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https://www.readbyqxmd.com/read/28545165/highly-recurrent-h3f3a-mutations-with-additional-epigenetic-regulator-alterations-in-giant-cell-tumor-of-bone
#1
Koichi Ogura, Fumie Hosoda, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Shoko Ohashi, Hirofumi Rokutan, Erina Takai, Shinichi Yachida, Akira Kawai, Sakae Tanaka, Tatsuhiro Shibata
Recurrent H3F3A and IDH2 mutations have been reported in giant cell tumor of bone (GCTB). However, the reported incidences have varied, and other molecular genetic alterations have not been identified due to the small number of cases analyzed with comprehensive methods. Moreover, the relative sensitivities of Sanger sequencing and next-generation sequencing (NGS) for the detection of H3F3A mutations in DNA extracted from archival formalin-fixed paraffin-embedded (FFPE) for clinical diagnosis have not been assessed...
May 25, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28545148/mitochondrial-genome-evolution-in-alismatales-size-reduction-and-extensive-loss-of-ribosomal-protein-genes
#2
Gitte Petersen, Argelia Cuenca, Athanasios Zervas, Gregory T Ross, Sean W Graham, Craig F Barrett, Jerrold I Davis, Ole Seberg
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant...
2017: PloS One
https://www.readbyqxmd.com/read/28544463/axonal-charcot-marie-tooth-neuropathy-concurrent-with-distal-and-proximal-weakness-by-translational-elongation-of-the-3-utr-in-nefh
#3
Da Eun Nam, Sung-Chul Jung, Da Hye Yoo, Sun Seong Choi, Sung-Yum Seo, Gwang Hoon Kim, Song-Ja Kim, Soo Hyun Nam, Byung-Ok Choi, Ki Wha Chung
Mutations in the NEFH gene encoding the heavy neurofilament protein are usually associated with neuronal damage and susceptibility to amyotrophic lateral sclerosis (ALS). Recently, frameshift variants in NEFH (p.Asp1004Glnfs*58 and p.Pro1008Alafs*56) have been reported to be the underlying cause of axonal Charcot-Marie-Tooth disease type 2CC (CMT2CC). The frameshift mutation resulted in a stop loss and translation of a cryptic amyloidogenic element (CAE) encoded by the 3' UTR. This study also identified a de novo c...
May 24, 2017: Journal of the Peripheral Nervous System: JPNS
https://www.readbyqxmd.com/read/28543388/environmental-constraints-on-the-compositional-and-phylogenetic-beta-diversity-of-tropical-forest-snake-assemblages
#4
Mario R Moura, Henrique C Costa, Antônio J S Argôlo, Walter Jetz
The ongoing biodiversity crisis increases the importance and urgency of studies addressing the role of environmental variation on the composition and evolutionary history of species assemblages, but especially the tropics and ectotherms remain understudied. In regions with rainy summers, coexistence of ectothermic species may be determined by the partitioning of the climatic niche, since ectotherms can rely on water availability and thermoregulatory behaviour to buffer constraints along their climatic niche...
May 22, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28542274/detecting-infection-hotspots-modeling-the-surveillance-challenge-for-elimination-of-lymphatic-filariasis
#5
Julie R Harris, Ryan E Wiegand
BACKGROUND: During the past 20 years, enormous efforts have been expended globally to eliminate lymphatic filariasis (LF) through mass drug administration (MDA). However, small endemic foci (microfoci) of LF may threaten the presumed inevitable decline of infections after MDA cessation. We conducted microsimulation modeling to assess the ability of different types of surveillance to identify microfoci in these settings. METHODS: Five or ten microfoci of radius 1, 2, or 3 km with infection marker prevalence (intensity) of 3, 6, or 10 times background prevalence were placed in spatial simulations, run in R Version 3...
May 19, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28541550/integrity-of-immunoglobulin-variable-region-is-supported-by-ganp-during-aid-induced-somatic-hypermutation-in-germinal-center-b-cells
#6
Mohammed Mansour Abbas Eid, Mayuko Shimoda, Shailendra Kumar Singh, Sarah Ameen Almofty, Phuong Pham, Myron F Goodman, Kazuhiko Maeda, Nobuo Sakaguchi
Immunoglobulin (Ig) affinity maturation depends on somatic hypermutation (SHM) in variable (V) regions initiated by activation-induced cytidine deaminase (AID). AID induces transition mutations by C→U deamination on both strands, causing C:G→T:A. Error-prone repairs of U by base excision and mismatch repairs create transversion mutations at C/G and mutations at A/T sites. In Neuberger's model, it remained to clarify how transition/transversion repair is regulated. We investigate role of AID-interacting GANP (germinal-center associated nuclear protein) in IgV SHM profile...
