keyword
MENU ▼
Read by QxMD icon Read
search

Essential genome

keyword
https://www.readbyqxmd.com/read/28339459/functional-classification-of-dna-variants-by-hybrid-minigenes-identification-of-30-spliceogenic-variants-of-brca2-exons-17-and-18
#1
Eugenia Fraile-Bethencourt, Beatriz Díez-Gómez, Valeria Velásquez-Zapata, Alberto Acedo, David J Sanz, Eladio A Velasco
Mutation screening of the breast cancer genes BRCA1 and BRCA2 identifies a large fraction of variants of uncertain clinical significance (VUS) whose functional and clinical interpretations pose a challenge for genomic medicine. Likewise, an increasing amount of evidence indicates that genetic variants can have deleterious effects on pre-mRNA splicing. Our goal was to investigate the impact on splicing of a set of reported variants of BRCA2 exons 17 and 18 to assess their role in hereditary breast cancer and to identify critical regulatory elements that may constitute hotspots for spliceogenic variants...
March 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28335576/genome-wide-identification-and-evolutionary-analysis-of-sarcocystis-neurona-protein-kinases
#2
Edwin K Murungi, Henry M Kariithi
The apicomplexan parasite Sarcocystis neurona causes equine protozoal myeloencephalitis (EPM), a degenerative neurological disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs) have been implicated in a myriad of critical functions, such as host cell invasion, cell cycle progression and host immune response evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans...
March 21, 2017: Pathogens
https://www.readbyqxmd.com/read/28335524/roles-of-cdk-and-ddk-in-genome-duplication-and-maintenance-meiotic-singularities
#3
REVIEW
Blanca Gómez-Escoda, Pei-Yun Jenny Wu
Cells reproduce using two types of divisions: mitosis, which generates two daughter cells each with the same genomic content as the mother cell, and meiosis, which reduces the number of chromosomes of the parent cell by half and gives rise to four gametes. The mechanisms that promote the proper progression of the mitotic and meiotic cycles are highly conserved and controlled. They require the activities of two types of serine-threonine kinases, the cyclin-dependent kinases (CDKs) and the Dbf4-dependent kinase (DDK)...
March 20, 2017: Genes
https://www.readbyqxmd.com/read/28335073/clinical-characteristics-and-whole-exome-transcriptome-sequencing-of-coexisting-chronic-myeloid-leukemia-and-myelofibrosis
#4
Malathi Kandarpa, Yi-Mi Wu, Dan Robinson, Patrick William Burke, Arul M Chinnaiyan, Moshe Talpaz
Myeloproliferative neoplasms (MPNs) are clonal hematopoietic stem cell (HSC) disorders that can be classified on the basis of genetic, clinical, phenotypic features. Genetic lesions such as JAK2 mutations and BCR-ABL translocation are often mutually exclusive in MPN patients and lead to essential thrombocythemia, polycythemia vera or myelofibrosis (ET/PV/MF) or chronic myeloid leukemia, respectively. Nevertheless, coexistence of these genetic aberrations in the same patient has been reported. Whether these aberrations occur in the same stem cell or a different cell is unclear, but an unstable genome in the HSCs seems to be the common antecedent...
