Biology subjects

Zhu, Z.-J.

Publications and source records attributed to Zhu, Z.-J..

8 recordsLinked to original sources

bioRxiv2025

CRISPR/Cas14a Combined with RPA for Visual Detection of Marek's Disease Virus

Mareks disease (MD), a highly contagious avian immunosuppressive disorder caused by the -herpesvirus MDV-1, poses a significant threat to poultry health. The development of rapid visual detection methods capable of distinguishing epidemic MDV-1 strains from vaccine strains is crucial for early disease warning, vaccine efficacy evaluation, and precise disease control. We developed a novel isothermal detection system that integrates recombinase polymerase amplification (RPA) with CRISPR/Cas14a technology for the visual identification of epidemic MDV-1 strains. This method operates at a constant temperature of 37{degrees}C and allows for either real-time analysis or endpoint visual readout without the need for complex instrumentation. Our results showed no cross-reactivity with Newcastle disease virus (NDV), infectious bursal disease virus (IBDV), MDV-1 vaccine strains, or herpesvirus of turkeys (HVT). Plasmid DNA standards were used to determine the sensitivity of the assay and the detection limit was 24.6 copies/L. Clinical evaluation using 24 field samples confirmed that the method successfully identified all MDV-positive cases, demonstrating its diagnostic reliability. In conclusion, we have developed a rapid, instrument-free, and highly specific nucleic acid detection platform for MDV-1 by combining the sensitivity of RPA with the specificity of CRISPR/Cas14a technology, offering promising potential for field-based diagnostics and disease surveillance. IMPORTANCEMareks disease virus (MDV-1) is a highly contagious and economically important avian pathogen. Existing diagnostic methods are unable to reliably distinguish between epidemic and vaccine strains in field settings, which hampers effective surveillance and evaluation of vaccination programs. To address this challenge, we developed a portable isothermal detection assay that combines recombinase polymerase amplification (RPA) with CRISPR/Cas14a technology. This approach enables highly sensitive (24.6 copies/L) and specific visual detection of epidemic MDV-1 strains without cross-reactivity with vaccine strains or related viruses. The assay demonstrated 100% agreement with reference methods when validated using clinical samples. As a cost-effective and instrument-free method, it offers a practical solution for rapid on-site diagnosis, facilitating enhanced outbreak control and improved poultry health management globally.

molecular biology↗

bioRxiv2024

CRISPR screens reveal ZBTB17/MIZ1 as a peroxisome regulator

Peroxisomes are integral metabolic organelles involved in both catabolic and anabolic processes in humans, with defects often linked to diseases. The functions of peroxisomes are regulated at transcriptional, translational, and post-translational levels. In this study, we employed the CRISPR/Cas9-based genetic screening of a ubiquitin ligase library to identify regulators of human peroxisomes. We discovered that ZBTB17 (also referred as MIZ1) plays a role in regulating the import of proteins into peroxisomes. Independent of its ubiquitin ligase activity, ZBTB17/MIZ1 operates as a transcription factor to directly modulate the expression of key importer PEX13, thereby influencing the localization of peroxisomal enzymes. Furthermore, metabolomic profiling reveals that the knockdown of ZBTB17 or PEX13 results in similar metabolic alterations, characterized by downregulated purine synthesis, suggesting that ZBTB17s role in metabolic regulation likely operates through peroxisomes. Collectively, we identify ZBTB17 as a key regulator of peroxisomal protein import, thereby affecting peroxisomal function and nucleotide metabolism. Our findings provide insights into the multifaceted regulation of peroxisomes in complex human cells and shed light on the molecular mechanisms underlying ZBTB17s role as a transcriptional regulator.

cell biology↗

bioRxiv2022

Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic network

Liquid chromatography - mass spectrometry (LC-MS) based untargeted metabolomics allows to measure both known and unknown metabolites in the metabolome. However, unknown metabolite annotation is a grand challenge in untargeted metabolomics. Here, we developed an approach, namely, knowledge-guided multi-layer network (KGMN), to enable global metabolite annotation from knowns to unknowns in untargeted metabolomics. The KGMN approach integrated three-layer networks, including knowledge-based metabolic reaction network, knowledge-guided MS/MS similarity network, and global peak correlation network. To demonstrate the principle, we applied KGMN in an in-vitro enzymatic reaction system and different biological samples, with [~]100-300 putative unknowns annotated in each data set. Among them, >80% unknown metabolites were validated with in-silico MS/MS tools. Finally, we successfully validated 5 unknown metabolites through the repository-mining and the syntheses of chemical standards. Together, the KGMN approach enables efficient unknown annotations, and substantially advances the discovery of recurrent unknown metabolites towards deciphering dark matters in untargeted metabolomics.

