Showing papers by "Jiaqi Li published in 2023"
TL;DR: Zhang et al. as discussed by the authors used weighted single-step GWAS to detect genetic regions and further candidate genes related to semen traits in Duroc boars and found a common candidate gene, STRA8, in sperm motility and sperm progressive motility, and common candidate genes ZSWIM7, TEKT3 and UBB in sperm abnormality rate, which confirms the hypothesis of gene pleiotropy.
Abstract: Simple Summary Due to the complexity of sperm cell reproduction and maturation, the genetic structure of semen traits remains largely unknown. In our study, we used weighted single-step GWAS to detect genetic regions and further candidate genes related to semen traits in Duroc boars. This study provides in-depth understanding of the genetic structure of semen traits and the biological information provided by gene networks, and can be applied to speed up the genetic process of semen traits in boars. The candidate genes CATSPER1, STRA8, ZSWIM7, TEKT3, UBB, PTBP2, EIF2B2, MLH3, and CCDC70 were associated with semen traits in Duroc pigs. Abstract Semen traits play a key role in the pig industry because boar semen is widely used in purebred and crossbred pigs. The production of high-quality semen is crucial to ensuring a good result in artificial insemination. With the wide application of artificial insemination in the pig industry, more and more attention has been paid to the improvement of semen traits by genetic selection. The purpose of this study was to identify the genetic regions and candidate genes associated with semen traits of Duroc boars. We used weighted single-step GWAS to identify candidate genes associated with sperm motility, sperm progressive motility, sperm abnormality rate and total sperm count in Duroc pigs. In Duroc pigs, the three most important windows for sperm motility—sperm progressive motility, sperm abnormality rate, and total sperm count—explained 12.45%, 9.77%, 15.80%, and 12.15% of the genetic variance, respectively. Some genes that are reported to be associated with spermatogenesis, testicular function and male fertility in mammals have been detected previously. The candidate genes CATSPER1, STRA8, ZSWIM7, TEKT3, UBB, PTBP2, EIF2B2, MLH3, and CCDC70 were associated with semen traits in Duroc pigs. We found a common candidate gene, STRA8, in sperm motility and sperm progressive motility, and common candidate genes ZSWIM7, TEKT3 and UBB in sperm motility and sperm abnormality rate, which confirms the hypothesis of gene pleiotropy. Gene network enrichment analysis showed that STRA8, UBB and CATSPER1 were enriched in the common biological process and participated in male meiosis and spermatogenesis. The SNPs of candidate genes can be given more weight in genome selection to improve the ability of genome prediction. This study provides further insight into the understanding the genetic structure of semen traits in Duroc boars.
1 citations
TL;DR: Zhang et al. as discussed by the authors identified the trans-regulatory lncRNA of ACTG1 (TRLA), which was epigenetically targeted by histone H3 lysine 4 acetylation (H3K4ac).
TL;DR: Wang et al. as mentioned in this paper conducted a systematic analysis on the process of chronic hepatitis B infection and found that a total of 18 m7G-related genes were altered in chronic HBV infection, and then they screened out CHB potential diagnostic biomarkers using machine learning and random forest methods.
Abstract: Chronic hepatitis B (CHB) is a major public health problem in the world. It is the main cause of liver cirrhosis and liver cancer. Although many important roles of RNA modification in stem cells or tumor diseases have been identified, the role of N7-methylguanosine (m7G) modification in the process of chronic HBV infection has not been clearly defined. Therefore, we conducted a systematic analysis on the process of chronic HBV infection. We found that a total of 18 m7G-related genes were altered in chronic HBV infection, and then we screened out CHB potential diagnostic biomarkers using machine learning and random forest methods. RT-qPCR was performed on the samples of healthy people and CHB, which further verified the possibility of being a diagnostic marker. Then, we typed CHB patients based on these 18 genes. We found that the immune microenvironment of different subtypes was different. Among them, patients with subtype-Ⅰ had severe immune response, that is, relatively serious immune cell infiltration, rich immune pathways, relatively many HLA genes, and immune checkpoints. Finally, we conducted an in-depth discussion on our m7G-related genes, and found that m7G gene related to immune cell infiltration may be involved in the disease progression of CHB patients, which was also confirmed in the GSE84044 dataset. In conclusion, m7G-related genes can not only serve as diagnostic markers of CHB, but also participate in the regulation of immune microenvironment and play an important role in the progression of CHB.
TL;DR: In this article , a Cox regression analysis was performed using GSE14520 chip data and a necroptosis-related genes survival prognosis score (NRGPS) was established for HBV-HCC patients.
