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mitochondrial copy number detect

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https://www.readbyqxmd.com/read/29130995/lncrna-uca1-promotes-mitochondrial-function-of-bladder-cancer-via-the-mir-195-arl2-signaling-pathway
#1
Hui-Jin Li, Xiao-Min Sun, Zheng-Kun Li, Qian-Wen Yin, Huan Pang, Jing-Jing Pan, Xu Li, Wei Chen
BACKGROUND/AIMS: This study aims to identify whether Urothelial Cancer Associated 1 (UCA1) regulates mitochondrial metabolic reprogramming in bladder cancer, and to explore how UCA1 participates in mitochondrial metabolism by the UCA1/miR-195/ARL2 signaling pathway; these findings may be aid in the development of tumor diagnostic and therapeutic strategies. METHODS: Bladder tissues were obtained from patients. Stable cell lines were constructed, with ectopic expression of UCA1 in UMUC2 cells and knockdown of UCA1 in 5637 cells...
November 1, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29070451/arctic-antibiotic-resistance-gene-contamination-a-result-of-anthropogenic-activities-and-natural-origin
#2
Lu Tan, Linyun Li, Nicholas Ashbolt, Xiaolong Wang, Yuxiao Cui, Xiao Zhu, Yan Xu, Yang Yang, Daqing Mao, Yi Luo
The increasing global prevalence of antibiotic resistance genes (ARGs) in the environment is attributed to anthropogenic activities, particularly the misuse of antimicrobial drugs in human care and animal production. In the present study, we first examined Arctic/sub-Arctic (polar) sediments for the abundance and diversity of 30 ARGs against sulfonamide, tetracycline, aminoglycoside, quinolone, macrolide, and β-lactam antibiotics. Polar sediment ARGs were detected by qPCR at relatively low levels (10(-9) to 10(-5) copies/16S rRNA gene copies) compared to the reference sites, which were heavily impacted regions of China (the Haihe River, the Tianjin Water Park water and the Qilihai Wetland water, at 10(-8) to 10(-2) copies/16S rRNA gene copies)...
October 22, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29045673/age-related-changes-in-the-mitochondria-of-human-mural-granulosa-cells
#3
Yifan Liu, Ming Han, Xiaoshuang Li, Hui Wang, Minyue Ma, Shihui Zhang, Yifan Guo, Shuling Wang, Yuanfen Wang, N Duan, Bing Xu, Jingwen Yin, Yuanqing Yao
STUDY QUESTION: What changes in the mitochondria of human mural granulosa cells (mGCs) with maternal aging? SUMMARY ANSWER: The mitochondrial membrane potential (MMP) and the ability of oxidative phosphorylation (OXPHOS) of mGCs declines with reproductive aging, accompanied with more abnormal mitochondria. WHAT IS KNOWN ALREADY: Mitochondria play an important role in the dialogue between the mGCs and oocytes. However, the underlying mechanism of mitochondrial dysfunction in mGCs in aging is still poorly understood...
October 17, 2017: Human Reproduction
https://www.readbyqxmd.com/read/29020391/association-between-mitochondrial-dna-copy-number-and-sudden-cardiac-death-findings-from-the-atherosclerosis-risk-in-communities-study-aric
#4
Yiyi Zhang, Eliseo Guallar, Foram N Ashar, Ryan J Longchamps, Christina A Castellani, John Lane, Megan L Grove, Josef Coresh, Nona Sotoodehnia, Leonard Ilkhanoff, Eric Boerwinkle, Nathan Pankratz, Dan E Arking
Aims: Sudden cardiac death (SCD) is a major public health burden. Mitochondrial dysfunction has been implicated in a wide range of cardiovascular diseases including cardiomyopathy, heart failure, and arrhythmias, but it is unknown if it also contributes to SCD risk. We sought to examine the prospective association between mtDNA copy number (mtDNA-CN), a surrogate marker of mitochondrial function, and SCD risk. Methods and results: We measured baseline mtDNA-CN in 11 093 participants from the Atherosclerosis Risk in Communities (ARIC) study...
