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https://www.readbyqxmd.com/read/28317860/gene-delivery-to-nile-tilapia-cells-for-transgenesis-and-the-role-of-pi3k-c2%C3%AE-in-angiogenesis
#1
Fernanda Maria Policarpo Tonelli, Samyra Maria Dos Santos Nassif Lacerda, Marcela Santos Procópio, Breno Luiz Sales Lemos, Luiz Renato de França, Rodrigo Ribeiro Resende
Microinjection is commonly performed to achieve fish transgenesis; however, due to difficulties associated with this technique, new strategies are being developed. Here we evaluate the potential of lentiviral particles to genetically modify Nile tilapia cells to achieve transgenesis using three different approaches: spermatogonial stem cell (SSC) genetic modification and transplantation (SC), in vivo transduction of gametes (GT), and fertilised egg transduction (ET). The SC protocol using larvae generates animals with sustained production of modified sperm (80% of animals with 77% maximum sperm fluorescence [MSF]), but is a time-consuming protocol (sexual maturity in Nile tilapia is achieved at 6 months of age)...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28317605/use-of-foodomics-for-control-of-food-processing-and-assessing-of-food-safety
#2
D Josić, Ž Peršurić, D Rešetar, T Martinović, L Saftić, S Kraljević Pavelić
Food chain, food safety, and food-processing sectors face new challenges due to globalization of food chain and changes in the modern consumer preferences. In addition, gradually increasing microbial resistance, changes in climate, and human errors in food handling remain a pending barrier for the efficient global food safety management. Consequently, a need for development, validation, and implementation of rapid, sensitive, and accurate methods for assessment of food safety often termed as foodomics methods is required...
2017: Advances in Food and Nutrition Research
https://www.readbyqxmd.com/read/28315989/rnai-inhibition-of-feruloyl-coa-6-hydroxylase-reduces-scopoletin-biosynthesis-and-post-harvest-physiological-deterioration-in-cassava-manihot-esculenta-crantz-storage-roots
#3
Shi Liu, Ima M Zainuddin, Herve Vanderschuren, James Doughty, John R Beeching
Cassava (Manihot esculenta Crantz) is a major world crop, whose storage roots provide food for over 800 million throughout the humid tropics. Despite many advantages as a crop, the development of cassava is seriously constrained by the rapid post-harvest physiological deterioration (PPD) of its roots that occurs within 24-72 h of harvest, rendering the roots unpalatable and unmarketable. PPD limits cassava's marketing possibilities in countries that are undergoing increased development and urbanisation due to growing distances between farms and consumers...
March 18, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28314283/stable-shrna-silencing-of-lactate-dehydrogenase-a-ldha-in-human-mda-mb-231-breast-cancer-cells-fails-to-alter-lactic-acid-production-glycolytic-activity-atp-or-survival
#4
Nzinga Mack, Elizabeth A Mazzio, David Bauer, Hernan Flores-Rozas, Karam F A Soliman
BACKGROUND: In the US, African Americans have a high death rate from triple-negative breast cancer (TNBC), characterized by lack of hormone receptors (ER, PR, HER2/ERRB2) which are otherwise valuable targets of chemotherapy. There is a need to identify novel targets that negatively impact TNBC tumorigenesis. TNBCs release an abundance of lactic acid, under normoxic, hypoxic and hyperoxic conditions; this referred to as the Warburg effect. Accumulated lactic acid sustains peri-cellular acidity which propels metastatic invasion and malignant aggressive transformation...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28301713/population-structure-and-genetic-basis-of-the-agronomic-traits-of-upland-cotton-in-china-revealed-by-a-genome-wide-association-study-using-high-density-snps
#5
Cong Huang, Xinhui Nie, Chao Shen, Chunyuan You, Wu Li, Wenxia Zhao, Xianlong Zhang, Zhongxu Lin
Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton producing and consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nation-wide population containing 503 G. hirsutum accessions was collected for a genome-wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high-density map based on this array were used for genotyping...
March 16, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28292625/-candidatus-dichloromethanomonas-elyunquensis-gen-nov-sp-nov-a-dichloromethane-degrading-anaerobe-of-the-peptococcaceae-family
#6
Sara Kleindienst, Steven A Higgins, Despina Tsementzi, Gao Chen, Konstantinos T Konstantinidis, E Erin Mack, Frank E Löffler
Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. We describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively...
December 21, 2016: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28289083/growth-tradeoffs-accompany-the-emergence-of-glycolytic-metabolism-in-shewanella-oneidensis-mr-1
#7
Lon M Chubiz, Christopher J Marx
Bacteria increase metabolic capacity via acquisition of genetic material or by mutation to genes already present in the genome. Here, we explore the mechanisms and tradeoffs involved when Shewanella oneidensis, a bacterium that typically consumes small organic and amino acids, rapidly evolves to expand its metabolic capacity to catabolize glucose after a short period of adaptation to a glucose-rich environment. Using whole-genome sequencing and genetic approaches, we discovered that deletions in a region including the transcriptional repressor (nagR) that regulates expression of genes associated with catabolism of N-acetylglucosamine is the common basis for evolved glucose metabolism across populations...
