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The Tibetan chicken is a native Chinese breed that lives at high elevations and has adapted to the extreme environmental conditions of the Tibetan Plateau. However, its hypoxic adaptation at the gene expression level is unclear. Here, we sequenced nine lung transcriptomes of the Tibetan chicken at three developmental stages (5 and 42 weeks and 4.5 years). A total of 1.02 billion clean reads were obtained. We identified 16 012 mRNAs and 6898 lncRNAs. The expression of mRNA showed that nine samples were significantly divided into three clusters, with higher correlation and closer relationship between the 5 and 42 week groups. We identified 399 differentially expressed genes (DEGs) between the 5 and 42 week groups, 3532 DEGs between the 5 week and 4.5 year groups, and 3909 DEGs between the 42 week and 4.5 year groups. The up-regulated DEGs in the 5 week group, compared with 42 week and 4.5 year groups, were enriched in GO terms associated with growth and development, whereas the up-regulated DEGs in the 4.5 year group were mainly enriched in many metabolic-related categories. Moreover, the enrichment results with up-regulated DEGs in the 5 and/or 42 week groups, compared with the 4.5 year group, were associated with hypoxic adaptation, such as oxygen transport, oxygen binding and oxygen carrier activity, and calcium signaling pathway. In addition, we identified 978 high-correlation lncRNA and protein-coding gene pairs, and 524 significant neighboring protein-coding genes were also DEGs. Our results provide new insights into gene expression of lung tissue in Tibetan chickens during the aging process., (© 2020 Stichting International Foundation for Animal Genetics.)

Background: To explore the disparity in glycosylphosphatidylinositol phospholipase D (GPI-PLD) expression levels between mononuclear cells of chronic myeloid leukemia (CML) and healthy controls, and clarify the certain relation of GPI-PLD expression levels to complement mediated killing of leukemic cells., Methods: Competitive RT-PCR was used to detect quantitatively the GPI-PLD mRNA in mononuclear cells. GPI-anchored CD55 and CD59 were analyzed by flow cytometry and Western blotting. Complement-mediated lysis was assessed by staining method of trypan blue dye., Results: The GPI-PLD activities and their mRNA copies in CML patients were significantly lower than those in healthy adults. At the tenth day after treatment with bone marrow transplantation (BMT), the GPI-PLD activities and copies of GPI-PLD mRNA almost recovered to the expression levels of healthy subjects. The expression of both CD55 and CD59 in CML patients were significantly higher than those in healthy subjects. After treatment with insulin (10(-7) mol/l) plus glucose (16.7 mmol/l) for 48 h, the cellular GPI-PLD activity and mRNA levels in K562 cells derived from the leukemic cells of a CML patient all increased about 3-fold. Simultaneously, the GPI-anchored CD55 and CD59 on cell surfaces were released into the culturing medium, and the killing rate of complement-mediated K562 cell lysis increased almost 3 times., Conclusion: The decreased GPI-PLD expression may reduce the release of GPI-anchored CD55 and CD59 in leukemia cells and finally decrease complement mediated killing of these cells in chronic phase of CML.

Fermentation with Bacillus subtilis significantly enhances the physiological activity and bioavailability of soymilk, but the resulting characteristic flavor seriously affects its industrial promotion. The objective of this study was to identify key proteins associated with characteristic flavors in B. subtilis BSNK-5-fermented soymilk using tandem mass tag (TMT) proteomics. The results showed that a total of 765 differentially expressed proteins were identified. Seventy differentially expressed proteins related to characteristic flavor were screened through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. After integrating metabolomics data, fifteen key proteases of characteristic flavor components in BSNK-5-fermented soymilk were further identified, and free ammonia was added. In addition, there were five main formation mechanisms, including the decomposition of urea to produce ammonia; the degradation of glutamate by glutamate dehydrogenase to produce ammonia; the degradation of threonine and non-enzymatic changes to form the derivative 2,5-dimethylpyrazine; the degradation of valine, leucine, and isoleucine to synthesize isovalerate and 2-methylbutyrate; and the metabolism of pyruvate and lactate to synthesize acetate. These results provide a theoretical foundation for the improvement of undesirable flavor in B. subtilis BSNK-5-fermented soy foods. [ABSTRACT FROM AUTHOR]

Nitrogen (N), as the main component of biological macromolecules, maintains the basic process of plant growth and development. GOGAT, as a key enzyme in the N assimilation process, catalyzes α-ketoglutaric acid and glutamine to form glutamate. In this study, six GOGAT genes in wheat (Triticum aestivum L.) were identified and classified into two subfamilies, Fd-GOGAT (TaGOGAT2s) and NADH-GOGAT (TaGOGAT3s), according to the type of electron donor. Subcellular localization prediction showed that TaGOGAT3-D was localized in mitochondria and that the other five TaGOGATs were localized in chloroplasts. Via the analysis of promoter elements, many binding sites related to growth and development, hormone regulation and plant stress resistance regulations were found on the TaGOGAT promoters. The tissue-specificity expression analysis showed that TaGOGAT2s were mainly expressed in wheat leaves and flag leaves, while TaGOGAT3s were highly expressed in roots and leaves. The expression level of TaGOGATs and the enzyme activity of TaGOGAT3s in the leaves and roots of wheat seedlings were influenced by the treatment of N deficiency. This study conducted a systematic analysis of wheat GOGAT genes, providing a theoretical basis not only for the functional analysis of TaGOGATs, but also for the study of wheat nitrogen use efficiency (NUE). [ABSTRACT FROM AUTHOR]