June 30, 2017: European Heart Journal
https://www.readbyqxmd.com/read/28973171/defective-mitochondrial-rrna-methyltransferase-mrm2-causes-melas-like-clinical-syndrome
#5
Caterina Garone, Aaron R D'Souza, Cristina Dallabona, Tiziana Lodi, Pedro Rebelo-Guiomar, Joanna Rorbach, Maria Alice Donati, Elena Procopio, Martino Montomoli, Renzo Guerrini, Massimo Zeviani, Sarah E Calvo, Vamsi K Mootha, Salvatore DiMauro, Ileana Ferrero, Michal Minczuk
Defects in nuclear-encoded proteins of the mitochondrial translation machinery cause early-onset and tissue-specific deficiency of one or more OXPHOS complexes. Here, we report a 7-year-old Italian boy with childhood-onset rapidly progressive encephalomyopathy and stroke-like episodes. Multiple OXPHOS defects and decreased mtDNA copy number (40%) were detected in muscle homogenate. Clinical features combined with low level of plasma citrulline were highly suggestive of mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome, however, the common m...
November 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28939701/rapid-targeted-genomics-in-critically-ill-newborns
#6
Cleo C van Diemen, Wilhelmina S Kerstjens-Frederikse, Klasien A Bergman, Tom J de Koning, Birgit Sikkema-Raddatz, Joeri K van der Velde, Kristin M Abbott, Johanna C Herkert, Katharina Löhner, Patrick Rump, Martine T Meems-Veldhuis, Pieter B T Neerincx, Jan D H Jongbloed, Conny M van Ravenswaaij-Arts, Morris A Swertz, Richard J Sinke, Irene M van Langen, Cisca Wijmenga
BACKGROUND: Rapid diagnostic whole-genome sequencing has been explored in critically ill newborns, hoping to improve their clinical care and replace time-consuming and/or invasive diagnostic testing. A previous retrospective study in a research setting showed promising results with diagnoses in 57%, but patients were highly selected for known and likely Mendelian disorders. The aim of our prospective study was to assess the speed and yield of rapid targeted genomic diagnostics for clinical application...
October 2017: Pediatrics
https://www.readbyqxmd.com/read/28936174/the-effect-of-velvet-antler-proteins-on-cardiac-microvascular-endothelial-cells-challenged-with-ischemia-hypoxia
#7
Xiang Xiao, Shuqiang Xu, Lin Li, Min Mao, Jinping Wang, Yanjun Li, Ziwei Wang, Fei Ye, Li Huang
Velvet antler (VA) is a precious traditional Chinese medicine that is capable of repeated regeneration. Based on the Chinese medicine theory of coordination the heart and kidneys, VA has been employed to treat heart diseases, including ischemic heart disease, heart failure, and arrhythmia. We examined the effects of VA proteins on primary cardiac microvascular endothelial cells (CMECs) that were subjected to ischemia-hypoxia (IH) to investigate their effects on and mechanism of action in the treatment of ischemic heart disease...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28914264/comprehensive-use-of-extended-exome-analysis-improves-diagnostic-yield-in-rare-disease-a-retrospective-survey-in-1-059-cases
#8
Gaber Bergant, Ales Maver, Luca Lovrecic, Goran Čuturilo, Alenka Hodzic, Borut Peterlin
PurposeWe sought to determine the analytical sensitivity of several extended exome variation analysis approaches in terms of their contribution to diagnostic yield and their clinical feasibility.MethodsWe retrospectively analyzed the results of genetic testing in 1,059 distinct cases referred for exome sequencing to our institution. In these, we routinely employed extended exome analysis approaches in addition to basic variant analysis, including (i) copy-number variation (CNV) detection, (ii) nonconsensus splice defect detection, (ii) genomic breakpoint detection, (iv) homozygosity mapping, and (v) mitochondrial variant analysis...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28910489/nucleoside-nucleotide-reverse-transcriptase-inhibitors-attenuate-angiogenesis-and-lymphangiogenesis-by-impairing-receptor-tyrosine-kinases-signalling-in-endothelial-cells
#9
Lin Song, Sha Ding, Zhen Ge, Xiaolong Zhu, Cong Qiu, Yuewen Wang, Enyin Lai, Weijun Yang, Yi Sun, Samson A Chow, Luyang Yu
BACKGROUND AND PURPOSE: Cardiovascular disease associated with antiretroviral therapy (ART) has become a major clinical challenge for HIV-positive patients. However, the role of ART in blood vessel growth is largely unknown. Here, we examined an integral component of ART, nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs), and investigated their effects on key microvascular functions, including angiogenesis and lymphangiogenesis. EXPERIMENTAL APPROACH: The angiogenesis/lymphangiogenesis capability of endothelial cells (ECs) was evaluated using migration, proliferation and tube formation assays in vitro, and mouse ear and Matrigel plug assays in vivo...
