Miracle-dz/UniFAR-FTUs huggingface dataset:
Protease‐resistant streptavidin for interaction proteomics

Streptavidin‐mediated enrichment is a powerful strategy to identify biotinylated biomolecules and their interaction partners; however, intense streptavidin‐derived peptides impede protein identification by mass spectrometry. Here, we present an approach to chemically modify streptavidin, thus rendering it resistant to proteolysis by trypsin and LysC. This modification results in over 100‐fold reduction of streptavidin contamination and in better coverage of proteins interacting with various biotinylated bait molecules (DNA, protein, and lipid) in an overall simplified workflow.
Morphology and Biology of Panagrolaimus Tipulae N. Sp. (Panagrolaimidae) and Rhabditis (Rhabditella) Tipulae N. Sp. (Rhabditidae), From Leatherjacket Larvae, Tipula Paludosa (Diptera: Tipulidae)

Two new species of nematode, described herein as Panagrolaimus tipulae and Rhabditis (Rhabditella) tipulae, were discovered from the cadavers of Tipula paludosa larvae collected from the field in British Columbia. They were cultured successfully on Galleria mellonella L. larvae in the laboratory. Tests on G. mellonella and T. paludosa larvae show that these nematodes are normally saprophytic in the soil. They feed on and multiply in the insect only after it is debilitated or dead.
IDENTIFICATION AND SIGNIFICANCE OF YEASTS ENCOUNTERED IN THE BREWERY

The methods of identifying and classifying yeasts are discussed and the writer's method for classifying strains of Saccharomyces cerevisiae is described. Twenty-seven different yeast species have been isolated from various stages of the brewing process, hops (12 species) and brewing yeast (11 species) having afforded the greatest number of these. Six species were obtained from priming solutions and these were unique in having very simple growth-factor requirements; two of them have been isolated from turbid beer on a previous occasion. Special media were necessary to isolate contaminants from the brewing yeast and it was this source which afforded those species most likely to cause turbidity in beer.
Describing adverse events in Swiss hospitalized oncology patients using the Global Trigger Tool

The occurrence rate of adverse events (AEs) related to care among hospitalized oncology patients in Switzerland remains unknown. The primary objective of this study was to describe, for the first time, the occurrence rate, type, severity of harm, and preventability of AEs related to care, reported in health records of hospitalized hematological and solid‐tumor cancer patients in three Swiss hospitals.
Cutaneous sensory nerve‐mediated microvascular vasodilation in normotensive and prehypertensive non‐Hispanic Blacks and Whites

Relative to non‐Hispanic Whites, non‐Hispanic Blacks are disproportionately affected by elevated blood pressure (BP). It is unknown whether race or subclinical increases in BP affect the ability of cutaneous sensory nerves to induce cutaneous microvascular vasodilation. Sixteen participants who self‐identified as non‐Hispanic Black (n = 8) or non‐Hispanic White (n = 8) were subgrouped as normotensive or prehypertensive. Participants were instrumented with three intradermal microdialysis fibers: (a) control, (b) 1 μM sodium nitroprusside (SNP), an exogenous nitric oxide (NO) donor, and (c) 20 mM NG‐nitro‐l‐arginine methyl ester (L‐NAME), a non‐selective NO synthase inhibitor. A slow local heating protocol (33–40°C, 0.1°C/min) was used to assess the onset of cutaneous sensory nerve‐mediated vasodilation (temperature threshold) and skin blood flow was measured using laser‐Doppler flowmetry. At control sites, the temperature threshold occurred at a higher temperature in non‐Hispanic Blacks (normotensive: 37.2 ± 0.6°C, prehypertensive: 38.9 ± 0.5°C) compared to non‐Hispanic Whites (normotensive: 35.2 ± 0.8°C, prehypertensive: 35.2 ± 0.9°C). L‐NAME shifted the temperature threshold higher in non‐Hispanic Whites (normotensive: 37.8 ± 0.7°C, prehypertensive: 38.2 ± 0.8°C), but there was no observed effect in non‐Hispanic Blacks. SNP did not affect temperature threshold in non‐Hispanic Whites, but shifted the temperature threshold lower in non‐Hispanic Blacks (normotensive: 34.6 ± 1.2°C, prehypertensive: 34.8 ± 1.1°C). SNP mitigated differences in temperature threshold across all groups. There was no effect found for BP status in either the non‐Hispanic Black or non‐Hispanic White groups. These data suggest that reduced NO bioavailability affects the ability of cutaneous sensory nerves to induce microvascular vasodilation in young, otherwise healthy non‐Hispanic Blacks.
The protein architecture of the endocytic coat analyzed by FRET microscopy

