Showing papers in "Genes & Genomics in 2019"

Genome-wide identification and expression analyses of WRKY transcription factor family members from chickpea (Cicer arietinum L.) reveal their role in abiotic stress-responses.

Abstract: WRKY proteins play a vital role in the regulation of several imperative plant metabolic processes and pathways, especially under biotic and abiotic stresses. Although WRKY genes have been characterized in various major crop plants, their identification and characterization in pulse legumes is still in its infancy. Chickpea (Cicer arietinum L.) is the most important pulse legume grown in arid and semi-arid tropics. In silico identification and characterization of WRKY transcription factor-encoding genes in chickpea genome. For this purpose, a systematic genome-wide analysis was carried out to identify the non-redundant WRKY transcription factors in the chickpea genome. We have computationally identified 70 WRKY-encoding non-redundant genes which were randomly distributed on all the chickpea chromosomes except chromosome 8. The evolutionary phylogenetic analysis classified the WRKY proteins into three major groups (I, II and III) and seven sub-groups (IN, IC, IIa, IIb, IIc, IId and IIe). The gene structure analysis revealed the presence of 2–7 introns among the family members. Along with the presence of absolutely conserved signatory WRKY domain, 19 different domains were also found to be conserved in a group-specific manner. Insights of gene duplication analysis revealed the predominant role of segmental duplications for the expansion of WRKY genes in chickpea. Purifying selection seems to be operated during the evolution and expansion of paralogous WRKY genes. The transcriptome data-based in silico expression analysis revealed the differential expression of CarWRKY genes in root and shoot tissues under salt, drought, and cold stress conditions. Moreover, some of these genes showed identical expression pattern under these stresses, revealing the possibility of involvement of these genes in conserved abiotic stress–response pathways. This genome-wide computational analysis will serve as a base to accelerate the functional characterization of WRKY TFs especially under biotic and abiotic stresses.

Genome-wide identification of WRKY family genes and their response to abiotic stresses in tea plant (Camellia sinensis)

Abstract: The WRKY transcription factors (TFs) family is one of the largest TF families in plants and plays a central role in diverse regulation and multiple stress responses. However, the systematical analysis of the WRKY gene family in tea plant (Camellia sinensis) based on genomic data has been lacking. The primary objective of this study was to set a systematic analysis of the WRKY gene family based on genomic data in tea plant and analyze their expression profiles under various abiotic stresses. We searched the tea plant genome using the consensus model of the WRKY domain (PF03106) and then used these search results to identify all the WRKY family members by SMART and the CDD program. Analyze their phylogeny, classification, structure, conserved motifs, Cis-elements, interactors and expression profiles. 56 putative WRKY genes were identified from the tea plant genome and divided into three main groups (I–III) and five subgroups (IIa–IIe) according to the WRKY domains and the zinc-finger structure. The gene structure and conserved motifs of the CsWRKY genes were also characterized and were consistent with the classification results. Annotation analysis showed that 34 CsWRKY genes may be involved in stress responses. Promoter analysis implied that CsWRKY genes, except for CsWRKY55, possessed at least one abiotic stress response cis-element. Expression profiles of CsWRKY genes in different tissues were analyzed with RNA-seq data. The results showed that 56 CsWRKY genes had differential expression in their transcript abundance. The expression profiles also showed that many identified CsWRKY genes were possibly involved in the response to cold, drought, salt, or ABA treatment. Tea plant genome contains at least 56 WRKY genes. These results provide useful information for further exploring the function and regulatory mechanism of CsWRKY genes in the growth, development, and adaption to abiotic stresses in tea plant.

Genomic signatures of high-altitude adaptation in Ethiopian sheep populations

Abstract: Ethiopian sheep populations such as Arsi-Bale, Horro and Adilo (long fat-tailed, LFT) inhabit mid to high-altitude areas; and Menz sheep (MZ, short fat-tailed) are adapted to cool sub-alpine environments. In contrast, Blackhead Somali sheep (BHS, fat-rumped) thrive well in arid and semi-arid areas characterized by high temperature and low precipitation. The genomic investigation of Ethiopian sheep populations may help to identify genes and biological pathways enable to adapt to the different ecological conditions. To uncover genomic regions and genes showing evidence of positive selection for altitude adaptation in Ethiopian sheep populations. A total of 72 animals inhabiting high-versus low-altitude environments were genotyped on an Ovine Infinium HD array (~ 600 K). Pairwise genetic differentiation (Fst) was calculated in sliding windows of 20 SNPs and the upper 1% smoothed Fst values were considered to represent positive selection signatures. Genes within < 25 kb of the most differentiated SNPs were considered as selection candidates. Signatures of selection were detected in genes known to be associated high with altitude adaptation in MZ–BHS pair comparison (PPP1R12A, RELN, PARP2, and DNAH9) and in LFT–BHS pair comparison (VAV3, MSRB3,EIF2AK4, MET, and TACR1). The candidate genes (MITF, FGF5, MTOR, TRHDE, and TUBB3) associated with altitude adaptation and shared between the MZ–BHS and LTF–BHS pair comparisons were also detected as under selection. Further functional analyses reveal that the candidate genes were involved in biological processes and pathways relevant to adaptation under extreme altitudes, including respiratory system development and smoothened signaling pathway. The results of the present study could aid in-depth understanding and exploitation of the underlying genetic mechanisms for sheep and other livestock species adaptation to high-altitude environments.

Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species.

