Biology subjects

Mason, C.

Publications and source records attributed to Mason, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2021

Linking Labs: Interconnecting Experimental Environments

We introduce the concept of LabLinking: a technology-based interconnection of experimental laboratories across institutions, disciplines, cultures, languages, and time zones - in other words experiments without borders. In particular, we introduce LabLinking levels (LLL), which define the degree of tightness of empirical interconnection between labs. We describe the technological infrastructure in terms of hard- and software required for the respective LLLs and present examples of linked laboratories along with insights about the challenges and benefits. In sum, we argue that linked labs provide a unique platform for a continuous exchange between scientists and experimenters, thereby enabling a time synchronous execution of experiments performed with and by decentralized user and researchers, improving outreach and ease of subject recruitment, allowing to establish new experimental designs and to incorporate a panoply of complementary biosensors, devices, hard- and software solutions.

neuroscience↗

bioRxiv2020

Engineering Radioprotective Human Cells Using the Tardigrade Damage Suppressor Protein, DSUP

Spaceflight has been documented to produce detrimental effects to physiology and genomic stability, partly a result of Galactic Cosmic Radiation (GCR). In recent years, extensive research into extremotolerant organisms has begun to reveal how they survive harsh conditions, such as ionizing radiation. One such organism is the tardigrade (Ramazzottius varieornatus) which can survive up to 5kGy of ionizing radiation and the vacuum of space. In addition to their extensive network of DNA damage response mechanisms, the tardigrade also possesses a unique damage suppressor protein (Dsup) that co-localizes with chromatin in both tardigrade and transduced human cells to protect against DNA damage from reactive oxygen species induced by ionizing radiation. While Dsup has been shown to confer human cells with increased radiotolerance; much of the mechanism of how it does this in the context of human cells remains unknown. Until now there is no knowledge yet of how introduction of Dsup into human cells can perturb molecular networks and if there are any systemic risks associated with foreign gene introduction. Here, we created a stable HEK293 cell line expressing Dsup, validated its radioprotective phenotype, and performed multi-omic analyses across different time points and doses of radiation to delineate molecular mechanism of the radioprotection and assess molecular network pertubations. Dsup expressing human cells showed an enrichment for pathways seen in cells overexpressing HMGN1, a chromosomal architectural protein that has a highly similar nucleosome binding motif. As HMGN1 binding to nucleosomes promotes a less transcriptionally repressed chromatin state, we further explored the hypothesis that Dsup could behave similarly via ATAC-seq analysis and discovered overall selective differential opening and closing of the chromatin landscape. Cut&Run analysis further revealed global increases in histone post translational modifications indicative of open chromatin and global decreases in repressive marks, with Dsup binding preferentially towards promoter regions marked by H3K27ac and H3K4me3. We further validated some of the enriched pathways via in-vitro assays and revealed novel phenotypes that Dsup confers to human cells such as reduction in apoptosis, increased cell proliferation, and increased cell adhesion properties. Our analysis provides evidence that the Dsup protein in the context of HEK293 cells may behave as a chromatin architectural protein and that in addition to its nucleosome shielding effect, may confer radio-resistance via chromatin modulation. These results provide future insight into mitigating some of the major challenges involved with long term spaceflight as well as understanding some of the molecular architectural underpinnings that lead to radioresistant cancer phenotypes back home.

synthetic biology↗

bioRxiv2020

Elevation of Gut-Derived p-Cresol Molecular Networks in Astronauts During Spaceflight Informs Drug Metabolism and Performance

