Reconstruction of a genome-scale metabolic network for Streptococcus pneumoniae R6

The gram-positive, lancet-shaped bacteria Streptococcus pneumoniae thrives in almost any environment. Under certain conditions this pathogen can cause several infections such as meningitis, otitis media, endocarditis or pneumonia. Genome-scale metabolic networks (GSMs) are commonly used to study phenotype-genotype relationships using biochemical, physiological and genomic information. These relationships might shed some light on identification of targets for metabolic engineering or, in the case of S. pneumoniae, determine if the bacteria´s increased invasiveness and virulence is dependent on specific genomic regions or determined by environmental conditions. In order to obtain a robust and reliable metabolic model, a proper, up-to-date genome annotation must be performed. In our work we aimed to re-annotate the genome of Streptococcus pneumoniae strain R6 and which would be used to reconstruct a metabolic network at a genomic level. For these tasks merlin was used, a software tool capable of performing automatic annotation of the genome using the amino acid sequences as well as reconstruction of the metabolic network. For validation purposes, another in-house tool (Optflux) capable of performing simulations and optimization tasks was used. Re-annotation of the genome was performed in accordance to an in-house generated pipeline which established rules for gene identification acceptance (and attribution of confidence levels) or rejection. Out of the 2043 genes present in S. pneumoniae´s genome, an initial 822 were identified as metabolic, representing an increase of almost 9 and 15% when compared to those of KEGG and Uniprot. An extended comparison revealed that a large number of genes (359 and 271 when compared to Uniprot and KEGG, respectively) were only present in our re-annotation. Although a significant amount of genes (113) were identified as only being present in KEGG and not in our study, this can be explained by the dismissal of genes associated to DNA and RNA processes from the statistical analysis. The metabolic network is comprised of 795 genes, 776 that only encode enzymes and 19 that only encode transporters. The biomass equation was adapted from close-related organisms such as B. subtilis and L. lactis cross-referenced with the biomass equation determined by ModelSEED for S. pneumoniae R6. Despite the considerable amount of essential genes in our model (83), only 38 were in accordance to literature regarding gene essentiality although it identified others (45) which have not been studied to date. The mismatch between results might be related to strain metabolic specificities, regulatory phenomena or even the dismissal of genes that affect DNA and RNA processes and capsule synthesis which should be addressed in future work. In order to validate the accuracy of the model, simulations were performed using experimental data retrieved from literature. The results obtained were very similar to the ones described in in vitro studies elevating the confidence level of the reconstructed model

Transthyretin binding to A-Beta peptide – Impact on A-Beta fibrillogenesis and toxicity

AbstractIt has been suggested that transthyretin (TTR) is involved in preventing A-Beta fibrillization in Alzheimer’s disease (AD). Here, we characterized the TTR/A-Beta interaction by competition binding assays. TTR binds to different A-Beta peptide species: soluble (Kd, 28nM), oligomers and fibrils; diverse TTR variants bind differentially to A-Beta. Transmission electron microscopy (TEM) analysis demonstrated that TTR is capable of interfering with A-Beta fibrillization by both inhibiting and disrupting fibril formation. Co-incubation of the two molecules resulted in the abolishment of A-Beta toxicity. Our results confirmed TTR as an A-Beta ligand and indicated the inhibition/disruption of A-Beta fibrils as a possible mechanism underlying the protective role of TTR in AD

Structural and functional diversification in the teleost S100 family of calcium-binding proteins

<p>Abstract</p> <p>Background</p> <p>Among the EF-Hand calcium-binding proteins the subgroup of S100 proteins constitute a large family with numerous and diverse functions in calcium-mediated signaling. The evolutionary origin of this family is still uncertain and most studies have examined mammalian family members.</p> <p>Results</p> <p>We have performed an extensive search in several teleost genomes to establish the <it>s100 </it>gene family in fish. We report that the teleost S100 repertoire comprises fourteen different subfamilies which show remarkable similarity across six divergent teleost species. Individual species feature distinctive subsets of thirteen to fourteen genes that result from local gene duplications and gene losses. Eight of the fourteen S100 subfamilies are unique for teleosts, while six are shared with mammalian species and three of those even with cartilaginous fish. Several S100 family members are found in jawless fish already, but none of them are clear orthologs of cartilaginous or bony fish <it>s100 </it>genes. All teleost <it>s100 </it>genes show the expected structural features and are subject to strong negative selection. Many aspects of the genomic arrangement and location of mammalian <it>s100 </it>genes are retained in the teleost <it>s100 </it>gene family, including a completely conserved intron/exon border between the two EF hands. Zebrafish <it>s100 </it>genes exhibit highly specific and characteristic expression patterns, showing both redundancy and divergence in their cellular expression. In larval tissue expression is often restricted to specific cell types like keratinocytes, hair cells, ionocytes and olfactory receptor neurons as demonstrated by <it>in situ </it>hybridization.</p> <p>Conclusion</p> <p>The origin of the S100 family predates at least the segregation of jawed from jawless fish and some extant family members predate the divergence of bony from cartilaginous fish. Despite a complex pattern of gene gains and losses the total repertoire size is remarkably constant between species. On the expression level the teleost S100 proteins can serve as precise markers for several different cell types. At least some of their functions may be related to those of their counterparts in mammals. Accordingly, our findings provide an excellent basis for future studies of the functions and interaction partners of <it>s100 </it>genes and finally their role in diseases, using the zebrafish as a model organism.</p

