Elevated calpain activity in acute myelogenous leukemia correlates with decreased calpastatin expression.

Calpains are intracellular cysteine proteases that have crucial roles in many physiological and pathological processes. Elevated calpain activity has been associated with many pathological states. Calpain inhibition can be protective or lethal depending on the context. Previous work has shown that c-myc transformation regulates calpain activity by suppressing calpastatin, the endogenous negative regulator of calpain. Here, we have investigated calpain activity in primary acute myelogenous leukemia (AML) blast cells. Calpain activity was heterogeneous and greatly elevated over a wide range in AML blast cells, with no correlation to FAB classification. Activity was particularly elevated in the CD34+CD38- enriched fraction compared with the CD34+CD38+ fraction. Treatment of the cells with the specific calpain inhibitor, PD150606, induced significant apoptosis in AML blast cells but not in normal equivalent cells. Sensitivity to calpain inhibition correlated with calpain activity and preferentially targeted CD34+CD38- cells. There was no correlation between calpain activity and p-ERK levels, suggesting the ras pathway may not be a major contributor to calpain activity in AML. A significant negative correlation existed between calpain activity and calpastatin, suggesting calpastatin is the major regulator of activity in these cells. Analysis of previously published microarray data from a variety of AML patients demonstrated a significant negative correlation between calpastatin and c-myc expression. Patients who achieved a complete remission had significantly lower calpain activity than those who had no response to treatment. Taken together, these results demonstrate elevated calpain activity in AML, anti-leukemic activity of calpain inhibition and prognostic potential of calpain activity measurement.

RAxML-Light: a tool for computing terabyte phylogenies.

MOTIVATION: Due to advances in molecular sequencing and the increasingly rapid collection of molecular data, the field of phyloinformatics is transforming into a computational science. Therefore, new tools are required that can be deployed in supercomputing environments and that scale to hundreds or thousands of cores. RESULTS: We describe RAxML-Light, a tool for large-scale phylogenetic inference on supercomputers under maximum likelihood. It implements a light-weight checkpointing mechanism, deploys 128-bit (SSE3) and 256-bit (AVX) vector intrinsics, offers two orthogonal memory saving techniques and provides a fine-grain production-level message passing interface parallelization of the likelihood function. To demonstrate scalability and robustness of the code, we inferred a phylogeny on a simulated DNA alignment (1481 taxa, 20 000 000 bp) using 672 cores. This dataset requires one terabyte of RAM to compute the likelihood score on a single tree. CODE AVAILABILITY: https://github.com/stamatak/RAxML-Light-1.0.5 DATA AVAILABILITY: http://www.exelixis-lab.org/onLineMaterial.tar.bz2 CONTACT: alexandros.stamatakis@h-its.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AID and RAG1 do not contribute to lymphomagenesis in Emu c-myc transgenic mice.

DNA breaks caused by recombination-activating gene 1 (RAG1) and activation-induced cytidine deaminase (AID) induce c-myc/immunoglobulin (Ig) heavy chain chromosomal translocations and thereby stimulate lymphomagenesis. However, constitutive expression of c-myc alone is not sufficient to induce lymphomas. Because RAG1 and AID activity occurs outside of Ig genes, we assessed whether these enzymes provide the secondary genetic lesions in Emu c-myc transgenic mice to promote lymphoma development. We found that the tumor incidence and tumor phenotype in Emu c-myc transgenic mice is similar in AID+/+, AID+/- and AID-/- backgrounds in both specific pathogen-free and conventional animal facilities, indicating that AID does not contribute to lymphoma development in Emu c-myc transgenic mice. To examine the role of RAG proteins in Emu c-myc mice, we examined Emu c-myc transgenic mice that harbor the Ig-HEL heavy- and light-chain transgenes, and thus have reduced RAG expression in B cells. We found that tumor incidence was not affected by these Ig transgenes. However, we found that RAG1-/- Emu c-myc mice exhibited accelerated tumor development compared to controls. This data combined with our finding that Emu c-myc mice lived longer in the conventional facility than in the specific pathogen-free facility suggest an immune-mediated activity that suppresses lymphoma development.

A phenomenological model for atherosclerotic plaque growth and rupture.

The objective of this communication is to develop a computer-based framework for the overall coupled phenomena leading to growth and rupture of atherosclerotic plaques. The modeling is purposely simplified to expose the dominant phenomenological controlling mechanisms, and their coupled interaction. The main ingredients of the present simplified modeling approach, describing the events that occur due to the presence and oxidation of excess low-density lipoprotein (LDL) in the intima, are: (i) adhesion of monocytes to the endothelial surface, which is controlled by the intensity of the blood flow and the adhesion molecules stimulated by the excess LDL, (ii) penetration of the monocytes into the intima and subsequent inflammation of the tissue, and (iii) rupture of the plaque accompanied with some degree of thrombus formation or even subsequent occlusive thrombosis. The set of resulting coupled equations, each modeling entirely different physical events, is solved using an iterative staggering scheme, which allows the equations to be solved in a computationally convenient decoupled fashion. Theoretical convergence properties of the scheme are given as a function of physical parameters involved. A numerical example is given to illustrate the modeling approach and an a priori prediction for time to rupture as a function of arterial geometry, diameter of the monocyte, adhesion stress, bulk modulus of the ruptured wall material, blood viscosity, flow rate and mass density of the monocytes.