Endocytosis is a fundamental cellular trafficking pathway, which requires an organized assembly of the multiprotein endocytic coat to pull the plasma membrane into the cell. Although the protein composition of the endocytic coat is known, its functional architecture is not well understood. Here, we determine the nanoscale organization of the endocytic coat by FRET microscopy in yeast Saccharomyces cerevisiae. We assessed pairwise proximities of 18 conserved coat‐associated proteins and used clathrin subunits and protein truncations as molecular rulers to obtain a high‐resolution protein map of the coat. Furthermore, we followed rearrangements of coat proteins during membrane invagination and their binding dynamics at the endocytic site. We show that the endocytic coat proteins are not confined inside the clathrin lattice, but form distinct functional layers above and below the lattice. Importantly, key endocytic proteins transverse the clathrin lattice deeply into the cytoplasm connecting thus the membrane and cytoplasmic parts of the coat. We propose that this design enables an efficient and regulated function of the endocytic coat during endocytic vesicle formation.
Root distribution patterns of white yam (Dioscorea rotundata Poir.): a field study

Abstract The productivity of white yam (Dioscorea rotundata Poir) must increase to sustainably meet the demand of the increasing populations in the developing world where this is a staple crop. Although this could be achieved through the use of mineral fertilizers, reports indicate limited effects of these inputs on tuber yield. We hypothesized (i) that D. rotundata has a small and shallow root system and (ii) that this root system does not respond to mineral fertilizer application. Two field experiments were conducted in Côte d'Ivoire in year 1 and in year 2 to test these hypotheses. In the first field experiment we measured biomass production, as well as root density during plant growth in fertilized and unfertilized plots while in the second experiment, we analysed the distribution pattern of roots in horizontal and vertical root profiles in fertilized plots. The root system of D. rotundata consisted of seminal, adventitious and tubercular roots. Only the adventitious roots remained alive until the end of the growth cycle. The root length density was very low with a maximum of 0.25 cm cm−3. No roots were observed in the 15–30 cm horizon at 50 cm from the plant's crown. The horizontal and vertical root maps revealed that roots were mostly distributed in clumps, and there was a good correlation between the two methods of root sampling for this species. Fertilizer application had no significant effect on plant biomass, fresh tuber yield or on root growth. However, thinner and longer roots and higher tuber yields were observed in year 1 than in year 2. The different weather conditions and more specifically the higher soil temperature might explain the results obtained in year 1. Therefore, it could be recommended to farmers not to fertilize D. rotundata.
Utilisation d'une technique d'empreinte moléculaire dans l'étude d'écosystèmes microbiens complexes. Application à la fabrication d'un fromage au lait cru "l'AOC Salers "

L'article presente la technique de SSCP (Single Strand Conformation Polymorphism) associee a une identification moleculaire de la microflore basee sur la sequence de l'ADNr 16S. Cette technique permet d'obtenir une empreinte moleculaire des ecosystemes microbiens. Cette empreinte permet de caracteriser sans mise en culture la diversite d'une microflore, de comparer des microflores semblables, d'en suivre la dynamique en terme de presence grâce a l'ADNr 16S et/ou en terme d'activite grâce a l'ARNr 16S. Ces nouvelles possibilites sont illustrees par des exemples pris sur la microflore d'un fromage AOC Salers ou a defaut sur la microflore d'un digesteur anaerobie.
Utilization of a computer-assisted sperm motion analysis system to examine effects of dinoseb on rat sperm.

