Proteomics, a systems biology based approach to investigations of Jatropha curcas seeds

Poster presentation from IUFRO Tree Biotechnology Conference 2011: From Genomes to Integration and Delivery Arraial dAjuda, Bahia, Brazil. 26 June - 2 July 2011(VLID)90651

EnzMet™: An Enzymatic Metallography Reagent for Accurately Delineating Neuronal Boundaries for Segmenting Gap Junction-Coupled Neurons in their Three-dimensional Space

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 - August 2, 201

Effectiveness of a real-life program (DIAfit) to promote physical activity in patients with type 2 diabetes: a pragmatic cluster randomized clinical trial.

INTRODUCTION The aim of this study was to evaluate the effectiveness of a real-life clinical physical activity program (DIAfit) on improving physical fitness, body composition, and cardiometabolic health in an unselected population with type 2 diabetes mellitus, and to compare the effects of two variants a different exercise frequencies on the same outcomes. RESEARCH DESIGN AND METHODS This was a cluster randomized-controlled assessor-blind trial conducted in 11 clinical centres in Switzerland. All participants in the clinical program with type 2 diabetes were eligible and were randomized to either standard (3 sessions/week for 12 weeks) or alternative (1 session/week for the first four weeks, then 2 sessions/week for the rest of 16 weeks) physical activity program each consisting of 36 sessions of combined aerobic and resistance exercise. Allocation was concealed by a central office unrelated to the study. The primary outcome was aerobic fitness. Secondary outcome measures included: body composition, BMI, HbA1c, muscle strength, walking speed, balance, flexibility, blood pressure, lipid profile. RESULTS All 185 patients with type 2 diabetes (mean age 59.7 +-10.2 years, 48% women) agreed to participate and were randomized in two groups: a standard group (n=88) and an alternative group (n=97)). There was an 11% increase in aerobic fitness after the program (12.5 Watts; 95% CI 6.76 to 18.25; p<0.001). Significant improvements in physical fitness, body composition, and cardiometabolic parameters were observed at the end of the DIAfit program (improvements between 2-29%) except for lean body mass, triglycerides and cholesterol. No differences were observed between both programs, except for a larger weight reduction of -0.97kg (95% CI -0.04 to -1.91; p=0.04) in the standard program. CONCLUSIONS Both frequency variants of the nation-wide DIAfit program had beneficial effects on physical fitness, HbA1c, body composition, and blood pressure in type 2 diabetes patients and differences were negligible. CLINICAL TRIAL REGISTRATION clinicaltrials.gov, identifier NCT01289587

D-Light on promoters : a client-server system for the analysis and visualization of cis-regulatory elements

Background: The binding of transcription factors to DNA plays an essential role in the regulation of gene expression. Numerous experiments elucidated binding sequences which subsequently have been used to derive statistical models for predicting potential transcription factor binding sites (TFBS). The rapidly increasing number of genome sequence data requires sophisticated computational approaches to manage and query experimental and predicted TFBS data in the context of other epigenetic factors and across different organisms. Results: We have developed D-Light, a novel client-server software package to store and query large amounts of TFBS data for any number of genomes. Users can add small-scale data to the server database and query them in a large scale, genome-wide promoter context. The client is implemented in Java and provides simple graphical user interfaces and data visualization. Here we also performed a statistical analysis showing what a user can expect for certain parameter settings and we illustrate the usage of D-Light with the help of a microarray data set. Conclusions: D-Light is an easy to use software tool to integrate, store and query annotation data for promoters. A public D-Light server, the client and server software for local installation and the source code under GNU GPL license are available at http://biwww.che.sbg.ac.at/dlight.Josef Laimer, Clemens J Zuzan, Tobias Ehrenberger, Monika Freudenberger, Simone Gschwandtner, Carina Lebherz and Peter Lackne

In silico design of Phl p 6 variants with altered Fold-Stability significantly impacts antigen processing, immunogenicity and immune polarization

