Oestrus and ovulation detection in pasture-based dairy herds: the role of new technologies

Automatic milking systems (AMS) are becoming increasingly popular due to the growing cost of labour and reduced labour availability. The voluntary cow traffic and resultant distribution of milkings throughout the day and night affects most aspects of herd and farm management in AMS. The literature review (Chapter 1) highlighted a need to evaluate the effects of milk yield and milking frequency during early lactation on reproductive performance. The analysis of a 5-year historic database from Australia’s first AMS research farm (Chapter 2) found no significant association of average milk yield and milking frequency during 100 days in milk with any of the reproductive measures. However, the interval from calving to first oestrus increased gradually within the study period and consequently influenced other reproductive outcomes. As a result, a series of studies were conducted with a multidisciplinary approach (both physiological and technological) to investigate the potential to improve oestrus detection on pasture-based AMS farms. A field study (Chapter 3) was conducted to allow for the development and application of an algorithm to assess the application accuracy of an infrared thermography (IRT) device when used to detect oestrus events or pending oestrus events by detecting the time of ovulation. Vulval and muzzle temperatures were measured by IRT in twenty synchronized cows (using a controlled internal drug release and prostaglandin F2α). Whilst the IRT showed some potential as an oestrus detection aid with higher sensitivity than visual observation (67%) and Estrotect activation (67%), the specificity and positive predictive value were lower with the IRT. The vulva and muzzle were the focus areas for the IRT application and some concern was generated with regard to the potential for the IRT data to impacted by faecal contamination, obscuring of the vulva by the tail and time since last drinking (affecting muzzle surface temperature). To address these concerns a further study (Chapter 5) was conducted to test the hypothesis that the specificity of IRT in detecting oestrus (or imminent oestrus) could be improved if other body parts were focused on. In that study (Chapter 5), an additional technology was incorporated to test the hypothesis that the combined activity and rumination data generated by an accelerometer (SCR heat and rumination long distance tags) would provide a more accurate indication of oestrus and/or ovulation than the activity and rumination data alone. Unfortunately the monitoring of eyes and/or ears did not provide the improvement in accuracy of IRT (as an oestrus detection aid) indicating that as an oestrus detection aid there was likely to be limited value in developing this as an automated stand-alone device. Alerts generated by accelerometer based on a lower activity threshold level had high sensitivity and may be able to detect a high proportion of cows in ovulatory periods in pasture-based system; however, the specificities and positive predictive value were lower than the visual assessment of mounting indicators and would still require the herd’s person to filter data to identify the false alerts to ensure that cows are not inseminated unnecessarily. Whilst the use of in-line milk monitoring has already been commercialized for the assessment of milk progesterone, there is potential for other biomarkers to provide further opportunities for the assessment of milk components. Biomarkers of oxidative stress were evaluated in plasma showing that plasma glutathione was lower in ovulated cows compared to those of an-ovulated cows (Chapter 4). Whilst baseline plasma data for oxidative stress biomarkers was a useful starting point, the real value of these biomarkers would be realised if their concentration in milk could be linked with oestrus (and or ovulation). Milk superoxide dismutase activity was shown to be higher in ovulated cows while lipoperoxides, glutathione peroxidase were lower in ovulated cows compared to those in an-ovulated cows (Chapter 6). Further work would be required to determine the accuracy with which these biomarkers could be used to identify oestrus cows but these results are promising and suggest that there may be some potential to develop in-line milk sampling technology to alert the herdsperson to cows that should be inseminated. In summary, this thesis provides very useful, scientifically based information on potential use of technologies for oestrus and ovulation detection in dairy cows, which should serve as a foundation to develop and upgrade automated on-farm technologies and biosensors for better reproductive management of cows in pasture-based AMS. However, it is noted that the most likely success with automated oestrus detection is to require a combination of different indicators that should be incorporated to truly increase the accuracy of detection beyond that which can be achieved by skilled and devoted herd’s people

