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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.

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At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Bulk segregant and QTL analysis of maltose metabolism in Saccharomyces eubayanus

This study investigates natural variation in maltose utilization among Saccharomyces eubayanus strains isolated from different tree hosts. An F2 population was generated from a cross between strain QC18 (Quercus-associated) and strain CL467.1 (Nothofagus-associated). Bulk segregant analysis (BSA) was performed on the F2 offspring, and QTL mapping was conducted by whole-genome sequencing of two pools of 30 segregants each, representing the lowest and highest growth in high maltose concentrations. For QTL analysis, the parental strains QC18 and CL467.1 were also sequenced.

evolutionary plasticity↗
DOE OSTI2024

Site-specific acetylation of polynucleotide kinase 3'-phosphatase regulates its distinct role in DNA repair pathways

Mammalian polynucleotide kinase 3'-phosphatase (PNKP), a DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, is involved in multiple DNA repair pathways, including base excision (BER), single-strand break (SSBR), and double-strand break repair (DSBR). However, little is known as to how PNKP functions in such diverse repair processes. Here we report that PNKP is acetylated at K142 (AcK142) by p300 constitutively but at K226 (AcK226) by CBP, only after DSB induction. Co-immunoprecipitation analysis using AcK142 or AcK226 PNKP-specific antibodies showed that AcK142-PNKP associates only with BER/SSBR, and AcK226 PNKP with DSBR proteins. Despite the modest effect of acetylation on PNKP’s enzymatic activity in vitro, cells expressing non-acetylable PNKP (K142R or K226R) accumulated DNA damage in transcribed genes. Intriguingly, in striatal neuronal cells of a Huntington's Disease (HD)-based mouse model, K142, but not K226, was acetylated. This is consistent with the reported degradation of CBP, but not p300, in HD cells. Moreover, transcribed genomes of HD cells progressively accumulated DSBs. Chromatin-immunoprecipitation analysis demonstrated the association of Ac-PNKP with the transcribed genes, consistent with PNKP’s role in transcription-coupled repair. Thus, our findings demonstrate that acetylation at two lysine residues, located in different domains of PNKP, regulates its distinct role in BER/SSBR versus DSBR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2

To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Additionally, based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10 -3 substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola

Anthracnose leaf blight (ALB) is an economically important disease of sorghum [Sorghum bicolor (L.) Moench] caused by the fungal pathogen Colletotrichum sublineola Henn. ex Sacc. & Trotter. Although qualitative and quantitative resistance have been identified for ALB, the usefulness of resistance loci differs depending on the pathogen pathotype. Identifying resistance effective against unique pathogen pathotypes is critical to managing ALB, as the disease is managed primarily through the deployment of host resistance. We isolated C. sublineola from ALB-infected leaves collected in Illinois and found that the strain was a novel pathotype, as it produced a unique combination of virulence against a set of differential lines. Using this isolate, we inoculated 579 temperate-adapted sorghum conversion lines in 2019 and 2020. We then conducted a genome-wide association study (GWAS) and a metabolic pathway analysis using the Pathway Associated Study Tool (PAST). We identified 47 significant markers distributed across all chromosomes except chromosome 8. We identified 32 candidate genes based on physical proximity with significant markers, some of which have a known role in host defense. We identified 47 pathways associated with ALB resistance, indicating a role for secondary metabolism in defense to ALB. Our results are important to improve the understanding of the genetic basis of ALB resistance in sorghum and highlight the importance of developing durable resistance to ALB.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale

The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota

Abstract The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

SSGUI v1.0

SSGUI is a web-based application that integrates the integrative genomics browser (IGV) with upstream alignment pipelines enabling rapid analysis of a batch of next-generation sequencing (NGS) samples. The input to SSGUI is an NGS file system directory that is organized by experiment and reference sequence. The output is an online dashboard containing various sequencing statistics for each sample and an integrated IGV plugin enabling rapid analysis of aligned NGS reads.

