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Search Results: 1 - 10 of 598 matches for " Ynte Hein Schukken "
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Microbial Diversity of Bovine Mastitic Milk as Described by Pyrosequencing of Metagenomic 16s rDNA
Georgios Oikonomou, Vinicius Silva Machado, Carlos Santisteban, Ynte Hein Schukken, Rodrigo Carvalho Bicalho
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0047671
Abstract: Dairy cow mastitis is an important disease in the dairy industry. Different microbial species have been identified as causative agents in mastitis, and are traditionally diagnosed by bacterial culture. The objective of this study was to use metagenomic pyrosequencing of bacterial 16S rRNA genes to investigate bacterial DNA diversity in milk samples of mastitic and healthy dairy cows and compare the results with those obtained by classical bacterial culture. One hundred and thirty-six milk samples were collected from cows showing signs of mastitis and used for microbiological culture. Additionally, 20 milk samples were collected from healthy quarters. Bacterial DNA was isolated from the same milk samples and the 16S rRNA genes were individually amplified and pyrosequenced. Discriminant analysis showed that the groups of samples that were most clearly different from the rest and thus easily discriminated were the normal milk samples from healthy cows and those characterised by culture as Trueperella pyogenes and Streptococcus spp. The mastitis pathogens identified by culture were generally among the most frequent organisms detected by pyrosequencing, and in some cases (Escherichia coli, Klebsiella spp. and Streptococcus uberis mastitis) the single most prevalent microorganism. Trueperella pyogenes sequences were the second most prevalent sequences in mastitis cases diagnosed as Trueperella pyogenes by culture, Streptococcus dysgalactiae sequences were the second most prevalent sequences in mastitis cases diagnosed as Streptococcus dysgalactiae by culture, and Staphyloccocus aureus sequences were the third most prevalent in mastitis cases diagnosed as Staphylococcus aureus by culture. In samples that were aerobic culture negative, pyrosequencing identified DNA of bacteria that are known to cause mastitis, DNA of bacteria that are known pathogens but have so far not been associated with mastitis, and DNA of bacteria that are currently not known to be pathogens. A possible role of anaerobic pathogens in bovine mastitis is also suggested.
Microbiota of Cow’s Milk; Distinguishing Healthy, Sub-Clinically and Clinically Diseased Quarters
Georgios Oikonomou, Marcela Lucas Bicalho, Enoch Meira, Rodolfo Elke Rossi, Carla Foditsch, Vinicius Silva Machado, Andre Gustavo Vieira Teixeira, Carlos Santisteban, Ynte Hein Schukken, Rodrigo Carvalho Bicalho
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0085904
Abstract: The objective of this study was to use pyrosequencing of the 16S rRNA genes to describe the microbial diversity of bovine milk samples derived from clinically unaffected quarters across a range of somatic cell counts (SCC) values or from clinical mastitis, culture negative quarters. The obtained microbiota profiles were used to distinguish healthy, subclinically and clinically affected quarters. Two dairy farms were used for the collection of milk samples. A total of 177 samples were used. Fifty samples derived from healthy, culture negative quarters with a SCC of less than 20,000 cells/ml (group 1); 34 samples derived from healthy, culture negative quarters, with a SCC ranging from 21,000 to 50,000 cells/ml (group 2); 26 samples derived from healthy, culture negative quarters with a SCC greater than 50,000 cells/ml (group 3); 34 samples derived from healthy, culture positive quarters, with a SCC greater than 400,000 (group 4, subclinical); and 33 samples derived from clinical mastitis, culture negative quarters (group 5, clinical). Bacterial DNA was isolated from these samples and the 16S rRNA genes were individually amplified and pyrosequenced. All samples analyzed revealed great microbial diversity. Four bacterial genera were present in every sample obtained from healthy quarters (Faecalibacterium spp., unclassified Lachnospiraceae, Propionibacterium spp. and Aeribacillus spp.). Discriminant analysis models showed that samples derived from healthy quarters were easily discriminated based on their microbiota profiles from samples derived from clinical mastitis, culture negative quarters; that was also the case for samples obtained from different farms. Staphylococcus spp. and Streptococcus spp. were among the most prevalent genera in all groups while a general multivariable linear model revealed that Sphingobacterium and Streptococcus prevalences were associated with increased 10 log SCC. Conversely, Nocardiodes and Paenibacillus were negatively correlated, and a higher percentage of the genera was associated with a lower 10 log SCC.
