Miracle-dz/UniFAR-FTUs huggingface dataset:
Rhizosphere competence of Pseudomonas sp. NBRI9926 and Rhizobium sp. NBRI9513 involved in the suppression of chickpea (Cicer arietinum L.) pathogenic fungi

In order to obtain chickpea (Cicer arietinum L.) rhizosphere-competent bacteria, 256 bacterial strains, representing different morphological types, were screened for their biocontrol activity against Fusarium oxysporum f.sp. ciceri, Rhizoctonia bataticola and Pythium sp. under in vitro conditions. Pseudomonas sp. NBRI9926 and Rhizobium sp. NBRI9513 were selected for further work because of their unique ability to inhibit all three fungi. Spontaneous rifampicin-resistant (Rifr) derivatives of Pseudomonas sp. NBRI9926 and Rhizobium sp. NBRI9513 showing a growth rate and membrane protein composition comparable to the wild-type were selected to elucidate their rhizosphere competence on chickpea. Both strains showed no difference to their corresponding wild-type strains in terms of chickpea rhizosphere competence. However, when Pseudomonas sp. NBRI9926P3 was mixed in an equal or lower ratio with Rhizobium sp. NBRI9513R7, both in sterile soil and non-sterile soil assays, Rhizobium sp. NBRI9513R7 consistently failed to achieve titres similar to Pseudomonas sp. NBRI9926P3. These results suggest that antibiotic resistance-marked strains should be compared with wild-type parents before being used as monitors of parental strain survival. Pseudomonas sp. NBRI9926P3 was a better chickpea rhizosphere coloniser compared to Rhizobium sp. NBRI9513R7. Greenhouse results demonstrated a superior biocontrol potential of Pseudomonas sp. NBRI9926P3 to control F.oxysporum f.sp. ciceri, R.bataticola and Pythium sp. compared to Rhizobium sp. NBRI9513R7. The screening method should prove useful in identifying rhizosphere bacteria with the greatest potential for controlling diseases caused by phytopathogenic fungi.
Trophic triangles and competition among vertebrate (Oncorhynchus nerka, Gasterosteus aculeatus) and macroinvertebrate (Neomysis mercedis) planktivores in Muriel Lake, British Columbia, Canada

ABSTRACT We investigated whether pelagic food web dynamics, expressed through a trophic triangle, could influence the potential success of whole-lake fertilization to enhance juvenile sockeye salmon growth. Muriel Lake (145 ha), located on Vancouver Island, was fertilized during 1984 with no apparent effect on juvenile sockeye growth. Unlike most sockeye nursery lakes, Muriel Lake contains a substantial population of the invertebrate zooplanktivore Neomysis mercedis. We hypothesized that competition for zooplankton prey between Neomysis and planktivorous fish (juvenile sockeye, threespine stickleback) could counteract beneficial effects of either natural or fertilizer-induced increases in food for fish. To test this, we assessed (1985–1986) biomass, production, and consumption of planktivorous mysids and fish and then used bioenergetics models to quantify potential competitive interactions. Our analysis suggested that N. mercedis consumed 7–8% of the zooplankton standing stock per day, while planktivorous fish consumed <1.0%·d−1. Although mysids were the main consumers of zooplankton, mysids were also consumed by fish. Late in 1986, an increase in mysid consumption by large, 1+ juvenile sockeye precipitated substantial declines in Neomysis biomass. Although this event came too late to reduce mysid competition with sockeye fry in Muriel Lake in 1986, it did highlight the potential importance of trophic triangles in pelagic food webs. We suggest that mysids may be held in check by juvenile sockeye when exogenous recruitment events result in high sockeye biomass. By contrast, recruitment failures and low sockeye biomass promote increases in Neomysis populations, which then control zooplankton communities such that sockeye gain little benefit from either natural or fertilizer-induced increases of zooplankton. For food web ecologists, the implication is that trophic triangles might produce alternate stable states that are mediated by external factors. For fisheries managers, the implication is that lakes containing mysids should only be fertilized when sockeye densities are high or mysid densities are low.
Stem water storage capacity and efficiency of water transport: their functional significance in a Hawaiian dry forest

