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Prions are proteinaceous infectious particles implicated in fatal neurodegenerative disorders known as prion diseases. Herein, we provide an overview of prion biology, emphasizing the structural, functional, and evolutionary aspects of prions, along with their potential applications in protein engineering. Understanding the structure-function relationships of both healthy and disease-associated prion proteins enables a deeper understanding of the mechanisms of prion-induced neurotoxicity. Furthermore, we describe how insights into prion evolution have begun to shed light on their ancient origins and evolutionary resilience, offering deeper insights into the potential roles of prions in primordial chemical processes., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

As the proportion of prime carcasses originating from dairy herds increases, the focus is shifting to the beef merit of the progeny from dairy herds. Several dairy cow total merit indexes include a negative weight on measures of cow size. However, there is a lack of knowledge on the effect of genetic selection, solely for lighter or smaller-sized dairy cows, on the beef performance of their progeny. Therefore, the objective of this study was to quantify the genetic correlations among cow size traits (i.e., cow BW, cow carcass weight [CW]), cow BCS, cow carcass conformation (CC), and cow carcass fat cover (CF), as well as the correlations between these cow traits and a series of beef performance slaughter-related traits (i.e., CW, CC, CF, and age at slaughter [AS]) in their progeny. After data editing, there were 52,950 cow BW and BCS records, along with 57,509 cow carcass traits (i.e., CW, CC, and CF); carcass records from 346,350 prime animals along with AS records from 316,073 prime animals were also used. Heritability estimates ranged from moderate to high (0.18-0.62) for all cow and prime animal traits. The same carcass trait in cows and prime animals were strongly genetically correlated with each other (0.76-0.85), implying that they are influenced by very similar genomic variants. Selecting exclusively for cows with higher BCS (i.e., fatter) will, on average, produce more conformed prime animal carcasses, owing to a moderate genetic correlation (0.30) between both traits. Genetic correlations revealed that selecting exclusively for lighter BW or CW cows will, on average, result in lighter prime animal carcasses of poor CC, while also delaying slaughter age. Nonetheless, selective breeding through total merit indexes should be successful in breeding for smaller dairy cows and desirable prime animal carcass traits concurrently, because of the nonunity genetic correlations between the cow and prime animal traits; this will help to achieve a more ethical, environmentally sustainable, and economically viable dairy-beef industry., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Escherichia coli can colonise the urogenital tract of individuals without causing symptoms of infection, in a condition referred to as asymptomatic bacteriuria (ABU). ABU isolates can protect the host against symptomatic urinary tract infections (UTIs) by bacterial interference against uropathogenic E. coli (UPEC). The aim of this study was to investigate the genotypic and phenotypic characteristics of five ABU isolates from midstream urine samples of adults. Comparative genomic and phenotypic analysis was conducted including an antibiotic resistance profile, pangenome analysis, and a putative virulence profile. Based on the genome analysis, the isolates consisted of one from phylogroup A, three from phylogroup B2, and one from phylogroup D. Two of the isolates, PUTS 58 and SK-106-1, were noted for their lack of antibiotic resistance and virulence genes compared to the prototypic ABU strain E. coli 83,972. This study provides insights into the genotypic and phenotypic profiles of uncharacterised ABU isolates, and how relevant fitness and virulence traits can impact their potential suitability for therapeutic bacterial interference., (© 2024. The Author(s).)

Molecular diagnostics has the potential to revolutionise the field of clinical microbiology. Microbial identification and nomenclature have, for too long, been restricted to phenotypic characterisation. However, this species-level view fails to wholly account for genetic heterogeneity, a result of lateral gene transfer, mediated primarily by mobile genetic elements. This genetic promiscuity has helped to drive virulence development, stress adaptation, and antimicrobial resistance in several important bacterial pathogens, complicating their detection and frustrating our ability to control them. We argue that, as clinical microbiologists at the front line, we must embrace the molecular technologies that allow us to focus specifically on the genetic elements that cause disease rather than the bacterial species that express them. This review focuses on the evolution of microbial taxonomy since the introduction of molecular sequencing, the role of mobile genetic elements in antimicrobial resistance, the current and emerging assays in clinical laboratories, and the comparison of phenotypic versus genotypic analyses. In essence, it is time now to refocus from species to genes as part of a new diagnostic paradigm.

