Life Sciences Commons^™

Methylation Controlled J Protein Is A Master Regulator Of Mitochondrial Metabolism, Devin Pierre Champagne

Graduate College Dissertations and Theses

Methylation controlled J protein (MCJ) is a negative regulator of mitochondrial metabolism that has a substantial impact on overall cell metabolism and function. MCJ is highly expressed by naïve CD8+ T cells, however its role in their immune effector functions was unknown. In this dissertation, it will be demonstrated that MCJ restricts the mitochondrial metabolism of CD8+ T cells, in part by reducing respiratory supercomplex formation. MCJ deficiency enhances the immune effector functions and memory responses of CD8+ T cells in a mitochondrial ATP dependent manner. As a consequence, protection to influenza virus infection is substantially improved. Reduced expression of …

Remote Sensing Methods And Applications For Detecting Change In Forest Ecosystems, David James Gudex-Cross

Graduate College Dissertations and Theses

Forest ecosystems are being altered by climate change, invasive species, and additional stressors. Our ability to detect these changes and quantify their impacts relies on detailed data across spatial and temporal scales. This dissertation expands the ecological utility of long-term satellite imagery by developing high quality forest mapping products and examining spatiotemporal changes in tree species abundance and phenology across the northeastern United States (US; the ‘Northeast’).

Species/genus-level forest composition maps were developed by integrating field data and Landsat images to model abundance at a sub-pixel scale. These abundance maps were then used to 1) produce a more detailed, accurate …

Labor On Vermont Dairy Farms: A Producer Perspective, Emily Irwin

Graduate College Dissertations and Theses

To compete with larger, more efficient dairy farms, build resilience against increasingly volatile milk prices, and increase farm income, farms in traditional dairy states such as New York, Wisconsin, and Vermont, have been forced to expand their herds and increase production. Many dairy farmers do not have formal training in human resources management, and find the transition to a larger, non-family workforce to be challenging. In addition, farmers who have transitioned to a primarily Latinx workforce also face considerable cultural and language barriers. The quality of human resource management can have a significant impact on a farm business, and evidence …

Investigating The Effects Of Ant-Hemipteran Mutualisms On The Invertebrate Community Structure And Their Host Plant, Honey Mesquite (Prosopis Glandulosa), Nabil Nasseri

Graduate College Dissertations and Theses

Ants are ubiquitous in most communities and many form opportunistic mutualisms with honeydew-producing hemipterans (e.g. treehoppers). Hemipterans excrete honeydew, a carbohydrate rich substance, that ants harvest and, in return, ants protect their honeydew-producing partners from parasitoids, predators, and competitors. Given the efficacy of tending ants in removing hemipteran antagonists, and the strong roles that ants play within their communities as predators, competitors, and seed dispersers, surprisingly little is known of the effects of ant-hemipteran mutualisms (AHM) on the invertebrate communities in which they are embedded or on the plants that host AHM. Using observational and manipulative field experiments, I examined …

A Proximity-Dependent Biotin Labeling Based Screen For Protein Kinase A Anchoring Proteins Within Focal Adhesion Complexes, Hannah Naughton

Graduate College Dissertations and Theses

Protein kinase A (PKA) regulates a diverse array of cellular activities including metabolism, differentiation, actomyosin contractility, and migration. The multifunctionality of this ubiquitous enzyme is achieved, in part, through subcellular targeting mediated by the A Kinase Anchoring Proteins (AKAP) family of proteins. AKAPs serve as scaffolding proteins that localize PKA to various cellular compartments and bring together specific targets and modulators of PKA activity.

