Showing 1 - 17 of 17 Items

Date: 2014-08-01

Creator: Amanda Howard

Access: Open access

Neuropeptides are small signaling molecules found throughout the nervous system that are responsible for influencing animal behavior. They consist of short amino acid chains and interact with cell-membrane receptors in order to regulate behavioral responses (Fig. 1a). The American lobster, Homarus americanus, has proven to be a strong model organism in which to study such activity due to the simplicity of the system and the wealth of existing knowledge about the animal. One neuropeptide found in H. americanus is a C-type allatostatin (AST-C). Allatostatins are a family of neuropeptides originally identified in insects that inhibits juvenile hormone production. The H. americanus AST-C has a pyroglutamate blocked N-terminus and an unmodified C-terminus (Fig. 1b). In addition to AST-C, a different, yet structurally similar neuropeptide has been found in H. americanus. This peptide has an unmodified N-terminus and an amidated C-terminus (Fig. 1c). Both forms of AST-C (referred to as ASTC-real and ASTC-like) also have a disulfide bond between their two cysteine residues. In the lobster, both peptides influence cardiac muscle contraction patterns and have been found in various tissues throughout the nervous system [1, 2]. In order to establish the purpose of the observed post-translational modifications, this study aims to find whether these peptides exist in other forms in the lobster and to determine their relative and absolute concentrations.Liquid chromatography-mass spectrometry (LC-MS) and tandem mass spectrometry (MS/MS) are often used in analytical chemistry to characterize complex samples and identify neuropeptides. First, sample components are separated by chromatography based on properties such as size and hydrophobicity. Using mass spectrometry (MS), peptides are protonated (positively charged) and their mass is determined from their measured mass-to-charge ratios. These peptides are lastly fragmented into many ions using MS/MS, which ultimately allows them to be sequenced in order to determine their identity. This summer, standards of the two AST-C peptides have been characterized by LC-MS/MS. The reduced forms of both peptides have been synthesized by chemically reducing the disulfide bond and were also analyzed by MS/MS. As expected, the structural stability provided by the disulfide bond prevented fragmentation during MS/MS analysis; that is, there was evidence of more fragmentation in the reduced forms than in the fully processed forms (Fig. 2). When looking for other forms of ASTC, these findings will facilitate the identification of the reduced forms in crustacean tissue.To assess the accuracy of the detection method used, detection limits were assessed by analyzing sample matrices augmented with known amounts of peptide standards. The smallest amount of peptide detected from a single injection was 25 fmol (2.5·10-14 mol) peptide. There appeared to be a strongly linear relationship between the amount of ASTC-real injected and the instrument response (chromatographic peak area) (R2=0.996, n=6). However, the relationship between the amount of ASTC-like injected and the instrument response was less linear (R2=0.802, n=5), and the calibration slope was more shallow, indicating that this peptide is more difficult to detect. This is possibly because ASTC-real, unlike ASTC-like, contains an arginine (R) and a histidine (H) residue, two basic amino acids susceptible to protonation. Therefore, it seems that ASTC-real is more easily protonated during the ionization process in MS analysis, causing it to be more readily detected.Lastly, ASTC-real has been identified in the pericardial organ (PO), a tissue responsible for delivering neuropeptides manufactured in the thoracic ganglion to the heart in order to control muscle contraction. ASTC-like is also believed to be present in the PO based on previous work in the Dickinson lab (E. Dickinson, unpublished data), but it is likely that it has not yet been detected in this study due to the detection limitations described above. To address these issues, more tissues will be pooled to increase the amount of peptide in each sample analyzed.Currently, tissue extraction methods are being optimized to eliminate phospholipid contamination and to maximize detection sensitivity. Specifically, two separate extraction solvents as well as a chloroform delipidation procedure are being tested. Future goals include quantifying peptide levels by adding a known amount of internal standard to the samples and comparing instrument responses for ASTC and for internal standard. Additionally, known amounts of peptide standard will be brought through the extraction process to determine the amount of peptide loss throughout this procedure. During the upcoming academic year, this study will be continued as an Honor’s project. Further research in these areas will ultimately help explain how neuropeptides interact to regulate behavior within the lobster and in more complex systems. Final Report of research funded by the Henry L. and Grace Doherty Charitable Foundation Coastal Studies Research Fellowship.

Date: 2014-08-01

Creator: Christine Walder

Access: Open access

Ascophyllum nodosum, the dominant intertidal macroalgal species from Maine to Canada, plays an important role in buffering intertidal stresses and supports a variety of organisms such as molluscs, crustaceans, fish and birds. A. nodosum is harvested commercially for use in fertilizers and food additives, and landings have been increasing in Maine in recent years. The ecological impact of removing the rockweed canopy was assessed in a comparative study between Kent Island in the Bay of Fundy, New Brunswick, Canada and Orr’s Island in Harpswell, ME, USA. Paired 2x2m control and experimental plots were set up, harvested, and surveyed monthly during the summers of 2013 (15 plots on Kent Island) and 2014 (an additional 9 plots on Kent Island and 20 on Orr’s Island) in a BACI design (Before, After, Control, Impact). One square meter surveys were conducted to determine algal species richness, algal percent secondary cover, and megafauna abundance and diversity. Surveys were designed to assess the overall diversity within plots and count/identify all present species. Initial t-tests of Kent Island data show a short-term reduction in amphipods and isopods, Carcinus maenas (green crabs), and Littorina obtusata (smooth periwinkles) and a short-term increase in Littorina littorea (common periwinkles) (p Final Report of research funded by the Rusack Coastal Studies Fellowship (2014).

