Search NASA⌕ Search

SEARCH · Search NASA

Results for “sequence analysis”

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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Spectroradiometric detection of competitor diatoms and the grazer Poteriochromonas in algal cultures

To address challenges in early detection of pond pests, we have extended a spectroradiometric monitoring method, initially demonstrated for measurement of pigment optical activity and biomass, to the detection of algal competitors and grazers. The method relies upon measurement and interpretation of pond reflectance spectra spanning from the visible into the near-infrared. Reflectance spectra are acquired every 5 min with a multi-channel, fiber-coupled spectroradiometer, providing monitoring of algal pond conditions with high temporal frequency. The spectra are interpreted via numerical inversion of a reflectance model, in which the above-water reflectance is expressed in terms of the absorption and backscatter coefficients of the cultured species, with additional terms accounting for the pigment fluorescence features and for the water-surface reflection of sunlight and skylight. With this method we demonstrate detection of diatoms and the predator Poteriochromonas in outdoor cultures of Nannochloropsis oceanica and Chlorella vulgaris, respectively. Further, the relative strength of these signatures is compared to microscopy and sequencing analysis. Spectroradiometric detection of diatoms is then further assessed on beaker-contained mixtures of Microchloropsis salina with Phaeodactylum tricornutum, Thalassiosira weissflogii, and Thalassiosira pseudonana, respectively, providing an initial evaluation of the sensitivity and specificity of detecting pond competitors.

09 BIOMASS FUELS↗
DOE OSTI2018

A novel lentiviral scFv display library for rapid optimization and selection of high affinity antibodies

Highlights: • We constructed a novel scFv display library based on lentivirus vector. • Stable transduced cell lines were obtained. • Characterization of mutants showed approximately upto three fold increase in antibody affinity. Antibody display libraries have become a popular technique to screen monoclonal antibodies for therapeutic purposes. An important aspect of display technology is to generate an optimization library by changing antibody affinity to antigen through mutagenesis and screening the high affinity antibody. In this study, we report a novel lentivirus display based optimization library antibody in which Agtuzumab scFv is displayed on cell membrane of HEK-293T cells. To generate an optimization library, hotspot mutagenesis was performed to achieve diverse antibody library. Based on sequence analysis of randomly selected clones, library size was estimated approximately to be 1.6 × 10{sup 6}. Lentivirus display vector was used to display scFv antibody on cell surface and flow cytometery was performed to check the antibody affinity to antigen. Membrane bound scFv antibodies were then converted to secreted antibody through cre/loxP recombination. One of the mutant clones, M8 showed higher affinity to antigen in flow cytometery analysis. Further characterization of cellular and secreted scFv through western blot showed that antibody affinity was increased by three fold after mutagenesis. This study shows successful construction of a novel antibody library and suggests that hotspot mutagenesis could prove a useful and rapid optimization tool to generate similar libraries with various degree of antigen affinity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Long-term hindlimb unloading causes a preferential reduction of medullary thymic epithelial cells expressing autoimmune regulator (Aire)

Highlights: • Two-week hindlimb unloading caused persistent reductions of thymocyte number. • Two-week hindlimb unloading did not alter percentage of CD4{sup +}CD8{sup +} cells in thymocytes. • Hindlimb unloading reduced cellularity of thymic epithelial cells expressing Aire. • Hindlimb unloading reduced ectopic expression of tissue specific antigens in thymus. Hindlimb unloading (HU) of rodents has been used as a ground-based model of spaceflight. In this study, we investigated the detailed impact of 14-day HU on the murine thymus. Thymic mass and cell number were significantly reduced after 14 days of hindlimb unloading, which was accompanied by an increment of plasma corticosterone. Although corticosterone reportedly causes selective apoptosis of CD4{sup +}CD8{sup +} thymocytes (CD4{sup +}CD8{sup +}DPs) in mice treated with short-term HU, the reduction of thymocyte cellularity after the 14-day HU was not selective for CD4{sup +}CD8{sup +}DPs. In addition to the thymocyte reduction, the cellularity of thymic epithelial cells (TECs) was also reduced by the 14-day HU. Flow cytometric and RNA-sequencing analysis suggested that medullary TECs (mTECs) were preferentially reduced after HU. Moreover, immunohistochemical staining suggested that the 14-day HU caused a reduction of the mTECs expressing autoimmune regulator (Aire). Our data suggested that HU impacts both thymocytes and TECs. Consequently, these data imply that thymic T cell repertoire formation could be disturbed during spaceflight-like stress.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Identification and characterization of circular RNAs in rapid atrial pacing dog atrial tissue

