Biology subjects

Su, M.

Publications and source records attributed to Su, M..

72 records · Page 4Linked to original sources

bioRxiv2020

Structural analysis of the Legionella pneumophila Dot/Icm Type IV Secretion System Core Complex

Legionella pneumophila is an opportunistic pathogen that causes the potentially fatal pneumonia Legionnaires Disease. This infection and subsequent pathology require the Dot/Icm Type IV Secretion System (T4SS) to deliver effector proteins into host cells. Compared to prototypical T4SSs, the Dot/Icm assembly is much larger, containing ~27 different components including a core complex reported to be composed of five proteins: DotC, DotD, DotF, DotG, and DotH. Using single particle cryo-electron microscopy (cryo-EM), we report reconstructions of the core complex of the Dot/Icm T4SS that includes a symmetry mismatch between distinct structural features of the outer membrane cap (OMC) and periplasmic ring (PR). We present models of known core complex proteins, DotC, DotD, and DotH, and two structurally similar proteins within the core complex, DotK and Lpg0657. This analysis reveals the stoichiometry and contact interfaces between the key proteins of the Dot/Icm T4SS core complex and provides a framework for understanding a complex molecular machine.

microbiology↗

bioRxiv2020

Comparative study of curvature sensing mediated by F-BAR domain and an intrinsically disordered region of FBP17

Membrane curvature has emerged as an intriguing physical organization principle underlying biological signaling and membrane trafficking. FBP17 of the CIP4/FBP17/Toca-1 F-BAR family is unique in the BAR family because its structurally folded F-BAR domain does not contain any hydrophobic motifs that insert into lipid bilayer. While it has been widely assumed so, whether the banana-shaped F-BAR domain alone can sense curvature has never been experimentally demonstrated. Using a nanopillar-supported lipid bilayer system, we found that the F-BAR domain of FBP17 displayed minimal curvature sensing in vitro. We further identified an alternatively spliced intrinsically disordered region (IDR) of FBP17 next to its F-BAR domain that is conserved in sequence across species. The IDR senses membrane curvature and its sensing ability greatly exceeds that of F-BAR domain alone. In living cells, presence of the IDR domain changed the dynamics of FBP17 recruitment in a curvature-coupled cortical wave system. Collectively, we propose that FBP17 does sense curvature but contrary to the common belief, its curvature sensing capability largely originates from its disordered region, not F-BAR domain itself.

biophysics↗

bioRxiv2020

Trantrace: a reliable, traceable, and collaborative solution to streamline the translation of emerging biomedical resources

BackgroundPrecision medicine is gaining popularity in routine health care, which heavily relies on the interpretation of emerging biomedical databases and professional guidelines. Translation of those biomedical materials, that is crucial to deliver research discovery to health interventions in non-native English-speaking countries, remains a large amount of work for biomedical practitioners. ResultsWe presented an application called Trantrace to facilitate the routine of large-scale long-running translation. Especially for the case that many people joined multiple translation projects, it has a rigorous task division and cooperation process: assignment, translation, review, release, and iteration. Trantrace empowers users to build own projects with different permissions, version control all the translation operation without specific skills, and further improve the translation efficiency through real-time task management tools. ConclusionsBy providing a working platform for collaborative translation and enabling long-time version correction, the Trantrace contributes towards the creation of a multilingual biomedical knowledge commons, which would be a valuable aid for personalized therapies. The source code is freely accessible at https://github.com/sgi-drylab/trantrace.

bioinformatics↗

bioRxiv2020

Influence of the lab adopted natural diet, environmental, and parental microbiota on life history and metabolic phenotype of Drosophila melanogaster larvae.

