Christopher Mason

SMARCA4 encodes one of two mutually exclusive ATPase subunits in the BRG/BRM associated factor (BAF) complex that is recruited by transcription factors (TFs) to drive chromatin accessibility and transcriptional activation. SMARCA4 is among the most recurrently mutated genes in human cancer, including ∼30% of germinal center (GC)-derived Burkitt lymphomas. In mice, GC-specific Smarca4 haploinsufficiency cooperated with MYC over-expression to drive lymphomagenesis. Furthermore, monoallelic Smarca4 deletion drove GC hyperplasia with centroblast polarization via significantly increased rates of centrocyte recycling to the dark zone. Mechanistically, Smarca4 loss reduced the activity of TFs that are activated in centrocytes to drive GC-exit, including SPI1 (PU.1), IRF family, and NF-κB. Loss of activity for these factors phenocopied aberrant BCL6 activity within murine centrocytes and human Burkitt …

Ten years ago, it was predicted that the multi-omics revolution would also revolutionize space pharmacogenomics. Current barriers related to the findable, accessible, interoperable, and reproducible use of space-flown pharmaceutical data have contributed to a lack of progress beyond application of earth-based principles. To directly tackle these challenges, we have produced a novel database of all the drugs flown into space, compiled from publicly available ontological and spaceflight-related datasets, to exemplify analyses for describing significant spaceflight-related targets. By focusing on mechanisms perturbed by spaceflight, we have provided a novel avenue for identifying the most relevant changes within the drug absorption, distribution, metabolism, and excretion pathways. We suggest a set of space genes, by necessity limited to available tissue types, that can be expanded and modified based on future tissue-specific and mechanistic-specific high-throughput assays. In sum, we provide the justification and a definitive starting point for pharmacogenomics guided spaceflight as a foundation of precision medicine, which will enable long-term human habitation of the Moon, Mars, and beyond.

Clinical testing has been a vital part of the response to and suppression of the COVID-19 pandemic; however, testing imposes significant burdens on a population. College students had to contend with clinical testing while simultaneously dealing with health risks and the academic pressures brought on by quarantines, changes to virtual platforms, and other disruptions to daily life. The objective of this study was to analyze whether wastewater surveillance can be used to decrease the intensity of clinical testing while maintaining reliable measurements of diseases incidence on campus. Twelve months of human health and wastewater surveillance data for eight residential buildings on a university campus were analyzed to establish how SARS-CoV-2 levels in the wastewater can be used to minimize clinical testing burden on students. Wastewater SARS-CoV-2 levels were used to create multiple scenarios, each with …

ARID1A, a subunit of the canonical BAF nucleosome remodeling complex, is commonly mutated in lymphomas. We show that ARID1A orchestrates B cell fate during the germinal center (GC) response, facilitating cooperative and sequential binding of PU.1 and NF-kB at crucial genes for cytokine and CD40 signaling. The absence of ARID1A tilts GC cell fate toward immature IgM+CD80−PD-L2− memory B cells, known for their potential to re-enter new GCs. When combined with BCL2 oncogene, ARID1A haploinsufficiency hastens the progression of aggressive follicular lymphomas (FLs) in mice. Patients with FL with ARID1A-inactivating mutations preferentially display an immature memory B cell-like state with increased transformation risk to aggressive disease. These observations offer mechanistic understanding into the emergence of both indolent and aggressive ARID1A-mutant lymphomas through the …

Introduction: Prior studies that use 16S rRNA amplicon sequencing to profile bacterial components of cerebral thrombi do not provide species-level taxonomic information or functional gene content, which are critical for the development of subsequent clinical applications. To determine the amount and taxonomic nature of non-human DNA in cerebral thrombi, shotgun metagenomic sequencing was performed on specimens retrieved from ischemic stroke patients. Methods: Thrombi were retrieved during standard of care thrombectomy and preserved in DNA/RNA Shield (Zymo), alongside environmental controls. DNA was extracted per manufacturer instructions, using Zymo kits. Quality control was carried out using Bowtie2 and the bbtools suite. To clump reads, bbmap was applied. Sequencing adapter contamination was removed with bbduk. Data was aligned to the human reference genome (hg38) using Bowtie2 …

COVID-19, the disease caused by SARS-CoV-2, has caused significant morbidity and mortality worldwide. The betacoronavirus continues to evolve with global health implications as we race to learn more to curb its transmission, evolution, and sequelae. The focus of this review, the second of a three-part series, is on the biological effects of the SARS-CoV-2 virus on post-acute disease in the context of tissue and organ adaptations and damage. We highlight the current knowledge and describe how virological, animal, and clinical studies have shed light on the mechanisms driving the varied clinical diagnoses and observations of COVID-19 patients. Moreover, we describe how investigations into SARS-CoV-2 effects have informed the understanding of viral pathogenesis and provide innovative pathways for future research on the mechanisms of viral diseases.

Background: Chimeric antigen receptor (CAR) T cell therapy is effective in treating B-cell malignancies, but factors influencing the persistence of functional CAR+ T cells, such as product composition, patients’ lymphodepletion, and immune reconstitution, are not well understood. To shed light on this issue, we conducted single-cell multi-omics analysis of transcriptional, clonal, and phenotypic profiles from pre- to 1-month post-infusion of CAR+ and CAR− T cells from patients who received a donor-derived 4-1BB CAR product targeting CD19. Methods: Longitudinal blood samples and infusion products were obtained from 10 individuals with large B cell lymphoma or B-cell acute lymphoblastic leukemia (CARTELL cohort in Sydney Australia1). CD45+ cells and enriched CAR+ T cells were single cell sorted for simultaneous scRNA-seq, 41 barcoded proteins (N=41) and T cell receptors, n= 115,000 cells across 21 …

Bacteriophages are recognized as the most abundant members of microbiomes and have therefore a profound impact on microbial communities through the interactions with their bacterial hosts. The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics, throwing light into these hitherto largely unexplored urban environments. MetaSUB focused primarily on the bacterial community. In this work, we explored MetaSUB metagenomic data in order to recover and analyze bacteriophage genomes. We recovered and analyzed 1714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. The recovered genomes were predicted to belong to temperate (69%) and lytic (31%) phages. Thirty-three of these genomes have more than 200 …

Abstract Mantle cell lymphoma (MCL) is an incurable B-cell non-Hodgkin lymphoma, and patients who relapse on targeted therapies have poor prognosis. Protein arginine methyltransferase 5 (PRMT5), an enzyme essential for B-cell transformation, drives multiple oncogenic pathways and is overexpressed in MCL. Despite the antitumor activity of PRMT5 inhibition (PRT-382/PRT-808), drug resistance was observed in a patient-derived xenograft (PDX) MCL model. Decreased survival of mice engrafted with these PRMT5 inhibitor–resistant cells vs treatment-naive cells was observed (P = .005). MCL cell lines showed variable sensitivity to PRMT5 inhibition. Using PRT-382, cell lines were classified as sensitive (n = 4; 50% inhibitory concentration [IC50], 20-140 nM) or primary resistant (n = 4; 340-1650 nM). Prolonged culture of sensitive MCL lines with drug escalation produced PRMT5 inhibitor–resistant …

The Spatial Atlas of Human Anatomy (SAHA) is a foundational effort to map 250 million cells and transcriptomes and proteomes of 30 non-diseased organs from healthy adults at two spatial scales: whole transcriptome of histological features (50 µm to 2 mm), and 1,000-plex RNA and 64-plex protein panels at spatial subcellular resolution (50 nm across 1 cm2). The project aims to establish and validate best practices in experimental design, sample processing, data analysis, and data standards for high-content spatial analysis across multiple human organs at whole transcriptome and proteome levels. The profiled samples will capture variability across genders and ancestries. All results, including raw and processed data, will be made available to the scientific community through the SAHA data portal and AtoMxTM Spatial Informatics Platform. Here we present the part of Phase I data collected specifically around …

Despite regulating overlapping gene enhancers and pathways, CREBBP and KMT2D mutations recurrently co-occur in germinal center (GC) B cell-derived lymphomas, suggesting potential oncogenic cooperation. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d induces a more severe mouse lymphoma phenotype (vs either allele alone) and unexpectedly confers an immune evasive microenvironment manifesting as CD8+ T-cell exhaustion and reduced infiltration. This is linked to profound repression of immune synapse genes that mediate crosstalk with T-cells, resulting in aberrant GC B cell fate decisions. From the epigenetic perspective, we observe interaction and mutually dependent binding and function of CREBBP and KMT2D on chromatin. Their combined deficiency preferentially impairs activation of immune synapse-responsive super-enhancers, pointing to a particular …

The increasing accessibility of commercial and private space travel necessitates a profound understanding of its impact on human health. The NASA Open Science Data Repository (OSDR) provides transparent and FAIR access to biological studies, notably the SpaceX Inspiration4 (I4) mission, which amassed extensive data from civilian astronauts. This dataset encompasses omics and clinical assays, facilitating comprehensive research on space-induced biological responses. These data allow for multi-modal, longitudinal assessments, bridging the gap between human and model organism studies.

Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology. Our findings demonstrated the strong geographical specificity of urban environmental resistome, and their correlation with various local socioeconomic and medical conditions. We also identified distinctive evolutionary patterns of …

Improving human healthspan in our rapidly aging population has never been more imperative. Telomeres, protective “caps” at the ends of linear chromosomes, are essential for maintaining genome stability of eukaryotic genomes. Due to their physical location and the “end-replication problem” first envisioned by Dr. Alexey Olovnikov, telomeres shorten with cell division, the implications of which are remarkably profound. Telomeres are hallmarks and molecular drivers of aging, as well as fundamental integrating components of the cumulative effects of genetic, lifestyle, and environmental factors that erode telomere length over time. Ongoing telomere attrition and the resulting limit to replicative potential imposed by cellular senescence serves a powerful tumor suppressor function, and also underlies aging and a spectrum of age-related degenerative pathologies, including reduced fertility, dementias, cardiovascular …

Culture is currently the gold standard for diagnosis of urinary tract infections (UTIs); however, it has poor sensitivity detecting urogenital pathogens, especially if patients have already initiated antimicrobial therapy, or have an infection from an organism that is not commonly cultured. False negative urine culture results can lead to the inappropriate use of antimicrobial therapies or to the progression to urosepsis in high-risk patients. Though not commonly applied to urine in a clinical setting, Next-generation sequencing (NGS)-based metagenomics offer a solution as a precision diagnostic. We developed and validated BIOTIA-ID, a clinical-grade NGS-based diagnostic pipeline for the detection and identification of pathogens in urine specimens. Remnant clinical urine specimens, and contrived sterile urine spiked with common UTI pathogens, were processed with our end-to-end assay including extraction, metagenomic library preparation and Illumina NextSeq 550 sequencing. We trained and applied a bioinformatic pipeline that uses machine learning (ML) to identify pathogens. Internal controls and other quality control measures were incorporated into the process to provide rigorous and standardized results. The assay was tested on 1,470 urine specimens and achieved 99.92% sensitivity, 99.95% specificity and a limit of detection (LoD) of <25,000 CFU/mL and <5,000 CFU/mL in bacteria and fungi, respectively. Discordant results were reconciled with additional testing by target-specific qPCR or 16S Sanger sequencing; 87% of the NGS results were ultimately determined to be the correct result. Overall, these data demonstrate that BIOTIA-ID is a …

The I4 mission, the first all-civilian orbital flight mission, investigated the physiological effects of short duration spaceflight through a multi-omic approach. We analyzed telomere length, clonal hematopoiesis of indeterminate potential (CHIP), whole genome stability, cell-free DNA (cfDNA) cell lysis, and immune cell gene expression. Our results revealed telomere length dynamics similar to those observed in the NASA Twins Study and in astronauts spending 6 months on the ISS, with lengthening in space and shortening upon return to Earth. Our cell-type of origin analysis of cfDNA fragments revealed an increased presence of innate and adaptive immune cell signatures that persisted over a month after return to earth. No significant relationship between spaceflight and CHIP-related or whole genome abnormalities were observed. Longitudinal mitochondrial, ribosomal and immune function gene expression changes occurred across both adaptive and innate immune cells, suggesting adaptations to the space environment can extend months after return from spaceflight and alter immune function. Our findings provide valuable insights into the physiological consequences of short duration spaceflight and will serve as a reference point for future space tourism, low Earth-orbit (LEO) missions, and deep-space exploration.

Motivation The acquisition of somatic mutations in hematopoietic stem and progenitor stem cells with resultant clonal expansion, termed clonal hematopoiesis (CH), is associated with increased risk of hematologic malignancies and other adverse outcomes. CH is generally present at low allelic fractions, but clonal expansion and acquisition of additional mutations leads to hematologic cancers in a small proportion of individuals. With high depth and high sensitivity sequencing, CH can be detected in most adults and its clonal trajectory mapped over time. However, accurate CH variant calling is challenging due to the difficulty in distinguishing low frequency CH mutations from sequencing artifacts. The lack of well-validated bioinformatic pipelines for CH calling may contribute to lack of reproducibility in studies of CH. Results Here, we developed ArCH, an Artifact filtering Clonal H …

In the era of renewed space exploration, comprehending the effects of the space environment on human health, particularly for deep space missions, is crucial. While extensive research exists on the impacts of spaceflight, there is a gap regarding female reproductive risks. We hypothesize that space stressors could have enduring effects on female health, potentially increasing risks for future pregnancies upon return to Earth, particularly related to small-for-gestational-age (SGA) fetuses. To address this, we identify a shared microRNA (miRNA) signature between SGA and the space environment, conserved across humans and mice. These miRNAs target genes and pathways relevant to diseases and development. Employing a machine learning approach, we identify potential FDA-approved drugs to mitigate these risks, including estrogen and progesterone receptor antagonists, vitamin D receptor antagonists, and DNA polymerase inhibitors. This study underscores potential pregnancy-related health risks for female astronauts and proposes pharmaceutical interventions to counteract the impact of space travel on female health.

Feline coronavirus type 1 (FCoV-1) is widely known for causing feline infectious peritonitis (FIP), a systemic infection that is often fatal, with the virus known as the FIPV biotype. However, subclinical disease also occurs, in which cats may not show signs and intermittently shed the virus, including in feces, possibly for long periods of time. This virus is known as the FECV biotype. Progression of FECV to FIPV has been linked to several genomic changes, however a specific region of the viral spike protein at the interface of the spike S1 and S2 domains has been especially implicated. In this study, we followed a cat (#576) for six years from 2017, at which time FCoV-1 was detected in feces and conjunctival swabs, until 2022, when the animal was euthanized based on a diagnosis of alimentary small cell lymphoma. Over this time period, the cat was clinically diagnosed with inflammatory bowel disease and chronic rhinitis, and cardiac problems were also suspected. Using hybridization capture targeting the spike (S) gene of FCoV followed by next-generation sequencing, we screened 27 clinical samples. We detected FCoV-1 in 4 samples taken in 2017 (intestine and nasal tissue, feces, and conjunctiva), and 3 samples taken in 2022 (feces, and intestinal and heart tissue), but not in fecal samples taken in 2019 and 2020. Next, we focused on the S1/S2 region within S, which contains the furin cleavage site (FCS), a key regulator of viral transmission and pathogenesis. We show that the FCoV-1 variants obtained from feces in 2017 and 2022 were identical, while the ones from conjunctiva (2017), heart (2022), and intestine (2017 and 2022) were distinct …

CAMbank: cfDNA BCT Field Processing v1 Page 1 protocols.io | https://dx.doi.org/10.17504/protocols.io.6qpvr33yovmk/v1 Aug 22 2023 1 AUG 22, 2023 CAMbank: cfDNA BCT Field Processing v1 Eliah G Overbey , Krista A Ryon , JangKeun Kim , Christopher E Mason Weill Cornell Medicine; BioAstra Eliah G Overbey Weill Cornell Medicine, BioAstra DOI: dx.doi.org/10.17504/protocols.io. 6qpvr33yovmk/v1 Protocol Citation: Eliah G Overbey, Krista A Ryon, JangKeun Kim, Christopher E Mason 2023. CAMbank: cfDNA BCT Field Processing v1. protocols.io https://dx.doi.org/10.17504/protoc ols.io.6qpvr33yovmk/v1 License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Protocol status: Working We use this protocol and it's working 1,…

Organismal adaptations to spaceflight have been characterized at the molecular level in model organisms, including Drosophila and C. elegans. Here we extend molecular work to energy metabolism and sex hormone signaling in mice and humans. We found spaceflight-induced changes in insulin and estrogen signaling in rodents and humans. Murine changes were most prominent in the liver, where we observed inhibition of insulin and estrogen receptor signaling with concomitant hepatic insulin resistance and steatosis. Based on the metabolic demand, metabolic pathways mediated by insulin and estrogen vary among muscles, specifically between the soleus and extensor digitorum longus. In humans, spaceflight induced changes in insulin and estrogen related genes and pathways. Pathway analysis demonstrated spaceflight-induced changes in insulin resistance, estrogen signaling, stress response, and viral infection. These data strongly suggest the need for further research on the metabolic and reproductive endocrinologic effects of space travel, if we are to become a successful interplanetary species

Introduction The ancient city of Tel Megiddo in the Jezreel Valley (Israel), which lasted from the Neolithic to the Iron Age, has been continuously excavated since 1903 and is now recognized as a World Heritage Site. The site features multiple ruins in various areas, including temples and stables, alongside modern constructions, and public access is allowed in designated areas. The site has been studied extensively since the last century; however, its microbiome has never been studied. We carried out the first survey of the microbiomes in Tel Megiddo. Our objectives were to study (i) the unique microbial community structure of the site, (ii) the variation in the microbial communities across areas, (iii) the similarity of the microbiomes to urban and archeological microbes, (iv) the presence and abundance of potential bio-corroding microbes, and (v) the presence and abundance of potentially pathogenic microbes. Methods We collected 40 swab samples from ten major areas and identified microbial taxa using next-generation sequencing of microbial genomes. These genomes were annotated and classified taxonomically and pathogenetically. Results We found that eight phyla, six of which exist in all ten areas, dominated the site (>99%). The relative sequence abundance of taxa varied between the ruins and the sampled materials and was assessed using all metagenomic reads mapping to a respective taxon. The site hosted unique taxa characteristic of the built environment and exhibited high similarity to the microbiome of other monuments. We identified acid-producing bacteria that may pose a risk to the site through biocorrosion and staining …

Mutations in IDH1, IDH2, and TET2 are recurrently observed in myeloid neoplasms. IDH1 and IDH2 encode isocitrate dehydrogenase isoforms, which normally catalyze the conversion of isocitrate to α-ketoglutarate (α-KG). Oncogenic IDH1/2 mutations confer neomorphic activity, leading to the production of D-2-hydroxyglutarate (D-2-HG), a potent inhibitor of α-KG-dependent enzymes which include the TET methylcytosine dioxygenases. Given their mutual exclusivity in myeloid neoplasms, IDH1, IDH2, and TET2 mutations may converge on a common oncogenic mechanism. Contrary to this expectation, we observed that they have distinct, and even opposite, effects on hematopoietic stem and progenitor cells in genetically engineered mice. Epigenetic and single-cell transcriptomic analyses revealed that Idh2R172K and Tet2 loss-of-function have divergent consequences on the expression and activity of key …

Missions into Deep Space are planned this decade. Yet the health consequences of exposure to microgravity and galactic cosmic radiation (GCR) over years-long missions on indispensable visceral organs such as the kidney are largely unexplored.

