Tissue-specific gene expression in soybean (Glycine max) detected by cDNA microarray analysis

We have constructed cDNA microarrays for soybean (Glycine max L. Merrill), containing approximately 4,100 Unigene ESTs derived from axenic roots, to evaluate their application and utility for functional genomics of organ differentiation in legumes. We assessed microarray technology by conducting studies to evaluate the accuracy of microarray data and have found them to be both reliable and reproducible in repeat hybridisations. Several ESTs showed high levels (>50 fold) of differential expression in either root or shoot tissue of soybean. A small number of physiologically interesting, and differentially expressed sequences found by microarray analysis were verified by both quantitative real-time RT-PCR and Northern blot analysis. There was a linear correlation (r(2) = 0.99, over 5 orders of magnitude) between microarray and quantitative real-time RT-PCR data. Microarray analysis of soybean has enormous potential not only for the discovery of new genes involved in tissue differentiation and function, but also to study the expression of previously characterised genes, gene networks and gene interactions in wild-type, mutant or transgenic; plants.

Electronic nose evaluation of onion headspace volatiles and bulb quality as affected by nitrogen, sulphur and soil type

Edaphic factors affect the quality of onions (Allium cepa). Two experiments were carried out in the field and glasshouse to investigate the effects of N (field: 0, 120 kg ha(-1); glasshouse: 0, 108 kg ha(-1)), S (field: 0, 20 kg ha(-1); glasshouse: 0, 4.35 kg ha(-1)) and soil type (clay, sandy loam) on onion quality. A conducting polymer sensor electronic nose (E-nose) was used to classify onion headspace volatiles. Relative changes in the E-nose sensor resistance ratio (%dR/R) were reduced following N and S fertilisation. A 2D Principal Component Analysis (PCA) of the E-nose data sets accounted for c. 100% of the variations in onion headspace volatiles in both experiments. For the field experiment, E-nose data set clusters for headspace volatiles for no N-added onions overlapped (D-2 = 1.0) irrespective of S treatment. Headspace volatiles of N-fertilised onions for the glasshouse sandy loam also overlapped (D-2 = 1.1) irrespective of S treatment as compared with distinct separations among clusters for the clay soil. N fertilisation significantly (P < 0.01) reduced onion bulb pyruvic acid concentration (flavour) in both experiments. S fertilisation increased pyruvic acid concentration significantly (P < 0.01) in the glasshouse experiment, especially for the clay soil, but had no effect on pyruvic acid concentration in the field. N and S fertilisation significantly (P < 0.01) increased lachrymatory potency (pungency), but reduced total soluble solids (TSS) content in the field experiment. In the glasshouse experiment, N and S had no effect on TSS. TSS content was increased on the clay by 1.2-fold as compared with the sandy loam. Onion tissue N:water-soluble SO42- ratios of between five and eight were associated with greater %dR/R and pyruvic acid concentration values. N did not affect inner bulb tissue microbial load. In contrast, S fertilisation reduced inner bulb tissue microbial load by 80% in the field experiment and between 27% (sandy loam) and 92% (clay) in the glasshouse experiment. Overall, onion bulb quality discriminated by the E-nose responded to N, S and soil type treatments, and reflected their interactions. However, the conventional analytical and sensory measures of onion quality did not correlate with %dR/R.

The relationship between antioxidant supplements and oxidative stress in renal transplant recipients: A review

Renal transplant recipients (RTRs) have elevated oxidative stress and a high incidence of cardiovascular morbidity and mortality. Although recent studies do not support the use of antioxidant supplements as a cardioprotectant in the general population, evidence suggests that RTRs may represent individuals that would benefit from this therapy. RTRs have elevated oxidative stress probably caused by the immunosuppressive therapy, and although only a small number of studies have examined the effects of antioxidant supplementation in these patients, most have reported beneficial findings. This review discusses these studies along with the rationale for the use of antioxidant supplements in RTRs and a call for more research to investigate this important topic.

