Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability

The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines

Mathematical Methods for studying DNA and Protein Interactions

Deoxyribnucleic Acid (DNA) damage can lead to health related issues such as developmental disorders, aging, and cancer. It has been estimated that damage rates may be as high as 100,000 per cell per day. Because of the devastating effects that DNA damage can have, DNA repair mechanisms are of great interest yet are not completely understood. To gain a better understanding of possible DNA repair mechanisms, my dissertation focused on mathematical methods for understanding the interactions between DNA and proteins. I developed a damaged DNA model to estimate the probabilities of damaged DNA being located at specific positions. Experiments were then performed that suggested that the damaged DNA may be repositioned. These experimental results were consistent with the model's prediction that damaged DNA has preferred locations. To study how proteins might be moving along the DNA, I studied the use of the uniform motion “n-step” model. The n-step model has been used to determine the kinetics parameters (e.g. rates at which a protein moves along the DNA, how much energy is required to move a protein along a specified amount of DNA, etc.) of proteins moving along the DNA. Monte Carlo methods were used to simulate proteins moving with different types of non-uniform motion (e.g. backward, jumping, etc.) along the DNA. Estimates for the kinetics parameters in the n-step model were found by fitting of the Monte Carlo simulation data. Analysis indicated that non-uniform motion of the protein may lead to over or underestimation of the kinetic parameters of this n-step model

Calculus-enhanced energy-first curriculum for introductory physics improves student performance locally and in downstream courses

Here we demonstrate the benefits of a new curriculum for introductory calculus-based physics that motivates classical mechanics using a modified version of Hamiltonian mechanics. This curriculum shifts the initial focus of instruction away from forces and the associated vector mathematics, which are known to be problematic for students, to the scalar quantity energy, which is more closely aligned with their previously established intuition, and associated differential and integral calculus. We show that implementation of this calculus-enhanced “energy-first” curriculum resulted in higher normalized gains on the Force Concept Inventory exam for all students and improved performance in downstream engineering courses for students with lower ACT math scores. In other words, the downstream benefits were largest for students with lower math abilities who also pose a larger retention risk. This new curriculum thus has the potential to improve student retention by specifically helping the students who need help the most, including traditionally underserved populations who often have weaker mathematics preparation. We propose future work to investigate whether this new curriculum has lowered the math transference barrier to learning in introductory physics, resulting concomitantly in improvements in student learning of classical mechanics and in student fluency with applied mathematics.Northrop Grumman Foundatio

Effects of nucleosome stability on remodeler-catalyzed repositioning

Chromatin remodelers are molecular motors that play essential roles in the regulation of nucleosome positioning and chromatin accessibility. These machines couple the energy obtained from the binding and hydrolysis of ATP to the mechanical work of manipulating chromatin structure through processes that are not completely understood. Here we present a quantitative analysis of nucleosome repositioning by the imitation switch (ISWI) chromatin remodeler and demonstrate that nucleosome stability significantly impacts the observed activity. We show how DNA damage induced changes in the affinity of DNA wrapping within the nucleosome can affect ISWI repositioning activity and demonstrate how assay-dependent limitations can bias studies of nucleosome repositioning. Together, these results also suggest that some of the diversity seen in chromatin remodeler activity can be attributed to the variations in the thermodynamics of interactions between the remodeler, the histones, and the DNA, rather than reflect inherent properties of the remodeler itself

Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability

The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines

A Comparison of Morphological and Molecular-Based Surveys to Estimate the Species Richness of <i>Chaetoceros</i> and <i>Thalassiosira</i> (Bacillariophyta), in the Bay of Fundy

<div><p>The goal of this study was to compare the ability of morphology and molecular-based surveys to estimate species richness for two species-rich diatom genera, <i>Chaetoceros</i> Ehrenb. and <i>Thalassiosira</i> Cleve, in the Bay of Fundy. Phytoplankton tows were collected from two sites at intervals over two years and subsampled for morphology-based surveys (2010, 2011), a culture-based DNA reference library (DRL; 2010), and a molecular-based survey (2011). The DRL and molecular-based survey utilized the 3′ end of the RUBISCO large subunit (<i>rbc</i>L-3P) to identify genetic species groups (based on 0.1% divergence in <i>rbc</i>L-3P), which were subsequently identified morphologically to allow comparisons to the morphology-based survey. Comparisons were compiled for the year (2011) by site (n = 2) and by season (n = 3). Of the 34 taxa included in the comparisons, 50% of taxa were common to both methods, 35% were unique to the molecular-based survey, and 12% were unique to the morphology-based survey, while the remaining 3% of taxa were unidentified genetic species groups. The morphology-based survey excelled at identifying rare taxa in individual tow subsamples, which were occasionally missed with the molecular approach used here, while the molecular methods (the DRL and molecular-based survey), uncovered nine cryptic species pairs and four previously overlooked species. The last mentioned were typically difficult to identify and were generically assigned to <i>Thalassiosira</i> spp. during the morphology-based survey. Therefore, for now we suggest a combined approach encompassing routine morphology-based surveys accompanied by periodic molecular-based surveys to monitor for cryptic and difficult to identify taxa. As sequencing technologies improve, molecular-based surveys should become routine, leading to a more accurate representation of species composition and richness in monitoring programs.</p></div

Example of a morphological species-discovery curve used to determine when colony isolation should discontinue.

<p>This curve was generated for colonies isolated from the Passamaquoddy Bay plankton tow subsamples on June 1, 2010 for development of the culture-based DNA reference library (DRL). Isolation was terminated after 60 mins (n = 42 colonies of 26 morphological species isolated) because 30 mins had elapsed with no new morphological types found.</p

Comparisons between the number of species found during the morphology (morph) and molecular-based (mol) surveys.

<p>Data were summarized for the 2011-monitoring year (<b>A</b>), and then by site (<b>B</b>), and by season (<b>C</b>). In the year summary (<b>A</b>), taxa were placed into five main categories in bold font (two of these were divided further into three subcategories each) as indicated on the figure and described in the text. In the by site (<b>B</b>) and by season (<b>C</b>) summaries, the taxa are placed in only three categories including taxa that were identified: in common to the morphology (morph) and molecular (mol) -based surveys (black); or in the morphology-based survey only (white); in the molecular-based survey only as unique (gray) or cryptic (vertical lines) species. Sites were Passamaquoddy Bay (PB) and The Wolves (WV). Seasons were Jan, Apr, May (winter), June–Sept (summer), and Oct–Dec (fall).</p

<i>Chaetoceros</i> and <i>Thalassiosira</i> diversity and abundance as recorded during the morphology-based surveys in 2010 and 2011.

<p>PB = Passamaquoddy Bay; WV = The Wolves; J = January; F = February; M = March; A = April; My = May; Jun = June; Jul = July; Aug = August; S = September; O = October; N = November; and D = December.</p>a<p>n indicates the number of tow subsamples in which each taxon was present (n = 59 for 2010 and n = 46 for 2011).</p>b<p>Months are the months each taxon was present.</p>c<p>n>1 are the number of tow subsamples with a HELCOM rating>1.</p>d<p>Months n>1 are the months in which the higher abundance occurred.</p