Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “gene sequencing”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Programming mRNA decay to modulate synthetic circuit resource allocation

Synthetic circuits embedded in host cells compete with cellular processes for limited intracellular resources. Here we show how funnelling of cellular resources, after global transcriptome degradation by the sequence-dependent endoribonuclease MazF, to a synthetic circuit can increase production. Target genes are protected from MazF activity by recoding the gene sequence to eliminate recognition sites, while preserving the amino acid sequence. The expression of a protected fluorescent reporter and flux of a high-value metabolite are significantly enhanced using this genome-scale control strategy. Proteomics measurements discover a host factor in need of protection to improve resource redistribution activity. A computational model demonstrates that the MazF mRNA-decay feedback loop enables proportional control of MazF in an optimal operating regime. Transcriptional profiling of MazF-induced cells elucidates the dynamic shifts in transcript abundance and discovers regulatory design elements. Altogether, our results suggest that manipulation of cellular resource allocation is a key control parameter for synthetic circuit design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates

Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual gene. Such an approach has led to many robustly supported but contradictory phylogenies. A close examination shows that the supermatrix approach often suffers from two shortcomings. The first is that MSA is rarely checked for reliability and, as will be illustrated, can be poor. The second is that, to alleviate the problem of homoplasy at the third codon position of protein-coding genes due to convergent evolution of nucleotide frequencies, phylogeneticists may remove or degenerate the third codon position but may do it improperly and introduce new biases. We performed extensive reanalysis of one of such “big data” sets to highlight these two problems, and demonstrated the power and benefits of correcting or alleviating these problems. Our results support a new group with Xiphosura and Arachnopulmonata (Tetrapulmonata + Scorpiones) as sister taxa. This favors a new hypothesis in which the ancestor of Xiphosura and the extinct Eurypterida (sea scorpions, of which many later forms lived in brackish or freshwater) returned to the sea after the initial chelicerate invasion of land. Our phylogeny is supported even with the original data but processed with a new “principled” codon degeneration. We also show that removing the 1673 codon sites with both AGN and UCN codons (encoding serine) in our alignment can partially reconcile discrepancies between nucleotide-based and AA-based tree, partly because two sequences, one with AGN and the other with UCN, would be identical at the amino acid level but quite different at the nucleotide level.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms

Strain SBT is a new, strictly anaerobic, gram-negative, nonmotile, non-sporeforming, rod-shaped bacterium that degrades benzoate and certain fatty acids in syntrophic association with hydrogen/formate-using microorganisms. Strain SBT produced approximately 3 mol of acetate and 0.6 mol of methane per mol of benzoate in coculture with Methanospirillum hungatei strain JF1. Saturated fatty acids, some unsaturated fatty acids, and methyl esters of butyrate and hexanoate also supported growth of strain SBT in coculture with Desulfovibrio strain G11. Strain SBT grew in pure culture with crotonate, producing acetate, butyrate, caproate, and hydrogen. The molar growth yield was 17 +/- 1 g cell dry mass per mol of crotonate. Strain SBT did not grow with fumarate, iron(III), polysulfide, or oxyanions of sulfur or nitrogen as electron acceptors with benzoate as the electron donor. The DNA base composition of strain SBT was 43.1 mol% G+C. Analysis of the 16 S rRNA gene sequence placed strain SBT in the delta-subdivision of the Proteobacteria, with sulfate-reducing bacteria. Strain SBT was most closely related to members of the genus Syntrophus. The clear phenotypic and genotypic differences between strain SBT and the two described species in the genus Syntrophus justify the formation of a new species, Syntrophus aciditrophicus.

