Miracle-dz/UniFAR-FTUs huggingface dataset:
Production of monoclonal antibodies for the detection of potato virus Y

SUMMARY Monoclonal antibodies (McAb) were obtained to potato virus Y (PVY) after immunisation of BALB/c mice with purified PVY, tobacco necrotic strain (PVYn). Spleen cells from a mouse showing a high serum titre were used for fusion with X63NS1 myeloma cells. Hybridomas were selected in medium containing HAT. Culture supernatants were screened for antibody production against PVY, ordinary strain (PVY0) and PVYn using indirect ELISA. Clones of interest were further cross-reacted with 12 isolates each of PVY0 and PVYn and two isolates of potato virus A (PVA) and healthy sap. For further trials, two clones which reacted specifically with PVYn isolates and one which detected all PVY isolates except two of potato virus C (PVC) were selected.
Distribution and modification of diatom assemblages in and around a warm core ring in the western North Pacific Frontal Zone east of Hokkaido

Spatial distribution relationships between diatom assemblages and water types were inves- tigated in and around a 2-year-old warm core ring in the western North Pacific Polar Frontal Zone off Hokkaido, Japan. From the oceanographic and diatom data, principal component analysis and a clustering technique identified four water types and four diatom assemblages. The Background Assemblage had a low standing stock and was distributed over the entire study area, including the core water of the ring. This assemblage was associated with water conditions that were not highly suitable for diatom growth. A Cold Assemblage, probably linked to submerging Oyashio Water, was found in sub-surface waters. Its standing crop was rather high. The two other assemblages also had relatively high standing stocks: one, the Stratified Assemblage, was found around the nutricline in the sub-surface layer and the other, the Warm Streamer Assemblage, in a warm streamer flowing along the outer edge of the warm core ring. We argue here that the Stratified Assemblage emerged from the Background Assemblage because of favorable local conditions (nutrient level), and, conversely, that in the downstream of the warm streamer, the Warm Streamer Assemblage reversed to the Back- ground Assemblage because the nutrient supply was depleted.
Applications of stable isotope techniques to the ecology of mammals

1 Stable isotope analysis (SIA) has the potential to become a widespread tool in mammalian ecology, because of its power in resolving the ecological and behavioural characteristics of animals. Although applications of the technique have enhanced our understanding of mammalian biology, it remains underused. Here we provide a review of previous applications to the study of extant mammals, drawing when appropriate on examples from the wider ecological literature, to identify the potential for future development of the approach. 2 Stable isotope analysis has been applied successfully to understanding the basic foraging decisions of mammals. However, SIA generates quantitative data on a continuous scale meaning that the approach can be particularly powerful in the characterization of community metrics, such as dimensions of resource partitioning within species assemblages or nutrient dynamics in food chains. Resolving spatial and temporal patterns of individual, intraspecific and interspecific resource use is of fundamental importance in animal ecology and evolutionary biology and SIA will emerge as a critical tool in these fields. 3 Geographical differences in naturally occurring stable isotopes have allowed ecologists to describe large-scale mammal migrations. Several isotopic gradients exist at smaller spatial scales, which can provide finer resolution of spatial ecology. 4 A combination of foraging and movement decisions is of prime importance in the study of ecotoxicology, since this discipline requires quantitative understanding of exposure risk.
Do myosins contribute to metastasis of prostate cancer cells

Prostate cancer is the second most common cause of death from cancer in men in the UK. Localised disease can be treated with surgery or radiotherapy, but metastasis remains a great therapeutic challenge. Cancer cell migration involves rearrangements of the actin cytoskeleton, which is mediated by its interaction with myosins, a large and diverse family of motor proteins involved in many processes crucial for cell migration, such as cell adhesion, cell polarity or endocytosis. It is likely that the activity of myosins contributes to metastatic spread. I investigated the myosin expression profile in prostate cancer cell lines and found that Myo1b, Myo9b, Myo10 and Myo18a were expressed at higher levels in cells with high metastatic potential. Using an siRNA-based approach, knockdown of each myosin resulted in distinct phenotypes. Myo10 knockdown drastically decreased filopodia of PC3 cells, Myo18a knockdown increased filaments of non-muscle myosin 2A, knockdown of Myo1b and Myo9b increased stress fibre formation. Loss of Myo10 affected cell migration in 2D. In all cases, cell spread area was increased and 3D migration potential was decreased for Myo1b, Myo10 and Myo18a. Myo1b, Myo10 and Myo18a were also expressed in benign prostatic hyperplasia although knockdown of these myosins in benign tissue did not have very clear effects. Glioblastoma cells expressed high levels of Myo10 and showed decreased protrusions after Myo10 knockdown. Taken together, myosins act as molecular motors but also directly influence actin organisation and cell morphology and migration, which can contribute to the metastatic phenotype of cancer cells.
Impacts of Human Disturbances on Biotic Communities in Hawaiian Streams