Angioimmunoblastic T cell lymphoma (AITL) is a peripheral T cell lymphoma that originates from T follicular helper (Tfh) cells and exhibits a prominent tumor microenvironment (TME). IDH2 and TET2 mutations co-occur frequently in AITL, but their contribution to tumorigenesis is poorly understood. We developed an AITL mouse model that is driven by Idh2 and Tet2 mutations. Malignant Tfh cells display aberrant transcriptomic and epigenetic programs that impair TCR signaling. Neoplastic Tfh cells bearing combined Idh2 and Tet2 mutations show altered cross-talk with germinal center B cells that promotes B cell clonal expansion while decreasing Fas-FasL interaction and reducing B cell apoptosis. The plasma cell count and angiogenesis are also increased in the Idh2-mutated tumors, implying a major relationship between Idh2 mutation and the characteristic AITL TME. Our mouse model recapitulates several …

Multiple Sclerosis (MS) is a complex disease of the CNS thought to require an environmental trigger. Gut dysbiosis is common in MS, but specifically causative species are unknown. To address this knowledge gap, we used sensitive and quantitative PCR detection to show that people with MS were more likely to harbor and show a greater abundance of epsilon toxin (ETX)-producing strains of C. perfringens within their gut microbiomes compared to healthy controls

Despite improvements in the treatment options, acute myeloid leukemia (AML) remains a fatal malignancy with an estimated 5-year relative survival rate of 31.7%. There is continued need for identification of new disease drivers to develop novel therapeutic options and improve clinical outcomes. Dysregulated transcriptional landscapes are associated with disease pathogenesis and treatment responses. To identify new disease drivers of AML, we analyzed RNA-Seq data from 59 patient-matched diagnosis and relapse (PAML) specimens (study cohort). A set of five differentially expressed genes (DEGs; STAT4, XRCC2, USP3, CEBPD, RBM47) with concordant changes in expression between diagnosis and relapse (Figure 1A) were selected for study using the following criteria: (a) concordant differential expression (DESeq2: log2FC > |1.2| and q < 0.05) in at least 25% of the relapsed patients in the study cohort (b …

1. The overall number of genes with recurrent oncogenic and likely oncogenic mutations in the study cohort was unchanged (Fig. 1A, B, Supplementary Fig. 2). 2. The comparison to BEAT AML data and the findings of a subset of mutations being enriched in the older AML patients remains unchanged (Fig. 1C, D). 3. Cytogenetics data was not originally available for the specimens excluded, thus these analyses and published results are unchanged.4. Conclusions from the somatic event co-occurrence analyses were unchanged (Fig. 1E, Supplementary Fig. 5). 5. Due to the smaller sample size, the threshold for inclusion in the regression tree analysis for association with overall survival was increased to keep the balance between false

The Polaris Dawn mission from SpaceX is set to launch this summer, and it will include some crew members who will also be taking the SpaceX Starship on its first mission in the next year or two in space. This is significant, as the Starship will likely be the first spacecraft to take humans back to the moon and then to the red planet. But if we do finally set foot on Mars, how long can we survive there and what resources (beyond potatoes) would we need to live on Mars long term? To answer such questions, we need to consider how much tweaking, adaptation, and engineering of life will be required (human, microbial, plant, fungal, and otherwise). We will also need to take evolutionary lessons from all creatures, big and small, with us. Related to this goal, nestled in a small bioreactor at Cornell University, New York, under eerie blue LED lights, are some very unusual cells that are prepared for such missions. These cells …

T cells are important in preventing severe disease from SARS-CoV-2, but scalable and field-adaptable alternatives to expert T-cell assays are needed. The interferon-gamma release assay QuantiFERON platform was developed to detect T-cell responses to SARS-CoV-2 from whole blood with relatively basic equipment and flexibility of processing timelines. Forty-eight participants with different infection and vaccination backgrounds were recruited. Whole blood samples were analysed using the QuantiFERON SARS-CoV-2 assay in parallel with the well-established ‘Protective Immunity from T Cells in Healthcare workers’ (PITCH) ELISpot, which can evaluate spike-specific T-cell responses. The primary aims of this cross-sectional observational cohort study were to establish if the QuantiFERON SARS-Co-V-2 assay could discern differences between specified groups and to assess the sensitivity of the assay …

BackgroundWastewater monitoring is increasingly used for community surveillance of infectious diseases, especially after the COVID-19 pandemic as the genomic footprints of pathogens shed by infected individuals can be traced in the environment. However, detection and concentration of pathogens in the environmental samples and their efficacy in predicting infectious diseases can be influenced by meteorological conditions and quality of samples.ObjectivesThis research examines whether meteorological conditions and sample pH affect SARS-CoV-2 concentrations in wastewater samples, and whether the association of SARS-CoV-2 with COVID-19 cases and mortality improves when adjusted for meteorological conditions and sample pH value in Miami-Dade County, FL.MethodsDaily wastewater samples were collected from Miami-Dade Wastewater Treatment Plant in Key Biscayne, Florida from August …

Sarcopenia is characterized by loss of muscle mass and strength in the elderly. Interestingly, astronauts suffer from a sarcopenic-like phenotype due to microgravity, thus effective countermeasures and preventive strategies are needed. Earth precision medicine combined with statistical, co-expression network and pathway analysis enables us to explore gene expression data from people with and without sarcopenia to obtain a list of 21 Key Genes (KGs). We then validated our KGs upon data from human endothelial cells cultured in the International Space Station, and astronauts’ samples from Japan Aerospace Exploration Agency and Inspiration 4 mission. Our results suggest that POMC and GOLGA8R are the most robust biomarkers identified for muscle loss. Finally, a pharmacological screening performed to target our KGs showed that POMC activity can be modulated using phase IV or approved drugs. Combining Earth’s precision medicine with space data is a promising approach to address common conditions related to accelerated aging.

Humans operating in extreme environments often conduct their operations at the edges of the limits of human performance. Sometimes, they are required to push these limits to previously unattained levels. As a result, their margins for error in execution are much smaller than that found in the general public. These same small margins for error that impact execution may also impact risk, safety, health, and even survival. Thus, humans operating in extreme environments have a need for greater refinement in their preparation, training, fitness, and medical care. Precision medicine (PM) is uniquely suited to address the needs of those engaged in these extreme operations because of its depth of molecular analysis, derived precision countermeasures, and ability to match each individual (and his or her specific molecular phenotype) with any given operating context (environment). Herein, we present an overview of a …

Wastewater-based epidemiology (WBE) has been utilized to track community infections of Coronavirus Disease 2019 (COVID-19) by detecting RNA of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), within samples collected from wastewater. The correlations between community infections and wastewater measurements of the RNA can potentially change as SARS-CoV-2 evolves into new variations by mutating. This study analyzed SARS-CoV-2 RNA and indicators of human waste in wastewater from two sewersheds of different scales (University of Miami (UM) campus and Miami-Dade County Central District wastewater treatment plant (CDWWTP)) during five internally defined COVID-19 variant dominant periods (Initial, Pre-Delta, Delta, Omicron, and Post-Omicron wave). SARS-CoV-2 RNA quantities were compared against COVID-19 clinical cases and hospitalizations to evaluate …

Molecular methods have been used to detect human pathogens in wastewater with sampling typically performed at wastewater treatment plants (WWTP) and upstream locations within the sewer system. A wastewater-based surveillance (WBS) program was established at the University of Miami (UM) in 2020, which included measurements of SARS-CoV-2 levels in wastewater from its hospital and within the regional WWTP. In addition to the development of a SARS-CoV-2 quantitative PCR (qPCR) assay, qPCR assays to detect other human pathogens of interest were also developed at UM. Here we report on the use of a modified set of reagents published by the CDC to detect nucleic acids of Monkeypox virus (MPXV) which emerged during May of 2022 to become a concern worldwide. Samples collected from the University hospital and from the regional WWTP were processed through DNA and RNA workflows …

Here, we performed shotgun metagenome sequencing of swab samples collected on floors at a train station in Narita City, Chiba, Japan. The taxonomic analysis revealed that Actinobacteria and Proteobacteria were the dominant phyla. The data will contribute to insight into the microbiome community on the surfaces of urban built environments.