Highlights: • Revealed the expression characterization of circRNAs in dog atrial tissue. • Compared differentially expressed circRNAs between atrial fibrillation and control dog. • Found extensive interaction among circRNAs and AF related miRNAs and mRNAs. Circular RNAs (circRNAs) have emerged as novel molecules of interest in gene regulation as other noncoding RNAs, and participating in the process of many diseases. However, the expression and functions of circRNAs in Rapid atrial pacing (RAP) dog atrial tissue still unknown. 12 canines were randomly assigned to control and pacing group. RAP at 500 beats per minute was maintained 14 days in the pacing group. The expression characterization of circRNAs were revealed by high-throughput sequencing. We totally predicted 15,990 circRNAs in dog atrial tissues. Moreover, we found 146 differentially expressed circRNAs between control and RAP dogs. Five circRNAs were selected for subsequent RT-PCR validation, and four circRNAs confirmed with the high throughput sequencing analysis. GO analysis showed that the differentially expressed circRNAs might involve in the process of “structural constituent of cytoskeleton, ion channel activity”. We explored the circRNA-miRNA interaction network, and found extensive interaction among differentially expressed circRNAs and AF related miRNAs and mRNAs. Our work firstly identified the characterization of circRNAs in the dog atrial, and revealed the differentially expressed circRNAs in the RAP dog, this might lay a solid foundation on the function of circRNA in the mechanisms of AF.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Dietary mung bean protein reduces high-fat diet-induced weight gain by modulating host bile acid metabolism in a gut microbiota-dependent manner

Highlights: • Mung bean protein intake reduces high fat diet-induced weight gain, fat accumulation, and hepatic steatosis. . • Mung bean protein intake increases plasma GLP-1 and intestinal secondary bile acids. • The anti-obesity effects occur via a mechanism that depends on the gut microbiota. The 8-globulin-rich mung bean protein (MPI) suppresses hepatic lipogenesis in rodent models and reduces fasting plasma glucose and insulin levels in obese adults. However, its effects on mitigating high fat diet (HFD)-induced obesity and the mechanism underlying these effects remain to be elucidated. Herein, we examined the metabolic phenotype, intestinal bile acid (BA) pool, and gut microbiota of conventionally raised (CONV-R) male C57BL/6 mice and germ-free (GF) mice that were randomized to receive either regular HFD or HFD containing mung bean protein isolate (MPI) instead of the dairy protein present in regular HFD. MPI intake significantly reduced HFD-induced weight gain and adipose tissue accumulation, and attenuated hepatic steatosis. Enhancement in the secretion of intestinal glucagon-like peptide-1 (GLP-1) and an enlarged cecal and fecal BA pool of dramatically elevated secondary/primary BA ratio were observed in mice that had consumed MPI. These effects were abolished in GF mice, indicating that the effects were dependent upon the presence of the microbiota. As revealed by 16S rRNA gene sequence analysis, MPI intake also elicited dramatic changes in the gut microbiome, such as an expansion of taxa belonging to the phylum Bacteroidetes along with a reduced abundance of the Firmicutes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

