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https://www.readbyqxmd.com/read/28640905/an-efficient-method-for-transgenic-callus-induction-from-vitis-amurensis-petiole
#1
Tingting Zhao, Zemin Wang, Lingye Su, Xiaoming Sun, Jun Cheng, Langlang Zhang, Sospeter Karanja Karungo, Yuepeng Han, Shaohua Li, Haiping Xin
Transformation is the main platform for genetic improvement and gene function studies in plants. However, the established somatic embryo transformation system for grapevines is time-consuming and has low efficiency, which limits its utilization in functional genomics research. Vitis amurensis is a wild Vitis species with remarkable cold tolerance. The lack of an efficient genetic transformation system for it has significantly hindered the functional identification of cold stress related genes in the species...
2017: PloS One
https://www.readbyqxmd.com/read/28638437/a-multiplex-pcr-for-rapid-identification-of-brassica-species-in-the-triangle-of-u
#2
Joshua C O Koh, Denise M Barbulescu, Sally Norton, Bob Redden, Phil A Salisbury, Sukhjiwan Kaur, Noel Cogan, Anthony T Slater
BACKGROUND: Within the Brassicaceae, six species from the genus Brassica are widely cultivated throughout the world as oilseed, condiment, fodder or vegetable crops. The genetic relationships among the six Brassica species are described by U's triangle model. Extensive shared traits and diverse morphotypes among Brassica species make identification and classification based on phenotypic data alone challenging and unreliable, especially when dealing with large germplasm collections. Consequently, a major issue for genebank collections is ensuring the correct identification of species...
2017: Plant Methods
https://www.readbyqxmd.com/read/28636585/microbiome-a-potential-component-in-the-origin-of-mental-disorders
#3
George B Stefano, Radek Ptacek, Jiri Raboch, Richard M Kream
It is not surprising to find microbiome abnormalities present in psychiatric disorders such as depressive disorders, bipolar disorders, etc. Evolutionary pressure may provide an existential advantage to the host eukaryotic cells in that it survives in an extracellular environment containing non-self cells (e.g., bacteria). This phenomenon is both positive and negative, as with other intercellular processes. In this specific case, the phenomenal amount of information gained from combined bacterial genome could enhance communication between self and non-self cells...
June 21, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28634825/a-rapid-and-cost-effective-approach-for-the-development-of-polymorphic-microsatellites-in-non-model-species-using-paired-end-rad-sequencing
#4
Dong-Xiu Xue, Yu-Long Li, Jin-Xian Liu
As one of the most informative and versatile DNA-based markers, microsatellites have been widely used in population and conservation genetic studies. However, the development of microsatellites has traditionally been laborious, time-consuming, and expensive. In the present study, a rapid and cost-effective "RAD-seq-Assembly-Microsatellite" approach was developed to identify abundant microsatellite markers in non-model species using the roughskin sculpin Trachidermus fasciatus as a representative. Overlapping paired-end Illumina reads generated by restriction-site-associated DNA sequencing (RAD-seq) were clustered based on the similarity of reads containing the restriction enzyme recognition site and then assembled into contigs, which were used for microsatellite discovery and primer design...
June 20, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28622802/rapid-multiplex-dna-amplification-on-an-inexpensive-microdevice-for-human-identification-via-short-tandem-repeat-analysis
#5
Jacquelyn A DuVall, Delphine Le Roux, Brandon L Thompson, Christopher Birch, Daniel A Nelson, Jingyi Li, Daniel L Mills, An-Chi Tsuei, Martin G Ensenberger, Cindy Sprecher, Douglas R Storts, Brian E Root, James P Landers
Forensic DNA analysis requires several steps, including DNA extraction, PCR amplification, and separation of PCR fragments. Intuitively, there are numerous situations where it would be beneficial to speed up the overall DNA analysis process; in this work, we focus on the most time-consuming component in the analysis pipeline, namely the polymerase chain reaction (PCR). Primers were specially designed to target 10 human genomic loci, all yielding amplicons shorter than 350 bases, for ease of downstream integration with on-board microchip electrophoresis...
August 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28621354/density-functional-theory-calculations-for-the-band-gap-and-formation-energy-of-pr4-xcaxsi12o3-xn18-x-a-highly-disordered-compound-with-low-symmetry-and-a-large-cell-size
#6
Sung Un Hong, Satendra Pal Singh, Myoungho Pyo, Woon Bae Park, Kee-Sun Sohn
A novel oxynitride compound, Pr4-xCaxSi12O3+xN18-x, synthesized using a solid-state route has been characterized as a monoclinic structure in the C2 space group using Rietveld refinement on synchrotron powder X-ray diffraction data. The crystal structure of this compound was disordered due to the random distribution of Ca/Pr and N/O ions at various Wyckoff sites. A pragmatic approach for an ab initio calculation based on density function theory (DFT) for this disordered compound has been implemented to calculate an acceptable value of the band gap and formation energy...
