Miracle-dz/UniFAR-FTUs huggingface dataset:
Escherichia coli cells containing the plasmid ColV produce the iron ionophore aerobactin

The first colicin to be described (colicin V) in 1925 was the product of a virulent Escherichia coli strain [1]. Since then studies have been performed with the aim of identifying the virulence factor associated with the ability to produce colicin V. ' Such a relationship has been established for humans, domestic animals and in experimental animal systems infected with pathogenic E. coli strains [2-7]. To date it is clear that several virulence enhancing factors are encoded by ColV plasmids. Synthesis of colicin V seems not to be essential for virulence enhancement [2,3] although it has been reported that colicin V inhibits macrophages [8]. E. coli strains harbouring ColV plasmids show an enhanced resistance to the bactericidal effects of serum [3,9], and their growth is supported by a new iron sequestering system [7,10,11]. It was shown that the iron ligand was of the hydroxamate type but ferrichrome, the only known ferric hydroxamate complex to be actively taken up by E. coli, was excluded [11 ]. In this paper it is reported that aerobactin is the new iron ligand produced by ColV-bearing E. coli strains. The search for the iron ligand was guided by the fact that other Enterobacteriaceae, Aerobacter aerogenes [12], Shigella flexneri [13] and Enterobacter cloacae [14] produce aerobactin. A new rapid isolation procedure was developed which is different from the one described by the discoverers of aerobactin, F. Gibson and D.I. Magrath [12], and which allows the isolation of large quantities in highly pure form.
Mining synthetic hexaploids for multiple disease resistance to improve bread wheat

A collection of 253 synthetic hexaploid wheats (SHWs) produced from 192 Aegilops tauschii accessions and 39 elite durum varieties were studied to identify, characterise, and evaluate potentially untapped diversity of disease resistance in wheat. The diseases for which resistance was sought included cereal cyst nematode (CCN), root lesion nematode (RLN), Stagonospora nodorum blotch (SNB), Septoria tritici blotch (STB), and the 3 rusts, leaf rust, stem rust, and stripe rust, all important diseases of bread wheat worldwide, which can severely reduce wheat yield and quality. The SHWs exhibited a wide spectrum of resistance to the 8 pathogens. The frequency of disease-resistant SHWs ranged from 1% for one species of RLN (Pratylenchus neglectus), 3% and 10% for Septoria nodorum leaf and glume blotch, 10% for seedling resistance to yellow leaf spot, 16% for CCN, 21% for the second species of RLN (Pratylenchus thornei), 73% for Septoria tritici blotch, and 15%, 40%, and 24% for leaf rust, stem rust, and stripe rust, respectively. Five SHWs, Aus26860, Aus30258, Aus30294, Aus30301, and Aus30304, exhibited high levels of resistance to CCN, YLP, STB, LR, and SR, while 56 SHWs showed resistance to either 3 or 4 diseases. The genetics of resistance to CCN in some of the SHWs revealed that some of the accessions carry the same CCN gene(s) against pathotype Ha13, while others may carry different resistance gene(s). Additional studies were carried out to understand the relationship between the resistances identified in SHWs and the ones already present in common wheat, in particular the resistance genes Cre1 and Cre3 against CCN. The use of perfect markers associated with Cre1 and Cre3 suggested that some SHWs may carry a new CCN resistance gene(s), which could be deployed in breeding programs to increase the diversity of available resistance. The identification of SHWs with resistance to a range of diseases provides an opportunity to generate genetic knowledge and resistant germplasm to be used in future variety development.
Growth Stage at Harvest of a Winter Rye Cover Crop Influences Soil Moisture and Nitrogen

