Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle.

When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI's database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists.

Genetic evaluations for endangered dual-purpose German Black Pied cattle using 50K SNPs, a breed-specific 200K chip, and whole-genome sequencing.

Genetic evaluations of local cattle breeds are hampered due to small reference groups or biased due to the utilization of SNP effects estimated in other large populations. Against this background, there is a lack of studies addressing the possible advantage of whole-genome sequences (WGS) or consideration of specific variants from WGS data in genomic predictions for local breeds with small population size. Consequently, the aim of this study was to compare genetic parameters and accuracies of genomic estimated breeding values (GEBV) for 305-d production traits, fat-to protein ratio (FPR), and somatic cell score (SCS) at the first test date after calving and confirmation traits of the endangered German Black Pied cattle (DSN) breed using 4 different marker panels: (1) the commercial 50K Illumina BovineSNP50 BeadChip, (2) a customized 200K chip designed for DSN (DSN200K) which considers the most important variants for DSN from WGS, (3) randomly generated 200K chips based on WGS data, and (4) a WGS panel. The same number of animals was considered for all marker panel analyses (i.e., 1,811 genotyped or sequenced cows for conformation traits, 2,383 cows for lactation production traits, and 2,420 cows for FPR and SCS). Mixed models for the estimation of genetic parameters directly included the respective genomic relationship matrix from the different marker panels plus the trait-specific fixed effects. For the calculation of GEBV accuracies, we applied repeated random subsampling validation. In the process of separate cross-validations per trait, we created a validation set including 20% of cows with masked phenotypes, and a training set comprising 80% of the cows. The cows were selected randomly in a procedure with 10 replicates considering replacements in the different scenarios. The accuracy was defined as the correlation between the direct GEBV and the phenotypes with subtracted corresponding fixed effects for the cows in the validation set. For FPR and SCS, as well as for lactation production traits, heritabilities were largest based on WGS data, but the increase compared with the 50K or DSN200K applications was quite small in the range from 0.01 to 0.03. Also, for most of the conformation traits, heritabilities were largest based on WGS and DSN200K data, but the increase was in the range of the corresponding standard error. Accordingly, GEBV accuracies for most of the studied traits were highest based on WGS data or when utilizing the DSN200K chip, but the accuracy differences across the marker panels were quite small and nonsignificant. In conclusion, WGS data and the DSN200K chip only contributed to minor improvements in genomic predictions, still justifying the use of the commercial 50K chip. Nevertheless, WGS and the 200KDSN chip harbor breed-specific variants, which are valuable for studying causal genetic mechanisms in the endangered DSN population.

Prediction of R Status in Resections for Pancreatic Cancer Using Simplified Radiological Criteria.

OBJECTIVE: Predicting R status before surgery for pancreatic cancer (PDAC) patients with upfront surgery and neoadjuvant therapy. SUMMARY BACKGROUND DATA: Negative surgical margins (R0) are a key predictor of long-term outcomes in PDAC. METHODS: Patients undergoing pancreatic resection with curative intent for PDAC were identified. Using the CT scans from the time of diagnosis, the 2019 NCCN borderline resectability criteria were compared to novel criteria: presence of any alteration of the superior mesenteric-portal vein (SMPV) and perivascular stranding of the superior mesenteric artery (SMA). Accuracy of predicting R status was evaluated for both criteria. Patient baseline characteristics, surgical, histopathological parameters, and long-term overall survival (OS) after resection were evaluated. RESULTS: A total of 593 patients undergoing pancreatic resections for PDAC between 2010 and 2018 were identified. Three hundred and twenty-five (54.8%) patients underwent upfront surgery, whereas 268 (45.2%) received neoadjuvant therapy. In upfront resected patients, positive SMA stranding was associated with 56% margin positive resection rates, whereas positive SMA stranding and SMPV alterations together showed a margin positive resection rate of 75%. In contrast to these criteria, the 2019 NCCN borderline criteria failed to predict margin status. In patients undergoing neoadjuvant therapy, only perivascular SMA stranding remained a predictor of margin positive resection, leading to a rate of 33% R+ resections. Perivascular SMA stranding was related to higher clinical T stage (P = 0.003) and clinical N stage (P = 0.043) as well as perineural invasion (P = 0.022). SMA stranding was associated with worse survival in both patients undergoing upfront surgery (36 vs 22 months, P = 0.002) and neoadjuvant therapy (47 vs 34 months, P = 0.050). CONCLUSIONS: The novel criteria were accurate predictors of R status in PDAC patients undergoing upfront resection. After neoadjuvant treatment, likelihood of positive resection margins is approximately halved, and only perivascular SMA stranding remained a predictive factor.

