Biology subjects

Lin, H.

Publications and source records attributed to Lin, H..

At least 217 records · Page 12Linked to original sources

bioRxiv2020

Pharmacologic inhibition of Protein Kinase C α and Protein Kinase C β halts renal function decline indirectly, by blunting hyperphagia, and directly reduces adiposity in the ZSF1 rat model of type 2 diabetes

Type 2 diabetes (T2D) and its complications can have debilitating, sometimes fatal consequences. Despite advances that address some of the metabolic aspects of T2D, for many patients these approaches do not sufficiently control the disease. As a result, an emerging therapeutic strategy is to target the pathobiological mechanisms downstream of T2D metabolic derangement that can result in organ damage, morbidity, and mortality in afflicted individuals. One such proposed mechanism involves the Protein Kinase C (PKC) family members PKC and PKC{beta}, which have been linked to diabetes-induced tissue damage to organs including the kidneys. To evaluate the therapeutic potential of dual inhibition of PKC and PKC{beta} in the context of T2D, we have evaluated a potent and orally bioavailable inhibitor, herein referred to as Cmpd 1, in the ZSF1 rat model of leptin-receptor deficiency, obesity-driven T2D. Therapeutic dosing of Cmpd 1 virtually halted renal function decline but did so indirectly by blunting the hyperphagia response of these animals. Beyond this clear but indirect effect, Cmpd 1 had direct and prominent effects on body weight and in liver and inguinal white adipose tissue (iWAT) when administered to ZSF1 obese rats.

pharmacology and toxicology↗

bioRxiv2020

Potentiating CD8+ T cell antitumor activity by targeting the PCSK9/LDLR axis

Metabolic regulation has proven to play a critical role in T cell antitumor immunity. Cholesterol metabolism is a key component of this response but remains largely unexplored. Herein, we found that the LDL receptor (LDLR), which has been previously identified as a transporter for cholesterol and fatty acids, plays a pivotal role in regulating CD8+ T cell antitumor activity, with the genetic ablation of LDLR significantly attenuating CD8+ T cell activation and clonal expansion. Additionally, we found that LDLR interacts with the T-cell receptor (TCR) signalosome and regulates TCR signaling, facilitating CD8+ T cell activation and effector function. Furthermore, we found that the tumor microenvironment downregulates CD8+ T cell LDLR levels and TCR signaling via tumor cell-derived PCSK9, which binds and prevents the recycling of LDLR and TCR into the plasma membrane. Our findings indicate that genetic deletion or pharmacological inhibition of PCSK9 in tumor cells can enhance the antitumor activity of CD8+ T cells by alleviating the tumor microenvironments suppressive effect on CD8+ T cells and consequently inhibit tumor progression. While previously established as a hyperlipidemia target, this study highlights PCSK9 as a potential target for cancer immunotherapy as well.

immunology↗

bioRxiv2020

β-cell SENP1 facilitates responsiveness to incretins and limits oral glucose intolerance in high fat fed mice

SUMOylation reduces oxidative stress and preserves islet mass; but this happens at the expense of robust insulin secretion. To investigate a role for the deSUMOylating enzyme sentrin-specific protease 1 (SENP1) in glycemia following metabolic stress, we put pancreas/gut-specific SENP1 knockout mice (pSENP1-KO) on an 8-10-week high fat diet (HFD). Male pSENP1-KO mice were more glucose intolerant following HFD than littermate controls, but this was only obvious in response to oral glucose, and a similar but milder phenotype was observed in females. Plasma incretin responses were identical, and glucose-dependent insulinotropic polypeptide (GIP) was equally upregulated after HFD, in pSENP1-KO and - WT littermates. Islet mass was not different, but insulin secretion and {beta}-cell exocytotic responses to Exendin4 (Ex4) and GIP were impaired in islets lacking SENP1. Glucagon secretion from pSENP1-KO islets was also reduced, consistent with the expected SENP1 knockout in all islet cells, so we generated {beta}-cell-specific SENP1 knockout mice ({beta}SENP1-KO). These phenocopied the pSENP1-KO mice with selective impairment in oral glucose tolerance following HFD, preserved islet mass expansion, and impaired {beta}-cell exocytosis and insulin secretion to Ex4 and GIP. Thus, {beta}-cell SENP1 limits glucose intolerance following HFD by ensuring a robust facilitation of insulin secretion by incretins such as GIP.

