Perspectives from the 2nd International Post-Tuberculosis Symposium: mobilising advocacy and research for improved outcomes.

In 2020, it was estimated that there were 155 million survivors of TB alive, all at risk of possible post TB disability. The 2nd International Post-Tuberculosis Symposium (Stellenbosch, South Africa) was held to increase global awareness and empower TB-affected communities to play an active role in driving the agenda. We aimed to update knowledge on post-TB life and illness, identify research priorities, build research collaborations and highlight the need to embed lung health outcomes in clinical TB trials and programmatic TB care services. The symposium was a multidisciplinary meeting that included clinicians, researchers, TB survivors, funders and policy makers. Ten academic working groups set their own goals and covered the following thematic areas: 1) patient engagement and perspectives; 2) epidemiology and modelling; 3) pathogenesis of post-TB sequelae; 4) post-TB lung disease; 5) cardiovascular and pulmonary vascular complications; 6) neuromuscular & skeletal complications; 7) paediatric complications; 8) economic-social and psychological (ESP) consequences; 9) prevention, treatment and management; 10) advocacy, policy and stakeholder engagement. The working groups provided important updates for their respective fields, highlighted research priorities, and made progress towards the standardisation and alignment of post-TB outcomes and definitions.

En 2020, il est estimé qu'il y a 155 millions de survivants de la TB dans le monde, tous exposés à un risque d'invalidité post-TB. Le deuxième Symposium International Post-Tuberculose (Stellenbosch, Afrique du Sud) a été organisé dans le but de sensibiliser davantage à l'échelle mondiale et de permettre aux communautés touchées par la TB de contribuer activement à la mise en œuvre de l'agenda. De plus, nous avons entrepris de mettre à jour les connaissances sur la vie et les maladies post-TB, de déterminer les domaines de recherche prioritaires, d'établir des partenariats de recherche et de souligner l'importance d'intégrer les résultats sur la santé pulmonaire dans les essais cliniques et les services de soins de la TB. Le symposium était une réunion de travail pluridisciplinaire rassemblant des praticiens, des chercheurs, des personnes ayant survécu à la TB, des donateurs, des décideurs politiques et d'autres acteurs clés. Dix groupes de travail académiques ont établi leurs propres objectifs et ont abordé les sujets thématiques suivants : 1) engagement et perspectives des patients ; 2) épidémiologie et modélisation ; 3) pathogénie des séquelles post-TB ; 4) maladie pulmonaire post-TB (PTLD, pour l'anglais «post-TB lung disease ¼) ; 5) complications cardiovasculaires et vasculaires pulmonaires ; 6) complications neuromusculaires et squelettiques ; 7) complications pédiatriques ; 8) conséquences économiques, sociales et psychologiques (ESP, pour l'anglais «economic-social and psychological¼) ; 9) prévention, traitement et gestion ; 10) plaidoyer, politique et engagement des parties prenantes. Les groupes de travail académiques ont apporté des mises à jour significatives dans leurs domaines respectifs, ont mis en évidence les priorités de recherche et ont avancé vers la normalisation et l'harmonisation des résultats et des définitions de la post-TB.

Genome assembly of the southern pine beetle (Dendroctonus frontalis Zimmerman) reveals the origins of gene content reduction in Dendroctonus.

Dendroctonus frontalis, also known as southern pine beetle (SPB), represents the most damaging forest pest in the southeastern United States. Strategies to predict, monitor and suppress SPB outbreaks have had limited success. Genomic data are critical to inform on pest biology and to identify molecular targets to develop improved management approaches. Here, we produced a chromosome-level genome assembly of SPB using long-read sequencing data. Synteny analyses confirmed the conservation of the core coleopteran Stevens elements and validated the bona fide SPB X chromosome. Transcriptomic data were used to obtain 39,588 transcripts corresponding to 13,354 putative protein-coding loci. Comparative analyses of gene content across 14 beetle and 3 other insects revealed several losses of conserved genes in the Dendroctonus clade and gene gains in SPB and Dendroctonus that were enriched for loci encoding membrane proteins and extracellular matrix proteins. While lineage-specific gene losses contributed to the gene content reduction observed in Dendroctonus, we also showed that widespread misannotation of transposable elements represents a major cause of the apparent gene expansion in several non-Dendroctonus species. Our findings uncovered distinctive features of the SPB gene complement and disentangled the role of biological and annotation-related factors contributing to gene content variation across beetles.

