REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform

Motivation: Proteins with solenoid repeats evolve more quickly than non-repetitive ones and their periodicity may be rapidly hidden at sequence level, while still evident in structure. In order to identify these repeats, we propose here a novel method based on a metric characterizing amino-acid properties (polarity, secondary structure, molecular volume, codon diversity, electric charge) using five previously derived numerical functions

TESE: generating specific protein structure test set ensembles

TESE is a web server for the generation of test sets of protein sequences and structures fulfilling a number of different criteria. At least three different use cases can be envisaged: (i) benchmarking of novel methods; (ii) test sets tailored for special needs and (iii) extending available datasets. The CATH structure classification is used to control structural/sequence redundancy and a variety of structural quality parameters can be used to interactively select protein subsets with specific characteristics, e.g. all X-ray structures of alpha-helical repeat proteins with more than 120 residues and resolution <2.0 A. The output includes FASTA-formatted sequences, PDB files and a clickable HTML index file containing images of the selected proteins. Multiple subsets for cross-validation are also supported. AVAILABILITY: The TESE server is available for non-commercial use at URL: http://protein.bio.unipd.it/tese/

Valutazione dei principali indicatori bibliometrici relativi alle riviste scientifiche internazionali peer-reviewed ad orientamento trapiantologico.

Introduzione \u2013 L\u2019adozione di specifici indicatori bibliometrici (IB) rappresenta una modalit\ue0 di valutazione quantitativa in grado di offrire elementi utili alla valutazione della rilevanza e penetranza delle informazioni veicolate attraverso il circuito delle riviste scientifiche internazionali peer-reviewed ad orientamento trapiantologico. Metodi \u2013 Nell\u2019ambito della base dati ISI (Institute for Scientific Information) \ue8 stata effettuata una ricerca per "subject category" finalizzata alla restituzione delle riviste di interesse trapiantologico indicizzate per il periodo 2000-2004 (n=19) [1]. Per ciascuna rivista sono stati considerati i seguenti IB/anno: numeri pubblicati, Total Cites (TC), Impact Factor (IF; n citazioni per l\u2019anno di riferimento dei lavori pubblicati nel biennio precedente/n articoli pubblicati nel biennio precedente); Immediacy Index (IMI); Overall Articles (OA); Cited Half-life (CedHL); Citing Half-life (CngHL); non-Review Articles (non-Rev); Reviews (Rev); non-Rev/Rev ratio. Gli IB sono stati analizzati mediante statistiche descrittive, confronto tra due o pi\uf9 gruppi (test di Mann-Whitney od ANOVA) e correlazione non parametrica di Spearman. Risultati \u2013 Le statistiche descrittive inerenti gli IB hanno presentato i seguenti valori medi/anno: numeri pubblicati: 10.04+/-5.8 (mediana [md]: 8; range: 4 \u2013 24); TC: 4195.66+/-6181.48 (md: 1482; range: 23 \u2013 25722); IF: 2.11+/-1.16 (md: 2.06; range: 0.25 \u2013 5.68); IMI: 0.34+/-0.29 (md: 0.308; range: 0.017 \u2013 1.49); OA: 248.68+/-318.81 (md: 107; range: 26 \u2013 1605); CedHL: 5.076+/-1.62 (md: 5; range: 1.2 \u2013 9.7); CngHL: 6.05+/-0.62 (md: 6; range: 4 \u2013 7.5); non-Rev: 241.2+/-319 (md: 99; range: 25 \u2013 1605); Rev: 7.48+/-7.37 (md: 5.5; range: 0 \u2013 32); non-Rev/Rev ratio: 43.93+/-76.08 (md: 19.6; range: 1.37 \u2013 507). Il confronto tra gli IB stratificati per anno non ha registrato alcuna significativit\ue0 statistica nel confronto tra due o pi\uf9 gruppi. L\u2019IF medio calcolato per l\u2019anno 2000 (2.00+/-0.97) \ue8 risultato privo di significativit\ue0 statistica nei confronti del medesimo parametro riferito all\u2019anno 2004 (2.26+/-1.28; P = 0.536). Una correlazione diretta significativa \ue8 stata individuata tra IF ed i seguenti IB: numeri pubblicati (r = 0.277; P = 0.013); TC (r = 0.29; P = 0.009); IMI (r = 0.763; P <0.0001); Rev (r = 0.33; P = 0.002). Una correlazione inversa significativa \ue8 stata riscontrata tra IF e CedHL (r = -0.748; P<0.0001), CngHL (r = 0.48; P<0.0001) e non-Rev/Rev ratio (r = -0.24; P = 0.031). Il coefficiente di variazione (CV) generale riferito all\u2019IF \ue8 risultato del 54.52%; il CV dell\u2019IF per singolo anno ha presentato per l\u2019anno 2000 un valore del 48.73%, mentre per l\u2019anno 2004 \ue8 risultato del 56.69%. Il CV dell\u2019IF per singola rivista \ue8 risultato compreso tra il 6.95% ed il 30.59%. Conclusioni \u2013 L\u2019IF delle riviste scientifiche internazionali ad orientamento trapiantologico \ue8 risultato direttamente correlato con il numero di Review pubblicate ed inversamente correlato con il non-Rev/Rev ratio. L\u2019elevato CV generale e per rivista dell\u2019IF pu\uf2 ostacolare a livello di singolo autore/gruppo di ricerca il processo decisionale circa la selezione della rivista a cui sottoporre un contributo scientifico. Bibliografia - [1]. http://jcr17.isiknowledge.com/JCR/JCR

