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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Impact of Polymicrobial Infection on Fitness of Streptococcus gordonii In Vivo

Pathogenic microbial ecosystems are often polymicrobial, and interbacterial interactions drive emergent properties of these communities. In the oral cavity, Streptococcus gordonii is a foundational species in the development of plaque biofilms, which can contribute to periodontal disease and, after gaining access to the bloodstream, target remote sites such as heart valves. Here, we used a transposon sequencing (Tn-Seq) library of S. gordonii to identify genes that influence fitness in a murine abscess model, both as a monoinfection and as a coinfection with an oral partner species, Porphyromonas gingivalis. In the context of a monoinfection, conditionally essential genes were widely distributed among functional pathways. Coinfection with P. gingivalis almost completely changed the nature of in vivo gene essentiality. Community-dependent essential (CoDE) genes under the coinfection condition were primarily related to DNA replication, transcription, and translation, indicating that robust growth and replication are required to survive with P. gingivalis in vivo. Interestingly, a group of genes in an operon encoding streptococcal receptor polysaccharide (RPS) were associated with decreased fitness of S. gordonii in a coinfection with P. gingivalis. Individual deletion of two of these genes (SGO_2020 and SGO_2024) resulted in the loss of RPS production by S. gordonii and increased susceptibility to killing by neutrophils. P. gingivalis protected the RPS mutants by inhibiting neutrophil recruitment, degranulation, and neutrophil extracellular trap (NET) formation. These results provide insight into genes and functions that are important for S. gordonii survival in vivo and the nature of polymicrobial synergy with P. gingivalis. Furthermore, we show that RPS-mediated immune protection in S. gordonii is dispensable and detrimental in the presence of a synergistic partner species that can interfere with neutrophil killing mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dual Targeting Factors Are Required for LXG Toxin Export by the Bacterial Type VIIb Secretion System

Bacterial type VIIb secretion systems (T7SSb) are multisubunit integral membrane protein complexes found in Firmicutes that play a role in both bacterial competition and virulence by secreting toxic effector proteins. The majority of characterized T7SSb effectors adopt a polymorphic domain architecture consisting of a conserved N-terminal Leu-X-Gly (LXG) domain and a variable C-terminal toxin domain. Recent work has started to reveal the diversity of toxic activities exhibited by LXG effectors; however, little is known about how these proteins are recruited to the T7SSb apparatus. In this work, we sought to characterize genes encoding domains of unknown function (DUFs) 3130 and 3958, which frequently cooccur with LXG effector-encoding genes. Using coimmunoprecipitation-mass spectrometry analyses, in vitro copurification experiments, and T7SSb secretion assays, we found that representative members of these protein families form heteromeric complexes with their cognate LXG domain and in doing so, function as targeting factors that promote effector export. Additionally, an X-ray crystal structure of a representative DUF3958 protein, combined with predictive modeling of DUF3130 using AlphaFold2, revealed structural similarity between these protein families and the ubiquitous WXG100 family of T7SS effectors. Interestingly, we identified a conserved FxxxD motif within DUF3130 that is reminiscent of the YxxxD/E “export arm” found in mycobacterial T7SSa substrates and mutation of this motif abrogates LXG effector secretion. Overall, our data experimentally link previously uncharacterized bacterial DUFs to type VIIb secretion and reveal a molecular signature required for LXG effector export.

24 antibacterial toxins↗
DOE OSTI2022

Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina

Outdoor cultivation of microalgae has promising potential for renewable bioenergy, but there is a knowledge gap on the structure and function of the algal microbiome that coinhabits these ecosystems. Here, we describe the assembly mechanisms, taxonomic structure, and metabolic potential of bacteria associated with Microchloropsis salina cultivated outdoors. Open mesocosms were inoculated with algal cultures that were either free of bacteria or coincubated with one of two different strains of alga-associated bacteria and were sampled across five time points taken over multiple harvesting rounds of a 40-day experiment. Using quantitative analyses of metagenome-assembled genomes (MAGs), we tracked bacterial community compositional abundance and taxon-specific functional capacity involved in algal-bacterial interactions. One of the inoculated bacteria (Alteromonas sp.) persisted and dispersed across mesocosms, whereas the other inoculated strain (Phaeobacter gallaeciensis) disappeared by day 17 while a taxonomically similar but functionally distinct Phaeobacter strain became established. The inoculated strains were less abundant than 6 numerically dominant newly recruited taxa with functional capacities for mutualistic or saprophytic lifestyles, suggesting a generalist approach to persistence. This includes a highly abundant unclassified Rhodobacteraceae species that fluctuated between 25% and 77% of the total community. Overall, we did not find evidence for priority effects exerted by the distinct inoculum conditions; all mesocosms converged with similar microbial community compositions by the end of the experiment. Instead, we infer that the 15 total populations were retained due to host selection, as they showed high metabolic potential for algal-bacterial interactions such as recycling alga-produced carbon and nitrogen and production of vitamins and secondary metabolites associated with algal growth and senescence, including B vitamins, tropodithietic acid, and roseobacticides.

