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The effects of stroke on the skeleton

Tue, 14 Feb 2006 00:00:00 GMT

Title: The effects of stroke on the skeleton Authors: Poole, Kenneth Abstract: Stroke is now a well-recognised risk factor for hip fracture. The aim of this study was to elucidate the pathophysiological mechanisms by which hip bone loss occurs in hemiplegia and to test the efficacy of a novel pharmaceutical strategy for preserving bone in stroke patients. Patients who were admitted acutely with a first-ever stroke and who remained unable to walk one week later were studied prospectively for 12 months, with a series of bone mineral density measurements of the hips (dual energy X-ray absorptiometry) in the context of a randomised controlled trial. Untreated patients (n=13) experienced a decline in bone mineral density at the hemiplegic hip that was rapid, with the greatest losses in the trochanteric region of the affected side. This bone loss was prevented by the administration of a single 4 mg dose of the intravenous bisphosphonate, zoledronate (n=14) within 35 days of stroke onset. Computed tomography of the hips in 8 untreated patients more than a year after stroke confirmed that the greatest difference between sides was in the trochanteric region. Serum vitamin D measurements in 44 patients with acute stroke were substantially lower than healthy elderly controls, with 77% of patients in the insufficient range, suggesting that vitamin D insufficiency preceded stroke. Histomorphometric analysis of iliac bone biopsies from hemiplegic patients 10 weeks following stroke showed normal erosion parameters, but a striking decrease in the surface extent of osteoid when compared with healthy reference values. Unexpectedly, treatment with zoledronate was associated with a significantly higher osteoid surface compared with placebo treated subjects in cancellous, endocortical and cortical bone. Sclerostin, a newly discovered osteocyte-derived protein was studied using immunohistochemical staining of the bone biopsies. Sclerostin is known to be an inhibitor of active osteoblasts, which led to the hypothesis that in stroke, the proportion of osteocytes expressing sclerostin would be inversely associated with the surface extent of bone formation. Histological analysis revealed widespread expression of sclerostin in osteocytes and their canaliculi in all subjects. However, examining individual osteocytes in relation to bone forming surfaces revealed that newly embedded osteocytes did not express sclerostin until after primary mineralisation. It is proposed that this precise pattern and timing of sclerostin expression by osteocytes allows bone formation to continue locally (during remodelling), but prevents excessive new bone formation elsewhere, as seen in the single gene disorder sclerosteosis.

FcyRIIb controls bone marrow plasma cell persistence and apoptosis.

Mon, 01 Jan 2007 00:00:00 GMT

Title: FcyRIIb controls bone marrow plasma cell persistence and apoptosis. Authors: Xiang, Zou; Cutler, Antony J; Brownlie, Rebecca J; Fairfax, Kirsten; Lawlor, Kate E; Severinson, Eva; Walker, Elizabeth U; Manz, Rudolf A; Tarlinton, David M; Smith, Kenneth G C Abstract: The survival of long-lived plasma cells, which produce most serum immunoglobulin, is central to humoral immunity. We found here that the inhibitory Fc receptor FcgammaRIIb was expressed on plasma cells and controlled their persistence in the bone marrow. Crosslinking FcgammaRIIb induced apoptosis of plasma cells, which we propose contributes to the control of their homeostasis and suggests a method for therapeutic deletion. Plasma cells from mice prone to systemic lupus erythematosus did not express FcgammaRIIb and were protected from apoptosis. Human plasmablasts expressed FcgammaRIIb and were killed by crosslinking, as were FcgammaRIIb-expressing myeloma cells. Our results suggest that FcgammaRIIb controls bone marrow plasma cell persistence and that defects in it may contribute to autoantibody production.

