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Background The role of microbiota in sinonasal inflammation can be further understood by targeted sampling of healthy and diseased subjects. We compared the microbiota of the middle meatus (MM) and inferior meatus (IM) in healthy, allergic rhinitis (AR), and chronic rhinosinusitis (CRS) subjects to characterize intrasubject, intersubject, and intergroup differences. Methods Subjects were recruited in the office, and characterized into healthy, AR, and CRS groups. Endoscopically-guided swab samples were obtained from the MM and IM bilaterally. Bacterial microbiota were characterized by sequencing the V3-V4 region of the 16S ribosomal RNA (rRNA) gene. Results Intersubject microbiome analyses were conducted in 65 subjects: 8 healthy, 11 AR, and 46 CRS (25 CRS with nasal polyps [CRSwNP]; 21 CRS without nasal polyps [CRSsNP]). Intrasubject analyses were conducted for 48 individuals (4 controls, 11 AR, 8 CRSwNP, and 15 CRSwNP). There was considerable intersubject microbiota variability, but intrasubject profiles were similar ( p = 0.001, nonparametric t test). Intrasubject bacterial diversity was significantly reduced in MM of CRSsNP subjects compared to IM samples ( p = 0.022, nonparametric t test). CRSsNP MM samples were enriched in Streptococcus, Haemophilus, and Fusobacterium spp. but exhibited loss of diversity compared to healthy, CRSwNP, and AR subject-samples ( p < 0.05; nonparametric t test). CRSwNP patients were enriched in Staphylococcus, Alloiococcus, and Corynebacterium spp. Conclusion This study presents the sinonasal microbiome profile in one of the larger populations of non-CRS and CRS subjects, and is the first office-based cohort in the literature. In contrast to healthy, AR, and CRSwNP subjects, CRSsNP MM samples exhibited decreased microbiome diversity and anaerobic enrichment. CRSsNP MM samples had reduced diversity compared to same-subject IM samples, a novel finding. [ABSTRACT FROM AUTHOR]

Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing. [ABSTRACT FROM AUTHOR]

The article focuses on the genetic basis of the spread of cholera in Haiti which clarifies both the climatic and human transmission hypotheses explaining the origin of the disease after the January 12, 2010 earthquake. Topics include the role of the nonpathogenic Vibrio cholerae in cholera, studies supporting the human transmission hypothesis, and molecular study on the origin of Vibrio cholerae in the country. The use of genome sequencing as a tool for molecular epidemiology is considered.

An introduction is presented in which the editor discusses various topics within the issue including National Science Advisory Board for Biosecurity (NSABB) criteria's for public health and safety, avian influenza virus to be the most dangerous and the concept of dual-use research of concern (DURC).

Abstract: The Bacillus anthracis genome reflects its close genetic ties to Bacillus cereus and Bacillus thuringiensis but has been shaped by its own unique biology and evolutionary forces. The genome is comprised of a chromosome and two large virulence plasmids, pXO1 and pXO2. The chromosome is mostly co-linear among B. anthracis strains and even with the closest near neighbor strains. An exception to this pattern has been observed in a large inversion in an attenuated strain suggesting that chromosome co-linearity is important to the natural biology of this pathogen. In general, there are few polymorphic nucleotides among B. anthracis strains reflecting the short evolutionary time since its derivation from a B. cereus-like ancestor. The exceptions to this lack of diversity are the variable number tandem repeat (VNTR) loci that exist in genic and non genic regions of the chromosome and both plasmids. Their variation is associated with high mutability that is driven by rapid insertion and deletion of the repeats within an array. A notable example is found in the vrrC locus which is homologous to known DNA translocase genes from other bacteria. [Copyright &y& Elsevier]

The development of human civilizations and global commerce has led to the emergence and worldwide circulation of many infectious diseases. Anthrax, plague and tularaemia are three zoonotic diseases that have been intensely studied through genome characterization of the causative species and phylogeographical analyses. A few highly fit genotypes in each species represent the causative agents for most of the observed disease cases. Together, mutational and selective forces create highly adapted pathogens, but this must be coupled with ecological opportunities for global expansion. This Review describes the distributions of the bacteria that cause anthrax, plague and tularaemia and investigates the forces that created clonal structures in these species. [ABSTRACT FROM AUTHOR]

This article discusses microbial forensics and the use of DNA fingerprinting to identify a single strain of anthrax, (Bacillus anthracis) found in bioterrorism letters mailed in the U.S. in 2001. According to the authors, there are several differences between microbial forensics and human DNA fingerprinting including clonal versus sexual reproduction and rates of mutation. For human forensics, the U.S. FBI has developed the Combined DNA Index System using single tandem repeats of restricted fragment length polymorphism. For bacteria, amplified fragment length polymorphism by pulse-field gel electrophoresis led to a sequential sequencing of variable natural tandem repeats. Due to slow mutation rates, canonical single nucleotide polymorphism and progressive hierarchial resolving assay with nucleic acids was used to identify the Ames strain.

