Miracle-dz/UniFAR-FTUs huggingface dataset:
Retinal degeneration and remodelling in experimental glaucoma

Glaucoma is an optic neuropathy characterised by the loss of retinal ganglion cells (RGC). Dendritic atrophy occurs early in the disease, prior to soma and axonal degeneration. RGCs exhibit reduced branching density and dendritic field size. This thesis seeks to further characterise dendritic atrophy in glaucoma in the context of two external factors that may contribute to the disease pathology – immune system effects mediated via complement and the influence of the perineuronal net (PNN), a specialised extracellular matrix that surrounds RGCs. RGC morphology was investigated in a rat bead model of experimental glaucoma using ballistic labelling techniques; morphological changes were related to synaptic loss and PNN composition using immunohistochemistry. A model was derived for the classification of diseased RGCs in order to prevent labelling bias in subsequent investigations. The immune system was modulated using a complement inhibitor (using a transgenic mouse and pharmacological agent in rats) and PNNs disrupted using the bacterial enzyme Chondroitinase ABC. Experimental glaucoma caused significant dendritic loss, with partial protection conferred by both complement inhibition and PNN digestion. Analysis of retinal sections also revealed partial protection of synapses. PNNs did not show any changes in their composition in the rat in experimental glaucoma but human glaucoma eyes showed increased glycosaminoglycan sulphation in the RGC layer which was correlated with visual deficit. Manipulation of the RGC external environment therefore proved successful in protecting from dendritic atrophy.
Phytochemical Regulation of Tumor Suppressive MicroRNA in Human Breast Cancer Cells

Author(s): Hargraves, Kristina G.H. | Advisor(s): Firestone, Gary L. | Abstract: MicroRNA post-transcriptionally regulate more than half of the transcribed human genome and could be potential targets of anti-cancer therapeutics. The microRNA family, miR-34, is a component of the p53 tumor suppressor pathway and has been shown to mediate induction of cell cycle arrest, senescence, and apoptosis in cancer cells. Indole-3-carbinol (I3C) derived from cruciferous vegetables, artemisinin isolated from the sweet wormwood plant and artesunate derived from the carbonyl reduction of artemisinin effect components of the p53 pathway to growth arrest human cancer cells, implicating a potential role for miR-34 in their anti-proliferative effects. Flow cytometry and Taqman semi-quantitative PCR analysis of I3C, artemisinin and artesunate treated human breast cancer cells indicate all three phytochemicals upregulate miR-34a in a dose and time-dependant manner that correlates with a pronounced G1 cell cycle arrest. Western blot analysis revealed miR-34a upregulation correlates with induction of functional p53 by I3C as well as artesunate and artemisinin mediated decreases in estrogen-receptor alpha and the cyclin-dependant kinase CDK4, a known target of miR-34a inhibition. Luciferase assays in which cells were transfected with the miR-34a binding site of CDK4 mRNA attached to the firefly luciferase reporter gene confirmed miR-34a directly inhibits CDK4 expression in cells growth arrested by artemisinin or artesunate. Functional miR-34a appears critical for the anti-proliferative effects of I3C and artemisinin as transfection of non-translatable miR-34a inhibitors prevented I3C mediated growth inhibition and reversed artemisinin mediated down-regulation of CDK4. Artemisinin mediated down-regulation of ERα was also reversed in cells transfected with miR-34a inhibitors, implicating a novel role for miR-34a in the regulation of hormonal signaling. Transfection of dominant negative p53 prevented I3C upregulation of miR-34a in growth arrested cells containing wild-type p53 yet had no effect on artemisinin regulation of miR-34a, indicating a p53-indepedent mechanism of miR-34a regulation. Artemisinin and artesunate also upregulate miR-34a expression levels in breast cancer cell lines containing non-functional p53. All of these data suggest that miR-34a plays a critical role in the anti-proliferative effects of artemisinin, artesunate and indole-3-carbinol in human breast cancer cells. Such evidence elucidates the therapeutic potential of each phytochemical to ectopically express tumor suppressive microRNA while implicating the use of miR-34a expression levels to determine the efficacy of phytochemical treatment. Artemisinin, artesunate and I3C could represent an efficacious means of increasing tumor suppressive microRNA in vivo.
Reptiles as principal prey? Adaptations for durophagy and prey selection by jaguar (Panthera onca)

