bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of global transcriptional responses of chicken following primary and secondary Eimeria acervulina infections
Authors: Kim Chul-Hong , Lillehoj Hyun S , Hong Yeong-Ho , Keeler Calvin L , Lillehoj Erik P
Published: June 2011

Background

Characterization of host transcriptional responses during coccidia infections can provide new clues for the development of alternative disease control strategies against these complex protozoan pathogens.

Methods

In the current study, we compared chicken duodenal transcriptome profiles following primary and secondary infections with Eimeria acervulina using a 9.6K avian intestinal intraepithelial lymphocyte cDNA microarray (AVIELA).

Results

Gene Ontology analysis showed that primary infection significantly modulated the levels of mRNAs for genes involved in the metabolism of lipids and carbohydrates as well as those for innate immune-related genes. By contrast, secondary infection increased the levels of transcripts encoded by genes related to humoral immunity and reduced the levels of transcripts for the innate immune-related genes. The observed modulation in transcript levels for gene related to energy metabolism and immunity occurred concurrent with the clinical signs of coccidiosis.

Conclusions

Our results suggest that altered expression of a specific set of host genes induced by Eimeria infection may be responsible, in part, for the observed reduction in body weight gain and inflammatory gut damage that characterizes avian coccidiosis.
Genome-wide identification of allele-specific expression (ASE) in response to Marek’s disease virus infection using next generation sequencing
Authors: MacEachern Sean , Muir William M , Crosby Seth , Cheng Hans H
Published: June 2011

Background

Marek’s disease (MD), a T cell lymphoma induced by the highly oncogenic α-herpesvirus Marek’s disease virus (MDV), is the main chronic infectious disease concern threatening the poultry industry. Enhancing genetic resistance to MD in commercial poultry is an attractive method to augment MD vaccines, which is currently the control method of choice. In order to optimally implement this control strategy through marker-assisted selection (MAS) and to gain biological information, it is necessary to identify specific genes that influence MD incidence.

Methods

A genome-wide screen for allele-specific expression (ASE) in response to MDV infection was conducted. The highly inbred ADOL chicken lines 6 (MD resistant) and 7 (MD susceptible) were inter-mated in reciprocal crosses and half of the progeny challenged with MDV. Splenic RNA pools at a single time after infection for each treatment group point were generated, sequenced using a next generation sequencer, then analyzed for allele-specific expression (ASE). To validate and extend the results, Illumina GoldenGate assays for selected cSNPs were developed and used on all RNA samples from all 6 time points following MDV challenge.

Results

RNA sequencing resulted in 11-13+ million mappable reads per treatment group, 1.7+ Gb total sequence, and 22,655 high-confidence cSNPs. Analysis of these cSNPs revealed that 5360 cSNPs in 3773 genes exhibited statistically significant allelic imbalance. Of the 1536 GoldenGate assays, 1465 were successfully scored with all but 19 exhibiting evidence for allelic imbalance.

Conclusions

ASE is an efficient method to identify potentially all or most of the genes influencing this complex trait. The identified cSNPs can be further evaluated in resource populations to determine their allelic direction and size of effect on genetic resistance to MD as well as being directly implemented in genomic selection programs. The described method, although demonstrated in inbred chicken lines, is applicable to all traits in any diploid species, and should prove to be a simple method to identify the majority of genes controlling any complex trait.
Preliminary association analysis of TLR9 gene polymorphisms and immune parameters in an Italian Holstein calves population
Authors: Catalani Elisabetta , Nardone Alessandro , Barone Antonino , Scicluna Maria Teresa , Autorino Gian Luca , Caprioli Andrea , Lacetera Nicola
Published: June 2011

Background

This preliminary study was aimed at evaluating the association between single nucleotide polymorphisms (SNPs) on Toll like receptor 9 (TLR9) gene and some immunological parameters in a population of Italian Holstein calves.

Methods

The study was carried out in a commercial farm on 68 Holstein calves aging about 6 months. Genomic DNA was extracted from peripheral blood mononuclear cells (PBMC) and genotyped for nine SNPs on TLR9. Immunological parameters considered were the immunoglobulin (Ig) G titers against bovine herpesvirus 1, and the proliferative response of peripheral blood mononuclear cells to mitogens. For the association study, only results relative to the SNP located in the promoter region have been discussed.

Results

Among the nine SNPs expected, only eight were detected. Considering the SNP located in the promoter region, all three possible genotypes were observed, and their distribution was as follows: genotype a (n=34), b (n=19), and c (n=8). On the basis of their response to vaccine, calves were categorized as low (L, n=8), medium (M, n=45) and high responders (H, n=8). Although no significant association was found between genotypes and L, M or H categories, the genotype estimated as the less represented within the population (c) had no calves categorized as H, the highest frequency of L (25%), and mean values of IgG lower (P < 0.005) compared to genotype b. Furthermore, IgG titers were positively correlated with responses of PBMC to mitogens.

