The nonhistone chromosomal proteins of vertebrate liver and kidney: A comparative study by gel electrophoresis

Summary The nonhistone chromosomal proteins (NHC proteins) probably include enzymes of chromosomal metabolism, general structural proteins, and possibly control elements. In theory, these proteins may have been strongly conserved during evolution, as the histones have. We have used sodium dodecyl sulfate (SDS) disc gel electrophoresis to analyze and compare the NHC proteins of two tissues, liver and kidney, from rat, cat, cow, chicken, turtle, and frog. The gel patterns indicate that the NHC proteins have changed much more during evolution than have the histones; the total pattern of NHC proteins has not been conserved. However, there does appear to be a conservation of a subset of bands for each tissue investigated. Further chemical analysis will be required to establish the significance of the results.Recipient of NIH Career Development Award NIH AI-20388     

Elucidation of the evolution and taxonomy of cultivated potatoes with electrophoresis

Summary A recently developed polyacrylamide gel electrophoresis technique for tuber proteins is used to help elucidate the evolution and taxonomy of some cultivated potatoes. The results substantiate the theory that Group Tuberosum evolved from Group Andigena, that Group Andigena evolved from a cultivated diploid × wild diploid hybrid, and that Group Phureja evolved from Group Stenotomum. Furthermore, the results suggest these groups are closely enough related to merit classification within a single species.Scientific Journal Series Article 10,172 of the Minnesota Agricultural Experiment Station     

A computer-assisted examination of the storage protein genetic variation in 841 accessions of Triticum dicoccoides

Summary Triticum turgidum L. var. dicoccoides (wild emmer) is an important genetic resource for increasing the protein content of common wheat (Triticum aestivum L.). Many studies have shown that the presence or absence of bands in sodium dodecyl sulfate polyacrylamide (SDS-PAGE) electrophoregrams of wheat storage proteins to be of a purely genetic character. A total protein extraction and SDS-PAGE technique was used to estimate the storage protein genetic variability among 841 accessions of wild emmer collected from various ecological regions in the Middle East. In addition, a computer data bank was developed, recording the onedimension electrophoregram bands for each accession by molecular weight (MW) and relative Coomassie Blue staining intensity as determined from densitometer scans. Analyses of this information are being used to identify specific accessions for further study by two dimension electrofocusing-electrophoresis and breeding and genetic analyses. The computer-assisted analyses indicated that the greatest genetic variability occurs for proteins in the high MW region (above 70,000 MW) followed by those in the medium range (70,000 to 33,300 MW). Comparatively little variability was revealed for protein subunits of below 33,300 MW.Scientific Paper No. 6591. College of Agriculture Research Center, Washington State University, Pullman, Project No. 1568. This work was supported in part by the U.S.-Israel Binational Agricultural Research and Development Fund (BARD)     

Feature selection for splice site prediction: A new method using EDA-based feature ranking

Background  

The identification of relevant biological features in large and complex datasets is an important step towards gaining insight in the processes underlying the data. Other advantages of feature selection include the ability of the classification system to attain good or even better solutions using a restricted subset of features, and a faster classification. Thus, robust methods for fast feature selection are of key importance in extracting knowledge from complex biological data.     

Hidden markov model for the prediction of transmembrane proteins using MATLAB

Since membranous proteins play a key role in drug targeting therefore transmembrane proteins prediction is active and challenging area of biological sciences. Location based prediction of transmembrane proteins are significant for functional annotation of protein sequences. Hidden markov model based method was widely applied for transmembrane topology prediction. Here we have presented a revised and a better understanding model than an existing one for transmembrane protein prediction. Scripting on MATLAB was built and compiled for parameter estimation of model and applied this model on amino acid sequence to know the transmembrane and its adjacent locations. Estimated model of transmembrane topology was based on TMHMM model architecture. Only 7 super states are defined in the given dataset, which were converted to 96 states on the basis of their length in sequence. Accuracy of the prediction of model was observed about 74 %, is a good enough in the area of transmembrane topology prediction. Therefore we have concluded the hidden markov model plays crucial role in transmembrane helices prediction on MATLAB platform and it could also be useful for drug discovery strategy. AVAILABILITY: The database is available for free at bioinfonavneet@gmail.comvinaysingh@bhu.ac.in.     

