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Functional mapping

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https://www.readbyqxmd.com/read/28821187/genetic-dissection-of-seedling-stage-salinity-tolerance-in-rice-using-introgression-lines-of-a-salt-tolerant-landrace-nona-bokra
#1
Venkata Ramana Rao Puram, John Ontoy, Steven Linscombe, Prasanta K Subudhi
Salinity is an important abiotic stress affecting rice production worldwide. Development of salt tolerant varieties is the most feasible approach for improving rice productivity in salt affected soils. In rice, seedling stage salinity tolerance is crucial for better crop establishment. Quantitative trait loci (QTL) mapping using introgression lines (ILs) is useful for identification and simultaneous transfer of desirable alleles into elite genetic background. In the present study, 138 ILs derived from the cross between a high yielding elite salt susceptible japonica rice cultivar Jupiter and a salt tolerant indica landrace Nona Bokra were evaluated for salt tolerance at seedling stage in a hydroponics experiment and were genotyped using 126 simple sequence repeat markers...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28821014/efficient-and-accurate-causal-inference-with-hidden-confounders-from-genome-transcriptome-variation-data
#2
Lingfei Wang, Tom Michoel
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations. Findr outperformed existing methods on the DREAM5 Systems Genetics challenge and on the prediction of microRNA and transcription factor targets in human lymphoblastoid cells, while being nearly a million times faster...
August 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28819924/dynamic-imaging-of-mitochondrial-membrane-proteins-in-specific-sub-organelle-membrane-locations
#3
REVIEW
Timo Appelhans, Karin B Busch
Mitochondria are cellular organelles with multifaceted tasks and thus composed of different sub-compartments. The inner mitochondrial membrane especially has a complex nano-architecture with cristae protruding into the matrix. Related to their function, the localization of mitochondrial membrane proteins is more or less restricted to specific sub-compartments. In contrast, it can be assumed that membrane proteins per se diffuse unimpeded through continuous membranes. Fluorescence recovery after photobleaching is a versatile technology used in mobility analyses to determine the mobile fraction of proteins, but it cannot provide data on subpopulations or on confined diffusion behavior...
August 17, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28819820/genome-wide-characterization-of-the-wrky-gene-family-in-radish-raphanus-sativus-l-reveals-its-critical-functions-under-different-abiotic-stresses
#4
Bernard Kinuthia Karanja, Lianxue Fan, Liang Xu, Yan Wang, Xianwen Zhu, Mingjia Tang, Ronghua Wang, Fei Zhang, Everlyne M'mbone Muleke, Liwang Liu
The radish WRKY gene family was genome-widely identified and played critical roles in response to multiple abiotic stresses. The WRKY is among the largest transcription factors (TFs) associated with multiple biological activities for plant survival, including control response mechanisms against abiotic stresses such as heat, salinity, and heavy metals. Radish is an important root vegetable crop and therefore characterization and expression pattern investigation of WRKY transcription factors in radish is imperative...
August 17, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28819229/cryo-em-analysis-of-homodimeric-full-length-lrrk2-and-lrrk1-protein-complexes
#5
Kushal Sejwal, Mohamed Chami, Hervé Rémigy, Renée Vancraenenbroeck, William Sibran, Rosmarie Sütterlin, Paul Baumgartner, Robert McLeod, Marie-Christine Chartier-Harlin, Veerle Baekelandt, Henning Stahlberg, Jean-Marc Taymans
Leucine-rich repeat kinase 2 (LRRK2) is a large multidomain protein implicated in the pathogenesis of both familial and sporadic Parkinson's disease (PD), and currently one of the most promising therapeutic targets for drug design in Parkinson's disease. In contrast, LRRK1, the closest homologue to LRRK2, does not play any role in PD. Here, we use cryo-electron microscopy (cryo-EM) and single particle analysis to gain structural insight into the full-length dimeric structures of LRRK2 and LRRK1. Differential scanning fluorimetry-based screening of purification buffers showed that elution of the purified LRRK2 protein in a high pH buffer is beneficial in obtaining high quality cryo-EM images...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818860/the-chickpea-early-flowering-1-efl1-locus-is-an-ortholog-of-arabidopsis-elf3
#6
Stephen Ridge, Amit Deokar, Robyn Lee, Ketema Daba, Richard C Macknight, James L Weller, Bunyamin Tar'an
In climates that experience short growing seasons due to drought, heat or end-of-season frost, early flowering is a highly desirable trait for chickpeas. In this study, we mapped, sequenced and characterized Efl1, an ortholog of Arabidopsis ELF3 that confers early flowering in chickpea. In a RIL population derived from a cross between CDC Frontier and ICCV 96029, this gene was mapped to the site of a QTL on Ca5 that explained 59% of flowering time variation under SD. Sequencing of ELF3 in ICCV 96029 revealed an 11-bp deletion in the first exon that was predicted to result in a premature stop codon...
