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https://www.readbyqxmd.com/read/28440405/copy-number-variation-analysis-in-familial-nonsyndromic-congenital-anomalies-of-the-kidney-and-urinary-tract-evidence-for-the-causative-role-of-a-transposable-element-associated-genomic-rearrangement
#1
Ekaterini Siomou, Artemis G Mitsioni, Vasileios Giapros, Ioanna Bouba, Dimitrios Noutsopoulos, Ioannis Georgiou
Most congenital anomalies of the kidney and urinary tract (CAKUT) are sporadic, but familial occurrence has been described, suggesting a genetic contribution. Copy‑number variations (CNVs) were detected in patients with CAKUT to identify possible novel genomic regions associated with CAKUT. CNVs were investigated in 7 children with CAKUT from three unrelated families using array comparative genomic hybridization: female monozygotic twins with bilateral duplex collecting system/vesicoureteral reflux (VUR)/unilateral renal hypodyspasia (URHD); two male siblings with VUR/URHD; 3 male second cousins, one with bilateral VUR/URHD, one with bilateral VUR and one with ureterovesical junction obstruction (UVJO)...
April 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28439519/structured-illumination-diffuse-optical-tomography-for-noninvasive-functional-neuroimaging-in-mice
#2
Matthew D Reisman, Zachary E Markow, Adam Q Bauer, Joseph P Culver
Optical intrinsic signal (OIS) imaging has been a powerful tool for capturing functional brain hemodynamics in rodents. Recent wide field-of-view implementations of OIS have provided efficient maps of functional connectivity from spontaneous brain activity in mice. However, OIS requires scalp retraction and is limited to superficial cortical tissues. Diffuse optical tomography (DOT) techniques provide noninvasive imaging, but previous DOT systems for rodent neuroimaging have been limited either by sparse spatial sampling or by slow speed...
April 2017: Neurophotonics
https://www.readbyqxmd.com/read/28437453/three-dominant-awnless-genes-in-common-wheat-fine-mapping-interaction-and-contribution-to-diversity-in-awn-shape-and-length
#3
Motohiro Yoshioka, Julio C M Iehisa, Ryoko Ohno, Tatsuro Kimura, Hiroyuki Enoki, Satoru Nishimura, Shuhei Nasuda, Shigeo Takumi
The awn is a long needle-like structure formed at the tip of the lemma in the florets of some grass species. It plays a role in seed dispersal and protection against animals, and can contribute to the photosynthetic activity of spikes. Three main dominant inhibitors of awn development (Hd, B1 and B2) are known in hexaploid wheat, but the causal genes have not been cloned yet and a genetic association with awn length diversity has been found only for the B1 allele. To analyze the prevalence of these three awning inhibitors, we attempted to predict the genotypes of 189 hexaploid wheat varieties collected worldwide using markers tightly linked to these loci...
2017: PloS One
https://www.readbyqxmd.com/read/28436918/an-integrated-and-highly-sensitive-ultrafast-acoustoelectric-imaging-system-for-biomedical-applications
#4
Beatrice Berthon, Pierre-Marc Dansette, Mickael Tanter, Mathieu Pernot, Jean Provost
PURPOSE: Direct imaging of cardiac electrical activation is crucial to better understand and diagnose diseases linked to arrhythmias. This work presents an Ultrafast Acoustoelectric Imaging (UAI) system for direct and non-invasive ultrafast mapping of propagating current densities. MATERIALS AND METHODS: Acoustoelectric imaging is based on the acoustoelectric effect, the modulation of the medium's electrical impedance by a propagating ultrasonic wave. UAI triggers this effect with plane wave emissions to image current densities...
April 24, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28432904/optimising-multi-frame-adf-stem-for-high-precision-atomic-resolution-strain-mapping
#5
Lewys Jones, Sigurd Wenner, Magnus Nord, Per Harald Ninive, Ole Martin Løvvik, Randi Holmestad, Peter D Nellist
Annular dark-field scanning transmission electron microscopy is a powerful tool to study crystal defects at the atomic scale but historically single slow-scanned frames have been plagued by low-frequency scanning-distortions prohibiting accurate strain mapping at atomic resolution. Recently, multi-frame acquisition approaches combined with post-processing have demonstrated significant improvements in strain precision, but the optimum number of frames to record has not been explored. Here we use a non-rigid image registration procedure before applying established strain mapping methods...