Introduction: Understanding, which factors determine the immunogenicity and immune polarizing properties of proteins, is an important prerequisite for designing better vaccines and immunotherapeutics. While extrinsic immune modulatory factors such as pathogen associated molecular patterns are well-understood, far less is known about the contribution of protein inherent features. Protein fold-stability represents such an intrinsic feature contributing to immunogenicity and immune polarization by influencing the amount of peptide-MHC II complexes (pMHCII). Here, we investigated how modulation of the fold-stability of the grass pollen allergen Phl p 6 affects its ability to stimulate immune responses and T cell polarization. Methods: MAESTRO software was used for in silico prediction of stabilizing or destabilizing point mutations. Mutated proteins were expressed in E. coli, and their thermal stability and resistance to endolysosomal proteases was determined. Resulting peptides were analyzed by mass spectrometry. The structure of the most stable mutant protein was assessed by X-ray crystallography. We evaluated the capacity of the mutants to stimulate T cell proliferation in vitro, as well as antibody responses and T cell polarization in vivo in an adjuvant-free BALB/c mouse model. Results: In comparison to wild-type protein, stabilized or destabilized mutants displayed changes in thermal stability ranging from −5 to +14°. While highly stabilized mutants were degraded very slowly, destabilization led to faster proteolytic processing in vitro. This was confirmed in BMDCs, which processed and presented the immunodominant epitope from a destabilized mutant more efficiently compared to a highly stable mutant. In vivo, stabilization resulted in a shift in immune polarization from TH2 to TH1/TH17 as indicated by higher levels of IgG2a and increased secretion of TNF-α, IFN-γ, IL-17, and IL-21. Conclusion: MAESTRO software was very efficient in detecting single point mutations that increase or reduce fold-stability. Thermal stability correlated well with the speed of proteolytic degradation and presentation of peptides on the surface of dendritic cells in vitro. This change in processing kinetics significantly influenced the polarization of T cell responses in vivo. Modulating the fold-stability of proteins thus has the potential to optimize and polarize immune responses, which opens the door to more efficient design of molecular vaccines

Cardiac rehabilitation in Austria: long term health-related quality of life outcomes

<p>Abstract</p> <p>Background</p> <p>The goal of cardiac rehabilitation programs is not only to prolong life but also to improve physical functioning, symptoms, well-being, and health-related quality of life (HRQL). The aim of this study was to document the long-term effect of a 1-month inpatient cardiac rehabilitation intervention on HRQL in Austria.</p> <p>Methods</p> <p>Patients (N = 487, 64.7% male, age 60.9 ± 12.5 SD years) after myocardial infarction, with or without percutaneous interventions, coronary artery bypass grafting or valve surgery underwent inpatient cardiac rehabilitation and were included in this long-term observational study (two years follow-up). HRQL was measured with both the MacNew Heart Disease Quality of Life Instrument [MacNew] and EuroQoL-5D [EQ-5D].</p> <p>Results</p> <p>All MacNew scale scores improved significantly (p < 0.001) and exceeded the minimal important difference (0.5 MacNew points) by the end of rehabilitation. Although all MacNew scale scores deteriorated significantly over the two year follow-up period (p < .001), all MacNew scale scores still remained significantly higher than the pre-rehabilitation values. The mean improvement after two years in the MacNew social scale exceeded the minimal important difference while MacNew scale scores greater than the minimal important difference were reported by 40-49% of the patients.</p> <p>Two years after rehabilitation the mean improvement in the EQ-5D Visual Analogue Scale score was not significant with no significant change in the proportion of patients reporting problems at this time.</p> <p>Conclusion</p> <p>These findings provide a first indication that two years following inpatient cardiac rehabilitation in Austria, the long-term improvements in HRQL are statistically significant and clinically relevant for almost 50% of the patients. Future controlled randomized trials comparing different cardiac rehabilitation programs are needed.</p

Effects of a carbohydrate-restricted diet on emerging plasma markers for cardiovascular disease

BACKGROUND: Increasing evidence supports carbohydrate restricted diets (CRD) for weight loss and improvement in traditional markers for cardiovascular disease (CVD); less is known regarding emerging CVD risk factors. We previously reported that a weight loss intervention based on a CRD (% carbohydrate:fat:protein = 13:60:27) led to a mean weight loss of 7.5 kg and a 20% reduction of abdominal fat in 29 overweight men. This group showed reduction in plasma LDL-cholesterol and triglycerides and elevations in HDL-cholesterol as well as reductions in large and medium VLDL particles and increases in LDL particle size. In this study we report on the effect of this intervention with and without fiber supplementation on plasma homocysteine, lipoprotein (a) [Lp(a)], C-reactive protein (CRP), interleukin-6 (IL-6), and tumor necrosis factor alpha (TNF-α). METHODS: Twenty nine overweight men [body mass index (BMI) 25–35 kg/m(2)] aged 20–69 years consumed an ad libitum CRD (% carbohydrate:fat:protein = 13:60:27) including a standard multivitamin every other day for 12 wk. Subjects were matched by age and BMI and randomly assigned to consume 3 g/d of either a soluble fiber supplement (n = 14) or placebo (n = 15). RESULTS: There were no group or interaction (fiber × time) main effects, but significant time effects were observed for several variables. Energy intake was spontaneously reduced (-30.5%). This was accompanied by an increase in protein intake (96.2 ± 29.8 g/d to 107.3 ± 29.7 g/d) and methionine intake (2.25 ± 0.7 g/d, to 2.71 ± 0.78 g/d; P < 0.001). Trans fatty acid intake was significantly reduced (-38.6%) while dietary folate was unchanged, as was plasma homocysteine. Bodyweight (-7.5 ± 2.5 kg) was reduced as was plasma Lp(a) (-11.3%). Changes in plasma Lp(a) correlated with reductions in LDL-cholesterol (r = .436, P < 0.05) and fat loss (r = .385, P < 0,05). At wk 12, both CRP (-8.1%) and TNF-α (-9.3%) were reduced (P < 0.05) independently of weight loss. IL-6 concentrations were unchanged. CONCLUSION: A diet based on restricting carbohydrates leads to spontaneous caloric reduction and subsequent improvement in emerging markers of CVD in overweight/obese men who are otherwise healthy

