New in Pubmed: Identification of Conserved and Novel MicroRNAs in the Pacific Oyster Crassostrea gigas by Deep Sequencing.

Identification of Conserved and Novel MicroRNAs in the Pacific Oyster Crassostrea gigas by Deep Sequencing.

PLoS One. 2014;9(8):e104371

Authors: Xu F, Wang X, Feng Y, Huang W, Wang W, Li L, Fang X, Que H, Zhang G

Abstract
MicroRNAs (miRNAs) play important roles in regulatory processes in various organisms. To date many studies have been performed in the investigation of miRNAs of numerous bilaterians, but limited numbers of miRNAs have been identified in the few species belonging to the clade Lophotrochozoa. In the current study, deep sequencing was conducted to identify the miRNAs of Crassostrea gigas (Lophotrochozoa) at a genomic scale, using 21 libraries that included different developmental stages and adult organs. A total of 100 hairpin precursor loci were predicted to encode miRNAs. Of these, 19 precursors (pre-miRNA) were novel in the oyster. As many as 53 (53%) miRNAs were distributed in clusters and 49 (49%) precursors were intragenic, which suggests two important biogenetic sources of miRNAs. Different developmental stages were characterized with specific miRNA expression patterns that highlighted regulatory variation along a temporal axis. Conserved miRNAs were expressed universally throughout different stages and organs, whereas novel miRNAs tended to be more specific and may be related to the determination of the novel body plan. Furthermore, we developed an index named the miRNA profile age index (miRPAI) to integrate the evolutionary age and expression levels of miRNAs during a particular developmental stage. We found that the swimming stages were characterized by the youngest miRPAIs. Indeed, the large-scale expression of novel miRNAs indicated the importance of these stages during development, particularly from organogenetic and evolutionary perspectives. Some potentially important miRNAs were identified for further study through significant changes between expression patterns in different developmental events, such as metamorphosis. This study broadened the knowledge of miRNAs in animals and indicated the presence of sophisticated miRNA regulatory networks related to the biological processes in lophotrochozoans.

PMID: 25137038 [PubMed - as supplied by publisher]



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[HTML] SNP Identification by Transcriptome Sequencing and Candidate Gene-Based Association Analysis for Heat Tolerance in the Bay Scallop Argopecten irradians

X Du, L Li, S Zhang, F Meng, G Zhang - PloS one, 2014
Abstract The northern bay scallop Argopecten irradians irradians (Lamarck) and the
southern bay scallop Argopecten irradians concentricus (Say) were introduced into China in
the 1980s and 1990s, and are now major aquaculture molluscs in China. Here, we report

[HTML] Transcriptome of American Oysters, Crassostrea virginica, in Response to Bacterial Challenge: Insights into Potential Mechanisms of Disease Resistance

IC McDowell, C Nikapitiya, D Aguiar, CE Lane, S Istrail… - PloS one, 2014
Abstract The American oyster Crassostrea virginica, an ecologically and economically
important estuarine organism, can suffer high mortalities in areas in the Northeast United
States due to Roseovarius Oyster Disease (ROD), caused by the gram-negative bacterial

[HTML] De Novo Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy

JD Farrell, S Byrne, C Paina, T Asp - PLOS ONE, 2014
Background Perennial ryegrass is a highly heterozygous outbreeding grass species used
for turf and forage production. Heterozygosity can affect de-Bruijn graph assembly making
de novo transcriptome assembly of species such as perennial ryegrass challenging.


