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https://www.readbyqxmd.com/read/29356213/a-multi-parent-advanced-generation-inter-cross-magic-population-for-genetic-analysis-and-improvement-of-cowpea-vigna-unguiculata-l-walp
#1
Bao-Lam Huynh, Jeffrey D Ehlers, Bevan Emma Huang, Maria Munoz-Amatriain, Stefano Lonardi, Jansen R P Santos, Arsenio Ndeve, Benoit J Batieno, Ousmane Boukar, Ndiaga Cisse, Issa Drabo, Christian Fatokun, Francis Kusi, Richard Y Agyare, Yi-Ning Guo, Ira Herniter, Sassoum Lo, Steve I Wanamaker, Shizhong Xu, Timothy J Close, Philip A Roberts
Multi-parent Advanced Generation Inter-Cross (MAGIC) populations are an emerging type of resource to dissect the genetic structure of traits and improve breeding populations. We developed a MAGIC population for cowpea (Vigna unguiculata L. Walp.) from eight founder parents which are genetically diverse and carry many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in the USA and sub-Saharan Africa, where cowpea is vitally important in the human diet and local economies...
January 21, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29355682/identification-of-cyp703a3-3-and-analysis-of-regulatory-role-of-cyp703a3-in-rice-anther-cuticle-and-pollen-exine-development
#2
Zhengfu Yang, Yingxin Zhang, Lianping Sun, Peipei Zhang, Ling Liu, Ping Yu, Dandan Xuan, Xiaojiao Xiang, Weixun Wu, Liyong Cao, Shihua Cheng
Anther cuticle and pollen exine are two elaborated lipid-soluble barriers protecting pollen grains from environmental and biological stresses. However, less is known about the mechanisms underlying the synthesis of these lipidic polymers. Here, we identified a no-pollen male-sterility mutant cyp703a3-3 from indica restorer line Zhonghui 8015 (Zh8015) mutant library treated with 60Coγ-ray radiation. Histological analysis indicated that cyp703a3-3 underwent abnormal tapetal cells development, produced few orbicules and secreted less sporopollenin precursors to anther locule, as well as cutin monomers on anther...
January 17, 2018: Gene
https://www.readbyqxmd.com/read/29355681/whole-exome-sequencing-identifies-a-novel-mutation-c-333%C3%A2-%C3%A2-2t%C3%A2-%C3%A2-c-of-tnni3k-in-a-chinese-family-with-dilated-cardiomyopathy-and-cardiac-conduction-disease
#3
Liang-Liang Fan, Hao Huang, Jie-Yuan Jin, Jing-Jing Li, Ya-Qin Chen, Shui-Ping Zhao, Rong Xiang
Dilated Cardiomyopathy (DCM) and cardiac conduction disease (CCD) are two kinds if diseases that can induce heart failure, syncope and even sudden cardiac death (SCD). DCM patients can experience CCD at the same time. In recent research, some disease-causing genes and variants have been identified in patients with DCM and CCD, such as Alpha-Actinin-2 and TNNI3 Interacting Kinase (TNNI3K). In this study, we employed whole-exome sequencing (WES) to explore the potential causative genes in a Chinese family with DCM and CCD...
January 17, 2018: Gene
https://www.readbyqxmd.com/read/29355665/scientific-underpinnings-of-biotechnology-regulatory-frameworks
#4
Savannah Gleim, Stuart J Smyth
Part of what is presently missing at domestic regulatory levels (and that is important at the international level as well) is a detailed understanding of what the rules of, and for, regulation should be, who the actors, stakeholders and major decision makers are and finally, how to get agreement about the rules. Greater insights into the system of rules that underpin regulatory frameworks for agri-food and biotechnology products in genetically modified (GM) crop- adopting nations will provide value by clarifying the evidence used to commercialize these technologies...
January 17, 2018: New Biotechnology
https://www.readbyqxmd.com/read/29355570/a-novel-plasmid-psaa0430-08-from-streptococcus-anginosus-subsp-anginosus-strain-0430-08
#5
Atsushi Tabata, Douglas Deutsch, Seiya Otsuka, Kathleen Verratti, Toshifumi Tomoyasu, Hideaki Nagamune, Vincent A Fischetti
Mobile genetic elements (MGEs) are the genetic material often involved in the interspecies and intraspecies genetic transduction in bacteria. However, little is known about MGEs in the Anginosus group of streptococci (AGS), one of the streptococcal groups found in the oral cavity of humans. We looked for the presence of MGEs in Streptococcus anginosus subsp. anginosus (SAA), a representative species belonging to AGS, and found a novel plasmid from SAA strain 0430-08. This plasmid was 7038bp and ~31% G/C content which we named pSAA0430-08, and examined its genetic structure and characteristics...
