A Preliminary internet survey of pet rabbit owners’ characteristics

[EN] This study aimed to conduct a preliminary survey to investigate basic ownership factors, frequency of microchipping and insurance and views of pet rabbit owners  n these areas and general rabbit management. More specifically, we aimed to investigate whether owners possess insurance, whether their rabbits are microchipped, and owners’ views on the recommendations relating to rabbits (e.g. recommended enclosure sizes) and the law. A questionnaire was designed and promulgated through social media sites and rabbit forums. A total of 1183 responses were received. Just over 29% of respondents sourced their rabbits through rescue centres. 73.9% (867/1174) of owners stated that they had no pet insurance for their rabbits. Concerning microchips, 78.3% (919/1173) of rabbits were not microchipped, while 21.7% (254/1173) were. This preliminary study found that the majority of individuals are of the opinion that the relevant law is insufficiently publicised. A more detailed study would be beneficial to investigate and provide further insight into rabbit owners and their views and concerns for rabbits. The results of such a study could help formulate rabbit-related information and guidelines which in turn could have a direct impact on pet rabbit welfare.Oxley, J.; Previti, A.; Alibrandi, A.; Briefer, E.; Passantino, A. (2015). A Preliminary internet survey of pet rabbit owners’ characteristics. World Rabbit Science. 23(4):289-293. doi:10.4995/wrs.2015.3771.SWORD289293234Bays TB, Lightfoot T, and Mayer J 2006 Exotic pet behavior: birds, reptiles, and small mammals. Elsevier Health Sciences: USA.Egenvall, A., Bonnett, B. N., Olson, P., & Hedhammar, Å. (1998). Validation of computerized Swedish dog and cat insurance data against veterinary practice records. Preventive Veterinary Medicine, 36(1), 51-65. doi:10.1016/s0167-5877(98)00073-7Lord, L. K., Wittum, T. E., Ferketich, A. K., Funk, J. A., & Rajala-Schultz, P. J. (2007). Search and identification methods that owners use to find a lost dog. Journal of the American Veterinary Medical Association, 230(2), 211-216. doi:10.2460/javma.230.2.211Oxley, J. A. (2013). Letter - Rabbit welfare and legislation in the UK. World Rabbit Science, 21(4). doi:10.4995/wrs.2013.1748RSPCA 2012 The time and costs involved in keeping rabbits: RSPCA companion animal pet care factsheet. RSPCA: West Sussex.RWAF (Rabbit Association and Fund) 2012 Survey reveals abandoned rabbit numbers have soared. The Veterinary Times. 42, 4.Schepers F, Koene P and Beerda B 2009 Welfare assessment in pet rabbits. Animal Welfare. 18: 477-485

Molecular Epidemiology and Genetic Diversity of Human Respiratory Syncytial Virus in Sicily during Pre- and Post-COVID-19 Surveillance Seasons

Human respiratory syncytial virus (hRSV) is an important pathogen of acute respiratory tract infection of global significance. In this study, we investigated the molecular epidemiology and the genetic variability of hRSV over seven surveillance seasons between 2015 and 2023 in Sicily, Italy. hRSV subgroups co-circulated through every season, although hRSV-B mostly prevailed. After the considerable reduction in the circulation of hRSV due to the widespread implementation of non- pharmaceutical preventive measures during the COVID-19 pandemic, hRSV rapidly re-emerged at a high intensity in 2022–2023. The G gene was sequenced for genotyping and analysis of deduced amino acids. A total of 128 hRSV-A and 179 hRSV-B G gene sequences were obtained. The phylogenetic analysis revealed that the GA2.3.5a (ON1) and GB5.0.5a (BA9) genotypes were responsible for the hRSV epidemics in Sicily.; only one strain belonged to the genotype GB5.0.4a. No differences were observed in the circulating genotypes during pre- and post-pandemic years. Amino acid sequence alignment revealed the continuous evolution of the G gene, with a combination of amino acid changes specifically appearing in 2022–2023. The predicted N-glycosylation sites were relatively conserved in ON1 and BA9 genotype strains. Our findings augment the understanding and prediction of the seasonal evolution of hRSV at the local level and its implication in the monitoring of novel variants worth considering in better design of candidate vaccines