Closed-loop insulin delivery in adults with type 1 diabetes

Mon, 08 Oct 2012 23:00:00 GMT

Title: Closed-loop insulin delivery in adults with type 1 diabetes Authors: Kumareswaran, Kavita Abstract: Achieving tight glucose control safely in type 1 diabetes with currently available methods of insulin delivery is challenging. Aggressive regimens carry an increased risk of hypoglycaemia, particularly overnight. Both alcohol consumption and exercise predispose further to low glucose levels. The demands are even greater in pregnancy where, in addition to limiting hypoglycaemia, avoidance of postprandial hyperglycaemia is critical to minimising adverse obstetric outcomes. The aim of my studies was to evaluate feasibility and safety of a closed-loop or ’artificial pancreas’ system linking insulin delivery with continuous glucose monitoring (CGM), in adults with type 1 diabetes in a controlled setting. Three randomised crossover studies compared closed-loop insulin delivery with conventional insulin pump therapy on two separate occasions, matched in meals and activities. During closed-loop visits, CGM values were entered into a computer containing a model predictive control algorithm which advised on basal insulin infusion for subcutaneous delivery, every 15 minutes. During control visits, usual insulin pump regimen was continued. The feasibility study evaluated overnight closed-loop in 12 adults (seven females, mean age 37.7 years, HbA1c 7.8%) following 60g- carbohydrate evening meal. A follow-up study assessed overnight closed-loop in 12 further adults (seven females, mean age 37.2 years, HbA1c 7.8%) following 100g-carbohydrate meal and (mean 564 ml) white wine. The third study evaluated 24 hours of closed-loop in 12 pregnant women (mean age 32.9 years, 19 to 23 weeks gestation, HbA1c 6.4%) during normal daily activities, including low and moderate intensity exercise. Activity and glucose levels were also measured during free-living. CGM performance during exercise was evaluated. Overnight closed-loop insulin delivery in adults, compared with conventional pump therapy, increased time spent with plasma glucose in target range (3.9−8.0 mmol/l) following both standard meal (81% versus 57%; p = 0.012) and large meal accompanied by alcohol (70% versus 46%; p = 0.012). Glycaemic variability, and time spent in hypo- and hyper- glycaemia were lowered. In pregnant women, day and night closed-loop insulin delivery was as effective as usual pump regimen (81% versus 81% time spent with plasma glucose 3.5−7.8 mmol/l; p = 0.754). Hypoglycaemia occurred following exercise, although closed-loop prevented nocturnal episodes. Glycaemic control during free-living was suboptimal, compared with controlled diet and exercise conditions. Accuracy of CGM was lower during exercise. In conclusion, these studies confirm the feasibility and efficacy of overnight closed-loop insulin delivery in adults with type 1 diabetes. Closed-loop is safe during pregnancy and may be beneficial in women with suboptimal glycaemic control. Meals and physical activity currently limit optimal daytime use of closed-loop.

Imaging atherosclerotic plaque inflammation with [18F]- fluorodeoxyglucose positron emission tomography

Mon, 06 Oct 2003 23:00:00 GMT

Title: Imaging atherosclerotic plaque inflammation with [18F]- fluorodeoxyglucose positron emission tomography Authors: Rudd, James H. F. Abstract: Inflammation is important in both the pathogenesis and outcome of atherosclerosis. Plaques containing numerous inflammatory cells, particularly macrophages, have a high risk of rupture, whereas those with fewer inflammatory cells are at lower risk. The current ‘gold standard’ technique for imaging atherosclerosis is x-ray contrast angiography, which provides high-resolution definition of the site and severity of luminal stenoses, but no information about plaque inflammation. Quantification of plaque inflammation is desirable both to predict risk of plaque rupture and to monitor the effects of atheroma-modifying therapies. This is important since recent studies strongly suggest that HMG Co-A reductase inhibitors promote plaque stability by decreasing plaque macrophage content and activity without substantially reducing plaque size and therefore angiographic appearance. FDG is a glucose analogue that is taken up by cells in proportion to their metabolic activity. In this work, the central hypothesis was that plaque inflammation could be visualised and quantified non-invasively using FDG-PET. Initially, THP-1 monocytes and buffy-coat macrophages were stimulated with cellular activators, and the effect on deoxyglucose uptake was observed. It was demonstrated that both types of cell accumulated deoxyglucose in proportion to their metabolic activity. Next, FDG uptake was assessed in endarterectomy specimens from patients with symptomatic carotid disease. Autoradiography of excised plaques confirmed accumulation of deoxyglucose in macrophage-rich areas. Subsequently, co-registered FDG-PET imaging was performed in patients with transient ischaemic attack. FDG accumulated within carotid plaques, with significantly more FDG being taken up into symptomatic plaques than contralateral asymptomatic lesions. Finally, a rabbit model of atherosclerosis was established to investigate two related questions: firstly, whether an animal PET scanner (MicroPet) might detect atheroma, and secondly whether FDG-PET could image and perhaps quantify both atheroma progression and regression. Aortic atheroma was identified by FDG-PET, but full quantification was not possible, because the microPet system is currently unable to perform studies with attenuation correction. In summary, it has been shown, both in vitro and in vivo, that inflammation within atherosclerotic plaques can be successfully imaged by FDG-PET. In addition, pilot data from an experimental study of atherosclerosis in rabbits suggested that serial imaging with this technique might be useful for monitoring the effects of anti-atheroma drugs.