A novel sequence-based method for phosphorylation site prediction with feature selection and analysis

Phosphorylation is one of the most important post-translational modifications, and the identification of protein phosphorylation sites is particularly important for studying disease diagnosis. However, experimental detection of phosphorylation sites is labor intensive. It would be beneficial if computational methods are available to provide an extra reference for the phosphorylation sites. Here we developed a novel sequence-based method for serine, threonine, and tyrosine phosphorylation site prediction. Nearest Neighbor algorithm was employed as the prediction engine. The peptides around the phosphorylation sites with a fixed length of thirteen amino acid residues were extracted via a sliding window along the protein chains concerned. Each of such peptides was coded into a vector with 6,072 features, derived from Amino Acid Index (AAIndex) database, for the classification/detection. Incremental Feature Selection, a feature selection algorithm based on the Maximum Relevancy Minimum Redundancy (mRMR) method was used to select a compact feature set for a further improvement of the classification performance. Three predictors were established for identifying the three types of phosphorylation sites, achieving the overall accuracies of 66.64%, 66.11%% and 66.69%, respectively. These rates were obtained by rigorous jackknife cross-validation tests.     

Molecular phylogeny of selected predaceous leeches with reference to the evolution of body size and terrestrialism

The phylogenetic relationships of erpobdellid leeches collected throughout Europe were investigated using newly obtained mitochondrial cytochrome c oxidase subunit I (CO-I) gene sequence data from 10 taxa. Monophyly of the five European Erpobdella species (sub-family Erpobdellinae) was supported, but a newly discovered leech, E. wuttkeit Kutschera, 2004 (the smallest member of its genus, discovered in an aquarium) was only distantly related to this clade. Three members of the semiaquatic Trochetinae were included in this study. The largest European leech species discovered so far, Trocheta haskonis Grosser, 2000, was found to be a terrestrial predator that feeds on earthworms. The rare species T. haskonis is the sister taxon of T. bykowskii Gedroyc, 1913, a well-known amphibious leech. Based on a comparison of body sizes and a phylogenetic tree the evolution of terrestrialism in the family Erpobdellidae is discussed.     

A simple and fast secondary structure prediction method using hidden neural networks

MOTIVATION: In this paper, we present a secondary structure prediction method YASPIN that unlike the current state-of-the-art methods utilizes a single neural network for predicting the secondary structure elements in a 7-state local structure scheme and then optimizes the output using a hidden Markov model, which results in providing more information for the prediction. RESULTS: YASPIN was compared with the current top-performing secondary structure prediction methods, such as PHDpsi, PROFsec, SSPro2, JNET and PSIPRED. The overall prediction accuracy on the independent EVA5 sequence set is comparable with that of the top performers, according to the Q3, SOV and Matthew's correlations accuracy measures. YASPIN shows the highest accuracy in terms of Q3 and SOV scores for strand prediction. AVAILABILITY: YASPIN is available on-line at the Centre for Integrative Bioinformatics website (http://ibivu.cs.vu.nl/programs/yaspinwww/) at the Vrije University in Amsterdam and will soon be mirrored on the Mathematical Biology website (http://www.mathbio.nimr.mrc.ac.uk) at the NIMR in London. CONTACT: kxlin@nimr.mrc.ac.uk     

Systematics and palaeoecology of middle Toarcian Asteroidea (Echinodermata) from the “Seuil du Poitou”, Western France

