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Genomics

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https://www.readbyqxmd.com/read/28634029/discovery-of-scors-anciently-derived-highly-conserved-gene-associated-repeats-in-stony-corals
#1
Huan Qiu, Ehud Zelzion, Hollie M Putnam, Ruth D Gates, Nicole E Wagner, Diane K Adams, Debashish Bhattacharya
Stony coral (Scleractinia) genomes are still poorly explored and many questions remain about their evolution and contribution to the success and longevity of reefs. We analyzed transcriptome and genome data from Montipora capitata, Acropora digitifera, and transcriptome data from 20 other coral species. To our surprise, we found highly conserved, anciently derived, Scleractinia COral-specific Repeat families (SCORs) that are abundant in all the studied lineages. SCORs form complex secondary structures and are located in untranslated regions and introns, but most abundant in intergenic DNA...
June 17, 2017: Genomics
https://www.readbyqxmd.com/read/28625866/genome-analysis-of-crude-oil-degrading-franconibacter-pulveris-strain-dj34-revealed-its-genetic-basis-for-hydrocarbon-degradation-and-survival-in-oil-contaminated-environment
#2
Siddhartha Pal, Anirban Kundu, Tirtha Das Banerjee, Balaram Mohapatra, Ajoy Roy, Riddha Manna, Pinaki Sar, Sufia K Kazy
Franconibacter pulveris strain DJ34, isolated from Duliajan oil fields, Assam, was characterized in terms of its taxonomic, metabolic and genomic properties. The bacterium showed utilization of diverse petroleum hydrocarbons and electron acceptors, metal resistance, and biosurfactant production. The genome (4,856,096bp) of this strain contained different genes related to the degradation of various petroleum hydrocarbons, metal transport and resistance, dissimilatory nitrate, nitrite and sulfite reduction, chemotaxy, biosurfactant synthesis, etc...
June 15, 2017: Genomics
https://www.readbyqxmd.com/read/28624536/microrna-dependent-regulation-of-metamorphosis-and-identification-of-micrornas-in-the-red-flour-beetle-tribolium-castaneum
#3
Wei Wu, Wenfeng Xiong, Chengjun Li, Mengfan Zhai, Yao Li, Fei Ma, Bin Li
To date, although some microRNAs (miRNAs) have been discovered in the holometabolism insect Tribolium castaneum, large numbers of miRNAs still require investigation. Knocking down Dicer-1 (Dcr-1) and Argonaute-1 (Ago-1) in late larvae impaired miRNA synthesis, affected the juvenile hormone pathway by up-regulating Methoprene-tolerant (Met) and Krüppel-homolog1 (Kr-h1) transcript levels, and resulted in a series of defects in T. castaneum development and metamorphosis. Thus, high-throughput Illumina/Solexa sequencing was performed with a mixed sample of eight key developmental stages of T...
June 14, 2017: Genomics
https://www.readbyqxmd.com/read/28579515/chrombisim-interactive-chromatin-biclustering-using-a-simple-approach
#4
Nighat Noureen, Hafiz Muhammad Zohaib, Muhammad Abdul Qadir, Sahar Fazal
Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics. We present ChromBiSim, an interactive tool for mining subsets of modifications from epigenomic profiles. ChromBiSim efficiently extracts biclusters with their genomic locations. It is the very first user interface based and multiple cell type handling tool for decoding the interplay of subsets of histone modifications combinations along their genomic locations...
June 1, 2017: Genomics
https://www.readbyqxmd.com/read/28579514/recognition-of-long-range-enhancer-promoter-interactions-by-adding-genomic-signatures-of-segmented-regulatory-regions
#5
Zhen-Xing Feng, Qian-Zhong Li
Enhancer-promoter interaction (EPI) is an important cis-regulatory mechanism in the regulation of tissue-specific gene expression. However, it still has limitation to precisely identity these interactions so far. In this paper, using diverse genomic features for various regulatory regions, we presented a computational approach to predict EPIs with improved accuracies. Meanwhile, we comprehensively studied more potential regulatory factors that are important to EPIs prediction, such as nucleosome occupancy, enhancer RNA; and found the cell line-specificity and region-specificity of the contributions of diverse regulatory signatures...
