Miracle-dz/UniFAR-FTUs huggingface dataset:
Host genes involved in the interaction between Aspergillus flavus and maize

Aflatoxin contamination caused by Aspergillus flavus is a major concern in maize production. Understanding the complex interrelationships of genes during the A. flavus–maize interaction may be the key to developing strategies to interrupt the aflatoxin contamination process. The A. flavus Genome Sequencing and Expressed Sequence Tags projects are providing opportunities to identify a number of candidate genes involved in plant invasion as well as aflatoxin biosynthesis. Many A. flavus hydrolase genes have been presumed to function in polymer degradation and nutrient capture. With the application of proteomics and genomics technology, many resistance-associated proteins and genes have also been identified by comparing resistant with susceptible maize lines. This research facilitates an understanding of defense mechanisms in maize kernels at physical and biochemical levels. Although environmental stress, such as drought and high temperature, has been observed to greatly enhance aflatoxin contamination of maize kernels, and the related genomics research has been initiated, more work needs to be done to determine the environmental impacts on gene expression in maize kernels.
Seed micromorphology in Dactylorhiza Necker ex Nevski (Orchidaceae) and allied genera

Seeds of 21 taxa of the genera Dactylorhiza (incl. Coeloglossum), Gymnadenia (incl. Nigritella) and Pseudorchis were examined by light microscope and SEM. Qualitative and quantitative characters were analyzed. In Dactylorhiza, the seeds are fusiform, but some populations of D. viridis show clavate seeds. According to the ornamentation of the periclinal walls, 3 types of seeds are recognized in this genus. The considerable variation in the seed coat ornamentation pattern in the taxa belonging to majalis, maculata, and praetermissa groups of the genus Dactylorhiza is congruent with the genetic processes that occurred during the history of this genus. Gymnadenia shows clavate seeds with stout and straight to slightly curved anticlinal walls, although these are straight to wavy in some taxa considered previously as Nigritella. These taxa also show low values of seed length. Pseudorchis has fusiform seeds without ornamentation in the periclinal walls and fine anticlinal walls. Our study supports the inclusion of the former genus Coeloglossum in Dactylorhiza.
Assessing and managing the risk posed by Salmonella in pig feed

Salmonella in pigs and derived pork is a significant food safety concern in Ireland. During commercial pig production, it is proposed that a number of risk factors including commercial feed can introduce Salmonella to fattening pig herds and may thereby cause human infections via consumption of contaminated pork. The objective of this work was to carry out an in-depth study on ten high Salmonella sero-prevalence pig farms to firstly identify which production stages were the principal harbours of Salmonella infection and secondly, to assess the occurrence of Salmonella in feed throughout the different production stages on these farms and thereby assess potential risks as well as epidemiological relationships. Isolates were characterized by serotyping, antibiotic resistance profiling, pulsed field gel electrophoresis (PFGE) and multiple locus VNTR analysis (MLVA). Eleven serotypes were recovered, with a monophasic variant of Typhimurium (4,[5],12:i:) accounting for 41.1% of all isolates recovered. Five Salmonella 4,[5],12:i:- isolates were recovered from the commercial feed mills supplying our pig farms. Typing of all isolates resulted in two common distinct MLVA profiles for both mills and farms. The Salmonella 4,[5],12:i:- variant that predominated in the pigs and feed is an emerging strain in Europe and are of increasing food safety concern. The objective of the final study was to determine the survival characteristics of Salmonella 4,[5],12:i:- strains. The thermal inactivation of the five feed strains at 55, 60 and 65°C was investigated using an immersed heating coil apparatus. The ability of the five strains to survive during storage on weaner pig feed premixed with Sodium Butyrate was also assessed over 28 day storage. The key findings in this study is the confirmation of monophasic Salmonella Typhimurium occurrence in new geographical settings and the indication of its possible role in the transmission of Salmonella from contaminated feed ingredients and feed to pigs.
The importance of low atmospheric CO2 and fire in promoting the spread of grasslands and savannas

