from B. Joseph Hinnebusch, Florent Sebbane, and Viveka Vadyvaloo writing in Yersinia: Systems Biology and Control:

DNA microarray technology enables a comprehensive, systems biology approach to investigate the microbial gene expression program associated with adaptation to different environments. Monitoring the whole-genome transcriptional response of pathogens within infected tissues has rarely been achieved, but has been possible with Yersinia pestis. The transcriptional profiles of Y. pestis in infective fleas and in the lymph node of rats during bubonic plague were compared to identify important adaptational responses associated with successful colonization of the flea, transmission, and the establishment of disease in the mammal. The differential patterns of gene expression indicate metabolic reprogramming, response to different stresses, and specific induction of virulence and transmission factors as Y. pestis alternates between its two hosts.

Further reading: Yersinia: Systems Biology and Control

from Reinhard Hoffmann, Ekaterina Lenk, and Jürgen Heesemann writing in Yersinia: Systems Biology and Control:

The infection of the host is a complex biological process which prompted infection biologists to pursue reductionist approaches to unravel molecular events of pathogen-host interaction. DNA microarray provides us with a systems biology approach to gain a more holistic picture. Transcriptional profiling of host cell-pathogen interactions results in vast data sets which have to be carefully analyzed by considering the pathogen on a clonal level, the particular cell type (cell lines or primary cells) and the infection model. Here we summarize and discuss the available transcriptional profiling data obtained from Yersinia enterocolitica infection models in relation to the general gene expression program of host cells to microbial infection.

Further reading: Yersinia: Systems Biology and Control

from Valerie A. Ray and Karen L. Visick writing in Two-Component Systems in Bacteria:

The symbiotic relationship between the marine bioluminescent bacterium Vibrio fischeri and its host, the Hawaiian bobtail squid Euprymna scolopes, depends upon the ability of the two partners to sense and respond to each other. V. fischeri colonizes a specialized squid organ called the light organ in three general stages: initiation, accommodation, and persistence. To respond to the different environments encountered during these stages of colonization, V. fischeri utilizes specialized two-component signal transduction systems to regulate processes such as biofilm formation, motility and chemotaxis, and luminescence. In this chapter, we discuss in detail the two component systems that regulate these processes and how they impact successful colonization of the squid host.

Further reading: Two-Component Systems in Bacteria

"This is a good review of how viruses can hijack a host cell and induce unrestrained cellular replication. It will serve as a good reference and review for scientists working in this field as well as those developing vaccines and therapies for tumor-promoting viruses." from Rebecca T. Horvat (University of Kansas, USA) writing in Doodys read more ...

Small DNA Tumour Viruses Edited by: Kevin Gaston ISBN: 978-1-904455-99-8 Publisher: Caister Academic Press Publication Date: March 2012 Cover: hardback "a good reference and review" (Doodys)

from David E. Whitworth writing in Bacterial Regulatory Networks:

Two-component systems (TCSs) are signalling pathways found abundantly in prokaryotes, and they are the dominant mechanism for stimulus-responsive adaptation in such organisms. An ever-increasing number of physiological phenomena are known to be regulated by TCSs, including cell cycle progression, pathogenesis, motility, and biofilm formation. The basic TCS comprises a receptor protein (sensor kinase) which autophosphorylates in response to a stimulus. The phosphoryl group is then directly transferred to a response regulator protein (the second component) that has a phosphorylation-dependent effector function. While the most basic TCSs are relatively well understood, there are many 'atypical' systems, which exhibit additional mechanistic features (for instance, regulation of sub-cellular location, intrinsic and extrinsic phosphatase activities, and cross-communication between TCSs), adding complexity to their signalling properties. The relatively recent availability of complete prokaryotic genome sequences has also provided new opportunities to appreciate global features of TCS function. For example, analyses have provided insights into TCS evolution, which in turn have yielded computational methods for evaluating TCS protein partnerships. This chapter provides an overview of the common features of TCSs from a historical perspective, and then describes current understanding regarding the mechanisms of TCS function. Finally, outstanding questions regarding TCS function are discussed.

Further reading: Bacterial Regulatory Networks   Related publications

from Karen Schrecke, Anna Staroń and Thorsten Mascher writing in Two-Component Systems in Bacteria:

The cell envelope stress response (CESR) network monitors and maintains envelope integrity to counteract the damaging effects of cell wall antibiotics and membrane perturbating agents. Two-component systems (2CSs) involved in orchestrating CESR in Firmicutes bacteria (low G+C Gram-positive) are characterized by so-called intramembrane-sensing histidine kinases (IM-HKs). The N-terminal input domain of these proteins consists of two transmembrane helices with a very short extracellular linker of less than 20 amino acids, which is insufficient for stimulus perception. It was originally thought that these HKs sense their stimuli within the membrane interface. But subsequent studies identified accessory membrane proteins for all IM-HKs described so far. This chapter will specifically summarize the current state of knowledge on BceRS- and LiaRS-like 2CSs, which are ubiquitously distributed in Firmicutes bacteria. While BceRSAB-like systems represent antibiotic-specific detoxification modules, LiaFSR-like three-component systems mount more general CESR. These two types of systems are genetically and functionally linked to BceAB-like ABC transporters and LiaF-like membrane-anchored regulatory proteins, respectively, which play a crucial role in sensing envelope stress and transferring the information to the cognate HKs. Accordingly, BceS- and LiaS-like IM-HKs do not function as sensor proteins, but rather as signal transfer relays between the sensor and the cognate response regulators.

Further reading: Two-Component Systems in Bacteria

from writing in Two-Component Systems in Bacteria:

Further reading: Two-Component Systems in Bacteria

"Cancer biology researchers interested in the transforming viruses will find the information contained in Small DNA Tumour Viruses to be highly applicable in terms of its strong molecular biology coverage. Virologists focused on this group of viruses will find this book invaluable for its multiple perspectives and concise summary of a large body of research in this area." from MedicalScienceBooks.com read more ...

Small DNA Tumour Viruses Edited by: Kevin Gaston ISBN: 978-1-904455-99-8 Publisher: Caister Academic Press Publication Date: March 2012 Cover: hardback "invaluable for its multiple perspectives and concise summary of a large body of research" (MedicalScienceBooks.com)

from Juan-Francisco Martín, Alberto Sola-Landa and Antonio Rodríguez-García writing in Two-Component Systems in Bacteria:

Two-component systems (TCS) play a very important role in the regulation of metabolism in Streptomyces species in response to different nutritional or environmental signals. Streptomyces are Gram-positive soil-dwelling filamentous bacteria with large genomes that have the ability to produce thousands of different secondary metabolites. Streptomyces genomes contain a large number of paired two-component systems (usually more than 70) and some additional orphan sensor kinases and response regulators. Several of these systems have been studied in detail in the model species Streptomyces coelicolor. Particular attention has been paid to the PhoR/PhoP and the orphan GlnR systems due to their relevance in the control of primary metabolism and secondary metabolite biosynthesis. The PhoP binding sequence in many phosphate regulated promoters is formed by 11 nucleotide direct-repeats. A cross-talk between PhoP and other global regulators such as AfsR or GlnR has been found. Other two-component systems, particularly AbsA1/AbsA2, also control antibiotic biosynthesis in S. coelicolor, while others control chitinase synthesis, stress responses or cellular differentiation. Finally, some orphan response regulators named atypical response regulators (e.g. RedZ in S. coelicolor and JadR1 in Streptomyces venezuelae) bind as ligands the final product of the antibiotic biosynthetic pathway and act as feedback regulators of the biosynthesis of these secondary metabolites.

Further reading: Two-Component Systems in Bacteria

from writing in Two-Component Systems in Bacteria:

Further reading: Two-Component Systems in Bacteria

from writing in Two-Component Systems in Bacteria:

Further reading: Two-Component Systems in Bacteria

Stress Response in Microbiology Edited by: Jose M. Requena ISBN: 978-1-908230-04-1 Publisher: Caister Academic Press Publication Date: June 2012 Cover: hardback

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from Daniela Keilberg, Stuart Huntley and Lotte Søgaard-Andersen writing in Two-Component Systems in Bacteria:

The Myxococcus xanthus lifecycle is characterized by many social interactions. In particular, M. xanthus forms cooperatively spreading colonies in the presence of nutrients and multicellular, spore-filled fruiting bodies in the absence of nutrients. Formation of both cellular patterns depends on two intact motility systems. Moreover, fruiting body formation depends on intercellular communication and temporally regulated gene expression. The M. xanthus genome encodes a staggering 272 putative proteins of two-component system and most aspects of the M. xanthus lifecycle are regulated by one or more of these proteins. Interestingly, many of the corresponding genes encoding two-component system proteins possess an unusual organization in complex genes clusters and as orphan genes. However, major strides have been made in our understanding of a large number of these proteins. Here, we focus on the function of well-studied proteins of two-component systems in motility and development in M. xanthus.

Further reading: Two-Component Systems in Bacteria

from Jorge Santo Domingo, Mary Schoen, Nicholas Ashbolt and Hodon Ryu writing in Quantitative Real-time PCR in Applied Microbiology:

Microbial risk assessment (MRA) has traditionally utilized microbiological data that was obtained by culture-based techniques that are expensive and time consuming. With the advent of PCR methods there is a realistic opportunity to conduct MRA studies economically, in less time, and simultaneously targeting multiple pathogens and their sources. More importantly, recently developed qPCR assays provide the opportunity to estimate the densities of the reference pathogens and their sources, which is critical to quantitative MRA (QMRA) analyses. In this chapter we discuss the use of qPCR-based methods to identify risks associated with exposure to water, namely, drinking and recreational waters. We discuss the advantages associated with the current qPCR approaches used in microbial water quality studies and critically evaluate some of the limitations as they relate to the use of QMRA in the assessment of microbial water quality and public health protection.

Further reading: Quantitative Real-time PCR in Applied Microbiology   Related publications

from Sergei Boichuk and Ole Gjoerup writing in Small DNA Tumour Viruses:

Incoming viral genomes, aberrant viral replication structures or individual viral proteins are potential triggers of DNA damage responses (DDRs). In an emerging theme, viruses interfere with, and frequently commandeer, DDR and repair signaling pathways to promote the viral life cycle. Here we review the diverse mechanisms that small DNA tumour viruses utilize to deregulate DDR pathways. Adenoviruses (Ad) encode gene products that specifically degrade the MRN (Mre11, Rad50, Nbs1) damage sensor or sequester it in nuclear tracks. This causes an inhibition of both ATM and ATR responses. Failure to inactivate MRN leads to attenuation of viral replication and concatemerization of the viral genome, thus preventing efficient packaging. Conversely, polyomaviruses, like SV40, as well as human papillomaviruses (HPVs) appear to exploit the DDR, since they use components of it to positively regulate their life cycle, while generally inhibiting downstream checkpoint responses. SV40, mouse polyomavirus and HPV activate ATM signaling and benefit from it. Complexities of the interplay between small DNA tumour viruses and the DDR are continuously evolving and illuminate both critical aspects of the viral life cycle as well as basic cellular mechanisms operating in a non-viral setting.

Further reading: Small DNA Tumour Viruses   Related publications

from Michael M. Goodin and Byoung-Eun Min writing in Rhabdoviruses: Molecular Taxonomy, Evolution, Genomics, Ecology, Host-Vector Interactions, Cytopathology and Control:

Rhabdoviruses belonging to the genus Nucleorhabdovirus are unique in that they have not only adapted to replication in both plant and invertebrate cells but they are nucleotrophic as well. Beyond their roles as plant pathogens, these viruses also serve as probes to provide insights into plant nuclear biology. Using data gained from studies with Sonchus yellow net virus and Potato yellow dwarf virus, this review will describe protein interaction and membrane dynamics in virus-infected cells, with particular emphasis on relating these findings to the mechanism of cell-to-cell movement. To date, five host factors have been implicated in the process of moving nucleocapsids from infected cells into adjacent ones. These host factors, in concert with several virus-encoded proteins, are thought to form a cytoplasmic complex that migrates from nuclei on microtubules and membranes towards the plasmodesmata where they dock onto plasmodesmata-localized protein 1. Prior to moving cell-to-cell, these viruses induce dramatic changes in nuclear membranes, particularly the inner nuclear membrane, during establishment of a nuclear viroplasm, were nascent nucleocapsids form on ring-shaped protein complexes before accumulating in the perinuclear space.

Further reading: Rhabdoviruses: Molecular Taxonomy, Evolution, Genomics, Ecology, Host-Vector Interactions, Cytopathology and Control

from Pranvera Lazo and Jaroslav Reif writing in Bioremediation of Mercury: Current Research and Industrial Applications:

North of Vlora in Albania is the site of a former chemical manufacturing complex consisting of a chlor-alkali factory and plants for the production of vinyl chloride monomer (VCM) and polyvinylchloride (PVC). The factory closed in 1992 and was completely destroyed during a civil uprising in 1997. It covers an area of approximately 1 km² located directly at the coast of the Adriatic Sea. The major environmental problems are the destroyed mercury cells of the chlor-alkali electrolysis plant, the waste-water which has been discharged into the Bay of Vlora without treatment in the past, and the sludge from the former production processes which was dumped in the area between the plant and the Bay. Hydrological, geochemical and geophysical investigations showed that mercury concentrations in ambient air exceeded the emission limit of 50 ng m^-3 in about 40% of measurements; the maximum was reached with 50 µg m^-3. The soils were found to be contaminated only within the unsaturated zone. Here the maximum mercury concentration was greater than 20,000 mg kg^-1. The mercury distribution in marine deposits of the Adriatic Sea did not indicate any influence of the discharged waste water. A significant contamination hot spot was the electrolysis building. Here, mercury concentration was higher than 60,000 mg kg^-1. Most of the mercury was present in elemental form. Therefore the impact of mercury pollution in the Bay of Vlora on humans and indicator organisms was small.

Further reading: Bioremediation of Mercury: Current Research and Industrial Applications

from Daniela Bassi, Fabrizio Cappa and Pier Sandro Cocconcelli writing in Bacterial Spores: Current Research and Applications:

Bacterial spore water uptake and solute permeability are hypothesised to play a central role during the sporulation and germination processes but the leading mechanisms are at now poorly understood. In this chapter, a state of the art and the last experiments to better study this topic are presented. In the first part, major questions are addressed to the role of water content in spore dormancy and resistance, to the mechanisms which lead to spore dehydration and to the permeability of the spore layers to water and solutes. In the second part, the attention is focused on the ion composition of spores and their importance for the spore life cycle, with particular attention to the leading mechanisms acting during spore formation in the mother cell and during the germination process and outgrowth.

Further reading: Bacterial Spores   Related publications

Quantitative Real-time PCR in Applied Microbiology Edited by: Martin Filion ISBN: 978-1-908230-01-0 Publisher: Caister Academic Press Publication Date: May 2012 Cover: hardback

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from Francisco Dionisio, Teresa Nogueira, Luís M. Carvalho, Helena Mendes-Soares, Sílvia C. M. Mendonça, Iolanda Domingues, Bernardino Moreira and Ana M. Reis writing in Horizontal Gene Transfer in Microorganisms:

The ubiquity of plasmids in nature contrasts with our ability to understand their maintenance. Despite the ability of plasmids to transfer across different bacterial taxonomic groups and to carry useful genes to bacterial cells, it is unclear which factors are responsible for plasmid maintenance among bacterial populations. In this review, we present several hypotheses aiming at explaining plasmid existence: efficiency of self-transfer, advantageous genes, transitory derepression of conjugative pili synthesis, compensatory mutations, the existence of amplifier strains, positive epistasis between chromosomal mutations and plasmids, selective sweeps, frequent cross-species transfer, as well as three types of social interactions (exploitation avoidance in the production of public goods, pathogen- or parasite-mediated harmful behavior, biofilm formation). These hypotheses imply that plasmids and their hosts are adaptable to variable conditions and even that plasmids can be irreplaceable under particular circumstances.

Further reading: Horizontal Gene Transfer in Microorganisms

from Ali Navid and Eivind Almaas writing in Yersinia: Systems Biology and Control:

Bubonic plague is one of the deadliest diseases known to man. Unfortunately, despite all of our medical advances, we still do not have a working vaccine against this disease. Worse yet, discovery of anti-microbial resistant strains of Yersinia pestis, the causative agent of plague, could soon render our current therapeutic means ineffective. Unique characteristics of bacterial metabolism constitute one of the primary sets of targets for drug design. Accordingly, metabolism of Y. pestis has been one of the most studied aspects of its physiology.

Further reading: Yersinia: Systems Biology and Control

from Michael Marceau and Michel Simonet writing in Yersinia: Systems Biology and Control:

Yersinia pseudotuberculosis is a septicemic pathogen for rodents and many other animals. However, in certain immunosuppressive conditions, it may also invade the human bloodstream and little is known about the physiological events that take place once the microorganism has entered this compartment. DNA arrays are powerful tools for comparing wide and complex RNA population samples and, therefore, are appropriate to gain insight into the metabolic pathways and virulence factors expressed by the bacterium in this situation. Using such a technology, we compared the overall gene transcription patterns (the transcriptome) of Y. pseudotuberculosis cultured in either human plasma or Luria-Bertani medium. In this chapter, we will try to decipher, and sometimes speculate a little bit, on the physiological events behind the most salient transcriptional regulatory events detected in our experiments, with the intention of making the story as less descriptive as possible. Discordances between our data and those obtained in identical conditions with Y. pestis will be discussed when necessary.

Further reading: Yersinia: Systems Biology and Control

The Helicobacter genus belongs to class Epsilonproteobacteria, orders Campylobacterales, family Helicobacteraceae and already involves >35 species. Recently, new gastric (Helicobacter suis and Helicobacter baculiformis) and enterohepatic (Helicobacter equorum) species have been reported. Helicobacter pylori is of primary importance for medicine, however, non-pylori Helicobacter species (NPHS), which naturally inhabit mammals (except humans) and birds, have been detected in human clinical specimens. NPHS encompass two (gastric and enterohepatic) groups, showing different organ specificity. Importantly, some species such as Helicobacter hepaticus, Helicobacter mustelae and, probably, Helicobacter bilis exhibit carcinogenic potential in animals. NPHS harbour many virulence genes and may cause diseases not only in animals but also in humans. Gastric NPHS such as H. suis (most often), Helicobacter felis, Helicobacter bizzozeronii and Helicobacter salomonis have been associated with chronic gastritis and peptic ulcers in humans and, importantly, with higher risk for MALT lymphoma compared to H. pylori. Enterohepatic species e.g., H. hepaticus, H. bilis and Helicobacter ganmani have been detected by PCR in, but still not isolated from, specimens of patients with hepatobiliary diseases. Moreover, NPHS may be associated with Crohn's disease, inflammatory bowel disease and ulcerative colitis. The significance of avian helicobacters (Helicobacter pullorum, Helicobacter anseris and Helicobacter brantae) also has been evaluated extensively. NPHS such as Helicobacter cinaedi and Helicobacter canis can cause severe infections, mostly in immunocompromised patients with animal exposure. Briefly, the role of NPHS in veterinary and human medicine is increasingly recognised. However, despite the growing interest in the possible association between NPHS and the chronic hepatobiliary or intestinal diseases in humans, more studies are still required to prove the suggested association. Several other topics such as isolation of still uncultured species, antibiotic resistance and treatment regimens for NPHS infections and, last but not least, NPHS pathogenesis and possible carcinogenesis in humans should be additionally evaluated.

Further reading: Helicobacter pylori

Lactobacilli can be found in very diverse environments, ranging from plants and fermented food products to the mucosal surfaces of the human body, including the Gastro Intestinal tract. Like many other lactic acid bacteria, they are traditionally used in food fermentation, serving food preservation as well as flavor and texture development. In this chapter we present an overview of the phylogenetic diversity, occurrence and industrial applications of lactobacilli. We then focus on genome sequence data and how this recent source of information changed our view of the genus Lactobacillus, largely improving our understanding of these bacteria and their particular properties. To end with, we compare lactobacilli from the viewpoint of surface exposed and secreted proteins, which may prove particularly important in the emerging field of bacteria?host interactions in the GI tract. We present a novel vision of what the proteinaceous component of the Lactobacillus cell surface may look like, and reveal differences between the different species in an attempt to establish a potentially important link in the interaction of the bacteria with their biotic and abiotic environment.

Further reading: Lactic Acid Bacteria and Bifidobacteria: Current Progress in Advanced Research

from Patrick Eichenberger writing in Bacillus: Cellular and Molecular Biology (Second edition):

Bacteria of the genera Bacillus and Clostridium can be found in two distinct states. In the vegetative state, bacteria are metabolically active and use available nutrients to grow and divide by binary fission, a process that generates two identical daughter cells. By contrast, when nutrients are scarce, a developmental program of endospore formation (sporulation) is initiated, resulting in the production of highly resistant spores. In the spore state, bacteria are metabolically dormant, and their genetic material, protected in the core of the spore, can endure a variety of challenges, including exposure to radiation, elevated temperatures and noxious chemicals. Sporulation is a complex process, which requires the generation of two distinct cell types: a forespore and a larger mother cell. The progression of the developmental program is controlled by two exquisitely regulated cell type-specific lines of gene expression that run in parallel and are connected at the post-translational level. Various genetic screens and genome-wide transcriptional analyses have identified more than 600 genes that are expressed in the course of sporulation. The function of several of these genes has been characterized in detail and subcellular localization data are available for at least 90 sporulation proteins. Thus, sporulation constitutes one of the best characterized developmental programs at the molecular and cellular levels.

