Exploring the functional domain and the target of the tetanus toxin light chain in neurohypophysial terminals

The tetanus toxin light chain blocks calcium induced vasopressin release from neurohypophysial nerve terminals. Here we show that histidine residue 233 within the putative zinc binding motif of the tetanus toxin light chain is essential for the inhibition of exocytosis, in the rat. The zinc chelating agent dipicolinic acid as well as captopril, an inhibitor of zinc-dependent peptidases, counteract the effect of the neurotoxin. Synthetic peptides, the sequences of which correspond to motifs present in the cytoplasmic domain of the synaptic vesicle membrane protein synaptobrevin 1 and 2, prevent the effect of the tetanus toxin light chain. Our results indicate that zinc bound to the zinc binding motif constitutes the active site of the tetanus toxin light chain. Moreover they suggest that cleavage of synaptobrevin by the neurotoxin causes the inhibition of exocytotic release of vasopressin from secretory granules

ProDGe: investigating protein-protein interactions at the domain level

An important goal of systems biology is the identification and investigation of known and predicted protein-protein interactions to obtain more information about new cellular pathways and processes. Proteins interact via domains, thus it is important to know which domains a protein contains and which domains interact with each other. Here we present the Java^TM^ program ProDGe (Protein Domain Gene), which visualizes existing and suggests novel domain-domain interactions and protein-protein interactions at the domain level. The comprehensive dataset behind ProDGe consists of protein, domain and interaction information for both layers, collected and combined appropriately from UniProt, Pfam, DOMINE and IntAct. Based on known domain interactions, ProDGe suggests novel protein interactions and assigns them to four confidence classes, depending on the reliability of the underlying domain interaction. Furthermore, ProDGe is able to identify potential homologous interaction partners in other species, which is particularly helpful when investigating poorly annotated species. We further evaluated and compared experimentally identified protein interactions from IntAct with domain interactions from DOMINE for six species and noticed that 31.13% of all IntAct protein interactions in all six species can be mapped to the actual interacting domains. ProDGe and a comprehensive documentation are freely available at http://www.cogsys.cs.uni-tuebingen.de/software/ProDGe

Malat Metabolismus und die Rolle der NADP-Malat Enzym Isoformen in der C3-Modellpflanze A. thaliana

Obwohl Malat und Fumarat in eine Vielzahl von Stoffwechselweg der Pflanze involviert sind, bleibt ihre Funktion als Kohlenstoffquelle in C3-Pflanzen weitgehend ungeklärt. In dieser Arbeit wurden Arabidopsis thaliana Pflanzen und Stärkefreimutanten adg1 (ADG-Glukose-Phyrophosphorylase1 null Mutante) und pgm1 und sft1 (Phosphoglucomutase1 null Mutante), die ein plastidäres Mais-NADP-ME (MEm) überexprimierten, wurden genutzt um die Auswirkung eines extrem niedrigen Malat- und Fumarat-Gehalt au die Physiologie von C3-Pflanzen zu untersuchen. Die MEm-Überexpressions-Pflanzen entwickelten einen Kohlenstoffmangel-Phänotypen besonders unter Kurz-Tag-Bedingungen. Die Beobachteten Ergebnisse dieses Phänotyp untermauern die physiologische Rolle von Malat und Fumarat als essenzielle transiente Kohlenstoffquellen in C3-Pflanzen wie A. thaliana. Wir postulieren, dass das niedrige Level von organischen Säuren, das einem Karbohydrat-Mangel am Ende der Nacht folgt, als initiales Signal dient und eine Kaskade von Abläufen verursacht, die letztlich zur veränderten Substratnutzung in der Respiration hin zu hoch reduzierten Substraten, wie Fettsäuren und Proteinen während der langen Nachtphase bewirken. Dem folgend unterstützen unsere Ergebnisse die Annahme, das die organischen Säuren, Malat und Fumarat, äußerst wichtige C-Quellen im Metabolismus von A. thaliana darstellen. NADP-Malat-Enzym (NADP-ME, E.C. 1.1.1.40) katalysiert die oxidative Dekarboxylierung von L-Malat unter Gewinnung von Pyruvat, CO2 und NADPH. Obwohl die Rolle von NADP-ME in der C4-Photosynthese bekannt ist, bleiben die physiologischen Funktionen der C3-Isoformen bisher ungeklärt. Die Analyse des transkriptionalen Coexpressionsmuster zeigt, dass NADP-ME2 in Verbindung mit Genen steht, die in die Pathogenabwehr involviert sind. Unsere Arbeit zeigt, dass die gesamte NADP-ME Aktivität nach Infiltration mit pilzlichen und bakteriellen Elizitoren und nach Infektion mit dem hemibiotrophen pilzlichen Pathogen Colletotrichum higginsianum induziert wurde. Des weiteren konnte mit Funktionsverlust-Mutanten und mehreren biochemischen und physiologischen Methoden gezeigt werden, dass die beobachtete Aktivitätsänderung durch NADP-ME2 verursacht wurde und der Verlust des zytosolischen NADP-ME2 eine erhöhte Empfindlichkeit gegenüber Infektionen zur Folge hat. Unsere Ergebnisse lassen vermuten, dass NADP-ME2 in Mechanismen involviert ist, die NADPH für die ROS-Produktion bereitstellen könnten. NADP-ME3 könnte eine mögliche Rolle im Abbau der primären oder sekundären PCM-Wand während Pollen Entwicklung

