Biology subjects

Zhao, Q.

Publications and source records attributed to Zhao, Q..

At least 145 records · Page 8Linked to original sources

bioRxiv2023

hURAT1 Transgenic Mouse Model for Evaluating Targeted Urate-Lowering Agents

ObjectiveUrate transporter 1 (URAT1), a well-established urate-lowering therapeutic target for hyperuricemia and gout treatment, expresses in the kidney proximal tubule and is responsible for uric acid (UA) reabsorption. However, non-primate animal models currently used in pharmacological studies failed to evaluate URAT1 inhibitors effectiveness because their URAT1 has a very low UA affinity compared to human URAT1, resulting in a lag in targeting drug screening and novel therapy development for gout treatment. We established a human URAT1 (hURAT1) transgenic knock-in (KI) mouse model to assess uricosuric agents effectiveness and characterize URAT1-caused pathogenesis. MethodsWe generated hURAT1 transgenic mice using CRISPR/Cas9 knock-in technique. mUrat1 knockout was achieved by replacing exon 1 coding sequence with a human SLC22A12 CDS-pA cassette. Based on the above transgenic mice, a hyperuricemia model was further established by hypoxanthine administration. ResultsThe hURAT1-KI mice successfully expressed hURAT1 protein to the apical side of the kidney proximal tubule epithelium, where a native human URAT1 kidney localization in human body. Upon hypoxanthine challenge, the blood UA level was elevated in hURAT1-KI mice, exhibiting an approximately 37% increase compared to wild-type (WT) mice. The elevated blood UA level could be alleviated by hURAT1 inhibitor benzbromarone treatment in the hURAT1-KI mice whereas no response was observed in WT littermates. Therefore, hURAT1 transgenic mice responded well to inhibitors and can be used to evaluate the therapeutic effects. ConclusionThe hURAT1-KI hyperuricaemia mouse model would be valuable for preclinical evaluation of urate-lowering agents toward gout treatment and studying UA metabolic complexities in humans.

pharmacology and toxicology↗

bioRxiv2023

NLRP3 Cys126 palmitoylation by ZDHHC7 Promotes Inflammasome Activation

NACHT-, leucine-rich-repeat- (LRR), and pyrin domain-containing protein 3 (NLRP3) mediates inflammasome activation in response to multiple pathogen and damage-associated molecular patterns in macrophages. Hyperactivation of NLRP3 inflammasome contributes to many human chronic inflammatory diseases. Understanding how NLRP3 inflammasome is regulated can potentially provide new strategies to treat inflammatory diseases. Here, we demonstrated that NLRP3 is palmitoylated on Cys126 by palmitoyl-acyltransferase ZDHHC7 in macrophages, which is critical for NLRP3-mediated inflammasome activation. Perturbating NLRP3 Cys126 palmitoylation by ZDHHC7 knockout, pharmacological inhibition, or modification site mutation, diminishes NLRP3 activation and the consequential Caspase-1 and Gasdermin D (GSDMD) cleavage, and IL-1{beta} and IL-18 secretion in mouse primary macrophages and human macrophages. Furthermore, NLRP3 Cys126 palmitoylation is vital for inflammasome activation in vivo, as Zdhhc7 knockout, pharmacological inhibition, or NLRP3 C126A mutation protects mice from LPS-induced endotoxic shock and monosodium urate (MSU)-induced peritonitis. Mechanistically, ZDHHC7-mediated NLRP3 Cys126 palmitoylation promotes resting NLRP3 localizing on the trans-Golgi network (TGN) and activated NLRP3 on the dispersed TGN (dTGN), which is indispensable for the recruitment and oligomerization of adaptor protein ASC after inflammasome activation. The activation of NLRP3 by ZDHHC7-mediated Cys126 palmitoylation is different from the previously reported inhibitory effect by ZDHHC12-mediated Cys841 palmitoylation, highlighting the versatile regulatory roles of S-palmitoylation. Therefore, our study identifies a new regulatory mechanism of NLRP3 activation and suggests targeting ZDHHC7 or NLRP3 Cys126 residue as a potential therapeutic strategy to treat NLRP3-related human disorders. HighlightsO_LINLRP3 Cys126 is palmitoylated by ZDHHC7. C_LIO_LIZDHHC7 promotes NLRP3 activation in macrophages, which can be inhibited by ZDHHCs inhibitors, 2-bromopalmitate and MY-D4. C_LIO_LICys126 palmitoylation of NLRP3 is critical for NLRP3 activation. C_LIO_LINLRP3 TGN/dTGN localization depends on ZDHHC7-mediated Cys126 palmitoylation, which is crucial for ASC recruitment and inflammasome assembly. C_LIO_LINLRP3 inflammasome activation by ZDHHC7 differs from ZDHHC12-mediated NLRP3 inhibition. C_LI

