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The sperm epigenome is thought to affect the developmental programming of the resulting embryo, influencing health and disease in later life. Age‐related methylation changes in the sperm of old fathers may mediate the increased risks for reproductive and offspring medical problems. The impact of paternal age on sperm methylation has been extensively studied in humans and, to a lesser extent, in rodents and cattle. Here, we performed a comparative analysis of paternal age effects on protein‐coding genes in the human and marmoset sperm methylomes. The marmoset has gained growing importance as a non‐human primate model of aging and age‐related diseases. Using reduced representation bisulfite sequencing, we identified age‐related differentially methylated transcription start site (ageTSS) regions in 204 marmoset and 27 human genes. The direction of methylation changes was the opposite, increasing with age in marmosets and decreasing in humans. None of the identified ageTSS was differentially methylated in both species. Although the average methylation levels of all TSS regions were highly correlated between marmosets and humans, with the majority of TSS being hypomethylated in sperm, more than 300 protein‐coding genes were endowed with species‐specifically (hypo)methylated TSS. Several genes of the glycosphingolipid (GSL) biosynthesis pathway, which plays a role in embryonic stem cell differentiation and regulation of development, were hypomethylated (<5%) in human and fully methylated (>95%) in marmoset sperm. The expression levels and patterns of defined sets of GSL genes differed considerably between human and marmoset pre‐implantation embryo stages and blastocyst tissues, respectively. [ABSTRACT FROM AUTHOR]

Colicin (Col) plasmid contains colicin encoding genes arranged in an operon controlled by an SOS inducible promoter. Therefore, any external stresses to the host cell can induce the expression of the downstream genes in the Col operon, including a lysis gene. The lysis protein is involved in the extracellular release of colicin through lysis of the producer cells, which causes a decline in culture turbidity. However, it is not yet known that E. coli cells with the native pColE9-J plasmid hold the same level of cell death at the population level following a set of induced conditions. In this study, using a mitomycin C sensitivity assay along with a live dead staining method of detection, we showed that the native pColE9-J plasmid, which unusually carries an extended Col operon (ColE9) containing two lysis genes, did not confer a rapid decline in the culture turbidity following induction with mitomycin C. Interestingly a subset of the cells suffered perturbation of their outer membrane, which was not observed from single lysis mutant (∆ celE or ∆ celI) cells. This observed heterogeneity in the colicin E9 release leading to differential outer membrane perforation may bring a competitive advantage to these cells in a mixed population. [ABSTRACT FROM AUTHOR]

The early specification and rapid growth of extraembryonic membranes are distinctive hallmarks of primate embryogenesis. These complex tasks are resolved through an intricate combination of signals controlling the induction of extraembryonic lineages and, at the same time, safeguarding the pluripotent epiblast. Here, we delineate the signals orchestrating primate epiblast and amnion identity. We encapsulated marmoset pluripotent stem cells into agarose microgels and identified culture conditions for the development of epiblast- and amnion-spheroids. Spatial identity mapping authenticated spheroids generated in vitro by comparison with marmoset embryos in vivo. We leveraged the microgel system to functionally interrogate the signalling environment of the post-implantation primate embryo. Single-cell profiling of the resulting spheroids demonstrated that activin/nodal signalling is required for embryonic lineage identity. BMP4 promoted amnion formation and maturation, which was counteracted by FGF signalling. Our combination of microgel culture, single-cell profiling and spatial identity mapping provides a powerful approach to decipher the essential cues for embryonic and extraembryonic lineage formation in primate embryogenesis. [ABSTRACT FROM AUTHOR]

