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https://www.readbyqxmd.com/read/28335474/coccolithoviruses-a-review-of-cross-kingdom-genomic-thievery-and-metabolic-thuggery
#1
Jozef I Nissimov, António Pagarete, Fangrui Ma, Sean Cody, David D Dunigan, Susan A Kimmance, Michael J Allen
Coccolithoviruses (Phycodnaviridae) infect and lyse the most ubiquitous and successful coccolithophorid in modern oceans, Emiliania huxleyi. So far, the genomes of 13 of these giant lytic viruses (i.e., Emiliania huxleyi viruses-EhVs) have been sequenced, assembled, and annotated. Here, we performed an in-depth comparison of their genomes to try and contextualize the ecological and evolutionary traits of these viruses. The genomes of these EhVs have from 444 to 548 coding sequences (CDSs). Presence/absence analysis of CDSs identified putative genes with particular ecological significance, namely sialidase, phosphate permease, and sphingolipid biosynthesis...
March 18, 2017: Viruses
https://www.readbyqxmd.com/read/28335465/schr%C3%A3-dinger-s-cheshire-cat-are-haploid-emiliania-huxleyi-cells-resistant-to-viral-infection-or-not
#2
Gideon J Mordecai, Frederic Verret, Andrea Highfield, Declan C Schroeder
Emiliania huxleyi is the main calcite producer on Earth and is routinely infected by a virus (EhV); a double stranded DNA (dsDNA) virus belonging to the family Phycodnaviridae. E. huxleyi exhibits a haplodiploid life cycle; the calcified diploid stage is non-motile and forms extensive blooms. The haploid phase is a non-calcified biflagellated cell bearing organic scales. Haploid cells are thought to resist infection, through a process deemed the "Cheshire Cat" escape strategy; however, a recent study detected the presence of viral lipids in the same haploid strain...
March 18, 2017: Viruses
https://www.readbyqxmd.com/read/28334887/avoidance-of-apobec3b-induced-mutation-by-error-free-lesion-bypass
#3
James I Hoopes, Amber L Hughes, Lauren A Hobson, Luis M Cortez, Alexander J Brown, Steven A Roberts
APOBEC cytidine deaminases mutate cancer genomes by converting cytidines into uridines within ssDNA during replication. Although uracil DNA glycosylases limit APOBEC-induced mutation, it is unknown if subsequent base excision repair (BER) steps function on replication-associated ssDNA. Hence, we measured APOBEC3B-induced CAN1 mutation frequencies in yeast deficient in BER endonucleases or DNA damage tolerance proteins. Strains lacking Apn1, Apn2, Ntg1, Ntg2 or Rev3 displayed wild-type frequencies of APOBEC3B-induced canavanine resistance (CanR)...
March 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334877/iron-mediates-catalysis-of-nucleic-acid-processing-enzymes-support-for-fe-ii-as-a-cofactor-before-the-great-oxidation-event
#4
C Denise Okafor, Kathryn A Lanier, Anton S Petrov, Shreyas S Athavale, Jessica C Bowman, Nicholas V Hud, Loren Dean Williams
Life originated in an anoxic, Fe2+-rich environment. We hypothesize that on early Earth, Fe2+ was a ubiquitous cofactor for nucleic acids, with roles in RNA folding and catalysis as well as in processing of nucleic acids by protein enzymes. In this model, Mg2+ replaced Fe2+ as the primary cofactor for nucleic acids in parallel with known metal substitutions of metalloproteins, driven by the Great Oxidation Event. To test predictions of this model, we assay the ability of nucleic acid processing enzymes, including a DNA polymerase, an RNA polymerase and a DNA ligase, to use Fe2+ in place of Mg2+ as a cofactor during catalysis...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334760/twin-primer-non-enzymatic-dna-assembly-an-efficient-and-accurate-multi-part-dna-assembly-method
#5
Jing Liang, Zihe Liu, Xi Z Low, Ee L Ang, Huimin Zhao
DNA assembly forms the cornerstone of modern synthetic biology. Despite the numerous available methods, scarless multi-fragment assembly of large plasmids remains challenging. Furthermore, the upcoming wave in molecular biological automation demands a rethinking of how we perform DNA assembly. To streamline automation workflow and minimize operator intervention, a non-enzymatic assembly method is highly desirable. Here, we report the optimization and operationalization of a process called Twin-Primer Assembly (TPA), which is a method to assemble polymerase chain reaction-amplified fragments into a plasmid without the use of enzymes...
