Relating pathogenic loss-of-function mutations in humans to their evolutionary fitness costs.

Causal loss-of-function (LOF) variants for Mendelian and severe complex diseases are enriched in 'mutation intolerant' genes. We show how such observations can be interpreted in light of a model of mutation-selection balance and use the model to relate the pathogenic consequences of LOF mutations at present to their evolutionary fitness effects. To this end, we first infer posterior distributions for the fitness costs of LOF mutations in 17,318 autosomal and 679 X-linked genes from exome sequences in 56,855 individuals. Estimated fitness costs for the loss of a gene copy are typically above 1%; they tend to be largest for X-linked genes, whether or not they have a Y homolog, followed by autosomal genes and genes in the pseudoautosomal region. We compare inferred fitness effects for all possible de novo LOF mutations to those of de novo mutations identified in individuals diagnosed with one of six severe, complex diseases or developmental disorders. Probands carry an excess of mutations with estimated fitness effects above 10%; as we show by simulation, when sampled in the population, such highly deleterious mutations are typically only a couple of generations old. Moreover, the proportion of highly deleterious mutations carried by probands reflects the typical age of onset of the disease. The study design also has a discernible influence: a greater proportion of highly deleterious mutations is detected in pedigree than case-control studies, and for autism, in simplex than multiplex families and in female versus male probands. Thus, anchoring observations in human genetics to a population genetic model allows us to learn about the fitness effects of mutations identified by different mapping strategies and for different traits.

Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies.

Ancient genomes anchor genealogies in directly observed historical genetic variation and contextualize ancestral lineages with archaeological insights into their geography and cultural associations. However, the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies. Here, we present a fast and scalable method, Colate, the first approach for inferring ancestral relationships through time between low-coverage genomes without requiring phasing or imputation. Our approach leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. For deeply sequenced ancient genomes, we additionally introduce an extension of the Relate algorithm for joint inference of genealogies incorporating such genomes. Application to 278 present-day and 430 ancient DNA samples of >0.5x mean coverage allows us to identify dynamic population structure and directional gene flow between early farmer and European hunter-gatherer groups. We further show that the previously reported, but still unexplained, increase in the TCC/TTC mutation rate, which is strongest in West Eurasia today, was already present at similar strength and widespread in the Late Glacial Period ~10k-15k years ago, but is not observed in samples >30k years old. It is strongest in Neolithic farmers, and highly correlated with recent coalescence rates between other genomes and a 10,000-year-old Anatolian hunter-gatherer. This suggests gene-flow among ancient peoples postdating the last glacial maximum as widespread and localizes the driver of this mutational signal in both time and geography in that region. Our approach should be widely applicable in future for addressing other evolutionary questions, and in other species.

ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair.

During meiosis, homologous chromosomes pair and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, double-strand breaks (DSBs) initiate recombination within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have been identified. We identified Zcwpw1, containing H3K4me3 and H3K36me3 recognition domains, as having highly correlated expression with Prdm9. Here, we show that ZCWPW1 has co-evolved with PRDM9 and, in human cells, is strongly and specifically recruited to PRDM9 binding sites, with higher affinity than sites possessing H3K4me3 alone. Surprisingly, ZCWPW1 also recognises CpG dinucleotides. Male Zcwpw1 knockout mice show completely normal DSB positioning, but persistent DMC1 foci, severe DSB repair and synapsis defects, and downstream sterility. Our findings suggest ZCWPW1 recognition of PRDM9-bound sites at DSB hotspots is critical for synapsis, and hence fertility.