Abstract Streams throughout the tropics have been altered by water diversion, channel modification, introduced species, and water quality degradation. The Hawaiian Islands, with watersheds ranging from the relatively pristine to the highly degraded, offer an opportunity to examine the impacts of human disturbance on native stream communities. For example, urbanization is often accompanied by stream-channel modification and reduced canopy cover, resulting in higher water temperatures and greater fluctuations in daily temperature. Even in relatively pristine watersheds, stream diversions can result in decreased flow velocity and water depth, reducing habitat availability. Dewatering of stream reaches can also inhibit downstream dispersal of larvae and upstream migration of juveniles and adults of native species. Many nonnative aquatic species are better adapted than native species to degraded habitats; once established in these habitats, they can cause further reduction in native populations through competition, predation, and the introduction of parasites or diseases. Understanding the relationship between habitat alteration and aquatic community structure is critical for developing sound management strategies.
Relative Quantitation of mRNA in β-Thalassemiamb E Using Real-Time Polymerase Chain Reaction

β-Thalassemia and Hb E patients, with seemingly identical genotypes, have a remarkable variability in severity. Reduction in red cell survival in β-thalas-semia is correlated with the amount of intracellular unmatched α-globin chains. However, it was only recently realized that mRNA, whose translation is prematurely terminated, is also unstable. No systematic attempts have been made to investigate mRNA stability in β-thalassemia arising from nonsense mutations located upstream from the normal termination codon. In this study, one-step real-time polymerase chain reaction has been employed to compare the levels of α- and β-globin mRNA in reticulocytes from β-thalassemia/Hb E subjects. The results showed the highest α/β-globin mRNA ratio (median = 5.70, n = 13) in frameshift codons 41/42 (-TTCT)/Hb E individuals compared to normal subjects (median = 1.02, n = 6), or those with Hb E trait (median = 2.15, n = 8). In addition, there was a concomitant increase in the α/β-globin mRNA ratio with decrease in hemoglobin level, ie. , increase in severity. The difference in the ratio among β-thalassemia/Hb E patients with the same genotype may be attributed to individual variations of efficiency in βE-globin mRNA splicing and in the destruction of prematurely terminated mRNA.
Comparative performance of sorghum hybrids and their parents under extreme water stress

Sorghum hybrids are generally considered to be drought tolerant based on their yield performance in multi-locational trials. The present study was undertaken to test this hypothesis. A short duration hybrid, CSH–6, a long duration hybrid, CSH–9, their common male parent and both female parents were evaluated in the field in India under both rainfed and irrigated conditions during the rainy seasons of 1986 and 1987. Due to the low rainfall received in these years, the unirrigated treatments experienced severe water stress during the vegetative and post-anthesis periods. The hybrids produced more leaf area and dry matter than their parents even under water stress. The values for the physiological traits examined either resembled those of one of their parents or were intermediate between them. The hybrid CSH–6 produced more grain than its female parent under rainfed conditions but, due to the severe water stress, neither CSH–9 nor its parents exhibited panicle emergence. The results suggest that crop phenology is very important for the production of grain yield under severe water stress. Given knowledge of rainfall characteristics and probable periods of drought within specific regions, it should be possible to breed phenologically and physiologically adapted hybrids for specific environments.
Dothistroma needle blight Mycosphaerella pini E. Rostrup, a new quarantine pathogen of pines in the CR

