The mammalian Nm23/NDPK family: from metastasis control to cilia movement

Nucleoside diphosphate kinases (NDPK) are encoded by the NME genes, also called NM23. They catalyze the transfer of γ-phosphate from nucleoside triphosphates to nucleoside diphosphates by a ping-pong mechanism involving the formation of a high energy phospho-histidine intermediate [1, 2]. Besides their known functions in the control of intracellular nucleotide homeostasis, they are involved in multiple physiological and pathological cellular processes such as differentiation, development, metastastic dissemination or cilia functions. Over the past 15 years, ten human genes have been discovered encoding partial, full length, and/or tandemly repeated Nm23/NDPK domains, with or without N-or C-terminal extensions and/or additional domains. These genes encode proteins exhibiting different functions at various tissular and subcellular localizations. Most of these genes appear late in evolution with the emergence of the vertebrate lineage. This review summarizes the present knowledge on these multitalented proteins.     

Middleware support for many-task computing

Many-task computing aims to bridge the gap between two computing paradigms, high throughput computing and high performance computing. Many-task computing denotes high-performance computations comprising multiple distinct activities, coupled via file system operations. The aggregate number of tasks, quantity of computing, and volumes of data may be extremely large. Traditional techniques found in production systems in the scientific community to support many-task computing do not scale to today’s largest systems, due to issues in local resource manager scalability and granularity, efficient utilization of the raw hardware, long wait queue times, and shared/parallel file system contention and scalability. To address these limitations, we adopted a “top-down” approach to building a middleware called Falkon, to support the most demanding many-task computing applications at the largest scales. Falkon (Fast and Light-weight tasK executiON framework) integrates (1) multi-level scheduling to enable dynamic resource provisioning and minimize wait queue times, (2) a streamlined task dispatcher able to achieve orders-of-magnitude higher task dispatch rates than conventional schedulers, and (3) data diffusion which performs data caching and uses a data-aware scheduler to co-locate computational and storage resources. Micro-benchmarks have shown Falkon to achieve over 15K+ tasks/s throughputs, scale to hundreds of thousands of processors and to millions of queued tasks, and execute billions of tasks per day. Data diffusion has also shown to improve applications scalability and performance, with its ability to achieve hundreds of Gb/s I/O rates on modest sized clusters, with Tb/s I/O rates on the horizon. Falkon has shown orders of magnitude improvements in performance and scalability than traditional approaches to resource management across many diverse workloads and applications at scales of billions of tasks on hundreds of thousands of processors across clusters, specialized systems, Grids, and supercomputers. Falkon’s performance and scalability have enabled a new class of applications called Many-Task Computing to operate at previously so-believed impossible scales with high efficiency.     

Effects of Menadione, Hydrogen Peroxide, and Quercetin on Apoptosis and Delayed Luminescence of Human Leukemia Jurkat T-Cells

Menadione (MD) is an effective cytotoxic drug able to produce intracellularly large amounts of superoxide anion. Quercetin (QC), a widely distributed bioflavonoid, can exert both antioxidant and pro-oxidant effects and is known to specifically inhibit cell proliferation and induce apoptosis in different cancer cell types. We have investigated the relation between delayed luminescence (DL) induced by UV-laser excitation and the effects of MD, hydrogen peroxide, and QC on apoptosis and cell cycle in human leukemia Jurkat T-cells. Treatments with 500 μM H₂O₂ and 250 μM MD for 20 min produced 66.0 ± 4.9 and 46.4 ± 8.6% apoptotic cell fractions, respectively. Long-term (24 h) pre-exposure to 5 μM, but not 0.5 μM QC enhanced apoptosis induced by MD, whereas short-term (1 h) pre-incubation with 10 μM QC offered 50% protection against H₂O₂-induced apoptosis, but potentiated apoptosis induced by MD. Since physiological levels of QC in the blood are normally less than 10 μM, these data can provide relevant information regarding the benefits of flavonoid-combined treatments of leukemia. All the three drugs exerted significant effects on DL. Our data are consistent with (1) the involvement of Complex I of the mitochondrial respiratory chain as an important source of delayed light emission on the 10 μs–10 ms scale, (2) the ability of superoxide anions to quench DL on the 100 μs–10 ms scale, probably via inhibition of reverse electron transfer at the Fe/S centers in Complex I, and (3) the relative insensitivity of DL to intracellular OH^? and H₂O₂ levels.     

