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Pax‐6 emerges as a critical transcription factor that guides the fate of stem cells towards neural lineages. Its expression influences the differentiation of neural progenitors into diverse neuronal subtypes, glial cells, and other neural cell types. Pax‐6 operates with other regulatory factors to ensure the precise patterning and organization of the developing nervous system. The intricate interplay between Pax‐6 and other signaling pathways, transcription factors, and epigenetic modifiers underpins the complicated balance between stem cell maintenance, proliferation, and differentiation in neuroectodermal and ocular contexts. Dysfunction of Pax‐6 can lead to a spectrum of developmental anomalies, underscoring its importance in these processes. This review highlights the essential role of Pax‐6 expression in neuroectodermal and ocular stem cells, shedding light on its significance in orchestrating the intricate journey from stem cell fate determination to the emergence of diverse neural and ocular cell types. The comprehensive understanding of Pax‐6 function gained from a developmental biology perspective offers valuable insights into normal development and potential therapeutic avenues for neuroectodermal and ocular disorders. [ABSTRACT FROM AUTHOR]

Summary: The root epidermis of tracheophytes consists of hair‐forming cells (HCs) and nonhair cells (NCs). The HC distribution pattern is classified into three types: random (Type I), vertically alternating (Type II), and radial (Type III). Type III is found only in core eudicots and is known to be position‐dependent in superrosids with HCs positioned between two underlying cortical cells. However, the evolution of Type III and the universality of its position dependency in eudicots remain unclear.We surveyed the HC distribution in basal and Type III‐exhibiting core eudicots and conducted genomic analyses to get insight into whether eudicots share the same genetic network to establish Type III.Our survey revealed no canonical Type III in basal eudicots but a reverse Type III, with NCs between two cortical cells and HCs on a single cortical cell, in Papaveraceae of basal eudicots. Type III‐exhibiting species from both superrosids and superasterids showed the canonical position dependency of HCs. However, some key components for Type III determination were absent in the genomes of Papaveraceae and Type III‐exhibiting superasterids.Our findings identify a novel position‐dependent type of HC patterning, reverse Type III, and suggest that Type III emerged independently or diversified during eudicot evolution. [ABSTRACT FROM AUTHOR]

Summary: Arsenic poses a global threat to living organisms, compromising crop security and yield. Limited understanding of the transcriptional network integrating arsenic‐tolerance mechanisms with plant developmental responses hinders the development of strategies against this toxic metalloid.Here, we conducted a high‐throughput yeast one‐hybrid assay using as baits the promoter region from the arsenic‐inducible genes ARQ1 and ASK18 from Arabidopsis thaliana, coupled with a transcriptomic analysis, to uncover novel transcriptional regulators of the arsenic response.We identified the GLABRA2 (GL2) transcription factor as a novel regulator of arsenic tolerance, revealing a wider regulatory role beyond its established function as a repressor of root hair formation. Furthermore, we found that ANTHOCYANINLESS2 (ANL2), a GL2 subfamily member, acts redundantly with this transcription factor in the regulation of arsenic signaling. Both transcription factors act as repressors of arsenic response. gl2 and anl2 mutants exhibit enhanced tolerance and reduced arsenic accumulation. Transcriptional analysis in the gl2 mutant unveils potential regulators of arsenic tolerance.These findings highlight GL2 and ANL2 as novel integrators of the arsenic response with developmental outcomes, offering insights for developing safer crops with reduced arsenic content and increased tolerance to this hazardous metalloid. [ABSTRACT FROM AUTHOR]

The Human Cell Atlas (HCA) is a global partnership "to create comprehensive reference maps of all human cells—the fundamental units of life – as a basis for both understanding human health and diagnosing, monitoring, and treating disease." (https://www.humancellatlas.org/) The atlas shall characterize cells from diverse individuals across the globe to better understand human biology. HCA proactively considers the priorities of, and benefits accrued to, contributing communities. Here, we lay out principles and action items that have been adopted to affirm HCA's commitment to equity so that the atlas is beneficial to all of humanity. The Human Cell Atlas (HCA) aims to characterize cells from diverse individuals across the globe to better understand human biology. Here, the authors lay out principles and action items that have been adopted to affirm HCA's commitment to equity so that the atlas is beneficial to all of humanity. [ABSTRACT FROM AUTHOR]

Root hairs (RHs) are an innovation of vascular plants whose development is coordinated by endogenous and environmental cues, such as ethylene and light conditions. However, the potential crosstalk between ethylene and light conditions in RH development is unclear. We report that Arabidopsis constitutive photomorphogenic 1 (COP1) integrates ethylene and light signaling to mediate RH development. Darkness suppresses RH development largely through COP1. COP1 inhibits both cell fate determination of trichoblast and tip growth of RHs based on pharmacological, genetic, and physiological analyses. Indeed, COP1 interacts with and catalyzes the ubiquitination of ACS2 and ACS6. COP1- or darkness-promoted proteasome-dependent degradation of ACS2/6 leads to a low ethylene level in underground tissues. The negative role of COP1 in RH development by downregulating ethylene signaling may be coordinated with the positive role of COP1 in hypocotyl elongation by upregulating ethylene signaling, providing an evolutionary advantage for seedling fitness. [Display omitted] • Root hairs respond to light or ethylene by increasing both density and length • Arabidopsis COP1, the light responsive factor, inhibits root hair development • COP1 catalyzes the ubiquitination of type I ACSs to reduce ethylene responses • Dark-induced 26S-proteasome-mediated degradation of type I ACSs largely depends on COP1 Yin et al. report that Arabidopsis constitutive photomorphogenic 1 (COP1), a light response factor, controls root hair development by catalyzing the ubiquitination of type I ACSs and degradation to inhibit ethylene biosynthesis. The negative role of COP1 in root hairs may coordinate with its positive role in hypocotyl elongation to promote seedling fitness. [ABSTRACT FROM AUTHOR]

TET-family members play a critical role in cell fate commitment. Indeed, TET3 is essential to postnatal development due to yet unknown reasons. To define TET3 function in cell differentiation, we have profiled the intestinal epithelium at single-cell level from wild-type and Tet3 knockout mice. We have found that Tet3 is mostly expressed in differentiated enterocytes. In the absence of TET3, enterocytes exhibit an aberrant differentiation trajectory and do not acquire a physiological cell identity due to an impairment in oxidative phosphorylation, specifically due to an ATP synthase assembly deficiency. Moreover, spatial metabolomics analysis has revealed that Tet3 knockout enterocytes exhibit an unphysiological metabolic profile when compared with their wild-type counterparts. In contrast, no metabolic differences have been observed between both genotypes in the stem cell compartment where Tet3 is mainly not expressed. Collectively, our findings suggest a mechanism by which TET3 regulates mitochondrial function and, thus, terminal cell differentiation at the metabolic level. TET3 is essential to postnatal development due to unknown reasons. Here Mulet et al. demonstrate that TET3 is required for ATP synthase assembly in differentiated cells and that its loss leads to an unphysiological metabolic profile. [ABSTRACT FROM AUTHOR]

