Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular regulation of thymic epithelial lineage specification

iii Table of contents. iv Abbreviations . xiii 1 Introduction. 1 1.1 Introduction to the thymus . 1 1.2 Function of the thymus . 1 1.3 Structure and morphology of the thymus. 3 1.3. 1 Thymic epithelial progenitor cells (TEPC). 3 1.3. 2 Thymic epithelial lineage cells . 4 1.3. 3 NC-derived thymic mesenchyme. 7 1.3. 4 Thymic vascularisation . 7 1.4 Intrathymic T-cell development. 8 1.5 Cellular regulation of early thymus organogenesis. 11 1.6 Molecular regulation of early thymus organogenesis . 14 1.6. 1 Formation of the third pharyngeal pouch (3PP). 14 1.6. 1.1 T-­‐box 1 (Tbx1) . 19 1.6. 1.2 Retinoic acid (RA). 20 1.6. 1.3 Fibroblast growth factor 8 (Fgf8). 20 1.6. 2 Regulation of third pharyngeal pouch (3PP) development. 21 1.6. 2.1 Homeobox protein A3 (Hoxa3) . 21 1.6. 2.2 Eyes Absent 1 (Eya1) and Sine oculis homeobox 1 (Six1) . 22 1.6. 3 Patterning of the third pharyngeal pouch (3PP) into thymus and parathyroid specific domains . 23
Relationship of incisor size to diet and anterior tooth use in sympatric sumatran anthropoids

Researchers often relate anthropoid incisor size to diet and ingestive behaviors. It is suggested that primates that frequently consume large, tough foods (i.e., fruits) require large incisors to process these items. This idea has been difficult to test because of a lack of data on anterior tooth use in wild primates, and a lack of understanding concerning the relationships between food properties and ingestive behaviors. The first field study of primate ingestive behaviors has recently been completed for four species of Sumatran anthropoids: Hylobates lar, Macaca fascicularis, Pongo pygmaeus, and Presbytis thomasi [Ungar, American Journal of Physical Anthropology 95:197–219, 1994; International Journal of Primatology 16:221–245, 1995]. This paper documents both relative and absolute incisor row width differences among these taxa, and evaluates the relationships between incisor size and feeding behaviors for specific taxa. Results indicate that differences in incisor size among these species cannot all be explained by degree of frugivory, food item size, or even degree of incisor use in ingestion alone. It is therefore suggested that inferences of dietary differences based on largely or solely on differences in incisor sizes of specific fossil anthropoid taxa should be approached with caution. © 1996 Wiley‐Liss, Inc.
Activity and Species Composition of Arbuscular Mycorrhizal Fungi Following Soil Removal

Large areas of the Everglades National Park have been invaded by exotic plant species, particularly Schinus terebinthifolius. In an attempt to return these areas to the former wetland vegetation, an experimental site was subjected to soil removal (SR). The objective of this study was to document the effect of SR on the activity-estimated by total propagule and spore numbers, and root colonization-and species composition of arbuscular mycorrhizal (AM) fungi. Soil and plant samples were collected in the spring (following the dry season) and fall (following the wet season) for 2 yr from full- and partial- SR plots, an adjacent site dominated by schinus, and the mature undisturbed glade. The mature glade had the lowest mycorrhizal activity, while the SR plots had the highest activity. Mycorrhizal activity in SR plots increased over the 2-yr period. These plots also had greater plant species richness than the mature glade. No relationship was found between root colonization and plant hydrological category. A total of 22 fungal species, belonging to four genera, were present as the most abundant AM species in individual plots. Temporal changes observed in these species were likely related to changes in host plants and the edaphic environment. We suggest that the complexity of both AM and vegetation succession on these plots will decrease with time after species richness of AM and plants peak and the site conditions stabilize.
Characterization and functional ecology of the extrafloral nectar of Cedrela odorata in contrasting growth environments in central Veracruz, Mexico