Producers may offset the cost associated with winter rye (Secale cereale L.) cover cropping by harvesting the rye as forage, but care must be taken to avoid yield suppression of a primary crop induced by soil water and nitrogen depletion by the rye. The objective was to determine the effect of rye growth stage in the spring on the soil moisture and soil nitrogen under a fall-sown cereal rye cover crop. Field studies were conducted in Morris and St. Paul, MN, from September 2007 through June 2008. Soil moisture and soil NO -N were monitored for eight rye harvest dates in the spring and summer of 2008. Soil moisture in late April and early May was similar for rye and fallow treatments. At boot stage, rye had depleted soil moisture by 10% and soil NO -N by 83% when averaged across locations. Rye reduced soil NO -N compared to the fallow at all growth stages. Harvest timing may be an important management tool to conserve soil moisture for the primary crop. Spring N fertilization is likely necessary when a non-legume such as corn (Zea mays L.) follows rye. Introduction Corn and soybean (Glycine max L.) are the most widely grown crops in the Upper Midwest. These annual crops have relatively short growing seasons with active plant growth and significant ground cover for as little as three or four months per year. The result is a landscape that is prone to off-site nutrient transport, increased soil erosion, and loss of soil organic matter. Planting cover crops after corn or soybean is one approach to addressing these concerns. In the Midwest, winter rye cover cropping has been shown to scavenge excess soil NO -N (11) and reduce NO -N leaching (14,26). Increased surface cover may also reduce soil erosion (16), while the cover crop biomass may help mitigate loss of soil organic matter (15,22). Rye is particularly well suited for use in the Upper Midwest because it grows well after harvest of the main crop in the fall, is winter hardy, and begins regrowth early in the spring (25). In addition, rye tends to reach optimum forage harvest stage sooner than other small grains, which makes it the preferred small grain species for early-season forage production (18). Producers are often reluctant to plant winter rye because of costs associated with rye management. If the environmental benefits associated with rye production are to be realized, there must be some immediate economic incentive for producers. Including rye as part of a double-crop forage production system may justify its cost. On farm research in the Upper Midwest has emphasized that rye can be an integral component of soil conservation and nutrient management, as well as provide producers a high-quality forage (10). Dairy farmers have reported high rye forage yields and increased milk 3
The plant vigor hypothesis applies to a holoparasitic plant on a drought-stressed host

Parasitic plants extract resources from host vascular tissues but their responses to environmental fluctuation experienced by the host are poorly studied. Three frequently-cited hypotheses for effects of environmental stress on plant resistance to herbivores predict decreased, increased, or fluctuation in herbivore performance in response to drought stress. We tested which hypothesis best accounts for how drought stress applied to a perennial herb affects growth of the holoparasite, Cuscuta gronovii Willd. ex Roem. & Schult. (common dodder), an obligate shoot parasite. Verbesina alternifolia (L.) Britton ex Kearney (wingstem) supporting single, young C. gronovii were exposed to continuous, pulsed, or no water stress for 32 days and then dry mass of each parasite was determined. Consistent with the plant vigor hypothesis, C. gronovii grew significantly better on well-watered hosts. Continuous and pulsed drought stress of the host resulted in similar growth reduction relative to no drought stress. In additi.
The use of practical diets and regression analyses to determine the utilization of lysine and phosphorus in corn distillers dried grains and solubles using Cobb 500 male broilers

SUMMARY Two experiments were conducted to evaluate the utilization of lysine (experiment 1) and phosphorus (experiment 2) in corn distillers dried grains and solubles (DDGS). In these experiments, we used a 5 × 3 factorial analysis with variations in diet formulations for digestible lysine (DLys) and available phosphorus (AP) with increasing DDGS levels. Common performance metrics observed in both experiments 1 and 2 were average BW, average live weight gain, feed intake (by pen), and FCR. On d 43 of experiment 1, two birds per pen were chosen for analysis of carcass characteristics, and on d 21 of experiment 2, tibias were excised to obtain tibia ash measurements. For both experiments 1 and 2, performance metrics improved with increasing levels of DLys and AP, respectively. In experiment 1, there was a DLys × DDGS interaction where performance was best for diets containing high DLys and low levels of DDGS, and in experiment 2, DDGS inclusion had no effect on performance. Regression equations were derived for each performance metric across DLys or AP levels and solved 2 ways: (1) using the observed metric resulting from each DDGS inclusion at the lowest DLys or AP level in the equation derived from no DDGS inclusion; and (2) selecting a common performance metric and comparing DLys or AP predictions across DDGS inclusions. Based on these data, the original DLys and AP coefficients for DDGS are justified, but may underestimate availability by up to 0.08 and 0.02 percentage points, respectively.
Leveraging neighborhood “structural holes” to identifying key spreaders in social networks