Abstract: Akkermansia muciniphila is an important bacterium that resides on the mucus layer of the intestinal tract. Akkermansia muciniphila has a high abundance in human feces and plays an important role in human health. In this article, 23 whole genome sequences of the Akkermansia genus were comparatively studied. Phylogenetic trees were constructed with three methods: All amino acid sequences of each strain were used to construct the first phylogenetic tree using the web server of Composition Vector Tree Version 3. The matrix of Genome-to-Genome Distances which were obtained from GGDC 2.0 was used to construct the second phylogenetic tree using FastME. The concatenated single-copy core gene-based phylogenetic tree was generated through MEGA. The single-copy genes were obtained using OrthoMCL. Population structure was assessed by STRUCTURE 2.3.4 using the SNPs in core genes. PROKKA and Roary were used to do pan-genome analyses. The biosynthetic gene clusters were predicted using antiSMASH 4.0. IalandViewer 4 was used to detect the genomic islands. The results of comparative genomic analysis revealed that: (1) The 23 Akkermansia strains formed 4 clades in phylogenetic trees. The A. muciniphila strains isolated from different geographic regions and ecological niches, formed a closely related clade. (2) The 23 Akkermansia strains were divided into 4 species based on digital DNA-DNA hybridization (dDDH) values. (3) Pan-genome of A. muciniphila is in an open state and increases with addition of new sequenced genomes. (4) SNPs were not evenly distributed throughout the A. muciniphila genomes. The genes in regions with high SNP density are related to metabolism and cell wall/membrane envelope biogenesis. (5) The thermostable outer-membrane protein, Amuc_1100, was conserved in the Akkermansia genus, except for Akkermansia glycaniphila PytT. Overall, applying comparative genomic and pan-genomic analyses, we classified and illuminated the phylogenetic relationship of the 23 Akkermansia strains. Insights of the evolutionary, population structure, gene clusters and genome islands of Akkermansia provided more information about the possible physiological and probiotic mechanisms of the Akkermansia strains, and gave some instructions for the in-depth researches about the use of Akkermansia as a gut probiotic in the future.

Analysis of synonymous codon usage of chloroplast genome in Porphyra umbilicalis

Abstract: Synonymous codon usage bias is noticed in the genome of every organism, influenced by mutation pressure and natural selection. The analysis of codon usage pattern in Porphyra umbilicalis chloroplast genome are inferred while previous study focused on codon bias in nuclear genome. To develop a better understanding of the factors affecting synonymous codon usage, codon usage patterns and nucleotide composition of 150 genes in P. umbilicalis cp genome, and provide a theoretical basis for genetic modification of chloroplast genome. In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS and Microsoft Excel. It shows that codon usage models are mainly influenced by compositional constraints under mutational pressure and synonymous codon prefers to use codons ending with A/T, comparing to C/G. The ENC value is slight low which shows the weak codon bias. For all coding genes of P. umbilicalis chloroplast genome except Photosystem I genes, a weak correlation between GC3 and GC12 suggests natural selection might play a significant role in synonymous codon usage bias. The codon usage bias in P. umbilicalis cp genome is low and in some way or other, influenced by natural selection, mutation pressure, nucleotide composition. Our results can provide a theoretical basis for codon modification of exogenous genes, accuracy of prediction about new members of chloroplast gene family and identification of unknown genome.

Deciphering genome-wide WRKY gene family of Triticum aestivum L. and their functional role in response to Abiotic stress

Abstract: WRKY transcription factors (TFs) act in regulating plant growth and development as well as in response to different stress Some earlier studies done by individual researchers reported different wheat WRKY TFs Although, the recently released wheat genome has opened an avenue to investigate wheat WRKYs (TaWRKY) TFs Prime objective of this study to performed genome-wide classifications of TaWRKYs and their functional annotation The classification of 107 individual identified characterized sequences of TaWRKY (IICS-TaWRKY) and 160 uncharacterized draft sequences of TaWRKY (UDS-TaWRKY), along with their gene structures and motifs analysis was performed Along with comparative sequence analysis and microarray analysis was performed to mimic out TaWRKYs functions in response to different abiotic stresses, accompanied by in-vitro validation The comparative phylogenetic analysis and estimation of Ka/Ks ratio with Triticum urartu, illustrate group based clasifications of TaWRKYs and evolutionary divergences Furthermore, motif-based and protein-DNA interaction analysis of TaWRKYs helps to identify, their putative function in target DNA recognition sites Subsequently, results of microarray and comparative sequence analysis provides the evidence of TaWRKYs involved in heat and/or drought stress Further, in-vitro results validates that TaWRKY014, TaWRKY090 are found to participate in response of drought stress, whereas TaWRKY008, TaWRKY122, and WRKY45 are involved in response of heat and drought stress These findings can be utilized in developing novel heat and drought-tolerant wheat cultivars using marker-assisted breeding and transgenic development

Comparative transcriptome analysis of salt-sensitive and salt-tolerant maize reveals potential mechanisms to enhance salt resistance

Abstract: Salt stress is a devastating environmental stress that causes plant growth inhibition and yield reduction. The identification of salt-tolerant genes brings hope for the generation of salinity-tolerant crop plants through molecular breeding. In this study, one salt-sensitive and one salt-tolerant maize inbred line were screened from 242 maize inbred lines. Reactive oxygen species (ROS)-related enzyme activities were detected and salt-responsive comparative transcriptome analysis was performed for control and 220 mM NaCl treated maize leaves. Salt-tolerant maize inbred line (L87) showed higher ROS-related enzyme (SOD, POD, APX and CAT) activities and accumulated relatively lower levels of ROS under salt stress. Of the total DEGs, 1856 upregulated DEGs were specific to L87, including stress tolerance-related members of the 70kDa family of heat shock proteins (Hsp70s) and aquaporins. The DEGs involved in the abscisic acid (ABA), ethylene, jasmonic acid (JA) and salicylic acid (SA) signal transduction pathways may determine the difference in salt tolerance between the two varieties, especially one central component SnRK2, that positively regulates ABA signaling and was only upregulated in L87. Analysis of DEGs related to ROS scavenging showed that some peroxidase (POD), glutathione S-transferase (GST), catalase (CAT) and superoxide dismutase (SOD) genes specific to L87 probably enhanced its salt tolerance. The analysis of differentially expressed transcription factors (TFs) suggested that WRKY TFs could contribute to the difference in salt tolerance between the two maize lines. Compared with Salt-sensitive maize inbred line (L29), L87 exhibits specific regulatory mechanisms related to salt tolerance, including plant hormone interactions, ROS scavenging and the regulation of TFs. Our study identifies new candidate genes that may regulate maize tolerance to salt stress and provides useful information for breeding maize with high salt resistance.

Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding

Abstract: Recent next generation sequencing-driven mass production of genomic data and multi-omics-integrated approaches have significantly contributed to broadening and deepening our knowledge on the molecular system of living organisms. Accordingly, translational genomics (TG) approach can play a pivotal role in creating an informational bridge between model systems and relatively less studied plants. This review focuses mainly on addressing recent advancement in omics-related technologies, a diverse array of bioinformatic resources and potential applications of TG for the crop breeding. To accomplish above objectives, information on omics data production, various DBs and high throughput technologies was collected, integrated, and used to analyze current status and future perspectives towards omics-assisted crop breeding. Various omics data and resources have been organized and integrated into the databases and/or bioinformatic infrastructures, and thereby serve as the ome’s information center for cross-genome translation of biological data. Although the size of accumulated omics data and availability of reference genomes are different among plant families, translational approaches have been actively progressing to access particular biological characteristics. When multi-layered omics data are integrated in a synthetic manner, it will allow providing a stereoscopic view of dynamic molecular behavior and interacting networks of genes occurring in plants. Consequently, TG approach will lead us to broader and deeper insights into target traits for the plant breeding. Furthermore, such systems approach will renovate conventional breeding programs and accelerate precision crop breeding in the future.

A transcriptome analysis uncovers Panax notoginseng resistance to Fusarium solani induced by methyl jasmonate.

Abstract: Panax notoginseng is a famous Chinese herbal medicine, but the root rot disease mainly caused by Fusarium solani severely reduces the yield and quality of its medicinal materials. The defense priming in P. notoginseng through exogenous application of signaling molecule will supply theoretical support for the exogenous regulation of disease resistance in P. notoginseng. In this study, the exogenous application of methyl jasmonate (MeJA) increased P. notoginseng’s resistance to F. solani. Furthermore, the P. notoginseng transcriptome during F. solani infection was investigated through next-generation sequencing to uncover the resistance mechanism of P. notogingseng induced by MeJA. The de novo assembly of transcriptome sequences produced 80,551 unigenes, and 36,771 of these unigenes were annotated by at least one database. A differentially expressed gene analysis revealed that a large number of genes related to terpenoid backbone biosynthesis, phenylalanine metabolism, and plant–pathogen interactions were predominantly up-regulated by MeJA. Moreover, jasmonic acid (JA) biosynthesis-related genes and the JA signaling pathway genes, such as linoleate 13S-lipoxygenase, allene oxide cyclase, allene oxide synthase, TIFY, defensin, and pathogenesis-related proteins, showed increased transcriptional levels after inoculation with F. solani. Notably, according to the gene expression analysis, JA and ethylene signaling pathways may act synergistically to positively regulate the defense responses of P. notoginseng to F. solani. JA signaling appears to play a vital role in P. notoginseng responses to F. solani infection, which will be helpful in improving the disease resistance of P. notoginseng cultivars as well as in developing an environmentally friendly biological control method for root rot disease.

Long noncoding RNA UCA1 inhibits ischaemia/reperfusion injury induced cardiomyocytes apoptosis via suppression of endoplasmic reticulum stress.

Abstract: Ischemia heart disease is one of the major causes of death worldwide which often associated with tissue infarction and limit the recovery of function. Multiple factors involved in the I/R-induced cardiomyocyte dysfunction which were consistent with a role of oxidative stress and altered endothelium-dependent responses. However, the pathogenic mechanisms in I/R injury remain unclear. The H9C2 cells were in the ischaemia/reperfusion (I/R) condition. After I/R, the cells were transfected with or without adenovirus-urothelial carcinoma associated 1(Ad-UCA1). Then qRT-PCR analysis was performed to quantify mRNA expression of different treatment groups. Cell apoptosis rate was assessed using flow cytometry and ER stress biomarker expression were measured by immunoblotting. Intracellular and mitochondrial ROS generation were assayed by fluorescence microscope after staining with the DCFDA or MitoSOX. I/R conditions trigger lncRNAs UCA1 expression, cellular and mitochondria ROS production, resulting in cell apoptosis through the induction of oxidative and ER stress. Overexpression of UCA1 protects H9C2 cells from I/R-induced ER stress and cell apoptosis. Moreover, UCA1 might be a potential regulator in the protective effect of I/R‑induced oxidative stress and mitochondria dysfunction. Subsequently, ER stress inhibitor attenuated the effect of siUCA1 induced injury in H9C2 cells. The expression of UCA1 against I/R induced oxidative stress and mitochondria dysfunction via suppression of endoplasmic reticulum stress. UCA1 might be a biomarker to improved diagnosis of I/R injury.

Sugar metabolism as input signals and fuel for leaf senescence

Abstract: Senescence in plants is an active and acquired developmental process that occurs at the last developmental stage during the life cycle of a plant. Leaf senescence is a relatively slow process, which is characterized by loss of photosynthetic activity and breakdown of macromolecules, to compensate for reduced energy production. Sugars, major photosynthetic assimilates, are key substrates required for cellular respiration to produce intermediate sources of energy and reducing power, which are known to be essential for the maintenance of cellular processes during senescence. In addition, sugars play roles as signaling molecules to facilitate a wide range of developmental processes as metabolic sensors. However, the roles of sugar during the entire period of senescence remain fragmentary. The purpose of the present review was to examine and explore changes in production, sources, and functions of sugars during leaf senescence. Further, the review explores the current state of knowledge on how sugars mediate the onset or progression of leaf senescence. Progress in the area would facilitate the determination of more sophisticated ways of manipulating the senescence process in plants and offer insights that guide efforts to maintain nutrients in leafy plants during postharvest storage.

MicroRNA-377-3p inhibits growth and invasion through sponging JAG1 in ovarian cancer.