Conclusions

Genotype c appeared to be “non advantageous” in terms of immune response. It was characterized by the presence of the mutation in homozygosity and, not surprisingly, it was the most rare genotype in the population. Larger studies are necessary in order to confirm these observations.
Identification of parental line specific effects of MLF2 on resistance to coccidiosis in chickens
Authors: Hong Yeong Ho , Kim Eui-Soo , Lillehoj Hyun S
Published: June 2011

Background

MLF2 was the candidate gene associated with coccidiosis resistance in chickens. Although single marker analysis supported the association between MLF2 and coccidiosis resistance, causative mutation relevant to coccidiosis was not identified yet. Thus, this study suggested segregation analysis of MLF2 haplotype and the association test of the other candidate genes using improved data transformation.

Results

A haplotype probably originated from one parental line was found out of 4 major haplotypes of MLF2. Frequency of this haplotype was 0.2 in parental chickens and its offspring in 12 families. Allele substitution effect of the MLF2 haplotype originated from a specific line was associated with increased body weight and fecal egg count explaining coccidiosis resistance. Nevertheless Box-Cox transformation was able to improve normality; association test did not produce obvious different results compared with analysis with log transformed phenotype.

Conclusion

Allele substitution effect analysis and classification of MLF2 haplotype identified the segregation of haplotype associated with coccidiosis resistance. The haplotype originated from a specific parental line was associated with improving disease resistance. Estimating effect of MLF2 haplotype on coccidiosis resistance will provide useful information for selecting animals or lines for future study.
Whole genome analysis of infectious bovine keratoconjunctivitis in Angus cattle using Bayesian threshold models
Authors: Kizilkaya Kadir , Tait Richard G , Garrick Dorian J , Fernando Rohan L , Reecy James M
Published: June 2011

Infectious bovine keratoconjunctivitis (IBK), also known as pinkeye, is characterized by damage to the cornea and is an economically important, lowly heritable, categorical disease trait in beef cattle. Scores of eye damage were collected at weaning on 858 Angus cattle. SNP genotypes for each animal were obtained from BovineSNP50 Infinium-beadchips. Simultaneous associations of all SNP with IBK phenotype were determined using Bayes-C that treats SNP effects as random with equal variance for an assumed fraction (π=0.999) of SNP having no effect on IBK scores. Bayes-C threshold models were used to estimate SNP effects by classifying IBK into two, three or nine ordered categories. Magnitudes of genetic variances estimated in localized regions across the genome indicated that SNP within the most informative regions accounted for much of the genetic variance of IBK and pointed out some degree of association to IBK. There are many candidate genes in these regions which could include a gene or group of genes associated with bacterial disease in cattle.
Expression of trypanotolerance in N’Dama x Boran crosses under field challenge in relation to N’Dama genome content
Authors: Orenge Caleb , Munga Leonard , Kimwele Charles , Kemp Steve , Korol Abraham , Gibson John , Hanotte Olivier , Soller Morris
Published: June 2011

Background

Animal trypanosomosis in sub-Saharan Africa is a major obstacle to livestock based agriculture. Control relies on drugs with increasing incidence of multiple-drug resistance. A previous mapping experiment in an F2 population derived from the indigenous trypanotolerant N’Dama cattle crossed to susceptible (Kenya)-Boran cattle under controlled challenge, uncovered a number of trypanotolerance QTL (T-QTL). The present study was to determine expression of N’Dama trypanotolerance in a backcross to the Boran under conditions of field challenge, and whether chromosomal regions associated with trypanotolerance in the F2 experiment showed similar effects in the BC population.

Methods

192 backcross animals to the Boran were produced in six batches from June 2001 to December 2006. At one year of age animals were moved to the field and exposed to natural challenge over about one year in Southwest Kenya (Narok). The animals were individually recorded weekly for body weight, packed cell volume, parasitaemia score, and drug treatments, and were genotyped using 35 microsatellite markers spanning 5 chromosomes found in the F2 study to harbour T-QTL.

Results

The F1 were most trypanotolerant, Boran least, and BC intermediate. Females showed distinctly higher trypanotolerance than males. There was a positive correlation in the BC population between trypanotolerance and number of N’Dama origin marker alleles. QTL mapping revealed T-QTL distributed among all five targeted chromosomes, corresponding in part to the results obtained in the F2 experiment.

Conclusions

N’Dama origin trypanotolerance is expressed in a BC population under field conditions in proportion to N’Dama origin marker alleles. Consequently, marker assisted selection in such populations may be a means of increasing trypanotolerance, while retaining the desirable productive qualities of the recurrent parent.
Comparison of DNA methylation levels of repetitive loci during bovine development
Authors: Kaneda Masahiro , Akagi Satoshi , Watanabe Shinya , Nagai Takashi
Published: June 2011

Background

DNA methylation of cytosine residues in CpG dinucleotide controls gene expression and dramatically changes during development. Its pattern is disrupted in cloned animals suggesting incomplete reprogramming during somatic cell nuclear transfer (the first reprogramming). However, the second reprogramming occurs in the germ cells and epigenetic errors in somatic cells of cloned animals should be erased. To analyze the DNA methylation changes on the spermatogenesis of bulls, we measured DNA methylation levels of three repetitive elements in blastocysts, blood and sperm.

