Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences

Motivation: In any macromolecular polyprotic system - for example protein, DNA or RNA - the isoelectric point - commonly referred to as the pI - can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall surface charge - and thus the electrophoretic mobility - of the ampholyte sums to zero. Different modern analytical biochemistry and proteomics methods depend on the isoelectric point as a principal feature for protein and peptide characterization. Protein separation by isoelectric point is a critical part of 2-D gel electrophoresis, a key precursor of proteomics, where discrete spots can be digested in-gel, and proteins subsequently identified by analytical mass spectrometry. Peptide fractionation according to their pI is also widely used in current proteomics sample preparation procedures previous to the LC-MS/MS analysis. Therefore accurate theoretical prediction of pI would expedite such analysis. While such pI calculation is widely used, it remains largely untested, motivating our efforts to benchmark pI prediction methods. Results: Using data from the database PIP-DB and one publically available dataset as our reference gold standard, we have undertaken the benchmarking of pI calculation methods. We find that methods vary in their accuracy and are highly sensitive to the choice of basis set. The machine-learning algorithms, especially the SVM-based algorithm, showed a superior performance when studying peptide mixtures. In general, learning-based pI prediction methods (such as Cofactor, SVM and Branca) require a large training dataset and their resulting performance will strongly depend of the quality of that data. In contrast with Iterative methods, machine-learning algorithms have the advantage of being able to add new features to improve the accuracy of prediction. Contact: yperez@ebi.ac.uk Availability and Implementation: The software and data are freely available at https://github.com/ypriverol/pIR. Supplementary information: Supplementary data are available at Bioinformatics online.

Optimised phase disposition pulse-width modulation strategy for hybrid-clamped multilevel inverters using switching state sequences

This study describes an optimised modulation strategy based on switching state sequences for the hybrid-clamped multilevel converter. Two key control variables defined as 'phase shift angle' and 'switching state change' for a five-level hybrid-clamped inverter are proposed to improve all switches' operation, and by changing their values, different control methods can be obtained for modulation optimisation purposes. Two example methods can solve the voltage imbalance problem of the dc-link capacitors and furthermore avoid two switches' simultaneous switching transitions and improve the inverter's performance as compared with the traditional phase disposition pulse-width modulation strategy. A 6 kW prototype inverter is developed and a range of simulation and experiments are carried out for validation. It is found that simulation and experimental results are in a good agreement and the proposed modulation strategy is verified in terms of low-order harmonic reduction.

Ammonite biostratigraphy, lithofacies variations, and paleoceanographic implications for Barremian-Aptian sequences of northeastern Mexico

Two Barremian-Aptian sequences studied in Durango and Nuevo Leon States, northeastern Mexico include three lithic units which have been described as the Cupido Formation of Barremian-early Early Aptian age, its lateral equivalent, the Lower Tamaulipas Formation, and the La Peña Formation extending through the early Albian. ^ The present work improves the existing ammonite Aptian biozonation by considering constraints associated with a discontinuous spatial and temporal record of the different taxa within the La Peña Formation. ^ Four ammonite biozones are established: (1) The Dufrenoyia justinae Zone for the late Early Aptian, (2) The Burckhardtites nazasensis/Rhytidoplites robertsi Zone for the middle Aptian, (3) The Cheloniceras inconstans Zone for the early Late Aptian, and (4) The Hypacanthoplites cf. leanzae Zone for the late late Aptian. ^ Also, a detailed sedimentological analysis of the sections shed further light on the possible causes that controlled intermittent occurrences of the ammonites in relation to the prevailing paleoceanographic and paleoecologic conditions in northeastern Mexico during the late Barremian-Aptian. ^ Microfacies analyses show that the upper part of the Cupido facies are represented by biocalcirudite with rudists, biocalcarenites with oolites and algae, and rich benthonic foraminifera assemblages with ostracods. These facies are related to paleoceanographic conditions of sedimentation within a shallow-marine carbonate platform. Its lateral equivalent, deep-water facies extended to the southeast and it is represented by the Lower Tamaulipas Formation, which includes planktonic foraminifera, ostracods, and mollusk and echinoid fragments. The beginning of deposition of the La Peña Formation in the late Early Aptian is characterized by an increase in terrigenous materials and significant decrease in the abundance of benthic fauna. The La Peña Formation is recognized by an alternation of marls and shale limestones containing ammonites, planktonic foraminifera, ostracods, and radiolaria toward the top. Accumulation of the La Peña continued throughout the end of the Aptian and records changes in conditions of sedimentation and productivity in the water column, which abruptly terminated the carbonate deposition in the Cupido Platform. ^ Results of carbon/carbonate content analyses show that changes from the Cupido to the La Peña facies are also characterized by an increase of organic carbon, which indicate the onset of enhanced dysoxic/anoxic conditions in the lower water column. ^

Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains

Background The HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation, among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method [1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal sequence data. We present serial evolutionary networks as a longitudinal representation of the mutational pathways of a viral population in a within-host environment. The longitudinal representation of the evolutionary networks was complemented with charts of clinical markers to facilitate correlation analysis between pertinent clinical information and the evolutionary relationships. Results Analysis based on the predicted networks suggests the following:: significantly stronger recombination signals (p = 0.003) for the inferred ancestors of the X4 strains, recombination events between different lineages and recombination events between putative reservoir virus and those from a later population, an early star-like topology observed for four of the patients who died of AIDS. A significantly higher number of recombinants were predicted at sampling points that corresponded to peaks in the viral load levels (p = 0.0042). Conclusion Our results indicate that serial evolutionary networks of HIV sequences enable systematic statistical analysis of the implicit relations embedded in the topology of the structure and can greatly facilitate identification of patterns of evolution that can lead to specific hypotheses and new insights. The conclusions of applying our method to empirical HIV data support the conventional wisdom of the new generation HIV treatments, that in order to keep the virus in check, viral loads need to be suppressed to almost undetectable levels.

Towards the prediction of mutations in genomic sequences

Bio-systems are inherently complex information processing systems. Furthermore, physiological complexities of biological systems limit the formation of a hypothesis in terms of behavior and the ability to test hypothesis. More importantly the identification and classification of mutation in patients are centric topics in today's cancer research. Next generation sequencing (NGS) technologies can provide genome-wide coverage at a single nucleotide resolution and at reasonable speed and cost. The unprecedented molecular characterization provided by NGS offers the potential for an individualized approach to treatment. These advances in cancer genomics have enabled scientists to interrogate cancer-specific genomic variants and compare them with the normal variants in the same patient. Analysis of this data provides a catalog of somatic variants, present in tumor genome but not in the normal tissue DNA. In this dissertation, we present a new computational framework to the problem of predicting the number of mutations on a chromosome for a certain patient, which is a fundamental problem in clinical and research fields. We begin this dissertation with the development of a framework system that is capable of utilizing published data from a longitudinal study of patients with acute myeloid leukemia (AML), who's DNA from both normal as well as malignant tissues was subjected to NGS analysis at various points in time. By processing the sequencing data at the time of cancer diagnosis using the components of our framework, we tested it by predicting the genomic regions to be mutated at the time of relapse and, later, by comparing our results with the actual regions that showed mutations (discovered at relapse time). We demonstrate that this coupling of the algorithm pipeline can drastically improve the predictive abilities of searching a reliable molecular signature. Arguably, the most important result of our research is its superior performance to other methods like Radial Basis Function Network, Sequential Minimal Optimization, and Gaussian Process. In the final part of this dissertation, we present a detailed significance, stability and statistical analysis of our model. A performance comparison of the results are presented. This work clearly lays a good foundation for future research for other types of cancer.^

A heuristic algorithm to generate test program sequences for moving probe electronic test equipment

The electronics industry, is experiencing two trends one of which is the drive towards miniaturization of electronic products. The in-circuit testing predominantly used for continuity testing of printed circuit boards (PCB) can no longer meet the demands of smaller size circuits. This has lead to the development of moving probe testing equipment. Moving Probe Test opens up the opportunity to test PCBs where the test points are on a small pitch (distance between points). However, since the test uses probes that move sequentially to perform the test, the total test time is much greater than traditional in-circuit test. While significant effort has concentrated on the equipment design and development, little work has examined algorithms for efficient test sequencing. The test sequence has the greatest impact on total test time, which will determine the production cycle time of the product. Minimizing total test time is a NP-hard problem similar to the traveling salesman problem, except with two traveling salesmen that must coordinate their movements. The main goal of this thesis was to develop a heuristic algorithm to minimize the Flying Probe test time and evaluate the algorithm against a "Nearest Neighbor" algorithm. The algorithm was implemented with Visual Basic and MS Access database. The algorithm was evaluated with actual PCB test data taken from Industry. A statistical analysis with 95% C.C. was performed to test the hypothesis that the proposed algorithm finds a sequence which has a total test time less than the total test time found by the "Nearest Neighbor" approach. Findings demonstrated that the proposed heuristic algorithm reduces the total test time of the test and, therefore, production cycle time can be reduced through proper sequencing.

