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https://www.readbyqxmd.com/read/30334804/svsr-a-program-to-simulate-structural-variations-and-generate-sequencing-reads-for-multiple-platforms
#1
Xiguo Yuan, Meihong Gao, Jun Bai, Junbo Duan
Structural variation accounts for a major fraction of mutations in the human genome and confers susceptibility to complex diseases. Next generation sequencing along with the rapid development of computational methods provides a cost-effective procedure to detect such variations. Simulation of structural variations and sequencing reads with real characteristics is essential for benchmarking the computational methods. Here, we develop a new program, SVSR, to simulate five types of structural variations (indels, tandem duplication, CNVs, inversions, and translocations) and SNPs for the human genome and to generate sequencing reads with features from popular platforms (Illumina, SOLiD, 454, and Ion Torrent)...
October 17, 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/30333848/detailed-structural-characterization-of-arabinans-and-galactans-of-14-apple-cultivars-before-and-after-cold-storage
#2
Daniel Wefers, Ramona Flörchinger, Mirko Bunzel
Physiological and textural properties of apples are greatly influenced by both cultivar and structural composition of their pectic polysaccharides. In previous studies, it was demonstrated that neutral pectic side chains (arabinans and galactans) play a major role during fruit development and postharvest processes. However, these complex polymers have a high structural heterogeneity, and some structural elements such as side chain substituents and substitution of neighboring residues cannot be analyzed by using conventional analytical methods...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/30328284/molecular-characterization-of-prkn-structural-variations-identified-through-whole-genome-sequencing
#3
Paloma Bravo, Hossein Darvish, Abbas Tafakhori, Luis J Azcona, Amir Hossein Johari, Faezeh Jamali, Coro Paisán-Ruiz
BACKGROUND: Early-onset Parkinson's disease (PD) is the most common inherited form of parkinsonism, with the PRKN gene being the most frequently identified mutated. Exon rearrangements, identified in about 43.2% of the reported PD patients and with higher frequency in specific ethnicities, are the most prevalent PRKN mutations reported to date in PD patients. METHODS: In this study, three consanguineous families with early-onset PD were subjected to whole-genome sequencing (WGS) analyses that were followed by Sanger sequencing and droplet digital PCR to validate and confirm the disease segregation of the identified genomic variations and to determine their parental origin...
October 16, 2018: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/30327465/characterization-of-nigerian-breast-cancer-reveals-prevalent-homologous-recombination-deficiency-and-aggressive-molecular-features
#4
Jason J Pitt, Markus Riester, Yonglan Zheng, Toshio F Yoshimatsu, Ayodele Sanni, Olayiwola Oluwasola, Artur Veloso, Emma Labrot, Shengfeng Wang, Abayomi Odetunde, Adeyinka Ademola, Babajide Okedere, Scott Mahan, Rebecca Leary, Maura Macomber, Mustapha Ajani, Ryan S Johnson, Dominic Fitzgerald, A Jason Grundstad, Jigyasa H Tuteja, Galina Khramtsova, Jing Zhang, Elisabeth Sveen, Bryce Hwang, Wendy Clayton, Chibuzor Nkwodimmah, Bisola Famooto, Esther Obasi, Victor Aderoju, Mobolaji Oludara, Folusho Omodele, Odunayo Akinyele, Adewunmi Adeoye, Temidayo Ogundiran, Chinedum Babalola, Kenzie MacIsaac, Abiodun Popoola, Michael P Morrissey, Lin S Chen, Jiebiao Wang, Christopher O Olopade, Adeyinka G Falusi, Wendy Winckler, Kerstin Haase, Peter Van Loo, John Obafunwa, Dimitris Papoutsakis, Oladosu Ojengbede, Barbara Weber, Nasiru Ibrahim, Kevin P White, Dezheng Huo, Olufunmilayo I Olopade, Jordi Barretina
Racial/ethnic disparities in breast cancer mortality continue to widen but genomic studies rarely interrogate breast cancer in diverse populations. Through genome, exome, and RNA sequencing, we examined the molecular features of breast cancers using 194 patients from Nigeria and 1037 patients from The Cancer Genome Atlas (TCGA). Relative to Black and White cohorts in TCGA, Nigerian HR + /HER2 - tumors are characterized by increased homologous recombination deficiency signature, pervasive TP53 mutations, and greater structural variation-indicating aggressive biology...
