Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematics and evolutionary history of the circum­Mediterranean genus Anagyris L. (Fabaceae) based on morphological and molecular data

A taxonomic survey of the relict and poorly known circum-Mediterranean Anagyris (Fabaceae) was conducted using a total evidence principle approach based on morphological and molecular data. Statistical analysis of both qualitative and quantitative morphological and chemically-derived traits allowed us to separate the Mediterranean A. foetida and the Canarian A. latifolia as independent species. Newly analyzed traits relating to the odour of leaves, number of inflorescences per branch, colour of fresh calyx, and degree of corolla opening, were diagnostic for identifying these two previously almost indistinguishable taxa. Significant differences in quantitative morphometric traits indicate that vegetative and floral characters are overall larger in A. latifolia than in A. foetida, supporting the hypothesis of increased size and woodiness of Macaronesian endemic plants compared to the reduced sizes of their continental counterparts adapted to the more xeric Mediterranean climate. Combined plastid trnLF and nuclear ribosomal ITS data recovered a monophyletic origin of Anagyris within the central-western Eurasian Thermopsideae clade and its split into two lineages. The dated divergences of the Anagyris lineages, calculated by Bayesian relaxed-clock methods with the combined sequence data, showed that Anagyris diverged in the late Miocene (8.2 ± 4.5 Ma), and that the origin of A. foetida (3.6 ± 3.2 Ma) pre-dated that of A. latifolia (1.9 ± 2.1 Ma).
First report of Artibeus bogotensis Andersen, 1906 (Chiroptera: Phyllostomidae) for Peru

Artibeus bogotensis (Phyllostomidae: Stenodermatinae) is reported for the first time for Peru. This record is based on the re-identification of a subadult female specimen collected at the Jenaro Herrera Research Center, District of Jenaro Herrera, Province of Requena, Department of Loreto, Peru. The comparative study between Artibeus bogotensis and other Artibeus species ( Artibeus glaucus and Artibeus anderseni ) was based on morphological and morphometric analyses. This noteworthy record means an expansion of its known distribution and, also, adds another bat species for Peru.
Genetic parameters for rank of the Santa Inês sheep in agricultural fairs using Bayesian procedures

Abstract The aim of this study was to estimate the genetic parameters for the ability of a sheep to rank among the top three in its age category (ABI3) and for its total score (TS) on the judgement championships held in different agricultural fairs in Brazil. Data files included 3180 records referring to 1896 animals for ABI3 and 4383 records referring to 2170 animals for TS. The relationship matrix was composed by 4069 animals. Variance components were estimated fitting threshold and linear animal models for ABI3 and TS, respectively, by Bayesian analysis using the Gibbs sampler. The posterior means of the heritability and repeatability were, respectively, 0.10 ± 0.07 and 0.57 ± 0.11 for ABI3 and 0.12 ± 0.04 and 0.31 ± 0.02 for TS. The low values for the heritabilities related to these traits reveal a strong influence of the environmental factors, as the differential management offered to the animals before and during the fair. The repeatability values for ABI3 suggest high correlation among the animal classifications in different fairs. However, for TS, the observed performance has moderate confidence to be repeated over time. We conclude that although reduced, there is genetic variability for the animal’s performance in agricultural fairs. Nevertheless, due to the low heritability estimates, the expected response to direct selection for ABI3 and TS will be low.
Effective application of next-generation sequencing (NGS) approaches in systematics and population genetics: case studies in Eucalyptus and Acacia

Abstract. Next-generation sequencing (NGS) provides numerous tools for population and systematic studies. These tools are a boon to researchers working with non-model and poorly characterised organisms where little or no genomic resources exist. Several techniques have been developed to subsample the genomes of multiple individuals from related populations and species, so as to discover variable regions. We describe here the use of a modified AFLPseq method that provides a rapid and cost-effective approach to screening variable gene regions (SNPs) for multiple samples. Our method provides an adaptable toolkit for multiple downstream applications, which can be scaled up or down depending on the needs of the research question and budget. Using minor modifications to the protocol, we successfully recovered variable and useful markers that were applied to three case studies examining different scales of biological organisation, namely, from within populations to phylogenetic questions at the genus level and above. The case studies on Acacia and Eucalyptus generated genomic data across multiple taxonomic hierarchies, including demonstrating the detection of Acacia pinguifolia J.M. Black individuals used in restoration and their population origins, regional phylogeography of Acacia pycnantha Benth. , and SNP-marker conservatism across some 70 million years of divergence among the Myrtaceae.
Hypotheses and trends on how body size affects trophic interactions in a guild of South American killifishes

