Read by QxMD icon Read

"structural variation"

Anton S Petrov, Elizabeth C Wood, Chad R Bernier, Ashlyn M Norris, Alan Brown, A Amunts
Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary history of mitoribosomes across the phylogenetic tree by combining three-dimensional structural information with a comparative analysis of the secondary structures of mitochondrial rRNAs (mt-rRNAs) and available proteomic data...
December 4, 2018: Molecular Biology and Evolution
Sen Ma, Wen Han, Li Li, Xueling Zheng, Xiaoxi Wang
Wheat bran dietary fiber (WBDF) has been reported to be responsible for the low quality of whole wheat flour products due to its destructive effect on the gluten matrix. Glutenin and gliadin are the major components of gluten protein and contribute to a proper gluten structure. In this study, the thermostability, surface hydrophobicity, fluorescence characteristics, free sulfhydryl contents, and molecular weight distributions of glutenin- and gliadin-rich fractions were determined after the addition of WBDF...
December 5, 2018: Food & Function
Yimin Mao, Peter Y Zavalij
Two ZnII -based coordination polymers (CPs) were synthesized by the hydrothermal method, using Zn(NO3 )2 ·6H2 O and furan-2,5-dicarboxylic acid (FDCA) in dimethylformamide (DMF) solvent, at 95 °C. Poly[tetrakis(dimethylazanium) [tetrakis(μ2 -furan-2,5-dicarboxylato-κ2 O2 :O5 )dizinc(II)]], {(C2 H8 N)4 [Zn2 (C6 H2 O5 )4 ]}n or {[DMA]4 [ZnII 2 (FDC)4 ]}n (DMA = dimethylazanium and FDC = furan-2,5-dicarboxylate), (1), was obtained with a 1:1 molar ratio of ZnII and FDCA. It crystallized in the monoclinic space group C2/c...
December 1, 2018: Acta Crystallographica. Section C, Structural Chemistry
Lily J Doershuk, Jaap P P Saers, Colin N Shaw, Tea Jashashvili, Kristian J Carlson, Jay T Stock, Timothy M Ryan
OBJECTIVE: This project investigates trabecular bone structural variation in the proximal humerus and femur of hunter-gatherer, mixed-strategy agricultural, medieval, and human groups to address three questions: (a) What is the extent of trabecular bone structural variation in the humerus and femur between populations with different inferred activity levels? (b) How does variation in the proximal humerus relate to variation in the proximal femur? (c) Are trabecular bone microstructural variables sexually dimorphic? METHODS: The proximal humerus and femur of 73 adults from five human groups with distinct subsistence strategies were scanned using a micro-computed tomography system...
January 2019: American Journal of Physical Anthropology
István Prazsák, Norbert Moldován, Zsolt Balázs, Dóra Tombácz, Klára Megyeri, Attila Szűcs, Zsolt Csabai, Zsolt Boldogkői
BACKGROUND: Varicella zoster virus (VZV) is a human pathogenic alphaherpesvirus harboring a relatively large DNA molecule. The VZV transcriptome has already been analyzed by microarray and short-read sequencing analyses. However, both approaches have substantial limitations when used for structural characterization of transcript isoforms, even if supplemented with primer extension or other techniques. Among others, they are inefficient in distinguishing between embedded RNA molecules, transcript isoforms, including splice and length variants, as well as between alternative polycistronic transcripts...
December 4, 2018: BMC Genomics
Yi Wang, Xiangyu Li, Yanping Lin, Yanfang Wang, Kangyu Wang, Chunyu Sun, Tiancheng Lu, Meiping Zhang
Ginseng ( C.A. Mey.) is one of the most important medicinal herbs for human health and medicine, for which ginsenosides are the major bioactive components. The cytochrome P450 genes, , form a large gene superfamily; however, only three genes have been identified from ginseng and shown to be involved in ginsenoside biosynthesis, indicating the importance of the gene superfamily in the process. Here we report genome-wide identification and systems analysis of the genes in ginseng, defined as genes. We identified 414 genes, including the three published genes...
November 2018: Plant Genome
Maojun Wang, Lili Tu, Daojun Yuan, De Zhu, Chao Shen, Jianying Li, Fuyan Liu, Liuling Pei, Pengcheng Wang, Guannan Zhao, Zhengxiu Ye, Hui Huang, Feilin Yan, Yizan Ma, Lin Zhang, Min Liu, Jiaqi You, Yicheng Yang, Zhenping Liu, Fan Huang, Baoqi Li, Ping Qiu, Qinghua Zhang, Longfu Zhu, Shuangxia Jin, Xiyan Yang, Ling Min, Guoliang Li, Ling-Ling Chen, Hongkun Zheng, Keith Lindsey, Zhongxu Lin, Joshua A Udall, Xianlong Zhang
Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete1-4 . Here we report reference-grade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3-79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques...