microRNA-9 selectively targets LMX1A to promote gastric cancer cell progression

Highlights: • miR-9 overexpression downregulates LMX1A, promoting gastric cancer (GC) cell proliferation. • miR-9 inhibition upregulates LMX1A to induce GC cell apoptosis. • LMX1A is the direct and primary target of miR-9 in GC cells. • miR-9 upregulation in human GC tissues correlates with LMX1A downregulation. LIM homeobox transcription factor 1, alpha (LMX1A) is downregulated in human gastric cancer (GC), functioning as a tumor suppressor. The current study aims to identify specific microRNA that can regulate LMX1A expression. By sequence analysis of LMX1A mRNA 3′-untranslated region (3′-UTR), we show that microRNA-9 (miR-9) putatively targets human LMX1A. In established (AGS cells) and primary human GC cells, ectopic overexpression of miR-9 by a lentiviral construct decreased LMX1A 3′-UTR activity, causing LMX1A mRNA and protein downregulation. Functional analyses show that miR-9 overexpression enhanced GC cell survival and proliferation. On the contrary, miR-9 inhibition by antagomir-9 lentivirus increased LMX1A 3′-UTR activity to upregulate LMX1A mRNA and protein expression, causing GC cell apoptosis. CRISPR/Cas9-mediated LMX1A knockout promoted AGS cell survival and proliferation. Importantly, miR-9 and antagomiR-9 were ineffective to the function of LMX1A-knockout AGS cells. In human GC tissues miR-9 is upregulated, which is negatively correlated with LMX1A downregulation. Together, we conclude that miR-9 selectively targets LMX1A to promote GC cell progression.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Long noncoding RNA LOXL1-AS1 regulates prostate cancer cell proliferation and cell cycle progression through miR-541-3p and CCND1

Highlights: • LOXL1-AS1 regulates proliferation and cell cycle in prostate cancer cells. • miR-541-3p regulates CCND1 expression in prostate cancer cells. • LOXL1-AS1 sponges and regulates the expression of miR-541-3p. • LOXL1-AS1 regulates proliferation and cell cycle through miR-541-3p and CCND1. Prostate cancer is one of the most frequent malignancies affecting men. Long non-coding RNAs (lncRNAs) are involved in the pathogenesis of prostate cancer. LncRNA LOXL1-AS1 participates in the pathogenesis of the exfoliation syndrome. However, the role of LOXL1-AS1 in cancer remains largely unknown. Here, we found that LOXL1-AS1 down-regulation inhibited prostate cancer cell proliferation and cell cycle progression. RNA sequencing analysis revealed that it regulates the expression of cell cycle-related genes. LOXL1-AS1 is predominantly distributed in the cytoplasm, where it interacts with miR-541-3p. In addition, miR-541-3p targets the cell cycle regulator CCND1 in prostate cancer cells. LOXL1-AS1 down-regulation inhibits the expression of CCND1 and cell cycle progression, whereas these effects are abolished upon miR-541-3p suppression. In summary, our study revealed that LOXL1-AS1 regulates prostate cancer cell proliferation and cell cycle progression through miR-541-3p and CCND1. Modulation of their levels may be used to treat prostate cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Targeting ninjurin 2 by miR-764 regulates hydrogen peroxide (H2O2)-induced neuronal cell death

Highlights: • MicroRNA-764 (miR-764) directly regulates ninjurin2 (NINJ2) expression. • Forced overexpression of miR-764 downregulates NINJ2 in human neuronal cells. • miR-764 inhibitor upregulates NINJ2 in human neuronal cells. • NINJ2 downregulation by miR-764 is cytotoxic to human neuronal cells. • NINJ2 overexpression by lentivirus or mir-764 inhibitor protects neuronal cells from H{sub 2}O{sub 2}. Ninjurin 2 (NINJ2) is a novel adhesion molecule expressed in neurons and glial cells. The current study determined if specific microRNA (miRNA) can regulate NINJ2 expression in human neuronal cells. Sequence analysis of NINJ2 mRNA 3′-untranslated region (3′-UTR) revealed that microRNA-764 (miR-764) putatively targets NINJ2. In SH-SY5Y/SK-N-BE neuronal cells and primary human neurons, lentivirus-mediated overexpression of miR-764 conferred significant repression on NINJ2 3′-UTR luciferase activity and downregulation of NINJ2 mRNA/protein. Conversely, transfection of the miR-764 inhibitor increased NINJ2 mRNA and protein expression in the neuronal cells. Function studies show that NINJ2 downregulation by miR-764 induced significant viability reduction and apoptosis in the neuronal cells. Further, CRISPR/Cas9-mediated NINJ2 knockout mimicked and abolished miR-764-induced actions in SH-SY5Y cells. Conversely, lentivirus-mediated NINJ2 overexpression or transfection of miR-764 inhibitor protected neuronal cells from hydrogen peroxide (H{sub 2}O{sub 2})-induced cell death and apoptosis. Collectively, these results show that NINJ2 is a pro-survival factor in human neuronal cells. miR-764 regulates NINJ2 expression and neuron functions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump

The multidrug efflux pumps of Gram-negative bacteria are a class of complexes that span the periplasm, coupling both the inner and outer membranes to expel toxic molecules. The best-characterized example of these tripartite pumps is the AcrAB-TolC complex of Escherichia coli. However, how the complex interacts with the peptidoglycan (PG) cell wall, which is anchored to the outer membrane (OM) by Braun’s lipoprotein (Lpp), is still largely unknown. In this work, we present molecular dynamics simulations of a complete, atomistic model of the AcrAB-TolC complex with the inner membrane, OM, and PG layers all present. We find that the PG localizes to the junction of AcrA and TolC, in agreement with recent cryo-tomography data. Free-energy calculations reveal that the positioning of PG is determined by the length and conformation of multiple Lpp copies anchoring it to the OM. The distance between the PG and OM measured in cryo-electron microscopy images of wild-type E. coli also agrees with the simulation-derived spacing. Finally, sequence analysis of AcrA suggests a conserved role for interactions with PG in the assembly and stabilization of efflux pumps, one that may extend to other trans-envelope complexes as well.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Effects of rigidity on the selectivity of protein kinase inhibitors

Established strategies for discovering selective kinase inhibitors are target-centric as they often target certain structural or reactive features in the target kinase. In the absence of such prominent features, there is a lack of general methods for discovering selective inhibitors. As such, here we describe a new strategy that exploits conformational flexibility of kinases for achieving selective kinase inhibition. Through ring closure, we designed and synthesized a panel of isoquinoline-containing compounds as rigidified analogs of an amidophenyl-containing parent compound. These analogs potently inhibit kinases including Abl and BRAF but have diminished inhibition against some other kinases compared to the parent compound. Sequence analysis reveals that many of the kinases that are potently inhibited by the isoquonoline-containing compounds contain a long insertion within their catalytic domains. A crystal structure of one rigid compound bound to BRAF confirmed its binding mode. Our findings highlight the potential of a novel strategy of rigidification for improving the selectivity of kinase inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

FTO regulates myoblast proliferation by controlling CCND1 expression in an m6A-YTHDF2-dependent manner

Highlights: • Silencing FTO delays cell cycle and inhibits cell proliferation. • FTO regulates cell proliferation depending on its m{sup 6}A demethylation activity. • Silencing FTO suppresses CCND1 expression via YTHDF2-mediated mRNA degradation. • Knockdown YTHDF2 eliminates the cell cycle arrest in FTO-deficient cells. N6-Methyladenosine (m{sup 6}A) modification is the most abundant chemical modification in mRNA, and it participates in various biological processes, such as cell differentiation and proliferation. However, little is known about the function of m{sup 6}A demethylase fat mass and obesity-associated (FTO) in myoblast proliferation. Here, we demonstrated that knockdown of FTO can significantly inhibit myoblast proliferation and promote apoptosis. RNA sequencing analysis revealed that a lot of downregulated genes in FTO knockdown cells are associated with cell cycle and apoptosis. Furthermore, silencing FTO drastically decreased cyclin D1 (CCND1) expression through YTHDF2-mediated mRNA degradation, thereby delaying the progression of G1 phase, and leading to impaired myoblast proliferation. These findings unraveled that FTO regulates myoblast proliferation by controlling CCND1 expression in an m{sup 6}A-YTHDF2-dependent manner, which highlights the critical roles of m{sup 6}A modification in myoblast proliferation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Genomic insights into the origin, domestication and diversification of Brassica juncea

Despite early domestication around 3000 BC, the evolutionary history of the ancient allotetraploid species Brassica juncea (L.) Czern & Coss remains uncertain. Here, we report a chromosome-scale de novo assembly of a yellow-seeded B. juncea genome by integrating long-read and short-read sequencing, optical mapping and Hi-C technologies. Nuclear and organelle phylogenies of 480 accessions worldwide supported that B. juncea is most likely a single origin in West Asia, 8,000–14,000 years ago, via natural interspecific hybridization. Subsequently, new crop types evolved through spontaneous gene mutations and introgressions along three independent routes of eastward expansion. Selective sweeps, genome-wide trait associations and tissue-specific RNA-sequencing analysis shed light on the domestication history of flowering time and seed weight, and on human selection for morphological diversification in this versatile species. Our data provide a comprehensive insight into the origin and domestication and a foundation for genomics-based breeding of B. juncea.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Lyophilization of ASFV vaccine candidate ASFV-G-ΔI177L offers long term stability

