Miracle-dz/UniFAR-FTUs huggingface dataset:
Four Novel Recombinant Peanut Allergens: More Information, More Problems

Peanuts are the cause of a number of different allergic symptoms with differing degrees of severity. These clinical symptoms are the oral allergy syndrome, atopic dermatitis, asthma, diarrhoea and anaphylactic reactions. It was recently shown that in peach allergy, the oral allergy syndrome is caused by the Bet v 1-analogous allergen, whereas severe clinical reactions are induced by the lipid transfer proteins [1]. Since peanuts contain several allergenic components, the not inept question arises whether these components are associated with distinct clinical symptoms or the severity of the clinical reaction. If so, this would be a starting point for improving the in vitro diagnostics of peanut allergy based on single allergenic components. Furthermore, the identification of ‘anaphylaxisinducing and -eliciting allergens’ would put the relevant allergens in focus for designing safe immunotherapeutic drugs. Results and Discussion
Cholesterol Oxidation in Egg Yolk Powder During Storage and Heating as Affected by Dietary Oils and Tocopherol

The effects of feeding flax, sunflower, palm and fish oils, with and without tocopherols, to laying hens was investigated on oxidative stability of cholesterol in egg yolk powders. Storage of spray-dried egg yolk powders at room temperature resulted in loss (p flax > sunflower > palm. Heating egg yolk powder increased (p <0.05) the amounts of total cholesterol oxides. Diets with tocopherol supplementation resulted in a decrease (p <0.05) of cholesterol oxides during storage and heating.
Inferring feeding patterns from stomach contents data

1. In this paper we show that analysis of changes in the distribution of stomach contents weights over time offers opportunities for improved understanding of fish feeding using data gathered from four of the larger fish species exploiting a sea-loch on the west coast of Scotland. 2. A simple dynamic model of the feeding and digestion process was developed to help understand complex feeding patterns, for which explanatory mechanisms are not immediately obvious. This model characterizes the 24-h cycle in food uptake rate by a small group of parameters whose values are estimated from the data set taken as a whole. 3. As a result of its higher immunity to noisy data, our model has advantages over previous methods for calculating food uptake rates.
Age-0 Lost River Sucker and Shortnose Sucker Nearshore Habitat Use in Upper Klamath Lake, Oregon: A Patch Occupancy Approach

Abstract We examined habitat use by age-0 Lost River suckers Deltistes luxatus and shortnose suckers Chasmistes brevirostris over six substrate classes and in vegetated and nonvegetated areas of Upper Klamath Lake, Oregon. We used a patch occupancy approach to model the effect of physical habitat and water quality conditions on habitat use. Our models accounted for potential inconsistencies in detection probability among sites and sampling occasions as a result of differences in fishing gear types and techniques, habitat characteristics, and age-0 fish size and abundance. Detection probability was greatest during mid- to late summer, when water temperatures were highest and age-0 suckers were the largest. The proportion of sites used by age-0 suckers was inversely related to depth (range = 0.4-3.0 m), particularly during late summer. Age-0 suckers were more likely to use habitats containing small substrate ( 64 mm) and habitats with vegetation than those with.
Simvastatin Potentiates TNF-α-Induced Apoptosis through the Down-Regulation of NF-κB-Dependent Antiapoptotic Gene Products: Role of IκBα Kinase and TGF-β-Activated Kinase-11

Numerous recent reports suggest that statins (hydroxy-3-methylglutaryl-CoA reductase inhibitors) exhibit potential to suppress tumorigenesis through a mechanism that is not fully understood. Therefore, in this article, we investigated the effects of simvastatin on TNF-α-induced cell signaling. We found that simvastatin potentiated the apoptosis induced by TNF-α as indicated by intracellular esterase activity, caspase activation, TUNEL, and annexin V staining. This effect of simvastatin correlated with down-regulation of various gene products that mediate cell proliferation (cyclin D1 and cyclooxygenase-2), cell survival (Bcl-2, Bcl-xL, cellular FLIP, inhibitor of apoptosis protein 1, inhibitor of apoptosis protein 2, and survivin), invasion (matrix mellatoproteinase-9 and ICAM-1), and angiogenesis (vascular endothelial growth factor); all known to be regulated by the NF-κB. We found that simvastatin inhibited TNF-α-induced NF-κB activation, and l-mevalonate reversed the suppressive effect, indicating the role of hydroxy-3-methylglutaryl-CoA reductase. Simvastatin suppressed not only the inducible but also the constitutive NF-κB activation. Simvastatin inhibited TNF-α-induced IκBα kinase activation, which led to inhibition of IκBα phosphorylation and degradation, suppression of p65 phosphorylation, and translocation to the nucleus. NF-κB-dependent reporter gene expression induced by TNF-α, TNFR1, TNFR-associated death domain protein, TNFR-associated factor 2, TGF-β-activated kinase 1, receptor-interacting protein, NF-κB-inducing kinase, and IκB kinase β was abolished by simvastatin. Overall, our results provide novel insight into the role of simvastatin in potentially preventing and treating cancer through modulation of IκB kinase and NF-κB-regulated gene products.
Antisense expression of a ω-3 fatty acid desaturase gene in tobacco plants enhances susceptibility against pathogens