August 17, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28818819/quantifying-human-movement-using-the-movn-smartphone-app-validation-and-field-study
#7
Ralph Maddison, Luke Gemming, Javier Monedero, Linda Bolger, Sarahjane Belton, Johann Issartel, Samantha Marsh, Artur Direito, Madeleine Solenhill, Jinfeng Zhao, Daniel John Exeter, Harshvardhan Vathsangam, Jonathan Charles Rawstorn
BACKGROUND: The use of embedded smartphone sensors offers opportunities to measure physical activity (PA) and human movement. Big data-which includes billions of digital traces-offers scientists a new lens to examine PA in fine-grained detail and allows us to track people's geocoded movement patterns to determine their interaction with the environment. OBJECTIVE: The objective of this study was to examine the validity of the Movn smartphone app (Moving Analytics) for collecting PA and human movement data...
August 17, 2017: JMIR MHealth and UHealth
https://www.readbyqxmd.com/read/28818682/the-epidemiology-of-driving-in-later-life-sociodemographic-health-and-functional-characteristics-predictors-of-incident-cessation-and-driving-expectations
#8
Kaarin J Anstey, Xiaolan Li, Diane E Hosking, Ranmalee Eramudugolla
AIM: To describe population-level characteristics of drivers and non-drivers in a cohort of older Australians and identify predictors of driving cessation and expectations. METHODS: The sample comprised the oldest cohort of the PATH Through Life project who were assessed 4 times between 2001 and 2013. At waves 3 and 4 questions on driving were included in the study interview. Data were also collected on health, physical and cognitive function and psychosocial wellbeing...
August 14, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28818390/three-novel-recessive-mutations-in-lama2-syne1-and-ttn-are-identified-in-a-single-case-with-congenital-muscular-dystrophy
#9
Liang Wu, Bingwu Xiang, Huan Zhang, Xiaoxiao He, Celina Shih, Xiang Chen, Tao Cai
Congenital muscular dystrophies (CMD) are a group of heterogeneous disorders. Here, targeted next generation sequencing of 168 CMD-associated genes was performed on collected clinic samples to identify potential mutations. A loss-of-function mutation (c.4676-4682delGCTGCAA; p.Cys1560Thrfs*33) of the LAMA2 gene in a consanguineous family was identified and confirmed by Sanger sequencing. The second recessive mutation in SYNE1 (c.2881C>T; p.Arg961Trp) was found in the SAP motif, which was predicted to be involved in chromosomal organization...
July 6, 2017: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/28818388/genetic-analysis-of-rootstock-mediated-nitrogen-n-uptake-and-root-to-shoot-signalling-at-contrasting-n-availabilities-in-tomato
#10
M J Asins, A Albacete, C Martinez-Andujar, F Pérez-Alfocea, I C Dodd, E A Carbonell, J A Dieleman
Selecting rootstocks for high nitrogen acquisition ability may allow decreased N fertilizer application without reducing tomato yields, minimizing environmental nitrate pollution. A commercial hybrid tomato variety was grafted on a genotyped population of 130 recombinant inbred lines (RILs) derived from Solanum pimpinellifolium, and compared with self- and non-grafted controls under contrasting nitrate availabilities (13.8 vs 1.0mM) in the nutrient solution. Grafting itself altered xylem sap composition under N-sufficient conditions, particularly Na(+) (8...
