Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation of Bacillus amyloliquefaciens JK6 and identification of its lipopeptides surfactin for suppressing tomato bacterial wilt

A rhizobacteria strain, B. amyloliquefaciens JK6, isolated from the rhizosphere soil of healthy tomato plants, significantly inhibited Ralstonia solanacearum (RS). The biocontrol efficacies (BCEs) of JK6 suppressing tomato bacterial wilt caused by RS were up to 58.6% and 52.9% in two greenhouse experiments. To evaluate the mechanisms of the antagonist, we found that JK6 could produce siderophores, protease, biofilm, cellulose, indole acetic acid (IAA) and ammonium (NH3). In addition, PCR was used to identify antimicrobial genes in JK6. Amplification products of the expected sizes were identified as srfAB, involved in surfactin synthesis; ituA, ituB, ituC and ituD, involved in iturin synthesis; fenD, involved in fengycin synthesis; and yndJ, involved in the biosynthesis of the Yndj protein. The concentration of the lipopeptides surfactin isolated from JK6 culture was 64.24 mg L−1 identified by liquid chromatography coupled with mass spectroscopy. Furthermore, the srfAB, fenD and yndJ DNA content (copy number per 100 ng of total soil DNA) in the JK6-treated soil was significantly higher than that of the controls, as determined through real-time PCR analysis. In summary, we estimated that the production of lipopeptides surfactin as well as the higher srfAB, fenD and yndJ DNA copy numbers detected in the rhizosphere soil may play major roles in the biocontrol mechanisms with which JK6 protects plants from pathogen attacking.
The control of escape behaviour in, and the histopathology of, the Norway lobster, Nephrops norvegicus (L.)

Nephrops norvegicus, like other lobsters and crayfish, react to threatening stimuli by producing of the tail-flip escape response. This response, which is important in both predator avoidance and capture by trawling, takes the form of repeated flexions and extensions of the abdomen, produced by the deep abdominal flexor and extensor muscles. Much research has been concentrated on both the metabolic and neuronal factors controlling and limiting the tail-flip swimming of decapod Crustacea, but little attention has been focused upon the interactions between these two areas. This study has examined the tail-flip swimming of N.norvegicus in terms of both metabolic and neuronal limitations. Results have indicated that prolonged swimming and its recovery are limited neither by the availability of energy (from direct, stored sources - endogenous muscle ATP; or from indirect sources - by glycolytic production of ATP from D-glucose),nor by alteration of inter- or intra-cellular conditions by the build up of the glycolytic end product L-lactate. However, the part played by phospho-L-arginine (another short-term energy reserve in muscle) in the limitation of tail-flipping has not been unequivocally defined, and the possibility remains that there may be some metabolic influence in determining the endurance and recovery of swimming. Despite the lack of definitive evidence against any metabolic limitation of escape swimming, the results of further experiments suggest that neuronal factors play a major role in the limitation of tail-flipping. These experiments were designed to assess the importance and site of action of neuronal factors, in particular habituation, in swimming. Furthermore, the waning of tail-flipping in response to repeated stimulation appears to represent true habituation. By the use of both histochemical and morphological techniques, the roles of the muscles of the thoraco-abdominal joint in both tail-flipping and postural control have been partially elucidated. These results suggest both bracing and steering functions for the larger muscles of the two groups examined (thoraco-abdominal extensors and abdominal abductors) and postural roles for the smaller muscles. These investigations also identify suitable areas for further research, not least an examination of the innervation and recruitment of these muscle groups during tail-flipping in order to determine unequivocally their bracing and steering functions.
Molecular phylogenetic analysis of Tulipa (Liliaceae) based on noncoding plastid and nuclear DNA sequences with an emphasis on Turkey

We investigated the phylogenetic relationships in Tulipa in Turkey using DNA sequences from the plastid trnL-trnF region and the internal transcribed spacer (ITS) of nuclear ribosomal DNA. We generated trnL-trnF and nuclear ITS sequences for 11 Tulipa spp. from Turkey and compared the utility of trnL-trnF and ITS sequences for phylogenetic analysis. Neighbor-joining, Bayesian and maximum parsimony methods were implemented using the same matrices. Our study of Tulipa based on molecular data revealed congruent results with previous studies. Despite the relatively lower resolution of trnL-trnF than that of ITS, both sequence matrices generated similar results. Three clades were clearly distinguished, corresponding to subgenera Tulipa, Eriostemones and Orithyia. It is not fully resolved whether Clusianae should be recognized as a separate section of subgenus Tulipa or a distinct subgenus. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172, 270–279.
Physiological response of common bean (Phaseolus vulgaris L.) to drought stress.

