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https://www.readbyqxmd.com/read/28647735/uniparental-disomy-of-chromosome-15-in-two-cases-by-chromosome-microarray-a-lesson-worth-thinking
#1
Shu Liu, Kaihui Zhang, Fengling Song, Yali Yang, Yuqiang Lv, Min Gao, Yi Liu, Zhongtao Gai
Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are neurogenetic disorders caused by loss of function of the imprinted genes at 15q11q13. A 5-7 Mb paternal/maternal deletion of chromosomal region 15q11.2q13 is the major genetic cause of PWS/AS, but in a small group of patients, the PWS/AS phenotype can result from maternal/paternal uniparental disomy (UPD) of chromosome 15. Various mechanisms leading to UPD include gametic complementation, trisomy rescue, and compensatory UPD, which can be inferred from the pattern of uniparental heterodisomy (heteroUPD) or uniparental isodisomy (isoUPD)...
June 24, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28647497/prediction-of-metastasis-in-advanced-colorectal-carcinomas-using-cgh-data
#2
Ehsan Saghapour, Mohammadreza Sehhati
Logistic Regression Model (LRM) and artificial neural networks (ANNs) as two nonlinear models have been used to establish a novel two-stage hybrid modeling procedure for prediction of metastasis in advanced colorectal carcinomas. Two different datasets were used in training and testing procedures. For the first stage of hybrid modeling procedure, LRM was used to evaluate the contribution of DNA sequence copy number aberrations detected by Comparative Genomic Hybridization in advanced colorectal carcinoma and its metastasis...
June 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28647451/association-of-mitochondrial-dna-in-peripheral-blood-with-depression-anxiety-and-stress-and-adjustment-disorders-in-primary-health-care-patients
#3
Xiao Wang, Kristina Sundquist, Hamideh Rastkhani, Karolina Palmér, Ashfaque A Memon, Jan Sundquist
Mitochondrial dysfunction may result in a variety of diseases. The objectives here were to examine possible differences in mtDNA copy number between healthy controls and patients with depression, anxiety or stress- and adjustment disorders; the association between mtDNA copy number and disease severity at baseline; and the association between mtDNA copy number and response after an 8-week treatment (mindfulness, cognitive based therapy). A total of 179 patients in primary health care (age 20-64 years) with depression, anxiety and stress- and adjustment disorders, and 320 healthy controls (aged 19-70 years) were included in the study...
June 21, 2017: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28647243/quantification-of-hookworm-ova-from-wastewater-matrices-using-quantitative-pcr
#4
Pradip Gyawali, Warish Ahmed, Jatinder P Sidhu, Paul Jagals, Simon Toze
A quantitative PCR (qPCR) assay was used to quantify Ancylostoma caninum ova in wastewater and sludge samples. We estimated the average gene copy numbers for a single ovum using a mixed population of ova. The average gene copy numbers derived from the mixed population were used to estimate numbers of hookworm ova in A. caninum seeded and unseeded wastewater and sludge samples. The newly developed qPCR assay estimated an average of 3.7×10(3) gene copies per ovum, which was then validated by seeding known numbers of hookworm ova into treated wastewater...
July 2017: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/28646449/occurrence-of-pepper-mild-mottle-virus-pmmov-in-groundwater-from-a-karst-aquifer-system-in-the-yucatan-peninsula-mexico
#5
Gabriela Rosiles-González, Gerardo Ávila-Torres, Oscar A Moreno-Valenzuela, Gilberto Acosta-González, Rosa María Leal-Bautista, Cinthya D Grimaldo-Hernández, Judith K Brown, Cristóbal Chaidez-Quiroz, Walter Q Betancourt, Charles P Gerba, Cecilia Hernández-Zepeda
The Yucatan Peninsula of Mexico hosts a karst aquifer system that is the only source of freshwater for the area; however, it is vulnerable to human-mediated contamination. Pepper mild mottle virus (PMMoV) is one of the most abundant RNA viruses associated with human feces, making it a viable indicator for tracking fecal pollution in aquatic environments, including groundwater. In this study, groundwater samples collected from a karst aquifer from fresh and brackish water locations were analyzed for fecal indicator bacteria, somatic and male F+ specific coliphages, and PMMoV during the rainy and dry seasons...