A reference quality genome assembly for the jewel scarab Chrysina gloriosa.

The jewel scarab Chrysina gloriosa is one of the most charismatic beetles in the United States and is found from the mountains of West Texas to the Southeastern Arizona sky islands. This species is highly sought by professional and amateur collectors worldwide due to its gleaming metallic coloration. However, the impact of the large-scale collection of this beetle on its populations is unknown, and there is a limited amount of genetic information available to make informed decisions about its conservation. As a first step, we present the genome of C. gloriosa, which we reconstructed using a single female specimen sampled from our ongoing effort to document population connectivity and the demographic history of this beetle. Using a combination of long-read sequencing and Omni-C data, we reconstructed the C. gloriosa genome at a near-chromosome level. Our genome assembly consisted of 454 scaffolds spanning 642 MB, with the 10 largest scaffolds capturing 98% of the genome. The scaffold N50 was 72 MB, and the BUSCO score was 95.5%. This genome assembly will be an essential tool to accelerate understanding C. gloriosa biology and help make informed decisions for the conservation of Chrysina and other species with similar distributions in this region. This genome assembly will further serve as a community resource for comparative genomic analysis.

Intravenous Reelin rescues despair-like behavior, Reelin cells in the dentate sub-granular zone, and spleen atrophy in the cyclic corticosterone model of recurring depressive episodes.

Novel antidepressants are predominantly evaluated preclinically in rodent models of chronic stress in which animals experience a single prolonged exposure to chronic stress prior to treatment. Rodent models of a single episode of chronic stress translate poorly to human depressive disorders, which are commonly marked by recurring depressive episodes. Intravenous administration of Reelin has previously been shown to resolve immobility in the forced swim test of rats exposed to a single prolonged exposure to chronic stress. To determine whether Reelin has antidepressant-like properties in a model of recurring depressive episodes, Long-Evans rats (N = 57) were exposed to multiple cycles of chronic stress and stress-free periods before the administration of a single injection of Reelin during the final cycle of chronic stress. The animals then performed in the forced swim test and open field test before the post-mortem evaluation of Reelin cell counts in the sub-granular zone of the dentate gyrus to determine the impact of treatment on hippocampal Reelin levels and spleen white pulp to evaluate the role of Reelin treatment in peripheral inflammation. The results show a single Reelin injection reversed elevated levels of immobility in the forced swim test in both male and female subjects exposed to the cyclic chronic stress model of recurring depressive episodes. Treatment with Reelin also restored Reelin-positive cell counts in the dentate gyrus sub-granular zone and reversed atrophy of spleen white pulp. The results shown here indicate that treatment with Reelin could effectively resolve alterations in forced swim test behavior caused by the cyclic corticosterone model of recurring depressive episodes and that Reelin homeostasis is important for regulating stress-related inflammation. Future preclinical antidepressant research should incorporate models of multiple depressive episodes to improve the translation of preclinical rodent research to human depressive disorders.

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography.

The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

The Genome of the Yellow Mealworm, Tenebrio molitor: It's Bigger Than You Think.

BACKGROUND: Insects are a sustainable source of protein for human food and animal feed. We present a genome assembly, CRISPR gene editing, and life stage-specific transcriptomes for the yellow mealworm, Tenebrio molitor, one of the most intensively farmed insects worldwide. METHODS: Long and short reads and long-range data were obtained from a T. molitor male pupa. Sequencing transcripts from 12 T. molitor life stages resulted in 279 million reads for gene prediction and genetic engineering. A unique plasmid delivery system containing guide RNAs targeting the eye color gene vermilion flanking the muscle actin gene promoter and EGFP marker was used in CRISPR/Cas9 transformation. RESULTS: The assembly is approximately 53% of the genome size of 756.8 ± 9.6 Mb, measured using flow cytometry. Assembly was complicated by a satellitome of at least 11 highly conserved satDNAs occupying 28% of the genome. The injection of the plasmid into embryos resulted in knock-out of Tm vermilion and knock-in of EGFP. CONCLUSIONS: The genome of T. molitor is longer than current assemblies (including ours) due to a substantial amount (26.5%) of only one highly abundant satellite DNA sequence. Genetic sequences and transformation tools for an insect important to the food and feed industries will promote the sustainable utilization of mealworms and other farmed insects.

