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Genomics

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https://www.readbyqxmd.com/read/28502702/deep-sequencing-reveals-complex-mechanisms-of-microrna-regulation-during-retinoic-acid-induced-neuronal-differentiation-of-mesenchymal-stem-cells
#1
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
#2
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
#3
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
#4
Shuhui Liu, Guangcan Chen, Haihua Huang, Wengting Lin, Guo Dan, Zhao Shukun, 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 6, 2017: Genomics
https://www.readbyqxmd.com/read/28487172/prediction-of-vaccine-candidates-against-pseudomonas-aeruginosa-an-integrated-genomics-and-proteomics-approach
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28435087/the-complete-mitochondrial-genome-of-clostera-anachoreta-lepidoptera-notodontidae-and-phylogenetic-implications-for-noctuoidea-species
#13
Xiao-Yu Zhu, Zhao-Zhe Xin, Ying Wang, Hua-Bin Zhang, Dai-Zhen Zhang, Zheng-Fei Wang, Chun-Lin Zhou, Bo-Ping Tang, Qiu-Ning Liu
In this study, the complete mitochondrial genome (mitogenome) of Clostera anachoreta (Lepidoptera: Notodontidae) was sequenced. It comprises 15,456 base pairs (bp), including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNA), 22 transfer RNAs (tRNA) and one non-coding control region (CR), as found in other lepidopterans. Gene order is identical to that of typical lepidopterans. There are 15 intergenic spacers ranging from 1 to 49bp, and 9 overlapping regions ranging from 1 to 8bp, occurring throughout the genome...
April 20, 2017: Genomics
https://www.readbyqxmd.com/read/28365388/comparative-analysis-of-mbd-seq-and-medip-seq-and-estimation-of-gene-expression-changes-in-a-rodent-model-of-schizophrenia
#14
Jennifer L Neary, Stephanie M Perez, Kara Peterson, Daniel J Lodge, Melanie A Carless
We conducted a comparative study of multiplexed affinity enrichment sequence methodologies (MBD-seq and MeDIP-seq) in a rodent model of schizophrenia, induced by in utero methylazoxymethanol acetate (MAM) exposure. We also examined related gene expression changes using a pooled sample approach. MBD-seq and MeDIP-seq identified 769 and 1771 differentially methylated regions (DMRs) between F2 offspring of MAM-exposed rats and saline control rats, respectively. The assays showed good concordance, with ~56% of MBD-seq-detected DMRs being identified by or proximal to MeDIP-seq DMRs...
March 29, 2017: Genomics
https://www.readbyqxmd.com/read/28347827/computational-prediction-of-functional-abortive-rna-in-e-coli
#15
Jeremy I Marcus, Soha Hassoun, Nikhil U Nair
Failure by RNA polymerase to break contacts with promoter DNA results in release of bound RNA and re-initiation of transcription. These abortive RNAs were assumed to be non-functional but have recently been shown to affect termination in bacteriophage T7. Little is known about the functional role of these RNA in other genetic models. Using a computational approach, we investigated whether abortive RNA could exert function in E. coli. Fragments generated from 3780 transcription units were used as query sequences within their respective transcription units to search for possible binding sites...
March 24, 2017: Genomics
https://www.readbyqxmd.com/read/28315383/genetic-equidistance-at-nucleotide-level
#16
Dejian Yuan, Shi Huang
The genetic equidistance phenomenon shows complex taxa to be all approximately equidistant to a less complex species in amino acid percentage identity. The overlooked mystery was re-interpreted by the maximum genetic diversity hypothesis (MGD). Here, we studied 14 proteomes and their coding DNA sequences (CDS) to see if the equidistance phenomenon also holds at the CDS level. We found that the outgroup taxon was equidistant to the two more complex taxa species. When two sister taxa were compared to human as the outgroup, the more complex taxon was closer to human, confirming species complexity to be the primary determinant of MGD...
March 14, 2017: Genomics
https://www.readbyqxmd.com/read/28286147/evaluation-and-assessment-of-read-mapping-by-multiple-next-generation-sequencing-aligners-based-on-genome-wide-characteristics
#17
Subazini Thankaswamy-Kosalai, Partho Sen, Intawat Nookaew
Massive data produced due to the advent of next-generation sequencing (NGS) technology is widely used for biological researches and medical diagnosis. The crucial step in NGS analysis is read alignment or mapping which is computationally intensive and complex. The mapping bias tends to affect the downstream analysis, including detection of polymorphisms. In order to provide guidelines to the biologist for suitable selection of aligners; we have evaluated and benchmarked 5 different aligners (BWA, Bowtie2, NovoAlign, Smalt and Stampy) and their mapping bias based on characteristics of 5 microbial genomes...
March 9, 2017: Genomics
https://www.readbyqxmd.com/read/28286146/altered-gene-expression-in-late-onset-alzheimer-s-disease-due-to-snps-within-3-utr-microrna-response-elements
#18
Jyoti Roy, Bibekanand Mallick
Late-onset Alzheimer's disease (LOAD) is a progressive and fatal neurodegenerative disease found in people older than 65years of age. Disease etiology is complex, as susceptibility has been linked to multiple gene variants conferred by single nucleotide polymorphisms (SNPs). However, the molecular mechanisms by which SNPs contribute to LOAD pathogenesis have not been extensively studied, particularly for SNPs within the 3' untranslated regions (3'UTRs), the hubs for microRNA binding. Therefore, we screened for SNPs within the 3'UTRs of LOAD-associated genes that may create or destroy microRNA response elements (MREs) and thus alter gene expression...
March 9, 2017: Genomics
https://www.readbyqxmd.com/read/28263792/a-genomic-approach-to-susceptibility-and-pathogenesis-leads-to-identifying-potential-novel-therapeutic-targets-in-androgenetic-alopecia
#19
R Dey-Rao, A A Sinha
We studied genome-wide gene expression from bald and haired scalp of individuals to evaluate pathogenic mechanisms underlying the development and progression of androgenetic alopecia (AGA). Unbiased analyses revealed a "bald pathology" based signature. Ontology enrichment analyses of the differentially expressed genes (DEGs) underscored apoptosis, cell proliferation, perturbed neurological pathways, and WNT signaling as central drivers of the hair loss process. Interactome analysis uncovered several known and novel key transcriptional regulators potentially affecting disease pathogenesis both within and "hidden" from the dataset...
March 2, 2017: Genomics
https://www.readbyqxmd.com/read/28235564/candidate-novel-long-noncoding-rnas-micrornas-and-putative-drugs-for-parkinson-s-disease-using-a-robust-and-efficient-genome-wide-association-study
#20
Zahra Mortezaei, Hossein Lanjanian, Ali Masoudi-Nejad
Parkinson's disease (PD) is a neurodegenerative disorder with serious symptoms of which, are not clearly demonstrated at the beginning stages of the disease, making treatment challenging. Understanding the genetic causes of PD can be useful for determining its mechanisms and proposing treatments and preventive methods. For different populations with different genetic backgrounds and lifestyles, genome-wide association studies (GWASs) represent a crucial approach for genetic analysis. In this study, a robust and efficient GWAS without dimensionality reduction applied to evaluate heritability and genetic causes of PD in the German and US populations...
February 21, 2017: Genomics
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