Measuring farmers' attitude towards breeding tools: the Livestock Breeding Attitude Scale

Under-use of genetic improvement tools and low participation in breeding programmes are key drivers of breeding programmes under-performance. Both aspects are heavily influenced by farmers attitudes which, to date, have not been analysed in an objective and systematic manner. A key factor constraining the implementation of attitudinal studies towards livestock breeding tools is the lack of a reference scale for measuring attitudes. In this research, we provide the livestock breeding sector with such a reference measure. We developed the scale following the standardized psychometric methodologies and statistical tools. Then, as a case study, we used the scale to explore the attitudes of beef and dairy sheep farmers in Australia, New Zealand and Spain and analysed farmer and farming system factors related to those attitudes. Fourteen sheep and beef breed associations facilitated the implementation of a survey of 547 farmers, generating data that was used for the scale evaluation. The relationship between attitudinal factors and farmer and farming system factors was analysed using generalized linear models across and within breeds. The results suggest that the 8-item definitive scale we have developed is appropriate to measure farmer attitudes. We found that attitudes towards genetic improvement tools have two components; i) traditional selection and ii) genetic and genomic selection combined. This means that positive attitudes towards traditional phenotypic selection do not necessarily imply a negative attitude towards genetic and genomic selection tools. Farmer attitudes varied greatly not only across the studied breeds, species and countries, but also within them. High-educated farmers of business-oriented farms tend to have the most negative attitude towards traditional selection. However, attitudes towards genetic and genomic selection tools could not be linked to these factors. Finally, we found that the breed raised had a large effect on farmer attitude. These findings may help in the evolution of breeding programmes by identifying both the farmers most inclined to uptake breeding innovations in the early stages of its establishment and the farmers who would be more reluctant to participate in such programmes, thus informing where to focus extension efforts

Analyzing the heterogeneity of farmers’ preferences for improvements in dairy cow traits using farmer typologies

AbstractGiving consideration to farmers’ preferences for improvements in animal traits when designing genetic selection tools such as selection indexes might increase the uptake of these tools. The increase in use of genetic selection tools will, in turn, assist in the realization of genetic gain in breeding programs. However, the determination of farmers’ preferences is not trivial because of its large heterogeneity. The aim of this study was to quantify Australian dairy farmers’ preferences for cow trait improvements to inform and ultimately direct the choice of traits and selection indexes in the 2014 review of the National Breeding Objective. A specific aim was to analyze the heterogeneity of preferences for cow trait improvements by determining whether there are farmer types that can be identified with specific patterns of preferences. We analyzed whether farmer types differed in farming system, socioeconomic profile, and attitudes toward breeding and genetic evaluation tools. An online survey was developed to explore farmers’ preferences for improvement in 13 cow traits. The pairwise comparisons method was used to derive a ranking of the traits for each respondent. A total of 551 farmers fully completed the survey. A principal component analysis followed by a Ward hierarchical cluster analysis was used to group farmers according to their preferences. Three types of farmers were determined: (1) production-focused farmers, who gave the highest preference of all for improvements in protein yield, lactation persistency, feed efficiency, cow live weight, and milking speed; (2) functionality-focused farmers with the highest preferences of all for improvements in mastitis, lameness, and calving difficulty; and (3) type-focused farmers with the highest preferences of all for mammary system and type. Farmer types differed in their age, their attitudes toward genetic selection, and in the selection criteria they use. Surprisingly, farmer types did not differ for herd size, calving, feeding system, or breed. These results support the idea that preferences for cow trait improvements are intrinsic to farmers and not to production systems or breeds. As a result of this study, and some bioeconomic modeling (not included in this study), the Australian dairy industry has implemented a main index and 2 alternative indexes targeting the different farmer types described here

Biodiversity and ecosystem services in quarries

Although covering less than 1% of the land surface, extraction activities have long‐lasting impacts on local ecosystems, inevitably damaging biological diversity and depleting ecosystem services. Many extractive companies are now aware of their impacts and, while pressured by society, demand concrete solutions from researchers to reverse the effects of exploitation and restore biodiversity and ecosystems services. In this article, we compile and synthesize the contributions of the latest available research on quarry restoration. We depict and discuss some of the most pressing issues regarding (1) the challenges of restoring quarries; (2) the opportunities for biodiversity and ecosystem services delivery; and (3) outline further research addressing current gaps. We conclude that quarries pose different abiotic and biotic constraints that act interdependently, hampering the attainment of effective restoration if considered solely. Such constraints need to be addressed holistically to lastly encourage the self‐sustainability of the system by reinstating ecological processes. However, a restored site does not have to specifically mimic the pristine situation, as under certain conditions alternative approaches may uphold valuable natural assets contributing to the conservation of rare, restricted, or protected species and habitats.Czech Grant Agency by the project no. 20-06065Sinfo:eu-repo/semantics/publishedVersio

Livestock keepers’ attitudes: Keystone of effective community-based breeding programs

Livestock keepers in southwestern Burkina Faso hold the local Lobi taurine breed, local Zebu cattle, and their crosses. Some communities in the region have begun to implement community-based cattle breeding programs (CBBPs), which involve animal tagging and recording and, potentially, also bull sharing. Based on the hypothesis that the participation of livestock keepers in CBBPs depends on their attitudes towards these programs, we used questionnaires to survey the attitudes of 125 farmers towards cattle breeding strategies and tools. Results were analyzed using principal component analysis. Farmers showed a highly positive attitude towards maintaining the features of their preferred cattle breed, but their attitudes varied substantially towards crossbreeding for breed improvement. Farmers generally agreed that performance was more important than animal appearance, and most of them were willing to cooperate with breeders’ associations but were skeptical about sharing their bulls with other farmers. The majority was reluctant to record performance data, which may be due to a capacity deficit and their confidence in being able to select the best animals based purely on phenotype. Our analysis suggests that breeders’ associations, as a key component of CBBPs, should lay down clear rules and obligations for their members from the outset. Timely consideration of farmers’ attitudes towards different breeding tools may improve their uptake and guarantee the sustainability of CBBPs

EcoCyc: fusing model organism databases with systems biology.

