Genetic analysis of the modern Australian labradoodle dog breed reveals an excess of the poodle genome.

The genomic diversity of the domestic dog is an invaluable resource for advancing understanding of mammalian biology, evolutionary biology, morphologic variation, and behavior. There are approximately 350 recognized breeds in the world today, many established through hybridization and selection followed by intense breeding programs aimed at retaining or enhancing specific traits. As a result, many breeds suffer from an excess of particular diseases, one of many factors leading to the recent trend of "designer breed" development, i.e. crossing purebred dogs from existing breeds in the hope that offspring will be enriched for desired traits and characteristics of the parental breeds. We used a dense panel of 150,106 SNPs to analyze the population structure of the Australian labradoodle (ALBD), to understand how such breeds are developed. Haplotype and admixture analyses show that breeds other than the poodle (POOD) and Labrador retriever (LAB) contributed to ALBD formation, but that the breed is, at the genetic level, predominantly POOD, with all small and large varieties contributing to its construction. Allele frequency analysis reveals that the breed is enhanced for variants associated with a poodle-like coat, which is perceived by breeders to have an association with hypoallergenicity. We observed little enhancement for LAB-specific alleles. This study provides a blueprint for understanding how dog breeds are formed, highlighting the limited scope of desired traits in defining new breeds.

Best practices for analyzing imputed genotypes from low-pass sequencing in dogs.

Although DNA array-based approaches for genome-wide association studies (GWAS) permit the collection of thousands of low-cost genotypes, it is often at the expense of resolution and completeness, as SNP chip technologies are ultimately limited by SNPs chosen during array development. An alternative low-cost approach is low-pass whole genome sequencing (WGS) followed by imputation. Rather than relying on high levels of genotype confidence at a set of select loci, low-pass WGS and imputation rely on the combined information from millions of randomly sampled low-confidence genotypes. To investigate low-pass WGS and imputation in the dog, we assessed accuracy and performance by downsampling 97 high-coverage (> 15×) WGS datasets from 51 different breeds to approximately 1× coverage, simulating low-pass WGS. Using a reference panel of 676 dogs from 91 breeds, genotypes were imputed from the downsampled data and compared to a truth set of genotypes generated from high-coverage WGS. Using our truth set, we optimized a variant quality filtering strategy that retained approximately 80% of 14 M imputed sites and lowered the imputation error rate from 3.0% to 1.5%. Seven million sites remained with a MAF > 5% and an average imputation quality score of 0.95. Finally, we simulated the impact of imputation errors on outcomes for case-control GWAS, where small effect sizes were most impacted and medium-to-large effect sizes were minorly impacted. These analyses provide best practice guidelines for study design and data post-processing of low-pass WGS-imputed genotypes in dogs.

Guideline on the peri-operative management of patients with sickle cell disease: Guideline from the Association of Anaesthetists.

Sickle cell disease is a multisystem disease characterised by chronic haemolytic anaemia, painful vaso-occlusive crises and acute and chronic end-organ damage. It is one of the most common serious inherited single gene conditions worldwide and has a major impact on the health of affected individuals. Peri-operative complications are higher in patients with sickle cell disease compared with the general population and may be sickle or non-sickle-related. Complications may be reduced by meticulous peri-operative care and transfusion, but unnecessary transfusion should be avoided, particularly to reduce the risk of allo-immunisation. Planned surgery and anaesthesia for patients with sickle cell disease should ideally be undertaken in centres with experience in caring for these patients. In an emergency, advice should be sought from specialists with experience in sickle cell disease through the haemoglobinopathy network arrangements. Emerging data suggest that patients with sickle cell disease are at increased risk of COVID-19 infection but may have a relatively mild clinical course. Outcomes are determined by pre-existing comorbidities, as for the general population.

Global Capnography Project (GCAP): implementation of capnography in Malawi - an international anaesthesia quality improvement project.

The Lancet Commission on Global Surgery emphasised the importance of access to safe anaesthesia care. Capnography is an essential monitor for safe anaesthesia, but is rarely available in low-income countries. The aim of this study was twofold: to measure the prevalence of capnography in the operating theatres and in intensive care units; and to determine whether its introduction was feasible and could improve the early recognition of critical airway incidents in a low-income country. This is the first project to do this. Forty capnographs were donated to eight hospitals in Malawi. Thirty-two anaesthesia providers received a 1-day capnography training course with pre- and post-course knowledge testing. Providers kept logbooks of capnography use and recorded their responses to abnormal readings. On follow-up at 6 months, providers completed questionnaires on any significant patient safety incidents identified using capnography. In January 2017, at the commencement of the project, only one operating theatre had a capnograph. Overall, 97% and 100% 'capnography gaps' were identified in the theatres and intensive care units, respectively. The mean (SD) scores of our capnography multiple choice questionnaires improved after training from 15.00 (3.16) to 18.70 (0.99), p = < 0.001. The capnography equipment was appropriately robust and performed well. Six months following implementation, 24 (77%) anaesthesia providers reported recognising 44 oesophageal intubations and 28 (90%) believed that capnography had saved lives. This study has shown it is feasible to introduce capnography in a low-income country, resulting in early recognition of critical airway incidents and ultimately helping to save lives. Building on the experience of the first trial of pulse oximetry implementation in low-income countries in 2007, we believe this is one of the most important projects in anaesthesia safety in the last decade.

