Using Object-Oriented Simulation to Assess the Impact of the Frequency and Accuracy of Mobility Scoring on the Estimation of Epidemiological Parameters for Lameness in Dairy Herds.

Mobility scoring data can be used to estimate the prevalence, incidence, and duration of lameness in dairy herds. Mobility scoring is often performed infrequently with variable sensitivity, but how this impacts the estimation of lameness parameters is largely unknown. We developed a simulation model to investigate the impact of the frequency and accuracy of mobility scoring on the estimation of lameness parameters for different herd scenarios. Herds with a varying prevalence (10, 30, or 50%) and duration (distributed around median days 18, 36, 54, 72, or 108) of lameness were simulated at daily time steps for five years. The lameness parameters investigated were prevalence, duration, new case rate, time to first lameness, and probability of remaining sound in the first year. True parameters were calculated from daily data and compared to those calculated when replicating different frequencies (weekly, two-weekly, monthly, quarterly), sensitivities (60-100%), and specificities (95-100%) of mobility scoring. Our results showed that over-estimation of incidence and under-estimation of duration can occur when the sensitivity and specificity of mobility scoring are <100%. This effect increases with more frequent scoring. Lameness prevalence was the only parameter that could be estimated with reasonable accuracy when simulating quarterly mobility scoring. These findings can help inform mobility scoring practices and the interpretation of mobility scoring data.

"I didn't see a sheep": perspectives of lecturers and students at veterinary schools in Great Britain on learning about lameness in sheep.

Introduction: Great Britain has over 15 million ewes. Lameness is one of the top three most economically important diseases for the sheep industry, costing about £80 million per annum. The prevalence of lameness reduced from 10% to 5% between 2004 and 2013 but further reduction is unlikely because many farmers and agricultural students still believe in, and use, ineffective practices to control lameness. Unfortunately, many veterinary practitioners consider themselves insufficiently knowledgeable to work confidently with sheep farmers, and many sheep farmers agree with them. Another route to improve control of lameness is to ensure that all new veterinary graduates are competent to advise farmers. Methods: Our study investigated how veterinary students are taught about management of lameness in sheep. Ten lecturers from eight veterinary schools were interviewed, and 33 students from four veterinary schools participated in four focus groups; all were recorded, transcribed, and analysed using directed qualitative content analysis. Results: Teaching time and opportunities for students to gain clinical experience of lameness were very limited. Students were not confident they could diagnose causes of lameness and listed many practices, including ineffective ones, to manage footrot. Discussion: We conclude that GB veterinary students are graduating without evidence-based understanding and clinical experience necessary to advise farmers on management of lameness in sheep. Given the importance of lameness in sheep in GB we conclude that an alternative approach to education on lameness in sheep could help to ensure that new graduate veterinarians can contribute to control of lameness in sheep.

Differences in composition of interdigital skin microbiota predict sheep and feet that develop footrot.

Footrot has a major impact on health and productivity of sheep worldwide. The current paradigm for footrot pathogenesis is that physical damage to the interdigital skin (IDS) facilitates invasion of the essential pathogen Dichelobacter nodosus. The composition of the IDS microbiota is different in healthy and diseased feet, so an alternative hypothesis is that changes in the IDS microbiota facilitate footrot. We investigated the composition and diversity of the IDS microbiota of ten sheep, five that did develop footrot and five that did not (healthy) at weekly intervals for 20 weeks. The IDS microbiota was less diverse on sheep 2 + weeks before they developed footrot than on healthy sheep. This change could be explained by only seven of > 2000 bacterial taxa detected. The incubation period of footrot is 8-10 days, and there was a further reduction in microbial diversity on feet that developed footrot in that incubation period. We conclude that there are two stages of dysbiosis in footrot: the first predisposes sheep to footrot and the second occurs in feet during the incubation of footrot. These findings represent a step change in our understanding of the role of the IDS microbiota in footrot pathogenesis.

Sites of persistence of Fusobacterium necrophorum and Dichelobacter nodosus: a paradigm shift in understanding the epidemiology of footrot in sheep.

