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https://www.readbyqxmd.com/read/29792819/distinct-mechanisms-of-transcription-initiation-by-rna-polymerases-i-and-ii
#1
Christoph Engel, Simon Neyer, Patrick Cramer
RNA polymerases I and II (Pol I and Pol II) are the eukaryotic enzymes that catalyze DNA-dependent synthesis of ribosomal RNA and messenger RNA, respectively. Recent work shows that the transcribing forms of both enzymes are similar and the fundamental mechanisms of RNA chain elongation are conserved. However, the mechanisms of transcription initiation and its regulation differ between Pol I and Pol II. Recent structural studies of Pol I complexes with transcription initiation factors provided insights into how the polymerase recognizes its specific promoter DNA, how it may open DNA, and how initiation may be regulated...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29792237/according-to-mitochondrial-dna-evidence-parascaris-equorum-and-parascaris-univalens-may-represent-the-same-species
#2
J F Gao, X X Zhang, X X Wang, Q Li, Y Li, W W Xu, Y Gao, C R Wang
Parascarosis is caused mainly by parasitic infections with Parascaris equorum and Parascaris univalens, the most common ascarid nematodes, in the small intestine of equines. Parascarosis often causes severe illness and even death in foals and yearlings. In this study, we obtained the complete sequence of the P. equorum mitochondrial (mt) genome and compared its organization and structure with that of P. equorum Japan isolate (nearly complete), and the complete mtDNA sequences of P. univalens Switzerland and USA isolates...
May 24, 2018: Journal of Helminthology
https://www.readbyqxmd.com/read/29791787/dna-barcoding-of-microgastrine-parasitoid-wasps-hymenoptera-braconidae-using-high-throughput-methods-more-than-doubles-the-number-of-species-known-for-australia
#3
Erinn P Fagan-Jeffries, Steven J B Cooper, Terry Bertozzi, Tessa M Bradford, Andrew D Austin
The Microgastrinae are a hugely diverse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents, and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Northern Hemisphere, the Australian fauna has received little attention. In total, 100 species have been described from or have been introduced into Australia, but the real species diversity for the region is clearly much larger than this...
May 23, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29789391/mst2-kinase-suppresses-rdna-transcription-in-response-to-dna-damage-by-phosphorylating-nucleolar-histone-h2b
#4
Dafni Eleftheria Pefani, Maria Laura Tognoli, Deniz Pirincci Ercan, Vassilis Gorgoulis, Eric O'Neill
The heavily transcribed rDNA repeats that give rise to the ribosomal RNA are clustered in a unique chromatin structure, the nucleolus. Due to its highly repetitive nature and transcriptional activity, the nucleolus is considered a hotspot of genomic instability. Breaks in rDNA induce a transient transcriptional shut down to conserve energy and promote rDNA repair; however, how nucleolar chromatin is modified and impacts on rDNA repair is unknown. Here, we uncover that phosphorylation of serine 14 on histone H2B marks transcriptionally inactive nucleolar chromatin in response to DNA damage...
May 22, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29788454/variation-in-human-chromosome-21-ribosomal-rna-genes-characterized-by-tar-cloning-and-long-read-sequencing
#5
Jung-Hyun Kim, Alexander T Dilthey, Ramaiah Nagaraja, Hee-Sheung Lee, Sergey Koren, Dawood Dudekula, William H Wood Iii, Yulan Piao, Aleksey Y Ogurtsov, Koichi Utani, Vladimir N Noskov, Svetlana A Shabalina, David Schlessinger, Adam M Phillippy, Vladimir Larionov
Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments from a single human chromosome 21 using transformation-associated recombination (TAR) cloning in yeast. Accurate long-read sequencing of 13 isolates covering ∼0.82 Mb of the chromosome 21 rDNA complement revealed substantial variation among tandem repeat rDNA copies, several palindromic structures and potential errors in the previous reference sequence...