Obesity is an increasing worldwide epidemic and contributes to physical and mental health losses. The development of obesity is caused by multiple factors including genotype, hormonal misregulation, psychological stress, and gut microbiota. Our project investigated the effects produced by microbiota community, acquired from the environment and horizontal transfer, on traits related to obesity. The study applied a novel approach of raising Drosophila melanogaster from ten, wild-derived genetic lines (DGRP) on naturally fermented peaches, thereby preserving genuine microbial conditions. Our results indicated that larvae raised on the natural and standard lab diets were significantly different from each other in every tested phenotype. In addition, sterilized larvae raised on the autoclaved peach diet, therefore exposed to natural nutritional stress but lacking natural microbiota community, were associated with adverse phenotypes such as low survival rate, longer developmental time, smaller weight, and elevated triglyceride and glucose levels. Our findings suggested that frozen peach food provided nutritional conditions similar to the natural ones and preserved key microbial taxa necessary for survival and development of Drosophila larvae. The presence of parental microbiota did not produce a significant effect on any of the tested phenotypes when larvae were raised on the lab diet. Contrarily, on the peach diet, the presence of parental microbiota increased the weight and development rate, even if the original peach microbiota were still present. In addition, we found that larvae raised on the peach diet formed a microbial community distinctive from larvae raised on the lab or peach autoclaved diets. The effect that individual microbial taxa produced on the host varied significantly with changing environmental and genetic conditions, occasionally to the degree of opposite correlations.

microbiology↗

bioRxiv2020

Quantitative secretome analysis establishes the cell type-resolved mouse brain secretome

To understand how cells communicate in the nervous system, it is essential to define their secretome, which is challenging for primary cells because of large cell numbers being required. Here, we miniaturized secretome analysis by developing the high-performance secretome-protein-enrichment-with-click-sugars method (hiSPECS). To demonstrate its broad utility, hiSPECS was used to identify the secretory response of brain slices upon LPS-induced neuroinflammation and to establish the cell type-resolved mouse brain secretome resource using primary astrocytes, microglia, neurons and oligodendrocytes. This resource allowed mapping the cellular origin of CSF proteins and revealed that an unexpectedly high number of secreted proteins in vitro and in vivo are proteolytically-cleaved membrane protein ectodomains. Two examples are neuronally secreted ADAM22 and CD200, which we identified as substrates of the Alzheimer-linked protease BACE1. hiSPECS and the brain secretome resource can be widely exploited to systematically study protein secretion, brain function and to identify cell type-specific biomarkers for CNS diseases.

neuroscience↗

bioRxiv2020

Structural basis of transcription-translation coupling

In bacteria, transcription and translation are coupled processes, in which movement of RNA polymerase (RNAP) synthesizing mRNA is coordinated with movement of the first ribosome translating mRNA. Coupling is modulated by the transcription factors NusG--which is thought to bridge RNAP and ribosome--and NusA. Here, we report cryo-EM structures of Escherichia coli transcription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P-site. Structures of TTCs containing short spacers show a state incompatible with NusG bridging and NusA binding (TTC-A; previously termed "expressome"). Structures of TTCs containing longer spacers reveal a new state compatible with NusG bridging and NusA binding (TTC-B) and reveal how NusG bridges and NusA binds. We propose that TTC-B mediates NusG- and NusA-dependent transcription-translation coupling. One Sentence SummaryCryo-EM defines states that mediate NusG- and NusA-dependent transcription-translation coupling in bacteria

molecular biology↗

bioRxiv2019

RatHat: A self-targeting printable brain implant system

There has not been a major change in how neuroscientists approach stereotaxic methods in decades. Here we present a new stereotaxic method that improves on traditional approaches by reducing costs, training, surgical time, and aiding repeatability. The RatHat brain implantation system is a 3D printable stereotaxic device for rats that is fabricated prior to surgery and fits to the shape of the skull. RatHat builds are directly implanted into the brain without the need for head-leveling or coordinate-mapping during surgery. The RatHat system can be used in conjunction with the traditional u-frame stereotaxic device, but does not require the use of a micromanipulator for successful implantations. Each RatHat system contains several primary components including the implant for mounting intracranial components, the surgical stencil for targeting drill sites, and the protective cap for impacts and debris. Each component serves a unique function and can be used together or separately. We demonstrate the feasibility of the RatHat system in four different proof-of-principle experiments: 1) a 3-pole cannula apparatus, 2) an optrode-electrode assembly, 3) a fixed-electrode array, and 4) a tetrode hyperdrive. Implants were successful, durable, and long-lasting (up to 9 months). RatHat print files are easily created, can be modified in CAD software for a variety of applications, and are easily shared, contributing to open science goals and replications. The RatHat system has been adapted to multiple experimental paradigms in our lab and should be a useful new way to conduct stereotaxic implant surgeries in rodents. Impact StatementWe demonstrate a new approach to rodent stereotaxic surgery. Rodent neurosurgery is a complex skill that requires expensive equipment for head stabilization and micromanipulators for localization. The RatHat is a 3D printable brain implant system that reduces costs and time using pre-mapped and printed surgical files. A surgical stencil allows for quick placement of drill holes, and a RatHat places components in the brain using atlas coordinates. The RatHat system is an easily shared resource facilitating open science goals for simple replications and archiving of specific experimental applications.

