Refining multiple sequence alignments with conserved core regions

Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their identification and classification. This article presents a new algorithm, REFINER, that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core (block) model of a protein family. Realignment of each sequence can correct misalignments between a given sequence and the rest of the profile and at the same time preserves the family's overall block model. Large-scale benchmarking studies showed a noticeable improvement of alignment after refinement. This can be inferred from the increased alignment score and enhanced sensitivity for database searching using the sequence profiles derived from refined alignments compared with the original alignments. A standalone version of the program is available by ftp distribution () and will be incorporated into the next release of the Cn3D structure/alignment viewer

Universality and its Origins at the Amorphous Solidification Transition

Systems undergoing an equilibrium phase transition from a liquid state to an amorphous solid state exhibit certain universal characteristics. Chief among these are the fraction of particles that are randomly localized and the scaling functions that describe the order parameter and (equivalently) the statistical distribution of localization lengths for these localized particles. The purpose of this Paper is to discuss the origins and consequences of this universality, and in doing so, three themes are explored. First, a replica-Landau-type approach is formulated for the universality class of systems that are composed of extended objects connected by permanent random constraints and undergo amorphous solidification at a critical density of constraints. This formulation generalizes the cases of randomly cross-linked and end-linked macromolecular systems, discussed previously. The universal replica free energy is constructed, in terms of the replica order parameter appropriate to amorphous solidification, the value of the order parameter is obtained in the liquid and amorphous solid states, and the chief universal characteristics are determined. Second, the theory is reformulated in terms of the distribution of local static density fluctuations rather than the replica order parameter. It is shown that a suitable free energy can be constructed, depending on the distribution of static density fluctuations, and that this formulation yields precisely the same conclusions as the replica approach. Third, the universal predictions of the theory are compared with the results of extensive numerical simulations of randomly cross-linked macromolecular systems, due to Barsky and Plischke, and excellent agreement is found.Comment: 10 pages, including 3 figures (REVTEX

Utilização de resíduos de batata-doce na alimentação de aves coloniais.

Na região produtora de batata-doce do RS, onde destaca-se o município de Mariana Pimentel, significativa parcela dos agricultores familiares são dependentes da renda gerada pela batatadoce e pelo fumo. A disponibilidade de resíduos de batata-doce estimulou a realização de uma experiência de seu processamento e secagem em estufa de fumo com o objetivo de sua posterior utilização na composição de ração para aves coloniais. A diversificação do sistema, com a autonomia na produção do componente energético da ração, poderia permitir maior autonomia aos avicultores coloniais. O trabalho foi conduzido utilizando metodologia participativa e em parceria entre o "Conjunto Agrotécnico Visconde da Graça" - CAVG/UFPel, Secretaria de Agricultura de Mariana Pimentel-RS, Fepagro-RS (Taquari), Brastec Nutrição, Senar-RS e Embrapa Clima Temperado. Os resultados obtidos mostraram bom desempenho zootécnico quanto ao ganho de peso, onde as aves atingiram 2.650 gr. na 14ª semana, superiores ao peso padrão esperado (2.601 gr/ave).Resumos do VI CBA e II CLAA

Measurement of Angular Distributions and R= sigma_L/sigma_T in Diffractive Electroproduction of rho^0 Mesons

Production and decay angular distributions were extracted from measurements of exclusive electroproduction of the rho^0(770) meson over a range in the virtual photon negative four-momentum squared 0.5< Q^2 <4 GeV^2 and the photon-nucleon invariant mass range 3.8< W <6.5 GeV. The experiment was performed with the HERMES spectrometer, using a longitudinally polarized positron beam and a ^3He gas target internal to the HERA e^{+-} storage ring. The event sample combines rho^0 mesons produced incoherently off individual nucleons and coherently off the nucleus as a whole. The distributions in one production angle and two angles describing the rho^0 -> pi+ pi- decay yielded measurements of eight elements of the spin-density matrix, including one that had not been measured before. The results are consistent with the dominance of helicity-conserving amplitudes and natural parity exchange. The improved precision achieved at 47 GeV, reveals evidence for an energy dependence in the ratio R of the longitudinal to transverse cross sections at constant Q^2.Comment: 15 pages, 15 embedded figures, LaTeX for SVJour(epj) document class Revision: Fig. 15 corrected, recent data added to Figs. 10,12,14,15; minor changes to tex

MMDB: annotating protein sequences with Entrez's 3D-structure database

Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's ‘Related Structure’ links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The ‘Related Structure’ service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB ()

The Distinct Metamorphic Stages and Structural Styles of the 1.94–1.86 Ga Snowbird Orogen, Northwest Territories, Canada