We investigated the contribution of internal water storage and efficiency of water transport to the maintenance of water balance in six evergreen tree species in a Hawaiian dry forest. Wood-saturated water content, a surrogate for relative water storage capacity, ranged from 70 to 105%, and was inversely related to its morphological correlate, wood density, which ranged between 0·51 and 0·65 g cm−3. Leaf-specific conductivity (kL) measured in stem segments from terminal branches ranged from 3 to 18 mmol m−1 s−1 MPa−1, and whole-plant hydraulic efficiency calculated as stomatal conductance (g) divided by the difference between predawn and midday leaf water potential (ΨL), ranged from 70 to 150 mmol m−2 s−1 MPa−1. Hydraulic efficiency was positively correlated with kL (r2 = 0·86). Minimum annual ΨL ranged from − 1·5 to − 4·1 MPa among the six species. Seasonal and diurnal variation in ΨL were associated with differences among species in wood-saturated water content, wood density and kL. The species with higher wood-saturated water content were more efficient in terms of long-distance water transport, exhibited smaller diurnal variation in ΨL and higher maximum photosynthetic rates. Smaller diurnal variation in ΨL in species with higher wood-saturated water content, kL and hydraulic efficiency was not associated with stomatal restriction of transpiration when soil water deficit was moderate, but avoidance of low minimum seasonal ΨL in these species was associated with a substantial seasonal decline in g. Low seasonal minimum ΨL in species with low kL, hydraulic efficiency, and wood-saturated water content was associated with higher leaf solute content and corresponding lower leaf turgor loss point. Despite the species-specific differences in leaf water relations characteristics, all six evergreen tree species shared a common functional relationship defined primarily by kL and stem water storage capacity.
Searching for Atlantic cod (Gadus morhua) spawning sites in the northwest Gulf of St Lawrence (Canada) using molecular techniques

Bui, A. O. V. , Castonguay, M. , Ouellet, P., and Sevigny, J-M. 2011. Searching for Atlantic cod (Gadus morhua) spawning sites in the northwest Gulf of St Lawrence (Canada) using molecular techniques. – ICES Journal of Marine Science, 68: 911–918.The overexploitation of Atlantic cod (Gadus morhua) in the Northwest Atlantic led to the collapse of most stocks and the demise of spawning components in the early 1990s. In the northern Gulf of St Lawrence, the spawning component of Northwest Atlantic Fishery Organization Division 4S was believed no longer to exist after the collapse. To verify this hypothesis, we used molecular techniques to identify cod, haddock, and witch flounder (CHW) eggs precisely, in an attempt to locate the potential remaining spawning sites for cod in the northwest Gulf. Ichthyoplankton surveys were conducted in spring from 2005 to 2008. Results were compared with those of surveys that took place in spring in the same area 20 years earlier to determine if there had been any changes in spawning location and egg abundance. Atlantic cod made up the majority (97%) of CHW eggs identified. The presence of stage I cod eggs proved that there is still a cod spawning component in the northwest Gulf of St Lawrence, but egg abundance has declined by about an order of magnitude compared with the 1980s. There was no obvious difference in the location of cod spawning grounds between the two decades.
Análise de desempenho econômico da produção orgânica de leite: estudo de caso no Distrito Federal

Neste trabalho, objetivou-se analisar economicamente a producao orgânica de leite. Para esta avaliacao foram utilizados os dados obtidos em uma propriedade certificada como orgânica, localizada no Distrito Federal, durante os periodos de 2002 e 2003. A Renda Liquida (RL) por litro de leite foi positiva no ano de 2002 e negativa no de 2003, considerando-se o preco do leite a R$ 0,40/ L, (preco historico pago ao produtor de leite convencional na regiao), apresentando resultados positivos com o preco simulado de R$ 0,80/L (preco pago aos produtores orgânicos nas Regioes Sul e Sudeste do pais). Os indices de produtividade foram semelhantes aos observados nas propriedades convencionais. A producao orgânica de leite pode ser uma alternativa economicamente viavel para a pecuaria, desde que haja uma remuneracao superior a praticada para o leite convencional.
Cellular phenology of annual ring formation of Abies balsamea in the Quebec boreal forest (Canada)