March 23, 2017: American Journal of Hematology
https://www.readbyqxmd.com/read/28334807/allele-specific-quantitative-proteomics-unravels-molecular-mechanisms-modulated-by-cis-regulatory-pparg-locus-variation
#5
Heekyoung Lee, Kun Qian, Christine von Toerne, Lena Hoerburger, Melina Claussnitzer, Christoph Hoffmann, Viktoria Glunk, Simone Wahl, Michaela Breier, Franziska Eck, Leili Jafari, Sophie Molnos, Harald Grallert, Ingrid Dahlman, Peter Arner, Cornelia Brunner, Hans Hauner, Stefanie M Hauck, Helmut Laumen
Genome-wide association studies identified numerous disease risk loci. Delineating molecular mechanisms influenced by cis-regulatory variants is essential to understand gene regulation and ultimately disease pathophysiology. Combining bioinformatics and public domain chromatin information with quantitative proteomics supports prediction of cis-regulatory variants and enabled identification of allele-dependent binding of both, transcription factors and coregulators at the type 2 diabetes associated PPARG locus...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334774/high-tolerance-to-self-targeting-of-the-genome-by-the-endogenous-crispr-cas-system-in-an-archaeon
#6
Aris-Edda Stachler, Israela Turgeman-Grott, Ella Shtifman-Segal, Thorsten Allers, Anita Marchfelder, Uri Gophna
CRISPR-Cas systems allow bacteria and archaea to acquire sequence-specific immunity against selfish genetic elements such as viruses and plasmids, by specific degradation of invader DNA or RNA. However, this involves the risk of autoimmunity if immune memory against host DNA is mistakenly acquired. Such autoimmunity has been shown to be highly toxic in several bacteria and is believed to be one of the major costs of maintaining these defense systems. Here we generated an experimental system in which a non-essential gene, required for pigment production and the reddish colony color, is targeted by the CRISPR-Cas I-B system of the halophilic archaeon Haloferax volcanii...
March 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334373/estimating-error-models-for-whole-genome-sequencing-using-mixtures-of-dirichlet-multinomial-distributions
#7
Steven H Wu, Rachel S Schwartz, David J Winter, Donald F Conrad, Reed A Cartwright
Motivation: Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease, and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-numbervariation, paralogous sequences, library preparation, sequencing error, and reference-mapping biases, among others. Results: We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334120/svpv-a-structural-variant-prediction-viewer-for-paired-end-sequencing-datasets
#8
Jacob E Munro, Sally L Dunwoodie, Eleni Giannoulatou
Motivation: A wide range of algorithms exist for the prediction of structural variants (SVs) from paired-end whole genome sequencing (WGS) alignments. It is essential for the purpose of quality control to be able to visualize, compare and contrast the data underlying the predictions across multiple different algorithms. Results: We provide the structural variant prediction viewer, a tool which presents a visual summary of the most relevant features for SV prediction from WGS data...
February 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334079/how-do-cold-adapted-plants-respond-to-climatic-cycles-interglacial-expansion-explains-current-distribution-and-genomic-diversity-in-primula-farinosa-l
#9
Spyros Theodoridis, Christophe Randin, Peter Szövényi, Florian C Boucher, Theofania S Patsiou, Elena Conti
Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model...
December 21, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28333921/bioenergetics-based-modeling-of-plasmodium-falciparum-metabolism-reveals-its-essential-genes-nutritional-requirements-and-thermodynamic-bottlenecks
#10
Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati-Favre, Vassily Hatzimanikatis
Novel antimalarial therapies are urgently needed for the fight against drug-resistant parasites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this complexity and allow integrative analyses of cell metabolism. In this study, we present a genome-scale metabolic model (iPfa) of the deadliest malaria parasite, Plasmodium falciparum, and its thermodynamics-based flux analysis (TFA). Using previous absolute concentration data of the intraerythrocytic parasite, we applied TFA to iPfa and predicted up to 63 essential genes and 26 essential pairs of genes...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28332623/identification-and-characterization-of-the-abscisic-acid-aba-receptor-gene-family-and-its-expression-in-response-to-hormones-in-the-rubber-tree
#11