Ammonite biostratigraphy, lithofacies variations, and paleoceanographic implications for barremian-aptian sequences of northeastern Mexico

Two Barremian-Aptian sequences studied in Durango and Nuevo Leon States, northeastern Mexico include three lithic units which have been described as the Cupido Formation of Barremian-early Early Aptian age, its lateral equivalent, the Lower Tamaulipas Formation, and the La Pena Formation extending through the early Albian. The present work improves the existing ammonite Aptian biozonation by considering constraints associated with a discontinuous spatial and temporal record of the different taxa within the La Pena Formation. Four ammonite biozones are established: 1) The Dufrenoyia justinae Zone for the late Early Aptian, 2) The Burckhardtites nazasensis/Rhytidoplites robertsi Zone for the middle Aptian, 3) The Cheloniceras inconstans Zone for the early Late Aptian, and 4) The Hypacanthoplites cf. leanzae Zone for the late late Aptian. Also, a detailed sedimentological analysis of the sections shed further light on the possible causes that controlled intermittent occurrences of the ammonites in relation to the prevailing paleoceanographic and paleoecologic conditions in northeastern Mexico during the late Barremian-Aptian. Microfacies analyses show that the upper part of the Cupido facies are represented by biocalcirudite with rudists, biocalcarenites with oolites and algae, and rich benthonic foraminifera assemblages with ostracods. These facies are related to paleoceanographic conditions of sedimentation within a shallow-marine carbonate platform. Its lateral equivalent, deep-water facies extended to the southeast and it is represented by the Lower Tamaulipas Formation, which includes planktonic foraminifera, ostracods, and mollusk and echinoid fragments. The beginning of deposition of the La Pena Formation in the late Early Aptian is characterized by an increase in terrigenous materials and significant decrease in the abundance of benthic fauna. The La Pena Formation is recognized by an alternation of marls and shale limestones containing ammonites, planktonic foraminifera, ostracods, and radiolaria toward the top. Accumulation of the La Pena continued throughout the end of the Aptian and records changes in conditions of sedimentation and productivity in the water column, which abruptly terminated the carbonate deposition in the Cupido Platform. Results of carbon/carbonate content analyses show that changes from the Cupido to the La Pena facies are also characterized by an increase of organic carbon, which indicate the onset of enhanced dysoxic/anoxic conditions in the lower water column.

(Table 1) Individual codes, haplotype codes, GenBank accession numbers for DNA sequences and sample locality of the analysed Betamorpha fusiformis specimens from the ANDEEP III expedition

Based on our current knowledge about population genetics, phylogeography and speciation, we begin to understand that the deep sea harbours more species than suggested in the past. Deep-sea soft-sediment environment in particular hosts a diverse and highly endemic invertebrate fauna. Very little is known about evolutionary processes that generate this remarkable species richness, the genetic variability and spatial distribution of deep-sea animals. In this study, phylogeographic patterns and the genetic variability among eight populations of the abundant and widespread deep-sea isopod morphospecies Betamorpha fusiformis [Barnard, K.H., 1920. Contributions to the crustacean fauna of South Africa. 6. Further additions to the list of marine isopods. Annals of the South African Museum 17, 319-438] were examined. A fragment of the mitochondrial 16S rRNA gene of 50 specimens and the complete nuclear 18S rRNA gene of 7 specimens were sequenced. The molecular data reveal high levels of genetic variability of both genes between populations, giving evidence for distinct monophyletic groups of haplotypes with average p-distances ranging from 0.0470 to 0.1440 (d-distances: 0.0592-0.2850) of the 16S rDNA, and 18S rDNA p-distances ranging between 0.0032 and 0.0174 (d-distances: 0.0033-0.0195). Intermediate values are absent. Our results show that widely distributed benthic deep-sea organisms of a homogeneous phenotype can be differentiated into genetically highly divergent populations. Sympatry of some genotypes indicates the existence of cryptic speciation. Flocks of closely related but genetically distinct species probably exist in other widespread benthic deep-sea asellotes and other Peracarida. Based on existing data we hypothesize that many widespread morphospecies are complexes of cryptic biological species (patchwork hypothesis).