January 17, 2018: Plasmid
https://www.readbyqxmd.com/read/29355479/mutations-in-l-type-amino-acid-transporter-2-support-slc7a8-as-a-novel-gene-involved-in-age-related-hearing-loss
#6
Meritxell Espino Gaurch, Mariona Font-Llitjós, Silvia Murillo-Cuesta, Ekaitz Errasti-Murugarren, Adelaida M Celaya, Giorgia Girotto, Dragana Vuckovic, Massimo Mezzavilla, Clara Vilches, Susanna Bodoy, Ignasi Sahún, Laura González, Esther Prat, Antonio Zorzano, Mara Dierssen, Isabel Varela-Nieto, Paolo Gasparini, Manuel Palacín, Virginia Nunes
Age related hearing loss (ARHL) is the most common sensory deficit in the elderly. The disease has a multifactorial etiology with both environmental and genetic factors involved being largely unknown. SLC7A8/SLC3A2 heterodimer is a neutral amino acid exchanger. Here, we demonstrated that SLC7A8 is expressed in the mouse inner ear and that its ablation resulted in ARHL, due to the damage of different cochlear structures. These findings make SLC7A8 transporter a strong candidate for ARHL in humans. Thus, a screening of a cohort of ARHL patients and controls was carried out revealing several variants in SLC7A8, whose role was further investigated by in vitro functional studies...
January 22, 2018: ELife
https://www.readbyqxmd.com/read/29354354/population-structure-and-association-analysis-of-heat-stress-relevant-traits-in-chickpea-cicer-arietinum-l
#7
Uday Chand Jha, Rintu Jha, Abhishek Bohra, Swarup Kumar Parida, Paresh Chandra Kole, Virevol Thakro, Deepak Singh, Narendra Pratap Singh
Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster...
January 2018: 3 Biotech
https://www.readbyqxmd.com/read/29353911/miscellanea-dependent-generalized-functional-linear-models
#8
S Jadhav, H L Koul, Q Lu
This paper considers testing for no effect of functional covariates on response variables in multivariate regression. We use generalized estimating equations to determine the underlying parameters and establish their joint asymptotic normality. This is then used to test the significance of the effect of predictors on the vector of response variables. Simulations demonstrate the importance of considering existing correlation structures in the data. To explore the effect of treating genetic data as a function, we perform a simulation study using gene sequencing data and find that the performance of our test is comparable to that of another popular method used in sequencing studies...
December 2017: Biometrika
https://www.readbyqxmd.com/read/29353152/tgf%C3%AE-c-509t-tgf%C3%AE-t869c-xrcc1-arg194trp-ikb%C3%AE-c642t-il4-c-590t-genetic-polymorphisms-combined-with-socio-economic-lifestyle-diet-factors-and-gastric-cancer-risk-a-case-control-study-in-south-indian-population
#9
Dhayalan Pavithra, Majumdar Gautam, Ranganathan Rama, Rajaraman Swaminathan, Gopisetty Gopal, Ayyalur Seshadri Ramakrishnan, Thangarajan Rajkumar
BACKGROUND: Gastric cancer is worldwide the third major cause of cancer related death. Risk factors for gastric cancer includes Helicobacter pylori infection, gastric ulcer, less hygienic condition, use of tobacco, alcohol consumption, use of salted, smoked food, genetic alterations etc. In order to identify the risk factors associated with gastric cancer in South Indian population a case-control study involving 200 proven gastric cancer cases and 400 controls was conducted. METHODS: A structured questionnaire was used to interview all the subjects who participated in our study...
January 17, 2018: Cancer Epidemiology
https://www.readbyqxmd.com/read/29353077/classification-of-heterogeneous-genetic-variations-of-microrna-regulome-in-cancer
#10
Karin Hrovatin, Tanja Kunej
Genetic variations and differential expression of miRNA regulome components are associated with cancer. Thus miRNA based diagnosis and treatments have been proposed. However, to better explore these options, the molecular changes in miRNA regulome must be understood. MicroRNAs can be involved in regulation of oncogenes and tumour suppressors. As each miRNA targets broad range of genes, minor changes in miRNAs can have great effects, contributing to cell transformation. Many genetic variants of miRNA regulome have been reported to be associated with cancer, but this information needs to be systematized...