October 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28818380/molecular-cloning-and-expression-analysis-of-duplicated-polyphenol-oxidase-genes-reveal-their-functional-differentiations-in-sorghum
#11
Song Yan, Sujuan Li, Guowei Zhai, Ping Lu, Hui Deng, Shan Zhu, Renliang Huang, Jianfeng Shao, Yuezhi Tao, Guihua Zou
Polyphenol oxidase (PPO) is believed to play a role in plant growth, reproduction, and resistance to pathogens and pests. PPO causes browning of grains in cereals. In this study, genetic mapping of sorghum grain for phenol color reaction (PHR) was performed using a recombinant inbred line population. Only one locus was detected between SSR markers SM06072 and Xtxp176 on chromosome 6. Two linked orthologous genes (Sb06PPO1 and Sb06PPO2) within the mapped region were discovered and cloned. Transformation experiments using Nipponbare (a PHR negative rice cultivar) showed that Sb06PPO1 from LTR108 and two Sb06PPO2 alleles from both varieties could complement Nipponbare, whereas Sb06PPO1 from 654 could not...
October 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28817608/data-driven-coarse-graining-of-large-biomolecular-structures
#12
Yi-Ling Chen, Michael Habeck
Advances in experimental and computational techniques allow us to study the structure and dynamics of large biomolecular assemblies at increasingly higher resolution. However, with increasing structural detail it can be challenging to unravel the mechanism underlying the function of molecular machines. One reason is that atomistic simulations become computationally prohibitive. Moreover it is difficult to rationalize the functional mechanism of systems composed of tens of thousands to millions of atoms by following each atom's movements...
2017: PloS One
https://www.readbyqxmd.com/read/28817568/an-optimal-strategy-for-epilepsy-surgery-disruption-of-the-rich-club
#13
Marinho A Lopes, Mark P Richardson, Eugenio Abela, Christian Rummel, Kaspar Schindler, Marc Goodfellow, John R Terry
Surgery is a therapeutic option for people with epilepsy whose seizures are not controlled by anti-epilepsy drugs. In pre-surgical planning, an array of data modalities, often including intra-cranial EEG, is used in an attempt to map regions of the brain thought to be crucial for the generation of seizures. These regions are then resected with the hope that the individual is rendered seizure free as a consequence. However, post-operative seizure freedom is currently sub-optimal, suggesting that the pre-surgical assessment may be improved by taking advantage of a mechanistic understanding of seizure generation in large brain networks...
August 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28817255/nonacene-generated-by-on-surface-dehydrogenation
#14
Rafal Zuzak, Ruth Dorel, Mariusz Krawiec, Bartosz Such, Marek Kolmer, Marek Szymonski, Antonio M Echavarren, Szymon Godlewski
The on-surface synthesis of nonacene has been accomplished by dehydrogenation of an air-stable partially saturated precursor, which could be aromatized by using a combined scanning tunneling and atomic force microscope (STM/AFM) as well as by on-surface annealing. This transformation allowed the in-detail analysis of the electronic properties of nonacene molecules physisorbed on Au(111) by scanning tunneling spectroscopy (STS) measurements. The spatial mapping of molecular orbitals was corroborated by density functional theory (DFT) calculations...
August 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/28817232/crystal-structure-of-the-melampsora-lini-effector-avrp-reveals-insights-into-a-possible-nuclear-function-and-recognition-by-the-flax-disease-resistance-protein-p
#15
Xiaoxiao Zhang, Nadya Farah, Laura Rolston, Daniel J Ericsson, Ann-Maree Catanzariti, Maud Bernoux, Thomas Ve, Katerina Bendak, Chunhong Chen, Joel P Mackay, Gregory J Lawrence, Adrienne Hardham, Jeffrey G Ellis, Simon J Williams, Peter N Dodds, David A Jones, Bostjan Kobe
The effector protein AvrP is secreted by the flax rust fungal pathogen (Melampsora lini) and recognized specifically by the flax (Linum usitatissimum) P disease resistance protein, leading to effector-triggered immunity. To investigate the biological function of this effector and mechanisms of specific recognition by the P resistance protein, we determined the crystal structure of AvrP. The structure reveals an elongated zinc-finger-like structure with a novel interleaved zinc-binding topology. The residues responsible for zinc binding are conserved in AvrP effector variants and mutations of these motifs result in loss of P-mediated recognition...
