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https://www.readbyqxmd.com/read/29677564/-omic-technologies-as-a-helpful-tool-in-radioecological-research
#1
REVIEW
Polina Yu Volkova, Stanislav A Geras'kin
This article presents a brief review of the modern 'omic' technologies, namely genomics, epigenomics, transcriptomics, proteomics, and metabolomics, as well as the examples of their possible use in radioecology. For each technology, a short description of advances, limitations, and instrumental applications is given. In addition, the review contains examples of successful use of 'omic' technologies in the assessment of biological effects of pollutants in the field conditions.
April 17, 2018: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/29677560/effective-discovery-of-rare-variants-by-pooled-target-capture-sequencing-a-comparative-analysis-with-individually-indexed-target-capture-sequencing
#2
Seungjin Ryu, Jeehae Han, Trina M Norden-Krichmar, Nicholas J Schork, Yousin Suh
Identification of all genetic variants associated with complex traits is one of the most important goals in modern human genetics. Genome-wide association studies (GWAS) have been successfully applied to identify common variants, which thus far explain only small portion of heritability. Interests in rare variants have been increasingly growing as an answer for this missing heritability. While next-generation sequencing allows detection of rare variants, its cost is still prohibitively high to sequence a large number of human DNA samples required for rare variant association studies...
March 30, 2018: Mutation Research
https://www.readbyqxmd.com/read/29677511/an-integrated-genome-wide-crispra-approach-to-functionalize-lncrnas-in-drug-resistance
#3
Assaf C Bester, Jonathan D Lee, Alejandro Chavez, Yu-Ru Lee, Daphna Nachmani, Suhani Vora, Joshua Victor, Martin Sauvageau, Emanuele Monteleone, John L Rinn, Paolo Provero, George M Church, John G Clohessy, Pier Paolo Pandolfi
Resistance to chemotherapy plays a significant role in cancer mortality. To identify genetic units affecting sensitivity to cytarabine, the mainstay of treatment for acute myeloid leukemia (AML), we developed a comprehensive and integrated genome-wide platform based on a dual protein-coding and non-coding integrated CRISPRa screening (DICaS). Putative resistance genes were initially identified using pharmacogenetic data from 760 human pan-cancer cell lines. Subsequently, genome scale functional characterization of both coding and long non-coding RNA (lncRNA) genes by CRISPR activation was performed...
April 19, 2018: Cell
https://www.readbyqxmd.com/read/29677510/physiological-and-genetic-adaptations-to-diving-in-sea-nomads
#4
Melissa A Ilardo, Ida Moltke, Thorfinn S Korneliussen, Jade Cheng, Aaron J Stern, Fernando Racimo, Peter de Barros Damgaard, Martin Sikora, Andaine Seguin-Orlando, Simon Rasmussen, Inge C L van den Munckhof, Rob Ter Horst, Leo A B Joosten, Mihai G Netea, Suhartini Salingkat, Rasmus Nielsen, Eske Willerslev
Understanding the physiology and genetics of human hypoxia tolerance has important medical implications, but this phenomenon has thus far only been investigated in high-altitude human populations. Another system, yet to be explored, is humans who engage in breath-hold diving. The indigenous Bajau people ("Sea Nomads") of Southeast Asia live a subsistence lifestyle based on breath-hold diving and are renowned for their extraordinary breath-holding abilities. However, it is unknown whether this has a genetic basis...
April 19, 2018: Cell
https://www.readbyqxmd.com/read/29677504/multi-regional-sequencing-elucidates-the-evolution-of-clear-cell-renal-cell-carcinoma
#5
Christopher J Ricketts, W Marston Linehan
Extensive multi-regional whole-genome and -exome sequencing performed in tumors from patients with localized, as well as metastatic, clear cell renal cell carcinoma provides a comprehensive description of the tumor origin, intratumoral heterogeneity, evolution, and route to metastasis, laying the foundation for the development of precision clinical management.
April 19, 2018: Cell
https://www.readbyqxmd.com/read/29677478/unfinished-business-evolution-of-the-mhc-and-the-adaptive-immune-system-of-jawed-vertebrates
#6
Jim Kaufman
The major histocompatibility complex (MHC) is a large genetic region with many genes, including the highly polymorphic classical class I and II genes that play crucial roles in adaptive as well as innate immune responses. The organization of the MHC varies enormously among jawed vertebrates, but class I and II genes have not been found in other animals. How did the MHC arise, and are there underlying principles that can help us to understand the evolution of the MHC? This review considers what it means to be an MHC and the potential importance of genome-wide duplication, gene linkage, and gene coevolution for the emergence and evolution of an adaptive immune system...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29677463/a-role-for-collagen-iv-in-cardiovascular-disease
#7
Lasse Bach Steffensen, Lars M Rasmussen
Over the past decade, studies have repeatedly found single nucleotide polymorphisms located in the COL4A1 and COL4A2 genes to be associated with cardiovascular disease (CVD), and the 13q34 locus harboring these genes is one of approximately 160 genome-wide significant risk loci for coronary artery disease. COL4A1 and COL4A2 encode the ⍺1- and ⍺2-chains of collagen IV, a major component of basement membranes in various tissues including arteries. In spite of the growing body of evidence indicating a role for collagen IV in CVD, remarkably few studies aim at directly investigating such a role...
