Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferring population history from genealogies

This thesis investigates a range of genealogical approaches to making quantitative inferences about the spatial and demographic history of populations with application to two insect systems: A local radiation of high alpine ground beetles (Carabidae) in the genus Trechus and major refugial populations of the oak gall parasitoid Cecidostiba fungosa (Pteromalidae). i) Summary statistics, which make explicit use of genealogical information are developed. Using simulations their power to detect a history of population growth is shown to be higher than that of standard measures such as Tajima’s D for single and multilocus data. The improvement arises from the fact that in contrast to pairwise measures, the new statistics are minimally confounded with the topology. ii) A Bayesian method to reconstructing character states is used to infer the Pleistocene history of populations of high alpine Trechus sampled along a single mountain range from mitochondrial and nuclear data. Despite evidence for some incomplete lineage sorting, a simple model of a series of extreme founder events out of two refugia during or before the last glacial maximum provides a good fit to the data. iii) A large set of exon-primed, intron-spanning (EPIC) loci is developed for Hymenoptera from EST and genomic data. Amplification success is screened on a range of Hymenopteran species associated with two insect-plant interactions: Oak galls and figs. iv) Borrowing model-based approaches developed to quantify species divergence, the new EPIC loci are used to investigate the relationships between three major European refugia in the oak gall parasitoid C. fungosa. These analyses reveal strong support for an eastern origin, effective ancestral population sizes comparable to insect model species and evidence for recent population divergence during the last interglacial. The results also suggest that there is significant information in minimal samples provided a large number of loci are available. v) Results for the probability of gene tree topologies are derived for a model of divergence with gene flow between three populations. I outline how the asymmetries in the frequency of gene tree topologies may be used to distinguish incomplete lineage sorting from migration and discuss the results in the context of next generation sequence data from D. melanogaster and humans and Neanderthals.
Reproductive ecology of the boreal riparian guild of Drosophila

The reproductive ecology of four sympatric Drosophila virths group species (Diptera Drosophilidae) was studied in the field to trace the factors maintaining species isolation There was a high probability of meeting a heterospecific individual belonging to the same species group on the basis of adult spatial occurrence Direct field observations revealed that the males court also females of the foreign species but interspecific courtships do not lead to mating The main mating period among these species lasted only several weeks and the timing of mating periods differed markedlv in the three most common species Reproductive character displacement between species may explain the observed differences in the timing of the mating periods but they could have arisen in the context of other selective pressures than the prevention of interspecific courtships and matings
The contribution of inorganic and organic nutrients to the growth of a North American isolate of the mixotrophic dinoflagellate, Dinophysis acuminata

Diarrhetic Shellfish Poisoning (DSP) is a globally significant human health syndrome most commonly caused by dinoflagellates of the genus Dinophysis. While ecosystem studies suggest that blooms of this mixotrophic dinoflagellate can be promoted by excessive nitrogen (N) loading, it is unclear whether these effects are direct (nutrient stimulation of Dinophysis) or indirect (nutrient stimulation of prey) since this alga is mixotrophic and culture studies investigating the effects of nutrients on Dinophysis have not been performed. We established an isolate of Dinophysis acuminata from New York waters and conducted controlled culture experiments to assess the effects of nutrients on the growth of this dinoflagellate with and without its prey, Mesodinium rubrum. Dinophysis was found to rapidly assimilate 15N‐labeled ammonium and urea, AND to a far lesser extent nitrate. Cultures grown with and without prey generally grew faster with ammonium, glutamine, or organic matter from sewage effluent added than respective controls, while nitrate grown cultures yielded significantly more rapid growth only when fed copious amounts of Mesodinium. Growth rates of Dinophysis also increased with the amount of Mesodinium available in cultures and achieved maximal growth rates (0.36 ± 0.01 d−1) when grown with high levels of Mesodinium and the amino acid, glutamine. Collectively, this study demonstrates that inorganic and organic N can directly promote the growth of Dinophysis and supports the hypothesis that accelerated N loading in coastal ecosystems can promote DSP producing blooms of this species and, thus, may be partly responsible for their recent expansion across the North America.
Is ornithogenic fertilization important for collembolan communities in Arctic terrestrial ecosystems?

