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HB-107, a nonbacteriostatic fragment of the antimicrobial peptide cecropin B, accelerates murine wound repair.

Antimicrobial peptides are essential to innate host defense as effectors of pathogen clearance and can modify host cell behaviors to promote wound repair. While these two functions appear interrelated, it is unclear whether the ability to aid in wound repair requires inherent antimicrobial function. We hypothesized that the influence of antimicrobial peptides on wound repair is not dependent on antimicrobial function. To explore this, we analyzed the microbial killing activity of peptide fragments and correlated this with the ability to influence wound repair in mice. HB-107, a peptide lacking antimicrobial activity and originally derived from the antimicrobial cecropin B, showed up to 64 percent improvement in wound repair compared to scrambled peptide and vehicle controls, an effect comparable to treatment with recombinant human platelet-derived growth factor-BB (formulated as Regranex). Wounds treated with HB-107 showed keratinocyte hyperplasia and increased leukocyte infiltration. Furthermore, HB-107 stimulated interleukin-8 secretion from cultured endothelial cells, an effect that may explain the increase in leukocyte migration. These findings confirm that antimicrobial peptides can function as effectors of cutaneous wound repair. Moreover, this study furthers our understanding of antimicrobial peptides by showing that their wound repair properties can be independent of antimicrobial function.

Animals↗

Microbial genomes--the untapped resource.

Although the 1990s have ushered in the genome, they have also exposed our limitations for deriving structural and functional information. In parallel, molecular phylogeny has demonstrated that the majority of microbial genomes are currently inaccessible. Key objectives for the next century are the development of techniques for accessing 'unculturable' genomes, exploiting their biotechnologically valuable genes and products, and linking genome-sequence data to molecular structure and function.

Eukaryota↗

Functional characterization of the putative Aspergillus nidulans poly(ADP-ribose) polymerase homolog PrpA.

Poly(ADP-ribose) polymerase (PARP) is a highly conserved enzyme involved in multiple aspects of animal and plant cell physiology. For example, PARP is thought to be intimately involved in the early signaling events that trigger the DNA damage response. However, the genetic dissection of PARP function has been hindered by the presence of multiple homologs in most animal and plant species. Here, we present the first functional characterization of a putative PARP homolog (PrpA) in a microbial system (Aspergillus nidulans). PrpA belongs to a group of PARP homologs that includes representatives from filamentous fungi and protists. The genetic analysis of prpA demonstrates that it is an essential gene whose role in the DNA damage response is sensitive to gene dosage. Notably, temporal patterns of prpA expression and PrpA-GFP nuclear localization suggest that PrpA acts early in the A. nidulans DNA damage response. Additional studies implicate PrpA in farnesol-induced cell death and in the initiation of asexual development. Collectively, our results provide a gateway for probing the diverse functions of PARP in a sophisticated microbial genetic system.

Aspergillus nidulans↗

Comparison of microbial populations in model and natural rumens using 16S ribosomal RNA-targeted probes.

