Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization and Modification of Genetically Encoded Indicators to Monitor Neural Activity in Drosophila melanogaster

Genetically encoded fluorescent indicators of neural activity represent promising tools for systems neuroscience. In the first part of my thesis, a comparative in vivo analysis of ten different genetically encoded calcium indicators as well as the pH-sensitive SynaptopHluorin is presented. The calcium indicators are either based on a single chromophore (GCaMP variants, Camgaroo variants, Pericam variants) or on two chromophores (Yellow Cameleon variants, Troponeon variants). I expressed these indicators in the cytosol of presynaptic boutons of the Drosophila larval neuromuscular junction and analyzed their fluorescence changes upon stimulation. GCaMP 1.3, GCaMP 1.6, Yellow Cameleon 2.0, 2.3, and 3.3, Inverse-Pericam, the troponin C-based calcium sensor TNL 15 and SynaptopHluorin allowed reliable detection of presynaptic fluorescence changes at the level of individual boutons. However, the response characteristics of all of these indicators differed considerably from each other. TNL 15 exhibited the most stable and fastest rising signals at lower activity rates, whereas GCaMP 1.6 produced the fastest signals at high rates of nerve activity with largest fluorescence changes. GCaMP 1.6 and GCaMP 1.3 signals, however, were complicated by bleaching, as was the case for Inverse Pericam. The fluorescence signals of the double-chromophore indicators were in general smaller but more photostable and reproducible. Camgaroo-1 and Camgaroo-2 showed little or no response, and Flash Pericam did not result in any detectable fluorescence. GCaMP 1.3 and YC 3.3 revealed fairly linear fluorescence changes and a corresponding linear increase in the signal-to-noise ratio (SNR) over an expanded range of neural activity. As expected, the expression level of the indicator had an influence on the signal kinetics and the SNR, whereas the signal amplitude was independent. In the second part of my thesis work I fused several genetically encoded calcium indicators to different signal sequences. The targeting of the indicators to distinct parts of the cell such as the membrane, vesicles or ion channels allows detection of calcium ions before they disperse in the cytosol. Specific signals can be extracted more efficiently and in a more relevant physiological context. Tagging of YC 2.3, GCaMP 1.6 and TNL 15 to transmembrane domains or proteins involved in the synaptic vesicle cycle did not result in functional targeting. TN XL fused to the transmembrane domain mCD8 at the N-terminus and eight amino acids from a calcium channel subunit at the C-terminus resulted in membrane association at the NMJ. Fractional fluorescence changes up to 6.5 % were recorded upon stimulation. In cells of the fly visual system scattered fluorescent puncta were observed. This fusion protein has the potential for monitoring calcium dynamics in close proximity of ion influx. The presented data will be useful for in vivo experiments with respect to the selection of an appropriate indicator, as well as for the correct interpretation of optical signals.
Characterization of microsatellite markers in sycamore (Acer pseudoplatanus L.)

Sycamore (Acer pseudoplatanus L.) is a tetraploid European hardwood tree species. The reproduction system of the insect-pollinated trees and patterns of genetic variation are largely unknown. We isolated and characterized eight polymorphic microsatellite markers for Acer pseudoplatanus L. The high degree of polymorphism observed at these markers makes them useful to observe genetic variation patterns at various spatial scales and to analyse gene flow and the mating system. Primers developed for the amplification of microsatellites in A. pseudoplatanus were tested for 21 different species of genus Acer. Amplification products of the expected size were obtained in most cases.
An Acid Protease Produced by Monilinia fructigena in vitro and in Infected Apple Fruits, and its Possible Role in Pathogenesis

