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https://www.readbyqxmd.com/read/28526069/xlf-mediated-nhej-activity-in-hepatocellular-carcinoma-therapy-resistance
#1
Sitian Yang, Xiao Qi Wang
BACKGROUND: DNA repair pathways are used by cancer cells to overcome many standard anticancer treatments, causing therapy resistance. Here, we investigated the role of XRCC4-like factor (XLF), a core member of the non-homologous end joining (NHEJ) repair pathway, in chemoresistance in hepatocellular carcinoma (HCC). METHODS: qRT-PCR analysis and western blotting were performed to detect expression levels of genes and proteins related to NHEJ. NHEJ repair capacity was assessed in vitro (cell-free) and in vivo by monitoring the activity of the NHEJ pathway...
May 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28525744/ctf4-prevents-genome-rearrangements-by-suppressing-dna-double-strand-break-formation-and-its-end-resection-at-arrested-replication-forks
#2
Mariko Sasaki, Takehiko Kobayashi
Arrested replication forks lead to DNA double-strand breaks (DSBs), which are a major source of genome rearrangements. Yet DSB repair in the context of broken forks remains poorly understood. Here we demonstrate that DSBs that are formed at arrested forks in the budding yeast ribosomal RNA gene (rDNA) locus are normally repaired by pathways dependent on the Mre11-Rad50-Xrs2 complex but independent of HR. HR is also dispensable for DSB repair at stalled forks at tRNA genes. In contrast, in cells lacking the core replisome component Ctf4, DSBs are formed more frequently, and these DSBs undergo end resection and HR-mediated repair that is prone to rDNA hyper-amplification; this highlights Ctf4 as a key regulator of DSB end resection at arrested forks...
May 18, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28523289/core-canonical-pathways-involved-in-developing-human-glioblastoma-multiforme-gbm
#3
Somiranjan Ghosh, Sisir Dutta, Gabriel Thorne, Ava Boston, Alexis Barfield, Narendra Banerjee, Rayshawn Walker, Hirendra Nath Banerjee
Glioblastoma multiforme (GBM) is the most common and aggressive type of the primary brain tumors with pathologic hallmarks of necrosis and vascular proliferation. The diagnosis of GBM is currently mostly based on histological examination of brain tumor tissues, after radiological characterization and surgical biopsy. The ability to characterize tumors comprehensively at the molecular level raises the possibility that diagnosis can be made based on molecular profiling with or without histological examination, rather than solely on histological phenotype...
February 2017: Int J Sci Res Sci Eng Technol
https://www.readbyqxmd.com/read/28521775/genome-wide-association-study-of-subclinical-interstitial-lung-disease-in-mesa
#4
Ani Manichaikul, Xin-Qun Wang, Li Sun, Josée Dupuis, Alain C Borczuk, Jennifer N Nguyen, Ganesh Raghu, Eric A Hoffman, Suna Onengut-Gumuscu, Emily A Farber, Joel D Kaufman, Dan Rabinowitz, Karen D Hinckley Stukovsky, Steven M Kawut, Gary M Hunninghake, George R Washko, George T O'Connor, Stephen S Rich, R Graham Barr, David J Lederer
BACKGROUND: We conducted a genome-wide association study (GWAS) of subclinical interstitial lung disease (ILD), defined as high attenuation areas (HAA) on CT, in the population-based Multi-Ethnic Study of Atherosclerosis Study. METHODS: We measured the percentage of high attenuation areas (HAA) in the lung fields on cardiac CT scan defined as voxels with CT attenuation values between -600 and -250 HU. Genetic analyses were performed in MESA combined across race/ethnic groups: non-Hispanic White (n = 2,434), African American (n = 2,470), Hispanic (n = 2,065) and Chinese (n = 702), as well as stratified by race/ethnicity...
May 18, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28516866/invasive-serotype-35b-pneumococci-including-an-expanding-serotype-switch-lineage-united-states-2015-2016
#5
Sopio Chochua, Benjamin J Metcalf, Zhongya Li, Hollis Walker, Theresa Tran, Lesley McGee, Bernard Beall
We used whole-genome sequencing to characterize 199 nonvaccine serotype 35B pneumococcal strains that caused invasive pneumococcal disease (IPD) in the United States during 2015-2016 and related these findings to previous serotype 35B IPD data obtained by Active Bacterial Core surveillance. Penicillin-nonsusceptible 35B IPD increased during post-pneumococcal 7-valent conjugate vaccine years (2001-2009) and increased further after implementation of pneumococcal 13-valent conjugate vaccine in 2010. This increase was caused primarily by the 35B/sequence type (ST) 558 lineage...