Genomic loci and genetic parameters for uterine diseases in first-parity Holstein cows and associations with milk production and fertility.

Based on the clinical stage (e.g., vaginal discharge) and bacterial species, several forms of uterine diseases (UD) exist and can be classified as different traits [i.e., different stages of endometritis (EM) and metritis (MET)], which may differ in their genetic background and causal physiological mechanisms. Consequently, the present study aimed to study (1) the effect of UD on 305-d lactation and fertility, (2) the estimation of heritabilities for UD traits using pedigree- and SNP-based relationships, and (3) genome-wide associations to detect significant SNP markers and to infer candidate genes for UD traits. The data set contained herd manager and veterinarian recorded UD traits of 14,810 first-lactating genotyped Holstein cows from 63 large-scale contract herds. Binary defined UD traits (healthy or diseased) according to the clinical stage were endometritis catarrhalis (EM I), endometritis mucopurulenta (EM II), endometritis purulenta (EM III), pyometra (EM IV), endometritis (EM_SOD; superordinate diagnosis = no specific clinical stage defined), and MET. The binary defined trait UDall included all EM and MET diagnoses. The prevalence of UDall was 26.7%. The effect of UD on 305-d lactation and fertility was estimated via linear and generalized linear mixed models. We applied linear single-trait animal models and threshold models to estimate pedigree- and SNP-based heritabilities for UD traits, and bivariate linear models for genetic correlation estimations between UDall with 305-d lactation and fertility traits. A diagnosis for UDall had significant unfavorable effects on the female fertility traits calving interval, interval from calving to first service, days open, and nonreturn rate after 90 d, but was unrelated to 305-d lactation records for production traits milk yield, protein yield, and fat yield. Heritabilities for UDall and EM stages were close to zero, displaying maximal values of 0.05 for pedigree and 0.07 for SNP-based relationship matrices. For MET, pedigree- and SNP-based heritabilities were <0.001 and 0.07, respectively. Genetic correlations ranged from 0.20 to 0.31 between UDall with 305-d milk, protein, and fat yield, and from 0.17 to 0.40 with fertility traits. The GWAS revealed 5 SNP on bovine chromosomes (BTA) 1, 8, 10, 23 for UDall, 5 SNP on BTA 26 for EM I, 1 SNP on BTA 19 for EM II, 4 SNP on BTA 2, 18, 20, 25 for EM III, and 4 SNP on BTA 4, 16, 20 for EM IV above the significance threshold. For EM_SOD, we identified 15 significantly associated SNP on 4 chromosomes, and 4 significant SNP on BTA 3, 20, 22, 28 for MET. Marker associations for UD traits were annotated to 24 potential candidate genes using the ENSEMBL database. Six of these genes were previously reported to be involved in uterine defense mechanisms or in endometritis. Further detected genes contribute to immune response mechanisms during bacterial infections. Different SNP significantly influenced different UD stages, explaining the inter-individual variations in clinical severity of uterine infections.

Genomic analyses of claw disorders in Holstein cows: Genetic parameters, trait associations, and genome-wide associations considering interactions of SNP and heat stress.