The trophoblast lineage safeguards fetal development by mediating embryo implantation, immune tolerance, nutritional supply and gas exchange. Human trophoblast stem cells (hTSCs) provide a platform to study lineage specification of placental tissues; however, the regulatory network controlling self-renewal remains elusive. Here, we present a single-cell atlas of human trophoblast development from zygote to mid-gestation together with single-cell profiling of hTSCs. We determine the transcriptional networks of trophoblast lineages in vivo and leverage probabilistic modelling to identify a role for MAPK signalling in trophoblast differentiation. Placenta- and blastoidderived hTSCs consistently map between late trophectoderm and early cytotrophoblast, in contrast to blastoid-trophoblast, which correspond to trophectoderm. We functionally assess the requirement of the predicted cytotrophoblast network in an siRNAscreen and reveal 15 essential regulators for hTSC self-renewal, including MAZ, NFE2L3, TFAP2C, NR2F2 and CTNNB1. Our human trophoblast atlas provides a powerful analytical resource to delineate trophoblast cell fate acquisition, to elucidate transcription factors required for hTSC self-renewal and to gauge the developmental stage of in vitro cultured cells. [ABSTRACT FROM AUTHOR]

SUMMARY: The photosynthetic capacity of mature leaves increases after several days' exposure to constant or intermittent episodes of high light (HL) and is manifested primarily as changes in chloroplast physiology. How this chloroplast‐level acclimation to HL is initiated and controlled is unknown. From expanded Arabidopsis leaves, we determined HL‐dependent changes in transcript abundance of 3844 genes in a 0–6 h time‐series transcriptomics experiment. It was hypothesized that among such genes were those that contribute to the initiation of HL acclimation. By focusing on differentially expressed transcription (co‐)factor genes and applying dynamic statistical modelling to the temporal transcriptomics data, a regulatory network of 47 predominantly photoreceptor‐regulated transcription (co‐)factor genes was inferred. The most connected gene in this network was B‐BOX DOMAIN CONTAINING PROTEIN32 (BBX32). Plants overexpressing BBX32 were strongly impaired in acclimation to HL and displayed perturbed expression of photosynthesis‐associated genes under LL and after exposure to HL. These observations led to demonstrating that as well as regulation of chloroplast‐level acclimation by BBX32, CRYPTOCHROME1, LONG HYPOCOTYL5, CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA‐105 are important. In addition, the BBX32‐centric gene regulatory network provides a view of the transcriptional control of acclimation in mature leaves distinct from other photoreceptor‐regulated processes, such as seedling photomorphogenesis. Significance Statement: Identifying genes that control plants' intrinsic photosynthetic capacity would provide opportunities for increasing crop productivity. Photosynthetic capacity in mature leaves increases after several days' exposure to episodes of high‐light intensity (HL), which is defined as HL acclimation. Using temporal transcriptomics data and dynamic modelling, we inferred a BBX32‐centric 47‐member Gene Regulatory Network, members of which control, in the first hours of HL exposure, cellular processes that result in enhanced photosynthetic capacity 5 days later. [ABSTRACT FROM AUTHOR]

Cover legend: The cover image is based on the Article Age‐related and species‐specific methylation changes in the protein‐coding marmoset sperm epigenome by Marcus Dittrich et al., https://doi.org/10.1111/acel.14200. [ABSTRACT FROM AUTHOR]

The uterus is the organ for embryo implantation and fetal development. Most current models of the uterus are centred around capturing its function during later stages of pregnancy to increase the survival in pre-term births. However, in vitro models focusing on the uterine tissue itself would allow modelling of pathologies including endometriosis and uterine cancers, and open new avenues to investigate embryo implantation and human development. Motivated by these key questions, we discuss how stem cell-based uteri may be engineered from constituent cell parts, either as advanced self-organising cultures, or by controlled assembly through microfluidic and print-based technologies. Bergmann et al. discuss the construction of synthetic uteri to model the earliest stages of human embryogenesis and associated pathologies. They highlight the constituent components from which a synthetic uterus may be engineered, propose a modular approach to assembling synthetic uteri and discuss how these technologies can shed light on implantation failure and uterine pathologies. [ABSTRACT FROM AUTHOR]

Background: The association between diet and head and neck cancer (HNC) survival is unclear. Methods: Cox proportional hazard models measured the association between fruit, vegetable, and deep‐fried food intake and HNC overall survival adjusting for clinical, social and lifestyle variables including smoking, alcohol, and HPV status. Results: Fruit and vegetable intake and improved survival were associated in minimally adjusted analyses. Following adjustment for smoking and alcohol consumption (fully adjusted analyses), the association with survival disappeared for fruit (HR 0.91, 95% CI 0.67, 1.23; P for trend = .55) and attenuated for vegetables (HR 0.79, 95% CI 0.61, 1.03; P for trend = .04). We observed no association between survival and deep‐fried food intake in minimally adjusted or fully adjusted analyses (HR 0.88 95% CI 0.72, 1.07; P for trend = .13). Conclusions: Vegetable intake and HNC survival are modestly associated. There is some confounding by tobacco and alcohol consumption. [ABSTRACT FROM AUTHOR]