Nm23-H1/NDP kinase folding intermediates and cancer: a hypothesis

The Nm23-H1/nucleoside diphosphate (NDP) kinase A is a metastasis suppressor, besides its enzymatic activity. The mutant S120G has been found in high-grade neuroblastomas. The mutant protein, once denatured in urea, is unable to refold in vitro. A size-exclusion chromatography analysis of the folding/association pathway showed that recombinant wild-type and S120G mutant human Nm23-H1/NDP kinase A unfold and refold passing through a molten globule state while typical hexameric NDP kinases unfold without dissociated species and refold through a native monomeric intermediate. A survey of the recent literature showed that several proteins involved in cancer, and their mutants, are marginally stable, like the wild-type Nm23-H1/NDP kinase A, or are misfolded, like its S120G mutant. We therefore suggest that the low thermodynamic stability and the folding intermediate of the Nm23-H1/NDP kinase A may be necessary for its regulatory properties.     

Size, motion, and function of the SecY translocon revealed by molecular dynamics simulations with virtual probes

We report a hybrid, coarse-grained and atomistic, molecular dynamics simulation study of the size, motion, and function of the SecY protein-conducting channel. Growing and pushing virtual soft ball constructs through the pore of SecY, we mimic the push-through of polypeptides, performed cotranslationally by the ribosome and posttranslationally by the SecA ATPase. Forced lateral opening of a "front gate" between transmembrane helices is also induced by the passage of the virtual probes, with implications for the membrane insertion of peptides. We conclude that the SecY channel can stretch to allow passage of peptides with transversal sizes of approximately 16 A. The observed motion of a transmembrane helical "plug" controlling the closed and open states of the channel is consistent with experimental results and confirms previous hypotheses. Additionally, the "hinge" region for front gate opening is observed to be highly mobile as postulated. Both the forced dilation of a "ring" of residues at the middle of the pore and the lateral opening of the front gate are shown to induce plug displacement, but neither accomplish a full-extent motion of the plug to the back of the channel. For probes whose passage does not destroy the resilience of the SecY, both lateral exit and full translocation are observed, despite the fact that applied forces were always in the direction along the pore axis. Lateral exit is accompanied by front gate opening and slight plug displacement, whereas full translocation is accompanied by large plug displacement but no apparent lateral opening. Simulations also reveal that dilating the pore ring is a more effective way to destabilize the plug than intercalation of a cylinder-like probe at the front gate. Based on the simulations, the existence of a family of diverse open states is proposed.     

A lubrication analysis of pharyngeal peristalsis: Application to flavour release

After eating a liquid or a semi-liquid food product, a thin film responsible for the dynamic profile of aroma release coats the pharyngeal mucosa. The aim of this article was to analyse the fluid mechanics of pharyngeal peristalsis and to develop a simple biomechanical model in order to understand the role of saliva and food bolus viscosity on the coating of pharyngeal mucosa. We began by analysing the physiology and the biomechanics of swallowing in order to determine relevant model assumptions. This analysis of the literature clarified the types of mechanical solicitations applied on the food bolus. Moreover, we showed that the pharyngeal peristalsis in the most occluded region is equivalent to a forward roll coating process, the originality of which is lubrication by a film of saliva. A model based on the lubrication theory for Newtonian liquids was developed in dimensionless form. The parametric study showed the strong influence of relative saliva thickness on the food bolus coating. A specific experimental device was designed that confirms the model predictions. Two sets of conditions that depend on the relative thickness of saliva were distinguished. The first is characterised by a relatively thin film of saliva: food bolus viscosity has a strong impact on mucosa coating. These phenomena are well represented by the model developed here. The second is obtained when the saliva film is relatively thick: hydrodynamic mixing with saliva, interdiffusion or instabilities may govern mucosa coating. Finally, these results were extrapolated to determine the influence of food bolus viscosity on the dynamic profile of flavour release according to physiological parameters.     