December 3, 2018: Nature Genetics
Kei Fujiwara, Kentaro Matsuura, Kayoko Matsunami, Etsuko Iio, Shunsuke Nojiri
BACKGROUND: Hepatitis B virus (HBV) infection is one of the most serious public health issues. Recent HBV genetic research has revealed novel genetic rearrangements termed complex structural variations (SVs), which are composed of combinations of SVs such as insertions, deletions, and duplications. An extensive search was made for complex SVs of HBV and their characteristics were analyzed. RESULTS: Fifty-five HBV strains with complex SVs were identified by analyzing genetic sequences of HBV with bioinformatical tools...
December 3, 2018: BMC Microbiology
Benjamin B Currall, Caroline W Antolik, Ryan L Collins, Michael E Talkowski
Precise tests for genomic structural variation (SV) are essential for accurate diagnosis of prenatal genome abnormalities. The two most ubiquitous traditional methods for prenatal SV assessment, karyotyping and chromosomal microarrays, do not provide sufficient resolution for some clinically actionable SVs. Standard whole-genome sequencing (WGS) overcomes shortcomings of traditional techniques by providing base-pair resolution of the entire accessible genome. However, while sequencing costs have continued to decline in recent years, conventional WGS costs remain high for most routine clinical applications...
2019: Methods in Molecular Biology
Nya Mehnwolo Boayue, Gábor Csifcsák, Oula Puonti, Axel Thielscher, Matthias Mittner
During the past decade, it became clear that the effects of non-invasive brain stimulation (NIBS) techniques such as transcranial direct current stimulation (tDCS) and transcranial magnetic stimulation (TMS) are substantially influenced by variations in individual head and brain anatomy. In addition to structural variations in the healthy, several psychiatric disorders are characterized by anatomical alterations that are likely to further constrain the intracerebral effects of NIBS. Here, we present high-resolution realistic head models derived from structural magnetic resonance imaging data of 19 healthy adults and 19 patients diagnosed with major depressive disorder (MDD)...
2018: F1000Research
Noelia Díaz, Kai Kruse, Tabea Erdmann, Annette M Staiger, German Ott, Georg Lenz, Juan M Vaquerizas
Chromatin conformation constitutes a fundamental level of eukaryotic genome regulation. However, our ability to examine its biological function and role in disease is limited by the large amounts of starting material required to perform current experimental approaches. Here, we present Low-C, a Hi-C method for low amounts of input material. By systematically comparing Hi-C libraries made with decreasing amounts of starting material we show that Low-C is highly reproducible and robust to experimental noise. To demonstrate the suitability of Low-C to analyse rare cell populations, we produce Low-C maps from primary B-cells of a diffuse large B-cell lymphoma patient...
November 29, 2018: Nature Communications
I-Te Chu, Chia-Chuan Wu, Ta-Chau Chang
BACKGROUND: Mitochondrial DNA (mtDNA) mutations could lead to mitochondrial dysfunction, which plays a major role in aging, neurodegeneration, and cancer. Recently, we have highlighted G-quadruplex (G4) formation of putative G4-forming (PQF) mtDNA sequences in cells. Herein, we examine structural variation of G4 formation due to mutation of mtDNA sequences in vitro. METHODS: The combined circular dichroism (CD), nuclear magnetic resonance (NMR), and polyacrylamide gel electrophoresis (PAGE) results provide complementary insights into the structural variation of the studied G-rich sequence and its mutants...
November 26, 2018: Biochimica et biophysica acta. General subjects
Lijie Zhou, Biao Ye, Siqing Xia
Chromate (CrO4 2- ) exposure, especially high concentration (mg/L), still probably occurs in the industrial and mining area due to industrial accidents or even illegal discharge, though CrO4 2- has been restricted to be discharged into wastewater treatment system (WWTS). Therefore, this study was applied to better understand the structural characteristics of cake layer in membrane bioreactor (MBR), which is one of best alternative for WWTS of industrial or mining area, with CrO4 2- exposure. Three submerged MBRs with CrO4 2- exposure (10 mg/L was normal high concentration CrO4 2- ; 50 mg/L as extreme level for better identification; 0 mg/L as control condition) were applied in this study...
November 23, 2018: Ecotoxicology and Environmental Safety
Lili Xing, Junwei Lucas Bao, Zhandong Wang, Xuetao Wang, Donald G Truhlar
Hydroperoxyalkylperoxy species (OOQOOH) are important intermediates that are generated during the autoignition of transport fuels. A key reaction of hydroperoxyalkylperoxy radicals is a [1,5] hydrogen shift, for which kinetics data are experimentally unavailable. Here we study two typical OOQOOH reactions and compare their kinetics to one another and to a previous study to learn the effect of structural variations of the alkyl group on the competition between alternative [1,5] hydrogen shifts of hydroperoxyalkylperoxy species...