Measurement of the 2νßß Decay Rate and Spectral Shape of

Neutrinoless double beta decay (0νßß) is a yet unobserved nuclear process that would demonstrate Lepton number violation, a clear evidence of beyond standard model physics. The process two neutrino double beta decay (2νßß) is allowed by the standard model and has been measured in numerous experiments. In this Letter, we report a measurement of 2νßß decay half-life of ^{100}Mo to the ground state of ^{100}Ru of [7.07±0.02(stat)±0.11(syst)]×10^{18} yr by the CUPID-Mo experiment. With a relative precision of ±1.6% this is the most precise measurement to date of a 2νßß decay rate in ^{100}Mo. In addition, we constrain higher-order corrections to the spectral shape, which provides complementary nuclear structure information. We report a novel measurement of the shape factor ξ_{3,1}=0.45±0.03(stat)±0.05(syst) based on a constraint on the ratio of higher-order terms from theory, which can be reliably calculated. This is compared to theoretical predictions for different nuclear models. We also extract the first value for the effective axial vector coupling constant obtained from a spectral shape study of 2νßß decay.

Generation of the iPSC line FINi002-A from a male Parkinson's disease patient carrying compound heterozygous mutations in the PRKN gene.

The most common cause of autosomal recessive familial Parkinson's disease (PD) are mutations in the PRKN/PARK2 gene encoding an E3 ubiquitin protein-ligase PARKIN. We report the generation of an iPSC cell line from the fibroblasts of a male PD patient carrying a common missense variant in exon 7 (p.Arg275Trp), and a 133 kb deletion encompassing exon 8, using transiently-present Sendai virus. The established line displays typical human primed iPSC morphology and expression of pluripotency-associated markers, normal karyotype without SNP array-detectable copy number variations and can give rise to derivatives of all three embryonic germ layers. We envisage the usefulness of this iPSC line, carrying a common and well-studied missense mutation in the RING1 domain of the PARKIN protein, for the elucidation of PARKIN-dependent mechanisms of PD using in vitro and in vivo models.

Tritium Beta Spectrum Measurement and Neutrino Mass Limit from Cyclotron Radiation Emission Spectroscopy.

The absolute scale of the neutrino mass plays a critical role in physics at every scale, from the subatomic to the cosmological. Measurements of the tritium end-point spectrum have provided the most precise direct limit on the neutrino mass scale. In this Letter, we present advances by Project 8 to the cyclotron radiation emission spectroscopy (CRES) technique culminating in the first frequency-based neutrino mass limit. With only a cm^{3}-scale physical detection volume, a limit of m_{ß}<155 eV/c^{2} (152 eV/c^{2}) is extracted from the background-free measurement of the continuous tritium beta spectrum in a Bayesian (frequentist) analysis. Using ^{83m}Kr calibration data, a resolution of 1.66±0.19 eV (FWHM) is measured, the detector response model is validated, and the efficiency is characterized over the multi-keV tritium analysis window. These measurements establish the potential of CRES for a high-sensitivity next-generation direct neutrino mass experiment featuring low background and high resolution.

A chromosome scale assembly of the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), genome.

OBJECTIVE: The tarnished plant bug (TPB), Lygus lineolaris (Palisot de Beauvois) (Hemiptera: Miridae), is a pest damaging many cultivated crops in North America. Although partial transcriptome data are available for this pest, a genome assembly was not available for this species. This assembly of a high-quality chromosome-length genome of TPB is aimed to develop the genetic resources that can provide the foundation required for advancing research on this species. RESULTS: The initial genome of TPB assembled with paired-end nucleotide sequences generated with Illumina technology was scaffolded with Illumina HiseqX reads generated from a proximity ligated (HiC) library to obtain a high-quality genome assembly. The final assembly contained 3963 scaffolds longer than 1 kbp to yield a genome of 599.96 Mbp. The N50 of the TPB genome assembly was 35.64 Mbp and 98.68% of the genome was assembled into 17 scaffolds larger than 1 Mbp. This megabase scaffold number is the same as the number of chromosomes observed in karyotyping of this insect. The TPB genome is known to have high repetitive DNA content, and the reduced assembled genome size compared to flowcytometric estimates of approximately 860 Mbp may be due to the collapsed assembly of highly similar regions.

Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture.