The aim of the present study was an in-depth genomic analysis to understand the genomic mechanisms of the 3 claw disorders dermatitis digitalis (DD), interdigital hyperplasia (HYP), and sole ulcer (SU). In this regard, we estimated genetic parameters based on genomic relationship matrices, performed genome-wide association studies, annotated potential candidate genes, and inferred genetic associations with breeding goal traits considering the most important chromosomal segments. As a further novelty of this study, we inferred possible SNP × heat stress interactions for claw disorders. The study consisted of 17,264 first-lactation Holstein Friesian cows kept in 50 large-scale contract herds. The disease prevalence was 15.96, 2.36, and 8.20% for DD, HYP, and SU, respectively. The remaining breeding goal traits consisted of type traits of the feet and leg composite, female fertility, health traits, and 305-d production traits. The final genotype data set included 44,474 SNPs from the 17,264 genotyped cows. Heritabilities for DD, HYP, and SU were estimated in linear and threshold models considering the genomic relationship matrix (G matrix). Genetic correlations with breeding goal traits based on G were estimated in a series of bivariate linear models, which were verified via SNP effect correlations for specific chromosome segments (i.e., segments harboring potential candidate genes for DD, HYP, and SU). Genome-wide association studies were performed for all traits in a case-control design by applying a single SNP linear mixed model. Furthermore, for DD, HYP, and SU, we modeled SNP × heat stress interactions in genome-wide association studies. Single nucleotide polymorphism-based heritabilities were 0.04 and 0.08 for DD, 0.03 and 0.10 for SU, and 0.03 and 0.23 for HYP from linear and threshold models, respectively. The genetic correlations between DD, HYP, and SU with conformation traits from the feet and leg composite were positive throughout, indicating the value of indirect selection on conformation traits to improve claw health. Genetic correlations between DD, SU, and HYP with other breeding goal traits indicated impaired female fertility, impaired udder health status, and productivity decline of diseased cows. Genetic correlations among DD, SU, and HYP were moderate to large, indicating that different claw disorders have similar genetic mechanisms. Nevertheless, we identified disease-specific potential candidate genes, and genetic associations based on the surrounding SNPs partly differed from the genetic correlations. Especially for candidate genes contributing to 2 traits simultaneously, correlations based on SNP effects from the respective chromosome segment were close to 1 or to -1. In this regard, we annotated the candidate genes KRT33A and KRT33B for HYP and DD, KIF27 for HYP and calving to first insemination, and MAN1A1 for SU and the production traits. For SNP × heat stress interactions, we identified significant SNPs on BTA 2, 4, 5, 7, 8, 9, 13, 22, 25, and 28, and we annotated the potential candidate genes FSIP2, CLCN1, ADGRV1, DOP1A, THBD, and RHOBTB1. Results indicate gene-specific mechanisms of the claw disorders only in specific environments.

[An Unexpected Complication: Contralateral Tension Pneumothorax following Transbronchial Forceps Biopsy]. / Eine unerwartete Komplikation: Kontralateraler Spannungspneumothorax nach transbronchialer Zangenbiopsie.

Ipsilateral pneumothoraces are a common complication after transbronchial forceps biopsy. In this case report, a contralateral tension pneumothorax and a pneumoperitoneum occurred following transbronchial forceps biopsy in addition to an ipsilateral pneumothorax.

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN).

BACKGROUND: German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN's genetic diversity and to provide avenues for genetic improvement. RESULTS: Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. CONCLUSION: The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

A simple preoperative stratification tool predicting the risk of postoperative pancreatic fistula after pancreatoduodenectomy.

BACKGROUND: Postoperative pancreatic fistula (POPF) after pancreatoduodenectomy (PD) can be associated with severe postoperative morbidity. This study aims to develop a preoperative POPF risk calculator that can be easily implemented in clinical routine. METHODS: Patients undergoing PD were identified from a prospectively-maintained database. A total of 11 preoperative baseline and CT-based radiological parameters were used in a binominal logistic regression model. Parameters remaining predictive for grade B/C POPF were entered into the risk calculator and diagnostic accuracy measures and ROC curves were calculated for a training and a test patient cohort. The risk calculator was transformed into a simple nomogram. RESULTS: A total of 242 patients undergoing PD in the period from 2012 to 2018 were included. CT-imaging-based maximum main pancreatic duct (MPD) diameter (p = 0.047), CT-imaging-based pancreatic gland diameter at the anticipated resection margin (p = 0.002) and gender (p = 0.058) were the parameters most predictive for grade B/C POPF. Based on these parameters, a risk calculator was developed to identify patients at high risk of developing grade B/C POPF. In a training cohort of PD patients this risk calculator was associated with an AUC of 0.808 (95%CI 0.726-0.874) and an AUC of 0.756 (95%CI 0.669-0-830) in the independent test cohort. A nomogram applicable as a visual risk scale for quick assessment of POPF grade B/C risk was developed. CONCLUSION: The preoperative POPF risk calculator provides a simple tool to stratify patients planned for PD according to the risk of developing postoperative grade B/C POPF. The nomogram visual risk scale can be easily integrated into clinical routine and may be a valuable model to select patients for POPF-preventive therapy or as a stratification tool for clinical trials.

