Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse

The production of bioethanol from non-food agricultural residues represents an alternative energy source to fossil fuels for incorporation into the world's economy. Within the context of bioconversion of plant biomass into renewable energy using improved enzymatic cocktails, Illumina RNA-seq transcriptome profiling was conducted on a strain of Aspergillus tamarii, efficient in biomass polysaccharide degradation, in order to identify genes encoding proteins involved in plant biomass saccharification. Enzyme production and gene expression was compared following growth in liquid and semi-solid culture with steam-exploded sugarcane bagasse (SB) (1% w/v) and glucose (1% w/v) employed as contrasting sole carbon sources. Enzyme production following growth in liquid minimum medium supplemented with SB resulted in 0.626 and 0.711 UI.mL−1 xylanases after 24 and 48 h incubation, respectively. Transcriptome profiling revealed expression of over 7120 genes, with groups of genes modulated according to solid or semi-solid culture, as well as according to carbon source. Gene ontology analysis of genes expressed following SB hydrolysis revealed enrichment in xyloglucan metabolic process and xylan, pectin and glucan catabolic process, indicating up-regulation of genes involved in xylanase secretion. According to carbohydrate-active enzyme (CAZy) classification, 209 CAZyme-encoding genes were identified with significant differential expression on liquid or semi-solid SB, in comparison to equivalent growth on glucose as carbon source. Up-regulated CAZyme-encoding genes related to cellulases (CelA, CelB, CelC, CelD) and hemicellulases (XynG1, XynG2, XynF1, XylA, AxeA, arabinofuranosidase) showed up to a 10-fold log2FoldChange in expression levels. Five genes from the AA9 (GH61) family, related to lytic polysaccharide monooxygenase (LPMO), were also identified with significant expression up-regulation. The transcription factor gene XlnR, involved in induction of hemicellulases, showed up-regulation on liquid and semi-solid SB culture. Similarly, the gene ClrA, responsible for regulation of cellulases, showed increased expression on liquid SB culture. Over 150 potential transporter genes were also identified with increased expression on liquid and semi-solid SB culture. This first comprehensive analysis of the transcriptome of A. tamarii contributes to our understanding of genes and regulatory systems involved in cellulose and hemicellulose degradation in this fungus, offering potential for application in improved enzymatic cocktail development for plant biomass degradation in biorefinery applications

Ethnoveterinary plants of Ankober District, North Shewa Zone, Amhara Region, Ethiopia

Background: Traditional herbal preparations for addressing veterinary problems have been applied in Ankober District, Ethiopia, for generations. However, the millennia-old ethnoveterinary knowledge of the community, and the plants are subjected to loss without being scientifically documented due to anthropogenic and environmental threats. Hence, this study aims at providing a comprehensive documentation on ethnoveterinary plant knowledge of the people in order to preserve the fast-eroding knowledge and resources of the area. Methods: Semi-structured interviews, focus group discussions, participant observation and walk-in-the-woods methods were used to gather ethnoveterinary data. Informant Consensus Factor (ICF) and Fidelity level (FL) values were calculated using quantitative approaches so as to check the level of informants' agreement on plant use and healing potential of ethnoveterinary medicinal plant species, respectively. Indigenous knowledge on use of medicinal plants for ethnoveterinary purposes among different informant groups was compared using One-way ANOVA and t-tests. Results: A total of 51 plant species representing 50 genera and 35 botanical families used in the treatment of 33 different ailments were identified. Medicinal plant species belonging to families Asteraceae, Asclepiadaceae, Euphorbiaceae and Ranunculaceae were reported to be of frequent use in the local ethnoveterinary medical system. Roots (65%, 33 species) were most often utilized for remedy preparation. Highest ICF values were recorded for gastro-intestinal (0.71) ailments depicting best agreement on knowledge of medicinal plants used to treat aliments in this category. Embelia schimperi Vatke showed highest fidelity level value (90%) to treat gastro-intestinal diseases showing conformity of knowledge on this species' healing potential. Significant difference (P<0.05) was observed in average number of therapeutic plants reported by senior members of the community than younger groups. Embelia schimperi Vatke and Rubus steudnerii Schweinf. were the most-preferred species to treat diarrhoea. Conclusion: The study indicated that indigenous knowledge on ethnoveterinary medicinal plant use is still rich and active in the District. Species with recorded highest consensus for curative role are a useful pool for further phytochemical and pharmacological validation for better utilization. Declining wild medicinal flora of the area calls for implementation of a coordinated complementary in situ and ex situ conservation strategy

