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https://www.readbyqxmd.com/read/29334241/transcriptional-regulation-on-the-gene-expression-signature-in-combined-allergic-rhinitis-and-asthma-syndrome
#1
Zhengdao Mao, Yujia Shi, Qi Cao, Yi Chen, Yun Sun, Zhiguang Liu, Qian Zhang, Mao Huang
AIM: This study was intended to evaluate transcriptional regulation of gene expression signatures in combined allergic rhinitis and asthma syndrome (CARAS). MATERIALS & METHODS: The blood samples of three patients with CARAS, three patients with allergic rhinitis and three normal controls were obtained. The cuffdiff, miRDeep2 and DEGseq were used to quantify the expression of genes and miRNAs, respectively. And p-value < 0.01 and false discovery rate < 0...
January 15, 2018: Epigenomics
https://www.readbyqxmd.com/read/29333267/type-1-diabetes-genome-wide-association-studies-not-to-be-lost-in-translation
#2
REVIEW
Flemming Pociot
Genetic studies have identified >60 loci associated with the risk of developing type 1 diabetes (T1D). The vast majority of these are identified by genome-wide association studies (GWAS) using large case-control cohorts of European ancestry. More than 80% of the heritability of T1D can be explained by GWAS data in this population group. However, with few exceptions, their individual contribution to T1D risk is low and understanding their function in disease biology remains a huge challenge. GWAS on its own does not inform us in detail on disease mechanisms, but the combination of GWAS data with other omics-data is beginning to advance our understanding of T1D etiology and pathogenesis...
December 2017: Clinical & Translational Immunology
https://www.readbyqxmd.com/read/29332309/how-have-leaves-of-mycoheterotrophic-plants-evolved-from-the-view-point-of-a-developmental-biologist
#3
Hirokazu Tsukaya
How mycoheterotrophs have evolved and how they are sustained are an enigma. Structural analyses of the plastid genome and phylogenetic analyses of mycoheterotrophs have been used to identify mycorrhizal fungi. Molecular genetic studies have also revealed the mechanism for plant-fungi interactions. However, the evolution of the small, scale-like vegetative leaves of mycoheterotrophs is unknown. As almost all genes determining leaf size affect the floral organ sizes, it is highly implausible that loss-of-function mutations in leaf size regulators caused the evolution of smaller foliage leaves in mycoheterotrophs...
January 14, 2018: New Phytologist
https://www.readbyqxmd.com/read/29332190/transcriptomic-profiling-of-developing-fiber-in-levant-cotton-gossypium-herbaceum-l
#4
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/29332143/conjunction-of-g-quadruplex-and-stem-loop-in-the-5-untranslated-region-of-mouse-hepatocyte-nuclear-factor-4-alpha1-mediates-strong-inhibition-of-protein-expression
#5
Shangdong Guo, Hong Lu
Hepatocyte nuclear factor 4-alpha (HNF4α) is a well-established master regulator of liver development and function. Restoration of HNF4α can treat multiple liver disorders and liver cancers. To date, HNF4α is still "undruggable" due to lack of known activating ligands. Thus, understanding the regulatory mechanism of HNF4α expression may help develop an alternative approach to modulate HNF4α protein levels. G-quadruplexes (G4) are non-canonical stable secondary structures discovered mostly in the promoters of oncogenes...
January 13, 2018: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/29331932/cnv-biology-in-neurodevelopmental-disorders
#6
REVIEW
Toru Takumi, Kota Tamada
Copy number variants (CNVs), characterized in recent years by cutting-edge technology, add complexity to our knowledge of the human genome. CNVs contribute not only to human diversity but also to different kinds of diseases including neurodevelopmental delay, autism spectrum disorder and neuropsychiatric diseases. Interestingly, many pathogenic CNVs are shared among these diseases. Studies suggest that pathophysiology of disease may not be simply attributed to a single driver gene within a CNV but also that multifactorial effects may be important...
