CiteULike: jyuh's Williams

Efficacy and Safety of Renal Tubule Cell Therapy for Acute Renal Failure

James Tumlin — 2008-07-04T10:52:06-00:00

J Am Soc Nephrol, Vol. 19, No. 5. (1 May 2008), pp. 1034-1040.

The mortality rate for patients with acute renal failure (ARF) remains unacceptably high. Although dialysis removes waste products and corrects fluid imbalance, it does not perform the absorptive, metabolic, endocrine, and immunologic functions of normal renal tubule cells. The renal tubule assist device (RAD) is composed of a conventional hemofilter lined by monolayers of renal cells. For testing whether short-term (up to 72 h) treatment with the RAD would improve survival in patients with ARF compared with conventional continuous renal replacement therapy (CRRT), a Phase II, multicenter, randomized, controlled, open-label trial involving 58 patients who had ARF and required CRRT was performed. Forty patients received continuous venovenous hemofiltration + RAD, and 18 received CRRT alone. The primary efficacy end point was all-cause mortality at 28 d; additional end points included all-cause mortality at 90 and 180 d, time to recovery of renal function, time to intensive care unit and hospital discharge, and safety. At day 28, the mortality rate was 33% in the RAD group and 61% in the CRRT group. Kaplan-Meier analysis revealed that survival through day 180 was significantly improved in the RAD group, and Cox proportional hazards models suggested that the risk for death was approximately 50% of that observed in the CRRT-alone group. RAD therapy was also associated with more rapid recovery of kidney function, was well tolerated, and had the expected adverse event profile for critically ill patients with ARF. 10.1681/ASN.2007080895

Systolic pressure is all that matters

Bryan Williams — 2008-07-02T06:31:16-00:00

The Lancet, Vol. 371, No. 9631., pp. 2219-2221.

Grading quality of evidence and strength of recommendations for diagnostic tests and strategies.

HJ Schünemann — 2008-06-14T03:09:10-00:00

BMJ (Clinical research ed.), Vol. 336, No. 7653. (17 May 2008), pp. 1106-1110.

Bioluminescence imaging of hollow fibers in living animals: its application in monitoring molecular pathways

Guo-Jun Zhang — 2008-05-20T03:52:12-00:00

Nat. Protocols, Vol. 3, No. 5. (May 2008), pp. 891-899.

Nutrition in End-Stage Liver Disease: Principles and Practice

Alastair O'Brien — 2008-05-17T03:16:02-00:00

Gastroenterology, Vol. 134, No. 6. (May 2008), pp. 1729-1740.

Discovery of a Cytokine and Its Receptor by Functional Screening of the Extracellular Proteome

Haishan Lin — 2008-05-13T01:59:36-00:00

Science, Vol. 320, No. 5877. (9 May 2008), pp. 807-811.

To understand the system of secreted proteins and receptors involved in cell-cell signaling, we produced a comprehensive set of recombinant secreted proteins and the extracellular domains of transmembrane proteins, which constitute most of the protein components of the extracellular space. Each protein was tested in a suite of assays that measured metabolic, growth, or transcriptional responses in diverse cell types. The pattern of responses across assays was analyzed for the degree of functional selectivity of each protein. One of the highly selective proteins was a previously undescribed ligand, designated interleukin-34 (IL-34), which stimulates monocyte viability but does not affect responses in a wide spectrum of other assays. In a separate functional screen, we used a collection of extracellular domains of transmembrane proteins to discover the receptor for IL-34, which was a known cytokine receptor, colony-stimulating factor 1 (also called macrophage colony-stimulating factor) receptor. This systematic approach is thus useful for discovering new ligands and receptors and assessing the functional selectivity of extracellular regulatory proteins. 10.1126/science.1154370

ACC/AHA/SCAI 2005 guideline update for percutaneous coronary intervention: a report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines (ACC/AHA/SCAI Writing Committee to Update 2001 Guidelines for Percutaneous Coronary Intervention).

SC Smith — 2008-05-12T01:57:12-00:00

Circulation, Vol. 113, No. 7. (21 February 2006)

ACC/AHA/ASNC guidelines for the clinical use of cardiac radionuclide imaging--executive summary: a report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines (ACC/AHA/ASNC Committee to Revise the 1995 Guidelines for the Clinical Use of Cardiac Radionuclide Imaging).

FJ Klocke — 2008-05-12T01:58:32-00:00

Journal of the American College of Cardiology, Vol. 42, No. 7. (1 October 2003), pp. 1318-1333.

High-throughput functional annotation and data mining with the Blast2GO suite

Stefan Gotz — 2008-04-29T11:39:18-00:00

Nucl. Acids Res. (29 April 2008), gkn176.

Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data. 10.1093/nar/gkn176

Amplification of complex gene libraries by emulsion PCR

Richard Williams — 2006-06-24T00:10:07-00:00

Nature Methods, Vol. 3, No. 7., pp. 545-550.

Type 1 fimbriate strains of escherichia coli initiate renal parenchymal scarring

N Topley — 2008-05-08T03:07:59-00:00

Kidney Int, Vol. 36, No. 4. (October 1989), pp. 609-616.

ProtQuant: a tool for the label-free quantification of MudPIT proteomics data.

SM Bridges — 2008-05-07T09:18:27-00:00

BMC bioinformatics, Vol. 8 Suppl 7 (2007)

BACKGROUND: Effective and economical methods for quantitative analysis of high throughput mass spectrometry data are essential to meet the goals of directly identifying, characterizing, and quantifying proteins from a particular cell state. Multidimensional Protein Identification Technology (MudPIT) is a common approach used in protein identification. Two types of methods are used to detect differential protein expression in MudPIT experiments: those involving stable isotope labelling and the so-called label-free methods. Label-free methods are based on the relationship between protein abundance and sampling statistics such as peptide count, spectral count, probabilistic peptide identification scores, and sum of peptide Sequest XCorr scores (SigmaXCorr). Although a number of label-free methods for protein quantification have been described in the literature, there are few publicly available tools that implement these methods. We describe ProtQuant, a Java-based tool for label-free protein quantification that uses the previously published SigmaXCorr method for quantification and includes an improved method for handling missing data. RESULTS: ProtQuant was designed for ease of use and portability for the bench scientist. It implements the SigmaXCorr method for label free protein quantification from MudPIT datasets. ProtQuant has a graphical user interface, accepts multiple file formats, is not limited by the size of the input files, and can process any number of replicates and any number of treatments. In addition, ProtQuant implements a new method for dealing with missing values for peptide scores used for quantification. The new algorithm, called SigmaXCorr*, uses "below threshold" peptide scores to provide meaningful non-zero values for missing data points. We demonstrate that SigmaXCorr* produces an average reduction in false positive identifications of differential expression of 25% compared to SigmaXCorr. CONCLUSION: ProtQuant is a tool for protein quantification built for multi-platform use with an intuitive user interface. ProtQuant efficiently and uniquely performs label-free quantification of protein datasets produced with Sequest and provides the user with facilities for data management and analysis. Importantly, ProtQuant is available as a self-installing executable for the Windows environment used by many bench scientists.

Cell cycle markers in clinical oncology.

GH Williams — 2008-04-27T02:08:29-00:00

Current opinion in cell biology, Vol. 19, No. 6. (December 2007), pp. 672-679.