physiology↗

bioRxiv2020

Interactions between SQUAMOSA and SVP MADS-box proteins regulate meristem transitions during wheat spike development

A better understanding of spike development can contribute to improving wheat productivity. MADS-box genes VRN1 and FUL2 (SQUAMOSA-clade) play critical and redundant roles in wheat spike and spikelet development, where they act as repressors of MADS-box genes of the SHORT VEGETATIVE PHASE (SVP) clade (VRT2, SVP1 and SVP3). Here, we show that wheat vrt2 svp1 mutants are late flowering, have shorter stems, increased number of spikelets per spike and unusual axillary inflorescences in nodes of the elongating stem. Constitutive expression of VRT2 resulted in leafy glumes and lemmas, reversion of basal spikelets to spikes, and down-regulation of MADS-genes involved in floral development. Moreover, constitutive expression of VRT2 enhanced spikelet defects of ful2, whereas vrt2 reduced vegetative characteristics in the spikelets of vrn1 ful2 mutants heterozygous for VRN-A1. These SVP-SQUAMOSA genetic interactions were paralleled by physical interactions among their encoded proteins. SVP proteins were able to reduce SQUAMOSA-SEPALLATA interactions in yeast-three-hybrid experiments. We propose that SQUAMOSA-SVP complexes act during the early reproductive phase to promote heading, formation of the terminal spikelet, and stem elongation, but that down-regulation of SVP genes is then necessary for the formation of SQUAMOSA-SEPALLATA complexes that are required for normal spikelet and floral development.

plant biology↗

bioRxiv2020

FGF2 disruption enhances thermogenesis in brown and beige fat to protect against obesity and hepatic steatosis

Since brown and beige fat expend energy in the form of heat via non-shivering thermogenesis, identifying key regulators of thermogenic functions represents a major goal for development of potential therapeutic avenues for obesity and associated disorders. Here, we identified fibroblast growth factor 2 (FGF2) as a novel thermogenic regulator. FGF2 gene disruption resulted in increased thermogenic capability in both brown and beige fat, which was supported by increased UCP1 expression, enhanced respiratory exchange ratio, and elevated thermogenic potential under cold challenge or {beta}-adrenergic stimulation. Thus, deletion of FGF2 protected mice from high fat-induced obesity and hepatic steatosis. Mechanistically, FGF2 acts in autocrine/paracrine fashions in vitro. Exogenous FGF2 supplementation inhibits both PGC-1 and PPAR{gamma} expression through ERK phosphorylation, thereby limiting PGC-1/PPAR{gamma} interactions, and leading to suppression of UCP1 expression and thermogenic activity in brown and beige adipocytes. These findings suggest a viable potential strategy for use of FGF2-selective inhibitors in treatment of combating obesity and related disorders.

cell biology↗

bioRxiv2020

Hyperpolyploidization of hepatocyte initiates preneoplastic lesion formation in the liver

Hepatocellular carcinoma (HCC) is the most predominant primary malignancy in the liver. Genotoxic and genetic models have revealed that HCC cells are derived from hepatocytes, but where the critical region for tumor foci emergence is and how this transformation occurs are still unclear. Here, hyperpolyploidization of hepatocytes around the centrilobular (CL) region was demonstrated to be closely linked with the development of HCC cells after diethylnitrosamine treatment. We identified the CL region as a dominant lobule for accumulation of hyperpolyploid hepatocytes and preneoplastic tumor foci formation. We also demonstrated that upregulation of Aurkb plays a critical role in promoting hyperpolyploidization. Increase of AURKB phosphorylation was detected on the midbody during cytokinesis, causing abscission failure and hyperpolyploidization. Pharmacological inhibition of AURKB dramatically reduced nucleus size and tumor foci number surrounding the CL region in diethylnitrosamine-treated liver. Our work reveals an intimate molecular link between pathological hyperpolyploidy of CL hepatocytes and transformation into HCC cells.

