Showing 71 - 80 of 583 Items
Quantification and Characterization of AST-C Peptides in Homarus americanus Using Mass Spectrometry
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.
Effects of octopamine and tyramine on the cardiac system of the lobster, Homarus americanus
Date: 2019-05-01
Creator: Casey Breslow
Access: Open access
- Modulation in neural systems is important for regulating physiology and behavior (Wright et al., 2010). Peptides, hormones, and amines are common neural modulators, acting on many neural systems across species. One group of neural networks that can be regulated are central pattern generators (CPGs), which generate rhythmic neural patterns, which drive behaviors (Marder and Bucher, 2001). Octopamine, and its precursor tyramine, are two amines that have been found to regulate (CPGs) across species (Cooke, 2002; Fussnecker et al., 2006). One role of octopamine in the decapod neurogenic heart is regulating the frequency and the duration of heart beats. However, the precise site of octopamine modulation within the cardiac system is not yet known (Kurumoto and Ebara, 1991). One possible site of action is the cardiac ganglion (CG), the CPG in decapod hearts. The transcripts for the enzymes required to synthesize octopamine from tyramine have been identified and localized in the CG (Christie et al., 2018). This would suggest that octopamine is produced in the CG, where it could have a direct action on those neurons, or it could be released peripherally. We have found individual variation in the response to octopamine and its precursor tyramine, and significant effects of frequency and contraction amplitude in the whole heart.
Midterm Decline in Comparative Perspective
Date: 2019-05-01
Creator: Duncan Gans
Access: Open access
Beyond Urban Bias: Peasant Movements and the State in Africa
Date: 2019-05-01
Creator: Connor Rockett
Access: Open access
- Focusing on sub-Saharan Africa, this study tests the hypothesis that state intervention in agrarian economies causes peasant movements to engage in broad-based contention, on regional and national levels. The study traces the connections between government land and agricultural institutions and the characteristics of rural movements that make claims on them. Case studies of regions of Tanzania, Senegal, Côte d’Ivoire, and Ethiopia show the ways in which rural movements are constructed in response to the political and social environments in which they arise. That is, the comparisons demonstrate that the character of political authority and social organization are important determinants of the form taken by peasant movements.
Ecological Effects of Rockweed (Ascophyllum nodosum) Harvesting
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).
Tension production and sarcomere length in lobster (Homarus americanus) cardiac muscles: the mechanisms underlying mechanical anisotropy Access to this record is restricted to members of the Bowdoin community. Log in here to view.
Date: 2019-05-01
Creator: Matthew Maguire
Access: Access restricted to the Bowdoin Community
The evolutionary response of populations of the blue mussel (Mytilus edulis) populations to climate change
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.
Active and Passive Spatial Learning and Memory in Human Navigation
Date: 2019-01-01
Creator: Caroline Rice
Access: Open access
- Previous studies show that active exploration of an environment contributes to spatial learning more than passive visual exposure (Chrastil & Warren, 2013; Chrastil & Warren, 2015). Active navigation and cognitive decision-making in a novel environment leads to increased spatial knowledge and memory of location compared to a passive exploration that removes the decision-making component. There is evidence of theta oscillations present in electroencephalography (EEG) recordings from the hippocampus and pre-frontal cortex (PFC). These low-frequency waves could reflect spatial navigation and memory performance, suggested by their involvement in communication between the formerly named brain regions. Through communication with the hippocampus, theta oscillations could be involved in the integration of new spatial information into memory. While undergoing EEG, subjects in this study either actively or passively explored a virtual maze, identified as the “Free” or “Guided” groups, respectively. After exploring, subjects’ spatial memory of the maze was tested through a task that required navigation from a starting object to a target object. Behavioral data show increased spatial memory for the Free group, indicated by significantly greater navigation to the correct target object in the memory task. EEG results indicate significantly greater theta oscillations in frontal regions for the Free group during the exploration phase. These results support those found in previous studies and could indicate a correlation between frontal theta oscillations during learning of novel environments and spatial memory.
An Assessment of pH and the Effects of Ocean Acidification in a Phippsburg, ME Clam Flat
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.
GIS analysis of historical cod fisheries in the Gulf of Maine
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