Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge discovery and modeling in genomic databases

This dissertation research is targeted toward developing effective and accurate methods for identifying gene structures in the genomes of high eukaryotes, such as vertebrate organisms. Several effective hidden Markov models (HMMs) are developed to represent the consensus and degeneracy features of the functional sites including protein-translation start sites, mRNA splicing junction donor and acceptor sites in vertebrate genes. The HMM system based on the developed models is fully trained using an expectation maximization (EM) algorithm and the system performance is evaluated using a 10-way cross-validation method. Experimental results show that the proposed HMM system achieves high sensitivity and specificity in detecting the functional sites. This HMM system is then incorporated into a new gene detection system, called GeneScout. The main hypothesis is that, given a vertebrate genomic DNA sequence S, it is always possible to construct a directed acyclic graph G such that the path for the actual coding region of S is in the set of all paths on G. Thus, the gene detection problem is reduced to the analysis of paths in the graph G. A dynamic programming algorithm is employed by GeneScout to find the optimal path in G. Experimental results on the standard test dataset collected by Burset and Guigo indicate that GeneScout is comparable to existing gene discovery tools and complements the widely used GenScan system.
Post-fledging body mass increase in Common Terns Sterna hirundo : influence of age, sex and year

We studied the inter-year and inter-sex variation of the post-fledging body mass development of Common Terns Sterna hirundo in 2000 and 2001 at the Banter See colony, northern Germany. Here, post-fledglings can be identified and weighed remotely and automatically by a transponder system that makes use of automated balances installed at the colony. Individuals were sexed with PCR amplification methods. After fledging, young generally continued to increase their mass. However, in 2000, the young did not significantly increase their mass during the post-fledging period. In 2001, conditions were more favourable and body mass increased continuously. Further, in 2001, male post-fledglings were significantly heavier than female post-fledglings. Once having left the colony area (on average 18-23 days after fledging in 2000, and 14-16 days after fledging in 2001), post-fledgling body mass had still not reached adult body mass. The longer a juvenile stayed at the colony, the higher was its final body mass, which if acting as a threshold level may control departure time. Neither brood size nor hatching order affected post-fledging mass or period. In the unfavourable year 2000, when many individuals were found dead after fledging, fledging age but not fledging mass was found to be a predictor of post-fledging survival before departure: individuals fledging when older had a lower survival probability. Our results stress the importance of the post-fledging period for body mass increase and survival prior to departure. The variation in post-fledging mass growth between years and between the sexes is discussed with respect to parental effort and a possible selective provisioning of sons over daughters.
The edge of a species' range : survival and space-use patterns of raccoons at the northern periphery of their distribution

The raccoon (Procyon lotor) is a species that has likely benefited from environmental conditions that followed European settlement of North America. As such, the raccoon has experienced vast range expansion during the past century, moving northward across the continent. However, little is known about the factors that currently govern the northern distribution and the ecology of raccoons at the northern edge of its range. Thus, I studied the population dynamics and social ecology of raccoons in southern Manitoba during spring, summer, and autumn, 2002-2005. To understand how intrinsic and extrinsic factors affected population dynamics, I examined how winter severity, body condition, age, and gender influenced over-winter survival of raccoons. Winter severity (measured by temperature and snow accumulation) was the most important factor influencing survival (β = 1.08, 95% CI = 0.99-1.17). Over-winter survival estimates ranged from 0.51 (95% CI: 0.41, 0.75) during the harshest winter to 0.84 (95% CI: 0.71, 0.97) during the mildest winter on record for Manitoba. There was no apparent relationship between autumn body condition and autumn food indices and no correlation between autumn and spring body condition. Adults experienced higher survival than yearlings while males had a greater chance of dying compared to females. Variation in abundance natural food items thought to be important during autumn hyperphagia are likely overwhelmed by the presence of grain as an alternative food source, as autumn body condition was constant across all years and plateaued at ca. 20% body fat. I conclude that changes in climatic conditions will likely have the greatest impact on raccoon demographics, with milder winters leading to higher survival.
Mapping of fruit shape and color development traits in eggplant (Solanum melongena L.) based on RAPD and AFLP markers