April 15, 2017: Ultramicroscopy
https://www.readbyqxmd.com/read/28430825/discovery-and-fine-mapping-of-adiposity-loci-using-high-density-imputation-of-genome-wide-association-studies-in-individuals-of-african-ancestry-african-ancestry-anthropometry-genetics-consortium
#6
Maggie C Y Ng, Mariaelisa Graff, Yingchang Lu, Anne E Justice, Poorva Mudgal, Ching-Ti Liu, Kristin Young, Lisa R Yanek, Mary F Feitosa, Mary K Wojczynski, Kristin Rand, Jennifer A Brody, Brian E Cade, Latchezar Dimitrov, Qing Duan, Xiuqing Guo, Leslie A Lange, Michael A Nalls, Hayrettin Okut, Salman M Tajuddin, Bamidele O Tayo, Sailaja Vedantam, Jonathan P Bradfield, Guanjie Chen, Wei-Min Chen, Alessandra Chesi, Marguerite R Irvin, Badri Padhukasahasram, Jennifer A Smith, Wei Zheng, Matthew A Allison, Christine B Ambrosone, Elisa V Bandera, Traci M Bartz, Sonja I Berndt, Leslie Bernstein, William J Blot, Erwin P Bottinger, John Carpten, Stephen J Chanock, Yii-Der Ida Chen, David V Conti, Richard S Cooper, Myriam Fornage, Barry I Freedman, Melissa Garcia, Phyllis J Goodman, Yu-Han H Hsu, Jennifer Hu, Chad D Huff, Sue A Ingles, Esther M John, Rick Kittles, Eric Klein, Jin Li, Barbara McKnight, Uma Nayak, Barbara Nemesure, Adesola Ogunniyi, Andrew Olshan, Michael F Press, Rebecca Rohde, Benjamin A Rybicki, Babatunde Salako, Maureen Sanderson, Yaming Shao, David S Siscovick, Janet L Stanford, Victoria L Stevens, Alex Stram, Sara S Strom, Dhananjay Vaidya, John S Witte, Jie Yao, Xiaofeng Zhu, Regina G Ziegler, Alan B Zonderman, Adebowale Adeyemo, Stefan Ambs, Mary Cushman, Jessica D Faul, Hakon Hakonarson, Albert M Levin, Katherine L Nathanson, Erin B Ware, David R Weir, Wei Zhao, Degui Zhi, Donna K Arnett, Struan F A Grant, Sharon L R Kardia, Olufunmilayo I Oloapde, D C Rao, Charles N Rotimi, Michele M Sale, L Keoki Williams, Babette S Zemel, Diane M Becker, Ingrid B Borecki, Michele K Evans, Tamara B Harris, Joel N Hirschhorn, Yun Li, Sanjay R Patel, Bruce M Psaty, Jerome I Rotter, James G Wilson, Donald W Bowden, L Adrienne Cupples, Christopher A Haiman, Ruth J F Loos, Kari E North
Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes...
April 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28428560/combination-of-high-density-microelectrode-array-and-patch-clamp-recordings-to-enable-studies-of-multisynaptic-integration
#7
David Jäckel, Douglas J Bakkum, Thomas L Russell, Jan Müller, Milos Radivojevic, Urs Frey, Felix Franke, Andreas Hierlemann
We present a novel, all-electric approach to record and to precisely control the activity of tens of individual presynaptic neurons. The method allows for parallel mapping of the efficacy of multiple synapses and of the resulting dynamics of postsynaptic neurons in a cortical culture. For the measurements, we combine an extracellular high-density microelectrode array, featuring 11'000 electrodes for extracellular recording and stimulation, with intracellular patch-clamp recording. We are able to identify the contributions of individual presynaptic neurons - including inhibitory and excitatory synaptic inputs - to postsynaptic potentials, which enables us to study dendritic integration...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28425624/a-statistical-approach-to-fine-mapping-for-the-identification-of-potential-causal-variants-related-to-bone-mineral-density
#8
Jonathan Greenbaum, Hong-Wen Deng
Although GWAS have been able to successfully identify dozens of genetic loci associated with bone mineral density (BMD) and osteoporosis related traits, very few of these loci have been confirmed to be causal. This is due to the fact that in a given genetic region there may exist many trait-associated SNPs that are highly correlated. While this correlation is useful for discovering novel associations, the high degree of linkage disequilibrium that persists throughout the genome presents a major challenge to discern which among these correlated variants has a direct effect on the trait...