Exposure to drought stress induces a cluster of physiological changes and has detrimental effects on several cell functions. Common bean is sensitive to drought stress, which can cause yield losses of more than 50 %. Different approaches to study physiological changes in leaves of two common bean varieties, Tiber and Starozagorski, subjected to drought stress were implemented. These included Total Radical-Trapping Potential (TRAP) test, PulseAmplitude-Modulation (PAM) fluorometry and reflectometry. The results of TRAP measurements and reflectometry indicate higher drought tolerance of the variety Tiber. Drought stress was not so intense as to cause irreversible damage of the photosynthetic apparatus in any of the varieties.
The fish fauna of the Vasse-Wonnerup and the impact of a substantial fish kill event

Despite the high community value placed on the Vasse-Wonnerup and the many issues it faces, very little was known on its fish communities. This report details the results of the first comprehensive study of the fish communities in the nearshore (shallow) waters of the Vasse-Wonnerup. Over the course of the two year project, over 174,000 fish belonging to 31 species were recorded. Most individuals (94%) were either silversides or gobies, both of which are small fish that spend their whole life in the estuary. However, 18 species of marine fish (and invertebrates such as blue-swimmer crabs) were also found, emphasizing that the Vasse-Wonnerup provides a valuable nursery area for species found in Geographe Bay, many of which are targeted by recreational fishers. The distribution and abundance of fishes in the estuary changes throughout the year, due to the massive increases in salinity that occur during summer and autumn. Generally, the number of species and individuals decreased with increasing distance from the ocean (i.e. in an upstream direction). Higher densities of fish were also recorded during spring and summer than in autumn and winter, as most fish breed during the former period. While the large fish kill in April 2013 was undoubtedly a disturbing event, our analysis of the nearshore fish community failed to detect a change in the fish fauna between the May of 2013 (several weeks after the fish kill) and that same season in 2012. This is because there is a ‘natural’ decrease in the fish fauna at this time of year. Although no data were available on the larger fishes living in the deeper waters, like Mullets and Black Bream before the fish kill, we now have baseline data of those fishes which will be valuable in the long-term monitoring of those stocks. Worryingly, there has been negligible successful breeding of that population since the fish kill. Those deeper waters were found to contain approximately equal numbers of Sea Mullet, Yelloweye Mullet and Black Bream. The oldest Black Bream (which was 38 cm in length) was 13 years old, having been born in 2000. Our preliminary analysis of the Black Bream from the Vasse-Wonnerup also indicated that they were slow growing, due to them consuming a low calorie diet of mainly plant material, rather than molluscs, worms and fish like they eat in other estuaries. The robust baseline data on the entire fish community gathered in the current report will prove extremely valuable in the long-term monitoring of the ecological health of the Vasse-Wonnerup. Moreover, it will allow more informed management decisions to be made, and also better assessment of the efficacy of those decisions. It is recommended that annual monitoring of the fish community occurs in February to detect any changes in the ecological condition of the system. It is also recommended that the biology of Black Bream be investigated further to help guide specific management of that recreationally valuable species to ensure that its stocks remain healthy.
Leaf gas exchange in water-stressed common bean and tepary bean

Tepary bean, Phaseolus acutifolius A. Gray var. latifolius G. Freeman, is adapted to hot arid conditions and might be a valuable source of genes to improve the drought tolerance of P. vulgaris L. We tested the hypothesis that P. acutifolius adaptation to arid environments relies on differences in gas exchange characteristics leading to greater water-use efficiency. Both species were subjected to controlled levels of water stress by enclosing the root systems in semipermeable membranes immersed in nutrient solutions osmotically adjusted with polyethylene glycol (.)
Disrupted phylogeographical microsatellite and chloroplast DNA patterns indicate a vicariance rather than long‐distance dispersal origin for the disjunct distribution of the Chilean endemic Dioscorea biloba (Dioscoreaceae) around the Atacama Desert