Mechanical effects of plant cell wall enzymes on cellulose/xyloglucan composites

Xyloglucan-acting enzymes are believed to have effects on type I primary plant cell wall mechanical properties. In order to get a better understanding of these effects, a range of enzymes with different in vitro modes of action were tested against cell wall analogues (bio-composite materials based on Acetobacter xylinus cellulose and xyloglucan). Tomato pericarp xyloglucan endo transglycosylase (tXET) and nasturtium seed xyloglucanase (nXGase) were produced heterologously in Pichia pastoris. Their action against the cell wall analogues was compared with that of a commercial preparation of Trichoderma endo-glucanase (EndoGase). Both 'hydrolytic' enzymes (nXGase and EndoGase) were able to depolymerise not only the cross-link xyloglucan fraction but also the surface-bound fraction. Consequent major changes in cellulose fibril architecture were observed. In mechanical terms, removal of xyloglucan cross-links from composites resulted in increased stiffness (at high strain) and decreased visco-elasticity with similar extensibility. On the other hand, true transglycosylase activity (tXET) did not affect the cellulose/xyloglucan ratio. No change in composite stiffness or extensibility resulted, but a significant increase in creep behaviour was observed in the presence of active tXET. These results provide direct in vitro evidence for the involvement of cell wall xyloglucan-specific enzymes in mechanical changes underlying plant cell wall re-modelling and growth processes. Mechanical consequences of tXET action are shown to be complimentary to those of cucumber expansin.

Hybrid 'Sinta' papaya exhibits unique ACC synthase 1 cDNA isoforms

Five ripening-related ACC synthase cDNA isoforms were cloned from 80% ripe papaya cv. 'Sinta' by reverse transcription-PCR using gene-specific primers. Clone 2 had the longest transcript and contained all common exons and three alternative exons. Clones 3 and 4 contained common exons and one alternative exon each, while clone 1, the most common transcript, contained only the common exons. Clone 5 could be due to cloning artifacts and might not be a unique cDNA fragment. Thus, there are only four isoforms of ACC synthase mRNA. Southern blot analysis indicates that all five clones came from only one gene existing as a single copy in the 'Sinta' papaya genome. Multiple sequence alignment indicates that the four isoforms arise from a single gene, possibly through alternative splicing mechanisms. All the putative alternative exons were present at the 5'-end of the gene comprising the N-terminal region of the protein. 'Sinta' ACC synthase cDNAs were of the capacs 1 type and are most closely related to a 1.4 kb capacs 1-type DNA (AJ277160) from Eksotika papaya. No capacs 2-type cDNAs were cloned from 'Sinta' by RT-PCR. This is the first report of possible alternative splicing mechanism in ripening-related ACC synthase genes in hybrid papaya, possibly to modulate or fine-tune gene expression relevant to fruit ripening.

Assessment of P availability in heavily fertilized soils using the diffusive gradient in thin films (DGT) technique

Phosphorus-availability tests typically provide an indication of quantity of P available (Colwell bicarbonate-extractable P), or of the intensity of supply (0.01 M CaCl2-extractable P). The soil's capacity to buffer P is more difficult to assess, and is generally estimated using a P-adsorption curve. The diffusive gradient in thin films (DGT) approach may provide a simpler means of assessing a soil's ability to maintain soil solution P. Optimal extraction conditions were found to be 24 h exposure of DGT samplers to saturated soil. The DGT approach was evaluated on a range of 24 soils, some of which had high Colwell- (>100 mu g g(-1)) and Bray 1- (>30 mu g g(-1)) extractable P content, but showed a tomato (Lycopersicon esculentum Mill.) yield response to the addition of P fertilizer. The DGT approach provided an excellent separation of soils on which tomato showed a yield response, from those where fertilizer P did not increase dry-matter yield. Phosphorus accumulation was strongly correlated with soil solution P concentration and anion exchange resin-extractable P, but showed poor correlation with Colwell- or Bray 1-extractable P. The DGT P accumulation rate of 3.62 x 10(-7) to 4.79 x 10(-5) mol s(-1) m(-3) for the soils tested was comparable to the uptake rate of roots of tomato plants that were adequately supplied with P (2.25 x 10(-5) mol s(-1) m(-3)).

