Conference Update: New Zealand Microbiological Society
November 30 - December 3, 2010 New Zealand Microbiological Society and New Zealand Society for Biochemistry and Molecular Biology joint meeting
Auckland, New Zealand Further information
This is a multidisciplinary conference generally attracting 200-300 delegates. Most participants are New Zealand-based, although the conference also has a range of renowned international plenary speakers, encompassing diverse fields such as medical microbiology, wine science, food microbiology, industrial microbiology, microbial ecology, systems biology and molecular evolution.
Suggested reading: Molecular Microbiology Books
Auckland, New Zealand Further information
This is a multidisciplinary conference generally attracting 200-300 delegates. Most participants are New Zealand-based, although the conference also has a range of renowned international plenary speakers, encompassing diverse fields such as medical microbiology, wine science, food microbiology, industrial microbiology, microbial ecology, systems biology and molecular evolution.
Suggested reading: Molecular Microbiology Books
Labels: New Zealand Microbiology Conference, NZ Microbiological Society, NZ Society for Biochemistry and Molecular Biology
Conference Update: Superbugs and Superdrugs
March 17 - 18, 2010 12th Annual Superbugs and Superdrugs
London, UK Further information
Organized by SMI. Keynote address from Professor Peter Hawkey, Professor of Public Health Bacteriology, University of Birmingham and Health Protection Agency.
Suggested reading: Microbiology Books
London, UK Further information
Organized by SMI. Keynote address from Professor Peter Hawkey, Professor of Public Health Bacteriology, University of Birmingham and Health Protection Agency.
Suggested reading: Microbiology Books
Labels: Health Protection Agency, Peter Hawkey, Superbugs, Superdrugs
Conference Update: International Papillomavirus Conference
July 3 - 8, 2010 26th International Papillomavirus Conference and Workshops
Montreal, Canada Further information
HPV 2010. Twenty-Sixth Annual International Papillomavirus Conference and Clinical Workshop
Suggested reading: Papillomavirus Research: From Natural History To Vaccines and Beyond
Montreal, Canada Further information
HPV 2010. Twenty-Sixth Annual International Papillomavirus Conference and Clinical Workshop
Suggested reading: Papillomavirus Research: From Natural History To Vaccines and Beyond
Labels: International Papillomavirus Conference, Papillomavirus
Conference update: Microbial Ecology and Disease
September 6 - 10, 2010 XXXIII International Congress of the Society for Microbial Ecology and Disease
Cruiseship Aegean Pearl, Greece Further information
1st Day,Medical Microbial Ecology; 2nd Day,Dental Microbial Ecology; 3rd Day,Nutrition, Probiotics, Food and Water Microbial Ecology Health Related 4th Day,Environmental Microbial Ecology. The cruise programme includes some of the most well known Greek Islands such as Cosmopolitan Myconos, Rhodes, Patmos, Crete, the fascinating island of Santorini and Ephesus and Kusadasi in Turkey.
Suggested reading: Environmental Molecular Microbiology
Cruiseship Aegean Pearl, Greece Further information
1st Day,Medical Microbial Ecology; 2nd Day,Dental Microbial Ecology; 3rd Day,Nutrition, Probiotics, Food and Water Microbial Ecology Health Related 4th Day,Environmental Microbial Ecology. The cruise programme includes some of the most well known Greek Islands such as Cosmopolitan Myconos, Rhodes, Patmos, Crete, the fascinating island of Santorini and Ephesus and Kusadasi in Turkey.
Suggested reading: Environmental Molecular Microbiology
Labels: International Congress of the Society for Microbial Ecology and Disease, Society for Microbial Ecology and Disease
Evolution of Plastids
Photosynthesis is one of the most successful energy production strategies on the planet and has been co-opted numerous times throughout evolutionary history via the uptake and retention of photosynthetic cells by non-photosynthetic eukaryotic heterotrophs. Whereas the result of this process is clear, what is not settled is the mode and tempo of plastid movement among eukaryotes, particularly plastids of red algal derivation. Recent changes in our understanding of the relationships between eukaryotic supergroups have only served to complicate the picture further. Of particular interest is the evolution of plastids, the relationships among photosynthetic eukaryotes, the process of endosymbiogenesis and the variation in ways plastids have been modified to suit the light harvesting needs of their hosts. The understanding of all of these factors is an active field of continued research that will undoubtedly lead to further discoveries in the coming years read more ...
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
- Molecular Phylogeny of Microorganisms
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- Metagenomics
Labels: Endosymbiogenesis, Evolution of plastids, Evolutionary history, Photosynthesis, Plastid
Microbial Phylogenetics: Horizontal Gene Transfer
Efforts to construct the tree of life take their conceptual motivation from Charles Darwin's theory of evolution. Until the advent of molecular biology, however, a universal tree of life was well beyond the scope of the data and methods of traditional organismal phylogeny. The rapid development of these methods and bodies of genetic sequence from the 1970s onwards resulted in major reclassifications of life and revived ambitions to represent all organismal lineages by one true tree of life. Subsequent realization of the significance of lateral gene transfer and other non-vertical processes has subtly reconceptualized and reoriented attempts to construct this universal phylogeny.
Gene transfer has affected the formation of groups of organisms. Gene transfer can make it more difficult to define and determine relationships. In those cases where many genes have been transferred between preferred partners, the majority of genes in a genome may reflect gene acquisition, and as a consequence, if a coherent signal is detected, one nevertheless might not be sure that the signal is due to organismal shared ancestry. However, the presence of a particular transferred gene has been shown, in several cases, to constitute a shared derived character useful in classification. Gene transfer can put together new metabolic pathways that open up new ecological niches, and consequently, the transfer of an adaptive gene might create a new group of organisms read more ...
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
Gene transfer has affected the formation of groups of organisms. Gene transfer can make it more difficult to define and determine relationships. In those cases where many genes have been transferred between preferred partners, the majority of genes in a genome may reflect gene acquisition, and as a consequence, if a coherent signal is detected, one nevertheless might not be sure that the signal is due to organismal shared ancestry. However, the presence of a particular transferred gene has been shown, in several cases, to constitute a shared derived character useful in classification. Gene transfer can put together new metabolic pathways that open up new ecological niches, and consequently, the transfer of an adaptive gene might create a new group of organisms read more ...
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
- Molecular Phylogeny of Microorganisms
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- Metagenomics
Labels: Gene transfer, horizontal gene transfer, Lateral Gene Transfer, Tree of life
Microbial Phylogenetics: Conserved Indels
Comparative analysis of genome sequences is leading to discovery of large numbers of novel molecular markers that are proving very helpful in understanding many important aspects of microbial phylogeny. Of these molecular markers, the conserved inserts or deletions (indels) in protein sequences provide particularly useful means for identifying different groups of microbes in clear molecular terms and for understanding how they have branched off from a common ancestor. Conserved indels and other novel molecular markers (viz. lineage-specific proteins) can be useful for understanding microbial phylogeny at different phylogenetic depths. Genetic and biochemical studies of these markers should also lead to identification of novel properties that are unique to different groups of microbes read more ...
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
- Molecular Phylogeny of Microorganisms
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- Metagenomics
Labels: Conserved indels, Conserved inserts or deletions, Groups of microbes, Indels, Lineage-specific proteins, Microbial phylogeny, Molecular markers, Phylogenetic depths
Rooting the Tree of Life
Defining the evolutionary relationships between groups of organisms is a major part of modern-day microbiology. With the continuing dramatic increase in the availability of genomic data, these techniques have been extended to describing an all-encompassing "tree of life". However, identifying the location of the root of this tree corresponding to the most recent common ancestor is a challenging and distinct problem that has yet to be solved. To date, many investigations have proposed various roots, using a wide diversity of biological data and techniques. A survey of the most promising of these models illustrates the difficulty faced in reaching a scientific consensus on the issue, as well as the additional philosophical complications posed by our emerging understanding of the role of horizontal gene transfer in genome evolution read more ...
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
- Molecular Phylogeny of Microorganisms
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- Metagenomics
Labels: Tree of Life
The Phyla of Prokaryotes
There is no official classification of prokaryotes. For the higher taxa there even is no official nomenclature: the rules of the International Code of Nomenclature of Prokaryotes do not cover taxa above the rank of class. The most commonly accepted division of the prokaryotes in two "subkingdoms" or "domains" (Bacteria and Archaea) and the classification of their species with validly published names in respectively 27 and 2 "phyla" or "divisions" (as of November 2009) is primarily based on 16S rRNA sequence comparisons. This type of classification was adopted in the latest edition of Bergey's Manual of Systematic Bacteriology. Alternative classifications have been proposed as well, based e.g. on the structure of the cell wall. Some 16S rRNA sequence-based phyla unite prokaryotes of similar physiological properties (for example Cyanobacteria, Chlorobi, Thermotogae); others (Euryarchaeota, Proteobacteria, Flavobacteria) contain organisms with highly disparate lifestyles. Some phyla based on deep 16S rRNA lineages are currently represented by one or a few species only. Environmental genomics/metagenomics approaches suggest existence of many more phyla based on the deep lineages of 16S rRNA gene sequences recovered. To obtain the organisms harboring these sequences and to study their properties is a major challenge of microbiology today read more ...
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
- Molecular Phylogeny of Microorganisms
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- Metagenomics
Labels: Bergeys Manual of Systematic Bacteriology, Classification of prokaryotes, International Code of Nomenclature of Prokaryotes
Microbial Phylogenetics: Global Markers
The introduction of comparative rRNA sequence analysis represents a major milestone in the history of microbiology. The current taxonomy of prokaryotes as well as modern probe and chip based identification methods are mainly based upon rRNA derived phylogenetic conclusions. Also of importance is single gene based phylogenetic inference and alternative global markers include elongation and initiation factors, RNA polymerase subunits, DNA gyrases, heat shock and recA proteins. Although the comparative analyses are hampered by the generally low phylogenetic information content, and different resolution power, and multiple copies of the individual markers, the domain and prokaryotic phyla concept is globally supported read more ...
