Selfish conflict underlies RNA-mediated parent-of-origin effects.

Genomic imprinting-the non-equivalence of maternal and paternal genomes-is a critical process that has evolved independently in many plant and mammalian species1,2. According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles3,4. Yet, how these epigenetic differences evolve in the first place is poorly understood3,5,6. Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals7-9. In reciprocal crosses between two Caenorhabditis tropicalis wild isolates, we found that the slow-1/grow-1 TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the slow-1 toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when slow-1/grow-1 is maternally inherited, slow-1 repression is halted by a translation-independent role of its maternal mRNA. That is, slow-1 transcripts loaded into eggs-but not SLOW-1 protein-are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation.

Pumping iron: A multi-omics analysis of two extremophilic algae reveals iron economy management.

Marine algae are responsible for half of the world's primary productivity, but this critical carbon sink is often constrained by insufficient iron. One species of marine algae, Dunaliella tertiolecta, is remarkable for its ability to maintain photosynthesis and thrive in low-iron environments. A related species, Dunaliella salina Bardawil, shares this attribute but is an extremophile found in hypersaline environments. To elucidate how algae manage their iron requirements, we produced high-quality genome assemblies and transcriptomes for both species to serve as a foundation for a comparative multiomics analysis. We identified a host of iron-uptake proteins in both species, including a massive expansion of transferrins and a unique family of siderophore-iron-uptake proteins. Complementing these multiple iron-uptake routes, ferredoxin functions as a large iron reservoir that can be released by induction of flavodoxin. Proteomic analysis revealed reduced investment in the photosynthetic apparatus coupled with remodeling of antenna proteins by dramatic iron-deficiency induction of TIDI1, which is closely related but identifiably distinct from the chlorophyll binding protein, LHCA3. These combinatorial iron scavenging and sparing strategies make Dunaliella unique among photosynthetic organisms.

Island-specific evolution of a sex-primed autosome in a sexual planarian.

The sexual strain of the planarian Schmidtea mediterranea, indigenous to Tunisia and several Mediterranean islands, is a hermaphrodite1,2. Here we isolate individual chromosomes and use sequencing, Hi-C3,4 and linkage mapping to assemble a chromosome-scale genome reference. The linkage map reveals an extremely low rate of recombination on chromosome 1. We confirm suppression of recombination on chromosome 1 by genotyping individual sperm cells and oocytes. We show that previously identified genomic regions that maintain heterozygosity even after prolonged inbreeding make up essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicates that this phenomenon has evolved specifically in populations from Sardinia and Corsica. We find that most known master regulators5-13 of the reproductive system are located on chromosome 1. We used RNA interference14,15 to knock down a gene with haplotype-biased expression, which led to the formation of a more pronounced female mating organ. On the basis of these observations, we propose that chromosome 1 is a sex-primed autosome primed for evolution into a sex chromosome.

Validation of the society of thoracic surgeons predicted risk of mortality score for long-term survival after cardiac surgery in Israel.

BACKGROUND: Long-term survival is an important metric in assessing procedural value. We previously confirmed that the Society of Thoracic Surgeons predicted risk of mortality score (PROM) accurately predicts 30-day mortality in Israeli patients. The present study investigated the ability of the PROM to reliably predict long-term survival. METHODS: Data on 1279 patients undergoing cardiac surgery were prospectively entered into our database and used to calculate PROM. Long-term mortality was obtained from the Israeli Social Security Database. Patients were stratified into five cohorts according to PROM (A: 0-0.99%, B: 1.0-1.99%, C: 2.0-2.99%, D: 3.0-4.99% and E: ≥ 5.0%). Kaplan-Meier estimates of survival were calculated for each cohort and compared by Wilcoxon signed-rank test. We used C-statistics to assess model discrimination. Cox regression analysis was performed to identify predictors of long-term survival. RESULTS: Follow-up was achieved for 1256 (98%) patients over a mean period of 62 ± 28 months (median 64, range 0-107). Mean survival of the entire cohort was 95 ± 1 (95% CI 93-96) months. Higher PROM was associated with reduced survival: A-104 ± 1 (103-105) months, B-96 ± 2 (93-99) months, C-93 ± 3 (88-98) months, D-89 ± 3 (84-94) months, E-74 ± 3 (68-80) months (p < 0.0001). The Area Under the Curve was 0.76 ± 0.02 indicating excellent model discrimination. Independent predictors of long-term mortality included advanced age, lower ejection fraction, reoperation, diabetes mellitus, dialysis and PROM. CONCLUSIONS: The PROM was a reliable predictor of long-term survival in Israeli patients undergoing cardiac surgery. The PROM might be a useful metric for assessing procedural value and surgical decision-making.

