Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell motility in microfluidic environments

Trypanosomes are single-celled bloodstream parasites and causative agents of African Sleeping Sickness in humans and Nagana disease in domestic livestock. The pathogen is transmitted by the bite of the tsetse fly and lethal to the infected host if left untreated. Eponymous for the Trypanosoma genus name (Trypanosoma: drilling body ) is the striking nature of their movement which is often described by the spiral motion of a corkscrew. However, looking at trypanosomes at high spatiotemporal resolution, we find that the way the cells move is more complex than described before and changes over time and cell. Apart from the question how trypanosomes move, we find ourselves confronted with the question why trypanosomes move at all? In this context, M. Engstler et al. have shown that active movement is essential for cells that are exposed to hostile antibodies. Hydrodynamic flow induced by active movement of the cell leads to a delocalization of antibodies that have bound to the cell surface: Antibodies exposed to the flow around a forward swimming cell are driven backwards into the flagellar pocket where they are taken up by endocytosis and rendered harmless by subsequent digestion. In contrary, a backward swimming cell is accumulating antibodies at the tip of the flagellum and gets digested itself by the host s immune system. If the described mechanism of hydrodynamic protein sorting is a ubiquitous feature in nature, it has to be proven in more detailed studies of cell motility as well as the involved hydrodynamic condition.The aim of this thesis is to study and quantify the movement of trypanosomes in their microfluidic environments in order to help understanding the mechanisms and reasons of their motility. To achieve this goal we constructed an optical trapping fluorescence microscope optimized for high spatiotemporal resolution and reduced phototoxicity. In combination with advanced microfluidic methods we were not only able to control hydrodynamic flow conditions and spatial confinement, but also to position, manipulate and measure forces on the single cell level, as well as to specifically label single living cells in the microflow.In this work we could show for the first time that using strongly focussed diode lasers it is possible to optically trap living trypanosomes over time scales of t < 15 min, without inducing significant photodamage. The optical stall forces acting on trypanosomes were determined and used to measure the propagation forces of single and dividing trypanosomes.In combination with automated image processing routines we also analyzed the positioning of trypanosomes within the optical trap and found distinct trapping loci which could be correlated to structural features of trypanosomes.
CHIRONOMID RESEARCH IN NORTHERN PATAGONIA

Patagonia is the southernmost territory of South America and was traditionally considered as belonging to the Neotropical region (Sclater 1858, Wallace 1876). Based on these zoogeographic schemes, the Argentinean biogeographer Raul Ringuelet (1961) divided Patagonia into the Araucanian Subregion, characterized by dominance of Austral or Notogeic fauna, and the Andean-Patagonian Subregion, having a dominant mixture of Notogeic, Brasilic, and Nearctic elements. Later, Cabrera & Willink (1973) proposed a biogeographic scheme for South America and the Caribbean in which the Andean-Patagonian region was part of the Neotropical region and Araucania. They named the region the SubAntarctic province, which was part of the Antarctic region and was based on the floristic and faunistic affinities of southwestern Patagonia with Antarctica, Australia and New Zealand. Further biogeographic schemes considered Patagonia as a part of a Holantarctic region (Takhtajan 1986) or Sub-Antarctic subregion and Patagonian subregion of the Andean Region (Morrone 2001). The extraordinary amount of different biogeographic schemes reflects the complexity of the affinities of the biota of Patagonia.
Processing of amyloid precursor protein and amyloid Peptide neurotoxicity.

Alzheimer's disease is characterized by the presence of two types of lesions in brain: neurofibrillary tangles and senile plaques. Intraneuronal neurofibrillary tangles are made of paired helical filaments containing hyperphosphorylated microtubule associated protein tau. Extracellular senile plaques contain a core of beta-amyloid peptide (Abeta), which is produced by cleavage of the Amyloid Precursor Protein (APP). Among the two catabolic pathways of APP, the amyloidogenic pathway producing Abeta peptides was intensively studied in different cellular models expressing human APP. Differences in APP processing and in toxicity resulting from Abeta accumulation can be observed from one cell type to another. In particular, primary cultures of neurons process APP differently compared with other cultured cells including neuronal cell lines. Neurons accumulate intraneuronal Abeta, which is neurotoxic, and in these cells, APP can be phosphorylated at specific residues. Recent studies suggest that APP phosphorylation can play an important role in its amyloidogenic processing. In addition, protein kinases that phosphorylate APP are also able to phosphorylate the neuronal protein tau. Biochemical analysis of these two proteins in primary cultures of neurons show that phosphorylation of both APP and tau can be a factor linking the two characteristic lesions of Alzheimer's disease.
EFFECT OF FLUCTUATING SALINITY AT DIFFERENT GROWTH STAGES ON PHYSIOLOGICAL AND YIELD RELATED PARAMETERS OF RICE (ORYZA SATIVA L.)

