We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the... more
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in... more
The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species' abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most h...
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Many microorganisms are unable to synthesize essential B vitamin-related enzyme cofactors de novo. The underlying mechanisms by which such microbes survive in multi-species communities are largely unknown. We previously reported the... more
Many microorganisms are unable to synthesize essential B vitamin-related enzyme cofactors de novo. The underlying mechanisms by which such microbes survive in multi-species communities are largely unknown. We previously reported the near-complete genome sequence of two ~18-member unicyanobacterial microbial consortia that maintain stable membership on defined medium lacking vitamins. Here we have used genome analysis and growth studies on isolates derived from the consortia to reconstruct pathways for biogenesis of eight essential cofactors and predict cofactor usage and precursor exchange in these communities. Our analyses revealed that all but the two Halomonas and cyanobacterial community members were auxotrophic for at least one cofactor. We also observed a mosaic distribution of salvage routes for a variety of cofactor precursors, including those produced by photolysis. Potentially bidirectional transporters were observed to be preferentially in prototrophs, suggesting a mechan...
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Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture... more
Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms, however little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity, and metabolic gradient measurements. Draft reconstructed genomes of 34 abundant organisms revealed three dominant cyanobacterial populations differentially distributed across the top layers of the mat suggesting niche separation along light and oxygen gradien...
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To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has... more
To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (est. >85% of gene complement) genome sequences for 17 of the 20 detected member species. Two Halomonas spp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds re...
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Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance because of its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of... more
Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance because of its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of the Trichodesmium erythraeum (strain IMS101) genome is predicted to encode protein, which is 20-25% less than the average for other cyanobacteria and nonpathogenic, free-living bacteria. We use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of the Trichodesmium genus, both in culture and in situ. Transcriptome analysis indicates that 86% of the noncoding space is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and twofold higher than that found in the gene-dense genomes of the sympatric cya...
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Research Interests: Molecular Evolution, Biology, DNA replication, DNA repair, Medicine, and 15 moreMultidisciplinary, Nature, Energy Metabolism, Phylogeny, Humans, Vibrio cholerae, Molecular Phylogenetics and Evolution, Cholera, Gram-negative bacteria, Genome sequence, Base Sequence, Cell Wall, Open Reading Frame, DNA sequence, and Molecular Sequence Data
We have applied âwhole-genome shotgun sequencingâ to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base... more
We have applied âwhole-genome shotgun sequencingâ to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.
Research Interests: Genomics, Computational Biology, Photosynthesis, Biology, Bacteriophages, and 15 moreCyanobacteria, Microbial diversity, Biodiversity, Multidisciplinary, Phylogeny, Atlantic Ocean, Archaea, Bacteria, Genome, Plasmids, Ecosystem, Microbial Diversity, Relative Abundance, Eukaryotic Cells, and Molecular Sequence Data
The 1,995,275-bp genome of Coxiella burnetii , Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This bacterium is an obligate intracellular... more
The 1,995,275-bp genome of Coxiella burnetii , Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This bacterium is an obligate intracellular acidophile that is highly adapted for life within the eukaryotic phagolysosome. Genome analysis revealed many genes with potential roles in adhesion, invasion, intracellular trafficking, host-cell modulation, and detoxification. A previously uncharacterized 13-member family of ankyrin repeat-containing proteins is implicated in the pathogenesis of this organism. Although the lifestyle and parasitic strategies of C. burnetii resemble that of Rickettsiae and Chlamydiae , their genome architectures differ considerably in terms of presence of mobile elements, extent of genome reduction, metabolic capabilities, and transporter profiles. The presence of 83 pseudogenes displays an ongoing process of gene degradation. Unlike other obligate intracellular bacteria,...
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Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have... more
Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In additi...
