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Full-Text Articles in Life Sciences

The Conservation Value Of Residential Landscapes For Native Bird Communities: Patterns, Processes, And Management Implications, Susannah Beth Lerman Sep 2011

The Conservation Value Of Residential Landscapes For Native Bird Communities: Patterns, Processes, And Management Implications, Susannah Beth Lerman

Open Access Dissertations

Urbanization, as it transforms natural biotic systems into human-dominated landscapes, is recognized as one of the greatest threats to biodiversity throughout the world. Furthermore, urban dwellers are becoming increasingly disconnected with the natural world. Here I investigate whether residential landscape designs that mimic the natural environment can provide habitat for native birds. First I uncover some of the patterns of bird distribution in residential yards by incorporating habitat features, urbanization measurements and socioeconomic factors with bird monitoring data into a multivariate analysis. The results indicate that native birds associate with neighborhoods with native plants and shrubs, neighborhoods closer to desert ...


Phylogenics And Patterns Of Molecular Evolution In Amoebozoa, Daniel J.G. Lahr Sep 2011

Phylogenics And Patterns Of Molecular Evolution In Amoebozoa, Daniel J.G. Lahr

Open Access Dissertations

My dissertation explores several aspects of the relationship between morphological and molecular evolution in amoeboid lineages:

Chapter 1 - General Introduction: This chapter provides an overview of the most pressing issues in Amoebozoa phylogeny that are dealt with in the remainder of the thesis

Chapter 2 - Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new generation high fidelity DNA polymerase: This chapter addresses the methodological difficulty in the study of large gene families, the generation of artifactual sequences by recombination during PCR.

Chapter 3 - Evolution of the actin gene family in testate lobose amoebae (Arcellinida ...


Cellular And Molecular Changes Following Skeletal Muscle Damage: A Role For Nf-Kb And Muscle Resident Pericytes, Robert H. Hyldahl Sep 2011

Cellular And Molecular Changes Following Skeletal Muscle Damage: A Role For Nf-Kb And Muscle Resident Pericytes, Robert H. Hyldahl

Open Access Dissertations

Skeletal muscle is dynamic and actively regenerates following damage or altered functional demand. Regeneration is essential for the maintenance of muscle mass and, when dysregulated as a result of disease or aging, can lead to losses in functional capacity and increased mortality. Limited data exist on the molecular mechanisms that govern skeletal muscle regeneration in humans. Therefore, the overall objective of this dissertation was to characterize early molecular alterations in human skeletal muscle to strenuous exercise known to induce a muscle regenerative response. Thirty-five subjects completed 100 eccentric (muscle lengthening) contractions (EC) of the knee extensors with one leg and ...


Components Of A Protein Machine: Allosteric Domain Assembly And A Disordered C-Terminus Enable The Chaperone Functions Of Hsp70, Robert G. Smock Sep 2011

Components Of A Protein Machine: Allosteric Domain Assembly And A Disordered C-Terminus Enable The Chaperone Functions Of Hsp70, Robert G. Smock

Open Access Dissertations

Hsp70 molecular chaperones protect proteins from aggregation, assist in their native structure formation, and regulate stress responses in the cell. A mechanistic understanding of Hsp70 function will be necessary to explain its physiological roles and guide the therapeutic modulation of various disease states. To this end, several fundamental features of the Hsp70 structure-function relationship are investigated. The central component of Hsp70 chaperone function is its capacity for allosteric signaling between structural domains and tunable binding of misfolded protein substrates. In order to identify a cooperative network of sites that mediates interdomain allostery within Hsp70, a mutational correlation analysis is performed ...