Analysis of complex and redundant pathways that control proliferation, differentiation, apoptosis and DNA damage response by global genome wide analysis is an intensive area of investigation aimed at identifying unique molecular signatures of prognostic significance in cancer. An alternative approach is to focus on the cell cycle machinery, which acts as an integration point for information transduced through upstream signalling pathways. Analysis of the DNA replication licensing pathway and the mitotic regulatory machinery in tumour biopsy material is now leading to the identification of novel biomarkers that are being exploited in cancer detection and prognostic assessment.

Data Mining in Genomics

Jae Lee — 2008-01-18T00:02:24-00:00

Clinics in Laboratory Medicine, Vol. 28, No. 1. (March 2008), pp. 145-166.

This article reviews important emerging statistical concepts, data mining techniques, and applications that have been recently developed and used for genomic data analysis. First, general background and some critical issues in genomic data mining are summarized. A novel concept of statistical significance is described, the so-called "false discovery rate"--the rate of false-positives among all positive findings--which has been suggested to control the error rate of numerous false-positives in large screening biological data analysis. Two recent statistical testing methods are then introduced: significance analysis of microarray and local pooled error tests. Statistical modeling in genomic data analysis is then presented, such as analysis of variance and heterogeneous error modeling approaches that have been suggested for analyzing microarray data obtained from multiple experimental or biological conditions. Two sections then describe data exploration and discovery tools largely termed as supervised learning and unsupervised learning. The former approaches include several multivariate statistical methods to investigate coexpression patterns of multiple genes, and the latter are the classification methods to discover genomic biomarker signatures for predicting important subclasses of human diseases. The last section briefly summarizes various genomic data mining approaches in biomedical pathway analysis and patient outcome or chemotherapeutic response prediction.

Some simple tests for spatial effects around putative sources of health risk.

AB Lawson — 2008-04-07T02:42:47-00:00

Biometrical journal. Biometrische Zeitschrift, Vol. 49, No. 4. (August 2007), pp. 493-504.

The need for tests dealing with different features of small area health data is less important with the increase in computation speed of computers and the access to MCMC methods. However there are many situations where exploratory testing could be useful and where MCMC methods are not readily usable or available. In this paper, a number of simple tests are derived for the logistic model for case events. This model assumes that a control disease is available and that the events have a binary label relating to case or control state. The tests are derived from likelihood considerations and Monte Carlo critical regions are examined. A simulated evaluation of the tests is presented in terms of Monte Carlo power. A data example is considered.

Activator Protein-1 Contributes to High NaCl-induced Increase in Tonicity-responsive Enhancer/Osmotic Response Element-binding Protein Transactivating Activity

Carlos Irarrazabal — 2008-04-02T01:38:58-00:00

J. Biol. Chem., Vol. 283, No. 5. (1 February 2008), pp. 2554-2563.

Tonicity-responsive enhancer/osmotic response element-binding protein (TonEBP/OREBP) is a Rel protein that activates transcription of osmoprotective genes at high extracellular NaCl. Other Rel proteins NFAT14 and NF-kappaB complex with activator protein-1 (AP-1) to transactivate target genes through interaction at composite NFAT/NF-kappaBmiddle dotAP-1 sites. TonEBP/OREBP target genes commonly have one or more conserved AP-1 binding sites near TonEBP/OREBP cognate elements (OREs). Also, TonEBP/OREBP and the AP-1 proteins c-Fos and c-Jun are all activated by high NaCl. We now find, using an OREmiddle dotAP-1 reporter from the target aldose reductase gene or the same reporter with a mutated AP-1 site, that upon stimulation by high extracellular NaCl, 1) the presence of a wild type, but not a mutated, AP-1 site contributes to TonEBP/OREBP-dependent transcription and 2) AP-1 dominant negative constructs inhibit TonEBP/OREBP-dependent transcription provided the AP-1 site is not mutated. Using supershifts and an OREmiddle dotAP-1 probe, we find c-Fos and c-Jun present in combination with TonEBP/OREBP. Also, c-Fos and c-Jun coimmunoprecipitate with TonEBP/OREBP, indicating physical association. Small interfering RNA knockdown of either c-Fos or c-Jun inhibits high NaCl-induced increase of mRNA abundance of the TonEBP/OREBP target genes AR and BGT1. Furthermore, a dominant negative AP-1 also reduces high NaCl-induced increase of TonEBP/OREBP transactivating activity. Inhibition of p38, which is known to stimulate TonEBP/OREBP transcriptional activity, reduces high NaCl-dependent transcription of an OREmiddle dotAP-1 reporter only if the AP-1 site is intact. Thus, AP-1 is part of the TonEBP/OREBP enhanceosome, and its role in high NaCl-induced activation of TonEBP/OREBP may require p38 activity. 10.1074/jbc.M703490200

Relationships between non-occupational cadmium exposure and expression of nine cytochrome P450 forms in human liver and kidney cortex samples.

JR Baker — 2008-03-25T09:15:03-00:00

Biochem Pharmacol, Vol. 62, No. 6. (15 September 2001), pp. 713-721.

This study was undertaken to assess associations between age, gender, cigarette smoke and non-workplace cadmium exposure, and liver pathology and inter-individual variation in cytochrome P450 (CYP) expression in human tissues. Autopsy specimens of twenty-eight Queensland residents whose ages ranged from 3 to 89 years were analyzed for the presence of nine CYP protein isoforms by immunoblotting. All subjects were Caucasians and their liver cadmium contents ranged from 0.11 to 3.95 microg/g wet weight, while their kidney cadmium contents were in the range of 2 to 63 microg/g wet weight. CYP1A2, CYP2A6, CYP2D6, CYP3A4, and CYP3A5 were detected in liver but not in kidney, and CYP1A1 and CYP1B1 were not found in liver or kidney. Lowered liver CYP2C8/19 protein contents were found to be associated with liver pathology. Importantly, we show elevated levels of CYP2C9 protein to be associated with cadmium accumulation in liver. No mechanism that explains this association is apparent, but there are two possibilities that require further study. One is that variation in CYP2C9 protein levels may be, in part, attributed to an individual's non-workplace exposure to cadmium, or an individual's CYP2C9 genotype may be a risk factor for cadmium accumulation. A positive correlation was found between liver CYP3A4 protein and subject age. Levels of liver CYP1A2 protein, but not other CYP forms, were increased in people more exposed to cigarette smoke, but there was no association between CYP1A2 protein and cadmium. CYP2A6 protein was found in all liver samples and CYP2A6 gene typing indicated the absence of CYP2A6 null allele (CYP2A6(D)) in this sample group, confirming very low prevalence of homozygous CYP2A6(D) in Caucasians. CYP2A6 gene types W/W, W/C, and C/C were not associated with variations in liver microsomal CYP2A6 protein. CYP2D6 protein was absent in all twenty-five kidney samples tested but was detectable in liver samples of all but two subjects, indicating the prevalence of the CYP2D6 null allele (CYP2D6(D)) in this sample group to be about 7%, typical of Caucasian populations.

Elevations in renal interstitial hydrostatic pressure and 20-hydroxyeicosatetraenoic acid contribute to pressure natriuresis.

JM Williams — 2008-03-25T09:11:15-00:00

Hypertension, Vol. 49, No. 3. (March 2007), pp. 687-694.