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
- Molecular Phylogeny of Microorganisms
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- Metagenomics
Labels: Chip based identification, DNA gyrase, Elongation factor, Global markers, Heat shock, Phylogenetic analysis, Phylogenetic inference, RecA, RNA polymerase, rRNA sequence analysis, Taxonomy of prokaryotes
Multilocus Sequence Analysis
Multilocus sequence analysis (MLSA) represents the novel standard in microbial molecular systematics. In this context, MLSA is implemented in a relatively straightforward way, consisting essentially in the concatenation of several sequence partitions for the same set of organisms, resulting in a "supermatrix" which is used to infer a phylogeny by means of distance-matrix or optimality criterion-based methods. This approach is expected to have an increased resolving power due to the large number of characters analyzed, and a lower sensitivity to the impact of conflicting signals (i.e. phylogenetic incongruence) that result from eventual horizontal gene transfer events. The strategies used to deal with multiple partitions can be grouped in three broad categories: the total evidence, separate analysis and combination approaches. The concatenation approach that dominates MLSAs in the microbial molecular systematics literature is known to systematists working with plants and animals as the "total molecular evidence" approach, and has been used to solve difficult phylogenetic questions such as the relationships among the major groups of cetaceans, that of microsporidia and fungi, or the phylogeny of major plant lineages. The total molecular evidence approach has been criticized because by directly concatenating all available sequence alignments, the evidence of conflicting phylogenetic signals in the different data partitions is lost along with the possibility to uncover the evolutionary processes that gave rise to such contradictory signals. The nature of these conflicts is varied, but in the microbial world the strongest conflicting signals often derive from the existence of horizontal gene transfer events in the dataset. If the individuals containing xenologous loci are not identified and removed from the supermatrix prior to phylogeny inference, the resulting hypothesis may be strongly distorted, since standard treeing methods assume a single underlying evolutionary history. Based on these arguments, the conditional data combination strategy is to be generally preferred in bacterial MLSA read more ...
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
- Molecular Phylogeny of Microorganisms
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- Metagenomics
Labels: horizontal gene transfer, Microbial molecular systematics, MLSA, Multilocus sequence analysis, Phylogenetic incongruence, Phylogeny
Microbial Phylogenetics Methods
The purpose of phylogenetic analysis is to understand the past evolutionary path of organisms. Even though we will never know for certain the true phylogeny of any organism, phylogenetic analysis provides best assumptions, thereby providing a framework for various disciplines in microbiology. Due to the technological innovation of modern molecular biology and the rapid advancement in computational science, accurate inference of the phylogeny of a gene or organism seems possible in the near future. There has been a flood of nucleic acid sequence information, bioinformatic tools and phylogenetic inference methods in public domain databases, literature and worldwide web space. Phylogenetic analysis has long played a central role in basic microbiology, for example in taxonomy and ecology. In addition, more recently emerging fields of microbiology, including comparative genomics and phylogenomics, require substantial knowledge and understanding of phylogenetic analysis and computational skills to handle the large-scale data involved. Methods of phylogenetic analysis and relevant computer software tools lend accuracy, efficiency and availability to the task.
There are four steps in general phylogenetic analysis of molecular sequences: (i) selection of a suitable molecule or molecules (phylogenetic marker), (ii) acquisition of molecular sequences, (iii) multiple sequence alignment (MSA) and (iv) phylogenetic treeing and evaluation. The first step of phylogenetic analysis is to choose a suitable homologous part of the genomes to be compared. Mechanisms of molecular evolution include mutations, duplication of genes, reorganization of genomes, and genetic exchanges such as recombination, reassortment and lateral gene transfer. Although all of this information can be used to infer phylogenetic relationships of genes or organisms, information on mutations, including substitution, insertion, and deletion, is most frequently used in phylogeny reconstruction. The aim is to infer a correct organismal phylogeny, using orthologous genetic loci, in which common ancestry of two sequences can be traced back to a speciation event. Phylogeny using homologous genetic loci derived by gene duplication (paralogy) or related through lateral gene transfer (xenology), cannot reflect evolutionary history of organisms.
Once DNA sequence data are generated, they are subjected to a multiple sequence alignment process. This involves finding homologous sites, that is, positions derived from the same ancestral organism in the molecules under study. A set of sequences can be aligned with another by introducing "alignment gaps" (known in brief as "gaps"). In general, multiple sequence alignment starts by aligning a pair of sequences (pairwise alignment), and is then expanded to multiple sequences using various algorithms.
Many algorithms and computer programs have been developed in the last few decades for multiple sequence alignment, but the original Clustal series programs are still most widely used and produce reasonably good quality MSA for small data sets. For a large dataset, such as massive pyrosequencing reads, the MUSCLE program can generate good compromise between accuracy and speed. The MAFFT program utilizes several different algorithmic approaches and can be used for either small or very large datasets. There are also other computer programs developed for general multiple sequence alignment, but the above three have been most popular and are routinely used in publications in various microbiological disciplines read more ...
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
There are four steps in general phylogenetic analysis of molecular sequences: (i) selection of a suitable molecule or molecules (phylogenetic marker), (ii) acquisition of molecular sequences, (iii) multiple sequence alignment (MSA) and (iv) phylogenetic treeing and evaluation. The first step of phylogenetic analysis is to choose a suitable homologous part of the genomes to be compared. Mechanisms of molecular evolution include mutations, duplication of genes, reorganization of genomes, and genetic exchanges such as recombination, reassortment and lateral gene transfer. Although all of this information can be used to infer phylogenetic relationships of genes or organisms, information on mutations, including substitution, insertion, and deletion, is most frequently used in phylogeny reconstruction. The aim is to infer a correct organismal phylogeny, using orthologous genetic loci, in which common ancestry of two sequences can be traced back to a speciation event. Phylogeny using homologous genetic loci derived by gene duplication (paralogy) or related through lateral gene transfer (xenology), cannot reflect evolutionary history of organisms.
Once DNA sequence data are generated, they are subjected to a multiple sequence alignment process. This involves finding homologous sites, that is, positions derived from the same ancestral organism in the molecules under study. A set of sequences can be aligned with another by introducing "alignment gaps" (known in brief as "gaps"). In general, multiple sequence alignment starts by aligning a pair of sequences (pairwise alignment), and is then expanded to multiple sequences using various algorithms.
Many algorithms and computer programs have been developed in the last few decades for multiple sequence alignment, but the original Clustal series programs are still most widely used and produce reasonably good quality MSA for small data sets. For a large dataset, such as massive pyrosequencing reads, the MUSCLE program can generate good compromise between accuracy and speed. The MAFFT program utilizes several different algorithmic approaches and can be used for either small or very large datasets. There are also other computer programs developed for general multiple sequence alignment, but the above three have been most popular and are routinely used in publications in various microbiological disciplines read more ...
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
- Molecular Phylogeny of Microorganisms
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- Metagenomics
Labels: Clustal, Comparative genomics, MAFFT, Multiple sequence alignment, MUSCLE, Phylogenetic analysis, Phylogenetic inference methods, Phylogenetic marker, Phylogenetic tree, Phylogenomics, Phylogeny of a gene
Microbial Phylogenetics: A Historical Overview
When at the end of the 19th century information began to accumulate about the diversity within the bacterial world, scientists started to include the bacteria in phylogenetic schemes to explain how life on Earth may have developed. Some of the early phylogenetic trees of the prokaryote world were morphology-based; others were based on the then-current ideas on the presumed conditions on our planet at the time that life first developed. Around 1950 many leading microbiologists had become pessimistic with respect to the possibility of ever reconstructing bacterial phylogeny. The concept of the prokaryote-eukaryote dichotomy did little to clarify phylogenetic relationships. The developing technology of nucleic acid sequencing, together with the recognition that sequences of building blocks in informational macromolecules (nucleic acids, proteins) can be used as "molecular clocks" that contain historical information, led to the development of the three-domain model (Archaea - Bacteria - Eucarya) in the late 1970s, primarily based on small subunit ribosomal RNA sequence comparisons. The information currently accumulating from complete genome sequences of an ever increasing number of prokaryotes are now leading to further modifications of our views on microbial phylogeny read more ...
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)
References
- Molecular Phylogeny of Microorganisms
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- Metagenomics
Labels: Bacterial phylogeny, Microbial phylogeny, Phylogenetic relationships, Phylogenetic schemes, Ribosomal RNA sequence comparison
Potential Risks of Nanotechnology on Human Health
The risk assessment of nanoparticles and nanomaterials is of key importance for the continuous development in the new field of nanotechnology. Humans are increasingly being exposed to nanoparticles and nanomaterials, placing stress on the development and validation of reproducible toxicity tests. Tests currently used include genotoxicity and cytotoxicity tests, and in vivo toxicity models. The unique characteristics of nanoparticles and nanomaterials are responsible for their toxicity and interaction with biological macromolecules within the human body. This may lead to the development of diseases and clinical disorders. A loss in cell viability and structure can also occur in exposed tissues as well as inflammation and granuloma formation. The future of nanotechnology depends on the responsible assessment of nanoparticles and nanomaterials read more ...
References:
References:
- Nanotechnology in Water Treatment Applications
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- PCR publications
- Environmental Microbiology publications
- Bacteriology
Labels: Biofilm-removal, Biomolecular-detection, Electrospinning Nanofibers, Nanobiocides, Nanobiotechnology, Nanofibers, Nanofiltration, Nanotechnology, Nanozymes, Reverse-Osmosis, Wastewater-treatment, Water treatment
Nanofibers for Water Treatment
Electrospinning is a highly versatile technique that can be used to create ultrafine fibres of various polymers and other materials, with diameters ranging from a few micrometers down to tens of nanometres. The nonwoven webs of fibers formed through this process typically have high specific surface areas, nano-scale pore sizes, high and controllable porosity and extreme flexibility with regard to the materials used and modification of the surface chemistry of the fibres. A combination of these features is utilized in the application of electrospun nanofibres to a variety of water treatment applications, including filtration, solid phase extraction and reactive membranes read more ...
