Testing competing explanations for the inverse productivity puzzle

We use plot-level data from ICRISAT to assess competing explanations for an old empirical regularity - the inverse relationship between land productivity and farm size. The presence of farmers who simultaneously crop multiple plots with di¤erent sizes is used to test (and reject) explanations based on household heterogeneity. The panel nature of the data is explored to test (and refuse) explanations based on plot fixed characteristics. We are then left with explanations based on time-varying plot features or measurement errors in the plot size. Theoretically, the input choices should reflect both plot-specific features and the true plot size. Empirically, the inverse relationship vanishes when we control for input use.Development, farm size, productivity.

The use of Fluorescence Resonance Energy Transfer (FRET) peptidesfor measurement of clinically important proteolytic enzymes

Proteolytic enzymes have a fundamental role in many biological processes and are associated with multiple pathological conditions. Therefore, targeting these enzymes may be important for a better understanding of their function and development of therapeutic inhibitors. Fluorescence Resonance Energy Transfer (FRET) peptides are convenient tools for the study of peptidases specificity as they allow monitoring of the reaction on a continuous basis, providing a rapid method for the determination of enzymatic activity. Hydrolysis of a peptide bond between the donor/acceptor pair generates fluorescence that permits the measurement of the activity of nanomolar concentrations of the enzyme. The assays can be performed directly in a cuvette of the fluorimeter or adapted for determinations in a 96-well fluorescence plate reader. The synthesis of FRET peptides containing ortho-aminobenzoic acid (Abz) as fluorescent group and 2, 4-dinitrophenyl (Dnp) or N-(2, 4-dinitrophenyl)ethylenediamine (EDDnp) as quencher was optimized by our group and became an important line of research at the Department of Biophysics of the Federal University of São Paulo. Recently, Abz/Dnp FRET peptide libraries were developed allowing high-throughput screening of peptidases substrate specificity. This review presents the consolidation of our research activities undertaken between 1993 and 2008 on the synthesis of peptides and study of peptidases specificities.As enzimas proteolíticas têm um papel fundamental em muitos processos biológicos e estão associadas a vários estados patológicos. Por isso, o estudo da especificidade das peptidases pode ser importante para uma melhor compreensão da função destas enzimas e para o desenvolvimento de inibidores. Os substratos com supressão intramolecular de fluorescência constituem uma excelente ferramenta, pois permitem o monitoramento da reação de forma contínua, proporcionando um método prático e rápido para a determinação da atividade enzimática. A hidrólise de qualquer ligação da cadeia peptídica entre o grupo doador e o grupo supressor gera fluorescência que permite detectar concentração nanomolar de enzima. Os ensaios podem ser acompanhados diretamente na cubeta ou adaptados para determinações de fluorescência em leitoras de placa. A síntese dos peptídeos com supressão intramolecular de fluorescência contendo o grupo fluorescente Abz (orto-aminobenzóico) e o grupo supressor EDDnp (N-[2, 4-dinitrofenil]-etilenodiamino ou Dnp (2, 4-dinitrophenyl) foi otimizada pelo nosso grupo e tornou-se uma importante linha de pesquisa no Departamento de Biofísica da Universidade Federal de São Paulo (UNIFESP). Recentemente, foram desenvolvidas bibliotecas de peptídeos fluorogênico contendo Abz/Dnp como grupo doador/supressor trazendo um grande avanço no estudo de especificidade das peptidases. Esta revisão apresenta o trabalho desenvolvido pelo nosso grupo entre 1993 e 2008 sobre a síntese de peptídeos e o estudo da especificidade de peptidases.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Universidade Federal de São Paulo (UNIFESP) Escola Paulista de Medicina Departamento de BiofísicaUNIFESP, EPM, Depto. de BiofísicaSciEL

Detection of the basement membrane-degrading proteolytic activity of Paracoccidioides brasiliensis after SDS-PAGE using agarose overlays containing Abz-MKALTLQ-EDDnp

