What you missed on twitter this week…

8 items   Favorite tweet by @douglaswr September 10, 2014 at 03:20PM #eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications #openaccess #openresearch #openscience — Douglas Robertson (@douglaswr) September 10, 2014 via Twitter http://ift.tt/WW1qhn September 09, 2014 at 05:04PM Favorite tweet by @neilfws September 11, 2014 at 05:21PM This is really good. “10 simple rules for better figures”: http://t.co/yPMUySHcb4 — Neil Saunders (@neilfws) September 12, 2014 via Twitter http://ift.tt/1mj6z9e September 11, 2014 at 05:00PM Favorite tweet by @rachelomics September 11, 2014 at 06:28PM Pretty visualization of methylation data. Yay! http://t.co/uRR4S5vOYO — Rachel Edgar (@rachelomics) September 11, 2014 via Twitter http://ift.tt/1AEgai2 September 11, 2014 at 04:54PM Favorite tweet by @mwilsonsayres September 12, 2014 at 03:39PM Is lecturing ethical? Storify of Scott Freeman’s interactive seminar: https://t.co/G31T3gFyG7 — Melissa WilsonSayres (@mwilsonsayres) September 12, 2014 via Twitter http://ift.tt/1cr4Itv September 12, 2014 at 03:07PM Favorite tweet by @TrevorABranch September 15, 2014 at 08:55PM Blue whale study by @UW researchers mentioned on @letterman show (at 2:40) http://t.co/biS3YEVYIT @UW_SAFS @UW_CoEnv @SHinesSci — Trevor A. Branch (@TrevorABranch) September 16, 2014 via Twitter http://ift.tt/1h3RSaI September 15, 2014 at 08:19PM Favorite tweet by @jeroenhjanssens September 17, 2014 at 03:39PM Unix pipes and filters beautifully explained by @psobot | http://t.co/xTnPlwmBoO — Jeroen Janssens (@jeroenhjanssens) September 17, 2014 via Twitter http://ift.tt/1dIz0IP September 17, 2014 at 01:44AM Favorite tweet by @GenomeBiology September 19, 2014 at 04:18AM Wang &co on the regulation of stress response in Arabidopsis thru repetitive elements and DNA #methylation http://t.co/DV2HNoY2ul #genomics — Genome Biology (@GenomeBiology) September 19, 2014 via Twitter http://ift.tt/1nMGjHN September 19, 2014 at 04:01AM Favorite tweet by @moorejh September 19, 2014 at 05:22AM Next-generation sequencing for chromatin biology - Nature Reviews http://t.co/miHPJeO5tB #genomics #ENCODE http://ift.tt/1rkdXrA — Jason H. Moore, Ph.D (@moorejh) September 17, 2014 via Twitter http://ift.tt/1gN5ncR September 17, 2014 at 06:53AM Put the internet to work for you. Turn off or edit this Recipe

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[ons] Similarities between two males

Similar:

SELECT *([M1ratio]+[M3ratio])/as meanmales
  FROM [che625@washington.edu].[M1.txt
  inner join [che625@washington.edu].[M3.txton [che625@washington.edu].[M1.txt].loci=[che625@washington.edu].[M3.txt].loci 
  where [M1ratio]-(([M1ratio]+[M3ratio])/2abs(.2
  and [M3ratio(([M1ratio]+[M3ratio])/2abs(.2


Different:
SELECT FROM [che625@washington.edu].[CgLarv_males]
  where
  ([M1ratio[M3ratio>= abs('0.30')
  or
  [M3ratio[M1ratio>= abs('0.30'))


Of the 446658 common loci between the two male samples, how many have the same methylation state?

421,569 similar loci




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New in Pubmed: Temperature influences histone methylation and mRNA expression of the Jmj-C histone-demethylase orthologues during the early development of the oyster Crassostrea gigas.

Temperature influences histone methylation and mRNA expression of the Jmj-C histone-demethylase orthologues during the early development of the oyster Crassostrea gigas.

Mar Genomics. 2014 Sep 12;

Authors: Fellous A, Favrel P, Riviere G

Abstract
In many groups, epigenetic mechanisms influence developmental gene regulation under environmental inputs. The Pacific oyster Crassostrea gigas belongs to lophotrochozoans and its larval development is highly dependent on temperature, but the role of epigenetic mechanisms in this context is unknown despite high levels of the recently characterized Jumonji histone demethylase (JHDM) orthologues (Cg_Jumonji) suggesting a physiological relevance of histone methylation in the oyster development. Because in other species alterations of the histone methylation pattern have deleterious outcomes, we investigated the influence of temperature during the oyster larval life on histone methylation and JHDM expression. To shed light on this point, oyster embryonic and early larval development experiments were carried out at different temperatures (18°C, 25°C and 32°C). Histone methylation levels were investigated using fluorescent ELISA at 6 and 24h post-fertilization. When compared to the 25°C group, at 18°C H3K4, H3K9 and H3K27 residues were hypomethylated at 6h post fertilization (hpf) and hypermethylated at 24hpf. In contrast, at 32°C, 6hpf animals present a dramatic hypermethylation (ca. 4-fold) of all examined residues, which is minored but sustained at 24hpf. RT-qPCR investigations of the mRNA expression of the nine oyster JHDMs, showed gene- and stage-specific temperature sensitivities throughout the early life of oysters. This study provides evidence of the biological significance of histone methylation during development in a lophotrochozoan species. Our results also indicate that temperature influences histone methylation, possibly through the expression level of putative actors of its regulation, which might participate in developmental control. To our knowledge, this is the first report indicating a direct relationship between an epigenetic mark and an environmental parameter in marine molluscs. Such investigations could help better understand the molecular mechanisms of development and adaptation in lophotrochozoans.