Date: 2014-08-01

Creator: Jenna Watling

Access: Open access

Since early July, I’ve been working on three projects. I’ve been studying parrotfish speciation, dissecting green crabs, and collecting samples of muscle tissue from blue mussels. My primary occupation is the study of parrotfish speciation with Dr. Carlon. He has found evidence of speciation through hybridization, which is has not been commonly observed. During the 2013-2014 academic year, he and I extracted DNA from fin or scale samples from Pacific parrotfish. Throughout the year and during this summer, we have been amplifying specific genes—nuclear and mitochondrial—using a polymerase chain reaction, confirming the amplification via gel electrophoresis, and preparing the samples for Sanger sequencing, which is done by the Nevada Genomics Center. Once we receive the sequencing results electronically, I use the program Geneious to check the quality of the individual sequences and resolve ambiguous calls (e.g., whether a specific base pair is an arginine or a cytosine) and align the sequences so we can compare them base pair by base pair. By examining both nuclear and mitochondrial genes, which evolve at different rates, we can hypothesize about the way in which different species arise. Green crab (Carcinus maenas) dissection is an early step in Aidan Short’s analysis of their diet. I assist in collecting tissue samples. We collect muscle tissue from the crabs’ claws. These samples will allow Aiden to differentiate between the crabs’ food and the crabs themselves. Then their carapaces are cut open and their entire stomachs are collected. In the near future, Aidan will use next-generation sequencing to identify any species present in the crab stomachs and quantify the abundance of these species’ DNA. Sequencing the crabs’ stomach contents is more precise and more complete than the older method of hard part analysis. The green crabs’ diet is of interest because green crabs are an invasive species and have been implicated in loss of sea grass beds and decreasing soft shell clam populations. Collection of tissue from blue mussels (Mytilus edulis) and bay mussels (M. trossulus) is a preliminary step for Dr. Sarah Kingston’s investigation of the genetic basis of variation in shell calcification rate under environmental conditions possible due to ocean acidification. She collects mussels from various sites along the Maine coast, marks each with a color and number, and records their buoyant weight. The buoyant weight allows Dr. Kingston to determine the mass of the shells without having to kill the mussels. In the first round of experiments, Dr. Kingston determined which of three experimental schemes (involving the manipulation of food levels, temperature, and pH) resulted in the greatest variation of shell calcification after two weeks. The harshest scheme—no food, high temperature, and low pH—resulted in the greatest variation, and this scheme will be used in the experiment going forward. After the experimental period, the mussels are re-weighed and tissue samples are collected. I assist in tissue sample collection; we cut open the mussels and remove the foot and the adductor muscle. In the next round of experiments, I will further assist by participating in mussel collection, monitoring tank conditions during the experimental period, and labeling and weighing the specimens. The DNA libraries obtained from the tissue samples will be sent away for next generation sequencing, and Dr. Kingston will begin looking for genetic variation associated with calcification rates. Final Report, summer 2014 student-faculty research.

Date: 2014-08-01

Creator: Lloyd Anderson

Access: Open access

Increased atmospheric CO2 due to the combustion of fossil fuels and subsequent oceanic uptake has led to a phenomenon known as ocean acidification: CO2 gas dissolved in the ocean lowers surface ocean pH and acidifies ocean waters, a process which has raised global concern. The purpose of my research was to investigate why a particular clam flat in Phippsburg, ME is not as productive as it used to be. This clam flat, located on “The Branch” in Phippsburg adjacent to Head Beach, has decreased to approximately a sixth of its former productivity in just over a decade. A possible explanation for this drop in clam bed productivity is acidification. I worked in a partnership with Bailey Moritz ’16, with the goal to measure indicators of ocean acidification in the clam flat and see if there was a difference in those indicators between productive and unproductive areas of the flat. Bailey’s focus was alkalinity, a quantification of the buffering capacity of seawater, where my specific research focus was on the effective collection of pH measurements. We were ultimately able to combine our alkalinity and pH measurements to calculate saturation state, an indicator of the susceptibility of clam shells to dissolution. I measured pH, a direct indicator of water acidity, from the top centimeter of the mudflat, the region where clam spat (juvenile clams) are seeded. The first few weeks of my fellowship time I spent researching the most accurate and precise way to measure pH in the field, and ultimately decided to measure pH on site using glass electrode probes. Sites 1 and 2 were located in a productive region of the flat, sites 4 and 5 were located in an unproductive region, and site 3 was located on the boundary between the two zones. Average pH values within the clam flat ranged from 6.9-7.5, and there was no significant difference in pH between productive and unproductive sites across the flat (Figure 1). The wide variations in pH across this clam flat could potentially be attributed to daily shifts in temperature, freshwater input, and biological productivity in the sediments. Low average pH values seen across all sites contribute to a low saturation state across the flat: our average calculated saturation state was 0.47, lower than similar data measured by Green et al. on a clam flat in South Portland in 2013, where average saturation state was 0.9. Our data indicate that the soft-shell clams at the productive sites in this particular Phippsburg clam flat are managing to survive in undersaturated (saturation state < 1) conditions. Since saturation state was low across both productive and unproductive sites, ocean acidification seems not to be the cause for the clams’ decline. However, other factors such as dissolved oxygen or sediment type may have combined with low saturation states to create a difference in productivity across the flat. In further research I would be interested to see how average pH at these same sites varies over a year-long period, which would give a better representation of the environment that the soft-shell clams are exposed to through yearly cycles. Final Report of research funded by the Rusack Coastal Studies Fellowship.

