Length-dependent prediction of protein intrinsic disorder

Background  

Due to the functional importance of intrinsically disordered proteins or protein regions, prediction of intrinsic protein disorder from amino acid sequence has become an area of active research as witnessed in the 6th experiment on Critical Assessment of Techniques for Protein Structure Prediction (CASP6). Since the initial work by Romero et al. (Identifying disordered regions in proteins from amino acid sequences, IEEE Int. Conf. Neural Netw., 1997), our group has developed several predictors optimized for long disordered regions (>30 residues) with prediction accuracy exceeding 85%. However, these predictors are less successful on short disordered regions (≤30 residues). A probable cause is a length-dependent amino acid compositions and sequence properties of disordered regions.     

Influences of age and maxillary anterior teeth status on patient's satisfaction with dental appearance and tooth colour

doi: 10.1111/j.1741‐2358.2011.00543.x Influences of age and maxillary anterior teeth status on patient’s satisfaction with dental appearance and tooth colour Objectives: To study the impact of age, gender, tooth colour and maxillary anterior teeth status on patient’s satisfaction with their dental appearance. Material and methods: A total of 259 Caucasian subjects participated in the study (119 men, mean age 56 years; 140 women, mean age 61 years) divided into three age groups (young <35 age; middle aged 35–54 age; old ≥55 age). Their maxillary anterior teeth status was classified into three groups: (1) natural teeth (NTG) group; (2) composite filling group (CFG) and (3) porcelain‐fused‐to‐metal fixed prosthodontic restoration group (FPDG). The participants judged appearance and tooth colour using a scale with three categories: completely dissatisfied, moderately dissatisfied and completely satisfied. Results: Almost half of the participants were completely satisfied with their dental appearance and tooth colour. Half of the ‘young’ and ‘middle‐aged’ participants with natural maxillary anterior teeth were completely satisfied and half of the ‘old’ participants were moderately satisfied with their dental appearance and tooth colour. The majority of participants with composite restorations (45–51%) were moderately satisfied with their dental appearance, one‐third of ‘young’ and ‘middle‐aged’ participants were moderately satisfied or dissatisfied with their tooth colour and more than 70% of older participants were dissatisfied with their tooth colour (p > 0.05). Conclusions: Satisfaction with the appearance of the maxillary anterior teeth differed both between individuals of different age and different dental status.     

Intrinsic disorder in putative protein sequences

Background

Intrinsically disordered proteins (IDPs) and regions (IDRs) perform a variety of crucial biological functions despite lacking stable tertiary structure under physiological conditions in vitro. State-of-the-art sequence-based predictors of intrinsic disorder are achieving per-residue accuracies over 80%. In a genome-wide study of intrinsic disorder in human genome we observed a big difference in predicted disorder content between confirmed and putative human proteins. We investigated a hypothesis that this discrepancy is not correct, and that it is due to incorrectly annotated parts of the putative protein sequences that exhibit some similarities to confirmed IDRs, which lead to high predicted disorder content.

Methods

To test this hypothesis we trained a predictor to discriminate sequences of real proteins from synthetic sequences that mimic errors of gene finding algorithms. We developed a procedure to create synthetic peptide sequences by translation of non-coding regions of genomic sequences and translation of coding regions with incorrect codon alignment.

Results

Application of the developed predictor to putative human protein sequences showed that they contain a substantial fraction of incorrectly assigned regions. These regions are predicted to have higher levels of disorder content than correctly assigned regions. This partially, albeit not completely, explains the observed discrepancy in predicted disorder content between confirmed and putative human proteins.

Conclusions

Our findings provide the first evidence that current practice of predicting disorder content in putative sequences should be reconsidered, as such estimates may be biased.

     

TSE clearance during plasma products separation process by Gradiflow(TM).

BACKGROUND AND OBJECTIVES: Recent experimental evidence from rodent models suggests a potential risk for transmissible spongiform encephalopathy (TSE) transmission by blood. The emergence of a new variant Creutzfeldt-Jakob disease (vCJD) has raised increased concerns about the safety of blood components and plasma products derived from vCJD-infected donors. Recent risk-minimisation strategies have included a ban on the use of UK-sourced plasma for the preparation of licensed blood products and leukodepletion of blood donations for fear of possible transmission of the human TSE via blood or blood components. The aim of this study was to investigate the capability and efficacy of a preparative electrophoresis system (Gradiflow) in the removal of TSE contaminants during the separation of plasma products. MATERIALS AND METHODS: Using hamster adapted scrapie 263 K as a model for TSE agent, albumin and IgG separation from human plasma by Gradiflow were performed separately by spiking a 263 K scrapie microsomal fraction to the feed material at each process step. Samples from pre- and post-Gradiflow separation process were titrated to the end-point for the detection of the disease-associated, proteinase K resistant form of the pathogenic prion protein (PrP(Sc)) by Western blot. RESULTS: Under all conditions tested, a greater than 3 log(10) reduction was achieved with no PrP(Sc) detected in any of the pooled products for either of the IgG or albumin separations. These data show that Gradiflow processing has clear advantages for concurrent purification of plasma products and in-process TSE removal. CONCLUSIONS: Our findings suggest that Gradiflow process is a viable alternative to remove causative TSE agents during plasma products separation, potentially eliminating the risk of TSE agents transmission.     