This study examined the role of changes in renal interstitial pressure on the renal levels of cytochrome P450 metabolites of arachidonic acid and compared the effects of inhibition of the formation of 20-hydroxyeicosatetraenoic acid (20-HETE) and epoxyeicosatrienoic acids with 1-aminobenzotriazole on the pressure-natriuretic response versus that seen after administration of HET0016, a more selective inhibitor of the formation of 20-HETE. Renal interstitial pressure rose by 3.4+/-0.3 mm Hg, and the levels of 20-HETE in renal cortical tissue doubled when renal perfusion pressure was increased from 100 to 160 mm Hg. Removal of the renal capsule prevented the increase in renal interstitial pressure and 20-HETE levels after an elevation in renal perfusion pressure. Urine flow and sodium excretion increased 5-fold when renal perfusion pressure was increased from 106 to 160 mm Hg. The administration of 1-aminobenzotriazole (50 mg/kg, IP) or HET0016 (10 mg/kg IV bolus plus 1 mg/kg per hour of infusion) decreased the pressure-natriuretic response by 50% and inhibited the renal formation of 20-HETE and epoxyeicosatrienoic acids by 90% and 50%, respectively. Administration of a lower dose of HET0016 (1 mg/kg per hour, IV) selectively reduced the formation of 20-HETE by 80% without inhibiting renal epoxygenase activity and blunted the pressure-natriuretic response by 42%. These results indicate that elevations in renal perfusion pressure increase 20-HETE levels in the kidney secondary to a rise in renal interstitial pressure. They also suggest that 20-HETE, rather than epoxyeicosatrienoic acids, modulates the pressure-natriuretic response, because selective blockade of the formation of 20-HETE with HET0016 blunts the response to the same extent as that seen after inhibition of the formation of 20-HETE and epoxyeicosatrienoic acids with 1-aminobenzotriazole.

YPED: a web-accessible database system for protein expression analysis.

MA Shifman — 2008-03-13T16:14:40-00:00

J Proteome Res, Vol. 6, No. 10. (October 2007), pp. 4019-4024.

We have developed an integrated web-accessible software system called the Yale Protein Expression Database (YPED) to address the need for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED is an open source system which integrates gel analysis results with protein identifications from DIGE experiments. The system associates the DIGE gel spots and image, analyzed with DeCyder, with mass spectrometric protein identifications from selected gel spots. Following in gel trypsin digestion, proteins in spots of interest are analyzed using MALDI-TOF/TOF on an AB 4700 or, more recently, on an AB 4800 with protein identifications performed by Mascot in conjunction with the AB GPS Explorer system. In addition to DIGE, YPED currently handles protein identifications from MudPIT, iTRAQ, and ICAT experiments. Sample descriptions are compatible with the evolving MIAPE standards. Tandem MS/MS results from MudPIT, and ICAT analyses are validated with the Trans-Proteomic Pipeline and then stored in the database for viewing and linking to the identified proteins. Researchers can view, subset, and download their data through a secure Web interface that includes a table containing proteins identified, a sample summary, the sample description, and a clickable gel image for DIGE samples. Tools are available to facilitate sample comparison and the viewing of phosphoproteins. A summary report with PANTHER Classification System annotations is also available to aid in biological interpretation of the results. The source code is open-source and is available from http://yped.med.yale.edu/yped_dist.

Hemodialyzed type I and type II diabetic patients in the US: Characteristics, glycemic control, and survival.

ME Williams — 2008-03-12T07:55:30-00:00

Kidney Int, Vol. 70, No. 8. (October 2006), pp. 1503-1509.

Diabetes mellitus (DM) constitutes a major end-stage renal disease (ESRD) health problem. Glycemic control is fundamental to the management of diabetes and its complications, and relies on monitoring of hyperglycemia. We therefore performed a primary data analysis of glycemic control and survival on a large national ESRD database. Ninety-five percent of patients with DM had type II diabetes (N = 23,504), and five percent had type I diabetes (N = 1,371). For the combined population, the mean hemoglobin A1c (HgbA1c) was 6.77%, and the mean random blood glucose was 168 mg/dl. Mean HgbA1c values were >7.0% in 35% and >8.5% in 14%. Mean HgbA1c values were below 5% in 11.3% of patients. Type I study patients tended to have higher HgbA1c values. Most patients (75.8%) had three or more random blood glucose determinations within 90 days preceding the HgbA1c measurement. The HgbA1c showed only a weak correlation with mean random glucose values (R2 0.3716; s.e. = 1.36). The survival rates in the subsequent 12-month period ranged from 80 to 85% across different HgbA1c strata. Kaplan-Meier survival curves grouped by HgbA1c levels showed no correlation between HgbA1c and survival at 12 months. More studies are needed to refine recommendations for the role of HgbA1c and glycemic control in this patient population.

Transgenic blockade of interleukin 6 transsignaling abrogates inflammation.

B Rabe — 2008-03-10T02:29:14-00:00

Blood, Vol. 111, No. 3. (1 February 2008), pp. 1021-1028.

The immunoregulatory cytokine interleukin6 (IL6) acts in a pro- and anti-inflammatory fashion. Synthesized by myeloid cells, fibroblasts and endothelial cells, IL6 on target cells, binds to the IL6 receptor (IL6R) and signals via complex formation with the ubiquitously expressed gp130 receptor. Paradoxically, most cells that respond to IL6 during inflammatory states do not express the IL6R and are themselves not directly responsive to the cytokine. A naturally occurring soluble form of the IL6R renders all cells responsive to IL6. This alternative signaling process is called IL6 transsignaling. Here we developed a transgenic strategy based on the overexpression of the soluble form of gp130, which specifically blocks all IL6 responses mediated by the soluble IL6R but does not affect IL6 responses via the membrane bound IL6R. In these mice, inflammatory processes are blocked as in IL6(-/-) mice, strongly arguing for a major role of the soluble IL6R during inflammation in vivo.

Agrin and neuregulin, expanding roles and implications for therapeutics.

Stacey Williams — 2008-03-10T02:25:43-00:00

Biotechnol Adv (4 December 2007)

Agrin and neuregulin are broadly expressed molecules that have significant developmental roles. Here we review the diverse temporal and spatial expression patterns and functions of these molecules and the impact that dysregulation may have on a number of disease states. Many know agrin as a modulator of synaptogenesis and the neuregulins for their prominent role in breast cancer; this review elaborates on many of the other proposed functions for these molecules both in the nervous system and elsewhere. In several instances we discuss the possible use of agrin, neuregulin and related molecules as therapeutic agents.

Coffee Consumption Is Associated With Higher Plasma Adiponectin Concentrations in Women With or Without Type 2 Diabetes: A prospective cohort study

Catherine Williams — 2008-03-03T02:24:44-00:00

Diabetes Care, Vol. 31, No. 3. (1 March 2008), pp. 504-507.