A chief structuring force in food webs is the hierarchy of trophic interactions, where bigger animals feed on smaller ones. The anatomic and physiological explanations of why body size determines this hierarchy are embodied within the concept of gape limitation. The relaxation of gape limitation and an increase in energetic demands due to predators' larger body size determine the size and diversity of prey species. However, these patterns may be related to further trends in trophic interactions with body size, which have been less considered. Specifically, the passive incorporation of prey should involve a nested distribution of prey among predator size classes. However, predators avoid smaller resources because of their low energy return, with a clumped distribution of prey potentially generating modular organization with qualitative changes in prey identity (e.g. zooplankton, macroinvertebrates and fishes). Finally, size-mediated interactions (such as direct and indirect competition) may cause predators of similar body size to differentiate among prey organisms, resulting in a checkerboard distribution of prey identity. Consequently, nestedness, modularity and checkerboard distributions of prey among predators of different size classes should form emergent network structures that are directly related to clear ecological mechanisms. We analyse these predictions in a killifish guild, where trends in trophic positions, prey richness, evenness and the number of energy sources systematically scale with body size. We found significant nestedness and segregation in diet among different size classes, supporting the progressive incorporation of prey items coupled with prey differentiation among similar classes. However, we also detected an ‘anti-modular’ trend, which contradicts theoretical expectations and previous results. We hypothesize that this anti-modularity is determined by the high biodiversity of the system and the continuous representation of prey size classes. These results reinforce the concept of size-mediated interactions and its connection with community biodiversity as a main structuring force of food webs.
Characterization of Salmonella isolates obtained from pigs slaughtered at Wambizzi Abattoir in Kampala, Uganda

Globally, non-typhoidal salmonellosis accounts for approximately 80.3 million cases of human infections annually. Estimates of salmonellosis due to consumption of pork or pork products is difficult to determine but, it ranges from < 1% to 25%. These invasive pathogens colonize intestinal mucosal surface but, they are self-limiting in health individuals due to a noble immunity. Utilization of antimicrobial agents in pig farming has been associated with the spread of resistant Salmonella species to man and the carrier status presents a major hazard to human health. This study examined 54 isolates for antimicrobial resistance, sequenced seven housekeeping genes, and performed Multi-Locus Sequence Type (MLST) analysis. We detected â-lactamase and tetA(B) genes in 100% and 80% of the isolates respectively. Data analysis using Codon-based Test of Neutrality analysis between sequences revealed P-value less than 0.05, an indication of strong forces of natural selection pressure acting at the sequence type level. Further data analysis using the Maximum Composite Likelihood Estimate of the Pattern of Nucleotide Substitution discovered frequencies of 0.177 (A), 0.244 (T/U), 0.263 (C), and 0.317 (G). The transition/transversion rate ratios were found to be k1 = 2.698 (purines) and k2 = 20.089 (pyrimidines) with an overall transition/transversion bias of R = 6.565, where R = [A*G*k1 + T*C*k2]/[(A+G)*(T+C)] further confirming that indeed the Salmonella isolates studied here were divergent. These results suggest that, sequence types (STs) coexist in the intestine thereby providing for an efficient intestinal colonization and multiple adaptations. Our results offer general and rapid approaches for identifying genetic diversity of Salmonella serotypes in individual pig carcasses which can be adopted for molecular epidemiological surveys of important food contaminating bacterial pathogens.
In silico analysis of subcellular localization of putative proteins of Mycobacterium tuberculosis H37Rv strain

