ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins

BACKGROUND: Profile-profile methods have been used for some years now to detect and align homologous proteins. The best such methods use information from the background distribution of amino acids and substitution tables either when constructing the profiles or in the scoring. This makes the methods dependent on the quality and choice of substitution table as well as the construction of the profiles. Here, we introduce a novel method called ProfNet that is used to derive a profile-profile scoring function. The method optimizes the discrimination between scores of related and unrelated residues and it is fast and straightforward to use. This new method derives a scoring function that is mainly dependent on the actual alignment of residues from a training set, and it does not use any additional information about the background distribution. RESULTS: It is shown that ProfNet improves the discrimination of related and unrelated residues. Further it can be used to improve the alignment of distantly related proteins. CONCLUSION: The best performance is obtained using superfamily related proteins in the training of ProfNet, and a classifier that is related to the distance between the structurally aligned residues. The main difference between the new scoring function and a traditional profile-profile scoring function is that conserved residues on average score higher with the new function

Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps

BACKGROUND: Protein sequence alignment is one of the basic tools in bioinformatics. Correct alignments are required for a range of tasks including the derivation of phylogenetic trees and protein structure prediction. Numerous studies have shown that the incorporation of predicted secondary structure information into alignment algorithms improves their performance. Secondary structure predictors have to be trained on a set of somewhat arbitrarily defined states (e.g. helix, strand, coil), and it has been shown that the choice of these states has some effect on alignment quality. However, it is not unlikely that prediction of other structural features also could provide an improvement. In this study we use an unsupervised clustering method, the self-organizing map, to assign sequence profile windows to "structural states" and assess their use in sequence alignment. RESULTS: The addition of self-organizing map locations as inputs to a profile-profile scoring function improves the alignment quality of distantly related proteins slightly. The improvement is slightly smaller than that gained from the inclusion of predicted secondary structure. However, the information seems to be complementary as the two prediction schemes can be combined to improve the alignment quality by a further small but significant amount. CONCLUSION: It has been observed in many studies that predicted secondary structure significantly improves the alignments. Here we have shown that the addition of self-organizing map locations can further improve the alignments as the self-organizing map locations seem to contain some information that is not captured by the predicted secondary structure

Assessing the role of large herbivores in the structuring and functioning of freshwater and marine angiosperm ecosystems

2 figuras, 3 tablasWhile large herbivores can have strong impacts on terrestrial ecosystems, much less is known of their role in aquatic systems. We reviewed the literature to determine: (1) which large herbivores (>10 kg) have a (semi-)aquatic lifestyle and are important consumers of submerged vascular plants, (2) their impact on submerged plant abundance and species composition and (3) their ecosystem functions. We grouped herbivores according to diet, habitat selection and movement ecology: (1) Fully aquatic species, either resident or migratory (manatees, dugongs, turtles), (2) Semi-aquatic species that live both in water and on land, either resident or migratory (swans), (3) Resident semi-aquatic species that live in water and forage mainly on land (hippopotamuses, beavers, capybara), (4) Resident terrestrial species with relatively large home ranges that frequent aquatic habitats (cervids, water buffalo, lowland tapir). Fully aquatic species and swans have the strongest impact on submerged plant abundance and species composition. They may maintain grazing lawns. Because they sometimes target belowground parts, their activity can result in local collapse of plant beds. Semi-aquatic species and turtles serve as important aquatic-terrestrial linkages, by transporting nutrients across ecosystem boundaries. Hippopotamuses and beavers are important geomorphological engineers, capable of altering the land and hydrology at landscape scales. Migratory species and terrestrial species with large home ranges are potentially important dispersal vectors of plant propagules and nutrients. Clearly, large aquatic herbivores have strong impacts on associated species and can be critical ecosystem engineers of aquatic systems, with the ability to modify direct and indirect functional pathways in ecosystems. While global populations of large aquatic herbivores are declining, some show remarkable local recoveries with dramatic consequences for the systems they inhabit. A better understanding of these functional roles will help set priorities for the effective management of large aquatic herbivores along with the plant habitats they rely on.This research was funded by the Spanish Ministry of Science and Innovation (CTM2013-48027-C3-3-R), an Intramural Project from the Spanish National Research Council (CSIC, 201330E062) and the Pew Marine Fellowship.Peer reviewe

Azimuthal anisotropy of charged jet production in root s(NN)=2.76 TeV Pb-Pb collisions

