A physical study on the thermal ice ridge in a closed deep lake: Lake Kuttara, Hokkaido, Japan

An ice-ridge line more than 2,000 m long was discovered in a closed, deep lake—Lake Kuttara, Hokkaido, Japan—in the ice-covered season of 1995. To clarify when and how the ice-ridge line built up, meteorology and ice and water temperatures were monitored, and the density, thermal conductivity, and thickness of the covered ice were measured from January through March 1995. The covered ice on 4 and 5 March 1995, which corresponded to the period with the thickest lake ice, consisted of snow ice 0.05- to 0.07-m thick and candle ice 0.18- to 0.21-m thick. Numerical simulations for the ice thickness and temperature were carried out using a one-dimensional, unsteady, three-layer model. The simulated results, which were reasonable to the observations, indicate that due to the ice contraction and expansion, the ice-ridge line started to construct on 2 February and was completed the next day.     

PredGPI: a GPI-anchor predictor

Background  

Several eukaryotic proteins associated to the extracellular leaflet of the plasma membrane carry a Glycosylphosphatidylinositol (GPI) anchor, which is linked to the C-terminal residue after a proteolytic cleavage occurring at the so called ω-site. Computational methods were developed to discriminate proteins that undergo this post-translational modification starting from their aminoacidic sequences. However more accurate methods are needed for a reliable annotation of whole proteomes.     

Solid-phase epitope recovery: a high throughput method for antigen identification and epitope optimization

Self tolerance to MHC class I-restricted nonmutated self Ags is a significant hurdle to effective cancer immunotherapy. Compelling evidence is emerging that altered peptide ligands can be far more immunogenic than their corresponding native epitopes; however, there is no way to reliably predict which modifications will lead to enhanced native epitope-specific immune responses. We reasoned that this limitation could be overcome by devising an empirical screen in which the nearly complete combinatorial spectrum of peptides of optimal length can be rapidly assayed for reactivity with a MHC class I-restricted cytotoxic T cell clone. This method, solid-phase epitope recovery, quantitatively ranks all reactive peptides in the library and allows selection of altered peptide ligands having desirable immunogenic properties of interest. In contrast to rationally designed MHC anchor-modified peptides, peptides identified by the present method are highly substituted in predicted TCR contact residues and can reliably activate and expand effector cell populations in vitro which lyse target cells presenting the wild-type epitope. We demonstrate that solid-phase epitope recovery peptides corresponding to a poorly immunogenic epitope of the melanoma Ag, gp100, can reliably induce wild-type peptide-specific CTL using normal donor T cells in vitro. Furthermore, these peptides can complement one another to induce these responses in an overwhelming majority of normal individuals in vitro. These data provide a rationale for the design of superior vaccines comprising a mixture of structurally diverse yet functionally convergent peptides.     

Mutations in a dominant Nef epitope of simian immunodeficiency virus diminish TCR:epitope peptide affinity but not epitope peptide:MHC class I binding

Viruses like HIV and SIV escape from containment by CD8(+) T lymphocytes through generating mutations that interfere with epitope peptide:MHC class I binding. However, mutations in some viral epitopes are selected for that have no impact on this binding. We explored the mechanism underlying the evolution of such epitopes by studying CD8(+) T lymphocyte recognition of a dominant Nef epitope of SIVmac251 in infected Mamu-A*02(+) rhesus monkeys. Clonal analysis of the p199RY-specific CD8(+) T lymphocyte repertoire in these monkeys indicated that identical T cell clones were capable of recognizing wild-type (WT) and mutant epitope sequences. However, we found that the functional avidity of these CD8(+) T lymphocytes for the mutant peptide:Mamu-A*02 complex was diminished. Using surface plasmon resonance to measure the binding affinity of the p199RY-specific TCR repertoire for WT and mutant p199RY peptide:Mamu-A*02 monomeric complexes, we found that the mutant p199RY peptide:Mamu-A*02 complexes had a lower affinity for TCRs purified from CD8(+) T lymphocytes than did the WT p199RY peptide:Mamu-A*02 complexes. These studies demonstrated that differences in TCR affinity for peptide:MHC class I ligands can alter functional p199RY-specific CD8(+) T lymphocyte responses to mutated epitopes, decreasing the capacity of these cells to contain SIVmac251 replication.     