Complete, articulated starfish fossils are rare. However, more frequently encountered dissociated skeletal elements (ossicles) permit reliable taxonomic identification, making them a valuable data source for diversity estimates. Nearly 300 asteroid ossicles, collected from the middle Toarcian marls in western France can be assigned to five species. Four species and two genera are described: Comptoniaster vrinensis nov. sp. (Goniasteridae), Poncetaster crateri nov. gen. nov. sp. (Stauranderasteridae), Galbaster recurrans nov. gen. nov. sp. (Goniasteridae) and Pentasteria? liasica nov. sp. (Astropectinidae). The known diversity of Early Jurassic asteroids is increased from 12 to 16 species. These taxa illustrate the diversification of crown-group asteroids early in the Jurassic, following the Permo-Triassic crisis. They also reflect bias of the fossil record, and imply the existence of numerous ghost lineages in the evolutionary trees of extant groups. Variation in asteroid diversity across the “Seuil du Poitou” was driven by ecological constraints. The relative frequency (abundance of ossicles and diversity) of goniasterids and stauranderasterids increases in shallower environments. The Benthopectinidae, represented by Plesiastropecten hallovensis, occurred primarily from deep-shelf sediments. Similar ecological patterns are observed for more recent fossil and extant relatives, which further supports the idea of conservative evolution in post-Palaeozoic starfishes since the Early Jurassic.     

Evolution of virulence: interdependence, constraints, and selection using nested models

Natural selection acts on virus populations at two distinct but interrelated levels: within individual hosts and between them. Studies of the evolution of virulence typically focus on selection acting at the epidemiological or between-host level and demonstrate the importance of trade-offs between disease transmission and virulence rates. Within-host studies reach similar conclusions regarding trade-offs between transmission and virulence at the level of individual cells. Studies which examine selection at both scales assume that between- and within-host selection are necessarily in conflict. We explicitly examine these ideas and assumptions using a model of within-host viral dynamics nested within a model of between-host disease dynamics. Our approach allows us to evaluate the direction of selection at the within- and between-host levels and identify situations leading to conflict and accord between the two levels of selection.     

A review and synthesis on the systematics and evolution of jellyfish blooms: advantageous aggregations and adaptive assemblages

Pelagic gelatinous invertebrates in many diverse phyla aggregate, bloom, or swarm. Although typically portrayed as annoying to humans, such accumulations probably are evolutionary adaptations to the environments of pelagic gelatinous zooplankton. We explore this proposition by systematic analysis completed in three steps. First, using the current morphological taxonomic framework for Scyphozoa, we summarize relevant information on species that aggregate, bloom, and swarm and on those species that do not. Second, we establish a molecular phylogenetic framework for assessing evolutionary relationships among classes and many orders of Medusozoa and among most families of Scyphozoa (particularly Discomedusae). Third, we interpret the phylogenetic distribution of taxa and of characteristics of jellyfish that aggregate, bloom, or swarm, in terms of species diversity—a proxy for evolutionary success. We found that: (1) Medusae that occur en masse are not randomly distributed within the Phylum Cnidaria but instead they are found primarily within the Scyphozoa which have a metagenic life history. (2) Midwater and deep-sea medusae rarely bloom or swarm. (3) Epibenthic medusae do not swarm. (4) Large carnivores that feed on large prey do not bloom strongly. (5) Large medusae that feed exclusively on small prey both bloom and swarm. (6) Pelagia, the only holoplanktonic, epipelagic scyphomedusan, both blooms and swarms, demonstrating that a metagenic life cycle is not required for blooming or swarming at sea. (7) Environmental change (overfishing, species introductions, and eutrophication) may induce or inhibit blooms. (8) Taxa that bloom or swarm are often more diverse than taxa that do not. (9) Speciation in scyphozoans can occur rapidly. (10) Morphological stasis in holozooplankton masks genetic variability. (11) Selection for convergent evolution in the sea is strong because mass occurrence has evolved multiple times in independent evolutionary lineages under similar circumstances. Thus, attributes possessed by many taxa that occur en masse appear to be evolutionarily advantageous, i.e., adaptations. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Guest editors: K. A. Pitt & J. E. Purcell Jellyfish Blooms: Causes, Consequences, and Recent Advances     

