ABSTRACT

INTRODUCTION Over the past several years our lab has experimented with a variety of high-throughput sequencing platforms with the ultimate goal of addressing important scientific questions. On a few occasions we have been successful. Some of our early work included Roche 454 GS-FLX pyrosequencing used to examine phenotypic plasticity in lake trout , identify single nucleotide polymorphisms in salmon and develop genomic resources for Pacific herring . - Morera D, Roher N, Ribas L, Balasch JC, Doñate C, Callol A, Boltaña A, Roberts SB, Goetz G, Goetz FW, Mackenzie SA. (2011) RNA-Seq reveals an integrated immune response in nucleated erythrocytes. PLoS ONE 6(10): e26998. doi:10.1371/journal.pone.0026998 - Gavery MR* and Roberts SB. (2012) Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 7:2 94-99 June 2012. doi:10.1016/j.cbd.2011.12.003 - Burge CA, Douglas N, Conti-Jerpe I, Weil E, Roberts SB, Friedman CS, CD Harvell. (2012) Friend or foe: the association of Labyrinthulomycetes with the Caribbean sea fan, Gorgonia ventalina. Diseases of Aquatic Organisms. 101:1-12 doi:10.3354/dao02487 - Gavery MR, Roberts SB. (2013) Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc. PeerJ 1:e215 doi:10.7717/peerj.215 However there are a number of efforts that have failed early on (_ie_ poor read quality) or just never gained enough momentum to see the light of the peer-review system. This paper is a final attempt to share these datasets in a manner where they have the potenial, however slim, to be useful to someone. We will not be providing fluffy background or in-depth over-analysis but strive to offer a sound _data description_. This current work will be organized by target species, which will often correspond to project. Species include - _Vibrio tubiashii_ - Olympia oyster (_Ostrea lurida_) - Yellow Perch (_Perca flavescens_) - Pacific herring (_Clupea pallasii_) - Abalone / Withering Syndrome (WS) - Hard clam (_Mercenaria mercenaria_)

AbstractWe tested the sensitivity of early life stages and the potential for geoduck clams to display acclimatization to ocean acidification through a series of  repeat exposure experiments.  First, we exposed larval geoducks to ambient (~8.0) and low pH (~7.4) for 10 days and found that larval mortality is decreased and shell size increased in low pH conditions. Second, we exposed juvenile geoduck to ambient (~8.0), low (~7.4) and lower (~7.0) pH for 23 days, placed them in ambient common garden for several months, then re-exposed them to ambient (~8.0) pH and low pH (~7.4) for another 23 days. In geoduck juveniles there was a size benefit of preconditioning to low pH. Juvenile growth initially declined at pH ~7.4 and 7.0 in the first exposure, but when replaced in the ambient conditions, the initial exposure to low pH resulted in compensatory growth, such that the juveniles grew larger. Growth in the pre-exposed juveniles was also more resistant to low pH in the second exposure. The role of DNA methylation as a mechanism of environmental memory was tested using reduced representation bisulfite sequencing. This suggests that acclimatization to OA can result in benefits to geoduck growth, with exposure memory that is potentially linked to epigenetic mechanisms such as DNA methylation.

1. Abstract

1. Abstract

INTRODUCTION - DNA Methylation - Function in bivalves - MERV - Relationship with expression

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YEAR 2 PROGRESS REPORT NOAA Award: NA13OAR4310107 University of Washington PI: Bart Nijssen Reporting Period: 07/01/2014 - 06/30/2015 Report date: 06/30/2015

