Biology subjects

Huang, F.

Publications and source records attributed to Huang, F..

115 records · Page 7Linked to original sources

bioRxiv2019

A Clostridia-rich microbiota contributes to increased excretion of bile acids in diarrhea-predominant irritable bowel syndrome

ObjectiveAn excess of fecal bile acids (BAs) is thought to be one of the mechanisms for diarrhea-predominant irritable bowel syndrome (IBS-D). However, the factors causing excessive BA excretion remains unclear. Given the importance of gut microbiota in BA metabolism, we hypothesized that gut dysbiosis might contribute to excessive BA excretion in IBS-D.\n\nDesignMetabolomic and metagenomic analyses were performed of specimens from 290 IBS-D patients and 89 healthy volunteers. By transplanting human microbiota and manipulating specific microbiome species in mice, the effects of microbiota on host BA metabolism were assessed at metabolic, genetic and protein levels. Effects of individual and mixed BAs on enterohepatic feedback pathways were also tested in vitro and in vivo.\n\nResultsTotal fecal BAs were excessively excreted in 24.5% of IBS-D patients. Their fecal metagenomes showed increased abundances of Clostridia and BA-transforming genes (hdhA and bais). The increases of Clostridia bacteria (e.g. C. scindens) were positively associated with the levels of fecal BAs and serum 7-hydroxy-4-cholesten-3-one (C4), while being negatively correlated with serum fibroblast growth factor 19 (FGF19). Both Clostridia-rich human microbiota and C. scindens enhanced levels of serum C4 and hepatic conjugated BAs in mice recipients and reduced ileal FGF19 expression. Inhibition of Clostridium species by vancomycin yielded opposite findings. Clostridia-derived BAs (e.g. conjugated and free ursodeoxycholic acid) significantly suppressed intestinal FGF19 expression.\n\nConclusionThe Clostridia-rich microbiota contributes to excessive BA excretion in IBS-D patients. This study provided the basis for more precise clinical diagnosis and management for IBS-D.

microbiology↗

bioRxiv2019

Enhanced 4Pi single-molecule localization microscopy with coherent pupil based localization and light sheet illumination

Over the last decades, super-resolution techniques have revolutionized the field of fluorescence microscopy. Among them, interferometric or 4Pi microscopy methods exhibit supreme resolving power in the axial dimension. Combining with single-molecule detection/localization and adaptive optics, iPALM/4PiSMS/W-4PiSMSN allowed 10-15 nm isotropic 3D resolution throughout the whole cell. However, further improving the achieved 3D resolution poses significantly challenges which, in part, is blocked by the complexity of single-molecule emission pattern generated by these systems rendering a large portion of information carrying photons unusable. Here we introduce a localization algorithm that achieves the theoretical information limit for 4Pi based single-molecule switching nanoscopy (4Pi-SMSN), and demonstrates improvements in resolution, accuracy as well as applicability comparing with the state of art 4Pi-SMSN methods. Further, with a novel 4Pi-compatible light-sheet illumination reducing the fluorescence background by >5-fold, we demonstrated the new system enables further improvement in the achievable resolution of 4Pi/interferometric single-molecule imaging systems.

biophysics↗

bioRxiv2019

Single-organelle quantification reveals the stoichiometric and structural variability of carboxysomes dependent on the environment

The carboxysome is a complex, proteinaceous organelle that plays essential roles in carbon assimilation in cyanobacteria and chemoautotrophs. It comprises hundreds of protein homologs that self-assemble in space to form an icosahedral structure. Despite its significance in enhancing CO2 fixation and potentials in bioengineering applications, the formation of carboxysomes and their structural composition, stoichiometry and adaptation to cope with environmental changes remain unclear. Here we use live-cell single-molecule fluorescence microscopy, coupled with confocal and electron microscopy, to decipher the absolute protein stoichiometry and organizational variability of single {beta}-carboxysomes in the model cyanobacterium Synechococcus elongatus PCC7942. We determine the physiological abundance of individual building blocks within the icosahedral carboxysome. We further find that the protein stoichiometry, diameter, localization and mobility patterns of carboxysomes in cells depend sensitively on the microenvironmental levels of CO2 and light intensity during cell growth, revealing cellular strategies of dynamic regulation. These findings, also applicable to other bacterial microcompartments and macromolecular self-assembling systems, advance our knowledge of the principles that mediate carboxysome formation and structural modulation. It will empower rational design and construction of entire functional metabolic factories in heterologous organisms, for example crop plants, to boost photosynthesis and agricultural productivity.\n\nOne Sentence SummaryDetermination of absolute protein stoichiometry reveals the organizational variability of carboxysomes in response to microenvironmental changes\n\nThe authors responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Author (www.plantcell.org) is: Lu-Ning Liu (luning.liu@liverpool.ac.uk).