Sickle cell blood flow in the microcirculation.

The clinical symptomology, as well as the subclinical sequela, of sickle-cell (S-C) disease, or anemia, is thought to be largely the consequence of abnormal events in the capillaries, resulting primarily from theological changes SC erythrocytes undergo when deoxygenated. A model of the flow of such RBCs in a single capillary was formulated taking into account the principal characteristics of the disease. This has been extended to a microcirculatory bed, generated in a pseudo-random manner. S-C disease is characterized by episodic painful and debilitating clinical events, called S-C "crisis". These studies, undertaken to evaluate possible causative mechanisms, suggest that the pressure available to drive the S-C RBCs through the microcirculation might be the control parameter.

A turbulence model for pulsatile arterial flows.

Difficulties in predicting the behavior of some high Reynolds number flows in the circulatory system stem in part from the severe requirements placed on the turbulence model chosen to close the time-averaged equations of fluid motion. In particular, the successful turbulence model is required to (a) correctly capture the "nonequilibrium" effects wrought by the interactions of the organized mean-flow unsteadiness with the random turbulence, (b) correctly reproduce the effects of the laminar-turbulent transitional behavior that occurs at various phases of the cardiac cycle, and (c) yield good predictions of the near-wall flow behavior in conditions where the universal logarithmic law of the wall is known to be not valid. These requirements are not immediately met by standard models of turbulence that have been developed largely with reference to data from steady, fully turbulent flows in approximate local equilibrium. The purpose of this paper is to report on the development of a turbulence model suited for use in arterial flows. The model is of the two-equation eddy-viscosity variety with dependent variables that are zero-valued at a solid wall and vary linearly with distance from it. The effects of transition are introduced by coupling this model to the local value of the intermittency and obtaining the latter from the solution of a modeled transport equation. Comparisons with measurements obtained in oscillatory transitional flows in circular tubes show that the model produces substantial improvements over existing closures. Further pulsatile-flow predictions, driven by a mean-flow wave form obtained in a diseased human carotid artery, indicate that the intermittency-modified model yields much reduced levels of wall shear stress compared to the original, unmodified model. This result, which is attributed to the rapid growth in the thickness of the viscous sublayer arising from the severe acceleration of systole, argues in favor of the use of the model for the prediction of arterial flows.

Mast cells stimulated by membrane-bound, but not soluble, steel factor are dependent on phospholipase C activation.

The steel factor (SLF) and c-Kit growth factor/receptor pair are key molecules governing mast cell development and survival. SLF is expressed on stromal cells as a membrane-bound molecule (mSLF) which can be cleaved by proteases to release a soluble form (sSLF). We investigated the importance of phospholipase C (PLC) activation in mast cells stimulated by sSLF and mSLF. PLC antagonists U73122, neomycin sulfate and oleic acid inhibited mast cell thymidine incorporation stimulated by mSLF, but not by sSLF. These antagonists suppressed sSLF-induced Ca2+ transients but did not significantly interfere with c-Kit phosphorylation or PLC-gamma2 recruitment. p85, the regulatory subunit of phosphatidylinositol 3-kinase (PI3-kinase), was found to be efficiently recruited to c-Kit following stimulation by sSLF or mSLF. However PKB/Akt, a kinase activated by PI3-kinase products, was phosphorylated following sSLF stimulation, but not with mSLF. Taken together, these studies demonstrate the importance of PLC activation by mSLF in supporting mast cells.

Numerical analysis of flow through a severely stenotic carotid artery bifurcation.

The results of computational simulations may supplement MR and other in vivo diagnostic techniques to provide an accurate picture of the hemodynamics in particular vessels, which may help demonstrate the risks of embolism or plaque rupture posed by particular plaque deposits. In this study, a model based on an endarterectomy specimen of the plaque in a carotid bifurcation was examined. The flow conditions include steady flow at Reynolds numbers of 300, 600, and 900 as well as unsteady pulsatile flow. Both dynamic pressure and wall shear stress are very high, with shear values up to 70 N/m2, proximal to the stenosis throat in the internal carotid artery, and both vary significantly through the flow cycle. The wall shear stress gradient is also strong along the throat. Vortex shedding is observed downstream of the most severe occlusion. Two turbulence models, the Chien and Goldberg varieties of k-epsilon, are tested and evaluated for their relevance in this geometry. The Chien model better captures phenomena such as vortex shedding. The flow distal to stenosis is likely transitional, so a model that captures both laminar and turbulent behavior is needed.