Metabolites produced by enteric microbes may have important effects on astronauts on long-duration missions. The NASA Twins Study provided the most comprehensive multi-scale omics data to date from which to extract molecular features of potential clinical significance to spaceflight. From the multivariate data, we identified an elevation of the uremic toxin p-cresol, which is produced by gut microbial fermentation of dietary tyrosine. p-Cresol has adverse metabolic effects via depletion of the hepatic sulfur pool, which impacts metabolism of drugs, endogenous metabolites, and xenobiotics. Moreover, p-cresol reshapes gut microbial community structure by facilitating survival of species such as clostridia and inhibition of butyrate producers. Spaceflight may also impact the genes responsible for the metabolism of p-cresol (e.g. SULT) and for the safe metabolism of common drugs used in space, such as acetaminophen (e.g. SULT, CYP4502E1, GST). Understanding p-cresol production and its related molecular networks in astronauts may lead to precision medicine advances that enhance astronaut safety and performance on long-duration missions.

molecular biology↗

bioRxiv2020

Telomere length dynamics in response to DNA damage in malaria parasites

Malaria remains a major cause of morbidity and mortality within the developing world. Recent work has implicated chromosome end stability and the repair of DNA breaks through telomere healing as potent drivers of variant antigen diversification, thus associating basic mechanisms for maintaining genome integrity with aspects of host-parasite interactions. Here we applied long-read sequencing technology to precisely examine the dynamics of telomere addition and chromosome end stabilization in response to double strand breaks within subtelomeric regions. We observed that the process of telomere healing induces the initial synthesis of telomere repeats well in excess of the minimal number required for end stability. However once stabilized, these newly created telomeres appear to function normally, eventually returning to a length nearing that of intact chromosome ends. These results parallel recent observations in humans, suggesting an evolutionarily conserved mechanism for chromosome end repair.

cell biology↗

bioRxiv2020

Cell-free DNA (cfDNA) and exosome profiling from a year-long humanspaceflight reveals circulating biomarkers

The health impact of prolonged space flight on the human body is not well understood. Liquid biopsies based on cell-free DNA (cfDNA) or exosome analysis provide a noninvasive approach to monitor the dynamics of genomic, epigenomic and proteomic biomarkers, and the occurrence of DNA damage, physiological stress, and immune responses. To study the molecular consequences of spaceflight we profiled cfDNA isolated from plasma of an astronaut (TW) during a year-long mission on the International Space Station (ISS), sampling before, during, and after spaceflight, and compared the results to cfDNA profiling of the subjects identical twin (HR) who remained on Earth, as well as healthy donors. We characterized cfDNA concentration and fragment size, and the positioning of nucleosomes on cfDNA, observing a significant increase in the proportion of cell-free mitochondrial DNA inflight, suggesting that cf-mtDNA is a potential biomarker for space flight-associated stress, and that this result was robust to ambient transit from the International Space Station (ISS). Analysis of exosomes isolated from post-flight plasma revealed a 30-fold increase in circulating exosomes and distinct exosomal protein cargo, including brain-derived peptides, in TW compared to HR and all known controls. This study provides the first longitudinal analysis of astronaut cfDNA during spaceflight, as well as the first exosome profiles, and highlights cf-mtDNA levels as a potential biomarker for physiological stress or immune system responses related to microgravity, radiation exposure, and other unique environmental conditions on the ISS.

cell biology↗

bioRxiv2020

Females and hermaphrodites of the gynodioecious Geranium maculatum respond similarly to soil nutrient availability.

Sexual dimorphism in plant growth and/or reproductive responses to the surrounding environment has been documented in some plant species. In gynodioecious plants, it is especially important to understand whether females and hermaphrodites differ in their response to environmental stressors, as the fitness of females relative to hermaphrodites determines the extent to which these separate sexes are maintained in natural populations. Soil nutrient availability is of particular importance given the different nutrient requirements of male and female sexual functions in plants. Here, we evaluated and compared the growth of females and hermaphrodites of Geranium maculatum in response to varying levels of nutrients. Using a greenhouse experiment, we manipulated the overall nutrient, nitrogen, and phosphorus levels in the soil and measured growth, allocation, and leaf quality responses in both females and hermaphrodites. We found that sexes responded similarly in their growth and allocation responses to nutrient availability, albeit evidence that female leaf chlorophyll content may have increased more than that of hermaphrodites across soil nitrogen levels. Our findings demonstrate that hermaphrodites differ from females in terms of their physiological response to varying nutrient levels, however these physiological differences did not translate into meaningful growth or reproduction differences.

