Biology Open最新文献

Precise genome editing remains a major challenge in functional genomics, particularly for generating knock-in (KI) alleles in model organisms. Here, we introduce the mini-golden system, a versatile Golden Gate-based subcloning platform that enables rapid assembly of donor constructs containing homology arms and a gene of interest. This system offers a library of middle entry vectors including diverse genes, enhancing the preparation of donor minicircles for KI applications. Using the mini-golden system, we efficiently generated a foxd3CreER KI zebrafish line, allowing conditional recombination in neural crest cells. To further improve genome editing precision, we developed a synthetic exon-based donor template strategy combined with fluorescence screening. Using this approach, we successfully engineered a targeted isoleucine-to-valine substitution (Ile-to-Val) in hbaa1.2, one of the two adult hemoglobin alpha genes in zebrafish. Importantly, despite the high sequence similarity between hbaa1.2 and its paralog hbaa1.1, our strategy specifically edited hbaa1.2, demonstrating the effectiveness of the synthetic exon approach. This method minimized undesired recombination and significantly improved the identification of lines carrying the edited genome. Together, we provide a robust toolkit for efficient and precise genome engineering in zebrafish, with broad applicability to other model systems.

Anthelmintic resistance (AR) poses an escalating threat to global soil-transmitted helminth control efforts, particularly in the context of mass drug administration (MDA) programs that rely heavily on benzimidazole drugs. To address the urgent need for novel therapeutics, a machine learning (ML) guided drug repurposing pipeline was developed to identify compounds effective against a multi-anthelmintic drug-resistant (MADR) isolate of Ancylostoma caninum. The computational strategy employed in this work involved training classifiers on curated datasets of anthelmintic actives and decoys, followed by screening all approved drugs from the online database, DrugBank. Selected compounds were tested using a tiered assay system comprising egg hatch assays (EHA), larval development assays (LDA), and adult survival assays. Among these, flutamide, a nonsteroidal antiandrogen approved for prostate cancer, demonstrated potent, egg- and larval-stage-specific activity against MADR hookworm. Flutamide exhibited a concentration-dependent inhibition of egg hatching and arrested larval development in MADR hookworm. These findings underscore the translational value of drug repurposing to accelerate therapeutic discovery against MADR helminths.

Drosophila compound eye is composed of approximately 800 ommatidia, and every ommatidium contains eight photoreceptor cells, six outer cells (R1-R6) and two inner cells (R7 and R8), and accessory cells (cone and pigment cells). Expression of rhodopsin genes in R7 and R8 is highly coordinated through an instructive signal from R7 to R8. The activity of the homeodomain protein Defective proventriculus in R1 is also required to transmit this instructive signal, suggesting that cell-cell communication between R7-R1-R8 is important to generate the pattern of Rh expression in R7/R8 (Rhodopsin coupling). As cell junctions play crucial roles in maintaining the structural and functional integrity of tissues, we tested whether cell-junction proteins are involved in the interactions between photoreceptor cells. Here we show that gap junction proteins Innexin2 (Inx2) and Inx7 are required in accessory cells to transmit a signal from R7 to R8. In addition, Notch-mediated accessory cell development and Rhodopsin coupling in R7/R8 are highly corelated. Our results provide evidence that functional coupling of two different neurons R7 and R8 is established through gap junction-mediated signaling from adjacent accessory cells.

In chordate embryos, placodes are ectodermal thickenings around the borders of the neural plate that give rise to various sensory organs and cell types. While generally thought to be a vertebrate-specific innovation, homologous placodes are proposed to exist in non-vertebrate chordates as well. In Ciona robusta, a solitary tunicate, the adult mouth (the oral siphon) is derived from one such "cranial-like" placode in the larva, which we term the oral siphon placode (OSP). At embryonic and larval stages, the OSP consists of a small rosette of cells that forms from the neuropore at the anteriormost extent of neural tube closure. While the morphogenesis of the OSP and its physical separation from other surface ectoderm structures have been described in detail, how this is regulated at the molecular level is currently unknown. Here we show the involvement of protocadherin-mediated cell-cell interactions in the proper morphogenesis of the OSP. Protocadherin.e (Pcdhe.e) is expressed specifically in the OSP but not in other surface ectoderm cells. CRISPR/Cas9-mediated disruption of Pcdh.e in these cells results in the failure of the OSP to physically separate from other structures derived from the same cell lineage. Overexpression of Pcdh.e throughout the anterior surface ectoderm results in similar loss of a physically separate and distinct OSP territory. This effect is likely mediated by homophilic adhesion in trans, as Pcdh.e with scrambled extracellular domains failed to recapitulate the phenotype. Finally, we show that Pcdh.e expression in the OSP depends on oral placode-specific transcription factors such as Six1/2 and Pitx. Our results suggest that OSP morphogenesis requires precise regulation of a homotypic cell-cell adhesion molecule, which might reflect a conserved mechanism for placode formation in chordates.

