EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

<p>Abstract</p> <p>Background</p> <p>Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds.</p> <p>Results</p> <p>We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization.</p> <p>Conclusion</p> <p>EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.</p

Strong exciton-photon coupling with colloidal nanoplatelets in an open microcavity

Colloidal semiconductor nanoplatelets exhibit quantum size effects due to their thickness of only few monolayers, together with strong optical band-edge transitions facilitated by large lateral extensions. In this article we demonstrate room temperature strong coupling of the light and heavy hole exciton transitions of CdSe nanoplatelets with the photonic modes of an open planar microcavity. Vacuum Rabi splittings of $66 \pm 1$ meV and $58 \pm 1$ meV are observed for the heavy and light hole excitons respectively, together with a polariton-mediated hybridisation of both transitions. By measuring the concentration of platelets in the film we compute the transition dipole moment of a nanoplatelet exciton to be $\mu = (575 \pm 110)$ D. The large oscillator strength and fluorescence quantum yield of semiconductor nanoplatelets provide a perspective towards novel photonic devices, combining polaritonic and spinoptronic effects.Comment: 9 pages, 4 figure

A data processing module for acoustic doppler current meters

This report describes the development of a Data Processing Module (DPM) designed for use with an RD Instruments Acoustic Doppler Current Meter (ADCM). The DPM is a self-powered unit in its own pressure case and its use requires no modification to the current meter. The motivation for this work was the desire for real-time monitoring and data transmission from an ADCM deployed at a remote site. The DPM serves as an interface between the ADCM and a satellite telemetry package consisting of a controller, an Argos Platform Transmit Terminal, and an antenna. The DPM accepts the data stream from the ADCM, processes the data and sends out the processed data upon request from the telemetry controller. The output of the ADCM is processed by eliminating unnecessary data combining quality control information into a small number of summary parameters, and averaging the remaining data in depth and time. For the implementation described here, eight data records of 719 bytes each, output from the ADCM at 15 minute intervals, were processed and averged over 2 hr intervals to produce a 34 byte output array.Funding was provided by the Office of Naval Research under Contract No. N00014-89-J-1288

BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results

<p>Abstract</p> <p>Background</p> <p>High-throughput screening (HTS) is one of the main strategies to identify novel entry points for the development of small molecule chemical probes and drugs and is now commonly accessible to public sector research. Large amounts of data generated in HTS campaigns are submitted to public repositories such as PubChem, which is growing at an exponential rate. The diversity and quantity of available HTS assays and screening results pose enormous challenges to organizing, standardizing, integrating, and analyzing the datasets and thus to maximize the scientific and ultimately the public health impact of the huge investments made to implement public sector HTS capabilities. Novel approaches to organize, standardize and access HTS data are required to address these challenges.</p> <p>Results</p> <p>We developed the first ontology to describe HTS experiments and screening results using expressive description logic. The BioAssay Ontology (BAO) serves as a foundation for the standardization of HTS assays and data and as a semantic knowledge model. In this paper we show important examples of formalizing HTS domain knowledge and we point out the advantages of this approach. The ontology is available online at the NCBO bioportal <url>http://bioportal.bioontology.org/ontologies/44531</url>.</p> <p>Conclusions</p> <p>After a large manual curation effort, we loaded BAO-mapped data triples into a RDF database store and used a reasoner in several case studies to demonstrate the benefits of formalized domain knowledge representation in BAO. The examples illustrate semantic querying capabilities where BAO enables the retrieval of inferred search results that are relevant to a given query, but are not explicitly defined. BAO thus opens new functionality for annotating, querying, and analyzing HTS datasets and the potential for discovering new knowledge by means of inference.</p

The relationship between forest cover and diet quality:a case study of rural southern Malawi

Peer reviewedPublisher PD

Effects of deer on woodland structure revealed through terrestrial laser scanning

