Biology subjects

Zhang, W.

Publications and source records attributed to Zhang, W..

At least 361 records · Page 20Linked to original sources

bioRxiv2024

Transcriptional memories mediate the plasticity of sulfide stress responses to enable acclimation in Urechis unicinctus

To cope with environmental stresses, organisms often adopt a memory response upon primary stress exposure to facilitate a quicker and/or stronger reaction to recurring stresses. Somatic stress memory is essential in dealing with contemporary stress. The earliest sign of somatic stress memory is a change in gene transcription levels, which alters physiology and phenotype to better cope with stress. Sulfide is a common environmental pollutant; however, some organisms have successfully colonized sulfur-rich environments. Whether stress memory plays important role in sulfide stress adaptation remains unclear. In this study, to determine whether Urechis unicinctus, a sulfur-tolerant organism, retains the memory of previous sulfide stress, we simulated a repetitive sulfide stress/recovery system. The results showed that the tolerance of U. unicinctus to sulfide stress was significantly increased after priming with 50 {micro}M sulfide. Further, transcriptional memory genes (TMGs) involved in regulating sulfide stress memory were identified, classified according to their expression patterns, and functionally analyzed. TMGs involved in sulfide metabolism, sugar metabolism, and protein homeostasis pathway showed an enhanced response, whereas those related to DNA repair pathway demonstrated a modified response pattern. Our study indicated that U. unicinctus retains memory of sulfide stress priming, which mediates plasticity to accelerate sulfide stress adaptation.

zoology↗

bioRxiv2024

FishCODE: a web-based information platform for comprehensive omics data exploration in fish research

In terms of the utilization of omics data, the current fish database analysis functions are primarily relatively simple tools at the transcriptional level, aimed at obtaining the co-expression levels of specified genes or the data visualization of multiple genes, and do not enable users to perform comprehensive omics data analysis. Furthermore, the gene-level information currently provided by these multispecies fish genomics databases is incomplete, and there is a lack of a comprehensive portal that can offer multidimensional genetic information. To address these challenges, we collected extensive multi-omics information on 35 fishes and established the primary comprehensive multi-omics data information platform for fish, FishCODE (http://bioinfo.ihb.ac.cn/fishcode). We have collected experimental background of dataset which pertaining to the target fishes, selected a range of datasets that encompass a broad spectrum of research areas, and downloaded the corresponding raw omics data from public repositories such as the Sequence Read Archive (SRA). Through a unified pipeline analysis, FishCODE contains 11,216 samples from 540 sets of genomic, transcriptomic, and methylomic datasets. These data encompass transcript structure and expression, gene methylation levels, protein domains, protein subcellular localization, protein interactions, best matched protein (Swiss-Prot), associated SNP site information (47,111,018), orthologous genes, phylogenetic tree and GO/KEGG annotations. To facilitate comparison, we annotated the experimental background data sets of the FishCODE, FishGET, PhyloFish, FishSED and FishSCT databases using the Fish Experimental Condition Ontology. Currently, the FishCODE database omics dataset includes 146 unique experimental condition words, 654 cumulative experimental condition words, and 13 species with rich experimental background (more than 20 unique FECO words). These data are 3.5 times (42), 8.3 times (74), and 6.5 times (2) those of the second-ranked databases respectively. We generated word cloud maps for the experimental condition vocabularies of FishCODE and FishGET, illustrating the superior richness of FishCODEs experimental background.

bioinformatics↗

bioRxiv2024

GPR30 in spinal cholecystokinin-positive neurons modulates neuropathic pain via mediating descending facilitation

