Identifying Genomic Regions Targeted During Eggplant Domestication Using Transcriptome Data.

Identifying genes and traits that have diverged during domestication provides key information of importance for maintaining and even increasing yield and nutrients in existing crops. A "bottom-up" population genetics approach was used to identify signatures of selection across the eggplant genome, to better understand the process of domestication. RNA-seq data were obtained for 4 wild eggplants (Solanum insanum L.) and 16 domesticated eggplants (S. melongena L.) and mapped to the eggplant genome. Single-nucleotide polymorphism (SNPs) exhibiting signatures of selection in domesticates were identified as those exhibiting high FST between the 2 populations (evidence of significant divergence) and low π for the domesticated population (indicative of a selective sweep). Some of these regions appear to overlap with previously identified quantitative trait loci for domestication traits. Genes in regions of linkage disequilibrium surrounding these SNPs were searched against the Arabidopsis thaliana and tomato genomes to find orthologs. Subsequent gene ontology (GO) enrichment analysis identified over-representation of GO terms related to photosynthesis and response to the environment. This work reveals genomic changes involved in eggplant domestication and improvement, and how this compares to observed changes in the tomato genome, revealing shared chromosomal regions involved in the domestication of both species.

Sexual wellbeing in early adolescence: a cross-sectional assessment among girls and boys in urban Indonesia.

BACKGROUND: Early adolescence (ages 10-14) is a critical period of physical, cognitive, social and emotional development, which affect sexual and reproductive health and rights (SRHR). Yet, little is known about positive or healthy aspects of sexuality development during this period of life, especially in South East Asia where sexual norms remain restrictive. The objective of this study is to assess the prevalence and correlates of sexual wellbeing among early adolescent girls and boys ages 10-14 years in Indonesia. METHODS: Data for this cross-sectional study were collected as part of the Global Early Adolescent Study via a school-based survey in three Indonesian urban sites in 2018 (N = 4309). We assessed the prevalence of multiple indicators of sexual wellbeing (e.g. SRHR knowledge and communication, gender attitudes, body satisfaction, self-efficacy, freedom from violence) and tested for differences by sex using Chi-square, Student t-test, and Wilcoxon rank-sum test. Multivariable logistic regression models were used to assess the adjusted odds ratio of selected indicators in relation to sociodemographic factors, romantic relationship status, and sexual activities. RESULTS: The mean age of students was 12 years (53% girls); 90% had started puberty. SRHR knowledge and communication was low overall, but higher among boys than girls. Boys were more likely than girls to report high body satisfaction, less feelings of guilt in relation to sexuality, but also to have experienced physical peer violence. In contrast, girls were more likely to hold gender equal attitudes, greater perceived self-efficacy to say 'no', and to report being bullied by boys. In multivariable models, romantic relationship experiences, perceived voice (boys and girls) and decision-making (girls) were associated with three or more indicators of sexual wellbeing. CONCLUSIONS: While young adolescents in Indonesia score high on some aspects of sexual wellbeing, misconceptions, feelings of guilt and uncertainties related to sexuality are common, with clear gender differences. These findings confirm the need for comprehensive sexuality education that begins early in adolescence.

Eggplant Domestication: Pervasive Gene Flow, Feralization, and Transcriptomic Divergence.

In the context of food security, examining the genomics of domestication will help identify genes underlying adaptive and economically important phenotypes, for example, larger fruit, improved taste, and loss of agronomically inferior phenotypes. Examination of genome-scale single nucleotide polymorphisms demonstrates the relationships between wild ancestors of eggplant (Solanum melongena L.), confirming that Solanum insanum L. is the wild progenitor. This species is split roughly into an Eastern (Malaysian, Thai, and Vietnamese) and Western (Indian, Madagascan, and Sri Lankan) group, with domesticates derived from the former. Additional "wild" accessions from India appear to be feral escapes, derived multiple times from domesticated varieties through admixture. Accessions with small egg-shaped fruit are generally found intermixed with East Asian Solanum insanum confirming they are primitive relative to the large-fruited domesticates. Comparative transcriptomics was used to track the loci under selection. Sequence analysis revealed a genetic bottleneck reducing variation by almost 50% in the primitive accessions relative to the wild species and a further 10% in the landraces. We also show evidence for selection on genes with a role in response to wounding and apoptosis. Genes showing a significant difference in expression between wild and primitive or between primitive and landrace genepools were mostly (>75%) downregulated in the derived populations and enriched for gene ontologies related to defense, flowering, signaling, and response to biotic and abiotic stimuli. This work reveals genomic changes involved in crop domestication and improvement, and the population genetics work explains why defining the eggplant domestication trajectory has been so challenging.