Abstract For over a century African swine fever (ASF) has been causing outbreaks leading to devastating losses for the swine industry. The current pandemic of ASF has shown no signs of stopping and continues to spread causing outbreaks in additional countries. Currently control relies mostly on culling infected farms, and strict biosecurity procedures. Recently a vaccine, ASFV-G-ΔI177L was approved for use in Vietnam. In this study we evaluate the long-term stability of lyophilized ASFV-G-ΔI177L. Understanding the stability of different formulations of vaccines is information necessary for deployment of vaccines to ASF outbreak areas, particularly those that do not have a reliable well established cold chain to ensure conservation of vaccine quality. In this report, we determined that ASFV-G-ΔI177L, when lyophilized under specific conditions, is stable for up to one year at 4 °C, with similar vaccine titers after storage. Next-generation sequencing analysis also determined that lyophilization and long-term storage under these conditions had no effect on the genome of ASFV as the genome remained genetically identical to the original non-lyophilized form.

Science & Technology - Other Topics↗
DOE OSTI2018

Short-term early exposure to thirdhand cigarette smoke increases lung cancer incidence in mice

Exposure to thirdhand smoke (THS) is a recently described health concern that arises in many indoor environments. However, the carcinogenic potential of THS, a critical consideration in risk assessment, remains untested. Here we investigated the effects of short-term early exposure to THS on lung carcinogenesis in A/J mice. Forty weeks after THS exposure from 4 to 7 weeks of age, the mice had increased incidence of lung adenocarcinoma, tumor size and, multiplicity, compared with controls. In vitro studies using cultured human lung cancer cells showed that THS exposure induced DNA double-strand breaks and increased cell proliferation and colony formation. RNA sequencing analysis revealed that THS exposure induced endoplasmic reticulum stress and activated p53 signaling. Activation of the p53 pathway was confirmed by an increase in its targets p21 and BAX. These data indicate that early exposure to THS is associated with increased lung cancer risk.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Protein cost minimization promotes the emergence of coenzyme redundancy

Metabolism relies on a small class of molecules (coenzymes) that serve as universal donors and acceptors of key chemical groups and electrons. Although metabolic networks crucially depend on structurally redundant coenzymes [e.g., NAD(H) and NADP(H)] associated with different enzymes, the criteria that led to the emergence of this redundancy remain poorly understood. Our combination of modeling and structural and sequence analysis indicates that coenzyme redundancy may not be essential for metabolism but could rather constitute an evolved strategy promoting efficient usage of enzymes when biochemical reactions are near equilibrium. Our work suggests that early metabolism may have operated with fewer coenzymes and that adaptation for metabolic efficiency may have driven the rise of coenzyme diversity in living systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Validation of Continuous-Energy ENDF/B-VIII.0 16 O, 56 Fe, and 63,65 Cu Cross Sections for Nuclear Criticality Safety Applications

Recently completed cross-section evaluations sponsored in part by the Nuclear Criticality Safety Program were incorporated into the 2018 release of the ENDF/B-VIII.0 cross-section library. Evaluated isotopes of interest to the nuclear data and criticality safety community include 16 O, 56 Fe, and 63,65 Cu. For performance validation, benchmark models defined in the International Criticality Safety Benchmark Evaluation Project Handbook were selected based on energy-integrated k eff sensitivities to total cross sections of interest and compared with experimental values. Of the 102 benchmark configurations that were utilized, 63 are sensitive to 16 O, 32 sensitive to 63,65 Cu, and 25 sensitive to 56 Fe. Selected benchmarks were modeled in SCALE 6.2.3 Criticality Safety Analysis Sequence (CSAS) continuous-energy Monte Carlo k eff calculations with ENDF/B-VII.1, with a hybrid ENDF/B-VII.1 with ENDF/B-VIII.0 data substituted for individual isotopes of interest, and with ENDF/B-VIII.0. ENDF/B-VIII.0 showed improved agreement with experimental k eff for 56 Fe, 63 Cu, elemental copper, and full library substitution while producing lessened agreement for 16 O and 65 Cu. Furthermore, with full library and isotope-specific ENDF/B-VIII.0 performance, a best-case ENDF library was formed by excluding underperforming isotopes’ ENDF/B-VIII.0 data, reverting 16 O and 65 Cu cross sections to ENDF/B-VII.1. This resulted in the average relative deviation between calculated and experimental data improving from 1.45σ for the ENDF/B-VIII.0 library to 1.32σ for the best-case library, relative to benchmark uncertainty.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Continuous-Energy ENDF/B-VIII.0 Cross Section and SCALE 6.2.4 Performance for Nuclear Criticality Safety Applications: 1 H, C, 58,60 Ni, 182,183,184,186 W, 235,238 U, 239 Pu

