Developmental Progression Research Articles

Tail-specific protease is an essential Chlamydia virulence factor that mediates the differentiation of elementary bodies into reticulate bodies.

Tail-specific proteases (Tsp) are members of a widely distributed family of serine proteases that commonly target and process periplasmic proteins in Gram-negative bacteria. The obligately intracellular, Gram-negative Chlamydia encode a highly conserved Tsp homolog whose target and function are unclear. We identified a Chlamydia muridarum mutant with a nonsense mutation in tsp. Differentiation of the tsp mutant elementary bodies into vegetative reticulate bodies was delayed at 37°C and completely blocked at 40°C. Tsp localized to C. muridarum cells but was not detected outside the inclusion, suggesting that it targets chlamydial rather than host proteins. The abundance of key chlamydia outer membrane complex and virulence-related proteins differed in wild-type and tsp mutant elementary bodies, consistent with the possibility that Tsp regulates developmental cycle progression. The altered abundances of chlamydial structural and virulence factors could explain why the mutant, but not an isogenic recombinant with wild-type tsp, was highly attenuated in a mouse intravaginal infection model. Thus, chlamydial Tsp is required for timely differentiation of elementary bodies into reticulate bodies in vitro and is an essential virulence factor in vivo.

Clinical characteristics of patients with P4HTM variant-associated epilepsy and therapeutic exploration: a case report and literature review

The P4HTM gene encodes a transmembrane prolyl 4-hydroxylase, which is responsible for the degradation of hypoxia-inducible transcription factors (HIF) under normoxia. Clinically, biallelic P4HTM variants have been identified in patients with hypotonia, hypoventilation, intellectual disabilities, dysautonomia, epilepsy, and eye abnormalities (HIDEA syndrome). Seizure was one of the most prominent symptoms. However, the clinical features of patients with epilepsy associated with P4HTM variants remain unclear. In this report, we describe a one-month-old infant with HIDEA syndrome caused by compound heterozygous P4HTM variants (c.300dupG/p.Gly103Argfs*22 and c.488C > T/p.Ala163Val). The infant presented with clonic seizures of focal onset that responded well to valproate, but with profound intellectual disability and global developmental delay at the last follow-up at 3 years old. A review of the existing literature indicates that seizures in this population typically begin early in infancy, manifest in multiple types, and are relatively well controlled. Epilepsy seemed unrelated to developmental outcomes or disease progression. Valproate, which has HIF-1α inhibiting properties, may be a promising treatment avenue for this population.

Single essential oils and their binary mixtures protect against ethanol-induced defects in a zebrafish fetal alcohol spectrum disorder model at the same level as folic acid

This study evaluated protective effects of clove (SEO), thyme white (TEO), oregano (OEO), and caraway (CEO) essential oils (EOs), and their binary mixtures, in a zebrafish fetal alcohol spectrum disorder model. Furthermore, folic acid (FA) was used for comparison as it had previously shown protection against ethanol (EtOH)-induced defects. The co-exposure of zebrafish embryos to EtOH (150 mM) and FA (75 μM) or EOs and their binary mixtures (0.5-1 mg/L) was carried out during 6 or 22 hours postfertilization (hpf). Different developmental endpoints (epiboly measurement, survival rate at 24 hpf, embryonic developmental progression measurement at 24 hpf, larval development at 48-96 hpf, and hatching rate at 72-96 hpf) were evaluated at 8-96 hpf. EtOH exposure reduced epiboly. Only FA and the SEO + TEO binary mixture protected against these defects, and SEO and TEO single exposure showed partial protection. Therefore, these groups were chosen for subsequent experiments. At 24 hpf, EtOH showed developmental delay and hatching rate was delayed at 72 hpf. FA, SEO, TEO, and SEO + TEO partially protected against these defects. This study supports the conclusion that FA partially protects against EtOH-induced defects. SEO and TEO single exposure partially protect against EtOH-induced defects. However, the binary mixture of SEO + TEO was more effective, showing similar efficacy as FA.

Genomic prediction of cereal crop architectural traits using models informed by gene regulatory circuitries from maize.