We have characterized, in the Paracoccidioides brasiliensis yeast phase, an exocellular SH-dependent serine proteinase activity against Abz-MKRLTL-EDDnp and analogous fluorescent-quenched peptides, and showed that it is also active against constituents of the basement membrane in vitro. In the present study, we separated the components of P. brasiliensis culture filtrates by electrophoresis and demonstrated that the serine-thiol exocellular proteinase has a diffuse and heterogeneous migration by SDS-PAGE, localizing in a region between 69 and 43 kDa. The hydrolytic activity was demonstrable after SDS-PAGE using buffered agarose overlays of Abz-MKALTLQ-EDDnp, following incubation at 37oC, and detection of fluorescent bands with a UV transilluminator. Hydrolysis was more intense when incubation was carried out at basic pH, and was completely inhibited with 2.5 mM PMSF and partially with sodium 7-hydroxymercuribenzoate (2.5 mM p-HMB), suggesting its serine-thiol nature. A proteolytic band with similar characteristics was observed in conventional gelatin zymograms, but could not be correlated with a silver-stained component. Detection of the serine-thiol proteinase in substrate gels after SDS-PAGE provides a useful way of monitoring purification of the basement membrane degrading enzyme.A01Universidade Federal de São Paulo (UNIFESP)UNIFESPSciEL

Extracellular ATP triggers proteolysis and cytosolic Ca²⁺ rise in Plasmodium berghei and Plasmodium yoelii malaria parasites.

BACKGROUND: Plasmodium has a complex cell biology and it is essential to dissect the cell-signalling pathways underlying its survival within the host. METHODS: Using the fluorescence resonance energy transfer (FRET) peptide substrate Abz-AIKFFARQ-EDDnp and Fluo4/AM, the effects of extracellular ATP on triggering proteolysis and Ca²⁺ signalling in Plasmodium berghei and Plasmodium yoelii malaria parasites were investigated. RESULTS: The protease activity was blocked in the presence of the purinergic receptor blockers suramin (50 μM) and PPADS (50 μM) or the extracellular and intracellular calcium chelators EGTA (5 mM) and BAPTA/AM (25, 100, 200 and 500 μM), respectively for P. yoelii and P. berghei. Addition of ATP (50, 70, 200 and 250 μM) to isolated parasites previously loaded with Fluo4/AM in a Ca²⁺-containing medium led to an increase in cytosolic calcium. This rise was blocked by pre-incubating the parasites with either purinergic antagonists PPADS (50 μM), TNP-ATP (50 μM) or the purinergic blockers KN-62 (10 μM) and Ip5I (10 μM). Incubating P. berghei infected cells with KN-62 (200 μM) resulted in a changed profile of merozoite surface protein 1 (MSP1) processing as revealed by western blot assays. Moreover incubating P. berghei for 17 h with KN-62 (10 μM) led to an increase in rings forms (82% ± 4, n = 11) and a decrease in trophozoite forms (18% ± 4, n = 11). CONCLUSIONS: The data clearly show that purinergic signalling modulates P. berghei protease(s) activity and that MSP1 is one target in this pathway

A glimpse on biological activities of tellurium compounds

Tellurium is a rare element which has been regarded as a toxic, non-essential trace element and its biological role is not clearly established to date. Besides of that, the biological effects of elemental tellurium and some of its inorganic and organic derivatives have been studied, leading to a set of interesting and promising applications. As an example, it can be highlighted the uses of alkali-metal tellurites and tellurates in microbiology, the antioxidant effects of organotellurides and diorganoditellurides and the immunomodulatory effects of the non-toxic inorganic tellurane, named AS-101, and the plethora of its uses. Inasmuch, the nascent applications of organic telluranes (organotelluranes) as protease inhibitors and its applications in disease models are the most recent contribution to the scenario of the biological effects and applications of tellurium and its compounds discussed in this manuscript.O telúrio é um elemento não-essencial raro que vem sendo considerado tóxico, e o seu papel biológico é ainda pouco esclarecido. Apesar disso, os efeitos biológicos do telúrio elementar e de alguns derivados inorgânicos e orgânicos que têm sido estudados revelam um conjunto de aplicações diversificadas interessantes e promissoras. Como exemplo, pode-se destacar os usos de teluritos e teluratos de metais alcalinos em microbiologia, o efeito antioxidante de teluretos e diteluretos orgânicos, os efeitos imunomodulatórios e a diversidade de usos correlacionados a este efeito de uma telurana inorgânica denominada AS-101. Ademais, as aplicações de teluranas orgânicas (organoteluranas) como inibidoras de proteases e as aplicações em modelos de doenças compõem a mais recente contribuição ao cenário dos efeitos e aplicações biológicas do telúrio e seus compostos discutidas neste manuscrito.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)UNIFESP Departamento de Ciências Exatas e da TerraUNIFESP Departamento de BiofísicaUNIFESP, Depto. de Ciências Exatas e da TerraUNIFESP, Depto. de BiofísicaSciEL

