A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry

Top-down mass spectrometry methods are becoming continuously more popular in the effort to describe the proteome. They rely on the fragmentation of intact protein ions inside the mass spectrometer. Among the existing fragmentation methods, electron transfer dissociation is known for its precision and wide coverage of different cleavage sites. However, several side reactions can occur under electron transfer dissociation (ETD) conditions, including nondissociative electron transfer and proton transfer reaction. Evaluating their extent can provide more insight into reaction kinetics as well as instrument operation. Furthermore, preferential formation of certain reaction products can reveal important structural information. To the best of our knowledge, there are currently no tools capable of tracing and analyzing the products of these reactions in a systematic way. In this Article, we present in detail masstodon: a computer program for assigning peaks and interpreting mass spectra. Besides being a general purpose tool, masstodon also offers the possibility to trace the products of reactions occurring under ETD conditions and provides insights into the parameters driving them. It is available free of charge under the GNU AGPL V3 public license

Ultrafast cooling reveals microsecond-scale biomolecular dynamics

The temperature-jump technique, in which the sample is rapidly heated by a powerful laser pulse, has been widely used to probe the fast dynamics of folding of proteins and nucleic acids. However, the existing temperature-jump setups tend to involve sophisticated and expensive instrumentation, while providing only modest temperature changes of ~10–15 °C, and the temperature changes are only rapid for heating, but not cooling. Here we present a setup comprising a thermally conductive sapphire substrate with light-absorptive nano-coating, a microfluidic device and a rapidly switched moderate-power infrared laser with the laser beam focused on the nano-coating, enabling heating and cooling of aqueous solutions by ~50 °C on a 1-μs time scale. The setup is used to probe folding and unfolding dynamics of DNA hairpins after direct and inverse temperature jumps, revealing low-pass filter behaviour during periodic temperature variations

On subset seeds for protein alignment

We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several different design methods and use them to construct several alphabets. We then perform a comparative analysis of seeds built over those alphabets and compare them with the standard BLASTP seeding method [2], [3], as well as with the family of vector seeds proposed in [4]. While the formalism of subset seeds is less expressive (but less costly to implement) than the cumulative principle used in BLASTP and vector seeds, our seeds show a similar or even better performance than BLASTP on Bernoulli models of proteins compatible with the common BLOSUM62 matrix. Finally, we perform a large-scale benchmarking of our seeds against several main databases of protein alignments. Here again, the results show a comparable or better performance of our seeds vs. BLASTP.Comment: IEEE/ACM Transactions on Computational Biology and Bioinformatics (2009

On consensus biomarker selection

<p>Abstract</p> <p>Background</p> <p>Recent development of mass spectrometry technology enabled the analysis of complex peptide mixtures. A lot of effort is currently devoted to the identification of biomarkers in human body fluids like serum or plasma, based on which new diagnostic tests for different diseases could be constructed. Various biomarker selection procedures have been exploited in recent studies. It has been noted that they often lead to different biomarker lists and as a consequence, the patient classification may also vary.</p> <p>Results</p> <p>Here we propose a new approach to the biomarker selection problem: to apply several competing feature ranking procedures and compute a consensus list of features based on their outcomes. We validate our methods on two proteomic datasets for the diagnosis of ovarian and prostate cancer.</p> <p>Conclusion</p> <p>The proposed methodology can improve the classification results and at the same time provide a unified biomarker list for further biological examinations and interpretation.</p

Batoid abundances, spatial distribution, and life history traits in the strait of sicily (Central mediterranean sea): Bridging a knowledge gap through three decades of survey