Tularemia is a disease caused by several subspecies of Francisella tularensis, although the severity of the disease varies greatly from subspecies to subspecies. Currently, there are four recognized subspecies ( tularensis, holarctica, mediasiatica, and novicida), in addition to a second Francisella species, F. philomiragia. It is clear from molecular sampling of the environment that these human pathogens are a mere fraction of the Francisella diversity. Taxonomic nomenclature is now being based upon several DNA-sequence-based approaches and this advance provides for robust phylogenetic models that are guiding the systematics of this genus. This in turn allows for better molecular epidemiological investigations and more precise ecological analysis. Tularemia ecology is still only partially understood, with many knowledge gaps about the disease reservoir and vectors. Molecular analysis has identified a major population split within F. tularensis subsp. tularensis that points toward distinctive ecological adaptations, vectors, and host species. Current medical practice does not rely upon subspecies or subpopulation identification, although this information may have predictive value for clinical outcome, especially in the United States. Combined molecular and epidemiological analyses suggest that the population split in F. tularensis subsp. tularensis matches two distinct human diseases in the United States with different mortality rates. DNA-sequence-based typing of F. tularensis subsp. holarctica from tularemia outbreaks in Europe and the United States proves regional identity among isolates and also demonstrates that this subspecies successfully disseminated worldwide in recent evolutionary time. [ABSTRACT FROM AUTHOR]

Precise identification of Bacillus anthracis isolates has aided forensic and epidemiological analyses of natural anthrax cases, bioterrorism acts and industrial scale accidents by state-sponsored bioweapons programs. Because there is little molecular variation among B. anthracis isolates, identifying and using rare variation is crucial for precise strain identification. We think that mutation is the primary diversifying force in a clonal, recently emerged pathogen, such as B. anthracis, since mutation rate is correlated with diversity on a per locus basis. While single nucleotide polymorphisms (SNPs) are rare, their detection is facilitated by whole genome discovery approaches. As highly stable phylogenetic markers, SNPs are useful for identifying long branches or key phylogenetic positions. Selection of single, diagnostic “Canonical SNPs” (canSNPs) for these phylogenetic positions allows for efficient and defining assays. We have taken a nested hierarchal strategy for subtyping B. anthracis, which is consistent with traditional diagnostics and applicable to a wide range of pathogens. Progressive hierarchical resolving assays using nucleic acids (PHRANA) uses a progression of diagnostic genomic loci that are initially highly stable but with low resolution and, ultimately, very unstable but with high resolution. This approach mitigates the need for data weighting and provides both a deeply rooted phylogenetic hypothesis and high resolution discrimination among closely related isolates. [Copyright &y& Elsevier]

This article reflects on the notion of time flowing from back to front, how it correlates with human experience, and leads to the complexity of eschatological language and the biblical poetics of hope. The literature of the Ancient Near East portrays a contrastly different orientation of time to that of the modern Western version. In the Ancient Near Eastern texts, there seems to be a cultural construction of time as flowing from back to front.

Examines the use of an aerosol containing Bacillus anthracis in bioterrorism by the religious group Aum Shinrikyo in Kameido, Tokyo, Japan in July 1993. Details of the incident; Laboratory findings of the fluid sample from Kameido; Cases of anthrax in humans.

Whole-genome sequencing is fundamental to understanding the genetic composition of an organism. Given the size and complexity of the soybean genome, an alternative approach is targeted random-gene sequencing, which provides an immediate and productive method of gene discovery. In this study, more than 120 000 soybean expressed sequence tags (ESTs) generated from more than 50 cDNA libraries were evaluated. These ESTs coalesced into 16 928 contigs and 17 336 singletons. On average, each contig was composed of 6 ESTs and spanned 788 bases. The average sequence length submitted to dbEST was 414 bases. Using only those libraries generating more than 800 ESTs each and only those contigs with 10 or more ESTs each, correlated patterns of gene expression among libraries and genes were discerned. Two-dimensional qualitative representations of contig and library similarities were generated based on expression profiles. Genes with similar expression patterns and, potentially, similar functions were identified. These studies provide a rich source of publicly available gene sequences as well as valuable insight into the structure, function, and evolution of a model crop legume genome.Key words: Glycine max, genome sequencing, functional genomics.Le séquençage de génomes complets est requis pour la compréhension de la composition génétique d'un organisme. Étant donné la taille et la complexité du génome du soja, le séquençage ciblé de gènes choisis au hasard constitue une approche alternative qui procure une méthode rapide et productive en vue d'identifier des gènes. Dans le cadre du présent travail, plus de 120 000 étiquettes de séquences exprimées (EST) du soja, provenant de 50 banques d'ADNc, ont été évaluées. Ces EST formaient 16 928 contigs et 17 336 étiquettes uniques. En moyenne, chaque contig comprenait 6 EST et totalisait 788 nucléotides. La taille moyenne des séquences soumises à dbEST était de 414 pb. En se limitant aux seules banques qui avaient contribué au moins 800 EST et aux seuls contigs comptant au moins 10 EST, des corrélations de l'expression génique ont pu être observées entre les banques et parmi des gènes. Des représentations qualitatives bidimensionnelles de la similarité des banques et des contigs ont été générées à partir des profils d'expression. Des gènes montrant des profils d'expression semblables, et potentiellement des fonctions similaires, ont été identifiés. Ces études contribuent un vaste éventail de séquences de gènes, dans le domaine publique, et apportent un éclairage nouveau sur la structure, la fonction et l'évolution du génome d'une légumineuse modèle.Mots clés : Glycine max, séquençage génomique, génomique fonctionnelle.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