We have constructed a linkage map of eggplant (Solanum melongena L.) using an F2 population derived from a cross between a breeding line, EPL-1 and an introduced line, WCGR112-8, from India. The two parental lines showed contrasting responses to several pathogens and differences in several morphological traits. Parental lines were screened with 1, 232 random primers for RAPD and 64 primer combinations for AFLP. The link-age map consisted of 181 loci, comprising 88 RAPD and 93 AFLP markers. These markers identified 21 linkage groups spanning 779.2cM with an average distance of 4.9cM. The linkage groups ranged from 1.9 to 95.6cM in length and included 2 to 32 markers, respectively. The fruit shape and color development trait were scored and the linkage to the markers was investigated. The fruit shape showed a significant association with markers on linkage group 2. Color development in fruit, stem and calyx showed a significant association with markers on linkage group 7. These markers may provide valuable information for eggplant breeding.
Markov vs. Hurst-Kolmogorov behaviour identification in hydroclimatic processes

Hydroclimatic processes are usually modelled either by exponential decay of the autocovariance function, i.e. Markovian behaviour, or power type decay, i.e. long-term persistence (or else Hurst-Kolmogorov behaviour). For the identification and quantification of such behaviours several graphical stochastic tools can be used such as the climacogram (i.e. plot of the variance of the averaged process vs. scale), autocovariance, variogram, power spectrum etc. with the former usually exhibiting smaller statistical uncertainty as compared to the others. However, most methodologies including these tools are based on the expected value of the process. In this analysis, we explore a methodology that combines both the practical use of a graphical representation of the internal structure of the process as well as the statistical robustness of the maximum-likelihood estimation. For validation and illustration purposes, we apply this methodology to fundamental stochastic processes, such as Markov and Hurst-Kolmogorov type ones.
Identifying signature whistles from recordings of groups of unrestrained bottlenose dolphins (Tursiops truncatus)

Bottlenose dolphins (Tursiops truncatus) have individually distinctive signature whistles. Each individual dolphin develops its own unique frequency modulation pattern and uses it to broadcast its identity. However, underwater sound localization is challenging, and researchers have had difficulties identifying signature whistles. The traditional method to identify them involved isolating individuals. In this context, the signature whistle is the most commonly produced whistle type of an animal. However, most studies on wild dolphins cannot isolate animals. We present a novel method, SIGnature IDentification (SIGID), that can identify signature whistles in recordings of groups of dolphins recorded via a single hydrophone. We found that signature whistles tend to be delivered in bouts with whistles of the same type occurring within 1–10 s of each other. Nonsignature whistles occur with longer or shorter interwhistle intervals, and this distinction can be used to identify signature whistles in a recording. We tested this method on recordings from wild and captive bottlenose dolphins and show thresholds needed to identify signature whistles reliably. SIGID will facilitate the study of signature whistle use in the wild, signature whistle diversity between different populations, and potentially allow signature whistles to be used in mark-recapture studies.
PHOTOPHYSIOLOGY IN TWO SOUTHERN OCEAN PHYTOPLANKTON TAXA: PHOTOSYNTHESIS OF PHAEOCYSTIS ANTARCTICA (PRYMNESIOPHYCEAE) AND FRAGILARIOPSIS CYLINDRUS (BACILLARIOPHYCEAE) UNDER SIMULATED MIXED‐LAYER IRRADIANCE 1