The importance of spatially restricted PKA signaling is particularly apparent in the context of cell motility. It has been observed that both anchoring through AKAPs and the subsequent localized activation of PKA at the leading edge …

Radically Different Lignin Composition In Posidonia Species May Link To Differences In Organic Carbon Sequestration Capacity, Joeri Kaal, Oscar Serrano, José C.Del Río, Jorge Rencoret

Research outputs 2014 to 2021

There is considerable variability in the ability of seagrass ecosystems to sequester organic carbon (C_org) in their sediments, which act as natural carbon sinks contributing to climate change mitigation. In this work, we studied the chemistry of two Posidonia seagrass species aiming to elucidate whether differences in chemical composition might explain differences in their C_org sequestration capacity. Pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) and Thermally assisted Hydrolysis and Methylation (THM) GC-MS data showed a remarkable difference in phenolic compound patterns between P. oceanica and P. australis bulk plants and individual organs (leaves, sheaths, roots and rhizomes). The lignin of …

Phylogenetic Analysis Of Apicomplexan Parasites Infecting Commercially Valuable Species From The North-East Atlantic Reveals High Levels Of Diversity And Insights Into The Evolution Of The Group, R. Xavier, R. Severino, M. Pérez-Losada, C. Gestal, R. Freitas, D. James Harris, Ana Verissimo, D. Rosado, J. Cable

VIMS Articles

Background: The Apicomplexa from aquatic environments are understudied relative to their terrestrial counterparts, and the seminal work assessing the phylogenetic relations of fish-infecting lineages is mostly based on freshwater hosts. The taxonomic uncertainty of some apicomplexan groups, such as the coccidia, is high and many genera were recently shown to be paraphyletic, questioning the value of strict morphological and ecological traits for parasite classification. Here, we surveyed the genetic diversity of the Apicomplexa in several commercially valuable vertebrates from the NorthEast Atlantic, including farmed fish. Results: Most of the sequences retrieved were closely related to common fish coccidia of Eimeria, …

Depth- And Range-Dependent Variation In The Performance Of Aquatic Telemetry Systems: Understanding And Predicting The Susceptibility Of Acoustic Tag-Receiver Pairs To Close Proximity Detection Interference, S R. Scherrer, B P. Rideout, G. Giorli, E M. Nosal, Kevin C. Weng

VIMS Articles

BACKGROUND:

Passive acoustic telemetry using coded transmitter tags and stationary receivers is a popular method for tracking movements of aquatic animals. Understanding the performance of these systems is important in array design and in analysis. Close proximity detection interference (CPDI) is a condition where receivers fail to reliably detect tag transmissions. CPDI generally occurs when the tag and receiver are near one another in acoustically reverberant settings. Here we confirm transmission multipaths reflected off the environment arriving at a receiver with sufficient delay relative to the direct signal cause CPDI. We propose a ray-propagation based model to estimate the arrival …

Characterizing The Preferences And Values Of Us Recreational Atlantic Bluefin Tuna Anglers, William Morris Goldsmith, Andrew M. Scheld, John Graves

VIMS Articles

The Atlantic Bluefin Tuna Thunnus thynnus is the target of a recreational fishery along the U.S. East Coast that is thought to be of considerable economic value. In some years, recreational landings have exceeded the sector’s annual subquota due to changes in fish availability, limited predictability of angler effort, and difficulties in realtime monitoring of catch. Understanding the drivers of angler behavior is critical for predicting how effort and harvest may vary as a function of changing fish availability, regulations, or costs. To investigate angler decision making, preferences, and values, we surveyed private recreational anglers from Maine to North Carolina …

Accuracy And Precision Of Tidal Wetland Soil Carbon Mapping In The Conterminous United States, Jr Holmquist, L Windham-Myers, N Bliss, S Crooks, Jt Morris, W. G. Reay, Et Al.

VIMS Articles

Tidal wetlands produce long-term soil organic carbon (C) stocks. Thus for carbon accounting purposes, we need accurate and precise information on the magnitude and spatial distribution of those stocks. We assembled and analyzed an unprecedented soil core dataset, and tested three strategies for mapping carbon stocks: applying the average value from the synthesis to mapped tidal wetlands, applying models fit using empirical data and applied using soil, vegetation and salinity maps, and relying on independently generated soil carbon maps. Soil carbon stocks were far lower on average and varied less spatially and with depth than stocks calculated from available soils …

Antibiotic Effects On Microbial Communities Responsible For Denitrification And N2o Production In Grassland Soils, M Semedo, Bk Song, T Sparrer, Rl Phillips

