Inositol Phosphate Metabolism Pathways Research Articles

Study on Action and Mechanism of Potentilla discolor Bunge using Patch-Clamp to Explore the Effect of the Main Components of Potentilla discolor Bunge on Myocardial Cell Membranes

Background Potentilla discolor Bunge (PDB) is a plant of the Rosaceae family. A wide range of pharmacological activities, such as antibacterial, hypoglycemic, and others, can be achieved through its chemical components, which include terpenes, steroids, polyphenols, and flavonoids. However, the effects of the herb on the heart are unclear. Purpose To explore the effect of the main components of PDB on myocardial cell membranes. Materials and Methods We investigated the role of different concentrations of PDB in cardiomyocytes by evaluating myocardial electrical activity. We used high-performance liquid chromatography to analyze the components. Patch-clamp experiments were conducted to detect the drugs’ impact on the ion channels of cardiomyocytes. Results PDB regulated 14 potential metabolites in mice. Interestingly, quercetin exerts certain effects on the heart by acting on the inositol phosphate metabolism pathway. Quercetin is a monomer compound that can enhance the activity of IK1 on the myocardium membrane. Conclusion This study showed that monomeric compounds of PDB can significantly enhance IK1 activity and influence ion channels in a concentration-dependent manner.

Identification and role of differentially expressed genes/proteins between pulmonary tuberculosis patients and controls across lung tissues and blood samples.

Differentially expressed genes/proteins (DEGs/DEPs) play critical roles in pulmonary tuberculosis (PTB) diagnosis and treatment. However, there is a scarcity of reports on DEGs/DEPs in lung tissues and blood samples in PTB patients. We aim to identify the DEGs/DEPs in lung tissues and blood samples of PTB patients and investigate their roles in PTB. The lung granulomas and normal tissues were collected from PTB patients for proteomic and transcriptomic analyses. Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) analyses annotated the functions of DEGs/DEPs. The GSE107994 data set was downloaded to identify the DEGs/DEPs in peripheral blood. The common DEGs and DEPs were identified. A nomogram was established. Pearson correlation analysis was conducted. Eighty-three DEGs/DEPs were identified. These DEGs/DEPs were mainly enriched in the movement of cell or subcellular components, regulation of cellular component biogenesis, and actin filament-based process as well as in the pathways of inositol phosphate metabolism, adherens junction, phosphatidylinositol signaling system, leukocyte transendothelial migration, regulation of actin cytoskeleton, and tight junction. There were eight common DEGs/DEPs (TYMP, LAP3, ADGRL2, SIL1, LMO7, SULF 1, ANXA3, and PACSIN3) between the lung tissues and blood samples. They were effective in predicting tuberculosis. Moreover, the activated dendritic cells, macrophages, monocytes, neutrophils, and regulatory T cells were significantly positively correlated with TYMP (r > .50), LAP3 (r > .50), SIL1 (r > .50), ANXA3 (r > .5), andPACSIN3 (r < .50), while negatively correlated with LMO7 (r < -0.50) (p < .05). ADGRL2 and SULF1 did not have a significant correlation (p > .05). The sample size was small. Eight common DEGs/DEPs of lung tissues and blood samples were identified. They were correlated with immune cells and demonstrated predictive value for PTB. Our data may facilitate the diagnosis and treatment of PTB.

Untargeted urine metabolomics and machine learning provide potential metabolic signatures in children with autism spectrum disorder.

Complementary to traditional biostatistics, the integration of untargeted urine metabolomic profiling with Machine Learning (ML) has the potential to unveil metabolic profiles crucial for understanding diseases. However, the application of this approach in autism remains underexplored. Our objective was to delve into the metabolic profiles of autism utilizing a comprehensive untargeted metabolomics platform coupled with ML. Untargeted metabolomics quantification (UHPLC/Q-TOF-MS) was performed for urine analysis. Feature selection was conducted using Lasso regression, and logistic regression, support vector machine, random forest, and extreme gradient boosting were utilized for significance stratification. Pathway enrichment analysis was performed to identify metabolic pathways associated with autism. A total of 52 autistic children and 40 typically developing children were enrolled. Lasso regression identified ninety-two urinary metabolites that significantly differed between the two groups. Distinct metabolites, such as prostaglandin E2, phosphonic acid, lysine, threonine, and phenylalanine, were revealed to be associated with autism through the application of four different ML methods (p<0.05). The alterations observed in the phosphatidylinositol and inositol phosphate metabolism pathways were linked to the pathophysiology of autism (p<0.05). Significant urinary metabolites, including prostaglandin E2, phosphonic acid, lysine, threonine, and phenylalanine, exhibit associations with autism. Additionally, the involvement of the phosphatidylinositol and inositol phosphate pathways suggests their potential role in the pathophysiology of autism.

Arsenite Mediates Selenite Resistance and Reduction in Enterobacter sp. Z1, Thereby Enhancing Bacterial Survival in Selenium Environments.