Sites of persistence of bacterial pathogens contribute to disease dynamics of bacterial diseases. Footrot is a globally important bacterial disease that reduces health and productivity of sheep. It is caused by Dichelobacter nodosus, a pathogen apparently highly specialised for feet, while Fusobacterium necrophorum, a secondary pathogen in footrot is reportedly ubiquitous on pasture. Two prospective longitudinal studies were conducted to investigate the persistence of D. nodosus and F. necrophorum in sheep feet, mouths and faeces, and in soil. Molecular tools were used to detect species, strains and communities. In contrast to the existing paradigm, F. necrophorum persisted on footrot diseased feet, and in mouths and faeces; different strains were detected in feet and mouths. D. nodosus persisted in soil and on diseased, but not healthy, feet; similar strains were detected on both healthy and diseased feet of diseased sheep. We conclude that D. nodosus and F. necrophorum depend on sheep for persistence but use different strategies to persist and spread between sheep within and between flocks. Elimination of F. necrophorum would be challenging due to faecal shedding. In contrast D. nodosus could be eliminated if all footrot-affected sheep were removed and fade out of D. nodosus occurred in the environment before re-infection of a foot.

Development and validation of a multiple locus variable number tandem repeat analysis (MLVA) scheme for Fusobacterium necrophorum.

Fusobacterium necrophorum is associated with various diseases in humans and animals. Reservoirs (sites where the pathogen persists in the absence of disease) of F. necrophorum are believed to be present in healthy individuals e.g. tonsillar epithelium, or their environment e.g. soil, but for most diseases the reservoir sites are unknown. Strain typing of F. necrophorum would facilitate linking specific reservoirs with a specific disease. The aim of this study was to develop multiple locus variable number tandem repeat analysis (MLVA) as a strain typing technique for F. necrophorum, and to test the use of this scheme to analyse both isolates and mixed communities of bacteria. Seventy-three tandem repeat regions were identified in the F. necrophorum genome; three of these loci were suitable and developed as a MLVA scheme. The MLVA scheme was sensitive, specific, and discriminatory for both isolates and communities of F. necrophorum. The MLVA scheme strain typed 46/52F. necrophorum isolates including isolates of both subspecies and from different countries, host species and sample sites within host. There were 12 unique MLVA strain types that clustered by subspecies. The MLVA scheme characterised the F. necrophorum community in DNA from 32/49 foot- and 28/33 mouth swabs from sheep. There were 17 community types in total. In 31/32 foot swabs, single strains of F. necrophorum were detected while in the 28 mouth swabs there were up to a maximum of 8 strains of F. necrophorum detected. The results demonstrate the potential for this method to elucidate reservoirs of F. necrophorum.

C(m)CGG methylation-independent parent-of-origin effects on genome-wide transcript levels in isogenic reciprocal F1 triploid plants.

Triploid F1 hybrids generated via reciprocal interploidy crosses between genetically distinct parental plants can display parent-of-origin effects on gene expression or phenotypes. Reciprocal triploid F1 isogenic plants generated from interploidy crosses in the same genetic background allow investigation on parent-of-origin-specific (parental) genome-dosage effects without confounding effects of hybridity involving heterozygous mutations. Whole-genome transcriptome profiling was conducted on reciprocal F1 isogenic triploid (3x) seedlings of A. thaliana. The genetically identical reciprocal 3x genotypes had either an excess of maternally inherited 3x(m) or paternally inherited 3x(p) genomes. We identify a major parent-of-origin-dependent genome-dosage effect on transcript levels, whereby 602 genes exhibit differential expression between the reciprocal F1 triploids. In addition, using methylation-sensitive DNA tiling arrays, constitutive and polymorphic CG DNA methylation patterns at CCGG sites were analysed, which revealed that paternal-excess F1 triploid seedling C(m)CGG sites are overall hypermethylated. However, no correlation exists between C(m)CGG methylation polymorphisms and transcriptome dysregulation between the isogenic reciprocal F1 triploids. Overall, our study indicates that parental genome-dosage effects on the transcriptome levels occur in paternal-excess triploids, which are independent of C(m)CGG methylation polymorphisms. Such findings have implications for understanding parental effects and genome-dosage effects on gene expression and phenotypes in polyploid plants.