PMID: 25224965 [PubMed - as supplied by publisher]



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New in Pubmed: [Effects of calcification on respiratory quotient of cultured oyster Crassostrea gigas and its fouling animals].

[Effects of calcification on respiratory quotient of cultured oyster Crassostrea gigas and its fouling animals].

Ying Yong Sheng Tai Xue Bao. 2014 Jun;25(6):1785-90

Authors: Ren LH, Zhang JH, Fang JG, Yao YF, Zhang YT, Gao ZK, Zhang ML

Abstract
Respiratory quotient (RQ) is one of the basic indices in physiology and energy metabolism of animals. When RQ is calculated, the amount of released CO2 is typically used directly. But for calcifying marine organisms, calcification which can affect dissolved inorganic carbon (DIC) content in the water may cause methodological error to some extent, if it is ignored. In this paper, RQ and O/N of cultured oyster Crassostrea gigas and 3 marine fouling animal species (Mytilus edulis, Ciona intestinalis, Styela clava) were measured in the respiratory chamber to discuss the effect of calcification in RQ determination. The results demonstrated that calcification rates of C. gigas and M. edulis were (56.37 +/- 14.85) and (17.95 +/- 7.21) micromol x g(-1) x h(-1), respectively. (3.72 +/- 0.80) and (1.48 +/- 0.14) mg x L(-1) DIC in the water were correspondingly decreased, which occupied about (60.9 +/- 7.6)% and (39.9 +/- 5.7)% of respired CO2, respectively. RQ values of 4 animals were C. gigas 1.38 +0.19, M. edulis 1.18 +/- 0.11, C. intestinalis 1.11 +/- 0.05 and S. clava 1.32 +/- 0.19, which agreed with the O/N values except C. intestinalis. Meanwhile, the uncorrected RQ values of C. gigas and M. edulis were 0.56 +/- 0.19 and 0.70 +/- 0.04, respectively, which were contrary to the O/N values. Therefore, it was obviously that calcification could result in a significant influence on the respiratory quotient by affecting water DIC concentration and should be accurately calculated in RQ measurement.

PMID: 25223039 [PubMed - in process]



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Evolution and origin of sympatric shallow-water morphotypes of Lake Trout, Salvelinus namaycush, in Canada’s Great Bear Lake

LN Harris, L Chavarie, R Bajno, KL Howland, SH Wiley… - Heredity, 2014
Abstract Range expansion in north-temperate fishes subsequent to the retreat of the
Wisconsinan glaciers has resulted in the rapid colonization of previously unexploited,
heterogeneous habitats and, in many situations, secondary contact among conspecific


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SeaPen Timelapse: September 15, 2014 at 06:12AM

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New in Pubmed: Genomic Analysis of the Pacific Oyster (Crassostrea gigas) Reveals Possible Conservation of Vertebrate Sex Determination Genes in a Mollusc.

Genomic Analysis of the Pacific Oyster (Crassostrea gigas) Reveals Possible Conservation of Vertebrate Sex Determination Genes in a Mollusc.

G3 (Bethesda). 2014 Sep 11;

Authors: Zhang N, Xu F, Guo X

Abstract
Despite the prevalence of sex in animal kingdom, we have only limited understanding of how sex is determined and evolved in many taxa. The mollusc Pacific oyster Crassostrea gigas exhibits complex modes of sexual reproduction that consists of protandric dioecy, sex change and occasional hermaphroditism. This complex system is controlled by both environmental and genetic factors through unknown molecular mechanisms. In this study, we investigated genes related to sex-determining pathways in C. gigas through transcriptome sequencing and analysis of female and male gonads. Our analysis identified novel homologs in the oyster of key sex-determining genes (SoxH or Sry-like and FoxL2) that were thought to be vertebrate-specific. Their expression profile in C. gigas is consistent with conserved roles in sex determination, under a proposed model where a novel testis-determining CgSoxH may serve as a primary regulator, directly or indirectly interacting with a testis-promoting CgDsx and an ovary-promoting CgFoxL2. Our findings suggest that key vertebrate sex-determining genes such as Sry and FoxL2 may not be inventions of vertebrates as suggested by previous studies. The presence of such genes in a mollusc with expression profiles consistent with expected roles in sex determination suggest that sex determination may be deeply conserved in animals, despite rapid evolution of the regulatory pathways that in C. gigas may involve both genetic and environmental factors.

PMID: 25213692 [PubMed - as supplied by publisher]



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[PDF] Evolution of innate immunity: clues from invertebrates via fish to mammals

K Buchmann - Name: Frontiers in Immunology, 2014
Copyright statement:© 2014 Buchmann. This is an open-access article distributed under the
terms of the Creative Commons Attribution License (CC BY). The use, distribution and
reproduction in other forums is permitted, provided the original author (s) or licensor are


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