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Functional & Integrative Genomics

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https://www.readbyqxmd.com/read/29332191/genome-wide-characterization-of-differentially-expressed-genes-provides-insights-into-regulatory-network-of-heat-stress-response-in-radish-raphanus-sativus-l
#1
Ronghua Wang, Yi Mei, Liang Xu, Xianwen Zhu, Yan Wang, Jun Guo, Liwang Liu
Heat stress (HS) causes detrimental effects on plant morphology, physiology, and biochemistry that lead to drastic reduction in plant biomass production and economic yield worldwide. To date, little is known about HS-responsive genes involved in thermotolerance mechanism in radish. In this study, a total of 6600 differentially expressed genes (DEGs) from the control and Heat24 cDNA libraries of radish were isolated by high-throughput sequencing. With Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, some genes including MAPK, DREB, ERF, AP2, GST, Hsf, and Hsp were predominantly assigned in signal transductions, metabolic pathways, and biosynthesis and abiotic stress-responsive pathways...
January 13, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29332190/transcriptomic-profiling-of-developing-fiber-in-levant-cotton-gossypium-herbaceum-l
#2
Mithil J Parekh, Sushil Kumar, Ranbir S Fougat, Harshvardhan N Zala, Ramesh J Pandit
Cotton (Gossypium spp.) is an imperative economic crop of the globe due to its natural textile fiber. Molecular mechanisms of fiber development have been greatly revealed in allotetraploid cotton but remained unexplored in Gossypium herbaceum. G. herbaceum can withstand the rigors of nature like drought and pests but produce coarse lint. This undesirable characteristic strongly needs the knowledge of fiber development at molecular basis. The present study reported the transcriptome sequence of the developing fiber of G...
January 13, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29322263/comparative-transcriptomic-analysis-of-skeletal-muscle-tissue-during-prenatal-stages-in-tongcheng-and-yorkshire-pig-using-rna-seq
#3
Huijing Liu, Yu Xi, Guorong Liu, Yuqiang Zhao, Ji Li, Minggang Lei
Myogenesis is accompanied by a number of changes in gene expression in mammals, and the transcriptional events that underlie these processes have not been yet fully elucidated. In this study, RNA-seq was used to comprehensively compare the transcription profiles of skeletal muscle between Tongcheng (TC) and Yorkshire (YK) pigs at 40, 55, 63, 70, and 90 days of gestation. One thousand three hundred seventeen and 691 differentially expressed genes (DEGs) were detected in TC and YK, respectively, among which 321 DEGs were shown to be common in TC and YK...
January 10, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29280022/molecular-characterization-and-expression-analysis-of-the-na-h-exchanger-gene-family-in-medicago-truncatula
#4
Devinder Sandhu, Manju V Pudussery, Rakesh Kaundal, Donald L Suarez, Amita Kaundal, Rajandeep S Sekhon
One important mechanism plants use to cope with salinity is keeping the cytosolic Na+ concentration low by sequestering Na+ in vacuoles, a process facilitated by Na+/H+ exchangers (NHX). There are eight NHX genes (NHX1 through NHX8) identified and characterized in Arabidopsis thaliana. Bioinformatics analyses of the known Arabidopsis genes enabled us to identify six Medicago truncatula NHX genes (MtNHX1, MtNHX2, MtNHX3, MtNHX4, MtNHX6, and MtNHX7). Twelve transmembrane domains and an amiloride binding site were conserved in five out of six MtNHX proteins...
December 26, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29275436/transcriptomic-profiles-of-the-bovine-mammary-gland-during-lactation-and-the-dry-period
#5
Wen-Ting Dai, Yi-Xuan Zou, Robin R White, Jian-Xin Liu, Hong-Yun Liu
The initiation and maintenance of lactation are complex phenomena governed by biochemical and endocrine processes in the mammary gland (MG). Although DNA-based approaches have been used to study the onset of lactation, more comprehensive RNA-based techniques may be critical in furthering our understanding of gene alterations that occur to support lactation in the bovine MG. To further determine how gene profiles vary during lactation compared with the dry period, RNA-seq transcriptomic analysis was used to identify differentially expressed genes (DEG) in bovine MG tissues from animals that were lactating and not lactating...