March 13, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28283358/identify-and-analysis-crotonylation-sites-in-histone-by-using-support-vector-machines
#8
Wang-Ren Qiu, Bi-Qian Sun, Hua Tang, Jian Huang, Hao Lin
OBJECTIVE: Lysine crotonylation (Kcr) is a newly discovered histone posttranslational modification, which is specifically enriched at active gene promoters and potential enhancers in mammalian cell genomes. Although lysine crotonylation sites can be correctly identified with high-resolution mass spectrometry, the experimental methods are time-consuming and expensive. Therefore, it is necessary to develop computational methods to deal with this problem. METHODS: We proposed a new encoding scheme named position weight amino acid composition to extract sequence information of histone around crotonylation sites...
March 7, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28273481/matching-dietary-amino-acid-balance-to-the-in-silico-translated-exome-optimizes-growth-and-reproduction-without-cost-to-lifespan
#9
Matthew D W Piper, George A Soultoukis, Eric Blanc, Andrea Mesaros, Samantha L Herbert, Paula Juricic, Xiaoli He, Ilian Atanassov, Hanna Salmonowicz, Mingyao Yang, Stephen J Simpson, Carlos Ribeiro, Linda Partridge
Balancing the quantity and quality of dietary protein relative to other nutrients is a key determinant of evolutionary fitness. A theoretical framework for defining a balanced diet would both reduce the enormous workload to optimize diets empirically and represent a breakthrough toward tailoring diets to the needs of consumers. Here, we report a simple and powerful in silico technique that uses the genome information of an organism to define its dietary amino acid requirements. We show for the fruit fly Drosophila melanogaster that such "exome-matched" diets are more satiating, enhance growth, and increase reproduction relative to non-matched diets...
March 7, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28272908/metabolomics-assisted-biotechnological-interventions-for-developing-plant-based-functional-foods-and-nutraceuticals
#10
Arun Kumar, Kareem A Mosa, Liyao Ji, Udaykumar Kage, Dhananjay Dhokane, Shailesh Karre, Deepa Madalageri, Neemisha Pathania
Today, the dramatic changes in types of food consumed have led to an increased burden of chronic diseases. Therefore, the emphasis of food research is not only to ensure quality food that can supply adequate nutrients to prevent nutrition related diseases, but also to ensure overall physical and mental-health. This has led to the concept of functional foods and nutraceuticals (FFNs), which can be ideally produced and delivered through plants. Metabolomics can help in getting the most relevant functional information, and thus has been considered the greatest -OMICS technology to date...
March 8, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28272456/computer-vision-and-machine-learning-for-robust-phenotyping-in-genome-wide-studies
#11
Jiaoping Zhang, Hsiang Sing Naik, Teshale Assefa, Soumik Sarkar, R V Chowda Reddy, Arti Singh, Baskar Ganapathysubramanian, Asheesh K Singh
Traditional evaluation of crop biotic and abiotic stresses are time-consuming and labor-intensive limiting the ability to dissect the genetic basis of quantitative traits. A machine learning (ML)-enabled image-phenotyping pipeline for the genetic studies of abiotic stress iron deficiency chlorosis (IDC) of soybean is reported. IDC classification and severity for an association panel of 461 diverse plant-introduction accessions was evaluated using an end-to-end phenotyping workflow. The workflow consisted of a multi-stage procedure including: (1) optimized protocols for consistent image capture across plant canopies, (2) canopy identification and registration from cluttered backgrounds, (3) extraction of domain expert informed features from the processed images to accurately represent IDC expression, and (4) supervised ML-based classifiers that linked the automatically extracted features with expert-rating equivalent IDC scores...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28266534/efficient-and-rapid-generation-of-large-genomic-variants-in-rats-and-mice-using-crismere
#12
Marie-Christine Birling, Laurence Schaeffer, Philippe André, Loic Lindner, Damien Maréchal, Abdel Ayadi, Tania Sorg, Guillaume Pavlovic, Yann Hérault
Modelling Down syndrome (DS) in mouse has been crucial for the understanding of the disease and the evaluation of therapeutic targets. Nevertheless, the modelling so far has been limited to the mouse and, even in this model, generating duplication of genomic regions has been labour intensive and time consuming. We developed the CRISpr MEdiated REarrangement (CRISMERE) strategy, which takes advantage of the CRISPR/Cas9 system, to generate most of the desired rearrangements from a single experiment at much lower expenses and in less than 9 months...
