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Understanding the farming system impact on animals is crucial for evaluating welfare. Rabbits exhibit distinct behaviours influenced by their surroundings. The conditions in which they are raised directly influence behaviour and stress responses, emphasizing the importance of providing an optimal environment for their overall well-being and growth. In this study, we assessed the behaviour and welfare of two Italian local rabbit populations, namely the grey rabbit of Carmagnola and the grey rabbit of Monferrato. These rabbits are not yet officially recognized as breeds, but they are commonly used in Italy for meat production and represent a distinctive phenotype and local heritage among farmers and consumers. We analysed the behavioural patterns, physiological responses, and blood parameters of the animals to assess the influence of both age and three distinct housing systems (traditional single cages, group farming, and a mixed system) on rabbits' welfare. In this study, 294 weaned males with 35 days old were divided into three housing systems with seven replicates each until reaching slaughtering age (100 days of age). A traditional single cage system, a group farming with 10 animals each replicate and a Mixed pilot system with 10 rabbits initially grouped, then transferred to single cages. The findings from the behavioural analysis and the evaluation of salivary and hair corticosterone levels demonstrate that both the housing system and the age of the rabbits exerted significant effects on their welfare. Rabbits in group housing displayed a wider range of behavioural patterns, including increased kinetic activities such as running, walking, and exploration. However, this housing system was associated with higher levels of both salivary and hair corticosterone, indicating a high acute and chronic stress condition. The single cage system was associated with higher levels of acute stress and a low frequency of kinetic activities and social interactions, with a predominant behaviour of turning on themselves. The age factor significantly influenced the occurrence of behaviours, with younger rabbits exhibiting higher levels of kinetic activities, while social behaviours such as attacks and dominance were more prevalent as the rabbits reached sexual maturity (around 80-85 days of age). Moreover, the attainment of sexual maturity coincided with an increase in salivary corticosterone levels. We found a significant association between attack behaviours, escape attempts, and elevated corticosterone levels, by demonstrating that these behaviours can be used as indicators of decreased animals' well-being. Our findings underscore the importance of considering both the housing environment and the temporal dimension in the study of behaviour and welfare. This enables a comprehensive assessment of appropriate rearing management techniques. By understanding the social dynamics and stress sources within housing systems, farmers can implement measures to enhance animal welfare and create a conducive environment for the health and behaviour of rabbits., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Ozella et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Pyrenean Mountain Dog (PMD) is an ancient dog breed firstly described in XIV century in the Pyrenees Region and nowadays diffused both in Europe and in the US. Hereditary Cataract (HC), defined as the inherited opacity of the lens, involves clinical signs ranging from reduced vision to glaucoma. A molecular basis of HC was firstly described in Staffordshire Bull Terriers and then reported in multiple canine breeds. The HC-associated variation is a single nucleotide deletion in HSF4 gene that introduces a premature stop codon (c.962del, p.Ala321*). Multifocal Retinopathy 1 (MR) is an ocular disorder characterized by multiple areas of retinal degeneration, caused in various dog breeds (including PMD) by a single nucleotide variant (SNV) in BEST1 gene that generates a premature stop codon (c.73G>A, p.Arg25*). Degenerative Myelopathy (DM) is an adult-onset, progressive neurodegenerative disease and it is associated to a SNV in SOD1 gene causing a change in aminoacidic sequence of the protein (c.118G>A, p.Glu40Lys). This causative variant has been described in various dog breeds, including PMD. Aim of this study was to determine the allele frequencies for the abovementioned three genetic diseases in the Italian breeding PMD population. The survey found no dogs carrying the allele (deletion) associated with HC, while three dogs (6 %) were heterozygous (G/A) for the MR-associated variant, and seven dogs (13 %) were heterozygous (G/A) for the DM-associated alteration, indicating that the variant alleles frequency were 0  %, 3 %, and 7 %, respectively. Appropriate mating management is suggested for the prevention of genetic diseases spreading in the PMD population., Competing Interests: Declaration of Competing Interest None of the authors has any financial or personal relationships that could inappropriately influence or bias the content of the paper., (Copyright © 2023. Published by Elsevier Inc.)

Objectives: The objectives of this study were to investigate the c.1024G>T SNP in the TRPV4 gene in Scottish Straight and Fold cats, and to evaluate the pattern of skeletal phenotype and the evolution of radiological signs of Scottish Fold osteochondrodysplasia (SFOCD) over time in heterozygous subjects., Methods: DNA was obtained from blood samples of 17 cats (Scottish Fold: n = 12; Scottish Straight: n = 5) and subsequently genotyped by sequencing in a 249 bp region of the TRPV4 gene (exon 6), including the known c.1024G>T causative mutation for osteochondrodysplasia. Orthopaedic and radiographic analyses were performed on animals carrying the mutant allele., Results: Genotyping by sequencing confirmed that all and only the Scottish Fold cats carried the mutant allele in a heterozygous asset. Furthermore, two other exon variants, already described in the literature as silent variants, were found in some of the sampled cats. Comparative orthogonal radiographic views of the shoulder, elbow, carpus, hip, stifle and tarsus were obtained. A mediolateral projection of the thoracic and lumbar column was also performed. Three out of four cats were clinically and radiographically examined again 1.5 years later., Conclusions and Relevance: Although the presence of the mutant allele in all the tested Scottish Fold cats was confirmed, only 1/12 showed clinical signs of SFOCD. Furthermore, no cats in the 1.5-year follow-up showed skeletal changes. Although significant, the c.1024G>T mutation in the TRPV4 gene, supposedly, is not the only cause or risk of developing SFOCD., Competing Interests: Conflict of interestThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Adopting a 300 μs long MD trajectory of the folding of villin headpiece (HP35) by D. E. Shaw Research, we recently constructed a Markov state model (MSM) based on inter-residue contacts. The model reproduces the folding time and predicts that the native basin and unfolded region consist of metastable substates that are structurally well-characterized. Recognizing the need to establish well-defined benchmark problems, we study to what extent and in what sense this MSM can be employed as a reference model. Hence, we test the robustness of the MSM by comparing it to models that use alternative combinations of features, dimensionality reduction methods, and clustering schemes. The study suggests some main characteristics of the folding of HP35 that should be reproduced by other competitive models. Moreover, the discussion reveals which parts of the MSM workflow matter most for the considered problem and illustrates the promises and pitfalls of state-based models for the interpretation of biomolecular simulations.