The distribution and abundance of trees can be strongly affected by disturbance such as fire. In mixed tree/grass ecosystems, recurrent grass‐fuelled fires can strongly suppress tree saplings and therefore control tree dominance. We propose that changes in atmospheric [CO2] could influence tree cover in such metastable ecosystems by altering their postburn recovery rates relative to flammable herbaceous growth forms such as grasses. Slow sapling recovery rates at low [CO2] would favour the spread of grasses and a reduction of tree cover. To test the possible importance of [CO2]/fire interactions, we first used a Dynamic Global Vegetation Model (DGVM) to simulate biomass in grassy ecosystems in South Africa with and without fire. The results indicate that fire has a major effect under higher rainfall conditions suggesting an important role for fire/[CO2] interactions. We then used a demographic model of the effects of fire on mesic savanna trees to test the importance of grass/tree differences in postburn recovery rates. We adjusted grass and tree growth in the model according to the DGVM output of net primary production at different [CO2] relative to current conditions. The simulations predicted elimination of trees at [CO2] typical of the last glacial period (180 ppm) because tree growth rate is too slow (15 years) to grow to a fire‐proof size of ca. 3 m. Simulated grass growth would produce an adequate fuel load for a burn in only 2 years. Simulations of preindustrial [CO2] (270 ppm) predict occurrence of trees but at low densities. The greatest increase in trees occurs from preindustrial to current [CO2] (360 ppm). The simulations are consistent with palaeo‐records which indicate that trees disappeared from sites that are currently savannas in South Africa in the last glacial. Savanna trees reappeared in the Holocene. There has also been a large increase in trees over the last 50–100 years. We suggest that slow tree recovery after fire, rather than differential photosynthetic efficiencies in C3 and C4 plants, might have been the significant factor in the Late Tertiary spread of flammable grasslands under low [CO2] because open, high light environments would have been a prerequisite for the spread of C4 grasses. Our simulations suggest further that low [CO2] could have been a significant factor in the reduction of trees during glacial times, because of their slower regrowth after disturbance, with fire favouring the spread of grasses.
A phylogenetic view on skull size and shape variation in the smooth newt (Lissotriton vulgaris, Caudata, Salamandridae)

In this study, we explore skull size and shape variation in the smooth newt, a taxon with substantial morphological differentiation and complex phylogeographic relations. By projecting phylogenies into the morphospace of the skull shape, we explore the variation in and differentiation of this complex morphological structure within a phylogenetic framework. For these analyses, we used a dataset that covers the most southern part of the species distribution range, including all conventionally recognized subspecies. The study revealed different patterns of divergence in skull shape between sexes, which is paralleled by intraspecific differentiation. The divergence in dorsal skull shape is concordant with the phylogenetic divergence, as the most diverged clades of the smooth newt (Lissotriton vulgaris kosswigi and Lissotriton vulgaris lantzi) exhibit a skull shape that significantly diverges from the smooth newts mean shape configuration. The results of this study also indicate that ventral skull portion, which is more directly related to feeding and foraging, shows higher variation between populations than dorsal skull portion, which appears to be less variable and phylogenetically informative.
Factors affecting the dispersal of large‐scale releases of the Queensland fruit fly, Bactrocera tryoni

This study investigated two factors potentially affecting the spatial distribution of Queensland fruit fly Bactrocera tryoni (Froggatt) after release from a single point. First, the effect of age at release was investigated using a single cohort of 205 000 males from a mass‐rearing strain used for sterile insect releases. Approximately half were released as immature males and the remainder as sexually mature males (1 week later). Males were collected over 3 weeks from a grid of 135 traps, each containing a pheromone/insecticide bait, positioned between 4 and 500 m from the release point. Variation in the distribution of fly density around the release point was assessed by regressing trapped fly counts against distance. Unexpectedly, no significant differences were found in the spatial distribution of the flies. Second, the effect of inbreeding on spatial distribution was investigated using replicated simultaneous releases of two strains of B. tryoni. One strain was the existing (inbred) mass‐rearing strain that has been selected for high productivity in a mass‐rearing facility. The second strain was deliberately outbred but also selected for high productivity. Almost 100 000 males of each strain were released over the two experiments. Regression of trappings against distance differed significantly between strains in only one of five releases, but in all cases the outbred strain had a greater dispersal distance. As our trapping grid was not regular but contained gaps of up to 100 m, a small preliminary experiment investigated whether flies move faster along tree rows or across open fields. At distances up to 100 m, we found no detectable difference in fly distributions. These results are primarily relevant to the large‐scale point releases carried out as part of an existing B. tryoni sterile insect programme and are discussed in that context.
Seed bank patterns in Restionaceae and Epacridaceae after wildfire in kwongan in southwestern Australia