Radiological prediction of portal vein infiltration in patients with pancreatic ductal adenocarcinoma.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive gastrointestinal malignancy characterized by early loco-regional invasion. Portal vein resection (PVR) during pancreatoduodenectomy (PD) for PDAC is performed if tumor cell invasion to the venous wall (PVI) is suspected. The aim of this study is to evaluate radiological criteria for predicting PVR and PVI. METHODS: Patients undergoing PD for PDAC were identified from a prospectively maintained database. On the basis of CT- and MRI-based imaging portal vein tumor contact (PV), stranding of the superior mesenteric artery (SMA) and any alterations of the superior mesenterico-portal vein (SMPV) were evaluated. The accuracy of PVI and PVR prediction based on the radiological parameters was calculated. RESULTS: 143 patients were included in the study. 48 patients underwent PVR (34%), PVI was diagnosed in 23 patients (16%). Median overall survival was 22 months. Prediction of PVR (sensitivity 79%, negative predictive value 88%, p = 0.010) and PVI (sensitivity 95%, negative predictive value 99%, p = 0.002) was most accurate for any SMPV alterations as compared to the other radiological parameters. SMPV alterations qualified as an independent prognostic parameter (26.5 months vs. 33.5months, p = 0.034). CONCLUSION: Radiological evaluation of any SMPV alterations is a simple preoperative method to accurately predict PVI. Assessing SMPV alterations may help to identify candidates for neoadjuvant therapy.

[IgG4-associated lung disease with granulomatous lesions : Coexistence of two entities or the spectrum of one disease?] / IgG4-assoziierte Lungenerkrankung mit granulomatösen Läsionen : Koexistenz zweier Entitäten oder das Spektrum einer Erkrankung?

A 54-year-old patient with a history of pulmonary tuberculosis and occupational exposure to dust in early adulthood presented with symptoms of coughing with sputum, weight loss, occasional night sweats, and thoracic pain. Non-necrotizing granulomatosis in lung and lymph-node biopsies indicated sarcoidosis. Combined immunosuppressive therapy did not lead to an improvement. An atypical lung resectate with fibroinflammatory changes and obliterative endothelialitis may finally lead to the diagnosis of IgG4-associated lung disease with a bronchovascular pattern of involvement. The question discussed here is whether this is a coexistence of IgG4-associated lung disease with sarcoidosis or the spectrum of one disease.

Genome-wide associations and functional gene analyses for endoparasite resistance in an endangered population of native German Black Pied cattle.

BACKGROUND: Gastrointestinal nematodes (GIN), liver flukes (Fasciola hepatica) and bovine lungworms (Dictyocaulus viviparus) are the most important parasitic agents in pastured dairy cattle. Endoparasite infections are associated with reduced milk production and detrimental impacts on female fertility, contributing to economic losses in affected farms. In quantitative-genetic studies, the heritabilities for GIN and F. hepatica were moderate, encouraging studies on genomic scales. Genome-wide association studies (GWAS) based on dense single nucleotide polymorphism (SNP) marker panels allow exploration of the underlying genomic architecture of complex disease traits. The current GWAS combined the identification of potential candidate genes with pathway analyses to obtain deeper insights into bovine immune response and the mechanisms of resistance against endoparasite infections. RESULTS: A 2-step approach was applied to infer genome-wide associations in an endangered dual-purpose cattle subpopulation [Deutsches Schwarzbuntes Niederungsrind (DSN)] with a limited number of phenotypic records. First, endoparasite traits from a population of 1166 Black and White dairy cows [including Holstein Friesian (HF) and DSN] naturally infected with GIN, F. hepatica and D. viviparus were precorrected for fixed effects using linear mixed models. Afterwards, the precorrected phenotypes were the dependent traits (rFEC-GIN, rFEC-FH, and rFLC-DV) in GWAS based on 423,654 SNPs from 148 DSN cows. We identified 44 SNPs above the genome-wide significance threshold (pBonf = 4.47 × 10- 7), and 145 associations surpassed the chromosome-wide significance threshold (range: 7.47 × 10- 6 on BTA 1 to 2.18 × 10- 5 on BTA 28). The associated SNPs identified were annotated to 23 candidate genes. The DAVID analysis inferred four pathways as being related to immune response mechanisms or involved in host-parasite interactions. SNP effect correlations considering specific chromosome segments indicate that breeding for resistance to GIN or F. hepatica as measured by fecal egg counts is genetically associated with a higher risk for udder infections. CONCLUSIONS: We detected a large number of loci with small to moderate effects for endoparasite resistance. The potential candidate genes regulating resistance identified were pathogen-specific. Genetic antagonistic associations between disease resistance and productivity were specific for specific chromosome segments. The 2-step approach was a valid methodological approach to infer genetic mechanisms in an endangered breed with a limited number of phenotypic records.