Introduction: Diabetic kidney disease (DKD) is one of the prominent microvascular complications of diabetes and the leading cause of end-stage renal disease. Inflammation plays a crucial role in the development and progression of DKD. Currently, only a few studies depict the landscape of infiltrating immune cells and their potential regulatory network in DKD. To gain a better understanding of the role of immune cells in the renal microenvironment, we sought to reveal the profile of infiltrating immune cells and their potential regulatory network in DKD. Methods: We obtained the transcriptomes and the corresponding clinical data of 19 DKD and 25 control samples from the Gene Expression Omnibus and Nephroseq databases, respectively. Thereafter, we conducted an analysis on the infiltrating immune cells and identified immune-related differentially expressed genes through bioinformatics. Finally, correlation analyses among immune cells, immune genes, and clinical manifestations were performed, and differentially infiltrating immune cell subsets were verified through multiplex immunofluorescence staining. Results: We demonstrated the landscape of infiltrating immune cells in patients with DKD and identified the top five hub immune regulatory genes (C3, IL7R, TYROBP, BMP2, and CXCL6). Three of the core genes (C3, BMP2, and CXCL6) were significantly correlated with the estimated glomerular filtration rate. Through multiplex immunofluorescence staining, we verified that macrophage numbers were remarkably elevated, whereas Treg cells were remarkably reduced in diabetic kidney tissues. Th2 cells were scarce in the kidney tissue. Conclusion: Collectively, our findings shed light on new, possible therapeutic strategies for DKD, from an immune microenvironment perspective. [ABSTRACT FROM AUTHOR]

The species Prunus mume consists of uniquely aromatic woody perennials with large amounts of free aromatic substances in the flower cells. Uridine diphosphate glycosyltransferase (UGT) modifies these free aromatic substances into water-soluble glycoside-bound volatiles (GBVs) which play an important role in regulating the use of volatiles by plants for information exchange, defense, and stress tolerance. To investigate the changes in the glycosidic state of aromatic substances during the flowering period of P. mume and discern the location and expression of glycoside synthesis genes, we extracted and enzymatically hydrolyzed GBVs of P. mume and then utilized gas chromatography–mass spectrometry (GC–MS) to characterize and analyze the types and contents of GBV glycosides. Further, we identified and classified the members of the UGT gene family of P. mume using the bioinformatic method and analyzed the correlation between the expression of the UGT family genes in P. mume and the changes in glycosidic content. The results showed that the benzenoids were the main aromatic substance that was glycosylated during flowering in P. mume and that glycosidic benzaldehyde was the most prevalent compound in different flower parts and at different flowering stages. The titer of glycoside benzaldehyde gradually increased during the bud stage and reached the highest level at the big bud stage (999.6 μg·g−1). Significantly, titers of glycoside benzaldehyde significantly decreased and stabilized after flowering while the level of free benzaldehyde, in contrast, significantly increased and then reached a plateau after the flowering process was completed. A total of 155 UGT family genes were identified in the P. mume genome, which were divided into 13 subfamilies (A–E, G–N); according to the classification of Arabidopsis thaliana UGT gene subfamilies, the L subfamily contains 17 genes. The transcriptome analysis showed that PmUGTL9 and PmUGTL13 were highly expressed in the bud stage and were strongly correlated with the content of the glycosidic form of benzaldehyde at all stages of flowering. This study provides a theoretical basis to elucidate the function of UGT family genes in P. mume during flower development, to explore the mechanism of the storage and transportation of aromatic compounds in flower tissues, and to exploit industrial applications of aromatic products from P. mume. [ABSTRACT FROM AUTHOR]

Objective: To determine the role of Tripterygium wilfordii multiglycoside (TGW) in the treatment of psoriatic dermatitis from a cellular immunological perspective. Methods: Mouse models of psoriatic dermatitis were established by imiquimod (IMQ). Twelve male BALB/c mice were assigned to IMQ or IMQ+TGW groups according to a random number table. Histopathological changes in vivo were assessed by hematoxylin and eosin staining. Ratios of immune cells and cytokines in mice, as well as PAM212 cell proliferation in vitro were assessed by flow cytometry. Pro-inflammatory cytokine expression was determined using reverse transcription quantitative polymerase chain reaction. Results: TGW significantly ameliorated the severity of IMQ-induced psoriasis-like mouse skin lesions and restrained the activation of CD45+ cells, neutrophils and T lymphocytes (all P<0.01). Moreover, TGW significantly attenuated keratinocytes (KCs) proliferation and downregulated the mRNA levels of inflammatory cytokines including interleukin (IL)-17A, IL-23, tumor necrosis factor α, and chemokine (C-X-C motif) ligand 1 (P<0.01 or P<0.05). Furthermore, it reduced the number of γ δ T17 cells in skin lesion of mice and draining lymph nodes (P<0.01). Conclusions: TGW improved psoriasis-like inflammation by inhibiting KCs proliferation, as well as the associated immune cells and cytokine expression. It inhibited IL-17 secretion from γ δ T cells, which improved the immune-inflammatory microenvironment of psoriasis. [ABSTRACT FROM AUTHOR]