References:
References:
- Nanotechnology in Water Treatment Applications
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- PCR publications
- Environmental Microbiology publications
- Bacteriology
Labels: Biofilm-removal, Biomolecular-detection, Electrospinning Nanofibers, Nanobiocides, Nanobiotechnology, Nanofibers, Nanofiltration, Nanotechnology, Nanozymes, Reverse-Osmosis, Wastewater-treatment, Water treatment
Reverse Osmosis
The membrane separation technologies of reverse osmosis (hyperfiltration) and nanofiltration are important in water treatment applications. Reverse osmosis is based on the basic principle of osmotic pressure, while nanofiltration makes use of molecule size for separation. Recent advances in the field of nanotechnology are opening a range of possibilities in membrane technologies. These include: new membrane preparation and cleaning methods, new surface and interior modification possibilities, the use of new nanostructured materials, and new characterization techniques read more ...
References:
References:
- Nanotechnology in Water Treatment Applications
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- PCR publications
- Environmental Microbiology publications
- Bacteriology
Labels: Biofilm-removal, Biomolecular-detection, Electrospinning Nanofibers, Nanobiocides, Nanobiotechnology, Nanofibers, Nanofiltration, Nanotechnology, Nanozymes, Reverse-Osmosis, Wastewater-treatment, Water treatment
Nanofiltration in Wastewater Treatment
Nanofiltration is a new type of pressure driven membrane process and used between reverse osmosis and ultrafiltration membranes. The most different speciality of nanofiltration membranes is the higher rejection of multivalent ions than monovalent ions. Nanofiltration membranes are used in softening water, brackish water treatment, industrial wastewater treatment and reuse, product separation in the industry, salt recovery and recently desalination as two pass nanofiltration system read more ...
References:
References:
- Nanotechnology in Water Treatment Applications
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- PCR publications
- Environmental Microbiology publications
- Bacteriology
Labels: Biofilm-removal, Biomolecular-detection, Electrospinning Nanofibers, Nanobiocides, Nanobiotechnology, Nanofibers, Nanofiltration, Nanotechnology, Nanozymes, Reverse-Osmosis, Wastewater-treatment, Water treatment
Nanozymes in Biofilm Removal
Sessile communities of bacteria encased in extracellular polymeric substances (EPS) are known as biofilms and causes serious problems in various areas, amongst other, the medical industry, industrial water settings, paper industry and food processing industry.
Although various methods of biofilm control exist, these methods are not without limitations and often fail to remove biofilms from surfaces. Biofilms often show reduced susceptibility to antimicrobials or chemicals and chemical by-products may be toxic to the environment, whereas mechanical methods may be labour intensive and expensive due to down-time required to clean the system. This has led to a great interest in the enzymatic degradation of biofilms. Enzymes are highly selective and disrupt the structural stability of the biofilm EPS matrix.
Various studies have focused on the enzymatic degradation of polysaccharides and proteins for biofilm detachment since these are the two dominant components of the EPS. Due to the structural role of proteins and polysaccharides in the EPS matrix, a combination of various proteases and polysaccharases may be successful in biofilm removal. The biodegradability and low toxicity of enzymes also make them attractive biofilm control agents. Regardless of all the advantages associated with enzymes, they also suffer from various drawbacks given that they are relatively expensive, show insufficient stability or activity under certain conditions, and cannot be reused. Various approaches are being used to increase the stability of enzymes, including enzyme modification, enzyme immobilization, protein engineering and medium engineering. Although these conventional methods have been used frequently to improve the stability of enzymes, various new techniques, such as self-immobilization of enzymes, the immobilization of enzymes on nano-scale structures and the production of single-enzyme nanoparticles, have been developed.
Self-immobilization of enzymes entails the cross-linking of enzyme molecules with each other and yields final preparations consisting of essentially pure proteins and high concentrations of enzyme per unit volume. The activity, stability and efficiency of immobilized enzymes can be improved by reducing the size of the enzyme-carrier. Nano-scale carrier materials allow for high enzyme loading per unit mass, catalytic recycling and a reduced loss of enzyme activity. Furthermore, enzymes can be stabilized by producing single-enzyme nanoparticles consisting of single-enzyme molecules surrounded by a porous organic-inorganic network of less than a few nanometers thick. All these new technologies of enzyme stabilization make enzymes even more attractive alternatives to other biofilm removal and control agents read more ...
References:
Although various methods of biofilm control exist, these methods are not without limitations and often fail to remove biofilms from surfaces. Biofilms often show reduced susceptibility to antimicrobials or chemicals and chemical by-products may be toxic to the environment, whereas mechanical methods may be labour intensive and expensive due to down-time required to clean the system. This has led to a great interest in the enzymatic degradation of biofilms. Enzymes are highly selective and disrupt the structural stability of the biofilm EPS matrix.
Various studies have focused on the enzymatic degradation of polysaccharides and proteins for biofilm detachment since these are the two dominant components of the EPS. Due to the structural role of proteins and polysaccharides in the EPS matrix, a combination of various proteases and polysaccharases may be successful in biofilm removal. The biodegradability and low toxicity of enzymes also make them attractive biofilm control agents. Regardless of all the advantages associated with enzymes, they also suffer from various drawbacks given that they are relatively expensive, show insufficient stability or activity under certain conditions, and cannot be reused. Various approaches are being used to increase the stability of enzymes, including enzyme modification, enzyme immobilization, protein engineering and medium engineering. Although these conventional methods have been used frequently to improve the stability of enzymes, various new techniques, such as self-immobilization of enzymes, the immobilization of enzymes on nano-scale structures and the production of single-enzyme nanoparticles, have been developed.
Self-immobilization of enzymes entails the cross-linking of enzyme molecules with each other and yields final preparations consisting of essentially pure proteins and high concentrations of enzyme per unit volume. The activity, stability and efficiency of immobilized enzymes can be improved by reducing the size of the enzyme-carrier. Nano-scale carrier materials allow for high enzyme loading per unit mass, catalytic recycling and a reduced loss of enzyme activity. Furthermore, enzymes can be stabilized by producing single-enzyme nanoparticles consisting of single-enzyme molecules surrounded by a porous organic-inorganic network of less than a few nanometers thick. All these new technologies of enzyme stabilization make enzymes even more attractive alternatives to other biofilm removal and control agents read more ...
References:
- Nanotechnology in Water Treatment Applications
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- PCR publications
- Environmental Microbiology publications
- Bacteriology
Labels: Biofilm-removal, Biomolecular-detection, Electrospinning Nanofibers, Nanobiocides, Nanobiotechnology, Nanofibers, Nanofiltration, Nanotechnology, Nanozymes, Reverse-Osmosis, Wastewater-treatment, Water treatment
Nanobiocides in Water Purification
Electrospun nanofibers and nanobiocides show potential in the improvement of water filtration membranes. Biofouling of membranes caused by the bacterial load in water reduces the quality of drinking water and has become a major problem. Several studies showed inhibition of these bacteria after exposure to nanofibers with functionalized surfaces. Nanobiocides such as metal nanoparticles and engineered nanomaterials are successfully incorporated into nanofibers showing high antimicrobial activity and stability in water read more ...
References:
References:
- Nanotechnology in Water Treatment Applications
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- PCR publications
- Environmental Microbiology publications
- Bacteriology
Labels: Biofilm-removal, Biomolecular-detection, Electrospinning Nanofibers, Nanobiocides, Nanobiotechnology, Nanofibers, Nanofiltration, Nanotechnology, Nanozymes, Reverse-Osmosis, Wastewater-treatment, Water treatment
Nanobiotechnology for the Detection of Microbial Pathogens
An adequate supply of safe drinking water is one of the major prerequisites for a healthy life, but waterborne diseases is still a major cause of death in many parts of the world, particularly in young children, the elderly, or those with compromised immune systems. As the epidemiology of waterborne diseases is changing, there is a growing global public health concern about new and reemerging infectious diseases that are occurring through a complex interaction of social, economic, evolutionary, and ecological factors. An important challenge is therefore the rapid, specific and sensitive detection of waterborne pathogens. Presently, microbial tests are based essentially on time-consuming culture methods. However, newer enzymatic, immunological and genetic methods are being developed to replace and/or support classical approaches to microbial detection. Moreover, innovations in nanotechnology and nanosciences are having a significant impact in biodiagnostics, where a number of nanoparticle-based assays and nanodevices have been introduced for biomolecular detection read more ...
References:
References:
- Nanotechnology in Water Treatment Applications
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- PCR publications
- Environmental Microbiology publications
- Bacteriology
Labels: Biofilm-removal, Biomolecular-detection, Electrospinning Nanofibers, Nanobiocides, Nanobiotechnology, Nanofibers, Nanofiltration, Nanotechnology, Nanozymes, Reverse-Osmosis, Wastewater-treatment, Water treatment
Nanotechnology in Water Treatment: Applications and Emerging Opportunities
Nanotechnology, the engineering and art of manipulating matter at the nanoscale (1-100 nm), offers the potential of novel nanomaterials for the treatment of surface water, groundwater and wastewater contaminated by toxic metal ions, organic and inorganic solutes and microorganisms. Due to their unique activity toward recalcitrant contaminants and application flexibility, many nanomaterials are under active research and development.