Allele substitution and dominance effects of CD166/ALCAM gene polymorphisms for endoparasite resistance and test-day traits in a small cattle population using logistic regression analyses.

The study investigated the effects of four single-nucleotide polymorphisms (SNPs) in the activated leukocyte cell adhesion molecule (ALCAM) gene on liver fluke (Fasciola hepatica) infections (FH-INF), gastrointestinal nematode infections (GIN-INF) and disease indicator traits [e.g. somatic cell score (SCS), fat-to-protein ratio (FPR)] in German dual-purpose cattle (DSN). A genome-wide association study inferred the chip SNP ALCAMc.73+32791A>G as a candidate for F. hepatica resistance in DSN. Because of the crucial function of ALCAM in immune responses, SNPs in the gene might influence further resistance and performance traits. Causal mutations were identified in exon 9 (ALCAMc.1017T>C) and intron 9 (ALCAMc.1104+10T>A, ALCAMc.1104+85T>C) in a selective subset of 94 DSN cows. We applied logistic regression analyses for the association between SNP genotypes with residuals for endoparasite traits (rINF-FH, rGIN-INF) and estimated breeding values (EBVs) for test-day traits. The probability of the heterozygous genotype was estimated in dependency of the target trait. Allele substitution effects for rFH-INF were significant for all four loci. The T allele of the SNPs ALCAMc.1017T>C and ALCAMc.1104+85T>C was the favourable allele when improving resistance against FH-INF. Significant allele substitution for rGIN-INF was only found for the chip SNP ALCAMc.73+32791A>G. We identified significant associations between the SNPs with EBVs for milk fat%, protein% and FPR. Dominance effects for the EBVs of test-day traits ranged from 0.00 to 0.47 SD and were in the direction of improved resistance for rFH-INF. We estimated favourable dominance effects from same genotypes for rFH-INF and FPR, but dominance effects were antagonistic between rFH-INF and SCS.

Genetic line comparisons and genetic parameters for endoparasite infections and test-day milk production traits.

Keeping dairy cows in grassland systems relies on detailed analyses of genetic resistance against endoparasite infections, including between- and within-breed genetic evaluations. The objectives of this study were (1) to compare different Black and White dairy cattle selection lines for endoparasite infections and (2) the estimation of genetic (co)variance components for endoparasite and test-day milk production traits within the Black and White cattle population. A total of 2,006 fecal samples were taken during 2 farm visits in summer and autumn 2015 from 1,166 cows kept in 17 small- and medium-scale organic and conventional German grassland farms. Fecal egg counts were determined for gastrointestinal nematodes (FEC-GIN) and flukes (FEC-FLU), and fecal larvae counts for the bovine lungworm Dictyocaulus viviparus (FLC-DV). The lowest values for gastrointestinal nematode infections were identified for genetic lines adopted to pasture-based production systems, especially selection lines from New Zealand. Heritabilities were low for FEC-GIN (0.05-0.06 ± 0.04) and FLC-DV (0.05 ± 0.04), but moderate for FEC-FLU (0.33 ± 0.06). Almost identical heritabilities were estimated for different endoparasite trait transformations (log-transformation, square root). The genetic correlation between FEC-GIN and FLC-DV was 1.00 ± 0.60, slightly negative between FEC-GIN and FEC-FLU (-0.10 ± 0.27), and close to zero between FLC-DV and FEC-FLU (0.03 ± 0.30). Random regression test-day models on a continuous time scale [days in milk (DIM)] were applied to estimate genetic relationships between endoparasite and longitudinal test-day production traits. Genetic correlations were negative between FEC-GIN and milk yield (MY) until DIM 85, and between FEC-FLU and MY until DIM 215. Genetic correlations between FLC-DV and MY were negative throughout lactation, indicating improved disease resistance for high-productivity cows. Genetic relationships between FEC-GIN and FEC-FLU with milk protein content were negative for all DIM. Apart from the very early and very late lactation stage, genetic correlations between FEC-GIN and milk fat content were negative, whereas they were positive for FEC-FLU. Genetic correlations between FEC-GIN and somatic cell score were positive, indicating similar genetic mechanisms for susceptibility to udder and endoparasite infections. The moderate heritabilities for FEC-FLU suggest inclusion of FEC-FLU into overall organic dairy cattle breeding goals to achieve long-term selection response for disease resistance.

