Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel roles of Celf1 and Tia1 during vegetal RNA localization in Xenopus laevis oocytes

The localization of certain mRNAs to the vegetal cortex of Xenopus oocytes is of crucial importance for germ cell development and germ layer formation of the future embryo. Vegetal RNA localization is mediated by signal sequences within the RNA. These so-called localization elements recruit certain proteins that direct transport to the vegetal cortex. Although numerous localization ribonucleoprotein (RNP) components have been identified, their full composition is yet unknown. The Xenopus RNA binding proteins Celf1 (CUGBP, Elav-like family) and Tia1 (T-cell internal antigen 1) are novel components of vegetal localization RNPs that we identified in an RNA affinity purification approach, using the dead end 1 (dnd1) RNA localization element. Both Celf1 and Tia1 are detected as parts of an RNP complex together with other known vegetal localization proteins and show specific interactions with localization elements from several vegetally localizing RNAs. Immunostaining experiments reveal co-localization of Celf1 and Tia1 with vegetally localizing RNA and with known localization factors. Inhibition of Celf1 protein binding by localization element mutagenesis as well as Celf1 overexpression interfere with vegetal RNA localization, suggesting an active role for Celf1 during vegetal RNA transport in Xenopus oocytes. Ectopic expression of Celf1 and Tia1 in Xenopus embryos counteracts somatic degradation of dnd1 localization element reporter RNAs. Furthermore, Tia1 protects several other localizing and germ cell specific mRNAs from somatic degradation and synergizes with the germ cell specific protein Dnd1. These results suggest that Celf1 and Tia1 are components of vegetal localization RNPs in oocytes that could have additional functions in the protection of germ cell specific RNAs in early embryos. Furthermore, Celf1 is enriched at the vegetal cortex in zebrafish oocytes and thus may play a conserved role in vegetal RNP complexes of fish and frogs. Celf1 loss of function approaches in zebrafish result in the primary development of males, indicating a role of Celf1 during zebrafish sex determination or female viability. Our results reveal Xenopus Celf1 and Tia1 as novel components of vegetal localization complexes. While Celf1 actively participates in vegetal RNA localization in oocytes, both Celf1 and Tia1 seem to act in germ cell specific RNA protection in embryos. These findings support the idea that both mechanisms share the same proteins and they highlight the functional link between RNA localization and germ cell formation.
Salmonella enterica, Listeria monocytogenes and Clostridium perfringens:

5 LIST OF ORIGINAL PUBLICATIONS 7 ABBREVIATIONS 8 INTRODUCTION 9 REVIEW OF THE LITERATURE 10 1. Food-borne infections and intoxication 10 1.1. Terminology 10 1.1.1. Infections 10 1.1.2. Intoxication 10 1.2. Clinical symptoms 10 1.3. Risk factors associated with food 12 1.4. Risk factors associated with humans 13 1.5. Factors associated with food-borne pathogens 13 1.6. Burden of diseases 15 1.7. Prevention 15 1.8. Surveillance in Finland 16 2. Common food-borne pathogens 16 2.1. Bacteria 16 2.1.1. Salmonella enterica 18 2.1.2. Clostridium perfringens 22 2.1.3. Listeria monocytogenes 24 2.2. Other bacteria 27 2.3. Viruses and parasites 31 3. Characterization of bacteria for epidemiological surveillance 32 3.1. Phenotyping methods 32 3.1.1. Biotyping 32 3.1.2. Serotyping 34 3.1.3. Phage typing 35 3.1.4. Determination of antimicrobial resistance patterns 35 3.1.5. Detection of toxin production 35 3.2. Genotyping methods 36 3.2.1. Plasmid analysis 36 3.2.2. Polymerase chain reaction (PCR) 37 3.2.3. Ribotyping 38 3.2. 4. Pulsed-field gel electrophoresis (PFGE) 38 AIMS OF THE STUDY 40
Biochemical mechanisms of insecticide resistance in the diamondback moth (DBM), Plutella xylostella L. (Lepidopterata: Yponomeutidae), in the Sydney region, Australia

