Condominium Conversions in the Bay Area

A Report to the Association of Bay Area Governments and the Department of City and Regional Planning in Partial Fulfillment of the Requirements for the Degree of Master of City Plannin

Archaeal DNA Polymerase-B as a DNA Template Guardian: Links between Polymerases and Base/Alternative Excision Repair Enzymes in Handling the Deaminated Bases Uracil and Hypoxanthine

In Archaea repair of uracil and hypoxanthine, which arise by deamination of cytosine and adenine, respectively, is initiated by three enzymes: Uracil-DNA-glycosylase (UDG, which recognises uracil); Endonuclease V (EndoV, which recognises hypoxanthine); and Endonuclease Q (EndoQ), (which recognises both uracil and hypoxanthine). Two archaeal DNA polymerases, Pol-B and Pol-D, are inhibited by deaminated bases in template strands, a feature unique to this domain. Thus the three repair enzymes and the two polymerases show overlapping specificity for uracil and hypoxanthine. Here it is demonstrated that binding of Pol-D to primer-templates containing deaminated bases inhibits the activity of UDG, EndoV, and EndoQ. Similarly Pol-B almost completely turns off EndoQ, extending earlier work that demonstrated that Pol-B reduces catalysis by UDG and EndoV. Pol-B was observed to be a more potent inhibitor of the enzymes compared to Pol-D. Although Pol-D is directly inhibited by template strand uracil, the presence of Pol-B further suppresses any residual activity of Pol-D, to near-zero levels. The results are compatible with Pol-D acting as the replicative polymerase and Pol-B functioning primarily as a guardian preventing deaminated base-induced DNA mutations

Matrix Big Brunch

Following the holographic description of linear dilaton null Cosmologies with a Big Bang in terms of Matrix String Theory put forward by Craps, Sethi and Verlinde, we propose an extended background describing a Universe including both Big Bang and Big Crunch singularities. This belongs to a class of exact string backgrounds and is perturbative in the string coupling far away from the singularities, both of which can be resolved using Matrix String Theory. We provide a simple theory capable of describing the complete evolution of this closed Universe.Comment: 15 pages, no figures. References adde

Winding String Condensation and Noncommutative Deformation of Spacelike Singularity

In a previous paper (hep-th/0509067) using matrix model, we showed that closed string tachyons can resolve spacelike singularity in one particular class of Misner space (with anti-periodic boundary conditions for fermions around the spatial circle). In this note, we show that for Misner space without closed string tachyons, there also exists a mechanism to resolve the singularity in the context of the matrix model, namely cosmological winding string production. We show that here space and time also become noncommutative due to these winding strings. Employing optical theorem, we study the bulk boundary coupling by calculating the four-open-string cylinder amplitudes.Comment: 16 pages, no figures, harvmac; references added; added a section of discussion on disk and cylinder amplitude

Effective Dynamics of the Matrix Big Bang

We study the leading quantum effects in the recently introduced Matrix Big Bang model. This amounts to a study of supersymmetric Yang-Mills theory compactified on the Milne orbifold. We find a one-loop potential that is attractive near the Big Bang. Surprisingly, the potential decays very rapidly at late times, where it appears to be generated by D-brane effects. Usually, general covariance constrains the form of any effective action generated by renormalization group flow. However, the form of our one-loop potential seems to violate these constraints in a manner that suggests a connection between the cosmological singularity and long wavelength, late time physics.Comment: 22 pages, LaTeX; some minor changes; an improved discussion of the potentia

Cosmologies with Null Singularities and their Gauge Theory Duals

We investigate backgrounds of Type IIB string theory with null singularities and their duals proposed in hep-th/0602107. The dual theory is a deformed N=4 Yang-Mills theory in 3+1 dimensions with couplings dependent on a light-like direction. We concentrate on backgrounds which become AdS_5 x S^5 at early and late times and where the string coupling is bounded, vanishing at the singularity. Our main conclusion is that in these cases the dual gauge theory is nonsingular. We show this by arguing that there exists a complete set of gauge invariant observables in the dual gauge theory whose correlation functions are nonsingular at all times. The two-point correlator for some operators calculated in the gauge theory does not agree with the result from the bulk supergravity solution. However, the bulk calculation is invalid near the singularity where corrections to the supergravity approximation become important. We also obtain pp-waves which are suitable Penrose limits of this general class of solutions, and construct the Matrix Membrane theory which describes these pp-wave backgrounds.Comment: 43 pages REVTeX and AMSLaTeX. v2: references adde

