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https://www.readbyqxmd.com/read/28437710/customised-nucleic-acid-libraries-for-enhanced-aptamer-selection-and-performance
#1
REVIEW
Franziska Pfeiffer, Malte Rosenthal, Julia Siegl, Jörg Ewers, Günter Mayer
Aptamers are short single-stranded oligo(deoxy)nucleotides that are selected to bind to target molecules with high affinity and specificity. Because of their sophisticated characteristics and versatile applicability, aptamers are thought to become universal molecular probes in biotechnological and therapeutic applications. However, the variety of possible interactions with a putative target molecule is limited by the chemical repertoire of the natural nucleobases. Consequently, many desired targets are not addressable by aptamers...
April 21, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28436093/genome-wide-association-studies-to-identify-rice-salt-tolerance-markers
#2
Juan Patishtan, Tom N Hartley, Raquel Fonseca de Carvalho, Frans Jm Maathuis
Salinity is an ever increasing menace that affects agriculture world-wide. Crops such as rice are salt sensitive but its degree of susceptibility varies widely between cultivars pointing to extensive genetic diversity which can be exploited to identify genes and proteins that are relevant in the response of rice to salt stress. We used a diversity panel of 306 rice accessions and collected phenotypic data after short (6 h), medium (7d) and long (30d) salinity treatment (50 mM NaCl). A genome wide association study (GWAS) was subsequently performed which identified around 1200 candidate genes from many functional categories but this was treatment period dependent...
April 23, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28435308/association-of-the-ppp3ca-c-249g-a-variant-with-clinical-outcomes-of-tacrolimus-based-therapy-in-kidney-transplant-recipients
#3
Patricia C Salgado, Fabiana Dv Genvigir, Claudia R Felipe, Helio Tedesco-Silva, Jose O Medina-Pestana, Sonia Q Doi, Mario H Hirata, Rosario Dc Hirata
BACKGROUND: The effects of genetic variants related to the pharmacodynamic mechanisms of immunosuppressive drugs on their therapeutic efficacy and safety have been poorly explored. This study was performed to investigate the influence of the PPP3CA c.249G>A variant on the clinical outcomes of kidney transplant recipients. PATIENTS AND METHODS: A total of 148 Brazilian patients received tacrolimus (TAC)-based immunosuppressive therapy for 90 days post-kidney transplantation...
2017: Pharmacogenomics and Personalized Medicine
https://www.readbyqxmd.com/read/28435307/comparison-of-cyp2c9-cyp2c19-cyp2d6-abcb1-and-slco1b1-gene-polymorphism-frequency-in-russian-and-nanai-populations
#4
Dmitrij Alekseevitch Sychev, Grigorij Nikolaevich Shuev, Salavat Shejhovich Suleymanov, Kristina Anatol'evna Ryzhikova, Karin Badavievich Mirzaev, Elena Anatol'evna Grishina, Natalia Evgenievna Snalina, Zhannet Alimovna Sozaeva, Anton Mikhailovich Grabuzdov, Irina Andreevna Matsneva
BACKGROUND: The efficiency and safety of drug therapy depends on the peculiarities of functioning of the P450 cytochrome group and transporting proteins. There are significant differences for single-nucleotide polymorphism (SNP) frequency. MATERIALS AND METHODS: We studied the peculiarities of P450 cytochrome polymorphisms, SLCO1B1 transporting protein, and P-glycoprotein carriage in healthy volunteers in the Nanai ethnic group living in Russia, and compared them to the carriage of SNPs in the Russian population according to literature data...
2017: Pharmacogenomics and Personalized Medicine
https://www.readbyqxmd.com/read/28434155/nitrogen-fertility-and-abiotic-stresses-management-in-cotton-crop-a-review
#5
Aziz Khan, Daniel Kean Yuen Tan, Muhammad Zahir Afridi, Honghai Luo, Shahbaz Atta Tung, Mir Ajab, Shah Fahad
This review outlines nitrogen (N) responses in crop production and potential management decisions to ameliorate abiotic stresses for better crop production. N is a primary constituent of the nucleotides and proteins that are essential for life. Production and application of N fertilizers consume huge amounts of energy, and excess is detrimental to the environment. Therefore, increasing plant N use efficiency (NUE) is important for the development of sustainable agriculture. NUE has a key role in crop yield and can be enhanced by controlling loss of fertilizers by application of humic acid and natural polymers (hydrogels), having high water-holding capacity which can improve plant performance under field conditions...
