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"structural variation"

Huijie Liu, Jian He, Chuanhua Ding, Rudan Lyu, Linying Pei, Jin Cheng, Lei Xie
Structural rearrangements of Anemone species' chloroplast genome has been reported based on genetic mapping of restriction sites but has never been confirmed by genomic studies. We used a next-generation sequencing method to characterize the complete chloroplast genomes of five species in the tribe Anemoneae. Plastid genomes were assembled using de novo assembling methods combined with conventional Sanger sequencing to fill the gaps. The gene order of the chloroplast genomes of tribe Anemoneae was compared with that of other Ranunculaceae species...
2018: Frontiers in Plant Science
Huijun Zhang, Xiong Fang, Qian Meng, Yujia Mao, Yan Xu, Tingting Fan, Jing An, Ziwei Huang
Microtubule has been an important target for anticancer drug development. Here we report the discovery and characterization of a series of fused 4-aryl-4H-chromene-based derivatives as highly potent microtubule inhibitors. Among a total of 37 derivatives synthesized, 23 exhibited strong in vitro anti-proliferative activities against A375 human melanoma cells. The relationship between the biological activities of these microtubule inhibitors and their chemical structure variations was analyzed. Studies of compounds 27a, 19a and 9a in parallel with colchicine as the positive control compound in a panel of biological assays revealed that these compounds blocked cell cycle progression, increased apoptosis, and inhibited HUVEC capillary tube formation at low nanomolar concentrations...
July 20, 2018: European Journal of Medicinal Chemistry
Xinjin He, Zilong Sun, Ram Kumar Manthari, Panhong Wu, Jundong Wang
Fluoride is known to affect the pro-inflammatory cytokines in the testis. Most of the recent literatures cited that cytokines regulate the blood-testis-barrier (BTB). However, the involvement of cytokines in the fluoride induced toxicity in BTB remains unclear. In order to study this, 60 male Sprague-Dawley (SD) rats were taken and randomly divided into 5 groups which included four fluoride groups exposed to 0, 25, 50, and 100 mg/L NaF in distilled water and one positive control group. On the 29th day of fluoride exposure, the positive control group rats were administered 0...
August 3, 2018: Chemosphere
Kristian Urh, Živa Kolenc, Maj Hrovat, Luka Svet, Peter Dovč, Tanja Kunej
Background: Cryptorchidism is one of the most frequent congenital birth defects in male children and is present in 2-4% of full-term male births. It has several possible health effects including reduced fertility, increased risk for testicular neoplasia, testicular torsion, and psychological consequences. Cryptorchidism is often diagnosed as comorbid; copresent with other diseases. It is also present in clinical picture of several syndromes. However, this field has not been systematically studied. The aim of the present study was to catalog published cases of syndromes which include cryptorchidism in the clinical picture and associated genomic information...
2018: Frontiers in Endocrinology
Hongwei Zhou, Mingsen Chen, Yuanli Liu, Si Wu
Ruthenium-containing polymers (RCPs) are a type of functional metallopolymer. Stimuli-responsive RCPs in which the responsive behaviors derive from the structure variation of Ru complexes are reviewed in this Feature Article, with particular focus on redox responsive RCPs and photoresponsive RCPs. On the basis of the recent progress, the response principle, syntheses, structures, properties, applications, and remaining challenges of such stimuli-responsive RCPs are discussed.
August 9, 2018: Macromolecular Rapid Communications
Kijong Yi, Young Seok Ju
Next-generation sequencing technology has enabled the comprehensive detection of genomic alterations in human somatic cells, including point mutations, chromosomal rearrangements, and structural variations (SVs). Using sophisticated bioinformatics algorithms, unbiased catalogs of SVs are emerging from thousands of human cancer genomes for the first time. Via careful examination of SV breakpoints at single-nucleotide resolution as well as local DNA copy number changes, diverse patterns of genomic rearrangements are being revealed...
August 7, 2018: Experimental & Molecular Medicine
David Jurnecka, Petr Man, Peter Sebo, Ladislav Bumba
Filamentous hemagglutinin (FHA) mediates adherence and plays an important role in lower respiratory tract infections by pathogenic Bordetellae . The mature FHA proteins of B. pertussis (Bp-FHA) and the B. bronchiseptica (Bb-FHA) are generated by processing of the respective FhaB precursors by the autotransporter subtilisin-type protease SphB1. We have used bottom-up proteomics with differential 16 O/18 O labeling and show that despite high-sequence conservation of the corresponding FhaB segments, the mature Bp-FHA (~ 230 kDa) and Bb-FHA (~ 243 kDa) proteins are processed at different sites of FhaB, after the Ala-2348 and Lys-2479 residues, respectively...
