Biomedical subjects

John Kelly

Publications and source records attributed to John Kelly.

At least 19 recordsLinked to original sources

PubMed2026

Investigating the relationship between Toll-like receptor activity, low-grade inflammation, cognitive deficits, and antipsychotic drug dose in schizophrenia patients: a moderation analysis.

BACKGROUND: Schizophrenia (SZ) is a debilitating psychiatric disorder where patients experience cognitive decline. Antipsychotic drugs alleviate positive symptoms but do not improve cognitive performance. We previously demonstrated that Toll-like receptors (TLRs), involved in cytokine production, can predict cognitive deficits in SZ patients. In this study, we aim to investigate the potential moderating effects of antipsychotic drugs on the associations between cytokines, TLRs, and cognition. METHODS: In total, 280 participants (201 controls and 79 cases of SZ) were recruited in Ireland. Venous blood from the participants was stimulated with TLR ligands. Levels of cytokines were measured from plasma and post-blood stimulation. The participants were administered a battery of cognitive tasks using the Cambridge Neuropsychological Test Automated Battery and Wechsler Adult Intelligence Scale-IIIR. Olanzapine equivalents were calculated using the defined daily dose method. RESULTS: The results indicate that antipsychotic drug dose does not predict TLR activity or cognition, indicating that antipsychotic drug dose does not have a direct effect on cognition or TLR activity. However, the relationship between TLR4 activity and visual learning and memory is moderated by the antipsychotic drug dose (B = -0.065; p < 0.001), where increasing doses have a decreasing impact on their relationship. CONCLUSIONS: Our data indicate that the dose of antipsychotic drugs alone cannot predict changes in cognitive performance and TLR4-activity. It also suggests that antipsychotic drug doses significantly affect TLR activity and its relationship with cognition. These effects are more pronounced on some domains than others. These findings open up new avenues for understanding the complex interplay between antipsychotic drugs, TLRs, and cognitive deficits in SZ.

Humans↗

PubMed2007

Protein markers of ischemic insult in brain endothelial cells identified using 2D gel electrophoresis and ICAT-based quantitative proteomics.

The blood-brain barrier (BBB) is formed by endothelial cells of cerebral microvessels sealed by tight junctions. Ischemic brain injury is known to initiate a series of biochemical and molecular processes that lead to the disruption of the BBB, development of vascular inflammation, and subsequent neurovascular remodeling including angiogenesis. Molecular effectors of these changes are multiple and are regulated in a dynamic fashion. The current study was designed to analyze changes in cellular and secreted proteins in rat brain endothelial cells (BEC) exposed to ischemic insult in vitro using two complementary quantitative proteomic approaches: two-dimensional gel electrophoresis (2DE) and isotope-coded affinity tag (ICAT)-based proteomics. We show a comprehensive qualitative and quantitative comparison between the two proteomic methods applied to the same experimental system with respect to their reproducibility, specificity, and the type of proteins identified. In total, >160 proteins showed differential expression in response to the ischemic insult, with 38 identified by 2DE and 138 by ICAT. Only 15 proteins were commonly identified. ICAT showed superior reproducibility over 2DE and was more suitable for detecting small, large, basic, hydrophobic, and secreted proteins than 2DE. However, positive identification of proteins by MS/MS was more reliably done using a 2DE-based method compared to ICAT. Changes in proteins involved in nucleic acid, protein, and carbohydrate metabolism, signal transduction, cell structure, adhesion and motility, immunity and defense, cell cycle, and apoptosis were observed. The functional significance of observed protein changes was evaluated through a multifaceted protein classification and validation process, which included literature mining and comparative evaluation of protein changes in analogous in vitro and in vivo ischemia models. The comparative analyses of protein changes between the in vitro and in vivo models demonstrated a significant correlative relationship, emphasizing the 'translational' value of in vitro endothelial models in neurovascular research.

Aldehyde Oxidoreductases↗

PubMed2006

Glycosylation of Pseudomonas aeruginosa strain Pa5196 type IV pilins with mycobacterium-like alpha-1,5-linked d-Araf oligosaccharides.