plant biology↗

bioRxiv2020

Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study

Massively parallel DNA sequencing is a critical tool for genomics research and clinical diagnostics. Here, we describe the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Phase II Study to measure quality and reproducibility of DNA sequencing. Replicates of human and bacterial reference DNA samples were generated across multiple sequencing platforms, including well-established technologies such as Illumina, ThermoFisher Ion Torrent, and Pacific Biosciences, as well as emerging technologies such as BGI, Genapsys, and Oxford Nanopore. A total of 202 datasets were generated to investigate the performance of a total of 16 sequencing platforms, including mappability of reads, coverage and error rates in difficult genomic regions, and detection of small-scale polymorphisms and large-scale structural variants. This study provides a comprehensive baseline resource for continual benchmarking as chemistries, methods, and platforms evolve for DNA sequencing.

genomics↗

bioRxiv2020

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 clades that have spread throughout the world. In this study, we investigated over 7,000 SARS-CoV-2 datasets to unveil both intrahost and interhost diversity. Our intrahost and interhost diversity analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights iSNV and SNP similarity, albeit with high variability in C>T changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of small indels fuel the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.

genomics↗

bioRxiv2020

Holobiont Urbanism: sampling urban beehives reveals cities' metagenomes

Over half of the worlds population lives in urban areas with, according to the United Nations (UN), nearly 70% expected to live in cities by 2050 (United Nations, 2019). 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 citys microbiome. Our design decisions for the built environment shape these invisible populations, and we interact with them on a constant basis. A growing body of evidence shows us that our 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. While the processing and sequencing of samples can be high-throughput, gathering samples is still very expensive, labor intensive, and can require mobilizing large numbers of volunteers to get a snapshot of the microbial landscape of a city, such as City Sampling Day (metasub.org). Here we postulate that honeybees may be effective collaborators in the sampling process, as they daily forage within a 2-mile radius of their hive. We describe the results of a pilot study conducted with 3 rooftop beehives in Brooklyn, NY, where we evaluated the potential of various hive materials (beeswax, honey, debris, pollen, propolis) to reveal information as to the surrounding metagenomic landscape, and where we conclude that the bee debris are the richest substrate. Based on these results, we profiled 4 additional cities in this manner: Sydney, Melbourne, Venice and Tokyo. While the molecular and computational methods used here were based on DNA analysis, it is possible they could be used to monitor RNA-based viruses such as Sars-Cov-2. Here we present the results of this study, and discuss them in terms of architectural implications, as well as the potential of this method for epidemic surveillance.

microbiology↗

bioRxiv2020

Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.

molecular biology↗

bioRxiv2020

Haplotype Diversity and Sequence Heterogeneity of Human Telomeres

Telomeres are regions of repetitive nucleotide sequences capping the ends of eukaryotic chromosomes that protect against deterioration, whose lengths can be correlated with age and disease risk factors. Given their length and repetitive nature, telomeric regions are not easily reconstructed from short read sequencing, making telomere sequence resolution a very costly and generally intractable problem. Recently, long-read sequencing, with read lengths measuring in hundreds of Kbp, has made it possible to routinely read into telomeric regions and inspect their structure. Here, we describe a framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference. We find that long telomeric stretches can be accurately captured with long-read sequencing, observe extensive sequence heterogeneity of human telomeres, discover and localize non-canonical motifs (both previously reported as well as novel), and report the first motif composition maps of human telomeric diplotypes on a multi-Kbp scale.

genomics↗

bioRxiv2019

The microbiomes of seven lichen genera reveal host specificity, a reduced core community and potential as source of antimicrobials