Neuropathic pain, a major health problem affecting 7-10% of the global population, lacks effective treatment due to its elusive mechanisms. Cholecystokinin-positive (CCK+) neurons in the spinal dorsal horn (SDH) are critical for neuropathic pain, yet the underlying molecular mechanisms remain unclear. Here, we show that the membrane estrogen receptor G-protein coupled estrogen receptor (GPER/GPR30) in spinal neurons was significantly upregulated in chronic constriction injury (CCI) mice and that inhibition of GPR30 in CCK+ neurons reversed CCI-induced neuropathic pain. Furthermore, GPR30 in spinal CCK+ neurons was essential for the enhancement of AMPA-mediated excitatory synaptic transmission in CCI mice. Moreover, GPR30 was expressed in spinal CCK+ neurons that received direct projection from the primary sensory cortex (S1-SDH). Chemogenetic inhibition of S1-SDH post-synaptic neurons alleviated CCI-induced neuropathic pain. Conversely, chemogenetic activation of these neurons mimicked neuropathic pain symptoms, which were attenuated by spinal inhibition of GPR30. Finally, we confirmed that GPR30 in S1-SDH post-synaptic neurons was required for CCI-induced neuropathic pain. Taken together, our findings suggest that GPR30 in spinal CCK+ neurons and S1-SDH postsynaptic neurons is pivotal for neuropathic pain, thereby representing a promising therapeutic target for neuropathic pain.

neuroscience↗

bioRxiv2024

An Atlas of Linkage Disequilibrium Across Species

Linkage disequilibrium (LD) is a key metric that characterizes populations in flux. To reach a genomic scale LD illustration, which has a substantial computational cost of[O] (nm2), we introduce a framework with two novel algorithms for LD estimation: X-LD, with a time complexity of[O] (n2m) suitable for small sample sizes (n < 104); X-LDR, a stochastic algorithm with a time complexity of[O] (nmB) for biobank-scale data (B iterations); n the sample size, and m the number of SNPs. These methods can refine the entire genome into high-resolution LD grids, such as more than 9 million grids for UK Biobank samples ([~]4.2 million SNPs). The efficient resolution for genome-wide LD leads to intriguing biological discoveries. I) High-resolution LD illustrations revealed how the pericentromeric regions and the HLA region lead to intense and extended LD patterns. II) Two universal LD patterns, identified as Norm I and Norm II patterns, provide insights on the evolutionary history of populations and can also highlight genomic regions of deviation, such as chromosomes 6 and 11 or ncRNA regions. III) The results of our innovative LD decay method aligned with the LD decay scores of 59.5 for Europeans, 60.2 for East Asians, and 33.2 for Africans; correspondingly, the length of the LD was approximately 2.85 Mb, 2.18 Mb, and 1.58 Mb for these three ethnicities. Rare or imputed variants universally increased LD. IV) An unprecedented LD atlas for 25 reference populations contoured interspecies diversity in terms of their Norm I and Norm II LD patterns, highlighting the impact of refined population structure, quality of reference genomes, and uncovered a profound status quo of these populations. The algorithms have been implemented in C++ and are freely available (https://github.com/gc5k/gear2).

genetics↗

bioRxiv2024

Germinated brown rice research: bibliometric analysis of progress, hotspots and trends

To gain a deeper understanding of global research trends and focal points in germinated brown rice, this article takes the relevant literature on germinated brown rice in the core database of Web of Science as the research object. By using bibliometric analysis, the literature on germinated brown rice published from 2003 to 2023 is deeply analyzed, and the global research progress, hotspots and future development trend of germinated brown rice are summarized. Since 2018, research on germinated brown rice has been rapidly developing, with a significant surge in interest since 2020. China leads in the number of publications, institutions, and core authors in this research area. The primary research topics include the nutritional value, physiological active components, and industrial applications of germinated brown rice. Current research frontiers involve identifying, evaluating, and enhancing bioactive substances in germinated brown rice for food applications. Research in this field remains active, and application scenarios are becoming increasingly diverse. Future studies may explore new directions in related equipment and ingredients.