Plant architecture is a major determinant of planting density, which enhances productivity potential for crops per unit area. Genomic prediction is well positioned to expedite genetic gain of plant architectural traits since they are typically highly heritable. Additionally, the adaptation of genomic prediction models to query predictive abilities of markers tagging certain genomic regions could shed light on the genetic architecture of these traits. Here, we leveraged transcriptional networks from a prior study that contextually described developmental progression during tassel and leaf organogenesis in maize (Zea mays) to inform genomic prediction models for architectural traits. Since these developmental processes underlie tassel branching and leaf angle, 2 important agronomic architectural traits, we tested whether genes prioritized from these networks quantitatively contribute to the genetic architecture of these traits. We used genomic prediction models to evaluate the ability of markers in the vicinity of prioritized network genes to predict breeding values of tassel branching and leaf angle traits for 2 diversity panels in maize and diversity panels from sorghum (Sorghum bicolor) and rice (Oryza sativa). Predictive abilities of markers near these prioritized network genes were similar to those using whole-genome marker sets. Notably, markers near highly connected transcription factors from core network motifs in maize yielded predictive abilities that were significantly greater than expected by chance in not only maize but also closely related sorghum. We expect that these highly connected regulators are key drivers of architectural variation that are conserved across closely related cereal crop species.

Recent Developments in Single-Cell Metabolomics by Mass Spectrometry─A Perspective.

Recent advancements in single-cell (sc) resolution analyses, particularly in sc transcriptomics and sc proteomics, have revolutionized our ability to probe and understand cellular heterogeneity. The study of metabolism through small molecules, metabolomics, provides an additional level of information otherwise unattainable by transcriptomics or proteomics by shedding light on the metabolic pathways that translate gene expression into functional outcomes. Metabolic heterogeneity, critical in health and disease, impacts developmental outcomes, disease progression, and treatment responses. However, dedicated approaches probing the sc metabolome have not reached the maturity of other sc omics technologies. Over the past decade, innovations in sc metabolomics have addressed some of the practical limitations, including cell isolation, signal sensitivity, and throughput. To fully exploit their potential in biological research, however, remaining challenges must be thoroughly addressed. Additionally, integrating sc metabolomics with orthogonal sc techniques will be required to validate relevant results and gain systems-level understanding. This perspective offers a broad-stroke overview of recent mass spectrometry (MS)-based sc metabolomics advancements, focusing on ongoing challenges from a biologist's viewpoint, aimed at addressing pertinent and innovative biological questions. Additionally, we emphasize the use of orthogonal approaches and showcase biological systems that these sophisticated methodologies are apt to explore.

Altering the redox status of Chlamydia trachomatis directly impacts its developmental cycle progression.

Chlamydia trachomatis is an obligate intracellular bacterial pathogen with a unique developmental cycle. It differentiates between two functional and morphological forms: elementary body (EB) and reticulate body (RB). The signals that trigger differentiation from one form to the other are unknown. EBs and RBs have distinctive characteristics that distinguish them, including their size, infectivity, proteome, and transcriptome. Intriguingly, they also differ in their overall redox status as EBs are oxidized and RBs are reduced. We hypothesize that alterations in redox may serve as a trigger for secondary differentiation. To test this, we examined the function of the primary antioxidant enzyme alkyl hydroperoxide reductase subunit C (AhpC), a well-known member of the peroxiredoxins family, in chlamydial growth and development. Based on our hypothesis, we predicted that altering the expression of ahpC would modulate chlamydial redox status and trigger earlier or delayed secondary differentiation. To test this, we created ahpC overexpression and knockdown strains. During ahpC knockdown, ROS levels were elevated, and the bacteria were sensitive to a broad set of peroxide stresses. Interestingly, we observed increased expression of EB-associated genes and concurrent higher production of EBs at an earlier time in the developmental cycle, indicating earlier secondary differentiation occurs under elevated oxidation conditions. In contrast, overexpression of AhpC created a resistant phenotype against oxidizing agents and delayed secondary differentiation. Together, these results indicate that redox potential is a critical factor in developmental cycle progression. For the first time, our study provides a mechanism of chlamydial secondary differentiation dependent on redox status.

Children's Selective Teaching and Informing: A Meta-Analysis.