1. Terrestrial laser scanning (TLS) captures the three-dimensional structure of habitats. Compared to traditional methods of forest mensuration, it allows quantification of structure at increased resolution, and the derivation of novel metrics with which to inform ecological studies and habitat management. 2. Lowland woodlands in the UK have altered in structure over the last century due to increased abundance of deer and a decline in management. We compared whole-canopy profiles between woodlands with high (>10 deer km−2) and low deer density (c. 1 deer km−2), and in stands with and without records of management interventions in the last 20 years, providing a test case for the application of TLS in habitat assessment for conservation and management. 3. Forty closed-canopy lowland woodlands (height range 16·5–29·4 m) were surveyed using TLS in two regions of the UK, divided into areas of high- and low-deer abundance, and between plots which had been recently managed or were unmanaged. Three-dimensional reconstructions of the woodlands were created to document the density of foliage and stem material across the entire vertical span of the canopy. 4. There was a 68% lower density of understorey foliage (0·5–2 m above-ground) in high-deer woodlands, consistent in both regions. Despite this, total amounts of foliage detected across the full canopy did not differ between deer density levels. High-deer sites were 5 m taller overall and differed in the distribution of foliage across their vertical profile. Managed woodlands, in contrast, exhibited relatively minor differences from controls, including a lower quantity of stem material at heights from 2 to 5 m, but no difference in foliage density. All main effects were replicated equally in both regions despite notable differences in stand structures between them. 5. Synthesis and applications. Terrestrial laser scanning allows ecologists to move beyond two-dimensional measures of vegetation structure and quantify patterns across complex, heterogeneous, three-dimensional habitats. Our findings suggest that reduction of deer populations is likely to have a strong impact on woodland structures and aid in restoring the complex understorey habitats required by many birds, whereas management interventions as currently practiced have limited and inconsistent effects

Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays

Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. A total of 3442 genes, called the set M AD, were found to be either up- or down-regulated by at least 2-fold between the two phenotypes. Genes assigned to a particular gene ontology term were found, in many cases, to be significantly unevenly distributed between the genes in and outside M AD. Terms that were overrepresented in M AD included functions directly implicated in the cancer cell metabolism. Based on their functional roles and expression profiles, genes in M AD were grouped into likely co-regulated gene sets. Highly conserved sequences in the 5 kb region upstream of the genes in these sets were identified with the motif discovery tool, MoDEL. Potential oncogenic transcription factors and their corresponding binding sites were identified in these conserved regions using the TRANSFAC 8.3 database. Several of the transcription factors identified in this study have been shown elsewhere to be involved in oncogenic processes. This study searched beyond phenotypic gene expression profiles in cancer cells, in order to identify the more important regulatory transcription factors that caused these aberrations in gene expressio

Transcriptional Response of Two Core Photosystem Genes in Symbiodinium spp. Exposed to Thermal Stress

Mutualistic symbioses between scleractinian corals and endosymbiotic dinoflagellates (Symbiodinium spp.) are the foundation of coral reef ecosystems. For many coral-algal symbioses, prolonged episodes of thermal stress damage the symbiont\u27s photosynthetic capability, resulting in its expulsion from the host. Despite the link between photosynthetic competency and symbiont expulsion, little is known about the effect of thermal stress on the expression of photosystem genes in Symbiodinium. This study used real-time PCR to monitor the transcript abundance of two important photosynthetic reaction center genes, psbA(encoding the D1 protein of photosystem II) and psaA (encoding the P700 protein of photosystem I), in four cultured isolates (representing ITS2-types A13, A20, B1, and F2) and two in hospite Symbiodinium spp. within the coral Pocillopora spp. (ITS2-types C1b-c and D1). Both cultured and in hospite Symbiodinium samples were exposed to elevated temperatures (32°C) over a 7-day period and examined for changes in photochemistry and transcript abundance. Symbiodinium A13 and C1b-c (both thermally sensitive) demonstrated significant declines in both psbA and psaA during the thermal stress treatment, whereas the transcript levels of the other Symbiodinium types remained stable. The downregulation of both core photosystem genes could be the result of several different physiological mechanisms, but may ultimately limit repair rates of photosynthetic proteins, rendering some Symbiodinium spp. especially susceptible to thermal stress

Ab Initio No Core Shell Model - Recent Results and Further Prospects

There has been significant recent progress in solving the long-standing problems of how nuclear shell structure and collective motion emerge from underlying microscopic inter-nucleon interactions. We review a selection of recent significant results within the ab initio No Core Shell Model (NCSM) closely tied to three major factors enabling this progress: (1) improved nuclear interactions that accurately describe the experimental two-nucleon and three-nucleon interaction data; (2) advances in algorithms to simulate the quantum many-body problem with strong interactions; and (3) continued rapid development of high-performance computers now capable of performing $20 \times 10^{15}$ floating point operations per second. We also comment on prospects for further developments.Comment: Invited paper presented at NTSE-2014 and published online in the proceedings (see footnote on p.1