Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetics of metabolic syndrome and related traits

In this thesis several aspects of metabolic syndrome are addressed. The focus involves questions concerning the genetics of obesity, TG and cholesterol and hyperglycemia. Since we hypothesized that obesity is the most important trigger of metabolic impairment, the MetS definition in this thesis was chosen to include the obesity measure waist circumference as an essential component. In the study described in chapter 2, the heritability of the metabolic syndrome was addressed and compared to the heritability of its individual components. Since the individual components of MetS were shown to be more heritable than MetS itself, the studies described in chapter 3 and 4 focused on the genetics of the individual MetS component plasma TG. For this purpose, a candidate gene approach was employed using HTG patients and healthy controls. The involvement of a series of candidate genes was confirmed. The study described in chapter 5 followed a similar approach to that used in the studies described in chapter 3 and 4. Several candidate genes were studied in patients suffering from hyperlipoproteinemia (HLP) type III, which is characterized by elevated levels of total plasma cholesterol and plasma TG. HLP type III is characterized by APOE2 homozygosity. Contributing genetic factors in the (metabolically stressed) APOE2/2 environment were confirmed. Plasma adiponectin, an adipose tissue secreted hormone (adipokine), has been suggested to be a biomarker for MetS. In chapter 6 we describe a study which particularly aimed to determine the effect of menopause on the discriminating accuracy of adiponectin to predict MetS. Especially low levels of plasma adiponectin in postmenopausal women were found to be a risk for MetS. However, the discriminating accuracy of adiponectin for the presence of MetS was exceeded by BMI in men and pre –and post menopausal women. Since plasma adiponectin levels are very well correlated with MetS components or related traits, the study described in chapter 7 addressed the question whether these correlations are caused by a genetic overlap (genetic correlation). The genetic correlation was mono-laterally validated with regard to the adiponectin gene (ADIPOQ). Chapter 8 describes a study towards finding novel loci associated with adiponectin or loci that are possibly involved in the genetic overlap between adiponectin and MetS components or related traits. This study followed a genome-wide association (GWA) approach. The results of this GWA were used in a joined analysis with two other cohorts in a meta-analysis. In addition, a selected proportion of SNPs was submitted for replication in several cohorts. Chapter 9 provides a general discussion by reviewing all previous chapters in the thesis. Furthermore, chapter 9 includes suggestions and proposals for future analyses towards unraveling genetic and environmental factors involved in the expression and manifestation of metabolic risk factors.
Distribution of burnet moths (Zygaena spp.) in relation to larval and adult resources on two spatial scales

Abstract. 1 Metapopulation theory predicts habitat patch area and isolation to be the main factors affecting the distribution of species dependent of patchily distributed habitats, but the need for multiple resources, which might be spatially separated, is often ignored. 2 Here, I studied the effect of host plant and nectar flower distributions on the spatial distribution of pupae and adults of two species of burnet moths (Zygaena filipendulae and Zygaena lonicerae), on two spatial scales. 3 At the landscape scale (10 × 12 km), moths were patchily distributed, but there was no effect of patch isolation on the occurrence of any of the species. On the local scale (2 × 2 km), I expected to find additive effects of the local abundances of larval and adult resources and their abundances in the surrounding areas, but instead, moth abundance decreased with increasing resource connectivity. I interpret this as an aggregation effect, such that at low resource abundances in the area, moths tend to aggregate in patches with higher flower densities. 4 My results also supported the hypothesis that the spatial distribution of individuals at one life stage is restricted by the requirement of other life stages, because the abundance of pupae of both species were associated with floral resources and abundance of imagos was related to larval resources. 5 I conclude that in studies aiming at understanding the relative importance of local and regional factors for species distributions, it is important to account for the habitat requirements of all life stages.
Quantifying the effects of temperature and flow regimes on 0+ cyprinid fish abundance in the upper Rhone River using Bayesian hierarchical modelling

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Quantifying the effects of temperature and flow regimes on 0+ cyprinid fish abundance in the upper Rhone River using Bayesian hierarchical modelling J. Piffady, Y. Souchon, H. Capra, E. Parent
Dynamic refugia and species persistence: tracking spatial shifts in habitat through time