In the Arctic, areas close to seabird colonies are often characterized by exceptionally rich vegetation communities linked with the high nutrient subsidies transported by seabirds from the marine environment to the land. These areas also support soil invertebrate communities of which springtails (Collembola) often represent the most abundant and diverse group. Our study focused on springtail community composition in the vicinity of seabird (little auk, great skua and glaucous gull) nesting areas in different parts of Svalbard (Magdalenefjorden, Isfjorden and Bjørnøya), and on their comparison with adjacent areas not impacted by seabirds. Out of a total of 35 springtail species recorded, seven were found only within the ornithogenically influenced sites. Although geographical location was the strongest factor differentiating these springtail communities, ornithogenic influence was also significant regardless of the location. When each location was considered separately, seabirds were responsible for a relatively small but strongly significant proportion (8.6, 5.2 and 3.9%, respectively, for each site) of total springtail community variability. Species whose occurrence was positively correlated with seabird presence were Folsomia coeruleogrisea, Friesea quinquespinosa, Lepidocyrtus lignorum and Oligaphorura groenlandica near Magdalenefjorden, Arrhopalites principalis, Folsomia bisetosella and Protaphorura macfadyeni in Isfjorden, and Folsomia quadrioculata on Bjørnøya.
Crumb pasting and staling properties of white and traditional Vakfıkebir breads

The crumb pasting properties of Vakfikebir bread (VB) produced by the sourdough method traditionally and standard white bread (WB) produced by the straight dough method were investigated. For both bread types, 2 different weights of loaf were produced (500 and 1500 g). One hour after removal from the oven the loaves were wrapped in 2-layer polyethylene bags and stored at room temperature (about 20 °C) for 5 days. During storage, crumb and crust aw, pH, softness, and pasting properties of bread crumb were determined for both bread types. The aims of this study were to compare the crumb pasting properties of VB and WB and to determine the causes of changes during storage. No previous study has examined the pasting properties of any sourdough bread crumb. The pH value of bread crumb exhibited a significant positive correlation with softness (r = 0.87) and bump area (r = 0.89), and a negative correlation with pasting temperature (r = -0.62) and peak viscosity (r = -0.48). In addition, the pasting properties of VB were completely different from those of WB.
Influence of liveweight, liveweight change, and diet on wool growth, staple strength, and fibre diameter in young sheep

The effects of initial liveweight, liveweight change, and composition of the diet on wool growth and staple strength in weaner sheep were investigated. Weaner wethers (64) were allocated to treatments in a factorial design (23). The factors were initial liveweight (heavy, 33 kg; light, 25 kg), liveweight change (fed at maintenance for 56 days, or 28 days at 0 ·6×maintenance then 28 days at 1·6×maintenance), and diet (lupin seed based diet or canola meal based diet). The heavier weaners grew approximately 1·9 g/day more wool than the light sheep during the experimental period and this resulted in a higher clean fleece weight (1·8 v. 1·4 kg), staple strength (37 v. 27·4 N/ktex), and fibre diameter (18·0 v. 17·4 µm). Substituting canola meal for lupin seed increased wool growth during the experiment and clean wool yield, but did not affect clean fleece weight or staple strength. The weaners fed to lose and then gain weight grew wool with a lower staple strength than the weaners fed to maintain weight through the experiment (28·6 v. 35·8 N/ktex), but there were no differences in any of the other fleece characteristics. The ratio of wool growth to dry matter intake (DMI) was higher in the sheep fed canola meal than those fed lupins (by approximately 1·5 g/kg DMI) and higher in weaners losing weight than those fed to maintain weight (by approximately 4·5 g/kg DMI). From a practical perspective, these results indicate that initial liveweight and liveweight change both influence staple strength and wool growth and need to be included in any management strategy to improve wool quality of young sheep.
SIFAT DASAR DAN POTENSI KEGUNAAN KAYU JABON MERAH

