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The objective of this randomized, placebo-controlled, double-blinded field trial was to investigate the effects of oral administration of purple coneflower (Echinacea purpurea L. (EP)) on performance, health and immune parameters in calves. Calves (n = 27) were enrolled to three groups (9 calves per group): 0.5 g EP/calf per day (ECL), 5 g EP/calf per day (ECH) or placebo. Calves were vaccinated with Bluetongue-Virus (BTV) serotype 4 vaccine to investigate EPs effects on seroconversion. Clinical and performance parameters, inter alia body weight, health and milk intake were recorded for 57 days. Blood samples were analyzed for BTV antibodies and IgG by ELISA, white and red blood cell counts by flow cytometry and mRNA abundance of various inflammatory markers in leukocytes (IL-1β, IL-8, tumor necrosis factor α (TNFα), cyclooxygenase 2 (Cox-2) and prostaglandin E synthase) was studied. The findings demonstrated no differences between groups regarding performance parameters. In all groups, calves suffered from diarrhea for a minimum of 2 days, but EP reduced the number of diarrhea days by 44% in ECL and increased the body temperature. Interestingly, ECL resulted in an increased number of respiratory disease days during the follow-up period. EP did not change blood cell and IgG counts, whereas eosinophil granulocytes were reduced in ECL. Decreased levels of hemoglobin and hematocrit were found in ECH. Prostaglandin E synthase levels in leukocytes were higher in ECL and ECH, whereas no differences were obtained for IL-1β, IL-8, TNFα and Cox-2. Due to the unexpected occurrence of BTV seropositive calves before the first vaccination, 13 calves were excluded from the evaluation on seroconversion and no statistical analyses could be performed regarding antibody production. BTV-4 antibodies were not produced in 4 placebo-calves, whereas 4 of 5 and 1 of 6 ECL- and ECH-calves produced antibodies. Further investigations are needed to draw final conclusions on mode of action and efficacy of EP in calves.

Autophagosomes are unique organelles that form de novo as double-membrane vesicles engulfing cytosolic material for destruction. Their biogenesis involves membrane transformations of distinctly shaped intermediates whose ultrastructure is poorly understood. Here, we combine cell biology, correlative cryo-electron tomography (cryo-ET), and extensive data analysis to reveal the step-by-step structural progression of autophagosome biogenesis at high resolution directly within yeast cells. The analysis uncovers an unexpectedly thin intermembrane distance that is dilated at the phagophore rim. Mapping of individual autophagic structures onto a timeline based on geometric features reveals a dynamical change of membrane shape and curvature in growing phagophores. Moreover, our tomograms show the organelle interactome of growing autophagosomes, highlighting a polar organization of contact sites between the phagophore and organelles, such as the vacuole and the endoplasmic reticulum (ER). Collectively, these findings have important implications for the contribution of different membrane sources during autophagy and for the forces shaping and driving phagophores toward closure without a templating cargo.

Protocol for sample preparation and live fluorescence imaging of yeast cells.

This protocol describes how to plunge-freeze yeast on EM grids and how to target autophagic structures by combining cryo confocal fluorescence data to FIB-milling and tomogram acquisition

Cryo-electron tomography (cryo-ET) has become the method of choice for investigating cellular ultrastructure and molecular complexes in their native, frozen-hydrated state. However, cryo-ET requires that samples are thin enough to not scatter or block the incident electron beam. For thick cellular samples, this can be achieved by cryo-focused ion beam (FIB) milling. This protocol describes how to target specific cellular sites during FIB milling using a 3D-correlative approach, which combines three-dimensional fluorescence microscopy data with information from the FIB-scanning electron microscope. Using this technique, rare cellular events and structures can be targeted with high accuracy and visualized at molecular resolution using cryo-transmission electron microscopy (cryo-TEM).

[Image: see text] In-cell distance determination by electron paramagnetic resonance (EPR) spectroscopy reveals essential structural information about biomacromolecules under native conditions. We demonstrate that the pulsed EPR technique RIDME (relaxation induced dipolar modulation enhancement) can be utilized for such distance determination. The performance of in-cell RIDME has been assessed at Q-band using stiff molecular rulers labeled with Gd(III)-PyMTA and microinjected into Xenopus laevis oocytes. The overtone coefficients are determined to be the same for protonated aqueous solutions and inside cells. As compared to in-cell DEER (double electron–electron resonance, also abbreviated as PELDOR), in-cell RIDME features approximately 5 times larger modulation depth and does not show artificial broadening in the distance distributions due to the effect of pseudosecular terms.