Diabetes mellitus in dialysis and renal transplantation.

Diabetes mellitus is the commonest cause of end-stage kidney failure worldwide and is a proven and significant risk factor for the development of cardiovascular disease. Renal impairment has a significant impact on the physiology of glucose homeostasis as it reduces tissue sensitivity to insulin and reduces insulin clearance. Renal replacement therapy itself affects glucose control: peritoneal dialysis may induce hyperglycaemia due to glucose-rich dialysate and haemodialysis often causes hypoglycaemia due to the relatively low concentration of glucose in the dialysate. Autonomic neuropathy which is common in chronic kidney disease (CKD) and diabetes increases the risk for asymptomatic hypoglycaemia. Pharmacological options for improving glycaemic control are limited due to alterations to drug metabolism. Impaired glucose tolerance and diabetes are also common in the post-kidney-transplant setting and increase the risk of graft failure and mortality. This review seeks to summarise the literature and tackle the intricacies of glycaemic management in patients with CKD who are either on maintenance haemodialysis or have received a kidney transplant. It outlines changes to glycaemic targets, monitoring of glycaemic control, the use of oral hypoglycaemic agents, the management of severe hyperglycaemia in dialysis and kidney transplantation patients.

Day-case open reduction for developmental dysplasia of the hip.

AIMS: Open reduction in developmental dysplasia of the hip (DDH) is regularly performed despite screening programmes, due to failure of treatment or late presentation. A protocol for open reduction of DDH has been refined through collaboration between surgical, anaesthetic, and nursing teams to allow same day discharge. The objective of this study was to determine the safety and feasibility of performing open reduction of DDH as a day case. METHODS: A prospectively collected departmental database was visited. All consecutive surgical cases of DDH between June 2015 and March 2020 were collected. Closed reductions, bilateral cases, cases requiring corrective osteotomy, and children with comorbidities were excluded. Data collected included demographics, safety outcome measures (blood loss, complications, readmission, reduction confirmation), and feasibility for discharge according to the Face Legs Activity Cry Consolidability (FLACC) pain scale. A satisfaction questionnaire was filled by the carers. Descriptive statistics were used for analysis. RESULTS: Out of 168 consecutive DDH cases, 16 patients fit the inclusion criteria (age range 10 to 26 months, 13 female). Intraoperative blood loss ranged from "minimal" to 120 ml, and there were no complications or readmissions. The FLACC score was 0 for all patients. The carers satisfaction questionnaire expressed high satisfaction from the experience with adequate information and support provided. CONCLUSION: Open reduction in DDH, without corrective osteotomy, is safe and feasible to be managed as a day case procedure. It requires a clear treatment pathway, analgesia, sufficient counselling, and communication with carers. It is even more important during the COVID-19 pandemic when reduced length of hospital stay is likely to be safer for both patient and their parents. Cite this article: Bone Joint Open 2021;2(4):271-277.

Whole-organism eQTL mapping at cellular resolution with single-cell sequencing.

Genetic regulation of gene expression underlies variation in disease risk and other complex traits. The effect of expression quantitative trait loci (eQTLs) varies across cell types; however, the complexity of mammalian tissues makes studying cell-type eQTLs highly challenging. We developed a novel approach in the model nematode Caenorhabditis elegans that uses single-cell RNA sequencing to map eQTLs at cellular resolution in a single one-pot experiment. We mapped eQTLs across cell types in an extremely large population of genetically distinct C. elegans individuals. We found cell-type-specific trans eQTL hotspots that affect the expression of core pathways in the relevant cell types. Finally, we found single-cell-specific eQTL effects in the nervous system, including an eQTL with opposite effects in two individual neurons. Our results show that eQTL effects can be specific down to the level of single cells.