SUMMARY: The fungus Monilinia fructigena grown in a liquid medium containing protein secreted a protease with many similarities to one extractable from apple fruits infected with this pathogen but absent from healthy fruit. Enzymes from both sources degraded several protein substrates optimally at pH 3·4. At this pH, haemoglobin was degraded optimally at 47 °C, while at 37 °C both enzymes were most stable at pH 5. The pI values for the enzymes were close to 4·0, and their action was inhibited by pepstatin and diazoacetyl-norleucine methyl ester plus copper ions but unaffected by p-hydroxymercuribenzoate, EDTA or trypsin inhibitors. Mercaptoethanol was essential for the recovery of enzyme activity from acrylamide gels in which the in vitro and in vivo enzymes were electrophoretically homogeneous. The in vitro enzyme gave a positive reaction for glycoproteins after purification with a Sepharose-haemoglobin affinity medium. Both enzymes were single units with a molecular weight of 37000–40000 on sodium dodecyl sulphate (SDS)-poryacrylamide gels; gel filtration indicated a molecular weight of 34000–38000. The purified in vitro enzyme had no aminopeptidase or carboxypeptidase activity; the products of haemoglobin digestion were peptides with molecular weights on SDS--polyacrylamide gels of 2000-12000. Purified in vitro protease did not damage apple fruit tissue or cultured apple cells, lyse plant protoplasts or release proteins from isolated fruit cell walls. The protease had no effect on active fungal or host enzymes that might have a role in host/pathogen interactions, and did not induce phaseollin formation in bean cotyledons. The plant proteins vicilin, legumin and heat-denatured peroxidase were hydrolysed at pH 3·5 and spinach nitrate reductase was inactivated. Nontural protease inhibitors were detected in healthy or infected apples. We suggest that in vivo the protease might be involved in the nutrition of the pathogen.
Bulked segregant analysis to detect quantitative trait loci (QTL) related to heat tolerance at grain filling rate in wheat using simple sequence repeat (SSR) markers

The grain-filling rate (GFR) plays an important role in determining grain yield. An F2 population of wheat was developed from a cross between the 2 wheat cultivars, Ksu106 (heat-tolerant) and Yecora Rojo (heat-sensitive). The parents and 205 F 2 plants were planted on the 20 th of January during the winter season of 2009 to evaluate heat tolerance during the grain-filling period. The sowing date in the present investigation represents the heat stress conditions in Saudi Arabia. Bulked – segregant analyses (BSA) was used in conjunction with simple sequence repeats (SSR) analysis to find markers linked to genes of heat tolerance. Composite interval mapping was used for mapping quantitative trait loci (QTL). The results reveal that 12 SSR markers: Wmc24, Wmc168, Wmc326, Xgwm30, Xgwm456, Wmc25, Wmc44, Wmc94, Wmc161, Wmc273, Wmc327 and Xgwm566 were linked to GFR by QTLs analysis of the F 2 population. The results show that regression analysis for the relationship between the 12 markers and the phenotypes of F 2 individuals were highly significant. The results demonstrate that SSR markers combined with bulked segregant analysis could be used to identify molecular markers linked to the grain filling rate as an indicator for heat tolerance in wheat. Keywords: Grain filling rate, QTL analysis, SSR marker, wheat
Thermal Stability of Chicken Keel Bone Collagen

Acid-soluble and pepsin-solubilized collagen were isolated from chicken keel bone and analyzed by electrophoresis and circular dichroism. The denaturation temperature of chicken keel bone was determined by circular dichroism and compared to denaturation temperature of black drum or alligator bone. Our results show that collagen from chicken keel bone is a mixture of type II and type I, has predominantly the amino acids glycine, proline and hydroxyproline, and its secondary structure is predominantly triple-helix. The onset of the denaturation temperature is 37C; at 44C, 50% of the collagen is denatured and the denaturation is complete at 48.8C making it the highest of vertebrate collagen denaturation temperatures reported in the literature. The high heat stability of chicken keel bone collagen may be in part ascribed to its imino acid content. Because of the high heat stability and low methionine content, chicken keel bone collagen is a high value-added product with several biochemical and biomedical applications. Practical Applications The denaturation temperature of chicken keel bone collagen is above body temperature and allows applications in cosmetics where other types of collagen may be denatured because of their low denaturation temperature. Chicken type II collagen is well tolerated by patients with rheumatoid arthritis and is effective in the treatment of rheumatoid arthritis. Methionine-restricted diet inhibits the growth of solid tumor such as gastric cancer, glioblastoma, medulloblastoma and neuroblastoma. Chicken type collagen may be a medical food for patients with solid tumors mentioned above.
Biological observations on the gulper shark Centrophorus granulosus (Chondrichthyes: Centrophoridae) off the coast of Galicia (north-western Spain, eastern Atlantic)