High-risk pulmonary embolism with right heart thrombi

Accuracy is essential to surface quality control when a range sensor is applied to measure the 3D shape of an automotive body part. A sensor's viewing pose, including location and orientation, is related to measurement accuracy. It is usually difficult to find an optimal solution by manual control of sensor viewpoints. A CAD-guided robot view planner developed previously can automatically generate viewpoints. Measurement accuracy can be satisfied in a certain range. However, the unpredictable image noises, especially in regions with low intensity contrast, cannot be compensated by the CADguided robot view planner. In another aspect, measurement accuracy is evaluated all over the part surface. The local accuracy of a small patch may exceed the measurement tolerance. In this paper, feedback design is applied to the CADguided robot sensor planning system. The feedback controller can evaluate the accuracy of obtained point clouds, identify problem regions, and generate new viewpoints. This process is recursively executed until the measurement accuracy reaches to a tolerant value. This feedback-based inspection system had been implemented in previous work to fill holes of a point cloud, which are caused by shadows and light reflections. In this paper, the feedback controller is specifically designed to improve the measurement accuracy. Experimental results show the success of applying this feedback system for dimensional inspection of an automotive body part. © 2007 IEEE.Link_to_subscribed_fulltex

Adult-onset autoimmune diabetes: comparative analysis of classical and latent presentation

Introduction: Adult-onset autoimmune diabetes (AID) has two different phenotypes: classic type 1 diabetes mellitus (T1DM), with insulin requirement just after diagnosis, and latent autoimmune diabetes in adults (LADA). The purpose of this study is to characterize patients with AID followed on a tertiary centre, comparing classic T1DM and LADA. Methods: We collected data from patients with diabetes and positive islet autoantibodies, aged 30 years old and over at diagnosis. Patients who started insulin in the first 6 months were classified as T1DM and patients with no insulin requirements in the first 6 months were classified as LADA. Data regarding clinical presentation, autoantibodies, A1C and C-peptide at diagnosis, pharmacologic treatment and complications were analysed. Results: We included 92 patients, 46 with classic T1DM and 46 with LADA. The percentage of females was 50% in T1DM group and 52.1% in LADA group. The median age at diagnosis was 38 years (IQR–15) for T1DM and 42 years (IQR–15) for LADA (p = 0.057). The median time between diagnosis of diabetes and diagnosis of autoimmune aetiology was 0 months in T1DM group and 60 months in LADA group (p < 0.001). The mean BMI at diagnosis was 24.1 kg/m2 in T1DM group and 26.1 kg/m2 in LADA group (p = 0.042). In T1DM group, 67.4% of the patients had more than one positive autoantibody, comparing to 41.3% of LADA patients (p = 0.012). There was no statistical difference in what concerns to title of GAD autoantibodies, A1C and C-peptide at diagnosis of autoimmune aetiology. The presence of symptoms at diagnosis was associated with T1DM group (p < 0.001). The median daily insulin dose was 40 IU for T1DM (0.58 IU/kg) and 33.5 IU for LADA (0.57 IU/kg), with no statistical difference. LADA patients were more often under non-insulin antidiabetic drugs (p = 0.001). At 10 years follow up, 21.1% of T1DM patients and 63.3% of LADA patients had microvascular complications (p = 0.004). Diabetic nephropathy was present in 23.5% of T1DM patients and 53.3% of LADA patients (p = 0.047). At the last evaluation, 55.6% of T1DM and 82.6% of LADA patients had metabolic syndrome and this difference was independent of diabetes duration. Conclusion: Patients with classic T1DM presented more often with symptoms, lower BMI and higher number of autoantibodies, which may be related to a more aggressive autoimmune process. Patients with LADA developed more frequently microvascular complications for the same disease duration, namely diabetic nephropathy, and had more often metabolic syndrome

