Caspase Cleavage Sites in the Human Proteome: CaspDB,a Database of Predicted Substrates

Caspases are enzymes belonging to a conserved family of cysteine-dependent aspartic-specific proteases that are involved in vital cellular processes and play a prominent role in apoptosis and inflammation. Determining all relevant protein substrates of caspases remains a challenging task. Over 1500 caspase substrates have been discovered in the human proteome according to published data and new substrates are discovered on a daily basis. To aid the discovery process we developed a caspase cleavage prediction method using the recently published curated MerCASBA database of experimentally determined caspase substrates and a Random Forest classification method. On both internal and external test sets, the ranking of predicted cleavage positions is superior to all previously developed prediction methods. The in silico predicted caspase cleavage positions in human proteins are available from a relational database: CaspDB. Our database provides information about potential cleavage sites in a verified set of all human proteins collected in Uniprot and their orthologs, allowing for tracing of cleavage motif conservation. It also provides information about the positions of disease-annotated single nucleotide polymorphisms, and posttranslational modifications that may modulate the caspase cleaving efficiency.     

Myocardial Metastases on 6-[18F] fluoro-L-DOPA PET/CT: A Retrospective Analysis of 116 Serotonin Producing Neuroendocrine Tumour Patients

Purpose

This study evaluates the prevalence of cardiac metastases in patients with serotonin producing neuroendocrine tumours (NET), examined with ¹⁸F-FDOPA PET/CT, and the relationship of these metastases to the presence of carcinoid heart disease (CHD) based on echocardiography.

Background

CHD occurs in patients with serotonin producing NET. The diagnostic method of choice remains echocardiography. The precise prevalence of cardiac metastases is unknown given the limitations of standard technologies. Nuclear medicine modalities have the potential to visualize metastases of NET.

Methods

All patients who underwent ¹⁸F-FDOPA PET/CT because of serotonin producing NET between November 2009 and May 2012 were retrospectively analyzed. The presence of cardiac metastasis was defined as myocardial tracer accumulation higher than the surrounding physiological myocardial uptake. Laboratory tests and transthoracic echocardiography (TTE) results were digitally collected.

Results

116 patients (62 male) underwent ¹⁸F-FDOPA PET/CT, mean age was 61±13 years. TTE was performed in 79 patients. Cardiac metastases were present in 15 patients, of which 10 patients also underwent TTE. One patient had both cardiac metastasis (only on ¹⁸F-FDOPA PET/CT) and echocardiographic signs of CHD. There were no differences in echocardiographic parameters for CHD between patients with and without cardiac metastases. TTE in none of the 79 patients showed cardiac metastases.

Conclusion

The prevalence of cardiac metastases detected with ¹⁸F-FDOPA PET/CT in this study is 13%. ¹⁸F-FDOPA PET/CT can visualize cardiac metastases in serotonin producing NET patients. There appears to be no relationship between the presence of cardiac metastases and TTE parameters of CHD.     

Regulation of tomato fruit pericarp development by an interplay between CDKB and CDKA1 cell cycle genes

Growth of tomato fruits is determined by cell division and cell expansion, which are tightly controlled by factors that drive the core cell cycle. The cyclin-dependent kinases (CDKs) and their interacting partners, the cyclins, play a key role in the progression of the cell cycle. In this study the role of CDKA1, CDKB1, and CDKB2 in fruit development was characterized by fruit-specific overexpression and down-regulation. CDKA1 is expressed in the pericarp throughout development, but is strongly up-regulated in the outer pericarp cell layers at the end of the growth period, when CDKB gene expression has ceased. Overexpression of the CDKB genes at later stages of development and the down-regulation of CDKA1 result in a very similar fruit phenotype, showing a reduction in the number of cell layers in the pericarp and alterations in the desiccation of the fruits. Expression studies revealed that CDKA1 is down-regulated by the expression of CDKB1/2 in CDKB1 and CDKB2 overexpression mutants, suggesting opposite roles for these types of CDK proteins in tomato pericarp development.     