Prickle1 is expressed in distinct cell populations of the central nervous system and contributes to neuronal morphogenesis.

Development of axons and dendrites constitutes a critical event in neuronal maturation and seems to require signaling through the planar cell polarity (PCP) pathway. Mutations in components of the PCP pathway lead to a spectrum of neurological phenotypes and disorders. For example, a missense mutation in Prickle 1 (Pk1) is associated with progressive myoclonus epilepsy (PME) in humans, and its reduced gene dosage increases sensitivity to induced seizure in mice. In an effort to unravel the role of the PCP pathway in mammalian neuronal development, we examined the expression of Pk1 in the central nervous system (CNS) using in situ hybridization (ISH) in combination with a genetic knock-in approach. We show that Pk1 transcripts are detected in the postmitotic cells of the subplate and cortical plate during mid- and late stages of cortical neurogenesis. In adult brain, Pk1 is expressed in distinct neuronal and glial cell populations, with dynamic formation of dendrites and glial processes during development. Of all the cell types in the mature retina, the highest expression of Pk1 is detected in cholinergic amacrine neurons. Knockdown of Pk1 by shRNA or dominant-negative constructs causes reduced axonal and dendritic extension in hippocampal neurons. Similarly, Pk1 knockdown in neonatal retina leads to defects in inner and outer segments and axon terminals of photoreceptors. Our studies implicate Pk1 function in axonal-dendritic development associated with the maturation of CNS neurons.

A comparison of virtual versus in-person delivery of SafeCare on parent and implementation outcomes.

BACKGROUND: Evidence-based prevention services for child abuse and neglect (CAN), typically delivered via home visiting (HV), pivoted to virtual delivery in 2020 to continue family services while adhering to the COVID-19 public health guidelines. OBJECTIVE: The study aims are to compare parent and implementation outcomes for the HV program, SafeCare©, delivered virtually versus in-person, across a 2-year period. METHODS: Three data sources were used to examine parent program engagement and skill mastery, as well as provider fidelity. Sources included: 1) quantitative service data collected as part of routine SafeCare implementation (in-person families, n = 923; virtual families, n = 1978), 2) qualitative survey data collected from SafeCare providers (n = 212) and 3) focus group data with SafeCare Providers (n = 9). RESULTS: Service data were examined using mixed models due to the nesting of the data, with all analyses controlling for time. Qualitative data from the survey and focus groups were analyzed using thematic coding. Data were triangulated from the three sources to answer the primary research question. Findings suggest that virtual delivery of SafeCare holds promise, with parents who participated virtually completing more modules at a faster pace than in-person clients. SafeCare parents demonstrated positive programmatic outcomes regardless of whether they participated in the program virtually or in-person. Provider fidelity remained high in the transition to virtual delivery. However, technology-related logistical issues and provider self-efficacy related to virtual delivery presented challenges to program success. CONCLUSIONS: The study has multiple implications for the HV field about the viability of virtual service delivery. Further research is warranted with data collected directly from parents, and a more critical analysis of what works best for whom and when to further advance the field.

Divergent patterns of healthy aging across human brain regions at single-cell resolution reveal links to neurodegenerative disease.

Age is a major common risk factor underlying neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Previous studies reported that chronological age correlates with differential gene expression across different brain regions. However, prior datasets have not disambiguated whether expression associations with age are due to changes in cell numbers and/or gene expression per cell. In this study, we leveraged single nucleus RNA-sequencing (snRNAseq) to examine changes in cell proportions and transcriptomes in four different brain regions, each from 12 donors aged 20-30 years (young) or 60-85 years (old). We sampled 155,192 nuclei from two cortical regions (entorhinal cortex and middle temporal gyrus) and two subcortical regions (putamen and subventricular zone) relevant to neurodegenerative diseases or the proliferative niche. We found no changes in cellular composition of different brain regions with healthy aging. Surprisingly, we did find that each brain region has a distinct aging signature, with only minor overlap in differentially associated genes across regions. Moreover, each cell type shows distinct age-associated expression changes, including loss of protein synthesis genes in cortical inhibitory neurons, axonogenesis genes in excitatory neurons and oligodendrocyte precursor cells, enhanced gliosis markers in astrocytes and disease-associated markers in microglia, and genes critical for neuron-glia communication. Importantly, we find cell type-specific enrichments of age associations with genes nominated by Alzheimer's disease and Parkinson's disease genome-wide association studies (GWAS), such as apolipoprotein E (APOE), and leucine-rich repeat kinase 2 (LRRK2) in microglia that are independent of overall expression levels across cell types. We present this data as a new resource which highlights, first, region- and cell type-specific transcriptomic changes in healthy aging that may contribute to selective vulnerability and, second, provide context for testing GWAS-nominated disease risk genes in relevant subtypes and developing more targeted therapeutic strategies. The data is readily accessible without requirement for extensive computational support in a public website, https://brainexp-hykyffa56a-uc.a.run.app/.

Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids.

Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.1 Although dogs of variable size are found in the archeological record,2-4 the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.5 Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFß signaling, and skeletal formation.6-10 Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.8 The identification of a functional mutation associated with IGF1 has thus far proven elusive.6,10,11 Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.

Whole Genome Analysis of a Single Scottish Deerhound Dog Family Provides Independent Corroboration That a SGK3 Coding Variant Leads to Hairlessness.

The breeds of domestic dog, Canis lupus familiaris, display a range of coat types with variation in color, texture, length, curl, and growth pattern. One trait of interest is that of partial or full hairlessness, which is found in a small number of breeds. While the standard for some breeds, such as the Xoloitzcuintli, requires sparse hair on their extremities, others are entirely bald, including the American Hairless Terrier. We identified a small, rare family of Scottish Deerhounds in which coated parents produced a mixed litter of coated and hairless offspring. To identify the underlying variant, we performed whole genome sequencing of the dam and five offspring, comparing single nucleotide polymorphisms and small insertions/deletions against an established catalog of 91 million canine variants. Of 325 homozygous alternative alleles found in both hairless dogs, 56 displayed the expected pattern of segregation and only a single, high impact variant within a coding region was observed: a single base pair insertion in exon two of SGK3 leading to a potential frameshift, thus verifying recently published findings. In addition, we observed that gene expression levels between coated and hairless dogs are similar, suggesting a mechanism other than non-sense mediated decay is responsible for the phenotype.

Failure to detect immunocytochemically reactive endogenous lectin on the cell surface of Dictyostelium discoideum.

The endogenous lectins of Dictyostelium discoideum, called discoidins I and II, have been implicated in cell cohesion during the associative phase of this organism. In an effort to repeat and extend the studies of these putative cell-surface proteins, we attempted a variety of immunocytochemical techniques. Antibodies to a mixture of the purified discoidins were raised in rabbit. Both living and fixed cells were examined by indirect immunoferritin labeling using whole antiserum and by direct immunolabeling using purified specific IgG adsorbed to colloidal gold. Cells, at the appropriate stage, of strains A3, NC-4, and WS-582 were tested. In no instance were cell surface antigens detected despite meticulous efforts to duplicate the published techniques and to extend and refine them. Specific localization was found only in the cytosol and on the cytoplasmic face of certain endomembrane vesicles, and much less so on outer nuclear and mitochondrial membranes, in inadvertently disrupted cells. In no case was specific label found on either side of the plasma membrane or on food vacuoles. Exogenously supplied discoidins, bound to cells, were successfully localized by our technique. We conclude that the discoidins are not present on the cell surface, or are there in undetectable quantities, during the associative phase. We suggest that previous demonstrations of these proteins at the cell surface were artifacts resulting from the way in which the cells were handled, which caused the binding of externalized discoidins, possibly those released from lysed cells. We believe that the current notion that the discoidins play a direct role in cell cohesion by virtue of their carbohydrate-binding capacity should be reexamined. We suggest that the true role of the discoidins is solely intracellular.

Global oximetry: an international anaesthesia quality improvement project.

Pulse oximetry is mandatory during anaesthesia in many countries, a standard endorsed by the World Health Organization 'Safe Surgery Saves Lives' initiative. The Association of Anaesthetists of Great Britain and Ireland, the World Federation of Societies of Anaesthesiologists and GE Healthcare collaborated in a quality improvement project over a 15-month period to investigate pulse oximetry in four pilot sites in Uganda, Vietnam, India and the Philippines, using 84 donated pulse oximeters. A substantial gap in oximeter provision was demonstrated at the start of the project. Formal training was essential for oximeter-naïve practitioners. After introduction of oximeters, logbook data were collected from over 8000 anaesthetics, and responses to desaturation were judged appropriate. Anaesthesia providers believed pulse oximeters were essential for patient safety and defined characteristics of the ideal oximeter for their setting. Robust systems for supply and maintenance of low-cost oximeters are required for sustained uptake of pulse oximetry in low- and middle-income countries.