A model rumen system, dual-flow continuous culture fermenters, was evaluated by two comparative criteria in two experiments using ribosomal (r)RNA-targeted DNA probes to compare key microbial groups in samples. The initial experiment measured temporal changes in population structure during adaptation of ruminal microbial populations in fermenters over 240 h. The fermenter inoculum contained 34.9% Bacteria, 60.1% Eukarya and 6.8% Archaea measured as a fraction of total small subunit (SSU) rRNA quantified using a universal probe. The cellulolytic bacterial genus Fibrobacter comprised 9.5% of total SSU rRNA in the inoculum. After 240 h of fermenter operation, the average abundance was 80.9% Bacteria, 6.1% Eukarya, 5.1% Archaea and Fibrobacter genus accounted for 6.6% of the total SSU rRNA. Divergence between ruminal and fermenter population structure was evaluated in the second experiment and samples were classified as ruminal, inoculum or fermenter (96, 120, 144 and 168 h of fermenter operation). Fermenter samples had higher relative abundances of Bacteria (84.5%) and Archaea (2.1%) and lower relative abundances of Eukarya (1.8%) than ruminal samples (average 48.0% Bacteria, 1.3% Archaea and 61.5% Eukarya). The relative abundance of Fibrobacter was similar in all samples, averaging 2.5%. The ruminal and fermenter samples had similar proportions of F. succinogenes and F. succinogenes subgroup 3 (as a percentage of Fibrobacter SSU rRNA). Fibrobacter succinogenes subgroup 1 and F. intestinalis proportions of Fibrobacter were lower in fermenter samples (8.2% and 0.7% respectively) than in ruminal samples (28.4% and 2.2% respectively). Fermenters were able to maintain a core prokaryotic community structure similar to the native microbial community in the rumen. Although protozoa populations were lost, maintenance of Fibrobacter and archaeal populations indicated that the model system supported a functional community structure similar to the rumen. This model rumen system may serve as a suitable tool for studying aspects of ruminal microbial ecology and may resolve some of the relationships between microbial community structure and function by providing control of experimental conditions.

Animals↗

Functions of antimicrobial peptides in host defense and immunity.

Antimicrobial peptides (AMPs) are effector molecules of the innate immune system. AMPs have a broad antimicrobial spectrum and lyse microbial cells by interaction with biomembranes. Besides their direct antimicrobial function, they have multiple roles as mediators of inflammation with impact on epithelial and inflammatory cells influencing diverse processes such as cytokine release, cell proliferation, angiogenesis, wound healing, chemotaxis, immune induction, and protease-antiprotease balance. Furthermore, AMPs qualify as prototypes of innovative drugs that may be used as antibiotics, anti-lipopolysaccharide drugs, or modifiers of inflammation. This review summarizes the current knowledge about the basic and applied biology of antimicrobial peptides and discusses features of AMPs in host defense and inflammation.

Amino Acid Sequence↗

Disorders of phagocyte function: biochemical aspects.

Intensive laboratory investigation of patients with recurrent infections, and with infections with microbial species not usually considered to be pathogenic, have led to the identification of several defects in granulocyte function. The two functions of granulocytes which have received most attention in the past decade have been locomotion (especially response to chemotactic stimulation) and microbicidal activity. Defective granulocyte chemotaxis has been demonstrated in patients with clinical manifestations suggesting abnormalities related to vasoactive amines, i.e., patients with eczema and extreme IgE hyperimmunoglobulinemia. The depressed granulocyte chemotactic responsiveness found in these patients can be reproduced in vitro when histamine and beta adrenergic agents are incubated with control granulocytes. Since these compounds have been shown to increase levels of intracellular cyclic AMP in other cells, there appears to be an association between cyclic nucleotide metabolism and regulation of granulocyte locomotion. Defective granulocyte microbicidal activity is found in patients with chronic granulomatous disease and it has been shown that there is little increase in oxidative metabolism during phagocytosis by these cells. Methods for quantitating the oxidative metabolism of granulocytes and monocytes include oxygen uptake, reduction of nitroblue tetrazolium, formate oxidation, and chemiluminescence response during phagocytosis. Since products of oxygen metabolism, i.e., hydrogen peroxide, superoxide or singlet oxygen do not accumulate in granulocyte phagocytic vacuoles, intracellular microbes are not killed (except bacterial species that produce hydrogen peroxide). The biochemical basis for defective oxidative metabolism in granulocytes from patients with chronic granulomatous disease appears to be associated with abnormal nucleotide oxidase activity.

Blood Bactericidal Activity↗

Structural and functional analysis of integrin alpha2I domain interaction with echovirus 1.

