Molecular dynamics simulations suggest that the Eco RI kink is an example of molecular strain

The energy surface in the vicinity of the "Eco RI kink" was investigated by conducting both in vacuo molecular dynamics simulations as well as a simulation with explicit solvent. The in vacuo simulations used the "all atom" AMBER 3.0 force field with a distant dependent dielectric function and "hydrated" counter ions while the simulation with explicit solvent used the AMBER 4.0 force field, fully charged phosphates and counter ions and a dielectric constant of 1.0. The thrust of the simulations was to discriminate between two models of the energy surface of the deformed DNA as found in the recognition complex with Eco RI endonuclease. In the intrinsic model, the kinked DNA is a local minimum of the energy surface intrinsic to the DNA itself while in the strained model there is no significant energy barrier separating kinked and regular B-DNA. The two models have significant implications for theories of indirect recognition of DNA based on sequence-dependent deformability. The simulations suggest that the Eco RI-kinked structure is an example of molecular strain because it is not near a minimum of any of the potential energy functions examined. The simulations leave the question of an energy barrier somewhat open and raise the possibility that the Eco RI kink is at (or near) a point of dynamic instability of the energy surface (either a true maximum or a saddle point).     

Preliminary evidence that cell death may contribute to separation of the trachea from the primitive foregut in the rat embryo

BACKGROUND/PURPOSE: The embryogenesis of many congenital tracheoesophageal abnormalities has been elucidated poorly, mainly because of an incomplete understanding of the normal mechanism of separation of the primitive foregut into the trachea and esophagus. There has been controversy about the existence and significance of the so-called tracheoesophageal septum. This study investigates the normal mechanism of tracheoesophageal separation in the rat. METHODS: Timed-pregnant Sprague-Dawley rats were killed on gestational days 11 to 16, respectively (the day on which the vaginal smear showed sperm was considered day 0 of gestation). Thirty-six embryos (six embryos from each age group) were fixed in 10% formalin. Fixed embryos from gestational day 13, 12, and 11 were sandwiched in melted agar to facilitate proper orientation before being processed. Half of the fetuses from each age group were sectioned serially in a transverse plane and the other half in a sagittal plane. The histological sections were stained with H&E. RESULTS: On gestational day 11, the foregut appears as a ventrodorsal slit in transverse section. Below the primitive pharynx, the epithelial cells on the ventral part of the foregut are actively proliferating, producing two lateral epithelial bulges (primitive bronchial buds). The epithelial cells of the dorsal aspect of the foregut show no sign of active growth. On day 12, the proximal trachea still shares a common lumen with the foregut. The distal trachea, the tracheal bifurcation, and both primary bronchi are recognized easily. At the point of tracheoesophageal separation, there is obvious debris of dead epithelial cells and condensed nuclei. These appearances were specifically located around the so-called tracheoesophageal septum and nearby grooves, resulting in enfolding cristae. There was no cell proliferation or inflammatory response in this region. On gestational day 13, the separation of the trachea and esophagus was almost complete. CONCLUSION: The present study demonstrates that a specific and consistent pattern of cell death in the region of the "tracheoesophageal septum" produced enfolding cristae that may be part of the mechanism of separation of the trachea and esophagus.     

Autoactivation of spore germination in mutant and wild type strains of Dictyostelium discoideum

Freshly formed wild type Dictyostelium discoideum spores are constitutively dormant, and thus require an activation treatment to germinate. Wild type spores may germinate without an activation treatment (autoactivate) after a period of ageing (maturation) in the intact fruiting body. Mutants have been isolated which autoactivate without the need for ageing. Autoactivation of mutant and aged wild type spores appears to occur by identical mechanisms; thus the mutation may involve premature maturation. Autoactivation is mediated by autoactivator substances released from spores as they spontaneously swell. These factors are readily chromatographed, and elute from a Biogel P2 column in three peaks of activity. One activity peak appears only after spores have begun to germinate. No autoactivator substances are released from heat activated spores. Autoactivation is sensitive to cychloheximide, and may result from altered spore permeability. Autoactivation is likely to be the mechanism of D. discoideum spore germination in nature.     