With the advent of long‑term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram‑stain‑positive bacteria, including two spore‑forming and three non‑spore‑forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed> 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited< 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA–DNA hybridization values, when compared to any known bacterial species, were< 94% and< 50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In‑depth annotation of the genomes unveiled a variety of genes …

Maintenance of astronaut health during spaceflight will require monitoring and potentially modulating their microbiomes, which play a role in some space-derived health disorders. However, documenting the response of microbiota to spaceflight has been difficult thus far due to mission constraints that lead to limited sampling. Here, we executed a six-month longitudinal study centered on a three-day flight to quantify the high-resolution microbiome response to spaceflight. Via paired metagenomics and metatranscriptomics alongside single immune profiling, we resolved a microbiome “architecture” of spaceflight characterized by time-dependent and taxonomically divergent microbiome alterations across 750 samples and ten body sites. We observed pan-phyletic viral activation and signs of persistent changes that, in the oral microbiome, yielded plaque-associated pathobionts with strong associations to immune cell …

Spaceflight poses a unique set of challenges to humans and the hostile Spaceflight environment can induce a wide range of increased health risks, including dermatological issues. The biology driving the frequency of skin issues in astronauts is currently not well understood. To address this issue, we used a systems biology approach utilizing NASA’s Open Science Data Repository (OSDR) on spaceflown murine transcriptomic datasets focused on the skin, biomedical profiles from fifty NASA astronauts, and confirmation via transcriptomic data from JAXA astronauts, the NASA Twins Study, and the first civilian commercial mission, Inspiration4. Key biological changes related to skin health, DNA damage & repair, and mitochondrial dysregulation were determined to be involved with skin health risks during Spaceflight. Additionally, a machine learning model was utilized to determine key genes driving Spaceflight …

The use of wastewater-based surveillance (WBS) for detecting pathogens within communities has been growing since the beginning of the COVID-19 pandemic with early efforts investigating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA in wastewater. Recent efforts have shed light on the utilization of WBS for alternative targets, such as fungal pathogens, like Candida auris, in efforts to expand the technology to assess non-viral targets. The objective of this study was to extend workflows developed for SARS-CoV-2 quantification to evaluate whether C. auris can be recovered from wastewater, inclusive of effluent from a wastewater treatment plant (WWTP) and from a hospital with known numbers of patients colonized with C. auris. Measurements of C. auris in wastewater focused on culture-based methods and quantitative PCR (qPCR). Results showed that C. auris can be cultured from …

Human space exploration is hazardous, causing molecular changes that can alter astronauts' health. This can include genomic instability, mitochondrial dysfunction, increased inflammation, homeostatic dysregulation, and epigenomic changes. These alterations are similar to changes during aging on Earth. However, little is known about the link between these changes and disease development in space. Frailty syndrome is a robust predictor associated with biological aging, however its existence during spaceflight has not been examined. We used murine data from NASA’s GeneLab and astronaut data from JAXA and Inspiration4 missions to evaluate the presence of biological markers and pathways related to frailty, aging and sarcopenia. We identified changes in gene expression that could be related to the development of a frailty-like condition. These results suggest that the parallels between spaceflight and aging may extend to frailty as well. Future studies examining the utility of a frailty index in monitoring astronaut health appear warranted.

BackgroundOver half of the world’s population lives in urban areas with, according to the United Nations, nearly 70% expected to live in cities by 2050. Our cities are built by and for humans, but are also complex, adaptive biological systems involving a diversity of other living species. The majority of these species are invisible and constitute the city’s microbiome. Our design decisions for the built environment shape these invisible populations, and as inhabitants we interact with them on a constant basis. A growing body of evidence shows us that human health and well-being are dependent on these interactions. Indeed, multicellular organisms owe meaningful aspects of their development and phenotype to interactions with the microorganisms—bacteria or fungi—with which they live in continual exchange and symbiosis. Therefore, it is meaningful to establish microbial maps of the cities we inhabit. While the …

BackgroundOral microbial therapy has been studied as an intervention for a range of gastrointestinal disorders. Though research suggests that microbial exposure may affect the gastrointestinal system, motility, and host immunity in a pediatric population, data have been inconsistent, with most prior studies being in neither a randomized nor placebo-controlled setting. The aim of this randomized, placebo-controlled study was to evaluate the efficacy of a synbiotic on increasing weekly bowel movements (WBMs) in constipated children.MethodsSixty-four children (3–17 years of age) were randomized to receive a synbiotic (n = 33) comprising mixed-chain length oligosaccharides and nine microbial strains, or placebo (n = 31) for 84 days. Stool microbiota was analyzed on samples collected at baseline and completion. The primary outcome was a change from baseline of WBMs in the treatment group compared to …

Antibiotic resistance is a growing problem worldwide—and in outer space. Spaceflight can promote biofilm formation and antimicrobial resistance development, and astronauts are especially vulnerable to infection due to the unique demands of spaceflight. To support future space travel, it is critical to understand exactly how spaceflight affects microbial diversity and virulence. To learn more, researchers recently used a machine learning algorithm to analyze sequencing data from the Microbial Tracking (MT)-1 mission, which sampled microbes at eight locations on the International Space Station during three flights. The model predicted the presence of hundreds of antibiotic resistance genes (ARGs) in the 226 bacterial strains isolated from the flights, including strains of the potentially very pathogenic bacterium Enterobacter bugandensis and the food poisoning-related bacterium Bacillus cereus. Antibiotic …

ObjectiveMetatranscriptomic analysis of RNA viromes on built-environment surfaces is hampered by low RNA yields and high abundance of rRNA. Therefore, we evaluated the quality of libraries, efficiency of rRNA depletion, and viral detection sensitivity using a mock community and a melamine-coated table surface RNA with levels below those required (< 5 ng) with a library preparation kit (NEBNext Ultra II Directional RNA Library Prep Kit).ResultsGood-quality RNA libraries were obtained from 0.1 ng of mock community and table surface RNA by changing the adapter concentration and number of PCR cycles. Differences in the target species of the rRNA depletion method affected the community composition and sensitivity of virus detection. The percentage of viral occupancy in two replicates was 0.259 and 0.290% in both human and bacterial rRNA-depleted samples, a 3.4 and 3.8-fold increase compared with …

Wastewater, which contains everything from pathogens to pollutants, is a geospatially- and temporally-linked microbial fingerprint of a given population. As a result, it can be leveraged for monitoring multiple dimensions of public health across locales and time. Here, we integrate targeted and bulk RNA sequencing (n=1,419 samples) to track the viral, bacterial, and functional content over geospatially distinct areas within Miami Dade County from 2020-2022. First, we used targeted amplicon sequencing (n=966) to track diverse SARS-CoV-2 variants across space and time, and we found a tight correspondence with clinical caseloads from University students (N = 1,503) and Miami-Dade County hospital patients (N = 3,939 patients), as well as an 8-day earlier detection of the Delta variant in wastewater vs. in patients. Additionally, in 453 metatranscriptomic samples, we demonstrate that different wastewater sampling locations have clinically and public-health-relevant microbiota that vary as a function of the size of the human population they represent. Through assembly, alignment-based, and phylogenetic approaches, we also detect multiple clinically important viruses (e.g., norovirus) and describe geospatial and temporal variation in microbial functional genes that indicate the presence of pollutants. Moreover, we found distinct profiles of antimicrobial resistance (AMR) genes and virulence factors across campus buildings, dorms, and hospitals, with hospital wastewater containing a significant increase in AMR abundance. Overall, this effort lays the groundwork for systematic characterization of wastewater to improve public health decision making …

The power of the ever-increasing tools and algorithms for prediction and their paradoxical effects on risk. The Age of Prediction is about two powerful, and symbiotic, trends: the rapid development and use of artificial intelligence and big data to enhance prediction, as well as the often paradoxical effects of these better predictions on our understanding of risk and the ways we live. Beginning with dramatic advances in quantitative investing and precision medicine, this book explores how predictive technology is quietly reshaping our world in fundamental ways, from crime fighting and warfare to monitoring individual health and elections. As prediction grows more robust, it also alters the nature of the accompanying risk, setting up unintended and unexpected consequences. The Age of Prediction details how predictive certainties can bring about complacency or even an increase in risks—genomic analysis might lead to unhealthier lifestyles or a GPS might encourage less attentive driving. With greater predictability also comes a degree of mystery, and the authors ask how narrower risks might affect markets, insurance, or risk tolerance generally. Can we ever reduce risk to zero? Should we even try? This book lays an intriguing groundwork for answering these fundamental questions and maps out the latest tools and technologies that power these projections into the future, sometimes using novel, cross-disciplinary tools to map out cancer growth, people’s medical risks, and stock dynamics.