In contrast to natural and historical diets of wild and domesticated ruminants, the diversity of plant species is limited in diets of modern dairy cows. Are "production diseases" linked to this? We conducted a trial to test the effects of a multicomponent herbal feed additive (HFA) on health, performance and fertility traits. A dose-finding study (DF) with 62 cows on 11 commercial farms compared a low (50 g) and a high (100 g) dose of HFA (HFA-50, HFA-100) with a placebo (PL). In a subsequent field trial (FT) with 280 cows on 30 commercial farms, HFA-100 was compared to PL. Cows were randomly assigned to HFA and PL groups and received HFA or PL individually daily from 14 days pre- to 300 days post-calving. Data were analysed with mixed effects models. No differences between HFA and PL were found regarding performance, body condition score and overall culling rates. A tendency towards lower milk urea for HFA-100 compared to PL (p = .06) was found in DF. HFA significantly reduced elevated milk acetone observations (≥10 mg/L) in the first 10 lactation weeks (HFA-100: 4%; HFA-50: 4%; PL: 12%) in DF. HFA-50 significantly reduced lameness incidence (HFA-100: 11%; HFA-50: 2%; PL: 14%) in DF. Calving intervals were 15 days shorter in HFA compared to PL in both trials, which could be confirmed by tendency (p = .07) in FT. In both trials, the proportion of test days with elevated somatic cell score (≥3.0) was significantly lower in HFA compared to PL (DF: HFA-100: 40%, HFA-50: 45% and PL: 55%; FT: HFA-100: 38% and PL: 55%) which is also reflected by tendency (p = .08) in lower culling rates due to udder diseases in FT. HFA showed no negative impact on any of the measured parameters. The effects of HFA indicate a potential of phytochemically rich and diverse feed additives for dairy cows' nutrition and physiology.

1. Ascarids (Ascaridia galli and Heterakis spp.) are highly prevalent in free-range laying hens. Ascarid eggs survive for long periods in soil, and one preventive measure is to add litter material to areas close to the henhouse. In this study, recovery rates of ascarid eggs from three common litter materials, namely pea gravel, beech (Fagus sylvatica) and spruce (Picea abies) wood chips were compared to recovery rates from soil. 2. Materials were mixed with faeces containing 1,408 ascarid eggs per g of faeces, placed in plastic fruit boxes and exposed to natural weather conditions in a randomised block design with six replicates per treatment. 3. Numbers of ascarid eggs were quantified at 28 time points over 3.5 years. Ascarid eggs were recovered for over three years from all materials and completely disappeared during the fourth winter of exposure. Time needed to get to a 50% reduction in ascarid eggs did not differ between litter materials and soil (242 to 269 days). A 99% reduction was reached significantly (P < 0.001) earlier in pea gravel (548 days) than in the three other materials, and earlier in the two wood chips (day 682 for beech, day 692 for spruce, P < 0.05) than in soil (1,277 days). 4. Accumulation of ascarid eggs in the area close to the henhouse can be reduced by any of the tested litter materials compared to bare soil. Adding litter to this area is highly recommended for free-range layer farmers in order to reduce numbers of infective ascarid eggs.

This study aimed to identify organic dairy major farm types (MFTs) in seven European countries, describe these MFTs in an open research database and assess central characteristics of the MFTs. This was conducted in a three-step procedure including (1) Identification of organic MFTs in seven European countries: Austria, Switzerland, Germany, Denmark, Lithuania, Poland and Sweden, based on existing data from dairy databases and consultations with experts within the respective fields of knowledge; (2) Collection of data on farm characteristics, management procedures, production level and herd health from at least 10 farms per MFT and country and (3) Creating an open research database on MFT characteristics, description of essential characteristics of MFTs and assessment of similarities and differences between farms within and across MFTs. The results indicate variations in herd characteristics such as production level, herd size, farm size, housing system, milking system and cow health status between organic dairy farms in these seven European countries. It also indicates variations in management strategies such as feeding, animal health management and recruitment strategies across the organic dairy sector in Europe. These variations seem to be associated with differences between regions and countries in the conditions for organic dairy production, such as topography, land availability and regulations.

This study investigated the effect of, and interactions between, US Brown Swiss (BS) genetics and season on milk yield, basic composition and fatty acid profiles, from cows on low-input farms in Switzerland. Milk samples (n = 1,976) were collected from 1,220 crossbreed cows with differing proportions of BS, Braunvieh and Original Braunvieh genetics on 40 farms during winter-housing and summer-grazing. Cows with more BS genetics produced more milk in winter but not in summer, possibly because of underfeeding potentially high-yielding cows on low-input pasture-based diets. Cows with more Original Braunvieh genetics produced milk with more (i) nutritionally desirable eicosapentaenoic and docosapentaenoic acids, throughout the year, and (ii) vaccenic and α-linolenic acids, total omega-3 fatty acid concentrations and a higher omega-3/omega-6 ratio only during summer-grazing. This suggests that overall milk quality could be improved by re-focussing breeding strategies on cows’ ability to respond to local dietary environments and seasonal dietary changes.

