Miracle-dz/UniFAR-FTUs huggingface dataset:
Incidence, survival and biocontrol of psychrotrophic Bacillus cereus and its potential for toxin production in milk and Tallaga cheese.

The incidence of Bacillus cereus, psychrotrophic character and the ability of isolates to produce haemolysin were investigated to evaluate their health potential in some dairy products. In total 125 samples (skim milk powder, white soft cheese, processed cheese, Kareish cheese and rice with milk) were analysed. Of these (39.2%) contained B. cereus. The viability of (reference and isolated strains) B. cereus and toxin production in sterilized milk was examined during storage at 10°C for 7 days. The two tested strains, when inoculated in milk with 10 5 cfu/mL, were shown to be capable of producing toxin at the end of the storage period. The antimicrobial activity of 7 strains of lactic acid bacteria against B. cereus was tested to select the effective starter to control the pathogen. Lactobacillus reuteri followed by Lb. rhamnosus were the most effective probiotic cultures. The choice was a mixed culture of Lactococcus lactis ssp. diacetylactis as a starter culture and Lb. rhamnosus as a probiotic culture (1:1) to use in manufacture of Tallaga cheese. The use of this starter resulted in reduction of viable count of B. cereus and so, no toxin was detected in these cheeses. In contrast, in the control cheese (inoculated with 10 5 cfu isolated strain of B. cereus), the viable counts of B. cereus increased and released detectable amount of enterotoxin at the end of refrigerated storage.
A computational model for asynchronous oocyte growth dynamics in a batch-spawning fish

A computational model of oocyte growth dynamics (i.e., oocyte recruitment, growth, and spawning) in a batch-spawning fish, fathead minnow (FHM, Pimephales promelas), has been developed. The model provides a quantitative link between oocyte growth dynamics and biochemical processes in FHMs through the absorption of vitellogenin (a lipoprotein precursor of egg yolk proteins) into oocytes, which contributes significantly to oocyte growth in fish. The model simulates the number and volume of oocytes in different batches within a FHM ovary. Model-predicted clutch sizes and spawning intervals matched the experimental data well for both unexposed FHMs and FHMs exposed to 17β-trenbolone (a relatively stable metabolite of trenbolone acetate, a synthetic androgen used as a growth promoter in livestock). Overall, the model presents a novel approach to simulating oocyte growth dynamics in a batch-spawning fish and meets an urgent need in ecotoxicological studies to link the effects of endocrine disrupting chemicals a.
Molecular effects of Mammalian Orthoreovirus (MRV) infection on hypoxic prostate tumor cells

Mammalian Orthoreovirus (MRV), a double-stranded RNA virus, is a potent oncolytic virus, which specifically replicates in tumor cells and consequently kills them. Hypoxia, a condition of low oxygen, is a characteristic feature of most solid tumors and develops due to tumor cells outgrowing their blood supply. Hypoxic cell survival is driven by the transcriptional activity of hypoxia inducible factor-1 (HIF-1). We examined the ability of MRV to infect hypoxic prostate tumor cells and found that not only did it successfully translate proteins and replicate in hypoxic prostate tumor cells, it also induced apoptosis. In addition, MRV induced downregulation of the HIF-1α protein, through a ubiquitin-dependent proteasome-mediated pathway, required the PAS domain of HIF-1α and was rescued by knockdown of the Receptor for Activated C Kinase 1 (RACK1). We investigated the direct involvement of any MRV proteins in the downregulation of HIF-1α and found that proteins μ1 and μ2 were able to downregulate HIF-1α independently. Strain specific difference (specifically the aa at 208 position of the protein) was found to affect the ability of μ2 to induce downregulation of HIF-1α; the T1L and T3D causing more downregulation than the T3D MRV strains. The region of μ2 containing aa 188-380 and the φ domain of μ1 were determined to be needed for HIF1α downregulation. The dependence of Prostate Cancer (PCa) on androgens for growth and survival is exploited by the hormone therapy, where androgen deprivation is used as a viable
Diversity of culturable moderately halophilic and halotolerant bacteria in a marsh and two salterns a protected ecosystem of Lower Loukkos (Morocco)

