Publications by authors named "James Womack"

84 Publications

Sequence analysis in reveals pervasiveness of X-Y arms races in mammalian lineages.

Genome Res 2020 12 18;30(12):1716-1726. Epub 2020 Nov 18.

Whitehead Institute, Cambridge, Massachusetts 02142, USA.

Studies of Y Chromosome evolution have focused primarily on gene decay, a consequence of suppression of crossing-over with the X Chromosome. Here, we provide evidence that suppression of X-Y crossing-over unleashed a second dynamic: selfish X-Y arms races that reshaped the sex chromosomes in mammals as different as cattle, mice, and men. Using super-resolution sequencing, we explore the Y Chromosome of (bull) and find it to be dominated by massive, lineage-specific amplification of testis-expressed gene families, making it the most gene-dense Y Chromosome sequenced to date. As in mice, an X-linked homolog of a bull Y-amplified gene has become testis-specific and amplified. This evolutionary convergence implies that lineage-specific X-Y coevolution through gene amplification, and the selfish forces underlying this phenomenon, were dominatingly powerful among diverse mammalian lineages. Together with Y gene decay, X-Y arms races molded mammalian sex chromosomes and influenced the course of mammalian evolution.
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http://dx.doi.org/10.1101/gr.269902.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7706723PMC
December 2020

The ONETEP linear-scaling density functional theory program.

J Chem Phys 2020 May;152(17):174111

Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA.

We present an overview of the onetep program for linear-scaling density functional theory (DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the density matrix and the NGWFs are optimized with localization constraints. By taking advantage of localization, onetep is able to perform calculations including thousands of atoms with computational effort, which scales linearly with the number or atoms. The code has a large and diverse range of capabilities, explored in this paper, including different boundary conditions, various exchange-correlation functionals (with and without exact exchange), finite electronic temperature methods for metallic systems, methods for strongly correlated systems, molecular dynamics, vibrational calculations, time-dependent DFT, electronic transport, core loss spectroscopy, implicit solvation, quantum mechanical (QM)/molecular mechanical and QM-in-QM embedding, density of states calculations, distributed multipole analysis, and methods for partitioning charges and interactions between fragments. Calculations with onetep provide unique insights into large and complex systems that require an accurate atomic-level description, ranging from biomolecular to chemical, to materials, and to physical problems, as we show with a small selection of illustrative examples. onetep has always aimed to be at the cutting edge of method and software developments, and it serves as a platform for developing new methods of electronic structure simulation. We therefore conclude by describing some of the challenges and directions for its future developments and applications.
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http://dx.doi.org/10.1063/5.0004445DOI Listing
May 2020

Mapping Genes Is Good for You.

Annu Rev Anim Biosci 2019 02 8;7:1-16. Epub 2018 Oct 8.

Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4467, USA; email:

I abandoned my original career choice of high school teaching to pursue dentistry and soon abandoned that path for genetics. The latter decision was due to a challenge by a professor that led to me reading Nobel speeches by pioneer geneticists before I had formal exposure to the subject. Even then, I was 15 years into my career before my interest in rodent genomes gave way to mapping cattle genes. Events behind these twists and turns in my career path comprise the first part of this review. The remainder is a review of the development of the field of bovine genomics from my personal perspective. I have had the pleasure of working with outstanding graduate students, postdocs, and colleagues to contribute my small part to a discipline that has evolved from a few individuals mapping an orphan genome to a discipline underlying a revolution in animal breeding.
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http://dx.doi.org/10.1146/annurev-animal-020518-114902DOI Listing
February 2019

Genomic Structure and Tissue Expression of the NK-Lysin Gene Family in Bison.

J Hered 2018 06;109(5):598-603

Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A & M University, College Station, TX.

Antimicrobial peptides (AMPs) are a class of natural peptides with varying numbers of amino acids. They are principal components of innate immunity in vertebrates, encoding natural antibiotics and providing a protective response against a broad range of microbes including those responsible for tuberculosis, an important disease in bison. NK-lysins are AMPs that have been described in various organisms and are coded by a single gene in several mammalian species, including human. Recently, we described a family of 4 NK-lysin genes in cattle. Here, we examined NK-lysin genes in bison and identified 4 bison paralogs (NK1, NK2A, NK2B, and NK2C), although the current bison genome assembly annotates only 2 (NK1 and NK2). Sequence and phylogenetic analysis support the triplication of NK2 prior to the most recent common ancestor of bison and cattle. Comparative mapping of bison and cattle paralogs indicates that the NK-lysin family is located on bison chromosome 11 with well-conserved synteny of flanking genes relative to cattle. The 3 bison NK-lysin2 genes share high sequence similarity with each other. RNA-seq analysis demonstrates that NK2A, NK2B, and NK2C are expressed primarily in the lung, whereas NK1 is expressed at low levels in all tissues studied. This tissue expression pattern differs from that previously reported for cattle, suggesting some divergence in function since the evolutionary separation of the 2 species.
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http://dx.doi.org/10.1093/jhered/esy022DOI Listing
June 2018

DL_MG: A Parallel Multigrid Poisson and Poisson-Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution.

J Chem Theory Comput 2018 Mar 2;14(3):1412-1432. Epub 2018 Mar 2.

