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PubMed2007

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding.

The thermodynamic properties and phase behavior of water in confined regions can vary significantly from that observed in the bulk. This is particularly true for systems in which the confinement is on the molecular-length scale. In this study, we use molecular dynamics simulations and a powerful solvent analysis technique based on inhomogenous solvation theory to investigate the properties of water molecules that solvate the confined regions of protein active sites. Our simulations and analysis indicate that the solvation of protein active sites that are characterized by hydrophobic enclosure and correlated hydrogen bonds induce atypical entropic and enthalpic penalties of hydration. These penalties apparently stabilize the protein-ligand complex with respect to the independently solvated ligand and protein, which leads to enhanced binding affinities. Our analysis elucidates several challenging cases, including the super affinity of the streptavidin-biotin system.

Amino Acid Motifs↗
PubMed2004

A policy analysis of funding for ambitious interventional gerontology: the possibility of rejuvenation research at the National Institute on Aging.

Issues related to the development of ambitious interventional gerontology-rejuvenation research-at the National Institute on Aging (NIA) within the National Institutes of Health (NIH) are discussed. Creating a separate branch for rejuvenation research within the NIA is probably neither feasible nor desirable at this time. However, it may be both feasible and desirable to begin rejuvenation research by establishing a bioengineering laboratory offering technologies that complement the disease-orientated focus of other NIA intramural laboratories. Such a bioengineering lab could use modern engineering tools for cell and gene therapies to uncover mechanisms of aging and to attempt to repair age-associated pathogenic damage. It is argued that, even in the absence of a full understanding of the complex causes and manifestations of human aging, interventional bioengineering could create methods for reversing aging processes. Exploring technical interventions may both reverse aging processes and significantly advance current disease-specific research.

Aged↗
PubMed2002

Genetic complexity of cellulose synthase a gene function in Arabidopsis embryogenesis.

The products of the cellulose synthase A (CESA) gene family are thought to function as isoforms of the cellulose synthase catalytic subunit, but for most CESA genes, the exact role in plant growth is still unknown. Assessing the function of individual CESA genes will require the identification of the null-mutant phenotypes and of the gene expression profiles for each gene. Here, we report that only four of 10 CESA genes, CESA1, CESA2, CESA3, and CESA9 are significantly expressed in the Arabidopsis embryo. We further identified two new mutations in the RADIALLY SWOLLEN1 (RSW1/CESA1) gene of Arabidopsis that obstruct organized growth in both shoot and root and interfere with cell division and cell expansion already in embryogenesis. One mutation is expected to completely abolish the enzymatic activity of RSW1(CESA1) because it eliminated one of three conserved Asp residues, which are considered essential for beta-glycosyltransferase activity. In this presumed null mutant, primary cell walls are still being formed, but are thin, highly undulated, and frequently interrupted. From the heart-stage onward, cell elongation in the embryo axis is severely impaired, and cell width is disproportionally increased. In the embryo, CESA1, CESA2, CESA3, and CESA9 are expressed in largely overlapping domains and may act cooperatively in higher order complexes. The embryonic phenotype of the presumed rsw1 null mutant indicates that the RSW1(CESA1) product has a critical, nonredundant function, but is nevertheless not strictly required for primary cell wall formation.

Amino Acid Sequence↗
PubMed2005

Characterization of alpha-synuclein aggregation and synergistic toxicity with protein tau in yeast.

A yeast model was generated to study the mechanisms and phenotypical repercussions of expression of alpha-synuclein as well as the coexpression of protein tau. The data show that aggregation of alpha-synuclein is a nucleation-elongation process initiated at the plasma membrane. Aggregation is consistently enhanced by dimethyl sulfoxide, which is known to increase the level of phospholipids and membranes in yeast cells. Aggregation of alpha-synuclein was also triggered by treatment of the yeast cells with ferrous ions, which are known to increase oxidative stress. In addition, data are presented in support of the hypothesis that degradation of alpha-synuclein occurs via autophagy and proteasomes and that aggregation of alpha-synuclein disturbs endocytosis. Reminiscent of observations in double-transgenic mice, coexpression of alpha-synuclein and protein tau in yeast cells is synergistically toxic, as exemplified by inhibition of proliferation. Taken together, the data show that these yeast models recapitulate major aspects of alpha-synuclein aggregation and cytotoxicity, and offer great potential for defining the underlying mechanisms of toxicity and synergistic actions of alpha-synuclein and protein tau.