Identification and characterization of non-pathogenic Fusarium oxysporum capable of increasing and decreasing Fusarium wilt severity

Fusarium wilt of banana is a potentially devastating disease throughout the world. Options for control of the causal organism, Fusarium oxysporum f.sp. cubense (Foc) are limited. Suppressive soil sites have previously been identified where, despite the presence of Foc, Fusarium wilt does not develop. In order to understand some aspects of this disease suppression, endophytic Fusarium oxysporum isolates were obtained from banana roots. These isolates were genetically characterized and compared with an isolate of Fusarium oxysporum previously identified as being capable of suppressing Fusarium wilt of banana in glasshouse trials. Three additional isolates were selected for glasshouse trials to assess suppression of Fusarium wilt in two different cultivars of banana, Cavendish and Lady Finger. One isolate (BRIP 29089) was identified as a potential biocontrol organism, reducing the disease severity of Fusarium wilt in Lady Finger and Cavendish cultivars. Interestingly, one isolate (BRIP 45952) increased Fusarium wilt disease severity on Cavendish. The implications of an isolate of Fusarium oxysporum, non-pathogenic on banana, increasing disease severity and the potential role of non-pathogenic isolates of Fusarium oxysporum in disease complexes are discussed. (c) 2006 Published by Elsevier Ltd on behalf of The British Mycological Society.

Acibenzolar-S-methyl and methyl jasmonate treatments of glasshouse-grown freesias suppress post-harvest petal specking caused by Botrytis cinerea

Compounds that activate host plant defence responses potentially offer socio-environmentally sound alternative methods for disease control. In a series of glasshouse trials over 2 years, pre-harvest sprays with acibenzolar-S-methyl (ASM) and methyl jasmonate (MeJA) were tested for suppression of post-harvest infection of cut Freesia hybrida L. flowers by Botrytis cinerea. For the ASM treatments, variability in reducing the incidence of B. cinerea disease was observed between years freesia varieties, incubation temperatures and ASM concentrations. In the first year, the greatest reductions in lesion numbers on ASM-treated var. 'Cote d'Azur' were recorded using 2.86 mM ASM. For three different post-harvest temperature regimes, the relative reductions in lesion numbers, compared to untreated controls, were 45% at 5 degrees C, 40% at 12 degrees C and 30% at 20 degrees C, respectively. In the second year, lesion numbers were most reduced using 1.43 mM ASM to treat freesia var. 'Dukaat' flowers. Here, the relative reductions were to 44% at 5 degrees C, 26% at 12 degrees C and 51% at 20 degrees C. MeJA treatments were, in general, more consistently effective than ASM treatments in reducing lesion numbers and lesion diameters on cut freesia flowers. MeJA-treated (0.2 mM) freesia flowers (var. 'Dukaat') incubated at 20 degrees C showed relative reductions of 62%, and 45% for lesion number and lesion diameter, respectively. The differing efficacy between ASM and MeJA treatments could be attributed to their differential abilities to induce the salicylic acid (SA)-mediated vs. the jasmonic acid (JA)-mediated host defence pathways, respectively.

DEVELOPMENT OF INTEGRATED BIOPROCESSING TECHNOLOGIES FOR THE PRODUCTION OF PECTIC OLIGOSACCHARIDES (POS) FROM AGRO-PROCESSING RESIDUES

