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https://www.readbyqxmd.com/read/29793041/-selenoproteins-in-colon-cancer
#1
REVIEW
Kristin M Peters, Bradley A Carlson, Vadim N Gladyshev, Petra A Tsuji
Selenocysteine-containing proteins (selenoproteins) have been implicated in the regulation of various cell signaling pathways, many of which are linked to colorectal malignancies. In this in-depth excurse into the selenoprotein literature, we review possible roles for human selenoproteins in colorectal cancer, focusing on the typical hallmarks of cancer cells and their tumor-enabling characteristics. Human genome studies of single nucleotide polymorphisms in various genes coding for selenoproteins have revealed potential involvement of glutathione peroxidases, thioredoxin reductases, and other proteins...
May 21, 2018: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29791254/a-genome-wide-mirna-screen-identifies-regulators-of-tetraploid-cell-proliferation
#2
Marc A Vittoria, Elizabeth M Shenk, Kevin P O'Rourke, Amanda F Bolgioni, Sanghee Lim, Victoria Kacprzak, Ryan J Quinton, Neil J Ganem
Tetraploid cells, which are most commonly generated by errors in cell division, are genomically unstable and have been shown to promote tumorigenesis. Recent genomic studies have estimated that ∼40% of all solid tumors have undergone a genome-doubling event during their evolution, suggesting a significant role for tetraploidy in driving the development of human cancers. To safeguard against the deleterious effects of tetraploidy, non transformed cells that fail mitosis and become tetraploid activate both the Hippo and p53 tumor suppressor pathways to restrain further proliferation...
May 23, 2018: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/29790070/genotyping-single-sperm-cells-by-universal-marsala-enables-the-acquisition-of-linkage-information-for-combined-pre-implantation-genetic-diagnosis-and-genome-screening
#3
Haitao Wu, Xiaoting Shen, Lei Huang, Yanhong Zeng, Yumei Gao, Lin Shao, Baomin Lu, Yiping Zhong, Benyu Miao, Yanwen Xu, Yali Wang, Yubin Li, Luoxing Xiong, Sijia Lu, X Sunney Xie, Canquan Zhou
PURPOSE: This paper aims to investigate the feasibility of performing pre-implantation genetic diagnosis (PGD) and pre-implantation genetic screening (PGS) simultaneously by a universal strategy without the requirement of genotyping relevant affected family members or lengthy preliminary work on linkage analysis. METHODS: By utilizing a universal Mutated Allele Revealed by Sequencing with Aneuploidy and Linkage Analyses (MARSALA) strategy based on low depth whole genome sequencing (~3x), not involving specific primers' design nor the enrichment of SNP markers for haplotype construction...
May 22, 2018: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/29789419/detection-of-bladder-cancer-via-microfluidic-immunoassay-and-single-cell-dna-copy-number-alteration-analysis-of-captured-urinary-exfoliated-tumor-cells
#4
Anqi Chen, Guanghou Fu, Zhijie Xu, Yukun Sun, Xiaoyi Chen, Kok Suen Cheng, Kuang Hong Neoh, Zhewen Tang, Shifu Chen, Ming Liu, Tanxiao Huang, Yun Dai, Qibo Wang, Jing Jin, Baiye Jin, Ray P S Han
The increasing incidence of bladder cancer (BC) and its high rate of recurrence over a 5-year period necessitate the need for diagnosis and surveillance amelioration. Cystoscopy and urinary cytology are the current tools, and molecular techniques such as BTA stat, NMP22, survivin mRNA, and urovysion FISH have attracted attention, however, they suf-fer from insufficient sensitivity or specificity. We developed a novel microfluidic approach for harvesting intact urinary-exfoliated tumor cells (UETCs), either individually or in clus-ters, in a clean and segregated environment, which is crucial to minimize cross-contamination and misreads...
May 22, 2018: Cancer Research
https://www.readbyqxmd.com/read/29789392/fam35a-associates-with-rev7-and-modulates-dna-damage-responses-of-normal-and-brca1-defective-cells
#5
Junya Tomida, Kei-Ichi Takata, Sarita Bhetawal, Maria D Person, Hsueh-Ping Chao, Dean G Tang, Richard D Wood
To exploit vulnerabilities of tumors, it is urgent to identify associated defects in genome maintenance. One unsolved problem is the mechanism of regulation of DNA double-strand break repair by REV7 in complex with 53BP1 and RIF1, and its influence on repair pathway choice between homologous recombination and non-homologous end-joining. We searched for REV7-associated factors in human cells and found FAM35A, a previously unstudied protein with an unstructured N-terminal region and a C-terminal region harboring three OB-fold domains similar to single-stranded DNA-binding protein RPA, as novel interactor of REV7/RIF1/53BP1...