Mantle cell lymphoma (MCL) is an incurable B-cell malignancy with an overall poor prognosis, particularly for patients that progress on targeted therapies. Novel, more durable treatment options are needed for patients with MCL. Protein arginine methyltransferase 5 (PRMT5) is overexpressed in MCL and plays an important oncogenic role in this disease via epigenetic and posttranslational modification of cell cycle regulators, DNA repair genes, components of prosurvival pathways, and RNA splicing regulators. The mechanism of targeting PRMT5 in MCL remains incompletely characterized. Here, we report on the antitumor activity of PRMT5 inhibition in MCL using integrated transcriptomics of in vitro and in vivo models of MCL. Treatment with a selective small-molecule inhibitor of PRMT5, PRT-382, led to growth arrest and cell death and provided a therapeutic benefit in xenografts derived from patients with …

RNA sequencing (RNA-seq) is a powerful technology for gene expression and functional genomics profiling. Expression profiles generated using this approach can be impacted by the methods utilised for cDNA library generation. Selection of the optimal parameters for each step during the protocol are crucial for acquisition of high-quality data. Polymerase chain reaction (PCR) amplification of transcripts is a common step in many RNA-seq protocols and, if not optimised, high PCR duplicate proportions can be generated, resulting in the inflation of transcript counts and introduction of bias. In this study, we investigate the impact of input amount and PCR cycle number on the PCR duplication rate and on the RNA-seq data quality using a broad range of inputs (1 ng - 1,000 ng) for RNA-seq library preparation with unique molecular identifiers (UMIs) and sequencing the data on four different short-read sequencing platforms: Illumina NovaSeq 6000, Illumina NovaSeq X, Element Biosciences AVITI, and Singular Genomics G4. Across all platforms, samples of input amounts greater than 125 ng had a negligible PCR duplication rate and the number of PCR cycles did not have a significant effect on data quality. However, for input amounts lower than 125ng we observed a strong negative correlation between input amount and the proportion of PCR duplicates; between 34% and 96% of reads were discarded via deduplication. Fortunately, UMIs were effective for removing in silico PCR duplicates without removing valuable biological information. Removal of PCR duplicates resulted in more comparable gene expression obtained from the different PCR …

Genomic footprints of pathogens shed by infected individuals can be traced in environmental samples, which can serve as a noninvasive method of infectious disease surveillance. The research evaluates the efficacy of environmental monitoring of SARS-CoV-2 RNA in air, surface swabs and wastewater to predict COVID-19 cases. Using a prospective experimental design, air, surface swabs, and wastewater samples were collected from a college dormitory housing roughly 500 students from March to May 2021 at the University of Miami, Coral Gables, FL. Students were randomly screened for COVID-19 during the study period. SARS-CoV-2 concentration in environmental samples was quantified using Volcano 2nd Generation-qPCR. Descriptive analyses were conducted to examine the associations between time-lagged SARS-CoV-2 in environmental samples and COVID-19 cases. SARS-CoV-2 was detected in …

High-linear energy transfer (LET) ionizing radiation is a major health hazard for astronauts who will be exposed to galactic cosmic rays during upcoming lunar and Mars missions. Predicting and mitigating this risk requires understanding the factors underlying individual radiation sensitivity. We started to address this challenge by identifying the genomic and phenotypic associations with sensitivity to low and high-LET ionizing radiation ex vivo in over 750 healthy human donors. We exposed primary human blood mononuclear cells to simulated galactic cosmic ray components: 350MeV/n (28)Si, 350MeV/n (40)Ar and 600MeV/n (56)Fe particles, at 1.1 and 3 particles/100µm^(2) fluences, as well as 0.1 Gy and 1 Gy doses of gamma rays, and analyzed the outcomes at 4 and 24 hours post-irradiation. We quantified DNA damage and repair responses based on 53BP1^(+) radiation-induced foci formation, together with oxidative stress and changes in secreted factors including immune cytokines and exosomes. We also analyzed phenotypic associations with spontaneous DNA repair foci at baseline prior to irradiation. We identified an increase in spontaneous DNA repair associated with age and latent viral infection, and observed that human spontaneous DNA repair foci at baseline can serve as a negative predictor of DNA repair and immunoregulatory cytokine production after irradiation. Furthermore, we observed a wide variability of subject- and LET-dependent radiation responses, with radiation-induced DNA repair foci increasing by dose and LET, and high-LET particle radiation resulting in more residual DNA damage compared to low-LET …

Lethal COVID-19 outcomes are most often attributed to classic cytokine storm and attendant excessive immune signaling. We re-visit this question using RNA sequencing in nasopharyngeal and 40 autopsy samples from COVID-19-positive and negative individuals. In nasal swabs, the top 100 genes which significantly correlated with COVID-19 viral load, include many canonical innate immune genes. However, 22 much less studied "non-canonical" genes are found and despite the absence of viral transcripts, subsets of these are upregulated in heart, lung, kidney, and liver, but not mediastinal lymph nodes. An important regulatory potential emerges for the non-canonical genes for over-activating the renin-angiotensin-activation-system (RAAS) pathway, resembling this phenomenon in hereditary angioedema (HAE) and its overlapping multiple features with lethal COVID-19 infections. Specifically, RAAS overactivation links increased fibrin deposition, leaky vessels, thrombotic tendency, and initiating the PANoptosis death pathway, as suggested in heart, lung, and especially mediastinal lymph nodes, with a tightly associated mitochondrial dysfunction linked to immune responses. For mediastinal lymph nodes, immunohistochemistry studies validate the transcriptomic findings showing abnormal architecture, excess fibrin and collagen deposition, and pathogenic fibroblasts. Further, our findings overlap findings in SARS-CoV-2 infected hamsters, C57BL/6 and BALB/c mouse models, and importantly peripheral blood mononuclear cell (PBMC) and whole blood samples from COVID-19 patients infected with early variants and later SARS-CoV-2 strains …

MicroRNAs (miRNAs) are small, non-coding RNA molecules that are post-transcriptional regulators of gene expression. miRNAs have been shown to be key regulators of complicated pathological processes and hence great biomarkers for the early prediction of diseases, such as cardiovascular diseases and radiation-associated alteration after spaceflight. In this study, we present possible antagomir treatments targeting three different miRNAs, miR-16-5p, miR-125b-5p, and let-7a-5p, to mitigate the activity of the spaceflight environment in cardiovascular diseases. We focus on three proteins of interest associated with fibrotic remodeling, TGF-β1, SMAD3, and COL1, analyzing the molecular outcomes of antagomir treatment when exposed to Galactic Cosmic Radiation (GCR), Solar Particle Events (SPE) radiation, and microgravity. These proteins have been shown to play different fibrotic and antifibrotic roles and show molecular changes associated with exposure to the space environment. Furthermore, our results demonstrate the therapeutic potential of antagomirs as a countermeasure for future spaceflight missions.

With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which …

Mutations in the SWI/SNF chromatin remodeling complex BAF are a recurring feature in many cancers, with a high prevalence in follicular lymphoma (FL; >19%) and diffuse large B-cell lymphoma (DLBCL; >34%). Despite this, the mechanism that links mutations in ARID1A, most frequently mutated BAF subunit, to the development of lymphoma is still not understood.To this aim, we crossed Arid1a-floxed mice with Cγ1-Cre mice to yield offspring with a conditional (cKO) Arid1a deletion in germinal center (GC) B cells, FL and DLBCL cell-of-origin. We immunized WT/WT ( Arid1a+/+; Cγ1Cre/+) and cKO/WT ( Arid1a+/-; Cγ1Cre/+) mice with sheep red blood cells and analyzed 10 days later at the peak of the GC reaction. Upon Arid1a deletion, we found a decrease in the total number of GC B cells relative to total B cells (WT/WT vs. cKO/WT; p<0.001). However, we observed skewing of GC polarity manifesting as increased …

The utility of using severe-acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA for assessing the prevalence of COVID-19 within communities begins with the design of the sample collection program. The objective of this study was to assess the utility of 24-hour composites as representative samples for measuring multiple microbiological targets in wastewater, and whether normalization of SARS-CoV-2 by endogenous targets can be used to decrease hour to hour variability at different watershed scales. Two sets of experiments were conducted, in tandem with the same wastewater, with samples collected at the building, cluster, and community sewershed scales. The first set of experiments focused on evaluating degradation of microbiological targets: SARS-CoV-2, Simian Immunodeficiency Virus (SIV) – a surrogate spiked into the wastewater, plus human waste indicators of Pepper Mild Mottle Virus …

Wastewater-based surveillance (WBS) is a noninvasive, epidemiological strategy for assessing the spread of COVID-19 in communities. This strategy was based upon wastewater RNA measurements of the viral target, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The utility of WBS for assessing the spread of COVID-19 has motivated research to measure targets beyond SARS-CoV-2, including pathogens containing DNA. The objective of this study was to establish the necessary steps for isolating DNA from wastewater by modifying a long-standing RNA-specific extraction workflow optimized for SARS-CoV-2 detection. Modifications were made to the sample concentration process and included an evaluation of bead bashing prior to the extraction of either DNA or RNA. Results showed that bead bashing reduced detection of RNA from wastewater but improved recovery of DNA as assessed by quantitative polymerase chain reaction (qPCR). Bead bashing is therefore not recommended for the quantification of RNA viruses using qPCR. Whereas for Mycobacterium bacterial DNA isolation, bead bashing was necessary for improving qPCR quantification. Overall, we recommend 2 separate workflows, one for RNA viruses that does not include bead bashing and one for other microbes that use bead bashing for DNA isolation. The experimentation done here shows that current-standing WBS program methodologies optimized for SARS-CoV-2 need to be modified and reoptimized to allow for alternative pathogens to be readily detected and monitored, expanding its utility as a tool for public health assessment.

The SpaceX Inspiration4 mission provided a unique opportunity to study the impact of spaceflight on the human body. Biospecimen samples were collected from the crew at different stages of the mission, including before (L-92, L-44, L-3 days), during (FD1, FD2, FD3), and after (R+ 1, R+ 45, R+ 82, R+ 194 days) spaceflight, creating a longitudinal sample set. The collection process included samples such as venous blood, capillary dried blood spot cards, saliva, urine, stool, body swabs, capsule swabs, SpaceX Dragon capsule HEPA filter, and skin biopsies, which were processed to obtain aliquots of serum, plasma, extracellular vesicles, and peripheral blood mononuclear cells. All samples were then processed in clinical and research laboratories for optimal isolation and testing of DNA, RNA, proteins, metabolites, and other biomolecules. This paper describes the complete set of collected biospecimens, their processing steps, and long-term biobanking methods, which enable future molecular assays and testing. As such, this study details a robust framework for obtaining and preserving high-quality human, microbial, and environmental samples for aerospace medicine in the Space Omics and Medical Atlas (SOMA) initiative, which can also aid future experiments in human spaceflight and space biology.

