Data management and analysis for high-throughput DNA sequencingprojects

The rapid advances in molecular biology have begun to shift many of the bottlenecks in genome research from the laboratory to the data analysis facility. The pace at which this has occurred creates a situation in which software development always has to catch up with the flow of data. Since such large-scale processes were not anticipated, the analysis infrastructure has not been fully established. Furthermore, most systems that have been built were designed by the biologists who collected the data. More recently, computer scientists, mathematicians, and engineers have taken an interest in this problem. This has had a positive effect, since it has created a tight synergy between the informatics and the biology. Several principles affected the design of the system developed at TIGR. Each of the sample preparation, sequencing, and analysis steps had to be managed, scheduled, and tracked. This information had to be made readily available to those who needed it for carrying out their tasks. Different skill levels of the users had to be taken into account. The degree of human intervention at each step had to be evaluated and built into the design. A mixed processing environment of Macintosh and Unix platforms had to be integrated. Most importantly, the system had to save time, reduce error, and ensure uniformity of the analysis and quality of the results. In the authors' experience, the tools they have built work well because of their early decisions as to which systems to use for development. The authors settled on a robust relational database management system (Sybase) and a portable development environment (C, C++)     

Actions of cisplatin on the electrophysiological properties of cultured dorsal root ganglion neurones from neonatal rats

In this study we have employed the whole cell patch clamp technique to investigate the effects of an anti-cancer drug cisplatin on basic electrophysiological properties of cultured dorsal root ganglion neurones from neonatal rats. The results show that within the clinical concentration range, cisplatin (0.1 to 10 microM) caused a decrease in input conductance, and complex changes in resting membrane potential in these cultured sensory neurones. The dominant effects of cisplatin on input conductance may be due to inhibition of leak conductances. Transplatin (5 microM) was significantly less effective than cisplatin at reducing input conductance which suggests a degree of stereoselectivity. Cisplatin (1 to 5 microM) transiently increased excitability of the cultured neurones as reflected by a reduction in the threshold for activation of action potentials by 8 mV. The rise time, peak amplitude and duration of action potentials were not changed by acute application of 5 microM cisplatin. Long term treatment of neurones with cisplatin (5 microM), for up to 1 week reduced the viability of the cultures, and attenuated neurone excitability, although input conductance of the cells was significantly increased to 322 +/- 49 M omega (n = 9) compared with controls of 210 +/- 20 M omega (n = 30; P < 0.05). Acute and chronic treatment of cultured neurones with cisplatin therefore produced contrasting actions.     

A New Image Analysis Based Method for Measuring Electrospun Nanofiber Diameter

In this paper, a new image analysis based method for electrospun nanofiber diameter measurement has been presented. The method was tested by a simulated image with known characteristics and a real web. Mean (M) and standard deviation (STD) of fiber diameter obtained using this method for the simulated image were 15.02 and 4.80 pixels respectively, compared to the true values of 15.35 and 4.47 pixels. For the real web, applying the method resulted in M and STD of 324 and 50.4 nm which are extremely close to the values of 319 and 42 nm obtained using manual method. The results show that this approach is successful in making fast, accurate automated measurements of electrospun fiber diameters.     

Phosphorus Inputs to Lake Simcoe from 1990 to 2003: Declines in Tributary Loads and Observations on Lake Water Quality

Total phosphorus (TP) inputs to Lake Simcoe have led to hypolimnetic dissolved oxygen (DO) depletion and loss of cold water fish habitat. Since 1990, efforts have been made to reduce the total TP input to the lake below a defined target of 75 t/year, which was predicted to lead to reductions in spring TP concentration and improvements in end-of-summer hypolimnetic DO concentrations. The total TP load to the lake during the most recent period of record (1998/99-2003/04) ranged from 53 to 76 t/yr and averaged 67 t/yr, compared to an average of 114 t/yr estimated between 1990/91 and 1997/98 (range 85-157 t/yr). Reductions in TP loads from the catchment via tributary discharge (∼26 t) accounted for the majority of the decrease in total load between the two time periods. Total P concentrations decreased significantly in four out of six long-term monitored tributaries; however, concentrations in all six tributaries remain above the level recommended to avoid nuisance plant growth (30 μg/L). Although TP loads to the lake are currently below the target 75 t/yr, excessive growths of filamentous algae and macrophytes continue to be a problem in the nearshore zone. End-of-summer minimum hypolimnetic DO concentrations (average 4.3 mg/L, 1998/99-2003/04) remain substantially below the level (7 mg/L) that is considered protective of lake trout. Efforts to reduce TP loads to the lake therefore need to continue.     

