Major Developmental Transitions Research Articles

Spatially resolved transcriptomic analysis of the germinating barley grain.

Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14000 genes differentially regulated during the first 24 hafter imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.

Future research directions of the model marine tubeworm Hydroides elegans and synthesis of developmental staging of the complete life cycle.

The biofouling marine tube worm, Hydroides elegans, is an indirect developing polychaete with significance as a model organism for questions in developmental biology and the evolution of host-microbe interactions. However, a complete description of the life cycle from fertilization through sexual maturity remains scattered in the literature, and lacks standardization. Here, we present a unified staging scheme synthesizing the major morphological changes that occur during the entire life cycle of the animal. These data represent a complete record of the life cycle, and serve as a foundation for connecting molecular changes with morphology. The present synthesis and associated staging scheme are especially timely as this system gains traction within research communities. Characterizing the Hydroides life cycle is essential for investigating the molecular mechanisms that drive major developmental transitions, like metamorphosis, in response to bacteria.

Untargeted Proteomics and Metabolomics Analysis of Plant Organ Development.

Our understanding of major developmental transitions in plants and animals has been transformed by the emergence of omics technologies. The majority of leaf growth research has been conducted at the transcriptional level. Although historically understudied, alterations at the protein and metabolite levels have begun to gain traction in recent years. Here, we present a protocol for metabolite and protein extraction followed by untargeted metabolomics and proteomics analysis of the growing leaves.

OR14-1 Preimplantation embryo development is associated with both birth size and post-natal growth and can predict adult cardiovascular risk

Abstract Background The link between birth-size, early childhood growth and later life cardiovascular (CV) risk is well recognised. The contribution to CV risk of growth and cell differentiation during pre-implantation embryo development is unknown. Aims Develop a transcriptomic model of developmental trajectory in the pre-implantation embryo and link this model to birthweight, child growth and CV risk in later life. Methods Single cell RNA velocity1 and pseudotime analyses were used to infer developmental trajectory in the preimplantation human embryo2. Time series clustering was used to identify genes with similar activity patterns. These data were compared with independent genomic data from four further data sets. I) Birthweight genome wide association study (GWAS)3. II) Genes correlated with gestation4. III) A previously identified set of 55 genes that classify pre-hypertensive young adults using their blood methylome at age 0, 7 and 17 years5. IV) A set of genes with differential methylation associated with linear childhood growth6. Data sets III) and IV) were derived from the Avon Longitudinal Study of Parents and Children (n=6487). Enrichment was assessed using the hypergeometric test and confirmed via random permutation (1×105-fold) and z-score analysis. Random Forest was used to determine the predictive value presented as the area under the curve (AUC) of the receiver operating characteristic. Results 8256 genes contributed to the velocity of mRNA change in the preimplantation embryo and a temporal wave pattern was revealed with peaks of velocity at 3, 4, and 5-days post-fertilisation. Genes associated with the velocity of the developmental trajectory formed 6 clusters, in which metabolic pathways were over-represented (adj. p<0.02). We found that 16/60 birthweight GWAS (I) and 3096/10521 gestation correlated genes (II) were associated with embryonic developmental trajectory (both 2-fold enrichment, p<5×10-3). Furthermore, 11/55 pre-hypertensive associated genes (III) were linked with embryonic developmental trajectory (>10-fold enrichment, p<1×10-8), these 11 genes predicted adult pre-hypertension in small for gestational age catch-up growth (cuSGA) with an AUC=0.98. Of the 8256 developmental trajectory genes, 307 were differentially methylated in linear childhood growth (IV) (2.3-fold over-enrichment, p<1×10-8). Conclusion Waves of gene expression velocity occur in preimplantation human embryos. These waves mark major developmental transitions and form a transcriptomic developmental trajectory which is associated with both birthweight and gestation. The transcriptomic developmental trajectory genes are over-enriched for genes associated with the linear phase of childhood growth and for genes associated with and predictive for the development of adult pre-hypertension in cuSGA. Pre-implantation gene expression can therefore be linked to the origins of adult disease. 1. LaManno, et al. (2018). Nature. 560(7719): 494-8. 2. Petropoulos, et al. (2016). Cell. 165(4): 1012-26. 3. Horikoshi, et al. (2016). Nature 538(7624): 248-252. 4. Rasmussen, et al. (2022). Nature. https://doi.org/10.1038/s41586-021-04249-w 5. Garner, et al (2021). JES. 5: A654–A655. 6. Garner, et al (2019) ESPE Abstracts 92FC12.6 Presentation: Sunday, June 12, 2022 11:00 a.m. - 11:15 a.m.

