Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular and kinetic characterisation of sugarcane pyrophosphate: fructose-6-phosphate 1-phosphotransferase and its possible role in the sucrose accumulation phenotype.

The amount of pyrophosphate: fructose-6-phosphate 1-phosphotransferase (PFP) activity in sugarcane internodal tissue is inversely correlated with sucrose content. To help elucidate this apparent role of PFP in sucrose accumulation in sugarcane we have determined its molecular and kinetic properties. Sugarcane PFP was purified 285-fold to a final specific activity of 4.23 µmol min-1 mg-1 protein. It contained two polypeptides of 63.2 and 58.0 kDa respectively, at near equal amounts that cross-reacted with potato PFP-α and -β antiserum. In gel filtration analyses the native enzyme eluted in three peaks of 129, 245 and 511 kDa, corresponding to dimeric, tetrameric and octameric forms, respectively and fructose 2,6-bisphosphate (Fru 2,6-P2) influenced this aggregation state. Both the glycolytic (forward) and gluconeogenic (reverse) reactions had relative broad pH optima between pH 6.7 and 8.0. The Fru 2,6-P2 saturation curves were hyperbolic with approximate Ka values of 69 and 82 nm for the forward and reverse reactions, respectively. The enzyme showed hyperbolic saturation curves for all its substrates with Km values comparable with that of other plant PFP, i.e. 150, 37, 39 and 460 µM for fructose 6-phosphate, inorganic pyrophosphate, fructose 1,6-bisphosphate and inorganic phosphate, respectively. Sugarcane PFP's molecular and kinetic characteristics differed slightly from that of other plant PFP in that: (i) Fru 2,6-P2 directly induced the octameric state from the dimeric state; (ii) Fru 2,6-P2 shifted the pH optimum for the forward reaction to a slightly more basic pH; and (iii) Fru 2,6-P2 increased the Vmax for the forward and reverse reactions by similar amounts.
Self-assembly in colloidal hard-sphere systems

In this thesis, we examine the phase behaviour and nucleation in a variety of hard-sphere systems. In Chapter 1 we present a short introduction and describe some of the simulation techniques used in this thesis. One of the main difficulties in predicting the phase behaviour in colloidal, atomic and nanoparticle systems is in determining the stable crystalline phases. To address this problem, in Chapters 2 and 4 we present two different methods for predicting possible crystal phases. In Chapter 2, we apply a genetic algorithm to binary hard-sphere mixtures and use it to predict the best-packed structures for this system. In Chapter 4 we present a novel method based on Monte Carlo simulations to predict possible crystalline structures for a variety of models. When the possible phases are known, full free-energy calculations can be used to predict the phase diagrams. This is the focus of Chapters 3 and 5. In Chapter 3, we examine the phase behaviour for binary hard-sphere mixtures with size ratios of the large and small spheres between 0.74 and 0.85. Between size ratios 0.76 and 0.84 we find regions where the binary Laves phases are stable, in addition to monodisperse face-centered-cubic (FCC) crystals of the large and small spheres and a binary liquid. For size ratios 0.74 and 0.85 we find only the monodisperse FCC crystals and the binary liquid. In Chapter 5 we examine the phase behaviour of binary hard-sphere mixtures with size ratios between 0.3 and 0.42. In this range, we find an interstitial solid solution (ISS) to be stable, as well as FCC crystals of the small and large spheres, and a binary fluid. The ISS phase consists of an FCC crystal of the large particles with some of the octahedral holes filled by smaller particles. We show that this filling fraction can be tuned from 0 to 100%. Additionally, we examine the diffusive properties of the small particles in the ISS for size ratio 0.3. In contrast to most systems, we find a region where the diffusion increases as a function of the packing fraction. Finally, in Chapters 6, 7, and 8 we examine nucleation in colloidal systems. In Chapter 6, we examine the crystal nucleation for hard spheres using a variety of simulation techniques, namely, umbrella sampling (US), forward flux sampling (FFS), and molecular dynamics (MD). We compare the resulting nucleation rates with previous experimental and simulated rates. and find agreement between all the theoretically predicted nucleation rates. However, the experimental results display a markedly different behaviour for low supersaturation. In Chapter 7, we examine in more detail the FFS technique, in particular, the effect measurement error has on the resulting nucleation rates. In Chapter 8, we examine the crystal nucleation of the Weeks-Chandler-Andersen (WCA) model with ? = 40 using Brownian dynamics, US and FFS. This WCA potential is softer than the hard-sphere potential, but is frequently used to approximate hard spheres. Our predicted nucleation rates for this potential are in agreement with those found for hard spheres.
Costs and benefits of hormone-regulated plant defences

