CiteULike: jyuh's Ward

Mutation detection and single-molecule counting using isothermal rolling-circle amplification.

PM Lizardi — 2008-07-19T03:19:36-00:00

Nature genetics, Vol. 19, No. 3. (July 1998), pp. 225-232.

Rolling-circle amplification (RCA) driven by DNA polymerase can replicate circularized oligonucleotide probes with either linear or geometric kinetics under isothermal conditions. In the presence of two primers, one hybridizing to the + strand, and the other, to the - strand of DNA, a complex pattern of DNA strand displacement ensues that generates 10(9) or more copies of each circle in 90 minutes, enabling detection of point mutations in human genomic DNA. Using a single primer, RCA generates hundreds of tandemly linked copies of a covalently closed circle in a few minutes. If matrix-associated, the DNA product remains bound at the site of synthesis, where it may be tagged, condensed and imaged as a point light source. Linear oligonucleotide probes bound covalently on a glass surface can generate RCA signals, the colour of which indicates the allele status of the target, depending on the outcome of specific, target-directed ligation events. As RCA permits millions of individual probe molecules to be counted and sorted using colour codes, it is particularly amenable for the analysis of rare somatic mutations. RCA also shows promise for the detection of padlock probes bound to single-copy genes in cytological preparations.

Single-Molecule DNA Sequencing of a Viral Genome

Timothy Harris — 2008-04-04T15:36:18-00:00

Science, Vol. 320, No. 5872. (4 April 2008), pp. 106-109.

The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of >25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of >150x and with 100% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing. 10.1126/science.1150427

Oxygen sensors in context.

JP Ward — 2008-07-16T09:59:33-00:00

Biochimica et biophysica acta, Vol. 1777, No. 1. (January 2008), pp. 1-14.

The ability to adapt to changes in the availability of O2 provides a critical advantage to all O2-dependent lifeforms. In mammals it allows optimal matching of the O2 requirements of the cells to ventilation and O2 delivery, underpins vital changes to the circulation during the transition from fetal to independent, air-breathing life, and provides a means by which dysfunction can be limited or prevented in disease. Certain tissues such as the carotid body, pulmonary circulation, neuroepithelial bodies and fetal adrenomedullary chromaffin cells are specialised for O2 sensing, though most others show for example alterations in transcription of specific genes during hypoxia. A number of mechanisms are known to respond to variations in PO2 over the physiological range, and have been proposed to fulfil the function as O2 sensors; these include modulation of mitochondrial oxidative phosphorylation and a number of O2-dependent synthetic and degradation pathways. There is however much debate as to their relative importance within and between specific tissues, whether their O2 sensitivity is actually appropriate to account for their proposed actions, and in particular their modus operandi. This review discusses our current understanding of how these mechanisms may operate, and attempts to put them into the context of the actual PO2 to which they are likely to be exposed. An important point raised is that the overall O2 sensitivity (P50) of any O2-dependent mechanism does not necessarily correlate with that of its O2 sensor, as the coupling function between the two may be complex and non-linear. In addition, although the bulk of the evidence suggests that mitochondria act as the key O2 sensor in carotid body, pulmonary artery and chromaffin cells, the signalling mechanisms by which alterations in their function are translated into a response appear to differ fundamentally, making a global unified theory of O2 sensing unlikely.

Dietary advice for reducing cardiovascular risk.

EJ Brunner — 2008-06-13T02:04:15-00:00

Cochrane database of systematic reviews (Online), No. 4. (2007)

BACKGROUND: Changes in population diet are likely to reduce cardiovascular disease and cancer, but the effect of dietary advice is uncertain. OBJECTIVES: To assess the effects of providing dietary advice to achieve sustained dietary changes or improved cardiovascular risk profile among healthy adults. SEARCH STRATEGY: We searched the Cochrane Central Register of Controlled Trials, DARE and HTA databases on The Cochrane Library (Issue 4 2006), MEDLINE (1966 to December 2000, 2004 to November 2006) and EMBASE (1985 to December 2000, 2005 to November 2006). Additional searches were done on CAB Health (1972 to December 1999), CVRCT registry (2000), CCT (2000) and SIGLE (1980 to 2000). Dissertation abstracts and reference lists of articles were checked and researchers were contacted. SELECTION CRITERIA: Randomised studies with no more than 20% loss to follow-up, lasting at least 3 months involving healthy adults comparing dietary advice with no advice or minimal advice. Trials involving children, trials to reduce weight or those involving supplementation were excluded. DATA COLLECTION AND ANALYSIS: Two reviewers independently assessed trial quality and extracted data. Study authors were contacted for additional information. MAIN RESULTS: Thirty-eight trials with 46 intervention arms (comparisons) comparing dietary advice with no advice were included in the review. 17,871 participants/clusters were randomised. Twenty-six of the 38 included trials were conducted in the USA. Dietary advice reduced total serum cholesterol by 0.16 mmol/L (95% CI 0.06 to 0.25) and LDL cholesterol by 0.18 mmol/L (95% CI 0.1 to 0.27) after 3-24 months. Mean HDL cholesterol levels and triglyceride levels were unchanged. Dietary advice reduced blood pressure by 2.07 mmHg systolic (95% CI 0.95 to 3.19) and 1.15 mmHg diastolic (95% CI 0.48 to 1.85) and 24-hour urinary sodium excretion by 44.2 mmol (95% CI 33.6 to 54.7) after 3-36 months. Three trials reported plasma antioxidants where small increases were seen in lutein and beta-cryptoxanthin, but there was heterogeneity in the trial effects. Self-reported dietary intake may be subject to reporting bias, and there was significant heterogeneity in all the following analyses. Compared to no advice, dietary advice increased fruit and vegetable intake by 1.25 servings/day (95% CI 0.7 to 1.81). Dietary fibre intake increased with advice by 5.99 g/day (95% CI 1.12 to 10.86), while total dietary fat as a percentage of total energy intake fell by 4.49 % (95% CI 2.31 to 6.66) with dietary advice and saturated fat intake fell by 2.36 % (95% CI 1.32 to 3.39). AUTHORS' CONCLUSIONS: Dietary advice appears to be effective in bringing about modest beneficial changes in diet and cardiovascular risk factors over approximately 10 months but longer term effects are not known.