June 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28618081/loss-of-the-ssra-genome-island-led-to-partial-debromination-in-the-pbde-respiring-dehalococcoides-mccartyi-strain-gy50
#7
Chang Ding, Matthew J Rogers, Kun-Lin Yang, Jianzhong He
Polybrominated diphenyl ethers (PBDEs), chemicals commonly used as flame-retardants in consumer products, are emerging persistent organic pollutants that are ubiquitous in the environment. In this study, we report the PBDE-respiring isolate - Dehalococcoides mccartyi strain GY50, which debrominates the most toxic tetra- and penta-BDE congeners (∼1.4 µM) to diphenyl ether within 12 days with hydrogen as the electron donor. The complete genome sequence revealed 26 reductive dehalogenase homologous genes (rdhAs), among which three genes (pbrA1, pbrA2, and pbrA3) were highly expressed during PBDE debromination...
June 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28610640/multi-country-outbreak-of-salmonella-enteritidis-infection-linked-to-the-international-ice-hockey-tournament
#8
T Pärn, V Dahl, T Lienemann, J Perevosčikovs, B DE Jong
In April 2015, Finnish public health authorities alerted European Union member states of a possible multi-country Salmonella enteritidis outbreak linked to an international youth ice-hockey tournament in Latvia. The European Centre for Disease Prevention and Control (ECDC), Finnish and Latvian authorities initiated an outbreak investigation to identify the source. The investigation included a description of the outbreak, retrospective cohort study, microbiological investigation and trace-back. We identified 154 suspected and 96 confirmed cases from seven countries...
June 14, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28608278/identification-and-characterization-of-eyk1-a-key-gene-for-erythritol-catabolism-in-yarrowia-lipolytica
#9
F Carly, H Gamboa-Melendez, M Vandermies, C Damblon, J M Nicaud, P Fickers
Erythritol is a four-carbon sugar alcohol synthesized by osmophilic yeasts, such as Yarrowia lipolytica, in response to osmotic stress. This metabolite has application as food additive due to its sweetening properties. Although Y. lipolytica can produce erythritol at a high level from glycerol, it is also able to consume it as carbon source. This ability negatively affects erythritol productivity and represents a serious drawback for the development of an efficient erythritol production process. In this study, we have isolated by insertion mutagenesis a Y...
June 12, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28597999/a-rapid-and-easy-protein-n-terminal-profiling-strategy-using-n-succinimidyloxycarbonylmethyl-tris-2-4-6-trimethoxyphenyl-phosphonium-bromide-tmpp-labeling-and-stagetip
#10
Yanchang Li, Zhiqiang Wang, Wenjing Zhou, Kun Zhang, Jie Ma, Feilin Wu, Jianguo Ji, Xuechuan Hong, Zixin Deng, Simin He, Ping Xu
Protein N-terminal profiling is crucial when characterizing biological functions and provides proteomic evidences for genome reannotations. However, most of the current N-terminal enrichment approaches involve multiple chemical derivatizations and chromatographic separation processes which are time consuming and can contribute to N-terminal peptide losses. In this study, a fast, one-step approach utilizing TMPP derivatization and StageTip separation was developed to enhance N-terminal peptide enrichment and analysis...
June 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28594572/effect-of-high-pressure-processing-on-human-noroviruses-in-laboratory-contaminated-oysters-by-bio-accumulation
#11
Saiki Imamura, Hiromi Kanezashi, Tomoko Goshima, Atsushi Suto, You Ueki, Naoko Sugawara, Hiroshi Ito, Bizhen Zou, Masashi Uema, Mamoru Noda, Keiko Akimoto
The contamination of oysters with human noroviruses poses a human health risk, since oysters are often consumed raw. In this study, human norovirus genogroup II was allowed to bio-accumulate in oysters, and then the effect of high-pressure processing (HPP) on human noroviruses in oysters was determined through a polymerase chain reaction (PCR)-based method with enzymatic pretreatment to distinguish infectious noroviruses. As a result, oysters could be artificially contaminated to a detectable level of norovirus genome by the reverse transcription-PCR...
June 8, 2017: Foodborne Pathogens and Disease
https://www.readbyqxmd.com/read/28592645/inbred-strain-variant-database-isvdb-a-repository-for-probabilistically-informed-sequence-differences-among-the-collaborative-cross-strains-and-their-founders
#12
Daniel Oreper, Yanwei Cai, Lisa M Tarantino, Fernando Pardo-Manuel de Villena, William Valdar
The Collaborative Cross (CC) is a panel of recently established multiparental recombinant inbred mouse strains. For the CC, as for any multiparental population (MPP), effective experimental design and analysis benefit from detailed knowledge of the genetic differences between strains. Such differences can be directly determined by sequencing, but until now whole-genome sequencing was not publicly available for individual CC strains. An alternative and complementary approach is to infer genetic differences by combining two pieces of information: probabilistic estimates of the CC haplotype mosaic from a custom genotyping array, and probabilistic variant calls from sequencing of the CC founders...