DNA sequences that differ between individuals often change the activation pattern of genes. That is, they change how, when, or why genes switch on and off. We call such DNA sequences 'expression quantitative trait loci', or eQTLs for short. Many of these eQTLs affect biological traits, but their effects are not always easy to predict. In fact, these effects can change with time, with different stress levels, and even in different types of cells. This makes studying eQTLs challenging, especially in organisms with many different types of cells. Standard methods of studying eQTLs involve separately measuring which genes switch on or off under every condition and in each cell. However, a technology called single cell sequencing makes it possible to profile many cells simultaneously, determining which genes are switched on or off in each one. Applying this technology to eQTL discovery could make a challenging problem solvable with a straightforward experiment. To test this idea, Ben-David et al. worked with the nematode worm Caenorhabditis elegans, a frequently-used experimental animal which has a small number of cells with well-defined types. The experiment included tens of thousands of cells from tens of thousands of genetically distinct worms. Using single cell sequencing, Ben-David et al. were able to find eQTLs across all the different cell types in the worms. These included many eQTLs already identified using traditional approaches, confirming that the new method worked. To understand the effects of some of these eQTLs in more detail, Ben-David et al. took a closer look at the cells of the nervous system. This revealed that eQTL effects not only differ between cell types, but also between individual cells. In one example, an eQTL changed the expression of the same gene in opposite directions in two different nerve cells. There is great interest in studying eQTLs because they provide a common mechanism by which changes in DNA can affect biological traits, including diseases. These experiments highlight the need to compare eQTLs in all conditions and tissues of interest, and the new technique provides a simpler way to do so. As single-cell technology matures and enables profiling of larger numbers of cells, it should become possible to analyze more complex organisms. This could one day include mammals.

A meta-analysis of level I evidence comparing tenotomy vs tenodesis in the management of long head of biceps pathology.

BACKGROUND: The ideal surgical treatment of long head of biceps pathology is unclear. This review evaluates Level I studies comparing tenotomy and tenodesis for the management of long head of biceps pathology. METHODS: Medline, EMBASE, and the Cochrane Library databases were searched from database inception though April 17, 2020. Clinical outcomes including Constant-Murley Shoulder Outcome Score, American Shoulder and Elbow Surgeons Standardized Shoulder Assessment Form (ASES) shoulder score, pain on visual analog scale, postoperative strength, and Popeye deformity were evaluated. Dichotomous outcomes were pooled into relative risk ratios whereas continuous outcomes were pooled into weighted mean differences using random effects meta-analysis. RESULTS: A total of 5 studies (227 tenotomy and 227 tenodesis patients) met the final inclusion criteria. Postoperative improvement across all outcomes was observed regardless of surgical treatment. Pooled analysis demonstrated no statistically significant difference for Constant-Murley Shoulder Outcome Score, ASES, pain, or flexion strength. Tenodesis was superior to tenotomy in reducing the risk of Popeye deformity (relative risk ratio 3.07, confidence interval 1.87, 5.02; P < .001). CONCLUSION: Tenotomy and tenodesis of the long head of the biceps results in comparable postoperative clinical and functional outcomes. Tenodesis is superior to tenotomy in preventing Popeye deformity postoperatively.

Ubiquitous Selfish Toxin-Antidote Elements in Caenorhabditis Species.

Toxin-antidote elements (TAs) are selfish genetic dyads that spread in populations by selectively killing non-carriers. TAs are common in prokaryotes, but very few examples are known in animals. Here, we report the discovery of maternal-effect TAs in both C. tropicalis and C. briggsae, two distant relatives of C. elegans. In C. tropicalis, multiple TAs combine to cause a striking degree of intraspecific incompatibility: five elements reduce the fitness of >70% of the F2 hybrid progeny of two Caribbean isolates. We identified the genes underlying one of the novel TAs, slow-1/grow-1, and found that its toxin, slow-1, is homologous to nuclear hormone receptors. Remarkably, although previously known TAs act during embryonic development, maternal loading of slow-1 in oocytes specifically slows down larval development, delaying the onset of reproduction by several days. Finally, we found that balancing selection acting on linked, conflicting TAs hampers their ability to spread in populations, leading to more stable genetic incompatibilities. Our findings indicate that TAs are widespread in Caenorhabditis species and target a wide range of developmental processes and that antagonism between them may cause lasting incompatibilities in natural populations. We expect that similar phenomena exist in other animal species.

Toxin-Antidote Elements Across the Tree of Life.

In life's constant battle for survival, it takes one to kill but two to conquer. Toxin-antitoxin or toxin-antidote (TA) elements are genetic dyads that cheat the laws of inheritance to guarantee their transmission to the next generation. This seemingly simple genetic arrangement-a toxin linked to its antidote-is capable of quickly spreading and persisting in natural populations. TA elements were first discovered in bacterial plasmids in the 1980s and have recently been characterized in fungi, plants, and animals, where they underlie genetic incompatibilities and sterility in crosses between wild isolates. In this review, we provide a unified view of TA elements in both prokaryotic and eukaryotic organisms and highlight their similarities and differences at the evolutionary, genetic, and molecular levels. Finally, we propose several scenarios that could explain the paradox of the evolutionary origin of TA elements and argue that these elements may be key evolutionary players and that the full scope of their roles is only beginning to be uncovered.

Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning.

We demonstrate that a deep neural network can be trained to virtually refocus a two-dimensional fluorescence image onto user-defined three-dimensional (3D) surfaces within the sample. Using this method, termed Deep-Z, we imaged the neuronal activity of a Caenorhabditis elegans worm in 3D using a time sequence of fluorescence images acquired at a single focal plane, digitally increasing the depth-of-field by 20-fold without any axial scanning, additional hardware or a trade-off of imaging resolution and speed. Furthermore, we demonstrate that this approach can correct for sample drift, tilt and other aberrations, all digitally performed after the acquisition of a single fluorescence image. This framework also cross-connects different imaging modalities to each other, enabling 3D refocusing of a single wide-field fluorescence image to match confocal microscopy images acquired at different sample planes. Deep-Z has the potential to improve volumetric imaging speed while reducing challenges relating to sample drift, aberration and defocusing that are associated with standard 3D fluorescence microscopy.

Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk.

Genetic studies of complex traits in animals have been hindered by the need to generate, maintain, and phenotype large panels of recombinant lines. We developed a new method, C. elegans eXtreme Quantitative Trait Locus (ceX-QTL) mapping, that overcomes this obstacle via bulk selection on millions of unique recombinant individuals. We use ceX-QTL to map a drug resistance locus with high resolution. We also map differences in gene expression in live worms and discovered that mutations in the co-chaperone sti-1 upregulate the transcription of HSP-90. Lastly, we use ceX-QTL to map loci that influence fitness genome-wide confirming previously reported causal variants and uncovering new fitness loci. ceX-QTL is fast, powerful and cost-effective, and will accelerate the study of complex traits in animals.

Are we losing future talent? A national survey of UK medical student interest and perceptions of cardiothoracic surgery.

OBJECTIVES: Cardiothoracic surgery appears to have become a significantly less popular career option among UK medical graduates. This study aimed to elucidate the current levels of interest in pursuing a career in cardiothoracic surgery among surgically orientated UK medical students and to determine the factors underlying this decision. METHODS: An online cross-sectional survey generated using the LimeSurvey was distributed to the surgical societies of all 32 UK medical schools. This assessed current career intentions, previous experience and perceptions of cardiothoracic surgery and the factors that attract or deter them to the speciality. RESULTS: A total of 352 responses were obtained. Although 31% of the total cohort was considering a career in cardiothoracic surgery, only 14% of the final year students were. Seventy-five percent felt that they had received inadequate exposure to cardiothoracic surgery during their undergraduate curriculum, with 74% having spent no time on a dedicated cardiothoracic placement. Extracurricular exposure to the specialty was poor with 13% having attended a cardiothoracic conference/careers day. Approximately 50% of students were aware of the publication of surgeon-specific mortality data and previous scandals affecting the speciality; however, 80% claimed that this did not deter them. The main factor attracting students was the ability to significantly influence or save lives, whereas the main deterring factor was perceived competition levels. CONCLUSIONS: Although there remains healthy interest among UK students to pursue a career in cardiothoracic surgery, there is a worrying decline in desire over the course of medical school which appears to stem from a lack of engagement with the specialty both within undergraduate curricula and through extracurricular events.

A genetic signature of the evolution of loss of flight in the Galapagos cormorant.

We have a limited understanding of the genetic and molecular basis of evolutionary changes in the size and proportion of limbs. We studied wing and pectoral skeleton reduction leading to flightlessness in the Galapagos cormorant (Phalacrocorax harrisi). We sequenced and de novo assembled the genomes of four cormorant species and applied a predictive and comparative genomics approach to find candidate variants that may have contributed to the evolution of flightlessness. These analyses and cross-species experiments in Caenorhabditis elegans and in chondrogenic cell lines implicated variants in genes necessary for transcriptional regulation and function of the primary cilium. Cilia are essential for Hedgehog signaling, and humans affected by skeletal ciliopathies suffer from premature bone growth arrest, mirroring skeletal features associated with loss of flight.

A maternal-effect selfish genetic element in Caenorhabditis elegans.

Selfish genetic elements spread in natural populations and have an important role in genome evolution. We discovered a selfish element causing embryonic lethality in crosses between wild strains of the nematode Caenorhabditis elegans The element is made up of sup-35, a maternal-effect toxin that kills developing embryos, and pha-1, its zygotically expressed antidote. pha-1 has long been considered essential for pharynx development on the basis of its mutant phenotype, but this phenotype arises from a loss of suppression of sup-35 toxicity. Inactive copies of the sup-35/pha-1 element show high sequence divergence from active copies, and phylogenetic reconstruction suggests that they represent ancestral stages in the evolution of the element. Our results suggest that other essential genes identified by genetic screens may turn out to be components of selfish elements.