The objective of the study was to quantify the association between the birth weight of a calf and the subsequent performance of its dairy dam in the absence of any recorded calving assistance. A total of 11,592 lactation records from 4,549 spring-calving dairy cows were used. The association between a series of quantitative cow performance metrics (dependent variable) and calf birth weight (independent variable) was determined using linear mixed models; logistic regression was used where the dependent variable was binary. Nuisance factors in the models were calf sex, heterosis coefficient of both the cow and calf, dry period length immediately before the birth of the calf, cow age at calving relative to the median cow age per parity, breed proportion of the cow, cow live weight between 100 and 200 d of lactation relative to the mean cow weight per parity, and contemporary group. Calf birth weight was included in the model as either a continuous or a categorical variable. Primiparous and multiparous cows were analyzed separately. Mean (SD) calf birth weight was 36.2 (6.8) kg. In primiparous cows, calf birth weight was associated with milk yield in the first 60 d of lactation, calving to first service interval, calving body weight (BW), and both nadir BW and body condition score (BCS). In multiparous cows, calf birth weight was associated with total milk, fat, and protein yield in the first 60 and 305 d of lactation, peak milk yield, total milk solids, both calving and nadir BW, and BCS loss from calving to nadir. Relative to primiparous cows that gave birth to calves weighing 34 to 37 kg (i.e., population mean), their contemporaries who gave birth to calves that weighed 15 to 29 kg produced 9.82 kg more milk in the first 60 d of lactation, had a 2-d shorter interval to first service, and were 8.08 kg and 5.51 kg lighter at calving and nadir BW, respectively; the former was also 0.05 units lower in BCS (5-point scale, 1 = emaciated and 5 = obese) at nadir. Relative to multiparous cows that gave birth to calves that were 34 to 37 kg birth weight, multiparous cows that gave birth to calves that were 15 to 29 kg yielded 59.63 kg, 2.44 kg, and 1.76 kg less milk, fat, and protein, respectively, in the first 60 d of lactation; produced 17.69 kg less milk solids throughout the 305-d lactation; and were also 10.49 kg lighter at nadir and lost 0.01 units more BCS to nadir. In a separate series of analyses, sire breed was added to the model as a fixed effect with and without calf birth weight. When calf birth weight was not adjusted for, 60-d milk yield for multiparous cows who gave birth to calves sired by a traditional beef breed (i.e., Angus, Hereford) produced 59.63 kg more milk than multiparous cows who gave birth to calves sired by a Holstein-Friesian. Hence, calf birth weight is associated with some subsequent dam performance measures; however, where associations do exist, the effect is biologically small., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Traditional bacteriocin screening methods often face limitations due to diffusion-related challenges in agar matrices, which can prevent the peptides from reaching their target organism. Turbidimetric techniques offer a solution to these issues, eliminating diffusion-related problems and providing an initial quantification of bacteriocin efficacy in producer organisms. This study involved screening the cell-free supernatant (CFS) from eight uncharacterized asymptomatic bacteriuria (ABU) isolates and Escherichia coli 83972 for antimicrobial activity against clinical uropathogenic E. coli (UPEC) strains using turbidimetric growth methods. ABU isolates exhibiting activity against five or more UPEC strains were further characterized (PUTS 37, PUTS 58, PUTS 59, S-07-4, and SK-106-1). The inhibition of the CFS by proteinase K suggested that the antimicrobial activity was proteinaceous in nature, potentially bacteriocins. The activity of E. coli PUTS 58 and SK-106-1 was enhanced in an artificial urine medium, with both inhibiting all eight UPECs. A putative microcin H47 operon was identified in E. coli SK-106-1, along with a previously identified microcin V and colicin E7 in E. coli PUTS 37 and PUTS 58, respectively. These findings indicate that ABU bacteriocin-producers could serve as viable prophylactics and therapeutics in the face of increasing antibiotic resistance among uropathogens., (© 2024 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Neuronal development is a highly regulated mechanism that is central to organismal function in animals. In humans, disruptions to this process can lead to a range of neurodevelopmental phenotypes, including Schizophrenia (SCZ). SCZ has a significant genetic component, whereby an individual with an SCZ affected family member is eight times more likely to develop the disease than someone with no family history of SCZ. By examining a combination of genomic, transcriptomic and epigenomic datasets, large-scale 'omics' studies aim to delineate the relationship between genetic variation and abnormal cellular activity in the SCZ brain. Herein, we provide a brief overview of some of the key omics methods currently being used in SCZ research, including RNA-seq, the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and high-throughput chromosome conformation capture (3C) approaches (e.g., Hi-C), as well as single-cell/nuclei iterations of these methods. We also discuss how these techniques are being employed to further our understanding of the genetic basis of SCZ, and to identify associated molecular pathways, biomarkers, and candidate drug targets., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Background: The role of the urobiome in health and disease remains an understudied area compared to the rest of the human microbiome. Enhanced culturing techniques and next-generation sequencing technologies have identified the urobiome as an untapped source of potentially novel antimicrobials. The aim of this study was to screen the urobiome for genes encoding bacteriocin production. Methods: The genomes of 181 bacterial urobiome isolates were screened in silico for the presence of bacteriocin gene clusters using the bacteriocin mining tool BAGEL4 and secondary metabolite screening tool antiSMASH7 . Results: From these isolates, an initial 263 areas of interest were identified, manually annotated, and evaluated for potential bacteriocin gene clusters. This resulted in 32 isolates containing 80 potential bacteriocin gene clusters, of which 72% were identified as class II, 13.75% as class III, 8.75% as class I, and 5% as unclassified bacteriocins. Conclusion: Overall, 53 novel variants were discovered, including nisin, gassericin, ubericin, and colicins., Competing Interests: All authors declared that there are no conflicts of interest., (© The Author(s) 2024.)

During the early stages of the COVID-19 pandemic, we called for mandatory public masking to 'flatten the curve'. We helped formulate a national standard (SWiFT 19) for barrier facemasks, and, using a novel laser-based approach, we determined that mask efficacy is dependent on both fabric and fit; with both variables being inversely related. Herein, we take a retrospective view of the role of masks during the pandemic and surmise that, on the balance of evidence to date, masks were effective at stemming the spread of SARS-CoV-2 and may well be an effective early control strategy for potential future respiratory pandemics.

Environmental contamination is estimated to contribute to up to 20% of all hospital acquired infections. Acinetobacter baumannii is an example of one the most prevalent opportunistic pathogens causing severe and persistent infections in immunocompromised patients. It has proven ability to form biofilms, has significant associated multi-drug resistance and is able to transfer mobile genetic elements to other clinically relevant pathogens. All of these factors point to a definite utility of A. baumannii as an indicator organism for effectiveness of decontamination regimens as well as environmental screening. There is an increased cost, both financial and clinical, associated with multi drug resistant organisms, carbapenem resistant A. baumannii . With a dearth of new antimicrobials in development, now is the time to radically transform and lead the introduction of scientifically based environmental screening and microbiological verified decontamination to control the dissemination of further resistance., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Fahy, O’Connor, Lucey and Sleator.)

The cumulative improvement achieved in the genetic merit for reproductive performance in dairy populations will likely improve dairy cow longevity; therefore, it is time to reassess whether linear type traits are still suitable predictors of survival in an aging dairy cow population. The objective of the present study was therefore to estimate the genetic correlations between linear type traits and survival from one parity to the next and, in doing so, evaluate if those genetic correlations change with advancing parity. After edits, 152,894 lactation survival records (first to ninth parity) were available from 52,447 Holstein-Friesian cows, along with linear type trait records from 52,121 Holstein-Friesian cows. A series of bivariate random regression models were used to estimate the genetic covariances between survival in different parities and each linear type trait. Heritability estimates for survival per parity ranged from 0.02 (SE = 0.004; first parity) to 0.05 (SE = 0.01; ninth parity). Pairwise genetic correlations between survival among different parities varied from 0.42 (first and ninth parity) to 1.00 (eighth to ninth parity), with the strength of these genetic correlations being inversely related to the interval between the compared parities. The genetic correlations between survival and the individual linear type traits varied across parities for 9 of the 20 linear type traits examined, but the correlations with only 3 of these linear type traits strengthened as the cows aged; these 3 traits were rear udder height, teat length, and udder depth. Given that linear type traits are frequently scored in first parity and are genetically correlated with survival in older parities, they may be suitable early predictors of survival, especially for later parity cows. Additionally, the direction of the genetic correlations between survival and rear udder height, teat length, and udder depth did not change between parities; hence, selection for survival in older parities using these linear type traits should not hinder genetic improvement for survival in younger parities., (© 2022, The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Genomic imprinting is an epigenetic phenomenon defined as the silencing of an allele, at least partially, at a given locus based on the sex of the transmitting parent. The objective of the present study was to detect the presence of SNP-phenotype imprinting associations for carcass weight ( CW ), carcass conformation ( CC ) and carcass fat ( CF ) in cattle. The data used comprised carcass data, along with imputed, high-density genotype data on 618,837 single nucleotide polymorphisms ( SNPs ) from 23,687 cattle; all animal genotypes were phased with respect to parent of origin. Based on the phased genotypes and a series of single-locus linear models, 24, 339, and 316 SNPs demonstrated imprinting associations with CW, CC, and CF, respectively. Regardless of the trait in question, no known imprinted gene was located within 0.5 Mb of the SNPs demonstrating imprinting associations in the present study. Since all imprinting associations detected herein were at novel loci, further investigation of these regions may be warranted. Nonetheless, knowledge of these associations might be useful for improving the accuracy of genomic evaluations for these traits, as well as mate allocations systems to exploit the effects of genomic imprinting., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Kenny, Sleator, Murphy, Evans and Berry.)