Aim The Chilean endemic Dioscorea biloba (Dioscoreaceae) is a dioecious geophyte that shows a remarkable 600 km north–south disjunction in the peripheral arid area of the Atacama Desert. Its restricted present‐day distribution and probable Neogene origin indicate that its populations have a history linked to that of the Atacama Desert, making this an ideal model species with which to investigate the biogeography of the region.
Southern hybridization and PCR for specific detection of phytopathogenic Clavibacter michiganensis subsp. michiganensis

Clavibacter michiganensis subsp. michiganensis is the causal agent of bacterial wilt and canker in tomato (Lycopersicon esculentum). Specific detection of this important bacterial pathogen was possible using Southern hybridization with DNA-probes derived from plasmid-borne genes, celA encoding an endocellulase and pat-I involved in pathogenicity. The celA probe differentiated the C. m. subsp. michiganensis, insidiosus, nebraskensis, tessellarius, and sepedonicus; moreover, the pat-1 probe distinguished virulent from avirulent strains of C. m. michiganensis. A polymerase chain reaction based on primers derived from the pat-1 region was developed. Virulent strains were detectable in homogenates prepared from infected tomato plants, naturally contaminated seeds, and healthy lant homogenates containing as few as 2 × 10 2 bacteria per milliliter
Détermination du niveau de contamination de l'ochratoxine A (OTA) dans les fèves de cacao à l'exportation

L’evaluation du niveau de contamination du cacao a l’exportation par l’ochratoxine A (OTA) a ete initiee pour satisfaire a des dispositions legales et reglementaires. Des prelevements d’importants echantillons de cacao (300), effectues selon le reglement No 401/2006 (CE) ont ete doses par la methode CLHP pour la recherche de l’OTA apres extraction et purification sur colonnes d’immunoaffinite. Les resultats globaux indiquent que 33 echantillons sur les 300 feves de cacao se situent a une limite superieure a 2 μg/kg, ce qui represente un pourcentage de 11,04%. Sur le port d’Abidjan la probabilite de rejet serait de l’ordre de 15,65% si la norme etait fixee a 2 μg/kg. Les resultats au niveau du port de San Pedro indiquent une probabilite de rejet plus faible (6, 67%). Si l’on considere selon la legislation ivoirienne que les lots classes sous grade (SG) ne doivent pas etre exportes (c’est-a-dire les feves de cacao sechees dont le taux de moisissure est superieur a 4%), le taux de feves ardoisees est superieur a 8% et le taux de defectuosite est egalement superieur a 6%). Les rejets ne seraient plus que de l’ordre de 9,50% pour les 2 ports, a savoir 11% sur le port d’Abidjan et 8% pour le port de San Pedro. Cette contamination des feves de cacao par l’OTA peut etre controlee ou reduite par la mise en place effective et la vulgarisation de bonnes pratiques de production du cacao, si les points critiques de production de l’OTA par les champignons ochratoxicogenes sont bien identifies. Determination du niveau de contamination de l’ochratoxine A (OTA) dans les feves de cacao a l’exportation
Candidatus Liberibacter asiaticus and Huanglongbing effects on citrus seeds and seedlings.