February 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334749/ctg-repeat-targeting-oligonucleotides-for-down-regulating-huntingtin-expression
#6
Eman M Zaghloul, Olof Gissberg, Pedro M D Moreno, Lee Siggens, Mattias Hällbrink, Anna S Jørgensen, Karl Ekwall, Rula Zain, Jesper Wengel, Karin E Lundin, C I Edvard Smith
Huntington's disease (HD) is a fatal, neurodegenerative disorder in which patients suffer from mobility, psychological and cognitive impairments. Existing therapeutics are only symptomatic and do not significantly alter the disease progression or increase life expectancy. HD is caused by expansion of the CAG trinucleotide repeat region in exon 1 of the Huntingtin gene (HTT), leading to the formation of mutant HTT transcripts (muHTT). The toxic gain-of-function of muHTT protein is a major cause of the disease...
February 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28333574/cytosolic-nucleic-acid-sensors-and-innate-immune-regulation
#7
Daisuke Ori, Motoya Murase, Taro Kawai
During viral and bacterial infections, pathogen-derived cytosolic nucleic acids are recognized by the intracellular RNA sensors retinoic acid-inducible gene I and melanoma-differentiated gene 5 and intracellular DNA sensors, including cyclic-di-GMP-AMP synthase, absent in melanoma 2, interferon (IFN)-gamma inducible protein 16, polymerase III, and so on. Binding of intracellular nucleic acids to these sensors activates downstream signaling cascades, resulting in the production of type I IFNs and pro-inflammatory cytokines to induce appropriate systematic immune responses...
March 23, 2017: International Reviews of Immunology
https://www.readbyqxmd.com/read/28333044/effects-of-c-n-ratio-on-nitrous-oxide-production-from-nitrification-in-a-laboratory-scale-biological-aerated-filter-reactor
#8
Qiang He, Yinying Zhu, Leilei Fan, Hainan Ai, Xiaoliu Huangfu, Mei Chen
Emission of nitrous oxide (N2O) during biological wastewater treatment is of growing concern. This paper reports findings of the effects of carbon/nitrogen (C/N) ratio on N2O production rates in a laboratory-scale biological aerated filter (BAF) reactor, focusing on the biofilm during nitrification. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and microelectrode technology were utilized to evaluate the mechanisms associated with N2O production during wastewater treatment using BAF...
March 2017: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/28332898/herpes-simplex-virus-1-and-cytomegalovirus-dnas-detection-in-the-inner-ear-of-implanted-patients-with-non-congenital-infection
#9
Walter Di Nardo, Roberta Anzivino, Paola Cattani, Rosaria Santangelo, Eugenio De Corso, Gaetano Paludetti
CONCLUSIONS: The detection of cytomegalovirus (CMV) and herpes simplex virus-1 (HSV-1) genome in perilymph of patients with negative serology or clinical history for congenital infections supports the hypothesis that Herpesviridae, even after acquired postnatal infections, could remain in latent phase in the spiral ganglion and damage the cochlea by a possible subsequent reactivation. Further studies are needed to identify the markers of such reactivation. OBJECTIVE: To identify the presence of certain viral species in the endolabyrinthic fluid of deaf patients with non-congenital infection...
March 23, 2017: Acta Oto-laryngologica
https://www.readbyqxmd.com/read/28332162/isolation-of-taxol-producing-endophytic-fungi-from-iranian-yew-through-novel-molecular-approach-and-their-effects-on-human-breast-cancer-cell-line
#10
Abdollah Kasaei, Mohsen Mobini-Dehkordi, Foruzandeh Mahjoubi, Behnaz Saffar
Taxol or paclitaxel, an approved drug by the Food and Drug Administration, is being used for the treatment of human cancers. This study aimed to isolate and determine different species of native endophytic fungi from Iranian Taxus baccata (yew) plants located in the northern forests of Iran. To do so, a novel molecular screening approach was performed for 50 isolated endophytic fungi through amplification of exon No. 1 of taxadine synthase as a key gene in taxol production pathway. We used effective colony-polymerase chain reaction technique for rapid screening of potent taxol-producing fungi instead of genomic DNA extraction...
March 23, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28331418/optimization-of-pcr-condition-the-first-study-of-high-resolution-melting-technique-for-screening-of-apoa1-variance
#11
Hesty Wahyuningsih, Ferdy K Cayami, Udin Bahrudin, Mochamad A Sobirin, Farmaditya Ep Mundhofir, Sultana Mh Faradz, Ichiro Hisatome
BACKGROUND: High resolution melting (HRM) is a post-PCR technique for variant screening and genotyping based on the different melting points of DNA fragments. The advantages of this technique are that it is fast, simple, and efficient and has a high output, particularly for screening of a large number of samples. APOA1 encodes apolipoprotein A1 (apoA1) which is a major component of high density lipoprotein cholesterol (HDL-C). This study aimed to obtain an optimal quantitative polymerase chain reaction (qPCR)-HRM condition for screening of APOA1 variance...