Assessing differential attrition in Clinical Trials: self-monitoring of oral anticoagulation and type II diabetes

Carl Heneghan — 2007-05-02T17:13:34-00:00

BMC Medical Research Methodology, Vol. 7 (02 May 2007), 18.

The minimum information about a genome sequence (MIGS) specification

Dawn Field — 2008-05-08T23:35:18-00:00

Nat Biotech, Vol. 26, No. 5. (May 2008), pp. 541-547.

Protein Function Assignment through Mining Cross-Species Protein-Protein Interactions.

XW Chen — 2008-02-22T19:05:03-00:00

PLoS ONE, Vol. 3, No. 2. (2008)

BACKGROUND: As we move into the post genome-sequencing era, an immediate challenge is how to make best use of the large amount of high-throughput experimental data to assign functions to currently uncharacterized proteins. We here describe CSIDOP, a new method for protein function assignment based on shared interacting domain patterns extracted from cross-species protein-protein interaction data. METHODOLOGY/PRINCIPAL FINDINGS: The proposed method is assessed both biologically and statistically over the genome of H. sapiens. The CSIDOP method is capable of making protein function prediction with accuracy of 95.42% using 2,972 gene ontology (GO) functional categories. In addition, we are able to assign novel functional annotations for 181 previously uncharacterized proteins in H. sapiens. Furthermore, we demonstrate that for proteins that are characterized by GO, the CSIDOP may predict extra functions. This is attractive as a protein normally executes a variety of functions in different processes and its current GO annotation may be incomplete. CONCLUSIONS/SIGNIFICANCE: It can be shown through experimental results that the CSIDOP method is reliable and practical in use. The method will continue to improve as more high quality interaction data becomes available and is readily scalable to a genome-wide application.

Biomarker method validation in anticancer drug development.

J Cummings — 2008-04-25T04:36:36-00:00

British journal of pharmacology, Vol. 153, No. 4. (February 2008), pp. 646-656.

Over recent years the role of biomarkers in anticancer drug development has expanded across a spectrum of applications ranging from research tool during early discovery to surrogate endpoint in the clinic. However, in Europe when biomarker measurements are performed on samples collected from subjects entered into clinical trials of new investigational agents, laboratories conducting these analyses become subject to the Clinical Trials Regulations. While these regulations are not specific in their requirements of research laboratories, quality assurance and in particular assay validation are essential. This review, therefore, focuses on a discussion of current thinking in biomarker assay validation. Five categories define the majority of biomarker assays from 'absolute quantitation' to 'categorical'. Validation must therefore take account of both the position of the biomarker in the spectrum towards clinical end point and the level of quantitation inherent in the methodology. Biomarker assay validation should be performed ideally in stages on 'a fit for purpose' basis avoiding unnecessarily dogmatic adherence to rigid guidelines but with careful monitoring of progress at the end of each stage. These principles are illustrated with two specific examples: (a) absolute quantitation of protein biomarkers by mass spectrometry and (b) the M30 and M65 ELISA assays as surrogate end points of cell death.

Linkage and association analysis of angiotensin I-converting enzyme (ACE)-gene polymorphisms with ACE concentration and blood pressure.

X Zhu — 2008-03-31T12:53:12-00:00

Am J Hum Genet, Vol. 68, No. 5. (May 2001), pp. 1139-1148.

Considerable effort has been expended to determine whether the gene for angiotensin I-converting enzyme (ACE) confers susceptibility to cardiovascular disease. In this study, we genotyped 13 polymorphisms in the ACE gene in 1,343 Nigerians from 332 families. To localize the genetic effect, we first performed linkage and association analysis of all the markers with ACE concentration. In multipoint variance-component analysis, this region was strongly linked to ACE concentration (maximum LOD score 7.5). Likewise, most of the polymorphisms in the ACE gene were significantly associated with ACE (P<.0013). The two most highly associated polymorphisms, ACE4 and ACE8, accounted for 6% and 19% of the variance in ACE, respectively. A two-locus additive model with an additive x additive interaction of these polymorphisms explained most of the ACE variation associated with this region. We next analyzed the relationship between these two polymorphisms (ACE4 and ACE8) and blood pressure (BP). Although no evidence of linkage was detected, significant association was found for both systolic and diastolic BP when a two-locus additive model developed for ACE concentration was used. Further analyses demonstrated that an epistasis model provided the best fit to the BP variation. In conclusion, we found that the two polymorphisms explaining the greatest variation in ACE concentration are significantly associated with BP, through interaction, in this African population sample. Our study also demonstrates that greater statistical power can be anticipated with association analysis versus linkage, when markers in strong linkage disequilibrium with a trait locus have been identified. Furthermore, allelic interaction may play an important role in the dissection of complex traits such as BP.

Socioeconomic status and the incidence of ESRD.

MM Ward — 2008-03-31T10:05:51-00:00

Am J Kidney Dis, Vol. 51, No. 4. (April 2008), pp. 563-572.

