New insights into probiotic mechanisms: a harvest from functional and metagenomic studies

There has been continued and expanding recognition of probiotic approaches for treating gastrointestinal and systemic disease, as well as increased acceptance of probiotic therapies by both the public and the medical community. A parallel development has been the increasing recognition of the diverse roles that the normal gut microbiota plays in the normal biology of the host. This advance has in turn has been fed by implementation of novel investigative technologies and conceptual paradigms focused on understanding the fundamental role of the microbiota and indeed all commensal bacteria, on known and previously unsuspected aspects of host physiology in health and disease. This review discusses current advances in the study of the host-microbiota interaction, especially as it relates to potential mechanisms of probiotics. It is hoped these new approaches will allow more rational selection and validation of probiotic usage in a variety of clinical conditions.

Ecophysiological and bioclimatic foundations for a global plant functional classification

Question: What plant properties might define plant functional types (PFTs) for the analysis of global vegetation responses to climate change, and what aspects of the physical environment might be expected to predict the distributions of PFTs? Methods: We review principles to explain the distribution of key plant traits as a function of bioclimatic variables. We focus on those whole-plant and leaf traits that are commonly used to define biomes and PFTs in global maps and models. Results: Raunkiær's plant life forms (underlying most later classifications) describe different adaptive strategies for surviving low temperature or drought, while satisfying requirements for reproduction and growth. Simple conceptual models and published observations are used to quantify the adaptive significance of leaf size for temperature regulation, leaf consistency for maintaining transpiration under drought, and phenology for the optimization of annual carbon balance. A new compilation of experimental data supports the functional definition of tropical, warm-temperate, temperate and boreal phanerophytes based on mechanisms for withstanding low temperature extremes. Chilling requirements are less well quantified, but are a necessary adjunct to cold tolerance. Functional traits generally confer both advantages and restrictions; the existence of trade-offs contributes to the diversity of plants along bioclimatic gradients. Conclusions: Quantitative analysis of plant trait distributions against bioclimatic variables is becoming possible; this opens up new opportunities for PFT classification. A PFT classification based on bioclimatic responses will need to be enhanced by information on traits related to competition, successional dynamics and disturbance.

Destructive behaviours and leadership: the source of the shift from a functional to dysfunctional workplace?

Destructive leadership behaviour often results in damage to the organisations that the individual is entrusted to lead. Although accurately pinpointing the type of destructive behaviour is difficult, this article seeks to offer suggestions as to why leaders spiral into such unattractive behaviour. After reviewing the literature, this paper highlights four drivers for destructive ways that people act based on detailed qualitative scenarios that involve how those who experienced such behaviour reacted and felt. The study reveals a noticeable human experience from which nobody can escape, and offers understanding of the study participants’ experiences. Out of respect to the participants, the authors keep their identity anonomous. We drew our subjects from a cross-section of organisations that function internationally within one area of the manufacturing industry. The article presents a model comprising two dimensions: 1) the leader’s attitude to the organisation he or she leads and 2) adequacy of his or her leadership capabilities. The models offer us understanding of the drivers of the destructive actions that the leader exhibits. Understanding allows us to provide managers with tactical methods to protect them against destructive behaviour and help them lessen the worst aspects of destructive behaviour in both their colleagues and themselves.

A framework for designing multi-functional cover crops

Cover crops are sown to provide a number of ecosystem services including nutrient management, mitigation of diffuse pollution, improving soil structure and organic matter content, weed suppression, nitrogen fixation and provision of resources for biodiversity. Although the decision to sow a cover crop may be driven by a desire to achieve just one of these objectives, the diversity of cover crops species and mixtures available means that there is potential to combine a number of ecosystem services within the same crop and growing season. Designing multi-functional cover crops would potentially help to reconcile the often conflicting agronomic and environmental agendas and contribute to the optimal use of land. We present a framework for integrating multiple ecosystem services delivered by cover crops that aims to design a mixture of species with complementary growth habit and functionality. The optimal number and identity of species will depend on the services included in the analysis, the functional space represented by the available species pool and the community dynamics of the crop in terms of dominance and co-existence. Experience from a project that applied the framework to fertility building leys in organic systems demonstrated its potential and emphasised the importance of the initial choice of species to include in the analysis