Date: 2014-08-01

Creator: Nora Hefner

Access: Open access

Gulf of Maine cod fisheries, once essential to Maine’s economy and culture, are currently in a state of collapse. Following a long decline throughout the 1800s and two collapses in the 1900s – one in the middle of the century and one in the 1990s, cod populations along the coast exist now as small fractions of their former bounty. Though the connection was largely forgotten in the twentieth century, fishermen in the nineteenth century attributed the decline of the cod fishery to the loss of alewives, an anadromous river herring upon which cod prey. Alewives have been cut off from their spawning and nursery habitat along much of the Gulf of Maine due to the damming of rivers that empty into the Gulf. My research is a part of an ongoing study that aims to establish the historical relationship between cod and other gadoid groundfish fisheries, their ecosystems, and anadromous alewives using spatial data from geographic information systems (GIS). GIS maps were created with the positions of 466 historical Gulf of Maine cod fishing grounds, identified using a database developed by fisheries scientist Ted Ames (whose work is largely responsible for fisheries scientists’ renewed interest in the groundfish-alewife connection). The spatial database generated from these data will be analyzed using a logistical regression to identify characteristics of fishing grounds that define them as fishing grounds, as well as characteristics that determine the relative quality of individual fishing grounds. The Ames database contains data in two main categories: biophysical (ecosystem characteristics) and socioeconomic (infrastructure). The focus of my research was on generating two specific data sets from historical literature, government reports, and experts in the field, and on mapping that data using GIS software (see Figure 1). The first was a list of rivers that supported annual alewife runs before the mid-twentieth century cod groundfish fishery collapse. Using GIS software, I mapped the locations at which these rivers enter the ocean, creating spatial data that show the point at which cod in the Gulf and alewives in the rivers would meet. The second data set was a list of ports and harbors that supported the groundfish industry, also before the mid-twentieth century collapse. These locations were mapped as the areas from which fishing boats would set out in pursuit of groundfish, again creating a set of spatial data points. Both of these data sets were added to the existing spatial database. My data and Ames’ data will be used to calculate distances between individual groundfish fishing grounds and historic alewife runs and between fishing grounds and ports and harbors. Statistical analyses will determine both whether those two factors have any significant relationship with fishing ground quality and the nature of their effects, if any. Ultimately, the results of these analyses will contribute to an increasingly detailed picture of the Gulf of Maine as it existed – physically, ecologically, and economically – when it still supported astoundingly large populations of cod and other groundfish. With a better idea of what the system looked like when it worked properly, we can make a more informed and focused attempt to rebuild it. This research provided me with opportunities to develop practical skills like use of GIS software, contacting and collaborating with scientists, researchers, and government agencies in my field, and data management. I also gained a greater understanding of and appreciation for the complexity and challenge of trying to bring research from the science level to management policy and action. Final Report of research funded by the Cooke Environmental Research Fellowship

Date: 2014-08-01

Creator: Xuan Qu

Access: Open access

Central pattern generators are networks of neurons that produce rhythmic and repetitiveoutputs. These outputs control behaviors such as walking, breathing and digestion. In the Americanlobster, central pattern generators control the behavior of muscles in its foregut, which allows thedigestion of a variety of food types. The stomatogastric ganglion (STG) is a bundle of about thirtyneurons in the foregut of American lobsters. It has been studied extensively since each one of theneurons in it is both identifiable and produces simple patterned outputs. The analysis of American lobster’s stomach behaviors and the neural mechanisms controlling them could provide general insights into how rhythmic motor patterns for locomotion are produced. A large number of the neurons in the STG are modulatory neurons that use neuromodulators for at least part of their synaptic receptions. These neuromodulators are released by neurons and cause long-lasting changes in the synaptic efficacies of the targets. At present, many types of neuropeptides have been identified within the crustacean stomatogastric nervous system. The pyrokinins are members of one peptide family, PBAN. PBAN peptides all share the common Cterminalpentapeptide FXPRL-amide, in which X can be S, T, G, N, or V. Previous studies, using immunohistochemistry, have found that there are pyrokinin peptides present in both the STG and the cardiac ganglion (CG) of American lobsters. My research tests five different kinds of pyrokinin peptides, including PevPK1 (DFAFSPRLamide) and PevPK2 (ADFAFNPRLamide) from the shrimp L.vannamei (Torfs et al., 2001; Ma et al., 2010), CabPK1 (TNFAFSPRLamide) and CabPK2(SGGFAFSPRLamide from the crab C.borealis (Saideman et al., 2007;Ma et al., 2009) and Conserved Sequence (FSPRLamide) from the lobster, H.americanus (Ma, et al, 2008). ConservedSequence, the only pyrokinin identified in the American lobster so far, is highly conserved among many other pyrokinin peptides. Therefore, it is believed to be just a fragment with the complete sequence yet to be identified. Thus, we predicted that it might produce a weaker effect on the STG. Previous studies on the pyrokinin peptides have shown that in crabs, CabPK1, CabPK2 and LeucoPK (identified in an insect), all had a virtually identical effect on the CG, suggesting that the differences among these pyrokinin peptides are not important and the receptors for these peptides are the same. However, research done by Bowdoin students in 2011-2012 showed that among PevPK1,PevPK2, CabPK1, CabPK2, and Conserved Sequence, all but Conserved Sequence (not yet tested) had strong effects on the STG. However, only PevPK2 had an effect on the CG. My goal for this summer research was to determine whether or not there are differences between the responses of the STG to the different peptides in order to further determine the cause for the differences between the responses of the CG and those of the STG. The results from the extracellular recordings from the identified neurons in my research have shown that none of the five kinds of pyrokinin peptides affect the pyloric rhythm, which controls the pumping and filtering of food through the pylorus in Americanlobsters. They all, however, excite the gastric mill rhythm, which controls the movements of the teeth that grind up the food before it is transferred into the pylorus. Moreover, there is no significant difference among the effects of these five kinds of pyrokinin peptides. Conserved Sequence, which was predicted to produce a relatively weaker effect, proved to produce virtually identical effect asfour other kinds of pyrokinin peptides. Future research will focus on studying the differences between the STG and CG to determine the cause of the varied responses between them. Final Report of research funded by the Doherty Coastal Studies Research Fellowship.

Date: 2024-03-20

Creator: Katharine Kurtz

Access: Open access

Cities need more green spaces to adapt to climate change and facilitate community resilience. However, successfully managing green spaces is challenging. City governments consistently employ top-down management practices that limit the benefits, usage, and perception of such spaces as Nature. Further, current management practices overlook socio-cultural factors important to residents. Using the existing categories of urban green spaces (UGS) and informal green spaces (IGS), this article situates the cultural practice prendersi cura as a way to conceptualize successful, bottom-up green space management. The term prendersi cura, meaning “to take care of” in Italian, emerged through interviews in Perugia, Italy, and reflects the socio-ecological value of IGS and the disconnect between residents and city-managed UGS. This study employed mixed methods, combining 10 weeks of participant observation, 13 interviews, and GIS analysis to understand the relationship between Perugians and their green spaces. Results indicate that interviewees did not describe city-supported UGS (i.e. top-down green spaces like parks or historic gardens) as Nature, even if they were areas of dense vegetation and recognized by the City of Perugia in GIS analyses. In contrast, interviewees described IGS (i.e. community gardens, vacant lots, or potted plants) that were unrecognized in city GIS visualizations as Nature, indicating a stronger attachment to green spaces when interviewees had active roles in their management or witnessed community-based management practices. This paper demonstrates the importance of managing green spaces through a socio-ecological framework that considers user perceptions and cultural values. To allow greening initiatives to reach their full potential, it is critical to embrace local values and participation in management practices.

