Conformational Dependence of a Protein Kinase Phosphate Transfer Reaction

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In the TC, we calculate that the reactants and products are nearly isoenergetic with a 0.2 eV barrier; while phosphate transfer is unfavorable by over 1.2 eV in the RC, with an even higher barrier. With the protein in the TC, the motions involved in reaction are small, with only P$_\gamma$ and the catalytic proton moving more than 0.5 \AA. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an \AA in the catalytic site.Comment: revtex4, 7 pages, 4 figures, to be submitted to Scienc

Geometric Aspects of the Moduli Space of Riemann Surfaces

This is a survey of our recent results on the geometry of moduli spaces and Teichmuller spaces of Riemann surfaces appeared in math.DG/0403068 and math.DG/0409220. We introduce new metrics on the moduli and the Teichmuller spaces of Riemann surfaces with very good properties, study their curvatures and boundary behaviors in great detail. Based on the careful analysis of these new metrics, we have a good understanding of the Kahler-Einstein metric from which we prove that the logarithmic cotangent bundle of the moduli space is stable. Another corolary is a proof of the equivalences of all of the known classical complete metrics to the new metrics, in particular Yau's conjectures in the early 80s on the equivalences of the Kahler-Einstein metric to the Teichmuller and the Bergman metric.Comment: Survey article of our recent results on the subject. Typoes corrrecte

Effective Lagrangian Approach to Weak Radiative Decays of Heavy Hadrons

Motivated by the observation of the decay $\bar{B}\to \bar{K}^*\gamma$ by CLEO, we have systematically analyzed the two-body weak radiative decays of bottom and charmed hadrons. There exist two types of weak radiative decays: One proceeds through the short-distance $b\to s\gamma$ transition and the other occurs through $W$-exchange accompanied by a photon emission. Effective Lagrangians are derived for the $W$-exchange bremsstrahlung processes at the quark level and then applied to various weak electromagnetic decays of heavy hadrons. Predictions for the branching ratios of $\bar{B}^0\to D^{*0} \gamma,~\Lambda_b^0\to\Sigma_c^0\gamma,~\Xi_b^0\to \Xi_c^0\gamma$ and \Xi_b^0\to\xip_c^0\gamma are given. In particular, we found ${\cal B}(\bar{B}^0 \to D^{*0}\gamma)\approx 0.9\times 10^{-6}$. Order of magnitude estimates for the weak radiative decays of charmed hadrons: $~D^0\to \bar{K}^{*0}\gamma,~\Lambda_c^+\to\Sigma^+\gamma$ and $\Xi_c^0\to\Xi^0\gamma$ are also presented. Within this approach, the decay asymmetry for antitriplet to antitriplet heavy baryon weak radiative transitions is uniquely predicted by heavy quark symmetry. The electromagnetic penguin contribution to $\Lambda_b^0\to\Lambda\gamma$ is estimated by two different methods and its branching ratio is found to be of order $1\times 10^{-5}$. We conclude that weak radiative decays of bottom hadrons are dominated by the short-distance $b\to s\gamma$ mechanism.Comment: 28 pages + 3 figures (not included), CLNS 94/1278, IP-ASTP-04-94. [Main changes in this revised version: (i) Sect 2 and subsection 4.1 are revised, (ii) A MIT bag method for calculating the decay rate of $Lambda_b \to\Lambda+gamma$ is presented, (iii) All predictions are updated using the newly available 1994 Particle Data Group, and (iv) Appendix and subsections 3.3 and 4.4 are deleted.