Insights into the Specificity of Thioredoxin Reductase-Thioredoxin Interactions. A Structural and Functional Investigation of the Yeast Thioredoxin System

The enzymatic activity of thioredoxin reductase enzymes is endowed by at least two redox centers: a flavin and a dithiol/disulfide CXXC motif. The interaction between thioredoxin reductase and thioredoxin is generally species-specific, but the molecular aspects related to this phenomenon remain elusive. Here, we investigated the yeast cytosolic thioredoxin system, which is composed of NADPH, thioredoxin reductase (ScTrxR1), and thioredoxin 1 (ScTrx1) or thioredoxin 2 (ScTrx2). We showed that ScTrxR1 was able to efficiently reduce yeast thioredoxins (mitochondrial and cytosolic) but failed to reduce the human and Escherichia coli thioredoxin counterparts. To gain insights into this specificity, the crystallographic structure of oxidized ScTrxR1 was solved at 2.4 angstrom resolution. The protein topology of the redox centers indicated the necessity of a large structural rearrangement for FAD and thioredoxin reduction using NADPH. Therefore, we modeled a large structural rotation between the two ScTrxR1 domains (based on the previously described crystal structure, PDB code 1F6M). Employing diverse approaches including enzymatic assays, site-directed mutagenesis, amino acid sequence alignment, and structure comparisons, insights were obtained about the features involved in the species-specificity phenomenon, such as complementary electronic parameters between the surfaces of ScTrxR1 and yeast thioredoxin enzymes and loops and residues (such as Ser(72) in ScTrx2). Finally, structural comparisons and amino acid alignments led us to propose a new classification that includes a larger number of enzymes with thioredoxin reductase activity, neglected in the low/high molecular weight classification.

Structural Aspects of the Distinct Biochemical Properties of Glutaredoxin 1 and Glutaredoxin 2 from Saccharomyces cerevisiae

Glutaredoxins (Grxs) are small (9-12 kDa) heat-stable proteins that are ubiquitously distributed. In Saccharomyces cerevisiae, seven Grx enzymes have been identified. Two of them (yGrx1 and yGrx2) are dithiolic, possessing a conserved Cys-Pro-Tyr-Cys motif. Here, we show that yGrx2 has a specific activity 15 times higher than that of yGrx1, although these two oxidoreductases share 64% identity and 85% similarity with respect to their amino acid sequences. Further characterization of the enzymatic activities through two-substrate kinetics analysis revealed that yGrx2 possesses a lower Km for glutathione and a higher turnover than yGrx1. To better comprehend these biochemical differences, the pK(a) of the N-terminal active-site cysteines (Cys27) of these two proteins and of the yGrx2-C30S mutant were determined. Since the pK(a) values of the yGrx1 and yGix2 Cys27 residues are very similar, these parameters cannot account for the difference observed between their specific activities. Therefore, crystal structures of yGrx2 in the oxidized form and with a glutathionyl mixed disulfide were determined at resolutions of 2.05 and 1.91 angstrom, respectively. Comparisons of yGrx2 structures with the recently determined structures of yGrx1 provided insights into their remarkable functional divergence. We hypothesize that the substitutions of Ser23 and Gln52 in yGrx1 by Ala23 and Glu52 in yGrx2 modify the capability of the active-site C-terminal cysteine to attack the mixed disulfide between the N-terminal active-site cysteine and the glutathione molecule. Mutagenesis studies supported this hypothesis. The observed structural and functional differences between yGrx1 and yGrx2 may reflect variations in substrate specificity. (C) 2008 Elsevier Ltd. All rights reserved.

Semiconductor nanoparticle modeling via density functional theory

In this work, a 2.0 nm nanoparticle (low limit synthesized system) is compared to possible simplified models: passivated clusters, small (1.3 nm) nanoparticles and sets of plane surfaces. Our density functional theory results suggest that even when geometric aspects are properly described by the simplifications considered, electronic properties might be very different, especially when edge atoms are not properly taken into account in the nanoparticle`s modeling. In addition, we propose a protocol that might help future theoretical descriptions of nanoparticles.