Systematic revision of the Neotropical catfish genus Scleronema (Siluriformes: Trichomycteridae), with descriptions of six new species from Pampa grasslands

The Neotropical genus Scleronema is revised based on the re-examination of the type specimens and 1,713 newly collected specimens. Scleronema is diagnosed from other trichomycterids by the following unambiguous derived characters: fleshy flap at the base of the maxillary barbell; skin flap in the posterior margin of the opercle; articulation between the autopalatine and the vomer ventrally located, with the medial margins of the autopalatines very close to each other; and autopalatine with an interrupted or not interrupted ossified arch-shaped process on its dorsal surface forming a canal. Scleronema minutum and S. operculatum are redescribed, S. angustirostre is considered a junior synonym of S. minutum, and six new species are described. A lectotype is designated for Trichomycterus minutus. The type localities of S. angustirostre, S. minutum, and S. operculatum are reviewed in order to correct erroneous information cited in articles and catalogs subsequent to the original descriptions. Species of Scleronema are geographically distributed in the La Plata basin and Atlantic coastal drainages from Southern Brazil, Southern Paraguay, Northeastern Argentina and Uruguay. They inhabit rivers or streams with sand- or gravel-bottoms across the Pampa grasslands. We provide evidences to recognize two putative monophyletic units within the genus, namely the S. minutum species group and the S. operculatum species group, and discuss the distribution patterns of their species.O gênero Neotropical Scleronema é revisado com base na análise do material-tipo e outros 1.713 espécimes recentemente coletados. Scleronema é diagnosticado de outros tricomicterídeos pelos seguintes caracteres derivados não ambíguos: aba de pele na base do barbilhão maxilar; aba de pele na margem posterior do opérculo; articulação entre o autopalatino e o vômer posicionada ventralmente, deixando as margens mediais dos autopalatinos muito próximas entre si; e o autopalatino com um processo com formato de arco na sua superfície dorsal. Scleronema minutum e S. operculatum são redescritas, S. angustirostre é considerada um sinônimo júnior de S. minutum e seis novas espécies são descritas. Um lectótipo é designado para S. minutum. As localidades-tipo de S. angustirostre, S. minutum e S. operculatum são revisadas com o intuito de corrigir informações errôneas citadas em artigos e catálogos após suas descrições. As espécies de Scleronema distribuem-se na bacia do rio da Plata e drenagens costeiras atlânticas no sul do Brasil, sul do Paraguai, nordeste da Argentina e Uruguai, habitando rios e riachos ao longo do Pampa com fundos de areia ou cascalho. Dois grupos de espécies supostamente monofiléticos, o grupo S. minutum e o grupo S. operculatum, são reconhecidos no gênero e os padrões de distribuição de suas espécies são discutidos

Foot-and-mouth disease virus leader proteinase: Structural insights into the mechanism of intermolecular cleavage

Translation of foot-and-mouth disease virus RNA initiates at one of two start codons leading to the synthesis of two forms of leader proteinase L(pr)o (Lab(pro) and Lb(pro)). These forms free themselves from the viral polyprotein by intra- and intermolecular self-processing and subsequently cleave the cellular eukaryotic initiation factor (eIF) 4G. During infection, Lb(pro) removes six residues from its own C-terminus, generating sLb(pro). We present the structure of sLb(pro) bound to the inhibitor E64-R-P-NH2, illustrating how sLb(pro) can cleave between Lys/Gly and Gly/Arg pairs. in intermolecular cleavage on polyprotein substrates, Lb(pro) was unaffected by P1 or P1' substitutions and processed a substrate containing nine eIF4GI cleavage site residues whereas sLb(pro) failed to cleave the eIF4GI containing substrate and cleaved appreciably more slowly on mutated substrates. Introduction of 70 eIF4GI residues bearing the Lb(pro) binding site restored cleavage. These data imply that Lb(pro) and sLb(pro) may have different functions in infected cells. (C) 2014 the Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).Austrian Science FoundationFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Med Univ Vienna, Max F Perutz Labs, A-1030 Vienna, AustriaUniv Vienna, Dept Struct & Computat Biol, Max F Perutz Labs, A-1030 Vienna, AustriaUniversidade Federal de São Paulo, Escola Paulista Med, Dept Biophys, BR-0404420 São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, Dept Biophys, BR-0404420 São Paulo, BrazilAustrian Science Foundation: P20889Austrian Science Foundation: P24038FAPESP: 12/50191-4RCNPq: 471340/2011-1CNPq: 470388/2010-2Web of Scienc

Editorial

Editoria