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https://www.readbyqxmd.com/read/27911492/rolling-circle-amplification-with-chemically-modified-nucleoside-triphosphates
#1
Marcel Hollenstein, Masad J Damha
Modified nucleoside triphosphates (dN*TPs) represent facile and versatile precursors for the introduction of chemical diversity into nucleic acids. While dN*TPs have been utilized in a plethora of practical applications, very little attention has been devoted to the assessment of their compatibility with isothermal amplification strategies. In this context, rolling circle amplification (RCA) is a wide-spread enzymatic replication method in which small single-stranded DNA (ssDNA) circles serve as templates in primer extension reactions yielding very long, ssDNA products...
December 1, 2016: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/27910773/giant-oyster-mushroom-pleurotus-giganteus-agaricomycetes-enhances-adipocyte-differentiation-and-glucose-uptake-via-activation-of-ppar%C3%AE-and-glucose-transporters-1-and-4-in-3t3-l1-cells
#2
Puvaneswari Paravamsivam, Chua Kek Heng, Sri Nurestri Abdul Malek, Vikineswary Sabaratnam, Ravishankar Ram M, Umah Rani Kuppusamy
The edible mushroom Pleurotus giganteus was tested for its effect on adipocyte differentiation and glucose uptake activity in 3T3-L1 cells. The basidiocarps of P. giganteus were soaked in methanol to obtain a crude methanol extract and then fractionated to obtain an ethyl acetate extract. In this study, cell proliferation was measured using an MTT assay, lipid accumulation using an Oil Red O assay, and glucose uptake using a fluorescence glucose uptake assay. Gene expression was measured via real-time polymerase chain reaction analysis with TaqMan primer...
2016: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/27910762/genetic-diversity-and-relationships-of-24-strains-of-genus-auricularia-agaricomycetes-assessed-using-srap-markers
#3
Ping Du, Tian-Xu Cao, Bao-Kai Cui, Yuan Yuan, Yu-Cheng Dai
Auricularia species are well known for their traditional edible and medicinal importance. In this study, sequence-related amplified polymorphism (SRAP) markers were used to evaluate the genetic diversity and relationships of 24 Auricularia strains obtained from different ecological regions of China. A total of 402 polymorphic loci were detected using 11 SRAP primer combinations with 100% polymorphic loci. The similarity coefficient ranged from 0.662 to 0.903, with an average of 0.73. Cluster analysis using the pair-group method using arithmetic average, based on the data from SRAP loci amplified by 11 primer pairs, showed that 24 Auricularia strains were distinguished into 4 groups with 73% similarity...
2016: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/27908771/molecular-detection-and-genetic-characterization-of-babesia-theileria-and-anaplasma-amongst-apparently-healthy-sheep-and-goats-in-the-central-region-of-turkey
#4
Mo Zhou, Shinuo Cao, Ferda Sevinc, Mutlu Sevinc, Onur Ceylan, Sepil Ekici, Charoonluk Jirapattharasate, Paul Franck Adjou Moumouni, Mingming Liu, Guanbo Wang, Aiko Iguchi, Patrick Vudriko, Hiroshi Suzuki, Xuenan Xuan
Babesia spp., Theileria spp. and Anaplasma spp. are significant tick-borne pathogens of livestock globally. In this study, we investigated the presence and distribution of Babesia ovis, Theileria ovis and Anaplasma ovis in 343 small ruminants (249 sheep and 94 goats) from 13 towns in the Central Anatolia region of Turkey using species-specific PCR assays. The PCR were conducted using the primers based on the B. ovis ssu rRNA (BoSSUrRNA), T. ovis ssu rRNA (ToSSUrRNA) and A. ovis major surface protein 4 (AoMSP4) genes, respectively...
November 16, 2016: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/27908595/polymerase-chain-reaction-with-nearby-primers
#5
Ravil R Garafutdinov, Aizilya A Galimova, Assol R Sakhabutdinova
DNA analysis of biological specimens containing degraded nucleic acids such as mortal remains, archaeological artefacts, forensic samples etc. has gained more attention in recent years. DNA extracted from these samples is often inapplicable for conventional polymerase chain reaction (PCR), so for its amplification the nearby primers are commonly used. Here we report the data that clarify the features of PCR with nearby and abutting primers. We have shown that the proximity of primers leads to significant reduction of the reaction time and ensures the successful performance of DNA amplification even in the presence of PCR inhibitors...
