Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.

Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half-lives, proteins, and protein half-lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160-fold among genes, most of the known factors had little impact on translation efficiency.

Government veterinarians' perceptions of routine biosecurity focused on dairy cattle farms in north-western and north-eastern Spain.

The implementation of biosecurity measures in livestock production systems can be affected by the psychosocial factors of its stakeholders, which can be observed through their knowledge, attitudes and perceptions/practices. In Spain, there are no regulations to promote biosecurity. Of all stakeholders, farmers and veterinarians have been addressed in previous biosecurity studies, but not veterinarians belonging specifically to the government services.

Influence on the implementation of biosecurity measures in dairy cattle farms: Communication between veterinarians and dairy farmers.

This study was carried out in two regions in Spain (Catalonia and Galicia) through eight focus groups; four for dairy farmers and four for veterinarians. The results showed that dairy farmers and veterinarians attributed responsibility to one another for not following biosecurity practices. The study brings to light contradictions among veterinarians and certain individual veterinary practices that participated in the study, which lead to doubt and confusion on the part of dairy farmers.

Quantitative risk assessment of introduction of BVDV and BoHV-1 through indirect contacts based on implemented biosecurity measures in dairy farms of Spain.

A stochastic quantitative risk assessment model was developed to estimate the annual probability of introduction of bovine viral diarrhea virus (BVDV) and bovine herpesvirus 1 (BoHV-1) on 127 dairy farms through indirect contacts. Vehicles transporting calves, cattle to slaughterhouse, dead animals, and mixture of feed, as well as visits by veterinarians and hoof trimmers, farm workers and contacts with neighbors were considered in the model. Data from biosecurity questionnaires of each farm, scientific literature and expert opinion from field veterinarians, animal vehicle drivers, hoof trimmers and personnel from rendering transport companies were used to estimate values for input parameters.

Factors Associated with the Introduction of spp. Paratuberculosis (MAP) into Dairy Herds in Galicia (North-West Spain): The Perception of Experts.

This study aimed at quantifying expert opinions on the risk factors involved in subsp. (MAP) infection in dairy cattle herds. For this purpose, potential risk factors associated with the introduction of MAP into dairies were chosen based on a literature review and discussions with researchers and veterinarians.

A survey of biosecurity measures and serological status for bovine viral diarrhoea virus and bovine herpesvirus 1 on dairy cattle farms in north-west and north-east Spain.

Background: Biosecurity is a key measure to reduce and prevent the introduction of diseases to farms and minimise spread of diseases within a herd. The aim of the study was to characterise the current application of biosecurity measures on dairy cattle farms in Spain along with their bovine viral diarrhoea and infectious bovine rhinotracheitis status.

Methods: Data on biosecurity measures for 124 dairy herds were collected using a questionnaire.

Short communication: Risk factors associated with Mycobacterium avium ssp. paratuberculosis introduction into dairy herds in Galicia, northwestern Spain.

This study assessed potential risk factors associated with introduction of Mycobacterium avium ssp. paratuberculosis (MAP) into dairy cattle herds in the Galicia region, northwestern Spain. The study was carried out with data collected from 93 dairies enrolled in a voluntary MAP control program.

Impact of C-terminal amino acid composition on protein expression in bacteria.

The C-terminal sequence of a protein is involved in processes such as efficiency of translation termination and protein degradation. However, the general relationship between features of this C-terminal sequence and levels of protein expression remains unknown. Here, we identified C-terminal amino acid biases that are ubiquitous across the bacterial taxonomy (1,582 genomes).

Development of a quantitative risk assessment of bovine viral diarrhea virus and bovine herpesvirus-1 introduction in dairy cattle herds to improve biosecurity.

A quantitative risk assessment model was developed to estimate the annual probability of introducing bovine viral diarrhea virus (BVDV) and bovine herpesvirus 1 (BoHV-1) at the farm level through animal movements. Data from 2017 official animal movements, biosecurity questionnaires, scientific literature, and expert opinion from field veterinarians were taken into consideration for model input parameters. Purchasing or introducing cattle, rearing replacement heifers offsite, showing cattle at competitions, sharing transport vehicles with other herds, and transporting cattle in vehicles that have not been cleaned and disinfected were considered in the model.

Dairy farmers' decision-making to implement biosecurity measures: A study of psychosocial factors.

Biosecurity measures are a set of management procedures that prevent the risk of introducing and spreading infectious diseases to a farm, although these measures are rarely implemented in dairy farms. There are some studies that have identified that the decision to implement biosecurity measures can be influenced by several psychosocial factors (attitudes and behaviours). Thus, the objective of this study was to examine the psychosocial factors (and their interactions) influencing the implementation of biosecurity measures in dairy farms in Spain, through the views of dairy farmers and veterinarians from Catalonia (northeast Spain) and Galicia (northwest Spain).

Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors.

Here, we determined the relative importance of different transcriptional mechanisms in the genome-reduced bacterium Mycoplasma pneumoniae, by employing an array of experimental techniques under multiple genetic and environmental perturbations. Of the 143 genes tested (21% of the bacterium's annotated proteins), only 55% showed an altered phenotype, highlighting the robustness of biological systems. We identified nine transcription factors (TFs) and their targets, representing 43% of the genome, and 16 regulators that indirectly affect transcription.

Robot milking and relationship with culling rate in dairy cows.