This research was carried out to examine basic properties (anatomical structure, chemical, physical and mechanical) of jabon merah wood (Anthocephalus macrophyllus (Roxb.) Havil) taken from natural forest in Luwu Timur District South Sulawesi Province. Potential uses of wood were determined by considering those properties and wood uses which the local inhabitants have currently employed. Results revealed that jabon merah heartwood is yellowish rather tend to red in colour and not clearly distinct from the sapwood, texture is rather fine and even, grain is straight and sometimes rather interlocked, wood surface is rather glossy, rather smooth to smooth in touch, and moderate in hardness. Fiber is remarkably long with very thin wall thickness. High in cellulose and extractive, moderate in lignin and low in pentose content. Moderate in specific gravity (0.48), very low in shrinkage and classified in wood strength class III. Potential uses are for light construction material under roof, cheap furniture, handicraft, measuring and drawing instruments, pencil, box and stick of matches, toothpick, spoon and handles of ice cream, moulding, wood composites, pulp and paper, pallet, packing box and concrete forms. Keywords: Anatomical, chemical, mechanical, uses of wood, jabon merah
Relação entre radiação fotossinteticamente ativa e radiação global

Medidas simultâneas de radiacao global (K) (MJ/m².dia) e de radiacao fotossinteticamente ativa (RFA) (E/m² .dia) foram obtidas, no periodo de um ano, nas condicoes climaticas de Pelotas, RS. A analise dos dados permitiu o estabelecimento de uma equacao linear para expressar a relacao entre RFA e K na forma RFA = 2,23 K. Verificou-se que a radiacao de onda curta na faixa de RFA (400-700 nm) foi cerca de 47% do espectro solar. A radiacao fotossinteticamente ativa pode ser estimada com base na medida da radiacao global (X2,23) com erro relativo medio da mesma ordem de grandeza das medidas das duas variaveis.
A new species of Prosansanosmilus: implications for the systematic relationships of the family Barbourofelidae new rank (Carnivora, Mammalia)

A new barbourofelid species, Prosansanosmilus eggeri, is described from the Middle Miocene (MN 5) locality of Sandelzhausen, Germany. It differs from all other European barbourofelid species in being smaller and showing a more plesiomorphic morphology, especially in the relatively less developed sabretooth adaptations, low accessory cusps on the premolars, and the remnant of a very small talonid on the carnassial. The species is, however, stratigraphically later than the more apomorphic P. peregrinus, which is known from MN 4 of Germany and France. A phylogenetic analysis based on dental characters of early nimravids, barbourofelids and felids supports previous results on skull morphology of Barbourofelis that Barbourofelinae is not closely related to the Late Eocene and Oligocene Nimravinae. Instead, both subfamilies should be treated as separate families, with the Barbourofelidae closely related to the Felidae. The Barbourofelidae differ from the Felidae as well as from the Nimravidae s.s. , particularly in the unique morphology of their basicranium. They presumably originated in Africa; P. eggeri sp. nov. is interpreted as part of a Miocene immigration of African faunal elements into Europe that took place at the beginning of MN 5. © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society, 2004, 140, 43−61.
Transgenic and Gene-Knockout Rodents as Research tools for Cardiovascular Disorders

Summary Cardiovascular disorders like hypertension, cerebral stroke, heart failure and thromboembolism account for a high degree of morbidity and mortality all over the World. As the regulation of the cardiovascular system is complex, the study of cardiovascular disorders has been limited to whole-organism models. The last decade has witnessed an upsurge in transgenic and gene knockout technologies, which have played a major role in the discovery of a particular gene, or its product, implicated in various cardiovascular disorders. Knockout and transgenic animals are likely to become important tools in drug development to determine the physiological sites of action for newly developed pharmacological agents. The present review will briefly discuss the methods and types of genetically engineered rodents (transgenic and gene knockout models) with alterations in second messenger systems involved in cardiovascular disorders.
Regulation of Hemoglobin β-Chain Synthesis in Bone Marrow Erythroid Cells by α Chains

