The role of mismatch repair in mediating cellular sensitivity to cisplatin : the Escherichia coli methyl-directed repair paradigm

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2006.Includes bibliographical references (v. 2, leaves 195-258).The anticancer drug cisplatin is in widespread use but its mechanism of action is only poorly understood. Moreover, human cancers acquire resistance to the drug, which limits its clinical utility. A paradox in the field is how loss of mismatch DNA repair leads to clinical resistance to this widely used drug. The phenomenon of cisplatin tolerance in mismatch repair deficient cells was initially discovered in E. coli, where methylation deficient dam mutants show high sensitivity to cisplatin and dam mutants with an additional mutation in either of the mismatch repair genes mutS or mutL show near wildtype levels of resistance. A prevalent explanation for this observation is the abortive repair model, which proposes that in dam mutants, where the strand discrimination signal is lost, mismatch repair attempts futile cycles of repair opposite cisplatin-DNA adducts. Previous findings have supported this model to the extent that MutS, the E. coli mismatch recognition protein, specifically recognizes DNA modified with cisplatin. However it has recently been shown that MutS binding to cisplatin adducts may contribute to toxicity by instead preventing the recombinational repair of a cisplatin-modified substrate, and we have previously shown that recombination is an essential mechanism for tolerating cisplatin damage.(cont.) In the present study, we examined the global transcriptional responses of wildtype, dam, dam mutS, and mutS mutant E. coli after treatment with a toxic dose of cisplatin. We also determined any dose-response at the transcriptional level of several SOS response genes and other genes involved in DNA repair by real time RT-PCR. Furthermore, we performed single-cell electrophoresis in order to determine the effect of mismatch repair on the level of double-strand break formation in cisplatin-treated cells. Our results show that Dam-deficient strains exhibit unique gene regulation that may be due to mismatch-repair induced DNA damage in the absence of adenine methylation. In addition, cisplatin treatment induces double-strand break formation and the SOS response in a dose-dependent manner, and both break formation and the SOS response are greatest in the hypersensitive dam mutant strain. The higher level of cisplatin-induced double-strand breaks in the dam mutant may be dependent on functional mismatch repair.by Jennifer L. Robbins.Ph.D

Psychological and physiological correlates of sleep in HIV infection

Insomnia, a common problem associated with HIV disease, is most likely caused by a multitude of factors. This study investigated the correlations between a selected group of physiological and psychological factors and sleep quality in an HIV-infected population. A convenience sample of 79 ethnically diverse HIVpositive adults, ages 24 to 63, completed a number of questionnaires and released their laboratory records for CD4+ cell count and viral load information. Variables significantly related to sleep quality were HIV-related symptoms, total pain, fatigue, depression, state anxiety, and the number of adults in the household. Findings support the need for health care providers to consider factors that contribute to impaired sleep when developing effective care for HIV-infected individuals with sleep disturbance

Shape and Stereoselective Cyclopropanation of Alkenes Catalyzed by Iron Porphyrins

Iron porphryin complexes are active catalysts for the cyclopropanation of alkenes by ethyl diazoacetate. Fe(TIP) (TIP = meso-tetra-p-tolylporphyrin), an isolated iron(II) porphyrin complex, can be used as the catalyst, or the iron(III) complexes of several porphyrins can be reduced in situ. The reactions produce synthetically useful excesses of the trans cyclopropyl ester products. This stereoselectivity exhibits a modest solvent dependence, with donor solvents giving higher ratios of the trans cyclopropane products. The diastereoselectivity exhibits only a modest dependence on the steric bulk of the porphyrin. The reactions are selective for 1-alkenes and 1, 1-disubstituted alkenes. Conjugated substrates and enol ethers react more rapidly than simple aliphatic alkenes. A mechanistic model for the iron-mediated reactions is proposed which is consistent with the data presented herein

Development and Validation of a Socioeconomic Kidney Transplant Derailers Index

Background: Socioeconomic barriers can prevent successful kidney transplant (KT) but are difficult to measure efficiently in clinical settings. We created and validated an individual-level, single score Kidney Transplant Derailers Index (KTDI) and assessed its association with waitlisting and living donor KT (LDKT) rates. Methods: The dataset included 733 patients presenting for KT evaluation in a transplant center in California. Exploratory factor analysis was used to identify socioeconomic barriers to KT (derailers) to include in the index. Potential KT derailers included health insurance, employment, financial insecurity, educational attainment, perception of neighborhood safety, access to a vehicle, having a washer/dryer, and quality of social support. Validity was tested with associations between KTDI scores and the following: (1) the Area Deprivation Index (ADI) and (2) time to KT waitlisting and LDKT. Results: Nine derailers were retained, omitting only social support level from the original set. The KTDI was scored by summing the number of derailers endorsed (mean: 3.0; range: 0–9). Black patients had higher estimated KTDI scores than other patient groups (versus White patients, 3.8 versus 2.1; P \u3c 0.001, effect size = 0.81). In addition, the KTDI was associated with the ADI (γ = 0.70, SE = 0.07; P \u3c 0.001). Finally, in comparison to the lower tertile, patients in the upper and middle KTDI tertiles had lower hazard of waitlisting (upper tertile hazard ratio [HR]: 0.34, 95% confidence interval [CI]: 0.25-0.45; middle tertile HR: 0.54, 95% CI: 0.40-0.72) and receiving an LDKT (upper tertile HR: 0.15, 95% CI: 0.08-0.30; middle tertile HR: 0.35, 95% CI: 0.20-0.62). These associations remained significant when adjusting for the ADI and other patient characteristics. Conclusions: The KTDI is a valid indicator of socioeconomic barriers to KT for individual patients that can be used to identify patients at risk for not receiving a KT