References:
References:
- Nanotechnology in Water Treatment Applications
- Lab-on-a-Chip Technology
- Real-Time PCR: Current Technology and Applications
- Environmental Molecular Microbiology
- PCR publications
- Environmental Microbiology publications
- Bacteriology
Labels: Biofilm-removal, Biomolecular-detection, Electrospinning Nanofibers, Nanobiocides, Nanobiotechnology, Nanofibers, Nanofiltration, Nanotechnology, Nanozymes, Reverse-Osmosis, Wastewater-treatment, Water treatment
Iron in Yeasts
Yeasts take up iron by three main mechanisms. In the reductive uptake mechanism, specialized flavo-hemoproteins (Fre) dissociate extracellular ferric complexes by reduction involving trans-plasma membrane electron transfer. The resulting free iron is then imported by a high-affinity permease system (Ftr), coupled to a copper-dependent oxidase (Fet), which channels iron through the plasma membrane. As a consequence, iron uptake by this mechanism is dependent on the availability of copper. In the siderophore-mediated mechanism, siderophores excreted by the cells or produced by other bacterial or fungal species are taken up without prior dissociation, via specific, copper-independent high-affinity receptors. The iron is then dissociated from the siderophores intracellularly, probably by reduction. In the heme uptake mechanism, free heme or heme bound to hemoglobin is taken up as such, probably by endocytosis. Iron is released intracellularly after hydrolysis of the porphyrin ring catalyzed by heme oxygenase. Within the cell, iron is stored in vacuoles or in siderophores.
Iron can be mobilized from vacuoles by a reductive mechanism homologous to that found at the plasma membrane. Regulation of iron uptake and iron use are mediated by transcriptional regulators acting either as activators in iron-deficient conditions or as repressors in iron-rich conditions, according to the yeast species; these regulators thus adjust the iron uptake flux to the cell's requirements. In the baker's yeast, Saccharomyces cerevisiae, a post-transcriptional mechanism is active under low iron conditions, involving the degradation of RNAs encoding inessential iron-utilizing proteins. Other fungi have mechanisms serving a similar purpose at the transcriptional level. Studies in S. cerevisiae show that mitochondria are central to regulating cellular iron homeostasis, through the synthesis of iron-sulfur clusters.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Iron can be mobilized from vacuoles by a reductive mechanism homologous to that found at the plasma membrane. Regulation of iron uptake and iron use are mediated by transcriptional regulators acting either as activators in iron-deficient conditions or as repressors in iron-rich conditions, according to the yeast species; these regulators thus adjust the iron uptake flux to the cell's requirements. In the baker's yeast, Saccharomyces cerevisiae, a post-transcriptional mechanism is active under low iron conditions, involving the degradation of RNAs encoding inessential iron-utilizing proteins. Other fungi have mechanisms serving a similar purpose at the transcriptional level. Studies in S. cerevisiae show that mitochondria are central to regulating cellular iron homeostasis, through the synthesis of iron-sulfur clusters.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: fungal, fungi, Iron acquisition mechanisms, Iron transporters, Iron uptake in Yeasts, Iron uptake systems, Iron-homeostasis, Iron-uptake, mycology, Siderophores, yeast, Yeasts
Iron in Staphylococci
Staphylococcus aureus causes a significant amount of human morbidity and mortality. The ability of S. aureus to cause disease is dependent upon its acquisition of iron from the host. S. aureus can obtain iron from various sources during infection, including heme and transferrin. The most abundant iron source in humans is heme-iron bound by hemoglobin contained within erythrocytes. S. aureus is known to lyse erythrocytes through secretion of pore-forming toxins, providing access to host hemoglobin.
Proteins of the iron-regulated surface determinant (Isd) system bind host hemoproteins, remove the heme cofactor, and shuttle heme into the cytoplasm for use as a nutrient iron source. Deletion of Isd system components decreases staphylococcal virulence, underscoring the importance of heme-iron acquisition during infection. In addition to heme, S. aureus can utilize transferrin-iron through the secretion of siderophores. Several staphylococcal siderophores have been described, some of which have defined roles during the pathogenesis of staphylococcal infections. A greater understanding of staphylococcal iron acquisition may lead to the development of novel therapeutic strategies that target nutrient uptake and decrease the threat of this increasingly drug-resistant bacterial pathogen.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Proteins of the iron-regulated surface determinant (Isd) system bind host hemoproteins, remove the heme cofactor, and shuttle heme into the cytoplasm for use as a nutrient iron source. Deletion of Isd system components decreases staphylococcal virulence, underscoring the importance of heme-iron acquisition during infection. In addition to heme, S. aureus can utilize transferrin-iron through the secretion of siderophores. Several staphylococcal siderophores have been described, some of which have defined roles during the pathogenesis of staphylococcal infections. A greater understanding of staphylococcal iron acquisition may lead to the development of novel therapeutic strategies that target nutrient uptake and decrease the threat of this increasingly drug-resistant bacterial pathogen.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: Heme, Heme uptake, Iron acquisition mechanisms, Iron transporters, Iron uptake in Staphylococci, Iron uptake systems, Iron-homeostasis, Iron-uptake, Siderophore, Siderophores, Staphylococci
Iron in Bacillus
Bacillus subtilis is a metabolically versatile soil microbe and Gram-positive model organism that displays a sophisticated adaptive response to conditions of iron limitation. The endogenous siderophore of B. subtilis is bacillibactin, a trimeric catecholate siderophore similar in structure to enterobactin. In addition to bacillibactin, B. subtilis can obtain iron from several xenosiderophores, ferric citrate, heme, and through a newly discovered elemental iron permease.
The regulation of iron homeostasis in B. subtilis is complex and involves a ferric uptake regulator (Fur) protein as master regulator and at least two subsidiary regulatory systems. The most significant of these is an iron-sparing/prioritization response controlled by the small RNA FsrA and three auxiliary proteins (FbpABC). In addition, the bacillibactin uptake system is transcriptionally activated by an AraC family activator, Btr that directly senses bacillibactin. Iron uptake and homeostasis systems in B. anthracis and related organisms are largely similar to those in B. subtilis with some additional components. These include a second siderophore synthesis operon for petrobactin, which is important for virulence, and a more elaborate (or at least better understood) heme uptake system.
Further reading: Iron Uptake and Homeostasis in Microorganisms
The regulation of iron homeostasis in B. subtilis is complex and involves a ferric uptake regulator (Fur) protein as master regulator and at least two subsidiary regulatory systems. The most significant of these is an iron-sparing/prioritization response controlled by the small RNA FsrA and three auxiliary proteins (FbpABC). In addition, the bacillibactin uptake system is transcriptionally activated by an AraC family activator, Btr that directly senses bacillibactin. Iron uptake and homeostasis systems in B. anthracis and related organisms are largely similar to those in B. subtilis with some additional components. These include a second siderophore synthesis operon for petrobactin, which is important for virulence, and a more elaborate (or at least better understood) heme uptake system.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: bacillus, Iron acquisition mechanisms, Iron deficiency, Iron transporters, Iron uptake in Bacillus, Iron uptake systems, Iron-homeostasis, Iron-uptake, Siderophore, Siderophores
Iron in Cyanobacteria
Cyanobacteria are dependent on but can also be compromised by metals such as iron. On the one hand the demand for iron for photosystem functionality represents a challenge for the iron uptake machinery in iron limiting environments. On the other hand intoxication by iron causes a severe problem for growth and reproduction. To overcome this dilemma cyanobacteria have developed a regulatory network controlling iron uptake. They produce siderophores, which are distinct from that of other bacteria. Furthermore, the iron metabolism is linked to the nitrogen metabolism as documented for example in Anabaena sp. PCC 7120.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: Anabaena, cyanobacteria, Iron acquisition mechanisms, Iron deficiency, Iron transporters, Iron uptake in Cyanobacteria, Iron uptake systems, Iron-homeostasis, Iron-uptake, Siderophore, Siderophores
Iron in Campylobacter
Iron is known to catalyze a wide range of biochemical reactions essential for most living organisms, including Campylobacter jejuni. Paradoxically, this iron reactivity is also responsible for the generation of hydroxyl radicals (·OH), which are particularly biotoxic. In order to avoid iron toxicity, microorganisms must achieve an effective iron homeostasis by tightly regulating the expression of genes encoding the proteins involved in iron acquisition, metabolism and oxidative stress defences in response to iron availability. Interestingly, in addition to the classical ferric uptake regulator Fur, C. jejuni carries another member of the Fur family of metalloregulators, PerR. PerR is a peroxide-sensing regulator and typically regulates peroxide stress response in Gram-positive bacteria. Recent work indicates that the regulatory functions of Fur and PerR extend beyond their classically ascribed roles. These diverse functions include energy metabolism, protein glycosylation and flagella biogenesis. Moreover, the Fur and PerR regulons appear to overlap and co-regulate key genes at specific junctions.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: Campylobacter, Iron acquisition mechanisms, Iron transporters, Iron uptake in Campylobacter, Iron uptake systems, Iron-homeostasis, Iron-metabolism, Iron-uptake
Iron in Bacteroides
Bacteroides spp. have an essential requirement for heme and non-heme iron. They cannot synthesize the tetrapyrrole macrocycle ring due to a lack of genes for the heme biosynthetic pathway. It is remarkable that heme-dependent organisms outnumber heme-independent organisms in the lower intestinal tract suggesting that heme biosynthesis is not essential for colonization of the colonic environment. However, this colonization advantage may be due to the fact that under anaerobic conditions in the presence of heme, B. fragilis can generate nearly the double amount of ATP than Escherichia coli per mol of glucose. This high energy yield is linked to a rudimentary heme-induced fumarate reductase and cytochrome b-dependent electron transport energy metabolism pathway which uses fumarate as the terminal electron acceptor. Moreover, Bacteroides spp. can incorporate iron-deuteroporphyrin and iron-mesoporphyrin into a functional type-b cytochrome. Heme can be demetalated without cleaving the tetrapyrrole ring releasing free iron and free protoporphirin IX. The ability of the opportunistic human pathogen B. fragilis to cause infections seems to be due in part to its ability to scavenge heme and iron from host proteins. The in-frame translated intergenic region of the fused FeoAB proteins are exclusively present in gastro-intestinal colonizers belonging to the Bacteroidetes, Firmicutes and Actinobacteria phyla. Several members of the Bacteroides group have three orthologs of the mammalian-type bacterial ferritin gene, ftnA. FtnA may play an important role in protection against iron-induced oxidative stress in this group of highly aerotolerant anaerobes.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: Bacteroides, Iron acquisition mechanisms, Iron transporters, Iron uptake in Bacteroides, Iron uptake systems, Iron-homeostasis, Iron-metabolism, Iron-uptake
