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Ribosomal DNA

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https://www.readbyqxmd.com/read/28813669/the-phage-nucleus-and-tubulin-spindle-are-conserved-among-large-pseudomonas-phages
#1
Vorrapon Chaikeeratisak, Katrina Nguyen, MacKennon E Egan, Marcella L Erb, Anastasia Vavilina, Joe Pogliano
We recently demonstrated that the large Pseudomonas chlororaphis bacteriophage 201φ2-1 assembles a nucleus-like structure that encloses phage DNA and segregates proteins according to function, with DNA processing proteins inside and metabolic enzymes and ribosomes outside the nucleus. Here, we investigate the replication pathway of the Pseudomonas aeruginosa bacteriophages φKZ and φPA3. Bacteriophages φKZ and φPA3 encode a proteinaceous shell that assembles a nucleus-like structure that compartmentalizes proteins and DNA during viral infection...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28811661/myst2-kat7-histone-acetyltransferase-interaction-proteomics-reveals-tumour-suppressor-niam-as-a-novel-binding-partner-in-embryonic-stem-cells
#2
Mercedes Pardo, Lu Yu, Shihpei Shen, Peri Tate, Daniel Bode, Blake L Letney, Dawn E Quelle, William Skarnes, Jyoti S Choudhary
MYST histone acetyltransferases have crucial functions in transcription, replication and DNA repair and are hence implicated in development and cancer. Here we characterise Myst2/Kat7/Hbo1 protein interactions in mouse embryonic stem cells by affinity purification coupled to mass spectrometry. This study confirms that in embryonic stem cells Myst2 is part of H3 and H4 histone acetylation complexes similar to those described in somatic cells. We identify a novel Myst2-associated protein, the tumour suppressor protein Niam (Nuclear Interactor of ARF and Mdm2)...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28810700/a-single-mini-barcode-test-to-screen-for-australian-mammalian-predators-from-environmental-samples
#3
Elodie Modave, Anna J MacDonald, Stephen D Sarre
Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28808135/mutations-in-eif5b-confer-thermosensitive-and-pleiotropic-phenotypes-via-translation-defects-in-arabidopsis-thaliana
#4
Liyuan Zhang, Xinye Liu, Kishor Gaikwad, Xiaoxia Kou, Fei Wang, Xuejun Tian, Mingming Xin, Zhongfu Ni, Qixin Sun, Huiru Peng, Elizabeth Vierling
The conserved eukaryotic translation initiation factor 5B, eIF5B, is a GTPase that acts late in translation initiation. We found that an Arabidopsis thaliana mutant sensitive to hot temperatures 3 (hot3-1), which behaves as wild type in the absence of stress but is unable to acclimate to high temperature, carries a missense mutation in eIF5B1 gene (At1g76810),, producing a temperature sensitive protein. A more severe, T-DNA insertion allele (hot3-2) causes pleiotropic developmental phenotypes. Surprisingly, Arabidopsis has three other eIF5B genes that do not substitute for eIF5B1; two of these appear to be in the process of pseudogenization...
August 14, 2017: Plant Cell
https://www.readbyqxmd.com/read/28807005/first-records-of-triatoma-rubrofasciata-de-geer-1773-hemiptera-reduviidae-in-foshan-guangdong-province-southern-china
#5
Qin Liu, Yun-Hai Guo, Yi Zhang, Zheng-Bin Zhou, Liang-Liang Zhang, Dan Zhu, Xiao-Nong Zhou
BACKGROUND: Triatomines, also known as kissing bugs, which are found throughout the world and especially in Latin America, are well known natural vectors that transmit American trypanosomiasis, also called Chagas disease. In China, the presence of two species of Triatoma (Triatoma rubrofasciata and T. sinica) was recorded in the past. Due to the growing population and the increasing risk of the global spread of Chagas disease, triatomines became a potential public health nuisance, and in 2016, we started monitoring triatomine activities in southern China...
