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https://www.readbyqxmd.com/read/28749613/linked-selection-demography-and-the-evolution-of-correlated-genomic-landscapes-in-birds-and-beyond
#1
Reto Burri
Selection has a deep impact on the distribution of genetic diversity and population differentiation along the genome (the genomic landscapes of diversity and differentiation), reducing diversity and elevating differentiation not only at the sites it targets, but also at linked neutral sites. Fuelled by the high-throughput sequencing revolution, these genomic footprints of selection have been extensively exploited over the past decade with the aim to identify genomic regions involved in adaptation and speciation...
August 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28749611/morphology-ultrastructure-and-molecular-phylogeny-of-rozella-multimorpha-a-new-species-in-cryptomycota
#2
Peter M Letcher, Joyce E Longcore, Timothy Y James, Domingos S Leite, D Rabern Simmons, Martha J Powell
Increasing numbers of sequences of basal fungi from environmental DNA studies are being deposited in public databases. Many of these sequences remain unclassified below the phylum level because sequence information from identified species is sparse. Lack of basic biological knowledge due to a dearth of identified species is extreme in Cryptomycota, a new phylum widespread in the environment and phylogenetically basal within the fungal lineage. Consequently, we are attempting to fill gaps in the knowledge of Rozella, the best-known genus in this lineage...
July 27, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28749586/patient-decisions-to-receive-secondary-pharmacogenomic-findings-and-development-of-a-multidisciplinary-practice-model-to-integrate-results-into-patient-care
#3
J Kevin Hicks, Amy Shealy, Allison Schreiber, Marissa Coleridge, Ryan Noss, Marvin Natowicz, Rocio Moran, Timothy Moss, Angelika Erwin, Charis Eng
Whole exome sequencing (WES) has the potential of identifying secondary findings that are predictive of poor pharmacotherapy outcomes. The purpose of this study was to investigate patients' wishes regarding the reporting of secondary pharmacogenomic findings. WES results (n = 106 patients) were retrospectively reviewed to determine the number of patients electing to receive secondary pharmacogenomic results. Phenotypes were assigned based on Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines...
July 27, 2017: Clinical and Translational Science
https://www.readbyqxmd.com/read/28749585/mir3954-is-a-trigger-of-phasirnas-that-affects-flowering-time-in-citrus
#4
Yuanlong Liu, Lili Ke, Guizhi Wu, Yuantao Xu, Xiaomeng Wu, Rui Xia, Xiuxin Deng, Qiang Xu
In plant, a few 22 nt miRNAs direct cleavages of their targets and trigger the biogenesis of phased small interfering RNAs (phasiRNAs) in plant. In this study, we characterized a miRNA triggering phasiRNAs generation, miR3954, and explored its downstream target genes and potential function. Our results demonstrated that miR3954 showed specific expression in the flowers of citrus species and it targeted a NAC transcription factor (Cs7g22460) and two non-coding RNA transcripts (lncRNAs, Cs1g09600 and Cs1g09635)...
July 27, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28749583/chiral-sulfur-functional-groups-as-definers-of-the-chirality-at-the-metal-in-ir-and-rh-half-sandwich-complexes-a-combined-cd-x-ray-study
#5
Miguel A Sierra, Maria C de la Torre, Roberto Fernandez de la Pradilla, Alma Viso, Maria Frutos, Marta G Avello, Marina Velado, Heinz Gornitzka, Catherine Hemmert
Mesoionic carbenes (MIC) derived from triazolium salts containing chiral sulfoxide or sulfoximine functional groups lead to enantiopure chiral-at-metal Ir(III) and Rh(III) half-sandwich complexes, through the sequence MIC complexation-C-H aromatic activation. The process is efficient and totally diastereoselective in the formation of enantiopure five membered metallacycles. The use of the enantiomers of the sulfur chiral groups allows to prepare complexes having opposite configurations at the metal. Complete retention of the configuration at the metal center is observed during the formation of cationic Ir(III) complexes and upon insertion of alkynes into the Ir(III)-C bond, as demonstrated by a combined Circular Dichroism (CD)-X-ray study...