Conserved and novel functions for Arabidopsis thaliana MIA40 in assembly of proteins in mitochondria and peroxisomes.

The disulfide relay system of the mitochondrial intermembrane space has been extensively characterized in Saccharomyces cerevisiae. It contains two essential components, Mia40 and Erv1. The genome of Arabidopsis thaliana contains a single gene for each of these components. Although insertional inactivation of Erv1 leads to a lethal phenotype, inactivation of Mia40 results in no detectable deleterious phenotype. A. thaliana Mia40 is targeted to and accumulates in mitochondria and peroxisomes. Inactivation of Mia40 results in an alteration of several proteins in mitochondria, an absence of copper/zinc superoxide dismutase (CSD1), the chaperone for superoxide dismutase (Ccs1) that inserts copper into CSD1, and a decrease in capacity and amount of complex I. In peroxisomes the absence of Mia40 leads to an absence of CSD3 and a decrease in abnormal inflorescence meristem 1 (Aim1), a ß-oxidation pathway enzyme. Inactivation of Mia40 leads to an alteration of the transcriptome of A. thaliana, with genes encoding peroxisomal proteins, redox functions, and biotic stress significantly changing in abundance. Thus, the mechanistic operation of the mitochondrial disulfide relay system is different in A. thaliana compared with other systems, and Mia40 has taken on new roles in peroxisomes and mitochondria.

Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana.

Natural genetic variation in Arabidopsis thaliana exists for many traits and often reflects acclimation to local environments. Studying natural variation has proven valuable in the characterization of phenotypic traits and, in particular, in identifying genetic factors controlling these traits. It has been previously shown that chromatin compaction changes during development and biotic stress. To gain more insight into the genetic control of chromatin compaction, we investigated the nuclear phenotype of 21 selected Arabidopsis accessions from different geographic origins and habitats. We show natural variation in chromatin compaction and demonstrate a positive correlation with latitude of geographic origin. The level of compaction appeared to be dependent on light intensity. A novel approach, combining Quantitative Trait Locus (QTL) mapping and microscopic examination, pointed at PHYTOCHROME-B (PHYB) and HISTONE DEACETYLASE-6 (HDA6) as positive regulators of light-controlled chromatin compaction. Indeed, mutant analyses demonstrate that both factors affect global chromatin organization. HDA6, in addition, strongly promotes the light-mediated compaction of the Nucleolar Organizing Regions (NORs). The accession Cape Verde Islands-0 (Cvi-0), which shows sequence polymorphism in the PHYB gene and in the HDA6 promotor, resembles the hda6 mutant in having reduced chromatin compaction and decreased methylation levels of DNA and histone H3K9 at the NORs. We provide evidence that chromatin organization is controlled by light intensity. We propose that chromatin plasticity is associated with acclimation of Arabidopsis to its environment. The polymorphic alleles such as PHYB and HDA6 control this process.

Alternative oxidase: a target and regulator of stress responses.

The alternative oxidase (AOX) is found in all plants examined to date, fungi and lower invertebrates. We propose that AOX is not only part of the stress response in plants, but it also plays a central role in defining the stress response. Three lines of evidence support this proposal: (1) The absence of AOX leads to an alteration of stress defences in normal and stress conditions, (2) the expression of AOX is triggered by a variety of signals indicating that it is a common response and (3) AOX acts as a buffer that determines the threshold for the induction of programmed cell death. Therefore, AOX is not only one of many components involved in the defence response, its activity or lack of activity leads to a radical alteration of the defence equilibrium at a cellular level and thus it plays a central role in programming the stress response. This programming role of AOX can be achieved directly by its ability to suppress the induction of reactive oxygen species (ROS) and indirectly by causing changes in the energy status of cells owing to the non-phosphorylating nature of the alternative respiratory pathway. The latter is likely achieved in combination with a variety of alternative NAD(P)H dehydrogenases, that are co-regulated with AOX. Additionally, we explore the possible function of AOX as a component of the stress response beyond the plant frontier.

