“Micronuclei and Disease” special issue: Aims, scope, and synthesis of outcomes

[Abastract] The purpose of the “Micronuclei and Disease” special issue (SI) is to: (i) Determine the level of evidence for association of micronuclei (MN), a biomarker of numerical and structural chromosomal aberrations, with risk of specific diseases in humans; (ii) Define plausible mechanisms that explain association of MN with each disease; (iii) Identify knowledge gaps and research needed to translate MN assays into clinical practice. The “MN and Disease” SI includes 14 papers. The first is a review of mechanisms of MN formation and their consequences in humans. 11 papers are systematic reviews and/or meta-analyses of the association of MN with reproduction, child health, inflammation, auto-immune disease, glycation, metabolic diseases, chronic kidney disease, cardiovascular disease, eleven common cancers, ageing and frailty. The penultimate paper focuses on effect of interventions on MN frequency in the elderly. A road map for translation of MN data into clinical practice is the topic of the final paper. The majority of reviewed studies were case-control studies in which the ratio of mean MN frequency in disease cases relative to controls, i.e. the mean ratio (MR), was calculated. The mean of these MR values, estimated by meta-analyses, for lymphocyte and buccal cell MN in non-cancer diseases were 2.3 and 3.6 respectively, and for cancers they were 1.7 and 2.6 respectively. The highest MR values were observed in studies of cancer cases in which MN were measured in the same tissue as the tumour (MR = 4.9–10.8). This special issue is an important milestone in the evidence supporting MN as a reliable genomic biomarker of developmental and degenerative disease risk. These advances, together with results from prospective cohort studies, are helping to identify diseases in which MN assays can be practically employed in the clinical setting to better identify high risk patients and to prioritise them for preventive therapy

Correlation of LNCR rasiRNAs Expression with Heterochromatin Formation during Development of the Holocentric Insect Spodoptera frugiperda

Repeat-associated small interfering RNAs (rasiRNAs) are derived from various genomic repetitive elements and ensure genomic stability by silencing endogenous transposable elements. Here we describe a novel subset of 46 rasiRNAs named LNCR rasiRNAs due to their homology with one long non-coding RNA (LNCR) of Spodoptera frugiperda. LNCR operates as the intermediate of an unclassified transposable element (TE-LNCR). TE-LNCR is a very invasive transposable element, present in high copy numbers in the S. frugiperda genome. LNCR rasiRNAs are single-stranded RNAs without a prominent nucleotide motif, which are organized in two distinct, strand-specific clusters. The expression of LNCR and LNCR rasiRNAs is developmentally regulated. Formation of heterochromatin in the genomic region where three copies of the TE-LNCR are embedded was followed by chromatin immunoprecipitation (ChIP) and we observed this chromatin undergo dynamic changes during development. In summary, increased LNCR expression in certain developmental stages is followed by the appearance of a variety of LNCR rasiRNAs which appears to correlate with subsequent accumulation of a heterochromatic histone mark and silencing of the genomic region with TE-LNCR. These results support the notion that a repeat-associated small interfering RNA pathway is linked to heterochromatin formation and/or maintenance during development to establish repression of the TE-LNCR transposable element. This study provides insights into the rasiRNA silencing pathway and its role in the formation of fluctuating heterochromatin during the development of one holocentric organism

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems

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

Yacon concentrate NZFOS+, its phytochemical contents, health-related properties and potential applications

Yacon (Smallanthus sonchifolius), a sustainable foodstuff, is perceived as a functional food because it contains biologically active components e.g. fructooligosaccharides (FOS), inulin, and phenolic compounds that may provide physiological benefits beyond basic nutrition to reduce the risk of chronic diseases. There is a growing public interest in why and how to use yacon. Yacon, originally from South America, has been grown in New Zealand since 1980’s. NZ-produced yacon concentrate NZFOS+ contains the purest natural prebiotic FOS. Our study aimed to examine the phytochemical contents of NZFOS+ and its health-related properties. The glycemic index of yacon concentrate was measured by ISO 26642:2010(E) (n=10). Total phenolic and flavonoid contents were measured by spectrometric method. The chlorogenic acid content and phenolic profiling were measured using the liquid chromatography coupled with mass spectrometry (LC-MS). The antioxidant activity of the yacon concentrate and Manuka honey were compared using the cupric reducing antioxidant capacity (CUPRAC), Ferric-ion reducing antioxidant power (FRAP) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays. The results indicated that compared to Manuka honey, yacon concentrate has a lower glycemic index (40 vs 52); a higher content of total phenolic (5430mg vs 744mg GAE/100g), total flavonoid (329mg vs 22mg QE/100g), and chlorogenic acid (11.88μg vs 0.08μg CA/g); across all assays observed, a significantly higher antioxidant capacity (CUPRAC assay, 892mg vs 52.6mg TE/100g; FRAP assay, 633mg vs 47mg TE/100g; DPPH assay, 383mg vs 22mg TE/100g, respectively). Yacon concentrate has proven potential health benefits and applications associated with the maintenance of health and wellbeing and prevention of chronic diseases. Further investigations are needed for human studies and new applications and use of yacon concentrate. Yacon concentrate (NZFOS+) has potential markets in the development of new food products and new dietotherapy applications, e.g. in the form of syrup, and functional prebiotic drinks