April 20, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28424708/quantitative-trait-locus-mapping-for-verticillium-wilt-resistance-in-an-upland-cotton-recombinant-inbred-line-using-snp-based-high-density-genetic-map
#9
Koffi Kibalou Palanga, Muhammad Jamshed, Md Harun Or Rashid, Juwu Gong, Junwen Li, Muhammad Sajid Iqbal, Aiying Liu, Haihong Shang, Yuzhen Shi, Tingting Chen, Qun Ge, Zhen Zhang, Tussipkan Dilnur, Weijie Li, Pengtao Li, Wankui Gong, Youlu Yuan
Verticillium wilt (VW) caused by Verticillium dahlia Kleb is one of the most destructive diseases of cotton. Numerous efforts have been made to improve the resistance of upland cotton against VW, with little progress achieved due to the paucity of upland cotton breeding germplasms with high level of resistance to VW. Gossypium barbadense was regarded as more resistant compared to upland cotton; however, it is difficult to apply the resistance from G. barbadense to upland cotton improvement because of the hybrid breakdown and the difficulty to fix resistant phenotype in their interspecific filial...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28424525/genome-wide-detection-of-copy-number-variation-in-chinese-indigenous-sheep-using-an-ovine-high-density-600%C3%A2-k-snp-array
#10
Qing Ma, Xuexue Liu, Jianfei Pan, Lina Ma, Yuehui Ma, Xiaohong He, Qianjun Zhao, Yabin Pu, Yingkang Li, Lin Jiang
Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28422147/construction-of-a-high-density-linkage-map-and-fine-mapping-of-qtls-for-growth-and-gonad-related-traits-in-blunt-snout-bream
#11
Shi-Ming Wan, Hong Liu, Bo-Wen Zhao, Chun-Hong Nie, Wei-Min Wang, Ze-Xia Gao
High-density genetic maps based on SNPs are essential for fine mapping loci controlling specific traits for fish species. Using restriction-site associated DNA tag sequencing (RAD-Seq) technology, we identified 42,784 SNPs evenly distributed across the Megalobrama amblycephala genome. Based on 2 parents and 187 intra-specific hybridization progenies, a total of 14,648 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs) of maternal and paternal map. The total length of the integrated map was 3,258...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28420407/understanding-phlebotomus-perniciosus-abundance-in-south-east-spain-assessing-the-role-of-environmental-and-anthropic-factors
#12
José Risueño, Clara Muñoz, Pedro Pérez-Cutillas, Elena Goyena, Moisés Gonzálvez, María Ortuño, Luis Jesús Bernal, Juana Ortiz, Bulent Alten, Eduardo Berriatua
BACKGROUND: Leishmaniosis is associated with Phlebotomus sand fly vector density, but our knowledge of the environmental framework that regulates highly overdispersed vector abundance distributions is limited. We used a standardized sampling procedure in the bioclimatically diverse Murcia Region in Spain and multilevel regression models for count data to estimate P. perniciosus abundance in relation to environmental and anthropic factors. METHODS: Twenty-five dog and sheep premises were sampled for sand flies using adhesive and light-attraction traps, from late May to early October 2015...
April 19, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28418866/investigation-of-hypoxia-conditions-using-oxygen-enhanced-magnetic-resonance-imaging-measurements-in-glioma-models
#13
Qi Fan, Cheuk Ying Tang, Di Gu, Jinyu Zhu, Guojun Li, Yingwei Wu, Xiaofeng Tao
The objective of this study was to determine whether using oxygen-enhanced magnetic resonance imaging (OE-MRI) to assess hypoxia is feasible and whether historical measurements, pO2 changes, and percentage of signal intensity changes (PSIC) are correlated in an animal model of glioma. A total of 25 Sprague-Dawley rats were used to establish C6 brain or subcutaneous glioma model. Nine rats with brain gliomas underwent OE-MRI followed by histopathologic analysis to assess microvessel density and hypoxia. Another 11 rats were underwent OE-MRI and were followed for a survival analysis...