Department of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom.

The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential-a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions. The analytic solutions generally used to solve the Poisson equation in vacuum (or with homogeneous permittivity) are not applicable in these circumstances, and numerical methods must be used. In this work, we present DL_MG, a flexible, scalable, and accurate solver library, developed specifically to tackle the challenges of solving the Poisson equation in modern large-scale electronic structure calculations on parallel computers. Our solver is based on the multigrid approach and uses an iterative high-order defect correction method to improve the accuracy of solutions. Using two chemically relevant model systems, we tested the accuracy and computational performance of DL_MG when solving the generalized Poisson and Poisson-Boltzmann equations, demonstrating excellent agreement with analytic solutions and efficient scaling to ∼10 unknowns and 100s of CPU cores. We also applied DL_MG in actual large-scale electronic structure calculations, using the ONETEP linear-scaling electronic structure package to study a 2615 atom protein-ligand complex with routinely available computational resources. In these calculations, the overall execution time with DL_MG was not significantly greater than the time required for calculations using a conventional FFT-based solver.
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http://dx.doi.org/10.1021/acs.jctc.7b01274DOI Listing
March 2018

Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory.

J Chem Theory Comput 2017 Nov 17;13(11):5572-5581. Epub 2017 Oct 17.

Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States.

We present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The solvent-solute electrostatic interactions are computed by numerical solution of the nonhomogeneous Poisson equation and incorporated at the Hartree-Fock stage of the EOM-CCSD calculation by modification of the electrostatic potential. We demonstrate the method by computing excited state transition energies and solvent shifts for several small molecules in water. Results are presented for solvated HO, formaldehyde, acetone, and trans-acrolein, which have low-lying n → π* transitions and associated blue shifts in aqueous solution. Comparisons are made with experimental data and other theoretical approaches, including popular implicit solvation models and QM/MM methods. We find that our approach provides surprisingly good agreement with both experiment and the other models, despite its comparative simplicity. This approach only requires modification of the Fock operator and total energy expressions at the Hartree-Fock level-solvation effects enter into the EOM-CCSD calculation only through the Hartree-Fock orbitals. Our model provides a theoretically and computationally simple route for accurate simulations of excited state spectra of molecules in solution, paving the way for studies of larger and more complex molecules.
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http://dx.doi.org/10.1021/acs.jctc.7b00833DOI Listing
November 2017

Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals.

J Phys Chem Lett 2017 Jan 12;8(1):35-40. Epub 2016 Dec 12.

Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California , Berkeley, California 94720, United States.

The VV10 and rVV10 nonlocal correlation functionals are consistently implemented and assessed, with the goal of determining if the rVV10 nonlocal correlation functional can replace the VV10 nonlocal correlation functional in the recently developed B97M-V density functional, to give the B97M-rV density functional. Along the way, four density functionals are simultaneously tested: VV10, rVV10, B97M-V, and B97M-rV. An initial assessment is carried out across the S22 data set, and the short-range damping variable, b, is varied for all four density functionals in order to determine the sensitivity of the functionals to the empirical parameter. The results of this test indicate that a value of b = 6 (fortuitously the same as that in B97M-V) is suitable for B97M-rV. The functionals are then compared across an extensive database of interaction energies, and it is demonstrated that B97M-rV either matches or outperforms B97M-V for all of the tests considered. Finally, the optimization of b across the S22 data set is extended to two range-separated hybrid density functionals, ωB97X-V and ωB97M-V, and a value of b = 6.2 is recommended for both ωB97X-rV and ωB97M-rV.
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http://dx.doi.org/10.1021/acs.jpclett.6b02527DOI Listing
January 2017

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package.

J Chem Phys 2016 Nov;145(20):204114

School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom.

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.
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http://dx.doi.org/10.1063/1.4967960DOI Listing
November 2016

Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination.

Proc Natl Acad Sci U S A 2016 11 14;113(48):13815-13820. Epub 2016 Nov 14.

Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843;

Defensins constitute an evolutionary conserved family of cationic antimicrobial peptides that play a key role in host innate immune responses to infection. Defensin genes generally reside in complex genomic regions that are prone to structural variation, and defensin genes exhibit extensive copy number variation in humans and in other species. Copy number variation of defensin genes was examined in inbred lines of Leghorn and Fayoumi chickens, and a duplication of defensin7 was discovered in the Fayoumi breed. Analysis of junction sequences confirmed the occurrence of a simple tandem duplication of defensin7 with sequence identity at the junction, suggesting nonallelic homologous recombination between defensin7 and defensin6 The duplication event generated two chimeric promoters that are best explained by gene conversion followed by homologous recombination. Expression of defensin7 was not elevated in animals with two genes despite both genes being transcribed in the tissues examined. Computational prediction of promoter regions revealed the presence of several putative transcription factor binding sites generated by the duplication event. These data provide insight into the evolution and possible function of large gene families and specifically, the defensins.
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http://dx.doi.org/10.1073/pnas.1616948113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5137700PMC
November 2016

Tissue expression and antibacterial activity of host defense peptides in chicken.

BMC Vet Res 2016 Oct 13;12(1):231. Epub 2016 Oct 13.

WCU Biomodulation Major, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.