BACKGROUND: Persons of low socioeconomic status (SES) may be at increased risk of end-stage renal disease (ESRD). This study examines the association between SES and incidence of ESRD caused by all primary renal diseases and caused by 3 diseases that differ in the availability of effective treatment: diabetes mellitus, lupus nephritis, and autosomal dominant polycystic kidney disease (ADPKD). STUDY DESIGN: Retrospective cohort study. SETTING & PARTICIPANTS: Adults with incident ESRD in the United States from January 1, 1996, to June 30, 2004 (N = 747,556). PREDICTOR: SES, based on characteristics of the patient's ZIP code of residence. OUTCOMES: Incidence of ESRD. RESULTS: In all sex-race groups, the incidence of ESRD caused by all primary renal diseases was greatest in those in the lowest SES score quartile and decreased progressively with higher SES. For example, for white women, the incidence of ESRD was 388.9 per million in the lowest quartile of SES and 200.8 per million in the highest quartile of SES (relative risk, 1.92; 95% confidence interval, 1.89 to 1.95). However, this association differed among patients with primary renal diseases. There were strong associations between SES and ESRD caused by diabetes mellitus, weaker associations for ESRD caused by lupus nephritis, and generally no associations for ESRD caused by ADPKD. For example, for white women, relative risks of ESRD in the lowest compared with the highest SES quartile were 2.84 for ESRD caused by diabetes mellitus, 1.63 for ESRD caused by lupus nephritis, and 1.27 for ESRD caused by ADPKD. LIMITATIONS: Use of an area-based measure of SES. CONCLUSIONS: The strength of the association between SES and ESRD differs among patients with diabetes mellitus, lupus nephritis, and ADPKD, suggesting that socioeconomic factors act differently in the progression of chronic kidney disease in these conditions.

Big results from small samples: evaluation of amplification protocols for gene expression profiling.

A Viale — 2007-09-04T16:18:01-00:00

J Biomol Tech, Vol. 18, No. 3. (July 2007), pp. 150-161.

Microarrays have revolutionized many areas of biology due to our technical ability to quantify tens of thousands of transcripts within a single experiment. However, there are still many areas that cannot benefit from this technology due to the amount of biological material needed for microarray analysis. In response to this demand, chemistries have been developed that boast the capability of generating targets from nanogram amounts of total RnA, reflecting minimal amounts of biological material, on the order of several hundred or thousand cells. Herein, we describe the evaluation of four chemistries for RnA amplification in terms of reproducibility, sensitivity, accuracy, and comparability to results from a single round of T7 amplification. No evidence for false-positive measurements of differential expression was observed. In contrast, clear differences between chemistries in sensitivity and accuracy were detected. PCR validation showed an interaction of probe sequence on the array and target labeling chemistry, resulting in a chemistry-dependent probe set sensitivity varying over an order of magnitude.

Glucose transporters in human renal proximal tubular cells isolated from the urine of patients with non-insulin-dependent diabetes.

H Rahmoune — 2008-02-20T04:55:42-00:00

Diabetes, Vol. 54, No. 12. (December 2005), pp. 3427-3434.

The bulk of glucose that is filtered by the renal glomerulus is reabsorbed by the glucose transporters of the proximal convoluted tubular epithelium. However, it has been difficult to investigate this in diseases such as type 2 diabetes because of the inability to isolate primary renal cells from patients without a renal biopsy. We report here a method for the immunomagnetic isolation and novel primary culture of human exfoliated proximal tubular epithelial cells (HEPTECs) from fresh urine. The primary isolates are highly enriched and differentiated and express characteristic proximal tubular phenotypic markers. They continue to express the proximal tubular markers CD13/aminopeptidase-N, sodium glucose cotransporter (SGLT) 2, and alkaline phosphatase through up to six subsequent subcultures in a similar way to human proximal cells isolated from renal biopsies. In a hyperglycemic environment, HEPTECs isolated from patients with type 2 diabetes expressed significantly more SGLT2 and the facilitative glucose transporter GLUT2 than cells from healthy individuals. We also demonstrated a markedly increased renal glucose uptake in HEPTECs isolated from patients with type 2 diabetes compared with healthy control subjects. Our findings indicate for the first time in a human cellular model that increased renal glucose transporter expression and activity is associated with type 2 diabetes.

Primer: measuring the effects of treatment in clinical trials.

MM Ward — 2008-02-13T08:14:07-00:00

Nat Clin Pract Rheumatol, Vol. 3, No. 5. (May 2007), pp. 291-297.

The results of clinical trials are often used as the basis for changes in clinical practice. Proper execution and interpretation of the results of trials are, therefore, of paramount importance to the welfare of patients. The results of a clinical trial are based on four key elements: the choice of the primary study end point, the method used to compare end points between groups, the clinically meaningful difference in the primary end point selected a priori by the investigators, and the power of the study to detect as statistically significant a difference between groups that is as large as the preselected clinically meaningful difference. These key elements directly follow from the primary hypothesis tested by the trial. This article reviews the basic features of these four elements, and the influence they have on the interpretation of clinical trials.

PGC-1alpha: a key regulator of energy metabolism.

Huiyun Liang — 2006-11-20T20:29:10-00:00

Adv Physiol Educ, Vol. 30, No. 4. (December 2006), pp. 145-151.

Peroxisome proliferator-activated receptor-gamma coactivator (PGC)-1alpha is a member of a family of transcription coactivators that plays a central role in the regulation of cellular energy metabolism. It is strongly induced by cold exposure, linking this environmental stimulus to adaptive thermogenesis. PGC-1alpha stimulates mitochondrial biogenesis and promotes the remodeling of muscle tissue to a fiber-type composition that is metabolically more oxidative and less glycolytic in nature, and it participates in the regulation of both carbohydrate and lipid metabolism. It is highly likely that PGC-1alpha is intimately involved in disorders such as obesity, diabetes, and cardiomyopathy. In particular, its regulatory function in lipid metabolism makes it an inviting target for pharmacological intervention in the treatment of obesity and Type 2 diabetes.