Novel Progestin Signaling Molecules In The Brain: Distribution, Regulation And Molecular Mechanism Of Action, Karlie A. Intlekofer May 2011

Novel Progestin Signaling Molecules In The Brain: Distribution, Regulation And Molecular Mechanism Of Action, Karlie A. Intlekofer

Open Access Dissertations

Progesterone regulates female reproduction in many ways, yet it is still unclear how signals are conveyed through nuclear and extranuclear receptors. The traditional notion was that progesterone binds classical progesterone receptors to alter gene transcription. This view has been challenged by the discovery of additional progesterone signaling molecules important for progesterone actions in non-neural cells. In granulosa cells, the progesterone receptor membrane component 1 (Pgrmc1) mediates progesterone effects by forming a receptor complex with binding partner, Serpine mRNA binding protein 1, but it is unknown whether these molecules function similarly in the brain. To begin to address these issues, I ...


Metformin And/Or Exercise Training Affect Metabolic Health In Men And Women With Prediabetes, Steven K. Malin May 2011

Metformin And/Or Exercise Training Affect Metabolic Health In Men And Women With Prediabetes, Steven K. Malin

Open Access Dissertations

Prediabetes is defined by elevated blood glucose concentrations not high enough to meet criteria for type 2 diabetes. Exercise or metformin, a common “anti-diabetes” medication, may attenuate the progression from prediabetes to type 2 diabetes by improving insulin sensitivity and cardio-metabolic health. Because each treatment has its primary action in different tissues, combining exercise (muscle) with metformin (liver) may further enhance insulin sensitivity and cardio-metabolic health. Purpose: To determine the efficacy of combining exercise training with metformin on insulin sensitivity and cardio-metabolic health in men and women with prediabetes. We hypothesized that the combined treatment would improve insulin sensitivity and ...


Investigation Of A Sulfur-Utilizing Perchlorate-Reducing Bacterial Consortium, Teresa Anne Conneely May 2011

Investigation Of A Sulfur-Utilizing Perchlorate-Reducing Bacterial Consortium, Teresa Anne Conneely

Open Access Dissertations

We present research investigating how, with in depth knowledge of the community, microbial communities may be harnessed for bioremediation of hazardous water contaminants. We focused on the bacterial reduction of perchlorate, a common water contaminant. For this we studied the structure and capabilities of a novel sulfur-utilizing, perchlorate-reducing bacterial (SUPeRB) consortium. Initially, we characterized the minimal consortium that retained functional capabilities, using 16S rRNA and functional gene analysis. A diverse functional consortium dominated by Beta-Proteobacteria of the family Rhodocyclaceae and sulfur-oxidizing Epsilon-Proteobacteria was found. We also examined the optimal growth conditions under which perchlorate degradation occurred and uncovered the upper ...


Movin' & Groovin' Salamanders: Conservation Implications Of Large Scales And Quirky Sex, Noah D. Charney May 2011

Movin' & Groovin' Salamanders: Conservation Implications Of Large Scales And Quirky Sex, Noah D. Charney

Open Access Dissertations

Mole salamanders (Ambystoma) and woodfrogs (Lithobates sylvaticus) are abundant in New England and depend on ephemeral wetlands for breeding. Their aquatic habitats have been well studied and are protected by several local and regional regulations. State endangered species laws also protect mabled salamanders (A. opacum), Jefferson salamanders (A. jeffersonianum), and blue-spotted salamanders (A. laterale). However, these amphbibians spend most of their adult lives in terrestrial habitats that remain poorly protected and elusive to researchers.

In chapter 1, I developed a novel technique using passive integrated transponders for tracking small animals. I used this technique to track marbled salamanders walking up ...


Effects Of Free Fatty Acids, Mono- And Diacylglycerols On Oxidative Stability Of Soybean Oil-In-Water Emulsions, Thaddao Waraho May 2011

Effects Of Free Fatty Acids, Mono- And Diacylglycerols On Oxidative Stability Of Soybean Oil-In-Water Emulsions, Thaddao Waraho

Open Access Dissertations

Even though edible oils undergo refining processes to remove undesirable components, commercial oils still contain small amounts of minor components that can contribute to either prooxidant and antioxidant pathways which ultimately affect the quality of the oils. The objective of this research was to determine the role of free fatty acids and mono- and diacylglycerols on the oxidative stability of oil-in-water emulsions.

