Tissue Expression Profiles Research Articles

Identification and function of the Pax gene Bmgsb in the silk gland of Bombyx mori.

Paired box (Pax) genes are highly conserved throughout evolution, and the Pax protein is an important transcription factor of embryonic development. The Pax gene Bmgsb is expressed in the silk glands of silkworm, but its biological functions remain unclear. This study aimed to investigate the expression pattern of Bmgsb in the silk gland and explore its functions using RNA interference (RNAi). Here, we identified eight Pax genes in Bombyx mori. Phylogenetic analysis showed that the B. mori Pax genes were highly homologous to the Pax genes in other insects and highly evolutionarily conserved. The tissue expression profile showed that Bmgsb was expressed in the anterior silk gland and anterior part of the middle silk gland (AMSG). RNAi of Bmgsb resulted in defective development of the AMSG, and the larvae were mostly unable to cocoon in the wandering stage. RNA-seq analysis showed that the fibroin genes fib-l, fib-h and p25, cellular heat shock response-related genes and phenol oxidase genes were considerably upregulated upon Bmgsb knockdown. Furthermore, quantitative reverse transcription-PCR results showed that the fibroin genes and ubiquitin proteolytic enzyme-related genes were significantly upregulated in the AMSG after Bmgsb knockdown. This study provides a foundation for future research on the biological functions of B. mori Pax genes. In addition, it demonstrates the important roles of Bmgsb in the transcriptional regulation of fibroin genes and silk gland development.

Diagnostic Model for Alzheimer's Disease Based on PANoptosis-Related Genes.

The pathophysiology of Alzheimer's disease (AD) involves the interplay of three different processes: pyroptosis, apoptosis, and necroptosis. To explore role of PANoptosis, a novel pro-inflammatory programmed cell death pathway, in AD patients. We performed a consensus clustering analysis to identify distinct transcriptional profiles in the samples using the R package "ConsensusClusterPlus". The PANoptosis key genes were obtained by crossing the WGCNA brown module and differentially expressed PANoptosis genes. We accomplished regression analyses using the LASSO-Cox method, combined with pathological status and gene expression data. At the same time, we also constructed PANscore system. The expression of PANoptosis hub genes were validated by qRT-PCR in AD transgenic mice. Our study utilized tissue expression profile data from AD patients to construct three distinct PANoptosis patterns, each with unique molecular and clinical characteristics. We have created a risk scoring system called PANscore, which can analyze patterns specific for each AD patient. Additionally, we observed significantly lower levels of follicular helper T (Tfh) cells in the high PANscore and AD patients. Further analysis revealed a significant negative correlation of Tfh with GSDMD and MLKL. These findings provide a roadmap for personalized patient stratification, enabling clinicians to develop personalized treatment plans for AD patients and advance the field of precision medicine.

Obesity modulates the cellular and molecular microenvironment in the peritoneal cavity: implication for ovarian cancer risk.

Abdominal obesity increases the risk of developing ovarian cancer but the molecular mechanisms of how obesity supports ovarian cancer development remain unknown. Here we investigated the impact of obesity on the immune cell and gene expression profiles of distinct abdominal tissues, focusing on the peritoneal serous fluid (PSF) and the omental fat band (OFB) as critical determinants for the dissemination of ovarian metastases and early metastatic events within the peritoneal cavity. Female C57BL/6 mice were fed a low-fat (LFD) or a high-fat diet (HFD) for 12 weeks until the body weights in the HFD group were significantly higher and the mice displayed an impaired glucose tolerance. Then the mice were injected with the murine ovarian cancer cells (MOSE-LTICv) while remaining on their diets. After 21 days, the mice were sacrificed, tumor burden was evaluated and tissues were harvested. The immune cell composition of abdominal tissues and changes in gene expression in the PSF and OFB were evaluated by flow cytometry and qPCR RT2-profiler PCR arrays and confirmed by qRT-PCR, respectively. Other peritoneal adipose tissues including parametrial and retroperitoneal white adipose tissues as well as blood were also investigated. While limited effects were observed in the other peritoneal adipose tissues, feeding mice the HFD led to distinct changes in the immune cell composition in the PSF and the OFB: a depletion of B cells but an increase in myeloid-derived suppressor cells (MDSC) and mono/granulocytes, generating pro-inflammatory environments with increased expression of cyto- and chemokines, and genes supporting adhesion, survival, and growth, as well as suppression of apoptosis. This was associated with a higher peritoneal tumor burden compared to mice fed a LFD. Changes in cellular and genetic profiles were often exacerbated by the HFD. There was a large overlap in genes that were modulated by both the HFD and the cancer cells, suggesting that this 'genetic fingerprint' is important for ovarian metastases to the OFB. In accordance with the 'seed and soil' theory, our studies show that obesity contributes to the generation of a pro-inflammatory peritoneal environment that supports the survival of disseminating ovarian cancer cells in the PSF and the OFB and enhances the early metastatic adhesion events in the OFB through an increase in extracellular matrix proteins and modulators such as fibronectin 1 and collagen I expression as well as in genes supporting growth and invasion such as Tenacin C. The identified genes could potentially be used as targets for prevention strategies to lower the ovarian cancer risk in women with obesity.

