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Lu Lu, Jinfeng Chen, Sofia M C Robb, Yutaka Okumoto, Jason E Stajich, Susan R Wessler
To understand the success strategies of transposable elements (TEs) that attain high copy numbers, we analyzed two pairs of rice ( Oryza sativa ) strains, EG4/HEG4 and A119/A123, undergoing decades of rapid amplification (bursts) of the class 2 autonomous Ping element and the nonautonomous miniature inverted repeat transposable element (MITE) mPing Comparative analyses of whole-genome sequences of the two strain pairs validated that each pair has been maintained for decades as inbreds since divergence from their respective last common ancestor...
December 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
Adi Aran, Reeval Segel, Kota Kaneshige, Suleyman Gulsuner, Paul Renbaum, Scott Oliphant, Tomer Meirson, Ariella Weinberg-Shukron, Yair Hershkovitz, Sharon Zeligson, Ming K Lee, Abraham O Samson, Stanley M Parsons, Mary-Claire King, Ephrat Levy-Lahad, Tom Walsh
OBJECTIVE: To identify the genetic basis of a recessive congenital neurologic syndrome characterized by severe hypotonia, arthrogryposis, and respiratory failure. METHODS: Identification of the responsible gene by exome sequencing and assessment of the effect of the mutation on protein stability in transfected rat neuronal-like PC12A123.7 cells. RESULTS: Two brothers from a nonconsanguineous Yemeni Jewish family manifested at birth with severe hypotonia and arthrogryposis...
March 14, 2017: Neurology
Mingzi Wang, Wei Zhang, Weikai Xu, Yuemao Shen, Liangcheng Du
As an accelerated evolutionary tool, genome shuffling is largely dependent on the high fusion frequency of different parental protoplasts. However, it was unclear how many types of parental protoplasts would afford the highest fusion frequency. Here, we applied the Monte Carlo method to simulate the simplified processes of protoplast fusion, to achieve maximal useful fusions in genome shuffling. The basic principle of this simulation is that valid fusions would take place when the minimum distance between two different types of parent protoplasts is smaller than that between two of the same types...
September 2016: Applied Microbiology and Biotechnology
Fariha Shafi, Syed Zaidi, Purnima Mehta, Harpreet Singh Ahluwalia, Shahzada K Ahmed
PURPOSE: Surgical approaches to the medial orbit especially within the cone of orbital muscles necessitate great precision and care to avoid damage to surrounding structures-most importantly the optic nerve. The authors present a novel technique in which access to the medial orbital contents was achieved through an entirely endoscopic approach. METHODS: A 72-year-old Caucasian female presented with loss of vision in the right eye and reduced extraocular movements...
May 2016: Ophthalmic Plastic and Reconstructive Surgery
Kathryn M Sibley, Dina Brooks, Paula Gardner, Tania Janaudis-Ferreira, Mandy McGlynn, Sachi OʼHoski, Sara McEwen, Nancy M Salbach, Jennifer Shaffer, Paula Shing, Sharon E Straus, Susan B Jaglal
BACKGROUND: Effective balance reactions are essential for avoiding falls, but are not regularly measured by physical therapists. Physical therapists report wanting to improve reactive balance assessment, and theory-based approaches are recommended as the foundation for the development of interventions. This article describes how a behavior change theory for health care providers, the theoretical domains framework (TDF), was used to develop an intervention to increase reactive balance measurement among physical therapists who work in rehabilitation settings and treat adults who are at risk of falls...
April 2016: Journal of Neurologic Physical Therapy: JNPT
Bin Shen, Michelle L James, Lauren Andrews, Christopher Lau, Stephanie Chen, Mikael Palner, Zheng Miao, Natasha C Arksey, Adam J Shuhendler, Shawn Scatliffe, Kota Kaneshige, Stanley M Parsons, Christopher R McCurdy, Ahmad Salehi, Sanjiv S Gambhir, Frederick T Chin
BACKGROUND: This study aims to further evaluate the specificity and selectivity of [(18)F]FTC-146 and obtain additional data to support its clinical translation. METHODS: The binding of [(19)F]FTC-146 to vesicular acetylcholine transporter (VAChT) was evaluated using [(3)H]vesamicol and PC12(A123.7) cells in an in vitro binding assay. The uptake and kinetics of [(18)F]FTC-146 in S1R-knockout mice (S1R-KO) compared to wild-type (WT) littermates was assessed using dynamic positron emission tomography (PET) imaging...
December 2015: EJNMMI Research
Thomas H Dubaniewicz, Joseph P DuCarme
National Institute for Occupational Safety and Health (NIOSH) researchers continue to study the potential for lithium and lithium-ion battery thermal runaway from an internal short circuit in equipment for use in underground coal mines. Researchers conducted cell crush tests using a plastic wedge within a 20-L explosion-containment chamber filled with 6.5% CH4 -air to simulate the mining hazard. The present work extends earlier findings to include a study of LiFePO4 cells crushed while under charge, prismatic form factor LiCoO2 cells, primary spiral-wound constructed LiMnO2 cells, and crush speed influence on thermal runaway susceptibility...