November 23, 2018: Journal of the American Chemical Society
Qizong Lao, Marcia Des Jardin, Rahul Jayakrishnan, Monique Ernst, Deborah P Merke
CYP21A2 defects result in congenital adrenal hyperplasia (CAH), an autosomal recessive disorder characterized by impaired adrenal steroidogenesis. CYP21A2 lies within the major histocompatibility complex in an area of the genome highly susceptible to genetic variation. Alterations in the neighboring complement component 4 isotypes C4A and C4B have been associated with psychiatric and autoimmune disease. The purpose of this study was to evaluate C4A and C4B in patients with CAH in relation to CYP21A2 genotype and psychiatric and autoimmune comorbidity...
December 2018: Human Genetics
Hui-Chen Wu, Victor P Bulgakov, Tsung-Luo Jinn
Heat stress (HS) is expected to be of increasing worldwide concern in the near future, especially with regard to crop yield and quality as a consequence of rising or varying temperatures as a result of global climate change. HS response (HSR) is a highly conserved mechanism among different organisms but shows remarkable complexity and unique features in plants. The transcriptional regulation of HSR is controlled by HS transcription factors (HSFs) which allow the activation of HS-responsive genes, among which HS proteins (HSPs) are best characterized...
2018: Frontiers in Plant Science
Markus Mayrhofer, Bram De Laere, Tom Whitington, Peter Van Oyen, Christophe Ghysel, Jozef Ampe, Piet Ost, Wim Demey, Lucien Hoekx, Dirk Schrijvers, Barbara Brouwers, Willem Lybaert, Els Everaert, Daan De Maeseneer, Michiel Strijbos, Alain Bols, Karen Fransis, Steffi Oeyen, Pieter-Jan van Dam, Gert Van den Eynden, Annemie Rutten, Markus Aly, Tobias Nordström, Steven Van Laere, Mattias Rantalainen, Prabhakar Rajan, Lars Egevad, Anders Ullén, Jeffrey Yachnin, Luc Dirix, Henrik Grönberg, Johan Lindberg
BACKGROUND: There are multiple existing and emerging therapeutic avenues for metastatic prostate cancer, with a common denominator, which is the need for predictive biomarkers. Circulating tumor DNA (ctDNA) has the potential to cost-efficiently accelerate precision medicine trials to improve clinical efficacy and diminish costs and toxicity. However, comprehensive ctDNA profiling in metastatic prostate cancer to date has been limited. METHODS: A combination of targeted and low-pass whole genome sequencing was performed on plasma cell-free DNA and matched white blood cell germline DNA in 364 blood samples from 217 metastatic prostate cancer patients...
November 21, 2018: Genome Medicine
Telmo Graça, Pei-Shin Ku, Marta G Silva, Joshua E Turse, Kenitra G Hammac, Wendy C Brown, Guy H Palmer, Kelly A Brayton
Anaplasma marginale is a prototypical highly antigenically variant bacterial pathogen, dependent on sequential generation of Major Surface Protein-2 (Msp2) outer membrane variants to establish persistent infection. Msp2 is encoded by a single expression site and diversity is achieved by gene conversion of chromosomally encoded msp2 pseudogenes. Analysis of the full complement of msp2 pseudogenes in the St. Maries strain revealed identical sequences in different loci. The Florida strain shared the same locus structure but in the loci where the St...
November 19, 2018: Infection and Immunity
Xiaopeng Bian, Bin Zhu, Mingyi Wang, Ying Hu, Qingrong Chen, Cu Nguyen, Belynda Hicks, Daoud Meerzaman
BACKGROUND: High-throughput sequencing has rapidly become an essential part of precision cancer medicine. But validating results obtained from analyzing and interpreting genomic data remains a rate-limiting factor. The gold standard, of course, remains manual validation by expert panels, which is not without its weaknesses, namely high costs in both funding and time as well as the necessarily selective nature of manual validation. But it may be possible to develop more economical, complementary means of validation...
November 19, 2018: BMC Bioinformatics
Jie Li, Zhuowen Liang, Shuang Wang, Zhe Wang, Xu Zhang, Xueyu Hu, Kaige Wang, Qingli He, Jintao Bai
Confocal Raman microspectral imaging (CRMI) in combination with multivariate analysis was used to study pathological progression after spinal cord injury (SCI). By establishing moderate contusion in rat models, ex vivo longitudinal spinal cord tissue sections were prepared for microspectroscopic analysis. Comparative studies were then performed to determine the pathological distinctions among before injury (BI), one day post-injury (1 DPI), seven days post-injury (7 DPI), and 14days post-injury (14 DPI) groups...
November 13, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"