June 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28516862/non-essential-mcm-related-proteins-mediate-a-response-to-dna-damage-in-the-archaeon-methanococcus-maripaludis
#6
Alison D Walters, James P J Chong
The single minichromosome maintenance (MCM) protein found in most archaea has been widely studied as a simplified model for the MCM complex that forms the catalytic core of the eukaryotic replicative helicase. Organisms of the order Methanococcales are unusual in possessing multiple MCM homologues. The Methanococcus maripaludis S2 genome encodes four MCM homologues, McmA-McmD. DNA helicase assays reveal that the unwinding activity of the three MCM-like proteins is highly variable despite sequence similarities and suggests additional motifs that influence MCM function are yet to be identified...
May 18, 2017: Microbiology
https://www.readbyqxmd.com/read/28514311/trends-in-esophageal-and-esophagogastric-junction-cancer-research-from-2007-to-2016-a-bibliometric-analysis
#7
Yan Miao, Ran Liu, Yuepu Pu, Lihong Yin
BACKGROUND: This study aimed to analyze the scientific outputs of esophageal and esophagogastric junction (EGJ) cancer and construct a model to quantitatively and qualitatively evaluate pertinent publications from the past decade. METHODS: Publications from 2007 to 2016 were retrieved from the Web of Science Core Collection database. Microsoft Excel 2016 (Redmond, WA) and the CiteSpace (Drexel University, Philadelphia, PA) software were used to analyze publication outcomes, journals, countries, institutions, authors, research areas, and research frontiers...
May 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28510608/the-biomphalaria-glabrata-dna-methylation-machinery-displays-spatial-tissue-expression-is-differentially-active-in-distinct-snail-populations-and-is-modulated-by-interactions-with-schistosoma-mansoni
#8
Kathrin K Geyer, Umar H Niazi, David Duval, Céline Cosseau, Chad Tomlinson, Iain W Chalmers, Martin T Swain, David J Cutress, Utibe Bickham-Wright, Sabrina E Munshi, Christoph Grunau, Timothy P Yoshino, Karl F Hoffmann
BACKGROUND: The debilitating human disease schistosomiasis is caused by infection with schistosome parasites that maintain a complex lifecycle alternating between definitive (human) and intermediate (snail) hosts. While much is known about how the definitive host responds to schistosome infection, there is comparably less information available describing the snail's response to infection. METHODOLOGY/PRINCIPLE FINDINGS: Here, using information recently revealed by sequencing of the Biomphalaria glabrata intermediate host genome, we provide evidence that the predicted core snail DNA methylation machinery components are associated with both intra-species reproduction processes and inter-species interactions...
May 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28509989/the-dna-sequence-specificity-of-bleomycin-cleavage-in-a-systematically-altered-dna-sequence
#9
Shweta D Gautam, Jon K Chen, Vincent Murray
Bleomycin is an anti-tumour agent that is clinically used to treat several types of cancers. Bleomycin cleaves DNA at specific DNA sequences and recent genome-wide DNA sequencing specificity data indicated that the sequence 5'-RTGT*AY (where T* is the site of bleomycin cleavage, R is G/A and Y is T/C) is preferentially cleaved by bleomycin in human cells. Based on this DNA sequence, we constructed a plasmid clone to explore this bleomycin cleavage preference. By systematic variation of single nucleotides in the 5'-RTGT*AY sequence, we were able to investigate the effect of nucleotide changes on bleomycin cleavage efficiency...