The increasing availability of ultrabright Light Sources is facilitating the study of smaller crystals at faster timescales but with an increased risk of severe X-ray damage, leading to developments in multi-crystal methods such as serial crystallography (SX). SX studies on crystals with small unit cells are challenging as very few reflections are recorded in a single data image, making it difficult to determine the orientation matrix for each crystal and thus preventing the combination of the data from all crystals for structure solution. We herein present a Small-Rotative Fixed-Target Serial Synchrotron Crystallography (SR-FT-SSX) methodology, in which rotation of the serial target through a small diffraction angle (φ) at each crystal delivers high-quality data, facilitating ab initio unit cell determination and atomic-scale structure solution. The method is benchmarked using microcrystals of the small-molecule photoswitch sodium nitroprusside dihydrate, obtaining complete data to dmin = 0.6 Å by combining just 66 partial datasets selected against rigorous quality criteria. Multi-crystal methods such as serial crystallography can provide a complete 3D structure of the target material before radiation damage becomes significant, but the methods are challenging for small molecule crystals with small unit cells, where very few reflections are recorded in a single data image. Here, the authors present a small-rotative fixed-target serial synchrotron crystallography (SR-FT-SSX) methodology, in which rotation of the serial target through a small diffraction angle (φ) at each crystal delivers high-quality data, facilitating ab initio unit cell determination and atomic-scale structure solution. [ABSTRACT FROM AUTHOR]

Production of cultivated meat requires defined medium formulations for the robust differentiation of myogenic cells into mature skeletal muscle fibres in vitro. Although these formulations can drive myogenic differentiation levels comparable to serum-starvation-based protocols, the resulting cultures are often heterogeneous, with a significant proportion of cells not participating in myofusion, limiting maturation of the muscle. To address this problem, we employed RNA sequencing to analyse heterogeneity in differentiating bovine satellite cells at single-nucleus resolution, identifying distinct cellular subpopulations including proliferative cells that fail to exit the cell cycle and quiescent 'reserve cells' that do not commit to myogenic differentiation. Our findings indicate that the MEK/ERK, NOTCH, and RXR pathways are active during the initial stages of myogenic cell fate determination, and by targeting these pathways, we can promote cell cycle exit while reducing reserve cell formation. This optimised medium formulation consistently yields fusion indices close to 100% in 2D culture. Furthermore, we demonstrate that these conditions enhance myotube formation and actomyosin accumulation in 3D bovine skeletal muscle constructs, providing proof of principle for the generation of highly differentiated cultivated muscle with excellent mimicry to traditional muscle. Single-nucleus RNA sequencing gives insights into heterogeneity during bovine skeletal muscle differentiation, informing the design of improved medium formulations for cultivated meat production. [ABSTRACT FROM AUTHOR]

ABSTRACT Notch1 and Notch2, transmembrane receptors belonging to the Notch family, are pivotal mediators of intercellular communication and have profound implications including cell fate determination, embryonic development, and tissue homeostasis in various cellular processes. Despite their structural homology, Notch1 and Notch2 exhibit discrete phenotypic characteristics and functional nuances that necessitate their individualized targeting in specific medical scenarios. Aberrant Notch signaling, often driven by the dysregulated activity of one receptor over the other, is implicated under various pathological conditions. Notch1 dysregulation is frequently associated with T‐cell acute lymphoblastic leukemia, whereas Notch2 perturbations are linked to B‐cell malignancies and solid tumors, including breast cancer. Hence, tailored therapeutic interventions that selectively inhibit the relevant Notch receptor need to be devised to disrupt the signaling pathways driving the specific disease phenotype. In this review, we emphasize the importance of distinct tissue‐specific expression patterns, functional divergence, disease‐specific considerations, and the necessity to minimize off‐target effects that collectively underscore the significance of “individualized” targeting for Notch1 and Notch2. This comprehensive review sheds light on the receptor‐specific characteristics of Notch1 and Notch2, providing insights into their roles in cellular processes and offering opportunities for developing tailored therapeutic interventions in the fields of biomedical research and clinical practice. [ABSTRACT FROM AUTHOR]

Glioma associated macrophages/microglia (GAMs) play an important role in glioblastoma (GBM) progression, due to their massive recruitment to the tumor site and polarization to a tumor promoting phenotype. GAMs secrete a variety of cytokines, which facilitate tumor cell growth and invasion, and prevent other immune cells from mounting an immune response against the tumor. Here, we demonstrate that zinc finger and BTB containing domain 18 (ZBTB18), a transcriptional repressor with tumor suppressive function in glioblastoma, impairs the production of key cytokines, which function as chemoattractant for GAMs. Consistently, we observe a reduced migration of GAMs when ZBTB18 is expressed by glioblastoma cells, both in cell culture and in vivo experiments. Moreover, RNA sequencing analysis shows that the presence of ZBTB18 in glioblastoma cells alters the commitment of conditioned microglia, suggesting the loss of the immune-suppressive phenotype and the acquisition of pro-inflammatory features. Thus, therapeutic approaches to increase ZBTB18 expression in GBM cells could represent an effective adjuvant to immune therapy in GBM. In vitro, in vivo and in silico studies identify the transcriptional repressor ZBTB18 as a negative regulator of tumor associated macrophage recruitment and of their tumor promoting phenotype in glioblastoma [ABSTRACT FROM AUTHOR]

Background Objectives Methods Results Conclusion DNA repair plays a major role in maintaining genomic stability, thus limiting the transformation of normal cells into cancer cells. However, in cancer patients treated with DNA‐targeting drugs, DNA repair can decrease efficacy by removing the damage generated by such molecules that is needed to induce pharmacological activity. Inhibiting DNA repair thus represents an interesting approach to potentiating the activity of chemotherapy in this setting.Here, we continue the characterization of an inhibitor of the interaction between Excision Repair Cross‐Complementing Rrodent repair deficiency complementation group 1 (ERCC1) and Xeroderma Pigmentousum group F (XPF) (B9), two key proteins of nucleotide excision repair.We used various cell lines and co‐incubation studies for the determination of cell survival and DNA repair capacities.We show that it is synergistic with other platinum derivatives than previously described, and that synergy is lacking in cells not expressing ERCC1 or XPF. Finally, a series of experiments show that potentiation is observed only in cells expressing wild‐type p53.Our results confirm the mechanism of action of our ERCC1–XPF inhibitor and give important additional data on this approach to enhance the activity of already existing cancer drugs. [ABSTRACT FROM AUTHOR]

Cyst nematodes use a stylet to secrete CLE-like peptide effector mimics into selected root cells of their host plants to hijack endogenous plant CLE signaling pathways for feeding site (syncytium) formation. Here, we identified ATHB8, encoding a HD-ZIP III family transcription factor, as a downstream component of the CLE signaling pathway in syncytium formation. ATHB8 is expressed in the early stages of syncytium initiation, and then transitions to neighboring cells of the syncytium as it expands; an expression pattern coincident with auxin response at the infection site. Conversely, MIR165a, which expresses in endodermal cells and moves into the vasculature to suppress HD-ZIP III TFs, is down-regulated near the infection site. Knocking down HD-ZIP III TFs by inducible over-expression of MIR165a in Arabidopsis dramatically reduced female development of the sugar beet cyst nematode (Heterodera schachtii). HD-ZIP III TFs are known to function downstream of auxin to promote cellular quiescence and define stem cell organizer cells in vascular patterning. Taken together, our results suggest that HD-ZIP III TFs function together with a CLE and auxin signaling network to promote syncytium formation, possibly by inducing root cells into a quiescent status and priming them for initial syncytial cell establishment and/or subsequent cellular incorporation. Author summary: Plant-parasitic cyst nematodes are one of the most damaging pathogens impacting crop production. These nematodes establish a permanent feeding site called a syncytium to withdraw nutrients from plant roots, causing plant malnutrition and reduced crop yield. The syncytium is induced by nematode stylet-secreted effectors, many of which hijack innate plant developmental programs to convert a normal plant cell to a syncytial cell. One such group of effectors functions by mimicking plant CLE peptide hormones, which are important in plant cell fate determination, and play a crucial role in syncytium formation. In this study, we show that nematode secreted CLE-like effectors induce the expression of the ATHB8 gene, a member of the Class III HD-ZIP transcription factor family, at early stages of syncytium formation. Reducing the level of HD-ZIP III family genes compromised the nematode's ability to feed on plants, indicating that HD-ZIP III transcription factors are important for cyst nematode parasitism. [ABSTRACT FROM AUTHOR]

