We recently reported on the radio-frequency attenuation length of cold polar ice at Summit Station, Greenland, based on bi-static radar measurements of radio-frequency bedrock echo strengths taken during the summer of 2021. Those data also allow studies of (a) the relative contributions of coherent (such as discrete internal conducting layers with sub-centimeter transverse scale) vs incoherent (e.g. bulk volumetric) scattering, (b) the magnitude of internal layer reflection coefficients, (c) limits on signal propagation velocity asymmetries (‘birefringence’) and (d) limits on signal dispersion in-ice over a bandwidth of ~100 MHz. We find that (1) attenuation lengths approach 1 km in our band, (2) after averaging 10 000 echo triggers, reflected signals observable over the thermal floor (to depths of ~1500 m) are consistent with being entirely coherent, (3) internal layer reflectivities are ≈–60$\to$–70 dB, (4) birefringent effects for vertically propagating signals are smaller by an order of magnitude relative to South Pole and (5) within our experimental limits, glacial ice is non-dispersive over the frequency band relevant for neutrino detection experiments.

Over the last 25 years, radiowave detection of neutrino-generated signals, using cold polar ice as the neutrino target, has emerged as perhaps the most promising technique for detection of extragalactic ultra-high energy neutrinos (corresponding to neutrino energies in excess of 0.01 Joules, or 1017 electron volts). During the summer of 2021 and in tandem with the initial deployment of the Radio Neutrino Observatory in Greenland (RNO-G), we conducted radioglaciological measurements at Summit Station, Greenland to refine our understanding of the ice target. We report the result of one such measurement, the radio-frequency electric field attenuation length $L_\alpha$. We find an approximately linear dependence of $L_\alpha$ on frequency with the best fit of the average field attenuation for the upper 1500 m of ice: $\langle L_\alpha \rangle = ( ( 1154 \pm 121) - ( 0.81 \pm 0.14) \, ( \nu /{\rm MHz}) ) \,{\rm m}$ for frequencies ν ∈ [145 − 350] MHz.

The Pueblo population of Chaco Canyon during the Bonito Phase (AD 800–1130) employed agricultural strategies and water-management systems to enhance food cultivation in this unpredictable environment. Scepticism concerning the timing and effectiveness of this system, however, remains common. Using optically stimulated luminescence dating of sediments and LiDAR imaging, the authors located Bonito Phase canal features at the far west end of the canyon. Additional ED-XRF and strontium isotope (87Sr/86Sr) analyses confirm the diversion of waters from multiple sources during Chaco’s occupation. The extent of this water-management system raises new questions about social organisation and the role of ritual in facilitating responses to environmental unpredictability.

Bovine tuberculosis (bTB) is an important disease of cattle caused by infection with Mycobacterium bovis, a pathogen that may be extremely difficult to eradicate in the presence of a true wildlife reservoir. Our objective was to identify and review relevant literature and provide a succinct summary of current knowledge of risk factors for transmission of infection of cattle. Search strings were developed to identify publications from electronic databases to February 2015. Abstracts of 4255 papers identified were reviewed by three reviewers to determine whether the entire article was likely to contain relevant information. Risk factors could be broadly grouped as follows: animal (including nutrition and genetics), herd (including bTB and testing history), environment, wildlife and social factors. Many risk factors are inter-related and study designs often do not enable differentiation between cause and consequence of infection. Despite differences in study design and location, some risk factors are consistently identified, e.g. herd size, bTB history, presence of infected wildlife, whereas the evidence for others is less consistent and coherent, e.g. nutrition, local cattle movements. We have identified knowledge gaps where further research may result in an improved understanding of bTB transmission dynamics. The application of targeted, multifactorial disease control regimens that address a range of risk factors simultaneously is likely to be a key to effective, evidence-informed control strategies.

In this paper, we describe improvements to the in situ cosmogenic radiocarbon extraction system at SUERC made since 2004, highlighting the factors that potentially control the reduction of analytical variability. We also present new results on system blanks and of measurements of in situ14C in shielded quartz and a surface quartz sample used at the University of Arizona as an in situ14C standard (PP-4). The SUERC in situ14C extraction system was built in 2001 and is based on a combustion technique following the design of the extraction system at the University of Arizona. Our preliminary results suggest that the continuous running of the extraction system and the monitoring of gas collecting time and of the temperature of the cryogenic traps used in the gas cleaning steps are key to maintaining low and stable system blanks. Our latest average system blank is 2.02 ± 0.23 x 10514C atoms. This is consistent with those recently published by the University of Arizona and ETH in situ14C labs. Measurements of in situ14C concentrations in sample PP-4 yield an average of 3.82 ± 0.23 x 105 atoms g–1 quartz, again consistent with published values.