Free fatty acids acted as a strong prooxidants in stripped soybean oil-in-water emulsions. Concentrations as low as 0.1% of the lipid accelerated lipid oxidation rate by both shortening the lag phase of lipid hydroperoxide and hexanal formation ...


Bacterial Toxicity Of Oxide Nanoparticles And Their Effects On Bacterial Surface Biomolecules, Wei Jiang May 2011

Bacterial Toxicity Of Oxide Nanoparticles And Their Effects On Bacterial Surface Biomolecules, Wei Jiang

Open Access Dissertations

Toxicity of nano-scaled Al2O3, SiO2, TiO2 and ZnO to bacteria (Bacillus subtilis, Escherichia coli and Pseudomonas fluorescens) was examined and compared to that of their respective bulk (micro-scaled) counterparts. All nanoparticles (NPs) but TiO2 showed higher toxicity than their bulk counterparts. Toxicity of released metal ions was differentiated from that of the oxide particles. ZnO was the most toxic among the three NPs, causing 100% mortality to the three tested bacteria. TEM images showed attachment of NPs to the bacteria, suggesting that the toxicity was affected by bacterial attachment.

The effects of oxide NPs on bacteria cells and bacterial surface ...


The Role Of The Suprmam1 Locus In Responses To Ionizing Radiation And Susceptibility To Mammary Tumors, Nicholas B. Griner May 2011

The Role Of The Suprmam1 Locus In Responses To Ionizing Radiation And Susceptibility To Mammary Tumors, Nicholas B. Griner

Open Access Dissertations

Loss of p53 function can lead to a variety of cancers, including breast cancer. Mice heterozygous for the p53 gene (designated Trp53+/-) develop spontaneous mammary tumors, but this depends on the strain background and has been linked to a locus on chromosome 7 (designated SuprMam1). Mammary tumors are common in BALB/c-Trp53+/-females, but are rare in C57BL/6-Trp53+/- mice. Prevalence of genomic instability appears to contribute to the phenotype as loss of heterozygosity (LOH) is significantly more common among tumors arising in BALB/c-Trp53+/- mice compared to C57BL/6J-Trp53+/- mice. This increased LOH in BALB/c-Trp53+/- tumors was shown ...


Developing An Efficient Cover Cropping System For Maximum Nitrogen Recovery In Massachusetts, Ali Farsad May 2011

Developing An Efficient Cover Cropping System For Maximum Nitrogen Recovery In Massachusetts, Ali Farsad

Open Access Dissertations

Time of planting plays a critical role in nitrogen (N) uptake by rye cover crop (CC). Even a few days of delay in planting can severely decrease CC performance. Evaluating the amount of N accumulation related to time of planting is critical to the farmer who has to optimize the winter rye planting date based on completion of corn harvest, suitable weather conditions and time availability for fall manure application. Winter rye cover crop was planted at 6 planting dates in fall from mid August to early October at weekly intervals from 2004 to 2009.

The results suggest that delay ...


Armillaria In Massachusetts Forests: Ecology, Species Distribution, And Population Structure, With An Emphasis On Mixed Oak Forests, Nicholas Justin Brazee May 2011

Armillaria In Massachusetts Forests: Ecology, Species Distribution, And Population Structure, With An Emphasis On Mixed Oak Forests, Nicholas Justin Brazee

Open Access Dissertations

The ecology, species distribution, and population structure of Armillaria was investigated in the forests of Massachusetts. From 64 plots at 16 sites, 640 isolates of Armillaria were collected from six forest types (northern hardwoods, mixed oak, pitch pine, white pine, white pine/mixed oak, and eastern hemlock). Armillaria gallica proved to be the most abundant species, making up 316/640 (52%) of all isolations. This was followed by A. solidipes (219/640; 34%), A. mellea (46/640; 7%), A. calvescens (36/640; 6%), A. gemina (16/640; 3%), and A. sinapina (7/640; 1%). Armillaria gallica was routinely encountered causing ...