Mycobacterium tuberculosis is a facultative intracellular pathogen that has evolved the ability to survive and multiply within human macrophages. These bacteria comprise of significant proteins, which were involve in the pathogenesis and regulation of cell activity. The insilico prediction of protein subcellular localization has been extensively studied for prokaryotic, virus and eukaryotic organisms. But, in the case of Mycobacterium, proteins are often involved in extensive interactions at various subcellular localizations in cell. Total thirty-nine putative proteins of M. tuberculosis were predicted for four locations viz cytoplasmic, integral membrane, secretory and protein attached to membrane by Lipid anchor in the subcellular localization. Such predictions provide a method to annotate Mycobacterium proteomes with subcellular localization information rapidly. They have widespread applications in function of proteins in the host cell and in designing the tuberculosis drugs.
Isolation and characterization of polymorphic microsatellite DNA Markers from an Amazonian white-sand vegetation specialist bird, Xenopipo atronitens (Aves: Pipridae)

ABSTRACT Thirteen novel polymorphic microsatellite loci were isolated and characterized from the Amazonian Black Manakin, Xenopipo atronitens. The loci were screened using 30 samples from Brazil. A total of 13 loci were variable with number of alleles per locus ranging from 2 to 17, whilst the observed and expected heterozygosities varied from 0.067–0.900 and 0.310–0.910, respectively. Five loci deviated significantly from the Hardy–Weinberg equilibrium, whereas one pair of loci deviated significantly from linkage disequilibrium. The set of markers will be a useful tool for future population genetic and kinship studies of X. atronitens, an Amazonian white-sand vegetation specialist.
Cloning, regulation and purification of cellulase-free xylanase from Bacillus circulans Teri-42

The isolate, Bacillus circulans Teri-42 was found to produce higher xylanase on oat spelt xylan (OSX) than any other substrate. The enzyme was constitutive showing no catabolite repression when grown on glucose, xylose and other soluble substrates. Xylanase purified to homogeneity by Q-Sepharose and Sephadex G-50 chromatography from the culture supernatant was found to have molecular weight of 71 Da with the Km value of 2.86 mg mL - 1 . Xylanase was stable over a wide range of pH (6-8) and maximum activity was at 50°C. Cloning of xylanase gene of B. circulans in E. coli (pAQ4) showed that the latter excreted 88% of the xylanase. The 1.7 kb insert had internal sites for Eco RI, Pst I and Sph I.
Narrative competence of bilingual children: an exploratory study of Franco-Chinese children aged 5 to 10 years old in France

The aim of this paper is to analyze and to describe the narrative competence of bilingual children, who speak both Chinese and French and are living in France. This study is focused on two aspects: the differences in narrative competence of the two languages of bilingual children aged 5 to 10 years old and the development of the narrative competence of this group. In the research, the narrative competence of children in both languages will be measured by using an object-oriented story.
Rats’ Metabolic Responses to Chronic Intervention with Cantonese Herbal Tea

Cantonese Herbal Tea (CHT) is consumed in south China to alleviate feelings of discomfort due to the over-heat and humidity in the body, but the related molecular mechanisms behind its effects remain obscure. The urinary metabolic responses to CHT over time in rats were investigated during a 38-day-period using GC-MS-based metabonomics. Integrated with student’s t-test and Orthogonal Projection on Latent Structures Discriminant Analysis (OPLS-DA) at each time point revealed that the process could be divided into two stages. In the first stage, the bioefficacy was characterized by elevated antioxidant activity and the depletion of oxidative stresses. However, the effect was reduced with time and replaced by a second stage characterized by the decreased flow of energy metabolism and an imbalance in gut microbiota. In conclusion, metabonomics study gained insight into the metabolic changes induced by CHT intake and the extent to which CHT intake influences the urinary metabolome, which also provides a powerful method for understanding the mechanism of CHT.
Manufacture of Functional Labneh Using Uf-Retentate and Artichoke Puree