Post-Acute Sequelae of SARS-CoV-2 infection (PASC or "Long COVID"), includes numerous chronic conditions associated with widespread morbidity and rising healthcare costs. PASC has highly variable clinical presentations, and likely includes multiple molecular subtypes, but it remains poorly understood from a molecular and mechanistic standpoint. This hampers the development of rationally targeted therapeutic strategies. The NIH-sponsored "Researching COVID to Enhance Recovery" (RECOVER) initiative includes several retrospective/prospective observational cohort studies enrolling adult, pregnant adult and pediatric patients respectively. RECOVER formed an "OMICS" multidisciplinary task force, including clinicians, pathologists, laboratory scientists and data scientists, charged with developing recommendations to apply cutting-edge system biology technologies to achieve the goals of RECOVER. The task force met biweekly over 14 months, to evaluate published evidence, examine the possible contribution of each "omics" technique to the study of PASC and develop study design recommendations. The OMICS task force recommended an integrated, longitudinal, simultaneous systems biology study of participant biospecimens on the entire RECOVER cohorts through centralized laboratories, as opposed to multiple smaller studies using one or few analytical techniques. The resulting multi-dimensional molecular dataset should be correlated with the deep clinical phenotyping performed through RECOVER, as well as with information on demographics, comorbidities, social determinants of health, the exposome and lifestyle factors that may contribute to the clinical presentations of PASC. This approach will minimize lab-to-lab technical variability, maximize sample size for class discovery, and enable the incorporation of as many relevant variables as possible into statistical models. Many of our recommendations have already been considered by the NIH through the peer-review process, resulting in the creation of a systems biology panel that is currently designing the studies we proposed. This system biology strategy, coupled with modern data science approaches, will dramatically improve our prospects for accurate disease subtype identification, biomarker discovery and therapeutic target identification for precision treatment. The resulting dataset should be made available to the scientific community for secondary analyses. Analogous system biology approaches should be built into the study designs of large observational studies whenever possible. [ABSTRACT FROM AUTHOR]

Background: Burkholderia pseudomallei, causative agent of melioidosis, is a One Health concern as it is acquired directly from soil and water and causes disease in humans and agricultural and wild animals. We examined B. pseudomallei in soil and goats at a single farm in the Northern Territory of Australia where >30 goats acquired melioidosis over nine years. Methodology/Principal findings: We cultured 45 B. pseudomallei isolates from 35 goats and sampled soil in and around goat enclosures to isolate and detect B. pseudomallei and evaluate characteristics associated with its occurrence; 33 soil isolates were obtained from 1993–1994 and 116 in 2006. Ninety-two goat and soil isolates were sequenced; mice were challenged with six soil isolates to evaluate virulence. Sampling depth and total N/organic C correlated with B. pseudomallei presence. Twelve sequence types (STs) were identified. Most goat infections (74%) were ST617, some with high similarity to 2006 soil isolates, suggesting ST617 was successful at persisting in soil and infecting goats. ST260 and ST266 isolates were highly virulent in mice but other isolates produced low/intermediate virulence; three of these were ST326 isolates, the most common soil ST in 2006. Thus, virulent and non-virulent lineages can co-occur locally. Three genes associated with virulence were present in ST260 and ST266, absent in most ST326 isolates, and present or variably present in ST617. Conclusions/Significance: Agricultural animals can influence B. pseudomallei abundance and diversity in local environments. This effect may persist, as B. pseudomallei was detected more often from soil collected inside and adjacent to goat enclosures years after most goats were removed. Following goat removal, the low virulence ST326, which was not isolated from soil when goats were present, became the predominant ST in soil by 2006. Although multiple diverse lineages of B. pseudomallei may exist in a given location, some may infect mammals more efficiently than others. Author summary: We studied genomic diversity in the environmental bacterial pathogen, Burkholderia pseudomallei, which caused the disease melioidosis in goats at a small farm in northern Australia. By comparing genomes from 92 B. pseudomallei isolates from goats and soil, we discovered 12 diverse lineages at this location, three of which infected the majority of goats and were cultured from the soil of goat enclosures. We also conducted a mouse challenge experiment using six isolates from this farm and determined that two soil isolates displayed much greater virulence than the others. Finally, we investigated soil factors associated with B. pseudomallei occurrence and found 1) most B. pseudomallei isolates were sampled from irrigated soils, and 2) B. pseudomallei was much more likely to be encountered at soil depths of 30 cm than 10 cm. The presence of this pathogen in the soil severely impacted maintenance of the goat herd due to high mortality and emphasizes its One Health implications for other livestock operations in tropical countries where B. pseudomallei is endemic. Our findings provide insight into the importance of more fully understanding soil habitats that promote B. pseudomallei presence, thereby increasing the risk of melioidosis to humans and agricultural animals. [ABSTRACT FROM AUTHOR]

Describes a high density map in soybean using a 300 recombinant inbred line population from BSR-101 x PI437.654 by constructing a restriction fragment length polymorphism scaffold map based on the entire population. Identification of length differences; Primer products; Uncorrelated linkage groups.

Presents information on a study which optimized the standard random amplified polymorphic DNA procedure to generate reliable markers for mapping in soybeans. Materials and methods of the study; How restriction digested template increases polymorphism.

Discusses the use of DNA to differentiate individuals and populations of mule deer in regions adjacent to the north and south rims of the Grand Canyon in Arizona. Nuclear genetic analysis; Mitochondrial genetic analysis; Nuclear DNA fingerprinting; Mitochondrial DNA; Management implications of study results.

Focuses on a study which compared the phylogenetic relationships of several pairs of mitochondrial cytochrome b gene, acquired from three species of extant peccaries. Identification of the species; Details on phylogenetic analyses which used parsimony and maximum likelihood; Methodology used to conduct the study; Results of the study.