Batoid species play a key role in marine ecosystems but unfortunately they have globally declined over the last decades. Given the paucity of information, abundance data and the main life history traits for batoids, obtained through about three decades of bottom trawl surveys, are presented and discussed. The surveys were carried out in two areas of the Central Mediterranean (South of Sicily and Malta Island), in a timeframe ranging from 1990 to 2018. Excluding some batoids, the abundance trends were stable or increasing. Only R. clavata, R. miraletus, and D. oxyrinchus showed occurrence and abundance indexes notable enough to carry out more detailed analysis. In particular, spatial distribution analysis of these species highlighted the presence of two main hotspots in Sicilian waters whereas they seem more widespread in Malta. The lengths at first maturity (L50) were 695 and 860, 635 and 574, and 364 and 349 mm total length (TL), respectively, for females and males of D. oxyrinchus, R. clavata, and R. miraletus. The asymptotic lengths (L∞) and the curvature coefficients (K) were 1365 and 1240 (K = 0.11 and 0.26), 1260 and 1100 (K = 0.16 and 0.26), and 840 and 800 mm TL (K = 0.36 and 0.41), respectively, for females and males of D. oxyrinchus, R. clavata, and R. miraletus. The lack of detailed quantitative historical information on batoids of Sicily and Malta does not allow to analytically judge the current status of the stocks, although the higher abundance of some species within Malta raises some concern for the Sicilian counterpart. In conclusion, suitable actions to protect batoids in the investigated area are recommended

Drag forces on inclusions in classical fields with dissipative dynamics

We study the drag force on uniformly moving inclusions which interact linearly with dynamical free field theories commonly used to study soft condensed matter systems. Drag forces are shown to be nonlinear functions of the inclusion velocity and depend strongly on the field dynamics. The general results obtained can be used to explain drag forces in Ising systems and also predict the existence of drag forces on proteins in membranes due to couplings to various physical parameters of the membrane such as composition, phase and height fluctuations.Comment: 14 pages, 7 figure

Correlations Between Parental Inbred Lines and Derived Hybrid Performance for Grain Filling Traits in Maize

Individual kernel weight (KW) is largely genetically determined, and its variability is achieved through different combinations of rate and duration of kernel growth. Genetic variability for grain-filling patterns has been observed among inbred lines and commercial hybrids, and there is current interest on dissecting its genetic basis. However, suitable grain filling phenotyping protocols are still to be determined, such as the value to study traits at the inbred or hybrid levels. The objective of our study was to evaluate the correlation between parental inbred line and derived hybrid performance for several grain-filling traits in maize (Zea mays L.). We hypothesized that there would be high correlations due to the relative high heritability of grainfilling traits. Three trials were conducted (two in Argentina and one in the United States) with commercial relevant germplasm (totaling 25 parental inbreds and 31 single-cross hybrids). Traits were KW, kernel growth rate (KGR), grainfilling duration (GFD), maximum water content (MWC), moisture concentration at physiological maturity (MCPM), and kernel desiccation rate (KDR) during the effective grain filling. Both heterosis and correlations between midparental value and hybrid performance were significant (p < 0.05) for all traits (r values of 0.63, 0.71, 0.81, 0.83, 0.61, and 0.71 for KW, KGR, GFD, MWC, KDR, and MCPM, respectively). Our results confirm that studying inbred lines for grain-filling traits generates valuable information for derived hybrid performanceFil: Alvarez Prado, Santiago. Universidad Nacional de Rosario. Facultad de Cs.agrarias. Departamento de Producción Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gambin, Brenda Laura. Universidad Nacional de Rosario. Facultad de Cs.agrarias. Departamento de Producción Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Novoa, A. Daniel. Nidera S. A; ArgentinaFil: Foster, Daniel. Syngenta Seeds; Estados UnidosFil: Senior, M. Lynn. Syngenta Biotechnology,; Estados UnidosFil: Zinselmeier, Christopher. Syngenta Seeds; Estados UnidosFil: Otegui, Maria Elena. Universidad de Buenos Aires. Facultad de Agronomía; ArgentinaFil: Borras, Lucas. Universidad Nacional de Rosario. Facultad de Cs.agrarias. Departamento de Producción Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Reply to comment by C. Morhange, C. Flaux, P.A. Pirazzoli, M.B. Carre on \u201cHolocene Sea level Change in Malta\u201d

The pits of Birzebbugia are located near the present-day mean sea level, and some are partially submerged. They were dated using pottery discovered in an archaeological site close to the coast, dated to the Bronze Age (Zammit, 1928; Abela, 1999). As they have been interpreted as sites for the retting of flax, during their utilization they should have remained dry and the sea could not submerge them. This is the reason why these structures are not directly related to the sea level, as suggested by Biolchi et al. (2011), so they represent an upper limit.peer-reviewe