Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.

Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here, we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X = 52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this intergenomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high-resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.

Imprisonment for South Ethiopian people living with HIV presents a double health burden: lived experiences of prisoners.

BACKGROUND: Optimal adherence is crucial for ensuring both therapeutic and preventative benefits of antiretroviral therapy (ART). Sub-optimal adherence is common in prisoners and little information is available about its predisposing circumstances in resource-limited settings. We explored lived experiences of inmates living with HIV (ILWH) and experiential accounts of service providers in South Ethiopia to identify barriers to and facilitators of HIV care use in the prison context. METHODS: We conducted qualitative in-depth interviewing with eleven ILWH and eleven service providers. Audio recorded interview data were transcribed verbatim in Amharic language, translated into English and coded based on emerging concepts. We employed a descriptive phenomenological approach to abstract meaning attributed to the prisoners' lived experiences in relation to HIV care use and service providers' experiential account regarding care provision as presented to our consciousness. FINDINGS: Several concepts emerged as barriers to HIV care use amongst ILWH in South Ethiopia including: limited access to standard care, insufficient health staff support, uncooperative security system, loss of patient privacy, a lack of status disclosure due to social stigma, and food supply insufficiency. In addition to a unique opportunity offered by an imprisonment for some ILWH to refrain from health damaging behaviours, the presence of social support in the prison system facilitated care use. CONCLUSIONS: This study identified important structural and social contexts that can both hinder and enhance HIV care use amongst ILWH in South Ethiopia. Given the disproportionate burden of HIV in prisoners and the potential of transmission to others during and after incarceration, development of contextually-responsive strategies is required to address the barriers and to also strengthen the enablers.

Variation in cytonuclear expression accommodation among allopolyploid plants.

Cytonuclear coevolution is a common feature among plants, which coordinates gene expression and protein products between the nucleus and organelles. Consequently, lineage-specific differences may result in incompatibilities between the nucleus and cytoplasm in hybrid taxa. Allopolyploidy is also a common phenomenon in plant evolution. The hybrid nature of allopolyploids may result in cytonuclear incompatibilities, but the massive nuclear redundancy created during polyploidy affords additional avenues for resolving cytonuclear conflict (i.e. cytonuclear accommodation). Here we evaluate expression changes in organelle-targeted nuclear genes for 6 allopolyploid lineages that represent 4 genera (i.e. Arabidopsis, Arachis, Chenopodium, and Gossypium) and encompass a range in polyploid ages. Because incompatibilities between the nucleus and cytoplasm could potentially result in biases toward the maternal homoeolog and/or maternal expression level, we evaluate patterns of homoeolog usage, expression bias, and expression-level dominance in cytonuclear genes relative to the background of noncytonuclear expression changes and to the diploid parents. Although we find subsets of cytonuclear genes in most lineages that match our expectations of maternal preference, these observations are not consistent among either allopolyploids or categories of organelle-targeted genes. Our results indicate that cytonuclear expression evolution may be subtle and variable among genera and genes, likely reflecting a diversity of mechanisms to resolve nuclear-cytoplasmic incompatibilities in allopolyploid species.

Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels.

Mitochondrial and plastid functions depend on coordinated expression of proteins encoded by genomic compartments that have radical differences in copy number of organellar and nuclear genomes. In polyploids, doubling of the nuclear genome may add challenges to maintaining balanced expression of proteins involved in cytonuclear interactions. Here, we use ribo-depleted RNA sequencing (RNA-seq) to analyze transcript abundance for nuclear and organellar genomes in leaf tissue from four different polyploid angiosperms and their close diploid relatives. We find that even though plastid genomes contain <1% of the number of genes in the nuclear genome, they generate the majority (69.9 to 82.3%) of messenger RNA (mRNA) transcripts in the cell. Mitochondrial genes are responsible for a much smaller percentage (1.3 to 3.7%) of the leaf mRNA pool but still produce much higher transcript abundances per gene compared to nuclear genome. Nuclear genes encoding proteins that functionally interact with mitochondrial or plastid gene products exhibit mRNA expression levels that are consistently more than 10-fold lower than their organellar counterparts, indicating an extreme cytonuclear imbalance at the RNA level despite the predominance of equimolar interactions at the protein level. Nevertheless, interacting nuclear and organellar genes show strongly correlated transcript abundances across functional categories, suggesting that the observed mRNA stoichiometric imbalance does not preclude coordination of cytonuclear expression. Finally, we show that nuclear genome doubling does not alter the cytonuclear expression ratios observed in diploid relatives in consistent or systematic ways, indicating that successful polyploid plants are able to compensate for cytonuclear perturbations associated with nuclear genome doubling.

Parental legacy versus regulatory innovation in salt stress responsiveness of allopolyploid cotton (Gossypium) species.