Identification of regulatory pathways controlling gene expression of stress-responsive mitochondrial proteins in Arabidopsis.

In this study we analyzed transcript abundance and promoters of genes encoding mitochondrial proteins to identify signaling pathways that regulate stress-induced gene expression. We used Arabidopsis (Arabidopsis thaliana) alternative oxidase AOX1a, external NADP H-dehydrogenase NDB2, and two additional highly stress-responsive genes, At2g21640 and BCS1. As a starting point, the promoter region of AOX1a was analyzed and functional analysis identified 10 cis-acting regulatory elements (CAREs), which played a role in response to treatment with H(2)O(2), rotenone, or both. Six of these elements were also functional in the NDB2 promoter. The promoter region of At2g21640, previously defined as a hallmark of oxidative stress, shared two functional CAREs with AOX1a and was responsive to treatment with H(2)O(2) but not rotenone. Microarray analysis further supported that signaling pathways induced by H(2)O(2) and rotenone are not identical. The promoter of BCS1 was not responsive to H(2)O(2) or rotenone, but highly responsive to salicylic acid (SA), whereas the promoters of AOX1a and NDB2 were unresponsive to SA. Analysis of transcript abundance of these genes in a variety of defense signaling mutants confirmed that BCS1 expression is regulated in a different manner compared to AOX1a, NDB2, and At2g21640. These mutants also revealed a pathway associated with programmed cell death that regulated AOX1a in a manner distinct from the other genes. Thus, at least three distinctive pathways regulate mitochondrial stress response at a transcriptional level, an SA-dependent pathway represented by BCS1, a second pathway that represents a convergence point for signals generated by H(2)O(2) and rotenone on multiple CAREs, some of which are shared between responsive genes, and a third pathway that acts via EDS1 and PAD4 regulating only AOX1a. Furthermore, posttranscriptional regulation accounts for changes in transcript abundance by SA treatment for some genes.

The absence of ALTERNATIVE OXIDASE1a in Arabidopsis results in acute sensitivity to combined light and drought stress.

Treatment of Arabidopsis (Arabidopsis thaliana) alternative oxidase1a (aox1a) mutant plants with moderate light under drought conditions resulted in a phenotypic difference compared with ecotype Columbia (Col-0), as evidenced by a 10-fold increase in the accumulation of anthocyanins in leaves, alterations in photosynthetic efficiency, and increased superoxide radical and reduced root growth at the early stages of seedling growth. Analysis of metabolite profiles revealed significant changes upon treatment in aox1a plants typical of combined stress treatments, and these were less pronounced or absent in Col-0 plants. These changes were accompanied by alteration in the abundance of a variety of transcripts during the stress treatment, providing a molecular fingerprint for the stress-induced phenotype of aox1a plants. Transcripts encoding proteins involved in the synthesis of anthocyanins, transcription factors, chloroplastic and mitochondrial components, cell wall synthesis, and sucrose and starch metabolism changed, indicating that effects were not confined to mitochondria, where the AOX1a protein is located. Microarray and quantitative reverse transcription-polymerase chain reaction analysis revealed that transcripts typically induced upon stress treatment or involved in antioxidant defense systems, especially chloroplast-located antioxidant defense components, had altered basal levels in untreated aox1a plants, suggesting a significant change in the basal equilibrium of signaling pathways that regulate these components. Taken together, these results indicate that aox1a plants have a greatly altered stress response even when mitochondria or the mitochondrial electron transport chain are not the primary target of the stress and that AOX1a plays a broad role in determining the normal redox balance in the cell.

Characterization of the regulatory and expression context of an alternative oxidase gene provides insights into cyanide-insensitive respiration during growth and development.