Cell formation in growth rings of balsam fir (Abies balsamea (L.) Mill) in the boreal forest was studied to describe the timing of ring formation and the development patterns of earlywood and latewood. Wood micro-cores were extracted during the growing season from 1998 to 2000. The micro-cores were stained with cresyl fast violet to facilitate counting the number of cells in the radial enlargement, wall thickening phases, and mature cell phases. The periods required to complete these various phases were then estimated. Variations in the beginning of the growing season (May 7 - June 7), the earlywood-latewood transition (July 2 - July 19), and the end of the growing season (August 20 - September 20) were observed. Short cell enlargement durations of less than a week for earlywood and 5-10 days for latewood were observed. Time required for cell wall thickening was about 20 days for earlywood and longer than 10-15 days for latewood. A certain flexibility was observed in the ring formation patterns and in the cell development rate, providing an advantage in the boreal forest where optimal growth conditions change from year to year. These findings on the spatial and temporal patterns of ring development may be useful for understanding tree relationships with climate or other environmental parameters. La formation des cellules dans les cernes annuels du sapin baumier (Abies balsamea (L.) Mill. ) en foret boreale a ete etudiee pour decrire la chronologie de la formation des cernes et le developpement du bois initial et final. Des micro-carottes ont ete extraites pendant les saisons 1998 a 2000. Des sections ont ete colorees a l'aide du « cresyl fast violet » pour faciliter le denombrement des cellules dans les phases d'accroissement radial, de formation des parois secondaires et les cellules matures. Le temps requis pour que les cellules pour completent ces phases a ete estime. Des variations dans le debut de la croissance (7 mai au 7 juin), dans la transition du bois initial au bois final (2 juillet au 19 juillet) et dans la fin de la croissance (20 aout au 20 septembre) ont ete observees. De courtes periodes d'accrois sement, de moins d'une semaine pour le bois initial et de 5 a 10 jours pour le bois final ont ete observees. Le temps necessaire a l'epais sissement des parois secondaires etait d'environ 20 jours pour le bois initial et plus de 30 a 35 jours pour le bois final respectivement. Les resultats mettent en evidence une certaine flexibilite dans le developpement des cernes, ce qui procure un avantage en foret boreale ou les conditions optimales de croissance changent d'annees en annees. Ces resultats pourront etre utiles pour mieux comprendre la relation entre les arbres et le climat ou d'autres parametres environnementaux.
Novel Roles for Arginine Modifying Enzymes in Immune Regulation

Arginine modifying enzymes are important transcriptional regulators involved in many cellular processes. Cytokine expression by immune cells is a highly regulated process, since cytokine imbalance is associated with severe pathological consequences including autoimmunity, autoinflammation and asthma. Th2 mediated IL-4 expression is a tightly regulated process. The NFAT interacting protein NIP45 is an essential regulator of IL-4 expression by Th2 cells. Furthermore, NIP45-mediated IL-4 expression is enhanced by arginine methylation of NIP45. Here, I demonstrate that arginine deimination of NIP45 by PAD4 negatively regulates IL-4 expression. PAD4 can deiminate NIP45 both in vitro and in vivo. Overexpression of PAD4 can suppress NIP45-mediated IL-4 expression. Interestingly, the suppressive activity of PAD4 is independent of its catalytic activity. Furthermore, Th2 cells from PAD4-deficient mice that I generated for this thesis display elevated IL-4 secretion. Taken together, I have established that PAD4 is a negative regulator of IL-4 expression. Although PAD4 can deiminate NIP45, the catalytic activity of PAD4 is not required for suppression of NIP45-mediated IL-4 secretion. CARM1 coactivates NFkB-mediated transcription of several proinflammatory genes including IL-6, TNFa, and IP-10 in MEFs. In contrast, I demonstrate that CARM1 is a negative regulator of NFkB-mediated proinflammatory cytokine secretion in macrophages. CARM1-deficient BMDMs secrete significantly more IL-6 and TNFa upon LPS stimulation than CARM1-sufficient BMDMs, without exhibiting a difference in IL-10 secretion. In addition, CARM1 is reported to coactivate glucocorticoid-receptor mediated transcription. Here, I show that glucocorticoid mediated trans-repression of NFkB in BMDMs is not regulated by CARM1. In conclusion, the results from this thesis reveal novel roles for arginine modifying enzymes in cytokine expression by Th2 cells and macrophages. PAD4 is a negative regulator of NIP45-mediated IL-4 secretion in Th2 cells. In addition, the generation of the PAD4 conditional knockout strain will allow a more detailed analysis of PAD4 in immune regulation. Furthermore, CARM1 is a negative regulator of NFkB-mediated proinflammatory cytokine secretion in macrophages, revealing cell-type specific differences for CARM1 function in macrophages and MEFs.
Non-chemical control of the Red-billed Quelea (Quelea Quelea) and use of the birds as a food resource