May 22, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29788371/selective-nanopore-sequencing-of-human-brca1-by-cas9-assisted-targeting-of-chromosome-segments-catch
#6
Tslil Gabrieli, Hila Sharim, Dena Fridman, Nissim Arbib, Yael Michaeli, Yuval Ebenstein
Next generation sequencing (NGS) is challenged by structural and copy number variations larger than the typical read length of several hundred bases. Third-generation sequencing platforms such as single-molecule real-time (SMRT) and nanopore sequencing provide longer reads and are able to characterize variations that are undetected in NGS data. Nevertheless, these technologies suffer from inherent low throughput which prohibits deep sequencing at reasonable cost without target enrichment. Here, we optimized Cas9-Assisted Targeting of CHromosome segments (CATCH) for nanopore sequencing of the breast cancer gene BRCA1...
May 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29788099/biomarkers-for-homologous-recombination-deficiency-in-cancer
#7
Michal M Hoppe, Raghav Sundar, David S P Tan, Anand D Jeyasekharan
Defective DNA repair is a common hallmark of cancer. Homologous recombination is a DNA repair pathway of clinical interest due to the sensitivity of homologous recombination-deficient cells to poly-ADP ribose polymerase (PARP) inhibitors. The measurement of homologous recombination deficiency (HRD) in cancer is therefore vital to the appropriate design of clinical trials incorporating PARP inhibitors. However, methods to identify HRD in tumors are varied and controversial. Understanding existing and new methods to measure HRD is important to their appropriate use in clinical trials and practice...
May 18, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29787441/exome-sequencing-discloses-ionizing-radiation-induced-dna-variants-in-the-genome-of-human-gingiva-fibroblasts
#8
Neetika Nath, Jennifer Esche, Jessica Müller, Lars R Jensen, Matthias Port, Mario Stanke, Lars Kaderali, Harry Scherthan, Andreas W Kuss
Ionizing radiation can induce genomic lesions such as DNA double-strand breaks whose incomplete or faulty repair can result in mutations, which in turn can influence cellular functions and alter the fate of affected cells and organ systems. Ionizing-radiation-induced sequence alterations/mutations occur in a stochastic manner, which contributes to an increased cancer risk in irradiated individuals. Ionizing radiation exposure, and particularly acute doses at high dose rates (as often observed in radiation accidents), induce alterations in the genome that in part will reflect specific characteristics of the DNA damage response and the repair mechanisms involved...
July 2018: Health Physics
https://www.readbyqxmd.com/read/29787419/a-locus-at-7p14-3-predisposes-to-refractory-celiac-disease-progression-from-celiac-disease
#9
Barbara Hrdlickova, Chris J Mulder, Georgia Malamut, Bertrand Meresse, Mathieu Platteel, Yoichiro Kamatani, Isis Ricaño-Ponce, Roy L J van Wanrooij, Maria M Zorro, Marc Jan Bonder, Javier Gutierrez-Achury, Christophe Cellier, Alexandra Zhernakova, Petula Nijeboer, Pilar Galan, Sebo Withoff, Mark Lathrop, Gerd Bouma, Ramnik J Xavier, Bana Jabri, Nadine C Bensussan, Cisca Wijmenga, Vinod Kumar
BACKGROUND: Approximately 5% of patients with celiac disease (CeD) do not respond to a gluten-free diet and progress to refractory celiac disease (RCD), a severe progression that is characterized by infiltration of intraepithelial T lymphocytes. Patients with RCD type II (RCDII) show clonal expansions of intraepithelial T lymphocytes that result in a poor prognosis and a high mortality rate through development of aggressive enteropathy-associated T-cell lymphoma. It is not known whether genetic variations play a role in severe progression of CeD to RCDII...
