Miracle-dz/UniFAR-FTUs huggingface dataset:
GENETIC IDENTIFICATION OF THE NORTHEASTERN ATLANTIC SPINY SPIDER CRAB AS MAJA BRACHYDACTYLA BALSS, 1922

Abstract The northeastern Atlantic spiny spider crab occurs from the British Islands to Senegal, where it is an important fishery resource. From morphological characters this crab has recently been proposed as a distinct species, Maja brachydactyla, although for commercial purposes it is still considered the same species as its Mediterranean congener M. squinado. We have studied variation at two mitochondrial genes in several crab populations from the Atlantic (putatively M. brachydactyla) and Mediterranean (M. squinado and M. crispata) basins, in order to clarify the taxonomic status of this crab in the northeastern Atlantic and Mediterranean regions. Phylogenetic analysis revealed that each of these three taxa forms a distinct and well-defined clade. While the divergence within each taxon was 0% for 16S and 0-0.3% for COI, divergence between taxa was 0.6-2.5% for 16S and 5.3-8.7% for COI; values that are in the range of the differences observed between other crustacean species. These results confirm the genetic distinctiveness of each taxa and support their designation as different species. Therefore, the Atlantic spider crab should be referred as M. brachydactyla, a fact that should be taken into account for conservation and commercial purposes.
Effect of Dietary Lipid Sources on Production of Leukotriene B by Head Kidney of Channel Catfish Held at Different Water Temperatures

Abstract Separate and combined effects of dietary fatty acids and water temperature on the production of leukotriene B (LTB) by the head kidney of channel catfish Ictalurus punctatus were investigated. Fish were fed semipurified diets containing 7% lipid as beef tallow, corn oil, linseed oil, menhaden oil, or a mixture (1:1:1) of menhaden oil, beef tallow, and corn oil. At 28°C, fish fed corn oil produced the greatest amount of LTB, and fish fed beef tallow produced the least. At 17°C, production of LTB by fish fed the beef tallow diet was again lowest; production of LTB by fish fed the corn oil diet was highest but was not significantly different from that obtained with the mixed-oil or menhaden oil diet. Production of LTB for the other diets was intermediate. This is the first report that the head kidney of channel catfish produces LTB; this production was affected by dietary lipid sources but not by the two water temperatures tested. Production of LTB was not related to weight gain. Moreover, the patte.
Cellulase production by two fungal strains isolated from Taif in Saudi Arabia.

Among 17 fungal isolates isolated from soil of El-hawia, El-hada, El-kaym and Karwa in Taif governorate in Saudi Arabia, two isolates showed high efficacy in producing cellulases enzymes. They were identified to be Alternaria alternata and Aspergillus wentii. Some factors such as carbon and wheat bran as a raw material, nitrogen, pH and incubation temperature were investigated. Results indicated that glucose and cellulose were the most effective as a carbon source while, urea was the best nitrogen source for cellulases production. Initial pH 5.0 and incubation temperatures at 25 or 35oC achieved high cellulases production.
Effect of Temperature, Light, Nutrients and Dehardening on Abscisic Acid Induced Cold Hardiness in Bromus inermis Leyss Suspension Cultured Cells

The effects of culture conditions on abscisic acid (ABA)-induced freezing tolerance were determined in smooth bromegrass (Bromus inermis Leyss cv. Manchar) cell suspension cultures. Bromegrass cultures initiated with 2g fr wt of cells achieved maximum freezing tolerances (greater than —32°C) at 25 to 30°C in the presence of 75 to 100^M ABA. High levels of freezing tolerance induced by ABA were correlated with high growth rates at 25 and 30°C. In control cells, incubation at 10°C induced optimum levels of hardiness with minimal growth. Prolonged exposure (6 weeks) of cells to 3°C, with or without ABA, increased freezing tolerance only by several degrees. Exogenous ABA concentrations greater than IOO^M were not inhibitory to growth. Repeated exposure to ABA, however, retarded growth and made the cells tolerant to temperatures below — 40°C. Removal of ABA from the medium resulted in dehardening of the cells both at 25 and 3°C. Nitrogen had a marginal effect on ABA-induced hardening at 25°C, but inhibited age-dependent hardening of control cell cultures. Light had no effect on the freezing tolerance of cultured cells. Addition of 10% sucrose, 30 min prior to freezing, to bromegrass cells treated with ABA for 4 days increased freezing tolerance more than 15°C. These observations are discussed in relation to the contrasting behaviour of the low temperature and photoperiod dependent cold acclimation of plants.
Gro-mate soil amendment improves growth of greenhouse-grown 'Chardonnay' grapevines