May 24, 2017: International Immunology
https://www.readbyqxmd.com/read/28540987/lack-of-aberrant-methylation-in-an-adjacent-area-of-left-sided-colorectal-cancer
#7
Otgontuya Sambuudash, Hyun Soo Kim, Mee Yon Cho
PURPOSE: The molecular nature and the rate-limiting step of epigenetic field defects in the evolution of left-sided colorectal cancer (LCA) remain uncertain. MATERIALS AND METHODS: The methylation status of 27 candidate field defect markers, six classic CpG island methylator phenotype (CIMP) markers, and LINE-1 were determined in LCA and adjacent normal mucosas (ADJs) from 33 LCA patients and in left normal colorectal mucosa (LNM) from 33 age- and sex-matched controls...
July 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/28539631/phylogeography-of-the-tyrrhenian-red-deer-cervus-elaphus-corsicanus-resolved-using-ancient-dna-of-radiocarbon-dated-subfossils
#8
K Doan, F E Zachos, B Wilkens, J-D Vigne, N Piotrowska, A Stanković, B Jędrzejewska, K Stefaniak, M Niedziałkowska
We present ancient mitochondrial DNA analyses of 31 complete cytochrome b gene sequences from subfossil red deer remains from the Tyrrhenian islands (Corsica and Sardinia) and mainland Italy in a European-wide phylogeographic framework. Tyrrhenian and North African red deer, both going back to human introductions, were previously the only red deer to harbour the mitochondrial B lineage whose origin, however, remained unknown. Our ancient Italian samples from the central part of the peninsula that were radiocarbon-dated to an age of ca...
May 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28537069/life-cycle-assessment-and-release-studies-for-15-nanosilver-enabled-consumer-products-investigating-hotspots-and-patterns-of-contribution
#9
Leila Pourzahedi, Marina Eller Vance, Matthew J Eckelman
Increasing use of silver nanoparticles (AgNPs) in consumer products as antimicrobial agents has prompted extensive research towards evaluation of their potential release to the environment and subsequent ecotoxicity to aquatic organisms. It has also been shown that AgNPs can pose significant burdens to the environment from life cycle emissions associated with their production, but these impacts must be considered in the context of actual products that contain nanosilver. Here a cradle-to-gate life cycle assessment for production of 15 different AgNP-enabled consumer products was performed, coupled with release studies of those same products, thus providing a consistent analytical platform for investigation of nanosilver impacts across a range of product types and concentrations...
May 24, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28533636/comparison-of-spect-ct-and-planar-lympho-scintigraphy-in-sentinel-node-biopsies-of-oral-cavity-squamous-cell-carcinomas
#10
Piyush Chandra, Sanket Dhake, Sneha Shah, Archi Agrawal, Nilendu Purandare, Venkatesh Rangarajan
INTRODUCTION: Evidence supporting the use of Sentinel node biopsy (SNB) for nodal staging of early oral squamous cell carcinomas (OSCC) appears to be very promising. Pre-operative lymphatic mapping using planar lymphoscinitigraphy (PL) with or without SPECT/CT in the SNB procedure is useful in sentinel node localization and for planning appropriate surgery. Recently, a large prospective multi-centric study evaluating SNB in cutaneous melanoma, breast and pelvic malignancies, demonstrated that adding SPECT to PL leads to surgical adjustments in a considerable number of patients...
April 2017: Indian Journal of Nuclear Medicine: IJNM: the Official Journal of the Society of Nuclear Medicine, India
https://www.readbyqxmd.com/read/28533537/novel-mutations-and-phenotypic-associations-identified-through-apc-mutyh-nthl1-pold1-pole-gene-analysis-in-indian-familial-adenomatous-polyposis-cohort
#11
Nikhat Khan, Anuja Lipsa, Gautham Arunachal, Mukta Ramadwar, Rajiv Sarin
Colo-Rectal Cancer is a common cancer worldwide with 5-10% cases being hereditary. Familial Adenomatous Polyposis (FAP) syndrome is due to germline mutations in the APC or rarely MUTYH gene. NTHL1, POLD1, POLE have been recently reported in previously unexplained FAP cases. Unlike the Caucasian population, FAP phenotype and its genotypic associations have not been widely studied in several geoethnic groups. We report the first FAP cohort from South Asia and the only non-Caucasian cohort with comprehensive analysis of APC, MUTYH, NTHL1, POLD1, POLE genes...