Camellia rubriflora (C. rubriflora), a member of the genus Camellia, is an endemic species in the northern mountainous region of Vietnam. However, overexploitation of this species has placed it at risk of extinction, and conservation strategies need to be implemented to ensure its continued survival. This study evaluated the ex-vitro propagation potential of C. rubriflora using cuttings obtained from a nursery. The effects of seasonality, rooting media, and NAA concentration on survival rate, bud break rate, rooting ability of cuttings were investigated. Spring propagation of cuttings performed significantly better than those in other seasons. Using a rooting medium composed of soil and carbonized rice husk, combined with 150 ppm NAA, significantly enhanced growth parameters, achieving a 77.8% survival rate, 94.4% bud break rate, and 72.2% rooting rate, significantly higher than the control using soil without NAA. Root number and root length were also significantly increased under optimal conditions, reaching 5.2±1.0 roots per cutting and 9.4±0.9 mm, respectively. The high correlation between survival rate, bud break rate, and rooting rate was observed, especially when using Soil+CRH, ranging from 0.709 to 0.843, showing the simultaneous impact of experimental factors on the evaluation criteria. Evaluating optimal conditions for the propagation of C. rubriflora played an important role in enhancing the conservation potential of this endemic species at risk of extinction.

The Loke Centre for Trophoblast Research Annual Meeting, 'The Placenta at Term', was held on 7-8 July, 2025, at the University of Cambridge, UK. The meeting brought together leading clinical and basic scientists from around the world to explore how robust research methods can improve understanding of placental complications such as preeclampsia, fetal growth restriction, and gestational diabetes. This Meeting Review highlights emerging research directions and emphasises the remarkable potential of the placenta, not only as a window into obstetrical complications, but also as a diagnostic tool for predicting the short- and long-term health of both mother and child.

The flatworm Macrostomum lignano is a versatile invertebrate model organism with a growing molecular toolbox. Genome assembly and detailed karyotyping revealed that M. lignano is a hidden polyploid species with a recent whole-genome duplication. Its karyotype consists of six small and two large chromosomes (2n=8), with the large chromosomes originating from the fusion of duplicated ancestral chromosomes. However, 2n=9 and 2n=10 karyotypes with duplicated large chromosomes were also observed in animals from both laboratory cultures and field samples, prompting us to further investigate this phenomenon. To this end, we optimized a flow cytometric approach that enables easy and rapid studies of tens or even hundreds of animals simultaneously to gain insight into the karyotype polymorphisms present in a culture and consistently tracked karyotype dynamics in multiple cultures over a period of 26 months. We demonstrate that de novo duplications of the large chromosome in M. lignano can spontaneously appear under laboratory conditions and can become dominant in laboratory cultures. Since uncontrolled chromosomal duplications can complicate genetic studies in laboratory model organisms, we propose an approach to easily control the karyotype of experimental cultures by regularly karyotyping M. lignano subcultures using flow cytometry and replacing cultures with de novo chromosome duplications as needed.

Mediterranean corals living in coastal habitats are subjected to natural fluctuations in temperature and nutrient availability, including substantial iron (Fe) inputs via terrestrial runoff (up to 14.5 nM). While Fe is essential for coral and symbiont metabolism, the assimilation rate, physiological thresholds, and spatial allocation of Fe within coral compartments, and its interactive effects with warming, remain poorly understood. Here, we provide the first characterization of oxygen (O2) dynamics, trace metal content, and microbial community composition in two Mediterranean corals, Cladocora caespitosa and Eunicella singularis, exposed to chronic warming (18-24°C) and Fe(III) supplementation (20 nM day-1). We show that although these corals are not Fe-limited, increased temperature enhanced the Fe uptake in the algal symbionts of C. caespitosa. In C. caespitosa, Fe supplementation reduced the O2 availability within the gastrovascular cavity (GVC) and altered the composition and diversity of GVC microbial communities. In E. singularis, interactive effects of Fe and warming reduced GVC O2 availability within the GVC, and warming increased metal content, while the microbiome resembled the surrounding seawater. These intraspecific differences in the sensitivity of the coral holobiont to warming and Fe supplementation could have important implications for the resilience of Mediterranean corals to ongoing climate stress, underscoring the importance of considering coral compartments in ecophysiological research.

The 2025 EMBO Workshop 'Beyond the standard: Unconventional vertebrate models in biomedicine' took place in Edinburgh, UK, in June 2025, and gathered a diverse group of researchers, veterinarians and animal technicians to explore the biological insights that can be unlocked from studying diverse, non-traditional vertebrates. This second iteration of the workshop focused on stem cells and regeneration, reproductive biology, immunology, ageing, and the latest technological advances and ongoing challenges in bringing non-model vertebrates to the forefront of biomedical research. The workshop also housed the first meeting for the growing spiny mouse research community.

Low reprogramming efficiency and high phenotypic variability hinder the regenerative medicine applications of human pluripotent stem cells. Understanding the mechanisms that regulate pluripotency is crucial to overcoming these challenges. This study investigated the relationship between lactylation, a newly identified regulator of gene expression, pluripotency, metabolism, and lactate transport in human embryonic stem cells (hESCs). Histone lactylation levels were significantly higher in hESCs than in differentiated cells. Further, exogenous lactate increased histone lactylation and acetylation levels and altered pluripotency gene expression, notably increasing KLF4, KLF5, GBX2, and DMNT3L in hESCs. Finally, naïve-like hESC colonies exhibited higher lactylation levels peripherally, coinciding with elevated peripheral SOX2 levels. Conversely, lactate transport and production protein levels were higher centrally. This study suggests that elevated histone lysine lactylation levels are a newly identified characteristic of human pluripotency. The spatial distribution findings are consistent with a positive relationship between histone lactylation and SOX2 expression in naïve-like hESCs.