Membrane lipids in higher plants contain a high proportion of trienoic fatty acids. ω-3 Fatty acid desaturases act on membrane lipids to catalyze the formation of trienoic acids. We isolated a wound-inducible Arabidopsis plastid ω-3 fatty acid desaturase (fad7) gene, and generated transgenic tobacco plants constitutively expressing the antisense fad7 RNA. Selected transgenic lines showed significant reductions in the content of trienoic fatty acids compared with control plants. The transgenic lines showed enhanced susceptibility against Tobacco mosaic virus infection, where necrotic lesions with brown halos developed much earlier and were larger in the transgenic lines than in control plants. After Tobacco mosaic virus infection, expression and protein accumulations of the wound-inducible protein kinase WIPK, as well as defense-response gene expressions such as lipoxygenase (lox) and defensin (pdf1.2), were retarded in the transgenic lines compared with control plants. Increased susceptibility of the tran.
Characterization of a Novel RING-Type Ubiquitin E3 Ligase GhRING2 Differentially Expressed in Cotton Fiber

The ubiquitin-proteasome proteolysis pathway is responsible for the degradation of abnormal and short-lived proteins to regulate many important biochemical activities in eukaryotes. By employing affymetrix microarray analysis, we have identified a novel ubiquitin ligase E3 gene GhRING2 that is differentially expressed between two Gossypium hirsutum lines-Texas Marker-1 (TM-1) and Chromosome Substitution Line CS-B25. The CS-B25 line has chromosome 25 from G. barbadense substituted into TM-1. The complete nucleotide sequences of GhRING2 along with its 5’-flanking region were obtained by genomic walking. GhRING2 was highly expressed in elongating fiber, and GUS expression directed by the GhRING2 promoter was found in hypocotyls and young stems of transgenic Arabidopsis plants. Using a yeast two-hybrid assay GhRING2 was found to interact with a PROTODERMAL FACTOR1 (GhPDF1) protein. GhPDF1 was expressed preferentially in immature ovules and fiber initials, and the GhPDF1 gene had been suggested to play a role in cell fate determination and fiber development. Pull down and plasmid swap assays further confirmed the interaction between GhRING2 and GhPDF1. The expression and protein interaction data indicate that GhRING2 may be involved in the turnover of GhPDF1 and participation in the transition from initiation to elongation stages during fiber development. Our data strongly suggest that the ubiquitin-proteasome pathway may regulate cotton fiber growth and development. The nucleotide sequence data of GhRING2 in this article have been submitted to the Gen Bank Nucleotide Sequence Data Bases under the accession number BankIt 1,742,008 SeqKM 108,000.
Cascading biodiversity and functional consequences of a global change–induced biome switch

Aim At a regional scale, across southern Africa, woody thickening of savannas is becoming increasingly widespread. Using coupled vegetation and faunal responses (ants), we explore whether major changes in woody cover in savannas represent an increase in the density of savanna trees (C4 grass layer remains intact) or a ‘regime shift’ in system state from savanna to thicket (=dry forest) where broad‐leaved, forest‐associated trees shade out C4 grasses.
Interleukin-17A Induces Extracellular Matrix Protein Expression in Osteoblastic ROS17/2.8 Cells

