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.
Monday, February 9, 2009
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The Computational Versatility of Proteomic Signaling Networks
ReplyDeleteSniffers, 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
The Contents of Adenine Nucleotides, Phosphagens and
ReplyDeletesome 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 - www.biomedcentral.com/1752-0509/3/22
Dendritic spikes and activity-dependent synaptic plasticity
ReplyDeleteDirectional and quantitative phosphorylation networks
Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks
http://synthbio.mshri.on.ca/linding.eu/Publications_files/eln001.pdf
Quantitative genome-scale analysis of protein
ReplyDeletelocalization in an asymmetric bacterium - PNAS
Cellular and subcellular localization of PDE10A, a striatum-enriched phosphodiesterase
ReplyDeleteCELL SIGNALLING DYNAMICS IN TIME AND SPACE
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
Diffusion control of protein phosphorylation in signal transduction pathways
ReplyDeleteSignaling 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
Plastid-to-Nucleus Retrograde Signaling
ReplyDeleteMitochondrial-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 (www.pnas.org/content/102/43/15500.abstract)
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
Calcium dynamics in dendritic spines, modeling and experiments
ReplyDeleteORGANELLES AND TRAFFICKING MACHINERY FOR POSTSYNAPTIC PLASTICITY
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
Lipid Binding Domains: More than Simple Lipid Effectors
ReplyDeleteMembrane Tubulation by Lattices of Amphiphysin
Two distinct but interchangeable mechanisms for flipping of lipid-linked oligosaccharides
The origins of phagocytosis and eukaryogenesis
ReplyDeletethe 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
http://jcs.biologists.org/cgi/content/full/117/13/2769
ReplyDeletehttp://jcb.rupress.org/cgi/content/full/183/4/583
http://www.nature.com/ng/journal/v29/n1/abs/ng708.html
http://hydra.icgeb.trieste.it/~pongor/biophys-homepage/Graphs/Podani.pdf
http://www.pnas.org/content/105/29/10011.full
ReplyDeleteDetermination of cytosolic ADP and AMP concentrations and the free energy of ATP hydrolysis in human muscle and brain tissues with 31P NMR spectroscopy
ReplyDeleteInterrelations of ATP synthesis and proton handling in ischaemically exercising human forearm muscle studied by 31P magnetic resonance spectroscopy
http://www.jbc.org/cgi/reprint/254/14/6538
ReplyDeleteOxidative ATP synthesis in skeletal muscle is controlled by substrate feedbackSkeletal Muscle Fatigue: Cellular MechanismsPROTECTING THE CELLULAR ENERGY STATE DURING CONTRACTIONS: ROLE OF AMP DEAMINASEAdenylate Kinase and AMP Signaling Networks: Metabolic Monitoring, Signal Communication and Body Energy Sensing RB
ReplyDeletePhilosophical Basis and Some Historical Aspects of Systems Biology: From Hegel to Noble - Applications for Bioenergetic Research
RB
Modulation of cell motility by spatial repositioning of enzymatic ATP/ADP exchange capacity RB
Pharmacological Findings on the Biochemical Bases of Memory Processes: A General View
ReplyDeleteClinical Pharmacology of Memory
ReplyDeletePathological Changes in Memory Processing
Opiate States of Memory: Receptor Mechanisms
The influence of central administration of dopaminergic and cholinergic agents on morphine-induced amnesia in morphine-sensitized mice
Amnesic trace locked into the benzodiazepine state of memory
The locus coeruleus–noradrenergic system: modulation of behavioral state and state-dependent cognitive processes
Nicotine does not produce state-dependent effects on learning in a Pavlovian appetitive goal-tracking task with rats
Neurobiology of Memory and Anxiety: From Genes to Behavior
NATURALLY ARISING CD4+ REGULATORY T CELLS FOR IMMUNOLOGIC SELF-TOLERANCE AND NEGATIVE CONTROL OF IMMUNE RESPONSES
ReplyDeleteNeuronal control of swimming in jellyfish: a comparative story
ReplyDeleteCentral 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)
Root fungi turn rock into soil
ReplyDeletePlant-driven fungal weathering: Early stages of mineral alteration at the nanometer scale paywall
The late Precambrian greening of the Earth paywall
Late Precambrian Oxygenation; Inception of the Clay Mineral Factory registration
Molecular Evidence for the Early Colonization of Land by Fungi and Plants registration
Effect of cyanobacterial growth on biotite surfaces under laboratory nutrient-limited conditions paywall
Mineralogical transformation of bioweathered granitic biotite, studied by HRTEM; evidence for a new pathway in lichen activity paywall
The early development of terrestrial ecosystems
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