Iron in Francisella
Francisella tularensis is unusual among Gram-negative bacteria in that its genome does not encode orthologs for TonB, ExbB and ExbD that typically energize the uptake of iron across the outer membrane. This organism secretes however a siderophore similar in structure to rhizoferrin. The fsl operon of six genes encodes functions for biosynthesis and uptake of the siderophore. Two of these genes encode a siderophore synthetase belonging to the nonribosomal peptide synthetase (NRPS)-independent synthetase (NIS)-family and a protein belonging to the pyridoxyl phosphate-dependent decarboxylase family, and both are required for siderophore production. Siderophore utilization involves the product of the fslE gene, a protein unique to Francisella species that could function as a siderophore receptor. Additionally, genes related in sequence to fslE also play a role in siderophore acquisition. The mechanism for TonB-independent iron uptake in this microorganism remains to be elucidated.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: Francisella, Iron acquisition mechanisms, Iron transporters, Iron uptake in Francisella, Iron uptake systems, Iron-homeostasis, Iron-metabolism, Iron-uptake
Iron in Vibrio and Aeromonas
Vibrio and Aeromonas species are ubiquitous bacteria in aquatic environments worldwide. Many of the species are important pathogens for humans and/or aquatic animals. Several iron acquisition strategies have been developed by vibrios and aeromonads in order to get this essential element for surviving in their host and in aquatic habitats. All species studied so far have the ability to synthesize siderophores to sequester iron from the cell environment and transport it through their respective cognate outer membrane receptors. It has been demonstrated that this capacity is a relevant virulence factor for human and animal pathogens. Furthermore, all species studied can utilize exogenous siderophores, made by other bacteria. Another iron acquisition system described in both genera involves the use of heme as a source of iron, by a mechanism very well conserved among all species, which involves a heme transporter that includes a specific TonB-dependent outer membrane receptor(s) and an ABC-type inner membrane transporter. Alternative systems based on ferrous or ferric iron transporters have been reported in V. cholerae. How the different iron acquisition systems work together to supply iron to the cell and how they are used in the different environments where vibrios and aeromonads can be found is still an open question.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: Aeromonas, Exogenous heme, Heme biosynthesis pathway, Heme degradation, Heme efflux, Heme uptake, Iron acquisition strategies, Iron deficiency, Iron extraction, Iron uptake in Vibrio, vibrio
Iron in Erwinia
The critical role of iron in host-pathogen relationships has been elucidated in infectious diseases of mammals, where the importance of siderophores in microbial pathogenesis has been demonstrated. Our group has established the role of iron and its ligands in the virulence of the plant pathogenic bacteria Dickeya dadantii (Erwinia chrysanthemi) and Erwinia amylovora. The genomes of the two pectinolytic enterobacterial species Pectobacterium atrosepticum SCRI1043 and D. dadantii 3937 have been sequenced and annotated. This review focuses on the functions involved in iron acquisition in both species. Besides the production and utilization of siderophores, P. atrosepticum and D. datantii have the capacity to use other iron sources. Indeed, both species are able to use haem iron, whereas only P. atrosepticum can transport the ferric citrate complex and only D. dadantii can acquire ferrous iron. These different modes of iron capture indicate that these species have to cope with various environmental and ecological conditions during their pathogenic life cycle.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: Erwinia, Iron capture, Iron transport systems, Iron uptake in Erwinia, Iron uptake systems, Iron-homeostasis, Iron-metabolism, Iron-uptake
Iron Shigella and E. coli
Shigella spp. and pathogenic E. coli are characterized by a variety and abundance of iron transport systems. Although members of this group of bacteria are closely related genetically, they differ widely in the iron transport systems they use. This may reflect the different niches occupied by different strains and the nature of the source of iron available in a specific environment. Only the ferrous iron transporter Feo is common to all the commensals and pathogens. All members of this group produce one or more siderophore, but no single siderophore is produced by all. Other iron transport systems include heme transporters and the ferrous iron transporters Sit and Efe. With the exception of the genes for enterobactin and the Feo system, the iron transport genes in the enterics are found within pathogenicity islands or on plasmids and their presence often increases pathogenicity or colonization of niches within the host.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: E. coli, Iron transport systems, Iron-homeostasis, Iron-metabolism, Iron-uptake, Shigella
Iron in Bordetella
Upon colonization of the mammalian respiratory epithelium by mucosal pathogens of the genus Bordetella, the host-pathogen interaction causes inflammatory changes, immune activation, and host cell injury. In this dynamic environment, Bordetella cells scavenge the nutritional iron necessary for growth. The three classical Bordetella species produce the siderophore alcaligin. In addition, they can utilize xenosiderophores that could be produced by commensals or other microbes that transiently inhabit the nasopharynx.
As infection progresses, extravasation of immune cells, erythrocytes and serum to the mucosal surface can occur, exacerbated by the damaging action of Bordetella toxins, thus providing iron sources such as transferrin and heme compounds to the microbe. The three characterized Bordetella iron systems for utilization of alcaligin, enterobactin and heme are each inducible by the cognate iron source. The ability to sense and respond to the presence of available iron sources allows these pathogens to adapt to temporal changes in iron source availability, and this ability is important for successful in vivo growth.
Further reading: Iron Uptake and Homeostasis in Microorganisms
As infection progresses, extravasation of immune cells, erythrocytes and serum to the mucosal surface can occur, exacerbated by the damaging action of Bordetella toxins, thus providing iron sources such as transferrin and heme compounds to the microbe. The three characterized Bordetella iron systems for utilization of alcaligin, enterobactin and heme are each inducible by the cognate iron source. The ability to sense and respond to the presence of available iron sources allows these pathogens to adapt to temporal changes in iron source availability, and this ability is important for successful in vivo growth.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: Bordetella, Iron acquisition mechanisms, Iron deficiency, Iron extraction, Iron transporters, pertussis, Siderophore, Siderophores
Iron in the Rhizobia
The rhizobia live as free-living soil bacteria or in symbiosis with leguminous plants. The success of these organisms in each milieu involves the ability to sense the environment to assess the availability of nutrients, and to optimize cellular systems for their acquisition. Iron in the rhizosphere is mostly inaccessible due to low solubility, and microorganisms must compete for this limited nutrient. Rhizobia belong to the alpha-Proteobacteria, a diverse taxonomic group that includes numerous species that form close or intracellular associations with eukaryotic hosts in a symbiotic or pathogenic context.
Thus, in addition to their agricultural and economic importance, rhizobia are model organisms that have given new insights into related, but less tractable animal pathogens. In particular, genetic control of iron homeostasis in the rhizobia and other alpha-Proteobacteria has moved away from the Fur paradigm to an iron sensing mechanism responding to the metal indirectly. Moreover, utilization of heme as an iron source is not unique to animal pathogens, but is an acquisition strategy employed by the rhizobia with some interesting novel features.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Thus, in addition to their agricultural and economic importance, rhizobia are model organisms that have given new insights into related, but less tractable animal pathogens. In particular, genetic control of iron homeostasis in the rhizobia and other alpha-Proteobacteria has moved away from the Fur paradigm to an iron sensing mechanism responding to the metal indirectly. Moreover, utilization of heme as an iron source is not unique to animal pathogens, but is an acquisition strategy employed by the rhizobia with some interesting novel features.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: Iron transporters, Iron uptake in Rhizobia, Iron uptake systems, Iron-homeostasis, Iron-metabolism, Iron-uptake, Proteobacteria, Rhizobia, Rhizobium
Heme Uptake and Iron Extraction by Bacteria
Heme is ubiquitous, abundant and necessary for energy metabolism. Most bacteria have a heme biosynthesis pathway, but nevertheless, since heme is a major source of iron (an essential metal), microbes take up exogenous heme to retrieve iron. To grab heme, microbes extract it from host hemoproteins. This is achieved by two non-exclusive distinct pathways. One pathway involves proteins secreted by bacteria (hemophores) that scavenge heme from host hemoproteins. The second pathway involves microbial cell surface receptors that catch hemoproteins circulating in the vicinity of the cell surface. Both pathways lead to heme docking to cell surface receptors. In Gram-negative bacteria, docked heme is transported through the outer membrane by an energy-dependent process. In Gram-positive bacteria, docked heme is transferred to membrane-anchored heme binding lipoproteins. In all thus far described systems, heme is actively transported through the plasma membrane by an ATP hydrolysis-powered ABC transporter. Heme is either degraded into biliverdin, CO and iron by heme oxygenases, or iron is retrieved from heme, keeping the tetrapyrrol ring intact by recently identified enzymes. As excess heme is toxic, heme uptake, efflux and degradation are usually highly regulated. In most cases, intracytoplasmic heme or iron released during heme degradation are cofactors along with transcriptional regulators. In several cases, heme uptake and efflux are regulated by extracellular heme.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: Exogenous heme, Haeme, Heme, Heme biosynthesis pathway, Heme degradation, Heme efflux, Heme uptake
Iron Uptake and Homeostasis in Microorganisms
Iron is essential for almost all living organisms as it is involved in a wide variety of important metabolic processes. However, iron is not readily available and microorganisms therefore employ various iron uptake systems to secure sufficient supplies from their surroundings. There is considerable variation in the range of iron transporters and iron sources utilised by different microbial species. Pathogens, in particular, require efficient iron acquisition mechanisms to enable them to compete successfully for iron in the highly iron-restricted environment of the host's tissues and body fluids.
Further reading: Iron Uptake and Homeostasis in Microorganisms
Further reading: Iron Uptake and Homeostasis in Microorganisms
Labels: Iron acquisition mechanisms, Iron transporters, Iron uptake systems, Iron-homeostasis, Iron-metabolism, Iron-uptake
9th European Nitrogen Fixation Conference
September 6 - 10, 2010 9th European Nitrogen Fixation Conference
Geneva, Switzerland Further information
Topics include: Applied aspects of biological nitrogen fixation; Evolution and diversity of diazotrophs and hosts; Genomics and post-genomics of diazotrophs and hosts; Interactions of proteobacteria with legumes; Interactions of diazotrophs with non-legume hosts; Novel tools and technologies to study diazotrophy; Physiology of free-living and symbiotic diazotrophs; Regulation of nitrogen fixation; Structure and function of nitrogenase.