Plants activate defence responses to protect themselves against microbial pathogens and herbivorous insects. However, induction of defences comes at a price, as the associated allocation costs, autotoxicity costs and ecological costs form fitness penalties. Upon pathogen or insect attack, resources are allocated to defences instead of to plant growth and reproduction, while above- and below-ground interactions with beneficial organisms may also be disturbed. The phytohormones salicylic acid and jasmonic acid are major players in the regulation of induced defences and their associated fitness costs. Hormone-controlled signalling pathways cross-communicate, providing the plant with a finely tuned defence regulatory system that can contribute to a reduction of fitness costs by repressing ineffective defences. However, this sophisticated regulatory system causes ecological costs, because activated resistance to one organism can suppress resistance to another. Moreover, the system can be hijacked by invading organisms that manipulate it for their own benefit. Priming for enhanced defence emerged as a defence mechanism with limited fitness costs. Because priming results in a faster and stronger activation of defence only after pathogen or insect attack, the limited costs of the primed state are often outweighed by the benefits in environments with pathogen or herbivore pressure. The balance between protection and fitness is crucial for a plant’s success and is therefore of great interest for plant breeders and farmers. By combining molecular knowledge and ecological relevance of defence mechanisms, one can gain fundamental insight into how and why plants integrate different immune signals to cope with their natural multitrophic environment in a cost-effective manner.
The plant‐growth‐promoting rhizobacteria Bacillus pumilus and Bacillus licheniformis produce high amounts of physiologically active gibberellins

The plant-growth-promoting rhizobacteria (PGPR), Bacillus pumilus and Bacillus licheniformis, isolated from the rhizosphere of alder (Alnus glutinosa [L.] Gaertn.) have a strong growth-promoting activity. Bioassay data showed that the dwarf phenotype induced in alder seedlings by paclobutrazol (an inhibitor of gibberellin [GA] biosynthesis) was effectively reversed by applications of extracts from media incubated with both bacteria and also by exogenous GA 3 , Full-scan gas chromatography-mass spectrometry analyses on extracts of these media showed the presence of GA 1 , GA 3 , GA 4 and GA 20 , in addition to the isomers 3-epi-GA 1 and iso-GA 3 . Isotope dilution analysis indicated that epi-GA 1 was an artefact. Likewise, iso-GA 3 is also probably an artifact spontaneously formed during extraction and/or analysis. In both culture media, GA 1 was present in higher concentrations (130-150 ng ml -1 ) than GA 3 (50-60 ng ml -1 ), GA 4 (8-12 ng ml -1 ) and GAS (2-3 ng ml -1 ). The data indicated that culture of both bacteria accumulate bioactive C 19 -gibberellins in relative high amounts and that these GAs appear to be physiologically active in the host plant. The evidence suggests that the promotion of stem elongation induced by the PGPR could be mediated by bacterial GAs.
Possible bloom of free trichomes in the Bay of Marseille, NW Mediterranean Sea: an anomaly evidenced by flow cytometry

The composition of ultraphytoplankton ( 7 × 104 events mL−1), with both orange and red fluorescence intensities like Synechococcus, but with a size signal larger than that of 2 µm fluorospheres (beads). These unknown particles were sorted out by flow cytometry and then observed by epifluorescence microscopy: they appeared to be chain-forming microorganisms, just like trichomes of some diazotroph cyanobacteria with one heterocyst, but not unambiguously distal. The chains observed after cell sorting were not straight, but rather folded. To our knowledge, this is the first report of a possible bloom of such free trichomes. The small sample volume available for the delayed analysis and the limited resolution of our photomicrography did not allow for species identification. The brief occurrence of free trichomes in the Bay of Marseille with such a high abundance remains to be explained. High temperature in summer, induced stratification of the water column and nitrate depletion may be related to this event. High-frequency surveys of ultraphytoplankton assemblages at the single cell level appear to be necessary to observe such phenomenon more efficiently and document their dynamics.
Endosulfan-enhanced crest induction in Daphnia longicephala: evidence for cholinergic innervation of kairomone receptors