Cloning and spatio-temporal expression of CsKr-h1 encoding the juvenile hormone response gene in Coccinella septempunctata L.

The gene encoding juvenile hormone response (Krüppel homolog1, Kr-hl) in Coccinella septempunctata was investigated by cloning and analysing expression profiles in different developmental stages and tissues by quantitative real-time polymerase chain reaction (PCR). C. septempunctata Kr-hl (CsKr-hl) encoded a 1338 bp open reading frame (ORF) with a predicted protein product of 445 amino acids; the latter showed high similarity to orthologs in other species and contained eight highly-conserved Zn-finger motifs for DNA-binding. CsKr-hl was expressed in different developmental stages of C. septempunctata. The expression levels of CsKr-hl in eggs, 2nd, 3rd, 4th instar larvae, and pupa were 3.31, 2.30, 7.09, 0.58, and 7.48 times the number of 1st instar larvae, respectively. CsKr-hl expression levels in female adults gradually increased at 25-30 days and were significantly higher than expression at 1-20 days. CsKr-hl expression in 20-30 days-old male adults was significantly higher than males aged 1-15 days. CsKr-hl expression levels in heads of male and female adults were significantly higher than expression levels in the thorax, adipose, and reproductive system. Interestingly, CsKr-hl expression levels in the adipose and reproductive system of female adults were significantly higher than in adult male corresponding organs, which suggest that CsKr-hl plays an important role in regulating reproductive development in C. septempunctata.

CloudProteoAnalyzer: scalable processing of big data from proteomics using cloud computing.

Shotgun proteomics is widely used in many system biology studies to determine the global protein expression profiles of tissues, cultures, and microbiomes. Many non-distributed computer algorithms have been developed for users to process proteomics data on their local computers. However, the amount of data acquired in a typical proteomics study has grown rapidly in recent years, owing to the increasing throughput of mass spectrometry and the expanding scale of study designs. This presents a big data challenge for researchers to process proteomics data in a timely manner. To overcome this challenge, we developed a cloud-based parallel computing application to offer end-to-end proteomics data analysis software as a service (SaaS). A web interface was provided to users to upload mass spectrometry-based proteomics data, configure parameters, submit jobs, and monitor job status. The data processing was distributed across multiple nodes in a supercomputer to achieve scalability for large datasets. Our study demonstrated SaaS for proteomics as a viable solution for the community to scale up the data processing using cloud computing. This application is available online at https://sipros.oscer.ou.edu/ or https://sipros.unt.edu for free use. The source code is available at https://github.com/Biocomputing-Research-Group/CloudProteoAnalyzer under the GPL version 3.0 license.

Genome-wide characterization of SDR gene family and its potential role in seed dormancy of Brassica napusL.

Rapeseed (Brassica napus L.) with short or no dormancy period are easy to germinate before harvest (pre-harvest sprouting, PHS). PHS has seriously decreased seed weight and oil content in B. napus. Short-chain dehydrogenase/ reductase (SDR) genes have been found to related to seed dormancy by promoting ABA biosynthesis in rice and Arabidopsis. In order to clarify whether SDR genes are the key factor of seed dormancy in B. napus, homology sequence blast, protein physicochemical properties, conserved motif, gene structure, cis-acting element, gene expression and variation analysis were conducted in present study. Results shown that 142 BnaSDR genes, unevenly distributed on 19 chromosomes, have been identified in B. napus genome. Among them, four BnaSDR gene clusters present in chromosome A04、A05、C03、C04 were also identified. These 142 BnaSDR genes were divided into four subfamilies on phylogenetic tree. Members of the same subgroup have similar protein characters, conserved motifs, gene structure, cis-acting elements and tissue expression profiles. Specially, the expression levels of genes in subgroup A, B and C were gradually decreased, but increased in subgroup D with the development of seeds. Among seven higher expressed genes in group D, six BnaSDR genes were significantly higher expressed in weak dormancy line than that in nondormancy line. And the significant effects of BnaC01T0313900ZS and BnaC03T0300500ZS variation on seed dormancy were also demonstrated in present study. These findings provide a key information for investigating the function of BnaSDRs on seed dormancy in B. napus.

