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https://www.readbyqxmd.com/read/28214969/attached-and-suspended-denitrifier-communities-in-pristine-limestone-aquifers-harbor-high-fractions-of-potential-autotrophs-oxidizing-reduced-iron-and-sulfur-compounds
#1
M Herrmann, S Opitz, R Harzer, K U Totsche, K Küsel
Oxygen and nitrate availability as well as the presence of suitable organic or inorganic electron donors are strong drivers of denitrification; however, the factors influencing denitrifier abundance and community composition in pristine aquifers are not well understood. We explored the denitrifier community structure of suspended and attached groundwater microorganisms in two superimposed limestone aquifer assemblages with contrasting oxygen regime in the Hainich Critical Zone Exploratory (Germany). Attached communities were retrieved from freshly crushed parent rock material which had been exposed for colonization in two groundwater wells (12...
February 18, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28213542/plant-community-and-nitrogen-deposition-as-drivers-of-%C3%AE-and-%C3%AE-prokaryotic-diversity-in-reconstructed-oil-sands-soils-and-natural-boreal-forest-soils
#2
Jacynthe Masse, Cindy E Prescott, Sébastien Renaut, Yves Terrat, Sue J Grayston
The Athabasca Oil Sands deposit is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil-like profiles that can support the previous land capabilities. The objective of this study was to assess if soil prokaryotic α- and β-diversity in oil-sands soils reconstructed 20-30 years previously, and planted to one of three vegetation types (coniferous or deciduous trees and grassland) were similar to those found in natural boreal-forest soils subject to wildfire disturbance...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28212593/micrornas-and-endometriosis-distinguishing-drivers-from-passengers-in-disease-pathogenesis
#3
Warren B Nothnick
Endometriosis is a disease common in women of reproductive age, characterized by pelvic pain and infertility. Despite its prevalence, the factors and mechanisms which contribute to the development and survival of ectopic lesions remain uncertain. MicroRNAs (miRNAs) are small RNA molecules that regulate posttranscriptional gene regulation which have been proposed to contribute to the pathogenesis of many diseases including that of endometriosis. This review summarizes the results of initial studies describing differentially expressed miRNAs between endometriotic lesion tissue and eutopic endometrium...
February 17, 2017: Seminars in Reproductive Medicine
https://www.readbyqxmd.com/read/28210881/comprehensive-genomic-profiling-of-malignant-phyllodes-tumors-of-the-breast
#4
Sahar Nozad, Christine E Sheehan, Laurie M Gay, Julia A Elvin, Jo-Anne Vergilio, James Suh, Shakti Ramkissoon, Alexa B Schrock, Kim M Hirshfield, Nadia Ali, Shridar Ganesan, Siraj M Ali, Vincent A Miller, Philip J Stephens, Jeffrey S Ross, Jon H Chung
PURPOSE: Malignant phyllodes tumors (MPT) are exceptionally rare, and the genomic drivers of these tumors are still being elucidated. We performed comprehensive genomic profiling (CGP) of MPT to identify genomic alterations that will inform approaches to targeted therapy for patients with MPT, including relapsed, refractory, and metastatic disease. METHODS: DNA was extracted from formalin-fixed, paraffin-embedded samples from 24 consecutive patient cases of MPT...
February 17, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28209901/vitamin-b3-modulates-mitochondrial-vulnerability-and-prevents-glaucoma-in-aged-mice
#5
Pete A Williams, Jeffrey M Harder, Nicole E Foxworth, Kelly E Cochran, Vivek M Philip, Vittorio Porciatti, Oliver Smithies, Simon W M John
Glaucomas are neurodegenerative diseases that cause vision loss, especially in the elderly. The mechanisms initiating glaucoma and driving neuronal vulnerability during normal aging are unknown. Studying glaucoma-prone mice, we show that mitochondrial abnormalities are an early driver of neuronal dysfunction, occurring before detectable degeneration. Retinal levels of nicotinamide adenine dinucleotide (NAD(+), a key molecule in energy and redox metabolism) decrease with age and render aging neurons vulnerable to disease-related insults...