T cells develop in the thymus by expressing a diverse repertoire of either αβ‐ or γδ‐T cell receptors (TCR). While many studies have elucidated how TCR signaling and gene expression control T cell ontogeny, the role of nutrient metabolism is just emerging. Here, we discuss how metabolic reprogramming and nutrient availability impact the fate of developing thymic T cells. We focus on how the PI3K/mTOR signaling mediates various extracellular inputs and how this signaling pathway controls metabolic rewiring during highly proliferative and anabolic developmental stages. We highlight the role of the hexosamine biosynthetic pathway that generates metabolites that are utilized for N‐ and O‐linked glycosylation of proteins and how it impacts TCR expression during T cell ontogeny. We consider the dichotomy in metabolic needs during αβ‐ versus γδ‐T cell lineage commitment as well as how metabolism is also coupled to molecular signaling that controls cell fate. [ABSTRACT FROM AUTHOR]

AbstractHere we report a colorimetric cytosensor for osteosarcoma CTCs based on mesenchymal marker cell surface vimentin monoclonal antibody 84-1 (mAb 84-1) and jaboticaba-inspired signal amplification. The linear range of our cytosensor ranges from 50 to 1.0 × 106 cells/mL and the limit of detection is 18 cells/mL for the human osteosarcoma cell line. The cytosensor also exhibits good selectivity for epithelial- derived cancer compared to mesenchymal-derived sarcomas, and has been successfully applied to detection CTCs in blood from osteosarcoma patients. In summary, an accurate, sensitive, and controllable colorimetric sensing platform has been developed, with promise for the early diagnosis and prognostic of osteosarcoma. [ABSTRACT FROM AUTHOR]

Competitive athletes are often exposed to extreme physiological loading, resulting in over excessive mechanotransduction during their acute intensive training sessions and competitions. Individual differences in their genetics often affect how they cope with these challenges, as reflected in their high performances. Olympic Medalists are prohibited from providing atypical values in the Hematological Module of the Athlete Biological Passport. Since there was no aphysiological result and the Athlete maintained his innocence, a whole genome sequence analysis was carried out on him and his parents, with the primary focus on the PIEZO ion channels encoding gene. PIEZO1 is known to participate in homeostatic regulation even on a whole-body level, including the regulation of physical performance, circulatory longevity of red blood cells and cell fate determination of mesenchymal stem cells in relation to hydrostatic pressure. However, PIEZO2 was found to be the principal mechanosensory ion channel for proprioception. These regulatory mechanisms play a pivotal role in mechanotransduction and intensive exercise moments. Interestingly, two variances of uncertain significance of PIEZO1 were found that may explain the atypical values of the Athlete. Furthermore, two additional variances in SDC2, the syndcan-2 encoding gene, were identified in trans position that may influence the crosstalk between PIEZO2 and PIEZO1, with more likely relevance to the detected atypical values. After all, based on the found variances of PIEZO1 and syndecan-2, it cannot be ruled out that these VUS variants may have caused or impacted the exhibited outlier findings of the ABP Hematological Module of the Athlete. [ABSTRACT FROM AUTHOR]

Teeth are comprised of epithelial and mesenchymal cells, and regenerative teeth rely on the regeneration of both cell types. Transcription factors play a pivotal role in cell fate determination. In this study, we establish fluorescence models based on transcription factors to monitor and analyze dental epithelial cells. Using Pitx2-P2A-copGFP mice, we observe that Pitx2+ epithelial cells, when combined with E14.5 dental mesenchymal cells, are sufficient for the reconstitution of teeth. Induced-Pitx2+ cells, directly isolated from the embryoid body that employs the Pitx2-GFP embryonic stem cell line, exhibit the capacity to differentiate into ameloblasts and develop into teeth when combined with dental mesenchymal cells. The regenerated teeth exhibit a complete structure, including dental pulp, dentin, enamel, and periodontal ligaments. Subsequent exploration via RNA-seq reveals that induced-Pitx2+ cells exhibit enrichment in genes associated with FGF receptors and WNT ligands compared with induced-Pitx2- cells. Our results indicate that both primary Pitx2+ and induced Pitx2+ cells possess the capability to differentiate into enamel-secreting ameloblasts and grow into teeth when combined with dental mesenchymal cells. [ABSTRACT FROM AUTHOR]

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Post-transcriptional regulation has emerged as a keymechanismfor regulating stem cell renewal and differentiation, which is essential for understanding tissue regeneration and homeostasis. Poly(A)-binding proteins are a family of RNA-binding proteins that play a vital role in post-transcriptional regulation by controlling mRNA stability and protein synthesis. The involvement of poly(A) binding proteins in a wide range of cellular functions is increasingly being investigated. In this study, we used the regenerative model planarian organism Schmidtea mediterranea to demonstrate the critical role of poly(A)-binding protein 2 (PABP2) in regulating neoblast maintenance and differentiation. A deficit in PABP2 blocks the transition of neoblasts toward immediate early progenitors, leading to an enhanced pool of non-committed neoblasts and a decreased progenitor population. This is reflected in variations in the transcriptome profile, providing evidence of downregulation in multiple lineages. Thus, an insufficiency of PABP2 resulted in defective formation and organization of tissue, leading to abnormal regeneration. Our study reveals the essential role of PABP2 in regulating genes that mediate stem cell commitment to early progenitors during tissue regeneration. [ABSTRACT FROM AUTHOR]

Epigenetic regulation of metabolism profoundly influences cell fate commitment. During osteoclast differentiation, the activation of RANK signaling is accompanied by metabolic reprogramming, but the epigenetic mechanisms by which RANK signaling induces this reprogramming remain elusive. By transcriptional sequence and ATAC analysis, this study identifies that activation of RANK signaling upregulates PRMT6 by epigenetic modification, triggering a metabolic switching from fatty acids oxidation toward glycolysis. Conversely, Prmt6 deficiency reverses this shift, markedly reducing HIF‐1α‐mediated glycolysis and enhancing fatty acid oxidation. Consequently, PRMT6 deficiency or inhibitor impedes osteoclast differentiation and alleviates bone loss in ovariectomized (OVX) mice. At the molecular level, Prmt6 deficiency reduces asymmetric dimethylation of H3R2 at the promoters of genes including Ppard, Acox3, and Cpt1a, enhancing genomic accessibility for fatty acid oxidation. PRMT6 thus emerges as a metabolic checkpoint, mediating metabolic switch from fatty acid oxidation to glycolysis, thereby supporting osteoclastogenesis. Unveiling PRMT6's critical role in epigenetically orchestrating metabolic shifts in osteoclastogenesis offers a promising target for anti‐resorptive therapy. [ABSTRACT FROM AUTHOR]

While cell fate determination and maintenance are important in establishing and preserving tissue identity and function during development, aberrant cell fate transition leads to cancer cell heterogeneity and resistance to treatment. Here, we report an unexpected role for the transcription factor p63 (Trp63/TP63) in the fate choice of the squamous versus neuroendocrine lineage in esophageal development and malignancy. Deletion of p63 results in extensive neuroendocrine differentiation in the developing mouse esophagus and esophageal progenitors derived from human embryonic stem cells. In human esophageal neuroendocrine carcinoma (eNEC) cells, p63 is transcriptionally silenced by EZH2-mediated H3K27 trimethylation (H3K27me3). Up-regulation of the major p63 isoform Np63a, through either ectopic expression or EZH2 inhibition, promotes squamous transdifferentiation of eNEC cells. Together, these findings uncover p63 as a rheostat in coordinating the transition between squamous and neuroendocrine cell fates during esophageal development and tumor progression. [ABSTRACT FROM AUTHOR]

