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https://www.readbyqxmd.com/read/28545255/frozen-accident-pushing-50-stereochemistry-expansion-and-chance-in-the-evolution-of-the-genetic-code
#1
Eugene V Koonin
Nearly 50 years ago, Francis Crick propounded the frozen accident scenario for the evolution of the genetic code along with the hypothesis that the early translation system consisted primarily of RNA. Under the frozen accident perspective, the code is universal among modern life forms because any change in codon assignment would be highly deleterious. The frozen accident can be considered the default theory of code evolution because it does not imply any specific interactions between amino acids and the cognate codons or anticodons, or any particular properties of the code...
May 23, 2017: Life
https://www.readbyqxmd.com/read/28545254/bacterial-virus-ontology-coordinating-across-databases
#2
Chantal Hulo, Patrick Masson, Ariane Toussaint, David Osumi-Sutherland, Edouard de Castro, Andrea H Auchincloss, Sylvain Poux, Lydie Bougueleret, Ioannis Xenarios, Philippe Le Mercier
Bacterial viruses, also called bacteriophages, display a great genetic diversity and utilize unique processes for infecting and reproducing within a host cell. All these processes were investigated and indexed in the ViralZone knowledge base. To facilitate standardizing data, a simple ontology of viral life-cycle terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address unique viral replication cycle processes, and existing terminology was modified and adapted...
May 23, 2017: Viruses
https://www.readbyqxmd.com/read/28545252/cpg-and-non-cpg-methylation-in-epigenetic-gene-regulation-and-brain-function
#3
REVIEW
Hyun Sik Jang, Woo Jung Shin, Jeong Eon Lee, Jeong Tae Do
DNA methylation is a major epigenetic mark with important roles in genetic regulation. Methylated cytosines are found primarily at CpG dinucleotides, but are also found at non-CpG sites (CpA, CpT, and CpC). The general functions of CpG and non-CpG methylation include gene silencing or activation depending on the methylated regions. CpG and non-CpG methylation are found throughout the whole genome, including repetitive sequences, enhancers, promoters, and gene bodies. Interestingly, however, non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells...
May 23, 2017: Genes
https://www.readbyqxmd.com/read/28545226/emergence-of-cd26-cancer-stem-cells-with-metastatic-properties-in-colorectal-carcinogenesis
#4
Alvin Ho-Kwan Cheung, Deepak Narayanan Iyer, Colin Siu-Chi Lam, Lui Ng, Sunny K M Wong, Hung-Sing Lee, Timothy Wan, Johnny Man, Ariel K M Chow, Ronnie T Poon, Roberta Pang, Wai-Lun Law
Colorectal cancer results from genetic aberrations which accumulate over a long period of time, with malignant and metastatic properties acquired at a relatively late stage. A subpopulation of CD26+ colorectal cancer stem cells are known to be implicated in metastasis. We quantified CD26+ cancer cells in 11 primary tumor samples by flow cytometry, and showed that tumors having confirmed or suspected metastases harbored a relatively high CD26+ level in these samples. We hypothesized that this subpopulation of cancer stem cells arises in the late stage of carcinogenesis from the bulk of tumor daughter cells which are CD26-...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28545225/state-of-art-of-cancer-pharmacogenomics-in-latin-american-populations
#5
REVIEW
Andrés López-Cortés, Santiago Guerrero, María Ana Redal, Angel Tito Alvarado, Luis Abel Quiñones
Over the past decades, several studies have shown that tumor-related somatic and germline alterations predicts tumor prognosis, drug response and toxicity. Latin American populations present a vast geno-phenotypic diversity due to the great interethnic and interracial mixing. This genetic flow leads to the appearance of complex characteristics that allow individuals to adapt to endemic environments, such as high altitude or extreme tropical weather. These genetic changes, most of them subtle and unexplored, could establish a mutational profile to develop new pharmacogenomic therapies specific for Latin American populations...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28545206/the-performance-of-an-efficient-dairy-system-using-a-combination-of-nitrogen-leaching-mitigation-strategies-in-a-variable-climate
#6
P C Beukes, A J Romera, P Gregorini, K A Macdonald, C B Glassey, M A Shepherd
An efficient dairy system, that implemented a combination of nitrogen (N) leaching mitigation strategies including lower N fertilizer input, standing cows off pasture for part of the day in autumn and winter (stand-off), and importing limited amounts of low protein supplements was evaluated over four consecutive years of a farmlet study. This efficient system consistently demonstrated a lower measured annual N leaching of 40 to 50% compared with a baseline system representing current practice with no mitigations...