Influences of land use/cover on water quality in the upper and middle reaches of River Njoro, Kenya

Data from 10 sampling sites along the River Njoro are used to examine the contribution of nutrients from upstream land uses draining each of the sampling sites. The data also are used to assess whether both the proportion of land uses and the size of the subwatersheds account for the variability in water quality in the River Njoro watershed. Geographical Information System analysis was used to determine the spatial distribution of land‐cover types and subwatersheds contributing run‐off to the sampling sites in the River Njoro. Standard Digital Elevation Model‐based routines were used to establish the watershed area contributing run‐off to each sampling site. Water and sediment samples were collected for chemical analysis, and the nutrient levels were related to the upstream land‐use types and the size of the subwatersheds. The mid‐stream portion of the River Njoro (near Egerton University) accounts for the highest nutrient contributions. The percentage contribution is magnified by additions from industrial, human settlements and agricultural land uses around the University. There is a significant decrease in nutrient levels downstream, however, indicating natural purification as the river flows through an area of large‐scale farming with intense, well‐preserved riparian and in‐stream vegetation. Steep slopes of the land upstream of Egerton University enhance erosion and nutrient losses from those subwatersheds. Mixed small‐scale agricultural and bare lands contribute over 55% of the phosphorus load to the upper and mid‐reaches of the River Njoro. The size of the subwatershed accounts for about 53% of the variability in the soluble phosphorus in the river. The land‐use subwatershed proportions are important for characterizing and modelling water quality in the River Njoro watershed. Upland land uses are as important as near‐stream land uses. We suggest that conservation of intact riparian corridor along the river and its tributaries contributes significantly to natural purification processes and recovery of the ecological integrity of the River Njoro ecosystem.     

Performance of a non‐load‐bearing steel stud gypsum board wall assembly: Experiments and modelling

A gypsum wall assembly was exposed to an intense real‐scale compartment fire. For the wall assembly, temperatures were measured at the exposed face, within the stud cavity, and at the unexposed face during the fire exposure. Total heat flux gauges were used to measure the temporal variation of the energy incident on the walls, and cameras, both visual and infrared, were used to image the unexposed face of the wall assembly during the fire exposure. The behaviour of the wall assembly under the fire load is discussed as are current model results for a simulation of the fire test. Copyright © 2006 John Wiley & Sons, Ltd.     

Mutagenicity of three agricultural soils

A chemical and biological testing protocol was employed to evaluate the mutagenic potential of the organic compounds extracted from three agricultural soils. The analytical procedures used included bioassays with Salmonella typhimurium and Aspergillus nidulans for the detection of point mutations and a gas chromatography/mass spectrometry/computer system to identify major organic constituents. The extracts of all three soils exhibited mutagenic response in the bioassays. At a dose level of 1000 micrograms per plate, the organic extract of the Bastrop clay induced 434 net revertants; while at the same dose level the Norwood sandy clay and the Sassafrass sandy loam induced 35 and 178 net revertants, respectively, in the Salmonella assay with metabolic activation. In the Aspergillus assay, the extract of the Norwood and Bastrop soils induced a positive response without metabolic activation; this effect was reduced or eliminated in the presence of metabolic activation. Chemical analysis identified a variety of initiators, promotors, inhibitors, and cocarcinogens; however, there were no mutagenic compounds identified in any of the soil extracts. The results of this combined testing protocol indicate that the agricultural soils tested had an inherent level of mutagenic activity, which was not detected by GC/MS analysis alone, and this activity may be related to the past history of agricultural practices, including biocide applications, fertilization, and cultivation.     

Case Study of an Aerosol Explosion and a Method to Determine Explosion Temperatures

A failure analysis case study is presented for a two-piece aerosol containing tetrafluoroethane, commonly referred to as Refrigerant 134a. A gentleman was preparing to recharge the air conditioning system of an automobile when the bottom exploded off the aerosol container, propelling the body of the aerosol container like a rocket, which hit the man in the eye and blinded him in that eye. The aerosol was never connected to the air conditioner, therefore backpressure from the air conditioner (AC) compressor was ruled out as a cause for the explosion. The objective of the study was to determine why the aerosol exploded. Several recently developed test methods were used, including two types of heat-to-burst tests and a puncture chamber to measure the pressure-versus-temperature behavior of aerosols. More common test methods were also used, such as water bath pressure tests, hydro pressure burst tests, pneumatic pressure burst tests, hardness measurements, weight measurements, metallography, scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS), and an accident scenario recreation. A semi-empirical correlation between the hardness and weights of the container bottoms was used to determine the explosion temperature and/or pressure. This semi-empirical correlation agrees in principle with an analysis of the explosion pressures using finite-element analysis (FEA). The root cause for the explosion was determined to be a lack of strength of the bottom of the two-piece aerosol coupled with heating the aerosol to temperatures significantly above room temperature.     

Prediction of Undrained Sinkhole Collapse

Sinkholes are surface depressions or shafts resulting from the collapse of a submerged cavity in soil. The cavities that lead to sinkholes form as a result of underlying geology in limestone areas, or as a result of human activity such as mining or leakage from a sewer. The formation of sinkholes is often sudden and can lead to extensive damage and loss of life, especially in urban areas. Much of the literature on the subject of sinkhole formation is empirical in nature, often being associated with specific locations. This paper presents the results of a study, using numerical modeling, of the undrained stability of the submerged cavities that lead to sinkhole formation. Finite-element limit analysis techniques (using programs developed at the University of Newcastle) are used to obtain upper and lower bound values of a suitable load parameter, which bracket the exact solution. The results are compared to analytical solutions, both from literature and derived independently.