EcoCyc (http://EcoCyc.org) is a model organism database built on the genome sequence of Escherichia coli K-12 MG1655. Expert manual curation of the functions of individual E. coli gene products in EcoCyc has been based on information found in the experimental literature for E. coli K-12-derived strains. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc

Multidimensional annotation of the Escherichia coli K-12 genome

The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns biochemical functions to 76%, and 66% of all genes had their functions determined experimentally. EcoCyc assigns E. coli genes to Gene Ontology and to MultiFun. Seventy-five percent of gene products contain reviews authored by the EcoCyc project that summarize the experimental literature about the gene product. EcoCyc information was derived from 15 000 publications. The database contains extensive descriptions of E. coli cellular networks, describing its metabolic, transport and transcriptional regulatory processes. A comparison to genome annotations for other model organisms shows that the E. coli genome contains the most experimentally determined gene functions in both relative and absolute terms: 2941 (66%) for E. coli, 2319 (37%) for Saccharomyces cerevisiae, 1816 (5%) for Arabidopsis thaliana, 1456 (4%) for Mus musculus and 614 (4%) for Drosophila melanogaster. Database queries to EcoCyc survey the global properties of E. coli cellular networks and illuminate the extent of information gaps for E. coli, such as dead-end metabolites. EcoCyc provides a genome browser with novel properties, and a novel interactive display of transcriptional regulatory networks

Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis

The preterm gut microbiome is a complex dynamic community influenced by genetic and environmental factors and is implicated in the pathogenesis of necrotising enterocolitis (NEC) and sepsis. We aimed to explore the longitudinal development of the gut microbiome in preterm twins to determine how shared environmental and genetic factors may influence temporal changes and compared this to the expressed breast milk (EBM) microbiome. Stool samples (n = 173) from 27 infants (12 twin pairs and 1 triplet set) and EBM (n = 18) from 4 mothers were collected longitudinally. All samples underwent PCR-DGGE (denaturing gradient gel electrophoresis) analysis and a selected subset underwent 454 pyrosequencing. Stool and EBM shared a core microbiome dominated by Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae. The gut microbiome showed greater similarity between siblings compared to unrelated individuals. Pyrosequencing revealed a reduction in diversity and increasing dominance of Escherichia sp. preceding NEC that was not observed in the healthy twin. Antibiotic treatment had a substantial effect on the gut microbiome, reducing Escherichia sp. and increasing other Enterobacteriaceae. This study demonstrates related preterm twins share similar gut microbiome development, even within the complex environment of neonatal intensive care. This is likely a result of shared genetic and immunomodulatory factors as well as exposure to the same maternal microbiome during birth, skin contact and exposure to EBM. Environmental factors including antibiotic exposure and feeding are additional significant determinants of community structure, regardless of host genetics

Influence of Milk-Feeding Type and Genetic Risk of Developing Coeliac Disease on Intestinal Microbiota of Infants: The PROFICEL Study

Interactions between environmental factors and predisposing genes could be involved in the development of coeliac disease (CD). This study has assessed whether milk-feeding type and HLA-genotype influence the intestinal microbiota composition of infants with a family history of CD. The study included 164 healthy newborns, with at least one first-degree relative with CD, classified according to their HLA-DQ genotype by PCR-SSP DQB1 and DQA1 typing. Faecal microbiota was analysed by quantitative PCR at 7 days, and at 1 and 4 months of age. Significant interactions between milk-feeding type and HLA-DQ genotype on bacterial numbers were not detected by applying a linear mixed-model analysis for repeated measures. In the whole population, breast-feeding promoted colonization of C. leptum group, B. longum and B. breve, while formula-feeding promoted that of Bacteroides fragilis group, C. coccoides-E. rectale group, E. coli and B. lactis. Moreover, increased numbers of B. fragilis group and Staphylococcus spp., and reduced numbers of Bifidobacterium spp. and B. longum were detected in infants with increased genetic risk of developing CD. Analyses within subgroups of either breast-fed or formula-fed infants indicated that in both cases increased risk of CD was associated with lower numbers of B. longum and/or Bifidobacterium spp. In addition, in breast-fed infants the increased genetic risk of developing CD was associated with increased C. leptum group numbers, while in formula-fed infants it was associated with increased Staphylococcus and B. fragilis group numbers. Overall, milk-feeding type in conjunction with HLA-DQ genotype play a role in establishing infants' gut microbiota; moreover, breast-feeding reduced the genotype-related differences in microbiota composition, which could partly explain the protective role attributed to breast milk in this disorder

Senescent cells as a source of inflammatory factors for tumor progression

Cellular senescence, which is associated with aging, is a process by which cells enter a state of permanent cell cycle arrest, therefore constituting a potent tumor suppressive mechanism. Recent studies show that, despite the beneficial effects of cellular senescence, senescent cells can also exert harmful effects on the tissue microenvironment. The most significant of these effects is the acquisition of a senescent-associated secretory phenotype (SASP), which entails a striking increase in the secretion of pro-inflammatory cytokines. Here, we summarize our knowledge of the SASP and the impact it has on tissue microenvironments and ability to stimulate tumor progression