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Ribosomal DNA

Zachary Villarreal, Nicole Stephenson, Janet Foley
Increasing rates of Rocky Mountain spotted fever (RMSF) in the southwestern United States and northern Mexico underscore the importance of studying the ecology of the brown dog tick, Rhipicephalus sanguineus, the vector in that region. This species is reported to comprise distinct tropical and temperate lineages which may differ in vectorial capacity for RMSF and which are hypothesized to be limited in their geographical range by climatic conditions. In this study, lineage was determined for ticks from nine locations in California, Arizona, and Mexico by DNA sequencing of 12S, 16S, and D-loop ribosomal RNA...
March 19, 2018: Journal of Parasitology
Gustavo F Paz, Jeronimo M N Rugani, Andreza P Marcelino, Célia M F Gontijo
The aim of this study was to evaluate the relationship between naturally occurring Leishmania spp. infections in dogs (Canis familiaris) and the practical implications of the use of serological and molecular methods to confirm diagnoses. The study population consisted of 96 domestic dogs in southeastern Brazil. Serum samples were tested for the presence of anti-Leishmania immunoglobulin G (IgG) antibodies using four commercial canine visceral leishmaniasis kits. Dogs confirmed positive by immunofluorescence antibody test (IFAT) were culled and samples from mesenteric lymph nodes, spleen border, bone marrow and ear skin were taken and submitted to DNA extraction...
March 12, 2018: Acta Tropica
Stephen S Curran, Eric E Pulis, Michael J Andres, Robin M Oversteet
Two cryptic species of haploporid digeneans belonging in Saccocoelioides are described from Costa Rica; one from a poeciliid fish Poecilia gillii and the other from a characid fish, Astyanx aeneus. Traditional morphological features are examined and found to be largely inefficient for differentiate among new species and 20 New World congeners. Comparison of ribosomal DNA sequences among the 2 new species, 2 North American, 4 Middle American, and 3 South American species of Saccocoelioides, including the type-species Saccocoelioides nanii from Argentina and Saccocoelioides sogandaresi from Texas, is effective for differentiating among these species...
March 16, 2018: Journal of Parasitology
Amit Gaba, Lisanework E Ayalew, Amrutlal Patel, Pankaj Kumar, Suresh K Tikoo
Adenovirus protein VIII appears to connect core with the inner surface of the adenovirus capsid. Since protein- protein interactions are central to virus replication, identification of proteins interacting with protein VIII may help in understanding their role in adenovirus infection. Our yeast two hybrid assay indicated that protein VIII interacts with eukaryotic initiation factor 6 (eIF6). These findings were confirmed by GST-pull down assay, bimolecular fluorescent complementation assay and co-immunoprecipitation assay in plasmid DNA transfected and BAdV-3 infected cells...
March 15, 2018: Cellular Microbiology
Bouchra Trari, Mohamed Dakki
The Anopheles maculipennis complex has been implicated in the transmission of malaria, which was endemic in Morocco until 2010. Climate change, intensification of international travel and the permanent presence of the vector increase the risk of malaria re-emergence. Using polymerase chain reaction assay (PCR), this study attempts to identify the possible presence of the Maculipennis complex in several areas of Morocco, based on the concept of risk. Eighty-six mosquito specimens were analyzed using PCR amplification of the ITS2 (Internal Transcribed Spacer 2) sequence of ribosomal DNA...
March 5, 2018: Eastern Mediterranean Health Journal, la Revue de Santé de la Méditerranée Orientale
Sarmila Majumder, Kalpana Ghoshal, Jharna Datta, David Spencer Smith, Shoumei Bai, Samson T Jacob
No abstract text is available yet for this article.
March 9, 2018: Journal of Biological Chemistry
Davide Moiani, Daryl A Ronato, Chris A Brosey, Andrew S Arvai, Aleem Syed, Jean-Yves Masson, Elena Petricci, John A Tainer
For inhibitor design, as in most research, the best system is question dependent. We suggest structurally defined allostery to design specific inhibitors that target regions beyond active sites. We choose systems allowing efficient quality structures with conformational changes as optimal for structure-based design to optimize inhibitors. We maintain that evolutionarily related targets logically provide molecular avatars, where this Sanskrit term for descent includes ideas of functional relationships and of being a physical embodiment of the target's essential features without requiring high sequence identity...