Daphnia longicephala were reared from early embryogenesis in the presence or absence of crest-inducing kairomones released by Anisops grants (Notonectidae) and from birth in one of five concentrations of the organochlorine pesticide, endosulfan (0,0.1,1.0,10 or 100 ug I*1). The morph- ology of the daphnids was measured 3 days after birth and on production of the first brood of eggs. The reproductive parameters, first brood size, age at first reproduction, mean egg volume and total egg volume, were also measured. Endosulfan significantly induced crest development in 3-day-old daphnids at 0.1,1.0 and 10 ug I"1 in the presence and absence of Anisops kairomone, although crest size in the absence of kairomone was only marginally greater than controls. A concentration of 10 ug 1~' endosulfan significantly enhanced crest growth of kairomone-exp osed daphnids at maturity. The Anisops kairomone alone induced a large crest in D.longicephala, reduced first brood size, mean egg volume and total egg volume, and increased age at maturity. The coefficient of variation of mean egg volume was significantly reduced by Anisops kairomone. It is hypothesized that endosulfan enhances crest development by inhibition of y-aminobutyric acid (GABA), an inhibitory neurotransmitter at cholinergic nerve junctions.
Les virus de plantes et les virus des animaux : deux mondes totalement différents ?

Auteur(s) :, M Keller1, G Jonard1 1Institut de biologie moleculaire des plantes, CNRS-UPR2357, Universite Louis Pasteur, 12 rue du General Zimmer, 67084 Strasbourg Cedex. Historiquement, les virus de plantes ont joue un role determinant dans la naissance et l’essor d’une nouvelle science, la virologie, a la fin du XIXe siecle. En effet, les etudes menees sur la maladie de la mosaique du tabac ont permis de montrer que celle-ci etait due a un agent infectieux ayant des [. ]
The contribution of stored water to transpiration in Scots pine

Abstract. The amount of water available diurnally and annually from the storage tissues was measured in plots of Scots pine trees with four different population densities (608–3281 trees per ha) in a 40-year-old plantation in north eastern Scotland. The water storage capacity of stems, branches, and foliage was estimated from equations derived from harvested trees and measurements of relative water content. On average 64% of the water considered to be available for transpiration was in the stem sapwood and less than 5% in the phloem, cambium and foliage. Trees on the plot with the highest population density had a water storage capacity of 212 m3 ha−1 (21.2 mm), whereas those on the plot with the lowest population density had a water storage capacity of 124 m3 ha−1 (12.4 mm). The utilization of stored water in transpiration was estimated from seasonal and diurnal measurements of the relative water content of foliage and stem sapwood. The largest change in sapwood relative water content over a 2-week period was a reduction of 27% corresponding to extraction from the sapwood of 2.5 and 5.1 mm of water on the plots with the lowest and highest population densities, respectively. In rapidly changing weather conditions 1–1.5 mm day−1 could be removed from the stem sapwood alone. Since transpiration rarely exceeded 3 mm day−1, 30–50% of the transpired water was extracted from water stored in the stem sapwood over short periods. Trees on the plot with the lowest population density occasionally had slightly higher relative water contents and exhibited larger diurnal fluctuations than those on the plot with the highest population density, possibly because of differences in wood density. Sapwood water content was generally lower at times of high transpiration rate and in winter during freezing conditions. Resaturation took several months to complete during the winter.
TWO DISTINCT COLONIAL MORPHOTYPES OF AMPHORA COFFEAEFORMIS (BACILLARIOPHYCEAE) CULTURED ON SOLID MEDIA 1