Supraorbital ridge and masticatory apparatus I: Primates

The supraorbital ridge formation in apes is a result of the traction of the masticatory force exerted by the anterior part of the temporalis muscle. This force varies inversely with the ratio of the power arm to the load arm of the mandible. The smaller this ratio, the greater the anterior part of the temporalis muscle and the larger the supraorbital ridge. The size of the ridge is independent of the actual size of the skull. The orang has a larger skull but the smallest brow ridge of the three species studied: gorilla, chimpanzee and orang. Pearson’s correlation coefficient shows a positive correlation between the anterior temporalis muscle and the ridge as well as between the ridge/sinus and anterior/whole temporalis muscle. The correlation is negative between the power/load arms and anterior/whole muscle and also between the power/load arms and the ridge/sinus ratio.     

PPO: predictor for prokaryotic operons

SUMMARY: We present an operon predictor for prokaryotic operons (PPO), which can predict operons in the entire prokaryotic genome. The prediction algorithm used in PPO allows the user to select binary particle swarm optimization (BPSO), a genetic algorithm (GA) or some other methods introduced in the literature to predict operons. The operon predictor on our web server and the provided database are easy to access and use. The main features offered are: (i) selection of the prediction algorithm; (ii) adjustable parameter settings of the prediction algorithm; (iii) graphic visualization of results; (iv) integrated database queries; (v) listing of experimentally verified operons; and (vi) related tools. Availability and implementation: PPO is freely available at http://bio.kuas.edu.tw/PPO/.     

Pepitope: epitope mapping from affinity-selected peptides

Identifying the epitope to which an antibody binds is central for many immunological applications such as drug design and vaccine development. The Pepitope server is a web-based tool that aims at predicting discontinuous epitopes based on a set of peptides that were affinity-selected against a monoclonal antibody of interest. The server implements three different algorithms for epitope mapping: PepSurf, Mapitope, and a combination of the two. The rationale behind these algorithms is that the set of peptides mimics the genuine epitope in terms of physicochemical properties and spatial organization. When the three-dimensional (3D) structure of the antigen is known, the information in these peptides can be used to computationally infer the corresponding epitope. A user-friendly web interface and a graphical tool that allows viewing the predicted epitopes were developed. Pepitope can also be applied for inferring other types of protein-protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure. AVAILABILITY: http://pepitope.tau.ac.il/     

TEpredict: Software for T-Cell epitope prediction

The program TEpredict was developed for T-cell epitope prediction. The used models for T-cell epitope prediction were constructed by the partial least squares regression method using the data extracted from the IEDB (Immune Epitope Database), the most complete resource of experimental peptide-MHC binding data. TEpredict is also able to predict proteasomal processing of protein antigens and the ability of produced oligopeptides to bind to the transporters associated with antigen processing, to discard the peptides sharing local similarity with human proteins from the set of predicted epitopes, and to estimate the expected population coverage by the selected peptides using the data on HLA allele genotypic frequencies. The main part of the constructed models demonstrated a high prediction sensitivity (0.50–0.80) in combination with a high specificity (0.75–0.99). Comparative testing demonstrated that TEpredict was competitive with or even superior to the programs ProPred1, SVRMHC, SVMHC, and SYFPEITHI. Thus, TEpredict can become an efficient tool for developing polyepitope vaccines, including the vaccines against various human pathogens, such as HIV and the influenza virus. TEpredict and the source code are available at http://tepredict.source- forge.net.     

