Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

Epistasis refers to the interaction between genes. Although high-throughput epistasis data from model organisms are being generated and used to construct genetic networks(1-3), the extent to which genetic epistasis reflects biologically meaningful interactions remains unclear(4-6). We have addressed this question through in silico mapping of positive and negative epistatic interactions amongst biochemical reactions within the metabolic networks of Escherichia coli and Saccharomyces cerevisiae using flux balance analysis. We found that negative epistasis occurs mainly between nonessential reactions with overlapping functions, whereas positive epistasis usually involves essential reactions, is highly abundant and, unexpectedly, often occurs between reactions without overlapping functions. We offer mechanistic explanations of these findings and experimentally validate them for 61 S. cerevisiae gene pairs.

Analysis on the high luminous flux white light from GaN-based laser diode

We fabricated a phosphor-conversion white light using an InGaN laser diode that emits 445 nm and phosphor that emits in the yellow region when excited by the blue laser light. At 500 mA injection current the luminous flux and the luminous efficacy were 113 lm and 44 lm/W, respectively. The relationship of the luminous flux and the luminous efficacy of the white light with an injection current were discussed. Based on the evaluation method for luminous efficacy of light sources established by the Commission International de I'Eclairage (CIE) and the phosphor used in this experiment, a theoretical analysis of the experiment results and the maximum luminous efficacy of this white light fabrication method were also presented.

Wave Propagation Analysis in a Pressure-Wave-Refrigerator

Pressure wave refrigerators (PWR) refrigerate the gas through periodical expansion waves. Due to its simple structure and robustness, PWR may have many potential applications if the efficiency becomes competitive with existing alternative devices. In order to improve the efficiency, the characteristics of wave propagation in a PWR are studied by experiment, numerical simulation and theoretical analysis. Based on the experimental results and numerical simulation, a simplified model is suggested, which includes the assumptions of flux-equilibrium and conservation of the free energy. This allows the independent analysis of the operation parameters and design specifics. Furthermore, the optimum operation condition can be deduced. Some considerations to improve the PWR efficiency are also given.

Chemical equilibrium analysis and CFD simulation of coal combustion and NOx formation

A full two-fluid model of reacting gas-particle flows with an algebraic unified second-order moment (AUSM) turbulence-chemistry model is used to simulate Beijing coal combustion and NOx formation. The sub-models are the k-epsilon-kp two-phase turbulence model, the EBU-Arrhenius volatile and CO combustion model, the six-flux radiation model, coal devolatilization model and char combustion model. The blocking effect on NOx formation is discussed. In addition, the chemical equilibrium analysis is used to predict NOx concentration at different temperature. Results of CID simulation and chemical equilibrium analysis show that, optimizing air dynamic parameters can delay the NOx formation and decrease NOx emission, but it is effective only in a restricted range. In order to decrease NOx emission near to zero, the re-burning or other chemical methods must be used.

Wave Propagation Analysis in a Pressure-Wave-Refrigerator

Pressure wave refrigerators (PWR) refrigerate the gas through periodical expansion waves. Due to its simple structure and robustness, PWR may have many potential applications if the efficiency becomes competitive with existing alternative devices. In order to improve the efficiency, the characteristics of wave propagation in a PWR are studied by experiment, numerical simulation and theoretical analysis. Based on the experimental results and numerical simulation, a simplified model is suggested, which includes the assumptions of flux-equilibrium and conservation of the free energy. This allows the independent analysis of the operation parameters and design specifics. Furthermore, the optimum operation condition can be deduced. Some considerations to improve the PWR efficiency are also given.

Sand storms: CFD analysis of Reynolds stress and collision stress of particles near sand bed

Sand storm is a serious environmental threat to humans. Sand particles are transported by saltation and suspension, causing soil erosion in one place and deposition in another. In order to prevent and predict sand storms, the causes and the manners of particle motions must be studied in detail. In this paper a standard k-epsilon model is used for the gas phase simulation and the discrete element method (DEM) is used to predict the movements of particles using an in-house procedure. The data are summarized in an Eulerian-Eulerian regime after simulation to get the statistical particle Reynolds stress and particle collision stress. The results show that for the current case the Reynolds stress and the air shear stress predominate in the region 20-250 mm above the initial sand bed surface. However, in the region below 3 mm, the collision stress must be taken into account in predicting particle movement. (C) 2010 Chinese Society of Particuology and Institute of Process Engineering, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Metabolic profiling studies on the toxicological effects of realgar in rats by H-1 NMR spectroscopy