Background: The house cricket, Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry using insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of reports on climate change and biodiversity loss largely driven by agriculture. As with other crops, genetic resources are needed to improve crickets for food and other applications. Methods: We present the first high quality annotated genome assembly of A. domesticus from long read data and scaffolded to chromosome level, providing information needed for genetic manipulation. Results: Gene groups related to immunity were annotated and will be useful for improving value to insect farmers. Metagenome scaffolds in the A. domesticus assembly, including Invertebrate Iridescent Virus 6 (IIV6), were submitted as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of A. domesticus and discuss implications for the food, pharmaceutical, and other industries. RNAi was demonstrated to disrupt the function of the vermilion eye-color gene producing a useful white-eye biomarker phenotype. Conclusions: We are utilizing these data to develop technologies for downstream commercial applications, including more nutritious and disease-resistant crickets, as well as lines producing valuable bioproducts, such as vaccines and antibiotics.

Post-TB health and wellbeing.

TB affects around 10.6 million people each year and there are now around 155 million TB survivors. TB and its treatments can lead to permanently impaired health and wellbeing. In 2019, representatives of TB affected communities attending the '1st International Post-Tuberculosis Symposium´ called for the development of clinical guidance on these issues. This clinical statement on post-TB health and wellbeing responds to this call and builds on the work of the symposium, which brought together TB survivors, healthcare professionals and researchers. Our document offers expert opinion and, where possible, evidence-based guidance to aid clinicians in the diagnosis and management of post-TB conditions and research in this field. It covers all aspects of post-TB, including economic, social and psychological wellbeing, post TB lung disease (PTLD), cardiovascular and pericardial disease, neurological disability, effects in adolescents and children, and future research needs.

Cost analysis of COVID-19 test result notification using an automated messaging system compared to a staff caller practice in Alberta.

SETTING: In Alberta, polymerase chain reaction (PCR) COVID-19 tests were an important step in detecting and isolating contagious individuals throughout the pandemic. Initially, a staff member provided results to all PCR COVID-19 test clients by phone. As the number of tests increased, new approaches were essential for timely result notification. INTERVENTION: An innovative automated IT system was introduced during the pandemic to reduce workloads and support timely result notification. At the time of the COVID-19 test booking and again following swabbing, clients had an option to consent to receive their test results via an automated text or voice message. Prior to implementation, a privacy impact assessment was approved, a pilot was undertaken, and changes to lab information systems were made. OUTCOMES: Health administration data were used in a cost analysis to compare the unique costs associated with the novel automated IT practice (e.g., administration, integration, messages, staffing costs) and a hypothetical staff caller practice (e.g., administration, staffing costs) for negative test results. The costs of sharing 2,161,605 negative test results in 2021 were assessed. The automated IT practice demonstrated a cost savings of $6,272,495 over the staff caller practice. A follow-up analysis determined the cost savings threshold of 46,463 negative tests to break even. IMPLICATIONS: Using an automated IT practice for consenting clients can be a cost-effective approach to reach clients in a timely manner during a pandemic or other instances warranting direct notification. This approach is being explored for test result notification of other communicable diseases in other contexts.

RéSUMé: LIEU: En Alberta, les tests de réaction de polymérisation en chaîne (PCR) pour la COVID-19 ont représenté une étape importante dans la détection et l'isolement des personnes contagieuses tout au long de la pandémie. Au début, un membre du personnel communiquait par téléphone les résultats de tous les tests PCR de la COVID-19 aux usagers et usagères. Avec l'augmentation du nombre de tests, il a absolument fallu trouver de nouvelles façons de communiquer les résultats rapidement. INTERVENTION: Un système de TI automatisé novateur a été introduit durant la pandémie pour alléger la charge de travail et favoriser la communication rapide des résultats des tests. Au moment de la réservation d'un test de dépistage de la COVID-19 et après l'écouvillonnage, les usagers et usagères pouvaient consentir à recevoir leurs résultats via un message texte automatisé ou un message vocal. Avant la mise en œuvre, une évaluation des facteurs relatifs à la vie privée a été approuvée, un projet pilote a été mené, et des changements ont été apportés aux systèmes d'information des laboratoires. RéSULTATS: Les données administratives sanitaires ont servi à effectuer une analyse des coûts visant à comparer les coûts spécifiquement associés à la nouvelle pratique de TI automatisée (p. ex. frais d'administration, d'intégration, de messages, de personnel) et ceux d'une hypothétique pratique d'appel par un membre du personnel (p. ex. frais d'administration, de personnel) pour les tests négatifs. Les coûts de communication des résultats de 2 161 605 tests négatifs en 2021 ont été évalués. La pratique de TI automatisée a représenté des économies de 6 272 495 $ par rapport à la pratique d'appel par un membre du personnel. Selon une analyse de suivi, le seuil de rentabilité était atteint après 46 463 tests négatifs. CONSéQUENCES: L'utilisation d'une pratique de TI automatisée pour les usagers et usagères ayant consenti à cette option peut être une méthode efficace par rapport au coût pour joindre rapidement les usagères et usagers lors d'une pandémie ou dans d'autres cas où une notification directe est justifiée. Cette méthode est explorée pour la communication des résultats de tests d'autres maladies transmissibles dans d'autres contextes.