The Red-billed Quelea Quelea quelea is the most numerous terrestrial bird and the most destructive avian pest of small-grain crops throughout sub-Saharan Africa. The birds occur in 60% of the cereal production areas of Tanzania almost every year. Quelea can cause serious local damage to millet, rice, wheat and sorghum and cause considerable hardship to subsistence farmers. Spraying with the organophosphate avicide Queletox®, (60% fenthion a.i.) remains the preferred control measure despite its negative impact on the environment and high cost. As an alternative control measure, the mass trapping of quelea and harvesting their chicks to use both as a source of protein and for income generation was investigated. Two traps using very large nets, based on designs used successfully to catch birds in Tunisia and the USA, failed with quelea; but success was achieved with four other methods. With traditional basket traps made of grass, an average of 286 birds could be caught per trap per day, this increased to 574 birds by using a replica wire mesh version. When using mist nets in a breeding colony the number of birds caught per day per 12 m long net varied from 445 for the first day to 231 on the tenth day. Trials with a roost trap yielded 5,000 to 17,000 birds per day. Cooking and preservation methods were investigated to maximise the potential utilization of quelea meat as a food resource. The best preservation method was achieved by boiling with added salt and drying, while the cooked product rated most highly by volunteer tasters was fresh meat. Proximate analysis was conducted on preserved, milled, quelea meat which confirmed the highly nutritive value of quelea for human consumption. It was concluded that mass-trapping and chick harvesting methods were more environmentally friendly control methods than spraying or use of explosives, with the added benefits of providing high-quality proteinaceous, uncontaminated, food and income generation for the trappers and their families.
An evaluation of the anticancer activity in Hopea odorata extracts

Possible anticancer characteristics of Hopea Odorata extracts were investigated by cell proliferation and viability studies of cells in culture. The mechanism of action was studied by determining the rate of apoptosis and expression of protein involved in signal transduction. The result indicated that the butanol extract of H. Odorata had selective inhibition to both Hep G2 and Chang cells with IC50 of 20.14 and 377 µg/ml, respectively. Growth inhibition by the extract showed an increased of apoptosis at concentration of 25 µg/ml. Cell study demonstrated morphologic changes characteristic of apoptosis such as chromatin condensation and fragmentation, as well as formation of apoptotic bodies. However, MAPK kinase signal transduction pathway indicated no difference in ERK1 and ERK2 expression level after exposure at varying time. P53 protein level also showed no changes in expression compared to control. In conclusion, the increase in apoptosis observed was not due to changes in MAPK pathways involving ERK1, ERK 2 and p53 but may involve other pathway, which require further investigation. Key words: Antiproliferation, Hopea Odorata, apoptosis.
Tolerance to heavy metals in Littorina saxatilis from a metal contaminated estuary in the Isle of Man

Population differences were measured in the tolerance of Littorina saxatilis from sites around the Isle of Man, to acute exposure to zinc, lead, copper and cadmium. Animals from a site influenced by disused mine run-off in Laxey estuary (high zinc) were compared with animals from less contaminated estuaries (Peel-high lead, but lower zinc), and the relatively uncontaminated Castletown and Ramsey estuaries, plus the open coast near Derbyhaven. Median lethal times (LT50) were estimated for each test concentration (5, 10, 20 mg l−1 Zn; 5, 10 mg l−1 Pb; 0·5, 1·0, 2·0 mg l−1 Cu and Cd) except for those that did not produce sufficient mortalities. Individuals from Laxey estuary showed significantly higher tolerances to zinc (10 mg l−1) and lead (5 mg l−1) than animals from the unpolluted sites. No co-tolerance to copper or cadmium was apparent. Population tolerance to zinc was correlated with reduced accumulation rates. Lead tolerance may result from the ability of the tolerant individuals to sequester the metal and detoxify it in their tissues; the littorinids from Laxey had significantly higher rates of lead accumulation.
STUDIES ON VASCULAR INFECTION OF FUSARIUM OXYSPORUM F. SP. CUBENSE RACE 4 IN BANANA BY FIELD SURVEY AND GREEN FLUORESCENT PROTEIN REPORTER