Post-fire seed germination, seedling mortality and seed banks were investigated in scrub-heath (kwongan) in SW Australia. Study species included herbaceous and woody, obligate seeders and resprouters in two non-bradysporous but significant plant families (Restionaceae and Epacridaceae). In all species, seedlings were recruited only in the first autumn-spring after fire and occurred in similar densities as the estimated germinable annual seed input. Seedlings were absent from unburnt vegetation. Although most species retained some residual seeds after fire, tests (excised embryo culture) indicated that a negligible number of seeds were germinable. Regardless of fire response or species, there appeared to be a large loss of seeds each year and in most cases, only a small proportion of the annual seed production was used in post-fire recovery of plants. Based on seedling: parent ratios, all species had the capacity to reconstitute parent densities from germinants in the first year after fire, but high seedling mortality and no further recruitment resulted in less seedlings than replacements for four resprouter Restionaceae and three Epacridaceae (all obligate seeders) at the end of the third year after fire.
Geranylgeranyl pyrophosphate stimulates γ‐secretase to increase the generation of Aβ and APP‐CTFγ

Cleavage of the amyloid precursor protein (APP) by β‐ and γ‐secretases results in generation of the amyloid‐β protein (Aβ), which is characteristically deposited in the brain of Alzheimer's disease patients. Inhibitors of 3‐hydroxy‐3‐methyl‐glutaryl (HMG)‐CoA reductase (the statins) reduce levels of cholesterol and isoprenoids such as geranylgeranyl pyrophosphate (GGPP). Previous studies have demonstrated that cholesterol increases and statins reduce Aβ levels mostly by regulating β‐secretase activity. In this study, we focused on the role of geranylgeranyl isopre‐noids GGPP and geranylgeraniol (GGOH) in regulating Aβ production. Our data show that the inhibition of GGPP synthesis by statins plays an important role in statin‐mediated reduction of Aβ secretion. Consistent with this finding, the geranylgeranyl isoprenoids preferentially increase the yield of Aβ of 42 residues (Aβ42) in a dose‐dependent manner. Our studies further demonstrated that geranylgeranyl iso‐prenoids increase the yield of APP‐CTFγ (a.k.a. AICD) as well as Aβ by stimulating γ‐secretase‐mediated cleavage of APP‐CTFα and APP‐CTFβ in vitm. Furthermore, GGOH increases the levels of the active γ‐secretase complex in the detergent‐insoluble membrane fraction along with its substrates, APP‐CTFα and APP‐CTFβ. Our results indicate that geranylgeranyl isoprenoids may be an important physiological facilitator of γ‐secretase activity that can foster production of the pathologically important Aβ42. — Zhou, Y. , Suram, A. , Venugopal, C. , Prakasam, A. , Lin, S. , Su, Y. , Li, B. , Paul, S. M. , Sambamurti, K. Geranylgeranyl pyrophos‐phate stimulates γ‐secretase to increase the generation of Aβ and APP‐CTFγ. FASEB J. 22, 47–54 (2008)
Food-anticipatory Activity as a Cue for Local Enhancement in Golden Shiners (Pisces: Cyprinidae, Notemigonus crysoleucas)