May 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28532501/pik3ca-hotspot-mutations-differentially-impact-responses-to-met-targeting-in-met-driven-and-non-driven-preclinical-cancer-models
#12
Lluís Nisa, Pascal Häfliger, Michaela Poliaková, Roland Giger, Paola Francica, Daniel Matthias Aebersold, Roch-Philippe Charles, Yitzhak Zimmer, Michaela Medová
BACKGROUND: The MET receptor tyrosine kinase represents a promising target in cancer. PIK3CA activating mutations are common in several tumor types and can potentially confer resistance to anti-receptor tyrosine kinase therapy. METHODS: MET and/or PI3K pathway inhibition was assessed in NIH3T3 cells harboring MET-activating point mutation with or without ectopic expression of PIK3CA(E545K) and PIK3CA(H1047R), as well as in MET-expressing head and neck cancer cells with endogenous PIK3CA mutations...
May 22, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28531315/the-interaction-between-cytosine-methylation-and-processes-of-dna-replication-and-repair-shape-the-mutational-landscape-of-cancer-genomes
#13
Rebecca C Poulos, Jake Olivier, Jason W H Wong
Methylated cytosines (5mCs) are frequently mutated in the genome. However, no studies have yet comprehensively analysed mutation-methylation associations across cancer types. Here we analyse 916 cancer genomes, together with tissue type-specific methylation and replication timing data. We describe a strong mutation-methylation association across colorectal cancer subtypes, most interestingly in samples with microsatellite instability (MSI) or Polymerase epsilon (POLE) exonuclease domain mutations. By analysing genomic regions with differential mismatch repair (MMR) efficiency, we suggest a possible role for MMR in the correction of 5mC deamination events, potentially accounting for the high rate of 5mC mutation accumulation in MSI tumours...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28531088/influence-of-patient-mispositioning-on-sar-distribution-and-simulated-temperature-in-regional-deep-hyperthermia
#14
Bassim Aklan, Pia Gierse, Josefin Hartmann, Oliver J Ott, Rainer Fietkau, Christoph Bert
Patient positioning plays an important role in regional deep hyperthermia to obtain a successful hyperthermia treatment. In this study, the influence of possible patient mispositioning was systematically assessed on specific absorption rate (SAR) and temperature distribution. With a finite difference time domain approach, the SAR and temperature distributions were predicted for six patients at 312 positions. Patient displacements and rotations as well as the combination of both were considered inside the Sigma-Eye applicator...
May 22, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28529012/the-epidemiology-and-hotspots-of-road-traffic-injuries-in-moshi-tanzania-an-observational-study
#15
Joseph M Reardon, Luciano Andrade, Julian Hertz, George Kiwango, Anneth Teu, Msafiri Pesambili, Deena El-Gabri, Michael Hocker, Mark Mvungi, João Ricardo N Vissoci, Catherine A Staton
Road traffic injuries (RTIs) continue to increase with the proliferation of motor vehicles, especially in low-income countries where safe road infrastructure is lacking. Knowing where and why RTIs occur would allow for increased safety and prevention planning. In this study, police records of 300 motor vehicle collisions which occurred between February 2013 and January 2014 in Moshi, Tanzania were reviewed. Analysis of variables including victim age, gender, type of collision, conditions, and use of safety equipment were analyzed...
May 3, 2017: Injury
https://www.readbyqxmd.com/read/28528867/a-pan-cancer-proteogenomic-atlas-of-pi3k-akt-mtor-pathway-alterations
#16
Yiqun Zhang, Patrick Kwok-Shing Ng, Melanie Kucherlapati, Fengju Chen, Yuexin Liu, Yiu Huen Tsang, Guillermo de Velasco, Kang Jin Jeong, Rehan Akbani, Angela Hadjipanayis, Angeliki Pantazi, Christopher A Bristow, Eunjung Lee, Harshad S Mahadeshwar, Jiabin Tang, Jianhua Zhang, Lixing Yang, Sahil Seth, Semin Lee, Xiaojia Ren, Xingzhi Song, Huandong Sun, Jonathan Seidman, Lovelace J Luquette, Ruibin Xi, Lynda Chin, Alexei Protopopov, Thomas F Westbrook, Carl Simon Shelley, Toni K Choueiri, Michael Ittmann, Carter Van Waes, John N Weinstein, Han Liang, Elizabeth P Henske, Andrew K Godwin, Peter J Park, Raju Kucherlapati, Kenneth L Scott, Gordon B Mills, David J Kwiatkowski, Chad J Creighton
Molecular alterations involving the PI3K/AKT/mTOR pathway (including mutation, copy number, protein, or RNA) were examined across 11,219 human cancers representing 32 major types. Within specific mutated genes, frequency, mutation hotspot residues, in silico predictions, and functional assays were all informative in distinguishing the subset of genetic variants more likely to have functional relevance. Multiple oncogenic pathways including PI3K/AKT/mTOR converged on similar sets of downstream transcriptional targets...
