SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments

MOTIVATION: The complex program of gene expression allows the cell to cope with changing genetic, developmental and environmental conditions. The accumulating large-scale measurements of gene knockout effects and molecular interactions allow us to begin to uncover regulatory and signaling pathways within the cell that connect causal to affected genes on a network of physical interactions. RESULTS: We present a novel framework, SPINE, for Signaling-regulatory Pathway INferencE. The framework aims at explaining gene expression experiments in which a gene is knocked out and as a result multiple genes change their expression levels. To this end, an integrated network of protein-protein and protein-DNA interactions is constructed, and signaling pathways connecting the causal gene to the affected genes are searched for in this network. The reconstruction problem is translated into that of assigning an activation/repression attribute with each protein so as to explain (in expectation) a maximum number of the knockout effects observed. We provide an integer programming formulation for the latter problem and solve it using a commercial solver. We validate the method by applying it to a yeast subnetwork that is involved in mating. In cross-validation tests, SPINE obtains very high accuracy in predicting knockout effects (99%). Next, we apply SPINE to the entire yeast network to predict protein effects and reconstruct signaling and regulatory pathways. Overall, we are able to infer 861 paths with confidence and assign effects to 183 genes. The predicted effects are found to be in high agreement with current biological knowledge. AVAILABILITY: The algorithm and data are available at http://cs.tau.ac.il/~roded/SPINE.html.     

Short communication. A high level of atmospheric oxygen, as occurred toward the end of the Cretaceous period, increases leaf diffusion conductance

Leaf diffusion conductance much increased when Xanthium strumarium (C3), Atriplex prostata (C3) and Flaveria pringlei (C3), F. sonorensis (C3/C4), F. floridana (C3/C4), and F. trinervia (C4) plants were grown under relatively high (28 kPa) ambient oxygen. This phenomenon, which increases sensitivity to water stress, could have adversely affected vegetation during the late Cretaceous, high O2 episode.Keywords: Palaeo-atmosphere, stomata, oxygen, Cretaceous.      

Temporal fluxomics reveals oscillations in TCA cycle flux throughout the mammalian cell cycle

Cellular metabolic demands change throughout the cell cycle. Nevertheless, a characterization of how metabolic fluxes adapt to the changing demands throughout the cell cycle is lacking. Here, we developed a temporal‐fluxomics approach to derive a comprehensive and quantitative view of alterations in metabolic fluxes throughout the mammalian cell cycle. This is achieved by combining pulse‐chase LC‐MS‐based isotope tracing in synchronized cell populations with computational deconvolution and metabolic flux modeling. We find that TCA cycle fluxes are rewired as cells progress through the cell cycle with complementary oscillations of glucose versus glutamine‐derived fluxes: Oxidation of glucose‐derived flux peaks in late G1 phase, while oxidative and reductive glutamine metabolism dominates S phase. These complementary flux oscillations maintain a constant production rate of reducing equivalents and oxidative phosphorylation flux throughout the cell cycle. The shift from glucose to glutamine oxidation in S phase plays an important role in cell cycle progression and cell proliferation.     

BioCloneDB

BioCloneDB is a user-friendly database with a web interface to assist molecular genetics laboratories in managing a local repository of sequence information linked to DNA clones. This tool is designed to assist in high-throughput sequence and gene expression projects, providing a link between both types of information. The unique feature of the application is the automation of batch sequence annotation following BLAST((R)) searches, which is supported by easy-to-use web interfaces. Furthermore, any set of sequences can be annotated against any sequence database. This replaces the need to perform and analyse individual web BLAST((R)) searches or the need to learn how to produce batch searches and perform analysis in a UNIX((R)) operating system. BioCloneDB is open-source software that can be installed on Linux or UNIX((R)) operating systems. To test the application, we used 1400 expressed sequence tags obtained from the filamentous fungus Neurospora crassa. The results were analysed and compared with published results and they show a significant change due to the accumulation of the data in the nr database (ftp://ftp.ncbi.nih.gov/blast/db/). AVAILABILITY: BioCloneDB is available for academic use along with documentation, screenshots, database scheme and readme files at http://bioclonedb.agri.huji.ac.il/ CONTACT: Oded Yarden (Oded.Yarden@huji.ac.il).     

The consequence of natural selection on genetic variation in the mouse

Laboratory mouse strains are known to have emerged from recent interbreeding between individuals of Mus musculus isolated populations. As a result of this breeding history, the collection of polymorphisms observed between laboratory mouse strains is likely to harbor the effects of natural selection between reproductively isolated populations. Until now no study has systematically investigated the consequences of this breeding history on gene evolution. Here we have used a novel, unbiased evolutionary approach to predict the founder origin of laboratory mouse strains and to assess the balance between ancient and newly emerged mutations in the founder subspecies. Our results confirm a contribution from at least four distinct subspecies. Additionally, our method allowed us to identify regions of relaxed selective constraint among laboratory mouse strains. This unique structure of variation is likely to have significant consequences on the use of mouse to find genes underlying phenotypic variation.     

