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Genomics

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https://www.readbyqxmd.com/read/30316740/secret-aar-a-web-server-to-assess-the-antigenic-density-of-proteins-and-homology-search-against-bacterial-and-parasite-secretome-proteins
#1
Fernanda Cornejo-Granados, Juan Manuel Hurtado-Ramírez, Rogelio Hernández-Pando, Adrián Ochoa-Leyva
The secretome refers to all the Excreted/Secreted (ES) proteins, and these are involved in critical biological processes, such as cell-cell communication, and host immune response. Recently, we introduced the abundance of antigenic regions (AAR) value to assess the protein antigenic density and to evaluate the antigenic potential of secretomes. Here, to facilitate the AAR calculation, we implemented it as a user-friendly webserver. We extended the webserver capabilities implementing a sequence-based tool for searching homologous proteins across secretomes, including experimental and predicted secretomes of Mycobacterium tuberculosis and Taenia solium...
October 11, 2018: Genomics
https://www.readbyqxmd.com/read/30316739/effects-of-polymethylmethacrylate-nanoplastics-on-dicentrarchus-labrax
#2
I Brandts, M Teles, A Tvarijonaviciute, M L Pereira, M A Martins, L Tort, M Oliveira
The present study aimed to evaluate the effects of ~45 nm nanoplastics (NPs) on the marine fish Dicentrarchus labrax after a short-term exposure. Animals were exposed to a concentration range of NPs for 96 h and liver, plasma and skin mucus sampled. Assessed endpoints included biochemical biomarkers and expression of genes related to lipid metabolism, immune system and general cell stress. Molecular signaling pathways related to lipid metabolism, pparα and pparγ were significantly increased after exposure to NPs...
October 11, 2018: Genomics
https://www.readbyqxmd.com/read/30315899/identification-of-dna-methylation-regulated-novel-host-genes-relevant-to-inhibition-of-virus-replication-in-porcine-pk15-cell-using-double-stranded-rna-mimics-and-dna-methyltransferase-inhibitor
#3
Xiaoshuo Wang, Hong Ao, Minyan Song, Lijing Bai, Weiyong He, Chuduan Wang, Ying Yu
During RNA viruses's replication, double-stranded RNA (dsRNA) is normally produced and induce host innate immune response. Most of gene activation due cytokine mediated but which are due to methylation mediated is still unknown. In the study, DNA methylome was integrated with our previous transcriptome data to investigate the differentially methylated regions and genes using MeDIP-chip technology. We found that the transcriptional expressions of 15, 37 and 18 genes were negatively related with their promoter DNA methylation levels in the cells treated by PolyI:C, Aza-CdR, as well as PolyI:C plus Aza-CdR, respectively, compared with the untreated cells...
October 10, 2018: Genomics
https://www.readbyqxmd.com/read/30312661/performance-evaluation-measures-for-protein-complex-prediction
#4
REVIEW
Asma Ivazeh, Javad Zahiri, Maseud Rahgozar, Sriganesh Srihari
Protein complexes play a dominant role in cellular organization and function. Prediction of protein complexes from the network of physical interactions between proteins (PPI networks) has thus become one of the important research areas. Recently, many computational approaches have been developed to identify these complexes. Various performance assessment measures have been proposed for evaluating the efficiency of these methods. However, there are many inconsistencies in the definitions and usage of the measures across the literature...
October 9, 2018: Genomics
https://www.readbyqxmd.com/read/30308223/snp-markers-for-the-genetic-characterization-of-mexican-shrimp-broodstocks
#5
Ricardo Perez-Enriquez, Diego Robledo, Ross D Houston, Raúl Llera-Herrera
Selective breeding of shrimp has major potential to enhance production traits, including growth and disease resistance. Genetic characterization of broodstock populations is a key element of breeding programs, as it enables decisions on inbreeding restrictions, family structure, and the potential use of genomic selection. Single Nucleotide Polymorphisms (SNPs) are suitable genetic markers for this purpose. A set of SNPs was developed to characterize commercial breeding stocks in Mexico. Individuals from local and imported lines were selected for sequencing using the nextRAD technique, resulting in the identification of 2619 SNPs...