To test whether the beneficial effects of coffee consumption in metabolism might be explained by changes in circulating levels of adiponectin, we evaluated self-reported habitual coffee and tea consumption and caffeine intake as predictors of plasma adiponectin concentrations among 982 diabetic and 1,058 nondiabetic women without cardiovascular disease from the Nurses' Health Study. Women with and without diabetes who drank [≥]4 cups of coffee per day had significantly higher adiponectin concentrations than those who didn't drink coffee regularly (7.7 vs. 6.1 microg/ml, respectively, in diabetic women, P = 0.004; 15.0 vs. 13.2 microg/ml in nondiabetic women, P = 0.04). Similar associations were observed for caffeine intake. We confirm previously reported inverse associations of coffee consumption with inflammatory markers, C-reactive protein, and tumor necrosis factor-alpha receptor II. Adjustment for adiponectin did not weaken these associations, and adjustment for inflammatory markers did not attenuate the association between coffee consumption and adiponectin concentrations. High consumption of caffeine-containing coffee is associated with higher adiponectin and lower inflammatory marker concentrations. 10.2337/dc07-1952

Factors affecting survival in advanced chronic kidney disease patients who choose not to receive dialysis.

CF Wong — 2008-02-13T07:12:39-00:00

Ren Fail, Vol. 29, No. 6. (2007), pp. 653-659.

INTRODUCTION: Non-dialytic treatment (NDT) has become a recognized and important modality of treatment in end stage renal disease (ESRD) in certain groups of chronic kidney disease (CKD) patients. However, little is known about the prognosis of these NDT patients in terms of hospitalization rates and survival. We analyzed our experience in managing these NDT with a multidisciplinary team (MDT) approach over a three-year period. PATIENTS AND METHODS: The Renal Unit at the Royal Liverpool University Hospital set up a dedicated MDT clinic to manage NDT patients in January 2003. Patients approaching end stage chronic kidney disease who chose not to dialyse were recruited from other nephrologists. The study group was classified according to age band (<70 years, 71-80 years, and >80 years), estimated glomerular filtration rate (eGFR) (<10 ml/min, 11-20 ml/min, and >20 ml/min) according to the Modified Diet In Renal Disease formula and Stoke comorbidity grade (SCG). The SCG is a validated scoring system for the survival of patients on renal replacement therapy. We also used the ERA-EDTA primary renal diagnosis codes. As there are no existing standards for NDT patients, we used the U.K. national set for haemodialysis patients as a reference and target for our NDT patients. Data was collected prospectively. RESULTS: The median age was 79 years and the male: female ratio was approximately 1. The most common primary cause of kidney disease in the NDT study population was chronic renal failure of unknown cause n = 22 (31%), but the most common identifiable cause was diabetic nephropathy, n = 20 (28%). The most common comorbidity was ischaemic heart disease n = 25 (34%). Those achieving the standards for anaemia were 78% at referral. Only 30% of the NDT patients achieved the standard for blood pressure (<130/80 mmHg) at referral. Forty-three patients (60%) had no admissions at all. There were a total of 30 patients admitted on 58 occasions. Thirty-one (53%) of these were due to a non-renal cause. The median length of stay for the other NDT patients was 10 days. The median overall survival (life expectancy) was 1.95 years. The one-year overall survival was 65%. SCG was an independent prognostic factor in predicting survival in NDT patients studied (p = 0.005), the hazard ratio being 2.53, for each incremental increase in the SCG. At one year, the survival for comorbidity grade 0, 1 and 2 were 83%, 70% and 56% respectively. Of the 28 patients who died, 20 did so at home (71%). DISCUSSION: The NDT of ESRD has become an important alternative modality in renal replacement therapy. With the emergence of epidemic proportions of CKD, more elderly patients with progressive renal disease will need to make informed decisions regarding renal replacement therapy. There is likely to be increasing number of elderly patients that will tolerate dialysis badly and who will be very dependent on others. We believe that there should be a multidisciplinary approach to assist the ESRD patients in choosing their modality of renal replacement therapy, and with an agreed care plan to support these patients in managing their chosen modality to achieve the best possible quality of life. There should be integrated services with primary care, community nurses, and palliative care teams to enable the majority of the patient's treatment to be carried out at home and to allow a dignified death. However. there was a statistically significant trend for shorter survival among those with greater comorbidities, as determined by the SCG. This is the first report of the potential importance of SCG as an independent prognostic factor in NDT patients. This will help us to counsel our patients in the future about their prognosis if they choose NDT as their modality of renal replacement therapy. CONCLUSION: Our prospective study is the first and currently the largest observational study of a multidisciplinary approach in the management of NDT patients. SCG was an independent prognostic factor in predicting survival. In those patients who chose not to dialyse, SCG provides a potentially useful indication of expected prognosis.

Correction of disturbed pathophysiology of hepatic failure by albumin dialysis.

R Williams — 2008-02-08T07:48:14-00:00

Hepatobiliary Pancreat Dis Int, Vol. 7, No. 1. (February 2008), pp. 19-24.

Hypertension and impaired renal function accompany juvenile obesity: The effect of prenatal diet

PJ Williams — 2008-01-23T09:27:36-00:00

Kidney Int, Vol. 72, No. 3. (11 April 2007), pp. 279-289.

Discovery of tissue-specific exons using comprehensive human exon microarrays

Tyson Clark — 2007-04-25T00:43:39-00:00

Genome Biology, Vol. 8 (24 April 2007), R64.

Best practice in primary care pathology: review 6

WSA Smellie — 2008-01-02T09:53:38-00:00

J Clin Pathol, Vol. 60, No. 3. (1 March 2007), pp. 225-234.

This sixth best practice review examines four series of common primary care questions in laboratory medicine: (1) laboratory monitoring in hypertension and heart failure abnormalities; (2) markers of inflammatory joint disease; (3) laboratory investigation of chronic diarrhoea; and (4) mumps and chickenpox. The review is presented in question-answer format, referenced for each question series. The recommendations represent a precis of guidance found using a standardised literature search of national and international guidance notes, consensus statements, health policy documents and evidence-based medicine reviews, supplemented by Medline Embase searches to identify relevant primary research documents. They are not standards but form a guide to be set in the clinical context. Most are consensus based rather than evidence based. They will be updated periodically to take account of new information. 10.1136/jcp.2006.040014

Evaluation of nausea and vomiting.

K Scorza — 2008-01-02T08:37:35-00:00

Am Fam Physician, Vol. 76, No. 1. (1 July 2007), pp. 76-84.

A comprehensive history and physical examination can often reveal the cause of nausea and vomiting, making further evaluation unnecessary. Acute symptoms generally are the result of infectious, inflammatory, or iatrogenic causes. Most infections are self-limiting and require minimal intervention; iatrogenic causes can be resolved by removing the offending agent. Chronic symptoms are usually a pathologic response to any of a variety of conditions. Gastrointestinal etiologies include obstruction, functional disorders, and organic diseases. Central nervous system etiologies are primarily related to conditions that increase intracranial pressure, and typically cause other neurologic signs. Pregnancy is the most common endocrinologic cause of nausea and must be considered in any woman of childbearing age. Numerous metabolic abnormalities and psychiatric diagnoses also may cause nausea and vomiting. Evaluation should first focus on detecting any emergencies or complications that require hospitalization. Attention should then turn to identifying the underlying cause and providing specific therapies. When the cause cannot be determined, empiric therapy with an antiemetic is appropriate. Initial diagnostic testing should generally be limited to basic laboratory tests and plain radiography. Further testing, such as upper endoscopy or computed tomography of the abdomen, should be determined by clinical suspicion based on a complete history and physical examination.