Arsenic (As) is widely present in the environment, and virtually all bacteria possess a conserved ars operon to resist As toxicity. High selenium (Se) concentrations tend to be cytotoxic. Se has an uneven regional distribution and is added to mitigate As contamination in Se-deficient areas. However, the bacterial response to exogenous Se remains poorly understood. Herein, we found that As(III) presence was crucial for Enterobacter sp. Z1 to develop resistance against Se(IV). Se(IV) reduction served as a detoxification mechanism in bacteria, and our results demonstrated an increase in the production of Se nanoparticles (SeNPs) in the presence of As(III). Tandem mass tag proteomics analysis revealed that the induction of As(III) activated the inositol phosphate, butanoyl-CoA/dodecanoyl-CoA, TCA cycle, and tyrosine metabolism pathways, thereby enhancing bacterial metabolism to resist Se(IV). Additionally, arsHRBC, sdr-mdr, purHD, and grxA were activated to participate in the reduction of Se(IV) into SeNPs. Our findings provide innovative perspectives for exploring As-induced Se biotransformation in prokaryotes.

Effects of a liquid and dry Saccharomyces cerevisiae fermentation product feeding program on ruminal fermentation, total tract digestibility, and plasma metabolome of Holstein steers receiving a grain-based diet.

The study aimed to determine the effects of a postbiotic feeding program consisting of liquid and dry Saccharomyces cerevisiae fermentation product (SCFP) on ruminal fermentation, digestibility, and plasma metabolome of Holstein steers receiving a grain-based diet. Eight Holstein steers (body weight, BW, 467 ± 13.9kg) equipped with rumen cannulas were used in a crossover design study, with 21 d per period and a 7-d washout period in between periods. Steers were stratified by initial BW and assigned to 1 of 2 treatments. The treatments were 1) Control, basal finishing diet only (CON); 2) SCFP, 1-d feeding of liquid SCFP (infused into the rumen via the cannula at 11mL/100kg BW) followed by daily feeding of dry SCFP (12g/d, top-dressed). Feed and spot fecal samples were collected during days 17 to 20 for determination of digestibility and fecal excretion of N, P, Cu, and Zn. Digestibility was measured using acid-insoluble ash as an internal marker. Blood samples were collected on day 21 before the morning feeding. Rumen fluid samples were collected on days 0, 1, 2, 3, 5, and 21 via rumen cannula. Results were analyzed with the GLIMMIX procedure of SAS 9.4 (SAS, 2023). Treatment did not affect dry matter intake (P = 0.15) and digestibility (P ≥ 0.62). The fecal output and absorption of Zn, Cu, P, and N were not affected (P > 0.22) by treatment. On day 1, the liquid SCFP supplementation tended to reduce (P = 0.07) ruminal VFA concentration and increased (P < 0.01) the molar proportion of valerate. Feeding SCFP tended to increase total ruminal VFA on day 5 (P = 0.08) and significantly increased total VFA on day 21 (P = 0.05). Ruminal NH3-N was reduced (P = 0.02) on day 21 by supplementing SCFP. Treatment did not affect the production of proinflammatory cytokines, interleukin (IL)-1β (P > 0.19), and IL-6 (P > 0.12) in the whole blood in response to various toll-like receptor stimulants in vitro. Feeding SCFP enriched (P ≤ 0.05) plasma metabolic pathways, including citric acid cycle, pyrimidine metabolism, glycolysis/gluconeogenesis, retinol metabolism, and inositol phosphate metabolism pathways. In summary, supplementing liquid SCFP with subsequent dry SCFP enhanced ruminal total VFA production and reduced NH3-N concentration in the rumen. Furthermore, feeding SCFP enriched several important pathways in lipid, protein, and glucose metabolism, which may improve feed efficiency of energy and protein in Holstein steers.

PSI-6 Effects of a Postbiotic Program Consisting of Liquid and Solid Saccharomyces Cerevisiae Fermentation Products on Digestibility, Ruminal Fermentation, and Plasma Metabolome of Finishing Beef Steers

