1,430 research outputs found
Constraints, Histones, and the 30 Nanometer Spiral
We investigate the mechanical stability of a segment of DNA wrapped around a
histone in the nucleosome configuration. The assumption underlying this
investigation is that the proper model for this packaging arrangement is that
of an elastic rod that is free to twist and that writhes subject to mechanical
constraints. We find that the number of constraints required to stabilize the
nuclesome configuration is determined by the length of the segment, the number
of times the DNA wraps around the histone spool, and the specific constraints
utilized. While it can be shown that four constraints suffice, in principle, to
insure stability of the nucleosome, a proper choice must be made to guarantee
the effectiveness of this minimal number. The optimal choice of constraints
appears to bear a relation to the existence of a spiral ridge on the surface of
the histone octamer. The particular configuration that we investigate is
related to the 30 nanometer spiral, a higher-order organization of DNA in
chromatin.Comment: ReVTeX, 15 pages, 18 figure
Sequence Effects on DNA Entropic Elasticity
DNA stretching experiments are usually interpreted using the worm-like chain
model; the persistence length A appearing in the model is then interpreted as
the elastic stiffness of the double helix. In fact the persistence length
obtained by this method is a combination of bend stiffness and intrinsic bend
effects reflecting sequence information, just as at zero stretching force. This
observation resolves the discrepancy between the value of A measured in these
experiments and the larger ``dynamic persistence length'' measured by other
means. On the other hand, the twist persistence length deduced from
torsionally-constrained stretching experiments suffers no such correction. Our
calculation is very simple and analytic; it applies to DNA and other polymers
with weak intrinsic disorder.Comment: LaTeX; postscript available at
http://dept.physics.upenn.edu/~nelson/index.shtm
N-[4-Cyano-3-(trifluoromethyl)phenyl]-2-methoxybenzamide
In the title compound, C16H11F3N2O2, the carboxamide group connecting the two aromatic rings is in a syn-periplanar configuration; the molecule is non-planar; the dihedral angle between the two aromatic rings is 13.95 (18)°. Intramolecular N—H⋯O and C—H⋯O hydrogen bonds occur. In the crystal, molecules are linked by intermolecular C—H⋯O hydrogen bonds
SPECULOOS exoplanet search and its prototype on TRAPPIST
One of the most significant goals of modern science is establishing whether
life exists around other suns. The most direct path towards its achievement is
the detection and atmospheric characterization of terrestrial exoplanets with
potentially habitable surface conditions. The nearest ultracool dwarfs (UCDs),
i.e. very-low-mass stars and brown dwarfs with effective temperatures lower
than 2700 K, represent a unique opportunity to reach this goal within the next
decade. The potential of the transit method for detecting potentially habitable
Earth-sized planets around these objects is drastically increased compared to
Earth-Sun analogs. Furthermore, only a terrestrial planet transiting a nearby
UCD would be amenable for a thorough atmospheric characterization, including
the search for possible biosignatures, with near-future facilities such as the
James Webb Space Telescope. In this chapter, we first describe the physical
properties of UCDs as well as the unique potential they offer for the detection
of potentially habitable Earth-sized planets suitable for atmospheric
characterization. Then, we present the SPECULOOS ground-based transit survey,
that will search for Earth-sized planets transiting the nearest UCDs, as well
as its prototype survey on the TRAPPIST telescopes. We conclude by discussing
the prospects offered by the recent detection by this prototype survey of a
system of seven temperate Earth-sized planets transiting a nearby UCD,
TRAPPIST-1.Comment: Submitted as a chapter in the "Handbook of Exoplanets" (editors: H.
Deeg & J.A. Belmonte; Section Editor: N. Narita). 16 pages, 4 figure
Automated Annotation of Functional Imaging Experiments via Multi-Label Classification
Identifying the experimental methods in human neuroimaging papers is important for grouping meaningfully similar experiments for meta-analyses. Currently, this can only be done by human readers. We present the performance of common machine learning (text mining) methods applied to the problem of automatically classifying or labeling this literature. Labeling terms are from the Cognitive Paradigm Ontology (CogPO), the text corpora are abstracts of published functional neuroimaging papers, and the methods use the performance of a human expert as training data. We aim to replicate the expert’s annotation of multiple labels per abstract identifying the experimental stimuli, cognitive paradigms, response types, and other relevant dimensions of the experiments. We use several standard machine learning methods: naive Bayes (NB), k -nearest neighbor, and support vector machines (specifically SMO or sequential minimal optimization). Exact match performance ranged from only 15% in the worst cases to 78% in the best cases. NB methods combined with binary relevance transformations performed strongly and were robust to overfitting. This collection of results demonstrates what can be achieved with off-the-shelf software components and little to no pre-processing of raw text
Chromatin: a tunable spring at work inside chromosomes
This paper focuses on mechanical aspects of chromatin biological functioning.
Within a basic geometric modeling of the chromatin assembly, we give for the
first time the complete set of elastic constants (twist and bend persistence
lengths, stretch modulus and twist-stretch coupling constant) of the so-called
30-nm chromatin fiber, in terms of DNA elastic properties and geometric
properties of the fiber assembly. The computation naturally embeds the fiber
within a current analytical model known as the ``extensible worm-like rope'',
allowing a straightforward prediction of the force-extension curves. We show
that these elastic constants are strongly sensitive to the linker length, up to
1 bp, or equivalently to its twist, and might locally reach very low values,
yielding a highly flexible and extensible domain in the fiber. In particular,
the twist-stretch coupling constant, reflecting the chirality of the chromatin
fiber, exhibits steep variations and sign changes when the linker length is
varied.
We argue that this tunable elasticity might be a key feature for chromatin
function, for instance in the initiation and regulation of transcription.Comment: 38 pages 15 figure
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