Macaques (genus Macaca) are the most widely distributed non‐human primates, and their evolutionary history, gene expression profiles, and genetic differences have been extensively studied. However, the DNA methylomes of macaque species are not available in public databases, which hampers understanding of epigenetic differences among macaque species. Epigenetic modifications can potentially affect development, physiology, behavior, and evolution. Here, we investigated the methylation patterns of the Tibetan macaque (M. thibetana; TM), Chinese rhesus macaque (M. mulatta lasiota; CR), and crab‐eating macaque (M. fascicularis; CE) through whole‐genome bisulfite sequencing from peripheral blood. We compared genome‐wide methylation site information for the three species. We identified 12,128 (CR vs. CE), 59,165 (CR vs. TM), and 39,751 (CE vs. TM) differentially methylated regions (DMRs) in the three macaques. Furthermore, we obtained the differentially expressed genes (DEGs) among the three macaque species. The differences between CR and CE were smaller at both the methylome and transcriptome levels than compared with TM (CR vs. TM and CE vs. TM). We also found a change in the density of single nucleotide mutations in DMRs relative to their flanking regions, indicating a potential mechanism through which genomic alterations may modulate methylation landscapes, thereby influencing the transcriptome. Functional enrichment analyses showed the DMR‐related genes were enriched in developmental processes and neurological functions, such as the growth hormone‐related pathway, insulin secretion pathway, thyroid hormone synthesis pathway, morphine addiction, and GABAergic synapses. These differences may be associated with variations in physiology and habitat among the macaques. Our study provides one of the first genome‐wide comparisons of genetic, gene expression, and epigenetic variations across different macaques. Our results should facilitate further research on comparative genomic and genetic differences in macaque species. [ABSTRACT FROM AUTHOR]

High temperature around flowering has a serious impact on the growth and development of maize. However, few maize genes related to flowering under heat stress have been confirmed, and the regulatory mechanism is unclear. To reveal the molecular mechanism of heat tolerance in maize, two maize hybrids, ZD309 and XY335, with different heat resistance, were selected to perform transcriptome and metabolomics analysis at the flowering stage under heat stress. In ZD309, 314 up-regulated and 463 down-regulated differentially expressed genes (DEGs) were detected, while 168 up-regulated and 119 down-regulated DEGs were identified in XY335. By comparing the differential gene expression patterns of ZD309 and XY335, we found the "frontloaded" genes which were less up-regulated in heat-tolerant maize during high temperature stress. They included heat tolerance genes, which may react faster at the protein level to provide resilience to instantaneous heat stress. A total of 1062 metabolites were identified via metabolomics analysis. Lipids, saccharides, and flavonoids were found to be differentially expressed under heat stress, indicating these metabolites' response to high temperature. Our study will contribute to the identification of heat tolerance genes in maize, therefore contributing to the breeding of heat-tolerant maize varieties. [ABSTRACT FROM AUTHOR]

Acute myeloid leukemia (AML) is a common hematological malignancy. Circular RNAs (circRNAs) are newly discovered endogenous non-coding RNAs that play important roles in regulating gene expression in cancer biology. The aim of this study was to identify novel prognostic and therapeutic targets associated with AML. The expression levels of circRNA Plexin B2 (circPLXNB2), microRNA-654-3p (miR-654-3p) and cyclin D1 protein (CCND1) mRNA were detected by real-time quantitative polymerase chain reaction (qRT-PCR). The stability of circPLXNB2 was determined by RNase R and Actinomycin D assays. Cell counting kit-8 (CCK-8) and 5′-ethynyl-2′-deoxyuridine (EDU) assays were used to detect cell proliferation. Western blot was used to detect protein content. Cell apoptosis and cell cycle distribution were detected by flow cytometry. The relationship between miR-654-3p and circPLXNB2 or CCND1 was confirmed by dual-luciferase reporter assay. CircPLXNB2 was highly expressed in AML patients and cells, and circPLXNB2 was more stable than linear PLXNB2. Knockdown of circPLXNB2 affected the proliferation, apoptosis and cell cycle distribution of AML cells. CircPLXNB2 acted as a sponge for miR-654-3p and affected the progression of AML cells by targeting miR-654-3p. CCND1 was targeted by miR-654-3p, and miR-654-3p suppressed AML progression by targeting CCND1. CircPLXNB2 regulated CCND1 expression through sponging miR-654-3p. In conclusion, circPLXNB2 was highly expressed in AML patients and cells and modulated tumor progression by regulating the circPLXNB2/miR-654-3p/CCND1 axis, suggested that circPLXNB2 might be a new therapeutic target for AML treatment. [ABSTRACT FROM AUTHOR]