Organogenesis, the phase of embryonic development that starts at the end of gastrulation and continues until birth is the critical process for understanding cellular differentiation and maturation during organ development. The rapid development of single‐cell transcriptomics technology has led to many novel discoveries in understanding organogenesis while also accumulating a large quantity of data. To fill this gap, OrganogenesisDB (http://organogenesisdb.com/), which is a comprehensive database dedicated to exploring cell‐type identification and gene expression dynamics during organogenesis, is developed. OrganogenesisDB contains single‐cell RNA sequencing data for more than 1.4 million cells from 49 published datasets spanning various developmental stages. Additionally, 3324 cell markers are manually curated for 1120 cell types across 9 human organs and 4 mouse organs. OrganogenesisDB leverages various analysis tools to assist users in annotating and understanding cell types at different developmental stages and helps in mining and presenting genes that exhibit specific patterns and play key regulatory roles during cell maturation and differentiation. This work provides a critical resource and useful tool for deciphering cell lineage determination and uncovering the mechanisms underlying organogenesis. [ABSTRACT FROM AUTHOR]

One of the most critical axes for cell fate determination is how cells respond to excessive reactive oxygen species (ROS)--oxidative stress. Extensive lipid peroxidation commits cells to death via a distinct cell death paradigm termed ferroptosis. However, the molecular mechanism regulating cellular fates to distinct ROS remains incompletely understood. Through siRNA against human receptor-interacting protein kinase (RIPK) family members, we found that RIPK4 is crucial for oxidative stress and ferroptotic death. Upon ROS induction, RIPK4 is rapidly activated, and the kinase activity of RIPK4 is indispensable to induce cell death. Specific ablation of RIPK4 in kidney proximal tubules protects mice from acute kidney injury induced by cisplatin and renal ischemia/reperfusion. RNA sequencing revealed the dramatically decreased expression of acyl-CoA synthetase medium-chain (ACSM) family members induced by cisplatin treatment which is compromised in RIPK4-deficient mice. Among these ACSM family members, suppression of ACSM1 strongly augments oxidative stress and ferroptotic cell death with induced expression of ACS long-chain family member 4, an important component for ferroptosis execution. Our lipidome analysis revealed that overexpression of ACSM1 leads to the accumulation of monounsaturated fatty acids, attenuation of polyunsaturated fatty acid (PUFAs) production, and thereby cellular resistance to ferroptosis. Hence, knockdown of ACSM1 resensitizes RIPK4 KO cells to oxidative stress and ferroptotic death. In conclusion, RIPK4 is a key player involved in oxidative stress and ferroptotic death, which is potentially important for a broad spectrum of human pathologies. The link between the RIPK4-ASCM1 axis to PUFAs and ferroptosis reveals a unique mechanism to oxidative stress-induced necrosis and ferroptosis. [ABSTRACT FROM AUTHOR]

Methylation profiles of animals are known to differ by age and disease status. Bovine respiratory disease (BRD), a complex infectious disease, primarily affects calves and has significant impact on animal welfare and the cattle industry, due to production losses, increased veterinary costs as well as animal losses. BRD susceptibility is multifactorial, influenced by both environmental and genetic factors. We have performed a pilot study to investigate the epigenetic profile of BRD susceptibility in six calves (three healthy versus three diagnosed with BRD) and age-related methylation differences between healthy calves and adult dairy cows (three calves versus four adult cows) using Reduced Representation Bisulfite Sequencing (RRBS). We identified 2537 genes within differentially methylated regions between calves and adults. Functional analysis revealed enrichment of developmental pathways including cell fate commitment and tissue morphogenesis. Between healthy and BRD affected calves, 964 genes were identified within differentially methylated regions. Immune and vasculature regulatory pathways were enriched and key candidates in BRD susceptibility involved in complement cascade regulation, vasoconstriction and respiratory cilia structure and function were identified. Further studies with a greater sample size are needed to validate these findings and formulate integration into breeding programmes aiming to increase animal longevity and disease resistance. Epigenetic profiling using reduced representation bisulfite sequencing provides preliminary insights into the role of DNA methylation in ageing and bovine respiratory disease in UK dairy cattle. [ABSTRACT FROM AUTHOR]

Cardiac mononuclear phagocytic cells (Cardiac MPCs) participate in maintaining homeostasis and orchestrating cardiac responses upon injury. However, the function of specific MPC subtypes and the related cell fate commitment mechanisms remain elusive in regenerative and nonregenerative hearts due to their cellular heterogeneities. Using spatiotemporal single- cell epigenomic analysis of cardiac MPCs in regenerative (P1) and nonregenerative (P10) mouse hearts after injury, we found that P1 hearts accumulate reparative Arg1+ macrophages, while proinflammatory S100a9+Ly6c+ monocytes are uniquely abundant during nonregenerative remodeling. Moreover, blocking chemokine CXCR2 to inhibit the specification of the S100a9+Ly6c+ -biased inflammatory fate in P10 hearts resulted in elevated wound repair responses and marked improvements in cardiac function after injury. Single-cell RNA-Seq further confirmed an increased Arg1+ macrophage subpopulation after CXCR2 blockade, which was accomplished by increased expression of wound repair–related genes and reduced expression of proinflammatory genes. Collectively, our findings provide instructive insights into the molecular mechanisms underlying the function and fate specification of heterogeneous MPCs during cardiac repair and identify potential therapeutic targets for myocardial infarction. [ABSTRACT FROM AUTHOR]

Enhancers are regulatory elements that determine the temporal and spatial specificity of gene transcription. Enhancers serve as hubs for the transient assembly of transcription factor/coactivator clusters during the induction of transcriptional bursting. Transcriptional activation by enhancers does not always accompany an increased physical proximity to target promoters. The formation of higher-order genome architectures fosters ultra-long-range enhancer–promoter communication during cell fate determination. Enhancers are noncoding regulatory elements that instruct spatial and temporal specificity of gene transcription in response to a variety of intrinsic and extrinsic signals during development. Although it has long been postulated that enhancers physically interact with target promoters through the formation of stable loops, recent studies have changed this static view: sequence-specific transcription factors (TFs) and coactivators are dynamically recruited to enhancers and assemble so-called transcription hubs. Dynamic assembly of transcription hubs appears to serve as a key scaffold to integrate regulatory information encoded by surrounding genome and biophysical properties of transcription machineries. In this review, we outline emerging new models of transcriptional regulation by enhancers and discuss future perspectives. [ABSTRACT FROM AUTHOR]

A recent study published in Cell by Liu et al. introduced a new dual homologous recombinase‐mediated genetic profiling tracer technique to track lung epithelial cells accurately, shedding light on the regenerative origin and regulatory mechanism of adult alveolar epithelial stem cells. The research highlights the importance of alveolar regeneration for maintaining lung homeostasis and facilitating post‐injury healing, emphasizing the role of club cells and bronchioalveolar stem cells in promoting alveolar regeneration after lung injury. By developing a novel dual homologous recombination tool, the authors were able to identify club cells as the primary source of alveolar stem cell regeneration, offering new insights for lung stem cell therapy and potential treatment approaches for lung damage healing. [Extracted from the article]

Metabolism has been implicated in cell fate determination, particularly through epigenetic modifications. Similarly, lipid remodeling also plays a role in regulating cell fate. Here, we present comprehensive lipidomics analysis during BMP4-driven primed to naive pluripotency transition or BiPNT and demonstrate that lipid remodeling plays an essential role. We further identify Cpt1a as a rate-limiting factor in BiPNT, driving lipid remodeling and metabolic reprogramming while simultaneously increasing intracellular acetyl-CoA levels and enhancing H3K27ac at chromatin open sites. Perturbation of BiPNT by histone acetylation inhibitors suppresses lipid remodeling and pluripotency transition. Together, our study suggests that lipid remodeling promotes pluripotency transitions and further regulates cell fate decisions, implicating Cpt1a as a critical regulator between primed-naive cell fate control. The metabolomic landscape characterizing the PNT process elucidates the crucial role of CPT1A in driving lipid remodeling, thereby regulating the transition of cellular fate [ABSTRACT FROM AUTHOR]