The effect of glibenclamide on the pathogenesis of melioidosis

Tue, 06 Mar 2012 00:00:00 GMT

Title: The effect of glibenclamide on the pathogenesis of melioidosis Authors: Koh, Gavin Christian Kia Wee Abstract: Melioidosis is an important cause of community-acquired sepsis, endemic to Southeast Asia and Northern Australia. Melioidosis is caused by the soil saprophyte, Burkholderia pseudomallei, a motile Gram-negative bacillus, and is associated with a mortality rate that approaches 50% in Northeast Thailand. The most important risk factor for melioidosis is diabetes mellitus, and two-thirds of all adult patients with melioidosis have diabetes as a risk factor. It has been noted previously, however, that patients with diabetes have lower mortality than patients without diabetes. In this dissertation, we look at a cohort of 1160 consecutive adult melioidosis patients presenting to Sappasithiprasong Hospital in Ubon Ratchathani, Thailand, 410 (35%) of whom were diagnosed with diabetes prior to admission. We confirmed previous findings that diabetes protected from mortality in melioidosis, but also found that this protective effect was confined to a smaller subset of patients (208 patients) who were treated with glibenclamide prior to admission. Patients with hyperglycaemia (but no diagnosis of diabetes prior to admission) had the same mortality rate as patients without diabetes. In vitro experiments found no inhibitory effect of glibenclamide on bacterial growth, and we therefore looked for evidence of an effect of glibenclamide on the host. We conducted a gene expression study of circulating blood leukocytes in melioidosis patients and compared them to uninfected controls. In this study, we found that glibenclamide was associated with an anti-inflammatory effect on the host response to melioidosis. To further elucidate a mechanism for the action of glibenclamide, we studied the effect of glibenclamide therapy in a mouse model of melioidosis and found that the effect of glibenclamide was specific to interleukin-1β secretion. This reduction in interleukin-1β secretion was associated with reduced cellular influx into the lungs as well as lower bacterial loads in blood, liver and spleen.

Molecular detection and speciation of pathogenic Leptospira spp. in blood from patients with culture-negative leptospirosis

Tue, 13 Dec 2011 00:00:00 GMT

Title: Molecular detection and speciation of pathogenic Leptospira spp. in blood from patients with culture-negative leptospirosis Authors: Boonsilp, Siriphan; Thaipadungpanit, Janjira; Amornchai, Premjit; Wuthiekanun, Vanaporn; Chierakul, Wirongrong; Limmathurotsakul, Direk; Day, Nicholas P; Peacock, Sharon J Abstract: Abstract Background Pathogenic Leptospira spp. present in the blood of patients with leptospirosis during the first week of symptoms can be detected using culture or PCR. A proportion of patients who are positive by PCR are negative by culture. Leptospira spp. are fastidious bacteria, and we hypothesized that a false-negative culture result may represent infection with a distinct bacterial subset that fail to grow in standard culture medium. Methods We evaluated our hypothesis during a prospective study of 418 consecutive patients presenting to a hospital in northeast Thailand with an acute febrile illness. Admission blood samples were taken for Leptospira culture and PCR. A single tube nested PCR that amplified a region of the rrs gene was developed and applied, amplicons sequenced and a phylogenetic tree reconstructed. Results 39/418 (9%) patients were culture-positive for Leptospira spp., and 81/418 (19%) patients were culture-negative but rrs PCR-positive. The species associated with culture-positive leptospirosis (37 L. interrogans and 2 L. borgpetersenii) were comparable to those associated with culture-negative, PCR-positive leptospirosis (76 L. interrogans, 4 L. borgpetersenii, 1 unidentified, possibly new species). Conclusion Molecular speciation failed to identify a unique bacterial subset in patients with culture-negative, PCR-positive leptospirosis. The rate of false-negative culture was high, and we speculate that antibiotic pre-treatment is the most likely explanation for this. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.

