A novel application of gene arrays: Escherichia coli array provides insight into the biology of the obligate endosymbiont of tsetse flies

Symbiotic associations with microorganisms are pivotal in many insects. Yet, the functional roles of obligate symbionts have been difficult to study because it has not been possible to cultivate these organisms in vitro. The medically important tsetse fly (Diptera: Glossinidae) relies on its obligate endosymbiont, Wigglesworthia glossinidia, a member of the Enterobacteriaceae, closely related to Escherichia coli, for fertility and possibly nutrition. We show here that the intracellular Wigglesworthia has a reduced genome size smaller than 770 kb. In an attempt to understand the composition of its genome, we used the gene arrays developed for E. coli. We were able to identify 650 orthologous genes in Wigglesworthia corresponding to ≈85% of its genome. The arrays were also applied for expression analysis using Wigglesworthia cDNA and 61 gene products were detected, presumably coding for some of its most abundant products. Overall, genes involved in cell processes, DNA replication, transcription, and translation were found largely retained in the small genome of Wigglesworthia. In addition, genes coding for transport proteins, chaperones, biosynthesis of cofactors, and some amino acids were found to comprise a significant portion, suggesting an important role for these proteins in its symbiotic life. Based on its expression profile, we predict that Wigglesworthia may be a facultative anaerobic organism that utilizes ammonia as its major source of nitrogen. We present an application of E. coli gene arrays to obtain broad genome information for a closely related organism in the absence of complete genome sequence data.

Evidence from disruption of the lmcpb gene array of Leishmania mexicana that cysteine proteinases are virulence factors.

The mammalian form of the protozoan parasite Leishmania mexicana contains high activity of a cysteine proteinase (LmCPb) encoded on a tandem array of 19 genes (lmcpb). Homozygous null mutants for lmcpb have been produced by targeted gene disruption. All life-cycle stages of the mutant can be cultured in vitro, demonstrating that the gene is not essential for growth or differentiation of the parasite. However, the mutant exhibits a marked phenotype affecting virulence-- its infectivity to macrophages is reduced by 80%. The mutants are as efficient as wild-type parasites in invading macrophages but they only survive in a small proportion of the cells. However, those parasites that successfully infect these macrophages grow normally. Despite their reduced virulence, the mutants are still able to produce subcutaneous lesions in mice, albeit at a slower rate than wild-type parasites. The product of a single copy of lmcpb re-expressed in the null mutant was enzymatically active and restored infectivity toward macrophages to wild-type levels. Double null mutants created for lmcpb and lmcpa (another cathepsin L-like cysteine proteinase) have a similar phenotype to the lmcpb null mutant, showing that LmCPa does not compensate for the loss of LmCPb.

Optimizing the number of stations in arrays measurements: experimental outcomes for different array geometries and the f-k method

Array measurements have become a valuable tool for site response characterization in a non-invasive way. The array design, i.e. size, geometry and number of stations, has a great influence in the quality of the obtained results. From the previous parameters, the number of available stations uses to be the main limitation for the field experiments, because of the economical and logistical constraints that it involves. Sometimes, from the initially planned array layout, carefully designed before the fieldwork campaign, one or more stations do not work properly, modifying the prearranged geometry. Whereas other times, there is not possible to set up the desired array layout, because of the lack of stations. Therefore, for a planned array layout, the number of operative stations and their arrangement in the array become a crucial point in the acquisition stage and subsequently in the dispersion curve estimation. In this paper we carry out an experimental work to analyze which is the minimum number of stations that would provide reliable dispersion curves for three prearranged array configurations (triangular, circular with central station and polygonal geometries). For the optimization study, we analyze together the theoretical array responses and the experimental dispersion curves obtained through the f-k method. In the case of the f-k method, we compare the dispersion curves obtained for the original or prearranged arrays with the ones obtained for the modified arrays, i.e. the dispersion curves obtained when a certain number of stations n is removed, each time, from the original layout of X geophones. The comparison is evaluated by means of a misfit function, which helps us to determine how constrained are the studied geometries by stations removing and which station or combination of stations affect more to the array capability when they are not available. All this information might be crucial to improve future array designs, determining when it is possible to optimize the number of arranged stations without losing the reliability of the obtained results.

