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https://www.readbyqxmd.com/read/28213379/slowed-decay-of-mrnas-enhances-platelet-specific-translation
#1
Eric W Mills, Rachel Green, Nicholas T Ingolia
Platelets are anucleate cytoplasmic fragments that lack genomic DNA, but continue to synthesize protein using a pool of mRNAs, ribosomes, and regulatory small RNAs inherited from the precursor megakaryocyte (MK). The regulatory processes that shape the platelet transcriptome and the full scope of platelet translation have remained elusive. Using RNA-Seq and ribosome profiling of primary human platelets, we show the platelet transcriptome encompasses a subset of transcripts detected by RNA-Seq analysis of in vitro derived MK cells and these platelet-enriched transcripts are broadly occupied by ribosomes...
February 17, 2017: Blood
https://www.readbyqxmd.com/read/28212567/ribosomal-dna-status-inferred-from-dna-cloud-assays-and-mass-spectrometry-identification-of-agarose-squeezed-proteins-interacting-with-chromatin-aspic-ms
#2
Kamil Krol, Justyna Jendrysek, Janusz Debski, Marek Skoneczny, Anna Kurlandzka, Joanna Kaminska, Michal Dadlez, Adrianna Skoneczna
Ribosomal RNA-encoding genes (rDNA) are the most abundant genes in eukaryotic genomes. To meet the high demand for rRNA, rDNA genes are present in multiple tandem repeats clustered on a single or several chromosomes and are vastly transcribed. To facilitate intensive transcription and prevent rDNA destabilization, the rDNA-encoding portion of the chromosome is confined in the nucleolus. However, the rDNA region is susceptible to recombination and DNA damage, accumulating mutations, rearrangements and atypical DNA structures...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28210845/whipworm-diversity-in-west-african-rodents-a-molecular-approach-and-the-description-of-trichuris-duplantieri-n-sp-nematoda-trichuridae
#3
Alexis Ribas, Christophe Diagne, Caroline Tatard, Mamoudou Diallo, Srisupaph Poonlaphdecha, Carine Brouat
Whipworms were collected from rodents (Muridae) from six West African countries: Burkina-Faso, the Islamic Republic of Mauritania, and the Republics of Benin, Guinea, Mali and Senegal. Molecular sequences (ITS-1, 5.8S and ITS-2 of the ribosomal DNA gene) and morphometric characters were analysed in Trichuris (Nematoda: Trichuridae) specimens found in seven host species: Arvicanthis niloticus, Gerbilliscus gambianus, Gerbillus gerbillus, G. tarabuli, Mastomys erythroleucus, M. huberti and M. natalensis. Phylogenetic analyses revealed three clades, one recognised as Trichuris mastomysi, previously recorded in M...
February 16, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28205355/trametes-polyzona-an-emerging-filamentous-basidiomycete-in-r%C3%A3-union-island
#4
Alexandre Gauthier, Julien Jaubert, Nicolas Traversier, Jérôme Lemant, Laurent Balu, Dea Garcia-Hermoso, Stephane Welti, Anne Favel, Sandrine Picot, Gautier Hoarau
We describe two serious Trametes polyzona pulmonary infections, which occurred in Réunion Island, in critically ill patients. The identification was performed using sequencing of the internal transcribed spacer region of ribosomal DNA and D1/D2 region of 28S rDNA. In one case, the significance of T. polyzona in the pathological process was certain, proven by histopathological evidence of fungal lung infection. T. polyzona, an emerging filamentous basidiomycete, prevalent in tropical areas, has not been described so far in human infections...
February 16, 2017: Mycoses
https://www.readbyqxmd.com/read/28204512/ribosomal-rna-genes-contribute-to-the-formation-of-pseudogenes-and-junk-dna-in-the-human-genome
#5
Brent M Robicheau, Edward Susko, Amye M Harrigan, Marlene Snyder
No abstract text is available yet for this article.
February 15, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28199101/fungal-identification-using-molecular-tools-a-primer-for-the-natural-products-research-community
#6
Huzefa A Raja, Andrew N Miller, Cedric J Pearce, Nicholas H Oberlies
Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi...