Estrogens Determine Adherens Junction Organization and E-Cadherin Clustering in Breast Cancer Cells via Amphiregulin

Estrogens play an important role in the development and progression of human cancers, particularly in breast cancer. Breast cancer progression depends on the malignant destabilization of adherens junctions (AJs) and disruption of tissue integrity. We found that estrogen receptor alpha (ER alpha) inhibition led to a striking spatial reorganization of AJs and microclustering of E-Cadherin (E-Cad) in the cell membrane of breast cancer cells. This resulted in increased stability of AJs and cell stiffness and a reduction of cell motility. These effects were actomyosindependent and reversible by estrogens. Detailed investigations showed that the ERa target gene and epidermal growth factor receptor (EGFR) ligand Amphiregulin (AREG) essentially regulates AJ reorganization and E-Cad microclustering. Our results not only describe a biological mechanism for the organization of AJs and the modulation of mechanical properties of cells but also provide a new perspective on how estrogens and anti-estrogens might influence the formation of breast tumors

Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies

<p>Abstract</p> <p>Background</p> <p>To understand the dynamic behavior of cellular systems, mathematical modeling is often necessary and comprises three steps: (1) experimental measurement of participating molecules, (2) assignment of rate laws to each reaction, and (3) parameter calibration with respect to the measurements. In each of these steps the modeler is confronted with a plethora of alternative approaches, e. g., the selection of approximative rate laws in step two as specific equations are often unknown, or the choice of an estimation procedure with its specific settings in step three. This overall process with its numerous choices and the mutual influence between them makes it hard to single out the best modeling approach for a given problem.</p> <p>Results</p> <p>We investigate the modeling process using multiple kinetic equations together with various parameter optimization methods for a well-characterized example network, the biosynthesis of valine and leucine in <it>C. glutamicum</it>. For this purpose, we derive seven dynamic models based on generalized mass action, Michaelis-Menten and convenience kinetics as well as the stochastic Langevin equation. In addition, we introduce two modeling approaches for feedback inhibition to the mass action kinetics. The parameters of each model are estimated using eight optimization strategies. To determine the most promising modeling approaches together with the best optimization algorithms, we carry out a two-step benchmark: (1) coarse-grained comparison of the algorithms on all models and (2) fine-grained tuning of the best optimization algorithms and models. To analyze the space of the best parameters found for each model, we apply clustering, variance, and correlation analysis.</p> <p>Conclusion</p> <p>A mixed model based on the convenience rate law and the Michaelis-Menten equation, in which all reactions are assumed to be reversible, is the most suitable deterministic modeling approach followed by a reversible generalized mass action kinetics model. A Langevin model is advisable to take stochastic effects into account. To estimate the model parameters, three algorithms are particularly useful: For first attempts the settings-free Tribes algorithm yields valuable results. Particle swarm optimization and differential evolution provide significantly better results with appropriate settings.</p

Ghosts of the past and dreams of the future: the impact of temporal focus on responses to contextual ingroup devaluation.