Abstract Synthesis of α and β chains of hemoglobin was studied in vitro in intact reticulocytes and bone marrow cells. The cells were from rabbits having a variant form of hemoglobin in which L-isoleucine is in the α but not in the β chains. This characteristic permitted a selective inhibition of α-chain synthesis to be produced by addition to the incubation medium of L-O-methylthreonine, an inhibitor of protein synthesis that is a specific antagonist of L-isoleucine. In studies with reticulocytes, 25 mM L-O-methylthreonine produced a 60-70% inhibition of α-chain synthesis, but β-chain synthesis was unaffected even after incubation times for 4 hr. Because reticulocytes contain a pool of uncombined α chains which might have obscured the demonstration of an α chain-dependent mechanism for β-chain synthesis, subsequent studies were done with bone marrow cells. The latter had little or no detectable α-chain pool. A substantial inhibition of α-chain synthesis by the bone marrow cells was produced by the isoleucine antagonist but was also accompanied by a significantly decreased rate of β-chain synthesis. These findings suggest that the coordinated synthesis of the complementary α- and β-globin chains of hemoglobin may reflect in part a modifying effect of α-chain synthesis on the synthesis of β chains.
Functional and applied aspects of the DOWNY MILDEW RESISTANT 1 and 6 genes in Arabidopsis

Plants are constantly exposed to micro-organisms including pathogens. They are resistant to the vast majority of potential pathogens due to a multilayered defence system. Plant disease susceptibility, on the other hand, is determined by virulence factors from the pathogen, their targets in the host and the successful suppression of plant defences. To gain insight into the molecular mechanisms underlying disease susceptibility, we study the interaction between the oomycete pathogen Hyaloperonospora arabidopsidis, causing downy mildew, and its host Arabidopsis. A forward genetic screen resulted in several downy mildew resistant (dmr) Arabidopsis mutants of which dmr1 and dmr6 were further characterized. Chapter 2 described the cloning of DMR1 that encodes for homoserine kinase (HSK), a key enzyme in the Aspartate pathway. Mutation of HSK in the dmr1 mutant resulted in accumulation of the amino acid homoserine. Exogenous application of homoserine proved to be sufficient to induce resistance against H. arabidopsidis. No known defence-related pathways were associated with the observed resistance, indicating homoserine accumulation triggers a novel form of plant resistance. HSK was further analysed in chapter 3 where a reverse genetics approach (TILLING) resulted in additional hsk alleles. One mutant accumulated homoserine and is resistant to downy mildew infection. Another mutant did not develop beyond the seedling stage suggesting HSK is an essential plant gene. We also identified HSK orthologs for a number of crop species making them candidates for mutagenesis to further explore dmr1-mediated resistance. Chapter 4 described the characterization of the DMR6 gene, coding for a 2-oxoglutarate Fe(II)-dependent oxygenase. Absence of a functional DMR6 gene resulted in resistance that requires a functional salicylic acid pathway. On the other hand, overexpression of DMR6 resulted in enhanced susceptibility towards biotrophic pathogens indicating DMR6 acts as negative regulator of defence. A 3-dimensional model was constructed of the DMR6 protein that facilitated in the identification of important residues in the substrate pocket. Chapter 5 described the family of DMR6-like oxygenases (DLOs) and their role in plant defence. Two Arabidopsis DLOs, identified through phylogenetic analysis, have a similar molecular function as DMR6. Also, we have identified DMR6 orthologs in several crop species that are able to complement the dmr6-mediated resistance. A DMR6/DLO-specific motif is identified that could be used for the identification of crop DMR6 or DLO proteins. The presence of this conserved motif could determine the specificity for a particular substrate that is shared between different species.
Cetacean brains have a structure similar to the brains of primitive mammals; does this imply limits in function?