How parenting pre‐teens compares to other child stages: Identifying opportunities to enhance adolescent mental health and wellbeing

AbstractBackgroundEarly adolescence is a key stage for parents and children before increasing child independence, yet little research has explored parents' experiences during this time.MethodsSecondary analysis using a broadly representative survey of 2600 parents explored challenges and opportunities for parents of 10–12 year‐olds relative to other child ages.ResultsParents of pre‐teens are mostly confident in their parenting, satisfied with children's sleep and they were more confident in knowing where to seek professional help than parents of younger and older children. Nevertheless, there were several challenges, including the use of positive discipline and partner support. Parents of adolescents reported less favourable experiences in several areas, including concerns about children's use of electronic devices, confidence and help‐seeking.ConclusionsFindings highlight the importance of pre‐adolescence as an opportune time to support parents prior to major developmental transitions associated with adolescence.

Past accomplishments and future challenges of the multi-omics characterization of leaf growth.

The advent of omics technologies has revolutionized biology and advanced our understanding of all biological processes, including major developmental transitions in plants and animals. Here, we review the vast knowledge accumulated concerning leaf growth in terms of transcriptional regulation before turning our attention to the historically less well-characterized alterations at the protein and metabolite level. We will then discuss how the advent of biochemical methods coupled with metabolomics and proteomics can provide insight into the protein–protein and protein–metabolite interactome of the growing leaves. We finally highlight the substantial challenges in detection, spatial resolution, integration, and functional validation of the omics results, focusing on metabolomics as a prerequisite for a comprehensive understanding of small-molecule regulation of plant growth.

Epigenetic Mechanisms of Senescence in Plants.

Senescence is a major developmental transition in plants that requires a massive reprogramming of gene expression and includes various layers of regulations. Senescence is either an age-dependent or a stress-induced process, and is under the control of complex regulatory networks that interact with each other. It has been shown that besides genetic reprogramming, which is an important aspect of plant senescence, transcription factors and higher-level mechanisms, such as epigenetic and small RNA-mediated regulators, are also key factors of senescence-related genes. Epigenetic mechanisms are an important layer of this multilevel regulatory system that change the activity of transcription factors (TFs) and play an important role in modulating the expression of senescence-related gene. They include chromatin remodeling, DNA methylation, histone modification, and the RNA-mediated control of transcription factors and genes. This review provides an overview of the known epigenetic regulation of plant senescence, which has mostly been studied in the form of leaf senescence, and it also covers what has been reported about whole-plant senescence.

Exploring the Utility of the Emerging Adulthood Theory Among Military Members and Veterans with Risky Substance Use

Emerging adult (EA; aged 18–29) military members experience major career, life, and developmental transitions. The conglomeration of these changes may influence or exacerbate anxiety or stress, produce challenges, and lead to negative coping mechanisms, such as substance use. This study sought to understand the utility of the five Emerging Adulthood Theory (EAT) dimensions among a sample of military members and veterans with risky substance use. To our knowledge, the applicability of EAT has not been explored with United States military populations. During 2019, we completed 24 semi-structured interviews. On average, participants were 24.9 years old, male, white, and in the United States Marine Corps. We asked about experiences transitioning into adulthood, military culture, and experiences of the five EAT dimensions. Three coders employed rigorous theory-driven thematic analysis procedures to piece together themes. We report EA military members’ experiences with the EAT dimensions, focusing on nuances related to the influence of military culture.