Characterization of dynamic speckle sequences using principal component analysis and image descriptors

Speckle is being used as a characterization tool for the analysis of the dynamic of slow varying phenomena occurring in biological and industrial samples. The retrieved data takes the form of a sequence of speckle images. The analysis of these images should reveal the inner dynamic of the biological or physical process taking place in the sample. Very recently, it has been shown that principal component analysis is able to split the original data set in a collection of classes. These classes can be related with the dynamic of the observed phenomena. At the same time, statistical descriptors of biospeckle images have been used to retrieve information on the characteristics of the sample. These statistical descriptors can be calculated in almost real time and provide a fast monitoring of the sample. On the other hand, principal component analysis requires longer computation time but the results contain more information related with spatial-temporal pattern that can be identified with physical process. This contribution merges both descriptions and uses principal component analysis as a pre-processing tool to obtain a collection of filtered images where a simpler statistical descriptor can be calculated. The method has been applied to slow-varying biological and industrial processes

Soliton based DPSK encoded sequences:stability and dynamical properties

We study the dynamical properties of the RZ-DPSK encoded sequences of bits, focusing on the instabilities in the train leading to the bit stream corruption. The problem is studied within the framework of the complex Toda chain model for optical solitons. We show how the bit composition of the pattern affects the initial stage of the train dynamics and explain the general mechanisms of the appearance of unstable collective soliton modes. Then we discuss the nonlinear regime using the asymptotic properties of the pulse stream at large propagation distances and analyze the dynamical behavior of the train elucidating different scenarios for the pattern instabilities. ©2010 Crown.

Geochemistry and radiogenic isotope ratios of the volcanic sequences from Izu-Bonin Arc, Japan

New radiogenic isotope and trace element data are presented for the volcanic sequences along 600 km of the active Izu-Bonin arc, the Oligocene Izu arc, and their associated rift basins. As with many intra-oceanic island arcs, the Pliocene-Recent Izu-Bonin frontal-arc lavas are highly depleted in Zr, Nb and the rare-earth elements relative to typical mid-ocean ridge basalt (MORB), indicating that the mantle wedge source has undergone a previous episode of melting. Ratios between these elements (such as Nb/Zr and La/Sm), as well as 143Nd/144Nd, do not vary significantly along the length of the frontal-arc. These parameters suggest that each of the arc volcanoes is derived from similar melt fractions of the mantle wedge. However, Ba/Zr, Ba/Rb and 87Sr/86Sr increase along the frontal-arc to the north. This leads us to propose that a variable enrichment in Ba and radiogenic Sr is superimposed on the mantle wedge. Sr-Nd and Pb-Nd isotope variation indicate that both Sr and Pb become more radiogenic after fluid addition. However, Pb isotope ratios do not correlate with increases in Pb concentration or ratios such as Ba/Zr and Nb/Pb. In other words, the Pb isotopic composition of the arc lavas appears to be independent of the amount of Pb introduced by subduction fluids into the mantle source. This buffering of Pb isotopes along the frontal-arc means that the isotopic composition of the lavas is indistinguishable from that of the fluid. Isotopic mixing models presented for the arc are only illustrative of the many plausible combinations of components and quantities. Despite this, we are able to determine that the mantle wedge has isotopic characteristics similar to Indian Ocean MORB, and that the subduction-fluid solute is primarily derived from subducted oceanic basalt with a <2% contribution from subducted sediment. Lavas in the Oligocene Izu arc and fore-arc basin were derived from a mantle wedge of similar composition to the active arc. Despite levels of Pb enrichment comparable to those of the modern arc, the Pb isotopes of the Oligocene volcanics indicate a lower sediment input into the melting region.