May 20, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28545182/breast-cancer-in-australian-indigenous-women-incidence-mortality-and-risk-factors
#7
Kriscia A Tapia, Gail Garvey, Mark Mc Entee, Mary Rickard, Patrick Brennan
The Indigenous people of Australia face significant health gaps compared with the general population, with lower life expectancies, higher rates of death, and chronic illness occurring more often than in non-indigenous Australians. Cancer is the second largest contributor to the burden of disease with breast cancer being the most common invasive cancer diagnosed for females. Despite a lower breast cancer incidence compared with non-indigenous women, fatalities occur at an elevated rate and breast cancers have an earlier age of onset...
April 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28545165/highly-recurrent-h3f3a-mutations-with-additional-epigenetic-regulator-alterations-in-giant-cell-tumor-of-bone
#8
Koichi Ogura, Fumie Hosoda, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Shoko Ohashi, Hirofumi Rokutan, Erina Takai, Shinichi Yachida, Akira Kawai, Sakae Tanaka, Tatsuhiro Shibata
Recurrent H3F3A and IDH2 mutations have been reported in giant cell tumor of bone (GCTB). However, the reported incidences have varied, and other molecular genetic alterations have not been identified due to the small number of cases analyzed with comprehensive methods. Moreover, the relative sensitivities of Sanger sequencing and next-generation sequencing (NGS) for the detection of H3F3A mutations in DNA extracted from archival formalin-fixed paraffin-embedded (FFPE) for clinical diagnosis have not been assessed...
May 25, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28545141/prion-pathogenesis-is-unaltered-in-the-absence-of-sirp%C3%AE-mediated-don-t-eat-me-signaling
#9
Mario Nuvolone, Marta Paolucci, Silvia Sorce, Veronika Kana, Rita Moos, Takashi Matozaki, Adriano Aguzzi
Prion diseases are neurodegenerative conditions caused by misfolding of the prion protein, leading to conspicuous neuronal loss and intense microgliosis. Recent experimental evidence point towards a protective role of microglia against prion-induced neurodegeneration, possibly through elimination of prion-containing apoptotic bodies. The molecular mechanisms by which microglia recognize and eliminate apoptotic cells in the context of prion diseases are poorly defined. Here we investigated the possible involvement of signal regulatory protein α (SIRPα), a key modulator of host cell phagocytosis; SIRPα is encoded by the Sirpa gene that is genetically linked to the prion gene Prnp...
2017: PloS One
https://www.readbyqxmd.com/read/28545131/major-changes-in-microbial-diversity-and-community-composition-across-gut-sections-of-a-juvenile-panchlora-cockroach
#10
Erin A Gontang, Frank O Aylward, Camila Carlos, Tijana Glavina Del Rio, Mansi Chovatia, Alison Fern, Chien-Chi Lo, Stephanie A Malfatti, Susannah G Tringe, Cameron R Currie, Roberto Kolter
Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica...
2017: PloS One
https://www.readbyqxmd.com/read/28545126/pheromone-sensing-neurons-regulate-peripheral-lipid-metabolism-in-caenorhabditis-elegans
#11
Rosalind Hussey, Jon Stieglitz, Jaleh Mesgarzadeh, Tiffany T Locke, Ying K Zhang, Frank C Schroeder, Supriya Srinivasan
It is now established that the central nervous system plays an important role in regulating whole body metabolism and energy balance. However, the extent to which sensory systems relay environmental information to modulate metabolic events in peripheral tissues has remained poorly understood. In addition, it has been challenging to map the molecular mechanisms underlying discrete sensory modalities with respect to their role in lipid metabolism. In previous work our lab has identified instructive roles for serotonin signaling as a surrogate for food availability, as well as oxygen sensing, in the control of whole body metabolism...