To study the biodiversity of halophilic bacteria in a protected wetland located in Loukkos (Northwest, Morocco), a total of 124 strains were recovered from sediment samples from a marsh and salterns. 120 isolates (98%) were found to be moderately halophilic bacteria; growing in salt ranges of 0.5 to 20%. Of 124 isolates, 102 were Gram-positive while 22 were Gram negative. All isolates were identified based on 16S rRNA gene phylogenetic analysis and characterized phenotypically and by screening for extracellular hydrolytic enzymes. The Gram-positive isolates were dominated by the genus Bacillus (89%) and the others were assigned to Jeotgalibacillus, Planococcus, Staphylococcus and Thalassobacillus. The Gram negative isolates were dominated by the genus Vibrio (41%) and the others were assigned to Halomonas, Psychrobacter, Marinobacterium, Pseudoalteromonas, Salinivibrio and Photobacterium. The growth of strains obtained under different physico-chemical conditions and the screening for hydrolytic enzymes showed a high diversity even within the same species.
Should males come first? The relationship between offspring hatching order and sex in the black‐headed gull Larus ridibundus

In birds with hatching asynchrony and sexual size dimorphism, chicks hatched earlier and later in the laying sequence usually suffer different mortalities due to uneven abilities to compete for food, especially in poor years. If sexes differ in vulnerability to environmental conditions, e.g., by having different food requirements due to differential growth rates, mothers can increase fitness by allocating sex according to the laying order, producing less vulnerable sex later rather than early in the clutch. By analysing variation in primary sex ratio using a PCR-based DNA technique, we tested this prediction in black-headed gull Larus ridibundus chicks where males may be the less viable sex under adverse conditions. The overall primary sex ratio of the population did not depart from parity. However, first hatched chicks were more likely to be males whereas last hatched chicks were more likely to be females. Both egg volume and hatchling body mass decreased with laying order irrespective of sex. Time of breeding had no effect on offspring sex or hatchling sex ratios.
INTERCOLONY AND ANNUAL DIFFERENCES IN THE DIET AND FEEDING ECOLOGY OF LITTLE TERN ADULTS AND CHICKS IN PORTUGAL

Abstract We used pellets and prey dropped near nests to study the diet and feeding ecology of Little Tern (Sterna albifrons) adults and chicks in northern and southern Portugal during 2000–2004. We compared diets among study areas, years, and birds breeding in two main habitat types: sandy beaches and salinas (man-made salt-pans). We also sampled prey fish in one study area and used published data from another area to examine whether the diet of Little Tern adults and chicks corresponded with the abundance of prey found in primary foraging habitats. Adult Little Terns fed mainly on sand-smelts (Atherina spp.) and gobies (Pomatoschistus spp.), which were the most abundant fish species in our estuarine and lagoon study areas. Despite some differences among colonies we did not find clear differences in adult diets among study areas and habitat types. Little Tern chicks also ate primarily Atherina spp. , but their diet was more diverse than that of the adults, and characterized by a significantly higher proportion of prey with a high energetic value such as sardines (Sardina pilchardus), garfish (Belone belone), and killifish (Fundulus spp.). Chick diets differed significantly between habitat types, which may be a consequence of the limited foraging range of adult breeding birds. Both adult and chick diets matched the abundance of the main prey in our study areas, confirming the opportunistic foraging character of this species. We suggest that annual variation in prey availability may be the most important factor explaining annual variation in adult diets.
FLAG tag module for PCR based gene targeting

Epitope tagging of yeast proteins has become an efficient tool for biochemical analysis of protein of interest. The epitope-tagged proteins can be used for western blotting, immunoprecipitation and immunofluorescence experiments without the need to raise specific antibodies, thus saving considerable time and expense. We have constructed plasmid containing FLAG tag with kanMX6 module, which allows selection of G418-resistant cells in yeast. The same set of primers that amplify module constructed by Bahler et al. (1998) can be used to amplify the FLAG tag module constructed in this study. The linear DNA fragment containing FLAG tag module with flanking homology region of gene of interest can be efficiently integrated on the yeast genome, using homologous recombination. We have successfully FLAG tag wat1/pop3 gene at its chromosomal locus and confirmed by western blot analysis. This construct can be very useful for generating C terminal tagging of desired genes at its normal chromosomal locus without interfering with their function.
LIPID CHANGES AND SENSORY QUALITY OF WHOLE- AND GUTTED RAINBOW TROUT DURING STORAGE IN ICE