Date: 2014-08-01

Creator: Tricia Hartley

Access: Open access

In many animals, there are groups of neurons, known as central pattern generators (CPGs), which are capable of controlling major everyday life functions. CPGs are responsible for functions that require patterned rhythmic activity, such as the heartbeat, digestion and locomotion. A CPG called the cardiac ganglion, consisting of only nine neurons, controls the rhythmic beating of the heart of the American lobster, Homarus americanus, by stimulating the muscle cells of the heart.My summer consisted of two separate projects in Patsy Dickinson’s neurophysiology lab, both studying the interaction of the cardiac ganglion with neuropeptides. These neuropeptides, GYSDRNYLRFamide (GYS) and SGRNFLRFamide (SGRN) are released hormonally into the cardiac neuromuscular system. The overarching goal of both projects was to determine the role of these neuropeptides in the lobster’s cardiac neuromuscular system.For my first project, I studied the interaction of the neuropeptide GYS with the stretch receptors of the lobster heart. Previous research has found these stretch receptors to be a form of excitatory feedback from the lobster heart to the cardiac ganglion, as heartbeat amplitude and frequency increase as heart is stretched. Further, the dendrites along the cardiac ganglion have been found to be stretch-sensitive, meaning when these dendrites were cut, this excitatory response is no longer observed. By stretching the heart with the dendrites intact and with GYS and next when the dendrites were cut and with GYS, the goal of this project was to determine if GYS would alter the feedback of the stretch receptors back to the cardiac ganglion to change heartbeat frequency and amplitude. Unfortunately, the intricacy involved in being able to cut the dendrites while allowing the heart to continue to beat proved very difficult and I moved on to my next project.The goal of my next project was to examine the interactions of the neuropeptides GYS and SGRN with the decreased and increased presence of nitric oxide, the second form of feedback from the heart muscle to the cardiac ganglion. Previous research shows nitric oxide as having an inhibitory effect, decreasing heartbeat amplitude and frequency. By applying both GYS and SGRN to both the isolated cardiac ganglion and the whole heart in the presence of both a nitric oxide inhibitor and donor, the hope is to be able to determine the interaction of these peptides with and without the presence of the feedback of nitric oxide. Because I started this project later in the summer, with the assistance of Sophie Janes’ data, I have been able to look at the effects of GYS on the whole heart, in addition to the combination of GYS with L-NA, a nitric oxide inhibitor. So far, the data has shown that the combination of GYS with L-NA causes less of a decrease in heartbeat frequency than GYS alone, which shows a significant decrease. We predict this is because GYS enhances the nitric oxide pathway, while L-NA is blocking the nitric oxide pathway, thus giving insight into the role of GYS within the lobster’s cardiac neuromuscular system. For my senior independent study I hope to continue this research and be able to continue to compile data for both SGRN and GYS on the isolated cardiac ganglion as well as on the whole heart, with a nitric oxide inhibitor and donor. Final Report of research funded by a Doherty Coastal Studies Research Fellowship.

Date: 2015-03-01

Creator: Aidan W. Short, David B. Carlon

Access: Open access

A new wave of green crabs Carcinus maenus is sweeping through the Gulf of Maine (GOM). While first reports of green crabs in the GOM date from the early 1900s, populations in southern GOM have exploded in the last five years. In the Casco Bay region, this unusually high abundance is associated with poor commercial shellfish landings and the decline of eel grass habitat (Zostera marina). To determine the mechanistic roles green crabs play in direct and indirect ecological interactions, it is important to understand diet breadth, and how feeding preferences change in response to ecological context. Since green crabs are omnivorous, traditional approaches to diet analysis via hard parts suffer from substantial bias. We are using DNA barcoding and next generation sequencing (NGS) to analyze green crab diets from a longitudinal sampling design in Casco Bay. In addition to a temporal dimension, our design includes two habitats: clam flats and eel grass beds. We have now sampled ~ 1000 crabs and have processed 460 individual stomachs from a range of sizes and both sexes. Here we will present: our sampling design, our NGS pipeline, and preliminary analysis from a lobster-specific (Homarus americanus) probe. Presenting author status: Undergraduate Preferred presentation type: Poster Preferred topics: 3. Biological invasions; 18. Molecular ecology Benthic Ecology Meeting, 2015 Quebec City, Canada Aidan Short was an undergraduate student at Bowdoin College when this research was conducted.