QTL Mapping of a High Protein Digestibility Trait in Sorghum bicolor

Compared with other cereal grains, Sorghum bicolor shows lower protein digestibility. The low digestibility is thought to result from disulfide cross linking in the β- and γ-kafirins. In contrast, the single recessive high digestibility/high lysine content (HD) mutation which confers greater grain digestibility exists in sorghum that is thought to result from reduced accumulation of γ-kafirin that allows greater access to the high digestible α-kafarin fraction. In an effort to both clearly define the molecular basis for the HD trait and develop tools to improve the introgression of this difficult-to-screen trait, this study focuses on mapping the QTLs linked to this trait. While the HD trait has been defined as a single recessive gene, our results uncovered that two major QTLs on chromosome 1 are associated with protein digestibility—one QTL (locus 1 from the HD parent) unfavorably affects digestibility and one QTL (locus 2 from the HD parent) only 20 cM away favorably affects digestibility. A contrast analysis between genotypic groups at these two loci shows that a higher level of protein digestibility may be obtained when this linkage in repulsion is broken and favorable alleles are allowed to recombine

The effect of coastal landform development on decadal- to millennial-scale longshore sediment fluxes: Evidence from the Holocene evolution of the central mid-Atlantic coast, USA - Sediment Core and Chronology Data

These data are sediment core, radiocarbon, and optically stimulated luminescence (OSL) data from the barrier islands and backbarrier lagoons, bays, and marshes of Assateague Island (VA, USA), Chincoteague Island (VA, USA), and Wallops Island (VA, USA). Vibracore data from Tom’s Cove, a backbarrier bay, were collected using a vibracore system with the ability to core through a ‘moonhole’ on a flat bottom boat. Geoprobe cores were collected using a track-mounted 66DT Geoprobe direct-push drill rig. Select samples from the sediment cores (associated with figures and tables in Shawler et al., 2021) were analyzed using a Beckman-Coulter Laser Diffraction Particle Size Analyzer (LS 13 320 Aqueous Liquid Module) with an applied calculation model that uses Fraunhöfer theory. Data are available as Microsoft Excel Workbooks and can be opened using Excel or numerous free and open sources products such as Google Sheets. Each sediment core data spreadsheet contains a “READ ME” tab with additional detail. The full OSL report from co-author Sebastien Huot is also included and can be accessed with a PDF reader

Computed cardiopulmonography and the idealized lung clearance index, iLCI2.5, in early-stage cystic fibrosis

This study explored the use of computed cardiopulmonography (CCP) to assess lung function in early-stage cystic fibrosis (CF). CCP has two components. The first is a particularly accurate technique for measuring gas exchange. The second is a computational cardiopulmonary model where patient-specific parameters can be estimated from the measurements of gas exchange. Twenty-five participants (14 healthy controls, 11 early-stage CF) were studied with CCP. They were also studied with a standard clinical protocol to measure the lung clearance index (LCI2.5). Ventilation inhomogeneity, as quantified through CCP parameter σlnCl, was significantly greater (P < 0.005) in CF than in controls, and anatomical deadspace relative to predicted functional residual capacity (DS/FRCpred) was significantly more variable (P < 0.002). Participant-specific parameters were used with the CCP model to calculate idealized values for LCI2.5 (iLCI2.5) where extrapulmonary influences on the LCI2.5, such as breathing pattern, had all been standardized. Both LCI2.5 and iLCI2.5 distinguished clearly between CF and control participants. LCI2.5 values were mostly higher than iLCI2.5 values in a manner dependent on the participant’s respiratory rate (r = 0.46, P < 0.05). The within-participant reproducibility for iLCI2.5 appeared better than for LCI2.5, but this did not reach statistical significance (F ratio = 2.2, P = 0.056). Both a sensitivity analysis on iLCI2.5 and a regression analysis on LCI2.5 revealed that these depended primarily on an interactive term between CCP parameters of the form σlnCL*(DS/FRC). In conclusion, the LCI2.5 (or iLCI2.5) probably reflects an amalgam of different underlying lung changes in early-stage CF that would require a multiparameter approach, such as potentially CCP, to resolve

Placental syncytiotrophoblast constitutes a major barrier to vertical transmission of Listeria monocytogenes.

Listeria monocytogenes is an important cause of maternal-fetal infections and serves as a model organism to study these important but poorly understood events. L. monocytogenes can infect non-phagocytic cells by two means: direct invasion and cell-to-cell spread. The relative contribution of each method to placental infection is controversial, as is the anatomical site of invasion. Here, we report for the first time the use of first trimester placental organ cultures to quantitatively analyze L. monocytogenes infection of the human placenta. Contrary to previous reports, we found that the syncytiotrophoblast, which constitutes most of the placental surface and is bathed in maternal blood, was highly resistant to L. monocytogenes infection by either internalin-mediated invasion or cell-to-cell spread. Instead, extravillous cytotrophoblasts-which anchor the placenta in the decidua (uterine lining) and abundantly express E-cadherin-served as the primary portal of entry for L. monocytogenes from both extracellular and intracellular compartments. Subsequent bacterial dissemination to the villous stroma, where fetal capillaries are found, was hampered by further cellular and histological barriers. Our study suggests the placenta has evolved multiple mechanisms to resist pathogen infection, especially from maternal blood. These findings provide a novel explanation why almost all placental pathogens have intracellular life cycles: they may need maternal cells to reach the decidua and infect the placenta