Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion.

Classic molecular motion simulation techniques, such as Monte Carlo (MC) simulation, generate motion pathways one at a time and spend most of their time in the local minima of the energy landscape defined over a molecular conformation space. Their high computational cost prevents them from being used to compute ensemble properties (properties requiring the analysis of many pathways). This paper introduces stochastic roadmap simulation (SRS) as a new computational approach for exploring the kinetics of molecular motion by simultaneously examining multiple pathways. These pathways are compactly encoded in a graph, which is constructed by sampling a molecular conformation space at random. This computation, which does not trace any particular pathway explicitly, circumvents the local-minima problem. Each edge in the graph represents a potential transition of the molecule and is associated with a probability indicating the likelihood of this transition. By viewing the graph as a Markov chain, ensemble properties can be efficiently computed over the entire molecular energy landscape. Furthermore, SRS converges to the same distribution as MC simulation. SRS is applied to two biological problems: computing the probability of folding, an important order parameter that measures the "kinetic distance" of a protein's conformation from its native state; and estimating the expected time to escape from a ligand-protein binding site. Comparison with MC simulations on protein folding shows that SRS produces arguably more accurate results, while reducing computation time by several orders of magnitude. Computational studies on ligand-protein binding also demonstrate SRS as a promising approach to study ligand-protein interactions.     

SVR angiosarcomas can be rejected by CD4 costimulation dependent and CD8 costimulation independent pathways

PURPOSE: We wished to determine whether virally- induced endothelial tumors are rejected by CD4 and CD8 lymphocytes, and whether there are differences in requirements for costimulation in the rejection of these tumors by lymphocyte subsets. EXPERIMENTAL DESIGN: We have developed a model of endothelial tumorigenesis through the sequential introduction of SV40 large T antigen and oncogenic H-ras into endothelial cells. These cells (SVR cells) form highly aggressive angiosarcomas in immunocompromised mice, but do not grow in syngeneic C57BL/6 mice. Using both acute blockade with systemic administration of antibodies and mice genetically deficient in the costimulatory molecules CD28, CD40, and CD40L, we have delineated the requirements of costimulation required to reject this virally-induced endothelial tumor. RESULTS: Control of SVR angiosarcoma is mediated through T lymphocytes, and both CD4 and CD8 lymphocytes are capable of controlling SVR angiosarcoma growth in vivo. Mice genetically deficient in CD28, CD40, and CD40L were able to reject SVR tumors, but depletion of these mice of CD8, but not CD4 cells led to rapid tumor growth. This data suggests that CD4 mediated rejection has a greater dependence of costimulation than CD8 mediated rejection. Surprisingly, acute depletion of costimulatory molecules in immunocompetent C57BL/6 mice led to rapid tumor growth. CONCLUSIONS: Significant differences exist in the immune status of mice acutely depleted of costimulatory molecules versus genetically deficient mice. Our results suggest that acute depletion is more immunosuppressive than genetic depletion. Humans who undergo costimulatory blockade may require periodic surveillance for virally-induced tumors.     

Proinflammatory gene induction by platelet-activating factor mediated via its cognate nuclear receptor

It has been postulated that intracellular binding sites for platelet-activating factor (PAF) contribute to proinflammatory responses to PAF. Isolated nuclei from porcine cerebral microvascular endothelial cells (PCECs) produced PAF-molecular species in response to H(2)O(2). Using FACS analysis, we demonstrated the expression of PAF receptors on cell and nuclear surfaces of PCECs. Confocal microscopy studies performed on PCECs, Chinese hamster ovary cells stably overexpressing PAF receptors, and isolated nuclei from PCECs also showed a robust nuclear distribution of PAF receptors. Presence of PAF receptors at the cell nucleus was further revealed in brain endothelial cells by radioligand binding experiments, immunoblotting, and in situ in brain by immunoelectron microscopy. Stimulation of nuclei with methylcarbamate-PAF evoked a decrease in cAMP production and a pertussis toxin-sensitive rise in nuclear calcium, unlike observations in plasma membrane, which exhibited a pertussis toxin-insensitive elevation in inositol phosphates. Moreover, on isolated nuclei methylcarbamate-PAF evoked the expression of proinflammatory genes inducible nitric oxide synthase and cyclooxygenase-2 (COX-2) and was associated with augmented extracellular signal-regulated kinase 1/2 phosphorylation and NF-kappaB binding to the DNA consensus sequence. COX-2 expression was prevented by mitogen-activated protein kinase kinase/extracellular signal-regulated kinase 1/2 and NF-kappaB inhibitors. This study describes for the first time the nucleus as a putative organelle capable of generating PAF and expresses its receptor, which upon stimulation induces the expression of the proinflammatory gene COX-2.     

Gel beads composed of collagen reconstituted in alginate

Spherical gel beads of collagen/alginate were prepared by discharging droplets of a mixture containing collagen (1.07-1.9 mg/ml) and alginate (1.2-1.5% w/v) into 1.5% w/v CaCl2 solution at 4°C. Collagen in the gel beads was reconstituted by raising the temperature to 37°C after alginate was liquefied by citrate. Scanning electron microscopy of the beads revealed the characteristic fibrous structure of collagen. To demonstrate the application of this new technique in cell culture, GH3 rat pituitary tumor cells were entrapped and grown in the gel beads. The immobilized cells proliferated to a density of 1.95 x 106 cell/ml which is about an order of magnitude higher than that grown in the alginate beads.     

