Behaviour-based assessments in the special forces environment: a procedural review

The South African Special Forces is a grouping of highly trained, motivated and dedicated soldiers who execute specialised tasks that ordinary infantry soldiers are not trained or required to conduct. The milieu in which Special Forces operators function is notoriously challenging as these forces could deploy for a few days or several months or longer in any type of environment. It is therefore essential that the correct candidates be selected to function in these environments. The aim of the officer’s potential assessment (OPA) is thus to select candidates with the physical, cognitive, emotional and psychological fitness to be trained as South African Special Forces operators and officers. The study on which this article is based, explored the development of the behavioural assessments during the South African Special Forces officers’ selection process as a method and model for the review and design of assessment centres from a holistic, detailed perspective.Keywords: Behavioural observation, Special Forces, assessment centres, rating scales, officer

Identification and characterization of a QTL for growth of Fusarium circinatum on pine-based medium

SUPPLEMENTARY FILE S1: HPLC and GC-MS results showing the broad overview and primary metabolites identified in the pine-based media. SUPPLEMENTARY FILE S2: The primer sequences and PCR protocols used to amplify gene regions in this study. SUPPLEMENTARY FILE S3: Reference mapping of F. circinatum Illumina and MinIon raw reads mapped to the genomes of F circinatum KS17 and F. temperatum. SUPPLEMENTARY FILE S4: Genic information of the identified genes and indel region in the QTL region of F. circinatum. InterProScan and gene ontology information are provided for all genes in this region. Further information on the retrotransposons and repeats that are characteristic of the indel within the QTL region is provided.Fusarium circinatum is an economically important pathogen of pine and resides in the Fusarium fujikuroi species complex. Here we investigated the molecular processes underlying growth in F. circinatum by exploring the association between growth and the nutritional environment provided by the pine host. For this purpose, we subjected a mapping population consisting of F. circinatum X F. temperatum hybrid progeny to an analysis of growth rate on a pine-tissue derived medium. These data, together with the available genetic linkage map for F. circinatum, were then used to identify Quantitative Trait Loci (QTLs) associated with growth. The single significant QTL identified was then characterized using the available genome sequences for the hybrid progeny’s parental isolates. This revealed that the QTL localized to two non-homologous regions in the F. circinatum and F. temperatum genomes. For one of these, the F. circinatum parent contained a two-gene deletion relative to the F. temperatum parent. For the other region, the two parental isolates encoded different protein products. Analysis of repeats, G+C content, and repeat-induced point (RIP) mutations further suggested a retrotransposon origin for the two-gene deletion in F. circinatum. Nevertheless, subsequent genome and PCR-based analyses showed that both regions were similarly polymorphic within a collection of diverse F. circinatum. However, we observed no clear correlation between the respective polymorphism patterns and growth rate in culture. These findings support the notion that growth is a complex multilocus trait and raise the possibility that the identified QTL contains multiple small-effect QTLs, of which some might be dependent on the genetic backgrounds. This study improved our current knowledge of the genetic determinants of vegetative growth in F. circinatum and provided an important foundation for determining the genes and processes underpinning its ability to colonize its host environment.The South African Department of Science and Innovation’s South African Research Chair Initiative and the DSI-NRF Centre of Excellence in Plant Health Biotechnology at the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria.https://www.mdpi.com/journal/jofam2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyZoology and Entomolog

Intra-species genomic variation in the pine pathogen Fusarium circinatum

Fusarium circinatum is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of F. circinatum. These genomes were analysed together with previously published genomes of F. circinatum isolates, FSP34 and KS17. Multi-sample variant calling identified a total of 461,683 micro variants (SNPs and small indels) and a total of 1828 macro structural variants of which 1717 were copy number variants and 111 were inversions. The variant density was higher on the sub-telomeric regions of chromosomes. Variant annotation revealed that genes involved in transcription, transport, metabolism and transmembrane proteins were overrepresented in gene sets that were affected by high impact variants. A core genome representing genomic elements that were conserved in all the isolates and a non-redundant pangenome representing all genomic elements is presented. Whole genome alignments showed that an average of 93% of the genomic elements were present in all isolates. The results of this study reveal that some genomic elements are not conserved within the isolates and some variants are high impact. The described genome-scale variations will help to inform novel disease management strategies against the pathogen.DATA AVAILABILTY STATEMENT : The Whole Genome Shotgun project for Fusarium circinatum CMWF1803 has been deposited at DDBJ/ENA/GenBank under the accession JAEHFH000000000. The version described in this paper is version JAEHFH010000000. The Whole Genome Shotgun project for Fusarium circinatum CMWF560 has been deposited at DDBJ/ENA/GenBank under the accession JAEHFI000000000. The version described in this paper is version JAEHFI010000000. The Whole Genome Shotgun project for Fusarium circinatum CMWF567 has been deposited at DDBJ/ENA/GenBank under the accession JADZLS000000000. The version described in this paper is version JADZLS010000000. The Whole Genome Shotgun project for Fusarium circinatum UG27 has been deposited at DDBJ/ENA/ GenBank under the accession JAELVK000000000. The version described in this paper is version JAELVK010000000. The Whole Genome Shotgun project for Fusarium circinatum UG10 has been deposited at DDBJ/ENA/GenBank under the accession JAGJRQ000000000. The version described in this paper is version JAGJRQ010000000.The South African Department of Science and Innovation’s South African Research Chair Initiative and the DSI-NRF Centre of Excellence in Plant Health Biotechnology at the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria.http://www.mdpi.com/journal/jofBiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