Efficacy of intervention for engaging youth and families into treatment and some variables that may contribute to differential effectiveness.

This study reports data on the efficacy of Strategic Structural Systems Engagement (SSSE), which is designed to bring hard-to-reach families into treatment. The study also explores variables that may contribute to differential effectiveness. Participants were 193 Hispanic families, who were randomly assigned to either experimental or control conditions. Several important findings emerged. First, the overall results replicated earlier findings showing the superiority of SSSE: 81% of SSSE families, compared to 60% of control families, were successfully engaged, χ–2(1, N?=?193)?=?7.5, p?N?=?51)?=?7.53, p?=?.006. Third, an analysis of intervention failure suggests a mechanism by which culture and ethnicity influence clinical processes (resistance to engagement) and may result in differential effectiveness. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Iron and copper nutrition-dependent changes in protein expression in a tomato wild type and the nicotianamine-free mutant chloronerva

The nicotianamine-deficient mutant chloronerva resembles phenotypically an Fe-deficient plant despite the high accumulation of Fe in the leaves, whereas if suffers from Cu deficiency in the shoot. Two-dimensional electrophoretic separation of proteins from root tips and leaves of wild-type Lycopersicon esculentum Mill. cv Bonner Beste and the mutant grown with and without Fe showed a number of consistent differences. In root tips of the Fe-deficient wild type and the Fe-sufficient as well as the Fe-deficient mutant, the expression of glyceraldehyde-3-phosphate dehydrogenase, formate dehydrogenase, and ascorbate peroxidase was increased. In leaves of the Fe-sufficient and -deficient mutant, Cu-containing chloroplastic and cytosolic superoxide dismutase (Cu-Zn) and plastocyanin (Cu) were nearly absent. This low plastocyanin content could be restored by supplying Cu via the xylem, but the superoxide dismutase levels could not be increased by this treatment. The differences in the protein patterns between wild type and mutant indicate that the apparent Fe deficiency of mutant plants led to an increase in enzymes involved in anaerobic metabolism as well as enzymes involved in stress defense. The biosynthesis of plastocyanin was diminished in mutant leaves, but it was differentially induced by increased Cu content.     

Variants of smooth Salmonella enterica serovar Enteritidis that grow to higher cell density than the wild type are more virulent

Salmonella enterica serovar Enteritidis that grows to a higher cell density (SE-HCD) than wild type while retaining O-chain lipopolysaccharide was isolated by transforming wild type serovar Enteritidis with the cell density sensor plasmid pSB402 and selecting for bioluminescence. A luminescent strain, SE-HCD, that emitted light in proportion with cell density and opacity through stationary phase was isolated. After a peak cell density of 1.5 x 10(11) CFU/ml was observed, luminescence decreased, although opacity continued to increase. Scanning electron microscopy revealed that changes in luminescence and opacity past peak cell density were associated with lysis of a swarming hyperflagellated coccobacillary cell type and emergence of a 10-to-30-fold-elongated rod cell type that lacked cell surface structures. Vigorous aeration was required to induce this dramatic cellular differentiation. The virulence of two isogenic variants with different patterns of light emission at an opacity of 0.2 after the culture was diluted 10-fold (1/10 OD) was assessed in animal models. Whereas SE-HCD1 killed 70% of 6-day-old chicks challenged subcutaneously, the same dose of SE-HCD2 did not kill any chicks. Conversely, subcutaneous challenge of hens with SE-HCD2 contaminated eggs five and seven times more often, respectively, than did SE-HCD1 or wild type serovar Enteritidis. Intravenous challenge with SE-HCD2 contaminated 22% of eggs versus 0. 5% with wild type, depressed egg production for 4 weeks, and caused clinical signs of Gallinarum Disease (Fowl Typhoid) in hens. SE-HCD2 produced no contaminated eggs following oral infection, whereas wild type contaminated 1.3% of eggs. Thus, SE-HCD2 is better at contaminating eggs than wild type, but only by parenteral challenge. These results suggest that it may be possible to separate luminescent serovar Enteritidis into groups that infect different age groups and organs and contaminate eggs.     

Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge

It is known that anionic surface residues play a role in the long-range electrostatic attraction between acetylcholinesterase and cationic ligands. In our current investigation, we show that anionic residues also play an important role in the behavior of the ligand within the active site gorge of acetylcholinesterase. Negatively charged residues near the gorge opening not only attract positively charged ligands from solution to the enzyme, but can also restrict the motion of the ligand once it is inside of the gorge. We use Brownian dynamics techniques to calculate the rate constant kon, for wild type and mutant acetylcholinesterase with a positively charged ligand. These calculations are performed by allowing the ligand to diffuse within the active site gorge. This is an extension of previously reported work in which a ligand was allowed to diffuse only to the enzyme surface. By setting the reaction criteria for the ligand closer to the active site, better agreement with experimental data is obtained. Although a number of residues influence the movement of the ligand within the gorge, Asp74 is shown to play a particularly important role in this function. Asp74 traps the ligand within the gorge, and in this way helps to ensure a reaction.     

Antigenic and molecular characterization of wild type 1 poliovirus causing outbreaks of poliomyelitis in Albania and neighboring countries in 1996

Mass vaccination has led poliomyelitis to become a rare disease in a large part of the world, including Western Europe. However, in the past 20 years wild polioviruses imported from countries where polio is endemic have been responsible for outbreaks in otherwise polio-free European countries. We report on the characterization of poliovirus isolates from a large outbreak of poliomyelitis that occurred in Albania in 1996 and that also spread to the neighboring countries of Yugoslavia and Greece. The epidemics involved 145 subjects, mostly young adults, and caused persisting paralysis in 87 individuals and 16 deaths. The agent responsible for the outbreak was isolated from 74 patients and was identified as wild type 1 poliovirus by both immunological and molecular methods. Sequence analysis of the genome demonstrated the involvement of a single virus strain throughout the epidemics, and genotyping analysis showed 95% homology of the strain with a wild type 1 poliovirus strain isolated in Pakistan in 1995. Neutralization assays with both human sera and monoclonal antibodies were performed to analyze the antigenic structure of the epidemic strain, suggesting its peculiar antigenic characteristics. The presented data underline the current risks of outbreaks due to imported wild poliovirus and emphasize the need to improve vaccination efforts and also the need to implement surveillance in countries free of indigenous wild poliovirus.     

Evidence that HLA class II-restricted human CD4+ T cells specific to p53 self peptides respond to p53 proteins of both wild and mutant forms

By stimulating peripheral blood mononuclear cells of four healthy donors with a mixture of overlapping peptides representing the core domain of p53, we established two CD4+ alphabeta T cell clones and four lines that recognized wild-type and mutant p53 proteins as well as p53 self peptides in an HLA class II-restricted fashion. Two T cell lines established from two unrelated donors reacted to the p53 peptide (p)153-166 and p108-122, respectively, in the context of DP5 molecules. Two T cell clones established from two other unrelated donors were specific for p193-204 in the context of DRB1*1401 and for p153-165 in the context of DP5, respectively. These two T cell clones responded almost equally to both wild-type and four mutant recombinant p53 proteins. The proliferative responses of these T cell clones to p53 recombinant proteins were augmented by heat denaturing, thereby suggesting that altered conformation of the protein facilitates proteolytic processing to produce antigenic peptides. The DRB1*1401-restricted T cell clone specific for p193-204 killed a B lymphoblastoid cell line homozygous for HLA-DRB1*1401 when the cell line was pre-pulsed with p53 protein as well as peptide. These results indicate that CD4+ T cells reactive to p53 do exist in healthy individuals and the epitopes are probably ignored by the immune system under physiological conditions. It is suggested that such epitopes stimulate T cells to induce anti-p53 antibody production in cancer patients as previously reported by others. The possible involvement of p53-reactive T cells in anti-tumor immunity is discussed.     

