Production and carcass quality of ten beef cattle breeds of the southwest of Europe

A sample of about 70 young bulls of each of ten beef cattle breeds reared in their typical production systems has been studied regarding growth and carcass quality traits. Breeds included were Asturiana de los Valles (AV), Asturiana de la Montaña (AM), Avileña-Negra Ibérica (A-NI), Bruna dels Pirineus (BP), Morucha (Mo), Pirenaica (Pi) and Retinta (Re) from Spain, and Aubrac (Au), Gasconne (Ga) and Salers (Sal) from France. There existed large differences between breeds and also within breeds. AV and Pi were the breeds with more muscle and less fat, whereas A-NI, Mo and Re were in the opposite side. BP and AM occupied an intermediate position. This allows to classify the Spanish breeds in three groups: AV and Pi would belong to the group of late maturity, A-NI, Mo and Re, would be early maturing breeds, whereas BP and AM, despite the small size of the last, will be of intermediate maturity. In the French populations, Au was the breed with the highest carcass weight and Ga exhibited the lowest. Sal occupied an intermediate position, showing the longer and thinner thigh. In a wide range of carcass weight, the general relationships among carcass traits have been confirmed. Animals with the better conformation were also the leaner and longer carcasses tended to be lowly associated with a poorer conformation and fatter carcasses. Bone content was clearly opposed to carcass conformation and muscle content and was associated with longer carcasses

Meat quality of ten cattle breeds of the Southwest of Europe

A sample of about 70 young bulls of each of ten beef cattle breeds reared in their typical production systems has been characterised with respect to meat quality traits. Breeds included were Asturiana de los Valles, Asturiana de la Montaña, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica and Retinta from Spain, and Aubrac, Gasconne and Salers from France. As was previously showed regarding carcass traits, there exist large differences both between and within breed – systems. In general, rustic breeds tended to present darker and redder meats with higher haematin contents, whereas less precocious and more specialised breeds showed brighter meats with bigger water losses. Protein content was similar, whereas intramuscular fat presented the larger variations both between and within breeds. ICDH content was higher in the more rustic breeds, showing the predominantly oxidative character of their fibres. Texture measurements showed in general large within breed-system variations, the differences between breeds being less evident. Within breed-system, daily gain weight was positively associated with brighter and tender meats. In the range studied, increasing slaughter weight within breed did not have influence on meat quality. Conformation was related to lower water holding capacity and less dry matter and intramuscular fat, as well as to a lower haematin content giving brighter meats. The increase in fatness scores was related to an augment of toughness in meat specialised breeds, although in Avileña-Negra Ibérica breed fatness carcasses were related to more tender meats. Redness parameter a* was positively related to fatter animals and opposed to conformation, the opposite being true for the L* (lightness) parameter. There was a small trend of fatter carcasses to be related to oxidative fibres, whereas the muscular fibres of the more conformed carcasses were more glycolytic. Texture measurements maximum load, maximum stress and toughness were very closely related. Shear force was opposed to tenderness. Losses at cooking were opposed to juiciness, but only in the Spanish breeds. No consistent trends regarding relationships between carcass characteristics and tenderness could be observed. Overall acceptability was primarily related with tenderness and flavour, and later on juiciness.

La paletina: un pinzell pla i prim

Treball de recerca realitzat per una alumna d'ensenyament secundari i guardonat amb un Premi CIRIT per fomentar l'esperit científic del Jovent l'any 2009. L’origen de l’autora és la Sénia, un poble d'uns 6000 habitants de la província de Tarragona, on, tot i el predomini actual de la fabricació de mobles, les primeres mostres d'industrialització foren el paper i els pinzells. L’arrelament de la indústria pinzellera de la seva família, ha estat el motiu que l’ha portat a desenvolupar aquest treball sobre la paletina, un tipus de pinzell. L'objectiu del treball ha estat dissenyar un model de paletina, a partir de proves pràctiques i d'estudis estadístics sobre quins són els components més adients. En primer lloc, es fa una descripció detallada dels components de la paletina. A continuació, s’estudia el seu procés de fabricació, primer des del punt de vista manual i després d'acord amb els procediments moderns. Finalment, a partir d'un experiment i amb el corresponent estudi estadístic, s’arriba a una nova proposta de paletina amb unes condicions òptimes de qualitat i rendiment. A més també es descriu el procés de fabricació de la paletina que es duia a terme uns cinquanta anys enrere i es pot valorar, així, tant el mèrit del procés en aquella època com també l'evolució tecnològica que s'ha dut a terme fins al moment.