June 1, 2017: Genomics
https://www.readbyqxmd.com/read/28577791/plantenrichment-a-tool-for-enrichment-analysis-of-transposable-elements-in-plants
#6
Gökhan Karakülah, Aslı Suner
Transposable elements (TEs) are mobile DNA sequences that play roles in gene regulation, and have a potential to influence the expression of nearby genes by functioning as cis-regulatory sequences. However, bioinformatics tools facilitating analysis of the associations between TEs and nearby genes in plants are still lacking. We therefore reanalyzed the comprehensive annotation data of gene models and TEs of 11 plant species available in Ensembl Plants database, and built an up-to-date, unique tool called PlanTEnrichment, enabling enrichment analysis of TEs located within the upstream regions of a given gene list...
June 1, 2017: Genomics
https://www.readbyqxmd.com/read/28577792/genome-wide-analysis-of-gene-expression-of-ems-induced-short-fiber-mutant-ligon-lintless-y-liy-in-cotton-gossypium-hirsutum-l
#7
Marina Naoumkina, Efrem Bechere, David D Fang, Gregory N Thyssen, Christopher B Florane
In this work we describe a chemically-induced short fiber mutant cotton line, Ligon-lintless-y (liy), which is controlled by a single recessive locus and affects multiple traits, including height of the plant, and length and maturity of fiber. An RNAseq analysis was used to evaluate global transcriptional changes during cotton fiber development at 3, 8 and 16days post anthesis. We found that 613, 2629 and 3397 genes were significantly down-regulated, while 2700, 477 and 3260 were significantly up-regulated in liy at 3, 8 and 16 DPA...
May 31, 2017: Genomics
https://www.readbyqxmd.com/read/28533192/in-vitro-effects-of-reprogramming-factors-on-the-expressions-of-pluripotent-genes-and-cd34-gene-in-human-acute-promyelocytic-leukemia-hl-60-cells
#8
Liang-Fang Zhu, Min Xiao, Yong-Quan Chen, Ling-Yan Wang, Xiao-Feng Luo, Xiao-Hong Yuan, Jin-Hua Ren, Zhi-Zhe Chen, Jian-Da Hu, Ting Yang
OBJECTIVE: Our study aims to explore the in vitro effects of reprogramming factors on the expressions of pluripotent genes and CD34 gene in HL-60 cells. METHODS: According to the construction of retroviral vector LV-OSCK of reprogramming factors (Oct-4, Sox2, Klf4, c-Myc), 293T cells were transfected to detect virus titer. The endogenous pluripotent genes (Oct4, SOX2, c-Myc and Klf4) and CD34 mRNA and protein expressions were detected by AP staining, immunofluorescence staining, qRT-PCR and flow cytometry...
May 19, 2017: Genomics
https://www.readbyqxmd.com/read/28502702/deep-sequencing-reveals-complex-mechanisms-of-microrna-regulation-during-retinoic-acid-induced-neuronal-differentiation-of-mesenchymal-stem-cells
#9
Feihu Hu, Peng Xu, Bo Sun, Gaojun Teng, Zhongdang Xiao
Retinoic acid (RA) has an important role in nervous system development; exogenous RA could induce stem cells towards neural lineage cells. However, the miRNA regulation mechanism and biological process of this induction require further exploration. In this study, using high-throughput sequencing results, we evaluated the microRNA profiles of neurally differentiated adipose-derived mesenchymal stem cells (ASCs), summarized several crucial microRNAs that profoundly contributed to the differentiation process, and speculated that several miRNAs were likely to mimic RA or other factors to induce the neuronal differentiation of stem cells...
May 12, 2017: Genomics
https://www.readbyqxmd.com/read/28502701/fastpcr-an-in-silico-tool-for-fast-primer-and-probe-design-and-advanced-sequence-analysis
#10
Ruslan Kalendar, Bekbolat Khassenov, Erlan Ramanculov, Olga Samuilova, Konstantin I Ivanov
Polymerase chain reaction (PCR) is one of the most important laboratory techniques used in molecular biology, genetics and molecular diagnostics. The success of a PCR-based method largely depends on the correct nucleic acid sequence analysis in silico prior to a wet-bench experiment. Here, we report the development of an online Java-based software for virtual PCR on linear or circular DNA templates and multiple primer or probe search from large or small databases. Primer or probe sensitivity and specificity are predicted by searching a database to find sequences with an optimal number of mismatches, similarity and stability...