The observed Centrophorus granulosus were caught with bottom trawl and longline between 500 and 1300 m depth off the continental slope of Galicia and the Galician Bank (north-eastern Atlantic) between 1996 and 1998. The main biological data obtained were: a maximum recorded size of 166 cm TL (total length); females mature at 147 cm TL; between 1 and 10 mature oocytes by females of 55–80 mm diameter and as many as 6 pups per litter, and size at birth ranging between 35–47 cm TL. These results differ greatly from those compiled in the literature suggesting different populations or perhaps a possible misidentification.
Patagonicola: a new genus of xeromelissine bee from Argentina (Hymenoptera: Apoidea: Colletidae)

Abstract Patagonicola Packer new genus is described for two species of xeromelissine bee (Hymenoptera: Colletidae) from Patagonian Argentina. One species, P. graveli Packer new species is described; the second species, P. aenigma (Packer) new combination, originally placed in Chilicola Spinola, 1851 subgenus Chilioediscelis Toro and Moldenke, 1979, is designated as the type species. The new genus is superficially most similar to Xenochilicola Toro and Moldenke, 1979 but possesses none of the derived characteristics that were originally used to define that genus. Results of a phylogenetic analysis, based upon 114 morphological characters, are presented and suggest that the new genus is the sister clade to (Geodiscelis Michener and Rozen, 1999 + Xeromelissa Cockerell, 1926). An illustrated key is provided for the genera of Xeromelissinae and for the two species of Patagonicola. Résumé Patagonicola Packer nouveau genre est décrit pour deux espèces d'abeilles xéromelissines (Hymenoptera: Colletidae) de la Patagonie argentine. Une espèce, P. graveli Packer nouvelle espèce, est décrite; la seconde, P. aenigma (Packer) nouvelle combinaison, originalement placée dans Chilicola Spinola, 1851, sous-genre Chilioediscelis Toro et Moldenke, 1979, est l'espèce type. Le nouveau genre est superficiellement plus similaire à Xenochilicola, Toro et Moldenke, 1979, mais ne possède aucune des caractéristiques dérivées qui étaient initialement utilisées pour définir ce genre. Les résultats de l'analyse phylogénétique, basée sur 114 caractères morphologiques, sont présentés et suggèrent que ce nouveau genre est sœur à (Geodiscelis Rozen et Michener, 1999 + Xeromelissa Cockerell, 1926). Une clé d'identification illustrée est fournie pour les genres de Xeromelissinae et pour les deux espèces de Patagonicola.
Two Clip Domain Family of Serine Proteases and a Serine Protease Homolog from the Fall Webworm, Hyphantria cunea; cDNA Cloning and Characterization

Two types of serine proteases and a serine protease homologue cDNAs were isolated from Hyphantria cunea larvae induced immune response due to an injection of a microorganism through RT‐PCR and cDNA library screening, and their characteristics were examined. The isolated cDNAs are composed 2.1 kb, 2.2 kb, and 2.5 kb nucleotide each, which encoded 388, 390, 580 amino acid residues, and were designated as HcPE‐1, HcPE‐2 and HcPE‐3, respectively. They were revealed as serine proteases or a serine protease homologue with the clip domain through a database search. The deduced amino acid sequence comparison showed high homology of 72‐78% among them. Six Cys residues of the N‐terminal clip domain forming the disulfide bond, Cys residues of the catalytic domain, and Cys residues forming inter‐bridge between clip domain and catalytic domain were also well preserved. Three amino acid residues, His, Asp, and Ser, within the active site were perfectly conserved in HcPE‐2 and HcPE‐3, however, His was replaced with Gln178 in HcPE‐1. The Arg residues (HcPE‐1, Arg132; HcPE‐2, Arg134; HcPE‐3, Arg325) known as the activation sites by proteolytic cleavage were preserved well in all three types of protein. In case of HcPE‐3, three continuous clip‐like domains existed in the N terminal. As the result of phylogenetic analysis, three clip domain family of protein from H. cunea make groups with arthropod proclotting enzyme precursor. Northern blot analysis showed all three genes were induced through an injection of Escherichia coli, but expression patterns were varied.
The Inhibitory Effect of 5‐Bromodeoxyuridine on the Programmed Cell Death in the Chick Limb

