Inferring sub-cellular localization through automated lexical analysis

MOTIVATION: The SWISS-PROT sequence database contains keywords of functional annotations for many proteins. In contrast, information about the sub-cellular localization is available for only a few proteins. Experts can often infer localization from keywords describing protein function. We developed LOCkey, a fully automated method for lexical analysis of SWISS-PROT keywords that assigns sub-cellular localization. With the rapid growth in sequence data, the biochemical characterisation of sequences has been falling behind. Our method may be a useful tool for supplementing functional information already automatically available. RESULTS: The method reached a level of more than 82% accuracy in a full cross-validation test. Due to a lack of functional annotations, we could infer localization for fewer than half of all proteins in SWISS-PROT. We applied LOCkey to annotate five entirely sequenced proteomes, namely Saccharomyces cerevisiae (yeast), Caenorhabditis elegans (worm), Drosophila melanogaster (fly), Arabidopsis thaliana (plant) and a subset of all human proteins. LOCkey found about 8000 new annotations of sub-cellular localization for these eukaryotes.     

Fully automated proteomic detection of cervical dysplasia

OBJECTIVE: To evaluate the efficacy of two biomarkers, transferrin receptor (TfR) and epidermal growth factor receptor (EGFR), for the early detection of cervical dysplasia and to explore the relationship of E5, one of three viral oncogenes expressed by the human papillomavirus (HPV), to TfR and EGFR. STUDY DESIGN: Two hundred seventy-four patients were evaluated in two separate preclinical studies using EGFR and TfR in fluorescent antibody-based assays. Cervical epithelial monolayers on glass slides were immunostained and scanned using an automated microscope platform and proprietary analysis software. Sensitivity and specificity were calculated in patient cohorts for both assays. RESULTS: Sensitivity for high grade dysplasia (HSIL) and invasive cancer in the EGFR study was 100%; specificity was 73.3%. The TfR assay, which is completely automated, demonstrated sensitivity for HSIL and invasive cancer of 96.3%, with a specificity of 81.3% in 211 patients, from five different clinical sites. CONCLUSION: Both EGFR and TfR assays detected HSIL with very high accuracy (100% and 96.3%, respectively). Specificity of the TfR assay was slightly higher (81.3%) than that of the EGFR assay (73.3%). HPV E5-induced disruption of intracellular endosomal acidification and its effects upon both EGFR and TfR may provide the specific mechanistic connection between overexpression of these receptor proteins, and HPV in fection and integration. EGFR and especially TfR show great promise as biomarkers in a highly sensitive and specific, fully automated assay for the early detection of cervical dysplasia.     

Specific-primer-directed DNA sequencing using automated fluorescence detection.

Automated fluorescence-based DNA sequence analysis offers the possibility to undertake very large scale sequencing projects. Directed strategies, such as the specific-primer-directed sequencing approach ('gene walking'), should prove useful in such projects. Described herein is a study involving the use of this approach in conjunction with automated fluorescence detection on a commercial instrument (ABI 370A DNA sequencer). This includes procedures for the rapid chemical synthesis and purification of labeled primers, the design of primer sequences that are compatible with the commercial analysis software, and automated DNA sequence analysis using such primers. A set of four fluorophore-labeled primers can be reliably synthesized in a twenty-four hour period, and greater than 300 nucleotides of analyzed new sequence obtained using this set in an additional twenty-four hours. Scale-up of these procedures to take advantage of the full capabilities of the sequencer is, at present, too slow and costly to be suitable for routine sequencing, and therefore the use of specific-primers is best suited to the closure of gaps in extended sequence produced using random cloning and sequencing strategies.     

Tendon extracellular matrix damage detection and quantification using automated edge detection analysis

The accumulation of sub-rupture tendon fatigue damage in the extracellular matrix, particularly of type I collagen fibrils, is thought to contribute to the development of tendinopathy, a chronic and degenerative pathology of tendons. Quantitative assessment of collagen fibril alignment is paramount to understanding the importance of matrix injury to cellular function and remodeling capabilities. This study presents a novel application of edge detection analysis to calculate local collagen fibril orientation in tendon. This technique incorporates damage segmentation and stratification by severity which will allow future analysis of the direct effect of matrix damage severity on the cellular and molecular response.     