Methods

DNA from PBLs (peripheral blood leukocytes), sperm and individual IVF (in vitro fertilized) and parthenogenetic blastocysts was isolated and bisulfite converted. Three repetitive elements; Satellite I, Satellite II and art2 sequences were amplified by PCR with specific pairs of primers. The PCR product was then cut by restriction enzymes and analyzed by agarose gel electrophoresis for determining the DNA methylation levels.

Results

Both Satellite I and Satellite II sequences were highly methylated in PBLs, whereas hypo-methylated in sperm and blastocysts. The art2 sequence was half methylated both in PBLs and sperm but less methylated in blastocysts. There was no difference in DNA methylation levels between IVF and parthenogenetic blastocysts.

Conclusions

These results suggest that there is a dynamic change of DNA methylation during embryonic development and spermatogenesis in cattle. Satellite I and Satellite II regions are methylated during embryogenesis and then de-methylated during spermatogenesis. However, art2 sequences are not de-methylated during spermatogenesis, suggesting that this region is not reprogrammed during germ cell development. These results show dynamic changes of DNA methylation levels during bovine embryogenesis, especially genome-wide reprogramming in germ cells.
Deciphering the genetic control of innate and adaptive immune responses in pig: a combined genetic and genomic study
Authors: Flori Laurence , Gao Yu , Oswald Isabelle P , Lefevre François , Bouffaud Marcel , Mercat Marie-José , Bidanel Jean-Pierre , Rogel-Gaillard Claire
Published: June 2011

Improving animal robustness and resistance to pathogens by adding health criteria in selection schemes is one of the challenging objectives of the next decade. In order to better understand the genetic control of immunity in French Large White pigs, we have launched a program combining genetic and genomic studies not focussing on any particular pathogen. Animals recorded for production traits were scored for a wide range of immunity parameters three weeks after vaccination againstMycoplasma hyopneumoniae: i) total white blood cells and lymphocyte counts and proportions of various leucocyte subsets including cells harbouring IgM, γδTCR, CD4/CD8, CD16/CD2 and CD16/CD172a/MHCII, ii) innate immune response parameters (phagocytosis andin vitroproduction of IL1B, IL6, IL8, TNF, IL12 and IFNαafter blood stimulation), iii) adaptive immune response parameters (lymphocyte proliferation,in vitroproduction of IL2, IL4, IL10 and IFNγ after blood stimulation, total IgG, IgA, IgM and specific IgG levels) and iv) two acute phase proteins (C-reactive protein and haploglobin). Across traits, heritability estimates reached 0.4 on average (se=0.1) and 42 of the 54 measured parameters showed moderate to high heritabilities (≥0.2), confirming that many parameters are under genetic control and could be included in selection protocols. Functional analyses revealed that the blood transcriptome is informative for part of the immunity traits and should provide relevant phenotypic information to better characterize some immunity traits.
Contribution of the genetic background to the immune response of broilers vaccinated or challenged with LPAI H9N2
Authors: Vervelde Lonneke , de Geus Eveline , Jansen Christine , Heller Dan E
Published: June 2011

Background

The knowledge on the immune responses to LPAI is limited. The purpose of this study was to investigate the immune responses of two divergently selected lines of broilers, a line responding with high antibody response to antigens (HH), and a line responding with low antibody titers (LL) to antigen.

Methods

Day old chicks from each line were divided in two groups, one vaccinated with inactivated H9N2 vaccine and one non-vaccinated. At 21 days of age all the chicks were challenged with field isolate of H9N2, 1X106.5 ELD50 per chick by drops to the eye, nose and beak. Twenty four hours and 14 days post challenge (PC), the chickens were weighed blood spleen and lungs were taken and leukocytes were isolated. The leukocytes were stained with monoclonal antibodies for surface markers and analyzed by flow cytometry. We used Elispot assay to identify the number of antibody producing cells in each of the organs. mRNA was extracted using TRIsol reagent in order to assess the cytokine production level by qRT-PCR using the SYBR green methods.

Results

Our results showed that LL-vaccinated group gained more weight than any of the other group. Using IDEXX kit, no antibody titers could be identified in vaccinated chicks 21 days post vaccination while 14 days PC vaccinated HH chickens demonstrated the highest average antibody titers. LL vaccinated chickens demonstrated higher average antibody titer than non-vaccinated LL. Using the Elispot assay no difference were found between the groups either cells producing IgA, IgM or IgY beside of a high number of IgY producing cells in the lungs of vaccinated HH birds.

Conclusions

Further data on leukocytes subpopulations using flow cytometry, cytokines production (IFNγ, IL-6, IL-18, IL-2 and IL-4) isotype specific antibody responses and number and functionality of NK cells are in process.
Down-regulation of promoter methylation level of CD4 gene after MDV infection in MD-susceptible chicken line
Authors: Luo Juan , Yu Ying , Zhang Huanmin , Tian Fei , Chang Shuang , Cheng Hans H , Song Jiuzhou
Published: June 2011

Background

Marek’s disease virus (MDV) is an oncovirus that induces lymphoid tumors in susceptible chickens, and may affect the epigenetic stability of theCD4gene. The purpose of this study was to find the effect of MDV infection on DNA methylation status of theCD4gene differed between MD-resistant (L63) and –susceptible (L72) chicken lines.