2018: Methods in Enzymology
G Schiavo, M G Strillacci, A Ribani, S Bovo, S I Roman-Ponce, S Cerolini, F Bertolini, A Bagnato, L Fontanesi
Mitochondrial DNA (mtDNA) insertions have been detected in the nuclear genome of many eukaryotes. These sequences are pseudogenes originated by horizontal transfer of mtDNA fragments into the nuclear genome, producing nuclear DNA sequences of mitochondrial origin (numt). In this study we determined the frequency and distribution of mtDNA-originated pseudogenes in the turkey (Meleagris gallopavo) nuclear genome. The turkey reference genome (Turkey_2.01) was aligned with the reference linearized mtDNA sequence using last...
March 9, 2018: Animal Genetics
Emma K Wear, Elizabeth G Wilbanks, Craig E Nelson, Craig A Carlson
Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re-evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time-series of DNA samples from the temperate coastal Santa Barbara Channel...
March 9, 2018: Environmental Microbiology
Miranda Prats-van der Ham, Juan Tatay-Dualde, Ángel Gómez-Martín, Juan Carlos Corrales, Antonio Contreras, Antonio Sánchez, Christian de la Fe
Mycoplasma capricolum subsp. capricolum (Mcc) is one of the causative agents of contagious agalactia, and antimicrobial therapy is the most commonly applied measure to treat outbreaks of this disease. Macrolides and lincosamides bind specifically to nucleotides at domains II and V of the 23S rRNA. Furthermore, rplD and rplV genes encode ribosomal proteins L4 and L22, which are also implicated in the macrolide binding site. The aim of this work was to study the relationship between mutations in these genes and the acquisition of macrolide and lincosamide resistance in Mcc...
March 2018: Veterinary Microbiology
Lauriane Simon, Fernando A Rabanal, Tristan Dubos, Cecilia Oliver, Damien Lauber, Axel Poulet, Alexander Vogt, Ariane Mandlbauer, Samuel Le Goff, Andreas Sommer, Hervé Duborjal, Christophe Tatout, Aline V Probst
Organized in tandem repeat arrays in most eukaryotes and transcribed by RNA polymerase III, expression of 5S rRNA genes is under epigenetic control. To unveil mechanisms of transcriptional regulation, we obtained here in depth sequence information on 5S rRNA genes from the Arabidopsis thaliana genome and identified differential enrichment in epigenetic marks between the three 5S rDNA loci situated on chromosomes 3, 4 and 5. We reveal the chromosome 5 locus as the major source of an atypical, long 5S rRNA transcript characteristic of an open chromatin structure...
March 6, 2018: Nucleic Acids Research
Radka Symonová, Iva Vrbová, Dunja K Lamatsch, Jürgen Paar, Renate Matzke-Karasz, Olivier Schmit, Koen Martens, Stefan Müller
Transitions from sexual to asexual reproduction are often associated with polyploidy and increased chromosomal plasticity in asexuals. We investigated chromosomes in the freshwater ostracod species Eucypris virens (Jurine, 1820), where sexual, asexual and mixed populations can be found. Our initial karyotyping of multiple populations from Europe and North Africa, both sexual and asexual, revealed a striking variability in chromosome numbers. This would suggest that chromosomal changes are likely to be accelerated in asexuals because the constraints of meiosis are removed...
March 8, 2018: Genes
Rafael R C Cuadrat, Danny Ionescu, Alberto M R Dávila, Hans-Peter Grossart
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations...
2018: Frontiers in Microbiology
Meriem Bekliz, Said Azza, Hervé Seligmann, Philippe Decloquement, Didier Raoult, Bernard La Scola
Acanthamoeba polyphaga mimivirus is the first giant virus ever described, with a 1.2-Mb genome which encodes 979 proteins including central components of the translation apparatus. One of these proteins, R458, was predicted to initiate translation, although its specific role remains unknown.We silenced the R458 gene using siRNA and compared viral fitness and protein expression in silenced versus wild-type mimivirus. Silencing decreased growth rate but viral particle production at the end of the viral cycle was unaffected...