In-herd prevalence of Fasciola hepatica and Calicophoron / Paramphistomum spp. infections in German dairy cows with comparison of two coproscopical methods and establishment of real-time pyrosequencing for rumen fluke species differentiation.

Infections with liver and rumen flukes are among the most frequent parasitic diseases in cattle worldwide. In Europe, the predominant liver fluke species is Fasciola hepatica, and the recently rapidly spreading rumen flukes are mostly Calicophoron daubneyi and occasionally Paramphistomum leydeni. In this study, 1638 faecal samples from individual dairy cows from 24 northern and 18 southern German farms as well as one central German farm, all preselected for potential F. hepatica infection, were examined to determine in-herd prevalences of liver and rumen fluke infections. Furthermore, individual faecal egg counts (FECs) were determined in the northern and central German cows. On farms with patent F. hepatica infections, the mean in-herd prevalence was 15.8% in northern Germany, 41.6% in southern Germany and 14.0% in the central German farm. Rumen fluke infections resulted in high in-herd prevalences in all regions with a mean prevalence of 46.0% in northern, 48.4% in southern and 40.0% in central Germany. Individual FECs varied between 0.1 and 4.1 (mean 0.4) eggs per gram faeces (EPG) for F. hepatica and between 0.1 and 292.4 (mean 16.9) EPG for rumen flukes. Mean in-herd prevalence and mean FECs did not differ significantly between mono- and coinfected farms for either fluke species. Comparison of the classical sedimentation technique and the Flukefinder® method on a subset of 500 faecal samples revealed a similar number of positive samples, however, Flukefinder® mean FECs were three to four times higher for liver and rumen fluke eggs, respectively, with an increasing gap between EPG levels with rising egg counts. Fluke egg size measurement confirmed P. leydeni eggs on average to be larger in length and width (161.0 µm x 87.1 µm) than those of C. daubneyi (141.8 µm x 72.9 µm). However, due to overlap of measurements, morphological species identification based on egg size proved unreliable. For accurate identification, a real-time pyrosequencing approach was established, offering the advantage over classical Sanger sequencing of unambiguously identifying rumen fluke mixed species infections. Real-time pyrosequencing confirmed C. daubneyi (78.1% [50/64]) as the predominant rumen fluke species in Germany, while P. leydeni was detected in 12.5% (8/64) of sampled cows. A total of 9.4% (6/64) cows were infected with both C. daubneyi and P. leydeni, representing the first finding of a mixed infection in domestic ruminants in Europe to date.

Genomic Selection for Dairy Cattle Behaviour Considering Novel Traits in a Changing Technical Production Environment.

Cow behaviour is a major factor influencing dairy herd profitability and is an indicator of animal welfare and disease. Behaviour is a complex network of behavioural patterns in response to environmental and social stimuli and human handling. Advances in agricultural technology have led to changes in dairy cow husbandry systems worldwide. Increasing herd sizes, less time availability to take care of the animals and modern technology such as automatic milking systems (AMSs) imply limited human-cow interactions. On the other hand, cow behaviour responses to the technical environment (cow-AMS interactions) simultaneously improve production efficiency and welfare and contribute to simplified "cow handling" and reduced labour time. Automatic milking systems generate objective behaviour traits linked to workability, milkability and health, which can be implemented into genomic selection tools. However, there is insufficient understanding of the genetic mechanisms influencing cow learning and social behaviour, in turn affecting herd management, productivity and welfare. Moreover, physiological and molecular biomarkers such as heart rate, neurotransmitters and hormones might be useful indicators and predictors of cow behaviour. This review gives an overview of published behaviour studies in dairy cows in the context of genetics and genomics and discusses possibilities for breeding approaches to achieve desired behaviour in a technical production environment.

A Case Report of Acute Hepatitis Involving the Medicinal Herb Tinospora cordifolia Along with Other Variables.