Roles of plant growth regulators on flowering of rose (Rosa hybrida L.’Red Rose’)

Rose is the most popular ornamental flower all over the world, which is used as garden plants and cut flowers. In the case of Rosa hybrida L. ’Red Rose’, flowering provides the major developmental transition from the vegetative to the reproductive stage, and reproduction is one of the most important phases in an organism’s life cycle. In this study, the morphological and physiological changes during the flower development of rose, which is planted in the garden, and roles of plant growth regulators on the flowering of in vitro vegetative shoots of rose were analyzed. The development of a flower includes three stages: the shoot apical meristem, floral meristem, floral bud. Levels of cytokinin, auxins, and gibberellins increased in the transition of meristem from the shoot apical meristem to the floral meristem stage. Plant growth regulators have important effects on the shoot apical meristem cell division and flowering. The combination of 0.5 mg.L−1 GA3, 0.1 mg.L−1 NAA, 2.5 or 3.0 mg.L−1 BA to Murashige and Skoog (MS) medium induces the floral transition of the in vitro vegetative shoots with the highest percentage (41%) as well as growth and development in comparison to the other treatments after 10 weeks. Then, the in vitro floral meristem continuously developed into a flower bud after 12 weeks.

Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis

Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant.

Drosophila E93 promotes adult development and suppresses larval responses to ecdysone during metamorphosis

Pulses of the steroid hormone ecdysone act through transcriptional cascades to direct the major developmental transitions during the Drosophila life cycle. These include the prepupal ecdysone pulse, which occurs 10 ​hours after pupariation and triggers the onset of adult morphogenesis and larval tissue destruction. E93 encodes a transcription factor that is specifically induced by the prepupal pulse of ecdysone, supporting a model proposed by earlier work that it specifies the onset of adult development. Although a number of studies have addressed these functions for E93, little is known about its roles in the salivary gland where the E93 locus was originally identified. Here we show that E93 is required for development through late pupal stages, with mutants displaying defects in adult differentiation and no detectable effect on the destruction of larval salivary glands. RNA-seq analysis demonstrates that E93 regulates genes involved in development and morphogenesis in the salivary glands, but has little effect on cell death gene expression. We also show that E93 is required to direct the proper timing of ecdysone-regulated gene expression in salivary glands, and that it suppresses earlier transcriptional programs that occur during larval and prepupal stages. These studies support the model that the stage-specific induction of E93 in late prepupae provides a critical signal that defines the end of larval development and the onset of adult differentiation.

Negative evaluation of role transitions is associated with perceived stress and alcohol consequences: Examination of the Transitions Overload Model in young adulthood using two years of monthly data.

Young adulthood is characterized by transitions into and out of social roles in multiple domains. Consistent with self-medication models of alcohol use, the Transitions Overload Model (J Stud Alcohol Suppl, 14, 2002, 54) hypothesizes that one cause of increased alcohol use during young adulthood may be the stress of navigating simultaneous role transitions. This study examined the simultaneous occurrence of major developmental role transitions in the domains of education, employment, romantic relationships, and residential status and their associations with perceived stress, heavy episodic drinking (HED), and negative alcohol-related consequences. Further, we extended the Transitions Overload Model to explore whether the number of transitions rated as having a negative impact on one's life was related to perceived stress, HED, and alcohol-related consequences. A community sample of young adult drinkers (N=767, 57% women, ages 18 to 25years) in the Pacific Northwest provided monthly data across 2years. Multilevel models were used to assess the average (between-person) and month-to-month (within-person) associations of role transitions with perceived stress, HED, and negative alcohol-related consequences. Although having more role transitions was positively associated with HED frequency and alcohol-related consequences at both the between- and within-person (monthly) levels, it was not associated with increased stress. The number of transitions rated as having a negative impact on one's life, however, was positively associated with stress. Thus, rather than the total number of transitions, it is the number of negatively perceived major developmental role transitions that is associated with perceived stress and increased risk for negative alcohol-related consequences. Contrary to Transitions Overload Model assumptions, more transitions were not a significant predictor of more perceived stress; rather, the evaluation of the transition as negative was associated with stress and negative alcohol-related outcomes. This distinction may help elucidate the etiology of stress and subsequent alcohol consequences and identify individuals at-risk of these effects.

Genome Expression Dynamics Reveal the Parasitism Regulatory Landscape of the Root-Knot Nematode Meloidogyne incognita and a Promoter Motif Associated with Effector Genes

Root-knot nematodes (genus Meloidogyne) are the major contributor to crop losses caused by nematodes. These nematodes secrete effector proteins into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effector genes. The details of how root-knot nematodes regulate transcription remain sparse. Here, we report a life stage-specific transcriptome of Meloidogyne incognita. Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands, providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus, and we name it Mel-DOG. Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode and identify a new set of candidate effector genes that will guide future functional analyses.