Further reading: Bacillus: Cellular and Molecular Biology (Second edition)

from Marcel W. Coolen and Susan J. Clark writing in Epigenetics: A Reference Manual:

Over the past decades it has become ever more apparent that understanding the genome did not stop with unravelling the genetic code. Regulatory mechanisms are needed to determine which parts of the genome are active or inactive, and to form a memory system that can be passed on over multiple cell divisions for proper functioning of the cell. These mechanisms underpinning heritable gene regulation are encapsulated by the term "epigenetics" and include histone modifications, miRNA and non-coding RNA expression, and methylation of cytosine residues in DNA. In this review, we compare the various methods that can be used to analyse DNA methylation patterns throughout the genome, and discuss their advantages and disadvantages. In addition, we present a detailed protocol for genome-wide DNA methylation analysis based on the capture of methylated DNA using a methyl-CpG binding domain-based (MBD) protein combined with second generation sequencing.

Further reading: Epigenetics: A Reference Manual

Genome sequence comparison has been an important method for understanding gene function and genome evolution since the early days of gene sequencing. Alignment of DNA sequences is the core process in comparative genomics. In recent years, an important new sequence-analysis task has emerged: comparing an entire genome with another. Several powerful alignment algorithms have been developed to align two or more sequences.

MUMmer
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. MUMmer can also align incomplete genomes; it can handle thousands of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included within the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program within the environment can generate alignments based upon the six-frame translations of both input sequences. The original MUMmer system, version 1.0, was described in a 1999 Nucleic Acids Research paper. Version 2.1 appeared a few years later and was described in a 2002 Nucleic Acids Research paper , and the most recent version MUMmer 3.0 was described in a 2004 Genome Biology paper.

BLAT
BLAT (The BLAST-Like Alignment Tool) is a new tool for sequence alignment, which is similar in many ways to BLAST. The program rapidly scans for relatively short matches (hits), and extends these into high-scoring pairs (HSPs). However, BLAT differs from BLAST in several significant ways. Specifically, where BLAST builds an index of the query sequence and then scans linearly through the database, BLAT builds an index of the database and then scans linearly through the query sequence. Where BLAST triggers an extension when one or two hits occur in proximity to each other, BLAT can trigger extensions on any number of perfect or near-perfect hits. Where BLAST returns each area of homology between two sequences as separate alignments, BLAT stitches them together into a larger alignment. Both the client/server and the stand-alone can do comparisons at the nucleotide, protein, or translated nucleotide level.

MEGABlast
Mega BLAST uses the greedy algorithm of Zhang et al. for nucleotide sequence alignment search and concatenates many queries to save time spent scanning the database. This program is optimized for aligning sequences that differ slightly as a result of sequencing or other similar "errors". It is up to 10 times faster than more common sequence similarity search and alignment programs and therefore can be used to swiftly compare two large sets of sequences against each other.

Comparative analysis is an increasingly important step in the annotation and analysis process of genome sequence data, allowing phenotypic differences between strains and species to be correlated with changes in the chromosomes. For example, comparative sequence analysis has enabled the identification of cis-regulatory regions and location of coding exons using purely computational means. Visual front-ends are necessary and important to make the process of viewing alignments intuitive and easy to facilitate discovery of conserved sequences for functionally significant regions. Below we describe a few visualization tools for genome comparisons.

PipMaker and MultiPipMaker
PipMaker is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree of similarity for each aligning segment between the two sequences in a compact and easily understandable form. The web site also provides a plot of the locations of those segments in both species. PipMaker is appropriate for comparing genomic sequences from any two related species, although the types of information that can be inferred (e.g., protein-coding regions and cis-regulatory elements) depend on the level of conservation and the time and divergence rate since the separation of the species. PipMaker supports analysis of unfinished or working draft sequences by permitting one of the two sequences to be in un-oriented and unordered contigs. Similarly, MultiPipMaker allows the user to visualize relationships among more than two sequences. All pairwise alignments with the first sequence are computed and then returned as interleaved pips. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.

ACT
ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer, such as parsed BLAST alignments based on Artemis - an annotation tool. Similar to other Artemis tools, ACT is written in Java and runs on Unix, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequence in FASTA or raw sequence format. Other types of readable sequence input files include EMBL, GENBANK and GFF formats. The sequence comparison displayed by ACT is usually the result of running a blastn or tblastx search.

VISTA
Vista (Visualization and Alignment Software for Comparative Genomics) is a visualization tool for alignments, which displays GLASS alignments. It is a program to depict long alignments of DNA sequences from two or more organisms with various types of annotation in a clear and easily interpretable format. Originally it was developed to locate conserved sequences in syntenic regions of different genomes. The key features of the VISTA program are mainly the following:
1. Clean graphical output, allowing for easy identification of sequence similarities and differences.
2. Easily configurable, enabling the visualization of alignments of up to several million bases at different levels of resolution.
3. Displays alignments of draft sequences.
4. Displays sequence annotations such as repeats, coding exons, UTRs and more.
The VISTA plot is based on moving a user-specified window over the entire alignment and calculating the percent identity over the window at each base pair.

SynPlot
Synplot (displays DIALIGN and GLASS alignments) is an application program, written in Perl, for viewing global alignments of syntenic regions of genomic DNA sequence. The alignment is used to calculate the percentage identity along the alignment within a sliding window, the width of which can be specified by the user. This information is used to draw a picture of the alignment in postscript format. The sequences are rendered as lines interrupted by spaces corresponding to the gaps introduced by the alignment, with a plot of the percentage identity underneath. Features can also be drawn on the sequence lines. This program uses a GFF format file output by ACeDB from the annotated genomic sequence, and a configuration file which specifies the color, height and order in which the rectangles representing the features are drawn.

from Mikael Kubista, Vendula Rusnakova, David Svec, Björn Sjögreen and Ales Tichopad writing in Quantitative Real-time PCR in Applied Microbiology:

As the qPCR field advances, the design of experiments and the analysis of data is becoming more important and more challenging. Calculation of relative expression of a reporter gene to a reference gene in pairs of samples using the ΔΔCq method is no longer sufficient. Studies are now designed using multiple markers, nested levels, exploring or confirming the effect of multiple factors, occasionally in paired designs, etc. Proper handling of such data requires software that support the planning and design of experiments, and data analysis. Several software with these capacities are emerging. This chapter describes some of the features of one of the most powerful of those: GenEx from MultiD Analysis.

Further reading: Quantitative Real-time PCR in Applied Microbiology   Related publications

from Tarja Sironen and Alexander Plyusnin writing in Bunyaviridae: Molecular and Cellular Biology:

Hantaviruses are globally important human pathogens. They are emerging viruses, and both the number of different hantavirus species discovered, and the amount of human infections are increasing. The hantaviral sequence data set is rapidly growing, and several fully sequenced genomes have been reported. Until recently, rodents have been regarded as the main reservoir and evolutionary scene of hantaviruses. These viruses have indeed proven to be an excellent model to study virus evolution and co-evolution of a virus with its host. During the last couple of years, however, majority of novel hantaviruses have been discovered from insectivore hosts instead of rodents, thus challenging some of the earlier views on hantavirus evolution. In the following paragraphs we summarize the current knowledge on the genome organization, genetic diversity, and evolution of hantaviruses from the major groups associated with Cricetidae and Muridae rodents and Soricomorph insectivores.

Further reading: Bunyaviridae: Molecular and Cellular Biology

from Andre Irsigler and Karen M. McGinnis writing in Epigenetics: A Reference Manual:

Maize has served as an excellent model for the study of epigenetic gene regulation for the past several decades. The pioneering work of maize geneticists like Barbara McClintock, Alexander Brink, Marcus Rhoades, and others led to the observation of many fascinating phenomena that were later demonstrated to be epigenetically regulated events. Since these observations were made, a great deal of progress has been made in determining the underlying causes of the phenomena, and many of these examples of epigenetic gene regulation are currently being used to elucidate the mechanisms of epigenetic heritability in plants. Today, these phenomena and the mutants that impact them serve as resources for studying how DNA methylation, chromatin structure, and small RNAs act to influence paramutation, gene silencing, and parent-of-origin dependent dosage compensation. The key attributes and potential contributions of each resource are discussed in the context of understanding the mechanisms and significance of epigenetic gene regulation in large, complex genomes.

Further reading: Epigenetics: A Reference Manual

from Gavin K. Paterson and Duncan J. Maskell writing in Bacterial Pathogenesis: Molecular and Cellular Mechanisms:

Determinants of bacterial pathogenicity are encoded by different types of genetic elements. Of particular note are large loci including pathogenicity islands, bacteriophages, integrative and conjugative elements, plasmids and integrons. Gene loss can also play a significant role in determining bacterial pathogenicity and should not be disregarded. Here we discuss these main genetic determinants of bacterial pathogenicity and how they influence the behaviour of important human and veterinary pathogens. The chapter illustrates the vast diversity and adaptability of bacterial pathogens, features that will ensure their continued medical and veterinary importance for quite some time to come.

Further reading: Bacterial Pathogenesis: Molecular and Cellular Mechanisms

from Kürşad Turgay writing in Bacillus: Cellular and Molecular Biology (Second edition):

Proteolysis is an important part of many fundamental cellular processes. The intricate involvement of proteases and peptidases in protein quality control, general stress response, control of regulatory networks and development in Bacillus subtilis are introduced in this review. Especially the more recent developments on the role of AAA+ proteins and their adaptor proteins in regulated and general proteolysis and the role of regulated intra-membrane proteolysis and membrane proteases in signal transduction are discussed.

Further reading: Bacillus: Cellular and Molecular Biology (Second edition)

from Eduardo A. Robleto, Holly A. Martin, Amber M. Pepper and Mario Pedraza-Reyes writing in Bacterial Spores: Current Research and Applications:

Endospore formation in the Bacilli has been used extensively as a proxy for cell growth and differentiation. Research that spans many years has revealed that endospore formation is a complex and elegant process that exquisitely coordinates the development of a dormant spore. The spore structure allows survival when nutrients and moisture are scarce. Once growth-conducive conditions are restored, the process of germination gives rise to vegetative cells. The cell differentiation program of sporulation is activated upon cessation of growth. Comparison of gene regulons activated during sporulation and stress survival suggest that the mode of regulation of endospore formation is well conserved between Bacilli and Clostridia.

Further reading: Bacterial Spores   Related publications

from Vijay J. Gadkar and Martin Filion writing in Quantitative Real-time PCR in Applied Microbiology:

Real time-quantitative PCR (RT-qPCR) technology has revolutionized the detection landscape in every area of molecular biology. The fundamental basis of this technology has remained unchanged since its inception, however various modifications have enhanced the overall performance of this highly versatile technology. These improvements have ranged from changes in the individual components of the enzymatic reaction cocktail (polymerizing enzymes, reaction buffers, probes, etc.) to the detection system itself (instrumentation, software, etc). The RT-qPCR technology currently available to researchers is more sensitive, faster and affordable than when this technology was first introduced. In this chapter, we summarize the developments of the last few years in RT-qPCR technology and nucleic acid amplification.

Further reading: Quantitative Real-time PCR in Applied Microbiology   Related publications

"a solid and critical review of the impact that extremophiles have in biotechnology. It discusses the adaptation of thermophilic, psychrophilic, acidophilic, and radiation-resistant microorganisms in their respective habitats ... the book offers newcomers to the biotechnology industry a good overview and a simple introduction to the subject, above all on future trends and web sources. " from Sonja Albers (Marburg) writing in BIOspektrum (2012) 18: 224. read more ...

Extremophiles: Microbiology and Biotechnology Edited by: Roberto Paul Anitori ISBN: 978-1-904455-98-1 Publisher: Caister Academic Press Publication Date: January 2012 Cover: hardback "a good overview" (Biospektrum)

Systems Microbiology: Current Topics and Applications Edited by: Brian D. Robertson and Brendan W. Wren ISBN: 978-1-908230-02-7 Publisher: Caister Academic Press Publication Date: June 2012 Cover: hardback

read more ...

from Liping Zhao and Jian Shen writing in Metagenomics: Current Innovations and Future Trends:

A devastating epidemic of chronic diseases is threatening the public health worldwide. Preventive healthcare systems require novel types of health assessment technologies which focus on the early warning biomarkers before the clinical onset of chronic diseases. In light of the systems theory, emergent functions of the human body should be measured for health evaluation. Humans are superorganisms harbouring two integrated genomes, the human genome and the microbiome which is the collective genomes of all symbiotic microorganisms, particularly those inhabiting the gut. The gut microbiota and the host interact intimately. The structure and functions of the gut microbiota, together with the host metabolism as reflected in urine metabolite profiles, are the emergent functions of the human body. Metagenomics and metabonomics can be used to monitor the dynamics of gut microbiota and host metabolism. Large scale cohort studies in which urine and faecal samples are analyzed by the whole body systems approaches may lead to the discovery of patterns of gut microbiota and host metabotypes which can in turn be used as a biomarker for diagnosis or target for developing new therapeutics for chronic diseases. The application of these systems approaches in traditional Chinese medicine and nutritional studies may lead to a significant paradigm shift in modern medicine and nutritional sciences.

Further reading: Metagenomics: Current Innovations and Future Trends

from Krista M. Giglio and Anthony G. Garza writing in Bacterial Spores: Current Research and Applications:

The myxobacteria are Gram-negative spore formers. Although the spores of myxobacteria and those of Bacillus species, which are Gram-positive bacteria, have many properties in common, the developmental processes that lead to their formation are fundamentally different. In this chapter, we give a general overview of sporulation in the model myxobacterium Myxoccocus xanthus. We discuss the developmental process that yields M. xanthus spores, the structural and biochemical properties of the spores and the genes that are associated with sporulation in this organism, and we compare each to its counterpart in Bacillus.

Further reading: Bacterial Spores   Related publications

Real-time PCR requires monitoring the reaction during amplification. Fluorescence is a convenient method of interrogation that only requires a clear optical path for excitation and emission. Double-stranded DNA (dsDNA) dyes and fluorescently-labeled probes are both commonly used. dsDNA dyes directly measure the amount of double-stranded product produced. Probes used in real-time PCR function indirectly through fluorescence resonance energy transfer (FRET) or fluorescence quenching. Initially proposed in the late 1940s, it was not until the 1980s that FRET was applied to DNA (Wittwer and Farrar, 2011 in PCR Troubleshooting and Optimization). However, real-time monitoring with probes was only achieved several years later after dsDNA dyes were established in real-time PCR. One advantage of probes over dsDNA dyes is multiplexing by color with different fluorescent dyes. Nevertheless, this advantage comes at a cost in instrumentation and analysis complexity. Furthermore, multiplex analysis with dsDNA dyes is possible by melting temperature separation of products and/or probes.

Flow cytometry (FC) detects and quantify light scattering from fluorescent-labeled cells that have crossed a laser beam. A single sample can be analysed within 3-5 min with a quantification limit of approximately 200 cells/ml. FC, although an optical detection method, is used in combination with molecular techniques. Bacterial cells in water have been monitored with flow cytometry through nucleic acid staining or targeting specific cells with antibodies or FISH hybridization.

FC is a valuable tool to differentiate between viable, intermediate and nonviable cells. Baclightbacterial viability kit (Live/Dead kit), widely used in flow cytometry, double stains nucleic acid with SYTO dyes (green fluorescence) and propidium iodide (PI) (red fluorescence). SYTO dyes stain the nucleic acid of all the cells, resulting in green fluorescence. The cells are afterwards stained with PI which can only move into membrane compromised cells, staining the nucleic acid and resulting in red fluorescence. The disadvantage is that cells can be dead without showing membrane damage and hence is this rather an assay representing membrane damage than cell viability. Calculating the nucleic acid content has also been used as an indicator of cell viability. The theory is that cells with higher cell viability reproduces at a higher rate and therefore will contain more copies of their genome. Care must be taken with the interpretation of results obtained from this approach. Bouvier et al. investigated the varied correlation between different nucleic acid contents and metabolic activities of subpopulations from a wide range of environmental communities.

FC combined with nucleic acid staining enable researchers to investigate the growth potential of microbial pathogens in natural waters. Vibrio cholerae, the causative agent of cholera, was shown through FC and SYBR Green nucleic acid staining to grow in different freshwater samples. This contradicted previous opinions that natural waters do not have sufficient nutrients to support the growth of this pathogen. Combining these experiments with assimilable organic carbon (AOC) concentrations it was concluded that V. cholerae would proliferate in water with a minimum AOC of 60 mg/l. The same research group investigated the growth potential of E. coli O157 in freshwater samples using the same methodology. E. coli O157 was able to grow in freshwater samples with low carbon concentrations, once again contradicting previous opinions.

Fluorescence activated cell sorting (FACS) makes FC even more indispensible for detecting and differentiating between microbial pathogens in water. Cells with specific nucleic acid targets can be labeled with FISH probes, quantified and separated with FC-FACS. These cells can then be subjected for further genetic and biochemical analysis. Catalyzed fluorescent reporter disposition-FISH and molecular beacons are now incorporated into FC-FACS to increase stain sensitivity and overcome the problem of sorting cells present in low numbers. FC-FACS-FISH has also been applied to sequence previously unsequenced microorganisms and cultured previously uncultured microorganisms from environmental samples.

from Duane J Gubler writing in Molecular Virology and Control of Flaviviruses:

The flaviviruses (genus Flavivirus) are among the most important pathogens infecting humans and domestic animals, causing hundreds of millions of infections annually. They have a global distribution and cause a broad spectrum of illness ranging from mild viral syndrome to severe and fatal hemorrhagic and neurologic disease. The genus is made up of a diverse group of 53 viral species that have evolved into three distinct groups with very different transmission cycles. The vector-borne group is transmitted among vertebrate hosts by hematophagous arthropods (mosquitoes and ticks), the no-known vector group is transmitted directly among vertebrate animals and the arthropod group is transmitted directly among arthropods. This chapter reviews the history, the present status and future trends of flaviviruses, using some of the more important species as case studies.

Further reading: Molecular Virology and Control of Flaviviruses

from Ken E. Olson and Carol D. Blair writing in Molecular Virology and Control of Flaviviruses:

Flaviviruses such as dengue, yellow fever and West Nile viruses continue to cause a significant amount of disease in humans. Most flaviviruses are maintained in nature by cycling between hematophagus arthropod vectors and vertebrate hosts, and the viruses need to replicate in both vectors and hosts. This review focuses on flavivirus-vector interactions to present a current understanding of events and processes that lead to vector infection, virus amplification and dissemination, transmission. This chapter will focus mainly on DENVs and their interactions with Aedes aegypti, but will include interactions between other flaviviruses and their vectors where approriate. Flavivirus-mosquito cell interactions will be discussed first to give the reader a cellular view of the infection process but this will be followed with a view of the infection process in vectors. This review will describe flavivirus interactions with the vector's innate immune (Toll, Jak-Stat, apoptosis) and antiviral (RNA interference) pathways and discuss flavivirus evolution and its consequences for vector infection, DENV transmission and genotype displacement. The review will dicuss how our understanding of vector genetics is enhanced by the availability of genome databases for A. aegypti and Culex quinquefasciatus, tissue-specific transcriptomes and microarrays and small RNA databases. The chapter will also discuss RNA silencing and vector transgenesis as tools for defining gene function. Finally, we will review several recently described vector-based approaches that may result in new strategies for flavivrus disease control.

Further reading: Molecular Virology and Control of Flaviviruses

"Overall, this book provides a timely and useful review of topics relevant to the interface of small RNA biology and virology. Chapters were written to stand alone and are therefore best read individually ... a good addition to institutional libraries." from Eva Gottwein (Chicago, USA) writing in The Quarterly Review of Biology (2012) 87: 66-67. read more ...

RNA Interference and Viruses: Current Innovations and Future Trends Edited by: Miguel Angel Martínez ISBN: 978-1-904455-56-1 Publisher: Caister Academic Press Publication Date: February 2010 Cover: hardback "a timely and useful review" (Quart. Rev. Biol.)

" a useful overview on the tools and concepts in bacterial population biology" from Edward J. Feil (Bath, UK) writing in The Quarterly Review of Biology (2012) 87: 71. read more ...

Microbial Population Genetics Edited by: Jianping Xu ISBN: 978-1-904455-59-2 Publisher: Caister Academic Press Publication Date: March 2010 Cover: hardback "a useful overview " (Quart. Rev. Biol.)

"a must-have for anyone interested in Brucella spp and brucellosis ... a comprehensive and detailed review of the most recent advances regarding Brucella ... This well-referenced book will be a welcome addition to the libraries of researchers, laboratory workers, molecular biologists, microbiologists, and veterinarians ... For those looking for a single, detailed reference on Brucella organisms, purchasing this book will be money well spent." from Angela Arenas writing in J. Vet. Med. Assoc. (2012) 240: 686. read more ...

Brucella: Molecular Microbiology and Genomics Edited by: Ignacio López-Goñi and David O'Callaghan ISBN: 978-1-904455-93-6 Publisher: Caister Academic Press Publication Date: February 2012 Cover: hardback "a must-have for anyone interested in Brucella" (J. Vet. Med. Assoc.)

"The book contains some very high quality diagrams and figures ... It also comes with useful Internet tools ... This comprehensive book presents current scientific studies on the cellular processes of Bacillus species ... The book is well organized" from Rebecca T. Horvat (University of Kansas, USA) writing in Doodys read more ...