Abstract: Ovarian cancer is the one of the most deadly gynecologic malignancy among cancer related death in women. However, the treatment for ovarian cancer is still limited. In this study, we aimed to explore the inhibition potential of miR-377-3p in ovarian cancer and explore the mechanism of this effect. Quantitative real-time PCR was used to detect the mRNA or microRNA (miRNA) levels. CCK-8, wound-healing, transwell assay were used to detect cell proliferation, migration and invasion. The protein levels were examined by western blot. The dual luciferase reporter assay was conducted to examine the luciferase activity. Tumor volume was measured and Ki67 was detected via immunohistochemistry. qRT-PCR results showed that miR-377-3p was downregulated in ovarian cancer patients. MiR-377-3p mimics suppressed cell proliferation, migration, invasion and decreased the JAG1 level. However, miR-377-3p inhibitor promoted these appearances. Interestingly, we found JAG1 was a target gene of miR-377-3p. JAG1 overexpression reversed the miR-377-3p-induced inhibition of proliferation and invasion. In addition, miR-377-3p inhibited ovarian cancer tumorigenesis in vivo, indicating by decreased tumor volume and staining of Ki67. The results showed that miR-377-3p inhibited growth and invasion of ovarian cancer cells by targeting JAG1.

Physiological responses and small RNAs changes in maize under nitrogen deficiency and resupply

Abstract: Maize is an important crop in the world, nitrogen stress severely reduces maize yield. Although a large number of studies have identified the expression changes of microRNAs (miRNAs) under N stress in several species, the miRNAs expression patterns of N-deficient plants under N resupply remain unclear. The primary objective of this study was to identify miRNAs in response to nitrogen stress and understand relevant physiological changes in nitrogen-deficient maize after nitrogen resupply. Physiological parameters were measured to study relevant physiological changes under different nitrogen conditions. Small RNA sequencing and qRT-PCR analysis were performed to understand the response of miRNAs under different nitrogen conditions. The content of chlorophyll, soluble protein and nitrate nitrogen decreased than CK by 0.52, 0.49 and 0.82 times after N deficiency treatment and increased than ND by 0.52, 1.36 and 0.65 times after N resupply, respectively. Conversely, the activity of superoxide dismutase (SOD) and peroxidase (POD) increased by 0.67 and 1.64 times than CK after N deficiency, respectively, and decreased by 0.09 and 0.35 times than ND after N resupply. A total of 226 known miRNAs were identified by sRNA sequencing; 106 miRNAs were differentially expressed between the control and N-deficient groups, and 103 were differentially expressed between the N-deficient and N-resupply groups (P < 0.05). Real-time quantitative PCR (qPCR) was used to further validate and analyze the expression of the identified miRNAs. A total of 1609 target genes were identified by target prediction, and some differentially expressed miRNAs were predicted to target transcription factors and functional proteins. Gene Ontology (GO) analysis was used to determine the biological function of these targets and revealed that some miRNAs, such as miR169, miR1214, miR2199, miR398, miR408 and miR827 might be involved in nitrogen metabolism regulation. Our study comprehensively provides important information on miRNA functions and molecular mechanisms in response to N stress. These findings may assist to improve nitrogen availability in plants.

Expression and function analysis of a rice OsHSP40 gene under salt stress.

Abstract: Heat shock proteins (HSPs) play essential roles in both plant growth and abiotic stress tolerance. In rice, OsHSP40 was recently reported to regulate programmed cell death (PCD) of suspension cells under high temperature. However, the expression and functions of OsHSP40 under normal growth or other abiotic stress conditions is still unknown. We reported the expression and function of a rice OsHSP40 gene under salt stress. Homologous proteins of OsHSP40 were collected from the NCBI database and constructed the neighbor-joining (NJ) phylogenetic tree. The expression pattern of OsHSP40 was detected by qRT-PCR under NaCl (150 mM) treatment. Then, identified a rice T-DNA insertion mutant oshsp40. At last, we compared and analyzed the phenotypes of oshsp40 and wild type under salt stress. OsHSP40 was a constitutively expressed small HSP (sHSP) gene and was close related to other plant sHSPs. Moreover, the expression of OsHSP40 was regulated by salt, varying across time points and tissues. Furthermore, the growth of T-DNA insertion mutant of OsHSP40 (designated as oshsp40) was suppressed by NaCl (150 mM) compared with that of the WT at seedling stage. Detailed measurement showed root and shoot length of the oshsp40 seedlings were significantly shorter than those of the WT seedlings under NaCl stress. In addition, the pot experiment results revealed that seedlings of oshsp40 withered more seriously compared with those of WT after NaCl treatment and recovery, and that survival rate and fresh weight of oshsp40 seedlings were significantly reduced. Taken together, these data suggested that OsHSP40 had multiple functions in rice normal growth and abiotic stress tolerance.

Association study of the three functional polymorphisms (TAS2R46G>A, OR4C16G>A, and OR4X1A>T) with recurrent pregnancy loss

Abstract: This study was purposed to investigate whether genetic polymorphisms in the function of stop-gain are associated with a fetal or placental development play roles and a development of idiopathic recurrent pregnancy loss (RPL) in Korean females. Three stop-gain polymorphisms were selected using next-generation sequencing screening, which allows for the rigorous examination and discovery of previously uncharacterized stop-gain genes and stop-gain expression profiles. Accordingly, we investigated the association of stop-gain polymorphisms in Korean women with RPL. Three functional polymorphisms in the TAS2R46G>A (rs2708381), OR4C16G>A (rs1459101), and OR4X1A>T (rs10838851) genes were genotyped using polymerase chain reaction (PCR)—restriction fragment length polymorphism assays and real-time PCR analysis. We determined that the OR4C16G>A polymorphism was associated with idiopathic RPL in Korean women (Adjusted odds ratio [AOR] 1.782; 95% confidence interval [CI] 1.004–3.163; P = 0.048, and AOR 1.766; 95% CI 1.020–3.059; P = 0.042). In addition, the prevalence of RPL was increased in women with the OR4C16GA + AA genotype and blood coagulation measures of prothrombin time (PT) > 10.4 s (AOR 8.292; 95% CI 2.744–25.054). We suggest that the OR4C16G>A polymorphism might serve as a clinically useful biomarker for the development, prevention, and prognosis of RPL.