August 15, 2017: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/28806924/essential-genome-of-campylobacter-jejuni
#6
Rabindra K Mandal, Tieshan Jiang, Young Min Kwon
BACKGROUND: Campylobacter species are a leading cause of bacterial foodborne illness worldwide. Despite the global efforts to curb them, Campylobacter infections have increased continuously in both developed and developing countries. The development of effective strategies to control the infection by this pathogen is warranted. The essential genes of bacteria are the most prominent targets for this purpose. In this study, we used transposon sequencing (Tn-seq) of a genome-saturating library of Tn5 insertion mutants to define the essential genome of C...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28804492/population-genetic-differentiation-and-taxonomy-of-three-closely-related-species-of-saxifraga-saxifragaceae-from-southern-tibet-and-the-hengduan-mountains
#7
Qing-Bo Gao, Yan Li, Zhuo-Ma Gengji, Richard J Gornall, Jiu-Li Wang, Hai-Rui Liu, Liu-Kun Jia, Shi-Long Chen
The effects of rapid, recent uplift of the Hengduan Mountains on evolution and diversification of young floristic lineages still remain unclear. Here, we investigate diversification of three closely related Saxifraga species with a distribution restricted to the Hengduan Mountains (HM) and southern Tibet, and comment on their taxonomy based on molecular evidence. Three chloroplast DNA fragments (rbcL, trnL-F, trnS-G) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to study genetic structure across 104 individuals from 12 populations of Saxifraga umbellulata, S...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28792370/molecular-diagnosis-of-rhino-orbito-cerebral-mucormycosis-from-fresh-tissue-samples
#8
Kamran Zaman, Shivaprakash Mandya Rudramurthy, Ashim Das, Naresh Panda, Prasanna Honnavar, Harsimran Kaur, Arunaloke Chakrabarti
PURPOSE: We aimed to evaluate a PCR-based technique for the diagnosis of mucormycosis and the identification of fungi from fresh tissue specimens in patients with rhino-orbito-cerebral-mucormycosis (ROCM). METHODOLOGY: Fifty cases of ROCM were included in the study. Conventional identification was performed using microscopy and culture. Molecular diagnosis was performed by amplifying the ribosomal DNA using pan-fungal ITS primers and semi-nested Mucorales-specific primers of the 18S region...
August 9, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28781096/morphology-morphogenesis-and-molecular-phylogeny-of-a-new-soil-ciliate-paragonostomoides-xianicum-n-sp-ciliophora-hypotrichia-gonostomatidae
#9
Jingyi Wang, Jiyang Ma, Shuyan Qi, Chen Shao
A hypotrichous ciliate, Paragonostomoides xianicum n. sp., was discovered in soil on the surface of the Xi'an Circumvallation, Xi'an, China. Its morphology and some major ontogenetic stages were studied and the phylogenetic position was estimated using standard methods Paragonostomoides xianicum n. sp. is characterized as follows: body size about 75-90×15-25μm in vivo, elliptical and flexible; colourless mitochondrion-like cortical granules scattered throughout cell surface, about 0.8×0.6μm in size; contractile vacuole positioned at mid-body; frontoventral row IV extends beyond buccal vertex and frontoventral row VI extends to about body end; frontoventral cirri not in pairs; transverse cirri absent; three caudal cirri; two macronuclear nodules and one to four micronuclei...
July 12, 2017: European Journal of Protistology
https://www.readbyqxmd.com/read/28777931/biallelic-mutations-in-mrps34-lead-to-instability-of-the-small-mitoribosomal-subunit-and-leigh-syndrome
#10
Nicole J Lake, Bryn D Webb, David A Stroud, Tara R Richman, Benedetta Ruzzenente, Alison G Compton, Hayley S Mountford, Juliette Pulman, Coralie Zangarelli, Marlene Rio, Nathalie Bodaert, Zahra Assouline, Mingma D Sherpa, Eric E Schadt, Sander M Houten, James Byrnes, Elizabeth M McCormick, Zarazuela Zolkipli-Cunningham, Katrina Haude, Zhancheng Zhang, Kyle Retterer, Renkui Bai, Sarah E Calvo, Vamsi K Mootha, John Christodoulou, Agnes Rötig, Aleksandra Filipovska, Ingrid Cristian, Marni J Falk, Metodi D Metodiev, David R Thorburn
The synthesis of all 13 mitochondrial DNA (mtDNA)-encoded protein subunits of the human oxidative phosphorylation (OXPHOS) system is carried out by mitochondrial ribosomes (mitoribosomes). Defects in the stability of mitoribosomal proteins or mitoribosome assembly impair mitochondrial protein translation, causing combined OXPHOS enzyme deficiency and clinical disease. Here we report four autosomal-recessive pathogenic mutations in the gene encoding the small mitoribosomal subunit protein, MRPS34, in six subjects from four unrelated families with Leigh syndrome and combined OXPHOS defects...
