Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics.

The emergence of robust single-cell 'omics techniques enables studies of uncultivable species, allowing for the (re)discovery of diverse genomic features. In this study, we combine single-cell genomics and transcriptomics to explore genome evolution in ciliates (a > 1 Gy old clade). Analysis of the data resulting from these single-cell 'omics approaches show: 1) the description of the ciliates in the class Karyorelictea as "primitive" is inaccurate because their somatic macronuclei contain loci of varying copy number (i.e., they have been processed by genome rearrangements from the zygotic nucleus); 2) gene-sized somatic chromosomes exist in the class Litostomatea, consistent with Balbiani's (1890) observation of giant chromosomes in this lineage; and 3) gene scrambling exists in the underexplored Postciliodesmatophora (the classes Heterotrichea and Karyorelictea, abbreviated here as the Po-clade), one of two major clades of ciliates. Together these data highlight the complex evolutionary patterns underlying germline genome architectures in ciliates and provide a basis for further exploration of principles of genome evolution in diverse microbial lineages

Insights into Transgenerational Epigenetics from Studies of Ciliates

Epigenetics, a term with many meanings, can be broadly defined as the study of dynamic states of the genome. Ciliates, a clade of unicellular eukaryotes, can teach us about the intersection of epigenetics and evolution due to the advantages of working with cultivable ciliate lineages, plus their tendency to express extreme phenotypes such as heritable doublet morphology. Moreover, ciliates provide a powerful model for studying epigenetics given the presence of dimorphic nuclei – a somatic macronucleus and germline micronucleus – within each cell. Here, we exemplify the power of studying ciliates to learn about epigenetic phenomena. We highlight “classical” examples from morphology and physiology including cortical inheritance, mating type determination, and serotype expression. In addition, we detail molecular studies of epigenetic phenomena, including: DNA elimination; alternative processing and unscrambling; and copy number determination. Based on the implications of these studies, we discuss epigenetics as a possible functional mechanism for rapid speciation in ciliates

Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘Omics

The emergence of robust single-cell ‘omics techniques enables studies of uncultivable species, allowing for the (re)discovery of diverse genomic features. In this study, we combine single-cell genomics and transcriptomics to explore genome evolution in ciliates (a \u3e 1 Gy old clade). Analysis of the data resulting from these single-cell ‘omics approaches show: 1) the description of the ciliates in the class Karyorelictea as “primitive”is inaccurate because their somatic macronuclei contain loci of varying copy number (i.e., they have been processed by genome rearrangements from the zygotic nucleus); 2) gene-sized somatic chromosomes exist in the class Litostomatea, consistent with Balbiani’s (1890) observation of giant chromosomes in this lineage; and 3) gene scrambling exists in the underexplored Postciliodesmatophora (the classes Heterotrichea and Karyorelictea, abbreviated here as the Po-clade), one of two major clades of ciliates. Together these data highlight the complex evolutionary patterns underlying germline genome architectures in ciliates and provide a basis for further exploration of principles of genome evolution in diverse microbial lineages

Straight-sided beer and cider glasses to reduce alcohol sales for on-site consumption: A randomised crossover trial in bars.

BackgroundStraight-sided glasses can slow the rate of lager consumption in a laboratory setting compared with curved glasses. Slower drinking rates may lower overall alcohol consumption. Glass shape is therefore a potential target for intervention. The aim of this randomised crossover trial was to estimate the impact of serving draught beer and cider in straight-sided glasses, compared with usual, predominantly curved glasses, on alcohol sales for on-site consumption in bars.MethodsTwenty-four bars in England completed two intervention periods (A) and two control periods (B) in a randomised order: 1) BABA; 2) BAAB; 3) ABBA; or 4) ABAB. Each period lasted two weeks and involved serving draught beer and cider in either straight-sided glasses (A) or the venue's usual glasses (≥75% curved; B). The primary outcome was the mean volume (in litres) of draught beer and cider sold weekly, compared between A and B periods using a paired-samples t-test on aggregate data. A regression model adjusted for season, order, special events, and busyness.FindingsMean weekly volume sales of draught beer and cider was 690·9 L (SD 491·3 L) across A periods and 732·5 L (SD 501·0 L) across B periods. The adjusted mean difference (A minus B) was 8·9 L per week (95% CI -45·5 to 63·3; p = 0·737).InterpretationThis study provides no clear evidence that using straight-sided glasses, compared with usual, predominantly curved glasses, reduces the volume of draught beer and cider sold for on-site consumption in bars

Exploring genome architecture, protein evolution and epigenetic processes in ciliates