Studies the geographic patters of mitochondrial-DNA variation in peccaries. Difference in the frequencies of haplotypes across regions; Indication of partitioning of mtDNA haplotypes; Colonization of Arizona by three mtDNA lineages.

Reports on the molecular characterization of bacillus anthracis and selected related bacillus species by using amplified fragment length polymorphism (AFLP) markers. Origin of Bacillus anthracis; Genetic relationships among Bacillus anthracis strains.

Pneumonic plague (PP) is characterized by high infection rate, person-to-person transmission, and rapid progression to severe disease. In 2017, a PP epidemic occurred in 2 Madagascar urban areas, Antananarivo and Toamasina. We used epidemiologic data and Yersinia pestis genomic characterization to determine the sources of this epidemic. Human plague emerged independently from environmental reservoirs in rural endemic foci >20 times during August-November 2017. Confirmed cases from 5 emergences, including 4 PP cases, were documented in urban areas. Epidemiologic and genetic analyses of cases associated with the first emergence event to reach urban areas confirmed that transmission started in August; spread to Antananarivo, Toamasina, and other locations; and persisted in Antananarivo until at least mid-November. Two other Y. pestis lineages may have caused persistent PP transmission chains in Antananarivo. Multiple Y. pestis lineages were independently introduced to urban areas from several rural foci via travel of infected persons during the epidemic. [ABSTRACT FROM AUTHOR]

An interview with acting U.S. National Science Advisory Board for Biosecurity (NSABB) chairman Paul S. Keim is presented. When asked about his comments on papers reporting experimental adaptations of influenza viruses, he asserts that they demonstrate segments of the 2009 pandemic influenza. He affirms that the major benefit of the work is to alert humanity to the threat posed by H5N1. He states that they remain concern about any type of research that enhances the virulence of Influenza virus.

Background: Diagnostic tools designed to target Burkholderia pseudomallei, the causative agent of melioidosis that was classified as a Tier 1 Select Agent by the U.S. Centers for Disease Control and Prevention, have typically suffered from false-positive and false-negative results because of a lack of understanding of the genomic diversity of B. pseudomallei and its genetic near neighbors. Objective: In this review, we discuss a strategy for using comparative genomics to guide the design of inclusivity and exclusivity panels for the validation of assays as defined by the Standard Method Performance Requirement (SMPR®). Methods: Based upon a literature review, comparative genomic analyses, and hands-on experience with diagnostic development and testing, we describe important factors to consider when developing inclusivity and exclusivity panels for testing diagnostic and/or detection tools. Results: The genomic diversity of B. pseudomallei is substantial, with the genome characterized by horizontal gene transfer, including the acquisition of genomic islands from near-neighbor species. This genomic diversity, core genome reduction, and signal erosion can complicate molecular diagnostic tool development and validation. Conclusions: Accurate diagnostic and/or detection tools targeting B. pseudomallei, an important pathogen from a public health and biodefense perspective, are needed for many applications. Utilizing whole genome sequencing data and comparative genomic techniques can guide the development and validation of such tools. Amplicon sequencing assays and assay redundancy can provide improved assay performance. Highlights: When developing and validating diagnostic and/or detection tools targeting B. pseudomallei, it is important to consider genomic diversity, genome reduction, and signal erosion to reduce the effects of typical diagnostic errors. [ABSTRACT FROM AUTHOR]

Background: The role of microbes in chronic rhinosinusitis (CRS) is poorly understood. We hypothesize that analyzing prior microbial exposures via assessing microbial protein serological reactivity in CRS versus controls may offer insights for CRS etiopathogenesis. Methods: We profiled IgG and IgA antibodies to individual microbial proteins in serum samples of CRS patients and controls using a novel high‐throughput microarray protein technology, Nucleic Acid Programmable Protein Array (NAPPA). The study was conducted on 118 subjects (39 CRS, 79 controls). A CRS‐focused NAPPA array, with 1557 potentially sero‐reactive microbial proteins elected from a pre‐screening of 6500 genes of interest was constructed. It included membrane‐associated proteins from 47 bacterial species and all proteins from 43 viral strains. Differences between CRS and controls were compared across individual antimicrobial antibodies and the species. Results: Chronic rhinosinusitis patients had significantly elevated antimicrobial antibodies compared with controls. One bacterium (Staphylococcus aureus) and three viral strains (human metapneumovirus, human herpesvirus 5, and human herpesvirus 4) were identified as sources of the proteins that showed significantly elevated sero‐reactivity in CRS patients. Within CRS, patients with polyps had elevated antibodies against S. aureus, influenza A virus (H1N1, H3N2), and rhinovirus B14. CRS patients without polyps showed more antibodies against human herpesvirus 1 and vaccinia virus WR. Conclusions: Compared with healthy controls, CRS patients' serum samples showed significantly increased sero‐reactivity to both bacterial and viral proteins, reflecting recent or current infection or active colonization. Significantly higher antibodies against S. aureus, human metapneumovirus, human herpesvirus 5, and human herpesvirus 4 in CRS need further study. [ABSTRACT FROM AUTHOR]

Exposure to soil or water contaminated with the urine of Leptospirainfected animals is the most common way in which humans contract leptospirosis. Entire populations can be at high risk of leptospirosis while working in inundated fields, when engaging in aquatic sports, or after periods of heavy rainfall. The risk of infection after contact with these environmental sources depends on the ability of Leptospira bacteria to survive, persist, and infect new hosts. Multiple variables such as soil and water pH, temperature, and even environmental microbial communities are likely to shape the environmental conditions needed by the pathogen to persist. Here we review what is known about the environmental phase of the infectious Leptospira transmission cycle and identify knowledge gaps that will serve as a guide for future research. [ABSTRACT FROM AUTHOR]