A genome wide association study of pulmonary tuberculosis susceptibility in Indonesians

Fri, 13 Jan 2012 00:00:00 GMT

Title: A genome wide association study of pulmonary tuberculosis susceptibility in Indonesians Authors: Png, Eileen; Alisjahbana, Bachti; Sahiratmadja, Edhyana; Marzuki, Sangkot; Nelwan, Ron; Balabanova, Yanina; Nikolayevskyy, Vladyslav; Drobniewski, Francis; Nejentsev, Sergey; Adnan, Iskandar; van de Vosse, Esther; Hibberd, Martin L; van Crevel, Reinout; Ottenhoff, Tom HM; Seielstad, Mark Abstract: Abstract Background There is reason to expect strong genetic influences on the risk of developing active pulmonary tuberculosis (TB) among latently infected individuals. Many of the genome wide linkage and association studies (GWAS) to date have been conducted on African populations. In order to identify additional targets in genetically dissimilar populations, and to enhance our understanding of this disease, we performed a multi-stage GWAS in a Southeast Asian cohort from Indonesia. Methods In stage 1, we used the Affymetrix 100 K SNP GeneChip marker set to genotype 259 Indonesian samples. After quality control filtering, 108 cases and 115 controls were analyzed for association of 95,207 SNPs. In stage 2, we attempted validation of 2,453 SNPs with promising associations from the first stage, in 1,189 individuals from the same Indonesian cohort, and finally in stage 3 we selected 251 SNPs from this stage to test TB association in an independent Caucasian cohort (n = 3,760) from Russia. Results Our study suggests evidence of association (P = 0.0004-0.0067) for 8 independent loci (nominal significance P < 0.05), which are located within or near the following genes involved in immune signaling: JAG1, DYNLRB2, EBF1, TMEFF2, CCL17, HAUS6, PENK and TXNDC4. Conclusions Mechanisms of immune defense suggested by some of the identified genes exhibit biological plausibility and may suggest novel pathways involved in the host containment of infection with TB. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.

COPD association and repeatability of blood biomarkers in the ECLIPSE cohort

Fri, 04 Nov 2011 00:00:00 GMT

Title: COPD association and repeatability of blood biomarkers in the ECLIPSE cohort Authors: Dickens, Jennifer A; Miller, Bruce E; Edwards, Lisa D; Silverman, Edwin K; Lomas, David A; Tal-Singer, Ruth; (ECLIPSE) study investigators, Evaluation of COPD Longitudinally to Identify Surrogate ENDPOINTS Abstract: Abstract Background There is a need for biomarkers to better characterise individuals with COPD and to aid with the development of therapeutic interventions. A panel of putative blood biomarkers was assessed in a subgroup of the Evaluation of COPD Longitudinally to Identify Surrogate Endpoints (ECLIPSE) cohort. Methods Thirty-four blood biomarkers were assessed in 201 subjects with COPD, 37 ex-smoker controls with normal lung function and 37 healthy non-smokers selected from the ECLIPSE cohort. Biomarker repeatability was assessed using baseline and 3-month samples. Intergroup comparisons were made using analysis of variance, repeatability was assessed through Bland-Altman plots, and correlations between biomarkers and clinical characteristics were assessed using Spearman correlation coefficients. Results Fifteen biomarkers were significantly different in individuals with COPD when compared to former or non-smoker controls. Some biomarkers, including tumor necrosis factor-α and interferon-γ, were measurable in only a minority of subjects whilst others such as C-reactive protein showed wide variability over the 3-month replication period. Fibrinogen was the most repeatable biomarker and exhibited a weak correlation with 6-minute walk distance, exacerbation rate, BODE index and MRC dyspnoea score in COPD subjects. 33% (66/201) of the COPD subjects reported at least 1 exacerbation over the 3 month study with 18% (36/201) reporting the exacerbation within 30 days of the 3-month visit. CRP, fibrinogen interleukin-6 and surfactant protein-D were significantly elevated in those COPD subjects with exacerbations within 30 days of the 3-month visit compared with those individuals that did not exacerbate or whose exacerbations had resolved. Conclusions Only a few of the biomarkers assessed may be useful in diagnosis or management of COPD where the diagnosis is based on airflow obstruction (GOLD). Further analysis of more promising biomarkers may reveal utility in subsets of patients. Fibrinogen in particular has emerged as a potentially useful biomarker from this cohort and requires further investigation. Trial Registration SCO104960, clinicaltrials.gov identifier NCT00292552 Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.

