Miracle-dz/UniFAR-FTUs huggingface dataset:
Cannabinoids and zebrafish

Cannabinoids are a group of terpenophenolic compounds and are naturally found in the cannabis plant (Cannabis sativa L). Δ9-Tetrahydrocannabinol (Δ9-THC) is the psychoactive cannabinoid. The high lipophilicity of Δ9-THC is a hindering factor in the further development of this compound into a large scale pharmaceutical product. In an effort to generate highly polar derivatives of Δ9-THC, we screened 206 alkane degrading bacterial strains. In total, eight derivatives were produced on milligram. All of these biotransformation products harbored modified alkyl chains, with hydroxy, carboxy and ester functionalities. We also investigated the potential of cell suspension culture of Catharanthus Roseus to transform Δ9-THC. Unlike bacterial strains, Catharanthus Roseus cells transformed Δ9-THC to its glycosylated and additionally hydroxylated derivatives. The behavioral effects of ∆9-THC are mediated by the centra l CB1 receptor in rats. CB1 receptors show high degree of sequence conservation in vertebrates. We used zebrafish embryos as a model to study the behavioral effects of cannabinoids. We conclude that cannabinoids have behavioural effects in zebrafish that are comparable to some of those reported in the literature for mammals. In particular, the acute exposure response resembles behavioural effects reported for adult. This suggests that some similarity in cannabinoid response pathways between zebrafish and mammals exists. We also performed the metabolomic profiling of zebrafish embryos treated with the concentrations of CB1 agonist and antagonist used in behavioural assays. The results of behavioural assays were successfully correlated with the metabolomic data of zebrafish embryos.
Analysis of the cis-regulatory structure of developmentally regulated genes in zebrafish embryo

Wahrend der embryonalen Entwicklung vertebrater Organismen wird die Genexpression durch cis-regulatorische Elemente streng kontrolliert. Die Interaktion dieser Elemente, gefolgt von der Rekrutierung der RNA Polymerase II Maschinerie, fuhrt zur Initiation der Transkription, einer der bedeutendsten Schritte in der Regulation der Genexpression. Seit der Fertigstellung mehrer Sauger- und vertebrater Genome ist phylogenetic footprinting einer der am Haufigsten angewandten Methoden um cis-regulatorische Sequenzelemente zu identifizieren. Dadurch konnte gezeigt werden, dass nicht-kodierende Sequenzelemente, teilweise mit extremer Konserviertheit, Enhancer Funktionen besitzen konnen. In der hier vorgestellten Arbeit zeige ich die Identifizierung von konservierten nicht-kodierenden Elementen und die Untersuchung ihrer Funktionalitat als Enhancer in vivo in transient transgenen Zebrafischembryonen am Beispiel des pax2 Locus. Konservierte nicht-kodierende Sequenzen die als Enhancer fungieren, zeigen ein signifikant erhohtes Vorkommen in der Nahe von entwicklungsspezifischen Regulatoren und Transkriptionsfaktoren. Im zweiten Teil meiner Arbeit stelle ich eine Methode vor, die eine Kombination aus globalem- und lokalem Alignment darstellt und zur Identifizierung einer groseren Anzahl konservierter nicht-kodierender Sequenzelemente mit Enhancer-Funktion fuhrt als bisherig verwendete Methoden. Die Mehrzahl der identifizierten Elemente wurde wahrend der Evolution durcheinander gemischt („shuffled“). Obwohl die Mehrzahl dieser shuffled-konservierten Elemente auch hier der Ontologieklasse von Transkriptionsfaktoren und Entwicklungsregulatoren zugewiesen werden konnte, wurde jedoch auch ein erhohtes Vorkommen in anderen Ontologieklassen festgestellt, die Gene beinhalten, die fur extrazellulare Regionen und Verhalten kodieren. Eines der Hauptprobleme, das sich nach der Identifizierung neuer Enhancer stellt, ist die Zuweisung von Genen, deren Expression durch den jeweiligen Enhancer beeinflusst werden, da diese durch grose Sequenzbereiche voneinander getrennt sein konnen. Neuere Studien zeigen auserdem, dass die Diversitat von Promotoren viel groser ist als ursprunglich angenommen. Da die Interaktion von Promotoren mit Enhancern durch Multiproteinkomplexe vermittelt wird, sollte die Zusammensetzung dieser Komplexe von der Eigenschaft des jeweiligen cis-regulatorischen Elements abhangig sein. Um zu ermitteln, ob die Sequenz des Kernpromoters und Enhancer die Spezifikation der Interaktion bestimmen, wurde ein high throughput screen durchgefuhrt, in dem 20 Kernpromotoren und 13 Enhancer zum Einsatz kamen, um 160 verschiedene Promoter/Enhancer Kombinationen zu generieren. Die Datenanalyse nach der automatisierten Bildgebung zeigte, dass die Enhancer-Funktion eindeutig promoterspezifisch ist und dass Promotoren die sich durch eine gute EST-Abdeckung auszeichnen signifikant aktiver sind und eine hohere Anzahl an Interaktionspartnern aufweisen.
APOPTOSIS INDUCTION EFFECT OF CURCUMIN AND ITS ANALOGS PENTAGAMAVUNON-0 AND PENTAGAMAVUNON-1 ON CANCER CELL LINES