Besides its primary informational role, the sequence of the mRNA (mRNA) including its 5′- and 3′- untranslated regions (UTRs), contains important features that are relevant for post-transcriptional and translational regulation of gene expression. In this work a number of bacterial twister motifs are characterized both in vitro and in vivo. The analysis of their genetic contexts shows that these motifs have the potential of being transcribed as part of polycistronic mRNAs, thus we suggest the involvement of bacterial twister motifs in the processing of mRNA. Our data show that the ribozyme-mediated cleavage of the bacterial 3′-UTR has major effects on gene expression. While the observed effects correlate weakly with the kinetic parameters of the ribozymes, they show dependence on motif-specific structural features and on mRNA stabilization properties of the secondary structures that remain on the 3′-UTR after ribozyme cleavage. Using these principles, novel artificial twister-based riboswitches are developed that exert their activity via ligand-dependent cleavage of the 3′-UTR and the removal of the protective intrinsic terminator. Our results provide insights into possible biological functions of these recently discovered and widespread catalytic RNA motifs and offer new tools for applications in biotechnology, synthetic biology and metabolic engineering. published

Copy Number Variations (CNVs) are DNA sequences of 50 bp up to several Mb long, which can vary in number of copies in comparison with a reference genome. CNVs can be used in association studies to disclose genetic basis of quantitative traits phenotypic variation. Up to date, no genome-wide association study (GWAS) with CNVs and quantitative traits in such a large Brown Swiss population (i.e. with 1116 samples) has been described. The purpose of this study was to perform a GWAS using CNVs with functional, health and productive traits and to asses the impact on farming and breeding practices. The CNV – association studies were performed with the Golden Helix SVS 8.4.4 software using a correlation-trend test model. Genes within significant associated CNVs for each trait were annotated with a GO analysis using the DAVID Bioinformatics Resources 6.7. A total of 56 CNVs were significantly associated with one or more of the eight evaluated traits. The greatest association signals were given by three CNVs on chromosome 12 for the fat yield trait and on BTA23 for udder traits. The associated CNVs overlap with 23 different genes annotated on the Bos taurus genome assembly (UMD3.1).

Supernumerary teats (SNT) are any abnormal teats found on a calf in addition to the usual and functional 4 teats. The presence of SNT has also been termed “hyperthelia” since the end of the 19th century. Supernumerary teats can act as an incubator for bacteria, infecting the whole udder, and can interfere with the positioning of the milking machine, and consequently, have economic relevance. Different types of SNT are observed at different positions on the udder. Caudal teats are in the rear, ramal teats are attached to another teat, and intercalary teats are found between 2 regular teats. Not all teats are equally developed; some are completely functional but most are rudimentary and not attached to any mammary gland tissue. Recently, different studies showed the poly/oligogenic character of these malformations in cattle as well as in other mammalian species. The objective of this study was to analyze the genetic architecture and incidence of hyperthelia in Swiss Brown Swiss cattle using both traditional genetic evaluation as well as imputed whole genome sequence variant information. First, phenotypes collected over the last 20 yr were used together with pedigree information for estimation of genetic variance. Second, breeding values of Brown Swiss bulls were estimated applying the BLUP algorithm. The BLUP-EBV were deregressed and used as phenotypes in genome-wide association studies. The gene LGR5 on chromosome 5 was identified as a candidate for the presence of SNT. Using alternative trait coding, genomic regions on chromosome 17 and 20 were also identified as being involved in the development of SNT with their own supernumerary mammary gland tissue. Implementing knowledge gained in this study as a routine application allows a more accurate evaluation of the trait and reduction of SNT prevalence in the Swiss Brown Swiss cattle population.

Although the use of local breeds is recommended by organic regulations, breed comparisons performed under organic production conditions with similar production intensities are scarce. Therefore, we compared data of local and widely used Holstein dairy cattle breeds from 2011 to 2015 regarding production, fertility and health from German and Swedish organic farms with similar management intensities within country. In Germany, the energy-corrected total milk yield tended to be lower in the local breed Original Angler Cattle (AAZ, 5193 kg) compared to the modern German Holstein Friesian breed (HO, 5620 kg), but AAZ showed higher milk fat and protein contents (AAZ v. HO: 5.09% v. 4.18% and 3.61% v. 3.31%, respectively). In Sweden, the widely used modern Swedish Holstein (SH) breed had the highest milk yield (9209 kg, fat: 4.10%, protein: 3.31%), while the local Swedish Polled (SKB) showed highest milk yield, fat and protein contents (6169 kg, 4.47%, 3.50%, respectively), followed by the local breed Swedish Red (SRB, 8283 kg, 4.33%, 3.46%, respectively). With regard to fertility characteristics, the German breeds showed no differences, but AAZ tended to have less days open compared to HO (−17 days). In Sweden, breeds did not differ with regard to calving interval, but both local breeds showed a lower number of days open (−10.4 in SRB and −24.1 in SKB compared to SH), and SKB needed fewer inseminations until conception (−0.5 inseminations) compared to SH. Proportion of test day records with a somatic cell count content of ≥100 000 cells per ml milk did not reveal breed differences in any of the two countries. German breeds did not differ regarding the proportion of cows with veterinary treatments. In Sweden, SRB showed the lowest proportion of cows with general veterinary treatment as well as specific treatment due to udder problems (22.8 ± 6.42 and 8.05 ± 2.18, respectively), but the local breed SKB did not differ from SH in either of the two traits. In Sweden, we found no breed differences regarding veterinary treatments due to fertility problems or diagnosis of claw or leg problems during claw trimming. Our results indicate a stronger expression of the antagonism between production and functional traits with increasing production intensity. Future breed comparisons, therefore, need to consider different production intensities within organic farming in order to derive practical recommendations as to how to implement European organic regulations with regard to a suitable choice of breeds.