Effect of lactation therapy on Staphylococcus aureus transmission dynamics in two commercial dairy herds
John W Barlow, Ruth N Zadoks, Ynte H Schukken
BMC Veterinary Research , 2013, DOI: 10.1186/1746-6148-9-28
Abstract: The direct effect of 8?days intramammary lactation therapy with pirlimycin hydrochloride was demonstrated by an increased proportion of cure and a reduction in duration of infection in quarters receiving treatment compared to untreated controls. The indirect effect of lactation therapy was demonstrated by reduction of new S. aureus intramammary infections (IMI) caused by the dominant strain type in both herds. Strain typing of representative isolates taken over the duration of all IMI, including pre- and post-treatment isolates, provided more precise estimates of new infection, cure, and re-infection rates. New S. aureus infections in recovered susceptible quarters and the emergence of a new strain type in one herd influenced incidence measures.In addition to demonstrating positive direct effects of lactation therapy, this study provides evidence that treatment of subclinical S. aureus mastitis during lactation can have indirect effects including preventing new IMI and reducing incidence of clinical mastitis within dairy herds. Strain specific transmission parameter estimates for S. aureus MLST clonal complexes 5, 97 and 705 in 2 commercial dairy herds are also reported.Mastitis continues to be recognized as one of the most economically important health problems of dairy cattle [1,2]. Subclinical mastitis, which can be characterized by an elevated milk somatic cell count (SCC), is the dominant form affecting cows. A number of authors have suggested that dairy producers frequently leave subclinical mastitis undetected or untreated for extended periods during lactation [3-5].Mastitis control interventions are intended to reduce the duration of infection and prevent new infections. Examples of effective mastitis control practices include the use of long acting antibiotics at the end of lactation (dry-cow therapy), application of a post-milking teat disinfectant following each milking, and segregation or culling of infected individuals [6,7]. Treatment of mastitis durin
Impact of Intramammary Treatment on Gene Expression Profiles in Bovine Escherichia coli Mastitis
Anja Sipka, Suzanne Klaessig, Gerald E. Duhamel, Jantijn Swinkels, Pascal Rainard, Ynte Schukken
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0085579
Abstract: Clinical mastitis caused by E. coli accounts for significant production losses and animal welfare concerns on dairy farms worldwide. The benefits of therapeutic intervention in mild to moderate cases are incompletely understood. We investigated the effect of intramammary treatment with cefapirin alone or in combination with prednisolone on gene expression profiles in experimentally-induced E. coli mastitis in six mid-lactating Holstein Friesian cows. Cows were challenged with E. coli in 3 quarters and received 4 doses of 300 mg cefapirin in one quarter and 4 doses of 300 mg cefapirin together with 20 mg prednisolone in another quarter. At 24 h (n = 3) or 48 h (n = 3) post-challenge, tissue samples from control and treated quarters were collected for microarray analysis. Gene expression analysis of challenged, un-treated quarters revealed an up-regulation of transcripts associated with immune response functions compared to un-challenged quarters. Both treatments resulted in down-regulation of these transcripts compared to challenged, un-treated quarters most prominently for genes representing Chemokine and TLR-signaling pathways. Gene expression of Lipopolysaccharide Binding Protein (LBP), CCL2 and CXCL2 were only significantly down-regulated in cefapirin-prednisolone-treated quarters compared to un-treated controls. Down-regulation of chemokines was further confirmed on the basis of protein levels in milk whey for CXCL1, CXCL2 and CXCL8 in both treatments with a greater decrease in cefapirin-prednisolone-treated quarters. The data reveal a significant effect of treatment on cell recruitment with a more pronounced effect in cefapirin-prednisolone treated quarters. Provided a rapid bacteriological clearance, combination therapy may prevent neutrophil-induced tissue damage and promote recovery of the gland.
Evolution of the Bovine TLR Gene Family and Member Associations with Mycobacterium avium Subspecies paratuberculosis Infection
Colleen A. Fisher, Eric K. Bhattarai, Jason B. Osterstock, Scot E. Dowd, Paul M. Seabury, Meenu Vikram, Robert H. Whitlock, Ynte H. Schukken, Robert D. Schnabel, Jeremy F. Taylor, James E. Womack, Christopher M. Seabury
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0027744
Abstract: 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.
Numerical extraction of a macroscopic pde and a lifting operator from a lattice Boltzmann model
Ynte Vanderhoydonc,Wim Vanroose
Physics , 2011, DOI: 10.1137/110842739
Abstract: Lifting operators play an important role in starting a lattice Boltzmann model from a given initial density. The density, a macroscopic variable, needs to be mapped to the distribution functions, mesoscopic variables, of the lattice Boltzmann model. Several methods proposed as lifting operators have been tested and discussed in the literature. The most famous methods are an analytically found lifting operator, like the Chapman-Enskog expansion, and a numerical method, like the Constrained Runs algorithm, to arrive at an implicit expression for the unknown distribution functions with the help of the density. This paper proposes a lifting operator that alleviates several drawbacks of these existing methods. In particular, we focus on the computational expense and the analytical work that needs to be done. The proposed lifting operator, a numerical Chapman-Enskog expansion, obtains the coefficients of the Chapman-Enskog expansion numerically. Another important feature of the use of lifting operators is found in hybrid models. There the lattice Boltzmann model is spatially coupled with a model based on a more macroscopic description, for example an advection-diffusion-reaction equation. In one part of the domain, the lattice Boltzmann model is used, while in another part, the more macroscopic model. Such a hybrid coupling results in missing data at the interfaces between the different models. A lifting operator is then an important tool since the lattice Boltzmann model is typically described by more variables than a model based on a macroscopic partial differential equation.