July 27, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28749553/myelopathy-in-beh%C3%A3-et-s-disease-the-bagel-sign
#6
Ugur Uygunoglu, Burcu Zeydan, Yesim Ozguler, Serdal Ugurlu, Emire Seyahi, Naci Kocer, Civan Islak, Kejal Kantarci, Sabahattin Saip, Aksel Siva, Orhun H Kantarci
OBJECTIVE: To describe the clinical and distinctive imaging features of myelopathy associated with Behçet's disease. METHODS: We evaluated the records of patients meeting the following criteria: a) fulfillment of the International Study Group criteria for Behçet's disease; b) clinically suggestive of myelopathy; c) simultaneous spinal cord and brain MRIs within 1 month of acute worsening of myelopathy; d) follow-up duration ≥1 year after initial MRI evaluation...
July 27, 2017: Annals of Neurology
https://www.readbyqxmd.com/read/28749551/a-novel-allele-hla-b-27-149-identified-by-sequence-based-typing-in-a-chinese-individual
#7
J Wang, Y Zhang, Q Li, K Ru, X Wang
HLA-B*27:149 differs from HLA-B*27:04:01 (488C->T, exon 3, A139V).
July 27, 2017: HLA
https://www.readbyqxmd.com/read/28749517/synthesis-of-3-acylindoles-by-oxidative-rearrangement-of-2-aminochalcones-using-a-hypervalent-iodine-reagent-and-cyclization-sequence
#8
Akira Nakamura, Satoshi Tanaka, Akira Imamiya, Reo Takane, Chiaki Ohta, Kazuma Fujimura, Tomohiro Maegawa, Yasuyoshi Miki
An efficient one-pot method was developed for the construction of 3-acylindoles via oxidative rearrangement of 2-aminochalcones followed by intramolecular cyclization. The reaction was used to convert a variety of 2-aminochalcones into 3-acylindoles in moderate to high yields.
July 27, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28749478/molecular-autopsy-in-maternal-fetal-medicine
#9
Hanan E Shamseldin, Wesam Kurdi, Fatima Almusafri, Maha Alnemer, Alya Alkaff, Zeneb Babay, Amal Alhashem, Maha Tulbah, Nada Alsahan, Rubina Khan, Bahauddin Sallout, Elham Al Mardawi, Mohamed Zain Seidahmed, Niema Meriki, Yasser Alsaber, Alya Qari, Ola Khalifa, Wafaa Eyaid, Zuhair Rahbeeni, Ahmed Kurdi, Mais Hashem, Tarfa Alshidi, Eman Al-Obeid, Firdous Abdulwahab, Niema Ibrahim, Nour Ewida, Karen El-Akouri, Mariam Al Mulla, Tawfeg Ben-Omran, Matthias Pergande, Sebahattin Cirak, Saeed Al Tala, Ranad Shaheen, Eissa Faqeih, Fowzan S Alkuraya
PurposeThe application of genomic sequencing to investigate unexplained death during early human development, a form of lethality likely enriched for severe Mendelian disorders, has been limited.MethodsIn this study, we employed exome sequencing as a molecular autopsy tool in a cohort of 44 families with at least one death or lethal fetal malformation at any stage of in utero development. Where no DNA was available from the fetus, we performed molecular autopsy by proxy, i.e., through parental testing.ResultsPathogenic or likely pathogenic variants were identified in 22 families (50%), and variants of unknown significance were identified in further 15 families (34%)...
July 27, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28749476/the-wide-genetic-landscape-of-clinical-frontotemporal-dementia-systematic-combined-sequencing-of-121-consecutive-subjects
#10
Cornelis Blauwendraat, Carlo Wilke, Javier Simón-Sánchez, Iris E Jansen, Anika Reifschneider, Anja Capell, Christian Haass, Melissa Castillo-Lizardo, Saskia Biskup, Walter Maetzler, Patrizia Rizzu, Peter Heutink, Matthis Synofzik
PurposeTo define the genetic spectrum and relative gene frequencies underlying clinical frontotemporal dementia (FTD).MethodsWe investigated the frequencies and mutations in neurodegenerative disease genes in 121 consecutive FTD subjects using an unbiased, combined sequencing approach, complemented by cerebrospinal fluid Aβ1-42 and serum progranulin measurements. Subjects were screened for C9orf72 repeat expansions, GRN and MAPT mutations, and, if negative, mutations in other neurodegenerative disease genes, by whole-exome sequencing (WES) (n = 108), including WES-based copy-number variant (CNV) analysis...