Enzyme-linked immunosorbent assay-based selection and optimization of elution buffer for TAG72-affinity chromatography

An enzyme-linked immunosorbent assay (ELISA)-elution assay was developed to screen a large variety of elution buffers for selection of a suitable one for purification of the fusion protein FV/TNF-α by affinity chromatography. Various commonly used buffer systems utilizing widely differing conditions such as extreme pH, denaturants, chaotropic ions and polarity reducing reagents were investigated. Ammonia solution (1 M, pH 11.5) proved to exert the most suitable influence on dissociation of the FV/TNF-α/TAG72 complex while having a minimal protein denaturing effect on FV/TNF-α. The total yield of purified FV/TNF-α using the TAG72-affinity column with this elution system was 300-fold higher than that using the common elution buffer, 0.1 M glycine, 0.5 M NaCl, pH 2.7. Our study indicates that the ELISA-elution assay will be most useful in the selection of suitable elution buffers for affinity chromatography.     

A likelihood method for the detection of selection and recombination using nucleotide sequences

Different regions along nucleotide sequences are often subject to different evolutionary forces. Recombination will result in regions having different evolutionary histories, while selection can cause regions to evolve at different rates. This paper presents a statistical method based on likelihood for detecting such processes by identifying the regions which do not fit with a single phylogenetic topology and nucleotide substitution process along the entire sequence. Subsequent reanalysis of these anomalous regions may then be possible. The method is tested using simulations, and its application is demonstrated using the primate psi eta-globin pseudogene, the V3 region of the envelope gene of HIV-1, and argF sequences from Neisseria bacteria. Reanalysis of anomalous regions is shown to reveal possible immune selection in HIV-1 and recombination in Neisseria. A computer program which implements the method is available.      

Separation of proteins and viruses using two-phase aqueous micellar systems

We discuss the utilization of a novel two-phase aqueous nonionic micellar system for the purification and concentration of biomolecules, such as proteins and viruses, by liquid–liquid extraction. The nonionic surfactant n-decyl tetra(ethylene oxide), C₁₀E₄, phase separates in water into two coexisting aqueous micellar phases by increasing temperature. The mild interactions of the C₁₀E₄ nonionic surfactant with biomolecules, combined with the high water content of the two coexisting micellar phases, suggest the potential utility of two-phase aqueous C₁₀E₄ micellar systems for the purification and concentration of biomolecules. In this paper, we review our recent experimental and theoretical studies involving the partitioning of several water-soluble proteins, including cytochrome c, soybean trypsin inhibitor, ovalbumin, bovine serum albumin, and catalase, in the two-phase aqueous C₁₀E₄ micellar system. In addition, we present results of our preliminary experimental investigation on the partitioning of bacteriophages, including φX174, P22, and T4.     

Anisogamy,sexual selection,and the evolution and maintenance of sex

Summary In the present paper we distinguish between two aspects of sexual reproduction. Genetic recombination is a universal features of the sexual process. It is a primitive condition found in simple, single-celled organisms, as well as in higher plants and animals. Its function is primarily to repair genetic damage and eliminate deleterious mutations. Recombination also produces new variation, however, and this can provide the basis for adaptive evolutionary change in spatially and temporally variable environments.The other feature usually associated with sexual reproduction, differentiated male and female roles, is a derived condition, largely restricted to complex, diploid, multicellular organisms. The evolution of anisogamous gametes (small, mobile male gametes containing only genetic material, and large, relatively immobile female gametes containing both genetic material and resources for the developing offspring) not only established the fundamental basis for maleness and femaleness, it also led to an asymmetry between the sexes in the allocation of resources to mating and offspring. Whereas females allocate their resources primarily to offspring, the existence of many male gametes for each female one results in sexual selection on males to allocate their resources to traits that enhance success in competition for fertilizations. A consequence of this reproductive competition, higher variance in male than female reproductive success, results in more intense selection on males.The greater response of males to both stabilizing and directional selection constitutes an evolutionary advantage of males that partially compensates for the cost of producing them. The increased fitness contributed by sexual selection on males will complement the advantages of genetic recombination for DNA repair and elimination of deleterious mutations in any outcrossing breeding system in which males contribute only genetic material to their offspring. Higher plants and animals tend to maintain sexual reproduction in part because of the enhanced fitness of offspring resulting from sexual selection at the level of individual organisms, and in part because of the superiority of sexual populations in competition with asexual clones.     