VIMS Articles

Antibiotics in soils may affect the structure and function of microbial communities. In this study, we investigated the acute effects of tetracycline on soil microbial community composition and production of nitrous oxide (N2O) and dinitrogen (N-2) as the end-products of denitrification. Grassland soils were pre-incubated with and without tetracycline for 1-week prior to measurements of N2O and N-2 production in soil slurries along with the analysis of prokaryotic and fungal communities by quantitative polymerase chain reaction (qPCR) and next-generation sequencing. Abundance and taxonomic composition of bacteria carrying two genotypes of N2O reductase genes (nosZ-I and nosZ-II) were evaluated through qPCR …

New Constraints On Coseismic Slip During Southern Cascadia Subduction Zone Earthquakes Over The Past 4600 Years Implied By Tsunami Deposits And Marine Turbidites, Gr Priest, Rc Witter, Yinglong J. Zhang, C Goldfinger, Kl Wang, Jc Allen

VIMS Articles

This correction stands to correct Figure 7c listing a low minimum slip of 12 m for Case 2 instead of the correct value of 8 m, as stated in the body of the text and depicted on the chart of cumulative slip. The corrected chart explanation and caption are shown below. This error did not affect any of the findings of the paper or the chart itself. This is a correction to the original article.

Spatial Distribution And Morphological Responses To Predation In The Salt Marsh Periwinkle, Aj Rietl, Mg Sorrentino, Bj Roberts

VIMS Articles

The salt marsh periwinkle (Littoraria irrorata) is a common and often abundant mollusk in marshes of the Gulf and Atlantic coasts of the United States. Several studies have focused on the effects of periwinkles on Spartina alterniflora production and the effects of oil on periwinkle survivability, yet the general ecology of the snail has been underreported. In this study, we measured spatial distributions, biomass, shell repair frequency, and a suite of morphological characteristics of L. irrorata at three sites in each of five regions spanning the southeastern Louisiana Coast between the Atchafalaya and Mississippi rivers. Sampling was conducted along 50 …

Time Trends Of Polybrominated Diphenyl Ethers (Pbdes) In Antarctic Biota, E Markham, Ek Brault, M Khairy, Ar Robuck, Me Goebel, Mg Cantwell, Rm Dickhut, R Lohmann

VIMS Articles

Polybrominated diphenyl ethers (PBDEs) are "emerged" contaminants that were produced and used as flame retardants in numerous consumer and industrial applications for decades until banned. They remain ubiquitously present in the environment today. Here, a unique set of >200 biotic samples from the Antarctic was analyzed for PBDEs, including phytoplankton, krill, fish, and fur seal milk, spanning several sampling seasons over 14 years. PBDE-47 and -99 were the dominant congeners determined in all samples, constituting > 60% of total PBDEs. A temporal trend was observed for Sigma 7PBDE concentrations in fur seal milk, where concentrations significantly increased (R-2 = 0.57, p < 0.05) over time (2000-2014). Results for krill and phytoplankton also suggested increasing PBDE concentrations over time. Trends of PBDEs in fur seal milk of individual seals sampled 1 or more years apart showed no clear temporal trends. Overall, there was no indication of PBDEs decreasing in Antarctic biota yet, whereas numerous studies have reported decreasing trends in the northern hemisphere. Similar PBDE concentrations in perinatal versus nonperinatal milk implied the importance of local PBDE sources for bioaccumulation. These results indicate the need for continued assessment of contaminant trends, such as PBDEs, and their replacements, in Antarctica.

Effects-Based Spatial Assessment Of Contaminated Estuarine Sediments From Bear Creek, Baltimore Harbor, Md, Usa, Se Hartzell, Michael A. Unger, Bl Mcgee, Lt Yonkos

VIMS Articles

The original publication of this paper contains an error. The correct image of figure 5 is shown in this paper.