February 17, 2017: Science
https://www.readbyqxmd.com/read/28209658/relevance-of-id3-tcf3-ccnd3-pathway-mutations-in-pediatric-aggressive-b-cell-lymphoma-treated-according-to-the-nhl-bfm-protocols
#6
Marius Rohde, Bettina R Bonn, Martin Zimmermann, Jonas Lange, Anja Möricke, Wolfram Klapper, Ilske Oschlies, Monika Szczepanowski, Inga Nagel, Martin Schrappe, Markus Loeffler, Reiner Siebert, Alfred Reiter, Birgit Burkhardt
Mature B-cell Non-Hodgkin lymphoma is the most common subtype of Non-Hodgkin lymphoma in childhood and adolescence. B-cell Non-Hodgkin lymphoma are further classified into histological subtypes, with Burkitt lymphoma and Diffuse large B-cell lymphoma being the most common subgroups in pediatric patients. Translocations involving the MYC oncogene are known as relevant but not sufficient hit for Burkitt lymphoma pathogenesis. Recently published large-scale next-generation sequencing studies unveiled sets of additional recurrently mutated genes in samples of pediatric and adult B-cell Non-Hodgkin lymphoma patients...
February 16, 2017: Haematologica
https://www.readbyqxmd.com/read/28207957/phylogenetic-relatedness-explains-highly-interconnected-and-nested-symbiotic-networks-of-woody-plants-and-arbuscular-mycorrhizal-fungi-in-a-chinese-subtropical-forest
#7
Liang Chen, Yong Zheng, Cheng Gao, Xiang-Cheng Mi, Ke-Ping Ma, Tesfaye Wubet, Liang-Dong Guo
Elucidating symbiotic relationships between arbuscular mycorrhizal fungi (AMF) and plants contributes to a better understanding of their reciprocally dependent co-existence and community assembly. However, the main drivers of plant and AMF community assembly remain unclear. In this study, we examined AMF communities from 166 root samples of 17 woody plant species from 10 quadrats in a Chinese subtropical forest using 454 pyrosequencing of 18S rRNA gene to describe symbiotic AMF-plant association. Our results show the woody plant-AMF networks to be highly interconnected and nested, but in anti-modular and anti-specialized manners...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28207896/rna-seq-analysis-of-chikungunya-virus-infection-and-identification-of-granzyme-a-as-a-major-promoter-of-arthritic-inflammation
#8
Jane A C Wilson, Natalie A Prow, Wayne A Schroder, Jonathan J Ellis, Helen E Cumming, Linden J Gearing, Yee Suan Poo, Adam Taylor, Paul J Hertzog, Francesca Di Giallonardo, Linda Hueston, Roger Le Grand, Bing Tang, Thuy T Le, Joy Gardner, Suresh Mahalingam, Pierre Roques, Phillip I Bird, Andreas Suhrbier
: Chikungunya virus (CHIKV) is an arthritogenic alphavirus causing epidemics of acute and chronic arthritic disease. Herein we describe a comprehensive RNA-Seq analysis of feet and lymph nodes at peak viraemia (day 2 post infection), acute arthritis (day 7) and chronic disease (day 30) in the CHIKV adult wild-type mouse model. Genes previously shown to be up-regulated in CHIKV patients were also up-regulated in the mouse model. CHIKV sequence information was also obtained with up to ≈8% of the reads mapping to the viral genome; however, no adaptive viral genome changes were apparent...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28202506/recurrent-patterns-of-dna-copy-number-alterations-in-tumors-reflect-metabolic-selection-pressures
#9
Nicholas A Graham, Aspram Minasyan, Anastasia Lomova, Ashley Cass, Nikolas G Balanis, Michael Friedman, Shawna Chan, Sophie Zhao, Adrian Delgado, James Go, Lillie Beck, Christian Hurtz, Carina Ng, Rong Qiao, Johanna Ten Hoeve, Nicolaos Palaskas, Hong Wu, Markus Müschen, Asha S Multani, Elisa Port, Steven M Larson, Nikolaus Schultz, Daniel Braas, Heather R Christofk, Ingo K Mellinghoff, Thomas G Graeber
Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions across diverse cancer types. These patterns are suggestive of conserved selection pressures during tumor evolution but cannot be fully explained by known oncogenes and tumor suppressor genes. Using a pan-cancer analysis of CNA data from patient tumors and experimental systems, here we show that principal component analysis-defined CNA signatures are predictive of glycolytic phenotypes, including (18)F-fluorodeoxy-glucose (FDG) avidity of patient tumors, and increased proliferation...
February 15, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28197728/linezolid-resistant-enterococci-in-polish-hospitals-species-clonality-and-determinants-of-linezolid-resistance
#10
I Gawryszewska, D Żabicka, W Hryniewicz, E Sadowy
The significant increase of the linezolid-resistant enterococci (LRE) has been observed in Polish hospitals since 2012 and our study aimed at elucidating the possible reasons for this phenomenon. Polish LRE isolates were analysed by multilocus-sequence typing (MLST) and multiple locus variable-number tandem repeat (VNTR) analysis (MLVA), polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP) to establish clonal relatedness and mechanism of linezolid resistance, respectively...