Sexual reproduction ­ that is, the combination of sex cells from two different individuals to produce an embryo ­ is one of the many mechanisms that have evolved to maintain genetic diversity. Most human cells contain 23 pairs of chromosomes, with each chromosome in a pair carrying either a paternal or maternal copy of the same gene. To form an embryo with the right number of chromosomes, each sex cell (the egg or sperm cell) must only contain one chromosome from each pair. Sex cells are produced from parent cells containing two sets of paternal and maternal chromosomes: these cells then divide twice to form four sex cells which contain only one chromosome from each pair. Before the parent cell divides, a process known as 'recombination' takes place, which allows chromosomes in a pair to exchange bits of genetic information. This reshuffling ensures that each chromosome in a sex cell is unique. A protein called PRDM9 helps control which sections of genetic information are recombined by modifying proteins attached to the chromosomes, marking them as locations for exchange. The DNA at each of these sites is then broken and repaired using the genetic sequence of the chromosome it is paired with as a template, thus causing the two chromosomes to swap genes. In 2019, a group of researchers found a set of genes in the testis of mice that are expressed at the same time as the gene for PRDM9. This suggested that another protein called ZCWPW1 is likely involved in recombination, but the precise role of this protein was unclear. To answer this question, Wells, Bitoun et al. ­ including many of the researchers involved in the 2019 study ­ examined human cells grown in the laboratory to determine where ZCWPW1 binds to in the chromosome. This revealed that ZCWPW1 can be found at the same sites as PRDM9, which is responsible for bringing it there. Furthermore, cells from male mice lacking the gene for ZCWPW1 cannot complete the exchange of genetic information between chromosomes, meaning that the mice are infertile. As such, ZCWPW1 seems to connect location selection by PRDM9 to the DNA repair mechanisms needed for gene exchange between chromosomes. Infertility is a significant issue for humans affecting as many as one in every six couples. Fertility is complex and many of the biological mechanisms involved are not fully understood. This work suggests that both PRDM9 and ZCWPW1 are key to the production of sex cells and may be worth investigating as factors that affect fertility in humans.

A method for genome-wide genealogy estimation for thousands of samples.

Knowledge of genome-wide genealogies for thousands of individuals would simplify most evolutionary analyses for humans and other species, but has remained computationally infeasible. We have developed a method, Relate, scaling to >10,000 sequences while simultaneously estimating branch lengths, mutational ages and variable historical population sizes, as well as allowing for data errors. Application to 1,000 Genomes Project haplotypes produces joint genealogical histories for 26 human populations. Highly diverged lineages are present in all groups, but most frequent in Africa. Outside Africa, these mainly reflect ancient introgression from groups related to Neanderthals and Denisovans, while African signals instead reflect unknown events unique to that continent. Our approach allows more powerful inferences of natural selection than has previously been possible. We identify multiple regions under strong positive selection, and multi-allelic traits including hair color, body mass index and blood pressure, showing strong evidence of directional selection, varying among human groups.

A high-resolution map of non-crossover events reveals impacts of genetic diversity on mammalian meiotic recombination.

During meiotic recombination, homologue-templated repair of programmed DNA double-strand breaks (DSBs) produces relatively few crossovers and many difficult-to-detect non-crossovers. By intercrossing two diverged mouse subspecies over five generations and deep-sequencing 119 offspring, we detect thousands of crossover and non-crossover events genome-wide with unprecedented power and spatial resolution. We find that both crossovers and non-crossovers are strongly depleted at DSB hotspots where the DSB-positioning protein PRDM9 fails to bind to the unbroken homologous chromosome, revealing that PRDM9 also functions to promote homologue-templated repair. Our results show that complex non-crossovers are much rarer in mice than humans, consistent with complex events arising from accumulated non-programmed DNA damage. Unexpectedly, we also find that GC-biased gene conversion is restricted to non-crossover tracts containing only one mismatch. These results demonstrate that local genetic diversity profoundly alters meiotic repair pathway decisions via at least two distinct mechanisms, impacting genome evolution and Prdm9-related hybrid infertility.

Unified single-cell analysis of testis gene regulation and pathology in five mouse strains.

