AllerTool: a web server for predicting allergenicity and allergic cross-reactivity in proteins

Assessment of potential allergenicity and patterns of cross-reactivity is necessary whenever novel proteins are introduced into human food chain. Current bioinformatic methods in allergology focus mainly on the prediction of allergenic proteins, with no information on cross-reactivity patterns among known allergens. In this study, we present AllerTool, a web server with essential tools for the assessment of predicted as well as published cross-reactivity patterns of allergens. The analysis tools include graphical representation of allergen cross-reactivity information; a local sequence comparison tool that displays information of known cross-reactive allergens; a sequence similarity search tool for assessment of cross-reactivity in accordance to FAO/WHO Codex alimentarius guidelines; and a method based on support vector machine (SVM). A 10-fold cross-validation results showed that the area under the receiver operating curve (A(ROC)) of SVM models is 0.90 with 86.00% sensitivity (SE) at specificity (SP) of 86.00%. Availability: AllerTool is freely available at http://research.i2r.a-star.edu.sg/AllerTool/.     

Prediction of food protein allergenicity: a bioinformatic learning systems approach

Food hypersensitivity is constantly increasing in Western societies with a prevalence of about 1-2% in Europe and in the USA. Among children, the incidence is even higher. Because of the introduction of foods derived from genetically modified crops on the marketplace, the scientific community, regulatory bodies and international associations have intensified discussions on risk assessment procedures to identify potential food allergenicity of the newly introduced proteins. In this work, we present a novel biocomputational methodology for the classification of amino acid sequences with regard to food allergenicity and non-allergenicity. This method relies on a computerised learning system trained using selected excerpts of amino acid sequences. One example of such a successful learning system is presented which consists of feature extraction from sequence alignments performed with the FASTA3 algorithm (employing the BLOSUM50 substitution matrix) combined with the k-Nearest-Neighbour (kNN) classification algorithm. Briefly, the two features extracted are the alignment score and the alignment length and the kNN algorithm assigns the pair of extracted features from an unknown sequence to the prevalent class among its k nearest neighbours in the training (prototype) set available. 91 food allergens from several specialised public repositories of food allergy and the SWALL database were identified, pre-processed, and stored, yielding one of the most extensively characterised repositories of allergenic sequences known today. All allergenic sequences were classified using a standard one-leave-out cross validation procedure yielding about 81% correctly classified allergens and the classification of 367 non-allergens in an independent test set resulted in about 98% correct classifications. The biocomputational approach presented should be regarded as a significant extension and refinement of earlier attempts suggested for in silico food safety assessment. Our results show that the framework described here is powerful enough to become useful as part of a multiple-procedure test scheme that also depicts other evaluation approaches such as solid phase immunoassay and tests for stability to digestions.     

Sources of stress among nurses: an empirical investigation

The effect of personality, demographic, and professional variables on nurses' experienced stress is examined through the use of the Nursing Stress Inventory in a midwestern Catholic hospital. Findings indicate that age, nursing role status, length of time since graduation, job tenure, area of nursing, and interpersonal needs are associated with various dimensions of stress.     

Characteristics of glottis-induced turbulence in oscillatory flow: an empirical investigation.

Turbulence inducement from the glottis was scrutinized by employing an idealized model of the larynx and trachea for oscillatory flow conditions. The characterization of turbulence was achieved with the two-component velocity measurements of split-film probe anemometry and with the flow visualization of a smoke-wire technique. The apertures of two different (triangular and circular) shapes were utilized in the airway model to address the distinct effects of the triangular-shaped glottal aperture on the generation, development, and decay of turbulence. One of the salient turbulence characteristics for the triangular aperture case was found to be the relatively high turbulence levels around the center region (2r/D approximately 0) in conjunction with the asymmetric mean axial velocity across the frontal-rear (A-O-P) plane of the trachea at one tracheal diameter (x/D = 1) downstream from the glottis. The detailed turbulence properties such as the Reynolds shear stresses and turbulence intensities for the triangular aperture case differed significantly from those for the circular aperture case within a few tracheal diameters (x/D < 7) downstream from the apertures. The glottis-induced turbulence was incipient during the acceleration phase of inspiration and convected downstream with the traits of decaying turbulence.     

Search for the determinants of allergenicity in proteins of the lipocalin family

Three different lines of analysis have been applied to approach the problem of the allergenicity of certain proteins: biological functions, molecular structures and immunological properties. It is immediately obvious that these three are interdependent. The lipocalin family of proteins includes a significant number of allergens. A considerable amount of data is already available of lipocalins and some insights about allergenic determinants can now be presented. However, more information on the molecular structures and immunological parameters of lipocalin allergens is required.     