Bacillus: Cellular and Molecular Biology (Second edition) Edited by: Peter Graumann ISBN: 978-1-904455-97-4 Publisher: Caister Academic Press Publication Date: February 2012 Cover: hardback "high quality diagrams and figures" (Doodys)

from Richard J. Kuhn writing in Molecular Virology and Control of Flaviviruses:

Flavivirus virions form in the endoplasmic reticulum (ER) with the recruitment of genome RNA, capsid protein, and the envelope (E) and precursor to the membrane proteins (prM). The nascent particles acquire a lipid bilayer as they bud into the ER lumen in an immature form. Glycosylation and subsequent processing of the particles occur as they proceed through the cellular secretory system. In the low pH that is encountered in the trans-Golgi network, cellular furin activates the particles by cleavage of prM into M. The particles are released from the cell in a mature and infectious form. The observations demonstrate the significant conformational and translational movements of the viral structural proteins during the virus life cycle and suggest the particles have substantial dynamic capabilities. These properties have been substantiated by analyses of antibody binding to virions and suggest novel targets for future therapeutic intervention strategies.

Further reading: Molecular Virology and Control of Flaviviruses

from Scott B. Halstead writing in Molecular Virology and Control of Flaviviruses:

Eight flaviviruses cause significant morbidity and mortality around the globe: yellow fever (YF), Japanese encephalitis (JE), Tick-borne encephalitis (TBE), dengue 1, 2, 3, 4 and West Nile (WN). Four, YF, JE, TBE and WN are zoonoses, with the consequence that vaccines are the only means of protecting humans. The successful YF 17D vaccine, introduced in 1937, produced dramatic reductions in epidemic activity. Effective killed JE and TBE vaccines were introduced in the middle of the 20th century. Unacceptable adverse events have prompted change from a mouse-brain killed JE vaccine to safer and more effective second generation JE vaccines. These may come into wide use to effectively prevent this severe disease in the huge populations of Asia - North, South and Southeast. The dengue viruses produce many millions of infections annually due to transmission by a successful global mosquito vector. As mosquito control has failed, several dengue vaccines are in varying stages of development. A tetravalent chimeric vaccine that splices structural genes of the four dengue viruses onto a 17D YF backbone is in Phase III clinical testing. For each of the eight flaviviruses, clinical disease, epidemiology, vaccine development history, vaccine useage, precautions and adverse events are briefly presented.

Further reading: Molecular Virology and Control of Flaviviruses

from Justin A. Roby, Anneke Funk, and Alexander A. Khromykh writing in Molecular Virology and Control of Flaviviruses:

The replication and assembly of Flaviviruses are complex procedures, which require the efficient coordination of a number of different steps. These stages are highly organized temporally and spatially in the infected cell and require the virus-induced establishment of host-derived membrane structures. Flavivirus RNA structures, non-structural proteins and host factors actively participate in the replication of genomic RNA within vesicle packets (VP). Progeny (+) strand RNA exits the VP pore and is incorporated into nucleocapsids by the capsid protein. Nucleocapsids are then presumably transported into the lumen of the endoplasmic reticulum at sites directly opposed to the VP pore during formation of the prM-E studded lipid envelope. These immature virions are trafficked to the Golgi network in individual vesicles for glycoprotein maturation and furin-directed prM cleavage. Mature virions (with associated, cleaved prM) are then secreted into the extracellular milieu.

Further reading: Molecular Virology and Control of Flaviviruses

from Gregory D. Ebel and Laura D. Kramer writing in Molecular Virology and Control of Flaviviruses:

Flavivirus fitness is inextricably linked to the ability of a particular agent to be efficiently transmitted among relevant hosts in natural transmission cycles. Thus, fitness is an inherent component of the virus-host relationship. The mechanisms through which virus fitness is maximized are poorly understood, but have recently been examined in increasing detail. This chapter examines recent developments in the study of flavivirus fitness from both observational and experimental studies, highlighting important emergent and/or resurgent tick- and mosquito-borne members of the flavivirus genus.

Further reading: Molecular Virology and Control of Flaviviruses

from Elizabeth Hunsperger writing in Molecular Virology and Control of Flaviviruses:

Within the family of Flaviviridae there are many medically important viruses that cause human disease worldwide. These viruses were originally categorized based on phenotype due to their antigenic relatedness and placed within groups, subgroups and types and later confirmed with nucleic acid sequence analysis. Diagnosis of disease caused by flaviviruses has been primarily based on serological identification of anti-viral antibodies and virus isolation. Some of the classic serological techniques of hemagglutination inhibition assay and complement fixation were replaced with the enzyme linked immunosorbent assay (ELISA) for the detection of IgM, IgG and IgA antibodies primarily due to ease-of-use. The plaque reduction neutralization test (PRNT) provided the specificity needed for virus identification following a positive serological test by ELISA. The development of polymerase chain reaction (PCR) assays improved the ability to detect virus nucleic acid sequence when viral isolates were not obtained. Because reverse transcriptase PCR (RT-PCR) assays are easy to perform, have increased sensitivity and provide virus identification in a short period of time, RT-PCR has essentially replaced isolation techniques for rapid diagnosis. However, virus isolation is still essential for genetic analysis. The future of flaviviral disease diagnosis is new platforms for antibody and nucleic acid detection as well as the development of point-of-care diagnostics for clinical management

Further reading: Molecular Virology and Control of Flaviviruses

from Qing-Yin Wang, Yen-Liang Chen, Siew Pheng Lim, and Pei-Yong Shi writing in Molecular Virology and Control of Flaviviruses:

Many flaviviruses are human pathogens of global importance, but no clinically approved antiviral therapy is currently available to manage these diseases. Both pharmaceutical industry and academia have invested considerable efforts over the past decade on finding the flavivirus antivirals using modern drug discovery. Various high-throughput compatible target-based and cell-based assays have been developed and implemented. In this chapter, we describe in details the methodologies developed for screening inhibitors against dengue virus, and the lessons learned from our screening campaigns. Based on our experience on dengue virus and the status of hepatitis C virus drug discovery, we propose that a combined target-based approach (e.g., viral polymerase, protease, and envelope) and a cell-based approach (e.g., virus infection and replicon assays) should be persistently pursued to develop flavivirus antiviral therapy.

Further reading: Molecular Virology and Control of Flaviviruses

from Hae Joo Kang, Edward N. Baker and Thomas Proft writing in Bacterial Pathogenesis: Molecular and Cellular Mechanisms:

As an important step for the successful and continuous colonization of the host, bacterial pathogens express a variety of specific adhesins on their cell surface, which allows them to interact with receptors on host cells. However, this close interaction might also be detrimental for the bacteria, as it could trigger infiltration and activation of immune cells and eventually lead to phagocytosis. Another obstacle for colonization is electrostatic repulsion due to the negative surface charge on both the bacteria and the host cell. Many bacteria have overcome this problem by expressing adhesins at the tip of a long fibril structure that extends from the bacterial cell surface. These structures are known as fimbriae or pili. Despite their diversity in structure and biogenesis, pili/fimbriae typically consist of a long fiber formed by homopolymerised subunits or pilins, and accessory pilins that often function as adhesins. Some pili are also involved in cell aggregation, biofilm formation, DNA uptake, phage transduction and gliding motility.

Further reading: Bacterial Pathogenesis: Molecular and Cellular Mechanisms

from Mark Paul Taylor, Lonnie Van Zyl, Marla Tuffin and Don Cowan writing in Extremophiles: Microbiology and Biotechnology:

In principle, extremophiles have much to offer the biotechnology industry, from robust, process hardy enzymes to metabolically and physiologically diverse whole cell biocatalysts. However, the penetration of extremophilic organisms and their products into biotechnology markets has been modest at best, with preference given to engineered, cost effective enzyme variants and organisms for which established genetic tools are widely available. Interest in 'xtreme' products has often been dissuaded due to the unattractive need for the sometimes costly and complicated cultivation equipment and the complexities of culture maintenance. The lack of suitable genetic tools by which to improve, adapt or engineer a process involving an extremophilic host further complicates the issue. Legislative controls over national biological resources and allegations of biopiracy have also retarded commercialisation and industry-academia collaborations. However, commercial success stories have been described and form part of this review. Future prospects are optimistic, as several new biotechnology companies involved in the production of biomolecules from renewable resources have based their platform technology on extremophiles.

Further reading: Extremophiles: Microbiology and Biotechnology

"a comprehensive update and review of the most promising strategies and technologies used in vaccine research since the dawn of the genomic era ... a quite effective title worthy of consideration from all those involved with the manufacture of vaccines ... Clearly any laboratory personnel working with vaccines specifically or using related principles of immunology in their work should read this book. Additionally, clinicians with a particular interest in infectious disease prevention can find valuable insight into the lines of investigation that will likely yield a new group of vaccines in the near future. " from Medical Science Books read more ...

Vaccine Design: Innovative Approaches and Novel Strategies Edited by: Rino Rappuoli and Fabio Bagnoli ISBN: 978-1-904455-74-5 Publisher: Caister Academic Press Publication Date: February 2011 Cover: hardback "a comprehensive update" (Med. Sci. Books)

from Hans Kristian Kotlar writing in Extremophiles: Microbiology and Biotechnology:

In the deep biosphere, extraordinary new types of microorganisms, sedimented or buried 200 - 500 million years ago, can be found. These organisms can be identified and characterized. The information obtained can be developed into novel tools for searching for new oil in sensitive regions like the Arctic, Antarctica and jungle areas. Relatively few enzymes are used in large-scale industrial applications. Enzymes isolated from these extremophile/ thermophile organisms might provide “game changing” new possibilities. They may furnish new incentives for the development of entirely new technical processes. These microbes provide opportunities for new technologies in second generation biofuel production. Several companies are working on alternative routes for the production of fuels using biomass as the raw source material. Traditional heavy oil extraction methods have major difficulties in justifying their high energy usage, CO₂ emissions and soil and environment pollution. The first company implementing a large-scale process based on biotechnology principles in enhanced oil recovery will gain huge strategic and economic benefits. The knowledge of this huge subsurface population of diverse microorganisms provides excellent opportunities for bioprospecting. There should be a multitude of spin-offs outside the oil industry. The world is desperately in need of new enzymes, new antibiotics, new immunosuppressant, new anticancer agents, etc. This chapter reviews just some of the areas we have been working on at Statoil. Hopefully some of these investigations could one day solve some of the problems we will face in the future. One day these extremophiles could be on the payroll of many different companies.

Further reading: Extremophiles: Microbiology and Biotechnology

from Anna M. Romaní, Joan Artigas and Irene Ylla writing in Microbial Biofilms: Current Research and Applications:

Biofilms in aquatic ecosystems colonize various compartments (sand, rocks, leaves) and play a key role in the uptake of inorganic and organic nutrients. Due to their extracellular enzyme capabilities, biofilm microorganisms are able to use organic matter from the surrounding water and increasing activities are related to the availability of biodegradable organic carbon. The most common extracellular enzymes analysed are those involved in the decomposition of polysaccharides, peptides and organic phosphorus compounds, and changes in enzyme expression have been related to the use of different sources of organic matter available in the ecosystem (i.e., during drought-storm and/or pollution episodes). Enzymes important for microbial acquisition of nitrogen and phosphorus also respond to nutrient content and/or imbalances in the flowing water. Additionally, biofilm extracellular enzyme activities are modified by the internal recycling of organic matter and microbial interactions (competition/synergism) within the biofilm, such as algal-bacterial and fungal-bacterial interactions. Although an extensive knowledge of the biofilm structure is required for the interpretation of extracellular enzyme activities in aquatic biofilms, they give a very useful, integrative measure of the biofilm community function in relation to organic matter use and cycling.

Further reading: Microbial Biofilms: Current Research and Applications

"... excellent volume ... This book is an essential reference for anyone interested in antibiotic resistance or discovery but also contains interesting chapters on the human microbiota and on current strategies for vaccine development. I highly recommend that you add this to your shelves." from Matt Hutchings (University of East Anglia, UK) writing in Microbiology Today (2012) read more ...

Emerging Trends in Antibacterial Discovery: Answering the Call to Arms Edited by: Alita A. Miller and Paul F. Miller ISBN: 978-1-904455-89-9 Publisher: Caister Academic Press Publication Date: August 2011 Cover: hardback "I highly recommend that you add this to your shelves" (Microbiol. Today)

from Luis Carlos de Souza Ferreia and Wolfgang Schumann writing in Bacterial Spores: Current Research and Applications:

Surface display of peptides and proteins on recombinant phages and bacterial cells has developed into a powerful technique to identify proteins with desired properties with multiple applications. This technique is of utmost importance as a tool for fundamental and applied research in the fields of microbiology, biotechnology and vaccination. Another promising bioparticle are spores produced by Bacillus subtilis cells that allow fusion of recombinant proteins to one of several outer spore coat proteins. There are several reports were antigens and proteins of biotechnological interest have been successfully displayed on the outside of spores. A major advantage of spores over bacterial cells is their intracellular biogenesis that does not require specific secretion sequences of the cellular apparatus. Therefore, heterologous proteins do not have to cross membranes and correct folding of these proteins can be achieved with the aid of cytoplasmic folder chaperones.

Further reading: Bacterial Spores   Related publications

"Highly recommended is the chapter on interactions between plants and biofilms" from Hans-Curt Flemming (Duisburg, Germany) writing in Biospektrum (2012) 18: 109. read more ...

Microbial Biofilms: Current Research and Applications Edited by: Gavin Lear and Gillian D. Lewis ISBN: 978-1-904455-96-7 Publisher: Caister Academic Press Publication Date: February 2012 Cover: hardback "Highly recommended" (Biospektrum)

CFGP
CFGP (Comparative Fungal Genomics Platform) is a web-based multifunctional informatics workbench. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the 'fill-in-the-form-and-press-SUBMIT' user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI.

MicroScope
MicroScope is a microbial genomes annotation and comparative analysis platform, which was developed by the French National Sequencing Center located at Genoscope. It is made of three major components : (i) a set of syntactic and functional annotation tools, (ii) a relational database, the Prokaryotic Genome DataBase, (PkGDB) which is linked to metabolic pathway databases (MicroCyc) created using the Pathway Tools software, and (iii) a graphical interface, the Magnifying Genome (MaGe), which allows performing relevant expert annotation that combine synteny results with metabolic network predictions.

"This book covers a topic in bacterial pathogenesis that is not often covered ... should be essential to any scientist working in the area of bacterial pathogenesis." from Rebecca T. Horvat (University of Kansas, USA) writing in Doodys read more ...

Bacterial Glycomics: Current Research, Technology and Applications Edited by: Christopher W. Reid, Susan M. Twine, and Anne N. Reid ISBN: 978-1-904455-95-0 Publisher: Caister Academic Press Publication Date: February 2012 Cover: hardback "essential" (Doodys)

from Yoshiyuki Nagai, Akira Takakura, Takashi Irie, Yoshikazu Yonemitsu and Bin Gotoh writing in The Biology of Paramyxoviruses:

Sendai virus (SeV) is not just an old mouse pathogen. SeV has been an irreplaceable tool in basic research to understand paramyxovirus replication and pathogenesis. SeV has further made an entrance into the scene of technological innovation in delivering foreign genes of interest to target cells and tissues. In this context, there are two different approaches. One is to make good use of the fusogenic capacity of inactivated SeV virions and the other is to generate a non-genotoxic (non-integrating) cytoplasmic RNA vector by reverse genetics. Here, we review the long history of SeV research focusing on its contribution to basic virology and technological development. We also highlight some old discoveries that have mostly vanished from recent textbooks but provided crucial momentum to the development of the current concepts and technologies.

Further reading: The Biology of Paramyxoviruses

from Ernesto Perez-Rueda, Nancy Rivera-Gomez, Mario Alberto Martinez-Nuñez and Silvia Tenorio-Salgado writing in Bacterial Regulatory Networks:

The capabilities of organisms to contend with environmental changes depend on their repertoire of genes and their ability to regulate their expression. DNA-binding transcription factors have a fundamental role in this process, because they regulate transcription positively or negatively as a consequence of environmental signals. In this chapter we briefly describe some of the most recent findings on regulatory network evolution from the perspective of DNA-binding transcription factors. We explore diverse elements associated with the evolution of regulatory networks, such as gene duplication, where new interactions can emerge together with their upstream and downstream binding sites. The chapter is divided into sections covering the evolution of transcription factors and their domains, their evolution, and a global analysis. Hypotheses concerning a comprehensive picture of how regulatory networks have evolved in prokaryotes and the role of transcription factors in this organization are discussed.

Further reading: Bacterial Regulatory Networks   Related publications

Viral hemorrhagic fever, a clinical syndrome characterized by fever, shock and bleeding, can be caused in humans by members of several RNA virus families, including filoviruses, bunyaviruses, arenaviruses and flaviviruses. None of the hemorrhagic fever viruses uniformly cause hemorrhage in humans. However, some viruses show greater propensity to cause severe, life threatening disease than do others. Because of their potential to cause life threatening disease, these viruses are public health concerns and many of the hemorrhagic fever viruses are considered to be potential weapons of terror. Recent emphasis on these viruses has prompted research into the mechanisms by which they interact with and evade host innate immune responses, particularly antiviral interferon (IFN) responses. Research has identified a variety of mechanisms of innate immune antagonism, and data from filovirus and bunyavirus systems links these functions to virulence. This sets the stage for studies to evaluate how specific mechanisms of IFN evasion contribute to the clinical manifestations of viral hemorrhagic fever.

Further reading: Viruses and Interferon: Current Research

from Sandra N. Oliver and E. Jean Finnegan writing in Epigenetics: A Reference Manual:

Polycomb-group (PcG) complexes are essential regulators of plant development. These multiprotein complexes repress gene expression by establishing and maintaining trimethylation of lysine 27 at histone H3, a modification that is associated with repressive chromatin. Recent studies have indicated that plant PcG complexes regulate key genes involved in responses to low temperature. Vernalization is a long-term response to low temperatures whereby plants coordinate their seasonal flowering to occur after winter. In contrast, acclimation of plants to low temperatures, a key step in the establishment of frost tolerance, involves rapid activation of cold-acclimation genes. In this chapter, we describe the dynamics of PcG-mediated gene regulation underlying these two important agronomic traits that are triggered by low temperatures.

Further reading: Epigenetics: A Reference Manual

H. pylori causes the second most common chronic bacterial infection in humans. As a result of the childhood-acquired and usually life-long (unless eradicated) infection, about 12-24% of the H. pylori positive subjects develop severe diseases e.g. peptic ulcers or gastric malignancy. In developed countries, the infection usually spreads intrafamilially; however, in developing countries or underdeveloped rural areas, it can be acquired often extrafamilially or via environmental contamination, leading to higher infection prevalence and greater intrafamiliar diversity of the strains there. Infected mother and older siblings are important factors for H. pylori transmission to children. The transmission routes are oral-oral (by saliva), which prevails in the developed world, faecal-oral (person-to-person or by contaminated water, or maybe food), mainly in the developing countries or gastro-oral (by vomiting and regurgitation). Role of viable but not culturable coccoids forms and biofilms appears to be important. Oral H. pylori seems to be associated with combined oral and gastric infections, probably more often in the developing countries. However, PCR accuracy for detection of extra-gastric H. pylori needs improvement. As a whole, the infection prevalence is still high in countries/groups with poor socio-economic status. In many developing countries, ≥50% of children and ≥70% of adults have been H. pylori positive vs. only >15% of children and ≤20-40% of adults in most developed countries. Detection of anti-CagA antibodies has been used to spot infections by virulent strains and the importance of East Asian CagA testing has been stressed. Both reinfection and infection clearance also have been reported, mainly in children, although in high-prevalence countries, the infection clearance is unimportant. Many risk factors for the infection mirror poor socioeconomic status and a strong birth cohort effect. Both dietary and environmental factors are likely to modify the infection prevalence and should be further evaluated. In brief, improved hygiene and living conditions, urbanisation and growing antibiotic use for H. pylori and many other infections, all have led to a decrease in both infection and reinfection rates in the developed countries and, already, in some developing countries. However, the infection still affects every second person worldwide. Moreover, many important questions on the infection transmission routes and reservoirs still need elucidation.

Further reading: Helicobacter pylori

from Helena Nevalainen, Ron Bradner, Sania Wadud, Suja Mohammed, Christopher McRae and Junior Te'o writing in Extremophiles: Microbiology and Biotechnology:

Fungi are eukaryotic organisms and considered to be less adaptable to extreme environments when compared to bacteria. While there are no thermophilic microfungi in a strict sense, some fungi have adapted to life in the cold. Cold-active microfungi have been isolated from the Antarctic and their enzyme activities explored with a view to finding new candidates for industrial use. On another front, environmental pollution by petroleum products in the Antarctic has led to a search for, and the subsequent discovery of, fungal isolates capable of degrading hydrocarbons. The work has paved the way to developing a bioremedial approach to containing this type of contamination in cold climates. Here we discuss our efforts to map the capability of Antarctic microfungi to degrade oil and also introduce a novel cold-active fungal lipase enzyme.

Further reading: Extremophiles: Microbiology and Biotechnology

from Benjamin Chanrion, Yurong Xin and Fatemeh Haghighi writing in Epigenetics: A Reference Manual:

DNA methylation plays an essential role in normal human development, where abnormalities in proper establishment and maintenance of DNA methylation patterns result in human disease. Many experimental approaches have been developed for assaying DNA methylation patterns, including enzymatic-based approaches. In this chapter, we highlight some of these approaches and describe their relative advantages and disadvantages. We also describe advances in microarray and sequencing technologies that have improved resolution of enzymatic-based methods, providing expanded coverage of CpG dinucleotides throughout the genome. These approaches are important tools in characterizing the role of DNA methylation in genome organization and function.