Pepitope: epitope mapping from affinity-selected peptides

Identifying the epitope to which an antibody binds is central for many immunological applications such as drug design and vaccine development. The Pepitope server is a web-based tool that aims at predicting discontinuous epitopes based on a set of peptides that were affinity-selected against a monoclonal antibody of interest. The server implements three different algorithms for epitope mapping: PepSurf, Mapitope, and a combination of the two. The rationale behind these algorithms is that the set of peptides mimics the genuine epitope in terms of physicochemical properties and spatial organization. When the three-dimensional (3D) structure of the antigen is known, the information in these peptides can be used to computationally infer the corresponding epitope. A user-friendly web interface and a graphical tool that allows viewing the predicted epitopes were developed. Pepitope can also be applied for inferring other types of protein-protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure. AVAILABILITY: http://pepitope.tau.ac.il/     

Cranial neural crest cells regulate head muscle patterning and differentiation during vertebrate embryogenesis

In the vertebrate head, mesoderm cells fuse together to form a myofiber, which is attached to specific cranial neural crest (CNC)-derived skeletal elements in a highly coordinated manner. Although it has long been recognized that CNC plays a role in the formation of the head musculature, the precise molecular underpinnings of this process remain elusive. In the present study we explored the nature of the crosstalk between CNC and mesoderm cells during head muscle development, employing three models for genetic perturbations of CNC development in mice, as well as experimental ablation of CNC in chick embryos. We demonstrate that although early myogenesis is CNC-independent, the migration, patterning and differentiation of muscle precursors are regulated by CNC. In the absence of CNC cells, accumulated myoblasts are kept in a proliferative state, presumably because of an increase of Fgf8 in adjacent tissues, which leads to abnormalities in both differentiation and subsequent myofiber organization in the head. These results have uncovered a surprising degree of complexity and multiple distinct roles for CNC in the patterning and differentiation of muscles during craniofacial development. We suggest that CNC cells control craniofacial development by regulating positional interactions with mesoderm-derived muscle progenitors that together shape the cranial musculoskeletal architecture in vertebrate embryos.     

IFN-gamma regulation of vacuolar pH, cathepsin D processing and autophagy in mammary epithelial cells

In this study we examined the ability of interferon-gamma (IFN-gamma) to regulate mammary epithelial cell growth and gene expression, with particular emphasis on two genes: Maspin (a member of serine protease inhibitor superfamily), and the lysosomal aspartyl endopeptidase cathepsin D (CatD). The protein products of these genes are critically involved in regulation of multitude of biological functions in different stages of mammary tissue development and remodeling. In addition, the expression of Maspin is down-regulated in primary breast cancer and is lost in metastatic disease, while CatD is excessively produced and aberrantly secreted by breast cancer cells. We report that IFN-gamma receptors are expressed in mammary epithelial cells, and receptor engagement by IFN-gamma transduces the IFN-gamma signal via Stat-1 resulting in decreased vacuolar pH. This change in vacuolar pH alters CatD protein processing and secretion concurrent with increased Maspin secretion. In addition, IFN-gamma exerts a suppressive effect on cell growth and proliferation, and induces morphological changes in mammary epithelial cells. Our studies also reveal that breast cancer cells, which are devoid of Maspin, are refractory to IFN-gamma with respect to changes in vacuolar pH and CatD. However, Maspin transfection of breast cancer cells partially sensitizes the cells to IFN-gamma's effect, thus providing new therapeutic implications.     

Manganese enhances the phosphorylation of membrane-associated proteins isolated from barley roots

Microsomal membranes isolated from barley roots (Hordeum vulgare L. cv. CM72) contained endogenous protein phosphorylation activities that were greatly enhanced by Mn²⁺. Mg²⁺ions also stimulated protein phosphorylation, but to a lesser extent than Mn²⁺. Ca²⁺ enhanced Mg²⁺, but not Mn²⁺-dependent phosphorylation. It is proposed that this strong enhancement by Mn²⁺ may be due to a greater affinity of Mn²⁺ than either Ca²⁺ or Mg²⁺ for both the Ca²⁺ and Mg²⁺ binding sites of certain kinases. Some Mn²⁺ stimulated kinase activity was eliminated from the membrane by washing with 0.2 mol/L KCl. The KCl extract contained histone and casein kinase activities, and 4 major phosphoproteins that were phosphorylated on serine and threonine residues. Phosphorylation of a 52 kDa polypeptide corresponded with the characteristics of the histone kinase activity and may represent the autophosphorylation of a CDPK-type kinase. Phosphorylation of a 36 kDa polypeptide was Ca²⁺ stimulated and may represent the autophosphorylation of a different type of unknown kinase. Polypeptides of 18 and 15 kDa had characteristics that suggest they were autophosphorylating subunits of a membrane bound nucleotide di-phosphokinase.     

Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states

Variation in gene expression levels on a genomic scale has been detected among different strains, among closely related species, and within populations of genetically identical cells. What are the driving forces that lead to expression divergence in some genes and conserved expression in others? Here we employ flux balance analysis to address this question for metabolic genes. We consider the genome-scale metabolic model of Saccharomyces cerevisiae, and its entire space of optimal and near-optimal flux distributions. We show that this space reveals underlying evolutionary constraints on expression regulation, as well as on the conservation of the underlying gene sequences. Genes that have a high range of optimal flux levels tend to display divergent expression levels among different yeast strains and species. This suggests that gene regulation has diverged in those parts of the metabolic network that are less constrained. In addition, we show that genes that are active in a large fraction of the space of optimal solutions tend to have conserved sequences. This supports the possibility that there is less selective pressure to maintain genes that are relevant for only a small number of metabolic states.