February 14, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28196873/lymphotoxin-beta-interacts-with-methylated-egfr-to-mediate-acquired-resistance-to-cetuximab-in-head-and-neck-cancer
#11
Dennis Shin-Shian Hsu, Wei-Lun Hwang, Chiou-Hwa Yuh, Chen-Hsi Chu, Yang-Hui Ho, Pon-Bo Chen, Han-Syuan Lin, Hua-Kuo Lin, Shih-Pei Wu, Chih-Yi Lin, Wen-Hao Hsu, Hsin-Yi Lan, Hsiao-Jung Wang, Shyh-Kuan Tai, Mien-Chie Hung, Muh-Hwa Yang
PURPOSE: In head and neck squamous cell carcinoma (HNSCC), the incidence of RAS mutation, which is the major cause of cetuximab resistance, is relatively rare compared with the other types of cancers, and the mechanism mediating acquired resistance is unclear compared with the driver gene mutation-mediated de novo resistance. Here we investigated the driver gene mutation-independent mechanism for cetuximab resistance in HNSCC. EXPERIMENTAL DESIGN: We used the in vitro-selected and in vivo-selected cetuximab-resistant sublines of HNSCC cell lines for investigating the mechanism of acquired resistance to cetuximab...
February 14, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28196587/pheochromocytomas-and-paragangliomas-genetically-diverse-and-minimalist-all-at-once
#12
Patricia L M Dahia
Pheochromocytomas and paragangliomas are infrequent, genetically heterogeneous neuroendocrine tumors. In this issue of Cancer Cell, Fishbein et al. report novel driver genes, pathogenic mechanisms, and markers of malignancy. Notably, the new findings support the long-held view that these tumors distinctively arise from a single driver event, either inherited or acquired.
February 13, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28193878/thada-fusion-is-a-mechanism-of-igf2bp3-activation-and-igf1r-signaling-in-thyroid-cancer
#13
Federica Panebianco, Lindsey M Kelly, Pengyuan Liu, Shan Zhong, Sanja Dacic, Xiaosong Wang, Aatur D Singhi, Rajiv Dhir, Simion I Chiosea, Shih-Fan Kuan, Rohit Bhargava, David Dabbs, Sumita Trivedi, Manoj Gandhi, Rachel Diaz, Abigail I Wald, Sally E Carty, Robert L Ferris, Adrian V Lee, Marina N Nikiforova, Yuri E Nikiforov
Thyroid cancer development is driven by known point mutations or gene fusions found in ∼90% of cases, whereas driver mutations in the remaining tumors are unknown. The insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) plays an important role in cancer, yet the mechanisms of its activation in cancer cells remain poorly understood. Using whole-transcriptome and whole-genome analyses, we identified a recurrent fusion between the thyroid adenoma-associated (THADA) gene on chromosome 2 and the LOC389473 gene on chromosome 7 located 12 kb upstream of the IGF2BP3 gene...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193728/mobile-introns-shape-the-genetic-diversity-of-their-host-genes
#14
Jelena Repar, Tobias Warnecke
Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. In fungi, many of these introns have retained their ability to spread to intron-free target sites, often assisted by intron-encoded endonucleases that initiate the homing process. Here, leveraging population genomic data from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Lachancea kluyveri, we expose non-random patterns of genetic diversity in exons that border self-splicing introns. In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approaches a mobile intron...
February 13, 2017: Genetics
https://www.readbyqxmd.com/read/28193224/microrna-mir-29-controls-a-compensatory-response-to-limit-neuronal-iron-accumulation-during-adult-life-and-aging
#15
Roberto Ripa, Luca Dolfi, Marco Terrigno, Luca Pandolfini, Aurora Savino, Valeria Arcucci, Marco Groth, Eva Terzibasi Tozzini, Mario Baumgart, Alessandro Cellerino
BACKGROUND: A widespread modulation of gene expression occurs in the aging brain, but little is known as to the upstream drivers of these changes. MicroRNAs emerged as fine regulators of gene expression in many biological contexts and they are modulated by age. MicroRNAs may therefore be part of the upstream drivers of the global gene expression modulation correlated with aging and aging-related phenotypes. RESULTS: Here, we show that microRNA-29 (miR-29) is induced during aging in short-lived turquoise killifish brain and genetic antagonism of its function induces a gene-expression signature typical of aging...
