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https://www.readbyqxmd.com/read/28550049/recovery-of-ethanol-induced-akkermansia-muciniphila-depletion-ameliorates-alcoholic-liver-disease
#1
Christoph Grander, Timon E Adolph, Verena Wieser, Patrick Lowe, Laura Wrzosek, Benedek Gyongyosi, Doyle V Ward, Felix Grabherr, Romana R Gerner, Alexandra Pfister, Barbara Enrich, Dragos Ciocan, Sophie Macheiner, Lisa Mayr, Matthias Drach, Patrizia Moser, Alexander R Moschen, Gabriel Perlemuter, Gyongyi Szabo, Anne Marie Cassard, Herbert Tilg
OBJECTIVE: Alcoholic liver disease (ALD) is a global health problem with limited therapeutic options. Intestinal barrier integrity and the microbiota modulate susceptibility to ALD. Akkermansia muciniphila, a Gram-negative intestinal commensal, promotes barrier function partly by enhancing mucus production. The aim of this study was to investigate microbial alterations in ALD and to define the impact of A. muciniphila administration on the course of ALD. DESIGN: The intestinal microbiota was analysed in an unbiased approach by 16S ribosomal DNA (rDNA) sequencing in a Lieber-DeCarli ALD mouse model, and faecal A...
May 26, 2017: Gut
https://www.readbyqxmd.com/read/28549457/atp8-is-in-the-ground-pattern-of-flatworm-mitochondrial-genomes
#2
Bernhard Egger, Lutz Bachmann, Bastian Fromm
BACKGROUND: To date, mitochondrial genomes of more than one hundred flatworms (Platyhelminthes) have been sequenced. They show a high degree of similarity and a strong taxonomic bias towards parasitic lineages. The mitochondrial gene atp8 has not been confidently annotated in any flatworm sequenced to date. However, sampling of free-living flatworm lineages is incomplete. We addressed this by sequencing the mitochondrial genomes of the two small-bodied (about 1 mm in length) free-living flatworms Stenostomum sthenum and Macrostomum lignano as the first representatives of the earliest branching flatworm taxa Catenulida and Macrostomorpha respectively...
May 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28548703/microsporidians-xenomas-of-anglerfish-from-ne-atlantic-waters
#3
M Llarena-Reino, E Abollo, S Pascual
The presence of emergent visible parasites at commercial valuable fish species is increasingly causing problems at fisheries and seafood industries. Microsporidians have been previously reported to appear forming apparent xenomas complexes in anglerfish species, but no effort has been carried out to simultaneously integrate epidemiological data, phenotypic, genotypic and fine structural characterizations in the same parasite sample. In this work, specimens of Lophius budegassa and Lophius piscatorius from NE Atlantic waters were sampled and examined to provide information about specific site of infection and demographic data of two groups of different sizes of xenomas present at both fish species...
May 26, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28545148/mitochondrial-genome-evolution-in-alismatales-size-reduction-and-extensive-loss-of-ribosomal-protein-genes
#4
Gitte Petersen, Argelia Cuenca, Athanasios Zervas, Gregory T Ross, Sean W Graham, Craig F Barrett, Jerrold I Davis, Ole Seberg
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant...
2017: PloS One
https://www.readbyqxmd.com/read/28543018/multiple-ice-binding-proteins-of-probable-prokaryotic-origin-in-an-antarctic-lake-alga-chlamydomonas-sp-ice-mdv-chlorophyceae
#5
James A Raymond
Ice-associated algae produce ice-binding proteins (IBPs) to prevent freezing damage. The IBPs of the three chlorophytes that have been examined so far share little similarity across species, making it likely that they were acquired by horizontal gene transfer (HGT). To clarify the importance and source of IBPs in chlorophytes, we sequenced the IBP genes of another Antarctic chlorophyte, Chlamydomonas sp. ICE-MDV (Chlamy-ICE). Genomic DNA and total RNA were sequenced and screened for known ice-associated genes...
