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3 items   Favorite tweet by @genetics_blog July 28, 2014 at 07:21AM Corset: differential gene expression analysis for de novo assembled transcriptomes http://t.co/6ju9VFpO5M — Stephen Turner (@genetics_blog) July 28, 2014 via Twitter http://ift.tt/1j3Xxjc July 28, 2014 at 07:00AM Favorite tweet by @fperez_org July 29, 2014 at 08:11PM Exploratory computing with Python: a beautiful self-contained course as IPython notebooks, by M. Bakker of U. Delft: http://t.co/Olnqq4PD1f — Fernando Perez (@fperez_org) July 29, 2014 via Twitter http://ift.tt/Yv21B0 July 29, 2014 at 02:05PM Favorite tweet by @genetics_blog August 01, 2014 at 10:59AM Buster - #Rstats pkg for bagging hierarchical clustering http://t.co/HnkW4nlN0I — Stephen Turner (@genetics_blog) August 1, 2014 via Twitter http://ift.tt/1j3Xxjc August 01, 2014 at 10:01AM Put the internet to work for you. Turn off or edit this Recipe

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New in Pubmed: Infection of Manila clams Ruditapes philippinarum from Galicia (NW Spain) with a Mikrocytos-like parasite.

Infection of Manila clams Ruditapes philippinarum from Galicia (NW Spain) with a Mikrocytos-like parasite.

Dis Aquat Organ. 2014 Jul 24;110(1):71-9

Authors: Ramilo A, Iglesias D, Abollo E, González M, Darriba S, Villalba A

Abstract
The name ‘microcells’ is frequently used to refer to small-sized unicellular stages of molluscan parasites of the genera Bonamia (Rhizaria, Haplosporidia) and Mikrocytos (Rhizaria). Histological examination of Manila clams Ruditapes philippinarum revealed microcells in the connective tissue of adductor muscle, foot, mantle, gills, siphon and visceral mass. The clams had been collected from 4 beds on the coast of Galicia, Spain. The prevalence of these microcells ranged from 73 to 93% in surface clams and from 3 to 33% in buried clams. However, the detection of brown ring disease signs in clams from every bed prevented us from making the assumption that the microcells alone were responsible for clam mortality. PCR assays using primer pairs designed to detect Bonamia spp. and haplosporidians gave negative results, whereas positive results were obtained with primers for the genus Mikrocytos. A consensus sequence of 1670 bp of the ribosomal gene complex of the microcells was obtained. It contained a section of the 18S region, the whole first internal transcribed spacer, the 5.8S region, the second internal transcribed spacer and a section of the 28S region. Comparison of this sequence with those of M. mackini infecting Crassostrea gigas and Mikrocytos sp. infecting Ostrea edulis showed that the microcells of Galician clams were the most divergent among the compared parasites. This is the first report of a Mikrocytos-like parasite infecting Manila clams. Care must be taken to avoid the spread of this parasite through Manila clam transfers.

PMID: 25060499 [PubMed - in process]



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New in Pubmed: Molecular taxonomy of Mikrocytos boweri sp. nov. from Olympia oysters Ostrea lurida in British Columbia, Canada.

Molecular taxonomy of Mikrocytos boweri sp. nov. from Olympia oysters Ostrea lurida in British Columbia, Canada.

Dis Aquat Organ. 2014 Jul 24;110(1):65-70

Authors: Abbott CL, Meyer GR, Lowe G, Kim E, Johnson SC

Abstract
Mikrocytos mackini is a microcell parasite that usually infects Crassostrea gigas distributed along the Pacific Northwest coast of North America. For many years, M. mackini was the only known species in the genus, but there have been multiple recent findings of genetically divergent forms of Mikrocytos in different hosts and in distantly located geographic locations. This note describes M. boweri sp. nov. found in Olympia oysters Ostrea lurida collected from and native to British Columbia, Canada, primarily using a molecular taxonomic approach.

PMID: 25060498 [PubMed - in process]



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[ons] Lineage sp and developmentally different barplot revisited



















library(plotly)

p <- plotly(username="claire.olson", key="piczb54zao")

trace1 <- list(
x = c("Genes", "Transposable Elements", "Promoter Regions"),
y = c(3.91, 8.85, -1.26),
name = "Developmentally Different Loci",
type = "bar"
)

trace2 <- list(
x = c("Genes", "Transposable Elements", "Promoter Regions"),
y = c(1.71, 10.76, -0.92),
name = "Lineage-specific Loci",
type = "bar"
)

data <- list(trace1, trace2)
layout <- list(
xaxis = list(type = "category"),
yaxis = list(title= "Percent of total genomic regions"),
barmode = "group",
categories = c("Genes", "Transposable Elements", "Promoter Regions")
)

response <- p$plotly(data, kwargs=list(layout=layout, filename="Lineage_Devel_Loci", fileopt="overwrite"))
url <- response$url
filename <- response$filename






from Claire’s lab notebook http://ift.tt/UGAS2l
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New in Pubmed: Evolution of the AKH/corazonin/ACP/GnRH receptor superfamily and their ligands in the Protostomia.

Evolution of the AKH/corazonin/ACP/GnRH receptor superfamily and their ligands in the Protostomia.

Gen Comp Endocrinol. 2014 Jul 21;

Authors: Hauser F, Grimmelikhuijzen CJ

Abstract
In this review we trace the evolutionary connections between GnRH receptors from vertebrates and the receptors for adipokinetic hormone (AKH), AKH/corazonin-related peptide (ACP), and corazonin from arthropods. We conclude that these G protein-coupled receptors (GPCRs) are closely related and have a common evolutionary origin, which dates back to the split of Proto- and Deuterostomia, about 700 million years ago. We propose that in the protostomian lineage, the ancestral GnRH-like receptor gene duplicated as did its GnRH-like ligand gene, followed by diversification, leading to (i) a corazonin receptor gene and a corazonin-like ligand gene, and (ii) an AKH receptor gene and an AKH-like ligand gene in the Mollusca and Annelida. Subsequently, the AKH receptor and ligand genes duplicated once more, yielding the situation that we know from arthropods today, where three independent hormonal systems exist, signalling with AKH, ACP, and corazonin. Our model for the evolution of GnRH signaling in the Protostomia is a striking example of receptor-ligand co-evolution. This model has been developed using several bioinformatics tools (TBLASTN searches, phylogenetic tree analyses), which also helped us to annotate six novel AKH preprohormones and their corresponding AKH sequences from the following molluscs: The sea hare Aplysia californica (AKH sequence: pQIHFSPDWGTamide), the sea slug Tritonia diomedea (pQIHFSPGWEPamide), the fresh water snail Bithynia siamensis goniomphalos (pQIHFTPGWGSamide), the owl limpet Lottia gigantea (pQIHFSPTWGSamide), the oyster Crassostrea gigas (pQVSFSTNWGSamide), and the freshwater pearl mussel Hyriopsis cumingii (pQISFSTNWGSamide). We also found AKHs in the tardigrade Hysibius dujardini (pQLSFTGWGHamide), the rotifer Brachionus calycifloros (pQLTFSSDWSGamide), and the penis worm Priapulus caudatus (pQIFFSKGWRGamide). This is the first report, showing that AKH signaling is widespread in molluscs.

PMID: 25058364 [PubMed - as supplied by publisher]



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