A guide to naming human non-coding RNA genes.

Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.

Detection of male genital schistosomiasis (MGS) associated with human, zoonotic and hybrid schistosomes in Southern Malawi.

BACKGROUND: Male Genital Schistosomiasis (MGS) remains an often-overlooked chronic sequela of urogenital schistosomiasis in endemic areas of sub-Saharan Africa. As part of a 2-year longitudinal study on Hybridization of UroGenital Schistosomiasis (HUGS) in Malawi, a MGS sub-study was conducted to assess whether hybrid schistosomes were incriminated. METHODS: During recruitment, demographic, health and socio-economic data were collected through individual questionnaire interviews in Mthawira community from Nsanje District along Shire River and Samama community from Mangochi District along Lake Malawi shoreline. Urine and semen samples were collected and analysed to determine the identity of schistosome infection. Urine filtration and microscopy, direct microscopy of semen and its sediments (after centrifugation) were performed. Thereafter, the sediments were examined by molecular DNA analysis with a novel two-tube real-time PCR assay. The participants were also screened for Human papilloma virus (HPV) and other sexually transmitted infections (STIs). RESULTS: Twenty-two men were recruited for the sub-study, 8 in Nsanje District and 14 in Mangochi District, with a median age of 22.0 years. By microscopy, ten (45.7%) participants had Schistosoma ova in their urine, 11 (50.0%) in semen while 16 (72.7%) were positive by real-time PCR. One participant had both S. haematobium and S. mattheei ova in his semen, three showed symptoms, and one had a mixed infection of S. mansoni and possible S. haematobium-S. mattheei hybrid. Twelve men had detectable high-risk HPV serotypes 16, 18 and others while six had Trichomonas vaginalis and other STIs. CONCLUSION: Zoonotic and hybrid schistosomes can cause MGS similar to human schistosomes, which can be co-infected with HPV and STIs, thereby posing a new challenge in diagnosis, management and control measures in resource poor settings. Increased awareness of these infections among local communities and primary healthcare workers and improvement of disease management are needed and advocated.

Rapid identification of mosquito species and age by mass spectrometric analysis.

BACKGROUND: A rapid, accurate method to identify and to age-grade mosquito populations would be a major advance in predicting the risk of pathogen transmission and evaluating the public health impact of vector control interventions. Whilst other spectrometric or transcriptomic methods show promise, current approaches rely on challenging morphological techniques or simple binary classifications that cannot identify the subset of the population old enough to be infectious. In this study, the ability of rapid evaporative ionisation mass spectrometry (REIMS) to identify the species and age of mosquitoes reared in the laboratory and derived from the wild was investigated. RESULTS: The accuracy of REIMS in identifying morphologically identical species of the Anopheles gambiae complex exceeded 97% using principal component/linear discriminant analysis (PC-LDA) and 84% based on random forest analysis. Age separation into 3 different age categories (1 day, 5-6 days, 14-15 days) was achieved with 99% (PC-LDA) and 91% (random forest) accuracy. When tested on wild mosquitoes from the UK, REIMS data could determine the species and age of the specimens with accuracies of 91 and 90% respectively. CONCLUSIONS: The accuracy of REIMS to resolve the species and age of Anopheles mosquitoes is comparable to that achieved by infrared spectroscopy approaches. The processing time and ease of use represent significant advantages over current, dissection-based methods. Importantly, the accuracy was maintained when using wild mosquitoes reared under differing environmental conditions, and when mosquitoes were stored frozen or desiccated. This high throughput approach thus has potential to conduct rapid, real-time monitoring of vector populations, providing entomological evidence of the impact of alternative interventions.

The importance of place-kicking in Women's International Rugby Union.