November 2014: Journal of Loss Prevention in the Process Industries
Hui Liu, Hongjun Jin, Junfeng Li, Xiang Zhang, Kota Kaneshige, Stanley M Parsons, Joel S Perlmutter, Zhude Tu
The loss of cholinergic neurons and synapses relates to the severity of dementia in several neurodegenerative pathologies; and the vesicular acetylcholine transporter (VAChT) provides a reliable biomarker of cholinergic function. We recently characterized and (11)C-labeled a new VAChT inhibitor, (-)-TZ659. Here we report the in vitro and ex vivo characterization of (-)-TZ659. A stably transfected PC12(A123.7) cell line which expresses human VAChT (hVAChT) was used for the in vitro binding characterization of (-)-[(3)H]TZ659...
April 5, 2015: European Journal of Pharmacology
Ruairidh Martin, Andrew Owens, Mauro Santibanez Koref, Bernard Keavney
UNLABELLED: : Genome-wide association studies (GWAS) have identified genetic variants in nine chromosomal regions that are associated with atrial fibrillation (AF). The mechanisms underlying these associations are unknown. To investigate these mechanisms, we mapped associations between single nucleotide polymorphisms (SNPs) and allelic expression of candidate genes in the region of interest. METHODS: Whole blood was collected for DNA and RNA extraction from 447 patients at the time of cardiac catheterisation or cardiac surgery...
June 2014: Heart: Official Journal of the British Cardiac Society
Wei Zhang, Liyan Xu, Lishan Yang, Yaojian Huang, Shengying Li, Yuemao Shen
One novel pentacyclic depsidone containing an oxetane unit, phomopsidone A (1), together with the reported excelsione (also named as phomopsidone) (2), and four known isobenzofuranones (3-6) were isolated from the mangrove endophytic fungus Phomopsis sp. A123. Their structures were elucidated by 1D and 2D NMR spectroscopic analysis and high resolution mass spectrometry. The bioactivity assays showed that these compounds possess cytotoxic, antioxidant, and antifungal activities.
July 2014: Fitoterapia
Sheila T Angeles-Han, Courtney McCracken, Mina Pichavant, Kirsten Jenkins, Lori Ponder, Erica Myoung, Kelly Rouster Stevens, Larry B Vogler, Christine Kennedy, Steven Yeh, Spencer Cope, John F Bohnsack, Aimee O Hersh, Susan D Thompson, Sampath Prahalad
BACKGROUND/PURPOSE: Studies have shown that HLA-DRB1*8, 11 and 13 are strong risk alleles for various juvenile idiopathic arthritis (JIA) subtypes. There are few studies investigating the role of HLADRB1 alleles in children with uveitis. Our objective is to determine the association of these alleles with uveitis in a matched cohort of children with JIA and JIAassociated uveitis (JIA-U). We will also explore associations with uveitis complications and the need for antitumor necrosis factor (TNF) agents...
March 2014: Arthritis & Rheumatology
Cerrone Cabanos, Naoki Kato, Yoshiki Amari, Keigo Fujiwara, Tomoki Ohno, Kousuke Shimizu, Tsuyoshi Goto, Masaya Shimada, Masaharu Kuroda, Taro Masuda, Fumio Takaiwa, Shigeru Utsumi, Satoshi Nagaoka, Nobuyuki Maruyama
Soybean 7S globulin, known as β-conglycinin, has been shown to regulate human plasma cholesterol and triglyceride levels. Furthermore, the α' subunit of β-conglycinin has specifically been shown to possess low-density lipoprotein (LDL)-cholesterol-lowering activity. Therefore, accumulation of the α' subunit of β-conglycinin in rice seeds could lead to the production of new functional rice that could promote human health. Herein, we used the low-glutelin rice mutant 'Koshihikari' (var. a123) and suppressed its glutelins and prolamins, the major seed storage proteins of rice, by RNA interference...
August 2014: Transgenic Research
Taiji Kawakatsu, Yoshihiro Kawahara, Takeshi Itoh, Fumio Takaiwa
Genetic modification (GM) by Agrobacterium-mediated transformation is a robust and widely employed method to confer new traits to crops. In this process, a transfer DNA is delivered into the host genome, but it is still unclear how the host genome is altered by this event at single-base resolution. To decipher genomic discrepancy between GM crops and their host, we conducted whole-genome sequencing of a transgenic rice line OSCR11. This rice line expresses a seed-based edible vaccine containing two major pollen allergens, Cry j 1 and Cry j 2, against Japanese cedar pollinosis...