Empirical studies on selective teaching and informing indicate that children may vary what they teach depending on whom they are teaching, taking into account how helpful the information is for a given audience. The current meta-analysis quantifies the effect of selective informing and teaching in 2-7-year-olds by examining the relationship between the helpfulness of the information and the frequency of information transmission. Through a systematic search that yielded 1483 results, 28 studies (104 effect sizes, N=2716) met the inclusion criteria. Using robust variance estimation, we found a medium average effect, Hedges' g=0.578, 95% CI (0.331, 0.825), suggesting that children selectively share information based on its perceived helpfulness to the listener. Moderator analyses revealed that age and communicative context were significant factors. Children were more informative in their communication when asked to teach compared to other nonpedagogical prompts. This finding supports and extends natural pedagogy theory-young children not only interpret pedagogical information differently than information acquired through other means, but they are more selective in their informing when teaching. Additionally, we observed a key developmental progression at age 4. Four- to 7-year-olds, but not 2-3-year-olds, selectively shared information that was most helpful for a given learner. This coincides with the development of false-belief understanding, which undergoes significant development at around age 4. Taken together, the present synthesis suggests that young children actively engage in selective social learning from both sides, that of beneficiaries and benefactors of valuable information.

Dynamics of flavonoid metabolites in coconut water based on metabolomics perspective.

Coconut meat and coconut water have garnered significant attention for their richness in healthful flavonoids. However, the dynamics of flavonoid metabolites in coconut water during different developmental stages remain poorly understood. This study employed the metabolomics approach using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to investigate the changes in flavonoid metabolite profiles in coconut water from two varieties, 'Wenye No.5'(W5) and Hainan local coconut (CK), across six developmental stages. The results showed that a total of 123 flavonoid metabolites including chalcones, dihydroflavonoids, dihydroflavonols, flavonoids, flavonols, flavonoid carboglycosides, and flavanols were identified in the coconut water as compared to the control. The total flavonoid content in both types of coconut water exhibited a decreasing trend with developmental progression, but the total flavonoid content in CK was significantly higher than that in W5. The number of flavonoid metabolites that differed significantly between the W5 and CK groups at different developmental stages were 74, 74, 60, 92, 40 and 54, respectively. KEGG pathway analysis revealed 38 differential metabolites involved in key pathways for flavonoid biosynthesis and secondary metabolite biosynthesis. This study provides new insights into the dynamics of flavonoid metabolites in coconut water and highlights the potential for selecting and breeding high-quality coconuts with enhanced flavonoid content. The findings have implications for the development of coconut-based products with improved nutritional and functional properties.

Transcriptional regulation of postnatal aortic development

The aorta exhibits tremendous changes in geometry, composition, and mechanical properties during postnatal development. These changes are necessarily driven by transcriptional changes, both genetically programmed and mechano-responsive, but there has not been a careful comparison of time-course changes in the transcriptional profile and biomechanical phenotype. Here, we show that the greatest period of differential gene expression in the normal postnatal mouse aorta occurs prior to weaning at three weeks of age though with important evolution of many transcripts thereafter. We identify six general temporal patterns, including transcripts that monotonically decrease to lower or increase to higher steady state values as well as those that either peak or dip prior to or near weaning. We show that diverse transcripts within individual groupings correlate well over time, and that sub-sets of these groups correlate well with the developmental progression of different biomechanical metrics that are expected to be involved in mechano-sensing. In particular, expression of genes for elastin and elastin-associated glycoproteins tend to correlate well with the ratio of systolic-to-diastolic stress whereas genes for collagen fibers correlate well with the daily rate of change of systolic stress and genes for mechano-sensing proteins tend to correlate well with the systolic stress itself. We conclude that different groupings of genes having different temporal expression patterns correlate well with different measures of the wall mechanics, hence emphasizing a need for age-dependent, gene-specific computational modeling of postnatal development.

LINE1 and PRC2 control nucleolar organization and repression of the 8C state in human ESCs.