FFT Interpolation From Nonuniform Samples Lying in a Regular Grid

This paper presents a method to interpolate a periodic band-limited signal from its samples lying at nonuniform positions in a regular grid, which is based on the FFT and has the same complexity order as this last algorithm. This kind of interpolation is usually termed “the missing samples problem” in the literature, and there exists a wide variety of iterative and direct methods for its solution. The one presented in this paper is a direct method that exploits the properties of the so-called erasure polynomial and provides a significant improvement on the most efficient method in the literature, which seems to be the burst error recovery (BER) technique of Marvasti’s The paper includes numerical assessments of the method’s stability and complexity.

Rigorous design of distillation columns using surrogate models based on Kriging interpolation

The economic design of a distillation column or distillation sequences is a challenging problem that has been addressed by superstructure approaches. However, these methods have not been widely used because they lead to mixed-integer nonlinear programs that are hard to solve, and require complex initialization procedures. In this article, we propose to address this challenging problem by substituting the distillation columns by Kriging-based surrogate models generated via state of the art distillation models. We study different columns with increasing difficulty, and show that it is possible to get accurate Kriging-based surrogate models. The optimization strategy ensures that convergence to a local optimum is guaranteed for numerical noise-free models. For distillation columns (slightly noisy systems), Karush–Kuhn–Tucker optimality conditions cannot be tested directly on the actual model, but still we can guarantee a local minimum in a trust region of the surrogate model that contains the actual local minimum.

Regional subsidence modelling in Murcia city (SE Spain) using 1-D vertical finite element analysis and 2-D interpolation of ground surface displacements

Subsidence is a hazard that may have natural or anthropogenic origin causing important economic losses. The area of Murcia city (SE Spain) has been affected by subsidence due to groundwater overexploitation since the year 1992. The main observed historical piezometric level declines occurred in the periods 1982–1984, 1992–1995 and 2004–2008 and showed a close correlation with the temporal evolution of ground displacements. Since 2008, the pressure recovery in the aquifer has led to an uplift of the ground surface that has been detected by the extensometers. In the present work an elastic hydro-mechanical finite element code has been used to compute the subsidence time series for 24 geotechnical boreholes, prescribing the measured groundwater table evolution. The achieved results have been compared with the displacements estimated through an advanced DInSAR technique and measured by the extensometers. These spatio-temporal comparisons have showed that, in spite of the limited geomechanical data available, the model has turned out to satisfactorily reproduce the subsidence phenomenon affecting Murcia City. The model will allow the prediction of future induced deformations and the consequences of any piezometric level variation in the study area.

Optimization of Chemical Processes Using Surrogate Models Based on a Kriging Interpolation

Superstructure approaches are the solution to the difficult problem which involves the rigorous economic design of a distillation column. These methods require complex initialization procedures and they are hard to solve. For this reason, these methods have not been extensively used. In this work, we present a methodology for the rigorous optimization of chemical processes implemented on a commercial simulator using surrogate models based on a kriging interpolation. Several examples were studied, but in this paper, we perform the optimization of a superstructure for a non-sharp separation to show the efficiency and effectiveness of the method. Noteworthy that it is possible to get surrogate models accurate enough with up to seven degrees of freedom.

Data and Code archive for the interpolation of surface ocean carbon dioxide

We have developed a statistical gap-filling method adapted to the specific coverage and properties of observed fugacity of surface ocean CO2 (fCO2). We have used this method to interpolate the Surface Ocean CO2 Atlas (SOCAT) v2 database on a 2.5°×2.5° global grid (south of 70°N) for 1985-2011 at monthly resolution. The method combines a spatial interpolation based on a 'radius of influence' to determine nearby similar fCO2 values with temporal harmonic and cubic spline curve-fitting, and also fits long term trends and seasonal cycles. Interannual variability is established using deviations of observations from the fitted trends and seasonal cycles. An uncertainty is computed for all interpolated values based on the spatial and temporal range of the interpolation. Tests of the method using model data show that it performs as well as or better than previous regional interpolation methods, but in addition it provides a near-global and interannual coverage.

An approach to the compilation of array expressions in the OL/2 language.

Originally presented as the author's thesis, University of Illinois at Urbana-Champaign.

Prepaging and applications to structured array problems /

Vita.