Reversine induces caspase-dependent apoptosis of human osteosarcoma cells through extrinsic and intrinsic apoptotic signaling pathways

Abstract: The 2-(4-morpholinoanilino)-6-cyclohexylaminopurine (reversine) acts as a chemopreventive agent and induces apoptotic cell death in various cancer cells. However, the anticancer effects of reversine on osteosarcoma cells are not clearly established. The purpose of this study was to investigate the effect of reversine on cell proliferation and induction of apoptosis in human osteosarcoma cells. Cell viability assay, histological analysis, DAPI staining, caspase activation analysis, flow cytometric analysis and immunoblotting were carried out in MG-63 osteosarcoma cells. Reversine inhibited the growth of cells in a dose-dependent manner and induced nuclear condensation and fragmentation. Reversine-treated cells showed caspase-3/7 activation and increased apoptosis versus control cells. FasL, a death ligand associated with extrinsic apoptotic signaling pathways, was significantly up-regulated by reversine treatment. Moreover, the caspase-8, a part of the extrinsic apoptotic pathway, was activated by reversine treatments. Expressions of anti-apoptotic factors such as Bcl-2 and Bcl-xL, components of the mitochondria dependent intrinsic apoptosis pathway, significantly decreased following reversine treatment. The expressions of pro-apoptotic factors such as BAX, BAD and caspase-9 increased by reversine treatments. In addition, reversine activated caspase-3 and Poly (ADP-ribose) polymerase (PARP) to induce cell death. The Z-VAD-fmk significantly inhibited cell death through the suppression of caspase-3 expression in MG-63 cells treated with reversine. These results suggest that the reversine may inhibit cell proliferation and induce apoptotic cell death in MG-63 osteosarcoma cells through both the mitochondria-mediated intrinsic pathway and the death receptor-mediated extrinsic pathway, and may have potential properties for the discovery of anti-cancer agents.

Genetic analysis of roots and shoots in rice seedling by association mapping

Abstract: The vigorous shoots and roots help to improve drought resistance and post-transplanting recovery in rice seedlings (Oryza sativa L.). Hundreds of loci related to root system have been identified recently, but little research has been done on shoot traits, and the relationship between roots and shoots development is also still unclear. The objective of this study was to identify associated loci for roots and shoots in rice seedlings as well as to screen pleiotropic QTLs involved in coordinated development of roots and shoots. Using mini core collection of 273 cultivated rice accessions and 280 simple-sequence repeat markers, we investigated six traits [root length (RL), root thickness (RT), root weight (RW), shoot length (SL), shoot weight (SW) and ratio of root-to-shoot mass] in seedlings. Study was performed in hydroponic medium and genetic analysis was performed by association mapping using general linear model (GLM) with population structure (Q) and mixed linear model (MLM) involving Q and familial relatedness (K). Two subgroups indica and japonica showed significant differences in RT, RW and SW. Maximum correlation was observed between RW and SW. Using GLM 65 QTLs for root and 43 QTLs associated with shoot traits were detected. Among them, seven QTLs were present between RL and RW and five common QTLs were detected between SL and SW with high phenotypic variation effects (PVEs). Two key pleiotropic QTLs were also identified involved in collaborative development of roots and shoots in rice seedlings. Importantly, 17 and 10 QTLs were identified for root and shoot traits respectively in both studies of GLM and MLM. More common QTLs with high PVEs between root and shoot traits suggested that longitudinal growth (RL and SL) played an important role in accumulation of biomass (RW and SW). Considering the obvious phenotypic differences and fewer common QTLs between indica and japonica, we suggested that there could be different mechanisms of seedling development between both subpopulations. Key pleiotropic QTLs and QTLs identified for root and shoot traits in both studies of GLM and MLM could be preferentially used in marker-assisted breeding for strong rice seedling.

Proteome-wide subtractive approach to prioritize a hypothetical protein of XDR-Mycobacterium tuberculosis as potential drug target

Abstract: Among the resistant isolates of MTB, multidrug resistant tuberculosis (MDR-TB) and extensively drug resistant tuberculosis (XDR-TB) have been the areas of growing concern. The genomic analysis showed that the respective genomic pool of the XDR-MTB proteome contains more than 30% of the hypothetical proteins for which no functions have been annotated yet. This class of proteins presumably have their own importance to complete genome and proteome information. The bioinformatics advancements have helped to annotate those hypothetical proteins by using various computational tools and have potential to classify them functionally. The objective of this study was to propose a new and unique drug target against the deadly Mycobacterium tuberculosis using Bioinformatics approaches to characterize the hypothetical proteins. We stepwise reduced the hypothetical proteins (total number: 1256) out of the complete proteome to only 26 essential hypothetical proteins. Out of those 26 proteins, the protein WP_003401246.1 was computationally characterized as the druggable target. The study proposed a hypothetical protein from complete proteome of the XDR-MTB as a new drug target against which new drug candidates can be proposed. Hence, the study opens up the new avenues in the areas of drug discovery against deadly M. tuberculosis.

Genetic diversity and population structure analysis in Perilla crop and their weedy types from northern and southern areas of China based on simple sequence repeat (SSRs)

Abstract: Identification of genetic variation is an essential ability for the long-term success of breeding programs and maximizes the use of germplasm resources. In East Asia, China has a long history of the cultivation of Perilla crop, but there has been little research on the genetic diversity and genetic relationships among accessions of Perilla crop and their weedy types. To better understand the genetic variations of the cultivated and weedy types of Perilla crop in China, the 91 accessions were evaluated for genetic diversity by 21 simple sequence repeat (SSR) markers. SSR amplifications were conducted in a total volume of 20 µL, consisting of 20 ng genomic DNA, 1X PCR buffer, 0.5 µM forward and reverse primers, 0.2 mM dNTPs, and 1 U Taq polymerase. Power Marker version 3.25 was applied to obtain the information on the number of alleles, allele frequency, major allele frequency, gene diversity (GD), and polymorphic information content (PIC). The similarity matrix was used to construct an unweighted pair group method with arithmetic mean dendrogram by the application of SAHN-Clustering from NTSYS-pc.V.2.1. A total of 147 alleles were identified with an average of 7 alleles per locus. The average values of PIC and GD were 0.577 and 0.537, respectively. The genetic diversity level of accessions from Northern China was lower than accessions from Southern China. The genetic diversity level and PIC values for accessions of var. crispa were the highest. For accessions of cultivated var. frutescens, genetic diversity in Southern China was higher than that in Northern China. Most cultivated Perilla accessions were clearly separated from weedy Perilla accessions, but there was no clear geographic structure between cultivated Perilla crop and weedy types based on their regional distribution. This study demonstrated the utility of SSR analysis for performing genetic and population analysis of cultivated and weedy types of Perilla accessions in China.

