Maine Impact Week 2021 Faculty Mentor Impact Awards : Kristina Cammen

Earlier this year, we asked students to nominate faculty members who had an important impact on them and the response was incredible. Through online videos and announcements, we are featuring the nine faculty members who won 2021 Faculty Mentor Impact Awards. Click the download button for a machine-generated, English transcript

Interdisciplinary Research Collaborative Trains Students to See Through Turbulent Systems

Despite the availability of interdisciplinary academic training programs, the practice of environmental science is often hampered by a lack of convergence across diverse disciplines. This gap is particularly salient in settings characterized by complex environmental issues, such as multiple-use coastal ecosystems. In response, we developed and implemented a training, research, and communication framework to provide undergraduates with an authentic operative experience working at the interface of interdisciplinary science and public decision-making within a case study of marine renewable energy. In our program, students gained hands-on experience with the scientific process and learned how to make information relevant, useful, and accessible to diverse stakeholder groups. Application of this framework demonstrates that the process of integrating data from biological (visual and acoustic monitoring of fish and marine mammals), physical (hydrodynamics), and social (local ecological knowledge) sciences can provide a more complete understanding of complex and turbulent ecosystems for better informed decision-making. We offer several recommendations to facilitate the adaptation and implementation of our interdisciplinary framework to diverse research contexts, with a focus on interdisciplinary training for the next generation of marine scientists

Maine EPSCoR, vol. 1, issue 1

The University of Maine recently gained Carnegie R1 status, a level of recognition that speaks to the quality and scale of research happening at Maine’s land grant, sea grant, and space grant institution, and across the state as a whole. Research institutes, centers and labs established because of NSF EPSCoR RII Track-1 grants have created a significant and lasting impact in Maine. These entities include the Advanced Structures and Composites Center, Frontier Institute for Research in Sensor Technologies, Forest Bioproducts Research Institute, and Mitchell Center for Sustainability Solutions, which have generated over 500 million dollars in new R&D funding for the state following the completion of their RII Track-1 support. Maine EPSCoR’s current NSF EPSCoR RII Track-1 grant, Maine-eDNA, is set to embark on a full field season with work occurring throughout the state. We recognize the researchers, staff, graduate students, and undergraduate students who continue to actively participate in this work. Their effort and resilience in the face of uncertain and changing circumstances is inspiring and makes real contributions in our efforts to expand educational opportunities in STEM, drive workforce development, and strengthen research capacity in the state of Maine

Harbor seal SNPs

Catalog of single nucleotide polymorphisms (SNPs) identified in ddRAD loci among 55 harbor seals from the Northwest Atlantic. SNPs were identified and genotyped using a bounded maximum-likelihood model in Stacks v1.21 with no minimum minor allele frequency. LocusID refers to the locus ID in RAD loci catalog FASTA file; Column refers to the position of the variable nucleotide within the locus

RAD locus allele frequencies

Allele frequencies for 7,431 polymorphic (single SNP) RAD loci that were assessed for an association with bottlenose dolphin survival following exposure to harmful algal blooms. Allele frequencies for each sample pool were calculated based on the proportion of reads sequenced for each SNP variant (see “Stacks analysis of RAD data” Dryad file). Depth indicates the total number of reads per locus and sample pool; sample size indicates the number of individuals sequenced in the sample pool (note this varies for PLC and CWU because individuals of good and excellent quality DNA were separated during library preparation)

Harbor seal RAD loci

Catalog of 195,906 RAD loci consensus sequences resulting from ddRAD sequencing of genomic DNA from 55 bycaught harbor seals sampled in the Northeast United States between 1992 and 2015. The details of the ddRAD protocol and bioinformatic processing are described in detail in the Methods section and Appendix S1 of Cammen et al. (2018). In brief, ddRAD was conducted with restriction enzymes SBfI-HF and MspI, size selection by 1.5x beads, and 50-bp single-end read Illumina Hiseq 2500 sequencing. Sequences were processed using Stacks v1.21 to build loci de novo using the following parameters, selected using the r80 optimization approach: m = 2, M = 2, and n = 2. File is in FASTA format and each sequence is identified by a numerical locus ID

Gray seal genotypes

A genepop file containing ddRAD genotypes for 252 gray seals from the Northwest Atlantic. All including loci were genotyped in at least 80% of the individuals in each sample group. Gray seals samples represent three breeding colonies and up to five cohorts per colony. Locus names are composed of the LocusID that corresponds to the RAD loci catalog FASTA file and the position of the variable nucleotide within the locus

Harbor seal genotypes

A genepop file containing ddRAD genotypes for 55 harbor seals from the Northeast US. All including loci were genotyped in at least 80% of the individuals in each sample group. Harbor seals samples represent three cohorts sampled since 1992. Locus names are composed of the LocusID that corresponds to the RAD loci catalog FASTA file and the position of the variable nucleotide within the locus

Gray seal SNPs

Catalog of single nucleotide polymorphisms (SNPs) identified in ddRAD loci among 252 gray seals from the Northwest Atlantic. SNPs were identified and genotyped using a bounded maximum-likelihood model in Stacks v1.21 with no minimum minor allele frequency. LocusID refers to the locus ID in RAD loci catalog FASTA file; Column refers to the position of the variable nucleotide within the locus

The Influence of Genetic Variation on Susceptibility of Common Bottlenose Dolphins (<italic>Tursiops truncatus</italic>) to Harmful Algal Blooms

<p>The capacity of marine organisms to adapt to natural and anthropogenic stressors is an integral component of ocean health. Harmful algal blooms (HABs), which are one of many growing threats in coastal marine ecosystems, represent a historically present natural stressor that has recently intensified and expanded in geographic distribution partially due to anthropogenic activities. In the Gulf of Mexico, HABs of <italic>Karenia brevis</italic> occur almost annually and produce neurotoxic brevetoxins that have been associated with large-scale mortality events of many marine species, including the common bottlenose dolphin (<italic>Tursiops truncatus</italic>). The factors resulting in large-scale dolphin mortality associated with HABs are not well understood, particularly in regards to the seemingly different impacts of HABs in geographically disjunct dolphin populations. My dissertation investigates a genetic basis for resistance to HABs in bottlenose dolphins in central-west Florida and the Florida Panhandle. I used both genome-wide and candidate gene approaches to analyze genetic variation in dolphins that died putatively due to brevetoxicosis and live dolphins from the same geographic areas that survived HAB events. Using restriction site-associated DNA sequencing, I identified genetic variation that suggested both a common genetic basis for resistance to HABs in bottlenose dolphins across the Gulf coast of Florida and regionally specific resistance. Many candidate genes involved in the immune, nervous, and detoxification systems were found in close genomic proximity to survival-associated polymorphisms throughout the bottlenose dolphin genome. I further investigated two groups of candidate genes, nine voltage-gated sodium channel genes selected because of their putative role in brevetoxin binding and four major histocompatibility complex (MHC) loci selected because of their genomic proximity to a polymorphism exhibiting a strong association with survival. I found little variation in the sodium channel genes and conclude that bottlenose dolphins have not evolved resistance to HABs via mutations in the toxin binding site. The immunologically relevant MHC loci were highly variable and exhibited patterns of genetic differentiation among geographic regions that differed from neutral loci; however, genetic variation at the MHC also could not fully explain variation in survival of bottlenose dolphins exposed to HABs. In my final chapter, I consider the advantages and drawbacks of the genome-wide approach in comparison to a candidate gene approach and, as laid out in my dissertation, I recommend using both complementary approaches in future investigations of adaptation in genome-enabled non-model organisms.</p>Dissertatio