Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of saline irrigation on yield and qualitative characterization of seed of an amaranth accession grown under Mediterranean conditions

SUMMARY Yield responses of a grain amaranth accession to different irrigation strategies were evaluated in Naples, Italy. Field experiments were carried out to evaluate the quantitative and qualitative response of amaranth under combined abiotic stresses (salinity and drought) in a Mediterranean environment of South Italy affected by problems due to groundwater salinization from seawater intrusion. A comparison was made in 2009 and 2010 between a fully irrigated treatment (1·00), with the restitution of all of the water necessary to replenish to field capacity the soil layer explored by roots (0·00–0·36 m), and two treatments with restitution of 0·50 and 0·25 of the water volume used for the fully irrigated treatment. The three levels of irrigation volume were combined with two levels of salinity, either fresh or salt water, with electrical conductivity (EC) of the irrigation water of 0·64 and 22 dS/m respectively, in a factorial experiment thus harbouring six treatments in a randomized complete block design. The results showed good adaptation of amaranth to drought. It was possible to obtain high yields even if groundwater with infiltrated seawater was used for irrigation (50% yield reduction when the EC of soil saturated paste extract (ECe) was 13·97 dS/m). A reduction of 50% in the volume of irrigation did not cause a significant reduction in yield, whether using fresh or saline water, compared to the treatment fully irrigated with fresh water. The chemical composition of amaranth seeds, however, was significantly affected by the treatments. Starch and ash content decreased with increasing drought while protein content was increased by both salt and drought. In view of the increased presence of salinity and drought stress in the Mediterranean area and the scarce information on amaranth response to salt and water stress, the aim of the present work is evaluation of the quantitative and qualitative response of amaranth grown in a Mediterranean environment of South Italy under combined drought and salinity stress.
Patterns and complexity in biological systems: a study of sequence structure and ontology-based networks

Biological information can be explored at many different levels, with the most basic information encoded in patterns within the DNA sequence. Through molecular level processes, these patterns are capable of controlling the states of genes, resulting in a complex network of interactions between genes. Key features of biological systems can be determined by evaluating properties of this gene regulatory network. More specifically, a network-based approach helps us to understand how the collective behavior of genes corresponds to patterns in genetic function. We combine Chromatin-Immunoprecipitation microarray (ChIP-chip) data with genomic sequence data to determine how DNA sequence works to recruit various proteins. We quantify this information using a value termed "nmer-association. " "Nmer-association" measures how strongly individual DNA sequences are associated with a protein in a given ChIP-chip experiment. We also develop the "split-motif" algorithm to study the underlying structural properties of DNA sequence independent of wet-lab data. The "split-motif" algorithm finds pairs of DNA motifs which preferentially localize relative to one another. These pairs are primarily composed of known transcription factor binding sites and their co-occurrence is indicative of higher-order structure. This kind of structure has largely been missed in standard motif-finding algorithms despite emerging evidence of the importance of complex regulation. In both simple and complex regulation, two genes that are connected in a regulatory fashion are likely to have shared functions. The Gene Ontology (GO) provides biologists with a controlled terminology with which to describe how genes are associated with function and how those functional terms are related to each other. We introduce a method for processing functional information in GO to produce a gene network. We find that the edges in this network are correlated with known regulatory interactions and that the strength of the functional relationship between two genes can be used as an indicator of how informationally important that link is in the regulatory network. We also investigate the network structure of gene-term annotations found in GO and use these associations to establish an alternate natural way to group the functional terms. These groups of terms are drastically different from the hierarchical structure established by the Gene Ontology and provide an alternative framework with which to describe and predict the functions of experimentally identified groups of genes.
Preference-performance relationships in herbivorous insects feeding on oilseed rape inoculated with soil-borne fungi