Cohesive And Mixed Sediment In The Regional Ocean Modeling System (Roms V3.6) Implemented In The Coupled Ocean-Atmosphere-Wave-Sediment Transport Modeling System (Coawst R1234), Cr Sherwood, Al Aretxabaleta, Courtney K. Harris, Jp Rinehimer, R Verney, B Ferre

VIMS Articles

We describe and demonstrate algorithms for treating cohesive and mixed sediment that have been added to the Regional Ocean Modeling System (ROMS version 3.6), as implemented in the Coupled Ocean-Atmosphere-Wave- Sediment Transport Modeling System (COAWST Subversion repository revision 1234). These include the following: floc dynamics (aggregation and disaggregation in the water column); changes in floc characteristics in the seabed; erosion and deposition of cohesive and mixed (combination of cohesive and non-cohesive) sediment; and biodiffusive mixing of bed sediment. These routines supplement existing noncohesive sediment modules, thereby increasing our ability to model fine-grained and mixed-sediment environments. Additionally, we describe changes to …

The Competing Impacts Of Climate Change And Nutrient Reductions On Dissolved Oxygen In Chesapeake Bay, Id Irby, Marjorie A.M. Friedrichs, F Da, Ke Hinson

VIMS Articles

The Chesapeake Bay region is projected to experience changes in temperature, sea level, and precipitation as a result of climate change. This research uses an estuarine-watershed hydrodynamic-biogeochemical modeling system along with projected mid-21st-century changes in temperature, freshwater flow, and sea level rise to explore the impact climate change may have on future Chesapeake Bay dissolved-oxygen (DO) concentrations and the potential success of nutrient reductions in attaining mandated estuarine water quality improvements. Results indicate that warming bay waters will decrease oxygen solubility year-round, while also increasing oxygen utilization via respiration and remineralization, primarily impacting bottom oxygen in the spring. Rising sea …

Estimating Fishing And Natural Mortality Rates, And Catchability Coefficient, From A Series Of Observations On Mean Length And Fishing Effort, Ay Then, Jm Hoenig, Qc Huynh

VIMS Articles

Gedamke and Hoenig (2006) (Transactions of the American Fisheries Society, 135: 476-487) developed a non-equilibrium version of the Beverton and Holt estimator of total mortality rate, Z, based on mean length and thereby increased the usefulness of length-based methods. In this study, we extend their model by replacing period-specific Z parameters with the year-specific parameterization Z(y) = qf(y) + M where q is the catchability coefficient, f(y) is the fishing effort in year y, F (= qf) is the fishing mortality rate, and M is the natural mortality rate. Thus, the problem reduces to estimating just three parameters: q, M …

Assimilating Bio-Optical Glider Data During A Phytoplankton Bloom In The Southern Ross Sea, De Kaufman, Marjorie A.M. Friedrichs, Jcp Hemmings, Walker O. Smith Jr.

VIMS Articles

The Ross Sea is a region characterized by high primary productivity in comparison to other Antarctic coastal regions, and its productivity is marked by considerable variability both spatially (1-50 km) and temporally (days to weeks). This variability presents a challenge for inferring phytoplankton dynamics from observations that are limited in time or space, which is often the case due to logistical limitations of sampling. To better understand the spatio-temporal variability in Ross Sea phytoplankton dynamics and to determine how restricted sampling may skew dynamical interpretations, high-resolution bio-optical glider measurements were assimilated into a one-dimensional biogeochemical model adapted for the Ross …

Saltmarsh Plants, But Not Fertilizer, Facilitate Invertebrate Recolonization After An Oil Spill, David S. Johnson, Jw Fleeger, Mr Riggio, Ia Mendelssohn, Qx Lin, Dr Deis, A Hou

VIMS Articles

Foundation species contribute to the recovery of animal communities from disturbance by engineering, by improving habitat quality, and by regulating food availability. In a salt marsh impacted by the Deepwater Horizon oil spill, we tested the hypothesis that nutrient subsidies would enhance the positive effects of the foundation species Spartina alterniflora on the initial recolonization of benthic invertebrate communities (e.g., copepods, annelids, nematodes) by augmenting food (i.e., microalgae) availability. After two months, plantings of S.alterniflora significantly elevated the densities of the polychaete Capitella capitata, meiofauna-sized annelids, and total macroinfauna over unplanted plots. After 7months, the significant effect of plantings persisted …