October 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/30322920/single-molecule-dna-mapping-and-whole-genome-sequencing-of-individual-cells
#5
Rodolphe Marie, Jonas N Pedersen, Loic Bærlocher, Kamila Koprowska, Marie Pødenphant, Céline Sabatel, Maksim Zalkovskij, Andrej Mironov, Brian Bilenberg, Neil Ashley, Henrik Flyvbjerg, Walter F Bodmer, Anders Kristensen, Kalim U Mir
To elucidate cellular diversity and clonal evolution in tissues and tumors, one must resolve genomic heterogeneity in single cells. To this end, we have developed low-cost, mass-producible micro-/nanofluidic chips for DNA extraction from individual cells. These chips have modules that collect genomic DNA for sequencing or map genomic structure directly, on-chip, with denaturation-renaturation (D-R) optical mapping [Marie R, et al. (2013) Proc Natl Acad Sci USA 110:4893-4898]. Processing of single cells from the LS174T colorectal cancer cell line showed that D-R mapping of single molecules can reveal structural variation (SV) in the genome of single cells...
October 15, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30318446/extensive-structural-differences-of-closely-related-3-mrna-isoforms-links-to-pab1-binding-and-mrna-stability
#6
Zarmik Moqtaderi, Joseph V Geisberg, Kevin Struhl
Alternative polyadenylation generates numerous 3' mRNA isoforms that can vary in biological properties, such as stability and localization. We developed methods to obtain transcriptome-scale structural information and protein binding on individual 3' mRNA isoforms in vivo. Strikingly, near-identical mRNA isoforms can possess dramatically different structures throughout the 3' UTR. Analyses of identical mRNAs in different species or refolded in vitro indicate that structural differences in vivo are often due to trans-acting factors...
September 26, 2018: Molecular Cell
https://www.readbyqxmd.com/read/30315635/trabecular-bone-structural-variation-in-the-proximal-sacrum-among-primates
#7
Gabrielle A Russo
The sacrum occupies a functionally important anatomical position as part of the pelvic girdle and vertebral column. Sacral orientation and external morphology in modern humans are distinct from that in other primates and compatible with the demands of habitual bipedal locomotion. Among nonhuman primates, however, the relationship between external sacral morphology and positional behaviors is less clear. As an alternative to evaluation of the sacrum's external morphology, this study assesses if the sacrum's internal morphology differs among extant primates...
October 13, 2018: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/30314258/wing-polymorphism-in-anaphothrips-graminum-thysanoptera-thripidae
#8
Kambiz Minaei
Of the 83 species of Anaphothrips in the world (ThripsWiki 2018), only four are recorded in Iran so far (Alavi et al. 2018): A. microptera, A. obscurus, A. sineconus and A. sudanensis. Among these, A. sineconus was collected from Haloxylon persicum (Amaranthaceae) while the others are related to various grasses (Poaceae). Color and structural variation among and within the species of Anaphothrips have been demonstrated by several authors (Kudo, 1989, Nakao 1996, Mound Masumoto 2009). In this paper a fifth species, A...
July 27, 2018: Zootaxa
https://www.readbyqxmd.com/read/30313912/nothogreniera-new-genus-for-two-species-of-australian-paracnephia-diptera-simuliidae
#9
Douglas A Craig, Douglas C Currie, John K Moulton
Two species of Australian Simuliidae known only from adult females and currently assigned to "Paracnephia" are re-described, as are their now-known males and immature stages. Morphological character states of "Paracnephia" fergusoni (Tonnoir) and "P." fergusoni var. (Mackerras Mackerras) reveal that they are markedly distinct from all other Australian species, and are here assigned to the new genus-Nothogreniera-the most plesiomorphic Gondwanan Australian simuliid. Structural variation among populations of N...
July 11, 2018: Zootaxa
https://www.readbyqxmd.com/read/30312931/l-8-naphthalimide-based-dna-intercalators-and-anticancer-agents-a-systematic-review-from-2007-to-2017
#10
REVIEW
Mateusz D Tomczyk, Krzysztof Z Walczak
In this review, we describe a detailed investigation about the structural variations and relative activity of 1,8-naphthalimide based intercalators and anticancer agents. The 1,8-naphthalimides binds to the DNA via intercalation, and exert their antitumor activities through Topoisomerase I/II inhibition, photoinduced DNA damage or related mechanism. Here, our discussion focused on works published over the last ten years (2007-2017) related to therapeutic applications, in the order of cancer treatment followed by other properties of 1,8-naphthalimides...