The National Aeronautics and Space Administration (NASA) has been monitoring the microbial burden of spacecraft since the 1970's Viking missions. Originally culture-based and then focused 16S sequencing techniques were used, but we have now applied whole metagenomic sequencing to a variety of cleanroom samples at the Jet Propulsion Lab (JPL), including the Spacecraft Assembly Facility (SAF) with the goals of taxonomic identification and for functional assignment. Our samples included facility pre-filters, cleanroom vacuum debris, and surface wipes. The taxonomic composition was carried out by three different analysis tools to contrast marker, k-mer, and true alignment approaches. Hierarchical clustering analysis of the data separated vacuum particles from other SAF DNA samples. Vacuum particle samples were the most diverse while DNA samples from the ISO (International Standards Organization) compliant facilities and the SAF were the least diverse; all three were dominated by Proteobacteria. Wipe samples had higher diversity and were predominated by Actinobacteria, including human commensals Cutibacterium acnes and Corynebacterium spp. Taxa identified by the three methods were not identical, supporting the use of multiple methods for metagenome characterization. Likewise, functional annotation was performed using multiple methods. Vacuum particles and SAF samples contained strong signals of the tricarboxylic acid cycle and of amino acid biosynthesis, suggesting that many of the identified microorganisms have the ability to grow in nutrient-limited environments. In total, 18 samples generated high quality metagenome assembled genomes (MAG), which were dominated by Moraxella osloensis or Malassezia restricta. One M. osloensis MAG was assembled into a single circular scaffold and gene annotated. This study includes a rigorous quantitative determination of microbial loads and a qualitative dissection of microbial composition. Assembly of multiple specimens led to greater confidence for the identification of particular species and their predicted functional roles. [ABSTRACT FROM AUTHOR]

Background: Melioidosis is a disease caused by the bacterium Burkholderia pseudomallei, infecting humans and non-human primates (NHP) through contaminated soil or water. World-wide there are an estimated 165,000 human melioidosis cases each year, but recordings of NHP cases are sporadic. Clinical detection of melioidosis in humans is primarily by culturing B. pseudomallei, and there are no standardized detection protocols for NHP. NHP are an important animal model for melioidosis research including clinical trials and development of biodefense countermeasures. Methodology/Principle findings: We evaluated the diagnostic potential of the multiple antigen serological assay, BurkPx, in NHP using two sera sets: (i) 115 B. pseudomallei-challenged serum samples from 80 NHP collected each week post-exposure (n = 52) and at euthanasia (n = 47), and (ii) 126 B. pseudomallei-naïve/negative serum samples. We observed early IgM antibody responses to carbohydrate antigens followed by IgG antibody recognition to multiple B. pseudomallei protein antigens during the second week of infection. B. pseudomallei negative serum samples had low to intermediate antibody cross reactivity to the antigens in this assay. Infection time was predicted as the determining factor in the variation of antibody responses, with 77.67% of variation explained by the first component of the principal component analysis. A multiple antigen model generated a binary prediction metric (p^), which when applied to all data resulted in 100% specificity and 63.48% sensitivity. Removal of week 1 B. pseudomallei challenged serum samples increased the sensitivity of the model to 95%. Conclusion/Significance: We employed a previously standardized assay for humans, the BurkPx assay, and assessed its diagnostic potential for detection of B. pseudomallei exposure in NHP. The assay is expected to be useful for surveillance in NHP colonies, in investigations of suspected accidental releases or exposures, and for identifying vaccine correlates of protection. Author summary: Melioidosis is a disease caused by the soil-dwelling bacterium Burkholderia pseudomallei, a Tier 1 Select Agent by the US Centers for Disease Control and Prevention (CDC), with the ability to naturally infect humans and non-human primates (NHP). Although melioidosis diagnosis in humans has been formally outlined, there is no standardized test available for B. pseudomallei exposure and melioidosis in NHP. NHP are important animal models in melioidosis research in addition to other scientific research. The goal of this study was to formally evaluate the first extensive serodiagnostic test for detection of B. pseudomallei exposure in NHP. The BurkPx assay comprised 21 B. pseudomallei specific antigens and was previously standardized in humans. Early IgM antibody responses were noted to carbohydrates whilst IgG antibody responses were mounted to multiple proteins during the second week of infection. The assay elicited low background reactivity to B. pseudomallei-naive NHP. Data collected from the BurkPx assay was fed into a multiple antigen model, which produced a p^ score used to classify the assay via thresholding. The final model produced a 100% specificity and 63.48% sensitivity among all samples; however, removal of early infection samples increased sensitivity to 95%. [ABSTRACT FROM AUTHOR]

