161 research outputs found
Effects of different biochar application rates on soil fertility and soil water retention in on-farm experiments on smallholder farms in Kenya
Biochar is produced through pyrolysis, the thermo-chemical degradation of biomass under anaerobic or oxygen-limited conditions. Due to its properties related to surface area and porosity, bulk density, nutrient content, stability, cation exchange capacity (CEC), pH value, and carbon content, biochar has the potential to improve physical as well as chemical soil properties and thus improve crop productivity and contribute to carbon sequestration. This study determined the effects of four different biochar rates on retention of plant available soil water, soil bulk density and availability of macronutrients. The research was conducted on smallholder farms in two counties in Kenya, namely Siaya and Embu. Maize cobs and stover biochar was applied in Siaya and coffee husk biochar was applied in Embu. Spectra of soil samples and maize leaves were taken with a visible near infrared (VNIR) spectroradiom-eter in order to determine soil moisture and available macronutrients. Also, bulk density and soil moisture at different suction pressures were determined.
Regarding plant available water, a trend of increasing soil moisture with biochar rate and significance for the two highest biochar rates compared to control was found in Siaya. For soil moisture at different water tensions, a notable difference between presence and absence of biochar was observed at the two lower water tensions (pF of 1.7 and 3) in Siaya, but not on a significant level. No significant differences or trends in plant available water were observed in Embu. For bulk density, no trend for decreasing bulk density with biochar rate was found and significant differences found were not conclusive for both Siaya and Embu. As to availability of macronutrients, no conclusive significant differences and trends for increasing nutrient content of maize leaves with biochar rate were found in either Siaya or Embu
The pyrroloquinoline quinone biosynthesis pathway revisited: A structural approach
<p>Abstract</p> <p>Background</p> <p>The biosynthesis pathway of Pyrroloquinoline quinone, a bacterial redox active cofactor for numerous alcohol and aldose dehydrogenases, is largely unknown, but it is proven that at least six genes in <it>Klebsiella pneumoniae </it>(PqqA-F) are required, all of which are located in the PQQ-operon.</p> <p>Results</p> <p>New structural data of some PQQ biosynthesis proteins and their homologues provide new insights and functional assignments of the proteins in the pathway. Based on sequence analysis and homology models we propose the role and catalytic function for each enzyme involved in this intriguing biosynthesis pathway.</p> <p>Conclusion</p> <p>PQQ is derived from the two amino acids glutamate and tyrosine encoded in the precursor peptide PqqA. Five reactions are necessary to form this quinone cofactor. The PqqA peptide is recognised by PqqE, which links the C9 and C9a, afterwards it is accepted by PqqF which cuts out the linked amino acids. The next reaction (Schiff base) is spontaneous, the following dioxygenation is catalysed by an unknown enzyme. The last cyclization and oxidation steps are catalysed by PqqC. Taken together the known facts of the different proteins we assign a putative function to all six proteins in PQQ biosynthesis pathway.</p
Uso de emissão de ondas de tensão para avaliação não destrutiva de árvores e da madeira de Pinus taeda L.
Orientador:Jorge L.M. de MatosDissertaçao (mestrado) - Universidade Federal do Paraná. Setor de Ciências Agrárias. Curso de Pós-Graduação em Engenharia FlorestalInclui bibliografiaÁrea de concentração: Tecnologia e Utilização de Produtos FlorestaisA aplicação de tecnologias inovadoras como a de emissão de ondas de tensão na avaliação da qualidade da madeira, pode transformar em material de maior valor econômico para outros setores, as árvores plantadas comercialmente para produção de fibras, ampliando substancialmente o mercado para a madeira. Como objetivo deste trabalho tem-se: Avaliar a eficiência da utilização do método não destrutivo de emissão de ondas de tensão na qualificação de árvores, toras, tábuas e lâminas de madeira de Pinus taeda. Foram utilizadas 25 árvores para realização das medidas efetivas de propagação de ondas acústicas com o aparelho Stress Wave Timer METRIGUARD, modelo 239A. Adotou-se com base na fase preliminar do experimento (13 árvores) os seguintes procedimentos: construção e utilização de aparato com objetivo de padronizar a força de impacto para emissão da onda de tensão; realização da aplicação e recepção das ondas de tensão nas árvores em pé na altura do DAP diretamente na madeira, procedendo à prévia retirada da casca; realização da tomada da onda de tensão em três posições: "horizontal", "diagonal" e "vertical". Nas toras traçadas, procedeu-se à aplicação da onda de tensão no sentido de seu comprimento (longitudinal), em duas faixas: próximo à medula, e próximo à casca, e ainda através da medula. A tomada nas lâminas das leituras de propagação das ondas de tensão deu-se nos sentidos longitudinal e transversal às fibras, posicionando os transdutores no ponto médio do comprimento e largura das mesmas. A tomada, nas tábuas, das leituras de propagação das ondas de tensão realizou-se no sentido longitudinal às fibras. Na fase 1 as lâminas foram classificadas visualmente pelas funcionárias da laminadora em duas classes: A e B. Os melhores valores obtidos a um nível de significância de 95%, foram: de 796/0 entre as variáveis volume de lâminas classe A e a propagação da onda de tensão na árvore em pé, na altura do DAP; de -84% entre as leituras de tempo de propagação