March 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28418033/a-genome-wide-snp-based-genetic-map-and-qtl-mapping-for-agronomic-traits-in-chinese-cabbage
#14
Li Huang, Yafei Yang, Fang Zhang, Jiashu Cao
The aim of this work was to construct a high-resolution genetic map for the dissection of complex morphological and agronomic traits in Chinese cabbage (Brassica rapa L. syn. B. campestris). Chinese cabbage, an economically important vegetable, is a good model plant for studies on the evolution of morphologic variation. Herein, two high-generation inbred Chinese cabbage lines, 'Huangxiaoza' and 'Bqq094-11', were crossed. Then restriction-site-associated DNA sequencing (RAD-seq) was performed on the parents and 120 F2 individuals...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28417941/mapping-patterns-and-trends-in-the-spatial-availability-of-alcohol-using-low-level-geographic-data-a-case-study-in-england-2003-2013
#15
Colin Angus, John Holmes, Ravi Maheswaran, Mark A Green, Petra Meier, Alan Brennan
Much literature examines the relationship between the spatial availability of alcohol and alcohol-related harm. This study aims to address an important gap in this evidence by using detailed outlet data to examine recent temporal trends in the sociodemographic distribution of spatial availability for different types of alcohol outlet in England. Descriptive analysis of measures of alcohol outlet density and proximity using extremely high resolution market research data stratified by outlet type and quintiles of area-level deprivation from 2003, 2007, 2010 and 2013 was undertaken and hierarchical linear growth models fitted to explore the significance of socioeconomic differences...
April 12, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28417558/the-tcn2-variant-of-rs9606756-ile23val-acts-as-risk-loci-for-obesity-related-traits-and-mediates-by-interacting-with-apo-a1
#16
Prashantha Hebbar, Fadi Alkayal, Rasheeba Nizam, Motasem Melhem, Naser Elkum, Sumi Elsa John, Mohamed Abufarha, Osama Alsmadi, Thangavel Alphonse Thanaraj
OBJECTIVE: Despite alarming obesity levels in the Arabian Peninsula, its population lacks convincingly identified genetic determinants of obesity. A genome-wide association study was performed for obesity-related anthropometric traits in Arabs and to decipher mechanisms by which the variants mediate traits. METHODS: The Illumina HumanOmniExpress BeadChip was used to genotype 1,353 Arab individuals (largely with Class I obesity) from Kuwait. Genome-wide association tests for obesity-related anthropometric traits were performed...
April 17, 2017: Obesity
https://www.readbyqxmd.com/read/28416035/measuring-the-autocorrelation-function-of-nanoscale-three-dimensional-density-distribution-in-individual-cells-using-scanning-transmission-electron-microscopy-atomic-force-microscopy-and-a-new-deconvolution-algorithm
#17
Yue Li, Di Zhang, Ilker Capoglu, Karl A Hujsak, Dhwanil Damania, Lusik Cherkezyan, Eric Roth, Reiner Bleher, Jinsong S Wu, Hariharan Subramanian, Vinayak P Dravid, Vadim Backman
Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction...
April 18, 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28414801/probabilistic-fluorescence-based-synapse-detection
#18
Anish K Simhal, Cecilia Aguerrebere, Forrest Collman, Joshua T Vogelstein, Kristina D Micheva, Richard J Weinberg, Stephen J Smith, Guillermo Sapiro
Deeper exploration of the brain's vast synaptic networks will require new tools for high-throughput structural and molecular profiling of the diverse populations of synapses that compose those networks. Fluorescence microscopy (FM) and electron microscopy (EM) offer complementary advantages and disadvantages for single-synapse analysis. FM combines exquisite molecular discrimination capacities with high speed and low cost, but rigorous discrimination between synaptic and non-synaptic fluorescence signals is challenging...
April 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28413851/detecting-peatland-drains-with-object-based-image-analysis-and-geoeye-1-imagery
#19
J Connolly, N M Holden
BACKGROUND: Peatlands play an important role in the global carbon cycle. They provide important ecosystem services including carbon sequestration and storage. Drainage disturbs peatland ecosystem services. Mapping drains is difficult and expensive and their spatial extent is, in many cases, unknown. An object based image analysis (OBIA) was performed on a very high resolution satellite image (Geoeye-1) to extract information about drain location and extent on a blanket peatland in Ireland...
December 2017: Carbon Balance and Management
https://www.readbyqxmd.com/read/28411394/improved-magnetic-resonance-fingerprinting-reconstruction-with-low-rank-and-subspace-modeling
#20
Bo Zhao, Kawin Setsompop, Elfar Adalsteinsson, Borjan Gagoski, Huihui Ye, Dan Ma, Yun Jiang, P Ellen Grant, Mark A Griswold, Lawrence L Wald
PURPOSE: This article introduces a constrained imaging method based on low-rank and subspace modeling to improve the accuracy and speed of MR fingerprinting (MRF). THEORY AND METHODS: A new model-based imaging method is developed for MRF to reconstruct high-quality time-series images and accurate tissue parameter maps (e.g., T1 , T2 , and spin density maps). Specifically, the proposed method exploits low-rank approximations of MRF time-series images, and further enforces temporal subspace constraints to capture magnetization dynamics...
April 15, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
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