Delays in Admittance-Controlled Haptic Devices Make Simulated Masses Feel Heavier

In an admittance-controlled haptic device, input forces are used to calculate the movement of the device. Although developers try to minimize delays, there will always be delays between the applied force and the corresponding movement in such systems, which might affect what the user of the device perceives. In this experiment we tested whether these delays in a haptic human-robot interaction influence the perception of mass. In the experiment an admittance-controlled manipulator was used to simulate various masses. In a staircase design subjects had to decide which of two virtual masses was heavier after gently pushing them leftward with the right hand in mid-air (no friction, no gravity). The manipulator responded as quickly as possible or with an additional delay (25 or 50 ms) to the forces exerted by the subject on the handle of the haptic device. The perceived mass was ~10% larger for a delay of 25 ms and ~20% larger for a delay of 50 ms. Based on these results, we estimated that the delays that are present in nowadays admittance-controlled haptic devices (up to 20ms) will give an increase in perceived mass which is smaller than the Weber fraction for mass (~10% for inertial mass). Additional analyses showed that the subjects’ decision on mass when the perceptual differences were small did not correlate with intuitive variables such as force, velocity or a combination of these, nor with any other measured variable, suggesting that subjects did not have a consistent strategy during guessing or used other sources of information, for example the efference copy of their pushes.     

Plant-associated bacteria and their role in the success or failure of metal phytoextraction projects: first observations of a field-related experiment

Phytoextraction has been reported as an economically and ecologically sound alternative for the remediation of metal-contaminated soils. Willow is a metal phytoextractor of interest because it allows to combine a gradual contaminant removal with production of biomass that can be valorized in different ways. In this work two willow clones growing on a metal-contaminated site were selected: ‘Belgisch Rood’ (BR) with a moderate metal extraction capacity and ‘Tora’ (TO) with a twice as high metal accumulation. All cultivable bacteria associated with both willow clones were isolated and identified using 16SrDNA ARDRA analysis followed by 16SrDNA sequencing. Further all isolated bacteria were investigated for characteristics that might promote plant growth (production of siderophores, organic acids and indol acetic acid) and for their metal resistance. The genotypic and phenotypic characterization of the isolated bacteria showed that the TO endophytic bacterial population is more diverse and contains a higher percentage of metal-resistant plant growth promoting bacteria than the endophytic population associated with BR. We hypothesize that the difference in the metal accumulation capacity between BR and TO clones might be at least partly related to differences in characteristics of their associated bacterial population.     

Optogenetic fUSI for brain-wide mapping of neural activity mediating collicular-dependent behaviors

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Hydroxychloroquine decreases human MSC‐derived osteoblast differentiation and mineralization in vitro

We recently showed that patients with primary Sjögren Syndrome (pSS) have significantly higher bone mineral density (BMD) compared to healthy controls. The majority of those patients (69%) was using hydroxychloroquine (HCQ), which may have favourable effects on BMD. To study the direct effects of HCQ on human MSC‐derived osteoblast activity. Osteoblasts were cultured from human mesenchymal stromal cells (hMSCs). Cultures were treated with different HCQ doses (control, 1 and 5 µg/ml). Alkaline phosphatase activity and calcium measurements were performed to evaluate osteoblast differentiation and activity, respectively. Detailed microarray analysis was performed in 5 µg/ml HCQ‐treated cells and controls followed by qPCR validation. Additional cultures were performed using the cholesterol synthesis inhibitor simvastatin (SIM) to evaluate a potential mechanism of action. We showed that HCQ inhibits both MSC‐derived osteoblast differentiation and mineralization in vitro. Microarray analysis and additional PCR validation revealed a highly significant up‐regulation of the cholesterol biosynthesis, lysosomal and extracellular matrix pathways in the 5 µg/ml HCQ‐treated cells compared to controls. Besides, we demonstrated that 1 µM SIM also decreases MSC‐derived osteoblast differentiation and mineralization compared to controls. It appears that the positive effect of HCQ on BMD cannot be explained by a stimulating effect on the MSC‐derived osteoblast. The discrepancy between high BMD and decreased MSC‐derived osteoblast function due to HCQ treatment might be caused by systemic factors that stimulate bone formation and/or local factors that reduce bone resorption, which is lacking in cell cultures.     

Maternal effects and parent–offspring conflict

Maternal effects can provide offspring with reliable information about the environment they are likely to experience, but also offer scope for maternal manipulation of young when interests diverge between parents and offspring. To predict the impact of parent–offspring conflict, we model the evolution of maternal effects on local adaptation of young. We find that parent–offspring conflict strongly influences the stability of maternal effects; moreover, the nature of the disagreement between parents and young predicts how conflict is resolved: when mothers favor less extreme mixtures of phenotypes relative to offspring (i.e., when mothers stand to gain by hedging their bets), mothers win the conflict by providing offspring with limited amounts of information. When offspring favor overproduction of one and the same phenotype across all environments compared to mothers (e.g., when offspring favor a larger body size), neither side wins the conflict and signaling breaks down. Only when offspring favor less extreme mixtures relative to their mothers (something no current model predicts), offspring win the conflict and obtain full information about the environment. We conclude that a partial or complete breakdown of informative maternal effects will be the norm rather than the exception in the presence of parent–offspring conflict.