immunology↗

bioRxiv2023

Is M1-L121E a good mimic on microbial rhodopsin? A viewpoint from excited-state dynamics

Microbial rhodopsin, an important photoreceptor protein, has been widely used in several fields, such as optogenetics, biotechnology, and biodevices etc. However, current microbial rhodopsins are all transmembrane proteins, which both complicates the investigation on the photoreaction mechanism and limits their further applications. Therefore, a suitable mimic for microbial rhodopsin can not only provide a better model for understanding the mechanism, but also can extend the applications. The human protein CRABPII turns out to be a good template for design mimics on rhodopsin, due to the convenience in synthesis and the stability after mutations. Recently, Geiger et al. designed a new CRABPII-based mimic M1-L121E on microbial rhodopsin with the correct 13-cis (13C) isomerization after irritation. However, it still remains a question how similar it is compared with the natural microbial rhodopsin, in particular in the aspect of the photoreaction dynamics. In this article, we investigated the excited-state dynamics of this mimic by measuring its transient absorption spectra. Our results reveal that there are two components in the solution of mimic M1-L121E at PH=8, known as protonated Schiff base (PSB) and unprotonated Schiff base (USB) states. In both states, the photoreaction process from 13-cis (13C) to all-trans (AT) is faster than that from the inverse direction. In addition, the photoreaction process in PSB state is faster than that in the USB state. In the end, we compared the isomerization time of the PSB state with the properties of the microbial rhodopsin, and confirmed that the mimic M1-L121E indeed captures the main feature of the rhodopsin and is a good model of microbial rhodopsin in the photoreaction dynamics. However, our results also reveal significant differences in the excited-state dynamics of the mimic relative to the natural microbial rhodopsin, including the slower PSB isomerization rates in both 13C-AT and AT-13C directions, as well as the unusual USB photoreaction dynamics at PH=8. Such unique properties have not been observed in the natural rhodopsin, which could further deepen the understanding in photoreaction mechanism of the photosensitive proteins.

biophysics↗

bioRxiv2023

CellPie: a fast spatial transcriptomics topic discovery method via joint factorization of gene expression and imaging data

Spatially resolved transcriptomics has enabled the study of expression of genes within tissues while retaining their spatial identity. Most spatial transcriptomics technologies generate a matched histopathological image as part of the standard pipeline, providing morphological information that can complement the transcriptomics data. Here we present CellPie, a fast, unsupervised factor discovery method, based on joint non-negative matrix factorisation of spatial RNA transcripts and histological image features.CellPie employs the accelerated hierarchical least squares method to significantly reduce the computational time, enabling efficient application to high-dimensional spatial transcriptomics datasets. We assessed CellPie on two different human cancer types and spatial resolutions, showing an improved performance against published factorisation methods. Additionally, we applied CellPie to a highly resolved Visium HD dataset, demonstrating its high computational efficiency compared to standard non-negative matrix factorisation and other existing methods. Availabilityhttps://github.com/ManchesterBioinference/CellPie

bioinformatics↗

bioRxiv2023

starTracer: An Accelerated Approach for Precise Marker Gene Identification in Single-Cell RNA-Seq Analysis