May 19, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28542495/dna-barcoding-and-lc-ms-metabolite-profiling-of-the-lichen-forming-genus-melanelia-specimen-identification-and-discrimination-focusing-on-icelandic-taxa
#6
Maonian Xu, Starri Heidmarsson, Margret Thorsteinsdottir, Finnur F Eiriksson, Sesselja Omarsdottir, Elin S Olafsdottir
Taxa in the genus Melanelia (Parmeliaceae, Ascomycota) belong to a group of saxicolous lichens with brown to black foliose thalli, which have recently undergone extensive changes in circumscription. Taxa belonging to Parmeliaceae are prolific producers of bioactive compounds, which have also been traditionally used for chemotaxonomic purposes. However, the chemical diversity of the genus Melanelia and the use of chemical data for species discrimination in this genus are largely unexplored. In addition, identification based on morphological characters is challenging due to few taxonomically informative characters...
2017: PloS One
https://www.readbyqxmd.com/read/28541477/mitochondrial-retroprocessing-promoted-functional-transfers-of-rpl5-to-the-nucleus-in-grasses
#7
Zhiqiang Wu, Daniel B Sloan, Colin W Brown, Mónica Rosenblueth, Jeffrey D Palmer, Han Chuan Ong
Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus...
May 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28534309/environmental-monitoring-and-assessment-of-antibacterial-metabolite-producing-actinobacteria-screened-from-marine-sediments-in-south-coastal-regions-of-karnataka-india
#8
Sinosh Skariyachan, Shruthi Garka, Sushmitha Puttaswamy, Shobitha Shanbhogue, Raksha Devaraju, Rajeswari Narayanappa
Assessment of the therapeutic potential of secondary metabolite producing microorganisms from the marine coastal areas imparts scope and application in the field of environmental monitoring. The present study aims to screen metabolites with antibacterial potential from actionbacteria associated with marine sediments collected from south coastal regions of Karnataka, India. The actinobacteria were isolated and characterized from marine sediments by standard protocol. The metabolites were extracted, and antibacterial potential was analyzed against eight hospital associated bacteria...
June 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28533985/metabarcoding-monitoring-analysis-the-pros-and-cons-of-using-co-extracted-environmental-dna-and-rna-data-to-assess-offshore-oil-production-impacts-on-benthic-communities
#9
Olivier Laroche, Susanna A Wood, Louis A Tremblay, Gavin Lear, Joanne I Ellis, Xavier Pochon
Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes...
2017: PeerJ
https://www.readbyqxmd.com/read/28533967/divergent-evolutionary-histories-of-dna-markers-in-a-hawaiian-population-of-the-coral-montipora-capitata
#10
Hollie M Putnam, Diane K Adams, Ehud Zelzion, Nicole E Wagner, Huan Qiu, Tali Mass, Paul G Falkowski, Ruth D Gates, Debashish Bhattacharya
We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2-3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies...
2017: PeerJ
https://www.readbyqxmd.com/read/28529264/communities-of-putative-ericoid-mycorrhizal-fungi-isolated-from-alpine-dwarf-shrubs-in-japan-effects-of-host-identity-and-microhabitat
#11
Takahiko Koizumi, Kazuhide Nara
Dwarf shrubs of the family Ericaceae are common in arctic and alpine regions. Many of these plants are associated with ericoid mycorrhizal (ERM) fungi, which allow them to take nutrients and water from the soil under harsh environmental conditions and, thus, affect host plant survival. Despite the importance of ERM fungi to alpine plant communities, limited information is available on the effects of microhabitat and host identity on ERM fungal communities. We investigated the communities of putative ERM fungi isolated from five dwarf shrub species (Arcterica nana, Diapensia lapponica, Empetrum nigrum, Loiseleuria procumbens, and Vaccinium vitis-idaea) that co-occur in an alpine region of Japan, with reference to distinct microhabitats provided by large stone pine (Pinus pumila) shrubs (i...