Methods

Chickens from each line were divided into two groups with one group infected by MDV and the other group as uninfected controls. Then, promoter DNA methylation levels of theCD4gene were measured by Pyrosequencing; and gene expression analysis was performed by quantitative PCR.

Results

Promoter methylation of theCD4gene was found to be down-regulated in L72chickens only after MDV infection. The methylation down-regulation of theCD4promoter is negatively correlated with up-regulation ofCD4gene expression in the L72spleen at 21 dpi.

Conclusions

The methylation fluctuation and mRNA expression change ofCD4gene induced by MDV infection suggested a unique epigenetic mechanism existed in MD-susceptible chickens.
Porcine type I interferons: polymorphic sequences and activity against PRRSV
Authors: Sang Yongming , Rowland Raymond RR , Blecha Frank
Published: June 2011

Background

Type I interferons (IFN) are a heterogeneous group of cytokines central to innate and adaptive antiviral immune responses. We have recently reported that porcine type I IFNs comprise at least 39 functional genes with diverse antiviral activity against porcine reproductive and respiratory syndrome virus (PRRSV). Here we report that potential cytokine polymorphisms exist in several genes of porcine type I IFNs.

Results

We have detected more than 100 potential polymorphic mutations, which include nucleotide substitutions and deletions, within the coding regions of porcine type I IFNs. Approximately 50% of the nucleotide changes were mutations that resulted in non-conserved amino acid substitution, as well as deletions that produced frame shifts in the open reading frames (ORFs). We have identified more than 20 polymorphic mutants that showed alterations in anti-PRRSV and anti-vesicular stomatitis virus (VSV) activity in vitro. In particular, some mutations in IFN-α2, IFN-α3, IFN-α8, IFN-α12 and IFN-ω5 significantly altered the antiviral activity of expressed proteins in comparison to the wild-type or variant with more similarity to the wild-type.

Conclusions

Multiple polymorphic isoforms potentially exist within subtypes of the porcine type I IFN family. Polymorphic mutations are more common in multiple-member subtypes than single-member subtypes, and most are found within the IFN-α subclass. Some polymorphic isoforms have altered amino acid composition and shifted ORFs, which show significantly different antiviral activity in vitro.
Acid polishing of lead glass
Authors: Ward Jonathan A , Fowler Andrew C , O’Brien Stephen BG
Published: June 2011

Purpose

The polishing of cut lead glass crystal is effected through the dowsing of the glass in a mixture of two separate acids, which between them etch the surface and as a result cause it to be become smooth. In order to characterise the resultant polishing the rate of surface etching must be known, but when this involves multicomponent surface reactions it becomes unclear what this rate actually is.

Methods

We develop a differential equation based discrete model to determine the effective etching rate by means of an atomic scale model of the etching process.

Results

We calculate the etching rate numerically and provide an approximate asymptotic estimate.

Conclusions

The natural extension of this work would be to develop a continuum advection-diffusion model.
Fluid-fiber-interactions in rotational spinning process of glass wool production
Authors: Arne Walter , Marheineke Nicole , Schnebele Johannes , Wegener Raimund
Published: June 2011

The optimal design of rotational production processes for glass wool manufacturing poses severe computational challenges to mathematicians, natural scientists and engineers. In this paper we focus exclusively on the spinning regime where thousands of viscous thermal glass jets are formed by fast air streams. Homogeneity and slenderness of the spun fibers are the quality features of the final fabric. Their prediction requires the computation of the fluid-fiber-interactions which involves the solving of a complex three-dimensional multiphase problem with appropriate interface conditions. But this is practically impossible due to the needed high resolution and adaptive grid refinement. Therefore, we propose an asymptotic coupling concept. Treating the glass jets as viscous thermal Cosserat rods, we tackle the multiscale problem by help of momentum (drag) and heat exchange models that are derived on basis of slender-body theory and homogenization. A weak iterative coupling algorithm that is based on the combination of commercial software and self-implemented code for flow and rod solvers, respectively, makes then the simulation of the industrial process possible. For the boundary value problem of the rod we particularly suggest an adapted collocation-continuation method. Consequently, this work establishes a promising basis for future optimization strategies.
Susceptibility to tuberculosis is associated with TLR1 polymorphisms resulting in a lack of TLR1 cell surface expression
Authors: Uciechowski Peter , Imhoff Heidi , Lange Christoph , Meyer Christian G , Browne Edmund N , Kirsten Detlef K , Schröder Anja K , Schaaf Bernhard , Al-Lahham Adnan , Reinert Ralf René , Reiling Norbert , Haase Hajo , Hatzmann Adelheid , Fleischer Daniela , Heussen Nicole , Kleines Michael , Rink Lothar
Published: June 2011

