Biology subjects

Johnson, J.

Publications and source records attributed to Johnson, J..

At least 91 records · Page 5Linked to original sources

bioRxiv2020

Genetic variation for plant growth traits in a common wheat population is dominated by known variants and novel QTL

Genetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characterized in wheat genetics. While the major variants for these traits have been cloned, the importance of these variants in contributing to genetic variation for plant growth over time is not fully understood. Here we develop a biparental population segregating for major variants for both plant height and flowering time to characterize the genetic architecture of the traits and identify additional novel QTL. We find that additive genetic variation for both traits is almost entirely associated with major and moderate-effect QTL, including four novel heading date QTL and four novel plant height QTL. FT2 and Vrn-A3 are proposed as candidate genes underlying QTL on chromosomes 3A and 7A, while Rht8 is mapped to chromosome 2D. These mapped QTL also underlie genetic variation in a longitudinal analysis of plant growth over time. The oligogenic architecture of these traits is further demonstrated by the superior trait prediction accuracy of QTL-based prediction models compared to polygenic genomic selection models. In a population constructed from two modern wheat cultivars adapted to the southeast U.S., almost all additive genetic variation in plant growth traits is associated with known major variants or novel moderate-effect QTL. Major transgressive segregation was observed in this population despite the similar plant height and heading date characters of the parental lines. This segregation is being driven primarily by a small number of mapped QTL, instead of by many small-effect, undetected QTL. As most breeding populations in the southeast U.S. segregate for known QTL for these traits, genetic variation in plant height and heading date in these populations likely emerges from similar combinations of major and moderate effect QTL. We can make more accurate and cost-effective prediction models by targeted genotyping of key SNPs.

genetics↗

bioRxiv2020

The meadow jumping mouse genome and transcriptome suggest mechanisms of hibernation

Hibernating mammals exhibit medically relevant phenotypes, but the genetic basis of hibernation remains poorly understood. Using the meadow jumping mouse (Zapus hudsonius), we investigated the genetic underpinnings of hibernation by uniting experimental and comparative genomic approaches. We assembled a Z. hudsonius genome and identified widespread expression changes during hibernation in genes important for circadian rhythm, membrane fluidity, and cell cycle arrest. Tissue-specific gene expression changes during torpor encompassed Wnt signaling in the brain and structural and transport functions in the kidney brush border. Using genomes from the closely related Zapus oregonus (previously classified as Z. princeps) and leveraging a panel of hibernating and non-hibernating rodents, we found selective pressure on genes involved in feeding behavior, metabolism, and cell biological processes potentially important for function at low body temperature. Leptin stands out with elevated conservation in hibernating rodents, implying a role for this metabolic hormone in triggering fattening and hibernation. These findings illustrate that mammalian hibernation requires adaptation at all levels of organismal form and function and lay the groundwork for future study of hibernation phenotypes.

genomics↗

bioRxiv2020

NG2+/Nestin+ mesenchymal stem cells dictate DTC dormancy in the bone marrow through TGFβ2

In the bone marrow (BM) microenvironment, NG2+/Nestin+ mesenchymal stem cells (MSCs) promote hematopoietic stem cell (HSC) quiescence1,2. Importantly, the BM can also harbour disseminated tumour cells (DTCs) from multiple cancers, which, like HSCs, can remain dormant3. The BM signals are so growth-restrictive that dormant BM DTCs can persist for years to decades only to awaken and fuel lethal metastasis3-10. The mechanisms and niche components regulating DTC dormancy remain largely unknown. Here, we reveal that periarteriolar BM-resident NG2+/Nestin+ MSCs can instruct breast cancer (BC) DTCs to enter dormancy. NG2+/Nestin+ MSCs produce TGF{beta}2 and BMP7 and activate a quiescence pathway dependent on TGFBRIII and BMPRII, which via p38-kinase result in p27-CDK inhibitor induction. Importantly, genetic depletion of the NG2+/Nestin+ MSCs or conditional knock-out of TGF{beta}2 in the NG2+/Nestin+ MSCs led to awakening and bone metastatic expansion of otherwise dormant p27+/Ki67- DTCs. Our results provide a direct proof that HSC dormancy niches control BC DTC dormancy. Given that aged NG2+/Nestin+ MSCs can lose homeostatic control of HSC dormancy, our results suggest that aging or extrinsic factors that affect the NG2+/Nestin+ MSC niche may result in a break from dormancy and BC bone relapse.