Historical climate is known to influence contemporary patterns of biological diversity. Species distribution modeling methods, combined with paleoclimatic surfaces, have been used to identify regions that were likely stable across long periods of time. To date, this approach has produced a static representation of refugia by identifying regions of suitable climate across a series of time-slices. However, suitable habitat for a given species (or suite of species) may have shifted contiguously in response to changing climates through geologic time. We develop a new approach that takes into consideration habitat connectivity through time. We use the Australian Wet Tropics as a case study to demonstrate how our method works and suggest additional insights the method might give for understanding the determinants of biological diversity.
Histopathology of the Digestive Tissues and Whole-Body Anaerobic Bacteria Counts of the Eastern Oyster, Crassostrea virginica, After Experimental Exposure to Anoxia

ABSTRACT The Eastern oyster, Crassostrea virginica, is a sensitive bio-indicator of environmental changes ranging from tidal flux to heavy-metal pollution. Extreme fluctuations in dissolved oxygen levels are well documented in Mobile Bay, AL. Extended periods of low dissolved oxygen occurring during the summer months have been shown to cause oyster mortality. The current study examined the effects of anoxia on tubule morphology of the digestive gland in the Eastern oyster as well as the quantity and quality of whole-body anaerobic bacteria counts. Oysters were exposed to anoxic conditions (<0.1 mg/L O2) at 28°C in a laboratory setting and sampled at 0 h (preexposure), 24 h, 48 h, and 60 h, and after a 4-wk recovery interval. The whole-body anaerobic bacteria count for test oysters (Mean = 1.11 × 106 cfu/mL) from the 60-h interval was significantly higher than counts for the preexposure oysters, 24-h, and 48-h experimental intervals. The most common bacteria isolated were Clostridium sp. Histological examination of oysters exposed to anoxic conditions indicated stress in the digestive gland. Changes in shape and size of digestive tubule epithelial cells occurred, as well as sloughing of secretory absorptive cells into the digestive tubule lumen. Necrosis and inflammation composed of aggregates of hemocytes along with bacterial infiltration into digestive tissue was noted in oysters exposed to anoxic conditions. Digestive tubule lumen ratios of oysters sampled after a 60-h exposure to anoxia were increased significantly in comparison with preexposure oysters. Digestive tubule lumen ratios returned to preexposure morphology after a 4-wk week recovery period. Oysters have the ability to regenerate digestive gland tissue if environmental conditions return to normal. These findings indicate that anoxia exposure at summer temperatures contributes to digestive gland atrophy and necrosis in C. virginica. The combination of digestive gland atrophy, necrosis, and bacterial infiltration into digestive tissues suggests that oysters may be succumbing to infection during periods of anoxic stress.
The Monash Simple Climate Model: An interactive climate model for teaching

The Monash university interactive simple climate model is a web-based interface that allows students and the general public to explore the physical simulation of the climate system with a real global climate model. It is based on the Globally Resolved Energy Balance (GREB) model that simulates most of the main physical processes in the climate system in a very simplistic way and therefore allows very fast and simple climate model simulations. Despite its simplicity the model simulates the mean climate and its response to external forcings, such as doubling of the CO 2 concentrations very realistically. The Monash simple climate model web-interface allows you to explore thousands of experiments, scenarios and tutorials in an interactive way. You can do some entertaining and educational puzzles about the interaction of climate dynamics. By turning switches OFF and ON you control physical processes in the climate system ansd see how the interaction of the processes builds up the climate. By testing a number of experiments you learn about the interactions in the climate system and thereby ﬁgure out which switch controls what process in the climate system. The presentation will illustrate how this web-base tool works and what are the possibilities in teaching students with this tool are.
Reconstructed paternal genotypes reveal variable rates of multiple paternity at three rookeries of loggerhead sea turtles (Caretta caretta) in Western Australia