The discovery of microbial communities in the urinary tract (the urobiome) has fundamentally altered the previous doctrine regarding urine sterility and associated urinary disorders. Recent advances in culturing and culture-independent DNA sequencing technologies have characterised the resident microbial community in the urobiome, and has, in turn, demonstrated how community imbalances potentially contribute to infection and disease. As we enter a post-antibiotic era, the effectiveness of standard antimicrobial treatments against multi-drug resistant (MDR) uropathogens is vastly diminished. Preliminary research is accumulating surrounding microbiome-based therapies, and their potential as non-antibiotic therapeutics. In this context, the urobiome is significantly underexplored, and knowledge regarding the fundamental role of its constituents is lacking. Herein, we review the current state of the art concerning the urobiome; specifically, how it impacts health and disease states, in the context of urinary tract infections (UTIs). Furthermore, we discuss the development of novel biological therapeutics that may have the potential to provide significant advancements in UTI therapy, with a particular focus on bacterial interference, probiotics, antimicrobial peptides, bacteriocins, and bacteriophage., (Copyright © 2022 The Authors. Published by Elsevier GmbH.. All rights reserved.)

The inclusion of reproductive performance in dairy cow breeding schemes has resulted in a cumulative improvement in genetic merit for reproductive performance; this improvement should manifest in longer productive lives through a reduced requirement for involuntary culling. Nonetheless, the average length of dairy cow productive life has not changed in most populations, suggesting that risk factors for culling, especially in older cows, are possibly more associated with lower yield or high somatic cell score (SCS) than compromised reproductive performance. The objective of the present study was to understand the dynamics of lactation yields and SCS in dairy cows across parities and, in doing so, quantify the potential to alter this trajectory through breeding. After edits, 3,470,520 305-d milk, fat, and protein yields, as well as milk fat and protein percentage and somatic cell count records from 1,162,473 dairy cows were available for analysis. Random regression animal models were used to identify the parity in which individual cows reached their maximum lactation yields, and highest average milk composition and SCS; also estimated from these models were the (co)variance components for yield, composition, and SCS per parity across parities. Estimated breeding values for all traits per parity were calculated for cows reaching ≥fifth parity. Of the cows included in the analyses, 91.0%, 92.2%, and 83.4% reached maximum milk, fat, and protein yield in fifth parity, respectively. Conversely, 95.9% of cows reached their highest average fat percentage in first parity and 62.9% of cows reached their highest average protein percentage in third parity. In contrast to both milk yield and composition traits, 98.4% of cows reached their highest average SCS in eighth parity. Individual parity estimates of heritability for milk yield traits, milk composition, and SCS ranged from 0.28 to 0.44, 0.47 to 0.69, and 0.13 to 0.23, respectively. The strength of the genetic correlations per trait among parities was inversely related to the interval between the parities compared; the weakest genetic correlation was 0.67 (standard error = 0.02) between milk yield in parities 1 and 8. Eigenvalues and eigenfunctions of the additive genetic covariance matrices for all investigated traits revealed potential to alter the trajectory of parity profiles for milk yield, milk composition, and SCS. This was further demonstrated when evaluating the trajectories of animal estimated breeding values per parity., (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

The objective of the present study was to quantify the association between both pedigree and genome-based measures of global heterozygosity and carcass traits, and to identify single nucleotide polymorphisms ( SNPs ) exhibiting non-additive associations with these traits. The carcass traits of interest were carcass weight ( CW ), carcass conformation ( CC ) and carcass fat ( CF ). To define the genome-based measures of heterozygosity, and to quantify the non-additive associations between SNPs and the carcass traits, imputed, high-density genotype data, comprising of 619,158 SNPs, from 27,213 cattle were used. The correlations between the pedigree-based heterosis coefficient and the three defined genomic measures of heterozygosity ranged from 0.18 to 0.76. The associations between the different measures of heterozygosity and the carcass traits were biologically small, with positive associations for CW and CC, and negative associations for CF. Furthermore, even after accounting for the pedigree-based heterosis coefficient of an animal, part of the remaining variability in some of the carcass traits could be captured by a genomic heterozygosity measure. This signifies that the inclusion of both a heterosis coefficient based on pedigree information and a genome-based measure of heterozygosity could be beneficial to limiting bias in predicting additive genetic merit. Finally, one SNP located on Bos taurus ( BTA ) chromosome number 5 demonstrated a non-additive association with CW. Furthermore, 182 SNPs (180 SNPs on BTA 2 and two SNPs on BTA 21) demonstrated a non-additive association with CC, while 231 SNPs located on BTA 2, 5, 11, 13, 14, 18, 19 and 21 demonstrated a non-additive association with CF. Results demonstrate that heterozygosity both at a global level and at the level of individual loci contribute little to the variability in carcass merit., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Kenny, Carthy, Murphy, Sleator, Evans and Berry.)

Measuring dry matter intake (DMI) in grazing dairy cows using currently available techniques is invasive, time consuming, and expensive. An alternative to directly measuring DMI for use in genetic evaluations is to identify a set of readily available animal features that can be used in a multitrait genetic evaluation for DMI. The objectives of the present study were thus to estimate the genetic correlations between readily available body-related linear type traits and DMI in grazing lactating Holstein-Friesian cows, but importantly also estimate the partial genetic correlations between these linear traits and DMI, after adjusting for differences in genetic merit for body weight. Also of interest was whether the predictive ability derived from the estimated genetic correlations materialized upon validation. After edits, a total of 8,055 test-day records of DMI, body weight, and milk yield from 1,331 Holstein-Friesian cows were available, as were chest width, body depth, and stature from 47,141 first lactation Holstein-Friesian cows. In addition to considering the routinely recorded linear type traits individually, novel composite traits were defined as the product of the linear type traits as an approximation of rumen volume. All linear type traits were moderately heritable, with heritability estimates ranging from 0.27 (standard error = 0.14) to 0.49 (standard error = 0.15); furthermore, all linear type traits were genetically correlated (0.29 to 0.63, standard error 0.14 to 0.12) with DMI. The genetic correlations between the individual linear type traits and DMI, when adjusted for genetic differences in body weight, varied from -0.51 (stature) to 0.48 (chest width). These genetic correlations between DMI and linear type traits suggest linear type traits may be useful predictors of DMI, even when body weight information is available. Nonetheless, estimated genetic merit of DMI derived from a multitrait genetic evaluation of linear type traits did not correlate strongly with actual DMI in a set of validation animals; the benefit was even less if body weight data were also available., (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Seaweeds are potentially sustainable crops and are receiving significant interest because of their rich bioactive compound content; including fatty acids, polyphenols, carotenoids, and complex polysaccharides. However, there is little information on the in vivo effects on gut health of the polysaccharides and their low-molecular-weight derivatives. Herein, we describe the first investigation into the prebiotic potential of low-molecular-weight polysaccharides (LMWPs) derived from alginate and agar in order to validate their in vivo efficacy. We conducted a randomized; placebo-controlled trial testing the impact of alginate and agar LWMPs on faecal weight and other markers of gut health and on composition of gut microbiota. We show that these LMWPs led to significantly increased faecal bulk (20-30%). Analysis of gut microbiome composition by sequencing indicated no significant changes attributable to treatment at the phylum and family level, although FISH analysis showed an increase in Faecalibacterium prausnitzii in subjects consuming agar LMWP. Sequence analysis of gut bacteria corroborated with the FISH data, indicating that alginate and agar LWMPs do not alter human gut microbiome health markers. Crucially, our findings suggest an urgent need for robust and rigorous human in vivo testing-in particular, using refined seaweed extracts.