neuroscience↗

bioRxiv2019

Cryo-EM structure of the human Mixed Lineage Leukemia-1 complex bound to the nucleosome

Mixed Lineage Leukemia (MLL) family histone methyltransferases are the key enzymes that deposit histone H3 Lys4 (K4) mono-/di-/tri-methylation and regulate gene expression in mammals. Despite extensive structural and biochemical studies, the molecular mechanism by which the MLL complexes recognize histone H3K4 within the nucleosome core particle (NCP) remains unclear. Here, we report the single-particle cryo-electron microscopy (cryo-EM) structure of the human MLL1 core complex bound to the NCP. The MLL1 core complex anchors on the NCP through RbBP5 and ASH2L, which interacts extensively with nucleosomal DNA as well as the surface close to histone H4 N-terminal tail. Concurrent interactions of RbBP5 and ASH2L with the NCP uniquely align the catalytic MLL1SET domain at the nucleosome dyad, allowing symmetrical access to both H3K4 substrates within the NCP. Our study sheds light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity.

biochemistry↗

bioRxiv2019

Eurotium cristatum, a new fungi probiotic from Fuzhuan brick tea, alleviated obesity in mice by modulating gut microbiota

Obesity is one of the major public health problems worldwide, mainly resulting from unhealthy lifestyles and diet. Gut microbiota dysbiosis may also lead to obese humans and animals. Modulating gut bacteria through fecal transplantation, the use of probiotics or certain dietary supplements, could normalize gut microbiota and subsequently alleviate obesity. Daily consumption of Fuzhuan brick tea (FBT) or its extracts have been observed to alleviate obesity in humans and experimental animals. In this study, high-fat diet-induced dysbiosis of gut microbiota in C57BL/6J mice was partially reversed by consumption of Eumtium cristatum, the dominant fungi during the manufacturing and storage of FBT. E. cristatum was able to modulate both gut fungi and bacteria composition, based on the analysis of microbiota composition of mice fecal samples. E. cristatum increased acetate and butyrate-producing bacteria in mice gut, and produced five times more butyrate than both obese and normal mice. Our results suggested that E. cristatum may be used as a fungi probiotic to beneficially modulate gut microbiota and to alleviate obesity in humans.

microbiology↗

bioRxiv2018

Inferring novel lncRNA associated with Ventricular septal defect by DNA methylation interaction network

Ventricular septal defect (VSD) is one of the most common types of congenital heart disease. To find more and more molecular alteration is conducive to explore the mechanism and biomarker in VSD. Herein we devised a predictive strategy to uncover novel lncRNA of VSD integrating DNA methylation, gene expression and lncRNA expression of early embryo and VSD by profiles from GEO database. In totally, 175 lncRNAs, 7290 genes and 3002 DNA methylation genes were obtained by logistic regression analysis associated with embryonic development. Moreover, 7304 DMGs were significant differential methylated by Wilcoxon rank test and Students test in VSD. We constructed the lncRNA-mRNA co-expression network in embryo (LMCNe). Then, a reconstructed co-expression weighted network (RCWN) was built integrated LMCNe and the DNA methylation associated network (DMAN) based on the correlation of the DNA methylation level and protein interaction network between embryonic development and VSD. We extracted top 10 lncRNAs with higher score performing DRaWR from the weight network, which as potential VSD related lncRNAs. Six lncRNAs showed a high level of expression in the heart tissue recorded in the NONOCOND database. Furthermore, associated lncRNA genes DCAF8L1, NIT1, SH2D7 and DOCK9-AS2 in validated samples showed a prominently association with VSD. These outcomes provide a reference for lncRNA involved in VSD initialization and a new insight for studies of VSD-associated lncRNAs. Author SummaryVentricular septal defect (VSD) is one of the most common types of congenital heart disease and has a high mortality rate in infants. Many molecular markers have proved effective as biomarker in VSD like DNA methylation and lncRNA. lncRNA is a type of non-coding RNA which has important effect in regulation gene expression and disease occurrence. VSD is an embryonic stage developmental disease. Therefore we hypothesized that lncRNA which was associated with DNA methylation and mRNA in early embryonic development may also affect the occurrence of VSD. So in this work, from the perspective of embryonic development, we devised a predictive strategy to uncovering novel lncRNA of VSD. In our result, four lncRNA associated genes were found differential expressed in VSD and normal samples by qPCR validation. The identification of lncRNA associated with ventricular septal defect is beneficial to further study the mechanism of VSD from the molecular level and also provides a good molecular marker for clinical therapeutic and diagnosis. At the same time, it also provides a new insight for the researches of lncRNA associated with VSD.

