Expectation-Maximization Binary Clustering for Behavioural Annotation

The growing capacity to process and store animal tracks has spurred the development of new methods to segment animal trajectories into elementary units of movement. Key challenges for movement trajectory segmentation are to (i) minimize the need of supervision, (ii) reduce computational costs, (iii) minimize the need of prior assumptions (e.g. simple parametrizations), and (iv) capture biologically meaningful semantics, useful across a broad range of species. We introduce the Expectation-Maximization binary Clustering (EMbC), a general purpose, unsupervised approach to multivariate data clustering. The EMbC is a variant of the Expectation-Maximization Clustering (EMC), a clustering algorithm based on the maximum likelihood estimation of a Gaussian mixture model. This is an iterative algorithm with a closed form step solution and hence a reasonable computational cost. The method looks for a good compromise between statistical soundness and ease and generality of use (by minimizing prior assumptions and favouring the semantic interpretation of the final clustering). Here we focus on the suitability of the EMbC algorithm for behavioural annotation of movement data. We show and discuss the EMbC outputs in both simulated trajectories and empirical movement trajectories including different species and different tracking methodologies. We use synthetic trajectories to assess the performance of EMbC compared to classic EMC and Hidden Markov Models. Empirical trajectories allow us to explore the robustness of the EMbC to data loss and data inaccuracies, and assess the relationship between EMbC output and expert label assignments. Additionally, we suggest a smoothing procedure to account for temporal correlations among labels, and a proper visualization of the output for movement trajectories. Our algorithm is available as an R-package with a set of complementary functions to ease the analysis.     

RATT: Rapid Annotation Transfer Tool

Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net.     

UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents

RNA interference (RNAi) is a widely adopted tool for loss-of-function studies but RNAi results only have biological relevance if the reagents are appropriately mapped to genes. Several groups have designed and generated RNAi reagent libraries for studies in cells or in vivo for Drosophila and other species. At first glance, matching RNAi reagents to genes appears to be a simple problem, as each reagent is typically designed to target a single gene. In practice, however, the reagent–gene relationship is complex. Although the sequences of oligonucleotides used to generate most types of RNAi reagents are static, the reference genome and gene annotations are regularly updated. Thus, at the time a researcher chooses an RNAi reagent or analyzes RNAi data, the most current interpretation of the RNAi reagent–gene relationship, as well as related information regarding specificity (e.g., predicted off-target effects), can be different from the original interpretation. Here, we describe a set of strategies and an accompanying online tool, UP-TORR (for Updated Targets of RNAi Reagents; www.flyrnai.org/up-torr), useful for accurate and up-to-date annotation of cell-based and in vivo RNAi reagents. Importantly, UP-TORR automatically synchronizes with gene annotations daily, retrieving the most current information available, and for Drosophila, also synchronizes with the major reagent collections. Thus, UP-TORR allows users to choose the most appropriate RNAi reagents at the onset of a study, as well as to perform the most appropriate analyses of results of RNAi-based studies.     

Gclust:A Parallel Clustering Tool for Microbial Genomic Data

The accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources.Building databases for non-redundant reference sequences from massive microbial genomic data based on clustering analysis is essential.However,existing clustering algorithms perform poorly on long genomic sequences.In this article,we present Gclust,a parallel program for clustering complete or draft genomic sequences,where clustering is accelerated with a novel parallelization strategy and a fast sequence comparison algorithm using sparse suffix arrays(SSAs).Moreover,genome identity measures between two sequences are calculated based on their maximal exact matches(MEMs).In this paper,we demonstrate the high speed and clustering quality of Gclust by examining four genome sequence datasets.Gclust is freely available for non-commercial use at https://github.com/niu-lab/gclust.We also introduce a web server for clustering user-uploaded genomes at http://niulab.scgrid.cn/gclust.     

Thermotherapy for Harding-Passey melanoma: light and electron microscopic study

The changes of implanted Harding-Passey melanoma in C57Bl/6J mice following treatment with wholebody hyperthermia were studied. The treated tumours showed a progressive growth delay, cellular and architectural irregularities as well as cell injury characteristics. The presence of distended and irregular blood vessels, the peripheral localization of the melanosomes and the melanosome complexes were constant.     

CHAP: A Versatile Tool for the Structural and Functional Annotation of Ion Channel Pores

The control of ion channel permeation requires the modulation of energetic barriers or “gates” within their pores. However, such barriers are often simply identified from the physical dimensions of the pore. Such approaches have worked well in the past, but there is now evidence that the unusual behavior of water within narrow hydrophobic pores can produce an energetic barrier to permeation without requiring steric occlusion of the pathway. Many different ion channels have now been shown to exploit “hydrophobic gating” to regulate ion flow, and it is clear that new tools are required for more accurate functional annotation of the increasing number of ion channel structures becoming available. We have previously shown how molecular dynamics simulations of water can be used as a proxy to predict hydrophobic gates, and we now present a new and highly versatile computational tool, the Channel Annotation Package (CHAP) that implements this methodology.     