Selección de péptidos sintéticos del Virus de la Hepatitis G (GBV-C/HGV) inhibidores del Péptido de Fusión HIV-I

El GB virus C (GBV-C) o virus de l'hepatitis G (HGV) es un virus format per una única cadena de RNA que pertany a la familia Flaviviridae. En els últims anys, s'han publicat nombrosos treballs en els quals s'associa la coinfecció del GBV-C i del virus de la immunodeficiència humana (VIH) amb una menor progressió de l'esmentada malaltia així com amb una major supervivència dels pacients una vegada que la SIDA s'ha desenvolupat. El mecanisme pel qual el virus GBV-C/HGV exerceix un “efecte protector” en els pacients amb VIH encara no està descrit. L’estudi de la interacció entre els virus GBVC/HGV i VIH podria donar lloc al desenvolupament de nous agents terapèutics per al tractament de la SIDA.Treballs recents mostren com la capacitat inhibitòria del virus del GBV-C/HGV és deguda a la seva glicoproteina estructural E2. S’ha vist que aquesta proteina seria capaç d’inhibir la primera fase de replicació de VIH, així com la unió i la fusió amb les membranes cel•lulars. Sobre la base d’aquests estudis, l’objectiu d’aquest treball ha estat seleccionar inhibidors del pèptid de fusió del VIH utilitzant pèptids sintètics de la proteina E2 del GBV-C/HGV. El treball realitzat ha consistit en estudiar, utilitzant assajos biofísics de leakage i de lipid mixing, la capacitat dels pèptids de la proteina estructural del virus del GBV-C/HGV per inhibir la interacció i el procés de desestabilització de membranes induïdes pel pèptid de fusió de la glicoproteina de l’embolcall, GP41, del VIH. Aquests assajos, com es descriu en treballs anteriors, han resultat útils per a la selecció i la identificació de compostos amb activitat específica anti-GP41. Es pot afirmar que efectivament els pèptids seleccionats de la proteina E2 del virus del GBV-C/HGV inhibeixen l’activitat del pèptid de fusió del VIH probablement com a consequència d’un canvi conformacional en aquest darrer.

Conformations of poly{G}-poly{C} π stacks with high hole mobility

Charge transfer properties of DNA depend strongly on the π stack conformation. In the present paper, we identify conformations of homogeneous poly-{G}-poly-{C} stacks that should exhibit high charge mobility. Two different computational approaches were applied. First, we calculated the electronic coupling squared, V2, between adjacent base pairs for all 1 ps snapshots extracted from 15 ns molecular dynamics trajectory of the duplex G15. The average value of the coupling squared 〈 V2 〉 is found to be 0.0065 eV2. Then we analyze the base-pair and step parameters of the configurations in which V2 is at least an order of magnitude larger than 〈 V2 〉. To obtain more consistent data, ∼65 000 configurations of the (G:C)2 stack were built using systematic screening of the step parameters shift, slide, and twist. We show that undertwisted structures (twist<20°) are of special interest, because the π stack conformations with strong electronic couplings are found for a wide range of slide and shift. Although effective hole transfer can also occur in configurations with twist=30° and 35°, large mutual displacements of neighboring base pairs are required for that. Overtwisted conformation (twist38°) seems to be of limited interest in the context of effective hole transfer. The results may be helpful in the search for DNA based elements for nanoelectronics

Electronic and vibrational contributions to first hyperpolarizability of donor-acceptor-substituted azobenzene