Following the detection of resistant diamondback moth (DBM) populations to synthetic pyrethroid, organophosphorus and indoxacarb insecticides in the Sydney Basin, a study of the major biochemical mechanisms was conducted to determine the type of resistance in these populations. The activity of cytochrome P450 monooxygenases increased two- to sixfold when compared with the susceptible strain. Up to a 1.9-fold increase in esterase activity in resistant strains compared with the susceptible strain was observed. In vitro inhibition studies showed that profenofos, methamidophos and chlorpyrifos strongly inhibited the esterases while permethrin and esfenvalerate resulted in less than 30% inhibition. Qualitative analysis of the esterases using native polyacrylamide gel electrophoresis showed four bands in both the susceptible and resistant individuals with more intense staining in the resistant individuals. The development of these bands was inhibited by methamidophos and chlorpyrifos pretreatment of the protein extract while permethrin and esfenvalerate did not exhibit this effect. Glutathione S-transferase (GST) activity was significantly higher in two field populations compared with the remaining populations. Overall, the study showed that the mechanisms of insecticide resistance in the DBM populations in the area studied were due to cytochrome P450 monooxygenases, esterase and GSTs, and possibly other non-metabolic mechanisms that were not investigated in the present study.
There are no minimal homeomorphisms of the multipunctured plane

The main results of this paper are the following theorem and its corollary. Theorem 0.1. Suppose that f: S2 → S2 is an orientation-preserving homeomorphism of the two-dimensional sphere and that Fix (f) is a finite set containing at least three points. If f has a dense orbit then the number of periodic points of period n for some iterate of f grows exponentially in n.
Proactive Conservation Management of an Island-Endemic Bird Species in the Face of Global Change

Biodiversity conservation in an era of global change and scarce funding benefits from approaches that simultaneously solve multiple problems. Here, we discuss conservation management of the island scrub-jay (Aphelocoma insularis), the only island-endemic passerine species in the continental United States, which is currently restricted to 250-square-kilometer Santa Cruz Island, California. Although the species is not listed as threatened by state or federal agencies, its viability is nonetheless threatened on multiple fronts. We discuss management actions that could reduce extinction risk, including vaccination, captive propagation, biosecurity measures, and establishing a second free-living population on a neighboring island. Establishing a second population on Santa Rosa Island may have the added benefit of accelerating the restoration and enhancing the resilience of that island's currently highly degraded ecosystem. The proactive management framework for island scrub-jays presented here illustrates how strategies for species protection, ecosystem restoration, and adaptation to and mitigation of climate change can converge into an integrated solution.
MODELING THE CONSEQUENCES OF ANTARCTIC KRILL HARVESTING ON ANTARCTIC FUR SEALS

In terms of the convention governing the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR), management advice for the Antarctic krill (Euphausia superba) fishery should take the needs of the predators of krill into account in order to reduce the risk of deleterious impacts on such predators (e.g., baleen whales and numerous fish, seal, penguin, and flying bird species). A single species yield model is currently being used by the CCAMLR Scientific Committee to recommend an annual krill catch limit, which is expressed as a proportion (γ = 0.116) of a survey biomass estimate. This approach takes the needs of predators into account in only a crude way by assuming that a median krill escapement of 75% of its unexploited biomass would be sufficient to meet the needs of predators. A krill–predator modeling procedure is presented that could be used to directly assess the impact of krill harvesting on krill predator populations and therefore to revise this recommended harvesting level (γ) for Antarctic krill. Application of a deterministic form of this model to an Antarctic fur seal (Arctocephalus gazella) data set from Bird Island, South Georgia, Antarctica, indicates that the level of krill fishing intensity (γ) that would reduce this population to half the equilibrium size in the absence of krill fishing (γhalf) lies between 0.03 and 0.18, which includes the level recommended by CCAMLR. This large range results primarily from the sensitivity of the model to the maximum growth rate parameter, for which a range of 5–15%/yr is investigated. A plausible range of values for this parameter (5–15%/yr) results in estimated γhalf values from 0.04 to 0.23. Stochastic calculations (which take account of interannual fluctuations in the abundance of the krill population due to recruitment variability) yield higher estimated γhalf values than the less realistic deterministic calculations. However, simulation tests indicate that the estimated γhalf values are biased upward; this modeling approach is therefore likely to yield γhalf values that would lead to a depletion of the Antarctic fur seal population to more than half its pristine size.
Oferta hídrica de la cuenca forestal Tapalpa, Jalisco, orientada hacia los servicios ambientales