The identifying of influential nodes in large-scale complex networks is an important issue in optimizing network structure and enhancing robustness of a system. To measure the role of nodes, classic methods can help identify influential nodes, but they have some limitations to social networks. Local metric is simple but it can only take into account the neighbor size, and the topological connections among the neighbors are neglected, so it can not reflect the interaction between the nodes. The global metrics is difficult to use in large social networks because of the high computational complexity. Meanwhile, in the classic methods, the unique community characteristics of the social networks are not considered. To make a trade off between affections and efficiency, a local structural centrality measure is proposed which is based on nodes' a nd their ‘neighbors’ structural holes. Both the node degree and “bridge” property are reflected in computing node constraint index. SIR (Susceptible-Infected-Recovered) model is used to evaluate the ability to spread nodes. Simulations of four real networks show that our method can rank the capability of spreading nodes more accurately than other metrics. This algorithm has strong robustness when the network is subjected to sybil attacks.
Genetic variation in populations of Western Australian wild radish

Raphanus raphanistrum L. (wild radish) is a major problematic weed worldwide. Random amplified polymorphic DNA (RAPD) was used to estimate the degree of genetic diversity between and within 2 populations of wild radish (WARR 5 and WARR 6), found to exhibit multiple herbicide resistance compared with a susceptible population (WARR 7). It is believed that weed species with high degrees of genetic variation show potential for developing resistance to herbicides. Of the 13 RAPD primers screened, 9 primers generated 97 polymorphic bands concomitant with a high level of polymorphism (82%) between the wild radish populations, characteristics of an outbreeding species. Analysis of molecular variance (AMOVA) showed a markedly higher proportion of diversity within populations (87%) as opposed to between populations (13%). Principal component analysis (PCA) further highlighted the large amount of variation between individuals within populations. Only one marker, OPC19-8, was found to be unique to the WARR 7 population but absent in WARR 5 and in most individuals of the WARR 6 populations. This marker may potentially be correlated with herbicide susceptibility. The 2 resistant wild radish populations were found to be closely related (0.7% dissimilar) to each other, whereas the susceptible population was genetically dissimilar to them by 2.3%. This higher level of dissimilarity between the susceptible and resistant populations may be explained by limited gene flow between them since the susceptible population is geographically located further away from the resistant populations. Hence, it may be concluded that the underlying genetic structure of the 3 wild radish populations seems to be similar despite WARR 6 and WARR 5 having been exposed to mixed herbicide usage for over 17 years.
Controlling bacterial persister cells and biofilms by synthetic brominated furanones

Bacteria are well known to obtain tolerance to antibiotics by forming multicellular structures, known as biofilms, and by entering dormancy and forming persister cells. Both mechanisms allow bacteria to tolerate antibiotics at concentrations hundreds to thousands of times higher than the lethal dose for regular planktonic cells of the same genotype. Persister formation increases in biofilms; thus, effective control of persister cells, especially those in biofilms is critically important to infection control. Over the past decades, a bacterial signaling system based on cell density, named quorum sensing (QS), has been found to regulate biofilm formation and, in Pseudomonas aeruginosa, the level of persistence. In this study, we characterized the effects of synthetic brominated furanones, a group of QS inhibitors, on the persistence of P. aeruginosa and Escherichia coli. Our results revealed that (Z)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) can reduce persister formation in P. aeruginosa PAO1 and E. coli RP437 and restore the antibiotic susceptibility of isolated persister cells at growth non-inhibitory concentrations. In addition to planktonic persister cells, BF8 was also found to reduce persister formation in the biofilms of P. aeruginosa PAO1 and E. coli RP437. Study at the genetic level using DNA microarrays demonstrated that BF8 induced the gene mdaB in both strains and 7 genes encoding oxidoreductases in P. aeruginosa. In E. coli RP437 persister cells, BF8 was also found to repress the genes for synthesizing indole, a signaling molecule reported to induce persister formation in E. coli. Interestingly, although BF8 is a QS inhibitor, the QS signal 3-oxo-C12- acyl homoserine-lactone also rendered the persister cells of P. aeruginosa PAO1 and its mucoid mutant PDO300 more sensitive to antibiotics. Furthermore, BF8 was found to have cidal effects on PDO300. Besides BF8, some other BFs were also found to restore the susceptibility of P. aeruginosa PAO1 persister cells to ciprofloxacin. Collectively, these results indicate that this group of QS inhibitors has promising activities to control multidrug tolerant persister cells; and there might be other bacterial targets of BFs in addition to QS inhibition.
Improvements in nematophagous fungi to control gastro-intestinal parasites : this thesis is presented in partial fulfilment of the requirements for the degree of Master of Veterinary Studies in Veterinary Parasitology, Massey University, Palmerston North, New Zealand

