242 research outputs found
Use of annexin-V to demonstrate the role of phosphatidylserine exposure in the maintenance of haemostatic balance by endothelial cells
A high-frequency, long-term data set of hydrology and sediment yield: the alpine badland catchments of Draix-Bléone Observatory
Draix-Bléone critical zone observatory was created in
1983 to study erosion processes in a mountainous badland region of the
French Southern Alps. Six catchments of varying size (0.001 to 22 km2)
and vegetation cover are equipped to measure water and sediment fluxes, both
as bedload and suspended load. This paper presents the core dataset of the
observatory, including rainfall and meteorology, high-frequency discharge
and suspended-sediment concentration, and event-scale bedload volumes. The
longest records span almost 40 years. Measurement and data-processing
methods are presented, as well as data quality assessment procedures and
examples of results. All the data presented in this paper are available on
the open repository https://doi.org/10.17180/obs.draix (Draix-Bleone
Observatory, 2015), and a 5-year snapshot is available for review at
https://doi.org/10.57745/BEYQFQ (Klotz et al., 2023).</p
Persistence of Environmental DNA in Freshwater Ecosystems
The precise knowledge of species distribution is a key step in conservation biology. However, species detection can be extremely difficult in many environments, specific life stages and in populations at very low density. The aim of this study was to improve the knowledge on DNA persistence in water in order to confirm the presence of the focus species in freshwater ecosystems. Aquatic vertebrates (fish: Siberian sturgeon and amphibian: Bullfrog tadpoles) were used as target species. In control conditions (tanks) and in the field (ponds), the DNA detectability decreases with time after the removal of the species source of DNA. DNA was detectable for less than one month in both conditions. The density of individuals also influences the dynamics of DNA detectability in water samples. The dynamics of detectability reflects the persistence of DNA fragments in freshwater ecosystems. The short time persistence of detectable amounts of DNA opens perspectives in conservation biology, by allowing access to the presence or absence of species e.g. rare, secretive, potentially invasive, or at low density. This knowledge of DNA persistence will greatly influence planning of biodiversity inventories and biosecurity surveys
Solvent Effects on Ionization Potentials of Guanine Runs and Chemically Modified Guanine in Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to Solvent
We examined the ionization potential (IP) corresponding to the free energy of a hole on duplex DNA by semiempirical molecular orbital theory with a continuum solvent model. As for the contiguous guanines (a guanine run), we found that the IP in the gas phase significantly decreases with the increasing number of nucleotide pairs of the guanine run, whereas the IP in water (OP, oxidation potential) only slightly does. The latter result is consistent with the experimental result for DNA oligomers in water. This decrease in the IP is mainly due to the attractive electrostatic interaction between the hole and a nucleotide pair in the duplex DNA. This interaction is reduced in water, which results in the small decrease in the IP in water. This mechanism explains the discrepancy between the experimental result and the previous computational results obtained by neglecting the solvent. As for the chemically modified guanine, the previous work showed that the removal of some solvent (water) molecules due to the attachment of a neutral functional group to a guanine in a duplex DNA stabilizes the hole on the guanine. One might naively have expected the opposite case, since a polar solvent usually stabilizes ions. This mechanism also explains this unexpected stabilization of a hole as follows. When some water molecules are removed, the attractive electrostatic interaction stabilizing the hole increases, and thus, the hole is stabilized. In order to design the hole energetics by a chemical modification of DNA, this mechanism has to be taken into account and can be used. 1
Analysis of the effects of exposure to acute hypoxia on oxidative lesions and tumour progression in a transgenic mouse breast cancer model
<p>Abstract</p> <p>Background</p> <p>Tumour hypoxia is known to be a poor prognostic indicator, predictive of increased risk of metastatic disease and reduced survival. Genomic instability has been proposed as one of the potential mechanisms for hypoxic tumour progression. Both of these features are commonly found in many cancer types, but their relationship and association with tumour progression has not been examined in the same model.</p> <p>Methods</p> <p>To address this issue, we determined the effects of 6 week <it>in vivo </it>acute hypoxic exposure on the levels of mutagenic lipid peroxidation product, malondialdehyde, and 8-oxo-7,8-dihydro-2'-deoxyguanosine DNA (8-oxo-dG) lesions in the transgenic polyomavirus middle T (PyMT) breast cancer mouse model.</p> <p>Results</p> <p>We observed significantly increased plasma lipid peroxidation and 8-oxo-dG lesion levels in the hypoxia-exposed mice. Consumption of malondialdehyde also induced a significant increase in the PyMT tumour DNA lesion levels, however, these increases did not translate into enhanced tumour progression. We further showed that the <it>in vivo </it>exposure to acute hypoxia induced accumulation of F4/80 positive tumour-associated macrophages (TAMs), demonstrating a relationship between hypoxia and macrophages in an experimental model.</p> <p>Conclusion</p> <p>These data suggest that although exposure to acute hypoxia causes an increase in 8-oxo-dG lesions and TAMs in the PyMT tumours, these increases do not translate into significant changes in tumour progression at the primary or metastatic levels in this strong viral oncogene-driven breast cancer model.</p