In order to assess the feasibility of creating a water market in the Tapalpa, Jalisco, Mexico watershed, the SWAT model was fitted to obtain the watershed water balance. The model was calibrated in one of the five subwatersheds included in the Tapalpa watershed with a good fit (R 2 = 0,85). All five forestry subwatersheds had good hydrologic behavior, allowing high infiltration water rates, which later on emerges as surface runoff with low sediment yields. The subwatersheds with high percentage of agriculture and grasslands yield more surface runoff as well as more sediment yields. The evapotranspiration from the forestry subwatersheds were higher than agricultural subwatersheds. The water supply from the Tapalpa watershed is 42’963,900 m 3 per year on average.
Twelve microsatellite loci in Manilkara huberi (Ducke) Standl (Sapotaceae), an Amazonian timber species

Manilkara huberi is a timber species, found and intensely exploited in the Amazonian forest. Twelve highly polymorphic microsatellite loci were developed from a genomic library enriched for AG/TC repeats. Levels of polymorphism were evaluated using a total of 12 adult trees from a natural population. An average of 6.43 alleles per locus were detected, and expected heterozygosity ranged from 0.721 to 0.862. These loci represent a powerful tool in investigating the mating system, gene flow, parentage and population dynamics in natural populations of M. huberi, all of which are needed to implement sound management.
Performance of Starter Broilers Fed Anaerobically Fermented and Lyle Treated Delonix regia Seed Meal

One hundred and twenty day-old Hubbard broiler birds were used to study the effects of anaerobic fermentation and lyle treatment of Delonix seed meal on the performance of starter broilers. The experimental period spanned 5 weeks. The birds were divided into four treatment groups of three replicates each using complete randomized design. The anaerobically fermented and lyle treated Delonix seed meal (AFLTDSM) was used to replace groundnut cake (GNC) at 0%, 5% and 7.5% level. Untreated raw Delonix seed meal (URDSM) was also used at 5% level in order to evaluate its effects on starter broiler performance. The four treatments were designated as T , T , T and T respectively. Parameters evaluated were mean body 1 2 3 4 weight, daily body weight gain, mean feed intake, mean feed conversion ratio as well as apparent nutrient digestibility. The results showed that mean body weight, daily body weight gain, mean feed intake and mean feed conversion ratio were not significantly affected (p>0.05) by the substitution of GNC with AFLTDSM in the diets. However, apparent nutrient digestibility of dry matter (DM), crude protein (CP), ash, ether extract (EE) and Nitrogen free extract (NFE) were significantly affected (p 0.05) by the inclusion of Delonix seed meal in the diets. It wa s concluded that AFLTDSM could be used as a substitute for GNC in starter broilers diet without any significant effect on the performance of the birds.
Performance and Carcass Composition of Broilers Fed Different Carbohydrate and Protein Sources in the Prestarter Phase

Abstract Chicken growth rate has increased substantially in the past decades, causing slaughter weight to be attained sooner and increasing the representativeness of the first days of life. Prestarter diets are presently used in a variety of situations in poultry production and are interpreted as investment, not a cost in production. Studies to define the nutrient requirements in the prestarter period are seconded by the necessity to search for ingredients with high nutrient availability that will result in improved animal performance associated with good carcass quality. Alternative ingredients with excellent digestibility must be used in diets for newly hatched chicks, because their digestive system is not completely adapted to the digestion and absorption of feeds. This research evaluated the effects of alternative carbohydrate and protein sources in prestarter broiler chicken diets on the performance, digestive organ morphometry, and carcass composition and yield. The effects of different carbohydrate and protein sources found at the prestarter phase were not maintained in subsequent phases.
Estimation of Nutrient Equivalency Values of Natuzyme and Its Effects on Broiler Chick Performance