Human TLR1 plays an important role in host defense against Mycobacterium tuberculosis. Our aim was to analyze the association of the loss of TLR1 surface expression and TLR1 SNPs with susceptibility to TB. TLR1neg and TLR1pos cells from healthy individuals were identified by flow cytometry and compared by sequencing. TLR1 expression was measured using quantitative real-time PCR and immunoblotting. TLR1 SNP analyses of healthy individuals and TB patients from EU-C and Ghana were performed, and association of the TLR1 genotypes with increased risk of developing TB was statistically evaluated. Lack of TLR1 surface expression accompanied by impaired function was strongly associated with TLR1 SNP G743A. Genotyping of EU-C controls and TB patients revealed an association of TLR1 743A/1805G alleles [OR 2.37 (95% CI 1.13, 4.93), P=0.0219; OR 2.74 (95% CI 1.26, 6.05), P=0.0059] as well as TLR1neg 743AA/1805GG versus TLR1pos genotypes 743AG/1805TG [OR 4.98 (95% CI 1.64, 15.15), P=0.0034; OR 5.70 (95% CI 1.69, 20.35), P=0.0015] and 743AG + GG/1805TG + TT [OR 3.54 (95% CI 1.29, 9.90), P=0.0086; OR 4.17 (95% CI 1.52, 11.67), P=0.0025] with increased susceptibility to TB. No association of G743A with TB was found in Ghana as a result of a low frequency of genotype 743AA. Our data gain new insights in the role of TLR1 in M. tuberculosis defense and provide the first evidence that TLR1 variants are associated with susceptibility to TB in a low-incidence country.
3D controlled-source electromagnetic edge-based finite element modeling of conductive and permeable heterogeneities
Authors: Mukherjee Souvik , Everett Mark E.
Published: June 2011

A new 3D controlled-source electromagnetic finite element (FE) modeling algorithm is presented which is capable of handling local inhomogeneities in the magnetic permeability and electrical conductivity distribution of buried geologic and anthropogenic structures. An ungauged, coupled-potential formulation of the governing electromagnetic vector diffusion and scalar continuity equations is used. The formulation introduces magnetic reluctivity, the inverse of magnetic permeability, to facilitate a separation of secondary and primary potentials. The governing equations are solved using a tetrahedral edge-based FE method. The postprocessing steps to obtain electromagnetic fields are outlined. The code is validated for non-magnetic and permeable conductive structures by comparisons against analytic and previously published numerical solutions. Some limitations of the implementation are explored and directions are proposed for its further development.
Heterogeneous aquifer characterization from ground-penetrating radar tomography and borehole hydrogeophysical data using nonlinear Bayesian simulations
Authors: Dubreuil-Boisclair Camille , Gloaguen Erwan , Marcotte Denis , Giroux Bernard
Published: June 2011

It is known that the heterogeneity of hydraulic conductivity drives the groundwater flow and the transport of contaminants. However, in conventional characterization methods, the lack of densely sampled hydrological data does not permit us to describe the aquifer heterogeneity at an appropriate scale. In this study, we integrate ground-penetrating radar (GPR) tomographic data with hydraulic conductivity logs to estimate the hydraulic conductivity of a heterogeneous unconsolidated aquifer at a decimetric scale between two boreholes. The integration of these different data sets is achieved using a nonlinear Bayesian simulation algorithm. The prior hydraulic conductivity distribution is estimated, under Gaussian hypothesis, by simple kriging of the hydraulic well data. The likelihood of hydraulic conductivity given the relative permittivity and the electrical conductivity functions is obtained from a kernel probability density function estimator that describes the in-situ relationship between the electric and the hydraulic properties measured along boreholes. The proposed method is tested on a synthetic heterogeneous model of permeability to validate the methodology. We show that permeability realizations obtained from the proposed algorithm present a higher correlation with the synthetic model than other classical simulation methods. The method is then applied on data acquired over an unconsolidated aquifer located in Saint-Lambert-de-Lauzon, Quebec, Canada. The data set consists of measurements from (i) GPR crosshole acquisition, (ii) cone penetration testing with pressure measurement combined with soil moisture resistivity, and (iii) a borehole electromagnetic flowmeter. By using the presented Bayesian approach, we generated multiple hydraulic conductivity realizations that are in good agreement with the hydrogeological model of the area.
Laboratory measurements of the acoustic and transport properties of carbonate rocks and their link with the amount of microcrystalline matrix
Authors: Vanorio Tiziana , Mavko Gary
Published: June 2011

Laboratory data and computer tomography (CT) scan image analysis of carbonate rocks were combined demonstrating a quantitative link between acoustic and transport properties, the fraction of microcrystalline calcite (micrite) in the matrix, and the grain-to-micrite matrix ratio. Samples from the Monte Acuto formation, Gargano, Italy, a transgressive system tract (TST) whose microstructure ranges from basal pelagic mudstones to coarse calciturbidites, were analyzed. Results indicate that high micrite rocks with low grain-to- micrite matrix ratios, typical of low-energy depositional settings, are relatively stiffer and more impermeable. In contrast, lower amounts of micrite, due to high-energy depositional settings or its removal from intergranular macropores by progressive leaching of the matrix, leads to high grain-to-micrite matrix ratios. This process will increase porosity and reduce rock stiffness, both of which reduce velocity. Decreasing micrite content correlates well with increasing macroporosity. Permeability increases with macroporosity, as microporosity within micrite does contribute less significantly to fluid flow. Study results, the mechanisms producing porosity, and the classifications describing carbonate rocks in the literature prompted us to address the characterization of these rocks from a different perspective: linking the transport and acoustic properties directly to the content of the microcrystalline matrix rather than to the type and/or geometry of the pore space left behind. These trends of the acoustic and transport properties particularly apply to cycles deposited in transgressive system tracts.
Controlled-source interferometric redatuming by crosscorrelation and multidimensional deconvolution in elastic media
Authors: van der Neut Joost , Thorbecke Jan , Mehta Kurang , Slob Evert , Wapenaar Kees
Published: June 2011