Gastro-intestinal parasites are a major cause of production loss in New Zealand livestock, and the continuing development of anthelmintic-resistant strains represents a significant threat to the future New Zealand agricultural economy. This has led to an increased interest in alternative (non-chemotherapeutic) controls, including potential application of the nematode-trapping fungi Duddingtonia jlagrans and Arthrobotrys oligospora. These species are capable of reducing the number of free-living stages of trichostrongylid nematodes developing in faeces, following oral administration or the addition of fungal material to faeces. However, high spore mortality through the gastro-intestinal tract currently limits the development of a commercial product, even for the robust chlamydospores of D. flagrans. The potential to reduce spore mortality by applying a protective coating to the spores was investigated, and an in vitro rumen simulation bioassay was used to quantitatively evaluate and compare the survival of D. jlagrans and A. oligospora spores in a series of experiments. These experiments revealed that unprotected D. jlagrans chlamydospores were superior to A . oligospora conidia in their ability to withstand the debilitating effects of rumen fluid. However, the survival of A. oligospora was improved by integration into a biopolymer formulation. Dried D. jlagrans chlamydospores were more resistant to a simulated rumen environment than freshly harvested chlamydospores, and exposure to water as an incubation medium was less detrimental than rumen fluid to the survival of both fresh and dried D. jlagrans chlamydospores. The application of a stearic acid coating to dried D. jlagrans chlamydospores failed to improve spore survival in either a simulated rumen environment, or efficacy during subsequent in vivo testing. However, as the application of a biopolymer formulation successfully improved the survival of A. oligospora conidia, it is likely that similar formulations may be successfully applied to other fungal species. These results highlight the potential for development of formulations containing multiple species of nematophagous fungi, including the application of fungal species that were previously unsuitable due to very high spore mortality.
Analysis of the coat protein gene and untranslated region of RNA3 of Cucumber Mosaic Virus isolates infecting various Lilium species and hybrids: association of the isolate infecting asiatic hybrid lily with subgroup II

The variability in the coat protein gene of Cucumber mosaic virus (CMV) isolates from various Lilium species and hybrids namely L. longiflorum, L. tigrinum, Asiatic hybrid and Oriental hybrid lilies was studied by sequence comparison of ∼900 bp regions spanning the entire coat protein, intercistronic regions and 3′-UTR. CMV isolate characterised from Asiatic hybrid lily showed the highest homology with subgroup II isolates (94 – 97%), whereas 73 – 76% homology was observed with those belonging to subgroup I. Similarly, another three isolates showed 91 – 98% amino acid sequence homology with subgroup I and 74 – 76% sequence homology with subgroup II. Based on the criteria for classification of CMV isolates all the Indian isolates fall in subgroup I, except the one characterized from Asiatic Hybrid lily which falls into subgroup II. Other lily isolates from world were placed in subgroup II. This is the first case of Asiatic hybrid lily CMV isolate belonging to subgroup II.
Nest habitat selection by the Austral parakeet in north-western Patagonia

Fil: Diaz, Soledad. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Patagonia Norte. Instituto de Investigacion en Biodiversidad y Medioambiente; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche. Laboratorio de Ecotono; Argentina
U4 snRNA variants of Bombyx mori

