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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Tracking ebolavirus genomic drift with a resequencing microarray

Filoviruses are emerging pathogens that cause acute fever with high fatality rate and present a global public health threat. During the 2013–2016 Ebola virus outbreak, genome sequencing allowed the study of virus evolution, mutations affecting pathogenicity and infectivity, and tracing the viral spread. In 2018, early sequence identification of the Ebolavirus as EBOV in the Democratic Republic of the Congo supported the use of an Ebola virus vaccine. However, field-deployable sequencing methods are needed to enable a rapid public health response. Resequencing microarrays (RMA) are a targeted method to obtain genomic sequence on clinical specimens rapidly, and sensitively, overcoming the need for extensive bioinformatic analysis. This study presents the design and initial evaluation of an ebolavirus resequencing microarray (Ebolavirus-RMA) system for sequencing the major genomic regions of four Ebolaviruses that cause disease in humans. The design of the Ebolavirus-RMA system is described and evaluated by sequencing repository samples of three Ebolaviruses and two EBOV variants. The ability of the system to identify genetic drift in a replicating virus was achieved by sequencing the ebolavirus glycoprotein gene in a recombinant virus cultured under pressure from a neutralizing antibody. Comparison of the Ebolavirus-RMA results to the Genbank database sequence file with the accession number given for the source RNA and Ebolavirus-RMA results compared to Next Generation Sequence results of the same RNA samples showed up to 99% agreement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Development of a Protein-based Human Identification Capability from a Single Hair

Shed human hair (lacking root nuclear DNA) frequently contributes important information to forensic investigations involving human identification. Detection of genetic variation observed in amino acid sequences of hair proteins provides a new suite of identity markers that augment microscopic hair analysis and mitochondrial DNA sequencing. In this study, a new method that completely dissolves single hairs using a combination of heat, ultrasonication, and surfactants was developed. Dissolved proteins were digested and genetically variant peptide (GVP) profiles were obtained for single hairs (25 mm) via high–resolution nanoflow liquid chromatography–based mass spectrometry and a novel exome–driven bioinformatic approach. Overall, 6519 unique peptides were identified and a total of 57 GVPs were confirmed. Random match probabilities ranged between 2.6 × 10 –2 and 6.0 × 10 –9 . In conclusion, the new bioinformatic strategy and ability to analyze GVPs in forensically relevant samples sizes demonstrate applicability of this approach to distinguish individuals in forensic contexts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Analysis of electron capture process in charge pumping sequence using time domain measurements

A method for analyzing the electron capture process in the charge pumping (CP) sequence is proposed and demonstrated. The method monitors the electron current in the CP sequence in time domain. This time-domain measurements enable us to directly access the process of the electron capture to the interface defects, which are obscured in the conventional CP method. Using the time-domain measurements, the rise time dependence of the capture process is systematically investigated. We formulate the capture process based on the rate equation and derive an analytic form of the current due to the electron capture to the defects. Based on the formula, the experimental data are analyzed and the capture cross section is obtained. In addition, the time-domain data unveil that the electron capture process completes before the electron channel opens, or below the threshold voltage in a low frequency range of the pulse.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2012

Strategic Sequencing for State Distributed PV Policies: A Quantitative Analysis of Policy Impacts and Interactions

State and local policymakers show increasing interest in spurring the development of customer-sited distributed generation (DG), in particular solar photovoltaic (PV) markets. Prompted by that interest, this analysis examines the use of state policy as a tool to support the development of a robust private investment market. This analysis builds on previous studies that focus on government subsidies to reduce installation costs of individual projects and provides an evaluation of the impacts of policies on stimulating private market development.

14 SOLAR ENERGY↗
DOE OSTI2021

Analysis of Previously Classified White Dwarf–Main-sequence Binaries Using Data from the APOGEE Survey