Maternal Separation Induced Alterations of Neurogenesis in the Rat Rostral Migratory Stream

1. The aim of our study was to investigate the possibility that maternal separation, an experimental model for studies of early environmental influences, has an effect on postnatal neurogenesis in neurogenic pathway—the rostral migratory stream (RMS). 2. Rat pups were subjected to maternal separation daily for 3 h, starting from the first postnatal day (P1) till P14 or P21. In the first two groups, brains were analyzed at the age of P14 and P21, respectively. In the third group, after 3 weeks of maternal separation, 1 week of normal rearing was allowed, and the brains were analyzed at P28. The controls matched the age of maternally separated animals. Dividing cells were labeled by bromodeoxyuridine; dying cells were visualized by Fluoro-Jade C and nitric oxide (NO) producing cells by NADPH-diaphorase histochemistry. 3. Quantitative analysis of proliferating cells in the RMS showed that maternal separation decreased the number of dividing cells in all experimental groups. This decrease was most prominent in the caudal part of the RMS. The amount of dying cells was increased at the end of 3 weeks of maternal separation as well as 1 week later. The number of differentiated nitrergic cells in the RMS was increased at the end of 2 or 3 weeks of maternal separation, respectively. Besides quantitative changes, maternally separated animals showed an accelerated maturation of nitrergic cells. 4. Our results indicate that an exposure of rats to adverse environmental factors in early postnatal periods may induce acute site-specific changes in the RMS neurogenesis.     

Comprehensible Predictive Modeling Using Regularized Logistic Regression and Comorbidity Based Features

Different studies have demonstrated the importance of comorbidities to better understand the origin and evolution of medical complications. This study focuses on improvement of the predictive model interpretability based on simple logical features representing comorbidities. We use group lasso based feature interaction discovery followed by a post-processing step, where simple logic terms are added. In the final step, we reduce the feature set by applying lasso logistic regression to obtain a compact set of non-zero coefficients that represent a more comprehensible predictive model. The effectiveness of the proposed approach was demonstrated on a pediatric hospital discharge dataset that was used to build a readmission risk estimation model. The evaluation of the proposed method demonstrates a reduction of the initial set of features in a regression model by 72%, with a slight improvement in the Area Under the ROC Curve metric from 0.763 (95% CI: 0.755–0.771) to 0.769 (95% CI: 0.761–0.777). Additionally, our results show improvement in comprehensibility of the final predictive model using simple comorbidity based terms for logistic regression.     

Changes in cardiac Na<Superscript>+</Superscript>/K<Superscript>+</Superscript>-ATPase expression and activity in female rats fed a high-fat diet

The aim of this study was to investigate whether the presence of endogenous estradiol alters the effects of a high-fat (HF) diet on activity/expression of the cardiac Na⁺/K⁺-ATPase, via PI3K/IRS and RhoA/ROCK signalling cascades in female rats. For this study, female Wistar rats (8 weeks old, 150–200 g) were fed a standard diet or a HF diet (balanced diet for laboratory rats enriched with 42% fat) for 10 weeks. The results show that rats fed a HF diet exhibited a decrease in phosphorylation of the α₁ subunit of Na⁺/K⁺-ATPase by 30% (p < 0.05), expression of total α₁ subunit of Na⁺/K⁺-ATPase by 31% (p < 0.05), and association of IRS1 with p85 subunit of PI3K by 42% (p < 0.05), while the levels of cardiac RhoA and ROCK2 were significantly increased by 84% (p < 0.01) and 62% (p < 0.05), respectively. Our results suggest that a HF diet alters cardiac Na⁺/K⁺-ATPase expression via molecular mechanisms involving RhoA/ROCK and IRS-1/PI3K signalling in female rats.     

States of productive and reproductive imagination reflected in the local synchronization of alpha and theta EEG frequencies

Healthy subjects (n = 83) performed a task involving reproductive imagination (remembrances): they were asked to remember and to have an imaginary walk along a well-known road (a real walk, the reproductive imagination state, RIS). Then the subjects performed a task involving productive imagination: they were asked to imagine a city that does not actually exist and to have an imaginary walk through it (a fictitious walk, productive imagination state, PIS). The reference values were measured at rest with the eyes open (REO). Monopolar EEGs were recorded from 19 areas of the scalp surface (10–20 system). An increase in EEG power in the α₂ frequency range during RIS and even more pronounced increase during PIS as compared with REO were considered to reflect the internalization of attention. We also observed multidirectional dynamics of EEG power in the θ and α1 ranges during PIS and RIS as compared with REO, which suggests the dominance of free associative manipulation of visual images in PIS in contrast to RIS, where algorithmically ordered operations with visual images stored in the memory were dominant.