It is known that the spliceosome's catalytic core is composed of U2, U6 and U5 small nuclear (sn)RNAs. U6 is chaperoned and held inactive by intermolecular base‐pair interactions by the U4 snRNA molecule until its incorporation into the spliceosomal complex. In previous studies, a number of variant forms of U1, U2 and U6 were detected in the silk moth Bombyx mori. Considering U4's unique role as a modulator of U6's activity, the aim of the present study was to determine if the multiplicity of U6 variants observed in B. mori is complemented in U4. Five U4 variants were identified in the B. mori Whole Genome Shotgun (WGS) database and were used to design internal U4 snRNA primers. These oligonucleotides were subsequently used to create four U4 reverse transcription (RT)‐polymerase chain reaction (PCR) libraries with RNA extracted from the silk gland of B. mori. Two major U4 variants were identified from these libraries. The majority of the variation among genomic and transcript‐derived U4 variant sequences is located in stem‐loop II and III as well as at the 3′‐end. No differences between the isoforms are located in the critical U4/U6 intermolecular binding regions. Sequence comparison analyses based on U4 intraspecific and interspecific variability delineate several evolutionarily conserved regions.
Conflict management in protected areas: The Lazar Canyon natural monument, Eastern Serbia

In recent decades, increasing utilisation pressure on forests and emphasis on the need for nature conservation has resulted in numerous conflicts between local communities and the institutions responsible for implementing nature conservation policy in Serbia. One example of these conflicts occurs in the Lazar Canyon natural monument in Eastern Serbia. This contains exceptional floristic and animal diversity as well as landscape diversity and beauty. After presenting the conservation policy in Serbia, the organisational structure of the institutions related to this case study, and the relevant stakeholders, this paper presents an approach to participatory management planning and conservation. It discusses potential solutions to the problem, and the feasibility of applying them. The study is based on a small survey with relevant stakeholders to explore their attitudes towards forests as natural resources and nature conservation policy. Findings suggest that these conflicts could be overcome through the involvement of all stakeholders and jointly agreed activities.
Nutritional Status and Total Phenols of Passiflora Genotypes Related to Nitrogen Fertilization

This paper was developed in order to verify the influence of nitrogen fertilization and different genotypes in the nutritional aspect and in the production of total phenols in passifloraceae. The experimental design was randomized blocks in a 5 × 2 × 2 factorial scheme, being five genotypes of Passiflora (three genotypes of Passiflora edulis, a genotype of Passiflora alata and a genotype of Passiflora ligularis), two levels of cow manure (with and without) and two doses of N (20 and 80 g), with four replicates. At 120 days after sowing, levels of foliar nutrient and total phenols were determined. Foliar N content varied depending on N doses, organic fertilization and the genotypes used. Foliar levels of P and K were higher when all genotypes received organic fertilization, while the levels of Fe and Mn were similar regardless of this fertilization. The levels of Ca and Mg were higher related to organic fertilization and the genotypes, in isolation. But the foliar contents of S, Zn and Cu increased only in relation to the used genotypes, and the average foliar content of total phenols found was 19.4 g·kg-1, ranging from 13.1 to 23.2 g·kg-1, being the lowest value observed in Passiflora alata without fertilization with cow manure. It is concluded that the nutritional requirement for N is greater for genotypes of the species Passiflora edulis in relation to the species Passiflora alata and Passiflora ligulares, and that the organic fertilization influences positively in the production of total phenols only for the genotype of sweet passion fruit.
Wind and honey bee pollination of kiwifruit (Actinidia chinensis ‘HORT16A’)

Abstract The aim of this study was to determine the factors required to pollinate ‘Hort16A’ (Actinidia chinensis Planch. var. chinensis) kiwifruit. Pistillate flowers (88%) opened between 0500 and 1200 h. There was no indication of nectar production or viable pollen on pistillate flowers. Stigma receptivity peaked on the second day after anthesis and then declined. Excluding honey bees (Apis mellifera L.) significantly (p<0.05) reduced fruit set and seed number. Flowers exposed to wind pollination for 5 days produced fruit with an average of 110 seeds. When equal numbers of staminate and pistillate flowers were presented on a tray, only 2.8% of visits were to staminate ‘Sparkler’ flowers and 2.2% to staminate ‘Meteor’ flowers. Single bee visits to pistillate flowers produced averages of 51–61.7 seeds. The percentage of staminate pollen carried by honey bees significantly decreased with increasing distance from staminate vines (0.8%/m). Average seed number decreased by 0.75%/m.