Integrins are cell surface receptors for several microbial pathogens including echovirus 1 (EV1), a picornavirus. Cryo-electron microscopy revealed that the functional domain (alpha(2)I) of human alpha(2)beta(1) integrin binds to a surface depression on the EV1 capsid. This three-dimensional structure of EV1 bound to alpha(2)I domain provides the first structural details of an integrin interacting with a picornavirus. The model indicates that alpha(2)beta(1) integrin cannot simultaneously bind both EV1 and the physiological ligand collagen. Compared with collagen binding to the alpha(2)I domain, the virus binds with a 10-fold higher affinity but in vitro uncoating of EV1 was not observed as a result of attachment of alpha(2)I. A molecular model, constructed on the basis of the EV1-integrin complex, shows that multiple alpha(2)beta(1) heterodimers can bind at adjacent sites around the virus 5-fold symmetry axes without steric hindrance. In agreement with this, virus attachment to alpha(2)beta(1) integrin on the cell surface was found to result in integrin clustering, which can give rise to signaling and facilitate the initiation of the viral entry process that takes place via caveolae-mediated endocytosis.

Capsid↗

Establishing the ELIXIR Microbiome Community.

Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and identifying solutions to the computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine microbiome studies, but are broadly applicable to other biomes. Thus, expanding this Marine Metagenomics Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broader range of biomes and link expertise across 'omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.

Computational Biology↗

Strain-specific ureolytic microbial calcium carbonate precipitation.

During a study of ureolytic microbial calcium carbonate (CaCO(3)) precipitation by bacterial isolates collected from different environmental samples, morphological differences were observed in the large CaCO(3) crystal aggregates precipitated within bacterial colonies grown on agar. Based on these differences, 12 isolates were selected for further study. We hypothesized that the striking differences in crystal morphology were the result of different microbial species or, alternatively, differences in the functional attributes of the isolates selected. Sequencing of 16S rRNA genes showed that all of the isolates were phylogenetically closely related to the Bacillus sphaericus group. Urease gene diversity among the isolates was examined by using a novel application of PCR-denaturing gradient gel electrophoresis (DGGE). This approach revealed significant differences between the isolates. Moreover, for several isolates, multiple bands appeared on the DGGE gels, suggesting the apparent presence of different urease genes in these isolates. The substrate affinities (K(m)) and maximum hydrolysis rates (V(max)) of crude enzyme extracts differed considerably for the different strains. For certain isolates, the urease activity increased up to 10-fold in the presence of 30 mM calcium, and apparently this contributed to the characteristic crystal formation by these isolates. We show that strain-specific calcification occurred during ureolytic microbial carbonate precipitation. The specificity was mainly due to differences in urease expression and the response to calcium.

Bacteria↗

Using DNA microarrays to study host-microbe interactions.

Complete genomic sequences of microbial pathogens and hosts offer sophisticated new strategies for studying host-pathogen interactions. DNA microarrays exploit primary sequence data to measure transcript levels and detect sequence polymorphisms, for every gene, simultaneously. The design and construction of a DNA microarray for any given microbial genome are straightforward. By monitoring microbial gene expression, one can predict the functions of uncharacterized genes, probe the physiologic adaptations made under various environmental conditions, identify virulence-associated genes, and test the effects of drugs. Similarly, by using host gene microarrays, one can explore host response at the level of gene expression and provide a molecular description of the events that follow infection. Host profiling might also identify gene expression signatures unique for each pathogen, thus providing a novel tool for diagnosis, prognosis, and clinical management of infectious disease.

Algorithms↗

Functional genomics databases on the web.

Experiments involving high-throughput methods for measuring transcripts, proteins and metabolites constitute the area of functional genomics. These experiments are highly context dependent and require much more detail about the experimental design, sample and protocols used than in genomics. Functional genomics databases are needed that follow established and emerging standards. Functional genomic databases are not yet very common; however, there are a few focused on microbial genomes and a couple integrative systems are available for setting up functional genomics databases.

Computational Biology↗

Polycystic kidney disease: an unrecognized emerging infectious disease?