April 22, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28434117/associations-of-tim-1-genetic-polymorphisms-with-asthma-a-meta-analysis
#6
Xiaochuan Xie, Xiaohan Shi, Peng Chen, Li Rao
PURPOSE: Recently, the roles of TIM-1 genetic polymorphisms in asthma have been extensively studied, with conflicting results. Therefore, we performed the present meta-analysis to better assess potential associations of TIM-1 genetic polymorphisms with asthma. METHODS: Eligible articles were searched in PubMed, Medline, EMBASE, Google Scholar, and CNKI up to December 2016. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to detect any potential associations between TIM-1 genetic polymorphisms and asthma...
April 22, 2017: Lung
https://www.readbyqxmd.com/read/28433721/optimizing-the-restored-chemotactic-behavior-of-anticancer-agent-salmonella-enterica-serovar-typhimurium-vnp20009
#7
Katherine M Broadway, Seungbeum Suh, Bahareh Behkam, Birgit E Scharf
Bacteria, including strains of Salmonella, have been researched and applied as therapeutic cancer agents for centuries. Salmonella are particularly of interest due to their facultative anaerobic nature, facilitating colonization of differentially oxygenated tumor regions. Additionally, Salmonella can be manipulated with relative ease, resulting in the ability to attenuate the pathogen or engineer vectors for drug delivery. It was recently discovered that the anti-cancer Salmonella enterica serovar Typhimurium strain VNP20009 is lacking in chemotactic ability, due to a non-synonymous single nucleotide polymorphism in cheY...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28433686/mitochatting-if-only-we-could-be-a-fly-on-the-cell-wall
#8
REVIEW
Michal Eisenberg-Bord, Maya Schuldiner
Mitochondria, cellular metabolic hubs, perform many essential processes and are required for the production of metabolites such as ATP, iron-sulfur clusters, heme, amino acids and nucleotides. To fulfill their multiple roles, mitochondria must communicate with all other organelles to exchange small molecules, ions and lipids. Since mitochondria are largely excluded from vesicular trafficking routes, they heavily rely on membrane contact sites. Contact sites are areas of close proximity between organelles that allow efficient transfer of molecules, saving the need for slow and untargeted diffusion through the cytosol...
April 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28433457/spatial-and-temporal-expression-patterns-of-genes-around-nine-neuroticism-associated-loci
#9
Kazutaka Ohi, Takamitsu Shimada, Toshiki Yasuyama, Kohei Kimura, Takashi Uehara, Yasuhiro Kawasaki
Neuroticism is a high-order personality trait. Individuals with higher neuroticism have increased risks of various psychiatric disorders and physical health outcomes. Neuroticism is related to physiological differences in the brain. A recent genome-wide association study identified nine distinct genomic loci that contribute to neuroticism. Brain development and function depend on the precise regulation of gene expression, which is differentially regulated across brain regions and developmental stages. Using multiple publicly available human post-mortem databases, we investigated, in brain and non-brain tissues and across several developmental life stages, the spatial and temporal expression patterns of genes arising from nine neuroticism-associated loci...
April 19, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28432611/comparison-of-human-erythrocyte-purine-nucleotide-metabolism-and-blood-purine-and-pyrimidine-degradation-product-concentrations-before-and-after-acute-exercise-in-trained-and-sedentary-subjects
#10
Wioleta Dudzinska, M Suska, A Lubkowska, K Jakubowska, M Olszewska, K Safranow, D Chlubek
This study aimed at evaluating the concentration of erythrocyte purine nucleotides (ATP, ADP, AMP, IMP) in trained and sedentary subjects before and after maximal physical exercise together with measuring the activity of purine metabolism enzymes as well as the concentration of purine (hypoxanthine, xanthine, uric acid) and pyrimidine (uridine) degradation products in blood. The study included 15 male elite rowers [mean age 24.3 ± 2.56 years; maximal oxygen uptake (VO2max) 52.8 ± 4.54 mL/kg/min; endurance and strength training 8...
