The Effect of Diversification on the Dynamics of Mobile Genetic Elements in Prokaryotes: The Birth-Death-Diversification Model

Mobile genetic elements (MGEs) are ubiquitous among prokaryotes, and have important implications to many areas, such as the evolution of certain genes, bioengineering and the spread of antibiotic resistance. In order to understand the complex dynamics of MGEs, mathematical models are often used. One model that has been used to describe the dynamics of mobile promoters (a class of MGEs) is the birth-death-diversification model. This model is unique in that it allows MGEs to diversify to create new families. In this thesis, I analyze the dynamics of this model; in particular, I examine equilibrium distributions, extinction probabilities and mean time until extinction for MGE lineages. I find that diversification indirectly increases MGE propagation through increased horizontal gene transfer rates; therefore, diversification increases population growth rates and decreases extinction probability. Overall, this work indicates that diversification of elements should be considered in order to fully understand the dynamics of MGEs in prokaryotes

Do assumptions about the central density of subhaloes affect dark matter annihilation and lensing calculations?

A growing body of evidence suggests that the central density of cuspy dark matter subhaloes is conserved in minor mergers. However, empirical models of subhalo evolution, calibrated from simulations, often assume a drop in the central density. Since empirical models of subhaloes are used in galaxy-galaxy lensing studies and dark matter annihilation calculations, we explore the consequences of assuming different subhalo models. We find that dark matter annihilation calculations are very sensitive to the assumed subhalo mass profile, and different models can give more than a magnitude difference in the J-factor and boost factor in individual haloes. On the other hand, the shear and convergence profiles used in galaxy-galaxy lensing are sensitive to the initial profile assumed (e.g., NFW versus Einato) but are otherwise well-approximated by a simple model in which the original profile is sharply truncated. We conclude that since the innermost parts of haloes are difficult to resolve in simulations, it is important to have a theoretical understanding of how subhaloes evolve to make accurate predictions of the dark matter annihilation signal.Comment: 15 pages, 13 figures. Submitted to MNRA

Etiology of Anemia in Patients With Advanced Heart Failure

ObjectivesWe prospectively investigated the causes of anemia in patients with advanced congestive heart failure (CHF).BackgroundAnemia is common in patients with advanced CHF, and its etiology is generally considered to be multifactorial. However, despite its importance, precise information is lacking regarding the prevalence of putative etiologic factors.MethodsPatients who were hospitalized for decompensated advanced CHF and who were stabilized after their initial treatment underwent evaluation of “clinically significant” anemia, defined as a hemoglobin content <12 g/dl for men and <11.5 g/dl for women. Patients with a serum creatinine concentration >3 mg/dl or patients with concurrent diseases that are known to cause anemia were not included. The initial evaluation included measurements of vitamin B12, folic acid, thyroid-stimulating hormone, erythropoietin, lactate dehydrogenase, Coombs test, multiple fecal occult tests, and bone marrow aspiration. Patients without diagnosis by these methods underwent red cell mass measurement with 51Cr assay.ResultsThe mean age of the 37 patients was 57.9 ± 10.9 years and mean left ventricular ejection fraction 22.5 ± 5.9%. Iron deficiency anemia was confirmed by bone marrow aspiration in 27 patients (73%), 2 patients (5.4%) had dilutional anemia, and 1 patient (2.7%) had drug-induced anemia. No specific cause was identified in 7 patients (18.9%) who were considered to have “anemia of chronic disease.” Serum ferritin for the iron-deficient patients was not a reliable marker of iron deficiency in this population.ConclusionsIn this group of patients, iron deficiency was the most common cause of anemia. The iron status of patients with end-stage chronic CHF should be thoroughly evaluated and corrected before considering other therapeutic interventions

A p53-independent role for the MDM2 antagonist Nutlin-3 in DNA damage response initiation.

BACKGROUND: The mammalian DNA-damage response (DDR) has evolved to protect genome stability and maximize cell survival following DNA-damage. One of the key regulators of the DDR is p53, itself tightly regulated by MDM2. Following double-strand DNA breaks (DSBs), mediators including ATM are recruited to the site of DNA-damage. Subsequent phosphorylation of p53 by ATM and ATM-induced CHK2 results in p53 stabilization, ultimately intensifying transcription of p53-responsive genes involved in DNA repair, cell-cycle checkpoint control and apoptosis. METHODS: In the current study, we investigated the stabilization and activation of p53 and associated DDR proteins in response to treatment of human colorectal cancer cells (HCT116p53+/+) with the MDM2 antagonist, Nutlin-3. RESULTS: Using immunoblotting, Nutlin-3 was observed to stabilize p53, and activate p53 target proteins. Unexpectedly, Nutlin-3 also mediated phosphorylation of p53 at key DNA-damage-specific serine residues (Ser15, 20 and 37). Furthermore, Nutlin-3 induced activation of CHK2 and ATM - proteins required for DNA-damage-dependent phosphorylation and activation of p53, and the phosphorylation of BRCA1 and H2AX - proteins known to be activated specifically in response to DNA damage. Indeed, using immunofluorescent labeling, Nutlin-3 was seen to induce formation of γH2AX foci, an early hallmark of the DDR. Moreover, Nutlin-3 induced phosphorylation of key DDR proteins, initiated cell cycle arrest and led to formation of γH2AX foci in cells lacking p53, whilst γH2AX foci were also noted in MDM2-deficient cells. CONCLUSION: To our knowledge, this is the first solid evidence showing a secondary role for Nutlin-3 as a DDR triggering agent, independent of p53 status, and unrelated to its role as an MDM2 antagonist

Impact of Mechanical Unloading on Microvasculature and Associated Central Remodeling Features of the Failing Human Heart

ObjectivesThis study investigates alterations in myocardial microvasculature, fibrosis, and hypertrophy before and after mechanical unloading of the failing human heart.BackgroundRecent studies demonstrated the pathophysiologic importance and significant mechanistic links among microvasculature, fibrosis, and hypertrophy during the cardiac remodeling process. The effect of left ventricular assist device (LVAD) unloading on cardiac endothelium and microvasculature is unknown, and its influence on fibrosis and hypertrophy regression to the point of atrophy is controversial.MethodsHemodynamic data and left ventricular tissue were collected from patients with chronic heart failure at LVAD implant and explant (n = 15) and from normal donors (n = 8). New advances in digital microscopy provided a unique opportunity for comprehensive whole-field, endocardium-to-epicardium evaluation for microvascular density, fibrosis, cardiomyocyte size, and glycogen content. Ultrastructural assessment was done with electron microscopy.ResultsHemodynamic data revealed significant pressure unloading with LVAD. This was accompanied by a 33% increase in microvascular density (p = 0.001) and a 36% decrease in microvascular lumen area (p = 0.028). We also identified, in agreement with these findings, ultrastructural and immunohistochemical evidence of endothelial cell activation. In addition, LVAD unloading significantly increased interstitial and total collagen content without any associated structural, ultrastructural, or metabolic cardiomyocyte changes suggestive of hypertrophy regression to the point of atrophy and degeneration.ConclusionsThe LVAD unloading resulted in increased microvascular density accompanied by increased fibrosis and no evidence of cardiomyocyte atrophy. These new insights into the effects of LVAD unloading on microvasculature and associated key remodeling features might guide future studies of unloading-induced reverse remodeling of the failing human heart