Timing the Juvenile-Adult Neurohormonal Transition: Functions and Evolution.

Puberty and metamorphosis are two major developmental transitions linked to the reproductive maturation. In mammals and vertebrates, the central brain acts as a gatekeeper, timing the developmental transition through the activation of a neuroendocrine circuitry. In addition to reproduction, these neuroendocrine axes and the sustaining genetic network play additional roles in metabolism, sleep and behavior. Although neurohormonal axes regulating juvenile-adult transition have been classically considered the result of convergent evolution (i.e., analogous) between mammals and insects, recent findings challenge this idea, suggesting that at least some neuroendocrine circuits might be present in the common bilaterian ancestor Urbilateria. The initial signaling pathways that trigger the transition in different species appear to be of a single evolutionary origin and, consequently, many of the resulting functions are conserved with a few other molecular players being co-opted during evolution.

Zygotic Genome Activation: Critical Prelude to the Most Important Time of Your Life.

Activation of the embryonic genome during development represents a major developmental transition in all species. The history of its exploration began in the 1950s-1960s, when this idea was put forward and proven experimentally by Alexander Neyfakh. He observed the aberrant development of fish embryos upon X-ray irradiation and noted the different developmental outcomes depending on the stage when fertilized eggs were subjected to irradiation. Neyfakh also discriminated a regional difference of X-irradiation between the nucleus and the cytoplasm. By selecting the X-ray dose causing nuclear damage, he determined the beginning of zygotic transcription, which at that time became known as the morphogenetic function of nuclei. His team defined the link of zygotic transcription with the asynchronization of cell division and cell migration, the two other hallmarks, which along with the morphogenetic function (or the zygotic genome activation), are at the core of the mid-blastula transition during development. Within this framework, current studies using maternal mutants and application of modern methods of whole-embryo and single-cell transcriptomics begin to decipher the molecular mechanisms of the mid-blastula transition (or the maternal-zygotic transition).

Dissecting the roles of FTZ-F1 in larval molting and pupation, and the sublethal effects of methoxyfenozide on Helicoverpa armigera.

In holometabolous insects, the major developmental transitions - larval molting and pupation - are triggered by a pulse of 20-hydroxyecdysone (20E) and coordinated by juvenile hormone. Methoxyfenozide (MF), an ecdysteroid agonist, represents a new class of insect growth regulators and is effective against lepidopteran pests. Fushi-tarazu factor 1 (FTZ-F1) is an ecdysone-inducible transcription factor. To date, the effect of MF on 20E-response genes remains unclear, and we speculate the involvement of FTZ-F1 in MF's growth regulating effect. MF at LC25 and LC10 caused severe ecdysis failure in Helicoverpa armigera, extended their larval duration, lowered their pupal weight, and reduced the respiratory, pupation and emergence rates. Furthermore, sublethal doses of MF inhibited ecdysteroidogenesis and lowered the intrinsic 20E titer, but showed an inductive effect on 20E-response genes including HaFTZ-F1. HaFTZ-F1, predominantly expressed in larval epidermis, was markedly upregulated before or right after larval ecdysis, and maintained a high level in prepupal stage. Knockdown of HaFTZ-F1 in 4th-instar larvae severely impaired larval ecdysis, whereas its knockdown in final-instar larvae caused abnormal pupation. Moreover, knocking down HaFTZ-F1 downregulated three critical ecdysteroidogenesis genes, lowered 20E titer, and suppressed the expression of 20E receptors and 20E-response genes. The introduction of 20E into HaFTZ-F1-RNAi larvae partly relieved the negative effects on the 20E-induced signaling cascade. Our findings reveal the adverse effects of sublethal doses of MF on the development of H. armigera and elucidate the resulting perturbations on the 20E-induced signaling cascade; we propose that HaFTZ-F1 regulates ecdysis and pupation by mediating 20E titer and its signaling pathway. © 2020 Society of Chemical Industry.

Interorgan communication in the control of metamorphosis.