Abstract The objective of this study was to determine the effects of a postbiotic feeding program consisting of liquid and solid Saccharomyces cerevisiae fermentation products (SCFP) on digestibility, ruminal fermentation, and plasma metabolome of finishing beef steers. Eight Holstein steers (BW 467 ± 13.9 kg) equipped with rumen cannulas were used in a crossover design study, with 21-d per period and 7-d washout period in between periods. Steers were blocked based on initial BW to one of two treatments: 1) Control, basal diet only (CON), or 2) SCFP, one day feeding of LiquiCare RTU (Diamond V, dosed via rumen cannula at 11 mL/100 kg BW) followed by daily feeding of 12 g NaturSafe (Diamond V, top-dressed). Feed and fecal samples were collected during d 17 to 20 for determination of digestibility and fecal excretion of N, P, Cu and Zn using acid-insoluble ash as an internal marker. Blood samples were collected on d 21 before morning feeding. Rumen fluid samples were collected on d 0, 1, 2, 3, 5 and 21 at 0, 4, 8, or 12 h post morning feeding via rumen cannula. Results were analyzed with the GLIMMIX procedure of SAS 9.4 (SAS, 2022). BW, DMI and digestibility were not affected by treatment. There was a tendency of treatment by period interaction (P = 0.09) on feed efficiency, which was improved by feeding SCFP only in period 1. Feeding SCFP did not affect (P &amp;gt; 0.10) ruminal pH. Feeding SCFP tended to reduce ruminal lactate concentration on d 21 (0.09 vs. 0.02 mM, P = 0.10). Supplementing SCFP reduced ruminal NH3-N concentration on d 2 (4.24 vs. 7.31 mg/dL, P = 0.03) and d 21 (4.86 vs. 6.83 mg/dL, P = 0.04). By feeding SCFP, ruminal total VFA concentration was increased 4-h post-feeding on d 5 (139.7 vs. 126.7 mM, P = 0.01) and numerically increased 4-h post-feeding on d 21 (151.2 vs. 133.3 mM, P = 0.12). For VFA composition, no treatment differences were observed on day 21. However, feeding SCFP reduced (P = 0.01) propionate proportion and increased (P = 0.05) butyrate proportion on day 3. The enriched plasma metabolic pathways (P ≤ 0.05) by feeding SCFP are citric acid cycle, pyrimidine metabolism, glycolysis/gluconeogenesis, retinol metabolism, and inositol phosphate metabolism pathways. Overall, our results indicated potential benefits of the SCFP feeding program on improving ruminal fermentation, preventing acidosis and improving N utilization in the rumen. Furthermore, feeding SCFP enriched several important pathways in lipid, protein, and glucose metabolism, which may improve feed efficiency of energy and protein in finishing beef cattle.

Genome sequencing-based transcriptomic analysis reveals novel genes in Peucedanum praeruptorum

BackgroundPeucedanum praeruptorum Dunn, a traditional Chinese herbal medicine, contains coumarin and volatile oil components that have clinical application value. However, early bolting often occurs in the medicinal materials of Apiaceae plants. The rhizomes of the medicinal parts are gradually lignified after bolting, resulting in a sharp decrease in the content of coumarins. At present, the link between coumarin biosynthesis and early bolting in P. praeruptorum has not been elucidated.ResultsCombining the genome sequencing and the previous transcriptome sequencing results, we reanalyzed the differential transcripts of P. praeruptorum before and after bolting. A total of 62,088 new transcripts were identified, of which 31,500 were unknown transcripts. Functional classification and annotation showed that many genes were involved in the regulation of transcription, defense response, and carbohydrate metabolic processes. The main domains are the pentatricopeptide repeat, protein kinase, RNA recognition motif, leucine-rich repeat, and ankyrin repeat domains, indicating their pivotal roles in protein modification and signal transduction. Gene structure analysis showed that skipped exon (SE) was the most dominant alternative splicing, followed by the alternative 3’ splice site (A3SS) and the alternative 5’ splice site (A5SS). Functional enrichment of differentially expressed genes showed that these differentially expressed genes mainly include transmembrane transporters, channel proteins, DNA-binding proteins, polysaccharide-binding proteins, etc. In addition, genes involved in peroxisome, hexose phosphate pathway, phosphatidylinositol signaling system, and inositol phosphate metabolism pathway were greatly enriched. A protein-protein interaction network analysis discoverd 1,457 pairs of proteins that interact with each other. The expression levels of six UbiA genes, three UGT genes, and four OMT genes were higher during the bolting stage. This observation suggests their potential involvement in the catalytic processes of prenylation, glycosylation, and methylation of coumarins, respectively. A total of 100 peroxidase (PRX) genes were identified being involved in lignin polymerization, but only nine PRX genes were highly expressed at the bolting stage. It is worth noting that 73 autophagy-related genes (ATGs) were first identified from the KEGG pathway-enriched genes. Some ATGs, such as BHQH00009837, BHQH00013830, and novel8944, had higher expression levels after bolting.ConclusionsComparative transcriptome analysis and large-scale genome screening provide guidance and new opinions for the identification of bolting-related genes in P. praeruptorum.

OsIPK2, a rice inositol polyphosphate kinase gene, is involved in phosphate homeostasis and root development.

Phosphorus (P) is one kind of growth-limiting nutrient for plants, which is taken up by root tissue from the environment as inorganic phosphate (Pi). To maintain an appropriate status of cellular Pi, plants have developed sophisticated strategies to sense Pi level and modulate their root system architecture (RSA) under the ever-changing growth condition. However, the molecular basis underlying the mechanism remains elusive. Inositol polyphosphate kinase (IPK2) is a key enzyme in the inositol phosphate metabolism pathway, which catalyzes the phosphorylation of IP3 into IP5 by consuming ATP. In this study, the function of a rice inositol polyphosphate kinase gene (OsIPK2) in plant Pi homeostasis and thus physiological response to Pi signal were characterized. As a biosynthetic gene for phytic acid in rice, overexpression of OsIPK2 led to distinct changes of inositol polyphosphate profiles and an excessive accumulation of Pi level in transgenic rice under Pi-sufficient conditions. The inhibitory effects of OsIPK2 on root growth were alleviated by Pi-deficient treatment compared with wild-type plants, suggesting the involvement of OsIPK2 in the Pi-regulated reconstruction of RSA. In OsIPK2-overexpressing plants, the altered acid phosphatase (APases) activities and misregulation of Pi starvation induced (PSI) genes were observed in roots under different Pi supply conditions. Notably, the expression of OsIPK2 also altered the Pi homeostasis and root system architecture in transgenic Arabidopsis. Taken together, our findings demonstrated that OsIPK2 plays an important role in Pi homeostasis and root system architecture adjustment in response to different environmental Pi levels in plant.