ABSTRACT We examined the evidence supporting the hypothesis that jaguars (Panthera onca) have morphological and behavioural adaptations to facilitate reptile predation. Jaguars’ head and bite features show adaptations to durophagy (consumption of hard-integumented prey) that are very unusual within the genus Panthera. These include: thick canines, well-developed head muscles and a fatal bite directed to braincase or nape. These characteristics have been previously considered an adaptation for the consumption of reptilian prey, whose thick integument poses a challenge to predation. Although causation of any trait as result of natural selection is hard to demonstrate with ecological evidence, its consequences can be suggested and predictions made. Here, through a review of the literature on jaguar predatory habits, we tallied the evidence for saurophagy against environmental characteristics correlated with jaguar predation on reptiles. We offer a new explanation for the presence of those traits, based on the selection patterns, prey abundances and main predation habits over the geographic range of the jaguar. We believe that these features allow jaguars to overcome dangerous and/or armoured prey by dispatching them rapidly through a bite to the head or nape. Reptile consumption is restricted to areas of high reptile abundance while dangerous or armoured prey is consistently preyed upon throughout the jaguar’s distribution, and selected even when their abundance is low. This questions the validity of the saurophagy hypothesis. We believe that these results are relevant to jaguar conservation and management, because some of the main prey species are severely threatened over their range, and because threatened reptiles are also consumed as prey.
Factors that affect parasitism of black‐tailed prairie dogs by fleas

Fleas (Insecta: Siphonaptera) are hematophagous ectoparasites that feed on vertebrate hosts. Fleas can reduce the fitness of hosts by interfering with immune responses, disrupting adaptive behaviors, and transmitting pathogens. The negative effects of fleas on hosts are usually most pronounced when fleas attain high densities. In lab studies, fleas desiccate and die under dry conditions, suggesting that populations of fleas will tend to decline when precipitation is scarce under natural conditions. To test this hypothesis, we compared precipitation vs. parasitism of blacktailed prairie dogs (Cynomys ludovicianus) by fleas at a single colony during May and June of 13 consecutive years (1976–1988) at Wind Cave National Park, South Dakota, USA. The number of fleas on prairie dogs decreased with increasing precipitation during both the prior growing season (April through August of the prior year) and the justcompleted winter–spring (January through April of current year). Due to the reduction in available moisture and palatable forage in dry years, herbivorous prairie dogs might have been foodlimited, with weakened behavioral and immunological defenses against fleas. In support of this hypothesis, adult prairie dogs of low mass harbored more fleas than heavier adults. Our results have implications for the spread of plague, an introduced bacterial disease, transmitted by fleas, that devastates prairie dog colonies and, in doing so, can transform grassland ecosystems.
A Temperature Effect on the Expression of Genotypic Differences in Flowering Induction in Antirrhinum majus

Three inbred lines of Antirrhinum majus and the Fi generations of crosses between them were scored for flowering time in nine greenhouse and garden experiments. The inbreds fell into two groups, the difference between which showed a marked interaction with environments. The two lines (An 105, An 106) which were similar were earlier flowering than the third line (An 101) in those environments which produced generally early flowering, but were later than An 101 when the environmental conditions led to late flowering. In all cases the Ft generations were at least as early as the earlier parent. Cabinet experiments identified temperature as the important environmental factor when day length was kept constant at 16 h. At 25 °C, An 105 and An 106 were earlier than An 101 while at 12 °C, at which temperature the average flowering time was much later, An 101 was earlier. The Fi generations were like An 105 and An 106 at 25 °C but showed heterosis at 12 °C. The differences in flowering time between genotypes were in all cases established by the time the first reproductive buds became visible (budding time). Thus a temperature difference well outside the range of vernalizing temperatures is having a striking effect on the phenotypic expression of genotypic differences determining the transition from vegetative to flowering development.
Fire History and Western Juniper Encroachment in Sagebrush Steppe