Impact of bioactive substances on the gastrointestinal tract and performance of weaned piglets: a review

The EU ban on in-feed antibiotics has stimulated research on weaning diets as a way of reducing post-weaning gut disorders and growth check in pigs. Many bioactive components have been investigated but only few have shown to be effective. Amongst these, organic acids (OA) have been shown to exert a bactericidal action mediated by non-dissociated OA, by lowering gastric pH, increasing gut and pancreas enzyme secretion and improving gut wall morphology. It has been postulated that they may also enhance non-specific immune responses and improve disease resistance. In contrast, relatively little attention has been paid to the impact of OA on the stomach but recent data show they can differently affect gastric histology, acid secretion and gastric emptying. Butyrate and precursors of butyric acid have received special attention and although promising results have been obtained, their effects are dependent upon the dose, treatment duration, initial age of piglets, gastrointestinal site and other factors. The amino acids (AA) like glutamine, tryptophan and arginine are supportive in improving digestion, absorption and retention of nutrients by affecting tissue anabolism, stress and (or) immunity. Glutamine, cysteine and threonine are important for maintaining mucin and permeability of intestinal barrier function. Spray-dried plasma (SDP) positively affects gut morphology, inflammation and reduces acquired specific immune responses via specific and a-specific influences of immunoglobulins and other bioactive components. Effects are more pronounced in early-weaned piglets and under poorer health conditions. Little interaction between plasma protein and antibiotics has been found, suggesting distinct modes of action and additive effects. Bovine colostrum may act more or less similarly to SDP The composition of essential oils is highly variable, depending on environmental and climatic conditions and distillation methods. These oils differ widely in their antimicrobial activity in vitro and some components of weaning diets may decrease their activity Results in young pigs are highly variable depending upon the product and doses used. These studies suggest that relatively high concentrations of essential oils are needed for beneficial effects to be observed and it has been assumed that these plant extracts mimic most of the effects of antibiotics active on gut physiology, microbiology and immunology. Often, bioactive substances protective to the gut also stimulate feed intake and growth performance. New insights on the effects of selected OA and AA, protein sources (especially SDP bovine colostrum) and plant extracts with anti-bacterial activities on the gut are reported in this review

Metal and metalloid foliar uptake by various plant species exposed to atmospheric industrial fallout: Mechanisms involved for lead

Fine and ultrafine metallic particulatematters (PMs) are emitted frommetallurgic activities in peri-urban zones into the atmosphere and can be deposited in terrestrial ecosystems. The foliar transfer ofmetals andmetalloids and their fate in plant leaves remain unclear, although this way of penetration may be a major contributor to the transfer of metals into plants. This study focused on the foliar uptake of various metals and metalloids from enriched PM(Cu, Zn, Cd, Sn, Sb, As, and especially lead (Pb)) resulting fromthe emissions of a battery-recycling factory.Metal and metalloid foliar uptake by various vegetable species, exhibiting different morphologies, use (food or fodder) and life-cycle (lettuce, parsley and rye-grass) were studied. The mechanisms involved in foliar metal transfer from atmospheric particulate matter fallout, using lead (Pb) as a model element was also investigated. Several complementary techniques (micro-X-ray fluorescence, scanning electron microscopy coupled with energy dispersive X-ray microanalysis and time-of-flight secondary ion mass spectrometry) were used to investigate the localization and the speciation of lead in their edible parts, i.e. leaves. The results showed lead-enriched PM on the surface of plant leaves. Biogeochemical transformations occurred on the leaf surfaces with the formation of lead secondary species (PbCO3 and organic Pb). Some compounds were internalized in their primary form (PbSO4) underneath an organic layer. Internalization through the cuticle or penetration through stomata openings are proposed as two major mechanisms involved in foliar uptake of particulate matter

The dual nature of trehalose in citrus canker disease: A virulence factor for Xanthomonas citri subsp. citri and a trigger for plant defence responses