Huanglongbing (HLB) is devastating disease of citrus and threatens the citrus industry worldwide. The suspected causal agent of the disease is a phloem-limited bacterium of the genus Cana'idatus Liberibacter transmitted through insect vector or grafting with diseased budwood. Currently, most seed source trees For citrus rootstock propagation are located outdoors and unprotected from disease transmission. In addition, fruit from HLB-affected scion varieties in Florida containing seeds enter the commercial trade and move into other citrus-growing areas. The objective of this study was to determine how Ca. L. asiaticus infection affects seed quality and seedling development and whether the disease appears in seedlings grown from infected fruit. Two experiments were conducted involving thousands of seedlings produced from seeds from infected rootstock seed source trees and 'Valencia' sweet orange trees, respectively. Infection of trees and fruit with Ca. L. asiaticus significantly reduced seed weight, seed germination, and seedling height. Seedlings did not develop symptoms typical of HLB throughout the experiment. Polymerase chain reaction (PCR) analysis initially identified two of 686 rootstock seedlings and three of 431 sweet orange seedlings positive for the pathogen when they were ver y young. Resampling and PCR analysis of these five seedlings at older ages consistently indicated they were negative for the pathogen and none of these plants ever developed symptoms of HLB. It is suggested that Ca. L. asiaticus may have been translocated into some part of the embryo during seed development but that it was not present in cells or tissue, which permitted replication or disease development as the seedling grew.
The effect of diluents containing glycine, and glycine and glycerol, on the fertility of diluted bovine semen

Abstract The conception rate of semen diluted in four experimental diluents containing glycine, C.U. E. , C.U. E.G. (C.U.E. plus 1.25 per cent glycerol), 14 (a simpler egg yolk-citrate-glycine-glucose diluent formulated in this laboratory), and 14G (14 plus 1.25 per cent glycerol, also formulated in this laboratory) gave significantly higher results than 2.9 per cent sodium citrate with semen used on the day of and day after collection. The superiority of the four diluents over 2.9 per cent sodium citrate was 2.2 per cent, 2.5 per cent, 2.2 per cent, and 2.1 per cent respectively with semen used on the day of collection, and 4.4 per cent, 4.1 per cent, 2.7 per cent, and 4.1 per cent respectively with semen used on the day after collection. The effect of glycerol addition to the two basic diluents, C.U. E. and 14, was estimated as + 0.1 per cent with semen used on the day of collection, and + 0.7 per cent with semen used on the day after collection. Neither difference was significant. However, there was a sign.
Preliminary comparisons of several annual Trifolium species on Kangaroo Island, South Australia

The growth and persistence of a number of accessions of seven species of Trifolium were measured. For the first three years the plots were grazed only to remove excess herbage after sampling. For the following three years they were grazed continuously under commercial conditions. In ungrazed swards the annual dry matter production of accessions of T. cherleri, T. globosum, and T. purpureurn was similar to T. subterraneum cultivars Yarloop and Woogenellup. T. cherleri, T. globosum, and Woogenellup made the bulk of their growth during the spring whereas T. purpureum and Yarloop produced half of their total dry matter during the winter. Good plant densities of T. argutum, T. cherleri, T. purpureum, and T. subterraneum were present at the end of three years continuous grazing, but Woogenellup and all other species were markedly inferior to Yarloop in their contribution to total production at the end of this period. Yarloop and T. purpureum were found to be very susceptible to clover scorch (Kabatiella caulivora) ; Woogenellup was moderately susceptible and the other species were unaffected in the field. All test species had low levels of formononetin in their leaves.
Changes in Sexual Expression as Result of Defoliation and Environment in a Monoecious Shrub in Mexico: Implications for Pollination

Folivory may indirectly impact plant reproduction through changes in sexual expression (i.e., number or proportion of male and female flowers produced), which influence plant–pollinator interactions via changes in pollinator preference or efficiency. This study is an experimental evaluation of the effect that defoliation has on sex expression in the monoecious shrub Cnidoscolus aconitifolius, how such effect varies across sites, as well as how such changes indirectly affect pollinator visitation rates. The present study used three populations of C. aconitifolius, each one located in a different site in Yucatán (México): pasture, deciduous forest and subdeciduous medium height forest and three levels of defoliation: 50 percent, 100 percent, and a control (no damage). Results showed that defoliation reduced significantly the total number of male flowers produced in two of the sites. Defoliation did not impact female flower production or the proportion of female flowers produced. Finally, floral visit rates were not affected by defoliation via changes in sexual expression and neither by site or by the interaction site × defoliation. Findings showed that defoliation had an effect on sex expression in C. aconitifolius, although apparently this change did not affect the plant–pollinator interactions.
Mechanistic Approaches to Community Ecology: A New Reductionism