FUCA1 is induced by wild-type p53 and expressed at different levels in thyroid cancers depending on p53 status

Fucose residues of cell surface glycans, which play important roles in growth, invasion and metastasis, are added by fucosyltransferases (FUTs) and removed by α-L-fucosidases (FUCAs). By the differential display method, we isolated a 3' non-coding region of α-L-fucosidase-1 (FUCA1) (a gene coding for the lysosomal fucosidase-1 enzyme) as a wild-type p53-inducible gene: 18S and 20S FUCA1 mRNA species were induced in Saos-2 cells transfected with a temperature-sensitive p53 mutant at the permissive temperature. By microarray analyses of thyroid cancer biopsy samples, FUCA1 RNA expression levels were found to be lower in anaplastic thyroid cancer samples (ATCs), while they were higher in papillary thyroid cancer samples (PTCs) and in normal thyroid tissues. Since most ATCs were reported to carry the mutated form of p53, while PTCs carry mostly the wild-type form of p53, it is likely that FUCA1 expression levels are regulated, at least in part, by the p53 status in thyroid cancers. In order to better understand the role played by FUCA genes in thyroid tumorigenesis, we examined the clonogenic potential in vitro of thyroid cell lines transfected with either FUCA1 or FUCA2 (the latter gene coding for a secreted, non-lysosomal enzyme). We found that α-L-fucosidases did not suppress grossly cell growth. Contrary to what we observed with the expression of FUCA1, the FUT8 expression levels were found high in ATCsbut lower in PTCs and normal thyroid tissues. Taken together, these results suggest the possibility that the higher fucose levels on cell surface glycans of aggressive ATCs, compared to those of less aggressive PTCs, may be at least in part responsible for the more aggressive and metastatic phenotype of ATCs compared to PTCs, as the expression levels of FUCA1 and FUT8 were inversely related in these two types of cancers. Fucose residues of cell surface glycans, which play important roles in growth, invasion and metastasis, are added by fucosyltransferases (FUTs) and removed by α-L-fucosidases (FUCAs). By the differential display method, we isolated a 3' non-coding region of α-L-fucosidase-1 (FUCA1) (a gene coding for the lysosomal fucosidase-1 enzyme) as a wild-type p53-inducible gene: 18S and 20S FUCA1 mRNA species were induced in Saos-2 cells transfected with a temperature-sensitive p53 mutant at the permissive temperature. By microarray analyses of thyroid cancer biopsy samples, FUCA1 RNA expression levels were found to be lower in anaplastic thyroid cancer samples (ATCs), while they were higher in papillary thyroid cancer samples (PTCs) and in normal thyroid tissues. Since most ATCs were reported to carry the mutated form of p53, while PTCs carry mostly the wild-type form of p53, it is likely that FUCA1 expression levels are regulated, at least in part, by the p53 status in thyroid cancers. In order to better understand the role played by FUCA genes in thyroid tumorigenesis, we examined the clonogenic potential in vitro of thyroid cell lines transfected with either FUCA1 or FUCA2 (the latter gene coding for a secreted, non-lysosomal enzyme). We found that α-L-fucosidases did not suppress grossly cell growth. Contrary to what we observed with the expression of FUCA1, the FUT8 expression levels were found high in ATCs but lower in PTCs and normal thyroid tissues. Taken together, these results suggest the possibility that the higher fucose levels on cell surface glycans of aggressive ATCs, compared to those of less aggressive PTCs, may be at least in part responsible for the more aggressive and metastatic phenotype of ATCs compared to PTCs, as the expression levels of FUCA1 and FUT8 were inversely related in these two types of cancers

Novel inhibition of archaeal family-D DNA polymerase by uracil.

International audienceArchaeal family-D DNA polymerase is inhibited by the presence of uracil in DNA template strands. When the enzyme encounters uracil, following three parameters change: DNA binding increases roughly 2-fold, the rate of polymerization slows by a factor of ≈ 5 and 3'-5' proof-reading exonuclease activity is stimulated by a factor of ≈ 2. Together these changes result in a significant decrease in polymerization activity and a reduction in net DNA synthesis. Pol D appears to interact with template strand uracil irrespective of its distance ahead of the replication fork. Polymerization does not stop at a defined location relative to uracil, rather a general decrease in DNA synthesis is observed. 'Trans' inhibition, the slowing of Pol D by uracil on a DNA strand not being replicated is also observed. It is proposed that Pol D is able to interact with uracil by looping out the single-stranded template, allowing simultaneous contact of both the base and the primer-template junction to give a polymerase-DNA complex with diminished extension ability