Extrafloral nectar (EFN) is a plant secretion known to mediate interactions between insects and plants. Here we present the ecological characterization of the EFN of Cedrela odorata, in terms of sugar composition, as well as its importance in attracting ant visitors to extrafloral nectaries. We also studied the influence of different plant water conditions on the quality of EFN. We found site (forest, agroecosystem, plantation) and season (i.e., rainy, dry) effects for both water balance and the quality of EFN. Our results show that (i) water has a significant influence on EFN quality and (ii) environmental disturbance that differed at each site was associated with differences in loss of water through transpiration. Season also affected the levels of dissolved sugars in EFN. This had a direct, site-dependent impact on the abundance of ants foraging on EFN. Only at the most disturbed site (where higher damage by shoot borer occurred) was the abundance of ants foraging on EFN higher during the rainy season,.
Negative effects of tropospheric ozone on the feed value of rice straw are mitigated by an ozone tolerance QTL

High surface ozone concentrations are recognized as an emerging threat to food security in Asia. This study aimed at determining the effects of ozone on the nutritive quality of rice straw, a by‐product of rice grain production and a major feed resource for ruminant livestock. Further, the question was addressed whether negative effects of ozone can be mitigated through molecular breeding. Rice plants from three different genotypes were exposed to four different ozone treatments in fumigation chambers from transplanting to maturity. These genotypes were (i) IR64, one of the most wide spread indica varieties in the world, (ii) Nipponbare, a typical japonica variety, and (iii) SL41, an ozone tolerant breeding line that carried chromosomal inserts at the ozone tolerance QTL OzT9 in the genetic background of Nipponbare. The treatments consisted of (i) charcoal filtered air, (ii) simulated ambient ozone concentration, (iii) 2 × ambient ozone concentration, and (iv) 2.5 × ambient ozone concentration. The effects of ozone on the chemical composition of straw were clearly dependent of the ozone level, and were significant even at ambient ozone concentration. Increases in crude ash, lignin and phenolics concentration adversely affected the digestibility as demonstrated in incubation experiments simulating rumen digestion in vitro. Negative ozone effects included reductions in the rate and extent of gas production due to inhibition of microbial fermentation, reduced formation of short chain fatty acids (SCFA), and a decrease in the true organic matter digestibility. The ozone tolerant genotype SL41 was less responsive to ozone than its more susceptible recurrent parent Nipponbare in terms of lignin and phenolics formation, organic matter digestibility and SCFA production. These data demonstrate that the feed quality of rice straw is affected by ozone even at ambient concentration, and that these negative effects are mitigated by the ozone tolerance QTL OzT9.
Feather mites on group-living Red-billed Choughs : a non-parasitic interaction ?

Most reports of interactions between feather mites and their avian hosts have assumed that mites have detrimental effects on their hosts, i.e. that they behave as parasites. We investigate the effects of feather mites Gabucinia delibata on the body condition of Red-billed Choughs Pyrrhocorax pyrrhocorax, a highly social, mediumsized corvid species. Feather mites were absent in fledglings at the nest and were probably acquired by Choughs from 1 to 5 months after fledging, when they joined communal roosts. The abundance of feather mites on both wing and tail increased with age and development of social habits in non-breeding Choughs, but decreased when they reached breeding status. Mated Choughs had similar abundances of feather mites. The abundance of mites correlated positively with body condition (computed as the residuals of mass on a "size factor") in both males and females, and body condition was in general better for Choughs holding mites than for those lacking mites. The conclusion that feather mites do not have detrimental effects on Choughs was reinforced by the fact that feather mite abundance did not differ between Choughs with normal and crossed bills, respectively, suggesting that preening does not remove mites from the feathers. This particular association thus could be labelled as non-parasitic, suggesting at least a commensal, and possibly a mutualistic relationship. In the latter case, the hypothesised benefits accrued to Chough hosts from their association with mites may derive from an improved feather cleaning, and from the supposed protection against pathogenic organisms achieved primarily by preemption of resources by more benign species, such as feather mites.
Effect of UV Irradiance on Utilization of Inorganic Nitrogen by the Antarctic Diatom Odontella weissflogii (Janisch) Grunow