Pseudomonas aeruginosa is a gram-negative bacterium that uses polar type IV pili for adherence to various materials and for rapid colonization of surfaces via twitching motility. Within the P. aeruginosa species, five distinct alleles encoding variants of the structural subunit PilA varying in amino acid sequence, length, and presence of posttranslational modifications have been identified. In this work, a combination of mass spectrometry and nuclear magnetic resonance spectroscopy was used to identify a novel glycan modification on the pilins of the group IV strain Pa5196. Group IV pilins continued to be modified in a lipopolysaccharide (wbpM) mutant of Pa5196, showing that, unlike group I strains, the pilins of group IV are not modified with the O-antigen unit of the background strain. Instead, the pilin glycan was determined to be an unusual homo-oligomer of alpha-1,5-linked d-arabinofuranose (d-Araf). This sugar is uncommon in prokaryotes, occurring mainly in the cell wall arabinogalactan and lipoarabinomannan (LAM) polymers of mycobacteria, including Mycobacterium tuberculosis and Mycobacterium leprae. Antibodies raised against M. tuberculosis LAM specifically identified the glycosylated pilins from Pa5196, confirming that the glycan is antigenically, as well as chemically, identical to those of Mycobacterium. P. aeruginosa Pa5196, a rapidly growing strain of low virulence that expresses large amounts of glycosylated type IV pilins on its surface, represents a genetically tractable model system for elucidation of alternate pathways for biosynthesis of d-Araf and its polymerization into mycobacterium-like alpha-1,5-linked oligosaccharides.

Amino Acid Sequence↗

PubMed2006

Calpain-cleaved collapsin response mediator protein-3 induces neuronal death after glutamate toxicity and cerebral ischemia.

Collapsin response mediator proteins (CRMPs) mediate growth cone collapse during development, but their roles in adult brains are not clear. Here we report the findings that the full-length CRMP-3 (p63) is a direct target of calpain that cleaves CRMP-3 at the N terminus (+76 amino acid). Interestingly, activated calpain in response to excitotoxicity in vitro and cerebral ischemia in vivo also cleaved CRMP-3, and the cleavage product of CRMP-3 (p54) underwent nuclear translocation during neuronal death. The expression of p54 was colocalized with the terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling-positive nuclei in glutamate-treated cerebellar granule neurons (CGNs) and in ischemic neurons located in the infarct core after focal cerebral ischemia, suggesting that p54 might be involved in neuronal death. Overexpression studies showed that p54, but not p63, caused death of human embryonic kidney cells and CGNs, whereas knock-down CRMP-3 expression by selective small interfering RNA protected neurons against glutamate toxicity. Collectively, these results reveal a novel role of CRMP-3 in that calpain cleavage of CRMP-3 and the subsequent nuclear translocation of the truncated CRMP-3 evokes neuronal death in response to excitotoxicity and cerebral ischemia. Our findings also establish a novel route of how calpain signals neuron death.

Animals↗

PubMed2006

Clinical laboratories, the select agent program, and biological surety (biosurety).

The threat of bioterrorism has led to increased concerns over the availability of biological select agents and toxins (BSAT). Congress has implemented several public laws that have led to the development of federal regulations by the Centers for Disease Control and Prevention (CDC) and the US Department of Agriculture. The CDC regulation 42 CFR 73 has a direct impact on all clinical laboratories that may at some time identify BSAT in a clinical specimen. The Department of Defense has imposed a more stringent layer of regulation called biological surety (biosurety) on top of the requirements of 42 CFR 73 for military laboratories that possess BSAT. However,42 CFR 73 falls into the framework of biosurety. Both sets of regulations have four pillars (safety, physical security, agent account-ability, and personnel reliability) that are built on a foundation of training and covered by a roof of management (operations and plans).

Bioterrorism↗

PubMed2006

Changes in flagellin glycosylation affect Campylobacter autoagglutination and virulence.