Own-rooted, glasshouse-grown 'Chardonnay' vines ( Vitis vinifera L.) were planted in a sand medium to which was added one of five levels of granular Gro-Mate (GM), a commercial humate (0, 8, 16, 32, 64 g/pot; 0 to 35 g a.i./pot). Two other treatments consisted of weekly (1× W) or twice-weekly (2× W) applications of liquid GM, whose cumulative addition over the 28 weeks of the experiment totaled 6.7 and 13.4 g a.i., respectively. Shoot length responded to increasing level of GM in a predominantly cubic fashion, with 32 g/pot resulting in the longest shoots. Fresh and dry weights of leaves, shoots, and roots, as well as leaf count and area, exhibited increasing linear or quadratic trends in response to increased level of granular GM. GM increased soil organic matter, K, Ca, Mg, Fe, Mn, Cu, Na, and S and also increased petiole Fe and lamina P, K, and Fe. Liquid treatment resulted in lower soil pH, organic matter, bulk density, and Fe and higher soil conductivity, NO3, P, K, Mg, Cu, Zn, Na, and S than the granular treatments, as well as higher petiole and lamina N and K, lower petiole and lamina P, and lower petiole Zn. Compared to the 1× W treatment, the 2× W produced lower soil bulk density and higher P, lower lamina K, Mn, and Fe; lower petiole Mn; and higher petiole Cu. Plant tissues contained extremely high levels of Mn irrespective of treatment, whereas liquid treatments resulted in high soil NO 3 levels. Although liquid GM cannot be recommended for young grapevines under an application regime such as described here, preplant applications of granular GM may have potential for improving growth of young vines in coarse-textured soils. High granular or excessive liquid applications may result in leaf necrosis and retarded growth.
Reconstructing Gene Function and Gene Regulatory Networks in Prokaryotes

The ability of a bacterial cell to respond to a complex environment lies with the network of genetic interactions that process information regarding the state of the cell and its local environment. The object of this study has been to better understand bacterial genetic regulatory networks, which conceptually consist of nodes (the genes) and edges (the interactions between the genes). Two problems are addressed, one focusing on the nodes in the network, the other focusing on the edges. The problem concerning the nodes in the network is that a large fraction of genes from bacteria have an unknown function. Even the most studied microbe, E. coli, still has around 30 percent of its genes uncharacterised. Using phenotype data and genomic data, a method for gene function prediction is improved and implemented in a tool called GeneTrawler. The gene function prediction tool is validated against a number of well studied phenotypes, and successfully predicts the majority of genes known to be involved in each phenotype when the phenotype is well defined. In addition, it can suggest genes that are dependent on a phenotype, but not directly involved. The second problem addressed in this thesis is reconstructing gene networks from DNA microarray data. DNA microarrays can measure the expression levels of thousands of genes simultaneously. Elucidating the topology of biochemical or genetic regulatory networks is a common problem in molecular biology, but piecing together gene regulatory networks with standard molecular methods not only requires significant time and effort, but may also miss the global or modular structure of the network. In addition, different stimuli can substantially change the "wiring" of a network, meaning that understanding how a network functions in time requires a global analysis of its dynamics combined with a detailed fine-grained approach. There has been much interest in the possibility of reconstructing genetic regulatory interactions from microarray data. We investigate the limitations of such reconstruction procedures, in terms of what kinds of networks can (and cannot) be reconstructed. A method of reconstruction is investigated that uses evolutionary computation for "evolving" a population of networks to resemble a target network. The results demonstrate that the topology of gene regulatory network structures can be reconstructed from time series data if the network displays dynamics of a particular category where negative feedback loops determine the dynamical behaviour of the network.
Can seed characteristics or species distribution be used to predict the stratification requirements of herbs in the Australian Alps

