Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region

Mycobacterium tuberculosis, the causative agent of most human tuberculosis, infects one third of the world's population and kills an estimated 1.7 million people a year. With the world-wide emergence of drug resistance, and the finding of more functional genetic diversity than previously expected, there is a renewed interest in understanding the forces driving genome evolution of this important pathogen. Genetic diversity in M. tuberculosis is dominated by single nucleotide polymorphisms and small scale gene deletion, with little or no evidence for large scale genome rearrangements seen in other bacteria. Recently, a single report described a large scale genome duplication that was suggested to be specific to the Beijing lineage. We report here multiple independent large-scale duplications of the same genomic region of M. tuberculosis detected through whole-genome sequencing. The duplications occur in strains belonging to both M. tuberculosis lineage 2 and 4, and are thus not limited to Beijing strains. The duplications occur in both drug-resistant and drug susceptible strains. The duplicated regions also have substantially different boundaries in different strains, indicating different originating duplication events. We further identify a smaller segmental duplication of a different genomic region of a lab strain of H37Rv. The presence of multiple independent duplications of the same genomic region suggests either instability in this region, a selective advantage conferred by the duplication, or both. The identified duplications suggest that large-scale gene duplication may be more common in M. tuberculosis than previously considere

WeatherBench 2: A benchmark for the next generation of data-driven global weather models

WeatherBench 2 is an update to the global, medium-range (1-14 day) weather forecasting benchmark proposed by Rasp et al. (2020), designed with the aim to accelerate progress in data-driven weather modeling. WeatherBench 2 consists of an open-source evaluation framework, publicly available training, ground truth and baseline data as well as a continuously updated website with the latest metrics and state-of-the-art models: https://sites.research.google/weatherbench. This paper describes the design principles of the evaluation framework and presents results for current state-of-the-art physical and data-driven weather models. The metrics are based on established practices for evaluating weather forecasts at leading operational weather centers. We define a set of headline scores to provide an overview of model performance. In addition, we also discuss caveats in the current evaluation setup and challenges for the future of data-driven weather forecasting

Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

<p>Abstract</p> <p>Background</p> <p>The sequence of the pathogen <it>Mycobacterium tuberculosis </it>(<it>Mtb</it>) strain <it>H37Rv </it>has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other <it>Mtb </it>strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of <it>Mtb </it>pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org), including 8 strains of <it>Mtb </it>and <it>M. bovis</it>, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, <it>Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes</it>, and <it>Bifidobacterium longum</it>.</p> <p>Results</p> <p>Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four.</p> <p>Conclusions</p> <p>Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of <it>Mtb </it>in a comparative context, and are available online and through TBDB.org.</p

Social rearing environment influences dog behavioral development

Early life experiences are known to influence behavior later in life. In dogs, environmental influences of early home rearing could be exploited to improve the chances of developing adult behavior most suited to the adult environment. For working dog organizations, such as Guide Dogs, suitable adult behavior is important to ensure that dogs can fulfill their role as guides for people with visual impairment. Here, we test the hypothesis that dogs' home rearing environment will influence behavioral development. To investigate this hypothesis, carers of potential guide dogs (puppy walkers) completed a questionnaire, termed the Puppy Walker Questionnaire (PWQ), about the dog's behavior at 5, 8, and 12 months of age. An additional 11 questions were answered about the home environment at the last assessment. Because no questionnaire existed which measured behavior most relevant to Guide Dogs, questions from an existing questionnaire (Canine Behaviour and Research Questionnaire) were combined with additional questions. Thus, a subsidiary aim of the study was to test the reliability of the PWQ for measuring behavioral development of potential guide dogs. The PWQ, scored on a 100-mm visual analogue scale, grouped into 5 new scales: trainability, distractibility, general anxiety, body sensitivity, and stair anxiety, with 4 Canine Behaviour and Research Questionnaire scales: excitability, separation-related behavior, attachment and attention seeking, and energy level. For each reliable scale, multivariate linear regression identified significant predictors from the home environmental questions. The results suggest that home rearing environment is indeed important for behavioral development: 9 of 11 environmental variables were significant predictors of behavioral scores. Those environmental variables that appeared most important were social in nature. Dogs were scored as higher in energy level, excitability, and distractibility if they had been raised in a home with children, lower on energy level and distractibility the more experience of puppy walking their carer had, and lower on separation-related behavior the more they had been able to play with other dogs. These findings have implications for matching between dogs' early and later home environments. Follow-up of dogs in this study could help to elucidate effects on guiding suitability and matching between dog and guide dog owner