Early-Holocene Greening Of The Afro-Asian Dust Belt Changed Sources Of Mineral Dust In West Asia, A Sharifi, Ln Murphy, A Pourmand, Ac Clement, Elizabeth A. Canuel

VIMS Articles

Production, transport and deposition of mineral dust have significant impacts on different components of the Earth systems through time and space. In modern times, dust plumes are associated with their source region(s) using satellite and land -based measurements and trajectory analysis of air masses through time. Reconstruction of past changes in the sources of mineral dust as related to changes in climate, however, must rely on the knowledge of the geochemical and mineralogical composition of modern and paleodust, and that of their potential source origins. In this contribution, we present a 13,000-yr record of variations in radiogenic Sr-Nd-Hf isotopes and …

Detection Of “Xisco” Gene For Identification Of Streptococcus Pneumoniae Isolates, Francisco Salvà-Serra, Gwendolyn Connolly, Edward Moore, Lucia Gonzales-Siles

Articles

We describe a PCR-assay differentiating Streptococcus pneumoniae from closely-related species of the Mitis group of the genus Streptococcus and identification of pneumococcus clinical isolates, based on the “Xisco” gene discriminatory marker. The complete “Xisco” gene sequence was observed in all S. pneumoniae genomes analyzed and absent in all non-pneumococcus genomes.

Measurement & Analysis Of The Temporal Discrimination Threshold Applied To Cervical Dystonia, Rebecca B. Beck, Eavan M. Mcgovern, John Butler, Dorina Birsanu, Brendan Quinlivan, Ines Beiser, Shrut Narasimham, Sean O'Riordan, Michael Hutchinson, Richard B. Reilly

Other resources

The temporal discrimination threshold (TDT) is the shortest time interval at which an observer can discriminate two sequential stimuli as being asynchronous (typically 30-50 ms). It has been shown to be abnormal (prolonged) in neurological disorders, including cervical dystonia, a phenotype of adult onset idiopathic isolated focal dystonia. The TDT is a quantitative measure of the ability to perceive rapid changes in the environment and is considered indicative of the behavior of the visual neurons in the superior colliculus, a key node in covert attentional orienting. This article sets out methods for measuring the TDT (including two hardware options and …

Recognizing Food As Part Of Ireland’S Intangible Cultural Heritage, Máirtín Mac Con Iomaire

Articles

Drawing on evidence from across a range of disciplines (literature, folklore, history, sociology, etc.), this paper explores the lack of an iconic link between Ireland and food, explaining the reasons why Ireland and food are not immediately linked in the popular imagination. It argues for recognition of foodways as a significant element in Ireland’s intangible cultural heritage. It highlights and interrogates constructs, such as ‘national’ and ‘regional’ cuisines, charting the growing scholarship around Irish food history from the ground breaking work of A.T. Lucas and Louis Cullen to a recent emerging cluster of doctoral researchers. The paper identifies the potential …

Arsenic In Groundwater In South West Ireland - Occurrence, Controls, And Hydrochemistry, Ellen R. Mcgrory, Emma Holian, Alberto Alvarez-Iglesias, Norma Bargary, Eoin Mcgillicuddy, Henry Tiernan, Liam Morrison

Articles

Globally numerous regions have been identified with elevated arsenic within groundwater which can result in potential adverse health risks. In Ireland, a previous national-scale research assessment of groundwater identified isolated clusters of elevated arsenic and indicated that lithology was a major controlling factor on arsenic in groundwater. Complementary comparisons of national-scale and regional-scale groundwater assessments of arsenic are lacking in Europe when compared to other global regions. The aims of this study were to demonstrate the value of a regional-scale groundwater hydrochemistry dataset with an existing national-scale approach, describe anomalies that can become the focus of attention for public health …