: The impact of UV-B irradiation on unialgal cultures of the temperate marine diatom Odontella sinensis and of the Antarctic Odontella weissflogii was tested under controlled laboratory conditions. Uptake rates of inorganic nitrogen by Odontella sinensis were more affected by UV-B radiation than those of Odontella weissflogii. Utilization of 15N-ammonium was reduced after 3 h of UV-B exposure. Values of Km from several marine phytoplankton species were estimated from algae not exposed to UV-B and from those after 3 h of UV-B radiation. Calculation of Lineweaver-Burk plot showed, under UV-B stress, a noncompetitive inhibition for 15NH+4 uptake and a competitive inhibitory effect for 15NO−3 by Odontella weissflogii. The damage to 15NH+4 uptake by UV-B was more pronounced under red than blue light; a contradictory result was obtained for 15NO−3 utilization by Odontella weissflogii. Reduction of the pigments by UV-B under white light was dependent on the exposure time; a strong depression of the contents of chlorophyllide a, chlorophyll c, diatoxanthin and the fucoxanthins was found. Contents of the chlorophylls are markedly affected by UV-B under red light whereas the chlorophyll a concentration is enhanced in blue and green light. UV-B exposure in conjunction with blue and green light led to a reduction of the protein content and an increase in the amino acid contents. The pattern of pool sizes of free amino acids varied after UV-B exposure. UV-A irradiance had no effect. The possible targets of UV-B irradiation on the uptake system of inorganic nitrogen are discussed in detail. Adaptation to the environmental conditions, e.g. via synthesis of UV stress proteins or mycosporine-like amino acids, were also considered.
Performance of Muscovy Ducks under Three Management Systems in South Eastern Nigeria

A study was conducted to evaluate the performance of Nigerian native muscovy ducks in terms of growth and feed utilization in a Randomized Complete Block Design (RCBD) under semi intensive system (SI), Intensive system with wallow (IW), and intensive system without wallow (IO). Eighteen males and equal number of female ducklings were allotted to two replicates each of the three treatments and fed from week 5 to week 20 with diet containing 17% CP and 2848.9 kcal/kg energy. Weekly weights were measured and compared using two-way analysis of variance. Final body weights were SI (males: 2507.07g, females: 1733.83g), IW (males: 2466.67g, females: 1641.17g) and IO (males: 2464.84g, females: 1657.67g). Average daily gains of drakes were 16.07g (SI), 16.39g (IW) 15.87g (IO); while those of females were 10.18g, 11.03g and 9.91g respectively. Average daily gain of drakes was significantly higher (P 0.05) on performance of muscovy ducks in the region.
Development of In Vitro Systems for Switchgrass (Panicum virgatum) - Final Report for 1992 to 2002

Our project began on July 1, 1992, with the objective of developing systems that could be used in biotechnological approaches to switchgrass improvement. Within six months after initiation of the project, we had worked out protocols in which plants could be regenerated from callus cultures through both organogenesis and somatic embryogenesis. Documentation for both modes of regeneration was provided in our progress reports and in publications. One thousand regenerated plants were established in the field during the first year. We found that Alamo (lowland type) was much more amenable to in vitro culture, and plants could be regenerated much more easily than from Cave-in-Rock (upland type). During the first three years of the project, we studied the influence of genotype, culture medium components, explant type, etc., on regeneration. As mentioned, we found that the lowland cultivars Alamo and Kanlow were much easier to regenerate than upland cultivars, such as Trailblazer, Blackwell, and Cave-in-Rock. For callus induction, we initially used mature caryopses, young leaf tissue, and portions of seedlings. We were successful in inducing callus and regenerating plants from all explants. Two other systems developed during the 4th to 6th year period of the project included multiple shoot formation initiated from germinated seedlings and regenerable suspension cultures. The latter were initiated from embryogenic calluses produced from in vitro developed inflorescences. An important factor for producing multiple shoots was the presence of thidiazuron in the medium. The shoots could be easily rooted and numerous plantlets produced. The last 3 to 4 years of the project focused on anther and microspore culture experiments to produce haploid plants and on genetic transformation. Although thousands of putative haploid plants were produced from a few anthers, they were very weak and difficult to keep alive. Chromosome counts revealed the gametic number in cells where it was possible to count chromosomes. The isolated microspore culture experiments were not successful.
Systematics and geographic variation of Ethiopian Arvicanthis (Rodentia, Muridae)