May 20, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28527138/application-of-hyper-branched-rolling-circle-amplification-hrca-and-hrca-based-strip-test-for-the-detection-of-chattonella-marina
#12
Xiaoli Nie, Chunyun Zhang, Yuanyuan Wang, Changlu Guo, Jin Zhou, Guofu Chen
Harmful algal blooms (HABs) are global threats to marine ecosystems, fisheries, and human health. Therefore, developing effective and accurate methods for identifying causative algae and monitoring seawater quality is urgent. However, traditional, microscopy-based methods are complex, inaccurate, and time-consuming. Here, we present a novel method for effective and sensitive detection of Chattonella marina using hyper-branched rolling circle amplification (HRCA) and HRCA-based strip test (HBST). The large subunit (LSU) ribosomal DNA (rDNA) D1-D2 region of C...
May 19, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28526989/first-molecular-detection-and-characterization-of-hepatozoon-and-sarcocystis-spp-in-field-mice-and-voles-from-japan
#13
Mohamed Abdallah Mohamed Moustafa, Michito Shimozuru, Wessam Mohamed, Kyle Rueben Taylor, Ryo Nakao, Mariko Sashika, Toshio Tsubota
Sarcocystis and Hepatozoon species are protozoan parasites that are frequently detected in domestic and wild animals. Rodents are considered common intermediate and paratenic hosts for several Sarcocystis and Hepatozoon species. Here, blood DNA samples from a total of six rodents, including one Myodes rutilus, one Myodes rufocanus, and four Apodemus speciosus, collected from Hokkaido, Japan, were shown by conventional PCR of the 18S ribosomal RNA (rRNA) gene to contain Sarcocystis and Hepatozoon DNA. Sequencing of the DNA detected one Sarcocystis sp...
May 19, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28525744/ctf4-prevents-genome-rearrangements-by-suppressing-dna-double-strand-break-formation-and-its-end-resection-at-arrested-replication-forks
#14
Mariko Sasaki, Takehiko Kobayashi
Arrested replication forks lead to DNA double-strand breaks (DSBs), which are a major source of genome rearrangements. Yet DSB repair in the context of broken forks remains poorly understood. Here we demonstrate that DSBs that are formed at arrested forks in the budding yeast ribosomal RNA gene (rDNA) locus are normally repaired by pathways dependent on the Mre11-Rad50-Xrs2 complex but independent of HR. HR is also dispensable for DSB repair at stalled forks at tRNA genes. In contrast, in cells lacking the core replisome component Ctf4, DSBs are formed more frequently, and these DSBs undergo end resection and HR-mediated repair that is prone to rDNA hyper-amplification; this highlights Ctf4 as a key regulator of DSB end resection at arrested forks...
May 18, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28521734/higher-order-organisation-of-extremely-amplified-potentially-functional-and-massively-methylated-5s-rdna-in-european-pikes-esox-sp
#15
Radka Symonová, Konrad Ocalewicz, Lech Kirtiklis, Giovanni Battista Delmastro, Šárka Pelikánová, Sonia Garcia, Aleš Kovařík
BACKGROUND: Pikes represent an important genus (Esox) harbouring a pre-duplication karyotype (2n = 2x = 50) of economically important salmonid pseudopolyploids. Here, we have characterized the 5S ribosomal RNA genes (rDNA) in Esox lucius and its closely related E. cisalpinus using cytogenetic, molecular and genomic approaches. Intragenomic homogeneity and copy number estimation was carried out using Illumina reads. The higher-order structure of rDNA arrays was investigated by the analysis of long PacBio reads...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28521470/new-role-of-human-ribosomal-protein-s3-regulation-of-cell-cycle-via-phosphorylation-by-cyclin-dependent-kinase-2
#16
Se Hee Han, Ji Hyung Chung, Joon Kim, Key-Sun Kim, Ye Sun Han