MiR-100-5p is upregulated in multiple myeloma and involves in the pathogenesis of multiple myeloma through targeting MTMR3

ABSTRACTObjectives:MicroRNA (miRNA) is a kind of highly conserved single-stranded small endogenous non-coding RNA associated with multiple diseases, particularly cancer. The miRNAs expression profile in multiple myeloma (MM) has been barely elucidated.Methods:The miRNAs expression profiles in bone marrow plasma cells of 5 MM individuals and 5 iron-deficiency anemia volunteers were analyzed using RNA-sequencing. Quantitative polymerase chain reaction (QPCR) was performed to validate the expression of selected miR-100-5p. The biological function of selected miRNA was predicated by bioinformatics analysis. Finally, the function of miR-100-5p and its target on MM cells were evaluated.Results:MiRNA-sequencing showed that miR-100-5p was obviously upregulated in MM patients, which was further validated in an expanded cohort. Receiver operating characteristic curve analysis characterized miR-100-5p as a valuable biomarker of MM. Bioinformatics analysis predicted that miR-100-5p is targeted to CLDN11, ICMT, MTMR3, RASGRP3, and SMARCA5, and their low expression are associated with poor prognosis of MM patients. Kyoto encyclopedia of genes and genomes analysis suggested that the major interacting proteins of these five targets are mainly enriched in inositol phosphate metabolism and phosphatidylinositol signaling system pathway. In vitro study showed that miR-100-5p inhibition promoted the expression of these targets, especially MTMR3. In addition, miR-100-5p inhibition declined living number and metastasis, whereas promoted apoptosis of RPMI 8226 and U266 MM cells. The function of miR-100-5p inhibition was weakened by MTMR3 inhibition.Conclusion:These results indicates that miR-100-5p is a promising biomarker for MM, and that it may involve in the pathogenesis of MM by targeting MTMR3.

Oncometabolite-Independent Anti-Apoptotic Feature Via Phospholipid Metabolic Adaptation in IDH2 Mutant AML Cells

Isocitrate dehydrogenase (IDH) gene mutation is found in approximately 20% of adult acute myeloid leukemia (AML) patients. IDH gene mutations give a pathological enzymatic activity producing oncometabolite, which impair hematopoietic differentiation while promoting leukemogenesis via epigenetic changes. Targeting mutant (mut) form of IDH enzymes, small molecule inhibitors have been developed. Among these inhibitors, AG-221 (enasidenib), which is the first-in-class, selective and orally available mut IDH2 inhibitor (Yen et al., Cancer Discov. 2017), has been tested in clinical trial. The clinical trial showed overall response rate was approximately 40% and more than half of the patient didn't respond to the treatment. This clinical study also showed clear correlation between clearance of IDH2 mut clones and complete clinical response rate (Stein et al., Blood 2019). Relapse cases under the AG-221 treatment, in which additional mutation in IDH2 or IDH1 gene occurred in the residual IDH2 mut clone have been reported (Intlekofer et al., Nature 2018, Harding et al., Cancer Discov. 2018). These reports suggested that IDH2 mut cells have an oncometabolite-independent survival advantage which contributes to refractoriness and relapse. However, most of the studies on IDH mut AML have been focused on oncometabolite-related mechanisms and oncometabolite-independent mechanism has not been investigated in detail so far. IDH gene mutations frequently coexist with other oncogenic mutations in AML patient cells, which make it difficult to analyze the precise role of IDH gene mutation in leukemogenesis. To address this issue, we utilized the cytokine-dependent AML cell line, TF-1 cells and its isogenic cell line with IDH2 gene mutation, which showed cytokine independent growth. Though AG-221 suppressed the cytokine independent growth in IDH2 mut cells, the growth of AG-221 treated IDH2 mut cells remained significantly faster than IDH2 wild type (WT) cells. These data indicated that IDH2 mut cells have a growth advantage machinery in an oncometabolite-independent manner. Metabolome analysis clearly separated AG-221 treated IDH2 mut cells from IDH2 WT cells and identified that inositol phosphate metabolism pathway showed significant difference between these two groups. High throughput drug screening using metabolic inhibitors also revealed that inositol phosphate related enzyme, phospholipase C (PLC) specific inhibitor promoted IDH2 mut cell proliferation. These data suggested that suppressed PLC activity induced oncometabolite-independent growth advantage in IDH2 mut AML cells. Since PLC indirectly release free arachidonic acid (AA) from phospholipid bilayer of cellular membrane and intracellular AA level has positive correlation to apoptosis (Cao et al. PNAS 2000), we analyzed intracellular AA and apoptosis in IDH2 mut cells. As expected, these analyses showed significantly lower intracellular AA and reduced Annexin V+ apoptotic cells in IDH2 mut cells irrespective of AG-221 treatment. Supporting these data, PLC activity related gene sets were negatively enriched and anti-apoptosis related genes were positively enriched in IDH2 mut cells in RNA seq analysis. Based on these novel mechanisms, we tested FDA-approved anti-inflammatory drugs, COX-2 and 5-LOX specific inhibitors (celecoxib and zileuton) to upregulate intracellular AA and induce apoptosis of TF-1 cells in vitro and in vivo xenograft. These drugs in combination with AG-221 successfully suppressed IDH2 mut cell proliferation and induced apoptosis both in vitro and in vivo. The mice treated with these triple drugs showed no sign of cytopenia nor therapy-associated complication, securing safety of this combination therapy. In this study, we identified unappreciated oncometabolite-independent anti-apoptotic feature acquisition via phospholipid metabolic adaptation in IDH2 mut AML cells. Moreover, targeting this metabolic adaptation, we identified that FDA-approved anti-inflammatory drugs in combination with mut IDH2 inhibitor could eradicate IDH2 mut AML cells by efficiently inducing apoptosis. Since these anti-inflammatory drugs have a track record of safety in clinical practice, the triple drug combination therapy could be an alternative therapeutic option for the IDH2 mut AML patients who couldn't tolerate existing therapy.