Corrections to Chiral Dynamics of Heavy Hadrons: (I) 1/M Correction

In earlier publications we have analyzed the strong and radiative decays of heavy hadrons in a formalism which incorporates both heavy-quark and chiral symmetries. In particular, we have derived a heavy-hadron chiral Lagrangian whose coupling constants are related by the heavy-quark flavor-spin symmetry arising from the QCD Lagrangian with infinitely massive quarks. In this paper, we re-examine the structure of the above chiral Lagrangian by including the effects of $1/m_Q$ corrections in the heavy quark effective theory. The relations among the coupling constants, originally derived in the heavy-quark limit, are modified by heavy quark symmetry breaking interactions in QCD. Some of the implications are discussed.Comment: PHYZZX, 45 pages, 1 figure (not included), CLNS 93/1192, IP-ASTP-02-93, ITP-SB-93-0

Predictions for s-Wave and p-Wave Heavy Baryons from Sum Rules and Constituent Quark Model (I): Strong Interactions

We study the strong interactions of the L=1 orbitally excited baryons with one heavy quark in the framework of the Heavy Hadron Chiral Perturbation Theory. To leading order in the heavy mass expansion, the interaction Lagrangian describing the couplings of these states among themselves and with the ground state heavy baryons contains 46 unknown couplings. We derive sum rules analogous to the Adler-Weisberger sum rule which constrain these couplings and relate them to the couplings of the s-wave heavy baryons. Using a spin 3/2 baryon as a target, we find a sum rule expressing the deviation from the quark model prediction for pion couplings to s-wave states in terms of couplings of the p-wave states. In the constituent quark model these couplings are related and can be expressed in terms of only two reduced matrix elements. Using recent CLEO data on $\Sigma_c^{*}$ and $\Lambda_{c1}^+$ strong decays, we determine some of the unknown couplings in the chiral Lagrangian and the two quark model reduced matrix elements. Specific predictions are made for the decay properties of all L=1 charmed baryons.Comment: 50 pages, REVTeX with 4 included figures; predictions for additional decay modes included; 1 reference adde

Nasopharyngeal carcinoma: time lapse before diagnosis and treatment

This is a descriptive study of 168 patients with nasopharyngeal carcinoma who were referred to public oncology departments for primary treatment between July and September 1996. The mean duration from the onset of the symptoms to histological diagnosis was 5.0 months; the duration ranged from 6.1 months (for patients presenting with nasal symptoms) to 1.8 months (for those with cranial nerve dysfunction). The mean period between the onset of symptoms and the seeking of medical advice was 2.9months. For 54% of the patients, there was a further delay of up to 2.4 months between the initial medical consultation and referral to the appropriate specialist. The majority (84%) of patients attended public institutions for histological confirmation. The mean total time taken from the onset of symptoms to the commencement of radiotherapy was 6.5 months (range, 1.3-74.0 months)---45% of the delay was attributed to the patient, 20% to initial consultations, 14% to diagnostic arrangement, and 21% to preparation for radiotherapy. Concerted efforts are needed to minimise further the time between the onset of symptoms and treatment. A substantial reduction in this delay can be achieved if both public and primary care doctors were made more aware of the significance of relevant symptoms.published_or_final_versio

Extracting density-density correlations from in situ images of atomic quantum gases

We present a complete recipe to extract the density-density correlations and the static structure factor of a two-dimensional (2D) atomic quantum gas from in situ imaging. Using images of non-interacting thermal gases, we characterize and remove the systematic contributions of imaging aberrations to the measured density-density correlations of atomic samples. We determine the static structure factor and report results on weakly interacting 2D Bose gases, as well as strongly interacting gases in a 2D optical lattice. In the strongly interacting regime, we observe a strong suppression of the static structure factor at long wavelengths.Comment: 15 pages, 5 figure