Mitochondrial Dna Polymerase Ib: Functional Characterization Of A Putative Drug Target For African Sleeping Sickness, David F. Bruhn May 2011

Mitochondrial Dna Polymerase Ib: Functional Characterization Of A Putative Drug Target For African Sleeping Sickness, David F. Bruhn

Open Access Dissertations

Trypanosoma brucei and related parasites are causative agents of severe diseases that affect global health and economy. T. brucei is responsible for sleeping sickness in humans (African trypanosomiasis) and a wasting disease in livestock. More than 100 years after T. brucei was identified as the etiological agent for sleeping sickness, available treatments remain inadequate, complicated by toxicity, lengthy and expensive administration regiments, and drug-resistance. There is clear need for the development of a new antitrypanosomal drugs. Due to the unique evolutionary position of these early diverging eukaryotes, trypanosomes posses a number of biological properties unparalleled in other organisms, including humans ...


Novel Systems For The Functional Characterization Of Genes Related To Paclitaxel Metabolism In Taxus Cell Cultures, Khamkeo Vongpaseuth May 2011

Novel Systems For The Functional Characterization Of Genes Related To Paclitaxel Metabolism In Taxus Cell Cultures, Khamkeo Vongpaseuth

Open Access Dissertations

Human society has benefited greatly from plant secondary metabolites, often utilizing a variety of compounds as dyes, food additives, and drugs. In particular, pharmaceutical development has benefited greatly from plant secondary metabolites. One example of this utility is paclitaxel, a highly substituted diterpene approved in the treatment of breast cancer, ovarian cancer, non-small cell lung cancer, and the AIDSrelated Kaposi’s sarcoma. Demand of paclitaxel is likely to increase, due to the current examination of paclitaxel in numerous clinical trials against a variety of other cancers.

Taxus cell culture represents a production source of paclitaxel to meet future demand. However ...


Adaptations To Running While Footwear Cushioning And Surface Are Manipulated, Trampas M. Tenbroek May 2011

Adaptations To Running While Footwear Cushioning And Surface Are Manipulated, Trampas M. Tenbroek

Open Access Dissertations

Minimal footwear sales have encountered rapid growth over the last several years. Minimal footwear are often constructed with thin basic uppers and thin, flexible midsoles. It is likely that running in minimal footwear will require adaptation and adjustments as the amount of cushioning and the geometry of the foot/ground interface will be substantially different than what many are accustomed to. This research investigated the effect footwear cushioning amount and the running surface had on running patterns. Study 1 (Chapter IV) utilized two different running footwear conditions and two different cushioned treadmill conditions, as well as a barefoot condition, to ...


Consequence Of Functioning At The End Range Of Joint Motion: Implications On Anterior Knee Pain, Pedro A. Rodrigues May 2011

Consequence Of Functioning At The End Range Of Joint Motion: Implications On Anterior Knee Pain, Pedro A. Rodrigues

Open Access Dissertations

“Excessive” and/or “delayed” subtalar joint (STJ) pronation has been linked to overuse injuries because of its influence on tibial internal rotation (TIR). The transfer of STJ pronation to TIR occurs via the talocrual joint, believed to have limited transverse plane motion. However, studies have shown the talocrural joint to have more transverse plane motion than once believed, therefore it is feasible that the STJ will only influence the motion of the tibia once this motion has been exhausted.

Currently, studies evaluating this relationship have focused on peak joint angles and excursion without reference to the amount of motion available ...


The Roles Of Notch1 And Pkc-Θ In Immune Mediated Bone Marrow Failure, Justine E. Roderick May 2011

The Roles Of Notch1 And Pkc-Θ In Immune Mediated Bone Marrow Failure, Justine E. Roderick

Open Access Dissertations

We sought to evaluate the individual contributions of Notch1 and PKC-ζ to disease progression in a mouse model of immune-mediated bone marrow failure and to define a mechanism for their potential cellular cooperation. We transferred parental bulk splenocytes into F1-hybrid recipients to induce a robust immune-mediated bone marrow failure (BMF) that we could partially rescue by administering a pharmacological inhibitor of Notch activation. Transferring splenocytes from PKC--ζ-/- animals did not induce disease, and treating animals with a pharmacological inhibitor of PKC-ζ also provided full protection from disease. We found that inhibiting Notch1 resulted in PKC-ζ down-regulation, and blocking PKC-ζ reduced ...