The mechanisms that ensure developmental progression in the early human embryo remain largely unknown. Here, we show that the family of long interspersed nuclear element 1 (LINE1) transposons prevents the reversion of naive human embryonic stem cells (hESCs) to 8-cell-like cells (8CLCs). LINE1 RNA contributes to maintenance of H3K27me3 levels, particularly at chromosome 19 (Chr19). Chr19 is enriched for key 8C regulators, H3K27me3, and genes derepressed upon LINE1 knockdown or PRC2 inhibition. Moreover, Chr19 is strongly associated with the nucleolus in hESCs but less in 8CLCs. Direct inhibition of PRC2 activity induces the 8C program and leads to a relocalization of Chr19 away from the nucleolus. LINE1 KD or PRC2 inhibition induces nucleolar stress, and disruption of nucleolar architecture is sufficient to de-repress the 8C program. These results indicate that LINE1 RNA and PRC2 maintain H3K27me3-mediated gene repression and 3D nuclear organization to prevent developmental reversion of hESCs.

Perkembangan Morfologi dan Tingkah Laku Larva Ikan Tuna Sirip Kuning Yellowfin Tuna (Thunnus albacares)

The yellowfin tuna (Thunnus albacares) is a pelagic fish with distinct morphological development and behavioral traits. Understanding the early stages of morphology and behavior in yellowfin tuna larvae is crucial for successful cultivation efforts, particularly during the hatchery phase. This study aimed to observe and document the developmental progression and behaviors of yellowfin tuna larvae at the Tuna Laboratory of Balai Besar Riset Budidaya Laut and Penyuluhan Perikanan Gondol, Bali. Yellowfin tuna larvae were reared in 700 L round tanks at a density of 10,000 larvae per tank. Larval rearing was monitored over a period of 13 days, specifically on days 1 (D1), 3 (D3), 5 (D5), 7 (D7), 10 (D10) and 13 (D13) post-hatching. Morphological changes in the larvae were observed over time. On day 1, the larvae were transparent and planktonic, with closed mouths and eyes and the presence of melanophore pigments in their bodies. By day 3, the larvae had opened their mouths and eyes, becoming capable of feeding. The mouth opening measured between 0.34-0.68 mm (90°) and 0.18-0.37 mm (45°) on day 5 post-hatching. As the larvae grew, improvements in swimming ability were noted, correlating with the development of the swim bladder, tail fin, and dorsal fin.

Development of Mycobacterium tuberculosis Enoyl Acyl Reductase (InhA) Inhibitors: A Mini-Review

This review article delves into the critical role of Enoyl acyl carrier protein Reductase (InhA; ENR), a vital enzyme in the NADH-dependent acyl carrier protein reductase family, emphasizing its significance in fatty acid synthesis and, more specifically, the biosynthesis of mycolic acid. The primary objective of this literature review is to elucidate diverse scaffolds and their developmental progression targeting InhA inhibition, thereby disrupting mycolic acid biosynthesis. Various scaffolds, including thiourea, piperazine, thiadiazole, triazole, quinazoline, benzamide, rhodanine, benzoxazole, and pyridine, have been systematically explored for their potential as InhA inhibitors. Noteworthy findings highlight thiadiazole and triazole derivatives, demonstrating promising IC50 values within the nanomolar concentration range. The review offers comprehensive insights into InhA's structure, structure-activity relationships, and a detailed overview of distinct scaffolds as effective inhibitors of InhA.

MTOR activity paces human blastocyst stage developmental progression.

Many mammals can temporally uncouple conception from parturition by pacing down their development around the blastocyst stage. In mice, this dormant state is achieved by decreasing the activity of the growth-regulating mTOR signaling pathway. It is unknown whether this ability is conserved in mammals in general and in humans in particular. Here, we show that decreasing the activity of the mTOR signaling pathway induces human pluripotent stem cells (hPSCs) and blastoids to enter a dormant state with limited proliferation, developmental progression, and capacity to attach to endometrial cells. These invitro assays show that, similar to other species, the ability to enter dormancy is active in human cells around the blastocyst stage and is reversible at both functional and molecular levels. The pacing of human blastocyst development has potential implications for reproductive therapies.

Using a Previsit Questionnaire for Initial Visits in a Pediatric Mitochondrial Clinic: Perspectives of Parents, a Specialty Physician, and a Clinical Coordinator.