Various researchers have shown that accurate redatuming of controlled seismic sources to downhole receiver locations can be achieved without requiring a velocity model. By placing receivers in a horizontal or deviated well and turning them into virtual sources, accurate images can be obtained even below a complex near-subsurface. Examples include controlled-source interferometry and the virtual-source method, both based on crosscorrelated signals at two downhole receiver locations, stacked over source locations at the surface. Because the required redatuming operators are taken directly from the data, even multiple scattered waveforms can be focused at the virtual-source location, and accurate redatuming can be achieved. To reach such precision in a solid earth, representations for elastic wave propagation that require multicomponent sources and receivers must be implemented. Wavefield decomposition prior to crosscorrelation allows us to enforce virtual sources to radiate only downward or only upward. Virtual-source focusing and undesired multiples from the overburden can be diagnosed with the interferometric point-spread function (PSF), which can be obtained directly from the data if an array of subsurface receivers is deployed. The quality of retrieved responses can be improved by filtering with the inverse of the PSF, a methodology referred to as multidimensional deconvolution.
A finite difference scheme for solving the eikonal equation including surface topography
Authors: Sun Jianguo , Sun Zhangqing , Han Fuxing
Published: June 2011

For solving the eikonal equation in the regions near the curved earth’s surface and the curved interface, we find a second order upwind finite difference scheme that uses nonuniform grid spacing in the regions near the earth’s surface and the interface, respectively. Specifically, in the direct neighborhood of the earth’s surface and of the considered interface, we replace the regular grid spacing in the vertical direction by the vertical distance between the surface (interface) point and the grid point under consideration. For the horizontal direction, however, only the regular grid points are used. As a result, the conventional upwind finite difference formulas are changed into the ones with nonuniform grid spacing. Furthermore, for capturing and propagating the local wavefront near the curved earth’s surface (interface), we adapt the fast marching method by introducing new point types, namely the surface point, the point above the surface, the interface point, and the point under the interface. If we use the scheme in a multistage fashion, we can compute not only the traveltimes of the first arrivals but also the traveltimes of the reflected and transmitted events. In comparison to the published schemes, our scheme has the following two advantages: (1) there is no need to construct a local unstructured grid for suturing the surface or the interface points to the neighboring regular grid points; (2) there is no need to make a local coordinate transform for capturing the local wavefront. Numerical results show that our scheme can treat the irregular region problem caused by the curved earth’s surface and by the curved interface with satisfactory effectiveness and flexibility.
Modeling elastic properties and assessing uncertainty of fracture parameters in the Middle Bakken Siltstone
Authors: Spikes Kyle T.
Published: June 2011

A statistical rock-physics technique, based on well data that provides estimates and associated uncertainty of fracture density in the Middle Bakken Siltstone, is presented. Geologic and hydrocarbon-charging history of the Middle Bakken indicate multiple sets of fractures that justify treating this unit as elastically isotropic. The generalized n-phase self-consistent model relates the elastic properties to composition, matrix porosity, and fracture porosity, where an assigned aspect ratio and volumetric fraction corresponds to each input. The modeling of bulk density as a function of total porosity supplies deterministic estimates of the composition. Analysis of in situ stress and pore-stiffness calculations provide a range of fracture aspect ratios, corresponding to open fractures. Stochastic simulation of fracture porosity initiates the statistical nature of the technique. This treatment of fracture porosity enables the rock-physics model to be treated statistically through multiple realizations. Modeling results explain the measured bulk and shear moduli, with the bulk modulus more accurately described, and the results also provide statistical estimates of fracture porosity. Calculations using these estimates of fracture porosity, along with fracture aspect ratios, result in statistical estimates of fracture density for each depth value in the Middle Bakken unit. Values of fracture density fall within imposed limits (< 0.10). The results and technique demonstrated here could be applied to field seismic data to identify locations of increased fracture density. These locations might indicate areas of increased permeability in the Middle Bakken Siltstone.
Characterizing seismic bright spots in deeply buried, Ordovician Paleokarst strata, Central Tabei uplift, Tarim Basin, Western China
Authors: Zeng Hongliu , Wang Guizhong , Janson Xavier , Loucks Robert , Xia Yiping , Xu Ligui , Yuan Bingheng
Published: June 2011