May 21, 2018: European Journal of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/29785042/inducible-high-efficiency-crispr-cas9-targeted-gene-editing-and-precision-base-editing-in-african-trypanosomes
#10
Eva Rico, Laura Jeacock, Julie Kovářová, David Horn
The Cas9 endonuclease can be programmed by guide RNA to introduce sequence-specific breaks in genomic DNA. Thus, Cas9-based approaches present a range of novel options for genome manipulation and precision editing. African trypanosomes are parasites that cause lethal human and animal diseases. They also serve as models for studies on eukaryotic biology, including 'divergent' biology. Genome modification, exploiting the native homologous recombination machinery, has been important for studies on trypanosomes but often requires multiple rounds of transfection using selectable markers that integrate at low efficiency...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29785013/genetic-identification-of-brain-cell-types-underlying-schizophrenia
#11
Nathan G Skene, Julien Bryois, Trygve E Bakken, Gerome Breen, James J Crowley, Héléna A Gaspar, Paola Giusti-Rodriguez, Rebecca D Hodge, Jeremy A Miller, Ana B Muñoz-Manchado, Michael C O'Donovan, Michael J Owen, Antonio F Pardiñas, Jesper Ryge, James T R Walters, Sten Linnarsson, Ed S Lein, Patrick F Sullivan, Jens Hjerling-Leffler
With few exceptions, the marked advances in knowledge about the genetic basis of schizophrenia have not converged on findings that can be confidently used for precise experimental modeling. By applying knowledge of the cellular taxonomy of the brain from single-cell RNA sequencing, we evaluated whether the genomic loci implicated in schizophrenia map onto specific brain cell types. We found that the common-variant genomic results consistently mapped to pyramidal cells, medium spiny neurons (MSNs) and certain interneurons, but far less consistently to embryonic, progenitor or glial cells...
May 21, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29785002/using-single-molecule-mrna-fluorescent-in-situ-hybridization-rna-fish-to-quantify-mrnas-in-individual-murine-oocytes-and-embryos
#12
Fang Xie, Kelsey A Timme, Jennifer R Wood
Changes in abundance of mRNAs during oocyte growth and maturation and during pre-implantation embryo development have been documented using quantitative real-time RT-PCR (qPCR), microarray analyses, and whole genome sequencing. However, these techniques require amplification of mRNAs, normalization using housekeeping genes, can be biased for abundant transcripts, and/or require large numbers of oocytes and embryos which can be difficult to acquire from mammalian species. We optimized a single molecule RNA fluorescence in situ hybridization (RNA-FISH) protocol, which amplifies fluorescence signal to detect candidate transcripts, for use with individual oocytes and embryos...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784674/clinically-relevant-cytotoxic-immune-cell-signatures-and-clonal-expansion-of-t-cell-receptors-in-high-risk-mycn-not-amplified-human-neuroblastoma
#13
Jun S Wei, Igor B Kuznetsov, Shile Zhang, Young K Song, Shahab Asgharzadeh, Sivasish Sindiri, Xinyu Wen, Rajesh Patidar, Sushma Nagaraj, Ashley Walton, Jaime M Guidry Auvil, Daniela S Gerhard, Aysen Yuksel, Daniel R Catchpoole, Stephen M Hewitt, Paul M Sondel, Robert C Seeger, John M Maris, Javed Khan
PURPOSE: High-risk neuroblastoma is an aggressive disease. DNA sequencing studies have revealed a paucity of actionable genomic alterations and a low mutation burden, posing challenges to develop effective novel therapies. We used RNA sequencing (RNA-seq) to investigate the biology of this disease including a focus on tumor-infiltrating lymphocytes (TILs). EXPERIMENTAL DESIGN: We performed deep RNA-seq on pre-treatment diagnostic tumors from 129 high-risk and 21 low- or intermediate-risk patients with neuroblastomas...
May 21, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29783949/gene-copy-number-variation-in-natural-populations-of-plasmodium-falciparum-in-eastern-africa
#14
Joan Simam, Martin Rono, Joyce Ngoi, Mary Nyonda, Sachel Mok, Kevin Marsh, Zbynek Bozdech, Margaret Mackinnon
BACKGROUND: Gene copy number variants (CNVs), which consist of deletions and amplifications of single or sets of contiguous genes, contribute to the great diversity in the Plasmodium falciparum genome. In vitro studies in the laboratory have revealed their important role in parasite fitness phenotypes such as red cell invasion, transmissibility and cytoadherence. Studies of natural parasite populations indicate that CNVs are also common in the field and thus may facilitate adaptation of the parasite to its local environment...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783762/live-cell-imaging-of-early-steps-of-single-hiv-1-infection
#15
REVIEW
Ashwanth C Francis, Gregory B Melikyan
Live-cell imaging of single HIV-1 entry offers a unique opportunity to delineate the spatio-temporal regulation of infection. Novel virus labeling and imaging approaches enable the visualization of key steps of HIV-1 entry leading to nuclear import, integration into the host genome, and viral protein expression. Here, we discuss single virus imaging strategies, focusing on live-cell imaging of single virus fusion and productive uncoating that culminates in HIV-1 infection.