cancer biology↗

bioRxiv2020

Immune modulatory effects of probiotic streptococcuc thermophilus on human monocytes

Ingesting probiotics contributes to the development of a healthy microflora in the gastrointestinal tract with established benefits to human health. Some of these beneficial effects may be through modulating of the immune system and probiotics have become more common in the treatment of many inflammatory and immune disorders. We demonstrate a range of immune modulating effects of Streptococcus thermophilus by human monocytes, including, decreased mRNA expression of IL-1R, IL-18, IFN{gamma}R1, IFNR1, CCL2, CCR5, TLR-1, TLR-2, TLR-4, TLR-5, TLR-6, TLR-8, CD14, CD86, CD4, ITGAM, LYZ, TYK2, IFNR1, IRAK-1, NOD2, MYD88, ITGAM, SLC11A1, and, increased expression of IL-1, IL-1{beta}, IL-2, IL-6, IL-8, IL-23, IFN{gamma}, TNF, CSF-2. Routine administration of Streptococcus thermophilus in fermented dairy products, and their consumption may be beneficial to the treatment/management of inflammatory and autoimmune diseases.

immunology↗

bioRxiv2020

Discovery of A New Class of Integrin Antibodies for Fibrosis

Lung fibrosis, or the scarring of the lung, is a devastating disease with huge unmet medical need. There are limited treatment options and its prognosis is worse than most types of cancer. We previously discovered that MK-0429 is an equipotent pan-inhibitor of all v integrins that reduces proteinuria and kidney fibrosis in a preclinical model. In the present study, we further demonstrated that MK-0429 significantly inhibits fibrosis progression in a bleomycin-induced lung injury model. In search of newer integrin inhibitors for fibrosis, we characterized monoclonal antibodies discovered using Adimabs yeast display platform. We identified several potent neutralizing integrin antibodies with unique human and mouse cross-reactivity. Among these, Ab-31 blocked the binding of multiple v integrins to their ligands with IC50s comparable to those of MK-0429. Furthermore, both MK-0429 and Ab-31 suppressed integrin-mediated cell adhesion and latent TGF{beta} activation. In IPF patient lung fibroblasts, TGF{beta} treatment induced profound SMA expression in phenotypic imaging assays and Ab-31 demonstrated superior in vitro activity at inhibiting SMA expression, suggesting that the integrin antibody is able to modulate TGF{beta} action though mechanisms beyond the inhibition of latent TGF{beta} activation. Together, our results highlight the potential to develop newer integrin therapeutics for the treatment of fibrotic lung diseases. One Sentence Summarytargeting integrin in lung fibrosis

pharmacology and toxicology↗

bioRxiv2020

Mapping of DNA damage genome-wide at nucleotide resolution by circle damage sequencing (CD-seq)

To establish relationships between mutations, for example in cancer genomes, and possible mechanisms linked to DNA damage, it is necessary to know at what sequence positions of the genome the damage occurs. However, it has been challenging to specifically map DNA damage at the nucleotide level of resolution and genome-wide with high sensitivity. Here, we describe a new method, which we named circle damage sequencing (circle-damage-seq), to accomplish this goal. The method is based on circularization of DNA molecules and DNA damage-selective cleavage of the circularized DNA followed by adapter ligation and sequencing. Based on the design of this approach, only DNA damage-containing molecules are sequenced. We conducted proof-of-principle studies to show that mapping of ultraviolet B-induced cyclobutane pyrimidine dimers (CPDs) can easily be achieved and show a specific tetranucleotide sequence context for CPDs (5PyPy<>PyT/A) with no further sequence enrichment outside of this context. Our approach shows strongly reduced levels of CPDs near transcription start sites and a spike of this damage near the transcription end sites of genes. We then show that 1,N6-etheno-deoxyadenosine DNA adducts formed after treatment of cells with the lipid peroxidation product 4-hydroxynonenal can be mapped genome-wide at adenine positions within a preferred sequence context of 5TAC/G3. The circle-damage-seq method can be adapted for a variety of DNA lesions for which specific excision enzymes are available.

genomics↗

bioRxiv2020

Development of a Coronavirus Disease 2019 Nonhuman Primate Model Using Airborne Exposure