We present analyses of near-infrared spectroscopic data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) survey for 45 previously confirmed or candidate white dwarf–main-sequence (WDMS) binaries identified by the optical Sloan Digital Sky Survey (SDSS) and LAMOST surveys. Among these 45 systems, we classify three as having red giant primaries in the LAMOST sample and 14 as young stellar object contaminants in the photometrically identified SDSS sample. From among the subsample of 28 systems that we confirm to have MS primaries, we derive and place limits on orbital periods and velocity amplitudes for 14. Seven systems have significant velocity variations that warrant a post-common-envelope (PCE) binary classification, four of which are newly classified, three of which are newly confirmed, and five for which we can derive full orbital parameters. If confirmed, one of these newly discovered systems (2M14544500+4626456) will have the second-longest orbital period reported for a typical compact PCE WDMS binary (P = 15.1 days). In addition to the seven above, we also recover and characterize with APOGEE data the well-known PCE WDMS systems EG UMa and HZ 9. We also investigate the overall metallicity distribution of the WDMS sample, which is a parameter space not often explored for these systems. Of note, we find one system (2M14244053+4929580) to be extremely metal-poor ([Fe/H] = − 1.42) relative to the rest of the near-solar sample. Additionally, the PCE systems in our sample are found to be, on average, higher in metallicity than their wide-binary counterparts, though we caution that with this small number of systems, the sample may not be representative of the overall distribution of WDMS systems.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Host analysis-guided selection and targeted engineering (HASTE) of Lipomyces tetrasporus for the conversion of CO2-derived feedstocks

Efficient and cost-competitive bioproduction calls for utilizing CO2-derived feedstocks, such as products from electro-reduction of CO2 and hydrolysate from lignocellulosic biomass. However, efficiently using all their carbon components, including acetate, glucose, and xylose, remains a challenge. Here, we characterize Lipomyces tetrasporus, a novel, robust yeast strain capable of effectively assimilating these carbon sources. We used an integrated systems biology approach combining ¹³C metabolic flux analysis, dynamic labeling experiments, and RNA sequencing. We conducted the first metabolic flux analysis for glucose, xylose, and acetate catabolism in this species. Dynamic labeling revealed a highly active TCA cycle during acetate metabolism, evidenced by rapid citrate and malate accumulation. The strain demonstrated strong NADH/NADPH production and acetyl-CoA synthase activity. Using insights and gene targets from this analysis, we engineered L. tetrasporus for malate production. The engineered strain produced 7.5 g/L malic acid (0.25 g/g yield) in shake flasks with glucose-acetate media and 28.8 g/L malic acid at a yield of 0.20 g/g in fed-batch mode with corn-stover hydrolysate. Together, these insights and rational strain engineering establish L. tetrasporus as a versatile, Crabtree-negative platform that is an energy-CO2-bioproduction nexus for channeling CO2 carbon into value-added bioproducts.

Xiao, Zhengyang↗
DOE OSTI2024

Genomic factors shaping codon usage across the Saccharomycotina subphylum

Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. It has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. We characterized codon usage across 1,154 strains from 1,051 species from the fungal subphylum Saccharomycotina to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns. We found a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is distinct between the 12 orders to such a degree that yeasts can be classified with an accuracy >90% using a machine learning algorithm. We also characterized the degree to which codon usage bias is impacted by translational selection. We found it was influenced by a combination of features, including the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that avoidance of the CGN codons is associated with a decline in arginine tRNA function. Consistent with previous findings, codon usage bias within the Saccharomycotina is shaped by genomic features and GC bias. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Cost-Effectiveness Analysis of Preoperative Versus Postoperative Radiation Therapy in Extremity Soft Tissue Sarcoma

Purpose: Surgery combined with radiation therapy (RT) is the cornerstone of multidisciplinary management of extremity soft tissue sarcoma (STS). Although RT can be given in either the preoperative or the postoperative setting with similar local recurrence and survival outcomes, the side effect profiles, costs, and long-term functional outcomes are different. The aim of this study was to use decision analysis to determine optimal sequencing of RT with surgery in patients with extremity STS. Methods and Materials: A cost-effectiveness analysis was conducted using a state transition Markov model, with quality-adjusted life years (QALYs) as the primary outcome. A time horizon of 5 years, a cycle length of 3 months, and a willingness-to-pay threshold of $50,000/QALY was used. One-way deterministic sensitivity analyses were performed to determine the thresholds at which each strategy would be preferred. The robustness of the model was assessed by probabilistic sensitivity analysis. Results: Preoperative RT is a more cost-effective strategy ($26,633/3.00 QALYs) than postoperative RT ($28,028/2.86 QALYs) in our base case scenario. Preoperative RT is the superior strategy with either 3-dimensional conformal RT or intensity-modulated RT. One-way sensitivity analyses identified the relative risk of chronic adverse events as having the greatest influence on the preferred timing of RT. The likelihood of preoperative RT being the preferred strategy was 82% on probabilistic sensitivity analysis. Conclusions: Preoperative RT is more cost effective than postoperative RT in the management of resectable extremity STS, primarily because of the higher incidence of chronic adverse events with RT in the postoperative setting.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2015