August 3, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28774889/a-dynamic-ribosomal-biogenesis-response-is-not-required-for-igf-1-mediated-hypertrophy-of-human-primary-myotubes
#11
Hannah Crossland, James A Timmons, Philip J Atherton
Increased ribosomal DNA transcription has been proposed to limit muscle protein synthesis, making ribosome biogenesis central to skeletal muscle hypertrophy. We examined the relationship between ribosomal RNA (rRNA) production and IGF-1-mediated myotube hypertrophy in vitro Primary skeletal myotubes were treated with IGF-1 (50 ng/ml) with or without 0.5 µM/L CX-5461 (CX), an inhibitor of RNA polymerase I. Myotube diameter, total protein, and RNA and DNA levels were measured along with markers of RNA polymerase I regulatory factors and regulators of protein synthesis...
August 3, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28771547/evaluation-of-multifarious-plant-growth-promoting-traits-antagonistic-potential-and-phylogenetic-affiliation-of-rhizobacteria-associated-with-commercial-tea-plants-grown-in-darjeeling-india
#12
Jintu Dutta, Debajit Thakur
Plant growth promoting rhizobacteria (PGPR) are studied in different agricultural crops but the interaction of PGPR of tea crop is not yet studied well. In the present study, the indigenous tea rhizobacteria were isolated from seven tea estates of Darjeeling located in West Bengal, India. A total of 150 rhizobacterial isolates were screened for antagonistic activity against six different fungal pathogens i.e. Nigrospora sphaerica (KJ767520), Pestalotiopsis theae (ITCC 6599), Curvularia eragostidis (ITCC 6429), Glomerella cingulata (MTCC 2033), Rhizoctonia Solani (MTCC 4633) and Fusarium oxysporum (MTCC 284), out of which 48 isolates were antagonist to at least one fungal pathogen used...
2017: PloS One
https://www.readbyqxmd.com/read/28769637/phylogeny-of-the-genus-yumtaax-boucher-coleoptera-passalidae-proculini-taxonomic-and-evolutionary-implications-with-descriptions-of-three-new-species
#13
Cristian Fernando Beza-Beza, James Beck, Pedro Reyes-Castillo, Mary Liz Jameson
Yumtaax Boucher (Coleoptera: Passalidae) is an endemic genus from the temperate sierras of Mexico and includes six narrowly distributed species. Yumtaax species have been assigned to several genera of Passalidae throughout history, and a phylogenetic approach is necessary to understand species delimitation and interspecific relationships. This study reconstructed the molecular phylogeny of six Yumtaax morphotypes using parsimony and Bayesian analysis of DNA sequence data from the ribosomal nuclear gene region 28S and the mitochondrial gene regions 12S and cytochrome oxidase I (COI) in addition to morphological characters...
2017: ZooKeys
https://www.readbyqxmd.com/read/28768523/genetic-signature-analysis-of-perkinsus-marinus-in-mexico-suggests-possible-translocation-from-the-atlantic-ocean-to-the-pacific-coast-of-mexico
#14
Juan Pablo Ek-Huchim, Ma Leopoldina Aguirre-Macedo, Monica Améndola-Pimenta, Victor Manuel Vidal-Martínez, Juan Antonio Pérez-Vega, Raúl Simá-Alvarez, Isabel Jiménez-García, Roberto Zamora-Bustillos, Rossanna Rodríguez-Canul
BACKGROUND: The protozoan Perkinsus marinus (Mackin, Owen & Collier) Levine, 1978 causes perkinsosis in the American oyster Crassostrea virginica Gmelin, 1791. This pathogen is present in cultured C. virginica from the Gulf of Mexico and has been reported recently in Saccostrea palmula (Carpenter, 1857), Crassostrea corteziensis (Hertlein, 1951) and Crassostrea gigas (Thunberg, 1793) from the Mexican Pacific coast. Transportation of fresh oysters for human consumption and repopulation could be implicated in the transmission and dissemination of this parasite across the Mexican Pacific coast...
August 2, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28766039/fungal-and-bacterial-diversity-of-airway-microbiota-in-adults-with-cystic-fibrosis-concordance-between-conventional-methods-and-ultra-deep-sequencing-and-their-practical-use-in-the-clinical-laboratory
#15
Françoise Botterel, Cécile Angebault, Odile Cabaret, Franziska A Stressmann, Jean-Marc Costa, Frédéric Wallet, Benoit Wallaert, Kenneth Bruce, Laurence Delhaes
Given the complexity of the airway microbiota in the respiratory tract of cystic fibrosis (CF) patients, it seems crucial to compile the most exhaustive and exact list of the microbial communities inhabiting CF airways. The aim of the present study was to compare the bacterial and fungal diversity of sputa from adult CF patients during non-exacerbation period by culture-based and molecular methods, and ultra-deep-sequencing (UDS). Sputum samples from four CF patients were cultured and analysed by DNA extractions followed by terminal restriction fragment length polymorphism analysis through resolution of bacterial ribosomal gene (rDNA) fragments, and cloning plus sequencing of part of fungal rRNA genes...