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Research Interests: Evolutionary Biology, Genetics, Microbiology, Genomics, Biology, and 15 moreEcology, Drosophila melanogaster, Medicine, Biological Sciences, DNA, Lipopolysaccharide, Elements, Animals, Genome Analysis, Glycolysis, Genome, Gene Duplication, Lateral Gene Transfer, Adenosine Triphosphate, and Medical and Health Sciences
Research Interests: Genetics, Developmental Biology, Molecular Evolution, Biology, Horizontal Gene Transfer, and 13 moreMedicine, Chlamydia pneumoniae, Biological Sciences, Virulence, Environmental Sciences, Nucleic Acids, Plasmids, Gram-negative bacteria, Genome sequence, Amino Acid Sequence, Chlamydia Psittaci, Biochemistry and cell biology, and Molecular Sequence Data
Research Interests: Computer Science, Genomics, Computational Biology, Comparative Genomics, Biology, and 15 moreMedicine, Biological Sciences, Software, Phylogeny, Environmental Sciences, Gene ontology, hidden Markov model, Evolutionary History, Genome, Nucleic Acids, Protein Function, Computer User Interface Design, Biological Process, Internet, and Lateral Gene Transfer
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Research Interests: Water Purification, Proteomics, Gene expression, Multidisciplinary, Nature, and 15 moreSequence alignment, Genome Analysis, Chromium, Electron Transport, Plasmids, Metals, Protein Sequence Analysis, Metal ion, Genome sequence, Species Specificity, Amino Acid Sequence, Open Reading Frame, Organic Chemicals, Shewanella, and Molecular Sequence Data
φCbK is a B3 morphotype bacteriophage of the Siphoviridae family that infects Caulobacter crescentus , the preeminent model system for bacterial cell cycle studies. The last 4 decades of research with φCbK as a genetic and cytological... more
φCbK is a B3 morphotype bacteriophage of the Siphoviridae family that infects Caulobacter crescentus , the preeminent model system for bacterial cell cycle studies. The last 4 decades of research with φCbK as a genetic and cytological tool to study the biology of the host warrant an investigation of the phage genome composition. Herein, we report the complete genome sequence of φCbK and highlight unusual features that emerged from its annotation. The complete genome analysis of the φCbK phage provides new insight into its characteristics and potential interactions with its Caulobacter crescentus host, setting the stage for future functional studies with φCbK.
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The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames... more
The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synt...
Research Interests: Genetics, Microbiology, Genomics, Bacteriology, Comparative Genomics, and 15 moreBiology, DNA replication, Medicine, Biological Sciences, GC content, Genome, Enzyme, Amino Acid Profile, Genome sequence, Host Range, Amino Acid Sequence, Open Reading Frame, Bacteriophage, Molecular Sequence Data, and Medical and Health Sciences
Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order... more
Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic var...
Research Interests: Immune response, Bacteriology, Polymorphism, Biology, Medicine, and 15 moreBiological Sciences, Phylogeny, Humans, Sequence alignment, Mycobacterium tuberculosis, Genome, Gene Polymorphism, Genome Comparison, Single Nucleotide Polymorphism, Genetic variation, Gene Family, Genetic Variability, Phospholipase C, Molecular Sequence Data, and Medical and Health Sciences
Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes... more
Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis . Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial...
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The genomes of the two closely related freshwater thermophilic cyanobacteria Synechococcus sp. strain JA-3-3Ab and Synechococcus sp. strain JA-2-3B′a(2-13) each host several families of insertion sequences (ISSoc families) at various copy... more
The genomes of the two closely related freshwater thermophilic cyanobacteria Synechococcus sp. strain JA-3-3Ab and Synechococcus sp. strain JA-2-3B′a(2-13) each host several families of insertion sequences (ISSoc families) at various copy numbers, resulting in an overall high abundance of insertion sequences in the genomes. In addition to full-length copies, a large number of internal deletion variants have been identified. ISSoc2 has two variants (ISSoc2∂-1 and ISSoc2∂-2) that are observed to have multiple near-exact copies. Comparison of environmental metagenomic sequences to the Synechococcus genomes reveals novel placement of copies of ISSoc2, ISSoc2∂-1, and ISSoc2∂-2. Thus, ISSoc2∂-1 and ISSoc2∂-2 appear to be active nonautonomous mobile elements derived by internal deletion from ISSoc2. Insertion sites interrupting genes that are likely critical for cell viability were detected; however, most insertions either were intergenic or were within genes of unknown function. Most nove...
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A new grass carp reovirus strain, tentatively named GCReV-109, was isolated in Hubei, China, and its complete genome sequence was determined. The genome contained 11 double-stranded RNA segments (S1-S11) covering 24,620 base pairs. All of... more
A new grass carp reovirus strain, tentatively named GCReV-109, was isolated in Hubei, China, and its complete genome sequence was determined. The genome contained 11 double-stranded RNA segments (S1-S11) covering 24,620 base pairs. All of the segments had conserved terminal nucleotides, with GUAA(U)/CU at the 5' end and UCAUC at the 3' end. Protein sequence comparison showed that GCReV-109 was most closely related to GCRV-GD108 and shared 96.6-99.5 % protein sequence identity but only shared 16.7-46.1 and 15.1-45.4 % identity with GCRV-873 and HGDRV, respectively. Phylogenetic analysis showed that grass carp reovirus strains in China can be divided into three genotypes. Further analysis revealed homology between the GCRV-109 VP56 and HGDRV VP55 proteins, as well as GCReV-109 NS38, GCRV-873 NS38, and HGDRV VP39. The results of these comparisons also indicated that the homology between viruses was not necessarily linked to their geographical distribution. Our study will help in recognizing and understanding the genome structure and genetic diversity of grass carp reovirus.