April 20, 2018: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/29677450/complete-programmable-decoding-of-oxidized-5-methylcytosine-nucleobases-in-dna-by-chemoselective-blockage-of-universal-tale-binders
#8
Mario Giess, Anna Witte, Julia Jasper, Oliver Koch, Daniel Summerer
5-methylcytosine (5mC) and its oxidized derivatives are regulatory elements of mammalian genomes involved in development and disease. These nucleobases do not selectively modulate Watson-Crick pairing, preventing their programmable targeting and analysis by traditional hybridiza-tion probes. Transcription-activator-like effectors (TALEs) can be engineered for use as programmable probes with epi-genetic nucleobase selectivity. However, only partial selectivi-ties for oxidized 5mC have been achieved so far, preventing unambiguous target binding...
April 20, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29677397/two-ancestral-genes-shaped-the-xanthomonas-campestris-tal-effector-gene-repertoire
#9
Nicolas Denancé, Boris Szurek, Erin L Doyle, Emmanuelle Lauber, Lisa Fontaine-Bodin, Sébastien Carrère, Endrick Guy, Ahmed Hajri, Aude Cerutti, Tristan Boureau, Stéphane Poussier, Matthieu Arlat, Adam J Bogdanove, Laurent D Noël
Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome)...
April 20, 2018: New Phytologist
https://www.readbyqxmd.com/read/29677353/humoral-immune-response-after-intravitreal-but-not-after-subretinal-aav8-in-primates-and-patients
#10
Felix F Reichel, Tobias Peters, Barbara Wilhelm, Martin Biel, Marius Ueffing, Bernd Wissinger, Karl U Bartz-Schmidt, Reinhild Klein, Stylianos Michalakis, M Dominik Fischer
Purpose: To study longitudinal changes of anti-drug antibody (ADA) titers to recombinant adeno-associated virus serotype 8 (rAAV8) capsid epitopes in nonhuman primates (NHP) and patients. Methods: Three groups of six NHP each received subretinal injections (high dose: 1 × 1012 vector genomes [vg], low dose: 1 × 1011 vg, or vehicle only). Four additional animals received intravitreal injections of the high dose (1 × 1012 vg). Three patients received 1 × 1010 vg as subretinal injections...
April 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29677208/modeling-the-dynamics-and-kinetics-of-hiv-1-gag-during-viral-assembly
#11
Michael D Tomasini, Daniel S Johnson, Joshua S Mincer, Sanford M Simon
We report a computational model for the assembly of HIV-1 Gag into immature viral particles at the plasma membrane. To reproduce experimental structural and kinetic properties of assembly, a process occurring on the order of minutes, a coarse-grained representation consisting of a single particle per Gag molecule is developed. The model uses information relating the functional interfaces implicated in Gag assembly, results from cryo electron-tomography, and biophysical measurements from fluorescence microscopy, such as the dynamics of Gag assembly at single virions...
2018: PloS One
https://www.readbyqxmd.com/read/29677189/progress-in-the-pharmacological-treatment-of-human-cystic-and-alveolar-echinococcosis-compounds-and-therapeutic-targets
#12
Mar Siles-Lucas, Adriano Casulli, Roberto Cirilli, David Carmena
Human cystic and alveolar echinococcosis are helmintic zoonotic diseases caused by infections with the larval stages of the cestode parasites Echinococcus granulosus and E. multilocularis, respectively. Both diseases are progressive and chronic, and often fatal if left unattended for E. multilocularis. As a treatment approach, chemotherapy against these orphan and neglected diseases has been available for more than 40 years. However, drug options were limited to the benzimidazoles albendazole and mebendazole, the only chemical compounds currently licensed for treatment in humans...
April 20, 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29677183/divergent-genome-evolution-caused-by-regional-variation-in-dna-gain-and-loss-between-human-and-mouse
#13
Reuben M Buckley, R Daniel Kortschak, David L Adelson
The forces driving the accumulation and removal of non-coding DNA and ultimately the evolution of genome size in complex organisms are intimately linked to genome structure and organisation. Our analysis provides a novel method for capturing the regional variation of lineage-specific DNA gain and loss events in their respective genomic contexts. To further understand this connection we used comparative genomics to identify genome-wide individual DNA gain and loss events in the human and mouse genomes. Focusing on the distribution of DNA gains and losses, relationships to important structural features and potential impact on biological processes, we found that in autosomes, DNA gains and losses both followed separate lineage-specific accumulation patterns...
April 20, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29677173/what-does-this-mutation-mean-the-tools-and-pitfalls-of-variant-interpretation-in-lymphoid-malignancies
#14
REVIEW
Guillermin Yann, Lopez Jonathan, Chabane Kaddour, Hayette Sandrine, Bardel Claire, Salles Gilles, Sujobert Pierre, Huet Sarah
High throughput sequencing (HTS) is increasingly important in determining cancer diagnoses, with subsequent prognostic and therapeutic implications. The biology of cancer is becoming increasingly deciphered and it is clear that therapy needs to be individually tailored. Whilst translational research plays an important role in lymphoid malignancies, few guidelines exist to guide biologists and routine laboratories through this constantly evolving field. In this article, we review the challenges of interpreting HTS in lymphoid malignancies and provide a toolkit to interpret single nucleotide variants obtained from HTS...
