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https://www.readbyqxmd.com/read/28231340/the-widely-used-nicotiana-benthamiana-16c-line-has-an-unusual-t-dna-integration-pattern-including-a-transposon-sequence
#1
Joshua G Philips, Fatima Naim, Michał T Lorenc, Kevin J Dudley, Roger P Hellens, Peter M Waterhouse
Nicotiana benthamiana is employed around the world for many types of research and one transgenic line has been used more extensively than any other. This line, 16c, expresses the Aequorea victoria green fluorescent protein (GFP), highly and constitutively, and has been a major resource for visualising the mobility and actions of small RNAs. Insights into the mechanisms studied at a molecular level in N. benthamiana 16c are likely to be deeper and more accurate with a greater knowledge of the GFP gene integration site...
2017: PloS One
https://www.readbyqxmd.com/read/28231235/near-real-time-surveillance-of-u-s-norovirus-outbreaks-by-the-norovirus-sentinel-testing-and-tracking-network-united-states-august-2009-july-2015
#2
Minesh P Shah, Mary E Wikswo, Leslie Barclay, Anita Kambhampati, Kayoko Shioda, Umesh D Parashar, Jan Vinjé, Aron J Hall
Norovirus is the leading cause of endemic and epidemic acute gastroenteritis in the United States (1). New variant strains of norovirus GII.4 emerge every 2-4 years (2-4) and are often associated with increased disease and health care visits (5-7). Since 2009, CDC has obtained epidemiologic data on norovirus outbreaks from state health departments through the National Outbreak Reporting System (NORS) (8) and laboratory data through CaliciNet (9). NORS is a web-based platform for reporting waterborne, foodborne, and enteric disease outbreaks of all etiologies, including norovirus, to CDC...
February 24, 2017: MMWR. Morbidity and Mortality Weekly Report
https://www.readbyqxmd.com/read/28230975/tuning-of-recombinant-protein-expression-in-escherichia-coli-by-manipulating-transcription-translation-initiation-rates-and-incorporation-of-non-canonical-amino-acids
#3
Orr Schlesinger, Yonatan Chemla, Mathias Heltberg, Eden Ozer, Ryan Marshall, Vincent Noireaux, Mogens Hogh Jensen, Lital Alfonta
Protein synthesis in cells has been thoroughly investigated and characterized over the past 60 years. However, some fundamental issues remain unresolved, including the reasons for genetic code redundancy and codon bias. In this study, we changed the kinetics of the E. coli transcription and translation processes by mutating the promoter and ribosome binding domains and by using genetic code expansion. The results expose a counterintuitive phenomenon, whereby an increase in the initiation rates of transcription and translation lead to a decrease in protein expression...
February 23, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28230768/bioinformatic-analysis-reveals-archaeal-trna-tyr-and-trna-trp-identities-in-bacteria
#4
Takahito Mukai, Noah M Reynolds, Ana Crnković, Dieter Söll
The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNA(Tyr) and tRNA(Trp) genes reveal bacterial or archaeal origins...
February 21, 2017: Life
https://www.readbyqxmd.com/read/28230599/a-targeted-next-generation-genetic-sequencing-study-on-tetralogy-of-fallot-combined-with-cleft-lip-and-palate
#5
Lin Liu, Haisong Bu, Yifeng Yang, Zhiping Tan, Fei Zhang, Shijun Hu, Tianli Zhao
BACKGROUND: Congenital heart disease (CHD), plus cleft lip and palate (CLP) are currently the most common types of structural malformation in infants. Many genes have been investigated for their involvement in CHD with CLP. Targeted next-generation sequencing can analyze large amounts of genetic information rapidly, and thus address this question. METHODS: The authors designed a targeted, next-generation sequencing gene panel for 455 genes previously implicated in CHD or CLP...
February 22, 2017: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/28229928/an-expanded-genetic-code-for-probing-the-role-of-electrostatics-in-enzyme-catalysis-by-vibrational-stark-spectroscopy
#6
REVIEW
Jan-Stefan Völler, Hernan Biava, Peter Hildebrandt, Nediljko Budisa
BACKGROUND: To find experimental validation for electrostatic interactions essential for catalytic reactions represents a challenge due to practical limitations in assessing electric fields within protein structures. SCOPE OF REVIEW: This review examines the applications of non-canonical amino acids (ncAAs) as genetically encoded probes for studying the role of electrostatic interactions in enzyme catalysis. MAJOR CONCLUSIONS: ncAAs constitute sensitive spectroscopic probes to detect local electric fields by exploiting the vibrational Stark effect (VSE) and thus have the potential to map the protein electrostatics...