The goal of this study was to test whether food-anticipatory activity, which is more subtle than feeding activity, can be used as a cue for local enhancement by fish. Golden shiners, Notemigonus crysoleucas, were offered a choice between spending time near a shoal of conspecifics normally fed at that time of day or a shoal normally fed at another time. Despite the fact that no food was delivered during the tests, the shoal that was normally fed at that time had more fish moving and more fish close to the surface, where food usually appeared, than the other shoal. This is evidence of food-anticipatory activity. The choosing shiners, after being deprived of food for 24-48 h, preferred to stay near the anticipating shoal rather than near the other one. When satiated, the shiners chose both shoals at random, indicating that hunger promotes the use of food-anticipatory cues in shoal choice and local enhancement. The results also support the idea that food-anticipatory activity can attract competitors for food and may therefore be costly. Food-anticipatory activity might also attract predators, but the fact that satiated shiners did not actively avoid anticipating shoals indicates that the potential cost of predator attraction would be either low or mitigated by other factors.
Contribution of organic matter sources to cyprinid fishes in the Chany Lake–Kargat River estuary, western Siberia

Although omnivorous cyprinid fish often dominate fish communities in shallow eutrophic lakes, their role in the food web is poorly known. In the present study, carbon sources of six cyprinid species were examined in a littoral freshwater habitat in a saline lake complex (Lake Chany, western Siberia, Russia) using stable isotope analyses (SIA). In this habitat, microalgae (phytoplankton and epiphytes), macrophytes and riparian vegetation comprised the major producer groups with distinctive δ13C values. Zooplankton and most benthic invertebrates functioned primarily as microalgae-based consumers, whereas the amphipod Gammarus lacustris depended largely on macrophytes or macrophyte-derived detritus. Cyprinids, Carassius carassius L. , Car. auratus gibelio Bloch. and Abramis brama L. , mainly utilised microalgae-derived carbon (δ13C-based isotope mixing model: 66–97%) via zooplanktonic trophic mediations. In contrast, Cyprinus carpio L. , Leuciscus idus L. and Rutilus rutilus L. depended more on macrophytic and/or riparian production (52–80%) than on microalgal production. Observations and SIA of foregut contents indicated highly opportunistic feeding habits of R. rutilus and L. idus and preference for macrophytes. These results suggested that cyprinid fishes link pelagic, benthic and riparian food webs in this shallow, eutrophic lake ecosystem.
INFLUÊNCIA DA INOCULAÇÃO DE Fusarium spp. E NÍVEIS DE SOMBREAMENTO NO CRESCIMENTO E DESENVOLVIMENTO DA ERVA-MATE

The “erva-mate” ( Ilex paraguariensis A. St.-Hill) is a species broadly cultivated in southern Brazil and neighboring countries, whose leaves and fine branches, prepared according to the appropriate method, make the “mate” or “chimarrao”, the most popular tea consumed in Brazil and exported around the world. With an increasing planted area, mainly in the last decade, phytosanitary problems caused by pests and disease have increased in this crop and root-rot is becoming one of the main problems. The disease is caused by Fusarium spp. and it causes serious damage to the roots, in the most serious cases, leading to the death of the plant. The “erva-mate” is a species that inhabits the forest underwood, and cultivation in a homogeneous way to full sun can be a stressful factor for the species causing less growth and development and, also, more susceptibility to root-rot. Therefore, experiments were conducted in the Forest Nursery area belonging to Forest Sciences Department of the Federal University Santa Maria with the objective of confirming these assumptions. The experiment was conducted in a factorial design (2 x 5), composed by Fusarium spp. inoculation and by shading levels. It was verified that plants submitted to lower shading levels or full sun had less development and were more susceptible to the disease. The plants inoculated with Fusarium spp. had less development in comparison with non-inoculated plants, mainly at the lower shading levels.
RECENT OCCURRENCES OF OPAH, LAMPRIS GUTTATUS (ACTINOPTERYGII, LAMPRIFORMES, LAMPRIDAE), IN THE WESTERN MEDITERRANEAN SEA

The first records of Lampris guttatus in the Mediterranean Sea date back to 1807. Yet, until now it has been considered as a rare species (less than 25 specimens recorded in the literature). Since 2008, at least 23 spec- imens have been fished or observed along the French Mediterranean coast. In this paper, we present an updated review of records in the Mediterranean and discuss the possible link with the present sea water warming. We hypothesise that the recent Mediterranean specimens could come from the Atlantic, throughout the Gibraltar Strait, following a northward migration along the Northeast Atlantic coast due to present global warming. K eywords: new records, first record, Algeria, Mediterranean, rare species, SST, w arming
Survey of soil chemical properties across a landscape in the Namib Desert