ABSTRACT Objectives: This experiment aims to investigate the apoptosis effect of curcumin and its analogs pentagamavunon-0 (PGV-0) and PGV-1 on normal and other cancer cell lines. Methods: Growth inhibition effect was investigated using the MTT method. Double staining used acridine orange, 2-(4-aminodiphenyl)-6- indolcarbamidine dihydrochloride and ethidium bromide was performed to determine morphological changes of cells. Detection of PARP, caspase-3, PUMA and BAX using a western blot method was conducted to elucidate the apoptosis effect of the compounds. Results: PGV-1 (2.5 μM) and PGV-0 (5.0 μM) could inhibit T47D-cell growth on 72 h observation, but not for curcumin. DNA staining showed PGV-1 has the strongest apoptosis induction effect on T47D-cells compared to PGV-0 and curcumin as well. Western blot analysis resulted in cleavage PARP (83 kD) on HeLa, T47D, and MCF-7 cells treated with PGV-1 (2.5 μM), PGV-0 (5.0 μM). Curcumin (10.0 μM) just induced apoptosis on T47D-cell and MCF-7 cell, but not HeLa cell. Cleavage PARP resulted by apoptosis process in the cell. PGV-1 (2.5 μM) had a stronger apoptosis effect compared to PGV-0 (5.0 μM) and curcumin (10.0 μM) based on cleaved PARP result qualitatively. On the normal cell (NH3T3), cells that were treated with the compounds resulted in a negative cleavage PARP. This result indicated that the compounds were part of a selectively induced cancer cell line apoptosis process. Conclusion: Curcumin, PGV-0 and PGV-1 could inhibit cell growth by induce apoptosis on cancer cells but not on normal cells, which PGV-1 has strongest apoptosis induction effect on cancer cell lines. Keywords: Curcumin and analogs, Apoptosis, Cancer cell lines.
Age Related Response of Tobacco Caterpillar, Spodoptera litura (Fabricius) (Lepidoptera:Noctuidae) to Biovirus-S, a Commercial Formulation of Nuclear Polyhedrosis Virus

Laboratory tests were carried out to evaluate the effectiveness of Biovirus-S, a commercial formulation of nuclear polyhedrosis virus ( Sl NPV) against the different age groups of Spodoptera litura (Fabricius) larvae. The susceptibility of the larvae correlated negatively with the larval period of development. LC 50 values of one day old larvae were found 2.7, 277.0 and 61951.2 times more susceptible than three, five and eight day old larvae, respectively. Ten-day-old larvae required comparatively higher concentrations of Biovirus-S (1.39x10 10 POBs/ml), thereby indicating decreased susceptibility.
Optimised microwave-assisted synthesis of methylcarbonate salts: a convenient methodology to prepare intermediates for ionic liquid libraries

The reaction of 1-butylpyrrolidine with dimethyl carbonate to yield the ionic liquid precursor, 1-butyl-1-methylpyrrolidinium methylcarbonate, has been investigated under microwave heating conditions and the reaction parameters optimised to achieve 100% yield of the pyrrolidinium salt with no by-products in under 1 h. The reactions of tributylamine, trioctylphosphine, and 1-butylimidazole with dimethyl carbonate under comparable conditions have also been evaluated, yielding the corresponding methylcarbonate salts which can be used as intermediates for the preparation of halide-free ionic liquids without generating any undesirable salt wastes.
Host community similarity and geography shape the diversity and distribution of haemosporidian parasites in Amazonian birds