Suggested reading: Microbiology Books
Geneva, Switzerland Further information
Topics include: Applied aspects of biological nitrogen fixation; Evolution and diversity of diazotrophs and hosts; Genomics and post-genomics of diazotrophs and hosts; Interactions of proteobacteria with legumes; Interactions of diazotrophs with non-legume hosts; Novel tools and technologies to study diazotrophy; Physiology of free-living and symbiotic diazotrophs; Regulation of nitrogen fixation; Structure and function of nitrogenase.
Suggested reading: Microbiology Books
Labels: Nitrogen Fixation, Nitrogen Fixation Conference
14th Workshop of the International Study Group for Systems Biology 2010
September 6 - 10, 2010 14th Workshop of the International Study Group for Systems Biology 2010
Vladimir, RussiaFurther information
The International Study Group for Systems Biology is a collective of international researchers interested in advancing the biological sciences through exploring the interplay between theory and experiment. The general theme is theoretical approaches to understanding the behaviour of cell systems, particularly transport, metabolism and signal transduction.
Suggested reading: Molecular Biology Books
Vladimir, Russia
The International Study Group for Systems Biology is a collective of international researchers interested in advancing the biological sciences through exploring the interplay between theory and experiment. The general theme is theoretical approaches to understanding the behaviour of cell systems, particularly transport, metabolism and signal transduction.
Suggested reading: Molecular Biology Books
Labels: Systems Biology, Systems Biology 2010, Workshops
Advances in Plant Virology Conference
September 5 - 7, 2010 Advances in Plant Virology
Wageningen, The Netherlands Further information
A conference organized by Association of Applied Biologists and the Dutch Society of Plant Virologists.
Suggested reading: Virology Books
Wageningen, The Netherlands Further information
A conference organized by Association of Applied Biologists and the Dutch Society of Plant Virologists.
Suggested reading: Virology Books
Labels: Plant Virology
IMC9 The Biology of Fungi Conference
August 1 - 6, 2010 IMC9 The Biology of Fungi
Edinburgh, UK Further information
9th International Mycological Congress hosted by the British Mycological Society
Suggested reading: Mycology Books
Edinburgh, UK Further information
9th International Mycological Congress hosted by the British Mycological Society
Suggested reading: Mycology Books
Labels: Fungal Conference, Mycology Conference
46th Annual Meeting of British Society for Medical Mycology
April 18 - 20, 2010 46th Annual Meeting of British Society for Medical Mycology (BSMM)
Exeter, UK Further information
The meeting generally attracts 80-120 delegates and covers topics from many areas of Medical Mycology. A range of international experts are contributing to this year‚s meeting, including a Special Retirement lecture from Professor Frank Odds (Aberdeen University) and the President's lecture from Professor Joe Heitman (Duke University).
Suggested reading: Mycology Books
Exeter, UK Further information
The meeting generally attracts 80-120 delegates and covers topics from many areas of Medical Mycology. A range of international experts are contributing to this year‚s meeting, including a Special Retirement lecture from Professor Frank Odds (Aberdeen University) and the President's lecture from Professor Joe Heitman (Duke University).
Suggested reading: Mycology Books
Labels: Fungal Conference, Mycology Conference
Rabbit Hemorrhagic Disease Virus and Other Lagoviruses
Rabbit hemorrhagic disease virus (RHDV) is a pathogen of rabbits that causes major problems throughout the world where rabbits are reared for food and clothing, make a significant contribution to ecosystem ecology, and where they support valued wildlife as a food source. The high mortality caused by RHDV has driven research in protecting rabbits from infection. However, RHDV is an unusual calicivirus in that it has served also as an important model in the family Caliciviridae by providing a range of beneficial outcomes as diverse as the creation of virus-like particles (VLPs) for vaccine and therapeutics delivery, the elucidation of calicivirus replication and structural features at the molecular level, and the biological control of a vertebrate pest.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Caliciviridae, Lagoviruses, Rabbit viruses, RHDV, Virus-like particles, VLPs
Murine Norovirus Translation, Replication and Reverse Genetics
Murine norovirus, currently the only norovirus that replicates efficiently in tissue culture, has offered scientists the first chance to study the entire norovirus life cycle in the laboratory. In addition, the development of reverse genetics for murine norovirus has provided the ideal opportunity for researchers to determine how variation at the genetic level affects pathogenicity in the natural host. Despite differences in the diseases caused by human and murine noroviruses, they possess a significant amount of genetic similarity; hence the general mechanisms of viral genome translation and replication are likely to be highly conserved.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Caliciviridae, Caliciviruses, Norovirus
Murine Norovirus Pathogenesis and Immunity
The first murine norovirus, murine norovirus 1 (MNV-1), was discovered in 2003. Since then, numerous murine norovirus strains have been identified and they were assigned a new genogroup in the genus Norovirus. Murine noroviruses share pathogenic properties with human noroviruses. Specifically, they are infectious orally, they spread between mice, and at least one strain, MNV-1, causes mild diarrhea in wild-type hosts. Furthermore, primary MNV-1 infection fails to elicit protection from a secondary challenge with homologous virus in at least some situations, which is similar to the lack of long-term protective immunity elicited by primary human norovirus infection. Investigators have now begun to extend basic knowledge of norovirus infection and immunity using this system. In particular, studies of murine norovirus infection have provided valuable information regarding the critical nature of innate immunity in controlling infection. Mice deficient in components of the interferon signaling pathway are highly susceptible to MNV-1-induced gastroenteritis, systemic infection, and ultimately death. The precise mechanisms by which interferon protects from serious murine norovirus infection are beginning to be elucidated and will provide potential antiviral targets for combating human norovirus infections. In addition, murine norovirus infection of mice provides a useful model with which to define conditions to elicit protective immunity, potentially providing important information for human norovirus vaccine design. For example, repeated exposure to high doses of MNV-1 may provide protection from mucosal re-infection.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: MNV, MNV-1, Murine Norovirus, Norovirus, Noroviruses
Caliciviruses in Swine
Viruses in three of the four established genera of the family Caliciviridae have been detected in pigs (Sapovirus, Norovirus and Vesivirus), making this animal species of particular interest in the study of calicivirus pathogenesis and host range. The Cowden strain of porcine enteric calicivirus (PEC), a sapovirus, was discovered in a diarrheic pig fecal sample in the US in 1980. Since then, sapoviruses have become recognized as a predominant calicivirus detected in pigs. The Cowden PEC strain grows efficiently in a unique cell culture system, and a reverse genetics system has been developed for elucidation of the mechanisms of replication and pathogenesis at the molecular level. Porcine noroviruses share genetic relatedness with those from humans, and recent studies have shown that pigs are susceptible to infection and mild diarrheal disease when experimentally challenged with related human norovirus strains. Research on porcine caliciviruses has yielded new insights into the mechanisms of pathogenesis, replication, and evolution of the family Caliciviridae.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Norovirus, Pig Caliciviruses, Sapovirus, Swine calicivirus, Vesivirus
Feline Calicivirus
Feline calicivirus (FCV) represents an important pathogen of cats that has been studied extensively on the molecular level. FCV was the first calicivirus for which milestones like a reverse genetics system or the identification of a verified virus receptor were reached. Recently, great efforts were made to investigate unusual mechanisms of translation initiation driven by the RNA bound protein VPg or an RNA structure named TURBS.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Calicivirus, FCV
Calicivirus Reverse genetics and Replicon Systems
Recently, reverse genetics and replicon systems have been developed and are starting to be used in the elucidation of the calicivirus replication and pathogenicity. Reverse genetics systems are available for feline calicivirus, porcine enteric calicivirus, murine norovirus, rabbit hemorrhagic disease virus and a rhesus monkey calicivirus. For uncultivable caliciviruses, such as human norovirus, cell-based replicon systems have been established. Norovirus replicon systems are used to screen potential antivirals and therapeutic options against norovirus infection. Replicon systems with reporter genes such as those encoding green fluorescent protein or luciferase allows quantitative analysis of cellular and viral factors that promote virus replication. Further studies with reverse genetics and replicon system could yield important information for cell culture adaptation of human noroviruses which is crucial for development of efficient vaccines and antivirals.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Caliciviridae, Lagovirus, Norovirus, Sapovirus, Vesivirus
Virus-Host Interaction and Cellular Receptors of Caliciviruses
Caliciviruses are a diverse virus family with a wide range of host and tissue tropisms. Most calicivirus genera recognize a carbohydrate ligand for attachment, including the A, B, H and Lewis histo-blood group antigens (HBGAs) and heparan sulfate for the human noroviruses, the H type 2 antigen for the rabbit hemorrhagic disease virus (genus Lagovirus), the type B antigen for the Tulane virus (a potential new genus), and sialic acid for feline calicivirus (FCV; genus Vesivirus) and murine norovirus (MNV; genus Norovirus). Following attachment, FCV recognizes also a cell surface protein, the junctional adhesion molecule 1 (JAM-1), as a functional receptor or co-receptor potentially for penetration or entry into host cells. Some human noroviruses interact also with a 105 kDa membrane protein, but its role in viral penetration/entry into host cells remains unknown. The genetic and structural analyses of selected strains of norovirus and FCV have generated new insights into virus-host interactions that chart the course for innovative research in the development of effective strategies to control and prevent calicivirus infection and illness.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Caliciviridae, Caliciviruses, Norovirus
Calicivirus Protein Structures
Sequence analysis and experimentally determined three-dimensional structures of structural and nonstructural proteins from a range of caliciviruses help to provide a molecular framework for understanding many aspects of their replication strategies. Structures of intact virions, virus-like particles and capsid fragments, as well as capsid-receptor complexes help to explain basic mechanisms of capsid assembly and receptor recognition. Structural studies of the recombinant viral proteinase and polymerase in complex with substrates and inhibitors provide a basis for understanding substrate recognition and enzymatic mechanisms, thus setting the stage for the design of new antiviral compounds.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Caliciviridae, Calicivirus, Caliciviruses, Lagovirus, Norovirus, Sapovirus, Vesivirus
