Biology subjects

liu, h.

Publications and source records attributed to liu, h..

8 recordsLinked to original sources

bioRxiv2025

ShenQi Compound improves diabetes by modulating pancreatic mitochondrial energy metabolism in GK rats

PurposeShenQi Compound (SQC) is a traditional herbal formula that has long been utilized in the treatment of type 2 diabetes and its complications. The purpose of this study was to investigate the effect of SQC on mitochondrial energy metabolism in pancreatic tissues of spontaneously type 2 diabetic Goto-Kakizaki (GK) rats. MethodsGK rats were induced into a diabetic model using a high-fat diet. They were randomly divided into 3 groups (n=8): diabetes model group, SQC group (14.4 g/kg/d) and metformin (Met) group (0.1 g/kg/d). Another 8 Wistar rats were taken as controls. Weight, Blood glucose was monitored weekly in each group,After 12 weeks of gavage. Fasting blood glucose and lipid levels were evaluated, and histopathological changes in the pancreas were assessed by hematoxylin-eosin (HE) staining, serum fasting insulin(FINS) and pancreatic mitochondrial respiratory chain complex I-V (complexI-V) levels were measured by enzyme-linked immunosorbent assay (ELISA), reactive oxygen species ((ROS)) levels were detected by chemiluminescence, superoxide dismutase (SOD) levels were detected by xanthine oxidase, and glutathione (GSH) and adenosine triphosphate (ATP) levels were detected by colorimetric assay. And the uncoupling protein(UCP-2) protein and mRNA expression levels were detected by protein blotting and real-time quantitative PCR. ResultsSQC treatment significantly decreased (P<0.01) the levels of FBS, FINS,triglyceride s(TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-C) (P<0.01) and significantly increased (P<0.01) the levels of denser lipoprotein cholesterol (HDL-C) in GK rats. Pancreatic histopathological damage was improved after SQC treatment, and complexI to complexIV significantly decreased (P<0.05) and complexV, SOD and GSH significantly increased (P<0.05) in pancreatic tissues. In addition, SQC reduced the content of ROS and ATP in pancreatic tissues (P<0.01) and down-regulated UCP-2 protein and mRNA expression (P<0.01). ConclusionSQC improves glucose-lipid metabolism and attenuates pathological damage of pancreatic tissues in T2DM rats, possibly by regulating mitochondrial energy metabolism in pancreatic tissues. The effects of SQC are not well understood. These findings provide new insights into the mechanism of action of SQC in the treatment of T2DM and its associated neurodegenerative effects.

zoology↗

bioRxiv2024

Individual connectivity-based parcellations reflect functional properties of human auditory cortex

Neuroimaging studies of the functional organization of human auditory cortex have focused on group-level analyses to identify tendencies that represent the typical brain. Here, we mapped auditory areas of the human superior temporal cortex (STC) in 30 participants by combining functional network analysis and 1-mm isotropic resolution 7T functional magnetic resonance imaging (fMRI). Two resting-state fMRI sessions, and one or two auditory and audiovisual speech localizer sessions, were collected on 3-4 separate days. We generated a set of functional network-based parcellations from these data. Solutions with 4, 6, and 11 networks were selected for closer examination based on local maxima of Dice and Silhouette values. The resulting parcellation of auditory cortices showed high intraindividual reproducibility both between resting state sessions (Dice coefficient: 69-78%) and between resting state and task sessions (Dice coefficient: 62-73%). This demonstrates that auditory areas in STC can be reliably segmented into functional subareas. The interindividual variability was significantly larger than intraindividual variability (Dice coefficient: 57%-68%, p<0.001), indicating that the parcellations also captured meaningful interindividual variability. The individual-specific parcellations yielded the highest alignment with task response topographies, suggesting that individual variability in parcellations reflects individual variability in auditory function. Connectional homogeneity within networks was also highest for the individual-specific parcellations. Furthermore, the similarity in the functional parcellations was not explainable by the similarity of macroanatomical properties of auditory cortex. Our findings suggest that individual-level parcellations capture meaningful idiosyncrasies in auditory cortex organization.

neuroscience↗

bioRxiv2022

Dissecting the genetic basis of the heterosis of Y900, an elite super-hybrid rice

Y900 is one of the top hybrid rice varieties with a yield exceeding 15 t/hm2. To dissect the mechanism of heterosis, the male parent line R900 and female parent line Y58S were sequenced using long-read and Hi-C technology. High-quality reference genomes of sizes of 396.41 Mb and 398.24 Mb were obtained for R900 and Y58S, respectively. Genome-wide variations between the parents were systematically identified, including 1,367,758 SNPs and 299,149 Indels. No megabase level structural variations exist. >75% of genes exhibited variation between the two parents. Compared with other two-line hybrids sharing the same female parent, the Geng/japonica-type genetic components from different male parents showed an increasing trend from phase 2-4 super-hybrid rice; Transcriptome analysis revealed that additive and dominance effects are the main genetic effects that constitute the heterosis of Y900. Allele-specific expression patterns and expression regulation patterns are quite dynamic in different tissues. For young panicle tissues, cis-regulation is dominant, while trans-regulation is more popular in leaf issues. Overdominance is more likely regulated by the trans-regulation mechanism. The differential gene expression and regulation pattern are closely related to Geng/japonica introgression. Additionally, R900 contained several excellent japonica haplotypes, such as NAL1, OsSPL13, Ghd8, OsBRI1, and DTH2, which make a good complement to Y58S. The fine tune mechanism through dynamic expression or regulation pattern change, especially on some key functional genes, is the base for heterosis.