SUMMARY Two experiments were carried out to estimate nutrient equivalency of a commercial multienzyme (Natuzyme) and its effects on broiler chick performance. Experiment 1 was carried out using a completely randomized design to evaluate the response of chicks to Natuzyme (with different equivalency values assigned by the producer) in corn-soybean meal-based diets. Dietary treatments 1 and 6 were negative and positive controls, respectively. Diets 2 through 5 were graded levels of nutrient equivalency values of Natuzyme. Each diet was offered to 5 replicates of 16 chicks (n = 480). In experiment 2, a total of 480 male Ross 308 broiler chicks were used in a completely randomized design. Treatment 1 to 4 varied in ME, CP, and nonphytate P content, but in all cases, the ratio between these nutrients remained constant, and treatments 5 to 8 included graded levels of Natuzyme from 0.1 to 0.4 g/kg. Results of experiment 1 show that multi-enzyme supplementation could not restore chick performance to the levels equal to positive control. Equivalency values of Natuzyme for ME, nonphytate P, and CP obtained were 195,180 kcal/kg and 188.45 and 1,170%, respectively. As obtained in the first experiment, performance of chicks in the second experiment showed that Natuzyme did not liberate nutrient equivalency values recommended by the producer for broiler chicks when fed corn-soybean meal-based diets.
Stream Drift as a Chronobiological Phenomenon in Running Water Ecosystems

Waters (141) made a thorough review of stream drift, particularly with regard to insects, in the Annual Review of Entomology (141), providing an excellent survey of the historical development within this special field of running water ecology. This review gives an interpretation of the phenomenon of drift and its function in running water, as well as a presentation of the relevant literature up to 1972. The context in which I take up these problems is one concerning stream drift as a chronobiologic phenomenon. The starting point for this presentation consists of a number of independent studies, performed in various parts of the world, which have shown that stream drift occurs with a diel rhythmic pattern. This finding is based on the extensive investigation of Tanaka (125) in a Japanese stream, Waters (134) in Minnesota, Muller (75) in central Europe, Elliott (23, 25-27, 29, 31, 33) in the British Isles, and Levanidova & Levandov (63, 64) in eastern Siberia. The 24 hr cycle with its continuously changing light-dark periods (depending on the time of year and latitude) causes, directly or indirectly, variations in the physical and chemical factors in running water. It also governs the development and locomotory processes of unicellular algae and the development and behavior of various aquatic invertebrates (including insects) and fish. Stream drift and those activities that underlie it have been found to possess a time-regulated component in running water ecosystems. The above investigations, which have appeared in the last ten years, show that the invertebrates in running water are able to perceive the differentiated day and night length. The duration of activity is positively correlated to the length of the periods of light or darkness.
Trocas gasosas influenciam na morfogênese in vitro de duas cultivares de oliveira (Olea europaea L.)

The objectives of this work were to establish cultivars of Olea europaea L. , namely 'Arbequina' and 'Maria da Fe', and to evaluate the influence of gas exchange on in vitro morphogenesis of these cultivars. Under aseptic conditions, single-bud nodal segments were previously decontaminated using disinfestation protocol developed in this work. The treatments followed a completely randomized design, in a 23 factorial scheme: two cultivars and two olive (Olive medium) culture media (OM) (OM + 20 µ M zeatin [1]; and OM + 20 µ M zeatin + 10 µM GA3 [2]); and two types of sealing (rigid lid without orifice and porous membrane) in five repetitions/treatment. The experimental unit consisted of four tubes. The following parameters were assessed: percentage of total contamination; percentage of fungal and bacterial contamination; number of explants with swollen buds; number of axillary buds, and oxidation percentages. At 30 days of cultivation, the total contamination indexes of 15% and 8.8% were recorded for 'Arbequina' and 'Maria da Fe', respectively. For bacterial and fungal contamination percentages, respectively, 'Arbequina' had 33.3% and 66.7%, whereas 'Maria da Fe' presented 71.4% and 28.6%. Regarding the number of responsive cultures showing swollen buds, there was no difference between cultivars when rigid lids without porous membranes were used. However, lids with porous membranes led to statistically superior values for 'Arbequina' as compared to 'Maria da Fe'. For the number of shoots, culture medium 1 was statistically superior to 2. There was no statistical difference for oxidation percentages among treatments. Thus, because of the low level of contamination, it is suggested to use the disinfestation protocol developed in this work. In addition, the use of culture medium 1 and lids with porous membranes did favoured further development of axillary buds into plants.
An evaluation of a method to differentiate the species of origin of meats on the basis of the contents of anserine, balenine and carnosine in skeletal muscle