Researchers Misunderstand Confidence Intervals and Standard Error Bars

Sarah Belia — 2006-03-03T14:09:23-00:00

Psychological Methods, Vol. 10, No. 4. (December 2005), pp. 389-396.

Little is known about researchers' understanding of confidence intervals (CIs) and standard error (SE) bars. Authors of journal articles in psychology, behavioral neuroscience, and medicine were invited to visit a Web site where they adjusted a figure until they judged 2 means, with error bars, to be just statistically significantly different (p SE bars, and do not appreciate the importance of whether the 2 means are independent or come from a repeated measures design. Better guidelines for researchers and less ambiguous graphical conventions are needed before the advantages of CIs for research communication can be realized.

Gene Profiling of Keloid Fibroblasts Shows Altered Expression in Multiple Fibrosis-Associated Pathways.

Joan C Smith — 2007-12-29T09:55:27-00:00

J Invest Dermatol (8 November 2007)

Keloids are benign tumors of the dermis that form during a protracted wound healing process. Susceptibility to keloid formation occurs predominantly in people of African and Asian descent. The key alteration(s) responsible for keloid formation has not been identified and there is no satisfactory treatment for this disorder. The altered regulatory mechanism is limited to dermal wound healing, although several diseases characterized by an exaggerated response to injury are prevalent in individuals of African ancestry. We have observed a complex pattern of phenotypic differences in keloid fibroblasts grown in standard culture medium or induced by hydrocortisone (HC). In this study Affymetrix-based microarray was performed on RNA obtained from fibroblasts cultured from normal scars and keloids grown in the absence and presence of HC. We observed differential regulation of approximately 500 genes of the 38,000 represented on the Affymetrix chip. Of particular interest was increased expression of several IGF-binding and IGF-binding-related proteins and decreased expression of a subset of Wnt pathway inhibitors and multiple IL-1-inducible genes. Increased expression of connective tissue growth factor and insulin-like growth factor binding protein-3 was observed in keloid fibroblasts only in the presence of HC. These findings support a role for multiple fibrosis-related pathways in the pathogenesis of keloids.Journal of Investigative Dermatology advance online publication, 8 November 2007; doi:10.1038/sj.jid.5701149.

Mesenchymal to epithelial transition in development and disease.

CL Chaffer — 2007-12-29T07:17:19-00:00

Cells Tissues Organs, Vol. 185, No. 1-3. (2007), pp. 7-19.

Cellular plasticity is fundamental to embryonic development. The importance of cellular transitions in development is first apparent during gastrulation when the process of epithelial to mesenchymal transition transforms polarized epithelial cells into migratory mesenchymal cells that constitute the embryonic and extraembryonic mesoderm. It is now widely accepted that this developmental pathway is exploited in various disease states, including cancer progression. The loss of epithelial characteristics and the acquisition of a mesenchymal-like migratory phenotype are crucial to the development of invasive carcinoma and metastasis. However, given the morphological similarities between primary tumour and metastatic lesions, it is likely that tumour cells re-activate certain epithelial properties through a mesenchymal to epithelial transition (MET) at the secondary site, although this is yet to be proven. MET is also an essential developmental process and has been extensively studied in kidney organogenesis and somitogenesis. In this review we describe the process of MET, highlight important mediators, and discuss their implication in the context of cancer progression.

Epithelial--mesenchymal and mesenchymal--epithelial transitions in carcinoma progression.

H Hugo — 2007-12-29T07:16:31-00:00

J Cell Physiol, Vol. 213, No. 2. (November 2007), pp. 374-383.

Like a set of bookends, cellular, molecular, and genetic changes of the beginnings of life mirror those of one of the most common cause of death--metastatic cancer. Epithelial to mesenchymal transition (EMT) is an important change in cell phenotype which allows the escape of epithelial cells from the structural constraints imposed by tissue architecture, and was first recognized by Elizabeth Hay in the early to mid 1980's to be a central process in early embryonic morphogenesis. Reversals of these changes, termed mesenchymal to epithelial transitions (METs), also occur and are important in tissue construction in normal development. Over the last decade, evidence has mounted for EMT as the means through which solid tissue epithelial cancers invade and metastasize. However, demonstrating this potentially rapid and transient process in vivo has proven difficult and data connecting the relevance of this process to tumor progression is still somewhat limited and controversial. Evidence for an important role of MET in the development of clinically overt metastases is starting to accumulate, and model systems have been developed. This review details recent advances in the knowledge of EMT as it occurs in breast development and carcinoma and prostate cancer progression, and highlights the role that MET plays in cancer metastasis. Finally, perspectives from a clinical and translational viewpoint are discussed.

2007 chronic angina focused update of the ACC/AHA 2002 guidelines for the management of patients with chronic stable angina: a report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines Writing Group to develop the focused update of the 2002 guidelines for the management of patients with chronic stable angina.

TD Fraker — 2007-12-17T02:22:00-00:00

J Am Coll Cardiol, Vol. 50, No. 23. (4 December 2007), pp. 2264-2274.

Community screening for non-insulin-dependent diabetes mellitus: self-testing for post-prandial glycosuria.

MJ Davies — 2007-12-15T15:46:50-00:00

Q J Med, Vol. 86, No. 10. (October 1993), pp. 677-684.

Recent requirements of the GP contract have included the testing of random urine samples from all patients aged 16-75 years for glycosuria. As a means of detecting diabetes this will be both inefficient and wasteful of resources, because of the method employed and age group screened. We examined a simple method for screening large populations for non-insulin-dependent diabetes mellitus using self-testing for post-prandial glycosuria, and compared its performance to that using fasting plasma glucose and haemoglobin A1. The study involved five general practices, screening over 13,000 subjects aged between 45 and 70 years. Of the 13,795 subjects screened, 10,348 responded (75%). Glycosuria was detected in 343 subjects (3.3%), of whom 330 (95.9%) attended for oral glucose tolerance testing. Of these 99 (30%) had newly diagnosed diabetes, 56 (17%) had impaired glucose tolerance. A further 65 subjects were identified as having diabetes but were not on a register of cases. Prevalence of diabetes in this age group rose from 2.26% to 4.1%. In a normal population control group (442 subjects from Ely), this system gave a sensitivity of 43%, specificity of 98% and positive predictive value of 53%, and compared favourably to the use of a fasting plasma glucose of 6 mmol/l, which gave a sensitivity of 65%, but only a specificity of 64% and positive predictive value of 9%. These results support the use of this simple system in large population screening for diabetes.

Effects of a fixed combination of perindopril and indapamide on macrovascular and microvascular outcomes in patients with type 2 diabetes mellitus (the ADVANCE trial): a randomised controlled trial.

A Patel — 2007-12-14T12:54:47-00:00

Lancet, Vol. 370, No. 9590. (8 September 2007), pp. 829-840.