The characterization of complex continuous norms of reaction

Recent focus on the array of phenotypes expressed under differing environmental conditions, or phenotypic plasticity, has led to increased understanding of its genetic basis as well as its adaptive significance. However, the quantification of plasticity has proven difficult, hampered by both the limited number of environments over which plasticity may typically be assessed and by the need to assume, a priori, the general form of reaction norms under study. Our understanding of the shapes of continuous norms of reaction and, consequently, the subtle differences that may exist in shapes among genotypes or populations is rudimentary. Here, we propose the use of the loess smoothing function to analyze complex norms of reaction and to quantify total plasticity over many environments. A thermogradient incubator offers an ideal means to provide many environments for a demonstration of the use of the loess method. We test seed germination in three populations of two monocarpic plant species for population differentiation in plasticity to temperature. First, we test for differentiation in norms of reaction to 30 temperature environments among three populations of the monocarpic perennial, Lobelia inflata . The second demonstration assesses plasticity to eight temperature environments of three populations of the arctic-alpine annual, Koenigia islandica . Our demonstration shows that the loess technique can detect significant genetic differentiation among populations in complex norms of reaction for both species studied, and suggests that the use of this procedure should be considered where the form of norms of reaction might be complex. The general applicability of the approach is discussed.     

A Gene Signature to Determine Metastatic Behavior in Thymomas

Purpose

Thymoma represents one of the rarest of all malignancies. Stage and completeness of resection have been used to ascertain postoperative therapeutic strategies albeit with limited prognostic accuracy. A molecular classifier would be useful to improve the assessment of metastatic behaviour and optimize patient management.

Methods

qRT-PCR assay for 23 genes (19 test and four reference genes) was performed on multi-institutional archival primary thymomas (n = 36). Gene expression levels were used to compute a signature, classifying tumors into classes 1 and 2, corresponding to low or high likelihood for metastases. The signature was validated in an independent multi-institutional cohort of patients (n = 75).

Results

A nine-gene signature that can predict metastatic behavior of thymomas was developed and validated. Using radial basis machine modeling in the training set, 5-year and 10-year metastasis-free survival rates were 77% and 26% for predicted low (class 1) and high (class 2) risk of metastasis (P = 0.0047, log-rank), respectively. For the validation set, 5-year metastasis-free survival rates were 97% and 30% for predicted low- and high-risk patients (P = 0.0004, log-rank), respectively. The 5-year metastasis-free survival rates for the validation set were 49% and 41% for Masaoka stages I/II and III/IV (P = 0.0537, log-rank), respectively. In univariate and multivariate Cox models evaluating common prognostic factors for thymoma metastasis, the nine-gene signature was the only independent indicator of metastases (P = 0.036).

Conclusion

A nine-gene signature was established and validated which predicts the likelihood of metastasis more accurately than traditional staging. This further underscores the biologic determinants of the clinical course of thymoma and may improve patient management.     

Mixed Convection Boundary Layer Flow over a Moving Vertical Flat Plate in an External Fluid Flow with Viscous Dissipation Effect

The steady boundary layer flow of a viscous and incompressible fluid over a moving vertical flat plate in an external moving fluid with viscous dissipation is theoretically investigated. Using appropriate similarity variables, the governing system of partial differential equations is transformed into a system of ordinary (similarity) differential equations, which is then solved numerically using a Maple software. Results for the skin friction or shear stress coefficient, local Nusselt number, velocity and temperature profiles are presented for different values of the governing parameters. It is found that the set of the similarity equations has unique solutions, dual solutions or no solutions, depending on the values of the mixed convection parameter, the velocity ratio parameter and the Eckert number. The Eckert number significantly affects the surface shear stress as well as the heat transfer rate at the surface.