Neuroprotective effect of miR-410-3p against sevoflurane anesthesia-induced cognitive dysfunction in rats through PI3K/Akt signaling pathway via targeting C-X-C motif chemokine receptor 5.

Abstract: Postoperative cognitive dysfunction (POCD) is a neurodegenerative disorder with impairment of cognition. Sevoflurane anesthesia has been found to lead to CD and microRNAs (miRNAs) were reported to affect cognitive function. This study investigates the neuroprotective effect against sevoflurane anesthesia-induced CD. HE staining was used to detect the pathological change of hippocampal neuron. Morris water maze test was used to analyze latency time, platform crossing and swimming speed. Quantitative real-time PCR (qRT-PCR) and western blotting were performed to examine the mRNA and protein expression of miR-410-3p, IL-6, TNF-α, IL-1β and C–X–C motif chemokine receptor 5 (CXCR5). Dual-luciferase reporter assay was used to detect the relationship between miR-410-3p and CXCR5. MiR-410-3p was downregulated in sevoflurane anesthesia-induced rats and cells and act as a suppressor in sevoflurane anesthesia-induced hippocampal neuron apoptosis and inflammation. Furthermore, miR-410-3p was identified to bind with CXCR5. Further analysis showed that CXCR5 expression was increased by sevoflurane treatment, whereas was repressed by miR-410-3p overexpression. Moreover, miR-410-3p could inhibit sevoflurane anesthesia-induced hippocampal neuron apoptosis by phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) pathway. These data indicated that miR-410-3p exhibited its neuroprotective effect on sevoflurane anesthesia-induced CD by targeting CXCR5 via PI3K/Akt signaling pathway. Our study may potentially provide a new light on the pathogenesis and therapeutic method for sevoflurane anesthesia-induced CD.

Pattern recognition receptors and their interactions with bacterial type III effectors in plants.

Abstract: Innate immune signaling of plants is initiated by pattern recognition receptors (PRRs) at the plasma membrane. Upon pathogen attack, PRRs recognize pathogen-associated molecular patterns (PAMPs) via ectodomain and lead to signaling cascade via cytoplasmic kinase domain. PAMP-triggered immunity (PTI) activates basal defense responses sufficient to confer broad-spectrum disease resistance by inhibiting pathogen entry and growth. On the other hand, one of the major virulence factors in plant-pathogenic bacteria is type III secretion system, which can deliver effector proteins into the host cell and modulate host cellular processes. Most type III effectors are implicated in PTI suppression, and PRRs have been identified as targets of multiple type III effectors. Mutants defective in T3SS lack pathogenicity in many bacterial species, revealing that T3SS-mediated PTI suppression is critical for host colonization and subsequent disease development. This review summarizes molecular basis of bacterial pathogen perception by plant PRRs and also interaction between PRRs and type III effectors during early stages of plant-pathogen interaction.

Construction of genetic linkage map and identification of QTLs related to agronomic traits in DH population of maize ( Zea mays L.) using SSR markers

Abstract: In this study, we used phenotypic and genetic analysis to investigate Double haploid (DH) lines derived from normal corn parents (HF1 and 11S6169). DH technology offers an array of advantages in maize genetics and breeding as follows: first, it significantly shortens the breeding cycle by development of completely homozygous lines in two or three generations; and second, it simplifies logistics, including requiring less time, labor, and financial resources for developing new DH lines compared with the conventional RIL population development process. In our study, we constructed a maize genetic linkage map using SSR markers and a DH population derived from a cross of normal corn (HF1) and normal corn (11S6169). The DH population used in this study was developed by the following methods: we crossed normal corn (HF1) and normal corn (11S6169), which are parent lines of a normal corn cultivar, in 2014; and the next year, the F1 hybrids were crossed with a tropicalized haploid inducer line (TAIL), which is homozygous for the dominant marker gene R1-nj (Nanda and Chase in Crop Sci 6:213–215, 1966), and we harvested seeds of the haploid lines. A total of 200 SSR markers were assigned to 10 linkage groups that spanned 1145.4 cM with an average genetic distance between markers of 5.7 cM. 68 SSR markers showed Mendelian segregation ratios in the DH population at a 5% significance threshold. A total of 15 quantitative trait loci (QTLs) for plant height (PH), ear height (EH), ear height ratio (ER), leaf length (LL), ear length (EL), set ear length (SEL), set ear ratio (SER), ear width (EW), 100 kernel weight (100 KW), and cob color (CC) were found in the 121 lines in the DH population. The results of this study may help to improve the detection and characterization of agronomic traits and provide great opportunities for maize breeders and researchers using a DH population in maize breeding programs.

The structural and functional roles of CTCF in the regulation of cell type-specific and human disease-associated super-enhancers.

Abstract: Super-enhancers play critical roles in cell-type specific gene controls and human disease progression. CCCTC-binding factor (CTCF), a transcriptional repressor that insulates the expression of neighboring genes and is involved in chromatin interactions, is frequently present in the boundary regions of or within super-enhancers. However, the structural and functional roles of CTCF in regulating super-enhancers remain elusive. To provide a comprehensive review describing the distinct chromatin features and functional roles of CTCF within super-enhancers. This review compares the various tools used to study the three-dimensional (3D) chromatin architecture of super-enhancers; summarizes the chromatin features of CTCF within cell-type specific super-enhancers and their in vivo biological activities, as determined by CRISPR/Cas9 genome editing; and describes the structural and functional activities of CTCF within human disease-associated super-enhancers. This review provides fundamental insights into the regulatory mechanisms of super-enhancers and facilitates studies of tissue-specific developmental processes and human disease progression.

