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Functional & Integrative Genomics

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https://www.readbyqxmd.com/read/29134405/cell-type-specific-gene-expression-patterns-in-the-knee-cartilage-in-an-osteoarthritis-rat-model
#1
Michal Korostynski, Natalia Malek, Marcin Piechota, Katarzyna Starowicz
Osteoarthritis (OA) is a chronic degenerative disease that leads to joint failure, pain, and disability. Gene regulation is implicated as a driver of the imbalance between the expression of catabolic and anabolic factors that eventually leads to the degeneration of osteoarthritic cartilage. In our model, knee-joint OA was induced in male Wistar rats by intra-articular sodium monoiodoacetate (MIA) injections. Whole-genome microarrays were used to analyse the alterations in gene expression during the time-course of OA development (at 2, 14, and 28 days post-injection) in rat knee joints...
November 13, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28993898/dynamic-transcriptomic-analysis-in-hircine-longissimus-dorsi-muscle-from-fetal-to-neonatal-development-stages
#2
Siyuan Zhan, Wei Zhao, Tianzeng Song, Yao Dong, Jiazhong Guo, Jiaxue Cao, Tao Zhong, Linjie Wang, Li Li, Hongping Zhang
Muscle growth and development from fetal to neonatal stages consist of a series of delicately regulated and orchestrated changes in expression of genes. In this study, we performed whole transcriptome profiling based on RNA-Seq of caprine longissimus dorsi muscle tissue obtained from prenatal stages (days 45, 60, and 105 of gestation) and neonatal stage (the 3-day-old newborn) to identify genes that are differentially expressed and investigate their temporal expression profiles. A total of 3276 differentially expressed genes (DEGs) were identified (Q value < 0...
October 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28986655/gilp-family-a-stress-responsive-group-of-plant-proteins-containing-a-litaf-motif
#3
C Cabreira-Cagliari, D G S Fagundes, N C F Dias, B Bohn, M Margis-Pinheiro, M H Bodanese-Zanettini, Alexandro Cagliari
Lipopolysaccharide-induced tumor necrosis factor-α (LITAF) is a membrane protein that is highly dependent on correct location to exert transcription factor activity and protein quality control. In humans, LITAF, PIG7 (p53-inducible gene 7), and SIMPLE (small integral membrane protein of the lysosome/late endosome) refer to the same gene, which acts as a tumor suppressor. Several studies have shown that the transcription factor activity and nuclear translocation of LITAF protein are critical for the induction of several immune cells via classical pathways...
October 6, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28956210/identification-of-drought-responsive-micrornas-in-tomato-using-high-throughput-sequencing
#4
Minmin Liu, Huiyang Yu, Gangjun Zhao, Qiufeng Huang, Yongen Lu, Bo Ouyang
Drought is a major abiotic stress affecting crop productivity and quality. As a class of noncoding RNA, microRNA (miRNA) plays important roles in plant growth, development, and stress response. However, their response and roles in tomato drought stress is largely unknown. Here, by using high-throughput sequencing, we compared the miRNA profiles before and after drought treatment in two tomato genotypes: M82, a drought-sensitive cultivated tomato (Solanum lycopersicum), and IL2-5, a drought-tolerant introgression line derived from M82 and the tomato wild species S...
September 28, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28918562/crispr-cas9-genome-editing-in-wheat
#5
Dongjin Kim, Burcu Alptekin, Hikmet Budak
Genome editing has been a long-term challenge for molecular biology research, particularly for plants possess complex genome. The recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a versatile tool for genome editing which enables editing of multiple genes based on the guidance of small RNAs. Even though the efficiency of CRISPR/Cas9 system has been shown with several studies from diploid plants, its application remains a challenge for plants with polyploid and complex genome...
September 16, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28900766/diversity-and-distribution-of-cyp-gene-family-in-bactrian-camel
#6
Surong Hasi, Jirimutu Yao, Siriguleng Yu, Yanan Tian
Cytochrome P450 (CYP) enzymes belong to a superfamily of monooxygenases which are phase I enzymes responsible for the first pass metabolism of about 90% of drugs in animals. However, these enzymes are often polymorphic and metabolism of the same drug in different species or different individuals is influenced by genetic and non-genetic factors. Bactrian camels are capable of survival in harsh living environments, being able to consume diets that are often toxic to other mammals and can tolerate extreme water and food deprivation...