Shelf-life extension of watermelon juice preserved by hyperbaric storage at room temperature compared to refrigeration

This work reports Hyperbaric Storage (HS) preservation of raw watermelon juice at variable/uncontrolled room temperature (RT,z21 C) for 7 days at 100 MPa and compared it with refrigeration (RF). At the end of storage, there was an increase in microbial counts (total aerobic mesophiles, psychrophiles, and yeasts and moulds) to above 6 log10 CFU/mL for samples stored at atmospheric pressure (RF and RT), while juice stored under HS/RT showed maximum values of about 2 log10 CFU/mL for total aerobic mesophiles/ psychrophiles and below the detection limit for yeasts and moulds. HS/RT juice showed also physicochemical parameters at levels similar to the initial juice. Thus, HS/RT can not only be used to preserve foods with no refrigeration energetic costs (since it does not require temperature control), but additionally, has also a great potential to extend the shelf-life of food products, compared to RF. This is the first case in the literature showing this additional potential/advantage of HS/RT

High pressure and thermal pasteurization effects on sweet cherry juice microbiological stability and physicochemical properties

This study evaluated high pressure processing (P1 – 400 MPa/5 min; P2 – 550 MPa/2 min) and thermal pasteurization (TP – 70°C/30 s) effects on sweet cherry juice’s microbiological and physicochemical parameters, during four weeks of refrigerated storage. All treatments reduced the microbiological load to undetectable levels not affecting total soluble solids and titratable acidity. The pH increased with all treatments, however, it decreased during storage. Phenols were differently affected: TP increased them by 6%, P1 had no effect while P2 decreased them by 11%. During storage, phenols in control and TP samples decreased by 26% and 20%, P1 samples decreased them by 11% whereas P2 showed no variation. TP had no effect on anthocyanins, while pressure treatments increased them by 8%. Anthocyanins decreased during storage, particularly in the control and P1 (decreasing 41%). All treatments had no effect on antioxidant activity until the 14th day, thereafter high pressure processing samples showed the highest antioxidant activity

Effect of temperature and compression/decompression rates on high pressure inactivation of Listeria

The main objective of the present study was to evaluate the effect of temperature and different compression/ decompression rates on the efficiency of Listeria inactivation by HPP. Stationary phase cultures of Listeria innocua were subjected to 300 MPa for 5 min at 4, 10, and 20 °C using different compression and decompression rates. Inactivation was more efficient at low temperature and with lowest compression and decompression rates (1.5 MPa s–1 and 3.2 MPa s–1, respectively). Kinetics of pressure building up and decompression, as well as temperature, have a significant impact on the outcome of Listeria inactivation by HPP. The results may contribute to the design of HPP protocols that ensure food safety, while preserving nutritional and organoleptic properties better

Peripheral Attentional Targets under Covert Attention Lead to Paradoxically Enhanced Alpha Desynchronization in Neurofibromatosis Type 1

The limited capacity of the human brain to process the full extent of visual information reaching the visual cortex requires the recruitment of mechanisms of information selection through attention. Neurofibromatosis type-1 (NF1) is a neurodevelopmental disease often exhibiting attentional deficits and learning disabilities, and is considered to model similar impairments common in other neurodevelopmental disorders such as autism. In a previous study, we found that patients with NF1 are more prone to miss targets under overt attention conditions. This finding was interpreted as a result of increased occipito-parietal alpha oscillations. In the present study, we used electroencephalography (EEG) to study alpha power modulations and the performance of patients with NF1 in a covert attention task. Covert attention was required in order to perceive changes (target offset) of a peripherally presented stimulus. Interestingly, alpha oscillations were found to undergo greater desynchronization under this task in the NF1 group compared with control subjects. A similar pattern of desynchronization was found for beta frequencies while no changes in gamma oscillations could be identified. These results are consistent with the notion that different attentional states and task demands generate different patterns of abnormal modulation of alpha oscillatory processes in NF1. Under covert attention conditions and while target offset was reported with relatively high accuracy (over 90% correct responses), excessive desynchronization was found. These findings suggest an abnormal modulation of oscillatory activity and attentional processes in NF1. Given the known role of alpha in modulating attention, we suggest that alpha patterns can show both abnormal increases and decreases that are task and performance dependent, in a way that enhanced alpha desynchronization may reflect a compensatory mechanism to keep performance at normal levels. These results suggest that dysregulation of alpha oscillations may occur in NF1 both in terms of excessive or diminished activation patterns