Yacon concentrate NZFOS+, its phytochemical contents, health-related properties and potential applications

Yacon (Smallanthus sonchifolius), a sustainable foodstuff, is perceived as a functional food because it contains biologically active components, e.g., fructooligosaccharides (FOS), inulin, and phenolic compounds that may provide physiological benefits beyond basic nutrition to reduce the risk of chronic diseases. There is a growing public interest in why and how to use yacon. Yacon, originally from South America, has been grown in New Zealand (NZ) since the 1980’s. NZ-produced yacon concentrate NZFOS+ contains the purest natural prebiotic FOS. Our study aimed to examine the phytochemical contents of NZFOS+ and its health-related properties. The glycemic index of yacon concentrate was measured by ISO 26642:2010(E) (n = 10). Total phenolic and flavonoid contents were measured by the spectrometric method. The chlorogenic acid content and phenolic profiling were measured using the liquid chromatography coupled with mass spectrometry (LC-MS). The antioxidant activity of the yacon concentrate and Manuka honey were compared using the cupric reducing antioxidant capacity (CUPRAC), ferric ion reducing antioxidant power (FRAP), and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays. The results indicated that compared to Manuka honey, yacon concentrate has a lower glycemic index (40 vs. 52); a higher content of total phenolic (5430 mg vs. 744 mg GAE/100 g), total flavonoid (329 mg vs. 22 mg QE/100 g), and chlorogenic acid (11.88 μg vs. 0.08 μg CA/g); and across all assays observed, a significantly higher antioxidant capacity (CUPRAC assay, 892 mg vs. 52.6 mg TE/100 g; FRAP assay, 633 mg vs. 47 mg TE/100 g; DPPH assay, 383 mg vs. 22 mg TE/100 g, respectively). Yacon concentrate has proven potential health benefits and applications associated with the maintenance of health and wellbeing and prevention of chronic diseases. Further investigations are needed for human studies and new applications and use of yacon concentrate. Yacon concentrate (NZFOS+) has potential markets in the development of new food products and new diet therapy applications, e.g., in the form of syrup, and functional prebiotic drink

Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements

The recent assembly of the silkworm Bombyx mori genome with 432 Mb on 28 holocentric chromosomes has become a reference in the genomic analysis of the very diverse Order of Lepidoptera. We sequenced BACs from two major pests, the noctuid moths Helicoverpa armigera and Spodoptera frugiperda, corresponding to 15 regions distributed on 11 B. mori chromosomes, each BAC/region being anchored by known orthologous gene(s) to analyze syntenic relationships and genome rearrangements among the three species. Nearly 300 genes and numerous transposable elements were identified, with long interspersed nuclear elements and terminal inverted repeats the most abundant transposable element classes. There was a high degree of synteny conservation between B. mori and the two noctuid species. Conserved syntenic blocks of identified genes were very small, however, approximately 1.3 genes per block between B. mori and the two noctuid species and 2.0 genes per block between S. frugiperda and H. armigera. This corresponds to approximately two chromosome breaks per Mb DNA per My. This is a much higher evolution rate than among species of the Drosophila genus and may be related to the holocentric nature of the lepidopteran genomes. We report a large cluster of eight members of the aminopeptidase N gene family that we estimate to have been present since the Jurassic. In contrast, several clusters of cytochrome P450 genes showed multiple lineage-specific duplication events, in particular in the lepidopteran CYP9A subfamily. Our study highlights the value of the silkworm genome as a reference in lepidopteran comparative genomics