Genetic diversity of the endangered Faucaria tigrina (Aizoaceae) through ISSR “fingerprinting” using automated fragment detection

Faucaria tigrina (Haw.) Schwantes is a rare, threatened succulent found exclusively on the outskirts of Grahamstown, Eastern Cape, South Africa. There are three extant populations of the species; two large ones (approximately 300 and 620 adults) separated by under two kilometres, and a third very much smaller one slightly further away. Genetic theory expects that smaller, isolated populations face a loss in genetic variation through inbreeding and genetic drift and that as declining genetic variation is linked to a loss in fitness, this species may face extinction in the long term. This study used the ISSR-PCR genetic methods linked to an automated detection platform to determine if these populations are genetically distinct, and whether they are genetically depauperate. Two ISSR primers were used, and the automated detection system identified a total of 572 ISSR loci. An UPGMA clustering analysis showed each population to be genetically distinct, and that the genetic diversity of each population does not appear to be particularly low. F. tigrina is separable from the related Faucaria britteniae L. Bolus using the ISSR method, suggesting that this method may be appropriate for systematic studies in the Aizoaceae, which comprises many genera with closely related species.     

Identification of core allosteric sites through temperature- and nucleus-invariant chemical shift covariance

Allosteric regulation is essential to control biological function. In addition, allosteric sites offer a promising venue for selective drug targeting. However, accurate mapping of allosteric sites remains challenging since allostery relies on often subtle, yet functionally relevant, structural and dynamical changes. A viable approach proposed to overcome such challenge is chemical shift covariance analysis (CHESCA). Although CHESCA offers an exhaustive map of allosteric networks, it is critical to define the core allosteric sites to be prioritized in subsequent functional studies or in the design of allosteric drugs. Here, we propose two new CHESCA-based methodologies, called temperature CHESCA (T-CHESCA) and CLASS-CHESCA, aimed at narrowing down allosteric maps to the core allosteric residues. Both T- and CLASS-CHESCAs rely on the invariance of core inter-residue correlations to changes in the chemical shifts of the active and inactive conformations interconverting in fast exchange. In T-CHESCA the chemical shifts of such states are modulated through temperature changes, while in CLASS-CHESCA through variations in the spin-active nuclei involved in pairwise correlations. T- and CLASS-CHESCAs, as well as complete-linkage CHESCA, were applied to the cAMP-binding domain of the exchange protein directly activated by cAMP (EPAC), which serves as a prototypical allosteric switch. Residues consistently identified by the three CHESCA methods were found in previously identified EPAC allosteric core sites. Hence, T-, CLASS-, and CL-CHESCA provide a toolset to establish allosteric site hierarchy and triage allosteric sites to be further analyzed by mutations and functional assays. Furthermore, the core allosteric networks selectively revealed through T- and CLASS-CHESCA are expected to facilitate the mechanistic understanding of disease-related mutations and the design of selective allosteric modulators.     

Fast multi-blind modification search through tandem mass spectrometry

With great biological interest in post-translational modifications (PTMs), various approaches have been introduced to identify PTMs using MS/MS. Recent developments for PTM identification have focused on an unrestrictive approach that searches MS/MS spectra for all known and possibly even unknown types of PTMs at once. However, the resulting expanded search space requires much longer search time and also increases the number of false positives (incorrect identifications) and false negatives (missed true identifications), thus creating a bottleneck in high throughput analysis. Here we introduce MODa, a novel "multi-blind" spectral alignment algorithm that allows for fast unrestrictive PTM searches with no limitation on the number of modifications per peptide while featuring over an order of magnitude speedup in relation to existing approaches. We demonstrate the sensitivity of MODa on human shotgun proteomics data where it reveals multiple mutations, a wide range of modifications (including glycosylation), and evidence for several putative novel modifications. Based on the reported findings, we argue that the efficiency and sensitivity of MODa make it the first unrestrictive search tool with the potential to fully replace conventional restrictive identification of proteomics mass spectrometry data.     

galaxieEST: addressing EST identity through automated phylogenetic analysis

Background  

Research involving expressed sequence tags (ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology.     