When cultured on different types of solid media, the marine‐fouling diatom Amphora coffeaeformis (Ag.) Kütz. consistently formed two distinct colonial morphotypes named tight and fuzzy. Tight colonies were comprised mainly of small, morphologically distorted, nonmotile cells, whereas morphologically normal and highly motile cells formed the fuzzy colonies. Cells from tight colonies were less adherent to glass, grew more slowly in liquid media, and had a slightly decreased viability on plates with copper than cells from fuzzy colonies. Whereas the protein profiles of the two types of cells were nearly identical in polyacrylamide gels stained with Coomassie blue, cells from tight colonies produced a significantly lower amount of a protease‐resistant, low Mr polysaccharide or glycoconjugate as detected in silver‐stained gels. The frequency of appearance of the fuzzy and tight morphotypes was not influenced by the mode of nutrition or the type of substratum to which the algal cells adhered. However, certain formulations of solid medium and the presence of growth‐inhibitory concentrations of copper in agar plates favored the formation of tight colonies. Due to their frequencies and patterns of appearance, it was clear that the two naturally formed morphotypes were not the consequence of spontaneous mutations, genetic rearrangement, or selection of stable natural variants, and we have hypothesized that they were linked to a normal physiological behavior. The tight colonial morphotype was used as a valuable marker to screen for true motility/adhesion mutants within an ultraviolet‐mutagenized population of A. coffeaeformis. Seven mutants were isolated that were non‐motile on agar plates, poorly adherent to glass, and distinguished from naturally formed cells from tight colonies by their inability to form fuzzy colonies upon subculture on solid media.
Antioxidant activity and phenolic content of germinated lentil (Lens culinaris)

In this study, the changes in phenolic compounds and antioxidant activity of lentil seeds before and after germination were investigated. Lentil seeds were germinated in dark chambers maintained near 100% relative humidity at 20°C. Three different solvents were employed to extract the phenolic compounds present in lentil seeds and sprouts. Total content of phenolic compounds were measured by Folin-Ciocalteau method and antioxidant activity determined by two different methods: assay of hydroxyl radical scavenging activity method and oven test method. For the later method, two different concentrations of extracts (0.02 and 0.1% w/w) were added to sheep tallow and the stabilities of the treatments were determined. Peroxide value and induction period measurements were used to evaluate the in vivo antioxidant activities. The results indicated that germination modifies the quantity and quality of phenolic composition of lentil, and the solvent used for extraction influence the antioxidant activity. The evaluation of in vivo antioxidant activity of the extracts measured by delay in tallow oxidation indicated that the activity was dependent on the phenolics concentration of extract which increased when higher concentrations of the extracts were applied. These data suggested that lentil sprout flour or extract can be used as a source of natural antioxidants in functional foods.
Hyperspectral Imaging on the International Space Station: An Innovative Approach to Commercial Development of Space

NASA s Space Partnership Division (SPD) was established to promote the commercial development of space by providing access to space ai opportunity to perform commercial research in the microgravity environment. NASA, through SPD, has established Research Partnership Centers (RPC s) that bring the government, universities at private industry together to perform research in space for commercial applica! lons. The SPD Office has fostered a re! ationship between an RPC and an aerospace company to perform hyperspectral imaging on the Window Observational Research Facility (WORF) on board the International Space Station (ISS). As a result of this relationship and M the capabilities of the WORF, the ISS will serve the private sector with platform to conduct hyperspectral imaging for commercial research.
Cation Transport in Escherichia coli

The intracellular Cl concentration in E. coli has been studied as a function of the Cl concentration in the growth medium and the age of the bacterial culture. The ratio of extracellular to intracellular Cl concentration is shown to be 3.0 in the logarithmic phase and 1.13 in the stationary phase, both ratios being independent of the extracellular Cl concentration. If it may be assumed that Cl is passively distributed in this organism, these results are consistent with a transmembrane P.D. of 29 mv, interior negative, during the logarithmic phase, and 3 mv, interior negative, in the stationary phase.
Utilization of organic and inorganic nitrogen sources by ectomycorrhizal fungi in pure culture and in symbiosis with Pinus contorta Dougl. ex Loud.