September 14, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28851493/evaluation-of-quantitative-ftd-pneumocystis-jirovecii-kit-for-pneumocystis-infection-diagnosis
#10
Gautier Hoarau, Solène Le Gal, Patricia Zunic, Patrice Poubeau, Emmanuel Antok, Julien Jaubert, Gilles Nevez, Sandrine Picot
We evaluated the Fast track Diagnostics (FTD) Pneumocystis PCR kit, targeting the mitochondrial large subunit ribosomal RNA gene (mtLSU rRNA) of Pneumocystis jirovecii (P. jirovecii). A hundred and thirty-three patients were prospectively enrolled. Respiratory specimens were examined using both microscopy and the PCR assay. Twenty-six patients led to P. jirovecii detection. Fourteen patients presented with Pneumocystis pneumonia (PCP) whereas 12 patients were considered to be colonized. The median copy numbers in bronchoalveolar lavage fluid were significantly different in the PCP and colonization groups (1...
August 9, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28818680/clinical-validation-of-copy-number-variant-detection-from-targeted-next-generation-sequencing-panels
#11
Jennifer Kerkhof, Laila C Schenkel, Jack Reilly, Sheri McRobbie, Erfan Aref-Eshghi, Alan Stuart, C Anthony Rupar, Paul Adams, Robert A Hegele, Hanxin Lin, David Rodenhiser, Joan Knoll, Peter J Ainsworth, Bekim Sadikovic
Next-generation sequencing (NGS) technology has rapidly replaced Sanger sequencing in the assessment of sequence variations in clinical genetics laboratories. One major limitation of current NGS approaches is the ability to detect copy number variations (CNVs) approximately >50 bp. Because these represent a major mutational burden in many genetic disorders, parallel CNV assessment using alternate supplemental methods, along with the NGS analysis, is normally required, resulting in increased labor, costs, and turnaround times...
August 15, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28810700/a-single-mini-barcode-test-to-screen-for-australian-mammalian-predators-from-environmental-samples
#12
Elodie Modave, Anna J MacDonald, Stephen D Sarre
Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28807237/mitochondrial-dysfunctions-in-bladder-cancer-exploring-their-role-as-disease-markers-and-potential-therapeutic-targets
#13
REVIEW
Antonella Cormio, Francesca Sanguedolce, Clara Musicco, Vito Pesce, Giuseppe Calò, Pantaleo Bufo, Giuseppe Carrieri, Luigi Cormio
Bladder cancer (BC) is a major cause of mortality worldwide as it currently lacks fully reliable markers of disease outcome and effective molecular targets for therapy. Mitochondria play a key role in cell metabolism but the role of mitochondrial dysfunctions in BC has been scarcely investigated. In this review, we explored current evidence for the potential role of mitochondrial DNA (mtDNA) alterations (point mutations and copy number) as disease markers in BC. Some germline mtDNA mutations detectable in blood could represent a non-invasive tool to predict the risk of developing BC...
September 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28803790/utility-of-the-cytochrome-c-oxidase-subunit-i-gene-for-the-diagnosis-of-toxoplasmosis-using-pcr
#14
Xue Feng, Kazumi Norose, Kexin Li, Kenji Hikosaka
Toxoplasmosis is caused by the protozoan parasite Toxoplasma gondii, which belongs to the phylum Apicomplexa. Since this parasite causes severe clinical symptoms in immunocompromised patients, early diagnosis of toxoplasmosis is essential. PCR is currently used for early diagnosis, but there is no consensus regarding the most effective method for amplifying Toxoplasma DNA. In this study, we considered the utility of the cytochrome c subunit I (cox1) gene, which is encoded in the mitochondrial DNA of this parasite, as a novel target of PCR for the diagnosis of toxoplasmosis...
August 10, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28767123/complete-mitochondrial-genome-of-the-lappet-moth-kunugia-undans-lepidoptera-lasiocampidae-genomic-comparisons-among-macroheteroceran-superfamilies
#15
Min Jee Kim, Jun Seong Jeong, Jong Seok Kim, Su Yeon Jeong, Iksoo Kim
The mitochondrial genome (mitogenome) characteristics of the monotypic Lasiocampoidea are largely unknown, because only limited number of mitogenomes is available from this superfamily. In this study, we sequenced the complete mitogenome of the lappet moth, Kunugia undans (Lepidoptera: Lasiocampidae) and compared it to those of Lasiocampoidea and macroheteroceran superfamilies (59 species in six superfamilies). The 15,570-bp K. undans genome had one additional trnR that was located between trnA and trnN loci and this feature was unique in Macroheterocera, including Lasiocampoidea...