Ciliates are a diverse clade of unicellular eukaryotes that differ in size, morphology, and nuclear organization; they are characterized by both cilia and dimorphic nuclei. Three classes of ciliates extensively fragment their somatic macronuclear genome, a process that is associated with elevated rates of protein evolution. Although ciliates in the class Heterotrichea are not known to extensively fragment their somatic genome, they do show high levels of genome amplification. In this study, I examine how genome architecture affects patterns of molecular evolution within the class Heterotrichea. I use a combination of molecular and bioinformatic tools to determine copy number of paralogs and analyze patterns of protein evolution. The genome (PCR) data suggest that heterotrichs have few paralogs, and those that are present exhibit high levels of amino acid conservation. The transcriptome (high throughput sequence; HTS) data suggest that heterotrichs have many paralogs, which are variably conserved. Moreover, the qPCR data suggest Blepharisma americanum (Heterotrichea) has a high copy number of the SSU rDNA gene and a similar copy number among selected actin, α-tub and Ef1α paralogs. In contrast, the copy number varies significantly between genes of other ciliates that amplify their somatic genomes. Ciliates, with their unusual nuclei, can teach us about genome architecture and protein evolution

How are milk substitutes labelled in the UK? Would consumers be confused by adding the term ‘milk’ to milk substitute labelling? Evidence from observational and online experimental studies.

This study comprises two studies exploring milk substitute labelling. Study 1 was an online observational study that assessed the absolute (total number of products) and relative (proportion compared to dairy milk) availability of plant-based milk substitutes in online supermarkets in the UK. Study 2 was an online experimental study that assessed the impact of using the term ‘milk’ on milk substitute labelling. In this study, 352 UK adults were randomised to one of two conditions where they saw milk substitutes that were either labelled with UK regulations (e.g., soya drink) or using the term ‘milk’ (e.g., soya milk). The protocol and analysis plan for Study 2 were pre-registered on the Open Science Framework (https://osf.io/c74ka/)

The impact of introducing alcohol-free beer options in bars and public houses on alcohol sales and revenue: A randomised crossover field trial.

Publication status: PublishedFunder: Bristol Health Partners Academic Health Science Centre Drug and Alcohol Health Integration TeamAIMS: The study aimed to estimate the impact of introducing a draught alcohol-free beer, thereby increasing the relative availability of these products, on alcohol sales and monetary takings in bars and pubs in England. DESIGN: Randomised crossover field trial. SETTING: England. PARTICIPANTS: Fourteen venues that did not previously sell draught alcohol-free beer. INTERVENTION AND COMPARATOR: Venues completed two intervention periods and two control periods in a randomised order over 8 weeks. Intervention periods involved replacing one draught alcoholic beer with an alcohol-free beer. Control periods operated business as usual. MEASUREMENTS: The primary outcome was mean weekly volume (in litres) of draught alcoholic beer sold. The secondary outcome was mean weekly revenue [in GBP (£)] from all drinks. Analyses adjusted for randomised order, special events, season and busyness. FINDINGS: The adjusted mean difference in weekly sales of draught alcoholic beer was -20 L [95% confidence interval (CI) = -41 to +0.4], equivalent to a 4% reduction (95% CI = 8% reduction to 0.1% increase) in the volume of alcoholic draught beer sold when draught alcohol-free beer was available. Excluding venues that failed at least one fidelity check resulted in an adjusted mean difference of -29 L per week (95% CI = -53 to -5), equivalent to a 5% reduction (95% CI = 8% reduction to 0.8% reduction). The adjusted mean difference in weekly revenue was +61 GBP per week (95% CI = -328 to +450), equivalent to a 1% increase (95% CI = 5% decrease to 7% increase) when draught alcohol-free beer was available. CONCLUSIONS: Introducing a draught alcohol-free beer in bars and pubs in England reduced the volume of draught alcoholic beer sold by 4% to 5%, with no evidence of the intervention impacting net revenue

Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies.

In Brazil, Leishmania braziliensis is the main causative agent of the neglected tropical disease, cutaneous leishmaniasis (CL). CL presents on a spectrum of disease severity with a high rate of treatment failure. Yet the parasite factors that contribute to disease presentation and treatment outcome are not well understood, in part because successfully isolating and culturing parasites from patient lesions remains a major technical challenge. Here we describe the development of selective whole genome amplification (SWGA) for Leishmania and show that this method enables culture-independent analysis of parasite genomes obtained directly from primary patient skin samples, allowing us to circumvent artifacts associated with adaptation to culture. We show that SWGA can be applied to multiple Leishmania species residing in different host species, suggesting that this method is broadly useful in both experimental infection models and clinical studies. SWGA carried out directly on skin biopsies collected from patients in Corte de Pedra, Bahia, Brazil, showed extensive genomic diversity. Finally, as a proof-of-concept, we demonstrated that SWGA data can be integrated with published whole genome data from cultured parasite isolates to identify variants unique to specific geographic regions in Brazil where treatment failure rates are known to be high. SWGA provides a relatively simple method to generate Leishmania genomes directly from patient samples, unlocking the potential to link parasite genetics with host clinical phenotypes

<i>L. braziliensis</i> genomic variants.

Frame-shift and missense variants enriched in L. braziliensis parasites present in Northeast Brazil. (XLSX)</p

Genome-wide coverage by SWGA.

Coverage plots for 35 L. braziliensis chromosomes in SWGA data from a single patient (#7; blue lines) compared to whole genome sequencing (WGS) of pure, cultured L. braziliensis (orange lines). Data were merged from all SWGA primer sets to maximize coverage. (TIFF)</p