March 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28261177/the-histidine-decarboxylase-gene-cluster-of-lactobacillus-parabuchneri-was-gained-by-horizontal-gene-transfer-and-is-mobile-within-the-species
#13
Daniel Wüthrich, Hélène Berthoud, Daniel Wechsler, Elisabeth Eugster, Stefan Irmler, Rémy Bruggmann
Histamine in food can cause intolerance reactions in consumers. Lactobacillus parabuchneri (L. parabuchneri) is one of the major causes of elevated histamine levels in cheese. Despite its significant economic impact and negative influence on human health, no genomic study has been published so far. We sequenced and analyzed 18 L. parabuchneri strains of which 12 were histamine positive and 6 were histamine negative. We determined the complete genome of the histamine positive strain FAM21731 with PacBio as well as Illumina and the genomes of the remaining 17 strains using the Illumina technology...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28261168/common-distribution-of-gad-operon-in-lactobacillus-brevis-and-its-gada-contributes-to-efficient-gaba-synthesis-toward-cytosolic-near-neutral-ph
#14
Qinglong Wu, Hein Min Tun, Yee-Song Law, Ehsan Khafipour, Nagendra P Shah
Many strains of lactic acid bacteria (LAB) and bifidobacteria have exhibited strain-specific capacity to produce γ-aminobutyric acid (GABA) via their glutamic acid decarboxylase (GAD) system, which is one of amino acid-dependent acid resistance (AR) systems in bacteria. However, the linkage between bacterial AR and GABA production capacity has not been well established. Meanwhile, limited evidence has been provided to the global diversity of GABA-producing LAB and bifidobacteria, and their mechanisms of efficient GABA synthesis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28250912/identification-and-preliminary-validation-of-radiation-response-protein-s-in-human-blood-for-a-high-throughput-molecular-biodosimetry-technology-for-the-future
#15
Saibadaiahun Nongrum, S Thangminlal Vaiphei, Joshua Keppen, Mandahakani Ksoo, Ettrika Kashyap, Rajesh N Sharan
The absence of a rapid and high-throughput technology for radiation biodosimetry has been a great obstacle in our full preparedness to cope with large-scale radiological incidents. The existing cytogenetic technologies have limitations, primarily due to their time-consuming methodologies, which include a tissue culture step, and the time required for scoring. This has seriously undermined its application in a mass casualty scenario under radiological emergencies for timely triage and medical interventions. Recent advances in genomics and proteomics in the postgenomic era have opened up new platforms and avenues to discover molecular biomarkers for biodosimetry in the future...
2017: Genome Integrity
https://www.readbyqxmd.com/read/28245842/knocking-out-consumer-concerns-and-regulator-s-rules-efficient-use-of-crispr-cas-ribonucleoprotein-complexes-for-genome-editing-in-cereals
#16
Felix Wolter, Holger Puchta
Selection-free genome editing using Cas9 ribonucleoprotein embryo bombardment has been achieved for maize and wheat. This is a breakthrough that should make new breeding technologies more acceptable for worldwide use.
February 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/28242343/biomedical-applications-of-cell-and-tissue-specific-metabolic-network-models
#17
REVIEW
Hamideh Fouladiha, Sayed-Amir Marashi
The essential goal of biomedical research is to understand the underlying mechanism of disease development. Unfortunately, achieving this goal requires expensive and time-consuming efforts in medical biotechnology. This review focuses on how context-specific genome-scale metabolic network models may facilitate reaching this goal. Such models provide an in silico framework for computational simulation of cellular metabolism, predicting the outcome of experiments. Therefore, by using these models at the initial stages of experimental design, time and cost in biomedical researches may be reduced...
February 24, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28238212/development-a-rapid-and-accurate-multiplex-real-time-pcr-method-for-the-detection-chlamydia-trachomatis-and-mycoplasma-hominis
#18
Roya Safarkar, Jalil Fallah Mehrabadi, Zahra Noormohammadi, Reza Mirnejad
BACKGROUND: Sexually transmitted diseases easily spread among sexually active people and often have no symptoms. Rapid and accurate method for detecting these infections are necessary in early stages. The traditional detection methods of them are difficult and time-consuming. METHODS: In this study, multiplex real time PCR was optimized for rapid identification of Chlamydia trachomatis and Mycoplasma hominis in a single tube and was performed with our designed primers...
February 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28231382/accurate-measurement-of-transgene-copy-number-in-crop-plants-using-droplet-digital-pcr
#19
Ray Collier, Kasturi Dasgupta, Yan-Ping Xing, Bryan Tarape Hernandez, Min Shao, Dominica Rohozinski, Emma Kovak, Jeanie Lin, Maria Luiza P de Oliveira, Ed Stover, Kent F McCue, Frank G Harmon, Ann Blechl, James G Thomson, Roger Thilmony
Genetic transformation is a powerful means for the improvement of crop plants, but requires labor and resource intensive methods. An efficient method for identifying single copy transgene insertion events from a population of independent transgenic lines is desirable. Currently transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes...
February 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28231290/mapping-the-sensory-perception-of-apple-using-descriptive-sensory-evaluation-in-a-genome-wide-association-study
#20
Beatrice Amyotte, Amy J Bowen, Travis Banks, Istvan Rajcan, Daryl J Somers
Breeding apples is a long-term endeavour and it is imperative that new cultivars are selected to have outstanding consumer appeal. This study has taken the approach of merging sensory science with genome wide association analyses in order to map the human perception of apple flavour and texture onto the apple genome. The goal was to identify genomic associations that could be used in breeding apples for improved fruit quality. A collection of 85 apple cultivars was examined over two years through descriptive sensory evaluation by a trained sensory panel...
2017: PloS One
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