BACKGROUND: Blood pressure is an important determinant of the risks of macrovascular and microvascular complications of type 2 diabetes, and guidelines recommend intensive lowering of blood pressure for diabetic patients with hypertension. We assessed the effects of the routine administration of an angiotensin converting enzyme (ACE) inhibitor-diuretic combination on serious vascular events in patients with diabetes, irrespective of initial blood pressure levels or the use of other blood pressure lowering drugs. METHODS: The trial was done by 215 collaborating centres in 20 countries. After a 6-week active run-in period, 11 140 patients with type 2 diabetes were randomised to treatment with a fixed combination of perindopril and indapamide or matching placebo, in addition to current therapy. The primary endpoints were composites of major macrovascular and microvascular events, defined as death from cardiovascular disease, non-fatal stroke or non-fatal myocardial infarction, and new or worsening renal or diabetic eye disease, and analysis was by intention-to-treat. The macrovascular and microvascular composites were analysed jointly and separately. This trial is registered with ClinicalTrials.gov, number NCT00145925. FINDINGS: After a mean of 4.3 years of follow-up, 73% of those assigned active treatment and 74% of those assigned control remained on randomised treatment. Compared with patients assigned placebo, those assigned active therapy had a mean reduction in systolic blood pressure of 5.6 mm Hg and diastolic blood pressure of 2.2 mm Hg. The relative risk of a major macrovascular or microvascular event was reduced by 9% (861 [15.5%] active vs 938 [16.8%] placebo; hazard ratio 0.91, 95% CI 0.83-1.00, p=0.04). The separate reductions in macrovascular and microvascular events were similar but were not independently significant (macrovascular 0.92; 0.81-1.04, p=0.16; microvascular 0.91; 0.80-1.04, p=0.16). The relative risk of death from cardiovascular disease was reduced by 18% (211 [3.8%] active vs 257 [4.6%] placebo; 0.82, 0.68-0.98, p=0.03) and death from any cause was reduced by 14% (408 [7.3%] active vs 471 [8.5%] placebo; 0.86, 0.75-0.98, p=0.03). There was no evidence that the effects of the study treatment differed by initial blood pressure level or concomitant use of other treatments at baseline. INTERPRETATION: Routine administration of a fixed combination of perindopril and indapamide to patients with type 2 diabetes was well tolerated and reduced the risks of major vascular events, including death. Although the confidence limits were wide, the results suggest that over 5 years, one death due to any cause would be averted among every 79 patients assigned active therapy.

Exercise Testing in Asymptomatic Adults: A Statement for Professionals From the American Heart Association Council on Clinical Cardiology, Subcommittee on Exercise, Cardiac Rehabilitation, and Prevention

Michael Lauer — 2007-11-28T14:45:29-00:00

Circulation, Vol. 112, No. 5. (2 August 2005), pp. 771-776.

Along with coronary artery calcium scanning, ankle-brachial index measurement, and carotid artery ultrasound, exercise electrocardiography has been proposed as a screening tool for asymptomatic subjects thought to be at intermediate risk for developing clinical coronary disease. A wealth of data indicate that exercise testing can be used to assess and refine prognosis, particularly when emphasis is placed on nonelectrocardiographic measures such as exercise capacity, chronotropic response, heart rate recovery, and ventricular ectopy. Nevertheless, randomized trial data on the clinical value of screening exercise testing are absent; that is, it is not known whether a strategy of routine screening exercise testing in selected subjects reduces the risk for premature mortality or major cardiac morbidity. The writing group believes that a large-scale randomized trial of such a strategy should be performed. 10.1161/CIRCULATIONAHA.105.166543

Biological stress response terminology: Integrating the concepts of adaptive response and preconditioning stress within a hormetic dose-response framework.

EJ Calabrese — 2007-11-24T10:14:54-00:00

Toxicol Appl Pharmacol, Vol. 222, No. 1. (1 July 2007), pp. 122-128.

Many biological subdisciplines that regularly assess dose-response relationships have identified an evolutionarily conserved process in which a low dose of a stressful stimulus activates an adaptive response that increases the resistance of the cell or organism to a moderate to severe level of stress. Due to a lack of frequent interaction among scientists in these many areas, there has emerged a broad range of terms that describe such dose-response relationships. This situation has become problematic because the different terms describe a family of similar biological responses (e.g., adaptive response, preconditioning, hormesis), adversely affecting interdisciplinary communication, and possibly even obscuring generalizable features and central biological concepts. With support from scientists in a broad range of disciplines, this article offers a set of recommendations we believe can achieve greater conceptual harmony in dose-response terminology, as well as better understanding and communication across the broad spectrum of biological disciplines.

TGF-beta1 stimulates the release of pre-formed bFGF from renal proximal tubular cells.

SG Jones — 2007-11-20T01:14:41-00:00

Kidney Int, Vol. 56, No. 1. (July 1999), pp. 83-91.

BACKGROUND: It is now clear that the progression of renal disease is closely correlated to the degree of renal interstitial fibrosis. We have previously demonstrated that the renal proximal tubular epithelial cell may contribute to the fibrotic response by the generation of profibrotic cytokines. Transforming growth factor-beta1 (TGF-beta1) and basic fibroblast growth factor (bFGF) are two of a group of profibrotic cytokines that have been associated with the development of renal interstitial fibrosis. In this study, we have examined the influence of TGF-beta1 on the generation of bFGF by renal tubular epithelial cells. METHODS: HK2 cells were grown to confluence and were serum deprived and stimulated with recombinant TGF-beta1 under serum-free conditions. Subsequently, supernatant, cell-associated, intracellular, and matrix-associated bFGF concentrations were determined by enzyme-linked immunosorbent assay (ELISA). bFGF mRNA expression was examined by reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: The exposure of confluent serum-deprived HK2 cells to TGF-beta1 led to a significant increase in bFGF concentration in the cell culture supernatant. Twenty-four hours following the addition of 10 ng/ml TGF-beta1, this represented a twofold increase in bFGF concentration (control, 102 pg/ml, N = 24, vs. 202 pg/ml, N = 19, P = 0.0001). Despite the increase in bFGF concentration in the supernatant, there was no change in the expression of bFGF mRNA following the addition of TGF-beta1. The addition of 10 ng/ml of TGF-beta1 led to a 30% decrease in the total cell-associated bFGF concentration (control, 8.51 ng/ml, N = 16, TGF-beta1, 6.01 ng/ml, N = 13, P = 0.0042). This decrease in intracellular bFGF was associated with a 15% reduction in anti-bFGF antibody binding to fixed permeabilized cells, following the addition of 10 ng/ml of recombinant TGF-beta1 (N = 9, P = 0.0007), suggesting that the mechanism of stimulation of bFGF by TGF-beta1 involved the release of preformed bFGF from within the cells. In addition, following the addition of TGF-beta1, there was a significant dose-dependent decrease in the amount of bFGF sequestered in the extracellular matrix. At a dose of 10 ng/ml TGF-beta, this represented a greater than sevenfold decrease (N = 9, P = 0.0007) in matrix-bound bFGF, although this represented less than 3% of the total bFGF released into the supernatant. CONCLUSION: The data presented suggest that the main mechanism by which TGF-beta1 stimulates bFGF generation by proximal tubular epithelial cells is by stimulation of the secretion of preformed cytokine from within the cells.

Effects of pyridoxamine in combined phase 2 studies of patients with type 1 and type 2 diabetes and overt nephropathy.

ME Williams — 2007-11-15T09:31:59-00:00

Am J Nephrol, Vol. 27, No. 6. (2007), pp. 605-614.