Airborne transmission is predicted to be a prevalent route of human exposure with SARS-CoV-2. Aside from African green monkeys, nonhuman primate models that replicate airborne transmission of SARS-CoV-2 have not been investigated. A comprehensive and comparative evaluation of COVID-19 in African green monkeys, rhesus macaques, and cynomolgus macaques following airborne exposure to SARS-CoV-2 was performed to define parameters critical to disease progression and the extent to which they correlate with human COVID-19. Respiratory abnormalities and viral shedding were noted for all animals, indicating successful infection. Cynomolgus macaques developed fever, and thrombocytopenia was measured for African green monkeys and rhesus macaques. Type II pneumocyte hyperplasia and alveolar fibrosis were more frequently observed in lung tissue from cynomolgus macaques and African green monkeys. The data indicate that, in addition to African green monkeys, macaques can be successfully infected by airborne SARS-CoV-2, providing viable macaque natural transmission models for medical countermeasure evaluation. One Sentence SummaryNonhuman primates develop COVID-19 following airborne virus exposure.

microbiology↗

bioRxiv2020

Expression and T cell Regulatory Action of the PD-1 Immune Checkpoint in the Ovary and Fallopian Tube

The Programmed Cell Death Protein-1 (PD-1/PDCD-1/CD279) checkpoint has powerful immunomodulatory action, including in the context of cancer. PD-1 receptor activation by its ligands (PD-L1/2) is associated with downregulated immune response, and tumor cells can avoid surveillance via PD-1 and/or ligand expression. While receptor expression is largely limited to lymphoid, myeloid, and tumor cells, we show that membrane bound and soluble variants of PD-1 and ligands are also expressed by permanent constituent cell types of the human ovary and fallopian tube, including granulosa cells and oocytes. PD-1 and soluble ligands were highly enriched in exosome fractions in human follicular fluid at bioactive levels that can control T cell PD-1 activation. PD-1 checkpoint signaling may be involved in physiological ovarian functions including follicle, and ultimately, germline and embryo immune-privilege.Competing Interest StatementThe authors have declared no competing interest.View Full Text

physiology↗

bioRxiv2020

Eliciting OTUD3/RIPK-Dependent Necroptosis to Prevent Epithelial Ovarian Cancer

BackgroundThere is an urgent need for early prevention strategies against high grade serous ovarian carcinoma (HGSOC), the deadliest gynecologic malignancy. Transformed p53-null fallopian tube epithelium (FTE) cells are precursors of HGSOC that may be eliminated by inducing necroptosis, a programmed form of inflammatory cell death. Induction of necroptosis is dependent upon activation of receptor-interacting serine/threonine-protein kinases 1 and 3 (RIPK1/3). TNF and progesterone (P4) effectively promote necroptosis. In this study, we explore the activation of necroptosis as an approach to inhibit HGSOC progression. MethodsUsing gene ontology sets as a reference, we analyzed publicly available datasets of HGSOC to correlate the expression of necroptosis effectors to clinical outcomes. Using in vitro models of HGSOC we evaluated the effect of TNF, P4, and -eleostearic acid on necroptosis. In parallel, the necroptosis inhibitor Necrostatin-1 was used to confirm necroptosis-specific cell death. ResultsExpression of the P4 receptor (PGR) was sharply reduced in a HGSOC cohort compared to normal, nonmalignant FTE. However, several genes involved in necroptosis signaling were elevated in HGSOC, including TNF and RIPK1. Increased expression of PGR, the necroptosis effectors TNF and RIPK1/3, as well as ovarian tumor domain-containing deubiquitinase 3 (OTUD3) were associated with higher overall survival in 484 HGSOC cases. HGSOC cells activated necroptosis in response to P4, TNF, and -eleostearic acid treatment, while P4 or TNF treatment of HGSOC cells increased TNF, RIPK1, and OTUD3 expression. OTUD3 is a putative tumor suppressor that stabilizes PTEN and is hypothesized to be functionally similar to the necroptosis inducer, OTUD7B. shRNA knockdown of OTUD3 resulted in decreased PTEN protein and RIPK1 protein. ConclusionsWe conclude that necroptosis activation may be a viable prevention strategy that leads to the elimination of transformed FTE "founder" cells and prevents HGSOC tumorigenesis. Our data indicate that HGSOC cells activate necroptosis in response to P4, TNF, and -eleostearic acid, suggesting that established HGSOC cells may also be eliminated by activating necroptosis.