February 13, 2017: BMC Biology
https://www.readbyqxmd.com/read/28192371/somatic-mutations-in-telomerase-promoter-counterbalance-germline-loss-of-function-mutations
#16
Lindley Maryoung, Yangbo Yue, Ashley Young, Chad A Newton, Cindy Barba, Nicolai S C van Oers, Richard C Wang, Christine Kim Garcia
Germline coding mutations in different telomere-related genes have been linked to autosomal-dominant familial pulmonary fibrosis. Individuals with these inherited mutations demonstrate incomplete penetrance of clinical phenotypes affecting the lung, blood, liver, skin, and other organs. Here, we describe the somatic acquisition of promoter mutations in telomerase reverse transcriptase (TERT) in blood leukocytes of approximately 5% of individuals with inherited loss-of-function coding mutations in TERT or poly(A)-specific ribonuclease (PARN), another gene linked to telomerase function...
February 13, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28191677/uvb-represses-melanocyte-cell-migration-and-acts-through-%C3%AE-catenin
#17
Juliette U Bertrand, Valérie Petit, Elke Hacker, Irina Berlin, Nicholas K Hayward, Marie Pouteaux, Evelyne Sage, David C Whiteman, Lionel Larue
The exposure of skin to ultraviolet (UV) radiation can have both beneficial and deleterious effects: it can lead, for instance, to increased pigmentation and vitamin D synthesis but also to inflammation and skin cancer. UVB may induce genetic and epigenetic alterations, and have reversible effects associated with post-translational and gene regulation modifications. β-catenin is a main driver in melanocyte development; although infrequently mutated in melanoma, its cellular localization and activity is frequently altered...
February 13, 2017: Experimental Dermatology
https://www.readbyqxmd.com/read/28188144/elevated-rate-of-genome-rearrangements-in-radiation-resistant-bacteria
#18
Jelena Repar, Fran Supek, Tin Klanjscek, Tobias Warnecke, Ksenija Zahradka, Davor Zahradka
A number of bacterial, archaeal, and eukaryotic species are known for their resistance to ionizing radiation. One of the challenges these species face is a potent environmental source of DNA double-strand breaks, potential drivers of genome structure evolution. Efficient and accurate DNA double-strand break repair systems have been demonstrated in several unrelated radiation-resistant species and are putative adaptations to the DNA damaging environment. Such adaptations are expected to compensate for the genome-destabilizing effect of environmental DNA damage and may be expected to result in a more conserved gene order in radiation-resistant species...
February 10, 2017: Genetics
https://www.readbyqxmd.com/read/28187448/impact-of-country-of-birth-on-genetic-testing-of-metastatic-lung-adenocarcinomas-in-france-african-women-exhibit-a-mutational-spectrum-more-similar-to-asians-than-to-caucasians
#19
Raphael Saffroy, Jean-François Morère, Nelly Bosselut, Pasquale F Innominato, Jocelyne Hamelin, Jean Trédaniel, Sophie Masse, Véronique Dussaule-Duchatelle, André Balaton, Pierre Validire, Catherine Guettier, Mohamed Bouchahda, Antoinette Lemoine
BACKGROUND: Limited data are available on the prevalence of oncogenic driver mutations in Caucasian populations, and especially in Europeans. AIM: To evaluate the targetable mutational spectra in unselected patients with lung adenocarcinoma in routine clinical practice from several French hospitals, using the same molecular platform. PATIENTS AND METHODS: Samples from 2,219 consecutive patients with histologically-proven advanced lung adenocarcinoma were centrally analysed at a referenced and certified diagnostic platform in order to test for activating and resistance mutations in EGFR, KRAS, BRAF, ERBB2 and PI3KCA...
February 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28187158/role-of-the-long-non-coding-rna-pvt1-in-the-dysregulation-of-the-cerna-cerna-network-in-human-breast-cancer
#20
Federica Conte, Giulia Fiscon, Matteo Chiara, Teresa Colombo, Lorenzo Farina, Paola Paci
Recent findings have identified competing endogenous RNAs (ceRNAs) as the drivers in many disease conditions, including cancers. The ceRNAs indirectly regulate each other by reducing the amount of microRNAs (miRNAs) available to target messenger RNAs (mRNAs). The ceRNA interactions mediated by miRNAs are modulated by a titration mechanism, i.e. large changes in the ceRNA expression levels either overcome, or relieve, the miRNA repression on competing RNAs; similarly, a very large miRNA overexpression may abolish competition...
2017: PloS One
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