Functional timing analysis of VLSI circuits containing complex gates

The recent advances in CMOS technology have allowed for the fabrication of transistors with submicronic dimensions, making possible the integration of tens of millions devices in a single chip that can be used to build very complex electronic systems. Such increase in complexity of designs has originated a need for more efficient verification tools that could incorporate more appropriate physical and computational models. Timing verification targets at determining whether the timing constraints imposed to the design may be satisfied or not. It can be performed by using circuit simulation or by timing analysis. Although simulation tends to furnish the most accurate estimates, it presents the drawback of being stimuli dependent. Hence, in order to ensure that the critical situation is taken into account, one must exercise all possible input patterns. Obviously, this is not possible to accomplish due to the high complexity of current designs. To circumvent this problem, designers must rely on timing analysis. Timing analysis is an input-independent verification approach that models each combinational block of a circuit as a direct acyclic graph, which is used to estimate the critical delay. First timing analysis tools used only the circuit topology information to estimate circuit delay, thus being referred to as topological timing analyzers. However, such method may result in too pessimistic delay estimates, since the longest paths in the graph may not be able to propagate a transition, that is, may be false. Functional timing analysis, in turn, considers not only circuit topology, but also the temporal and functional relations between circuit elements. Functional timing analysis tools may differ by three aspects: the set of sensitization conditions necessary to declare a path as sensitizable (i.e., the so-called path sensitization criterion), the number of paths simultaneously handled and the method used to determine whether sensitization conditions are satisfiable or not. Currently, the two most efficient approaches test the sensitizability of entire sets of paths at a time: one is based on automatic test pattern generation (ATPG) techniques and the other translates the timing analysis problem into a satisfiability (SAT) problem. Although timing analysis has been exhaustively studied in the last fifteen years, some specific topics have not received the required attention yet. One such topic is the applicability of functional timing analysis to circuits containing complex gates. This is the basic concern of this thesis. In addition, and as a necessary step to settle the scenario, a detailed and systematic study on functional timing analysis is also presented.

Insights into the Specificity of Thioredoxin Reductase-Thioredoxin Interactions. A Structural and Functional Investigation of the Yeast Thioredoxin System

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structural Aspects of the Distinct Biochemical Properties of Glutaredoxin 1 and Glutaredoxin 2 from Saccharomyces cerevisiae

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structural aspects of the fermion-boson mapping in two-dimensional gauge and anomalous gauge theories with massive fermions

Using a synthesis of the functional integral and operator approaches we discuss the fermion-buson mapping and the role played by the Bose field algebra in the Hilbert space of two-dimensional gauge and anomalous gauge field theories with massive fermions. In QED, with quartic self-interaction among massive fermions, the use of an auxiliary vector field introduces a redundant Bose field algebra that should not be considered as an element of the intrinsic algebraic structure defining the model. In anomalous chiral QED, with massive fermions the effect of the chiral anomaly leads to the appearance in the mass operator of a spurious Bose field combination. This phase factor carries no fermion selection rule and the expected absence of Theta-vacuum in the anomalous model is displayed from the operator solution. Even in the anomalous model with massive Fermi fields, the introduction of the Wess-Zumino field replicates the theory, changing neither its algebraic content nor its physical content. (C) 2002 Elsevier B.V. (USA).

Molecular and functional characterization of a new non-hemorrhagic metalloprotease from Bothrops jararacussu snake venom with antiplatelet activity