As part of the nuclear data evaluation and validation cycle, the ENDF/B-VIII.0 cross-section library released in 2018 requires testing to determine areas of improvement and deterioration. Previous work by the authors investigated the performance of 16 O, 56 Fe, and 63,65 Cu cross sections, with this study acting as an extension of the prior work. In addition to the isotopes and nuclear criticality safety benchmarks of interest to the prior work, benchmarks from the International Criticality Safety Benchmark Evaluation Project Handbook were selected for their k eff sensitivity to 1 H, C, 58,60 Ni, 182,183,184,186 W, 235,238U, or 239 Pu cross sections and were modeled in the SCALE code system maintained by Oak Ridge National Laboratory. In total, 253 benchmark configurations were selected for their sensitivities and modeled using SCALE 6.2.4 Criticality Safety Analysis Sequences (CSAS) continuous-energy Monte Carlo k eff calculations. This collection includes and expands upon the 99 benchmarks in the prior work. The AMPX-processed ENDF/B-VIII.0 library was decomposed into individual ENDF/B-VIII.0 datum libraries for each isotope of interest. Doing so allowed for the individual substitution of an ENDF/B-VIII.0 cross section in the place of ENDF/B-VII.1, determining isotope-specific effects of ENDF/B-VIII.0 relative to ENDF/B-VII.1. Full library calculations with entirely ENDF/B-VII.1 data or entirely ENDF/B-VIII.0 data were also executed. As a measure of performance, the average relative deviation was determined as the ratio of the deviation between calculated and experimental keff to the propagated calculational and experimental uncertainty. With calculated full library and isotope-specific ENDF/B-VIII.0 k eff ’s, an optimized combination of data libraries was estimated and confirmed with SCALE calculations. This showed that reverting 239 Pu, 58 Ni, 16 O, and 65 Cu cross sections to ENDF/B-VII.1 resulted in improved performance relative to the full ENDF/B-VIII.0 library. Across all 253 benchmarks, the average relative deviation was 1.29σ for the full ENDF/B-VII.1 library, 1.17σ for the full ENDF/B-VIII.0 library, and 0.97σ for the optimized combination. The reversion of 239 Pu, 58 Ni, 16 O, and 65 Cu cross sections to ENDF/B-VII.1 in the 99 benchmarks of the prior work resulted in further improved experimental agreement compared to the previously reported improvement from 16 O and 65 Cu alone. Therefore, it is suggested that applications with significant sensitivities to 239 Pu, 58 Ni, 16 O, and 65 Cu consider their choice of nuclear data library.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2025

Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters

Abstract Motivation The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutation events in sequences relative to a reference. Two versions of this method are available as a webtool. Neither of these methods consider multistate characters or gaps in the sequence alignment. Results Here, we present an updated, user-friendly web and command-line version of Hypermut with functionality to handle multistate characters and gaps in the sequence alignment. This tool allows for straightforward integration of hypermutation detection into sequence analysis pipelines. As with the previous tool, while the main purpose is to identify G to A hypermutation events, any mutational pattern and context can be specified. Availability and implementation Hypermut 3 is written in Python 3. It is available as a command-line tool at https://github.com/MolEvolEpid/hypermut3 and as a webtool at https://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermutv3.html.

59 BASIC BIOLOGICAL SCIENCES↗