November 5, 2018: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/30310315/difference-of-molecular-alterations-in-her2-positive-and-her2-negative-gastric-cancers-by-whole-genome-sequencing-analysis
#11
Chenfei Zhou, Xiaojing Feng, Fei Yuan, Jun Ji, Min Shi, Yingyan Yu, Zhenggang Zhu, Jun Zhang
Objective: The aim of this study was to compare the molecular profiling, including somatic mutation and somatic copy number variation (SCNV), between human epidermal growth factor receptor 2 (HER2)-positive (HER2+) and HER2-negative (HER2-) gastric cancer patients. Patients and methods: Tumor samples were collected from 15 gastric cancer patients, including 10 HER2+ samples and five HER2- samples, which were diagnosed by immunohistochemistry. Whole-genome sequencing was performed by Illumina HiSeq PE150 instrument, along with somatic single nucleotide variant (SNV), somatic structural variation (SV) and SCNV analyses...
2018: Cancer Management and Research
https://www.readbyqxmd.com/read/30305022/cloning-and-characterization-of-the-homoeologous-genes-for-the-rec8-like-meiotic-cohesin-in-polyploid-wheat
#12
Guojia Ma, Wei Zhang, Liwang Liu, Wun S Chao, Yong Qiang Gu, Lili Qi, Steven S Xu, Xiwen Cai
BACKGROUND: Meiosis is a specialized cell division critical for gamete production in the sexual reproduction of eukaryotes. It ensures genome integrity and generates genetic variability as well. The Rec8-like cohesin is a cohesion protein essential for orderly chromosome segregation in meiotic cell division. The Rec8-like genes and cohesins have been cloned and characterized in diploid models, but not in polyploids. The present study aimed to clone the homoeologous genes (homoeoalleles) for Rec8-like cohesin in polyploid wheat, an important food crop for humans, and to characterize their structure and function under a polyploid condition...
October 11, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/30304834/migration-energy-barriers-for-the-surface-and-bulk-of-self-assembly-zno-nanorods
#13
Feng-Ming Chang, Zhong-Zhe Wu, Jing-Heng Huang, Wei-Ting Chen, Sanjaya Brahma, Kuang Yao Lo
Post-annealing treatment is a necessary process to create/eliminate/repair defects in self⁻assembly (SA) metal oxide by providing enough thermal energy to the O atoms to overcome the migration energy barrier in ZnO. The height of migration energy barrier is dependent on the depth from the surface, which is hard to be estimated by theoretical calculations, as well as the optical analyses. SA ZnO nanorods (ZNRs) have high surface-to-volume ratio to provide complete picture between the optical and surface properties obtained by photoluminescence (PL) and ultraviolet/X-ray photoemission spectroscopy (UPS/XPS), which is used to investigate the evolution of structure and chemical states of the surface layers to reveal mutual agreement on all observations in PL, XPS, and UPS...
October 9, 2018: Nanomaterials
https://www.readbyqxmd.com/read/30302553/a-specific-allele-of-myb14-in-grapevine-correlates-with-high-stilbene-inducibility-triggered-by-al-3-and-uv-c-radiation
#14
Ru Bai, Yangyang Luo, Lixin Wang, Jing Li, Kerun Wu, Guifang Zhao, Dong Duan
The structural differences of MYB14 promoter in two grapevine genotypes affect the expression of MYB14 and stilbene synthesis in response to Al3+ and UV-C radiation. Grapevines provide an important fruit crop worldwide, but production is often limited by pathogen infection. Stilbenes, a class of secondary metabolite, represent phytoalexins that contribute to defence against pathogens in many plants, including grapevine. It is known that the transcription factors MYB14 and MYB15 are required for the activation of the promoters of resveratrol synthase to regulate stilbene biosynthesis...
October 9, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/30298665/genetic-study-of-immunoglobulin-a-nephropathy-from-research-to-clinical-application
#15
REVIEW
Ming Li, Xueqing Yu
Immunoglobulin A nephropathy (IgAN) is one of the most common primary glomerulonephritis throughout the world and a major cause of end-stage renal disease among East Asian population. It is widely considered that genetic factors play an important role in the pathogenesis of IgAN. The genetic studies of IgAN, is from the association studies of candidate genes and family-based designs, to the genome-wide association studies. Altogether there are five large genome-wide association studies performed, which have identified multiple susceptibility loci for IgAN, including several novel loci found in Chinese population...