July 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28722338/hdr-del-a-tool-based-on-hamming-distance-for-prioritizing-pathogenic-chromosomal-deletions-in-exome-sequencing
#16
Atsuko Imai-Okazaki, Masakazu Kohda, Kaori Kobayashi, Tomoko Hirata, Yasushi Sakata, Kei Murayama, Akira Ohtake, Yasushi Okazaki, Akihiro Nakaya, Jurg Ott
High-density oligonucleotide arrays have widely been used to detect pathogenic chromosomal deletions. In addition to high-density oligonucleotide arrays, programs using whole-exome sequencing have become available for estimating copy-number variations using depth of coverage. Here, we propose a new statistical method, HDR-del, to prioritize pathogenic chromosomal deletions based on Hamming distance in exome sequencing. In vcf (variant call format) files generated from exome sequencing, hemizygous chromosomal deletion regions lack heterozygous variants and lead to apparent long runs of homozygosity (ROH)...
December 2017: Human Mutation
https://www.readbyqxmd.com/read/28677739/protein-profiling-and-functional-analysis-of-liver-mitochondria-from-rats-with-nonalcoholic-steatohepatitis
#17
Yanting You, Yuxing Zhang, Yuanyuan Lu, Keke Hu, Xiaohu Qu, Yongzhag Liu, Bin Lu, Liqin Jin
Mitochondrial dysfunction is closely associated with the pathogenesis of nonalcoholic steatohepatitis (NASH). The aim of the present study was to comprehensively determine mitochondrial abnormalities in NASH by detecting the proteomics in liver mitochondria in a NASH rat model, which was induced for 16 weeks by the provision of a high fat and high cholesterol diet (HFD). Serum parameters, including triglycerides, total cholesterol, low‑density lipoprotein cholesterol and high‑density lipoprotein cholesterol were determined, and hematoxylin and eosin staining of liver tissues was examined to evaluate the NASH rat model...
September 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28659721/mtdna-as-a-cancer-marker-a-finally-closed-chapter
#18
REVIEW
Elmar Kirches
Sequence alterations of the mitochondrial DNA (mtDNA) have been identified in many tu-mor types. Their nature is not entirely clear. Somatic mutation or shifts of heteroplasmic mtDNA vari-ants may play a role. These sequence alterations exhibit a sufficient frequency in all tumor types investi-gated thus far to justify their use as a tumor marker. This statement is supported by the high copy num-ber of mtDNA, which facilitates the detection of aberrant tumor-derived DNA in bodily fluids. This will be of special interest in tumors, which release a relatively high number of cells into bodily fluids, which are easily accessible, most strikingly in urinary bladder carcinoma...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28652445/increased-copy-number-variation-of-mtdna-in-an-array-based-digital-pcr-assay-predicts-ulcerative-colitis-associated-colorectal-cancer
#19
Toshiaki Tanaka, Takashi Kobunai, Yoko Yamamoto, Koji Murono, Kensuke Otani, Koji Yasuda, Takeshi Nishikawa, Tomomichi Kiyomatsu, Kazushige Kawai, Keisuke Hata, Hiroaki Nozawa, Soichiro Ishihara, Toshiaki Watanabe
AIM: Mitochondrial dysfunction plays a central role in carcinogenesis in numerous cancer-related diseases. We examined the copy number variation of mitochondrial DNA (mtDNA) and the expression of energy-producing genes in relation to ulcerative colitis (UC)-associated carcinogenesis. MATERIALS AND METHODS: We studied 17 patients with UC-associated adenocarcinoma (UC-Ca) and 16 without UC-associated adenocarcinoma (UC-nonCa). The copy number of mtDNA in non-dysplastic mucosa in both groups was quantified by an array-based digital polymerase chain reaction (PCR) assay...
July 2017: In Vivo
https://www.readbyqxmd.com/read/28551263/identification-of-a-chicken-gallus-gallus-endogenous-reference-gene-actb-and-its-application-in-meat-adulteration
#20
Wenjin Xiang, Ying Shang, Qin Wang, Yuancong Xu, Pengyu Zhu, Kunlun Huang, Wentao Xu
The genes commonly used to determine meat species are mainly mitochondrial, but the copy numbers of such genes are high, meaning they cannot be accurately quantified. In this paper, for the first time, the chromosomal gene Actb was selected as an endogenous reference gene for chicken species. It was assayed in four different chicken varieties and 16 other species using both qualitative and quantitative PCR. No amplification of the Actb gene was found in species other than chicken and no allelic variations were detected in chicken...
November 1, 2017: Food Chemistry
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