Flowering time is an important agronomic trait in cabbage (Brassica oleracea L. var. capitata), but the molecular regulatory mechanism underlying flowering time regulation in cabbage remains unclear. In this study, transcriptome analysis was performed using two sets of cabbage materials: (1) the early-flowering inbred line C491 (P1) and late-flowering inbred line B602 (P2), (2) the early-flowering individuals F2-B and late-flowering individuals F2-NB from the F2 population. The analysis revealed 9508 differentially expressed genes (DEGs) common to both C491_VS_ B602 and F2-B_VS_F2-NB. The Kyoto Encyclopedia of Genes and Genomes (KEGGs) analysis showed that plant hormone signal transduction and the MAPK signaling pathway were mainly enriched in up-regulated genes, and ribosome and DNA replication were mainly enriched in down-regulated genes. We identified 321 homologues of Arabidopsis flowering time genes (Ft) in cabbage. Among them, 25 DEGs (11 up-regulated and 14 down-regulated genes) were detected in the two comparison groups, and 12 gene expression patterns closely corresponded with the different flowering times in the two sets of materials. Two genes encoding MADS-box proteins, Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2), showed significantly reduced expression in the late-flowering parent B602 compared with the early-flowering parent C491 via qRT-PCR analysis, which was consistent with the RNA-seq data. Next, the expression levels of Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2) were analyzed in two other groups of early-flowering and late-flowering inbred lines, which showed that their expression patterns were consistent with those in the parents. Sequence analysis revealed that three and one SNPs between B602 and C491 were identified in Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2), respectively. Therefore, BoSEP2-1 and BoSEP2-2 were designated as candidates for flowering time regulation through a potential new regulatory pathway. These results provide new insights into the molecular mechanisms underlying flowering time regulation in cabbage. [ABSTRACT FROM AUTHOR]

Lipoxygenases (LOX) play pivotal roles in plant resistance to stresses. However, no study has been conducted on LOX gene identification at the whole genome scale in rose (Rosa chinensis). In this study, a total of 17 RcLOX members were identified in the rose genome. The members could be classified into three groups: 9-LOX, Type I 13-LOX, and Type II 13-LOX. Similar gene structures and protein domains can be found in RcLOX members. The RcLOX genes were spread among all seven chromosomes, with unbalanced distributions, and several tandem and proximal duplication events were found among RcLOX members. Expressions of the RcLOX genes were tissue-specific, while every RcLOX gene could be detected in at least one tissue. The expression levels of most RcLOX genes could be up-regulated by aphid infestation, suggesting potential roles in aphid resistance. Our study offers a systematic analysis of the RcLOX genes in rose, providing useful information not only for further gene cloning and functional exploration but also for the study of aphid resistance. [ABSTRACT FROM AUTHOR]

Background: Currently, miRNAs are involved in the development of amyotrophic lateral sclerosis (ALS), and identifying circulating miRNAs that are causally associated with ALS risk as biomarkers is imperative. Methods: We performed a two-sample Mendelian randomization study to evaluate the causal relationship between miRNAs and ALS. Our analysis was conducted using summary statistics from miRNA expression quantitative loci (eQTL) data of the Framingham Heart Study and ALS genome-wide association studies data. Another independent miRNA data was used to further validate. Results: We identified eight unique miRNAs that were causally associated with ALS risk. Using expression data of miRNAs from an independent study, we validated three high-confidence miRNAs, namely hsa-miR-27b-3p, hsa-miR-139-5p, and hsa-miR-152-3p, which might have a potential causal effect on ALS risk. Conclusion: We suggested that higher levels of hsa-miR-27b-3p and hsa-miR-139-5p had protective effects on ALS, whereas higher levels of hsa-miR-152-3p might act as a risk factor for ALS. The analytical framework presented in this study helps to understand the role of miRNAs in the development of ALS and to identify the biomarkers for ALS risk. [ABSTRACT FROM AUTHOR]

Quorum‐sensing (QS) is an essential mechanism of microbial self‐regulation. In this work, the presence of QS in Acetobacter pasteurianus was demonstrated, and N‐acyl‐homoserine lactones N‐C4‐HSL and N‐C8‐HSL were identified as the signal molecules. The exogenous addition of N‐C4‐HSL, N‐C8‐HSL, N‐C10‐HSL, and N‐C12‐HSL result in the reduction in biomass, and lead to 11.56%, 11.91%, 7.94%, and 4.69% decrease in acetic acid production, respectively, when compared with the control. A hypothetical N‐acylhomoserine lactonase (AHL lactonase) 0046 was overexpressed in A. pasteurianus CGMCC 3089, and the recombinant strain exhibites a 17.38% and 12.75% increase in the biomass and the acetic acid production rate, respectively. Those results prove the negative regulation of QS on acetic acid fermentation, and overexpression of 0046 protein alleviates this negative effect. [ABSTRACT FROM AUTHOR]