December 23, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29270875/physiological-and-transcriptomic-analyses-of-a-yellow-green-mutant-with-high-photosynthetic-efficiency-in-wheat-triticum-aestivum-l
#6
Yu Wang, Wei Zheng, Weijun Zheng, Jianchu Zhu, Zhenshan Liu, Jinxia Qin, Hongxia Li
Optimizing the antenna size by reducing the chlorophyll (Chl) content is an effective strategy to improve solar energy conversion efficiencies in dense crop monocultures. To elucidate the physiological and molecular mechanisms that regulate Chl biosynthesis and understand the effects of lower Chl content on the photosynthetic process, a light-intensity-dependent yellow-green wheat mutant (Jimai5265yg) was characterized to determine its morphological, histological, physiological, and transcriptional differences with wild type...
December 21, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29264749/effect-of-salt-stress-on-gene-expression-in-citrus-roots-revealed-by-rna-seq
#7
Rangjin Xie, Xiaoting Pan, Jing Zhang, Yanyan Ma, Shaolan He, Yongqiang Zheng, Yingtao Ma
Citrus, as one of the most economically important fruits worldwide, is adversely affected by salinity stress. However, its molecular mechanisms underlying salinity tolerance are still not clear. In this study, next-generation RNA-seq technology was applied to analyze the gene expression profiling of citrus roots at 3 time points over a 24-h period of salt treatment. A total of 1831 differentially expressed genes (DEGs) were identified. Among them, 1195 and 1090 DEGs were found at 4 and 24 h, of which 454 were overlapped...
December 20, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29260344/integrative-network-based-approach-identifies-central-genetic-and-transcriptomic-elements-in-triple-negative-breast-cancer
#8
Ramireddy Sriroopreddy, C Sudandiradoss
Triple-negative breast cancer (TNBC) has gained considerable attention as it oversteps about 15% of the deaths caused by breast cancer in women and is well known for its aggressive impact, high proliferation rate, intensity of tumor, and metastasis. In this study, we have given a new insight into TNBC, by introducing an integrative network methodology to understand the complexity of the candidate genes in TNBC. In the course of this analysis, the central network was constructed by refining the candidate genes present in the various databases...
December 19, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29250708/identification-characterization-expression-profiling-and-virus-induced-gene-silencing-of-armadillo-repeat-containing-proteins-in-tomato-suggest-their-involvement-in-tomato-leaf-curl-new-delhi-virus-resistance
#9
Arunava Mandal, Awdhesh Kumar Mishra, Priya Dulani, Mehanathan Muthamilarasan, Shweta Shweta, Manoj Prasad
Armadillo repeat family is well-characterized in several plant species for their involvement in multiple regulatory processes including growth, development, and stress response. We have previously shown a three-fold higher expression of ARM protein-encoding in tomato cultivar tolerant to tomato leaf curl New Delhi virus (ToLCNDV) compared to susceptible cultivar upon virus infection. This suggests the putative involvement of ARM proteins in defense response against virus infection; however, no comprehensive investigation has been performed to address this inference...
December 17, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29188477/crispr-cas9-mediated-efficient-editing-in-phytoene-desaturase-pds-demonstrates-precise-manipulation-in-banana-cv-rasthali-genome
#10
Navneet Kaur, Anshu Alok, Shivani, Navjot Kaur, Pankaj Pandey, Praveen Awasthi, Siddharth Tiwari
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has been reported for precise genome modification in many plants. In the current study, we demonstrate a successful mutation in phytoene desaturase (RAS-PDS) of banana cv. Rasthali using the CRISPR/Cas9 system. Two PDS genes were isolated from Rasthali (RAS-PDS1 and RAS-PDS2), and their protein sequence analysis confirmed that both PDS comprises conserved motifs for enzyme activity. Phylogenetic analysis of RAS-PDS1 and RAS-PDS2 revealed a close evolutionary relationship with other monocot species...
November 29, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29134405/cell-type-specific-gene-expression-patterns-in-the-knee-cartilage-in-an-osteoarthritis-rat-model
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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