BACKGROUND/AIMS: Treatments of diabetic nephropathy (DN) delay the onset of end-stage renal disease. We report the results of safety/tolerability studies in patients with overt nephropathy and type 1/type 2 diabetes treated with pyridoxamine, a broad inhibitor of advanced glycation. METHODS: The two 24-week studies were multicenter Phase 2 trials in patients under standard-of-care. In PYR-206, patients were randomized 1:1 and had baseline serum creatinine (bSCr) <or=2.0 mg/dl. In PYR-205/207, randomization was 2:1 and bSCr was <or=2.0 for PYR-205 and >or=2.0 but <or=3.5 mg/dl for PYR-207. Treated patients (122 active, 90 placebo) received 50 mg pyridoxamine twice daily in PYR-206; PYR-205/207 patients were escalated to 250 mg twice daily. RESULTS: Adverse events were balanced between the groups (p = NS). Slight imbalances, mainly in the PYR-205/207 groups, were noted in deaths (from diverse causes, p = NS) and serious adverse events (p = 0.05) that were attributed to pre-existing conditions. In a merged data set, pyridoxamine significantly reduced the change from baseline in serum creatinine (p < 0.03). In patients similar to the RENAAL/IDNT studies (bSCr >or=1.3 mg/dl, type 2 diabetes), a treatment effect was observed on the rise in serum creatinine (p = 0.007). No differences in urinary albumin excretion were seen. Urinary TGF-beta1 also tended to decrease with pyridoxamine (p = 0.049) as did the CML and CEL AGEs. CONCLUSION: These data provide a foundation for further evaluation of this AGE inhibitor in DN.

Screening for type 2 diabetes: literature review and economic modelling.

N Waugh — 2007-11-15T03:30:11-00:00

Health Technol Assess, Vol. 11, No. 17. (May 2007)

OBJECTIVES: To reconsider the aims of screening for undiagnosed diabetes, and whether screening should be for other abnormalities of glucose metabolism such as impaired glucose tolerance (IGT), or the 'metabolic syndrome'. Also to update the previous review for the National Screening Committee (NSC) on screening for diabetes, including reviewing choice of screening test; to consider what measures would be taken if IGT and impaired fasting glucose (IFG) were identified by screening, and in particular to examine evidence on treatment to prevent progression to diabetes in these groups; to examine the cost-effectiveness of screening; and to consider groups at higher risk at which screening might be targeted. DATA SOURCES: Electronic databases were searched up to the end of June 2005. REVIEW METHODS: Literature searches and review concentrated on evidence published since the last review of screening, both reviews and primary studies. The review of economic studies included only those models that covered screening. The new modelling extended an existing diabetes treatment model by developing a screening module. The NSC has a set of criteria, which it applies to new screening proposals. These criteria cover the condition, the screening test or tests, treatment and the screening programme. Screening for diabetes was considered using these criteria. RESULTS: Detection of lesser degrees of glucose intolerance such as IGT is worthwhile, partly because the risk of cardiovascular disease (CVD) can be reduced by treatment aimed at reducing cholesterol level and blood pressure, and partly because some diabetes can be prevented. Several trials have shown that both lifestyle measures and pharmacological treatment can reduce the proportion of people with IGT who would otherwise develop diabetes. Screening could be two-stage, starting with the selection of people at higher risk. The second-stage choice of test for blood glucose remains a problem, as in the last review for NSC. The best test is the oral glucose tolerance test (OGTT), but it is the most expensive, is inconvenient and has weak reproducibility. Fasting plasma glucose would miss people with IGT. Glycated haemoglobin does not require fasting, and may be the best compromise. It may be that more people would be tested and diagnosed if the more convenient test was used, rather than the OGTT. Five economic studies assessed the costs and short-term outcomes of using different screening tests. None examined the long-term impact of different proportions of false negatives. All considered the costs that would be incurred and the numbers identified by different tests, or different cut-offs. Results differed depending on different assumptions. They did not give a clear guide as to which test would be the best in any UK screening programme, but all recognised that the choice of cut-off would be a compromise between sensitivity and specificity; there is no perfect test. The modelling exercise concluded that screening for diabetes appears to be cost-effective for the 40-70-year age band, more so for the older age bands, but even in the 40-49-year age group, the incremental cost-effectiveness ratio for screening versus no screening is only 10,216 pounds per quality-adjusted life-year. Screening is more cost-effective for people in the hypertensive and obese subgroups and the costs of screening are offset in many groups by lower future treatment costs. The cost-effectiveness of screening is determined as much by, if not more than, assumptions about the degree of control of blood glucose and future treatment protocols than by assumptions relating to the screening programme. The very low cost now of statins is also an important factor. Although the prevalence of diabetes increases with age, the relative risk of CVD falls, reducing the benefits of screening. Screening for diabetes meets most of the NSC criteria, but probably fails on three: criterion 12, on optimisation of existing management of the condition; criterion 13, which requires that there should be evidence from high-quality randomised controlled trials (RCTs) showing that a screening programme would reduce mortality or morbidity; and criterion 18, that there should be adequate staffing and facilities for all aspects of the programme. It is uncertain whether criterion 19, that all other options, including prevention, should have been considered, is met. The issue here is whether all methods of improving lifestyles in order to reduce obesity and increase exercise have been sufficiently tried. The rise in overweight and obesity suggests that health promotion interventions have not so far been effective. CONCLUSIONS: The case for screening for undiagnosed diabetes is probably somewhat stronger than it was at the last review, because of the greater options for reduction of CVD, principally through the use of statins, and because of the rising prevalence of obesity and hence type 2 diabetes. However, there is also a good case for screening for IGT, with the aim of preventing some future diabetes and reducing CVD. Further research is needed into the duration of undiagnosed diabetes, and whether the rise in blood glucose levels is linear throughout or whether there may be a slower initial phase followed by an acceleration around the time of clinical diagnosis. This has implications for the interval after which screening would be repeated. Further research is also needed into the natural history of IGT, and in particular what determines progression to diabetes. An RCT of the type required by NSC criterion 13 is under way but will not report for about 7 years.

Proteomic identification of proteins associated with the osmoregulatory transcription factor TonEBP/OREBP: functional effects of Hsp90 and PARP-1.

Y Chen — 2007-11-10T23:10:22-00:00

Am J Physiol Renal Physiol, Vol. 292, No. 3. (March 2007)

Hypertonicity (e.g., high NaCl) activates the transcription factor tonicity-responsive enhancer/osmotic response element-binding protein (TonEBP/OREBP), increasing transcription of protective genes. In the present studies, by stably expressing amino acids 1-547 of TonEBP/OREBP in HEK 293 cells and immunoprecipitating it plus associated proteins from the nuclei of cells exposed to high NaCl, we identify 14 proteins that are physically associated with TonEBP/OREBP. The associated proteins fall into several classes: 1) DNA-dependent protein kinase, both its catalytic subunit and regulatory subunit, Ku86; 2) RNA helicases, namely RNA helicase A, nucleolar RNA helicase II/Gu, and DEAD-box RNA helicase p72; 3) small or heterogeneous nuclear ribonucleoproteins (snRNPs or hnRNPs), namely U5 snRNP-specific 116 kDa protein, U5 snRNP-specific 200 kDa protein, hnRNP U, hnRNP M, hnRNP K, and hnRNP F; 4) heat shock proteins, namely Hsp90beta and Hsc70; and 5) poly(ADP-ribose) polymerase-1 (PARP-1). We confirm identification of most of the proteins by Western analysis and also demonstrate by electrophoretic mobility-shift assay that they are present in the large complex that binds specifically along with TonEBP/OREBP to its cognate DNA element. In addition, we find that PARP-1 and Hsp90 modulate TonEBP/OREBP activity. PARP-1 expression reduces TonEBP/OREBP transcriptional activity and the activity of its transactivating domain. Hsp90 enhances those activities and sustains the increased abundance of TonEBP/OREBP protein in cells exposed to high NaCl.