summary The growth of ten species of ectomycorrhizal fungi was measured in liquid media containing different organic and inorganic nitrogen sources. All fungi grew well on ammonium. Growth on nitrate was generally lower, although there was considerable variation between different isolates of the same species. Suillus variegatus, Piloderma croceum, Paxillus involutus, Hebeloma crustuliniforme and unidentified pink and white isolates often grew as well on organic nitrogen sources as on ammonium. Growth of the other species was more variable. Isolates of Thelephora terrestris and Lactarius rufus varied in their ability to use bovine serum albumen (BSA) but two Laccaria species were poor at using the protein as a nitrogen source. The ability of mycorrhizal and non-mycorrhizal Pinus contorta Dougl. ex Loud, plants to utilize BSA was also examined. Non-mycorrhizal plants and mycorrhizal plants infected with either T. terrestris or the unidentified pink ectomycorrhizal symbiont were supplied either with ammonium or with BSA. Growth of plants supplied with BSA was significantly increased by mycorrhizal infection with the pink symbiont and not significantly different from that of plants supplied with ammonium, but non-mycorrhizal plants were unable to use the protein as a nitrogen source and had significantly lower yields and nitrogen contents than infected plants. In contrast, mycorrhizal infection with T. terrestris had no effect on growth or nitrogen contents of plants supplied with protein. The results are discussed in relation to possible physiological differences between ectomycorrhizal fungi occurring at different successional stages of forest development.
Degeneracy and additional alloreactivity of drug-specific human αβ+ T cell clones

It has been well established that T cells can recognize small mol. wt compounds such as drugs. Results from previous studies revealing a high heterogeneity and cross-reactivity of drug-specific T cell clones (TCC) in individual patients prompted us to analyze the degeneracy of drug-reactive TCR in detail. Hence, we analyzed the MHC restriction pattern of a panel of 100 drug-specific TCC isolated from different drug-allergic donors. We found that 28 of the tested clones showed an MHC allele-unrestricted drug recognition. Most of these clones were at the same time highly drug specific, i.e. they could only be stimulated by the original drug and not by any drug derivatives. In contrast, TCC with the ability to interact with different drug derivatives displayed a clearly MHC allele-restricted drug recognition. Therefore, we concluded that the TCR of these clones is mainly interacting with side chains of the appropriate drug molecules and hence able to tolerate alterations in the MHC molecule. Moreover, we tested all clones for additional alloreactivity and found that 27 clones could be stimulated by a self-MHC‐peptide‐drug complex as well as by a non-self-MHC‐peptide complex. This cross-reactivity with allogeneic MHC molecules was substantially higher in drug-specific TCC compared to tetanus toxoid-specific clones from the same donors. This suggests that from the point of view of drug-specific TCR, non-self-MHC‐ peptide complexes have a higher incidence to mimic the ‘original’ self-MHC‐peptide‐drug complex and this may occur for TCR recognizing self-MHC‐pathogen-derived peptide complexes. Finally, the biological functions of bispecific TCC were not influenced by the nature of the stimulating ligand. Both drug as well as allogeneic stimulation led to similar reaction patterns in the analyzed TCC.
Characterization of porcine endothelial cell determinants recognized by human natural antibodies

Abstract: Organs transplanted from pigs to primates are subject to hyperacute rejection. This immunologic reaction is initiated by the recipient's natural antibodies that bind to endothelial cell antigens of the organ, resulting in the activation of the complement system and rapid destruction of the graft. Various lines of evidence, particularly blocking studies, using purified carbohydrates have suggested that the endothelial cell determinant recognized by human natural antibodies is a terminal galactose in an α configuration (α‐Gal). Although these studies are compelling, they fall short of proof because xenoreactive natural antibodies, being polyreactive, might bind to structures other than those used for blocking. Moreover, in vivo evidence that anti‐α‐Gal antibodies participate in hyperacute rejection has not been reported. Here we report that an enzyme specific for α‐Gal, α‐galactosidase, removes α‐galactose residues from both intact porcine aortic endothelial cells and immobilized porcine aortic endothelial cell membrane extracts and that as a result of this, xenoreactive natural antibody binding is lowered by 70 to 80%. This decrease in binding of human IgM causes a corresponding decrease in complement activation. Similar results were obtained using the sera of other Old World primates. Digestion of immobilized porcine aortic endothelial cell membrane extracts with α‐galactosidase produced a similar reduction in human IgM binding to gp 115/135. These results indicate that a terminal α‐galactose is an important component of the gp 115/135 porcine endothelial cell antigen. We also report that perfusion of porcine organs I with primate serum removes anti‐α‐Gal IgM from the serum.