Objective: In this study, we assessed the usefulness of a previsit questionnaire for children who were referred for an initial evaluation in a mitochondrial subspecialty clinic. We explored the themes regarding parent's questions, concerns, and goals. We aimed to add to existing knowledge about the usefulness of previsit questionnaires in a pediatric specialty setting from the perspective of parents, the specialist, and the clinical coordinator. Method: We enrolled 25 patients and their parent(s) over 25 months. Questionnaires were completed by the parent(s), the clinical coordinator, and the mitochondrial specialist. Descriptive statistics and thematic analysis were used to summarize results. Results: Parental responses suggested that they are most concerned about their child's clinical problems, communication, language and developmental delays, disease progression and prognosis, understanding mitochondrial disease, quality of life, and physical challenges including muscle and energy problems. Parents felt the previsit questionnaire was very helpful for both the doctor and for themselves to be prepared for their visit. The specialist and the clinical coordinator also found it to be helpful. Parental comments suggested that they felt that writing down the story of their child's life was helpful for the provider, allowed time for reflection, and improved the appointment experience. Some felt it was a difficult or redundant activity. Conclusion: Parents were often pleased to complete the previsit questionnaire. This allowed them to highlight concerns and share information that they wanted the care team to know about their child. We revised the tool based on feedback from parents and the specialist and will continue to use it in our clinic.

P65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation

Most gene functions have been discovered through phenotypic observations under loss of function experiments that lack temporal control. However, cell signaling relies on limited transcriptional effectors, having to be re-used temporally and spatially within the organism. Despite that, the dynamic nature of signaling pathways have been overlooked due to the difficulty on their assessment, resulting in important bottlenecks. Here, we have utilized the rapid and synchronized developmental transitions occurring within the zebrafish embryo, in conjunction with custom NF-kB reporter embryos driving destabilized fluorophores that report signaling dynamics in real time. We reveal that NF-kB signaling works as a clock that controls the developmental progression of hematopoietic stem and progenitor cells (HSPCs) by two p65 activity waves that inhibit cell cycle. Temporal disruption of each wave results in contrasting phenotypic outcomes: loss of HSPCs due to impaired specification versus proliferative expansion and failure to delaminate from their niche. We also show functional conservation during human hematopoietic development using iPSC models. Our work identifies p65 as a previously unrecognized contributor to cell cycle regulation, revealing why and when pro-inflammatory signaling is required during HSPC development. It highlights the importance of considering and leveraging cell signaling as a temporally dynamic entity.

Limb reduction in an Esco2 cohesinopathy mouse model is mediated by p53-dependent apoptosis and vascular disruption

Roberts syndrome (RBS) is an autosomal recessive disorder with profound growth deficiency and limb reduction caused by ESCO2 loss-of-function variants. Here, we elucidate the pathogenesis of limb reduction in an Esco2fl/fl;Prrx1-CreTg/0 mouse model using bulk- and single-cell-RNA-seq and gene co-expression network analyses during embryogenesis. Our results reveal morphological and vascular defects culminating in hemorrhage of mutant limbs at E12.5. Underlying this abnormal developmental progression is a pre-apoptotic, mesenchymal cell population specific to mutant limb buds enriched for p53-related signaling beginning at E9.5. We then characterize these p53-related processes of cell cycle arrest, DNA damage, cell death, and the inflammatory leukotriene signaling pathway in vivo. In utero treatment with pifithrin-α, a p53 inhibitor, rescued the hemorrhage in mutant limbs. Lastly, significant enrichments were identified among genes associated with RBS, thalidomide embryopathy, and other genetic limb reduction disorders, suggesting a common vascular etiology among these conditions.

The chlamydial transcriptional regulator Euo is a key switch in cell form developmental progression but is not involved in the committed step to the formation of the infectious form.

Bacterial species in the Chlamydiales order infect a variety of vertebrate animals and are a global health concern. They cause various diseases in humans, including genital and respiratory infections. The bacteria are obligate intracellular parasites that rely on a complex infectious cycle involving multiple cell forms. All species share the same life cycle, transitioning through different states to form the infectious elementary body (EB) to spread infections to new hosts. The Euo gene, encoding a DNA-binding protein, is involved in regulating this cycle. This study showed that ectopic expression of Euo halted the cycle at an early stage. This arrest depended on continued Euo expression. When Euo expression was reversed, the developmental cycle resumed. Additionally, this study suggests that high levels of Euo expression affect the formation of the infectious EB but not the production of the cell form committed to EB formation.