To fully exploit the potential of single-cell functional genomics in the study of development and disease, robust methods are needed to simplify the analysis of data across samples, time-points and individuals. Here we introduce a model-based factor analysis method, SDA, to analyze a novel 57,600 cell dataset from the testes of wild-type mice and mice with gonadal defects due to disruption of the genes Mlh3, Hormad1, Cul4a or Cnp. By jointly analyzing mutant and wild-type cells we decomposed our data into 46 components that identify novel meiotic gene-regulatory programs, mutant-specific pathological processes, and technical effects, and provide a framework for imputation. We identify, de novo, DNA sequence motifs associated with individual components that define temporally varying modes of gene expression control. Analysis of SDA components also led us to identify a rare population of macrophages within the seminiferous tubules of Mlh3-/- and Hormad1-/- mice, an area typically associated with immune privilege.

Microsurgery Competency During Plastic Surgery Residency: An Objective Skills Assessment of an Integrated Residency Training Program.

Objective: Microsurgical education is an integral aspect of plastic surgery training. Like most traditional surgical education models, microsurgical skills are taught on an apprenticeship model. This study aims at evaluating microsurgery skill acquisition within an integrated plastic surgery residency using electromagnetic hand-motion analysis and a global rating scale. Methods: This is a cross-sectional study of an integrated plastic surgery residency program. Participants performed microsurgical arterial anastomoses on cryopreserved rat aortas. Hand-motion analysis was recorded using a trakSTAR hand-motion tracker. Total time to complete the task, number of hand movements, and path length (mm) were recorded. Participant videos were graded using a subjective global rating scale (scored 0-100). Results: The data demonstrated construct validity, as hand-motion analysis outcome measures statistically varied according to the level of skill. Mean global rating scale scores increased with level of experience but lacked statistical significance. Conclusions: These data suggest that the objective assessment of hand motion is a valid tool for the evaluation of microsurgical skill. It is more accurate and reflective of the level of skill than a global rating scale. Identifying the predictive validity of hand-motion analysis will be a useful tool to establish clinical safe training and practice thresholds, and the application of both assessment tools simultaneously can yield better evaluation.

A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis.

PRDM9 binding localizes almost all meiotic recombination sites in humans and mice. However, most PRDM9-bound loci do not become recombination hotspots. To explore factors that affect binding and subsequent recombination outcomes, we mapped human PRDM9 binding sites in a transfected human cell line and measured PRDM9-induced histone modifications. These data reveal varied DNA-binding modalities of PRDM9. We also find that human PRDM9 frequently binds promoters, despite their low recombination rates, and it can activate expression of a small number of genes including CTCFL and VCX. Furthermore, we identify specific sequence motifs that predict consistent, localized meiotic recombination suppression around a subset of PRDM9 binding sites. These motifs strongly associate with KRAB-ZNF protein binding, TRIM28 recruitment, and specific histone modifications. Finally, we demonstrate that, in addition to binding DNA, PRDM9's zinc fingers also mediate its multimerization, and we show that a pair of highly diverged alleles preferentially form homo-multimers.

The Benslimane's Artistic Model for Females' Gaze Beauty: An Original Assessment Tool.

BACKGROUND: The aim of this paper is to analyze the aesthetic characteristics of the human females' gaze using anthropometry and to present an artistic model to represent it: "The Frame Concept." In this model, the eye fissure represents a painting, and the most peripheral shadows around it represent the frame of this painting. The narrower the frame, the more aesthetically pleasing and youthful the gaze appears. MATERIALS AND METHOD: This study included a literature review of the features that make the gaze appear attractive. Photographs of models with attractive gazes were examined, and old photographs of patients were compared to recent photographs. The frame ratio was defined by anthropometric measurements of modern portraits of twenty consecutive Miss World winners. The concept was then validated for age and attractiveness across centuries by analysis of modern female photographs and works of art acknowledged for portraying beautiful young and older women in classical paintings. RESULTS: The frame height inversely correlated with attractiveness in modern female portrait photographs. The eye fissure frame ratio of modern idealized female portraits was similar to that of beautiful female portraits idealized by classical artists. In contrast, the eye fissure frames of classical artists' mothers' portraits were significantly wider than those of beautiful younger women. CONCLUSION: The Frame Concept is a valid artistic tool that provides an understanding of both the aesthetic and aging characteristics of the female periorbital region, enabling the practitioner to plan appropriate aesthetic interventions. LEVEL OF EVIDENCE III: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the A3 online Instructions to Authors. www.springer.com/00266 .