May 11, 2017: Genomics
https://www.readbyqxmd.com/read/28502783/evolution-expression-analysis-and-functional-verification-of-catharanthus-roseus-rlk1-like-kinase-crrlk1l-family-proteins-in-pear-pyrus-bretchneideri
#11
Xiaobing Kou, Kaijie Qi, Xin Qiao, Hao Yin, Xing Liu, Shaoling Zhang, Juyou Wu
The Catharanthus roseus RLK1-like kinase (CrRLK1L) family is involved in multiple processes during plant growth. However, little is known about CrRLK1L in the wood of the pear fruit tree Pyrus bretchneideri. In this study, 26 CrRLK1L gene members were identified in pear and were grouped into six subfamilies according to phylogenetic analyses. Evolutionary analysis indicated that recent whole genome duplication (WGD) and dispersed gene duplications may contribute to the expansion of the CrRLK1L gene family in pear...
May 10, 2017: Genomics
https://www.readbyqxmd.com/read/28487173/patrilineal-background-of-the-she-minority-population-from-chaoshan-fenghuang-mountain-an-isolated-mountain-region-in-china
#12
Shuhui Liu, Guangcan Chen, Haihua Huang, Wenting Lin, Dan Guo, Shukun Zhao, Dongping Tian, Min Su
The She ethnic minority population is distributed in southern China. The origin of the She population has been controversial. The purpose of this work was to investigate the genomic diversity of She. The Chaoshan She population living in the Chaoshan Fenghuang mountain is a relatively isolated population. We detected 14 Y chromosome biallelic markers (Y-SNPs) and 6 Y chromosome short tandem repeat (Y-STR) loci in Chaoshan She people. Y-SNP analysis showed the Chaoshan She was closely related to the Chaoshan Hakka, Chaoshanese, Tujia and Gaoshan national minority...
May 7, 2017: Genomics
https://www.readbyqxmd.com/read/28487172/prediction-of-vaccine-candidates-against-pseudomonas-aeruginosa-an-integrated-genomics-and-proteomics-approach
#13
Muhammad Ibrahim Rashid, Anam Naz, Amjad Ali, Saadia Andleeb
Pseudomonas aeruginosa is among top critical nosocomial infectious agents due to its persistent infections and tendency for acquiring drug resistance mechanisms. To date, there is no vaccine available for this pathogen. We attempted to exploit the genomic and proteomic information of P. aeruginosa though reverse-vaccinology approaches to unveil the prospective vaccine candidates. P. aeruginosa strain PAO1 genome was subjected to sequential prioritization approach following genomic, proteomics and structural analyses...
May 6, 2017: Genomics
https://www.readbyqxmd.com/read/28476431/identification-and-characterization-of-known-and-novel-micrornas-in-three-tissues-of-chinese-giant-salamander-base-on-deep-sequencing-approach
#14
Yong Huang, Hong Tao Ren, Jian Li Xiong, Xiao Chan Gao, Xi Hong Sun
MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although animal miRNAs have been extensively studied in model systems, less is known in other animal with limited genome sequence data, including Chinese giant salamander (Andrias davidianus). The identification of the full repertoire of miRNAs expressed in the liver, spleen and muscle of A. davidianus would significantly increase our understanding for physiological function of A. davidianus, in this ancient and endangered urodele amphibian...
May 2, 2017: Genomics
https://www.readbyqxmd.com/read/28476430/imprinted-control-regions-include-composite-dna-elements-consisting-of-the-zfp57-binding-site-overlapping-mll1-morphemes
#15
Minou Bina
Mammalian genomes include DNA segments that are imprinted (CpG-methylated) only on one of the two parental chromosomes, leading to parent-of-origin-specific gene expression. The process is regulated by Imprinting Control Regions (ICRs) and germline Differentially Methylated Regions (gDMRs). Previously, ZFP57 was shown to recognize a methylated hexanucleotide in ICRs to maintain allele-specific gene repression. In Bioinformatics analyses, I found that the hexamer occurred frequently in mouse chromosomal DNA, suggesting that beside the ZFP57 binding site (ZFBS), ICRs contained sequence features with unknown characteristics...