February 15, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28198673/diversity-and-enterotype-in-gut-bacterial-community-of-adults-in-taiwan
#7
Chao Liang, Han-Chi Tseng, Hui-Mei Chen, Wei-Chi Wang, Chih-Min Chiu, Jen-Yun Chang, Kuan-Yi Lu, Shun-Long Weng, Tzu-Hao Chang, Chao-Hsiang Chang, Chen-Tsung Weng, Hwei-Ming Wang, Hsien-Da Huang
BACKGROUND: Gastrointestinal microbiota, particularly gut microbiota, is associated with human health. The biodiversity of gut microbiota is affected by ethnicities and environmental factors such as dietary habits or medicine intake, and three enterotypes of the human gut microbiome were announced in 2011. These enterotypes are not significantly correlated with gender, age, or body weight but are influenced by long-term dietary habits. However, to date, only two enterotypes (predominantly consisting of Bacteroides and Prevotella) have shown these characteristics in previous research; the third enterotype remains ambiguous...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28196871/identification-of-a-transcriptional-activation-domain-in-yeast-repressor-activator-protein-1-rap1-using-an-altered-dna-binding-specificity-variant
#8
Amanda N Johnson, P Anthony Weil
Repressor Activator Protein 1 (Rap1) performs multiple vital cellular functions in the budding yeast Saccharomyces cerevisiae. These include regulation of telomere length, transcriptional repression of both telomere-proximal genes and the silent mating type loci, and transcriptional activation of hundreds of mRNA-encoding genes, including the highly transcribed ribosomal protein- and glycolytic enzyme-encoding genes. Studies of the contributions of Rap1 to telomere length regulation and transcriptional repression have yielded significant mechanistic insights...
February 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28196718/the-neuropeptide-galanin-is-up-regulated-during-cholestasis-and-contributes-to-cholangiocyte-proliferation
#9
Matthew McMillin, Gabriel Frampton, Stephanie Grant, Sharon DeMorrow
During the course of cholestatic liver diseases, mitotically dormant cholangiocytes proliferate and subsequently acquire a neuroendocrine phenotype. Galanin is a neuroendocrine factor responsible for regulation of physiological responses, such as feeding behavior and mood, and has been implicated in the development of fatty liver disease, although its role in biliary hyperplasia is unknown. Biliary hyperplasia was induced in rats via bile duct ligation (BDL) surgery, and galanin was increased in serum and liver homogenates from BDL rats...
February 11, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28196664/new-records-of-ornithodoros-puertoricensis-fox-1947-ixodida-argasidae-parasitizing-humans-in-rural-and-urban-dwellings-panama
#10
Sergio E Bermúdez, Eduardo Castillo, Tyler D Pohlenz, Alexander Kneubehl, Aparna Krishnavajhala, Lillian Domínguez, Antonio Suárez, Job E López
The presence of ticks inside human constructions was evaluated in two localities from Colon province (Charco La Piedra and Espinar) and one from Panama province (Ancon, City of Panama). In two of houses, eight people from Charco La Piedra and one from Ancón reported "insect bites," which produced blisters for several weeks. The investigation resulted in the collection of argasid ticks, which were identified by morphology and sequencing the 16s ribosomal RNA gene, and later evaluated for the presence of relapsing fever Borrelia DNA...
February 5, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28196275/symbiodinium-dinophyceae-community-patterns-in-invertebrate-hosts-from-inshore-marginal-reefs-of-the-southern-great-barrier-reef-australia
#11
Linda Tonk, Eugenia M Sampayo, Aaron Chai, Verena Schrameyer, Ove Hoegh-Guldberg
The broad range in physiological variation displayed by Symbiodinium spp. has proven imperative during periods of environmental change and contribute to the survival of their coral host. Characterizing how host and Symbiodinium community assemblages differ across environmentally distinct habitats provides useful information to predict how corals will respond to major environmental change. Despite the extensive characterizations of Symbiodinium diversity found amongst reef cnidarians on the Great Barrier Reef substantial biogeographic gaps exist, especially across inshore habitats...
February 14, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28195642/functional-mucous-layer-and-healing-of-proximal-colonic-anastomoses-in-an-experimental-model
#12
J W A M Bosmans, A C H M Jongen, G M H Birchenough, E E L Nyström, M J J Gijbels, J P M Derikx, N D Bouvy, G C Hansson
BACKGROUND: Anastomotic leakage (AL) is the most dreaded complication after colorectal surgery, causing high morbidity and mortality. Mucus is a first line of defence against external factors in the gastrointestinal tract. In this study, the structural mucus protein Muc2 was depleted in genetically engineered mice and the effect on healing of colonic anastomoses studied in an experimental model. METHODS: Mice of different Muc2 genotypes were used in a proximal colonic AL model...
February 13, 2017: British Journal of Surgery
https://www.readbyqxmd.com/read/28188552/enhanced-biodegradation-of-low-and-high-density-polyethylene-by-novel-bacterial-consortia-formulated-from-plastic-contaminated-cow-dung-under-thermophilic-conditions
#13
Sinosh Skariyachan, Anagha Shamsundar Setlur, Sujay Yashwant Naik, Ashwini Amaresh Naik, Makam Usharani, Kiran S Vasist
The current study aimed to devise eco-friendly, safe, and cost-effective strategies for enhanced degradation of low- and high-density polyethylene (LDPE and HDPE) using newly formulated thermophilic microbial consortia from cow dung and to assess the biodegradation end products. The plastic-degrading bacteria from cow dung samples gathered from highly plastic-acclimated environments were enriched by standard protocols. The degradation ability was comprehended by zone of clearance method, and the percentage of degradation was monitored by weight reduction process...