May 19, 2018: Viruses
https://www.readbyqxmd.com/read/29783694/adaptive-mutations-in-influenza-a-california-07-2009-enhance-polymerase-activity-and-infectious-virion-production
#16
Patrick D Slaine, Cara MacRae, Mariel Kleer, Emily Lamoureux, Sarah McAlpine, Michelle Warhuus, André M Comeau, Craig McCormick, Todd Hatchette, Denys A Khaperskyy
Mice are not natural hosts for influenza A viruses (IAVs), but they are useful models for studying antiviral immune responses and pathogenesis. Serial passage of IAV in mice invariably causes the emergence of adaptive mutations and increased virulence. Here, we report the adaptation of IAV reference strain A/California/07/2009(H1N1) (also known as CA/07) in outbred Swiss Webster mice. Serial passage led to increased virulence and lung titers, and dissemination of the virus to brains. We adapted a deep-sequencing protocol to identify and enumerate adaptive mutations across all genome segments...
May 18, 2018: Viruses
https://www.readbyqxmd.com/read/29783088/evaluation-of-genotoxicity-and-mutagenic-effects-of-vector-dna-nanocomplexes-in-transfected-mesenchymal-stem-cells-by-flow-cytometry
#17
Alireza Nomani, Xuguang Chen, Arash Hatefi
In recent years, there has been a great deal of interest in ex-vivo genetic modification of mesenchymal stem cells (MSCs) to meet various biomedical needs. Considering the self-renewal potential of MSCs, it is critically important to ensure that transfection vectors (gene carriers) do not induce genotoxicity because they could theoretically turn a single stem cell into a cancer-initiating cell. Unfortunately, there is currently no reliable, unbiased, and quantitative method to measure genotoxicity (micronuclei formation) of gene carriers directly in transfected MSCs...
May 18, 2018: Acta Biomaterialia
https://www.readbyqxmd.com/read/29782554/hijacking-of-multiple-phospholipid-biosynthetic-pathways-and-induction-of-membrane-biogenesis-by-a-picornaviral-3cd-protein
#18
Sravani Banerjee, David Aponte-Diaz, Calvin Yeager, Suresh D Sharma, Gang Ning, Hyung S Oh, Qingxia Han, Masato Umeda, Yuji Hara, Robert Y L Wang, Craig E Cameron
RNA viruses induce specialized membranous structures for use in genome replication. These structures are often referred to as replication organelles (ROs). ROs exhibit distinct lipid composition relative to other cellular membranes. In many picornaviruses, phosphatidylinositol-4-phosphate (PI4P) is a marker of the RO. Studies to date indicate that the viral 3A protein hijacks a PI4 kinase to induce PI4P by a mechanism unrelated to the cellular pathway, which requires Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1, GBF1, and ADP ribosylation factor 1, Arf1...
May 21, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29780504/gene-specific-loci-quantitative-and-single-base-resolution-analysis-of-5-formylcytosine-by-compound-mediated-polymerase-chain-reaction
#19
Yafen Wang, Chaoxing Liu, Xiong Zhang, Wei Yang, Fan Wu, Guangrong Zou, Xiaocheng Weng, Xiang Zhou
5-Formylcytosine (5fC) is known as one of the key players in the process of active DNA demethylation and displays essential epigenetic functions in mammals. In spite of the blooming development of whole genome sequencing methods for this modified cytosine base, the easily operated gene specific-loci detection of 5fC has rarely been reported. Herein, we present a compound-mediated analysis of the content and site of 5fC by the polymerase chain reaction (PCR) assay. The molecule, namely azi-BP, which can selectively label 5fC and form a huge group through a click chemistry reaction, hindering the amplification activity of Taq DNA polymerase, acts as a "roadblock" and enables the quantitative analysis of 5fC by quantitative polymerase chain reaction (qPCR)...
April 21, 2018: Chemical Science
https://www.readbyqxmd.com/read/29780001/automated-typing-of-red-blood-cell-and-platelet-antigens-a-whole-genome-sequencing-study
#20
William J Lane, Connie M Westhoff, Nicholas S Gleadall, Maria Aguad, Robin Smeland-Wagman, Sunitha Vege, Daimon P Simmons, Helen H Mah, Matthew S Lebo, Klaudia Walter, Nicole Soranzo, Emanuele Di Angelantonio, John Danesh, David J Roberts, Nick A Watkins, Willem H Ouwehand, Adam S Butterworth, Richard M Kaufman, Heidi L Rehm, Leslie E Silberstein, Robert C Green
BACKGROUND: There are more than 300 known red blood cell (RBC) antigens and 33 platelet antigens that differ between individuals. Sensitisation to antigens is a serious complication that can occur in prenatal medicine and after blood transfusion, particularly for patients who require multiple transfusions. Although pre-transfusion compatibility testing largely relies on serological methods, reagents are not available for many antigens. Methods based on single-nucleotide polymorphism (SNP) arrays have been used, but typing for ABO and Rh-the most important blood groups-cannot be done with SNP typing alone...
May 17, 2018: Lancet Haematology
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