cancer biology↗

bioRxiv2020

The Past, Present and Future of Elephant Landscapes in Asia

Habitat loss drives species declines worldwide, but is seldom quantified over centennial timescales. We constructed ecological niche models for Asian elephants based on land-use change between 850-2015, and predictions under six different climate/socioeconomic scenarios from 2015-2099. We find that over 64% of suitable natural habitat across diverse ecosystems was lost over the past three centuries. Average patch size dropped 83% from approximately 99,000 km2 to 16,000 km2 and the area occupied by the largest patch decreased 83% from ~ 4 million km2 (45% of area) to 54,000 km2 (~7.5% of area). Over half of current elephant range appears unsuitable. Habitat availability is predicted to decline further this century across all scenarios. The most severe losses occur under RCP3.4-SSP4, representing mid-range emissions but high regional inequities. We conclude that climate change mitigation measures must include policies to ensure inter-regional socioeconomic equity to safeguard landscapes for elephants, humans, and other species.

ecology↗

bioRxiv2020

Survey of metaproteomics software tools for functional microbiome analysis.

To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional role of expressed microbial genes/proteins. This can be accomplished through metaproteomics, which characterizes the protein complement of the microbiome. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, so that researchers can make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental carie plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! Tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN6, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the Universal Protein Knowledgebase revealed that the sensitivity and specificity of functional annotation differed between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated the most precise GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.

bioinformatics↗

bioRxiv2019

Perceived Stress in First-Year Medical Students and its Effect on Gut Microbiota

Medical students are constantly under stress caused by strenuous medical programs, which may exert persistent physical and psychological effects on their well-being. Using medical students as a model population, this work explores the gut microbiome as a potential contributing mechanism for why individuals exposed to similar stimuli react variably. We evaluated the relationship of gut microbiome composition of first year medical students and stress resilience over a period of 4 months. Our objective was to identify gut microbiome characteristics of individuals that showed long-term stress resilience. Students were voluntarily recruited and screened for lifestyle and environmental factors at 3 timepoints during the first semester. Fecal samples were also collected at each timepoint. In order to identify candidates with stress resilience, their perceived stress and depression levels were normalized and summed to produce a psychologic index score. The most notable finding is a correlation between psychologic resiliency of Bacteriodete:Firmicute abundance as well as a relationship between durable resiliency and microbiome stability. Phylogenetic assembly of participants by microbiome relatedness found that 100% of subjects who were resilient to stress across all timepoints (n=8) were phylogenetically clustered in adjacent positions, showing a high degree of temporal stability. Of participants who were not durably resilient to stress, only 62% of participants (n=8) showed microbiomes that were phylogenetically related across the same 4 month period. We identified 2,102 Operational Taxonomic Units (OTUs) which were unique to the durable resilience group and 94 OTUs which were unique to the susceptible group. Of the 4,794 observed OTUs, 6.1% (n=294) were significantly different between groups. These findings support that the gut microbiome may play an important role in stress resilience at a time scale of 4 months. A better understanding of the role of the gut microbiome in stress resilience may shed light on potential treatment to reduce stress/anxiety in general, as well as to promote wellbeing of our future health care providers and physicians.

neuroscience↗

bioRxiv2019

A sectioning and database enrichment approach for improved peptide spectrum matching in large, genome-guided protein sequence databases

Multi-omics approaches focused on mass-spectrometry (MS)-based data, such as metaproteomics, utilize genomic and/or transcriptomic sequencing data to generate a comprehensive protein sequence database. These databases can be very large, containing millions of sequences, which reduces the sensitivity of matching tandem mass spectrometry (MS/MS) data to sequences to generate peptide spectrum matches (PSMs). Here, we describe a sectioning method for generating an enriched database for those protein sequences that are most likely present in the sample. Our evaluation demonstrates how this method helps to increase the sensitivity of PSMs while maintaining acceptable false discovery rate statistics. We demonstrate increased true positive PSM identifications using the sectioning method when compared to the traditional large database searching method, whereas it helped in reducing the false PSM identifications when compared to a previously described two-step method for reducing database size. The sectioning method for large sequence databases enables generation of an enriched protein sequence database and promotes increased sensitivity in identifying PSMs, while maintaining acceptable and manageable FDR. Furthermore, implementation in the Galaxy platform provides access to a usable and automated workflow for carrying out the method. Our results show the utility of this methodology for a wide-range of applications where genome-guided, large sequence databases are required for MS-based proteomics data analysis.

bioinformatics↗

bioRxiv2019

Delineation of the SUMO-Modified Proteome Reveals Regulatory Functions Throughout Meiosis