August 2018: FEBS Open Bio
Przemyslaw Szafranski, Ewelina Kośmider, Qian Liu, Justyna A Karolak, Lauren Currie, Sandhya Parkash, Stephen G Kahler, Elizabeth Roeder, Rebecca O Littlejohn, Thomas S DeNapoli, Felix R Shardonofsky, Cody Henderson, George Powers, Virginie Poisson, Denis Bérubé, Luc Oligny, Jacques L Michaud, Sandra Janssens, Kris De Coen, Jo Van Dorpe, Annelies Dheedene, Matthew T Harting, Matthew D Weaver, Amir M Khan, Nina Tatevian, Jennifer Wambach, Kathleen A Gibbs, Edwina Popek, Anna Gambin, Paweł Stankiewicz
Transposable elements modify human genome by inserting into new loci or by mediating homology-, microhomology-, or homeology-driven DNA recombination or repair, resulting in genomic structural variation. Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare, lethal, neonatal developmental lung disorder caused by point mutations or copy-number variant (CNV) deletions of FOXF1 or its distant tissue specific enhancer. Eighty five per cent of 45ACDMPV-causative CNV deletions, of which junctions have been sequenced, had at least one of their two breakpoints located in a retrotransposon, with more than half of them being Alu elements...
August 6, 2018: Human Mutation
Jenny Arnling Bååth, Scott Mazurkewich, Rasmus Meland Knudsen, Jens-Christian Navarro Poulsen, Lisbeth Olsson, Leila Lo Leggio, Johan Larsbrink
Background: Lignocellulose is highly recalcitrant to enzymatic deconstruction, where the recalcitrance primarily results from chemical linkages between lignin and carbohydrates. Glucuronoyl esterases (GEs) from carbohydrate esterase family 15 (CE15) have been suggested to play key roles in reducing lignocellulose recalcitrance by cleaving covalent ester bonds found between lignin and glucuronoxylan. However, only a limited number of GEs have been biochemically characterized and structurally determined to date, limiting our understanding of these enzymes and their potential exploration...
2018: Biotechnology for Biofuels
Laura B Scheinfeldt, Kelly Hodges, Jonathan Pevsner, Dorit Berlin, Nahid Turan, Norman P Gerry
OBJECTIVE: Lymphoblastoid cell lines are widely used in genetic and genomic studies. Previous work has characterized variant stability in transformed culture and across culture passages. Our objective was to extend this work to evaluate single nucleotide polymorphism and structural variation across cell line expansions, which are commonly used in biorepository distribution. Our study used DNA and cell lines sampled from six research participants. We assayed genome-wide genetic variants and inferred structural variants for DNA extracted from blood, from transformed cell cultures, and from three generations of expansions...
August 3, 2018: BMC Research Notes
Nicholas B Stephens, Tracy L Kivell, Dieter H Pahr, Jean-Jacques Hublin, Matthew M Skinner
Hand bone morphology is regularly used to link particular hominin species with behaviors relevant to cognitive/technological progress. Debates about the functional significance of differing hominin hand bone morphologies tend to rely on establishing phylogenetic relationships and/or inferring behavior from epigenetic variation arising from mechanical loading and adaptive bone modeling. Most research focuses on variation in cortical bone structure, but additional information about hand function may be provided through the analysis of internal trabecular structure...
July 30, 2018: Journal of Human Evolution
Yuxuan Yuan, Zbyněk Milec, Philipp E Bayer, Jan Vrána, Jaroslav Doležel, David Edwards, William Erskine, Parwinder Kaur
We selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs . Daliak and Yarloop. The structural variations (SVs) discovered by Bionano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions containing deletions and 19 regions containing insertions in Yarloop. The 12 large-scale regions contained 71 small deletions when validated by Illumina short reads. The results suggest that BOM could detect the total size of deletions and insertions, but it could not precisely report the location and actual quantity of SVs in the genome...