Cow routines and behavioral responses are altered substantially following the installation of robot milking. The present study was designed to analyze the effect that switching from milking parlor to automatic milking system (AMS) had on the culling rate (due to various causes) of dairy cattle. For this purpose, culling records and causes for culling were tracked in 23 dairy farms in the Galicia region (NW Spain).

A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants.

Quantitative analysis of the sequence determinants of transcription and translation regulation is relevant for systems and synthetic biology. To identify these determinants, researchers have developed different methods of screening random libraries using fluorescent reporters or antibiotic resistance genes. Here, we have implemented a generic approach called ELM-seq (expression level monitoring by DNA methylation) that overcomes the technical limitations of such classic reporters.

Short communication: Correlation between within-herd antibody-prevalence and bulk tank milk antibody levels to Mycobacterium avium ssp. paratuberculosis using 2 commercial immunoassays.

The objective of this study was to determine the correlation between the results obtained with the ELISA technique for antibodies to Mycobacterium avium ssp. paratuberculosis in serum and bulk tank milk at the herd level. For this purpose, 203 samples of bulk tank milk were analyzed with 2 commercial ELISA from dairy herds with a prevalence of seropositive animals that was also determined.

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae.

DNA-binding proteins are central regulators of chromosome organization; however, in genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of such bacteria adopt defined three-dimensional structures remains unexplored. Here we combine Hi-C and super-resolution microscopy to determine the structure of the Mycoplasma pneumoniae chromosome at a 10 kb resolution.

Genetic diversity of bovine viral diarrhea viruses from the Galicia region of Spain.

This study examined the frequency and diversity of bovine viral diarrhoea viruses (BVDVs) infecting cattle in Galicia (northwestern Spain). A total of 86 BVDV strains were typed in samples of serum from 79 persistently infected animals and 3 viraemic animals and of abomasal fluid from 4 fetuses. Samples came from 73 farms participating in a voluntary BVDV control programme.

Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium.

Coordination of transcription in bacteria occurs at supra-operonic scales, but the extent, specificity, and mechanisms of such regulation are poorly understood. Here, we tackle this problem by profiling the transcriptome of the model organism Mycoplasma pneumoniae across 115 growth conditions. We identify three qualitatively different levels of co-expression corresponding to distinct relative orientations and intergenic properties of adjacent genes.

Study on some risk factors and effects of bovine ketosis on dairy cows from the Galicia region (Spain).

The study was designed to determine the relation between β-hydroxybutyrate (BHB) concentrations in milk from dairy cows after calving and the length of the previous lactation, the dry period and the 305-day normalized production, and to assess the influence of BHB concentrations on culling and test-day milk productions and somatic cell counts (SCC) throughout the lactation that followed the BHB measurement. The data used in the study were obtained from 59 187 cows in the Galicia region (Spain). BHB determination was performed using Fourier-transformed infrared spectrometry from the milk samples collected from each cow on the first post-partum test day.

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.

We developed a comprehensive resource for the genome-reduced bacterium Mycoplasma pneumoniae comprising 1748 consistently generated '-omics' data sets, and used it to quantify the power of antisense non-coding RNAs (ncRNAs), lysine acetylation, and protein phosphorylation in predicting protein abundance (11%, 24% and 8%, respectively). These factors taken together are four times more predictive of the proteome abundance than of mRNA abundance. In bacteria, post-translational modifications (PTMs) and ncRNA transcription were both found to increase with decreasing genomic GC-content and genome size.

Bovine herpesvirus 1: within-herd seroprevalence and antibody levels in bulk-tank milk.

The aim of the present study was to establish a relationship between the results obtained with the enzyme-linked immunosorbent assay (ELISA) technique for antibodies (against bovine herpesvirus 1) in serum and those in milk at the herd level. For this purpose, 275 samples of bulk-tank milk were analysed with glycoprotein E (gE) antibody ELISA and 207 more were analysed with glycoprotein B (gB) antibody ELISA (482 in total). All of these samples came from dairy herds whose seroprevalence was also evaluated.

Associations between Mycobacterium paratuberculosis sero-status, milk quality parameters, and reproduction in dairy cows.

The objective of this study was to investigate the influence of Mycobocterium avium subsp. paratuberculosis (MAP) sero-status of dairy cows on different milk production variables and reproductive traits. The study was carried out on 40 herds from the region of Galicia (North-West Spain).

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.

Identifying all essential genomic components is critical for the assembly of minimal artificial life. In the genome-reduced bacterium Mycoplasma pneumoniae, we found that small ORFs (smORFs; < 100 residues), accounting for 10% of all ORFs, are the most frequently essential genomic components (53%), followed by conventional ORFs (49%). Essentiality of smORFs may be explained by their function as members of protein and/or DNA/RNA complexes.

MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae.

MyMpn (http://mympn.crg.eu) is an online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections.

Monitoring the bulk milk antibody response to bovine viral diarrhea in dairy herds vaccinated with inactivated vaccines.

This study was designed to determine long-term responses in dairy herds after vaccination with 1 of 3 inactivated bovine viral diarrhea virus (BVDV) vaccines with regard to antibodies against p80 protein in bulk tank milk samples, as detected by ELISA. In the present study, 29 dairy herds were vaccinated with Bovilis BVD (MSD Animal Health, Milton Keynes, UK), 11 with Hiprabovis Balance (Laboratorios Hipra, Amer, Spain), and 9 with Pregsure BVD (Zoetis, Florham Park, NJ). In these herds, bulk tank milk samples were collected and examined at the time of the first vaccination and every 6 mo during a 3-yr period.