Biology subjects

Sung, J.

Publications and source records attributed to Sung, J..

30 records · Page 2Linked to original sources

bioRxiv2022

GMHI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling

SummaryWe recently introduced the Gut Microbiome Health Index (GMHI), a stool-based indicator for monitoring health given the state of ones gut microbiome. GMHI depends on health-prevalent and health-scarce species determined and validated using a pooled dataset of 5,026 stool shotgun metagenomic samples from 43 independent studies. Encouragingly, GMHI has already been utilized in various studies focusing on identifying differences in the gut microbiome between cases and controls. However, current computational barriers and logistical issues prevent researchers from computing, interpreting, and contextualizing GMHI, thereby limiting its further widespread utilization. Herein, we introduce the GMHI-webtool, a user-friendly browser application that computes GMHI, health-prevalent/scarce species, -diversities, and taxonomic distributions of the gut microbiome from stool samples. Users of our interactive online tool can visualize their results and compare side-by-side with those from our pooled reference dataset, as well as export data in .csv format and high-resolution figures. Availability and implementationGMHI-webtool is freely available here: https://gmhi-webtool.github.io/. Source code: https://github.com/danielchang2002/GMHI-webtool.

bioinformatics↗

bioRxiv2021

Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C

Robust regulatory signals in the cell often depend on interactions between short linear motifs (SLiMs) and globular proteins. Many of these interactions are poorly characterized because the binding proteins cannot be produced in the amounts needed for traditional methods. To address this problem, we developed a single-molecule off-rate (SMOR) assay based on microscopy of fluorescent ligand binding to immobilized protein partners. We used it to characterize substrate binding to the Anaphase-Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that triggers chromosome segregation. We find that SLiMs in APC/C substrates (the D box and KEN box) display distinct affinities and specificities for the substrate-binding subunits of the APC/C, and we show that multiple SLiMs in a substrate generate a high-affinity multivalent interaction. The remarkably adaptable substrate-binding mechanisms of the APC/C have the potential to govern the order of substrate destruction in mitosis.

biophysics↗

bioRxiv2021

TaxiBGC: a Taxonomy-guided Approach for the Identification of Experimentally Verified Microbial Biosynthetic Gene Clusters in Shotgun Metagenomic Data

Biosynthetic gene clusters (BGCs) in microbial genomes encode for bioactive secondary metabolites (SMs), which can play important roles in microbe-microbe and host-microbe interactions. Given the biological significance of SMs and the current profound interest in the metabolic functions of microbiomes, the unbiased identification of BGCs from high-throughput metagenomic data could offer novel insights into the complex chemical ecology of microbial communities. Currently available tools for predicting BGCs from shotgun metagenomes have several limitations, including the need for computationally demanding read-assembly; predicting a narrow breadth of BGC classes; and not providing the SM product. To overcome these limitations, we developed TaxiBGC (Taxonomy-guided Identification of Biosynthetic Gene Clusters), a command-line tool for predicting experimentally characterized BGCs (and inferring their known SMs) in metagenomes by first pinpointing the microbial species likely to harbor them. We benchmarked TaxiBGC on various simulated metagenomes, showing that our taxonomy-guided approach could predict BGCs with much-improved performance (mean F1 score: 0.56, mean PPV score: 0.80) compared to directly identifying BGCs by mapping sequencing reads onto the BGC genes (mean F1 score: 0.49, mean PPV score: 0.41). Next, by applying TaxiBGC on 2,650 metagenomes from the Human Microbiome Project and various case-control gut microbiome studies, we were able to associate BGCs (and their SMs) with different human body sites and with multiple gastrointestinal diseases, including Crohns disease and liver cirrhosis. In all, TaxiBGC provides an in silico platform to predict experimentally characterized BGCs and their SM production potential in metagenomic data while demonstrating important advantages over existing techniques. IMPORTANCECurrently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally-oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding for bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared amongst multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.

bioinformatics↗

bioRxiv2021

Cytolytic memory CD4+ T cell clonotypes are expanded during Plasmodium falciparum infection