bioinformatics↗

bioRxiv2024

A toolbox for ablating excitatory and inhibitory synapses

Recombinant optogenetic and chemogenetic proteins are potent tools for manipulating neuronal activity and controlling neural circuit function. However, there are few analogous tools for manipulating the structure of neural circuits. Here, we introduce three rationally designed genetically encoded tools that use E3 ligase-dependent mechanisms to trigger the degradation of synaptic scaffolding proteins, leading to functional ablation of synapses. First, we developed a constitutive excitatory synapse ablator, PFE3, analogous to the inhibitory synapse ablator GFE3. PFE3 targets the RING domain of the E3 ligase Mdm2 and the proteasome-interacting region of Protocadherin 10 to the scaffolding protein PSD-95, leading to efficient ablation of excitatory synapses. In addition, we developed a light-inducible version of GFE3, paGFE3, using a novel photoactivatable complex based on the photocleavable protein PhoCl2c. paGFE3 degrades Gephyrin and ablates inhibitory synapses in response to 400 nm light. Finally, we developed a chemically inducible version of GFE3, chGFE3, which degrades inhibitory synapses when combined with the bio-orthogonal dimerizer HaloTag ligand-trimethoprim. Each tool is specific, reversible, and capable of breaking neural circuits at precise locations.

neuroscience↗

bioRxiv2024

Tenascin-C in the early lung cancer tumor microenvironment promotes progression through integrin activation and FAK

Pre-cancerous lung lesions are commonly initiated by activating mutations in the RAS pathway, but do not transition to lung adenocarcinomas (LUAD) without additional oncogenic signals. Here, we show that expression of the extracellular matrix protein Tenascin-C (TNC) is increased in and promotes the earliest stages of LUAD development in oncogenic KRAS-driven lung cancer mouse models and in human LUAD. TNC is initially expressed by fibroblasts and its expression extends to tumor cells as the tumor becomes invasive. Genetic deletion of TNC in the mouse models reduces early tumor burden and high-grade pathology and diminishes tumor cell proliferation, invasion, and focal adhesion kinase (FAK) activity. TNC stimulates cultured LUAD tumor cell proliferation and migration through engagement of v-containing integrins and subsequent FAK activation. Intringuingly, lung injury causes sustained TNC accumulation in mouse lungs, suggesting injury can induce additional TNC signaling for early tumor cell transition to invasive LUAD. Biospecimens from patients with stage I/II LUAD show TNC in regions of FAK activation and an association of TNC with tumor recurrence after primary tumor resection. These results suggest that exogenous insults that elevate TNC in the lung parenchyma interact with tumor-initiating mutations to drive early LUAD progression and local recurrence.

cancer biology↗

bioRxiv2024

Integrating collecting systems in kidney organoids through fusion of distal nephron to ureteric bud.

The kidney maintains homeostasis through an array of parallel nephrons, which all originate in development as isolated epithelial structures that later fuse through their distal poles to a system of collecting ducts (CD). This connection is required to generate functional nephrons by providing a pathway for excretion of metabolic waste and byproducts. Currently, methods for differentiating human pluripotent stem cells into kidney organoids generate nephrons that lack CDs and instead terminate as blind-ended tubules. Here we describe a developmentally inspired system that addresses this deficiency through assembly of induced nephrogenic mesenchyme with ureteric bud (UB) tissues, the embryonic building blocks of the kidneys collecting system. The UB progenitors grow and develop into a network of CDs within the organoid, and importantly, they functionally integrate with the nephrons through recapitulating fusion between the distal tubule and CD to create a continuous epithelial lumen. We further showed that proximal-distal nephron specification, fusion frequency, and maturation of the CD can be augmented through temporal manipulation of developmental signaling pathways. This work provides a platform for interrogating the principles and mechanisms underlying nephron-UB fusion and a framework for engineering unobstructed nephrons with patterned collecting systems, an important step toward the de novo generation of functional kidney tissue.