Test-retest reliability and predictive validity of a juvenile guide dog behavior test

The ability to measure stable and consistent behavioral traits in dogs would facilitate selection and assessment of working dogs, such as guide dogs. Ideally, these measures should predict suitability for the working role from a young age. This study assessed test-retest reliability of a juvenile guide dog behavior test and predictive validity using qualification or withdrawal from guide dog training. Ninety-three guide dog puppies (52 female; 41 male) were tested at 5 (mean 4.78; ±0.73 SD) and 8 (mean 7.98; ±0.78 SD) months of age. The dogs were exposed to a sequence of 11 stimuli designed to assess the dogs’ reactions to meeting a stranger, obedience commands, body sensitivity, scavenging, and “animal” and human distractions. The behavior of dogs was digitally recorded and analyzed using an ethogram incorporating both frequency of behavior and specific reactions to stimuli. Test-retest reliability indicated interindividual consistency in many of the behavioral measures such as jumping, barking, and “low” greeting posture, as defined in our ethogram. Behavior measures that did not show interindividual consistency between tests included obedience responses, lip licking, body shaking, and scratching. Binary logistic regression models revealed 7 behavioral measures at 5 months and 5 measures at 8 months that were significantly associated with qualification or withdrawal. Uncorrelated measures and principal component scores of correlated measures were combined in a logistic regression model that showed great potential for predicting the probability of a dog qualifying or being withdrawn from guide dog training

Characterising the refractive error in paediatric patients with congenital stationary night blindness: a multicentre study

BACKGROUND/AAIMS: Congenital stationary night blindness (CSNB) is an inherited retinal disease that is often associated with high myopia and can be caused by pathological variants in multiple genes, most commonly CACNA1F, NYX and TRPM1. High myopia is associated with retinal degeneration and increased risk for retinal detachment. Slowing the progression of myopia in patients with CSNB would likely be beneficial in reducing risk, but before interventions can be considered, it is important to understand the natural history of myopic progression. METHODS: This multicentre, retrospective study explored CSNB caused by variants in CACNA1F, NYX or TRPM1 in patients who had at least 6 measurements of their spherical equivalent of refraction (SER) before the age of 18. A mixed-effect model was used to predict progression of SER overtime and differences between genotypes were evaluated. RESULTS: 78 individuals were included in this study. All genotypes showed a significant myopic predicted SER at birth (-3.076D, -5.511D and -5.386D) for CACNA1F, NYX and TRPM1 respectively. Additionally, significant progression of myopia per year (-0.254D, -0.257D and -0.326D) was observed for all three genotypes CACNA1F, NYX and TRPM1, respectively. CONCLUSIONS: Patients with CSNB tend to be myopic from an early age and progress to become more myopic with age. Patients may benefit from long-term myopia slowing treatment in the future and further studies are indicated. Additionally, CSNB should be considered in the differential diagnosis for early-onset myopia

An evidence-based decision assistance model for predicting training outcome in juvenile guide dogs