Background: Vernalization, as a vital process in the life cycle of winter cereal, has important effects on floral organ formation and flowering time. Many morphological changes together with molecular changes occur during the vernalization period. Here, we used transcriptome sequencing to analyze the transcriptomic changes in wheat leaves before, during and after vernalization using the winter wheat cultivar 'Shiluan02-1'. Results: A total of 16,370 differentially expressed genes were obtained across different vernalization periods. Gene Ontology enrichment analysis revealed that photoperiodism, photoprotection, photosynthesis, lipid transport and biosynthetic process, and chlorophyll metabolic process were closely related to vernalization. In addition, AP2/ERF, C2H2, bHLH, WRKY, MYB, MYB-related, and NAC transcription factors were significantly enriched during vernalization, and the transcription factor expression patterns suggested the intricate regulation of transcription factor modules in plant vernalization pathways. Analysis of gene expression patterns of the MADS-box transcription factor genes showed different expression patterns during vernalization phases, among which VERNALIZATION1 (VRN1) genes were found to gradually increase during vernalization periods from V0 to V35, while decline in the V42 phase, then increase after vernalization. The Tavrt-2 gene cooperated with Tavrn1 to regulate flowering induced by vernalization, and its expression level was rapidly increased by vernalization but declined in the V42 phase and then increased after vernalization. Some genes from the ICE-CBF-COR pathway were also identified, and additional analysis indicated that some key genes related to phytohormone biosynthesis and signal transduction were enriched during the vernalization period, such as gibberellic acid, ethylene, abscisic acid and jasmonic acid biosynthesis and signaling pathway genes. Conclusions: Our study provides valuable molecular information for future studies on wheat vernalization regulation and also serves as an excellent reference for future wheat breeding. [ABSTRACT FROM AUTHOR]

Salt stress is one of the important environmental factors that inhibit the normal growth and development of plants. Plants have evolved various mechanisms, including signal transduction regulation, physiological regulation, and gene transcription regulation, to adapt to environmental stress. MicroRNAs (miRNAs) play a role in regulating mRNA expression. Nevertheless, miRNAs related to salt stress are rarely reported in bread wheat (Triticum aestivum L.). In this study, using high−throughput sequencing, we analyzed the miRNA expression profile of wheat under salt stress. We identified 360 conserved and 859 novel miRNAs, of which 49 showed considerable changes in transcription levels after salt treatment. Among them, 25 were dramatically upregulated and 24 were downregulated. Using real−time quantitative PCR, we detected significant changes in the relative expression of miRNAs, and the results showed the same trend as the sequencing data. In the salt−treated group, miR109 had a higher expression level, while miR60 and miR202 had lower expression levels. Furthermore, 21 miRNAs with significant changes were selected from the differentially expressed miRNAs, and 1023 candidate target genes were obtained through the prediction of the website psRNATarget. Gene ontology (GO) analysis of the candidate target genes showed that the expressed miRNA may be involved in the response to biological processes, molecular functions, and cellular components. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis confirmed their important functions in RNA degradation, metabolic pathways, synthesis pathways, peroxisome, environmental adaptation, global and overview maps, and stress adaptation and the MAPK signal pathway. These findings provide a basis for further exploring the function of miRNA in wheat salt tolerance. [ABSTRACT FROM AUTHOR]

Identifying essential genes in comparison states (EGS) is vital to understanding cell differentiation, performing drug discovery, and identifying disease causes. Here, we present a machine learning method termed Prediction of Essential Genes in Comparison States (PreEGS). To capture the alteration of the network in comparison states, PreEGS extracts topological and gene expression features of each gene in a five-dimensional vector. PreEGS also recruits a positive sample expansion method to address the problem of unbalanced positive and negative samples, which is often encountered in practical applications. Different classifiers are applied to the simulated datasets, and the PreEGS based on the random forests model (PreEGSRF) was chosen for optimal performance. PreEGSRF was then compared with six other methods, including three machine learning methods, to predict EGS in a specific state. On real datasets with four gene regulatory networks, PreEGSRF predicted five essential genes related to leukemia and five enriched KEGG pathways. Four of the predicted essential genes and all predicted pathways were consistent with previous studies and highly correlated with leukemia. With high prediction accuracy and generalization ability, PreEGSRF is broadly applicable for the discovery of disease-causing genes, driver genes for cell fate decisions, and complex biomarkers of biological systems. [ABSTRACT FROM AUTHOR]

Blood is an important non-reproductive tissue, but little is known about the sex-specific gene expressions in the blood. Therefore, we investigated sex-specific gene expression differences in the blood tissues of four primates, rhesus macaques (Macaca mulatta), Tibetan macaques (M. thibetana), yellow baboons (Papio cynocephalus), and humans. We identified seven sex-specific differentially expressed genes (SDEGs) in each non-human primate and 31 SDEGs in humans. The four primates had only one common SDEG, MAP7D2. In humans, immune-related SDEGs were identified as up-regulated, but also down-regulated in females. We also found that most of the X-Y gene pairs had similar expression levels between species, except pair EIF1AY/EIF1AX. The expression level of X-Y gene pairs of rhesus and Tibetan macaques showed no significant differential expression levels, while humans had six significant XY-biased and three XX-biased X-Y gene pairs. Our observed sex differences in blood should increase understanding of sex differences in primate blood tissue. • Identified the SDEGs of rhesus macaques, Tibetan macaques, yellow baboons, and humans. • The four primates had only one common SDEG, MAP7D2. • Most of the X-Y gene pairs showed X-biased (Y/X expression ratio < 1) expression levels in XY male individuals. • There were more XY-biased X-Y pair genes than XX-biased between XY male and XX female individuals. [ABSTRACT FROM AUTHOR]

