Structure and dynamics of the HIV-2 TAR RNA-argininamide complex by NMR spectroscopy

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1998.Includes bibliographical references (leaves 248-269).by Alexander S. Brodsky.Ph.D

NNLO corrections to top-pair production at hadron colliders: the all-fermionic scattering channels

This is a second paper in our ongoing calculation of the next-to-next-to-leading order (NNLO) QCD correction to the total inclusive top-pair production cross-section at hadron colliders. In this paper we calculate the reaction $q\bar q \to t\bar t + q\bar q$ which was not considered in our previous work on $q\bar q \to t\bar t +X$ due to its phenomenologically negligible size. We also calculate all remaining fermion-pair-initiated partonic channels $qq', q\bar q'$ and $qq$ that contribute to top-pair production starting from NNLO. The contributions of these reactions to the total cross-section for top-pair production at the Tevatron and LHC are small, at the permil level. The most interesting feature of these reactions is their characteristic logarithmic rise in the high energy limit. We compute the constant term in the leading power behavior in this limit, and achieve precision that is an order of magnitude better than the precision of a recent theoretical prediction for this constant. All four partonic reactions computed in this paper are included in our numerical program Top++. The calculation of the NNLO corrections to the two remaining partonic reactions, $qg\to t\bar t+X$ and $gg\to t\bar t+X$, is ongoing.Comment: 1+16 pages; 3 figure

Genome-Wide Identification of Functionally Distinct Subsets of Cellular mRNAs Associated with Two Nucleocytoplasmic-Shuttling Mammalian Splicing Factors

Background: Pre-mRNA splicing is an essential step in gene expression that occurs co-transcriptionally in the cell nucleus, involving a large number of RNA binding protein splicing factors, in addition to core spliceosome components. Several of these proteins are required for the recognition of intronic sequence elements, transiently associating with the primary transcript during splicing. Some protein splicing factors, such as the U2 small nuclear RNP auxiliary factor (U2AF), are known to be exported to the cytoplasm, despite being implicated solely in nuclear functions. This observation raises the question of whether U2AF associates with mature mRNA-ribonucleoprotein particles in transit to the cytoplasm, participating in additional cellular functions. Results: Here we report the identification of RNAs immunoprecipitated by a monoclonal antibody specific for the U2AF 65 kDa subunit (U2AF$^{65}$) and demonstrate its association with spliced mRNAs. For comparison, we analyzed mRNAs associated with the polypyrimidine tract binding protein (PTB), a splicing factor that also binds to intronic pyrimidine-rich sequences but additionally participates in mRNA localization, stability, and translation. Our results show that 10% of cellular mRNAs expressed in HeLa cells associate differentially with U2AF$^{65}$ and PTB. Among U2AF$^{65}$ -associated mRNAs there is a predominance of transcription factors and cell cycle regulators, whereas PTB-associated transcripts are enriched in mRNA species that encode proteins implicated in intracellular transport, vesicle trafficking, and apoptosis. Conclusion: Our results show that U2AF$^{65}$ associates with specific subsets of spliced mRNAs, strongly suggesting that it is involved in novel cellular functions in addition to splicing

Cisplatin resistant spheroids model clinically relevant survival mechanisms in ovarian tumors

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0151089, doi: 10.1371/journal.pone.0151089 .The majority of ovarian tumors eventually recur in a drug resistant form. Using cisplatin sensitive and resistant cell lines assembled into 3D spheroids we profiled gene expression and identified candidate mechanisms and biological pathways associated with cisplatin resistance. OVCAR-8 human ovarian carcinoma cells were exposed to sub-lethal concentrations of cisplatin to create a matched cisplatin-resistant cell line, OVCAR-8R. Genome-wide gene expression profiling of sensitive and resistant ovarian cancer spheroids identified 3,331 significantly differentially expressed probesets coding for 3,139 distinct protein-coding genes (Fc >2, FDR < 0.05) (S2 Table). Despite significant expression changes in some transporters including MDR1, cisplatin resistance was not associated with differences in intracellular cisplatin concentration. Cisplatin resistant cells were significantly enriched for a mesenchymal gene expression signature. OVCAR-8R resistance derived gene sets were significantly more biased to patients with shorter survival. From the most differentially expressed genes, we derived a 17-gene expression signature that identifies ovarian cancer patients with shorter overall survival in three independent datasets. We propose that the use of cisplatin resistant cell lines in 3D spheroid models is a viable approach to gain insight into resistance mechanisms relevant to ovarian tumors in patients. Our data support the emerging concept that ovarian cancers can acquire drug resistance through an epithelial-to-mesenchymal transition.This work was funded by the NIH NCRR supplement grant P41 RR001395-27S1 (J.W.H.), NSF DBI-1005378 “REU Site: Biological Discovery in Woods Hole”, faculty startup funds from the Office of Research at Oklahoma State University (W.C.), and the Mary Kay Foundation (A.S.B.)

Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells

BACKGROUND: Transcription by RNA polymerase II is regulated at many steps including initiation, promoter release, elongation and termination. Accumulation of RNA polymerase II at particular locations across genes can be indicative of sites of regulation. RNA polymerase II is thought to accumulate at the promoter and at sites of co-transcriptional alternative splicing where the rate of RNA synthesis slows. RESULTS: To further understand transcriptional regulation at a global level, we determined the distribution of RNA polymerase II within regions of the human genome designated by the ENCODE project. Hypophosphorylated RNA polymerase II localizes almost exclusively to 5' ends of genes. On the other hand, localization of total RNA polymerase II reveals a variety of distinct landscapes across many genes with 74% of the observed enriched locations at exons. RNA polymerase II accumulates at many annotated constitutively spliced exons, but is biased for alternatively spliced exons. Finally, RNA polymerase II is also observed at locations not in gene regions. CONCLUSION: Localizing RNA polymerase II across many millions of base pairs in the human genome identifies novel sites of transcription and provides insights into the regulation of transcription elongation. These data indicate that RNA polymerase II accumulates most often at exons during transcription. Thus, a major factor of transcription elongation control in mammalian cells is the coordination of transcription and pre-mRNA processing to define exons

Exon expression profiling reveals stimulus-mediated exon use in neural cells

Exon centric microarrays were used to resolve the calcium-modulated gene expression response into transcript-level an exon-level regulation

Identification of stromal ColXα1 and tumor-infiltrating lymphocytes as putative predictive markers of neoadjuvant therapy in estrogen receptor-positive/HER2-positive breast cancer

Patient characteristics. x indicates the case was included for the assay. (XLSX 44 kb

Four-fermion interaction from torsion as dark energy

The observed small, positive cosmological constant may originate from a four-fermion interaction generated by the spin-torsion coupling in the Einstein-Cartan-Sciama-Kibble gravity if the fermions are condensing. In particular, such a condensation occurs for quark fields during the quark-gluon/hadron phase transition in the early Universe. We study how the torsion-induced four-fermion interaction is affected by adding two terms to the Dirac Lagrangian density: the parity-violating pseudoscalar density dual to the curvature tensor and a spinor-bilinear scalar density which measures the nonminimal coupling of fermions to torsion.Comment: 6 pages; published versio

Dilepton production in proton-proton collisions at BEVALAC energies

The dilepton production in elementary ${pp\to e^{+}e^{-}X}$ reactions at BEVALAC energies $T_{lab}=1\div 5$ GeV is investigated. The calculations include direct ${e^{+}e^{-}}$ decays of the vector mesons $\rho ^{0}$, $\omega$, and $\phi$, Dalitz decays of the $\pi ^{0}$-, $\eta$-, $$-, $\omega$-, and $\phi$-mesons, and of the baryon resonances $$ $...$ . The subthreshold vector meson production cross sections in $pp$ collisions are treated in a way sufficient to avoid double counting with the inclusive vector meson production. The vector meson dominance model for the transition form factors of the resonance Dalitz decays $R\to e^{+}e^{-}N$ is used in an extended form to ensure correct asymptotics which are in agreement with the quark counting rules. Such a modification gives an unified and consistent description of both $R\to N\gamma$ radiative decays and $R\to N\rho (\omega)$ meson decays. The effect of multiple pion production on the experimental efficiency for the detection of the dilepton pairs is studied. We find the dilepton yield in reasonable agreement with the experimental data for the set of intermediate energies whereas at the highest energy $T_{lab}=4.88$ GeV the number of dilepton pairs is likely to be overestimated experimentally in the mass range $M=300\div 700$ MeV.Comment: 25 pages (IOP style), 5 figures, revised manuscript accepted for publication in JP