Further reading: Epigenetics: A Reference Manual

The fate of PCBs in soil and sediments is driven by a combination of interacting processes including several known biological processes. Under anaerobic conditions some bacteria use organohalides (including PCBs) as terminal acceptors. This process is responsible for the depletion of highly chlorinated congeners. Under aerobic conditions, PCBs are oxidized and mineralized by fungi through various pathways involving ligninolytic enzymes and monooxygenases and by bacteria through an initial dioxygenation reaction. Furthermore, several investigations have brought evidence that the rhizosphere provides a remarkable ecological niche to enhance the PCB degradation process by rhizobacteria. In this review, we will briefly summarize our current knowledge regarding the four above-mentioned biological processes involved in PCB degradation. Currently, the biochemistry of the anaerobic PCB-degrading process is still poorly understood. In the case of fungal enzymes, it is not yet clear which of the ligninolytic or monooxygenase systems prevails in PCB degradation. However, the bacterial oxidative enzymes have been investigated extensively. Furthermore, recent studies suggest that designing processes based on plant-microbe association are very promising avenues to remediate PCB-contaminated sites. In this review emphasis will be placed on the current state of knowledge regarding the strategies that are proposed to engineer PCB-degrading bacterial oxidative enzymes and PCB-degrading plant-microbe systems to degrade PCBs.

Further reading: Microbial Bioremediation of Non-metals: Current Research

In bacteria, many biological reactions are sustained by metabolic energy present in the form of phosphoester bonds, in compounds such as ATP and phosphoenolpyruvate (PEP), or in the form of ion gradients, such as the proton motive force (PMF) and the sodium motive force. The two forms of metabolic energy can be interconverted by FoF1-ATPases, which catalyze the translocation of H+ (or Na+) concomitant with either the hydrolysis or synthesis of ATP. Nutrient transport in bacteria is usually thought to consume metabolic energy; however, over the last two decades, a new class of nutrient transport reactions has been identified, in which substrate transport generates rather than consumes energy. The reaction consists of two steps: (1) electrogenic exchange of a precursor (amino acid or other organic acid) with its intracellular metabolic product produced by decarboxylation, and (2) intracellular decarboxylation of the transported precursor. The precursor:product exchange causes a net charge movement, which generates a membrane potential of physiological polarity, and the intracellular decarboxylation consumes cytoplasmic protons to generate both a pH gradient of physiological polarity and an outward concentration gradient of the end-product, which drives precursor uptake. The combined activities constitute a metabolically-driven proton pump (proton-motive metabolic cycle), which provides sufficient energy to generate ATP in a process called "decarboxylative phosphorylation". Thus, the proton-motive metabolic cycle can be recognized as a new class of ATP generation system that is distinct from substrate-level phosphorylation, oxidative phosphorylation, and photo-phosphorylation. We consider that the proton-motive metabolic cycle could be made available as an artificial energy-supply system in various industrial fermentation organisms with the use of recombinant DNA technology in the future.

Further reading: Lactic Acid Bacteria and Bifidobacteria: Current Progress in Advanced Research

from Koichi Nishio, Atsushi Kouzuma, Souichiro Kato and Kazuya Watanabe writing in Microbial Biofilms: Current Research and Applications:

Microbial fuel cells (MFCs) are devices that exploit microbial catabolic activities to generate electricity from a variety of starting materials, including complex organic waste and renewable biomass. The use of these energy sources provides MFCs with a great advantage over chemical fuel cells that utilize only purified reactive fuels (e.g., hydrogen). In an MFC bioreactor, microbes that respire using an anode with organics as electron donors grow preferentially, resulting in accelerated and increased current generation with time. The placement of an anode in either soil or sediment represents a simplified MFC system, known as a sediment MFC, which generates current as soil microbes utilize the anode as an electron acceptor. In addition, the irradiation of an MFC system results in the proliferation of photosynthetic microbes together with anode-respiring microbes, resulting in the syntrophic conversion of light energy into electricity. These examples demonstrate that the MFC system is based on a variety of fundamental and sustainable bioenergy processes, and we suggest that a deeper understanding of how microbes transfer electrons to anodes is essential for further developments of MFC systems.

Further reading: Microbial Biofilms: Current Research and Applications

Currently, the detection of microorganisms is largely based on time-consuming culture methods. However, newer enzymatic, immunological and genetic methods are being developed to replace and/or support classical approaches to microbial detection. Moreover, innovations in nanotechnology and nanosciences are having a significant impact in biodiagnostics, where a number of nanoparticle-based assays and nanodevices have been introduced for biomolecular detection. Accordingly, current and emerging molecular approaches for the detection of microbial pathogens as well as nanobiotechnologies that that will extend the limits of current molecular diagnostics are being developed.

from Olga Lomovskaya and Helen I. Zgurskaya writing in Emerging Trends in Antibacterial Discovery: Answering the Call to Arms:

Multidrug efflux pumps adversely affect both the clinical effectiveness of existing antibiotics as well as the discovery process to find new ones. In this chapter, we summarize recent advances in structural and functional analyses of multi-component efflux pumps from Gram-negative bacteria with the focus on transporters belonging to the Resistance-Nodulation-cell Division superfamily. The unquestionably significant impact of these pumps on the effectiveness of antibiotics in clinical settings and their emerging role in bacterial pathogenesis makes them attractive targets for inhibition. We discuss modes of inhibition and current efforts to develop effective inhibitors of multidrug efflux pumps.

Further reading: Emerging Trends in Antibacterial Discovery: Answering the Call to Arms

Studies on probiotic bacteria in the treatment or prevention of allergic rhinitis have shown encouraging results such as improved symptoms, reduced use of relief medication and modulated immunological parameters. Bacterial cells were shown to be sampled by intestinal immunocompetent cells and hence exerted diverse immunomodulatory effects on the hosts. Clinical studies using Bifidobacterium longum BB536 to prevent or treat allergic reactions to Japanese cedar pollen demonstrated possible involvement of gut microbiota in sensitization to allergens and development of symptoms, and the potential of probiotics in stabilizing the microbiota. Based on these studies, we suggest two possible mechanisms for the antiallergic activity of probiotics: 1) immunomodulatory effects via bacterial cell components mediated by intestinal antigen-presenting cells (biogenic effects); 2) immunomodulatory effects via generating or stabilizing a balanced gut microbiota (probiotic effects). These studies suggest that probiotics may serve as an alternative treatment for allergic rhinitis, although further studies are needed to determine this conclusively.

Further reading: Lactic Acid Bacteria and Bifidobacteria: Current Progress in Advanced Research

from Yuk Jing Loke and Jeffrey M. Craig writing in Epigenetics: A Reference Manual:

Epigenetics can appear as an impenetrable subject; not just to those encountering it for the first time, but to those within the field too. However, epigenetics, like any subject can be made easier to understand using a combination of clear language, creative illustrations and even animations and film clips. This chapter aims to point readers of all experiences towards helpful and easy-to-read resources that educate about epigenetics. It is split into two main sections, the first aimed at a lay audience including teachers and high school students and the second, at graduate and postgraduate students and beyond. Each section contains summaries of published articles and web sites. The chapter ends with a short section on epigenetic societies and research networks and a summary table of resources. It is intended to provide a sample of some of the best short to medium length reviews on general topics within the field of epigenetics and while we cover a wide variety of themes, we apologise for any areas not covered. We cite the URLs of freely-available articles wherever possible, but many articles will require library access. We also urge readers to contact authors or publishers if they wish to distribute any of the articles for teaching purposes.

Further reading: Epigenetics: A Reference Manual

from Karlijn C. Bastiaansen, Wilbert Bitter and María A. Llamas writing in Bacterial Regulatory Networks:

Gene expression in bacteria is mainly controlled at the level of transcription initiation. To achieve this process a number of different mechanisms have evolved, one of which is the utilization of alternative sigma factors. Sigma factors are small proteins that associate with the RNA polymerase core enzyme (RNAPc) and direct it to specific promoter sequences, where they initiate gene transcription. Bacteria are able to regulate transcription initiation by synthesizing and activating different sigma factors that recognize different promoter consensus sequences. The largest group of alternative sigma factors consists of the so-called extracytoplasmic function (ECF) sigma factors that regulate gene expression in response to cell envelope stresses or environmental stimuli. The activity of ECF sigma factors is controlled by anti-sigma factors and a complex cascade of regulated (proteolytic) modifications. In gram-negative bacteria, ECF sigma factors are also controlled by cell-surface signalling (CSS), a regulatory system that includes an outer membrane receptor in the signal transduction pathway. In this chapter we will discuss the general composition and function of ECF sigma factors and their role in cell envelope stress responses and CSS.

Further reading: Bacterial Regulatory Networks   Related publications

from Moshe Szyf writing in Epigenetics: A Reference Manual:

The DNA molecule contains within its chemical structure two layers of information. The DNA sequence that bears the ancestral genetic information and the pattern of distribution of covalently bound methyl groups to cytosines in DNA. While the genetic information is similar in all tissues in the individual, the pattern of distribution of methylation across the genome is cell-type specific. DNA methylation is an important regulator of gene function. Recent data that will be discussed here that supports the hypothesis that DNA methylation is a reversible biological signal. This expands the potential role of DNA methylation beyond embryogenesis to other time-points in life and to post mitotic tissues such as the brain. DNA methylation is proposed to act as a genomic response to both physical and social signals from the environment at different time points in life and to serve as a genomic memory of these exposures at different time scales, stably altering gene expression programming and thus modulating the physical and behavioral phenotypes to respond to these environments. It is hypothesized that DNA methylation provides within the structure of the DNA a dynamic interface between the changing world around us and the relatively fixed and stable genome.

Further reading: Epigenetics: A Reference Manual

from Scott B. Vande Pol writing in Small DNA Tumour Viruses:

Papillomavirus E6 oncoproteins are small zinc-binding proteins with a bewildering array of biological activities, including modulation of apoptosis, cellular transcription, host cell differentiation, growth factor dependence, DNA damage responses, and cell cycle progression. How can such a tiny protein do so much? This review examines insights from studies of oncogenic human papillomavirus E6 and bovine papillomavirus E6 to illuminate the mechanism by which E6 proteins interact with cellular binding partners. The origins of E6 and the history of its investigation are presented with the discovery of the major interaction partners that mediate E6 effects on DNA damage responses, cellular transcription, and modulation of keratinocyte differentiation.

Further reading: Small DNA Tumour Viruses   Related publications

from Begoña Carrasco, Paula P. Cardenas, Cristina Cañas, Tribuhwuan Yadav, Carolina E. César, Silvia Ayora and Juan C. Alonso writing in Bacillus: Cellular and Molecular Biology (Second edition):

All organisms have developed a variety of DNA repair mechanisms to cope with DNA lesions. Homologous recombination (HR), which uses a homologous template to restore lost information at the break site, is the ultimate step for repair of one- or two-ended double strands breaks (DSBs) and for promoting the re-establishment of replication forks. Genetic and cytological approaches were used to analyze the requirements of exponentially growing Bacillus subtilis cells to survive chemical or physical agents that generate one- or two-ended DSBs and the choreography of DSB repair. The damage-induced multi-protein complex (recombinosome), organised into focal assemblies, has been confirmed by biochemical approaches. HR is coordinated with other essential processes, such as DNA replication, transcription and chromosomal segregation. When DSB recognition or end resection is severely impaired or an intact homologous template is not available the DNA ends of two-ended DSBs are repaired via non-homologous end joining.

Further reading: Bacillus: Cellular and Molecular Biology (Second edition)

from Eivind Almaas, Per Bruheim, Rahmi Lale and Svein Valla writing in Systems Microbiology: Current Topics and Applications:

The functional repertoire of an organism's metabolic network is closely linked to its phenotype and potential for utility in metabolic engineering applications. In this chapter, we discuss a systems biology view of Escherichia coli metabolism by integrating current genome-scale computational modelling approaches with available molecular genetics tools, as well as the experimental framework for metabolite and metabolic flux determination.

Further reading: Systems Microbiology   Related publications

from Roger S. Lasken, Mary-Jane Lombardo, Mark Novotny, Joyclyn Yee-Greenbaum and Rashel V. Grindberg writing in Metagenomics: Current Innovations and Future Trends:

Development of a method to sequence DNA from a single cell has enabled new strategies to investigate the microbial world. Only a few years ago, sequencing from one cell was not feasible. A bacterium only contains a few femtograms of DNA which is insufficient for current sequencing technologies. This limitation was overcome with the development of a method to amplify DNA called multiple displacement amplification (MDA) which can generate micrograms of genomic sequence from one cell. Improvements have also been made in our ability to isolate cells by flow cytometry, micromanipulation and microfluidics and to lyse the cells to release the single genome copy as a template for MDA. Large portions of the genome can be obtained from each cell and this has opened up a new front in the effort to sequence uncultivated species. Cells can be isolated from an environment or clinical specimen and directly sequenced with no need to develop culture methods. This chapter will review the current methodologies, the strengths and limitations of the single cell approach and its application to microbial genomics.

Further reading: Metagenomics: Current Innovations and Future Trends

from Justin A. Fincher and Jonathan H. Dennis writing in Epigenetics: A Reference Manual:

DNA in eukaryotes is efficiently and compactly organized into chromatin, the fundamental subunit of which is the nucleosome: approximately 150 bp of DNA spooled 1.65 times around a histone octamer. The location and density of nucleosomes play a role in regulating nuclear processes including transcription, replication, recombination, and repair. Mechanisms acting in trans, like ATP-dependent remodelers and cellular memory complexes, as well as in cis features intrinsic to the DNA sequence itself regulate the location and density of nucleosomes. Here, we review the three cis acting DNA sequence features that affect the distribution of nucleosomes: (1) two frameworks defining the relationship between the histone octamer and the underlying DNA sequence (nucleosome occupancy and nucleosome position, then statistical positioning and a nucleosome positioning code), (2) the organization of DNA into the nucleosome core particle, and (3) specific DNA sequence features and DNA templates that promote or inhibit the formation of nucleosomes. We close by describing three computational algorithms trained on DNA sequence that have been used to predict nucleosome position and density. In summary, we hope to draw attention to multiple aspects of DNA sequence that specify organization of sequence into nucleosomes and influence the distribution of nucleosomes in eukaryotic genomes.

Further reading: Epigenetics: A Reference Manual

"This volume provides a good overview of how newer techniques are being used to study environmental microbial populations, primarily in water. It is a very useful starting point for those who are looking for an introduction to some of the methods or need to come up to speed on developments over the last decade or so ... The chapters are very well referenced ... it provides quite a comprehensive and useful look at the applications of a range of methodologies to aquatic microbiology in recent years. " from Jean MacRae (University of Maine, Orono, USA) writing in The Quarterly Review of Biology (2011) 86: 354-355. read more ...

Environmental Microbiology: Current Technology and Water Applications Edited by: Keya Sen and Nicholas J. Ashbolt ISBN: 978-1-904455-70-7 Publisher: Caister Academic Press Publication Date: January 2011 Cover: hardback "comprehensive and useful" (Quar. Rev. Biol.)

"a valuable book for both graduate students and mature scientists working in the field of bacterial pathogenesis. The authors are all highly accomplished scientists and have carefully shared their work in a logical and comprehensive manner ... useful to those in many areas of research" from Rebecca T. Horvat (University of Kansas, USA) writing in Doodys read more ...

Bacterial Pathogenesis: Molecular and Cellular Mechanisms Edited by: Camille Locht and Michel Simonet ISBN: 978-1-904455-91-2 Publisher: Caister Academic Press Publication Date: January 2012 Cover: hardback "useful to those in many areas of research" (Doodys)

from Samson Mani and Zdenko Herceg writing in Epigenetics: A Reference Manual:

DNA methylation is an important regulator of gene transcription and a large body of evidence has demonstrated that aberrant DNA methylation is associated with unscheduled gene silencing, and the genes with high levels of 5-methylcytosine in their promoter region are transcriptionally silent. DNA methylation is essential during embryonic development, and in somatic cells, patterns of DNA methylation are generally transmitted to daughter cells with a high fidelity. Aberrant DNA methylation patterns have been associated with a large number of human malignancies and found in two distinct forms: hypermethylation and hypomethylation compared to normal tissue. Hypermethylation is one of the major epigenetic modifications that repress transcription via promoter region of tumour suppressor genes. Hypermethylation typically occurs at CpG islands in the promoter region and is associated with gene inactivation. Global hypomethylation has also been implicated in the development and progression of cancer through different mechanisms. This chapter will focus on DNA methylation as the major epigenetic mechanism involved in normal biological processes and abnormal events leading to cancer development. It will also focus on the interaction between DNA methylation and other epigenetic mechanisms.

Further reading: Epigenetics: A Reference Manual

from Sainath Rao Shilpakala, Krishna Mohan V. Ketha and Chintamani D. Atreya writing in Bacterial Spores: Current Research and Applications:

Bacteria of several genera are able to form endospores when subjected to certain starvation conditions. The endospores are dormant forms that are structurally and biochemically different from the corresponding growing or vegetative cells. These bacterial endospores resist antibiotics, desciccation, and ordinary boiling than the vegetative cells. The detection of bacterial endospores can be important for a wide variety of purposes. In the sanitation and hygiene fields, detection of bacterial spores can be critical to monitor indoor environments, water quality and food quality. Similarly, in the public health perspective detection of bacterial spores is very important in ensuring regulation of safer transfusion and other therapeutic products, administered either orally or intravenously. Monitoring of bacterial spores is gaining importance even in other areas such as agriculture wherein soil or plant samples are periodically monitored for bacterial spores to ensure high levels of the bacterial population/toxin to be effective against insect pests. More recently, with the possibility of bacterial spores being used as bio-threat agents there has been an augmented effort in developing much more sensitive, specific and rapid detection systems for bacterial spores. The review discusses about current methods of bacterial spore detection and the challenges involved.

Further reading: Bacterial Spores   Related publications

from David L. Popham, Jared D. Heffron and Emily A. Lambert writing in Bacterial Spores: Current Research and Applications:

During spore germination, several spore components are broken down and are discarded or recycled. The first major degradative step in germination is depolymerization of the spore cortex peptidoglycan. This is essential to allow full hydration of the spore core and the resumption of cellular metabolism. The spore cortex is a thick layer of peptidoglycan with structural modifications that differentiate it from vegetative cell wall material. Germination-specific cortex lytic enzymes exhibit specificity for the muramic-δ-lactam modification of the peptidoglycan strands. As no protein synthesis can take place during germination prior to cortex breakdown, the cortex lytic enzymes must be produced during spore formation and packaged within the dormant spore in an inactive and highly stable form. A mechanism(s) must then exist for the activation of lytic enzymes during germination. This chapter will cover the current knowledge concerning the identities of cortex lytic enzymes in Bacilli and Clostridia, their expression and incorporation into dormant spores, the mechanisms that hold them inactive during spore dormancy and their activation during germination, and their specific lytic activities, substrates, and products.

Further reading: Bacterial Spores   Related publications

from J. Maxwell Dow, Yvonne McCarthy, Karen O'Donovan, Delphine Caly and Robert P. Ryan writing in Bacterial Regulatory Networks:

Cyclic di-GMP is now recognised as an almost universal second messenger in eubacteria that acts to regulate a wide range of functions including developmental transitions, adhesion, biofilm formation, motility and the synthesis of virulence factors. Cyclic di-GMP is synthesised from two GTP molecules by diguanylate cyclases that have a GGDEF domain and degraded by phosphodiesterases with either an EAL or HD-GYP domain. These proteins often have associated signal input domains, suggesting that their enzymatic activity may be modulated by different environmental or cellular cues. Cyclic di-GMP exerts a regulatory action through binding to diverse receptors that include a small protein domain called PilZ, transcription factors, enzymatically-inactive GGDEF, EAL or HD-GYP domains and riboswitches. The multiplicity of GGDEF, EAL and HD-GYP proteins together with a range of receptors within the same bacterial cell indicates the considerable complexity of cyclic di-GMP signalling. This has led to the concept of discrete pools of the nucleotide that are generated locally and act to influence intimately associated targets. A number of signalling proteins may be organised in a regulatory network to control a common function(s). Understanding cyclic di-GMP signalling may afford strategies for inhibition of biofilm formation and virulence factor synthesis in bacterial pathogens.

Further reading: Bacterial Regulatory Networks   Related publications

from Juan A. Ayala, Felipe Cava and Miguel A. de Pedro writing in Stress Response in Microbiology:

The cell envelope is the major line of defence against environmental threats. It is an essential but vulnerable structure that shapes the cell and counteracts the turgor pressure. It provides a sensory interface, a molecular sieve and a structural support, mediating information flow, transport and assembly of supramolecular structures. Therefore, maintenance of cell envelope integrity in the presence of deleterious conditions is crucial for survival. Several envelope stress responses, including two components regulatory systems (TCRS), of Escherichia coli are involved in the maintenance, adaptation and protection of the bacterial cell wall in response to a variety of stresses. Recent studies indicate that these stress responses exist in many Gram negative pathogens. Particular emphasis has been made on the identified TCRS and their activating signals. Another aspect of stress response is the generation of morphological modifications. Most bacteria alter shape when growth conditions change and upon symbiotic or parasitic processes. Any modification in cell shape is connected with cell wall metabolism and requires specific regulatory mechanisms. Recent advances support the existence of complex mechanisms mediating morphological responses to stress involving inter and intra-specific signalling.