Non-NASA Center↗
DOE OSTI2016

Characterization of Three Novel SXT/R391 Integrating Conjugative Elements ICE Mfu Ind1a and ICE Mfu Ind1b, and ICE Mpr Chn1 Identified in the Genomes of Marinomonas fungiae JCM 18476 T and Marinomonas profundimaris Strain D104

The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476 T (ICE Mfu Ind1a and ICE Mfu Ind1b) and in Marinomonas profundimaris strain D104 (ICE Mpr Chn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICE Mfu Ind1b and ICE Mpr Chn1 were inserted into the genome at 5'-end of an typical host prfC gene, while ICE Mfu Ind1a was inserted at 5'-end of an atypical hipA -like gene. Despite their coexistence, the ICE Mfu Ind1a and ICE Mfu Ind1b were not present in a tandem fashion in the genome of M. fungiae . Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their evolution from a common SXT ancestor. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE into the M. fungiae genome due to mutations. Our analysis showed the presence of 16, 25, and 27 variable genes in the hotspots of ICE Mfu Ind1a, ICE Mfu Ind1b, and ICE Mpr Chn1, respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hot spot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in either of the two ICEs from M. fungiae but were present within a transposon cassette in the HS-1 of the ICE Mpr Chn1 from M. profundimaris . Lastly, our data provided information on the genetic diversity and predicted functions encoded by variable genes present in the hotspot regions of these new ICEs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds

The objectives of this study are to determine the occurrence of antimicrobial resistance (AMR) genes using whole-genome sequence (WGS) of Streptococcus uberis (S. uberis) and Streptococcus dysgalactiae (S. dysgalactiae) isolates, recovered from dairy cows in the Canadian Maritime Provinces. A secondary objective included the exploration of the association between phenotypic AMR and the genomic characteristics (genome size, guanine–cytosine content, and occurrence of unique gene sequences). Initially, 91 isolates were sequenced, and of these isolates, 89 were assembled. Furthermore, 16 isolates were excluded due to larger than expected genomic sizes (>2.3 bp × 1,000 bp). In the final analysis, 73 were used with complete WGS and minimum inhibitory concentration records, which were part of the previous phenotypic AMR study, representing 18 dairy herds from the Maritime region of Canada (1). A total of 23 unique AMR gene sequences were found in the bacterial genomes, with a mean number of 8.1 (minimum: 5; maximum: 13) per genome. Overall, there were 10 AMR genes [ANT(6), TEM-127, TEM-163, TEM-89, TEM-95, Linb, Lnub, Ermb, Ermc, and TetS] present only in S. uberis genomes and 2 genes unique (EF-TU and TEM-71) to the S. dysgalactiae genomes; 11 AMR genes [APH(3'), TEM-1, TEM-136, TEM-157, TEM-47, TetM, bl2b, gyrA, parE, phoP, and rpoB] were found in both bacterial species. Two-way tabulations showed association between the phenotypic susceptibility to lincosamides and the presence of linB (P = 0.002) and lnuB (P < 0.001) genes and the between the presence of tetM (P = 0.015) and tetS (P = 0.064) genes and phenotypic resistance to tetracyclines only for the S. uberis isolates. The logistic model showed that the odds of resistance (to any of the phenotypically tested antimicrobials) was 4.35 times higher when there were >11 AMR genes present in the genome, compared with <7 AMR genes (P < 0.001). The odds of resistance was lower for S. dysgalactiae than S. uberis (P = 0.031). When the within-herd somatic cell count was >250,000 cells/mL, a trend toward higher odds of resistance compared with the baseline category of <150,000 cells/mL was observed. When the isolate corresponded to a post-mastitis sample, there were lower odds of resistance when compared with non-clinical isolates (P = 0.01). The results of this study showed the strength of associations between phenotypic AMR resistance of both mastitis pathogens and their genotypic resistome and other epidemiological characteristics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Geobacter sp. Strain IAE Dihaloeliminates 1,1,2-Trichloroethane and 1,2-Dichloroethane