We introduce starTracer, a novel R package designed to enhance the specificity and efficiency of marker gene identification in single-cell RNA-seq data analysis. The package consists of two primary functional modules: "searchMarker" and "filterMarker". The "searchMarker" module, operating as an independent pipeline, exhibits superior flexibility by accepting a variety of input file types. Its primary output is a marker gene matrix, where genes are sorted by their potential to function as cluster-specific markers, with those exhibiting the greatest potential positioned at the top of the matrix for each respective cluster. In contrast, the "filterMarker" module is designed as a complementary pipeline to the Seurat "FindAllMarkers" function, providing a more accurate marker gene list for each cluster in conjunction with Seurat results. Benchmark analyses demonstrate that starTracer not only achieves excellent specificity in identifying marker genes compared to Seurat but also significantly surpasses it in processing speed. Impressively, the speed improvement ranges by 1~2 orders of magnitude compared to Seurat, as observed across three independent datasets. It is worth noting that starTracer exhibits increasing speed improvement with larger data volumes. It also excels in identifying markers in smaller clusters. Furthermore, the "filterMarker" reordering process considerably enhances Seurats marker matrix specificity. These advantages solidify starTracer as an invaluable tool for researchers working with single-cell RNA-seq data, merging robust accuracy with exceptional speed.

bioinformatics↗

bioRxiv2023

TCCIA: A Comprehensive Resource for Exploring CircRNA in Cancer Immunotherapy

BackgroundImmunotherapies targeting immune checkpoints have gained increasing attention in cancer treatment, emphasizing the need for predictive biomarkers. Circular RNAs (circRNAs) have emerged as critical regulators of tumor immunity, particularly in the PD-1/PD-L1 pathway, and have shown potential in predicting immunotherapy efficacy. Yet, the detailed roles of circRNAs in cancer immunotherapy are not fully understood. While existing databases focus on either circRNA profiles or immunotherapy cohorts, there is currently no platform that enables the exploration of the intricate interplay between circRNAs and anti-tumor immunotherapy. A comprehensive resource combining circRNA profiles, immunotherapy responses, and clinical outcomes is essential to advance our understanding of circRNA-mediated tumor-immune interactions and to develop effective biomarkers. MethodsTo address these gaps, we constructed the Cancer CircRNA Immunome Atlas (TCCIA), the first database that combines circRNA profiles, immunotherapy response data, and clinical outcomes across multi-cancer types. The construction of TCCIA involved applying standardized preprocessing to the raw sequencing FASTQ files, characterizing circRNA profiles using an ensemble approach based on four established circRNA detection tools, analyzing tumor immunophenotypes, and compiling immunotherapy response data from diverse cohorts treated with immune-checkpoint blockades (ICBs). ResultsTCCIA encompasses over 4,000 clinical samples obtained from 25 cohorts treated with ICBs along with other treatment modalities. The database provides researchers and clinicians with a cloud-based platform that enables interactive exploration of circRNA data in the context of ICB. The platform offers a range of analytical tools, including browse of identified circRNAs, visualization of circRNA abundance and correlation, association analysis between circRNAs and clinical variables, assessment of the tumor immune microenvironment, exploration of tumor molecular signatures, evaluation of treatment response or prognosis, and identification of altered circRNAs in immunotherapy-sensitive and resistant tumors. To illustrate the utility of TCCIA, we showcase two examples, including circTMTC3 and circMGA, by employing analysis of large-scale melanoma and bladder cancer cohorts, which unveil distinct impacts and clinical implications of different circRNA expression in cancer immunotherapy. ConclusionsTCCIA represents a significant advancement over existing resources, providing a comprehensive platform to investigate the role of circRNAs in immuno-oncology. What is already known on this topicPrior knowledge indicated that circRNAs are involved in tumor immunity and have potential as predictive biomarkers for immunotherapy efficacy. However, there lacked a comprehensive database that integrated circRNA profiles and immunotherapy response data, necessitating this study. What this study addsThis study introduces TCCIA, a database that combines circRNA profiles, immunotherapy response data, and clinical outcomes. It provides a diverse collection of clinical samples and an interactive platform, enabling in-depth exploration of circRNAs in the context of checkpoint-blockade immunotherapy. How this study might affect research, practice or policyThe findings of this study offer valuable insights into the roles of circRNAs in tumor-immune interactions and provide a resource for researchers and clinicians in the field of immune-oncology. TCCIA has the potential to guide personalized immunotherapeutic strategies and contribute to future research, clinical practice, and policy decisions in checkpoint-blockade immunotherapy and biomarker development.