July 27, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28749474/racial-ethnic-differences-in-multiple-gene-sequencing-results-for-hereditary-cancer-risk
#11
Jennifer L Caswell-Jin, Tanya Gupta, Evan Hall, Iva M Petrovchich, Meredith A Mills, Kerry E Kingham, Rachel Koff, Nicolette M Chun, Peter Levonian, Alexandra P Lebensohn, James M Ford, Allison W Kurian
PurposeWe examined racial/ethnic differences in the usage and results of germ-line multiple-gene sequencing (MGS) panels to evaluate hereditary cancer risk.MethodsWe collected genetic testing results and clinical information from 1,483 patients who underwent MGS at Stanford University between 1 January 2013 and 31 December 2015.ResultsAsians and Hispanics presented for MGS at younger ages than whites (48 and 47 vs. 55; P = 5E-16 and 5E-14). Across all panels, the rate of pathogenic variants (15%) did not differ significantly between racial groups...
July 27, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28749451/characterization-of-two-historic-smallpox-specimens-from-a-czech-museum
#12
Petr Pajer, Jiri Dresler, Hana Kabíckova, Libor Písa, Pavel Aganov, Karel Fucik, Daniel Elleder, Tomas Hron, Vitezslav Kuzelka, Petr Velemínsky, Jana Klimentova, Alena Fucikova, Jaroslav Pejchal, Rita Hrabakova, Vladimir Benes, Tobias Rausch, Pavel Dundr, Alexander Pilin, Radomir Cabala, Martin Hubalek, Jan Stríbrny, Markus H Antwerpen, Hermann Meyer
Although smallpox has been known for centuries, the oldest available variola virus strains were isolated in the early 1940s. At that time, large regions of the world were already smallpox-free. Therefore, genetic information of these strains can represent only the very last fraction of a long evolutionary process. Based on the genomes of 48 strains, two clades are differentiated: Clade 1 includes variants of variola major, and clade 2 includes West African and variola minor (Alastrim) strains. Recently, the genome of an almost 400-year-old Lithuanian mummy was determined, which fell basal to all currently sequenced strains of variola virus on phylogenetic trees...
July 27, 2017: Viruses
https://www.readbyqxmd.com/read/28749433/hbv-drug-resistance-substitutions-existed-before-the-clinical-approval-of-nucleos-t-ide-analogues-a-bioinformatic-analysis-by-genbank-data-mining
#13
Xizhan Xu, Kuanhui Xiang, Mingze Su, Yao Li, Wei Ji, Yutang Li, Hui Zhuang, Tong Li
Naturally occurring nucleos(t)ide analogue resistance (NUCr) substitution frequencies in the reverse transcriptase (RT) of the hepatitis B virus (HBV) were studied extensively after the clinical approval of nucleos(t)ide analogues (NUCs; year of approval 1998). We aimed to study NUCr substitutions in HBV RT sequences obtained before 1998 and better understand the evolution of RT sequences without NUC pressures. Our strategy was to retrieve HBV sequences from GenBank deposited before 1998. The initial search used the keywords "hepatitis B virus" or "HBV" and 1139 sequences were found...
July 27, 2017: Viruses
https://www.readbyqxmd.com/read/28749380/handling-interference-effects-in-foraging-with-bucket-brigades
#14
Wonki Lee, DaeEun Kim
Many kinds of bio-inspired tasks have been tested with swarm robotics and task partitioning is one of challenging subjects. In nature, it is well known that some colonies of social insects such as honeybees, termites, and ants use task partitioning strategies for their survival. In this paper, we demonstrate an effect of task partitioning strategy called bucket brigade that uses the direct transfer of materials or food between a pair of workers. We propose a task partitioning strategy based on moving speeds of agents for the foraging task...
July 27, 2017: Bioinspiration & Biomimetics
https://www.readbyqxmd.com/read/28749355/hardware-accelerator-for-the-multifractal-analysis-of-dna-sequences
#15
Jorge E Duarte-Sanchez, Jaime Velasco-Medina, Pedro A Moreno
The multifractal analysis has allowed to quantify the genetic variability and non-linear stability along the human genome sequence. It has some implications in explaining several genetic diseases given by some chromosome abnormalities, among other genetic particularities. The multifractal analysis of a genome is carried out by dividing the complete DNA sequence in smaller fragments and calculating the generalized dimension spectrum of each fragment using the chaos game representation and the box-counting method...