Analysis of the complete flagellin glycosylation locus of Campylobacter jejuni strain 81-176 revealed a less complex genomic organization than the corresponding region in the genome strain, C. jejuni NCTC 11168. Twenty-four of the 45 genes found between Cj1293 and Cj1337 in NCTC 11168 are missing in 81-176. Mutation of six new genes, in addition to three previously reported, resulted in a non-motile phenotype, consistent with a role in synthesis of pseudaminic acid (PseAc) or transfer of PseAc to flagellin. Mutation of Cj1316c or pseA had been shown to result in loss of the acetamidino form of pseudaminic acid (PseAm). Mutation of a second gene also resulted in loss of PseAm, as well as a minor modification that appears to be PseAm extended with N-acetyl-glutamic acid. Previously described mutants in C. jejuni 81-176 and Campylobacter coli VC167 that produced flagella lacking PseAm or PseAc failed to autoagglutinate. This suggests that interactions between modifications on adjacent flagella filaments are required for autoagglutination. Mutants (81-176) defective in autoagglutination showed a modest reduction in adherence and invasion of INT407 cells. However, there was a qualitative difference in binding patterns to INT407 cells using GFP-labelled 81-176 and mutants lacking PseAm. A mutant lacking PseAm was attenuated in the ferret diarrhoeal disease model.

Agglutination↗

PubMed2006

Identification of genes involved in the biosynthesis and attachment of Methanococcus voltae N-linked glycans: insight into N-linked glycosylation pathways in Archaea.

N-linked glycosylation is recognized as an important post-translational modification across all three domains of life. However, the understanding of the genetic pathways for the assembly and attachment of N-linked glycans in eukaryotic and bacterial systems far outweighs the knowledge of comparable processes in Archaea. The recent characterization of a novel trisaccharide [beta-ManpNAcA6Thr-(1-4)-beta-GlcpNAc3NAcA-(1-3)-beta-GlcpNAc]N-linked to asparagine residues in Methanococcus voltae flagellin and S-layer proteins affords new opportunities to investigate N-linked glycosylation pathways in Archaea. In this contribution, the insertional inactivation of several candidate genes within the M. voltae genome and their resulting effects on flagellin and S-layer glycosylation are reported. Two of the candidate genes were shown to have effects on flagellin and S-layer protein molecular mass and N-linked glycan structure. Further examination revealed inactivation of either of these two genes also had effects on flagella assembly. These genes, designated agl (archaeal glycosylation) genes, include a glycosyl transferase (aglA) involved in the attachment of the terminal sugar to the glycan and an STT3 oligosaccharyl transferase homologue (aglB) involved in the transfer of the complete glycan to the flagellin and S-layer proteins. These findings document the first experimental evidence for genes involved in any glycosylation process within the domain Archaea.

Archaea↗

PubMed2006

Can spot urine protein/creatinine ratio replace 24 h urine protein in usual clinical nephrology?

BACKGROUND: This prospective study was designed to assess whether a single urine specimen, collected at the time of clinical assessment, could be used to estimate 24 h urinary protein excretion. METHODS: The spot urinary protein/creatinine ratio (P/Cr) and 24 h urine protein and creatinine excretion were determined from 103 patients attending a nephrology clinic. Using the spot urine P/Cr, a regression equation was derived, predicting 24 h protein excretion. The performance of the regression equation was tested on a new cohort of 85 patients. Within this new cohort, agreement between the predicted and the actual 24 h urinary protein excretion was assessed using the Bland-Altman technique. The ability of spot urine P/Cr and dipstick urinalysis to predict different threshold levels of protein excretion was assessed using a series of receiver operator curves. RESULTS: A logarithmic relationship exists between the spot P/Cr and 24 h protein excretion, with a correlation of 0.92, P < 0.0001. Agreement between the actual and predicted 24 h urine protein and between spot and 24 h urine P/Cr ratios was suboptimal at higher levels of protein excretion. Discriminant spot urine P/Cr values reliably predicted protein excretion thresholds of 0.3, 0.5, 1.0 and 3.0 g/day. Urinalysis was a poor test for quantitating protein excretion. CONCLUSION: Random spot urinary P/Cr predicts actual 24 h protein excretion with reasonable accuracy in patients with lower levels of protein excretion but is unreliable in patients with high protein excretion and should not be used in the clinical setting unless 24 h urine collection is unavailable.

Cohort Studies↗

PubMed2006

Progressive resistance training during hemodialysis: rationale and method of a randomized-controlled trial.

