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https://www.readbyqxmd.com/read/29353061/next-generation-sequencing-to-detect-deletion-of-rb1-and-erbb4-genes-in-chromophobe-renal-cell-carcinoma-a-potential-role-in-distinguishing-chromophobe-renal-cell-carcinoma-from-renal-oncocytoma
#1
Qingqing Liu, Kristine M Cornejo, Liang Cheng, Lloyd Hutchinson, Mingsheng Wang, Shaobo Zhang, Keith Tomaszewicz, Ediz F Cosar, Bruce A Woda, Zhong Jiang
Overlapping morphological, immunohistochemical, and ultrastructural features make it difficult to diagnose chromophobe renal cell carcinoma (ChRCC) and renal oncocytoma (RO). Since ChRCC is a malignant tumor, whereas RO is a tumor with benign behavior, it is important to distinguish these two entities. We aimed to identify genetic markers that distinguish ChRCC from RO by using next-generation sequencing (NGS). NGS for hotspot mutations or gene copy number changes was performed on 12 renal neoplasms including seven ChRCC and five RO cases...
January 15, 2018: American Journal of Pathology
https://www.readbyqxmd.com/read/29352723/which-hiv-infected-adults-with-high-cd4-t-cell-counts-benefit-most-from-immediate-initiation-of-antiretroviral-therapy-a-post-hoc-subgroup-analysis-of-the-start-trial
#2
Jean-Michel Molina, Birgit Grund, Fred Gordin, Ian Williams, Mauro Schechter, Marcello Losso, Matthew Law, Ernest Ekong, Noluthando Mwelase, Athanasios Skoutelis, Martin J Wiselka, Linos Vandekerckhove, Thomas Benfield, David Munroe, Jens D Lundgren, James D Neaton
BACKGROUND: Immediate initiation of antiretroviral therapy (ART) in asymptomatic adults with CD4 counts higher than 500 cells per μL, as recommended, might not always be possible in resource-limited settings. We aimed to identify subgroups of individuals who would benefit most from immediate treatment. METHODS: The START trial was a randomised controlled trial in asymptomatic, HIV-positive adults previously untreated with ART. Participants with CD4 counts higher than 500 cells per μL were randomly assigned to receive immediate ART or to defer ART until CD4 counts were lower than 350 cells per μL...
January 15, 2018: Lancet HIV
https://www.readbyqxmd.com/read/29352198/orid-structure-controls-repd-initiation-during-rolling-circle-replication
#3
Algirdas Toleikis, Martin R Webb, Justin E Molloy
Bacterial antibiotic resistance is often carried by circular DNA plasmids that are copied separately from the genomic DNA and can be passed to other bacteria, spreading the resistance. The chloramphenicol-resistance plasmid pC221 from Staphylococcus aureus is duplicated by a process called asymmetric rolling circle replication. It is not fully understood how the replication process is regulated but its initiation requires a plasmid-encoded protein called RepD that nicks one strand of the parent plasmid at the double-stranded origin of replication (oriD)...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352159/3-3-diaminobenzidine-staining-interferes-with-pcr-based-dna-analysis
#4
Christian Dölle, Laurence A Bindoff, Charalampos Tzoulis
3,3'-Diaminobenzidine (DAB) is a widely used chromogen in histological staining methods and stained tissue is often used in downstream molecular analyses such as quantitative PCR (qPCR). Using microdissected muscle fibers from sequential muscle sections stained by DAB-dependent and -independent methods, we show that DAB exerts a strong inhibitory effect on qPCR-based mitochondrial DNA quantification. This effect introduces a significant bias in the estimation of mitochondrial DNA copy number and deletion levels between DAB-positive and -negative fibers...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352111/hepatic-smarca4-predicts-hcc-recurrence-and-promotes-tumour-cell-proliferation-by-regulating-smad6-expression
#5
Zhiao Chen, Xinyuan Lu, Deshui Jia, Ying Jing, Di Chen, Qifeng Wang, Fangyu Zhao, Jinjun Li, Ming Yao, Wenming Cong, Xianghuo He
Hepatocellular carcinoma (HCC) is the most common form of liver cancer and is typically diagnosed at advanced stages. Identification and characterisation of genes within amplified and deleted chromosomal loci can provide new insights into the pathogenesis of cancer and lead to new approaches for diagnosis and therapy. In our previous study, we found a recurrent region of copy number amplification at 19p13.2 in hepatocellular carcinoma (HCC). In the present study, we performed integrated copy number analysis and expression profiling at this locus and a putative cancer gene, SMARCA4/BRG1, was uncovered in this region...