Dong Guo, Ying Zhou, Hui-Liang Li, Jia-Hong Zhu, Ying Wang, Xiong-Ting Chen, Shi-Qing Peng
Abscisic acid (ABA) is an essential phytohormone involved in diverse physiological processes. Although genome-wide analyses of the ABA receptor PYR/PYL/RCAR (PYL) protein/gene family have been performed in certain plant species, little is known about the ABA receptor protein/gene family in the rubber tree (Hevea brasiliensis). In this study, we identified 14 ABA receptor PYL proteins/genes (designated HbPYL1 through HbPYL14) in the most recent rubber tree genome. A phylogenetic tree was constructed, which demonstrated that HbPYLs can be divided into three subfamilies that correlate well with the corresponding Arabidopsis subfamilies...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28332257/exomic-variants-of-an-elderly-cohort-of-brazilians-in-the-abraom%C3%A2-database
#12
Michel Satya Naslavsky, Guilherme Lopes Yamamoto, Tatiana Ferreira de Almeida, Suzana A M Ezquina, Daniele Yumi Sunaga, Nam Pho, Daniel Bozoklian, Tatiana Orli Milkewitz Sandberg, Luciano Abreu Brito, Monize Lazar, Danilo Vicensotto Bernardo, Edson Amaro, Yeda A O Duarte, Maria Lúcia Lebrão, Maria Rita Passos-Bueno, Mayana Zatz
Brazilians are highly admixed with ancestry from Europe, Africa, America, and Asia yet still underrepresented in genomic databanks. We hereby present a collection of exomic variants from 609 elderly Brazilians in a census-based cohort (SABE609) with comprehensive phenotyping. Variants were deposited in ABraOM (Online Archive of Brazilian Mutations), a web-based public database. Population representative phenotype and genotype repositories are essential for variant interpretation through allele frequency filtering; since elderly individuals are less likely to harbor pathogenic mutations for early and adult-onset diseases, such variant databases are of great interest...
March 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28331549/dynamics-of-5-methylcytosine-and-5-hydroxymethylcytosine-during-pronuclear-development-in-equine-zygotes-produced-by-icsi
#13
Sonia Heras, Katrien Smits, Catharina De Schauwer, Ann Van Soom
BACKGROUND: Global epigenetic reprogramming is considered to be essential during embryo development to establish totipotency. In the classic model first described in the mouse, the genome-wide DNA demethylation is asymmetric between the paternal and the maternal genome. The paternal genome undergoes ten-eleven translocation (TET)-mediated active DNA demethylation, which is completed before the end of the first cell cycle. Since TET enzymes oxidize 5-methylcytosine to 5-hydroxymethylcytosine, the latter is postulated to be an intermediate stage toward DNA demethylation...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28331092/monkeypox-virus-host-factor-screen-in-haploid-cells-identifies-essential-role-of-garp-complex-in-extracellular-virus-formation
#14
Susan Realegeno, Andreas S Puschnik, Amrita Kumar, Cynthia Goldsmith, Jillybeth Burgado, Suryaprakash Sambhara, Victoria A Olson, Darin Carroll, Inger Damon, Tetsuya Hirata, Taroh Kinoshita, Jan E Carette, Panayampalli Subbian Satheshkumar
Monkeypox virus (MPXV) is a human pathogen that is a member of the Orthopoxvirus genus, which includes Vaccinia virus and Variola virus (the causative agent of smallpox). Human monkeypox is considered an emerging zoonotic infectious disease. To identify host factors required for MPXV infection, we performed a genome-wide insertional mutagenesis screen in human haploid cells. The screen revealed several candidate genes, including those involved in Golgi trafficking, glycosaminoglycan biosynthesis and glycosylphosphatidylinositol (GPI) - anchor biosynthesis...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28331049/achieving-precision-death-with-cell-cycle-inhibitors-that-target-dna-replication-and-repair
#15
Aimee Bence Lin, Samuel C McNeely, Richard P Beckmann
All cancers are characterized by defects in the systems that ensure strict control of the cell cycle in normal tissues. The consequent excess tissue growth can be countered by drugs that halt cell division and, indeed, the majority of chemotherapeutics developed during the last century work by disrupting processes essential for the cell cycle, particularly DNA synthesis, DNA replication, and chromatid segregation. In certain contexts the efficacy of these classes of drugs can be impressive but, because they indiscriminately block the cell cycle of all actively dividing cells, their side effects severely constrain the dose and duration with which they can be administered, allowing both normal and malignant cells to escape complete growth arrest...