Kulawik, Mark↗
DOE OSTI2020

yippee like 3 (ypel3) is a novel gene required for myelinating and perineurial glia development

Hypomyelination, a neurological disorder characterized by a decrease in the production of myelin sheets by glial cells, often has no known etiology. Elucidating the genetic causes of hypomyelination provides a better understanding of myelination, as well as means to diagnose, council, and treat patients. Here, we present evidence that YIPPEE LIKE 3 (YPEL3), a gene whose developmental role was previously unknown, is required for central and peripheral glial cell development. We identified a child with a constellation of clinical features including cerebral hypomyelination, abnormal peripheral nerve conduction, hypotonia, areflexia, and hypertrophic peripheral nerves. Exome and genome sequencing revealed a de novo mutation that creates a frameshift in the open reading frame of YPEL3 , leading to an early stop codon. We used zebrafish as a model system to validate that YPEL3 mutations are causative of neuropathy. We found that ypel3 isexpressed in the zebrafish central and peripheral nervous system. Using CRISPR/Cas9 technology, we created zebrafish mutants carrying a genomic lesion similar to that of the patient. Our analysis revealed that Ypel3 is required for specification and migration of myelinating oligodendrocytes, timely exit of the perineurial glial precursors from the central nervous system (CNS), formation of the perineurium, and Schwann cell maturation. Consistent with these observations, zebrafish ypel3 mutants have metabolomic signatures characteristic of oligodendrocyte and Schwann cell differentiation defects, show decreased levels of Myelin basic protein in the central and peripheral nervous system, and develop defasciculated peripheral nerves. Locomotion defects were observed in adult zebrafish ypel3 mutants. These studies demonstrate that Ypel3 is a novel gene required for perineurial cell differentiation and glial myelination.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides

An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of lignocellulosic carbon utilization in R. toruloides and reconstructed the genome-scale metabolic network of R. toruloides . High-quality metabolic network models for model organisms and orthologous protein mapping were used to build a draft metabolic network reconstruction. The reconstruction was manually curated to build a metabolic model using functional annotation and multi-omics data including transcriptomics, proteomics, metabolomics, and RB-TDNA sequencing. The multi-omics data and metabolic model were used to investigate R. toruloides metabolism including lipid accumulation and lignocellulosic carbon utilization. The developed metabolic model was validated against high-throughput growth phenotyping and gene fitness data, and further refined to resolve the inconsistencies between prediction and data. We believe that this is the most complete and accurate metabolic network model available for R. toruloides to date.

09 BIOMASS FUELS↗
DOE OSTI2023

A Re-Evaluation of African Swine Fever Genotypes Based on p72 Sequences Reveals the Existence of Only Six Distinct p72 Groups

The African swine fever virus (ASFV) is currently causing a world-wide pandemic of a highly lethal disease in domestic swine and wild boar. Currently, recombinant ASF live-attenuated vaccines based on a genotype II virus strain are commercially available in Vietnam. With 25 reported ASFV genotypes in the literature, it is important to understand the molecular basis and usefulness of ASFV genotyping, as well as the true significance of genotypes in the epidemiology, transmission, evolution, control, and prevention of ASFV. Historically, genotyping of ASFV was used for the epidemiological tracking of the disease and was based on the analysis of small fragments that represent less than 1% of the viral genome. The predominant method for genotyping ASFV relies on the sequencing of a fragment within the gene encoding the structural p72 protein. Genotype assignment has been accomplished through automated phylogenetic trees or by comparing the target sequence to the most closely related genotyped p72 gene. To evaluate its appropriateness for the classification of genotypes by p72, we reanalyzed all available genomic data for ASFV. We conclude that the majority of p72-based genotypes, when initially created, were neither identified under any specific methodological criteria nor correctly compared with the already existing ASFV genotypes. Based on our analysis of the p72 protein sequences, we propose that the current twenty-five genotypes, created exclusively based on the p72 sequence, should be reduced to only six genotypes. To help differentiate between the new and old genotype classification systems, we propose that Arabic numerals (1, 2, 8, 9, 15, and 23) be used instead of the previously used Roman numerals. Furthermore, we discuss the usefulness of genotyping ASFV isolates based only on the p72 gene sequence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

High throughput, accurate gene annotation through AI and HPC-enabled structural analysis