Immunoaffinity proteomics for kidney injury biomarkers in male beagle dogs.

Drug-induced kidney injury (DIKI) is a cause of drug development failure. Dogs represent a common non-rodent animal model in pre-clinical safety studies; however, biomarker assays for detecting nephrotoxicity in dogs are limited. To identify novel proteins and gain insight into the molecular mechanisms involved in DIKI, we developed an assay to evaluate proteomic changes associated with DIKI in male beagle dogs that received nephrotoxic doses of tobramycin for 10 consecutive days. Label-free quantitative discovery proteomics analysis on representative kidney cortex tissues collected on Day 11 showed that the tobramycin-induced kidney injury led to a significant differential regulation of 94 proteins mostly associated with mechanisms of nephrotoxicity such as oxidative stress and proteasome degradation. For verification of the proteomic results, we developed a multiplex peptide-centric immunoaffinity liquid chromatography tandem mass spectrometry assay (IA LC-MS/MS) to evaluate the association of eight DIKI protein biomarker candidates using kidney cortices collected on Day 11 and urine samples collected on Days -4, 1, 3, 7 and 10. The results showed that most biomarkers evaluated were detected in the kidney cortices and their expression profile in tissue aligned with the label-free data. Cystatin C was the most consistent marker regardless of the magnitude of the renal injury while fatty acid-binding protein-4 (FABP4) and kidney injury molecule-1 (KIM-1) were the most affected biomarkers in response to moderate proximal tubular injury in absence of changes in serum-based concentrations of blood urea nitrogen or creatinine. In the urine, clusterin is considered the most consistent biomarker regardless of the magnitude and time of the renal injury. To our knowledge, this is the most comprehensive multiplex assay for the quantitative analysis of mechanism-based proximal tubular injury biomarkers in dogs.

DNA methylation and gene expression profiling reveal potential association of retinol metabolism related genes with hepatocellular carcinoma development.

Aberrant DNA methylation patterns play a critical role in the development of hepatocellular carcinoma (HCC). However, the molecular mechanisms associated with these aberrantly methylated genes remain unclear. This study aimed to comprehensively investigate the methylation-driven gene expression alterations in HCC using a multi-omics dataset. Whole genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) techniques were used to assess the methylation and gene expression profiles of HCC tissues (HCCs) and normal adjacent tissues (NATs). The candidate genes' potential function was further investigated using single-cell RNA sequencing (scRNA seq) data. We observed widespread hypomethylation in HCCs compared to NATs. Methylation levels in distinct genomic regions exhibited significant differences between HCCs and NATs. We identified 247,632 differentially methylated regions (DMRs) and 4,926 differentially expressed genes (DEGs) between HCCs and NATs. Integrated analysis of DNA methylation and RNA-seq data identified 987 methylation-driven candidate genes, with 970 showing upregulation and 17 showing downregulation. Four genes involved in the retinol metabolic pathway, namely ADH1A, CYP2A6, CYP2C8, and CYP2C19, were identified as hyper-downregulated genes. Their expression levels could stratify HCCs into three subgroups with distinct survival outcomes, immune cell infiltration, and tumor microenvironments. Validation of these findings in an independent dataset yielded similar outcomes, confirming the high concordance and potential prognostic value of these genes. ScRNA seq data revealed the low expression of these genes in immune cells, emphasizing their role in promoting malignant cell proliferation and migration. In conclusion, this study provides insights into the molecular characteristics of HCC, revealing the involvement of retinol metabolism-related genes in the development and progression of HCC. These findings have implications for HCC diagnosis, prognosis prediction, and the development of therapeutic targets.

Development and evaluation of a chronic kidney disease risk prediction model using random forest.