January 19, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29351800/drug-resistance-genes-pvcrt-o-and-pvmdr-1-polymorphism-in-patients-from-malaria-endemic-south-western-coastal-region-of-india
#6
Shiny Joy, Benudhar Mukhi, Susanta K Ghosh, Rajeshwara N Achur, D Channe Gowda, Namita Surolia
BACKGROUND: Malaria is highly prevalent in many parts of India and is mostly caused by the parasite species Plasmodium vivax followed by Plasmodium falciparum. Chloroquine (CQ) is the first-line treatment for blood stage P. vivax parasites, but cases of drug resistance to CQ have been reported from India. One of the surveillance strategies which is used to monitor CQ drug resistance, is the analysis of single nucleotide polymorphisms (SNPs) of the associated gene markers. Susceptibility to CQ can also be determined by copy number assessment of multidrug resistant gene (mdr-1)...
January 19, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29351764/quantification-and-kinetics-of-viral-rna-transcripts-produced-in-orthohantavirus-infected-cells
#7
Julia Wigren Byström, Jonas Näslund, Fredrik Trulsson, Magnus Evander, Olivia Wesula Lwande, Clas Ahlm, Göran Bucht
BACKGROUND: Rodent borne viruses of the Orthohantavirus genus cause hemorrhagic fever with renal syndrome among people in Eurasia, and hantavirus cardiopulmonary syndrome in the Americas. At present, there are no specific treatments or efficient vaccines against these diseases. Improved understanding of viral transcription and replication may instigate targeted treatment of Orthohantavirus infections. For this purpose, we investigated the kinetics and levels of viral RNA transcription during an ongoing infection in-vitro...
January 19, 2018: Virology Journal
https://www.readbyqxmd.com/read/29351733/glutamate-synthases-from-conifers-gene-structure-and-phylogenetic-studies
#8
Ángel García-Gutiérrez, Francisco M Cánovas, Concepción Ávila
BACKGROUND: Plants synthesize glutamate from ammonium by the combined activity of the enzymes glutamine synthetase (GS) and glutamate synthase (GOGAT) through the glutamate synthase cycle. In plants, there are two forms of glutamate synthases that differ in their electron donors, NADH-GOGAT (EC 1.4.1.14) and Fd-GOGAT (EC 1.4.7.1), which have differential roles either in primary ammonia assimilation or in the reassimilation of ammonium from different catabolic processes. Glutamate synthases are complex iron-sulfur flavoproteins containing functional domains involved in the control and coordination of their catalytic activities in annual plants...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29351293/fibroblast-growth-factor-receptor-1-amplification-in-laryngeal-squamous-cell-carcinoma
#9
Jesus Monico, Brandon Miller, Luminita Rezeanu, Warren May, Donna C Sullivan
Fibroblast growth factor receptor 1 (FGFR1) has been noted to be amplified in a variety of squamous cell carcinomas (SCCa) of the head, neck, and lung and increased copy number (CN) is a predictor of poor outcomes. FGFR1 is a therapeutic target for lung SCCa and inhibition therapy is currently in clinical trials. Absolute quantification of FGFR1 from formalin fixed paraffin embedded (FFPE) tissue of laryngeal SCCa was examined in this retrospective study. A droplet digital polymerase chain reaction (ddPCR) was used for absolute quantitation of the FGFR1 gene CN...
2018: PloS One
https://www.readbyqxmd.com/read/29350171/the-dna-copy-number-landscape-of-a-collision-tumor
#10
Hugh Kearney, Jane B Cryan, Seamus Looby, Francesca M Brett, Michael A Farrell, Patrick G Buckley
Intracranial collision tumors are composed of two histologically distinct but merging components, and are rare. Their genetic profile has rarely been described. Comparative genome hybridization of a combined meningioma and oligodendroglioma demonstrated deletion of chromosome 22q and of 19q in both tumors. Somatic deletion of chromosome 22q and 19q is associated with development of an intracranial collision tumor.