The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in two Colombian Paramos using 16S rRNA gene analyses and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes were diverse, and in some cases were distinguished based on the identity of the lichen host. The majority of the lichen-associated microorganisms were not present in all lichens sampled and could be considered transient or specialists. We also uncovered sixteen shared taxa that suggest a core lichen microbiome among this diverse group of lichens, broadening our concept of these symbiotic structures. Additionally, we identified strains producing compounds active against clinically relevant pathogens. These results indicate that lichen microbiomes from the Paramo ecosystem are diverse and host-specific but share a taxonomic core and can be a source of new bacterial taxa and antimicrobials.

microbiology↗

bioRxiv2019

Single-Cell, Human Sperm Transcriptomes and Variants from Fathers of Autistic and Healthy Children

The human sperm is one of the smallest cells in the body, but also one of the most important, as it serves as the entire paternal genetic contribution to a child. This is especially relevant for diseases such as Autism Spectrum Disorders (ASD), which have been correlated with advance paternal age. Historically, most studies of sperm have focused on the assessment of a bulk sperm, wherein millions of individual sperm are present and only high-frequency variants can be detected. Using 10X Chromium single cell sequencing technology, we have assessed the RNA from >65,000 single sperm cells across 6 donors (scsperm-RNA-seq), including two of whom have autistic children and four that do not. Using multiple RNA-seq methods for differential expression and variant analysis, we found clusters of sperm mutations in each donor that are indicative of the sperm being produced by different stem cell pools. Moreover, by comparing the two groups, we have found expression changes that can separate out the two sets of donors. Finally, through our novel variant calling from single-cell RNA-seq methods, we have shown that we can detect mutation rates in sperm from ASD donors that is distinct from the controls, highlighting this method as a new means to characterize ASD risk.

genomics↗

bioRxiv2018

City-wide metagenomics uncover antibiotic resistance reservoirs in urban beach and sewage waters

BackgroundMicrobial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason a diverse variety of water environments are being analyzed using metagenomics to uncover public health threats. However, the composition of these communities along the coastal environment of a whole city where sewage and beach waters are mixed, is poorly understood.\n\nResultsWe shotgun-sequenced 20 coastal areas from the city of Montevideo (capital of Uruguay) including beach and sewage water samples to characterize bacterial communities and their virulence and antibiotic resistance repertories. We found that sewage and beach environments presented significantly different bacterial communities. Sewage waters harbored a higher prevalence and a more diverse repertory of virulence and antibiotic resistant genes mainly from well-known enterobacteria, including carbapenemases and extended-spectrum betalactamases reported in hospital infections in Montevideo. Additionally, we were able to genotype the presence of both globally-disseminated pathogenic clones as well as emerging antibiotic-resistant bacteria in sewage waters.\n\nConclusionsOur study represents the first in using metagenomics to jointly analyze beaches and the sewage system from an entire city, allowing us to characterize antibiotic-resistant pathogens circulating in urban waters. The data generated in this initial study represent a baseline metagenomic exploration to guide future longitudinal (time-wise) studies, whose systematic implementation will provide useful epidemiological information to improve public health surveillance.

genomics↗

bioRxiv2017

What are the most influencing factors in reconstructing a reliable transcriptome assembly?

Reconstructing the genome and transcriptome for a new or extant species are essential steps in expanding our understanding of the organisms active RNA landscape and gene regulatory dynamics, as well as for developing therapeutic targets to fight disease. The advancement of sequencing technologies has paved the way to generate high-quality draft transcriptomes. With many possible approaches available to accomplish this task, there is a need for a closer investigation of the factors that influence the quality of the results. We carried out an extensive survey of variety of elements that are important in transcriptome assembly. We utilized the human RNA-Seq data from the Sequencing Quality Control Consortium (SEQC) as a well-characterized and comprehensive resource with an available, well-studied human reference genome. Our results indicate that the quality of the library construction significantly impacts the quality of the assembly. Higher coverage of the genome is not as important as the quality of the input RNA-Seq data. Thus, once a certain coverage is attained, the quality of the assembly is mainly dependent on the base-calling accuracy of the input sequencing reads; and it is important to avoid saturating the assembler with extra coverage.