November 28, 2016: Analytical Biochemistry
https://www.readbyqxmd.com/read/27908244/free-initiation-factors-eif4a-and-eif4b-are-dispensable-for-translation-initiation-on-uncapped-mrnas
#6
P A Sakharov, S Ch Agalarov
The formation of ribosomal 48S initiation complexes at the start AUG codon of uncapped mRNA leader sequences was studied using the methodology of primer extension inhibition (toe-printing). The experiments were performed in the system composed of purified individual components required for translation initiation. The formation of ribosomal 48S initiation complexes at the initiation codon was tested depending on the presence of the initiation factors eIF4F, eIF4A, and eIF4B. Several mRNAs containing short leader sequences lacking the extended secondary structure were studied...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27907856/cdna-aflp-analysis-of-transcripts-induced-in-chickpea-plants-by-tio2-nanoparticles-during-cold-stress
#7
Saeed Amini, Reza Maali-Amiri, Rahmat Mohammadi, Seyyedeh-Sanam Kazemi-Shahandashti
We evaluated the effect of TiO2 nanoparticles (NPs) on cold tolerance (CT) development in two chickpea (Cicer arietinum L.) genotypes (Sel96Th11439, cold tolerant, and ILC533, cold susceptible) by using cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique during the first and sixth days of cold stress (CS) at 4 °C. Selective amplification by primer combinations generated 4200 transcript-derived fragments (TDFs) while 100 of them (2.62%) were differentially expressed. During CS, 60 differentially expressed TDFs of TiO2 NPs-treated plants were cloned and 10 of them produced successfully readable sequences...
November 22, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27907225/informativeness-of-ngs-analysis-for-vaginal-fluid-identification
#8
Saverio Giampaoli, Elisabetta DeVittori, Federica Valeriani, Andrea Berti, Vincenzo Romano Spica
The identification of vaginal fluids in forensic examinations plays an important role in crime scene reconstruction. Molecular detection of vaginal bacterial communities can lead to the correct discrimination of body fluids. These kinds of studies can be performed through multiplex real-time PCR using primers for a specific selection of bacteria. The availability of next-generation sequencing (NGS) protocols provided for the extension of the analysis to evaluate the prokaryotes present in specimens. In this study, DNA was extracted from 18 samples (vaginal, oral, fecal, yoghurt) and analyzed by real-time PCR and NGS...
December 1, 2016: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/27907089/detection-of-human-papillomavirus-infection-in-patients-with-vaginal-intraepithelial-neoplasia
#9
Cristina Lamos, Charlotte Mihaljevic, Sebastian Aulmann, Thomas Bruckner, Christoph Domschke, Markus Wallwiener, Carmen Paringer, Herbert Fluhr, Sarah Schott, Christine Dinkic, Janina Brucker, Michael Golatta, Lisa Gensthaler, Michael Eichbaum, Christof Sohn, Joachim Rom
INTRODUCTION: Vaginal intraepithelial neoplasia (VAIN) is a pre-malignant lesion, potentially leading to vaginal cancer. It is a rare disease, representing less than 1% of all intraepithelial neoplasia of the female genital tract. Similar to cervical intraepithelial neoplasia (CIN), there are three different grades of VAIN. VAIN 1 is also known as a low-grade squamous intraepithelial lesion (LSIL), whereas VAIN 2 and VAIN 3 both represent high-grade squamous intraepithelial lesions (HSIL)...
2016: PloS One
https://www.readbyqxmd.com/read/27907004/in-vitro-variant-surface-antigen-expression-in-plasmodium-falciparum-parasites-from-a-semi-immune-individual-is-not-correlated-with-var-gene-transcription
#10
Ellen Inga Bruske, Sandra Dimonte, Corinna Enderes, Serena Tschan, Matthias Flötenmeyer, Iris Koch, Jürgen Berger, Peter Kremsner, Matthias Frank
Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is considered to be the main variant surface antigen (VSA) of Plasmodium falciparum and is mainly localized on electron-dense knobs in the membrane of the infected erythrocyte. Switches in PfEMP1 expression provide the basis for antigenic variation and are thought to be critical for parasite persistence during chronic infections. Recently, strain transcending anti-PfEMP1 immunity has been shown to develop early in life, challenging the role of PfEMP1 in antigenic variation during chronic infections...
