Emma Timmins-Schiffman

Emma Timmins-Schiffman
University of Washington Seattle | UW · Department of Genome Sciences

Doctor of Philosophy

About

58
Publications
5,747
Reads
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661
Citations
Additional affiliations
March 2014 - present
University of Washington Seattle
Position
  • PostDoc Position
September 2009 - March 2014
University of Washington Seattle
Position
  • PhD Student
August 2007 - August 2009
Northwest Fisheries Science Center
Position
  • Fisheries Biologist
Education
September 2006 - June 2007
Stanford University
Field of study
  • Biological Sciences
September 2002 - May 2006
Hamilton College
Field of study
  • Biology, French

Publications

Publications (58)
Preprint
Zooplankton undergo a vertical migration which exposes them to gradients of light, temperature, oxygen and food availability on a predictable daily schedule. Anticipating and responding to these environmental conditions, which independently are known to influence metabolic rates, likely has an appreciable effect on the delivery of waste products to...
Article
Full-text available
Coral bleaching events are increasing with such frequency and intensity that many of the world’s reef-building corals are in peril. Some corals appear to be more resilient after bleaching but the mechanisms underlying their ability to recover from bleaching and persist are not fully understood. We used shotgun proteomics to compare the proteomes of...
Article
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Background Microbial communities are ubiquitous throughout ecosystems and are commensal with hosts across taxonomic boundaries. Environmental and species-specific microbiomes are instrumental in maintaining ecosystem and host health, respectively. The introduction of pathogenic microbes that shift microbiome community structure can lead to illness...
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Corals in nearshore marine environments are increasingly exposed to reduced water quality, which is the primary local threat to Hawaiian coral reefs. It is unclear if corals surviving in such conditions have adapted to withstand sedimentation, pollutants, and other environmental stressors. Lobe coral populations from Maunalua Bay, Hawaii showed cle...
Preprint
Full-text available
Background: Microbial communities are ubiquitous throughout ecosystems and are commensal with hosts across taxonomic boundaries. Environmental and species-specific microbiomes are instrumental in maintaining ecosystem and host health, respectively. The introduction of pathogenic microbes that shift microbiome community structure can lead to illness...
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Full-text available
Background Protein expression patterns underlie physiological processes and phenotypic differences including those occurring during early development. The Pacific oyster ( Crassostrea gigas ) undergoes a major phenotypic change in early development from free-swimming larval form to sessile benthic dweller while proliferating in environments with br...
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The innate immune response is active in invertebrate larvae from early development. Induction of immune response pathways may occur as part of the natural progression of larval development, but an up-regulation of pathways can also occur in response to a pathogen. Here, we took advantage of a protozoan ciliate infestation of a larval geoduck clam c...
Article
Full-text available
Pacific geoducks (Panopea generosa) are clams found along the northeast Pacific coast where they are important components of coastal and estuarine ecosystems and a major aquaculture product. The Pacific coastline, however, is also experiencing rapidly changing ocean habitat, including significant reductions in pH. To better understand the physiolog...
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The heterotrophic marine bacterium, Ruegeria pomeroyi, was experimentally cultured under environmentally realistic carbon conditions and with a tracer-level addition of ¹³C-labeled leucine to track bacterial protein biosynthesis through growth phases. A combination of methods allowed observation of real-time bacterial protein production to understa...
Preprint
Full-text available
Corals in nearshore marine environments are increasingly exposed to reduced water quality, which is the major local threat to coral reefs in Hawaii. Corals surviving in such conditions may have acclimatized and/or adapted to withstand sedimentation, pollutants, and other environmental stressors. Lobe coral ( Porites lobata ) populations from Maunal...
Article
Full-text available
We examined metaproteome profiles from two Arctic microbiomes during 10-day shipboard incubations to directly track early functional and taxonomic responses to a simulated algal bloom and an oligotrophic control. Using a novel peptide-based enrichment analysis, significant changes (p-value < 0.01) in biological and molecular functions associated wi...
Article
Pacific geoduck aquaculture is a growing industry, however, little is known about how geoduck respond to varying environmental conditions, or how the industry will fare under projected climate conditions. To understand how geoduck production may be impacted by low pH associated with ocean acidification, multi-faceted environmental heterogeneity nee...
Preprint
Full-text available
Pacific geoduck clams (Panopea generosa) are found along the Northeast Pacific coast where they are significant components of coastal and estuarine ecosystems and the basis of a growing and highly profitable aquaculture industry. The Pacific coastline, however, is also the sight of rapidly changing ocean habitat, including significant reductions in...
Article
Full-text available
Global climate change is rapidly altering coastal marine ecosystems that are important for food production. A comprehensive understanding of how organisms will respond to these complex environmental changes can come only from observing and studying species within their natural environment. To this end, the effects of environmental drivers — pH, dis...
Preprint
Full-text available
Global climate change is rapidly altering coastal marine ecosystems important for food production. A comprehensive understanding of how organisms will respond to these complex environmental changes can come only from observing and studying species within their natural environment. To this end, the effects of environmental drivers - pH, dissolved ox...
Preprint
Full-text available
Pacific geoduck aquaculture is a growing industry, however little is known about how geoduck respond to varying environmental conditions and how production might be impacted by low pH associated with ocean acidification. Ocean acidification research is increasingly incorporating multiple environmental drivers and natural pH variability into biologi...
Article
The diel vertical migration of zooplankton is a process during which individuals spend the night in surface waters and retreat to depth during the daytime, with substantial implications for carbon transport and the ecology of midwater ecosystems. The physiological consequences of this daily pattern have, however, been poorly studied beyond investig...