Optimal Control Of Human Running, Ross Herbert Miller May 2011

Optimal Control Of Human Running, Ross Herbert Miller

Open Access Dissertations

Humans generally use two modes of locomotion as adults. At slow speeds we walk, and at fast speeds we run. To perform either gait, we use our muscles. The central questions in this dissertation were: (1) Why do humans run the way they do, and (2) How do the mechanical properties of muscle influence running performance? Optimal control simulations of running were generated using a bipedal forward dynamics model of the human musculoskeletal system. Simulations of running and sprinting were posed as two-point boundary value problems where the muscle excitation signals were optimized to maximize an optimality criterion. In the ...


The Role Of Bacteriocins In Mediating Interactions Of Bacterial Isolates From Cystic Fibrosis Patients, Emine Suphan Bakkal Feb 2011

The Role Of Bacteriocins In Mediating Interactions Of Bacterial Isolates From Cystic Fibrosis Patients, Emine Suphan Bakkal

Open Access Dissertations

Cystic Fibrosis (CF) is a common autosomal genetic disorder in Caucasian populations. CF is caused by mutations in the cftr gene, which encodes the CF transmembrane conductance regulator (CFTR). CFTR regulates chloride and sodium ion transport across the epithelial cells lining the exocrine organs. Mutations in the cftr result in a failure to mediate chloride transport, which leads to dehydration of the mucus layer surrounding the epithelial cells. The mucus coating in the lung epithelia provides a favorable environment for invasion and growth of several opportunistic bacterial pathogens resulting in life threatening respiratory infections in CF patients. Pseudomonas aeruginosa(Pa ...


Xenopus Adam13 And Adam19 Are Important For Proper Convergence And Extension Of The Notochord, Russell David Neuner Feb 2011

Xenopus Adam13 And Adam19 Are Important For Proper Convergence And Extension Of The Notochord, Russell David Neuner

Open Access Dissertations

Gastrulation is a fundamental process that reorganizes the primary germ layers to shape the internal and external features of an early embryo. Morphogenetic movements underlying this process can be classified into a variety of different types of cellular movements. I will focus on investigating in this thesis two types of cell movements in the dorsal mesoderm; mediolateral cell intercalation and convergence and extension. During gastrulation, mesoderm cells send protrusions to gain traction on neighboring cells and the surrounding extracellular matrix; a process called mediolateral cell intercalation. Mesoderm cells use this type of cell movement to converge and extend the dorsal ...


Diversity Of Eukaryotes And Their Genomes, Laura Ellen Wegener Parfrey Feb 2011

Diversity Of Eukaryotes And Their Genomes, Laura Ellen Wegener Parfrey

Open Access Dissertations

My dissertation addresses two aspects of eukaryotic evolution, 1) the organization of eukaryotic diversity and 2) genomic variation in Foraminifera. The bulk of eukaryotic diversity is microbial with plants and animals representing just two of the estimated 75 lineages of eukaryotes. Among these microbial lineages, there are many examples of dynamic genome processes. Elucidating the origin and evolution of genome features requires a robust phylogenetic framework for eukaryotes. Taxon-rich molecular analyses provide a mechanism to test hypothesized evolutionary relationships and enable placement of diverse taxa on the tree of life. These analyses result in a well-resolved eukaryotic tree of life ...


New Genomic Approaches Reveal The Process Of Genome Reduction In Prochlorococcus, Zhiyi Sun Feb 2011

New Genomic Approaches Reveal The Process Of Genome Reduction In Prochlorococcus, Zhiyi Sun

Open Access Dissertations

Small bacterial genomes are believed to be evolutionarily derived from larger genomes through massive loss of genes and are usually associated with symbiotic or pathogenic lifestyles. It is therefore intriguing that a similar phenomenon of genome reduction has been reported within a group of free-living phototrophic marine cyanobacteria Prochlorococcus. Here I have investigated the roles of natural selection and mutation rate in the process of Prochlorococcus genome size reduction. Using a data set of complete cyanobacterial genomes including 12 Prochlorococcus and a sister group of 5 marine Synechococcus, I first reconstructed the steps leading to Prochlorococcus genome reduction in a ...