Artichoke, UF-retentate and Bifidobacteria were used in success to manufacture novel functional labneh treatments in this study. Artichoke (Cynara scolymus L.) puree was added in ratios of 0, 15, 30 and 45% of the formula. Bifidobacterium bifidum, Lactobacillus bulgaricus and Streptococcus thermophilus (1:1) were added to produce lactic acid and healthy compounds. Total solids, fat/dry matter, ash, pH values, Total Nitrogen (TN), Soluble Nitrogen (SN) contents and Total Volatile Fatty Acids (TVFA) were determined. All samples texture profile measurements were also carried out. Streptococcus thermophilus continuously increased in all treatments followed by slight decrease towards the end of the storage period especially with control. Also, Bifidobacterium bifidium numerous increased during storage period to reach up to log 9.00 CFU gG1 especially in the treatment that contained 30% artichoke puree. Results demonstrated that artichoke is a suitable food carrier that allows the survival of potentially probiotic strains. Preferences of treated samples 15 and 30% artichoke puree were as well as the control especially in outer appearance and flavour.
Studies on the Mechanism of Physiological Activity of Coronatine

Coronatine is an extracellular toxin produced by Pseudomonas coronafaciens var. atropurpurea (Reddy and Godkin) Stapp, the incitant of the chocolate spot disease on Italian ryegrass (Lolium multiflorum Lam.). Coronatine induced the necrosis with chlorotic halo symptoms of the disease in host leaves as well as in non-hosts and thus is nonspecific. Coronatine, at low concentration of 0.05 mM to 0.5 mM, also induced marked hypertrophy only on potato tuber tissues. When a potato tuber cylinder was incubated with coronatine before the extensibility measurment, the plasticity was greater than that of the control, suggesting that coronatine is required to increase the plasticity of the cell wall for cell expansion. Coronatine-induced water uptake was quantitatively inhibited by tree entirely different type of inhibitors, suggesting that water uptake by potato tuber tissue in the presence of coronatine externally added is linked to the general aerobic metabolism and corresponds closely to outgrowth of potato tuber tissue. Coronatine-induced tissue deformability of potato cylinder was reduced by treatment with actinomycin D and cycloheximide. These results suggest that RNA and protein syntheses seem to be essential prior to cell expansion and tissue deformation. It can be therefore concluded that coronatine may control the syntheses of enzymes which loosen the cell wall before expansion of the cell by turgor pressure. The rapid increase in cell expansion of potato tissue treated with coronatine was accompanied by disapperance of starch grains in the cell. We conclude from the experiments described above that the effect of coronatine on cell enlargement depends on both increases in the plasticity of the cell wall and in osmotic pressure in the cell sap. (Received August 25, 1979)
Effect of in ovo Feeding and Dietary Feeding of Silybum marianum Extract on Performance, Immunity and Blood Cation-Anion Balance of Broiler Chickens Exposed to High Temperatures

This experiment was conducted to investigate the effect of in ovo feeding (IOF) and dietary feeding of Silybum marianum (SM) extract on the immunity of chicken under heat stress conditions. A total of 360 fertile eggs from a commercial broiler breeder (Ross-308) farm was used for in ovo feeding of 0, 100 and 200 mg/L SM water extract at day 17.5 of incubation. After hatching, 240 chicks were transferred to the experimental cages. Two types of diet were used; one of them without extract and the other one containing 100 mg/kg of SM extract. Then chicks were exposed to elevated temperatures 4 ˚C above optimum from 7 to 28 days of age for 4 h daily and then they were kept at the optimum temperature. The chicks were divided into six treatments with four replicates as a completely randomized design with 2 × 3 factorial arrangement. The results showed that chicks fed diet containing the extract had the highest feed intake, daily weight gain and final body weight and lowest feed conversion ratio (P<0.01). At 28 and 42 days, dietary feeding of the extract increased the relative weights of bursa (P<0.05), thymus and spleen (P<0.01) significantly. Results showed a significant increase (P<0.05) in antibody titer against infectious bursal disease (IBD) by feeding extract. White blood cell counts was significantly higher (P<0.01), and heterophile/lymphocyte(Het/Lym) ratio was lower in dietary-feeding SMextract treatments (P<0.01). The dietary feeding of extract increased blood cationic charge (Na+ and K+) at 28 d and led to increase cation-anion equation (P<0.01). However at 42 d, effect of dietary feeding of extract on these parameters was not significant. The ash percentage was significantly higher in chicks fed 100 mg/kg of extract at 28 d (P<0.01). It seems that dietary feeding of the extract to broiler chickens considerably increased immunity response under elevated temperatures, but in ovo feeding of the extract had no much impact on immunity parameters.
Effect of spatial differences in habitat on home ranges of grizzly bears