pathology↗

bioRxiv2020

Statistics and classification of spatial rotations and projection directions considering molecular symmetry in 3D electron cryo-microscopy

Electron cryo-microscopy (cryoEM) three-dimensional (3D) reconstruction is based on estimations of orientations of projection images or 3D volumes. It is common that the macromolecules studied by cryoEM have molecular symmetry, which, unfortunately, has not been taken into consideration by any statistics for either spatial rotations or projection directions at this point. Meanwhile, there are growing needs to adopt advanced statistical methods, and further, modern machine learning techniques in cryoEM. Since those methodologies are built heavily upon statistical learning cornerstones, the absence of their domain-specific statistical justification limits their applications in cryoEM. In this research, based on the concept of non-unique-games (NUG), we propose two key statistical measurements, the mean and the variance, of both spatial rotations and projection directions when molecular symmetry is considered. Such methods are implemented in the open-source python package pySymStat.

biophysics↗

bioRxiv2020

SARS-CoV-2 manipulates the SR-B1-mediated HDL uptake pathway for its entry

The recently emerged pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly, leading to a global COVID-19 pandemic. Binding of the viral spike protein (SARS-2-S) to cell surface receptor angiotensin-converting enzyme 2 (ACE2) mediates host cell infection. In the present study, we demonstrate that in addition to ACE2, the S1 subunit of SARS-2-S binds to HDL and that SARS-CoV-2 hijacks the SR-B1-mediated HDL uptake pathway to facilitate its entry. SR-B1 facilitates SARS-CoV-2 entry into permissive cells by augmenting virus attachment. MAb (monoclonal antibody)-mediated blocking of SARS-2-S-HDL binding and SR-B1 antagonists strongly inhibit HDL-enhanced SARS-CoV-2 infection. Notably, SR-B1 is co-expressed with ACE2 in human pulmonary and extrapulmonary tissues. These findings revealed a novel mechanism for SARS-CoV-2 entry and could provide a new target to treat SARS-CoV-2 infection.

microbiology↗

bioRxiv2020

Development of a free radical scavenging probiotic to mitigate coral bleaching

Corals are colonized by symbiotic microorganisms that exert a profound influence on the animals health. One noted symbiont is a single-celled alga (from the family Symbiodiniaceae), which provides the coral with most of its fixed carbon. During thermal stress, hyperactivity of photosynthesis results in a toxic accumulation of reactive oxygen species (ROS). If not scavenged by the antioxidant network, ROS may trigger a signaling cascade ending with the coral host and algal symbiont disassociating; this process is known as bleaching. Our goal was to construct a probiotic comprised of host-associated bacteria able to neutralize free radicals such as ROS. Using the coral model, the anemone Exaiptasia diaphana, and pure bacterial cultures isolated from the model animal, we identified six strains with high free radical scavenging ability belonging to the families Alteromonadaceae, Rhodobacteraceae, Flavobacteriaceae, and Micrococcaceae. In parallel, we established a "negative" probiotic consisting of genetically related strains with poor free radical scavenging capacities. From their whole genome sequences, we explored genes of interest that may contribute to their potential beneficial roles, which may help facilitate the therapeutic application of a bacterial probiotic. In particular, the occurrence of key pathways that are known to influence ROS in each of the strains has been inferred from the genomes sequences and are reported here. IMPORTANCECoral bleaching is tightly linked to the production of reactive oxygen species (ROS), which accumulates to a toxic level in algae-harboring host cells leading to coral-algal dissociation. Interventions targeting ROS accumulation, such as the application of exogenous antioxidants, have shown promise for maintaining the coral-algal partnership. With the feasibility of administering antioxidants directly to corals being low, we aim to develop a probiotic to neutralize toxic ROS during a thermal stress event. This probiotic can be tested with corals or a coral model to assess its efficacy in improving coral resistance to environmental stress.