developmental biology↗

bioRxiv2024

Patterned wireless transcranial optogenetics generates artificial perception

Synthesizing perceivable artificial neural inputs independent of typical sensory channels remains a fundamental challenge in the development of next-generation brain-machine interfaces. Establishing a minimally invasive, wirelessly effective, and miniaturized platform with long-term stability is crucial for creating a clinically meaningful interface capable of mediating artificial perceptual feedback. In this study, we demonstrate a miniaturized fully implantable wireless transcranial optogenetic encoder designed to generate artificial perceptions through digitized optogenetic manipulation of large cortical ensembles. This platform enables the spatiotemporal orchestration of large-scale cortical activity for remote perception genesis via real-time wireless communication and control, with optimized device performance achieved by simulation-guided methods addressing light and heat propagation during operation. Cue discrimination during operant learning demonstrates the wireless genesis of artificial percepts sensed by mice, where spatial distance across large cortical networks and sequential order-based analyses of discrimination performance reveal principles that adhere to general perceptual rules. These conceptual and technical advancements expand our understanding of artificial neural syntax and its perception by the brain, guiding the evolution of next-generation brain-machine communication.

neuroscience↗

bioRxiv2024

Intra-hypothalamic circuit orchestrates β-endorphin release following coital ejaculation in male mice

Survey-based evidence suggests that men experience a distinct post-ejaculation affective state1,2, marked by intense pleasure sometimes compared to the euphoric rush from intravenous injection of opioid drugs such as heroin3. However, the intrinsic neural circuit mechanisms underlying the ejaculation-triggered affective state remain unclear. Here, we discovered that Calbindin1-expressing (Calb1+) neurons in the preoptic area (POA) of the hypothalamus, an evolutionarily conserved regulatory region for male mating behavior4, are specifically activated during ejaculation in male mice. Inhibiting POA Calb1+ neurons prolongs mating and delays ejaculation. Importantly, POA Calb1+ neurons transmit the ejaculation signal and activate proopiomelanocortin-expressing (Pomc+) neurons in the arcuate nucleus of the hypothalamus, which show robust and sustained activity lasting for tens of seconds, specifically upon ejaculation. This activity is accompanied by elevated levels of {beta}-endorphins5, opioid peptides secreted by Pomc+ neurons, post-ejaculation in male mice. Optogenetic activation of Pomc+ neurons increases {beta}-endorphins levels and conditioned placed preference, similar to ejaculation. Conversely, intracerebroventricular (i.c.v.) infusion of drugs blocking Pomc neuropeptides signaling eliminates ejaculation-conditioned place preference. Collectively, these results elucidate an intra-hypothalamic circuit from POA Calb1+ neurons to arcuate Pomc+ neurons that coordinate {beta}-endorphin release with ejaculation, shedding light on the neurobiological basis of the post-ejaculation affective state.

neuroscience↗

bioRxiv2024

Intranasal Lithium Chloride Nanoparticles Inhibit Inflammatory Pyroptosis in Brains and Ameliorate Memory Loss and Depression Behavior in 5xFAD mice