Dothistroma needle blight caused by Mycosphaerella pini E. Rostrup was observed for the first time in the Czech Republic on an imported Pinus nigra Arnold in 1999. In 2000, it was also found in the open planting. During three years, it became an important pathogen of pines in the Czech Republic. Its occurrence was noticed in more than 50 localities, above all in the region of Moravia and Silesia and eastern Bohemia. In total, it was found on 10 species of pine (P. nigra Arnold, P. banksiana Lamb., P. contorta Loudon, P. mugo Turra, P. leucodermis Ant., P. sylvestris L., P. cembra L., P. aristata Engelm., P. ponderosa P. et C. Lawson and P. jeffreyi Grev. et Balf.). Also Picea pungens Engelm. was noticed as a host species. In the Czech Republic, Pinus nigra is the most frequent host species of M. pini (80% localities) followed by Pinus mugo (27% localities). On Scots pine P. sylvestris, M. pini was noticed at two localities. The critical period for infection is in the Czech Republic from the second half of May until the end of June. The incubation period lasts about 2–4 months depending on climatic conditions. The first symptoms on the needles infected in the current year appear in August being clearly expressed from September to November. In the CR, Dothistroma needle blight spread probably with infected planting stock obtained from import at the end of the 80s and at the beginning of the 90s.
Effects of mannanoligosaccharide on different cecal parameters and on cecal concentrations of enteric pathogens in poultry

The ability of different enteric pathogens and coliforms to trigger agglutination of a yeast cell wall preparation (MOS), a yeast culture (Saccharomyces cerevisiae, NYCC 1026) and haemagglutination was studied. Three strains which agglutinated MOS (Salmonella typhimurium 29E, Salmonella dublin and Escherichia coli 15R) and one non-agglutinating strain (S. typhimurium 27A) were then selected as challenge organisms. The effects of dietary MOS on cecal concentrations of these challenge organisms and on activities and concentrations of the cecal microflora were evaluated in chicks under controlled conditions. Furthermore, the effects of MOS on ileal morphology were investigated. Five of seven strains of E. coli and seven of ten strains of S. typhimurium and Salmonella enteritidis agglutinated MOS and S. cerevisiae NYCC 1026. Strains of Salmonella choleraesuis, Salmonella pullorum and Campylobacter did not lead to agglutination. Agglutination of both yeast products could be inhibited by 25 mM of mannose. All strains that agglutinated the yeast products also triggered haemagglutination. However, haemagglutination of E. coli K99 could not be inhibited by mannose. Mannose sensitive agglutination of the yeast products and mannose resistant haemagglutination by £ coli K99 suggest that these strains express both a mannose sensitive (type-1) and a mannose resistant (K 99) type of fimbriae. In a series of three trials in which 3 d old chicks were orally challenged with 104 CFU of S. typhimurium 29E, birds receiving 4000 ppm of dietary MOS had reduced cecal S. typhimurium 29E concentrations (5.40 vs. 4.01 log CFU/g; P < 0.05) at d 10. In a second series of three trials with S. dublin as challenge organism the number of birds that tested salmonella positive in the ceca at d 10 was lower when MOS was part of the diet (90 % vs. 56 %; P < 0.05). Mannanoligosaccharide also reduced the number of birds from which the challenge organism £ coli 15R could be recovered (75 % vs. 15 %). In order to test the effect of MOS on concentrations of bacteria that do no express type-1 fimbriae, a challenge trial was conducted with S. typhimurium 27A. However, strain 27A did not colonize the birds sufficiently to evaluate if MOS affected its
Studies on Glutathione S-Transferases of Aspergillus Flavus Group in Relation to Aflatoxin Production