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The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria , the Cyanobacteria , and the Fungi. The... more
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria , the Cyanobacteria , and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N 2 fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class...
Research Interests: Microbiology, Biology, Cyanobacteria, Carbon Cycle, Fungi, and 15 moreMedicine, Applied, Applied Environmental Microbiology, Bacteria, Iron, Genome, Microorganism, Metabolic rate, Carbohydrate metabolism, Large classes, Carbon Source, Macrolides, Molecular Sequence Data, Major Facilitator Superfamily, and High Molecular Weight
ABSTRACTInsertion sequences (ISs) are simple mobile genetic elements capable of relocating within a genome. Through this transposition activity, they are known to create mutations which are mostly deleterious to the cell, although... more
ABSTRACTInsertion sequences (ISs) are simple mobile genetic elements capable of relocating within a genome. Through this transposition activity, they are known to create mutations which are mostly deleterious to the cell, although occasionally they are beneficial. Two closely related isolates of thermophilicSynechococcusspecies from hot spring microbial mats are known to harbor a large number of diverse ISs. To explore the mechanism of IS acquisition within natural populations and survival in the face of high IS abundance, we examined IS content and location in natural populations ofSynechococcusby comparing metagenomic data to the genomes of fully sequenced cultured isolates. The observed IS distribution in the metagenome was equivalent to the distribution in the isolates, indicating that the cultured isolates are appropriate models for the environmental population. High sequence conservation between IS families shared between the two isolates suggests that ISs are able to move bet...
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The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic... more
The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae , the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for ≈80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-...
Research Interests: Open Access, Design Research, Comparative Genomics, Biology, Medicine, and 15 moreGene expression, Multidisciplinary, Phylogeny, Sequence alignment, Genome Analysis, Genome, Genetic variation, Genome sequence, Amino Acid Sequence, Base Sequence, Genetic Variability, Group B Streptococcus, Multilocus sequence typing, Group A Streptococcus, and Molecular Sequence Data
The paper examines the capital structure decision of 3,432 US companies in the year 2006 and 2011. The paper employs quantile regression to explore the predictions of the trade-off and pecking order models. We find evidence of... more
The paper examines the capital structure decision of 3,432 US companies in the year 2006 and 2011. The paper employs quantile regression to explore the predictions of the trade-off and pecking order models. We find evidence of heterogeneity in the capital structure and the determinants of capital structure. We find the data more consistent with the trade-off theory than the pecking order theory in 2006 but find that only economic conditions matter in 2011.
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The novel fungal strain, Fusarium sp. strain DS 682, was isolated from the rhizosphere of the perennial grass, Bouteloua gracilis , at the Konza Prairie Biological Station in Kansas. This fungal strain is common across North American... more
The novel fungal strain, Fusarium sp. strain DS 682, was isolated from the rhizosphere of the perennial grass, Bouteloua gracilis , at the Konza Prairie Biological Station in Kansas. This fungal strain is common across North American grasslands and is resilient to environmental fluctuations. The draft genome is estimated to be 97.2% complete.
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To enable an in-depth survey of the metabolic potential of complex soil microbiomes, we performed ultra-deep metagenome sequencing, collecting >1 Tb of sequence data from three grassland soils representing different precipitation... more
To enable an in-depth survey of the metabolic potential of complex soil microbiomes, we performed ultra-deep metagenome sequencing, collecting >1 Tb of sequence data from three grassland soils representing different precipitation regimes.
Background: Technological advances in sequencing, assembly and segregation of resulting contigs into species-specific bins has enabled the reconstruction of individual genomes from environmental metagenomic data sets. Though a powerful... more
Background: Technological advances in sequencing, assembly and segregation of resulting contigs into species-specific bins has enabled the reconstruction of individual genomes from environmental metagenomic data sets. Though a powerful technique, it is shadowed by an inability to truly determine whether assembly and binning techniques are accurate, specific, and sensitive due to a lack of complete reference genome sequences against which to check the data. Errors in genome reconstruction, such as missing or mis-attributed activities, can have a detrimental effect on downstream metabolic and ecological modeling, and thus it is important to assess the accuracy of the process. Methods: We compared genomes reconstructed from metagenomic data to complete genome sequences of 10 organisms isolated from the same community to identify regions not captured by typical binning techniques. The nucleotide content, as %G+C and tetranucleotide frequencies, and sequence redundancy within both the ge...