February 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28228149/fasciolopsis-buski-digenea-fasciolidae-from-china-and-india-may-represent-distinct-taxa-based-on-mitochondrial-and-nuclear-ribosomal-dna-sequences
#7
Jun Ma, Miao-Miao Sun, Jun-Jun He, Guo-Hua Liu, Lin Ai, Mu-Xin Chen, Xing-Quan Zhu
BACKGROUND: Fasciolopsis buski is a zoonotic intestinal fluke infecting humans and pigs, but it has been seriously neglected. It is yet to know whether there is any genetic diversity among F. buski from different geographical locations, particularly in sequences of nuclear ribosomal DNA (rDNA) and mitochondrial (mt) DNA. Therefore, we determined the sequences of partial 18S, the complete internal transcribed spacer (ITS) rDNA and the complete mt genome of F. buski from China, compared the rDNA and mtDNA sequences with those of isolates from India and Vietnam, and assessed the phylogenetic relationships of this fluke and related fasciolid trematodes based on the mtDNA dataset...
February 22, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28228119/genetic-variation-of-the-toll-like-receptors-in-a-swedish-allergic-rhinitis-case-population
#8
V Henmyr, D Carlberg, E Manderstedt, C Lind-Halldén, T Säll, L O Cardell, C Halldén
BACKGROUND: Variation in the 10 toll-like receptor (TLR) genes has been significantly associated with allergic rhinitis (AR) in several candidate gene studies and three large genome-wide association studies. These have all investigated common variants, but no investigations for rare variants (MAF ≤ 1%) have been made in AR. The present study aims to describe the genetic variation of the promoter and coding sequences of the 10 TLR genes in 288 AR patients. METHODS: Sanger sequencing and Ion Torrent next-generation sequencing was used to identify polymorphisms in a Swedish AR population and these were subsequently compared and evaluated using 1000Genomes and Exome Aggregation Consortium (ExAC) data...
February 23, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28227475/label-free-detection-of-sex-determining-region-y-sry-via-capacitive-biosensor
#9
Shilpa Sivashankar, Christos Sapsanis, Sumeyra Agambayev, Ulrich Buttner, Khaled Nabil Salama, Shilpa Sivashankar, Christos Sapsanis, Sumeyra Agambayev, Ulrich Buttner, Khaled Nabil Salama, Khaled Nabil Salama, Shilpa Sivashankar, Sumeyra Agambayev, Christos Sapsanis, Ulrich Buttner
In this work, we present for the first time, the use of a simple fractal capacitive biosensor for the quantification and detection of sex-determining region Y (SRY) genes. This section of genetic code, which is found on the Y chromosome, finds importance for study as it causes fetuses to develop characteristics of male sex-like gonads when a mutation occurs. It is also an important genetic code in men, and disorders involving the SRY gene can cause infertility and sexual malfunction that lead to a variety of gene mutational disorders...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226217/sulfation-of-glycosaminoglycans-and-its-implications-in-human-health-and-disorders
#10
Diana Soares da Costa, Rui L Reis, Iva Pashkuleva
Sulfation is a dynamic and complex posttranslational modification process. It can occur at various positions within the glycosaminoglycan (GAG) backbone and modulates extracellular signals such as cell-cell and cell-matrix interactions; different sulfation patterns have been identified for the same organs and cells during their development. Because of their high specificity in relation to function,GAGsulfation patterns are referred to as the sulfation code. This review explores the role of GAG sulfation in different biological processes at the cell, tissue, and organism levels...