Skeletal muscle wasting in patients receiving maintenance hemodialysis (HD) has been well documented. The rationale for prescribing progressive resistance training (PRT) in this cohort in an attempt to reverse this catabolism and induce a wide spectrum of physiological, functional, and psychological health-related adaptations is extremely strong. Unfortunately, the barriers to exercise adoption in this cohort are many, which may explain the persisting sedentariness of this population and the lack of widespread clinical programs such as are now commonplace in cardiac rehabilitation and pulmonary rehabilitation units. Current health care practices for HD patients do not address the negative health issues of inactivity and muscle wasting. Therefore, we conducted the first randomized-controlled trial to prescribe PRT during maintenance HD treatment. The purpose of this paper is to present the rationale and methodology that we utilized for implementing intradialytic PRT in a conventional outpatient HD clinic. Potential areas for modification of PRT regimens in this setting are also presented.

Exercise Therapy↗

PubMed2006

Proteomic analysis of Campylobacter jejuni 11168 biofilms reveals a role for the motility complex in biofilm formation.

Campylobacter jejuni remains the leading cause of bacterial gastroenteritis in developed countries, and yet little is known concerning the mechanisms by which this fastidious organism survives within its environment. We have demonstrated that C. jejuni 11168 can form biofilms on a variety of surfaces. Proteomic analyses of planktonic and biofilm-grown cells demonstrated differences in protein expression profiles between the two growth modes. Proteins involved in the motility complex, including the flagellins (FlaA, FlaB), the filament cap (FliD), the basal body (FlgG, FlgG2), and the chemotactic protein (CheA), all exhibited higher levels of expression in biofilms than found in stationary-phase planktonic cells. Additional proteins with enhanced expression included those involved in the general (GroEL, GroES) and oxidative (Tpx, Ahp) stress responses, two known adhesins (Peb1, FlaC), and proteins involved in biosynthesis, energy generation, and catabolic functions. An aflagellate flhA mutant not only lost the ability to attach to a solid matrix and form a biofilm but could no longer form a pellicle at the air-liquid interface of a liquid culture. Insertional inactivation of genes that affect the flagellar filament (fliA, flaA, flaB, flaG) or the expression of the cell adhesin (flaC) also resulted in a delay in pellicle formation. These findings demonstrate that the flagellar motility complex plays a crucial role in the initial attachment of C. jejuni 11168 to solid surfaces during biofilm formation as well as in the cell-to-cell interactions required for pellicle formation. Continued expression of the motility complex in mature biofilms is unusual and suggests a role for the flagellar apparatus in the biofilm phenotype.

Bacterial Adhesion↗

PubMed2006

Biosynthesis of the N-linked glycan in Campylobacter jejuni and addition onto protein through block transfer.

In eukaryotes, N-linked protein glycosylation is a universal modification involving addition of preformed oligosaccharides to select Asn-Xaa-Ser/Thr motifs and influencing multiple biological events. We recently demonstrated that Campylobacter jejuni is the first member of the Bacteria to possess an N-linked glycan pathway. In this study, high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) was applied to probe and quantitate C. jejuni N-glycan biosynthesis in vivo. To confirm HR-MAS NMR findings, glycosylation mutants were screened for chicken colonization potential, and glycoproteins were examined by mass spectrometry and lectin blotting. Consistent with the mechanism in eukaryotes, the combined data indicate that bacterial glycans are assembled en bloc, emphasizing the evolutionary conservation of protein N glycosylation. We also show that under the conditions examined, PglG plays no role in glycan biosynthesis, PglI is the glucosyltransferase and the putative ABC transporter, and WlaB (renamed PglK) is required for glycan assembly. These studies underpin the mechanism of N-linked protein glycosylation in Bacteria and provide a simple model system for investigating protein glycosylation and for exploitation in glycoengineering.

Animals↗

PubMed2005

A role for TSLP in the development of inflammation in an asthma model.

Thymic stromal lymphopoietin (TSLP) is a cytokine that promotes CD4+ T cell homeostasis. We now demonstrate that TSLP is required to mount a normal CD4+ T cell-mediated inflammatory response. TSLP acts directly on naive, but not, memory CD4+ T cells, and promotes their proliferation in response to antigen. In addition, TSLP exerts an effect indirectly through DCs to promote Th2 differentiation of CD4+ T cells. Correspondingly, TSLP receptor (TSLPR) knockout (KO) mice exhibit strong Th1 responses, with high levels of interleukin (IL)-12, interferon-gamma, and immunoglobulin (Ig) G2a, but low production of IL-4, -5, -10, -13, and IgE; moreover, CD4+ T cells from these animals proliferate less well in response to antigen. Furthermore, TSLPR KO mice fail to develop an inflammatory lung response to inhaled antigen unless supplemented with wild-type CD4+ T cells. This underscores an important role for this cytokine in the development of inflammatory and/or allergic responses in vivo.