Background: Host defence peptides are a diverse group of small, cationic peptides and are important elements of the first line of defense against pathogens in animals. Expression and functional analysis of host defense peptides has been evaluated in chicken but there are no direct, comprehensive comparisons with all gene family and individual genes.

Results: We examined the expression patterns of all known cathelicidins, β-defensins and NK-lysin in multiple selected tissues from chickens. CATH1 through 3 were predominantly expressed in the bone marrow, whereas CATHB1 was predominant in bursa of Fabricius. The tissue specific pattern of β-defensins generally fell into two groups. β-defensin1-7 expression was predominantly in bone marrow, whereas β-defensin8-10 and β-defensin13 were highly expressed in liver. NK-lysin expression was highest in spleen. We synthesized peptide products of these gene families and analysed their antibacterial efficacy. Most of the host defense peptides showed antibacterial activity against E.coli with dose-dependent efficacy. β-defensin4 and CATH3 displayed the strongest antibacterial activity among all tested chicken HDPs. Microscopic analyses revealed the killing of bacterium by disrupting membranes with peptide treatment.

Conclusions: These results demonstrate dose-dependent antimicrobial effects of chicken HDPs mediated by membrane damage and demonstrate the differential tissue expression pattern of bioactive HDPs in chicken and the relative antimicrobial potency of the peptides they encode.
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http://dx.doi.org/10.1186/s12917-016-0866-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5064907PMC
October 2016

Expression of the Bovine NK-Lysin Gene Family and Activity against Respiratory Pathogens.

PLoS One 2016 13;11(7):e0158882. Epub 2016 Jul 13.

Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, United States of America.

Unlike the genomes of many mammals that have a single NK-lysin gene, the cattle genome contains a family of four genes, one of which is expressed preferentially in the lung. In this study, we compared the expression of the four bovine NK-lysin genes in healthy animals to animals challenged with pathogens known to be associated with bovine respiratory disease (BRD) using transcriptome sequencing (RNA-seq). The expression of several NK-lysins, especially NK2C, was elevated in challenged relative to control animals. The effects of synthetic peptides corresponding to functional region helices 2 and 3 of each gene product were tested on both model membranes and bio-membranes. Circular dichroism spectroscopy indicated that these peptides adopted a more helical secondary structure upon binding to an anionic model membrane and liposome leakage assays suggested that these peptides disrupt membranes. Bacterial killing assays further confirmed the antimicrobial effects of these peptides on BRD-associated bacteria, including both Pasteurella multocida and Mannhemia haemolytica and an ultrastructural examination of NK-lysin-treated P. multocida cells by transmission electron microscopy revealed the lysis of target membranes. These studies demonstrate that the expanded bovine NK-lysin gene family is potentially important in host defense against pathogens involved in bovine respiratory disease.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158882PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4943647PMC
August 2017

Bovine NK-lysin: Copy number variation and functional diversification.

Proc Natl Acad Sci U S A 2015 Dec 14;112(52):E7223-9. Epub 2015 Dec 14.

Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843;

NK-lysin is an antimicrobial peptide and effector protein in the host innate immune system. It is coded by a single gene in humans and most other mammalian species. In this study, we provide evidence for the existence of four NK-lysin genes in a repetitive region on cattle chromosome 11. The NK2A, NK2B, and NK2C genes are tandemly arrayed as three copies in ∼30-35-kb segments, located 41.8 kb upstream of NK1. All four genes are functional, albeit with differential tissue expression. NK1, NK2A, and NK2B exhibited the highest expression in intestine Peyer's patch, whereas NK2C was expressed almost exclusively in lung. The four peptide products were synthesized ex vivo, and their antimicrobial effects against both Gram-positive and Gram-negative bacteria were confirmed with a bacteria-killing assay. Transmission electron microcopy indicated that bovine NK-lysins exhibited their antimicrobial activities by lytic action in the cell membranes. In summary, the single NK-lysin gene in other mammals has expanded to a four-member gene family by tandem duplications in cattle; all four genes are transcribed, and the synthetic peptides corresponding to the core regions are biologically active and likely contribute to innate immunity in ruminants.
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http://dx.doi.org/10.1073/pnas.1519374113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702975PMC
December 2015

Single Pathogen Challenge with Agents of the Bovine Respiratory Disease Complex.

PLoS One 2015 16;10(11):e0142479. Epub 2015 Nov 16.

Department of Veterinary Pathobiology, Texas A & M University, College Station, Texas, 77843-4467, United States of America.

Bovine respiratory disease complex (BRDC) is an important cause of mortality and morbidity in cattle; costing the dairy and beef industries millions of dollars annually, despite the use of vaccines and antibiotics. BRDC is caused by one or more of several viruses (bovine respiratory syncytial virus, bovine herpes type 1 also known as infectious bovine rhinotracheitis, and bovine viral diarrhea virus), which predispose animals to infection with one or more bacteria. These include: Pasteurella multocida, Mannheimia haemolytica, Mycoplasma bovis, and Histophilus somni. Some cattle appear to be more resistant to BRDC than others. We hypothesize that appropriate immune responses to these pathogens are subject to genetic control. To determine which genes are involved in the immune response to each of these pathogens it was first necessary to experimentally induce infection separately with each pathogen to document clinical and pathological responses in animals from which tissues were harvested for subsequent RNA sequencing. Herein these infections and animal responses are described.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142479PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4646450PMC
June 2016

Mapping a Major Gene for Resistance to Rift Valley Fever Virus in Laboratory Rats.