Xanthomonas citri subsp. citri (Xcc) is a bacterial pathogen that causes citrus canker in susceptible Citrus spp. The Xcc genome contains genes encoding enzymes from three separate pathways of trehalose biosynthesis. Expression of genes encoding trehalose-6-phosphate synthase (otsA) and trehalose phosphatase (otsB) was highly induced during canker development, suggesting that the two-step pathway of trehalose biosynthesis via trehalose-6-phosphate has a function in pathogenesis. This pathway was eliminated from the bacterium by deletion of the otsA gene. The resulting XccΔotsA mutant produced less trehalose than the wild-type strain, was less resistant to salt and oxidative stresses, and was less able to colonize plant tissues. Gene expression and proteomic analyses of infected leaves showed that infection with XccΔotsA triggered only weak defence responses in the plant compared with infection with Xcc, and had less impact on the host plant's metabolism than the wild-type strain. These results suggested that trehalose of bacterial origin, synthesized via the otsA-otsB pathway, in Xcc, plays a role in modifying the host plant's metabolism to its own advantage but is also perceived by the plant as a sign of pathogen attack. Thus, trehalose biosynthesis has both positive and negative consequences for Xcc. On the one hand, it enables this bacterial pathogen to survive in the inhospitable environment of the leaf surface before infection and exploit the host plant's resources after infection, but on the other hand, it is a tell-tale sign of the pathogen's presence that triggers the plant to defend itself against infection.Fil: Piazza, Ainelén Melanie. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Zimaro, Tamara. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Garavaglia, Betiana Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Ficarra, Florencia Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Thomas, Ludivine. King Abdullah University of Science and Technology; Arabia SauditaFil: Marondedze, Claudius. King Abdullah University of Science and Technology; Arabia SauditaFil: Feil, Regina. Max Planck Institute of Molecular Plant Physiology; AlemaniaFil: Lunn, John E.. Max Planck Institute of Molecular Plant Physiology; AlemaniaFil: Gehring, Chris. King Abdullah University of Science and Technology; Arabia SauditaFil: Ottado, Jorgelina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Gottig Schor, Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentin

Potential of PM-selected components to induce oxidative stress and root system alteration in a plant model organism

Over the last years, various acellular assays have been used for the evaluation of the oxidative potential (OP) of particular matter (PM) to predict PM capacity to generate reactive oxygen (ROS) and nitrogen (RNS) species in biological systems. However, relationships among OP and PM toxicological effects on living organisms are still largely unknown. This study aims to assess the effects of atmospheric PM-selected components (brake dust - BD, pellet ash - PA, road dust - RD, certified urban dust NIST1648a - NIST, soil dust - S, coke dust - C and Saharan dust - SD) on the model plant A. thaliana development, with emphasis on their capacity to induce oxidative stress and root morphology alteration. Before growing A. thaliana in the presence of the PM-selected components, each atmospheric dust has been chemically characterized and tested for the OP through dithiothreitol (DTT), ascorbic acid (AA) and 2′,7′-dichlorofluorescin (DCFH) assays. After the exposure, element bioaccumulation in the A. thaliana seedlings, i.e., in roots and shoots, was determined and both morphological and oxidative stress analyses were performed in roots. The results indicated that, except for SD and S, all the tested dusts affected A. thaliana root system morphology, with the strongest effects in the presence of the highest OPs dusts (BD, PA and NIST). Principal component analysis (PCA) revealed correlations among OPs of the dusts, element bioaccumulation and root morphology alteration, identifying the most responsible dust-associated elements affecting the plant. Lastly, histochemical analyses of NO and O2•− content and distribution confirmed that BD, PA and NIST induce oxidative stress in A. thaliana, reflecting the high OPs of these dusts and ultimately leading to cell membrane lipid peroxidation

Assessment of socio-economic configuration of value chains : a proposed analysis framework to facilitate integration of small rural producers with global agribusiness

Value chain analysis is an important tool to assess and enhance the performance of agribusiness. This paper analyzes the empirical application of a conceptual framework known as the Rural Web to evaluate the socio-economic complexity of a specific agribusiness value chain. This can be used as a complementary approach to traditional value chain analysis. The proposed framework goes beyond linear descriptions of product flows and examines how supply chains are built, shaped and reproduced over time and space, while considering social, cultural, environmental and political aspects. The results demonstrate that the proposed framework is a suitable method for value chain analysis, principally for those whose early stages are based on small and medium-sized rural actors. The Rural Web analysis offers decision-makers a platform to identify key actors not traditionally considered in value chain analysis, as well as the social interrelationships that occur at different dimensions. It also enables the identification of corrective and preventive measures to enhance agribusiness value chains