BackgroundAlzheimers disease (AD) is a devastating neurodegenerative disease (AD) and has no treatment that can cure or halt the disease progression. This study explored the therapeutic potential of lithium salt dissolved in Ryanodex formulation vehicle (RFV) and delivered to the brain by intranasal application. We first compared lithium concentrations in the brain and blood of wild-type mice following intranasal or oral administration of lithium chloride (LiCl) dissolved in either RFV or water. The beneficial and side effects of intranasal versus oral LiCl in RFV in these mice were assessed and potential mechanisms underlying the efficacy of anti-inflammation and anti-pyroptosis in the brains were also investigated in both wild-type (WT) and 5XFAD Alzheimers Disease (AD) mice brains. MethodsFor the study of brain versus blood lithium concentrations, WT B6SJLF1/J mice at 2 months of age were treated with intranasal or oral LiCl (3 mmol/kg) dissolved in RFV or in water. Brain and blood lithium concentrations were measured at various times after drugs administration. Brain/blood lithium concentration ratios were then determined. For studying therapeutic efficacy versus side effects and their underlying mechanisms, 5XFAD and WT B6SJLF1/J mice were treated with intranasal LiCl (3 mmol/kg) daily, Monday to Friday each week, in RFV beginning at 2 or 9 months of age with a 12-week treatment duration. Animal behaviors were assessed for depression (tail suspension), cognition (fear conditioning and Y maze), olfaction (buried food test), and motor functions (rotarod) at the age of 5 and 12 months. Blood and brain tissue were harvested from these mice at 13 months. Blood biomarkers for the functions of thyroid (thyroid stimulating hormone, TSH) and kidney (creatinine) were measured using ELISA. Changes in protein expression levels of the endoplasmic reticulum Ca2+ release channels type 1 InsP3 receptors (InsP3R-1), malondialdehyde (MDA)-modified proteins and 4-hydroxy-2-nonenal (4-HNE), pyroptosis regulatory proteins (NLR family pyrin domain containing 3 (NLRP3), cleaved caspase-1, N-terminal of Gasdermin D (GSDMD)), cytotoxic (IL-1{beta}, IL-18, IL-6, TNF-) and cytoprotective (IL-10) cytokines and synapse proteins (PSD-95, synapsin-1) were determined using immunoblotting. Mouse body weights were monitored regularly. ResultsCompared to oral LiCl in RFV nanoparticles, intranasal treatment of WT mice with LiCl in RFV markedly decreased blood concentrations at the time frame of 30-120 minutes. The ratio of brain/blood lithium concentration after Intranasal lithium chloride in RFV significantly increased, in comparison to those after oral administration lithium chloride in RFV or intranasal administration of lithium chloride in water. Intranasal lithium chloride in RFV inhibited both memory loss and depressive behavior in adult and aged 5XFAD mice. Additionally intranasal treatment of aged 5XFAD mice with LiCl in RFV effectively suppressed the increases in InsP3R-1, intracellular oxidative stress markers (4-HNE-bound and MDA-modified proteins), pyroptosis activation proteins (NLRP3, cleaved caspase-1, N-terminal GSDMD) and cytotoxic cytokines (IL-1{beta}, IL-6, TNF-), but reversed the down-regulation of cytoprotective cytokine IL-10. Intranasal LiCl in RFV also alleviated the loss of the postsynaptic synapse protein PSD-95, but not synapsin-1, in aged 5XFAD mice. Blood level of the kidney function marker creatinine was significantly increased in 5XFAD than in WT mice in an age-dependent manner and this elevation was abolished by intranasal delivery of LiCl in RFV. Intranasal LiCl in RFV for 12 weeks in both WT or 5XFAD mice did not affect blood biomarkers for thyroid function, nor did it affect smell or muscle function or body weight. ConclusionIntranasal administration of LiCl in RFV significantly decreased lithium blood concentrations and increased brain/blood lithium concentration ratio, in comparison to its oral administration. Intranasal administration of LiCl in RFV robustly protected against both memory loss and depressive-like behavior, while had no side effects concerning thyroid and kidney toxicity in 5XFAD mice. These lithium-induced beneficial effects were strongly associated with lithiums suppression of InsP3R-1 Ca2+ channel receptor increase, pathological neuroinflammation and activation of the pyroptosis pathway, as well as the loss of some synaptic proteins. Intranasal delivery of lithium salt in RFV could become an effective and potent inhibitor of pathological inflammation/pyroptosis in the CNS and serve as a new treatment for both AD-associated dementia and depression with minimal unwanted side effects including peripheral organ toxicity.

neuroscience↗

bioRxiv2024

A brainstem circuit controls cough-like airway defensive behaviors in mice

The respiratory tract is subject to complex neural control for eupneic breathing and distinct airway defensive reflexes. Growing evidence has highlighted significant heterogeneity of airway-innervating vagal sensory neurons in mediating various respiratory functions, however, the central neuronal pathways and neural circuits involved in the airway regulation remain less understood. Combining whole-body plethysmography (WBP), audio, and video tracking to access breathing and airway defensive behaviors in conscious animals, we developed a quantitative paradigm implementing the mouse as a model to study cough-like defensive behaviors. Using TRAP2 transgenic mice and in vivo fiber photometry, we found that the neural activity in the caudal spinal trigeminal nucleus (SP5C) is strongly correlated with tussigen-evoked cough-like responses. Impairing synaptic outputs or chemogenetic inhibition of the SP5C effectively abolished these cough-like reflexes. Optogenetic stimulation of SP5C excitatory neurons or their projections to the ventral respiratory group (VRG) triggered robust cough-like behaviors without tussive stimuli. Notably, tonic elevation of SP5C excitability caused spontaneous cough-like activities chronically in mice. Together, our data provide strong evidence for a previously unrecognized brainstem circuit that controls cough-like defensive behaviors in mice.