There are limited murine models of cholestatic liver diseases characterized by chronic biliary obstruction and resumption of bile flow. While murine bile duct ligation (BDL) is a well‐established model of obstructive cholestasis, current models of BDL reversal (BDLR) alter biliary anatomy. We aimed to develop a more physiologic model of BDLR to evaluate the time course and mechanism for resolution of hepatic injury after biliary obstruction. In the present study, we restored bile flow into the duodenum without disruption of the gall bladder after murine BDL using biocompatible PE‐50 tubing. After establishing the technique, overall survival for BDLR at 7 or 14 days after BDL was 88%. Sham laparotomy was performed in control mice. Laboratory data, liver histology, and hepatic gene expression were compared among BDL, BDLR, and controls. Laboratory evidence of cholestatic liver injury was observed at day 7 after BDL and rapid improvement occurred within 48 hr of BDLR. After BDLR there was also enhanced gene expression for the bile acid transporter Abcb11, however, bile duct proliferation persisted. Assessment of the immune response showed increased gene and protein expression for the general immune cell marker Cd45 in BDLR versus BDL mice suggesting a reparative immune response after BDLR. In summary, we have established a novel murine model of BDLR that allows for the investigation into bile acid and immune pathways responsible for hepatic repair following obstructive cholestasis. Future studies with our model may identify targets for new therapies to improve outcome in pediatric and adult cholestatic liver disease. [ABSTRACT FROM AUTHOR]

Electrochemical methods allow fast and inexpensive analysis of enzymatic activity. Here, a simple and yet efficient 'signal-on' electrochemical assay for sensitive, label-free detection of DNA-related enzyme activity was established on the basis of terminal deoxynucleotidyl transferase (TdT)-mediated extension strategy. TdT, which is a template-independent DNA polymerase, can catalyze the sequential addition of deoxythymidine triphosphate (dTTP) at the 3'-OH terminus of single-stranded DNA (ssDNA); then, the TdT-yield T-rich DNA nanowires can be employed as the synthetic template of copper nanoclusters (CuNCs). Grown DNA nanowires-templated CuNCs (noted as DNA-CuNCs) were attached onto graphene oxide (GO) surface and exhibited unique electrocatalytic activity to HO reduction. Under optimal conditions, the proposed biosensor was utilized for quantitatively monitoring TdT activity, with the observed LOD of 0.1 U/mL. It also displayed high selectivity to TdT with excellent stability, and offered a facile, convenient electrochemical method for TdT-relevant inhibitors screening. Moreover, the proposed sensor was successfully used for BamHI activity detection, in which a new 3′-OH terminal was exposed by the digestion of a phosphate group. Ultimately, it has good prospects in DNA-related enzyme-based biochemical studies, disease diagnosis, and drug discovery. [ABSTRACT FROM AUTHOR]

Understanding the molecular mechanisms underlying cell migration, which plays an important role in tumor growth and progression, is critical for the development of novel tumor therapeutics. Overexpression of transmembrane protein 30A (TMEM30A) has been shown to initiate tumor cell migration, however, the molecular mechanisms through which this takes place have not yet been reported. Thus, we propose the integration of computational and experimental approaches by first predicting potential signaling networks regulated by TMEM30A using a) computational biology methods, b) our previous mass spectrometry results of the TMEM30A complex in mouse tissue, and c) a number of migration-related genes manually collected from the literature, and subsequently performing molecular biology experiments including the in vitro scratch assay and real-time quantitative polymerase chain reaction (qPCR) to validate the reliability of the predicted network. The results verify that the genes identified in the computational signaling network are indeed regulated by TMEM30A during cell migration, indicating the effectiveness of our proposed method and shedding light on the regulatory mechanisms underlying tumor migration, which facilitates the understanding of the molecular basis of tumor invasion. [ABSTRACT FROM AUTHOR]

Nucleostemin plays an essential role in the proliferation of some stem cells and cancer cells, but no research has been conducted to assess the link between Nucleostemin and ovarian cancer. To investigate the role of Nucleostemin in ovarian cancer tumorigenesis, we generated short hairpin (sh)RNA to knockdown the expression of the Nucleostemin gene in an ovarian cancer SKOV-3 cell line. We found that knockdown of this gene led to cell-cycle arrest, as well as to an increase in apoptosis. In addition, migration and invasion demonstrated significant inhibition in Nucleostemin-deficient cells. Furthermore, the knockdown of Nucleostemin dramatically suppressed xenograft progression in BALB/c nude mice. Our findings suggest that Nucleostemin is associated with malignancy in an ovarian cancer SKOV-3 cell line. [ABSTRACT FROM AUTHOR]

Isoflavones comprise a group of secondary metabolites produced almost exclusively by plants in the legume family, including soybean [Glycine max (L.) Merr.]. They play vital roles in plant defense and have many beneficial effects on human health. Isoflavone content is a complex quantitative trait controlled by multiple genes, and the genetic mechanisms underlying isoflavone biosynthesis remain largely unknown. Via a genome-wide association study (GWAS), we identified 28 single nucleotide polymorphisms (SNPs) that are significantly associated with isoflavone concentrations in soybean. One of these 28 SNPs was located in the 5’-untranslated region (5’-UTR) of an R2R3-type MYB transcription factor, GmMYB29, and this gene was thus selected as a candidate gene for further analyses. A subcellular localization study confirmed that GmMYB29 was located in the nucleus. Transient reporter gene assays demonstrated that GmMYB29 activated the IFS2 (isoflavone synthase 2) and CHS8 (chalcone synthase 8) gene promoters. Overexpression and RNAi-mediated silencing of GmMYB29 in soybean hairy roots resulted in increased and decreased isoflavone content, respectively. Moreover, a candidate-gene association analysis revealed that 11 natural GmMYB29 polymorphisms were significantly associated with isoflavone contents, and regulation of GmMYB29 expression could partially contribute to the observed phenotypic variation. Taken together, these results provide important genetic insights into the molecular mechanisms underlying isoflavone biosynthesis in soybean. [ABSTRACT FROM AUTHOR]