Exploring the Alberta Health Services COVID-19 provincial public health integrated outbreak prevention, preparedness, management, and response interventions to support congregate and communal living sites in Alberta.

SETTING: On March 17, 2020, a state of public health emergency was declared in Alberta under the Public Health Act in response to the COVID-19 pandemic. Congregate and communal living sites were environments with a high risk of exposure to and transmission of COVID-19. Consequently, provincial efforts to prevent and manage COVID-19 were required and prioritized. INTERVENTION: During the first 9 months of the pandemic, vaccines were unavailable and alternate strategies were used to prevent and manage COVID-19 (e.g., physical distancing, masking, symptom screening, testing, isolating cases). Alberta Health Services worked with local, provincial, and First Nations and Inuit Health Branch stakeholders to deliver interventions to support congregate and communal living sites. Interventions included resources and site visits to support prevention and preparedness, and the creation of a coordinated response line to serve as a single point of contact to access information and services in the event of an outbreak (e.g., guidance, testing, personal protective equipment, reporting). OUTCOMES: Data from an internal monitoring dashboard informed intervention uptake and use. Online survey results found high levels of awareness, acceptability, appropriateness, and use of the interventions among congregate and communal living site administrators (n = 550). Recommendations were developed from reported experiences, challenges, and facilitators, and processes were improved. IMPLICATIONS: Provincially coordinated prevention, preparedness, and outbreak management interventions supported congregate and communal living sites. Efforts to further develop adaptive system-level approaches for prevention and preparedness, in addition to communication and information sharing in complex rapidly changing contexts, could benefit future public health emergencies.

RéSUMé: LIEU: Le 17 mars 2020, un état d'urgence sanitaire a été déclaré en Alberta en vertu de la Loi sur la santé publique pour riposter à la pandémie de COVID-19. Les habitations collectives étaient des environnements qui présentaient un risque élevé d'exposition à la COVID-19 et de transmission du virus. Des efforts provinciaux pour prévenir et gérer la COVID-19 ont donc été nécessaires et se sont vu accorder la priorité. INTERVENTION: Comme des vaccins n'étaient pas disponibles au cours des neuf premiers mois de la pandémie, d'autres stratégies ont été utilisées pour prévenir et gérer la COVID-19 (p. ex. distanciation physique, port du masque, dépistage des symptômes, tests, isolation des cas). Les Services de santé de l'Alberta ont travaillé avec les acteurs locaux et provinciaux et les fonctionnaires de la Direction générale de la santé des Premières nations et des Inuits pour mener des interventions à l'appui des habitations collectives. Ces interventions ont compris des ressources et des visites sur place pour appuyer la prévention et la préparation, et la création d'une ligne d'intervention coordonnée qui a servi de guichet unique d'accès à l'information et aux services en cas d'éclosion (p. ex. conseils, tests, équipement de protection individuelle, déclaration des cas). RéSULTATS: Les données d'un tableau de bord interne ont permis d'en savoir plus sur la popularité et l'utilisation de ces interventions. Les résultats d'un sondage en ligne ont fait état de niveaux élevés de connaissance, d'acceptabilité, de pertinence et d'utilisation des interventions chez les administrateurs d'habitations collectives (n = 550). Des recommandations ont été élaborées à partir des expériences signalées et des éléments positifs et négatifs, et les processus ont été améliorés. CONSéQUENCES: Des interventions de prévention, de préparation et de gestion des éclosions coordonnées à l'échelle provinciale ont soutenu les habitations collectives. Il pourrait être utile pour les futures urgences sanitaires de développer ces approches d'adaptation systémiques pour la prévention et la préparation, en plus des communications et de l'échange d'informations dans des contextes en évolution rapide.