Abstract. Female sea turtles are promiscuous, with clutches of eggs often sired by multiple males and rates of multiple paternity varying greatly within and across species. We investigated levels of multiple paternity in loggerhead sea turtles (Caretta caretta) from three rookeries in Western Australia by analysing polymorphic species-specific genetic markers. We predicted that the level of multiple paternity would be related to female population size and hence the large rookery at Dirk Hartog Island would have higher rates of multiple paternity than two smaller mainland rookeries at Gnaraloo Bay and Bungelup Beach. Contrary to our prediction, we found highly variable rates of multiple paternity among the rookeries that we sampled, which was unrelated to female population size (25% at Bungelup Beach, 86% at Gnaraloo Bay, and 36% at Dirk Hartog Island). Approximately 45 different males sired 25 clutches and the average number of sires per clutch ranged from 1.2 to 2.1, depending on the rookery sampled. The variance in rates of multiple paternity among rookeries suggests that operational sex ratios are variable in Western Australia. Periodic monitoring would show whether the observed patterns of multiple paternity for these three rookeries are stable over time, and our data provide a baseline for detecting shifts in operational sex ratios.
Research of Klebsiella pneumoniae in dairy herds

Klebsiella pneumoniae is a common environmental agent of clinical and subclinical mastitis affecting dairy herds, and may be present in the final product decreasing its quality. Mastitis caused by K. pneumoniae is even more severe due to its poor response to antibiotic therapy, rapid evolution to toxic shock and death of the animal. This paper aimed to study the prevalence of this pathogen among dairy herds in ten farms located in different municipalities of Sao Paulo State based on size and use of milking technology. All mammary glands of all lactating cows were screened using the California Mastitis Test (CMT) and a strip cup. A single aseptic milk sample (20mL) was collected from all CMT-positive quarters and bulk tanks, whereas swab samples were collected from feces, hind limbs of the animals, bedding and milking parlor. Identification of K. pneumoniae was performed using conventional microbiology culture, biochemical assay and Polimerase Chain Reaction. The primers were designed and tested at the Laboratory of Molecular Biology applied to Zoonoses (FMVZ, Unesp-Botucatu) targeting the 16S rRNA gene. This study included 1067 animals. Six cases of intramammary infection by K. pneumoniae were detected in six different cows in two farms. Moreover, K. pneumoniae was isolated in 77 swabs (34 from bedding in 9 farms, 7 from waiting rooms in 5 farms, 6 from milking parlors in 4 farms, 11 from rectums in six farms, and 19 from hindlimbs in 7 farms. Molecular analysis confirmed the agent was K. pneumoniae. At least one strain of the agent was identified in a certain site in all farms, showing the need of maintaining the hygiene in dairy farms.
The twin arginine translocation pathway in Escherichia coli : mechanism and quality control

The bacterial twin-arginine translocation (Tat) pathway has the unique ability to export pre-folded proteins across the cytoplasmic membrane. Its name came from the almost invariant twin-arginine motif in the signal peptide of Tat substrates. Escherichia coli, a Gram-negative bacterium, is typically used to understand Tat function in bacteria. Until now, evidence has shown that TatA, TatB and TatC comprise the minimally functional unit, moreover, a quality control system exists to monitor the assembly of cofactors and the correctly folding state of proteins which avoids the futile export and initiates the degradation of rejected molecules. The research presented in this thesis sought to gain insight into the quality control mechanism of the Tat pathway in E. coli, and also study the relationship between transport and maturation of substrates. In the first place, a novel Tat substrate, YedY, was used to analyse the nature and variety of proofreading functions operating in conjunction with the Tat pathway. The single substitutions in three predicted ligands for the YedY molybdopterin centre led to complete inhibition of export and variable degradation of mutated YedY forms, indicating an effective proofreading activity. Circular dichroism spectroscopy and inductively coupled plasma mass spectrometry of purified proteins demonstrated the change of secondary structures between YedY and mutated variants, and also indicated the content of Mo in molybdopterin cofactor within proteins. The data suggested that the three mutated forms failed to correctly assemble cofactor which resulted in rejection by the Tat export pathway on the basis of the different changes of secondary structures. Further analysis shows that none of the known export chaperones for molybdenum cofactor-containing Tat substrates is required for YedY biogenesis; export is unaffected in cells lacking DmsD and TorD. In the second place, maturation of pre-YedY was blocked when an Ala>Leu substitution was made at the -1 position of the signal peptide, and a membrane-bound precursor form accumulated in the membrane. However, the mature domain had been transferred to the periplasm. The accumulation did not block transport of other Tat substrates, indicating the precursor exited from the translocation channel and integrated into the membrane bilayer. Since the precursor was not detected in the periplasm, it was suggested that the precursor has undergone lateral transfer into the bilayer during translocation. These results are discussed in relation to the overall mechanism of translocation and proofreading by the Tat pathway in E. coli.
The Prevalence of Three Viruses Infecting Fig in Southern Turkey