Plasmodium falciparum (Pf) malaria causes high rates of morbidity and mortality and lacks a sufficiently effective vaccine. Clinical immunity develops in residents of malaria endemic regions which confers reduced clinical symptoms during infection and protection against severe disease. We hypothesized that understanding the immune mechanisms of clinical immunity could inform vaccine design to improve efficacy. We compared the peripheral blood cellular and humoral immune responses during a mild episode of Pf malaria infection. Participants were classified as either clinically susceptible or clinically protected, based on the number of recurrent clinical infections over an 18-month longitudinal study in a malaria endemic region in Malawi. Susceptible participants had three or more recurrent clinical episodes while clinically immune individuals had one or none. Protected participants exhibited higher plasma immunoglobulin G (IgG) breadth and titers against Pf antigens, and greater antibody (Ab)-dependent Pf opsonization compared to susceptible participants. Using high dimensional mass cytometry (CyTOF), spectral flow cytometry and single-cell transcriptomic analyses, we identified expanded memory CD4+ T cell clones sharing identical T cell receptor clonotypes in the blood of protected participants during malaria infection. These cells express a strong cytolytic T helper 1 effector program with transcripts encoding granzymes (A, B, H, M), granulysin, NKG7 and the Zeb2 master transcriptional regulator of terminally differentiated effector T cells. Memory CD4+ T cells expressing Zeb2+ were CD39hiTIGIThi and expressed multiple chemotactic and checkpoint inhibitory receptors, although the cellular levels of several of these receptors were reduced in protected compared to susceptible individuals. We propose that clonally expanded Zeb2+ cytolytic memory CD4+ Th1 cells could represent essential contributors to clinical immunity against Pf malaria. One Sentence SummaryA population of cytolytic memory CD4+ T cells is clonally expanded in patients with Plasmodium falciparum malaria and has reduced chemotactic and inhibitory receptor expression in patients with naturally acquired clinical malaria immunity.

immunology↗

bioRxiv2020

Sensitivity of radio-photoluminescence glass dosimeters to accumulated doses

BackgroundThis study investigated the effect of accumulated doses on radio-photoluminescence glass dosimeters (RPLGDs) from measurements involving mega-voltage photons. MethodsForty-five commercially available RPLGDs were irradiated to estimate their dose responses. Photon beams of 6, 10, and 15 MV were irradiated onto the RPLGDs inside a phantom, which were divided into five groups with different doses and energies. Groups 1 and 2 were irradiated at 1, 5, 10, 50, and 100 Gy in a sequential manner; Group 3 was irradiated 10 times with a dose of 10 Gy; and Groups 4 and 5 followed the same method as that of Group 3, but with doses of 50 Gy and 100 Gy, respectively. ResultsFor the annealed Group 1, RPLGD exhibited a linearity response with variance within 5%. For the non-annealed Group 2, readings demonstrated hyperlinearity at 6 MV and 10 MV, and linearity at 15 MV. Following the 100 Gy irradiation, the readings for Group 2 were 118.7 {+/-} 1.9%, 112.2 {+/-} 2.7%, and 101.5 {+/-} 2.3% at 6, 10, and 15 MV, respectively. For Groups 3, 4, and 5, the responsiveness of the RPLGDs gradually decreased as the number of repeated irradiations increased. The percentage readings for the 10th beam irradiation with respect to the readings for the primary beam irradiation were 84.6 {+/-} 1.9%, 87.5 {+/-} 2.4%, and 93.0 {+/-} 3.0% at 6 MV, 10 MV, and 15 MV, respectively. ConclusionsThe non-annealed RPLGD response to dose was hyperlinear for the 6 MV and 10 MV photon beams but not for the 15 MV photon beam. Additionally, the annealed RPLGD exhibited a fading phenomenon when the measurement was repeated several times and demonstrated a relatively large fading effect at low energies than at high energies.

cancer biology↗

bioRxiv2020

Single-Cell Mass Cytometry on Peripheral Blood Identifies Immune Cell Subsets Associated with Primary Biliary Cholangitis