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Full-text available
Assigning links between microbial activity and biogeochemical cycles in the ocean is a primary objective for ecologists and oceanographers. Bacteria represent a small ecosystem component by mass, but act as the nexus for both nutrient transformation and organic matter recycling. There are limited methods to explore the full suite of active bacteria...
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Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil) to microbiome data from multicellular organisms (such as the human gut...
Article
Biological significance: This study investigated the proteomic changes that occurred after DON and ZEA (individually and in combination) short exposures at low cytotoxicity levels in proliferating HepaRG cells using LC-MS/MS. The obtained results showed that the cellular response is time- and mycotoxin or mixture-dependent. In particular, after 1h...
Article
Geoduck clams (Panopea generosa) are an increasingly important fishery and aquaculture product along the eastern Pacific coast from Baja California, Mexico to Alaska. These long-lived clams are highly fecund, though sustainable hatchery production of genetically diverse larvae is hindered by the lack of sexual dimorphism, resulting in asynchronous...
Preprint
Full-text available
Geoduck clams ( Panopea generosa ) are an increasingly important fishery and aquaculture product along the eastern Pacific coast from Baja California, Mexico to Alaska. These long-lived clams are highly fecund, though sustainable hatchery production of genetically diverse larvae is hindered by the lack of sexual dimorphism, resulting in asynchronou...
Article
Full-text available
Evaluations of human impacts on Earth's ecosystems often ignore evolutionary changes in response to altered selective regimes. Freshwater habitats for Snake River fall Chinook salmon (SRFCS), a threatened species in the U.S., have been dramatically changed by hydropower development and other watershed modifications. Associated biological changes in...
Article
In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genom...
Article
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A changing climate is altering many ocean properties that consequently will modify marine productivity. Previous phytoplankton manipulation studies have focused on individual or subsets of these properties. Here, we investigate the cumulative effects of multi-faceted change on a subantarctic diatom Pseudonitzschia multiseries by concurrently manipu...
Article
Full-text available
The mechanisms that allow psychrophilic bacteria to remain metabolically active at subzero temperatures result from form and function of their proteins. We present first proteomic evidence of physiological changes of the marine psychrophile Colwellia psychrerythraea 34H (Cp34H) after exposure to subzero temperatures (-1, and -10°C in ice) through 8...
Article
Full-text available
Background: Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end-of-century open ocean pH reductions. In order to assess the impact of ocean acidificati...
Preprint
Background. Ocean acidification as a result of increased anthropogenic CO 2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end of century open ocean pH reductions. Projected and current ocean acidification have wid...
Preprint
Full-text available
Background. Ocean acidification as a result of increased anthropogenic CO 2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end of century open ocean pH reductions. Projected and current ocean acidification have wid...
Article
Full-text available
Recognizing the genetic diversity within and among collections of allopatric rainbow trout is an important step in understanding and monitoring the dynamics of the metapopulation structure of a species like Oncorhynchus mykiss with resident and anadromous life history forms. Prior to the removal of a barrier and the recolonization of Icicle Creek w...
Data
Background. Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end of century open ocean pH reductions. Projected and current ocean acidification have wide...
Article
Full-text available
Shotgun proteomics offers an efficient means to characterize proteins in a complex mixture, particularly when sufficient genomic resources are available. In order to assess the practical application of shotgun proteomics in the Pacific oyster (Crassostrea gigas), liquid chromatography coupled with tandem mass spectrometry was used to characterize t...
Data
Increasing atmospheric CO2 equilibrates with surface seawater, elevating the concentration of aqueous hydrogen ions. This process, ocean acidification, is a future and contemporary concern for aquatic organisms, causing failures in Pacific oyster (Crassostrea gigas) aquaculture. This experiment determines the effect of elevated pCO2 on the early de...
Article
Full-text available
Effective conservation of threatened species depends on the ability to assess organism physiology and population demography. To develop genomic resources to better understand the dynamics of two ecologically vulnerable species in the Pacific Northwest of the United States, larval transcriptomes were sequenced for the pinto abalone, Haliotis kamtsch...
Article
Full-text available
Background The lipid signaling molecule, ceramide, is a key component of the vertebrate stress response, however, there is limited information concerning its role in invertebrate species. In order to identify genes involved in ceramide metabolism in bivalve molluscs, Pacific oyster genomic resources were examined for genes associated with ceramide...
Data
Contigs of ESTs corresponding to ceramide metabolism pathway genes identified in C. gigas. Contigs are listed by Gene ID and described in Table 1.
Data
Melting curves for qPCR done on the 4 genes. Panel A is the melting curve for Cg-3KDSR, panel B is for Cg-AC, panel C is for Cg-GlcCer, and panel D is for Cg-sptlc1.
Article
Full-text available
Increasing atmospheric CO2 equilibrates with surface seawater, elevating the concentration of aqueous hydrogen ions. This process, ocean acidification, is a future and contemporary concern for aquatic organisms, causing failures in Pacific oyster (Crassostrea gigas) aquaculture. This experiment determines the effect of elevated pCO2 on the early de...
Article
Full-text available
**This is a draft version of the following article: Timmins-Schiffman et al. (2012) Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas. Marine Biology, doi:10.1007/s00227-012-2055-x, which has been published in final form at the link provided below.** Increasing atmospheric CO2 equilibrates with surface seaw...
Conference Paper
Pacific oysters, Crassostrea gigas, are an important aquaculture species worldwide. Recent mass mortalities of C. gigas larvae in the Pacific Northwest have been linked to upwelling events and acidic water, as well as emerging diseases. High mortalities have created concern over how stocks of C. gigas will respond to a changing ocean environment. C...

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Project (1)
Project
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1829318&HistoricalAwards=false