In a survey of four fig-growing provinces of Turkey (Adana, Hatay, Sanliurfa and Mersin), 132 samples were tested by reverse transcription-polymerase chain reaction (RT-PCR) to assess the presence of Fig leaf mottle-associated virus 1 (FLMaV-1), Fig leaf mottleassociated virus 2 (FLMaV-2) and Fig mosaic virus (FMV). All samples were negative in PCR to FLMaV1, whereas FLMaV-2 and FMV were detected in six (4.5%) and 10 (7.6%) of the samples, respectively. Both viruses were found in fig trees collected in the provinces of Adana, Hatay and Sanliurfa, but no infection was found in Mersin province. Sequence analysis of amplified DNA showed a level of nucleotides variability ranging from 1 to 10% for FLMaV-2 and from 6 to 17% for FMV isolates. Phylogenetic analysis grouped the Turkish FLMaV-2 isolates in one cluster together with other near-eastern FLMaV-2 isolates previously reported in GenBank.
Ecology of parasites of Metynnis lippincottianus (Characiformes: Serrasalmidae) from the eastern Amazon region, Macapá, State of Amapá, Brazil

The present study provides the first investigation on the ecological aspects of the parasites M. lippincottianus from the Amazonian basin, as well as the parasite-host relationship . 76 out of the examined fish ( 98.7%) were parasitized by at least one species of parasites. A total of 8,774 parasites were collected, being Ichthyophthirius multifiliis , Anacanthorus jegui , Dadayius pacupeva , Digenea gen. sp. (metacercariae), Procamallanus ( Spirocamallanus ) inopinatus , Procamallanus ( Spirocamallanus ) sp. , Spinoxyuris oxydoras , Contracaecum sp. larvae, Dolops longicauda and Hirudinea gen. sp. Ichthyophthirius multifiliis was the dominant species, followed by A. jegui . Among the endoparasites, S. oxydoras and D. pacupeva were predominant. The mean diversity of parasites was HB = 0.96 ± 0.32 and there was aggregate distribution pattern. A positive correlation of body weight with the abundance of I. multifiliis and S. Oxydoras was observed, whereas a negative correlation of body weight with abundance of the Contracaecum sp. larvae was found. The relative condition factor (Kn) was not negatively affected by parasites, and a positive correlation between Kn and abundance of I. multifiliis , S. oxydoras and D. pacupeva was found. This study is the first one to record I. multifiliis , D. longicauda and A. jegui parasitizing M. lippincottianus , as well as the first record of D. pacupeva and S. oxydoras in the Amazonas river system.
INFLUENCE OF DIETARY ROSEMARY, MARJORAM AND GINGER SUPPLEMENTATION ON REPRODUCTIVE PERFORMANCE OF NEW ZEALAND WHITE RABBIT DOES UNDER SINAI CONDITIONS