Exogenous leptin promotes the recovery of regressed ovary in fasted ducks

The present study was undertaken to examine the effect of administered recombinant mouse leptin on the recovery of regressed ovary in fasted ducks. Twenty-eight ducks were divided into five groups: fed ad libitum (control; n = 5), fasted control (FC; n = 5), fasted + low dose of leptin (F + L; n = 5), fasted + medium dose of leptin (F + M; n = 5) and fasted + high dose of leptin (F + H; n = 3). All four fasted groups were fasted for 2 days and then ad libitum and the ducks were treated with leptin at doses of 0 (control and FC), 50 (F + L), 250 (F + M) and 1000 (F + H) μg/kg body weight/day on day 3–5. Results showed that a moderate dose of leptin (250 μg/kg body weight/day) injected during the re-feeding period: (i) promoted the recovery of the regressed ovary as evidenced by an increase in ovary weight and recovery of yellow hierarchical follicles; (ii) elevated the plasma 17β-estradiol (E₂) level; (iii) increased the mRNA levels of ovary follicle-stimulating hormone receptor (FSHR), luteinizing hormone receptor (LHR) and estrogen receptor-β (ER-β). Furthermore, the results also showed that a high dose of leptin (1000 μg/kg body weight/day) may have a negative effect on the recovery of the regressed ovary. In conclusion, this study indicates that, in ducks, leptin may be involved in the recovery of the regressed ovary caused by 2 days of fasting. This effect may be related to increased plasma E₂ levels and stimulation of the mRNA levels of ovarian FSHR, LHR and especially ER-β.     

BaCelLo: a balanced subcellular localization predictor

MOTIVATION: The knowledge of the subcellular localization of a protein is fundamental for elucidating its function. It is difficult to determine the subcellular location for eukaryotic cells with experimental high-throughput procedures. Computational procedures are then needed for annotating the subcellular location of proteins in large scale genomic projects. RESULTS: BaCelLo is a predictor for five classes of subcellular localization (secretory pathway, cytoplasm, nucleus, mitochondrion and chloroplast) and it is based on different SVMs organized in a decision tree. The system exploits the information derived from the residue sequence and from the evolutionary information contained in alignment profiles. It analyzes the whole sequence composition and the compositions of both the N- and C-termini. The training set is curated in order to avoid redundancy. For the first time a balancing procedure is introduced in order to mitigate the effect of biased training sets. Three kingdom-specific predictors are implemented: for animals, plants and fungi, respectively. When distributing the proteins from animals and fungi into four classes, accuracy of BaCelLo reach 74% and 76%, respectively; a score of 67% is obtained when proteins from plants are distributed into five classes. BaCelLo outperforms the other presently available methods for the same task and gives more balanced accuracy and coverage values for each class. We also predict the subcellular localization of five whole proteomes, Homo sapiens, Mus musculus, Caenorhabditis elegans, Saccharomyces cerevisiae and Arabidopsis thaliana, comparing the protein content in each different compartment. AVAILABILITY: BaCelLo can be accessed at http://www.biocomp.unibo.it/bacello/.     

Reshaping Cinderella's slipper: the shared epitope hypothesis

This issue of Arthritis Research and Therapy contains a succinct and elegant paper by Michou and colleagues that advances our understanding of the genetic basis of rheumatoid arthritis (RA) by reclassifying the contribution of RA susceptibility alleles according to their structure. This line of research is potentially important in our conceptualization of the mechanism of disease in RA, in predicting disease course and severity, and as a model for further studies on this topic. The author's approach to reassessing the molecular structure of the shared epitope redirects attention to using the binding properties of the major histocompatibility complex molecules associated with susceptibility to search for the peptides driving the autoimmune process underlying rheumatoid arthritis     

Peptide epitope mapping in vaccine development: Introduction

Protection from infectious disease by the host immune response requires specific molecular recognition of unique antigenic determinants of a given pathogen. An epitope is an antigenic determinant which: 1) specifically stimulates the immune response (either B or T cell mediated); and 2) is acted upon by the products of these protective mechanisms. In B cell immunity, antibodies produced from stimulation by specific epitopes recognize and bind to these same antigenic structures. Identification of protective epitopes is extremely valuable to successful vaccine development. In order to be protective these antibodies must, in addition to recognition and binding, interfere with some vital step in pathogenesis such as adherence or toxin action. Protein B cell epitopes are frequently composed of the side chains (R-groups) of the amino acids found at solvent-exposed surfaces. These epitopes are classified as continuous (also linear or sequential) if composed of a single antibody-recognizing element located at a single locus of the primary structure. They are discontinuous (or assembled) if more than one physically separated entity is involved. T cell epitopes are peptides on the surface of antigen-presenting cells (macrophages, dendritic cells, and B cells) that are bound to major histocompatibility proteins; the T cell recognizes this peptide-MHC complex. Received 12 August 1996/ Accepted in revised form 03 November 1996     