Despite the growing popularity of women's rugby, there is a lack of research understanding the contribution of place-kicking to match outcomes. This study aims to establish the characteristics and contribution of place-kicking to women's international Rugby Union and evaluate the performance of place-kickers while accounting for factors that contribute to kick difficulty. Data from 674 place-kicks across 80 matches were analysed. A binomial generalised linear mixed model (GLMM) was used to predict the probability of kick success. 60.5% of place-kicks were successful, and they contributed 23.9% of all points scored; conversions accounted for 16.8% and penalties 7.1%. Kick success percentages for conversions (56.9%) and penalties (78.3%) significantly differed (p < 0.01). Kick distance and angle were significant (p < 0.01) predictors of kick success and the GLMM had a prediction accuracy of 73.6%. The performance rankings of kickers changed when comparing observed and expected success, highlighting the need to consider contextual factors contributing to kick difficulty when evaluating performance. The GLMM results provide valuable insights for coaches and players to make informed decisions, for example, whether to attempt a place-kick when a penalty is awarded, by enabling predictions of place-kick success. This could enhance a team's chances of winning matches.

Post-traumatic stress disorder is more likely in younger patients undergoing lower limb arthroplasty: impact on function and quality of life.

INTRODUCTION: The aim of this study was to assess whether PTSD was associated with preoperative and/or postoperative joint-specific function and health-related quality of life (HRQoL) in patients undergoing total hip arthroplasty (THA) and total knee arthroplasty (TKA) and whether there were associated preoperative factors. METHODS: A retrospective study was conducted at a single centre using an established arthroplasty database over a 2-year period. Patients undergoing THA and TKA completed pre and 1-year postoperative Oxford hip/knee scores and EuroQoL questionnaire (EQ-5D) to assess joint specific function and HRQoL. Postoperatively, patients completed the self-reported PTSD Checklist for DSM-5 (PCL-5) questionnaire where a score of 31 or greater was used to determine a provisional diagnosis of PTSD. RESULTS: There were 1244 THA and 1356 TKA patients, of which 42 (3.4%) and 54 (4.0%) had a PCL-5 score of ≥ 31, respectively (PTSD groups). Younger age was associated (p < 0.001) with PTSD for both THA (mean difference (MD) 9.9, 95%CI 6.7-13.0) and TKA (MD 4.6, 95%CI 2.2-6.9), which remained significant when adjusting for confounding variables (THA: p < 0.001; TKA: p = 0.020). The preoperative Oxford (THA:MD 4.9, p < 0.001; TKA:MD 5.7, p < 0.001) and EQ-5D scores (THA:MD 0.378, p < 0.001; TKA:MD 0.276, p < 0.001) were significantly worse in the PTSD groups. Age (AUC 73.8%, p < 0.001) and EQ-5D (AUC 72.9%, p < 0.001) were independent factors that were predictive of PTSD in patients undergoing THA and TKA, respectively. When adjusting for confounding variables, PTSD was clinically and statistically significantly (p < 0.001) associated with a lower improvement in the Oxford (THA:MD 9.3; TKA:MD 10.0) and EQ-5D (THA:MD 0.375; TKA:MD 0.293) scores. CONCLUSIONS: One in 25 patients met a provisional PTSD diagnosis; they were younger and had worse preoperative and improvement in postoperative joint specific function and HRQoL. Age and EQ-5D could be used to identify patients at risk.

Quo vadis microRNAs?

Since 2002, published miRNAs have been collected and named by the online repository miRBase. However, with 11 000 annual publications this has become challenging. Recently, four specialized miRNA databases were published, addressing particular needs for diverse scientific communities. This development provides major opportunities for the future of miRNA annotation and nomenclature.

Gastrointestinal parasites in captive olive baboons in a UK safari park.

From the safety inside vehicles, Knowsley Safari offers visitors a close-up encounter with captive olive baboons. As exiting vehicles may be contaminated with baboon stool, a comprehensive coprological inspection was conducted to address public health concerns. Baboon stools were obtained from vehicles, and sleeping areas, inclusive of video analysis of baboon­vehicle interactions. A purposely selected 4-day sampling period enabled comparative inspections of 2662 vehicles, with a total of 669 baboon stools examined (371 from vehicles and 298 from sleeping areas). As informed by our pilot study, front-line diagnostic methods were: QUIK-CHEK rapid diagnostic test (RDT) (Giardia and Cryptosporidium), Kato­Katz coproscopy (Trichuris) and charcoal culture (Strongyloides). Some 13.9% of vehicles were contaminated with baboon stool. Prevalence of giardiasis was 37.4% while cryptosporidiosis was <0.01%, however, an absence of faecal cysts by quality control coproscopy, alongside lower than the expected levels of Giardia-specific DNA, judged RDT results as misleading, grossly overestimating prevalence. Prevalence of trichuriasis was 48.0% and strongyloidiasis was 13.7%, a first report of Strongyloides fuelleborni in UK. We advise regular blanket administration(s) of anthelminthics to the colony, exploring pour-on formulations, thereafter, smaller-scale indicator surveys would be adequate.

Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

Rfam is a database of RNA families where each of the 3444 families is represented by a multiple sequence alignment of known RNA sequences and a covariance model that can be used to search for additional members of the family. Recent developments have involved expert collaborations to improve the quality and coverage of Rfam data, focusing on microRNAs, viral and bacterial RNAs. We have completed the first phase of synchronising microRNA families in Rfam and miRBase, creating 356 new Rfam families and updating 40. We established a procedure for comprehensive annotation of viral RNA families starting with Flavivirus and Coronaviridae RNAs. We have also increased the coverage of bacterial and metagenome-based RNA families from the ZWD database. These developments have enabled a significant growth of the database, with the addition of 759 new families in Rfam 14. To facilitate further community contribution to Rfam, expert users are now able to build and submit new families using the newly developed Rfam Cloud family curation system. New Rfam website features include a new sequence similarity search powered by RNAcentral, as well as search and visualisation of families with pseudoknots. Rfam is freely available at https://rfam.org.

ON LIVER FLUKE (FASCIOLA HEPATICA) IN CAPTIVE VICUÑAS (VICUGNA VICUGNA) AT KNOWSLEY SAFARI, PRESCOT, UNITED KINGDOM.

Knowsley Safari (KS), Prescot, United Kingdom houses a variety of captive exotic ungulates. As part of their animal welfare plan, a prospective coprological survey was undertaken for liver fluke. In June 2021, 330 fecal samples, representative of 18 exotic ungulate species, were processed by sedimentation and filtration, with examination by coproscopy. Finding fascioliasis in all five vicuña alone, with fecal egg counts ranging from one to eight eggs per gram, anthelminthic treatment was attempted twice, with three coprological reviews. While the first anthelminthic treatment (oxyclozanide) was equivocal, the second anthelminthic treatment (triclabendazole) was proven effective upon two later follow-ups. An initial malacological survey of 16 freshwater sites in KS, first found Galba truncatula at two sites in June 2021, then upon more extensive searching subsequently within the vicuña's enclosure. It appears that F. hepatica was locally acquired, being the first report of fascioliasis within captive vicuñas in the United Kingdom. To develop a better fluke-management plan, regular coprological and malacological surveillance is justified, perhaps with molecular xenomonitoring of snails, alongside prompt administration of appropriate flukicide as required.

Predicting long-term trends in inflammatory neuropathy outcome measures using latent class modelling.

Immunoglobulin (Ig) is used to treat chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) and multifocal motor neuropathy with conduction block (MMNCB). Regular infusions may be used for symptom control. Disease activity is monitored with clinical outcome measurements. We examined outcome measure variation during clinically stable periods in Ig-treated CIDP and MMNCB patients. We explored utility of serial outcome measurement in long-term outcome prediction. Retrospective longitudinal analysis of a single neuroscience centre's Ig-treated CIDP and MMNCB patients, 2009-2020, was performed. Mean and percentage change for grip strength, Rasch-built overall disability scales (RODS) and MRC sum scores (MRC-SS) during periods of clinical stability were compared to score-specific minimal clinically important differences (MCID). Latent class mixed modelling (LCMM) was used to identify longitudinal trends and factors influencing long-term outcome. We identified 85 CIDP and 23 MMNCB patients (1423 datapoints; 5635 treatment-months). Group-averaged outcome measures varied little over time. Intra-individual variation exceeded MCID for RODS in 44.2% CIDP and 16.7% MMNCB datapoints, grip strength in 10.6% (CIDP) and 8.8%/27.2% (MMNCB right/left hand) and MRC-SS in 43.5% (CIDP) and 20% (MMNCB). Multivariate LCMM identified subclinical trends towards improvement (32 patients) and deterioration (73 patients) in both cohorts. At baseline, CIDP 'deteriorators' were older than 'improvers' (66.2 vs 57 years, P = .025). No other individual factors predicted categorisation. The best model for 'deteriorator' identification was contiguous sub-MCID decline in more than one outcome measure (CIDP: sensitivity 74%, specificity 59%; MMNCB: sensitivity 73%, specificity 88%). Outcome measure interpretation determines therapeutic decision-making in Ig-dependent neuropathy patients, but intra-individual variation is common, often exceeding MCID. Here we show sub-MCID contiguous changes in more than one outcome measurement are a better predictor of long-term outcome.