January 10, 2018: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29331642/protein-adaptations-in-extremophiles-an-insight-into-extremophilic-connection-of-mycobacterial-proteome
#7
REVIEW
Ashutosh Kumar, Anwar Alam, Deeksha Tripathi, Mamta Rani, Hafeeza Khatoon, Saurabh Pandey, Nasreen Z Ehtesham, Seyed E Hasnain
The biological paradox about how extremophiles persist at extreme ecological conditions throws a fascinating picture of the enormous potential of a single cell to adapt to homeostatic conditions in order to propagate. Unicellular organisms face challenges from both environmental factors and the ecological niche provided by the host tissue. Although the existence of extremophiles and their physiological properties were known for a long time, availability of whole genome sequence has catapulted the study on mechanisms of adaptation and the underlying principles that have enabled these unique organisms to withstand evolutionary and environmental pressures...
January 10, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29330501/novel-endogenous-simian-retroviral-integrations-in-vero-cells-implications-for-quality-control-of-a-human-vaccine-cell-substrate
#8
Chisato Sakuma, Tsuyoshi Sekizuka, Makoto Kuroda, Fumio Kasai, Kyoko Saito, Masaki Ikeda, Toshiyuki Yamaji, Naoki Osada, Kentaro Hanada
African green monkey (AGM)-derived Vero cells have been utilized to produce various human vaccines. The Vero cell genome harbors a variety of simian endogenous type D retrovirus (SERV) sequences. In this study, a transcriptome analysis showed that DNA hypomethylation released the epigenetic repression of SERVs in Vero cells. Moreover, comparative genomic analysis of three Vero cell sublines and an AGM reference revealed that the genomes of the sublines have ~80 SERV integrations. Among them, ~60 integrations are present within all three cell sublines and absent from the reference sequence...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330500/integration-of-gwas-pathway-and-network-analyses-reveals-novel-mechanistic-insights-into-the-synthesis-of-milk-proteins-in-dairy-cows
#9
Sara Pegolo, Núria Mach, Yuliaxis Ramayo-Caldas, Stefano Schiavon, Giovanni Bittante, Alessio Cecchinato
The quantities and proportions of protein fractions have notable effects on the nutritional and technological value of milk. Although much is known about the effects of genetic variants on milk proteins, the complex relationships among the set of genes and pathways regulating the different protein fractions synthesis and secretion into milk in dairy cows are still not completely understood. We conducted genome-wide association studies (GWAS) for milk nitrogen fractions in a cohort of 1,011 Brown Swiss cows, which uncovered 170 significant single nucleotide polymorphism (SNPs), mostly located on BTA6 and BTA11...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330297/characterization-and-evidence-of-the-mir-888-cluster-as-a-novel-cancer-network-in-prostate
#10
Tsuyoshi Hasegawa, Garrison Glavich, Mary Pahuski, Aleena M Short, Oliver John Semmes, Lifang Yang, Vitold Galkin, Richard R Drake, Aurora Esquela-Kerscher
Prostate cancer afflicts 1 in 7 men and is the second leading cause of male cancer-related deaths in the United States. MicroRNAs (miRNAs), an extensive class of ~22 nucleotide non-coding RNAs, are often aberrantly expressed in tissues and fluids from prostate cancer patients but the mechanism of how specific miRNAs regulate prostate tumorigenesis and metastasis are poorly understood. Here, miR-888 was identified as a novel prostate factor that promotes proliferation and migration. miR-888 resides within a genomic cluster of 7 miRNA genes (mir-892c, mir-890, mir-888, mir-892a, mir-892b, mir-891b, mir-891a) on human chromosome Xq27...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330284/novel-intergenically-spliced-chimera-nfatc3-pla2g15-is-associated-with-aggressive-t-all-biology-and-outcome
#11
Jonathan Bond, Christine Tran Quang, Guillaume Hypolite, Mohamed Belhocine, Aurélie Bergon, Gaëlle Cordonnier, Jacques Ghysdael, Elizabeth Macintyre, Nicolas Boissel, Salvatore Spicuglia, Vahid Asnafi