The recent expansion of juniper into sagebrush steppe communities throughout the semiarid Intermountain West is most frequently attributed to the reduced role of fire, introduction and overstocking of domestic livestock in the late 1800s, and mild and wet climate conditions around the turn of the century. This hypothesis has, however, limited quantitative support. There are few studies of fire history in the sagebrush steppe and none that examine the chronosequence of changes in mean fire intervals, introduction of livestock, and coincident climatic conditions with the initiation of post-settlement juniper expansion. This study was undertaken to test the hypothesis that the postsettlement expansion of juniper was synchronous with the introduction of domestic livestock, reduction in fire frequency, and optimal climate conditions for plant growth. We documented the fire history and western juniper (Juniperus occidentalis Hook). woodland chronology for a sagebrush steppe in a 5,000 ha watershed in south central Oregon. Regional tree ring data were used as proxy data for presettlement climatic conditions. Western juniper age distribution was determined by coring trees across the study area. Fire history was constructed from several small clusters of presettlement ponderosa pine (Pinus ponderosa Laws.) scattered across the study area. Samples were crossdated to determine fire occurrence to the calendar year. Mean fire intervals were computed for each cluster based on cumulative fire history of each tree sampled within the cluster. Fire events in low sagebrush (Artemisia arbuscula Nutt.) were documented by determining death dates of fire-killed western juniper trees. Records dating the introduction and buildup of livestock during the late 1800s and dates of initial fire suppression were summarized. Western juniper expansion began between 1875 and 1885, with peak expansion rates occurring between 1905 and 1925. The fire record spans 1601 to 1996. Before 1897, mean fire intervals within individual clusters ranged from 12 to 15 years with years between fires varying between 3 to 28. Nearly one third of the fires in the basin were large and usually proceeded by one year of above-average tree ring growth. Two fire events were recorded in the sparsely vegetated low sagebrush site, 1717 and 1855. The last large fire occurred in the study area in 1870 and the last small fire in 1897. The time sequence of wet climatic conditions between 1870 and 1915, introduction of livestock, and the reduced role of fire support the hypothesis that these factors contributed to the postsettlement expansions of western juniper.
Genome research activities in the EC

Etant donne leur cout, leur complexite et leur valeur universelle, les projets sur le genome se pretent particulierement bien a la collaboration internationale. La Commission des Communautes europeennes s'en preoccupe depuis pres de cinq ans deja. Plusieurs projets europeens ont vu le jour. Le sequencage du chromosome 3 de la levure, dans le cadre du programme BAP, livre deja des resultats surprenants
Design of an efficient fermentation process for the production of Metarhizium acridum blastospores

ABSTRACT Using a sequential approach, we described efficient blastospore production in a stirred tank bioreactor (3 L capacity). We used the response surface methodology to optimise the media ingredients and fermentation parameters to obtain the maximum production of blastospores by a locally collected isolate of Metarhizium acridum (Ascomycota: Hypocreales). The results showed that a liquid culture medium supplemented with monopotassium phosphate (15.17 g/L), corn steep liquor (69.25 g/L), and casamino acids (80.68 g/L) in a stirred tank bioreactor under operating conditions constant at 635 rpm, a temperature of 26°C, and pH 3.3 produced 1.25 × 108 blastospores (bls)/ml, with 93% viability after 120 h of fermentation. This bioreactor yield compares favourably with the yields obtained by shake flask production and confirms the suitability of the media and production parameters for the potential scale-up fermentation production of M. acridum.
Proline accumulation in response to high temperature in winter-acclimated shoots of Prunus persica: a response associated with growth resumption or heat stress?