The inhibitory effect of 5‐bromodeoxyuridine (BrdU) on the programmed cell death in interdigital mesenchyme of a chick leg bud was studied using vital staining and histological methods. A single administration of BrdU at day 6 1/3 specifically inhibited the programmed cell death in the mesenchyme of interdigital areas of a leg bud, resulting in the formation of a web‐like structure. No inhibitory effect was observed on general development of limb buds. Hoechst 33258 staining revealed that many cells of interdigits incorporated BrdU into their nuclei. The simultaneous administration of thymidine blocked the BrdU effect.
Human Risk Assessment of Endocrine-Disrupting Chemicals Derived from Plastic Food Containers

Abstract: In the manufacture of plastic containers, various materials such as additives (for example, plasticizers, stabilizers, antioxidants), polymers (for example, polystyrene [PS], polycarbonate [PC], polyvinyl chloride [PVC]) are widely used. Endocrine disrupting chemicals [EDCs] can migrate as residual monomers (for example, styrene for PS or bisphenol A [BPA] for PC) presented in polymers, as additives (for example, phthalates for PVC) used in polymer manufacturing, and/or as contaminants from the polymers depending on physicochemical conditions such as temperature, UV light, pH, microwave, and mechanical stress. Some phthalates (for example, DEHP, DBP), styrene, or bisphenol have been suspected to have endocrine disrupting effects, but human toxicological effects of these compounds are very controversial. For these reasons, a comprehensive review on toxicological and risk assessment studies for these chemicals (phthalates, BPA, and styrene) was carried out to evaluate their safety in humans. On the basis of exposure estimates for the these chemicals and reference doses (RfDs), we calculated hazard index (HI = chronic daily intake/tolerable daily intake [TDI] or RfD). A HI of less than 1 suggests an exposure lower than the safety limit of the chemicals. We showed that the HI values of these chemicals were lower then 1, but there are one or several exceptions for di(2-ethylhexyl) phthalate (DEHP), dibutyl phthalate (DBP), di-isodecyl phthalate (DIDP), and di-n-octyl phthalate (DnOP; for example, exposure via infant formula, packaged lunch, total exposure), where estimated their HI values are higher than 1, which suggests an exposure higher than the safety limits of the chemicals. However, the HI of BPA was 0.001–0.26 (3.57–1000 times lower than its safety limit), and the HI for styrene was 0.276 (3.62 times lower than its safety limit). In this article, we focused on recent issues concerning the endocrine-disrupting chemicals (EDCs) derived from plastic food containers or packaging. This review suggests that the use of plastic food containers might not exceed human safe limits n general with respect to endocrine disruptors aside from the exceptions of the phthalates mentioned earlier.
Condition–dependent variation in the blue–ultraviolet coloration of a structurally based plumage ornament

After years of investigation into the function of sexually dimorphic ornamental traits, researchers are beginning to understand how bright plumage colour in birds acts as an intraspecific signal. This work has focused primarily on pigment–based ornaments because they are highly variable in patch size, hue and brightness for some species. In contrast, structurally based ornaments have been little studied, in part because they do not appear to be as variable as pigment–based ornaments. We investigated a structurally based plumage ornament in a wild population of blue grosbeaks (Guiraca caerulea), a sexually dimorphic passerine. We report plumage variation that extends into the ultraviolet region of the spectrum. The pattern of covariation between four out of five elements of plumage variation suggests that structurally based ornamentation is pushed towards extreme expression of the trait as predicted by the sexual selection theory. The ‘bluest’birds have the highest percentage of blue feathers on the body. These ornamental feathers reflect light maximally at the shortest wavelengths (ultraviolet), with the greatest intensity and the greatest contrast. Age may have some effect on expression of blueness. In addition, plumage variables are correlated with growth bars in tail feathers (a record of nutritional condition during moult in a non–ornamental trait). This suggests that the ornament is partially condition dependent. Thus, blue plumage in male grosbeaks may serve as an honest indicator of age and quality.
Graphical and Statistical Methods for Determining the Consistency of Age Determinations

Abstract Many laboratories rely on periodic rereading of reference collections of scales or otoliths to ensure that their age readers remain consistent in their age interpretations, both through time and with other age readers. Measures of both systematic difference (bias) and precision are required for this purpose, because measures of bias are not suitable as measures of precision, and vice versa. Using data from an age comparison study of haddock Melanogrammus aeglefinus for demonstration purposes, we evaluated a variety of graphical and statistical approaches for making paired age comparisons from the standpoint of both detecting age differences and assessing precision. Parametric and nonparametric matched-pair tests, regression analysis, analysis of variance, and age difference plots were all capable of detecting systematic over- or underaging. However, only the age bias plot was sensitive to both linear and nonlinear biases. The coefficient of variation (CV = SD/mean) was a robust measure of precisi.
Recreational angling intensity correlates with alteration of vulnerability to fishing in a carnivorous coastal fish species