Background. The aquaculture rainbow trout may be a valuable source of long chain n-3 polyunsaturated fatty acid (LC n-3 PUFA). In the retail these fish are mainly present as a whole or gutted. The present study was aimed at comparing changes occurring in lipids of whole and gutted rainbow trout stored in ice. Materials and Methods. The analysis were performed after 0, 3, 7, and 14 days of storage in ice at 2°C and the following assays were carried out: proximate composition; lipid composition high pressure liquid chromatography (HPLC); fatty acid composition gas chromatography /mass spectrometry (GC/MS) by direct tissue saponification; contents of lipids extracted, using the Bligh-Dyer technique; UV-VIS, IR, and fluorescence lipid spectra; peroxide value (PV); anisidine value (AsV); and acid value (AC). Results. Gutting prior to storage made it possible to extend the sensory shelf-life by about 2–3 days and affected the quantitative fatty acid composition and oxidation level during storage in ice. The rainbow trout lipids are resistant to oxidation; oxidation product decomposition rather than lipid oxidation proceeds during storage, the decomposition being more intensive in whole than in gutted fish. It is only when the fish lose their eating quality (2 weeks) that a small increase in the level of oxidation occurs, accompanied by an about 15% loss of n-3 PUFA and a 20% loss of DHA, but only in the whole fish. Conclusion. Gutting rainbow trout prior to storage in ice is appropriate by the extending the shelf-life by about 2–3 days and keeping stable amount of n-3 PUFA during 2 weeks of storage.
Recovery of phytase produced by solid-state fermentation on citrus peel

The extraction of phytase produced by solid-state fermentation of citrus peel was studied employing a multistage leaching process. It was observed that the extracts containing EDTA retained over 90% of phytase activity at room temperature after 24 h after the leaching. A fractional design 22 (with 4 replicates at the central point) was carried out for testing the pH and agitation as process independent factors. Only the interaction between the pH and agitation showed a significant influence. These factors were optimized with a central composite design. Agitation at 300 rpm and pH at 5.0 were the best conditions to extract the enzyme from solid matrix. The modeling of the process indicated that diffusivity of the enzyme in the solvent was the controlling mechanism. The corresponding kinetic constant and saturation concentration in this process were 0.89 min-1 and 4.0 IU/mL, respectively. The multistage process indicated that after two steps, it was possible to recover 85% of total enzyme produced.
Quantitative analysis of biofilm formation by oropharyngeal Candida albicans isolates under static conditions by confocal scanning laser microscopy

Candida albicans may colonize natural or artificial surfaces, leading to formation of the biofilm. Infections associated with the biofilm formation are important therapeutic problem. In this paper, we present data concerning the biofilm formation under static conditions by oropharyngeal isolates of C. albicans on a glass surface using confocal scanning laser microscopy (CSLM). The areal parameters describing the architecture of biofilm and its development, i.e. the areal porosity, the length of edge line, the length of skeleton line, were calculated. The changes in values of these parameters during the biofilm formation by C. albicans were similar for biofilm consisting of only blastospores as well as the biofilm consisting of blastospores and filamentous elements (hyphae or/and pseudohyphae). However, the thickness of C. albicans biofilm consisting of blastospores and filamentous elements was much higher than that consisting of only blastospores. The heterogeneity may be regarded as an important feature of the yeast biofilm including C. albicans.
Toxicity of Biosal (Phytopesticide) and Permethrin (Pyrethroid) Against Common Carp, Cyprinus carpio

The objective of this study was to compare the toxicity of locally produced phytopesticide (Biosal) and synthetic pyrethroid (permethrin) against the fresh water fish Cyprinus carpio. Fry of Cyprinus carpio was treated with five different concentrations of Biosal and permethrin, separately for 24 hours. Experiment was repeated 10 times with each concentration, and mortality count was made. Mortality curve was drawn using regression line equation (y=a+bx) from the statistically computed results. It was found that LC50 of Biosal is 42133ppm (4.21 mg/L aquarium water) and LC50 of permethrin is 35.37ppm (35 µg/L aquarium water), indicating that permethrin was found nearly 1000 times more toxic than Biosal against fish fry as a non-target species.
Genotype Influences Body Composition of Developing Chicken Embryo