Further reading: Stress Response in Microbiology   Related publications

from Steve Flint and Gideon Wolfaardt writing in Microbial Biofilms: Current Research and Applications:

Biofilms can directly or indirectly be attributed to deterioration of the underlying substratum. Corrosion may result, particularly if the surface comprises metal or metal alloy. This phenomenon, referred to as microbially influenced corrosion (MIC) affects many industries from food manufacture to medicine. The economic impact of corrosion is significant due to the need for replacing corroded equipment, repairs and attempts to prevent corrosion. MIC is believed to be responsible for one third of all metallic corrosion. Although there have been many studies into the mechanisms of MIC, the process is relatively poorly understood. Most information relates to pure cultures, however biofilms are rarely composed of single species thus most models are a simplification of the real process. It is likely the MIC depends on the composition of the biofilm and the environment surrounding the biofilm. Prevention and control methods rely on mechanical cleaning of fouling and chemical removal and killing of biofilms. Future control measures are likely to focus on preventing biofilm formation.

Further reading: Microbial Biofilms: Current Research and Applications

from John M. Pfeffer, Patrick J. Moynihan, Chelsea A. Clarke, Chris Vandenende and Anthony J. Clarke writing in Bacterial Glycomics: Current Research, Technology and Applications:

Lytic transglycosylases are an important class of bacterial enzymes that act on peptidoglycan with the same substrate specificity as lysozyme. Unlike the latter enzymes however, the lytic transglycosylases are not hydrolases, but instead cleave the glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anydromuramyl product. They are ubiquitous in bacteria which produce a complement of different forms that are responsible for creating space within the peptidoglycan sacculus for its biosynthesis and recycling, cell division, and the insertion of cell-envelope spanning structures, such as flagella and secretion systems. Given their catastrophic autolytic potential, the activity of lytic transglycosylases must be tightly controlled within the producing cells. Three modes of control at the enzymatic level have been identified: the modification of substrate, membrane association and complex formation, and the production of proteinaceous inhibitors. These modes of control and their potential as new targets for antibacterials are discussed.

Further reading: Bacterial Glycomics: Current Research, Technology and Applications

from Berenike Maier writing in Bacillus: Cellular and Molecular Biology (Second edition):

Competence for transformation enables bacteria to take up exogenous DNA. The imported DNA can integrate into the chromosome by homologous recombination or anneal to form a self replicating plasmid. Development of competence in Bacillus subtilis is tightly regulated as a function of cell density during entry into the stationary growth phase. Additionally, competence occurs only in a small subpopulation of B. subtilis cells. Development of competence is switch-like and controlled by the concentration of the master regulator ComK. Quantitative analysis at the single cell level in conjunction with mathematical modeling allowed understanding of development and decline of competence at the systems level. In the current model, a complex regulatory network maintains the concentration of ComK below a threshold concentration for switching into the competent state. In the stationary growth phase, noisy expression of ComK triggers competence development as individual cells reach the threshold concentration due to random fluctuations. Competent cells express specialized proteins (late competence proteins) for binding, importing, and recombining external DNA. Cytosolic and transmembrane proteins accumulate at a single or both cell poles. Application of external DNA triggers movement of various proteins involved in recombination away from the pole, most likely undergoing search for homologous regions on the chromosome. These findings provide good evidence for a concerted action of DNA import and recombination, promoting the idea that a spatially organized and modular multiprotein machine has evolved for efficient transformation. This machine powers efficient and irreversible DNA import and can work against considerable external forces.

Further reading: Bacillus: Cellular and Molecular Biology (Second edition)

from Peter L. Graumann writing in Bacillus: Cellular and Molecular Biology (Second edition):

After a bit more than a decade of the use of GFP - or immuno-fluorescence microscopy to study bacterial chromosome segregation, it has become clear that this process is highly organized, temporally as well as spatially, and that a mitotic-like machinery exists that actively moves apart sister chromosomes. Several key factors in this process have been identified, and at least a rough overall picture can be drawn on how chromosomes are separated so highly rapidly and efficiently. Bacillus subtilis has a circular chromosome. Replication initiates at the origin of replication that is defined as 0 degrees, and two replication forks proceed bidirectionally to converge at the terminus region, which is defined as 180 degrees. All other regions on the chromosome are defined as the corresponding site on a circle. DNA replication occurs in the cell centre, and duplicated regions are moved away from the cell centre towards opposite cell poles. This process is driven by an active motor that involves bacterial actin-like proteins, whose mode of action is still unknown. A dedicated protein complex called SMC forms two subcellular centres that organize newly duplicated chromosome regions within each cell half, setting up the spatial organization that characterizes bacterial chromosome segregation. Several proteins, including topoisomerases, DNA translocases and recombinases, ensure that entangled sister chromosomes or chromosome dimers can be completely separated into the future daughter cells shortly before cell division occurs at the middle of the cells.

Further reading: Bacillus: Cellular and Molecular Biology (Second edition)

from T.A. Vishnivetskaya, B. Raman, T.J. Phelps, M. Podar and J.G. Elkins writing in Extremophiles: Microbiology and Biotechnology:

Conversion of lignocellulosic biomass to liquid fuels using biological processes offers a potential solution to partially offset the world's dependence on fossil fuels for energy. In nature, decomposition of organic plant biomass is brought about by the combined action of several interacting microorganisms existing in complex communities. Bioprospecting in natural environments with high cellulolytic activity (for example, thermal springs) may yield novel cellulolytic microorganisms and enzymes with elevated rates of biomass hydrolysis for use in industrial biofuel production. In this chapter, various cellulose-degrading microorganisms (in particular, thermophilic anaerobic bacteria), their hydrolytic enzymes, and recent developments in the application of biomass fermentations for production of sustainable bioenergy are reviewed. In this context, results from ongoing research at the Oak Ridge National Laboratory in the isolation and subsequent phylogenetic and metabolic characterization of thermophilic, anaerobic, cellulolytic bacteria from the hot springs of Yellowstone National Park are presented.

Further reading: Extremophiles: Microbiology and Biotechnology

from Frederico Gueiros-Filho writing in Bacillus: Cellular and Molecular Biology (Second edition):

Cell division is the process of generating two viable descendants from a progenitor cell. This involves two coordinated events: the replication and segregation of the bacterial chromosome and the splitting of the progenitor cell by cytokinesis, which in bacteria is also known as septum formation. Bacterial cells have developed a remarkably sophisticated protein machine capable of precisely splitting a progenitor cell at the right place and time in every cell cycle. This machine, which is known as the divisome or septalsome, is based on a contractile protein ring, as in the case of eukaryotes. In contrast to eukaryotic cells, however, which use actin and myosin in their contractile protein ring, the bacterial contractile machine is based on the tubulin-like protein FtsZ. Here we review the mechanism of cytokinesis in Bacillus subtilis.

Further reading: Bacillus: Cellular and Molecular Biology (Second edition)

from Rainer Gross, Andreas Schmid and Katja Buehler writing in Microbial Biofilms: Current Research and Applications:

Biofilms are mainly known for causing problems in medical and industrial settings due to their persistence towards treatment with bactericides, including antibiotics. However, in the area of bioremediation they are widely recognized for their ability to degrade hazardous or organic compounds to CO₂ and biomass. Biofilms represent a highly interesting biological concept since they unite important characteristics such as the ability of self-immobilization and increased robustness to various physical, chemical and biological stressors, which make them exceedingly attractive for productive catalysis. The following review provides a detailed survey of biofilm applications for productive biocatalysis on lab-, pilot-, and industrial scales, regarding fermentation as well as biotransformation reactions. It discusses technological as well as biological challenges of biofilm driven catalysis, presenting developments in the field of biofilm reactor technology and the latest findings in understanding biofilm dynamics. Biocatalysis related issues like genetic stability, evolution, uncontrolled growth as well as detachment, contamination risks, monitoring of biomass, EPS, chemical and biological heterogeneity are considered.

Further reading: Microbial Biofilms: Current Research and Applications

from Anne N. Reid and Leslie Cuthbertson writing in Bacterial Glycomics: Current Research, Technology and Applications:

Capsular polysaccharides (CPSs) and exopolysaccharides (EPSs) enhance bacterial survival in the environment, contribute to symbiotic interactions between plants and bacteria, and mediate interactions between plant and animal pathogens and their hosts. Bacteria express a wide array of CPS and EPS structures that are assembled by one of three distinct mechanisms. The Wzy-dependent polymerization system is characterized by the synthesis of lipid-linked repeat units in the cytoplasm, and their block-wise polymerization at the periplasmic face of the inner membrane. The resulting polymer is transported across the outer membrane (in Gram-negative organisms) via a channel formed by an outer membrane polysaccharide export (OPX) protein. The ATP-binding cassette (ABC) transporter-dependent system is defined by the synthesis of full-length CPS chains in the cytoplasm, their ABC transporter-dependent export across the inner membrane, and their subsequent transport across the outer membrane, presumably via a channel formed by an OPX protein. In the synthase-dependent system, a single enzyme achieves polymer initiation, synthesis and export across the membrane. This chapter describes these modes of CPS and EPS assembly, highlighting recent findings and identifying areas where further research is warranted.

Further reading: Bacterial Glycomics: Current Research, Technology and Applications

from Gabriele Pastorella, Giulio Gazzola, Seratna Guadarrama and Enrico Marsili writing in Microbial Biofilms: Current Research and Applications:

Bioremediation uses microorganisms to remove, detoxify, or immobilize pollutants, and does not require addition of harmful chemicals. Bioremediation is particularly suitable for large areas where contaminant concentrations are relatively low and the hydrology of the soil does not support an aggressive chemical remediation strategy. In the last few years, researchers have described the mechanisms of bioremediation for numerous priority pollutants, including chlorinated hydrocarbons, polyaromatic hydrocarbons, and heavy metals. However, most studies published to date have dealt with planktonic cultures grown under controlled laboratory conditions. Microorganisms in the environment occur mostly as biofilms, whose development is encouraged by the presence of solid surfaces and the limited amounts of organic carbon. Therefore, optimization of bioremediation processes in the field requires a thorough knowledge of biofilm structure, dynamic, and interaction with pollutants and other environmental factors. In this chapter, we describe the recent advances in bioremediation, with particular regard to the role of microbial biofilms. We discuss emerging technologies, such as bioelectroremediation and microbially produced surfactants. We also show how genetic engineering technologies may be employed to improve bioremediation effectiveness, both in laboratory and in field applications.

Further reading: Microbial Biofilms: Current Research and Applications

from G.A. Clark Ehlers and Susan J. Turner writing in Microbial Biofilms: Current Research and Applications:

Biofilms occur frequently inside various engineered systems for wastewater treatment. These include traditional trickling filter systems, modified lagoons, and specialized supplementary systems for nutrient removal or treatment of specialized wastes. The major advantages of biofilm systems over suspension treatment is the high microbial density that can be achieved, leading to smaller treatment system footprints, and the inherent development of aerobic, anoxic and anaerobic zones which enable simultaneous biological nutrient removal. The intrinsic resistance of biofilm communities to changing environmental conditions creates the added advantage that biofilm-based treatment systems are more resilient to influent variation in toxicity and nutrient concentrations. In contrast to biofilms of environmental or biomedical relevance comparatively little is known about development and stability in waste treatment systems. The advent of tools that enable the study of biofilms in reactor systems on a molecular level has enabled greater insight into the physiologically and biochemically relevant pathways that may facilitate optimized processes. In this chapter, the current literature on biofilms in wastewater treatment systems is reviewed and opportunities for further development in this field are identified.

Further reading: Microbial Biofilms: Current Research and Applications

from Gavin Lear, Andrew Dopheide, Pierre-Yves Ancion, Kelly Roberts, Vidya Washington, Jo Smith and Gillian D. Lewis writing in Microbial Biofilms: Current Research and Applications:

This chapter reviews our current understanding of the roles biofilm-associated microbial communities play in both maintaining and improving the ecological health of freshwater rivers and streams. Biofilms are where most of the bacteria present in freshwater systems are found, and have been identified as major sites for primary production, carbon and nutrient cycling. Advances in various scientific methodologies have recently been used to characterise the enormous diversity of biofilms, in terms of their structural, chemical and biological traits. The microbial life present within most natural biofilms, as well as associated exudates and lysates have been identified as a valuable, nutrient rich food source for a variety of benthic consumers. Furthermore, the diverse metabolic potential of these complex communities, in combination with various protective traits offered by the biofilm 'mode-of-life', provide biofilms with an excellent ability to degrade, or otherwise transform a vast array of freshwater pollutants. Despite this apparent resilience, we highlight the sensitivity of these poorly studied freshwater biofilm communities to various human activities, and consider their potential as a reliable and sensitive biological indicator of freshwater ecological health.

Further reading: Microbial Biofilms: Current Research and Applications

from James D. Bryers writing in Microbial Biofilms: Current Research and Applications:

Clinically related research on biofilms has expanded exponentially in the past ten years due to the pandemic of nosocomial (hospital-related) infections. Biofilms are thought to cause a significant amount of all human microbial infections, according to the Centers for Disease Control and Prevention. Nosocomial infections are the fifth leading cause of death in the U.S. with more than two million cases annually (or approximately 10% of American hospital patients). The difficulty of eradicating biofilm bacteria with classic systemic antibiotic treatments is a prime concern of medicine. Biofilm bacteria can be up to a thousand times less susceptible to antimicrobial stress than their freely suspended counterparts. This chapter discusses the pathogenesis of a number of biofilm-mediated infections, including: oral infections, biomedical device based infections, osteomyelitis, otitis media, and others. Emerging research in biofilm control and prevention is also reviewed.

Further reading: Microbial Biofilms: Current Research and Applications

from Leonardo G. Alonso, Lucía B. Chemes, María L. Cerutti, Karina I. Dantur, and Gonzalo de Prat-Gay writing in Small DNA Tumour Viruses:

The human papillomavirus E7 oncoprotein is the main transforming agent of this important pathogen. Although its primary action is binding and targeting the retinoblastoma tumour suppressor protein, over two decades of research has shown a much more complex mode of action where multiple cellular partners and cellular events take place before ultimate progression to carcinogenesis. In this chapter we describe the HPV16 E7 protein in biochemical terms in an attempt to understand some of the various interactions in which this protein participates. We describe its multiple equilibria and conformational species in solution and show that these can explain some of its puzzling promiscuous binding activities and we review the few interactions that have been addressed by biochemical and mechanistic approaches to date. We finally discuss the cellular localization of E7 conformers, how they influence its antigenic capacity, and how they can be exploited in therapeutic applications.

Further reading: Small DNA Tumour Viruses   Related publications

from Patricia C. Burrows, Simone C. Wiesler, Zhensheng Pan, Martin Buck and Sivaramesh Wigneshweraraj writing in Bacterial Regulatory Networks:

Amongst the many accessory factors that bind RNA polymerase (RNAp) and serve to control its activities, sigma (sigma) factors ubiquitously feature in programming of gene expression in response to abiotic and biotic cues. Here we review the role of the major variant sigma factor, sigma54, in the expression of gene sets used for establishing the virulence of a wide range of pathogenic bacteria. The tight coupling of sigma54-dependent transcription to signalling pathways underpins the regulation of such systems, and allows a wide dynamic range of gene expression.

Further reading: Bacterial Regulatory Networks   Related publications

from Arun K. Mishra, Sarah M. Batt, Luke J. Alderwick, Klaus Futterer, and Gurdyal Singh Besra writing in Bacterial Glycomics: Current Research, Technology and Applications:

Lipoarabinomannan is an amphipathic lipoglycan found in the cell wall of most Actinomycetes. The majority of bacteria from the sub-order Corynebacterineae, including Mycobacterium tuberculosis, Mycobacterium smegmatis and Corynebacterium glutamicum, and from genus Rhodococcus, Gordonia and Amycolatopsis; all possess lipoarabinomannan and related glycoconjugates, such as lipomannan and phosphatidyl-myo-inositol mannosides. In addition to their physiological function in these microorganisms, these glycoconjugates play a key immunomodulatory role for pathogenic bacteria during infection. Herein, we report the work from this laboratory and several others, which has led to the biochemical characterization of key enzymes involved in the biogenesis of these complex glycoconjugates.

Further reading: Bacterial Glycomics: Current Research, Technology and Applications

from Susan M. Twine and Susan M. Logan writing in Bacterial Glycomics: Current Research, Technology and Applications:

The biosynthesis and assembly of the flagellar apparatus has been the subject of extensive studies over many decades. More recently, glycosylation of the major structural protein, the flagellin, has been shown to be an important component of numerous flagellar systems in both Archaea and Bacteria, playing either an integral role in assembly and for a number of bacterial pathogens a role in virulence. Increasingly, it is apparent that bacteria elaborate a structurally diverse array of flagellin-modifying glycans. This chapter focuses firstly upon reviewing recent research on the structural diversity in Gram-positive and Gram-negative flagellar glycosylation systems. In the second part, the ways in which flagellin glycosylation and associated biosynthetic pathways can be exploited are discussed.

Further reading: Bacterial Glycomics: Current Research, Technology and Applications

from Kathryn A. Scott, Elizabeth E. Jefferys, Benjamin A. Hall, Mark A. J. Roberts and Judith P. Armitage writing in Bacterial Regulatory Networks:

Chemotaxis is the process by which bacteria migrate towards environments that are favourable for growth. Changes in the concentration of attractants or repellents are detected by receptors, which are usually transmembrane proteins. These receptors transduce the signal to the interior of the cell where a two-component system ultimately leads to changes in motile behaviour. Chemotaxis emerged as a beneficial trait for survival early in the evolution of bacteria and archaea. A core set of proteins is common to the chemosensory networks in many different species. During the evolution of bacteria this core network has diversified and expanded. Here we describe the conserved apparatus in the steps necessary for chemotaxis; sensing of chemoeffectors, signalling to the motility apparatus, rapid signal termination, and adaptation. We then highlight examples from species with complex chemosensory networks to illustrate the variations in chemotactic apparatus that have arisen from the common core.

Further reading: Bacterial Regulatory Networks   Related publications

from Diana Clausznitzer, Judith P. Armitage and Robert G. Endres writing in Systems Microbiology: Current Topics and Applications:

Bacterial chemotaxis is a paradigm for biological sensing and information transmission. The chemotaxis signal-transduction pathway allows cells to sense chemicals in their surroundings in order to regulate flagellated rotary motors, thus allowing them to swim towards nutrients and away from toxins. Importantly, cells are able to sense with remarkably high sensitivity over a wide range of chemical background concentrations. To make this possible, chemoreceptors do not signal independently but form clusters for amplification and integration of signals, as well as for adaptation to persistent stimulation. While chemotaxis in Escherichia coli has been exceptionally well characterised, new experimental facts still require revisions of existing models and thus further increase our understanding of sensing and signalling in bacteria. Additionally, experiments on other bacterial species such as Bacillus subtilis and Rhodobacter sphaeroides indicate that bacteria other than E. coli can have substantially different and more complex chemotaxis pathways, which provides renewed challenges for experimentalists and modellers alike. Here we discuss our current understanding as well as the frontiers of bacterial chemotaxis research.

Further reading: Systems Microbiology   Related publications

from J. Cuccui, R.H. Langdon, M.G. Moule and Brendan W. Wren writing in Bacterial Glycomics: Current Research, Technology and Applications:

Once thought to be restricted to eukaryotes and archaea, N-linked glycosylation has now been discovered in prokarytoes. Over the past decade, our understanding of bacterial N-linked glycosylations systems and their abundance has been expanding. This type of protein modification was first demonstrated in Campylobacter jejuni, a human gut pathogen, and we now know that N-linked glycosylation also exists in other &episilon;-proteobacteria ranging from the deep-sea vent Nitratiruptor spp. and Sulfurovum spp. to sulfate reducing δ-proteobacteria. A greater understanding of these systems is necessary in order to comprehend the evolutionary reasons for their development and maintenance. In addition, this knowledge may also be exploited for glycoengineering purposes to produce cheaper subunit vaccines as well as humanized proteins.

Further reading: Bacterial Glycomics: Current Research, Technology and Applications

from Warren Wakarchuk writing in Bacterial Glycomics: Current Research, Technology and Applications:

It is now accepted that complex glycans play major roles in biology, such as the development of the embryo, the function of the immune system, microbial and viral pathogenesis and cellular communication, to name just a few. The many faceted roles that glycans play in biology makes them a challenge to understand on functional level, and the complexity of the structures themselves makes them daunting targets for chemical synthesis, which is required for examination of their binding interactions and for future development of carbohydrate based therapeutics. In order to facilitate the synthesis of complex glycans, we have been examining glycosyltransferases which make strategic linkages in biologically active glycans. Many of the mammalian enzymes have not been as easy to express as active recombinant proteins, and many have a more restricted acceptor specificity that limits their use for synthesis. Our focus has been on the use of bacterial enzymes from pathogens which make molecular mimics of host glycans, and which have been shown to be potent catalystsfor carbohydrate synthesis. This chapter will provide a review on a variety of bacterial enzymes that we and others have enabled for in vitro synthetic carbohydrate chemistry, as well as some promising in vivo production strategies for bioactive carbohydrates.

