Energy efficient scheduling for parallel applications on mobile clusters

During the past decade, cluster computing and mobile communication technologies have been extensively deployed and widely applied because of their giant commercial value. The rapid technological advancement makes it feasible to integrate these two technologies and a revolutionary application called mobile cluster computing is arising on the horizon. Mobile cluster computing technology can further enhance the power of our laptops and mobile devices by running parallel applications. However, scheduling parallel applications on mobile clusters is technically challenging due to the significant communication latency and limited battery life of mobile devices. Therefore, shortening schedule length and conserving energy consumption have become two major concerns in designing efficient and energy-aware scheduling algorithms for mobile clusters. In this paper, we propose two novel scheduling strategies aimed at leveraging performance and power consumption for parallel applications running on mobile clusters. Our research focuses on scheduling precedence constrained parallel tasks and thus duplication heuristics are applied to schedule parallel tasks to minimize communication overheads. However, existing duplication algorithms are developed with consideration of schedule lengths, completely ignoring energy consumption of clusters. In this regard, we design two energy-aware duplication scheduling algorithms, called EADUS and TEBUS, to schedule precedence constrained parallel tasks with a complexity of O(n ²), where n is the number of tasks in a parallel task set. Unlike the existing duplication-based scheduling algorithms that replicate all the possible predecessors of each task, the proposed algorithms judiciously replicate predecessors of a task if the duplication can help in conserving energy. Our energy-aware scheduling strategies are conducive to balancing scheduling lengths and energy savings of a set of precedence constrained parallel tasks. We conducted extensive experiments using both synthetic benchmarks and real-world applications to compare our algorithms with two existing approaches. Experimental results based on simulated mobile clusters demonstrate the effectiveness and practicality of the proposed duplication-based scheduling strategies. For example, EADUS and TABUS can reduce energy consumption for the Gaussian Elimination application by averages of 16.08% and 8.1% with merely 5.7% and 2.2% increase in schedule length respectively.

Antiviral phagocytosis is regulated by a novel Rab-dependent complex in shrimp penaeus japonicus

Rab GTPases are involved in phagosome formation and maturation. However, the role of Rab GTPases in phagocytosis against virus infection remains unknown. In this study, it was found that a Rab gene ( PjRab) from marine shrimp was upregulated in virus-resistant shrimp, suggesting that Rab GTPase was involved in the innate response to virus. The RNAi and mRNA assays revealed that the PjRab protein could regulate shrimp hemocytic phagocytosis through a protein complex consisting of the PjRab, beta-actin, tropomyosin, and envelope protein VP466 of shrimp white spot syndrome virus (WSSV). It was further demonstrated that the PjRab gene silencing by RNAi caused the increase in the number of WSSV copies, indicating that the PjRab might be an intracellular virus recognition protein employed by a host to increase the phagocytic activity. Therefore, our study presents a novel Rab-dependent signaling complex, in which the Rab GTPase might detect virus infection as an intracellular virus recognition protein and trigger downstream phagocytic defense against virus in crustacean for the first time. This discovery would improve our understanding of the still poorly understood molecular events involved in innate immune response against virus infection of invertebrates.     

Regulation of c-Jun N-terminal kinase activation in hydrogen peroxide induced neurotoxicity

C-Jun N-terminal kinase 1 and 2 (JNK1/2) have been shown to be transiently activated and involved in neurotoxicity. We searched for possible upstream molecules, which are responsible for the regulation of hydrogen peroxide-(H₂O₂) induced JNK1/2 activation and JNK1/2-mediated apoptotic-like cell death in cultured rat cortical neurons. The results showed that JNK1/2 activation (monitored by anti-diphosphorylated JNK1/2 antibody) was largely prevented by elimination of extracellular Ca²⁺ or blockage of NMDA-receptors (NMDA-R), and was weakly but significantly decreased by blockage of L-type voltage-gated calcium channel (L-VGCC); furthermore, JNK1/2 activation was largely prevented by inhibition of Ca²⁺/calmodulin-dependent protein kinase-II (CaMKII) and protein-tyrosine kinases (PTK). We also found that H₂O₂-induced apoptotic-like cell death was partially prevented by elimination of extracellular Ca²⁺, or by inhibition of NMDA-R, L-VGCC, PTK and CaMKII, respectively. The above results suggest that in H₂O₂-induced neurotoxicity, JNK1/2 activation is mainly mediated by NMDA-R and L-VGCC. Consequently, PTK and CaMKII are critical intermediaries in JNK1/2 activation and are mainly responsible for JNK1/2-mediated apoptotic-like cell death.     