developmental biology↗

bioRxiv2018

Genetic signatures of human cytomegalovirus variants acquired by seronegative glycoprotein B vaccinees

Human cytomegalovirus (HCMV) is the most common congenital infection worldwide, and a frequent cause of hearing loss or debilitating neurologic disease in newborn infants. Thus, a vaccine to prevent HCMV-associated congenital disease is a public health priority. One potential strategy is vaccination of women of child-bearing age to prevent maternal HCMV acquisition during pregnancy. The glycoprotein B (gB) + MF59 adjuvant subunit vaccine is the most efficacious tested clinically to date, demonstrating approximately 50% protection against HCMV infection of seronegative women in multiple phase 2 trials. Yet, the impact of gB/MF59-elicited immune responses on the population of viruses acquired by trial participants has not been assessed. In this analysis, we employed quantitative PCR as well as multiple sequencing methodologies to interrogate the magnitude and genetic composition of HCMV populations infecting gB/MF59 vaccinees and placebo recipients. We identified several differences between the viral dynamics of acutely-infected vaccinees and placebo recipients. First, there was reduced magnitude viral shedding in the saliva of gB vaccinees. Additionally, employing a panel of tests for genetic compartmentalization, we noted tissue-specific gB haplotypes in the majority of vaccinees though only in a single placebo recipient. Finally, we observed reduced acquisition of genetically-related gB1, gB2, and gB4 genotype \"supergroup\" HCMV variants among vaccine recipients, suggesting that the gB1 genotype vaccine construct may have elicited partial protection against HCMV viruses with antigenically-similar gB sequences. These findings indicate that gB immunization may have had a measurable impact on viral intrahost population dynamics and support future analysis of a larger cohort.\n\nAuthor SummaryThough not a household name like Zika virus, human cytomegalovirus (HCMV) causes permanent neurologic disability in one newborn child every hour in the United States - more than Down syndrome, fetal alcohol syndrome, and neural tube defects combined. There are currently no established effective preventative measures to inhibit congenital HCMV transmission following acute or chronic HCMV infection of a pregnant mother. However, the glycoprotein B (gB) vaccine is the most effective HCMV vaccine tried clinically to date. Here, we utilized high-throughput, next-generation sequencing of viral DNA isolated from patients enrolled in a gB vaccine trial, and identified several impacts that this vaccine had on the size, distribution, and composition of the in vivo viral population. These results have increased our understanding of why the gB/MF59 vaccine was partially efficacious and will inform future rational design of a vaccine to prevent congenital HCMV.

microbiology↗

bioRxiv2018

goCTF: Geometrically optimized CTF determination for single-particle cryo-EM

Preferred particle orientation represents a recurring problem in single-particle cryogenic electron microcopy (cryo-EM). A specimen-independent approach through tilting has been attempted to increase particle orientation coverage, thus minimizing anisotropic three-dimensional (3D) reconstruction. However, focus gradient is a critical issue hindering tilt applications from being a general practice in single-particle cryo-EM. The present study describes a newly developed geometrically optimized approach, goCTF, to reliably determine the global focus gradient. A novel strategy of determining contrast transfer function (CTF) parameters from a sector of the signal preserved power spectrum is applied to increase reliability. Subsequently, per-particle based local focus refinement is conducted in an iterative manner to further improve the defocus accuracy. Novel diagnosis methods using a standard deviation defocus plot and goodness fitting heatmap have also been proposed to evaluate CTF fitting quality prior to 3D refinement. In a benchmark study, goCTF processed a published single-particle cryo-EM dataset for influenza hemagglutinin trimer collected at a 40-degree specimen tilt. The resulting 3D reconstruction map was improved from 4.1[A] to 3.7[A] resolution. The goCTF program is built on the open-source code of CTFFIND4, which adopts a consistent user interface ease of use.

biophysics↗

bioRxiv2018

High altitude adaptation mitigates anemia risk associated with diabetes among the Mosuo of Southwest China

Human populations native to high altitude regions ([≥]2500 m) exhibit numerous adaptations to hypoxic stress. On the Tibetan Plateau, these include modifications of the hypoxia inducible factor (HIF) pathway to essentially uncouple erythropoiesis (red blood cell production) and blood hemoglobin (Hb) concentration--which normally increase in response to low oxygen--from hypoxia. Uncoupling of erythropoiesis and hypoxia is also observed among people with diabetes due to damage to kidney tissues. This is hypothesized to result in elevated risk for anemia among diabetics, which increases risk for cardiovascular disease and death. We tested the hypothesis that the independence of erythropoiesis from HIF among high-altitude adapted populations of the Tibetan Plateau may protect against diabetes-associated anemia. We investigated this hypothesis among the Mosuo, a population living in Yunnan Province, China (at ~2800 m altitude) that is undergoing rapid market integration and lifestyle change, with concomitant increase in risk for type 2 diabetes. We found that, although diabetes (glycated hemoglobin, HbA1c [≥]6.5%) is associated with anemia (females: Hb<12g/dl; males: Hb<13g/dl) among the Chinese population as a whole (N: 5,606; OR: 1.48; p: 0.008), this is not the case among the Mosuo (N: 316; OR: 1.36; p: 0.532). Both pathways uncoupling hypoxia from erythropoiesis (diabetic disease and high altitude adaptation) are incompletely understood; their intersection in protecting Mosuo with diabetes from anemia may provide insight into the mechanisms underlying each. Further, these findings point to the importance of understanding how high-altitude adaptations interact with chronic disease processes, as populations like the Mosuo experience rapid market integration.

evolutionary biology↗

bioRxiv2018

Coiled Coil-Mediated Assembly of an Icosahedral Protein Cage with Extremely High Thermal and Chemical Stability

The organization of protein molecules into higher-order nanoscale architectures is ubiquitous in Nature and represents an important goal in synthetic biology. Here we describe the symmetry-directed design of a hollow protein cage with dimensions similar to those of many icosahedral viruses. The cage was constructed based on icosahedral symmetry by genetically fusing a trimeric protein (TriEst) to a small pentameric de novo-designed coiled coil domain, separated by a flexible oligo-glycine linker sequence. Screening a small library of designs in which the linker length varied from 2 to 12 residues identified a construct containing 8 glycine residues (Ico8) that formed well-defined cages. Characterization by dynamic light scattering, negative stain and cryo EM, and by atomic force and IR-photo-induced force microscopy established that Ico8 assembles into a flexible hollow cage with comprising 60-subunits with overall icosahedral geometry. Unexpectedly, the cages were found to encapsulate DNA, even though neither protein component binds nucleic acids on its own. Notably, the cages formed by Ico8 proved to be extremely stable towards thermal and chemical denaturation: whereas TriEst was unfolded by heating (Tm ~75 {degrees}C) or denatured by 1.5 M guanidine hydrochloride, the Ico8 cages remained folded even at 120 {degrees}C or in 8 M guanidine hydrochloride. The encapsulation of DNA and increased stability of the cages are new properties that emerge from the higher order structure of the protein cage, rather than being intrinsic to the components from which it is constructed.

synthetic biology↗

bioRxiv2018

Probing the Acyl Carrier Protein-Enzyme Interactions within Terminal Alkyne Biosynthetic Machinery

