2,777 research outputs found
Metastability of life
The physical idea of the natural origin of diseases and deaths has been
presented. The fundamental microscopical reason is the destruction of any
metastable state by thermal activation of a nucleus of a nonreversable change.
On the basis of this idea the quantitative theory of age dependence of death
probability has been constructed. The obtained simple Death Laws are very
accurately fulfilled almost for all known diseases.Comment: 3 pages, 4 figure
A combined tactile and Raman probe for tissue characterization - Design considerations
Histopathology is the golden standard for cancer diagnosis and involves the characterization of tissue components. It is labour intensive and time consuming. We have earlier proposed a combined fibre-optic near-infrared Raman spectroscopy (NIR-RS) and tactile resonance method (TRM) probe for detecting positive surgical margins as a complement to interoperative histopathology. The aims of this study were to investigate the effects of attaching an RS probe inside a cylindrical TRM sensor and to investigate how laser-induced heating of the fibre-optic NIR-RS affected the temperature of the RS probe tip and an encasing TRM sensor. In addition, the possibility to perform fibre-optic NIR-RS in a well-lit environment was investigated. A small amount of rubber latex was preferable for attaching the thin RS probe inside the TRM sensor. The temperature rise of the TRM sensor due to a fibre-optic NIR-RS at 270 mW during 20 s was less than 2 degrees C. Fibre-optic NIR-RS was feasible in a dimmed bright environment using a small light shield and automatic subtraction of a pre-recorded contaminant spectrum. The results are promising for a combined probe for tissue characterization
Use of high throughput sequencing to observe genome dynamics at a single cell level
With the development of high throughput sequencing technology, it becomes
possible to directly analyze mutation distribution in a genome-wide fashion,
dissociating mutation rate measurements from the traditional underlying
assumptions. Here, we sequenced several genomes of Escherichia coli from
colonies obtained after chemical mutagenesis and observed a strikingly
nonrandom distribution of the induced mutations. These include long stretches
of exclusively G to A or C to T transitions along the genome and orders of
magnitude intra- and inter-genomic differences in mutation density. Whereas
most of these observations can be explained by the known features of enzymatic
processes, the others could reflect stochasticity in the molecular processes at
the single-cell level. Our results demonstrate how analysis of the molecular
records left in the genomes of the descendants of an individual mutagenized
cell allows for genome-scale observations of fixation and segregation of
mutations, as well as recombination events, in the single genome of their
progenitor.Comment: 22 pages, 9 figures (including 5 supplementary), one tabl
Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers.
Microbial communities interplay with their environment through their functional traits that can be a response or an effect on the environment. Here, we explore how a functional trait-the decomposition of organic matter, can be addressed based on genetic markers and how the expression of these markers reflect ecological strategies of two fungal litter decomposer Gymnopus androsaceus and Chalara longipes. We sequenced the genomes of these two fungi, as well as their transcriptomes at different steps of Pinus sylvestris needles decomposition in microcosms. Our results highlighted that if the gene content of the two species could indicate similar potential decomposition abilities, the expression levels of specific gene families belonging to the glycoside hydrolase category reflected contrasting ecological strategies. Actually, C. longipes, the weaker decomposer in this experiment, turned out to have a high content of genes involved in cell wall polysaccharides decomposition but low expression levels, reflecting a versatile ecology compare to the more competitive G. androsaceus with high expression levels of keystone functional genes. Thus, we established that sequential expression of genes coding for different components of the decomposer machinery indicated adaptation to chemical changes in the substrate as decomposition progressed
Molecular dynamics simulation of nanocolloidal amorphous silica particles: Part II
Explicit molecular dynamics simulations were applied to a pair of amorphous
silica nanoparticles of diameter 3.2 nm immersed in a background electrolyte.
Mean forces acting between the pair of silica nanoparticles were extracted at
four different background electrolyte concentrations. Dependence of the
inter-particle potential of mean force on the separation and the silicon to
sodium ratio, as well as on the background electrolyte concentration, are
demonstrated. The pH was indirectly accounted for via the ratio of silicon to
sodium used in the simulations. The nature of the interaction of the
counter-ions with charged silica surface sites (deprotonated silanols) was also
investigated. The effect of the sodium double layer on the water ordering was
investigated for three Si:Na+ ratios. The number of water molecules trapped
inside the nanoparticles was investigated as the Si:Na+ ratio was varied.
Differences in this number between the two nanoparticles in the simulations are
attributed to differences in the calculated electric dipole moment. The
implications of the form of the potentials for aggregation are also discussed.Comment: v1. 33 pages, 7 figures (screen-quality PDF), submitted to J. Chem.
Phys v2. 15 pages, 4 tables, 6 figures. Content, author list and title
changed; single space
Glass transition in biomolecules and the liquid-liquid critical point of water
Using molecular dynamics simulations, we investigate the relation between the
dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and
thermodynamic properties of hydration water. We find that the dynamic
transition of the macromolecules, sometimes called a ``protein glass
transition'', occurs at the temperature of dynamic crossover in the diffusivity
of hydration water, and also coincides with the maxima of the isobaric specific
heat and the temperature derivative of the orientational order parameter.
We relate these findings to the hypothesis of a liquid-liquid critical point in
water. Our simulations are consistent with the possibility that the protein
glass transition results from crossing the Widom line, which is defined as the
locus of correlation length maxima emanating from the hypothesized second
critical point of water.Comment: 10 Pages, 12 figure
Ergodicity criteria for non-expanding transformations of 2-adic spheres
In the paper, we obtain necessary and sufficient conditions for ergodicity
(with respect to the normalized Haar measure) of discrete dynamical systems
on 2-adic spheres of radius
, , centered at some point from the ultrametric space of
2-adic integers . The map is
assumed to be non-expanding and measure-preserving; that is, satisfies a
Lipschitz condition with a constant 1 with respect to the 2-adic metric, and
preserves a natural probability measure on , the Haar measure
on which is normalized so that
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