The relationship between Primary Biliary Cholangitis (PBC), a chronic cholestatic autoimmune liver disease, and the peripheral immune system remains to be fully understood. Herein, we performed the first mass cytometry (CyTOF)-based, immunophenotyping analysis of the peripheral immune system in PBC at single-cell resolution. CyTOF was performed on peripheral blood mononuclear cells (PBMCs) from PBC patients (n=33) and age-/sex-matched healthy controls (n=33) to obtain immune cell abundance and marker expression profiles. Hiearchical clustering methods were applied to identify immune cell types and subsets significantly associated with PBC. Subsets of gamma-delta T cells (CD3+TCRgd+), CD8+ T cells (CD3+CD8+CD161+PD1+), and memory B cells (CD3-CD19+CD20+CD24+CD27+) were found to have lower abundance in PBC than in control. In contrast, higher abundance of subsets of monocytes and naive B cells were observed in PBC compared to control. Furthermore, several naive B cell (CD3-CD19+CD20+CD24-CD27-) subsets were significantly higher in PBC patients with cirrhosis (indicative of late-stage disease) than in those without cirrhosis. Alternatively, subsets of CD8+CD161+ T cells and memory B cells were lower in abundance in cirrhotic relative to non-cirrhotic PBC patients. Future immunophenotyping investigations could lead to better understanding of PBC pathogenesis and progression, and also to the discovery of novel biomarkers and treatment strategies.

bioinformatics↗

bioRxiv2020

A Novel Index for Predicting Health Status Using Species-level Gut Microbiome Profiling

The development of a biologically-interpretable and robust metric that provides clear insight into the general health status (i.e. healthy or non-healthy) of ones gut microbiome remains an important target in human microbiome research. We introduce the Gut Microbiome Health Index (GMHI), a mathematical formula that determines the degree to which a gut microbiome profile reflects good or adverse health. GMHI was formulated based on microbial species specific to healthy gut ecosystems. These species were identified through a multi-study, integrative analysis on 4,347 human stool metagenomes from 34 published studies across healthy and 12 different disease or abnormal bodyweight conditions. When demonstrated on our population-scale meta-dataset, GMHI is the most robust and consistent predictor of general health compared to -diversity indices commonly considered as markers for gut health. Validation of GMHI on 679 samples from 9 additional studies resulted in remarkable reproducibility in distinguishing healthy and non-healthy groups. Our findings suggest that gut taxonomic signatures can indeed serve as robust predictors of general health, and highlight the importance of how data sharing efforts can provide broadly-applicable novel discoveries.

bioinformatics↗

bioRxiv2019

Human Reference Genome and a High Contiguity Ethnic Genome AK1

Studies have shown that the current human reference genome (GRCh38) might miss information for some populations, but \"exactly what we miss\" is still elusive due to the lower contiguity of non-reference genomes. We juxtaposed the GRCh38 with high contiguity genome assemblies, AK1, to show that [~]1.8% ([~]53.4 Mbp) of AK1 sequences missed in GRCh38 with [~]0.76% ([~]22.2 Mbp) of ectopic chromosomes. The unique AK1 sequences harbored [~]1,390 putative coding elements. We found that [~]5.3Mb ([~]0.2%) of the AK1 sequences aligned and recovered the \"unmapped\" reads of fourteen individuals (5 East-Asians, 4 Europeans, and 5 Africans) as a reference. The regions that \"unmapped\" reads aligned included 110 common (shared between [≥]2 individuals) and 38 globally ([≥]7 individuals) missing regions with 25 candidate coding elements. We verified that many of the common missing regions exist in multiple populations and chimpanzees DNA. Our study illuminates not only the discovery of missing information but the use of highly precise ethnic genomes in understanding human genetics.

genomics↗

bioRxiv2019

Cryptococcus deuterogattii VGIIa infection associated with travel to the Pacific Northwest outbreak region in an anti-GM-CSF autoantibody positive patient in the United States

The Pacific Northwest (PNW), Vancouver Island, Oregon, and Washington have been the location of an ongoing Cryptococcus gattii outbreak since the 1990s, and there is evidence that the outbreak is expanding along the West Coast into California. Here we report a clinical case of a 69-year-old, HIV-negative man from North Carolina who was diagnosed with a fungal brain mass by magnetic resonance imaging (MRI) and pathology. He had traveled to Seattle and Vancouver three years earlier and Costa Rica four months prior to presentation. Phenotypic evidence shows the fungal mass isolated from the patients brain is C. gattii. In agreement with the phenotypic results, MLST provides genotypic evidence that assigns the infecting organism within in the C. gattii species complex and belonging to the C. deuterogattii VGIIa clade. Whole genome sequencing revealed >99.99% identity to the C. deuterogattii reference strain R265, indicating that the infecting strain is derived from the highly clonal outbreak strains in the PNW. We conclude the patient acquired the C. gattii infection during his travel to region three years prior and the infection was dormant for an extended period of time before causing disease. The patient tested positive for anti-granulocyte-macrophage colony-stimulating factor (GM-CSF) autoantibodies, supporting earlier reports that implicate these autoantibodies as a risk factor a risk factor associated with C. gattii infection.\n\nImportanceMortality rates associated with C. gattii infections are estimated to be between 13% and 33% depending on an individuals predisposition, and C. gattii has caused more at least 39 deaths in the PNW region. There have been four other international travel cases reported in patients from Europe and Asia with travel history to the PNW, but this study describes the first North American travel who acquired C. deuterogattii infection presenting within the United States, and the first case of a C. deuterogattii outbreak infection associated with anti-GM-CSF autoantibodies. Early and accurate diagnoses are important for disease prevention, treatment, and control of infectious diseases. Continual reporting of C. deuterogattii infections is necessary to raise awareness of the ongoing outbreak in the PNW and alert travelers and physicians to the endemic areas with potential risks.