In the Ross Sea, the prymnesiophyte Phaeocystis antarctica G. Karst. dominates deeply mixed water columns, while diatoms dominate shallower mixed layers. Understanding what controls the dynamics of these two phytoplankton taxa is essential because they dominate virtually all coastal polar waters, have different nutrient utilization characteristics, and support dissimilar food webs. We cultured two strains of P. antarctica and one strain of the diatom Fragilariopsis cylindrus (Grunow) Willi Krieg under three dynamic irradiance regimes that simulated different mixed‐layer depths and measured their photosynthetic characteristics, cellular pigment concentrations, and cellular carbon and nitrogen content. In both species, chl a–normalized maximum carbon uptake rate (Pm* ) and specific growth rate were highest in the deeply mixed treatment that had a dark period. In all irradiance treatments, both (Pm* ) and photosynthetic efficiency (α*) were greater for the two P. antarctica strains than for the F. cylindrus strain. In contrast, P. antarctica strains were more susceptible to photoinhibition (β*) than the F. cylindrus strain. When photosynthetic rates of each phytoplankton taxon were normalized by cellular particulate organic carbon (POC), the difference in the maximal photosynthetic rate () was generally reduced. In the dynamic irradiance treatment that simulated the shallowest mixed‐layer irradiance, all three phytoplankton had similar ; however, the diatom had a 2‐fold higher POC‐normalized photosynthetic efficiency (αC). Finally, we performed calculations using the measured POC‐normalized photosynthetic parameters to show that αC and can play a greater role than βC in determining the competitive outcome between P. antarctica and F. cylindrus in both shallow and deep mixed‐layer environments of the Ross Sea.
Contrasting spermatozoal ultrastructure in two thoracotreme crabs, cardisoma carnifex (gecarcinidae) and varunu litterata (grapsidae) (crustacea: Brachyura)

Despite its terrestrial mode of life, Cardisoma carnifex (Gecarcinidae) returns to the sea to breed, and its spermatozoon displays all of the diagnostic features of thoracotreme sperm: absence (clearly loss) of the acrosome ray zone; presence of an apical button filling an opercular perforation; concentric lamellation of the outer acrosome zone; and the near-horizontal accessory opercular ring. In contrast, Varuna litterata (Grapsidae, subfamily Varuninae), a freshwater species, though again returning to marine (or estuarine) conditions to breed, shows only a negative state, absence of acrosome rays (other than a questionable presence of concentric lamellae) which would place it in the Thoracotremata. It does not display the grapsid synapomorphy, loss of the thickened ring. The distinctness spermatologically of Varuna from other grapsids is susceptible to a number of explanations among which are: (1) it is not a grapsid but a thoracotreme descended from a stock which had not yet developed typical thoracotreme spermatozoal ultrastructure; (2) it is a grapsid which has lost typical thoracotreme spermatozoal ultrastructure; (3) it is a heterotreme which has developed a thoracotreme configuration of genital pores independently of true thoracotremes. Of these alternatives, (3) is considered unacceptable, but the choice between (1) and (2) is difficult, although classical taxonomy would favour alternative (2). Absence of a recognizable acrosome ray zone, in Varuna sperm, presence of which is a typical heterotreme feature is also noted for the heterotremes Potamonautes, Potamon (Potamidae), and Australocarcinus (Goneplacidae), all of which are freshwater genera.
First Record of Three Known Species of the Family Tylenchidae Örley, 1880 (Nematoda: Tylenchina) from Iran with New Morphological and Molecular Data

Three species belonging to three genera of the family Tylenchidae, namely, Cephalenchus leptus , Eutylenchus excretorius, and Lelenchus leptosoma were discovered as first reports for Iran's nematode fauna. They were characterized by morphological, morphometric and molecular phylogenetic studies. The two latter genera are new for Iran. Iranian population of Cephalenchus leptus is characterized by lateral field with six lines in females, stylet length of 16-20 µm and tail length of 153-290 µm with pointed tip. The recovered population of Eutylenchus excretorius is characterized by 848-1,038 µm long females’ body, stylet length of 20.0-21.5 µm, having advulval flaps and absence of male. The Iranian population of Lelenchus leptosoma is defined by its narrow slender body, flattened lip region, sinuous amphidial opening and absence of lateral field. The phylogenetic relationships of the three recovered species were studied using the partial sequences of 28S rDNA D2/D3 segment and revealed the genera Cephalenchus and Eutylenchus forming a monophyletic clade, while, Lelenchus was placed inside the clade of currently sequenced species of Malenchus in Bayesian tree.
Characterization of olfactory receptor gene expression in the olfactory epithelium of larval Xenopus laevis