da onda de tensão nas lâminas classe B no sentido longitudinal e nas toras de 2,6 m na região de aplicação da onda próximo à medula; e ainda de -92% entre as velocidades de propagação da onda nas lâminas classe A no sentido transversal às fibras e nas toras de 2,6 m na região de aplicação da onda próximo à medula. Na fase 2, com relação à aplicação do impacto na árvore em pé do martelo emissor da onda de tensão, a melhor alternativa é fazê-lo no sentido diagonal por este apresentar menor coeficiente de variação, e consequentemente medidas mais homogêneas. Nas toras, a emissão da onda de tensão pelo impacto é recomendada no sentido cruzado, através da medula, entre a emissão e recepção da onda. Concluiu-se que há eficiência no sortimento em classes de qualidade das árvores primeiramente, pelo método não destrutivo, resultando na correlação entre estas e seus produtos: toras, tábuas e lâminas. Recomenda-se ainda que seja realizado o estudo com o material após secagem (tábuas e lâminas), para verificar a influência da umidade neste processo e método de avaliação de qualidade da madeira.New technologies like non destructive evaluation (NDE) -acoustic waves can be used to access wood and other materials quality. The objective of this work was evaluate the NDE acoustic waves method to evaluate living trees, logs, veneer and boards of Pinus taeda using Metriguard Stress Wave Timer, model 239A. The final tests are made with 25 trees. By the pre tests using 13 trees, some guidelines were produced: an apparatus was built and used to standardizing the impact strength; in the living trees the impact wave was applied after removing the bark, in three directions: horizontal, diagonal, and vertical one. In the logs, the stress wave was applied through its length parallel near the bark and near the pith, and crossing the pith. The veneer wave measurements were made through its length and through its width, in the middle section of both positions. In the boards the wave measurements were made only at the length direction. At pre testing occasion, veneers were qualified by the Veneer Lumber Factory workers in A and B quality categories. The best correlation values at 95% confidence level were: 79% between veneer quality A volume and stress time propagation in living trees, at the breast height diameter (BHD), 84% by stress time propagation in veneer quality B length direction and 2,6 m long logs, near the pith application of stress wave; and 92% between wave speed propagation into veneer quality A, width direction, and 2,6 long logs, near the pith application of stress wave. The final tests show that the better way to apply the stress wave is, in living trees, through the wood in diagonal direction. To the log evaluation, the stress wave was best applied through its length crossing the pith. Conclusion is that non destructive evaluation works for wood quality assessment in living trees, with correlation with its products: logs, veneers and boards. Recommended complementary studies must be developed to identify moisture influence at the stress wave measurements, using this same material (veneers and boards) after drying
Purification, crystallization and X-ray diffraction analysis of human dynamin-related protein 1 GTPase-GED fusion protein
The mechano-enzyme dynamin-related protein 1 plays an important role in mitochondrial fission and is implicated in cell physiology. Dysregulation of Drp1 is associated with abnormal mitochondrial dynamics and neuronal damage. Drp1 shares structural and functional similarities with dynamin 1 with respect to domain organization, ability to self-assemble into spiral-like oligomers and GTP-cycle-dependent membrane scission. Structural studies of human dynamin-1 have greatly improved the understanding of this prototypical member of the dynamin superfamily. However, high-resolution structural information for full-length human Drp1 covering the GTPase domain, the middle domain and the GTPase effector domain (GED) is still lacking. In order to obtain mechanistic insights into the catalytic activity, a nucleotide-free GTPase-GED fusion protein of human Drp1 was expressed, purified and crystallized. Initial X-ray diffraction experiments yielded data to 2.67 angstrom resolution. The hexagonal-shaped crystals belonged to space group P2(1)2(1)2, with unit-cell parameters a = 53.59, b = 151.65, c = 43.53 angstrom, one molecule per asymmetric unit and a solvent content of 42%. Expression of selenomethionine-labelled protein is currently in progress. Here, the expression, purification, crystallization and X-ray diffraction analysis of the Drp1 GTPase-GED fusion protein are presented, which form a basis for more detailed structural and biophysical analysis
Molecular mechanism of enzymatic chlorite detoxification: insights from structural and kinetic studies
The heme enzyme chlorite dismutase (Cld) degrades chlorite to chloride and dioxygen. Although the structure and steady-state kinetics of pentameric Clds have been elucidated, many questions remain, such as the mechanism of chlorite cleavage and the pH dependence of the reaction. Here, we present high resolution X-ray crystal structures of a dimeric Cld at pH 6.5 and 8.5, its fluoride and isothiocyanate complexes and the neutron structure at pH 9.0 together with the pH dependence of the Fe(III)/Fe(II) couple and the UV-vis and resonance Raman spectral features. We demonstrate that the distal Arg127 cannot act as proton acceptor and is fully ionized even at pH 9.0 ruling out its proposed role in dictating the pH dependence of chlorite degradation. Stopped-flow studies show that (i) Compound I and hypochlorite cannot recombine and (ii) Compound II is the immediately formed redox intermediate that dominates during reaction. Homolytic cleavage of chlorite is propose