Liang-Ge decoction ameliorates acute lung injury in septic model rats through reducing inflammatory response, oxidative stress, apoptosis, and modulating host metabolism.

Liang-Ge decoction (LG) has been used in the treatment of early stage of spesis and can ameliorate sepsis-associated lung injury. However, the mechanism of LG on sepsis-associated lung injury remains unknown. In this study, we established a rat model of sepsis-associated lung injury using the cecal ligation and puncture (CLP) method, and investigated the therapeutic effects of LG on lung injury in rats with sepsis. In addition, the anti-inflammatory, anti-oxidative and anti-apoptotic effects of LG on sepsis-associated lung injury model rats were evaluated. Besides, untargeted metabolomics was used to investigate the regulation of metabolites in rats with sepsis-associated lung injury after LG treatment. Our results showed that LG could decrease the wet/dry (W/D) ratio in lung and the total cell count and total protein concentration in bronchoalveolar lavage fluid (BALF) in septic model rats. Hematoxylin and eosin (HE) staining showed that LG reduced the infiltration of pro-inflammatory cells in lung. In addition, LG treatmment down-regulated the gene and protein expression of pro-inflammatory cytokins in lung tissue and BALF. The activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) were increased and the level of methane dicarboxylic aldehyde (MDA) was decreased in lung tissue homogenate in septic model rats after LG treament. Moreover, the numbers of apoptotic cells in lung were reduced and the activity of lactic dehydrogenase (LDH) in BALF was decreased in septic model rats after LG treament. Untargeted metabolomics analysis showed that LG treatment affected the levels of 23 metabolites in lung in septic model rats such as citric acid, methionine, threonine, alpha-ketoglutaric acid, and inositol, these metabolites were associated with the glycine, serine and threonine metabolism, cysteine and methionine metabolism, inositol phosphate metabolism and citrate cycle (TCA cycle) pathways. In conclusion, our study demonstrated the therapeutic effetcts of LG on sepsis-associated lung injury model rats. Moreover, LG could inhibit the inflammatory response, oxidative stress, apoptosis and regulate metabolites related to glycine, serine and threonine metabolism, cysteine and methionine metabolism, inositol phosphate metabolism and TCA cycle in lung in sepsis-associated lung injury model rats.

Unbiased comparison and modularization identify time-related transcriptomic reprogramming in exercised rat cartilage: Integrated data mining and experimental validation.

Exercise is indispensable for maintaining cartilage integrity in healthy joints and remains a recommendation for knee osteoarthritis. Although the effects of exercise on cartilage have been implied, the detailed mechanisms, such as the effect of exercise time which is important for exercise prescription, remain elusive. In this study, bioinformatic analyses, including unbiased comparisons and modularization, were performed on the transcriptomic data of rat cartilage to identify the time-related genes and signaling pathways. We found that exercise had a notable effect on cartilage transcriptome. Exercise prominently suppressed the genes related to cell division, hypertrophy, catabolism, inflammation, and immune response. The downregulated genes were more prominent and stable over time than the upregulated genes. Although exercise time did not prominently contribute to the effects of exercise, it was a factor related to a batch of cellular functions and signaling pathways, such as extracellular matrix (ECM) homeostasis and cellular response to growth factors and stress. Two clusters of genes, including early and late response genes, were identified according to the expression pattern over time. ECM organization, BMP signaling, and PI3K-Akt signaling were early responsive in the exercise duration. Moreover, time-related signaling pathways, such as inositol phosphate metabolism, nicotinate/nicotinamide metabolism, cell cycle, and Fc epsilon RI signaling pathway, were identified by unbiased mapping and polarization of the highly time-correlated genes. Immunohistochemistry staining showed that Egfr was a late response gene that increased on day 15 of exercise. This study elucidated time-related transcriptomic reprogramming induced by exercise in cartilage, advancing the understanding of cartilage homeostasis.