Arvicanthis, the unstriped grass-rat, is a widespread genus occurring in many regions of Africa and is major pest in agricultural farmland. Despite its economic importance for developing countries, the taxonomy of the genus is stillin a chaotic state. We used univariate and multivariate morphometrics to investigate two species, A. abyssinicus and A. dembeensis, occurring in Ethiopia. Results show that these taxa are well separated, this contradicting authors who lump all Arvicanthis as A. niloticus. There is a longitudinal cline in the morphology of A. dembeensis from eastern regions along the Rift Valley. Differences between the species in morphlogy seem to reflect adaptation to different ecological niches at high (A. abyssinicus) and low (A. dembeensis) altitudes.
Radiographic anatomy aspects and gastrointestinal transit time in Podocnemis unifilis troschel, 1848 (Testudines, Podocnemididae).

The present study analyzed the radiographic anatomy and determined the gastrointestinal transit time of Podocnemis unifilis . We used ten animals belonging to LAPAS from the Federal University of Uberlândia, Uberlândia, Minas Gerais State, Brazil. The animals were orally fed with a barium sulphate suspension at 10 mL kg -1 mixed with mineral oil, at a ratio of 70% of barium sulphate for 30% of mineral oil. Afterwards, the animals underwent radiography in a dorsum ventriloquoal position, with the X-ray device adjusted at 72 Kv and 200 mA, in time intervals to follow the permanency of contrast in the organism. Five minutes after the contrast was supplied, the stomach was filled. After sixteen hours the contrast advanced to the small intestine. In 48 hours, the whole small intestine and part of the colon were fulfilled. On the 9 th day the stomach was empty and the contrast advanced to the colon. On the 11 th day, the colon was totally fulfilled, and the contrast was close to cloaca. On the 18 th day all contrast was eliminated by the animal. Total time for contrast elimination was, in average, 17.6 ± 2.4 days, with the minimum of 12 and maximum of 22 days, with temperature at 27°C. The digestion of the food was slower in the duodenum, and faster in the colon-rectum, which presents lower indices of repletion.
Is there a better chela to use for geometric morphometric differentiation in brachyuran crabs? A case study using Pachygrapsus marmoratus and Carcinus maenas

Landmark-based geometric morphometric methods were used to test which chela is most suitable to use in population differentiation of brachyuran crabs. Two species were analysed: Pachygrapsus marmoratus, a homochelous species, and Carcinus maenas, a heterochelous species. Variance analysis of shape variables and of each chela was calculated to determine which claw presents less variation within populations. The results showed that the right chela of P. marmoratus is more appropriate to use when the goal is to differentiate populations. In C. maenas, the males major chela and females right chela are more suitable to use, probably due to its heterochely. To test these results, specimens from different geographical locations were compared. Pachygrapsus marmoratus populations presented significant differences in manus shape, and C. maenas populations had differences in polex size and shape. Differences in carapace shape were also encountered between populations of both species. This phenotypic variation was not corroborated with genetic data, which were obtained using the mitochondrial DNA gene cytochrome oxidase I as a marker. These opposite results suggest that environmental factors, such as diet and parasitism, can be determining shape differentiation.
A field survey to investigate why nightjars frequent roads at night