AbstractAflatoxin synthesis in the mycelia of Aspergillus is positively correlated with the activity of cellular glutathione (GSH) S-transferases (Saxena, Manju, Mukerji, K.G., Raj, H.G. 1988, Biochem. J. 254, 567-570). This finding is further extended to the action of inducer and inhibitor of aflatoxin synthesis upon A. flavus GSH S-transferase. Phenobarbitone (PB) a known inducer of aflatoxin formation increases GST activity in toxigenic strain alone as compared to non-toxigenic strains. Tinaderm (Tolnaftate) an antifungal drug specifically inhibit aflatoxin synthesis. Tinaderm - treated A. flavus mycelium was found to have significantly diminished GSH S-transferase activity coupled with reduce levels of aflatoxin. These observations point out clearly that theendogenous aflatoxin is the main factor effecting specific induction of A. flavus GSH S-transferase. The inducing effect of aflatoxin appears to be different from phenobarbital pattern of induction of GSH S-transferase. In this connection, a direct.
Gynodioecy and Reproductive Trait Variation in Three Thymus Species (Lamiaceae)

We studied the general features of the reproductive system of two sympatric species Thymus zygis and Thymus mastichina (Lamiaceae) near Salamanca, Spain, and compare our data with previous and original data on the gynodioecious Thymus vulgaris studied near Montpellier, France. The frequency of females is high on average and strongly variable among natural populations and species: 51% (17–87) in T. zygis, 72% (41–99) in T. mastichina, and 63% (34–88) in T. vulgaris. The high female frequencies in some populations and the strong maternal inheritance of the sexual phenotype indicate a nuclear‐cytoplasmic determination of sex in both Spanish species, as already demonstrated in T. vulgaris. At the species level, we found a tendency for a positive association of the average frequency of females with both the relative fecundity of females and the relative allocation into male function in hermaphrodites. Among natural populations within each of the three species in contrast, these traits were not significantly related to each other. We propose that temporal variation of female frequency in natural populations prevents natural selection from adjusting female frequency and reproductive parameters.
Influence on Flax Fibers of Components in Enzyme Retting Formulations

A series of formulations with varying enzyme and chelator components is tested for flax fiber yield and properties using a recently developed enzyme retting system on Ariane flax grown as a winter crop in southeastern South Carolina. The levels of Viscozyme L, a commercial pectinase-rich enzyme mixture, and Mayoquest 200, a commercial chelator containing 38% ethylenediaminetetraacetic acid (EDTA) as tetrasodium salt, are varied. Enzyme retted flax straw is hand-carded and passed one time through a Shirley Analyzer for cleaning. The chelator level determines the fine fiber (i.e., Shirley cleaned) yield. Fiber strength measured by Stelometer is inversely proportional to enzyme level and not affected by chelator level. Fiber fineness measured by air flow methods is better with higher enzyme levels, and within enzyme levels the higher chelator levels tend to produce fibers with the highest degree of fineness. Relative cost calculations, taking into account fiber yield with costs of enzyme and chelators, provide a framework for determining retting efficiency and fiber quality. Results indicate that fiber properties can be tailored by enzyme or chelator levels. Further, commercial enzyme mixtures and chelators effectively ret flax and can serve as a basis for large scale retting tests.
Overwinter Mortality of Gizzard Shad: Evaluation of Starvation and Cold Temperature Stress

Abstract Overwinter mortality of gizzard shad Dorosoma cepedianum has been attributed to starvation, cold stress, and predation; however, the interactions among these factors are not well understood and can change across winter. We evaluated possible causes for overwinter mortality of age-0 gizzard shad through a combination of experiments and field sampling during the winters of 2005–2006 and 2006–2007. In the first experiment, gizzard shad were placed into cages in Oneida Lake, New York, during three time periods prior to ice formation. The fish exhibited low mortality at temperatures above 8°C but high mortality (>75%) in all cages as temperature dropped below 8°C. We observed no consistent patterns of length-dependent mortality or changes in total percent dry weight (DW). However, the viscerosomatic index (VSI) decreased during all time periods, indicating disproportionate use of visceral tissues. In the second experiment, gizzard shad were exposed to temperature treatments of 1, 2, and 4°C in experim.
Disproportionate importance of nearshore habitat for the food web of a deep oligotrophic lake