March 7, 2018: Journal of Virology
Shaghayegh Nasr, Mona Mohammadimehr, Marzieh Geranpayeh Vaghei, Mohammad Ali Amoozegar, Seyed Abolhassan Shahzadeh Fazeli
A new ascomycetous black yeast-like species was recovered from healthy plant (Avicennia marina) of Hara protected mangrove forests at Qeshm Island, Iran. Morphological, physiological analysis as well as a molecular analysis of the internal transcribed spacer (ITS) and partial large ribosomal subunit (D1/D2 domains) confirmed the placement of this strain in the genus Aureobasidium and based on considerable sequence divergence, distinguishable cardinal growth temperatures and salt tolerance a new species Aureobasidium mangrovei sp...
March 6, 2018: Antonie Van Leeuwenhoek
Zhen Chen, Phillip A Lichtor, Adrian P Berliner, Jonathan C Chen, David R Liu
The evolution of sequence-defined synthetic polymers made of building blocks beyond those compatible with polymerase enzymes or the ribosome has the potential to generate new classes of receptors, catalysts and materials. Here we describe a ligase-mediated DNA-templated polymerization and in vitro selection system to evolve highly functionalized nucleic acid polymers (HFNAPs) made from 32 building blocks that contain eight chemically diverse side chains on a DNA backbone. Through iterated cycles of polymer translation, selection and reverse translation, we discovered HFNAPs that bind proprotein convertase subtilisin/kexin type 9 (PCSK9) and interleukin-6, two protein targets implicated in human diseases...
March 5, 2018: Nature Chemistry
José Ferreira Saraiva, Raimundo Nonato Picanço Souto, Vera Margarete Scarpassa
Recent studies have shown that Anopheles oswaldoi sensu lato comprises a cryptic species complex in South America. Anopheles konderi, which was previously raised to synonymy with An. oswaldoi, has also been suggested to form a species complex. An. oswaldoi has been incriminated as a malaria vector in some areas of the Brazilian Amazon, Colombia, Peru and Venezuela, but was not recognized as a vector in the remaining regions in its geographic distribution. The role of An. konderi as a malaria vector is unknown or has been misattributed to An...
2018: PloS One
Matthew M Parks, Chad M Kurylo, Randall A Dass, Linda Bojmar, David Lyden, C Theresa Vincent, Scott C Blanchard
The ribosome, the integration point for protein synthesis in the cell, is conventionally considered a homogeneous molecular assembly that only passively contributes to gene expression. Yet, epigenetic features of the ribosomal DNA (rDNA) operon and changes in the ribosome's molecular composition have been associated with disease phenotypes, suggesting that the ribosome itself may possess inherent regulatory capacity. Analyzing whole-genome sequencing data from the 1000 Genomes Project and the Mouse Genomes Project, we find that rDNA copy number varies widely across individuals, and we identify pervasive intra- and interindividual nucleotide variation in the 5 S , 5...
February 2018: Science Advances
Jannigje G Kers, Francisca C Velkers, Egil A J Fischer, Gerben D A Hermes, J A Stegeman, Hauke Smidt
The initial development of intestinal microbiota in poultry plays an important role in production performance, overall health and resistance against microbial infections. Multiplexed sequencing of 16S ribosomal RNA gene amplicons is often used in studies, such as feed intervention or antimicrobial drug trials, to determine corresponding effects on the composition of intestinal microbiota. However, considerable variation of intestinal microbiota composition has been observed both within and across studies. Such variation may in part be attributed to technical factors, such as sampling procedures, sample storage, DNA extraction, the choice of PCR primers and corresponding region to be sequenced, and the sequencing platforms used...
2018: Frontiers in Microbiology
I Skrede, T Carlsen, T Schumacher
Helvella is a widespread, speciose genus of large apothecial ascomycetes ( Pezizomycete : Pezizales ) that are found in terrestrial biomes of the Northern and Southern Hemispheres. This study represents a beginning on assessing species limits and applying correct names for Helvella species based on type material and specimens in the university herbaria (fungaria) of Copenhagen (C), Harvard (FH) and Oslo (O). We use morphology and phylogenetic evidence from four loci - heat shock protein 90 ( hsp ), translation elongation factor alpha ( tef ), RNA polymerase II ( rpb2 ) and the nuclear large subunit ribosomal DNA (LSU) - to assess species boundaries in an expanded sample of Helvella specimens from Europe...
December 2017: Persoonia
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