Biology subjects

Zuo, B.

Publications and source records attributed to Zuo, B..

6 recordsLinked to original sources

bioRxiv2026

Scale dependence decouple life history traits from transposable element evolution in sauropsids

The Mutational Hazard Hypothesis (MHH) predicts that reduced effective population size weakens purifying selection and promotes transposable element (TE) accumulation. Because effective population size is difficult to estimate across broad taxonomic scales, body mass, generation time, and dN/dS are often used as proxies. We analyzed TE landscapes across 167 sauropsid genomes to test whether these proxies predict genomic TE proportion consistently across phylogenetic scales. All three showed strong scale dependence. Body mass was positively associated with TE proportion across clades, but this relationship broke down within clades: only snakes retained a significant negative Pearson correlation after multiple-testing correction, whereas the corresponding phylogenetically corrected slopes were not significant. Generation time showed a strong pooled association that disappeared within every major clade in both Pearson and PGLS analyses. The pooled dN/dS-TE relationship also disappeared after accounting for body mass and generation time in a structural equation model, with a robust within-clade association retained only in turtles. Lineage-specific TE dynamics, including LTR expansion in sea snakes, were not captured by these proxies. These results show that commonly used MHH proxies mainly reflect clade-level structure rather than consistent within-lineage mechanisms.

genomics↗

bioRxiv2023

Inflammasomes primarily restrict cytosolic Salmonella replication within human macrophages

Salmonella enterica serovar Typhimurium is a facultative intracellular pathogen that utilizes its type III secretion systems (T3SSs) to inject virulence factors into host cells and colonize the host. In turn, a subset of cytosolic immune receptors respond to T3SS ligands by forming multimeric signaling complexes called inflammasomes, which activate caspases that induce interleukin-1 (IL-1) family cytokine release and an inflammatory form of cell death called pyroptosis. Human macrophages mount a multifaceted inflammasome response to Salmonella infection that ultimately restricts intracellular bacterial replication. However, how inflammasomes restrict Salmonella replication remains unknown. We find that caspase-1 is essential for mediating inflammasome responses to Salmonella and restricting bacterial replication within human macrophages, with caspase-4 contributing as well. We also demonstrate that the downstream pore-forming protein gasdermin D (GSDMD) and Ninjurin-1 (NINJ1), a mediator of terminal cell lysis, play a role in controlling Salmonella replication in human macrophages. Notably, in the absence of inflammasome responses, we observed hyperreplication of Salmonella within the cytosol of infected cells as well as increased bacterial replication within vacuoles, suggesting that inflammasomes control Salmonella replication primarily within the cytosol and also within vacuoles. These findings reveal that inflammatory caspases and pyroptotic factors mediate inflammasome responses that restrict the subcellular localization of intracellular Salmonella replication within human macrophages.

microbiology↗

bioRxiv2022

Versican binds collagen via its G3 domain and regulates the organization and mechanics of collagenous matrices

Type I collagen is the most abundant structural protein in the body and, with other fibrillar collagens, forms the fibrous network of the extracellular matrix (ECM). Another group of ECM polymers, the glycosaminoglycans (GAGs) and GAG-modified proteoglycans, play important roles in regulating collagen behaviors and contribute to the compositional, structural and mechanical complexity of the ECM. While the binding between collagen and small leucine-rich proteoglycans (SLRPs) has been studied in detail, the interactions between collagen and the large bottlebrush proteoglycan versican are not well understood. Here, we report that versican binds collagen directly and regulates collagen structure and mechanics. Versican colocalizes with collagen fibers in vivo and binds to collagen via its C-terminal G3 domain (a non-GAG-modified domain present in all known versican isoforms) in vitro; it promotes the deposition of a highly-aligned collagen-rich matrix by fibroblasts. Versican also shows an unexpected effect on the rheology of collagen gels in vitro, causing decreased stiffness and attenuated shear strain stiffening, and the cleavage of versican in liver results in reduced tissue compression stiffening. Thus, versican is an important collagen binding partner, playing a role in modulating collagen organization and mechanics.

cell biology↗

bioRxiv2020

Targeted over-expression of PPARγ in pig skeletal muscle improves oxidative fiber formation and intramuscular fat deposition