INTRODUCTION PROBLEM 1 Relevant definitions: $$minimize\quad ^{6} ^{6} ^{6} ^{6} c_{ij}x_{ij}^{kl} \qquad \left ( i\neq j , k\neq l\right )$$ $$ b_{i}^{kl} = \left\{ b^{kl} & i = k \\ b^{kl} & i = l\\ 0 & otherwise \right. $$ $$^{6} \left ( ^{6} x_{ij}^{kl} - ^{6} x_{ji}^{kl} = b_{i}^{kl} \right ) \qquad \left ( i\neq j , k\neq l\right )$$ $$^{6} ^{6} x_{ij}^{kl} \le u_{i,j} \qquad \forall i,j \left ( i\neq j , k\neq l\right )$$ $$ x_{i,j} \ge 0 $$ $$ u_{i,j} &= 30 + 2(-1)^i + 3(-1)^j \\ c_{i,j} &= 50 + 10(-1)^{j+i} & i \ne j\\ b_{i,j} &= 10 + 2(-1)^{i+j} & i \ne j $$ PROBLEM 3 Relevant definitions: - Let xs, t be the amount of drugs bought from supplier s on month t - Let $y_{s,t} = \left\{ 1 & \\ 0 & \right. $ &: min ^{6}( c_{1,t}*x_{1,t} + c_{2,t}*x_{2,t}+ c_{3,t}*x_{3,t}- 7*E_t)\\ &\\ &y_{1,t} + y_{2,t} + y_{3,t} = 1 & t\in \{1, \dots ,6\}\\ &y_{s,t}*d_s \leq x_{s,t} & t\in \{1, \dots ,6\}, s \in \{1,2,3\}\\ &y_{s,t} \leq 1 & t\in \{1, \dots ,6\}, s \in \{1,2,3\}\\ &I_{t} \leq 40 & t\in \{1, \dots ,6\}\\ &I_{t-1} + x_{1,t} + x_{2,t} + x_{3,t} = d_t+I_t + E_t & t\in \{1, \dots ,6\}\\ Month t amp; c1, t amp; c2, t amp; c3, t amp; dt --------- ------------ ------------ ------------ ---------- 1 amp; 15 amp; 11 amp; 11 amp; 99 2 amp; 14 amp; 12 amp; 15 amp; 113 3 amp; 13 amp; 13 amp; 11 amp; 107 4 amp; 12 amp; 14 amp; 15 amp; 121 5 amp; 11 amp; 15 amp; 11 amp; 115 6 amp; 10 amp; 16 amp; 15 amp; 129 : Problem 3. Coefficients d₁ = 129; d₂ = 131, d₃ = 129 Month t amp; ys, t amp; xs, t amp; It amp; Et --------- ---------------- ------------------ -------------- -------------- 1 amp; y3, 1 = 1 amp; x3, 1 = 129 amp; I₁ = 0 amp; E₁ = 30 2 amp; y2, 2 = 1 amp; x2, 2 = 131 amp; I₂ = 0 amp; E₂ = 18 3 amp; y3, 3 = 1 amp; x3, 3 = 129 amp; I₃ = 16 amp; E₃ = 6 4 amp; y1, 4 = 1 amp; x1, 4 = 131 amp; I₄ = 26 amp; E₄ = 0 5 amp; y3, 5 = 1 amp; x3, 5 = 129 amp; I₅ = 40 amp; E₅ = 0 6 amp; y1, 6 = 1 amp; x1, 6 = 131 amp; I₆ = 0 amp; E₆ = 42 : Problem 3. Solution (All the other xs, t and ys, t not mentioned in the table are 0. )

AUTHORS: Joseph Hamman¹, Bart Nijssen¹ 1. Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA. SESSION H070: Modeling Hydrological Processes and Changes _Abstract to be submitted to the American Geophysical Uninion 2015 Fall Meeting_

AUTHORS: Joseph Hamman¹, Bart Nijssen¹ 1. Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA. SESSION C017: Frozen soil, its change, and the responses and feedbacks of the frozen soil change in atmosphere, hydrology and ecosystem or GC046: Land Surface, Snow and Soil moisture in Land-climate Feedback and Model Diagnosis _Abstract to be submitted to the American Geophysical Uninion 2015 Fall Meeting_

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I'm not digging all the white space... the lack of boundaries on the page makes the never ending white space to fill a little daunting. Also, where are you importing references from?