A simulation program for the timing of fungicides to control Sooty Blotch in organic apple growing. First results in 2003

A simulation program for infections by Sooty Blotch was developed based on literature data and expert judgements. The value of the model as tool for timing fungicide sprays to control Sooty Blotch was tested in 2003 in two randomized plot trials, and four “on farm” trials where the treatments where made by the growers. Disease pressure was relative low due to the warm and dry summer of 2003. Two to five post infection treatments with lime sulfur or coconut soap aimed at severe infection periods as indicated by the model provides 72 to 100 % control

Comparison of instrumental methods for measuring seed hardness of food-grade soybean

Seed hardness is an important factor in determining soybean suitability for natto production. There is no established methodology for testing seed texture of soybeans. The objective of this study was to develop an efficient method by examining different instruments and seed parameters that could be potentially used for testing soybean seed hardness. Five food-grade soybean genotypes with different seed sizes were used to determine seed hardness and water-absorption capacity. Water absorption capacity was expressed by swell ratios for seed weight, seed dimension, and volume of water changes before and after soaking. Seed hardness test was conducted by a one-bite method using two food-texture analyzers: a TMS-2000 equipped with shear cell (SC) and a TA-XT2i equipped with either a single blade (SB), a 2-mm probe (PB), a 75-mm cylinder (CY), or a 16-probe pea rigs (PR). The results showed that hardness testing by CY with ten seeds (CV=0.14), SB with 5 seeds (CV=0.11), and SC with 30 g steamed seeds (CV=0.14) produced dependable and consistent results with low coefficient of variance. However, SC may not be practical for early plant selection in a breeding program due to a relatively large sample requirement. Seed size was negatively, whereas swell ratio by weight and volume was positively, correlated with seed hardness, and therefore, can be used as indirect selection indicators for seed hardness

Influence in vitro de divers facteurs abiotiques (température, pH, salinité) sur la croissance mycélienne de trois souches locales de Trichoderma sp.

Les Trichoderma sont des champignons imparfaits saprophytes que l’on retrouve dans divers milieux comme le sol, le bois mort, les débris des végétaux et les organes aériens des plantes. Ils ont un rôle phytoprotecteur et stimulateur du développement des plantes associées. L’effet de différents facteurs abiotiques (température, pH, salinité) sur la croissance mycélienne de trois souches locales de Trichoderma a été évalué. Ces souches ont été isolées à partir de la rhizosphère de la tomate. Une étude préliminaire a été effectuée sur quatre milieux de culture (PDA, MEA, SB et DOX) pour la sélection du milieu d’étude. Les résultats obtenus montrent que le milieu PDA permet une meilleure croissance des souches de Trichoderma. La température optimale de croissance des différentes souches est de 29 °C et le pH 5 se révèle être le plus adéquat pour la culture des Trichoderma. Cette étude montre également que les souches de Trichoderma résistent à des concentrations de sel (NaCl) allant jusqu’à 3%.© 2016 International Formulae Group. All rights reserved.Mots clés: Trichoderma, facteurs limitant, température, pH, salinité, milieu de cultureEnglish Title:  In vitro influence of various abiotic factors (température, pH, salinity) on mycelium growth of three local strains of Trichoderma sp.English AbstractTrichoderma are saprophytic imperfect fungi that are found in various environments such as soil, dead wood, vegetable fragments and plant aerial organs. They protect and stimulate development of related plants. Effects of various abiotic factors (temperature, pH, salinity) on mycelium growth of three local Trichoderma strains were investigated. These strains were isolated from tomato rhizosphere. A preliminary study was performed on four culture media (PDA, MEA, SB and DOX) for the selection of the best media. The results  showed that PDA medium was highly growth of Trichoderma strains. The optimum temperature for growth of different strains is 29 °C and pH 5 was found to be most suitable for Trichoderma culture. Indeed, Trichoderma strains resistant to salt concentrations (NaCl) up to 3%.© 2016 International Formulae Group. All rights reserved.Keywords: Trichoderma, limiting factors, temperature, pH, salinity, culture medi