Fusarium wilt of banana ( Musa spp.) caused by Fusarium oxysporum f. sp. cubense ( Foc ) is one of the most serious banana fungal diseases in the world. Understanding the infection process of Foc is important for development of effective ways in disease control. In order to follow infection and colonization of this pathogen from root to rhizome and pseudostem tissues of banana, a highly pathogenic strain FJAT-3076 of Foc race 4 ( Foc 4) was transformed with gene encoding green fluorescent protein (GFP) and the fungus carrying gfp (FJAT-3076-GFP) was used to inoculate banana plants (Cavendish cv. B.F.). After inoculation for 3 to 10 d, it was observed that the conidia and their germ-tubes had penetrated into epidermis of young roots. The hyphae were found inside the root xylem 10 d after inoculation in the rhizome and pseudostem xylem after inoculation for 17 d. All plants infected by Foc died in 24 d after inoculation. It was also observed that Foc had spread all over the xylem and part of hyphae reached the pseudostem surface. Hyphal population was found the highest in the pseudostem, lower in root and least in rhizome. Field survey confirmed that Foc 4 were mostly present in the base of pseudostem and less in the rhizome. Thus, effective prevention of the Foc hyphae movement from the rhizome up to the pseudostem might delay or control banana wilt disease.
Role of the Murein Precursor UDP-N-Acetylmuramyl-l-Ala-γ-d-Glu- meso-Diaminopimelic Acid-d-Ala-d-Ala in Repression of β-Lactamase Induction in Cell Division Mutants

ABSTRACT Certain β-lactam antibiotics induce the chromosomal ampC β-lactamase of many gram-negative bacteria. The natural inducer, though not yet unequivocally identified, is a cell wall breakdown product which enters the cell via the AmpG permease component of the murein recycling pathway. Surprisingly, it has been reported that β-lactamase is not induced by cefoxitin in the absence of FtsZ, which is required for cell division, or in the absence of penicillin-binding protein 2 (PBP2), which is required for cell elongation. Since these results remain unexplained, we examined an ftsZ mutant and other cell division mutants (ftsA, ftsQ, and ftsI) and a PBP2 mutant for induction of β-lactamase. In all mutants, β-lactamase was not induced by cefoxitin, which confirms the initial reports. The murein precursor, UDP-N-acetylmuramyl-l-Ala-γ-d-Glu-meso-diaminopimelic acid-d-Ala-d-Ala (UDP-MurNAc-pentapeptide), has been shown to serve as a corepressor with AmpR to repress β-lactamase expression in vitro. Our results suggest that β-lactamase is not induced because the fts mutants contain a greatly increased amount of corepressor which the inducer cannot displace. In the PBP2(Ts) mutant, in addition to accumulation of corepressor, cell wall turnover and recycling were greatly reduced so that little or no inducer was available. Hence, in both cases, a high ratio of repressor to inducer presumably prevents induction.
Relationship between level of hydrophobic peptides and bitterness in cheese made from pasteurized and raw milk

Hydrophobic and hydrophilic peptides in the water-soluble fraction of 20 batches of Hispanico cheese made from pasteurized and raw milk were determined by reversed-phase HPLC, with detection at 214 and 280 nm. Cheese flavour characteristics were evaluated by a sensory panel, and regressions of bitterness scores on levels of hydrophobic and hydrophilic peptides and their ratio were calculated. The best fitting relationship for pasteurized milk cheese was the linear regression of mean panel bitterness scores on hydrophobic peptides at 280 nm (r2=0·791). The determination coefficient for the regression of hydrophobic peptides at 280 nm on panellist bitterness scores (r2=0·356) was lower, owing to individual differences in the perceived intensity of bitterness. In the case of raw milk cheese, the respective determination coefficients were 0·203 for panel scores and 0·034 for individual panellist scores.