Chiral Lagrangians for Radiative Decays of Heavy Hadrons

The radiative decays of heavy mesons and heavy baryons are studied in a formalism which incorporates both the heavy quark symmetry and the chiral symmetry. The chiral Lagrangians for the electromagnetic interactions of heavy hadrons consist of two pieces: one from gauging electromagnetically the strong-interaction chiral Lagrangian, and the other from the anomalous magnetic moment interactions of the heavy baryons and mesons. Due to the heavy quark spin symmetry, the latter contains only one independent coupling constant in the meson sector and two in the baryon sector. These coupling constants only depend on the light quarks and can be calculated in the nonrelativistic quark model. However, the charm quark is not heavy enough and the contribution from its magnetic moment must be included. Applications to the radiative decays $D^\ast \rightarrow D \gamma~,~B^\ast \rightarrow B \gamma~,~ \Xi^\prime_c \rightarrow \Xi_c \gamma~, \Sigma_c \rightarrow \Lambda_c \gamma$ and $\Sigma_c \rightarrow \Lambda_c \pi \gamma$ are given. Together with our previous results on the strong decay rates of $D^\ast \rightarrow D \pi$ and $\Sigma_c \rightarrow \Lambda_c \pi$, predictions are obtained for the total widths and branching ratios of $D^\ast$ and $\Sigma_c$. The decays $\Sigma^+_c \rightarrow \Lambda^+_c \pi^0 \gamma$ and $\Sigma^0_c \rightarrow \Lambda^+_c \pi^- \gamma$ are discussed to illustrate the important roles played by both the heavy quark symmetry and the chiral symmetry.Comment: 30 pages (one figure, available on request), CLNS 92/1158 and IP-ASTP-13-9

Rare B Decays with a HyperCP Particle of Spin One

In light of recent experimental information from the CLEO, BaBar, KTeV, and Belle collaborations, we investigate some consequences of the possibility that a light spin-one particle is responsible for the three Sigma^+ -> p mu^+ mu^- events observed by the HyperCP experiment. In particular, allowing the new particle to have both vector and axial-vector couplings to ordinary fermions, we systematically study its contributions to various processes involving b-flavored mesons, including B-Bbar mixing as well as leptonic, inclusive, and exclusive B decays. Using the latest experimental data, we extract bounds on its couplings and subsequently estimate upper limits for the branching ratios of a number of B decays with the new particle. This can serve to guide experimental searches for the particle in order to help confirm or refute its existence.Comment: 17 pages, 3 figures; discussion on spin-0 case modified, few errors corrected, main conclusions unchange

Dual role of immune cells in the testis: protective or pathogenic for germ cells?

The purpose of this review is to describe how the immune cells present in the testis interact with the germinal epithelium contributing to survival or apoptosis of germ cells (GCs). Physiologically, the immunosuppressor testicular microenvironment protects GCs from immune attack, whereas in inflammatory conditions, tolerance is disrupted and immune cells and their mediators respond to GC self antigens, inducing damage of the germinal epithelium. Considering that experimental models of autoimmune orchitis have clarified the local immune mechanisms by which protection of the testis is compromised, we described the following topics in the testis of normal and orchitic rats: (1) cell adhesion molecule expression of seminiferous tubule specialized junctions and modulation of blood-testis barrier permeability by cytokines (2) phenotypic and functional characteristics of testicular dendritic cells, macrophages, effector and regulatory T cells and mast cells and (3) effects of pro-inflammatory cytokines (TNF-α, IL-6 and FasL) and the nitric oxide-nitric oxide synthase system on GC apoptosis.Fil: Pérez, Cecilia Valeria. Universidad de Buenos Aires. Facultad de Medicina; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas; ArgentinaFil: Theas, Maria Susana. Universidad de Buenos Aires. Facultad de Medicina; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas; ArgentinaFil: Jacobo, Patricia Verónica. Universidad de Buenos Aires. Facultad de Medicina; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas; ArgentinaFil: Jarazo Dietrich, Sabrina Soledad. Universidad de Buenos Aires. Facultad de Medicina; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas; ArgentinaFil: Guazzone, Vanesa Anabella. Universidad de Buenos Aires. Facultad de Medicina; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas; ArgentinaFil: Lustig, Livia. Universidad de Buenos Aires. Facultad de Medicina; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas; Argentin