BjussuMP-II is an acidic low molecular weight metalloprotease (Mr similar to 24,000 and pI similar to 6.5), isolated from Bothrops jararacussu snake venom. The chromatographic profile in RP-HPLC and its N-terminal sequence confirmed its high purity level. Its complete cDNA was obtained by RT-PCR and the 615 bp codified for a mature protein of 205 amino acid residues. The multiple alignment of its deduced amino acid sequence and those of other snake venom metalloproteases showed a high structural similarity, mainly among class P-I proteases. The molecular modeling analysis of BjussuMP-II showed also conserved structural features with other SVMPs. BjussuMP-II did not induce hemorrhage, myotoxicity and lethality, but displayed dose-dependent proteolytic activity on fibrinogen, collagen, fibrin, casein and gelatin, keeping stable at different pHs, temperatures and presence of several divalent ions. BjussuMP-II did not show any clotting or anticoagulant activity on human citrated plasma, in contrast to its inhibitory effects on platelet aggregation. The aspects broached, in this work, provide data on the relationship between structure and function, in order to better understand the effects elicited by snake venom metalloproteases. (c) 2007 Elsevier B.V. All rights reserved.

Influence of forest cover and mesohabitat types on functional and taxonomic diversity of fish communities in Neotropical lowland streams

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Immunologic aspects of West syndrome and evidence of plasma inhibitory effects on T cell function

OBJETIVO: O objetivo deste estudo foi determinar o perfil da deficiência imune em um grupo bem definido de epilepsia: crianças com síndrome de West (SW) e seus padrões EEG de evolução, idade-dependentes, como os complexos onda-aguda- onda lenta generalizadas da síndrome de Lenox-Gastaut (SLG) e as pontas multifocais independentes (PMI). MÉTODO: Um grupo de 50 crianças, 33 com SW, 10 com SLG, 7 com PMI e 20 crianças sadias (controle) foram avaliadas em relação aos seguintes parâmetros:determinação de subpopulações de linfócitos T (CD1, CD3, CD4 e CD8), relação CD4/CD8 e resposta proliferativa de linfócitos frente a fitohemaglutinina (PHA), na presença de plasma autólogo ou de plasma AB (homólogo). A prova cutânea de sensibilização ao Dinitroclorobenzeno (DNCB) foi realizada apenas nos pacientes. Os níveis séricos de IgG, IgA e IgM foram comparados aos valores normais em crianças Brasileiras, em diferentes faixas etárias. RESULTADOS: A resposta ao DNCB foi ausente ou fracamente reativa em 76% dos pacientes. Níveis séricos elevados de IgG (45,7%) e de IgM (61,4%) e baixos de IgA (23,9%) foram detectados nos pacientes. A determinação das subpopulações de linfócitos T em sangue periférico mostrou: deficiência nas proporções de células CD3+ (p<0,05) e de CD4+ (p<0,05), aumento de CD8+ (p<0,01) e diminuição da relação CD4 / CD8 (p<0,001). A proporção de células CD1+ no grupo controle manteve-se menor que 3%, enquanto que em 18% dos pacientes esses níveis variaram entre 3 e 11%. A resposta proliferativa de linfócitos frente a PHA revelou índices blastogênicos significativamente mais baixos apenas quando células dos pacientes foram cultivadas na presença do próprio plasma (plasma autólogo). Quando estas células foram cultivadas na presença de plasma AB, não se evidenciou diferença significativa em relação ao grupo controle. CONCLUSÃO: A imunodeficiência na SW caracterizou-se por: anergia, alteração de imunidade mediada por células e dos níveis de imunoglobulinas, presença de timócitos imaturos na circulação periférica e deficiência funcional de linfócitos T induzida por fatores plasmáticos inibidores. Discutem-se as principais evidências de disfunção imune como imunodeficiência e autoimunidade.

Ultrastructural aspects of acid phosphatase activity in Malpighian tubules of Triatoma infestans Klug

Acid phosphatase activity was investigated ultrastructurally in Malpighian tubules of Triatoma infestans. Enzyme activity was demonstrated in laminated 'concretions' (distal cells) and in typical lysosomes, as well as in basal plasmalemma infoldings and basement membranes (especially in distal cells). This activity was assumed to be related to the excretory functions carried out mostly by the distal cells. Heterochromatin-nucleolus functional relationships involving RNA transcription may promote the nuclear reaction verified in the proximal cells and in some distal cells. A lead phosphate precipitate appeared free in the cytoplasm encircling the nuclei and was assumed to be a contamination from the nuclear precipitates.