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January 19, 2018: Clinical Neuropathology
https://www.readbyqxmd.com/read/29348864/the-macro-evolutionary-events-in-esophageal-squamous-cell-carcinoma
#11
Bin Yang, Ting Yan, Heyang Cui, Enwei Xu, Yanchun Ma, Caixia Cheng, Ling Zhang, Pengzhou Kong, Fang Wang, Yu Qian, Jian Yang, Yaoping Li, Hongyi Li, Yanghui Bi, Xiaoling Hu, Juan Wang, Bin Song, Jie Yang, Wei Gao, Jing Liu, Binbin Zou, Ruyi Shi, Yanyan Zhang, Haiyan Liu, Yiqian Liu, Yuanfang Zhai, Lu Chang, Yi Wang, Yingchun Zhang, Zhiwu Jia, Xing Chen, Yanfeng Xi, Guodong Li, Jianfang Liang, Jiansheng Guo, Shiping Guo, Rongsheng Zhang, Xiaolong Cheng, Yongping Cui
Understanding the evolutionary processes operative in cancer genome may provide insights into clinical outcome and drug-resistance. However, studies focus on genomic signatures, especially for macro-evolutionary events, in esophageal squamous cell carcinoma (ESCC) are limited. Here, we integrated published genomic sequencing data to investigate underlying evolutionary characteristics in ESCC. We found most of ESCC genomes were polyploidy with high genomic instability. Whole genome doubling that acts as one of mechanisms for polyploidy was predicted as a late event in the majority of ESCC genome...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348835/simultaneous-quantification-of-dna-damage-and-mitochondrial-copy-number-by-long-run-dna-damage-quantification-lord-q
#12
Benjamin Dannenmann, Simon Lehle, Sebastian Lorscheid, Stephan M Huber, Frank Essmann, Klaus Schulze-Osthoff
DNA damage and changes in the mitochondrial DNA content have been implicated in ageing and cancer development. To prevent genomic instability and tumorigenesis, cells must maintain the integrity of their nuclear and mitochondrial DNA. Advances in the research of DNA damage protection and genomic stability, however, also depend on the availability of techniques that can reliably quantify alterations of mitochondrial DNA copy numbers and DNA lesions in an accurate high-throughput manner. Unfortunately, no such method has been established yet...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348203/infectious-virus-in-exhaled-breath-of-symptomatic-seasonal-influenza-cases-from-a-college-community
#13
Jing Yan, Michael Grantham, Jovan Pantelic, P Jacob Bueno de Mesquita, Barbara Albert, Fengjie Liu, Sheryl Ehrman, Donald K Milton
Little is known about the amount and infectiousness of influenza virus shed into exhaled breath. This contributes to uncertainty about the importance of airborne influenza transmission. We screened 355 symptomatic volunteers with acute respiratory illness and report 142 cases with confirmed influenza infection who provided 218 paired nasopharyngeal (NP) and 30-minute breath samples (coarse >5-µm and fine ≤5-µm fractions) on days 1-3 after symptom onset. We assessed viral RNA copy number for all samples and cultured NP swabs and fine aerosols...
January 18, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29348129/genomic-cdkn2a-2b-deletions-in-adult-ph-all-are-adverse-despite-allogeneic-stem-cell-transplantation
#14
Heike Pfeifer, Katharina Raum, Sandra Markovic, Verena Nowak, Stephanie Fey, Julia Obländer, Jovita Pressler, Verena Böhm, Monika Brüggemann, Lydia Wunderle, Andreas Hüttmann, Ralph Wäsch, Joachim Beck, Matthias Stelljes, Andreas Viardot, Fabian Lang, Dieter Hoelzer, Wolf-Karsten Hofmann, Hubert Serve, Christel Weiss, Nicola Goekbuget, Oliver G Ottmann, Daniel Nowak
We investigated the role of copy number alterations to refine risk stratification in adult Philadelphia chromosome positive (Ph)+ ALL treated with tyrosine kinase inhibitors (TKI) and allogeneic stem cell transplantation (aSCT). 97 Ph+ ALL patients (median age 41 years, range 18-64 years) within the prospective multicenter GMALL studies 06/99 (n=8) and 07/2003 (n=89) were analysed. All patients received TKI and aSCT in first complete remission (CR1). Copy number analysis was performed with SNP arrays and validated by multiplex ligation-dependent probe amplification (MLPA)...