Characterization of O2 (1Δg)-derived oxidation products of tryptophan: A combination of tandem mass spectrometry analyses and isotopic labeling studies
Seasonal variation in environmental DNA detection in sediment and water samples
The use of aquatic environmental DNA (eDNA) to detect the presence of species depends on the seasonal activity of the species in the sampled habitat. eDNA may persist in sediments for longer than it does in water, and analysing sediment could potentially extend the seasonal window for species assessment. Using the great crested newt as a model, we compare how detection probability changes across the seasons in eDNA samples collected from both pond water and pond sediments. Detection of both aquatic and sedimentary eDNA varied through the year, peaking in the summer (July), with its lowest point in the winter (January): in all seasons, detection probability of eDNA from water exceeded that from sediment. Detection probability of eDNA also varied between study areas, and according to great crested newt habitat suitability and sediment type. As aquatic and sedimentary eDNA show the same seasonal fluctuations, the patterns observed in both sample types likely reflect current or recent presence of the target species. However, given the low detection probabilities found in the autumn and winter we would not recommend using either aquatic or sedimentary eDNA for year-round sampling without further refinement and testing of the methods
Interlaboratory comparison of methodologies for the measurement of urinary 8-oxo-7,8-dihydro-2′-deoxyguanosine
A neutron solution scattering study of the structure of annexin-V and its binding to lipid vesicles.
International audienceLow-angle neutron solution scattering has been used to study the structure of annexin-V and its interaction with small single-bilayer vesicles consisting of phosphatidylserine and phosphatidylcholine at a 33:66 (mol:mol) ratio. There was no evidence for a change in the state of aggregation of annexin-V, which remained as a monomer in the presence of 3 mM-free calcium. The only difference between presence and absence of free calcium was the increase of the radius of gyration, from 19(+/- 0.4) A to 22(+/- 0.4) A in 2H2O buffer and from 19.7(+/- 1.2) A to 22.2(+/- 1.2) A in H2O buffer. The relative molecular weight, outer radius and average surface area per lipid of vesicles alone were respectively 2.5(+/- 0.5) x 10(6), 127 A and 90(+/- 19) A2. These parameters were not modified in the presence of free calcium, which testified to the absence of vesicle coalescence. The calcium-dependent binding of annexin-V was essentially interfacial and therefore did not alter significantly the structural characteristics of the vesicles. At saturation, 80(+/- 10) annexin-V molecules were bound per vesicle, the available area per molecule being 2500(+/- 300) A2 thus covering approximately 28 lipid head groups. The protein shell was approximately 35 A thick. The apparent dissociation constant was probably less than 1 nM. These data contribute to a more accurate definition of annexin-V as a possible probe of those cytodynamic events involving exposure of sequestered membrane aminophospholipids.Low-angle neutron solution scattering has been used to study the structure of annexin-V and its interaction with small single-bilayer vesicles consisting of phosphatidylserine and phosphatidylcholine at a 33:66 (mol:mol) ratio. There was no evidence for a change in the state of aggregation of annexin-V, which remained as a monomer in the presence of 3 mM-free calcium. The only difference between presence and absence of free calcium was the increase of the radius of gyration, from 19(+/- 0.4) A to 22(+/- 0.4) A in 2H2O buffer and from 19.7(+/- 1.2) A to 22.2(+/- 1.2) A in H2O buffer. The relative molecular weight, outer radius and average surface area per lipid of vesicles alone were respectively 2.5(+/- 0.5) x 10(6), 127 A and 90(+/- 19) A2. These parameters were not modified in the presence of free calcium, which testified to the absence of vesicle coalescence. The calcium-dependent binding of annexin-V was essentially interfacial and therefore did not alter significantly the structural characteristics of the vesicles. At saturation, 80(+/- 10) annexin-V molecules were bound per vesicle, the available area per molecule being 2500(+/- 300) A2 thus covering approximately 28 lipid head groups. The protein shell was approximately 35 A thick. The apparent dissociation constant was probably less than 1 nM. These data contribute to a more accurate definition of annexin-V as a possible probe of those cytodynamic events involving exposure of sequestered membrane aminophospholipids
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