(98151)3822577. ABSTRACT: In order to evaluate salt stress impact on yield related parameters of rice Tarom Hashemi cultivar at different growth stages, an experiment was conducted at Sari Agricultural Sciences and Natural Resources University (Iran) during 2010, using randomized completely design with five replications. Treatments were considered four levels of salinity (control, 3, 6 and 9 dS.m -1 ) by adding or replacement of treatment at three stages (vegetative, flowering and grain filling) to resemble fluctuating salinity. The results indicated that increasing salinity levels caused marked differences between control and salinity treatments in which some morphological parameters such as leaf area and active leaf number rapidly influenced. Salinity could not effect on tiller number, while flag leaf area significantly affected during grain filling stage. Physiological traits such as chlorophyll a, b and a+b and relative water content (RWC) were determined 2 weeks after flowering. These parameters significantly decreased (up to 16.5%) for chlorophyll contents as well as RWC (up to 21%) compared to control. Among studied traits, biological, paddy and straw yield, total plant biomass, fertile tillers, plant height, filled grain and 1000-grain weight, length, volume and biomass of root, significantly decreased when salt stress increased. Salt stress induced a linear decrease in biological and paddy yield and total plant biomass, whereas a second degree equation was existed for harvest index. A positive and significant correlation was observed between biological yield and grain number per plant with paddy yield, while grain number per panicle had a negative and significant correlation. Results showed that the fluctuating salt stress especially at the early growth stages markedly reduced rice yield as compared to other stages.
Biological activity of polyketide pigments produced by the fungus Monascus

L. MART~NKOVA, P. JOZLOVA AND D. VESELV. 1995. The biological activity of the pigment extracts from Monascus purpureus included their antibiotic action not only against bacteria but also against some species of yeasts and filamentous fungi, as well as embryotoxicity and teratogenicity. These activities depended on the presence of the orange component (monascorubrin and rubropunctatin). The formation of these compounds was influenced by the composition of the culture medium and by cultivation of the fungus : when amino acids, peptides or proteins were available during cultivation, as in the case of solid-state cultivation on rice, wheat or pearl barley or submerged cultivation with an organic nitrogen source, the bioactive compounds were converted into inactive complexes and, to a lesser extent, into purple pigments (monascorubramine and rubropunctamine) which retained some biological activity. The toxicity of the orange pigments may reside in the same reaction as their detoxication, i.e. in their binding
Caribou encounters with wolves increase near roads and trails: a time‐to‐event approach

Summary 1. Caribou and reindeer Rangifer tarandus are declining across North America and Scandinavia in part from wolf Canis lupus-mediated apparent competition with more abundant ungulate prey species. While caribou generally persist in areas with low wolf density, wolf packs that overlap caribou ranges could trigger caribou declines. Moreover, anthropogenic linear features such as roads, trails and seismic lines are hypothesized to increase predation risk for caribou, yet few studies have examined the mechanistic effects of linear features or spatial overlap on wolf–caribou encounter rates and predation risk. 2. We used (a) time-to-event models of wolf–caribou encounters estimated from concurrent global positioning system (GPS) radio-collar data from wolves and caribou and (b) wolf resource selection models of travel locations, to determine the potential influence of wolf–caribou spatial overlap, linear features, elevation and season on encounter rates. Analyses were based on data from 35 adult female caribou and 37 male and female wolves from 11 wolf packs from Banff and Jasper National Parks, Canada, from 2002 until 2010. 3. Wolf–caribou encounter rates increased with high wolf–caribou overlap, proximity to linear features and lower elevations. Wolves strongly selected low elevations, especially during winter and spring. Selection for linear features as travel routes increased with elevation. 4. Caribou risk of encounter was highest during the summer and autumn when wolves spent the most time at high elevations. Most wolf-caused mortalities (n = 12) occurred during spring and summer. 5. Synthesis and applications. The presence of anthropogenic linear features and the amount of time wolves spend in caribou range could be equally as important as wolf density when prioritizing caribou recovery actions such as wolf or primary prey reductions or re-introductions. The use of GPS locations and time-to-event modelling offers a powerful tool for evaluating factors affecting predation risk of threatened and endangered species.
Securing the future of the natural environment: using scenarios to anticipate challenges to biodiversity, landscapes and public engagement with nature