Nutritional screening in patients on hemodialysis: is subjective global assessment an appropriate tool?

F Gurreebun — 2008-01-24T04:10:05-00:00

J Ren Nutr, Vol. 17, No. 2. (March 2007), pp. 114-117.

OBJECTIVE: Malnutrition is common in patients with chronic renal failure and should be screened for systematically. Subjective global assessment (SGA) is frequently used, but it is time-consuming. The aim of this study was to assess the sensitivity of SGA as a screening tool for malnutrition compared with the measurement of body mass index (BMI) and serum albumin combined with a history of unintentional weight loss. DESIGN: This was a cross-sectional study. SETTING: The study was undertaken in two hospital hemodialysis units. PATIENTS AND INTERVENTION: A total of 141 patients on hemodialysis were studied. Nutritional assessment was undertaken with a seven-point SGA, measurement of height, weight and serum albumin, and a record of unintentional weight loss. OUTCOMES: Patients were considered to be at risk of malnutrition if any of the following three criteria were met: a serum albumin less than 35 g/L, a BMI less than 18.5, and unintentional weight loss of edema free weight greater than 10% in the past 6 months. A diagnosis of malnutrition was made if the SGA score was between 1 and 5. RESULTS: A total of 41 patients had either a serum albumin less than 35 g/L or a BMI less than 18.5 or unintentional weight loss of edema free weight of more than 10% in the past 6 months. Of these 41 patients, 29 had a serum albumin less than 35 g/L, 9 had a BMI less than 18.5, and 15 had unintentional loss of edema free weight greater than 10% in the past 6 months. Thirteen patients were judged by SGA to be mild to moderately malnourished. All 13 were identified by serum albumin, BMI, or weight loss. CONCLUSIONS: In this study, measurement of SGA did not diagnose malnutrition in any patients in whom this had not already been potentially identified by measurement of serum albumin, BMI, and a history of weight loss. SGA did not therefore increase the sensitivity of nutritional screening in this cohort.

Vasopressin Directly Regulates Cyst Growth in Polycystic Kidney Disease

Xiaofang Wang — 2008-01-08T04:05:25-00:00

J Am Soc Nephrol, Vol. 19, No. 1. (1 January 2008), pp. 102-108.

The polycystic kidney diseases (PKD) are a group of genetic disorders causing renal failure and death from infancy to adulthood. Arginine vasopressin (AVP) V2 receptor antagonists inhibit cystogenesis in animal models of cystic kidney diseases, presumably by downregulating cAMP signaling, cell proliferation, and chloride-driven fluid secretion. For confirmation that the protective effect of these drugs is due to antagonism of AVP, PCK (Pkhd1/) and Brattleboro (AVP/) rats were crossed to generate rats with PKD and varying amounts of AVP. At 10 and 20 weeks of age, PCK AVP/ rats had lower renal cAMP and almost complete inhibition of cystogenesis compared with PCK AVP+/+ and PCK AVP+/ rats. The V2 receptor agonist 1-deamino-8-d-arginine vasopressin increased renal cAMP and recovered the full cystic phenotype of PCK AVP/ rats and aggravated the cystic disease of PCK AVP+/+ rats but did not induce cystic changes in wild-type rats. These observations indicate that AVP is a powerful modulator of cystogenesis and provide further support for clinical trials of V2 receptor antagonists in PKD. 10.1681/ASN.2007060688

Dissecting complex transcriptional responses using pathway-level scores based on prior information.

HJ Bussemaker — 2008-01-01T01:01:59-00:00

BMC Bioinformatics, Vol. 8 Suppl 6 (2007)

BACKGROUND: The genomewide pattern of changes in mRNA expression measured using DNA microarrays is typically a complex superposition of the response of multiple regulatory pathways to changes in the environment of the cells. The use of prior information, either about the function of the protein encoded by each gene, or about the physical interactions between regulatory factors and the sequences controlling its expression, has emerged as a powerful approach for dissecting complex transcriptional responses. RESULTS: We review two different approaches for combining the noisy expression levels of multiple individual genes into robust pathway-level differential expression scores. The first is based on a comparison between the distribution of expression levels of genes within a predefined gene set and those of all other genes in the genome. The second starts from an estimate of the strength of genomewide regulatory network connectivities based on sequence information or direct measurements of protein-DNA interactions, and uses regression analysis to estimate the activity of gene regulatory pathways. The statistical methods used are explained in detail. CONCLUSION: By avoiding the thresholding of individual genes, pathway-level analysis of differential expression based on prior information can be considerably more sensitive to subtle changes in gene expression than gene-level analysis. The methods are technically straightforward and yield results that are easily interpretable, both biologically and statistically.

Short tandem repeat profiling provides an international reference standard for human cell lines.

JR Masters — 2007-12-31T15:02:43-00:00

Proc Natl Acad Sci U S A, Vol. 98, No. 14. (3 July 2001), pp. 8012-8017.

Cross-contamination between cell lines is a longstanding and frequent cause of scientific misrepresentation. Estimates from national testing services indicate that up to 36% of cell lines are of a different origin or species to that claimed. To test a standard method of cell line authentication, 253 human cell lines from banks and research institutes worldwide were analyzed by short tandem repeat profiling. The short tandem repeat profile is a simple numerical code that is reproducible between laboratories, is inexpensive, and can provide an international reference standard for every cell line. If DNA profiling of cell lines is accepted and demanded internationally, scientific misrepresentation because of cross-contamination can be largely eliminated.

The PI3K inhibitor arsenal: choose your weapon!

T Crabbe — 2007-12-29T15:13:15-00:00

Trends Biochem Sci, Vol. 32, No. 10. (October 2007), pp. 450-456.