The germination requirements of 19 herbs in the Australian Alps were investigated to determine which species may be sensitive to predicted climate changes. Seeds were subjected to factorial treatments of cold stratification for 0, 4, 8 and 12 weeks, followed by incubation at constant temperatures of 10, 15, 20 and 25 °C and alternating temperatures of 20/5 and 20/10 °C. Germination responses were used to identify stratification-dependent species, to classify dormancy and to determine optimum conditions for laboratory germination. Ordinal logistic regression was used to determine whether the duration of stratification required for ≥ 50% germination could be predicted by seed weight, seed length, embryo : seed ratio or species distribution (latitudinal range, altitudinal range and maximum altitude). The Kruskal–Wallis test was used to determine any significant differences in stratification requirement between endospermic and non-endospermic seeds. Species varied considerably in their response to the treatment combinations, and therefore their dormancy class. No significant predictors of stratification requirement were identified by ordinal logistic regression (P > 0.9); however, there was a significant difference in stratification requirement between endospermic and non-endospermic seeds (P = 0.003). Species with non-endospermic seeds did not require any stratification to germinate well over a range of temperatures, and appear most likely to remain stable or expand in range in response to climate warming. Conversely, the need for ≥ 8 weeks of cold stratification was associated with the presence of endosperm and either a restricted distribution or upland ecotypes of widely distributed species. Alpine species with endospermic seed and a restricted distribution are most likely to contract in range under climate change and would be appropriate to prioritize for ex situ conservation. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172, 187–204.
Linking the physiological parameters of nitrate uptake with root morphology and topology in wheat (Triticum durum) and citrus (Citrus volkameriana) rootstock

The relationships between net nitrate uptake and root morphology and topology were investigated in wheat (Triticum durum Desf.) and citrus (Citrus volkameriana Ten. & Pasq.) seedlings in which root systems were modified by supplying different nutrient concentrations. Root morphological and topological changes were assessed by the number of root tips, the total root length, and the topological index. The net nitrate uptake process was evaluated during the induction and inhibition "feedback" regulation phases. In wheat seedlings, an increase in the external nitrate concentration, at either high or no phosphate, brought about an increase in number of root tips but did not affect total root length. A similar pattern was observed in citrus seedlings. Citrus seedlings also exhibited a shift in root branching pattern from herringbone to dichotomous with an increase in the external nitrate concentration. Conversely, wheat root topology was unaffected by nutrient treatments. A high level of nitrate supplied to whe.
EMERGÊNCIA E CRESCIMENTO INICIAL DA CANAFÍSTULA EM DIFERENTES SUBSTRATOS E MÉTODOS DE SUPERAÇÃO DE DORMÊNCIA

Objetivou-se com o presente trabalho avaliar a influencia de diferentes metodos de superacao de dormencia e tipos de substratos na emergencia e crescimento inicial de plântulas de canafistula (Peltophorum dubium (Spreng.) Taub. ). O experimento foi conduzido em delineamento de blocos casualizados no esquema fatorial 5x4, sendo cinco substratos, Bioplant®; 75% Bioplant® + 25% bagaco de cana-de-acucar (75B+25BC); 50% Bioplant® + 50% bagaco de cana-de-acucar (50B+50BC); 25% Bioplant® + 75% bagaco de cana-de-acucar (25B+75BC); bagaco de cana-de-acucar (100%) e quatro metodos de superacao de dormencia (testemunha, escarificacao mecânica com o uso de lixa, imersao em agua quente e escarificacao com acido sulfurico concentrado) com tres repeticoes de 12 sementes. Avaliaram-se o indice de velocidade de emergencia; tempo medio de emergencia; percentagem de emergencia aos 7, 14 e 28 dias apos a semeadura; massa seca da parte aerea e massa seca de raiz. A imersao em agua quente e a escarificacao quimica com acido sulfurico (98%) sao metodos eficientes para superacao de dormencia tegumentar em sementes de canafistula. Os substratos Bioplant® e 75B+25BC proporcionam crescimento inicial superior das plântulas.
Effects of an early application of sulphur or etephon as foliar spray on the growth and yield of spring barley in a Mediterranean environment