This is a 54-year-old woman from Germany of central European origin who developed an acute hepatitis while orally taking Ayurvedic herbal remedies, among those was the medicinal herb Tinospora cordifolia. She took the plant powders from July 1, 2021, to October 1, 2021, with the intention of relieving the symptoms of her subjectively irritated gastrointestinal tract. The patient's main symptoms of acute hepatitis were progressively increasing general fatigue, nausea, and exhaustion. During an inpatient hospital admission from November 4, 2021, to November 9, 2021, she was under clinical observation, but no specific therapeutic measures were deemed necessary; however, blood chemistry showed an acute toxic hepatitis. There was no clinical or laboratory evidence of acute liver failure. Aminotransferase values decreased to normal values on December 14, 2021, by themselves. This case report contributes to the ongoing discussion about the potential risks of triggering an acute hepatitis due to the intake of herbal remedies from the Tinospora genus in rare cases, differentiating other involved risk factors. The case also shows that causality assignments are not trivial in the context of multivariate clinical scenarios. In the case of known hepatic metabolism-associated risk factors, T. cordifolia should be used with more caution based on available case reports. At the same time, no hasty and exaggerated prejudgments should be made about this medicinal herb, which has been very successfully used in traditional South Asian systems of medicine for many centuries.

Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN).

German Black Pied (DSN) is considered an ancestral population of the Holstein breed. The goal of the current study was to fine-map genomic loci for milk production traits and to provide sequence variants for selection. We studied genome-wide associations for milk-production traits in 2160 DSN cows. Using 11.7 million variants from whole-genome sequencing of 304 representative DSN cattle, we identified 1980 associated variants (-log10(p) ≥ 7.1) in 13 genomic loci on 9 chromosomes. The highest significance was found for the MGST1 region affecting milk fat content (-log10(p) = 11.93, MAF = 0.23, substitution effect of the minor allele (ßMA) = -0.151%). Different from Holstein, DGAT1 was fixed (0.97) for the alanine protein variant for high milk and protein yield. A key gene affecting protein content was CSN1S1 (-log10(p) = 8.47, MAF = 049, ßMA = -0.055%) and the GNG2 region (-log10(p) = 10.48, MAF = 0.34, ßMA = 0.054%). Additionally, we suggest the importance of FGF12 for protein and fat yield, HTR3C for milk yield, TLE4 for milk and protein yield, and TNKS for milk and fat yield. Selection for favored alleles can improve milk yield and composition. With respect to maintaining the dual-purpose type of DSN, unfavored linkage to genes affecting muscularity has to be investigated carefully, before the milk-associated variants can be applied for selection in the small population.

Understanding the uptake of diagnostics for sustainable gastrointestinal nematode control by European dairy cattle farmers: a multi-country cross-sectional study.

To mitigate emerging anthelmintic resistance (AR) in cattle, sustainable gastrointestinal nematode control strategies should be adopted. A multi-centre study was set up to understand the factors affecting European dairy cattle farmers' adoption of diagnostics and to gauge for differences between regions. The data were collected through a multi-lingual survey by participating countries of the European Co-operation in Science and Technology (COST) action COMbatting Anthelmintic Resistance in ruminants (COMBAR). Four countries provided sufficient data to be included in the data analysis: Norway, Italy, Germany and Austria. Three models were estimated and validated through structural equation modelling. Norway, along with Germany and Austria (pooled dataset) showed similar trends that align with previous studies. AR risk perception had no influence on the adoption intention of diagnostics, a positive influence was found for attitude towards diagnostics and subjective norms (i.e., perceived opinion of others), and a negative influence of attitudes towards anthelminthics. Additionally, routine (i.e., perception of the current treatment) had an indirect effect on adoption intention through attitudes. Italy's data deviated from these findings, presenting a positive effect of the perceived severity of AR, and perceived behavioural control (i.e., perceived ability to perform a specific behaviour) on adoption intention of diagnostics. Finally, Norway's data set allowed for inclusion of a measurement of current behaviour in the model, identifying a direct positive effect of the perceived actual behaviour of other farmers on their own behaviour.