bioengineering↗

bioRxiv2020

Directed evolution reveals the mechanism of HitRS signal transduction in Bacillus anthracis

Bacterial two component systems (TCSs) have been studied for decades; however, most work has focused on individual domains or proteins. Systematic characterization of an entire TCS could provide a mechanistic understanding of these important signal transduction systems. Here, genetic selections were employed to dissect the molecular basis of signal transduction by the HitRS system that has been implicated in detecting cell envelope stress in the pathogen Bacillus anthracis. Numerous point mutations were isolated within HitRS, 17 of which were in a 50-residue HAMP domain. Mutational analysis revealed the importance of hydrophobic interactions within the HAMP domain and highlighted its essentiality in TCS signaling. In addition, these data defined residues critical for activities intrinsic to HitRS, uncovered specific interactions among individual domains and between the two signaling proteins, and revealed that phosphotransfer is the rate-limiting step for signal transduction. This study establishes the use of unbiased genetic selections to study TCS signaling, provides a comprehensive mechanistic understanding of an entire TCS, and lays the foundation for development of novel antimicrobial therapeutics against this important infectious threat.View Full Text

biochemistry↗

bioRxiv2020

Ultra-compact Dual-band Smart NEMS Magnetoelectric Antennas for Simultaneous Wireless Energy Harvesting and Magnetic Field Sensing

Ultra-compact wireless implantable medical devices (IMDs) are in great demand for healthcare applications, in particular for neural recording and stimulation. Current implantable technologies based on miniaturized micro-coils suffer from low wireless power transfer efficiency (PTE) and are not always compliant with the specific absorption rate imposed by the Federal Communications Commission, particularly for deep brain implantation where field attenuation and tissue loss are significant. Moreover, current implantable devices are reliant on recordings of voltage or current. This has two major weaknesses: 1) the necessary direct contact between electrode and tissue degrades over time due to electrochemical fouling and tissue reactions, and 2) the necessity for differential recordings across space. Here, we report, for the first time, an ultra-compact dual-band smart nanoelectromechanical systems magnetoelectric (ME) antenna with a size of 250×174 µm2 that can efficiently perform wireless energy harvesting and sense ultra-small magnetic fields such as those arising from neural activities. The proposed smart ME antenna has a wireless PTE 1∼2 orders of magnitude higher than any other reported miniaturized micro-coil, allowing the wireless IMDs to be compliant with the specific absorption rate (SAR) limit and to operate under safe exposure of radio frequency energy. Furthermore, the magnetic sensing capability of the proposed smart ME antenna, with a limit of detection of 300∼500pT at > 200Hz, should allow the IMDs to record neural magnetic fields from the brain without requiring differential recording.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioengineering↗

bioRxiv2020

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin in terrestrial and marine food webs. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet (SI), British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last by far the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicted that Marinimicrobia HgcAB proteins contain the highly conserved structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several SI putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognised.

microbiology↗

bioRxiv2020

Multivalent lipid targeting by the calcium-independent C2A domain of Slp-4/granuphilin

Synaptotagmin-like protein 4 (Slp-4), also known as granuphilin, is a Rab effector responsible for docking secretory vesicles to the plasma membrane before exocytosis. Slp-4 binds vesicular Rab proteins via an N-terminal Slp homology (SHD) domain, interacts with plasma membrane SNARE complex proteins via a central linker region, and contains tandem C-terminal C2 domains (C2A and C2B) with affinity for phosphatidylinositol-(4,5)-bisphosphate (PIP2). The Slp-4 C2A domain binds with low nanomolar apparent affinity to PIP2 in lipid vesicles that also contain background anionic lipids such as phosphatidylserine (PS), but much weaker when either the background anionic lipids or PIP2 are removed. Through computational and experimental approaches, we show that this high affinity membrane interaction arises from concerted interaction at multiple sites on the C2A domain. In addition to a conserved PIP2-selective lysine cluster, there exists a larger cationic surface surrounding the cluster which contributes substantially to the affinity for physiologically relevant lipid compositions. While mutations at the PIP2-selective site decrease affinity for PIP2, multiple mutations are needed to decrease binding to physiologically relevant lipid compositions. Docking and molecular dynamics simulations indicate several conformationally flexible loops that contribute to the nonspecific cationic surface. We also identify and characterize a covalently modified variant in the bacterially expressed protein, which arises through reactivity of the PIP2-binding lysine cluster with endogenous bacterial compounds and has a low membrane affinity. Overall, multivalent lipid binding by the Slp-4 C2A domain provides selective recognition and high affinity docking of large dense-core secretory vesicles to the plasma membrane.