June 23, 2017: Food and Environmental Virology
https://www.readbyqxmd.com/read/28645800/high-throughput-sequencing-of-the-entire-genomic-regions-of-ccm1-krit1-ccm2-and-ccm3-pdcd10-to-search-for-pathogenic-deep-intronic-splice-mutations-in-cerebral-cavernous-malformations
#6
Matthias Rath, Sönke E Jenssen, Konrad Schwefel, Stefanie Spiegler, Dana Kleimeier, Christian Sperling, Lars Kaderali, Ute Felbor
Cerebral cavernous malformations (CCM) are vascular lesions of the central nervous system that can cause headaches, seizures and hemorrhagic stroke. Disease-associated mutations have been identified in three genes: CCM1/KRIT1, CCM2 and CCM3/PDCD10. The precise proportion of deep-intronic variants in these genes and their clinical relevance is yet unknown. Here, a long-range PCR (LR-PCR) approach for target enrichment of the entire genomic regions of the three genes was combined with next generation sequencing (NGS) to screen for coding and non-coding variants...
June 20, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28645778/whole-genome-sequencing-of-monozygotic-twins-discordant-for-schizophrenia-indicates-multiple-genetic-risk-factors-for-schizophrenia
#7
Jinsong Tang, Yu Fan, Hong Li, Qun Xiang, Deng-Feng Zhang, Zongchang Li, Ying He, Yanhui Liao, Ya Wang, Fan He, Fengyu Zhang, Yin Yao Shugart, Chunyu Liu, Yanqing Tang, Raymond C K Chan, Chuan-Yue Wang, Yong-Gang Yao, Xiaogang Chen
Schizophrenia is a common disorder with a high heritability, but its genetic architecture is still elusive. We implemented whole-genome sequencing (WGS) analysis of 8 families with monozygotic (MZ) twin pairs discordant for schizophrenia to assess potential association of de novo mutations (DNMs) or inherited variants with susceptibility to schizophrenia. Eight nonsynonymous DNMs (including one splicing site) were identified and shared by twins, which were either located in previously reported schizophrenia risk genes (p...
June 8, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28645357/appreciating-the-population-wide-impact-of-copy-number-variants-on-cognition
#8
Joon-Yong An, Stephan J Sanders
No abstract text is available yet for this article.
July 15, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/28645267/a-rapid-and-quantitative-method-to-detect-human-circulating-tumor-cells-in-a-preclinical-animal-model
#9
Shih-Hsin Tu, Yi-Chen Hsieh, Li-Chi Huang, Chun-Yu Lin, Kai-Wen Hsu, Wen-Shyang Hsieh, Wei-Ming Chi, Chia-Hwa Lee
BACKGROUND: As cancer metastasis is the deadliest aspect of cancer, causing 90% of human deaths, evaluating the molecular mechanisms underlying this process is the major interest to those in the drug development field. Both therapeutic target identification and proof-of-concept experimentation in anti-cancer drug development require appropriate animal models, such as xenograft tumor transplantation in transgenic and knockout mice. In the progression of cancer metastasis, circulating tumor cells (CTCs) are the most critical factor in determining the prognosis of cancer patients...
June 23, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28645105/a-three-gene-immunohistochemical-panel-serves-as-an-adjunct-to-clinical-staging-of-patients-with-head-and-neck-cancer
#10
Chin-Ann J Ong, Nicholas B Shannon, Stefan Mueller, Sze Min Lek, Xuan Qiu, Fui Teen Chong, Ke Li, Kelvin K N Koh, Gerald C A Tay, Thakshayeni Skanthakumar, Jacqueline S G Hwang, Tony Kiat Hon Lim, Mei Kim Ang, Daniel S W Tan, Ngian-Chye Tan, Hiang Khoon Tan, Khee Chee Soo, N Gopalakrishna Iyer
BACKGROUND: Current management of head and neck squamous cell carcinoma (HNSCC) depends on tumor staging. Despite refinements in clinical staging algorithms, outcomes remain unchanged for the last two decades. In this study, we set out to identify a small, clinically applicable molecular panel to aid prognostication of patients with HNSCC. MATERIALS AND METHODS: Data from The Cancer Genome Atlas (TCGA) was used to derive copy number aberrations and expression changes to identify putative prognostic genes...