Postweaning diarrhoea (PWD) is one of the most serious problems in pig production, leading to a high antimicrobial use. Preventive oral administration of Allium sativum L. (AS, garlic) represents an option to reduce antimicrobial medication by improving health and performance in postweaning pigs. A trial was conducted on a commercial Swiss farm [1]. Six-hundred piglets were randomly assigned to three treatment groups. For the first two weeks post weaning, the piglets received orally 0.3 g dried AS-powder/kg body weight/day, 6 mg colistin-sulphate/kg body weight /day or a placebo (PL). Piglets were observed until the end of the third week post weaning. For the time of the study, daily weight gain (DWG) was measured weekly on individual basis. Data were analysed using generalized mixed effect models. DWG of placebo-treated piglets was significantly lower compared to AS (61 g; p=0.008) and colistin-treated piglets (61 g; p=0.001) on the third week post weaning [Fig. 1]. Due to severe diarrhoea, three out of nine (33%) of AS and the placebo pens were treated with antibiotics. In conclusion, oral administration of dried AS-powder does not prevent severe PWD but improves the growing performance compared to placebo. Thus, AS contributes to limiting the use of antimicrobials to strictly therapeutic indications.

Our aim was to map the performance of local (native) dairy cattle breeds in Austria, Switzerland, Poland, and Sweden with regard to production, fertility, longevity, and health-associated traits and to compare them with commercial (modern) breeds. For this purpose, we analyzed test-day records (July 1, 2011, to June 30, 2014) and treatment records (Austria, Sweden) of cows managed on organic farms. We performed country-wise comparisons of 123,415 lactations from Original Braunvieh (OB) and Grey Cattle (AL) with Braunvieh (BV; Brown Swiss blood >60%) in Switzerland; AL with BV (Brown Swiss blood >50%) in Austria; Polish Black and White (ZB), Polish Red and White (ZR), and Polish Red (RP) with Polish Holstein Friesian (PHF) in Poland; and Swedish Red (SRB) with Swedish Holstein (SH) in Sweden. Average milk yields were substantially lower for local compared with commercial breeds in all countries; differences ranged from 750 kg (Sweden) to 1,822 kg (Austria), albeit on very different average levels. Local breeds showed a longer productive lifetime by 0.64, 0.83, 1.42, and 0.20 lactations in Switzerland, Austria, Poland, and Sweden, respectively, again on very different levels in each country. Regarding fertility traits, calving interval was shorter in local than in commercial breeds by 13 (Sweden), 14 (Switzerland), and 20 d (Austria, Poland). Insemination index was lower in certain local breeds by 0.15 (Switzerland), 0.14 (Austria), 0.21 (Poland), and 0.13 (Sweden). Several local breeds showed a lower proportion of cows with >100,000 somatic cells/mL. This was the case in Switzerland (OB 24.2%; BV 35.8%), Austria (AL 25.3%; BV 36.9%), and Sweden (SRB 42.4%; SH 43.4%). In contrast, the respective proportion in Poland exceeded 82% in all breeds except the commercial PHF (76.1%). In Sweden, lactations with veterinary treatments were considerably less prevalent in SRB (15.6%) than in SH (21.7%). In Austria, breeds differed only in treatments for udder disorders, which favored AL. In conclusion, the markedly lower milk yields of local breeds are partly counterbalanced by (somewhat inconsistent) advantages in longevity, fertility, and health traits across 4 European countries. This indicates that the robustness of local breeds can contribute to improved sustainability of organic dairy systems.