Identifying the mechanisms driving the distribution and diversity of parasitic organisms and characterizing the structure of parasite assemblages are critical to understanding host-parasite evolution, community dynamics, and disease transmission risk. Haemosporidian parasites of the genera Plasmodium and Haemoproteus are a diverse and cosmopolitan group of bird pathogens. Despite their global distribution, the ecological and historical factors shaping the diversity and distribution of these protozoan parasites across avian communities and geographic regions remains unclear. Here we used a region of the mitochondrial cytochrome b gene to characterize the diversity, biogeographical patterns and phylogenetic relationships of Plasmodium and Haemoproteus infecting Amazonian birds. Specifically, we asked whether, and how, host community similarity and geography (latitude and area of endemism) structure parasite assemblages across 15 avian communities in the Amazon Basin. We identified 265 lineages of haemosporidians recovered from 2661 sampled birds from 330 species. Infection prevalence varied widely among host species, avian communities, areas of endemism, and latitude. Composition analysis demonstrated that both malarial parasites and host communities differed across areas of endemism and as a function of latitude. Thus, areas with similar avian community composition were similar in their parasite communities. Our analyses, within a regional biogeographic context, imply that host switching is the main event promoting diversification in malarial parasites. Although dispersal of haemosporidian parasites was constrained across six areas of endemism, these pathogens are not dispersal-limited among communities within the same area of endemism. Our findings indicate that the distribution of malarial parasites in Amazonian birds is largely dependent on local ecological conditions and host evolutionary relationships. This article is protected by copyright. All rights reserved.
Haematological parameters of pond bats (Myotis dasycneme Boie, 1825 Chiroptera: Vespertilionidae) in the Ural Mountains

AbstractHaematological parameters of pond bats (Myotis dasycneme, Chiroptera), the most numerous bat species in the Ural Mountains, were investigated. Blood samples were collected from 40 wild bats. Ten haematological parameters were determined using an automated haematological analyser. Morphological differentiation of leukocytes was performed in blood smears. No significant differences were revealed in the main parameters of peripheral blood between adult males and females of Myotis dasycneme except for the content of haemoglobin (p = 0.01) and leukocytes (p = 0.02). Data show that significant differences exist between adult and subadult females in erythropoiesis (RBC, HGB, HCT, and MCV). Thus, with age, the number of erythrocytes and the haemoglobin level increase (p < 0.05), but the leukocytic chain remains relatively stable. Changes in haematological parameters were observed in the bats caught in the season of preparation for long hibernation (6–7 months). Conclusion: The blood system of Myotis dasyc.
Molecular and morphological characterization of the Achnanthidium minutissimum complex (Bacillariophyta) in Petuniabukta (Spitsbergen, High Arctic) including the description of A. digitatum sp. nov.

ABSTRACT Recent morphology-based investigations of freshwater Arctic diatoms suggest that many species remain to be discovered, reflecting a unique polar flora. During a survey of the freshwater diatom flora of northern Billefjorden, including the Petuniabukta fjord region (Spitsbergen), several morphodemes belonging to the Achnanthidium minutissimum species complex were recorded. Molecular phylogenies based on rbcL, 28S and 18S sequences, including single cells from Canada and strains from Marion Island (sub-Antarctica) and GenBank revealed the presence of 12 distinct A. minutissimum complex lineages, of which three contained strains from Spitsbergen. One Arctic lineage is described as a new species. Achnanthidium digitatum sp. nov. is morphologically characterized by narrow, linear to only slightly lanceolate valves and usually two areolae per stria. The two remaining Arctic lineages are in need of a more complete morphological and molecular comparison with other representatives of the A. minutissimum complex to clarify their taxonomic identity. It is argued that implementation of molecular data in the taxonomy of Achnanthidium will be essential to solve the taxonomic problems associated with this group, eventually resulting in a better understanding of the biogeography and niche differentiation of different species belonging to the A. minutissimum complex. Ideally, this should be based on more variable genes than the currently widely used 18S, which does not have a species level resolution in the A. minutissimum complex.
Divergence between riparian seed banks and standing vegetation increases along successional trajectories

