Biology subjects

yu, y.

Publications and source records attributed to yu, y..

6 recordsLinked to original sources

bioRxiv2026

A two-step model of FtsZ-ring disassembly in Bacillus subtilis

Bacillus subtilis grows and divides by binary fission, directed by medial localization of cell division protein FtsZ. Disruption of either the Min system or EzrA results in aberrant FtsZ positioning. Here we compare FtsZ dynamics in cells disrupted for either MinD or EzrA when grown in microfluidic channels. Here we show that cells lacking MinD or EzrA appear to be similarly defective in Z-ring disassembly after septation, but play different roles as simultaneous disruption results in a synergistic defect in division. Moreover, we account for a low frequency of minicell formation in the absence of EzrA, as MinD but not EzrA is necessary for removal of ZapA from polar Z-rings. Finally, overexpression of MinCD results inhibits division through pervasive Z-ring disassembly but appears to concentrate ZapA through localized sequestration. Combined, our results indicate a closer relationship between MinCD and ZapA than previously recognized and show that Z-ring disassembly can be genetically separated into discrete steps. We propose a two-step model for Z-ring disassembly that mirrors the assembly process, such that after and/or during septation, the Z-ring separately decondenses and protofilaments are disassembled to monomers for recycling.

microbiology↗

bioRxiv2024

A high-quality de novo genome assembly of Asian Crested Ibis (Nipponia Nippon) using long-read and Hi-C data

We present TtaoRef1, the highest-quality de novo genome assembly of Asian Crested Ibis (Nipponia Nippon) to date consisting of 134 scaffolds with a length of 1.25 Gb and N50 of 101,183,595 bp. This assembly was generated through the utilization of long-read sequencing and Hi-C data. The assessment of assembly quality, conducted via Benchmarking Universal Single-Copy Orthologs (BUSCO), revealed the presence of 96.8% of completely predicted single-copy genes. TtaoRef1 had 18 times longer N50 value than the previous assembly (ASM70822v1), Furthermore, we conducted the annotation of 24,681 protein-coding genes within the newly assembled genome sequences.

bioinformatics↗

bioRxiv2024

A novel cell communication method reveals that grik4 and gabrd may be critical for inducing death in RGNNV-infected grouper.

To investigate the infectious mechanism of RGNNV, we adopted multi-omics methods to study the precise cellular interactions. We combined proteomic, bulk-RNA seq and sc-RNA seq to search for the secret of RGNNVs influence on the nervous system in grouper. Besides, we created a sc-RNA seq workflow for cell communication analysis that can be applied to those non-model organisms with a reference for the first time, which usually been done by comparing homologous genes in humans or mice in the past (Cheng, Chen et al. 2023), but we use stringdb database to predict interactions at the whole proteomic level (Szklarczyk, Kirsch et al. 2023), and we also build a R package of this procedure to help achieving this goal in other non-model organisms. The results shows that grik4 and gabrd might be the direct causes of death in RGNNV-infected groupers. We also present a mechanistic picture of RGNNV attacking the nervous system of grouper and causing nerve necrosis.

zoology↗

bioRxiv2023

SWI/SNF chromatin remodeling determines brassinosteroid-induced transcriptional activation

The brassinosteroid (BR) hormone is a central modulator of plant growth, development, and responses to stresses by activating or repressing the expression of thousands of genes through the transcription factor BRASSINAZOLE-RESISTANT 1 (BZR1) and its homologues. However, the molecular mechanism that determines the transcriptional activation versus repression activity of BZR1 remains largely unclear. Here, we show that BZR1-responsive transcriptional activation at thousands of loci requires the Switch defective/sucrose non-fermentable (SWI/SNF)-complexes-mediated chromatin accessibility regulation. BR-activated BZR1 controls the activation or repression of thousands of BZR1 target genes through reprograming genome-wide chromatin accessibility landscape in Arabidopsis thaliana. BZR1 physically interacts with the BRAHMA (BRM)-Associated SWI/SNF complexes (BAS), co-localizes with BRM on the genome, and enhances BRM occupancy at sites of increased accessibility by BR. Loss of BRM abrogates the capacity of BZR1 to increase but not decrease chromatin accessibility, blocks BR-induced hypocotyl elongation, and diminishes BZR1-mediated transcriptional activation rather than repression. Together, our work reveals that the BAS chromatin remodeling complex is a critical epigenetic regulatory partner in dictating BZR1-mediated transcriptional activation ability, thus providing a long sought mechanistic explanation for how BR signaling activates gene transcription in shaping diverse developmental programs. TeaserBZR1-responsive transcriptional activation activity at thousands of loci requires the SWI/SNF-complexes-mediated chromatin accessibility regulation.