This research aims to advance the detection of Chronic Kidney Disease (CKD) through a novel gene-based predictive model, leveraging recent breakthroughs in gene sequencing. We sourced and merged gene expression profiles of CKD-affected renal tissues from the Gene Expression Omnibus (GEO) database, classifying them into two sets for training and validation in a 7:3 ratio. The training set included 141 CKD and 33 non-CKD specimens, while the validation set had 60 and 14, respectively. The disease risk prediction model was constructed using the training dataset, while the validation dataset confirmed the model's identification capabilities. The development of our predictive model began with evaluating differentially expressed genes (DEGs) between the two groups. We isolated six genes using Lasso and random forest (RF) methods-DUSP1, GADD45B, IFI44L, IFI30, ATF3, and LYZ-which are critical in differentiating CKD from non-CKD tissues. We refined our random forest (RF) model through 10-fold cross-validation, repeated five times, to optimize the mtry parameter. The performance of our model was robust, with an average AUC of 0.979 across the folds, translating to a 91.18% accuracy. Validation tests further confirmed its efficacy, with a 94.59% accuracy and an AUC of 0.990. External validation using dataset GSE180394 yielded an AUC of 0.913, 89.83% accuracy, and a sensitivity rate of 0.889, underscoring the model's reliability. In summary, the study identified critical genetic biomarkers and successfully developed a novel disease risk prediction model for CKD. This model can serve as a valuable tool for CKD disease risk assessment and contribute significantly to CKD identification.

Antennal Transcriptome and Proteome Analysis of Olfactory Genes and Tissue Expression Profiling of Odorant Binding Proteins in Wohlfahrtia magnifica

Antennal Transcriptome and Proteome Analysis of Olfactory Genes and Tissue Expression Profiling of Odorant Binding Proteins in Wohlfahrtia magnifica

Genome-wide analysis of radish AHL gene family and functional verification of RsAHL14 in tomato.

The AT-hook motif nuclear localized (AHL) gene family is a highly conserved transcription factors involved in plant growth, development, and stress responses. However, AHLs have not been systematically analyzed in radish (Raphanus sativus). Therefore, we performed genome-wide identification and expression pattern, gene structure, and function verifications of radish AHLs. We identified 52 radish AHLs (RsAHL1-RsAHL52), which were unevenly distributed across nine chromosomes. Phylogenetic analysis showed that the RsAHLs were divided into two clades (A and B) and subdivided into three types (I, II, and III). Collinearity analysis revealed that the 52 RsAHLs produced 49 repeat events. Tissue expression profiles revealed differential expression of RsAHLs across different tissues, with higher expression observed in flower organs, particularly petals and anthers. qRT-PCR results indicated that RsAHLs responded to abscisic acid, methyl jasmonate, and abiotic stress (low and high temperatures and drought). Additionally, RsAHL14 induced a dwarf phenotype in tomato plants, and RsAHL14-overexpression tomato plants presented significantly decreased expression levels of the gibberellin (GA) synthetic genes ent-Copalyl diphosphatase, GA3ox-3/-4/-5, and GA20ox-1/-2/-3, but significantly increased expression of the degradation gene GA2ox-1/-3. Thus, RsAHL14 might affect plant growth by regulating GA content. Collectively, our study comprehensively identified RsAHLs in radish and provided a reference for further research on these genes.

Functional characterization of MaEXPA11 and its roles in response to biotic and abiotic stresses in mulberry

Mulberry is a traditional economic tree with various values in sericulture, ecology, food industry and medicine. Expansins (EXPs) are known as cell wall expansion related proteins and have been characterized to involve in plant development and responses to diverse stresses. In present study, twenty EXP and expansin-like (EXL) genes were identified in mulberry. RNA-seq results indicated that three EXP and EXL genes showed up-regulated expression level under sclerotiniose pathogen infection in three independent RNA-seq datasets. The most significant upregulated EXPA11 was selected as key EXP involving in response to sclerotiniose pathogen infection in mulberry. Furthermore, a comprehensive functional analysis was performed to reveal subcellular location, tissue expression profile of MaEXPA11 in mulberry. Down-regulation of MaEXPA11 using virus induced gene silence (VIGS) was performed to explore the function of MaEXPA11 in Morus alba. Results showed that MaEXPA11 can positively regulate mulberry resistance to Ciboria shiraiana infection and negatively regulate mulberry resistance to cold or drought stress.

Analysis of transcriptome differences between subcutaneous and intramuscular adipose tissue of Ningxiang pigs.