neuroscience↗

bioRxiv2024

De novo Design of A Fusion Protein Tool for GPCR Research

G protein-coupled receptors (GPCRs) play pivotal roles in cellular signaling and represent prominent drug targets. Structural elucidation of GPCRs is crucial for drug discovery efforts. However, structural studies of GPCRs remain challenging, particularly for inactive state structures, which often require extensive protein engineering. Here, we present a de novo design strategy termed "click fusion" for generating fusion proteins to facilitate GPCR structural studies. Our method involves the rational design of structurally stable protein domains rigidly linked to GPCRs. The resulting fusion protein enhances the thermostability of the target GPCR and aids in determining GPCR structures via cryo-electron microscopy (cryo-EM). We further demonstrate that the designed fusion protein can be transferred among structurally similar GPCRs with minor adjustments to the linker region. Our study introduces a promising approach for facilitating GPCR structural studies and advancing drug discovery efforts.

biophysics↗

bioRxiv2024

Zebrafish models of human-duplicated gene SRGAP2 reveal novel functions in microglia and visual system development

The expansion of the human SRGAP2 family, resulting in a human-specific paralog SRGAP2C, likely contributed to altered evolutionary brain features. The introduction of SRGAP2C in mouse models is associated with changes in cortical neuronal migration, axon guidance, synaptogenesis, and sensory-task performance. Truncated SRGAP2C heterodimerizes with the full-length ancestral gene product SRGAP2A and antagonizes its functions. However, the significance of SRGAP2 duplication beyond neocortex development has not been elucidated due to the embryonic lethality of complete Srgap2 knockout in mice. Using zebrafish, we show that srgap2 knockout results in viable offspring and that these larvae phenocopy "humanized" SRGAP2C larvae, including altered morphometric features (i.e., reduced body length and inter-eye distance) and differential expression of synapse-, axonogenesis-, and vision-related genes. Through single-cell transcriptome analysis, we demonstrate a skewed balance of excitatory and inhibitory neurons that likely contribute to increased susceptibility to seizures displayed by Srgap2 mutant larvae, a phenotype resembling SRGAP2 loss-of-function in a child with early infantile epileptic encephalopathy. Single-cell data also shows strong endogenous expression of srgap2 in microglia with mutants exhibiting altered membrane dynamics and likely delayed maturation of microglial cells. Microglia cells expressing srgap2 were also detected in the developing eye together with altered expression of genes related to axonogenesis in mutant retinal cells. Consistent with the perturbed gene expression in the retina, we found that SRGAP2 mutant larvae exhibited increased sensitivity to broad and fine visual cues. Finally, comparing the transcriptomes of relevant cell types between human (+SRGAP2C) and non-human primates (-SRGAP2C) revealed significant overlaps of gene alterations with mutant cells in our zebrafish models; this suggests that SRGAP2C plays a similar role altering microglia and the visual system in modern humans. Together, our functional characterization of conserved ortholog Srgap2 and human SRGAP2C in zebrafish uncovered novel gene functions and highlights the strength of cross-species analysis in understanding the development of human-specific features. Abstract (short)SRGAP2C has been implicated in contributing to altered brain features in the evolution of humans. However, the significance of SRGAP2 duplication beyond neocortex development has not been elucidated due to the embryonic lethality of complete Srgap2 knockout in mice. Using zebrafish, we show that srgap2 knockout results in viable offspring that phenocopy "humanized" SRGAP2C larvae. Morphometric, behavioral, and transcriptome analyses collectively suggest srgap2 impacts axonal guidance, synaptogenesis, and seizure susceptibility. Beyond neurons, Srgap2 functions in controlling membrane dynamics and maturation of microglial cells, possibly leading to altered axonogenesis in the developing retina and increased sensitivity to broad and fine visual cues. Comparing relevant transcriptomes between human and nonhuman primates suggests that SRGAP2C similarly impacts microglia and vision in modern humans. Our functional characterization of conserved ortholog Srgap2 and human SRGAP2C in zebrafish uncovered novel gene functions and highlights the strength of cross-species analysis in understanding the development of human-specific features.