rhodobacteraceae↗
DOE OSTI2020

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

ABSTRACT Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this “uncultivated majority” remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes . Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages. IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Influence of local river hydraulics on Kootenai River white sturgeon ( Acipenser transmontanus ) habitat selection during four spawning years, 2017–2020

Understanding fine-scale habitat selection of endangered Kootenai River white sturgeon ( Acipenser transmontanus) is an important component for monitoring and recovery efforts. Fine-scale habitat selection and quantifying temporal changes in suitable habitat contributes to the work of addressing recruitment failure within the Kootenai River population. Habitat suitability indices were developed using over 96 000 acoustic telemetry sturgeon detections and two-dimensional hydrodynamic model simulations near Bonners Ferry, Idaho, USA. The selected habitat was assessed to develop habitat suitability indices for sturgeon; females undergoing spawn migrations and non-spawners. The most frequented locations were 8–9 m deep and water velocities of 0.3–0.7 m·s −1 . These observations suggest sturgeon with different spawning capabilities selected similar habitat. Weighted usable area was calculated to understand temporal variability in habitat quality, which showed a positive relationship with increases in flow. Results help understand the habitat limiting factors in regulated hydrologic regimes; provide biologists insight for monitoring efforts in discrete habitat conditions; guidance for water managers and the regulation of upstream water resources; and guidance to restoration practitioners for in-stream structure designs.

Dudunake, Taylor J. (ORCID:0000000176502419)↗
DOE OSTI2022

Estella Atekwana: Autobiographical Notes

I describe my career journey from a young girl in Cameroon, West Africa, to a trailblazing geophysicist to my current role as dean. I chronicle my time as a student, the transition to being an early career faculty, launching my research career, and ultimately finding my way to administration. Along the way I helped pioneer biogeophysics as a subdiscipline in geophysics while simultaneously maintaining an international research program in continental rift tectonics. I also describe the many intersectionalities in my life including being the first Black woman in many spaces, being a champion for student success, developing a diverse talent pipeline by enhancing diversity in the geosciences, and navigating academic job searches as part of a dual-career couple. Finally, I acknowledge all those who helped shape my career including the many students I had the opportunity to mentor. • Many underrepresented minority geoscientists lack the social capital and professional networks critical for their success. • Geoscience departments must be intentional and deliberate in promoting and ensuring more inclusive workplace environments. • Dual-career couples remain a major challenge, impacting retention and recruitment of top talent; universities should provide resources to alleviate this challenge. • Biogeophysics has untapped potential for advancing understanding of subsurface biogeochemical processes and the search for life in extreme environments. • To date, considerable speculation remains regarding the fundamental geodynamic processes that initiate and sustain the evolution of magma-deficient rifts.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2022

Profile of Twenty-Three Human Milk Oligosaccharides in Han Chinese Mothers throughout Postpartum 1 year

Human milk oligosaccharides (HMOs) are multifunctional carbohydrates in breast milk, which are composed by a variety of structures. This study aimed to identified HMOs concentration profile, milk microbiota composition, and the associations with major maternal characteristics in Han Chinese mothers in the one-year lactation period. Seventeen healthy mothers aged from 28 to 36 years, who gave birth to healthy term infants, were recruited. Carbohydrates were detected using the MIRIS human milk analyzer (HMA), and twenty-three HMOs were quantified using ultra-performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-MS). Results showed that carbohydrates were relatively stable, while total HMO concentrations ranged from 1.74 to 9.72 g/L and decreased gradually over lactation in breast milk. Based on the structure, seven sialylated HMOs concentration showed the significant decline ( p < 0.05 ) after three months in lactation. In addition, the relationships between maternal factors, containing the lactation period, genetic status, delivery mode, parity, and milk microbiota profile, and the HMO composition in healthy women, which still need further investigations, were observed.