2016: PloS One
https://www.readbyqxmd.com/read/27905281/identification-of-acanthamoeba-genotypes-in-pools-and-stagnant-water-in-ponds-in-sistan-region-in-southeast-iran
#11
Ali Aghajani, Mansour Dabirzadeh, Yahya Maroufi, Hossein Hooshyar
OBJECTIVE: Acanthamoeba is one of the most abundant free-living amoebas that is widely distributed in natural and artificial environment resources. Acanthamoeba pathogenic genotypes cause chronic human diseases including amoebic keratitis and granulomatous amoebic encephalitis. The aim of this study was to determine and identify Acanthamoeba genotypes residing in pools and stagnant water in ponds in Sistan region in southeast Iran. This descriptive study was conducted at the Parasitology Laboratory, School of Medicine, Zabol University of Medical Sciences...
September 2016: Türkiye Parazitolojii Dergisi
https://www.readbyqxmd.com/read/27904520/a-diagnostic-one-step-real-time-reverse-transcription-polymerase-chain-reaction-method-for-accurate-detection-of-influenza-virus-type-a
#12
Mohammad Amin Behzadi, Mazyar Ziyaeyan, Abdolvahab Alborzi
INTRODUCTION: Influenza A is known as a public health concern worldwide. In this study, a novel one-step real-time reverse transcription polymerase chain reaction (rtRT-PCR) assay was designed and optimized for the detection of influenza A viruses. MATERIAL AND METHODS: The primers and probe were designed based on the analysis of 90 matrix nucleotide sequence data of influenza type A subtypes from the GenBank database of the National Center for Biotechnology Information (NCBI)...
December 1, 2016: Archives of Medical Science: AMS
https://www.readbyqxmd.com/read/27904465/simultaneous-detection-of-three-bacterial-seed-borne-diseases-in-rice-using-multiplex-polymerase-chain-reaction
#13
In Jeong Kang, Mi-Hyung Kang, Tae-Hwan Noh, Hyeong Kwon Shim, Dong Bum Shin, Suggi Heu
Burkholderia glumae (bacterial grain rot), Xanthomonas oryzae pv. oryzae (bacterial leaf blight), and Acidovorax avenae subsp. avenae (bacterial brown stripe) are major seedborne pathogens of rice. Based on the 16S and 23S rDNA sequences for A. avenae subsp. avenae and B. glumae, and transposase A gene sequence for X. oryzae pv. oryzae, three sets of primers had been designed to produce 402 bp for B. glumae, 490 bp for X. oryzae, and 290 bp for A. avenae subsp. avenae with the 63°C as an optimum annealing temperature...
December 2016: Plant Pathology Journal
https://www.readbyqxmd.com/read/27904399/identification-of-alleles-of-puroindoline-genes-and-their-effect-on-wheat-triticum-aestivum-l-grain-texture
#14
Mária Presinszká, Klára Štiasna, Tomáš Vyhnánek, Václav Trojan, Eva Mrkvicová, Luděk Hřivna, Ladislav Havel
Grain hardness is one of the most important quality characteristics of wheat (Triticum aestivum L.). It is a significant property of wheat grains and relates to milling quality and end product quality. Grain hardness is caused by the presence of puroindoline genes (Pina and Pinb). A collection of 25 genotypes of wheat with unusual grain colour (blue aleurone, purple and white pericarp, yellow endosperm) was studied by polymerase chain reaction (PCR) for the diversity within Pina and Pinb (alleles: Pina-D1a, Pina-D1b, Pinb-D1a, Pinb- -D1b, Pinb-D1c and Pinb-D1d)...