Abstract: Our previous study revealed that proline (Pro) accumulated in peach trees when cold-acclimated shoots were exposed to higher temperatures. In this study, we determined whether such Pro accumulation is indeed a high temperature-stress response or metabolic preparation for growth resumption. Two studies were conducted to address this question using ‘Daewol’ peach trees. In study 1 (February), Pro content of eco-dormant shoots increased when cold-acclimated plants were exposed to two heat treatments (HTs) but remained unchanged during the intervening cold treatment (CT). Concurrently, ornithine-delta-aminotransferase (OAT) and Δ1-pyrroline-5-carboxylate reductase (P5CR) genes were up- and down-regulated after two HTs and the CT, respectively. Study 2, conducted with growing trees (May), showed that Pro did not change and expression of P5CR and OAT was down-regulated when trees were subjected to either HT or CT; HT and CT used here constituted ‘stress’ treatments as revealed by the decline in chlorophyll fluorescence. Taken together, these results suggest that Pro accumulation (study 1) may be associated with the preparation for growth resumption and not ‘stress’. Furthermore, results from parallel gene expression studies suggest that the ornithine, rather than glutamate, pathway may be the primary Pro biosynthesis route both during growth resumption and high temperature stress in ‘Daewol’ peach.
Cuticular microstructures of abdominal tergites and sternites of Cloeon sp. (Ephemeroptera; Baetidae) during post-embryonic development

The postembryonic changes of the external microstructure of the cuticle on the abdominal tergites and sternites of Cloeon sp. (Ephemeroptera:Baetidae) are described. An inventory of the structures as the aquatic nymph grows and becomes transformed into a terrestrial subimago and then an imago, is provided. It is found that sensillar diversity on nymphal tergites increases with development, but remains unchanged on the stemites. While nymphs and subimago possess various types of sensilla trichoidea, sensilla basiconica are apparent on the imaginal abdomen only. Furthermore, the scaled and spiny cuticle of the nymph becomes relatively smooth in the adult stages. The distinct changes which structure and distribution of the scales as well as marginal spines on the abdominal tergites and stemites of the nymphs undergo during development, must find a reflection in behavioural changes of the larvae. Finally, the taxonomic implications of the observed changes are discussed.
Establishing a benchmarking for fish farming – Profitability, productivity and energy efficiency of German, Danish and Turkish rainbow trout grow-out systems

The promotion of Blue Growth in aquaculture requires an understanding of the economic drivers influencing the sector at farm level, but the collection of reliable and comparable data at this level is time-consuming and expensive. This study suggests an alternative strategy for qualitative sampling of freshwater trout farms in Germany, Denmark and Turkey, using a combination of existing data, group discussions and interviews with trout farmers, consultants and researchers. Nine ‘typical’ trout farming models are described, focusing on profitability, productivity and energy efficiency and allowing in-depth comparative economic analyses of different production systems at farm level, across regions. Our results show that the majority of the farms investigated have been profitable. Turkish farms benefit from competitive advantages due to low wages, low capital investment and favourable climate conditions. Large German farms profit from local market prices and advanced farm management. Danish farms using recirculating techniques remain competitive thanks to enhanced productivity and economy of scale. However, small traditional farms in Germany and Denmark may struggle to stay competitive in the long term. Organic farms in both countries face challenges of high feed costs and comparatively low productivity with mixed success. Using edible protein energy return on investment (epEROI) as an indicator of ecological sustainability, all surveyed farms compared very favourably with the terrestrial systems of animal meat production were investigated so far.
A winter dysentery (coronavirus infection) outbreak in a dairy herd in Galicia (northwestern Spain)

Bovine coronavirus infections in adult cattle are commonly referred as to winter dysentery and present as an epidemic outbreak characterised by the sudden onset of diarrhoea with fresh blood that presents with high morbidity but low mortality. Despite the low mortality, milk production may not return fully to expected levels until several weeks post infection. This case report demonstrates the symptoms, examination and evaluation of a referred outbreak of winter dysentery in adult and youngstock cattle in a dairy herd located in northwestern Spain, highlighting the importance of precise questioning and on-farm assessment for examining the biocontainment practices of a herd.
Nidificación de meliponinos (Hymenoptera: Apidae) de la Región Central de Colombia