In growing cattle, the phenotypic and genetic relationships between feeding behavior and both live animal ultrasound measures and subsequent carcass merit are generally poorly characterized. The objective of the current study was to quantify the phenotypic and genetic associations between a plethora of feeding behavior traits with both pre-slaughter ultrasound traits and post-slaughter carcass credentials in crossbred Bos taurus cattle. Carcass data were available on 3,146 young bulls, steers, and heifers, of which 2,795 and 2,445 also had records for pre-slaughter ultrasound muscle depth and intramuscular fat percentage, respectively; a total of 1,548 steers and heifers had information on all of the feeding behavior, ultrasound, and carcass traits. Young bulls were fed concentrates, while steers and heifers were fed a total mixed ration. Feeding behavior traits were defined based on individual feed events or meal events (i.e., individual feed events grouped into meals). Animal linear mixed models were used to estimate (co)variance components. Phenotypic correlations between feeding behavior and both ultrasound and carcass traits were generally weak and not different from zero, although there were phenotypic correlations of 0.40, 0.26, and 0.37 between carcass weight and feeding rate, energy intake per feed event, and energy intake per meal, respectively. Genetically, cattle that had heavier carcass weights, better carcass conformation, or a higher dressing percentage fed for a shorter time per day (genetic correlations [±SE] of -0.46 ± 0.12, -0.39 ± 0.11, and -0.50 ± 0.10, respectively). Genetic correlations of 0.43 ± 0.12 and 0.68 ± 0.13 were estimated between dressing difference (i.e., differential between live weight pre-slaughter and carcass weight) and energy intake per feed event and energy intake per meal, respectively. Neither intramuscular fat percentage measured on live animals nor carcass fat score (i.e., a measure of subcutaneous fat cover of the carcass) was genetically associated with any of the feeding behavior traits. The genetic associations between some feeding behavior traits and both ultrasound and carcass traits herein suggested that indirect responses in the feeding behavior of growing cattle from selection for improved carcass merit would be expected. Such changes in feeding behavior patterns in cattle may be reduced by measuring and including feeding behavior in a multiple-trait selection index alongside carcass traits., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Improvements in bacterial culturing and DNA sequencing techniques have revealed a diverse, and hitherto unknown, urinary tract microbiome (urobiome). The potential role of this microbial community in contributing to health and disease, particularly in the context of urinary tract infections (UTIs) is of significant clinical importance. However, while several studies have confirmed the existence of a core urobiome, the role of its constituent microbes is not yet fully understood, particularly in the context of health and disease. Herein, we review the current state of the art, concluding that the urobiome represents an important component of the body's innate immune defences, and a potentially rich resource for the development of alternative treatment and control strategies for UTIs., (Copyright © 2021. Published by Elsevier Ltd.)

The objective of this study was to determine whether response to selection for carcass weight (CW), conformation (CC) and fat (CF), and the association between heterosis and carcass performance varied by herd environment in cattle. Following edits, carcass information was available for 4,616,761 cattle, of which the majority were some crossbred combination of the following breeds: Angus, Aubrac, Belgian Blue, Blonde d'Aquitaine, Charolais, Hereford, Holstein-Friesian, Jersey, Limousin, Saler, Shorthorn and Simmental. Herd environment was defined separately for each carcass trait using herd solutions outputted from carcass trait genetic evaluations. A total of 3,859 herds were stratified, for each trait, into one of five strata based on their corresponding percentile herd solution rank, with the response to selection and the effect of heterosis then estimated within each stratum. The response in CW and CC from selection on the respective estimated breeding values (EBV) increased between the lowest (0.71 kg and 0.89 CC score increase per unit increase in the respective EBV) and highest (0.99 kg and 1.25 CC score increase per unit increase in the respective EBV) corresponding herd stratum. The response in CF from selection on CF EBV, however, reduced between the lowest and highest CF herd stratum (respective increases of 0.93 and 0.83 CF scores per unit increase in CF EBV). In addition, the effect of a unit increase in heterosis coefficient on CW, CC and CF also varied by herd stratum. Furthermore, results (i.e. the area under relative operating characteristic curves) from the present study demonstrated that the response to selection and heterosis effects estimated for the different herd stratum can be used, along with EBVs and the herd solutions themselves, to improve the accuracy of phenotypic predictions. Results from the present study could help producers to make more informed breeding decisions that are bespoke to their herd., (© 2021 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.)

The objectives of the present study were to estimate genetic parameters for several feeding behavior traits in growing cattle, as well as the genetic associations among and between feeding behavior and both performance and feed efficiency traits. An additional objective was to investigate the use of feeding behavior traits as predictors of genetic merit for feed intake. Feed intake and live-weight data on 6,088 growing cattle were used of which 4,672 had ultrasound data and 1,548 had feeding behavior data. Feeding behavior traits were defined based on individual feed events or meal events (where individual feed events were grouped into meals). Univariate and bivariate animal linear mixed models were used to estimate (co)variance components. Heritability estimates (± SE) for the feeding behavior traits ranged from 0.19 ± 0.08 for meals per day to 0.61 ± 0.10 for feeding time per day. The coefficient of genetic variation per trait varied from 5% for meals per day to 22% for the duration of each feed event. Genetically heavier cattle, those with a higher daily energy intake (MEI), or those that grew faster had a faster feeding rate, as well as a greater energy intake per feed event and per meal. Better daily feed efficiency (i.e., lower residual energy intake) was genetically associated with both a shorter feeding time per day and shorter meal time per day. In a validation population of 321 steers and heifers, the ability of estimated breeding values (EBV) for MEI to predict (adjusted) phenotypic MEI was demonstrated; EBVs for MEI were estimated using multi-trait models with different sets of predictor traits such as liveweight and/or feeding behaviors. The correlation (± SE) between phenotypic MEI and EBV for MEI marginally improved (P < 0.001) from 0.64 ± 0.03 to 0.68 ± 0.03 when feeding behavior phenotypes from the validation population were included in a genetic evaluation that already included phenotypic mid-test metabolic live-weight from the validation population. This is one of the largest studies demonstrating that significant exploitable genetic variation exists in the feeding behavior of young crossbred growing cattle; such feeding behavior traits are also genetically correlated with several performance and feed efficiency metrics. Nonetheless, there was only a marginal benefit to the inclusion of time-related feeding behavior phenotypes in a genetic evaluation for MEI to improve the precision of the EBVs for this trait., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Genetic evaluations separate phenotypes into their contributing additive genetic effects and non-(additive) genetic effects, with the former termed best linear unbiased predictions, and the latter termed best linear unbiased estimates (BLUEs). For the purpose of the present study, genetic evaluations, along with phenotypic data from 4 137 376 animals, were used to generate herd, year of slaughter and sex contemporary group BLUEs for various slaughter-related traits. These slaughter traits included carcass weight (CW), carcass conformation (CC) and carcass fat (CF). For the 4 665 herds that were consistently slaughtering ≥10 animals/year between the years 2014 and 2018, inclusive, all relevant contemporary group BLUEs were collapsed into a single herd-year value; results herein relate to these herds. The within-year herd-year BLUE correlations between CW and CC, between CW and CF, and between CC and CF were 0.51, 0.10 and -0.04, respectively. The repeatability across years of the herd-year BLUEs for CW, CC and CF was 0.66, 0.59 and 0.50, respectively. Furthermore, when the herds were stratified, within year, on the percentile rank of their herd-year BLUEs, herds had the greatest probability of remaining in the same BLUE stratum from one year to the next. In addition, results from the present study determined that various herd characteristics are associated with differences in the herd BLUEs. Results from the present study could be used to advise beef producers on the most promising strategy to improve the carcass merit of their animals., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