Growth Kinetics And Constraints Related To Metabolic Diversity And Abundances Of Hyperthermophiles In Deep-Sea Hydrothermal Vents, Helene Chavanne Ver Eecke Feb 2011

Growth Kinetics And Constraints Related To Metabolic Diversity And Abundances Of Hyperthermophiles In Deep-Sea Hydrothermal Vents, Helene Chavanne Ver Eecke

Open Access Dissertations

This dissertation research aims to show that there are deterministic microbial distribution patterns based on quantifiable environmental thresholds by determining and rationalizing the relative abundances of hyperthermophilic methanogens, autotrophic iron(III) oxide reducers, and heterotrophic sulfur reducers within deep-sea hydrothermal vents. Organisms of these metabolisms are predicted to be relatively more abundant in different regions depending on environmental conditions such as reduction potential, organic carbon, and hydrogen availability. The relative abundances of these metabolic groups within samples from the Endeavour Segment and Axial Volcano in the northeastern Pacific Ocean were determined. Iron(III) oxide reducers were detected in nearly all ...


The Role Of Dawn Song In Tree Swallows And Its Place In The Diversity Of Oscine Song Learning, Benjamin Nichols Taft Feb 2011

The Role Of Dawn Song In Tree Swallows And Its Place In The Diversity Of Oscine Song Learning, Benjamin Nichols Taft

Open Access Dissertations

Aspects of the behavioral ecology of bird song learning are examined in three parts. First, an approach from image analysis is extended to allow rapid, quantitative description of animal sounds. In this approach, sounds are summarized as sets of time-frequency-amplitude landmarks. Second, the role of dawn song in tree swallow (Tachycineta bicolor) breeding biology is examined. Song syllable sharing among tree swallows was found to be high among birds nesting at the same site, but sharing was lower between birds nesting at different sites. When birds nested at different sites, the distance between those sites was not related to the ...


Innate Immune Responses To B. Burgdorferi Mediated By Jnk1 And The Cochaperone, Methylation Controlled Dnaj (Mcj), Hooman Izadi Feb 2011

Innate Immune Responses To B. Burgdorferi Mediated By Jnk1 And The Cochaperone, Methylation Controlled Dnaj (Mcj), Hooman Izadi

Open Access Dissertations

The infections agent of Lyme disease, Borrelia Burgdorferi is a complex microorganism with a highly diverse genome. One of the most remarkable aspects of the B. burgdorferi genome is the large number of sequences encoding predicted or known lipoproteins, including outer-surface proteins. The B. burgdorferi genome encodes no recognizable toxins. Instead, this extracellular pathogen causes pathology by migration through tissues, adhesion to host cells, and evasion of immune clearance. Inflammation elicited by infection with B. burgdorferi depends on the ability of the spirochete to survive in the mammalian host, as well as the immune response that arises upon the interaction ...


Avian Ecology And Conservation In Tropical Agricultural Landscapes With Emphasis On Vermivora Chrysoptera, Richard Brooks Chandler Feb 2011

Avian Ecology And Conservation In Tropical Agricultural Landscapes With Emphasis On Vermivora Chrysoptera, Richard Brooks Chandler

Open Access Dissertations

The world's biodiversity is concentrated in tropical ecosystems, yet tropical forests are being converted for agriculture at a rapid rate. I evaluated the potential of an alternative coffee production system known as Integrated Open Canopy (IOC) to contribute to avian conservation. This study was conducted from 2005-2010 in the Cordillera de Tilarán, Costa Rica. My results indicate that species richness of forest-dependent birds was higher in IOC farms than in shade coffee farms, and was comparable to secondary forest sites. There was no difference in species richness of Neotropical-Nearctic migrants between IOC and shade coffee farms. Overall similarity was ...