Dimethyl Sulfoxide↗
PubMed2006

Order is needed to promote linear or quantum changes in nutrition and physical activity behaviors: a reaction to 'A chaotic view of behavior change' by Resnicow and Vaughan.

Recently, Drs. Ken Resnicow and Roger Vaughan published a thought-provoking paper in the International Journal of Behavioral Nutrition and Physical Activity (IJBNPA). They argue that the most often used social-cognition theories in behavioral nutrition and physical activity are of limited use. These models describe behavior change as a linear event, while Resnicow and Vaughan posit that behavior change is more likely to occur in quantum leaps that are impossible to predict. They introduce Chaos Theory into the behavioral nutrition and physical activity domain as a more valid framework to study the complex process of health behavior change. The present paper is a commentary on Resnicow and Vaughan's article by Resnicow's opponent in a recent debate-session at the annual meeting of the International Society of Behavioral Nutrition and Physical Activity. The chair of that meeting, Prof. Tom Baranowski, provides a separate commentary on Resnicow and Vaughan's paper also published recently in the IJBNPA. In the present commentary I relate Resnicow and Vaughan's paper to the other contributions to the Theory debate in the IJBNPA. I recognize the limited success of social cognition models, and, next to a better application of these models and more thorough research to test these model, also support research to further test the quantum and chaotic character of health behavior change. However, if such research supports the chaotic and quantum nature of health behavior change, the implications for behavioral nutrition and physical activity interventions may be limited, because even if behavior change is quantum rather than linear, the social cognition models are still relevant to inform interventions to promote quantum leaps in behavior change.

Comment↗
PubMed1984

Liposome facilitated xenogeneic approach for studying human colon cancer immunity: carrier and adjuvant effect of liposomes.

Liposomes prepared with human LS174T colon tumour cell membranes induce specific primary xenogeneic immune responses in BALB/c splenocytes in vitro. Characterization of the adjuvant role of these liposomes was accomplished by determining the effect on immune induction of several modifications on the liposomal carrier. The results showed that the carrier effect of liposomes was mediated primarily by tumour antigens exposed on the outer surface. Trypsin treatment of the liposomes eliminated 95% of the surface protein and significantly (P less than 0.05) reduced the ability of liposomes to induce cytotoxic splenocytes. The generation of cytolytic activity with liposomes was dose-dependent, with a 10 micrograms protein threshold and a maximal response at 100 micrograms. 'Rigid' liposomes were shown to be significantly (P less than 0.05) more efficacious than fluid liposomes in inducing cytotoxicity. In addition, the data indicate that the xenogeneic cell-mediated immunity exhibits identical classes of effector cells as found in murine-murine reactions. Lymphocytes bearing the THY-1, Lyt-1 and Lyt-2 surface markers were necessary for immune induction. The role of Lyt-123 subpopulation was suggested by the inability to achieve normal cytolytic levels by reconstitution with Lyt-1 plus Lyt-2 cells. Adherent cells were, as expected, necessary for the generation of primary immunity. Indeed, the interaction of I-A+ adherent cells with liposomes for at least 8 h was required to generate subsequent maximal T cell cytotoxic activity. The phenotype of the cytotoxic effector cell was Thy-1+, Lyt-2+, and I-Ad-. If this were an allo-or syngeneic, and not a xenogeneic system, this study would be of less interest. However, when coupled with the known molecular homologies between murine and human lymphocyte antigens, these results suggest that the concept of cross species major histocompatibility complex (MHC) restriction is tenable. Thus the liposome is not only an effective antigen carrier, but also a functional adjuvant for in vitro induced cell-mediated immunity.

Adjuvants, Immunologic↗
PubMed2002

Solution structure of a phage-derived peptide antagonist in complex with vascular endothelial growth factor.

Vascular endothelial growth factor (VEGF) is a potent endothelial cell-specific mediator of angiogenesis and vasculogenesis. VEGF is involved pathologically in cancer, proliferative retinopathy and rheumatoid arthritis, and as such represents an important therapeutic target. Three classes of disulfide-constrained peptides that antagonize binding of the VEGF dimer to its receptors, KDR and Flt-1, were identified previously using phage display methods. NMR studies of a representative peptide from the most potent class of these peptide antagonists, v107 (GGNECDAIRMWEWECFERL), were undertaken to characterize its interactions with VEGF. v107 has no defined structure free in solution, but binding to VEGF induces folding of the peptide. The solution structure of the VEGF receptor-binding domain-v107 complex was determined using 3940 (1970 per VEGF monomer) internuclear distance and 476 (238 per VEGF monomer) dihedral angle restraints derived from NMR data obtained using samples containing either (13)C/(15)N-labeled protein plus excess unlabeled peptide or (13)C/(15)N-labeled peptide plus excess unlabeled protein. Residual dipolar coupling restraints supplemented the structure determination of the complex and were found to increase significantly both the global precision of VEGF in the complex and the agreement with available crystal structures of VEGF. The calculated ensemble of structures is of high precision and is in excellent agreement with the experimental restraints. v107 has a turn-helix conformation with hydrophobic residues partitioned to one face of the peptide and polar or charged residues at the other face. Contacts between two v107 peptides and the VEGF dimer are mediated by primarily hydrophobic side-chain interactions. The v107-binding site on VEGF overlaps partially with the binding site of KDR and is similar to that for domain 2 of Flt-1. The structure of the VEGF-v107 complex provides new insight into how binding to VEGF can be achieved that may be useful for the design of small molecule antagonists.

Alanine↗
PubMed2006

Domain structure and protein interactions of the silent information regulator Sir3 revealed by screening a nested deletion library of protein fragments.

Transcriptional silencing in yeast is mediated by the interactions of silent information regulator (Sir) proteins with chromatin and with one another. The stable association of Sir3 with Sir4 is mediated by a C-terminal region of Sir3 that has additional functions including the dimerization of Sir3. We have developed a simple, robust expression screening methodology that allows for the unbiased identification of functional protein domains expressed from nested-deletion libraries of full-length genes. Using these methodologies, Sir3 dimerization was shown to be mediated by two separate domains. One of these domains also binds cooperatively to the C-terminal coiled-coil motif of Sir4 and dimerization further increases the affinity of Sir3 for Sir4. The resulting Sir3-Sir4 complexes form progressively higher order assemblies with increasing protein concentration, with implications for the mechanism of gene silencing.

Base Sequence↗
PubMed2005

Molecular dissection of the photoreceptor ribbon synapse: physical interaction of Bassoon and RIBEYE is essential for the assembly of the ribbon complex.

The ribbon complex of retinal photoreceptor synapses represents a specialization of the cytomatrix at the active zone (CAZ) present at conventional synapses. In mice deficient for the CAZ protein Bassoon, ribbons are not anchored to the presynaptic membrane but float freely in the cytoplasm. Exploiting this phenotype, we dissected the molecular structure of the photoreceptor ribbon complex. Identifiable CAZ proteins segregate into two compartments at the ribbon: a ribbon-associated compartment including Piccolo, RIBEYE, CtBP1/BARS, RIM1, and the motor protein KIF3A, and an active zone compartment including RIM2, Munc13-1, a Ca2+ channel alpha1 subunit, and ERC2/CAST1. A direct interaction between the ribbon-specific protein RIBEYE and Bassoon seems to link the two compartments and is responsible for the physical integrity of the photoreceptor ribbon complex. Finally, we found the RIBEYE homologue CtBP1 at ribbon and conventional synapses, suggesting a novel role for the CtBP/BARS family in the molecular assembly and function of central nervous system synapses.

Alcohol Oxidoreductases↗
PubMed2004

Identifying uniformly mutated segments within repeats.

Given a long string of characters from a constant size alphabet we present an algorithm to determine whether its characters have been generated by a single i.i.d. random source. More specifically, consider all possible n-coin models for generating a binary string S, where each bit of S is generated via an independent toss of one of the n coins in the model. The choice of which coin to toss is decided by a random walk on the set of coins where the probability of a coin change is much lower than the probability of using the same coin repeatedly. We present a procedure to evaluate the likelihood of a n-coin model for given S, subject a uniform prior distribution over the parameters of the model (that represent mutation rates and probabilities of copying events). In the absence of detailed prior knowledge of these parameters, the algorithm can be used to determine whether the a posteriori probability for n=1 is higher than for any other n>1. Our algorithm runs in time O(l4logl), where l is the length of S, through a dynamic programming approach which exploits the assumed convexity of the a posteriori probability for n. Our test can be used in the analysis of long alignments between pairs of genomic sequences in a number of ways. For example, functional regions in genome sequences exhibit much lower mutation rates than non-functional regions. Because our test provides means for determining variations in the mutation rate, it may be used to distinguish functional regions from non-functional ones. Another application is in determining whether two highly similar, thus evolutionarily related, genome segments are the result of a single copy event or of a complex series of copy events. This is particularly an issue in evolutionary studies of genome regions rich with repeat segments (especially tandemly repeated segments).