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we provide a first and comprehensive description of the core promoter repertoire and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal genome-wide rules of core promoter usage, structure, and dynamics, key to understanding the control of gene regulation during vertebrate ontogeny. They revealed the existence of multiple classes of pervasive intra- and intergenic post-transcriptionally processed RNA products and their developmental dynamics. Among these RNAs, we report splice donor site-associated intronic RNA (sRNA) to be specific to genes of the splicing machinery. For the identification of conserved features, we compared the zebrafish data sets to the first CAGE promoter map of Tetraodon and the existing human CAGE data. We show that a number of features, such as promoter type, newly discovered promoter properties such as a specialized purine-rich initiator motif, as well as sRNAs and the genes in which they are detected, are conserved in mammalian and Tetraodon CAGE-defined promoter maps. The zebrafish developmental promoterome represents a powerful resource for studying developmental gene regulation and revealing promoter features shared across vertebrates.publishedVersio

Identifying differentially methylated genes using mixed effect and generalized least square models

<p>Abstract</p> <p>Background</p> <p>DNA methylation plays an important role in the process of tumorigenesis. Identifying differentially methylated genes or CpG islands (CGIs) associated with genes between two tumor subtypes is thus an important biological question. The methylation status of all CGIs in the whole genome can be assayed with differential methylation hybridization (DMH) microarrays. However, patient samples or cell lines are heterogeneous, so their methylation pattern may be very different. In addition, neighboring probes at each CGI are correlated. How these factors affect the analysis of DMH data is unknown.</p> <p>Results</p> <p>We propose a new method for identifying differentially methylated (DM) genes by identifying the associated DM CGI(s). At each CGI, we implement four different mixed effect and generalized least square models to identify DM genes between two groups. We compare four models with a simple least square regression model to study the impact of incorporating random effects and correlations.</p> <p>Conclusions</p> <p>We demonstrate that the inclusion (or exclusion) of random effects and the choice of correlation structures can significantly affect the results of the data analysis. We also assess the false discovery rate of different models using CGIs associated with housekeeping genes.</p

Linking the Epigenome to the Genome: Correlation of Different Features to DNA Methylation of CpG Islands

DNA methylation of CpG islands plays a crucial role in the regulation of gene expression. More than half of all human promoters contain CpG islands with a tissue-specific methylation pattern in differentiated cells. Still today, the whole process of how DNA methyltransferases determine which region should be methylated is not completely revealed. There are many hypotheses of which genomic features are correlated to the epigenome that have not yet been evaluated. Furthermore, many explorative approaches of measuring DNA methylation are limited to a subset of the genome and thus, cannot be employed, e.g., for genome-wide biomarker prediction methods. In this study, we evaluated the correlation of genetic, epigenetic and hypothesis-driven features to DNA methylation of CpG islands. To this end, various binary classifiers were trained and evaluated by cross-validation on a dataset comprising DNA methylation data for 190 CpG islands in HEPG2, HEK293, fibroblasts and leukocytes. We achieved an accuracy of up to 91% with an MCC of 0.8 using ten-fold cross-validation and ten repetitions. With these models, we extended the existing dataset to the whole genome and thus, predicted the methylation landscape for the given cell types. The method used for these predictions is also validated on another external whole-genome dataset. Our results reveal features correlated to DNA methylation and confirm or disprove various hypotheses of DNA methylation related features. This study confirms correlations between DNA methylation and histone modifications, DNA structure, DNA sequence, genomic attributes and CpG island properties. Furthermore, the method has been validated on a genome-wide dataset from the ENCODE consortium. The developed software, as well as the predicted datasets and a web-service to compare methylation states of CpG islands are available at http://www.cogsys.cs.uni-tuebingen.de/software/dna-methylation/