The effect of genotype on postnatal efficiencies of chickens has been well documented. However, little is known about the effect of genotype on body composition and metabolic physiology of chickens during embryonic development. To test the hypothesis that even with equalised egg weight at setting during incubation, there could be some effect of genotype on body composition, an experiment was conducted with embryonic chicks of broiler and layer genotypes at four stages of development during incubation (viz. 12, 16, 18, 20 d). Wet weight (P<0.01) and dry weight (P<0.05) of embryos were higher th in broilers compared to layers. Irrespective of genotype, the wet and dry weights increased (P<0.01) progressively and significantly from day 12 to day 20. Water content was not found to be affected by genotype but goes progressively down till 20 d of incubation. Body nitrogen concentration was higher (P<0.05) in the pre-hatch chicks of broiler vs. layer genotype th but stage of development did not significantly influence the value of this parameter. Broiler had higher (P<0.05) ether extract than layer prehatch chicks. Ether extract increased progressively and significantly (P<0.01) during the entire period of pre- hatch development. Body ash content was neither affected by genotype nor stage of development during embryonic period. This appears to be the first report that demonstrates differences in the body composition of broiler and layer genotype during embryonic life life itself.
Density–dependent recruitment rates in great tits: the importance of being heavier

In birds, individuals with a higher mass at fledging have a higher probability of recruiting into the breeding population. This can be because mass is an indicator of general condition and thereby of the ability to survive adverse circumstances and/or because fledging mass is positively related to competitive strength in interactions with other fledglings. This latter explanation leads to two testable predictions: (i) there is stronger selection for fledging mass when there is more severe competition (i.e. at higher densities); and (ii) that besides absolute fledging mass, relative mass of fledglings within a cohort is important. We test these two predictions in two great tit (Parus major) populations. The first prediction was met for one of the populations, showing that competition affects the importance of mass–dependent recruitment. The second prediction, that fledglings recruit relatively well if they are heavy compared to the other fledglings, is met for both populations. The consequence of the importance of relative rather than absolute fledging mass is that the fitness consequences of reproductive decisions affecting fledging mass, such as clutch size, depend on the decisions of the other individuals in the population.
In vitro biochemical investigations of the effects of Carica papaya and Fagara zanthoxyloides on antioxidant status and sickle erythrocytes

Various works have identified a number of herbal applications that have ameliorating effects on sickle cell disorders. The antisickling activities of dried Carica papaya leaves and roots of Fagara zanthoxyloides are being investigated in this study to determine the antioxidant properties of the plant extracts and their effects on homozygous sickle cell (SS) erythrocytes in vitro. The antisickling activity of both extracts were determined as well as analyses of hematological parameters, hemolysis of SS cells and formation of membrane associated denatured hemoglobin (MADH) used to measure the effects of plant extracts on the erythrocyte. Folin-Ctotal phenol and beta-carotene methods of assay were used to determine antioxidant activity, while the effect of plant extracts on oxidative stress was measured by assaying for superoxide dismutase, catalase, gluthathione transferase levels and lipid peroxidation. Results confirmed the potent antisickling activity of both plants. The levels of the oxidative stress enzymes (superoxide dismutase (SOD), catalase (CAT) and glutathione (GST) and lipid peroxidation were reduced after blood samples had been incubated with the extracts. The extracts therefore protected membrane integrity resulting in a reduction of red blood cells (RBC) hemolysis without met-hemoglobin formation. Both plant extracts possess potent antioxidant activity which may be responsible for their observed antisickling action. Key words: Fagara, papaya, oxidative stress enzymes, antioxidant activity, hemolysis.
Intergeneric and interspecific hybridizations among Glebionis coronaria , G. segetum and Leucanthemum vulgare