Developmental Cajal-Retzius cell death contributes to the maturation of layer 1 cortical inhibition and somatosensory processing

The role of developmental cell death in the formation of brain circuits is not well understood. Cajal-Retzius cells constitute a major transient neuronal population in the mammalian neocortex, which largely disappears at the time of postnatal somatosensory maturation. In this study, we used mouse genetics, anatomical, functional, and behavioral approaches to explore the impact of the early postnatal death of Cajal-Retzius cells in the maturation of the cortical circuit. We find that before their death, Cajal-Retzius cells mainly receive inputs from layer 1 neurons, which can only develop their mature connectivity onto layer 2/3 pyramidal cells after Cajal-Retzius cells disappear. This developmental connectivity progression from layer 1 GABAergic to layer 2/3 pyramidal cells regulates sensory-driven inhibition within, and more so, across cortical columns. Here we show that Cajal-Retzius cell death prevention leads to layer 2/3 hyper-excitability, delayed learning and reduced performance in a multi-whisker-dependent texture discrimination task.

Development of algorithmic thinking skills in K-12 education: A comparative study of unplugged and digital assessment instruments

In the rapidly evolving landscape of digital competencies, the need for a robust and universal method to assess students’ algorithmic thinking (AT) skills has become increasingly pronounced. Algorithmic thinking refers to the ability to analyse a problem and develop a step-by-step process to solve it.This research investigates the efficacy of the Cross Array Task (CAT) as an assessment tool for AT skills within Switzerland’s compulsory education system. Originally conceptualised as an unplugged activity, where students performed the task without digital technologies (e.g., by using gestures on paper) and an administrator manually assessed them, the CAT evolved into a digital activity that runs on an iPad. The CAT’s digital transformation has automated the scoring of student responses and data collection, streamlining the assessment processes and facilitating efficient large-scale assessments. It has also enhanced scalability, making the CAT suitable for widespread use in educational settings. Furthermore, it provides immediate feedback to students and educators, supporting timely interventions and personalised learning experiences.Our study aims to comprehensively investigate algorithmic competencies in compulsory education, examining their variations and influencing factors. This research examines key variables, such as age, sex, educational environment and school characteristics (e.g., the level and grade of education), and regional factors (e.g., the canton of the school) in Switzerland, and characteristics related to the specific assessment tool, including the type of artefact used, the complexity of the algorithms generated, and the level of autonomy. Additionally, it seeks to analyse the effectiveness of the unplugged and digital approaches in assessing AT skills, specifically comparing the unplugged and virtual CAT versions, aiming to provide insights into their advantages and potential synergies.This investigation delineates the developmental progression of AT skills across compulsory education, emphasising the influence of age on algorithm development and problem-solving strategies. Furthermore, we reveal the impact of artefacts and the potential of digital tools to facilitate advanced AT skill development across diverse age groups. Finally, our investigation delves into the influence of school environments and sex disparities on AT performance, alongside the significant individual variability influenced by personal abilities and external circumstances.These findings underscore the importance of tailored educational interventions and equitable practices to accommodate diverse learning profiles and optimise student outcomes in AT across educational settings.

Poised PABP–RNA hubs implement signal-dependent mRNA decay in development

Signaling pathways drive cell fate transitions largely by changing gene expression. However, the mechanisms for rapid and selective transcriptome rewiring in response to signaling cues remain elusive. Here we use deep learning to deconvolve both the sequence determinants and the trans-acting regulators that trigger extracellular signal-regulated kinase (ERK)–mitogen-activated protein kinase kinase (MEK)-induced decay of the naive pluripotency mRNAs. Timing of decay is coupled to embryo implantation through ERK–MEK phosphorylation of LIN28A, which repositions pLIN28A to the highly A+U-rich 3′ untranslated region (3′UTR) termini of naive pluripotency mRNAs. Interestingly, these A+U-rich 3′UTR termini serve as poly(A)-binding protein (PABP)-binding hubs, poised for signal-induced convergence with LIN28A. The multivalency of AUU motifs determines the efficacy of pLIN28A–PABP convergence, which enhances PABP 3′UTR binding, decreases the protection of poly(A) tails and activates mRNA decay to enable progression toward primed pluripotency. Thus, the signal-induced convergence of LIN28A with PABP–RNA hubs drives the rapid selection of naive mRNAs for decay, enabling the transcriptome remodeling that ensures swift developmental progression.