Owing to its widespread activation in inflammation and cancer, a growing appreciation of the therapeutic potential of inhibitors of the phosphoinositide 3-kinase (PI3K) pathway has stimulated intense interest in compounds with suitable pharmacological profiles. These are primarily directed toward PI3K itself. However, as class I PI3Ks are also essential for a range of normal physiological processes, broad spectrum PI3K inhibition could be poorly tolerated. In recent years, patents describing a new generation of PI3K inhibitors have started to appear, with a particular focus on the development of compounds with enhanced isoform selectivity for use as anti-cancer and anti-inflammatory therapies. However, challenges remain for the efforts to pharmacologically target this enzyme family in a successful manner.

Predictive modeling of genome-wide mRNA expression: from modules to molecules.

HJ Bussemaker — 2007-11-21T07:05:41-00:00

Annu Rev Biophys Biomol Struct, Vol. 36 (2007), pp. 329-347.

Various algorithms are available for predicting mRNA expression and modeling gene regulatory processes. They differ in whether they rely on the existence of modules of coregulated genes or build a model that applies to all genes, whether they represent regulatory activities as hidden variables or as mRNA levels, and whether they implicitly or explicitly model the complex cis-regulatory logic of multiple interacting transcription factors binding the same DNA. The fact that functional genomics data of different types reflect the same molecular processes provides a natural strategy for integrative computational analysis. One promising avenue toward an accurate and comprehensive model of gene regulation combines biophysical modeling of the interactions among proteins, DNA, and RNA with the use of large-scale functional genomics data to estimate regulatory network connectivity and activity parameters. As the ability of these models to represent complex cis-regulatory logic increases, the need for approaches based on cross-species conservation may diminish.

Cytokine receptor signaling through the Jak-Stat-Socs pathway in disease.

LA O'Sullivan — 2007-11-19T09:45:44-00:00

Mol Immunol, Vol. 44, No. 10. (April 2007), pp. 2497-2506.

The complexity of multicellular organisms is dependent on systems enabling cells to respond to specific stimuli. Cytokines and their receptors are one such system, whose perturbation can lead to a variety of disease states. This review represents an overview of our current understanding of the cytokine receptors, Janus kinases (Jaks), Signal transducers and activators of transcription (Stats) and Suppressors of cytokine signaling (Socs), focussing on their contribution to diseases of an immune or hematologic nature.

Better understanding of organ dysfunction requires proteomic involvement.

X Wang — 2007-11-18T03:18:39-00:00

J Proteome Res, Vol. 5, No. 5. (May 2006), pp. 1060-1062.

Organ dysfunction is defined as a systemic consequence of acute and chronic diseases, a critical and important phase of disease development. The mortality of patients with severe illness is highly correlated with the number and duration of dysfunctional organs. There is still not an efficient and specific therapy to improve the prognosis of patients with organ dysfunction, due to the complexity and severity of the disease. There is a great need to understand molecular mechanisms of the disease, identify disease-related biomarkers, and validate therapeutic effects. Thus, it is important to have a special attention from proteomic scientists to explore the combination between advanced proteomic biotechnology, clinical proteomics, tissue imaging and profiling, and organ dysfunction score systems, to improve the clinical outcomes of these patients.

Phosphoinositide 3-kinase signalling in lung disease: leucocytes and beyond

Medina-Tato — 2007-07-06T05:14:28-00:00

Immunology, Vol. 121, No. 4. (August 2007), pp. 448-461.

Phosphatidylinositol 3-kinase mediates activation of ATM by high NaCl and by ionizing radiation: Role in osmoprotective transcriptional regulation.

Carlos E Irarrazabal — 2006-06-01T12:27:14-00:00

Proc Natl Acad Sci U S A (25 May 2006)

High NaCl causes DNA double-strand breaks and activates the transcription factor, TonEBP/OREBP, resulting in increased transcription of several protective genes, including those involved in accumulation of compatible organic osmolytes. Several kinases are known to contribute to signaling activation of TonEBP/OREBP, including ATM, which is a member of the phosphatidylinositol 3-kinase (PI3K)-like kinase family and is activated by DNA double-strand breaks. The purpose of the present studies was to investigate a possible role of PI3K Class IA (PI3K-IA). We found that high NaCl increases PI3K-IA lipid kinase activity. Inhibiting PI3K-IA either by expressing a dominant negative of its regulatory subunit, p85, or by small interfering RNA-mediated knockdown of its catalytic subunit, p110alpha, reduces high NaCl-induced increases in TonEBP/OREBP transcriptional activity and transactivation, but not nuclear translocation of TonEBP/OREBP, or increases in its abundance. Further, suppression of PI3K-IA inhibits the activation of ATM that is caused by either ionizing radiation or high NaCl. High NaCl-induced increase in TonEBP/OREBP activity is reduced equally by inhibition of ATM or PI3K-IA, and the effects are not additive. The conclusions are as follows: (i) PI3K-IA activity is necessary for both high NaCl- and ionizing radiation-induced activation of ATM and (ii) high NaCl activates PI3K-IA, which, in turn, contributes to full activation of TonEBP/OREBP via ATM.

Cardiovascular outcomes in high-risk hypertensive patients stratified by baseline glomerular filtration rate.

M Rahman — 2007-10-02T03:05:47-00:00

Ann Intern Med, Vol. 144, No. 3. (7 February 2006), pp. 172-180.