Alternative oxidase (AOX) is encoded in small multigene families in plants. Functional analysis of the Arabidopsis (Arabidopsis thaliana) alternative oxidase 1c (AtAOX1c) promoter, an AOX gene not induced by oxidative stress, indicated that regulation of expression was complex, with the upstream promoter region containing positive and negative response regions. Comparison to the promoter region of soybean (Glycine max) alternative oxidase 2b (GmAOX2b), another AOX gene not induced by oxidative stress, revealed that they contained seven sequence elements in common. All elements were active in the promoter region of AtAOX1c in suspension cells and in leaf tissue from Columbia and mutant plants, where a mitochondrial protein import receptor was inactivated. Analysis of coexpressed and putatively coregulated genes, the latter defined as containing five or more sequence elements functional in AtAOX1c, indicated that AtAOX1c was coregulated with components involved with cell division and growth. Consistent with this analysis, we demonstrated that site II elements, previously shown to regulate the proliferating cell nuclear antigen, are present in the upstream promoter region of AtAOX1c and were strong negative regulators of AtAOX1c expression. It was demonstrated that NDB4, a gene encoding an external NAD(P)H dehydrogenase, displayed strong coexpression with AtAOX1c. Overall, these results indicate that AtAOX1c is regulated by growth and developmental signals.

Plant mitochondrial transcriptomics by quantitative RT-PCR.

Transcriptomic analysis using quantitative reverse transcriptase polymerase chain reaction (QRT-PCR) facilitates analysis of nuclear and mitochondrial-encoded mitochondrial genes, enabling mechanisms and regulation of signaling pathways to be explored. To illustrate this technique, we use genes of the mitochondrial respiratory chain. We show that several components of the mitochondrial respiratory chain respond to stress, in particular the alternative oxidase. This chapter describes a method involving total ribonucleic acid (RNA) isolation and QRT-PCR for the detection and analysis of transcriptional changes that accompany seven commonly used chemical stresses. This methodology describes an accurate technique to determine quantitatively absolute transcript levels and a platform to facilitate comparison between responses to other stress stimuli.

Alternative oxidases in Arabidopsis: a comparative analysis of differential expression in the gene family provides new insights into function of non-phosphorylating bypasses.

The emergence of Arabidopsis as a model plant provides an opportunity to gain insights into the role of the alternative oxidase that cannot be as readily achieved in other plant species. The analysis of extensive mRNA expression data indicates that all five Aox genes (Aox1a, 1b, 1c, 1d and 2) are expressed, but organ and developmental regulation are evident, suggesting regulatory specialisation of Aox gene members. The stress-induced nature of the alternative pathway in a variety of plants is further supported in Arabidopsis as Aox1a and Aox1d are amongst the most stress responsive genes amongst the hundreds of known genes encoding mitochondrial proteins. Analysis of genes co-expressed with Aoxs from studies of responses to various treatments altering mitochondrial functions and/or from plants with altered Aox levels reveals that: (i) this gene set encodes more functions outside the mitochondrion than functions in mitochondria, (ii) several pathways for induction exist and there is a difference in the magnitude of the induction in each pathway, (iii) the magnitude of induction may depend on the endogenous levels of Aox, and (iv) induction of Aox can be oxidative stress-dependent or -independent depending on the gene member and the tissue analysed. An overall role for Aox in re-programming cellular metabolism in response to the ever changing environment encountered by plants is proposed.

Characterization of mitochondrial alternative NAD(P)H dehydrogenases in Arabidopsis: intraorganelle location and expression.