December 2013: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Bruno Ramos-Molina, Ana Lambertos, Andrés J López-Contreras, Rafael Peñafiel
BACKGROUND: Ornithine decarboxylase (ODC), the key enzyme in the polyamine biosynthetic pathway, is highly regulated by antizymes (AZs), small proteins that bind and inhibit ODC and increase its proteasomal degradation. Early studies delimited the putative AZ-binding element (AZBE) to the region 117-140 of ODC. The aim of the present work was to study the importance of certain residues of the region 110-142 that includes the AZBE region for the interaction between ODC and AZ1 and the ODC functionality...
November 2013: Biochimica et Biophysica Acta
Sofia M C Robb, Lu Lu, Elizabeth Valencia, James M Burnette, Yutaka Okumoto, Susan R Wessler, Jason E Stajich
Transposable elements (TEs) are dynamic components of genomes that often vary in copy number among members of the same species. With the advent of next-generation sequencing TE insertion-site polymorphism can be examined at an unprecedented level of detail when combined with easy-to-use bioinformatics software. Here we report a new tool, RelocaTE, that rapidly identifies specific TE insertions that are either polymorphic or shared between a reference and unassembled next-generation sequencing reads. Furthermore, a novel companion tool, CharacTErizer, exploits the depth of coverage to classify genotypes of nonreference insertions as homozygous, heterozygous or, when analyzing an active TE family, as rare somatic insertion or excision events...
June 2013: G3: Genes—Genomes—Genetics
Magali Maitre, Stéphanie Weidmann, Aurélie Rieu, Daphna Fenel, Guy Schoehn, Christine Ebel, Jacques Coves, Jean Guzzo
The ability of the small Hsp (heat-shock protein) Lo18 from Oenococcus oeni to modulate the membrane fluidity of liposomes or to reduce the thermal aggregation of proteins was studied as a function of the pH in the range 5-9. We have determined by size-exclusion chromatography and analytical ultracentrifugation that Lo18 assembles essentially as a 16-mer at acidic pH. Its quaternary structure evolves to a mixture of lower molecular mass oligomers probably in dynamic equilibrium when the pH increases. The best Lo18 activities are observed at pH 7 when the particle distribution contains a major proportion of dodecamers...
May 15, 2012: Biochemical Journal
W Zhang, M Wang, Y Huang, S K P Chea, Z Zheng, X Qian, Y Shen
AIMS: To establish a highly efficient methodology for screening high yield strains of cytotoxic deacetylmycoepoxydiene (DAM), to meet the need of research on its mechanism of anti-tumor properties and in vivo toxicity studies. METHODS AND RESULTS: A simple, sensitive, and highly repetitive screening procedure 'Antimicrobial-TLC-HPLC' (ATH) was established for the rapid obtaining of high-yielding DAM mutants to replace the time and labor intensive anti-tumor activity assay (MTT)...
May 2011: Letters in Applied Microbiology
Yancai Wang, Zhaoping Liu, Dianrui Zhang, Xihui Gao, Xiaoyu Zhang, Cunxian Duan, Lejiao Jia, Feifei Feng, Yaojian Huang, Yuemao Shen, Qiang Zhang
Deacety mycoepoxydiene (DM), extracted from Phomopsis sp. A123 of thalassiomycetes, is a novel and potent anti-cancer agent. Due to its physicochemical characteristics, the drug, a poorly water-soluble weak acid, shows poor solubility and dissolution characteristics. To improve the solubility and dissolution, formulation of DM as nanosuspension has been performed in this study. Nanosuspensions were developed by high-pressure homogenization (HPH) (DissoCubes(®) Technology) and transformed into dry powder by freeze-drying...
April 1, 2011: Colloids and Surfaces. B, Biointerfaces
Parul Khare, Anuprao Mulakaluri, Stanley M Parsons
Vesicular acetylcholine transporter (VAChT; TC 2.A.1.2.13) mediates storage of acetylcholine (ACh) by synaptic vesicles. A three-dimensional homology model of VAChT is available, but the binding sites for ACh and the allosteric inhibitor (-)-trans-2-(4-phenylpiperidino)cyclohexanol (vesamicol) are unknown. In previous work, mutations of invariant W331 in the lumenal beginning of transmembrane helix VIII (TM VIII) of rat VAChT led to as much as ninefold loss in equilibrium affinity for ACh and no loss in affinity for vesamicol...
November 2010: Journal of Neurochemistry
Parul Khare, Ana M Ojeda, Ananda Chandrasekaran, Stanley M Parsons
Invariant E309 is in contact with critical and invariant D398 in a three-dimensional homology model of vesicular acetylcholine transporter (VAChT, TC 2.A.1.2.13) [Vardy, E., et al. (2004) Protein Sci. 13, 1832-1840]. In the work reported here, E309 and D398 in human VAChT were mutated singly and together to test their functions, assign pK values to them, and determine whether the residues are close to each other in three-dimensional space. Mutants were stably expressed in the PC12(A123.7) cell line, and transport and binding properties were characterized at different pH values using radiolabeled ligands and filtration assays...
April 13, 2010: Biochemistry
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