genomics↗

bioRxiv2024

Discovery of novel 1,4-dicarbonylthiosemicarbazides as DNA gyrase inhibitors for the treatment of MRSA infection

Antibiotic resistance has become a serious threat to public health, thus novel antibiotics are urgently needed to combat drug-resistant bacteria including MRSA (methicillin-resistant S. aureus). The 1,4-dicarbonylthiosemicarbazide is an interesting chemotype that could exhibit antibacterial activity. However, the currently available compounds are not as potent as clinical antibiotics. Herein, we adopted the computer-aided drug design strategy, substructure search, to retrieve antibacterial 1,4-dicarbonylthiosemicarbazide derivatives, and identified compound B5 (Specs ID: AG-690/15432331) from the Specs chemical library that exhibited moderate activity (minimum inhibitory concentration (MIC): 6.25 {micro}g/mL) against S. aureus (ATCC 29213). Based on that compound, we further designed and synthesized 45 derivatives, and evaluated their antibacterial activity. Eight derivatives were more potent than or equivalent to vancomycin (MIC: 1.56 {micro}g/mL). We compared the three most potent ones for their cytotoxicity to HepG2 and HUVEC cells and selected compound 1b as our lead compound for comprehensive biological evaluation. As a result, compound 1b exhibited a bacteriostatic mode, and was active against a panel of gram-positive bacteria strains, metabolically stable, and effective to protect the mice from MRSA infection. More importantly, we applied 2D similarity calculation and reverse docking to predict potential targets of compound 1b. Through experimental validation and molecular dynamics simulation, we were able to confirm that compound 1b inhibited S. aureus DNA gyrase (IC50: 1.81 {micro}M) and DNA supercoiling, potentially by binding to the ATPase domain, where ASP81, GLU58 and GLN91 formed key hydrogen bonds. Taken together, we have discovered a new class of DNA gyrase inhibitors represented by compound 1b for the treatment of MRSA infection, through the design, synthesis, and biological evaluation of novel 1,4-dicarbonylthiosemicarbazides. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/611349v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@549dadorg.highwire.dtl.DTLVardef@13bff64org.highwire.dtl.DTLVardef@1fc2c00org.highwire.dtl.DTLVardef@acee76_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAn interesting 1,4-dicarbonylthiosemicarbazide derivative B5 with moderate antibacterial activity for S. aureus was discovered by substructure search. C_LIO_LIBased on B5, 45 new 1,4-dicarbonylthiosemicarbazides were designed, synthesized and biologically evaluated, which led to the discovery of a promising lead compound 1b. C_LIO_LICompound 1b exhibited good antibacterial activity for a panel of gram-positive bacteria strains, and was effective to protect mice from MRSA infection. C_LIO_LIThe 1,4-dicarbonylthiosemicarbazides represented by compound 1b were discovered as a new class of DNA gyrase inhibitors, by target prediction and experimental validation. C_LI

pharmacology and toxicology↗

bioRxiv2024

Repurposing the plant-derived compound apigenin for senomorphic effect in antiaging pipelines