Gene transcription is a stochastic process that occurs in all organisms. Transcriptional bursting, a critical molecular dynamics mechanism, creates significant heterogeneity in mRNA and protein levels. This heterogeneity drives cellular phenotypic diversity. Currently, the lack of a comprehensive quantitative model limits the research on transcriptional bursting. This review examines various gene expression models and compares their strengths and weaknesses to guide researchers in selecting the most suitable model for their research context. We also provide a detailed summary of the key metrics related to transcriptional bursting. We compared the temporal dynamics of transcriptional bursting across species and the molecular mechanisms influencing these bursts, and highlighted the spatiotemporal patterns of gene expression differences by utilizing metrics such as burst size and burst frequency. We summarized the strategies for modeling gene expression from both biostatistical and biochemical reaction network perspectives. Single-cell sequencing data and integrated multiomics approaches drive our exploration of cutting-edge trends in transcriptional bursting mechanisms. Moreover, we examined classical methods for parameter estimation that help capture dynamic parameters in gene expression data, assessing their merits and limitations to facilitate optimal parameter estimation. Our comprehensive summary and review of the current transcriptional burst dynamics theories provide deeper insights for promoting research on the nature of cell processes, cell fate determination, and cancer diagnosis. [ABSTRACT FROM AUTHOR]

Post-larval hematopoiesis in Drosophila largely depends upon the stockpile of progenitors present in the blood-forming organ/lymph gland of the larvae. During larval stages, the lymph gland progenitors gradually accumulate reactive oxygen species (ROS), which is essential to prime them for differentiation. Studies have shown that ROS triggers the activation of JNK (c-Jun Kinase), which upregulates fatty acid oxidation (FAO) to facilitate progenitor differentiation. Intriguingly, despite having ROS, the entire progenitor pool does not differentiate simultaneously in the late larval stages. Using expression analyses, genetic manipulation and pharmacological approaches, we found that the Drosophila NF-κB transcription factor Relish (Rel) shields the progenitor pool from the metabolic pathway that inducts them into the differentiation program by curtailing the activation of JNK. Although ROS serves as the metabolic signal for progenitor differentiation, the input from ROS is monitored by the developmental signal TAK1, which is regulated by Relish. This developmental circuit ensures that the stockpile of ROS-primed progenitors is not exhausted entirely. Our study sheds light on how, during development, integrating NF-κB-like factors with metabolic pathways seem crucial to regulating cell fate transition during development. Author summary: The determination of cell fate in stem/progenitor cells is crucial for normal development and various pathophysiological conditions. Our research focuses on the Drosophila larval blood-forming organ, the lymph gland, as a model to gain further insights into this intricate process. Interestingly, while the entire progenitor pool within this organ is enriched in Reactive Oxygen Species (ROS), which is a known trigger for differentiation, they do not differentiate entirely. We show that Relish, a component of the Immune Deficiency Pathway (IMD), plays a role in preventing premature differentiation of the progenitors. Relish hinders TAK1 (transforming growth factor-β-activated kinase 1), thereby reducing JNK activation downstream of ROS. This inhibition on JNK delays progenitor differentiation. Our study reveals an interplay between developmental signaling and metabolic factors that govern the fate specification and maintenance of blood progenitors. Given that the process of blood development in flies shares several similarities with mammalian hematopoiesis, including the presence of high ROS in the myeloid progenitors, it would be worth exploring whether similar interactions are at play in vertebrate hematopoiesis. In addition, it would be fascinating to investigate whether similar coordination between metabolic and developmental signals regulates the differentiation of stem/progenitor cells in other biological systems. [ABSTRACT FROM AUTHOR]

The thymus plays a pivotal role in generating a highly-diverse repertoire of T lymphocytes while preventing autoimmunity. Thymus seeding progenitors (TSPs) are a heterogeneous group of multipotent progenitors that migrate to the thymus via CCR7 and CCR9 receptors. While NOTCH guides thymus progenitors toward T cell fate, the absence or disruption of NOTCH signaling renders the thymus microenvironment permissive to other cell fates. Following T cell commitment, developing T cells undergo multiple selection checkpoints by engaging with the extracellular matrix, and interacting with thymic epithelial cells (TECs) and other immune subsets across the different compartments of the thymus. The different selection checkpoints assess the T cell receptor (TCR) performance, with failure resulting in either repurposing (agonist selection), or cell death. Additionally, environmental cues such as inflammation and endocrine signaling induce acute thymus atrophy, contributing to the demise of most developing T cells during thymic selection. We discuss the occurrence of acute thymus atrophy in response to systemic inflammation. The thymus demonstrates high plasticity, shaping inflammation by abrogating T cell development and undergoing profound structural changes, and facilitating regeneration and restoration of T cell development once inflammation is resolved. Despite the challenges, thymic selection ensures a highly diverse T cell repertoire capable of discerning between self and non-self antigens, ultimately egressing to secondary lymphoid organs where they complete their maturation and exert their functions. [ABSTRACT FROM AUTHOR]

This work aims to report the phytoplankton species composition and cell density in the Mazatlán coastal region (eastern entrance of the Gulf of California (GC), Mexico) during the strong El Niño event of 2023. Surface water samples (at 2 m depth) for phytoplankton cell determinations were collected in December of 2023, a month in which the numerical value of the Oceanic Niño Index was 2.0. The results showed a total of 197 species, including 113 diatoms (with a total cell density of 51,444 cells L-1), 76 dinoflagellates (with a total cell density of 31,260 cells L-1), four silicoflagellates (with a total cell density of 420 cells L-1), two cyanobacteria (with a total cell density of 2,020 cells L-1), one Euglenophyta (with a total cell density of 900 cells L-1) and one ciliate (with a total cell density of 7,820 cells L-1). The diatom Dactyliosolen phuketensis (B.G.Sundström) G.R. Hasle, 1996 and the dinoflagellate Gyrodinium fusiforme (Kofoid & Swezy, 1921) presented the highest cell densities with 4,100 and 5,900 cells L-1, respectively, species that have been previously reported in high abundances in Mexican waters in years of warming events, including El Niño. The results presented here contribute to understanding the effects of strong El Niño events on the phytoplankton community structure of the southeastern GC. This topic still needs to be fully addressed. This study also provides an update on the taxonomic lists available for the region of a group of organisms whose nomenclature has been constantly changing in recent years. [ABSTRACT FROM AUTHOR]

Osteochondral lesions may be due to trauma or congenital conditions. In both cases, therapy is limited because of the difficulty of tissue repair. Tissue engineering is a promising approach that relies on designed scaffolds with variable mechanical attributes to favor cell attachment and differentiation. Human adipose-derived stem cells (hASCs) are a very promising cell source in regenerative medicine with osteochondrogenic potential. Based on the assumption that stiffness influences cell commitment, we investigated three different scaffolds: a semisynthetic animal-derived GelMA hydrogel, a combined scaffold made of rigid PEGDA coated with a thin GelMA layer and a decellularized plant-based scaffold. We investigated the role of different biomechanical stimulations in the scaffold-induced osteochondral differentiation of hASCs. We demonstrated that all scaffolds support cell viability and spontaneous osteochondral differentiation without any exogenous factors. In particular, we observed mainly osteogenic commitment in higher stiffness microenvironments, as in the plant-based one, whereas in a dense and softer matrix, such as in GelMA hydrogel or GelMA-coated-PEGDA scaffold, chondrogenesis prevailed. We can induce a specific cell commitment by combining hASCs and scaffolds with particular mechanical attributes. However, in vivo studies are needed to fully elucidate the regenerative process and to eventually suggest it as a potential approach for regenerative medicine. [ABSTRACT FROM AUTHOR]