August 1, 2017: Mycopathologia
https://www.readbyqxmd.com/read/28765578/selection-of-reference-genes-for-expression-analysis-using-rt-qpcr-in-the-dissemination-system-of-heliothis-virescens-ascovirus-3%C3%A2-h-hvav-3h
#16
Zi-Shu Chen, Ning-Ning Han, Jian-Hong Li, Guo-Hua Huang, Hu Wan
Ascoviruses are double-stranded DNA viruses that mainly infect noctuid larvae, and are transmitted by the parasitoid wasp Microplitis similis Lyle. Ascovirus-parasitoids wasp-noctuid insects constitute the dissemination system. Selection of suitable reference genes for the dissemination system could play an important role in elucidating the pathogenic molecular mechanisms of ascovirus. Unfortunately, such studies on potential reference genes in the dissemination system of ascoviruses are lacking. In the present study, we evaluated 11 candidate reference genes: β-actin1 (ACT1), β-actin2 (ACT2), elongation factor 1 (EF1), elongation factor 2 (EF2), ribosomal protein L10 (L10), ribosomal protein L17A (L17A), superoxide dismutase (SOD), 28S ribosome (28S), Tubulin (TUB) and 18S ribosome (18S)...
August 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28764736/quadriacanthus-species-monogenea-dactylogyridae-from-catfishes-teleostei-siluriformes-in-eastern-africa-new-species-new-records-and-first-insights-into-interspecific-genetic-relationships
#17
Kateřina Francová, Mária Seifertová, Radim Blažek, Milan Gelnar, Zuheir N Mahmoud, Eva Řehulková
BACKGROUND: African catfishes of the families Bagridae and Clariidae are known to be parasitized with monogeneans of Quadriacanthus Paperna, 1961 (Dactylogyridae). The genus remains taxonomically challenging due to its speciose nature and relatively wide host range representing two fish orders, i.e. Siluriformes and Osteoglossiformes, in Africa and Asia. Here, we investigated diversity of Quadriacanthus spp. parasitizing Clarias gariepinus (Burchell), Heterobranchus bidorsalis Geoffroy Saint-Hilaire, and Bagrus docmak (Forsskål) collected in the Lake Turkana (Kenya) and Nile River Basin (Sudan)...
August 1, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28763741/expression-stability-and-selection-of-optimal-reference-genes-for-gene-expression-normalization-in-early-life-stage-rainbow-trout-exposed-to-cadmium-and-copper
#18
Kamran Shekh, Song Tang, Som Niyogi, Markus Hecker
Gene expression analysis represents a powerful approach to characterize the specific mechanisms by which contaminants interact with organisms. One of the key considerations when conducting gene expression analyses using quantitative real-time reverse transcription-polymerase chain reaction (qPCR) is the selection of appropriate reference genes, which is often overlooked. Specifically, to reach meaningful conclusions when using relative quantification approaches, expression levels of reference genes must be highly stable and cannot vary as a function of experimental conditions...
September 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28762997/investigating-the-biosynthesis-of-natural-products-from-marine-proteobacteria-a-survey-of-molecules-and-strategies
#19
REVIEW
Marshall L Timmermans, Yagya P Paudel, Avena C Ross
The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts...
August 1, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28761482/molecular-characterization-and-analysis-of-16s-ribosomal-dna-in-some-isolates-of-demodex-folicullorum
#20
Afrooz Daneshparvar, Gholamreza Mowlavi, Hamed Mirjalali, Homa Hajjaran, Iraj Mobedi, Saeed Reza Naddaf, Mohammadreza Shidfar, Mahsa Sadat Makki
BACKGROUND: Demodicosis is one of the most prevalent skin diseases resulting from infestation by Demodex mites. This parasite usually inhabits in follicular infundibulum or sebaceous duct and transmits through close contact with an infested host. METHODS: This study was carried from September 2014 to January 2016 at Tehran University of Medical Sciences, Tehran, Iran. DNA extraction and amplification of 16S ribosomal RNA was performed on four isolates, already obtained from four different patients and identified morphologically though clearing with 10% Potassium hydroxide (KOH) and microscopical examination...
April 2017: Iranian Journal of Parasitology
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