A thiosemicarbazone derivative induces triple negative breast cancer cell apoptosis: possible role of miRNA-125a-5p and miRNA-181a-5p.

Abstract: Breast cancer, the most commonly diagnosed malignancy in women, accounts for the highest cancer-related deaths worldwide. Triple negative breast cancer (TNBC), lacking the expression of estrogen, progesterone and HER2 receptors, has an aggressive clinical phenotype and is susceptible to chemotherapy but not to hormonal or targeted immunotherapy. In an attempt to identify potent and selective anti-TNBC agents, a set of thiosemicarbazone derivatives were screened for their cytotoxic activity against MDA-MB 231 breast cancer cell line. MTT assay was used to examine cell viability. P53 phosphorylation status, poly (ADP-ribose) polymerase (PARP) cleavage as well as Bcl2 and Bax protein levels were assessed by Western blot. Quantitative Real Time-PCR was carried out to characterize miRNAs expression levels. Combining Cisplatin + thiosemicarbazone compound 4 showed potent anti-TNBC potential. Cisplatin + compound 4 significantly enhanced p53 phosphorylation, induced Bax amount, reduced Bcl2 protein levels, enhanced PARP cleavage and modulated miRNAs expression profile in TNBCs, with a particular overexpression of miR-125a-5p and miR-181a-5p. Intriguingly, miR-125a-5p and miR-181a-5p could significantly downregulate BCL2 expression by binding to their target sites in the 3′UTR. Collectively, our results demonstrate an anti-TNBC activity of Cisplatin + thiosemicarbazone compound 4 combination mediated via induction of apoptosis.

C1q and TNF related protein 1 regulates expression of inflammatory genes in vascular smooth muscle cells.

Abstract: C1q and TNF related protein 1 (C1QTNF1) is known to be associated with coronary artery diseases. However, the molecular function of C1QTNF1 on the vascular smooth muscles remains to be investigated. This study was therefore undertaken to investigate the effect of C1QTNF1 on gene expression of human smooth muscle cells and to reveal potential molecular mechanisms mediated by C1QTNF1. Vascular smooth muscle cells were incubated with recombinant C1QTNF1 for 16 h, followed by determining any change in mRNA expressions by Affymetrix genechip. Gene ontology (GO), KEGG pathway, and protein–protein interaction (PPI) network were analyzed in differentially expressed genes. In addition, validation of microarray data was performed using quantitative real-time PCR. The mRNA expressions of annotated 74 genes were significantly altered after incubation with recombinant C1QTNF1; 41 genes were up-regulated and 33 down-regulated. The differentially expressed genes were enriched in biological processes and KEGG pathways associated with inflammatory responses. In the PPI network analysis, IL-6, CCL2, and ICAM1 were identified as potential key genes with relatively high degree. The cluster analysis in the PPI network identified a significant module composed of upregulated genes, such as IL-6, CCL2, NFKBIA, SOD2, and ICAM1. The quantitative real-time PCR results of potential key genes were consistent with microarray data. The results in the present study provide insights on the effects of C1QTNF1 on gene expression of smooth muscle cells. We believe our findings will help to elucidate the molecular mechanisms regarding the functions of C1QTNF1 on smooth muscle cells in inflammatory diseases.

Association analysis of polymorphism in the NR6A1 gene with the lumbar vertebrae number traits in sheep

Abstract: The vertebral number is an economically significant trait, which is associated with body length and carcass traits. Nuclear Receptor Subfamily 6, Group A, Member 1 (NR6A1) is a member of the nuclear receptor superfamily and it plays an important role in the early development of embryos. The NR6A1 gene was considered as an important candidate for influence vertebrae number, while the potential associations between this gene and the number of lumbar vertebrae traits of sheep have not been explored. In this study, we detected the genetic variants of NR6A1 gene and analyzed the associations of the polymorphisms with lumbar number traits in 130 Kazakh sheep. We use single-strand conformation polymorphism (SSCP) technique to detect single nucleotide polymorphism (SNP) of NR6A1 gene, and the association of the genotype and lumbar number variation was analyzed by independent Chi-square test. We detect SNP of NR6A1 gene by PCR-SSCP technique, and polymorphisms were only found in the coding region of exon-6 and exon-8 of NR6A1 gene. In order to investigate the connection between the SNP locus and lumbar number traits in sheep, we conducted a Chi-square test for independence for exon-6 and exon-8 of NR6A1 gene, respectively. Association analysis revealed significant associations between the SNP (rs414302710: A >C) in the exon-8 of NR6A1 gene with the number of lumbar vertebrae (P C) locus of exon-8 of NR6A1 gene in sheep possible influence the number of lumbar vertebrae, which has the potential to be applied in selective breeding of sheep.

Rheinic acid ameliorates radiation-induced acute enteritis in rats through PPAR-γ/NF-κB