Weekly food intake and body weight were measured from 3 to 17 weeks of age on mice selected 14 generations for increased and decreased values of one of three criteria: appetite (A) as measured by 4- to 6-week food intake, adjusted by phenotypic regression to minimize change in 4-week body weight; fat percentage (F), using the ratio of gonadal fat pad weight to body weight at 10 weeks of age and total lean mass (protein, P), using the index body weight in 10-week males— (8 × gonadal fat pad weight). Carcass composition analyses were undertaken on the 17-week-old mice, and are presented along with composition data for younger mice from earlier generations. The high intake A line mice are larger, eat more, have higher maintenance requirements and are slightly leaner than the low intake A line mice, but are no more efficient. The increased lean mass P line mice are much larger, eat more and are more efficient than the decreased lean mass P line mice, but show little difference in maintenance or carcass composition. The (much) fatter F line mice are larger, more efficient and eat more during the rapid growth period than their leaner F line counterparts, but show no difference in lean mass or maintenance requirements. These results provide implications about the relationships between the input (intake) and output (maintenance and lean and fat deposition) components of growth.

Forty Theileria schizont-infected lymphocyte culture isolates from Zimbabwe were characterized using a panel of antischizont monoclonal antibodies (MAbs) and 4 Theileria parva DNA probes containing cloned extrachromosomal element, Tpr repetitive, ribosomal and telomeric sequences. The Theileria isolates were assigned as T. parva or T. taurotragi on the basis of reactivities with MAbs and restriction fragment length polymorphisms (RFLPs) detected using the extra chromosomal element probe. Cattle-derived T. parva isolates were relatively homogeneous on the basis of reactivities with MAbs and RFLPs detected using Tpr repetitive and ribosomal DNA probes. In contrast to previous results from Kenya, most of the cattle-derived isolates from Zimbabwe exhibited very similar Tpr restriction fragment patterns, although the Tpr genotypes of buffalo-derived isolates were heterogeneous. This suggests that selection for a particular Tpr genotype may be occurring in cattle. Many isolates with similar Tpr genotypes were differentiated by RFLPs detected using the telomeric DNA probe. The T. parva Boleni immunizing stock was distinguished from all other isolates by telomeric RFLPs. The T. parva Boleni Tpr repetitive DNA probe cross-hybridized with T. taurotragi DNA and detected RFLPs between different T. taurotragi isolates.

Theileria-free waterbuck (Kobus defassa) born in captivity were successfully infected with Theileria parva sporozoites derived from ticks infected by feeding on African buffalo (Syncerus caffer). All waterbuck underwent mild infections with the development of sporadic schizont and piroplasm parasitosis when inoculated with sporozoite doses lethal to cattle. A carrier state of T. parva was demonstrated by feeding clean R. appendiculatus nymphs on two of these infected waterbuck. Tick batches from these waterbuck on 2 of 5 occasions transmitted lethal Theileria infections to cattle. In a separate experiment, waterbuck cells were infected and transformed in vitro by T. parva sporozoites derived from buffalo but not by cattle-derived T. parva (Muguga) sporozoites. Waterbuck cells infected in vitro with T. parva isolated from buffalo were inoculated into autologous waterbuck but no infections developed. Theileria parva isolates generated in this study from various sources were characterized using anti-T. parva schizont monoclonal antibodies (MAbs), and it was found that buffalo-derived and waterbuck-passaged isolates had different profiles. Species-specific synthetic oligonucleotide probes, restriction fragment length polymorphism (RFLP) analysis with cloned T. parva DNA probes, and DNA sequence analysis of the p67 sporozoite antigen gene confirmed that the waterbuck-passaged parasite was T. parva. The Tpr repetitive probe hybridization patterns from the waterbuck-passaged parasites were different from the other samples tested. The ribosomal genotype of the waterbuck-passaged T. parva was similar to that of cattle-derived T. parva Muguga. Analyses with both probes and MAbs suggested that a minor parasite population present within the T. parva 7014 buffalo- derived stock had been selected during waterbuck passage. A variable region of the p67 sporozoite antigen gene of the waterbuck-passaged T. parva was similar to that of cattle-derived T. parva stocks and different from that of buffalo- derived parasites. Based on these results, methods were suggested to confirm and quantitate the involvement of waterbuck in the epidemiology of cattle theileriosis.