Burkholderia pseudomallei, the causative agent of melioidosis, is a gram-negative soil bacterium well recognized in Southeast Asia and northern Australia. However, wider and expanding global distribution of B. pseudomallei has been elucidated. Early diagnosis is critical for commencing the specific therapy required to optimize outcome. Serological testing using the indirect hemagglutination (IHA) antibody assay has long been used to augment diagnosis of melioidosis and to monitor progress. However, cross reactivity and prior exposure may complicate the diagnosis of current clinical disease (melioidosis). The goal of our study was to develop and initially evaluate a serology assay (BurkPx) that capitalized upon host response to multiple antigens. Antigens were selected from previous studies for expression/purification and conjugation to microspheres for multiantigen analysis. Selected serum samples from non-melioidosis controls and serial samples from culture-confirmed melioidosis patients were used to characterize the diagnostic power of individual and combined antigens at two times post admission. Multiple variable models were developed to evaluate multivariate antigen reactivity, identify important antigens, and determine sensitivity and specificity for the diagnosis of melioidosis. The final multiplex assay had a diagnostic sensitivity of 90% and specificity of 93%, which was superior to any single antigen in side-by-side comparisons. The sensitivity of the assay started at >85% for the initial serum sample after admission and increased to 94% 21 days later. Weighting antigen contribution to each model indicated that certain antigen contributed to diagnosis more than others, which suggests that the number of antigens in the assay can be decreased. In summation, the BurkPx assay can facilitate the diagnosis of melioidosis and potentially improve on currently available serology assays. Further evaluation is now required in both melioidosis-endemic and non-endemic settings. Author summary: Melioidosis has a wide diversity of symptoms, making laboratory diagnosis essential. The diagnosis of melioidosis is primarily by culture of the causative bacterium, Burkholderia pseudomallei, which is problematic for locations with limited laboratory resources and for laboratories inexperienced in handling B. pseudomallei. Early diagnosis of melioidosis facilitates the specific antimicrobial therapy that optimizes outcomes and substantially lowers mortality. We have developed and evaluated a multiple antigen-antibody serology assay using serial samples from culture confirmed melioidosis patients including the first sample after patient admission, together with non-melioidosis serum controls. Multiantigen reactivity was compared to single antigens and to the indirect hemagglutination (IHA) antibody assay data collected from routine patient testing. The results from testing patients with culture-confirmed melioidosis suggest that using multiple individual antigen assays coupled with models can improve the sensitivity and specificity of serological diagnosis using the same antigens evaluated individually. In addition, all evaluated antigens may not be needed to improve assay performance. Further antigen down selection and evaluation of the utility of this assay is now required in both melioidosis-endemic and non-endemic settings. [ABSTRACT FROM AUTHOR]

Leptospirosis is a major zoonotic disease with widespread distribution and a large impact on human health. Carrier animals excrete pathogenic Leptospira primarily in their urine. Infection occurs when the pathogen enters a host through mucosa or small skin abrasions. Humans and other animals are exposed to the pathogen by direct contact with urine, contaminated soil or water. While many factors influence environmental cycling and the transmission of Leptospira to humans, the load of pathogenic Leptospira in the environment is likely to play a major role. Peridomestic rats are often implicated as a potential source of human disease; however exposure to other animals is a risk factor as well. The aim of this report is to highlight the importance of various carrier animals in terms of the quantity of Leptospira shed into the environment. For this, we performed a systematic literature review and a meta-analysis of the amount of pathogen that various animal species shed in their urine. Results: The quantity of pathogen has been reported for cows, deer, dogs, humans, mice, and rats, in a total of 14 research articles. We estimated the average Leptospira per unit volume shed by each animal species, and the daily environmental contribution by considering the total volume of urine excreted by each carrier animal. Rats excrete the highest quantity of Leptospira per millilitre of urine (median = 5.7 × 106 cells), but large mammals excrete much more urine and thus shed significantly more Leptospira per day (5.1 × 108 to 1.3 × 109 cells). Conclusions: Here we illustrate how, in a low-income rural Ecuadorian community, host population demographics, and prevalence of Leptospira infection can be integrated with estimates of shed Leptospira to suggest that peridomestic cattle may be more important than rats in environmental cycling and ultimately, transmission to humans. [ABSTRACT FROM AUTHOR]

We recently published a preliminary assessment of the activity of a poly (ADP-ribose) polymerase (PARP) inhibitor, stenoparib, also known as 2X-121, which inhibits viral replication by affecting pathways of the host. Here we show that stenoparib effectively inhibits a SARS-CoV-2 wild type (BavPat1/2020) strain and four additional variant strains; alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2) and gamma (P.1) in vitro, with 50% effective concentration (EC50) estimates of 4.1 μM, 8.5 μM, 24.1 μM, 8.2 μM and 13.6 μM, respectively. A separate experiment focusing on a combination of 10 μM stenoparib and 0.5 μM remdesivir, an antiviral drug, resulted in over 80% inhibition of the alpha variant, which is substantially greater than the effect achieved with either drug alone, suggesting at least additive effects from combining the different mechanisms of activity of stenoparib and remdesivir. [ABSTRACT FROM AUTHOR]

Bacillus anthracis, the causative agent of anthrax, is a proven biological weapon. In order to study this threat, a number of experimental surrogates have been used over the past 70 years. However, not all surrogates are appropriate for B. anthracis, especially when investigating transport, fate and survival. Although B. atrophaeus has been widely used as a B. anthracis surrogate, the two species do not always behave identically in transport and survival models. Therefore, we devised a scheme to identify a more appropriate surrogate for B. anthracis. Our selection criteria included risk of use (pathogenicity), phylogenetic relationship, morphology and comparative survivability when challenged with biocides. Although our knowledge of certain parameters remains incomplete, especially with regards to comparisons of spore longevity under natural conditions, we found that B. thuringiensis provided the best overall fit as a non-pathogenic surrogate for B. anthracis. Thus, we suggest focusing on this surrogate in future experiments of spore fate and transport modelling. [ABSTRACT FROM AUTHOR]