Human ribosomal protein S3 (hRpS3) is a component of the 40S ribosomal subunit that associated in protein synthesis. hRpS3 has additional ribosomal functions such as DNA repair, transcription, metastasis, and apoptosis via interaction with numerous signaling molecules and has different modifications. Cyclin-dependent kinases (CDKs) are heterodimeric serine/threonine protein kinases that regulate cell cycle progression. Among its members, the Cdk1-cyclin B complex is known to control cell progression in the G2/M phase, while Cdk2-cyclin E/A complexes function in G1/S and S/G2 transition...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28516032/a-case-of-respiratory-infection-possibly-caused-by-mycobacterium-triviale-current-problems-on-diagnostic-and-therapeutic-strategies
#17
Asako Okabayashi, Mizue Hasegawa, Akitoshi Sato, Hideki Katsura, Toshiko Kamata, Eitetsu Koh, Yasuo Sekine
Mycobacterium triviale is a subspecies of the Mycobacterium terrae complex, which rarely causes disease in humans. We encountered a case of respiratory infection, possibly caused by M. triviale, which was successfully treated by levofloxacin and clarithromycin. Although DNA-DNA hybridization identified M. triviale in one of three samples, clinical validations convinced us that it was the pathogen. 16s ribosomal RNA sequencing would have been reliable and ideal to perform in this case, although it is not covered by the insurance system in Japan...
2017: Respiratory Medicine Case Reports
https://www.readbyqxmd.com/read/28515326/semantic-closure-demonstrated-by-the-evolution-of-a-universal-constructor-architecture-in-an-artificial-chemistry
#18
Edward B Clark, Simon J Hickinbotham, Susan Stepney
We present a novel stringmol-based artificial chemistry system modelled on the universal constructor architecture (UCA) first explored by von Neumann. In a UCA, machines interact with an abstract description of themselves to replicate by copying the abstract description and constructing the machines that the abstract description encodes. DNA-based replication follows this architecture, with DNA being the abstract description, the polymerase being the copier, and the ribosome being the principal machine in expressing what is encoded on the DNA...
May 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28510184/footprint-of-the-eastern-euroasian-past-in-italian-populations-of-cryptotaenia-thomasii-ten-dc
#19
Anna Maria Palermo, Liliana Bernardo, Domenico Gargano, Giuseppe Pellegrino
BACKGROUND: The knowledge of the genetic architecture of closely related species and/or populations of a single species can be very useful to shed light on the processes that led to their current distributions. The present study provides a preliminary evaluation of the conservation status of the populations of Cryptotaenia thomasii, a very narrow endemic species occurring in southern Italy. Previous studies showed that C. thomasii was phylogenetically closely related to C. flahaultii, endemic species of Caucasus, and to evaluate its conservation status and the genetic variability of plant species the internal transcribed spacers (ITSs) of nuclear ribosomal DNA were sequenced and the SNPs were analyzed...
December 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28504693/cyclin-dependent-kinase-7-is-a-therapeutic-target-in-high-grade-glioma
#20
S A Greenall, Y C Lim, C B Mitchell, K S Ensbey, B W Stringer, A L Wilding, G M O'Neill, K L McDonald, D J Gough, B W Day, T G Johns
High-grade glioma (HGG) is an incurable brain cancer. The transcriptomes of cells within HGG tumors are highly heterogeneous. This renders the tumors unresponsive or able to adapt to therapeutics targeted at single pathways, thereby causing treatment failure. To overcome this, we focused on cyclin-dependent kinase 7 (CDK7), a ubiquitously expressed molecule involved in two major drivers of HGG pathogenesis: cell cycle progression and RNA polymerase-II-based transcription. We tested the activity of THZ1, an irreversible CDK7 inhibitor, on patient-derived primary HGG cell lines and ex vivo HGG patient tissue slices, using proliferation assays, microarray analysis, high-resolution respirometry, cell cycle analysis and in vivo tumor orthografts...
May 15, 2017: Oncogenesis
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