Summary 1. Maintaining and protecting biodiversity for the future under changing environmental and socio-political conditions is a major challenge. Scenarios are used as decision-making aids for natural resource management at local to global scales. Scenarios are underutilised by conservationists at a local level, where they can be highly effective for anticipating change. 2. People’s values and attitudes are crucial in determining the future, yet they are rarely placed at the centre of scenario exercises. Novel methods have been developed to fully integrate people’s worldviews into scenario planning. The ethnographic futures framework focuses on how changes occur through human agency and how they will be felt by society in the future. The three horizons approach considers how different ideas and paradigms become more, or less, dominant in society over time. 3. Natural England (NE), the statutory adviser to the UK Government on the natural environment in England, carried out a scenario planning process using these novel approaches. The scenarios consider a wide range of global and local factors and investigate their impact upon the natural environment in England, to 2060. 4. A set of four contrasting scenarios was produced. Despite their differences, nature was always highly valued in some form; ultimately, the state of the natural environment was determined not by natural forces but by societal choice. 5. Synthesis and applications. Scenario planning allows the development of key visions for the future. These can be used to establish, and influence, the direction of future trends and their impacts on the natural environment, particularly in the context of a shifting basis for conservation policy that seeks to enhance ecological resilience. The scenarios are being used within NE to help local communities shape the future of their natural environment; this process can be utilised by governments or environmental agencies elsewhere. This study demonstrates that across a range of scenarios the future state of the natural environment is very much a matter of societal choice. Decision-making frameworks for environmental conservation must take proper account of ecological knowledge, societal values, foresight and complexity.
Effects of auxin and anoxia on the cell wall yield threshold determined by negative pressure jumps in segments of cowpea hypocotyl.

In this paper, we report the determination of Y' not by such an extrapolation but directly by the negative pressure jump technique, in combination with the results of a pressure-probe study. The effects of auxin (IAA) and the metabolic control exerted by anoxia on Y' have also been investigated
Radiation-induced Autophagic Apoptosis of Rat Splenic Lymphocytes

The present investigation was undertaken with the aim of studying the relationship between apoptosis and autophagy through observation of the alternations in splenic lymphocytes after reversible sublethal cell injury. For this purpose, splenic lymphocytes of rats which were irradiated with γ-ray (total 800 rads), were studied by histochemistry and electron microscopy. After γ-ray irradiation, a large number of splenic lymphocytes developed apoptosis which was classified into two types, i. e. classical apoptosis or apoptosis and autophagic apoptosis. Ultra-structurally, classical apoptosis of lymphocyte assumed the aspects characterized by com-paction of nuclear chromatin and formation of cell fragments. 30-40 min after irradiation, classical apoptosis of lymphocytes was observed in spleen, and became most prominent 2-5hr after irradiation. 3-5hr later, most of apoptotic lymphocytes were phago-cytized by macrophages. Autophagic apoptosis was characterized by the formation of numerous autophagic vacuoles (autophagosomes). Early autophagosomes containing identifiable organelles e. g. mitochondria, ribosomes, smooth and rough endoplasmic reticulum were visible 2-24hr after γ-ray irradiation. The autophagosomes that contained multiplied organelles, nuclear fragments and portions of cytoplasm were formed through the enclosing of cisternae of endoplasmic reticulum around damaged organelles. In most of the autophagic apoptotic lymphocytes, their organelles were essentially increased in number. In addition, except that their nuclei were pyknotic, they did not shrink as other apoptotic cells. Thus, we considered the increase of organelles and formation of autophagic vacuoles in the apoptotic splenic lymphocytes was as one of the self-protective reactions against radiation damage. The results showed that part of the apoptotic cells exhibited marked enhancement of autophagic activity. After γ-ray irradiation, distinct organelle changes occurred in autophagic apoptotic lym-phocytes, and the autophagic apoptotic cells themselves perhaps took part in the elimination of apoptotic bodies. These indicated that the classical and the autophagic apoptosis are two types of cell death that assumed different morphological and functional aspects.
Bifurcation analysis in the flight dynamics design process? A view from the aircraft industry

Since 1977, various studies have been conducted to analyse the dynamics of aircraft by using continuation schemes and bifurcation analysis. The technique has not, however, been adopted as an engineering tool in the industry. After reviewing previous work, we apply bifurcation analysis to an industrial-scale aircraft model. The technique is shown to locate and identify key changes in the dynamic behaviour of the aircraft as its flight controls are varied. The issues facing the aircraft industry in implementing this technique are raised and a set of software improvements suggested. With these improvements the technique could be made into an engineering tool with important benefits to industry.
Modelling species competition in mixtures of perennial sow-thistle and spring barley based on shoot radiation use efficiency