biophysics↗

bioRxiv2020

Protein enhanced NIR-IIb emission of indocyanine green for functional imaging

Fluorescence imaging performed in the 1500-1700 nm spectral range (labeled as near-infrared IIb, NIR-IIb) promises high imaging contrast and spatial resolution for its little photon scattering effect and minimum auto-fluorescence. Though inorganic and organic probes have been developed for NIR-IIb bioimaging, most are in preclinical stage, hampering further clinical application. Herein, we showed that indocyanine green (ICG), an US Food and Drug Administration (FDA)-approved agent, exhibited remarkable amount of NIR-IIb emission when dissolved into different protein solutions, including human serum albumin, rat bile, and fetal bovine serum. We performed fluorescence imaging in NIR-IIb window to visualize structures of lymph system, extrahepatic biliary tract and cerebrovascular. Results demonstrated that proteins promoted NIR-IIb emission of ICG in vivo and that NIR-IIb imaging with ICG preserved higher signal-to-background ratio (SBR) and spatial resolution compared with the conventional near-infrared II (NIR-II) fluorescence imaging. Our findings confirm that NIR-IIb fluorescence imaging can be successfully performed using the clinically approved agent ICG. Further clinical application in NIR-IIb region would hopefully be carried out with appropriate ICG-protein solutions.

bioengineering↗

bioRxiv2020

"Select and retrieve via direct upsampling" network (SARDU-Net): a data-driven, model-free, deep learning approach for quantitative MRI protocol design

PurposeWe introduce "Select and retrieve via direct upsampling" network (SARDU-Net), a data-driven framework for model-free quantitative MRI (qMRI) protocol design, and demonstrate it on in vivo brain and prostate diffusion-relaxation imaging (DRI). MethodsSARDU-Net selects subsets of informative measurements within lengthy pilot scans, without the requirement to identify tissue parameters for which to optimise for. The algorithm consists of a selector, identifying measurement subsets, and a predictor, estimating fully-sampled signals from the subsets. We implement both using deep neural networks, which are trained jointly end-to-end. We demonstrate the algorithm on brain (32 diffusion-/T1-weightings) and prostate (16 diffusion-/T2-weightings) DRI scans acquired on 3 healthy volunteers on two separate 3T Philips systems each. We used SARDU-Net to identify sub-protocols of fixed size, assessing the reproducibility of the procedure and testing sub-protocols for their potential to inform multi-contrast analyses via T1-weighted spherical mean diffusion tensor (T1-SMDT, brain) and hybrid multi-dimensional MRI (HM-MRI, prostate) modelling. ResultsIn both brain and prostate, SARDU-Net identifies sub-protocols that maximise information content in a reproducible manner across training instantiations. The sub-protocols enable multi-contrast modelling for which they were not optimised explicitly, providing robust T1-SMDT and HM-MRI maps and goodness-of-fit in the top 5% against extensive sub-protocol comparisons. ConclusionsSARDU-Net gives new opportunities to identify economical but informative qMRI protocols from a subset of the pilot scans that can be used for acquisition-time-sensitive applications. The simple architecture makes the algorithm easy to train when exhaustive searches are intractable, and applicable to a variety of anatomical contexts.