May 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29788335/detection-of-hepatozoon-canis-in-the-brown-dog-tick-and-domestic-dogs-in-peninsular-malaysia
#6
Batah Kunalan Prakash, Van Lun Low, Tiong Kai Tan, Wei Yin Vinnie-Siow, Yvonne Ai-Lian Lim, Akhavan Rezaei Morvarid, Adzzie Shazleen Azman, Yze Shiuan Yeong, Sazaly AbuBakar, Mohd Sofian-Azirun
Hepatozoon canis has been widely reported in dogs. Its prevalence in ticks, however, has not been well-established. Here we determine the occurrence of Hepatozoon DNA in the brown dog tick Rhipicephalus sanguineus (Latreille) (Acari: Ixodidae) sensu lato (s.l.) and domestic dogs from Peninsular Malaysia using a polymerase chain reaction (PCR) assay based on amplification of the 18S ribosomal RNA coding sequence. Our results revealed a relatively low prevalence of H. canis DNA in both R. sanguineus s.l. (0.7%) and dogs (3...
May 17, 2018: Journal of Medical Entomology
https://www.readbyqxmd.com/read/29781415/mammomonogamus-nematodes-in-felid-carnivores-a-minireview-and-the-first-molecular-characterization
#7
Barbora Červená, Kristýna Hrazdilová, Peter Vallo, Jennifer Ketzis, Pompei Bolfa, Edgar Tudor, Estevam G Lux-Hoppe, Caroline Blanvillain, David Modrý
Five of the 13 known species of Mammomonogamus have been described in members of the family Felidae, including domestic cats, making felids the most frequent hosts of Mammomonogamus. The occurrence of Mammomonogamus in felids is geographically scattered and information on the life cycle and other aspects of infections is lacking. The paucity of data opens the questions on possible conspecificity of some of the described species of Mammomonogamus and on the existence of possible reservoirs for infections in domestic cats in geographically isolated endemic foci of infection...
May 21, 2018: Parasitology
https://www.readbyqxmd.com/read/29780376/diversity-novelty-and-antimicrobial-activity-of-endophytic-actinobacteria-from-mangrove-plants-in-beilun-estuary-national-nature-reserve-of-guangxi-china
#8
Zhong-Ke Jiang, Li Tuo, Da-Lin Huang, Ilya A Osterman, Anton P Tyurin, Shao-Wei Liu, Dmitry A Lukyanov, Petr V Sergiev, Olga A Dontsova, Vladimir A Korshun, Fei-Na Li, Cheng-Hang Sun
Endophytic actinobacteria are one of the important pharmaceutical resources and well known for producing different types of bioactive substances. Nevertheless, detection of the novelty, diversity, and bioactivity on endophytic actinobacteria isolated from mangrove plants are scarce. In this study, five different mangrove plants, Avicennia marina, Aegiceras corniculatum, Kandelia obovota, Bruguiera gymnorrhiza , and Thespesia populnea , were collected from Beilun Estuary National Nature Reserve in Guangxi Zhuang Autonomous Region, China...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29780369/identification-and-removal-of-contaminant-sequences-from-ribosomal-gene-databases-lessons-from-the-census-of-deep-life
#9
Cody S Sheik, Brandi Kiel Reese, Katrina I Twing, Jason B Sylvan, Sharon L Grim, Matthew O Schrenk, Mitchell L Sogin, Frederick S Colwell
Earth's subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29778198/molecular-characterization-of-dermatophytes-isolated-from-cattle-in-plateau-state-nigeria
#10
James S Dalis, Haruna M Kazeem, Jacob K P Kwaga, Clara N Kwanashie, Bitrus Yakubu, Olajide A Owolodun, Anvou R Jambol
Dermatophytes from cattle were successfully characterized to species and strain levels for the first time in Nigeria. This study was undertaken to isolate and characterize dermatophytes from cattle in Plateau State, Nigeria. Two molecular techniques were utilized. The first was the use of polymerase chain reaction (PCR) to amplify the internal transcribed spacer regions of the ribosomal DNA using ITS-1 and ITS-4 as primers. This was followed by restriction fragment length polymorphism analysis of the amplified ITS regions using the enzyme MvaI to identify dermatophyte species...