Background: People with head and neck cancer have higher comorbidity levels but it remains unclear if pretreatment comorbidity is an independent prognosticator in head and neck cancer. Methods: Survival analyses were performed using data from participants in a UK multicentre cohort study with cancers of the oral cavity (n = 668), oropharynx (n = 1074), and larynx (n = 530). Survival analyses were incrementally adjusted for age, sex, marital status, income, education, stage, alcohol, and smoking. Results: After adjusting for demographic, clinical, and behavioral confounders, higher baseline comorbidity was associated with reduced overall survival (mild comorbidity HR = 1.4, 95% CI = 1.1, 1.7; moderate comorbidity HR = 1.7, 95% CI = 1.3, 2.2; severe comorbidity HR = 2.8, 95% CI = 1.9, 4.; P‐trend<.001). Conclusions: Our findings suggest that comorbidity is an independent prognosticator for overall survival in head and neck cancer. Comorbid illnesses should be considered in the assessment and treatment planning of people with head and neck cancer. [ABSTRACT FROM AUTHOR]

Tobacco smoking and alcohol consumption are well‐established risk factors for head and neck cancer. The prognostic role of smoking and alcohol intake at diagnosis have been less well studied. We analysed 1,393 people prospectively enrolled into the Head and Neck 5000 study (oral cavity cancer, n=403; oropharyngeal cancer, n=660; laryngeal cancer, n=330) and followed up for a median of 3.5 years. The primary outcome was all‐cause mortality. We used Cox proportional hazard models to derive minimally adjusted (age and gender) and fully adjusted (age, gender, ethnicity, stage, comorbidity, body mass index, HPV status, treatment, education, deprivation index, income, marital status, and either smoking or alcohol use) mortality hazard ratios (HR) for the effects of smoking status and alcohol intake at diagnosis. Models were stratified by cancer site, stage and HPV status. The fully‐adjusted HR for current versus never‐smokers was 1.7 overall (95% confidence interval [CI] 1.1, 2.6). In stratified analyses, associations of smoking with mortality were observed for oropharyngeal and laryngeal cancers (fully adjusted HRs for current smokers: 1.8 (95% CI=0.9, 3.40 and 2.3 (95% CI=0.8, 6.4)). We found no evidence that people who drank hazardous to harmful amounts of alcohol at diagnosis had a higher mortality risk compared to non‐drinkers (HR=1.2 (95% CI=0.9, 1.6)). There was no strong evidence that HPV status or tumour stage modified the association of smoking with survival. Smoking status at the time of a head and neck cancer diagnosis influenced all‐cause mortality in models adjusted for important prognostic factors. [ABSTRACT FROM AUTHOR]

Leaf senescence involves degenerative but active biological processes that require balanced regulation of pro- and anti-senescing activities. Ethylene and cytokinin are major antagonistic regulatory hormones that control the timing and progression rate of leaf senescence. To identify the roles of these hormones in the regulation of leaf senescence in Arabidopsis, global gene expression profiles in detached leaves of the wild type, an ethylene-insensitive mutant (ein2/ore3), and a constitutive cytokinin response mutant (ahk3/ore12) were investigated during dark-induced leaf senescence. Comparative transcriptome analyses revealed that genes involved in oxidative or salt stress response were preferentially altered in the ein2/ore3 mutant, whereas genes involved in ribosome biogenesis were affected in the ahk3/ore12 mutant during dark-induced leaf senescence. Similar results were also obtained for developmental senescence. Through extensive molecular and physiological analyses in ein2/ore3 and ahk3/ore12 during darkinduced leaf senescence, together with responses when treated with cytokinin and ethylene inhibitor, we conclude that ethylene acts as a senescence-promoting factor via the transcriptional regulation of stress-related responses, whereas cytokinin acts as an anti-senescing agent by maintaining cellular activities and preserving the translational machinery. These findings provide new insights into how plants utilize two antagonistic hormones, ethylene and cytokinin, to regulate the molecular programming of leaf senescence. [ABSTRACT FROM AUTHOR]