plant biology↗

bioRxiv2020

Integrin-linked kinase is a key signal factor involved in Nogo-66-induced inhibition of neurite outgrowth

Nogo-66, the extracellular domain of Nogo-A, has been identified as the most important myelin-associated neuronal growth inhibitor. Evidence suggested that Nogo-66 exert its neurite inhibition effect via a Nogo-66/Protein kinase B (PKB)/Glycogen synthase kinase-3{beta} (GSK-3{beta})/tau signaling pathway. Integrin-linked kinase (ILK) is a serine/threonine kinase mediating axon upstream growth of PKB and GSK-3{beta}. However, the contribution of ILK to the Nogo-66-induced inhibition of neurite, is not clear. In this study, we set out to reveal the role of ILK on Nogo-66 signaling in vitro and in vivo. To deteremine this directly, Recombinant adenoviruses were constructed to upregulate or downregulate the expresioon of ILK in Neuro 2a (N2a)and analysis the change of downstream molecule and neurite length. The results showed that Nogo-66 inhibited the phosphorylation of ILK, while ILK regulated the phosphorylation of PKB and GSK-3{beta}, and the expression of tau in Nogo-66-treated N2a cells. ILK overexpression through lentivirus vector transfection reduced the inhibitory effect of neurite outgrowth induced by Nogo-66 in cortical neurons. The Tau expression in the complete spinal cord transection rat model was promoted by the overexpression of ILK. Our findings indicated that ILK is a key signal factor involved in Nogo-66-induced inhibition of neurite outgrowth. The mechanism of Nogo-66 signaling pathway was further explained and a proper target for the promotion of neural regeneration was also provided by this study.

neuroscience↗

bioRxiv2020

Selective Germline Genome Edited Pig Meninges Grafts for the Abdominal Wall Closure in Damage Control Surgery

Reconstruction of abdominal wall defects is still a big challenge in surgery, especially where there is insufficient fascia muscular or excessive tension of the defects in emergency and life-threatening scenarios. Indeed, the concept of damage control surgery has been advanced in the management of both traumatic and nontraumatic surgical settings. The strategy requires abridged surgery and quick back to intensive care units (ICU) for aggressive resuscitation. In the damage control laparotomy, patients are left with open abdomen or provisional closure of the abdomen with a planned return to the operating room for definitive surgery. So far, various techniques have been utilized to achieve early temporary abdominal closure, but there is no clear consensus on the ideal method or material for abdominal wall reconstruction. We recently successfully created the selective germline genome-edited pig (SGGEP) and here we aimed to explore the feasibility of in vivo reconstruction of the abdominal wall in a rabbit model with SGGEP meninges grafts (SGGEP-MGs). Our result showed that the SGGEP-MGs could restore the integrity of the defect very well. After 7 weeks of engraftment, there was no sign of herniation observed, the grafts were re-vascularized, and the defects were well repaired. Histologically, the boundary between the graft and the host was very well integrated and there was no strong inflammatory response. Therefore, this kind of closure could help restore the fluid and electrolyte balance and to dampen systemic inflammatory response in damge control surgery while ADM graft failed to establish re-vascularization as the same as the SGGEP-MG. It is concluded that the meninges of SGGEP could serve as a high-quality alternative for restoring the integrity of the abdominal wall, especially for damage control surgery.

synthetic biology↗