bioinformatics↗

bioRxiv2017

Minerva: An Alignment and Reference Free Approach to Deconvolve Linked-Reads for Metagenomics

Emerging Linked-Read technologies (aka Read-Cloud or barcoded short-reads) have revived interest in standard short-read technology as a viable way to understand large-scale structure in genomes and metagenomes. Linked-Read technologies, such as the 10X Chromium system, use a microfluidic system and a set of specially designed 3 barcodes (aka UIDs) to tag short DNA reads which were originally sourced from the same long fragment of DNA; subsequently, these specially barcoded reads are sequenced on standard short read platforms. This approach results in interesting compromises. Each long fragment of DNA is covered only sparsely by short reads, no information about the relative ordering of reads from the same fragment is preserved, and typically each 3 barcode matches reads from 2-20 long fragments of DNA. However, compared to long read platforms like those produced by Pacific Biosciences and Oxford Nanopore the cost per base to sequence is far lower, far less input DNA is required, and the per base error rate is that of Illumina short-reads.\n\nThe use of Linked-Reads presents a new set of algorithmic challenges. In this paper, we formally describe one particular issue common to all applications of Linked-Read technology: the deconvolution of reads with a single 3 barcode into clusters that correspond to a single long fragment of DNA. We introduce Minerva, A graph-based algorithm that approximately solves the barcode deconvolution problem for metagenomic data (where reference genomes may be incomplete or unavailable). Additionally, we develop two demonstrations where the deconvolution of barcoded reads improves downstream results: improving the specificity of taxonomic assignments, and by improving clustering of related sequences. To the best of our knowledge, we are the first to address the problem of barcode deconvolution in metagenomics.

bioinformatics↗

bioRxiv2017

Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers

BackgroundOne of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole genome shotgun sequencing data, comprehensive comparisons of these methods are limited. In this study, we use the largest (n=35) to date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of eleven metagenomics classifiers. We also assess the effects of filtering and combining tools to reduce the number of false positives.\n\nResultsTools were characterized on the basis of their ability to (1) identify taxa at the genus, species, and strain levels, (2) quantify relative abundance measures of taxa, and (3) classify individual reads to the species level. Strikingly, the number of species identified by the eleven tools can differ by over three orders of magnitude on the same datasets. However, various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Indeed, leveraging tools with different heuristics is beneficial for improved precision. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species and where customized tools may be required.\n\nConclusionsThe results of this study provide positive controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision and recall. We show that proper experimental design and analysis parameters, including depth of sequencing, choice of classifier or classifiers, database size, and filtering, can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.

genomics↗

bioRxiv2017

Differing strategies used by motor neurons and glia to achieve robust development of an adult neuropil in Drosophila

In both vertebrates and invertebrates, neurons and glia are generated in a stereotyped order from dedicated progenitors called neural stem cells, but the purpose of invariant lineages is not understood. Here we show that three of the stem cells that produce leg motor neurons in Drosophila also generate a specialized subset of glia, the neuropil glia, which wrap and send processes into the neuropil where motor neuron dendrites arborize. The development of the neuropil glia and leg motor neurons is highly coordinated. However, although individual motor neurons have a stereotyped birth order and transcription factor code, both the number and individual morphologies of the glia born from these lineages are highly plastic, even though the final structure they contribute to is highly stereotyped. We suggest that the shared lineages of these two cell types facilitates the assembly of complex neural circuits, and that the two different birth order strategies - hardwired for motor neurons and flexible for glia - are important for robust nervous system development and homeostasis.

neuroscience↗