Working dog organisations, such as Guide Dogs, need to regularly assess the behaviour of the dogs they train. In this study we developed a questionnaire-style behaviour assessment completed by training supervisors of juvenile guide dogs aged 5, 8 and 12 months old (n = 1,401), and evaluated aspects of its reliability and validity. Specifically, internal reliability, temporal consistency, construct validity, predictive criterion validity (comparing against later training outcome) and concurrent criterion validity (comparing against a standardised behaviour test) were evaluated. Thirty-nine questions were sourced either from previously published literature or created to meet requirements identified via Guide Dogs staff surveys and staff feedback. Internal reliability analyses revealed seven reliable and interpretable trait scales named according to the questions within them as: Adaptability; Body Sensitivity; Distractibility; Excitability; General Anxiety; Trainability and Stair Anxiety. Intra-individual temporal consistency of the scale scores between 5±8, 8±12 and 5±12 months was high. All scales excepting Body Sensitivity showed some degree of concurrent criterion validity. Predictive criterion validity was supported for all seven scales, since associations were found with training outcome, at at-least one age. Thresholds of z-scores on the scales were identified that were able to distinguish later training outcome by identifying 8.4% of all dogs withdrawn for behaviour and 8.5% of all qualified dogs, with 84% and 85% specificity. The questionnaire assessment was reliable and could detect traits that are consistent within individuals over time, despite juvenile dogs undergoing development during the study period. By applying thresholds to scores produced from the questionnaire this assessment could prove to be a highly valuable decision-making tool for Guide Dogs. This is the first questionnaire-style assessment of juvenile dogs that has shown value in predicting the training outcome of individual working dogs

Identification of CIITA Regulated Genetic Module Dedicated for Antigen Presentation

The class II trans-activator CIITA is a transcriptional co-activator required for the expression of Major Histocompatibility Complex (MHC) genes. Although the latter function is well established, the global target-gene specificity of CIITA had not been defined. We therefore generated a comprehensive list of its target genes by performing genome-wide scans employing four different approaches designed to identify promoters that are occupied by CIITA in two key antigen presenting cells, B cells and dendritic cells. Surprisingly, in addition to MHC genes, only nine new targets were identified and validated by extensive functional and expression analysis. Seven of these genes are known or likely to function in processes contributing to MHC-mediated antigen presentation. The remaining two are of unknown function. CIITA is thus uniquely dedicated for genes implicated in antigen presentation. The finding that CIITA regulates such a highly focused gene expression module sets it apart from all other transcription factors, for which large-scale binding-site mapping has indicated that they exert pleiotropic functions and regulate large numbers of genes

Caregiving process and caregiver burden: Conceptual models to guide research and practice

BACKGROUND: Parental care for a child with a developmental disability is an enormous responsibility, one that can far exceed that of typical parental care. While most parents adapt well to the situation of caring for a child with a disability, some do not. To understand parents' adaptations to their children's disabilities, the complex nature of stress processes must be accounted for and the constructs and factors that play a role in the caregiving must be considered. DISCUSSION: Evidence suggests that there is considerable variation in how caregivers adapt to their caregiving demands. Many studies have sought to qualify the association between caregiving and health outcomes of the caregivers. Contextual factors such as SES, child factors such as child behaviour problems and severity of disability, intra-psychic factors such as mastery and self-esteem, coping strategies and social supports have all been associated with psychological and/or physical outcome or parents or primary caregivers. In reviewing these issues, the literature appears to be limited by the use of traditional analytic approaches which examine the relationship between a factor and an outcome. It is clear, however, that changes to single factors, as represented in these studies, occur very rarely even in the experimental context. The literature has also been limited by lack of reliance on specific theoretical frameworks. SUMMARY: This conceptual paper documents the state of current knowledge and explores the current theoretical frameworks that have been used to describe the caregiving process from two diverse fields, pediatrics and geriatrics. Integration of these models into one comprehensive model suitable for this population of children with disabilities and their caregivers is proposed. This model may guide future research in this area

Conjugated linoleic acids: why the discrepancy between animal and human studies?

Conjugated linoleic acids (CLA) are positional and geometric isomers of linoleic acid. In animals, CLA consumption reduces body fat but results in humans are less conclusive. This review of the literature on CLA and loss of body fat or body weight in humans was conducted to explore the reasons for the discrepancy between animal and clinical trials. It indicates that the incongruity between human and animal data is largelyrelatedto methodological differences inthe experimental design, including age and gender and, to a lesser extent, to CLA dose and isomers. The relatively unknown metabolic fate of CLA in humans may also be a contributing factor that helps explain the lack of consistency for CLA efficacy across studies