Complete Mitochondrial Genome Sequence of the Magpie-Lark (Grallina cyanoleuca)

Here, we report the complete mitochondrial genome sequence of an Australian passerine bird, magpie-lark (Grallina cyanoleuca). The circular genome has a size of 16,933 bp and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. This study provides a reference mitochondrial genome of magpie-lark for further molecular studies

Characterization of the first mitochondrial genome of a little Corella (Cacatua sanguinea) and its phylogenetic implications

This study was designed to sequence the first complete mitochondrial genome from a little corella (Cacatua sanguinea). The mitogenome sequence was circular and 16,695 bp in length. In comparison to other available mitogenome sequences belongs to Psittacidae species, this mitogenome encoded a conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes. The lengths of 12S and 16S ribosomal RNA were 975 bp and 1582 bp, respectively. The overall base composition of the mitogenome of C. sanguinea was dominated by higher AT (53.0%) than GC (47.0%) content. The complete mitogenome sequence determined in this study is useful for understanding the more profound evolutionary history and the conservation of C. sanguinea

Complete Mitochondrial Genome Sequence of a Seabird, Wedge-Tailed Shearwater (Ardenna pacifica)

Here, we report the complete mitochondrial genome sequence of a seabird, wedge-tailed shearwater (Ardenna pacifica). The circular genome has a size of 16,434 bp and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The study provides a reference mitochondrial genome of wedge-tailed shearwater for further molecular studies

The first complete mitogenome of Indian ringneck (Psittacula krameri) demonstrates close phylogenetic relationship with Eclectus parrot

This study was aimed to sequence the first complete mitochondrial genome from an Indian ringneck parrot (Psittacula krameri). The mitogenome sequence was circular and 16,413 bp in length. In comparison to other available mitogenome sequences belonging to Psittacidae species, this mitogenome encoded a conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, 21 tRNA genes and a control region; however, this mitogenome missing a tRNA-Glu. The lengths of 12S and 16S ribosomal RNA were 975 bp and 1582 bp, respectively. The overall base composition of the mitogenome of P. krameri was dominated by higher AT (53.5%) than GC (46.5%) content. The complete mitogenome sequence determined in this study would be useful to track the more profound evolutionary history and the conservation of P. krameri

Estimation of nitrogen use efficiency for ryegrass-fed dairy cows: model development using diet and animal-based proxy measures

This study aimed to identify suitable predictors of nitrogen (N) use efficiency (NUE; milk N/N intake) for cows that differed in breeds and were fed with ryegrass pasture, using existing data from the scientific literature. Data from 16 studies were used to develop models based on the relationships between NUE and dietary and animal-based factors. Data from a further 10 studies were used for model validation. Milk urea N (MUN) and dietary water-soluble carbohydrate-to-crudeprotein ratio (WSC/CP) were the best and most practical animal- and diet-based proxies to predict NUE. The results indicate that it might be necessary to adopt separate models for different breeds when using WSC/CP to predict NUE but not when using MUN

The use of digital infrared thermography and measurement of oxidative stress biomarkers as tools to diagnose foot lesions in sheep

This study reports preliminary data on the use of digital infrared thermography (IRT) and biomarkers of oxidative stress (OS) to diagnose foot lesions in sheep. Interdigital space skin temperatures were obtained from crossbred rams with healthy (n=9) and with foot lesions (n=6) with a FLIR T620 series infrared camera. Interdigital space lesions were scored using a five point scoring system (0\u20134). Blood was sampled from all rams and plasma was analysed for reactive oxygen metabolites (ROMs), biological antioxidant potential (BAP), and advanced oxidation protein products (AOPP). The degree of OS was estimated by the ratio of ROMs/BAP (U.Carr./\u3bcmol/L) multiplied by 100 to give an OS index (OSI). Footrot scores were used to stratify the rams in 2 groups: Healthy Group (HG; n=9) or Foot Lesion (FL; n=6), if the lesions were recorded as absent or present, respectively. Differences in OS biomarkers and IRT temperatures between the two groups were analysed by a linear mixed model. A significant (P < 0.05) increase of IRT temperature was observed in rams with foot lesions compared with healthy rams. Rams that presented foot lesions had significantly higher values of ROMs (P < 0.05) and OSI (P < 0.001) and lower concentration of BAP than healthy rams (P < 0.05). In conclusion, IRT and biomarkers of oxidative stress were able to identify sheep with foot lesions