BACKGROUND: Chronic kidney disease is common in older patients with hypertension. OBJECTIVE: To compare rates of coronary heart disease (CHD) and end-stage renal disease (ESRD) events; to determine whether glomerular filtration rate (GFR) independently predicts risk for CHD; and to report the efficacy of first-step treatment with a calcium-channel blocker (amlodipine) or an angiotensin-converting enzyme inhibitor (lisinopril), each compared with a diuretic (chlorthalidone), in modifying cardiovascular disease (CVD) outcomes in high-risk patients with hypertension stratified by GFR. DESIGN: Post hoc subgroup analysis. SETTING: Multicenter randomized, double-blind, controlled trial. PARTICIPANTS: Persons with hypertension who were 55 years of age or older with 1 or more risk factors for CHD and who were stratified into 3 baseline GFR groups: normal or increased (> or = 90 mL/min per 1.73 m2; n = 8126 patients), mild reduction (60 to 89 mL/min per 1.73 m2; n = 18,109 patients), and moderate or severe reduction (< 60 mL/min per 1.73 m2; n = 5662 patients). INTERVENTIONS: Random assignment to chlorthalidone, amlodipine, or lisinopril. MEASUREMENTS: Rates of ESRD, CHD, stroke, and combined CVD (CHD, coronary revascularization, angina, stroke, heart failure, and peripheral arterial disease). RESULTS: In participants with a moderate to severe reduction in GFR, 6-year rates were higher for CHD than for ESRD (15.4% vs. 6.0%, respectively). A baseline GFR of less than 53 mL/min per 1.73 m2 (compared with >104 mL/min per 1.73 m2) was independently associated with a 32% higher risk for CHD. Amlodipine was similar to chlorthalidone in reducing CHD (16.0% vs. 15.2%, respectively; hazard ratio, 1.06 [95% CI, 0.89 to 1.27]), stroke, and combined CVD (CHD, coronary revascularization, angina, stroke, heart failure, and peripheral arterial disease), but less effective in preventing heart failure. Lisinopril was similar to chlorthalidone in preventing CHD (15.1% vs. 15.2%, respectively; hazard ratio, 1.00 [CI, 0.84 to 1.20]), but was less effective in reducing stroke, combined CVD events, and heart failure. LIMITATIONS: Proteinuria data were not available, and combination therapies were not tested. CONCLUSIONS: Older high-risk patients with hypertension and reduced GFR are more likely to develop CHD than to develop ESRD. A low GFR independently predicts increased risk for CHD. Neither amlodipine nor lisinopril is superior to chlorthalidone in preventing CHD, stroke, or combined CVD, and chlorthalidone is superior to both for preventing heart failure, independent of level of renal function.

The NCBI dbGaP database of genotypes and phenotypes

Matthew Mailman — 2007-10-01T16:01:33-00:00

Nat Genet, Vol. 39, No. 10. (October 2007), pp. 1181-1186.

Laboratory abnormalities at the onset of treatment of end-stage renal disease: are there racial or socioeconomic disparities in care?

MM Ward — 2007-08-08T08:16:13-00:00

Arch Intern Med, Vol. 167, No. 10. (28 May 2007), pp. 1083-1091.

BACKGROUND: Laboratory abnormalities at the start of treatment of end-stage renal disease (ESRD) have been reported as worse in racial/ethnic minorities than in white patients, suggesting racial disparities in care. It is not known whether these differences are attributable to racial/ethnic differences in socioeconomic status (SES). METHODS: We tested associations between race/ethnicity, SES, and type of medical insurance and serum creatinine level, estimated glomerular filtration rate, serum albumin level, and hematocrit at the start of treatment of ESRD and use of epoietin before ESRD treatment in a large national population-based sample. Data on 515 561 patients beginning ESRD treatment between January 1, 1996, and June 30, 2004, were obtained for this cross-sectional survey from the United States Renal Data System. RESULTS: Race/ethnicity had a much stronger association than SES with each laboratory measure. Adjusted mean serum creatinine levels were lowest in white patients (7.5 mg/dL [663.0 micromol/L]; 95% confidence interval [CI], 7.45-7.49) and highest in black patients (8.9 mg/dL [786.7 micromol/L]; 95% CI, 8.92-8.97) (P<.001 across racial/ethnic groups). Adjusted mean hematocrit for white patients (29.5%; 95% CI, 29.4%-29.6%) was significantly higher and for black patients (28.3%; 95% CI, 28.2%-28.4%) significantly lower than that of all other racial/ethnic groups (P<.001 across racial/ethnic groups). Less marked differences were present for estimated glomerular filtration rate and serum albumin level. In contrast, predialysis use of epoietin was associated with race/ethnicity (black vs white: odds ratio, 0.80; 95% CI, 0.78-0.81; Hispanic vs white: odds ratio, 0.87; 95% CI, 0.85-0.89) and showed a graded decrease with decreasing SES (odds ratio for the lowest vs highest socioeconomic quartile 0.68; 95% CI, 0.67-0.70). Patients without medical insurance had more abnormal laboratory values than those with insurance, but these associations were weaker than those of race/ethnicity. CONCLUSIONS: Minorities, particularly black patients, had more severe laboratory abnormalities at the start of ESRD treatment than white patients. These differences were not readily attributable to SES differences. Absence of medical insurance, SES, and race/ethnicity were associated with the likelihood of predialysis use of epoietin.

A systematic review and economic evaluation of statins for the prevention of coronary events.

S Ward — 2007-08-03T03:59:29-00:00

Health Technol Assess, Vol. 11, No. 14. (April 2007), pp. 1-178.