Algorithms↗
PubMedDate not supplied

Ward managers' perceptions of the role of healthcare assistants.

While unqualified nurses form an integral part of the UK's healthcare system, accounting for a large percentage of the workforce, there is limited evidence to identify the actual role of the healthcare assistant. This study explored hospital ward managers' views on the current and potential expansion of the healthcare assistant's role. A confidential survey was sent to all ward managers (n = 35) in one large acute hospital trust. A response rate of 94% (n = 33) was obtained. Data were analysed using descriptive statistics and open-ended questions were analysed for emerging themes. The results indicated that healthcare assistants are undertaking a wide diversity of procedures raging from general tidying to carrying out complex clinical procedures. Additionally, 82% (n = 27) of the managers reported that the healthcare assistant's role could be expanded, although concerns were raised regarding additional training and supervision.

Attitude of Health Personnel↗
PubMed2006

Growth factor signaling regulates elongation of RNA polymerase I transcription in mammals via UBF phosphorylation and r-chromatin remodeling.

Synthesis of the 45S rRNA by RNA polymerase I limits cell growth. Knowledge of the mechanism of its regulation is therefore key to understanding growth control. rRNA transcription is believed to be regulated solely at initiation/promoter release. However, we found that stimulation of endogenous 45S rRNA synthesis by epidermal growth factor (EGF) and serum failed to induce an increase in RNA polymerase I engagement on the rRNA genes, despite robust enhancement of 45S rRNA synthesis. Further, endogenous transcription elongation rates were measured and found to be directly proportional to 45S rRNA synthesis. Thus, elongation is a rate-limiting step for rRNA synthesis in vivo. ERK phosphorylation of the HMG boxes of UBF, an RNA polymerase I factor essential for transcription enhancement, was shown to directly regulate elongation by inducing the remodeling of ribosomal gene chromatin. The data suggest a mechanism for coordinating the cotranscriptional assembly of preribosomal particles.

Animals↗
PubMed2004

Brain activation associated with evaluative processes of guilt and embarrassment: an fMRI study.

We aimed to investigate the neural substrates associated with evaluative process of moral emotions. Using functional magnetic resonance imaging (fMRI), we examined the similarities and differences between evaluative process of guilt and that of embarrassment at the neural basis level. Study of the neural basis of judgments of moral emotions might contribute to a better understanding of the amoral behavior observed in neurological and psychiatric disorders. Nineteen healthy volunteers were studied. The participants read sentences carrying neutral, guilty, or embarrassing contents during the scans. Both guilt and embarrassment conditions commonly activated the medial prefrontal cortex (MPFC), left posterior superior temporal sulcus (STS), and visual cortex. Compared to guilt condition, embarrassment condition produced greater activation in the right temporal cortex (anterior), bilateral hippocampus, and visual cortex. Most of these regions have been implicated in the neural substrate of social cognition or Theory of Mind (ToM). Our results support the idea that both are self-conscious emotions, which are social emotions requiring the ability to represent the mental states of others. At the same time, our functional fMRI data are in favor of the notion that evaluative process of embarrassment might be a more complex process than that of guilt.

Adult↗
PubMed2002

The influence of evil on forensic clinical practice.

As the medicalization of criminal behaviour expands through forensic psychiatric practice it is reliant upon a therapeutic ideology based on clinical assessment and effective application of treatment strategies. When such criminal offenses are particularly heinous the perpetrators are often referred to as evil by non-professional accounts. However, the extent to which the concept of evil affects the perceptions of mental health professionals working with such offenders is little understood. This paper reports on research conducted in a high-security psychiatric hospital in the North-west of England and examines the construction of care plans in relation to a number of mentally disordered offenders who are considered by a group of mental health professionals as evil. Thematic analysis of mental health professionals' discourse pertaining to the care plans revealed a complex motivational and rational structuring of evil that dictated the switch from medical ideological discourse to lay notions of badness. From this, an Airaksinen model was constructed to display the types of evil manifestations.