BackgroundWith the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habits, and how microbes survive, proliferate and spread in space conditions, is coming more and more important. The Microbial Tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the International Space Station (ISS).ResultsThe analysis of their 16S rRNA gene sequences revealed< 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing (WGS) was undertaken. For all strains, the gyrB gene exhibited< 93 …

Results:To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed a module-based metagenomics analysis system written in Snakemake, a popular workflow management system, along with a standardized module and working directory architecture. Each module can be run independently or conjointly with a series of others to produce the target data format (ex. short-read preprocessing alone, or short-read preprocessing followed by de novo assembly), and outputs aggregated summary statistics reports and semi-guided Jupyter notebook-based visualizations, The module system is a bioinformatics-optimzied scaffold designed to be rapidly iterated upon by the research community at large.Availability:The module template as well as the modules described below can be found at https://github. com/MetaSUB-CAMP.

Background & AimsA number of genetic polymorphisms have been associated with susceptibility to or protection against non-alcoholic fatty liver disease (NAFLD), but the underlying mechanisms remain unknown. Here, we focused on the rs738409 C>G single nucleotide polymorphism (SNP), which produces the I148M variant of patatin-like phospholipase domain-containing protein 3 (PNPLA3) and is strongly associated with NAFLD.MethodsTo enable mechanistic dissection, we developed a human pluripotent stem cell (hPSC)-derived multicellular liver culture by incorporating hPSC-derived hepatocytes, hepatic stellate cells, and macrophages. We first applied this liver culture to model NAFLD by utilising a lipotoxic milieu reflecting the circulating levels of disease risk factors in affected individuals. We then created an isogenic pair of liver cultures differing only at rs738049 and compared NAFLD phenotype …

During the construction and assembly of the Mars 2020 mission components at two different NASA cleanrooms, several fungal strains were isolated. Based on their colony morphology, two strains that showed yeast-like appearance were further characterized for their phylogenetic position. The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. The strain FJI-L2-BK-P3T, isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility, was placed in the Naganishia albida clade …

Protein function prediction based on amino acid sequence alone is an extremely challenging but important task, especially in metagenomics/metatranscriptomics field, in which novel proteins have been uncovered exponentially from new microorganisms. Many of them are extremely low homology to known proteins and cannot be annotated with homology-based or information integrative methods. To overcome this problem, we proposed a Homology Independent protein Function annotation method (HiFun) based on a unified deep-learning model by reassembling the sequence as protein language. The robustness of HiFun was evaluated using the benchmark datasets and metrics in the CAFA3 challenge. To navigate the utility of HiFun, we annotated 2 212 663 unknown proteins and discovered novel motifs in the UHGP-50 catalog. We proved that HiFun can extract latent function related structure features …

Multiple sclerosis (MS) is a complex disease of the CNS thought to require an environmental trigger. Gut dysbiosis is common in MS, but specific causative species are unknown. To address this knowledge gap, we used sensitive and quantitative PCR detection to show that people with MS were more likely to harbor and show a greater abundance of epsilon toxin–producing (ETX-producing) strains of C. perfringens within their gut microbiomes compared with individuals who are healthy controls (HCs). Isolates derived from patients with MS produced functional ETX and had a genetic architecture typical of highly conjugative plasmids. In the active immunization model of experimental autoimmune encephalomyelitis (EAE), where pertussis toxin (PTX) is used to overcome CNS immune privilege, ETX can substitute for PTX. In contrast to PTX-induced EAE, where inflammatory demyelination is largely restricted to the …

From our previous work we have shown a key miRNA signature that is associated with spaceflight can be used as a biomarker and countermeasure to mitigate the damage caused by space radiation. Here, we have further expanded on this work to determine key biological factors that are being rescued by the countermeasure treatment. We performed RNA-sequencing and transcriptomic analysis on our established 3D microvessel cell cultures exposed to simulated deep space radiation (0.5 Gy of Galactic Cosmic Radiation) with and without the antagonists to three microRNAs (ie antagomirs). Significant reduction of inflammation and DNA DSBs activity is observed, along with key mitochondria functions being rescued after antagomir treatment. Lastly, we compared the key genes and pathways involved with the antagomirs with astronaut data from Inspiration4 and JAXA missions to demonstrate that the key genes and pathways associated with these experiments occur in humans and this countermeasure strategy can potentially be utilized in astronauts to mitigate the space radiation response.

The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called ‘probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of …

The COVID-19 pandemic revealed that global health, social systems, and economies can be surprisingly fragile in an increasingly interconnected and interdependent world. Yet, during the last half of 2022, and quite remarkably, we began dismantling essential infectious disease monitoring programs in several countries. Absent such programs, localized biological risks will transform into global shocks linked directly to our lack of foresight regarding emerging health risks. Additionally, recent studies indicate that more than half of all infectious diseases could be made worse by climate change, complicating pandemic containment. Despite this complexity, the factors leading to pandemics are largely predictable but can only be realized through a well-designed global early warning system. Such a system should integrate data from genomics, climate and environment, social dynamics, and healthcare infrastructure. The glue for such a system is community-driven modeling, a modern logistics of data, and democratization of AI tools. Using the example of dengue fever in Brazil, we can demonstrate how thoughtfully designed technology platforms can build global-scale precision disease detection and response systems that significantly reduce exposure to systemic shocks, accelerate science-informed public health policies, and deliver reliable healthcare and economic opportunities as an intrinsic part of the global sustainable development agenda.

Iron accumulation in cancer cells contributes to malignant progression and chemoresistance. While disrupting this process can influence various hallmarks of cancer, the immunomodulatory effects of chelating iron in tumors remain undefined. Here, we report that treatment with deferiprone, an FDA-approved iron chelator, elicits innate immune responses that control metastatic ovarian cancer. Deferiprone reprogrammed ovarian cancer cells towards an immunostimulatory state characterized by enhanced production of type I interferon (IFN) and surface overexpression of molecules that activate natural killer (NK) cells. Mechanistically, this reprogramming was driven by innate sensing of mitochondrial DNA in the cytosol and concomitant activation of nuclear DNA damage responses evoked upon iron chelation. Deferiprone administration synergized with chemotherapy and prolonged the survival of mice bearing metastatic ovarian cancer by bolstering intratumoral NK cell infiltration and type I IFN responses. Iron chelation may represent an alternative immunotherapeutic approach for malignancies that are normally refractory to T cell-centric modalities.

Mutations affecting enhancer chromatin regulators CREBBP and KMT2D are highly co-occurrent in germinal center (GC)-derived lymphomas and other tumors, even though regulating similar pathways. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d (C+K) indeed accelerated lymphomagenesis. C+K haploinsufficiency induced GC hyperplasia by altering cell fate decisions, skewing B cells away from memory and plasma cell differentiation. C+K deficiency particularly impaired enhancer activation for immune synapse genes involved in exiting the GC reaction. This effect was especially severe at super-enhancers for immunoregulatory and differentiation genes. Mechanistically, CREBBP and KMT2D formed a complex, were highly co-localized on chromatin, and were required for each-other’s stable recruitment to enhancers. Notably, C+K lymphomas in mice and humans manifested significantly reduced CD8+ T-cell abundance. Hence, deficiency of C+K cooperatively induced an immune evasive phenotype due at least in part to failure to activate key immune synapse super-enhancers, associated with altered immune cell fate decisions.SIGNIFICANCEAlthough CREBBP and KMT2D have similar enhancer regulatory functions, they are paradoxically co-mutated in lymphomas. We show that their combined loss causes specific disruption of super-enhancers driving immune synapse genes. Importantly, this leads to reduction of CD8 cells in lymphomas, linking super-enhancer function to immune surveillance, with implications for immunotherapy resistance.

Space biology research aims to understand fundamental spaceflight effects on organisms, develop foundational knowledge to support deep space exploration and, ultimately, bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals and humans for sustained multi-planetary life. To advance these aims, the field leverages experiments, platforms, data and model organisms from both spaceborne and ground-analogue studies. As research is extended beyond low Earth orbit, experiments and platforms must be maximally automated, light, agile and intelligent to accelerate knowledge discovery. Here we present a summary of decadal recommendations from a workshop organized by the National Aeronautics and Space Administration on artificial intelligence, machine learning and modelling applications that offer solutions to these space biology challenges. The integration of …

Background Immunosuppressed patients and those experiencing complicated UTIs are more susceptible to misdiagnosis by outdated standard of care (SOC) diagnostics; resulting in ineffective treatment and risk of severe complications. Shotgun metagenomic sequencing can act as a highly accurate tool in profiling urogenital pathogens in high-risk patients. We assessed the performance of a genomic-based urine assay in patients where the SOC failed to identify pathogens and compiled clinical metadata from medical records to evaluate if antimicrobial stewardship could be improved. Methods Culture negative (no growth or < 100k CFU/mL) urine specimens (n=140) were collected from patients with pyuria and UTI symptoms then processed with the BIOTIA-ID Urine NGS Assay including DNA extraction, library preparation, Illumina NextSeq sequencing and analysis by BIOTIA …