bioinformatics↗

bioRxiv2023

Crohn's patients and healthy infants share immunodominant B cell response to commensal flagellin peptide epitopes

About half of patients with Crohns disease (CD) develop selective serum IgG response to flagellin proteins of the Lachnospiraceae family. Here, we identified a dominant B cell peptide epitope in CD, locating in the highly conserved "hinge region" between the D0 and D1 domains at the amino-terminus of Lachnospiraceae flagellins. Serum IgG reactive to this epitope is present at an elevated level in adult CD patients and in pediatric CD patients at diagnosis. Most importantly, high levels of serum IgG to the hinge epitope were found in most infants from 3 different geographic regions (Uganda, Sweden, and the USA) at one year of age. This vigorous homeostatic response decrements with age as it is not present in healthy adults. These data identify a distinct subset of CD patients, united by a shared reactivity to this dominant flagellin epitope that may represent failure of a homeostatic response beginning in infancy.

immunology↗

bioRxiv2023

USP20 deubiquitinates and stabilizes the ER-phagy receptor FAM134B to drive ER-phagy

The endoplasmic reticulum (ER) serves as a hub for various essential cellular processes, and maintaining ER homeostasis is essential for cell function. ER-phagy is a selective process that removes impaired ER subdomains through autophagosomes and lysosomal degradation. While the involvement of ubiquitination in autophagy regulation is well-established, its role in ER-phagy remains unclear. In our study, we screened deubiquitinating enzymes involved in ER-phagy and identified USP20 (ubiquitin specific peptidase 20) as a key regulator of ER-phagy under stress conditions. USP20 specifically cleaves K63- and K48-linked ubiquitin chains on the ER-phagy receptor FAM134B/RETREG1 (reticulophagy regulator 1), thereby stabilizing the substrate and promoting ER-phagy. Remarkably, despite lacking a transmembrane domain, USP20 is recruited to the ER through its interaction with VAPs (vesicle-associated membrane proteins). VAPs facilitate the recruitment of early autophagy proteins, including WIPI2, to specific ER subdomains, where USP20 and FAM134B are enriched. This recruitment of WIPI2 and other proteins plays a crucial role in facilitating FAM134B-mediated ER-phagy in response to cellular stress. Our findings highlight the critical role of USP20 in maintaining ER homeostasis by deubiquitinating and stabilizing FAM134B at distinct ER subdomains, where USP20 further recruits VAPs and promotes efficient ER-phagy.

molecular biology↗

bioRxiv2023

Modeling Human Spine-Spinal Cord Organogenesis by hPSC-Derived Neuromesodermal Progenitors

Human trunk development, including spine and spinal cord organogenesis, is a coordinated, orderly, and interdependent process with spatiotemporal tissue patterning. However, the underlying cellular and molecular mechanisms remain largely unclear due to the lack of an effective model that can simulate the early development of human body axis. Here, we reported the long-term patterning and dynamic morphogenesis of human trunk through the formation of spine-spinal cord organoids (SSCOs) self-organized from three-dimensional culture of human PSC-derived neuromesodermal progenitors (NMPs). The SSCOs resembled the morphogenetic features of spine and spinal cord along the anterior-posterior axis, and showed the chondro-osteogenic and neural trajectories consistent with developmental dynamics of spine and spinal cord in gestational embryo through single-cell RNA sequencing (scRNA-seq). In addition, we identified a new HMMR+ bipotent cell population with self-renewal ability and neural/mesodermal competence but distinct from NMPs, which may be involved in trunk development and represent an invaluable tool for disease modeling of spine- and spinal cord-related disorders. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/549829v1_ufig1.gif" ALT="Figure 1"> View larger version (80K): org.highwire.dtl.DTLVardef@14bfd30org.highwire.dtl.DTLVardef@1db7fe8org.highwire.dtl.DTLVardef@1aa66a1org.highwire.dtl.DTLVardef@380932_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