Further reading: Bacterial Glycomics: Current Research, Technology and Applications

from Petra Tielen, Max Schobert, Elisabeth Hartig and Dieter Jahn writing in Bacterial Regulatory Networks:

Survival and growth during periods of low oxygen tension are essential for the successful colonization of natural habitats by bacteria. For the coordination of the necessary biochemical adaption processes upon oxygen deprivation bacteria employ a fine tuned interplay of various regulatory proteins and sRNAs. The iron sulfur cluster containing oxygen sensor Fnr and its multiple variants are often found involved in the corresponding regulatory networks throughout the bacterial kingdom. Similarly, the alternative electron acceptor nitrate is usually detected by the two-component system NarXL and its derivatives. In contrast, other systems including the quinone pool responsive two component system ArcBA, the ResDE system or the regulatory sRNAs FnrS and ArcZ are limited to certain bacterial groups. Here we describe the regulatory networks and their components underlying the adaption processes of the model bacteria Escherichia coli, Pseudomonas aeruginosa and Bacillus subtilis to an anaerobic life style.

Further reading: Bacterial Regulatory Networks   Related publications

from Mette Burmølle, Annelise Kjøller and Søren J. Sørensen writing in Microbial Biofilms: Current Research and Applications:

Biofilms in soil are composed of multiple species microbial consortia attached to soil particles and biotic surfaces including roots, fungal hyphae and decomposing organic material. The bacteria present in these biofilms gain several advantages including protection from predation, desiccation and exposure to antibacterial substances, and optimized acquisition of nutrients released in the mycosphere. Studies of soil biofilms are complicated by the composite structure of the soil environment; therefore, various simplified model systems have been applied to study succession and bacterial interactions in soil biofilms. Model system observations indicate an increased efficiency to degrade and decompose organic material and xenobiotic compounds by these multispecies bacterial communities. Consequently, soil biofilms may be valuable tools for bioremediation and biocontrol. However, soil biofilms may also provide survival sites for opportunistic pathogenic bacteria, providing enhanced protection and increasing their potential to survive and evolve in the soil environment. In this review, we provide evidence that biofilms are of major importance for the fitness of individual bacteria and the wider soil ecology, due to the accumulated selective advantage provided to bacteria by the biofilm mode-of-life.

Further reading: Microbial Biofilms: Current Research and Applications

from Stephen A Bustin, Sara Zaccara and Tania Nolan writing in Quantitative Real-time PCR in Applied Microbiology:

The real-time fluorescence-based quantitative polymerase chain reaction (qPCR) has become the benchmark technology for the detection of nucleic acids in every area of microbiology, biomedical research, biotechnology and in forensic applications. Unlike conventional (legacy) PCR, which is a qualitative end-point assay, qPCR allows accurate quantification of amplified DNA in real time during the exponential phase of the reaction. The cost of instruments and reagents is well within reach of individual laboratories, assays are easy to perform, capable of high throughput and combine high sensitivity with reliable specificity. It is possible to achieve accurate and biologically meaningful quantification if meticulous attention is paid to the details of every step of the qPCR assay, starting with sample selection, acquisition and handling through assay design, validation and optimisation. The growing awareness of the need for standardisation, quality control and the significant problems associated with inadequate reporting of the assay has resulted in the publication of guidelines for minimum information for the publication of qPCR experiments (MIQE).

Further reading: Quantitative Real-time PCR in Applied Microbiology   Related publications

from Amy S. Gardiner, Abigail I. Wald and Saleem A. Khan writing in Small DNA Tumour Viruses:

In recent years, microRNAs (miRNAs) have been found to play important roles in the regulation of gene expression in mammalian cells. MiRNAs regulate many processes, including cell cycle progression, cell differentiation and organogenesis. Human cells encode approximately 1,000 miRNAs, and their expression has been shown to be altered in a variety of human cancers. Human papillomaviruses (HPVs) are DNA tumour viruses that are associated with cancers, especially cancers of the cervix and oropharynx. Recently, several studies have shown altered expression of miRNAs in HPV-associated cervical and oral cancers. In this article, we discuss the role of HPVs and their oncogenes in altering cellular miRNA expression, possible targets of such miRNAs, and how miRNA changes may contribute to the pathogenesis of HPV-associated cancers.

Further reading: Small DNA Tumour Viruses   Related publications

from Laura White and G. Eric Blair writing in Small DNA Tumour Viruses:

Adenovirus (Ad)-based vectors have been frequently used as gene therapy vectors due to their ability to infect a wide range of dividing and non-dividing cells, their efficient growth to high titres in complementing cell lines and ease of genome manipulation. However, the transition of Ad vectors from in vitro studies to clinical application has been limited by sub-optimal efficacy and robust inflammatory responses elicited upon administration. In recent years it has become clear that multiple innate and adaptive responses limit the efficacy and safety of Ad vectors. In this review, we focus on the current understanding of the immune response to Ads with a particular focus on the innate immune response, and how this information can be used to design safer and more efficacious vectors.

Further reading: Small DNA Tumour Viruses   Related publications

from W. Brian Whitaker and E. Fidelma Boyd writing in Stress Response in Microbiology:

Members of the genus Vibrio are Gram-negative ubiquitous marine bacteria. They can be isolated directly from the water column but are perhaps most known for their association with eukaryotic organisms. In their association with eukaryotic hosts, be it pathogenic or symbiotic, these bacteria must respond to a variety of stress conditions present within the host environment. Often times, these stress response systems are vitally important for the vibrios to successfully establish in the host. Here, we will discuss the systems used by the three main human pathogens of the genus, V. cholerae, V. parahaemolyticus, and V. vulnificus as well as briefly discussing the stress response systems of V. fischeri, V. splendidus, and V. anguillarum, all of which form close associations with marine organisms.

Further reading: Stress Response in Microbiology   Related publications

Small DNA Tumour Viruses Edited by: Kevin Gaston ISBN: 978-1-904455-99-8 Publisher: Caister Academic Press Publication Date: March 2012 Cover: hardback

read more ...]]>http://www.horizonpress.com/blogger/2011/12/small-dna-tumour-viruses-book-available-very-soon.htmlhttp://www.horizonpress.com/blogger/2011/12/small-dna-tumour-viruses-book-available-very-soon.htmlFri, 16 Dec 2011 12:15:00 GMTToxoplasma gondii: Without Stress There Is No Life

from Maria J. Figueras, Sergio O. Angel, Verónica M. Cóceres and Maria L. Alomar writing in Stress Response in Microbiology:

Toxoplasma gondii is an important pathogen of human and domestic animals. It has a complex life cycle which includes the transition from one host to another, being only exposed to the environment during one stage, as highly resistant oocysts. Interestingly, in the intermediate host (non-feline mammalians and birds) the parasite presents an asexual cycle with two stages that can interconvert without its passage in the definite host (felines). The asexual cycle is very important in the establishment of the infection and on its pathogenesis and it could be driven by different kind of stressors. Therefore, the response to environmental and host stresses is essential to their viability and successful progression through their life cycle. The heat shock proteins are key molecules not only in the resistance to different stressors, but they are also involved in the optimal differentiation as well as in other biological processes in T. gondii. This chapter summarizes the findings on different aspects of T. gondii stress responses and the implication of these processes in the biology and pathogenesis of this parasite.

Further reading: Stress Response in Microbiology   Related publications

from Theresa Kouril, Alexey Kolodkin, Melanie Zaparty, Ralf Steuer, Peter Ruoff, Hans V. Westerhoff, Jacky Snoep, Bettina Siebers and the SulfoSYS consortium writing in Systems Microbiology: Current Topics and Applications:

Life at high temperature challenges the stability of macromolecules and cellular components, but also the stability of metabolites, which has received little attention. For the cell, the thermal instability of metabolites means it has to deal with the loss of free energy and carbon, or in more extremes, it might result in the accumulation of dead-end compounds. In order to elucidate the requirements and principles of metabolism at high temperature, we used a comparative blueprint modelling approach of the lower part of the glycolysis cycle. The conversion of glyceraldehyde 3-phosphate to pyruvate from the thermoacidophilic Crenarchaeon Sulfolobus solfataricus P2 (optimal growth-temperature 80ºC) was modelled based on the available blueprint model of the eukaryotic model organism Saccharomyces cerevisiae (optimal growth-temperature of 30ºC). In S. solfataricus only one reaction is different, namely glyceraldehyde-3-phosphate is directly converted into 3-phosphoglycerate by the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase, omitting the extremely heat-instable 1,3-bisphosphoglycerate. By taking the temperature dependent non-enzymatic (spontaneous) degradation of 1,3-bisphosphoglycerate in account, modelling reveals that a hot lifestyle requires a cool design.

Further reading: Systems Microbiology   Related publications

from Julia P. Swiercz and Marie A. Elliot writing in Bacterial Spores: Current Research and Applications:

Streptomyces are soil-dwelling Gram positive bacteria with a complex, multicellular life cycle. The latter stages of their life cycle are defined by the metamorphosis of multi-genomic aerial hyphae into chains of unigenomic exospores. Here, we discuss the classical studies that established a solid genetic understanding of aerial development and sporulation, and highlight important new advances in the areas of cell division and spore septum placement, chromosome segregation and condensation during sporulation, and spore maturation.

Further reading: Bacterial Spores   Related publications

from Eberhard Klauck and Regine Hengge writing in Bacterial Regulatory Networks:

The sigmaS (RpoS) sigma subunit is the master regulator of the general stress response in Escherichia coli, which controls the expression of more than 500 genes during entry into stationary phase or upon exposure to many different stress conditions. sigmaS is present at very low levels only in rapidly growing cells, but multiple stress signals are integrated in a way that results in strong sigmaS accumulation and efficient sigmaS-containing RNAP holoenzyme (EsigmaS) formation. The first part of this review summarizes the molecular control mechanisms of switching from the "low-sigmaS" to "high-sigmaS" state, which operate at the levels of rpoS transcription, rpoS mRNA turnover and translation, sigmaS proteolysis and EsigmaS formation, and outlines multiple stress signal integration into these highly interconnected regulatory processes. We then show that, despite its complexity, the sigmaS control network essentially is an intricate combination of a few typical network motifs. These are several key feedforward loops that control sigmaS expression, a central and homeostatic negative feedback loop that integrates post-transcriptional sigmaS control mechanisms, mutual inhibition of sigma factors competing for RNAP core enzyme governing sigmaS activity control, and a series of smaller positive feedback loops that seem to stabilize the "high-sigmaS" state.

Further reading: Bacterial Regulatory Networks   Related publications

from Olga M. Pena, John D. F. Hale and Robert E.W. Hancock writing in Emerging Trends in Antibacterial Discovery: Answering the Call to Arms:

The increasing problem of resistance to antimicrobial agents, combined with the limited development of novel agents to treat infectious diseases is a serious threat to human morbidity and mortality around the world. Among the available strategies available to create new therapeutic agents is the enhancement of the multifunctional properties of the natural anti-infectives, cationic host defense (antimicrobial) peptides (HDPs). This chapter will provide a summary of our current understanding of the different types of HDPs including natural and synthetic peptides and their antimicrobial and immunomodulatory modes of action. Additionally, we will describe new approaches to peptide design and discuss both the therapeutic potential and prospective challenges in the utilization of peptides for antibacterial

Further reading: Emerging Trends in Antibacterial Discovery: Answering the Call to Arms

Herpes simplex virus (HSV) establishes latent infections as a consequence of a non-cytolytic immune response that represses HSV replication, but fails to destroy neurons that harbor HSV's genetic material. It has become increasingly evident that, in both mice and men, the host interferon system plays a critical role in tipping HSV's latency-replication balance in favor of latency. HSV can resist interferon-induced repression provided that HSV's two interferon antagonists, ICP0 and ICP34.5, are synthesized. Failure to synthesize either protein renders HSV interferon-sensitive and prone to establishing latent infections. Intriguingly, ICP0 and ICP34.5 are encoded within HSV's latency-regulating RL regions. We propose that differential synthesis of ICP0 and ICP34.5 may endow HSV with the capacity to 'choose' between latency and replication in vivo. HSV may choose to establish a latent infection by downregulating ICP0 or ICP34.5, and render itself sensitive to the interferon-induced antiviral state. Conversely, synthesis of ICP0 and ICP34.5 may ensure that HSV resists interferon-induced repression and completes another cycle of replication.

Further reading: Viruses and Interferon: Current Research

from Mark Schreiber, Joel Leong, and Martin Hibberd writing in Molecular Virology and Control of Flaviviruses:

Dengue fever is an acute viral infection that can produce a wide spectrum of disease outcomes in patients, ranging from mild or even asymptomatic fever to severe manifestations including hemorrhagic fever and shock. With the incidence of the severe forms increasing in most tropical countries as well as an overall increase in dengue incidence, dengue fever is becoming a significant burden on the health systems of affected countries. In this review, we examine the clinical definitions and presentation of mild and severe dengue as well as recent research into the underlying molecular mechanisms of the differential host response. Finally, we will examine how host responses from the early phase of the disease might be useful as biomarkers for predicting the eventual disease outcome.

Further reading: Molecular Virology and Control of Flaviviruses

from Peter L. Collins writing in The Biology of Paramyxoviruses:

Human respiratory syncytial virus (RSV) is a ubiquitous pathogen that infects essentially everyone worldwide during infancy and early childhood and is a leading cause of pediatric hospitalization for respiratory disease. RSV also is a frequent cause of less severe disease in healthy adults and is an important cause of morbidity and mortality in the elderly and in severely immunosuppressed individuals. RSV is an enveloped nonsegmented negative strand RNA virus classified in the Paramyxoviridae family, and its genome organization is one of the more complex of this family. The genome includes: two separate genes encoding type I and type III interferon (IFN) antagonists (NS1 and NS2); a gene (M2) with two open reading frames encoding novel proteins (M2-1 and M2-2) involved in RNA synthesis; and an attachment protein G that has a number of unusual features, including high sequence variability, heavy glycosylation, cytokine mimicry, and a shed form that helps the virus evade neutralizing antibodies. RSV is able to efficiently infect and cause disease in very young infants, with the peak of hospitalization at 2-3 months of age, despite the presence of maternally derived virus-neutralizing serum antibodies. RSV has a single serotype but is able to re-infect symptomatically throughout life without the need for significant antigenic change, although immunity from prior infection reduces disease. It is widely thought that re-infection is due to an ability of RSV to inhibit or subvert the host immune response, but this remains largely speculative. The development of an effective vaccine or specific antiviral therapy against RSV is considered a high priority, but these goals remain unfulfilled. RSV is notable for a historic vaccine failure: a formalin-inactivated RSV vaccine that was evaluated in infants and children in the 1960's was poorly protective and paradoxically primed for enhanced RSV disease upon subsequent natural RSV infection. However, RSV also is notable because of the development of a successful strategy for passive immunoprophylaxis of infants at high risk for serious RSV disease using an RSV-neutralizing monoclonal antibody (MAb).

Further reading: The Biology of Paramyxoviruses

In contrast to hydrolysis probes, the fluorescence from hybridization probes is reversible and depends only on probe hybridization. The first hybridization probes used in real-time PCR were dual hybridization probes consisting of two oligonucleotides, one labeled at the 3'-end the other at the 5'-end. Upon hybridization to their complementary sequences and fluorescent excitation, FRET increases. Signal generation with dual hybridization probes requires annealing of four oligonucleotides (two primers and two probes), suggesting even better specificity than hydrolysis probes. Later, single hybridization probe designs were developed, including FRET between an internally labeled primer and a single-labeled probe and deoxyguanosine quenching of a single-labeled probe (Wittwer and Farrar, 2011 in PCR Troubleshooting and Optimization). In contrast to hydrolysis probes that are consumed during amplification, the fluorescence of hybridization probes is reversible, enabling melting analysis. The first FDA-approved genetic tests in the US (F5 and F2 single base variants) used dual hybridization probes and melting analysis for genotyping.

Hydrocarbons are the major representatives of non-metal pollutants found in many contaminated soils by natural or industrial and social activities. Their removal from polluted environmental niches depends to a great extent on microbial degradation, which can also be applied on several technological applications. The extended microbial diversity in soil has served as a rich source for the isolation of efficient PAH-degrading strains. Bacterial isolates with the ability to use PAHs as an alternative source of carbon and energy facilitate their mineralisation to harmless products. Culture-based approaches have resulted in the isolation of a range of soil hydrocarbon-degrading bacteria, which primarily are members of different subdivisions of Proteobacteria as well as of the high G+C Gram-positive bacteria. Generally, in polluted-soils Gram-negative bacteria such as Pseudomonas, Burkholderia and Sphingomonas seem to degrade preferentially lower molecular weight PAHs such as naphthalene and phenanthrene, while Gram-positive isolates are more specialized in the degradation of high molecular weight PAHs such as pyrene.

Further reading: Microbial Bioremediation of Non-metals: Current Research

In 1991, Holland and colleagues at the Cetus Corporation used the 5' to 3' exonuclease activity of Taq polymerase to detect amplification products post-PCR. An oligonucleotide probe complementary to the PCR product was used with a non-extendable 3'-end and a radioactively labeled 5'-end. During amplification the polymerase degraded the probe, releasing the radioactive label as smaller fragments of the probe. However, a post-PCR radiograph was required in order to visualize the degraded probe. By replacing the radioactive label with two fluorescent labels in a FRET relationship, successful allele discrimination and later real-time monitoring were achieved. These dual-labeled fluorescent probes were hydrolyzed by the 5' to 3' exonuclease activity of Taq during PCR, separating the fluorescent labels with a loss of FRET to generate fluorescence. Specificity was enhanced over dsDNA dyes because complementation to three independent oligonucleotides (two primers and one probe) was necessary for probe hydrolysis and signal generation. Hydrolysis probes (also known by the trademark TaqMan, among others) are the most commonly used probes today (Wittwer and Farrar, 2011 in PCR Troubleshooting and Optimization). Their popularity was advanced by simplified design and a strong commercial effort to provide synthesis services. Signal generation is produced by probe hydrolysis and is irreversible and cumulative.

from Kazem Kashefi writing in Extremophiles: Microbiology and Biotechnology:

The isolation and characterization of novel hyperthermophilic, microorganisms from modern hot environments have greatly increased our understanding of how microbes can live and thrive in such inhospitable environments. The finding that microorganisms have the ability to grow at these high temperature has implications for delimiting when and where life might have evolved on a hot, early Earth; the depth to which life exists in the Earth's subsurface; and the potential for life in hot, extraterrestrial environments. The study of hyperthermophilic microorganisms provides valuable insights into microbial respiration in a diversity of modern and ancient hydrothermal systems. In addition, it provides information about the fate of metals such as iron, uranium, technetium, and even gold. Reduction of these metals by hyperthermophiles provides, for example, a likely explanation for a number of geologically, environmentally and economically important ore deposits. This allows us to identify geological signatures for biological processes, something that may prove instrumental in our search for life on other planets. Finally, enzymes capable of functioning at high temperatures have a number of important applications in biomass conversion, in biotechnology, and in the pharmaceutical, food and cosmetic industries.

Further reading: Extremophiles: Microbiology and Biotechnology

from Nichollas E. Scott, Stuart J. Cordwell, John F. Kelly and Susan M. Twine writing in Bacterial Glycomics: Current Research, Technology and Applications:

There are increasing numbers of reports of bacterial glycosylation in pathogenic bacteria, with well-characterized bacterial glycoproteins including pilins, flagellin and other surface-associated proteins. However, the discovery of bacterial glycoproteins can be challenging due to the diversity of glycans bacteria use to modify proteins. At the protein level, so-called 'top-down' mass spectrometry studies of intact protein can rapidly characterize bacterial glycan ions. At the peptide level, interpretation of individual bacterial glycopeptide tandem mass spectra can be challenging, owing to the diverse range of bacterial glycans produced. Reports of methods to specifically isolate bacterial glycopeptides are advancing knowledge of bacterial glycoproteomes. Herein, we provide an overview of protein and peptide centric mass spectrometry and related analytical techniques for the enrichment and analysis of bacterial glycoproteins.