May 18, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28545104/pkng-senses-amino-acid-availability-to-control-metabolism-and-virulence-of-mycobacterium-tuberculosis
#12
Barbara Rieck, Giulia Degiacomi, Michael Zimmermann, Alessandro Cascioferro, Francesca Boldrin, Natalie R Lazar-Adler, Andrew R Bottrill, Fabien le Chevalier, Wafa Frigui, Marco Bellinzoni, María-Natalia Lisa, Pedro M Alzari, Liem Nguyen, Roland Brosch, Uwe Sauer, Riccardo Manganelli, Helen M O'Hare
Sensing and response to changes in nutrient availability are essential for the lifestyle of environmental and pathogenic bacteria. Serine/threonine protein kinase G (PknG) is required for virulence of the human pathogen Mycobacterium tuberculosis, and its putative substrate GarA regulates the tricarboxylic acid cycle in M. tuberculosis and other Actinobacteria by protein-protein binding. We sought to understand the stimuli that lead to phosphorylation of GarA, and the roles of this regulatory system in pathogenic and non-pathogenic bacteria...
May 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28545071/characterization-of-the-urinary-microbiome-in-healthy-dogs
#13
Erin N Burton, Leah A Cohn, Carol N Reinero, Hans Rindt, Stephen G Moore, Aaron C Ericsson
The urinary bladder in healthy dogs has dogmatically been considered free of bacteria. This study used culture independent techniques to characterize the healthy canine urinary microbiota. Urine samples collected by antepubic cystocentesis from dogs without urinary infection were used for DNA extraction. Genital tract and rectal samples were collected simultaneously from the same dogs. The V4 hypervariable region of the 16S rRNA bacterial gene was amplified and compared against Greengenes database for OTU assignment and relative abundance for urine, genital, and rectal samples...
2017: PloS One
https://www.readbyqxmd.com/read/28545070/pou4f3-mutation-screening-in-japanese-hearing-loss-patients-massively-parallel-dna-sequencing-based-analysis-identified-novel-variants-associated-with-autosomal-dominant-hearing-loss
#14
Tomohiro Kitano, Maiko Miyagawa, Shin-Ya Nishio, Hideaki Moteki, Kiyoshi Oda, Kenji Ohyama, Hiromitsu Miyazaki, Hiroshi Hidaka, Ken-Ichi Nakamura, Takaaki Murata, Rina Matsuoka, Yoko Ohta, Nobuhiro Nishiyama, Kozo Kumakawa, Sakiko Furutate, Satoshi Iwasaki, Takechiyo Yamada, Yumi Ohta, Natsumi Uehara, Yoshihiro Noguchi, Shin-Ichi Usami
A variant in a transcription factor gene, POU4F3, is responsible for autosomal dominant nonsyndromic hereditary hearing loss, DFNA15. To date, 14 variants, including a whole deletion of POU4F3, have been reported to cause HL in various ethnic groups. In the present study, genetic screening for POU4F3 variants was carried out for a large series of Japanese hearing loss (HL) patients to clarify the prevalence and clinical characteristics of DFNA15 in the Japanese population. Massively parallel DNA sequencing of 68 target candidate genes was utilized in 2,549 unrelated Japanese HL patients (probands) to identify genomic variations responsible for HL...
2017: PloS One
https://www.readbyqxmd.com/read/28545069/behavioral-alterations-are-associated-with-vitamin-b12-deficiency-in-the-transcobalamin-receptor-cd320-ko-mouse
#15
Kaveri Arora, Jeffrey M Sequeira, Alejandro I Hernández, Juan M Alarcon, Edward V Quadros
Vitamin B12 (cobalamin) deficiency is prevalent worldwide and causes megaloblastic anemia and neurologic deficits. While the anemia can be treated, the neurologic deficits can become refractive to treatment as the disease progresses. Therefore, timely intervention is critical for a favorable outcome. Moreover, the metabolic basis for the neuro-pathologic changes and the role of cobalamin deficiency in the pathology still remains unexplained. Using a transcobalamin receptor / CD320 knockout mouse that lacks the receptor for cellular uptake of transcobalamin bound cobalamin, we aimed to determine whether cobalamin deficiency in the central nervous system produced functional neurologic deficits in the mouse that would parallel those observed in humans...
2017: PloS One
https://www.readbyqxmd.com/read/28545030/mitochondrial-dna-sequencing-and-large-scale-genotyping-identifies-mt-nd4-gene-mutation-m-11696g-a-associated-with-idiopathic-oligoasthenospermia
#16
Juan Ji, Miaofei Xu, Zhenyao Huang, Lei Li, Hongxiang Zheng, Shuping Yang, Shilin Li, Li Jin, Xiufeng Ling, Yankai Xia, Chuncheng Lu, Xinru Wang
Genetic variants of mitochondrial DNA (mtDNA) were implicated to be associated with male infertility. Our previous whole mitochondrial genome sequencing and association study has identified two susceptibility mtDNA variants for oligoasthenospermia in Han Chinese men. In this study, we tested promising associations in an extended validation using 670 idiopathic oligoasthenospermia cases and 793 healthy controls to identify additional risk variants. We found that the genetic variant of m.11696G>A showed significantly higher frequency in the case group than that in the control group (odds ratio (OR) 2...