Background: Acute myeloid leukemia in patients over the age of 60 (aAML) is associated with poor prognosis. aAML patients are the majority diagnosed but are underrepresented in large molecular studies. We have identified two clinical subgroups of aAML patients with distinct survival outcomes (low-risk and high-risk) in ECOG-ACRIN Cancer Research Group's clinical trial E3999 (NCT00046930). We hypothesize that these two groups are characterized by distinct biological mechanisms that contribute to leukemogenesis. We also hypothesize that the low-risk group harbor molecular and phenotypic signatures characteristic of known better-risk AMLs.Methods: Diagnostic specimens were obtained from patients enrolled in NCT00046930. Disease enriched cells were isolated by negative selection of lymphocytes (magnetic beads). Flow cytometry was used to characterize the blast population. Bulk RNA-sequencing …

The role of the space environment in activating a diverse set of genes involved in regulating key cellular pathways is now widely recognized. This includes genes associated with blood control and erythropoiesis, with a particular emphasis on those involved in globin chain production. The comprehensive investigation of haemoglobin biology provides an intriguing model for studying space omics, as it has been extensively explored at multiple-omic levels, spanning DNA, RNA, and protein analyses, in both experimental and clinical contexts. In this study, we examined the developmental expression of haemoglobin over time and space using a unique suite of multi-omic tools available on NASA GeneLab. We analyzed human data from the NASA Twins Study, the JAXA CFE study, and the Inspiration4 mission. Our findings reveal significant variations in globin gene expression corresponding to the distinct spatiotemporal characteristics of the collected samples. This study sheds light on the dynamic nature of globin gene regulation in response to the space environment and provides valuable insights into the broader implications of space omics research.

The purpose of this study is to identify key regulatory pathways that potentially drive abnormal gene expression program in relapsed Acute Myeloid Leukemia (AML) patients, by integrative computational analyses on multi-omics molecular profiles. Relapsed AML remains a clinical challenge. Epigenetic heterogeneity may contribute to transcriptional dysregulation and disease progression in AML. However, what specific transcriptional programs and potential regulatory mechanisms contribute to disease relapse are not yet well understood. To characterize the global transcriptional landscapes in relapsed AML, we integrated genomics data from two cohorts of matched diagnosis and relapse patient specimens. We identified 5,416 differentially expressed genes (DEGs) between diagnosis and relapse in Cohort I. Unsupervised clustering yielded three distinct DEG groups: group A, B and C genes that were …

Cyanobacteria are photosynthetic organisms that play important roles in carbon cycling as well as promising bioproduction chassis. Here, we isolate two novel cyanobacteria, UTEX 3221 and UTEX 3222, from a unique marine environment with naturally elevated CO₂. We describe complete genome sequences for both isolates and, focusing on UTEX 3222 due to its planktonic growth in liquid, characterize biotechnologically-relevant growth and biomass characteristics. UTEX 3222 outpaces other fast-growing model strains on solid medium. It can double every 2.35 hours in a liquid medium and grows to high density (>31g/L biomass dry weight) in batch culture, nearly double that of Synechococcus sp. PCC 11901, whose high-density growth was recently reported. In addition, UTEX 3222 sinks readily, settling more quickly than other fast-growing strains, suggesting improved de-watering of UTEX 3222 biomass. This settling behavior can be explained in part by larger cell volume. These traits may make UTEX 3222 a compelling choice for photosynthetic bioproduction from CO₂. Overall, we find that bio-prospecting in environments with naturally elevated CO₂ may uncover novel CO₂-metabolizing organisms with unique characteristics.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating glycolysis. We analyzed mitochondrial gene expression in nasopharyngeal and autopsy tissues from patients with coronavirus disease 2019 (COVID-19). In nasopharyngeal samples with declining viral titers, the virus blocked the transcription of a subset of nuclear DNA (nDNA)–encoded mitochondrial OXPHOS genes, induced the expression of microRNA 2392, activated HIF-1α to induce glycolysis, and activated host immune defenses including the integrated stress response. In autopsy tissues from patients with COVID-19, SARS-CoV-2 was no longer present, and mitochondrial gene transcription had recovered in the lungs. However, nDNA mitochondrial gene expression remained suppressed in autopsy tissue from the heart and …

Antibiotic resistance is a global health challenge, urgently requiring solutions from multi-disciplinary studies. Existing researches have pinpointed the potential of greenness as a nature-based solution to reduce pathogen abundance. Nevertheless, it remains unknown whether this efficacy extends to antibiotic-resistant pathogens, and furthermore, how this effect varies across global climate zones and urbanization gradient. Here, using 2875 samples worldwide, we examined the effect of Normalized Difference Vegetation Index (NDVI) on the abundance of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens at the global scale, as well as in subgroups with samples of four different climate zones and urbanization statuses. Results showed that NDVI was significantly and negatively correlated with …

A third of patients with diffuse large B-cell lymphoma (DLBCL) present with extranodal dissemination, which is associated with inferior clinical outcomes. MYD88L265P is a hallmark extranodal DLBCL mutation that supports lymphoma proliferation. Yet extranodal lymphomagenesis and the role of MYD88L265P in transformation remain mostly unknown. Here, we show that B cells expressing Myd88L252P (MYD88L265P murine equivalent) activate, proliferate, and differentiate with minimal T-cell costimulation. Additionally, Myd88L252P skewed B cells toward memory fate. Unexpectedly, the transcriptional and phenotypic profiles of B cells expressing Myd88L252P, or other extranodal lymphoma founder mutations, resembled those of CD11c+T-BET+ aged/autoimmune memory B cells (AiBC). AiBC-like cells progressively accumulated in animals prone to develop lymphomas, and ablation of T-BET …

During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient viral surveillance tool that takes into account asymptomatic cases and can identify known and novel mutations and offers the opportunity to assign known virus lineages based on the detected mutations profiles. WWGS can also hint towards novel or cryptic lineages, but it is difficult to clearly identify and define novel lineages from wastewater (WW) alone. While WWGS has significant advantages in monitoring SARS-CoV-2 viral spread, technical challenges remain, including poor sequencing coverage and quality due to viral RNA degradation. As a result, the viral RNAs in wastewater have low concentrations and are often fragmented, making sequencing difficult. WWGS analysis requires advanced computational tools that are yet to be developed and benchmarked. The existing bioinformatics tools used to analyze wastewater sequencing data are often based on previously developed methods for quantifying the expression of transcripts or viral diversity. Those methods were not developed for wastewater sequencing data specifically, and are not optimized to address unique challenges associated with wastewater. While specialized tools for analysis of wastewater sequencing data have also been developed recently, it remains to be seen how they will perform given the ongoing evolution of SARS-CoV-2 and the decline in testing and patient-based genomic surveillance. Here, we discuss opportunities and challenges associated with WWGS, including sample preparation, sequencing technology, and bioinformatics methods.

Members of the family Trichomeriaceae, belonging to the Chaetothyriales order and the Ascomycota phylum, are known for their capability to inhabit hostile environments characterized by extreme temperatures, nutrient scarcity (oligotrophic conditions), presence of toxic compounds, or drought conditions. Within this family, the genus Knufia encompasses the vast majority of polyextremophilic species. In this report, the genomic and morphological features of the strain FJI-L2-BK-P2, identified as Knufia obscura, are presented. The identification is based on multi-locus sequence analysis and whole genome sequence phylogeny. The strain FJI-L2-BK-P2 was isolated from the Mars 2020 mission spacecraft assembly facility located at the Jet Propulsion Laboratory in Pasadena, California. Additionally, the type strain of K. obscura (CBS 148926T), originally isolated from a car's gas tank in Italy, has been sequenced and annotated. The morphological analysis and description of the genomic characteristics of K. obscura FJI-L2-BK-P2 may contribute to refining the taxonomy of Knufia species. Key morphological features are reported in this K. obscura strain, resembling microsclerotia and chlamydospore-like propagules. These features, known to be significant in black fungi, could potentially facilitate their adaptation to harsh environments.

Viruses in built environments (BEs) raise public health concerns, yet they are generally less studied than bacteria. To better understand viral dynamics in BEs, this study assesses viromes from 11 habitats across four types of BEs with low to high occupancy. The diversity, composition, metabolic functions, and lifestyles of the viromes are found to be habitat dependent. Caudoviricetes species are ubiquitous on surface habitats in the BEs, and some of them are distinct from those present in other environments. Antimicrobial resistance genes are identified in viruses inhabiting surfaces frequently touched by occupants and in viruses inhabiting occupants’ skin. Diverse CRISPR/Cas immunity systems and anti-CRISPR proteins are found in bacterial hosts and viruses, respectively, consistent with the strongly coupled virus–host links. Evidence of viruses potentially aiding host adaptation in a specific-habitat manner is …

Human exploration of deep space will involve missions of substantial distance and duration. To effectively mitigate health hazards, paradigm shifts in astronaut health systems are necessary to enable Earth-independent healthcare, rather than Earth-reliant. Here we present a summary of decadal recommendations from a workshop organized by NASA on artificial intelligence, machine learning and modelling applications that offer key solutions toward these space health challenges. The workshop recommended various biomonitoring approaches, biomarker science, spacecraft/habitat hardware, intelligent software and streamlined data management tools in need of development and integration to enable humanity to thrive in deep space. Participants recommended that these components culminate in a maximally automated, autonomous and intelligent Precision Space Health system, to monitor, aggregate and …