PPAR{gamma} is a master regulator of adipogenesis and lipogenesis. To understand its roles in fat deposition and fiber formation in skeletal muscle, we successfully generated muscle-specific overexpression of PPAR{gamma} by pig cloning procedures. The content of intramuscular fat was significantly increased in PPAR{gamma} transgenic pigs while the muscle mass as lean percentage of body weight was not changed. The proteomics analysis demonstrated oxidative metabolism of fatty acids and respiratory chain were increased in PPAR{gamma} pigs. Furthermore, expressions of oxidative muscle fiber-related genes such as MyHC1 and TNNT1 were enhanced. CAMK2, MEF2 and PGC1 were also significantly increased in skeletal muscle of PPAR{gamma} pigs, indicating that Ca2+-sensitive phosphatases and kinases may play an important role in the switch of muscle fiber types when PPAR{gamma} activity is elevated in skeletal muscle. The results support skeletal muscle-specific overexpression of PPAR{gamma} can promote oxidative fiber formation and intramuscular fat deposition in pigs.

genetics↗

bioRxiv2019

CRISPR screening of porcine sgRNA library identified host factors essential for Japanese encephalitis virus replication

Japanese encephalitis virus (JEV) is a mosquito-borne zoonotic flavivirus that causes encephalitis and reproductive disorders in mammalian species. However, key host genes involved in the JEV life cycle and cell death are poorly understood. Here, we designed 85,674 single guide RNAs (sgRNAs) targeting 17,743 protein-coding genes, 11,053 long ncRNAs (lncRNAs), and 551 microRNAs (miRNAs) in the porcine genome, and subsequently developed a porcine sgRNA library and genome-scale CRISPR/Cas9 knockout (PigGeCKO) system. These sgRNAs were delivered into porcine kidney-15 (PK-15) cells that constitutively express Cas9, positive selection screening of the resulting PigGeCKO cell collection for resistance to JEV-induced cell death led to the identification of several previously unreported genes required for JEV infection. We conducted follow-up studies to verify the dependency of JEV on these genes, and identified functional contributions for six of the many candidate JEV-related host genes, including an endoplasmic reticulum membrane protein complex subunit 3 (EMC3) and calreticulin (CALR). Additionally, we identified that four genes associated with heparan sulfate proteoglycans (HSPGs) metabolism, specifically those responsible for HSPG sulfurylation, facilitated JEV entry into PK-15 cells. Thus, beyond our development of the largest CRISPR-based functional genomic screening platform for pig research to date, this work deepens our basic understanding of flavivirus infection and identifies multiple potentially vulnerable targets for the development of medical and breeding technologies to prevent and treat diseases caused by Japanese encephalitis virus.

genetics↗

bioRxiv2019

Assessment of gibberellin (GA4+7) mediated changes on grain filling, hormonal behaviour and antioxidants in high-density maize (Zea Mays L.)

Dense plant cultivation is an efficient approach to improve the maize production by maximizing the utilization of energy and nutrient. However, dense plant populations may aggravate the abortion rate of young grains and result in fewer number of kernels per ear. Grain filling rate and duration play a decisive role in maize grain yield. Therefore, increasing plant density, consideration of enhancing the grain filling rate and duration of individual maize plant and regulating crop senescence would be the first priority. In this study, we examined the regulatory effects of GA4+7 under two application methods (shank-smearing and silk-smearing). Shank-soaking with GA4+7 at the rate of 0 (CK1), 10 (T1), 60 (T2), and 120 (T3) mg L-1, while silk-smearing at the rate of 0 (CK2), 10 (S1), 60 (S2), and 120 (S3) mg L-1 were used. The results showed that GA4+7 improved the grain filling rate by increasing the content of auxin, gibberellin and zeatin and abscisic acid in grains compared to control plants. In addition, The auxin, gibberellin and zeatin contents in the grains were positively and significantly correlated with the maximum grain weight and the maximum and mean grain-filling rates; the abscisic acid level was positively correlated with the maximum grain weight and the maximum and mean grain-filling rates. Moreover, GA4+7 increased the activities of superoxide dismutases, catalases, peroxidases, and reduced the malondialdehyde content in leaves compared with untreated plants. At the rate of 60 mg L-1, GA4+7 showed the greatest effect for shank-smearing and silk-smearing (T2 and S2), followed by 10 mg L-1 (T1) for shank-smearing and 120 mg L-1 (S3) for silk-smearing. Our results suggest that application of 60 mg L-1 GA4+7 for smearing application could efficiently be used for changed the level of hormones in grains and antioxidant enzymes in ear leaf, would be useful for enhancing grain filling rate and delaying leaves senescence, and resulting in an increasing of maize grain yield.

plant biology↗