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6 items   Favorite tweet by @profjsb August 08, 2014 at 08:08PM Here’s me on the educational revolution to be fostered by #IPython/#Jupyter married to Google Docs inside of Chrome http://t.co/uStyUpwpTO — Joshua Bloom (@profjsb) August 8, 2014 via Twitter http://ift.tt/KWQTMN August 08, 2014 at 03:40PM Favorite tweet by @dirtygeew August 08, 2014 at 08:28PM http://t.co/5Ydc4gUB9d @sr320 Something to consider… — sarah gw (@dirtygeew) August 8, 2014 via Twitter http://ift.tt/1uxCZ5y August 08, 2014 at 11:15AM Favorite tweet by @tangming2005 August 12, 2014 at 06:50PM Trim at phred score 5! not 20! http://t.co/nmzu0i3yZM — Ming Tang (@tangming2005) August 12, 2014 via Twitter http://ift.tt/1vgyjFp August 12, 2014 at 11:57AM Favorite tweet by @theRedShrimp August 13, 2014 at 08:13PM “You can live tweet me if you want” @sr320 @EIMD_fhl #seminars #notacompetition http://ift.tt/VnzmCK — Reyn Yoshioka (@theRedShrimp) August 14, 2014 via Twitter http://ift.tt/VnzmT0 August 13, 2014 at 07:29PM Favorite tweet by @LaurenFuess August 13, 2014 at 08:13PM Listening to @sr320 talk about epigenetics tonight at #fhl. #science #genomes http://ift.tt/VnzoKL — Lauren (@LaurenFuess) August 14, 2014 via Twitter http://ift.tt/VnzoKO August 13, 2014 at 07:30PM Favorite tweet by @communicating August 14, 2014 at 08:17PM iPython Notebook Vagrant Box - A simple skeleton for easily running iPython Notebooks on a local machine: https://t.co/5keLkVpbpv — Christopher (@communicating) August 15, 2014 via Twitter http://ift.tt/1uVoj0n August 14, 2014 at 08:04PM Put the internet to work for you. Turn off or edit this Recipe

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New in Pubmed: Evidence for accumulation of Synechococcus elongatus (Cyanobacteria: Cyanophyceae) in the tissues of the oyster Crassostrea gigas (Mollusca: Bivalvia).

Evidence for accumulation of Synechococcus elongatus (Cyanobacteria: Cyanophyceae) in the tissues of the oyster Crassostrea gigas (Mollusca: Bivalvia).

Tissue Cell. 2014 Jul 22;

Authors: Avila-Poveda OH, Torres-Ariño A, Girón-Cruz DA, Cuevas-Aguirre A

Abstract
Cyanobacteria appear to have direct relations with mollusks in several aspects. This is the first time, distinguishing Gram-negative cyanoprokaryotic Synechococcus elongatus as bright yellow-gold autofluorescence by Lillie’s and Hiss’ staining methods on paraffin-embedded tissues of Crassostrea gigas. Three diets: cyanoprokaryotes, cyanoprokaryotes with microalgae, and only microalgae were evaluated. Cyanoprokaryotes were intact, densely bundled, and immersed in the cytosol of the digestive gland, connective tissue, mantle, and gonad of C. gigas, revealing an accumulation systemic without tissue damage observed by histology. Unexpectedly, cyanoprokaryotes were slightly most accumulated with microalgae diet by each of the tissues of the C. gigas than with any other diets. Cyanoprokaryotes tend to be in mean slightly higher in the digestive gland than in any other tissues respectively for each diet, although these values are closely similar to connective tissue. A possible order of exposure of the oyster tissues to accumulation of cyanoprokaryotes was digestive gland, connective tissue, mantle, and gonad. Thereby, the digestive gland could be the major target tissue for the accumulation. Our observations provide a valuable insight regarding the ability of cyanoprokaryotes to penetrate, spread, and remain inside the oyster tissues, suggesting for S. elongatus: (1) a pre-accumulation in oyster tissues from the natural environment, (2) a phagocytosis and/or endocytosis process rather than ingestion and extracellular digestion, (3) an apparent cellular division in the cytosol of oyster tissues, (4) an apparent inter-tissue movement, and (5) a possible endosymbiosis between C. gigas and S. elongatus. Hereby, it is possible that S. elongatus have a well-developed host-endobiont relationship with oysters, and thereby support future work toward a description of the escape and spreading mechanisms of S. elongatus inside the tissues of mollusks, and put forward questions as why it is there? and are the cells active or inactive?

PMID: 25109761 [PubMed - as supplied by publisher]



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Behavior of Titanium Dioxide Nanoparticles in Three Aqueous Media Samples: Agglomeration and Implications for Benthic Deposition

JJ Doyle, V Palumbo, BD Huey, JE Ward - Water, Air, & Soil Pollution, 2014
Abstract Predicting the fate of nanoparticles in aquatic environments requires knowledge of
how these materials interact with the organic and inorganic constituents in aqueous media.
This work explored the behavior of three types of titanium dioxide nanoparticles (rutile and

[PDF] Bacterias autótrofas y heterótrofas asociadas a nieve marina lodosa en arrecifes con escorrentía continental

A Henao-Castro, N Comba González, EM Alvarado Ch… - Universitas Scientiarum, 2014
Abstract The density of heterotrophic bacteria is greater than autotrophic in marine snow
aggregates influenced by continental runoff. Four coral reef areas at different distances from
the Canal del Dique served to evaluate this premise; this canal is the main source of


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