Marker-assisted selection using ridge regression

In cross between inbred lines, linear regression can be used to estimate the correlation of markers with a trait of interest; these marker effects then allow marker assisted selection (MAS) for quantitative traits. Usually a subset of markers to include in the model must be selected: no completely satisfactory method of doing this exists. We show that replacing this selection of markers by ridge regression can improve the mean response to selection and reduce the variability of selection response.     

Anterior dorsal ventricular ridge in the lizard: Embryonic development

In lacertids the telencephalic vesicle starts its development at stage E = 30, at which time it is lined by a homogeneous nucleated zone in which particular ventricular zone territories or sulci cannot be distinguished. At stage E = 32 coinciding with the initial development of the anterior dorsal ventricular ridge (ADVR), one may distinguish the ventricular zone b in the dorsolateral wall of the ventricle adjacent to the sulcus lateralis. The ADVR continues growing by incorporation of cells produced in two proliferative zones (zone b and wall of the sulcus lateralis) and appears fully developed in postnatal lizards. Ultrastructural characteristics of young ADVR neurons between stages E-32 and E-33 are typical of those in immature cells. Beginning at stage E-34, some of these neurons appear to be degenerating (pycnotic). Thereafter, neurons of the ADVR develop abundant cytoplasmic organelles and the neuropile grows quickly. Myelination starts in the ADVR between stages E-38 and E-40, but is not observed in other striatal masses in the same period. Vascularization begins and is well developed at E-40. The first synaptic contacts were observed in embryos of stage E=38; they are chiefly axo-dendritic, although some are axo-somatic. Degenerating neurons were found in the ADVR up to hatching. From stage E-40 onward, the ADVR shows a greater and more rapid differentiation than all other striatal nuclei, including the ventral and amygdaloid complex.     

On marker-assisted prediction of genetic value: beyond the ridge

Marked-assisted genetic improvement of agricultural species exploits statistical dependencies in the joint distribution of marker genotypes and quantitative traits. An issue is how molecular (e.g., dense marker maps) and phenotypic information (e.g., some measure of yield in plants) is to be used for predicting the genetic value of candidates for selection. Multiple regression, selection index techniques, best linear unbiased prediction, and ridge regression of phenotypes on marker genotypes have been suggested, as well as more elaborate methods. Here, phenotype-marker associations are modeled hierarchically via multilevel models including chromosomal effects, a spatial covariance of marked effects within chromosomes, background genetic variability, and family heterogeneity. Lorenz curves and Gini coefficients are suggested for assessing the inequality of the contribution of different marked effects to genetic variability. Classical and Bayesian methods are presented. The Bayesian approach includes a Markov chain Monte Carlo implementation. The generality and flexibility of the Bayesian method is illustrated when a Lorenz curve is to be inferred.     

Balancing on a narrow ridge: biomechanics and control.

The balance of standing humans is usually explained by the inverted pendulum model. The subject invokes a horizontal ground-reaction force in this model and controls it by changing the location of the centre of pressure under the foot or feet. In experiments I showed that humans are able to stand on a ridge of only a few millimetres wide on one foot for a few minutes. In the present paper I investigate whether the inverted pendulum model is able to explain this achievement. I found that the centre of mass of the subjects sways beyond the surface of support, rendering the inverted pendulum model inadequate. Using inverse simulations of the dynamics of the human body, I found that hip-joint moments of the stance leg are used to vary the horizontal component of the ground-reaction force. This force brings the centre of mass back over the surface of support. The subjects generate moments of force at the hip-joint of the swing leg, at the shoulder-joints and at the neck. These moments work in conjunction with a hip strategy of the stance leg to limit the angular acceleration of the head-arms-trunk complex. The synchrony of the variation in moments suggests that subjects use a motor programme rather than long latency reflexes.