June 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28592553/accurate-and-rapid-differentiation-of-acinetobacter-baumannii-strains-by-raman-spectroscopy-a-comparative-study
#13
Meron Ghebremedhin, Rae Heitkamp, Shubha Yesupriya, Bradford Clay, Nicole J Crane
In recent years matrix-assisted laser ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become the standard for routine bacterial species identification due to its rapidity and low costs for consumables compared to traditional DNA-based methods. However, it has been observed that some bacterial species such as Acinetobacter baumannii strains cannot be reliably identified using mass spectrometry (MS). Raman spectroscopy is a rapid technique, as fast as MALDI-TOF, and has been shown to accurately identify bacterial strains and species...
June 7, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28589124/a-multidisciplinary-phenotyping-and-genotyping-analysis-of-a-mapping-population-enables-quality-to-be-combined-with-yield-in-rice
#14
Mariafe Calingacion, Roland Mumm, Kevin Tan, Lenie Quiatchon-Baeza, Jeanaflor C T Concepcion, Jos A Hageman, Sangeeta Prakash, Melissa Fitzgerald, Robert D Hall
In this study a mapping population (F8) of ca 200 progeny from a cross between the commercial rice varieties Apo and IR64 has been both genotyped and phenotyped. A genotyping-by-sequencing approach was first used to identify 2,681 polymorphic SNP markers which gave dense coverage of the genome with a good distribution across all 12 chromosomes. The coefficient of parentage was also low, at 0.13, confirming that the parents are genetically distant from each other. The progeny, together with both parents, were grown under irrigated and water restricted conditions in a randomised block design...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28587743/a-novel-alignment-free-vector-method-to-cluster-protein-sequences
#15
Lily He, Yongkun Li, Rong Lucy He, Stephen S-T Yau
Classification of protein are crucial topics in biology. The number of protein sequences stored in databases increases sharply in the past decade. Traditionally, comparison of protein sequences is usually carried out through multiple sequence alignment methods. However, these methods may be unsuitable for clustering of protein sequences when gene rearrangements occur such as in viral genomes. The computation is also very time-consuming for large datasets with long genomes. In this paper, based on three important biochemical properties of amino acids: the hydropathy index, polar requirement and chemical composition of the side chain, we propose a 24 dimensional feature vector describing the composition of amino acids in protein sequences...
June 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28587674/navise-superenhancer-navigator-integrating-epigenomics-signal-algebra
#16
Alex M Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta, Marcos J Araúzo-Bravo
BACKGROUND: Superenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration. Although there are pipelines which use independent pieces of software to predict the presence of superenhancers from genome-wide chromatin marks or DNA-interaction protein binding sites, there is not yet an integrated software tool that processes automatically algebra combinations of raw data sequencing into a comprehensive final annotated report of predicted superenhancers...
June 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28585934/crenothrix-are-major-methane-consumers-in-stratified-lakes
#17
Kirsten Oswald, Jon S Graf, Sten Littmann, Daniela Tienken, Andreas Brand, Bernhard Wehrli, Mads Albertsen, Holger Daims, Michael Wagner, Marcel Mm Kuypers, Carsten J Schubert, Jana Milucka
Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth's natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an 'unusual' methane monooxygenase (MMO), which was only distantly related to 'classical' MMO of gamma-proteobacterial methanotrophs...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28579981/assessing-the-risk-of-probiotic-dietary-supplements-in-the-context-of-antibiotic-resistance
#18
Min Zheng, Ruijia Zhang, Xuechen Tian, Xuan Zhou, Xutong Pan, Aloysius Wong
Probiotic bacteria are known to harbor intrinsic and mobile genetic elements that confer resistance to a wide variety of antibiotics. Their high amounts in dietary supplements can establish a reservoir of antibiotic resistant genes in the human gut. These resistant genes can be transferred to pathogens that share the same intestinal habitat thus resulting in serious clinical ramifications. While antibiotic resistance of probiotic bacteria from food, human and animal sources have been well-documented, the resistant profiles of probiotics from dietary supplements have only been recently studied...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28577084/integrated-analysis-of-leaf-morphological-and-color-traits-in-different-populations-of-chinese-cabbage-brassica-rapa-ssp-pekinensis
#19
Su Ryun Choi, Xiaona Yu, Vignesh Dhandapani, Xiaonan Li, Zhi Wang, Seo Yeon Lee, Sang Heon Oh, Wenxing Pang, Nirala Ramchiary, Chang Pyo Hong, Suhyoung Park, Zhongyun Piao, HyeRan Kim, Yong Pyo Lim
QTLs and candidate gene markers associated with leaf morphological and color traits were identified in two immortalized populations of Brassica rapa, which will provide genetic information for marker-assisted breeding. Brassica rapa is an important leafy vegetable consumed worldwide and morphology is a key character for its breeding. To enhance genetic control, quantitative trait loci (QTLs) for leaf color and plant architecture were identified using two immortalized populations with replications of 2 and 4 years...
June 2, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28575161/gatekeeper-a-new-hardware-architecture-for-accelerating-pre-alignment-in-dna-short-read-mapping
#20
Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan
Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads - that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and "candidate" locations in that reference genome. The similarity measurement, called alignment , formulated as an approximate string matching problem, is the computational bottleneck because: (1) it is implemented using quadratic-time dynamic programming algorithms, and (2) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity...
May 31, 2017: Bioinformatics
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