Polycystic kidney disease (PKD) is one of the most common genetic diseases in humans. We contend that it may be an emerging infectious disease and/or microbial toxicosis in a vulnerable human subpopulation. Use of a differential activation protocol for the Limulus amebocyte lysate (LAL) assay showed bacterial endotoxin and fungal (1-->3)-beta-D-glucans in cyst fluids from human kidneys with PKD. Fatty acid analysis of cyst fluid confirmed the presence of 3-hydroxy fatty acids characteristic of endotoxin. Tissue and cyst fluid from three PKD patients were examined for fungal components. Serologic tests showed Fusarium, Aspergillus, and Candida antigens. IgE, but not IgG, reactive with Fusarium and Candida were also detected in cyst fluid. Fungal DNA was detected in kidney tissue and cyst fluid from these three PKD patients, but not in healthy human kidney tissue. We examine the intertwined nature of the actions of endotoxin and fungal components, sphingolipid biology in PKD, the structure of PKD gene products, infections, and integrity of gut function to establish a mechanistic hypothesis for microbial provocation of human cystic disease. Proof of this hypothesis will require identification of the microbes and microbial components involved and multifaceted studies of PKD cell biology.

Communicable Diseases↗

Sludge population optimisation: a new dimension for the control of biological wastewater treatment systems.

The activated sludge comprises a complex microbiological community. The structure (what types of microorganisms are present) and function (what can the organisms do and at what rates) of this community are determined by external physico-chemical features and by the influent to the sewage treatment plant. The external features we can manipulate but rarely the influent. Conventional control and operational strategies optimise activated sludge processes more as a chemical system than as a biological one. While optimising the process in a short time period, these strategies may deteriorate the long-term performance of the process due to their potentially adverse impact on the microbial properties. Through briefly reviewing the evidence available in the literature that plant design and operation affect both the structure and function of the microbial community in activated sludge, we propose to add sludge population optimisation as a new dimension to the control of biological wastewater treatment systems. We stress that optimising the microbial community structure and property should be an explicit aim for the design and operation of a treatment plant. The major limitations to sludge population optimisation revolve around inadequate microbiological data, specifically community structure, function and kinetic data. However, molecular microbiological methods that strive to provide that data are being developed rapidly. The combination of these methods with the conventional approaches for kinetic study is briefly discussed. The most pressing research questions pertaining to sludge population optimisation are outlined.

DNA, Bacterial↗

Immunoactive peptides, FK-156 and FK-565. III. Enhancement of host defense mechanisms against infection.

We investigated the effect of immunoactive peptides, FK-156 and FK-565 on host defense mechanisms against microbial invasion. It was shown that these drugs given to normal mice increased the counts of phagocytes in both peripheral blood and peritoneal cavity, and enhanced the chemotactic, phagocytic and killing activities of peritoneal macrophages and polymorphonuclear leukocytes, and stimulated the phagocytic function of the reticuloendothelial system. Enhanced host resistance to microbial infection by these immunoactive peptides might be induced by both increase in counts and enhancement of functions of phagocytes. FK-156 restored decreased counts and functions of phagocytes in mice immunosuppressed by cyclophosphamide, hydrocortisone or tumor. These findings suggest that these immunoactive peptides could be applied to prevent intractable infection in immunocompromised hosts.

Adjuvants, Immunologic↗

Biogeochemistry of dihydrogen (H2).