J Hered 2015 Nov-Dec;106(6):728-33. Epub 2015 Nov 6.

From the Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 4467 TAMU, College Station, TX 77843-4467 (Busch and Womack); the Animal Resource Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9037 (Callicott); the Department of Pathology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0609 (Peters); and the Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0609 (Morrill).

The Rift Valley Fever virus (RVFV) presents an epidemic and epizootic threat in sub-Saharan Africa, Egypt, and the Arabian Peninsula, and has furthermore recently gained attention as a potential weapon of bioterrorism due to its ability to infect both livestock and humans. Inbred rat strains show similar characteristic responses to the disease as humans and livestock, making them a suitable model species. Previous studies had indicated differences in susceptibility to RVFV hepatic disease among various rat strains, including a higher susceptibility of Wistar-Furth (WF) compared to a more resistant Lewis (LEW) strain. Further study revealed that this resistance trait exhibits the pattern of a major dominant gene inherited in Mendelian fashion. A genome scan of a congenic WF.LEW strain, created from the susceptible WF and resistant LEW strains and itself resistant to infection with RVFV, revealed 2 potential regions for the location of the gene, 1 on chromosome 3 and the other on chromosome 9. Through backcrossing of WF.LEW rats to WF rats, genotyping offspring using SNPs and microsatellites, and viral challenges of 3 N1 litters, we have mapped the gene to the distal end of chromosome 3.
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http://dx.doi.org/10.1093/jhered/esv087DOI Listing
April 2016

Density fitting for three-electron integrals in explicitly correlated electronic structure theory.

J Chem Phys 2014 Jan;140(4):044118

Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom.

The principal challenge in using explicitly correlated wavefunctions for molecules is the evaluation of nonfactorizable integrals over the coordinates of three or more electrons. Immense progress was made in tackling this problem through the introduction of a single-particle resolution of the identity. Decompositions of sufficient accuracy can be achieved, but only with large auxiliary basis sets. Density fitting is an alternative integral approximation scheme, which has proven to be very reliable for two-electron integrals. Here, we extend density fitting to the treatment of all three-electron integrals that appear at the MP2-F12/3*A level of theory. We demonstrate that the convergence of energies with respect to auxiliary basis size is much more rapid with density fitting than with the traditional resolution-of-the-identity approach.
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http://dx.doi.org/10.1063/1.4863136DOI Listing
January 2014

Susceptibility loci revealed for bovine respiratory disease complex in pre-weaned holstein calves.

BMC Genomics 2014 Dec 22;15:1164. Epub 2014 Dec 22.

Division of Animal Sciences, University of Missouri, Columbia, USA.

Background: Bovine respiratory disease complex (BRDC) is an infectious disease of cattle that is caused by a combination of viral and/or bacterial pathogens. Selection for cattle with reduced susceptibility to respiratory disease would provide a permanent tool for reducing the prevalence of BRDC. The objective of this study was to identify BRDC susceptibility loci in pre-weaned Holstein calves as a prerequisite to using genetic improvement as a tool for decreasing the prevalence of BRDC. High density SNP genotyping with the Illumina BovineHD BeadChip was conducted on 1257 male and 757 female Holstein calves from California (CA), and 767 calves identified as female from New Mexico (NM). Of these, 1382 were classified as BRDC cases, and 1396 were classified as controls, with all phenotypes assigned using the McGuirk health scoring system. During the acquisition of blood for DNA isolation, two deep pharyngeal and one mid-nasal diagnostic swab were obtained from each calf for the identification of bacterial and viral pathogens. Genome-wide association analyses were conducted using four analytical approaches (EIGENSTRAT, EMMAX-GRM, GBLUP and FvR). The most strongly associated SNPs from each individual analysis were ranked and evaluated for concordance. The heritability of susceptibility to BRDC in pre-weaned Holstein calves was estimated.

Results: The four statistical approaches produced highly concordant results for 373 top ranked SNPs that defined 126 chromosomal regions for the CA population. Similarly, in NM, 370 SNPs defined 138 genomic regions that were identified by all four approaches. When the two populations were combined (i.e., CA + NM) and analyzed, 324 SNPs defined 116 genomic regions that were associated with BRDC across all analytical methods. Heritability estimates for BRDC were 21% for both CA and NM as individual populations, but declined to 13% when the populations were combined.

Conclusions: Four analytical approaches utilizing both single and multi-marker association methods revealed common genomic regions associated with BRDC susceptibility that can be further characterized and used for genomic selection. Moderate heritability estimates were observed for BRDC susceptibility in pre-weaned Holstein calves, thereby supporting the application of genomic selection to reduce the prevalence of BRDC in U.S. Holsteins.
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http://dx.doi.org/10.1186/1471-2164-15-1164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445561PMC
December 2014

Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes.

Cell 2014 Nov 30;159(4):800-13. Epub 2014 Oct 30.

Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA. Electronic address:

We sequenced the MSY (male-specific region of the Y chromosome) of the C57BL/6J strain of the laboratory mouse Mus musculus. In contrast to theories that Y chromosomes are heterochromatic and gene poor, the mouse MSY is 99.9% euchromatic and contains about 700 protein-coding genes. Only 2% of the MSY derives from the ancestral autosomes that gave rise to the mammalian sex chromosomes. Instead, all but 45 of the MSY's genes belong to three acquired, massively amplified gene families that have no homologs on primate MSYs but do have acquired, amplified homologs on the mouse X chromosome. The complete mouse MSY sequence brings to light dramatic forces in sex chromosome evolution: lineage-specific convergent acquisition and amplification of X-Y gene families, possibly fueled by antagonism between acquired X-Y homologs. The mouse MSY sequence presents opportunities for experimental studies of a sex-specific chromosome in its entirety, in a genetically tractable model organism.
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http://dx.doi.org/10.1016/j.cell.2014.09.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260969PMC
November 2014

Results of the BRD CAP project: progress toward identifying genetic markers associated with BRD susceptibility.

Anim Health Res Rev 2014 Dec 11;15(2):157-60. Epub 2014 Nov 11.

Department of Molecular and Cellular Medicine,Texas A&M Health Science Center College of Medicine, Texas A&M University,Bryan,Texas,USA.

The Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP) is a 5-year project funded by the United States Department of Agriculture (USDA), with an overriding objective to use the tools of modern genomics to identify cattle that are less susceptible to BRD. To do this, two large genome wide association studies (GWAS) were conducted using a case:control design on preweaned Holstein dairy heifers and beef feedlot cattle. A health scoring system was used to identify BRD cases and controls. Heritability estimates for BRD susceptibility ranged from 19 to 21% in dairy calves to 29.2% in beef cattle when using numerical scores as a semi-quantitative definition of BRD. A GWAS analysis conducted on the dairy calf data showed that single nucleotide polymorphism (SNP) effects explained 20% of the variation in BRD incidence and 17-20% of the variation in clinical signs. These results represent a preliminary analysis of ongoing work to identify loci associated with BRD. Future work includes validation of the chromosomal regions and SNPs that have been identified as important for BRD susceptibility, fine mapping of chromosomes to identify causal SNPs, and integration of predictive markers for BRD susceptibility into genetic tests and national cattle genetic evaluations.
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http://dx.doi.org/10.1017/S1466252314000231DOI Listing
December 2014

Genome-wide DNA methylation profiles and their relationships with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos taurine).

Sci Rep 2014 Oct 13;4:6546. Epub 2014 Oct 13.

College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi, People's Republic of China.

DNA methylation is a key epigenetic modification in mammals and plays important roles in muscle development. We sampled longissimus dorsi muscle (LDM) from a well-known elite native breed of Chinese Qinchuan cattle living within the same environment but displaying distinct skeletal muscle at the fetal and adult stages. We generated and provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA for fetal and adult muscle studies. Integration analysis revealed a total of 77 and 1,054 negatively correlated genes with methylation in the promoter and gene body regions, respectively, in both the fetal and adult bovine libraries. Furthermore, we identified expression patterns of high-read genes that exhibit a negative correlation between methylation and expression from nine different tissues at multiple developmental stages of bovine muscle-related tissue or organs. In addition, we validated the MeDIP-Seq results by bisulfite sequencing PCR (BSP) in some of the differentially methylated promoters. Together, these results provide valuable data for future biomedical research and genomic and epigenomic studies of bovine skeletal muscle that may help uncover the molecular basis underlying economically valuable traits in cattle. This comprehensive map also provides a solid basis for exploring the epigenetic mechanisms of muscle growth and development.
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http://dx.doi.org/10.1038/srep06546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194443PMC
October 2014

An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae.

BMC Genomics 2014 Jul 23;15:625. Epub 2014 Jul 23.

Key lab of animal genetics, breeding and reproduction of ministry education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.

Background: The domestic goat (Capra hircus), an important livestock species, belongs to a clade of Ruminantia, Bovidae, together with cattle, buffalo and sheep. The history of genome evolution and chromosomal rearrangements on a small scale in ruminants remain speculative. Recently completed goat genome sequence was released but is still in a draft stage. The draft sequence used a variety of assembly packages, as well as a radiation hybrid (RH) map of chromosome 1 as part of its validation.

Results: Using an improved RH mapping pipeline, whole-genome dense maps of 45,953 SNP markers were constructed with statistical confidence measures and the saturated maps provided a fine map resolution of approximate 65 kb. Linking RH maps to the goat sequences showed that the assemblies of scaffolds/super-scaffolds were globally accurate. However, we observed certain flaws linked to the process of anchoring chromosome using conserved synteny with cattle. Chromosome assignments, long-range order, and orientation of the scaffolds were reassessed in an updated genome sequence version. We also present new results exploiting the updated goat genome sequence to understand genomic rearrangements and chromosome evolution between mammals during species radiations. The sequence architecture of rearrangement sites between the goat and cattle genomes presented abundant segmental duplication on regions of goat chromosome 9 and 14, as well as new insertions in homologous cattle genome regions. This complex interplay between duplicated sequences and Robertsonian translocations highlights the rearrangement mechanism of centromeric nonallelic homologous recombination (NAHR) in mammals. We observed that species-specific shifts in ANKRD26 gene duplication are coincident with breakpoint reuse in divergent lineages and this gene family may play a role in chromosome stabilization in chromosome evolution.