Detecting genetic variation such as Copy Number Variants (CNVs) in cattle provides the opportunity to study their association with quantitative traits. CNVs are DNA sequences of 50 bp up to several Mb long, which can vary in copy number in comparison with a reference genome. The aim of this study was to investigate CNVs in 1410 samples of the Brown Swiss cattle breed using Illumina Bovine HD SNP chip information, which includes 777,962 SNPs. After stringent quality control, CNVs were called with the Golden Helix SVS 8.3.1 (SVS) and PennCNV software and were summarized to CNV regions (CNVRs) at a population level (i.e. overlapping CNVs), using BEDTools. Additionally, common CNVRs between the two software were set as consensus regions. Genes within consensus CNVRs were annotated with a GO analysis using the DAVID Bioinformatics Resources 6.7. In order to validate these results, quantitative PCRs were executed on 15 selected CNVRs. The SVS software identified 25,030 CNVs summarized to 398 CNVRs, which comprised 30 gains, 344 losses and 24 complex CNVRs (i.e. containing both losses and gains), covering 3.92% of the bovine genome. The PennCNV software identified 62,341 CNVs summarized to 5578 CNVRs, which comprised 2638 gains, 2404 losses and 537 complex CNVRs, covering 7.68% of the bovine genome. The length of these CNVRs ranged from 1244 bp to 1,381,355 bp. A total of 563 consensus CNVRs were found covering 2.29% of the UMD 3.1 bovine genome assembly. Of these, 24 were gains, 300 were losses and 239 were complex CNVRs. A total of 775 official gene IDs were annotated in the consensus CNVRs. Among the 537 genes with functional information, the GO and pathway analysis was reported for those who clustered with a p-value

Postweaning diarrhoea (PWD) due to

Nanometric distance measurements with EPR spectroscopy yield crucial information on the structure and interactions of macromolecules in complex systems. The range of suitable spin labels for such measurements was recently expanded with a new class of light-inducible labels: the triplet state of porphyrins. Importantly, accurate distance measurements between a triplet label and a nitroxide have been reported with two distinct light-induced spectroscopy techniques, (light-induced) triplet-nitroxide DEER (LiDEER) and laser-induced magnetic dipole spectroscopy (LaserIMD). In this work, we set out to quantitatively compare the two techniques under equivalent conditions at Q band. Since we find that LiDEER using a rectangular pump pulse does not reach the high modulation depth that can be achieved with LaserIMD, we further explore the possibility of improving the LiDEER experiment with chirp inversion pulses. LiDEER employing a broadband pump pulse results in a drastic improvement of the modulation depth. The relative performance of chirp LiDEER and Laser-IMD in terms of modulation-to-noise ratio is found to depend on the dipolar evolution time: While LaserIMD yields higher modulation-to-noise ratios than LiDEER at short dipolar evolution times ({\tau}=2 {\mu}s), the high phase memory time of the triplet spins causes the situation to revert at {\tau}=6 {\mu}s., Comment: 9 pages, 4 figures and supporting information (18 pages, 11 figures)

peer-reviewed H.D.D., A.J.C., P.J.B. and B.J.H. would like to acknowledge the Dairy Futures Cooperative Research Centre for funding. H.P. and R.F. acknowledge funding from the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr ‘Synbreed—Synergistic Plant and Animal Breeding’ (grant 0315527B). H.P., R.F., R.E. and K.-U.G. acknowledge the Arbeitsgemeinschaft Süddeutscher Rinderzüchter, the Arbeitsgemeinschaft Österreichischer Fleckviehzüchter and ZuchtData EDV Dienstleistungen for providing genotype data. A. Bagnato acknowledges the European Union (EU) Collaborative Project LowInputBreeds (grant agreement 222623) for providing Brown Swiss genotypes. Braunvieh Schweiz is acknowledged for providing Brown Swiss phenotypes. H.P. and R.F. acknowledge the German Holstein Association (DHV) and the Confederación de Asociaciones de Frisona Española (CONCAFE) for sharing genotype data. H.P. was financially supported by a postdoctoral fellowship from the Deutsche Forschungsgemeinschaft (DFG) (grant PA 2789/1-1). D.B. and D.C.P. acknowledge funding from the Research Stimulus Fund (11/S/112) and Science Foundation Ireland (14/IA/2576). M.S. and F.S.S. acknowledge the Canadian Dairy Network (CDN) for providing the Holstein genotypes. P.S. acknowledges funding from the Genome Canada project entitled ‘Whole Genome Selection through Genome Wide Imputation in Beef Cattle’ and acknowledges WestGrid and Compute/Calcul Canada for providing computing resources. J.F.T. was supported by the National Institute of Food and Agriculture, US Department of Agriculture, under awards 2013-68004-20364 and 2015-67015-23183. A. Bagnato, F.P., M.D. and J.W. acknowledge EU Collaborative Project Quantomics (grant 516 agreement 222664) for providing Brown Swiss and Finnish Ayrshire sequences and genotypes. A.C.B. and R.F.V. acknowledge funding from the public–private partnership ‘Breed4Food’ (code BO-22.04-011- 001-ASG-LR) and EU FP7 IRSES SEQSEL (grant 317697). A.C.B. and R.F.V. acknowledge CRV (Arnhem, the Netherlands) for providing data on Dutch and New Zealand Holstein and Jersey bulls. Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.