Markov state models represent a popular means to interpret molecular dynamics trajectories in terms of memoryless transitions between metastable conformational states. To provide a mechanistic understanding of the considered biomolecular process, these states should reflect structurally distinct conformations and ensure a time scale separation between fast intrastate and slow interstate dynamics. Adopting the folding of villin headpiece (HP35) as a well-established model problem, here we discuss the selection of suitable input coordinates or "features", such as backbone dihedral angles and interresidue distances. We show that dihedral angles account accurately for the structure of the native energy basin of HP35, while the unfolded region of the free energy landscape and the folding process are best described by tertiary contacts of the protein. To construct a contact-based model, we consider various ways to define and select contact distances and introduce a low-pass filtering of the feature trajectory as well as a correlation-based characterization of states. Relying on input data that faithfully account for the mechanistic origin of the studied process, the states of the resulting Markov model are clearly discriminated by the features, describe consistently the hierarchical structure of the free energy landscape, and─as a consequence─correctly reproduce the slow time scales of the process.

Heifers are a fundamental resource on farms, and their importance is reflected in both farm management and economy. Therefore, the selection of heifers to be reared on a farm should be carefully performed to select only the best animals. Genomic selection is available nowadays to evaluate animals in a fast and economic way. However, it is mainly used on the sire line and on performance traits. Ten farms were selected based on their 5-year records of average somatic cell count and evenly classified into high (>300,000 cells/mL) and low somatic cell count (<150,000 cells/mL). Genomic indexes (regarding both wellness and productive traits) were evaluated in 157 Italian Holstein heifers reared in the selected ten farms (90 from high-cells farms and 67 from low-cells ones). Linear mixed models were fitted to analyze the effects of the abovementioned genomic indexes on related phenotypes. Results have shown that farms classified into low somatic cell count had an overall better animal genomic pool compared to high somatic cell count ones. Additionally, the results shown in this study highlighted a difference in wellness genomic indexes in animals from farms with either a high or a low average somatic cell count. Applying genomic tools directly to heifer selection could improve economic aspects related to herd turnover.

The aim of the present study was to investigate the ability of two Italian slow-growing poultry breeds (namely, Bionda Piemontese , BP, and Bianca di Saluzzo , BS) to cope with a stressful event, such as collective grouping, using a multifactorial approach. A total of 120 hens of BP and BS breeds were homogenously distributed, according to breed, in 12 pens (10 hens/pen; 6 pens/breed), from 18 to 49 weeks of age. At 50 weeks of age, hens were regrouped (Stressful Farm Practice, SFP), by removing separators, both in indoor and outdoor areas. At 49 weeks of age, 24 hens/breed were randomly selected for the evaluation of welfare (ethological and physiological) parameters, at different time points: T0: 1-week pre-SPF; T1: 1-week post-SFP; T2: 3-week post-SFP; T3: 5-week post-SFP. Egg production was recorded from 38 to 56 weeks of age. Grouping produced a social stress in both BS and BP-laying hens, which was expressed in terms of productive traits (reduction of oviposition), behavioral modification (worsening of plumage condition due to feather peaking and extension of the duration of the tonic immobility test) and physiological modification (increased heterophil/lymphocyte ratio and corticosterone metabolites in droppings). Both breeds reacted in a similar way; in fact, no differences were attributed to the breed. At the end of the observation period, the egg rate fully recovered, while the behavioral and physiological parameters partially recovered but failed to recover to those recorded prior to the stressful event.

Small ruminant lentiviruses (SRLV) belong to the Retroviridae family and can cause various diseases. One of the most impacting diseases is visna-maedi, a complex disease characterized by long latencies and chronic progressive inflammatory events affecting the nervous system, lungs, mammary gland, and articular joints. A single nucleotide polymorphism (rs408593969, c.103G>A, missense mutation E35K) in the ovine transmembrane protein gene 154 (TMEM154) was identified as protective against small ruminant lentivirus infection in different herds worldwide. However, there is evidence in the scientific literature of a breed-specificity of this protective effect and, furthermore, there are still limited studies regarding the association between the animal genotype and the infecting virus genotype. Thus, the aim of this study was to further investigate the association between the animal genotype for the suggested protective mutation and the infecting virus genotype, in three different sheep breeds reared in northern Italy. The results obtained only partially confirmed the data available in the literature, as the protective effect was confirmed only for SRLV genotype A clusters, while other genotypes (namely B and E) infected AA and GA animals. Further studies with an experimental infection of specific virus genotypes in hosts with specific genotypes are required to confirm the larger number of cases the results obtained in this study., (© 2022. The Author(s).)