There is increasing evidence that plant-associated microorganisms are able to mediate plant-herbivorous insects-interactions. In this study, I evaluated the impact of two plant colonising fungi on three herbivorous insect species, using mycological, entomological and plant biochemistry techniques. In detail, my research focused on the mediation of two soil-borne fungi, the endophyte Acremonium alternatum and the fungal plant pathogen Verticillium longisporum on the preference and performance of three herbivorous insects with different feeding modes, Delia radicum L. (Diptera: Anthomyiidae), Plutella xylostella L. (Lepidoptera: Plutellidae) and Brevicoryne brassicae L. (Hemiptera: Aphididae). Two different cultivars of oilseed rape (Brassica napus and Brassica napus var.) were used. Host-preference of the herbivorous insects was tested by using mechanically damaged and intact plants either with endophyte infection (E+) or controls (E-) and plants inoculated with Verticillium (V+) or control (V-). Performance of insect feeding on infected /uninfected plants was evaluated by recording mortality of larvae, development time, pupal weight and fecundity. A field experiment was implemented to test the impact of endophyte inoculations on insect preference/performance relationships with regard to cabbage aphid population dynamics. Volatiles released from aerial plant part of infected or control plants were collected and analyzed qualitatively and quantitatively to explain host preference of adult herbivorous insects. The content and relative composition of four typical phytosterols, namely Sitosterol, Campesterol, Brassicasterol and Stigmasterol was quantified from the leaves and roots of infected and control plants to understand mechanisms of a fungal infection on insect performance.The results of the experiments can be summarized as follows:
MEKK1 activates both IκB kinase α and IκB kinase β

A critical step in the signal-induced activation of the transcription factor NF-κB is the site-specific phosphorylation of its inhibitor, IκB, that targets the latter for degradation by the ubiquitin–proteasome pathway. We have previously shown that mitogen-activated protein kinase/ERK kinase kinase 1 (MEKK1) can induce both this site-specific phosphorylation of IκBα at Ser-32 and Ser-36 in vivo and the activity of a high molecular weight IκB kinase complex in vitro. Subsequently, others have identified two proteins, IκB kinase α (IKK-α) and IκB kinase β (IKK-β), that are present in a tumor necrosis factor α-inducible, high molecular weight IκB kinase complex. These kinases are believed to directly phosphorylate IκB based on the examination of the kinase activities of IKK immunoprecipitates, but more rigorous proof of this has yet to be demonstrated. We show herein that recombinant IKK-α and IKK-β can, in fact, directly phosphorylate IκBα at Ser-32 and Ser-36, as well as homologous residues in IκBβ in vitro, and thus are bona fide IκB kinases. We also show that MEKK1 can induce the activation of both IKK-α and IKK-β in vivo. Finally, we show that IKK-α is present in the MEKK1-inducible, high molecular weight IκB kinase complex and treatment of this complex with MEKK1 induces phosphorylation of IKK-α in vitro. We conclude that IKK-α and IKK-β can mediate the NF-κB-inducing activity of MEKK1.
Reduction of soil-borne plant pathogens using lime and ammonia evolved from broiler litter.

In laboratory and micro-plots simulations and in a commercial greenhouse, soil ammonia (NH3) and pH were manipulated as means to control soil-borne fungal pathogens and nematodes. Soil ammonification capacity was increased by applying low C/N ratio broiler litter at 1–8% (w/w). Soil pH was increased using lime at 0.5–1% (w/w). This reduced fungi (Fusarium oxysporum f. sp. dianthi and Sclerotium rolfsii) and root-knot nematode (Meloidogyne javanica) in lab tests below detection. In a commercial greenhouse, broiler litter (25 Mg ha−1) and lime (12.5 Mg ha−1) addition to soil in combination with solarization significantly reduced M. javanica induced root galling of tomato test plants from 47% in the control plots (solarization only) to 7% in treated plots. Root galling index of pepper plants, measured 178 days after planting in the treated and control plots, were 0.8 and 1.5, respectively, which was statistically significantly different. However, the numbers of nematode juveniles in the root zone soil counted 83 and 127 days after pepper planting were not significantly different between treatments. Pepper fruit yield was not different between treatments. Soil disinfection and curing was completed within one month, and by the time of bell-pepper planting the pH and ammonia values were normal.
Quality preservation of salted, vacuum packaged and refrigerated mahi sefid (Rutilus frisii kutum) fillets using an onion (Allium cepa) extract