September 12, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28856505/comparative-analysis-of-constitutive-proteome-between-resistant-and-susceptible-tomato-genotypes-regarding-to-late-blight
#7
Bruno Soares Laurindo, Renata Dias Freitas Laurindo, Patrícia Pereira Fontes, Camilo Elber Vital, Fábio Teixeira Delazari, Maria Cristina Baracat-Pereira, Derly José Henriques da Silva
Late blight is one of the most destructive diseases of the tomato, resulting in substantial economic losses. There is difficulty in controlling this disease, so the molecular characterization of tomato genotypes may help in the selection of higher resistance tomato plants against Phytophthora infestans, late blight's pathogen. The objective was to analyze the differences with regard to the constitutive proteome between the access Vegetable Germplasm Bank (BGH)-2127, resistant genotype, and Santa Clara-susceptible genotype to late blight...
August 30, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28735352/long-noncoding-rna-expression-profiles-in-chondrogenic-and-hypertrophic-differentiation-of-mouse-mesenchymal-stem-cells
#8
Zhen Cao, Song Huang, Jianmei Li, Yun Bai, Ce Dou, Chuan Liu, Fei Kang, Xiaoshan Gong, Haibin Ding, Tianyong Hou, Shiwu Dong
Long noncoding RNAs (lncRNAs) are important regulators for a variety of biological processes. Chondrogenic differentiation of mesenchymal stem cells (MSCs) is a crucial stage in chondrogenesis while chondrocyte hypertrophy is related to endochondral ossification and osteoarthritis. However, the effects of lncRNAs on chondrogenic and hypertrophic differentiation of mouse MSCs are unclear. To explore the potential mechanisms of lncRNAs during chondrogenesis and chondrocyte hypertrophy, microarray was performed to investigate the expression profiles of lncRNA and mRNA in MSCs, pre-chondrocytes, and hypertrophic chondrocytes...
July 22, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28735351/multiple-correlation-analyses-revealed-complex-relationship-between-dna-methylation-and-mrna-expression-in-human-peripheral-blood-mononuclear-cells
#9
Fang-Fei Xie, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Hong Zhu, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Xiao-Wei Zhu, Wei Xia, Lan Wang, Pei He, Peng-Fei Bing, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei
DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes...
July 22, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28687892/transcriptome-and-metabolome-analysis-of-ferula-gummosa-boiss-to-reveal-major-biosynthetic-pathways-of-galbanum-compounds
#10
Ahmad Sobhani Najafabadi, Mohammad Reza Naghavi, Hamid Farahmand, Alireza Abbasi
Ferula gummosa Boiss. is an industrial and pharmaceutical plant that has been highly recognized for its valuable oleo-gum-resin, namely galbanum. Despite the fabulous value of galbanum, very little information on the genetic and biochemical mechanisms of its production existed. In the present study, the oleo-gum-resin and four organs (root, flower, stem, and leaf) of F. gummosa were assessed in terms of metabolic compositions and the expression of genes involved in their biosynthetic pathways. Results showed that the most accumulation of resin and essential oils were occurred in the roots (13...
July 7, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28674744/ectopic-expression-of-csd1-and-csd2-targeting-genes-of-mir398-in-grapevine-is-associated-with-oxidative-stress-tolerance
#11
XiangPeng Leng, Peipei Wang, Xudong Zhu, Xiaopeng Li, Ting Zheng, Lingfei Shangguan, Jinggui Fang
MicroRNAs (miRNAs) are endogenous small RNAs of -21 nucleotides that play an important role in diverse plant physiological processes at the post-transcriptional level by directing mRNA cleavage or translational inhibition. Previous studies have indicated that down-regulation of miR398 in response to oxidative stress allows up-regulation of the two target genes, cytosolic CSD1 and chloroplastic CSD2 (copper/zinc superoxide dismutase), resulting in protecting the plants to tolerate oxidative stress. In this study, we provide evidence that grapevine miR398 (Vv-miR398), by regulating the expression of its target genes, VvCSD1 and VvCSD2, mediates responses of grapevine to copper (Cu) stress which have been magnified due to increase in Cu-containing pesticide application...