Palaeoproterozoic orogenesis within the Archean southeastern Rae craton is related to the initial amalgamation of Laurentia. Characterizing the accompanying tectonic processes during this time has been complicated due to polymetamorphism, which results in the obscuring of the age record of the terranes involved. To improve the knowledge of the tectonic evolution of the South Rae Craton, petrologic and structural analyses are applied in conjunction with in situ trace element chemistry, inclusion barometry, U–Pb monazite and titanite, and Lu–Hf garnet chronology. The data robustly constrain Palaeoproterozoic pressure–temperature–time paths of major deformational events along the southeastern Rae craton margin. D1 occurred between 1.94 and 1.93 Ga in the Dodge-Snowbird domain, which included prograde burial of metasedimentary rocks, deposited at 2.2–2.0 Ga, and the development of migmatitic layering and east-southeast trending folds (S1, F1). Peak metamorphism is recorded in metasedimentary units at c. 1.93 Ga when rocks reached conditions of 9.0–10.5 kbar and 810–830°C. Within the Dodge-Snowbird domain, D2 imparted north-northeast trending open folds and associated axial planar cleavage (S2, F2) between 1.93 and 1.90 Ga during east-west compression that appears to have been synchronous with cooling and exhumation. Later D2 deformation, localized within the Wholdaia Lake shear zone (WLsz; ST1), developed in the footwall of this thrust-sense structure at 1,873 ± 5 Ma at conditions of 9.5–11.0 kbar and 820–850°C. The hangingwall Dodge-Snowbird domain had already cooled to below 300°C by then, indicating a significant structural and metamorphic break across the domain\u27s western boundary. A new phase of unroofing (D3) involved pervasive amphibolite- to greenschist facies extensional shearing (ST2) within the WLsz, which overprinted ST1 foliations between 1.87 and 1.86 Ga. Continued greenschist facies shearing younger than 1.86 Ga likely ended by c. 1.83 Ga when lamprophyre dykes cut the structure, which was followed by cooling until c. 1.80 Ga. This work highlights the utility and application of multiple chronometers (zircon, monazite, titanite, garnet) along with structural and petrologic analysis that together can resolve precise orogenic cycles in polymetamorphic terranes that may otherwise be undetected. The time-resolved P–T–D histories derived here enable more robust interpretations regarding the nature and evolution of 1.9 Ga tectonism along the southeast Rae craton margin, which may be used to refine models for Laurentian terrane amalgamation

MMDB: 3D structures and macromolecular interactions

Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure

Observation of a Coherence Length Effect in Exclusive Rho^0 Electroproduction

Exclusive incoherent electroproduction of the rho^0(770) meson from 1H, 2H, 3He, and 14N targets has been studied by the HERMES experiment at squared four-momentum transfer Q**2>0.4 GeV**2 and positron energy loss nu from 9 to 20 GeV. The ratio of the 14N to 1H cross sections per nucleon, known as the nuclear transparency, was found to decrease with increasing coherence length of quark-antiquark fluctuations of the virtual photon. The data provide clear evidence of the interaction of the quark- antiquark fluctuations with the nuclear medium.Comment: RevTeX, 5 pages, 3 figure

Determination of the Deep Inelastic Contribution to the Generalised Gerasimov-Drell-Hearn Integral for the Proton and Neutron

The virtual photon absorption cross section differences [sigma_1/2-sigma_3/2] for the proton and neutron have been determined from measurements of polarised cross section asymmetries in deep inelastic scattering of 27.5 GeV longitudinally polarised positrons from polarised 1H and 3He internal gas targets. The data were collected in the region above the nucleon resonances in the kinematic range nu < 23.5 GeV and 0.8 GeV**2 < Q**2 < 12 GeV**2. For the proton the contribution to the generalised Gerasimov-Drell-Hearn integral was found to be substantial and must be included for an accurate determination of the full integral. Furthermore the data are consistent with a QCD next-to-leading order fit based on previous deep inelastic scattering data. Therefore higher twist effects do not appear significant.Comment: 6 pages, 3 figures, 1 table, revte

Measurement of the Neutron Spin Structure Function g1ng_1^n with a Polarized ^3He Target

Results are reported from the HERMES experiment at HERA on a measurement of the neutron spin structure function $g_1^n(x,Q^2)$ in deep inelastic scattering using 27.5 GeV longitudinally polarized positrons incident on a polarized $^3$He internal gas target. The data cover the kinematic range $0.023<x<0.6$ and $1 (GeV/c)^2 < Q^2 <15 (GeV/c)^2$. The integral $\int_{0.023}^{0.6} g_1^n(x) dx$ evaluated at a fixed $Q^2$ of $2.5 (GeV/c)^2$ is $-0.034\pm 0.013(stat.)\pm 0.005(syst.)$. Assuming Regge behavior at low $x$, the first moment $\Gamma_1^n=\int_0^1 g_1^n(x) dx$ is $-0.037\pm 0.013(stat.)\pm 0.005(syst.)\pm 0.006(extrapol.)$.Comment: 4 pages TEX, text available at http://www.krl.caltech.edu/preprints/OAP.htm