plant biology↗

bioRxiv2021

Grp78 alleviates sodium iodate-induced retinal cell injury in vivo and in vitro

ObjectiveGlucose-regulated protein 78 (Grp78) has been regarded as a main member of the endoplasmic reticulum proteins, Grp78 could protect cells from apoptosis under stress conditions. However, whether Grp78 could protect retinal pigment epithelium (RPE) cells from oxidative injury and then protect retinas from morphological changes and functional abnormalities remain undetermined. Here, we try to explore the effect of Grp78 on retinal cell injury induced by sodium iodate in vivo and in vitro. MethodsTo investigate whether Grp78 has a protective effect on RPE injury in vitro, human retinal pigment epithelium (ARPE-19) cells were treated with sodium iodate. The cell proliferation, morphology, apoptosis and ROS production assays were detected. In vivo, We established sodium iodate-induced retinal injury model in mice by intravenous injection of sodium iodate into tail vein. After that, we examined the morphology and function of retina in mice by fundus photography, OCT and ERG. Finally, we removed the retina of mice for histological examination. ResultsGrp78 significantly inhibited sodium iodate-induced reactive oxygen species (ROS), and decreased apoptosis of RPE in vitro. Furthermore, Grp78 significantly decreased the apoptosis of retinal cells in vivo, resulting in the inhibition of morphological changes of retina, and improving the function of retina. The underlying mechanisms included inhibited caspase3 and Nos, and increased expression of Bcl2, thereby protecting RPE from SI-induced ROS and apoptosis. ConclusionGrp78 could reduce the injury of retinal cells induced by sodium iodate in vitro and in vivo. These findings suggested Grp78 may become a new therapeutic target for retinal injury in clinical practice.

molecular biology↗

bioRxiv2020

Computational analysis on the ACE2-derived peptides for neutralizing the ACE2 binding to the spike protein of SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19, is spreading globally and has infected more than 3 million people. It has been discovered that SARS-CoV-2 initiates the entry into cells by binding to human angiotensin-converting enzyme 2 (hACE2) through the receptor binding domain (RBD) of its spike glycoprotein. Hence, drugs that can interfere the SARS-CoV-2-RBD binding to hACE2 potentially can inhibit SARS-CoV-2 from entering human cells. Here, based on the N-terminal helix 1 of human ACE2, we designed nine short peptides that have potential to inhibit SARS-CoV-2 binding. Molecular dynamics simulations of peptides in the their free and SARS-CoV-2 RBD-bound forms allow us to identify fragments that are stable in water and have strong binding affinity to the SARS-CoV-2 spike proteins. The important interactions between peptides and RBD are highlighted to provide guidance for the design of peptidomimetics against the SARS-CoV-2.

biophysics↗

bioRxiv2019

In vitro Reconstitution Unveils the Phospho-regulated Ska-Ndc80 Macro-complex

The human Ska (spindle and kinetochore associated) complex is essential for proper kinetochore-microtubule interactions. Its loading onto the kinetochore complex Ndc80 (Ndc80C) plays a critical role in such function; however, the key determinant that docks Ska onto Ndc80C still remain elusive. Here, we address this question using biochemical reconstitution followed by functional analysis. We identified six Cdk1 sites in Ska3 distributed in three conserved regions. In vitro, Cdk1 phosphorylation on the Ska complex enhanced WT, not phospho-deficient 6A, binding to Ndc80C. Strikingly, the phospho-mimetic Ska 6D complex formed a stable macro-complex with Ndc80C, but Ska WT failed to do so, suggesting that Cdk1 phosphorylation is necessary and sufficient for the formation of the Ska-Ndc80 macro-complex. In cells, Ska3 6A completely lost its localization to kinetochores and its functions in chromosome segregation; whereas Ska3 6D partially restored them. Altogether, our findings not only for the first time reveal the key phospho-regulated Ska-Ndc80 macro-complex essential for faithful chromosome segregation, but also pave the way for mechanistic analyses of kinetochore-microtubule interactions.

cell biology↗

bioRxiv2019

Genome-wide developed microsatellites reveal a weak population differentiation in the hoverfly Eupeodes corollae (Diptera: Syrphidae) across China

The hoverfly, Eupeodes corollae, is a worldwide natural enemy of aphids and a plant pollinator. To provide insights into the biology of this species, we examined its population genetic structure by obtaining 1.15-GB random genomic sequences using next-generation sequencing and developing genome-wide microsatellite markers. A total of 79,138 microsatellite loci were initially isolated from the genomic sequences; after strict selection and further testing of 40 primer pairs in eight individuals, 24 polymorphic microsatellites with high amplification rates were developed. These microsatellites were used to examine the population genetic structure of 96 individuals from four field populations collected across southern to northern China. The number of alleles per locus ranged from 5 to 13 with an average of 8.75; the observed and expected heterozygosity varied from 0.235 to 0.768 and from 0.333 to 0.785, respectively. Population genetic structure analysis showed weak genetic differentiation among the four geographical populations of E. corollae, suggesting a high rate of gene flow reflecting likely widespread migration of E. corollae in China.

molecular biology↗

bioRxiv2018

NEPRE: a Scoring Function for Protein Structures based on Neighbourhood Preference

Protein structure prediction relies on two major components, a method to generate good models that are close to the native structure and a scoring function that can select the good models. Based on the statistics from known structures in the protein data bank, a statistical energy function is derived to reflect the amino acid neighbourhood preferences. The neighbourhood of one amino acid is defined by its contacting residues, and the energy function is determined by the neighbhoring residue types and relative positions. A scoring algorithm, Nepre, has been implemented and its performance was tested with several decoy sets. The results show that the Nepre program can be applied in model ranking to improve the success rate in structure predictions.

bioinformatics↗