Body condition scoring is a common tool to assess the subcutaneous fat reserves of dairy cows. Because of its subjectivity, which causes limits in repeatability, it is often discussed controversially. Aim of the current study was to evaluate the impact of considering the cows overall appearance on the scoring process and on the validity of the results. Therefore, two different methods to reveal body condition scores (BCS), 'independent BCS' (iBCS) and 'dependent BCS' (dBCS), were used to assess 1111 Swiss Brown Cattle. The iBCS and the dBCS systems were both working with the same flowchart with a decision tree structure for visual and palpatory assessment using a scale from 2 to 5 with increment units of 0.25. The iBCS was created strictly complying with the defined frames of the decision tree structure. The system was chosen due to its formularized approach to reduce the influence of subjective impressions. By contrast, the dBCS system, which was in line with common practice, had a more open approach, where - besides the decision tree - the overall impression of the cow's physical appearance was taken into account for generating the final score. Ultrasound measurement of the back fat thickness (BFT) was applied as a validation method. The dBCS turned out to be the better predictor of BFT, explaining 67.3% of the variance. The iBCS was only able to explain 47.3% of the BFT variance. Within the whole data set, only 31.3% of the animals received identical dBCS and iBCS. The pin bone region caused the most deviations between dBCS and iBCS, but also assessing the pelvis line, the hook bones and the ligaments led to divergences in around 20% of the scored animals. The study showed that during the assessment of body condition a strict adherence to a decision tree is a possible source of inexact classifications. Some body regions, especially the pin bones, proved to be particularly challenging for scoring due to difficulties in assessing them. All the more, the inclusion of the overall appearance of the cow into the assessment process counteracted these errors and led to a fair predictability of BFT with the flowchart-based BCS. This might be particularly important, if different cattle types and breeds are assessed.

Postweaning diarrhoea (PWD) due to Escherichia coli is an economically important disease in pig production. In this placebo-controlled study performed in Switzerland, the effects of oral supplementation of Allium sativum L. (garlic, AS) on performance (bodyweight (BW) and daily weight gain (DWG)) and health (body condition and clinical score) were investigated in postweaning piglets. Piglets (n=600) were randomly assigned to the treatment groups (placebo, AS or colistin) and observed from birth until three weeks postweaning. The treatments were administered for the first two weeks postweaning. Faecal dry matter (FDM) and coliform bacteria on pen level were measured weekly. Data were analysed using generalised mixed-effect models in R. BW and DWG of the AS group were significantly higher compared with placebo in the third week postweaning. No differences in body condition and FDM were observed. The clinical score of AS-treated animals was significantly better compared with the colistin group. About 33 per cent of the piglets of the AS and the placebo group had to be treated with antibiotics due to the occurrence of severe PWD. The major finding of this study showed that AS supplementation increased growth performance and improved clinical health, but did not reduce the incidence and severity of PWD.

The aim of this study was to estimate genetic parameters and accuracies of breeding values for a set of functional, behavior, and conformation traits in Brown Swiss cattle. These traits were milking speed, udder depth, position of labia, rank order in herd, general temperament, aggressiveness, milking temperament, and days to first heat. Data of 1,799 phenotyped Brown Swiss cows from 40 Swiss dairy herds were analyzed taking the complete pedigree into account. Estimated heritabilities were within the ranges reported in literature, with results at the high end of the reported values for some traits (e.g., milking speed: 0.42±0.06, udder depth: 0.42±0.06), whereas other traits were of low heritability and heritability estimates were of low accuracy (e.g., milking temperament: 0.04±0.04, days to first heat: 0.02±0.04). For most behavior traits, we found relatively high heritabilities (general temperament: 0.38±0.07, aggressiveness: 0.12±0.08, and rank order in herd: 0.16±0.06). Position of labia, arguably an indicator trait for pathological urovagina, was genetically analyzed in this study for the first time, and a moderate heritability (0.28±0.06) was estimated.

Detecting Copy Number Variation (CNV) in cattle provides the opportunity to study their association with quantitative traits (Winchester et al., 2009; Zhang et al., 2009; Hou et al., 2011; Clop et al., 2012; de Almeida et al., 2016;). The aim of this study was to map CNVs in 1,410 Brown Swiss males and females using Illumina BovineHD Genotyping BeadChip data and to perform a genome-wide association analysis for production functional and health traits. After quality control, CNVs were called with the GoldenHelix SVS 8.3.1 and PennCNV software and were summarized to CNV regions (CNVRs) at a population level, i.e. overlapping CNVs, using BEDTools. Additionally common CNVRs between the two software were set as consensus. CNV-association studies were executed with the CNVRuler software using a linear regression model. Genes within significant associated CNVRs for each trait were annotated with a GO analysis using the DAVID Bioinformatics Resources 6.7. The quality control filtered out 294 samples. The GoldenHelix SVS 8.3.1 software identified 25,030 CNVs summarized to 398 CNVRs while PennCNV identified 62,341 CNVs summarized to 5,578 CNVRs. A total of 311 CNVRs were identified to be significantly associated with one or more of the evaluated traits. The result of this study is a comprehensive genomic analysis of the Brown Swiss breed, which enriches the bovine CNV map in its genome. Finally, the results of the association studies deliver new information for quantitative traits considered in selection programs of the Brown Swiss breed., International Journal of Health, Animal Science and Food Safety, Vol 3, No 1s (2016)