Proteolytic Cleavage and Viral Proteins
Caliciviruses are icosahedral nonenveloped viruses with a positive-sense single strand RNA genome that does not exceed 8.6 kb. Despite its small size, the virus genome encodes a number of nonstructural proteins that successfully facilitate and regulate mechanisms required for efficient virus amplification. Although caliciviruses show significant genetic diversity, they share a common protein expression strategy. Recent findings have shown that the nonstructural proteins of caliciviruses are produced by autocatalytic cleavage of a polyprotein encoded by ORF1 of the virus genome. A single virus protease structurally similar to a class of viral chymotrypsin-like cysteine proteases mediates these cleavages, and in some caliciviruses, adds to a release of the virus capsid protein. The temporal regulation of viral protein synthesis relies on the specificity of the protease and may be modulated by additional viral and cellular factors. The proteolytic processing results not only in the synthesis of the mature virus proteins, but also their precursors, whose functions have yet to be determined. Almost all calicivirus proteins have been identified as components of the virus replication complexes; however, their roles in replication are not entirely understood and remain an active and crucial target of calicivirus research.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Caliciviridae, Calicivirus, Caliciviruses, Lagovirus, Norovirus, Sapovirus, Vesivirus
Genome Organization and Recombination
Recombination was first described in the human caliciviruses in 1997. Since then naturally occurring recombinants have been detected for all four genera of the Caliciviridae and has become an important mechanism in the emergence of new calicivirus variants. Due to similarities in genome organization between the different genera, recombination predomoninantly occurs at the start of the major structural gene which encodes the capsid, VP1. Knowledge of the mechanisms of calicivirus recombination is important as new variants can emerge, with potentially different pathogenesis and virulence.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Caliciviridae, Calicivirus, Caliciviruses, Lagovirus, Norovirus, Sapovirus, Vesivirus
Calicivirus Environmental Contamination
The virus family Caliciviridae contains four genera Norovirus, Sapovirus, Lagovirus and Vesivirus. Norovirus and sapovirus cause gastroenteritis in humans, while lagoviruses and vesiviruses mostly infect animals and cause a variety of diseases. Norovirus and sapoviruses can also infect a number of animals including cow and pig, respectively. Noroviruses are the dominant cause of human gastroenteritis around the world, infecting all age groups. Their low infectious dose and stability in the natural environment allows noroviruses to be easily spread. Contamination in food and water destined for human consumption has lead to numerous outbreaks of gastroenteritis. Noroviruses have been detected in shellfish, sandwiches, fruit, ice, drinking water and treated wastewater. Direct transmission from food and water to humans is well documented. Increased monitoring and improvements in detection methods may help to reduce the number of infections but regulations and standards need to be addressed in order to reduce viral contamination in the natural environment.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Caliciviridae, Calicivirus, Caliciviruses, Lagovirus, Norovirus, Sapovirus, Vesivirus
Norovirus Epidemiology
Noroviruses are the dominant cause of outbreaks as well as sporadic community cases of viral gastroenteritis in the world. Their very low infectious dose, combined with high levels of shedding and long persistence in the environment make noroviruses extremely infectious. Although generally norovirus related illness is regarded as mild and self-limiting, more severe outcomes are increasingly described among elderly and immuno-compromised patients. The combination of large and difficult to control outbreaks and severe illness in some patients leads to major problems in healthcare settings, such as hospitals and nursing homes. Additionally, some large and diffuse, multi-national and even multi-continent, foodborne-outbreaks have been described for norovirus, affecting up to thousands of people. With structured outbreak surveillance running in a number of regions across the world for the past ten years, it has become clear that the spread of noroviruses is global, although important information from developing countries is missing. At present, norovirus strains belonging to genogroup II genotype 4 (GII.4) are dominant worldwide. In the last ten years, at least three global pandemics involving GII.4 strains of different genetic variants occurred. Although a straightforward culturing method remains lacking for noroviruses, important progress has been made in immunological studies using virus-like particles. Thus it has been shown that the subsequent genetic variants of GII.4 are antigenically distinct, and that the GII.4 noroviruses evolved and continue to do so by a process known as epochal evolution, in which periods of genetic stasis are interrupted by rapid accumulation of mutations and the subsequent emergence of novel genetic variants. In norovirus evolution, this process is directed by population or herd immunity.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Caliciviridae, Calicivirus, Caliciviruses, Lagovirus, Norovirus, Sapovirus, Vesivirus
Caliciviruses
Members of the Caliciviridae family (caliciviruses) are positive-sense, single stranded RNA viruses containing four recognized genera: Norovirus, Sapovirus, Lagovirus and Vesivirus. They are ubiquitous in the environment and are a major cause of disease in humans and many animals. Examples include Norwalk virus, a norovirus, thought to be responsible for roughly 90% of epidemic, non-bacterial outbreaks of gastroenteritis in humans around the world. Lack of a suitable cell culture system for human caliciviruses limited studies in previous decades, however the recent application of modern genomic technologies has revolutionized the field, leading to an explosion in calicivirus publications.
Further reading: Caliciviruses: Molecular and Cellular Virology
Further reading: Caliciviruses: Molecular and Cellular Virology
Labels: Caliciviridae, Calicivirus, Caliciviruses, Lagovirus, Norovirus, Sapovirus, Vesivirus
Mononuclear phagocytes and virus infection
By Howard E. Gendelman (University of Nebraska Medical Centre, USA) writing in Lentiviruses and Macrophages: Molecular and Cellular Interactions
For chronic lentiviral infections mononuclear phagocytes remain an enigma. On the one hand they are among the first cells contacted by virus and, despite a virtual armada of immunological tools, still serve as means to both spread and contain infection. Virus particles can simultaneously assemble and hide in intracellular compartments, largely free from immune attack. Interestingly, the mononuclear phagocytes are not destroyed by the virus and throughout infection they still contribute to host immunity while at the same time perpetuating lentiviral dissemination. Infected mononuclear phagocytes are readily observed in lymph nodes and organs such as the lung and brain, where they produce cytotoxic mediators that contribute to the development of disease.
For human immunodeficiency virus (HIV) infection functional impairment of infected mononuclear phagocytes likely accelerates immune deficiency. Thus, the questions most asked are how can a cell that possesses so many intrinsic defence mechanisms harbour such viral pathogens for prolonged time periods? How can mononuclear phagocytes serve both as sentries and vehicles for disseminating infection and inducing disease? Indeed, in regards to biology, for both ontogeny and phylogeny, mononuclear phagocytes are the most primitive sensors of tissue injury and as such serve to clear debris and simultaneously protect the host's homeostatic environment. Their roles serve the host in non-specific defence (innate immunity) and in initiating cell-specific protection (adaptive immunity).
A consistent evolutionary role resides in the ability of mononuclear phagocytes to engulf, digest and destroy cell and tissue debris through phagolysosomal fusion. Interestingly, mononuclear phagocytes can affect neighbouring lymphocytes and other immunocytes to perform similar functions, albeit by divergent mechanisms. Control of viral growth occurs together with the mononuclear phagocyte's notable possession of a vast repertoire of immune secretory factors that include pro-inflammatory cytokines, chemokines, arachidonic acid and its metabolites, platelet activating factor, nitric oxide, quinolinic acid, amongst others. These serve to regulate immune defence, cell mobility, antigen presentation, immune activation, and cell differentiation. During disease such secretions are induced by infection and affect inflammatory processes that speed cell and tissue injury leading to clinical symptoms and morbidities. This, in the case of common lentiviral tissue injuries, leads to substantive lung, brain, blood, and joint diseases.
Clearly, the role played by mononuclear phagocytes in the pathogenesis of lentiviral infections is seemingly complex and quite multifaceted. Viral spread from mononuclear phagocytes to mononuclear phagocytes and from mononuclear phagocytes to T cells and across cell and tissue barriers is equally vast and complicated. Historically, how this primary mover for innate immunity serves as a source for restricted and productive lentiviral replication seems almost illogical.
First, with an armada of microbial clearance activities that include phagocytosis, intracellular killing, secretion of bioactive antiviral factors such as interferons and biodegradable enzymes, it is of great interest that lentiviruses can enter these cells and replicate over prolonged time periods measured in months or even years. How virus evades innate immune responses, nevertheless, remains poorly understood, even following nearly 30 years of study.
Second is the feature of transcriptional control for viral persistence. A host of factors control the viral life cycle and are regulated through the mononuclear phagocytes external environment which allows virus to continue to replicate in the face of often robust humoral and cellular immune responses and more recently during potent antiretroviral therapies for HIV. In this scenario, virus buds into endocytic compartments with limited cell surface expression of viral proteins and in this context parallels the ancient Trojan horse mythology of being protected inside a sheath of secrecy. It was such a stratagem that Odysseus employed which allowed the Greeks to enter the city of Troy and end a conflict which had lasted 10 years. The Greeks built a huge wooden figure of a horse and left it as a parting gift for Athena as they pretended to sail away from Troy. The jubilant Trojans pulled the wheeled horse into the city unaware of the armed Greek soldiers hiding in the Trojan horse's belly. The Greek soldiers poured out of a trap door in the horse's belly and quickly killed the Trojans, setting fire to the city and thereby winning the war. For lentiviruses, it is analogous to their strategy of entering the brain and overcoming the restrictions imposed by a seemingly impermeable blood-brain barrier through the establishment of a chemokine gradient. Certainly, lentiviruses use mononuclear phagocytes as a ploy to enter the host and evade immune surveillance thereby escaping detection in a similar manner to the Greek soldiers in the Trojan Horse.