October 8, 2018: Genomics
https://www.readbyqxmd.com/read/30304708/genomic-analysis-of-rna-seq-and-srna-seq-data-identifies-potential-regulatory-srnas-and-their-functional-roles-in-staphylococcus-aureus
#6
Devika Subramanian, Balu Bhasuran, Jeyakumar Natarajan
sRNAs are important post-transcriptional regulators in bacteria. The current study exploits potential of next-generation technology with computational analyses to develop a whole-genome sRNA-gene network for drug-resistant S. aureus by subjecting public expression-profiles to a novel analysis pipeline. Clustering and examination of the resultant global-interactome indicated a coordinated-regulation of numerous processes by various sRNAs with 9 sRNAs and 10 genes as potential hubs. 10 major sRNA-modules were annotated with various functions, among which a major module including of Rsa sRNAs was predicted to be a central regulatory unit...
October 7, 2018: Genomics
https://www.readbyqxmd.com/read/30300672/genome-wide-analysis-reveals-the-effects-of-artificial-selection-on-production-and-meat-quality-traits-in-qinchuan-cattle
#7
Chugang Mei, Hongcheng Wang, Qijun Liao, Rajwali Khan, Sayed Haidar Abbas Raza, Chunping Zhao, Hongbao Wang, Gong Cheng, Wanqiang Tian, Yaokun Li, Linsen Zan
A new strain of Qinchuan cattle (QNS) has been obtained after more than forty years of selective breeding, and it shows good performance and production traits. To characterize the genetic changes that have resulted from breeding, we sequenced 10 QNS and 10 of the original breed Qinchuan cattle (QCC) for the first time, with average of 12.5-fold depth. A total of 31,242,284 and 29,612,517 SNPs were identified in the QCC and QNS genomes, 47.81% and 44.36% of which were found to be novel, respectively. Furthermore, population structure analysis revealed the selection that these cattle had experienced...
October 6, 2018: Genomics
https://www.readbyqxmd.com/read/30292769/exploring-microrna-profiles-for-circadian-clock-and-flowering-development-regulation-in-himalayan-rhododendron
#8
Shruti Choudhary, Sapna Thakur, Aasim Majeed, Pankaj Bhardwaj
miRNA is a non-coding, yet crucial entity in remodeling the genetic architecture. Rhododendron arboreum of Himalayas grows and even flower under fluctuating climate. sRNA from leaves of vegetative and reproductive periods was sequenced to elucidate its seasonal associations. Conserved (256) and novel (210) miRNAs and their precursors were located based on homology with plant databases and transcriptome of the species. 27,139 predicted targets were involved with metabolism, reproduction, and response to abiotic stimuli...
October 4, 2018: Genomics
https://www.readbyqxmd.com/read/30287403/a-powerful-method-to-integrate-genotype-and-gene-expression-data-for-dissecting-the-genetic-architecture-of-a-disease
#9
Sarmistha Das, Partha Pratim Majumder, Raghunath Chatterjee, Aditya Chatterjee, Indranil Mukhopadhyay
To decipher the genetic architecture of human disease, various types of omics data are generated. Two common omics data are genotypes and gene expression. Often genotype data for a large number of individuals and gene expression data for a few individuals are generated due to biological and technical reasons, leading to unequal sample sizes for different omics data. Unavailability of standard statistical procedure for integrating such datasets motivates us to propose a two-step multi-locus association method using latent variables...
October 1, 2018: Genomics
https://www.readbyqxmd.com/read/30287402/pathogenicity-phylogenetic-relationship-and-ngs-based-identification-and-assembly-of-tumorigenic-agrobacterium-radiabacter-plasmidic-and-chromosomic-reads-isolated-from-prunus-duclcis
#10
Nesrine Nabi, Ahmed Ben Hafsa, Mohammed Salem Zellama, Maher Chaouachi
Although many Agrobacterium radiobacter strains have already been identified, only a few genomes of strains belonging to genomovar G4 have been sequenced so far. In this study, we report the first virulent genome sequence of Agrobacterium radiobacter strain tun 183, which is highly virulent to almond specie. The genome size was estimated to be 5.53 Mb, with 57.9%GC content. In total, 6486 genes encoding proteins and 61 genes encoding RNAs were identified in this genome. Comparisons with the available sequenced genomes of genomovar G4 as well as with other A...
October 1, 2018: Genomics
https://www.readbyqxmd.com/read/30287401/identification-and-comparative-analysis-of-the-mirna-expression-profiles-from-four-tissues-of-micropterus-salmoides-using-deep-sequencing
#11
Wangbao Gong, Yong Huang, Jun Xie, Guangjun Wang, Deguang Yu, Kai Zhang, Zhifei Li, Ermeng Yu, Jingjing Tian, Yun Zhu
In the present study, four small RNA libraries were constructed from an M. salmoides population and sequenced using deep sequencing technology. A total of 9,888,822; 8,519,365; 20,566,198; and 15,762,254 raw reads representing 666,097; 755,711; 978,923; and 840,175 unique sequences were obtained from the spleen, liver, kidney, and muscle libraries, respectively. As a result, 509 known miRNAs belonging to 143 families and 1157 novel miRNAs were identified. The miRNAs displayed diverse expression levels among the four libraries, among which most of the known miRNAs were expressed at higher levels than the novel miRNAs...