Background/Objectives: Induced pluripotent stem cells (iPSCs) reprogrammed from somatic cells into cells with most of the ESC (embryonic stem cell) characteristics show promise toward solving ethical problems currently facing stem cell research and eventually yield clinical grade pluripotent stem cells for therapies and regenerative medicine. In recent years, an increasing body of research suggests that the chemical induction of pluripotency (CIP) method can yield iPSCs in vitro, yet its application in avian species remains unreported. Methods: Herein, we successfully obtained stably growing chicken embryonic fibroblasts (CEFs) using the tissue block adherence method and employed 12 small-molecule compounds to induce chicken iPSC formation. Results: The final optimized iPSC induction system was bFGF (10 ng/mL), CHIR99021 (3 μM), RepSox (5 μM), DZNep (0.05 μM), BrdU (10 μM), BMP4 (10 ng/mL), vitamin C (50 μg/mL), EPZ-5676 (5 μM), and VPA (0.1 mM). Optimization of the induction system revealed that the highest number of clones was induced with 8 × 104 cells per well and at 1.5 times the original concentration. Upon characterization, these clones exhibited iPSC characteristics, leading to the development of a stable compound combination for iPSC generation in chickens. Concurrently, employing a deletion strategy to investigate the functionality of small-molecule compounds during induction, we identified CHIR99021 and BrdU as critical factors for inducing chicken iPSC formation. Conclusions: In conclusion, this study provides a reference method for utilizing small-molecule combinations in avian species to reprogram cells and establish a network of cell fate determination mechanisms. [ABSTRACT FROM AUTHOR]

The tendency for cell fate to be robust to most perturbations, yet sensitive to certain perturbations raises intriguing questions about the existence of a key path within the underlying molecular network that critically determines distinct cell fates. Reprogramming and trans-differentiation clearly show examples of cell fate change by regulating only a few or even a single molecular switch. However, it is still unknown how to identify such a switch, called a master regulator, and how cell fate is determined by its regulation. Here, we present CAESAR, a computational framework that can systematically identify master regulators and unravel the resulting canalizing kernel, a key substructure of interconnected feedbacks that is critical for cell fate determination. We demonstrate that CAESAR can successfully predict reprogramming factors for de-differentiation into mouse embryonic stem cells and trans-differentiation of hematopoietic stem cells, while unveiling the underlying essential mechanism through the canalizing kernel. CAESAR provides a system-level understanding of how complex molecular networks determine cell fates. [ABSTRACT FROM AUTHOR]

Avian Pasteurella multocida infection, can cause serious economic losses to the poultry industry every year. The inactivated vaccines of avian Pasteurella multocida are used to prevent infection. Increasing the cell density of avian Pasteurella multocida is the key to the application of these inactivated vaccines. This can be achieved by controlling the feeding strategy. This study aimed to achieve high-cell-density cultivation of avian Pasteurella multocida by applying an appropriate medium and a rational feeding strategy based on viable cell growth and dissolved oxygen level variation during a fermentation process. An optimized medium suited for the growth of avian P. multocida was used. Meanwhile, besides the online real-time determination of viable cell density, the concentration of glucose was maintained at 1.5 g/L using a glucose-stat feeding strategy after 2 h. The selected nutrient mixture, including yeast extract, tryptone, betaine, VB1, and VH, was fed using a dissolved oxygen feedback feeding strategy after 4 h. As a result, the viable cell density and cell count of avian P. multocida under optimized conditions were increased to OD600: 9.38 and 4.58×1010 CFU/mL, which were higher by 7.27 and 7.26 times than those under the original conditions, respectively. [ABSTRACT FROM AUTHOR]

Circadian clocks are biochemical timers regulating many physiological and molecular processes according to the day/night cycles. The function of the oscillator relies on negative transcriptional/translational feedback loops operated by the so-called clock genes and the encoded clock proteins. Previously, we identified the small GTPase LIGHT INSENSITIVE PERIOD 1 (LIP1) as a circadian-clock-associated protein that regulates light input to the clock in the model plant Arabidopsis thaliana. We showed that LIP1 is also required for suppressing red and blue light-mediated photomorphogenesis, pavement cell shape determination and tolerance to salt stress. Here, we demonstrate that LIP1 is present in a complex of clock proteins GIGANTEA (GI), ZEITLUPE (ZTL) and TIMING OF CAB 1 (TOC1). LIP1 participates in this complex via GUANINE EX-CHANGE FACTOR 7. Analysis of genetic interactions proved that LIP1 affects the oscillator via modulating the function of GI. We show that LIP1 and GI independently and additively regulate photomorphogenesis and salt stress responses, whereas controlling cell shape and photoperiodic flowering are not shared functions of LIP1 and GI. Collectively, our results suggest that LIP1 affects a specific function of GI, possibly by altering binding of GI to downstream signalling components. [ABSTRACT FROM AUTHOR]

Summary: The role of maternal tissue in embryogenesis remains enigmatic in many complex organisms. Here, we investigate the contribution of maternal tissue to apical–basal patterning in the kelp embryo.Focussing on Undaria pinnatifida, we studied the effects of detachment from the maternal tissue using microsurgery, staining of cell wall modifications, morphometric measurements, flow cytometry, genotyping and a modified kelp fertilisation protocol synchronising kelp embryogenesis.Detached embryos are rounder and often show aberrant morphologies. When a part of the oogonial cell wall remains attached to the zygote, the apical–basal patterning is rescued. Furthermore, the absence of contact with maternal tissue increases parthenogenesis, highlighting the critical role of maternal signals in the initial stages of development.These results show a key role for the connection to the maternal oogonial cell wall in apical–basal patterning in kelps. This observation is reminiscent of another brown alga, Fucus, where the cell wall directs the cell fate. Our findings suggest a conserved mechanism across phylogenetically distant oogamous lineages, where localised secretion of sulphated F2 fucans mediates the establishment of the apical–basal polarity. In this model, the maternal oogonial cell wall mediates basal cell fate determination by providing an extrinsic patterning cue to the future kelp embryo. [ABSTRACT FROM AUTHOR]

In this study, biomass-derived carbon quantum dots (CQDs) were synthesized by an one-step hydrothermal method using folium cycas as a carbon source. By optimizing the reaction conditions, the fluorescence quantum yield of CQDs was obtained to be as high as 8.91%, and strong blue emission light was emitted. The characterization results showed that the CQDs were quasi-spherical with an average particle size of 2.69 ± 0.08 nm and contained a large number of hydrophilic functional groups with excellent water solubility and photostability. The CQDs showed high selectivity and sensitivity for the detection of Fe3+, with a low limit of detection of 0.72 μM and a wide linear range of 0–200 μM. The practical applicability of the CQDs was further established by carrying out Fe3+ detection in environmental sample analysis. Besides, CQDs have been successfully applied to in vitro cell imaging and bioimaging. The final by-product of the hydrothermal reaction, biochar, is used for dye adsorption. This work identifies the importance of using a relatively green process and an inexpensive biomass precursor to produce high-quality CQDs that hold a promising future for use in metal ion detection, bioimaging, and practical sensing applications. [ABSTRACT FROM AUTHOR]

