Reuben John Pengelly

Background: Recombination rates can be estimated across the genome, underpinning genetic analyses such as identification of regions under selection. Accurate recombination mapping requires observing a large number of recombination events, necessitating large sample sizes to achieve high resolution. This can be prohibitive to some analyses, so population-based estimates can also be used, leveraging the increasing population genomic data available to researchers. Objective: This study aimed to determine the extent to which population-based recombination maps from different human populations are similar and assess to what extent they can be used interchangeably. Methods: Wavelet analysis was employed to decompose recombination rate signals along a chromosome and evaluate the proportion of variance explained at different scales. This method also enabled the assessment of correlations across scales and identification of regions with high coherence between datasets. The analysis focused on a region of chromosome 22 in human populations of European and African ancestry. Results: Recombination rates are not closely conserved across populations, with the greatest divergence observed at fine scales. Coherence between populations varied significantly across all scales. Conclusion: As recombination maps differ substantially between human populations, for genetic analyses involving recombination maps, it is recommended to use maps specific to the population under study.

Background: Multicystic mesothelioma (MCM) is a rare disease and there is debate about it’s neoplastic nature with a spectrum of disease behaviour and little known about the genomic profile. In contrast, the genomic profile of malignant peritoneal mesothelioma (MPeM) is characterised. Methods: We characterized 24 MCM and 18 MPeM cases across a panel of cancer related regions and expanded to whole-exome sequencing for 11 MCMs. Validation by amplicon sequencing and functional assessment by molecular dynamic simulation were carried out. Kaplan-Meier analysis was carried out to assess recurrence-free survival. Results: Few mutations were identified in MCMs across the panel. Exome sequencing revealed 28 genes mutated in >1 MCM case. We saw significant overrepresentation of mutations in the cohesin complex in SMC3 , SMC1A , and STAG3 . Multiple mutations in SMC3 at codon p.E1144 indicated a mutational hotspot. Molecular dynamics simulations showed mutation at this site impacts the protein function. Amplicon sequencing confirmed hotspot mutations in further MCMs. We observed a significant association ( p = 0.0302) of mutation in SMC3 or SMC1A with disease recurrence. Conclusions: We see recurrent somatic mutations in MCMs particularly at a novel mutational hotspot in SMC3 , consistent with a neoplastic process. Mutations in cohesin complex genes are associated with disease recurrence.

Background and Aims: Research into diabetic foot complications is extensive; it remains challenging to identify critical literature. Evolving interprofessional boundaries, alongside advances in molecular medicine and pathophysiological understanding, necessitates mapping of the scientific literature (corpus). Impact of these advances on podiatric medicine remains unclear. This study explores topics, research performance, and evolution across the literature and disciplines to understand the corpus in its current state.Method: A retrospective‐observational bibliometric analysis examined Web of Science publications using PRISMA search strategy (August 2023) to understand interconnectedness, direction, and intersectionality of subject disciplines, growth areas, and output. Curated phrases and disease focussed classification anchored investigation to diabetic peripheral neuropathy. Qualitative and quantitative approaches analysed publication meta‐data (authors, citations, keywords) to map key concepts and scientific developments.Results: Analysis of 589 records (1991–2023) revealed observational studies as the dominant design. Prominent concepts included risk, polyneuropathy, and prevalence, with authors favouring accessible terms (peripheral neuropathy) across specialisms. Leading research hubs were in England, Demark, USA, Qatar, Germany, and Italy. Diabetic Medicine and Diabetes Care remained the highest‐cited journals, whilst the International Journal of Molecular Science, Cell Stem Cell, and Nature Reviews Neurology provided contemporary insights. Post‐2016, methodological rigour and objectivity increased.Discussion: Recurring topics included enhancing pre‐clinical screening, addressing earlier diagnosis, pain management stratification with medicines optimisation, and reproducibility challenges. Case‐controls increasingly replaced larger prospective, longitudinal study designs to improve diagnostic test accuracy and detection of diabetic neuropathy, particularly for neuropathic pain affecting small nerve fibres. Molecular approaches gained prominence signalling a shift from purely clinically derived approaches. The corpus responded to subjectivity and variable diagnostic criteria by prioritising objectivity. Emerging insights into channelopathies and mitochondrial dysfunction may augment current assessment/screening approaches to refine risk stratification and management strategies.

Exonic sequences contain both protein-coding and RNA splicing information but the interplay of the protein and splicing code is complex and poorly understood. Here, we have studied traditional and auxiliary splicing codes of human exons that encode residues coordinating two essential divalent metals at the opposite ends of the Irving–Williams series, a universal order of relative stabilities of metal–organic complexes. We show that exons encoding Zn²⁺-coordinating amino acids are supported much less by the auxiliary splicing motifs than exons coordinating Ca²⁺. The handicap of the former is compensated by stronger splice sites and uridine-richer polypyrimidine tracts, except for position –3 relative to 3′ splice junctions. However, both Ca²⁺ and Zn²⁺ exons exhibit close-to-constitutive splicing in multiple tissues, consistent with their critical importance for metalloprotein function and a relatively small fraction of expendable, alternatively spliced exons. These results indicate that constraints imposed by metal coordination spheres on RNA splicing have been efficiently overcome by the plasticity of exon–intron architecture to ensure adequate metalloprotein expression.