Although it is understood that the composition of riparian trees can affect stream function through leaf litter fall, the potential effects of genetic variation within species are less understood. Using a naturally hybridizing cottonwood system, we examined tile hypothesis that genetic differences among two parental species (Populus fremontii and P. angustifolia) and two groups of their hybrids (F1 and backcrosses to P. angustifolia) would affect litter decomposition rates and the composition of the aquatic invertebrate community that colonizes leaves. Three major findings emerged: (1) parental and hybrid types differ in litter quality, (2) decomposition differs between two groups, a fast group (P. fremontii and F1 hybrid), and a slow group (P. angustifolia and backcross hybrids), and (3) aquatic invertebrate communities colonizing P. fremontii litter differed significantly in composition from all other cross types, even though P. fremontii and the F1 hybrid decomposed at similar rates. These findings are in agreement with terrestrial arthropod studies in the same cottonwood system. However, the effects are less pronounced aquatically than those observed in the adjacent terrestrial community, which supports a genetic diffusion hypothesis. Importantly, these findings argue that genetic interactions link terrestrial and aquatic communities and may have significant evolutionary and conservation implications. [ABSTRACT FROM AUTHOR]

Coccidioidomycosis is a common fungal disease that is endemic to arid and semi-arid regions of both American continents. Coccidioides immitis and Coccidioides posadasii are the etiological agents of the disease, also known as Valley Fever. For several decades, the C. posadasii strain Silveira has been used widely in vaccine studies, is the source strain for production of diagnostic antigens, and is a widely used experimental strain for functional studies. In 2009, the genome was sequenced using Sanger sequencing technology, and a draft assembly and annotation were made available. In this study, the genome of the Silveira strain was sequenced using single molecule real-time sequencing PacBio technology, assembled into chromosomal-level contigs, genotyped, and the genome was reannotated using sophisticated and curated in silico tools. This high-quality genome sequencing effort has improved our understanding of chromosomal structure, gene set annotation, and lays the groundwork for identification of structural variants (e.g. transversions, translocations, and copy number variants), assessment of gene gain and loss, and comparison of transposable elements in future phylogenetic and population genomics studies. [ABSTRACT FROM AUTHOR]

Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and northern Australia that causes the disease, melioidosis. Although the global genomic diversity of clinical B. pseudomallei isolates has been investigated, there is limited understanding of its genomic diversity across small geographic scales, especially in soil. In this study, we obtained 288 B. pseudomallei isolates from a single soil sample (~100g; intensive site 2, INT2) collected at a depth of 30cm from a site in Ubon Ratchathani Province, Thailand. We sequenced the genomes of 169 of these isolates that represent 7 distinct sequence types (STs), including a new ST (ST1820), based on multi-locus sequence typing (MLST) analysis. A core genome SNP phylogeny demonstrated that all identified STs share a recent common ancestor that diverged an estimated 796–1260 years ago. A pan-genomics analysis demonstrated recombination between clades and intra-MLST phylogenetic and gene differences. To identify potential differential virulence between STs, groups of BALB/c mice (5 mice/isolate) were challenged via subcutaneous injection (500 CFUs) with 30 INT2 isolates representing 5 different STs; over the 21-day experiment, eight isolates killed all mice, 2 isolates killed an intermediate number of mice (1–2), and 20 isolates killed no mice. Although the virulence results were largely stratified by ST, one virulent isolate and six attenuated isolates were from the same ST (ST1005), suggesting that variably conserved genomic regions may contribute to virulence. Genomes from the animal-challenged isolates were subjected to a bacterial genome-wide association study to identify genomic regions associated with differential virulence. One associated region is a unique variant of Hcp1, a component of the type VI secretion system, which may result in attenuation. The results of this study have implications for comprehensive sampling strategies, environmental exposure risk assessment, and understanding recombination and differential virulence in B. pseudomallei. Author summary: Burkholderia pseudomallei is the causative agent of melioidosis, a disease endemic to Southeast Asia and northern Australia. The evaluation of diversity within B. pseudomallei has largely been conducted utilizing clinical isolates despite almost all infections emerging from environmental exposure. In this study, we surveyed the genomic diversity of 169 isolates collected from a single soil sample in Ubon Ratchathani Province, Thailand. Seven different sequence types were identified, and substantial within-sequence-type gene diversity was observed. To test for differential virulence, 30 isolates were challenged in a mouse melioidosis model. A small number of isolates killed all mice, but most killed none, demonstrating the variable virulence potential of different B. pseudomallei isolates present in the single sample. A comparative genomics analysis identified multiple genes associated with virulence, including Hcp1, a component of the type VI secretion system and a known virulence factor. The results of this study have implications for the comprehensive environmental surveillance, environmental exposure, and differential virulence of B. pseudomallei. [ABSTRACT FROM AUTHOR]

Composite interval mapping was used to identify life-span QTL in F2 progeny of three crosses between different pairs of inbred lines. Each inbred line was derived from a different outbred population that had undergone long-term selection for either long or short life span. Microsatellite loci were used as genetic markers, and confidence intervals for QTL location were estimated by bootstrapping. A minimum of 10 QTL were detected, nine of which were located on the two major autosomes. Five QTL were present in at least two crosses and five were present in both sexes. Observation of the same QTL in more than one cross was consistent with the hypothesis that genetic variation for life span is maintained by balancing selection. For all QTL except one, allelic effects were in the direction predicted on the basis of outbred source population. Alleles that conferred longer life were always at least partially dominant. [ABSTRACT FROM AUTHOR]