Statistical analysis of end-points in cancer clinical trials

Tue, 01 Mar 1994 00:00:00 GMT

Title: Statistical analysis of end-points in cancer clinical trials Authors: Campbell, Ian Abstract: The major end-points arising from cancer clinical trials are reviewed. These are: tumour response, treatment morbidity, survival with related data, and quality of life. A survey of tumour response data from 81 published clinical trials found the most common statistical test in use to be a Chi squared test of the total response rate, but a total of 21 different statistical methods were used. The various statistical tests available are reviewed, including the Mann-Whitney test and the Chi squared test for trend which make use of all the categories of response and their intrinsic order. The assumptions underlying the tests are described. Theoretical considerations support the Mann-Whitney test as the optimum choice for the analysis of tumour response data. Methods for comparing alternative statistical tests are summarised, and a new method is described which uses a number of typical sets of data to estimate the relative efficiency of two statistical tests by the median value of the square of the ratio of the z-values. Using this technique, and data from the 81 trials, the Mann-Whitney test is found to be around 40% more efficient than the Chi squared test of the total response rate (this increased efficiency is equivalent to increasing the recruitment to the trial by 40%). This practical result is confirmed by mathematical modelling of tumour response using the power relation of the Mann-Whitney test for ordered categorical data, which is derived. Clinical data is found to fit best a shift model which assumes homogeneity of treatment effect across the different grades of response. On the basis of this model, the Mann-Whitney test is found to be 30% to 110% more efficient than a Chi squared test of the total response rate. The similarities of acute morbidity data to tumour response data lead to similar general conclusions on the optimum method of statistical analysis. In a survey of 36 published clinical trials, the most common method of statistical analysis was again a Chi squared test of a dichotomy (such as no morbidity versus morbidity of any grade). Analysis of data from these trials shows the Mann-Whitney test to be more efficient by around 30%. A survey of 81 papers reporting tumour response in clinical trials found that few of them used methods of estimation of the difference between the treatments, or derived confidence intervals of the size of such a difference. Methods of estimation and calculation of confidence intervals were found even less often in a survey of methods of presentation of morbidity results. The possible reasons for this are discussed. It is concluded that the current methods of analysis of tumour response data and many sets of acute treatment morbidity data are not optimum, and a change should be made from the Chi squared test to the Mann-Whitney test. Such a change could be equivalent to an increase in recruitment into many cancer clinical trials of around 40%.

Report from the Second Cytomegalovirus and Immunosenescence Workshop

Thu, 27 Oct 2011 23:00:00 GMT

Title: Report from the Second Cytomegalovirus and Immunosenescence Workshop Authors: Wills, Mark; Akbar, Arne; Beswick, Mark; Bosch, Jos A; Caruso, Calogero; Colonna-Romano, Giuseppina; Dutta, Ambarish; Franceschi, Claudio; Fulop, Tamas; Gkrania-Klotsas, Effrossyni; Goronzy, Joerg; Griffiths, Stephen J; Henson, Sian; Herndler-Brandstetter, Dietmar; Hill, Ann; Kern, Florian; Klenerman, Paul; Macallan, Derek; Macualay, Richard; Maier, Andrea B; Mason, Gavin; Melzer, David; Morgan, Matthew; Moss, Paul; Nikolich-Zugich, Janko; Pachnio, Annette; Riddell, Natalie; Roberts, Ryan; Sansoni, Paolo; Sauce, Delphine; Sinclair, John; Solana, Rafael; Strindhall, Jan; Trzonkowski, Piotr; van Lier, Rene; Vescovini, Rosanna; Wang, George; Westendorp, Rudi; Pawelec, Graham Abstract: Abstract The Second International Workshop on CMV & Immunosenescence was held in Cambridge, UK, 2-4th December, 2010. The presentations covered four separate sessions: cytomegalovirus and T cell phenotypes; T cell memory frequency, inflation and immunosenescence; cytomegalovirus in aging, mortality and disease states; and the immunobiology of cytomegalovirus-specific T cells and effects of the virus on vaccination. This commentary summarizes the major findings of these presentations and references subsequently published work from the presenter laboratory where appropriate and draws together major themes that were subsequently discussed along with new areas of interest that were highlighted by this discussion. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.