April 20, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29677156/divergent-roles-of-rpa-homologs-of-the-model-archaeon-halobacterium-salinarum-in-survival-of-dna-damage
#15
Jessica J Evans, Patrick E Gygli, Julienne McCaskill, Linda C DeVeaux
The haloarchaea are unusual in possessing genes for multiple homologs to the ubiquitous single-stranded DNA binding protein (SSB or replication protein A, RPA) found in all three domains of life. Halobacterium salinarum contains five homologs: two are eukaryotic in organization, two are prokaryotic and are encoded on the minichromosomes, and one is uniquely euryarchaeal. Radiation-resistant mutants previously isolated show upregulation of one of the eukaryotic-type RPA genes. Here, we have created deletions in the five RPA operons...
April 20, 2018: Genes
https://www.readbyqxmd.com/read/29677111/genome-characterization-of-a-pathogenic-porcine-rotavirus-b-strain-identified-in-buryat-republic-russia-in-2015
#16
Konstantin P Alekseev, Aleksey A Penin, Alexey N Mukhin, Kizkhalum M Khametova, Tatyana V Grebennikova, Anton G Yuzhakov, Anna S Moskvina, Maria I Musienko, Sergey A Raev, Alexandr M Mishin, Alexandr P Kotelnikov, Oleg A Verkhovsky, Taras I Aliper, Eugeny A Nepoklonov, Diana M Herrera-Ibata, Frances K Shepherd, Douglas G Marthaler
An outbreak of enteric disease of unknown etiology with 60% morbidity and 8% mortality in weaning piglets occurred in November 2015 on a farm in Buryat Republic, Russia. Metagenomic sequencing revealed the presence of rotavirus B in feces from diseased piglets while no other pathogens were identified. Clinical disease was reproduced in experimentally infected piglets, yielding the 11 RVB gene segments for strain Buryat15, with an RVB genotype constellation of G12-P[4]-I13-R4-C4-M4-A8-N10-T4-E4-H7. This genotype constellation has also been identified in the United States...
April 20, 2018: Pathogens
https://www.readbyqxmd.com/read/29677098/update-treatment-for-hbv-infection-and-persistent-risk-for-hepatocellular-carcinoma-prospect-for-an-hbv-cure
#17
REVIEW
Joseph Yoo, Hie-Won Hann, Robert Coben, Mitchell Conn, Anthony J DiMarino
Since the discovery of the hepatitis B virus (HBV) by Blumberg et al. in 1965, its genome, sequence, epidemiology, and hepatocarcinogenesis have been elucidated. Globally, hepatitis B virus (HBV) is still responsible for the majority of hepatocellular carcinoma (HCC). HCC is the sixth-most common cancer in the world and the second-most common cancer death. The ultimate goal of treating HBV infection is the prevention of HCC. Fortunately, anti-HBV treatment with nucleos(t)ide analogues (NAs), which began with lamivudine in 1998, has resulted in remarkable improvements in the survival of patients with chronic hepatitis B and a reduced incidence of HCC...
April 20, 2018: Diseases (Basel)
https://www.readbyqxmd.com/read/29677097/correction-kauppinen-a-miettinen-i-t-persistence-of-norovirus-gii-genome-in-drinking-water-and-wastewater-at-different-temperatures-pathogens-2017-6-4-48
#18
https://www.readbyqxmd.com/read/29676997/mining-tcga-database-for-genes-of-prognostic-value-in-glioblastoma-microenvironment
#19
Di Jia, Shenglan Li, Dali Li, Haipeng Xue, Dan Yang, Ying Liu
Glioblastoma (GBM) is one of the most deadly brain tumors. The convenient access to The Cancer Genome Atlas (TCGA) database allows for large-scale global gene expression profiling and database mining for potential correlation between genes and overall survival of a variety of malignancies including GBM. Previous reports have shown that tumor microenvironment cells and the extent of infiltrating immune and stromal cells in tumors contribute significantly to prognosis. Immune scores and stromal scores calculated based on the ESTIMATE algorithm could facilitate the quantification of the immune and stromal components in a tumor...
April 16, 2018: Aging
https://www.readbyqxmd.com/read/29676996/involvement-of-spata31-copy-number-variable-genes-in-human-lifespan
#20
Cemalettin Bekpen, Chen Xie, Almut Nebel, Diethard Tautz
The SPATA31 ( alias FAM75A) gene family belongs to the core duplicon families that are thought to have contributed significantly to hominoid evolution. It is also among the gene families with the strongest signal of positive selection in hominoids. It has acquired new protein domains in the primate lineage and a previous study has suggested that the gene family has expanded its function into UV response and DNA repair. Here we show that over-expression of SPATA31A1 in fibroblast cells leads to premature senescence due to interference with aging-related transcription pathways...
April 19, 2018: Aging
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