July 3, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28470340/comprehensive-strategy-for-the-design-of-precision-drugs-and-identification-of-genetic-signature-behind-proneness-of-the-disease-a-pharmacogenomic-approach
#12
REVIEW
Preethi M Iyer, S Karthikeyan, P Sanjay Kumar, P K Krishnan Namboori
The proneness of diseases and susceptibility towards drugs vary from person to person. At present, there is a strong demand for the personalization of drugs. The genetic signature behind proneness of the disease has been studied through a comprehensive 'octopodial approach'. All the genetic variants included in the approach have been introduced. The breast cancer associated with BRCA1 mutation has been taken as the illustrative example to introduce all these factors. The genetic variants associated with the drug action of tamoxifen have been fully illustrated in the manuscript...
July 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28285413/comprehensive-assessment-of-the-genes-involved-in-withanolide-biosynthesis-from-withania-somnifera-chemotype-specific-and-elicitor-responsive-expression
#13
Aditya Vikram Agarwal, Parul Gupta, Deeksha Singh, Yogeshwar Vikram Dhar, Deepak Chandra, Prabodh Kumar Trivedi
Withania somnifera (L.) Dunal (Family, Solanaceae), is among the most valuable medicinal plants used in Ayurveda owing to its rich reservoir of pharmaceutically active secondary metabolites known as withanolides. Withanolides are C28-steroidal lactones having a triterpenoidal metabolic origin synthesised via mevalonate (MVA) pathway and methyl-D-erythritol-4-phosphate (MEP) pathway involving metabolic intermediacy of 24-methylene (C30-terpenoid) cholesterol. Phytochemical studies suggest differences in the content and/or nature of withanolides in different tissues of different chemotypes...
July 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28236275/gene-expression-profiles-predictive-of-cold-induced-sweetening-in-potato
#14
Jonathan Neilson, M Lagüe, S Thomson, F Aurousseau, A M Murphy, B Bizimungu, V Deveaux, Y Bègue, J M E Jacobs, H H Tai
Cold storage (2-4 °C) used in potato production to suppress diseases and sprouting during storage can result in cold-induced sweetening (CIS), where reducing sugars accumulate in tuber tissue leading to undesirable browning, production of bitter flavors, and increased levels of acrylamide with frying. Potato exhibits genetic and environmental variation in resistance to CIS. The current study profiles gene expression in post-harvest tubers before cold storage using transcriptome sequencing and identifies genes whose expression is predictive for CIS...
July 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28224250/abscisic-acid-sucrose-and-auxin-coordinately-regulate-berry-ripening-process-of-the-fujiminori-grape
#15
Haifeng Jia, Zhenqiang Xie, Chen Wang, Lingfei Shangguan, Ning Qian, Mengjie Cui, Zhongjie Liu, Ting Zheng, Mengqi Wang, Jinggui Fang
The aim of this study was to examine the effect of abscisic acid (ABA), sucrose, and auxin on grape fruit development and to assess the mechanism of these three factors on the grape fruit ripening process. Different concentrations of ABA, sucrose, and auxin were used to treat the grape fruit, and the ripening-related indices, such as physiological and molecular level parameters, were analyzed. The activity of BG protein activity was analyzed during the fruit development. Sucrose, ABA, and auxin influenced the grape fruit sugar accumulation in different ways, as well as the volatile compounds, anthocyanin content, and fruit firmness...