Conclusions: We generated dense maps of the complete whole goat genome. The chromosomal maps allowed us to anchor and orientate assembled genome scaffolds along the chromosomes, annotate chromosome rearrangements and thereby get a better understanding of the genome evolution of ruminants and other mammals.
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http://dx.doi.org/10.1186/1471-2164-15-625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141111PMC
July 2014

Mapping and genotypic analysis of the NK-lysin gene in chicken.

Genet Sel Evol 2014 Jul 7;46:43. Epub 2014 Jul 7.

Department of Veterinary Pathobiology, Texas A & M University, College Station, TX 77843, USA.

Background: Antimicrobial peptides (AMP) are important elements of the first line of defence against pathogens in animals. NK-lysin is a cationic AMP that plays a critical role in innate immunity. The chicken NK-lysin gene has been cloned and its antimicrobial and anticancer activity has been described but its location in the chicken genome remains unknown. Here, we mapped the NK-lysin gene and examined the distribution of a functionally significant single nucleotide polymorphism (SNP) among different chicken inbred lines and heritage breeds.

Results: A 6000 rad radiation hybrid panel (ChickRH6) was used to map the NK-lysin gene to the distal end of chromosome 22. Two additional genes, the adipocyte enhancer-binding protein 1-like gene (AEBP1) and the DNA polymerase delta subunit 2-like (POLD2) gene, are located in the same NW_003779909 contig as NK-lysin, and were thus indirectly mapped to chromosome 22 as well. Previously, we reported a functionally significant SNP at position 271 of the NK-lysin coding sequence in two different chicken breeds. Here, we examined this SNP and found that the A allele appears to be more common than the G allele in these heritage breeds and inbred lines.

Conclusions: The chicken NK-lysin gene mapped to the distal end of chromosome 22. Two additional genes, AEBP1 and POLD2, were indirectly mapped to chromosome 22 also. SNP analyses revealed that the A allele, which encodes a peptide with a higher antimicrobial activity, is more common than the G allele in our tested inbred lines and heritage breeds.
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http://dx.doi.org/10.1186/1297-9686-46-43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4120735PMC
July 2014

Chicken NK-lysin is an alpha-helical cationic peptide that exerts its antibacterial activity through damage of bacterial cell membranes.

Poult Sci 2014 Apr;93(4):864-70

World Class University Biomodulation Major, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea 151-742.

The antimicrobial peptides (AMP) are important elements of the first line of defense against pathogens in animals, and an important constituent of innate immunity. Antimicrobial peptides act on a broad spectrum of microbial organisms. NK-Lysin is a cationic antibacterial peptide that was originally isolated from porcine intestinal tissue based on its antibacterial activity. We synthesized peptides corresponding to each helical region of chicken NK-lysin and analyzed their secondary structures in addition to their antimicrobial activity. Circular dichroism spectroscopy of the synthetic chicken NK-lysin (cNK-78) and 4 small peptides in negatively charged liposomes demonstrated transition in the conformation of α-helical peptides relative to the charged environment. Chicken NK-lysin inhibits the growth of a representative gram-negative bacterium, Escherichia coli. The antimicrobial activity of 2 peptides designated H23 and H34 was similar to that of mature NK-lysin, cNK-78. Microscopic analyses revealed the death of bacterium with disrupted membranes after peptide treatment, suggesting that chicken NK-lysin, an alpha-helical cationic peptide, exerts its antimicrobial activity by damaging the bacterial cell membrane.
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http://dx.doi.org/10.3382/ps.2013-03670DOI Listing
April 2014

Functional characterization of naturally occurring melittin peptide isoforms in two honey bee species, Apis mellifera and Apis cerana.

Peptides 2014 Mar 8;53:185-93. Epub 2014 Feb 8.

WCU Biomodulation Major, Department of Agricultural Biotechnology, College of Agriculture & Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea. Electronic address:

Insect-derived antimicrobial peptides (AMPs) have diverse effects on antimicrobial properties and pharmacological activities such as anti-inflammation and anticancer properties. Naturally occurring genetic polymorphism have a direct and/or indirect influence on pharmacological effect of AMPs, therefore information on single nucleotide polymorphism (SNP) occurring in natural AMPs provides an important clue to therapeutic applications. Here we identified nucleotide polymorphisms in melittin gene of honey bee populations, which is one of the potent AMP in bee venoms. We found that the novel SNP of melittin gene exists in these two honey bee species, Apis mellifera and Apis cerana. Nine polymorphisms were identified within the coding region of the melittin gene, of which one polymorphism that resulted in serine (Ser) to asparagine (Asp) substitution that can potentially effect on biological activities of melittin peptide. Serine-substituted melittin (Mel-S) showed more cytotoxic effect than asparagine-substituted melittin (Mel-N) against E. coli. Also, Mel-N and Mel-S had different inhibitory effects on the production of inflammatory factors such as IL-6 and TNF-α in BV-2 cells. Moreover, Mel-S showed stronger cytotoxic activities than Mel-N peptide against two human ovarian cancer cell lines. Using carbon nanotube-based transistor, we here characterized that Mel-S interacted with small unilamellar liposomes more strongly than Mel-N. Taken together, our present study demonstrates that there exist different characteristics of the gene frequency and the biological activities of the melittin peptide in two honey bee species, Apis mellifera and A. cerana.
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http://dx.doi.org/10.1016/j.peptides.2014.01.026DOI Listing
March 2014

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus).