Questions Plant community resilience largely depends on the secondary succession induced by species re-colonization from seed banks. Soil seed bank resilience is, however, poorly understood, especially in regularly disturbed habitats like riparian zones. Two questions were asked: what are the changes in species diversity experienced by riparian soil seed banks along successional trajectories, and to what extent do riparian soil seed banks promote vegetation resilience during secondary succession? Location Southeastern Quebec, Canada. Methods Soils were collected along five rivers in field edges and riverbanks of post-agricultural riparian zones with three contrasting successional stages (unplanted – planted with trees 15-17 years prior to sampling – natural riparian forests), and their seed bank composition determined with the seedling emergence method. Species richness in seed banks was assessed along successional trajectories for distinct ecological groups, using linear mixed models. The compositions of soil seed banks and standing vegetation (from botanical surveys) were compared based on NMDS and Indicator Species Analysis. Results Seed bank species richness decreased along successional trajectories. Tree-planted riparian zones were generally closer to unplanted riparian zones than to natural riparian forests, the latter being more species-rich for natives, trees, shrubs and zoochores, and species-poor for exotics, forbs and stress-tolerators. Likewise, seed bank species composition of unplanted and tree-planted riparian zones was similar but differed from those of natural riparian forests. Conversely, standing vegetation of tree-planted riparian zones was intermediate between early- and late-successional stages, at least at field edges. For the three successional stages, seed bank composition clearly differed from standing vegetation. Conclusions The high resilience of riparian plant communities appeared poorly related to the dynamics of their soil seed banks. This species shift between seed banks and standing vegetation during secondary succession is likely due to periodic flooding leading to the regular turnover of seeds. The resilience of riparian communities might thus be more influenced by spatial dispersal along rivers and across landscapes than by in situ temporal dispersal in soils. This article is protected by copyright. All rights reserved.
Integrating Biomarkers of Organophosphate Pesticides in an Agriculturally Exposed Population

Integrating Biomarkers of Organophosphate Pesticides in an Agriculturally Exposed Population Zachariah N Guerrette Chair of Supervisory Committee Professor Elaine M. Faustman Department of Environmental and Occupational Health Sciences Exposure biomonitoring of organophosphate (OP) pesticides is a common practice to protect the health of agricultural workers. However, few studies have examined the association between markers of exposure and cholinesterase inhibition, the standard marker of effect, for these compounds or how genetic variation in the metabolic pathways responsible for the activation and detoxification of OP pesticides affects these associations. We evaluated the potential for pesticide exposure and cholinesterase inhibition levels of apple orchard farmworkers and their children in relation to non-farmworker households in the same region. We tested the hypothesis that 1. ) OP pesticide exposure biomarkers were predictive of the inhibition of cholinesterase enzymes and 2. ) genetic variants for metabolizing genes, including paraoxonase-1 (PON1) and cytochrome P-450s (CYP450s) altered this association. Higher levels of azinphos methyl in blood and dimethylphosphate urinary metabolites were observed in farmworkers adults and children during periods of pesticide application (thinning season) compared to non-farmworkers. Levels of azinphos methyl in blood were significantly associated with higher levels of dimethyl phosphate metabolites in the urine. Significant associations between concentrations of these exposure biomarkers and levels of cholinesterase inhibition were observed during the thinning season. We observed no significant modification of these observations when incorporating PON1 phenotypic and genotypic information into our models in accordance with predictions from in vivo data. However, when considering quantification of exposure via urinary metabolites, we found significant modification of the exposure/effect relationship by genetic variants for a number of CYP450 enzymes. These observations suggest that significant differences in the level of activation or detoxification of OP pesticides occur between individuals differing in the genotype of certain CYP450s responsible for this metabolism. Despite not directly handling pesticides, individuals working in pomme orchards during periods of pesticide application and their children are exposed to OP pesticides and can experience cholinesterase inhibition. Furthermore, the risk of cholinesterase inhibition appears to be greater in individuals with certain genetic backgrounds. This information illustrates the significance of individual susceptibility and the metabolism of specific OP pesticides for cumulative risk assessments of these compounds.
RNA helicase, DDX27 regulates proliferation and myogenic commitment of muscle stem cells