July 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28190211/low-diversity-activity-and-density-of-transposable-elements-in-five-avian-genomes
#16
Bo Gao, Saisai Wang, Yali Wang, Dan Shen, Songlei Xue, Cai Chen, Hengmi Cui, Chengyi Song
In this study, we conducted the activity, diversity, and density analysis of transposable elements (TEs) across five avian genomes (budgerigar, chicken, turkey, medium ground finch, and zebra finch) to explore the potential reason of small genome sizes of birds. We found that these avian genomes exhibited low density of TEs by about 10% of genome coverages and low diversity of TEs with the TE landscapes dominated by CR1 and ERV elements, and contrasting proliferation dynamics both between TE types and between species were observed across the five avian genomes...
July 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28190210/identification-and-functional-characterization-of-four-novel-aldo-keto-reductases-in-anabaena-sp-pcc-7120-by-integrating-wet-lab-with-in-silico-approaches
#17
Chhavi Agrawal, Shivam Yadav, Shweta Rai, Antra Chatterjee, Sonia Sen, Ruchi Rai, L C Rai
Aldo/keto reductases (AKRs) constitute a multitasking protein family that catalyzes diverse metabolic transformations including detoxification of stress generated reactive aldehydes. Yet this important protein family is poorly understood particularly in cyanobacteria, the ecologically most diverse and significant group of micro-organisms. Present study is an attempt to characterize all putative AKRs of Anabaena sp. PCC 7120. In silico analysis, it revealed the presence of at least four putative AKRs in Anabaena PCC7120 genome...
July 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28011999/transcriptome-response-and-developmental-implications-of-rnai-mediated-odc-knockdown-in-tobacco
#18
Ami Choubey, M V Rajam
Polyamines (PAs) are ubiquitously present polycationic compounds that play a critical role in various growth and developmental processes including stress responses in plants. Yet, their specific functions and mode of action remain largely unknown. In the present study, we have targeted tobacco ornithine decarboxylase gene (ODC) by RNA interference to modulate cellular PA levels and study the effects at different developmental time points. Down-regulation of ODC resulted in significant physiological and morphological anomalies including reduced leaf size, reduced chlorophyll and carotene content, decreased abiotic stress tolerance, early onset of senescence, delayed flowering, partial male and female sterility, reduced seed setting, delayed seed germination, reduced seed viability, and poor in vitro regeneration response from leaf explants...
July 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27999965/genotypic-dependent-effects-of-n-fertilizer-glutathione-silicon-zinc-and-selenium-on-proteomic-profiles-amino-acid-contents-and-quality-of-rice-genotypes-with-contrasting-grain-cd-accumulation
#19
Fangbin Cao, Manman Fu, Runfeng Wang, Wangda Cheng, Guoping Zhang, Feibo Wu
Soil heavy metal (HM) contamination has posed a serious problem for safe food production. For restricting the translocation of HM into grain, many proteins were regulated to involve in the process. To identify these proteins, 2D-based proteomic analysis was carried out using different rice genotypes with distinct Cd accumulation in grains and as affected by an alleviating regulator (AR) in field experiments. AR application improved grain quality, with increased contents in Glu, Cys, His, Pro, and protein. Twenty-six low-grain HM accumulation-associated protein species were identified and categorized as physiological functions via two-dimensional gel electrophoresis (2DE) and mass spectrometry...
July 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28612136/identification-of-two-novel-chicken-gpr133-variants-and-their-expression-in-different-tissues
#20
Kai Tian, Qihai Xiao, Xueyou Zhang, Xi Lan, Xiaoling Zhao, Yan Wang, Diyan Li, Huadong Yin, Lin Ye, Qing Zhu
GPR133 (G protein-coupled receptor 133) plays significant roles in various physiological processes. Alternatively splicing (AS) variants of GPR133 in many species have been predicted in multiple databases, but there is no available information about the AS events of chicken GPR133 (cGPR133). In the present study, two chicken GPR133 variants, cGPR133-va and cGPR133-vb, were identified by a combination of reverse transcription PCR (RT-PCR) and rapid amplification of cDNA 5'-ends (5' RACE). Sequence analysis shows that cGPR133-va and cGPR133-vb are resulting from different AS modules and their sequences are predicted to encode two distinct putative proteins, respectively...
June 14, 2017: Functional & Integrative Genomics
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