Supernumerary teats (SNT) are any teats present on a cow`s udder other than the regular four. In Swiss Brown cows, 19.9% carry SNT. Different stages of development of SNT are observed from rudimentary appendices to functional and possibly lactating teats. SNT may promote mastatis, impeach good placement of the milking machine and lower market price of the animals. No genetic analysis of the trais has been done in this cattle population, althought SNT have been routinely recorded with other conformation traits since 1995 in Switzerland. This study aimed to investigate the genetic acrchitecture of this trait through genome-wide association studies (GWAS) performed with imputed whole-genome sequence. Two trait definitions were used: Udder Clearance (UCT) considering whether a cow is carrier of any SNT or has a clear udder and Presence of Supernumerary Mammary Gland (PMG) opposing animal carrier of completely developed and possibly functional SNT with animals with a clear udder or carrier of a rudimentary SNT. Breeding values were estimated for Brown Swiss sires of at least 20 daughters with SNT records using an animal model including the random effects expert-by-year, farm-by-year and animal. The animal's dam life stage—heifer or cow—during its parity was fitted as a fixed effect in the same model. Single SNP regression using deregressed proofs of 1519 bulls with genotypes imputed to the variant list of the 5thRun of the 1000 Bulls Genome Project permitted discovery of three important regions on BTA5, BTA17 and BTA20 associated with the presence or the development of SNT. Regions on BTA17 and BTA20 reached clearly lower p-values (10−7 vs. 10−4) when associated to PMG than UCT, while variants on BTA5 were significantly linked to both trait definitions. No candidate genes on BTA 17 and BTA20 were found after functional analysis. On BTA5, however, the leucine-rich repeat-containing G protein coupled receptor 5 (LGR5) can be considered as the major gene for our trait. Encoding a protein known as an up-regulator of the Wnt pathway and having an expression level impacting the mammary gland development, LGR5 also carries a synonymous mutation that is highly associated to SNT. To conclude, GWAS in the Swiss Brown Swiss population revealed LGR5 on BTA5 as a candidate gene influencing the presence and development stage of supernumerary teats.

This study investigated the effect of, and interactions between, contrasting crossbreed genetics (US Brown Swiss [BS] × Improved Braunvieh [BV] × Original Braunvieh [OB]) and feeding regimes (especially grazing intake and pasture type) on milk fatty acid (FA) profiles. Concentrations of total polyunsaturated FAs, total omega-3 FAs and trans palmitoleic, vaccenic, α-linolenic, eicosapentaenoic and docosapentaenoic acids were higher in cows with a low proportion of BS genetics. Highest concentrations of the nutritionally desirable FAs, trans palmitoleic, vaccenic and eicosapentaenoic acids were found for cows with a low proportion of BS genetics (0-24% and/or 25-49%) on high grazing intake (75-100% of dry matter intake) diets. Multivariate analysis indicated that the proportion of OB genetics is a positive driver for nutritionally desirable monounsaturated and polyunsaturated FAs while BS genetics proportion was positive driver for total and undesirable individual saturated FAs. Significant genetics × feeding regime interactions were also detected for a range of FAs.

Gastrointestinal nematodes (GIN) severely affect small ruminant production worldwide. Increasing problems of anthelmintic resistance have given strong impetus to the search for alternative strategies to control GIN. Selection of animals with an enhanced resistance to GIN has been shown to be successful in sheep. In goats, the corresponding information is comparatively poor. Therefore, the present study was designed to provide reliable data on heritabilities of and genetic correlations between phenotypic traits linked to GIN and milk yield in two major dairy goat breeds (Alpine and Saanen). In all, 20 herds totalling 1303 goats were enrolled in the study. All herds had (i) a history of gastrointestinal nematode infection, (ii) uniform GIN exposure on pasture and (iii) regular milk recordings. For all goats, individual recordings of faecal egg counts (FEC), FAMACHA© eye score, packed cell volume (PCV) and milk yield were performed twice a year with an anthelmintic treatment in between. The collected phenotypic data were multivariately modelled using animal as a random effect with its covariance structure inferred from the pedigree, enabling estimation of the heritabilities of the respective traits and the genetic correlation between them. The heritabilities of FEC, FAMACHA© and PCV were 0.07, 0.22 and 0.22, respectively. The genetic correlation between FEC and FAMACHA© was close to zero and -0.41 between FEC and PCV. The phenotypic correlation between FEC and milk yield was close to zero, whereas the genetic correlation was 0.49. Our data suggest low heritability of FEC in Saanen and Alpine goats and an unfavourable genetic correlation of FEC with milk yield.

