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https://www.readbyqxmd.com/read/28637276/repetitive-element-transcripts-are-elevated-in-the-brain-of-c9orf72-als-ftld-patients
#1
Mercedes Prudencio, Patrick K Gonzales, Casey N Cook, Tania F Gendron, Lillian M Daughrity, Yuping Song, Mark T W Ebbert, Marka van Blitterswijk, Yong-Jie Zhang, Karen Jansen-West, Matthew C Baker, Michael DeTure, Rosa Rademakers, Kevin B Boylan, Dennis W Dickson, Leonard Petrucelli, Christopher D Link
Significant transcriptome alterations are detected in the brain of patients with amyotrophic lateral sclerosis (ALS), including carriers of the C9orf72 repeat expansion and C9orf72-negative sporadic cases. Recently, the expression of repetitive element transcripts has been associated with toxicity and, while increased repetitive element expression has been observed in several neurodegenerative diseases, little is known about their contribution to ALS. To assess whether aberrant expression of repetitive element sequences are observed in ALS, we analyzed RNA sequencing data from C9orf72-positive and sporadic ALS cases, as well as healthy controls...
June 16, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28631163/evaluation-of-streck-bct-and-paxgene-stabilised-blood-collection-tubes-for-cell-free-circulating-dna-studies-in-plasma
#2
Kristina Warton, Nicole L Yuwono, Mark J Cowley, Mark J McCabe, Alwin So, Caroline E Ford
INTRODUCTION: Blood samples for studies of circulating DNA in disease are often collected in clinical settings where prompt processing of samples is not possible. In order to avoid problems associated with leukocyte lysis after prolonged blood storage, stabilised blood tubes have been developed containing preservatives that prevent cell lysis. We evaluated Streck BCT tubes and PAXgene ccfDNA tubes, as well as standard EDTA blood collection tubes, in terms of DNA yield and fragment size...
June 19, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28618811/vocal-repertoire-of-long-finned-pilot-whales-globicephala-melas-in-northern-norway
#3
Heike Vester, Sarah Hallerberg, Marc Timme, Kurt Hammerschmidt
The knowledge of the vocal repertoire of pilot whales is very limited. In this paper, the vocal repertoire of long-finned pilot whales recorded during different encounters in the Vestfjord in northern Norway between November 2006 and August 2010 are described. Sounds were analysed using two different methods: (1) an observer-based audio-visual inspection of FFT-derived spectrograms, with which, besides a general variety of clicks, buzzes, nonharmonic sounds, and whistles, 129 different distinct call types and 25 subtypes were distinguished...
June 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28618143/cedratvirus-lausannensis-digging-into-pithoviridae-diversity
#4
Claire Bertelli, Linda Mueller, Vincent Thomas, Trestan Pillonel, Nicolas Jacquier, Gilbert Greub
Amoeba-infecting viruses have raised scientists' interest due to their novel particle morphologies, their large genome size, and their genomic content challenging previously established dogma. We report here the discovery and the characterization of Cedratvirus lausannensis, a novel member of the Megavirales, with a 0.75-1 µm long amphora-shaped particle closed by two striped plugs. Among numerous host cell types tested, the virus replicates only in Acanthamoeba castellanii leading to host cell lysis within 24 hours...
June 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28614458/capacity-for-self-monitoring-reading-comprehension-in-elementary-school
#5
Gabriela Juliane Bueno, Carolina Alves Ferreira Carvalho, Clara Regina Brandão de Ávila
Purpose: To investigate the capacity for self-monitoring reading comprehension in Brazilian Elementary School students. Methods: Fifty-three Elementary students in the 5th and 9th grades from two Public Schools in the city of São Paulo were assessed. They were selected based on their oral reading rate and grouped according to their performance in reading comprehension in the following categories: Group with best comprehension: students with adequate rate and accuracy, without difficulties in reading comprehension; Group with worst comprehension: students with adequate rate and accuracy but with difficulties in reading comprehension...