Thirty five NZW rabbit does, aged 10 months and weighed 3.21 ± 0.06 kg were divided randomly into five comparable groups (7 each). Rabbits in the 1 group were fed the basal (CO) diet without medicinal plants. While those in the 2, 3, 4 and 5 groups were fed the basal pelleted diet containing 3% Rosemary (RS), 3% Marjoram (MR), 1.5% Ginger root (ZR) and 2.5% mixture (MX) of these medicinal plants, respectively which were replaced with control diet at the same levels (%) for each diet. Results showed that kindling rate was increased in does of RS, ZR and MX groups (87.5%); MR did not differ from the CO (77.8%). Litter size and weight at weaning was higher (P<0.05) in RS, MR and MX groups than those in the CO or ZR group. Average daily gain of bunnies at birth to weaning was higher (P<0.05) in medicinal plane groups compared to the control group. Doe rabbits fed medicinal plants had the highest (P<0.05) values of total milk yield during lactation period compared with the control rabbits. The mortality rate at all time intervals from birth to weaning tended (P>0.05) to be lower in RS, MR, ZR and MX (8.79, 11.54, 5.95 and 7.46, respectively) than in the CO group (16.84%). Blood plasma estradiol 17-β concentration was higher (P≤0.05) in RS and MX (19.3 and 17.9 pg/ml) than in CO, MR and ZR groups (12.97, 10.7 and 15.83 pg/ml), respectively. Relative economic efficiency increased by 143, 164, 123 and 152 in RS, MR, ZR and MX, respectively, compared with (100%) in CO group.
Chloromethyltetramethylrosamine (Mitotracker OrangeTM) Induces the Mitochondrial Permeability Transition and Inhibits Respiratory Complex I

We have investigated the interactions with isolated mitochondria and intact cells of chloromethyltetramethylrosamine (CMTMRos), a probe (Mitotracker OrangeTM) that is increasingly used to monitor the mitochondrial membrane potential (Δψm) in situ. CMTMRos binds to isolated mitochondria and undergoes a large fluorescence quenching. Most of the binding is energy-independent and can be substantially reduced by sulfhydryl reagents. A smaller fraction of the probe is able to redistribute across the inner membrane in response to a membrane potential, with further fluorescence quenching. Within minutes, however, this energy-dependent fluorescence quenching spontaneously reverts to the same level obtained by treating mitochondria with the uncoupler carbonylcyanide-p-trifluoromethoxyphenyl hydrazone. We show that this event depends on inhibition of the mitochondrial respiratory chain at complex I and on induction of the permeability transition pore by CMTMRos, with concomitant depolarization, swelling, and release of cytochrome c. After staining cells with CMTMRos, depolarization of mitochondriain situ with protonophores is accompanied by changes of CMTMRos fluorescence that range between small and undetectable, depending on the probe concentration. A lasting decrease of cellular CMTMRos fluorescence associated with mitochondria only results from treatment with thiol reagents, suggesting that CMTMRos binding to mitochondria in living cells largely occurs at SH groups via the probe chloromethyl moiety irrespective of the magnitude of Δψm. Induction of the permeability transition precludes the use of CMTMRos as a reliable probe of Δψm in situ and demands a reassessment of the conclusion that cytochromec release can occur without membrane depolarization and/or onset of the permeability transition.
Predição de Rankings de Artistas por Meio de Regressão

A construcao de rankings consiste na ordenacao de resultados recuperados de acordo com um determinado criterio. Os rankings podem fornecer informacoes relevantes para analistas de diferentes setores da industria. Na industria fonografica, os rankings possibilitam a compreensao de como os estilos musicais e a popularidade dos artistas e suas musicas evoluem com o tempo, permitindo analises de historicos de execucoes e de tendencias. Devido a importância da construcao de rankings no escopo musical, tecnicas de minera- cao de dados tem sido utilizadas para predizer os rankings atraves de informacoes contidas em midias sociais. Este trabalho avalia modelos de regressao para a predicao de rankings de artistas utilizando-se de dados historicos (rankings diarios de artistas) extraidos do website Vagalume. Tres tecnicas de regressao (k-Nearest Neighbors - k-NN, Regressao Linear Multipla - RLM e Random Forests - RF) foram avaliadas neste trabalho considerando-se diversos cenarios. Os resultados obtidos por meio de experimentos mostraram que predicoes com baixas taxas de erros podem ser obtidas, indicando que tecnicas de mineracao de dados podem ser utilizadas para obtencao de informacoes que auxiliem a industria fonografica na tomada de decisoes.