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https://www.readbyqxmd.com/read/28330166/a-molecular-phylogenetic-framework-for-bacillus-subtilis-using-genome-sequences-and-its-application-to-bacillus-subtilis-subspecies-stecoris-strain-d7xpn1-an-isolate-from-a-commercial-food-waste-degrading-bioreactor
#1
Joseph Adelskov, Bharat K C Patel
A thermophilic, heterotrophic and facultatively anaerobic bacterium designated strain D7XPN1 was isolated from Baku BakuKing™, a commercial food-waste degrading bioreactor (composter). The strain grew optimally at 45 °C (growth range between 24 and 50 °C) and pH 7 (growth pH range between pH 5 and 9) in Luria Broth supplemented with 0.3 % glucose. Strain D7XPN1 tolerated up to 7 % NaCl and showed amylolytic and xylanolytic activities. 16S rRNA gene analysis placed strain D7XPN1 in the cluster represented by Bacillus subtilis and the genome analysis of the 4...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327659/the-immunosuppressant-mycophenolic-acid-alters-nucleotide-and-lipid-metabolism-in-an-intestinal-cell-model
#2
Svenja Heischmann, Monika Dzieciatkowska, Kirk Hansen, Dieter Leibfritz, Uwe Christians
The study objective was to elucidate the molecular mechanisms underlying the negative effects of mycophenolic acid (MPA) on human intestinal cells. Effects of MPA exposure and guanosine supplementation on nucleotide concentrations in LS180 cells were assessed using liquid chromatography-mass spectrometry. Proteomics analysis was carried out using stable isotope labeling by amino acids in cell culture combined with gel-based liquid chromatography-mass spectrometry and lipidome analysis using (1)H nuclear magnetic resonance spectroscopy...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#3
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28326314/case-study-of-somaclonal-variation-in-resistance-genes-mlo-and-pme3-in-flaxseed-linum-usitatissimum-l-induced-by-nanoparticles
#4
Inese Kokina, Ilona Mickeviča, Marija Jermaļonoka, Linda Bankovska, Vjačeslavs Gerbreders, Andrejs Ogurcovs, Inese Jahundoviča
Nanoparticles influence on genome is investigated worldwide. The appearance of somaclonal variation is a cause of great concern for any micropropagation system. Somaclonal variation describes the tissue-culture-induced phenotypic and genotypic variations. This paper shows the results of somaclonal variation in two resistance genes pectin methylesterase and Mlo-like protein in all tissue culture development stages, as donor plant, calluses, and regenerants of Linum usitatissimum induced by gold and silver nanoparticles...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28303008/an-analysis-of-echinacea-chloroplast-genomes-implications-for-future-botanical-identification
#5
Ning Zhang, David L Erickson, Padmini Ramachandran, Andrea R Ottesen, Ruth E Timme, Vicki A Funk, Yan Luo, Sara M Handy
Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28302587/transcriptomic-changes-in-cho-cells-after-adaptation-to-suspension-growth-in-protein-free-medium-analysed-by-a-species-specific-microarray
#6
Smriti Shridhar, Gerald Klanert, Norbert Auer, Inmaculada Hernandez-Lopez, Maciej M Kańduła, Matthias Hackl, Johannes Grillari, Nancy Stralis-Pavese, David P Kreil, Nicole Borth
Chinese Hamster Ovary (CHO) cells are the preferred cell line for production of biopharmaceuticals. These cells are capable to grow without serum supplementation, but drastic changes in their phenotype occur during adaptation to protein-free growth, which typically include the change to a suspension phenotype with reduced growth rate. A possible approach to understand this transformation, with the intention to counteract the reduction in growth by targeted supplementation of protein-free media, is gene expression profiling...
March 14, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28292727/analysis-of-dna-from-post-blast-pipe-bomb-fragments-for-identification-and-determination-of-ancestry
#7
Esiri Tasker, Bobby LaRue, Charity Beherec, David Gangitano, Sheree Hughes-Stamm
Improvised explosive devices (IEDs) such as pipe bombs are weapons used to detrimentally affect people and communities. A readily accessible brand of exploding targets called Tannerite® has been identified as a potential material for abuse as an explosive in pipe bombs. The ability to recover and genotype DNA from such weapons may be vital in the effort to identify suspects associated with these devices. While it is possible to recover DNA from post-blast fragments using short tandem repeat markers (STRs), genotyping success can be negatively affected by low quantities of DNA, degradation, and/or PCR inhibitors...