Effects of extracellular matrix molecules on subepidermal neural crest cell migration in wild type and white mutant (dd) axolotl embryos

Sluzki's 1986 mental health model of the migratory process was tested with migrants (both refugees and immigrants), to New Zealand. Its central feature, suggesting an initial symptom free and euphoric phase after arrival in the country of settlement, followed by a crisis stage, was examined for 129 Southeast Asian refugees, 57 Pacific Island immigrants and 63 British immigrants. A questionnaire and the Hopkins Symptom Checklist-25, in English and in three Southeast Asian language translations, were administered face-to-face. All respondents had arrived in New Zealand within the last 15 years. The findings did not support Sluzki's model. Refugees and immigrants in the group with less than six months of residence were not symptom free. Neither did the group with six months to six years residence demonstrate a deterioration in mental health. However, mean depression levels were slightly lower for those who had lived in New Zealand for over six years, suggesting that mental health may improve the longer both refugees and immigrants reside in the host country.     

Diminished expression of CD40 ligand may contribute to the defective humoral immunity in patients with MHC class II deficiency

Major histocompatibility complex (MHC) class II deficiency (bare lymphocyte syndrome, BLS) is a rare primary immunodeficiency classified as a subgroup of severe combined immunodeficiency. We studied T and B lymphocyte function by examining the CD40 ligand/CD40 system in three BLS patients from two unrelated families. CD40 ligand expression by maximally activated BLS T cells was diminished. This abnormality may represent immunological na?veté rather than a general T cell defect, since expression of activation marker CD69 and proliferative responses to PHA or anti-CD3 were normal, and BLS T cells primed and restimulated in vitro expressed normal amounts of CD40 ligand. BLS B cells proliferated and produced IgE if stimulated with anti-CD40 or soluble CD40 ligand and IL-4. Activation of BLS B cells with soluble CD40 ligand and IL-4 induced normal expression of activation markers, although MHC class II expression remained absent. Depressed antibody titers, lack of amplification and failure to undergo isotype switching in response to immunization with bacteriophage phi x 174 demonstrated defective T cell help. We conclude that BLS B cells are functionally normal if appropriately stimulated, and that the defective humoral immunity observed may be related to diminished expression of CD40 ligand on BLS T cells.     

Crystal structure of the H256A mutant of rat testis fructose-6-phosphate,2-kinase/fructose-2,6-bisphosphatase. Fructose 6-phosphate in the active site leads to mechanisms for both mutant and wild type bisphosphatase activities

Fructose-6-phosphate,2-kinase/fructose-2,6-bisphosphatase (Fru-6-P, 2-kinase/Fru-2,6-Pase) is a bifunctional enzyme, catalyzing the interconversion of beta-D-fructose- 6-phosphate (Fru-6-P) and fructose-2,6-bisphosphate (Fru-2,6-P2) at distinct active sites. A mutant rat testis isozyme with an alanine replacement for the catalytic histidine (H256A) in the Fru-2,6-Pase domain retains 17% of the wild type activity (Mizuguchi, H., Cook, P. F., Tai, C-H., Hasemann, C. A., and Uyeda, K. (1998) J. Biol. Chem. 274, 2166-2175). We have solved the crystal structure of H256A to a resolution of 2. 4 A by molecular replacement. Clear electron density for Fru-6-P is found at the Fru-2,6-Pase active site, revealing the important interactions in substrate/product binding. A superposition of the H256A structure with the RT2K-Wo structure reveals no significant reorganization of the active site resulting from the binding of Fru-6-P or the H256A mutation. Using this superposition, we have built a view of the Fru-2,6-P2-bound enzyme and identify the residues responsible for catalysis. This analysis yields distinct catalytic mechanisms for the wild type and mutant proteins. The wild type mechanism would lead to an inefficient transfer of a proton to the leaving group Fru-6-P, which is consistent with a view of this event being rate-limiting, explaining the extremely slow turnover (0. 032 s-1) of the Fru-2,6-Pase in all Fru-6-P,2-kinase/Fru-2,6-Pase isozymes.     