In this study we report on the electronic and vibrational (hyper)polarizabilities of donor–acceptorsubstituted azobenzene. It is observed that both electronic and vibrational contributions to the electricdipole first hyperpolarizability of investigated photoactive molecule substantially depend on the conformation. The contributions to the nuclear relaxation first hyperpolarizability are found to be quite important in the case of two considered isomers (cis and trans). Although the double-harmonic term is found to be the largest in terms of magnitude, it is shown that the total value of the nuclear relaxation contribution to vibrational first hyperpolarizability is a result of subtle interplay of higher-order contributions. As a part of the study, we also assess the performance of long-range-corrected densityfunctional theory in determining vibrational contributions to electric dipole (hyper)polarizabilities. In most cases, the applied long-range-corrected exchange correlation potentials amend the drawbacks of their conventional counterparts

Understanding the two-component sensing System of virulent bacteria

Report for the scientific sojourn carried out at the l’ Institute for Computational Molecular Science of the Temple University, United States, from 2010 to 2012. Two-component systems (TCS) are used by pathogenic bacteria to sense the environment within a host and activate mechanisms related to virulence and antimicrobial resistance. A prototypical example is the PhoQ/PhoP system, which is the major regulator of virulence in Salmonella. Hence, PhoQ is an attractive target for the design of new antibiotics against foodborne diseases. Inhibition of the PhoQ-mediated bacterial virulence does not result in growth inhibition, presenting less selective pressure for the generation of antibiotic resistance. Moreover, PhoQ is a histidine kinase (HK) and it is absent in animals. Nevertheless, the design of satisfactory HK inhibitors has been proven to be a challenge. To compete with the intracellular ATP concentrations, the affinity of a HK inhibidor must be in the micromolar-nanomolar range, whereas the current lead compounds have at best millimolar affinities. Moreover, the drug selectivity depends on the conformation of a highly variable loop, referred to as the “ATP-lid, which is difficult to study by X-Ray crystallography due to its flexibility. I have investigated the binding of different HK inhibitors to PhoQ. In particular, all-atom molecular dynamics simulations have been combined with enhanced sampling techniques in order to provide structural and dynamic information of the conformation of the ATP-lid. Transient interactions between these drugs and the ATP-lid have been identified and the free energy of the different binding modes has been estimated. The results obtained pinpoint the importance of protein flexibility in the HK-inhibitor binding, and constitute a first step in developing more potent and selective drugs. The computational resources of the hosting institution as well as the experience of the members of the group in drug binding and free energy methods have been crucial to carry out this work.

Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations

Background: Recent advances on high-throughput technologies have produced a vast amount of protein sequences, while the number of high-resolution structures has seen a limited increase. This has impelled the production of many strategies to built protein structures from its sequence, generating a considerable amount of alternative models. The selection of the closest model to the native conformation has thus become crucial for structure prediction. Several methods have been developed to score protein models by energies, knowledge-based potentials and combination of both.Results: Here, we present and demonstrate a theory to split the knowledge-based potentials in scoring terms biologically meaningful and to combine them in new scores to predict near-native structures. Our strategy allows circumventing the problem of defining the reference state. In this approach we give the proof for a simple and linear application that can be further improved by optimizing the combination of Zscores. Using the simplest composite score () we obtained predictions similar to state-of-the-art methods. Besides, our approach has the advantage of identifying the most relevant terms involved in the stability of the protein structure. Finally, we also use the composite Zscores to assess the conformation of models and to detect local errors.Conclusion: We have introduced a method to split knowledge-based potentials and to solve the problem of defining a reference state. The new scores have detected near-native structures as accurately as state-of-art methods and have been successful to identify wrongly modeled regions of many near-native conformations.

Counter-ion effect on surfactant-DNA gel particles as controlled DNA delivery systems