January 15, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29352185/genetic-fingerprinting-of-salmon-louse-lepeophtheirus-salmonis-populations-in-the-north-east-atlantic-using-a-random-forest-classification-approach
#11
A Jacobs, M De Noia, K Praebel, Ø Kanstad-Hanssen, M Paterno, D Jackson, P McGinnity, A Sturm, K R Elmer, M S Llewellyn
Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic Lepeophtheirus salmonis, frustrating efforts to track louse populations and improve targeted control measures. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352182/chloroplast-genomic-resources-for-phylogeny-and-dna-barcoding-a-case-study-on-fritillaria
#12
Yu Bi, Ming-Fang Zhang, Jing Xue, Ran Dong, Yun-Peng Du, Xiu-Hai Zhang
The genus Fritillaria comprises approximately 130 perennial herbaceous species. In the Pharmacopoeia of the People's Republic of China, the bulbs of 11 Fritillaria species are used in Chinese herbal medicines. However, the traditional methods of morphological classification cannot accurately identify closely related species of Fritillaria. Previous studies have attempted to identify these species with universal molecular markers, but insufficient phylogenetic signal was available. In this study, the complete chloroplast genomes of eight Fritillaria species were compared...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352156/comprehensive-reduction-of-amino-acid-set-in-a-protein-suggests-the-importance-of-prebiotic-amino-acids-for-stable-proteins
#13
Rei Shibue, Takahiro Sasamoto, Masami Shimada, Bowen Zhang, Akihiko Yamagishi, Satoshi Akanuma
Modern organisms commonly use the same set of 20 genetically coded amino acids for protein synthesis with very few exceptions. However, earlier protein synthesis was plausibly much simpler than modern one and utilized only a limited set of amino acids. Nevertheless, few experimental tests of this issue with arbitrarily chosen amino acid sets had been reported prior to this report. Herein we comprehensively and systematically reduced the size of the amino acid set constituting an ancestral nucleoside kinase that was reconstructed in our previous study...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352136/gphenovision-a-ground-mobile-system-with-multi-modal-imaging-for-field-based-high-throughput-phenotyping-of-cotton
#14
Yu Jiang, Changying Li, Jon S Robertson, Shangpeng Sun, Rui Xu, Andrew H Paterson
Imaging sensors can extend phenotyping capability, but they require a system to handle high-volume data. The overall goal of this study was to develop and evaluate a field-based high throughput phenotyping system accommodating high-resolution imagers. The system consisted of a high-clearance tractor and sensing and electrical systems. The sensing system was based on a distributed structure, integrating environmental sensors, real-time kinematic GPS, and multiple imaging sensors including RGB-D, thermal, and hyperspectral cameras...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352088/an-archaeal-fluoride-responsive-riboswitch-provides-an-inducible-expression-system-for-hyperthermophiles
#15
Michael Clayton Speed, Brett W Burkhart, Jonathan W Picking, Thomas J Santangelo
Robust genetic systems for the hyperthermophilic Thermococcales have facilitated overexpression of native genes, allowed for the addition of sequences encoding secretion signals, epitope, and affinity tags to coding regions, and permitted the introduction of sequences encoding new proteins in these fast growing fermentative heterotrophs. Tightly controlled and easily manipulated systems permitting regulated gene expression are however limited for these hosts. Here we describe an alternative method for regulatory control reliant on a cis-encoded functional riboswitch in the model archaeon Thermococcus kodakarensis Despite the hyperthermophilic growth temperatures, the proposed structure of the riboswitch conforms to a fluoride-responsive riboswitch encoded in many bacteria, and similarly functions to regulate a component conserved fluoride export pathway...