Scalable Parallel Methods for Analyzing Metagenomics Data at Extreme Scale

The field of bioinformatics and computational biology is currently experiencing a data revolution. The exciting prospect of making fundamental biological discoveries is fueling the rapid development and deployment of numerous cost-effective, high-throughput next-generation sequencing technologies. The result is that the DNA and protein sequence repositories are being bombarded with new sequence information. Databases are continuing to report a Moore’s law-like growth trajectory in their database sizes, roughly doubling every 18 months. In what seems to be a paradigm-shift, individual projects are now capable of generating billions of raw sequence data that need to be analyzed in the presence of already annotated sequence information. While it is clear that data-driven methods, such as sequencing homology detection, are becoming the mainstay in the field of computational life sciences, the algorithmic advancements essential for implementing complex data analytics at scale have mostly lagged behind. Sequence homology detection is central to a number of bioinformatics applications including genome sequencing and protein family characterization. Given millions of sequences, the goal is to identify all pairs of sequences that are highly similar (or “homologous”) on the basis of alignment criteria. While there are optimal alignment algorithms to compute pairwise homology, their deployment for large-scale is currently not feasible; instead, heuristic methods are used at the expense of quality. In this dissertation, we present the design and evaluation of a parallel implementation for conducting optimal homology detection on distributed memory supercomputers. Our approach uses a combination of techniques from asynchronous load balancing (viz. work stealing, dynamic task counters), data replication, and exact-matching filters to achieve homology detection at scale. Results for a collection of 2.56M sequences show parallel efficiencies of ~75-100% on up to 8K cores, representing a time-to-solution of 33 seconds. We extend this work with a detailed analysis of single-node sequence alignment performance using the latest CPU vector instruction set extensions. Preliminary results reveal that current sequence alignment algorithms are unable to fully utilize widening vector registers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structure of the Intermediate Filament-Binding Region of Desmoplakin

Here, desmoplakin (DP) is a cytoskeletal linker protein that connects the desmosomal cadherin/plakoglobin/plakophilin complex to intermediate filaments (IFs). The C-terminal region of DP (DPCT) mediates IF binding, and contains three plakin repeat domains (PRDs), termed PRD-A, PRD-B and PRD-C. Previous crystal structures of PRDs B and C revealed that each is formed by 4.5 copies of a plakin repeat (PR) and has a conserved positively charged groove on its surface. Although PRDs A and B are linked by just four amino acids, B and C are separated by a 154 residue flexible linker, which has hindered crystallographic analysis of the full DPCT. Here we present the crystal structure of a DPCT fragment spanning PRDs A and B, and elucidate the overall architecture of DPCT by small angle X-ray scattering (SAXS) analysis. The structure of PRD-A is similar to that of PRD-B, and the two domains are arranged in a quasi-linear arrangement, and separated by a 4 amino acid linker. Analysis of the B-C linker region using secondary structure prediction and the crystal structure of a homologous linker from the cytolinker periplakin suggests that the N-terminal ~100 amino acids of the linker form two PR-like motifs. SAXS analysis of DPCT indicates an elongated but non-linear shape with R g = 51.5 Å and D max = 178 Å. These data provide the first structural insights into an IF binding protein containing multiple PRDs and provide a foundation for studying the molecular basis of DP-IF interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera ( Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae

Burkholderia sensu lato is a large and complex group, containing pathogenic, phytopathogenic, symbiotic and non-symbiotic strains from a very wide range of environmental (soil, water, plants, fungi) and clinical (animal, human) habitats. Its taxonomy has been evaluated several times through the analysis of 16S rRNA sequences, concantenated 4–7 housekeeping gene sequences, and lately by genome sequences. Currently, the division of this group into Burkholderia , Caballeronia , Paraburkholderia , and Robbsia is strongly supported by genome analysis. These new genera broadly correspond to the various habitats/lifestyles of Burkholderia s.l., e.g., all the plant beneficial and environmental (PBE) strains are included in Paraburkholderia (which also includes all the N 2 -fixing legume symbionts) and Caballeronia , while most of the human and animal pathogens are retained in Burkholderia sensu stricto. However, none of these genera can accommodate two important groups of species. One of these includes the closely related Paraburkholderia rhizoxinica and Paraburkholderia endofungorum , which are both symbionts of the fungal phytopathogen Rhizopus microsporus .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Description and Use of SCALE Sampler Parametric Capability for Engineering Analysis and Optimization