Date: 2014-08-01

Creator: Jack Mitchell

Access: Open access

DNA Barcoding is the identification of organisms through the use of a standardized portion of the genome, a concept first suggested by Hebert, et al (2003) and since developed to include standard databases and many campaigns internationally to identify and barcode all species in the world. Because DNA barcoding uses molecular data, rather than morphology, to identify organisms, it allows for the identification of organisms that are morphologically similar or have been processed to the point of unrecognizability. Barcoding has the potential to streamline and enhance conservation efforts drastically. Its "quick and easy" identification process allows better fisheries management, market regulation to ensure vendors are selling what they say they're selling (no more horsemeat burgers or dolphin sushi), and greater enforcement of regulations against the killing and selling of endangered animal products (Minhos et al., 2013). In my work this summer, I've been using DNA barcoding to examine the dynamics of a community of larval fish off the coast of Oahu through a seven-year longitudinal barcoding study. Fish larvae are very hard to identify morphologically because they lack obvious identifying characteristics. For this reason, barcoding is essential for accurately understanding the community structure of such fish. In my work, I analyze a set of sequences from the 5-prime region of the mitochondrial gene cytochrome oxidase subunit 1, widely used as a barcode in the animal kingdom, gathered from fish larvae collected off the coast of Oahu by the University of Hawaii Manoa Biology 301L class. The sampling consisted of a series of oblique plankton tows taken at three depths (5m, 25m, and 50m) between January and April every year from 2007 to 2013. During this period, a total of 833 fish larvae were sampled and sequenced. Using the Barcode of Life Data Systems (BOLD Systems) Identification Engine, I was able to identify 78% of all specimens to family-level or better, representing about 25% of the 202 families of shore fishes known to occur in Hawaiian coastal waters. The data stratification consisted of 7 years, each with three depths and 56 family groups, a 21 by 56 data matrix. In order to see the patterns of the matrix, I used Principal Components Analysis, a form of ordination, which distills multidimensional data to a form that is more easily visualized. This ordination revealed that 2009 and 2011 had highly anomalous community structure in which there were large increases in abundance (greater than three (3) Standard Deviations from the mean) of 12 family groups in each year, indicating concerted change in the structure of ichythoplankton in those years, though the families may be represented by a low number of specimens in the sample. Because these families had little to no representation in other years, we are able to rule out the possibility of results being skewed by a couple of families that showed up in our nets by chance that don't reflect the actual community structure. In these years, the highly anomalous families did not overlap, indicating that the factors causing the anomalies were non-identical. In 2009 there were eight families that deviated from the mean by over four (4) Standard Deviations, and in 2011 there were ten. Though the biggest groups of deviant families in both years were reef fish and mesopelagic fish, tropical habitat ranged from shallow water benthic (sea-bed) fish such as Ophichthidae, to bathypelagic (deep sea) fish such as the anglerfish family Ceratiidae. In my last few weeks working on this project I am exploring what environmental factors may have had a hand in such anomalies. El Niño cycles may have had a hand, as there was a weak La Niña (slightly cooler waters) anomaly leading into 2009, and a very strong La Niña (drastically cooler waters) anomaly leading into 2011 ("Cold and Warm Episodes by Season," 2014). The differences in community structure I detected had different signs, that is the co-variance of fish families was different for each of these years. This suggests that water temperature itself may not be causing these ecological patterns. A more likely hypothesis links the effects of El Niño/La Niña on oceanographic circulation throughout the Pacific and even near-shore in the Hawaiian Islands. These changes can drive differences in the delivery of larvae to the islands, as well as advection away from the islands. Further research in the remainder of the summer will attempt to gather more information on what may have caused the community structure anomalies. Final Report of research funded by Mary Lou Zeeman’s NSF grant - Computational Sustainability (NSF-CCF-0832788).

Date: 2014-08-01

Creator: Schuyler Nardelli

Access: Open access

Phytoplankton are the simple single-celled photosynthesizers that live in the ocean and form the base of the food chain. Cell size is a basic proxy for physiological rates as well as ecosystem structure. Thus, cell size can be used in a model framework to track changing environmental conditions that could potentially lead to harmful algal blooms (HABs, aka “red tides”)—events that can be detrimental to human health, marine life, and fisheries. HABs occur when a single algae (phytoplankton) species either grows unconstrained to a concentration such that it becomes toxic or causes low oxygen concentration in the water. In typical estuaries, less dense freshwater flows towards the ocean, and denser salty seawater flows into the estuary in the subsurface. However, Harpswell Sound is a reverse estuary that receives its freshwater input at its mouth from the upstream Kennebec River. This yields upstream surface low salinity flow and downstream deep high salinity flow. This rare dynamic allows phytoplankton located in the surface of seawater to be retained in the sound in conditions conducive to high growth and HABs, and can be used as a warning for conditions throughout the Gulf of Maine. To study the temporal and spatial dynamics of phytoplankton in the sound, we used the LISST-100, which uses light scattering properties to collect continuous in-situ water column observations of particle concentrations and size distributions. Although the LISST-100 was built to measure sediment size with a spherical shape, studies have been conducted that show it can accurately describe a diverse range of phytoplankton shapes and sizes, provided the population has sufficient size differences and is fairly concentrated, conditions found in Harpswell Sound. Weekly profiles of the water column were collected at the Bowdoin Buoy from 5/21/14-6/18/14, as well as a 20-day continuous time series collected at Bowdoin’s Coastal Studies Center dock from 5/30/14-6/18/14 along with supplementary oceanographic data. We determined that semi-diurnal tidal fluctuations are sufficient to move water masses past the buoy and dock with each tide, thereby connecting them. Phytoplankton were found to be in the 3-50 micron size range, with a peak diameter of approximately 7 microns. Additionally, three independent phytoplankton blooms were observed over the course of the 20-day time series as different water masses flowed through the sound. They were sourced in the oceanic water masses found under the freshened surface layer. Over the five-week period the populations gradually surfaced with their water mass as the overlying freshwater dissipated in the absence of rainfall. The LISST-100 served as a useful tool for determining phytoplankton distribution and dynamics within Harpswell Sound, and with further research there is great potential to continue to increase proficiency with the instrument in order to better understand phytoplankton dynamics and harmful algal blooms. Final Report of research funded by the Rusack Coastal Studies Fellowship.

Date: 2014-08-01

Creator: Sabine Y Berzins

Access: Open access

Eelgrass (Zostera marina) is a perennial seagrass that is widely distributed among the shallow subtidal and intertidal Atlantic coastline of the United States and Canada. A highly productive keystone species, eelgrass helps maintain healthy estuarine and ecosystem functions by stabilizing sediments, regulating water flow, absorbing nutrients, and providing critical habitat for animals including commercially important species like soft-shell clams, blue mussels, and migrating waterfowl. Loss of eelgrass beds can therefore result in degraded water quality, shoreline erosion, and reduced fish and wildlife populations. Historically, the Maine coast supported extensive eelgrass beds. However, between 2010 and 2013, eelgrass distribution in Casco Bay declined in area by over 55%. This decline in eelgrass distribution coincides with a regional population explosion of green crabs (Carcinus maenas), an invasive species that physically disturbs eelgrass while foraging for prey. This summer, I collaborated with several Casco Bay Eelgrass Partners including individuals from the Fish and Wildlife Service, Maine Department of Environmental Protection, and the Friends of Casco Bay. Led by U.S. Geological Survey biologist Dr. Hilary Neckles, this project identifies factors that make eelgrass more or less resilient to invasion by green crabs. In June, we established permanent eelgrass survey transects at five locations spanning eastern Casco Bay. Where possible, two transects were established in different types of sediment (fine or coarse/sandy). Most of the eelgrass loss observed over the past decade has been in fine sediments. The question remains; is eelgrass in coarse sediments prone to similar levels of damage? In addition to differences in substrate type, each site also exhibited varying degrees of eelgrass density, shoot height, green crab density and population structure, and other environmental stressors including light availability, temperature, nutrient availability, and natural physical disturbance. I made biweekly measurements of green crab densities at one site, Widgeon Cove in Harpswell. Crap trapping indicated few green crabs occurred near the Widgeon Cove transect, but traps at the other four Casco Bay sites collected as many as 300 crabs within a 24-hour period. Final measurements in the eelgrass transects will be taken in September and data collection will be completed in October. Data gathered this summer will provide information to help move forward with a plan to protect and potentially restore eelgrass in Casco Bay. Additionally, I identified patches of eelgrass in the Kennebec Estuary that might be viable sites for replanting next summer. I hope to continue working on this project next year, thinking about ways to restore eelgrass to the system while identifying ways to increase trapping pressure on green crabs such that their numbers might be reduced. Final Report of research funded by the Rusack Coastal Studies fellowship.

