30 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
Identification of a fall armyworm (Spodoptera frugiperda)-specific gene and development of a rapid and sensitive loop-mediated isothermal amplification assay
Open Access Journal; Published online: 18 Jan 2022The fall armyworm [FAW, Spodoptera frugiperda (J E Smith)], a moth native to America, has spread throughout the world since it was first discovered in Africa in 2016. The FAW is a polyphagous migratory pest that can travel over long distances using seasonal winds or typhoons because of its excellent flying ability, causing serious damage to many crops. For effective FAW control, accurate species identification is essential at the beginning of the invasion. In this study, the FAW-specific gene Sf00067 was discovered by performing bioinformatics to develop a fast and accurate tool for the species-specific diagnosis of this pest. An Sf00067 loop-mediated isothermal amplification (LAMP) assay was developed, and optimal conditions were established. The Sf00067 6 primer LAMP (Sf6p-LAMP) assay established in this study was able to diagnose various genotype-based strains of FAW captured in Korea and FAWs collected from Benin, Africa. Our FAW diagnostic protocol can be completed within 30 min, from the process of extracting genomic DNA from an egg or a 1st instar larva to species determination
Probing Polyelectrolyte Elasticity Using Radial Distribution Function
We study the effect of electrostatic interactions on the distribution
function of the end-to-end distance of a single polyelectrolyte chain in the
rodlike limit. The extent to which the radial distribution function of a
polyelectrolyte is reproduced by that of a wormlike chain with an adjusted
persistence length is investigated. Strong evidence is found for a universal
scaling formula connecting the effective persistence length of a
polyelectrolyte with its linear charge density and the Debye screening of its
self-interaction. An alternative definition of the electrostatic persistence
length is proposed based on matching of the maximum of the distribution with
that of an effective wormlike chain, as opposed to the traditional matching of
the first or the second moments of the distributions. It is shown that this
definition provides a more accurate probe of the affinity of the distribution
to that of the wormlike chains, as compared to the traditional definition. It
is also found that the length of a polyelectrolyte segment can act as a crucial
parameter in determining its elastic properties.Comment: 15 pages, 19 figure
The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
Renal cell carcinoma(RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival