A great first lab volunteering experience

I have never worked in an actual research lab before, but I have always
thought that research is what I want to do career-wise. So, I decided it
was time to get some experience and started volunteering in Steven’s lab.
So far I have mostly been working on data analysis with excel. I really am
actually enjoying it because I am learning a lot about not only how to make
easy-to-read graphs, but also what kind of data relationships are the
important ones to create visuals for based on the context of the research.
I have also counted some oyster larva, which was a nice change from data
analysis. While I enjoy data analysis and working with excel, I hope to
learn more about the other aspects of what all goes in to the research
process and more bench-work procedures. Everyone here is really nice and
very supportive. I feel no fear asking questions… even if I have to ask the
same one a couple times. This is all still pretty new to me, but everyone
has been ready and willing to help if I ask for it. This is a great place
to get some experience and an excellent learning environment.

New in Pubmed: Development of Genetic Markers for Triploid Verification of the Pacific Oyster, Crassostrea gigas.

Development of Genetic Markers for Triploid Verification of the Pacific Oyster, Crassostrea gigas.

Asian-Australas J Anim Sci. 2013 Jul;26(7):916-20

Authors: Kang JH, Lim HJ, Kang HS, Lee JM, Baby S, Kim JJ

Abstract
The triploid Pacific oyster, which is produced by mating tetraploid and diploid oysters, is favored by the aquaculture industry because of its better flavor and firmer texture, particularly during the summer. However, tetraploid oyster production is not feasible in all oysters; the development of tetraploid oysters is ongoing in some oyster species. Thus, a method for ploidy verification is necessary for this endeavor, in addition to ploidy verification in aquaculture farms and in the natural environment. In this study, a method for ploidy verification of triploid and diploid oysters was developed using multiplex polymerase chain reaction (PCR) panels containing primers for molecular microsatellite markers. Two microsatellite multiplex PCR panels consisting of three markers each were developed using previously developed microsatellite markers that were optimized for performance. Both panels were able to verify the ploidy levels of 30 triploid oysters with 100% accuracy, illustrating the utility of microsatellite markers as a tool for verifying the ploidy of individual oysters.

PMID: 25049868 [PubMed]



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New in Pubmed: Characterizations of Shell and Mantle Edge Pigmentation of a Pacific Oyster, Crassostrea gigas, in Korean Peninsula.

Characterizations of Shell and Mantle Edge Pigmentation of a Pacific Oyster, Crassostrea gigas, in Korean Peninsula.

Asian-Australas J Anim Sci. 2013 Dec;26(12):1659-64

Authors: Kang JH, Kang HS, Lee JM, An CM, Kim SY, Lee YM, Kim JJ

Abstract
The objectives of this study were to investigate color patterns of shell and mantle edge pigmentation of a Pacific oyster, C. gigas, and to estimate variance components of the two colors. A sample of 240 F0 oysters was collected from six aquaculture farms in Tongyeong, Korea to measure shell color and mantle edge pigmentation. Among the F0s, male and female individuals with black (white) shell and black (white) mantle edge were selected and mated to generate three F1 full-sib black (white) cross families (N = 265). Two and four F2 cross families (N = 286) were also produced from black and white F1 selected individuals, respectively. Variance component estimates due to residuals and families within color were obtained using SAS PROC VARCOMP procedures to estimate heritability of shell and mantle edge pigmentation. In the F0 generation, about 29% (11%) had black (white) color for both shell and mantle edge. However, in the F1 and F2 black (white) cross families, 75% (67%) and 100% (100%) of oysters had black (white) shell colors, and 59% (23%) and 79% (55%) had black (white) mantle edge, respectively. Spearman correlation coefficients between shell and mantle edge color were 0.25, 0.74, and 0.92 in F0, F1, and F2 generations, respectively, indicating that, with generations of selection process, an individual with black (white) shell color is more likely to have black (white) mantle edge pigmentation. This suggests that shell color could be a good indicator trait for mantle edge pigmentation if selection of both the colors is implemented for a couple of generations. Estimates of heritability were 0.41 and 0.77 for shell color and 0.27 and 0.08 for mantle edge pigmentation in the F1 and F2 generations, respectively, indicating that, in general, significant proportions of phenotypic variations for the shell and mantle edge colors are explained by genetic variations between individuals. These results suggest that the two color traits are inheritable and correlated, enabling effective selection on shell and mantle edge color.

PMID: 25049755 [PubMed]



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New in Pubmed: Positive Feedback Loop between Introductions of Non-native Marine Species and Cultivation of Oysters in Europe.

Positive Feedback Loop between Introductions of Non-native Marine Species and Cultivation of Oysters in Europe.