Cellular senescence is a cell fate triggered by inherent or environmental stress and characterized by stable cell cycle arrest accompanied by a hypersecretory feature, termed as the senescence-associated secretory phenotype (SASP). Senescent cell burden increases with natural aging, functionally contributing to age-related organ dysfunction and multiple disorders. In this study, we performed a large scale screening of a natural product library for senotherapeutic candidates by assessing their effects on human senescent cells. Apigenin, a dietary flavonoid previously reported with antioxidant and anti-inflammatory activities, exhibited a prominent capacity in targeting senescent cells as a senomorphic agent. In senescent cells, apigenin blocks the interactions between ATM/p38 and HSPA8, thus preventing transition of the acute stress-associated phenotype (ASAP) towards the SASP. Mechanistically, apigenin targets peroxiredoxin 6 (PRDX6), an intracellular redox-active molecule, suppressing the iPLA2 activity of PRDX6 and disrupting downstream reactions underlying the SASP development. Without reversing cellular senescence, apigenin deprives cancer cells of malignancy acquired from senescent stromal cells in culture, while reducing chemoresistance upon combination with chemotherapy in anticancer regimens. In preclinical trials, apigenin administration improves physical function of animals prematurely aged after whole body irradiation, alleviating physical frailty and cognitive impairment. Overall, our study demonstrates the potential of exploiting a naturally derived compound with senomorphic capacity to achieve geroprotective effects by modulating the SASP, thus providing a research platform for future exploration of novel natural agents against age-related conditions.

cell biology↗

bioRxiv2024

Distinct modes of coupling between VCP, an essential unfoldase, and deubiquitinases

Errors in proteostasis, which requires regulated degradation and recycling of diverse proteins, are linked to aging, cancer and neurodegenerative disease (1). In particular, recycling proteins from multiprotein complexes, organelles and membranes is initiated by ubiquitylation, extraction and unfolding by the essential mechanoenzyme VCP (2-4), and ubiquitin removal by deubiquitinases (DUBs), a class of [~]100 ubiquitin-specific proteases in humans (5, 6). As VCPs substrate recognition requires ubiquitylation, the removal of ubiquitins from substrates for recycling must follow extraction and unfolding. How the activities of VCP and different DUBs are coordinated for protein recycling or other fates is unclear. Here, we employ a photochemistry-based approach to profile proteome-wide domain-specific VCP interactions in living cells (7). We identify DUBs that bind near the entry, exit, or both sites of VCPs central pore, the channel for ATP-dependent substrate translocation (8-10). From this set of DUBs, we focus on VCPIP1, required for organelle assembly and DNA repair (11-13), that our chemical proteomics workflow indicates binds the central pores entry and exit sites. We determine a [~]3[A] cryo-EM structure of the VCP-VCPIP1 complex and find up to 3 VCPIP1 protomers interact with the VCP hexamer. VCPIP1s UBX-L domain binds VCPs N-domain in a down conformation, linked to VCPs ADP-bound state (2, 14), and the deubiquitinase domain is positioned at the central pores exit site, poised to remove ubiquitin following substrate unfolding. We find that VCP stimulates VCPIP1s DUB activity and use mutagenesis and single-molecule mass photometry assays to test the structural model. Together, our data suggest that DUBs bind VCP at distinct sites and reveal how the two enzyme activities can be coordinated to achieve specific downstream outcomes for ubiquitylated proteins.

biochemistry↗

bioRxiv2024

Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline

SummaryThe price, quality and throughout of DNA sequencing continue to improve. Algorithmic innovations have allowed inference of a growing range of features from DNA sequencing data, quantifying nuclear, mitochondrial and evolutionary aspects of both germline and somatic genomes. To automate analyses of the full range of genomic characteristics, we created an extensible Nextflow meta-pipeline called metapipeline-DNA. Metapipeline-DNA analyzes targeted and whole-genome sequencing data from raw reads through pre-processing, feature detection by multiple algorithms, quality-control and data- visualization. Each step can be run independently and is supported robust software engineering including automated failure-recovery, robust testing and consistent verifications of inputs, outputs and parameters. Metapipeline-DNA is cloud-compatible and highly configurable, with options to subset and optimize each analysis. Metapipeline-DNA facilitates high-scale, comprehensive analysis of DNA sequencing data. AvailabilityMetapipeline-DNA is an open-source Nextflow pipeline under the GPLv2 license and is available at https://github.com/uclahs-cds/metapipeline-DNA.

bioinformatics↗