August 17, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28816865/liquid-crystal-spatial-light-modulators-for-simulating-zonal-multifocal-lenses
#16
Yiyu Li, Arthur Bradley, Renfeng Xu, Pete S Kollbaum
SIGNIFICANCE: To maximize efficiency of the normally lengthy and costly multizone lens design and testing process, it is advantageous to evaluate the potential efficacy of a design as thoroughly as possible prior to lens fabrication and on-eye testing. The current work describes an ex vivo approach of optical design testing. PURPOSE: The aim of this study was to describe a system capable of examining the optical characteristics of multizone bifocal and multifocal optics by subaperture stitching using liquid crystal technologies...
August 14, 2017: Optometry and Vision Science: Official Publication of the American Academy of Optometry
https://www.readbyqxmd.com/read/28816805/development-of-a-mobile-app-for-family-planning-providers
#17
Viannella Halsall, Jennifer Rogers, Jacki Witt, Sejun Song, Hoang Duc Huy Nguyen, Patricia Kelly
PURPOSE: To provide an overview of lessons learned during the development process of an app for iOS and Android based on national recommendations for providing quality family planning services. STUDY AND DESIGN: After a review of existing apps was conducted to determine whether an app of clinical recommendations for family planning existed, a team of clinicians, training specialists, and app developers created a resource app by first drafting a comprehensive content map...
September 2017: MCN. the American Journal of Maternal Child Nursing
https://www.readbyqxmd.com/read/28816664/gradient-based-tone-mapping-for-rate-distortion-optimized-backward-compatible-high-dynamic-range-compression
#18
David Gommelet, Aline Roumy, Christine Guillemot, Michael Ropert, Julien Le Le Tanou
This paper addresses the problem of designing a global tone mapping operator for rate distortion optimized backward compatible compression of HDR images. We address the problem of tone mapping design for two different use cases leading to two different minimization problems. The first problem considered is the minimization of the distortion on the reconstructed HDR signal under a rate constraint on the SDR layer. The second problem remains the same minimization with an additional constraint to preserve a good quality for the SDR signal...
August 14, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28816646/chronic-cigarette-smoke-mediated-global-changes-in-lung-mucoepidermoid-cells-a-phosphoproteomic-analysis
#19
Hitendra S Solanki, Jayshree Advani, Aafaque Ahmad Khan, Aneesha Radhakrishnan, Nandini A Sahasrabuddhe, Sneha M Pinto, Xiaofei Chang, Thottethodi Subrahmanya Keshava Prasad, Premendu Prakash Mathur, David Sidransky, Harsha Gowda, Aditi Chatterjee
Proteomics analysis of chronic cigarette smoke exposure is a rapidly emerging postgenomics research field. While smoking is a major cause of lung cancer, functional studies using proteomics approaches could enrich our mechanistic understanding of the elusive lung cancer global molecular signaling and cigarette smoke relationship. We report in this study on a stable isotope labeling by amino acids in cell culture-based quantitative phosphoproteomic analysis of a human lung mucoepidermoid carcinoma cell line, H292 cells, chronically exposed to cigarette smoke...
August 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28816444/mapping-the-intricate-reactivity-of-nanojars-toward-molecules-of-varying-acidity-and-their-conjugate-bases-leading-to-exchange-of-pyrazolate-ligands
#20
Christian K Hartman, Gellert Mezei
A comprehensive reactivity study of nanojars toward 18 different acidic compounds with varying pKa, including 12 different carboxylic acids (both aliphatic and aromatic mono- and dicarboxylic acids), p-toluenesulfonic acid, hydrogen sulfate, hydrogen carbonate, carbonic acid, 1-decanethiol, and methanol, as well as four different conjugate bases (formate, acetate, benzoate, 2-bromoethanesulfonate) is carried out with the aid of electrospray-ionization mass spectrometry. Thus, the effect on nanojar substitution and breakdown pattern of a number of variables, such as concentration of reagent (acid or conjugate base), acidity of reagent (pKa), effect of acid vs conjugate base, steric effects, aromaticity, incarcerated anion and size of the nanojar, is evaluated...
August 17, 2017: Inorganic Chemistry
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