Epidermólisis ampollosa, reporte de un caso

Introduction: epidermolysis bullosa refers to a heterogeneous group of chronic hereditary pimple-like diseases affecting the skin and mucosae with blisters and vesicles after minimal injury, with variable involvement of other organs.Case report: 3-year-old female patient with exulcerated skin lesions and some erythema crust-plaques, with scaling at exposure sites such as hands, knees, feet, back of the neck and genitals. She was admitted to “Hermanos Cordové” Pediatric Teaching Hospital in Manzanillo. The medical care was based on maintaining the integrity of the skin avoiding trauma, temperature control, nutrition and prevention of secondary infections. A simple epidermolysis bullosa is diagnosed by skin biopsy.Conclusions: the disease is scarcely known with low incidence and prevalence. It is a major problem in the family and social environment, as parents are dealing with a rare disease of genetic origin and poor prognosis. Medical-social support helps to minimize the problems by means of information and coordination. Treatment requires the care of a multidisciplinary and specialized team.Introducción: la epidermólisis bulosa se refiere a un grupo heterogéneo de enfermedades hereditarias ampulosas crónicas, que afectan a la piel y las mucosas con formación de ampollas y vesículas tras mínimos traumatismos, con afectación variable de otros órganos.Presentación de caso: paciente femenina de 3 años de edad con lesiones de piel exulceradas y algunas eritematocostrosas en placas, con descamación en sitios de exposición como manos, rodillas, pies, parte posterior del cuello y genitales. Se encontraba ingresada en el Hospital Pediátrico Docente “Hermanos Cordové", de Manzanillo. Los cuidados médicos se basaron en mantener la entereza de la piel evitando traumatismo, control de la temperatura, nutrición y prevención de infecciones secundarias. Se diagnostica por biopsia de piel una epidermólisis bulosa simple. Conclusiones: la enfermedad es poco conocida con baja incidencia y prevalencia. Supone un problema de gran magnitud en el entorno familiar y social, al enfrentarse los padres a una enfermedad rara con origen genético y de mal pronóstico. El apoyo médico-social ayuda a minimizar los problemas, a través de la información y coordinación. Para su tratamiento es necesaria la atención de un equipo multidisciplinario y especializado.

Mutations in the histone methyltransferase gene KMT2B cause complex early-onset dystonia.

Histone lysine methylation, mediated by mixed-lineage leukemia (MLL) proteins, is now known to be critical in the regulation of gene expression, genomic stability, cell cycle and nuclear architecture. Despite MLL proteins being postulated as essential for normal development, little is known about the specific functions of the different MLL lysine methyltransferases. Here we report heterozygous variants in the gene KMT2B (also known as MLL4) in 27 unrelated individuals with a complex progressive childhood-onset dystonia, often associated with a typical facial appearance and characteristic brain magnetic resonance imaging findings. Over time, the majority of affected individuals developed prominent cervical, cranial and laryngeal dystonia. Marked clinical benefit, including the restoration of independent ambulation in some cases, was observed following deep brain stimulation (DBS). These findings highlight a clinically recognizable and potentially treatable form of genetic dystonia, demonstrating the crucial role of KMT2B in the physiological control of voluntary movement.Funding for the project was provided by the Wellcome Trust for UK10K (WT091310) and DDD Study. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund [grant number HICF-1009-003] - see www.ddduk.org/access.html for full acknowledgement. This work was supported in part by the Intramural Research Program of the National Human Genome Research Institute and the Common Fund, NIH Office of the Director. This work was supported in part by the German Ministry of Research and Education (grant nos. 01GS08160 and 01GS08167; German Mental Retardation Network) as part of the National Genome Research Network to A.R. and D.W. and by the Deutsche Forschungsgemeinschaft (AB393/2-2) to A.R. Brain expression data was provided by the UK Human Brain Expression Consortium (UKBEC), which comprises John A. Hardy, Mina Ryten, Michael Weale, Daniah Trabzuni, Adaikalavan Ramasamy, Colin Smith and Robert Walker, affiliated with UCL Institute of Neurology (J.H., M.R., D.T.), King’s College London (M.R., M.W., A.R.) and the University of Edinburgh (C.S., R.W.)