Expression of genes that contribute to proliferative and metastatic ability in breast cancer resected during various menstrual phases

BACKGROUND: Retrospective studies show significant improvements in survival among women who had breast cancer resected during the luteal phase of their menstrual cycle compared with the follicular phase. We hypothesised that tumour tissue would show cyclical changes in expression of genes whose products might contribute to metastatic potential. METHODS: We studied 32 premenopausal women with operable breast cancer. We assayed hormones to define more accurately the menstrual phase during which surgery was done. We used northern blot analysis of RNA from fresh-frozen tumour specimens to study the patterns of expression of genes for proteolytic enzymes (cysteine proteinase cathepsin L and aspartyl proteinase cathepsin D; matrix metalloproteinases MMP-9 and MMP-2), tissue inhibitors of metalloproteinases TIMP-1 and TIMP-2, and TP53. RESULTS: There was a significantly higher level of expression of RNA for cathepsin L, MMP-9, and TP53 (p=0.005, 0.03, 0.03, respectively) in tumours that were resected during the follicular and periovulatory phases of the menstrual cycle than at other times in the cycle. A similar but non-significant trend was seen for MMP-2 and cathepsin D. A non-significant trend in the opposite direction was seen for TIMP-1 and TIMP-2. INTERPRETATION: We found that tumour expression of genes that may contribute to proliferative capacity and metastatic potential can change in breast cancer during the course of the menstrual cycle. The finding could provide a molecular explanation for the reports of improved survival in some breast-cancer patients whose tumours were removed during the luteal phase of the menstrual cycle. Larger studies are required to extend our study, assess mechanisms of gene regulation, and verify any relevant influence in long-term survival.     

Identification of equivalent residues in the gamma, delta, and epsilon subunits of the nicotinic receptor that contribute to alpha-bungarotoxin binding

Cysteine was introduced from residues 116 to 121 of the gamma subunit of the fetal mouse acetylcholine receptor, and the mutant receptors were treated with methanethiosulfonate reagents and examined for changes in ligand binding properties. Of the 18 combinations of mutant and reagent, only receptors harboring gammaL119C treated with the quaternary ammonium reagent MTSET (trimethylammonium-ethyl methanethiosulfonate) show a decreased number of alpha-bungarotoxin (alpha-btx) sites. The decrease of 50% suggests that alpha-btx binding to the site harboring gammaL119C is blocked. Analysis of binding of the site-selective ligands dimethyl-d-tubocurarine (DMT) and alpha-conotoxin M1 (CTX) confirm specificity of modification for the site harboring gammaL119C. Cysteines placed at equivalent positions of the delta and epsilon subunits also lead to selective loss of alpha-btx binding following MTSET treatment. gammaL119C receptors treated with the primary amine reagent MTSEA (aminoethyl methanethiosulfonate) retain alpha-btx binding to both sites but show reduced affinity for DMT and CTX at the modified site. Lysine mutagenesis of Leugamma119, Leudelta121, and Leuepsilon119 mimics MTSEA treatment, whereas mutagenesis of Thralpha119 and Glnbeta119 is without effect, demonstrating subunit and residue specificity of MTSEA modification. MTSET modification of nearby gammaY117C does not block alpha-btx binding but markedly diminishes affinity for DMT and CTX. The overall findings indicate a localized point of interaction between alpha-btx and the modified gammaL119C, deltaL121C, and epsilonL119C.     