With the advances in next generation sequencing technologies, the number of sequenced genomes is growing exponentially, resulting in a technology bottleneck for the translation of sequence information into usable hypotheses about the function of each gene. We have proposed leveraging our leadership high-performance computing (HPC) resources to help break this annotation bottleneck. Here we design an HPC-based framework to infer gene function from gene sequence by incorporating information about protein structure and interactions predicted by deep learning approaches. Accurate functional prediction and gene annotation using computational methods will facilitate breakthroughs in the genomic sciences essential to understanding and harnessing life processes in bacteria, fungi and plants. The development and applications of the state-of-the-art deep neural networks to protein structural modeling, interaction prediction, sequence comparison, and quality assessment of protein structural models will be made possible by leadership computational resources. These HPC-enabled bioinformatics and molecular modeling tools will provide powerful insights into molecular functions of genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Extreme dimensions — how big (or small) can tailed phages be?

Bacteriophages (phages), that is, viruses that infect bacteria, represent an extremely diverse, yet under-characterized, group of viruses. Although most known phages harbour genomes that are shorter than 200 kb packaged into capsids with a diameter under 100 Å, more and more ‘extremely large’ phages are being discovered. Early reports of phages with genomes larger than 200 kb defined them as ‘jumbo phages’1. Phylogenetic analysis of these jumbo phages revealed that they form distinct and cohesive groups with multiple independent origins. This suggested that jumbo phages are not merely mistakes or aberrations of smaller phages that got too big, but that large genome size is generally a stable trait. In fact, a larger genome can be advantageous; almost all jumbo phages encode their own specific transcription factors, at least some parts of the replication machinery, and many also have their own tRNA genes, which enables increased independence from their host. Here, large genomes also provide more flexibility in terms of transcription strategy; smaller phage genomes tend to have a strict modular genome structure to increase efficiency, whereas jumbo phage genomes may be much less organized in the absence of a strong selection pressure to maintain a compact genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Trichoderma harzianum transcriptome in response to the nematode Pratylenchus brachyurus

The root-lesion nematode Pratylenchus brachyurus causes extensive damage in several crops of economic importance. Fungi of Trichoderma genus have been highlighted as biopesticide agents in the control of several plant diseases. Although it is already widely used in agriculture, there are few studies, especially at the molecular level, that evaluate T. harzianum in the control of P. brachyurus . The aim of the present study was to investigate how interaction with the nematode P. brachyurus influences gene expression of T. harzianum , by using RNA-Seq analysis. Of the 13,932 predicted genes in the T. harzianum genome, 2,922 (21%) were differentially expressed in the presence of P. brachyurus , in relation to the absence of the nematode. Among the differentially expressed genes, we found genes encoding Carbohydrate Active EnZymes (CAZy), MEROPS peptidases, and proteins related to secondary metabolite synthesis. 118 pathways were identified as related to the biosynthesis of secondary metabolites. Additionally, the analysis identified 136 metabolic pathways related to these differentially expressed genes, among which we highlight: aminobenzoate degradation, xenobiotic metabolism by cytochrome P450, and sesquiterpenoid and triterpenoid biosynthesis. Our results contribute to a better understanding of the response of T. harzianum to the nematode P. bracyurus , the potential for biocontrol by this fungus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

DRAM example narrative

DRAM example narrative DRAM on KBase let's anyone run annotations using DRAM in the cloud. DRAM is an annotation tool that can annotate bacterial, archaeal and viral genomes and distills those annotatios into represetations of the functional genomic potential of those organisms. If you want to read more about DRAM you can check out the GitHub, wiki and journal article. DRAM annotate assemblies In KBase Assembly objects contain nucleotide sequences from genomes or metagenomes. DRAM can predict genes and annotate their function from KBase Assembly objects which may be microbial isolate genomes, metagenome assembled genomes or metagenomes. This is done with the Annotate and Distill Assemblies with DRAM app. This app can also anntoate AssemblySet objects which contain collection of Assembly objects. It also generates a Genome object and a GenomeSet object which can be used for further analysis with other KBase apps. The full annotations and other DRAM files are also available for download in the app.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A single genomic region controls primocane fruiting in tetraploid blackberry