This paper reviews the evidence for host genetic variation in resistance to infectious diseases for a wide variety of diseases of economic importance in poultry, cattle, pig, sheep and Atlantic salmon. Further, it develops a method of ranking each disease in terms of its overall impact, and combines this ranking with published evidence for host genetic variation and information on the current state of genomic tools in each host species. The outcome is an overall ranking of the amenability of each disease to genomic studies that dissect host genetic variation in resistance. Six disease-based assessment criteria were defined: industry concern, economic impact, public concern, threat to food safety or zoonotic potential, impact on animal welfare and threat to international trade barriers. For each category, a subjective score was assigned to each disease according to the relative strength of evidence, impact, concern or threat posed by that particular disease, and the scores were summed across categories. Evidence for host genetic variation in resistance was determined from available published data, including breed comparison, heritability studies, quantitative trait loci (QTL) studies, evidence of candidate genes with significant effects, data on pathogen sequence and on host gene expression analyses. In total, 16 poultry diseases, 13 cattle diseases, nine pig diseases, 11 sheep diseases and three Atlantic salmon diseases were assessed. The top-ranking diseases or pathogens, i.e. those most amenable to studies dissecting host genetic variation, were Salmonella in poultry, bovine mastitis, Marek’s disease and coccidiosis, both in poultry. The top-ranking diseases or pathogens in pigs, sheep and Atlantic salmon were Escherichia coli, mastitis and infectious pancreatic necrosis, respectively. These rankings summarise the current state of knowledge for each disease and broadly, although not entirely, reflect current international research efforts. They will alter as more information becomes available and as genome tools become more sophisticated for each species. It is suggested that this approach could be used to rank diseases from other perspectives as well, e.g. in terms of disease control strategies.

Footrot is a highly contagious bacterial disease of sheep affecting the interdigital skin and surrounding soft and hard horn of a hoof, often resulting in severe lameness. This study was aimed at estimating the effect of footrot on weight gain of affected animals, and characterising the variation between animals in terms of phenotypic, environmental and genetic components. A general approach was developed describing the relationship between the disease and weight gain, defining new traits such as the maximum weight loss as a result of disease and the time after infection that this occurs. In two trials, 1267 Merino sheep were artificially challenged with footrot when 10 months old and re-infected through exposure to footrot on pasture 33 weeks later. Their feet were scored for footrot and live weights were measured approximately every 3 weeks. From data on animals that were not affected by footrot throughout each trial, normal growth curves were calculated and applied to affected animals to predict their growth had they remained healthy, so that weight loss as a result of footrot could be predicted. Animals with average footrot severity in the two trials suffered weight losses of 0.5 to 2.5 kg live weight, but most animals regained lost live weight later in the trials as footrot healed following vaccination. The estimates of the heritabilities of weight loss, adjusted for the severity of footrot, were about 0.30 and 0.15 in the experimental and natural challenge groups, respectively. Animals with higher genotypic values for weights at the start of each trial appeared to cope better with infections, in terms of lower weight losses. The time of highest footrot score and the time of maximum weight loss after infection had only very small genetic components.