The formation of stomata presents a compelling model system for comprehending the initiation, proliferation, commitment and differentiation of de novo lineage‐specific stem cells. Precise, timely and robust cell fate and identity decisions are crucial for the proper progression and differentiation of functional stomata. Deviations from this precise specification result in developmental abnormalities and nonfunctional stomata. However, the molecular underpinnings of timely cell fate commitment have just begun to be unravelled. In this review, we explore the key regulatory strategies governing cell fate commitment, emphasizing the distinctions between embryonic and postembryonic stomatal development. Furthermore, the interplay of transcription factors and cell cycle machineries is pivotal in specifying the transition into differentiation. We aim to synthesize recent studies utilizing single‐cell as well as cell‐type‐specific transcriptomics, epigenomics and chromatin accessibility profiling to shed light on how master‐regulatory transcription factors and epigenetic machineries mutually influence each other to drive fate commitment and maintenance. Summary statement: In this review, we delve into the molecular mechanisms underlying timely and precise cell fate commitment during stomatal development. Emphasis is made on the differences between embryonic and postembryonic stomatal differentiation. We highlight recent discoveries on the transcriptional circuits that initiate and fortify stomatal fate transitions, as well as the epigenetic processes that facilitate fate commitment and maintenance. [ABSTRACT FROM AUTHOR]

The transcription factors belonging to the Forkhead box (FOX) family are essential for the coordination of multiple cellular processes that are vital for the development of embryos, maintenance of tissue homeostasis, and the genesis of diseases. Of these, FOXC1 stands out as a crucial regulator that has a significant impact both during and after organogenesis. One of the several transcription factors that make up the FOX family, FOXC1, is known for its ability to control cellular motility, proliferation, differentiation, and cell fate determination. It is important for many organ systems, such as the ocular, central neurological, and cardiovascular systems, where it controls important developmental processes. Furthermore, new data highlights the role FOXC1 plays in a variety of clinical situations, from prenatal abnormalities to the advancement of cancer. FOXC1 also modulates gene expression networks critical for skeletal morphogenesis and cartilage integrity. This review attempts at exploring the role of FOXC1, elucidating its dynamics in organogenesis, developmental complexities, and numerous functions and providing insight into its critical role in determining biological complexity. [ABSTRACT FROM AUTHOR]

The completion of the Human Genome Project has provided a foundational blueprint for understanding human life. Nonetheless, understanding the intricate mechanisms through which our genetic blueprint is involved in disease or orchestrates development across temporal and spatial dimensions remains a profound scientific challenge. Recent breakthroughs in cellular omics technologies have paved new pathways for understanding the regulation of genomic elements and the relationship between gene expression, cellular functions, and cell fate determination. The advent of spatial omics technologies, encompassing both imaging and sequencing-based methodologies, has enabled a comprehensive understanding of biological processes from a cellular ecosystem perspective. This review offers an updated overview of how spatial omics has advanced our understanding of the translation of genetic information into cellular heterogeneity and tissue structural organization and their dynamic changes over time. It emphasizes the discovery of various biological phenomena, related to organ functionality, embryogenesis, species evolution, and the pathogenesis of diseases. This review summarizes how various spatial omics (transcriptomics, genomics, proteomics, epigenomics, translatomics, metabolomics, etc.) technologies are used at different scales, including the temporal scale, to understand how molecules and cells interact, their spatial distribution, and their dynamics. Their applications in studying development, disease, evolution, and clinical interventions, as well as areas for future improvement, are discussed in depth. [ABSTRACT FROM AUTHOR]

The development of multicellular organisms requires coordinated changes in gene expression that are often mediated by the interaction between transcription factors (TFs) and their corresponding cis-regulatory elements (CREs). During development and differentiation, the accessibility of CREs is dynamically modulated by the epigenome. How the epigenome, CREs, and TFs together exert control over cell fate commitment remains to be fully understood. In the Arabidopsis leaf epidermis, meristemoids undergo a series of stereotyped cell divisions, then switch fate to commit to stomatal differentiation. Newly created or reanalyzed scRNA-seq and ChIP-seq data confirm that stomatal development involves distinctive phases of transcriptional regulation and that differentially regulated genes are bound by the stomatal basic helix–loop–helix (bHLH) TFs. Targets of the bHLHs often reside in repressive chromatin before activation. MNase-seq evidence further suggests that the repressive state can be overcome and remodeled upon activation by specific stomatal bHLHs. We propose that chromatin remodeling is mediated through the recruitment of a set of physical interactors that we identified through proximity labeling—the ATPase-dependent chromatin remodeling SWI/SNF complex and the histone acetyltransferase HAC1. The bHLHs and chromatin remodelers localize to overlapping genomic regions in a hierarchical order. Furthermore, plants with stage-specific knockdown of the SWI/SNF components or HAC1 fail to activate specific bHLH targets and display stomatal development defects. Together, these data converge on a model for how stomatal TFs and epigenetic machinery cooperatively regulate transcription and chromatin remodeling during progressive fate specification. The development of multicellular organisms requires coordinated changes in gene expression. Here, the authors analyze transcriptional regulation in Arabidopsis during stomata development, revealing that cell fate decisions depend on complex interactions between master bHLH transcription factors and the epigenetic machinery. [ABSTRACT FROM AUTHOR]

The search for new Natural Products is one of the oldest interests for research in chemistry. The history of this discipline is very prolific, from its initial uses as medicine to advanced omics strategies to understand the mechanics of biological controls in living cells. The discoveries of morphine, penicillin, taxol and many other natural products revolutionized human health. During the last 40 years, excellent reviews published by Dr. David Newman and Dr. Gordon Crag have revealed that the pharmaceutical industry's research into natural products has lost some of its steam. Nevertheless, new natural products for antimicrobials, antifungals, and anticancer drugs remained the main alternative. Furthermore, research institutes have seen great vigor, and several startup companies have emerged worldwide, seeking therapeutic alternatives based in natural products. Innovations on spectrometric hardware, allowing broader coverage of chemical classes and spatial mapping, and in software, enabling the interpretation of large volumes of data, afforded a renewed interest in natural products and are considered the most important enabling technology for the new companies. In this perspective article we give some historical context to exciting developments, on software and spatial resolution, that promise to pave the way for a bright future of Natural Products research. [ABSTRACT FROM AUTHOR]

Purpose: To determine the effect of Lonicerae japonicae Caulis extract (LJCE) on the proliferation, apoptosis, and cycle distribution of human osteosarcoma U2OS cells. Methods: Human osteosarcoma U2OS cells were treated with LJCE at doses of 10, 20, 30 and 40 mg/mL, with untreated U2OS cells as the control group. Cell proliferation was measured using MTT method, while flow cytometric analysis was used for determination of apoptosis and cell cycle distribution. Results: As LJCE concentration increased, the viability of U2OS cells gradually decreased, while the apoptosis rate gradually increased. The LJCE treatment had no marked effect on G1 phase cells (p > 0.05). However, the population of G2 cells in each group increased with increasing LJCE concentration, while the S phase cells in each group decreased with increasing concentration. The cells were significantly blocked in the G2 phase (p < 0.05). Conclusion: Lonicerae japonicae Caulis extract inhibits the proliferation of U2OS cells and promotes apoptosis of U2OS cells. Therefore, LJCE possesses potentials as a novel therapeutic agent for osteosarcoma. [ABSTRACT FROM AUTHOR]

Due to importance of cell voltage and caustic current efficiency (CCE) in chlor-alkali industry, the necessity of accurate approach for prediction these parameters has become evident. In the current work, an extreme learning machine (ELM) approach is used to this end. Determination of the statistical qualities including R2 and different types of error reveals the fact that ELM method is suitable tool for calculation of CCE and cell voltage. The determined R2 values for CCE and cell voltage are equal to 1. Furthermore, RMSE values are 0.00002 and 1.3 × 10−6 for cell voltage and CCE, respectively. On the other hand, different graphical methods confirmed this acclaim. Moreover a sensitivity analysis is used to show effect of brine concentration, current density, operating temperature, electrolyte velocity, run time and pH on cell voltage and CCE. This analysis concluded to the fact that brine concentration and current density have the most effects on CCE and Cell voltage, respectively. [ABSTRACT FROM AUTHOR]