May 16, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/28508482/solving-efficiently-large-single-step-genomic-best-linear-unbiased-prediction-models
#10
I Strandén, K Matilainen, G P Aamand, E A Mäntysaari
Single-step genomic BLUP (ssGBLUP) requires a dense matrix of the size equal to the number of genotyped animals in the coefficient matrix of mixed model equations (MME). When the number of genotyped animals is high, solving time of MME will be dominated by this matrix. The matrix is the difference of two inverse relationship matrices: genomic (G) and pedigree (A22 ). Different approaches were used to ease computations, reduce computing time and improve numerical stability. Inverse of A22 can be computed as A22-1=A22-A21A11-1A12 where A(ij) , i, j = 1,2, are sparse sub-matrices of A(-1) , and numbers 1 and 2 refer to non-genotyped and genotyped animals, respectively...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508360/genome-to-phenome-a-systems-biology-approach-to-ptsd-using-an-animal-model
#11
Nabarun Chakraborty, James Meyerhoff, Marti Jett, Rasha Hammamieh
Post-traumatic stress disorder (PTSD) is a debilitating illness that imposes significant emotional and financial burdens on military families. The understanding of PTSD etiology remains elusive; nonetheless, it is clear that PTSD is manifested by a cluster of symptoms including hyperarousal, reexperiencing of traumatic events, and avoidance of trauma reminders. With these characteristics in mind, several rodent models have been developed eliciting PTSD-like features. Animal models with social dimensions are of particular interest, since the social context plays a major role in the development and manifestation of PTSD...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28507536/temporal-genomic-phylogeny-reconstruction-indicates-a-geospatial-transmission-path-of-salmonella-cerro-in-the-united-states-and-a-clade-specific-loss-of-hydrogen-sulfide-production
#12
Jasna Kovac, Kevin J Cummings, Lorraine D Rodriguez-Rivera, Laura M Carroll, Anil Thachil, Martin Wiedmann
Salmonella Cerro has become one of the most prevalent Salmonella serotypes isolated from dairy cattle in several U.S. states, including New York where it represented 36% of all Salmonella isolates of bovine origin in 2015. This serotype is commonly isolated from dairy cattle with clinical signs of salmonellosis, including diarrhea and fever, although it has also been identified in herds without evidence of clinical disease or decreased production. To better understand the transmission patterns and drivers of its geographic spread, we have studied the genomic similarity and microevolution of S...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28505376/evolutionary-re-wiring-of-p63-and-the-epigenomic-regulatory-landscape-in-keratinocytes-and-its-potential-implications-on-species-specific-gene-expression-and-phenotypes
#13
Isha Sethi, Christian Gluck, Huiqing Zhou, Michael J Buck, Satrajit Sinha
Although epidermal keratinocyte development and differentiation proceeds in similar fashion between humans and mice, evolutionary pressures have also wrought significant species-specific physiological differences. These differences between species could arise in part, by the rewiring of regulatory network due to changes in the global targets of lineage-specific transcriptional master regulators such as p63. Here we have performed a systematic and comparative analysis of the p63 target gene network within the integrated framework of the transcriptomic and epigenomic landscape of mouse and human keratinocytes...
May 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28503311/a-community-resource-for-exploring-and-utilizing-genetic-diversity-in-the-usda-pea-single-plant-plus-collection
#14
William L Holdsworth, Elodie Gazave, Peng Cheng, James R Myers, Michael A Gore, Clarice J Coyne, Rebecca J McGee, Michael Mazourek
Globally, pea (Pisum sativum L.) is an important temperate legume crop for food, feed and fodder, and many breeding programs develop cultivars adapted to these end-uses. In order to assist pea development efforts, we assembled the USDA Pea Single Plant Plus Collection (PSPPC), which contains 431 P. sativum accessions with morphological, geographic and taxonomic diversity. The collection was characterized genetically in order to maximize its value for trait mapping and genomics-assisted breeding. To that end, we used genotyping-by-sequencing-a cost-effective method for de novo single-nucleotide polymorphism (SNP) marker discovery-to generate 66 591 high-quality SNPs...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28500315/network-and-role-analysis-of-autophagy-in-phytophthora-sojae
#15
Linlin Chen, Xiong Zhang, Wen Wang, Xuejing Geng, Yan Shi, Risong Na, Daolong Dou, Honglian Li
Autophagy is an evolutionarily conserved mechanism in eukaryotes with roles in development and the virulence of plant fungal pathogens. However, few reports on autophagy in oomycete species have been published. Here, we identified 26 autophagy-related genes (ATGs) belonging to 20 different groups in Phytophthora sojae using a genome-wide survey, and core ATGs in oomycetes were used to construct a preliminary autophagy pathway model. Expression profile analysis revealed that these ATGs are broadly expressed and that the majority of them significantly increase during infection stages, suggesting a central role for autophagy in virulence...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28499008/rippminer-a-bioinformatics-resource-for-deciphering-chemical-structures-of-ripps-based-on-prediction-of-cleavage-and-cross-links
#16
Priyesh Agrawal, Shradha Khater, Money Gupta, Neetu Sain, Debasisa Mohanty
Ribosomally synthesized and post-translationally modified peptides (RiPPs) constitute a rapidly growing class of natural products with diverse structures and bioactivities. We have developed RiPPMiner, a novel bioinformatics resource for deciphering chemical structures of RiPPs by genome mining. RiPPMiner derives its predictive power from machine learning based classifiers, trained using a well curated database of more than 500 experimentally characterized RiPPs. RiPPMiner uses Support Vector Machine to distinguish RiPP precursors from other small proteins and classify the precursors into 12 sub-classes of RiPPs...
