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Biomedical subjects

John R Walker

Publications and source records attributed to John R Walker.

At least 19 recordsLinked to original sources
PubMed2006

Databases of free expression.

The rapid development of microarray technologies has led to a similar progression in gene expression analysis methods, gene expression applications, and gene expression databases. Public gene expression databases enable any researcher to examine expression of their favorite genes across a wide variety of samples, download sample data for development of new analysis methods, or answer broad questions about gene expression regulation, among other applications. A wide variety of public gene expression databases exist, and they vary in their content, analysis capabilities, and ease of use. This review highlights the current features and describes examples of two broad categories of mammalian microarray databases: tissue gene expression databases and data warehouses.

Animals↗
PubMed2006

The crystal structures of human calpains 1 and 9 imply diverse mechanisms of action and auto-inhibition.

Calpains are calcium activated cysteine proteases found throughout the animal, plant, and fungi kingdoms; 14 isoforms have been described in the human genome. Calpains have been implicated in multiple models of human disease; for instance, calpain 1 is activated in the brains of individuals with Alzheimer's disease, and the digestive tract specific calpain 9 is down-regulated in gastric cancer cell lines. We have solved the structures of human calpain 1 and calpain 9 protease cores using crystallographic methods; both structures have clear implications for the function of non-catalytic domains of full-length calpains in the calcium-mediated activation of the enzyme. The structure of minicalpain 1 is similar to previously solved structures of the protease core. Auto-inhibition in this system is most likely through rearrangements of a central helical/loop region near the active site cysteine, which occlude the substrate binding site. However, the structure of minicalpain 9 indicates that auto-inhibition in this enzyme is mediated through large intra-domain movements that misalign the catalytic triad. This disruption is reminiscent of the full-length inactive calpain conformation. The structures of the highly conserved, ubiquitously expressed human calpain 1 and the more tissue specific human calpain 9 indicate that although there are high levels of sequence conservation throughout the calpain family, isolated structures of family members are insufficient to explain the molecular mechanism of activation for this group of proteins.

Binding Sites↗
PubMed2006

Striatal function in generalized social phobia: a functional magnetic resonance imaging study.

BACKGROUND: Although evidence suggests the involvement of the amygdala in generalized social phobia (GSP), few studies have examined other neural regions. Clinical, preclinical, and dopamine receptor imaging studies demonstrating altered dopaminergic functioning in GSP suggest an association with striatal dysfunction. This is the first functional magnetic resonance imaging (fMRI) study to use a cognitive task known to involve the striatum to examine the neural correlates of GSP. We examined whether subjects with GSP had differential activation in striatal regions compared with healthy control subjects while engaged in a cognitive task that has been shown to activate striatal regions reliably. METHODS: Ten adult, unmedicated subjects with a primary DSM-IV diagnosis of GSP and 10 age-, gender-, and education-matched healthy comparison subjects underwent fMRI while performing the implicit sequence learning task. RESULTS: The GSP and healthy comparison subjects did not differ significantly on the behavioral performance of the task. Subjects with GSP, however, had significantly reduced neural activation related to implicit learning compared with healthy comparison subjects in the left caudate head, left inferior parietal lobe, and bilateral insula. CONCLUSIONS: These findings support the hypothesis that GSP is associated with striatal dysfunction and further the neurobiological understanding of this complex anxiety disorder.

Adult↗
PubMed2006

Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8).

Ubiquitin-specific protease 8 (USP8) hydrolyzes mono and polyubiquitylated targets such as epidermal growth factor receptors and is involved in clathrin-mediated internalization. In 1182 residues, USP8 contains multiple domains, including coiled-coil, rhodanese, and catalytic domains. We report the first high-resolution crystal structures of these domains and discuss their implications for USP8 function. The amino-terminal domain is a homodimer with a novel fold. It is composed of two five-helix bundles, where the first helices are swapped, and carboxyl-terminal helices are extended in an antiparallel fashion. The structure of the rhodanese domain, determined in complex with the E3 ligase NRDP1, reveals the canonical rhodanese fold but with a distorted primordial active site. The USP8 recognition domain of NRDP1 has a novel protein fold that interacts with a conserved peptide loop of the rhodanese domain. A consensus sequence of this loop is found in other NRDP1 targets, suggesting a common mode of interaction. The structure of the carboxyl-terminal catalytic domain of USP8 exhibits the conserved tripartite architecture but shows unique traits. Notably, the active site, including the ubiquitin binding pocket, is in a closed conformation, incompatible with substrate binding. The presence of a zinc ribbon subdomain near the ubiquitin binding site further suggests a polyubiquitin-specific binding site and a mechanism for substrate induced conformational changes.