March 2017: Yonago Acta Medica
https://www.readbyqxmd.com/read/28331161/isolation-of-cyanobacterial-mutants-exhibiting-growth-defects-under-microoxic-conditions-by-transposon-tagging-mutagenesis-of-synechocystis-sp-pcc-6803
#12
Kazuki Terauchi, Riho Sobue, Yuho Furutani, Rina Aoki, Yuichi Fujita
Cyanobacteria are photosynthetic prokaryotes that perform oxygenic photosynthesis by extracting electrons from water, with the generation of oxygen as a byproduct. Cyanobacteria use oxygen not only for respiration to produce energy in the dark but also for biosynthesis of various metabolites, such as heme and chlorophyll. Oxygen levels dynamically fluctuate in the field environments, from hyperoxic at daytime to almost anaerobic at night. Thus, adaptation to anaerobiosis should be important for cyanobacteria to survive in low-oxygen and anaerobic environments...
March 22, 2017: Journal of General and Applied Microbiology
https://www.readbyqxmd.com/read/28331082/kaposi-s-sarcoma-associated-herpesvirus-hijacks-rna-polymerase-ii-to-create-a-viral-transcriptional-factory
#13
Christopher Phillip Chen, Yuanzhi Lyu, Frank Chuang, Kazushi Nakano, Chie Izumiya, Di Jin, Mel Campbell, Yoshihiro Izumiya
Locally concentrated nuclear factors ensure efficient binding to the DNA templates, facilitating RNA polymerase II recruitment and frequent reutilization of stable pre-initiation complexes. Here we have uncovered a mechanism for effective viral transcription by focal assembly of RNA polymerase II around KSHV genomes in the host cell nucleus. Using immunofluorescent labeling of latent nuclear antigen (LANA) protein, together with fluorescence in situ RNA hybridization (RNA-FISH) of the intron region of immediate-early transcripts, we visualized active transcription of viral genomes in naturally infected cells...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28330330/a-combined-chloroplast-atpb-rbcl-and-trnl-f-phylogeny-unveils-the-ancestry-of-balsams-impatiens-spp-in-the-western-ghats-of-india
#14
P P Shajitha, N R Dhanesh, P J Ebin, Joseph Laly, Devassy Aneesha, John Reshma, Jomy Augustine, Mathew Linu
Only a few Impatiens spp. from South India (one of the five centers of diversity for Impatiens species) were included in the published datum of molecular phylogeny of the family Balsaminaceae. The present investigation is a novel attempt to reveal the phylogenetic association of Impatiens species of South India, by placing them in the global phylogeny of Impatiens based on a combined analysis of two chloroplast genes. Thirty species of genus Impatiens were collected from different locations of South India. Total genomic DNA was extracted from fresh plant leaf, and polymerase chain reaction was carried out using atpB-rbcL and trnL-F intergenic spacer-specific forward and reverse primers...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330158/a-simple-and-efficient-agrobacterium-tumefaciens-mediated-plant-transformation-of-brassica-rapa-ssp-pekinensis
#15
Venkidasamy Baskar, Baniekal H Gangadhar, Se Won Park, Shivraj Hariram Nile
The present study aims to investigate the numerous factors influencing Agrobacterium tumefaciens-mediated genetic transformation of Chinese cabbage (Brassica rapa ssp. pekinensis). Factors affecting transformation efficiency, such as age of explants, Agrobacterium concentration, and effect of acetosyringone, pre-cultivation, infection and co-cultivation time of Agrobacterium were examined. The pre-cultured hypocotyls from young seedlings prior to exposure to Agrobacterium showed higher shoot regeneration. The plant transformation with the modest A...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330131/an-efficient-protocol-for-isolation-of-inhibitor-free-nucleic-acids-even-from-recalcitrant-plants
#16
Mohammad Hossein Rezadoost, Mojtaba Kordrostami, Hassan Hassani Kumleh
For fast and easy isolation of inhibitor-free genomic DNA even from the toughest plant leaf samples, including those high in polyphenols and polysaccharides, a protocol has been developed. To prevent the solubility of polysaccharides in the DNA extract, high salt concentration (1.4 M) was used in the extraction buffer. Polyvinylpyrrolidone (PVP) was used for the removal of polyphenols as polymerase chain reaction (PCR) inhibitors. Proteins like various enzymes were degraded by proteinase K and removed by centrifugation from plant extracts during the isolation process resulting in pure DNA and RNA ready to use in downstream applications including PCR, quantitative polymerase chain reaction (qPCR), ligation, restriction and sequencing...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329680/major-roles-for-pyrimidine-dimers-nucleotide-excision-repair-and-atr-in-the-alternative-splicing-response-to-uv-irradiation