Xun, Yiping↗
DOE OSTI2021

NSU Hack-a-Thon Workshop v.2.0

SAND2021-6722 O This is a fitness tracking mobile application and server created to train college-level students to build full stack software. The front end is written using an open-source framework called Flutter. The API server is written using an open-source python framework called Flask. The app functions as a workout tracker and is intentionally partially functional for the purpose of training students during the live workshops hosted by Sandia's HR recruiting teams. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Carpenter, Logan↗
DOE OSTI2023

MetaBAT-LR v1.0.0

MetaBAT-LR is an extension to the metaBAT program, which adds functionalities to leverage various datasets (long-reads, Hi-C) to improve the completeness of metagenome binning while keeping contamination levels low. It trains a random forest model using the self-supervised training paradigm to predict linkage information among metagenome scaffolds, then uses this information to recruit unbinned scaffolds and merge incomplete bins that are from the same species.

Wang, Zhong↗
DOE OSTI2023

ShadeLab/PAPER_Howe_2023_switchgrass_MetaT

The raw data (metagenomes and metatranscriptomes) for this study are available in the Joint Genomes Institute Genome Portal (https://genome.jgi.doe.gov/portal/ Project ID 503249) with projects designated by year and product type. The MAG genomes analyzed in this paper are available on NCBI, as bioproject PRJNA800073. Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on field-grown switchgrass and miscanthus and to quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over representative time points in crop phenology. We curated 40 medium- and high-quality metagenome-assembled-genomes (MAGs) and focused analysis on seasonal transcript recruitment to them. Classes represented by these focal MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) were active and had increases in transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoids and isoprenoids) and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform both general and likely specialized activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues, and interactively engage in feedback with the plant. This analysis represented quality filtering of metagenomes and metatranscriptomes (data-preparation folder), metagenome assemblies (metagenome-assembly folder) and metagenome-assembled genome binning, curation, refinement, annotation (mag-evaluation folder). Abundances of sequencing libraries were calculated based on reads mapped (mapping folder). Additionallly, analysis of our annotated results are also included (analysis folder).

Howe, Adina↗
DOE OSTI2022

A Novel EGFRvIII T-Cell Bispecific Antibody for the Treatment of Glioblastoma

Abstract T-cell bispecific antibodies (TCB) are engineered molecules that bind both the T-cell receptor and tumor-specific antigens. Epidermal growth factor receptor variant III (EGFRvIII) mutation is a common event in glioblastoma (GBM) and is characterized by the deletion of exons 2–7, resulting in a constitutively active receptor that promotes cell proliferation, angiogenesis, and invasion. EGFRvIII is expressed on the surface of tumor cells and is not expressed in normal tissues, making EGFRvIII an ideal neoantigen target for TCBs. We designed and developed a novel 2+1 EGFRvIII-TCB with optimal pharmacologic characteristics and potent antitumor activity. EGFRvIII-TCB showed specificity for EGFRvIII and promoted tumor cell killing as well as T-cell activation and cytokine secretion only in patient-derived models expressing EGFRvIII. Moreover, EGFRvIII-TCB promoted T-cell recruitment into intracranial tumors. EGFRvIII-TCB induced tumor regression in GBM animal models, including humanized orthotopic GBM patient-derived xenograft models. Our results warrant the clinical testing of EGFRvIII-TCB for the treatment of EGFRvIII-expressing GBMs.

Oncology↗
DOE OSTI2025

Defining the Antitumor Mechanism of Action of a Clinical-stage Compound as a Selective Degrader of the Nuclear Pore Complex

Cancer cells are acutely dependent on nuclear transport due to elevated transcriptional activity, suggesting an unrealized opportunity for selective therapeutic inhibition of the nuclear pore complex (NPC). Through large-scale phenotypic profiling of cancer cell lines, genome-scale functional genomic modifier screens, and mass spectrometry–based proteomics, we discovered that the clinical drug PRLX-93936 is a molecular glue that binds and reprograms the TRIM21 ubiquitin ligase to degrade the NPC. Upon compound-induced TRIM21 recruitment, the nuclear pore is ubiquitylated and degraded, resulting in the loss of short-lived cytoplasmic mRNA transcripts and the induction of cancer cell apoptosis. Direct compound binding to TRIM21 was confirmed via surface plasmon resonance and X-ray crystallography, whereas compound-induced TRIM21–nucleoporin complex formation was demonstrated through multiple orthogonal approaches in cells and in vitro. Phenotype-guided optimization yielded compounds with 10-fold greater potency and drug-like properties, along with robust pharmacokinetics and efficacy against pancreatic cancer xenografts and patient-derived organoids.