May 8, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28528261/perfluoroalkylated-acids-in-the-eggs-of-great-tits-parus-major-near-a-fluorochemical-plant-in-flanders-belgium
#17
Thimo Groffen, Ana Lopez-Antia, Wendy D'Hollander, Els Prinsen, Marcel Eens, Lieven Bervoets
Perfluoroalkyl acids (PFAAs) are highly persistent substances which have been detected in wildlife around the world, including birds. Although bird eggs have often been used to determine and monitor PFAAs levels in the marine environment, this has rarely been done in the terrestrial environment. In the present study we examined the concentrations and composition profile of 12 PFAAs (4 perfluoroalkyl sulfonic acids (PFSAs) and 8 perfluoroalkyl carboxylic acids (PFCAs) in the eggs of great tits (Parus major) collected at a fluorochemical plant and in three other areas, representing a gradient in distance from the pollution source (from 1 to 70 km), in Antwerp, Belgium...
May 18, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28527418/atmospheric-pcdd-f-concentration-and-source-apportionment-in-typical-rural-agent-orange-hotspots-and-industrial-areas-in-vietnam
#18
Tuan Hung Ngo, To Thi Hien, Ngo Thi Thuan, Nguyen Hung Minh, Kai Hsien Chi
Vietnam has a double burden of dioxin from both industrial sources and historical sources. To evaluate the concentration of PCDD/Fs in ambient air in different areas of Vietnam and their possible sources, atmospheric samples were collected from three areas namely Son La (rural area) and Da Nang (harbor - Agent Orange hotspot area), and Ho Chi Minh City (metropolitan - industrial city). Vapor and solid phases of PCDD/Fs were collected and analyzed following the TO-9A sampling method. Principal Component Analysis and Positive Matrix Factorization model were applied to characterize the possible source...
May 11, 2017: Chemosphere
https://www.readbyqxmd.com/read/28527011/the-prdm9-krab-domain-is-required-for-meiosis-and-involved-in-protein-interactions
#19
Yukiko Imai, Frédéric Baudat, Miguel Taillepierre, Marcello Stanzione, Attila Toth, Bernard de Massy
PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. This role involves its DNA-binding domain, which is composed of a tandem array of zinc fingers, and PRDM9-dependent trimethylation of histone H3 at lysine 4. PRDM9 is a member of the PRDM family of transcription regulators, but unlike other family members, it contains a Krüppel-associated box (KRAB)-related domain that is predicted to be a potential protein interaction domain...
May 19, 2017: Chromosoma
https://www.readbyqxmd.com/read/28525363/targeted-sequencing-of-tonsillar-and-base-of-tongue-cancer-and-human-papillomavirus-positive-unknown-primary-of-the-head-and-neck-reveals-prognostic-effects-of-mutated-fgfr3
#20
Cinzia Bersani, Lars Sivars, Linnea Haeggblom, Sebastian DiLorenzo, Michael Mints, Andreas Ährlund-Richter, Nikolaos Tertipis, Eva Munck-Wikland, Anders Näsman, Torbjörn Ramqvist, Tina Dalianis
BACKGROUND: Human papillomavirus positive (HPV+) tonsillar cancer (TSCC), base of tongue cancer (BOTSCC) and unknown primary cancer of the head and neck (HNCUP) have better outcome than corresponding HPV- cancers. To find predictive markers for response to treatment, and correlations and differences in mutated oncogenes and suppressor genes between HPV+ TSCC/BOTSSCC and HPV+ HNCUP and HPV- TSCC/BOTSCC targeted next-generation sequencing was performed of frequently mutated regions in 50 cancer related genes...
May 23, 2017: Oncotarget
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