Hydrogen has had an important and evolving role in Earth's geo- and biogeochemistry, from prebiotic to modern times. On the earliest Earth, abiotic sources of H2 were likely stronger than in the present. Volcanic out-gassing and hydrothermal circulation probably occurred at several times the modern rate, due to presumably higher heat flux. The H2 component of volcanic emissions was likely buffered close to the modern value by an approximately constant mantle oxidation state since 3.9 billion years ago, and may have been higher before that, if the early mantle was more reducing. The predominantly ultramafic character of the early, undifferentiated crust could have led to increased serpentinization and release of H2 by hydrothermal circulation, as in modern ultramafic-hosted vents. At the same time, the reactive atmospheric sink for H2 was likely weaker. Collectively, these factors suggest that steady state levels of H2 in the prebiotic atmosphere were 3-4 orders of magnitude higher than at present, and possibly higher still during transient periods following the delivery of Fe and Ni by large impact events. These elevated levels had direct or indirect impacts on the redox state of the atmosphere, the radiation budget, the production of aerosol hazes, and the genesis of biochemical precursor compounds. The early abiotic cycling of H2 helped to establish the environmental and chemical context for the origins of life on Earth. The potential for H2 to serve as a source of energy and reducing power, and to afford a means of energy storage by the establishment of proton gradients, could have afforded it a highly utilitarian role in the earliest metabolic chemistry. Some origin of life theories suggest the involvement of H2 in the first energy-generating metabolism, and the widespread and deeply-branching nature of H2-utilization in the modern tree of life suggests that it was at least a very early biochemical innovation. The abiotic production of H2 via several mechanisms of water-rock interaction could have supported an early chemosynthetic biosphere. Such processes offer the continued potential for a deep, rock-hosted biosphere on Earth or other bodies in the solar system. The continued evolution of metabolic and community-level versatility among microbes led to an expanded ability to completely exploit the energy available in complex organic matter. Under the anoxic conditions that prevailed on the early Earth, this was accomplished through the linked and sequential action of several metabolic classes of organisms. By transporting electrons between cells, H2 provides a means of linking the activities of these organisms into a highly functional and interactive network. At the same time, H2 concentrations exert a powerful thermodynamic control on many aspects of metabolism and biogeochemical function in these systems. Anaerobic communities based on the consumption of organic matter continue to play an important role in global biogeochemistry even into the present day. As the principal arbiters of chemistry in most aquatic sediments and animal digestive systems, these microbes affect the redox and trace-gas chemistry of our oceans and atmosphere, and constitute the ultimate biological filter on material passing into the rock record. It is in such communities that the significance of H2 in mediating biogeochemical function is most strongly expressed. The advent of phototrophic metabolism added another layer of complexity to microbial communities, and to the role of H2 therein. Anoxygenic and oxygenic phototrophs retained and expanded on the utilization of H2 in metabolic processes. Both groups produce and consume H2 through a variety of mechanisms. In the natural world, phototrophic organisms are often closely juxtaposed with a variety of other metabolic types, through the formation of biofilms and microbial mats. In the few examples studied, phototrophs contribute an often swamping term to the H2 economy of these communities, with important implications for their overall function-including regulation of the redox state of gaseous products, and direct release of large quantities of H2 to the environment. As one of the dominant sources of biological productivity for as much as 2 billion years of Earth's history, these communities have been among the most important agents of long-term global biogeochemical change. On the modern Earth, H2 is present at only trace levels in the atmosphere and oceans. Nonetheless, its function as an arbiter of microbial interactions and chemistry ensures an important role in biogeochemical cycling. The significance of H2 in a global sense may soon increase, as the search for alternative fuels casts attention on the clean-energy potential of hydrogen fuel cells. Already, H2 utilization plays an important role in all three phylogenetic domains of life. Humans may soon add an important new term to this economy. Considerable research is focused on the H2-producing capacities of phototrophic and other microorganisms as potential contributors in this regard. Regardless of source, the large scale utilization of H2 as an energy source could carry important consequences for biogeochemistry.

Anaerobiosis↗

Protein microarrays: from serodiagnosis to whole proteome scale analysis of the immune response against pathogenic microorganisms.

Microbial diseases remain the most common cause of global mortality and morbidity. Scientific and technical achievements have dramatically improved the possibilities of investigating the humoral immune response against the whole proteome of microbial organisms. A number of genomes of microbial organisms responsible for diseases of worldwide medical importance such as Plasmodium, Toxoplasma, Mycobacterium, Streptococcus, Neisseria, Salmonella, Borrelia, and Rickettsia species have already been sequenced or will be available in the very near future. High-throughput assays such as protein microarrays have been clinically validated in serum for detecting the presence of antibodies directed against microbial antigens. Computational technologies for processing large sets of data are rapidly being developed. Such a powerful combination of genomic information and assays now offers the opportunity to identify the microbial antigens that, either alone or in combination, function as targets of natural acquired immunity against infectious diseases. This information will prove invaluable for developing vaccines against a series of microorganisms of medical relevance that are urgently needed, e.g., malaria. Additional applications of these technologies include the development of a microbial antigen array for the early serodiagnosis of both common and rare infectious diseases. This review will focus on technical and scientific issues concerning the use of antigen microarrays for vaccine development and the serodiagnosis of infectious diseases.