The protozoan parasite Cryptosporidium has emerged as a leading cause of diarrhoeal illness worldwide, posing a significant threat to young children and immunocompromised patients. While endemic in the vast majority of developing countries, Cryptosporidium also has the potential to cause waterborne epidemics and large scale outbreaks in both developing and developed nations. Anthroponontic and zoonotic transmission routes are well defined, with the ingestion of faecally contaminated food and water supplies a common source of infection. Microscopy, the current diagnostic mainstay, is considered by many to be suboptimal. This has prompted a shift towards alternative diagnostic techniques in the advent of the molecular era. Molecular methods, particularly PCR, are gaining traction in a diagnostic capacity over microscopy in the diagnosis of cryptosporidiosis, given the laborious and often tedious nature of the latter. Until now, developments in the field of Cryptosporidium detection and research have been somewhat hampered by the intractable nature of this parasite. However, recent advances in the field have taken the tentative first steps towards bringing Cryptosporidium research into the 21 st century. Herein, we provide a review of these advances., Competing Interests: There are no conflicts of interest, of which we are aware, relating to this body of work., (© 2021 The Authors.)

Awareness and interest in calf health and wellbeing is intensifying, prompting change in the management and breeding decisions of producers and associated policy-makers. The objectives of the present study were to 1) quantify the risk factors associated with subjectively measured scores of vigor and birth size as well as diagnoses of scour and pneumonia in a large national dataset of beef calves, and 2) to estimate the contribution of genetic variance to such phenotypic measures. After edits, the data consisted of health and birth size data subjectively scored by producers on 88,207 calves born in 6,126 Irish beef herds. Vigor was recorded on a scale of 1 (very poor) to 5 (very good). Birth size was also scored on a scale of 1 (very small) to 5 (very large). Scour and pneumonia were both scored independently based on the suspected number of occurrence of each (0 = no occurrence, 1 = one occurrence, or 2 = more than one occurrence). On average, 14.7% of calves were recorded as having had at least one occurrence of scour within the first 5 mo of life, whereas 6.4% of calves were recorded as having had at least one occurrence of pneumonia within the first 5 mo of life. Relative to female calves, male calves had a worse vigor score and a suspected greater incidence of both scour and pneumonia. Relative to singletons, twins were, on average, smaller at birth, they had a worse vigor score, and they were more prone to scour. Calves born in the later periods of the calving season (i.e., late and very late) had a greater incidence of scour relative to calves in the herd born earlier in the calving season. Heritability estimates for vigor, birth size, and pneumonia were 0.12 (0.02), 0.33 (0.03), and 0.08 (0.02), respectively; no genetic variance was detected for scour. Breeding for vigorous calves that are less susceptible to pneumonia could provide producers with an additional strategy to ensure consumer concerns regarding food quality, safety, and calf wellbeing are being met., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Validation of beef total merit breeding indexes for improving performance and profitability has previously been undertaken at the individual animal level; however, no herd-level validation of beef genetic merit and profit has been previously investigated. The objective of the present study was to quantify the relationship between herd profitability and both herd-average terminal and maternal genetic merit across 1,311 commercial Irish beef herds. Herd-level physical and financial performance data were available from a financial benchmarking tool used by Irish farmers and their extension advisors. Animal genetic merit data originated from the Irish Cattle Breeding Federation who undertake the national beef and dairy genetic evaluations. Herd-average genetic merit variables included the terminal index of young animals, the maternal index of dams, and the terminal index of service sires. The herds represented three production systems: 1) cow-calf to beef, 2) cow-calf to weanling/yearling, and 3) weanling/yearling to beef. Associations between herd financial performance metrics and herd average genetic merit variables were quantified using a series of linear mixed models with year, production system, herd size, stocking rate, concentrate input, and the two-way interactions between production system and herd size, stocking rate, and concentrate input included as nuisance factors. Herd nested within the county of Ireland ( n = 26) was included as a repeated effect. Herds with young cattle excelling in terminal index enjoyed greater gross and net profit per hectare (ha), per livestock unit (LU), and per kg net live-weight output. The change in gross profit per LU per unit change in the terminal index of young animals was €1.41 (SE = 0.23), while the respective regression coefficient for net profit per LU was €1.37 (SE = 0.30); the standard deviation of the terminal index is €37. Herd-average dam maternal index and sire terminal index were both independently positively associated with gross profit per ha and gross profit per LU. Each one unit increase in dam maternal index (standard deviation of €38) was associated with a €1.40 (SE = 0.48) and €0.76 (SE = 0.29) greater gross profit per ha and per LU, respectively. Results from the present study at the herd-level concur with previous validation studies at the individual animal level thus instilling further confidence among stakeholders as to the expected improvement in herd profitability with improving genetic merit., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Cryptosporidiosis remains the leading protozoan induced cause of diarrhoea-associated mortality worldwide. Cryptosporidium hominis, the anthroponotically transmitted species within the Cryptosporidium genus, contributes significantly to the global burden of infection, accounting for the majority of clinical cases in many countries. This study applied high resolution melting analysis, a post-real-time PCR application, to the differentiation of six globally prevalent C. hominisgp60-subtypes. This novel method targeted three microsatellite, tandem repeat containing genetic markers, gp60, the genetic marker upon which current Cryptosporidium subtype nomenclature is based, MSB, and MSE, by which to differentiate between C. hominis isolates. This multi-locus approach successfully differentiated between all six C. hominisgp60-subtypes studied, some of which, such as IbA10G2, are known to exhibit global ubiquity. Thus, this method has the potential to be universally employed as a sensitive, cost effective and highly reproducible means to rapidly differentiate between C. hominisgp60-subtypes. Such a method would be of particular utility in epidemiological studies and outbreak scenarios, providing cost effective, clinically accessible alternative to DNA sequencing. The success of this preliminary study also supports further analysis of an expanded C. hominisgp60-subtype range and the potential expansion of the multi-locus panel in order to improve the discriminatory power of this approach., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)