Abstract Perennial sow-thistle (Sonchus arvensis L.) may be a serious weed in organic and conventional farming. To assess the effects of radiation acquisition and resource allocation on competitive ability, S. arvensis was grown together with spring barley (Hordeum distichon L.) in six mixtures in a replacement series with initial above-ground biomass proportions of S. arvensis ranging from 2% to 96%. A one-season experiment was made outdoors in boxes in Uppsala, Sweden, at a low level of nitrogen supply (5 g N m−2). The study tested the predictability of shoot biomass of each species based on two principal assumptions: (i) growth model parameters derived from species in monocultures could be applied in mixtures, and (ii) radiation in the mixed stand was partitioned between species proportional to their leaf area. Calibration of two parameters, for scaling of shoot radiation use efficiency and radiation partitioning respectively, were the base for the evaluation. When the coefficients were close to unity, which was the case for all mixtures dominated by barley, and for one of the mixtures with high proportion of S. arvensis in the early season, observed and predicted shoot biomass coincided well. For the evenly composed mixtures, total shoot biomass was underestimated (the scaling coefficient of shoot radiation use efficiency was>1), whereas the relative composition among species was predicted well. In the late season the principal model assumptions were not applicable to S. arvensis, likely due to increasing root allocation not accounted for in the model. Sonchus arvensis in mixtures with high proportions was planted early in relation to sowing of barley, which resulted in a comparably late development stage of S. arvensis. Consequently the relation between species development stages varied with species composition suggesting a need to introduce effects of differences in development stage into the model.
Effet du nitrate d’ammonium sur le développement et l’activité des enzymes anti-oxydantes du fraisier (Fragaria x ananassa L.) micropropagé

L’ajout de nitrate d’ammonium (NH4NO3) aux doses de 500, 1000 et 1500 mg.l-1 au milieu de proliferation ameliore la vigueur et diminue la chlorose des microboutures de fraisier observee sur le milieu temoin preconise par Boxus ne contenant que de l’azote nitrique a la dose de 1250 mg.l-1. Les analyses realisees sur deux varietes « Chandler » et « Sweet Charlee » respectivement sensible et tolerante a la chlorose d’origine nutritionnelle, ont montre que NH4NO3 confere aux microboutures une situation nutritionnelle generant moins de stress. Une plus grande teneur en proteines solubles et l’amelioration de l’activite enzymatique des CAT (Catalase) et POD (Peroxydase) constituent les changements metaboliques particuliers qui ont ete observes chez les deux varietes cultivees en presence d’ammonium. Une telle situation leur etait plus favorable puisqu’elles ont montre une moindre peroxydation de leurs lipides membranaires suite a une meilleure activite des enzymes anti-oxydantes.
Gene flow and immigration rate in an island population of great tits

It is generally recognized that immigration and gene flow cannot be equated, but few detailed quantitative comparisons of these processes have been made over the entire lifetime of individual animals. We analyzed data collected in a longterm study of an island population of great tits Parus major, and tested two assumptions frequently made in population genetic studies. (1) The assumption that there is no difference in reproductive output between immigrant and resident breeding birds was refuted for females but not for males. Lifetime production of local recruits (LRS) was reduced by 37% in immigrant females, because female immigrants tended to leave the island after breeding, and thus reproduced for fewer years. Female LRS was density dependent, but the effect of density was independent of status (resident/immigrant). (2) The assumption that mating was random with respect to status was also refuted: assortative mating was found, even when temporal and spatial aggregation of immigrants was controlled for. Thus both assumptions were refuted, and gene flow was lower than immigration rate.
Phylogenetic relationships and pathogenicity of Colletotrichum acutatum isolates from grape in subtropical Australia

The identity of Colletotrichum acutatum as the causal pathogen of grape ripe-rot, which causes yield loss and a bitter taint that lowers wine quality in Australian subtropical wine-grape regions, was confirmed using species-specific primers. Cultural, morphological and molecular methods (RAPD-PCR and sequencing of parts of the 5·8S-ITS regions and the β-tubulin-2 gene) were used to determine the phylogenetic relationships of Australian C. acutatum isolates from wine grapes and other horticultural crops. A combination of RAPD-PCR and β-tubulin-2 gene data showed that all wine-grape ripe-rot isolates from northern regions of New South Wales (NSW) and Queensland belong to a proposed new C. acutatum group (A9), together with isolates from Australian strawberry, mango, blueberry and olive. The 5·8S-ITS sequences for these grape pathogens were identical to published sequences for an isolate from Cyclamen (the Netherlands) and differed by 1 bp from isolates from Capsicum (Taiwan) and orange (Costa Rica). The grape ripe-rot isolates from the Shoalhaven Valley (southern NSW) were clustered within two other C. acutatum groups: A2 and A5. In vitro infection studies showed that Australian C. acutatum isolates from almond, blueberry, chilli, grape, mango, olive, strawberry and tomato were able to infect grape and could also infect blueberry and strawberry, indicating a lack of host specificity. This lack of host specificity, the genetic similarity with non-grape isolates, and the fact that many of the non-grape hosts were isolated from wine-growing regions, suggest the potential for cross-infection between grape and other horticultural crops.