Interleukin (IL)-17 plays an important role in many autoimmune and inflammatory diseases. We recently demonstrated the various direct and indirect effects of IL-17A on osteoclastogenesis. However, the effect of IL-17A on bone matrix formation by osteoblasts is unclear. Therefore, we examined the effect of IL-17A on IL-17 receptor (IL-17R), extracellular matrix protein (ECMP), and cyclooxygenase (COX) expression; prostaglandin (PG) E2 production; alkaline phosphatase (ALPase) activity; and mineralized nodule formation in osteoblastic ROS17/2.8 cells. We also examined the indirect effect of PGE2 on IL-17-induced ECMP expression using NS398, a specific inhibitor of COX-2 activity. Cells were cultured with 0 (control), 1, 10, or 100 ng/mL IL-17A in the presence or absence of 50 ng/mL neutralizing anti-IL-17A antibodies or 1 μM NS398. IL-17RA, IL-17RC, type I collagen, bone sialoprotein (BSP), osteocalcin, osteopontin, COX-1, and COX-2 expression was examined by real-time PCR and Western blotting. PGE2 production was examined by ELISA. The expression of IL-17RA, type I collagen, BSP, osteocalcin, osteopontin, and COX-2, and PGE2 production were increased significantly in the presence of IL-17A, whereas the expression of IL-17RC and COX-1, cell proliferation, ALPase activity, and mineralized nodule formation were unaffected. Anti-IL-17 antibodies blocked IL-17Ainduced ECMP expression. NS398 blocked IL-17A-induced PGE2 production, but it did not affect IL-17A-induced ECMP expression. These results suggest that IL-17A stimulates ECMP expression via IL-17RC and/or IL-17A-induced IL-17RA in osteoblasts; however, mineralized nodule formation by the cells was unaffected by the addition of IL-17A. Furthermore, our results indicate that the stimulatory effect of IL-17A on ECMP expression is independent of the indirect effect of IL-17A-induced PGE2.
Diversity of Japanese Aphis gossypii and Comparison with Other Aphis Species Based on the Mitochondrial Cytochrome Oxidase I Sequence

ABSTRACT The sequence of the mitochondrial cytochrome oxidase I (COI) gene was analyzed in 168 individuals from seven Aphis (Hemiptera: Aphidini: Aphidina) species: Aphis gossypii Glover, Aphis glycines Matsumura, Aphis spiraecola Patch, Aphis craccivora Koch, Aphis fabae Scopoli, Aphis rumicis (L.), and Aphis nerii Boyer de Fenscolombe. One other Aphidina species, Toxoptera odinae (van der Goot), and two Macrosiphini species, Acyrthosiphon pisum (Harris) and Myzus persicae (Sulzer), were analyzed as out-groups. The coding region of the gene contains 1,563 bp in all of the species, and 272 sites were variable among the Aphis species. DNA sequence identities among individual aphids ranged from 91.4 to 100%, with greater identities among aphids in the same species (96.5–100%) than between different species (91.4–95.3%). Compared with some other species, A. gossypii showed little divergence in either nucleotide sequences or haplotypes, although intraspecific cytochrome oxidase I (COI) sequence divergence was observed in A. gossypii clones isolated from Commelina communis L. and Rubia cordfolia L. In the phylogenetic tree, every species formed a robust clade. The pairs A. gossypii and A. glycines, and A. rumicis and A. fabae showed robust sister relationships. T. odinae was located within the Aphis species clade, and this suggested that the Toxoptera classification should be reconsidered in the light of molecular data.
“The Greatness of the Smallest Ones”: The Most Valuable Attributes of Flies and Worms for the Study of Neurodegeneration

Over the last decades, a large number of experimental models have been developed to explore the mechanisms underlying neurodegenerative disorders. Invertebrate models of neurodegeneration, such as the fruit fly Drosophila melanogaster and the nematode Caenorhabtidis elegans, have emerged as successful complementary systems to mammalian models, facilitating identification of relevant pathways and novel diseaseassociated genes. These organisms provide reliable systems for identifying genetic modifiers of neuropathologies and the interesting possibility of screening and testing potential drugs for treatments to prevent and/or alleviate disease symptoms. This chapter will focus on the main experimental strategies used in Drosophila melanogaster and Caenorhabtidis elegans to study neurodegeneration. Insights from forward genetic approaches, transgenic models of human neurodegenerative disorders and studies of fly/worm homologs of human disease genes will be presented. The value of using invertebrate models for the study of neurodegeneration will be discussed, highlighting advantages and limitations associated with these studies.
Modelling short-term feeding behaviour