February 10, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28186364/rare-syndromes-of-the-head-and-face-mandibulofacial-and-acrofacial-dysostoses
#14
REVIEW
Karla Terrazas, Jill Dixon, Paul A Trainor, Michael J Dixon
Craniofacial anomalies account for approximately one-third of all congenital birth defects reflecting the complexity of head and facial development. Craniofacial development is dependent upon a multipotent, migratory population of neural crest cells, which generate most of the bone and cartilage of the head and face. In this review, we discuss advances in our understanding of the pathogenesis of a specific array of craniofacial anomalies, termed facial dysostoses, which can be subdivided into mandibulofacial dysostosis, which present with craniofacial defects only, and acrofacial dysostosis, which encompasses both craniofacial and limb anomalies...
February 10, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28186206/unbiased-k-mer-analysis-reveals-changes-in-copy-number-of-highly-repetitive-sequences-during-maize-domestication-and-improvement
#15
Sanzhen Liu, Jun Zheng, Pierre Migeon, Jie Ren, Ying Hu, Cheng He, Hongjun Liu, Junjie Fu, Frank F White, Christopher Toomajian, Guoying Wang
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185895/using-the-small-subunit-of-nuclear-ribosomal-dna-to-reveal-the-phylogenetic-position-of-the-plerocercoid-larvae-of-spirometra-tapeworms
#16
Xi Zhang, Jiang Yang Duan, Zhong Quan Wang, Peng Jiang, Ruo Dan Liu, Jing Cui
Although medically important, the systematics of Spirometra and the taxonomic position of S. erinaceieuropaei remain unclear. In this study, the 18S rDNA gene of S. erinaceieuropaei sparganum from naturally infected frogs caught in 14 geographical locations of China was sequenced. In addition, all available 18S sequences of the family Diphyllobothriidae in the Genbank database were included to reconstruct the phylogeny of diphyllobothriid tapeworms. The secondary structure model of the 18S rDNA was also predicated to further explore the sequence variation...
February 6, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28185825/amazonian-waters-harbour-an-ancient-freshwater-ceratomyxa-lineage-cnidaria-myxosporea
#17
Suellen A Zatti, Stephen D Atkinson, Jerri L Bartholomew, Antônio A M Maia, Edson A Adriano
A new species of Ceratomyxa parasitizing the gall bladder of Cichla monoculus, an endemic cichlid fish from the Amazon basin in Brazil, is described using morphological and molecular data. In the bile, both immature and mature myxospores were found floating freely or inside elongated plasmodia: length 304 (196-402) μm and width 35.7 (18.3-55.1) μm. Mature spores were elongated and only slightly crescent-shaped in frontal view with a prominent sutural line between two valve cells, which had rounded ends. Measurements of formalin-fixed myxospores: length 6...
February 7, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28184987/comparison-of-six-methods-for-the-recovery-of-pcr-compatible-microbial-dna-from-an-agricultural-biogas-plant
#18
L Stagnati, G Soffritti, A Lanubile, M Busconi
Six different commercial methods were compared to evaluate their efficiency in recovering high quantity/quality PCR compatible microbial DNA from an agricultural biogas plant. Within the last two decades, biogas plants have been developed to produce energy from organic wastes and from devoted biomass. The complex biotransformations are performed by a diverse consortium of microorganisms that is an important reserve of genes and enzymatic activities with a huge range of applications in various commercial fields...
February 9, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28182658/comparison-of-the-microbial-population-in-rabbits-and-guinea-pigs-by-next-generation-sequencing
#19
Edward J Crowley, Jonathan M King, Toby Wilkinson, Hilary J Worgan, Kathryn M Huson, Michael T Rose, Neil R McEwan
This study aimed to determine the microbial composition of faeces from two groups of caecotrophagic animals; rabbits and guinea pigs. In addition the study aimed to determine the community present in the different organs in the rabbit. DNA was extracted from seven of the organs in wild rabbits (n = 5) and from faecal samples from domesticated rabbits (n = 6) and guinea pigs (n = 6). Partial regions of the small ribosomal sub-unit were amplified by PCR and then the sequences present in each sample were determined by next generation sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28179023/optimization-of-dna-extraction-for-advancing-coral-microbiota-investigations
#20
Laura Weber, Emelia DeForce, Amy Apprill
BACKGROUND: DNA-based sequencing approaches are commonly used to identify microorganisms and their genes and document trends in microbial community diversity in environmental samples. However, extraction of microbial DNA from complex environmental samples like corals can be technically challenging, and extraction methods may impart biases on microbial community structure. METHODS: We designed a two-phase study in order to propose a comprehensive and efficient method for DNA extraction from microbial cells present in corals and investigate if extraction method influences microbial community composition...
February 8, 2017: Microbiome
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