A genome scan for ESRD in black families enriched for nondiabetic nephropathy.

BI Freedman — 2007-11-06T04:33:20-00:00

J Am Soc Nephrol, Vol. 15, No. 10. (October 2004), pp. 2719-2727.

Nephropathy is a complex disorder, with predisposition influenced by the interplay of both genetic and environmental factors. As part of an effort to map genes that predispose to ESRD, a genome scan was performed in 264 black pedigrees that contained 296 ESRD-affected sibling pairs using multipoint nonparametric linkage analysis methods. The cause of ESRD in index cases was consistent with hypertension-associated ESRD. Nonparametric linkage (NPL) regression provided modest evidence of linkage to 9p21.3 near D9S1121 (logarithm of odds [LOD] = 2.03), 1q25.1 near D1S1589 (LOD = 1.62), and 13q33.3 near D13S796 (LOD = 1.02). Adjusting for the evidence of linkage at the other loci through the NPL regression analysis provided evidence for linkage to 1q25.1, 6p23, and 9p21.3. The NPL regression and ordered subset analyses suggest that the evidence for linkage significantly increased with early onset of ESRD (2q32.1 LOD = 3.89, 13q13.1 LOD = 3.90), increased BMI (8p22 LOD = 3.37, 13q33.3 LOD = 5.20, 18p11.3 LOD = 2.38), early onset of hypertension (14q21.1 LOD = 3.19, 20q13.2 LOD = 2.32), and late onset of hypertension (4q13.1 LOD = 3.44, 5p15.33 LOD = 2.82). Multipoint single-locus linkage analysis provided modest evidence of linkage to nondiabetic ESRD on 9p21.3, 1q25.1 (in the region of the podocin gene), and 13q33.3. NPL regression and ordered subset analyses also identified loci on 13q13.1 and 13q33.3 as contributing to early-onset ESRD and ESRD in the presence of increased BMI, respectively. These regions should receive priority in the search for loci that contribute susceptibility to nondiabetic nephropathy.

A genome scan for diabetic nephropathy in African Americans.

DW Bowden — 2007-11-06T04:32:50-00:00

Kidney Int, Vol. 66, No. 4. (October 2004), pp. 1517-1526.

BACKGROUND: There is substantial evidence for a genetic contribution to diabetic nephropathy susceptibility in the African American population, but little is known about location or identity of susceptibility genes. METHODS: DNA samples were collected from 206 type 2 diabetes (T2DM) and end-stage renal disease (ESRD)/nephropathy-affected sib pairs from 166 African American families (355 affected individuals). A genome scan was performed and data analyzed using nonparametric linkage regression (NPLR) analysis and ordered subsets analysis (OSA) methods. RESULTS: In initial NPLR analyses no logarithm of odds (LOD) scores >2.0 were observed. Four loci had LOD scores > or =1.0, with LOD = 1.43 at 29 cM on chromosome 7p the highest. NPLR analyses of multilocus interactions detected 6 loci (7p, 12p, 14q, 16p, 18q, and 21q) with LOD scores 1.15 to 1.63. NPLR analyses evaluating phenotypic interactions revealed multiple locations with evidence (P < 0.05) for interactions with age-at-onset of ESRD (9 loci), duration of diabetes before onset of ESRD (19 loci), and age-at-onset of diabetes (14 loci). Several loci identified by NPLR analyses were also identified using OSA. OSA revealed evidence for a nephropathy locus at 135 cM on chromosome 3 in an estimated 29% of the families (LOD = 4.55 in the optimal subset). Additional linkage evidence, LOD = 3.59, was observed on chromosome 7p (37% of the families, longer duration of diabetes prior to diagnosis of ESRD), and 18q (max. LOD = 3.72; 64% of the families, early diabetes diagnosis). The 7p linkage has been observed in a recent genome scan of African American type 2 diabetes. CONCLUSION: This first genome scan of diabetic nephropathy in African Americans reveals evidence for susceptibility loci on chromosomes 3q, 7p, and 18q. The 7p locus may represent a type 2 diabetes susceptibility locus.

Mapping the genetic architecture of complex traits in experimental populations

Jian Yang — 2007-08-20T15:51:31-00:00

Bioinformatics, Vol. 23, No. 12. (15 June 2007), pp. 1527-1536.

Summary: Understanding how interactions among set of genes affect diverse phenotypes is having a greater impact on biomedical research, agriculture and evolutionary biology. Mapping and characterizing the isolated effects of single quantitative trait locus (QTL) is a first step, but we also need to assemble networks of QTLs and define non-additive interactions (epistasis) together with a host of potential environmental modulators. In this article, we present a full-QTL model with which to explore the genetic architecture of complex trait in multiple environments. Our model includes the effects of multiple QTLs, epistasis, QTL-by-environment interactions and epistasis-by-environment interactions. A new mapping strategy, including marker interval selection, detection of marker interval interactions and genome scans, is used to evaluate putative locations of multiple QTLs and their interactions. All the mapping procedures are performed in the framework of mixed linear model that are flexible to model environmental factors regardless of fix or random effects being assumed. An F-statistic based on Henderson method III is used for hypothesis tests. This method is less computationally greedy than corresponding likelihood ratio test. In each of the mapping procedures, permutation testing is exploited to control for genome-wide false positive rate, and model selection is used to reduce ghost peaks in F-statistic profile. Parameters of the full-QTL model are estimated using a Bayesian method via Gibbs sampling. Monte Carlo simulations help define the reliability and efficiency of the method. Two real-world phenotypes (BXD mouse olfactory bulb weight data and rice yield data) are used as exemplars to demonstrate our methods. Availability: A software package is freely available at http://ibi.zju.edu.cn/software/qtlnetwork Contact: jzhu@zju.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btm143

Measuring the secretion of heat shock proteins from cells

Elyse Ireland — 2007-10-29T04:12:54-00:00

Methods, Vol. 43, No. 3. (November 2007), pp. 176-183.

Heat shock proteins have been shown to be secreted from a number of cell types. Necrotic cells release heat shock proteins in a passive manner, whereas we, and others, have shown that viable cells secrete Hsp70 and Hsp60 through an active mechanism involving lysosomal vesicles and lipid rafts. This release of Hsp70 and Hsp60 is regulated, for example by being increased by elevated temperature. This article outlines procedures, using Hsp70 as the example, to: ensure the status of cells (viable, apoptotic or necrotic); identify the heat shock protein secreted; and quantify the secreted protein. Hsp70 has previously been quantified by ELISA, but newer methods are now being adopted, such as BIAcore and bead-based assays for use by FACS. These methods have the advantages of being more sensitive and requiring less sample than ELISA. The BIAcore has the potential to analyse Hsp70 ligands and provide affinity constants. The FACS bead assay system can be used to run multiplex assays.