Animals↗

PubMed2005

Huntingtin interacting protein 1 modulates the transcriptional activity of nuclear hormone receptors.

Internalization of activated receptors regulates signaling, and endocytic adaptor proteins are well-characterized in clathrin-mediated uptake. One of these adaptor proteins, huntingtin interacting protein 1 (HIP1), induces cellular transformation and is overexpressed in some prostate cancers. We have discovered that HIP1 associates with the androgen receptor through a central coiled coil domain and is recruited to DNA response elements upon androgen stimulation. HIP1 is a novel androgen receptor regulator, significantly repressing transcription when knocked down using a silencing RNA approach and activating transcription when overexpressed. We have also identified a functional nuclear localization signal at the COOH terminus of HIP1, which contributes to the nuclear translocation of the protein. In conclusion, we have discovered that HIP1 is a nucleocytoplasmic protein capable of associating with membranes and DNA response elements and regulating transcription.

Amino Acid Sequence↗

PubMed2005

Pretreatment and during treatment risk factors for dropout among patients with substance use disorders.

OBJECTIVE: The aim of this study was to use pretreatment and treatment factors to predict dropout from residential substance use disorder program and to examine how the treatment environment modifies the risk for dropout. METHOD: This study assessed 3649 male patients at entry to residential substance use disorder treatment and obtained information about their perceptions of the treatment environment. RESULTS: Baseline factors that predicted dropout included younger age, greater cognitive dysfunction, more drug use, and lower severity of alcohol dependence. Patients in treatment environments appraised as low in support or high in control also were more likely to drop out. Further, patients at high risk of dropout were especially likely to dropout when treated in a highly controlling treatment environment. CONCLUSION: Better screening of risk factors for dropout and efforts to create a less controlling treatment environment may result in increased retention in substance use disorder treatment.

Adult↗

PubMed2005

Identification and characterization of the unique N-linked glycan common to the flagellins and S-layer glycoprotein of Methanococcus voltae.

The flagellum of Methanococcus voltae is composed of four structural flagellin proteins FlaA, FlaB1, FlaB2, and FlaB3. These proteins possess a total of 15 potential N-linked sequons (NX(S/T)) and show a mass shift on an SDS-polyacrylamide gel indicating significant post-translational modification. We describe here the structural characterization of the flagellin glycan from M. voltae using mass spectrometry to examine the proteolytic digests of the flagellin proteins in combination with NMR analysis of the purified glycan using a sensitive, cryogenically cooled probe. Nano-liquid chromatography-tandem mass spectrometry analysis of the proteolytic digests of the flagellin proteins revealed that they are post-translationally modified with a novel N-linked trisaccharide of mass 779 Da that is composed of three sugar residues with masses of 318, 258, and 203 Da, respectively. In every instance the glycan is attached to the peptide through the asparagine residue of a typical N-linked sequon. The glycan modification has been observed on 14 of the 15 sequon sites present on the four flagellin structural proteins. The novel glycan structure elucidated by NMR analysis was shown to be a trisaccharide composed of beta-ManpNAcA6Thr-(1-4)-beta-Glc-pNAc3NAcA-(1-3)-beta-GlcpNAc linked to Asn. In addition, the same trisaccharide was identified on a tryptic peptide of the S-layer protein from this organism implicating a common N-linked glycosylation pathway.

Amino Acid Sequence↗

PubMed2005

The performance of SolarScan: an automated dermoscopy image analysis instrument for the diagnosis of primary melanoma.