July 24, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28749351/point-light-source-position-estimation-from-rgb-d-images-by-learning-surface-attributes
#16
Sezer Karaoglu, Yang Liu, Theo Gevers, Arnold W M Smeulders
Light source position estimation is a difficult yet an important problem in computer vision. A common approach for estimating the light source position (LSP) assumes Lambert's law. However, in real-world scenes, Lambert's law does not hold for all different types of surfaces. Instead of assuming all that surfaces follow Lambert's law, our approach classifies image surface segments based on their photometric and geometric surface attributes (i.e. glossy, matte, curved etc.) and assigns weights to image surface segments based on their suitability for LSP estimation...
July 24, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28749348/fast-simulation-of-dynamic-ultrasound-images-using-the-gpu
#17
Sigurd Storve, Hans Torp
Simulated ultrasound data is a valuable tool for development and validation of quantitative image analysis methods in echocardiography. Unfortunately, simulation time can become prohibitive for phantoms consisting of a large number of point-scatterers. The COLE algorithm by Gao et al. is a fast convolution-based simulator that trades simulation accuracy for improved speed. We present highly efficient parallelized CPU- and GPU-implementations of the COLE algorithm with an emphasis on dynamic simulations involving moving pointscatterers...
July 25, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28749336/ongoing-hepatitis-a-among-men-who-have-sex-with-men-msm-linked-to-outbreaks-in-europe-in-tel-aviv-area-israel-december-2016-june-2017
#18
Yael Gozlan, Itay Bar-Or, Aviya Rakovsky, Michal Savion, Ziva Amitai, Rivka Sheffer, Noa Ceder, Emilia Anis, Itamar Grotto, Ella Mendelson, Orna Mor
Between December 2016 and June 2017, 19 Hepatitis A virus (HAV)-positive cases, 17 of which were among men who have sex with men (MSM) were identified in the Tel Aviv area. Seven of the 15 sewage samples collected between January and June 2017 were also HAV-positive. All sequences clustered with two of the three strains identified in the current European HAV outbreak. We demonstrate that despite an efficient vaccination programme, HAV can still be transmitted to an unvaccinated high-risk population.
July 20, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28749329/in-vitro-efficacy-of-16-antimicrobial-drugs-against-a-large-collection-of-%C3%AE-lactamase-producing-isolates-of-extraintestinal-pathogenic-escherichia-coli-from-dogs-and-cats
#19
Takae Shimizu, Kazuki Harada, Yuzo Tsuyuki, Yui Kimura, Tadashi Miyamoto, Shingo Hatoya, Yoshiaki Hikasa
PURPOSE: The aim of this study was to assess the in vitro efficacy of candidate antimicrobials against extended-spectrum β-lactamase (ESBL)-producing isolates of extraintestinal pathogenic Escherichia coli (ExPEC) from companion animals. METHODOLOGY: A total of 90 ESBL-producing ExPEC isolates from dogs and cats were tested for susceptibility to 16 antimicrobials with the agar dilution method. We also identified the ESBLs and AmpC β-lactamases of these isolates with PCR and DNA sequencing...
July 28, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28749327/novel-adenoviruses-detected-in-british-mustelids-including-a-unique-aviadenovirus-in-the-tissues-of-pine-martens-martes-martes
#20
David Walker, William F Gregory, Dylan Turnbull, Mara Rocchi, Anna L Meredith, Adrian W Philbey, Colin P Sharp
Several adenoviruses are known to cause severe disease in veterinary species. Recent evidence suggests that canine adenovirus type 1 (CAV-1) persists in the tissues of healthy red foxes (Vulpes vulpes), which may be a source of infection for susceptible species. It was hypothesized that mustelids native to the UK, including pine martens (Martes martes) and Eurasian otters (Lutra lutra), may also be persistently infected with adenoviruses. Based on high-throughput sequencing and additional Sanger sequencing, a novel Aviadenovirus, tentatively named marten adenovirus type 1 (MAdV-1), was detected in pine marten tissues...
July 28, 2017: Journal of Medical Microbiology
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