April 21, 2017: Journal of Physiological Sciences: JPS
https://www.readbyqxmd.com/read/28432556/enzymes-that-hydrolyze-adenine-nucleotides-in-a-model-of-hypercholesterolemia-induced-by-triton-wr-1339-protective-effects-of-%C3%AE-caryophyllene
#11
Matheus D Baldissera, Carine F Souza, Pedro H Doleski, Daniela B R Leal, Lenita M Stefani, Aline A Boligon, Silvia G Monteiro
Purinergic system has been proven to play a critical role in the inflammatory process and to represent an important therapeutic target to improve the immune response during hypercholesterolemia. β-caryophyllene, a phytocannabinoid compound, has a powerful hypolipidemic and anti-inflammatory actions. However, the effects of β-caryophyllene on seric enzymes of purinergic system have not been evaluated. The purpose of this study was to investigate whether β-caryophyllene is able to ameliorate the seric activities of NTPDase and adenosine deaminase (ADA) in a model of hypercholesterolemia induced by Triton WR-1339...
April 21, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28432541/genome-characteristics-of-the-proteorhodopsin-containing-marine-flavobacterium-polaribacter-dokdonensis-dsw-5
#12
Kiyoung Yoon, Ju Yeon Song, Min-Jung Kwak, Soon-Kyeong Kwon, Jihyun F Kim
Bacteria in the genus Polaribacter, belonging to the family Flavobacteriaceae, are typically isolated from marine environments. Polaribacter dokdonensis DSW-5, the type strain of the species, is a Gram-negative bacterium isolated from the East Sea of Korea. Whole genome shotgun sequencing was performed with the HiSeq 2000 platform and paired-end reads were generated at 188-fold coverage. The sequencing reads were assembled into two contigs with a total length of 3.08 Mb. The genome sequences of DSW-5 contain 2,776 proteincoding sequences and 41 RNA genes...
April 22, 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28432259/probing-native-metal-ion-association-sites-through-quenching-of-fluorophores-in-the-nucleotide-binding-domains-of-the-abc-transporter-msba
#13
Daiki Tatsumi, Kei Nanatani, Yuto Koike, Kiyoto Kamagata, Satoshi Takahashi, Ayumu Konno, Tadaomi Furuta, Minoru Sakurai, Nobuyuki Uozumi
ATP binding cassette (ABC) transporters are ubiquitously present in prokaryotic and eukaryotic cells. Binding of ATP to the nucleotide binding domains (NBDs) elicits major conformational changes of the transporters resulting in the transport of the substrate across the membrane. The availability of a crystal structure of the NBDs enabled us to elucidate the local structure and small-scale dynamics in the NBDs. Here, we labeled the ABC transporter MsbA, a homodimeric flippase from E. coli , with a fluorescent probe, Alexa532, within the NBDs...
April 21, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28431990/a-common-polymorphism-decreases-lrp1-mrna-stability-and-is-associated-with-increased-plasma-factor-viii-levels
#14
Jiann-Der Lee, Kuang-Ming Hsiao, Pey-Jium Chang, Chih-Cheng Chen, Ya-Wen Kuo, Yen-Chu Huang, Huan-Lin Hsu, Ya-Hui Lin, Chih-Ying Wu, Ying-Chih Huang, Meng Lee, Chia-Yu Hsu, Yi-Ting Pan, Chih-Yu Kuo, Chun-Hsien Lin
The low-density lipoprotein receptor-related protein 1 (LRP1) gene is associated with increased levels of plasma factor VIII (FVIII). We aimed to explore eight functional genetic LRP1 variants for their potential roles in regulating FVIII levels and acute ischemic stroke (AIS). This genetic association study enrolled 192 patients with AIS and 134 controls. There were no significant differences in the genetic frequency of the eight functional single-nucleotide polymorphisms (SNPs) between the control and AIS groups...
April 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28431642/pcr-based-detection-methods-for-single-nucleotide-polymorphism-or-mutation-real-time-pcr-and-its-substantial-contribution-toward-technological-refinement
#15
Kazuyuki Matsuda
Single-nucleotide polymorphisms (SNPs) and single-nucleotide mutations result from the substitution of only a single base. The SNP or mutation can be relevant to disease susceptibility, pathogenesis of disease, and efficacy of specific drugs. It is important to detect SNPs or mutations clinically. Methods to distinguish/detect SNPs or mutations should be highly specific and sensitive. In this regard, polymerase chain reaction (PCR) has provided the necessary analytical performance for many molecular analyses...