Third, there is a curious balance of host defence and dissemination of viral infection. Dendritic cells and tissue macrophages are readily infected in body fluids and are the likely cellular source of viral spread both from animal to animal or person to person through seminal and blood macrophages and/or monocytes and dendritic cells and carriage of virus throughout the body.
Fourth are the severe and lasting functional consequences of viral infection and immune activation as it occurs during disease. This is typified by secretion of inflammatory toxins manufactured and released by mononuclear phagocytes that cause tissue injuries commonly in the lung, the joints, and the central nervous system. The latter perhaps has received the most intense study in regards to relationships between mononuclear phagocytes function, neuroinflammation, and neurodegeneration. The field spawned biomarker discovery in proteomics and metabolomics and adjunctive therapeutic developments aimed at better understanding and combating disordered mononuclear phagocytes function during lentiviral disease.
Fifth, intra- and inter-cellular mononuclear phagocytes mechanisms govern the viral life cycle. How lentiviruses hijack subcellular organelles and the cytoskeletal machinery to complete their life cycle is a fascinating area for research activities. Added to such complexities are the relationships between innate and adaptive immunity including spread of virus. Even more importantly, perhaps, is how regulatory and effector T cells amongst other cells that come in contact with macrophages affect macrophage function in disease and either exacerbate or control the tempo of disease.
By Howard E. Gendelman (University of Nebraska Medical Centre, USA) writing in Lentiviruses and Macrophages: Molecular and Cellular Interactions
For chronic lentiviral infections mononuclear phagocytes remain an enigma. On the one hand they are among the first cells contacted by virus and, despite a virtual armada of immunological tools, still serve as means to both spread and contain infection. Virus particles can simultaneously assemble and hide in intracellular compartments, largely free from immune attack. Interestingly, the mononuclear phagocytes are not destroyed by the virus and throughout infection they still contribute to host immunity while at the same time perpetuating lentiviral dissemination. Infected mononuclear phagocytes are readily observed in lymph nodes and organs such as the lung and brain, where they produce cytotoxic mediators that contribute to the development of disease.
For human immunodeficiency virus (HIV) infection functional impairment of infected mononuclear phagocytes likely accelerates immune deficiency. Thus, the questions most asked are how can a cell that possesses so many intrinsic defence mechanisms harbour such viral pathogens for prolonged time periods? How can mononuclear phagocytes serve both as sentries and vehicles for disseminating infection and inducing disease? Indeed, in regards to biology, for both ontogeny and phylogeny, mononuclear phagocytes are the most primitive sensors of tissue injury and as such serve to clear debris and simultaneously protect the host's homeostatic environment. Their roles serve the host in non-specific defence (innate immunity) and in initiating cell-specific protection (adaptive immunity).
A consistent evolutionary role resides in the ability of mononuclear phagocytes to engulf, digest and destroy cell and tissue debris through phagolysosomal fusion. Interestingly, mononuclear phagocytes can affect neighbouring lymphocytes and other immunocytes to perform similar functions, albeit by divergent mechanisms. Control of viral growth occurs together with the mononuclear phagocyte's notable possession of a vast repertoire of immune secretory factors that include pro-inflammatory cytokines, chemokines, arachidonic acid and its metabolites, platelet activating factor, nitric oxide, quinolinic acid, amongst others. These serve to regulate immune defence, cell mobility, antigen presentation, immune activation, and cell differentiation. During disease such secretions are induced by infection and affect inflammatory processes that speed cell and tissue injury leading to clinical symptoms and morbidities. This, in the case of common lentiviral tissue injuries, leads to substantive lung, brain, blood, and joint diseases.
Clearly, the role played by mononuclear phagocytes in the pathogenesis of lentiviral infections is seemingly complex and quite multifaceted. Viral spread from mononuclear phagocytes to mononuclear phagocytes and from mononuclear phagocytes to T cells and across cell and tissue barriers is equally vast and complicated. Historically, how this primary mover for innate immunity serves as a source for restricted and productive lentiviral replication seems almost illogical.
First, with an armada of microbial clearance activities that include phagocytosis, intracellular killing, secretion of bioactive antiviral factors such as interferons and biodegradable enzymes, it is of great interest that lentiviruses can enter these cells and replicate over prolonged time periods measured in months or even years. How virus evades innate immune responses, nevertheless, remains poorly understood, even following nearly 30 years of study.
Second is the feature of transcriptional control for viral persistence. A host of factors control the viral life cycle and are regulated through the mononuclear phagocytes external environment which allows virus to continue to replicate in the face of often robust humoral and cellular immune responses and more recently during potent antiretroviral therapies for HIV. In this scenario, virus buds into endocytic compartments with limited cell surface expression of viral proteins and in this context parallels the ancient Trojan horse mythology of being protected inside a sheath of secrecy. It was such a stratagem that Odysseus employed which allowed the Greeks to enter the city of Troy and end a conflict which had lasted 10 years. The Greeks built a huge wooden figure of a horse and left it as a parting gift for Athena as they pretended to sail away from Troy. The jubilant Trojans pulled the wheeled horse into the city unaware of the armed Greek soldiers hiding in the Trojan horse's belly. The Greek soldiers poured out of a trap door in the horse's belly and quickly killed the Trojans, setting fire to the city and thereby winning the war. For lentiviruses, it is analogous to their strategy of entering the brain and overcoming the restrictions imposed by a seemingly impermeable blood-brain barrier through the establishment of a chemokine gradient. Certainly, lentiviruses use mononuclear phagocytes as a ploy to enter the host and evade immune surveillance thereby escaping detection in a similar manner to the Greek soldiers in the Trojan Horse.
Third, there is a curious balance of host defence and dissemination of viral infection. Dendritic cells and tissue macrophages are readily infected in body fluids and are the likely cellular source of viral spread both from animal to animal or person to person through seminal and blood macrophages and/or monocytes and dendritic cells and carriage of virus throughout the body.
Fourth are the severe and lasting functional consequences of viral infection and immune activation as it occurs during disease. This is typified by secretion of inflammatory toxins manufactured and released by mononuclear phagocytes that cause tissue injuries commonly in the lung, the joints, and the central nervous system. The latter perhaps has received the most intense study in regards to relationships between mononuclear phagocytes function, neuroinflammation, and neurodegeneration. The field spawned biomarker discovery in proteomics and metabolomics and adjunctive therapeutic developments aimed at better understanding and combating disordered mononuclear phagocytes function during lentiviral disease.
Fifth, intra- and inter-cellular mononuclear phagocytes mechanisms govern the viral life cycle. How lentiviruses hijack subcellular organelles and the cytoskeletal machinery to complete their life cycle is a fascinating area for research activities. Added to such complexities are the relationships between innate and adaptive immunity including spread of virus. Even more importantly, perhaps, is how regulatory and effector T cells amongst other cells that come in contact with macrophages affect macrophage function in disease and either exacerbate or control the tempo of disease.
By Howard E. Gendelman (University of Nebraska Medical Centre, USA) writing in Lentiviruses and Macrophages: Molecular and Cellular Interactions
Labels: HIV infection, Howard E Gendelman, Human immunodeficiency virus, lentivirus, lentiviruses, Mononuclear phagocytes
Acclaim for new Aspergillus book
"an overview of the forefront of Aspergillus genomics - from bioinformatics and systems biology to gene regulation, secondary metabolism, and novel industrial applications ... (the book starts) with a superb holistic overview of the genus by its doyenne Joan Bennett ... a most stimulating volume ... The editors and publishers can be proud of having put together a volume that is produced to the highest scientific standards."
from David L. Hawksworth in Mycological Research 113: 1444-1445
Further reading: Aspergillus: Molecular Biology and Genomics
from David L. Hawksworth in Mycological Research 113: 1444-1445
Further reading: Aspergillus: Molecular Biology and Genomics
Labels: aspergillus, Aspergillus genomics, Aspergillus industrial applications
Industrial Applications of Aspergillus
"This feast of hugely topical science culminates with an overview of novel industrial applications of Aspergillus oryzaee genomics (Abe et. al., Chapter 10), inciting much enthusiasm for potential applications or exploitations of similar methodologies in other Aspergillus species. Not only does this conclude the suite of species examined with our recognised industrial work horse for heterologous enzyme production, it also presents the opportunity to consider the application of Aspergillus species to biodegradation of plastics and how cell sensing and signalling mechanisms are integral to maximising success in all of the applications under consideration; cue a trans-genus comparison of signal reception and transduction and its relevance to drug screening."
from Dr Elaine Bignell (Imperial College London) in Biotechnology March 2010
Further reading: Aspergillus: Molecular Biology and Genomics
from Dr Elaine Bignell (Imperial College London) in Biotechnology March 2010
Further reading: Aspergillus: Molecular Biology and Genomics
Labels: aspergillus, Aspergillus-Biotechnology, Biodegradation-of-plastics, book review, Book Reviews, fungi, Industrial-Applications-of-Aspergillus, mycology
Aspergillus book review
"...(a) feast of hugely topical science ... This book presents a modern-day dictionary of all things Aspergillus. It is highly readable and has been considerately crafted in terms of structure. From the very first chapter a sense of excitement about the new opportunities afforded by this fascinating genus is derived, which extends far beyond the interests of any single researcher but succeeds in capturing the relevance of genus-based findings for all who work with aspergilli. The essence of functional genomics and systems biology therefore permeates the volume, and ultimately the readers psyche. Not only does it provide a concise and highly current overview of Aspergillus genomics, it also manages to archive decades of relevant and highly insightful biology in a portable format. The book is a must-read for anyone whose work or study involves any member(s) of the Aspergillus genus. I, certainly, will be consulting it daily for a long time to come."
from Dr Elaine Bignell (Imperial College London) in Biotechnology March 2010
Further reading: Aspergillus: Molecular Biology and Genomics
from Dr Elaine Bignell (Imperial College London) in Biotechnology March 2010
Further reading: Aspergillus: Molecular Biology and Genomics
Labels: aspergillus, Aspergillus-Biotechnology, book review, Book Reviews, fungi, Industrial-Applications-of-Aspergillus, mycology
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