February 2, 2017: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/28222777/identification-of-somatic-and-germ-line-dicer1-mutations-in-pleuropulmonary-blastoma-cystic-nephroma-and-rhabdomyosarcoma-tumors-within-a-dicer1-syndrome-pedigree
#11
Lorena Fernández-Martínez, José Antonio Villegas, Íñigo Santamaría, Ana S Pitiot, Marta G Alvarado, Soledad Fernández, Héctor Torres, Ángeles Paredes, Pilar Blay, Milagros Balbín
BACKGROUND: DICER1 syndrome is a pediatric cancer predisposition condition causing a variety of tumor types in children and young adults. In this report we studied a family with two relatives presenting a variety of neoplastic conditions at childhood. METHODS: Germ-line mutation screening of the complete coding region of the DICER1 gene in genomic DNA from the proband was performed. The presence of somatic DICER1 mutation and further alterations in driver genes was investigated in genomic DNA obtained from available tumor samples...
February 21, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28222292/genomics-stentor-s-trumpet-sounds-anew
#12
Robert S Coyne
The amazing regenerative abilities of the giant ciliate Stentor coeruleus made it a favorite subject for classical embryologists. Now, its genome has been sequenced, enabling renewed experimental study and revealing unexpected surprises in mRNA splicing and the genetic code.
February 20, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28222234/transcriptome-analysis-of-the-brassica-napus-leptosphaeria-maculans-pathosystem-identifies-receptor-signalling-and-structural-genes-underlying-plant-resistance
#13
Michael G Becker, Xuehua Zhang, Philip L Walker, Joey C Wan, Jenna L Millar, Deirdre Khan, Matthew J Granger, Jacob D Cavers, Ainsley C Chan, Dilantha W G Fernando, Mark F Belmonte
The hemibiotrophic fungal pathogen Leptosphaeria maculans is the causal agent of blackleg disease in Brassica napus (canola, oilseed rape) and causes significant yield loss worldwide. While genetic resistance has been used to mitigate the disease using traditional breeding strategies, there is little knowledge about the genes contributing to blackleg resistance. RNA sequencing and a streamlined bioinformatics pipeline identified unique genes and plant defense pathways specific to plant resistance in the B. napus-L...
February 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28220771/expanding-the-genetic-code-of-mus-musculus
#14
Songmi Han, Aerin Yang, Soonjang Lee, Han-Woong Lee, Chan Bae Park, Hee-Sung Park
Here we report the expansion of the genetic code of Mus musculus with various unnatural amino acids including N(ɛ)-acetyl-lysine. Stable integration of transgenes encoding an engineered N(ɛ)-acetyl-lysyl-tRNA synthetase (AcKRS)/tRNA(Pyl) pair into the mouse genome enables site-specific incorporation of unnatural amino acids into a target protein in response to the amber codon. We demonstrate temporal and spatial control of protein acetylation in various organs of the transgenic mouse using a recombinant green fluorescent protein (GFPuv) as a model protein...
February 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28220625/predicting-gene-expression-in-massively-parallel-reporter-assays-a-comparative-study
#15
Anat Kreimer, Haoyang Zeng, Matthew D Edwards, Yuchun Guo, Kevin Tian, Sunyoung Shin, Rene Welch, Michael Wainberg, Rahul Mohan, Nicholas A Sinnott-Armstrong, Yue Li, Gökcen Eraslan, Talal Bin Amin, Jonathan Goke, Nikola S Mueller, Manolis Kellis, Anshul Kundaje, Michael A Beer, Sunduz Keles, David K Gifford, Nir Yosef
In many human diseases, associated genetic changes tend to occur within non-coding regions, whose effect might be related to transcriptional control. A central goal in human genetics is to understand the function of such non-coding regions: Given a region that is statistically associated with changes in gene expression (expression Quantitative Trait Locus; eQTL), does it in fact play a regulatory role? And if so, how is this role "coded" in its sequence? These questions were the subject of the Critical Assessment of Genome Interpretation eQTL challenge...
February 21, 2017: Human Mutation
https://www.readbyqxmd.com/read/28220606/lamarck-rises-from-his-grave-parental-environment-induced-epigenetic-inheritance-in-model-organisms-and-humans
#16
Yan Wang, Huijie Liu, Zhongsheng Sun
Organisms can change their physiological/behavioural traits to adapt and survive in changed environments. However, whether these acquired traits can be inherited across generations through non-genetic alterations has been a topic of debate for over a century. Emerging evidence indicates that both ancestral and parental experiences, including nutrition, environmental toxins, nurturing behaviour, and social stress, can have powerful effects on the physiological, metabolic and cellular functions in an organism...