The intramitochondrial location of putative type II NAD(P)H dehydrogenases (NDs) in Arabidopsis was investigated by measuring the ability of isolated mitochondria to take up precursor proteins generated from cDNAs using an in vitro translation system. The mature proteins of NDA1, NDA2 and NDC1 were judged to be located on the inside of the inner membrane because they were protected from protease added after the mitochondrial outer membrane had been ruptured. In contrast, NDB1, NDB2 and NDB4 were not protected from protease digestion in mitochondria with ruptured outer membranes and were deemed to be located on the outside of the inner membrane. Expression of all ND genes was measured using quantitative reverse transcription-PCR (RT-PCR) to determine transcript abundance, and compared with expression of alternative oxidase, uncoupler proteins and selected components of the oxidative phosphorylation complexes. NDA1 and NDB2 were the most prominently expressed members in a variety of tissues, and were up-regulated in the early daytime in a diurnal manner. Analysis of array data suggested that NDA1 clustered closest to the gene encoding the P-subunit of glycine decarboxylase. Taken together with the diurnal regulation of NDA1 observed here and in other studies, this suggests that NDA1 plays a role in integrating metabolic activities of chloroplasts and mitochondria. NDA2, NDB2 and Aox1a were up-regulated in a coordinated manner under various treatments, potentially forming a complete respiratory chain capable of oxidizing matrix and cytosolic NAD(P)H. NDB1 and NDC1 were down-regulated under the same conditions and may be regarded as housekeeping genes.

Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana.

Plant mitochondria contain non-phosphorylating bypasses of the respiratory chain, catalysed by the alternative oxidase (AOX) and alternative NADH dehydrogenases (NDH), as well as uncoupling (UCP) protein. Each of these components either circumvents or short-circuits proton translocation pathways, and each is encoded by a small gene family in Arabidopsis. Whole genome microarray experiments were performed with suspension cell cultures to examine the effects of various 3 h treatments designed to induce abiotic stress. The expression of over 60 genes encoding components of the classical, phosphorylating respiratory chain and tricarboxylic acid cycle remained largely constant when cells were subjected to a broad range of abiotic stresses, but expression of the alternative components responded differentially to the various treatments. In detailed time-course quantitative PCR analysis, specific members of both AOX and NDH gene families displayed coordinated responses to treatments. In particular, the co-expression of AOX1a and NDB2 observed under a number of treatments suggested co-regulation that may be directed by common sequence elements arranged hierarchically in the upstream promoter regions of these genes. A series of treatment sets were identified, representing the response of specific AOX and NDH genes to mitochondrial inhibition, plastid inhibition and abiotic stresses. These treatment sets emphasise the multiplicity of pathways affecting alternative electron transport components in plants.

Processing of the dual targeted precursor protein of glutathione reductase in mitochondria and chloroplasts.

Pea glutathione reductase (GR) is dually targeted to mitochondria and chloroplasts by means of an N-terminal signal peptide of 60 amino acid residues. After import, the signal peptide is cleaved off by the mitochondrial processing peptidase (MPP) in mitochondria and by the stromal processing peptidase (SPP) in chloroplasts. Here, we have investigated determinants for processing of the dual targeting signal peptide of GR by MPP and SPP to examine if there is separate or universal information recognised by both processing peptidases. Removal of 30 N-terminal amino acid residues of the signal peptide (GRDelta1-30) greatly stimulated processing activity by both MPP and SPP, whereas constructs with a deletion of an additional ten amino acid residues (GRDelta1-40) and deletion of 22 amino acid residues in the middle of the GR signal sequence (GRDelta30-52) could be cleaved by SPP but not by MPP. Numerous single mutations of amino acid residues in proximity of the cleavage site did not affect processing by SPP, whereas mutations within two amino acid residues on either side of the processing site had inhibitory effect on processing by MPP with a nearly complete inhibition for mutations at position -1. Mutation of positively charged residues in the C-terminal half of the GR targeting peptide inhibited processing by MPP but not by SPP. An inhibitory effect on SPP was detected only when double and triple mutations were introduced upstream of the cleavage site. These results indicate that: (i) recognition of processing site on a dual targeted GR precursor differs between MPP and SPP; (ii) the GR targeting signal has similar determinants for processing by MPP as signals targeting only to mitochondria; and (iii) processing by SPP shows a low level of sensitivity to single mutations on targeting peptide and likely involves recognition of the physiochemical properties of the sequence in the vicinity of cleavage rather than a requirement for specific amino acid residues.