To compare and analyze the molecular mechanisms of adipose deposition in subcutaneous fat (SAF)and intramuscular fat (IMF) tissues in Ningxiang pigs, differential gene expression profiles in SAF and IMF tissues of Ningxiang pigs were identified and analysed using RNA-seq technology. Six healthy 250-day-old male Ningxiang pigs with similar body weights (approximately 85 kg) of intraspecific individuals were selected as experimental material and samples of SAF and IMF tissues were collected. Differential genes associated with fat deposition and lipid metabolism were obtained by sequencing two adipose tissue transcriptomes and performing GO (Gene Ontology) functional annotation and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis. To verify the reliability of the sequencing results, six differential genes were randomly selected to validate using qRT-PCR. The results showed that we identified 2406 DEGs, with 1422 up-regulated and 984 down-regulated genes in two tissues. GO functional annotation analysis revealed that the differentially expressed genes were mainly involved in lipid metabolism related pathways, such as steroid biosynthesis, unsaturated fatty acid biosynthesis, glycerophospholipid metabolism and autophagy pathway. KEGG pathway enrichment showed that the differentially expressed genes were mainly enriched in the biological processes related to lipid binding, fatty acid metabolism, glycol ester metabolism, lipid biosynthesis and other biological processes related to lipid metabolism. Genes related to lipid metabolism, such as TCAP, NR4A1, ACACA, LPL, ELOVL6, DGAT1, PRKAA1, ATG101, TP53INP2, FDFT1, ACOX1 and SCD were identified by bioinformatic analyses and verified by qRT-PCR. Our results indicated that these genes may play important roles in the regulation of fat deposition and metabolism in the SAF and IMF tissue, providing the further mechanistic investigation of fat deposition in Ningxiang pigs.

Bioactives and metabolites of Tetrastigma hemsleyanum root extract alleviate DSS-induced ulcerative colitis by targeting the SYK protein in the B cell receptor signaling pathway

Tetrastigma hemsleyanum is an endemic Chinese herb with a wide range of pharmacological activities, including anti-inflammatory, antiviral, antioxidant, antitumor, and immunomodulatory activities. However, the effect and mechanisms of the anti-inflammatory activity of T. hemsleyanum root extract against dextran sodium sulfate (DSS)-induced ulcerative colitis (UC) have not yet been fully investigated. This study aimed to explore the therapeutic effect and molecular mechanisms of T. hemsleyanum root extract in DSS-induced UC mice and knockdown cells. T. hemsleyanum root extract was obtained and analyzed by high-performance liquid chromatography (HPLC). The therapeutic effects of T. hemsleyanum root extract on DSS-induced UC mice were evaluated by the disease activity index (DAI) score, colon length, serum inflammatory cytokines and oxidant/antioxidant levels, and histopathological features of the ileum and colon. Genome-wide gene expression profiles of ileal and colonic tissues were collected by transcriptomics, and signaling pathways were analyzed by the KEGG database. UC-related pathways were uploaded to the STRING database, then the protein-protein interactions (PPIs) were determined by Cytoscape, and the enriched genes were evaluated by real-time quantitative PCR (qPCR). The protein-ligand complexes were docked by AutoDock, and the genes were knocked down in Caco-2cells by shRNA. The non-targeted metabolomic profiling of ileal contents was analyzed by ultra-high-performance liquid chromatography (UHPLC), and gut microflora were sequenced by an Illumina MiSeq System. Ten components that alleviated UC symptoms in mice by decreasing the DAI and serum inflammatory cytokines and oxidant levels, promoting intestinal development, and increasing serum antioxidant levels were identified in T. hemsleyanum root extract. T. hemsleyanum root extract activated the B cell receptor signaling pathway in the colon tissue of UC mice, in which two components, rutin and astragaline, bound to the spleen tyrosine kinase (SYK) protein but also restored gut microflora diversity and increased the proportion of probiotics. Furthermore, metabolites of T. hemsleyanum root extract were involved in vitamin metabolism, fatty acid metabolism, and ferroptosis. The rutin and astragaline components of T. hemsleyanum root extract, by binding to SYK protein, activated the B cell receptor signaling pathway and restored gut microflora diversity to alleviate UC symptoms in mice.

MicroRNA PC-5p-3991_515 mediates triflumezopyrim susceptibility in the small brown planthopper through regulating the post-transcriptional expression of P450 CYP417A2.