Further reading: Bacterial Glycomics: Current Research, Technology and Applications

January 11 - 11, 2012: Climate Change and Imported Food. London, UK
January 13 - 14, 2012: Innovation in Severe Acute Respiratory Infections (SARI). Sitges, Spain
January 15 - 20, 2012: Drug Discovery for Protozoan Parasites. Santa Fe, NM, USA
January 15 - 20, 2012: Fungal Pathogens: From Basic Biology to Drug . Santa Fe, NM, USA
January 20 - 20, 2012: Exploiting bacteriophages for bioscience, biotechnology and medicine. London, UK
January 20 - 22, 2012: International Science Symposium on HIV and Infectious Diseases. Chennai, India
January 22 - 27, 2012: Biology of Spirochetes. Ventura, CA, USA
January 22 - 27, 2012: Genomics and Clinical Microbiology. Hinxton, Cambridge, UK
January 31 - February 3, 2012: IV International Giardia and Cryptosporidium Conference. Wellington, New Zealand

February 2012

February 4 - 7, 2012: International Conference Molecular Ecology. Vienna, Austria
February 7 - 12, 2012: Gene Silencing by Small RNAs. Vancouver, British Columbia, Canada
February 10 - 11, 2012: Update on Antibiotic Resistance from Laboratory to Clinical Practice. Al-Ain, UAE
February 13 - 24, 2012: Mathematical Models for Infectious Disease Dynamics. Hinxton, Cambridge, UK
February 21 - 23, 2012: International Scientific Conference on Bacteriocins and Antimicrobial Peptides. BAMP2012. Kosice, Slovakia
February 26 - 29, 2012: 10th ASM Biodefense and Emerging Diseases Research Meeting. Washington, DC , USA

March 2012

March 2 - 3, 2012: Problems in the Diagnosis and Treatment of Invasive Fungal Infections: Recent Advances in their Management. Athens, Greece
March 4 - 7, 2012: Amoebiasis: Exploring the biology and the pathogenesis of entamoeba. Khajuraho, India
March 4 - 9, 2012: The Microbiome. Keystone, CO, USA
March 4 - 10, 2012: Malaria Experimental Genetics. Hinxton, Cambridge, UK
March 7 - 10, 2012: Incorporating Bioinformatics Research in Undergraduate Education. Washington, DC , USA
March 9 - 9, 2012: Cell Culture Technology: recent advances, future prospects. Welwyn Garden City, UK
March 12 - 13, 2012: Bio-informatics and Computational Biology (BICB 2012). Bangkok, Thailand
March 14 - 17, 2012: 22nd Annual Meeting of the German Society for Virology. Essen, Germany
March 18 - 21, 2012: Annual Conference of the Association for General and Applied Microbiology (VAAM). Tubingen, Germany
March 19 - 21, 2012: Preparedness to new Emerging Infectious Threats: Avoiding Outbreaks in Europe. Marseille, France
March 19 - 23, 2012: Addressing the Challenges of Drug Discovery. Novel Targets, New Chemical Space and Emerging Approaches. Tahoe City, CA, USA
March 19 - 23, 2012: BSMM Diagnostic Medical Mycology Course. Leeds, UK
March 21 - 26, 2012: HIV Vaccines. Keystone, CO, USA
March 21 - 26, 2012: Viral Immunity and Host Gene Influence. Keystone, CO, USA
March 26 - 28, 2012: 3rd TNO Beneficial Microbes Conference. Noordwijkerhout, The Netherlands
March 26 - 29, 2012: SGM Spring Conference 2012. Dublin, Ireland
March 26 - 31, 2012: Cell Biology of Virus Entry, Replication and Pathogenesis. Whistler, BC, Canada
March 26 - 31, 2012: Frontiers in HIV Pathogenesis, Therapy and Eradication. Whistler, BC, Canada
March 28 - 29, 2012: Advances in Biodetection and Biosensors. Edinburgh, UK
March 28 - 29, 2012: Single Cell Analysis Europe . Edinburgh, UK
March 28 - 30, 2012: Advances in Plant Virology. Dublin, Ireland
March 29 - 31, 2012: Antimicrobial Stewardship: Measuring, Auditing and Improving. London, UK
March 29 - April 2, 2012: 11th ASM Conference on Candida and Candidiasis. San Francisco, CA, USA
March 30 - April 2, 2012: 11th European Conference on Fungal Genetics. Marburg, Germany
March 31 - April 3, 2012: 22nd European Congress of Clinical Microbiology and Infectious Diseases ECCMID. London, UK
March 31 - April 5, 2012: Non-Coding RNAs. Snowbird, UT, USA

April 2012

April 2 - 4, 2012: 5th International Biocuration Conference (Biocuration2012). Washington, DC, USA
April 2 - 4, 2012: Electron transfer at the microbe-mineral interface. Norwich, UK
April 10 - 12, 2012: Environmental Microbiology and Biotechnology Conference 2012. Bologna, Italy
April 15 - 18, 2012: 3rd Workshop on Microbial Sulfur Metabolism. Noorwijkerhout, The Netherlands
April 15 - 20, 2012: New Antibacterial Discovery and Development. Lucca, Italy
April 16 - 19, 2012: 5th European Spores Conference. London, UK
April 18 - 18, 2012: 6th Broadening Microbiology Horizons in Biomedical Science Meeting. Stratford-Upon-Avon, UK
April 24 - 27, 2012: Antigen presentation and processing. Amsterdam, The Netherlands
April 29 - May 10, 2012: Computational molecular evolution. Heraklion, Greece
April 30 - May 3, 2012: 34th Symposium on Biotechnology for Fuels and Chemical. New Orleans, LA, USA

May 2012

May 6 - 9, 2012: 8th International Symposium on Shiga Toxin (Verocytotoxin)-Producing Escherichia coli Infections. Amsterdam, The Netherlands
May 6 - 10, 2012: Cellular organization and functions and their subversion by pathogens. Villars-sur-Ollon, Switzerland
May 6 - 12, 2012: 4th ASM Conference on Prokaryotic Cell Biology and Development. Montreal, Canada
May 7 - 19, 2012: Bioinformatics and comparative genomes analyses. Napoli, Italy
May 8 - 10, 2012: Exploring Human Host-Microbiome Interactions in Health and Disease. Cambridge, UK
May 10 - 11, 2012: Microbiology and Biotechnology. Adapting to the Changing Microbial World. Cagayan De Oro City, Philippines
May 10 - 11, 2012: Molecular Diagnostics Europe . London, UK
May 10 - 13, 2012: Microbial Stress Responses: from Molecules to Systems. Maggiore Lake, Italy
May 13 - 18, 2012: Drug Resistance and Persistence in Tuberculosis. Kampala, Uganda
May 14 - 16, 2012: 8th Annual BioMalPar Conference. Biology and Pathology of the Malaria Parasite. Heidelberg, Germany
May 14 - 25, 2012: 13th Advanced Vaccinology Course ADVAC. Veyrier-du-Lac, France
May 19 - 22, 2012: New perspectives on immunity to infection. Heidelberg, Germany
May 30 - 31, 2012: European Lab Automation . Hamburg, Germany

June 2012

June 3 - 8, 2012: Anaerobes in Health and Disease; How to Isolate, Identify and Look for Resistance in a Cost-Effective Way. Szeged, Hungary
June 3 - 8, 2012: Biopolymers. Newport, RI, USA
June 10 - 15, 2012: Biology of Host-Parasite Interactions. Newport, RI, USA
June 11 - 16, 2012: Antiviral RNAi: From Molecular Biology Towards Applications. Pultusk, Poland
June 12 - 14, 2012: International Scientific Conference on Probiotics and Prebiotics - IPC2012. Kosice, Slovakia
June 13 - 15, 2012: The Third International Symposium On Antimicrobial Peptides, AMP2012. Lille, France
June 14 - 17, 2012: 19th Annual ASM Conference for Undergraduate Educators. San Mateo, CA, USA
June 16 - 19, 2012: ASM General Meeting ASM 2012. San Francisco, CA, USA
June 16 - 21, 2012: Gene transcription in yeast. Girona, Spain
June 17 - 20, 2012: 8th INRA-RRI Symposium on Gut Microbiology. Gut Microbiota: Friend or Foe?. Clermont-Ferrand, France
June 17 - 20, 2012: Antimicrobial Susceptibility Testing and Surveillance of Resistance in Gram-positive Cocci: Laboratory to Clinic. Zagreb, Croatia
June 18 - 29, 2012: Plant-microbe interactions. Norwich, UK
June 20 - 23, 2012: CSM 62nd Annual Conference . Vancouver, Canada
June 21 - 22, 2012: Swiss Joint Annual Meeting. St. Gallen, Switzerland
June 24 - 28, 2012: 5th International Symposium on Biosorption and Bioremediation. Prague, Czech Republic
June 24 - 28, 2012: Connecting Bioinformatics-Driven Hypotheses to Wet-Lab Projects . Hiram, OH, USA
June 24 - 29, 2012: Environmental Sciences: Water. Holderness, NH, USA
June 24 - 29, 2012: Marine Microbes. Lucca, Italy

July 2012

July 1 - 4, 2012: The Australian Society for Microbiology, Annual Scientific Meeting ASM 2012. Brisbane, Australia
July 2 - 5, 2012: Resistance, Adaptation and Biofilms. Edinburgh, UK
July 2 - 13, 2012: Molecular genetics with fission yeast. Paris, France
July 8 - 13, 2012: Microbial Toxins & Pathogenicity. Waterville Valley, NH, USA
July 9 - 13, 2012: 3rd Central European Summer Course on Mycology: Biology of Pathogenic Fungi. Szeged, Hungary
July 15 - 20, 2012: Microbial Stress Response. South Hadley, MA, USA
July 16 - 18, 2012: How bugs kill bugs: progress and challenges in bacteriocin research. Nottingham, UK
July 16 - 20, 2012: Viruses of microbes. Brussels, Belgium
July 21 - 25, 2012: ASV 2012. 31st Annual Meeting of American Society for Virology. Madison, WI, USA
July 29 - August 2, 2012: XV IS-MPMI Kyoto 2012. International Congress on Molecular Plant-Microbe Interactions. Kyoto, Japan
July 29 - August 3, 2012: Drug Resistance. Easton, MA, USA
July 30 - August 1, 2012: 2nd Annual International Symposia of Mycology (ISM-2012). Guangzhou, China
July 30 - August 1, 2012: 2nd Annual Symposia of Antimicrobial Research. Guangzhou, China
July 30 - August 1, 2012: 3rd Annual Symposia of Hepatitis Virus. Guangzhou, China

August 2012

August 5 - 10, 2012: Molecular Basis of Microbial One-Carbon Metabolism. Lewiston, ME, USA
August 12 - 16, 2012: SIM Society for Industrial Microbiology Annual Meeting. Washington DC, USA
August 18 - 22, 2012: The 30th World Congress of Biomedical Laboratory Science. Berlin, Germany
August 19 - 24, 2012: 14th International Symposium on Microbial Ecology, ISME14. Copenhagen, Denmark
August 20 - 22, 2012: 2nd World Congress on Virology. Las Vegas, NV, USA
August 26 - 30, 2012: 13th International Congress on Yeasts ICY2012. Madison, WI, USA
August 27 - 27, 2012: Medical Biofilm Techniques 2012. Copenhagen, Denmark

September 2012

September 3 - 5, 2012: SGM Autumn Conference 2012. Warwick, UK
September 4 - 9, 2012: 22nd IUBMB and 37th FEBS Congress. Sevilla, Spain
September 9 - 14, 2012: XVIIIth International Pathogenic Neisseria Conference IPNC. Wurzburg, Germany
September 10 - 14, 2012: 9th International Congress on Extremophiles. Sevilla, Spain
September 11 - 13, 2012: Influenza 2012. Oxford, UK
September 11 - 15, 2012: Tuberculosis 2012. Paris, France
September 16 - 19, 2012: Reconstructing the essential bacterial cell cycle machinery. Real Sitio de San Ildefonso, Spain
September 17 - 20, 2012: 7th Australasian Soilborne Diseases Symposium. Fremantle, Australia
September 23 - 26, 2012: Central European Symposium on Antimicrobials and Antimicrobial Resistance - CESAR 2012. Primosten, Croatia
September 25 - 28, 2012: Alternatives to antibiotics (ATA). Paris, France
September 25 - 28, 2012: Antimicrobial Susceptibility Testing and Surveillance: from Laboratory to Clinic - the EUCAST and ESGARS Perspective. Madrid, Spain

October 2012

October 17 - 21, 2012: Experimental approaches to evolution and ecology using yeast. Heidelberg, Germany
October 25 - 28, 2012: 13th Asia-Pacific Congress of Clinical Microbiology and Infection (13th APCCMI). Beijing, China
October 29 - November 3, 2012: Analysis of high-throughput sequencing data. Hinxton, Cambridge, UK

November 2012

November 7 - 10, 2012: 19th Annual Biomedical Research Conference for Minority Students. San Jose, CA, USA
November 7 - 12, 2012: Immunological Mechanisms of Vaccination. Ottawa, Canada

December 2012

December 19 - 21, 2012: Marine Microbiology and Biotechnology. Cork, Ireland ]]>http://www.horizonpress.com/blogger/2011/12/microbiology-conferences-2012.htmlhttp://www.horizonpress.com/blogger/2011/12/microbiology-conferences-2012.htmlThu, 01 Dec 2011 15:38:56 GMTBiotechnologyEmerging Molecular TechnologyHot Topics in Molecular Biologyfrom Theron et al. in Nanotechnology in Water Treatment Applications

Immunological methods are based on the specific recognition between antibodies and antigens, and the high affinity that is characteristic of this recognition reaction. Consequently, many different immunoassay methods have become available for both quantitative and qualitative analysis of pathogenic bacteria in water. These include immunocapture of cells or antigens by enzyme-linked immunosorbent assay (ELISA or EIA), or detection of targeted cells by immunofluorescence (IFA). These assays can be performed by a direct or indirect manner. In a direct immunoassay, the monoclonal or polyclonal antibodies, directed against antigens located on the surface of the target pathogen (such as capsid proteins, cell wall or flagellar antigens), are conjugated with a fluorochrome or fluorescent dye. Alternatively, secondary enzymatically- or fluorescently-labelled antibodies directed against the primary antibodies (now serving as antigens) can be used in an indirect immunoassay. The advantage of this procedure is that the secondary antibodies can easily be obtained from a commercial supplier with a range of conjugated fluorochromes and it leads to signal amplification as several labelled secondary antibodies can bind to a single unlabelled primary antibody. The antigen-antibody complex is detected and quantified by the ability of the enzyme to react with a substrate that produces either a coloured product for colorimetry or emits light for luminometry. The immunoassays are often performed on a solid phase to which the pathogen antigens have been applied, such as a membrane filter or the bottom of a microtitre plate well.

Studies have shown that solid-phase enzyme immunoassays generally are too insensitive for direct detection of microbial pathogens in water, as they require a minimum of 103 to 104 target microbes (or their antigens) for detection. In most situations drinking water and its sources rarely contain high enough levels of most target pathogens for direct immunoenzymatic detection. Nevertheless, enumeration of diluted specific cells can be obtained by means of immunomagnetic separation (IMS). Immunomagnetic separation, also termed immunocapture or antibody capture, is a method that uses paramagnetic synthetic beads or other magnetic particles that have been coated with monoclonal or polyclonal antibodies directed against the target microbes to recover the microbes from the sample by antigen-antibody reactions. The retained microbes can be analyzed directly or after they or their nucleic acids have been released or extracted from the antibody and solid phase by various physical or chemical methods. IMS methods have the advantage of selecting, separating and purifying specific target microbes from other microbes and from solutes, based on the specificity of the antigen-antibody reaction. This is a powerful approach for recovering, enriching, purifying and concentrating the target viruses, bacteria and parasites from the sample matrix. However, it is not applicable to some pathogens because of the lack of antisera or the antigenic diversity of a large pathogen group lacking a common antigen and thus requiring many antisera.

As an alternative to the above assays, agglutination methods can be used to detect pathogens by combining dispersed microorganisms with antibodies (on a slide, for example) and allowing for antigen-antibody reactions to produce agglutination (clumping) that can be scored as negative or various degrees of positive. One modification is latex bead agglutination in which antibodies against a specific microbial antigen are attached to latex beads. The beads are reacted with the sample and should the sample contain the specific antigen, agglutination occurs by the reaction of antigens with antibodies on the beads resulting in the beads clumping together. As with enzyme immunoassays, agglutination tests are too insensitive to directly detect and quantify most waterborne pathogens in drinking water and other aquatic samples. The target microbes must first be cultured in order to obtain a sufficient number of them or a sufficient amount of antigen to detect and antigenically characterize them by agglutination methods.

The use of immunological methods for the detection of specific microorganisms is a rapid and simple technique, the accuracy of which mainly depends on the specificity of the antibody. Nevertheless, its application to the detection of specific microorganisms from environmental water samples is limited. While IFA allows specific identification and detection at a single-cell level, it does not provide information on the physiological status or viability of the detected cells. The ELISA is a rapid, simple and quite sensitive test. However, assay limitations are often associated with the specificity of the antibody used, the concentration of both antibody and antigen, and the solid matrix often leads to non-specific binding of the antigen or of the secondary antibody.

Monoclonal antibodies are better suited for biosensors because of their higher specificity. Polyclonal antibodies recognize different epitopes on the same pathogen. False positives can be generated when these antigens are present in other closely-related non-pathogenic microorganisms. The thermal instability of antibodies, in particular monoclonal antibodies, is another drawback when applying them in environmental biosensors. Single domain antibodies (also referred to as nanobodies) have however been developed that are thermostable, even at temperatures as high as 90 degrees C. Their small size, high solubility and refolding capacity are other features that make them ideally situated for biosensing applications.

Helicobacter pylori infection induces almost all mechanisms of innate and acquired immunity. Different bacterial, environmental and host factors may influence the balance between the protective role of the immune mechanisms and their role in gastric mucosal damage, respectively, the possibility of lifelong asymptomatic colonisation of gastric mucosa or clinical manifestation and H. pylori infection. Bacterial virulence factors stimulate Toll-like and Nod-like receptors to induce innate and adaptive cell mediated and humoral immune response. Balance of Th1/Th2 response is of great importance in host protection and in pathogenesis of H. pylori-mediated diseases. The polarised Th1 response is not sufficient to clear the bacteria. Moreover, a predominant activation of Th1 cells plays a key role in tissue damage. Th2 response appears to be protective against gastric inflammation. Cytotoxic activities of T cells are important for the outcome of H. pylori infection. Protection due to anti-H. pylori humoral local and systemic immune response is minimal. Furthermore, the antibodies may promote colonisation of gastric mucosa.

Further reading: Helicobacter pylori

Influenza viruses are the etiological agents of seasonal influenza outbreaks as well as three devastating influenza pandemics in the 20th century and the 2009 swine-origin H1N1 pandemic. Like most viruses that cause significant disease, influenza viruses have developed means to circumvent the induction and effects of the innate immune system. Unlike most other RNA viruses, influenza viruses replicate in the nucleus, rather than in the cytoplasm. This distinguishing feature makes the interactions of influenza viruses with their hosts both complex and unique, and requires a well-orchestrated manipulation of many cellular processes. This includes the interferon (IFN) response, a key innate immune pathway, critical for limiting virus replication. To cope with the IFN burden, influenza viruses express non-structural protein 1 (NS1), which is largely dedicated to antagonism of the host IFN response. This chapter describes how influenza viruses induce the IFN response and the ample means they have developed to intersect with it at all three stages of the pathway. The molecular details of NS1-mediated IFN antagonism are discussed, as well as new vaccination and antiviral drug strategies that target NS1 to attenuate virus replication.

Further reading: Viruses and Interferon: Current Research

from Maudry Laurent-Rolle, Juliet Morrison and Adolfo García-Sastre writing in Molecular Virology and Control of Flaviviruses:

Flaviviruses, along with the distantly related Hepacivirus and Pestiviruses, belong to the Flaviviridae family. Currently, more than 70 flaviviruses have been reported, including dengue virus serotypes 1 to 4 (DENV1-4), yellow fever virus (YFV), West Nile virus (WNV), Japanese encephalitis virus (JEV) and tick-borne encephalitis virus (TBEV). Flaviviruses are significant human and animal pathogens, creating a global public health challenge with more than 100 million people infected yearly. Typical manifestations of flaviviral disease in humans include jaundice, an acute febrile illness, hemorrhagic disease, encephalitis, and even death. Currently, there are no specific antiviral treatments for infection with any of the flaviviruses. An understanding of the interplay between the virus and the host immune system would aid in the development of flaviviral therapeutics. The innate immune system is the host's first line of defense against invading pathogens. Critical components of the innate immune system include natural killer (NK) cells, the complement system, and the ability to recognize pathogens like viruses and induce antiviral cytokines. These components of the innate immune system play complementary roles in limiting viral replication and dissemination, as well as initiation of the adaptive immune response. While all flaviviruses examined thus far suppress host innate immune responses to viral infection, the mechanisms by which this occurs differ among viruses. In this chapter, we will examine the roles that the different arms of the innate immune system play in protecting the host against flavivirus infection. We will also discuss the mechanisms that flaviviruses use to subvert the innate immune system and establish infection.

Further reading: Molecular Virology and Control of Flaviviruses

from Jan Maarten van Dijl, Annette Dreisbach, Marcin J. Skwark, Mark J.J.B. Sibbald, Harold Tjalsma, Jessica C. Zweers and Girbe Buist writing in Bacillus: Cellular and Molecular Biology (Second edition):

Bacterial homeostasis is largely determined by a phospholipid bilayer that encloses the cytoplasm. The proteins residing in this cytoplasmic membrane are responsible for communication between the cytoplasm and extracytoplasmic cell compartments or the extracellular milieu of the cell. This chapter deals with the cytoplasmic membrane proteome of Bacillus subtilis. Specifically, we address current views on the roles of membrane proteins in homeostasis, their membrane targeting and retention signals, machinery for membrane insertion, localization of membrane proteins, membrane protein degradation and, finally, the identified and predicted composition of the B. subtilis membrane proteome. Known mechanisms and knowledge gaps are discussed to give a comprehensive overview of the ins and outs of the B. subtilis membrane proteome.