Previous analyses of feeding behaviour have either ignored the bouted structure of that behaviour or used log-survivorship analysis for the estimation of bout criteria. The latter is based on the null hypothesis that feeding behaviour is random within as well as between bouts. We falsify this null hypothesis by analysing how specific feeding events (such as visits to a feeder) by animals of a number species are distributed in time. They all show bouted, but non-random, feeding behaviour with a similar structure. This is caused by satiety at the end of feeding bouts, followed by an increase in the probability of animals starting to eat with time since feeding last. This results in a skewed normal distribution of the population of longer between-feeding, i.e. between-meal, intervals, which can be (almost) normalised by log-transformation of interval lengths. We show that either a Gaussian (for pooled data sets) or a Weibull (for individuals or data pooled across animals with similar feeding strategies) give excellent descriptions of the distribution of this population of log-transformed interval lengths. Depending on species, methodology and individual animal habits there may be one or more population(s) of shorter (i.e. within-meal) intervals. We developed methods that allow estimation of meal criteria even if the number of within-meal interval populations and their shape are not exactly known. Because the structure of feeding behaviour is the same across species, similar models to estimate bout criteria can be applied to data obtained with animals of species as diverse as cows, pigs, chickens, turkeys, ducks and dolphins. We demonstrate how analysis of data subsets, following disaggregation of pooled data, can elucidate underlying mechanisms that would otherwise remain obscure. The developed models can also be applied to other forms of animal behaviour that are affected by satiety-like principles.
Arthropod Galls Found on the Krakatau Islands and in Adjacent Areas of Indonesia, with Reference to Faunistic Disharmony between the Islands and the Whole of Indonesia

Up to 2000, a total of 147 sorts of arthropod gall were found on the Krakatau Islands and in adjacent areas since the world famous volcanic eruption in 1883. They were induced on at least 109 plant species belonging to 81 genera of 42 families and are listed in alphabetical order of host plant families, except one belonging to Pteridophyta. On the Krakataus, Docters van Leeuwen recorded 63 sorts of arthropod gall in 1919-1922. Thereafter, Yukawa and Partomihardjo collected 15 sorts in 1982 and 45 in 1991-1993, and Partomihardjo, Uechi, and Abe collected 22 in 2000. The cumulative number of different gall sorts found on the islands from 1982 to 2000 was 52, consisting of 31 insect and 21 eriophyoid galls, which is equivalent to 3.4% of 1536 sorts of arthropod galls recorded from Indonesia. We also refer to disharmony between galling-arthropod fauna of the Krakataus and that of the whole of Indonesia. During the surveys in 1991-1993 and 2000, we found 16 sorts of arthropod gall that are new to Indonesia. They are briefly described together with photographs and illustrations.
Effect of taurine on excitation-induced changes in brain and hemolymph octopamine levels in Periplaneta americana

Injection of adult male cockroaches with 16 nmol taurine reduces excitationinduced elevation of hemolymph octopamine levels. Taurine-treated insects have higher concentrations of octopamine in the brain following excitation than nontreated cockroaches. Isolated brains, incubated in taurine-containing saline, release less octopamine in response to electrical stimulation than those incubated in saline. The effect of taurine injection on excitation-induced octopamine release is manifested with physiological concentrations of taurine and persists for at least 15 h following injection. Excitation also causes a rapid increase in hemolymph taurine levels. The results indicate that taurine inhibits the release of octopamine from the insect nervous system and may form part of a dual control mechanism for excitation, with octopamine serving as a positive effector and taurine serving as an inhibitory modulator of octopamine release.
Wood Decay By Inonotus Rickii and Bjerkandera Adusta: A Micro- And Ultra-Structural Approach

Bjerkandera adusta (Willd.) P. Karst. and Inonotus rickii (Pat.) D.A. Reid. are important xylophagous fungi affecting street trees in Buenos Aires City, Argentina. The objective of this paper is to describe the decay patterns produced by these species in London plane wood (Platanus acerifolia (Ait.) Willd. ), which is one of the most abundant tree species in the city, through light microscopy (LM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). A better knowledge of the decay patterns of these fungi at early stages would provide useful information for optimizing tree management programs. Microscopic observations showed that B. adusta, having caused an important loss of dry weight, showed more extensive degradation of wood after three months than I. rickii, affecting mainly fiber walls with potential consequences in tree strength and stiffness. Inonotus rickii, on the other hand, selectively affected vessel walls and middle lamellae between fibers. Rays remained virtually unaltered in all decayed wood.
Morphometric sexing of Mediterranean Yellow-legged Gulls Larus michahellis michahellis breeding in the Gulf of Gabès, southern Tunisia