The toxicological effects of realgar after intragastrical administration (1 g/kg body weight) were investigated over a 21 day period in male Wistar rats using metabonomic analysis of H-1 NMR spectra of urine, serum and liver tissue aqueous extracts. Liver and kidney histopathology examination and serum clinical chemistry analyses were also performed. H-1 NMR spectra and pattern recognition analyses from realgar treated animals showed increased excretion of urinary Kreb's cycle intermediates, increased levels of ketone bodies in urine and serum, and decreased levels of hepatic glucose and glycogen, as well as hypoglycemia and hyperlipoidemia, suggesting the Perturbation of energy metabolism. Elevated levels of choline containing metabolites and betaine in serum and liver tissue aqueous extracts and increased serum creatine indicated altered transmethylation. Decreased urinary levels of trimethylamine-N-oxide, phenylacetylglycine and hippurate suggested the effects on the gut microflora environment by realgar.

Metabolic profiling of serum from gadolinium chloride-treated rats by H-1 NMR spectroscopy

Metabolic profiling of serum from gadolinium chloride (GdCl3, 10 and 50 mg/kg body weight, intraperitoneal [i.p.])-treated rats was investigated by the NMR spectroscopic-based metabonomic strategy. Serum samples were collected at 48, 96, and 168 h postdose (p.d.) after exposure to GdCl3. H-1 NMR spectra of serum were analyzed by pattern recognition using principal components analysis. The studies showed that there was a dose-related biochemical effect of GdCl3 treatment on the levels of a range of low-molecular weight compounds in serum. The liver damage induced by GdCl3 was characterized by the elevation of lactate, pyruvate, and creatine as well as the decrease of branched-chain amino acids (valine and isoleucine), alanine, glucose, and trimethylamine-N-oxide concentration in serum samples. The biochemical effects of GdCl3 in rats could be consulted when evaluating the biochemical profile of gadolinium-containing compounds that are being developed for nuclear magnetic resonance imaging.

Sequence analysis of Arthrospira maxima based on fosmid library

Arthrospira (Spirulina) (Setchell& Gardner) is an important cyanobacterium not only in its nutritional potential but in its special biological characteristics. An unbiased fosmid library of Arthrospira maxima FACHB438 that contains 4300 clones was constructed. The size distribution of insert fragments is from 15.5 to 48.9 kb and the average size is 37.6 kb. The recombination frequency is 100%. Therefore the library is 29.9 equivalents to the Arthrospira genome size of 5.4 Mb. A total of 719 sample clones were randomly chosen from the library and 602 available sequences, which consisted of 307,547 bases, covering 5.70% of the whole genome. The codon usage of A. maxima was not strongly biased. GC content at the first position of codons (46.9%) was higher than the second (39.8%) and the third (45.5%) positions. GC content of the genome was 43.6%. Of these sequences, 287 (47.7%) showed high similarities to known genes, 63 (10.5%) to hypothetical genes and the remaining 252 (41.8%) had no significant similarities. The assigned genes were classified into 22 categories with respect to different biological roles. Remarkably, the high presence of 25 sequences (4.2%) encoding reverse transcriptase indicates the RT gene may have multiple copies in the A. maxima genome and might play an important role in the evolutionary history and metabolic regulation. In addition, the sequences encoding the ATP-binding cassette transport system and the two-component signal transduction system were the second and third most frequent genes, respectively. These genomic features provide some clues as to the mechanisms by which this organism adapts to the high concentration of bicarbonate and to the high pH environment.

Sedimentation rates and provenance analysis in the Southwestern Okinawa Trough since the mid-Holocene