A selection of soils were sampled in the Central Namib Desert to investigate the importance of landscape and associated plant communities on soil nutrient status. Soils were sampled in an ephemeral river, a wash, and at two dune sites. The soils in the lower landscape positions, the Kuiseb River and an associated wash, had significantly higher nutrient levels than those at the dune sites. These lower landscape positions also had the most stable plant communities, Faidherbia albida and Welwitschia mirabilis, respectively. The two dune soils, which both support perennial herbaceous species, had extremely low nutrient levels. Only the wash showed nutrient enrichment of the soil under plants, as measured by a relative enrichment factor. This community is the most established, with plants being hundreds of years old; this time factor may be crucial for nutrient accumulation by plants in this extremely arid system. The lack of enrichment under the F. albida community suggests that the fluvial inputs and exports, both organic and inorganic, tend to homogenize the nutrient levels within this system. These results indicate that soil nutrient levels in the Namib Desert are closely linked to landscape position and less so with the associated plant communities.
OPTIMIZED LACTOBACILLUS PLANTARUM LP6 SOLID-STATE FERMENTATION AND PROTEOLYTIC HYDROLYSIS IMPROVE SOME NUTRITIONAL ATTRIBUTES OF SOYBEAN PROTEIN MEAL

ABSTRACT The solid-state fermentation of soybean protein meal (SPM) by Lactobacillus plantarum Lp6 was studied to evaluate the influence of soluble starch, acid protease and time on the degree of hydrolysis (DH) and viable cell counts (VCC). The fermented SPM (FSPM) was optimized for maximum DH and VCC using response surface methodology. The optimum conditions determined were the following: soluble starch (0.4 g/g of SPM), acid protease (0.1 g/g of SPM) and time (66 h). The optimized values were 22.58% and 9.08 (log cfu/g) for DH and VCC, respectively. Fermentation using the optimized process conditions increased the amount of low molecular weight peptides ( 97.4 kDa). The protein content (60.15%) of FSPM increased following fermentation of SPM. The free amino acids profile (0.32 to 8.03 g/100 g protein) and protein solubility (29.33% to 38.35%) increased significantly (P < 0.01) during fermentation due to the hydrolytic actions of L. plantarum Lp6 and acid protease. PRACTICAL APPLICATIONS Soybean is one of the best known vegetable protein in the world. During solid-state fermentation process, this study demonstrated that the nutritional attributes of soybean protein meal (SPM) could be enhanced by fermentation with Lactobacillus plantarum Lp6. These results would encourage production of bioactive peptides with the possible cheap source of protein in an industrial scale to improve the nutritional value of SPM. This is bound to increase the volume of SPM as a by-product of soybean oil-processing industries.
Etude de l'ovogenèse chez Centropages typicus (Copepoda, Calanoida)

We carried out a complete study of oogenesis in Centropages typicus using structural, ultrastructural and cytochemical data. The usual stages of oogenesis, i.e. germinative phase, premeiosis, primary and secondary vitellogenesis, were found. The latter two stages were the most typical. Primary vitellogenesis consisted of endogenous yolk accumulations; these substances, probably of lipoprotein or lipoglycoprotein nature, were produced at the granular endoplasmic reticulum level and then stocked in the reticulum cavities. During secondary vitellogenesis, endogenous yolk production continued, but we mainly observed the development of exogenous yolk accumulation (lipid droplets and protein globules) in the ooplasm. These accumulations resulted from the fusion of very numerous pinocytotic vesicles arising from the oolemma and containing substances probably brought to the oocytes by the hemolymph. The effect of various proteases on the vitellus globules caused a more or less marked digestion of their contents, tending to prove their protein nature. The end of vitellogenesis was marked by the appearance of vacuolar formations with dense lamellae which could correspond to cortical granules.