Introduction to the symposium on search and detection

[First paragraph...] Those managing biosecurity at borders or eradicating weeds, pests and diseases share a common problem. Unless the unwanted organism is highly conspicuous, it can be extremely difficult to find the first few invaders, or the last few survivors. Thus, non- detection after a search does not necessarily mean the animal, plant or disease is not in fact present. Depending on the effectiveness of the search, the absence of evidence may provide only weak evidence of absence. These uncertainties create risks for managers. Falsely declaring an unwanted organism absent when it is in fact present but undetected is likely to have adverse, and potentially major, biological, economic and political consequences. Conversely, it is obviously wasteful to continue with management and surveillance when in truth the organism is no longer present.     

Phosphopeptide detection using automated online IMAC-capillary LC-ESI-MS/MS

IMAC has become a commonly used technique in phosphoprotein analysis because of its affinity for phosphopeptides. However, the commonly used strategy combining offline IMAC enrichment with desalting procedures prior to MS/MS makes this method laborious. Here we report the development of a robust and automatic IMAC-capillary RP HPLC-ESI MS/MS technology platform, by which all procedures needed in phosphopeptide analysis including IMAC enrichment, RP HPLC separation and nanospray MS/MS can be done automatically controlled by the MassLynx program. The platform was optimized by analyzing standard phosphopeptide, and was then applied to the identification of phosphorylation sites of recombinant human telomeric repeat binding factor 1 treated with kinase in vitro, and two phosphorylation sites are defined.     

Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology

MOTIVATION: Two proteins can have a similar 3-dimensional structure and biological function, but have sequences sufficiently different that traditional protein sequence comparison algorithms do not identify their relationship. The desire to identify such relations has led to the development of more sensitive sequence alignment strategies. One such strategy is the Intermediate Sequence Search (ISS), which connects two proteins through one or more intermediate sequences. In its brute-force implementation, ISS is a strategy that repetitively uses the results of the previous query as new search seeds, making it time-consuming and difficult to analyze. RESULTS: Saturated BLAST is a package that performs ISS in an efficient and automated manner. It was developed using Perl and Perl/Tk and implemented on the LINUX operating system. Starting with a protein sequence, Saturated BLAST runs a BLAST search and identifies representative sequences for the next generation of searches. The procedure is run until convergence or until some predefined criteria are met. Saturated BLAST has a friendly graphic user interface, a built-in BLAST result parser, several multiple alignment tools, clustering algorithms and various filters for the elimination of false positives, thereby providing an easy way to edit, visualize, analyze, monitor and control the search. Besides detecting remote homologies, Saturated BLAST can be used to maintain protein family databases and to search for new genes in genomic databases.     

Accurate annotation of peptide modifications through unrestrictive database search

Proteins are extensively modified after translation due to cellular regulation, signal transduction, or chemical damage. Peptide tandem mass spectrometry can discover post-translational modifications, as well as sequence polymorphisms. Recent efforts have studied modifications at the proteomic scale. In this context, it becomes crucial to assess the accuracy of modification discovery. We discuss methods to quantify the false discovery rate from a search and demonstrate how several features can be used to distinguish valid modifications from search artifacts. We present a tool, PTMFinder, which implements these methods. We summarize the corpus of post-translational modifications identified on large data sets. Thousands of known and novel modification sites are identified, including site-specific modifications conserved over vast evolutionary distances.     