OBJECTIVES: To evaluate the clinical effectiveness and cost-effectiveness of statins for the primary and secondary prevention of cardiovascular events in adults with, or at risk of, coronary heart disease (CHD). DATA SOURCES: Electronic databases were searched between November 2003 and April 2004. REVIEW METHODS: A review was undertaken to identify and evaluate all literature relating to the clinical and cost effectiveness of statins in the primary and secondary prevention of CHD and cardiovascular disease (CVD) in the UK. A Markov model was developed to explore the costs and health outcomes associated with a lifetime of statin treatment using a UK NHS perspective. RESULTS: Thirty-one randomised studies were identified that compared a statin with placebo or with another statin, and reported clinical outcomes. Meta-analysis of the available data from the placebo-controlled studies indicates that, in patients with, or at risk of, CVD, statin therapy is associated with a reduced relative risk of all cause mortality, cardiovascular mortality, CHD mortality and fatal myocardial infarction (MI), but not of fatal stroke. It is also associated with a reduced relative risk of morbidity [non-fatal stroke, non-fatal MI, transient ischaemic attack (TIA), unstable angina] and of coronary revascularisation. It is hardly possible, on the evidence available from the placebo-controlled trials, to differentiate between the clinical efficacy of atorvastatin, fluvastatin, pravastatin and simvastatin. However, there is some evidence from direct comparisons between statins to suggest that atorvastatin may be more effective than pravastatin in patients with symptomatic CHD. There is limited evidence for the effectiveness of statins in different subgroups. Statins are generally considered to be well tolerated and to have a good safety profile. This view is generally supported both by the evidence of the trials included in this review and by postmarketing surveillance data. Increases in creatinekinase and myopathy have been reported, but rhabdomyolysis and hepatotoxicity are rare. However, some patients may receive lipid-lowering therapy for as long as 50 years, and long-term safety over such a timespan remains unknown. In secondary prevention of CHD, the incremental cost-effectiveness ratios (ICERs) increase with age varying between pound10,000 and pound17,000 per quality adjusted life year (QALY) for ages 45 and 85 respectively. Sensitivity analyses show these results are robust. In primary prevention of CHD there is substantial variation in ICERs by age and risk. The average ICERs weighted by risk range from pound20,000 to pound27,500 for men and from pound21,000 to pound57,000 for women. The results are sensitive to the cost of statins, discount rates and the modelling time frame. In the CVD analyses, which take into account the benefits of statins on reductions in stroke and TIA events, the average ICER weighted by risk level remains below pound20,000 at CHD risk levels down to 0.5%. Limitations of the analyses include the requirement to extrapolate well beyond the timeframe of the trial period, and to extrapolate effectiveness results from higher risk primary prevention populations to the treatment of populations at much lower risk. Consequently, the results for the lower age bands and lower risks are subject to greater uncertainty and need to be treated with caution. CONCLUSIONS: There is evidence to suggest that statin therapy is associated with a statistically significant reduction in the risk of primary and secondary cardiovascular events. As the confidence intervals for each outcome in each prevention category overlap, it is not possible to differentiate, in terms of relative risk, between the effectiveness of statins in primary and secondary prevention. However, the absolute risk of CHD death/non-fatal MI is higher, and the number needed to treat to avoid such an event is consequently lower, in secondary than in primary prevention. The generalisability of these results is limited by the exclusion, in some studies, of patients who were hypersensitive to, intolerant of, or known to be unresponsive to, statins, or who were not adequately compliant with study medication during a placebo run-in phase. Consequently, the treatment effect may be reduced when statins are used in an unselected population. The results of the economic modelling show that statin therapy in secondary prevention is likely to be considered cost-effective. In primary prevention, the cost-effectiveness ratios are dependent on the level of CHD risk and age, but the results for the CVD analyses offer support for the more aggressive treatment recommendation issued by recent guidelines in UK. Evidence on clinical endpoints for rosuvastatin is awaited from on-going trials. The potential targeting of statins at low-risk populations is however associated with major uncertainties, particularly the likely uptake and long-term compliance to lifelong medication by asymptomatic younger patients. The targeting, assessment and monitoring of low-risk patients in primary care would be a major resource implication for the NHS. These areas require further research.

Renal outcomes in high-risk hypertensive patients treated with an angiotensin-converting enzyme inhibitor or a calcium channel blocker vs a diuretic: a report from the Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial (ALLHAT).

M Rahman — 2007-07-29T03:12:01-00:00

Arch Intern Med, Vol. 165, No. 8. (25 April 2005), pp. 936-946.

BACKGROUND: This study was performed to determine whether, in high-risk hypertensive patients with a reduced glomerular filtration rate (GFR), treatment with a calcium channel blocker or an angiotensin-converting enzyme inhibitor lowers the incidence of renal disease outcomes compared with treatment with a diuretic. METHODS: We conducted post hoc analyses of the Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial (ALLHAT). Hypertensive participants 55 years or older with at least 1 other coronary heart disease risk factor were randomized to receive chlorthalidone, amlodipine, or lisinopril for a mean of 4.9 years. Renal outcomes were incidence of end-stage renal disease (ESRD) and/or a decrement in GFR of 50% or more from baseline. Baseline GFR, estimated by the simplified Modification of Diet in Renal Disease equation, was stratified into normal or increased (> or =90 mL /min per 1.73 m(2), n = 8126), mild reduction (60-89 mL /min per 1.73 m(2), n = 18 109), or moderate-severe reduction (<60 mL /min per 1.73 m(2), n = 5662) in GFR. Each stratum was analyzed for effects of the treatments on outcomes. RESULTS: In 448 participants, ESRD developed. Compared with patients taking chlorthalidone, no significant differences occurred in the incidence of ESRD in patients taking amlodipine in the mild (relative risk [RR], 1.47; 95% confidence interval [CI], 0.97-2.23) or moderate-severe (RR, 0.92; 95% CI, 0.68-1.24) reduction in GFR groups. Compared with patients taking chlorthalidone, no significant differences occurred in the incidence of ESRD in patients taking lisinopril in the mild (RR, 1.34; 95% CI, 0.87-2.06) or moderate-severe (RR, 0.98; 95% CI, 0.73-1.31) reduction in GFR groups. In patients with mild and moderate-severe reduction in GFR, the incidence of ESRD or 50% or greater decrement in GFR was not significantly different in patients treated with chlorthalidone compared with those treated with amlodipine (odds ratios, 0.96 [P = .74] and 0.85 [P = .23], respectively) and lisinopril (odds ratios, 1.13 [P = .31] and 1.00 [P = .98], respectively). No difference in treatment effects occurred for either end point for patients taking amlodipine or lisinopril compared with those taking chlorthalidone across the 3 GFR subgroups, either for the total group or for participants with diabetes at baseline. At 4 years of follow-up, estimated GFR was 3 to 6 mL /min per 1.73 m(2) higher in patients assigned to receive amlodipine compared with chlorthalidone, depending on baseline GFR stratum. CONCLUSIONS: In hypertensive patients with reduced GFR, neither amlodipine nor lisinopril was superior to chlorthalidone in reducing the rate of development of ESRD or a 50% or greater decrement in GFR. Participants assigned to receive amlodipine had a higher GFR than those assigned to receive chlorthalidone, but rates of development of ESRD were not different between the groups.