Conserv Biol. 2014 Jul 21;

Authors: Mineur F, Roux AL, Maggs CA, Verlaque M

Abstract
With globalization, agriculture and aquaculture activities are increasingly affected by diseases that are spread through movement of crops and stock. Such movements are also associated with the introduction of non-native species via hitchhiking individual organisms. The oyster industry, one of the most important forms of marine aquaculture, embodies these issues. In Europe disease outbreaks affecting cultivated populations of the naturalized oyster Crassostrea gigas caused a major disruption of production in the late 1960s and early 1970s and mitigation procedures involved massive imports of stock from the species’ native range in the northwestern Pacific from 1971 to 1977. We assessed the role stock imports played in the introduction of non-native marine species (including pathogens) from the northwestern Pacific to Europe through a methodological and critical appraisal of record data. The discovery rate of non-native species (a proxy for the introduction rate) from 1966 to 2012 suggests a continuous vector activity over the entire period. Disease outbreaks that have been affecting oyster production since 2008 may be a result of imports from the northwestern Pacific, and such imports are again being considered as an answer to the crisis. Although successful as a remedy in the short and medium terms, such translocations may bring new diseases that may trigger yet more imports (self-reinforcing or positive feedback loop) and lead to the introduction of more hitchhikers. Although there is a legal framework to prevent or reduce these introductions, existing procedures should be improved. Ciclo de Retroalimentación Positiva entre la Introducción de Especies Marinas No-Nativas y el Cultivo de Ostras en Europa.

PMID: 25047099 [PubMed - as supplied by publisher]



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Scholar Alert: New citation

Scholar Alert: New citations to my articles

Molecular cloning and characterization of cathepsin L from freshwater mussel,< i> Cristaria plicata</i>

X Hu, X Hu, B Hu, C Wen, Y Xie, D Wu, Z Tao, A Li… - Fish & Shellfish Immunology, 2014
Abstract Cathepsin L is one of the crucial enzyme superfamilies and involved in the immune
responses. The Cathepsin L cDNA and genome of Cristaria plicata (CpCL) was cloned from
the hemocytes using degenerate primers by the rapid amplification of cDNA ends (RACE)

[PDF] Bis-class: a new classification tool of methylation status using bayes classifier and local methylation information

I Huh, X Yang, T Park, VY Soojin - BMC Genomics, 2014
Background Whole genome sequencing of bisulfite converted DNA (‘methylC-seq’) method
provides comprehensive information of DNA methylation. An important application of these
whole genome methylation maps is classifying each position as a methylated versus non-


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citation ifttt

[ons] Lineage sp and developmentally different loci- bar plot



















library(plotly)

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

trace1 <- list(
x = c("Genes", "Transposable Elements", "Promoter Regions"),
y = c(43.15, 14.73, 4.65),
name = "Developmentally Different",
type = "bar"
)

trace2 <- list(
x = c("Genes", "Transposable Elements", "Promoter Regions"),
y = c(40.96, 16.63, 4.99),
name = "Lineage-specific",
type = "bar"
)

trace3 <- list(
x = c("Genes", "Transposable Elements", "Promoter Regions"),
y = c(39.24, 5.87, 5.91),
name = "All CG",
type = "bar"
)

data <- list(trace1, trace2, trace3)
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$plotly(data, kwargs=list(layout=layout, filename="Lineage_Devel_Sp_Loci", fileopt="overwrite"))
url <- response$url
filename <- response$filename






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New in Pubmed: Identification and functional characterization of SIMPL in Crassostrea gigas reveals its ancient origin and involvement in the regulation of Rel/NF-κB transcription activity.

Identification and functional characterization of SIMPL in Crassostrea gigas reveals its ancient origin and involvement in the regulation of Rel/NF-κB transcription activity.

Fish Shellfish Immunol. 2014 Jul 16;

Authors: Zhang Y, Li J, Yu F, Tong Y, Zhang Y, Xiang Z, Yu Z

Abstract
SIMPL (Signaling Molecule that associates with the mouse Pelle-Like Kinase) has been recently identified as a co-regulator of NF-κB dependent transcription. Here, we report the discovery and functional analysis of the SIMPL in a mollusk, Crassostrea gigas, which terms as CgSIMPL. CgSIMPL is comprised of 252 amino acids and shares significant homology with vertebrate homologs. Over-expression of CgSIMPL does not activate the NF-κB reporter in the HEK293 cell line, but can enhance Rel-dependent NF-κB transactivation. The dominant-negative effect of CgSIMPL was observed after the deletion of NLS, strongly suggesting that NLS is required for the enhancement of Rel-dependent NF-κB transactivation. Furthermore, CgSIMPL mRNA is constitutively expressed in various tissues and is inducible at late stages of infection, supporting its regulatory function in innate immunity. Altogether, our studies reveal that SIMPL is reserved and co-evolved with NF-κB in chordate and mollusk, supporting its ancient origin and involvement in regulation of NF-κB signaling pathway.

PMID: 25038279 [PubMed - as supplied by publisher]



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