Increased timidity is a behavioral response to exploitation caused by a combination of learning and fisheries-induced selection favoring shy fish. In our study, the potential for angling-induced change in fish behavior was examined in two marine coastal fishes exploited by boat recreational fishing in the Mediterranean (Mallorca, Spain). It was expected that the mean vulnerability to capture of surviving individuals would differ across a gradient of previous exposure to recreational angling and that this effect would be present in multiple species. The prediction received partial empirical support. Recreational angling intensity was correlated with enhanced gear-avoidance behavior in only one of the two study species, the carnivorous painted comber (Serranus scriba). By contrast, the omnivorous fish species in our study, the annular seabream (Diplodus annularis), did not differ in its behavior towards hooks in exploited compared with unexploited sites. These results suggest that recreational angling may c.
Evidencia serológica de infección por Neospora caninum en rebaños lecheros del Sur de Chile

Los abortos bovinos causan importantes perdidas economicas a la ganaderia mundial. Una parte importante de ellos permanecen aun con etiologia desconocida, y de los diagnosticados, la mayoria corresponden a causas infecciosas. Dentro de ellos los abortos ocasionados por protozoo s han tomado relevancia mundial. En Chile hasta ahora se desconocia su presencia. En este trabajo se presenta evidencia que vacas con antecedentes de abortos presentaron anticuerpos contra N. Caninum detectados mediante la tecnica 1FA y se discute la posibilidad de que hayan ocurrido como consecuencia de la infeccion por este protozoo.
Compensatory Mechanisms and T Cell Migration In Mouse Models of Dopaminergic Loss

We previously showed that chronic administration for 35 days of L-3,4dihydroxyphenylalanine (L-DOPA) or BL-1023 [an L-DOPA-gamma-aminobutyric acid (GABA) conjoined compound] improved locomotor function and increased numbers of tyrosine hydroxylase (TH) immunoreactive (TH+) neurons in the substantia nigra of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated mice compared to those given no drug. We therefore sought to identify whether the increase in TH+ neurons was a consequence of neurogenesis or rather from a phenotypic shift of surviving neurons in the substantia nigra. Using the thymidine analogue bromodeoxyuridine (BrdU), we sought to identify newly formed neurons after 21 days of L-DOPA or BL-1023 treatment, but were unable to do so. Dual immunofluorescent analysis of tissues for TH and glutamic acid decarboxylase-67 (GAD67), a marker for GABAergic neurons revealed that mice treated with either L-DOPA or BL-1023 showed significant increases in the numbers of TH+GAD67+ neurons in the substantia nigra compared to controls. These findings support the notion that numbers of GAD67+ neurons upregulate TH expression and effectively increase the numbers of TH+ neurons in response to MPTP-intoxication, loss of dopaminergic neurons, and/or chronic administration of dopamine-replacement drugs.
Comparative evidence for a positive correlation between haematozoan prevalence and mortality in waterfowl

Hamilton and Zuk (1982) suggested a new hypothesis to explain the evolution of secondary sexual characters, namely that male ornaments may represent honest signals of male capacity to resist parasites. Since then several authors have addressed the question of the role played by parasites in the evolution of host secondary sexual characters. Comparative analyses of Hamilton and Zuk's hypothesis have, however, failed to show the predicted positive association between parasitism levels and sexually‐selected traits. One possible explanation for this discrepancy involves a low pathogenicity of the parasites used to test the hypothesis. Here we show that haemosporidians are positively correlated with mortality rates in a sample of waterfowl, and that the correlation between the two variables is of similar magnitude in both males and females. Contrary to the expectations based on the Hamilton and Zuk's hypothesis, we did not find any correlation between plumage brightness and haemosporidian prevalence. These results indicate that haemosporidians may have a pathogenic effect on their avian hosts and that plumage brightness is likely to have evolved in response to ecological factors other than parasitism infections.