The computer-assisted sperm motion analysis (CASA) system has been used as one of the useful means for reproductive toxicity studies in male animals. Since various parameters of sperm motility are measured by the CASA system, we investigated the effects of a herbicide dinoseb, a testicular toxicant, and which parameter was the most appropriate for detecting changes. Crj:CD(SD)IGS mature male rats were administered dinoseb at a dose of 0 (corn oil), 5 or 7.5 mg/kg for 3 consecutive days, and were necropsied for cauda epididymal sperm analysis after a 12-day (Day15) or 19-day (Day 22) withdrawal period (Experiment I). No sperm motility parameters of dinoseb-treated rats were changed on Day 15, but on Day 22, the percentage of motile sperm (MOT) was significantly decreased in rats treated with dinoseb at 7.5 mg/kg. Other parameters, such as path velocity (VAP), curvilinear velocity (VCL), and amplitude of lateral head displacement (ALH) were significantly decreased as well. In Experiment II, no parameters of sperm motility showed any change in rats treated with dinoseb at 7.5 mg/kg three times per week when evaluated on Day 21. It was concluded that MOT, VAP, VCL, and ALH were more sensitive to dinoseb effects on sperm in the CASA system.
Depth-dependent vertebral number of Atlantic cod (Gadus morhua) on the Magdalen Shallows and Scotian Shelf: stock mixing or microgeographic trends within populations?

We examined spatial variation in the vertebral number of Atlantic cod (Gadus morhua) during the summer feeding season in the southern Gulf of St. Lawrence and on the Scotian Shelf. Mean vertebral number increased significantly with depth in the southern Gulf and on the northeastern Scotian Shelf but not on the southwestern Scotian Shelf. In the southern Gulf, where sampling was most extensive, mean vertebral number increased steadily as depth increased from 25 m to over 175 m. Mean vertebral number was also strongly related to relative length within age-classes, with the larger fish at age having more vertebrae. However, the association between vertebral number and depth could not be attributed to confounding between depth and size at age. These results indicate either unexpected mixing between neighbouring cod populations or unexpected structure at fine spatial scales within cod populations.
MECHANISTIC AND SELECTIVE CAUSES OF LIFE HISTORY TRADE-OFFS AND PLASTICITY

We discuss the mechanistic ("proximate") and selective ("ultimate") factors that cause life history trade-offs such as the trade-off between offspring quality and quantity and that between current and future reproduction. We point out that key concepts in life history theory and evolutionary biology such as negative genetic correlations and trade-offs can be understood in terms of physiological mechanisms. More specifically, negative genetic correlations causing trade-offs between life history traits are caused by hormones and their regulatory genes that have multiple and opposing, pleiotropic effects on two or more traits. Consequently, investigations of these mechanisms is a natural complement to the classical population genetical approach. We critically dissect the argument, put forward by other workers, that experimental manipulations of organismal physiology or other phenotypic traits do not reveal genetic life history trade-offs, but only reflects phenotypic plasticity. We reject this idea and discuss the proposed alternative approach: laboratory selection experiments. We point out some problems associated with laboratory selection experiments and suggest that experimental manipulations of life history traits and secondary sexual characters in natural populations is an important and invaluable empirical method if one aims to get a better understanding of life history evolution in the wild. Finally, we discuss the proximate-ultimate dichotomy, the physiology of phylogenetic constraints, the role of physiological mechanisms in population differentiation in life history trade-offs and the importance of phenotypic plasticity in shaping such trade-offs. We suggest that life history plasticity in many cases may stem from the same endocrine mechanisms (gonadotropin, gonadal steroids, and adrenal glucocorticoids) as those involved in life history trade-offs. In particular, attempts to dichotomize life history trade-offs and life history plasticity may be unrealistic as the hormones governing both life history phenomena are likely to share key mechanisms in common.
Establishment of Populus deltoides under simulated alluvial groundwater declines