March 22, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28330158/a-simple-and-efficient-agrobacterium-tumefaciens-mediated-plant-transformation-of-brassica-rapa-ssp-pekinensis
#16
Venkidasamy Baskar, Baniekal H Gangadhar, Se Won Park, Shivraj Hariram Nile
The present study aims to investigate the numerous factors influencing Agrobacterium tumefaciens-mediated genetic transformation of Chinese cabbage (Brassica rapa ssp. pekinensis). Factors affecting transformation efficiency, such as age of explants, Agrobacterium concentration, and effect of acetosyringone, pre-cultivation, infection and co-cultivation time of Agrobacterium were examined. The pre-cultured hypocotyls from young seedlings prior to exposure to Agrobacterium showed higher shoot regeneration. The plant transformation with the modest A...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328998/combinatorial-selection-for-replicable-rna-by-q%C3%AE-replicase-while-maintaining-encoded-gene-function
#17
Mio Yumura, Natsuko Yamamoto, Katsushi Yokoyama, Hirotada Mori, Tetsuya Yomo, Norikazu Ichihashi
Construction of a complex artificial self-replication system is challenging in the field of in vitro synthetic biology. Recently, we developed a translation-coupled RNA replication system, wherein an artificial genomic RNA replicates with the Qβ RNA replicase gene encoded on itself. The challenge is to introduce additional genes into the RNA to develop a complex system that mimics natural living systems. However, most RNA sequence encoding genes are not replicable by the Qβ replicase owing to its requirement for strong secondary structures throughout the RNA sequence that are absent in most genes...
2017: PloS One
https://www.readbyqxmd.com/read/28328880/swine-models-genomic-tools-and-services-to-enhance-our-understanding-of-human-health-and-diseases
#18
Eric M Walters, Kevin D Wells, Elizabeth C Bryda, Susan Schommer, Randall S Prather
The pig is becoming increasingly important as a biomedical model. Given the similarities between pigs and humans, a greater understanding of the underlying biology of human health and diseases may come from the pig rather than from classical rodent models. With an increasing need for swine models, it is essential that the genomic tools, models and services be readily available to the scientific community. Many of these are available through the National Swine Resource and Research Center (NSRRC), a facility funded by the US National Institutes of Health at the University of Missouri...
March 22, 2017: Lab Animal
https://www.readbyqxmd.com/read/28328372/psychiatric-genomics-and-mental-health-treatment-setting-the-ethical-agenda
#19
Camillia Kong, Michael Dunn, Michael Parker
Realizing the benefits of translating psychiatric genomics research into mental health care is not straightforward. The translation process gives rise to ethical challenges that are distinctive from challenges posed within psychiatric genomics research itself, or that form part of the delivery of clinical psychiatric genetics services. This article outlines and considers three distinct ethical concerns posed by the process of translating genomic research into frontline psychiatric practice and policy making...
April 2017: American Journal of Bioethics: AJOB
https://www.readbyqxmd.com/read/28327113/low-cell-number-single-tube-amplification-sta-of-total-rna-revealed-transcriptome-changes-from-pluripotency-to-endothelium
#20
Yi-Hsuan Lee, Ya-Wen Hsueh, Yao-Hung Peng, Kung-Chao Chang, Kuen-Jer Tsai, H Sunny Sun, Ih-Jen Su, Po-Min Chiang
BACKGROUND: In addition to messenger RNA (mRNA), noncoding RNAs (ncRNAs) are essential components in cellular machineries for translation and splicing. Besides their housekeeping functions, ncRNAs are involved in cell type-specific regulation of translation, mRNA stability, genome structure, and accessibility. To have a comprehensive understanding of the identities and functions of different cell types, a method to comprehensively quantify both mRNA and ncRNA in a sensitive manner is highly desirable...
March 21, 2017: BMC Biology
keyword
keyword
63878
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"