#17
Manuel J Muñoz, Nicolás Nieto Moreno, Luciana E Giono, Adrián E Cambindo Botto, Gwendal Dujardin, Giulia Bastianello, Stefania Lavore, Antonio Torres-Méndez, Carlos F M Menck, Benjamin J Blencowe, Manuel Irimia, Marco Foiani, Alberto R Kornblihtt
We have previously found that UV irradiation promotes RNA polymerase II (RNAPII) hyperphosphorylation and subsequent changes in alternative splicing (AS). We show now that UV-induced DNA damage is not only necessary but sufficient to trigger the AS response and that photolyase-mediated removal of the most abundant class of pyrimidine dimers (PDs) abrogates the global response to UV. We demonstrate that, in keratinocytes, RNAPII is the target, but not a sensor, of the signaling cascade initiated by PDs. The UV effect is enhanced by inhibition of gap-filling DNA synthesis, the last step in the nucleotide excision repair pathway (NER), and reduced by the absence of XPE, the main NER sensor of PDs...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28328323/an-adaptable-high-throughput-technology-enabling-the-identification-of-specific-transcription-modulators
#18
Tim Bergbrede, Emily Hoberg, Nils-Göran Larsson, Maria Falkenberg, Claes M Gustafsson
Mitochondria harbor the oxidative phosphorylation (OXPHOS) system, which under aerobic conditions produces the bulk of cellular adenosine triphosphate (ATP). The mitochondrial genome encodes key components of the OXPHOS system, and it is transcribed by the mitochondrial RNA polymerase, POLRMT. The levels of mitochondrial transcription correlate with the respiratory activity of the cell. Therefore, compounds that can increase or decrease mitochondrial gene transcription may be useful for fine-tuning metabolism and could be used to treat metabolic diseases or certain forms of cancer...
April 2017: SLAS Discov
https://www.readbyqxmd.com/read/28327808/prevalence-and-distribution-of-angiostrongylus-cantonensis-nematoda-angiostrongylidae-in-achatina-fulica-mollusca-gastropoda-in-baixada-santista-s%C3%A3-o-paulo-brazil
#19
Laura Rocha Guerino, Iracy Lea Pecora, Marcel Sabino Miranda, Cryslaine Aguiar-Silva, Omar Dos Santos Carvalho, Roberta Lima Caldeira, Reinaldo José da Silva
INTRODUCTION: Angiostrongylus cantonensis is causes eosinophilic meningoencephalitis in humans. Worldwide expansion of this nematode is linked to the dispersion of their hosts. This study aimed to determine the prevalence of A. cantonensis infection in Achatina fulica in the nine municipalities that make up Baixada Santista, São Paulo, Brazil. METHODS: Angiostrongylus cantonensis larvae were analyzed using optical microscopy. We performed polymerase chain reaction and restriction fragment length polymorphism using restriction endonuclease ClaI, directed to the internal transcribed spacer region 2 of A...
January 2017: Revista da Sociedade Brasileira de Medicina Tropical
https://www.readbyqxmd.com/read/28327800/trypanosoma-cruzi-i-genotype-among-isolates-from-patients-with-chronic-chagas-disease-followed-at-the-evandro-chagas-national-institute-of-infectious-diseases-fiocruz-brazil
#20
Tatiana da Silva Fonseca de Oliveira, Barbara Neves Dos Santos, Tainah Silva Galdino, Alejandro Marcel Hasslocher-Moreno, Otilio Machado Pereira Bastos, Maria Auxiliadora de Sousa
INTRODUCTION: Trypanosoma cruzi is the etiologic agent of Chagas disease in humans, mainly in Latin America. Trypanosome stocks were isolated by hemoculture from patients followed at Evandro Chagas National Institute of Infectious Diseases (FIOCRUZ) and studied using different approaches. METHODS: For species and genotype identification, the stocks were analyzed by parasitological techniques, polymerase chain reaction assays targeted to specific DNA sequences, isoenzyme patterns, besides sequencing of a polymorphic locus of TcSC5D gene (one stock)...
January 2017: Revista da Sociedade Brasileira de Medicina Tropical
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