Protein modification by SUMO helps orchestrate the elaborate events of meiosis to faithfully produce haploid gametes. To date, only a handful of meiotic SUMO targets have been identified. Here we delineate a multidimensional SUMO-modified meiotic proteome in budding yeast, identifying 2747 conjugation sites in 775 targets, and defining their relative levels and dynamics. Modified sites cluster in disordered regions and only a minority match consensus motifs. Target identities and modification dynamics imply that SUMOylation regulates all levels of chromosome organization and each step of homologous recombination. Execution-point analysis confirms these inferences, revealing functions for SUMO in S-phase, the initiation of recombination, chromosome synapsis and crossing over. K15-linked SUMO chains become prominent as chromosomes synapse and recombine, consistent with roles in these processes. SUMO also modifies ubiquitin, forming hybrid oligomers with potential to modulate ubiquitin signaling. We conclude that SUMO plays diverse and unanticipated roles in regulating meiotic chromosome metabolism.

genetics↗

bioRxiv2019

Challenges in Peptide-Spectrum Matching: a Robust and Reproducible Statistical Framework for Removing Low-Accuracy, High-Scoring Hits

Workflows for large-scale (MS)-based shotgun proteomics can potentially lead to costly errors in the form of incorrect peptide spectrum matches (PSMs). To improve robustness of these workflows, we have investigated the use of the precursor mass discrepancy (PMD) to detect and filter potentially false PSMs that have, nonetheless, a high confidence score. We identified and addressed three cases of unexpected bias in PMD results: time of acquisition within a LC-MS run, decoy PSMs, and length of peptide. We created a post-analysis Bayesian confidence measure based on score and PMD, called PMD-FDR. We tested PMD-FDR on four datasets across three types of MS-based proteomics projects: standard (single organism; reference database), proteogenomics (single organism; customized genomic-based database plus reference), and metaproteomics (microorganism community; customized conglomerate database). On a ground truth dataset and other representative data, PMD-FDR was able to detect 60-80% of likely incorrect PSMs (false-hits) while losing only 5% of correct PSMs (true-hits). PMD-FDR can also be used to evaluate data quality for results generated within different experimental PSM-generating workflows, assisting in method development. Going forward, PMD-FDR should provide detection of high-scoring but likely false-hits, aiding applications which rely heavily on accurate PSMs, such as proteogenomics and metaproteomics.

bioinformatics↗

bioRxiv2019

The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene

Diverse wild and weedy crop relatives hold genetic variants underlying key evolutionary innovations of crops under domestication. Here, we provide genome resources and probe the genetic basis of domestication traits in green millet (Setaria viridis), a close wild relative of foxtail millet (S. italica). Specifically, we develop and exploit a platinum-quality genome assembly and de novo assemblies for 598 wild accessions to identify loci underlying a) response to climate, b) a key loss of shattering trait that permits mechanical harvest, and c) leaf angle, a major predictor of yield in many grass crops. With CRISPR-Cas9 genome editing, we validated Less Shattering1 (SvLES1) as a novel gene for seed shattering, which is rendered non-functional via a retrotransposon insertion in SiLes1, the domesticated loss-of-shattering allele of S. italica. Together these results and resources project S. viridis as a key model species for complex trait dissection and biotechnological improvement of panicoid crops.

genomics↗

bioRxiv2019

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

Cactus, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequence. We describe progressive extensions to Cactus that enable reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We show that Cactus is capable of scaling to hundreds of genomes and beyond by describing results from an alignment of over 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment yet created. Further, we show improvements in orthology resolution leading to downstream improvements in annotation.

genomics↗

bioRxiv2019

Collagen Production and Niche Engineering: A Novel Strategy for Cancer Cells to Survive Acidosis and Evolve

Ductal Carcinoma in situ (DCIS) is an avascular disease characterized by profound acidosis. Pre-malignant cells within this niche must adapt to acidosis to survive and thrive. A component of this acid-adaptation involves extracellular matrix remodeling leading to niche construction and remodeling. Using discovery proteomics, we identified that collagen producing enzyme PLODs are upregulated in acid-adapted breast cancer cells. Second harmonic generation microscopy showed significant collagen deposition within DCIS lesions of patients. In vitro analyses identified that acid-adaptation involves production of rare collagens that can be regulated by Ras and SMAD pathway. Secretome analysis showed upregulation ECM remodeling enzymes such as TGM2 and LOXL2. Comparison of acid induced collagens in vitro and in patient data showed correlation between rare collagens production and survival of patients. We conclude acidosis induces collagen production by cancer cells and promote growth independent of basal membrane attachment. The independently produced collagen can be used for niche construction and engineering as an adaptation strategy of cancer cells to survive and evolve.

cancer biology↗