Constrained Runs algorithm as a lifting operator for the Boltzmann equation
Ynte Vanderhoydonc,Wim Vanroose
Computer Science , 2014,
Abstract: Lifting operators play an important role in starting a kinetic Boltzmann model from given macroscopic information. The macroscopic variables need to be mapped to the distribution functions, mesoscopic variables of the Boltzmann model. A well-known numerical method for the initialization of Boltzmann models is the Constrained Runs algorithm. This algorithm is used in literature for the initialization of lattice Boltzmann models, special discretizations of the Boltzmann equation. It is based on the attraction of the dynamics toward the slow manifold and uses lattice Boltzmann steps to converge to the desired dynamics on the slow manifold. We focus on applying the Constrained Runs algorithm to map density, average flow velocity, and temperature, the macroscopic variables, to distribution functions. Furthermore, we do not consider only lattice Boltzmann models. We want to perform the algorithm for different discretizations of the Boltzmann equation and consider a standard finite volume discretization.
Initialization of lattice Boltzmann models with the help of the numerical Chapman-Enskog expansion
Ynte Vanderhoydonc,Wim Vanroose
Computer Science , 2014, DOI: 10.1016/j.procs.2013.05.269
Abstract: We extend the applicability of the numerical Chapman-Enskog expansion as a lifting operator for lattice Boltzmann models to map density and momentum to distribution functions. In earlier work [Vanderhoydonc et al. Multiscale Model. Simul. 10(3): 766-791, 2012] such an expansion was constructed in the context of lifting only the zeroth order velocity moment, namely the density. A lifting operator is necessary to convert information from the macroscopic to the mesoscopic scale. This operator is used for the initialization of lattice Boltzmann models. Given only density and momentum, the goal is to initialize the distribution functions of lattice Boltzmann models. For this initialization, the numerical Chapman-Enskog expansion is used in this paper.
How to React to the Subprime Crisis? - The Impact of an Interest Rate Freeze on Residential Mortgage Backed  [PDF]
Julia Hein, Thomas Weber
Journal of Service Science and Management (JSSM) , 2009, DOI: 10.4236/jssm.2009.24035
Abstract: Several policy options have been discussed to mitigate the current subprime mortgage crisis. This paper analyses an interest rate freeze on adjustable rate mortgages as one possible reaction. In particular, the implications on Residential Mortgage Backed Securities (RMBS) are studied. We examine shifts in the underlying portfolio’s discounted cash flow distributions as well as changes in the payment profile of RMBS-tranches. We show that the positive effects of a rate freeze, e.g. less foreclosures and a stabilizing housing market, can outweigh the negative effect of lower interest income such that investors might be better off.
From GWAS to the clinic: risk factors for intracranial aneurysms
Ynte M Ruigrok, Gabriel JE Rinkel
Genome Medicine , 2010, DOI: 10.1186/gm182
Abstract: Subarachnoid hemorrhage (SAH) from a ruptured intracranial aneurysm is a devastating subset of stroke. Intracranial aneurysms are mostly situated on the larger arteries supplying the brain. These arteries run through the so-called subarachnoid space, which is the very small space between the brain and the skull. If such an aneurysm ruptures, a bleed under arterial pressure occurs in this subarachnoid space. Clinically, patients have a sudden, unusual severe headache, which is combined with a sudden loss of consciousness in half of them. The mean age at time of SAH is around 50 years, and the incidence is around 1 per 10,000 people per year, with highest rates in Japan and Finland and higher rates in women than in men [1]. Despite improvements in patient management and improved prognosis, around a third of patients still die in the initial months after the hemorrhage [2].Because of the relatively young age of onset and its poor prognosis, the socioeconomic burden of SAH is considerable. The number of productive life years lost in the population from SAH is as large as that lost from ischemic stroke [3] and, according to a recent study, a total of 80,356 life years and 74,807 quality-adjusted life years were lost as a result of SAH in the UK in 2005 [4]. Further improvements in prognosis in SAH patients on a population level will be difficult to achieve, because one in eight patients dies immediately, before reaching the hospital [5]. Therefore, prevention seems an attractive option to reduce the burden of SAH, and knowledge on risk factors is essential for the development of preventive measures.Risk factors for SAH can be divided into modifiable - or environmental - and non-modifiable risk factors. Established environmental risk factors for SAH are smoking, hypertension and excessive alcohol intake [6]. Non-modifiable risk factors include a familial preponderance of SAH, female gender and systemic diseases, such as polycystic kidney disease and the vascular type of E
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