An mTOR/RNA pol I axis shapes chromatin architecture in response to fasting

Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom. Yet, how it impacts on 3D genome organization is unknown. Here, we show that fasting induces a reversible and large-scale spatial reorganization of chromatin in C. elegans. This fasting-induced 3D genome reorganization requires inhibition of the nutrient-sensing mTOR pathway, a major regulator of ribosome biogenesis. Remarkably, loss of transcription by RNA Pol I, but not RNA Pol II nor Pol III, induces a similar 3D genome reorganization in fed animals, and prevents the restoration of the fed-state architecture upon restoring nutrients to fasted animals. Our work documents the first large-scale chromatin reorganization triggered by fasting and reveals that mTOR and RNA Pol I shape genome architecture in response to nutrients.

cell biology↗

bioRxiv2023

Nanobead-based single-molecule pulldown for single cells

Investigation of cell-to-cell variability holds critical physiological and clinical implications. Thus, numerous new techniques have been developed for studying cell-to-cell variability, and these single-cell techniques can also be used to investigate rare cells. Moreover, for studying protein-protein interactions (PPIs) in single cells, several techniques have been developed based on the principle of the single-molecule pulldown (SiMPull) assay. However, the applicability of these single-cell SiMPull (sc-SiMPull) techniques is limited because of their high technical barrier and special requirements for target cells and molecules. Here, we report a highly innovative nanobead-based approach for sc-SiMPull that is based on our recently developed microbead-based, improved version of SiMPull for cell populations. In our sc-SiMPull method, single cells are captured in microwells and lysed in situ, after which commercially available, pre-surface-functionalized magnetic nanobeads are placed in the microwells to specifically capture proteins of interest together with their binding partners from cell extracts; subsequently, the PPIs are examined under a microscope at the single-molecule level. Relative to previously published methods, nanobead-based sc-SiMPull is considerably faster, easier to use, more reproducible, and more versatile for distinct cell types and protein molecules, and yet provides similar sensitivity and signal-to-background ratio. These crucial features should enable universal application of our method to the study of PPIs in single cells. Statement of SignificanceHeterogeneity between single cells holds critical physiological and clinical implications. Characterization of protein-protein interactions (PPIs) and identification of the interacting partners of a specific protein are critical for elucidating the function and regulation of the protein. However, the applicability of the currently available techniques for studying PPIs in single cells is limited by their high technical barrier and special requirements for cell/proteins types. Our single-cell single-molecule pulldown (sc-SiMPull) assay in this study is not only substantially simpler and faster than existing sc-SiMPull methods, but also considerably more widely applicable--to all cell types and to both soluble and transmembrane proteins. These two crucial features should enable universal application of our method to the study of PPIs in single cells.

bioengineering↗

bioRxiv2023

GDF15 is a Critical Renostat in the Defense Against Hypoglycemia

Episodic hypoglycemia is one of the best honed, evolutionary conserved phenomena in biology, because of the constant feast-fast cycles that have characterized most of history. The counterregulatory response to hypoglycemia, mobilizing substrate stores to produce glucose, is the primary adaptive mechanism to enable survival. Catecholamines and glucagon have long been considered the key hypoglycemia counterregulatory hormones, but here we identify a new hypoglycemia counterregulatory factor. We employed the insulin tolerance test (ITT) and hyperinsulinemic-hypoglycemic clamp to mimic the two common settings in which hypoglycemia can occur in patients: postprandial insulin overdose and elevated basal insulin administration, respectively. We found that Growth Differentiation Factor 15 (GDF15) production is induced in the S3 segment of the renal proximal tubules and its release increases hepatic gluconeogenesis by increasing intrahepatic lipolysis in a beta-adrenergic receptor-2 (Adrb2)-dependent manner. In addition, mice exposed to recurrent hypoglycemia and patients with T1D exhibit impaired GDF15 production in the setting of hypoglycemia. These data demonstrate that GDF15 acts acutely as a gluco-counterregulatory hormone and identify a critical role for kidney-derived GDF15 in glucose homeostasis under physiological and pathophysiological conditions.