2018: Frontiers in Plant Science
Athena Andreou, Petros Giastas, Elias Christoforides, Elias E Eliopoulos
Functional and folding constraints impose interdependence between interacting sites along the protein chain that are envisaged through protein sequence evolution. Studying the influence of structure in phylogenetic models requires detailed and reliable structural models. Polysaccharide deacetylases (PDAs), members of the carbohydrate esterase family 4, perform mainly metal-dependent deacetylation of O - or N -acetylated polysaccharides such as peptidoglycan, chitin and acetylxylan through a conserved catalytic core termed the NodB homology domain...
July 31, 2018: Genes
Yanting Shen, Jing Liu, Haiying Geng, Jixiang Zhang, Yucheng Liu, Haikuan Zhang, Shilai Xing, Jianchang Du, Shisong Ma, Zhixi Tian
Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding. Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data...
July 27, 2018: Science China. Life Sciences
Silong Sun, Yingsi Zhou, Jian Chen, Junpeng Shi, Haiming Zhao, Hainan Zhao, Weibin Song, Mei Zhang, Yang Cui, Xiaomei Dong, Han Liu, Xuxu Ma, Yinping Jiao, Bo Wang, Xuehong Wei, Joshua C Stein, Jeff C Glaubitz, Fei Lu, Guoliang Yu, Chengzhi Liang, Kevin Fengler, Bailin Li, Antoni Rafalski, Patrick S Schnable, Doreen H Ware, Edward S Buckler, Jinsheng Lai
Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines...
July 30, 2018: Nature Genetics
Anouk Schurink, Vinicius H da Silva, Brandon D Velie, Bert W Dibbits, Richard P M A Crooijmans, Liesbeth Franҫois, Steven Janssens, Anneleen Stinckens, Sarah Blott, Nadine Buys, Gabriella Lindgren, Bart J Ducro
BACKGROUND: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide...
July 30, 2018: BMC Genetics
Anne B Arnett, Sandy Trinh, Raphael A Bernier
Autism spectrum disorder (ASD) is a behaviorally heterogeneous disorder with a strong genetic component, as evidenced by decades of twin and family studies. In recent years, enhanced methods of genomic sequencing have revealed that structural variation and mutations to both coding and non-coding regions of single, candidate genes may account for more than 30% of ASD cases. The current review highlights a genotype-first approach that builds upon these molecular findings to parse the heterogeneity of ASD. Advantages of this approach include strong potential for precision medicine diagnosis and treatment, as well as opportunity to advance basic science research on neurodevelopmental disorders...
July 21, 2018: Current Opinion in Psychology
D Vollhardt
The introduction of the highly-sensitive imaging technique Brewster angle microscopy (BAM) has given rise to new knowledges about the mesoscopic topology and ordering of condensed phase domains formed in the two-phase coexistence region of Langmuir monolayers. Besides fatty acids, monoalkanoylglycerols are the most studied amphiphiles at the air-water interface. In this review, the mesoscopic characterization of amphiphilic monoglycerol monolayers is surveyed to demonstrate the striking effect of the position of the glycerol backbone at which the polar head group is substituted...
July 22, 2018: Advances in Colloid and Interface Science
Dengying Liu, Zhenliang Chen, Zhe Zhang, Hao Sun, Peipei Ma, Kai Zhu, Guanglei Liu, Qishan Wang, Yuchun Pan
Objective: The Shanghai Holstein cattle breed is susceptible to severe mastitis and other diseases and suffers from hot weather and long-term humidity in Shanghai, where the main centre for providing Holstein semen for farms distributed throughout China is located. Our objective was to determine the genetic mechanisms influencing important economic traits, especially diseases that heavily impact the yield and quality of milk and reproduction. Methods: In our study, we detected the structural variations of 1092 Shanghai Holstein cows by using next-generation sequencing...
July 26, 2018: Asian-Australasian Journal of Animal Sciences
Darine Villela, Claudia K Suemoto, Renata Leite, Carlos Augusto Pasqualucci, Lea T Grinberg, Peter Pearson, Carla Rosenberg
Aging is a complex process strongly determined by genetics. Previous reports have shown that the genome of neuronal cells displays somatic genomic mosaicism including DNA copy number variations (CNVs). CNVs represent a significant source of genetic variation in the human genome and have been implicated in several disorders and complex traits, representing a potential mechanism that contributes to neuronal diversity and the etiology of several neurological diseases and provides new insights into the normal, complex functions of the brain...
2018: Neural Plasticity
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