Organic geochemical parameters (biomarker) in sedimentary sequences and sediment traps

For the reconstruction of sea-ice variability, a biomarker approach which is based on (1) the determination of sea-ice diatom-specific highly-branched isoprenoid (IP25) and (2) the coupling of phytoplankton biomarkers and IP25 has been used. For the first time, such a data set was obtained from an array of two sediment traps deployed at the southern Lomonosov Ridge in the central Arctic Ocean at water depth of 150 m and 1550 m and recording the seasonal variability of sea ice cover in 1995/1996. These data indicate a predominantly permanent sea ice cover at the trap location between November 1995 and June 1996, an ice-edge situation with increased phytoplankton productivity and sea-ice algae input in July/August 1996, and the start of new-ice formation in late September. The record of modern sea-ice variability is then used to better interpret data from sediment core PS2458-4 recovered at the Laptev Sea continental slope close to the interception with Lomonosov Ridge and recording the post-glacial to Holocene change in sea-ice cover. Based on IP25 and phytoplankton biomarker data from Core PS2458-4, minimum sea-ice cover was reconstructed for the Bølling/Allerød warm interval between about 14.5 and 13 calendar kyr BP, followed by a rapid and distinct increase in sea-ice cover at about 12.8 calendar kyr BP. This sea-ice event was directly preceded by a dramatic freshwater event and a collapse of phytoplankton productivity, having started about 100 years earlier. These data are the first direct evidence that enhanced freshwater flux caused enhanced sea-ice formation in the Arctic at the beginning of the Younger Dryas. In combination with a contemporaneous, abrupt and very prominent freshwater/meltwater pulse in the Yermak Plateau/Fram Strait area these data may furthermore support the hypothesis that strongly enhanced freshwater (and ice) export from the Arctic into the North Atlantic could have played an important trigger role for the onset of the Younger Dryas cold reversal. During the Early Holocene, sea-ice cover steadily increased again (ice-edge situation), reaching modern sea-ice conditions (more or less permanent sea-ice cover) probably at about 7-8 calendar kyr BP.

Evaluating demographic models for goat domestication using mtDNA sequences

Routes of migration and exchange are important factors in the debate about how the Neolithic transition spread into Europe. Studying the genetic diversity of livestock can help in tracing back some of these past events. Notably, domestic goat (Capra hircus) did not have any wild progenitors (Capra aegagrus) in Europe before their arrival from the Near East. Studies of mitochondrial DNA have shown that the diversity in European domesticated goats is a subset of that in the wild, underlining the ancestral relationship between both populations. Additionally, an ancient DNA study on Neolithic goat remains has indicated that a high level of genetic diversity was already present early in the Neolithic in northwestern Mediterranean sites. We used coalescent simulations and approximate Bayesian computation, conditioned on patterns of modern and ancient mitochondrial DNA diversity in domesticated and wild goats, to test a series of simplified models of the goat domestication process. Specifically, we ask if domestic goats descend from populations that were distinct prior to domestication. Although the models we present require further analyses, preliminary results indicate that wild and domestic goats are more likely to descend from a single ancestral wild population that was managed 11,500 years before present, and that serial founding events characterise the spread of Capra hircus into Europe.

Diversity of luciferase sequences and bioluminescence production in Baltic Sea Alexandrium ostenfeldii

The toxic dinoflagellate Alexandrium ostenfeldii is the only bioluminescent bloom-forming phytoplankton in coastal waters of the Baltic Sea. We analysed partial luciferase gene (lcf) sequences and bioluminescence production in Baltic A. ostenfeldii bloom populations to assess the distribution and consistency of the trait in the Baltic Sea, and to evaluate applications for early detection of toxic blooms. Lcf was consistently present in 61 Baltic Sea A. ostenfeldii strains isolated from six separate bloom sites. All Baltic Sea strains except one produced bioluminescence. In contrast, the presence of lcf and the ability to produce bioluminescence did vary among strains from other parts of Europe. In phylogenetic analyses, lcf sequences of Baltic Sea strains clustered separately from North Sea strains, but variation between Baltic Sea strains was not sufficient to distinguish between bloom populations. Clustering of the lcf marker was similar to internal transcribed spacer (ITS) sequences with differences being minor and limited to the lowest hierarchical clusters, indicating a similar rate of evolution of the two genes. In relation to monitoring, the consistent presence of lcf and close coupling of lcf with bioluminescence suggests that bioluminescence can be used to reliably monitor toxic bloom-forming A. ostenfeldii in the Baltic Sea.