380 research outputs found
Echinoderms have bilateral tendencies
Echinoderms take many forms of symmetry. Pentameral symmetry is the major
form and the other forms are derived from it. However, the ancestors of
echinoderms, which originated from Cambrian period, were believed to be
bilaterians. Echinoderm larvae are bilateral during their early development.
During embryonic development of starfish and sea urchins, the position and the
developmental sequence of each arm are fixed, implying an auxological
anterior/posterior axis. Starfish also possess the Hox gene cluster, which
controls symmetrical development. Overall, echinoderms are thought to have a
bilateral developmental mechanism and process. In this article, we focused on
adult starfish behaviors to corroborate its bilateral tendency. We weighed
their central disk and each arm to measure the position of the center of
gravity. We then studied their turning-over behavior, crawling behavior and
fleeing behavior statistically to obtain the center of frequency of each
behavior. By joining the center of gravity and each center of frequency, we
obtained three behavioral symmetric planes. These behavioral bilateral
tendencies might be related to the A/P axis during the embryonic development of
the starfish. It is very likely that the adult starfish is, to some extent,
bilaterian because it displays some bilateral propensity and has a definite
behavioral symmetric plane. The remainder of bilateral symmetry may have
benefited echinoderms during their evolution from the Cambrian period to the
present
Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress
BACKGROUND: In our previous studies, we found that the sites in prokaryotic genomes which are most susceptible to duplex destabilization under the negative superhelical stresses that occur in vivo are statistically highly significantly associated with intergenic regions that are known or inferred to contain promoters. In this report we investigate how this structural property, either alone or together with other structural and sequence attributes, may be used to search prokaryotic genomes for promoters. RESULTS: We show that the propensity for stress-induced DNA duplex destabilization (SIDD) is closely associated with specific promoter regions. The extent of destabilization in promoter-containing regions is found to be bimodally distributed. When compared with DNA curvature, deformability, thermostability or sequence motif scores within the -10 region, SIDD is found to be the most informative DNA property regarding promoter locations in the E. coli K12 genome. SIDD properties alone perform better at detecting promoter regions than other programs trained on this genome. Because this approach has a very low false positive rate, it can be used to predict with high confidence the subset of promoters that are strongly destabilized. When SIDD properties are combined with -10 motif scores in a linear classification function, they predict promoter regions with better than 80% accuracy. When these methods were tested with promoter and non-promoter sequences from Bacillus subtilis, they achieved similar or higher accuracies. We also present a strictly SIDD-based predictor for annotating promoter sequences in complete microbial genomes. CONCLUSION: In this report we show that the propensity to undergo stress-induced duplex destabilization (SIDD) is a distinctive structural attribute of many prokaryotic promoter sequences. We have developed methods to identify promoter sequences in prokaryotic genomes that use SIDD either as a sole predictor or in combination with other DNA structural and sequence properties. Although these methods cannot predict all the promoter-containing regions in a genome, they do find large sets of potential regions that have high probabilities of being true positives. This approach could be especially valuable for annotating those genomes about which there is limited experimental data
A novel DSPP mutation causes dentinogenesis imperfecta type II in a large Mongolian family
<p>Abstract</p> <p>Background</p> <p>Several studies have shown that the clinical phenotypes of dentinogenesis imperfecta type II (DGI-II) may be caused by mutations in <it>dentin sialophosphoprotein </it>(<it>DSPP</it>). However, no previous studies have documented the clinical phenotype and genetic basis of DGI-II in a Mongolian family from China.</p> <p>Methods</p> <p>We identified a large five-generation Mongolian family from China with DGI-II, comprising 64 living family members of whom 22 were affected. Linkage analysis of five polymorphic markers flanking <it>DSPP </it>gene was used to genotype the families and to construct the haplotypes of these families. All five DSPP exons including the intron-exon boundaries were PCR-amplified and sequenced in 48 members of this large family.</p> <p>Results</p> <p>All affected individuals showed discoloration and severe attrition of their teeth, with obliterated pulp chambers and without progressive high frequency hearing loss or skeletal abnormalities. No recombination was found at five polymorphic markers flanking DSPP in the family. Direct DNA sequencing identified a novel AâG transition mutation adjacent to the donor splicing site within intron 3 in all affected individuals but not in the unaffected family members and 50 unrelated Mongolian individuals.</p> <p>Conclusion</p> <p>This study identified a novel mutation (IVS3+3AâG) in <it>DSPP</it>, which caused DGI-II in a large Mongolian family. This expands the spectrum of mutations leading to DGI-II.</p
The Hubble Constant
I review the current state of determinations of the Hubble constant, which
gives the length scale of the Universe by relating the expansion velocity of
objects to their distance. There are two broad categories of measurements. The
first uses individual astrophysical objects which have some property that
allows their intrinsic luminosity or size to be determined, or allows the
determination of their distance by geometric means. The second category
comprises the use of all-sky cosmic microwave background, or correlations
between large samples of galaxies, to determine information about the geometry
of the Universe and hence the Hubble constant, typically in a combination with
other cosmological parameters. Many, but not all, object-based measurements
give values of around 72-74km/s/Mpc , with typical errors of 2-3km/s/Mpc.