Catalytic Domain↗
PubMed2006

Structure of human protein kinase C eta (PKCeta) C2 domain and identification of phosphorylation sites.

Protein kinase C eta (PKCeta) is one of several PKC isoforms found in humans. It is a novel PKC isoform in that it is activated by diacylglycerol and anionic phospholipids but not calcium. The crystal structure of the PKCeta-C2 domain, which is thought to mediate anionic phospholipid sensing in the protein, was determined at 1.75 A resolution. The structure is similar to that of the PKC epsilon C2 domain but with significant variations at the putative lipid-binding site. Two serine residues within PKC eta were identified in vitro as potential autophosphorylation sites. In the unphosphorylated structure both serines line the putative lipid-binding site and may therefore play a role in the lipid-regulation of the kinase.

Amino Acid Sequence↗
PubMed2006

Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus.

The Archaeoglobus fulgidus gene af0721 encodes CbiX(S), a small cobaltochelatase associated with the anaerobic biosynthesis of vitamin B12 (cobalamin). The protein was shown to have activity both in vivo and in vitro, catalyzing the insertion of Co2+ into sirohydrochlorin. The structure of CbiX(S) was determined in two different crystal forms and was shown to consist of a central mixed beta-sheet flanked by four alpha-helices, one of which originates in the C-terminus of a neighboring molecule. CbiX(S) is about half the size of other Class II tetrapyrrole chelatases. The overall topography of CbiX(S) exhibits substantial resemblance to both the N- and C-terminal regions of several members of the Class II metal chelatases involved in tetrapyrrole biosynthesis. Two histidines (His10 and His74), are in similar positions as the catalytic histidine residues in the anaerobic cobaltochelatase CbiK (His145 and His207). In light of the hypothesis that suggests the larger chelatases evolved via gene duplication and fusion from a CbiX(S)-like enzyme, the structure of AF0721 may represent that of an "ancestral" precursor of class II metal chelatases.

Archaeal Proteins↗
PubMed2006

Structural and biochemical study of effector molecule recognition by the E.coli glyoxylate and allantoin utilization regulatory protein AllR.

The interaction of Escherichia coli AllR regulator with operator DNA is disrupted by the effector molecule glyoxylate. This is a general, yet uncharacterized regulatory mechanism for the large IclR family of transcriptional regulators to which AllR belongs. The crystal structures of the C-terminal effector-binding domain of AllR regulator and its complex with glyoxylate were determined at 1.7 and 1.8 A, respectively. Residues involved in glyoxylate binding were explored in vitro and in vivo. Altering the residues Cys217, Ser234 and Ser236 resulted in glyoxylate-independent repression by AllR. Sequence analysis revealed low conservation of amino acid residues participating in effector binding among IclR regulators, which reflects potential chemical diversity of effector molecules, recognized by members of this family. Comparing the AllR structure to that of Thermotoga maritima TM0065, the other representative of the IclR family that has been structurally characterized, indicates that both proteins assume similar quaternary structures as a dimer of dimers. Mutations in the tetramerization region, which in AllR involve the Cys135-Cys142 region, resulted in dissociation of AllR tetramer to dimers in vitro and were functionally inactive in vivo. Glyoxylate does not appear to function through the inhibition of tetramerization. Using sedimentation velocity, glyoxylate was shown to conformationally change the AllR tetramer as well as monomer and dimer resulting in altered outline of AllR molecules.

Allantoin↗
PubMed2006

A functional genomics approach to the mode of action of apratoxin A.

The cyanobacterial metabolite apratoxin A (1) demonstrates potent cytotoxicity against tumor cell lines by a hitherto unknown mechanism. We have used functional genomics to elucidate the molecular basis for this activity. Gene expression profiling and DNA content analysis showed that apratoxin A induces G1-phase cell cycle arrest and apoptosis. Cell-based functional assays with a genome-wide collection of expression cDNAs showed that ectopic induction of fibroblast growth factor receptor (FGFR) signaling attenuates the apoptotic activity of apratoxin A. This natural product inhibited phosphorylation and activation of STAT3, a downstream effector of FGFR signaling. It also caused defects in FGF-dependent processes during zebrafish development, with concomitant reductions in expression levels of the FGF target gene mkp3. We conclude that apratoxin A mediates its antiproliferative activity through the induction of G1 cell cycle arrest and an apoptotic cascade, which is at least partially initiated through antagonism of FGF signaling via STAT3.

Animals↗
PubMed2006

The relationship of inflammatory bowel disease type and activity to psychological functioning and quality of life.