Abstract: The number of patients with hepatocellular carcinoma (HCC) caused by hepatitis B virus (HBV) infection remains large, despite the remarkable effectiveness of antiviral drugs and vaccines for HBV in preventing and treating HBV infection. Necroptosis is closely related to the occurrence of inflammation, clearance of viral infection, and tumor progression. Presently, little is known about the changes in necroptosis-related genes in the progression from chronic HBV infection (CHI) to HBV-related hepatic fibrosis (HBV-HF) and HBV-related hepatocellular carcinoma (HBV-HCC). In this study, Cox regression analysis was performed using GSE14520 chip data and a necroptosis-related genes survival prognosis score (NRGPS) was established for HBV-HCC patients. NRGPS was constructed using three model genes (G6PD, PINK1 and LGALS3), and verified by data sequencing in the TCGA database. The HBV-HCC cell model was established by transfection of pAAV/HBV1.2C2, constructed by homologous recombination, into HUH7 and HEPG2 cells. The expression levels of G6PD, PINK1, and LGALS3 were detected using RT-qPCR. We further analyzed the expression of the model genes in GSE83148, GSE84044, and GSE14520 and found that LGALS3 was consistently highly expressed in CHI, high fibrosis score and high NRGPS. In addition, immune microenvironment analysis showed that LGALS3 was not only associated with the infiltration of regulatory T cells in the immune microenvironment but also with expression of CCL20 and CCR6. The expression levels of model genes, FOXP3 and CCR6, were analyzed using RT-qPCR in peripheral blood mononuclear cells of 31 hepatitis B surface antibody positive patients, 30 CHI, 21 HBV-HF, and 20 HBV-HCC. In further cell-model experiments, we analyzed the expression of CCL20 by RT-qPCR and the changes in cell proliferation and migration by CCK8 and transwell assays, respectively, in HBV-HCC cell models after LGALS3 knockdown. The findings of this study suggest that LGALS3 could be a biomarker for adverse progression following chronic HBV infection and may also be involved in the regulation of the immune microenvironment, making it a potential therapeutic target.
TL;DR: In this paper , a single-cell transcriptome atlas of adult pigs encompassing 229,268 high-quality nuclei from 19 tissues, annotated to 67 major cell types, including muscle, epithelial, and immune cells.
Abstract: The systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell transcriptome atlas of adult pigs encompassing 229,268 high-quality nuclei from 19 tissues, annotated to 67 major cell types. Besides cellular heterogeneity within and across tissues, we further characterize prominent tissue-specific features and functions of muscle, epithelial, and immune cells. Through deconvoluting 3,921 bulk RNA-seq samples from 17 matching tissues, we dissect thousands of genetic variants with cell-type interaction effects on gene expression (ieQTL). By colocalizing these ieQTL with variants associated with 268 complex traits, we provide new insights into the cellular mechanisms behind these traits. Moreover, we highlight that orthologous genes with cell-type-specific regulation in pigs exhibit significant heritability enrichment for some human complex phenotypes. Altogether, our work provides a valuable resource and highlights novel insights in cellular regulation of complex traits for accelerating pig precision breeding and human biomedical research.
30 May 2023
TL;DR: In this article , the authors investigate the pool boiling performance of micro channel microporous copper structures grown scalably on silicon wafers and develop guidelines for the scalable and facile development of high-capillarity conductive porous structures.
Abstract: Efficient thermal management of semiconductor devices is critical to enable the growth of computational power. Over the past few decades, transistor volumetric packing densities (number of transistors per unit volume) have been increasing, enabling further miniaturization of electronic chips. To address thermal constraints, the development of scalable and robust manufacturing techniques for chip-scale integrated two-phase cooling has been a topic of interest over the past decade. Copper and silicon microchannels have been studied to enable near-junction phase change heat transfer, which show a substantial increase in allowable heat flux due to enhanced evaporation, increased three phase contact line length, and more efficient pool and flow boiling. Electrodeposited metal layers as well as sintering have been used to incorporate roughness on these microchannels. Previous studies have used standard photolithography, laser etching, and deep reactive ion etching for fabricating microchannels. Due to fabrication limitations, these studies have been able to achieve channel and fin widths on the order of 5 µm to 300 µm and fin heights ranging from 10 µm to 350 µm, Here, we investigate the pool boiling performance of micro channel microporous copper structures grown scalably on silicon wafers. Unlike previous approaches, we fabricate the structure using mask-less photoresist pattern writing and electrodeposition of porous copper. Optimized design guidelines are predicted by exploring the micro channel width and microporous copper structure thickness ranging from 10 µm to 400 µm, while structure heights are kept in the range of 25 µm to 50 µm, We demonstrate an optimized pore size can be predicted in terms of durability and improved heat transfer coefficient by varying current density from 20 mA/cm2 to 1 A/cm2 during fabrication. We analyze bubble dynamics during water pool boiling on the fabricated structures to find out the reason behind the results found. The results show prominent increases in critical heat flux and heat transfer coefficient due to escalated capillary activation stemming from the porous interconnected structures. Our work not only explores a distinctive, durable and scalable fabrication method for cooling devices on semiconductors, but also develops guidelines for the scalable and facile development of high-capillarity conductive porous structures.