June 2018: Veterinary Microbiology
https://www.readbyqxmd.com/read/29776339/differential-gene-transcription-across-the-life-cycle-in-daphnia-magna-using-a-new-all-genome-custom-made-microarray
#11
Bruno Campos, Danielle Fletcher, Benjamín Piña, Romà Tauler, Carlos Barata
BACKGROUND: Unravelling the link between genes and environment across the life cycle is a challenging goal that requires model organisms with well-characterized life-cycles, ecological interactions in nature, tractability in the laboratory, and available genomic tools. Very few well-studied invertebrate model species meet these requirements, being the waterflea Daphnia magna one of them. Here we report a full genome transcription profiling of D. magna during its life-cycle. The study was performed using a new microarray platform designed from the complete set of gene models representing the whole transcribed genome of D...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29774971/3d-dna-origami-crystals
#12
Tao Zhang, Caroline Hartl, Kilian Frank, Amelie Heuer-Jungemann, Stefan Fischer, Philipp C Nickels, Bert Nickel, Tim Liedl
3D crystals assembled entirely from DNA provide a route to design materials on a molecular level and to arrange guest particles in predefined lattices. This requires design schemes that provide high rigidity and sufficiently large open guest space. A DNA-origami-based "tensegrity triangle" structure that assembles into a 3D rhombohedral crystalline lattice with an open structure in which 90% of the volume is empty space is presented here. Site-specific placement of gold nanoparticles within the lattice demonstrates that these crystals are spacious enough to efficiently host 20 nm particles in a cavity size of 1...
May 18, 2018: Advanced Materials
https://www.readbyqxmd.com/read/29774288/molecular-analysis-of-giardia-duodenalis-isolates-from-symptomatic-and-asymptomatic-children-from-la-habana-cuba
#13
Luis Enrique Jerez Puebla, Fidel A Núñez, Lissette Pérez Santos, Lázara Rojas Rivero, Isabel Martínez Silva, Lucía Ayllón Valdés, Iraís Atencio Millán, Norbert Müller
Giardiasis is considered the most common intestinal parasitic disease in humans worldwide. In Cuba, this infection has particularly a strong clinical impact on the child population. Giardia duodenalis is a highly diverse protozoan, which comprises a complex of eight morphologically identical genetic assemblages, further divided into sub-assemblages. The present study used triose phosphate isomerase ( tpi ) and small-subunit ribosomal RNA (SSU rRNA) genes as genetic markers for the identification of G. duodenalis assemblages and sub-assemblages in correlation with clinical and epidemiological data in children attended at the Paediatric Hospital "William Soler" and at Pedro Kouri Institute, between 2015 and 2016...
August 2017: Parasite Epidemiology and Control
https://www.readbyqxmd.com/read/29773434/tinea-blepharo-ciliaris-in-a-13-year-old-girl-caused-by-trichophyton-benhamiae
#14
Fang-Ying Wang, Pei-Lun Sun
Tinea blepharo-ciliaris is a rare form of dermatophyte infection which involves eyelids and associated eyelashes. We report a 13-year-old girl with type I diabetes mellitus who had right eyelid swelling and eyelash loss for two weeks. The lesions were presented as erythematous patches with scales and tiny pustules on the right upper and lower eyelids with broken eyelashes. Two additional annular erythematous patches with scaly active borders were found on her right forearm and right thigh. Microscopic examination of broken eyelashes demonstrated many chains of arthroconidia and hyaline hyphae in an endothrix invasion pattern...
May 14, 2018: Journal de Mycologie Médicale
https://www.readbyqxmd.com/read/29772600/an-accurate-bacterial-dna-quantification-assay-for-hts-library-preparation-of-human-biological-samples
#15
Sarah Seashols-Williams, Raquel Green, Denise Wohlfahrt, Angela Brand, Antonio Limjuco Tan-Torres, Francy Nogales, J Paul Brooks, Baneshwar Singh
Sequencing and classification of microbial taxa within forensically relevant biological fluids has the potential for applications in the forensic science and biomedical fields. The quantity of bacterial DNA from human samples is currently estimated based on quantity of total DNA isolated. This method can miscalculate bacterial DNA quantity due to the mixed nature of the sample, and consequently library preparation is often unreliable. We developed an assay that can accurately and specifically quantify bacterial DNA within a mixed sample for reliable 16S ribosomal DNA (16S rDNA) library preparation and high throughput sequencing (HTS)...