Occurrence of copper proteins through the three domains of life: a bioinformatic approach

In high-throughput genome-level protein investigation efforts, such as Structural Genomics, the systematic experimental characterization of metal-binding properties (i.e., the investigation of the metalloproteome) is not always pursued and remains far from trivial. In the present work, we have applied a bioinformatic approach to investigate the occurrence of (putative) copper-binding proteins in 57 different organisms spanning the entire tree of life. We found that the size of the copper proteome is generally less than 1% of the total proteome of an organism, in both eukaryotes and prokaryotes. The occurrence of copper-binding proteins is relatively scarce when compared to that of zinc-binding proteins and of non-heme iron proteins. This may be due to both poorer bioavailability (in particular with respect to iron in the ancient world) and the complexity of copper chemistry and the risks associated with it, which may have adversely affected natural selection of copper-binding proteins. The present analysis shows that there is a strong relationship between the metal coordination sphere and protein function. A network involving proteins having roles in both copper transport and respiration was identified, parts or all of which are detected in the majority of the organisms examined.     

预测蛋白质可结晶性研究进展

解析蛋白质的三维结构具有重要的生物学意义,更是蛋白质功能研究和理性药物设计的基础。目前解析蛋白质结构最重要的方法是X-射线衍射晶体学解析技术。但是运用该技术解析蛋白质结构的关键是获得高质量的蛋白质晶体。然而,据统计仅有42%的可溶纯化蛋白质能够得到晶体,即不同蛋白质的可结晶性表现不同。由于实验方法验证蛋白质的可结晶性耗时耗力,因此,有研究者运用计算机模拟的方法预测蛋白质的可结晶性,从而节省资源与成本并且提高实验的成功率。本文结合我们的研究工作,介绍了几种目前较为成功的蛋白质可结晶性预测方法及其研究途径。     

Iron-binding proteins in human colorectal adenomas and carcinomas: an immunocytochemical investigation.

By immunocytochemistry, the presence of major iron-binding proteins (lactoferrin, transferrin and ferritin) was investigated in tubular adenomas (12 cases), villous adenomas (7 cases), carcinomas of the large bowel and rectum (39 cases) and lymph nodes involved in carcinomas (8 cases); 5 samples of colonic inflammatory pseudopolyps were also studied. Dysplastic areas of tubular and villous adenomas as well as adenocarcinomas and colloid carcinomas showed a variable cytoplasmic immunoreactivity for all antisera, although no staining was noted in some cases; tubular adenomas without dysplasia and colonic inflammatory pseudopolyps were always unstained. Metastatic elements present in lymph nodes maintained the immunohistochemical staining for iron-binding proteins. An autoctone production of lactoferrin, transferrin and ferritin by tumour cells may be hypothesized in relation to the increased requirement of iron for the turnover of rapidly dividing cells.     

Gerotranscendence in the second half of life: first empirical investigation in Flanders

Tornstam regards gerotranscendence as the final stage in a natural process towards maturity and wisdom, that can be described as a shift in meta-perspective which accompanies the process of aging: from a materialistic and rational perspective to a more cosmic and transcendent one. The present study contributes to the development of a by Tornstam used gerotranscendence scale, and looks for theoretically expected relations between gerotranscendence and psychosocial variables such as life satisfaction, death attitude, and recently experienced life crises. The relation between gerotranscendence and dimensions of religion and faith will also be examined. Participants were 120 older adults, 58 men and 62 women, aged 45-92 years. The scores on the gerotranscendence scale were not congruent, neither with the hypothetical threefold apriori scales, nor with the factor structure Tornstam had found in his research. An exploratory factor analysis yielded three factors which were to a certain extent reconcilable with the gerotranscendence theory. The subscales are Transcendent connection, Active involvement and coherence, and Attachment to life and material goods. Older respondents and respondents who experienced one or more life crises, have higher scores on Transcendent connection. The experience of connection seems to be related to dimensions of religion and faith. The results warrant further research into a measurement of gerotranscendence and the relation with dimensions of religion and faith.     

BEPITOPE: predicting the location of continuous epitopes and patterns in proteins

In growing need of obtaining highly specific monoclonal antibodies against novel proteins, we developed new functions implemented in the program BEPITOPE to predict continuous protein epitopes. This program not only can compute, combine, display and print prediction profiles, but also provides a list of suggested linear peptides to be synthesized. Novel facilities incorporated in BEPITOPE include the treatment of a whole genome, the search for a user-defined pattern, and the combination of prediction to pattern profiles. This latter approach is useful to remove unwanted predictions such as those including glycosylation sites.     

Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid

Background  

Safety assessment of genetically modified (GM) food, with regard to allergenic potential of transgene-encoded xenoproteins, typically involves several different methods, evaluation by digestibility being one thereof. However, there are still debates about whether the allergenicity of food allergens is related to their resistance to digestion by the gastric fluid. The disagreements may in part stem from classification of allergens only by their sources, which we believe is inadequate, and the difficulties in achieving identical experimental conditions for studying digestion by simulated gastric fluid (SGF) so that results can be compared. Here, we reclassify allergenic food allergens into alimentary canal-sensitized (ACS) and non-alimentary canal-sensitized (NACS) allergens and use a computational model that simulates gastric fluid digestion to analyze the digestibilities of these two types.     

Identification and bioinformatic analysis of the membrane proteins of synechocystis sp. PCC 6803

Background  

The membranes of Synechocystis sp. PCC 6803 play a central role in photosynthesis, respiration and other important metabolic pathways. Comprehensive identification of the membrane proteins is of importance for a better understanding of the diverse functions of its unique membrane structures. Up to date, approximately 900 known or predicted membrane proteins, consisting 24.5% of Synechocystis sp. PCC 6803 proteome, have been indentified by large-scale proteomic studies.     

TMBHMM: a frequency profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane residues

Transmembrane beta barrel (TMB) proteins are found in the outer membranes of bacteria, mitochondria and chloroplasts. TMBs are involved in a variety of functions such as mediating flux of metabolites and active transport of siderophores, enzymes and structural proteins, and in the translocation across or insertion into membranes. We present here TMBHMM, a computational method based on a hidden Markov model for predicting the structural topology of putative TMBs from sequence. In addition to predicting transmembrane strands, TMBHMM also predicts the exposure status (i.e., exposed to the membrane or hidden in the protein structure) of the residues in the transmembrane region, which is a novel feature of the TMBHMM method. Furthermore, TMBHMM can also predict the membrane residues that are not part of beta barrel forming strands. The training of the TMBHMM was performed on a non-redundant data set of 19 TMBs. The self-consistency test yielded Q(2) accuracy of 0.87, Q(3) accuracy of 0.83, Matthews correlation coefficient of 0.74 and SOV for beta strand of 0.95. In this self-consistency test the method predicted 83% of transmembrane residues with correct exposure status. On an unseen, non-redundant test data set of 10 proteins, the 2-state and 3-state TMBHMM prediction accuracies are around 73% and 72%, respectively, and are comparable to other methods from the literature. The TMBHMM web server takes an amino acid sequence or a multiple sequence alignment as an input and predicts the exposure status and the structural topology as output. The TMBHMM web server is available under the tmbhmm tab at: http://service.bioinformatik.uni-saarland.de/tmx-site/.     

PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins

A novel tool for computer-aided design of single-site mutations in proteins and peptides is presented. It proceeds by performing in silico all possible point mutations in a given protein or protein region and estimating the stability changes with linear combinations of database-derived potentials, whose coefficients depend on the solvent accessibility of the mutated residues. Upon completion, it yields a list of the most stabilizing, destabilizing or neutral mutations. This tool is applied to mouse, hamster and human prion proteins to identify the point mutations that are the most likely to stabilize their cellular form. The selected mutations are essentially located in the second helix, which presents an intrinsic preference to form beta-structures, with the best mutations being T183-->F, T192-->A and Q186-->A. The T183 mutation is predicted to be by far the most stabilizing one, but should be considered with care as it blocks the glycosylation of N181 and this blockade is known to favor the cellular to scrapie conversion. Furthermore, following the hypothesis that the first helix might induce the formation of hydrophilic beta-aggregates, several mutations that are neutral with respect to the structure's stability but improve the helix hydrophobicity are selected, among which is E146-->L. These mutations are intended as good candidates to undergo experimental tests.     

Proteomic analysis of mouse brain microsomes: identification and bioinformatic characterization of endoplasmic reticulum proteins in the mammalian central nervous system

The endoplasmic reticulum (ER) is the main source for the storage and release of intracellular calcium in neurons and, thus, contributes to the functionality of a diverse set of pathways that control critical aspects of central nervous system function including but not limited to gene expression, neurotransmission, learning, and memory. ER-derived proteins obtained after subcellular fractionation of mouse brain homogenate were digested with trypsin and the corresponding peptides fractionated by strong cation exchange chromatography followed by LC-MS/MS analysis on a hybrid linear ion trap--Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. A comprehensive catalogue representing 1914 proteins was generated from this particular proteomic analysis using identification criteria that corresponded to a false positive identification rate of 0.4%. Various molecular functions and biological processes relevant to the ER were identified upon gene ontology (GO)-based analysis including pathways associated with molecular transport, protein trafficking and localization, and cell signaling. Comparison of the 2D-LC-MS/MS results with those obtained from shotgun LC-MS/MS analyses demonstrated that most molecular functions and biological processes were represented via GO analysis using either methodology. Results from this comparison as well as a focused investigation into components of calcium-mediated signaling in the mouse brain ER are also presented.