The combined effect of light salting, vacuum packaging and onion extract on the shelf life of mahi sefid (Rutilus frisii kutum) fillets under refrigeration was assessed using chemical, microbiological and sensory methods. The shelf life of control, air-packaged, salted (APS), vacuum-packaged, salted (VPS) and vacuum-packaged, salted with onion extract (VPSOE) samples was determined to be up to 6, 9, 15 and 18 days respectively. The values of total volatile basic nitrogen, free fatty acid and thiobarbituric acid increased progressively during the storage period for all the treatments. However, the preservative methods applied led to an extended shelf life of fillets based on chemical indices and sensory attributes in the following order: VPSOE>VPS>APS>control group. The assay of the total viable count (TVC) revealed that 2% and 4%VPSOE produced a decrease in TVC throughout the storage period. According to the results obtained, the best method to preserve the mahi sefid fillet was by 4%VPSOE treatment.
Low‐molecular‐weight carbohydrates in some salt‐stressed plants

A study was made of the effects of salinity on the concentrations of free sugars, glycinebetaine, proline and other chemical components of Aster tripolium L. , Daucus carota L. , Honkenya peploides (L.) Ehr. and Plantago coronopus L. (Dicotyledones); and Carex extensa Good. , Eleocharis uniglumis (Link) Schutt. , Juncus maritima Lam. and Schoenoplectus tabernaemontani (C. C. Gmel.) Palla (Monocotyledones) grown in the laboratory. In Plantago coronopus the level of the polyol sorbitol increased when the plants were subjected to NaCl stress, while in Honkenya peploides the cyclitol pinitol accumulated. No consistent pattern emerged with respect to the changes in free sugar contents in either the monocotyledonous or dicotyledonous plants, though the monocotyledonous plants generally had higher sugar contents.
Effects of pre-rigour filleting on quality aspects of Atlantic cod (Gadus morhua L.)

Aquaculture is promising in increasing the amount of fresh Atlantic cod available all year around. The aim of this study was to investigate the effects of pre-rigour filleting on fillet quality of wild and farmed cod. Pre-rigour filleting resulted in significantly less fillet gaping than in fillets produced post rigour. The pre-rigour fillets were, however, 12–13% shorter post rigour. In spite of the significantly lower water content of the muscle 6 days post mortem, a significantly higher liquid loss was seen in the pre-rigour group. Differences in gaping score and muscle pH were dependent on whether the fish were wild or fed. Fillet gaping increased with storage time and was particularly pronounced for well-fed cod. Fed cod had a significantly higher hydroxyproline (Hyp) content and significantly lower amount of glycosaminoglycans (GAGs) than wild cod. The ratio between GAGs and Hyp was thus significantly lower in fed cod. A connection between connective tissue components and fillet gaping may exist. However, further investigations are required.
Biosynthesis of the cyclohexanecarboxylic acid starter unit of .omega.-cyclohexyl fatty acids in Alicyclobacillus acidocaldarius

The formation of the cyclohexanecarboxylic acid starter unit of ω-cyclohexyl fatty acids from shikimic acid in Alicyclobacillus acidocaldarius (formerly Bacillus acidocaldarius) has been studied. Feeding experiments with 13 C- and 2 H-labeled samples of shikimic acid and potential intermediates in the wild type and two blocked mutants demonstrated that the formation of cyclohexanecarboxylic acid in this organism follows the same pathway as in Streptomyces collinus (J. Am. Chem. Soc., preceding paper in this issue). (1S,3S)-3-Hydroxycyclohexanecarboxylic acid (20) is accumulated by blocked mutant 2, indicating that 5-hydroxycyclohex-1-enecarboxylic acid (6) is first reduced to the hydroxy acid 20 and then dehydrated to 2-cyclohexenecarboxylic acid (8)
Environmental impact of the establishment of exotic prawn pathogens in Australia

This study was commissioned by the Australian Quarantine and Inspection Service (AQIS) to evaluate the potential impact on the natural environment of the establishment of exotic prawn diseases, using White Spot Syndrome Virus (WSSV) and Infectious Hypodermal and Hematopoietic Necrosis Virus (IHHNV) as examples.
Ambulacral growth allometry in edrioasteroids: functional surface-volume change in ontogeny and phylogeny