The ability to entrap drugs within vehicles and subsequently release them has led to new treatments for a number of diseases. Based on an associative phase separation and interfacial diffusion approach, we developed a way to prepare DNA gel particles without adding any kind of cross-linker or organic solvent. Among the various agents studied, cationic surfactants offered particularly efficient control for encapsulation and DNA release from these DNA gel particles. The driving force for this strong association is the electrostatic interaction between the two components, as induced by the entropic increase due to the release of the respective counter-ions. However, little is known about the influence of the respective counter-ions on this surfactant-DNA interaction. Here we examined the effect of different counter-ions on the formation and properties of the DNA gel particles by mixing DNA (either single- (ssDNA) or double-stranded (dsDNA)) with the single chain surfactant dodecyltrimethylammonium (DTA). In particular, we used as counter-ions of this surfactant the hydrogen sulfate and trifluoromethane sulfonate anions and the two halides, chloride and bromide. Effects on the morphology of the particles obtained, the encapsulation of DNA and its release, as well as the haemocompatibility of these particles, are presented, using the counter-ion structure and the DNA conformation as controlling parameters. Analysis of the data indicates that the degree of counter-ion dissociation from the surfactant micelles and the polar/hydrophobic character of the counter-ion are important parameters in the final properties of the particles. The stronger interaction with amphiphiles for ssDNA than for dsDNA suggests the important role of hydrophobic interactions in DNA.

MMPBSA decomposition of the binding energy throughout a molecular dynamics simulation of Amyloid-Beta (Aß10-35) aggregation

Recent experiments with amyloid-beta (Aß) peptides indicate that the formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Aß oligomers depend on their structure, which is governed by assembly dynamics. However, a detailed knowledge of the structure of at the atomic level has not been achieved yet due to limitations of current experimental techniques. In this study, replica exchange molecular dynamics simulations are used to identify the expected diversity of dimer conformations of Aß10-35 monomers. The most representative dimer conformation has been used to track the dimer formation process between both monomers. The process has been characterized by means of the evolution of the decomposition of the binding free energy, which provides an energetic profile of the interaction. Dimers undergo a process of reorganization driven basically by inter-chain hydrophobic and hydrophilic interactions and also solvation/desolvation processes.

The role of Cysteine 6.47 in class A GPCRs

Abstract Background: The CWxP motif of transmembrane helix 6 (x: any residue) is highly conserved in class A GPCRs. Within this motif, W6.48 is a big star in the theory of the global “toggle switch” because of its key role in the activation mechanism of GPCRs upon ligand binding. With all footlights focused on W6.48, the reason why the preceding residue, C6.47, is largely conserved is still unknown. The present study is aimed to fill up this lack of knowledge by characterizing the role of C6.47 of the CWxP motif. Results: A complete analysis of available crystal structures has been made alongside with molecular dynamics simulations of model peptides to explore a possible structural role for C6.47. Conclusions: We conclude that C6.47 does not modulate the conformation of the TM6 proline kink and propose that C6.47 participates in the rearrangement of the TM6 and TM7 interface accompanying activation.

Diagnosi del canvi d'usos i cobertes del sòl a Sant Pere de Vilamajor (Vallès Oriental) : analitzant el passat per a entendre el present (1956-2010)

El projecte es centra en analitzar les transformacions en els usos i cobertes del sòl al municipi de Sant Pere de Vilamajor, com a conseqüència d’un conjunt de forces inductores de canvi global. Primerament, s’ha realitzat la caracterització social, econòmica, demogràfica i ambiental de la zona d’estudi des de mitjans del segle passat fins a l’actualitat. Posteriorment, l’estudi es centra en l’anàlisi cartogràfica de la zona, realitzat a través de Sistemes d’Informació Geogràfica (SIG), utilitzant el programa MiraMon, per tal de comparar els usos i cobertes del sòl entre 1956 i 2010. Les principals transformacions experimentades són la transició dels estatges de vegetació herbacis i matollars a bosc i la transformació dels cultius en sòl urbà. L’abandonament de les pràctiques agràries conjuntament amb el desenvolupament de les urbanitzacions a l’àmbit d’estudi són els principals agents de canvi, fruit del procés de la industrialització i terciarització de l’economia.