Title: Comprendre l'adoption des diagnostics pour le contrôle durable des nématodes gastro-intestinaux par les producteurs laitiers européens : une étude transversale multi-pays. Abstract: Pour atténuer la résistance émergente aux anthelminthiques (RA) chez les bovins, des stratégies durables de contrôle des nématodes gastro-intestinaux devraient être adoptées. Une étude multicentrique a été réalisée pour comprendre les facteurs affectant l'adoption des diagnostics par les éleveurs de bovins laitiers européens, et pour évaluer les différences entre les régions. Les données ont été recueillies au moyen d'une enquête multilingue menée par les pays participants à l'action de European Co-operation in Science and Technology (COST) COMbatting Anthelmintic Resistance in ruminants (COMBAR). Quatre pays ont collecté suffisamment de données pour être inclus dans l'analyse statistique : la Norvège, l'Italie, l'Allemagne et l'Autriche. Trois modèles ont été estimés et validés par modélisation d'équations structurelles. La Norvège, et d'autre part l'Allemagne et l'Autriche (données regroupées) ont montré des tendances similaires qui correspondent aux études précédentes. La perception de la RA n'avait aucune influence sur l'intention d'adoption des diagnostics, une influence positive a été trouvée pour l'attitude envers les diagnostics et les normes subjectives (c'est-à-dire l'opinion perçue des autres), et une influence négative des attitudes envers les anthelminthiques. De plus, la routine (c'est-à-dire la perception du traitement actuel) a eu un effet indirect sur l'intention d'adoption par le biais des attitudes. Les données de l'Italie s'écartaient des résultats précédents, présentant un effet positif de la gravité perçue du risque de la RA, et du contrôle comportemental perçu (c'est-à-dire la capacité perçue à adopter un comportement spécifique) sur l'intention d'adoption de diagnostic. Enfin, l'ensemble de données de la Norvège a permis d'inclure une mesure du comportement actuel dans le modèle, identifiant un effet positif direct du comportement réel perçu des autres agriculteurs sur son propre comportement.

Key parameters of head-heart electrical stunning need to be adapted to improve stunning effectiveness and meat quality in pigs of different genetic lines.

Adjustment of key parameters of electrical stunning of pigs is necessary to better respect animal welfare and avoid impairments of meat quality. In the present study, we analysed the effect of genetic line, stunning program and genetic line × stunning program interactions on stunning effectiveness, carcass and meat quality traits in 10,338 pigs from five different genetic lines in a German slaughterhouse using electrical stunning (two-cycle method head/heart current). Genetic line, stunning program and its interaction significantly influenced stunning effectiveness and pH in the semimembranosus muscle. Backup stunning rates ranged from 1.59 to 5.01% in the five genetic lines, and were significantly decreased (2.85%) in program 1 using a current of 1.3 to 1.35 A, 800 Hz and 1 s for the head-cycle compared to program 2 (4.73%) with 1.8 A, 100 Hz and 4.5 s. We suggest to consider genetic line × stunning program interactions when adjusting officially defined stunning parameters for head-heart electrical stunning.

Pasture rewetting in the context of nature conservation shows no long-term impact on endoparasite infections in sheep and cattle.

BACKGROUND: Nature conservation with reduced drainage of pastures has been increasingly promoted in agriculture in recent years. However, moisture on pastures is a crucial factor for the development of free-living stages of many parasite species in ruminants. Hence, for the first time, we conducted a field study between 2015 and 2017 at the German North Sea coast to investigate the long-term effect of pasture rewetting (since 2004) on endoparasite infections in sheep and cattle. METHODS: We examined faecal samples of 474 sheep and 646 cattle from five farms in spring, summer and autumn each year for the presence of endoparasite infections. Animals were kept on conventionally drained, undrained and rewetted pastures. The association between pasture rewetting and endoparasite infection probability was analysed in generalized linear mixed models and including further potential confounders. RESULTS: Infection frequencies for gastrointestinal strongyles, Eimeria spp. and Strongyloides papillosus were significantly higher in sheep (62.9%, 31.7% and 16.7%) than in cattle (39.0%, 19.7% and 2.6%). Fasciola hepatica was detected with a frequency of 13.3% in sheep and 9.8% in cattle, while rumen fluke frequency was significantly higher in cattle (12.7%) than in sheep (3.8%). Nematodirus spp., lungworms (protostrongylids, Dictyocaulus viviparus), Moniezia spp., Trichuris spp. and Dicrocoelium dendriticum were identified in less than 7% of samples. Co-infection with more than three endoparasite taxa was present significantly more often in sheep than in cattle. We identified significant positive correlations above 0.2 for excretion intensities between S. papillosus with strongyles, Eimeria spp. and Nematodirus spp. in sheep and between strongyles and Nematodirus spp. in cattle. Pasture rewetting had no long-term effect on endoparasite infections, neither in sheep nor in cattle. Interestingly, F. hepatica infections decreased significantly in sheep and cattle from 2015 (10.9% and 13.9%) to 2017 (1.4% and 2.1%). CONCLUSIONS: Pasture rewetting for nature conservation did not increase endoparasite infection probability in ruminants in the long term. This finding should be confirmed in ongoing studies aimed at further animal welfare parameters. The rapid decrease in F. hepatica infections over 3 years may suggest climatic impact or competition with rumen flukes in addition to potential anthelmintic treatment after feedback of the results to the farmers.