Date: 2014-08-01

Creator: Bailey Moritz

Access: Open access

With increased CO2 in the atmosphere from the burning of fossil fuels, more is absorbed into the surface ocean, causing a reaction that leads to lower pH. This process is known as ocean acidification, which has raised global concern. Over the past decade, the clam flat near Head Beach in Phippsburg has been reduced to approximately a sixth of its former productive area. The town of Phippsburg allots money every spring to seed the clam flat with juvenile soft-shell clams (Mya arenaria) in order to support the local clamming economy, but the clams are no longer growing in much of the mud flat. A possible explanation for this loss is acidification. In order to understand if ocean acidification is the cause, I collected water samples from the mud to test for alkalinity along a transect of 5 sites spanning productive and non-productive areas of the flat. Alkalinity is a measurement of the waters ability to buffer pH changes. Lower alkalinity could mean that clams would have more difficulty forming their calcium carbonate shells due to dissolution in low pH waters. Combined with the pH measurements gathered by my peer, Lloyd Anderson ‘16, we were able to calculate aragonite saturation state. Water with a saturation state below 1 is capable of dissolving calcium carbonate (aragonite) shells. A large portion of this research project was figuring out the best methodology to use for collecting data on the clam flat. The tested water needs to represent that which the clams are actually using while they are embedded in the mud. Additionally, juvenile clams only live in the upper centimeter or so of sediment. We followed methodologies used in past studies in Maine (Green et al 2013). Three pore water samples from each site were extracted and brought back to the lab to be filtered on 7 separate days throughout July. We began sampling 2 hours prior to low tide. I determined alkalinity using an automated titration system. Average alkalinity ranged from 2200-2500 μeq/kg. The results indicated that there was not a significant difference or pattern in alkalinity or saturation state between productive and unproductive areas of the clam flat (Fig. 1). Error bars in the figure represent variability at each site over the entire study period, while analytical reproducibility was ± 9.04 μeq/L. Large changes were observed merely from one day to another. Coastal ecosystems are complex and variations such as time of day, temperature, or productivity may have influences on the porewater characteristics (Duarte 2013). While ocean acidification does not appear to be the primary driving force behind the clams’ decline at this location, the saturation state was consistently quite low ( Final Report of research funded by the Rusack Coastal Studies Fellowship.

Date: 2014-08-01

Creator: Anna Hall

Access: Open access

High-latitude peatlands store a large stock of carbon in accumulated belowground biomass, estimated at 500 ± 100 Gt C (Yu 2012). For comparison, the atmospheric C pool is estimated at about 775 Gt (IPCC 2007) making the peatland carbon pool a potentially significant player in the global carbon cycle. Peatland carbon storage is controlled by a balance between plant productivity and decomposition, with plant matter produced during the summer months accumulating from year to year rather than fully decomposing. Peatlands are sensitive to changes in climatic regime and have the potential to shift from a net sink of atmospheric C to a net source of C with future disturbance by climate warming (Yu 2012).There are two major predictions as to how climate change could affect peatland C accumulation. Warmer temperatures could cause faster decomposition of plant biomass and lead to C release to the atmosphere and a positive feedback effect on climate change (Schuur et al. 2008). If this is the case, current warming trends suggest that peatlands could release up to 100 Gt C to the atmosphere by the year 2100 (Davidson and Janssens 2006). Alternatively, warmer summer temperatures and a longer growing season could lead to faster peat production and therefore CO2 drawdown from the atmosphere, somewhat mitigating the effects of climate change (Schuur et al. 2008). A detailed study of past C accumulation rates over a known historical warm period gives insight into how peatlands may respond to future climate warming. This project focuses on C accumulation in peatlands in Labrador, Canada, over the past 8,000 years. Because Canadian peatlands store approximately 150 Gt C, approximately 1/3 of the global peatland carbon pool, it is important to understand how the dynamics of these peatlands could be affected by present and future climate warming (Tarnocai 2006). However, the majority of research has focused on central Canada, leaving significant knowledge gaps surrounding coastal Eastern Canada (vanBellen et al. 2012). Particular emphasis in this study was given to the Holocene Thermal Maximum (HTM) which occurred from 4-6 thousand years ago in Labrador, when summer temperatures were 0.5 – 1°C warmer than at present (Kerwin et al. 2004). This study also attempts to determine the effect of fires on rates of C storage in these peatlands. Lightning-ignited peat fires have the potential to consume stored biomass and release significant CO2 to the atmosphere (Tarnocai 2006). Six peat cores (out of a total of 14 collected in Labrador in 2013) were used for this study. Throughout the following year, calibrated radiocarbon dates, bulk density, and percent carbon were used to calculate carbon accumulation rates. This summer, areal charcoal concentration (a measure of macroscopic charcoal used as a proxy for fire severity) was used to determine the influence of fires in this region. From 8,000 years ago to the present, rates of C accumulation averaged 23.1 ± 6.7 gC m-2 yr-1. Accumulation rates were highest during the HTM, averaging 29.6 ± 2.4 g C m-2 yr-1. Samples containing macroscopic charcoal had an average concentration of 0.62 mm2 cm-3 with a maximum concentration found of 3.51 mm2 cm-3. These consistently low charcoal concentrations indicate that fire was neither common nor severe in Labrador peatlands. While Kuhry (1994) and Payette et al. (2012) found that fires in Canada occurred twice as frequently during the HTM than at present, no trends in fire severity were found in these cores, and there was no evidence that fires had a significant influence on C accumulation. Therefore, the C accumulation trend we see in Labrador is not controlled by fire and is likely either a direct result of temperature variation or of vegetational and hydrological shifts caused by changes in climate. This work supports a growing body of evidence from high latitude peatlands suggesting that future warming conditions could lead to increased soil C sequestration. Final Report of research funded by the Freedman Coastal Studies Fellowship.