February 20, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/28220022/using-metaphors-to-explain-molecular-testing-to-cancer-patients
#17
Ana P M Pinheiro, Rachel H Pocock, Margie D Dixon, Walid L Shaib, Suresh S Ramalingam, Rebecca D Pentz
BACKGROUND: Molecular testing to identify targetable molecular alterations is routine practice for several types of cancer. Explaining the underlying molecular concepts can be difficult, and metaphors historically have been used in medicine to provide a common language between physicians and patients. Although previous studies have highlighted the use and effectiveness of metaphors to help explain germline genetic concepts to the general public, this study is the first to describe the use of metaphors to explain molecular testing to cancer patients in the clinical setting...
February 20, 2017: Oncologist
https://www.readbyqxmd.com/read/28219780/diversification-of-mitochondrial-genome-of-daphnia-galeata-cladocera-crustacea-comparison-with-phylogenetic-consideration-of-the-complete-sequences-of-clones-isolated-from-five-lakes-in-japan
#18
Shin-Ichi Tokishita, Hiroyuki Shibuya, Taku Kobayashi, Masaki Sakamoto, Jin-Yong Ha, Shin-Ichi Yokobori, Hideo Yamagata, Takayuki Hanazato
To characterize genetic diversity and gene flow among Daphnia galeata populations, the complete nucleotide (nt) sequences of the mitochondrial (mt) DNAs of D. galeata clones isolated from five lakes in Japan (Lakes Shirakaba, Suwa, Kizaki, Kasumigaura, and Biwa) were determined. Comparison of non-synonymous (amino acid altering) substitution rates with synonymous substitution rates of D. galeata mt protein-coding genes demonstrated that ATPase8 and COI genes were the most and least susceptible, respectively, to the evolutional forces selecting the aa substitutions...
February 17, 2017: Gene
https://www.readbyqxmd.com/read/28219393/molecular-and-genetic-alterations-associated-with-therapy-resistance-and-relapse-of-acute-myeloid-leukemia
#19
REVIEW
Hubert Hackl, Ksenia Astanina, Rotraud Wieser
BACKGROUND: The majority of individuals with acute myeloid leukemia (AML) respond to initial chemotherapy and achieve a complete remission, yet only a minority experience long-term survival because a large proportion of patients eventually relapse with therapy-resistant disease. Relapse therefore represents a central problem in the treatment of AML. Despite this, and in contrast to the extensive knowledge about the molecular events underlying the process of leukemogenesis, information about the mechanisms leading to therapy resistance and relapse is still limited...
February 20, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28219347/aquaculture-genomics-genetics-and-breeding-in-the-united-states-current-status-challenges-and-priorities-for-future-research
#20
EDITORIAL
Hisham Abdelrahman, Mohamed ElHady, Acacia Alcivar-Warren, Standish Allen, Rafet Al-Tobasei, Lisui Bao, Ben Beck, Harvey Blackburn, Brian Bosworth, John Buchanan, Jesse Chappell, William Daniels, Sheng Dong, Rex Dunham, Evan Durland, Ahmed Elaswad, Marta Gomez-Chiarri, Kamal Gosh, Ximing Guo, Perry Hackett, Terry Hanson, Dennis Hedgecock, Tiffany Howard, Leigh Holland, Molly Jackson, Yulin Jin, Karim Kahlil, Thomas Kocher, Tim Leeds, Ning Li, Lauren Lindsey, Shikai Liu, Zhanjiang Liu, Kyle Martin, Romi Novriadi, Ramjie Odin, Yniv Palti, Eric Peatman, Dina Proestou, Guyu Qin, Benjamin Reading, Caird Rexroad, Steven Roberts, Mohamed Salem, Andrew Severin, Huitong Shi, Craig Shoemaker, Sheila Stiles, Suxu Tan, Kathy F J Tang, Wilawan Thongda, Terrence Tiersch, Joseph Tomasso, Wendy Tri Prabowo, Roger Vallejo, Hein van der Steen, Khoi Vo, Geoff Waldbieser, Hanping Wang, Xiaozhu Wang, Jianhai Xiang, Yujia Yang, Roger Yant, Zihao Yuan, Qifan Zeng, Tao Zhou
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships...
February 20, 2017: BMC Genomics
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