Abstract Between May 1995 and June 1999 we equipped 81 barren-ground grizzly bears (Ursus arctos) with satellite radio-collars within a study area of 235,000 km2, centred 400 km northeast of Yellowknife, Northwest Territories. We estimated 71 annual ranges of radio-tracked animals (≥ 38 locations year-1) using the 95% fixed kernel technique with least squares cross-validation. Annual ranges of males ( x= 7,245 km2, SE = 1,158, n = 26) were larger than ranges of females (X= 2,100 km2, SE = 279, n = 45). Ranges increased in size as the proportional amount of exposed bedrock and other marginal habitats in the environment increased. Annual ranges are the largest reported for grizzly bears in North America.
Changes in fatty acid composition, cholesterol contents and quality attributes of bolti (Tilapia nilotica) fingerlings in relation to dietary lipid levels and sources in feeding regime

Summary This study was carried out to determine the fatty acids composition, cholesterol levels and quality attributes in muscle tissue (filet) of bolti (Tilapia nilotica) fingerlings as affected by feeding different sources and levels of lipids during 90 days. Corn oil and cod liver oil were added to the feeding regime (2 %, 4 % and 6 %) alone or as mixtures (1 : 1, w/w). The total lipids and cholesterol contents were found in the range of 2.55-8.14 g/100 g and 42-53 mg/100 g fish, respectively. All feeding treatments presented oleic acid C18:1n-9, as predominant fatty acid fol- lowed by linoleic C18 : 2n-6, palmitic acid C16 : 0 and stearic acid C18 : 0, respectively. The highest amount of total polyunsaturated fatty acids was detected when a mixture of 1 % corn oil and 1 % fish oil was enclosed in the fish diet. Concerning quality parameters (pH, TVN, TMA and TBA), there were no effects for dietary fat levels and sources on the quality at- tributes of the fish flesh.
Recovery of lakes and coastal marine ecosystems from eutrophication: A global meta‐analysis

In order to inform policies aimed at reducing nutrient emissions to surface waters, it is essential to understand how aquatic ecosystems respond to eutrophication management. Using data from 89 studies worldwide, we examined responses to the reduction or cessation of anthropogenic nutrient inputs relative to baseline conditions. Baseline conditions were pre‐disturbance conditions, undisturbed reference sites, restoration targets, or experimental controls. We estimated recovery completeness (% baseline conditions reached) and recovery rate (annual % change relative to baseline conditions) for plant and animal abundance and diversity and for ecosystem functions. Categories were considered fully recovered if the 95% confidence interval (CI) of recovery completeness overlapped 100% and partially recovered if the CI did not overlap either 100% or zero. Cessation of nutrient inputs did not result in more complete or faster recovery than partial nutrient reductions, due likely to insufficient passage of time, nutrients from other sources, or shifting baselines. Together, lakes and coastal marine areas achieved 34% (±16% CI) and 24% (±15% CI) of baseline conditions decades after the cessation or partial reduction of nutrients, respectively. One third of individual response variables showed no change or worsened conditions, suggesting that achieving baseline conditions may not be possible in all cases. Implied recovery times after cessation of nutrient inputs varied widely, from < 1 yr to nearly a century, depending on response. Our results suggest that long‐term monitoring is needed to better understand recovery timescales and trajectories and that policy measures must consider the potential for slow and partial recovery.
Controlled-release Fertilizers Affect Nitrate Nitrogen Runoff from Container Plants

Container plant runoff N O3-N levels varied with sampling time and were periodically higher than the 10-ppm federal drinking water standard during 4.5 months following fertilizer application, even though controlled-release fertilizers Nutricote 18N-2.6P-6.6K Osmocote 18N-2.6P-10K, Prokote 20N-1.3P8. 3K, and Woodace 19N-2.6P-10K were used. Leachate collected from containers had a higher NO3-N level than runoff regardless of sampling time. Leachate NO3-N ranged from 278 ppm for Nutricote 3.5 months after application to 6 ppm for Prokote 1 week after application.