Reconstructing promoter activity from Lux bioluminescent reporters.

The bacterial Lux system is used as a gene expression reporter. It is fast, sensitive and non-destructive, enabling high frequency measurements. Originally developed for bacterial cells, it has also been adapted for eukaryotic cells, and can be used for whole cell biosensors, or in real time with live animals without the need for euthanasia. However, correct interpretation of bioluminescent data is limited: the bioluminescence is different from gene expression because of nonlinear molecular and enzyme dynamics of the Lux system. We have developed a computational approach that, for the first time, allows users of Lux assays to infer gene transcription levels from the light output. This approach is based upon a new mathematical model for Lux activity, that includes the actions of LuxAB, LuxEC and Fre, with improved mechanisms for all reactions, as well as synthesis and turn-over of Lux proteins. The model is calibrated with new experimental data for the LuxAB and Fre reactions from Photorhabdus luminescens-the source of modern Lux reporters-while literature data has been used for LuxEC. Importantly, the data show clear evidence for previously unreported product inhibition for the LuxAB reaction. Model simulations show that predicted bioluminescent profiles can be very different from changes in gene expression, with transient peaks of light output, very similar to light output seen in some experimental data sets. By incorporating the calibrated model into a Bayesian inference scheme, we can reverse engineer promoter activity from the bioluminescence. We show examples where a decrease in bioluminescence would be better interpreted as a switching off of the promoter, or where an increase in bioluminescence would be better interpreted as a longer period of gene expression. This approach could benefit all users of Lux technology.

Working with young peer researchers in sexuality studies: benefits, challenges and lessons learnt.

Involvement as peer researchers provides young people with an opportunity to exercise their right to participation and can facilitate unique insights into young people's lives, social contexts, choices and negotiations. However, evidence on the approach has to date included little in-depth discussion on the complexities presented by sexuality research. Here, engaging young people as researchers is influenced by intersecting cultural discourses, particularly regarding youth agency and sexual freedom. This article provides practice-based insights from involving young people as peer researchers within two rights-based sexuality-focused research projects in Indonesia and the Netherlands. Drawing on two contrasting cultural contexts, it explores benefits and challenges regarding youth-adult power dynamics, the taboo nature of sexuality, research quality and dissemination. Recommendations for future studies include ongoing training and capacity strengthening for peer researchers which recognise cultural and educational backgrounds, strong youth-adult partnerships creating an enabling environment for the engagement of peer researchers, careful consideration of how young people are involved and critical reflection on adult-centric views of what constitutes "academic" research.

The role of laparoscopic surgery in the management of children and adolescents with inflammatory bowel disease.

Although laparoscopic surgery is readily used in the management of inflammatory bowel disease (IBD) in adults, its role in the surgical treatment of IBD in the pediatric population is not well established. The aim of this narrative review was to analyze the published evidence comparing laparoscopic and open resection in the management of children and adolescents with IBD. The Pubmed and Embase databases were searched using the terms "inflammatory bowel disease," "children," "adolescents," "laparoscopic," and "colectomy." The review identified 10 appropriate studies. Even though laparoscopic surgery generally resulted in longer operating times (between a mean of 40 and 140 min), benefits included reduced postoperative pain (mean duration of opiate use 3 vs 6 days) and reduced length of stay (median length of stay 5-8 vs 10.5-19 days) compared with open surgery. Postoperative complication rates were similar following both approaches. Due to the limited available data and the small sample size of the published series, definite recommendations are not able to be drawn. Nevertheless, current evidence indicates that laparoscopic colorectal resection is safe and feasible in the management of IBD in the paediatric population, with reductions in postoperative pain and length of hospital stay achievable.