Nat Biotechnol 2013 Feb 23;31(2):135-41. Epub 2012 Dec 23.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

We report the ∼2.66-Gb genome sequence of a female Yunnan black goat. The sequence was obtained by combining short-read sequencing data and optical mapping data from a high-throughput whole-genome mapping instrument. The whole-genome mapping data facilitated the assembly of super-scaffolds >5× longer by the N50 metric than scaffolds augmented by fosmid end sequencing (scaffold N50 = 3.06 Mb, super-scaffold N50 = 16.3 Mb). Super-scaffolds are anchored on chromosomes based on conserved synteny with cattle, and the assembly is well supported by two radiation hybrid maps of chromosome 1. We annotate 22,175 protein-coding genes, most of which were recovered in the RNA-seq data of ten tissues. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat reveal 51 genes that are differentially expressed between the two types of hair follicles. This study, whose results will facilitate goat genomics, shows that whole-genome mapping technology can be used for the de novo assembly of large genomes.
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http://dx.doi.org/10.1038/nbt.2478DOI Listing
February 2013

Genomics of complex traits.

Ann N Y Acad Sci 2012 Oct;1271:33-6

Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.

The analysis of complex genetic traits, including mapping and identification of causative genes, has long been an enigma of genetic biology, whether in the animal sciences or in medical sciences. Traits of agricultural interest and traits of medical interest are often under the influence of both environmental factors and multiple genes, each with modest contributions to the total variance in the trait. Although the number of known mutations underlying complex traits is still relatively small, advances in genomics have greatly enhanced traditional pathways to their analysis and gene mining. The candidate gene approach, linkage analysis, and association studies are all significantly more powerful with recent advances in genome mapping, sequencing, and analysis of individual variation. Avenues to gene discovery are discussed with emphasis on genome wide association studies (GWAS) and the use of single nucleotide polymorphisms (SNPs) as revealed by increasingly powerful commercially available microarrays.
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http://dx.doi.org/10.1111/j.1749-6632.2012.06733.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483623PMC
October 2012

Effects of a single nucleotide polymorphism in the chicken NK-lysin gene on antimicrobial activity and cytotoxicity of cancer cells.

Proc Natl Acad Sci U S A 2012 Jul 10;109(30):12087-92. Epub 2012 Jul 10.

World Class University Biomodulation Major, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea.

NK-lysin is an effector protein of the innate immune system and an important component of host protection. We isolated a SNP in the NK-lysin coding sequence among different chicken breeds. This A to G substitution at the position 271 nucleotide in the ORF results in an Asn (N) to Asp (D) amino acid alteration. We synthesized two 30-aa peptides (N29N and N29D) to compare the biological activity of the helix 2-loop-helix 3 region of NK-lysin resulting from the polymorphic gene. Both peptides were found to be cytotoxic in bacteria and tumor cell cultures at micromolar concentrations. The N29N peptide, however, exhibited greater antibacterial and anticancer activity than the N29D peptide. Circular dichroism spectroscopy of the two peptides in negatively charged single unilamellar vesicles showed spectra typical of α-helical peptides. The helical profile of N29D was reduced substantially compared with that of N29N. However, no structural change was observed in neutral vesicles. ζ-Potential measurements of liposomes incubated with increasing peptide concentrations allowed surface charge neutralization with a negatively charged lipid, but not with a zwitterionic lipid. This result suggests that a difference in electrostatic interaction between lipid membranes and the helical peptides results from the polymorphic gene and is subsequently an important factor in cell lytic activity of variant NK-lysin peptides.
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http://dx.doi.org/10.1073/pnas.1209161109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409721PMC
July 2012

First steps: bovine genomics in historical perspective.

Authors:
James E Womack

Anim Genet 2012 Jul;43 Suppl 1:2-8

Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843-4467, USA.

The vision of Morris Soller was instrumental in launching the field of bovine genomics. This study is a review of the early years of bovine gene mapping leading up to the sequencing and assembly of the bovine genome in 2009. A historical perspective of parasexual, linkage and physical mapping is provided with a focus on the contribution of these maps to the eventual assignment and orientation of genes and sequence to cattle chromosomes.
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http://dx.doi.org/10.1111/j.1365-2052.2012.02382.xDOI Listing
July 2012

Gene expression and DNA methylation status of chicken primordial germ cells.

Mol Biotechnol 2013 Jun;54(2):177-86

Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.