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Harms, Craig A., Mark A. Babcock, Steven R. McClaran, David F. Pegelow, Glenn A. Nickele, William B. Nelson, and Jerome A. Dempsey.Respiratory muscle work compromises leg blood flow during maximal exercise. J. Appl. Physiol.82(5):... more
Harms, Craig A., Mark A. Babcock, Steven R. McClaran, David F. Pegelow, Glenn A. Nickele, William B. Nelson, and Jerome A. Dempsey.Respiratory muscle work compromises leg blood flow during maximal exercise. J. Appl. Physiol.82(5): 1573–1583, 1997.—We hypothesized that during exercise at maximal O2 consumption (V˙o 2 max), high demand for respiratory muscle blood flow (Q˙) would elicit locomotor muscle vasoconstriction and compromise limb Q˙. Seven male cyclists (V˙o 2 max 64 ± 6 ml ⋅ kg−1 ⋅ min−1) each completed 14 exercise bouts of 2.5-min duration atV˙o 2 max on a cycle ergometer during two testing sessions. Inspiratory muscle work was either 1) reduced via a proportional-assist ventilator, 2) increased via graded resistive loads, or 3) was not manipulated (control). Arterial (brachial) and venous (femoral) blood samples, arterial blood pressure, leg Q˙ (Q˙legs; thermodilution), esophageal pressure, and O2 consumption (V˙o 2) were measured. Within each subject and across all subje...
Research Interests: Medicine, Biological Sciences, Humans, Epinephrine, Blood Pressure, and 15 moreApplied, Male, Heart rate, Applied Physiology, Respiration, Norepinephrine, Respiratory Muscles, Oxygen, Adult, Leg, Reproducibility of Results, Sympathetic Nervous System, Oxygen Consumption, Medical and Health Sciences, and physical exertion
Racial/ethnic disparities in the associations of body fatness with hormones and metabolic factors remain poorly understood. Therefore, we evaluated whether the associations of overall and central body fatness with circulating sex steroid... more
Racial/ethnic disparities in the associations of body fatness with hormones and metabolic factors remain poorly understood. Therefore, we evaluated whether the associations of overall and central body fatness with circulating sex steroid hormones and metabolic factors differ by race/ethnicity. Data from 1,243 non-Hispanic white (NHW), non-Hispanic black (NHB) and Mexican-American (MA) adult men in the third national health and nutrition examination survey (NHANES III) were analyzed. Waist circumference (central body fatness) was measured during the physical examination. Percent body fat (overall body fatness) was calculated from bioelectrical impedance. Associations were estimated by using weighted linear regression models to adjust the two measures of body fatness for each other. Waist circumference, but not percent body fat was inversely associated with total testosterone and SHBG in all three racial/ethnic groups after their mutual adjustment (all P < 0.0001). Percent body fat...
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Hyporheic zones (HZ) are active biogeochemical regions where groundwater and surface water mix. N transformations in HZ sediments were investigated in columns with a focus on understanding how the dynamic changes in groundwater and... more
Hyporheic zones (HZ) are active biogeochemical regions where groundwater and surface water mix. N transformations in HZ sediments were investigated in columns with a focus on understanding how the dynamic changes in groundwater and surface water mixing affect microbial community and its biogeochemical function with respect to N transformations. The results indicated that denitrification, DNRA, and nitrification rates and products changed quickly in response to changes in water and sediment chemistry, fluid residence time, and groundwater-surface water exchange. These changes were accompanied by the zonation of denitrification functional genes along a 30 cm advective flow path after a total of 6 days' elution of synthetic groundwater with fluid residence time >9.8 h. The shift of microbial functional potential toward denitrification was correlated with rapid NO3(-) reduction collectively affected by NO3(-) concentration and fluid residence time, and was resistant to short-term...
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Temperature is a key environmental driver of Anopheles mosquito population dynamics; understanding its central role is important for these malaria vectors. Mosquito population responses to temperature fluctuations, though important across... more
Temperature is a key environmental driver of Anopheles mosquito population dynamics; understanding its central role is important for these malaria vectors. Mosquito population responses to temperature fluctuations, though important across the life history, are poorly understood at a population level. We used stage-structured, temperature-dependent delay-differential equations to conduct a detailed exploration of the impacts of diurnal and annual temperature fluctuations on mosquito population dynamics. The model allows exploration of temperature-driven temporal changes in adult age structure, giving insights into the population's capacity to vector malaria parasites. Because of temperature-dependent shifts in age structure, the abundance of potentially infectious mosquitoes varies temporally, and does not necessarily mirror the dynamics of the total adult population. In addition to conducting the first comprehensive theoretical exploration of fluctuating temperatures on mosquito...