Leaf area development, biomass production and yield of four spring barley varieties grown in a Mediterranean environment (southern Spain) in response to an early application of foliar sulphur or etephon have been studied. Both sulphur and etephon produced similar results compared to the control. Thus, whereas the maximum leaf area index on untreated plots was reached at the beginning of shooting, the growth of foliar area in the treated ones was extended until anthesis and its decline during maturity was similarly retarded. This led to a significant improvement in the biomass at anthesis (which was closely correlated with grain yield) as well as in the leaf area duration during grain filling. These effects were principally due to variations in the number of leaves per plant, caused by a higher tiller production in the treated plants and not by an increase in the number of leaves per tiller or by leaf size. An application of sulphur or etephon at tillering increases grain yield by raising both the number of ears per plant and per plot, without modifying the number of grains per ear or 1000-grain weight. The similarity between the effects of sulphur and etephon may be due to the fact that sulphur absorbed by the leaves results in an increase in methyonine, the biological precursor or ethylene. The positive correlation between biomass at anthesis and number of ears over grain yield suggests that sink capacity and source activity are closely related and both simultaneously limited by the environment.
Expression of the Mucosal Homing Receptor α4β7 Correlates with the Ability of CD8+ Memory T Cells To Clear Rotavirus Infection

ABSTRACT The integrin α4β7 plays an important role in lymphocyte homing to mucosal lymphoid tissues and has been shown to define a subpopulation of memory T cells capable of homing to intestinal sites. Here we have used a well-characterized intestinal virus, murine rotavirus, to investigate whether memory/effector function for an intestinal pathogen is associated with α4β7 expression. α4β7hi memory phenotype (CD44hi), α4β7 −memory phenotype, and presumptively naive (CD44lo) CD8+ T lymphocytes from rotavirus-infected mice were sorted and transferred into Rag-2 (T- and B-cell-deficient) recipients that were chronically infected with murine rotavirus. α4β7 hi memory phenotype CD8+ cells were highly efficient at clearing rotavirus infection, α4β7 − memory cells were inefficient or ineffective, depending on the cell numbers transferred, and CD44lo cells were completely unable to clear chronic rotavirus infection. These data demonstrate that functional memory for rotavirus resides primarily in memory phenotype cells that display the mucosal homing receptor α4β7.
Investigating the mechanism of cystogenesis in TSC and ADPKD

Tuberous sclerosis complex (TSC) is characterised by the development of benign growths across the body and is caused by mutations in TSC1 or TSC2. The TSC gene products have an established role in the regulation of mammalian target of Rapamycin (mTOR) signalling. Clinical trials are underway for the treatment of TSC- associated tumours using mTOR inhibitors. Here, we show that many of the earliest renal lesions from Tsc1+, and Tsc2+/' mice (cysts) do not exhibit mTOR activation, suggesting alternative pathways should be targeted to prevent tumour formation. Patients with TSC often develop renal cysts (derived from dilated tubules) and those with inherited co-deletions of the autosomal dominant polycystic kidney disease (ADPKD) gene 1 (PKD1) develop severe, early onset polycystic kidneys. Using mouse models, we have shown that the Tsc and Pkd1 gene products are required for correct cell polarisation during renal tubule and bile duct elongation. When polarity is disrupted in Tsc1+I', Tsc2+, and Pkd1+' mice, we found significant alterations in the length of primary cilia projecting from pre-cystic tubule and duct cells (consistent with the highly polar nature of this organelle). The primary cilium is proposed to facilitate many signalling events and provides a mechanosensory input into renal tubule cells. Despite widespread defects in cell polarity and primary cilia in the developing kidney of a Tsc1+I , Tsc2+/ or Pkd1+I' mouse, we found no evidence of tubule dilation, occlusion or cyst formation until around 3-6 months of age. On the basis of this delay period, combined with our data showing significantly higher levels of cleaved caspase-3 in pre-cystic renal tubules from these mice, we suggest that apoptosis destroys these misaligned cells to protect against cyst formation. We found that almost all cysts without mTOR-activation failed to stain for cleaved caspase-3, and therefore sought activation of a pro-survival pathway. There was strong upregulation of Bcl2 in mTOR inactive cysts that were not undergoing apoptosis, suggesting this was the mediator of survival in our cysts. In cysts without activation of mTOR or apoptosis, we found significant activation of Jak2 and its downstream target Stat3. We finally sought gain-of-function mutations in this pathway, and found several somatic Jak2 mutations with likely oncogenic potential in Tsc-associated cysts. These data suggest that defective cell polarity in the context of abnormal Jak2 signalling can drive Tsc-associated cystogenesis in the absence of mTOR dysregulation and targeting of this pathway may be of key therapeutic benefit.
Cellular and Biochemical Regulation of Cdc25A Phosphatase by Nitrosative Stress