Motivation: Time course data are often used to study the changes to a biological process after perturbation. Statistical methods have been developed to determine whether such a perturbation induces changes over time, e.g. comparing a perturbed and unperturbed time course dataset to uncover differences. However, existing methods do not provide a principled statistical approach to identify the specific time when the two time course datasets first begin to diverge after a perturbation; we call this the perturbation time. Estimation of the perturbation time for different variables in a biological process allows us to identify the sequence of events following a perturbation and therefore provides valuable insights into likely causal relationships. Results: We propose a Bayesian method to infer the perturbation time given time course data from a wild-type and perturbed system. We use a non-parametric approach based on Gaussian Process regression. We derive a probabilistic model of noise-corrupted and replicated time course data coming from the same profile before the perturbation time and diverging after the perturbation time. The likelihood function can be worked out exactly for this model and the posterior distribution of the perturbation time is obtained by a simple histogram approach, without recourse to complex approximate inference algorithms. We validate the method on simulated data and apply it to study the transcriptional change occurring in Arabidopsis following inoculation with Pseudomonas syringae pv. tomato DC3000 versus the disarmed strain DC3000hrpA. [ABSTRACT FROM AUTHOR]

Background: This study's objectives were to investigate the prevalence of self-reported knee and hip osteoarthritis (OA) stratified by age and sex and to examine the association of modifiable factors with knee and hip OA prevalence. The study was conducted using randomly sampled data gathered from four communities in the province of Alberta, Canada.Methods: A large adult population sample (N = 4733) of individuals ≥18 years were selected. Health-related information was collected through telephone interviews and community measurement clinics for which a sub-sample (N = 1808) attended. Participants self-reported OA during telephone interviews. Clinic interviews further assessed if the diagnosis was made by a health care professional. Statistical analyses compared prevalence of OA between sexes and across age categories. Associations between modifiable factors for OA and the prevalence of knee and hip OA were assessed using binary logistic regression modelling.Results: Overall prevalence of self-reported OA in the total sample was 14.8 %, where 10.5 % of individuals reported having knee OA and 8.5 % reported having hip OA. Differences in prevalence were found for males and females across age categories for both knee and hip OA. In terms of modifiable factors, being obese (BMI >30 kg/m2) was significantly associated with the prevalence of knee (OR: 4.37; 95 % CI: 2.08,9.20) and hip (OR: 2.52; 95 % CI: 1.17,5.43) OA. Individuals who stand or walk a lot, but do not carry or lift things during their occupational activities were 2.0 times less likely to have hip OA (OR: 0.50; 95 % CI: 0.26,0.96). Individuals who usually lift or carry light loads or have to climb stairs or hills were 2.2 times less likely to have hip OA (OR: 0.45; 95 % CI: 0.21,0.95). The odds of having hip OA were 1.9 times lower in individuals consuming recommended or higher vitamin C intake (OR: 0.52; 95 % CI: 0.29,0.96). Significant differences in prevalence were found for both males and females across age categories.Conclusion: The prevalence of knee and hip OA obtained in this study is comparable to other studies. Females have greater knee OA prevalence and a greater proportion of women have mobility limitations as well as hip and knee pain; it is important to target this sub-group. [ABSTRACT FROM AUTHOR]

Here we introduce the causal structure identification (CSI) package, a Gaussian process based approach to inferring gene regulatory networks (GRNs) from multiple time series data. The standard CSI approach infers a single GRN via joint learning from multiple time series datasets; the hierarchical approach (HCSI) infers a separate GRN for each dataset, albeit with the networks constrained to favor similar structures, allowing for the identification of context specific networks. The software is implemented in MATLAB and includes a graphical user interface (GUI) for user friendly inference. Finally the GUI can be connected to high performance computer clusters to facilitate analysis of large genomic datasets. [ABSTRACT FROM AUTHOR]