May 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28498961/range-wide-snow-leopard-phylogeography-supports-three-subspecies
#17
Jan E Janecka, Jan E Janecka, Zhang Yu-Guang, Li Di-Qiang, Bariushaa Munkhtsog, Munkhtsog Bayaraa, Naranbaatar Galsandorj, Tshewang R Wangchuk, Dibesh Karmacharya, Thomas McCarthy, Juan Li, Lu Zhi, Kubanychbek Zhumabai Uulu, Ajay Gaur, Satish Kumar, B Kesav Kumar, Shafqat Hussain, Ghulam Muhammad, Matthew Jevit, Charlotte Hacker, Pamela Burger, Claudia Wultsch, Mary J Janecka, Kristofer Helgen, William J Murphy, Rodney Jackson
The snow leopard, Panthera uncia, is an elusive high-altitude specialist that inhabits vast, inaccessible habitat across Asia. We conducted the first range-wide genetic assessment of snow leopards based on noninvasive scat surveys. Thirty-three microsatellites were genotyped and a total of 683-bp of mitochondrial DNA sequenced in 70 individuals. Snow leopards exhibited low genetic diversity at microsatellites (AN = 5.8, HO = 0.433, HE = 0.568), virtually no mtDNA variation, and underwent a bottleneck in the Holocene (~8,000 years ago) coinciding with increased temperatures, precipitation, and upward treeline shift in the Tibetan Plateau...
May 4, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28498372/comparative-transcriptomics-analyses-reveal-the-conservation-of-an-ancestral-infectious-strategy-in-two-bacteriophage-genera
#18
Bob G Blasdel, Anne Chevallereau, Marc Monot, Rob Lavigne, Laurent Debarbieux
Although the evolution of tailed bacteriophages has increasingly been better understood through comparisons of their DNA sequences, the functional consequences of this evolution on phage infectious strategies have remained unresolved. In this study, we comprehensively compared the transcriptional strategies of two related myoviruses, PAK_P3 and PAK_P4, infecting the same Pseudomonas aeruginosa host strain. Outside of the conservation of their structural clusters, their highly syntenic genomes display only limited DNA similarity...
May 12, 2017: ISME Journal
https://www.readbyqxmd.com/read/28494807/concordant-clear-cell-mesonephric-carcinoma-of-the-bladder-and-lung-adenocarcinoma-with-clear-cell-features-multiple-primaries-versus-metastatic-neoplasms-a-case-report
#19
Sarmad H Jassim, Amer Khiyami, Jane K Nguyen, Santhi Ganesan, Joseph Tomashefski, Joram Sawady
BACKGROUND: Clear cell carcinoma of the bladder is a rare variant of urinary bladder adenocarcinoma. We report a case of a patient with clear cell carcinoma of the bladder and a concordant right upper lobe pulmonary adenocarcinoma with clear cell features, and we address the role of immunohistochemistry and cytogenetic analysis in distinguishing the two primary malignancies. CASE PRESENTATION: Our patient was a 59-year-old African American woman who presented with hematuria...
May 12, 2017: Journal of Medical Case Reports
https://www.readbyqxmd.com/read/28491820/endoplasmic-reticulum-stress-unfolded-protein-response-and-cancer-cell-fate
#20
REVIEW
Marco Corazzari, Mara Gagliardi, Gian Maria Fimia, Mauro Piacentini
Perturbation of endoplasmic reticulum (ER) homeostasis results in a stress condition termed "ER stress" determining the activation of a finely regulated program defined as unfolded protein response (UPR) and whose primary aim is to restore this organelle's physiological activity. Several physiological and pathological stimuli deregulate normal ER activity causing UPR activation, such as hypoxia, glucose shortage, genome instability, and cytotoxic compounds administration. Some of these stimuli are frequently observed during uncontrolled proliferation of transformed cells, resulting in tumor core formation and stage progression...
2017: Frontiers in Oncology
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