The high performance liquid chromatographic method proposed by Carnegie for determining the species of origin of meats in cooked products has been evaluated. The dipeptides anserine, balenine (ophidine) and carnosine have been extracted from the skeletal muscle of animals in New Zealand and compared with results obtained in Australia. The presence of significant quantities of balenine in red deer meat is reported for the first time. Limitations of the method are discussed.
Lignocellulose-degrading actinomycetes

Abstract Increasing interest in the exploitation of plant biomass as a renewable resource has provided an impetus for research on microbial degradation of lignocellulose. This has traditionally been concentrated on the fungi, but lignocellulose-degrading prokaryotes are beginning to receive more attention. Strain improvement by genetic manipulation, and large-scale cultivation are more easily achieved in prokaryotes, and the actinomycetes are no exception. In addition, their growth as branching hyphae is well adapted to the penetration and degradation of insoluble substrates such as lignocellulose. Actinomycetes form an important part of the microbial community responsible for nutrient recycling in natural substrates. Their specific contribution to lignocellulose degradation in the environment has received only limited attention but their importance can be inferred from the ubiquity and diversity of species in which activity against lignocellulose has been demonstrated. Characterisation of the cellulolytic activity of actinomycetes has understandably received most attention, since cellulose is the major component of plant biomass and a potentially utilisable source of glucose. Actinomycete cellulases are inducible extracellular enzymes which appear to attack cellulose in much the same way as fungal hydrolytic cellulases. Actinomycete xylanases similarly conform to the basic patterns of production and activity established in other bacteria and fungi, but they have been relatively little-studied. Evidence for activity against lignin has only recently been obtained for actinomycetes, with the development of sensitive radiometric assays which permit detection of limited ligninolytic activity. There is little doubt that actinomycetes compare poorly with the whiterot fungi in relation to the extent of delignification achieved, particularly with wood lignocelluloses. Nevertheless, their ability to solubilise grass lignins may have a role in humification and biotechnological applications of lignocellulose conversion. The biochemistry of lignin degradation by actinomycetes remains poorly understood and the enzymes involved have yet to be identified. There is more information on the enzymology of cellulose and hemicellulose degradation, but how these different groups of enzymes and their component proteins interact to solubilise lignocellulose is largely unknown. Elucidation of the biochemistry of lignocellulose degradation and development of actinomycete-based systems for lignocellulose conversion should be greatly assisted by the application of the recombinant DNA techniques recently developed for this group of organisms.
Media dependence of translational mutant phenotype

We have measured the growth rates of some ribosomal mutants of Escherichia coli in different growth media. The mutants are a streptomycin resistant (SmR) mutation in rpsL; a partially streptomycin dependent (SmP) mutation in rpsL; a ribosome ambiguity mutant (ram) in rpsD; a ram mutant in rpsE as well as a mutant defective in tRNA modification, mia A. The data show that the growth rates of all mutants are less inhibited in poor media than they are in rich ones. The translation rates and nonsense suppression levels for each mutant are not significantly different in rich and poor media, which shows that the ribosomal mutant phenotypes are maintained under different growth conditions. These results suggest that the degree of growth inhibition for mutants with altered translation machinery is dependent on the growth conditions. In addition, the data suggest that bacteria are able to physiologically compensate for the loss of growth efficiency in such mutants, particularly, under poor growth conditions.