Transcriptome profiling of mRNAs in muscle tissue of Pinan cattle and Nanyang cattle.

Mammalian muscle development is regulated by complex gene networks at the molecular level. The revelation of gene regulatory mechanisms is an important basis for the study of muscle development and molecular breeding. To analyze the excellent meat performance of Pinan cattle at the molecular level, we performed high-throughput RNA sequencing to analyze the key regulatory genes that determine the muscle quality traits in Pinan cattle (n=3) and Nanyang cattle (n=3). We identified 57 differentially expressed genes in muscle tissue of Pinan cattle compared to that of Nanyang cattle, including 32 upregulated and 25 downregulated genes. GO enrichment analysis showed that these genes were significantly enriched in 'molecular function', including voltage-gated ion channel activity, calcium channel activity and calcium ion binding, and KEGG pathway analysis results revealed that adrenergic signaling in cardio myocytes, cell adhesion molecules and inositol phosphate metabolism pathway were significantly enriched. We identified the reliability of RNA-Seq data through RT-qPCR. Meanwhile, we found that GSTA3, PLCB1 and ISYNA1 genes are highly expressed in muscle tissue of Pinan cattle, and these genes play important roles in PI3K/Akt, MEK1/2-ERK and p53-ISYNA1 signaling pathway. In summary, our results suggested that these differentially expressed genes may play important roles in muscle development in Pinan cattle. However, the functions and mechanism of these significantly differential expressed genes should be investigated in future studies.

Identifying key genes in milk fat metabolism by weighted gene co-expression network analysis

Milk fat is the most important and energy-rich substance in milk, and its content and composition are important reference elements in the evaluation of milk quality. However, the current identification of valuable candidate genes affecting milk fat is limited. IlluminaPE150 was used to sequence bovine mammary epithelial cells (BMECs) with high and low milk fat rates (MFP), the weighted gene co-expression network (WGCNA) was used to analyze mRNA expression profile data in this study. As a result, a total of 10,310 genes were used to construct WGCNA, and the genes were classified into 18 modules. Among them, violet (r = 0.74), yellow (r = 0.75) and darkolivegreen (r = − 0.79) modules were significantly associated with MFP, and 39, 181, 75 hub genes were identified, respectively. Combining enrichment analysis and differential genes (DEs), we screened five key candidate DEs related to lipid metabolism, namely PI4K2A, SLC16A1, ATP8A2, VEGFD and ID1, respectively. Relative to the small intestine, liver, kidney, heart, ovary and uterus, the gene expression of PI4K2A is the highest in mammary gland, and is significantly enriched in GO terms and pathways related to milk fat metabolism, such as monocarboxylic acid transport, phospholipid transport, phosphatidylinositol signaling system, inositol phosphate metabolism and MAPK signaling pathway. This study uses WGCNA to form an overall view of MFP, providing a theoretical basis for identifying potential pathways and hub genes that may be involved in milk fat synthesis.

Genetic architecture of the high‐inorganic phosphate phenotype derived from a low‐phytate mutant in winter wheat

AbstractPhytic acid (myo‐inositol 1,2,3,4,5,6‐hexakisphosphate) in grains and legumes reduces bioavailability and absorption of minerals in the gut via chelation of divalent minerals such as iron and zinc. In wheat (Triticum aestivum L.), a low‐phytate mutant (lpa1‐1), developed by ethyl methanesulfonate mutagenesis, was reported to reduce phytate in wheat grain by up to 35% and to elevate free inorganic phosphate (Pi). Little is known about the genetic architecture conditioning this high‐Pi (HIP) phenotype in wheat. Inheritance of the HIP phenotype was evaluated in three segregating populations developed with the lpa1‐1 derivative A02568WS‐A‐12‐10 as a common parent. Distinct genotypic classes were not identified in these populations. To identify quantitative trait loci (QTL) and develop molecular markers for the HIP phenotype, 171 recombinant inbred lines (RILs) from a winter wheat cross ‘Danby’ × A02568WS‐A‐12‐10 were phenotyped for Pi concentration and genotyped by reduced‐representation sequencing. A total of 1,246 nonredundant, high‐quality single‐nucleotide polymorphisms (SNPs) were used to construct a linkage map spanning 3,272 cM. Two major‐effect QTL were identified on chromosomes 4D and 5A, accounting for 23 and 33% of the total phenotypic variation, respectively. Multiple interval mapping (MIM) identified synergistic additive × additive epistasis between these QTL, and the full MIM model accounted for 54% of the phenotypic variation in grain Pi. Ten candidate genes were identified within or in close proximity to the genomic locations of the QTL, five of which encode proteins within the inositol phosphate metabolism pathway. Site‐specific marker assays were developed for marker‐assisted breeding.

Deep Metabolomic Profiling Reveals Alterations in Fatty Acid Synthesis and Ketone Body Degradations in Spermatozoa and Seminal Plasma of Astheno-Oligozoospermic Bulls.