The role of highlighting in visual search through maps

Two experiments were conducted in which participants performed a vehicle dispatching task. The intensity of one information source (vehicles in Experiment 1, destinations in Experiment 2) was varied to examine the effects of salience and discrimination on both searching for and processing the information in a cluttered display. Response times were recorded for questions either requiring focused attention on or divided attention between the different information domains in the map. The results of the present experiments indicate that it is possible to declutter a display without erasing any information. By 'lowlighting' one information domain and keeping the other domain at a fairly high intensity level, dividing attention between the information sources is optimal, as is focusing attention on either of the information domains exclusively. These results are discussed in conjunction with a computational model of confusion and salience which serves to predict search and integration performance in a cluttered display with separate domains of information displayed at different intensities.     

Archeal lectins: An identification through a genomic search

Forty‐six lectin domains which have homologues among well established eukaryotic and bacterial lectins of known three‐dimensional structure, have been identified through a search of 165 archeal genomes using a multipronged approach involving domain recognition, sequence search and analysis of binding sites. Twenty‐one of them have the 7‐bladed β‐propeller lectin fold while 16 have the β‐trefoil fold and 7 the legume lectin fold. The remainder assumes the C‐type lectin, the β‐prism I and the tachylectin folds. Acceptable models of almost all of them could be generated using the appropriate lectins of known three‐dimensional structure as templates, with binding sites at one or more expected locations. The work represents the first comprehensive bioinformatic study of archeal lectins. The presence of lectins with the same fold in all domains of life indicates their ancient origin well before the divergence of the three branches. Further work is necessary to identify archeal lectins which have no homologues among eukaryotic and bacterial species. Proteins 2016; 84:21–30. © 2015 Wiley Periodicals, Inc.     

Singularity-free finite element model of bone through automated voxel-based reconstruction

Computed tomography (CT) provides both anatomical and density information about tissues. Bone is segmented by raw images and Finite Element Method (FEM) voxel-based meshing technique is achieved by matching each CT voxel to a single finite element (FE). As a consequence of the automated model reconstruction, unstable elements – i.e. elements insufficiently anchored to the whole model and thus potentially involved in partial rigid body motion – can be generated, a crucial problem in obtaining consistent FE models, hindering mechanical analyses. Through the classification of instabilities on topological connections between elements, a numerical procedure is proposed in order to avoid unconstrained models.     

Assessing ecological risk through automated drainage extraction and watershed delineation

Decision makers are frequently involved in projects requiring ecological risk definition, which are inherent to biological conservation process. It is important to recognize these risks in order to invest wisely in the management and protection of biological resources. In this matter, Geographic Information System tools and remote sensing data have been used frequently as important components in planning and management of conservation units, Rabus et al. (2003), Valeriano et al. (2009) and Valeriano et al. (2010) stressed the advantages of using data that were gathered during the Shuttle Radar Topographic Mission (SRTM) for biological and geomorphologic purposes. For Brazil's national territory, the SRTM data were refined (Valeriano, 2008) and offered as free access on the TOPODATA Project website (http://www.dsr.inpe.br/topodata) where geomorphometric information (including elevation data) at a resolution of 30 m are provided. The aim of this paper is to demonstrate an example of how TOPODATA products have been applied in order to determine the ecological risk of the border of a Conservation Unit, located in the State of São Paulo—Brazil, in the Brazilian Atlantic Forest, using automated drainage network and watershed extraction. A comparison between SRTM, TOPODATA, and ASTER DEM was carried out, showing an advantage of TOPODATA drainage network product. The vectors generated using this data are more similar to the official drainage network vectors than the drainage network extracted using ASTER-DEM or SRTM. The network product generated using ASTER-DEM produced many commission errors and the one generated using SRTM produced a poor network, with generalized vectors, less detailed than the others. The results showed that using the TOPODATA Project‘s Digital Elevation Model (DEM) can provide important data for ecological analysis and significant additional information for decision making, regarding drainage networks and watershed features. The produced map for border ecological risk showed to fit perfectly to the field work analyses, produced in other works. Furthermore, the extracted watershed polygons might furnish important information unrevealing best conservation unit boundaries, which means more efficient management and best biological conservation results.