We review the evidence for the concept of the "initial" or prototype brain. We outline four possible modes of brain evolution suggested by our new findings on the evolutionary status of the dolphin brain. The four modes involve various forms of deviation from and conformity to the hypothesized initial brain type. These include examples of conservative evolution, progressive evolution, and combinations of the two in which features of one or the other become dominant. The four types of neocortical organization in extant mammals may be the result of selective pressures on sensory/motor systems resulting in divergent patterns of brain phylogenesis. A modular "modification/multiplication" hypothesis is proposed as a mechanism of neocortical evolution in eutherians. Representative models of the initial ancestral group of mammals include not only extant basal Insectivora but also Chiroptera; we have found that dolphins and large whales have also retained many features of the archetypal or initial brain. This group evolved from the initial mammalian stock and returned to the aquatic environment some 50 million years ago. This unique experiment of nature shows the effects of radical changes in environment on brain-body adaptations and specializations. Although the dolphin brain has certain quantitative characteristics of the evolutionary changes seen in the higher terrestrial mammals, it has also retained many of the conservative structural features of the initial brain. Its neocortical organization is accordingly different, largely in a quantitative sense, from that of terrestrial models of the initial brain such as the hedgehog.
High-Level Production of Functional Muscle α-Tropomyosin in Pichia pastoris☆

Abstract Although numerous studies have reported the production of skeletal muscle α-tropomyosin in E. coli, the protein needs to be modified at the amino terminus in order to be active. Without these modifications the protein does not bind to actin, does not exhibit head-to-tail polymerization, and does not inhibit the actomyosin Mg2+-ATPase in the absence of troponin. On the other hand, the protein produced in insect cells using baculovirus as an expression vector (Urbancikova, M., and Hitchcock-DeGregori, S. E., J. Biol. Chem., 269, 24310–24315, 1994) is only partially acetylated at its amino terminal and therefore is not totally functional. In an attempt to produce an unmodified functional recombinant muscle α-tropomyosin for structure–function correlation studies we have expressed the chicken skeletal α-tropomyosin cDNA in the yeast Pichia pastoris. Recombinant protein was produced at a high level (20 mg/L) and was similar to the wild type muscle protein in its ability to polymerize, to bind to actin and to regulate the actomyosin S1 Mg2+-ATPase.
Low microsatellite variation in Aphanius fasciatus from the Tarquinia Salterns

1 - The Tarquinia Salterns (Latium, central Italy) provided the opportunity to analyse the impact of environmental stress on the genetic structure of the resident population of the killifish Aphanius fasciatus. Indeed, after the salt production ceased in 1997, the salterns have undergone habitat degradation due to lack of maintenance. The ecological restoration carried out from 2003 to 2006 reverted the environmental conditions to those of ten years before. 2 - The temporal variation of the gene pool of the population of A. fasciatus inhabiting the Tarquinia Salterns was investigated using microsatellite markers in samples collected in 1998 and 2003. The results obtained showed a low genetic variability and a genetic homogeneity of the population, which appears not divided in sub-demes. 3 - Microsatellites revealed a surprisingly low level of genetic variability when compared to allozyme data obtained in previous studies. This is likely due to a difference in the time of response of the two markers to environmental degradation. Microsatellites would lose genetic variability earlier and faster because of their usually high polymorphisms. Conversely, allozymes would be more resistant to genetic erosion, being moderately variable markers. 4 - Selection probably contributed in maintaining allozyme polymorphism, while microsatellites, being neutral markers, did not benefit from the action of selection and lost diversity earlier and more rapidly. Accordingly, the population appeared subdivided in distinct demes based on allozyme data but spatially homogeneous following microsatellites results.