January 19, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29352045/eliminating-glutamatergic-input-onto-horizontal-cells-changes-the-dynamic-range-and-receptive-field-organization-of-mouse-retinal-ganglion-cells
#16
Sebastian Ströh, Christian Puller, Sebastian Swirski, Maj-Britt Hölzel, Lea I S van der Linde, Jasmin Segelken, Konrad Schultz, Christoph Block, Hannah Monyer, Klaus Willecke, Reto Weiler, Martin Greschner, Ulrike Janssen-Bienhold, Karin Dedek
In the mammalian retina, horizontal cells receive glutamatergic inputs from many rod and cone photoreceptors and return feedback signals to them, thereby changing photoreceptor glutamate release in a light-dependent manner. Horizontal cells also provide feedforward signals to bipolar cells. It is unclear, however, how horizontal cell signals also affect the temporal, spatial and contrast tuning in retinal output neurons, the ganglion cells. To study this, we generated a genetically modified mouse line in which we eliminated the light dependency of feedback by deleting glutamate receptors from mouse horizontal cells...
January 19, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29351992/involvement-of-aryl-hydrocarbon-receptor-in-myelination-and-in-human-nerve-sheath-tumorigenesis
#17
Ghjuvan'Ghjacumu Shackleford, Nirmal Kumar Sampathkumar, Mehdi Hichor, Laure Weill, Delphine Meffre, Ludmila Juricek, Ingrid Laurendeau, Aline Chevallier, Nicolas Ortonne, Frédérique Larousserie, Marc Herbin, Ivan Bièche, Xavier Coumoul, Mathieu Beraneck, Etienne-Emile Baulieu, Frédéric Charbonnier, Eric Pasmant, Charbel Massaad
Aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor involved in xenobiotic metabolism. Plexiform neurofibromas (PNFs) can transform into malignant peripheral nerve sheath tumors (MPNSTs) that are resistant to existing therapies. These tumors are primarily composed of Schwann cells. In addition to neurofibromatosis type 1 (NF1) gene inactivation, further genetic lesions are required for malignant transformation. We have quantified the mRNA expression levels of AHR and its associated genes in 38 human samples...
January 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29351920/exceptional-response-to-pembrolizumab-in-a-metastatic-chemotherapy-radiation-resistant-ovarian-cancer-patient-harboring-a-cd274-pd-l1-genetic-rearrangement
#18
Stefania Bellone, Natalia Buza, Jungmin Choi, Luca Zammataro, Laurie Gay, Julia A Elvin, David L Rimm, Yuting Liu, Elena Ratner, Peter E Schwartz, Alessandro D Santin
PURPOSE: Ovarian carcinoma no longer responsive to surgery and chemotherapy remains an incurable disease. Alternative therapeutic options remain desperately needed. EXPERIMENTAL DESIGN: We describe a heavily pretreated ovarian cancer patient with recurrent disease experiencing a remarkable clinical response to treatment with the anti-PD1 immune check-point inhibitor pembrolizumab. The clinical, pathological, and genomic characteristics of this exceptional ovarian cancer responder were carefully investigated using immunohistochemistry (IHC), quantitative multiplex fluorescence methods (ie, automated quantitative analysis, AQUA) and whole exome sequencing (WES) techniques...
January 19, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29351730/population-structure-of-venturia-inaequalis-a-causal-agent-of-apple-scab-in-response-to-heterogeneous-apple-tree-cultivation
#19
Monika Michalecka, Sylwester Masny, Thibault Leroy, Joanna Puławska
BACKGROUND: Tracking newly emergent virulent populations in agroecosystems provides an opportunity to increase our understanding of the co-evolution dynamics of pathogens and their hosts. On the one hand host plants exert selective pressure on pathogen populations, thus dividing them into subpopulations of different virulence, while on the other hand they create an opportunity for secondary contact between the two divergent populations on one tree. The main objectives of the study were to explore whether the previously reported structure between two Venturia inaequalis population types, virulent or avirulent towards Malus x domestica cultivars carrying Rvi6 gene, is maintained or broken several years after the first emergence of new virulent strains in Poland, and to investigate the relationship between 'new' and 'native' populations derived from the same commercial orchards...
January 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29351600/gtc-how-to-maintain-huge-genotype-collections-in-a-compressed-form
#20
Agnieszka Danek, Sebastian Deorowicz
Motivation: Nowadays, genome sequencing is frequently used in many research centers. In projects, such as the Haplotype Reference Consortium or the Exome Aggregation Consortium, huge databases of genotypes in large populations are determined. Together with the increasing size of these collections, the need for fast and memory frugal ways of representation and searching in them becomes crucial. Results: We present GTC, a novel compressed data structure for representation of huge collections of genetic variation data...
January 16, 2018: Bioinformatics
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