January 18, 2018: Blood
https://www.readbyqxmd.com/read/29347590/emergent-l%C3%A3-vy-behavior-in-single-cell-stochastic-gene-expression
#15
Chen Jia, Michael Q Zhang, Hong Qian
Single-cell gene expression is inherently stochastic; its emergent behavior can be defined in terms of the chemical master equation describing the evolution of the mRNA and protein copy numbers as the latter tends to infinity. We establish two types of "macroscopic limits": the Kurtz limit is consistent with the classical chemical kinetics, while the Lévy limit provides a theoretical foundation for an empirical equation proposed in N. Friedman et al., Phys. Rev. Lett. 97, 168302 (2006)PRLTAO0031-900710.1103/PhysRevLett...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346604/unique-genetic-profiles-from-cerebrospinal-fluid-cell-free-dna-in-leptomeningeal-metastases-of-egfr-mutant-non-small-cell-lung-cancer-a-new-medium-of-liquid-biopsy
#16
Y S Li, B Y Jiang, J J Yang, X C Zhang, Z Zhang, J Y Ye, W Z Zhong, H Y Tu, H J Chen, Z Wang, C R Xu, B C Wang, H J Du, S Chuai, H Han-Zhang, J Su, Q Zhou, X N Yang, W B Guo, H H Yan, Y H Liu, L X Yan, B Huang, M M Zheng, Y L Wu
Background: Leptomeningeal metastases (LM) are more frequent in non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations. Due to limited access to leptomeningeal lesions, the purpose of this study was to explore the potential role of cerebrospinal fluid (CSF) as a source of liquid biopsy in patients with LM. Patients and methods: Primary tumor, CSF, and plasma in NSCLC with LM were tested by next-generation sequencing. In total, 45 patients with suspected LM underwent lumbar puncture, and those with EGFR mutations diagnosed with LM were enrolled...
January 15, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29346534/microbial-community-structure-of-sea-spray-aerosols-at-three-california-beaches
#17
Katherine Graham, Linsey C Marr, Lauren M Sassoubre, Alexandria B Boehm
We characterized the microbial communities in SSA, water, and sand of three beaches in central California (Cowell Beach, Baker Beach, and Lovers Point) by sequencing the V4 region of the 16S rRNA gene. Average concentrations of 16S rRNA genes in SSA ranged from 2.4 × 104 to 1.4 × 105 gene copies per m3 of air. A total of 9,781 distinct OTUs were identified in SSA and of these, 1,042 OTUs were found in SSA of all beaches. SSA microbial communities included marine taxa, as well as some associated with the terrestrial environment...
January 15, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29346492/author-response-increased-mtdna-copy-number-protects-against-lhon
#18
Angelica Bianco, Luigi L Palese, Silvana Guerriero, Vittoria Petruzzella
No abstract text is available yet for this article.
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29346491/increased-mtdna-copy-number-does-not-protect-against-lhon
#19
Josef Finsterer, Sinda Zarrouk-Mahjoub
No abstract text is available yet for this article.
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29346449/within-host-selection-for-faster-replicating-bacterial-symbionts
#20
Ewa Chrostek, Luis Teixeira
Wolbachia is a widespread, intracellular symbiont of arthropods, able to induce reproductive distortions and antiviral protection in insects. Wolbachia can also be pathogenic, as is the case with wMelPop, a virulent variant of the endosymbiont of Drosophila melanogaster. An extensive genomic amplification of the 20kb region encompassing eight Wolbachia genes, called Octomom, is responsible for wMelPop virulence. The Octomom copy number in wMelPop can be highly variable between individual D. melanogaster flies, even when comparing siblings arising from a single female...
2018: PloS One
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