Nightjars throughout the Afrotropical Region regularly frequent roads at night and during the twilight of dusk and dawn. Most species exhibit this behaviour and numerous individuals are killed by road traffic. Many theories have been advanced to explain the presence of nightjars on roads at night, but very little fieldwork has been carried out to test them. For a period of a year we carried out a weekly survey of nightjars on a selected road network near Harare in Zimbabwe. All nightjar encounters were documented in relation to variations in road surface, road width, adjacent habitat, arc of sky visible and other variables, such as the time of night, moon phase and weather conditions. None of these factors provided a complete explanation for the presence of nightjars on the roads surveyed. Neither were any of the nightjars seen dust bathing, taking grit or picking up insects from the road. Many were seen actively hunting flying insects, especially at dusk, and palpation of the stomachs of those caught confirmed that they had fed well during the evening hours. They were clearly using the road as an observation platform for hunting during the first few hours after sunset and then as a convenient place for resting and digesting. A nightjar sitting on an open road is certainly in a good position to see flying insects silhouetted against the twilight sky.
Effect of Dominant Shade Trees on Coffee Production in Manasibu District, West Oromia, Ethiopia

Effect of shade trees species on coffee production in Manasibu district, West Ethiopia was assessed by the current study. It was aimed to (i) identify the most suitable dominant shade tree species for coffee production; (ii) assess the status of coffee production under different dominant coffee shade trees and unshaded areas and (iii) evaluate the relationship of top soil properties with coffee production in coffee based Agroforestry system. In this study, randomized complete block design with three replications was used for data collection. 48 circular samples were taken from areas around four dominant coffee shade tree species at 3, 5 and 7 m from tree trunk and unshaded zone. There was no observed significant difference in coffee production between shaded and unshaded zone of coffee farms. However, among the species, coffee bean yield (3.1Mg ha -1 ) was observed significantly higher under Croton macrostachyus than the others. There were significant positive correlations between coffee weight and soil acidity (r=0.44135), between coffee weight and electric conductivity (r=0.34302), between coffee weight and soil moisture content (r=0.44738). The influence of top soil plant nutrients on coffee production is not linear. Available Potassium was not supposed to influence coffee yield since highest reading was observed with lowest yield. It can be possible to conclude that coffee based Agroforestry system is the better production system when there is no intensive agronomic managements. Soil acidity status and moisture content have significant effect on coffee production than top soil macro nutrients. If choosing is needed, it appears to be a better option selecting C. macrostachyus than another dominant shade tree species for higher coffee production in shade coffee production system due to its coffee favorable environmental conditions (having normal soil pH and good soil moisture content). Keywords : Shade trees Croton macrostachyus Soil property Coffee yield Shaded system Manasibu District
Developing monitoring protocols for cost-effective surveillance of lichens

Abstract The criteria set out by the International Union for Conservation of Nature to identify threatened species requires information on population trends which, for priority lichen species within Scotland, is lacking. Collecting such data is problematic as there is a lack of empirical information on the performance of different sampling designs and survey methodologies. Using Pseudocyphellaria norvegica as an example species, we tested differences in the efficiency of 3 transect patterns and a 20 minute search for surveying 100×100 m cells of potentially suitable habitat. The methods were not intended to census the total population of the cells but, rather, to provide a standardized, repeatable estimate of the population density to allow detection of trends through time. We also tested the repeatability of the methods between surveyors. The results provided no evidence to suggest that controlled survey methodologies using fixed transect patterns were any better in terms of consistency between surveyors or numbers of occupied trees found than 20 minute searches of the areas within each 100×100 m cell deemed suitable for the target species by an experienced surveyor. Given that following the fixed transect patterns took approximately twice as long as a 20 minute search, the search method would clearly be more cost-effective when there are large numbers of cells to survey. For all survey methods variability between surveyors was high, meaning that it would be extremely difficult to detect temporal changes in populations, and hence identify population trends. We also examined the extent to which recording presence/absence at the 1 ha scale might improve consistency between surveyors and found that it reduced, but did not eliminate, the surveyor variability. Recording only presence/absence would allow greater numbers of cells to be surveyed using the same level of resources, but would reduce the amount of information available per cell for use in analysis of population trends. We conclude that controlling inter-surveyor variability while collecting adequate data for population trend analysis is a major issue when planning and implementing any large-scale survey of lichen species.