Numerous reports correlate nitric oxide (•NO) production with stalled S-phase progression, but the molecular mechanism(s) of cell cycle arrest remains elusive. Paradoxically numerous human tumors are exposed to vast quantities of nitric oxide and its reactive byproducts in situ, yet they continue to grow and proliferate. The dual-specificity phosphatase Cdc25A promotes cell cycle progression by dephosphorylating and activating cyclin-dependent kinases. Deregulation of Cdc25A is characteristic of human tumors, accelerates the cell cycle, and confers resistance to apoptosis, highlighting the importance of stringent Cdc25A control. Biochemical and structural analyses of Cdc25A indicate the potential for inhibition by S-nitrosation of the catalytic cysteine, providing a linkage between •NO and cytostatic signaling. Thus, the overall hypothesis examined in this dissertation was that Cdc25A is a target and transducer of signaling by •NO and •NO-derived reactive species. The specific aims were to: 1) probe the susceptibility of Cdc25A to enzymatic regulation by •NO-derived reactive species; 2) examine regulation of Cdc25A protein in nitrosatively challenged cells; and 3) determine whether Cdc25A activity was limiting for S-phase progression in nitrosatively-challenged tumor cells. My studies identified novel mechanisms controlling Cdc25A abundance and activity. S-Nitrosothiols rapidly S-nitrosated and inactivated Cdc25A in vitro, and Cdc25A activity was restored by reductants. Generation of nitrosative stress in cells either by iNOS-derived •NO or the cell-permeable S-nitrosating agent S-nitrosocysteine ethyl ester (SNCEE) caused translational inhibition of Cdc25A via hyperphosphorylation and inhibition of the eukaryotic translational regulator eIF2a. Although iNOS-derived •NO and SNCEE inhibited DNA synthesis coincident with Cdc25A loss, restoration of Cdc25A activity in nitrosatively-challenged cells did not alter DNA synthesis inhibition, distinguishing nitrosative inhibition of DNA synthesis from the canonical intra-S-phase checkpoint. SNCEE decoupled Cdc25A from ASK-1 and sensitized cells to chemotherapeutic-induced apoptosis, suggesting that Cdc25A suppression by nitrosative stress may lower the apoptotic threshold in nitrosatively-challenged cells by priming ASK-1 for activation. In summary, these studies describe novel regulation of Cdc25A translation and activity, and a model wherein selective inhibition of Cdc25A phosphatase-dependent and independent activities can occur under nitrosative stress, and implicate Cdc25A as a regulator of apoptotic threshold following nitrosative insult via priming of ASK-1.
Responses of stream macroinvertebrates and ecosystem function to conventional, integrated and organic farming

Summary 1. Organic farming practices can benefit a wide range of terrestrial biota in comparison to conventional farming but we do not know whether this benefit extends to streams flowing through farmed landscapes. 2. We measured the impacts of organic, integrated management and conventional farming on the taxonomic and trait composition of macroinvertebrate communities and on stream ecosystem functioning (algal accrual on tiles and leaf breakdown). Our study design included five replicates of each farming practice, arranged in blocks, in agricultural land dedicated to the farming of sheep and beef cattle on pasture in southern New Zealand. In each farm stream, we studied both upstream and downstream reaches within the farm’s boundaries. 3. The different farming practices were reflected in contrasting stream physicochemistry (total dissolved nitrogen, fine sediment on the bed and glyphosate concentrations in the bed sediment) and in differences in both the taxonomic organization and trait representation of stream invertebrate communities. Conventional farm streams showed the strongest negative responses, whilst the condition of organic and integrated farm streams was similar. 4. Invertebrate trait measures proved as effective as taxonomic measures in their response to agricultural intensity, whereas ecosystem function measures were least sensitive. 5. There were no overall physicochemical differences between upstream and downstream sites within the farms and few notable longitudinal patterns in ecological response variables. 6. Synthesis and applications. Conventional farming had the strongest adverse consequences for stream condition in our study. In contrast, an integrated management system (aimed at reducing pesticide use, increasing beneficial pest predators and encouraging environmentally responsible soil, water and energy management) proved at least as effective as organic farming and, together with organic farming, can be considered better practice.