Developmental processes depend on the combined efforts of epigenetic, transcriptional and post-transcriptional processes that lead to the production of specific proteins that are important determinants of cellular identity and developmental processes. Ribosomes are a central component of the protein biosynthesis machinery in cells; however, their regulatory roles in the translational control of gene expression in an organ specific context during development remain to be defined. In a genetic screen to identify critical regulators of myogenesis, we identified a DEAD-Box RNA helicase, DDX27, that is required for the proliferation and myogenic commitment of skeletal muscle stem cells. DDX27 deficient skeletal muscle exhibits hypotrophy and impaired regeneration potential. We demonstrate that DDX27 regulates ribosomal RNA (rRNA) maturation, and thereby the ribosome biogenesis and the translation of specific transcripts that are required to maintain pluripotency and myogenic differentiation of satellite cells. These findings provide insight into the translational regulation of gene expression in myogenesis and suggest novel functions for ribosomes in regulating gene expression during skeletal muscle development. AUTHOR SUMMARY Inherited skeletal muscle diseases are the most common form of genetic disorders with primary abnormalities in the structure and function of skeletal muscle resulting in the impaired locomotion in affected patients. A major hindrance to the development of effective therapies is a lack of understanding of biological processes that promote skeletal muscle growth. By performing a forward genetic screen in zebrafish we have identified mutation in a RNA helicase that leads to perturbations of ribosomal biogenesis pathway and impairs skeletal muscle growth and regeneration. Therefore, our studies have identified novel ribosome-based disease processes that may be therapeutic modulated to restore muscle function in skeletal muscle diseases.
Influencia de la temperatura sobre el ciclo de vida de la especie necrofaga Compsomyiops arequipensis Mello, 1968 (Diptera: Calliphoridae)

Se determino como influye la variacion de la temperatura en la duracion del ciclo de vida de C. arequipensis y se establecieron los requerimientos caloricos de la especie para cada estadio de desarrollo. La captura se realizo en el Centro Ambiental Chimayoy, Pasto-Narino, se procedio a su cria masiva “in vitro” y se sometieron a cuatro tratamientos en camaras de cria con reguladores electronicos de temperatura para determinar su ciclo de vida a niveles constantes de 25, 19, 13 y 7oC, considerados como valores usuales en la region. Se obtuvieron curvas de crecimiento y desarrollo, la duracion del ciclo total y de cada fase, y los grados dia acumulados (ADDs) necesarios para la culminacion de cada etapa del ciclo vital hasta obtener el imago. A 25oC la duracion del ciclo fue de 19,7 dias; a 19oC de 25,87 dias y a 13oC de 61,95 dias. A 7oC eclosiono el 5% de los huevos, pero murieron en el primer instar ya que esta temperatura se encuentra por debajo de la temperatura umbral minima de desarrollo. Los ADDs a 25oC fueron de 290,90; a 19oC de 234,34 y a 13oC de 185,50. Se amplia los registros de C. arequipensis en Colombia y se propone como especie util en investigaciones forenses para la determinacion del intervalo post mortem (IPM) en el municipio de Pasto y posiblemente en regiones de Colombia con altitudes y condiciones climatologicas similares.
Molecular Characterization, Tissue, and Developmental Expression Profiles of MagR and Cryptochrome Genes in Agrotis ipsilon (Lepidoptera: Noctuidae)

Abstract Light and temperature are the major environmental signals for insect circadian rhythms, and it is widely believed that magnetoreceptor (MagR) and cryptochromes (CRYs) participate in orientation behavior of organisms navigating or migrating long distances. Potential mechanisms for the coupling of circadian rhythm and magnetic detection have been discussed but are not known for the serious agricultural pest Agrotis ipsilon (Hufnagel). In this study, one novel MagR gene, designated Ai-MagR, was cloned from A. ipsilon by reverse transcription polymerase chain reaction and RACE-PCR strategies. It encodes a protein that has 131 amino acids and one conserved iron–sulfur cluster-binding domain. In a phylogenetic analysis, Ai-MagR was closely related to its orthologs in the noctuid family. The results of quantitative polymerase chain reaction showed that Ai-crys and Ai-MagR were present in all tested organs and life stages of the moths and that the daily levels of the three genes fluctuated. In 16 h light and 8 h dark, expression of Ai-crys and Ai-MagR followed a circadian rhythm throughout the day, and constant light or dark disturbed this rhythm. At 25 ± 1 ° C, expression of Ai-crys and Ai-MagR also had a circadian rhythm through the day, which was disrupted by cold or high temperature conditions. Based on the results, the two CRYs and MagR may play different roles during the migration of A. ipsilon. Overall, these findings have significant importance for further study of the functions of Ai-crys and Ai-MagR genes and potential control of the black cutworm.