This study employed the post-real-time PCR application, high resolution melting (HRM) analysis, in order to differentiate between characterised clinical and reference Cryptosporidium parvum samples obtained from Cork University Hospital (Cork, Ireland) and the Cryptosporidium Reference Unit (Swansea, Wales). A sample set composed of 18 distinct C. parvum gp60-subtypes of the IIa gp60-subtype family (an allele family accounting for over 80% of all cryptosporidiosis cases in Ireland) was employed. HRM analysis-based interrogation of the gp60, MM5 and MS9-Mallon tandem repeat loci was found to completely differentiate between 10 of the 18 studied gp60-subtypes. The remaining eight gp60-subtypes were differentiated into three distinct groupings, with the designations within these groupings resolved to two to three potential gp60-subtypes. The current study aimed to develop a novel, reproducible, real-time PCR based multi-locus genotyping method to distinguish between C. parvum gp60-subtypes. These preliminary results support the further expansion of the multi-locus panel in order to increase the discriminatory capabilities of this novel method., (Copyright © 2021 The Author(s). Published by Elsevier GmbH.. All rights reserved.)

The way in which computer code is perceived and used in biological research has been a source of some controversy and confusion, and has resulted in sub-optimal outcomes related to reproducibility, scalability and productivity. We suggest that the confusion is due in part to a misunderstanding of the function of code when applied to the life sciences. Code has many roles, and in this paper we present a three-dimensional taxonomy to classify those roles and map them specifically to the life sciences. We identify a "sweet spot" in the taxonomy-a convergence where bioinformaticians should concentrate their efforts in order to derive the most value from the time they spend using code. We suggest the use of the "inverse Conway maneuver" to shape a research team so as to allow dedicated software engineers to interface with researchers working in this "sweet spot." We conclude that in order to address current issues in the use of software in life science research such as reproducibility and scalability, the field must reevaluate its relationship with software engineering, and adapt its research structures to overcome current issues in bioinformatics such as reproducibility, scalability and productivity.

Objective: The microbiome contributes to the pathogenesis of inflammatory bowel disease (IBD) but the relative contribution of different lifestyle and environmental factors to the compositional variability of the gut microbiota is unclear., Design: Here, we rank the size effect of disease activity, medications, diet and geographic location of the faecal microbiota composition (16S rRNA gene sequencing) in patients with Crohn's disease (CD; n=303), ulcerative colitis (UC; n = 228) and controls (n=161), followed longitudinally (at three time points with 16 weeks intervals)., Results: Reduced microbiota diversity but increased variability was confirmed in CD and UC compared with controls. Significant compositional differences between diseases, particularly CD, and controls were evident. Longitudinal analyses revealed reduced temporal microbiota stability in IBD, particularly in patients with changes in disease activity. Machine learning separated disease from controls, and active from inactive disease, when consecutive time points were modelled. Geographic location accounted for most of the microbiota variance, second to the presence or absence of CD, followed by history of surgical resection, alcohol consumption and UC diagnosis, medications and diet with most (90.3%) of the compositional variance stochastic or unexplained., Conclusion: The popular concept of precision medicine and rational design of any therapeutic manipulation of the microbiota will have to contend not only with the heterogeneity of the host response, but also with widely differing lifestyles and with much variance still unaccounted for., Competing Interests: Competing interests: MTB reports grants and personal fees from AbbVie Canada, grants and personal fees from Janssen Canada, grants and personal fees from Pfizer Canada, grants from Shire Canada, grants and personal fees from Takeda Canada, personal fees from Mylan Pharmaceuticals, other from AbbVie, Janssen, Pfizer, Boerhinger Ingelheim, Celgene, outside the submitted work; FS reports other from Alimentary Health/Precision Biotics, other from 4D pharma, Cork, other from Atlantia Food Clinical Trials, personal fees from Kaleido Biosciences, outside the submitted work; MJC reports personal fees from Mars PetCare, other from Second Genome, outside the submitted work., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

A key phenotypic characteristic of the Gram-positive bacterial pathogen, Staphylococcus aureus, is its ability to grow in low a w environments. A homology transfer based approach, using the well characterised osmotic stress response systems of Bacillus subtilis and Escherichia coli, was used to identify putative osmotolerance loci in Staphylococcus aureus ST772-MRSA-V. A total of 17 distinct putative hyper and hypo-osmotic stress response systems, comprising 78 genes, were identified. The ST772-MRSA-V genome exhibits significant degeneracy in terms of the osmotic stress response; with three copies of opuD, two copies each of nhaK and mrp/mnh, and five copies of opp. Furthermore, regulation of osmotolerance in ST772-MRSA-V appears to be mediated at the transcriptional, translational, and post-translational levels., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Aim: Face masks are an important addition to our arsenal in the fight against COVID-19. The aim of this study is to present a novel method of measuring mask performance which can simultaneously assess both fabric penetration and leakage due to poor fit. Materials & methods: A synthetic aerosol is introduced into the lung of a medical dummy. A conical laser sheet surrounds the face of the dummy where it illuminates the aerosol emitted during a simulated breath. The system is demonstrated with five mask types. Conclusions: The curved laser sheet highlights both penetration through the mask fabric and leakage around the edges of the mask. A large variation in both material penetration and leakage was observed.

Lactation yield estimates standardized to common lactation lengths of 270-d or 305-d equivalents are commonly used in management decision support tools and dairy cow genetic evaluations. The use of such measurements to quantify the (genetic) merit of individual cows fails to penalize cows that do not reach the standardized lactation length, or indeed reward cows that lactate for more than the standardized lactation length. The objective of the present study was to quantify the genetic and nongenetic factors associated with lactation length in seasonal-calving, pasture-based dairy cows. A total of 616,350 lactation length records from 285,598 Irish cows were used. Linear mixed models were used to quantify the associations between lactation length and calving month, parity, age at calving, previous dry period length, calving difficulty score, heterosis, recombination loss, breed, and herd size, as well as to estimate the genetic and residual variance components of lactation length. The median lactation length in the edited data set was 288 d, with 27% of cows achieving lactations of at least 305 d. Relative to cows calving in January, the lactations of cow calving in February, March, or April was, on average, 4.2, 12.7, and 21.9 d shorter, respectively. The lactation length of a first parity cow was, on average, 7.8, 8.6, and 8.4 d shorter than that of second, third, and fourth parity cows, respectively. Norwegian Red and Montbéliarde cows had, on average, a 4.7- and 1.6-d shorter lactation than Holstein-Friesian cows, respectively. The heritability estimate, coefficient of genetic variation, and repeatability estimate of lactation length were 0.02, 1.2%, and 0.04, respectively. Based on the genetic standard deviation for lactation length estimated in the present study (3.3 d), cows ranked in the top 20% for genetic merit for lactation length would be expected to have lactations 9.2 d longer than cows in the bottom 20%, demonstrating exploitable genetic variability. Given the vast array of genetic and nongenetic factors associated with lactation length, an approach which combines improved management practices and selective breeding may be an efficient and effective strategy to lengthen lactations., (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).)