bioengineering↗

bioRxiv2020

Assessment of NR4A Ligands that Directly Bind and Modulate the Orphan Nuclear Receptor Nurr1

ABSTRACTNurr1/NR4A2 is an orphan nuclear receptor transcription factor implicated as a potential drug target for neurological disorders including Alzheimer’s and Parkinson’s diseases. Previous studies identified small molecule modulators of NR4A nuclear receptors including Nurr1 and Nur77/NR4A1; it remains unclear whether these ligands affect Nurr1 through direct binding or indirect non-binding mechanisms. We assessed a panel of twelve ligands reported to affect NR4A activity for Nurr1-dependent and Nurr1-independent transcriptional effects and binding to the Nurr1 ligand-binding domain (LBD). Most of the NR4A ligands show Nurr1-independent effects on transcription in a cell type-specific manner, suggesting they may function through binding to effector proteins whose downstream activities influence Nurr1 function. Protein NMR spectroscopy structural footprinting data show that 4-amino-7-chloroquinoline derivatives (amodiaquine and chloroquine) and cytosporone B directly bind the Nurr1 LBD. In contrast, other NR4A ligands including commercially available compounds such as C-DIM12, celastrol, camptothecin, IP7e, isoalantolactone, and TMPA do not bind the Nurr1 LBD. Interestingly, previous crystal structures indicate that cytosporone B analogs bind to surface pockets in the Nur77 LBD, but protein NMR data indicate cytosporone B likely binds to the Nurr1 orthosteric pocket. These findings should influence medicinal chemistry efforts that desire to optimize Nurr1-binding ligands as opposed to ligands that function through binding to Nurr1 effector proteins.Competing Interest StatementThe authors have declared no competing interest.View Full Text

pharmacology and toxicology↗

bioRxiv2020

A role for neutral variation in the evolution of C4 photosynthesis

Convergent trait evolution is a recurrent phenomenon in all domains of the tree of life. While some convergent traits are caused by simple sequence changes, many are associated with extensive changes to the sequence and regulation of large cohorts of genes. It is unknown how organisms traverse this expansive genotype space to assemble such complex convergent phenotypes. C4 photosynthesis is a paradigm of large-scale phenotypic convergence. Conceptual and mathematical models propose that C4 photosynthesis evolved from ancestral C3 photosynthesis through sequential adaptive changes. These adaptive changes could have been rapidly assembled if modifications to the activity and abundance of enzymes of the C4 cycle was neutral in C3 plants. This neutrality would enable populations of C3 plants to maintain genotypes with expression levels of C4 enzymes analogous to those in C4 species and thus enable rapid assembly of a functional C4 cycle from naturally occurring genotypes given shared environmental selection. Here we show that there is substantial natural variation in expression of genes encoding C4 cycle enzymes between natural accessions of the C3 plant Arabidopsis thaliana. We further show through targeted transgenic experiments in the C3 crop Oryza sativa, that high expression of the majority of C4 cycle enzymes in rice is neutral with respect to growth, development, biomass and photosynthesis. Thus, substantial variation in the abundance and activity of C4 cycle enzymes is permissible within the limits of operation of C3 photosynthesis and the emergence of component parts of this complex convergent trait can be facilitated by neutral variation.

plant biology↗

bioRxiv2020

When effort matters: Expectations of reward and efficacy guide cognitive control allocation

The amount of mental effort we invest in a task is influenced by the reward we can expect if we perform that task well. However, some of the rewards that have the greatest potential for driving these efforts (e.g., jobs, grants) are partly determined by factors beyond ones control. In such cases, effort has more limited efficacy for obtaining rewards. We have proposed that people integrate information about the expected reward and efficacy for effort to determine the expected value of control, and then adjust their control allocation (i.e. mental effort) accordingly. Here we test this theorys key behavioral and neural predictions. We show that participants invest more control when this control is more rewarding and more efficacious, and that these incentive components separately modulate EEG signatures of incentive evaluation and proactive control allocation. Our findings support the prediction that people combine worth and worthwhileness to determine how much effort to invest.

neuroscience↗