Male fertility is extremely important in dairy animals because semen from a single bull is used to inseminate several thousand females. Asthenozoospermia (reduced sperm motility) and oligozoospermia (reduced sperm concentration) are the two important reasons cited for idiopathic infertility in crossbred bulls; however, the etiology remains elusive. In this study, using a non-targeted liquid chromatography with tandem mass spectrometry-based approach, we carried out a deep metabolomic analysis of spermatozoa and seminal plasma derived from normozoospermic and astheno-oligozoospermic bulls. Using bioinformatics tools, alterations in metabolites and metabolic pathways between normozoospermia and astheno-oligozoospermia were elucidated. A total of 299 and 167 metabolites in spermatozoa and 183 and 147 metabolites in seminal plasma were detected in astheno-oligozoospermic and normozoospermic bulls, respectively. Among the mapped metabolites, 75 sperm metabolites were common to both the groups, whereas 166 and 50 sperm metabolites were unique to astheno-oligozoospermic and normozoospermic bulls, respectively. Similarly, 86 metabolites were common to both the groups, whereas 45 and 37 seminal plasma metabolites were unique to astheno-oligozoospermic and normozoospermic bulls, respectively. Among the differentially expressed metabolites, 62 sperm metabolites and 56 seminal plasma metabolites were significantly dysregulated in astheno-oligozoospermic bulls. In spermatozoa, selenocysteine, deoxyuridine triphosphate, and nitroprusside showed significant enrichment in astheno-oligozoospermic bulls. In seminal plasma, malonic acid, 5-diphosphoinositol pentakisphosphate, D-cysteine, and nicotinamide adenine dinucleotide phosphate were significantly upregulated, whereas tetradecanoyl-CoA was significantly downregulated in the astheno-oligozoospermia. Spermatozoa from astheno-oligozoospermic bulls showed alterations in the metabolism of fatty acid and fatty acid elongation in mitochondria pathways, whereas seminal plasma from astheno-oligozoospermic bulls showed alterations in synthesis and degradation of ketone bodies, pyruvate metabolism, and inositol phosphate metabolism pathways. The present study revealed vital information related to semen metabolomic differences between astheno-oligozoospermic and normospermic crossbred breeding bulls. It is inferred that fatty acid synthesis and ketone body degradations are altered in the spermatozoa and seminal plasma of astheno-oligozoospermic crossbred bulls. These results open up new avenues for further research, and current findings can be applied for the modulation of identified pathways to restore sperm motility and concentration in astheno-oligozoospermic bulls.

ITRAQ-based quantitative proteomic reveals proteomic changes in Serratia sp. CM01 and mechanism of Cr(Ⅵ) resistance

ObjectiveSerratia sp. CM01 is a wild strain with the resistance and reduction ability of chromium(Ⅵ). The aim of this study it to investigate the underlying mechanisms of the Cr(Ⅵ) tolerance and reduction of strain CM01, and to explore its response to environmental pollution pressure at the molecular level. MethodsThe iTRAQ technique was utilized to investigate the differentially expressed protein patterns related to the Cr(Ⅵ)-resistance in wild-type strain CM01 and domesticated CM01. RT-qPCR was used to verify the expression levels of several functional genes. The cell surface hydrophobicity and autoaggregation, the intracellular glucose content, and the total superoxide dismutase (SOD) activity were determined. ResultsIn total, 2750 proteins were detected and identified in WT CM01 and domesticated CM01. Compared with WT CM01, the iTRAQ results of 646 proteins were found to be significantly differentially expressed in domesticated CM01. There were 343 up-regulated and 303 down-regulated proteins, which mainly related to carbohydrate metabolism, stress responses, amino acid metabolism and some other systems. RT-qPCR results showed that the expression level of seven genes in domesticated CM01 were consistent with the iTRAQ proteomic profiles. The cell surface hydrophobicity, self-aggregation, intracellular glucose content and total SOD activity of domesticated CM01 with Cr(Ⅵ) treatment were significantly higher than without Cr(Ⅵ) treatment. ConclusionDomesticated CM01 displayed a complex biological network to exhibit the tolerance of Cr(Ⅵ), which may be attributed to the following aspects: (a) CM01 reduced the consumption of glucose by inhibiting the metabolism of carbohydrates, which was an energy-saving survival mode. (b) The inositol phosphate metabolism pathway played an important role. (c) Oxidative stress proteins enhanced the adaptability. (d) CM01 enhanced biosynthesis of hydrophobic amino acids to resistance to Cr(Ⅵ). (e) Several key systems and proteins, such as UvrABC system, Lon protease, porin OmpC, also may play an important role.

Serum Metabolomic Profiling Reveals the Amelioration Effect of Methotrexate on Imiquimod-Induced Psoriasis in Mouse.