A strategy for annotating the human milk glycome.

MR Ninonuevo — 2007-07-28T10:23:30-00:00

J Agric Food Chem, Vol. 54, No. 20. (4 October 2006), pp. 7471-7480.

Oligosaccharides in human milk represent a group of bioactive molecules that have evolved to be an abundant and diverse component of human milk, even though they have no direct nutritive value to the infant. A recent hypothesis proposes that they could be substrates for the development of the intestinal microflora and the mucosal immune system. The inability to determine the exact composition of these oligosaccharides limits research and the ability to understand their biological functions. Oligosaccharides isolated from the lipids and proteins of individual human milk samples were analyzed by a combination of techniques including microchip liquid chromatography mass spectrometry (HPLC-Chip/MS) and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT ICR MS). Accurate mass measurements obtained using an orthogonal time-of-flight (o-TOF) mass spectrometry provided oligosaccharide composition for approximately 200 individual molecular species. Comparison of HPLC-Chip/MS profiles from five different women revealed variations in milk oligosaccharide compositions. HPLC-Chip/MS profiling provides a method for routinely identifying milk oligosaccharides. Tandem MS in combination with exoglycosidase digestion provides unambiguous differentiation of structural isomers.

A new noninvasive method to determine central venous pressure

Kevin Ward — 2007-07-18T06:14:18-00:00

Resuscitation, Vol. 70, No. 2. (August 2006), pp. 238-246.

Summary Knowledge of central venous pressure (CVP) is considered valuable in the assessment and treatment of various states of critical illness and injury.Objectives We tested a noninvasive means of determining CVP (NICVP), by monitoring forearm volume changes in response to externally applied circumferential pressure to the upper arm veins.Methods Sixteen patients who were undergoing CVP monitoring as a part of their care had NICVP determined and compared with CVP. Volume changes were measured in the forearm with mercury-in-silastic strain gauge plethysmography. A pressure cuff is placed in the upper extremity. The cuff is inflated over 5 s to a pressure above CVP but below diastolic arterial pressure (40 mmHg). This allows blood into the forearm but prevents venous return. After 45-60 s the cuff is rapidly deflated. NICVP was determined as the cuff pressure noted at the maximum derivative of the forearm volume decrease during deflation. NICVP was then compared to invasively measured CVP taken during the same period.Results A total of 48 trials (three per subject) were performed on 16 patients. The range of CVP recorded was 0-22 mmHg. The correlation between CVP and NICVP was 0.98 (95% CI: 0.95-0.98) (p < 0.001). The bias between methods was 0.26 mmHg with the limits of agreement being 3.4 to -2.89 mmHg. When the average of three trials per patients was analysed the bias stayed at 0.26 mmHg but the limits of agreement improved to 2.54 and -2.03 mmHg.Conclusion NICVP as determined in this study may be a clinically useful substitute for traditional CVP measurement and may offer a valid tool for early diagnosis and treatment of acute states in which knowledge of CVP would be helpful.

PGC-1alpha-Induced Mitochondrial Alterations in 3T3 Fibroblast Cells

Huiyun Liang — 2007-07-15T14:53:04-00:00

Ann NY Acad Sci, Vol. 1100, No. 1. (1 April 2007), pp. 264-279.

Peroxisome proliferation activator receptor (PPAR) gamma-coactivator 1alpha (PGC-1alpha), a transcription coactivator, functions as a master regulator of a wide array of metabolic and physiological processes and is an essential factor in the process of mitochondrial biogenesis. Transfection of NIH 3T3 fibroblasts with a mouse cDNA for PGC-1alpha led to the induction of markers of mitochondrial biogenesis, that is, mitochondrial transcription factor A (mtTFA), cytochrome c, and mitochondrial DNA (mtDNA). Mitochondrial biogenesis-associated net protein synthesis appears to be accomplished by a reduction in the rate of mitochondrial protein degradation with little or no change in the rate of protein synthesis. Overexpression of PGC-1alpha did not adversely affect cellular proliferation. Cellular ATP levels were increased in the transfected cells and they were more resistant to oxidative stress than the control nontransfected 3T3 cells. This resistance to oxidative stress was manifested by both an improved viability and the maintenance of mitochondrial membrane potential in the transfected cells when exposed to t-butyl hydroperoxide (t-BOOH). It therefore appears that PGC-1alpha overexpression stimulates mitochondrial biogenesis in 3T3 cells making them more resistant to oxidative stressors. 10.1196/annals.1395.028

Changes in the serum proteome associated with the development of hepatocellular carcinoma in hepatitis C-related cirrhosis

DG Ward — 2006-01-11T15:43:59-00:00

British Journal of Cancer, Vol. aop, No. current. (10 January 2006)