Prediction of phenprocoumon maintenance dose and phenprocoumon plasma concentration by genetic and non-genetic parameters
Evaluation of the Allergenicity Potential of TcPR-10 Protein from Theobroma cacao
Background: The pathogenesis related protein PR10 (TcPR-10), obtained from the Theobroma cacao-Moniliophthora perniciosa interaction library, presents antifungal activity against M. perniciosa and acts in vitro as a ribonuclease. However, despite its biotechnological potential, the TcPR-10 has the P-loop motif similar to those of some allergenic proteins such as Bet v 1 (Betula verrucosa) and Pru av 1 (Prunus avium). The insertion of mutations in this motif can produce proteins with reduced allergenic power. The objective of the present work was to evaluate the allergenic potential of the wild type and mutant recombinant TcPR-10 using bioinformatics tools and immunological assays. Methodology/Principal Findings: Mutant substitutions (T10P, I30V, H45S) were inserted in the TcPR-10 gene by sitedirected mutagenesis, cloned into pET28a and expressed in Escherichia coli BL21(DE3) cells. Changes in molecular surface caused by the mutant substitutions was evaluated by comparative protein modeling using the three-dimensional structure of the major cherry allergen, Pru av 1 as a template. The immunological assays were carried out in 8-12 week old female BALB/c mice. The mice were sensitized with the proteins (wild type and mutants) via subcutaneous and challenged intranasal for induction of allergic airway inflammation. Conclusions/Significance: We showed that the wild TcPR-10 protein has allergenic potential, whereas the insertion of mutations produced proteins with reduced capacity of IgE production and cellular infiltration in the lungs. On the other hand, in vitro assays show that the TcPR-10 mutants still present antifungal and ribonuclease activity against M. perniciosa RNA. In conclusion, the mutant proteins present less allergenic potential than the wild TcPR-10, without the loss of interesting biotechnological properties. (Résumé d'auteur
Novel transcripts reveal a complex structure of the human TRKA gene and imply the presence of multiple protein isoforms
Publisher Copyright: © 2015 Luberg et al.Background: Tropomyosin-related kinase A (TRKA) is a nerve growth factor (NGF) receptor that belongs to the tyrosine kinase receptor family. It is critical for the correct development of many types of neurons including pain-mediating sensory neurons and also controls proliferation, differentiation and survival of many neuronal and non-neuronal cells. TRKA (also known as NTRK1) gene is a target of alternative splicing which can result in several different protein isoforms. Presently, three human isoforms (TRKAI, TRKAII and TRKAIII) and two rat isoforms (TRKA L0 and TRKA L1) have been described. Results: We show here that human TRKA gene is overlapped by two genes and spans 67 kb-almost three times the size that has been previously described. Numerous transcription initiation sites from eight different 5' exons and a sophisticated splicing pattern among exons encoding the extracellular part of TRKA receptor indicate that there might be a large variety of alternative protein isoforms. TrkA genes in rat and mouse appear to be considerably shorter, are not overlapped by other genes and display more straightforward splicing patterns. We describe the expression profile of alternatively spliced TRKA transcripts in different tissues of human, rat and mouse, as well as analyze putative endogenous TRKA protein isoforms in human SH-SY5Y and rat PC12 cells. We also characterize a selection of novel putative protein isoforms by portraying their phosphorylation, glycosylation and intracellular localization patterns. Our findings show that an isoform comprising mainly of TRKA kinase domain is capable of entering the nucleus. Conclusions: Results obtained in this study refer to the existence of a multitude of TRKA mRNA and protein isoforms, with some putative proteins possessing very distinct properties.publishersversionPeer reviewe
Genomic organisation of the Mal d 1 gene cluster on linkage group 16 in apple
European populations exhibit progressive sensitisation to food allergens, and apples are one of the foods for which sensitisation is observed most frequently. Apple cultivars vary greatly in their allergenic characteristics, and a better understanding of the genetic basis of low allergenicity may therefore allow allergic individuals to increase their fruit intake. Mal d 1 is considered to be a major apple allergen, and this protein is encoded by the most complex allergen gene family. Not all Mal d 1 members are likely to be involved in allergenicity. Therefore, additional knowledge about the existence and characteristics of the different Mal d 1 genes is required. In the present study, we investigated the genomic organisation of the Mal d 1 gene cluster in linkage group 16 of apple through the sequencing of two bacterial artificial chromosome clones. The results provided new information on the composition of this family with respect to the number and orientation of functional and pseudogenes and their physical distances. The results were compared with the apple and peach genome sequences that have recently been made available. A broad analysis of the whole apple genome revealed the presence of new genes in this family, and a complete list of the observed Mal d 1 genes is supplied. Thus, this study provides an important contribution towards a better understanding of the genetics of the Mal d 1 family and establishes the basis for further research on allelic diversity among cultivars in relation to variation in allergenicity
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