Salvia miltiorrhiza is a traditional Chinese herbal medicine, whose quality and yield are often affected by diseases and environmental stresses during its growing season. Salicylic acid (SA) plays a significant role in plants responding to biotic and abiotic stresses, but the involved regulatory factors and their signaling mechanisms are largely unknown. In order to identify the genes involved in SA signaling, the RNA sequencing (RNA-seq) strategy was employed to evaluate the transcriptional profiles in S. miltiorrhiza cell cultures. A total of 50,778 unigenes were assembled, in which 5,316 unigenes were differentially expressed among 0-, 2-, and 8-h SA induction. The up-regulated genes were mainly involved in stimulus response and multi-organism process. A core set of candidate novel genes coding SA signaling component proteins was identified. Many transcription factors (e.g., WRKY, bHLH and GRAS) and genes involved in hormone signal transduction were differentially expressed in response to SA induction. Detailed analysis revealed that genes associated with defense signaling, such as antioxidant system genes, cytochrome P450s and ATP-binding cassette transporters, were significantly overexpressed, which can be used as genetic tools to investigate disease resistance. Our transcriptome analysis will help understand SA signaling and its mechanism of defense systems in S. miltiorrhiza. [ABSTRACT FROM AUTHOR]

Adhesion molecules expressed on the uterine endometrium are potential receptive markers in embryo implantation. RL95-2 and HEC-1A cell lines represent the high- and low-receptive endometrial epithelium respectively. LeY (Lewis Y) is a difucosylated oligosaccharide highly expressed in the endometrium of some species during implantation. α1, 3 fucosylation of LeY is catalysed by FUT4 (fucosyltransferase IV), the key synthesis enzyme for LeY. We investigated whether the difference in receptivity between the 2 cell lines was related to different expressions of LeY and FUT4. RL95-2 cells expressed a higher level of LeY and FUT4 than HEC-1A cells, as shown by immunofluorescent staining, RT-PCR (reverse transcription-PCR) or Western blotting. FUT4-siRNA (small interfering RNA) transfection down-regulated FUT4 and LeY in RL95-2 cells, and inhibited the adhesion of the embryonic cells (JAR) to RL95-2 cell monolayer. FUT4-cDNA, however, increased the expression of FUT4 and LeY in HEC-1A cells, and increased the adhesion of embryonic cells to HEC-1A cell monolayer. Alterations of LeY level by up- or down-regulation of FUT4 also mediated EGFR (epidermal growth factor receptor)/MAPK (mitogen-activated protein kinase) signalling pathway. To conclude, the expression of LeY and FUT4 correlates with endometrial receptivity, making them potential new markers for the evaluation of endometrial receptivity. [ABSTRACT FROM AUTHOR]

CD73, a cell-surface protein encoded by the gene NT5E, is overexpressed in glioblastoma (GBM), where it contributes to the tumor's pathophysiology via the generation of immunosuppressive adenosine. Adenosinergic signaling, in turn, drives immunosuppression of natural killer (NK) cells through metabolic and functional reprogramming. The correlation of CD73 with patient survival in relation to GBM pathology and the intratumoral infiltration of NK cells has not been comprehensively studied before. Here, we present an analysis of the prognostic relevance of CD73 in GBM based on transcriptional gene expression from patient data from The Cancer Genome Atlas (TCGA) database. Utilizing bioinformatics data mining tools, we explore the relationship between GBM prognosis, NT5E expression, and intratumoral presence of NK cells. Our analysis demonstrates that CD73 is a negative prognostic factor for GBM and that presence of NK cells may associate with improved prognosis. Moreover, the interplay between expression of NT5E and specific NK genes hints to potential functional effects of CD73 on NK cell activation. [ABSTRACT FROM AUTHOR]

Aging is a very complicated biological process that can change gene expressions. The Chinese rhesus macaque (Macaca mulatta lasiota ; CR) is closely related to humans. We explored gene expression with increasing age and DNA methylation changes in young and old CRs. Results showed blood transcriptome and DNA methylome significantly changed from young to old CRs. The age-associated differentially expressed genes (DEGs) and differentially methylated regions (DMRs) were associated with age-related biological features, such as immunity, blood coagulation, and biosynthetic process. The measurements of coagulation indicators confirmed old CRs had shorter coagulation time than young CRs, and the activities of coagulation factor II (FII) and factor VIII (FVIII) were enhanced in old CRs. Humans and CRs exhibited the same enhanced blood coagulation with age phenotype. Our study found aging is a critical factor affecting gene expression in CRs, and also provided new insights into the blood coagulation changes in non-human primates. • Identified the age-related differentially expressed genes (DEGs) and differentially methylated regions (DMRs) of rhesus macaques in peripheral blood. • Comparison of the age-related DEGs provides a similar aging pattern between rhesus macaques and humans. • Associated pathways enriched by age-related DEGs and DMRs is consistent with other mammals regarding metabolism and immunity. • Enhanced blood coagulation in macaques with increasing age verified by both omics and physiological indices. [ABSTRACT FROM AUTHOR]