In large deep oligotrophic lakes, multiple lines of evidence suggest that the shallow nearshore water provides disproportionately important feeding and breeding habitat for the whole-lake food web. We examined the trophic importance of the nearshore environment, human impacts nearshore, and several approaches to disturbance detection in a deep (190m) oligotrophic lake with relatively modest residential development. In Lake Crescent, on the Olympic Peninsula of Washington (USA), stable isotope analysis demonstrated that apex salmonid predators derived more than 50%oftheircarbonfromnearshorewaters,eventhoughthisnearshorewateraccountedforonly2.5%oftotallakevolume. Unfortunately, it is this land-water interface that is initially degraded as shorelines are developed. We hypothesised that undertheseconditionsofrelativelymodestdisturbance,theeffectsofresidentialdevelopmentwouldbestronglylocalised neartoshore.Indeed,wefoundstrikingdifferencesbetweendevelopedandundevelopedsitesinperiphytonandassociated organic matter, though there were no offshore signals of human impact in water nutrient analysis or paleolimnological investigations. Together, these results suggest that nearshore biological monitoring should be integrated in lake management plans to provide 'early warning' of potential food-web repercussions before pollution problems are evident in open water and comparatively intractable.
Comparative and functional genome analysis of fungi for development of the protein production host Trichoderma reesei

Filamentous fungi of the subphylum Pezizomycotina are well known as protein and secondary metabolite producers. Various industries take advantage of these capabilities. However, the molecular biology of yeasts, i.e. Saccharomycotina and especially that of Saccharomyces cerevisiae, the bakers yeast, is much better known. In an effort to explain fungal phenotypes through their genotypes we have compared protein coding gene contents of Pezizomycotina and Saccharomycotina. Only biomass degradation and secondary metabolism related protein families seem to have expanded recently in Pezizomycotina. Of the protein families clearly diverged between Pezizomycotina and Saccharomycotina, those related to mitochondrial functions emerge as the most prominent. However, the primary metabolism as described in S. cerevisiae is largely conserved in all fungi. Apart from the known secondary metabolism, Pezizomycotina have pathways that could link secondary metabolism to primary metabolism and a wealth of undescribed enzymes. Previous studies of individual Pezizomycotina genomes have shown that regardless of the difference in production efficiency and diversity of secreted proteins, the content of the known secretion machinery genes in Pezizomycotina and Saccharomycotina appears very similar. Genome wide analysis of gene products is therefore needed to better understand the efficient secretion of Pezizomycotina. We have developed methods applicable to transcriptome analysis of non-sequenced organisms. TRAC (Transcriptional profiling with the aid of affinity capture) has been previously developed at VTT for fast, focused transcription analysis. We introduce a version of TRAC that allows more powerful signal amplification and multiplexing. We also present computational
Linkage of root physiology and morphology as an adaptation to soil phosphorus impoverishment in tropical montane forests

Summary Tropical forests in Borneo maintain a high level of productivity/biomass even under phosphorus (P)-limited conditions. The P-acquisition properties of roots may be an important factor that contributes to forest productivity, but they have not been well evaluated compared with above-ground properties of plants. In this study, we analysed root acid phosphatase activity and morphological properties (surface area, diameter and tissue density of roots) of dominant tree species in three tropical montane forests on Mt. Kinabalu, Borneo, to investigate changes in root properties along a soil P availability gradient. We found at the community level that root phosphatase activity and specific root surface area (root surface area per gram root biomass) increased, and root diameter decreased, with decreasing soil P availability at the community level, and the relationship was not changed in general even if we focused on a single-tree species distributed across multiple study sites that differ in soil P availability. Root acid phosphatase was significantly positively correlated with specific root surface area, and negatively correlated with root diameter, suggesting that finer roots have higher phosphatase activities. Furthermore, we compared root acid phosphatase activity with leaf P concentration of a given tree species and found a significant negative correlation between them. The significant correlation suggested that root P-acquisition properties could influence leaf P concentration, and/or vice versa. Below-ground properties (i.e. root P-acquisition properties) might be directly/indirectly linked to above-ground properties (i.e. leaf P concentration) of a tree individual. In conclusion, the root physiological and morphological properties change along a gradient of soil P availability in the tropical montane forests. In addition, the changes in the root properties are coordinated with the changes in leaf P concentrations. The adaptive changes in the above-ground and below-ground properties along the soil P gradient could contribute to the maintenance of forest productivity in the tropical montane forest in Borneo.