Leukemias are frequently characterized by the expression of oncogenic fusion chimeras that normally arise due to chromosomal rearrangements. Intergenically-spliced chimeric RNAs (ISCs) are transcribed in the absence of structural genomic changes, and aberrant ISC expression is now recognized as a potential driver of cancer. To better understand these potential oncogenic drivers, high-throughput RNA-sequencing (RNA-seq) was performed on T-acute lymphoblastic leukemia (T-ALL) patient specimens (n=24) and candidate T-ALL-related ISCs were identified (n=55; a median of 4 per patient)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330282/population-dependent-intron-retention-and-dna-methylation-in-breast-cancer
#12
Dongwook Kim, Manu Shivakumar, Seonggyun Han, Michael S Sinclair, Youngji Lee, Yonglan Zheng, Olufunmilayo I Olopade, Dokyoon Kim, Younghee Lee
Regulation of gene expression by DNA methylation in gene promoter regions is well-studied; however, the effects of methylation in the gene body (exons and introns) on gene expression are comparatively understudied. Recently, hyper-methylation has been implicated in the inclusion of alternatively spliced exons; moreover, exon recognition can be enhanced by recruiting the methyl-CpG-binding protein (MeCP2) to hyper-methylated sites. This study examines if methylation status of an intron is correlated with how frequently the intron is retained during splicing using DNA methylation and RNA sequencing (RNA-seq) data from breast cancer tissue specimens in The Cancer Genome Atlas (TCGA)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330202/high-risk-tp53-mutations-are-associated-with-extra-nodal-extension-ene-in-oral-cavity-squamous-cell-carcinoma-oscc
#13
Vlad C Sandulache, Chieko Michikawa, Pranav Kataria, Frederico O Gleber-Netto, Diana Bell, Sanchit Trivedi, Xiayu Rao, Jing Wang, Mei Zhao, Samar A Jasser, Jeffrey N Myers, Curtis R Pickering
PURPOSE:   Development of extra-nodal extension (ENE) has been associated with poor survival in patients with oral cavity squamous cell carcinoma (OSCC). Here we sought to confirm the role of ENE as a poor prognostic factor, and identify genomic and epigenetic markers of ENE in order to develop a predictive model and improve treatment selection. EXPERIMENTAL DESIGN: An institutional cohort (University of Texas MD Anderson Cancer Center) was utilized to confirm the impact of ENE on clinical outcomes and evaluate the genomic signature of primary and ENE containing tissue...
January 12, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29330178/development-of-an-efficient-genome-editing-tool-in-bacillus-licheniformis-using-crispr-cas9-nickase
#14
Kaifeng Li, Dongbo Cai, Zhangqian Wang, Zhili He, Shouwen Chen
Bacillus strains are important industrial bacteria that can produce various biochemical products. However, low transformation efficiencies and a lack of effective genome editing tools have hindered its widespread application. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)/cas9 techniques have been utilized in many organisms as genome editing tools because of their high efficiency and easy manipulation. In this study, an efficient genome editing method was developed for Bacillus licheniformis using a CRISPR-Cas9 nickase integrated into the genome of B...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29329552/correction-to-linkage-whole-genome-sequence-and-biological-data-implicate-variants-in-rab10-in-alzheimer-s-disease-resilience
#15
Perry G Ridge, Celeste M Karch, Simon Hsu, Ivan Arano, Craig C Teerlink, Mark T W Ebbert, Josue D Gonzalez Murcia, James M Farnham, Anna R Damato, Mariet Allen, Xue Wang, Oscar Harari, Victoria M Fernandez, Rita Guerreiro, Jose Bras, John Hardy, Ronald Munger, Maria Norton, Celeste Sassi, Andrew Singleton, Steven G Younkin, Dennis W Dickson, Todd E Golde, Nathan D Price, Nilüfer Ertekin-Taner, Carlos Cruchaga, Alison M Goate, Christopher Corcoran, JoAnn Tschanz, Lisa A Cannon-Albright, John S K Kauwe
The original version of this article [1] unfortunately contained a typographical error. The 'Alzheimer's Disease Neuroimaging Initiative' was erroneously included as 'Alzheimer's Disease Neuroimaging Initative' in the author list of the article.