Polyploidy provides an opportunity for evolutionary innovation and species diversification, especially under stressful conditions. In allopolyploids, the conditional dynamics of homoeologous gene expression can be either inherited from ancestral states pre-existing in the parental diploids or novel upon polyploidization, the latter potentially permitting a wider range of phenotypic responses to stresses. To gain insight into regulatory mechanisms underlying the diversity of salt resistance in Gossypium species, we compared global transcriptomic responses to modest salinity stress in two allotetraploid (AD-genome) cotton species, Gossypium hirsutum and G. mustelinum, relative to their model diploid progenitors (A-genome and D-genome). Multivariate and pairwise analyses of salt-responsive changes revealed a profound alteration of gene expression for about one third of the transcriptome. Transcriptional responses and associated functional implications of salt acclimation varied across species, as did species-specific coexpression modules among species and ploidy levels. Salt responsiveness in both allopolyploids was strongly biased toward the D-genome progenitor. A much lower level of transgressive downregulation was observed in the more salt-tolerant G. mustelinum than in the less tolerant G. hirsutum. By disentangling inherited effects from evolved responses, we show that expression biases that are not conditional upon salt stress approximately equally reflect parental legacy and regulatory novelty upon allopolyploidization, whereas stress-responsive biases are predominantly novel, or evolved, in allopolyploids. Overall, our work suggests that allopolyploid cottons acquired a wide range of stress response flexibility relative to their diploid ancestors, most likely mediated by complex suites of duplicated genes and regulatory factors.

Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms.

Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary "mismatches" between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.

Lifestyle Interventions through Participatory Research: A Mixed-Methods Systematic Review of Alcohol and Other Breast Cancer Behavioural Risk Factors.

Breast cancer is one of the most frequently diagnosed cancers in women globally. Sex and advancing age represent the dominant risk factors, with strong evidence of alcohol as a modifiable risk factor. The carcinogenic nature of alcohol has been known for over twenty years; however, this has failed to translate into significant behavioural, practice, or policy change. As a result, women have not benefitted from this research and, by extension, have been exposed to unnecessary breast cancer risk. Participatory research presents a solution to research translation in public health through the collaboration of impacted populations with academics in research. This systematic review examines peer-reviewed research studies where participants were involved in the research process and the outcomes related to breast cancer prevention (either alcohol or broader lifestyle modification). Seven of the eight studies reported positive effects, and the collaboration between academic researchers and impacted populations may have supported positive outcomes. Women were receptive and responsive to participatory approaches, and their participation is important to address socially entrenched behaviours such as alcohol consumption. Participatory research presents opportunities for future interventions to improve (or address) modifiable risk factors for breast cancer.

Revisiting Candidacy: What Might It Offer Cancer Prevention?

The notion of candidacy emerged three decades ago through Davison and colleagues' exploration of people's understanding of the causes of coronary heart disease. Candidacy was a mechanism to estimate one's own or others risk of disease informed by their lay epidemiology. It could predict who would develop illness or explain why someone succumbed to it. Candidacy's predictive ability, however, was fallible, and it was from this perspective that the public's reticence to adhere to prevention messages could be explained, as ultimately anybody could be 'at-risk'. This work continues to resonate in health research, with over 700 citations of Davison's Candidacy paper. Less explored however, is the candidacy framework in its entirety in other illness spheres, where prevention efforts could potentially impact health outcomes. This paper revisits the candidacy framework to reconsider it use within prevention. In doing so, candidacy within coronary heart disease, suicide prevention, diabetes, and cancer will be examined, and key components of candidacy and how people negotiate their candidacy within differing disease contexts will be uncovered. The applicability of candidacy to address modifiable breast cancer risk factors or cancer prevention more broadly will be considered, as will the implications for public health policy.

Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number.

The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication (WGD) events in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follows WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated the organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.

How Are the Links between Alcohol Consumption and Breast Cancer Portrayed in Australian Newspapers?: A Paired Thematic and Framing Media Analysis.

A dose-dependent relationship between alcohol consumption and increased breast cancer risk is well established, even at low levels of consumption. Australian women in midlife (45-64 years) are at highest lifetime risk for developing breast cancer but demonstrate low awareness of this link. We explore women's exposure to messages about alcohol and breast cancer in Australian print media in the period 2002-2018. METHODS: Paired thematic and framing analyses were undertaken of Australian print media from three time-defined subsamples: 2002-2004, 2009-2011, and 2016-2018. RESULTS: Five key themes arose from the thematic framing analysis: Ascribing Blame, Individual Responsibility, Cultural Entrenchment, False Equilibrium, and Recognition of Population Impact. The framing analysis showed that the alcohol-breast cancer link was predominantly framed as a behavioural concern, neglecting medical and societal frames. DISCUSSION: We explore the representations of the alcohol and breast cancer risk relationship. We found their portrayal to be conflicting and unbalanced at times and tended to emphasise individual choice and responsibility in modifying health behaviours. We argue that key stakeholders including government, public health, and media should accept shared responsibility for increasing awareness of the alcohol-breast cancer link and invite media advocates to assist with brokering correct public health information.

Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton.

The two cultivated allopolyploid cottons, Gossypium hirsutum and Gossypium barbadense, represent a remarkable example of parallel independent domestication, both involving dramatic morphological transformations under selection from wild perennial plants to annualized row crops. Deep resequencing of 643 newly sampled accessions spanning the wild-to-domesticated continuum of both species, and their allopolyploid relatives, are combined with existing data to resolve species relationships and elucidate multiple aspects of their parallel domestication. It is confirmed that wild G. hirsutum and G. barbadense were initially domesticated in the Yucatan Peninsula and NW South America, respectively, and subsequently spread under domestication over 4000-8000 years to encompass most of the American tropics. A robust phylogenomic analysis of infraspecific relationships in each species is presented, quantify genetic diversity in both, and describe genetic bottlenecks associated with domestication and subsequent diffusion. As these species became sympatric over the last several millennia, pervasive genome-wide bidirectional introgression occurred, often with striking asymmetries involving the two co-resident genomes of these allopolyploids. Diversity scans revealed genomic regions and genes unknowingly targeted during domestication and additional subgenomic asymmetries. These analyses provide a comprehensive depiction of the origin, divergence, and adaptation of cotton, and serve as a rich resource for cotton improvement.

Alcohol Consumption and Perceptions of Health Risks During COVID-19: A Qualitative Study of Middle-Aged Women in South Australia.

Australian women's alcohol consumption has increased in frequency during COVID-19. Research suggests this is to cope with stress resulting from the pandemic and COVID-19 countermeasures that require social distancing. This is a critical public health concern because increased alcohol consumption, even for a short period, increases the myriad longer-term health risks associated with cumulative exposure to alcohol. This paper provides unique qualitative evidence of how health risk perceptions are re-focused toward the shorter-term during the pandemic, through analysis of interviews with 40 middle-aged Australian women (aged 45-64) representing a range of self-perceived drinking status' ("occasional"/"light"/"moderate"/"heavy") before and then during the pandemic (n = 80 interviews). Our analysis captures women's risk horizons drifting away from the uncertain longer-term during COVID-19, toward the immediate need to "get through" the pandemic. We show how COVID-19 has increased the perceived value of consuming alcohol among women, particularly when weighed up against the social and emotional "costs" of reducing consumption. Our findings have implications for the delivery of alcohol-related health risk messages designed for middle-aged women both during, and into the recovery phases of the pandemic, who already consume more alcohol and experience more alcohol-related health risk than women in other age groups.

Effect of antenatal depression on adverse birth outcomes in Gondar town, Ethiopia: A community-based cohort study.

BACKGROUND: The impact of antenatal depression on pregnancy outcomes has been well investigated in developed countries, but few studies have been conducted in low-income countries. As depression is significantly affected by socio-economic and cultural factors, it would be difficult to generalize evidence from high-income countries to low-income countries. We conducted a community-based cohort study to estimate the incidence of adverse birth outcomes and the direct and indirect pathways via which depression and other psychosocial risk factors may impact such birth outcomes within Gondar town, Ethiopia. METHODS: The study followed 916 pregnant women who were screened for antenatal depression using the Edinburgh Postnatal Depression Scale (EPDS). We also assessed the incidence of preterm births, Low Birth Weight (LBW) and stillbirths. Modified Poisson regression was used to estimate the relative risk of predictors on adverse birth outcomes and a Generalized Structural Equation Model (GSEM) was used to estimate the direct and indirect effect of antenatal depression and other psychological risk factors on adverse birth outcomes. RESULTS: The cumulative incidence of stillbirth, LBW and preterm was 1.90%, 5.25%, and 16.42%, respectively. The risk of preterm birth was 1.61, 1.46, 1.49, and 1.77 times higher among participants who identified as Muslim, reported being fearful of delivery, were government employee's, and who had no antenatal care services, respectively. Partner support moderated the association between depression, preterm birth, and LBW. Depression had no direct effect on birth outcomes but indirectly affected preterm birth via partner support. Religion had both direct and indirect effects on preterm birth, while occupation and fear of delivery had direct effects. The risk of LBW was 9.44 and 2.19 times higher among preterm births and those who had exposure to tobacco, respectively. Stress coping was indirectly associated, and preterm birth and tobacco exposure were directly associated with LBW. The risk of stillbirth was 3.22 times higher in women with antenatal depression and 73% lower in women with higher coping abilities. CONCLUSIONS: There was a high incidence of all adverse birth outcomes in Gondar Town. Depression and psychosocial risk factors had important indirect negative effects on risk, while partner support provided a positive indirect effect on the incidence of adverse birth outcomes. Interventions that focus on increasing partner engagement and participation in antenatal support may help reduce adverse birth outcomes by enhancing maternal resilience.