Further reading: Bacillus: Cellular and Molecular Biology (Second edition)

from Brian W.J. Mahy writing in The Biology of Paramyxoviruses:

There is no abstract for this chapter, however the first paragraph is presented here instead. The chapters in this excellent book provide a truly comprehensive account of all known paramyxoviruses, a group whose members include highly pathogenic viruses affecting the human population, as well as animals and birds. In the early days of virology, the word "myxovirus" was coined for a group of viruses that had common features, namely an affinity for mucoproteins, and an enzyme activity that attacks the mucoprotein substrate (Andrewes et al, 1955). This group of viruses included fowl plague, first discovered in 1901 (Centanni, 1901), and later shown to be a highly virulent form of avian influenza virus (Davenport et al, 1960), as well as the human viruses, influenza, para-influenza, mumps, and avian Newcastle disease virus. Soon after this group was named, however, a number of biological differences as well as structural differences were noted between influenza and fowl plague viruses, on the one hand, and para-influenza, mumps and Newcastle disease viruses on the other (Andrewes and Worthington, 1959; Franklin and Wecker, 1959). This led to the concept of two kinds of myxovirus (Waterson, 1962), now known as the families Orthomyxoviridae and Paramyxoviridae. With hindsight, we now know that orthomyxoviruses are totally different in their structure and replication from paramyxoviruses, and their only features in common are the properties of binding to mucoproteins by a virion envelope protein and release by a receptor destroying enzyme, the neuraminidase, as originally recognized (Andrewes et al, 1955). The orthomyxovirus genome consists of negative-stranded RNA which is segmented, and transcription of this genome occurs within the nucleus and requires capped oligonucleotide primer RNAs (10-13 nucleotides long) that are derived from newly synthesized host cell mRNAs by endonuclease activity of the virus PB2 protein. Because of this intimate involvement with host cell transcription, orthomyxovirus replication is blocked by substances such as actinomycin D or alpha-amanitin, which do not affect paramyxovirus replication.

Further reading: The Biology of Paramyxoviruses

We tend to think of parasites as a nuisance, but they are in fact very serious disease-causing agents. Despite advances of veterinary medicine, parasitic diseases have remained a major cause of morbidity, mortality and economic losses, worldwide. With the increasing burden of parasites on human and animal suffering, study of "parasitology" has become an important and rapidly growing discipline of science. Veterinarians' awareness of parasitic diseases is undoubtedly more critical now than at any time in the history of veterinary medical practice. This chapter provides a short introduction to parasites and their unique properties.

Further reading: Essentials of Veterinary Parasitology

from Kelley R. Gwin and John R. Battista writing in Extremophiles: Microbiology and Biotechnology:

Of all the phenotypes associated with microorganisms, ionizing radiation resistance - the ability to survive exposure to high dose gamma radiation - is perhaps the most difficult to rationalize in terms of the natural world. There is no obvious selective advantage to being ionizing radiation resistant on Earth, as average yearly exposures to ionizing radiation from cosmic rays and radioactive decay are extremely low. Yet a significant number of genera exhibit this characteristic, displaying a remarkable capacity to tolerate levels of damage to cellular macromolecules that eradicates other forms of life. We argue that ionizing radiation resistance is an incidental characteristic, an inadvertent consequence of an evolutionary path that permitted these species to survive a selective pressure capable of damaging the cell in a manner similar to that of ionizing radiation. The phylogenetic distribution of ionizing radiation resistant species argues that these events occurred multiple times during the evolution of the Bacteria and Archaea, suggesting that different mechanisms may mediate ionizing radiation resistance.

Further reading: Extremophiles: Microbiology and Biotechnology

Extremophiles: Microbiology and Biotechnology Edited by: Roberto Paul Anitori ISBN: 978-1-904455-98-1 Publisher: Caister Academic Press Publication Date: March 2012 Cover: hardback

read more ... ]]>http://www.horizonpress.com/blogger/2011/11/extremophiles.htmlhttp://www.horizonpress.com/blogger/2011/11/extremophiles.htmlMon, 21 Nov 2011 16:40:09 GMTfrom David J. Bartley and Hany M. Elsheikha writing in Essentials of Veterinary Parasitology:

Accurate diagnosis of parasitic infections is a prerequisite for successful treatment and control of these pathogens. Errors in the diagnosis can lead to the initiation of unnecessary therapies, or delays in initiating the correct therapy. Thus, the clinicians must maintain a sharp index of suspicion and must rely on detailed history and clinical manifestations, to raise the possibility of a parasitic disease. Even though the diagnosis can be difficult, and definitive identification of the parasites can be challenging particularly in the non-endemic settings. Therefore, laboratory testing for detection and identification of the parasitic agents is required to complement clinical judgement, enhance the clinician's ability to select specific anti-parasitic drugs, and ultimately improve patient care. A wide range of laboratory procedures are available for the diagnosis of parasitic infections. These procedures vary in methodology, expense, availability, sensitivity, and specificity. In this chapter, the standard techniques used in the laboratory diagnosis of parasitic infections are discussed.

Further reading: Essentials of Veterinary Parasitology

Bacteriocins produced by lactobacilli from the lactic acid bacteria (LAB) group have been reported since about 1990 in the same time period when similar bacteriocins were reported in other bacterial species. Almost all of the bacteriocins from lactobacilli belong to class II bacteriocins except for a class III helveticin J produced by Lactobacillus helveticus 481 (37kDa, 333 amino acid residues, using an unknown antibacterial mechanism; Joerger and Klaenhammer, 1990). Interestingly, there have been few reports of class I lantibiotics from lactobacilli. In this chapter, the chemical structure, genetics, mode of action, immunity, and topics concerning lactobacilli bacteriocins are described from the recent decade. Other lactobacilli bacteriocins are referred to from many published papers and reviews.

Further reading: Lactic Acid Bacteria and Bifidobacteria: Current Progress in Advanced Research

Lactococcus is one of the most important genera of lactic acid bacteria (LAB), because of the widespread use in dairy fermentation foods. Since nisin produced by Lactococcus lactis was discovered in 1928 (Rogers and Whittier, 1928), many bacteriocin-producing Lactococcus strains have been reported and studied so far (Cotter et al., 2005a). Here, recent studies on lactococcal bacteriocins, mainly nisin, are summarized in their diversities and structures, biosynthesis, antimicrobial mechanisms, and applications.

Further reading: Lactic Acid Bacteria and Bifidobacteria: Current Progress in Advanced Research

from Sarah A. Kinkel and Hamish S. Scott writing in Epigenetics: A Reference Manual:

DNMT3L (DNA methyltransferase 3 like) is member of the DNA methyltransferase family of enzymes responsible for the methylation of CpG dinucleotides. Biochemical studies have revealed that while DNMT3L lacks DNA methyltransferase activity, it can bind to and stimulate the activity of de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3L has also been shown to interact directly with chromatin via its plant homeodomain (PHD)-like zinc finger domain. Studies in Dnmt3L-deficient mice have revealed that DNMT3L is essential for establishing correct methylation patterns at RetroTransposable Elements (RTE), unique loci and parentally imprinted genes in germ cells, and mice without DNMT3L are rendered infertile. Female Dnmt3L^-/- mice have apparently normal meiosis but in male Dnmt3L-/- germ cells there is asynapsis of chromosomes, and "meiotic catastrophe". Dnmt3L was among the first mammalian genes shown to have a paternal effect, where the genotype of the father (Dnmt3L^+/-) affects sex chromosome aneuploidy in adult and embryonic offspring. This chapter will discuss the role of DNMT3L in establishing DNA methylation patterns during gametogenesis, as well as the proven and potential consequences of DNMT3L-deficiency to fertility and somatic and germline genetic disease in light of the increasing evidence that epigenetic reprogramming is a dose sensitive and partially stochastic process.

Further reading: Epigenetics: A Reference Manual

from Leslie Cuthbertson writing in Bacterial Glycomics: Current Research, Technology and Applications:

Lipopolysaccharide (LPS) constitutes the major portion of the outer leaflet of the outer membrane and plays a major role in the physiology of Gram-negative bacteria. LPS can be divided into three structurally distinct regions: lipid A, core oligosaccharide and O-antigenic polysaccharide. Each of these regions as well as regulated modifications, are important in the overall functions of the LPS molecule. Synthesis of lipid A and the core oligosaccharide occurs in the cytoplasm and is separate from that of the O-antigenic polysaccharide. These two portions of the LPS molecule are then ligated in the periplasm prior to transport to the outer membrane. This chapter will describe the structure and cytoplasmic synthesis of LPS, modifications to these structures regulated by environmental conditions or phage-encoded genes, and the transfer of LPS to its final destination at the cell surface.

Further reading: Bacterial Glycomics: Current Research, Technology and Applications

from Brian P. Chadwick writing in Epigenetics: A Reference Manual:

The recent completion of several mammalian genome sequences makes obvious that we share a near-identical collection of genes. What defines us as human must therefore be encoded within regions of the genome where we differ, providing an added level of complexity that probably influences the spatial and temporal expression of genes. Most DNA sequence variation occurs within the repetitive DNA, once called 'Junk DNA' that accounts for at least half of the human genome, and evidence is mounting for its important role in genome function. Although some repeat elements are conserved to some extent between mammals, their precise copy number and genomic location typically are not. In addition, some repeats are not conserved, including the large tandem repeats. This chapter focuses on two large tandem arrays in the human genome that can adopt quite different chromatin configurations as a result of epigenetic changes; one as a direct consequence of X chromosome inactivation and the other in the context of disease susceptibility. Both cases highlight how alternate packaging of these unusual DNA sequences probably results in differing functions. In each instance, common denominators are the acquisition of the epigenetic organizer protein CTCF and a distinct change in transcripts originating from the array.

Further reading: Epigenetics: A Reference Manual

In contrast to gold nanoparticles and QDs, magnetic nanoparticles have not been used in many biological applications. Nevertheless, advances in the synthesis of monodispersed magnetic nanoparticles, ranging in size from 2 to 20 nm, has provided a basis from which to explore applications of magnetic nanoparticles in diagnostics. Magnetic nanoparticles are produced from materials that can be strongly attracted by magnets or be magnetized. They can be prepared in the form of single domain or superparamagnetic (Fe₃O₄), greigite (Fe₃S₄), maghemite (gamma-Fe₂O₃), and various types of ferrites (MeO.Fe₂O₃, where Me = Ni, Co, Mg, Zn, Mn, etc.). Bound to biorecognition molecules, magnetic nanoparticles can be used to facilitate the separation, purification and concentration of different biomolecules. To do so, biorecognition molecules such as antibodies can be immobilized on the surface of magnetic nanoparticles through covalent or electrostatic interactions. After reacting these magnetic nanoparticles with sample solutions, targeted molecules can be bound by or captured on the surface of these magnetic nanoparticles. By applying a magnetic field, these nanoparticles can subsequently be concentrated and separated from the bulk solution and identified.

Biofunctional magnetic nanoparticles, in which thiolated vancomycin was attached to FePt nanoparticles, have been used to capture and detect of a wide range of bacteria at very low concentrations within 60 min. These included capturing and detection of Staphylococcus aureus at 8 cfu/ml, S. epidermidis at 10 cfu/ml, Enterococcus faecalis at 26 cfu/ml, and E. coli at 15 cfu/ml. Although the sensitivity achieved using magnetic nanoparticles is comparable to PCR-based assays, the direct capture protocol is faster than PCR when the bacterium count is low since it obviates the need for pre-enrichment of bacteria through culturing. In an alternative approach, Ho et al. reported combining biofunctional magnetic nanoparticles with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to detect pathogenic bacteria in water. Biofunctional nanoparticles were fabricated by attaching human immunoglobulin (IgG), which binds selectively to IgG-binding sites on the cell walls of pathogens, onto the surfaces of magnetite (Fe₃O₄) nanoparticles. Using this assay, both S. saprophyticus and S. aureus were detected at concentrations of 3 x 10⁵ cfu/ml in aqueous sample solutions. Measuring adenosine triphosphate (ATP) bioluminescence of bacteria captured onto magnetic nanoparticles is another proposed method for detecting microorganisms. E coli was detected in milk by Cheng et al. within a short period (1 h) and with a low detection limit (20 cfu/ml).

Biofunctional magnetic glyconanoparticles have also been engineered by covently binding unmodified monosaccharide d-mannose onto iron oxide nanoparticles. These particles had the ability to recognize mannose-specific receptor sites on E. coli. Magnetic nanoparticles have been developed to sequester DNA in water and capture the DNA-nanoparticles complexes by the application of high-gradient magnetic separation. Modifying magnetite clusters with poly(hexamethylene biguanide)- and polyethyleneimine resulted in strong cationic nanoparticles which enabled the binding with DNA molecules through electrostatic forces. The cationic nanoparticles can also serve as a disinfectant by binding to the negatively charged cell envelopes of bacteria. These particles were colloidally stable in fresh and ocean water for weeks at a pH <= 10.

Magnetic microparticle-antibody conjugates (Dynabeads) are commercially available and kits have been developed for the detection of Legionella species, Cryptosporidium oocysts and Giardia cysts from concentrated water samples. Dynabeads are also available for the detection of E. coli, Salmonella and Listeria species; however the samples must be grown for 6 - 8 h in a pre-enrichment broth. Streptavidin coated Dynabeads allow researchers to design their own magnetic microparticle-antibody conjugates for specialized assays (www.invitrogen.com). Biotinylated organism-specific antibodies will bind covalently onto the streptavidin coated Dynabeads. A wide range of biotin-labeled antibodies are available from companies such as Abcam (www.abcam.com).

Despite the promise shown by biofunctional magnetic nanoparticles, some challenges regarding their widespread use have yet to be overcome. In addition to requiring a robust surface chemistry to attach bioactive molecules onto magnetic nanoparticles without laborious synthetic efforts, more precise control of the numbers and orientations of the molecules on the surfaces of magnetic nanoparticles is also required.

Cestoda is a class of parasitic flatworms (Platyhelminthes), commonly called tapeworms or cestodes. All tapeworms use vertebrates as a definitive host, and vertebrates or invertebrates (arthropods, crustaceans) as an intermediate host, depending on the species. The definitive host harbors the adult, sexual, or mature stages of parasite. Larval 'metacestode' development occurs in the intermediate host (I.H.), which will be eaten by definitive host. In the latter, larval stages attach to the gut mucosa and mature to adult tapeworms via a process called 'strobilation'. Most tapeworms are found in the small intestine of their host as adults or, with Thysanosoma spp., have access to the intestine.

Further reading: Essentials of Veterinary Parasitology

Dicrocoeliosis is caused by Dicrocoelium dendriticum, which is also known as 'lancet fluke' or 'small liver fluke'. It can infect sheep, goats, cattle, deer and rabbits, and occasionally horses and pigs. Dicrocoeliasis is a widespread problem worldwide in grazing livestock. The epidemiology of Dicrocoelium depends upon the environment and on the presence of its intermediate and definitive hosts. Dicrocoelium spp. do pose a zoonotic risk but are very uncommon in humans, most cases are likely to be non-symptomatic.

Further reading: Essentials of Veterinary Parasitology

Bacterial Glycomics: Current Research, Technology and Applications Edited by: Christopher W. Reid, Susan M. Twine, and Anne N. Reid ISBN: 978-1-904455-95-0 Publisher: Caister Academic Press Publication Date: February 2012 Cover: hardback

read more ...]]>http://www.horizonpress.com/blogger/2011/11/bacterial-glycomics-book-available-very-soon.htmlhttp://www.horizonpress.com/blogger/2011/11/bacterial-glycomics-book-available-very-soon.htmlTue, 08 Nov 2011 12:18:15 GMTfrom Hany M. Elsheikha writing in Essentials of Veterinary Parasitology:

Classification of nematodes has been traditionally based on the presence or absence of a posterior cuticular chemoreceptor called 'phasmid'. Nematode species with phasmid are known as phasmidea (Secernentea) and nematodes that lack phasmid are called aphasmidea (Adenophera). It is important to realize that the parasite taxonomy is an evolving field and there is no a single scheme that is always acceptable. Class Nematoda encompasses numerous species that infect livestock and companion animals. This chapter focuses only on the most economically important nematode infections in livestock and companion animals. General taxonomy of nematodes considered in this chapter is given to the genus level.

Further reading: Essentials of Veterinary Parasitology

from Sibylle Schneider-Schaulies and W. Paul Duprex writing in The Biology of Paramyxoviruses:

Measles virus (MV) infections continue to be of high clinical relevance as they can be associated with severe disease processes such as pneumonia and central nervous system (CNS) complications, but also because they cause a generalized transient immunosuppression. Though characterized and causatively linked to MV decades ago, the pathogenesis of these diseases including the prime target cells in the respiratory tract is far from being understood. The advent of reverse genetics systems for both vaccine and wild-type viruses alongside the establishment of suitable tissue culture and animal models has helped to provide new insights into mechanisms of viral entry and tissue targeting both in vitro and in vivo. Furthermore, there is an increasing understanding of mechanisms underlying the disruption of immune functions towards secondary infections in the face of the induction of an efficient virus-specific immune response. For the latter, the interaction of MV with professional antigen-presenting cells and the consequences for T cell activation and/or inhibition, have received particular attention. The detailed knowledge of MV gene functions together with the definition of the interaction of MV with cells of the hematopoietic system is critical to improve the success of vaccination, particularly in young infants and in immunocompromised individuals, but also to use MV as a vector for targeted gene therapy.

Further reading: The Biology of Paramyxoviruses

from Kevin Moreau and Frank Lafont writing in Bacterial Pathogenesis: Molecular and Cellular Mechanisms:

Most invading bacteria enter the host cell by using either a triggered or a zippered mechanism. The former depends on membrane ruffles induced by injection of bacteria-derived effectors into the eukaryotic cell. A hallmark of the latter is a "sliding" of the bacteria into the cell through a clathrin-mediated structure, which is distinct from the pits in conventional clathrin-mediated endocytosis. Bacteria hijacking either of these mechanisms can also take advantage of signalling platforms activated within specialized membrane domains (lipid rafts). At the entry site, activated signalling pathways regulate the fate of the invading microorganism. Bacteria may then replicate in either cytoplasmic or vacuolar niches. Alternatively, the host immune system can deal with the infection and target the pathogen for elimination via several degradation pathways (notably including autophagy).

Further reading: Bacterial Pathogenesis: Molecular and Cellular Mechanisms

Melting curve analysis is a powerful and practical extension of real-time PCR. While real-time PCR focuses on collecting fluorescence at a single temperature each PCR cycle, melting analysis monitors fluorescence over time as the temperature is changing. Melting analysis fits nicely into the kinetic paradigm of PCR. Duplexes melt as the temperature increases, and the hybridization of both PCR products and probes can be monitored. Similar to "old" (slow) PCR being considered an equilibrium process, "old" (dot blot) hybridizations were performed at a single temperature. Dynamic monitoring of the entire melting curve as the temperature changes defines the entire melting transition, not just a single point (Wittwer and Farrar, 2011 in PCR Troubleshooting and Optimization). Melting curve analysis was first integrated with real-time PCR on the LightCycler. No separations or reagent additions were required and melting analysis was fast (typically 2-15 min). The dye SYBR Green I conveniently provided quantification during PCR and melting analysis after PCR. The melting temperature of a DNA duplex is determined in large part by its sequence, G/C content and length. Specific PCR products can be easily distinguished from nonspecific PCR products. In many cases melting analysis eliminates the need for post-PCR processing such as gel electrophoresis. Genotyping by melting analysis was first demonstrated with a single hybridization probe and FRET to monitor probe melting. Different single base variants produced different probe stabilities, which were revealed by melting analysis. Later, dual hybridization probes were used for genotyping and both color and temperature multiplexing exploited. The use of a single fluorescein-labeled probe instead of two probes was a further simplification. Genotyping by melting without labeled probes was first shown with allele-specific PCR and SYBR Green I. Three primers were used, one with a GC-tail to discriminate alleles by melting temperature. Genotyping without GC-tails or labeled probes became possible with the availability of saturation dyes that detect heteroduplexes. These methods are detailed later in the section on high resolution melting analysis.

from Elizaveta Bonch-Osmolovskaya writing in Extremophiles: Microbiology and Biotechnology:

Thermophilic microorganisms, though known since the beginning of the 20th century, were intensively studied in its last three decades. Natural terrestrial and submarine thermal environments were found to be populated by moderate, extreme and hyperthermophilic microorganisms representing diverse metabolic groups. However, during the past few years this knowledge has been extended, and new metabolic groups of thermophilic prokaryotes described. Among these are ammonia-oxidizing archaea, thermoacidophilic methanotrophs of the phylum Verrucomicrobia, microorganisms gaining energy for growth from the disproportionation of sulfur species, and archaea and bacteria metabolizing one carbon (C1) compounds. Other novel metabolic groups, such as thermophilic anammox bacteria, nitrite-oxidizing thermophiles, and microorganisms performing anaerobic methane oxidation in thermal ecosystems, have been detected using molecular or geochemical approaches. These data will, certainly, stimulate further cultivation and isolation efforts.

Further reading: Extremophiles: Microbiology and Biotechnology

from Danielle H. Dube writing in Bacterial Glycomics: Current Research, Technology and Applications:

Though long believed to be absent from bacteria, glycoproteins are now known to be synthesized in a number of bacterial species. Traditional methods to study glycoproteins have revealed fascinating glycan structures that are exclusively found in bacteria and are frequently linked to pathogenesis. In recent years, these methods have been augmented by a complementary approach, termed metabolic oligosaccharide engineering (MOE), to facilitate large scale systematic studies of the entire complement of glycan structures in bacteria, referred to as bacterial glycomics. In MOE, bacterial glycans are metabolically labeled with unique chemical functionalities, called chemical reporters. Labeling bacterial glycans in this manner facilitates glycoprotein detection and enrichment. In addition to enabling glycoprotein profiling, the labeled glycans can undergo selective covalent bond formation, thereby permitting further applications. For example, labeled glycans are poised to disrupt the bacterial surface coat, target bacterial cells with toxins, trap glycan-based host-pathogen interactions, and image dynamic changes in glycosylation. This chapter focuses on MOE methodology, its application to the study of bacterial glycoproteins, and its future role in treating infectious disease.

Further reading: Bacterial Glycomics: Current Research, Technology and Applications