Shaping retroviral genomes

Sun, 02 Oct 2011 23:00:00 GMT

Title: Shaping retroviral genomes Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.

LCZ696, an angiotensin receptor neprilysin inhibitor (ARNI): clinical development in heart failure and hypertension

Sun, 31 Jul 2011 23:00:00 GMT

Title: LCZ696, an angiotensin receptor neprilysin inhibitor (ARNI): clinical development in heart failure and hypertension Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.

Phosphoinositide 3-kinase: a critical signalling event in pulmonary cells

Wed, 07 Jun 2000 23:00:00 GMT

Title: Phosphoinositide 3-kinase: a critical signalling event in pulmonary cells Abstract: Abstract Phosphoinositide 3-kinases (PI-3Ks) are enzymes that generate lipid second messenger molecules, resulting in the activation of multiple intracellular signalling cascades. These events regulate a broad array of cellular responses including survival, activation, differentiation and proliferation and are now recognised to have a key role in a number of physiological and pathophysiological processes in the lung. PI-3Ks contribute to the pathogenesis of asthma by influencing the proliferation of airways smooth muscle and the recruitment of eosinophils, and affect the balance between the harmful and protective responses in pulmonary inflammation and infection by the modulation of granulocyte recruitment, activation and apoptosis. In addition they also seem to exert a critical influence on the malignant phenotype of small cell lung cancer. PI-3K isoforms and their downstream targets thus provide novel therapeutic targets for intervention in a broad spectrum of respiratory diseases. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.

The genetics of chronic obstructive pulmonary disease

Thu, 11 Jan 2001 00:00:00 GMT

Title: The genetics of chronic obstructive pulmonary disease Abstract: Abstract Chronic obstructive pulmonary disease (COPD) is a significant cause of global morbidity and mortality. Previous studies have shown that COPD aggregates in families, suggesting a genetic predisposition to airflow obstruction. Many candidate genes have been assessed, but the data are often conflicting. We review the genetic factors that predispose smokers to COPD and highlight the future role of genomic scans in identifying novel susceptibility genes. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.

High-throughput sequencing identifies STAT3 as the DNA-associated factor for p53 - NF-kappaB - complex-dependent gene expression in human heart failure

Sun, 13 Jun 2010 23:00:00 GMT

Title: High-throughput sequencing identifies STAT3 as the DNA-associated factor for p53 - NF-kappaB - complex-dependent gene expression in human heart failure Authors: Choy, Mun-Kit; Movassagh, Mehregan; Siggens, Lee; Vujic, Ana; Goddard, Martin; Sanchez, Ana; Perkins, Neil; Figg, Nichola; Bennett, Martin; Carroll, Jason; Foo, Roger S-Y Abstract: Abstract Background Genome-wide maps of DNA regulatory elements and their interaction with transcription factors may form a framework for understanding regulatory circuits and gene expression control in human disease, but how these networks, comprising transcription factors and DNA-binding proteins, form complexes, interact with DNA and modulate gene expression remains largely unknown. Methods Using microRNA-21 (mir-21), which is an example of genes that are regulated in heart failure, we performed chromatin immunoprecipitation (ChIP) assays to determine the occupancy of transcription factors at this genetic locus. Tissue ChIP was further performed using human hearts and genome-wide occupancies of these transcription factors were analyzed by high-throughput sequencing. Results We show that the transcription factor p53 piggy-backs onto NF-κB/RELA and utilizes the κB-motif at a cis-regulatory region to control mir-21 expression. p53 behaves as a co-factor in this complex because despite a mutation in its DNA binding domain, mutant p53 was still capable of binding RELA and the cis-element, and inducing mir-21 expression. In dilated human hearts where mir-21 upregulation was previously demonstrated, the p53-RELA complex was also associated with this cis-element. Using high-throughput sequencing, we analyzed genome-wide binding sites for the p53-RELA complex in diseased and control human hearts and found a significant overrepresentation of the STAT3 motif. We further determined that STAT3 was necessary for the p53-RELA complex to associate with this cis-element and for mir-21 expression. Conclusions Our results uncover a mechanism by which transcription factors cooperate in a multi-molecular complex at a cis-regulatory element to control gene expression.

Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates

Thu, 26 Aug 2010 23:00:00 GMT

Title: Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates Authors: Sim, Bernice Meng Qi; Chantratita, Narisara; Ooi, Wen Fong; Nandi, Tannistha; Tewhey, Ryan; Wuthiekanun, Vanaporn; Thaipadungpanit, Janjira; Tumapa, Sarinna; Ariyaratne, Pramila; Sung, Wing-Kin; Sem, Xiao Hui; Chua, Hui Hoon; Ramnarayanan, Kalpana; Lin, Chi Ho; Liu, Yichun; Feil, Edward J; Glass, Mindy B; Tan, Gladys; Peacock, Sharon J; Tan, Patrick Abstract: Abstract Background Burkholderia thailandensis is a non-pathogenic environmental saprophyte closely related to Burkholderia pseudomallei, the causative agent of the often fatal animal and human disease melioidosis. To study B. thailandensis genomic variation, we profiled 50 isolates using a pan-genome microarray comprising genomic elements from 28 Burkholderia strains and species. Results Of 39 genomic regions variably present across the B. thailandensis strains, 13 regions corresponded to known genomic islands, while 26 regions were novel. Variant B. thailandensis isolates exhibited isolated acquisition of a capsular polysaccharide biosynthesis gene cluster (B. pseudomallei-like capsular polysaccharide) closely resembling a similar cluster in B. pseudomallei that is essential for virulence in mammals; presence of this cluster was confirmed by whole genome sequencing of a representative variant strain (B. thailandensis E555). Both whole-genome microarray and multi-locus sequence typing analysis revealed that the variant strains formed part of a phylogenetic subgroup distinct from the ancestral B. thailandensis population and were associated with atypical isolation sources when compared to the majority of previously described B. thailandensis strains. In functional assays, B. thailandensis E555 exhibited several B. pseudomallei-like phenotypes, including colony wrinkling, resistance to human complement binding, and intracellular macrophage survival. However, in murine infection assays, B. thailandensis E555 did not exhibit enhanced virulence relative to other B. thailandensis strains, suggesting that additional factors are required to successfully colonize and infect mammals. Conclusions The discovery of such novel variant strains demonstrates how unbiased genomic surveys of non-pathogenic isolates can reveal insights into the development and emergence of new pathogenic species. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.

Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling

Fri, 30 Jan 2004 00:00:00 GMT

Title: Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling Authors: Naderi, Ali; Ahmed, Ahmed A; Barosa-Morais, Nuno L; Aparicio, Samuel; Brenton, James D; Caldas, Carlos Abstract: Abstract Background Expression microarrays have evolved into a powerful tool with great potential for clinical application and therefore reliability of data is essential. RNA amplification is used when the amount of starting material is scarce, as is frequently the case with clinical samples. Purification steps are critical in RNA amplification and labelling protocols, and there is a lack of sufficient data to validate and optimise the process. Results Here the purification steps involved in the protocol for indirect labelling of amplified RNA are evaluated and the experimentally determined best method for each step with respect to yield, purity, size distribution of the transcripts, and dye coupling is used to generate targets tested in replicate hybridisations. DNase treatment of diluted total RNA samples followed by phenol extraction is the optimal way to remove genomic DNA contamination. Purification of double-stranded cDNA is best achieved by phenol extraction followed by isopropanol precipitation at room temperature. Extraction with guanidinium-phenol and Lithium Chloride precipitation are the optimal methods for purification of amplified RNA and labelled aRNA respectively. Conclusion This protocol provides targets that generate highly reproducible microarray data with good representation of transcripts across the size spectrum and a coefficient of repeatability significantly better than that reported previously. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.