[O III]λ5007\lambda 5007 and X-ray Properties of a Complete Sample of Hard X-ray Selected AGNs in the Local Universe

We study the correlation between the [O III]$\lambda 5007$ and X-ray luminosities of local Active Galactic Nuclei (AGNs), using a complete, hard X-ray ($>10$ keV) selected sample in the Swift/BAT 9-month catalog. From our optical spectroscopic observations at the South African Astronomical Observatory and the literature, a catalog of [O III]$\lambda 5007$ line flux for all 103 AGNs at Galactic latitudes of $|b|>15^\circ$ is complied. Significant correlations with intrinsic X-ray luminosity ($L_{\rm X}$) are found both for observed ($L_{\rm [O~III]}$) and extinction-corrected ($L_{\rm [O~III]}^{\rm cor}$) luminosities, separately for X-ray unabsorbed and absorbed AGNs. We obtain the regression form of $L_{\rm [O~III]}$ $\propto L_{\rm 2-10\; keV}^{1.18\pm0.07}$ and $L_{\rm [O~III]}^{\rm cor}$ $\propto L_{\rm 2-10\; keV}^{1.16\pm0.09}$ from the whole sample. The absorbed AGNs with low ($<$0.5\%) scattering fractions in soft X-rays show on average smaller $L_{\rm [O~III]}/L_{\rm X}$ and $L_{\rm [O~III]}^{\rm cor}/L_{\rm X}$ ratios than the other absorbed AGNs, while those in edge-on host galaxies do not. These results suggest that a significant fraction of this population are buried in tori with small opening angles. By using these $L_{\rm [O~III]}$ vs. $L_{\rm X}$ correlations, the X-ray luminosity function of local AGNs (including Compton thick AGNs) in a standard population synthesis model gives much better agreement with the [O III]$\lambda 5007$ luminosity function derived from the Sloan Digital Sky Survey than previously reported. This confirms that hard X-ray observations are a very powerful tool to find AGNs with high completeness.Comment: 14 pages including 11 figures and 3 tables, accepted for publication in ApJ. In this manuscript, the observed 14-195 keV luminosities in Table 1 have been corrected to be exactly the same as in the original Swift/BAT 9-month catalog. Accordingly, Figures 2(a) and 3(a) and a part of Tables 2 and 3 have been updated. The changes from the previous version are small and do not affect the tex

Applying Latent Class Analysis on Cancer Registry Data to Identify and Compare Health Disparity Profiles in Colorectal Cancer Surgical Treatment Delay

Context: Colorectal cancer (CRC) surgical treatment delay (TD) has been associated with mortality and morbidity; however, disparities by TD profiles are unknown. Objectives: This study aimed to identify CRC patient profiles of surgical TD while accounting for differences in sociodemographic, health insurance, and geographic characteristics. Design: We used latent class analysis (LCA) on 2005-2015 Tennessee Cancer Registry data of CRC patients and observed indicators that included sex/gender, age at diagnosis, marital status (single/married/divorced/widowed), race (White/Black/other), health insurance type, and geographic residence (non-Appalachian/Appalachian). Setting: The state of Tennessee in the United States that included both Appalachian and non-Appalachian counties. Participants: Adult (18 years or older) CRC patients (N = 35 412) who were diagnosed and surgically treated for in situ (n = 1286) and malignant CRC (n = 34 126). Main Outcome Measure: The distal outcome of TD was categorized as 30 days or less and more than 30 days from diagnosis to surgical treatment. Results: Our LCA identified a 4-class solution and a 3-class solution for in situ and malignant profiles, respectively. The highest in situ CRC patient risk profile was female, White, aged 75 to 84 years, widowed, and used public health insurance when compared with respective profiles. The highest malignant CRC patient risk profile was male, Black, both single/never married and divorced/separated, resided in non-Appalachian county, and used public health insurance when compared with respective profiles. The highest risk profiles of in situ and malignant patients had a TD likelihood of 19.3% and 29.4%, respectively. Conclusions: While our findings are not meant for diagnostic purposes, we found that Blacks had lower TD with in situ CRC. The opposite was found in the malignant profiles where Blacks had the highest TD. Although TD is not a definitive marker of survival, we observed that non-Appalachian underserved/underrepresented groups were overrepresented in the highest TD profiles. The observed disparities could be indicative of intervenable risk