Metabolism in 1,3‐propanediol fed‐batch fermentation by a D‐lactate deficient mutant of Klebsiella pneumoniae

Klebsiella pneumoniae HR526, a new isolated 1,3‐propanediol (1,3‐PD) producer, exhibited great productivity. However, the accumulation of lactate in the late‐exponential phase remained an obstacle of 1,3‐PD industrial scale production. Hereby, mutants lacking D ‐lactate pathway were constructed by knocking out the ldhA gene encoding fermentative D ‐lactate dehydrogenase (LDH) of HR526. The mutant K. pneumoniae LDH526 with the lowest LDH activity was studied in aerobic fed‐batch fermentation. In experiments using pure glycerol as feedstock, the 1,3‐PD concentrations, conversion, and productivity increased from 95.39 g L^?1, 0.48 and 1.98 g L^?1 h^?1 to 102. 06 g L^?1, 0.52 mol mol^?1 and 2.13 g L^?1 h^?1, respectively. The diol (1,3‐PD and 2,3‐butanediol) conversion increased from 0.55 mol mol^?1 to a maximum of 0.65 mol mol^?1. Lactate would not accumulate until 1,3‐PD exceeded 84 g L^?1, and the final lactate concentration decreased dramatically from more than 40 g L^?1 to <3 g L^?1. Enzymic measurements showed LDH activity decreased by 89–98% during fed‐batch fermentation, and other related enzyme activities were not affected. NADH/NAD⁺ enhanced more than 50% in the late‐exponential phase as the D ‐lactate pathway was cut off, which might be the main reason for the change of final metabolites concentrations. The ability to utilize crude glycerol from biodiesel process and great genetic stability demonstrated that K. pnemoniae LDH526 was valuable for 1,3‐PD industrial production. Biotechnol. Bioeng. 2009; 104: 965–972. © 2009 Wiley Periodicals, Inc.     

Large gradient high magnetic field affects the association of MACF1 with actin and microtubule cytoskeleton

The intense inhomogeneous magnetic fields acting on the diamagnetic materials naturally present in cells can generate strong magnetic forces. We have developed a superconducting magnet platform with large gradient high magnetic field (LG‐HMF), which can produce three magnetic force fields of ?1360, 0, and 1312 T²/m, and three corresponding apparent gravity levels, namely 0, 1, and 2‐g for diamagnetic materials. In this study, the effects of different magnetic force fields on osteoblast‐like cells (MG‐63 and MC3T3‐E1) viability, microtubule actin crosslinking factor 1 (MACF1) expression and its association with cytoskeleton were investigated. Results showed that cell viability increased to different degrees after exposure to 0 or 1‐g conditions for 24 h, but it decreased by about 30% under 2‐g conditions compared with control conditions. An increase in MACF1 expression at the RNA or protein level was observed in osteoblast‐like cells under the magnetic force field of ?1360 T²/m (0‐g) relative to 1312 T²/m (2‐g). Under control conditions, anti‐MACF1 staining was scattered in the cytoplasm and partially colocalized with actin filaments (AFs) or microtubules (MTs) in the majority of osteoblast‐like cells. Under 0‐g conditions, MACF1 labeling was concentrated at perinuclear region and colocalization was not apparent. The patterns of anti‐MACF1 labeling on MTs varied with MTs' changing under LG‐HMF environment. In conclusion, LG‐HMF affects osteoblast‐like cell viability, MACF1 distribution, expression, and its association with cytoskeleton to some extent. Bioelectromagnetics 30:545–555, 2009. © 2009 Wiley‐Liss, Inc.     

