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