Footrot is a costly endemic disease of sheep. This study investigates the potential to decrease its prevalence through selective breeding for decreased lesion score. Pedigreed mule and Scottish Blackface (SBF) ewes were scored for lesions on each hoof on a 0 to 4 scale for up to 2 (SBF ewes) or 4 (mules) times over 2 years. One score was obtained for SBF lambs. An animal was deemed to have lesions (severe lesions) if at least one hoof had a score of at least 1 (2). The prevalence of lesions was 34% in lambs, 17% in SBF ewes and 51% in mules. The heritability of lesions (severe lesions) analysed as repeated measurements of the same trait in a threshold model was 0.19 (0.26) in SBF ewes and 0.12 (0.19) in mules. Estimates for the sum and maximum of scores as well as the number of feet affected were much lower, as were estimates for permanent animal effects (i.e. non-genetic effects associated with an animal). When successive scores on the same animal were analysed as correlated traits, heritability estimates for most traits tended to be higher, except for severe footrot in mules where estimates varied greatly over time. The phenotypic correlations between successive scores in SBF ewes were close to 0, genetic correlations were moderately positive (0.18 to 0.55). Correlations in mules were generally of a similar size, but some genetic correlations were higher (up to 0.92). There was a clear trend for heritabilities for lesions and severe lesions to increase with higher prevalence of lesions, even when analysed in a threshold model. Heritability estimates for traits that combine scores over several events in mules, identifying the more persistently affected animals, ranged from 0.12 to 0.23 with the highest estimates for the average number of feet that were (severely) affected in animals scored for a minimum at two events. The heritability of all lesion traits in lambs was estimated as 0. It is concluded that selection for lower lesions is possible in ewes but not lambs, and that a simple binary score at an animal level is at least as effective as a comprehensive score at hoof level. Given the low repeatability of lesion scores, repeated measures over time will improve effectiveness of selection. Selection across environments (flocks, seasons) with different prevalences of lesions scores will need to take account of variation in the heritability.

Breeding indices that combine carcass and maternal performance traits have been tested in practice and result in significant improvements in lamb growth. However, subjective carcass grades for fatness and conformation did not differ as a result of 7 years of selection on the index (Conington et al., 2006). Instrumental grading systems with the potential to objectively and accurately predict carcass composition and muscularity using video image scanning (VIA) may become standard in the UK for lamb carcass grading in the future. The use of computer tomography (CT) scanning of lambs in sheep breeding programmes is likely to better predict the carcass and prime cut VIA-assessed traits and hence lead to accelerated progress in carcass traits. This paper assesses the impact of including CT-derived carcass traits in breeding programmes for hill sheep and the consequences on traits related to maternal traits and lamb survival.

A multi-trait selection index designed to improve the overall economic performance of hill sheep, including both maternal and lamb traits, has been developed and tested in a selection experiment over 7 years. Two versions of the index were tested, with different economic weights applied to the traits, on two different hill farms: one version including maternal and growth traits; the other version with additional breeding goals of carcass weight, fatness and conformation scores. Responses to selection, using both versions of the index, suggest that improvements are being made in overall index score and lamb growth. This study investigated the indirect effects of these selection indices on lamb carcass composition and muscularity traits, as measured using X-ray computed tomography (CT) scanning. A total of 499 lambs from the two hill farms were CT scanned at weaning (approximately 120 days of age). Approximately half of the lambs from each farm were from the selection line (S, animals with highest index scores selected for breeding), while the other half were from a control line (C, animals with average index scores selected). Composition and muscularity traits were estimated on each lamb from CT data and differences between genetic lines investigated, within farm, using restricted maximum likelihood analyses, adjusting for either live weight or age. Results showed that the selection index without carcass traits produced lambs with carcass composition that was not significantly different to control lambs at a given live weight or age. Including carcass traits in the index resulted in lambs with no compositional differences (except for a slight increase in bone) at a set age compared with controls. At a given live weight however, selection lambs had less fat and lower carcass weights and killing-out percentage. Muscularity (3-D muscle shape) and muscle area shape (2-D) were not improved as a result of selection on either version of the index (including carcass weight and grades in the breeding goals or not) and, at a fixed live weight, muscularity in hind leg and lumbar regions tended to be higher in the C line. To accelerate changes in carcass composition and muscularity within the context of a multi-trait selection index for hill sheep, consideration should therefore be given to including objective CT-derived carcass traits in the index in addition to the Meat and Livestock Commission (MLC) carcass grades or ultrasound measurements.