A new species of Gigaspora from desert soils of Rajasthan,India

A new species of the endogonaceous fungus Gigaspora, isolated from the Indian semi-arid region, is described. The fungus, named G. tuberculata, produces rusty-brown azygospores with septate subtending hypha. The azygospores bear warts all over the outer wall. The shape, size and general appearance of these spores resemble those of Scutellospora persica.Neeraj and A.K. Varma are with the Microbiology Unit, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India; K.G. Mukerji is with the Applied Mycology Laboratory, Botany Department, University of Delhi, Delhi 110 006, India. B.C. Sharma is with the Department of Textile Engineering, Indian Institute of Technology, New Delhi 110 016, India.     

Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors

Metabolism of living cells converts substrates into metabolic energy, redox potential and metabolic end products that are essential to maintain cellular function. The flux distribution among the various biochemical pathways is determined by the kinetic properties of enzymes which are subject to strict regulatory control. Simulation of metabolic behavior therefore requires the complete knowledge of biochemical pathways, enzyme kinetics as well as their regulation. Unfortunately, complete kinetic and regulatory information is not available for microbial cells, thus preventing accurate dynamic simulation of their metabolic behavior. However, it is possible to define wider limits on metabolic behavior based solely on flux balances of biochemical pathways. We present here comprehensive information about the catabolic pathways of the bacterium Escherichia coli. Using this biochemical database, we formulate a stoichiometric model of the bacterial network of fueling reactions. After logical structural reduction, the network consists of 53 metabolic fluxes and 30 metabolites. The solution space of this under-determined system of equations presents the bounds of metabolic flux distribution that the bacterial cell can achieve. We use specific objective functions and linear optimization to investigate the capability of E. coli catabolism to maximally produce the 12 biosynthetic precursors and three key cofactors within this solution space. For the three cofactors, the maximum yields are calculated to be 18.67 ATP, 11.6 NADH and 11 NADPH per glucose molecule, respectively. The yields of NADH and NADPH are less than 12 owing to the energy costs of importing glucose. These constraints are made explicit by the interpretation of shadow prices. The optimal yields of the 12 biosynthetic precursors are computed. Four of the 12 precursors (3-phosphoglycerate, phosphoenolpyruvate, pyruvate and oxaloacetate) can be made by E. coli with complete carbon conversion. Conversely, none of the sugar monophosphates can be made with 100% carbon conversion and analysis of the shadow prices reveals that this conversion is constrained by the energy cost of importing glucose. Three of the 12 precursors (acetyl-coA, α-ketoglutarate, and succinyl-coA) cannot be made with full carbon conversion owing to stoichiometric constraints; there is no route to these compounds without carrying out a decarboxylation reaction. Metabolite flux balances and linear optimization have thus been used to determine the catabolic capabilities of E. coli .     

Apoptosis and DNA fragmentation precede TNF-induced cytolysis in U937 cells.

The hypothesis that activation of apoptosis and DNA fragmentation is involved in TNF-mediated cytolysis of U937 tumor cells was investigated. Morphological, biochemical, and kinetic criteria established that TNF activates apoptosis as opposed to necrosis. Within 2-3 h of exposure to TNF, U937 underwent the morphological alterations characteristic of apoptosis. This was accompanied by cleavage of DNA into multiples of nucleosome size fragments. Both of these events occurred 1-2 h prior to cell death as defined by trypan blue exclusion or 51Cr release. DNA fragmentation was not a non-specific result of cell death since U937 cells lysed under hypotonic conditions did not release DNA fragments. The percentage of cells undergoing apoptosis depended on the concentration of TNF and was augmented by the addition of cycloheximide. A TNF-resistant variant derived from U937 did not undergo apoptosis in response to TNF, even in the presence of cycloheximide. Furthermore, TNF could still activate NFkB in this variant, suggesting that this pathway is not involved in TNF-mediated cytotoxicity. Two agents known to inhibit TNF-mediated cytotoxicity, ZnSO4 and 3-aminobenzamide, were shown to inhibit TNF-induced apoptosis. Taken altogether, these data support the hypothesis that activation of apoptosis is at least one essential step in the TNF lytic pathway in the U937 model system.     

Morphogenetic and apoptotic changes in diabetic cataract: Prevention by pyruvate

Studies have been conducted to ascertain the preventive effect of pyruvate against diabetes induced damage to DNA and associated morphogenetic changes in the mouse lens. Such changes were characterized by DNA nicks as well as by gross morphological changes in the nuclei, evident respectively by TUNEL and Hoechst staining procedures. Morphogenetic changes were also apparent by abnormal diferentiation of the germinal epithelial cells and errors in their migratory pathway. These changes were prevented by simultaneous administration of pyruvate to the diabetic animals. The preventive effect of this agent is attributable to its property of scavenging oxy-radicals generated by high levels of the sugars.     

Dynein: An ancient motor protein involved in multiple modes of transport

Cytoplasmic dynein has long been thought to be responsible for retrograde axonal transport. As the number of cellular roles for this multifunctional protein has expanded, the complexity of its contribution to axonal transport has increased. In this article the increasing evidence for a role for cytoplasmic dynein in anterograde as well as retrograde transport is discussed. The current status of the complex dynein cargo-binding mechanism is evaluated. Finally, recent genetic evidence supporting a role in axonal transport and revealing a role in neurodegenerative conditions is reviewed.