microbiology↗

bioRxiv2018

TMEM16F activation by Ca2+ triggers plasmalemma expansion and directs PD-1 trafficking

TMEM16F, an ion channel gated by high cytoplasmic Ca2+, is required for cell surface phosphatidylserine exposure during platelet aggregation and T cell activation. Here we demonstrate in Jurkat T cells and HEK293 cells that TMEM16F activation triggers large-scale surface membrane expansion in parallel with lipid scrambling. Following TMEM16F mediated scrambling and surface expansion, cells undergo extensive membrane shedding. The membrane compartment that expands the cell surface does not involve endoplasmic reticulum or acidified lysosomes. Surprisingly, T cells lacking TMEM16F expression not only fail to expand surface membrane, but instead rapidly internalize membrane via massive endocytosis (MEND). The T cell co-receptor PD-1 is selectively shed when TMEM16F triggers membrane expansion, while it is selectively internalized in the absence of TMEM16F. Its participation in this trafficking is determined by its single transmembrane domain. Thus, we establish a fundamental role for TMEM16F as a regulator of Ca2+-activated membrane trafficking.

cell biology↗

bioRxiv2017

High accuracy measurements of nanometer-scale distances between fluorophores at the single-molecule level

To uncover the mechanisms of molecular machines it is useful to probe their structural conformations. Single-molecule Forster resonance energy transfer (smFRET) is a powerful tool for measuring intra-molecular shape changes of single-molecules, but is confined to distances of 2-8 nm. Current super-resolution measurements are error prone at <25 nm. Thus, reliable high-throughput distance information between 8-25 nm is currently difficult to achieve. Here, we describe methods that utilize information about localization and imaging errors to measure distances between two different color fluorophores with [~]1 nm accuracy at any distance >2 nm, using a standard TIRF microscope and open-source software. We applied our two-color localization method to uncover a [~]4 nm conformational change in the \"stalk\" of the motor protein dynein, revealing unexpected flexibility in this antiparallel coiled-coil domain. These new methods enable high-accuracy distance measurements of single-molecules that can be used over a wide range of length scales.

biophysics↗

bioRxiv2017

Insulin resistance in cavefish as an adaptation to a nutrient-limited environment

Periodic food shortage is one of the biggest challenges organisms face in natural habitats. How animals cope with nutrient limited conditions is an active area of study, of particular relevance in the context of the current increasing destabilization of global climate. Caves represent an extreme setting where animals have adapted to nutrient-limited conditions, as most cave environments lack a primary energy source. Here we show that cave-adapted populations of the Mexican Tetra, Astyanax mexicanus, have dysregulated blood glucose homeostasis and are insulin resistant compared to the river-adapted population. We found that multiple cave populations carry a mutation in the insulin receptor that leads to decreased insulin binding in vitro. Surface/cave hybrid fish carrying the allele weigh more than non-carriers, and zebrafish genetically engineered to carry the mutation similarly have increased body weight and insulin resistance. Higher bodyweight may be advantageous in the cave as a strategy to cope with infrequent food. In humans, the identical mutation in the insulin receptor leads to a severe form of insulin resistance and dramatically reduced life-span. However, cavefish have a similar lifespan to surface fish (of greater than fourteen years) and do not accumulate advanced glycated end products (AGEs) in the blood that are typically associated with progression of diabetes-associated pathologies. Our findings raise the intriguing hypothesis that cavefish have acquired compensatory mechanisms that allow them to circumvent the typical negative effects associated with failure to regulate blood glucose.

evolutionary biology↗