Fruit maturity is an important agronomic trait of fruit crops. Although in previous studies, several molecular markers are developed for the trait, the knowledge about its candidate genes is particularly limited. In this study, a total of 357 peach accessions were re-sequenced to obtain 949,638 SNPs. Combing with 3-year fruit maturity dates, a genome-wide association analysis was performed, and 5, 8, and 9 association loci were identified. To screen the candidate genes for those year-stable loci on chromosomes 4 and 5, two maturity date mutants were used for transcriptome sequencing. Gene expression analysis indicated that Prupe.4G186800 and Prupe.4G187100 on chromosome 4 were essential to fruit ripening in peaches. However, the expression analysis of different tissues showed that the first gene has no tissue-specific character, but transgenic studies showed that the latter is more likely to be a key candidate gene than the first for the maturity date in peach. The yeast two-hybrid assay showed that the proteins encoded by the two genes interacted and then regulated fruit ripening. Moreover, the previously identified 9 bp insertion in Prupe.4G186800 may affect their interaction ability. This research is of great significance for understanding the molecular mechanism of peach fruit ripening and developing practical molecular markers in a breeding program. [Display omitted] • Using re-sequencing data of 357 accessions and 3 years of the maturity date, a total of 22 associated signals were identified. • Two candidate genes for peach fruit maturity date on chromosome 4 were screened by using RNA-seq data. • Transgenic experiments indicated that Prupe.4G187100 may be a key candidate gene for peach fruit maturity date. • The interaction between these two NAC genes was proved to be involved in regulating fruit mature in peach. [ABSTRACT FROM AUTHOR]

Abstract: In quantitative real-time PCR assay, the appropriate reference genes are essential to reduce the potential errors in quantification of gene expression. To date, there is not a well-defined and validated set of reference genes for skin tissue of cashmere goat. In the present work, based on the geNorm and NormFinder procedures, the expression stabilities of eight candidate housekeeping genes were assessed in skin tissue of Liaoning cashmere goat during hair follicle cycle including 18S, ACTB, B2M, GAPDH, TBP, UBC, YWHAZ, and SDHA. Both geNorm and NormFinder identified SDHA, YWHAZ and UBC as the most stable genes in skin of Liaoning cashmere goat. Also, we further validated the suitability of SDHA, YWHAZ and UBC in combination as references in skin of Liaoning cashmere goat via detecting the relative expression of TGFβR2, BMP2, MSX2 and Hoxc13 as target genes. Significant differences were revealed in the relative expression of TGFβR2, BMP2, MSX2, and Hoxc13 at anagen and telogen when a combination of SDHA, YWHAZ and UBC, versus single SDHA were used as reference genes. These results suggested that the combined use of three genes (SDHA, YWHAZ, and UBC) as references would be more reliable than that of a single SDHA for Q-PCR data normalization in skin tissue of Liaoning Cashmere goat. Therefore, we strongly recommended that these three genes can be used as a combined reference for normalization of gene expression in future longitudinal studies on skin of Liaoning cashmere goat associated with import cashmere traits. [Copyright &y& Elsevier]

Abstract: Follicular helper T (Tfh) cells are dedicated to providing help to B cells and are strongly associated with antibody-mediated autoimmune disease. B cell lymphoma 6 (Bcl-6) is a key transcription factor of Tfh cells, and IL-21 is known to be a critical cytokine produced by Tfh cells. We silenced Bcl-6 gene expression using RNA interference (RNAi) delivered by a lentiviral vector, to evaluate the therapeutic role of Bcl-6 short hairpin RNAs (shRNAs) in experimental autoimmune myasthenia gravis (EAMG). Our data demonstrate that CD4(+)CXCR5(+)PD-1(+) Tfh cells, Bcl-6 and IL-21 were significantly increased in EAMG mice, compared with controls. In addition, we found that frequencies of Tfh cells were positively correlated with the levels of serum anti-AChR Ab. In-vivo transduction of lenti-siRNA-Bcl6 ameliorates the severity of ongoing EAMG with decreased Tfh cells, Bcl-6 and IL-21 expression, and leads to decreased anti-AChR antibody levels. Furthermore, we found that siRNA knockdown of Bcl-6 expression increases the expression of Th1(IFN-γ, T-bet) and Th2 markers (IL-4 and GATA3), but failed to alter the expression of Th17-related markers (RORγt, IL-17) and Treg markers (FoxP3). Our study suggests that Tfh cells contribute to the antibody production and could be one of the most important T cell subsets responsible for development and progression of EAMG or MG. Bcl-6 provides a promising therapeutic target for immunotherapy not only for MG, but also for other antibody-mediated autoimmune diseases. [Copyright &y& Elsevier]