Cryptosporidium species subtypes are generally identified via DNA sequencing of the gp60 gene tandem repeat motif region. Due to the immunogenic nature of its glycoprotein products, gp60 is subject to host selective pressures, genetic recombination and evolutionary processes that drive extensive polymorphism at this locus. The elucidation of the polymorphic nature of this gene has led to the current mainstay in Cryptosporidium subtyping nomenclature. This study aimed to develop a real-time polymerase chain reaction based method utilising a post-PCR application, high resolution melting (HRM) analysis, in conjunction with the abovementioned gp60 nomenclature system, in order to differentiate between Cryptosporidium parvum gp60 subtypes. Subtype differentiation is based on the difference between the melting temperatures of individual subtypes conferred by variations in the polymorphic region of gp60 . • Nested gp60 primers were designed to amplify a target region of <200 base pairs for effective HRM analysis • This method presents a rapid, sensitive, cost effective alternative to conventional sequencing. • This method is highly flexible and may be applied to other loci in order to facilitate multi-locus analysis and improve the discriminative abilities of the method., Competing Interests: There are no conflicts of interest, of which we are aware, relating to this body of work., (© 2020 The Authors. Published by Elsevier B.V.)

Background: Carbapenems are a family of end line antibiotics with increasing levels of resistance that are a cause for concern., Aim: To ascertain whether the CPE screening programme employed in an acute tertiary hospital is fit for purpose., Method: We outlined the current working algorithm employed using a universal screening programme over a 26-month screening period. Rectal swabs are cultured on arrival. Those with suspicious growth are further investigated using NG-Carba 5 lateral flow tests and Vitek 2.0 sensitivity cards. These practices were compared with NHS guidelines., Findings & Conclusions: In all, 53 true positives were detected from 45 patients since the screening was implemented in early 2018 (46 OXA-48, 6 KPC, 1 NDM). As the rate of screening increased, the number of positive screens decreased over time. There were a lot of similarities between the HSE guidelines and the published NHS CPE toolkit. It was evident that there is no standard practice being employed across all hospitals. Comparing the MUH to national guidelines it appears to be quicker and more effective with universal screening in place at reducing the potential contacts and identifying carriers. Cost analysis indicates that the need to confirm all positive strains in a reference lab is costly, unnecessary and time consuming. There are adequate confirmatory tests available in-house for routine positive screens. It was concluded that infection prevention and control are key to identifying and controlling possible outbreaks in a hospital setting., (© 2020 The Authors.)

Cryptosporidium is a leading cause of gastroenteritis (cryptosporidiosis), with significant morbidity and mortality worldwide. Irish cryptosporidiosis incidence rates are consistently the highest reported in Europe. A retrospective, longitudinal study of clinical Cryptosporidium isolates was conducted from 2015 to 2018 in Cork, southern Ireland. Overall, 86.5% of cases were attributed to C. parvum , while the remaining 13.5% were caused by C. hominis Despite the widespread implications of this protozoan parasite in sporadic and outbreak-related illness in Ireland, the current dearth of species-level epidemiological surveillance and clinical studies needs to be addressed in order to elucidate the national impact of this enteric pathogen., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. No commercial re-use. See rights and permissions. Published by BMJ.)

Reported incidence rates of cryptosporidiosis in Ireland are consistently among the highest in Europe. Despite the national prevalence of this enteric parasite and the compulsory nature of incidence surveillance and reporting, in-depth analyses seeking to genotype clinical isolates of Cryptosporidium on an intra-species level are rarely undertaken in Ireland. This molecular epidemiology study of 163 clinical Cryptosporidium isolates was conducted in Southern Ireland, from 2015 to 2018, in order to ascertain population subtype heterogeneity. Analysis was conducted via real-time PCR amplification and gp60 gene sequencing, which successfully determined the subtype designation of 149 of the 163 (91.4%) tested isolates. Overall, 12 C. parvum and five C. hominis subtypes were identified, with the incidence of the regionally predominant C. parvum species found to primarily occur during springtime months, while C. hominis incidence was largely confined to late summer and autumnal months. Additionally, one C. parvum and four C. hominis subtypes were newly reported by this study, having not been previously identified in clinical or livestock infection in Ireland. Overall, these data give insight into the diversification of the Cryptosporidium population and emergent subtypes, while also allowing comparisons to be made with clinical epidemiological profiles reported previously in Ireland and elsewhere., (Copyright © 2020 Elsevier Inc. All rights reserved.)

I would like to commend Prescott and Bland [...].