BioCluster:Tool for Identification and Clustering of Enterobacteriaceae Based on Biochemical Data

Presumptive identification of different Enterobacteriaceae species is routinely achieved based on biochemical properties. Traditional practice includes manual comparison of each biochemical property of the unknown sample with known reference samples and inference of its identity based on the maximum similarity pattern with the known samples. This process is laborintensive, time-consuming, error-prone, and subjective. Therefore, automation of sorting and similarity in calculation would be advantageous. Here we present a MATLAB-based graphical user interface(GUI) tool named Bio Cluster. This tool was designed for automated clustering and identification of Enterobacteriaceae based on biochemical test results. In this tool, we used two types of algorithms, i.e., traditional hierarchical clustering(HC) and the Improved Hierarchical Clustering(IHC), a modified algorithm that was developed specifically for the clustering and identification of Enterobacteriaceae species. IHC takes into account the variability in result of 1–47 biochemical tests within this Enterobacteriaceae family. This tool also provides different options to optimize the clustering in a user-friendly way. Using computer-generated synthetic data and some real data, we have demonstrated that Bio Cluster has high accuracy in clustering and identifying enterobacterial species based on biochemical test data. This tool can be freely downloaded at http://microbialgen.du.ac.bd/biocluster/.     

RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool (RGAAT), a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNA-seq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool (RATT), RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification, genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/ and https://github.com/wushyer/RGAAT_v2 at no cost.     

Telocytes in liver: electron microscopic and immunofluorescent evidence

Hepatic interstitial cells play a vital role in regulating essential biological processes of the liver. Telocytes (TCs), a novel type of interstitial cells firstly identified by Popescu and his coworkers, have been reported in many tissues and organs, but not yet in liver (go to http://www.telocytes.com ). We used transmission electron microscopy and immunofluorescence (double labelling for CD34 and c‐kit/CD117, or vimentin, or PDGF Receptor‐α, or β) to provide evidence for the existence of TCs in mice liver. The distribution of TCs in liver was found to be of similar density in the four hepatic lobes. In conclusion, here we show the presence of TCs in mice liver. It remains to be determined the possible roles of TCs in the control of liver homeostasis and regeneration, the more so as a close special relationship was found between TCs and hepatic putative stem (progenitor) cells.     

Melting of myosin and tropomyosin: electron microscopic observations

A method was devised to maintain a very low angle (2-3 degrees) during the metal casting of specimens for electron microscopy. With this modified rotary shadowing procedure the melting of myosin and tropomyosin (TM) was investigated. When protein solutions were sprayed on mica sheets and then heated to melt alpha-helices, myosin molecules did not show any sign of chain separation but appeared to have collapsed into loose clumps. A few molecules showed separation of the two chains at the light meromyosin-heavy meromyosin hinge region. Heating myosin in bulk solution at 65 degrees C before spraying caused extensive fusing of the myosin heads. In contrast, in the case of TM, separation of the chains appeared to occur at temperatures at which the unfolding of alpha-helices had been shown by circular dichroism. Dissolution of TM and myosin in 0.5% SDS followed by 150-fold dilution led to single chain species. This method capable of detecting single chain peptides of melting TM whose thickness is of the order of 1 nm may be applicable to the study of the structure of proteins previously not considered possible.     

Consideration of the three dimensional structure of the adenovirus hexon from electron microscopy and computer modelling

A three-dimensional model of the adenovirus hexon has been built up from electron microscopic observations and information obtained by computer modelling. It has been shown that the hexons (in upright position) are negatively stained from below and that stain layer after drying is only 1–2nm high. Thus the top, i.e. the external part, of the hexon is triangular, the waist is hexagonal and the bottom is ‘round’ with a large axial hole. The top is twisted through 30° with respect to the waist. This morphological polarity is accompanied by differences in physico-chemical properties: the top appears to be negatively charged at neutral pH, whereas the bottom is rather hydrophobic. Because of the hexagonal region at the waist of the hexon the virus capsid becomes sealed allowing passage of small molecules only, presumably via a narrow central channel.     

NORMA: The Network Makeup Artist — A Web Tool for Network Annotation Visualization

The Network Makeup Artist (NORMA) is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Precalculated annotations (e.g., Gene Ontology, Pathway enrichment, community detection, or clustering results) can be uploaded and visualized in a network, either as colored pie-chart nodes or as color-filled areas in a 2D/3D Venn-diagram-like style. In the case where no annotation exists, algorithms for automated community detection are offered. Users can adjust the network views using standard layout algorithms or allow NORMA to slightly modify them for visually better group separation. Once a network view is set, users can interactively select and highlight any group of interest in order to generate publication-ready figures. Briefly, with NORMA, users can encode three types of information simultaneously. These are 1) the network, 2) the communities or annotations of interest, and 3) node categories or expression values. Finally, NORMA offers basic topological analysis and direct topological comparison across any of the selected networks. NORMA service is available at http://norma.pavlopouloslab.info, whereas the code is available at https://github.com/PavlopoulosLab/NORMA.     

Scanning and transmission electron microscopic observations on the stomach of three mysid species (Crustacea)

Epithelial and cuticular linings of the stomach investigated in three species representing different genera of the Mysidacea are elaborated into a set of structural specializations dividing the stomach longitudinally into one dorsal and two ventral channels. The dorsal, or food, channel contains ingested food and retains coarse particles, which eventually are transported into the midgut through a funnel. The ventral, or filtration, channels, which are separated by an anterior and a posterior median ridge (anteromedianum, inferomedianum), contain fine particles and soluble materials extracted from the dorsal channel through two filter systems: primary filters, which lie anteriorly on either side of the anteromedianum, and posterior secondary filters, which are located on the inferomedianum. The final filtrate is transported into the ventral caeca or midgut glands. The ultrastructure of the cuticle lining the lumen of the stomach shows several specializations, the most prominent of which are stout spines and delicate filter devices. The epithelium is multilayered in circumscribed areas (the lateralia). The basement lamina is extremely developed in the inferomedianum. Detailed knowledge of the microscopic anatomy and the ultrastructure of the stomach allows identification of several homologous gastric structures among different peracaridean groups and in Decapoda.