Background: Diagnostic testing for primary ciliary dyskinesia (PCD) started in 2013 in Palestine. We aimed to describe the diagnostic, genetic and clinical spectrum of the Palestinian PCD population.Methods: Individuals with symptoms suggestive of PCD were opportunistically considered for diagnostic testing: nasal nitric oxide (nNO) measurement, transmission electron microscopy (TEM) and/or PCD genetic panel or whole-exome testing. Clinical characteristics of those with a positive diagnosis were collected close to testing including forced expiratory volume in 1 s (FEV₁) Global Lung Index z-scores and body mass index z-scores.Results: 68 individuals had a definite positive PCD diagnosis, 31 confirmed by genetic and TEM results, 23 by TEM results alone, and 14 by genetic variants alone. 45 individuals from 40 families had 17 clinically actionable variants and four had variants of unknown significance in 14 PCD genes. CCDC39,DNAH11andDNAAF11were the most commonly mutated genes. 100% of variants were homozygous. Patients had a median age of 10.0 years at diagnosis, were highly consanguineous (93%) and 100% were of Arabic descent. Clinical features included persistent wet cough (99%), neonatal respiratory distress (84%) and situs inversus (43%). Lung function at diagnosis was already impaired (FEV₁z-score median −1.90 (−5.0–1.32)) and growth was mostly within the normal range (z-score mean −0.36 (−3.03–2.57). 19% individuals had finger clubbing.Conclusions: Despite limited local resources in Palestine, detailed geno- and phenotyping forms the basis of one of the largest national PCD populations globally. There was notable familial homozygosity within the context of significant population heterogeneity.

Auxilliary splicing sequences in exons, known as enhancers (ESEs) and silencers (ESSs), have been subject to strong selection pressures at the RNA and protein level. The protein component of this splicing code is substantial, recently estimated at ∼50% of the total information within ESEs, but remains poorly understood. The ESE/ESS profiles were previously associated with the Irving-Williams (I-W) stability series for divalent metals, suggesting that the ESE/ESS evolution was shaped by metal binding sites. Here, we have examined splicing activities of exonic sequences that encode protein binding sites for Ca2+, a weak binder in the I-W affinity order. We found that predicted exon inclusion levels for the EF-hand motifs and for Ca2+-binding residues in nonEF-hand proteins were higher than for average exons. For canonical EF-hands, the increase was centred on the EF-hand chelation loop and, in particular, on Ca2+-coordinating residues, with a 1>12>3∼5>9 hierarchy in the 12-codon loop consensus and usage bias at codons 1 and 12. The same hierarchy but a lower increase was observed for noncanonical EF-hands, except for S100 proteins. EF-hand loops preferentially accumulated exon splits in two clusters, one located in their N-terminal halves and the other around codon 12. Using splicing assays and published crosslinking and immunoprecipitation data, we identify candidate trans-acting factors that preferentially bind conserved GA-rich motifs encoding negatively charged amino acids in the loops. Together, these data provide evidence for the high capacity of codons for Ca2+-coordinating residues to be retained in mature transcripts, facilitating their exon-level expansion during eukaryotic evolution.

Ca²⁺-insensitive and -sensitive E1 subunits of the 2-oxoglutarate dehydrogenase complex (OGDHC) regulate tissue-specific NADH and ATP supply by mutually exclusive OGDH exons 4a and 4b. Here we show that their splicing is enforced by distant lariat branch points (dBPs) located near the 5′ splice site of the intervening intron. dBPs restrict the intron length and prevent transposon insertions, which can introduce or eliminate dBP competitors. The size restriction was imposed by a single dominant dBP in anamniotes that expanded into a conserved constellation of four dBP adenines in amniotes. The amniote clusters exhibit taxon-specific usage of individual dBPs, reflecting accessibility of their extended motifs within a stable RNA hairpin rather than U2 snRNA:dBP base-pairing. The dBP expansion took place in early terrestrial species and was followed by a uridine enrichment of large downstream polypyrimidine tracts in mammals. The dBP-protected megatracts permit reciprocal regulation of exon 4a and 4b by uridine-binding proteins, including TIA-1/TIAR and PUF60, which promote U1 and U2 snRNP recruitment to the 5′ splice site and BP, respectively, but do not significantly alter the relative dBP usage. We further show that codons for residues critically contributing to protein binding sites for Ca²⁺ and other divalent metals confer the exon inclusion order that mirrors the Irving-Williams affinity series, linking the evolution of auxiliary splicing motifs in exons to metallome constraints. Finally, we hypothesize that the dBP-driven selection for Ca²⁺-dependent ATP provision by E1 facilitated evolution of endothermy by optimizing the aerobic scope in target tissues.