Should Deep-Sequenced Amplicons Become the New Gold Standard for Analyzing Malaria Drug Clinical Trials?

Regulatory clinical trials are required to ensure the continued supply and deployment of effective antimalarial drugs. Patient follow-up in such trials typically lasts several weeks, as the drugs have long half-lives and new infections often occur during this period. "Molecular correction" is therefore used to distinguish drug failures from new infections. The current WHO-recommended method for molecular correction uses length-polymorphic alleles at highly diverse loci but is inherently poor at detecting low-density clones in polyclonal infections. This likely leads to substantial underestimates of failure rates, delaying the replacement of failing drugs with potentially lethal consequences. Deep-sequenced amplicons (AmpSeq) substantially increase the detectability of low-density clones and may offer a new "gold standard" for molecular correction. Pharmacological simulation of clinical trials was used to evaluate the suitability of AmpSeq for molecular correction. We investigated the impact of factors such as the number of amplicon loci analyzed, the informatics criteria used to distinguish genotyping "noise" from real low-density signals, the local epidemiology of malaria transmission, and the potential impact of genetic signals from gametocytes. AmpSeq greatly improved molecular correction and provided accurate drug failure rate estimates. The use of 3 to 5 amplicons was sufficient, and simple, nonstatistical criteria could be used to classify recurrent infections as drug failures or new infections. These results suggest AmpSeq is strongly placed to become the new standard for molecular correction in regulatory trials, with potential extension into routine surveillance once the requisite technical support becomes established.

miRBase: from microRNA sequences to function.

miRBase catalogs, names and distributes microRNA gene sequences. The latest release of miRBase (v22) contains microRNA sequences from 271 organisms: 38 589 hairpin precursors and 48 860 mature microRNAs. We describe improvements to the database and website to provide more information about the quality of microRNA gene annotations, and the cellular functions of their products. We have collected 1493 small RNA deep sequencing datasets and mapped a total of 5.5 billion reads to microRNA sequences. The read mapping patterns provide strong support for the validity of between 20% and 65% of microRNA annotations in different well-studied animal genomes, and evidence for the removal of >200 sequences from the database. To improve the availability of microRNA functional information, we are disseminating Gene Ontology terms annotated against miRBase sequences. We have also used a text-mining approach to search for microRNA gene names in the full-text of open access articles. Over 500 000 sentences from 18 542 papers contain microRNA names. We score these sentences for functional information and link them with 12 519 microRNA entries. The sentences themselves, and word clouds built from them, provide effective summaries of the functional information about specific microRNAs. miRBase is publicly and freely available at http://mirbase.org/.

Large-scale profiling of noncoding RNA function in yeast.