OBJECTIVE: To describe the diagnostic performance of SolarScan (Polartechnics Ltd, Sydney, Australia), an automated instrument for the diagnosis of primary melanoma. DESIGN: Images from a data set of 2430 lesions (382 were melanomas; median Breslow thickness, 0.36 mm) were divided into a training set and an independent test set at a ratio of approximately 2:1. A diagnostic algorithm (absolute diagnosis of melanoma vs benign lesion and estimated probability of melanoma) was developed and its performance described on the test set. High-quality clinical and dermoscopy images with a detailed patient history for 78 lesions (13 of which were melanomas) from the test set were given to various clinicians to compare their diagnostic accuracy with that of SolarScan. SETTING: Seven specialist referral centers and 2 general practice skin cancer clinics from 3 continents. Comparison between clinician diagnosis and SolarScan diagnosis was by 3 dermoscopy experts, 4 dermatologists, 3 trainee dermatologists, and 3 general practitioners. PATIENTS: Images of the melanocytic lesions were obtained from patients who required either excision or digital monitoring to exclude malignancy. MAIN OUTCOME MEASURES: Sensitivity, specificity, the area under the receiver operator characteristic curve, median probability for the diagnosis of melanoma, a direct comparison of SolarScan with diagnoses performed by humans, and interinstrument and intrainstrument reproducibility. RESULTS: The melanocytic-only diagnostic model was highly reproducible in the test set and gave a sensitivity of 91% (95% confidence interval [CI], 86%-96%) and specificity of 68% (95% CI, 64%-72%) for melanoma. SolarScan had comparable or superior sensitivity and specificity (85% vs 65%) compared with those of experts (90% vs 59%), dermatologists (81% vs 60%), trainees (85% vs 36%; P =.06), and general practitioners (62% vs 63%). The intraclass correlation coefficient of intrainstrument repeatability was 0.86 (95% CI, 0.83-0.88), indicating an excellent repeatability. There was no significant interinstrument variation (P = .80). CONCLUSIONS: SolarScan is a robust diagnostic instrument for pigmented or partially pigmented melanocytic lesions of the skin. Preliminary data suggest that its performance is comparable or superior to that of a range of clinician groups. However, these findings should be confirmed in a formal clinical trial.

Algorithms↗

PubMed2005

Comparative performance of 4 dermoscopic algorithms by nonexperts for the diagnosis of melanocytic lesions.

OBJECTIVE: To assess 4 dermoscopy methods in a nonexpert setting. DESIGN: Sixty-one medical practitioners, mainly primary care physicians in Australia, were trained in 4 dermoscopy algorithms. Participants then assessed macroscopic and dermoscopic images of 40 melanocytic skin lesions. Each of the dermoscopic images was assessed with pattern analysis, the 7-point checklist, the ABCD rule, and the Menzies method. RESULTS: The Menzies method showed the highest sensitivity, 84.6%, for the diagnosis of melanoma, followed by the 7-point checklist (81.4%), the ABCD rule (77.5%), pattern analysis (68.4%), and assessment of a macroscopic image (60.9%). Pattern analysis and assessment of the macroscopic image showed the highest specificity, 85.3% and 85.4%, respectively. The ABCD rule showed a specificity of 80.4%; the Menzies method, 77.7%; and the 7-point checklist, 73%. The Menzies method had a diagnostic accuracy of 81.1%; the ABCD rule, 79.0%; the 7-point checklist, 77.2%; pattern analysis, 76.8%; and clinical assessment, 73.2%. CONCLUSIONS: All algorithms performed well in the hands of relatively inexpert practitioners who had undertaken self-guided training provided on compact disc. The Menzies method showed the highest diagnostic accuracy and sensitivity for melanoma diagnosis and was preferred by study participants.

Algorithms↗

PubMed2005

Best practice recommendations for surgical care in weight loss surgery.

OBJECTIVE: To establish evidence-based guidelines for best practices for surgical care in weight loss surgery (WLS). RESEARCH METHODS AND PROCEDURES: We carried out a systematic search of English-language literature on WLS in MEDLINE and the Cochrane Library. Key words were used to narrow the field for a selective review of abstracts. Data extraction was performed, and evidence categories were assigned according to a grading system based on established evidence-based models. RESULTS: We assessed types of WLS, recommended guidelines for appropriateness, developed strategies for medical error reduction, established criteria for credentialing of systems and practitioners, and specified research needed for the future. DISCUSSION: Surgeon training, credentialing, and type of surgery performed were identified as key factors in patient safety. Other important issues in the delivery of best practice care included appropriate patient selection; use of a multidisciplinary treatment team; facility staffing, equipment, and administrative support; and early recognition and proper management of complications.

Biliopancreatic Diversion↗