This is in mild discrepancy with CMB-based measurements, in particular those
from the Planck satellite, which give values of 67-68km/s/Mpc and typical
errors of 1-2km/s/Mpc. The size of the remaining systematics indicate that
accuracy rather than precision is the remaining problem in a good determination
of the Hubble constant. Whether a discrepancy exists, and whether new physics
is needed to resolve it, depends on details of the systematics of the
object-based methods, and also on the assumptions about other cosmological
parameters and which datasets are combined in the case of the all-sky methods.Comment: Extensively revised and updated since the 2007 version: accepted by
Living Reviews in Relativity as a major (2014) update of LRR 10, 4, 200
Recommended from our members
Bioavailability in soils
The consumption of locally-produced vegetables by humans may be an important exposure pathway for soil contaminants in many urban settings and for agricultural land use. Hence, prediction of metal and metalloid uptake by vegetables from contaminated soils is an important part of the Human Health Risk Assessment procedure. The behaviour of metals (cadmium, chromium, cobalt, copper, mercury, molybdenum, nickel, lead and zinc) and metalloids (arsenic, boron and selenium) in contaminated soils depends to a large extent on the intrinsic charge, valence and speciation of the contaminant ion, and soil properties such as pH, redox status and contents of clay and/or organic matter. However, chemistry and behaviour of the contaminant in soil alone cannot predict soil-to-plant transfer. Root uptake, root selectivity, ion interactions, rhizosphere processes, leaf uptake from the atmosphere, and plant partitioning are important processes that ultimately govern the accumulation ofmetals and metalloids in edible vegetable tissues. Mechanistic models to accurately describe all these processes have not yet been developed, let alone validated under field conditions. Hence, to estimate risks by vegetable consumption, empirical models have been used to correlate concentrations of metals and metalloids in contaminated soils, soil physico-chemical characteristics, and concentrations of elements in vegetable tissues. These models should only be used within the bounds of their calibration, and often need to be re-calibrated or validated using local soil and environmental conditions on a regional or site-specific basis.Mike J. McLaughlin, Erik Smolders, Fien Degryse, and Rene Rietr
A review of elliptical and disc galaxy structure, and modern scaling laws
A century ago, in 1911 and 1913, Plummer and then Reynolds introduced their
models to describe the radial distribution of stars in `nebulae'. This article
reviews the progress since then, providing both an historical perspective and a
contemporary review of the stellar structure of bulges, discs and elliptical
galaxies. The quantification of galaxy nuclei, such as central mass deficits
and excess nuclear light, plus the structure of dark matter halos and cD galaxy
envelopes, are discussed. Issues pertaining to spiral galaxies including dust,
bulge-to-disc ratios, bulgeless galaxies, bars and the identification of
pseudobulges are also reviewed. An array of modern scaling relations involving
sizes, luminosities, surface brightnesses and stellar concentrations are
presented, many of which are shown to be curved. These 'redshift zero'
relations not only quantify the behavior and nature of galaxies in the Universe
today, but are the modern benchmark for evolutionary studies of galaxies,
whether based on observations, N-body-simulations or semi-analytical modelling.
For example, it is shown that some of the recently discovered compact
elliptical galaxies at 1.5 < z < 2.5 may be the bulges of modern disc galaxies.Comment: Condensed version (due to Contract) of an invited review article to
appear in "Planets, Stars and Stellar
Systems"(www.springer.com/astronomy/book/978-90-481-8818-5). 500+ references
incl. many somewhat forgotten, pioneer papers. Original submission to
Springer: 07-June-201
- âŠ