October 1, 2018: Genomics
https://www.readbyqxmd.com/read/30268779/genome-wide-differential-expression-of-long-noncoding-rnas-and-mrnas-in-ovarian-follicles-of-two-different-chicken-breeds
#12
Yongdong Peng, Li Chang, Yaqi Wang, Ruining Wang, Lulu Hu, Ziya Zhao, Liying Geng, Zhengzhu Liu, Yuanfang Gong, Jingshi Li, Xianglong Li, Chuansheng Zhang
Bashang long-tail chickens are an indigenous breed with dual purpose in China (meat and eggs) but have low egg laying performance. To improve the low egg laying performance, a genome-wide analysis of mRNAs and long noncoding RNAs (lncRNAs) from Bashang long-tail chickens and Hy-Line brown layers was performed. A total of 16,354 mRNAs and 8691 lncRNAs were obtained from ovarian follicles. Between the breeds, 160 mRNAs and 550 lncRNAs were found to be significantly differentially expressed. Integrated network analysis suggested some differentially expressed genes were involved in ovarian follicular development through oocyte meiosis, progesterone-mediated oocyte maturation, and the cell cycle...
September 27, 2018: Genomics
https://www.readbyqxmd.com/read/30267765/transcriptome-analysis-of-soybean-wrky-tfs-in-response-to-peronospora-manshurica-infection
#13
Hang Dong, Jie Tan, Mei Li, Yue Yu, Shirong Jia, Chong Zhang, Yuanhua Wu, Yuhui Liu
Soybean downy mildew (SDM) caused by Peronospora manshurica (Pm) is a common disease of soybean that occurs wherever soybean is grown. In order to provide new insights about the defense mechanism of soybean response to Pm infection, differential expression of WRKY transcription factors (TFs) in SDM-high resistant (HR) and SDM-high susceptible (HS) genotypes were analyzed in this study. Totally, 22 WRKY TFs were differentially expressed in HR and HS genotype, while 16 WRKY TFs were found to be specific in response to fungal inoculation...
September 27, 2018: Genomics
https://www.readbyqxmd.com/read/30261316/transcriptomic-evidence-of-adaptive-tolerance-to-high-environmental-ammonia-in-mudskippers
#14
Xinxin You, Jieming Chen, Chao Bian, Yunhai Yi, Zhiqiang Ruan, Jia Li, Xinhui Zhang, Hui Yu, Junmin Xu, Qiong Shi
Mudskippers are typical amphibious fishes and possess various strategies to ameliorate ammonia toxicity during exposure to environmental ammonia. The present study aimed to provide transcriptomic evidence through profiling the gill and liver transcriptomes of Boleophthalmus pectinirostris (BP) and Periophthalmus magnuspinnatus (PM), which were subjected to treatment with high environmental ammonia for up to 72 h. The results of gene function annotation showed that most of the differentially expressed genes were involved in metabolic pathways...
September 24, 2018: Genomics
https://www.readbyqxmd.com/read/30261315/proportions-of-resting-memory-t-cells-and-monocytes-in-blood-have-prognostic-significance-in-idiopathic-pulmonary-fibrosis
#15
Yao-Zhong Liu, Shigeki Saito, Gilbert F Morris, Charles A Miller, Jian Li, John J Lefante
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease characterized by progressive decline of lung function. Here, we tested the importance of differential proportions of blood immune cells to IPF clinical outcomes. We used Cibersort to deconvolute immune cell components based on PBMCs or whole blood IPF genomics datasets. We found that a higher proportion of resting memory (RM) T cells was associated with a better survival and a higher DLco (diffusing capacity for carbon monoxide) in IPF patients. The association was also found in opposite direction for monocytes...
September 24, 2018: Genomics
https://www.readbyqxmd.com/read/30248490/whole-genome-methylation-profiling-from-pbmcs-in-acute-exacerbation-copd-patients-with-good-and-poor-responses-to-corticosteroid-treatment
#16
Shih-Wei Lee, Hwa-Hwan Hwang, Paul Wei-Che Hsu, Tzu-Yi Chuang, Chi-Wei Liu, Lawrence Shih-Hsin Wu
Identifying heterogeneity in chronic obstructive pulmonary disease (COPD) phenotypes is important for the development of personalized medicine. Genome-wide analysis was used to compare the methylation levels of peripheral blood mononuclear cell (PBMC) samples from 24 acute-exacerbation (AE) COPD patients with good/poor response to corticosteroid therapy and 12 non-COPD controls. Pyrosequencing was employed to validate the genome-wide analysis. In the dataset specific to COPD patients with a good response, enrichment was identified for the following: genes in the Ubl conjugation pathway, nicotinamide nucleotide metabolism, the alkaloid metabolic process, and regulation of the glucose metabolic process...
September 21, 2018: Genomics
https://www.readbyqxmd.com/read/30248489/identification-of-genes-involved-in-steroid-alkaloid-biosynthesis-in-fritillaria-imperialis-via-de-novo-transcriptomics
#17
Mahsa Eshaghi, Behrouz Shiran, Hossein Fallahi, Rudabeh Ravash, Bojana Banović Đeri
Crown imperial (CI) has been used in traditional medicine. Today it is known that such beneficial effects are due to its richness in steroidal alkaloids (SA). Using de novo transcriptomics, orthologues/paralogues finder, phylogenetic analysis and tissue- and developmental stage-specific expression analysis, we identified ten genes and several TFs involved in the biosynthesis of SA in CI. The comparative analysis of ten genes expression profiles revealed the possibility of their co-regulation, which may imply the possibility of their organization in metabolic gene clusters...
September 21, 2018: Genomics
https://www.readbyqxmd.com/read/30248488/molecular-pathology-of-adverse-local-tissue-reaction-caused-by-metal-on-metal-implants-defined-by-rna-seq
#18
Christopher G Salib, Eric A Lewallen, Christopher R Paradise, Meagan E Tibbo, Joseph X Robin, William H Trousdale, Logan M Morrey, Jason Xiao, Travis W Turner, Afton K Limberg, Anthony G Jay, Roman Thaler, Amel Dudakovic, Joaquin Sanchez-Sotelo, Mark E Morrey, Daniel J Berry, David G Lewallen, Andre J van Wijnen, Matthew P Abdel
Total hip arthroplasty (THA) alleviates hip pain and improves joint function. Current implant design permits long-term survivorship of THAs, but certain metal-on-metal (MoM) articulations can portend catastrophic failure due to adverse local tissue reactions (ALTR). Here, we identified biological and molecular differences between periacetabular synovial tissues of patients with MoM THA failure undergoing revision THA compared to patients undergoing primary THA for routine osteoarthritis (OA). Analysis of tissue biopsies by RNA-sequencing (RNA-seq) revealed that MoM patient samples exhibit significantly increased expression of immune response genes but decreased expression of genes related to extracellular matrix (ECM) remodeling...
September 21, 2018: Genomics
https://www.readbyqxmd.com/read/30244142/identification-and-expression-analysis-of-phosphatidy-ethanolamine-binding-protein-pebp-gene-family-in-cotton
#19
Min Wang, Yangguang Tan, Caiping Cai, Baohong Zhang
The phosphatidy ethanolamine-binding proteins (PEBP) play an important role in controlling flower development and phase change. Here, a total of 61 PEBP genes were identified, in which 20, 21, 10, and 10 were from tetraploid Gossypium hirsutum (AD1) and G. barbadense (AD2), and diploid G. raimondii (D5) and G. arboreum (A2), respectively. In G. hirsutum, 20 identified PEBP genes were unevenly distributed on 12 chromosomes. The identified PEBP genes were classified into four groups (TFL1, MFT, FT and FT-like)...
September 20, 2018: Genomics
https://www.readbyqxmd.com/read/30244141/characterization-and-function-of-the-t-box-1-gene-in-chinese-giant-salamander-andrias-davidianus
#20
Qiaomu Hu, Yan Meng, Dan Wang, Haifeng Tian, Hanbing Xiao
We characterized the Andrias davidianus T-box 1 (Tbx1) gene. Tbx1 expression was high in testis and low in other examined tissues. Immunohistochemistry detected tbx1 expression in somatic and germ cells 62 days post-hatching (dph), prior to gonad differentiation. At 210 dph, after gonad differentiation, tbx1 was expressed in spermatogonia and testis somatic cells and in granulosa cells in ovary. Tbx1 expression was up-regulated in ovary after high temperature treatment. In the neomale, tbx1 expression showed a similar profile to normal males, and vice-versa for genetic male...
September 20, 2018: Genomics
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