We report that chlorinated ethanes, including 1,2-dichloroethane (1,2-DCA) and 1,1,2-trichloroethane (1,1,2-TCA), are widespread groundwater contaminants. Enrichment cultures XR DCA and XR TCA derived from river sediment dihaloeliminated 1,2-DCA to ethene and 1,1,2-TCA to vinyl chloride (VC), respectively. The XR TCA culture subsequently converted VC to ethene via hydrogenolysis. Microbial community profiling demonstrated the enrichment of Geobacter 16S rRNA gene sequences in both the XR DCA and XR TCA cultures, and Dehalococcoides mccartyi (Dhc) sequences were only detected in the ethene-producing XR TCA culture. The presence of a novel Geobacter population, designated as Geobacter sp. strain IAE, was identified by the 16S rRNA gene-targeted polymerase chain reaction and Sanger sequencing. Time-resolved population dynamics attributed the dihaloelimination activity to strain IAE, which attained the growth yields of 0.93 ± 0.06 x 10 7 and 1.18 ± 0.14 x 10 7 cells per μmol Cl -1 released with 1,2-DCA and 1,1,2-TCA as electron acceptors, respectively. In contrast, Dhc growth only occurred during VC-to-ethene hydrogenolysis. Our findings discover a Geobacter sp. strain capable of respiring multiple chlorinated ethanes and demonstrate the involvement of a broader diversity of organohalide-respiring bacteria in the detoxification of 1,2-DCA and 1,1,2-TCA.

1,1,2-trichloroethane↗
DOE OSTI2013

Towards uncovering the roles of switchgrass peroxidases in plant processes

Herbaceous perennial plants selected as potential biofuel feedstocks had been understudied at the genomic and functional genomic levels. Recent investments, primarily by the U.S. Department of Energy, have led to the development of a number of molecular resources for bioenergy grasses, such as the partially annotated genome for switchgrass (Panicum virgatum L.), and some related diploid species. In its current version, the switchgrass genome contains 65,878 gene models arising from the A and B genomes of this tetraploid grass. The availability of these gene sequences provides a framework to exploit transcriptomic data obtained from next-generation sequencing platforms to address questions of biological importance. One such question pertains to discovery of genes and proteins important for biotic and abiotic stress responses, and how these components might affect biomass quality and stress response in plants engineered for a specific end purpose. It can be expected that production of switchgrass on marginal lands will expose plants to diverse stresses, including herbivory by insects. Class III plant peroxidases have been implicated in many developmental responses such as lignification and in the adaptive responses of plants to insect feeding. Here, we have analyzed the class III peroxidases encoded by the switchgrass genome, and have mined available transcriptomic datasets to develop a first understanding of the expression profiles of the class III peroxidases in different plant tissues. Lastly, we have identified switchgrass peroxidases that appear to be orthologs of enzymes shown to play key roles in lignification and plant defense responses to hemipterans.

09 BIOMASS FUELS↗
NASA NTRS2022

Tracing the Path of Carbon Export in the Ocean though DNA Sequencing of Individual Sinking Particles

Surface phytoplankton communities were linked with the carbon they export into the deep ocean by comparing 18 S rRNA gene sequence communities from surface seawater and individually isolated sinking particles. Particles were collected in sediment traps deployed at locations in the North Pacific subtropical gyre and the California Current. DNA was isolated from individual particles, bulk-collected trap particles, and the surface seawater. The relative sequence abundance of exported phytoplankton taxa in the surface water varied across functional groups and ecosystems. Of the sequences detected in sinking particles, about half were present in large (>300 μm), individually isolated particles and primarily belonged to taxa with small cell sizes (<50 μm). Exported phytoplankton taxa detected only in bulk trap samples, and thus presumably packaged in the smaller sinking size fraction, contained taxa that typically have large cell sizes (>500 m). The effect of particle degradation on the detectable 18 S rRNA gene community differed across taxa, and differences in community composition among individual particles from the same location largely reflected differences in relative degradation state. Using these data and particle imaging, we present an approach that incorporates genetic diversity into mechanistic models of the ocean's biological carbon pump, which will lead to better quantification of the ocean’s carbon cycle.