Mechanistic approaches to community ecology are those which employ individual— ecological concepts—those of behavioral ecology, physiological ecology, and ecomorphology— as theoretical bases for understanding community patterns. Such approaches, which began explicitly about a decade ago, are just now coming into prominence. They stand in contrast to more traditional approaches, such as MacArthur and Levins (1967),which interpret community ecology almost strictly in terms of “megaparameters. ”. Mechanistic approaches can be divided into those which use population dynamics as a major component of the theory and those which do not; examples of the two are about equally common. The first approach sacrifices a highly detailed representation of individual— ecological processes; the second sacrifices an explicit representation of the abundance and persistence of populations. Three subdisciplines of ecology—individual, population and community ecology—form a “perfect” hierarchy in Beckner's (1974) sense. Two other subdisciplines—ecosystem ecology and evolutionary ecology—lie somewhat laterally to this hierarchy. The modelling of community phenomena using sets of population-dynamical equations is argued as an attempt at explanation via the reduction of community to population ecology. Much of the debate involving Florida State ecologists is over whether or not such a relationship is additive (or conjunctive), a very strong form of reduction. I argue that reduction of community to individual ecology is plausible via a reduction of population ecology to individual ecology. Approaches that derive the population-dynamical equations used in population and community ecology from individual-ecological considerations, and which provide a decomposition of megaparameters into behavioral and physiological parameters, are cited as illustrating how the reduction might be done. I argue that “sufficient parameters” generally will not enhance theoretical understanding in community ecology. A major advantage of the mechanistic approach is that variation in population and community patterns can be understood as variation in individual-ecological conditions. In addition to enriching the theory, this allows the best functional form to be chosen for modeling higher-level phenomena, where “best” is defined as biologically most appropriate rather than mathematically most convenient. Disadvantages of the mechanistic approach are that it may portend an overly complex, massive and special theory, and that it naturally tends to avoid many-species phenomena such as indirect effects. The paper ends with a scenario for a mechanistic-ecological utopia.
Genetic correlations in S4 families of popcorn (Zea mays). Cien. Inv. Agr. (In English) 33(2):105-110.

The objective of this work was to study the genetic correlations of the popping expansion (PE), 100 kernel weight (100KW), grain production (GP) and proportion of ears attacked by pests (PEAP) and diseases (PEAD). The study was conducted at Vicosa, Brazil during the 2001-2002 growing season, using 106 S 4 families of a Beija-Flor popcorn population. The experiment was designed as incomplete blocks. PE showed a positive correlation with grain production. Furthermore, a direct effect of PEAD on PE was estimated, with a correlation value of 0.56. PEAP and PEAD traits showed a high correlation (0.76), indicating that ears with high pest incidence were positively associated with grain disease damages. 100KW was not correlated with the other traits. Positively correlated responses were found between yield and popping expansion considering a simultaneous selections to both characters in previous selections cycles. El objetivo de este trabajo fue estudiar las correlaciones geneticas entre los caracteres capacidad de expansion (CE), peso de 100 granos (PCG), produccion de granos (PG) y porcentaje de mazorcas atacadas por plagas y enfermedades (PMAP) y (PMAE), respectivamente, en 106 familias S 4 de la poblacion de maiz popcorn Beija-Flor. El experimento fue conducido en un diseno de bloques incompletos, en Vicosa, Brasil, en la temporada agricola 2001-2002. La CE presento una correlacion positiva con la produccion. Tambien fue estimado un efecto directo de PMAE sobre CE, con un valor de 0,56. Las caracteristicas PMAP y PMAE estuvieron altamente correlacionadas (0,76), indicando que, en general, las mazorcas con mayor incidencia de plagas tambien presentaron mayor incidencia de enfermedades en los granos. PCG no presento correlacion con las demas caracteristicas. A traves de la seleccion simultanea en la produccion de granos y capacidad de expansion, en previos ciclos de seleccion, respuestas positivamente correlacionadas entre ambas caracteristicas pueden ser encontradas, aspecto relevante en el mejoramiento de la especie.