Date: 2014-08-01

Creator: Sasha Kramer

Access: Open access

Phytoplankton require certain essential nutrients for growth. The Redfield ratio (Redfield, 1934) dictates an ideal element proportion of 106 carbon: 16 nitrogen: 1 phosphorus in order to maintain balanced phytoplankton growth through photosynthesis (Li et al., 2008). Under typical conditions, the concentration of nutrients present in the water directly controls the attainable phytoplankton yield (i.e. one inorganic nitrogen from nitrate yields one organic nitrogen in cellular form). While plankton that are starved of nutrients tend to die off quickly, plankton that are simply nutrient limited can adjust to constant but low levels of nutrient concentration (Cullen et al., 1992), often by adjusting their Redfield ratio. As an essential nutrient, nitrogen is a limiting factor for phytoplankton growth in the ocean (Dugdale, 1967). In oceanic and coastal ecosystems, dissolved nitrate (NO3-) is the most commonly available form of nitrogen (Zielinski et al., 2011). The formation of nutrients through microbial processes such as denitrification in deep water creates a source of nitrogen in the deep ocean (Arrigo, 2005). Phytoplankton growth is limited by both light and nutrients: therefore, the transport of nitrate into the euphotic zone controls the rate of primary production. In the Gulf of Maine, nitrate concentration varies with depth and season. Water density is determined by temperature and salinity; these qualities in turn control the depth of mixing and stratification, and thus the depth of the nitracline, the depth at which the high-nutrient deep waters are found (Townsend, 1998). An instrument known as the In Situ Ultraviolet Spectrophotometer (ISUS by Satlantic, Inc.) offers the ability to quantify nitrate concentrations based on optical properties. The instrument specifically measures the magnitude of absorption of ultraviolet light by dissolved nitrate molecules in the water. The concentration is determined from the ratio of the measured absorption coefficient to the molar absorption coefficient of nitrate. The ISUS is placed directly into the water at a site of specific interest—it measures the absorption and computes the nitrate concentration at this site every hour. This method of analysis gives superior stability, precision, and accuracy in data compared to a typical water sample analysis in a laboratory setting (Johnson & Coletti, 2002). For the past 4 years, an ISUS sensor has been deployed on the Bowdoin Buoy in Harpswell Sound collecting hourly observations of nitrate concentration concurrent with hourly observations of chlorophyll fluorescence (which can be used as a proxy for phytoplankton biomass). Once per week between May 21, 2014 and June 18, 2014, measurements of the depth distribution of salinity, temperature, density, chlorophyll fluorescence, and dissolved oxygen content were taken at the Bowdoin Buoy. Water samples were collected at five discrete depths each week, and were returned to the lab for analysis of chlorophyll concentration on the Turner fluorometer and nutrient concentration on the SmartChem. These laboratory analyses were used to calibrate and validate the buoy- and boat-based optical observations. The analysis of nitrate observations was performed in two phases. First, the variability in nitrate measured on the buoy since 2007 along with co-located discrete water samples was compared to a published historical dataset in order to place Harpswell Sound in the broader context of the Gulf of Maine. Second, the timeseries buoy observations of nitrate and chlorophyll were analyzed to determine temporal covariability. The historical nutrient and water quality data for the Gulf of Maine gathered by Rebuck et al. 2009 for 1990-2009 (in addition to unpublished data from 2010-2012) provided a broader spatial and temporal range for comparison with data from the Bowdoin Buoy in Harpswell Sound, Maine from 2007-2012. The historical nutrient data for the Gulf of Maine were measured in the lab; the nutrient data for Harpswell Sound was measured by the ISUS. There are relatively few match-ups for validation, but these points did show the correlation between the two methods. However, the similarity of the distribution of measured nitrate from water samples in lab and the in situ temperature and salinity characteristics of the sampled waters were very coherent with those measured by the ISUS, providing some quantitative validation. Future analysis of the ISUS data from summer 2014, in comparison to nutrient data from the water samples taken over the course of this summer, will further justify the validity of the ISUS data. A clear relationship between nitrate concentration and water temperature and nitrate concentration and salinity for both the Gulf of Maine and Harpswell Sound emerged (Figure 1). The highest concentrations of nitrate are found in the saltiest water (between 30-34 psu) and coldest water (between 3 and 12 degrees Celsius). This pattern was observed both generally in the Gulf of Maine and more specifically in Harpswell Sound, indicating that processes observed in Harpswell Sound are connected to broader scale oceanographic processes. These results also indicate that nutrients generated by deep ocean processes are dominant and river sources are negligible, a result that is not found in most areas. For both chlorophyll data and ISUS nitrate data, 2010 proved to be a model year with a clear and thorough timeseries from early February to late November. After analysis, the relationship between nitrate and chlorophyll showed a strong preliminary correlation of chlorophyll concentration (once again, as a proxy for phytoplankton biomass) increasing as nitrate concentration decreases (Figure 2). The low levels of phytoplankton consume the high levels of nitrate and therefore, as the bloom grows, the concentration of nitrate decreases proportionally. The expected dependence of chlorophyll concentration on nitrate concentration becomes incredibly clear through these results, similar to the results presented in Li et al., 2010. The ISUS data from 2007-2012 requires further processing in order to fully explore the relationship between chlorophyll and nitrate concentration on a pertinent timescale to bloom growth dynamics. While it is possible to construct a full time-series from the newly manipulated ISUS dataset after this summer work, it would be important and interesting to further examine the relationship between chlorophyll concentration and nitrate concentration in Harpswell Sound on daily, weekly, seasonal, and yearly timescales. This next step of investigation will require more time for data processing, but the work done this summer to validate the ISUS data and show the correlation between Harpswell Sound and the Gulf of Maine is incredibly promising for future work. Final report of research funded by the Doherty Coastal Studies Research Fellowship.