Genetic parameters were estimated between current UK hill sheep breeding goals and lamb carcass composition and muscularity traits derived using X-ray computed tomography (CT). To produce these estimates, a total of 648 lambs from two hill farms were CT scanned at weaning (ca 120 days of age), over 3 years, and total weights of carcass muscle (MUSC), fat (CFAT) and bone (BONE) and internal fat (IFAT) were predicted. Previously derived muscularity indices were also calculated for the hind leg (HLMI) and lumbar (LRMI) regions, to assess muscle shape. Data for current breeding goals (lamb performance and maternal traits) were also included from a total of 10 297 lamb records and 12 704 ewe records. Heritabilities were estimated for each trait and genetic and phenotypic correlations were calculated between each CT trait and other lamb or ewe traits. Moderate to high positive genetic correlations were found between CT-predicted tissue weights and breeding goals, which were also weights (lamb weaning weight, carcass weight, mature ewe weight, average weight of lambs reared by the ewe). CFAT was positively genetically correlated with ultrasound backfat depth at weaning (UFD) and subjective fatness grade at slaughter (MLCF), suggesting that carcass fat could be decreased using selection on any of these predictors. Ultrasound muscle depth at weaning (UMD) and subjective conformation score at slaughter (MLCC) had high genetic correlations with the muscularity indices (HLMI and LRMI), but correlations with MUSC were not significantly different from zero. This implies that selection to improve MLCC is likely to be increasing the ‘roundness’ of muscle shape in the high-priced carcass region, but having little impact on total lean meat yield. Correlations of CT traits with the other ewe traits (number of lambs weaned, number of lambs lost, longevity, fleece weight) were generally small or not significantly different from zero. The genetic parameters generated in this study can now be used in selection index calculations to assess the benefits of including lamb CT traits in future selection programmes for hill sheep.

The presence of footrot in a flock can have serious implications for animal health, welfare and productivity. Associated increases in treatment and prevention costs, as well as losses in performance, have led to a notable interest in using breeding to control footrot in sheep. Current breeding indexes for UK hill sheep such as the Scottish Blackface, include both lamb and maternal traits, and have led to improvements in economic returns. So that breeding for resistance to footrot can be evaluated in the context of multi-trait selection programmes, the genetic relationships with current breeding goal traits must be quantified. The objective of this study was to identify important environmental factors affecting footrot prevalence and to estimate genetic parameters between footrot severity and other traits used in current UK hill sheep breeding indexes.

Genetic parameters for eating quality assessed by trained taste panellists were estimated on longissimus thoracis et lumborum (LTL) muscle in Scottish Blackface lambs, comprising lines previously divergently selected for carcass lean content (FAT and LEAN lines) as well as crosses between these lines. Also, relationships between eating quality assessments and fatty acid composition were investigated. Eating quality and fatty acid phenotypic measurements were made on 350 male lambs, at ca. 8 months of age. Eating quality measurements included 18 descriptive terms and fatty acid composition measurements included in total 17 fatty acids of three types: saturated, monounsaturated and polyunsaturated. The FAT line had juicier meat and more vegetable flavour than the LEAN line. Most of the eating quality traits were moderately to highly heritable, with heritabilities ranging from 0.21 (lamb flavour) to 0.92 (sweet flavour). Lamb flavour, juiciness and overall liking were strongly negatively correlated with individual polyunsaturated fatty acids, with the correlations being significantly different from zero. Overall liking was strongly positively correlated with the proportion of total monounsaturated fatty acids. This study provides new information on genetic parameters for eating quality traits in sheep, which may lead to novel opportunities for genetically improving these traits.

We observed an outbreak of necrotizing fasciitis associated with Streptococcus agalactiae infection in a group of juvenile saltwater crocodiles (Crocodylus porosus). We undertook screening of crocodiles and the environment to clarify the source of the outbreak and evaluated the isolates cultured from post-mortem specimens with molecular methods to assess clonality and the presence of known group B streptococcal virulence determinants. The isolates were indistinguishable by pulsed-field gel electrophoresis. They were a typical serotype Ia strain with the Cα-like protein gene, epsilon (or alp1), the mobile genetic elements IS381 ISSag1 and ISSag2, and belonged to multi-locus sequence type (ST) 23. All of these characteristics suggest they were probably of human origin. We review the medical and veterinary literature relating to S. agalactiae necrotizing fasciitis, epidemiology and virulence determinants.

Infection of sheep with the abomasal nematode Teladorsagia circumcincta can cause a relative protein deficiency and reduce growth rate in growing lambs. A key event appears to be the destruction of junctions between epithelial cells. If the infection is heavy or prolonged, this leads to increased mucus production, hyperplasia, decreased acid production, gastrinemia, inappetance and pepsinogenemia. The severity of the infection depends upon the extent of concurrent infection, the nutritional status of the host and genetically controlled variation in the ability to mount protective immune responses.