Cytochrome P450 monooxygenases (P450s) are recognized as a major contributor to metabolic resistance in insects to most insecticides, through gene overexpressions and protein mutations. MicroRNA (miRNA), an important post-transcriptional regulator, has been reported to promote insecticide resistance by mediating the expression of detoxification enzyme genes. In the present study, we reported that a novel microRNA PC-5p-3991_515 was involved in the post-transcriptional regulation of CYP417A2 and mediated the triflumezopyrim susceptibility in the small brown planthopper (SBPH), Laodelphax striatellus (Fallén). The tissue expression profiles showed that CYP417A2 was highly expressed in fat body. CYP417A2 was significantly up-regulated at 12, 36, 60, 84 and 108 h after the triflumezopyrim treatment. RNA interference (RNAi) against CYP417A2 significantly increased triflumezopyrim susceptibility in SBPH. According to the prediction by miRanda and TargetScan software, three miRNAs were indicated to bind to CYP417A2. However, when oversupply of agomir, only two miRNAs, PC-3p-625_4405 and PC-5p-3991_515, significantly increased the susceptibility to triflumezopyrim and decreased CYP417A2 levels. Furthermore, PC-5p-3991_515 was confirmed to be involved in the post-transcriptional regulation of CYP417A2 by dual luciferase reporter assay. Meanwhile, PC-5p-3991_515 was co-localized with CYP417A2 in the midgut in situ hybridization. Our findings revealed that the novel microRNA, PC-5p-3991_515, post-transcriptionally regulated CYP417A2 expression, which then mediated the triflumezopyrim susceptibility in SBPH. © 2023 Society of Chemical Industry.

Genome-wide analysis of UDP-glycosyltransferase gene family and identification of a flavonoid 7-O-UGT (AhUGT75A) enhancing abiotic stress in peanut (Arachis hypogaea L.)

BackgroundGlycosylation, catalyzed by UDP-glycosyltransferase (UGT), was important for enhancing solubility, bioactivity, and diversity of flavonoids. Peanut (Arachis hypogaea L.) is an important oilseed and cash crop worldwide. In addition to provide high quality of edible oils and proteins, peanut seeds contain a rich source of flavonoid glycosides that benefit human health. However, information of UGT gene family was quite limited in peanut.ResultsIn present study, a total of 267 AhUGTs clustered into 15 phylogenetic groups were identified in peanut genome. Group I has greatly expanded to contain the largest number of AhUGT genes. Segmental duplication was the major driving force for AhUGT gene family expansion. Transcriptomic analysis of gene expression profiles in various tissues and under different abiotic stress treatments indicated AhUGTs were involved in peanut growth and abiotic stress response. AhUGT75A (UGT73CG33), located in mitochondria, was characterized as a flavonoid 7-O-UGT by in vitro enzyme assays. The transcript level of AhUGT75A was strongly induced by abiotic stress. Overexpression of AhUGT75A resulted in accumulating less amount of malondialdehyde (MDA) and superoxide, and enhancing tolerance against drought and/or salt stress in transgenic Arabidopsis. These results indicated AhUGT75A played important roles in conferring abiotic stress tolerance through reactive oxygen species scavenging.ConclusionsOur research only not provides valuable information for functional characterization of UGTs in peanut, but also gives new insights into potential applications in breeding new cultivars with both desirable stress tolerance and health benefits.

Comprehensive expression profiling analysis to investigate salt and drought responding genes in wild barley (Hordeum spontaneum L.)

Drought and salinity are among the most affecting abiotic stress factors that limit the productivity in economically important plants. Understanding drought and salt tolerance mechanism is pivotal for developing drought and salt tolerant crop cultivars. Here, we monitored the changes in gene expression profiles of leaf and root tissues of two wild barley (Hordeum spontaneum L.) accessions after treatment with salt and drought stresses. We identified a total of 641 DEGs across 24 conditions (2 accessions, 2 stress conditions, 2 tissues and 3 time-points). Interestingly, there was a relatively little overlap between the leaf and the root stress responsive gene expression patterns, suggesting that different stress associated processes might be operating in these tissues during stress adaptation. In hierarchical clustering, the genes with distinct expression patterns were nearly half found in Cluster 1 and Cluster 9 and DEGs found in Cluster 9 were significantly enriched for metabolic processes and organic substance metabolic process. Gene ontology (GO) annotations of biological process of salt and drought analysis identified genes in categories including, catabolic processes, oxidation–reduction and organic substance metabolic process. Molecular function analyses significantly detected transcripts associated with oxidoreductase activity and nucleotide binding. Overall, our results revealed a number of candidate genes and plant processes associated with stress tolerance in wild barley. Determination of responsive genes will shed light on other barley studies aiming to elucidate molecular mechanism of drought or salt tolerance.