Given the current status of coronavirus disease 2019 (COVID-19) as a global pandemic, it is of high priority to gain a deeper understanding of the disease's development and how the virus impacts its host. Adenosine (A)-to-Inosine (I) RNA editing is a post-transcriptional modification, catalyzed by the ADAR family of enzymes, that can be considered part of the inherent cellular defense mechanism as it affects the innate immune response in a complex manner. It was previously reported that various viruses could interact with the host's ADAR enzymes, resulting in epigenetic changes both to the virus and the host. Here, we analyze RNA-seq of nasopharyngeal swab specimens as well as whole-blood samples of COVID-19 infected individuals and show a significant elevation in the global RNA editing activity in COVID-19 compared to healthy controls. We also detect specific coding sites that exhibit higher editing …

Mutations in chromatin modifiers are a hallmark of many tumors, especially lymphomas arising from germinal center (GC) B cells. Given that most of these lymphoma mutations induce aberrant gene repression, it is surprising that they often co-occur in individual patients. The most common pairing are mutations affecting CREBBP and KMT2D, even though regulating overlapping gene enhancers and pathways. Hence their co-occurrence is especially puzzling. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d (C+K) do indeed induce a more severe lymphoma phenotype (vs either allele alone) and unexpectedly conferred an immune evasive phenotype manifesting as reduced CD8+ T cell infiltration. This was linked to profound repression of immune synapse genes that provide costimulatory effects to T-cells and others. Repression of immune synapse genes was reflected in impaired response …

A single strain from the family Paenibacillaceae was isolated from the wall behind the Waste Hygiene Compartment aboard the International Space Station (ISS) in April 2018, as part of the Microbial Tracking mission series. This strain was identified as a gram-positive, rod-shaped, oxidase-positive, catalase-negative motile bacterium in the genus Cohnella, designated as F6_2S_P_1T. The 16S sequence of the F6_2S_P_1T strain places it in a clade with C. rhizosphaerae and C. ginsengisoli, which were originally isolated from plant tissue or rhizosphere environments. The closest 16S and gyrB matches to strain F6_2S_P_1T are to C. rhizosphaerae with 98.84 and 93.99% sequence similarity, while a core single-copy gene phylogeny from all publicly available Cohnella genomes places it as more closely related to C. ginsengisoli. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values to any described Cohnella species are <89 and <22%, respectively. The major fatty acids for strain F6_2S_P_1T are anteiso-C15:0 (51.7%), iso-C16:0 (23.1%), and iso-C15:0 (10.5%), and it is able to metabolize a wide range of carbon compounds. Given the results of the ANI and dDDH analyses, this ISS strain is a novel species within the genus Cohnella for which we propose the name Cohnella hashimotonis, with the type strain F6_2S_P_1T (=NRRL B-65657T and DSMZ 115098T). Because no closely related Cohnella genomes were available, this study generated the whole-genome sequences (WGSs) of the type strains for C. rhizosphaerae and C. ginsengisoli. Phylogenetic and pangenomic analysis reveals that F6_2S_P_1T, C …

The longer astronauts spend in space, the more their bodies tend to change—sometimes in undesirable ways. Long-term space flight has been linked to muscle and bone loss, vision problems, and even an overactive immune system. Now, a new study confirms bacteria aboard the International Space Station (ISS) are undergoing changes of their own. The difference is that they might actually be growing stronger in space. Data collected over 8 space flights tracked the evolution of strains of Acinetobacter pittii from the ISS. opportunistic bacteria perhaps best known for causing hospital-acquired infections on Earth. Findings revealed that these cosmic strains (red box) have become genetically distinct from strains found on Earth, even evolving functions that could help them thrive in space, such as a mechanism for repairing DNA damaged by radiation. One of the most concerning changes is the ISS strains’ ability to …

Mutations in IDH1, IDH2, and TET2 are recurrently observed in myeloid neoplasms. IDH1 and IDH2 encode isocitrate dehydrogenase isoforms, which normally catalyze the conversion of isocitrate to α-ketoglutarate (α-KG). Oncogenic IDH1/2 mutations confer neomorphic activity, leading to the production of D-2-hydroxyglutarate (D-2-HG), a potent inhibitor of α-KG-dependent enzymes which include the TET methylcytosine dioxygenases. Given their mutual exclusivity in myeloid neoplasms, IDH1, IDH2, and TET2 mutations may converge on a common oncogenic mechanism. Contrary to this expectation, we observed that they have distinct, and even opposite, effects on hematopoietic stem and progenitor cells in genetically engineered mice. Endogenous Idh2R172K caused much higher D-2-HG production compared to Idh1R132H and Idh2R140Q. This led to profound alterations in hematopoietic progenitor …

Lake Hillier is a hypersaline lake known for its distinctive bright pink color. The cause of this phenomenon in other hypersaline sites has been attributed to halophiles, Dunaliella, and Salinibacter, however, a systematic analysis of the microbial communities, their functional features, and the prevalence of pigment-producing-metabolisms has not been previously studied. Through metagenomic sequencing and culture-based approaches, our results evidence that Lake Hillier is composed of a diverse set of microorganisms including archaea, bacteria, algae, and viruses. Our data indicate that the microbiome in Lake Hillier is composed of multiple pigment-producer microbes, including Dunaliella, Salinibacter, Halobacillus, Psychroflexus, Halorubrum, many of which are cataloged as polyextremophiles. Additionally, we estimated the diversity of metabolic pathways in the lake and determined that many of these are …

Spatial omics technologies enable a deeper understanding of cellular organizations and interactions within a tissue of interest. These assays can identify specific compartments or regions in a tissue with differential transcript or protein abundance, delineate their interactions, and complement other methods in defining cellular phenotypes. A variety of spatial methodologies are being developed and commercialized; however, these techniques differ in spatial resolution, multiplexing capability, scale/throughput, and coverage. Here, we review the current and prospective landscape of single cell to subcellular resolution spatial omics technologies and analysis tools to provide a comprehensive picture for both research and clinical applications.

BackgroundThe cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples.ResultsWe systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput …

BackgroundMonitoring the adaptation of microorganisms to the extreme environment of the International Space Station (ISS) is crucial to understanding microbial evolution and infection prevention. Acinetobacter pittii is an opportunistic nosocomial pathogen, primarily impacting immunocompromised patients, that was recently isolated from two missions aboard the ISS.ResultsHere, we report how ISS-associated A. pittii (n = 20 genomes) has formed its own genetically and functionally discrete clade distinct from most Earth-bound isolates (n = 291 genomes). The antimicrobial susceptibility testing of ISS strains and two related clinical isolates demonstrated that ISS strains acquired more resistance, specifically with regard to expanded-spectrum cephalosporins, despite no prediction of increased resistance based on genomic analysis of resistance genes. By investigating 402 longitudinal environmental and host …

Pathogenic bacteria and viruses in medical environments can lead to treatment complications and hospital-acquired infections. Current disinfection protocols do not address hard-to-access areas or may be beyond line-of-sight treatment, such as with ultraviolet radiation. The COVID-19 pandemic further underscores the demand for reliable and effective disinfection methods to sterilize a wide array of surfaces and to keep up with the supply of personal protective equipment (PPE). We tested the efficacy of Sani Sport ozone devices to treat hospital equipment and surfaces for killing Escherichia coli, Enterococcus faecalis, Bacillus subtilis, and Deinococcus radiodurans by assessing Colony Forming Units (CFUs) after 30 min, 1 h, and 2 h of ozone treatment. Further gene expression analysis was conducted on live E. coli K12 immediately post treatment to understand the oxidative damage stress response transcriptome profile. Ozone treatment was also used to degrade synthetic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA as assessed by qPCR CT values. We observed significant and rapid killing of medically relevant and environmental bacteria across four surfaces (blankets, catheter, remotes, and syringes) within 30 min, and up to a 99% reduction in viable bacteria at the end of 2 h treatment cycles. RNA-seq analysis of E. coli K12 revealed 447 differentially expressed genes in response to ozone treatment and an enrichment for oxidative stress response and related pathways. RNA degradation of synthetic SARS-CoV-2 RNA was seen an hour into ozone treatment as compared to non-treated controls, and a non-replicative …

National Aeronautics and Space Administration’s (NASA) spacecraft assembly facilities are monitored for the presence of any bacteria or fungi that might conceivably survive a transfer to an extraterrestrial environment. Fungi present a broad and diverse range of phenotypic and functional traits to adapt to extreme conditions, hence the detection of fungi and subsequent eradication of them are needed to prevent forward contamination for future NASA missions. During the construction and assembly for the Mars 2020 mission, three fungal strains with unique morphological and phylogenetic properties were isolated from spacecraft assembly facilities. The reconstruction of phylogenetic trees based on several gene loci (ITS, LSU, SSU, RPB, TUB, TEF1) using multi-locus sequence typing (MLST) and whole genome sequencing (WGS) analyses supported the hypothesis that these were novel species. Here we report the genus or species-level classification of these three novel strains via a polyphasic approach using phylogenetic analysis, colony and cell morphology, and comparative analysis of WGS. The strain FJI-L9-BK-P1 isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) exhibited a putative phylogenetic relationship with the strain Aaosphaeria arxii CBS175.79 but showed distinct morphology and microscopic features. Another JPL-SAF strain, FJII-L3-CM-DR1, was phylogenetically distinct from members of the family Trichomeriaceae and exhibited morphologically different features from the genera Lithohypha and Strelitziana. The strain FKI-L1-BK-DR1 isolated from the Kennedy Space Center facility was …