Effect of Microvascular Anastomosis Technique on End Product Outcome in Simulated Training: A Prospective Blinded Randomized Controlled Trial.

Background The aim of this article is to evaluate the difference in skills acquisition of two end-to-end microvascular anastomosis techniques-the triangulation and biangulation-in early microsurgery training. Method In this study, 32 candidates ranging from medical students to higher surgical trainees underwent a 5-day basic microsurgery course. On days 3 and 5 of the course, candidates performed two end-to-end anastomoses on cryopreserved rat aortas. One anastomosis was performed using the biangulation technique and the other using the triangulation technique. Candidates were randomized to the order of technique performed. Structural patency, errors performed, and suture distribution were evaluated randomly by a blinded reviewer using the anastomosis lapse index score and ImageJ (U.S. National Institutes of Health, Bethesda, MD) Software. Results A total of 128 anastomoses were evaluated during the study period. A total of six anastomoses performed with the biangulation technique, and four anastomoses with the triangulation technique, were physically occluded on day 3 of the course. On day 5, two biangulation technique anastomoses and one triangulation technique produced a nonpatent outcome. There was a statistically significant difference of patency rate between the 2 days of evaluation confirming evidence of skill acquisition but no statistically significant difference between the two techniques in relation to anastomotic patency, errors performed, or suture placement quality. Conclusion The biangulation and triangulation techniques of microvascular anastomosis produce similar outcomes in relation to vessel structural patency and quality of anastomosis when taught in early stages of microsurgery training. Our results suggest that both techniques are equally suitable in training novices, basic microsurgical skills.

Twelve tips for postgraduate or undergraduate medics building a basic microsurgery simulation training course.

Microsurgery is used in a variety of surgical specialties, including Plastic Surgery, Maxillofacial Surgery, Ophthalmic Surgery, Otolaryngology and Neurosurgery. It is considered one of the most technically challenging fields of surgery. Microsurgical skills demand fine, precise and controlled movements, and microsurgical skill acquisition has a steep initial learning curve. Microsurgical simulation provides a safe environment for skill acquisition before operating clinically. The traditional starting point for anyone wanting to pursue microsurgery is a basic simulation training course. We present twelve tips for postgraduate and undergraduate medics on how to set up and run a basic ex-vivo microsurgery simulation training course suitable for their peers.

Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice.

The DNA-binding protein PRDM9 directs positioning of the double-strand breaks (DSBs) that initiate meiotic recombination in mice and humans. Prdm9 is the only mammalian speciation gene yet identified and is responsible for sterility phenotypes in male hybrids of certain mouse subspecies. To investigate PRDM9 binding and its role in fertility and meiotic recombination, we humanized the DNA-binding domain of PRDM9 in C57BL/6 mice. This change repositions DSB hotspots and completely restores fertility in male hybrids. Here we show that alteration of one Prdm9 allele impacts the behaviour of DSBs controlled by the other allele at chromosome-wide scales. These effects correlate strongly with the degree to which each PRDM9 variant binds both homologues at the DSB sites it controls. Furthermore, higher genome-wide levels of such 'symmetric' PRDM9 binding associate with increasing fertility measures, and comparisons of individual hotspots suggest binding symmetry plays a downstream role in the recombination process. These findings reveal that subspecies-specific degradation of PRDM9 binding sites by meiotic drive, which steadily increases asymmetric PRDM9 binding, has impacts beyond simply changing hotspot positions, and strongly support a direct involvement in hybrid infertility. Because such meiotic drive occurs across mammals, PRDM9 may play a wider, yet transient, role in the early stages of speciation.