Alcohol and breast cancer risk: Middle-aged women's logic and recommendations for reducing consumption in Australia.

BACKGROUND: We aimed to understand the factors shaping alcohol consumption patterns in middle-aged women (45-64), and to identify participant-driven population- and policy-level strategies that may be used to addresses alcohol consumption and reduce breast cancer risk. METHODS: Semi-structured interviews (n = 35) were conducted with 'middle-aged' women conversant in English and living in South Australia with no history of breast cancer diagnosis. Data were deductively coded using a co-developed framework including variables relevant to our study objectives. Women were asked about their current level of awareness of the association between alcohol and breast cancer risk, and their personal recommendations for how to decrease consumption in middle-aged Australian women. RESULTS: Women discussed their previous efforts to decrease consumption, which we drew on to identify preliminary recommendations for consumption reduction. We identified a low level of awareness of alcohol and breast cancer risk, and confusion related to alcohol as a risk for breast cancer, but not always causing breast cancer. Participants suggested that education and awareness, through various means, may help to reduce consumption. CONCLUSIONS: Participants' description of strategies used to reduce their own consumption lead us to suggest that campaigns might focus on the more salient and immediate effects of alcohol (e.g. on physical appearance and mental health) rather than longer-term consequences. Critical considerations for messaging include addressing the personal, physical and social pleasures that alcohol provides, and how these may differ across socio-demographics.

Does Resilience Moderate the Relationship Between Stress and Smoking Status?

BACKGROUND: There is a growing evidence that resilience to stress can promote nonsmoking. However, few studies have undertaken quantitative research to investigate whether resilience, generated by internal and external factors, moderates the impact of stress on the likelihood of smoking. OBJECTIVE: This study aims to help fill this knowledge gap in relation to smokers and ex-smokers, and those people who have never smoked. METHODS: A large online cross-sectional survey was administered in Australia (2015-2016) to collect data on demographic variables, levels of internal and external resilience, and stress from current and past smokers (n = 400) and those who have never-smoked (n = 921). Logistic regressions were employed to test our hypotheses. RESULTS: Most participants were female (82%) and ranged between 18 and 77 years. Higher levels of reported perceived stress and stress-related variables did significantly predict smoking. The combined impact of internal and external resilience factors predicted never-smoking and lessened the relationship between perceived stress and stress-related variables, and the likelihood of smoking. CONCLUSION: These results are important because they suggest that the social environment should be developed to augment social support and internal properties such as developing "a strong sense of purpose in life" to encourage people not to commence smoking, rather than focus on smoking cessation.

Message on a bottle: are alcohol warning labels about cancer appropriate?

BACKGROUND: Although most Australians are unaware of the risk, there is strong evidence for a direct link between alcohol consumption and many types of cancer. Warning labels on alcohol products have been proposed as a cost-effective strategy to inform the community of this health risk. We aimed to identify how Australians might respond to such an approach. METHODS: We conducted a national online survey canvassing responses to four separate cancer warning messages on labels. The graphically presented messages were informed by qualitative data from a series of focus groups among self-identified 'light-to-moderate' drinkers. For each label, participants were asked their level of agreement with impact statements about raising awareness, prompting conversation, influencing drinking behaviour and educating others about cancer risk. We analysed responses according to demographic and other factors, including self-reported drinking behaviour (using the 3-item Alcohol Use Disorder Test - AUDIT-C - scores). RESULTS: Approximately 1600 participants completed the survey, which was open to all Australian adults over a period of 1 month in 2014. Overall, the labels were well received, with the majority (>70 %) agreeing all labels could raise awareness and prompt conversations about the cancer risk associated with alcohol. Around 50 % or less agreed that the labels could influence drinking behaviour, but larger proportions agreed that the labels would prompt them to discuss the issue with family and friends. Although sex, AUDIT-C score and age were significantly associated with agreement on bivariate analysis, multivariate analyses demonstrated that being inclined to act upon warning label recommendations in general was the most important predictor of agreement with all of the impact statements. Having a low AUDIT-C score also predicted agreement that the labels might prompt behaviour change in friends. CONCLUSIONS: The findings suggest that providing detailed warnings about cancer risk on alcohol products is a viable means of increasing public awareness of the health risks associated with alcohol consumption. Further research is needed to explore the ability of such warnings to influence behavioural intentions and actual drinking behaviour.