Abstract: Acute radiation enteritis (ARE), a common complication of intestinal caused by abdominal and pelvic radiation therapy. Rheinic acid is a major active ingredient derived from Rhubarb. Rhubarb could suppress inflammation, tumor, fibrosis oxidative damage. However, RA as the main active component and extract monomer of Rhubarb, the pharmacological activity and the underlying molecular mechanism on various diseases has not yet been revealed. To determine the potential role of rheinic acid (RA) in ameliorating inflammation of rats with acute radiation enteritis (ARE), and explore the underlying mechanism. ARE rat model was established by irradiated with single-dose 10 Gy X-rays at a rate of 0.62 Gy/min to the abdomen. The rats were executed after orally administered with Rheinic acid 7 days and used in the subsequent experiments. Body weight, fecal characteristics and bloody of rats were used to assess the disease activity index. Histological analysis of the jejunum and colon were evaluated using H&E staining. The pro-inflammatory cytokines levels were measured by immunohistochemistry and ELISA. The levels of nitric oxide (NO), malondialdehyde (MDA), superoxide dismutase (SOD) and glutathione (GSH) were also determined. The mRNA and protein expression were examined by real-time polymerase chain reaction (qRT-PCR) and western blot, respectively. Rheinic acid promoted intestinal functional recovery, and ameliorated intestinal damage and bloody stool in ARE rats. Rheinic acid strongly decreased the levels of tumor necrosis factor-α, interleukin-1, interleukin-6, NO, and MDA, whereas increased levels of anti-oxidants, SOD and GSH. Moreover, the expression of apoptosis-related proteins, cleaved caspase-3 and cleaved poly (ADP-ribose) polymerase (PARP), were decreased with RA treatment. Further study indicated that PPAR-γ was activated and thereby NF-κB and p38 MAPK signaling pathway were suppressed after rheinic acid treatment. Rheinic acid could ameliorate acute radiation enteritis and the underlying molecular mechanism is, at least partially, through PPAR-γ/NF-κB and p38 MAPK/JNK pathways.

MicroRNA-340-5p relieved chronic constriction injury-induced neuropathic pain by targeting Rap1A in rat model.

Abstract: Neuropathic pain (NP) is one of the main challenges towards NP syndrome treatment. miR-340-5p exhibit different expression levels in NP models. Its effects on NP remained unclear. The objective of this study was to explore the potential regulation mechanisms of miR-340-5p in NP. Rat model of chronic constriction injury (CCI) was established to induce NP in vivo. NP levels were assessed using mechanical withdrawal threshold (MWT). The inflammation response in CCI rats were determined by HE staining and ELISA assay. The target genes of miR-340-5p were verified by luciferase report assays. In CCI rats, level of miR-340-5p was down-regulated both in spinal cord tissues and isolated microglial cells. Paw withdrawal threshold (PWT) and paw withdrawal latency (PWL) were decreased in CCI rats, which were restored upon miR-340-5p overexpression. miR-340-5p overexpression also decreased inflammation as well as expression levels of COX-2, IL-1β, TNF-α and IL-6 in CCI rats. Luciferase report assays revealed Rap1A was a target gene of miR-340-5p in the experimental model. Elevated miR-340-5p decreased Rap1A expression level in vitro and in vivo. Overexpression of Rap1A protein restored expression levels of COX-2, IL-1β, TNF-α and IL-6, reduced the PWT and PWL and increased inflammation response in CCI rats. miR-340-5p alleviated CCI-induced NP by targeting Rap1A. miR-340-5p and Rap1A may be the potential treatment targets for NP therapeutics.

Improving classification accuracy of cancer types using parallel hybrid feature selection on microarray gene expression data

Abstract: Data mining techniques are used to mine unknown knowledge from huge data. Microarray gene expression (MGE) data plays a major role in predicting type of cancer. But as MGE data is huge in volume, applying traditional data mining approaches is time consuming. Hence parallel programming frameworks like Hadoop, Spark and Mahout are necessary to ease the task of computation. Not all the gene expressions are necessary in prediction, it is very essential to select important genes for improving classification accuracy. So feature selection algorithms are parallelized and executed on Spark framework to eliminate unnecessary genes and identify only predictive genes in very less time without affecting prediction accuracy. Parallelized hybrid feature selection (HFS) method is proposed to serve the purpose. This method includes parallelized correlation feature subset selection followed by rank-based feature selection methods. The selected subset of genes is evaluated using parallel classification algorithms. The accuracy values obtained are compared with existing rank-weight feature selection, parallelized recursive feature selection methods and also with the values obtained by executing parallelized HFS on DistributedWekaSpark. The classification accuracy obtained with the proposed parallelized HFS method is 97% and 79% for gastric cancer and childhood leukemia respectively. The proposed parallelized HFS method produced ~ 4% to ~ 15% improvement in classification accuracy when compared with previous methods. The results reveal the fact that the proposed parallelized feature selection algorithm is scalable to growing medical data and predicts cancer sub-types in lesser time with higher accuracy.

Genome-wide identification of the HKT genes in five Rosaceae species and expression analysis of HKT genes in response to salt-stress in Fragaria vesca

Abstract: The high-affinity potassium transporter (HKT) gene family is implicated in the regulation of response to salt stress in different plants. Yet, knowledge remains very limited for them in the Rosaceae species. The whole genome sequences of the five Rosaceae species, including Fragaria vesca (woodland strawberry), Malus domestica (apple), Pyrus communis (pear), Prunus mume (mei) and Prunus persica (peach), give the opportunity to uncover the evolutionary pattern of the HKT genes among Rosaceae genomes. The primary objective of this study was to identify the HKT genes in five Rosaceae species and understand the potential biological functions of the HKT genes in response to salt stress in Fragaria vesca. In this study, the HKT genes in five Rosaceae species were identified by bioinformatics. The phylogenetic tree was constructed and Ka and Ks values were calculated by MEGA 5.0. Genetic mapping of these genes were processed by MapInspect software. In addition, the physico-chemical properties, the cis-acting elements, the intron/exon structures, and the conserved domain motifs of these genes were analyzed and predicted by the websites of ProtParam, Pfam, PlantCARE, GSDS, MEME, and Motif Scan. In the present study, a total of 12 HKT genes were identified from five Rosaceae species. In the phylogenetic tree, orthologous genes were clustering together rather than paralogous genes and PcHKTs underwent two species-specific duplications before the divergence of pear and apple.. Furthermore, various expression levels of FvHKT genes revealed that woodland strawberry HKT genes are associated in responding to the salt stress. The activities of ROS-scavenging enzymes, superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were also measured in different treatments of salt-stressed woodland strawberry leaves, which suggested that the three enzymes may also take part in response to salt stress. The Ka/Ks ratio demonstrated that purifying selection played a major role in the evolutionary processes of HKT genes among the Rosaceae species, and FvHKT genes are involved in response to salt stress.