Role of oxidant?antioxidant balance in reproduction of domestic animals

Reproductive process leads to dynamic changes in metabolism and energy consumption, which may be responsible for the excessive production of free radicals (oxidants) that are generated during the physiological process of oxygen consumption. As the ovary is a metabolically active organ, it produces oxidants. Growing follicles, granulose cells of Graffian follicles and ovulated follicles all produce both enzymatic and non-enzymatic antioxidants to preserve themselves from the oxidative damage of oxidants. Oxidants and antioxidants are involved in several reproductive functions such as the regulation of follicular fluid environment, folliculogenesis, steroidogenesis, corpus luteum function, and luteolysis. In this article, the currently available literature is reviewed in relation to the roles of oxidants and oxidative stress in both normal and abnormal reproductive physiological processes

Development of Thresholds to Predict Grazing Behaviour of Dairy Cows from Motion Sensor Data and Application in a Pasture-Based Automatic Milking System

The monitoring and measurement of animal behaviour may be valuable for improving animal production and welfare. This study was designed to develop thresholds to predict the grazing, standing, walking, and lying behaviour of dairy cows from motion sensor (IceTag) output. The experiment included 29 lactating cows grazed in a pasture-based dairy production system with voluntary cow movement in northern Victoria, Australia. Sensors recorded motion data at 1 min intervals. A total of 5818 min of cow observations were used. Two approaches were developed using (1) the IceTag lying index and steps only and (2) the IceTag lying index, steps, and motion index for each behaviour. Grazing behaviour was best predicted by the second approach, which had a sensitivity of 92% and specificity of 60%. The thresholds were then used to predict cow behaviour during two periods. On average, across both time periods, cows spent 38% of the day grazing, 38% lying, 19% standing, and 5% walking. Predicted individual cow grazing time was positively correlated with both milk production and milking frequency. The thresholds developed were effective at predicting cow behaviours and can be applied to measure behaviour in pasture-based dairy production

Unravelling Bile Viromes of Free-Range Laying Chickens Clinically Diagnosed with Spotty Liver Disease: Emergence of Many Novel Chaphamaparvoviruses into Multiple Lineages

Spotty liver disease (SLD) causes substantial egg production losses and chicken mortality; therefore, it is a disease that concerns Australian egg farmers. Over the last few decades, much research has been conducted to determine the etiologic agents of SLD and to develop potential therapeutics; however, SLD still remains a major issue for the chicken industries globally and remained without the elucidation of potentially multiple pathogens involved. To help fill this gap, this study was aimed at understanding the viral diversity of bile samples from which the SLD-causing bacterium, Campylobacter hepaticus, has been isolated and characterised. The collected samples were processed and sequenced using high-throughput next-generation sequencing. Remarkably, this study found 15 galliform chaphamaparvoviruses (GaChPVs), of which 14 are novel under the genus Chaphamaparvovirus. Among them, nine were complete genomes that showed between 41.7% and 78.3% genome-wide pairwise similarities to one another. Subsequent phylogenetic analysis using the NS1 gene exhibited a multiple incursion of chaphamaparvovirus lineages, including a novel lineage of unknown ancestral history in free-range laying chickens in Australia. This is the first evidence of circulating many parvoviruses in chickens in Australia, which has increased our knowledge of the pathogen diversity that may have an association with SLD in chickens