addresses: University of Exeter, Exeter, UK. [email protected]: Journal Article; Research Support, Non-U.S. Gov'tCopyright © 2012 SAGE Publications. Author's draft version; post-print. Final version published by Sage available on Sage Journals Online http://online.sagepub.com/The authors investigated the impact of temporal focus on group members' responses to contextual ingroup devaluation. Four experimental studies demonstrated that following an induction of negative ingroup evaluation, participants primed with a past temporal focus reported behavioral intentions more consistent with this negative appraisal than participants primed with a future temporal focus. This effect was apparent only when a negative (but not a positive) evaluation was induced, and only among highly identified group members. Importantly, the interplay between temporal focus and group identification on relevant intentions was mediated by individual self-esteem, suggesting that focus on the future may be conducive to separating negative ingroup appraisals from individual self-evaluations. Taken together, the findings suggest that high identifiers' responses to ingroup evaluations may be predicated on their temporal focus: A focus on the past may lock such individuals within their group's history, whereas a vision of the future may open up opportunities for change

Observation of isotonic symmetry for enhanced quadrupole collectivity in neutron-rich 62,64,66Fe isotopes at N=40

The transition rates for the 2_{1}^{+} states in 62,64,66Fe were studied using the Recoil Distance Doppler-Shift technique applied to projectile Coulomb excitation reactions. The deduced E2 strengths illustrate the enhanced collectivity of the neutron-rich Fe isotopes up to N=40. The results are interpreted by the generalized concept of valence proton symmetry which describes the evolution of nuclear structure around N=40 as governed by the number of valence protons with respect to Z~30. The deformation suggested by the experimental data is reproduced by state-of-the-art shell calculations with a new effective interaction developed for the fpgd valence space.Comment: 4 pages, 2 figure

Lifetime determination of excited states in Cd-106

Two separate experiments using the Differential Decay Curve Method have been performed to extract mean lifetimes of excited states in 106 Cd. The inedium-spin states of interest were populated by the Mo-98(C-12, 4n) Cd-106 reaction performed at the Wright Nuclear Structure Lab., Yale University. From this experiment, two isomeric state mean lifetimes have been deduced. The low-lying states were populated by the Mo-96(C-13, 3n)Cd-106 reaction performed at the Institut fur Kernphysik, Universitat zu Koln. The mean lifetime of the I-pi = 2(1)(+) state was deduced, tentatively, as 16.4(9) ps. This value differs from the previously accepted literature value from Coulomb excitation of 10.43(9) ps

Strontium Isotopic Composition of Paleozoic Carbonate Rocks in the Nevada Test Site Vicinity, Clark, Lincoln, and Nye Counties, Nevada and Inyo County, California.

Ground water moving through permeable Paleozoic carbonate rocks represents the most likely pathway for migration of radioactive contaminants from nuclear weapons testing at the Nevada Test Site, Nye County, Nevada. The strontium isotopic composition (87Sr/86Sr) of ground water offers a useful means of testing hydrochemical models of regional flow involving advection and reaction. However, reaction models require knowledge of 87Sr/86Sr data for carbonate rock in the Nevada Test Site vicinity, which is scarce. To fill this data gap, samples of core or cuttings were selected from 22 boreholes at depth intervals from which water samples had been obtained previously around the Nevada Test Site at Yucca Flat, Frenchman Flat, Rainier Mesa, and Mercury Valley. Dilute acid leachates of these samples were analyzed for a suite of major- and trace-element concentrations (MgO, CaO, SiO2, Al2O3, MnO, Rb, Sr, Th, and U) as well as for 87Sr/86Sr. Also presented are unpublished analyses of 114 Paleozoic carbonate samples from outcrops, road cuts, or underground sites in the Funeral Mountains, Bare Mountain, Striped Hills, Specter Range, Spring Mountains, and ranges east of the Nevada Test Site measured in the early 1990's. These data originally were collected to evaluate the potential for economic mineral deposition at the potential high-level radioactive waste repository site at Yucca Mountain and adjacent areas (Peterman and others, 1994). Samples were analyzed for a suite of trace elements (Rb, Sr, Zr, Ba, La, and Ce) in bulk-rock powders, and 87Sr/86Sr in partial digestions of carbonate rock using dilute acid or total digestions of silicate-rich rocks. Pre-Tertiary core samples from two boreholes in the central or western part of the Nevada Test Site also were analyzed. Data are presented in tables and summarized in graphs; however, no attempt is made to interpret results with respect to ground-water flow paths in this report. Present-day 87Sr/86Sr values are compared to values for Paleozoic seawater present at the time of deposition. Many of the samples have 87Sr/86Sr compositions that remain relatively unmodified from expected seawater values. However, rocks underlying the northern Nevada Test Site as well as rocks exposed at Bare Mountain commonly have elevated 87Sr/86Sr values derived from post-depositional addition of radiogenic Sr most likely from fluids circulating through rubidium-rich Paleozoic strata or Precambrian basement rocks