The retroviral RNA dimer linkage: different structures may reflect different roles

Tue, 17 Aug 2004 23:00:00 GMT

Title: The retroviral RNA dimer linkage: different structures may reflect different roles Authors: Greatorex, Jane S Abstract: Abstract Retroviruses are unique among virus families in having dimeric genomes. The RNA sequences and structures that link the two RNA molecules vary, and these differences provide clues as to the role of this feature in the viral lifecycles. This review draws upon examples from different retroviral families. Differences and similarities in both secondary and tertiary structure are discussed. The implication of varying roles for the dimer linkage in related viruses is considered. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.

Blockade of chemokine-induced signalling inhibits CCR5-dependent HIV infection in vitrowithout blocking gp120/CCR5 interaction

Sun, 03 Apr 2005 23:00:00 GMT

Title: Blockade of chemokine-induced signalling inhibits CCR5-dependent HIV infection in vitrowithout blocking gp120/CCR5 interaction Authors: Grainger, David J; Lever, Andrew M L Abstract: Abstract Background Cellular infection with human immunodeficiency virus (HIV) both in vitro and in vivo requires a member of the chemokine receptor family to act as a co-receptor for viral entry. However, it is presently unclear to what extent the interaction of HIV proteins with chemokine receptors generates intracellular signals that are important for productive infection. Results In this study we have used a recently described family of chemokine inhibitors, termed BSCIs, which specifically block chemokine-induced chemotaxis without affecting chemokine ligands binding to their receptors. The BSCI termed Peptide 3 strongly inhibited CCR5 mediated HIV infection of THP-1 cells (83 ± 7% inhibition assayed by immunofluoresence staining), but had no effect on gp120 binding to CCR5. Peptide 3 did not affect CXCR4-dependent infection of Jurkat T cells. Conclusion These observations suggest that, in some cases, intracellular signals generated by the chemokine coreceptor may be required for a productive HIV infection.

Identification of unique reciprocal and non reciprocal cross packaging relationships between HIV-1, HIV-2 and SIV reveals an efficient SIV/HIV-2 lentiviral vector system with highly favourable features for in vivo testing and clinical usage

Thu, 15 Sep 2005 23:00:00 GMT

Title: Identification of unique reciprocal and non reciprocal cross packaging relationships between HIV-1, HIV-2 and SIV reveals an efficient SIV/HIV-2 lentiviral vector system with highly favourable features for in vivo testing and clinical usage Authors: Strappe, Padraig M; Hampton, David W; Brown, Douglas; Gonzales, Begona-cachon; Caldwell, Maeve; Fawcett, James W; Lever, Andrew M L Abstract: Abstract Background Lentiviral vectors have shown immense promise as vehicles for gene delivery to non-dividing cells particularly to cells of the central nervous system (CNS). Improvements in the biosafety of viral vectors are paramount as lentiviral vectors move into human clinical trials. This study investigates the packaging relationship between gene transfer (vector) and Gag-Pol expression constructs of HIV-1, HIV-2 and SIV. Cross-packaged vectors expressing GFP were assessed for RNA packaging, viral vector titre and their ability to transduce rat primary glial cell cultures and human neural stem cells. Results HIV-1 Gag-Pol demonstrated the ability to cross package both HIV-2 and SIV gene transfer vectors. However both HIV-2 and SIV Gag-Pol showed a reduced ability to package HIV-1 vector RNA with no significant gene transfer to target cells. An unexpected packaging relationship was found to exist between HIV-2 and SIV with SIV Gag-Pol able to package HIV-2 vector RNA and transduce dividing SV2T cells and CNS cell cultures with an efficiency equivalent to the homologous HIV-1 vector however HIV-2 was unable to deliver SIV based vectors. Conclusion This new non-reciprocal cross packaging relationship between SIV and HIV-2 provides a novel way of significantly increasing bio-safety with a reduced sequence homology between the HIV-2 gene transfer vector and the SIV Gag-Pol construct thus ensuring that vector RNA packaging is unidirectional. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.