March 1, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28288142/serine-hydroxymethyl-transferase-1-stimulates-pro-oncogenic-cytokine-expression-through-sialic-acid-to-promote-ovarian-cancer-tumor-growth-and-progression
#8
R Gupta, Q Yang, S K Dogra, N Wajapeyee
High-grade serous (HGS) ovarian cancer accounts for 90% of all ovarian cancer-related deaths. However, factors that drive HGS ovarian cancer tumor growth have not been fully elucidated. In particular, comprehensive analysis of the metabolic requirements of ovarian cancer tumor growth has not been performed. By analyzing The Cancer Genome Atlas mRNA expression data for HGS ovarian cancer patient samples, we observed that six enzymes of the folic acid metabolic pathway were overexpressed in HGS ovarian cancer samples compared with normal ovary samples...
March 13, 2017: Oncogene
https://www.readbyqxmd.com/read/28277784/association-between-mthfr-c677t-polymorphism-and-methotrexate-treatment-outcome-in-rheumatoid-arthritis-patients-a-systematic-review-and-meta-analysis
#9
Wenjing Shao, Yi Yuan, Yuying Li
PURPOSE: Methotrexate (MTX) is one of the most widely used disease-modifying antirheumatic drugs for the treatment of rheumatoid arthritis (RA). However, its efficacy in RA patients is variable and unpredictable. Methylene tetrahydrofolate reductase (MTHFR) is an important enzyme in the MTX pathway and is involved in folate metabolism and DNA synthesis. Several studies have examined the association between the MTHFR C677T polymorphism and MTX toxicity and efficacy in RA, but their conclusions remain controversial...
March 9, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28270450/ssb1-and-ssb2-cooperate-to-regulate-mouse-hematopoietic-stem-and-progenitor-cells-by-resolving-replicative-stress
#10
Wei Shi, Therese Vu, Didier Boucher, Anna Biernacka, Jules Nde, Raj K Pandita, Jasmin Straube, Glen M Boyle, Fares Al-Ejeh, Purba Nag, Jessie Jeffery, Janelle L Harris, Amanda L Bain, Marta Grzelak, Magdalena Skrzypczak, Abhishek Mitra, Norbert Dojer, Nicola Crosetto, Nicole Cloonan, Olivier J Becherel, John Finnie, Jeffrey R Skaar, Carl R Walkley, Tej K Pandita, Maga Rowicka, Krzysztof Ginalski, Steven W Lane, Kum Kum Khanna
Hematopoietic stem and progenitor cells (HSPCs) are vulnerable to endogenous damage and defects in DNA repair can limit their function. The two single-stranded DNA binding proteins SSB1 and SSB2 are crucial regulators of the DNA damage response; however their overlapping roles during normal physiology are incompletely understood. We generated mice where both Ssb1 and Ssb2 were constitutively or conditionally deleted. Constitutive Ssb1/Ssb2 double knockout (DKO) caused early embryonic lethality, while conditional Ssb1/Ssb2 double knockout (cDKO) in adult mice resulted in acute lethality due to bone marrow failure and intestinal atrophy featuring stem and progenitor cell depletion, a phenotype unexpected from the previously reported single knockout models of Ssb1 or Ssb2 Mechanistically, cDKO HSPCs showed altered replication fork dynamics, massive accumulation of DNA damage, genome-wide double strand breaks (DSBs) enriched at Ssb binding regions and CpG islands, together with the accumulation of R-loops and cytosolic ssDNA...