June 8, 2017: CoDAS
https://www.readbyqxmd.com/read/28611826/the-evolution-of-bacterial-genome-architecture
#6
REVIEW
Louis-Marie Bobay, Howard Ochman
The genome architecture of bacteria and eukaryotes evolves in opposite directions when subject to genetic drift, a difference that can be ascribed to the fact that bacteria exhibit a mutational bias that deletes superfluous sequences, whereas eukaryotes are biased toward large insertions. Expansion of eukaryotic genomes occurs through the addition of non-functional sequences, such as repetitive sequences and transposable elements, whereas variation in bacterial genome size is largely due to the acquisition and loss of functional accessory genes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28608356/-the-influence-of-spanish-neuropsychiatry-on-the-improbable-medicine-of-ramon-gomez-de-la-serna
#7
REVIEW
G Delgado-Garcia, C Rodriguez-Navarez, T Corona, B Estanol-Vidal
INTRODUCTION: El doctor inverosimil (The Improbable Doctor) is a novel by Ramon Gomez de la Serna (1888-1963) in which the reader follows, by means of a series of different clinical cases, the adventures of Doctor Vivar. AIMS: To present and discuss, for the first time, the influence that Spanish neuropsychiatry had on this novel, taking the following short stories as study models: 'Casos cerebrales' ('Brain Cases') and 'La risita' ('The Giggles'). DEVELOPMENT: In these two tales, the improbable doctor embodies the three defining elements of Spanish neuropsychiatry...
June 16, 2017: Revista de Neurologia
https://www.readbyqxmd.com/read/28605751/improved-maize-reference-genome-with-single-molecule-technologies
#8
Yinping Jiao, Paul Peluso, Jinghua Shi, Tiffany Liang, Michelle C Stitzer, Bo Wang, Michael S Campbell, Joshua C Stein, Xuehong Wei, Chen-Shan Chin, Katherine Guill, Michael Regulski, Sunita Kumari, Andrew Olson, Jonathan Gent, Kevin L Schneider, Thomas K Wolfgruber, Michael R May, Nathan M Springer, Eric Antoniou, W Richard McCombie, Gernot G Presting, Michael McMullen, Jeffrey Ross-Ibarra, R Kelly Dawe, Alex Hastie, David R Rank, Doreen Ware
Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping...
June 12, 2017: Nature
https://www.readbyqxmd.com/read/28599536/effect-of-a-serrated-trailing-edge-on-sound-radiation-from-nearby-quadrupoles
#9
Mahmoud Karimi, Paul Croaker, Roger Kinns, Nicole Kessissoglou
A periodic boundary element technique is implemented to study the noise reduction capability of a plate with a serrated trailing edge under quadrupole excitation. It is assumed for this purpose that the quadrupole source tensor is independent of the trailing edge configuration and that the effect of the trailing edge shape is to modify sound radiation from prescribed boundary layer sources. The flat plate is modelled as a continuous structure with a finite repetition of small spanwise segments. The matrix equation formulated by the periodic boundary element method for this 3D acoustic scattering problem is represented as a block Toeplitz matrix...
May 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28596713/performances-of-different-fragment-sizes-for-reduced-representation-bisulfite-sequencing-in-pigs
#10
Xiao-Long Yuan, Zhe Zhang, Rong-Yang Pan, Ning Gao, Xi Deng, Bin Li, Hao Zhang, Per Torp Sangild, Jia-Qi Li
BACKGROUND: Reduced representation bisulfite sequencing (RRBS) has been widely used to profile genome-scale DNA methylation in mammalian genomes. However, the applications and technical performances of RRBS with different fragment sizes have not been systematically reported in pigs, which serve as one of the important biomedical models for humans. The aims of this study were to evaluate capacities of RRBS libraries with different fragment sizes to characterize the porcine genome. RESULTS: We found that the MspI-digested segments between 40 and 220 bp harbored a high distribution peak at 74 bp, which were highly overlapped with the repetitive elements and might reduce the unique mapping alignment...
2017: Biological Procedures Online
https://www.readbyqxmd.com/read/28595343/sequencing-de-novo-assembling-and-annotating-the-genome-of-the-endangered-chinese-crocodile-lizard-shinisaurus-crocodilurus
#11
Jian Gao, Qiye Li, Zongji Wang, Yang Zhou, Paolo Martelli, Fang Li, Zijun Xiong, Jian Wang, Huanming Yang, Guojie Zhang
The Chinese crocodile lizard, Shinisaurus crocodilurus, is the only living representative of the monotypic family Shinisauridae under the order Squamata. It is an obligate semi-aquatic, viviparous, diurnal species restricted to specific portions of mountainous locations in southwestern China and northeastern Vietnam. However, in the past several decades, this species has undergone a rapid decrease in population size due to illegal poaching and habitat disruption, making this unique reptile species endangered and listed in CITES Appendix II since 1990...