Yuan, Linjie [Stanford School of Medicine, CA (Uni↗
DOE OSTI2023

COVID-19-Related Experiences and Perspectives of Peruvian College Students: A Descriptive Study

The COVID-19 pandemic drastically affected higher education and higher education students around the world, but few studies of college students’ experiences during the COVID-19 pandemic have been conducted in Latin America. This study describes the COVID-19-related experiences and perspectives of Peruvian college students. We surveyed 3,427 full-time college students (average age: 23 years) attending a multi-campus Peruvian university in fall 2020. Participants were recruited through the digital platform of the learning management system at their university, email, and social media. We asked participants how they were managing risks related to COVID-19; the continuity of social, educational, and work activities; and the psychological and economic impacts of the pandemic on their lives. Since March 2020, 73.0% of participants reported COVID-19-related symptoms, but only 33.9% were tested for COVID-19. During the national quarantine imposed by the Peruvian government (March 15–June 30, 2020), 64.3% of participants remained in their house. Furthermore, while 44.0% of participants were working in February 2020 (95% CI: [41.7%, 46.4%]), only 23.6% (95% CI: [21.7%, 25.7%]) were working immediately after the pandemic began (i.e., at the end of April 2020). Participants were more stressed about the health and educational implications of COVID-19 for Peruvian society and their families than about themselves. The public health, economic, and educational implications of COVID-19 on college students are continuing to unfold. This study informed Peruvian higher education institutions’ continued response to the COVID-19 pandemic, the progressive return to postpandemic activities, as well as other future pandemics and other crises.

Bazo-Alvarez, Juan Carlos↗
DOE OSTI2020

Opinion: Lighting Research During and After the Pandemic

For many lighting researchers, the recent restrictions related to COVID-19 have paused most in-person laboratory or field experiments. In certain countries, regulatory institutions have allowed such experiments to resume but issued safety recommendations like pre-checking participants for disease symptoms and excluding those that are especially vulnerable. To avoid potential complications and delays, researchers are likely to resort to other research designs that enable remote research — eliminating the need for the experimenter and subjects to be in the same room. While unanticipated, this shift to remote research methods is an opportunity to revisit and further develop remote experimental techniques, which can have beneficial long-lasting implications on lighting research during and after the pandemic. Perhaps the most common type of remote research is online experiments; which can greatly benefit from improved techniques to allow for greater control or characterization of experimental conditions, like those proposed by Villa and Labayrade . These techniques require validation specific to the type of response collected and context, e.g. space type and attributes. New research techniques continue to emerge and will enable remote collection of objective measures such as gaze direction and high dynamic range images (HDRIs) without specialized equipment. In fact, many of these methods and techniques are commonly used in other disciplines, like vision science and psychology, and can be adapted for lighting research. Not all lighting studies can be conducted online, but in the age of ubiquitous and connected technologies, there is a largely missed opportunity to utilize crowdsourced responses to lighting conditions in real environments where people live and go about their daily lives without the research being limited to a certain time and laboratory locations. For instance, outdoor street luminaires can be rated by passersby using ecological momentary assessments on mobile phones. While this approach does not provide laboratory-level control over experimental conditions, it can provide more contextual responses resulting from ‘normal’ dynamic gaze, behavior, and interactions. Further, it can also reduce bias related to the experimental setting. Further development of remote research methods and their use in lighting research can improve the quality of lighting research. Given that sample sizes in most lighting research are relatively small, remote research can substantially increase sample sizes, reduce research costs, and shorten study duration, all while reducing interaction between experimenter and subjects. Another benefit is reaching a wider audience and including under-represented individuals who typically are not reachable using common recruitment methods. The pandemic has set back our plans for in-lab experiments, but can it inspire us to think of new and creative ways to expand lighting research?