Beef carcasses in Europe are classified on measures of carcass weight, conformation, and fat cover. These measurements provide the basis for payment to producers, with financial penalties for carcasses that do not conform to desirable characteristics. The objective of the present study was to identify animal-level factors associated with the achievement of a desirable carcass weight, conformation score, fat score, and age at harvest, as stipulated by Irish beef processors in accordance with the EUROP carcass classification system. The stipulated specifications were a EUROP conformation score ≥O=, a carcass weight between 270 and 380 kg, a EUROP fat score between 2+ and 4=, and an age at harvest ≤ 30 mo. In the present study, 59% of cattle failed to achieve at least one of these desired specifications. The logit of the probability of achieving the desired specifications was estimated using multivariable logistic regression and carcass data from 4,717,989 cattle finished and harvested in Ireland between the years 2003 and 2017. In comparison to beef-origin carcasses and after accounting for breed differences, the likelihood of dairy-origin carcasses achieving the desired age, conformation, fat, and weight specifications was 0.97, 0.88, 1.14, and 1.05, respectively. In comparison to heifer carcasses, the odds ratio (OR) of bull and steer carcasses simultaneously achieving all of the desired specifications (i.e. the overall specification) was 0.35 and 0.95, respectively. Additionally, after accounting for breed differences, heifers from the dairy herd were half as likely as heifers from the beef herd to achieve the overall specification, whereas the odds of dairy-origin bulls (OR = 3.46) and steers (OR = 2.41) achieving the overall specification was greater than that of their respective beef-origin counterparts. Finally, cattle with a greater breed proportion of Angus were most likely to achieve the overall specification. Results from the present study could provide a deeper understanding as to why animals fail to achieve desirable carcass specifications and could be implemented into the management decisions made on farm to ensure that the supply of beef carcasses that achieve the desired metrics is maximized., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The purpose of this study was to define an extensive suite of feeding behavior traits in growing crossbred cattle and to investigate their phenotypic inter-relationships as well as relationships with other performance and efficiency traits. Time-series feeding behavior data, as well as feed intake and liveweight records, were available for 624 growing crossbred cattle, of which 445 were steers and 179 were heifers. Feeding behavior repeatability estimates were calculated using linear mixed models. Additionally, partial Spearman correlations were estimated among 14 feeding behavior traits, as well as between feeding behavior with both performance and feed efficiency traits, using residuals retained from linear mixed models. The marginal contribution of several feeding behavior traits to the variability in metabolizable energy intake (MEI) was also determined. Repeatability estimates of 0.57, 0.36, and 0.48 were calculated for the number of feed events per day, the total time spent feeding per day, and the feeding rate, respectively. Cattle that ate more frequently each day, ate at a faster rate and consumed less energy in each visit to the feed bunk. More efficient cattle fed less often per day and fed for a shorter duration per day; they also had a slower feeding rate and fed for longer in each visit to the feed bunk. Moreover, heavier cattle fed for a longer duration per day had a faster feeding rate, but fed less often per day; heavier animals also fed first in the pen after the fresh feed was offered. The number of feed events per day and feeding time per day together explained an additional 13.4 percentage points of the variability in MEI above that already explained by all of growth rate, liveweight, and backfat depth. The results from the present study suggest that several repeatable time-series-related feeding behavior traits, that are less resource intensive to measure, may have a role as useful predictor traits of important but relatively difficult to record traits, such as feed intake and efficiency., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Few studies have attempted to quantify the association between a terminal total merit index with phenotypic feed and production efficiency in beef cattle, particularly when feed efficiency is itself explicitly absent as a goal trait in the index. The objective of the present study was to quantify the differences in phenotypic performance for feed intake, feed efficiency, and carcass traits of crossbred bulls, steers, and heifers differing in a terminal total merit index. A validation population of 614 bulls, steers, and heifers that were evaluated for feed intake and efficiency in the same feedlot and subsequently slaughtered at the end of their test period was constructed. The Irish national genetic evaluations for a terminal index of calving performance, docility, feed intake, and carcass traits were undertaken with the phenotypic records of animals present in the validation population masked. The validation population animals were subsequently stratified into four groups, within sex, according to their terminal index value. Mixed models were used to quantify the association between terminal genetic merit and phenotypic performance; whether the associations differed by sex were also investigated. The regression coefficient of phenotypic feed intake, carcass weight, carcass conformation, or carcass fat on its respective estimated breeding values was 0.86 kg dry matter 0.91 kg, 1.01 units, and 1.29 units, respectively, which are close to the expectation of one. On average, cattle in the very high terminal index stratum had a 0.63 kg DM/d lower feed intake, a 25.05 kg heavier carcass, a 1.82 unit better carcass conformation (scale 1 to 15), and a 1.24 unit less carcass fat score (scale 1 to 15), relative to cattle in the very low terminal index stratum. Cattle of superior total genetic merit were also more feed efficient (i.e., had a lower energy conversion ratio, lower residual feed intake, and greater residual gain), had a greater proportion of their live-weight as carcass weight (i.e., better dressing percentage) and were slaughtered at a younger age relative to their inferior total genetic merit counterparts. This study provides validation of an all-encompassing total merit index and demonstrates the benefits of selection on a total merit index for feed and production efficiency, which should impart confidence among stakeholders in the contribution of genetic selection to simultaneous improvements in individual animal performance and efficiency., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Today, thanks to advances in cloud computing, it is possible for small teams of software developers to produce internet-scale products, a feat that was previously the preserve of large organizations. Herein, we describe how these advances in software engineering can be made more readily available to bioinformaticians. In the same way that cloud computing has democratized access to distributed systems engineering for generalist software engineers, access to scalable and reproducible bioinformatic engineering can be democratized for generalist bioinformaticians and biologists. We present solutions, based on our own efforts, to achieve this goal., (© The Author(s) 2020. Published by Oxford University Press.)

The objective of the present study was to estimate the genetic parameters associated with the achievement of desirable weight, conformation, and fat specifications, represented by a series of binary traits. The desired specifications were those stipulated by Irish beef processors, in accordance with the EUROP carcass grading system, and were represented by a carcass weight between 270 and 380 kg, a fat score between 2+ and 4= (between 6 and 11 on a 15-point scale), and a conformation score of O= or better (≥5 on a 15-point scale). Using data from 58,868 beef carcasses, variance components were estimated using linear mixed models for these binary traits, as well as their underlying continuous measures. Heritability estimates for the continuous traits ranged from 0.63 to 0.73; heritability estimates for the binary traits ranged from 0.05 to 0.19. An additional trait was defined to reflect if all desired carcass specifications were met. All genetic correlations between this trait and the individual contributing binary traits were positive (0.38 to 0.87), while all genetic correlations between this trait and the continuous carcass measures were negative (-0.87 to -0.07). The genetic parameters estimated in the present study signify that potential exists to breed cattle that more consistently achieve desirable carcass metrics at harvest., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Some definitions of feed efficiency such as residual energy intake (REI) and residual gain (RG) may not truly reflect production efficiency. The energy sinks used in the derivation of the traits include metabolic live-weight; producers finishing cattle for slaughter are, however, paid on the basis of carcass weight, as opposed to live-weight. The objective of the present study was to explore alternative definitions of REI and RG which are more reflective of production efficiency, and quantify their relationship with performance, ultrasound, and carcass traits across multiple breeds and sexes of cattle. Feed intake and live-weight records were available on 5,172 growing animals, 2,187 of which also had information relating to carcass traits; all animals were fed a concentrate-based diet representative of a feedlot diet. Animal linear mixed models were used to estimate (co)variance components. Heritability estimates for all derived REI traits varied from 0.36 (REICWF; REI using carcass weight and carcass fat as energy sinks) to 0.50 (traditional REI derived with the energy sinks of both live-weight and ADG). The heritability for the RG traits varied from 0.24 to 0.34. Phenotypic correlations among all definitions of the REI traits ranged from 0.90 (REI with REICWF) to 0.99 (traditional REI with REI using metabolic preslaughter live-weight and ADG). All were different (P < 0.001) from one suggesting reranking of animals when using different definitions of REI to identify efficient cattle. The derived RG traits were either weakly or not correlated (P > 0.05) with the ultrasound and carcass traits. Genetic correlations between the REI traits with carcass weight, dressing difference (i.e., live-weight immediately preslaughter minus carcass weight) and dressing percentage (i.e., carcass weight divided by live-weight immediately preslaughter) implies that selection on any of the REI traits will increase carcass weight, lower the dressing difference and increase dressing percentage. Selection on REICW (REI using carcass weight as an energy sink), as opposed to traditional REI, should increase the carcass weight 2.2 times slower but reduce the dressing difference 4.3 times faster. While traditionally defined REI is informative from a research perspective, the ability to convert energy into live-weight gain does not necessarily equate to carcass gain, and as such, traits such as REICW and REICWF provide a better description of production efficiency for feedlot cattle., (© The Author(s) 2019. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Changes that occur naturally throughout the ageing process place the elderly population at greater risk of malnourishment. This review discusses the significance, causes, consequences and assessment of malnutrition in the elderly.

Campylobacter fetus is a Gram-negative, zoonotic pathogen and a member of the class Epsilonproteobacteria We report the draft genome sequence of C. fetus subsp. fetus CITCf01, isolated from a patient with subacute bacterial endocarditis. CITCf01 grew under aerobic, microaerobic, and anaerobic conditions, and at 42°C, an unusual combination of growth conditions., (Copyright © 2019 Culligan et al.)