Steroid hormones control major developmental transitions such as metamorphosis in insects and puberty in mammals. The juvenile must attain a sufficient size before it begins maturation in order to give rise to a properly sized and reproductively fit adult. Studies in the insect Drosophila have begun to reveal a remarkable example of the complex interplay between different organs and the neuroendocrine system that controls the production of the steroid ecdysone, which triggers metamorphosis. This review discusses the inter-organ signals mediating this crosstalk, which allows the neuroendocrine system to assess nutrient availability and growth status of internal organs, ensuring that maturation is initiated at the appropriate time. We discuss how the neuroendocrine system integrates signals from different tissues to coordinate growth and maturation. These studies are still unraveling the organ-to-organ signaling networks that control the timing of metamorphosis, defining important principles underlying the logic of growth and maturation coordination in animals.

Genetic growth potential, rather than phenotypic size, predicts migration phenotype in Atlantic salmon.

Knowledge of the relative importance of genetic versus environmental determinants of major developmental transitions is pertinent to understanding phenotypic evolution. In salmonid fishes, a major developmental transition enables a risky seaward migration that provides access to feed resources. In Atlantic salmon, initiation of the migrant phenotype, and thus age of migrants, is presumably controlled via thresholds of a quantitative liability, approximated by body size expressed long before the migration. However, how well size approximates liability, both genetically and environmentally, remains uncertain. We studied 32 Atlantic salmon families in two temperatures and feeding regimes (fully fed, temporarily restricted) to completion of migration status at age 1 year. We detected a lower migrant probability in the cold (0.42) than the warm environment (0.76), but no effects of male maturation status or feed restriction. By contrast, body length in late summer predicted migrant probability and its control reduced migrant probability heritability by 50-70%. Furthermore, migrant probability and length showed high heritabilities and between-environment genetic correlations, and were phenotypically highly correlated with stronger genetic than environmental contributions. Altogether, quantitative estimates for the genetic and environmental effects predicting the migrant phenotype indicate, for a given temperature, a larger importance of genetic than environmental size effects.

Impact of COVID-19 on the Perinatal Period Through a Biopsychosocial Systemic Framework.

The perinatal period involves major developmental transitions which can be conceptualized through a biopsychosocial (BPS; Engel in Science 196:129–136, 1977, 10.1126/science.847460, in The American Journal of Psychiatry 137:535–544, 1980, 10.1176/ajp.137.5.535), systemic (von Bertalanffy, General system theory: Foundations, development, applications, George Braziller, New York, 1968) framework. Thus, no one domain of health in the perinatal period can be understood without exploring how the other domains are both impacted by and impacting the others. As a result of COVID-19, popular media is paying special attention to the biomedical domain of women in the perinatal period as it relates to health outcomes and changes in perinatal healthcare policies; however, considerably less attention is being paid to the other BPS health domains and systemic impacts. This paper will outline U.S. changes in healthcare as a result of the COVID-19 pandemic for individuals, couples, and families within the perinatal period (i.e., family planning and conception, prenatal, labor and delivery, and postpartum) and explore the unique psychosocial, systemic impacts. Recommendations for care, including telehealth and virtual support options, and future directions for research will be provided.

Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq

BackgroundPlasmodium parasites undergo several major developmental transitions during their complex lifecycle, which are enabled by precisely ordered gene expression programs. Transcriptomes from the 48-h blood stages of the major human malaria parasite Plasmodium falciparum have been described using cDNA microarrays and RNA-seq, but these assays have not always performed well within non-coding regions, where the AT-content is often 90–95%.ResultsWe developed a directional, amplification-free RNA-seq protocol (DAFT-seq) to reduce bias against AT-rich cDNA, which we have applied to three strains of P. falciparum (3D7, HB3 and IT). While strain-specific differences were detected, overall there is strong conservation between the transcriptional profiles. For the 3D7 reference strain, transcription was detected from 89% of the genome, with over 78% of the genome transcribed into mRNAs. We also find that transcription from bidirectional promoters frequently results in non-coding, antisense transcripts. These datasets allowed us to refine the 5′ and 3′ untranslated regions (UTRs), which can be variable, long (> 1000 nt), and often overlap those of adjacent transcripts.ConclusionsThe approaches applied in this study allow a refined description of the transcriptional landscape of P. falciparum and demonstrate that very little of the densely packed P. falciparum genome is inactive or redundant. By capturing the 5′ and 3′ ends of mRNAs, we reveal both constant and dynamic use of transcriptional start sites across the intraerythrocytic developmental cycle that will be useful in guiding the definition of regulatory regions for use in future experimental gene expression studies.