Recently organic agriculture is more and more recognized as a food system that provides added economic and environmental services to the society as whole. Consequently the growth of organic agriculture has been accelerated changing its nature form alternative to mainstream food production distribution and consumption system. To support this change the stronger cooperation of scarce and disperse expertise is required to develop pull of very specific information knowledge technologies and innovations. One step in this direction is integration of organic agriculture issues into the official agricultural academic education. That process is in fact focus of the project SCOPES (2009/12) „Advancing training and teaching of organic agriculture in South East Europe (Albania Bosnia and Herzegovina Kosovo Bulgaria Hungary)“ financed by Swiss National Science Foundation and implemented by FiBL (CH) Faculty of Agriculture and Food Sciences Sarajevo (BA) Agricultural University Tirana (AL) Agricultural University in Plovdiv (BG) Department of Ecological and Sustainable Farming Systems of the Corvinus University of Budapest (HU) University of Prishtina Kosovo. The main project results are: multi language curriculum and teaching material which can be easily integrated within existing official academic education on B.Sc. or M.Sc level in SEE region and interactive e platform for on line teaching which connects researchers teachers experts students and other stakeholders and forms innovative social network able to communicate exchange experience innovate and think „out of box“ to face existing and future challenges regarding organic agriculture development. Keywords: Organic agriculture agricultural academic education SEE region.

In this study, direct genomic values for the functional traits general temperament, milking temperament, aggressiveness, rank order in herd, milking speed, udder depth, position of labia, and days to first heat in Brown Swiss dairy cattle were estimated based on ~777,000 (777 K) single nucleotide polymorphism (SNP) information from 1,126 animals. Accuracy of direct genomic values was assessed by a 5-fold cross-validation with 10 replicates. Correlations between deregressed proofs and direct genomic values were 0.63 for general temperament, 0.73 for milking temperament, 0.69 for aggressiveness, 0.65 for rank order in herd, 0.69 for milking speed, 0.71 for udder depth, 0.66 for position of labia, and 0.74 for days to first heat. Using the information of ~54,000 (54K) SNP led to only marginal deviations in the observed accuracy. Trying to predict the 20% youngest bulls led to correlations of 0.55, 0.77, 0.73, 0.55, 0.64, 0.59, 0.67, and 0.77, respectively, for the traits listed above. Using a novel method to estimate the accuracy of a direct genomic value (defined as correlation between direct genomic value and true breeding value and accounting for the correlation between direct genomic values and conventional breeding values) revealed accuracies of 0.37, 0.20, 0.19, 0.27, 0.48, 0.45, 0.36, and 0.12, respectively, for the traits listed above. These values are much smaller but probably also more realistic than accuracies based on correlations, given the heritabilities and samples sizes in this study. Annotation of the largest estimated SNP effects revealed 2 candidate genes affecting the traits general temperament and days to first heat.

Cryo-electron tomography (cryo-ET) has the potential to revolutionize our understanding of the building blocks of life since it provides the unique opportunity to study molecules and membrane architectures in the context of cellular interaction. In particular, the combination of fluorescence imaging with focused ion beam (FIB) milling allows the targeting of specific structures in thick cellular samples by preparing thin lamellae that contain a specific fluorescence marker. This technique has conventionally been time-consuming, as it requires sample transfer to multiple microscopes and presents several technical challenges that currently limit its success. Here we describe METEOR, a FIB-integrated microscopy solution that streamlines the correlative cryo-ET workflow. It protects the sample from ice contamination by minimizing handling steps, thus increasing the likelihood of high-quality data. It also allows for monitoring of the milling procedure to ensure the molecule of interest is captured and can then be imaged by cryo-ET.

There is a serious need for significant and fundamental improvements to the way we currently produce and consume food if we are going to respond meaningfully to the enormous global environmental challenges that face us. The role of animal farming in particular is faced with the challenge of balancing their potential positive contribution to our food system within an effective circular economy while ensuring that the animals on our farms exist as living, sentient beings that are treated in ways that allow their lives, from their perspective, to be worth living.This paper draws on evidence from a recently published book3 on organic animal farming as well as one recent and five on-going research projects across Europe funded via the H2020 ERA-net project, CORE Organic Cofund4. The presentation discusses the following approaches to future sustainable organic animal farming: 1) integrating diversified multi-speciessystems; 2) developing sustainable foraging, agroforestry and pastoralism; 3) finding new potential for home grown protein feeds; 4) adopting resilience as a core of health principle and developing strategies to significantly lower or phase out the use of antibiotics; 5) emphasising appropriate breeding and breeds, including multipurpose breeds; and 6) enabling enhanced mother-infant contact.Throughout we emphasise diversity as a key element for the future development of organic animal farming. Adopting innovations such as those described, that are guided by ethical principles, can offer multiple practical contextual applications and improved opportunity for sustainability. However, it is abundantly clear that there are no current farming systems that can be considered sustainable without the adoption of relevant supporting policies and the wider society undergoing fundamental changes in the way we demand, consume and waste food.