The fresh-market blackberry ( Rubus subgenus Rubus ) industry has expanded dramatically in the past 2 decades, driven in part by improved cultivars. Introgression of the primocane-fruiting (PF; annual flowering) trait into elite germplasm has enabled dual cropping in a single year, season extension, and cultivation in tropical and subtropical regions. Despite its economic performance, the genetic basis of PF is not well understood. It has been proposed that the PF trait is controlled by a major recessive locus, but its genomic location is unclear. Here, a genome-wide association study (GWAS) of 365 tetraploid blackberry genotypes identified a single genomic region on chromosome Ra03 (∼33 Mb) strongly associated with PF. Genetic linkage analysis in a biparental population confirmed that the same interval (32–35 Mb) was linked to the PF phenotype. Ten putative candidate genes were identified in this region. Allele mining using whole-genome resequencing of 17 genotypes highlighted 2 high-priority candidates: a CCCH-type zinc finger gene and an ubiquitin-specific protease gene. Use of an improved Rubus argutus “Hillquist” genome annotation (v1.2) enabled refined variant interpretation, including identification of regulatory 3′ UTR polymorphisms in the zinc finger homolog. Two diagnostic KASP markers (PF1 and PF2), designed from the most significant GWAS SNPs, predicted the PF phenotype with over 96% accuracy in a validation panel of 494 tetraploid blackberries from multiple breeding programs. Together, these results provide the first high-resolution mapping of the PF locus in blackberry, identify candidate genes for flowering regulation in Rubus , and deliver diagnostic markers that can be immediately deployed in breeding programs.

GWAS↗
DOE OSTI2022

The International Space Station Environment Triggers Molecular Responses in Aspergillus niger

Due to immense phenotypic plasticity and adaptability, Aspergillus niger is a cosmopolitan fungus that thrives in versatile environments, including the International Space Station (ISS). This is the first report of genomic, proteomic, and metabolomic alterations observed in A. niger strain JSC-093350089 grown in a controlled experiment aboard the ISS. Whole-genome sequencing (WGS) revealed that ISS conditions, including microgravity and enhanced irradiation, triggered non-synonymous point mutations in specific regions, chromosomes VIII and XII of the JSC-093350089 genome when compared to the ground-grown control. Proteome analysis showed altered abundance of proteins involved in carbohydrate metabolism, stress response, and cellular amino acid and protein catabolic processes following growth aboard the ISS. Metabolome analysis further confirmed that space conditions altered molecular suite of ISS-grown A. niger JSC-093350089. After regrowing both strains on Earth, production of antioxidant—Pyranonigrin A was significantly induced in the ISS-flown, but not the ground control strain. In summary, the microgravity and enhanced irradiation triggered unique molecular responses in the A. niger JSC-093350089 suggesting adaptive responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

Abstract Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Genotype–environment associations across spatial scales reveal the importance of putative adaptive genetic variation in divergence

Abstract Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide‐ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotype–environment associations in the hermit thrush ( Catharus guttatus ), a North American songbird, at broad (across the breeding range) and narrow spatial scales (at a hybrid zone). We begin by building a genoscape or map of genetic variation across the breeding range and find five distinct genetic clusters within the species, with the greatest variation occurring in the western portion of the range. Genotype–environment association analyses indicate higher allelic turnover in the west than in the east, with measures of temperature surfacing as key predictors of putative adaptive genomic variation rangewide. Since broad patterns detected across a species' range represent the aggregate of many locally adapted populations, we investigate whether our broadscale analysis is consistent with a finer scale analysis. We find that top rangewide temperature‐associated loci vary in their clinal patterns (e.g., steep clines vs. fixed allele frequencies) across a hybrid zone in British Columbia, suggesting that the environmental predictors and the associated candidate loci identified in the rangewide analysis are of variable importance in this particular region. However, two candidate loci exhibit strong concordance with the temperature gradient in British Columbia, suggesting a potential role for temperature‐related barriers to gene flow and/or temperature‐driven ecological selection in maintaining putative local adaptation. This study demonstrates how patterns identified at the broad (macrogeographic) scale can be validated by investigating genotype–environment correlations at the local (microgeographic) scale. Furthermore, our results highlight the importance of considering the spatial distribution of putative adaptive variation when assessing population‐level sensitivity to climate change and other stressors.

59 BASIC BIOLOGICAL SCIENCES↗