West Nile encephalitis in Israel, 1999: the New York connection.

We describe two cases of West Nile (WN) encephalitis in a married couple in Tel Aviv, Israel, in 1999. Reverse transcription-polymerase chain reaction performed on a brain specimen from the husband detected a WN viral strain nearly identical to avian strains recovered in Israel in 1998 (99.9% genomic sequence homology) and in New York in 1999 (99.8%). This result supports the hypothesis that the 1999 WN virus epidemic in the United States originated from the introduction of a strain that had been circulating in Israel.

Differential stimulation of c-Kit mutants by membrane-bound and soluble Steel Factor correlates with leukemic potential.

The authors investigated the roles of PI3-kinase and PLC-gamma in stimulation by Steel Factor (SLF) through c-Kit. c-Kit mutants YF719, YF728, and a YF719/YF728 double mutant were expressed in 32D myelomonocytic cells. KitYF719 fails to recruit PI3-kinase after stimulation with SLF, whereas KitYF728 fails to stimulate PLC-gamma phosphorylation or mobilize Ca(++). Both single mutants responded mitogenically to soluble SLF (sSLF) in a manner indistinguishable from wild type (WT), although sSLF failed to stimulate or promote the survival of cells expressing the double mutant. In contrast, although cells expressing WT or YF719 were mitogenically stimulated by membrane-bound SLF (mSLF), stimulation of cells expressing KitYF728 was impaired. Similarly, cells expressing WT or YF719 receptors were stimulated by plate-bound anti-Kit antibodies, whereas cells expressing the YF728 receptor were not stimulated. Neomycin sulfate, a PLC antagonist, inhibited cells expressing YF719 receptors stimulated by sSLF. Neomycin also inhibited cells expressing the WT receptor that were stimulated by mSLF or immobilized anti-Kit antibodies but did not inhibit stimulation of cells expressing WT or YF719 receptors by sSLF. 32D cells expressing KitWT, KitYF719, or KitYF728 were injected into mice and the presence of cells was evaluated by colony assays 6 to 7 weeks later. Although both KitWT and KitYF719 expressing cells could be recovered from the spleen and bone marrow, recovery of KitYF728 cells from these organs was severely reduced. These results indicate that Kit tyrosine 728 is of particular importance for mitogenic stimulation by mSLF or immobilized ligand and is required for full maintenance of cells in vivo, likely through activation of PLC-gamma. (Blood. 2000;96:3734-3742)

Clinical significance and antibiotic resistance patterns of Leminorella spp., an emerging nosocomial pathogen.

Although Leminorella spp., members of the family Enterobacteriaceae, were previously isolated from feces and urine specimens, clinical correlates have not been studied. We conducted a retrospective study to investigate the clinical significance and disease spectrum of these organisms, as well as their antibiotic susceptibility patterns. Identification and susceptibility testing were performed by an automated system. Eighteen cases were identified retrospectively during a 28-month period (1/97 to 4/99), representing an incidence of 11 cases per 100,000 patient admissions. The medical records of 14 patients were reviewed. The average patient age was 67 years, and 78% were males. Patients had multiple and diverse underlying conditions which might have predisposed them to infection. Leminorella spp. were classified as definite pathogens in 43% of the cases, probable pathogens in 29%, and possible pathogens in 21%. In one case of asymptomatic bacteriuria, the isolate had no clinical significance. All infections but one were nosocomial. Clinical syndromes included urinary tract infection in six patients, surgical site infection in three patients, and primary bacteremia, peritonitis, respiratory tract infection, and soft tissue infection in one patient each. Isolates were uniformly susceptible to imipenem. Other beta-lactam agents had poor activity against the isolates. We conclude that Leminorella spp. are significant nosocomial pathogens that are capable of causing a variety of clinical syndromes and are resistant to multiple antibiotic agents.

Epo regulates erythroid proliferation and differentiation through distinct signaling pathways: implication for erythropoiesis and Friend virus-induced erythroleukemia.