BACKGROUND & AIMS: We aimed to assess the relationship of disease type and disease activity with psychological functioning and quality of life (QOL) in a population-based cohort of patients with recently diagnosed inflammatory bowel disease (IBD). METHODS: A total of 388 individuals diagnosed within 7 years were recruited from a population-based registry of IBD patients for the Manitoba IBD Cohort Study. Participants completed a clinical interview and standardized self-report measures of positive and negative psychological functioning, and QOL. Disease activity was determined by symptom self-report over the prior 6 months; Harvey-Bradshaw or Powell-Tuck disease activity indices also were used. Disease type was determined through chart verification. RESULTS: Seventy-four percent of Crohn's disease and 66% of ulcerative colitis participants had active disease during the previous 6 months. Multivariate regression showed that those with active disease had higher levels of distress, health anxiety, and perceived stress, lower social support, well-being and mastery, and poorer disease-specific QOL, relative to those with inactive disease. Disease type was not contributory to psychological functioning or QOL. Pain anxiety (fear of pain) and pain-specific catastrophizing were not associated with disease activity, after controlling for other psychological variables. Participants with either active or inactive disease had suboptimal general QOL. CONCLUSIONS: Ulcerative colitis and Crohn's disease participants were not differentiated in their psychological profiles. Given the strong association between disease-specific QOL, psychological functioning, and disease activity, it is important to be aware of related difficulties in patients with active IBD. There is a continued impact on QOL by the disease, even when it is inactive.

Adaptation, Psychological↗
PubMed2006

On studying the connection between stress and IBD.

A number of investigators over the years have attempted to determine if a relationship exists between flares of inflammatory bowel disease (IBD) and stress. There are many complexities to addressing this issue, including determining the appropriate tools to measure stress, determining the appropriate measures of quantifying a disease flare and also determining the point at which the timing of the stress could be seen to be reasonably related to the onset of the flare. While advances have been made in understanding physiological responses to acute stress, it is unclear whether it is acute, chronic, or recurrent stress that might most impact on a chronic inflammatory disease. In the case of IBD, the disease itself poses a stress to the individual further clouding the issue.

Humans↗
PubMed2005

Illumination of the melanopsin signaling pathway.

In mammals, a small population of intrinsically photosensitive retinal ganglion cells (ipRGCs) plays a key role in the regulation of nonvisual photic responses, such as behavioral responses to light, pineal melatonin synthesis, pupillary light reflex, and sleep latency. These ipRGCs also express melanopsin (Opn4), a putative opsin-family photopigment that has been shown to play a role in mediating these nonvisual photic responses. Melanopsin is required for the function of this inner retinal pathway, but its precise role in generating photic responses has not yet been determined. We found that expression of melanopsin in Xenopus oocytes results in light-dependent activation of membrane currents through the Galpha(q)/Galpha(11) G protein pathway, with an action spectrum closely matching that of melanopsin-expressing ipRGCs and of behavioral responses to light in mice lacking rods and cones. When coexpressed with arrestins, melanopsin could use all-trans-retinaldehyde as a chromophore, which suggests that it may function as a bireactive opsin. We also found that melanopsin could activate the cation channel TRPC3, a mammalian homolog of the Drosophila phototransduction channels TRP and TRPL. Melanopsin therefore signals more like an invertebrate opsin than like a classical vertebrate rod-and-cone opsin.

Animals↗
PubMed2005

RNA profiling in circadian biology.

DNA arrays have become indispensable tools in the study of transcriptional output of the circadian clock and have enabled an increase in the number of outputs from tens to thousands. However, despite their widespread use, many challenges exist in accurately and sensitively identifying all transcriptional targets of the clock. This article discusses aspects of experimental design, including RNA-amplification strategies, data condensation methods, and other aspects that impact the use of these tools for the study of circadian biology.

Algorithms↗
PubMed2005

Hierarchical model of vulnerabilities for anxiety: replication and extension with a clinical sample.

This study served to replicate and extend our previously obtained hierarchical model of the relationships among general anxiety vulnerabilities, specific anxiety vulnerabilities and specific anxiety manifestations including panic symptoms, health anxiety, obsessive-compulsive symptoms and worry. Questionnaires assessing these variables, as well as positive affectivity and depressiveness, were administered to 125 outpatients seeking treatment for panic disorder, social anxiety disorder, obsessive-compulsive disorder, generalized anxiety disorder or major depressive disorder. The results, using a clinical sample, were highly consistent with the hierarchical model obtained in the previous study using a student sample. A more elaborate model, based on published theoretical and empirical evidence, was identified and tested, and similar results were obtained. Negative affectivity had expected direct positive effects on all of the specific anxiety and depression manifestations, with the exception of health anxiety, which showed a negative relationship, and OCD symptoms, which showed no relationship. Positive affectivity was found to be a specific risk factor for depression, while intolerance of uncertainty was found to be a specific risk factor for worry and depression. Finally, anxiety sensitivity appears to be a significant risk factor for panic and health anxiety.