March 7, 2017: Blood
https://www.readbyqxmd.com/read/28242083/association-of-five-snps-with-human-hair-colour-in-the-polish-population
#11
A Siewierska-Górska, A Sitek, E Żądzińska, G Bartosz, D Strapagiel
Twenty-two variants (single nucleotide polymorphisms - SNPs) of the genes involved in hair pigmentation (OCA2, HERC2, MC1R, SLC24A5, SLC45A2, TPCN2, TYR, TYRP1) were genotyped in a group of 186 Polish participants, representing a range of hair colours (45 red, 64 blond, 77 dark). A genotype-phenotype association analysis was performed. Using z-statistics we identified three variants highly associated with different hair colour categories (rs12913832:A>G in HERC2, rs1805007:T>C and rs1805008:C>T in MC1R)...
February 4, 2017: Homo: Internationale Zeitschrift Für die Vergleichende Forschung Am Menschen
https://www.readbyqxmd.com/read/28224923/high-throughput-sequencing-reveals-modulation-of-micrornas-in-vigna-mungo-upon-mungbean-yellow-mosaic-india-virus-inoculation-highlighting-stress-regulation
#12
Anirban Kundu, Sujay Paul, Avishek Dey, Amita Pal
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28223907/comparative-bioavailability-and-utilization-of-particular-forms-of-b12-supplements-with-potential-to-mitigate-b12-related-genetic-polymorphisms
#13
REVIEW
Cristiana Paul, David M Brady
CONTEXT: Three natural forms of vitamin B12 are commercially available: methylcobalamin (MeCbl), adenosylcobalamin (AdCbl), and hydroxycobalamin (OHCbl), all of which have been shown in clinical studies to improve vitamin B12 status. They are bioidentical to the B12 forms occurring in human physiology and animal foods. In contrast, cyanocobalamin (CNCbl), a synthetic B12 compound used for food fortification and in some supplements, occurs only in trace amounts in human tissues as a result of cyanide intake from smoking or other sources...
February 2017: Integrative Medicine
https://www.readbyqxmd.com/read/28210467/diversity-and-distribution-of-culturable-lactic-acid-bacterial-species-in-indonesian-sayur-asin
#14
Wibowo Mangunwardoyo, Abinawanto, Andi Salamah, Endang Sukara, Sulistiani, Achmad Dinoto
BACKGROUND AND OBJECTIVES: Lactic acid bacteria (LAB) play important roles in processing of Sayur Asin (spontaneously fermented mustard). Unfortunately, information about LAB in Indonesian Sayur Asin, prepared by traditional manufactures which is important as baseline data for maintenance of food quality and safety, is unclear. The aim of this study was to describe the diversity and distribution of culturable lactic acid bacteria in Sayur Asin of Indonesia. MATERIALS AND METHODS: Four Sayur Asin samples (fermentation liquor and fermented mustard) were collected at harvesting times (3-7 days after fermentation) from two traditional manufactures in Tulung Agung (TA) and Kediri (KDR), East Java provinces, Indonesia...
August 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/28206858/genetic-polymorphism-of-aedes-albopictus-population-inferred-from-nd5-gene-variabilities-in-subang-jaya-malaysia
#15
Nurul Adilah-Amrannudin, Mayamin Hamsidi, Nurul-Ain Ismail, Rodziah Ismail, Nazri Che Dom, Abu Hassan Ahmad, Mohd Fahmi Mastuki, Tengku Shahrul Anuar Tengku Ahmad Basri, Adira Khalid, Mohammad Muslim, Nurul Amalina Ahmad Daud, Siti Nazrina Camalxaman
This study was performed to establish the genetic variability of Aedes albopictus within Subang Jaya, Selangor, Malaysia, by using the nicotinamide adenine dinucleotide dehydrogenase 5 subunit (ND5) mitochondrial DNA (mtDNA) marker. A total of 90 samples were collected from 9 localities within an area of the Subang Jaya Municipality. Genetic variability was determined through the amplification and sequencing of a fragment of the ND5 gene. Eight distinct mtDNA haplotypes were identified. The evolutionary relationship of the local haplotypes alongside 28 reference strains was used to construct a phylogram, the analysis of which revealed low genetic differentiation in terms of both nucleotide and haplotype diversity...
