Monday, February 9, 2009

Starting out

This is to introduce my blog and describe what I hope to accomplish.

Basically, when I find something that strikes my interest, I'll write a few thoughts about it on a new thread. I'll try to keep up with feedback (if any), but no promises.


  1. The Computational Versatility of Proteomic Signaling Networks

    Sniffers, buzzers, toggles and blinkers: dynamics of regulatory
    and signaling pathways in the cell

    Quantitative analysis ofsignaling networks

    Coupled positive and negative feedback circuits form an essential building block of cellular signaling pathways

  2. The Contents of Adenine Nucleotides, Phosphagens and
    some Glycolytic Intermediates in Resting Muscles from
    Vertebrates and Invertebrates

    Roles of the creatine kinase system and myoglobin in maintaining energetic state in the working heart -

  3. Dendritic spikes and activity-dependent synaptic plasticity

    Directional and quantitative phosphorylation networks

    Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks

  4. Quantitative genome-scale analysis of protein
    localization in an asymmetric bacterium - PNAS

  5. Cellular and subcellular localization of PDE10A, a striatum-enriched phosphodiesterase


    Phosphoinositide-metabolizing enzymes at the interface between membrane traffic and cell signalling

    Membrane lipids: where they are
    and how they behave

    The function of tight junctions in maintaining differences in lipid composition between the apical and the basolateral cell surface domains of MDCK cells.

    Complex N-Glycan Number and Degree of Branching Cooperate to Regulate Cell Proliferation and Differentiation

    The vertebrate primary cilium is a sensory organelle

    Vertebrate Smoothened functions at the primary cilium (quotes: ciliary localization

    A Core Complex of BBS Proteins Cooperates with the GTPase Rab8 to Promote Ciliary Membrane Biogenesis

    Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene

    The Chlamydomonas genome reveals the evolution of key animal and plant functions

    The Mother Centriole Plays an Instructive Role in Defining Cell Geometry

  6. Diffusion control of protein phosphorylation in signal transduction pathways

    Signaling cascades as cellular devices for spatial computations

    Signaling gradients in cascades of two-state reaction-diffusion systemsEnzyme Localization Can Drastically Affect Signal Amplification in Signal Transduction Pathways

    Intrinsic Fluctuations, Robustness, and Tunability in Signaling Cycles

    Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors

    Modeling the signaling endosome hypothesis: Why a drive to the nucleus is better than a (random) walk: timing, ca 500-1000 msec for 15 micron cell. See fig 9 for graph.

    Calcium Microdomains in Aspiny Dendrites example of localized channeling signal

    Signaling in Small Subcellular Volumes. I. Stochastic and Diffusion Effects on Individual Pathways sets lower limit on size (at fixed concentrations)

    Why the Phosphotransferase System of Escherichia coli Escapes Diffusion Limitation

  7. Plastid-to-Nucleus Retrograde Signaling

    Mitochondrial-Nuclear Communications (MITOCHONDRIA AS INTEGRATORS OF INTRACELLULAR SIGNALING: rafting localization in plasma membrane and mt)

    Perinuclear, perigranular and sub-plasmalemmal mitochondria have distinct functions in the regulation of cellular calcium transport(De)constructing Mitochondria: What For?

    Emerging functions of mammalian mitochondrial fusion and fission

    Heterologous mitochondrial DNA recombination in human cells

    Organization and dynamics of human mitochondrial DNA

    Mitochondrial Fusion in Human Cells Is Efficient, Requires the Inner Membrane Potential, and Is Mediated by Mitofusins

    Mitochondrial Regulation of Intracellular Ca2+ Signaling: More Than Just Simple Ca2+ Buffers (very localized buffering activity: helps localize responses to calcium signals)

    Mitochondria: The Hub of Cellular Ca2+ Signaling (not only localize calcium signals, but intook calcium stimulates increased energy production. Thus, calcium may be used by a variety of different processes whose onset will require more energy)

    H-ras, K-ras, and inner plasma membrane raft proteins operate in nanoclusters with differential dependence on the actin cytoskeleton (

    Dynamic molecular confinement in the plasma membrane by microdomains and the cytoskeleton meshwork

    Mitochondria: More Than Just a Powerhouse

    Mitochondrial Morphology and Dynamics in Yeast and Multicellular Eukaryotes

    Mitochondrial fusion and fission in mammals

    Mitochondria: Dynamic Organelles in Disease, Aging, and Development

    Functions and dysfunctions of mitochondrial dynamics

    Peroxisome Fission in Hansenula polymorpha Requires Mdv1 and Fis1, Two Proteins Also Involved in Mitochondrial Fission

    Transcriptional Paradigms in Mammalian Mitochondrial Biogenesis and Function

    Expression and Maintenance of Mitochondrial DNA

  8. Calcium dynamics in dendritic spines, modeling and experiments


    Modeling calcium dynamics in dendritic spines

    Calcium Signaling

    Synaptotagmin arrests the SNARE complex before triggering fast, efficient membrane fusion in response to Ca2+

    Phosphatidylinositol 4,5-bisphosphate regulates SNARE-dependent membrane fusion

    Intracellular Trafficking in the Trypanosomatids

    Intracellular Membrane Transport Systems in Trypanosoma brucei

    Resurgence of Cardiac T-Tubule Research

    t-tubules and sarcoplasmic reticulum function in cardiac ventricular myocytes

  9. Lipid Binding Domains: More than Simple Lipid Effectors

    Membrane Tubulation by Lattices of Amphiphysin

    Two distinct but interchangeable mechanisms for flipping of lipid-linked oligosaccharides

  10. The origins of phagocytosis and eukaryogenesis

    the last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner

    The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa

    The Phagosome: Compartment with a License to Kill

    The many faces of actin: matching assembly factors with cellular structures

    Arp2/3 complex interactions and actin network turnover in lamellipodia

    The Bacterial Cytoskeleton

    The Deep Archaeal Roots of Eukaryotes

    Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode

    Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode

    Components of Coated Vesicles and Nuclear Pore Complexes Share a Common Molecular Architecture

    Rooting the tree of life by transition analyses

    Eukaryotic Cells and their Cell Bodies: Cell Theory Revised



  13. Determination of cytosolic ADP and AMP concentrations and the free energy of ATP hydrolysis in human muscle and brain tissues with 31P NMR spectroscopy

    Interrelations of ATP synthesis and proton handling in ischaemically exercising human forearm muscle studied by 31P magnetic resonance spectroscopy


  15. Pharmacological Findings on the Biochemical Bases of Memory Processes: A General View

  16. Neuronal control of swimming in jellyfish: a comparative story

    Central neural circuitry in the jellyfish Aglantha: a model 'simple nervous system'

    Rhopalia are integrated parts of the central nervous system in box jellyfish

    Bilateral symmetric organization of neural elements in the visual system of a coelenterate, Tripedalia cystophora (Cubozoa)

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