Discriminant analysis functions have previously been determined for sexing Mediterranean Yellow-legged Gulls Larus michahellis michahellis from the western Mediterranean basin. However, data from eastern Mediterranean populations are lacking. In this work, we used morphometric data from a sample of 81 Mediterranean Yellow-legged Gulls (39 males and 42 females) breeding in the Gulf of Gabès in south-eastern Tunisia to (1) determine a discriminant function useful for sex discrimination, and (2) assess the accuracy of previously published functions in sexing Mediterranean Yellow-legged Gulls from our study area. Our results showed marked sexual differences in all morphological measurements, with males being significantly larger than females. The best discriminant function included head length, bill depth and wing length, and accurately classified 93% of sampled birds. We also found that Mediterranean Yellow-legged Gulls from the Gulf of Gabès could accurately be sexed using discriminant functions determined for another North African population, but not with a function determined for a South European population, although distances between sites are almost the same.
Salmonella typhimurium infection in broilers and its effects on gastrointestinal health and performance

i Abbreviations.iii List of Tables.v List of Figures.xxiii Chapter 1: Introduction.1 Chapter 2: Literature review.4 2.1) Salmonella.4 2.2) Antibiotic Growth Promoters.17 2.3) Immunity.21 2.4) Cyclophosphamide.23 2.5) Gut microflora.24 Chapter 3: Pilot trial for determining optimum conditions to obtain Salmonella typhimurium infection in broiler chicks.27 3.1) Materials and methods.28 3.1. 1) Chickens.28 3.1. 2) Experimental design.28 3.1. 3) Bacteria.28 3.1. 4) Cyclophosphamide.28 3.1. 5) Husbandry.29 3.1. 6) Diets.29 3.1. 7) Measurements, sampling and sample analysis.30 3.1. 7) Statistical analysis.32 3.2) Results.32 3.2.1) Organ weights.32 3.2.2) Broiler Performance.41 3.2.3) Serum biochemical profile.66 3.2.4) Intestinal damage.74 3.2.5) Histopathology.77 3.3) Discussion.77 3.3.1) Organ weights.86 3.3.2) Broiler performance.86 3.3.3) Serum biochemical profile.86 3.3.4) Intestinal damage: lesions.88 3.3. 5) Histopathological results.88 3.4) Conclusion.89 Chapter 4: Salmonella Typhimurium infection in boilers and its effects on gastrointestinal health and function.90 4.1) Materials and methods.91 4.1. 1) Chickens.91 4.1. 2) Experimental design.91 4.1. 3) Bacteria.92 4.1. 4) Husbandry.92 4.1. 5) Diets.92 4.1. 6) Measurements, sampling and sample analysis.92 4.1. 7) Statistical analysis.95 4.2) Results.96 4.2.1) Organ weights.96 4.2.2) Broiler Performance.96 4.2.3) Serum biochemical profile.96 4.2.4) Intestinal damage.112 4.2.5) Histopathology.114 4.2. 6) Villous morphological measurements.114 4.3) Discussion.126 4.3.1) Organ weights.126 4.3.2) Broiler performance.126 4.3.2.1) Body weight and daily gain.126 4.3.2.2) Feed intake.127 4.3.2.3) Feed conversion ratio.127 4.3.3) Serum biochemical profile.127 4.3.4) Intestinal damage: lesions.128 4.3. 5) Histopathological results.129 4.3. 6) Villous morphological measurements.130 4.4) Conclusion.130 Chapter 5: General discussion and conclusions.132 Chapter 6: References.134 Appendix.149 Millonig’s buffered formalin solution.149 Rambach agar.149 Rappaport-Vassiliadis broth.150
Mark–recapture of Agriotes obscurus and Agriotes lineatus with dense arrays of pheromone traps in an undisturbed grassland population reservoir

The present study was conducted using mark–released populations of male Agriotes obscurus (AO) and Agriotes lineatus (AL) adults to simulate the spatial and temporal capture rates of wild beetle populations in dense arrays of pheromone traps in a confined, nonfarmed habitat. Two parallel rows of traps, spaced 3 m apart along corridors of grassy dyke, recaptured 85.6% of AO and 77.8% of AL with arrays of their respective pheromone traps, mostly within the first week of release. In arrays of mixed AO and AL traps, recapture rates were 77.8% and 83.3%, respectively. In arrays with only AO traps, 31.2% of AL males released within the arrays mistakenly entered the AO traps, which declined to only 2.2% when released in arrays with both AO and AL traps. In arrays with only AL traps, only 0.7% of released AO were mistakenly taken in the AL traps, and only 0.3% mistakenly entered AL traps in mixed AO and AL trap arrays. Between 34.4–38.9% of AO and 21.1–25.6% of AL released in areas immediately adjacent to the trapping arrays were caught, mostly in the outermost traps. The implications of these results for determining the efficacy of mass trapping as a click beetle management approach are discussed.