A randomized controlled trial of mental health interventions for survivors of systematic violence in Kurdistan, Northern Iraq

BACKGROUND: Experiencing systematic violence and trauma increases the risk of poor mental health outcomes; few interventions for these types of exposures have been evaluated in low resource contexts. The objective of this randomized controlled trial was to assess the effectiveness of two psychotherapeutic interventions, Behavioral Activation Treatment for Depression (BATD) and Cognitive Processing Therapy (CPT), in reducing depression symptoms using a locally adapted and validated version of the Hopkins Symptom Checklist and dysfunction measured with a locally developed scale. Secondary outcomes included posttraumatic stress, anxiety, and traumatic grief symptoms. METHODS: Twenty community mental health workers, working in rural health clinics, were randomly assigned to training in one of the two interventions. The community mental health workers conducted baseline assessments, enrolled survivors of systematic violence based on severity of depression symptoms, and randomly assigned them to treatment or waitlist-control. Blinded community mental health workers conducted post-intervention assessments on average five months later. RESULTS: Adult survivors of systematic violence were screened (N = 732) with 281 enrolled in the trial; 215 randomized to an intervention (114 to BATD; 101 to CPT) and 66 to waitlist-control (33 to BATD; 33 to CPT). Nearly 70% (n = 149) of the intervention participants completed treatment and post-intervention assessments; 53 (80%) waitlist-controls completed post-intervention assessments. Estimated effect sizes for depression and dysfunction were 0.60 and 0.55 respectively, comparing BATD participants to all controls and 0.84 and 0.79 respectively, compared to BATD controls only. Estimated effect sizes for depression and dysfunction were 0.70 and 0.90 respectively comparing CPT participants to all controls and 0.44 and 0.63 respectively compared to CPT controls only. Using a permutation-based hypothesis test that is robust to the model assumptions implicit in regression models, BATD had significant effects on depression (p = .003) and dysfunction (p = .007), while CPT had a significant effect on dysfunction only (p = .004). CONCLUSIONS: Both interventions showed moderate to strong effects on most outcomes. This study demonstrates effectiveness of these interventions in low resource environments by mental health workers with limited prior experience. TRIAL REGISTRATION: ClinicalTrials.Gov NCT00925262. Registered June 3, 2009

Draft genome sequence of Annulohypoxylon stygium, Aspergillus mulundensis, Berkeleyomyces basicola (syn. Thielaviopsis basicola), Ceratocystis smalleyi, two Cercospora beticola strains, Coleophoma cylindrospora, Fusarium fracticaudum, Phialophora cf. hyalina, and Morchella septimelata

Draft genomes of the species Annulohypoxylon stygium, Aspergillus mulundensis, Berkeleyomyces basicola (syn. Thielaviopsis basicola), Ceratocystis smalleyi, two Cercospora beticola strains, Coleophoma cylindrospora, Fusarium fracticaudum, Phialophora cf. hyalina and Morchella septimelata are presented. Both mating types (MAT1-1 and MAT1-2) of Cercospora beticola are included. Two strains of Coleophoma cylindrospora that produce sulfated homotyrosine echinocandin variants, FR209602, FR220897 and FR220899 are presented. The sequencing of Aspergillus mulundensis, Coleophoma cylindrospora and Phialophora cf. hyalina has enabled mapping of the gene clusters encoding the chemical diversity from the echinocandin pathways, providing data that reveals the complexity of secondary metabolism in these different species. Overall these genomes provide a valuable resource for understanding the molecular processes underlying pathogenicity (in some cases), biology and toxin production of these economically important fungi

