Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes

Background Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evolutionary history. However, this is impeded by both the fragmented nature of the majority of genome assemblies and the limitations of the available software to work with them. These limitations are particularly apparent in birds, with only 10 chromosome-level assemblies reported thus far. Algorithmic approaches applied to fragmented genome assemblies can nonetheless help define patterns of chromosomal change in defined taxonomic groups. Results Here, we make use of the DESCHRAMBLER algorithm to perform the first large-scale study of ancestral chromosome structure and evolution in birds. This algorithm allows us to reconstruct the overall genome structure of 14 key nodes of avian evolution from the Avian ancestor to the ancestor of the Estrildidae, Thraupidae and Fringillidae families. Conclusions Analysis of these reconstructions provides important insights into the variability of rearrangement rates during avian evolution and allows the detection of patterns related to the chromosome distribution of evolutionary breakpoint regions. Moreover, the inclusion of microchromosomes in our reconstructions allows us to provide novel insights into the evolution of these avian chromosomes, specifically

Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models

Advances in reporters for gene expression have made it possible to document and quantify expression patterns in 2D–4D. In contrast to microarrays, which provide data for many genes but averaged and/or at low resolution, images reveal the high spatial dynamics of gene expression. Developing computational methods to compare, annotate, and model gene expression based on images is imperative, considering that available data are rapidly increasing. We have developed a sparse Bayesian factor analysis model in which the observed expression diversity of among a large set of high-dimensional images is modeled by a small number of hidden common factors. We apply this approach on embryonic expression patterns from a Drosophila RNA in situ image database, and show that the automatically inferred factors provide for a meaningful decomposition and represent common co-regulation or biological functions. The low-dimensional set of factor mixing weights is further used as features by a classifier to annotate expression patterns with functional categories. On human-curated annotations, our sparse approach reaches similar or better classification of expression patterns at different developmental stages, when compared to other automatic image annotation methods using thousands of hard-to-interpret features. Our study therefore outlines a general framework for large microscopy data sets, in which both the generative model itself, as well as its application for analysis tasks such as automated annotation, can provide insight into biological questions

Face-selective electrostatic control of hydrothermal zinc oxide nanowire synthesis

Rational control over the morphology and the functional properties of inorganic nanostructures has been a long-standing goal in the development of bottom-up device fabrication processes. We report that the geometry of hydrothermally grown zinc oxide nanowires can be tuned from platelets to needles, covering more than three orders of magnitude in aspect ratio (~0.1–100). We introduce a classical thermodynamics-based model to explain the underlying growth inhibition mechanism by means of the competitive and face-selective electrostatic adsorption of non-zinc complex ions at alkaline conditions. The performance of these nanowires rivals that of vapour-phase-grown nanostructures and their low-temperature synthesis (<60 °C) is favourable to the integration and in situ fabrication of complex and polymer-supported devices. We illustrate this capability by fabricating an all-inorganic light-emitting diode in a polymeric microfluidic manifold. Our findings indicate that electrostatic interactions in aqueous crystal growth may be systematically manipulated to synthesize nanostructures and devices with enhanced structural control.National Science Foundation (U.S.) (MIT Center for Bits and Atoms (NSF CCR0122419))Massachusetts Institute of Technology. Media LaboratoryKorea Foundation for Advanced StudiesSamsung Electronics Co. (research internship)Harvard University. Society of FellowsWallace H. Coulter Foundation (Early Career Award)Brain & Behavior Research Foundation (Young Investigator Award)National Science Foundation (U.S.)National Institutes of Health (U.S.) (Director’s New Innovator Award