We have recently isolated the erythroleukemic cell line, HB60-5, that proliferates in the presence of erythropoietin (Epo) and stem cell factor (SCF), but undergoes terminal differentiation in the presence of Epo alone. Ectopic expression of the ets related transcription factor Fli-1 in these cells resulted in the establishment of the Epo-dependent cell line HB60-ED that proliferates in the presence of Epo. In this study, we utilized these two cell lines to examine the signal transduction pathways that are activated in response to Epo and SCF stimulation. We demonstrate that Epo, but not SCF, phosphorylates STAT-5 in both HB60-5 and HB60-ED cells. Interestingly, SCF activates the Shc/ras pathway in HB60-5 cells while Epo does not. However, both Epo and SCF are capable of activating the Shc/ras pathway in HB60ED cells. Furthermore, enforced expression of gp55 in HB60-5 cells by means of infection with the Spleen Focus Forming virus-P (SFFV-P), confers Epo independent growth, which is associated with the up-regulation of Fli-1. Activation of the Shc/ras pathway is readily detected in gp55 expressing cells in response to both Epo and SCF, and is associated with a block in STAT-5B tyrosine phosphorylation. These results suggest that STAT-5 activation, in the absence of Shc/ras activation, plays a role in erythroid differentiation. Moreover, Fli-1 is capable of switching Epo-induced differentiation to Epo-induced proliferation, suggesting that this ets factor regulated genes whose products modulate the Epo-Epo-R signal transduction pathway.

Influence of stenosis morphology on flow through severely stenotic vessels: implications for plaque rupture.

Flow patterns and flow-related stresses contribute to the characterization of health risks, particularly the risk of plaque rupture, posed by a particular atherosclerotic stenosis. Blood flow in the presence of significant plaque deposits is investigated, and the influence of factors such as stenosis morphology and surface irregularity is evaluated. Solutions for three-dimensional, unsteady flow in these stenotic vessels are obtained for an incompressible, Newtonian fluid. The equations of motion are solved numerically using a finite volume formulation. The resulting flow patterns and shear and normal stresses are interpreted with respect to diagnostic implications, including the possibility of plaque rupture. The inadequacy of "percent stenosis" to characterize the risks posed by a particular plaque is demonstrated. Surface irregularity, stenosis aspect ratio, and the shape of the pulsatile waveform all have considerable influence on the flow field and on the stresses on the plaque. A measure of surface irregularity or plaque symmetry, in particular, may complement percent stenosis in diagnosing the risk of plaque rupture.

A transforming mutation enhances the activity of the c-Kit soluble tyrosine kinase domain.

An activating mutation (DY814) located in the catalytic domain of the c-Kit receptor has been found in mastocytomas from human, mouse and rat. We evaluated the enzymic properties of purified wild-type (WT) and DY814 tyrosine kinase domains expressed in Pichia pastoris. A linker encoding the Flag epitope was fused to c-Kit cDNA species, enabling affinity purification of the proteins with anti-Flag antibodies. Yeast lysates expressing DY814 contained multiple tyrosine-phosphorylated proteins, whereas WT lysates had no detectable tyrosine phosphorylation. Purification of the WT and mutant kinases in the presence of vanadate demonstrated that both enzymes undergo autophosphorylation. Kinetic analyses of WT and DY814 kinases indicated that at 20 nM enzyme concentration the mutation increases the specific activity 10-fold and decreases the apparent Km for ATP 9-fold. WT activity displayed a hyperbolic dependence on enzyme concentration, consistent with a requirement for dimerization or aggregation for activity. This activity was also enhanced by anti-Flag antibodies. In contrast, the dependence of DY814 activity on enzyme concentration was primarily linear and only marginally enhanced by anti-Flag antibodies. Gel-filtration analysis showed that the WT kinase migrated as a monomer, whereas the DY814 mutant migrated as a dimer. These results indicate that this point mutation promotes dimerization of the c-Kit kinase, potentially contributing to its transforming potential in mast cells.

Protection from apoptosis by steel factor but not interleukin-3 is reversed through blockade of calcium influx.

Steel factor (SLF), the ligand for the c-Kit receptor, protects hemopoietic progenitors and mast cells from apoptosis. We show here that protection of 32D-Kit cells or mast cells from apoptosis by SLF is abrogated through concurrent inhibition of Ca2+ influx. In contrast, cell survival promoted by interleukin-3 is not affected by Ca2+ influx blockers. In the presence of blockers, increasing stimulation by SLF leads to greater levels of cell death in the population, indicating that it is the combination of activation by SLF with concurrent blockade of Ca2+ influx that results in apoptosis. The p815 mastocytoma, which expresses a mutated, constitutively active c-kit receptor, dies apoptotically in the presence of Ca2+ influx blockers alone. Ionomycin protects cells from SLF plus blocker-induced apoptosis, confirming specificity for Ca2+ ion blockade in cell death induction. Overexpression of bcl-2, which protects 32D-Kit cells from factor withdrawal, does not protect cells from apoptosis by SLF plus blocker. In contrast, caspase inhibitors YVAD-CHO, DEVD-FMK, and Boc-Asp-FMK protect cells from SLF plus blocker-induced death. These observations highlight the importance of SLF-stimulated Ca2+ influx in the protection of cells from apoptosis and demonstrate a new mechanism for inducing bcl-2 insensitive, caspase-dependent apoptosis through the combination of SLF stimulation with Ca2+ influx blockade.