May 17, 2018: Electrophoresis
https://www.readbyqxmd.com/read/29772229/polybacterial-community-analysis-in-human-conjunctiva-through-16s-rrna-gene-libraries
#16
Deepthi KrishnanNair Geetha, Jayasudha Rajagopalaboopathi, Girish Rameshan Nair, Manikandan Palanisamy, Ram Rammohan, Narendran Venkatapathy, Prabagaran Solai Ramatchandirane
The conjunctival sac of healthy human harbours a variety of microorganisms. When the eye is compromised, an occasional inadvertent spread happens to the adjacent tissue, resulting in bacterial ocular infections. Microbiological investigation of the conjunctival swab is one of the broadly used modality to study the aetiological agent of conjunctiva. However, most of the time such methods yield unsatisfactory results. Hence, the present study intends to identify the bacterial community in human conjunctiva of pre-operative subjects through 16S rRNA gene libraries...
May 14, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29768494/a-new-method-based-on-snp-of-nrdna-its-to-identify-saccharum-spontaneum-and-its-progeny-in-the-genus-saccharum
#17
Shan Yang, Xueting Li, Fei Huang, Yongji Huang, Xinlong Liu, Jiayun Wu, Qinnan Wang, Zuhu Deng, Rukai Chen, Muqing Zhang
The identification of germplasm resources is an important aspect of sugarcane breeding. The aim of this study was to introduce a new method for identifying Saccharum spontaneum and its progeny. First, we cloned and sequenced nuclear ribosomal DNA internal transcribed spacer (nrDNA-ITS) sequences from 20 Saccharum germplasms. Analysis of these nrDNA-ITS sequences showed a stable mutation at base 89. Primers (FO13, RO13, FI16, and RI16) were then designed for tetra-primer amplification refractory mutation system (ARMS) PCR based on mutations at base 89 of the nrDNA-ITS sequence...
2018: PloS One
https://www.readbyqxmd.com/read/29767361/making-and-sequencing-heavily-multiplexed-high-throughput-16s-ribosomal-rna-gene-amplicon-libraries-using-a-flexible-two-stage-pcr-protocol
#18
Ankur Naqib, Silvana Poggi, Weihua Wang, Marieta Hyde, Kevin Kunstman, Stefan J Green
Deep sequencing of polymerase chain reaction (PCR)-amplified small subunit (16S or 18S) ribosomal RNA (rRNA) genes fragments is commonly employed to characterize the composition and structure of microbial communities. Preparing genomic DNA for sequencing of such gene fragments on Illumina sequencers can be performed in a straightforward, two-stage PCR method, described herein. The protocol described allows for up to 384 samples to be sequenced simultaneously, and provides great flexibility in choice of primers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29764204/biotechnological-potential-of-microbial-consortia-and-future-perspectives
#19
Shashi Kant Bhatia, Ravi Kant Bhatia, Yong-Keun Choi, Eunsung Kan, Yun-Gon Kim, Yung-Hun Yang
Design of a microbial consortium is a newly emerging field that enables researchers to extend the frontiers of biotechnology from a pure culture to mixed cultures. A microbial consortium enables microbes to use a broad range of carbon sources. It provides microbes with robustness in response to environmental stress factors. Microbes in a consortium can perform complex functions that are impossible for a single organism. With advancement of technology, it is now possible to understand microbial interaction mechanism and construct consortia...
May 15, 2018: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/29762744/forensically-relevant-blow-flies-in-lebanon-survey-and-identification-using-molecular-markers-diptera-calliphoridae
#20
Salman Shayya, Régis Debruyne, André Nel, Dany Azar
Calliphoridae are among the first insects associated to decomposing animal remains. We have collected 1,841 specimens of three calliphorid genera: Calliphora, Lucilia, and Chrysomya, from different Lebanese localities as a first step in implementing a database of insects of forensic relevance for the country. Blow-flies are crucial for the estimation of the postmortem interval. DNA-based identification is a rapid and accurate method, often used for morphologically similar species, especially for immatures or incomplete specimens...
May 12, 2018: Journal of Medical Entomology
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