Adult↗
PubMed2004

A gene atlas of the mouse and human protein-encoding transcriptomes.

The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom arrays that interrogate the expression of the vast majority of protein-encoding human and mouse genes and have used them to profile a panel of 79 human and 61 mouse tissues. The resulting data set provides the expression patterns for thousands of predicted genes, as well as known and poorly characterized genes, from mice and humans. We have explored this data set for global trends in gene expression, evaluated commonly used lines of evidence in gene prediction methodologies, and investigated patterns indicative of chromosomal organization of transcription. We describe hundreds of regions of correlated transcription and show that some are subject to both tissue and parental allele-specific expression, suggesting a link between spatial expression and imprinting.

Animals↗
PubMed2004

X-ray crystal structure of a galactose-specific C-type lectin possessing a novel decameric quaternary structure.

Rattlesnake venom lectin (RSL) from the western diamondback rattlesnake (Crotalus atrox) is an oligomeric galactose-specific C-type lectin. The X-ray crystal structure of RSL, in complex with lactose and thiodigalactoside, at 2.2 and 2.3 A resolution, respectively, reveals a decameric protein composed of two 5-fold symmetric pentamers arranged in a staggered, back-to-back orientation. Each monomer corresponds to a single canonical C-type lectin carbohydrate recognition domain devoid of accessory domains and is disulfide-bonded to a monomer in the other pentamer. The structure is the first example of that of a carbohydrate complex of a vertebrate galactose-specific C-type lectin. The 10 carbohydrate-binding sites, located on the rim of the decamer, suggest a role for multivalent interactions and a mechanism for RSL's ability to promote receptor cross-linking and cell aggregation.

Amino Acid Sequence↗
PubMed2004

Does elimination of placebo responders in a placebo run-in increase the treatment effect in randomized clinical trials? A meta-analytic evaluation.

The use of a placebo run-in phase, in which placebo responders are withdrawn from a study before random assignment to treatment condition, has been criticized as favoring the active treatment in clinical trials. We compared the effect size of randomized, placebo-controlled clinical trials (in the treatment of depression with selective serotonin reuptake inhibitors [SSRIs]) that include a placebo run-in phase with those that do not, using a meta-analytic approach. This study differed from earlier meta-analytic studies in that it considered only SSRIs and included only studies using continuous measures of depression, allowing for a more refined assessment of effect size. An extensive literature search identified 43 datasets published between 1980 and 2000 comparing placebo with SSRI and using a continuous measure of depression (usually the Hamilton Depression Rating Scale). We included only studies of at least 6 weeks' duration focusing on treatment for primary acute major depression in adults 18-65 years of age. Studies focusing on depression in specific medical illnesses were not included. Analysis of efficacy was based on 3047 subjects treated with an SSRI antidepressant and 3740 subjects treated with a placebo. There was no statistically significant difference in effect size between the clinical trials that had a placebo run-in phase followed by withdrawal of placebo responders and those trials that did not. Despite the lack of a statistically significant difference between studies of withdrawing early placebo responders and those not using this procedure, this approach is likely to continue to be used widely because it produces large absolute effect sizes. It is recommended that future studies clearly describe these procedures and report the number of subjects dropped from the study for early placebo response and other reasons.

Antidepressive Agents, Second-Generation↗
PubMed2004

Deficits in perceived social support associated with generalized social phobia.

Social phobia is a common anxiety disorder associated with significant impairment in social and occupational functioning. To date, few studies have examined the relationship between social phobia and perceived social support, a construct with important relationships to physical and mental health. The present study examined data from 2 widely used measures of perceived social support administered to 132 individuals with DSM-IV generalized social phobia. These data were compared with those obtained from a healthy control group and from several clinical and non-clinical samples reported in the literature. Persons with generalized social phobia scored significantly lower on both measures of social support compared with all other groups. It is suggested that deficits in perceived social support associated with generalized social phobia may play a role in the development of co-morbid problems and should be explicitly targeted by treatments for social phobia. Low correlations between perceived social support and social anxiety measures suggest that perceived support should be specifically evaluated in this population.

Adult↗