Differential Gene Expression of Innate Immune Response Genes Consequent to Solenopsis invicta Virus-3 Infection

The red imported fire ant Solenopsis invicta Buren (fire ant hereafter) is a global pest that inflicts billions of dollars in damages to the United States economy and poses a major threat on a global scale. Concerns with the broad-spectrum application of insecticides have facilitated the hunt for natural enemy-mediated controls. One of these, the virus Solenopsis invicta virus-3 (SINV-3 hereafter) is exceptionally virulent in laboratory settings. However, despite high mortality rates in the laboratory and documented widespread SINV-3 prevalence in the southern United States, the fire ant remains a major pest. To explore this paradox, we document the immune response elicited by the fire ant when infected with SINV-3. We sequence the fire ant transcriptome prior to and following infection with SINV-3, and identify and discuss in detail genes in immune response pathways differentially expressed following infection with SINV-3. This information provides insights into genes and pathways involved in the SINV-3 infection response in the fire ant and offers avenues to pursue, to suppress key immune response genes and force the fire ant to succumb to SINV-3 infection in the field.

Genomic diversification of the specialized parasite of the fungus-growing ant symbiosis.

Fungi shape the diversity of life. Characterizing the evolution of fungi is critical to understanding symbiotic associations across kingdoms. In this study, we investigate the genomic and metabolomic diversity of the genus Escovopsis, a specialized parasite of fungus-growing ant gardens. Based on 25 high-quality draft genomes, we show that Escovopsis forms a monophyletic group arising from a mycoparasitic fungal ancestor 61.82 million years ago (Mya). Across the evolutionary history of fungus-growing ants, the dates of origin of most clades of Escovopsis correspond to the dates of origin of the fungus-growing ants whose gardens they parasitize. We reveal that genome reduction, determined by both genomic sequencing and flow cytometry, is a consistent feature across the genus Escovopsis, largely occurring in coding regions, specifically in the form of gene loss and reductions in copy numbers of genes. All functional gene categories have reduced copy numbers, but resistance and virulence genes maintain functional diversity. Biosynthetic gene clusters (BGCs) contribute to phylogenetic differences among Escovopsis spp., and sister taxa in the Hypocreaceae. The phylogenetic patterns of co-diversification among BGCs are similarly exhibited across mass spectrometry analyses of the metabolomes of Escovopsis and their sister taxa. Taken together, our results indicate that Escovopsis spp. evolved unique genomic repertoires to specialize on the fungus-growing ant-microbe symbiosis.

A scoping review of interventions to mitigate common non-communicable diseases among people with TB.

BACKGROUND: Recommendations have been made to integrate screening for common non-communicable diseases (NCDs) within TB programs. However, we must ensure screening is tied to evidence-based interventions before scale-up. We aimed to map the existing evidence regarding interventions that address NCDs that most commonly affect people with TB.METHODS: We systematically searched PubMed, Medline, and Embase for studies that evaluated interventions to mitigate respiratory disease, cardiovascular disease, alcohol and substance use disorder, and mental health disorders among people with TB. We excluded studies that only screened for comorbidity but resulted in no further intervention. We also excluded studies focusing on smoking cessation interventions for which evidence-based guidelines are well established.RESULTS: The search identified 20 studies that met our inclusion criteria. The most commonly evaluated intervention was referral for diabetes care (6 studies). Other interventions included pulmonary rehabilitation (5 studies), care programs for alcohol use disorder (4 studies), and psychosocial support or individual counselling (5 studies).CONCLUSION: There is limited robust evidence to support identified interventions in changing individual outcomes, and a significant knowledge gap remains on the long-term durability of the interventions´ clinical benefit, reach, and effectiveness. Implementation research demonstrating feasibility and effectiveness is needed before scaling up.

The Genomic Basis of Evolutionary Novelties in a Leafhopper.