A simple method for selection of trypsin chromogenic substrates using combinatorial chemistry approach

A tetrapeptide combinatorial library, considered as chromogenic substrates of bovine beta-trypsin, was synthesized by the solid phase method. The peptides contain an analog of p-nitroanilide, obtained by attaching 5-amino-2-nitrobenzoic acid (Anb(5,2)) to the C-termini. Deconvolution of the peptide library, performed in solution using an iterative method, yielded four efficient trypsin substrates. The most active one, Phe-Val-Pro-Arg-Anb(5,2)-NH(2), appeared to be 125-fold more active than Bz-D,L-Arg-pNA (BAPNA) used as a reference compound. The reported method of designing trypsin chromogenic substrate libraries is straightforward. Such p-nitroanilides may be useful for the investigation of any protease substrate specificity.     

A modified pedigree method of selection

Summary A dismal 81% failure of newly bulked lines against checks was observed in Indian wheat material evolved by the pedigree method. This is considered to be the consequence of selection in space planting in early generations followed by yield tests in a competitive environment which did not allow any scope of selection for competitive ability. Thus, most of the homozygous lines, which were until now raised and carried forward under space planting, failed to compete with the checks for yield in close planting. It is, therefore, necessary to modify the method to combine both the competitive ability and identity of selected plants. The proposed modified procedure involves raising the population under spaced planting as well as under drilling from F₂ onwards. Evaluation for tiller index marks an important step. On the basis of tiller index, single plants are isolated from spaced populations. Steps of the modified procedure are outlined in detail. The modified method, which economises on breeders' workload and other physical inputs, besides having other advantages, can also be used for certain other grain crops. Preliminary results based on the modified method during the past two seasons have indicated its utility.     

A neural network method for prediction of beta-turn types in proteins using evolutionary information

MOTIVATION: The prediction of beta-turns is an important element of protein secondary structure prediction. Recently, a highly accurate neural network based method Betatpred2 has been developed for predicting beta-turns in proteins using position-specific scoring matrices (PSSM) generated by PSI-BLAST and secondary structure information predicted by PSIPRED. However, the major limitation of Betatpred2 is that it predicts only beta-turn and non-beta-turn residues and does not provide any information of different beta-turn types. Thus, there is a need to predict beta-turn types using an approach based on multiple sequence alignment, which will be useful in overall tertiary structure prediction. RESULTS: In the present work, a method has been developed for the prediction of beta-turn types I, II, IV and VIII. For each turn type, two consecutive feed-forward back-propagation networks with a single hidden layer have been used where the first sequence-to-structure network has been trained on single sequences as well as on PSI-BLAST PSSM. The output from the first network along with PSIPRED predicted secondary structure has been used as input for the second-level structure-to-structure network. The networks have been trained and tested on a non-homologous dataset of 426 proteins chains by 7-fold cross-validation. It has been observed that the prediction performance for each turn type is improved significantly by using multiple sequence alignment. The performance has been further improved by using a second level structure-to-structure network and PSIPRED predicted secondary structure information. It has been observed that Type I and II beta-turns have better prediction performance than Type IV and VIII beta-turns. The final network yields an overall accuracy of 74.5, 93.5, 67.9 and 96.5% with MCC values of 0.29, 0.29, 0.23 and 0.02 for Type I, II, IV and VIII beta-turns, respectively, and is better than random prediction. AVAILABILITY: A web server for prediction of beta-turn types I, II, IV and VIII based on above approach is available at http://www.imtech.res.in/raghava/betaturns/ and http://bioinformatics.uams.edu/mirror/betaturns/ (mirror site).