The Sampler sequence was introduced into the SCALE nuclear modeling and simulation suite in SCALE 6.2 to perform uncertainty quantification via random sampling of nuclear data, material number densities, and dimensions. Sampler was expanded with the introduction of a parametric capability in SCALE 6.2.2. This paper discusses input for the Sampler parametric sequence and presents two case studies of analyses performed using the sequence. These case studies include preconceptual design of a package for transporting high assay low-enriched uranium (HALEU) oxide and scoping calculations to support subcritical limit development for a future update of the ANSI/ANS-8.1 (ANS-8.1) standard. The parametric capability within Sampler provides many benefits to analysts. For instance, parametric sweeps are frequently used to identify optimum parameter values as part of safety analysis or system design, but such sweeps can require substantial engineering time or may rely on custom-written scripts or scripts such as Write One, Run Many (or WORM) developed outside of any software quality assurance program. With the parametric capabilities in Sampler, however, a large number of inputs can be generated automatically without recourse to scripting by individual analysts. The parametric capability can also be used in lieu of the CSAS5S search sequence to identify optimum parameters more simply with straightforward inputs and outputs. Sampler can also be used to calculate input parameters from engineering specifications. For example, diameters can be converted to radii, or masses can be used to calculate number densities. Overall, the Sampler parametric capability provides a robust feature within SCALE, eliminating the need for user-developed scripting.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

CovS inactivation reduces CovR promoter binding at diverse virulence factor encoding genes in group A Streptococcus

The control of virulence gene regulator (CovR), also called caspsule synthesis regulator (CsrR), is critical to how the major human pathogen group A Streptococcus fine-tunes virulence factor production. CovR phosphorylation (CovR~P) levels are determined by its cognate sensor kinase CovS, and functional abrogating mutations in CovS can occur in invasive GAS isolates leading to hypervirulence. Presently, the mechanism of CovR-DNA binding specificity is unclear, and the impact of CovS inactivation on global CovR binding has not been assessed. Thus, we performed CovR chromatin immunoprecipitation sequencing (ChIP-seq) analysis in the emm1 strain MGAS2221 and its CovS kinase deficient derivative strain 2221-CovS-E281A. We identified that CovR bound in the promoter regions of nearly all virulence factor encoding genes in the CovR regulon. Additionally, direct CovR binding was observed for numerous genes encoding proteins involved in amino acid metabolism, but we found limited direct CovR binding to genes encoding other transcriptional regulators. The consensus sequence AATRANAAAARVABTAAA was present in the promoters of genes directly regulated by CovR, and mutations of highly conserved positions within this motif relieved CovR repression of the hasA and MGAS2221_0187 promoters. Analysis of strain 2221-CovS-E281A revealed that binding of CovR at repressed, but not activated, promoters is highly dependent on CovR~P state. CovR repressed virulence factor encoding genes could be grouped dependent on how CovR~P dependent variation in DNA binding correlated with gene transcript levels. Taken together, the data show that CovR repression of virulence factor encoding genes is primarily direct in nature, involves binding to a newly-identified DNA binding motif, and is relieved by CovS inactivation. These data provide new mechanistic insights into one of the most important bacterial virulence regulators and allow for subsequent focused investigations into how CovR-DNA interaction at directly controlled promoters impacts GAS pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

High-Precision Characterization of Seismicity from the 2022 Hunga Tonga-Hunga Ha'apai Volcanic Eruption