bioinformatics↗

bioRxiv2021

metID: A R package for automatable compound annotation for LC-MS-based data

SummaryAccurate and efficient compound annotation is a long-standing challenge for LC-MS-based data (e.g. untargeted metabolomics and exposomics). Substantial efforts have been devoted to overcoming this obstacle, whereas current tools are limited by the sources of spectral information used (in-house and public databases) and are not automated and streamlined. Therefore, we developed metID, an R package that combines information from all major databases for comprehensive and streamlined compound annotation. metID is a flexible, simple, and powerful tool that can be installed on all platforms, allowing the compound annotation process to be fully automatic and reproducible. A detailed tutorial and a case study are provided in Supplementary Materials. Availability and implementationhttps://jaspershen.github.io/metID/. Contactjiangzhu@sioc.ac.cn and mpsnyder@stanford.edu

bioinformatics↗

bioRxiv2020

MS-DIAL 4: accelerating lipidomics using an MS/MS, CCS, and retention time atlas

To the EditorWe formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry (MS/MS) to provide a comprehensive lipidome atlas with retention time, collision cross section, and MS/MS information. The all-in-one solution from import of raw MS data to export of a common output format (mztab-M) was packaged in MS-DIAL 4 (http://prime.psc.riken.jp/) providing an enhanced standardized untargeted lipidomics procedure following lipidomics standards initiative (LSI) semi-quantitative definitions and shorthand notation system of lipid structures with a 1-2% estimated false discovery rate, which will contribute to harmonizing lipidomics data across laboratories to accelerate lipids research.

bioinformatics↗

bioRxiv2019

Membrane association of VAMP2 SNARE motif in cells and its regulation by different lipid phases of synaptic vesicle membrane

Vesicle associated membrane protein 2 (VAMP2) contains a conserved SNARE motif that forms helix bundles with the homologous motifs of syntaxin-1 and SNAP25 to assemble into a SNARE complex for the exocytosis of synaptic vesicles (SV). Prior to SNARE assembly, the structure of VAMP2 is unclear. Here, using in-cell NMR spectroscopy, we described the dynamic membrane association of VAMP2 SNARE motif in mammalian cells at atomic resolution, and further tracked the intracellular structural changes of VAMP2 upon the lipid environmental changes. The underlying mechanistic basis was then investigated by solution NMR combined with mass-spectrometry-based lipidomic profiling. We analyzed the lipid compositions of lipid-raft and non-raft phases of SV membrane and revealed that VAMP2 configures distinctive conformations in different phases of SV membrane. The phase of cholesterol-rich lipid rafts could largely weaken the association of SNARE motif with SV membrane and thus, facilitate vesicle docking; While in the non-raft phase, the SNARE motif tends to hibernate on SV membrane with minor activity. Our work provides a spatial regulation of different lipid membrane phases to the structure of core SNARE proteins, which deepens our knowledge on the modulation of SNARE machinery.

biophysics↗

bioRxiv2018

Metabolic Reaction Network-based Recursive Metabolite Identification for Untargeted Metabolomics

Metabolite identification is a long-standing challenge in untargeted metabolomics and a major hurdle for functional metabolomics studies. Here, we developed a metabolic reaction network-based recursive algorithm and webserver called MetDNA for the large-scale and unambiguous identification of metabolites (available at http://metdna.zhulab.cn). We showcased the versatility of our workflow using different instrument platforms, data acquisition methods, and biological sample types and demonstrated that over 2,000 metabolites could be identified from one experiment.

bioinformatics↗

bioRxiv2018

Epigenetic Drift of H3K27me3 in Aging Links Glycolysis to Healthy Longevity

Epigenetic alteration has been implicated in aging. However, the mechanism by which epigenetic change impacts aging is unclear. H3K27me3, a highly conserved histone modification signifying transcriptional repression, is marked and maintained by Polycomb Repressive Complexes (PRCs). Here, we explore the mechanism by which age-modulated increase of H3K27me3 impacts adult lifespan. Using Drosophila, we reveal that aging leads to loss of fidelity in epigenetic marking and drift of H3K27me3 and consequential reduction in the expression of glycolytic genes with negative effects on energy production and redox state. Moreover, we show that a reduction of H3K27me3 by PRCs-deficiency promotes glycolysis and healthy lifespan. While perturbing glycolysis by gene mutation diminishes the pro-lifespan benefits mediated by PRCs-deficiency, transgenic increase of glycolytic genes in wild-type animals extends longevity. Together, we propose that epigenetic drift of H3K27me3 defines a new aging mechanism and that stimulation of glycolysis promotes metabolic health and longevity.

molecular biology↗