Evolutionary innovations generate phenotypic and species diversity. Elucidating the genomic processes underlying such innovations is central to understanding biodiversity. In this study, we addressed the genomic basis of evolutionary novelties in the glassy-winged sharpshooter (Homalodisca vitripennis, GWSS), an agricultural pest. Prominent evolutionary innovations in leafhoppers include brochosomes, proteinaceous structures that are excreted and used to coat the body, and obligate symbiotic associations with two bacterial types that reside within cytoplasm of distinctive cell types. Using PacBio long-read sequencing and Dovetail Omni-C technology, we generated a chromosome-level genome assembly for the GWSS and then validated the assembly using flow cytometry and karyotyping. Additional transcriptomic and proteomic data were used to identify novel genes that underlie brochosome production. We found that brochosome-associated genes include novel gene families that have diversified through tandem duplications. We also identified the locations of genes involved in interactions with bacterial symbionts. Ancestors of the GWSS acquired bacterial genes through horizontal gene transfer (HGT), and these genes appear to contribute to symbiont support. Using a phylogenomics approach, we inferred HGT sources and timing. We found that some HGT events date to the common ancestor of the hemipteran suborder Auchenorrhyncha, representing some of the oldest known examples of HGT in animals. Overall, we show that evolutionary novelties in leafhoppers are generated by the combination of acquiring novel genes, produced both de novo and through tandem duplication, acquiring new symbiotic associations that enable use of novel diets and niches, and recruiting foreign genes to support symbionts and enhance herbivory.

High-quality, chromosome-scale genome assemblies: comparisons of three Diaphorina citri (Asian citrus psyllid) geographic populations.

The Asian citrus psyllid, Diaphorina citri, is the insect vector of the causal agent of huanglongbing (HLB), a devastating bacterial disease of commercial citrus. Presently, few genomic resources exist for D. citri. In this study, we utilized PacBio HiFi and chromatin confirmation contact (Hi-C) sequencing to sequence, assemble, and compare three high-quality, chromosome-scale genome assemblies of D. citri collected from California, Taiwan, and Uruguay. Our assemblies had final sizes of 282.67 Mb (California), 282.89 Mb (Taiwan), and 266.67 Mb (Uruguay) assembled into 13 pseudomolecules-a reduction in assembly size of 41-45% compared with previous assemblies which we validated using flow cytometry. We identified the X chromosome in D. citri and annotated each assembly for repetitive elements, protein-coding genes, transfer RNAs, ribosomal RNAs, piwi-interacting RNA clusters, and endogenous viral elements. Between 19,083 and 20,357 protein-coding genes were predicted. Repetitive DNA accounts for 36.87-38.26% of each assembly. Comparative analyses and mitochondrial haplotype networks suggest that Taiwan and Uruguay D. citri are more closely related, while California D. citri are closely related to Florida D. citri. These high-quality, chromosome-scale assemblies provide new genomic resources to researchers to further D. citri and HLB research.

The Spruce Budworm Genome: Reconstructing the Evolutionary History of Antifreeze Proteins.

Insects have developed various adaptations to survive harsh winter conditions. Among freeze-intolerant species, some produce "antifreeze proteins" (AFPs) that bind to nascent ice crystals and inhibit further ice growth. Such is the case of the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae), a destructive North American conifer pest that can withstand temperatures below -30°C. Despite the potential importance of AFPs in the adaptive diversification of Choristoneura, genomic tools to explore their origins have until now been limited. Here we present a chromosome-scale genome assembly for C. fumiferana, which we used to conduct comparative genomic analyses aimed at reconstructing the evolutionary history of tortricid AFPs. The budworm genome features 16 genes homologous to previously reported C. fumiferana AFPs (CfAFPs), 15 of which map to a single region on chromosome 18. Fourteen of these were also detected in five congeneric species, indicating Choristoneura AFP diversification occurred before the speciation event that led to C. fumiferana. Although budworm AFPs were previously considered unique to the genus Choristoneura, a search for homologs targeting recently sequenced tortricid genomes identified seven CfAFP-like genes in the distantly related Notocelia uddmanniana. High structural similarity between Notocelia and Choristoneura AFPs suggests a common origin, despite the absence of homologs in three related tortricids. Interestingly, one Notocelia AFP formed the C-terminus of a "zonadhesin-like" protein, possibly representing the ancestral condition from which tortricid AFPs evolved. Future work should clarify the evolutionary path of AFPs between Notocelia and Choristoneura and assess the role of the "zonadhesin-like" protein as precursor of tortricid AFPs.