5,144 research outputs found
Seevolution: visualizing chromosome evolution
Summary: Genome evolution underpins all of biology, yet its principles can be difficult to communicate to the non-specialist. To facilitate broader understanding of genome evolution, we have designed an interactive 3D environment that enables visualization of diverse genome evolution processes. The system can intuitively and interactively animate mutation histories involving genome rearrangement, point mutation, recombination, insertion and deletion. Multiple organisms related by a phylogeny can be visualized simultaneously. As methods to infer evolutionary histories of genomes become increasingly complex, visualization of the evolutionary process will not only be useful for communication, but will also serve as an exploratory tool for discovering new patterns of genome evolution
Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria).
Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum Actinobacteria, isolated from a restaurant chair cushion. The assembly contains 3,791,485Â bp (G+C content of 73%) and is contained in 68 scaffolds
Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria).
Here we present the draft genome of an actinobacterium, Curtobacterium flaccumfaciens strain UCD-AKU, isolated from a residential carpet. The genome assembly contains 3,692,614Â bp in 130 contigs. This is the first member of the Curtobacterium genus to be sequenced
Hidden breakpoints in genome alignments
During the course of evolution, an organism's genome can undergo changes that
affect the large-scale structure of the genome. These changes include gene
gain, loss, duplication, chromosome fusion, fission, and rearrangement. When
gene gain and loss occurs in addition to other types of rearrangement,
breakpoints of rearrangement can exist that are only detectable by comparison
of three or more genomes. An arbitrarily large number of these "hidden"
breakpoints can exist among genomes that exhibit no rearrangements in pairwise
comparisons.
We present an extension of the multichromosomal breakpoint median problem to
genomes that have undergone gene gain and loss. We then demonstrate that the
median distance among three genomes can be used to calculate a lower bound on
the number of hidden breakpoints present. We provide an implementation of this
calculation including the median distance, along with some practical
improvements on the time complexity of the underlying algorithm.
We apply our approach to measure the abundance of hidden breakpoints in
simulated data sets under a wide range of evolutionary scenarios. We
demonstrate that in simulations the hidden breakpoint counts depend strongly on
relative rates of inversion and gene gain/loss. Finally we apply current
multiple genome aligners to the simulated genomes, and show that all aligners
introduce a high degree of error in hidden breakpoint counts, and that this
error grows with evolutionary distance in the simulation. Our results suggest
that hidden breakpoint error may be pervasive in genome alignments.Comment: 13 pages, 4 figure
Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria).
Here, we present the draft genome sequence of an actinobacterium, Dietzia sp. strain UCD-THP, isolated from a residential toilet handle. The assembly contains 3,915,613 bp. The genome sequences of only two other Dietzia species have been published, those of Dietzia alimentaria and Dietzia cinnamea
Inferring Latent Structure From Mixed Real and Categorical Relational Data
We consider analysis of relational data (a matrix), in which the rows correspond to subjects (e.g., people) and the columns correspond to attributes. The elements of the matrix may be a mix of real and categorical. Each subject and attribute is characterized by a latent binary feature vector, and an inferred matrix maps each row-column pair of binary feature vectors to an observed matrix element. The latent binary features of the rows are modeled via a multivariate Gaussian distribution with low-rank covariance matrix, and the Gaussian random variables are mapped to latent binary features via a probit link. The same type construction is applied jointly to the columns. The model infers latent, low-dimensional binary features associated with each row and each column, as well correlation structure between all rows and between all columns
Elastic and thermodynamic properties of the shape-memory alloy AuZn
The current work reports on the elastic shear moduli, internal friction, and
the specific heat of the B2 cubic ordered alloy AuZn as a function of
temperature. Measurements were made on single-crystal and polycrystalline
samples using Resonant Ultrasound Spectroscopy (RUS), semi-adiabatic
calorimetry and stress-strain measurements. Our results confirm that this alloy
exhibits the shape-memory effect and a phase transition at 64.75 K that appears
to be continuous (second-order) from the specific heat data. It is argued that
the combination of equiatomic composition and a low transformation temperature
constrain the chemical potential and its derivatives to exhibit behavior that
lies at the borderline between that of a first-order (discontinuous) and a
continuous phase transition. The acoustic dissipation does not peak at the
transtion temperature as expected, but shows a maximum well into the
low-temperature phase. The Debye temeprature value of 219 K, obtained from the
low-temperature specific heat data is in favorable agreement with that
determined from the acoustic data (207 K) above the transition.Comment: 25 pages, 6 figures, submitted to Phys. Rev.
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