The alkyne functionality has attracted much interest due to its diverse chemical and biological applications. We recently elucidated an acyl carrier protein (ACP)-dependent alkyne biosynthetic pathway, however, little is known about ACP interactions with the alkyne biosynthetic enzymes, an acyl-ACP ligase (JamA) and a membrane-bound bi-functional desaturase/acetylenase (JamB). Here, we showed that JamB has a more stringent interaction with ACP than JamA. In addition, site directed mutagenesis of a non-cognate ACP significantly improved its compatibility with JamB, suggesting a possible electrostatic interaction at the ACP-JamB interface. Finally, error-prone PCR and screening of a second non-cognate ACP identified hot spots on the ACP that are important for interacting with JamB and yielded mutants which were better recognized by JamB. Our data thus not only provide insights into the ACP interactions in alkyne biosynthesis, but it also potentially aids in future combinatorial biosynthesis of alkyne-tagged metabolites for chemical and biological applications.\n\nTopical HeadingBiomolecular Engineering, Bioengineering, Biochemicals, Biofuels, and Food

bioengineering↗

bioRxiv2018

Generative adversarial networks as a tool to recover structural information from cryo-electron microscopy data

Cryo-electron microscopy (cryo-EM) is a powerful structural biology technique capable of determining atomic-resolution structures of biological macromolecules. Despite this ability, the low signal-to-noise ratio of cryo-EM data continues to remain a hurdle for assessing raw cryo-EM micrographs and subsequent image analysis. To help address this problem, we have performed proof-of-principle studies with generative adversarial networks, a form of artificial intelligence, to denoise individual particles. This approach effectively recovers global structural information for both synthetic and real cryo-EM data, facilitating per-particle assessment from noisy raw images. Our results suggest that generative adversarial networks may be able to provide an approach to denoise raw cryo-EM images to facilitate particle selection and raw particle interpretation for single particle and tomography cryo-EM data.

biochemistry↗

bioRxiv2017

Missing Value Imputation Approach for Mass Spectrometry-based Metabolomics Data

IntroductionMissing values exist widely in mass-spectrometry (MS) based metabolomics data. Various methods have been applied for handling missing values, but the selection of methods can significantly affect following data analyses and interpretations. According to the definition, there are three types of missing values, missing completely at random (MCAR), missing at random (MAR), and missing not at random (MNAR).\n\nObjectivesThe aim of this study was to comprehensively compare common imputation methods for different types of missing values using two separate metabolomics data sets (977 and 198 serum samples respectively) to propose a strategy to deal with missing values in metabolomics studies.\n\nMethodsImputation methods included zero, half minimum (HM), mean, median, random forest (RF), singular value decomposition (SVD), k-nearest neighbors (kNN), and quantile regression imputation of left-censored data (QRILC). Normalized root mean squared error (NRMSE) and NRMSE-based sum of ranks (SOR) were applied to evaluate the imputation accuracy for MCAR/MAR and MNAR correspondingly. Principal component analysis (PCA)/partial least squares (PLS)-Procrustes sum of squared error were used to evaluate the overall sample distribution. Students t-test followed by Pearson correlation analysis was conducted to evaluate the effect of imputation on univariate statistical analysis.\n\nResultsOur findings demonstrated that RF imputation performed the best for MCAR/MAR and QRILC was the favored one for MNAR.\n\nConclusionCombining with \"modified 80% rule\", we proposed a comprehensive strategy and developed a public-accessible web-tool for missing value imputation in metabolomics data.

bioinformatics↗

bioRxiv2017

Collective membrane dynamics emerging from curvature-dependent spatial coupling

Membrane curvature has been recognized as an active participant of fundamental biological processes including vesicular transport and organelle biogenesis, but its effects on membrane remodeling are typically local. Here we show membrane curvature plays a critical role in propagating cortical waves and modulating mesoscale dynamics in living cells. We employ a membrane shape-dependent mechanochemical feedback model to account for the observed oscillatory travelling waves of Cdc42, F-BAR proteins and actin. We demonstrate that oscillatory membrane shape changes accompany and are required for such spatiotemporal patterns. In addition, modulating the curvature preference of the F-BAR proteins or membrane tension perturbs wave propagation. Our findings identify a distinct role of membrane curvature in mediating collective dynamics of cortical proteins and provide a molecular framework for integrating membrane mechanics and biochemical signaling in the context of subcellular pattern formation.

biophysics↗