Antigens↗

Bacterial contamination of keyboards: efficacy and functional impact of disinfectants.

BACKGROUND: Computers are ubiquitous in the healthcare setting and have been shown to be contaminated with potentially pathogenic microorganisms. This study was performed to determine the degree of microbial contamination, the efficacy of different disinfectants, and the cosmetic and functional effects of the disinfectants on the computer keyboards. METHODS: We assessed the effectiveness of 6 different disinfectants (1 each containing chlorine, alcohol, or phenol and 3 containing quaternary ammonium) against 3 test organisms (oxacillin-resistant Staphylococcus aureus [ORSA], Pseudomonas aeruginosa, and vancomycin-resistant Enterococcus species) inoculated onto study computer keyboards. We also assessed the computer keyboards for functional and cosmetic damage after disinfectant use. RESULTS: Potential pathogens cultured from more than 50% of the computers included coagulase-negative staphylococci (100% of keyboards), diphtheroids (80%), Micrococcus species (72%), and Bacillus species (64%). Other pathogens cultured included ORSA (4% of keyboards), OSSA (4%), vancomycin-susceptible Enterococcus species (12%), and nonfermentative gram-negative rods (36%). All disinfectants, as well as the sterile water control, were effective at removing or inactivating more than 95% of the test bacteria. No functional or cosmetic damage to the computer keyboards was observed after 300 disinfection cycles. CONCLUSIONS: Our data suggest that microbial contamination of keyboards is prevalent and that keyboards may be successfully decontaminated with disinfectants. Keyboards should be disinfected daily or when visibly soiled or if they become contaminated with blood.

Aspergillus↗

Distinct roles for the NF-kappaB1 and c-Rel transcription factors in the differentiation and survival of plasmacytoid and conventional dendritic cells activated by TLR-9 signals.

Reticuloendotheliosis viral oncogene homolog/nuclear factor of kappa light polypeptide gene enhancer in B cells 1 (Rel/NF-kappaB) activation is a ubiquitous outcome of engaging Toll-like receptors (TLRs), yet the cell-type-specific functions of this pathway in response to particular microbial signals remain poorly defined. Here we show that NF-kappaB1 and C-Rel, Rel/NF-kappaB proteins induced in conventional dendritic cells (cDCs) and plasmacytoid dendritic cells (pDCs) by cytosine-phosphate-guanosine (CpG) DNA, a TLR-9 ligand, serve markedly different functions in these DC subsets. With the exception of impaired interleukin-12 (IL-12) production, cultured Nfkb1(-/-)C-Rel(-/-) cDCs responded relatively normally to CpG DNA. In contrast, CpG-treated Nfkb1(-/-)C-Rel(-/-) pDCs, which were still able to produce type I interferon and regulated on activation normal T-cell expressed and secreted (RANTES), but not IL-6 or IL-12, failed to acquire an activated dendritic phenotype and underwent apoptosis. Although the TLR-9-mediated death of Nfkb1(-/-)C-Rel(-/-) pDCs, which coincided with a failure to up-regulate the prosurvival proteins B-cell lymphoma apoptosis regulator xL (Bcl-x(L)) and A1, was blocked by Bcl-2 transgene expression, this inhibition of apoptosis still failed to rescue the differentiation defects. This indicated that these NF-kappaB transcription factors independently regulate TLR-9-mediated pDC morphogenesis and survival. Collectively, these findings establish that NF-kappaB1 and c-Rel, while largely dispensable for TLR-9-induced cDC activation, are critical for regulating differentiation and survival programs during pDC activation.

Animals↗