June 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28644839/genomic-introgression-mapping-of-field-derived-multiple-anthelmintic-resistance-in-teladorsagia-circumcincta
#11
Young-Jun Choi, Stewart A Bisset, Stephen R Doyle, Kymberlie Hallsworth-Pepin, John Martin, Warwick N Grant, Makedonka Mitreva
Preventive chemotherapy has long been practiced against nematode parasites of livestock, leading to widespread drug resistance, and is increasingly being adopted for eradication of human parasitic nematodes even though it is similarly likely to lead to drug resistance. Given that the genetic architecture of resistance is poorly understood for any nematode, we have analyzed multidrug resistant Teladorsagia circumcincta, a major parasite of sheep, as a model for analysis of resistance selection. We introgressed a field-derived multiresistant genotype into a partially inbred susceptible genetic background (through repeated backcrossing and drug selection) and performed genome-wide scans in the backcross progeny and drug-selected F2 populations to identify the major genes responsible for the multidrug resistance...
June 23, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28644430/the-clinical-landscape-for-sma-in-a-new-therapeutic-era
#12
REVIEW
K Talbot, E F Tizzano
Despite significant advances in basic research, the treatment of degenerative diseases of the nervous system remains one of the greatest challenges for translational medicine. The childhood onset motor neuron disorder spinal muscular atrophy (SMA) has been viewed as one of the more tractable targets for molecular therapy, due to a detailed understanding of the molecular genetic basis of the disease. In SMA, inactivating mutations in the SMN1 gene can be partially compensated for by limited expression of SMN protein from a variable number of copies of the SMN2 gene, which provides both a molecular explanation for phenotypic severity and a target for therapy...
June 23, 2017: Gene Therapy
https://www.readbyqxmd.com/read/28644390/the-electrosome-a-surface-displayed-enzymatic-cascade-in-a-biofuel-cell-s-anode-and-a-high-density-surface-displayed-biocathodic-enzyme
#13
Alon Szczupak, Dror Aizik, Sarah Moraïs, Yael Vazana, Yoav Barak, Edward A Bayer, Lital Alfonta
The limitation of surface-display systems in biofuel cells to a single redox enzyme is a major drawback of hybrid biofuel cells, resulting in a low copy-number of enzymes per yeast cell and a limitation in displaying enzymatic cascades. Here we present the electrosome, a novel surface-display system based on the specific interaction between the cellulosomal scaffoldin protein and a cascade of redox enzymes that allows multiple electron-release by fuel oxidation. The electrosome is composed of two compartments: (i) a hybrid anode, which consists of dockerin-containing enzymes attached specifically to cohesin sites in the scaffoldin to assemble an ethanol oxidation cascade, and (ii) a hybrid cathode, which consists of a dockerin-containing oxygen-reducing enzyme attached in multiple copies to the cohesin-bearing scaffoldin...
June 23, 2017: Nanomaterials
https://www.readbyqxmd.com/read/28643557/pooled-sample-testing-for-bonamia-ostreae-a-tale-of-two-sybr-green-real-time-pcr-assays
#14
Henry S Lane, J Brian Jones, Wendy L McDonald
Pooled testing of samples is a common laboratory practice to increase efficiency and reduce expenses. We investigated the efficacy of 2 published SYBR Green real-time PCR assays when used to detect the haplosporidian parasite Bonamia ostreae in pooled samples of infected oyster tissue. Each PCR targets a different gene within the B. ostreae genome: the actin 1 gene or the 18S rRNA gene. Tissue homogenates (150 mg) of the New Zealand flat oyster Ostrea chilensis were spiked with ~1.5 × 10(3) purified B. ostreae cells to create experimental pools of 3, 5, and 10...