TL;DR: In this article , using widely available metal meshes with variable dimensions and by controlling the patterning pressure, scalably fabricating hybrid surfaces having spot and grid-like patterns using stamping, the authors show that optimized hybrid surfaces have a ∼37% higher fog harvesting rate when compared to homogeneous super-hydrophobic surfaces.
Abstract: Juxtaposing hydrophilicity and hydrophobicity on the same surface, known as hybrid surface engineering, can enhance phase-change heat transfer. However, controlling hydrophilicity on hybrid surfaces in a scalable fashion is a challenge, limiting their application. Here, using widely available metal meshes with variable dimensions and by controlling the patterning pressure, we scalably fabricate hybrid surfaces having spot and gridlike patterns using stamping. Using fog harvesting in a controlled chamber, we show that optimized hybrid surfaces have a ∼37% higher fog harvesting rate when compared to homogeneous superhydrophobic surfaces. Furthermore, condensation frosting experiments reveal that, on grid-patterned hybrid surfaces, frost propagates at ∼160% higher velocity and provides ∼20% less frost coverage when compared to homogeneous superhydrophobic surfaces. During defrost, our hybrid surfaces retain more water when compared to superhydrophobic surfaces due to the presence of hydrophilic patterns and melt water pinning. We adapt our fabrication technique to roll-to-roll patterning, demonstrating wettability contrast on round metallic geometries via atmospheric water vapor condensation. This work provides guidelines for the rapid, substrate-independent, and scalable fabrication of hybrid wettability surfaces for a wide variety of applications.
TL;DR: In this article , the authors used whole-genome and transcriptome sequencing technologies to identify potential candidate genes affecting growth and carcass traits in Duroc pigs and found that the identified candidate genes were significantly enriched for biological processes involved in the cell and organ development, lipids catabolic process and phosphatidylinositol 3-kinase signalling.
Abstract: Growth and carcass traits are of economic importance in the pig production, which affect pork quality and profitability of finishing pig production. This study used whole-genome and transcriptome sequencing technologies to identify potential candidate genes affecting growth and carcass traits in Duroc pigs. The medium (50-60 k) single nucleotide polymorphism (SNP) arrays of 4 154 Duroc pigs from three populations were imputed to whole-genome sequence data, yielding 10 463 227 markers on 18 autosomes. The dominance heritabilities estimated for growth and carcass traits ranged from 0.000 ± 0.041 to 0.161 ± 0.054. Using non-additive genome-wide association study (GWAS), we identified 80 dominance quantitative trait loci for growth and carcass traits at genome-wide significance (false discovery rate < 5%), 15 of which were also detected in our additive GWAS. After fine mapping, 31 candidate genes for dominance GWAS were annotated, and 8 of them were highlighted that have been previously reported to be associated with growth and development (e.g. SNX14, RELN and ENPP2), autosomal recessive diseases (e.g. AMPH, SNX14, RELN and CACNB4) and immune response (e.g. UNC93B1 and PPM1D). By integrating the lead SNPs with RNA-seq data of 34 pig tissues from the Pig Genotype-Tissue Expression project (https://piggtex.farmgtex.org/), we found that the rs691128548, rs333063869, and rs1110730611 have significantly dominant effects for the expression of SNX14, AMPH and UNC93B1 genes in tissues related to growth and development for pig, respectively. Finally, the identified candidate genes were significantly enriched for biological processes involved in the cell and organ development, lipids catabolic process and phosphatidylinositol 3-kinase signalling (P < 0.05). These results provide new molecular markers for meat production and quality selection of pig as well as basis for deciphering the genetic mechanisms of growth and carcass traits.
TL;DR: In this paper , the effect of various parameters, including the layouts of micro pin fin and TSV, TSV diameter, oxide thickness, and pin fin structures, on electrothermal coupling behaviors were analyzed.