Cross-hybridizations between Glebionis coronalia (L.) Spach and G. segetum (L.) Fourr. , G. coronalia and Leucanthemum vulgare Lam. and G. segetum and L. vulgare by using ovule culture were successfully made the hybrid seedlings. RAPD primer OPA20 was found to isolate respective bands specific to G. coronalia, G. segetum, and L. vulgare. The F1 hybrids between G. coronalia and L. vulgare and G. segetum and L. vulgare showed morphologically rather the maternal-side leaf characters.
Interspecific and Inter‐site Variation in Wood Specific Gravity of Tropical Trees

Variation in climate and soils results in inter‐site differences in the assemblages of tree life history strategies within a community, which has important implications for ecosystem structure and dynamics. I investigated interspecific and inter‐site variation in wood specific gravity–an easily measured indicator of tree life history strategy–in four Neotropical forests and analyzed its correlates. Mean wood specific gravity (oven‐dry weight divided by fresh volume, sometimes also referred to as wood density in the literature) differed significantly among sites, varying inversely with soil fertility and independently of rainfall, seasonality, and temperature. Mean wood specific gravity values were much higher at Kilometer 41, Manaus, Brazil, where soils are extremely poor, than at Cocha Cashu, Peru, Barro Colorado Island, Panama, or La Selva, Costa Rica, where soils are better and mortality rates of trees are higher. Within sites, wood specific gravity varied widely among species. On Barro Colorado Island, among‐species variation was significantly, albeit weakly, negatively correlated with sapling and tree mortality and relative growth rates. Altogether, the results suggest that the distribution of tree life history strategies in a community varies substantially among sites, with important consequences for community and ecosystem properties such as aboveground carbon stores.
GENETICS AND CELL BIOLOGY PROTECTIVE EFFECTS OF SERICIN PROTEIN ON ALCOHOL-MEDIATED LIVER DAMAGE IN MICE

Aims: The purpose of this study was to investigate the protective effects of sericin protein (SP) on alcohol-induced hepatic injury in mice and the possible mechanisms. Methods: SP (0.375, 0.75 and 1.50 g/kg body weight) was dissolved in distilled water and given to mice by gavage 1 hour before the alcohol (56% wt/vol, 14.2 ml/kg b.w.) treatment for 30 days, then blood, urine and liver were collected, processed and used for alcohol concentration mensuration, various biochemical estimations and histopathological examination. Results: The concentration of alcohol evidently decreased in serum and increased in urine in SP treated mice as compared to alcohol-administered animals. Chronic alcohol administration resulted in significantly increase in the levels of transaminase (AST and ALT) and malondialdehyde (MDA) but decrease of glutathione (GSH), glutathione peroxidase (GSH-PX), catalase (CAT) and superoxide dismutase (SOD) in the serum and liver. Hepatic triglyceride (TG) also increased. When mice ingested high doses of SP (0.75 and 1.50 g/kg b.w.) the levels of antioxidant enzymes in the serum were restored to normal. However, hepatic CAT and GSH were still below normal, although a trend of significant increases was observed in comparison with alcohol treatment group. Conclusions: The results indicated that SP was able to hasten the alcohol elimination through urine directly and enhance the ethanol oxidation rate in liver. Simultaneously, SP may exert a protective effect against lipid peroxidation by scavenging reactive oxygen species and elevating the activity of antioxidant enzymes, in consequence prevented the peroxidative deterioration of structural lipids in membranous organelles, especially mitochondria and karyon.
Systematic placement of the recently discovered beetle family Meruidae (Coleoptera: Dytiscoidea) based on molecular data

The family Meruidae has been established recently for the newly discovered species Meru phyllisae Spangler & Steiner, 2005 from Southern Venezuela. These beetles are morphologically highly distinct and at a body length of 0.8 mm represent the perhaps smallest individuals of Adephaga. Here, we use DNA sequence data to place this enigmatic taxon relative to other aquatic groups in this suborder. Meruidae was most closely associated with Noteridae, supporting a previous analysis of morphological structures which had suggested this sister relationship, albeit with weak support. While different alignment strategies did not affect the topology, the precise placement of Meruidae was affected by the choice of tree reconstruction method. Bayesian inference suggests a sister relationship of Meruidae + Noteridae, while parsimony analyses retrieve Meruidae + Notomicrus (a basal noterid genus), which combined are the sister group of all remaining Noteridae. Considering morphological evidence, the former placement appears more plausible.