June 8, 2017: GigaScience
https://www.readbyqxmd.com/read/28594634/dissemination-of-blaoxa-23-blaoxa-24-blaoxa-58-and-blandm-1-genes-of-acinetobacter-baumannii-isolates-from-four-tertiary-hospitals-in-thailand
#12
Udomluk Leungtongkam, Rapee Thummeepak, Suchada Wongprachan, Pollawat Thongsuk, Thawatchai Kitti, Kwanjai Ketwong, Chakkaphan Runcharoen, Narisara Chantratita, Sutthirat Sitthisak
Acinetobacter baumannii is a major threat to public health due to the emergence and dissemination of antibiotic-resistant strains. The purpose of this study was to determine the molecular epidemiology of antibiotic-resistant A. baumannii isolates collected from four tertiary hospitals in Thailand during the period November 2013-February 2015. We screened 339 A. baumannii, nonrepetitive clinical isolates to determine drug susceptibility. Among all isolates, we found that 7.9% was nondrug-resistant A. baumannii (NR-AB)...
June 8, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28593481/molecular-survey-of-coxiella-burnetii-in-wildlife-and-ticks-at-wildlife-livestock-interfaces-in-kenya
#13
David Ndeereh, Gerald Muchemi, Andrew Thaiyah, Moses Otiende, Samer Angelone-Alasaad, Michael J Jowers
Coxiella burnetii is the causative agent of Q fever, a zoonotic disease of public health importance. The role of wildlife and their ticks in the epidemiology of C. burnetii in Kenya is unknown. This study analysed the occurrence and prevalence of the pathogen in wildlife and their ticks at two unique wildlife-livestock interfaces of Laikipia and Maasai Mara National Reserve (MMNR) with the aim to determine the potential risk of transmission to livestock and humans. Blood from 79 and 73 animals in Laikipia and MMNR, respectively, and 756 and 95 ixodid ticks in each of the areas, respectively, was analysed...
June 7, 2017: Experimental & Applied Acarology
https://www.readbyqxmd.com/read/28589117/xmrv-and-public-health-the-retroviral-genome-is-not-a-suitable-template-for-diagnostic-pcr-and-its-association-with-myalgic-encephalomyelitis-chronic-fatigue-syndrome-appears-unreliable
#14
Simona Panelli, Lorenzo Lorusso, Alessandro Balestrieri, Giuseppe Lupo, Enrica Capelli
A few years ago, a highly significant association between the xenotropic murine leukemia virus-related virus (XMRV) and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), a complex debilitating disease of poorly understood etiology and no definite treatment, was reported in Science, raising concern for public welfare. Successively, the failure to reproduce these findings, and the suspect that the diagnostic PCR was vitiated by laboratory contaminations, led to the retraction of the paper. Notwithstanding, XMRV continued to be the subject of researches and public debates...
2017: Frontiers in Public Health
https://www.readbyqxmd.com/read/28586511/factors-affecting-dance-exercise-performance-among-students-at-a-special-needs-school
#15
Yukiko Ito, Izumi Hiramoto, Hideya Kodama
BACKGROUND: In Japan, dance exercise has been introduced as a compulsory element of health and physical education. However, there is a considerable discrepancy in the levels of performance among students with intellectual disabilities (ID) at a special needs school. AIM: To demonstrate factors affecting the performance of dance exercise in students with ID. METHODS: A 4-month dance exercise program was implemented for junior high school students at a special needs school, and performance of 32 students at 22 sessions was assessed quantitatively by amount of calorie use by exercise and the proficiency scores of performances...