As a high-sedimentation rate depocenter along the path of the Kuroshio Current, the southwesternmost part of the Okinawa Trough is a key area to understand the Kuroshio history and sediments transportation. A 34.17-m-long sediment core was obtained by the advanced piston corer of Marco Polo/IMAGES XII MARION DUFRESNE during the May 2005 from the Southern Okinawa Trough at site MD05-2908. The recovered sediments were analyzed by AMS C-14 dating, coarse size fraction (> 63 mu m) extraction and moisture content determination in order to study its sedimentation flux and provenance. The depth-age relationship of core MD05-2908 was well constrained by 17 C-14 dating points. The sediments span across the mid-Holocene (6.8 ka B.P.) and have remarkablely high sedimentation rates between 1.8 and 21-2 m/ka, which is well consistent with the modern observations from sediment traps. We identified five 70-200 a periods of abnormally rapid sedimentation events at 6790-6600 a B.P., 5690-5600 a B.P., 4820-4720 a B.P., 1090-880 a B.P., and 260-190 a B.P., during which the highest sedimentation rate is up to 21-2 m/ka. In general, the lithology of the sediments were dominated by silt and clay, associated with less than 5% coarse size fraction (a parts per thousand << 63 mu m). As the most significant sediment source, the Lanyang River in northeastern Taiwan annually deliver about 10Mt materials to the coastal and offshore region of northeast Taiwan, a portion of which could be carried northward by currents toward the study area. Therefore, we concluded that the 5 abnormally rapid sedimentation events may be related to intensified rainfall in Taiwan and thus increased materials to our study area at that time. However, a few extreme-rapid sedimentation events cannot be explained by normal river runoff alone. The large earthquakes or typhoons induced hyperpycnal discharge of fluvial sediment to the ocean may also act as a potential source supply to the Okinawa Trough.

Interannual horizontal heat advection in the surface mixed layer over the equatorial Pacific Ocean: assimilation versus TAO analysis

The interannual anomalies of horizontal heat advection in the surface mixed layer over the equatorial Pacific Ocean in an assimilation experiment are studied and compared with existing observational analyses. The assimilation builds upon a hindcast study that has produced a good simulation of the observed equatorial currents and optimizes the simulation of the Reynolds sea surface temperature (SST) data. The comparison suggests that the assimilation has improved the simulation of the interannual horizontal heat advection of the surface mixed layer significantly. During periods of interrupted current measurements, the assimilation is shown to produce more meaningful anomalies of the heat advection than the interpolation of the observational data does. The assimilation also shows that the eddy heat flux due to the correlation between high-frequency current and SST variations, which is largely overlooked by the existing observational analyses, is important for the interannual SST balance over the equatorial Pacific. The interannual horizontal heat advection anomalies are found to be sensitive to SST errors where oceanic currents are strong, which is a challenge for ENSO prediction. The study further suggests that the observational analyses of the tropical SST balance based on the TAO and the Reynolds SST data contain significant errors due to the large gradient errors in the Reynolds SST data, which are amplified into the advection anomalies by the large equatorial currents.

Monitoring and simulation of water, heat,and CO2 fluxes in terrestrial ecosystems based on the APEIS-FLUX system

The Integrated Environmental Monitoring (IEM) project, part of the Asia-Pacific Environmental Innovation Strategy (APEIS) project, developed an integrated environmental monitoring system that can be used to detect, monitor, and assess environmental disasters, degradation, and their impacts in the Asia-Pacific region. The system primarily employs data from the moderate resolution imaging spectrometer (MODIS) sensor on the Earth Observation System- (EOS-) Terra/Aqua satellite,as well as those from ground observations at five sites in different ecological systems in China. From the preliminary data analysis on both annual and daily variations of water, heat and CO2 fluxes, we can confirm that this system basically has been working well. The results show that both latent flux and CO2 flux are much greater in the crop field than those in the grassland and the saline desert, whereas the sensible heat flux shows the opposite trend. Different data products from MODIS have very different correspondence, e.g. MODIS-derived land surface temperature has a close correlation with measured ones, but LAI and NPP are quite different from ground measurements, which suggests that the algorithms used to process MODIS data need to be revised by using the local dataset. We are now using the APEIS-FLUX data to develop an integrated model, which can simulate the regional water,heat, and carbon fluxes. Finally, we are expected to use this model to develop more precise high-order MODIS products in Asia-Pacific region.

Microfluidic devices for the analysis of apoptosis

Apoptosis is the outcome of a metabolic cascade that results in cell death in a controlled manner. Due to its important role in maintaining balance in organisms, in mechanisms of diseases, and tissue homeostasis, apoptosis is of great interest in the emerging fields of systems biology. Research into cell death regulation and efforts to model apoptosis processes have become powerful drivers for new technologies to acquire ever more comprehensive information from cells and cell populations. The microfluidic technology promises to integrate and miniaturize many bioanalytical processes, which offers an alternative platform for the analysis of apoptosis. This review aims to highlight the recent developments of microfluidic devices in measuring the hallmarks as well as the dynamic process of cellular apoptosis. The potential capability and an outlook of microfluidic devices for the study of apoptosis are addressed.