MetaTM - a consensus method for transmembrane protein topology prediction

Transmembrane (TM) proteins are proteins that span a biological membrane one or more times. As their 3-D structures are hard to determine, experiments focus on identifying their topology (i. e. which parts of the amino acid sequence are buried in the membrane and which are located on either side of the membrane), but only a few topologies are known. Consequently, various computational TM topology predictors have been developed, but their accuracies are far from perfect. The prediction quality can be improved by applying a consensus approach, which combines results of several predictors to yield a more reliable result. RESULTS: A novel TM consensus method, named MetaTM, is proposed in this work. MetaTM is based on support vector machine models and combines the results of six TM topology predictors and two signal peptide predictors. On a large data set comprising 1460 sequences of TM proteins with known topologies and 2362 globular protein sequences it correctly predicts 86.7% of all topologies. CONCLUSION: Combining several TM predictors in a consensus prediction framework improves overall accuracy compared to any of the individual methods. Our proposed SVM-based system also has higher accuracy than a previous consensus predictor. MetaTM is made available both as downloadable source code and as DAS server at http://MetaTM.sbc.su.se

The Multifunctional Sorting Protein PACS-2 Regulates SIRT1-Mediated Deacetylation of p53 to Modulate p21-Dependent Cell-Cycle Arrest

SIRT1 regulates the DNA damage response by deacetylating p53, thereby repressing p53 transcriptional output. Here, we demonstrate that the sortingprotein PACS-2 regulates SIRT1-mediated deacetylation of p53 to modulate the DNA damage response. PACS-2 knockdown cells failed to efficiently undergo p53-induced cell-cycle arrest in response to DNA damage. Accordingly, p53 acetylation was reduced both in PACS-2 knockdown cells and thymocytes from Pacs-2-/- mice, thereby blunting induction of the cyclin-dependent kinase inhibitor p21 (CDKN1A). The SIRT1 inhibitor EX-527 or SIRT1 knockdown restored p53 acetylation and p21 induction as well as p21-dependent cell-cycle arrest in PACS-2 knockdown cells. Traffickingstudies revealed that cytoplasmic PACS-2 shuttled to the nucleus, where it interacted with SIRT1 andrepressed SIRT1-mediated p53 deacetylation. Correspondingly, invitro assays demonstrated that PACS-2 directly inhibited SIRT1-catalyzed p53 deacetylation. Together, these findings identify PACS-2 as an invivo mediator of the SIRT1-p53-p21 axis that modulates the DNA damage response

A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing

<p>Abstract</p> <p>Background</p> <p>The structurally complex network of minicircles and maxicircles comprising the mitochondrial DNA of kinetoplastids mirrors the complexity of the RNA editing process that is required for faithful expression of encrypted maxicircle genes. Although a few of the guide RNAs that direct this editing process have been discovered on maxicircles, guide RNAs are mostly found on the minicircles. The nuclear and maxicircle genomes have been sequenced and assembled for <it>Trypanosoma cruzi</it>, the causative agent of Chagas disease, however the complement of 1.4-kb minicircles, carrying four guide RNA genes per molecule in this parasite, has been less thoroughly characterised.</p> <p>Results</p> <p>Fifty-four CL Brener and 53 Esmeraldo strain minicircle sequence reads were extracted from <it>T. cruzi </it>whole genome shotgun sequencing data. With these sequences and all published <it>T. cruzi </it>minicircle sequences, 108 unique guide RNAs from all known <it>T. cruzi </it>minicircle sequences and two guide RNAs from the CL Brener maxicircle were predicted using a local alignment algorithm and mapped onto predicted or experimentally determined sequences of edited maxicircle open reading frames. For half of the sequences no statistically significant guide RNA could be assigned. Likely positions of these unidentified gRNAs in <it>T. cruzi </it>minicircle sequences are estimated using a simple Hidden Markov Model. With the local alignment predictions as a standard, the HMM had an ~85% chance of correctly identifying at least 20 nucleotides of guide RNA from a given minicircle sequence. Inter-minicircle recombination was documented. Variable regions contain species-specific areas of distinct nucleotide preference. Two maxicircle guide RNA genes were found.</p> <p>Conclusion</p> <p>The identification of new minicircle sequences and the further characterization of all published minicircles are presented, including the first observation of recombination between minicircles. Extrapolation suggests a level of 4% recombinants in the population, supporting a relatively high recombination rate that may serve to minimize the persistence of gRNA pseudogenes. Characteristic nucleotide preferences observed within variable regions provide potential clues regarding the transcription and maturation of <it>T. cruzi </it>guide RNAs. Based on these preferences, a method of predicting <it>T. cruzi </it>guide RNAs using only primary minicircle sequence data was created.</p

Functional septorhinoplasty alters brain structure and function: Neuroanatomical correlates of olfactory dysfunction