We present measurements of the azimuthal dependence of charged jet production in central and semi-central root s(NN) = 2.76 TeV Pb-Pb collisions with respect to the second harmonic event plane, quantified as nu(ch)(2) (jet). Jet finding is performed employing the anti-k(T) algorithm with a resolution parameter R = 0.2 using charged tracks from the ALICE tracking system. The contribution of the azimuthal anisotropy of the underlying event is taken into account event-by-event. The remaining (statistical) region-to-region fluctuations are removed on an ensemble basis by unfolding the jet spectra for different event plane orientations independently. Significant non-zero nu(ch)(2) (jet) is observed in semi-central collisions (30-50% centrality) for 20 <p(T)(ch) (jet) <90 GeV/c. The azimuthal dependence of the charged jet production is similar to the dependence observed for jets comprising both charged and neutral fragments, and compatible with measurements of the nu(2) of single charged particles at high p(T). Good agreement between the data and predictions from JEWEL, an event generator simulating parton shower evolution in the presence of a dense QCD medium, is found in semi-central collisions. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Peer reviewe

Production of He-4 and (4) in Pb-Pb collisions at root(NN)-N-S=2.76 TeV at the LHC

Results on the production of He-4 and (4) nuclei in Pb-Pb collisions at root(NN)-N-S = 2.76 TeV in the rapidity range vertical bar y vertical bar <1, using the ALICE detector, are presented in this paper. The rapidity densities corresponding to 0-10% central events are found to be dN/dy4(He) = (0.8 +/- 0.4 (stat) +/- 0.3 (syst)) x 10(-6) and dN/dy4 = (1.1 +/- 0.4 (stat) +/- 0.2 (syst)) x 10(-6), respectively. This is in agreement with the statistical thermal model expectation assuming the same chemical freeze-out temperature (T-chem = 156 MeV) as for light hadrons. The measured ratio of (4)/He-4 is 1.4 +/- 0.8 (stat) +/- 0.5 (syst). (C) 2018 Published by Elsevier B.V.Peer reviewe

Forward-central two-particle correlations in p-Pb collisions at root s(NN)=5.02 TeV

Two-particle angular correlations between trigger particles in the forward pseudorapidity range (2.5 2GeV/c. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B. V.Peer reviewe

Event-shape engineering for inclusive spectra and elliptic flow in Pb-Pb collisions at root(NN)-N-S=2.76 TeV

Peer reviewe

Pseudorapidity and transverse-momentum distributions of charged particles in proton-proton collisions at root s=13 TeV

The pseudorapidity (eta) and transverse-momentum (p(T)) distributions of charged particles produced in proton-proton collisions are measured at the centre-of-mass energy root s = 13 TeV. The pseudorapidity distribution in vertical bar eta vertical bar <1.8 is reported for inelastic events and for events with at least one charged particle in vertical bar eta vertical bar <1. The pseudorapidity density of charged particles produced in the pseudorapidity region vertical bar eta vertical bar <0.5 is 5.31 +/- 0.18 and 6.46 +/- 0.19 for the two event classes, respectively. The transverse-momentum distribution of charged particles is measured in the range 0.15 <p(T) <20 GeV/c and vertical bar eta vertical bar <0.8 for events with at least one charged particle in vertical bar eta vertical bar <1. The evolution of the transverse momentum spectra of charged particles is also investigated as a function of event multiplicity. The results are compared with calculations from PYTHIA and EPOS Monte Carlo generators. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Peer reviewe

Elliptic flow of muons from heavy-flavour hadron decays at forward rapidity in Pb-Pb collisions at root s(NN)=2.76TeV

The elliptic flow, v(2), of muons from heavy-flavour hadron decays at forward rapidity (2.5 <y <4) is measured in Pb-Pb collisions at root s(NN)= 2.76TeVwith the ALICE detector at the LHC. The scalar product, two- and four-particle Q cumulants and Lee-Yang zeros methods are used. The dependence of the v(2) of muons from heavy-flavour hadron decays on the collision centrality, in the range 0-40%, and on transverse momentum, p(T), is studied in the interval 3 <p(T)<10 GeV/c. A positive v(2) is observed with the scalar product and two-particle Q cumulants in semi-central collisions (10-20% and 20-40% centrality classes) for the p(T) interval from 3 to about 5GeV/c with a significance larger than 3 sigma, based on the combination of statistical and systematic uncertainties. The v(2) magnitude tends to decrease towards more central collisions and with increasing pT. It becomes compatible with zero in the interval 6 <p(T)<10 GeV/c. The results are compared to models describing the interaction of heavy quarks and open heavy-flavour hadrons with the high-density medium formed in high-energy heavy-ion collisions. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B.V.Peer reviewe