Anomalous seismic-amplitude bright spots are a common feature in deeply buried (5500 to 6500 m) Ordovician limestone strata in the Central Tabei Uplift area of the Tarim Basin in northwest China. Those anomalies have proven to be useful indicators of reservoir quality. The bright spots as seen on seismic data are tied to high-gamma ray, low-velocity zones in wireline logs, and correspond to clastic cave sediment-fills in the host limestone in core. Synthetic seismic models confirm this relationship between seismic bright spots and cave-sediment fills. A seismic traveltime map of the top Ordovician unconformity illustrates erosional topography and seismic geomorphologic patterns associated with the unconformity with numerous sinuous fluvial channels and canyons, fluvial valleys, sinkholes, and tower karsts and hills. A mature surface drainage system interacted with a near-surface karst system and allowed terrigenous sediments to enter an underground cave system. Karst-related bright spots probably correspond to paleocaves that initiated along an early regional fracture network and later were enhanced and altered by additional discharges in the surface drainage system. A few examples of bright spots are interpreted to be related to postkarstification faults that might have had a hydrothermal origin. Distribution of bright spots provides a useful reference in mapping regional collapsed-paleokarst systems. Bright spots typically are associated with circular and linear faults, and V-shaped depression patterns are related to a collapsed paleocave complex. Seismic-scale mapping and visualization of the paleokarst system can be achieved by interpreting circular and linear faults using continuity attributes and by analyzing the relationship among faults, local depressions, and bright spots.
The simulation of finite ERT electrodes using the complete electrode model
Authors: Rücker Carsten , Günther Thomas
Published: June 2011

Direct-current resistivity surveys usually are performed using steel rods of finite extent and grounding resistance. However, in modeling, electrodes are commonly treated as ideal point sources. We present an approach for numerical computation applying the complete electrode model (CEM), which is known from medical imaging. The electrode surface was discretized, and the partial-differential equations were extended by additional relations incorporating a contact impedance and a condition for the current flow through the electrode surface. We verified the modeling of the electrical potential using an analytical solution for a perfectly coupled half-ellipsoid current source. To quantify the influence of a finite electrode, we computed the electrode effect as the ratio between CEM and point-source solution and investigated its dependence on geometry and contact impedance. Surface measurements using rods of typical spatial extent showed electrode effects on the order of the measuring accuracy for an electrode length/spacing ratio lower than 0.2. However, the effects are more significant for closed geometries such as experimental tanks. A comparison with a point approximation for finite electrodes using point-source locations along the electrode axis showed the best agreement, with points at about 60% of the electrode extension. The contact impedance played a minor role for four-point measurements, contributing only a few percent to the electrode effect. In addition to penetrating electrodes, we investigated surface electrodes with galvanic or capacitive coupling, showing electrode effects on the same order as for penetrating electrodes. An inhomogeneous resistivity distribution clearly increased the size of the effects. We also investigate the use of CEM to simulate current injected through steel-cased boreholes. Finally, we applied the approach with buried ring electrodes to calculate effects caused mainly by geometric disturbances from the borehole.
Improving the efficiency of elastic wave-mode separation for heterogeneous tilted transverse isotropic media
Authors: Yan Jia , Sava Paul
Published: June 2011

Wave-mode separation for TI (transversely isotropic) models can be carried out by nonstationary filtering the elastic wavefields with localized filters. These filters are constructed based on the polarization vectors obtained by solving the Christoffel equation using local medium parameters. This procedure, although accurate, is computationally expensive, especially in 3D. We develop an efficient method for wave-mode separation, which exploits the same general idea of projecting wavefields onto polarization vectors. The method consists of two steps: (1) separate wave modes in the wavenumber domain at a number of reference models to obtain the same number of partially separated wavefields; then transform all the wavefields to the space domain; (2) interpolate the wavefields (obtained in step 1) in the space domain using the spatially-variable model parameters. The new method resembles the phase-shift plus interpolation (PSPI) technique, which interpolates the wavefields that are reconstructed at several reference velocities. Synthetic examples indicate that the separation followed by interpolation is effective for models with complex geology. The new technique has the benefits of speed and accuracy.
Wave propagation in heterogeneous porous media formulated in the frequency-space domain using a discontinuous Galerkin method
Authors: Dupuy Bastien , De Barros Louis , Garambois Stephane , Virieux Jean
Published: June 2011

Biphasic media with a dynamic interaction between fluid and solid phases must be taken into account to accurately describe seismic wave amplitudes in subsurface and reservoir geophysical applications. Consequently, the modeling of the wave propagation in heteregeneous porous media, which includes the frequency-dependent phenomena of the fluid-solid interaction, is considered for 2D geometries. From the Biot-Gassmann theory, we have deduced the discrete linear system in the frequency domain for a discontinuous finite-element method, known as the nodal discontinuous Galerkin method. Solving this system in the frequency domain allows accurate modeling of the Biot wave in the diffusive/propagative regimes, enhancing the importance of frequency effects. Because we had to consider finite numerical models, we implemented perfectly matched layer techniques. We found that waves are efficiently absorbed at the model boundaries, and that the discretization of the medium should follow the same rules as in the elastodynamic case, that is, 10 grids per minimum wavelength for a P0 interpolation order. The grid spreading of the sources, which could be stresses or forces applied on either the solid phase or the fluid phase, did not show any additional difficulties compared to the elastic problem. For a flat interface separating two media, we compared the numerical solution and a semianalytic solution obtained by a reflectivity method in the three regimes where the Biot wave is propagative, diffusive/propagative, and diffusive. In all cases, fluid-solid interactions were reconstructed accurately, proving that attenuation and dispersion of the waves were correctly accounted for. In addition to this validation in layered media, we have explored the capacities of modeling complex wave propagation in a laterally heterogeneous porous medium related to steam injection in a sand reservoir and the seismic response associated to a fluid substitution.
Effects of low-pass filtering on the calculated structural index from magnetic data
Authors: Davis Kristofer , Li Yaoguo , Nabighian Misac N.
Published: June 2011