December 2016: Journal of the American Mosquito Control Association
https://www.readbyqxmd.com/read/28197413/mechanism-of-reduced-susceptibility-to-fosfomycin-in-escherichia-coli-clinical-isolates
#16
Yasuo Ohkoshi, Toyotaka Sato, Yuuki Suzuki, Soh Yamamoto, Tsukasa Shiraishi, Noriko Ogasawara, Shin-Ichi Yokota
In recent years, multidrug resistance of Escherichia coli has become a serious problem. However, resistance to fosfomycin (FOM) has been low. We screened E. coli clinical isolates with reduced susceptibility to FOM and characterized molecular mechanisms of resistance and reduced susceptibility of these strains. Ten strains showing reduced FOM susceptibility (MIC ≥ 8 μg/mL) in 211 clinical isolates were found and examined. Acquisition of genes encoding FOM-modifying enzyme genes (fos genes) and mutations in murA that underlie high resistance to FOM were not observed...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28191013/quercetin-and-quercetin-rich-red-onion-extract-alter-pgc-1%C3%AE-promoter-methylation-and-splice-variant-expression
#17
Prasad P Devarshi, Aarin D Jones, Erin M Taylor, Barbara Stefanska, Tara M Henagan
Pgc-1α and its various isoforms may play a role in determining skeletal muscle mitochondrial adaptations in response to diet. 8 wks of dietary supplementation with the flavonoid quercetin (Q) or red onion extract (ROE) in a high fat diet (HFD) ameliorates HFD-induced obesity and insulin resistance in C57BL/J mice while upregulating Pgc-1α and increasing skeletal muscle mitochondrial number and function. Here, mice were fed a low fat (LF), high fat (HF), high fat plus quercetin (HF + Q), or high fat plus red onion extract (HF + RO) diet for 9 wks and skeletal muscle Pgc-1α isoform expression and DNA methylation were determined...
2017: PPAR Research
https://www.readbyqxmd.com/read/28188256/mgdg-pg-and-sqdg-regulate-the-activity-of-light-dependent-protochlorophyllide-oxidoreductase
#18
Michal Gabruk, Beata Myśliwa-Kurdziel, Jerzy Kruk
Light-dependent protochlorophyllide oxidoreductase (POR) is a plant enzyme involved in the chlorophyll biosynthesis pathway. POR reduces one of the double bonds of the protochlorophyllide (Pchlide) using NADPH and light. In the present paper, we found out that PG and SQDG are allosteric regulators of the nucleotide binding, which increase the affinity towards NADPH a hundred fold. Moreover, we showed for the first time that NADH can, like NADPH, form active complexes with Pchlide and POR, however at much higher concentrations...
February 10, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28186827/exploration-of-the-perceived-and-actual-benefits-of-omega-3-fatty-acids-and-the-impact-of-fads1-and-fads2-genetic-information-on-dietary-intake-and-blood-levels-of-epa-and-dha
#19
Kaitlin Roke
From a global health perspective, increased intake of omega-3 fatty acids (FAs), in particular eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are beneficial for human health. However, the consumption of EPA- and DHA-rich foods such as fatty fish is low in the Western diet. Therefore, finding new ways to motivate people to increase their consumption of omega-3 FAs is essential. To find effective ways to motivate individuals, understanding people's awareness of omega-3 FAs and how they obtain their knowledge about nutrition and health is critical...
March 2017: Applied Physiology, Nutrition, and Metabolism, Physiologie Appliquée, Nutrition et Métabolisme
https://www.readbyqxmd.com/read/28168762/developing-a-new-nonbinary-snp-fluorescent-multiplex-detection-system-for-forensic-application-in-china
#20
Yanfang Liu, Huidan Liao, Ying Liu, Juanjuan Guo, Yi Sun, Xiaoliang Fu, Ding Xiao, Jifeng Cai, Lingmei Lan, Pingli Xie, Lagabaiyila Zha
Nonbinary single-nucleotide polymorphisms (SNPs) are potential forensic genetic markers because that their discrimination power is greater than that of normal binary SNPs, and that they can detect highly degraded samples. We previously developed a nonbinary SNP multiplex typing assay. In the present study, we selected additional 20 nonbinary SNPs from the NCBI SNP database and verified them through pyrosequencing. These 20 nonbinary SNPs were analyzed using the fluorescent-labeled SNaPshot multiplex SNP typing method...
February 6, 2017: Electrophoresis
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