Biology subjects

ZHOU, J.

Publications and source records attributed to ZHOU, J..

4 recordsLinked to original sources

bioRxiv2026

TracePheno Enables Function-First Inference of Trace-ElementPhenotypes from Microbiome Profiles

Microbiome phenotype analysis usually captures broad organism-level traits, yet clinically and ecologically important programmes for trace-element acquisition, storage, detoxification, and cofactor biosynthesis remain difficult to summarize because the underlying loci are often strain-variable and only partly reflected by taxonomy. We present TracePheno, a function-first framework for inferring microbial phenotypes related to eight common trace elements from gene- or KO-level evidence. The current phenotype panels span iron, zinc, manganese, copper, cobalt/vitamin B12, nickel, molybdenum, and selenium. The implementation combines curated core/accessory/ambiguous marker tiers, cohort-invariant bounded support transforms, deterministic core-gated calling, presence/absence-oriented genome trait inference, and a publicationoriented visualization bundle. The bundled release covers ten phenotype panels and three complementary workflows: direct scoring of function matrices, genome-to-trait construction, and taxon-abundance scoring with a precomputed trait matrix. Using the current release, we analysed two local demonstrations that were regenerated for this manuscript. In 11 representative human-gut genomes from the MGnify catalogue, copper homeostasis/resistance and iron acquisition were the most prevalent high-scoring programmes, whereas Firmicutes in this small panel showed stronger cobalamin biosynthesis and selenium-utilization signals than Bacteroidota. In a PICRUSt2-style KO example, zinc acquisition was higher in the case group, whereas iron acquisition, corrinoid transport/cobalt uptake, and selenium utilization were relatively higher in controls. Together, these analyses show that TracePheno can convert genome annotations and predicted KO tables into interpretable, publication-ready trace-element phenotype landscapes while keeping the decision rules explicit, portable, and biologically constrained.

microbiology↗

bioRxiv2025

Voltage-dependent anion channels are mitophagy receptors mediating the recycling of depolarized mitochondria in Arabidopsis

The mitochondrion is an essential organelle in eukaryotic cells, playing crucial roles in cellular respiration and intracellular signaling pathways. To maintain a healthy population of mitochondria, dysfunctional and excess mitochondria are selectively removed through an autophagic process known as mitophagy. Over the past few decades, various autophagy-related (ATG) proteins involved in mitophagy have been well characterized in yeast and mammalian cells since it has significance to the survival of eukaryotes. While the core autophagy machinery responsible for autophagosome formation is conserved among eukaryotes, the homologs of key regulators of mammalian system is absent in plant. In this study, we identified a unique mitophagy mechanism in plant, that three voltage-dependent anion channel (VDAC) family proteins in the mitochondria outer membrane -- specifically VDAC1, VDAC2, and VDAC3 -- as mitophagy receptors in Arabidopsis. These proteins were required for translocation of ATG8 from the cytosol to the mitochondria surface, when Arabidopsis cells were treated with an uncoupler, 2,4-dinitrophenol (DNP). The VDACs interacted directly with ATG8 through an ATG8-interacting motif (AIM) located in their amino (N) termini. Furthermore, vdac mutants exhibited impaired uncoupler-induced mitophagy and accumulated damaged mitochondria. These mitophagy-related phenotypes were more pronounced in vdac double and triple mutant lines. Altogether, our results indicated that VDAC1, 2, and 3 recruit ATG8 to depolarized mitochondria, facilitating the formation of mitophagosomes, presenting a distinguishing mitophagy pathway with mammalian system.

plant biology↗

bioRxiv2024

ISCO: Intelligent Framework for Accurate Segmentation and Comparative Analysis of Organoids

Organoids are self-organizing 3D cell clusters that closely mimic the structure and function of in vivo tissues and organs. Quantifying organoid morphology is critical for advancing our understanding of organ development, drug discovery, and toxicity assessment. Recent advances in microscopy have provided powerful tools to capture detailed morphological features of organoids, yet manual image analysis remains labor-intensive and time-consuming. In response, we present a comprehensive microscopy-based analysis pipeline that utilizes SegmentAnything 2.1 to accurately segment individual organoids. Additionally, we introduce a suite of morphological features--including perimeter, area, radius, non-smoothness, and non-circularity--that enable researchers to quantitatively and automatically analyze organoid structures. To further standardize organoid analysis across the field, Intelligent segmentation and comparison of organoids(ISCO), an intelligent AI-driven open-source algorithm, is developed with the aim of establishing a comprehensive toolset for organoid characterization.

bioengineering↗

bioRxiv2021

A survey of Chinese pig farms and human healthcare isolates reveals separate human and animal MRSA populations

There has been increasing concern that the overuse of antibiotics in livestock farming is contributing to the burden of antimicrobial resistance in people. Farmed animals in Europe and North America, particularly pigs, provide a reservoir for livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA, ST398) found in people. This study was designed to investigate the contribution of MRSA from Chinese pig farms to human infection and carriage.A collection of 603 S. aureus were isolated from 55 pig farms and 4 hospitals (MRSA= 285, 198; MSSA= 50, 70) in central China, a high pig farming density area, during 2017-2018. CC9 MRSA accounting for 93% of all farm MRSA isolates, while no was found in hospitals. ST398 isolates were found on three farms (n = 23) and three hospitals (n = 12). None of the ST398 from this study belong to the livestock clade of the LA-MRSA commonly found in Europe and North America. The hospital ST398 MRSA isolates formed a clade that was clearly separate from the farm ST398 MRSA and MSSA isolates, and all possessed human immune evasion cluster genes which were absent from all the pig farm ST398 isolates. Despite the presence of high levels of MRSA found on Chinese pig farms we found no evidence of them spilling over to the human population. Nevertheless, the ST398 MRSA obtained from human samples appear to be part of a widely distributed lineage in China. And the new animal adapted ST398 lineage that emerged in China should also be alarmed. ImportanceWe disclosed the fact that although the high MRSA positive rate in Chinese hospitals and pig farms should be alarmed, they might be two separate issues. The new CC398 clades we identified highlight that the host adaption of the MRSA lineage is kept changing. These results suggest that continued surveillance of MRSA in livestock is necessary. We found that the pig farm MRSA isolates had unique antimicrobial resistance genes while most of the hospital MRSA isolates had human immune evasion cluster genes. These features could be used to distinguish the pig farm associated S. aureus in clinical laboratories. The policies of reducing antimicrobials use in livestock were implemented in China since 2020. Our study described the situation of MRSA populations in pig farms and hospitals in Central China before 2020, which provides a potential opportunity for future studies to evaluate the effects of the policies.

microbiology↗