Abboushi, Belal K.↗
DOE OSTI2024

The TLK-ASF1 histone chaperone pathway plays a critical role in IL-1β–mediated AML progression

Identifying and targeting microenvironment-driven pathways that are active across acute myeloid leukemia (AML) genetic subtypes should allow the development of more broadly effective therapies. The proinflammatory cytokine interleukin-1β (IL-1β) is abundant in the AML microenvironment and promotes leukemic growth. Through RNA-sequencing analysis, we identify that IL-1β–upregulated ASF1B (antisilencing function-1B), a histone chaperone, in AML progenitors compared with healthy progenitors. ASF1B, along with its paralogous protein ASF1A, recruits H3-H4 histones onto the replication fork during S-phase, a process regulated by Tousled-like kinase 1 and 2 (TLKs). Although ASF1s and TLKs are known to be overexpressed in multiple solid tumors and associated with poor prognosis, their functional roles in hematopoiesis and inflammation-driven leukemia remain unexplored. In this study, we identify that ASF1s and TLKs are overexpressed in multiple genetic subtypes of AML. We demonstrate that depletion of ASF1s significantly reduces leukemic cell growth in both in vitro and in vivo models using human cells. Using a murine model, we show that overexpression of ASF1B accelerates leukemia progression. Moreover, Asf1b or Tlk2 deletion delayed leukemia progression, whereas these proteins are dispensable for normal hematopoiesis. Through proteomics and phosphoproteomics analyses, we uncover that the TLK-ASF1 pathway promotes leukemogenesis by affecting the cell cycle and DNA damage pathways. Collectively, our findings identify the TLK1-ASF1 pathway as a novel mediator of inflammatory signaling and a promising therapeutic target for AML treatment across diverse genetic subtypes. Finally, selective inhibition of this pathway offers potential opportunities to intervene effectively, address intratumoral heterogeneity, and ultimately improve clinical outcomes in AML.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

Abstract Background Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes. Results Members of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria. Conclusion We find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Epidemiological surveillance of common respiratory viruses in patients with suspected COVID-19 in Southwest China

Abstract Background The outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the peak season of common respiratory viral infections. However, the clinical symptoms of most SARS-CoV-2 infected patients are not significantly different from those of common respiratory viral infections. Therefore, knowing the epidemiological patterns of common respiratory viruses may be valuable to improve the diagnostic and therapeutic efficacy of patients with suspected COVID-19, especially in Southwest China (a mild epidemic area). Methods A total of 2188 patients with clinically suspected of COVID-19 in Southwest China were recruited from January 21 to February 29, 2020. Nasopharyngeal swabs, throat swabs and sputum specimens were collected to detect SARS-CoV-2 by using real-time reverse transcription-polymerase chain reaction (RT-PCR) and other 12 viruses via PCR fragment analysis combined with capillary electrophoresis. Clinical characteristics and laboratory test findings were acquired from electronic medical records. All data were analyzed to unravel the epidemiological patterns. Results Only 1.1% (24/2188) patients with suspected COVID-19 were eventually confirmed to have SARS-CoV-2 infection, and the most frequently observed symptoms were fever (75.0%, 18/24) and cough (20.8%, 5/24). The overall detection rate of other respiratory pathogens was 10.3% (226/2188). Among them, human rhinovirus (3.2%, 71/2188), human parainfluenza viruses (1.6%, 35/2188), influenza B virus (1.2%, 26/2188) and mycoplasma pneumonia (1.2%, 26/2188) were the predominantly detected pathogens in this study. Moreover, the co-infection was observed in 22 specimens. Notably, one COVID-19 case had a coexisting infection with human parainfluenza virus (4.2%, 1/24) and bocavirus was the most common virus tending to occur in co-infection with other respiratory pathogens. Conclusions This study reveals the epidemiological features of common respiratory viruses and their clinical impact during the ongoing outbreak of COVID-19 in a mild epidemic area. The findings highlight the importance of understanding the transmission patterns of the common respiratory virus in COVID-19 regions, which can provide information support for the development of appropriate treatment plans and health policies, while eliminating unnecessary fear and tension.

Si, Yanjun↗
DOE OSTI2022

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

Background: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. Results: We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark. Conclusions: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome.

59 BASIC BIOLOGICAL SCIENCES↗