Olfactory receptors comprise the largest multigene family of G protein-coupled receptors in organisms ranging from fish to primates and are the detectors of thousands of odorant molecules. As they are crucial elements for odor recognition, much effort was put into the analysis of how olfactory receptor neurons express olfactory receptor genes and how odorant information is encoded by the receptor proteins. It is nowadays expected that each olfactory receptor neuron expresses only a single odorant receptor gene and that each receptor can be activated by multiple stimuli. According to this, a combinatorial code for odor detection was proposed to explain peripheral coding of odorant stimuli in the olfactory system. However, some mostly recent studies point towards a revision of this scheme, especially with regard to the one receptor-one neuron hypothesis. Consequently, this thesis aims to investigate this discrepancy. In order to answer whether a single or multiple olfactory receptors are expressed in single olfactory receptor neurons of Xenopus larvae, a single cell reverse transcription PCR protocol was developed. The obtained data propose, that, at least during the developmental phase of Xenopus, a subset of olfactory receptor neurons exists exhibiting oligogenic expression of olfactory receptors. In addition to this straight expression assay, ligand-sensitivities of olfactory receptors were characterized. In order to retrospectively identify receptors that recognize a particular odorant of interest, an assay was established that combined Ca2+ imaging and single cell reverse transcription PCR. Expressed transcripts of olfactory receptor genes were thereby amplified from those olfactory neurons that showed odorant responsiveness to certain amino acids. This functional strategy led to the finding of one candidate receptor that may be sensitive to these stimuli.
Constituintes das sementes de Copaifera officinalis L.

Copaifera L. is one of the most economically important plant genera in the Amazon Region, since it exudes a resin-oil named copaiba oil possessing several confirmed pharmacological properties. In spite of that, phytochemical studies of the seeds from this genus are rare. Copaifera officinalis L. was the first species in the genus Copaifera to be described. This paper describes the chemical composition of the hexane and ethyl acetate extracts of the seeds from this species. In the hexane extract, gas chromatography and mass spectrometry analyses enabled us to identify squalene, tetradecane, hexadecane, campesterol, stigmasterol and b-sitosterol; hexadecanoic, 9-octadecenoic and octadecanoic acids (major substances); as well as decanoic, eicosanoic, docosanoic and tetracosanoic (minor substances) acids. Coumarin was detected in the ethyl acetate extract, isolated and identified by NMR.
Hypoacousie due au bruit : la réglementation évolue

Les deficits auditifs dus au bruit comptent parmi les premieres maladies professionnelles dans les pays industrialises, que ce soit en nombre ou en cout de compensation financiere, car ces atteintes sont irreversibles. En France, ce sont en moyenne 6,8 % des travailleurs qui sont soumis a des bruits nocifs. Sur les 5 millions de Francais ayant des problemes auditifs, 2 millions sont âges de moins de 55 ans. Les signes de souffrance auditive ou d’alerte sont notamment des difficultes a la comprehension en milieu bruyant qui peuvent s’ajouter aux effets de la presbyacousie. Une recente directive europeenne, applicable des fevrier 2006, abaisse le niveau maximum de bruit admissible de 90 a 87 dBA (soit une intensite sonore diminuee de moitie), et introduit un niveau declenchant un plan de prevention a 80 dBA. Enfin, le tableau relatif aux surdites professionnelles a ete recemment modifie. Cette modification du calcul de l’indicateur medico-legal sera susceptible de multiplier par 4 le nombre de surdites professionnelles qui pourraient beneficier d’une compensation financiere.
Optimization of the Marker-Based Procedures for Pyramiding Genes from Multiple Donor Lines: I. Schedule of Crossing between the Donor Lines