Carbon Expert↗
DOE OSTI2015

Thermocrinis jamiesonii sp. nov., a thiosulfate-oxidizing, autotropic thermophile isolated from a geothermal spring

An obligately thermophilic, chemolithotrophic, microaerophilic bacterium, designated strain GBS1T, was isolated from the water column of Great Boiling Spring, Nevada, USA. Thiosulfate was required for growth. Although capable of autotrophy, growth of GBS1T was enhanced in the presence of acetate, peptone, or Casamino acids. Growth occurred at 70-85 °C with an optimum at 80 °C, at pH 6.5-7.75 with an optimum at pH 7.25, at 0.5-8% oxygen with an optimum at 1-2%, and at ≤200 mM sodium chloride. The doubling time under optimal growth conditions was 1.3 hrs, with a final cell density of 6.2±0.5 x 107 cells/mL. Non-motile, rod-shaped cells 1.4-2.4 x 0.4-0.6 µm occurred singly or in pairs. Major cellular fatty acids (>5% of total) were C20:1ω9c (44.8%), C18:0 (26.0%), C16:0 (9.9%) and C20:0 (5.4%). Phylogenetic analysis of the GBS1T 16S rRNA gene sequence indicated an affiliation with Thermocrinis ruber and other Thermocrinis spp., but comparisons of 16S rRNA gene identity (≤97.10%) and in silico estimated DNA-DNA hybridization values (≤18.4%) with Thermocrinis spp. indicate that his strain is distinct from described species. Based on phenotypic, genotypic, and phylogenetic characteristics, the name Thermocrinis jamiesonii sp. nov. is proposed, with GBS1T (= JCM 19133T = DSM 27162T) as the type strain.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2011

Community profiling and gene expression of fungal assimilatory nitrate reductases in agricultural soil

Although fungi contribute significantly to the microbial biomass in terrestrial ecosystems, little is known about their contribution to biogeochemical nitrogen cycles. Agricultural soils usually contain comparably high amounts of inorganic nitrogen, mainly in the form of nitrate. Many studies focused on bacterial and archaeal turnover of nitrate by nitrification, denitrification and assimilation, whereas the fungal role remained largely neglected. To enable research on the fungal contribution to the biogeochemical nitrogen cycle tools for monitoring the presence and expression of fungal assimilatory nitrate reductase genes were developed. To the B100 currently available fungal full-length gene sequences, another 109 partial sequences were added by amplification from individual culture isolates, representing all major orders occurring in agricultural soils. The extended database led to the discovery of new horizontal gene transfer events within the fungal kingdom. The newly developed PCR primers were used to study gene pools and gene expression of fungal nitrate reductases in agricultural soils. The availability of the extended database allowed affiliation of many sequences to known species, genera or families. Energy supply by a carbon source seems to be the major regulator of nitrate reductase gene expression for fungi in agricultural soils, which is in good agreement with the high energy demand of complete reduction of nitrate to ammonium.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2012

Draft Genome Sequences for Two Metal-Reducing Pelosinus fermentans Strains Isolated from a Cr(VI) Contaminated Site and for Type Strain R7

Pelosinus fermentans 16S rRNA gene sequences have been reported from diverse geographical sites since the recent isolation of the type strain. We present the genome sequence of the P. fermentans type strain R7 (DSM 17108) and genome sequences for two new strains with different abilities to reduce iron, chromate, and uranium.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns

Abstract Forest trees may harbor naturally occurring exon disruptive variants (DVs) in their gene sequences, which potentially impact important ecological and economic phenotypic traits. However, the abundance and molecular regulation of these variants remain largely unexplored. Here, 24,420 DVs were identified by screening 1014Populus trichocarpafull genomes. The identified DVs were predominantly heterozygous with allelic frequencies below 5% (only 26% of DVs had frequencies greater than 5%). Using common garden‐grown trees, DVs were assessed for gene expression variation in the developing xylem, revealing that their gene expression can be significantly altered, particularly for homozygous DVs (in the range of 27%–38% of cases depending on the studied common garden). DVs were further investigated for their correlations with 13 wood quality traits, revealing that, among the 148 discovered DV associations, 15 correlated with more than one wood property and six genes had more than one DV in their coding sequences associated with wood traits. Approximately one‐third of DVs correlated with wood property variation also showed significant gene expression variation, confirming their non‐spurious impact. These findings offer potential avenues for targeted introduction of homozygous mutations using tree biotechnology, and while the exact mechanisms by which DVs may directly influence wood formation remain to be unraveled, this study lays the groundwork for further investigation.

Genetics & Heredity↗
DOE OSTI2016

Human transbodies to VP40 inhibit cellular egress of Ebola virus-like particles

A direct acting anti-Ebola agent is needed. VP40, a conserved protein across Ebolavirus (EBOV) species has several pivotal roles in the virus life cycle. Inhibition of VP40 functions would lessen the virion integrity and interfere with the viral assembly, budding, and spread. In this study, cell penetrable human scFvs (HuscFvs) that bound to EBOV VP40 were produced by phage display technology. Gene sequences coding for VP40-bound-HuscFvs were subcloned from phagemids into protein expression plasmids downstream to a gene of cell penetrating peptide, i.e., nonaarginine (R9). By electron microscopy, transbodies from three clones effectively inhibited egress of the Ebola virus-like particles from human hepatic cells transduced with pseudo-typed-Lentivirus particles carrying EBOV VP40 and GP genes. Computerized simulation indicated that the effective HuscFvs bound to multiple basic residues in the cationic patch of VP40 C-terminal domain which are important in membrane-binding for viral matrix assembly and virus budding. The transbodies bound also to VP40 N-terminal domain and L domain peptide encompassed the PTAPPEY (WW binding) motif, suggesting that they might confer VP40 function inhibition through additional mechanism(s). The generated transbodies are worthwhile tested with authentic EBOV before developing to direct acting anti-Ebola agent for preclinical and clinical trials. - Highlights: • Cell penetrable human scFvs (transbodies) to Ebolavirus (EBOV) VP40 were produced. • The transbodies inhibited egress of EBOV-like particles (VLPs) from human hepatocytes. • They interacted with VP40 CTD basic residues important for plasma membrane binding. • And hence interfere with viral matrix assembly and viral progeny budding. • This is the first report on human antibodies that target intracellular EBOV VP40.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

High‐density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe

Abstract Miscanthus is a perennial C 4 grass that has recently become an important bioenergy crop. The efficiency of breeding improved Miscanthus biomass cultivars could be greatly increased by marker‐assisted selection. Thus, a high‐density genetic map is critical to Miscanthus improvement. In this study, a mapping population of 261 F 1 progeny was developed from a cross between two diploid M. sinensis cultivars, ‘Strictus’ and ‘Kaskade’. High‐density genetic maps for the two parents were produced with 3044 newly developed single nucleotide polymorphisms ( SNP s) obtained from restriction site‐associated DNA sequencing, and 138 previously mapped GoldenGate SNP s. The female parent (‘Strictus’) map spanned 1599 cM, with 1989 SNP s on 19 linkage groups, and an average intermarker spacing of 0.8 cM. The length of the male parent (‘Kaskade’) map was 1612 cM, with 1821 SNP s, and an average intermarker spacing of 0.9 cM. The utility of the map was confirmed by locating quantitative trait loci ( QTL ) for the zebra‐striped trait, which was segregating in this population. Three QTL for zebra‐striped presence/absence ( zb1 , zb2 on LG 7, and zb3 on LG 10) and three for zebra‐striped intensity ( zbi1 , zbi2 , zbi3 on LG s 7, 10, 3) were identified. Each allele that caused striping was recessive. Incomplete penetrance was observed for each zb QTL , but penetrance was greatest when two or more zb QTL were homozygous for the causative alleles. Similarly, the intensity of striping was greatest when two or more zbi QTL were homozygous for alleles that conferred the trait. Comparative mapping indicated putative correspondence between zb3 and/or zbi2 on LG 10 to previously sequenced genes conferring zebra stripe in maize and rice. These results demonstrate that the new map is useful for identifying marker–trait associations. The mapped markers will become a valuable community resource, facilitating comparisons among studies and the breeding of Miscanthus .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria , MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon -, Delta -, and Gammaproteobacteria in methane seep ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh

Influenza virus surveillance, poultry outbreak investigations and genomic sequencing were assessed to understand the ecology and evolution of low pathogenicity avian influenza (LPAI) A viruses in Bangladesh from 2007 to 2013. We analyzed 506 avian specimens collected from poultry in live bird markets and backyard flocks to identify influenza A viruses. Virus isolation-positive specimens (n = 50) were subtyped and their coding-complete genomes were sequenced. The most frequently identified subtypes among LPAI isolates were H9N2, H11N3, H4N6, and H1N1. Less frequently detected subtypes included H1N3, H2N4, H3N2, H3N6, H3N8, H4N2, H5N2, H6N1, H6N7, and H7N9. Gene sequences were compared to publicly available sequences using phylogenetic inference approaches. Among the 14 subtypes identified, the majority of viral gene segments were most closely related to poultry or wild bird viruses commonly found in Southeast Asia, Europe, and/or northern Africa. LPAI subtypes were distributed over several geographic locations in Bangladesh, and surface and internal protein gene segments clustered phylogenetically with a diverse number of viral subtypes suggesting extensive reassortment among these LPAI viruses. H9N2 subtype viruses differed from other LPAI subtypes because genes from these viruses consistently clustered together, indicating this subtype is enzootic in Bangladesh. The H9N2 strains identified in Bangladesh were phylogenetically and antigenically related to previous human-derived H9N2 viruses detected in Bangladesh representing a potential source for human infection. In contrast, the circulating LPAI H5N2 and H7N9 viruses were both phylogenetically and antigenically unrelated to H5 viruses identified previously in humans in Bangladesh and H7N9 strains isolated from humans in China. In Bangladesh, domestic poultry sold in live bird markets carried a wide range of LPAI virus subtypes and a high diversity of genotypes. Here these findings, combined with the seven year timeframe of sampling, indicate a continuous circulation of these viruses in the country.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2005

Microbial assessment of cabin air quality on commercial airliners

The microbial burdens of 69 cabin air samples collected from commercial airliners were assessed via conventional culture-dependent, and molecular-based microbial enumeration assays. Cabin air samples from each of four separate flights aboard two different carriers were collected via air-impingement. Microbial enumeration techniques targeting DNA, ATP, and endotoxin were employed to estimate total microbial burden. The total viable microbial population ranged from 0 to 3.6 x10 4 cells per 100 liters of air, as assessed by the ATP-assay. When these same samples were plated on R2A minimal medium, anywhere from 2% to 80% of these viable populations were cultivable. Five of the 29 samples examined exhibited higher cultivable counts than ATP derived viable counts, perhaps a consequence of the dormant nature (and thus lower concentration of intracellular ATP) of cells inhabiting these air cabin samples. Ribosomal RNA gene sequence analysis showed these samples to consist of a moderately diverse group of bacteria, including human pathogens. Enumeration of ribosomal genes via quantitative-PCR indicated that population densities ranged from 5 x 10 1 ' to IO 7 cells per 100 liters of air. Each of the aforementioned strategies for assessing overall microbial burden has its strengths and weaknesses; this publication serves as a testament to the power of their use in concert.

microbe↗