Coregulator Control of Androgen Receptor Action by a Novel Nuclear Receptor-Binding Motif

The androgen receptor (AR) is a ligand-activated transcription factor that is essential for prostate cancer development. It is activated by androgens through its ligand-binding domain (LBD), which consists predominantly of 11 α-helices. Upon ligand binding, the last helix is reorganized to an agonist conformation termed activator function-2 (AF-2) for coactivator binding. Several coactivators bind to the AF-2 pocket through conserved LXXLL or FXXLF sequences to enhance the activity of the receptor. Recently, a small compound-binding surface adjacent to AF-2 has been identified as an allosteric modulator of the AF-2 activity and is termed binding function-3 (BF-3). However, the role of BF-3 in vivo is currently unknown, and little is understood about what proteins can bind to it. Here we demonstrate that a duplicated GARRPR motif at the N terminus of the cochaperone Bag-1L functions through the BF-3 pocket. These findings are supported by the fact that a selective BF-3 inhibitor or mutations within the BF-3 pocket abolish the interaction between the GARRPR motif(s) and the BF-3. Conversely, amino acid exchanges in the two GARRPR motifs of Bag-1L can impair the interaction between Bag-1L and AR without altering the ability of Bag-1L to bind to chromatin. Furthermore, the mutant Bag-1L increases androgen-dependent activation of a subset of AR targets in a genome-wide transcriptome analysis, demonstrating a repressive function of the GARRPR/BF-3 interaction. We have therefore identified GARRPR as a novel BF-3 regulatory sequence important for fine-tuning the activity of the AR.

Buccodental health and oral mucositis. Clinical study in patients with hematological diseases

Objectives: The objective of the present study is to assess whether a good buccodental status (evaluated by means of dentogingival indices), is associated with a lower incidence and severity of oral mucositis in patients with hematological diseases who receive treatment with chemotherapy or bone marrow transplant. Study design: The study was carried out on 97 patients admitted to the Hematology Service of the Hospital Duran y Reynals in Barcelona during 2002-2003. These patients received treatment with chemotherapy or conditioning prior to bone marrow transplant. A descriptive study was made, analyzing oral hygiene, one dental index, and two gingivales indices, and evaluating their relationship with the appearance of mucositis. Results: The patients with high plaque (PI) and gingival (GI) indices during chemotherapy presented a higher percentage of mucositis (77.4% and 65.7% respectively) against those who had little or no visible plaque. In the case of the PI, the differences were statistically significant (p=0.015). Likewise, patients who brushed their teeth 3 times/day presented mucositis in only 26.7% of cases, against those who did not brush, or brushed only once a day (65.9% and 68.4%), these differences also being statistically significant (p=0.013). The CAO showed similar results in patients with or without mucositis (7.59 and 7.03 respectively). Conclusions: In our study, a good gingival status as well as good oral hygiene during chemoradiotherapy is associated with a lower incidence and severity of mucositis.

Allosteric conversation in the androgen receptor ligand-binding domain surfaces

Androgen receptor (AR) is a major therapeutic target that plays pivotal roles in prostate cancer (PCa) and androgen insensitivity syndromes. We previously proposed that compounds recruited to ligand-binding domain (LBD) surfaces could regulate AR activity in hormone-refractory PCa and discovered several surface modulators of AR function. Surprisingly, the most effective compounds bound preferentially to a surface of unknown function [binding function 3 (BF-3)] instead of the coactivator-binding site [activation function 2 (AF-2)]. Different BF-3 mutations have been identified in PCa or androgen insensitivity syndrome patients, and they can strongly affect AR activity. Further, comparison of AR x-ray structures with and without bound ligands at BF-3 and AF-2 showed structural coupling between both pockets. Here, we combine experimental evidence and molecular dynamic simulations to investigate whether BF-3 mutations affect AR LBD function and dynamics possibly via allosteric conversation between surface sites. Our data indicate that AF-2 conformation is indeed closely coupled to BF-3 and provide mechanistic proof of their structural interconnection. BF-3 mutations may function as allosteric elicitors, probably shifting the AR LBD conformational ensemble toward conformations that alter AF-2 propensity to reorganize into subpockets that accommodate N-terminal domain and coactivator peptides. The induced conformation may result in either increased or decreased AR activity. Activating BF-3 mutations also favor the formation of another pocket (BF-4) in the vicinity of AF-2 and BF-3, which we also previously identified as a hot spot for a small compound. We discuss the possibility that BF-3 may be a protein-docking site that binds to the N-terminal domain and corepressors. AR surface sites are attractive pharmacological targets to develop allosteric modulators that might be alternative lead compounds for drug design.