Recent exploitation of DNA markers of desirable trait genes facilitates construction of high-degree, gene-pyramided lines via assembling markers from multiple donor lines. In such a program, a plant that has all the target markers in a heterozygous state must be produced first. Efficient procedures for that are discussed. When pyramiding the genes onto the genetic background of a particular recipient line, the backcross should be performed separately for each donor before the crossing between the donors. The plants produced through the backcross should be crossed in a schedule with structure and disposition of the plants as symmetric as possible. When four such plants (A, B, C, and D) are produced, for instance, they should be crossed in a schedule like (A x B) x (C x D) in which the number of target markers of A plus B should be as similar as possible to that of C plus D. Ideal-type schedules in the presence of four to eight donors are presented. A contrastingly different guideline applies when the donors themselves are crossed without the backcross; they should be crossed in a schedule with completely tandem structure in which donors with fewer target markers enter the schedule in earlier stages. The disposition of donors in the schedule should be modified in the presence of linked or redundant markers. Donors should be disposed in a pattern to minimize the occurrence of repulsion linkages. Formulae for the modification under a high redundancy are presented.
Formation and distribution of food reserves during autumn and their subsequent utilization in jack pine

Five Pinus banksiana (Lamb.) seedlings were fed 50 μCi of 14CO2 (1 Ci = 37 GBq) per seedling in August and at 2-week intervals another set of five trees was fed until December for a total of 10 feedings. Trees of each set were sampled from January to June, in their dormant frost hardy phase and in their growing phase. Sampled trees were separated into needles, bark, xylem, and roots, freeze-dried, and ground. Samples of ground tissues were extracted sequentially for saponifiable and nonsaponifiable lipids, starch, lignin, hemicelluloses, and cellulose. Some protein, amino acids, and sugars were also extracted.In the dormant trees the total amount of 14C in the tissues decreased from August to December except for the needles where it increased towards December. Considerable amounts of 14C occurred in the structural components of the early feedings. The 14C distribution among the chemical components within the tissues was fairly similar over the entire feeding period except for an increase in root starch, x.
The intracellular source, composition and regulatory functions of nanosized vesicles from bovine milk-serum

A hypothesis that the source of milk-serum derived vesicles (MSDVs) is the Golgi apparatus (GA) was examined. Using dynamic light scattering and electron microscopy, it was shown that MSDVs are composed of globular structures with hydrodynamic sizes of 70 ± 15 nm. More than 60% of the total protein content of MSDVs was associated with the MSDV lumen and 30% was associated with the MSDV membrane. Casein was the major protein found in the MSDV lumen. The conclusive markers of the GA, lactose synthase components (α-lactalbumin and galactosyltransferase) and activity (synthesis of lactose from glucose and UTP-galactose), the presence of casein in micellar form in the MSDV lumen, and a high luminal content of citric acid, were demonstrated in the lumen of MSDVs. Though MSDVs composed only 0.7% of the milk mass, they accounted for a high proportion of the total milk content of reactive (15% Cu and 18% Fe) and toxic minerals (60% Cd and 65% Pb), which strongly suggests that MSDVs serve as an avenue to protect mammary epithelial cells from the toxic effects of these minerals by storing them intraluminally and secreting them into milk. The presence of micellar casein in the MSDV lumen, along with the presence of metal transporters in their membranes, is responsible for this impressive capacity for storing reactive and toxic minerals. Exposing a single mammary gland to lipopolysaccharide challenge induced changes in regulatory proteins stored in the lumen of MSDVs (tissue plasminogen activators, plasminogen and plasmin) and in the activity of xanthine oxidase and alkaline phosphatase attached to the outer membrane of MSDVs. Thus, we have demonstrated that MSDVs are under the regulation of the nucleus and respond to extracellular signals.
Productivité et Stabilité Phénotypique de l'Épinette Rouge au Québec

Fifteen red spruce provenances were planted in 1959 on abandoned farmland in Quebec. Volume productivity and phenotypic stability parameters, 25 years after planting, are presented. Provenance-environment interaction is significant in red spruce. However, the importance of the phenotypic instability may have been influenced by the southern origin of some provenances and by an unequal damage caused by a yellowheaded spruce sawfly outbreak in one of the sites. Three provenances are of average stability and perform relatively well on all sites. They could be recommended for reforestation under certain conditions. However, the productivity of even these provenances is much lower than expected, probably owing to the susceptibility of the species to winter desiccation and severe frost damage when planted on exposed sites. Key words: Provenance-environment interaction, winter desiccation, bud freezing injury, provenances, combined regression analysis.