Taurine supplementation alters gene expression profiles in white adipose tissue of obese C57BL/6J mice: Inflammation and lipid synthesis perspectives

This work aimed to identify the mechanisms by which taurine exerts its anti-obesity effects in the C57BL/6J ob/ob mice model and determine if taurine supplementation increases the amelioration of inflammation and lipogenesis linked genes in the adipose and liver tissues. Three groups of C57BL/6J mice were fed a standard chow diet for a period of 10 weeks the C57BL/6J normal group, the C57BL/6J ob/ob negative control group with no taurine intake and C57BL/6J ob/ob taurine group with taurine intake. Real time PCR was used to examine the gene expression profile in the experimental groups intrascapular brown adipose tissue (BAT), inguinal white adipose tissue (WAT) and liver. TNF-alpha, Ccl2, Adgre and illb genes that are associated with inflammation were found to have varying level of expression in the three tissues. In comparison to BAT and liver these genes were expressed at a much lower level in WAT, with enhanced serum adiponectin levels.

New Insights into the TIFY Gene Family of Brassica napus and Its Involvement in the Regulation of Shoot Branching

As plant-specific transcription factors, the TIFY family genes are involved in the responses to a series of biotic and abiotic stresses and the regulation of the development of multiple organs. To explore the potential roles of the TIFY gene family in shoot branching, which can shape plant architecture and finally determine seed yield, we conducted comprehensive genome-wide analyses of the TIFY gene family in Brassica napus. Here, HMMER search and BLASTp were used to identify the TIFY members. A total of 70 TIFY members were identified and divided into four subfamilies based on the conserved domains and motifs. These TIFY genes were distributed across 19 chromosomes. The predicted subcellular localizations revealed that most TIFY proteins were located in the nucleus. The tissue expression profile analyses indicated that TIFY genes were highly expressed in the stem, flower bud, and silique at the transcriptional level. High-proportioned activation of the dormant axillary buds on stems determined the branch numbers of rapeseed plants. Here, transcriptome analyses were conducted on axillary buds in four sequential developing stages, that is, dormant, temporarily dormant, being activated, and elongating (already activated). Surprisingly, the transcription of the majority of TIFY genes (65 of the 70) significantly decreased on the activation of buds. GO enrichment analysis and hormone treatments indicated that the transcription of TIFY family genes can be strongly induced by jasmonic acid, implying that the TIFY family genes may be involved in the regulation of jasmonic acid-mediated branch development. These results shed light on the roles of TIFY family genes in plant architecture.

Classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles.

Knee osteoarthritis (OA) involves a variety of tissues in the joint. Gene expression profiles in different tissues are of great importance in order to understand OA. First, we obtained gene expression profiles of cartilage, synovium, subchondral bone, and meniscus from the Gene Expression Omnibus (GEO). Several datasets were standardized by merging and removing batch effects. Then, we used unsupervised clustering to divide OA into three subtypes. The gene ontology and pathway enrichment of three subtypes were analyzed. CIBERSORT was used to evaluate the infiltration of immune cells in different subtypes. Finally, OA-related genes were obtained from the Molecular Signatures Database for validation, and diagnostic markers were screened according to clinical characteristics. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the effectiveness of markers. C1 subtype is mainly concentrated in the development of skeletal muscle organs, C2 lies in metabolic process and immune response, and C3 in pyroptosis and cell death process. Therefore, we divided OA into three subtypes: bone remodelling subtype (C1), immune metabolism subtype (C2), and cartilage degradation subtype (C3). The number of macrophage M0 and activated mast cells of C2 subtype was significantly higher than those of the other two subtypes. COL2A1 has significant differences in different subtypes. The expression of COL2A1 is related to age, and trafficking protein particle complex subunit 2 is related to the sex of OA patients. This study linked different tissues with gene expression profiles, revealing different molecular subtypes of patients with knee OA. The relationship between clinical characteristics and OA-related genes was also studied, which provides a new concept for the diagnosis and treatment of OA.