March 2016: Food Technology and Biotechnology
https://www.readbyqxmd.com/read/27902725/antimicrobial-potential-identification-and-phylogenetic-affiliation-of-wild-mushrooms-from-two-sub-tropical-semi-evergreen-indian-forest-ecosystems
#15
Lallawmsanga, Ajit Kumar Passari, Vineet Kumar Mishra, Vincent Vineeth Leo, Bhim Pratap Singh, Geetha Valliammai Meyyappan, Vijai Kumar Gupta, Sivakumar Uthandi, Ramesh Chandra Upadhyay
The diversity of wild mushrooms was investigated from two protected forest areas in India and 231 mushroom specimens were morphologically identified. Among them, 76 isolates were screened for their antimicrobial potential against seven bacterial and fungal pathogens. Out of 76 isolates, 45 isolates which displayed significant antimicrobial activities were identified using ITS rRNA gene amplification and subsequently phylogenetically characterized using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers...
2016: PloS One
https://www.readbyqxmd.com/read/27902440/synechococcus-diversity-along-a-trophic-gradient-in-the-osterseen-lake-district-bavaria
#16
Joachim Ruber, Franziska Bauer, Andrew Millard, Uta Raeder, Jürgen Geist, Katrin Zwirglmaier
Picocyanobacteria are important primary producers in freshwater, however there is still a knowledge gap regarding their diversity at the strain level. For this reason, the microbial diversity of four lakes with different trophic states was investigated by sequencing of the 16S rRNA gene using universal primers. The study was performed in selected lakes of the Osterseen Lake District, Germany, from 2012 to 2014 (Lake Schiffhuettensee: eutrophic; Lake Ostersee: meso-oligotrophic; Lake Groebensee: oligotrophic; Lake Lustsee: oligotrophic)...
November 1, 2016: Microbiology
https://www.readbyqxmd.com/read/27900685/assessing-bacterial-and-fungal-diversity-in-the-plant-endosphere
#17
Bernd Wemheuer, Franziska Wemheuer
Plants are colonized various microorganisms including endophytes. These microbes can play an important role in agricultural production as they promote plant growth and/or enhance the resistance of their host plant against diseases and environmental stress conditions. Although culture-independent molecular approaches such as DNA barcoding have greatly enhanced our understanding of bacterial and fungal endophyte communities, there are some methodical problems when investigating endophyte diversity. One main issue are sequence contaminations such as plastid-derived rRNA gene sequences which are co-amplified due to their high homology to bacterial 16S rRNA genes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900264/a-genomic-study-on-distribution-of-human-leukocyte-antigen-hla-a-and-hla-b-alleles-in-lak-population-of-iran
#18
Farhad Shahsavar, Ali-Mohammad Varzi, Seyyed Amir Yasin Ahmadi
Anthropological studies based on the highly polymorphic gene, human leukocyte antigen (HLA), provide useful information for bone marrow donor registry, forensic medicine, disease association studies, as well as infertility treatment, designing peptide vaccines against tumors, and infectious or autoimmune diseases. The aim of this study was to determine HLA-A and HLA-B allele frequencies in 100 unrelated Lak/lᴂk/individuals from Lorestan province of Iran. Finally, we compared the results with that previously described in Iranian population...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27899967/heteroplasmy-of-mutant-mitochondrial-dna-a10398g-and-analysis-of-its-prognostic-value-in-non-small-cell-lung-cancer
#19
Yuexiao Qi, Yuehua Wei, Qiaoli Wang, Hui Xu, You Wang, Anqi Yao, Hui Yang, Yan Gao, Fuxiang Zhou
Mitochondrial dysfunction is associated with pathogenic mitochondrial (mt)DNA mutations. The majority of mtDNA point mutations have a heteroplasmic status, which is defined as the coexistence of wild-type and mutated DNA within a cell or tissue. Previous findings demonstrated that certain mtDNA heteroplasmic mutations contribute to widely spread chronic diseases, including cancer, and alterations in the heteroplasmy level are associated with the clinical phenotype and severity of cancer. In the present study, the proportions of mutant mtDNA 10398G were assessed using amplification-refractory mutation system-quantitative polymerase chain reaction (PCR) assay in 129 non-small cell lung cancer (NSCLC) tissue samples...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899620/mrprimerv-a-database-of-pcr-primers-for-rna-virus-detection
#20
Hyerin Kim, NaNa Kang, KyuHyeon An, Doyun Kim, JaeHyung Koo, Min-Soo Kim
Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database...
November 29, 2016: Nucleic Acids Research
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