biophysics↗

bioRxiv2018

Hyocholic acid species and the risk of type 2 diabetes

Hyocholic acid (HCA) and its derivatives are found in only trace amounts in human blood, but constitute approximately 76 % of the bile acid (BA) pool in the pig, a species known for its exceptional resistance to type 2 diabetes mellitus (T2DM). Here we show that HCA species play a crucial role in maintaining glucose homeostasis and preventing T2DM. We found that in two cohort studies (n=1,213), both obesity and diabetes were associated with lower serum concentrations of HCA species. Serum HCA levels in apparently healthy individuals (n=132) were found to be strong predictors for metabolic health 10 years later. Oral administration of HCA increased serum fasting GLP-1, to a greater extent than metformin, in healthy and diabetic mouse models. HCA upregulated GLP-1 secretion in intestinal enteroendocrine cells via simultaneously activating G-protein-coupled BA receptor, TGR5, and inhibiting farnesoid X receptor, a unique mechanism that is not found in other BA species.

systems biology↗

bioRxiv2018

Pixel Quantum Efficiency Differences and Variance Stabilization for sCMOS Single Molecule Localization Microscopy Data Analysis

Optimal analysis of single molecule localization microscopy (SMLM) data acquired with a CMOS camera requires compensation for single pixel differences in gain, offset and readout noise. For some CMOS cameras we found that it is also necessary to compensate for pixel differences in sensitivity or relative quantum efficiency (RQE). We present the modifications to the original sCMOS analysis algorithm necessary to correct for these RQE differences. We also discuss the use of the Anscombe transform (AT) for variance stabilization. Removing the variance dependence on the mean allows simpler least squares fitting approaches to achieve the Cramer-Rao bound on the mixed Poisson and Gaussian distributed data typically acquired with an sCMOS camera.

biophysics↗

bioRxiv2018

Aerobic removal of microcystin-LR by a novel native effective bacterial community designated as YFMCD4 isolated from Lake Taihu

Microcystins (MCs) are a group of monocyclic heptapeptide hepatotoxins produced by species of cyanobacteria. MC-LR is the most toxic and frequently detected MCs variant in water, which poses a great threat to the natural ecosystem and public health. Its important to seek environment-friendly and cost-efficient methods to remove MC-LR. To investigate the MC-degrading capacities of a novel indigenous bacterial community designated as YFMCD4 and the influence of environmental factors including various temperatures, MC concentrations and pH on the MC-degrading activities, the concentration of MC-LR was measured by high performance liquid chromatography. In addition, the MC-degrading mechanism containing the degradation pathway and products of YFMCD4 was studied using HPLC coupled with an ultra-high resolution LTQ Orbitrap Velos Pro ETD mass spectrometry equipped with electrospray ionization interface. The data showed MC-LR can be removed at the maximum rate of 0.5 {micro}g/(ml{middle dot}h) by YFMCD4 containing Alcaligenes faecalis and Stenotrophomonas acidaminiohila. The MC-degrading rates of YFMCD4 were significantly affected by different temperatures, pH and MC-LR concentrations. Two intermediates of a tetrapeptide and Adda appeared in the degradation process. These results illustrate that the novel bacterial community YFMCD4 can remove MC-LR effectively and completely, which indicates YFMCD4 possesses a significant potential to be used in bioremediation of water bodies contaminated by MC-LR.

ecology↗

bioRxiv2018

HIV protease inhibitor Saquinavir inhibits toll-like receptor 4 activation by targeting receptor dimerization

Toll like receptor 4 (TLR4) is crucial in induction of innate immune response through recognition of invading pathogens or endogenous alarming molecules.Ligand-induced dimerization of TLR4 is required for the activation of downstream signaling pathways. TLR4 dimerization induces the activation of NF-kB and IRF3 through MyD88- or TRIF-dependent pathways. Saquinavir (SQV), a FDA-approved HIV protease inhibitor, has been shown to suppress the activation of NF-kB induced by HMGB1 by blocking TLR4-MyD88 association in proteasome-independent pathway. However, it remains nknown whether SQV is a HMGB1-specific and MyD88-dependent TLR4 signaling inhibitor and which precise signaling element of TLR4 is targeted by SQV. Our results showed that SQV inhibits both MyD88- and TRIF-dependent pathways in response to LPS, a critical sepsis inducer and TLR4 agonist, leading to downregulation of NF-kB and IRF3. SQV did not suppress MyD88-dependent pathway triggered by TLR1/2 agonist Pam3csk4. In the only TRIF-dependent pathway, SQV did not attenuate IRF3 activation induced by TLR3 agonist Poly(I:C). Furthermore, dimerization of TLR4 induced by LPS and HMGB1 was decreased by SQV. These results suggest that TLR4 receptor complex is the molecular target of SQV and shed light on that TLR4-mediated inmune responses and consequent risk for uncontrolled inflammation could be modulated by FDA-approved drug SQV.

immunology↗