Background:The imiquimod (IMQ)-induced psoriasis mouse model has been used as a model for pathogenic mechanism research, and methotrexate (MTX) is widely employed to treat various clinical manifestations of psoriasis. We explored the underlying pathogenesis of psoriasis and the treatment mechanism of the conventional drugs from the metabolic perspective of the psoriasis mouse model.Methods:Male BALB/c mice were smeared IMQ for 7 days to induce treatment-resistant psoriasis and intragastrically administered 1 mg/kg MTX. We evaluated inflammation of psoriasis-like lesions and therapeutic effects of MTX based on histological changes and immunohistochemistry. Based on gas chromatography-mass spectrometer detection of serum samples, a comprehensive metabolomics analysis was carried out to identify alterations of metabolites.Results:It was found that MTX ameliorated psoriatic lesions (representative erythema, scaling, and thickening) by inhibiting proliferation and differentiation of keratinocytes. Using multivariate statistical analysis to process metabolomics data, the results displayed alterations in serum metabolites among mice of the control group, IMQ group, and MTX group. Compared with group, psoriasis mice had the higher level of d-galactose and lower expression of myo-inositol, 9,12-octadecadienoic acid, and cholesterol. In contrast with the model set, serum levels of glycine, pyrrolidone carboxylic acid, d-galactose, and d-mannose were significantly decreased in the MTX group.Conclusion:The differential metabolites, reflecting the perturbation in the pathways of inositol phosphate metabolism; galactose metabolism; glyoxylate and dicarboxylate metabolism; glycine, serine, and threonine metabolism; and glutathione metabolism, may lead to the pathogenesis of psoriasis, and they are also related to the pharmacological treatment effect of MTX on psoriasis. This study established the foundation for further research on the mechanism and therapeutic targets of psoriasis.

Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves.

Alternative splicing (AS) is a post-transcriptional process common in plants and essential for regulation of environmental fitness of plants. In the present study, we focus on the AS events in poplar leaves to understand their effects on plant growth and development. The hybrid poplar (P.alba×P.glandulosa cv.84K) leaves were collected for RNA extraction. The extracted RNA was sequenced using on an Illumina HiSeq™ 2000 platform. Using the Populus trichocarpa genome as the reference, a total of 3810 AS genes were identified (9225 AS events), which accounted for 13.51% of all the expressed genes. Intron retention was the most common AS event, accounting for 43.86% of all the AS events, followed by alternative 3' splice sites (23.75%), alternative 5' splice sites (23.71%), and exon skipping (8.68%). Chromosomes 10 had the most condensed AS events (33.67 events/Mb) and chromosome 19 had the least (12.42 events/Mb). Association analysis showed that AS in the poplar leaves was positively correlated with intron length, exon number, exon length, and gene expression level, and was negatively correlated with GC content. AS genes in the poplar leaves were associated mainly with inositol phosphate metabolism and phosphatidylinositol signaling system pathways that would be significant on wooden plant production.

Effect of Concentrate Supplementation on the Expression Profile of miRNA in the Ovaries of Yak during Non-Breeding Season.

Simple SummaryYak (Bos grunniens) is an important and remarkable livestock species that survives in the challenging environment of the Qinghai–Tibetan Plateau. However, its growth rate is slower and reproductive ability is generally lower than cattle. This may be due to the yak living in high altitudes all year round where in the whole year, grasses are only available in July, August, and September (warm season), and from November to the next year of May (cold season), there is a scarcity of pastures. So, the reproductive efficiency of yak is very low. Meanwhile, it has been reported that enhanced nutrition improves the reproductive efficiency of animals. Therefore, this study aimed to explore the effects of supplemental nutrition on the growth traits and reproductive performance of yaks in the cold season. In addition, miRNAs related to yak reproductive traits were screened by miRNA sequencing technology. This research might be helpful for improving the reproductive potential of yak during the non-breeding season.Yak (Bos grunniens) is an important and remarkable livestock species that survives in the challenging environment of the Qinghai–Tibetan Plateau. However, its growth rate is slower and reproductive potential is generally lower than cattle. Meanwhile, it has been reported that enhanced nutrition improves the reproductive efficiency of animals. The purpose of this study was to investigate the effect of concentrate supplementation on the miRNA expression profile in the ovaries of yak during the non-breeding season. The study displayed that non-breeding season supplementation significantly improved growth performance, serum biochemical indicators, and reproductive hormone concentrations in yaks. In this study, we also examined the differential expression analysis of miRNA in the ovaries of yak during non-breeding seasons using Illumina Hiseq sequencing technology. As a result, 51 differentially expressed miRNAs were found in the experimental group (CS) and control group (CON). Gene Ontology (go) and Kyoto Genome Encyclopedia (KEGG) analysis of target genes showed that beta-alanine metabolism; tryptophan metabolism; sphingolipid metabolism; alanine, aspartate and glutamate metabolism; and the inositol phosphate metabolism pathway attracted our attention. Based on qRT-PCR, seven miRNAs were assessed to verify the accuracy of the library database. We predicted and identified potential miRNA target genes, including LEP, KLF7, VEGFA, GNAQ, GTAT6, and CCND2. miRNA and corresponding target genes may regulate yaks’ seasonal reproduction through their nutritional status. This study will provide an experimental basis for improving the reproductive efficiency of yaks by supplementation in the non-breeding season.