October 2018: Nephrology
https://www.readbyqxmd.com/read/30292630/targeted-exome-sequencing-identified-a-novel-mutation-hotspot-and-a-deletion-in-chinese-primary-hypertrophic-osteoarthropathy-patients
#16
Yulin Chen, Guoqiang Li, Yufei Xu, Tingting Yu, Yi Zhang, Niu Li, Ru-En Yao, Yunfang Zhou, Xiumin Wang, Yiping Shen, Lei Yin, Jian Wang
BACKGROUND: Primary hypertrophic osteoarthropathy (PHO) is a genetically and clinically heterogeneous systematic disorder caused by mutations in genes HPGD and SLCO2A1. The purpose of the present study is to provide useful information for the early and precise diagnosis of PHO and identify causative mutations in Chinese PHO children. METHODS AND RESULTS: The clinical manifestations, radiographic features of seven Chinese pediatric patients were systematically analyzed...
October 4, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/30291452/snort-acoustic-structure-codes-for-positive-emotions-in-horses
#17
Mathilde Stomp, Maël Leroux, Marjorie Cellier, Séverine Henry, Martine Hausberger, Alban Lemasson
While the vocal coding of human and animal internal states has been widely studied, the possible acoustic expression of "positive" emotions remains poorly known. Recent studies suggest that snorts (non-vocal sounds produced by the air expiration through the nostrils) appear to be reliable indicators of positive internal states in several ungulate species. Here, we hypothesised in horses that the acoustic structure of the snort could vary with the subjects' current emotional state. Indeed, a preliminary sound analysis of snorts let us suggest structure variations related to the presence of pulsations...
September 12, 2018: Die Naturwissenschaften
https://www.readbyqxmd.com/read/30289694/small-structural-variations-have-large-effects-on-the-assembly-properties-and-spin-state-of-room-temperature-high-spin-fe-ii-iminopyridine-cages
#18
Tabitha F Miller, Lauren R Holloway, Phoebe P Nye, Yana Lyon, Gregory J O Beran, W Hill Harman, Ryan R Julian, Richard J Hooley
Small changes in steric bulk at the terminus of bis-iminopyridine ligands can effect large changes in the spin state of self-assembled Fe(II)-iminopyridine cage complexes. If the added bulk is properly matched with ligands that are either sufficiently flexible to allow twisted octahedral geometries at the Fe centers or can assemble with unusual mer configurations at the metals, room temperature high spin Fe(II) cages can be synthesized. These complexes maintain their high spin state in solution at low temperatures and have been characterized by X-ray crystallographic and computational methods...
October 5, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/30289191/neutral-mechanisms-and-niche-differentiation-in-steady-state-insular-microbial-communities-revealed-by-single-cell-analysis
#19
Zishu Liu, Nicolas Cichocki, Thomas Hübschmann, Christine Süring, Irina Dana Ofiţeru, William T Sloan, Volker Grimm, Susann Müller
In completely insular microbial communities, evolution of community structure cannot be shaped by the immigration of new members. Also, when those communities are run in steady-state, the influence of environmental factors on their assembly is reduced. Therefore, one would expect similar community structures under steady-state conditions. Yet, in parallel setups variability does occur. To reveal ecological mechanisms behind this phenomenon, five parallel reactors were studied at the single-cell level for about 100 generations and community structure variations were quantified by ecological measures...
October 5, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/30270606/comparative-genomic-and-genetic-functional-analysis-of-industrial-l-leucine-and-l-valine-producing-corynebacterium-glutamicum-strains
#20
Yuechao Ma, Qixin Chen, Yi Cui, Lihong Du, Tuo Shi, Qingyang Xu, Qian Ma, Xixian Xie, Ning Chen
Corynebacterium glutamicum is an excellent platform for the production of amino acids, and is widely used in the fermentation industry. Most industrial strains are traditionally obtained by repeated processes of random mutation and selection, but the genotype of these strains is often unclear owing to the absence of genomic information. As such, it is difficult to improve the growth and amino-acid production of these strains via metabolic engineering. In this study, we generated a complete genome map of an industrial L-valine-producing strain C...
September 20, 2018: Journal of Microbiology and Biotechnology
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