-Establishment, growth and survival of seedlings of Populus deltoides subsp. monilifera (plains cottonwood) were examined in an experimental facility simulating five rates of declining alluvial groundwater. The treatments were permanent saturation, drawdown rates of 0.4, 0.7, 2.9 cm/d and immediate drainage. The experiment was conducted outdoors in planters near Fort Collins, Colorado. Seedling survival was highest under the two slowest drawdown rates and declined significantly with faster drawdown rates. The highest growth rate was associated with the drawdown rate of 0.4 cm/d, in which mean shoot height was 2.4 cm and mean root length was 39 cm 98 days after planting. Growth of shoots and roots was reduced both by saturated conditions and by the more rapid drawdown rates of 0.7 and 2.9 cm/d. No establishment was observed in the immediate drawdown treatment. Whereas maximum biomass accumulation is associated with the most gradual drawdown or saturated conditions, seedlings establishing naturally under such conditions are also most likely to be removed by ice or subsequent flooding. Seedlings establishing in higher topographic positions, in contrast, are subject to increased mortality and reduced shoot growth, resulting from reduced soil moisture. Rapid root extension following establishment allows P. deltoides seedlings to grow across a wide range of groundwater drawdown rates, and thus a variety of positions across a gradient of riparian soil moisture. Our results indicate that in coarse alluvial sands of low fertility, 47% of germinating P. deltoides seeds were able to survive in association with a drawdown rate of 2.9 cm/d and a final water table depth of 80 cm.
Amelioration of detrimental effects of waterlogging by foliar nutrient sprays in barley.

Six barley (Hordeum vulgare L.) cultivars contrasting in their waterlogging tolerance were subjected to waterlogging for 2 weeks under glasshouse conditions. The adverse effects of waterlogging were significantly alleviated by the foliar spray of nutrients (quarter- or full-strength Hoagland solution) in all cultivars. Beneficial effects of nutrient sprays included improved shoot and root growth and reduced leaf senescence. Chlorophyll content was increased, as was net CO2 assimilation, photochemical efficiency of PSII, and adventitious root production compared with waterlogged plants with no added foliar nutrients. Auxin was found accumulated at the shoot base in waterlogged plants, and the spray of foliar nutrients significantly increased this accumulation in waterlogged plants after 14 days of treatment. Foliar application of 1-NAA also promoted the production of adventitious roots. The highest concentration of auxin was measured in the stem region between 1.2 and 1.6 cm above the shoot-root junction. Foliar nutrient application also improved nitrogen and potassium content in both shoot and root, but calcium content was hardly affected. It is concluded that the improvement of waterlogged plant growth by foliar nutrient sprays could be related to both the improved plant nutrition and increased auxin accumulation in the shoot base, responsible for development of adventitious roots.
Positional Information and Positional Signalling in Hydra

A model is proposed for regulation and regeneration of the head end of hydra in terms of positional information, which involves two gradients. One is a diffusible substance made at the head end, which may be regarded as a positional signal. The other is a more stable cellular parameter which is the positional value. The rule for head end formation is that the concentration of the diffusible substance falls a threshold amount below the positional value. This model, for which some computer simulation is provided, can account for head end formation in a wide variety of grafts. Evidence for a diffusable signal is provided by experiments in which the time/distance relationships for head inhibition by a grafted head are determined. Changes in positional value during regulation have been assayed and are much slower away from the boundary. Polarity is interpreted in terms of the interaction between the two gradients. The biochemical basis of the gradients is not known, but an approach to the problem has been made by treating hydra with a variety of chemical agents.
The impact of catastrophic channel change on freshwater mussels in the Hunter River system, Australia: a conservation assessment

1. Australia has a distinct suite of endemic freshwater mussel species, several of which are restricted to south-eastern Australia, an intensively modified region supporting much of the nation's population and where pressures on freshwater ecosystems are increasing. 2. Surveys were made of 78 sites in the Hunter River system to determine the distribution and abundance of the six mussel species occurring in the region, to identify threatening processes and to locate populations of high conservation value. 3. Mussel populations were mainly distributed in the hydrologically stable southern Barrington rivers, where those in the Williams River have the highest conservation value. Strongholds for Hyridella drapeta were found in Wollombi Brook. 4. Mussels were not detected at 40% of the sites, some of which supported mussels in the past. These were mainly reaches that have undergone river metamorphosis. 5. Where found, most mussel populations had low densities and were highly fragmented. Major threats to these remnant populations are degradation of riparian and instream condition from agricultural activities, extreme climatic events (flood and drought) and the introduced macrophyte, Salvinia molesta. 6. While threat mitigation can be achieved by habitat protection and strategies to reconnect mussel populations, managers are largely unaware of this invertebrate group. Formal recognition of regionally threatened mussel populations would do much to focus efforts on conservation. 7. The proposed construction of a large dam on the Williams River is a potential threat to the most important mussel populations in the Hunter River system. Copyright © 2009 John Wiley & Sons, Ltd.
Alterations in fatty acid composition and fluidity of cell membranes affect the accumulation of PCB congener 2,2', 5,5'-tetrachlorobiphenyl by Ralstonia eutropha H850