McKinney, M. L. & Sumrall, C. D. 2010: Ambulacral growth allometry in edrioasteroids: functional surface-volume change in ontogeny and phylogeny. Lethaia, Vol. 44, pp. 102–108. Most organisms do not maintain geometric similarity as they grow, in large part because of surface-volume interactions. Because respiratory and food-acquiring organs are dependent on surface area, which increases more slowly than volume, organisms have evolved many strategies to increase the efficiency of, and/or the functional surface areas of these organs. Here, we report some preliminary results comparing area of the feeding apparatus (ambulacra) versus the volume of the theca for a suite of isorophid edrioasteroid species at various ontogenetic sizes. Regression of log (ambulacral area) on log (thecal volume) indicates a strongly constrained allometric pattern whereby the ontogenies of all measured species fall on or near the same line (r2 = 0.962, n = 55), with a slope (k) = 0.654 (± 0.018). This slope and associated 0.05 standard error (0.618–0.690) is within the bounds of that expected from increasing surface area to keep pace with the metabolic demands of increasing thecal size. This allometric value is also comparable to the size scaling of metabolism and respiratory and feeding surfaces in many living and a few fossil invertebrates (k ∼ 0.5–0.9). The edrioasteroid species analysed show a very wide variety of changes in ambulacral length, width and sinuosity, documenting many different patterns for achieving the same goal of increasing surface area to keep pace with volume increase. There is no evidence of increasing feeding efficiency. □Edrioasteroid, allometry, ambulacrum, surface-volume, echinoderm.
Investigating microbial community structure in soils by physiological, biochemical and molecular fingerprinting methods

Several biochemical and molecular methods are used to investigate the microbial diversity and changes in microbial community structure in rhizospheres and bulk soils resulting from changes in management. We have compared the effects of plants on the microbial community, using several methods, in three different types of soils. Pots containing soil from three contrasting sites were planted with Lolium perenne (rye grass). Physiological (Biolog), biochemical (PLFA) and molecular (DGGE and TRFLP) fingerprinting methods were employed to study the change in soil microbial communities caused by the growth of rye grass. Different methods of DNA extraction and nested PCR on TRFLP profiles were examined to investigate whether they gave different views of community structure. Molecular methods were used for both fungal and bacterial diversity. Principal component analysis of Biolog data suggested a significant effect of the plants on the microbial community structure. We found significant effects of both soil type and plants on microbial communities in PLFA data. Data from TRFLP of soil bacterial communities showed large effects of soil type and smaller but significant effects of plants. Effects of plant growth on soil fungal communities were measured by TRFLP and DGGE. Multiple Procrustes analysis suggested that both methods gave similar results, with only soil types having a significant effect on fungal communities. However, TRFLP was more discriminatory as it generated more ribotype fragments for each sample than the number of bands detected by DGGE. Neither methods of DNA extraction nor the nested PCR had any effect on the evaluation of soil microbial community structure. In conclusion, the different methods of microbial fingerprinting gave qualitatively similar results when samples were processed consistently and compatible statistical methods used. However, the molecular methods were more discriminatory than the physiological and biochemical approaches. We believe results obtained from this experiment will have a major impact on soil microbial ecology in general and rhizosphere–microbial interaction studies in particular, as we showed that the different fingerprinting methods for microbial communities gave qualitatively similar results.
SUPPRESSION OF N-NITROSODIETHYLAMINE INDUCED OXIDATIVE RENAL TOXICITY BY SULPHATEDPOLYSACCHARIDE AND AQUEOUS EXTRACT OF ULVA LACTUCA IN RATS