Doxycycline enhances the Ras‐MAPK signaling and proliferation of mouse thymic epithelial cells

Depletion of T‐cell‐dependent immunity is a major consideration for patients suffering from infections of human immunodeficiency virus (HIV), those undergoing organ transplantation, and those receiving anti‐cancer chemotherapy and/or radiotherapy. In general, T‐cell regeneration occurs in the thymus through thymopoiesis. We have found that doxycycline (Dox), a tetracycline derivative, enhances the proliferation of mouse thymic epithelial cells, which are unique in their capacity to support positive selection and are essential throughout the development of thymocytes. Cell cycle analysis indicates that the increased cell proliferation is due to a shortened G₀/G₁ phase. To reveal the underlying mechanisms, we examined the expression of an array of molecules that regulate the cell cycle. The results show that in mouse thymic medullary‐type epithelial cell line 1 (MTEC1) Dox leads to elevated levels of H‐Ras, phosphorylated extracellular signal‐regulated kinase 1/2 (p‐ERK1/2), cyclin E, cyclin dependent kinase 4/2 (CDK4/CDK2), E2F3, and c‐myc. These data, and the observation that the proliferation‐enhancing effect is largely abolished following treatment with an ERK inhibitor support an active role of the Ras‐ERK/mitogen‐activated protein kinase (MAPK) signaling pathway. In conclusion, the present study reveals a new activity of an old family of antibiotics. The in vivo effect of Dox on immune reconstitution warrants further exploration. J. Cell. Biochem. 107: 494–503, 2009. © 2009 Wiley‐Liss, Inc.     

Direct electrochemistry of myoglobin based on ionic liquid-clay composite films

The direct electron transfer of myoglobin (Mb) was realized by immobilizing Mb onto ionic liquid (1-butyl-3-methyl imidazolium tetrafluoraborate, [bmim][BF(4)])-clay composite film modified glassy carbon electrode. A pair of well-defined redox peaks of Mb with a formal potential (E(o)') of -0.297 V (vs. Ag/AgCl) was observed in 0.1M phosphate buffer solution (pH 6.0). The ionic liquid-clay composite film showed good biocompatibility and an obvious promotion capability for the direct electron transfer between Mb and electrode. The electron transfer rate constant (k(s)) of Mb was calculated to be (3.58+/-0.12)s(-1). UV-vis spectrum suggested that Mb retained its native conformation in the ionic liquid-clay system. Basal plane spacing of clay obtained by X-ray diffraction (XRD) indicated that there was an intercalation-exfoliation-restacking process, in ionic liquid and clay during the drying process of the modification, and the ionic liquid played the key role for promotion of the direct electron transfer between Mb and the ionic liquid-clay composite film modified electrode. The biocatalytic activity of Mb in the composite film was exemplified by the reduction of hydrogen peroxide. Under the optimal conditions, the reduction peak currents of Mb increased linearly with the concentration of H(2)O(2) in the range of 3.90 x 10(-6) to 2.59 x 10(-4)M, with a detection limit of 7.33 x 10(-7)M. The kinetic parameter I(max) and the apparent Michaelis constant (K(m)) for the electrocatalytic reactions were 3.87 x 10(-8)A and 17.6 microM, respectively. The proposed method would be valuable for the construction of a new third-generation H(2)O(2) sensor.     

Proteomic analysis of the triglyceride-rich lipoprotein-laden foam cells

In hypertriglyceridaemic individuals, atherosclerogenesis is associated with the increased concentrations of very low density lipoprotein (VLDL) and VLDL-associated remnant particles. In vitro studies have suggested that VLDL induces foam cells formation. To reveal the changes of the proteins expression in the process of foam cells formation induced by VLDL, we performed a proteomic analysis of the foam cells based on the stimulation of differentiated THP-1 cells with VLDL. Using two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, 14 differentially expressed proteins, containing 8 up-regulated proteins and 6 down-regulated proteins were identified. The proteins are involved in energy metabolism, oxidative stress, cell growth, differentiation and apoptosis, such as adipose differentiation-related protein (ADRP), enolase, S100A11, heat shock protein 27 and so on. In addition, the expression of some selected proteins was confirmed by Western blot and RT-PCR analysis. The results suggest that VLDL not only induces lipid accumulation, but also brings about foam cells diverse characteristics by altering the expression of various proteins.