This research deals with the production of pectic oligosaccharides (POS) from agro-industrial residues, with specific focus on development of continuous cross flow enzyme membrane reactor. Pectic oligosaccharides have recently gained attention due to their prebiotic activity. Lack of information on the continuous production of POS from agro-industrial residues formed the basis for the present study. Four residues i.e sugar beet pulp, onion hulls, pressed pumpkin cake and berry pomace were taken to study their pectin content. Based on the presence of higher galacturonic acid and arabinose (both homogalacturonan and rhamnogalacturonan) in sugar beet pulp and galacturonic acid (only homogalacturonan) in onion hulls, further optimization of different extraction methods of pectin (causing minimum damage to pectic chain) from these residues were done. The most suitable extractant for sugar beet pulp and onion hulls were nitric acid and sodium hexametaphosphate respectively. Further the experiments on the continuous production of POS from sugar beet pulp in an enzyme membrane reactor was initiated. Several optimization experiments indicated the optimum enzyme (Viscozyme) as well as feed concentration (25 g/L) to be used for producing POS from sugar beet pulp in an enzyme membrane reactor. The results highlighted that steady state POS production with volumetric and specific productivity of 22g/L/h and 11 g/gE/h respectively could be achieved by continuous cross flow filtration of sugar beet pulp pectic extract over 10 kDa membrane at residence time of 20 min. The POS yield of about 80% could be achieved using above conditions. Also, in this thesis preliminary experiments on the production and characterization of POS from onion hulls were conducted. The results revelaed that the most suitable enzyme for POS production from onion hulls is endo-polygalacturonase M2. The POS produced from onion hulls were present in the form of DP1 -DP10 in substituted as well as unsubstituted forms. This study clearly demonstrates that continuous production of POS from pectin rich sources can be achieved by using cross flow continuous enzyme membrane reactor.

Modelling and experimental verification of a solar-powered liquid desiccant cooling system for greenhouse food production in hot climates

Experiments and theoretical modelling have been carried out to predict the performance of a solar-powered liquid desiccant cooling system for greenhouses. We have tested two components of the system in the laboratory using MgCl2 desiccant: (i) a regenerator which was tested under a solar simulator and (ii) a desiccator which was installed in a test duct. Theoretical models have been developed for both regenerator and desiccator and gave good agreement with the experiments. The verified computer model is used to predict the performance of the whole system during the hot summer months in Mumbai, Chittagong, Muscat, Messina and Havana. Taking examples of temperate, sub-tropical, tropical and heat-tolerant tropical crops (lettuce, soya bean, tomato and cucumber respectively) we estimate the extensions in growing seasons enabled by the system. Compared to conventional evaporative cooling, the desiccant system lowers average daily maximum temperatures in the hot season by 5.5-7.5 °C, sufficient to maintain viable growing conditions for lettuce throughout the year. In the case of tomato, cucumber and soya bean the system enables optimal cultivation through most summer months. It is concluded that the concept is technically viable and deserves testing by means of a pilot installation at an appropriate location.

Características bioativas, funcionais e efeito protetor do resíduo desidratado de camu-camu (Myrciaria dubia H.B.K. (McVaugh)) sobre doenças degenerativas utilizando modelos in vivo C. elegans

Camu-camu (Myrciaria dubia H.B.K. (McVaugh)) is a native Amazon fruit, recognized worldwide as one of the main natural sources of ascorbic acid. Due to its great acidity, this fruit is generally consumed after processing into juice or as ingredient in food preparations. As a co-product of the camu-camu processing, a significant amount of agroindustrial residue is generated. Despite the studies showing the bioactive value and biological potential of the fruit, few studies have approached the possible processing techniques, transformation and preservation of camu-camu fruits and its agroindustrial pomace. Therefore, the present work has the objective of evaluating two different drying processes applied to camu-camu pomace (peel and seeds with residual pulp), freeze drying and hot air drying, in order to obtain a functional fruit product. This thesis was divided into three stages: the first one shows the studies related to the freeze drying and hot air drying, where we demonstrated the impact of the selected drying techniques on the bioactive components of camu-camu, taking the fresh pomace as the control group. Among the investigated conditions, the groups obtained at 50ºC and 4 m/s (SC50) and 80ºC and 6 m/s (SC80) were selected as for further studies, based on their ascorbic acid final content and Folin-Ciocalteau reducing capacity. In addition to SC50 and SC80, the fresh pomace (RF) and freeze dried (RL) samples were also evaluated in these further stages of the research. Overall, the results show higher bioactive concentration in the RF samples, followed by RL, SC50 and SC80. On the second step of the research, the antioxidant, antimicrobial and antienzymatic activities were evaluated and the same tendency was observed. It was also reported, for the first time in the literature, the presence of syringic acid in dried camu-camu pomace. In the third and final stage of the research, it was investigated the effect of dried camu-camu on aging and neuroprotective disorders, using the in vivo model C.elegans. It was observed that camu-camu extracts were able to modulate important signaling genes relevant to thermal and oxidative stresses (p < 0.05). The polar acid, polar basic and polar neutral fractions obtained from the low molecular extracts of SC50 were able to extend the lifespan of wild type N2 C. elegans in 20% and 13% (p < 0.001). Results also showed that the paralysis induced by the β1-42 amyloid was significantly (p < 0.0001) retarded in CL4176 worms. Similarly, the camu-camu extracts attenuated the dopaminergic induction associated to Parkinson’s disease. Finally, a global analysis of the data presented here reveal that the camu-camu pomace, a co-product obtained from the industrial processing of a native Brazilian fruit, is a relevant natural source of health relevant compounds. This thesis, shows for the first time, the multifunctionality of camu-camu pomace, a natural resource still underexploited for scientific, commercial and technological purposes.

Effects of vermicomposted spent mushroom compost on growing medium characteristics, plant growth, yield and abiotic stress tolerance

Treatment of agricultural biodegradable wastes and by-products can be carried out using composting or vermicomposting, or a combination of both treatment methods, to create a growing medium amendment suitable for horticultural use. When compared to traditional compost-maturation, vermicompost-maturation resulted in a more mature growing medium amendment i.e. lower C/N and pH, with increased nutrient content and improved plant growth response, increasing lettuce shoot fresh and dry weight by an average of 15% and 14%, respectively. Vermicomposted horse manure compost was used as a growing medium amendment for lettuce and was found to significantly increase lettuce shoot and root growth, and chlorophyll content. When used as a growing medium amendment for tomato fruit production, vermicomposted spent mushroom compost increased shoot growth and marketable yield, and reduced blossom end rot in two independent studies. Vermicompost addition to peat-based growing media increased marketable yield by an average of 21%. Vermicompost also improved tomato fruit quality parameters such as acidity and sweetness. Fruit sweetness, as measured using Brix value, was significantly increased in fruits grown with 10% or 20% vermicompost addition by 0.2 in truss one and 0.3 in truss two. Fruit acidity (% citric acid) was significantly increased in plants grown with vermicompost by an average of 0.65% in truss one and 0.68% in truss two. These changes in fruit chemical parameters resulted in a higher tomato fruit overall acceptability rating as determined by a consumer acceptance panel. When incorporated into soil, vermicomposted spent mushroom compost increased plant growth and reduced plant stress under conditions of cold stress, but not salinity or heat stress. The addition of 20% vermicompost to cold-stressed plants increased plant growth by an average of 30% and increased chlorophyll fluorescence by an average of 21%. Compared to peat-based growing medium, vermicompost had consistently higher nutrient content, pH, electrical conductivity and bulk density, and when added to a peat-based growing medium, vermicomposted spent mushroom compost altered the microbial community. Vermicompost amendment increased the microbial activity of the growing medium when incorporated initially, and this increased microbial activity was observed for up to four months after incorporation when plants were grown in it. Vermicomposting was shown to be a suitable treatment method for agricultural biodegradable wastes and by-products, with the resulting vermicompost having suitable physical, chemical and biological properties, and resulting in increased plant growth, marketable yield and yield quality, when used as an amendment in peat-based growing medium.

Unraveling the function of bacterial-type phosphoenolpyruvate carboxylase in vascular plants

