Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments

Background  

Time-course microarray experiments produce vector gene expression profiles across a series of time points. Clustering genes based on these profiles is important in discovering functional related and co-regulated genes. Early developed clustering algorithms do not take advantage of the ordering in a time-course study, explicit use of which should allow more sensitive detection of genes that display a consistent pattern over time. Peddada et al. [1] proposed a clustering algorithm that can incorporate the temporal ordering using order-restricted statistical inference. This algorithm is, however, very time-consuming and hence inapplicable to most microarray experiments that contain a large number of genes. Its computational burden also imposes difficulty to assess the clustering reliability, which is a very important measure when clustering noisy microarray data.     

Envelope structure of Synechococcus sp. WH8113, a nonflagellated swimming cyanobacterium

Background  

Many bacteria swim by rotating helical flagellar filaments [1]. Waterbury et al. [15] discovered an exception, strains of the cyanobacterium Synechococcus that swim without flagella or visible changes in shape. Other species of cyanobacteria glide on surfaces [2,7]. The hypothesis that Synechococcus might swim using traveling surface waves [6,13] prompted this investigation.     

Comparative genomics of lactic acid bacteria reveals a niche-specific gene set

Background  

The recently sequenced genome of Lactobacillus helveticus DPC4571 [1] revealed a dairy organism with significant homology (75% of genes are homologous) to a probiotic bacteria Lb. acidophilus NCFM [2]. This led us to hypothesise that a group of genes could be determined which could define an organism's niche.     

On Hill et al's conjecture for calculating the subtree prune and regraft distance between phylogenies

Background  

Recently, Hill et al. [1] implemented a new software package--called SPRIT--which aims at calculating the minimum number of horizontal gene transfer events that is needed to simultaneously explain the evolution of two rooted binary phylogenetic trees on the same set of taxa. To this end, SPRIT computes the closely related so-called rooted subtree prune and regraft distance between two phylogenies. However, calculating this distance is an NP-hard problem and exact algorithms are often only applicable to small- or medium-sized problem instances. Trying to overcome this problem, Hill et al. propose a divide-and-conquer approach to speed up their algorithm and conjecture that this approach can be used to compute the rooted subtree prune and regraft distance exactly.     

Feature selection and classification for microarray data analysis: Evolutionary methods for identifying predictive genes

Background  

In the clinical context, samples assayed by microarray are often classified by cell line or tumour type and it is of interest to discover a set of genes that can be used as class predictors. The leukemia dataset of Golubet al.[1] and the NCI60 dataset of Rosset al.[2] present multiclass classification problems where three tumour types and nine cell lines respectively must be identified. We apply an evolutionary algorithm to identify the near-optimal set of predictive genes that classify the data. We also examine the initial gene selection step whereby the most informative genes are selected from the genes assayed.     

Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays

Background  

The Audic-Claverie method [1] has been and still continues to be a popular approach for detection of differentially expressed genes in the SAGE framework. The method is based on the assumption that under the null hypothesis tag counts of the same gene in two libraries come from the same but unknown Poisson distribution. The problem is that each SAGE library represents only a single measurement. We ask: Given that the tag count samples from SAGE libraries are extremely limited, how useful actually is the Audic-Claverie methodology? We rigorously analyze the A-C statistic that forms a backbone of the methodology and represents our knowledge of the underlying tag generating process based on one observation.     

The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif

Background  

Argonaute (Ago) proteins interact with small regulatory RNAs to mediate gene regulatory pathways. A recent report by Kiriakidou et al. [1] describes an MC sequence region identified in Ago2 that displays similarity to the cap-binding motif in translation initiation factor 4E (eIF4E). In a cap-bound eIF4E structure, two important aromatic residues of the motif stack on either side of a 7-methylguanosine 5'-triphosphate (m⁷Gppp) base. The corresponding Ago2 aromatic residues (F450 and F505) were hypothesized to perform the same cap-binding function. However, the detected similarity between the MC sequence and the eIF4E cap-binding motif was questionable.     

Methodology for systematic analysis and improvement of manufacturing unit process life cycle inventory (UPLCI) CO2PE! initiative (cooperative effort on process emissions in manufacturing). Part 2: case studies

Purpose  

This report presents two case studies, one for both the screening approach and the in-depth approach, demonstrating the application of the life cycle assessment-oriented methodology for systematic inventory analysis of the machine tool use phase of manufacturing unit processes, which has been developed in the framework of the CO₂PE! collaborative research programme (CO₂PE! 2011) and is described in part 1 of this paper (Kellens et al. 2011).     

Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees

Background  

Non-parametric bootstrapping is a widely-used statistical procedure for assessing confidence of model parameters based on the empirical distribution of the observed data [1] and, as such, it has become a common method for assessing tree confidence in phylogenetics [2]. Traditional non-parametric bootstrapping does not weigh each tree inferred from resampled (i.e., pseudo-replicated) sequences. Hence, the quality of these trees is not taken into account when computing bootstrap scores associated with the clades of the original phylogeny. As a consequence, traditionally, the trees with different bootstrap support or those providing a different fit to the corresponding pseudo-replicated sequences (the fit quality can be expressed through the LS, ML or parsimony score) contribute in the same way to the computation of the bootstrap support of the original phylogeny.     