2017: Advances in Clinical Chemistry
https://www.readbyqxmd.com/read/28431403/association-of-the-vdac3-gene-polymorphism-with-sperm-count-in-han-chinese-population-with-idiopathic-male-infertility
#16
Lianjun Pan, Qingzhen Liu, Jingyun Li, Wei Wu, Xinru Wang, Dan Zhao, Jiehua Ma
Voltage-dependent anion channel (VDAC) is a multifunctional channel protein across the outer mitochondrial membrane of somatic cells and participates in many physiological and pathophysiological processes. Up to now, only a few studies, including our previous studies, showed that VDAC exists in mammalian spermatozoa and is involved in spermatogenesis and sperm functions. There is no report about VDAC genetic variants in germinal tissues or cells. To investigate the possible association between VDAC genetic variants and human sperm quality, we performed semen analysis and variant Genotyping of VDAC3 subtype (rs7004637, rs16891278 and rs6773) of 523 Han-Chinese males with idiopathic infertility respectively by computer assisted semen analysis (CASA) and single nucleotide polymorphism (SNP) Genotyping assay...
April 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28431244/bacterial-metabolism-affects-the-c-%C3%A2-elegans-response-to-cancer-chemotherapeutics
#17
Aurian P García-González, Ashlyn D Ritter, Shaleen Shrestha, Erik C Andersen, L Safak Yilmaz, Albertha J M Walhout
The human microbiota greatly affects physiology and disease; however, the contribution of bacteria to the response to chemotherapeutic drugs remains poorly understood. Caenorhabditis elegans and its bacterial diet provide a powerful system to study host-bacteria interactions. Here, we use this system to study how bacteria affect the C. elegans response to chemotherapeutics. We find that different bacterial species can increase the response to one drug yet decrease the effect of another. We perform genetic screens in two bacterial species using three chemotherapeutic drugs: 5-fluorouracil (5-FU), 5-fluoro-2'-deoxyuridine (FUDR), and camptothecin (CPT)...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28430929/promoter-polymorphism-rs886205-genotype-interacts-with-dna-methylation-of-the-aldh2-regulatory-region-in-alcohol-dependence
#18
Hansi Pathak, Helge Frieling, Stefan Bleich, Alexander Glahn, Annemarie Heberlein, Mani Haschemi Nassab, Thomas Hillemacher, Alexandra Burkert, Mathias Rhein
Aims: Aldehyde dehydrogenase 2 (ALDH2) protects cells from ethanol toxicity by metabolizing acetaldehyde. We studied the single nucleotide polymorphism (SNP) rs886205s located between a negative and a positive regulating promoter element in the ALDH2 gene. The negative regulatory region was already associated with differential DNA methylation in the two allele variations of rs886205 SNP. Another CpG island, in the positive regulatory region of the ALDH2 promoter, extends through the SNP rs886205 and a nuclear receptor response element...
May 1, 2017: Alcohol and Alcoholism: International Journal of the Medical Council on Alcoholism
https://www.readbyqxmd.com/read/28430100/discovery-of-african-bat-polyomaviruses-and-infrequent-recombination-in-the-large-t-antigen-in-the-polyomaviridae
#19
Michael Carr, Gabriel Gonzalez, Michihito Sasaki, Kimihito Ito, Akihiro Ishii, Bernard M Hang'ombe, Aaron S Mweene, Yasuko Orba, Hirofumi Sawa
Bat species represent natural reservoirs for a number of high-consequence human pathogens. The present study investigated the diversity of polyomaviruses (PyVs) in Zambian insectivorous and fruit bat species. We describe the complete genomes from four newly proposed African bat PyV species employing the recently recommended criteria provided by the Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses. A comprehensive phylogenetic and recombination analysis was performed to determine genetic relationships and the distribution of recombination events in PyV from mammalian and avian species...
April 22, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28428839/population-genomics-meet-lagrangian-simulations-oceanographic-patterns-and-long-larval-duration-ensure-connectivity-among-paracentrotus-lividus-populations-in-the%C3%A2-adriatic-and-ionian-seas
#20
Marta Paterno, Marcello Schiavina, Giorgio Aglieri, Jamila Ben Souissi, Elisa Boscari, Renato Casagrandi, Aurore Chassanite, Mariachiara Chiantore, Leonardo Congiu, Giuseppe Guarnieri, Claudia Kruschel, Vesna Macic, Ilaria A M Marino, Chiara Papetti, Tomaso Patarnello, Lorenzo Zane, Paco Melià
Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long-distance dispersal, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic-Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b-RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal...
April 2017: Ecology and Evolution
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