January 12, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29329372/enrichment-analysis-with-epiannotator
#16
Yoann Pageaud, Christoph Plass, Yassen Assenov
Motivation: Deciphering relevant biological insights from epigenomic data can be a challenging task. One commonly used approach is to perform enrichment analysis. However, finding, downloading and using the publicly available functional annotations requires time, programming skills and IT infrastructure. Here we describe the online tool EpiAnnotator for performing enrichment analyses on epigenomic data in a fast and user-friendly way. Results: EpiAnnotator is an R Package accompanied by a web interface...
January 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29328914/rewiring-of-the-fruit-metabolome-in-tomato-breeding
#17
Guangtao Zhu, Shouchuang Wang, Zejun Huang, Shuaibin Zhang, Qinggang Liao, Chunzhi Zhang, Tao Lin, Mao Qin, Meng Peng, Chenkun Yang, Xue Cao, Xu Han, Xiaoxuan Wang, Esther van der Knaap, Zhonghua Zhang, Xia Cui, Harry Klee, Alisdair R Fernie, Jie Luo, Sanwen Huang
Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes...
January 11, 2018: Cell
https://www.readbyqxmd.com/read/29328507/genetics-of-immune-mediated-inflammatory-diseases
#18
REVIEW
Trixy David, Stephanie Ling, Anne Barton
Immune-mediated inflammatory diseases (IMIDs) are characterised by dysregulation of the normal immune response, which leads to inflammation. Together, they account for a high disease burden in the population, given that they are usually chronic conditions with associated co-morbidities. Examples include systemic lupus erythematosus, rheumatoid arthritis, Crohn's disease and type 1 diabetes. Since the advent of genome-wide association studies, evidence of considerable genetic overlap in the loci predisposing to a wide range of IMIDs has emerged...
January 12, 2018: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/29328442/identification-of-differentially-expressed-genes-and-regulatory-relationships-in-huntington-s-disease-by-bioinformatics-analysis
#19
Xiaoyu Dong, Shuyan Cong
Huntington's disease (HD) is an inherited, progressive neurodegenerative disease caused by a CAG expansion in the huntingtin (HTT) gene; various dysfunctions of biological processes in HD have been proposed. However, at present the exact pathogenesis of HD is not fully understood. The present study aimed to explore the pathogenesis of HD using a computational bioinformatics analysis of gene expression. GSE11358 was downloaded from the Gene Expression Omnibus andthe differentially expressed genes (DEGs) in the mutant HTT knock‑in cell model STHdhQ111/Q111 were predicted...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328377/feature-genes-in-metastatic-breast-cancer-identified-by-metade-and-svm-classifier-methods
#20
Youlin Tuo, Ning An, Ming Zhang
The aim of the present study was to investigate the feature genes in metastatic breast cancer samples. A total of 5 expression profiles of metastatic breast cancer samples were downloaded from the Gene Expression Omnibus database, which were then analyzed using the MetaQC and MetaDE packages in R language. The feature genes between metastasis and non‑metastasis samples were screened under the threshold of P<0.05. Based on the protein‑protein interactions (PPIs) in the Biological General Repository for Interaction Datasets, Human Protein Reference Database and Biomolecular Interaction Network Database, the PPI network of the feature genes was constructed...
January 9, 2018: Molecular Medicine Reports
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