Noncoding RNAs (ncRNAs) are emerging as key regulators of cellular function. We have exploited the recently developed barcoded ncRNA gene deletion strain collections in the yeast Saccharomyces cerevisiae to investigate the numerous ncRNAs in yeast with no known function. The ncRNA deletion collection contains deletions of tRNAs, snoRNAs, snRNAs, stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs) and other annotated ncRNAs encompassing 532 different individual ncRNA deletions. We have profiled the fitness of the diploid heterozygous ncRNA deletion strain collection in six conditions using batch and continuous liquid culture, as well as the haploid ncRNA deletion strain collections arrayed individually onto solid rich media. These analyses revealed many novel environmental-specific haplo-insufficient and haplo-proficient phenotypes providing key information on the importance of each specific ncRNA in every condition. Co-fitness analysis using fitness data from the heterozygous ncRNA deletion strain collection identified two ncRNA groups required for growth during heat stress and nutrient deprivation. The extensive fitness data for each ncRNA deletion strain has been compiled into an easy to navigate database called Yeast ncRNA Analysis (YNCA). By expanding the original ncRNA deletion strain collection we identified four novel essential ncRNAs; SUT527, SUT075, SUT367 and SUT259/691. We defined the effects of each new essential ncRNA on adjacent gene expression in the heterozygote background identifying both repression and induction of nearby genes. Additionally, we discovered a function for SUT527 in the expression, 3' end formation and localization of SEC4, an essential protein coding mRNA. Finally, using plasmid complementation we rescued the SUT075 lethal phenotype revealing that this ncRNA acts in trans. Overall, our findings provide important new insights into the function of ncRNAs.

Enhanced genome assembly and a new official gene set for Tribolium castaneum.

BACKGROUND: The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality. RESULTS: Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI. CONCLUSIONS: The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.

A Computer Modelling Approach To Evaluate the Accuracy of Microsatellite Markers for Classification of Recurrent Infections during Routine Monitoring of Antimalarial Drug Efficacy.

Antimalarial drugs have long half-lives, so clinical trials to monitor their efficacy require long periods of follow-up to capture drug failure that may become patent only weeks after treatment. Reinfections often occur during follow-up, so robust methods of distinguishing drug failures (recrudescence) from emerging new infections are needed to produce accurate failure rate estimates. Molecular correction aims to achieve this by comparing the genotype of a patient's pretreatment (initial) blood sample with that of any infection that occurs during follow-up, with matching genotypes indicating drug failure. We use an in silico approach to show that the widely used match-counting method of molecular correction with microsatellite markers is likely to be highly unreliable and may lead to gross under- or overestimates of the true failure rates, depending on the choice of matching criterion. A Bayesian algorithm for molecular correction was previously developed and utilized for analysis of in vivo efficacy trials. We validated this algorithm using in silico data and showed it had high specificity and generated accurate failure rate estimates. This conclusion was robust for multiple drugs, different levels of drug failure rates, different levels of transmission intensity in the study sites, and microsatellite genetic diversity. The Bayesian algorithm was inherently unable to accurately identify low-density recrudescence that occurred in a small number of patients, but this did not appear to compromise its utility as a highly effective molecular correction method for analyzing microsatellite genotypes. Strong consideration should be given to using Bayesian methodology to obtain accurate failure rate estimates during routine monitoring trials of antimalarial efficacy that use microsatellite markers.

An explanation for the isotopic offset between soil and stem water in a temperate tree species.

A growing number of field studies report isotopic offsets between stem water and its potential sources that prevent the unambiguous identification of plant water origin using water isotopes. We explored the causes of this isotopic offset by conducting a controlled experiment on the temperate tree species Fagus sylvatica. We measured δ2 H and δ18 O of soil and stem water from potted saplings growing on three soil substrates and subjected to two watering regimes. Regardless of substrate, soil and stem water δ2 H were similar only near permanent wilting point. Under moister conditions, stem water δ2 H was 11 ± 3‰ more negative than soil water δ2 H, coherent with field studies. Under drier conditions, stem water δ2 H became progressively more enriched than soil water δ2 H. Although stem water δ18 O broadly reflected that of soil water, soil-stem δ2 H and δ18 O differences were correlated (r = 0.76) and increased with transpiration rates indicated by proxies. Soil-stem isotopic offsets are more likely to be caused by water isotope heterogeneities within the soil pore and stem tissues, which would be masked under drier conditions as a result of evaporative enrichment, than by fractionation under root water uptake. Our results challenge our current understanding of isotopic signals in the soil-plant continuum.