June 6, 2017: Pediatrics International: Official Journal of the Japan Pediatric Society
https://www.readbyqxmd.com/read/28582417/genome-wide-alteration-in-dna-hydroxymethylation-in-the-sperm-from-bisphenol-a-exposed-men
#16
Huajun Zheng, Xiaoyu Zhou, De-Kun Li, Fen Yang, Hongjie Pan, Tianqi Li, Maohua Miao, Runsheng Li, Wei Yuan
Environmental BPA exposure has been shown to impact human sperm concentration and motility, as well as rodent spermatogenesis. However, it is unclear whether BPA exposure is associated with alteration in DNA hydroxymethylation, a marker for epigenetic modification, in human sperm. A genome-wide DNA hydroxymethylation study was performed using sperm samples of men who were occupationally exposed to BPA. Compared with controls who had no occupational BPA exposure, the total levels of 5-hydroxymethylcytosine (5hmc) increased significantly (19...
2017: PloS One
https://www.readbyqxmd.com/read/28581499/high-quality-de-novo-assembly-of-the-apple-genome-and-methylome-dynamics-of-early-fruit-development
#17
Nicolas Daccord, Jean-Marc Celton, Gareth Linsmith, Claude Becker, Nathalie Choisne, Elio Schijlen, Henri van de Geest, Luca Bianco, Diego Micheletti, Riccardo Velasco, Erica Adele Di Pierro, Jérôme Gouzy, D Jasper G Rees, Philippe Guérif, Hélène Muranty, Charles-Eric Durel, François Laurens, Yves Lespinasse, Sylvain Gaillard, Sébastien Aubourg, Hadi Quesneville, Detlef Weigel, Eric van de Weg, Michela Troggio, Etienne Bucher
Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago...
June 5, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28580940/accurate-prediction-of-x-ray-pulse-properties-from-a-free-electron-laser-using-machine-learning
#18
A Sanchez-Gonzalez, P Micaelli, C Olivier, T R Barillot, M Ilchen, A A Lutman, A Marinelli, T Maxwell, A Achner, M Agåker, N Berrah, C Bostedt, J D Bozek, J Buck, P H Bucksbaum, S Carron Montero, B Cooper, J P Cryan, M Dong, R Feifel, L J Frasinski, H Fukuzawa, A Galler, G Hartmann, N Hartmann, W Helml, A S Johnson, A Knie, A O Lindahl, J Liu, K Motomura, M Mucke, C O'Grady, J-E Rubensson, E R Simpson, R J Squibb, C Såthe, K Ueda, M Vacher, D J Walke, V Zhaunerchyk, R N Coffee, J P Marangos
Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate...
June 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28577881/gene-enriched-draft-genome-of-the-cattle-tick-rhipicephalus-microplus-assembly-by-the-hybrid-pacific-biosciences-illumina-approach-enabled-analysis-of-the-highly-repetitive-genome
#19
Roberto A Barrero, Felix D Guerrero, Michael Black, John McCooke, Brett Chapman, Faye Schilkey, Adalberto A Pérez de León, Robert J Miller, Sara Bruns, Jason Dobry, Galina Mikhaylenko, Keith Stormo, Callum Bell, Quanzhou Tao, Robert Bogden, Paula M Moolhuijzen, Adam Hunter, Matthew I Bellgard
The genome of the cattle tick Rhipicephalus microplus, an ectoparasite with global distribution, is estimated to be 7.1Gbp in length and consists of approximately 70% repetitive DNA. We report the draft assembly of a tick genome that utilized a hybrid sequencing and assembly approach to capture the repetitive fractions of the genome. Our hybrid approach produced an assembly consisting of 2.0Gbp represented in 195,170 scaffolds with a N50 of 60,284bp. The Rmi v2.0 assembly is 51.46% repetitive with a large fraction of unclassified repeats, short interspersed elements, long interspersed elements and long terminal repeats...
June 1, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28574624/proper-reprogramming-of-imprinted-and-non-imprinted-genes-in-cloned-cattle-gametogenesis
#20
Masahiro Kaneda, Shinya Watanabe, Satoshi Akagi, Yasushi Inaba, Masaya Geshi, Takashi Nagai
Epigenetic abnormalities in cloned animals are caused by incomplete reprogramming of the donor nucleus during the nuclear transfer step (first reprogramming). However, during the second reprogramming step that occurs only in the germline cells, epigenetic errors not corrected during the first step are repaired. Consequently, epigenetic abnormalities in the somatic cells of cloned animals should be erased in their spermatozoa or oocytes. This is supported by the fact that offspring from cloned animals do not exhibit defects at birth or during postnatal development...
June 2, 2017: Animal Science Journal, Nihon Chikusan Gakkaihō
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