physiology↗

bioRxiv2023

Endosome-ER Interactions Define a Cellular Energy Landscape to Guide Cargo Transport

Molecular motor-driven cargo must navigate a complex intracellular environment, which is often crowded, heterogeneous and fluctuating, to fulfill their diverse functions in a cell. To meet these challenges, most cargo display qualitatively similar transport behavior, that is, random switching between states of diffusive "jiggling" movement (off-state) and states of directed "runs" (on-state). The physical picture of this 2-state motion and their regulation in a cell are not well understood. Here, by using single-particle tracking and motion-states dissection, we present a statistical analysis of the 2-state motion of epidermal growth factor receptor (EGFR)-endosomes in living cells. From a thorough analysis of a large volume of EGFR-endosome trajectories, we reveal that their lifetime in both states feature an exponential distribution with its probability density function (PDF)-amplitude varied by more than three decades. We show that their characteristic time, on-state probability, velocity and off-state diffusion coefficient are spatially regulated, and are probably contributed by the endoplasmic reticulum (ER) network via its spatially varying membrane densities and interactions with the cargo. We further propose a 2-state transport model to describe the complex, spatially varying transport dynamics of EGFR-endosomes in a cell. Our findings suggest that the ER network may play an essential role in constructing a cellular-level free-energy landscape {Delta}G(r) to spatially guide cargo transport.

biophysics↗

bioRxiv2023

Deciphering molecular heterogeneity and dynamics of neural stem cells in human hippocampal development, aging, and injury

While accumulated publications support the existence of neurogenesis in the adult human hippocampus, the homeostasis and developmental potentials of neural stem cells (NSCs) under different contexts remain unclear. Based on our generated single-nucleus atlas of the human hippocampus across neonatal, adult, aging and injury, we dissected the molecular heterogeneity and transcriptional dynamics of human hippocampal NSCs under different contexts. We further identified new specific neurogenic lineage markers that overcome the lack of specificity found in some well-known markers. Based on developmental trajectory and molecular signatures, we found that a subset of NSCs exhibit quiescent properties after birth, and most NSCs become deep quiescence during aging. Furthermore, certain deep quiescent NSCs are re-activated following stroke injury. Together, our findings provide valuable insights into the development, aging, and re-activation of the human hippocampal NSCs, and help to explain why adult hippocampal neurogenesis is infrequently observed in humans.

neuroscience↗

bioRxiv2023

Diazo-carboxyl click chemistry enables rapid and sensitive quantification of carboxylic acid metabolites

Carboxylic acids are central metabolites in bioenergetics, signal transduction and post-translation protein regulation. Unlike its genomic and transcriptomic counterparts, the quest for metabolomic profiling in trace amounts of biomedical samples is prohibitively challenging largely due to the lack of sensitive and robust quantification schemes for carboxylic acids. Based on diazo-carboxyl click chemistry, here we demonstrate DQmB-HA method as a rapid derivatization strategy for the sensitive analysis of hydrophilic, low-molecular-weight carboxylic acids. To the investigated metabolites, DQmB-HA derivatization method renders 5 to 2,000-fold higher response on mass spectrometry along with improved chromatographic separation on commercial UHPLC-MS machines. Using this method, we present the near-single-cell analysis of carboxylic acid metabolites in mouse egg cells before and after fertilization. Malate, fumarate and {beta}-hydroxybutyrate were found to decrease in mouse zygotes. We also showcase the kinetic profiling of TCA-cycle intermediates inside adherent cells cultured in one well of 96-well plates during drug treatment. FCCP and AZD3965 were shown to have overlapped but different effects on the isotope labeling of carboxylic acids. Finally, we apply DQmB-HA method to plasma or serum samples (down to 5 L) from mice and humans collected on pathological and physiological conditions. The measured changes of succinate, {beta}-hydroxybutyrate, and lactate in blood corroborate previous literatures in ischemia-reperfusion injury mouse model, acute fasting-refeeding mouse model, and human individuals diagnosed with mitochondrial dysfunction diseases, respectively. Overall, DQmB-HA method offers a sensitive, rapid and user-friendly quantification scheme for carboxylic acid metabolites, paving the road toward the ultimate goals of single-cell metabolomic analysis and bedside monitoring of biofluid samples.

