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Full-Text Articles in Life Sciences

X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar Nov 2016

X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar

Doctoral Dissertations

We think of DNA as double-stranded helices (duplex), but the polymer exists in many conformations. Several triplex and quadruplex DNA structures can be formed in laboratory settings and exist in nature. This thesis first provides a brief description of the nature of the order in arrays of duplex DNA under biologically relevant molecular crowding conditions. Then we compare the duplex DNA mesophases with the corresponding liquid crystalline phase behavior of the triplex and quadruplex DNA analogues. In particular, we focus on G-quadruplexes.

Observed in the folds of guanine-rich oligonucleotides, G-quadruplex structures are based on G-quartets formed by hydrogen bonding and ...


Ecological Consequences Of Lost Anadromous Forage Fish In Freshwater Ecosystems, Steven R. Mattocks Nov 2016

Ecological Consequences Of Lost Anadromous Forage Fish In Freshwater Ecosystems, Steven R. Mattocks

Masters Theses

Beginning in the early 1600s, dam construction in New England obstructed anadromous fish access to spawning grounds during migration. As a result, anadromous forage fish populations have declined, which has impacted freshwater, marine, and terrestrial ecosystems. To determine the impacts of dams on anadromous forage fish and freshwater ecosystems, I used historical and current data to estimate population changes in alewives (Alosa pseudoharengus) from 1600-1900. A significant reduction in spawning habitat occurred in New England as a result of 1,642 dams constructed between 1600 and 1900, resulting in 14.8% and 16.6% lake and stream habitat remaining by ...


Factors Affecting Habitat Quality For Wintering Wood Thrushes In A Coffee Growing Region In Honduras, Brett A. Bailey Nov 2016

Factors Affecting Habitat Quality For Wintering Wood Thrushes In A Coffee Growing Region In Honduras, Brett A. Bailey

Masters Theses

Amongst the diversity of taxa that occur in the Neotropics, 200 migratory bird species that breed in temperate North America can be found. Many of these populations have seen significant declines since the 1960s. The Wood Thrush, Hylocichla mustelina, is one such species. Shade coffee and other agroforestry practices show potential for benefiting migratory species, but the quality of coffee habitat and optimal habitat characteristics for Wood Thrushes remain unknown.

I surveyed a spatially complex, agricultural landscape in Honduras outside the recognized winter range of the Wood Thrush and radio-tagged 46 individuals within rustic coffee farms during the winters of ...


Morphological And Material Effects In Van Der Waals Interactions, Jaime C. Hopkins Jul 2016

Morphological And Material Effects In Van Der Waals Interactions, Jaime C. Hopkins

Doctoral Dissertations

Van der Waals (vdW) interactions influence a variety of mesoscale phenomena, such as surface adhesion, friction, and colloid stability, and play increasingly important roles as science seeks to design systems on increasingly smaller length scales. Using the full Lifshitz continuum formulation, this thesis investigates the effects of system materials, shapes, and configurations and presents open-source software to accurately calculate vdW interactions.

In the Lifshitz formulation, the microscopic composition of a material is represented by its bulk dielectric response. Small changes in a dielectric response can result in substantial variations in the strength of vdW interactions. However, the relationship between these ...


Photolysis Of Triazenylbenzoic Acids For Click Chemistry, Adam Gann Jul 2016

Photolysis Of Triazenylbenzoic Acids For Click Chemistry, Adam Gann

Doctoral Dissertations

Copper catalyzed cycloaddition of terminal alkynes and azides has revolutionized the field of bioconjugate chemistry. Unfortunately, typical copper catalysts are known to disrupt relevant biological systems, so it has become necessary to develop new, copper-free methods that are less cytotoxic. particular interest are "click" probes which can be activated with an outside light source, giving the user spatial and temporal control over the system being investigated. We have developed a method in which an aryl diazonium salt is rapidly generated using photolysis of the triazene functional group, and subsequently coupled with an electron rich aromatic nucleophile to yield an azobenzene ...


The Application Of Hydrogen/Deuterium Exchange And Covalent Labeling Coupled With Mass Spectrometry To Examine Protein Structure, Nicholas B. Borotto Mar 2016

The Application Of Hydrogen/Deuterium Exchange And Covalent Labeling Coupled With Mass Spectrometry To Examine Protein Structure, Nicholas B. Borotto

Doctoral Dissertations

Thorough insight into a protein’s structure is necessary to understand how it functions and what goes wrong when it malfunctions. The structure of proteins, however, is not easily analyzed. The analysis must take place under a narrow range of conditions or risk perturbing the very structure being probed. Furthermore, the wide diversity in size and chemistry possible in proteins significantly complicates this analysis. Despite this numerous methods have been developed in order to analyze protein structure. In this work, we demonstrate that mass spectrometry (MS)-based techniques are capable of characterizing the structure of particularly challenging proteins. This is ...