DNA methylation reprogramming of primordial germ cells (PGCs) in mammals establishes monoallelic expression of imprinting genes, maintains retrotransposons in an inactive state, inactivates one of the two X chromosomes, and suppresses gene expression. However, the roles of DNA methylation in chickens PGCs are unknown. In this study, we found a 1.5-fold or greater difference in the expression of 261 transcripts when comparing PGCs and chicken embryonic fibroblasts (CEFs) using an Affymetrix GeneChip Chicken Genome Array. In addition, we analyzed the methylation patterns of the regions ~5-kb upstream of 261 sorted genes, 51 of which were imprinting homologous loci and 49 of which were X-linked homologous loci in chicken using the MeDIP Array by Roche NimbleGen. Seven hypomethylated and five hypermethylated regions within the 5-kb upstream regions of 261 genes were found in PGCs when compared with CEFs. These differentially methylated regions were restrictively matched to differentially expressed genes in PGCs. We also detected 203 differentially methylated regions within imprinting and X-linked homologous regions between male PGCs and female PGCs. These differentially methylated regions may be directly or indirectly associated with gene expression during early embryonic development, and the epigenetic difference could be evolutionally conserved between mammals and birds.
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http://dx.doi.org/10.1007/s12033-012-9560-5DOI Listing
June 2013

Mechanical properties and elution characteristics of polymethylmethacrylate bone cement impregnated with antibiotics for various surface area and volume constructs.

Iowa Orthop J 2012 ;32:104-15

Department of Surgery, Section of Orthopaedics, The University of Kansas School of Medicine- Wichita, 929 N St Francis, Wichita, KS, USA.

Background: Numerous studies have examined the elution characteristics and the effects of antibiotics from bone cement. this study seeks to determine the effect that surface area and volume have on the elution characteristics and bioavailability of tobramycin and vancomycin when mixed in polymethylmethacralate (PMMA) bone cement in various combinations. It also investigates the mechanical properties of antibiotic-impregnated bone cement and its relationship to surface area and volume.

Methods: Three antibiotic-bone cement combinations were used, and these consisted of PMMA mixed with tobramycin and vancomycin or tobramycin alone. Four groups of specimens (different surface area and volume) were made. the elution characteristics of the different specimens were examined using the minimum inhibitory concentration (MIc) method at different time intervals. the bacteria used during testing were methicillin-sensitive staphylococcus aureus (MssA). the ultimate compressive strength (Ucs) of the specimens was also determined at various time intervals.

Results: the bactericidal activity of a tobramycin/vancomycin combination against MssA was not significantly greater than tobramycin alone. tobramycin was more effective than vancomycin against MssA (average: 168%, p<0.05). the inhibitory capabilities of tobramycin and vancomycin individually were not found to be additive. combination 2 (1.0 g tobramycin/1.0 g vancomycin) had a higher antibiotic elution mass and rate for all sample sizes compared to the other two combinations (average: 170%, p<0.05). surface area and volume did not have a significant effect on the elution rate of the antibiotics. the Ucs of all samples tested was greater than 70 MPa at all three testing intervals.

Discussion: Mixing tobramycin and vancomycin did not have a synergistic effect against the bacteria as expected. Increasing the concentration of antibiotics in bone cement increases both elution mass and elution rate over time. Although the Ucs of the antibiotic-impregnated bone cement was affected by antibiotic elution and sample geometry, all testing results fell within previously accepted standards.

Clinical Relevance: This study advanced our overall understanding of the elution characteristics and biomechanics of PMMA bone cement impregnated with tobramycin and vancomycin.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565390PMC
July 2013

Evolution of the bovine TLR gene family and member associations with Mycobacterium avium subspecies paratuberculosis infection.

PLoS One 2011 30;6(11):e27744. Epub 2011 Nov 30.

Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.

Members of the Toll-like receptor (TLR) gene family occupy key roles in the mammalian innate immune system by functioning as sentries for the detection of invading pathogens, thereafter provoking host innate immune responses. We utilized a custom next-generation sequencing approach and allele-specific genotyping assays to detect and validate 280 biallelic variants across all 10 bovine TLR genes, including 71 nonsynonymous single nucleotide polymorphisms (SNPs) and one putative nonsense SNP. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and specialized beef and dairy breeds could not be differentiated despite an average polymorphism density of 1 marker/158 bp. Collectively, 160 tagSNPs and two tag insertion-deletion mutations (indels) were sufficient to predict 100% of the variation at 280 variable sites for both Bos subspecies and their hybrids, whereas 118 tagSNPs and 1 tagIndel predictively captured 100% of the variation at 235 variable sites for B. t. taurus. Polyphen and SIFT analyses of amino acid (AA) replacements encoded by bovine TLR SNPs indicated that up to 32% of the AA substitutions were expected to impact protein function. Classical and newly developed tests of diversity provide strong support for balancing selection operating on TLR3 and TLR8, and purifying selection acting on TLR10. An investigation of the persistence and continuity of linkage disequilibrium (r2≥0.50) between adjacent variable sites also supported the presence of selection acting on TLR3 and TLR8. A case-control study employing validated variants from bovine TLR genes recognizing bacterial ligands revealed six SNPs potentially eliciting small effects on susceptibility to Mycobacterium avium spp paratuberculosis infection in dairy cattle. The results of this study will broadly impact domestic cattle research by providing the necessary foundation to explore several avenues of bovine translational genomics, and the potential for marker-assisted vaccination.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027744PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227585PMC
May 2012
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