Field observations of 34 species of stingless bees in 303 nests in Cundinamarca, Colombia, included the following parameters: construction site, presence or absence of a specialized entrance structure, degree of exposure, heigth of nest above the ground and altitudinal distribution. A trend to nest in live trees, usually with a especialized entrance structure was found. Most species build unexposed nests.
Species-independent height-age models for British Columbia

Species-specific height-age models abound in the scientific literature. Some researchers have used Zeide's two-point system to reduce the number of models in service. However, this system requires two height-age pairs which are not always available. The purpose of this research isto develop a height-age model for British Columbia, Canada, that is independent of species. From a large database of stem analysis data, 15 plots from three coastal and seven interior species were chosen to uniformly cover the range of site index for each species. After converting the stem analysis data into height-age data, a model based on the logistic function was fit to each plot. A preliminary analysis showed that site index, geographic region (coast, interior), and shade tolerance (tolerant, intolerant) are potentially good predictors of height. These variables, along with breast height age, were incorporated into a species-independent height-age model based on the log-logistic function. An additional ten plots per species were chosen to test the model. The testing showed that the species-independent model had approximately the same accuracy as the species-specific models. Future endeavors can be directed at improving the model by incorporating more species into the analysis and including other important climatic and ecological variables.
Significance of gut-blood barrier in health and disease

The gut microbiota produces a number of biologically active compounds that may have both, positive and negative effects on health. To enter the circulation, microbiota-derived molecules need to pass the gut-blood barrier (GBB), a complex multi-layer system that prevents the free passage form the gut lumen to the blood. The integrity and permeability of the GBB depends on numerous factors, and may be disturbed in gastrointestinal, metabolic, cardiovascular and other diseases. An increased permeability of the GBB results in easier access of gut-derived molecules to the circulation. This may exert a significant effect on the course of the underlying disease and may alter functioning of various organs. Here, we discuss physiological significance of the GBB and available methods of assessing the GBB permeability.
Estimating Transpiration for Three Woody Ornamental Tree Species using Stem-flow Gauges and Lysimetry

We compared transpiration estimates of three common desert landscape tree species using stem-flow gauges and lysimetry. Argentine mesquite (Prosophis alba Grisebach), desert willow [Chilopsis linearis (cav.) Sweet var. linearis], and southern live oak virginiana Mill. , seedling selection) were subjected to three irrigation regimes. Leaching fractions of +0.25, 0.00, and -0.25 were imposed for 2 years. During the summer of the second year, we conducted a comparative transpiration study. Trees growing in 190-liter plastic containers had a highly linear correlation (r=0.98, P=0.001) between transpiration estimated by stem-flow gauges and lysimetry [. ]
Effects of peatland size and exposure on two species of Diptera inhabiting the pitcher plant Sarracenia purpurea L.1

Abstract We explore how broad-scale landscape structure (size and exposure of peatlands) influences mosquitoes (Wyeomyia smithii [Coq.]) and midges (Metriocnemus knabi Coq.) that inhabit the pitcher plant (Sarracenia purpurea L.) in coastal peatlands. After accounting for fine-scale (pitcher volume, water volume, detritus) and medium-scale variables (distance to peatland edge, plant density), we show that incidence and abundance of both species decrease with peatland size, but more so in peatlands surrounded by vegetation less than 2 m tall. As peatland size increases, more pitchers experience extinction of midges (but not mosquitoes) over winter, but only in peatlands surrounded by vegetation less than 2 m tall. The density of mosquitoes (but not midges) in the spring was positively related to incidence in the fall (after emergence and oviposition). There was no relationship between the cardinal orientation of the edge and incidence in either species. In a variance components analysis, maximum variance is explained at the scale of the leaf for both species, but mosquitoes show peaks in additional variance at scales broader than midges. Collectively the results suggest that broad-scale forces (interactions between demography and landscape) structure these populations at different spatial scales. We emphasize that landscape studies must be performed at sufficiently broad spatial and long temporal scales in order to capture the full range of dynamics of any system.