Effects of habitual physical activity on microsurgical performance.

We investigated the effect of physical activity on microsurgical performance. Forty novice candidates and 6 expert controls did a series of consecutive end-to-end microvascular anastomoses. To assess performance, we did a hand motion analysis and correlated the results with levels of habitual physical activity. Higher levels of activity in the novice candidates correlated with slower completion of anastomosis for medical students on day 1 (p=0.0035) and day 5 (p=0.0003). The same pattern was seen for postgraduate trainees on day 1 (p=0.024) and day 5 (p=0.0063). Higher level of activity also correlated with an increase in path length (total distance travelled and direction of travel) and in total movements on day 1 for medical students (p=0.016 and p=0.0021, respectively), and in total path length on day 1 for postgraduate trainees (p=0.0305).

Non-crossover gene conversions show strong GC bias and unexpected clustering in humans.

Although the past decade has seen tremendous progress in our understanding of fine-scale recombination, little is known about non-crossover (NCO) gene conversion. We report the first genome-wide study of NCO events in humans. Using SNP array data from 98 meioses, we identified 103 sites affected by NCO, of which 50/52 were confirmed in sequence data. Overlap with double strand break (DSB) hotspots indicates that most of the events are likely of meiotic origin. We estimate that a site is involved in a NCO at a rate of 5.9 × 10(-6)/bp/generation, consistent with sperm-typing studies, and infer that tract lengths span at least an order of magnitude. Observed NCO events show strong allelic bias at heterozygous AT/GC SNPs, with 68% (58-78%) transmitting GC alleles (p = 5 × 10(-4)). Strikingly, in 4 of 15 regions with resequencing data, multiple disjoint NCO tracts cluster in close proximity (∼20-30 kb), a phenomenon not previously seen in mammals.

Recombination in the human Pseudoautosomal region PAR1.

The pseudoautosomal region (PAR) is a short region of homology between the mammalian X and Y chromosomes, which has undergone rapid evolution. A crossover in the PAR is essential for the proper disjunction of X and Y chromosomes in male meiosis, and PAR deletion results in male sterility. This leads the human PAR with the obligatory crossover, PAR1, to having an exceptionally high male crossover rate, which is 17-fold higher than the genome-wide average. However, the mechanism by which this obligatory crossover occurs remains unknown, as does the fine-scale positioning of crossovers across this region. Recent research in mice has suggested that crossovers in PAR may be mediated independently of the protein PRDM9, which localises virtually all crossovers in the autosomes. To investigate recombination in this region, we construct the most fine-scale genetic map containing directly observed crossovers to date using African-American pedigrees. We leverage recombination rates inferred from the breakdown of linkage disequilibrium in human populations and investigate the signatures of DNA evolution due to recombination. Further, we identify direct PRDM9 binding sites using ChIP-seq in human cells. Using these independent lines of evidence, we show that, in contrast with mouse, PRDM9 does localise peaks of recombination in the human PAR1. We find that recombination is a far more rapid and intense driver of sequence evolution in PAR1 than it is on the autosomes. We also show that PAR1 hotspot activities differ significantly among human populations. Finally, we find evidence that PAR1 hotspot positions have changed between human and chimpanzee, with no evidence of sharing among the hottest hotspots. We anticipate that the genetic maps built and validated in this work will aid research on this vital and fascinating region of the genome.

Development of a five-day basic microsurgery simulation training course: a cost analysis.

The widespread use of microsurgery in numerous surgical fields has increased the need for basic microsurgical training outside of the operating room. The traditional start of microsurgical training has been in undertaking a 5-day basic microsurgery course. In an era characterised by financial constraints in academic and healthcare institutions as well as increasing emphasis on patient safety, there has been a shift in microsurgery training to simulation environments. This paper reviews the stepwise framework of microsurgical skill acquisition providing a cost analysis of basic microsurgery courses in order to aid planning and dissemination of microsurgical training worldwide.