Introduction: We previously demonstrated functionally significant structural plasticity within the central olfactory networks, in association with improved olfaction after surgical treatment of chronic rhinosinusitis (CRS). In order to confirm and expand on these findings, the primary aim of this study was to determine whether these same regions undergo functionally significant structural plasticity following functional septorhinoplasty (fSRP), in patients with non-CRS olfactory dysfunction (OD) of mixed cause. fSRP has previously been shown to improve olfactory function, and the secondary aim of this study was to provide initial insights into the mechanism by which fSRP affects olfaction.// Methods: We performed a pilot prospective, multimodal neuroimaging study in 20 participants undergoing fSRP, including patients with non-CRS OD of mixed cause, as well as normosmic surgical controls. Participants underwent psychophysical olfactory testing, assessment of nasal airway, structural and functional neuroimaging. This was performed pre- and postoperatively in patients, and preoperatively in controls.// Results: There was a statistically and clinically significant improvement in mean psychophysical olfactory scores after surgery. This was associated with structural and functional plasticity within areas of the central olfactory network (anterior cingulate, orbitofrontal cortex, insula, temporal pole). Improved psychophysical scores were significantly correlated with change in bilateral measures of nasal airflow, not measures of airflow symmetry, suggesting that improved overall airflow was more important than correction of septal deviation.// Conclusion: This work highlights the importance of these neuroanatomical regions as potential structural correlates of olfactory function and dysfunction. Our results also provide initial insight into the mechanistic effects of fSRP on olfaction. Further work could investigate the utility of these regions as personalised biomarkers of OD, as well as the role of fSRP in treating OD

Parents’ experiences of health visiting for children with Down syndrome

© MA Healthcare Limited.Children with Down syndrome have an increased likelihoodof experiencing serious health conditions. Health visitors canhave an important role in monitoring and promoting healthand development for young children with Down syndrome.This study aimed to explore parents’ experiences of healthvisiting services for children with Down syndrome. Twentyfour parents of children with Down syndrome aged 0–5 yearscompleted a brief questionnaire about the number and natureof visits from health visitors in the previous 12 months andtheir support needs. Some parents commented that otherprofessionals met the needs of their child, whereas others saidthat they would like more advice and support from healthvisitors. A further exploration of broader health serviceprovision, including health visiting, for young children withDown syndrome is needed.Peer reviewedFinal Accepted Versio

Investigating changes in blood-cerebrospinal fluid barrier function in a rat model of chronic hypertension using non-invasive magnetic resonance imaging

Chronic hypertension is a major risk factor for the development of neurodegenerative disease, yet the etiology of hypertension-driven neurodegeneration remains poorly understood. Forming a unique interface between the systemic circulation and the brain, the blood-cerebrospinal fluid barrier (BCSFB) at the choroid plexus (CP) has been proposed as a key site of vulnerability to hypertension that may initiate downstream neurodegenerative processes. However, our ability to understand BCSFB’s role in pathological processes has, to date, been restricted by a lack of non-invasive functional measurement techniques. In this work, we apply a novel Blood-Cerebrospinal Fluid Barrier Arterial Spin Labeling (BCSFB-ASL) Magnetic resonance imaging (MRI) approach with the aim of detecting possible derangement of BCSFB function in the Spontaneous Hypertensive Rat (SHR) model using a non-invasive, translational technique. SHRs displayed a 36% reduction in BCSFB-mediated labeled arterial water delivery into ventricular cerebrospinal fluid (CSF), relative to normotensive controls, indicative of down-regulated choroid plexus function. This was concomitant with additional changes in brain fluid biomarkers, namely ventriculomegaly and changes in CSF composition, as measured by T1 lengthening. However, cortical cerebral blood flow (CBF) measurements, an imaging biomarker of cerebrovascular health, revealed no measurable change between the groups. Here, we provide the first demonstration of BCSFB-ASL in the rat brain, enabling non-invasive assessment of BCSFB function in healthy and hypertensive rats. Our data highlights the potential for BCSFB-ASL to serve as a sensitive early biomarker for hypertension-driven neurodegeneration, in addition to investigating the mechanisms relating hypertension to neurodegenerative outcomes

Non-monotonic field-dependence of the ZFC magnetization peak in some systems of magnetic nanoparticles

We have performed magnetic measurements on a diluted system of gamma-Fe2O3 nanoparticles (~7nm), and on a ferritin sample. In both cases, the ZFC-peak presents a non-monotonic field dependence, as has already been reported in some experiments,and discussed as a possible evidence of resonant tunneling. Within simple assumptions, we derive expressions for the magnetization obtained in the usual ZFC, FC, TRM procedures. We point out that the ZFC-peak position is extremely sensitive to the width of the particle size distribution, and give some numerical estimates of this effect. We propose to combine the FC magnetization with a modified TRM measurement, a procedure which allows a more direct access to the barrier distribution in a field. The typical barrier values which are obtained with this method show a monotonic decrease for increasing fields, as expected from the simple effect of anisotropy barrier lowering, in contrast with the ZFC results. From our measurements on gamma-Fe2O3 particles, we show that the width of the effective barrier distribution is slightly increasing with the field, an effect which is sufficient for causing the observed initial increase of the ZFC-peak temperatures.Comment: LaTeX file 19 pages, 9 postscript figures. To appear in Phys. Rev. B (tentative schedule: Dec.97

Decisions at the end of life: have we come of age?

Decision making is a complex process and it is particularly challenging to make decisions with, or for, patients who are near the end of their life. Some of those challenges will not be resolved - due to our human inability to foresee the future precisely and the human proclivity to change stated preferences when faced with reality. Other challenges of the decision-making process are manageable. This commentary offers a set of approaches which may lead to progress in this field