May 2, 2017: Genomics
https://www.readbyqxmd.com/read/28450240/correlation-of-fcgrt-genomic-structure-with-serum-immunoglobulin-albumin-and-farletuzumab-pharmacokinetics-in-patients-with-first-relapsed-ovarian-cancer
#16
Daniel J O'Shannessy, Katie Bendas, Charles Schweizer, Wenquan Wang, Earl Albone, Elizabeth B Somers, Susan Weil, Rhonda K Meredith, Jason Wustner, Luigi Grasso, Mark Landers, Nicholas C Nicolaides
Farletuzumab (FAR) is a humanized monoclonal antibody (mAb) that binds to folate receptor alpha. A Ph3 trial in ovarian cancer patients treated with carboplatin/taxane plus FAR or placebo did not meet the primary statistical endpoint. Subgroup analysis demonstrated that subjects with high FAR exposure levels (Cmin>57.6μg/mL) showed statistically significant improvements in PFS and OS. The neonatal Fc receptor (fcgrt) plays a central role in albumin/IgG stasis and mAb pharmacokinetics (PK). Here we evaluated fcgrt sequence and association of its promoter variable number tandem repeats (VNTR) and coding single nucleotide variants (SNV) with albumin/IgG levels and FAR PK in the Ph3 patients...
April 24, 2017: Genomics
https://www.readbyqxmd.com/read/28438488/whole-genome-sequencing-predicts-novel-human-disease-models-in-rhesus-macaques
#17
Benjamin N Bimber, Ranjani Ramakrishnan, Rita Cervera-Juanes, Ravi Madhira, Samuel M Peterson, Robert B Norgren, Betsy Ferguson
Rhesus macaques are an important pre-clinical model of human disease. To advance our understanding of genomic variation that may influence disease, we surveyed genome-wide variation in 21 rhesus macaques. We employed best-practice variant calling, validated with Mendelian inheritance. Next, we used alignment data from our cohort to detect genomic regions likely to produce inaccurate genotypes, potentially due to either gene duplication or structural variation between individuals. We generated a final dataset of >16 million high confidence variants, including 13 million in Chinese-origin rhesus macaques, an increasingly important disease model...
April 23, 2017: Genomics
https://www.readbyqxmd.com/read/28442363/the-global-expression-profiling-in-esophageal-squamous-cell-carcinoma
#18
Fuqiang Dai, Longyong Mei, Shenglan Meng, Zheng Ma, Wei Guo, Jinghai Zhou, Jingge Zhang
Esophageal squamous cell carcinoma (ESCC) is the dominant subtype of esophageal cancer worldwide. This study aimed to explore the aberrant global expression profiling and construct regulatory network in ESCC for understanding tumorigenesis of ESCC. The expression pattern of long non-coding RNA (lncRNA), microRNA (miRNA) and mRNA was measured by RNA-sequencing in ESCC. Differentially expressed lncRNAs/miRNAs/mRNAs (DELs/DEMs/DEMIs) were identified in ESCC. DEMIs-DEMs network was constructed; hsa-miR-424-5p and hsa-miR-450b-5p were the hub miRNAs in the network, which negatively regulated 19 and 17 DEMs...
April 22, 2017: Genomics
https://www.readbyqxmd.com/read/28438487/processdriver-a-computational-pipeline-to-identify-copy-number-drivers-and-associated-disrupted-biological-processes-in-cancer
#19
Brittany Baur, Serdar Bozdag
Copy number amplifications and deletions that are recurrent in cancer samples harbor genes that confer a fitness advantage to cancer tumor proliferation and survival. One important challenge in computational biology is to separate the causal (i.e., driver) genes from passenger genes in large, aberrated regions. Many previous studies focus on the genes within the aberration (i.e., cis genes), but do not utilize the genes that are outside of the aberrated region and dysregulated as a result of the aberration (i...
April 21, 2017: Genomics
https://www.readbyqxmd.com/read/28435088/improving-prediction-accuracy-using-decision-tree-based-meta-strategy-and-multi-threshold-sequential-voting-exemplified-by-mirna-target-prediction
#20
Bi Zhao, Bin Xue
Lots of computational predictors have been developed for fast and large-scale analysis of biological data. However, many of them were developed long time ago when training datasets or sets of input features were rather small. Consequently, the utility of these predictors in much large datasets, which are very common in nowadays, need to be examined carefully. In addition, with the rapid development of scientific research, the expectation on the prediction accuracy of computational predictors is continuously uplifting...
April 20, 2017: Genomics
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