Synthesis, Characterisation And Dna Intercalation Studies Of Regioisomers Of Ruthenium (Ii) Polypyridyl Complexes, Laura Perdisatt, Samar Moqadasi, Luke O'Neill, Gary Hessman, Alessandra Ghion, Muhammad Qasim Mushtaq Warraich, Alan Casey, Christine O'Connor

Articles

Regioisomers of the functional group of the main ligand (L) on a series of [Ru(phen)2L]2+and [Ru(bpy)2L]2+ complexes, where phen is 1,10 phenanthroline and bpy is 2,2′-bipyridine, were synthesised to investigate the interaction with deoxyribonucleic acid (DNA) as potential therapeutics. UV–Vis binding titrations, thermal denaturation and circular dichroism were used to evaluate their interaction with DNA. The conclusions indicated the significance of the auxiliary ligand; especially 1,10-phenanthroline has on the binding constants (Kb). The systematic variation of auxiliary ligand(phen or bpy), and polypyridyl ligand (4-(1H-Imidazo[4,5-f][1,10]phenanthrolin-2-yl)benzonitrile (CPIP), 2-(4-formylphenyl)imidazo[4,5-f] [1,10] phenanthroline (FPIP), 2-(4-bromophenyl)imidazo[4,5-f][1,10]phenanthroline (BPIP) and 2-(4-nitrophenyl)imidazo[4,5-f] [1,10] phenanthroline (NPIP), split in terms of …

Raman Spectroscopic Analysis Of High Molecular Weight Proteins In Solution - Considerations For Sample Analysis And Data Pre-Processing, Drishya Rajan Parachalil, Brenda B. Brankin, Jennifer Mcintyre, Hugh Byrne

Articles

This study explores the potential of Raman spectroscopy, coupled with multivariate regression techniques and a protein separation technique (ion exchange chromatography), to quantitatively monitor diagnostically relevant changes in high molecular weight proteins in liquid plasma. Measurement protocols to detect the imbalances in plasma proteins as an indicator of various diseases using Raman spectroscopy are optimised, such that strategic clinical applications for early stage disease diagnostics can be evaluated. In a simulated plasma protein mixture, concentrations of two proteins of identified diagnostic potential (albumin and fibrinogen) were systematically varied within physiologically relevant ranges. Scattering from the poorly soluble fibrinogen fraction is …

Current And Future Technologies For Microbiological Decontamination Of Cereal Grains, Agatha Los, Dana Ziuzina, Paula Bourke

Articles

Cereal grains are the most important staple foods for mankind worldwide. The constantly increasing annual production and yield is matched by demand for cereals, which is expected to increase drastically along with the global population growth. A critical food safety and quality issue is to minimize the microbiological contamination of grains as it affects cereals both quantitatively and qualitatively. Microorganisms present in cereals can affect the safety, quality, and functional properties of grains. Some molds have the potential to produce harmful mycotoxins and pose a serious health risk for consumers. Therefore, it is essential to reduce cereal grain contamination to …

Chlorate And Other Oxychlorine Contaminants Within The Dairy Supply Chain, William P. Mccarthy, Tom F. O'Callaghan, Martin Danaher, David Gleeson, Christine O'Connor, Mark A. Fenelon, John Tobin

Articles

The presence of chlorate in milk and dairy products can arise from the use of chlorinated water and chlorinated detergents for cleaning and sanitation of process equipment at both farm and food processor level. Chlorate and other oxychlorine species have been associated with inhibition of iodine uptake in humans and the formation of methemoglobin, with infants and young children being a high‐risk demographic. This comprehensive review of chlorate and chlorine derivatives in dairy, highlights areas of concern relative to the origin and/or introduction of chlorate within the dairy supply chain. This review also discusses the associated health concerns, regulations, and …

Hatch & Sons Menu 2018, Hatch & Sons

Menus of the 21st Century

Roark Cassidy’s stellar operational insight spans high-end and casual dining. The Kemp girls Domini and Peaches, who together with Roark own ITSA, Feast Catering, Alchemy & Joe's and journalist and consultant Hugo Arnold. We’ve cooked for each other and a frightening number of people over the years. At heart, however, we are all devoted to the joys of the kitchen table and good Irish grub.