Three selection experiments were used to identify chromosome regions that contain QTL affecting late-life and early-life fitness in Drosophila melanogaster. The selection experiments were initiated by crossing pairs of inbred lines that had been derived from outbred laboratory populations that had different mean life spans. QTL regions were located by association with microsatellite markers that showed significant selection responses. Regions between recombination map positions 54 and 81 on chromosome 2, between 0 and 30 on chromosome 3, and near locations 49 and 81 on chromosome 3 had the strongest support as locations of life-span QTL. There was good general agreement between the life-span QTL regions that were identified by selection and those that were identified in a companion recombination mapping experiment that used the same fly stocks. Many marker loci responded in opposite directions to selection for late- and early-life fitness, indicating negative genetic correlations or trade-offs between those traits. Indirect evidence suggested that some negative genetic correlations were due to antagonistic pleiotropy. [ABSTRACT FROM AUTHOR]

SUMMARY 1. Dispersal ability is an important ecological factor that can influence population structure. In an attempt to determine the extent that the pattern of genetic differentiation is correlated with dispersal ability in stream-dwelling aquatic insects, we used the amplified fragment length polymorphism (AFLP) technique to characterise genetic variation in four aquatic insect species: Gumaga griseola (Trichoptera: Sericostomatidae), Helicopsyche mexicana (Trichoptera: Helicopsychidae), Psephenus montanus (Coleoptera: Psephenidae) and Ambrysus thermarum (Hemiptera: Naucoridae). Individuals were sampled from several sites within two adjacent catchments in the Arizona White Mountains. In addition to the genetic analyses, a 20-week-long trapping study was used to determine the relative dispersal ability of adults of the four species examined. 2. We obtained hierarchical indicators of genetic differentiation for catchments, sites within catchments and sites across the region examined. Overall, average estimators of genetic differentiation (F -statistics) were consistent with direct observations of organismal movement, although it was our direct observations on adult insect flight that permitted us to interpret our results correctly. This was because of the fact that a lack of genetic differentiation across watersheds can be interpreted in two ways. 3. In contrast to F -statistics, patterns of genetic isolation by distance for each species more clearly reflected dispersal ability, suggesting that such analytical approaches provide less ambiguous information about the importance of gene flow in the hierarchical partitioning of genetic variation in stream organisms. [ABSTRACT FROM AUTHOR]

Examines the ability of muscles to adapt to locomotion. Elastic strain energy storage; Mechanism of muscle spring adaptation to eccentric contraction; Function of the protein titin in muscle spring.

AbstractInterspecific hybridization represents a dynamic evolutionary phenomenon and major conservation problem in salmonid fishes. In this study we used amplified fragment length polymorphisms (AFLP) and mitochondrial DNA (mtDNA) markers to describe the extent and characterize the pattern of hybridization and introgression between coastal rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki). Hybrid individuals were initially identified using principle coordinate analysis of 133 polymorphic AFLP markers. Subsequent analysis using 23 diagnostic AFLP markers revealed the presence of F1, rainbow trout backcross, cutthroat trout backcross and later-generation hybrids. mtDNA analysis demonstrated equal numbers of F1 hybrids with rainbow and cutthroat trout mtDNA indicating reciprocal mating of the parental types. In contrast, rainbow and cutthroat trout backcross hybrids always exhibited the mtDNA from the recurrent parent, indicating a male hybrid mating with a pure female. This study illustrates the usefulness of the AFLP technique for generating large numbers of species diagnostic markers. The pattern of hybridization raises many questions concerning the existence and action of reproductive isolating mechanisms between these two species. Our findings are consistent with the hypothesis that introgression between anadromous populations of coastal rainbow and coastal cutthroat trout is limited by an environment-dependent reduction in hybrid fitness. [ABSTRACT FROM AUTHOR]

Distinct Burkholderia strains were isolated from soil samples collected in tropical northern Australia (Northern Territory and the Torres Strait Islands, Queensland). Phylogenetic analysis of 16S rRNA and whole genome sequences revealed these strains were distinct from previously described Burkholderia species and assigned them to two novel clades within the B. pseudomallei complex (Bpc). Because average nucleotide identity and digital DNA-DNA hybridization calculations are consistent with these clades representing distinct species, we propose the names Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov. Strains assigned to B. mayonis sp. nov. include type strain BDU6T (=TSD-80; LMG 29941; ASM152374v2) and BDU8. Strains assigned to B. savannae sp. nov. include type strain MSMB266T (=TSD-82; LMG 29940; ASM152444v2), MSMB852, BDU18, and BDU19. Comparative genomics revealed unique coding regions for both putative species, including clusters of orthologous genes associated with phage. Type strains of both B. mayonis sp. nov. and B. savannae sp. nov. yielded biochemical profiles distinct from each other and from other species in the Bpc, and profiles also varied among strains within B. mayonis sp. nov. and B. savannae sp. nov. Matrix-assisted laser desorption ionization time-of-flight (MLST) analysis revealed a B. savannae sp. nov. cluster separate from other species, whereas B. mayonis sp. nov. strains did not form a distinct cluster. Neither B. mayonis sp. nov. nor B. savannae sp. nov. caused mortality in mice when delivered via the subcutaneous route. The addition of B. mayonis sp. nov. and B. savannae sp. nov. results in a total of eight species currently within the Bpc. [ABSTRACT FROM AUTHOR]