The effect of alterations in fatty acid composition and fluidity of cell membranes on the accumulation of PCB congener 2,2′,5,5′-tetrachlorobiphenyl (TeCB) by Ralstonia eutropha (formerly Alcaligenes eutrophus) H850 was studied. Cells of R eutropha H850 grown on either biphenyl or fructose were used. Significant increases in saturated fatty acid composition and decreases in membrane fluidity of bacteria grown on biphenyl at 28 °C were observed compared with those grown on fructose at 17 or 28 °C. The ratio of saturated fatty acids to unsaturated fatty acids and membrane fluidity of R eutropha H850 grown on biphenyl at 28 °C resembled those of cells grown on fructose at 37 °C. No inhibition effect of the uncoupler 2,4-dinitrophenol (2,4-DNP) on TeCB accumulation was observed, suggesting an energy-independent mechanism for TeCB accumulation in cells of R eutropha H850. The amount of TeCB accumulated was considerably higher in R eutropha H850 grown on fructose at 17 and 28 °C than when grown on biphenyl at 28 °C. Similar amounts of TeCB accumulated in bacteria grown on biphenyl at 28 °C as compared with those grown on fructose at 37 °C. These results suggest the alterations in fatty acid composition and membrane fluidity of R eutropha H850 may affect the accumulation of TeCB. © 2002 Society of Chemical Industry
Kwanghwana miscanthi Karun., C.H.Kuo & K.D.Hyde, gen. et sp. nov. (Phaeosphaeriaceae, Pleosporales) on Miscanthus floridulus (Labill.) Warb. ex K.Schum. & Lauterb. (Poaceae)

ABSTRACT We are studying microfungi growing on Poaceae hosts in different geographical regions and in this study we introduce Kwanghwana miscanthi Karun. , C.H. Kuo & K.D. Hyde, gen. et sp. nov., based on phylogenetic analyses of DNA sequences of four loci used in combination (three ribosomal (LSU, SSU and ITS) and one protein coding region (TEF1-α)) and on morphological characters. This new genus, including a single species isolated from Miscanthus floridulus (Labill.) Warb. ex K.Schum. & Lauterb. , is molecularly distinct from closely related genera, Neostagonosporella C.L. Yang, X.L. Xu & K.D. Hyde, Setophoma Gruyter, Aveskamp & Verkley and Edenia M.C. González, A.L. Anaya, Glenn, Saucedo & Hanlin. Kwanghwana miscanthi Karun. , C.H. Kuo & K.D. Hyde, sp. nov., also differs from Neostagonosporella and Setophoma by having subglobose ascomata, irregularly thickened peridium, cellular, septate and branched pseudoparaphyses, and fusiform, broadly fusoid, 3-septate ascospores.
Pros and Cons of Denosumab Treatment for Osteoporosis and Implication for RANKL Aptamer Therapy

Osteoporosis is age-related deterioration in bone mass and micro-architecture. Denosumab is a novel human monoclonal antibody for osteoporosis. It is a receptor activator of nuclear factor-κB ligand (RANKL) inhibitor, which binds to and inhibits osteoblast-produced RANKL, in turn reduces the binding between RANKL and osteoclast receptor RANK, therefore decreases osteoclast-mediated bone resorption and turnover. However, adverse events have also been reported after denosumab treatment, including skin eczema, flatulence, cellulitis and osteonecrosis of the jaw (ONJ). Extensive researches on the mechanism of adverse reactions caused by denosumab have been conducted and may provide new insights into developing new RANKL inhibitors that achieve better specificity and safety. Aptamers are single-stranded oligonucleotides that can bind to target molecules with high specificity and affinity. They are screened from large single-stranded synthetic oligonucleotides and enriched by a technology named SELEX (systematic evolution of ligands by exponential enrichment). With extra advantages such as high stability, low immunogenicity and easy production over antibodies, aptamers are hypothesized to be promising candidates for therapeutic drugs targeting RANKL to counteract osteoporosis. In this review, we focus on the pros and cons of denosumab treatment in osteoporosis and the implication for novel aptamer treatment.