The earthquake swarm accompanying the January 2022 Hunga Tonga-Hunga Ha'apai (HTHH) volcanic eruption includes a large number of posteruptive moderate-magnitude seismic events and presents a unique opportunity to use remote monitoring methods to characterize and compare seismic activity with other historical caldera-forming eruptions. We compute improved epicentroid locations, magnitudes, and regional moment tensors of seismic events from this earthquake swarm using regional to teleseismic surface-wave cross correlation and waveform modeling. Precise relative locations of 91 seismic events derived from 59,047 intermediate-period Rayleigh- and Love-wave cross-correlation measurements collapse into a small area surrounding the volcano and exhibit a southeastern time-dependent migration. Regional moment tensors and observed waveforms indicate that these events have a similar mechanism and exhibit a strong positive compensated linear vector dipole component. Precise relative magnitudes agree with regional moment tensor moment magnitude ($M_w$) estimates while also showing that event sizes and frequency increase during the days after the eruption followed by a period of several weeks of less frequent seismicity of a similar size. The combined information from visual observation and early geologic models indicate that the observed seismicity may be the result of a complex series of events that occurred after the explosive eruption on 15 January, possibly involving rapid resupply of the magma chamber shortly after the eruption and additional faulting and instability in the following weeks. In addition, we identify and characterize an $M_w$ 4.5 event five days before the paroxysmal explosion on 15 January, indicating that additional seismic events preceding the main eruption could have been identified with improved local monitoring. As a result, our analysis of the HTHH eruption sequence demonstrates the value of potentially utilizing teleseismic surface-wave cross correlation and waveform modeling methods to assist in the detailed analysis of remote volcanic eruption sequences.

58 GEOSCIENCES↗
DOE OSTI2016

Molecular cloning and expression analysis of cytochrome c oxidase subunit II from Sitophilus zeamais

Cytochrome c oxidase subunit II (COX II) containing a dual core CuA active site is one of the core subunits of mitochondrial Cytochrome c oxidase (Cco), which plays a significant role in the physiological process. In this report, the full-length cDNA of COXII gene was cloned from Sitophilus zeamais, which had an open reading frame (ORF) of 684 bp encoding 227 amino acids residues. The predicted COXII protein had a molecular mass of 26.2 kDa with pI value of 6.37. multiple sequence alignment and phylogenetic analysis indicated that Sitophilus zeamais COXII had high sequence identity with the COXII of other insect species. The gene was subcloned into the expression vector pET-32a, and induced by isopropyl β-D-thiogalactopyranoside (IPTG) in E. coli Transetta (DE3) expression system. Finally the recombinant COXII with 6-His tag was purified using affinity chromatography with Ni{sup 2+}-NTA agarose. Western Blotting (WB) showed the recombinant protein was about 44 kD, and the concentration of fusion protein was 50 μg/mL. UV-spectrophotometer and infrared spectrometer analysis showed that recombinant COXII could catalyze the oxidation of substrate Cytochrome C (Cyt c), and influenced by allyl isothiocyanate (AITC). By using molecular docking method, It was found that a sulfur atom of AITC structure could form a length of 2.9 Å hydrogen bond with Leu-31. These results suggested that tag-free COXII was functional and one of the action sites of AITC, which will be helpful to carry out a point mutation in binding sites for the future research. - Highlights: • A full-length cDNA of COXII was cloned from the Sitophilus zeamais. • We were successfully expressed the recombinant COXII and optimized the expression conditions. • After enterokinase digesting, the tag-free COXII was functional and affected by AITC. • Through the relevant data analysis, The COXII of Sitophilus zeamais might be one of the action sites of AITC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Similarities and differences between variants called with human reference genome HG19 or HG38

Reference genome selection is a prerequisite for successful analysis of next generation sequencing (NGS) data. Current practice employs one of the two most recent human reference genome versions: HG19 or HG38. To date, the impact of genome version on SNV identification has not been rigorously assessed. We conducted analysis comparing the SNVs identified based on HG19 vs HG38, leveraging whole genome sequencing (WGS) data from the genome-in-a-bottle (GIAB) project. First, SNVs were called using 26 different bioinformatics pipelines with either HG19 or HG38. Next, two tools were used to convert the called SNVs between HG19 and HG38. Lastly we calculated conversion rates, analyzed discordant rates between SNVs called with HG19 or HG38, and characterized the discordant SNVs. The conversion rates from HG38 to HG19 (average 95%) were lower than the conversion rates from HG19 to HG38 (average 99%). The conversion rates varied slightly among the various calling pipelines. Around 1.5% SNVs were discordantly converted between HG19 or HG38. The conversions from HG38 to HG19 had more SNVs which failed conversion and more discordant SNVs than the opposite conversion (HG19 to HG38). Most of the discordant SNVs had low read depth, were low confidence SNVs as defined by GIAB, and/or were predominated by G/C alleles (52% observed versus 42% expected). A significant number of SNVs could not be converted between HG19 and HG38. Based on careful review of our comparisons, we recommend HG38 (the newer version) for NGS SNV analysis. To summarize, our findings suggest caution when translating identified SNVs between different versions of the human reference genome.

59 BASIC BIOLOGICAL SCIENCES↗