Euler and extended Euler deconvolution applications use an assumed structural index (SI) or calculate the SI, respectively, for magnetic anomaly data within a specified window. The structural index depends on the source type: specifically, the rate at which the field produced by the source decays. We have examined the effects that the application of low-pass filtering to magnetic data has on estimating the SI. Using a simple low-pass filter, we derived the SI for filtered-field solutions directly over, and away from, a target based on the magnetic potential of a vertical dipole [Formula: see text]. We validated this approach by applying extended Euler deconvolution to synthetic and field examples. In general, filtered magnetic data will decrease the numerically determined SI to a value lower than the theoretical one. The slope and cutoff wavelength of the filter directly affect the estimated SI solutions. The results prove that one must take into account filtering for the application of Euler deconvolution to locate dipole anomalies for unexploded ordnance detection.
Quasi-2D inversion of DCR and TDEM data for shallow investigations
Authors: Monteiro Santos Fernando A. , El-Kaliouby Hesham M.
Published: June 2011

Joint or sequential inversion of direct current resistivity (DCR) and time-domain electromagnetic (TDEM) data commonly are performed for individual soundings assuming layered earth models. DCR and TDEM have different and complementary sensitivity to resistive and conductive structures, making them suitable methods for the application of joint inversion techniques. This potential joint inversion of DCR and TDEM methods has been used by several authors to reduce the ambiguities of the models calculated from each method separately. A new approach for joint inversion of these data sets, based on a laterally constrained algorithm, was found. The method was developed for the interpretation of soundings collected along a line over a 1D or 2D geology. The inversion algorithm was tested on two synthetic data sets, as well as on field data from Saudi Arabia. The results show that the algorithm is efficient and stable in producing quasi-2D models from DCR and TDEM data acquired in relatively complex environments.
How reliable is statistical wavelet estimation?
Authors: Edgar Jonathan A. , van der Baan Mirko
Published: June 2011

Well logs often are used for the estimation of seismic wavelets. The phase is obtained by forcing a well-derived synthetic seismogram to match the seismic, thus assuming the well log provides ground truth. However, well logs are not always available and can predict different phase corrections at nearby locations. Thus, a wavelet-estimation method that reliably can predict phase from the seismic alone is required. Three statistical wavelet-estimation techniques were tested against the deterministic method of seismic-to-well ties. How the choice of method influences the estimated wavelet phase was explored, with the aim of finding a statistical method which consistently predicts a phase in agreement with well logs. It was shown that the statistical method of kurtosis maximization by constant phase rotation consistently is able to extract a phase in agreement with seismic-to-well ties. A statistical method based on a modified mutual-information-rate criterion was demonstrated to provide frequency-dependent phase wavelets where the deterministic method could not. Time-varying statistical wavelets also were estimated with good results — a challenge for deterministic approaches because of the short logging sequence. It was concluded that statistical techniques can be used as quality control tools for the deterministic methods, as a way of extrapolating phase away from wells, or to act as standalone tools in the absence of wells.
Metalliferous mining geophysics — State of the art after a decade in the new millennium
Authors: Vallée Marc A. , Smith Richard S. , Keating Pierre
Published: June 2011

Mining exploration was very active during the first decade of the twenty-first century because there were numerous advances in the science and technology that geophysicists were using for mineral exploration. Development came from different sources: instrumentation improvements, new numerical algorithms, and cross-fertilization with the seismic industry. In gravity, gradiometry kept its promise and is on the cusp of becoming a key technology for mining exploration. In potential-field methods in general, numerous techniques have been developed for automatic interpretation, and 3D inversion schemes came into frequent use. These inversions will have even greater use when geologic constraints can be applied easily. In airborne electromagnetic (EM) methods, the development of time-domain helicopter EM systems changed the industry. In parallel, improvements in EM modeling and interpretation occurred; in particular, the strengths and weaknesses of the various algorithms became better understood. Simpler imaging schemes came into standard use, whereas layered inversion seldom is used in the mining industry today. Improvements in ground EM methods were associated with the development of SQUID technology and distributed-acquisition systems; the latter also impacted ground induced-polarization (IP) methods. Developments in borehole geophysics for mining and exploration were numerous. Borehole logging to measure physical properties received significant interest. Perhaps one reason for that interest was the desire to develop links between geophysical and geologic results, which also is a topic of great importance to mining geologists and geophysicists.