Date: 2014-08-01

Creator: Sophie Janes

Access: Open access

The central pattern generator (CPG) is a neural network that controls the rhythmic patterned outputs, which generate locomotion as needed. The lobster provides a good model to study CPGs because it has a relatively simple CPG. The lobster CPG, or cardiac ganglion accommodates for a range of activities and changes in the environment (Cooke, 2002).The small lobster CG is made up of nine neurons that control the neurogenic heart. The lobster CG is located on the inner dorsal wall of the heart and forms long neurites that branch onto the heart muscle. The CG, through an intrinsic mechanism, generates patterned and rhythmic bursts to the heart (Cooke 2002).The H. americanus CG sends information to the heart muscle to regulate the heart beat. The patterned bursts from the CG need to be adjusted in response to changing demands, for example, activity level or blood volume. Two general mechanisms, intrinsic feedback and extrinsic neuromodulation, have been identified to facilitate this adjustment. Through an intrinsic feedback mechanism, the muscle sends information back to the CG via a positive pathway and a negative pathway. In the positive pathway, stretch-sensitive dendrites of cardiac neurons increase the frequency of heart contractions when stretched (Cooke 2002). In the negative pathway, nitric oxide (NO), produced by the cardiac muscle, slows the frequency (Mahadevan et al. 2004). The interplay between the negative and positive feedback pathways regulates the output of the CG. An extrinsic mechanism has also been identified to regulate the CG output. Chemical neuromodulators that are released either locally or as hormones signal to the heart or CG to modulate ganglion activity. The intrinsic and extrinsic mechanisms affect the contraction amplitude and frequency of the heart.Within this simple invertebrate organism, a complex layering of control exists. Studies of the effects of various extrinsic modulators suggest that these modulators may alter how the feedback pathways operate. I examined what effect the neuromodulator GYSDRNLRFamide (GYS), a peptide found in the lobster nervous system, has on the balance between the positive and negative pathways (Ma et al., 2008). Recent experiments have demonstrated that when GYS was applied at high concentrations in the whole heart, the frequency decreased. This suggests that GYS may play a role in the intrinsic feedback pathways, and likely enhances the negative pathway.I looked at if nitric oxide altered the modulation of the heartbeat frequency when enhanced by the extrinsic modulator, GYS. Based on previous experiments, I hypothesized that GYS allows the NO, or negative pathway to predominate. In order to test my hypothesis, I examined the effects of GYS when I removed nitric oxide, which allows the negative pathway to exist. I compared the characteristics of the heartbeat when saline was run through the heart to when GYS was run through the heart. I also compared the characteristics of the heartbeat when the NO inhibitor, L-NA, was applied to when GYS was applied in the presence of L-NA. I finally compared the changes in frequency between these two comparisons. I found a significant difference between the change in frequency of the heart perfused with GYS in saline as opposed to perfused with GYS in L-NA. GYS had a greater negative effect without L-NA. These results demonstrate that NO is likely the cause of the observed decrease in frequency. Final Report of research funded by the Doherty Coastal Studies Research Fellowship.

Date: 2014-08-01

Creator: Anna Bearman

Access: Open access

There are numerous anthropogenic pollutants present in both marine and terrestrial waters.1 Though many of these chemicals do not absorb light and therefore cannot undergo photolyic degradation on their own, dissolved organic matter (DOM), found alongside pollutants in natural aquatic waters, can act as a catalyst in the attenuating process of contaminants. DOM is a complex mixture of organic compounds derived from decaying plants, animals and microorganisms. Since DOM can absorb light, it can transfer energy to contaminants, allowing them to break into smaller and often less hazardous molecules. The behavior of DOM is largely determined by its functional chemical components, and the character of DOM is constantly changing with the environment. For example, two International Humic Substances Society standards Pony Lake DOM from Antarctica and Suwannee River DOM from Georgia demonstrate very different compositions and characteristics2. More important than simply identifying varying functional groups in DOM these standards, however, may be understanding how our local water in the Androscoggin River and Gulf of Maine behaves and attenuates contaminants. The goal for this project was to first isolate DOM from the Androscoggin River and the Gulf of Maine. DOM was extracted using the Thurman and Malcolm procedure,3 beginning with collection and filtration of water from the Androscoggin River boat launch and Simpson’s Point. The water was then run through a chromatography column, through the method of absorption chromatography the dissolved organic matter sticks to the resin within the column. DOM was then eluted from the column, concentrated, and protonated with an ion exchange column. The resulting concentrated DOM solution was then freeze-dried to obtain the final powdered DOM fraction. Because the quantity of DOM isolated from the Gulf of Maine was too small for characterization, we determined that a new collection method using equipment suited for sampling larger volumes of water will be necessary for future DOM characterization. Instead we focused on collecting samples from the Androscoggin on a weekly basis. Following isolation, the Androscoggin River DOM was dissolved in Type I water to make 3mg/L DOM samples and then characterized through UV-Vis absorption and 3D fluorescence Excitation-Emission Matrix (EEM) spectroscopy techniques. The data was then processed using the parallel factor analysis (PARAFAC) method.4 PARAFAC deconvolutes the fluorescence spectra into the distinct fluorescent components present in the complex DOM mixture (Figure 1). This preliminary analysis indicates that Androscoggin River DOM is made up of at least six specific fluorophores. In the future, I will identify the types of molecules responsible for each component signature and attempt to ascertain the relative concentration of each photoactive constituent in the DOM samples. This information will have significant implications for the photochemistry of natural and anthropogenic chemicals in natural waters. Funded by the Henry L. Grace Doherty Coastal Studies Research Fellowship and James Stacy Coles Summer Research Fellowship in Chemistry.