Towards a global understanding and standardisation of education and training in microsurgery.

With an increasing emphasis on microsurgery skill acquisition through simulated training, the need has been identified for standardised training programmes in microsurgery. We have reviewed microsurgery training courses available across the six continents of the World. Data was collected of relevant published output from PubMed, MEDLINE (Ovid), and EMBASE (Ovid) searches, and from information available on the Internet of up to six established microsurgery course from each of the six continents of the World. Fellowships and courses that concentrate on flap harvesting rather than microsurgical techniques were excluded. We identified 27 centres offering 39 courses. Total course length ranged from 20 hours to 1,950 hours. Student-to-teacher ratios ranged from 2:1 to 8:1. Only two-thirds of courses offered in-vivo animal models. Instructions in microvascular end-to-end and end-to-side anastomoses were common, but peripheral nerve repair or free groin flap transfer were not consistently offered. Methods of assessment ranged from no formal assessment, where an instructor monitored and gave instant feedback, through immediate assessment of patency and critique on quality of repair, to delayed re-assessment of patency after a 12 to 24 hours period. Globally, training in microsurgery is heterogeneous, with variations primarily due to resource and regulation of animal experimentation. Despite some merit to diversity in curricula, there should be a global minimum standard for microsurgery training.

Assessment of microsurgery competency-where are we now?

In the last decade surgical training is being revolutionized by two novel concepts that have been introduced to almost all branches of surgery including and most recently to microsurgery. These two concepts are: objective assessments of surgical skills and the nurturing of surgical skills in a simulation laboratory setting. Acquiring surgical skills in the laboratory setting can help move the microsurgical learning curve from the patient to the laboratory and this will in turn improve patient safety. In order to optimize microsurgical training through a competency based training programme, it is imperative for microsurgical educators to understand microsurgical skill acquisition. This requires accurate objective assessment tools that can define and quantify microsurgical competency. This article aims to review the current literature on the various objective assessment tools adapted for microsurgery and attempt to identify the gaps that need to be addressed by research in microsurgical education to establish the ideal objective assessment tool.

Epidermal repair results from activation of follicular and epidermal progenitor keratinocytes mediated by a growth factor cascade.

Reepithelialization of human suction blister wounds was examined in five normal human volunteers over a period of 14 days postwounding to understand the control of keratinocyte migration, proliferation, and differentiation in acute wound healing in a controlled model. The hypothesis that morphological changes and progenitor activation result from altered cytokines and growth factor expression [in particular interleukin-1 beta (IL-1beta), interleukin-6 (IL-6), transforming growth factor alpha (TGF-alpha), TGF-beta 1, and keratinocyte growth factor] was tested using semiquantitative immunohistochemistry combined with reverse transcriptase-polymerase chain reaction of samples from the blister roof, edge, and base. Parallel changes in keratin expression were examined using a wide range of well-established antibodies to multiple keratins and in situ hybridization for keratin 16 (K16), a marker of the hyperproliferative (mucoregenerative) phenotype. Longitudinal morphological, semiquantitative cytokine and growth factor expression, and histometric histone and cytokeratin profiles suggest three phases to reepithelialization: phase 1, or the acute activation phase, early in the first 24 hours postwounding is characterized by epidermal expression of IL-1beta and IL-6, and dermal expression of TGF-beta1, as basal, upper outer root sheath, and putative interfollicular transit amplifying keratinocytes become committed to mitosis; phase 2, or the early activation phase, late in the second 24 hours postwounding, characterized by epidermal expression of TGF-alpha and IL-6 with concurrent suprabasal K16 expression and migration with continued proliferation, and dermal expression of keratinocyte growth factor and IL-6; and phase 3 or restitution over the following 2 weeks, characterized by the return of normal homeostasis, including bulge activation as evidenced by K19 expression.