Towards realistic benchmarks for multiple alignments of non-coding sequences

<p><b>Abstract</b></p> <p>Background</p> <p>With the continued development of new computational tools for multiple sequence alignment, it is necessary today to develop benchmarks that aid the selection of the most effective tools. Simulation-based benchmarks have been proposed to meet this necessity, especially for non-coding sequences. However, it is not clear if such benchmarks truly represent real sequence data from any given group of species, in terms of the difficulty of alignment tasks.</p> <p>Results</p> <p>We find that the conventional simulation approach, which relies on empirically estimated values for various parameters such as substitution rate or insertion/deletion rates, is unable to generate synthetic sequences reflecting the broad genomic variation in conservation levels. We tackle this problem with a new method for simulating non-coding sequence evolution, by relying on genome-wide distributions of evolutionary parameters rather than their averages. We then generate synthetic data sets to mimic orthologous sequences from the <it>Drosophila </it>group of species, and show that these data sets truly represent the variability observed in genomic data in terms of the difficulty of the alignment task. This allows us to make significant progress towards estimating the alignment accuracy of current tools in an absolute sense, going beyond only a relative assessment of different tools. We evaluate six widely used multiple alignment tools in the context of <it>Drosophila </it>non-coding sequences, and find the accuracy to be significantly different from previously reported values. Interestingly, the performance of most tools degrades more rapidly when there are more insertions than deletions in the data set, suggesting an asymmetric handling of insertions and deletions, even though none of the evaluated tools explicitly distinguishes these two types of events. We also examine the accuracy of two existing tools for annotating insertions versus deletions, and find their performance to be close to optimal in <it>Drosophila </it>non-coding sequences if provided with the true alignments.</p> <p>Conclusion</p> <p>We have developed a method to generate benchmarks for multiple alignments of <it>Drosophila </it>non-coding sequences, and shown it to be more realistic than traditional benchmarks. Apart from helping to select the most effective tools, these benchmarks will help practitioners of comparative genomics deal with the effects of alignment errors, by providing accurate estimates of the extent of these errors.</p

Present and Future of Surface-Enhanced Raman Scattering.

The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article

Analyses of pig genomes provide insight into porcine demography and evolution

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model

THE S1(n,π∗S_1 (n,\pi^{*}) STATE OF 2-CYCLOHEXEN-1-ONE: CAVITY RINGDOWN ABSORPTION SPECTRUM AND DFT CALCULATIONS

Author Institution: Department of Chemistry, University of Wisconsin-\mbox{Eau Claire},; Eau Claire, WI 54702; Department of Chemistry, Hanyang University, Ansan 425-791,; Korea; Department of Chemistry, Texas A \& M University, College Station, TX 77843The cavity ringdown absorption spectra of 2-cyclohexen-1-one (2CHO) and a deuterated derivative were recorded near 380 nm in a room-temperature gas cell. The weak band system ($\epsilon \approx$ 20 $M^{-1}$ ${\rm cm}^{-1}$) in this region is due to the $S_1(n, \pi$*$) \leftarrow S_0$ electronic transition. The origin band was observed at \mbox{26,081(1) ${\rm cm}^{-1}$} for the undeuterated molecule and at \mbox{26,076(1) ${\rm cm}^{-1}$} for 2CHO-2,6,6-$d_3$. For the $d_0$ isotopomer, about 40 vibronic transitions have been assigned in a region from $-300$ to \mbox{$+700$ ${\rm cm}^{-1}$} relative to the origin band. Nearly every corresponding assignment was made for the $d_3$ species. Several fundamental vibrational frequencies in the $S_1$ state, as well as the five lowest ring-puckering (or inversion) energy levels in the $S_1$ state, have been determined for the $d_0/d_3$ isotopomers. The spectroscopic results are summarized below (frequencies in cm$^{-1}$, uncertainties $\pm 0.5$ cm$^{-1}$), along with results of a DFT calculation of the $d_0$ isotopomer: \begin{center}Vibrational frequencies of 2CHO in its $S_1$ state \end{center} \vspace{-3mm} \begin{displaymath} \begin{array}{cccccccc}\hline {\rm mode} & {\rm description} & d_0 & d_0 \hspace{0.02in}(\rm DFT \hspace{0.05in} calc) & d_3 & v'_{39} & d_0 & d_3 \\ \hline \rule[0mm]{0mm}{3mm} \nu'_{39} & {\rm inversion} & 122.1 & 120.8 & 114.4 & 1 & 122.1 & 114.4 \\ \nu'_{38} & {\rm ring \hspace{0.05in} bending} & 251.9 & 249.9 & 236.9 & 2 & 243.8 & 228.6\\ \nu'_{37} & {\rm C\hspace{-0.03in}=\hspace{-0.03in}C \hspace{0.05in} twisting} & 303.3 & 298.4 & 294.6 & 3 & 364.5 & 341.8\\ \nu'_{36} & {\rm carbonyl \hspace{0.05in} deformation} & 343.9 & 341.9 & 332.0 & 4 & 485.3 & 455.3\\ & & & & & 5 & 603.6 & 565.7\\ \hline \end{array} \end{displaymath} The inversion-level spacings in the $S_1$ state indicate a barrier to planarity that is significantly higher than the 2000-cm$^{-1}$ barrier height of the ground electronic state. Work is in progress to fit an $S_1$ inversion potential to the spectroscopic data