Objective: The ancient tradition habits of consuming seaweeds in Asian and Middle East countries have been made a key part of their diet, and as an antioxidant, sulphated polysaccharides have made a large number of researches as one of the ocean's greatest treasures. Therefore, the scope of the present study was conducted to investigate the chemopreventive actions of sulphated polysaccharides and aqueous extract of Ulva lactuca on N-nitrosodiethylamine (NDEA) promoted by phenobarbital (PB) induced renal toxicity in male albino rats. Methods: Adult male albino rats were divided into four groups. Group B received a single dose of NDEA intra peritonealy (200 mg/kg body weight) for 2, 12 and 24 weeks to induce renal toxicity. Groups (C& D) simultaneously received (50 mg/kg body weight) sulphated polysaccharides and aqueous extract of U. lactuca , respectively by oral gavage. Further, the B, C& D groups received PB (0.05%) in drinking water after two weeks of NDEA administration along the entire period of study. Saline (0.9%) treated control group (A) was also built-in. Several In vivo enzymatic antioxidant defense system like superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), glutathione-s-transferase (GST), myeloperoxidase (MPO), and non-enzymatic system like reduced glutathione (GSH) were evaluated to determine the reno-protective and antioxidant activity of U. lactuca extracts. The oxidative stress markers like lipid peroxidation (LPO) and nitric oxide (NOx) were also investigated as the products of NDEA metabolism. Results : NDEA followed by PB provoked renal and nephrotoxicity was evident from the decreased activity of almost antioxidant enzymes (SOD, CAT, GST, GR and MPO) and increased oxidants (LPO & NOx) in renal tissues. A significant rise in the levels of malondialdehyde (MDA) throughout the entire period of study along with the striking decline of the above enzymic and non-enzymic antioxidants marks the severity of oxidative stress in NDEA-induced rats. However, concomitant treatment with sulphated polysaccharides restored the above antioxidant enzyme levels in the kidneys near to normal better than the aqueous extract, and exhibited a significant dose dependent protective effect against NDEA induced nephrotoxicity, which might be attributed to the antioxidant properties of the extracts. Conclusion : The present study provides evidence, for the first time, that sulphated polysaccharides exert a chemoreceptive significant effect on NDEA-initiated nephrotoxicity through induction of apoptosis. In addition, the restoration effect of enzymic and non-enzymic antioxidant to their normal levels. The study justified the ethno-medicinal use of sulphated polysaccharide extract for protection against renal toxicity.
On the biology of potato tuber worm, Phthorimaea operculella Zeller (Lepidoptera, Gelechiidae)

The larval diet for the potato tuberworm, Ph. operculella, proved to have a profound effect on the duration and weight of larvae and pupae as well as on the percentage of moth emergence. The shortest periods, the heaviest weights of larvae and pupae and the highest percentage of moth emergence occurred when potato tubers were offered as food. With the same diet, adults of both sexes lived longer and females laid higher number of eggs and relatively longer oviposition periods than those offered potato or tomato leaves. Zusammenfassung Zur Biologie der Kartoffelmotte Phthorimaea operculella Zeller (Lep., Gelechiidae). I. Wirkung der Nahrung Die Nahrungskomponente hat fur P. operculella tiefgreifende Wirkungen auf die Entwick-lungsdauer und das Gewicht der Larven und Puppen sowie auf die Schlupfrate der Falter. Die Kurzeste Entwicklung, die huchsten Larven- und Puppengewichte und die groste Schlupfrate wurden nach Ernahrung der Raupen mit Kartoffelknollen festgestellt. Bei der gleichen Nahrung lebten die Falter beiderlei Geschlechts langer und war die Zahl der abge-legten Eier pro Weibchen hoher sowie die Eiablageperiode ausgedehnter als nach Fras der Larven an Kartoffel- und Tomatenblattern.
The biosynthesis of cyclopropane fatty acids. II. Mechanistic studies using methionine labelled with one, two, and three deuterium atoms in the methyl group

The mechanism of formation of monodeuterated cyclopropane fatty acids on administration of L-methione-methyl-d3 to L. plantarum has been investigated. It has been found that the extent of exchange is not affected by the presence of oxygen in the medium, that neither formate-d0 nor formaldehyde-d2 is significantly incorporated into the fatty acid, and that methionine reisolated from the intracellular pool does not contain any exchanged species. These experiments militate against any mechanism involving exchange prior to methyl group transfer. Parallel feeding experiments using methionine labelled in the methyl group with one, two, or three deuterium atoms were carried out and in this way that extent of exchange was quantitated. It was found that at least one-third of the cyclopropane fatty acid from methionine methyl-d3 experiments is derived from an exchanged methyl group. The intramolecular and intermolecular primary deuterium isotope effects for biological cyclopropane ring formation were measured and f.