May 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28545024/an-unusual-intragenic-promoter-of-piwil2-contributes-to-aberrant-activation-of-oncogenic-pl2l60
#17
Shan-Shan Liu, Ning Liu, Meng-Yao Liu, Lei Sun, Wu-Yan Xia, Hong-Min Lu, Yu-Jie Fu, Guo-Liang Yang, Juan-Jie Bo, Xiao-Xing Liu, Haizhong Feng, Hailong Wu, Lin-Feng Li, Jian-Xin Gao
PIWIL2-like (PL2L) protein 60 (PL2L60), a product of aberrantly activated PIWIL2 gene, is widely expressed in various types of tumors and may promote tumorigenesis. However, the mechanisms underlying the activation of expression of PL2L60 remain unknown. In this study, an intragenic promoter responsible for the activation of PL2L60 within the human PIWIL2 gene has been identified, cloned and characterized. The promoter of PL2L60 is located in the intron 10 of the host gene PIWIL2. Bioinformatic and mutagenic analysis reveals that this intragenic promoter within the sequence of 50 nucleotides contains two closely arranged cis-acting elements specific for the hepatic leukemia factor (HLF) in the positive strand and signal transducer and activator of transcription 3 (STAT3) in the negative strand...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28545018/fixed-differences-in-the-3-utr-of-buffalo-prnp-gene-provide-binding-sites-for-mirnas-post-transcriptional-regulation
#18
Hui Zhao, Siqi Wang, Lixia Guo, Yanli Du, Linlin Liu, Tengfei Ma, Newton O Otecko, Canpeng Li, Yaping Zhang
Bovine spongiform encephalopathy, a member of transmissible spongiform encephalopathies, has not been reported in buffaloes, Bubalus bubalis. Prion protein (PrP), encoded by the prion protein gene (PRNP), is fundamental in the pathogenesis of transmissible spongiform encephalopathies. We previously showed that buffaloes express more PrP proteins but lower PRNP mRNA than cattle in several pivotal tissues like the obex. Therefore, we sought to establish whether genetic variability in PRNP 3'UTR, mediated by miRNA down-regulation, causes PrP expression differences between cattle and buffaloes...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28545014/paracetamol-causes-endocrine-disruption-and-hepatotoxicity-in-male-fish-rhamdia-quelen-after-subchronic-exposure
#19
Izonete Cristina Guiloski, João Luiz Coelho Ribas, Laercio Dante Stein Piancini, Ana Carolina Dagostim, Silvana Maris Cirio, Luis Fernando Fávaro, Suelen Lúcio Boschen, Marta Margarete Cestari, Cláudio da Cunha, Helena Cristina Silva de Assis
Paracetamol is one of the most widely sold non-prescription drugs. This study aimed to evaluate the effects of the paracetamol on reproductive, biochemical, genetic, histopathological and hematogical biomarkers by waterborne exposure. Male fish of Rhamdia quelen were exposed to environmental concentrations of paracetamol (0, 0.25, 2.5μg/L) in a semi-static bioassay for 21days. Hemoglobin and hematocrit were reduced upon exposure to 0.25μg/L of paracetamol. Leukocytes and thrombocytes increased after paracetamol exposure...
May 8, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28545008/psychiatric-disorders-in-a-cohort-of-individuals-with-prader-willi-syndrome
#20
L Shriki-Tal, H Avrahamy, Y Pollak, V Gross-Tsur, L Genstil, H J Hirsch, F Benarroch
BACKGROUND: Psychiatric manifestations in Prader-Willi Syndrome (PWS) are common and often are the most debilitating problem in these individuals. We present an epidemiological nation-wide survey of psychiatric diagnoses in the PWS population, based on full-range psychiatric interviews. METHODS: We studied the distribution of psychiatric diagnoses (as opposed to a symptom-based approach) in the Israel national cohort of adolescents and adults with PWS. There was a total of 53 (32 males) ages 12 years and older...
April 5, 2017: European Psychiatry: the Journal of the Association of European Psychiatrists
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