Elevation of extracellular cortical noradrenaline may contribute to the antidepressant activity of zotepine: an in vivo microdialysis study in freely moving rats

The antipsychotic, zotepine, as well as possessing affinity for dopamine D1- and D2-1ike receptors, has high affinity for the noradrenaline (NA) transporter and inhibits [3H]NA uptake by rat frontal cortex synaptosomes, in vitro. The present studies investigated the effects of zotepine on extracellular NA in the frontal cortex of freely moving rats using in vivo microdialysis. Removal of calcium from the perfusate reduced extracellular NA by 70.5% and prevented the 50 mM KCl-stimulated increase in NA levels. Zotepine (0.5-1.5 mg kg(-1) i.p.), evoked biphasic, dose-dependent rises in extracellular NA with maximal increases observed at 60 min (+ 171.0%) and 240 min (+ 211.5%) post-treatment. The increases in NA levels were sustained for up to 100 min post-dosing. Clozapine (10.0 mg kg(-1) i.p.), resulted in a smaller, transient increase in NA levels (+ 72.0%) which lasted for 20 min post-treatment. Neither ziprasidone (3.0 mg kg(-1) i.p.) nor olanzapine (1.0 mg kg(-1) i.p.) influenced extracellular NA. Systemic treatment with the antidepressant desipramine (0.3 mg kg(-1) i.p.) resulted in a prolonged elevation of NA levels over 240 min (maximal increase of + 354.3%), whilst local infusion of nisoxetine (1-100 microM) through the dialysis probe increased NA levels in a concentration-dependent manner (up to 587.8% of control values). These data suggest that the inhibition of NA uptake by zotepine and its subsequent prolonged elevation of extracellular cortical NA may underlie the reported antidepressant properties of zotepine in schizophrenic patients.     

Coordination of the [2Fe-2S] cluster in wild type and molecular variants of Clostridium pasteurianum ferredoxin, investigated by ESEEM spectroscopy

The [2Fe-2S] ferredoxin from Clostridium pasteurianum contains five cysteine residues in positions 11, 14, 24, 56, and 60. This pattern is unique, and a combination of site-directed mutagenesis and spectroscopy is therefore being implemented to identify the ligands of the [2Fe-2S] cluster. The possible involvement of ligands other than cysteine in some molecular variants of this ferredoxin has been considered, histidines being likely candidates. Therefore, the three histidine residues in positions 6, 7, and 90 of the amino acid sequence have been individually and collectively replaced by alanine or valine. The mutated ferredoxins have been purified and were all found to contain [2Fe-2S] clusters of which the UV-visible absorption spectra were identical to that of the wild-type protein. The H6A/H7A/ H90A triply mutated ferredoxin was further characterized by EPR and by ESEEM spectroscopy and was found to differ only marginally from the wild-type protein. The ESEEM spectra of wild-type ferredoxin displayed weak 14N hyperfine interactions at the three principal g-factors of the [2Fe-2S] center. The estimated 14N coupling constants (Aiso = 0.6 MHz; e2qQ approximately 3.3 MHz) indicate that the ESEEM effect is most likely due to 14N from the polypeptide backbone. 2H2O ESEEM spectra showed that the [2Fe-2S] cluster is accessible for exchange with solvent deuterons. ESEEM spectra of the previously characterized C24A and C14A/C24A variants have been recorded and were also found to be very similar to those of the wild-type protein. There was no evidence for coordination of the [2Fe-2S] cluster by [14N]histidine or other 14N nuclei, in either wild-type or mutant forms of the ferredoxin. By these criteria, the environment of the [2Fe-2S] center is not distinguishable from those in plant-type ferredoxins. Non-cysteinyl coordination most probably occurs only in the C14A/C24A variant, which contains no more than three cysteine residues. The data shown here indicate that the fourth ligand of the [2Fe-2S] cluster is neither a histidine residue nor another nitrogenous ligand. The possibility of oxygenic coordination for this molecular variant is discussed.