N6-methyladenosine (m6A) represents the most prevalent and significant internal modification in mRNA, with its critical role in gene expression regulation and cell fate determination increasingly recognized in recent research. The immune system, essential for defense against infections and maintaining internal stability through interactions with other bodily systems, is significantly influenced by m6A modification. This modification acts as a key post-transcriptional regulator of immune responses, though its effects on different immune cells vary across diseases. This review delineates the impact of m6A modification across major system-related cancers—including those of the respiratory, digestive, endocrine, nervous, urinary reproductive, musculoskeletal system malignancies, as well as acute myeloid leukemia and autoimmune diseases. We explore the pathogenic roles of m6A RNA modifications within the tumor immune microenvironment and the broader immune system, highlighting how RNA modification regulators interact with immune pathways during disease progression. Furthermore, we discuss how the expression patterns of these regulators can influence disease susceptibility to immunotherapy, facilitating the development of diagnostic and prognostic models and pioneering new therapeutic approaches. Overall, this review emphasizes the challenges and prospective directions of m6A-related immune regulation in various systemic diseases throughout the body. [ABSTRACT FROM AUTHOR]

MicroRNAs play critical roles in multiple developmental processes in insects. Our previous study showed that CRISPR/Cas9‐mediated knock down of the microRNA let‐7 in silkworms increased the size of larvae and silk glands, thereby improving the silk production capacity. In this study, we elucidate the molecular mechanism underlying of let‐7 regulates growth. Identification of differentially expressed genes in response to let‐7 knock down revealed enrichment of pathways associated with cell proliferation and DNA replication. let‐7 dysregulation affected the cell cycle and proliferation of the Bombyx mori cell line BmN. Dual‐luciferase and target site mutation assays showed that BmCDK1 is a direct target gene of let‐7, with only 1 binding site on its 3′‐untranslated region. RNA interference of BmCDK1 inhibited cell proliferation, but this effect was counteracted by co‐transfection with let‐7 antagomir. Moreover, let‐7 knock down induced BmCDK1 expression and promoted cell proliferation in multiple tissues, and further induced endomitosis in the silk gland in vivo. Knock down of BmCDK1 resulted in abnormal formation of a new epidermis, and larval development was arrested at the 2nd or 3rd molt stage. Taken together, our results demonstrated that BmCDK1 is a novel target of let‐7 in cell fate determination, possessing potential for improving silk yield in silkworm. [ABSTRACT FROM AUTHOR]

The regeneration of plant somatic cells is a prerequisite for their biological breeding. Identification of key genes controlling embryogenic callus (EC) differentiation and investigation of the genetic mechanism of cell fate determination are important for improving plant variety. In this study, we used the maize inbred line KN5585 and its gene-edited mutants Zmprx19-1, Zmprx19-2 and Zmprx19-3 as plant materials. Three somatic regeneration-related traits, the embryogenic callus induction rate (EIR), green callus rate (GCR) and plantlet regeneration rate (PRR), were identified by tissue culture of immature embryos. Additionally, the ECs at different differentiation stages (0 d, 5 d, 10 d and 15 d) were subjected to RNA-seq, and comparative transcriptome analyses were performed. The results showed that the somatic regeneration traits of the mutants were all highly significantly lower than those of the wild type (p < 0.01). The PRR value of KN5585 was 75.25%, while the highest PRR of the mutants was only 15.08%, indicating that knockdown of ZmPRX19 inhibited EC regeneration. Transcriptome sequencing yielded a total of 200.30 Gb of clean data from 24 libraries, with an average of 6.53 Gb of clean data per library. Mutant and wild-type gene expression data were compared separately at four differentiation stages, and 689 common differentially expressed genes (DEGs) were screened. WGCNA was used to classify these genes into nine modules, which were subsequently subjected to GO and KEGG enrichment analyses. In total, 40, 23, 17 and 5 genes were significantly (q < 0.05) enriched in plant hormone signal transduction, the MAPK signaling pathway-plant, phenylpropanoid biosynthesis and photosynthesis, respectively. Moreover, protein–protein interaction (PPI) network analysis revealed five MAPKKK17_18 hub nodes involved in the MAPK pathway-plant, which may be the key genes controlling plantlet differentiation from ECs. The above results provide a basis for the final elucidation of the molecular mechanism of plant somatic regeneration. [ABSTRACT FROM AUTHOR]

Summary: Inter‐subspecific indica–japonica hybrid rice (Oryza sativa) has the potential for increased yields over traditional indica intra‐subspecies hybrid rice, but limited yield of F1 hybrid seed production (FHSP) hinders the development of indica–japonica hybrid rice breeding. Diurnal flower‐opening time (DFOT) divergence between indica and japonica rice has been a major contributing factor to this issue, but few DFOT genes have been cloned. Here, we found that manipulating the expression of jasmonate (JA) pathway genes can effectively modulate DFOT to improve the yield of FHSP in rice. Treating japonica cultivar Zhonghua 11 (ZH11) with methyl jasmonate (MeJA) substantially advanced DFOT. Furthermore, overexpressing the JA biosynthesis gene OPDA REDUCTASE 7 (OsOPR7) and knocking out the JA inactivation gene CHILLING TOLERANCE 1 (OsHAN1) in ZH11 advanced DFOT by 1‐ and 2‐h respectively; and knockout of the JA signal suppressor genes JASMONATE ZIM‐DOMAIN PROTEIN 7 (OsJAZ7) and OsJAZ9 resulted in 50‐min and 1.5‐h earlier DFOT respectively. The yields of FHSP using japonica male‐sterile lines GAZS with manipulated JA pathway genes were significantly higher than that of GAZS wildtype. Transcriptome analysis, cytological observations, measurements of elastic modulus and determination of cell wall components indicated that the JA pathway could affect the loosening of the lodicule cell walls by regulating their composition through controlling sugar metabolism, which in turn influences DFOT. This research has vital implications for breeding japonica rice cultivars with early DFOT to facilitate indica–japonica hybrid rice breeding. [ABSTRACT FROM AUTHOR]

It is well established that microRNA-21 (miR-21) targets phosphatase and tensin homolog (PTEN), facilitating epithelial-to-mesenchymal transition (EMT) and drug resistance in cancer. Recent evidence indicates that PTEN activates its pseudogene-derived long non-coding RNA, PTENP1, which in turn inhibits miR-21. However, the dynamics of PTEN, miR-21, and PTENP1 in the DNA damage response (DDR) remain unclear. Thus, we propose a dynamic Boolean network model by integrating the published literature from various cancers. Our model shows good agreement with the experimental findings from breast cancer, hepatocellular carcinoma (HCC), and oral squamous cell carcinoma (OSCC), elucidating how DDR activation transitions from the intra-S phase to the G2 checkpoint, leading to a cascade of cellular responses such as cell cycle arrest, senescence, autophagy, apoptosis, drug resistance, and EMT. Model validation underscores the roles of PTENP1, miR-21, and PTEN in modulating EMT and drug resistance. Furthermore, our analysis reveals nine novel feedback loops, eight positive and one negative, mediated by PTEN and implicated in DDR cell fate determination, including pathways related to drug resistance and EMT. Our work presents a comprehensive framework for investigating cellular responses following DDR, underscoring the therapeutic potential of targeting PTEN, miR-21, and PTENP1 in cancer treatment. [ABSTRACT FROM AUTHOR]