Attitude of Health Personnel↗
PubMed2002

Disruption of HSP90 function reverts tumor necrosis factor-induced necrosis to apoptosis.

Triggering tumor necrosis factor receptor-1 (TNFR1) induces apoptosis in various cell lines. In contrast, stimulation of TNFR1 in L929sA leads to necrosis. Inhibition of HSP90, a chaperone for many kinases, by geldanamycin or radicicol shifted the response of L929sA cells to TNF from necrosis to apoptosis. This shift was blocked by CrmA but not by BCL-2 overexpression, suggesting that it occurred through activation of procaspase-8. Geldanamycin pretreatment led to a proteasome-dependent decrease in the levels of several TNFR1-interacting proteins including the kinases receptor-interacting protein, inhibitor of kappa B kinase-alpha, inhibitor of kappa B kinase-beta, and to a lesser extent the adaptors NF-kappaB essential modulator and tumor necrosis factor receptor-associated factor 2. As a consequence, NF-kappa B, p38MAPK, and JNK activation were abolished. No significant decrease in the levels of mitogen-activated protein kinases, adaptor proteins TNFR-associated death domain and Fas-associated death domain, or caspase-3, -8, and -9 could be detected. These results suggest that HSP90 client proteins play a crucial role in necrotic signaling. We conclude that inhibition of HSP90 may alter the composition of the TNFR1 complex, favoring the caspase-8-dependent apoptotic pathway. In the absence of geldanamycin, certain HSP90 client proteins may be preferentially recruited to the TNFR1 complex, promoting necrosis. Thus, the availability of proteins such as receptor-interacting protein, Fas-associated death domain, and caspase-8 can determine whether TNFR1 activation will lead to apoptosis or to necrosis.

Amino Acid Substitution↗
PubMed2003

Classification of Ralstonia pickettii-like isolates from the environment and clinical samples as Ralstonia insidiosa sp. nov.

Thirteen Ralstonia pickettii-like isolates from the environment (water, soil and activated sludge) and human clinical samples (including respiratory secretions of cystic fibrosis patients) were investigated in a polyphasic taxonomic study that employed 16S rDNA sequence analysis, DNA-DNA hybridization, determination of DNA base composition, whole-cell protein analysis, biochemical characterization and PCR-based assays. All isolates were classified as a novel Ralstonia species, for which the name Ralstonia insidiosa sp. nov. is proposed. The type strain, LMG 21421T (= CCUG 46789T), was isolated from the sputum of a patient with acute lymphoblastic leukaemia. R. insidiosa can be differentiated from other species of the genus Ralstonia and phenotypically similar species (including the Burkholderia cepacia complex and Achromobacter xylosoxidans) by a variety of biochemical tests, whole-cell protein analysis and several PCR-based assays. Some outstanding issues in the taxonomy of the genus Ralstonia are also discussed.

Base Composition↗
PubMed2004

Normal values for a clinical test of letter-recognition contrast thresholds.

PURPOSE: To investigate the contrast thresholds (CTs) in normal subjects using a high-luminance, letter-recognition task under clinically relevant testing conditions. SETTING: Texas Tech University Health Sciences System, Lubbock, Texas, USA. METHODS: Sixty normal subjects aged 20 to 49 years with a best corrected visual acuity of 20/20 or better in both eyes participated. M & S Technologies software was used to display black-on-white Sloan letters at contrast levels of 25%, 20%, 15%, 12%, and 10% through 1% in 1% decrements. The effects of age, sex, optotype size, eye dominance, ambient illumination level (bright = 625 - 630 lux; dim = <3 lux), and direction of approach to threshold were analyzed using a multivariate, ordinary, least-squares analysis. RESULTS: Age and sex did not influence CTs. Ascending versus descending testing was not statistically significant (P>.5). The effects of room illumination and eye dominance were significant (P<.01). Significant differences were found between 20/30 and 20/50, 20/30 and 20/70, and 20/50 and 20/70 optotype sizes (P<.01 for all comparisons). CONCLUSIONS: A commercially available, computer-based test of CTs was easy to administer and apparently easy for inexperienced subjects to perform. The results suggest criteria for detecting visual problems concerned with familiar but complex spatial-image shapes. This information might be used to assess the effects of treatments such as laser refractive surgery on recognition contrast. Further study is warranted.

Adult↗