Varying Intolerance of Gene Pathways to Mutational Classes Explain Genetic Convergence across Neuropsychiatric Disorders.

Genetic susceptibility to intellectual disability (ID), autism spectrum disorder (ASD), and schizophrenia (SCZ) often arises from mutations in the same genes, suggesting that they share common mechanisms. We studied genes with de novo mutations in the three disorders and genes implicated in SCZ by genome-wide association study (GWAS). Using biological annotations and brain gene expression, we show that mutation class explains enrichment patterns more than specific disorder. Genes with loss-of-function mutations and genes with missense mutations were associated with different pathways across disorders. Conversely, gene expression patterns were specific for each disorder. ID genes were preferentially expressed in the cortex; ASD genes were expressed in the fetal cortex, cerebellum, and striatum; and genes associated with SCZ were expressed in the adolescent cortex. Our study suggests that convergence across neuropsychiatric disorders stems from common pathways that are consistently vulnerable to genetic variations but that spatiotemporal activity of genes contributes to specific phenotypes.

Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data.

The study of the genetics of gene expression is of considerable importance to understanding the nature of common, complex diseases. The most widely applied approach to identifying relationships between genetic variation and gene expression is the expression quantitative trait loci (eQTL) approach. Here, we increased the computational power of eQTL with an alternative and complementary approach based on analyzing allele specific expression (ASE). We designed a novel analytical method to identify cis-acting regulatory variants based on genome sequencing and measurements of ASE from RNA-sequencing (RNA-seq) data. We evaluated the power and resolution of our method using simulated data. We then applied the method to map regulatory variants affecting gene expression in lymphoblastoid cell lines (LCLs) from 77 unrelated northern and western European individuals (CEU), which were part of the HapMap project. A total of 2309 SNPs were identified as being associated with ASE patterns. The SNPs associated with ASE were enriched within promoter regions and were significantly more likely to signal strong evidence for a regulatory role. Finally, among the candidate regulatory SNPs, we identified 108 SNPs that were previously associated with human immune diseases. With further improvements in quantifying ASE from RNA-seq, the application of our method to other datasets is expected to accelerate our understanding of the biological basis of common diseases.

Imputing Phenotypes for Genome-wide Association Studies.

Genome-wide association studies (GWASs) have been successful in detecting variants correlated with phenotypes of clinical interest. However, the power to detect these variants depends on the number of individuals whose phenotypes are collected, and for phenotypes that are difficult to collect, the sample size might be insufficient to achieve the desired statistical power. The phenotype of interest is often difficult to collect, whereas surrogate phenotypes or related phenotypes are easier to collect and have already been collected in very large samples. This paper demonstrates how we take advantage of these additional related phenotypes to impute the phenotype of interest or target phenotype and then perform association analysis. Our approach leverages the correlation structure between phenotypes to perform the imputation. The correlation structure can be estimated from a smaller complete dataset for which both the target and related phenotypes have been collected. Under some assumptions, the statistical power can be computed analytically given the correlation structure of the phenotypes used in imputation. In addition, our method can impute the summary statistic of the target phenotype as a weighted linear combination of the summary statistics of related phenotypes. Thus, our method is applicable to datasets for which we have access only to summary statistics and not to the raw genotypes. We illustrate our approach by analyzing associated loci to triglycerides (TGs), body mass index (BMI), and systolic blood pressure (SBP) in the Northern Finland Birth Cohort dataset.

Oncogenes create a unique landscape of fragile sites.

Recurrent genomic instability in cancer is attributed to positive selection and/or the sensitivity of specific genomic regions to breakage. Among these regions are fragile sites (FSs), genomic regions sensitive to replication stress conditions induced by the DNA polymerase inhibitor aphidicolin. However, the basis for the majority of cancer genomic instability hotspots remains unclear. Aberrant oncogene expression induces replication stress, leading to DNA breaks and genomic instability. Here we map the cytogenetic locations of oncogene-induced FSs and show that in the same cells, each oncogene creates a unique fragility landscape that only partially overlaps with aphidicolin-induced FSs. Oncogene-induced FSs colocalize with cancer breakpoints and large genes, similar to aphidicolin-induced FSs. The observed plasticity in the fragility landscape of the same cell type following oncogene expression highlights an additional level of complexity in the molecular basis for recurrent fragility in cancer.