systems biology↗

bioRxiv2023

Mitochondrial GTP Metabolism Regulates Reproductive Aging

Healthy mitochondria are critical for reproduction. During aging, both reproductive fitness and mitochondrial homeostasis decline. Mitochondrial metabolism and dynamics are key factors in supporting mitochondrial homeostasis. However, how they are coupled to control reproductive health remains unclear. We report that mitochondrial GTP metabolism acts through mitochondrial dynamics factors to regulate reproductive aging. We discovered that germline-only inactivation of GTP- but not ATP-specific succinyl-CoA synthetase (SCS), promotes reproductive longevity in Caenorhabditis elegans. We further revealed an age-associated increase in mitochondrial clustering surrounding oocyte nuclei, which is attenuated by the GTP-specific SCS inactivation. Germline-only induction of mitochondrial fission factors sufficiently promotes mitochondrial dispersion and reproductive longevity. Moreover, we discovered that bacterial inputs affect mitochondrial GTP and dynamics factors to modulate reproductive aging. These results demonstrate the significance of mitochondrial GTP metabolism in regulating oocyte mitochondrial homeostasis and reproductive longevity and reveal mitochondrial fission induction as an effective strategy to improve reproductive health.

cell biology↗

bioRxiv2023

Experimentally induced active and quiet sleep engage non-overlapping transcriptomes in Drosophila

Sleep in mammals can be broadly classified into two different physiological categories: rapid eye movement (REM) sleep and slow wave sleep (SWS), and accordingly REM and SWS are thought to achieve a different set of functions. The fruit fly Drosophila melanogaster is increasingly being used as a model to understand sleep functions, although it remains unclear if the fly brain also engages in different kinds of sleep as well. Here, we compare two commonly used approaches for studying sleep experimentally in Drosophila: optogenetic activation of sleep-promoting neurons and provision of a sleep-promoting drug, Gaboxadol. We find that these different sleep-induction methods have similar effects on increasing sleep duration, but divergent effects on brain activity. Transcriptomic analysis reveals that drug-induced deep sleep ( quiet sleep) mostly downregulates metabolism genes, whereas optogenetic active sleep upregulates a wide range of genes relevant to normal waking functions. This suggests that optogenetics and pharmacological induction of sleep in Drosophila promote different features of sleep, which engage different sets of genes to achieve their respective functions.

neuroscience↗

bioRxiv2023

A hierarchical strategy to decipher protein dynamics in vivo with chemical cross-linking mass spectrometry

Protein dynamics are essential for their various functions. Meanwhile, the intracellular environment would affect protein structural dynamics, especially for the intrinsically disordered proteins (IDPs). Chemical cross-linking mass spectrometry (CXMS) can unbiasedly capture the protein conformation information in cells and can also represent the protein dynamics. Here, we proposed a hierarchy deciphering strategy for protein dynamics in vivo. With the prior structure from AlphaFold2, the steady local conformation can be extensively evaluated. On this basis, the full-length structure of multi-domain proteins with various dynamic features can be characterized using CXMS. Furthermore, the complementary strategy with unbiased sampling and distance-constrained sampling enables an objective description of the intrinsic motion of the IDPs. Therefore, the hierarchy strategy we presented herein could help us better understand the molecular mechanisms of protein functions in cells.

cell biology↗