Two distinct phosphoenolpyruvate carboxylase (PEPC) isozymes occur in vascular plants and green algae: plant-type PEPC (PTPC) and bacterial-type PEPC (BTPC). PTPC polypeptides typically form a tightly regulated cytosolic Class-1 PEPC homotetramer. BTPCs, however, appear to be less widely expressed and to exist only as catalytic and regulatory subunits that physically interact with co-expressed PTPC subunits to form hetero-octameric Class-2 PEPC complexes that are highly desensitized to Class-1 PEPC allosteric effectors. Yeast two-hybrid studies indicated that castor plant BTPC (RcPPC4) interacts with all three Arabidopsis thaliana PTPC isozymes, and that it forms stronger interactions with AtPPC2 and AtPPC3, suggesting that specific PTPCs are preferred for Class-2 PEPC formation. In contrast, Arabidopsis BTPC (AtPPC4) appeared to interact very weakly with AtPPC2 and AtPPC3, suggesting that BTPCs from different species may have different physical properties, hypothesized to be due to sequence dissimilarities within their ~10 kDa intrinsically disordered region. Recent RNA-seq and microarray data were analyzed to obtain a better understanding of BTPC expression patterns in different tissues of various monocot and dicot species. High levels of BTPC transcripts, polypeptides and Class-2 PEPC complexes were originally discovered in developing castor seeds, but the analysis revealed a broad range of diverse tissues where abundant BTPC transcripts are also expressed, such as the developing fruits of cucumber, grape, and tomato. Marked BTPC expression correlated well with the presence of ~116 kDa immunoreactive BTPC polypeptides, as well as Class-2 PEPC complexes in the immature fruit of cucumbers and tomatoes. It is therefore hypothesized that in vascular plants BTPC and thus Class-2 PEPC complexes maintain anaplerotic PEP flux in tissues with elevated malate levels that would potently inhibit ‘housekeeping’ Class-1 PEPCs. Elevated levels of malate can be used by biosynthetically active sink tissues such as immature tomatoes and cucumbers for rapid cell expansion, drought or salt stressed roots for osmoregulation, and developing seeds and pollen as a precursor for storage lipid and protein biosynthesis.

Nanotechnology in the food industry I: applications

Nanotechnology is a multidisciplinary science that is having a boom today, providing new products with attractive physicochemical properties for many applications. In agri/feed/food sector, nanotechnology offers great opportunities for obtaining products and innovative applications for agriculture and livestock, water treatment and the production, processing, storage and packaging of food. To this end, a wide variety of nanomaterials, ranging from metals and inorganic metal oxides to organic nanomaterials carrying bioactive ingredients are applied. This review shows an overview of current and future applications of nanotechnology in the food industry. Food additives and materials in contact with food are now the main applications, while it is expected that in the future are in the field of nano-encapsulated and nanocomposites in applications as novel foods, additives, biocides, pesticides and materials food contact.

Phosphate Deficiency Induces the Jasmonate Pathway and Enhances Resistance to Insect Herbivory.

During their life cycle, plants are typically confronted by simultaneous biotic and abiotic stresses. Low inorganic phosphate (Pi) is one of the most common nutrient deficiencies limiting plant growth in natural and agricultural ecosystems, while insect herbivory accounts for major losses in plant productivity and impacts ecological and evolutionary changes in plant populations. Here, we report that plants experiencing Pi deficiency induce the jasmonic acid (JA) pathway and enhance their defense against insect herbivory. Pi-deficient Arabidopsis (Arabidopsis thaliana) showed enhanced synthesis of JA and the bioactive conjugate JA-isoleucine, as well as activation of the JA signaling pathway, in both shoots and roots of wild-type plants and in shoots of the Pi-deficient mutant pho1 The kinetics of the induction of the JA signaling pathway by Pi deficiency was influenced by PHOSPHATE STARVATION RESPONSE1, the main transcription factor regulating the expression of Pi starvation-induced genes. Phenotypes of the pho1 mutant typically associated with Pi deficiency, such as high shoot anthocyanin levels and poor shoot growth, were significantly attenuated by blocking the JA biosynthesis or signaling pathway. Wounded pho1 leaves hyperaccumulated JA/JA-isoleucine in comparison with the wild type. The pho1 mutant also showed an increased resistance against the generalist herbivore Spodoptera littoralis that was attenuated in JA biosynthesis and signaling mutants. Pi deficiency also triggered increased resistance to S. littoralis in wild-type Arabidopsis as well as tomato (Solanum lycopersicum) and Nicotiana benthamiana, revealing that the link between Pi deficiency and enhanced herbivory resistance is conserved in a diversity of plants, including crops.