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants, respectively1-3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Repeat-induced point mutations in the Fusarium fujikuroispecies complex

The Repeat-Induced Point (RIP) mutation pathway is a fungal-specific genome defence mechanism that mitigates the deleterious consequences of repeated motifs and transposable elements (TEs). RIP is an ancient pathway that evolved early in the evolutionary history of fungi. It most likely evolved before the divergence of the fungal subkingdom Dikarya and has been observed in both Ascomycota and certain Basidiomycota. Despite its prevalence, the genetic consequences and taxonomic range of RIP remains ill defined. For these reasons this thesis particularly focusses on fungi representing varying degrees of divergence in order to investigate the influence of RIP on genome evolution, divergence and development of genomic regions underlying important fungal biological traits. The Fusarium fujikuroi species complex (FFSC) represents a diverse assemblage of fungi that are distributed globally. Many of these fungi can cause disease on numerous crops and plants and threaten tree health in both natural and plantations settings. Due to their agricultural importance, and the biological and genomic interest in this taxon, whole genome sequences have been determined for many FFSC species. The availability of this information assembled into chromosome-sized scaffolds allows for unique opportunities to study the occurrence and extent of RIP on a genome-wide level. Moreover, the availability of these genomes, in varying stages of divergence, will prove invaluable in the understanding of the genetic and molecular factors driving genome evolution, lineage divergence, and ultimately speciation. The first chapter of this thesis is a critical review of the literature on the developments made in studying the RIP process in fungi. The different aspects of fungal biology and genome content that can contribute to variation in RIP strength and capabilities are discussed. As this thesis deals with the evolutionary implications of RIP on the FFSC, the current research progress made on RIP in Fusarium lineages is reviewed. Attention is also given to the functional consequences brought about by RIP, particularly how RIP can contribute to reinforcing species boundaries and ultimately drive lineage divergence and speciation. Chapter two introduces The RIPper, a web-based set of tools for genome-wide investigation of RIP in fungi in the phylum Ascomycota. This chapter discusses the development of this software and further demonstrates the ability of this set of software tools to detect the occurrence and extent of RIP in known RIP affected fungal sequences. The work presented in xix Chapter 2 has been published in the journal PeerJ as an application for genome-wide RIP analyses of fungal sequences. Chapter three presents detailed investigation on the extent and occurrence of RIP in the genome of the pitch canker pathogen, Fusarium circinatum and its relatives in the FFSC. Comparative genome-wide RIP analyses were undertaken to determine the influence of RIP on genome divergence amongst these fungi. This chapter provides valuable information on the independent divergence of chromosomes and changes to chromosome architecture brought about by RIP among this economic important group of fungi. The work presented was published in the journal Pathogens. Fusarium pininemorale is a recently recognized member of the American clade of the FFSC and is the focus of chapter 4. Overall, little is known regarding the biology and genetics of this species, even less so for the genetic determinants of host range in the broader American clade of the FFSC. The aim of chapter four was to determine the full genome sequence for F. pininemorale which will allow further studies to investigate genomic aspects of not only genome evolution but will also provide information of its biology and evolution amongst members of the FFSC. The chapter has been published in the journal IMA Fungus. In chapter 5 data on the genome-wide occurrence and extent of RIP in the Ascomycota is presented. This study considered the effects of the RIP amongst these fungi using whole genome sequences. To overcome the typical challenges associated with RIP analyses, genomewide RIP data is produced by using an alignment-free method, based on a sliding-window approach. This study provides valuable information on the taxonomic distribution of RIP amongst the Ascomycetes, occurrence and extent of RIP in regions with TEs and repeats, as well as where RIP occurred due to leakage. This work provides valuable insights on the cumulative influence of RIP and its contribution to chromosome evolution of Ascomycete fungi. This chapter has been submitted to the journal Microorganisms for peer review. The cumulative influence of RIP on the overall base composition in the different genomic regions and sub-genomic compartments of F. circinatum is the focus of chapter six. The results of this study present important information on the manner that RIP drives genomic variation and contributes to the evolution of the genetic landscape and differentiation of diverse sub-genomic compartments of this important fungal pathogen.Thesis (PhD)--University of Pretoria, 2020.National research Foundation of South Africa; The Forestry and Agricultural Biotechnology Institute; Center of Plant Health and Biotechnology; Tree Protection co operative programmeMicrobiology and Plant PathologyPhDRestricte