TESE: generating specific protein structure test set ensembles

Abstract Summary: TESE is a web server for the generation of test sets of protein sequences and structures fulfilling a number of different criteria. At least three different use cases can be envisaged: (i) benchmarking of novel methods; (ii) test sets tailored for special needs and (iii) extending available datasets. The CATH structure classification is used to control structural/sequence redundancy and a variety of structural quality parameters can be used to interactively select protein subsets with specific characteristics, e.g. all X-ray structures of α-helical repeat proteins with more than 120 residues and resolution &lt;2.0 Å. The output includes FASTA-formatted sequences, PDB files and a clickable HTML index file containing images of the selected proteins. Multiple subsets for cross-validation are also supported. Availability: The TESE server is available for non-commercial use at URL: http://protein.bio.unipd.it/tese/. Contact: [email protected]

Wind-driven bottom currents and related sedimentary bodies in Lake Saint-Jean (Québec, Canada)

International audienceLakes are major depositional systems for which the related depositional processes have long been considered relatively simple. Breaking this statement, this study presents a detailed analysis of deposits in Lake Saint-Jean, the third largest natural lake in Québec. In addition to postglacial deltaic and coastal depositional systems fringing the lake, current-controlled features such as a large subaqueous prograding wedge and three sediment drifts have been identifi ed in its central portion based on two-dimensional (2-D) acoustic high-resolution subbottom profiles. The large subaqueous prograding wedge is a 4-km-long and up to 15-m-thick heterolithic shelf-like construction in the southeastern part of the lake. The three sediment drifts are 0.1–0.5-km-long and 2–5-mthick mud mounds distributed on the lake floor in the central portion of the lake. Diatom analyses and radiocarbon dating show that the development of these current-controlled features occurred during the lacustrine phase, after the disconnection with the postglacial marine Laflamme Gulf at 8.5 cal. k.y. B.P. Depositional facies show evidence of recurrent bottom-current activity. Related deposits alternate with pelagic sedimentation stages characterized by the settling of mud and biogenic accumulations. We investigated the origin of bottom currents using a numerical simulation (SYMPHONIE, an oceanographic model), with the aim of modeling wind-induced lake-scale water circulation. Simulations suggest that the subaqueous prograding wedge and the three sediment drifts result from wind-induced bottom currents generated by storm events having wind speed greater than 10 m s–1. Such strong winds are able to significantly affect sedimentation in the central portion of Lake Saint-Jean. Theresulting wind-induced sedimentary features were integrated into a refi ned lacustrine depositional model that summarizes the evolution of a group of water bodies referred to as “wind-driven water bodies.” This study applies a new tool for lake strata characterization and highlights the potential diffi cultyin differentiating them from marine deposits in the geological record

Genetic tests for low-and middle-income countries: a literature review

The aim of this review is to describe a series of ten genetic diseases with Mendelian inheritance pattern in people of low-or middle-income countries, which can be easily identified with simple and affordable methods. Recent information shows that although genetic diseases account for more than 10% of infant mortality in such countries, testing, counseling, and treatment of genetic diseases is not a priority. The selection criteria for the genetic tests that are discussed in this review are: i) the frequency of the genetic disease in the general population, ii) the cost and ease of execution, and iii) the report of validated methods in the literature for the diagnosis of these diseases. The goal is to promote diagnosis of genetic diseases at low-cost and with relative ease, thereby enabling appropriate treatments, reducing mortality, and preventing genetic diseases in high-risk families