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A general method for the calculation of distribution of demagnetization field in paramagnetic materials is described, and the demagnetization field is calculated for samples with spherical geometries. The results show high non-uniformity... more
A general method for the calculation of distribution of demagnetization field in paramagnetic materials is described, and the demagnetization field is calculated for samples with spherical geometries. The results show high non-uniformity for the demagnetization field inside the sample depending on the sample aspect ratio and the direction of the externally applied magnetic field.
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Policy issues facing electric utilities, consumers, and Federal and state agencies were analyzed. Conclusions are: (1) Demand growth should proceed at a lesser rate than in the past. The 1980 consumption may be 2.2 trillion kWh, rather... more
Policy issues facing electric utilities, consumers, and Federal and state agencies were analyzed. Conclusions are: (1) Demand growth should proceed at a lesser rate than in the past. The 1980 consumption may be 2.2 trillion kWh, rather than the 3.1 trillion kWh projected by the Natural Electric Reliability Councils. (2) Conservation programs should be continued and expanded, and applied to
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Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several... more
Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. "Housekeeping" genes and genes for biosynthesis of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose...
The Asian citrus psyllid (ACP) Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is the insect vector of the fastidious bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening disease, or Huanglongbing... more
The Asian citrus psyllid (ACP) Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is the insect vector of the fastidious bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening disease, or Huanglongbing (HLB). The widespread invasiveness of the psyllid vector and HLB in citrus trees worldwide has underscored the need for non-traditional approaches to manage the disease. One tenable solution is through the deployment of RNA interference technology to silence protein-protein interactions essential for ACP-mediated CLas invasion and transmission. To identify psyllid interactor-bacterial effector combinations associated with psyllid-CLas interactions, cDNA libraries were constructed from CLas-infected and CLas-free ACP adults and nymphs, and analyzed for differential expression. Library assemblies comprised 24,039,255 reads and yielded 45,976 consensus contigs. They were annotated (UniProt), classified using Gene Ontology, and subjected to in silico express...
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Abstract We present results from a comparison between time and frequency domain types of three-dimensional, commercial, finite element solvers of Maxwellpsilas equations. Both solvers are part of the Microwave Studioreg (MWS) suite of... more
Abstract We present results from a comparison between time and frequency domain types of three-dimensional, commercial, finite element solvers of Maxwellpsilas equations. Both solvers are part of the Microwave Studioreg (MWS) suite of tools, available from computer ...
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In 2012, dozens of patients of Exeter Hospital in New Hampshire contracted new hepatitis C infections that were tracked back to a cardiac technician who ultimately confessed to drug diversion. A multi-state epidemiological investigation... more
In 2012, dozens of patients of Exeter Hospital in New Hampshire contracted new hepatitis C infections that were tracked back to a cardiac technician who ultimately confessed to drug diversion. A multi-state epidemiological investigation of hepatitis C cases occurring in multiple hospitals revealed that the technician had been fired from prior institutions due to similar drug diversion activity about which Exeter Hospital had not been notified. In this article we highlight the institutional ethical issues raised by this outbreak, and propose a national centralized reporting system to support institutional fulfillment of the ethical obligation to protect the health of patients by preventing such nosocomial outbreaks.
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More than 1.2 million Americans live with absence of a limb. Modern prosthetic limbs, talented prosthetists, and enthusiastic therapists enable many motivated individuals with absent limbs to pursue very active lifestyles. This article... more
More than 1.2 million Americans live with absence of a limb. Modern prosthetic limbs, talented prosthetists, and enthusiastic therapists enable many motivated individuals with absent limbs to pursue very active lifestyles. This article presents a case report of a first-class pilot who had experienced a traumatic above-knee amputation and includes a brief review of recent U.S. limb loss and amputation data, as well as aeromedical issues associated with amputation.
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... It extends southward to Augustine Island (Burbank, 1977). The normal movement of water from the east to the west south of the Forelands can be expedited by the interaction of the tidal currents with the coastline configuration. ...
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Is an ideal of distributive justice, strong enough to require some redistribution, philosophically defensible? More, could such an ideal be made politically attractive? While it looks as if redistribution inevitably conflicts with... more
Is an ideal of distributive justice, strong enough to require some redistribution, philosophically defensible? More, could such an ideal be made politically attractive? While it looks as if redistribution inevitably conflicts with property rights, and while property rights have great popular and political appeal, it is argued here that property rights are, in fact, hard to defend philosophically. And what can be defended has indeterminate, even open ended, content. Indeed, a strong argument for redistribution is that, unless property is qualified in such a way that it does not automatically rule out redistributive taxation, property cannot be defended.