June 1, 2017: Journal of Veterinary Diagnostic Investigation
https://www.readbyqxmd.com/read/28643373/cytomegalovirus-dna-is-highly-prevalent-in-the-blood-of-patients-with-asthma-and-is-associated-with-age-and-asthma-traits
#15
Marek L Kowalski, Aleksandra Wardzynska, Miroslawa Studzinska, Malgorzata Pawelczyk, Zbigniew Jan Lesnikowski, Edyta Paradowska
CMV IgG antibodies have been associated with inflammageing and immunosenescence. We aimed to assess the presence of CMV DNA in the blood of adult and elderly patients with bronchial asthma to establish potential association of CMV DNAemia with asthma and asthma characteristics. Eighty-five elderly asthmatics, 74 younger asthma patients and 114 age-matched controls were recruited. The CMV DNA was detected using commercial artus assay in 10.7% of asthma patients, but was negative in all control individuals. The secondary assay identified CMV DNA in 41...
June 22, 2017: Allergy
https://www.readbyqxmd.com/read/28642746/virucidal-activity-of-fogged-chlorine-dioxide-and-hydrogen-peroxide-based-disinfectants-against-human-norovirus-and-its-surrogate-feline-calicivirus-on-hard-to-reach-surfaces
#16
Naim Montazeri, Clyde Manuel, Eric Moorman, Janak R Khatiwada, Leonard L Williams, Lee-Ann Jaykus
Human norovirus (NoV) is the leading cause of foodborne illnesses in the United States. Norovirus is shed in high numbers in the feces and vomitous of infected individuals. Contact surfaces contaminated with bodily fluids harboring infectious virus particles serve as vehicles for pathogen transmission. Environmental stability of NoV and its resistance to many conventional disinfectants necessitate effective inactivation strategies to control the spread of virus. We investigated the efficacy of two commercial disinfectants, hydrogen peroxide (7...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28642636/nucleotide-composition-determines-the-role-of-translational-efficiency-in-human-genes
#17
Binata Halder, Arup Kumar Malakar, Supriyo Chakraborty
The basic sequence features were analysed that influence gene expression via codon usage bias of the selected forty coding sequences of Homo sapiens in a simple prokaryotic model i.e. E. coli K-12 genome. The prime objective was to elucidate the interrelationships among tRNA gene copy numbers, synonymous codons, amino acids and translational efficiency using tRNA adaptation index. It was evident from RSCU scores and principal component analysis, that only those preferred codons were used by the isoacceptor tRNAs that had G and C base at their third codon position...
2017: Bioinformation
https://www.readbyqxmd.com/read/28642606/transposable-elements-in-cancer
#18
REVIEW
Kathleen H Burns
Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1)...
July 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/28642587/systematic-comparison-of-two-whole-genome-amplification-methods-for-targeted-next-generation-sequencing-using-frozen-and-ffpe-normal-and-cancer-tissues
#19
Pedro Mendez, Li Tai Fang, David M Jablons, Il-Jin Kim
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28641368/glomerular-hyperfiltration-in-obese-african-american-hypertensive-patients-is-associated-with-elevated-urinary-mitochondrial-dna-copy-number
#20
Alfonso Eirin, Ahmed Saad, John R Woollard, Luis A Juncos, David A Calhoun, Hui Tang, Amir Lerman, Stephen C Textor, Lilach O Lerman
BACKGROUND: Glomerular hyperfiltration may contribute to the high incidence of renal disease in Obese African Americans essential hypertensive (ObAAEH) patients, but the precise mechanisms responsible for renal injury have not been elucidated. Mitochondria are important determinants of renal injury in hypertension, and increased levels of mitochondrial DNA (mtDNA) in the urine may indicate renal mitochondrial injury. We hypothesized that urine mtDNA copy numbers would be higher in ObAAEH compared to Caucasian essential hypertensive (CEH) patients...
June 14, 2017: American Journal of Hypertension
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