Cationic hydrous thorium dioxide colloids - a useful tool for staining negatively charged surface matrices of bacteria for use in energy-filtered transmission electron microscopy

Background  

Synthesis of cationic hydrous thorium dioxide colloids (ca. 1.0 to 1.7 nm) has been originally described by Müller [22] and Groot [11] and these have been used by Groot to stain acidic glucosaminoglycans for ultrastructure research of different tissues by conventional transmission electron microscopy.     

Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server

Background  

DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2–5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study.     

Implications of considering metal bioavailability in estimates of freshwater ecotoxicity: examination of two case studies

Purpose  

Previous methods of estimating characterization factors (CFs) of metals in life cycle impact assessment (LCIA) models were based on multimedia fate, exposure, and effect models originally developed to address the potential impacts of organic chemicals. When applied to metals, the models neglect the influence of ambient chemistry on metal speciation, bioavailability and toxicity. Gandhi et al. (2010) presented a new method of calculating CFs for freshwater ecotoxicity that addresses these metal-specific issues. In this paper, we compared and assessed the consequences of using the new method versus currently available LCIA models for calculating freshwater ecotoxicity, as applied to two case studies previously examined by Gloria et al. (2006): (1) the production of copper (Cu) pipe and (2) a zinc (Zn) gutter system.     

Comment on and reply to "Analysis of variation of amplitudes in cell cycle gene expression" by Liu,Gaido and Wolfinger: On the analysis of gene expression during the normal,eukaryotic, cell cycle

Background  

The paper of Liu, Gaido and Wolfinger on gene expression during the division cycle of HeLa cells using the data of Whitfield et al. are discussed in order to see whether their analysis is related to gene expression during the division cycle.     

Embryonic stem cells and mice expressing different GFP variants for multiple non-invasive reporter usage within a single animal

Background  

Non-invasive autofluorescent reporters have revolutionized lineage labeling in an array of different organisms. In recent years green fluorescent protein (GFP) from the bioluminescent jellyfish Aequoria Victoria has gained popularity in mouse transgenic and gene targeting regimes [1]. It offers several advantages over conventional gene-based reporters, such as lacZ and alkaline phosphatase, in that its visualization does not require a chromogenic substrate and can be realized in vivo. We have previously demonstrated the utility and developmental neutrality of enhanced green fluorescent protein (EGFP) in embryonic stem (ES) cells and mice [2].     

CRK9 contributes to regulation of mitosis and cytokinesis in the procyclic form of Trypanosoma brucei

Background  

The Trypanosoma brucei cell cycle is regulated by combinations of cyclin/CRKs (cdc2 related kinases). Recently, two additional cyclins (CYC10, CYC11) and six new CRK (CRK7-12) homologues were identified in the T. brucei genome database [1,2].     

Target selection of soluble protein complexes for structural proteomics studies

Background  

Protein expression in E. coli is the most commonly used system to produce protein for structural studies, because it is fast and inexpensive and can produce large quantity of proteins. However, when proteins from other species such as mammalian are produced in this system, problems of protein expression and solubility arise [1]. Structural genomics project are currently investigating proteomics pipelines that would produce sufficient quantities of recombinant proteins for structural studies of protein complexes. To investigate how the E. coli protein expression system could be used for this purpose, we purified apoptotic binary protein complexes formed between members of the Caspase Associated Recruitment Domain (CARD) family.     

Karyopherin binding interactions and nuclear import mechanism of nuclear pore complex protein Tpr

Background  

Tpr is a large protein with an extended coiled-coil domain that is localized within the nuclear basket of the nuclear pore complex. Previous studies [1] involving antibody microinjection into mammalian cells suggested a role for Tpr in nuclear export of proteins via the CRM1 export receptor. In addition, Tpr was found to co-immunoprecipitate with importins α and β from Xenopus laevis egg extracts [2], although the function of this is unresolved. Yeast Mlp1p and Mlp2p, which are homologous to vertebrate Tpr, have been implicated in mRNA surveillance to retain unspliced mRNAs in the nucleus[3, 4]. To augment an understanding of the role of Tpr in nucleocytoplasmic trafficking, we explored the interactions of recombinant Tpr with the karyopherins CRM1, importin β and importin α by solid phase binding assays. We also investigated the conditions required for nuclear import of Tpr using an in vitro assay.     

Gene network interconnectedness and the generalized topological overlap measure

Background  

Network methods are increasingly used to represent the interactions of genes and/or proteins. Genes or proteins that are directly linked may have a similar biological function or may be part of the same biological pathway. Since the information on the connection (adjacency) between 2 nodes may be noisy or incomplete, it can be desirable to consider alternative measures of pairwise interconnectedness. Here we study a class of measures that are proportional to the number of neighbors that a pair of nodes share in common. For example, the topological overlap measure by Ravasz et al. [1] can be interpreted as a measure of agreement between the m = 1 step neighborhoods of 2 nodes. Several studies have shown that two proteins having a higher topological overlap are more likely to belong to the same functional class than proteins having a lower topological overlap. Here we address the question whether a measure of topological overlap based on higher-order neighborhoods could give rise to a more robust and sensitive measure of interconnectedness.