Open Biology最新文献

Recent work has shown that the prevalence and character of metabolic diseases differs between male and female mammals. This strongly suggests that the control mechanisms that govern, for example lipid metabolism, differ between the sexes. If true, a one-size-fits-all approach to treating metabolic disease will not be effective in all patients. We tested three hypotheses to understand how the lipid metabolism of male and female mammals may differ. First, whether endogenous fatty acid biosynthesis differed between tissues in the same male and female mice. Second, whether the system-level control of lipid pathways differed between the sexes. Third, whether lipid composition differs between males and females at a population level. We found that fatty acid biosynthesis was distinct in male and female mice across tissues. Systemic control of phospholipid and triglyceride metabolism also differed between the sexes. A human population showed that both phospholipid and triglyceride metabolism differed between males and females.

Microbial holozoans are the closest unicellular relatives of animals. They share a substantial gene repertoire with animals and exhibit complex life cycles. Studying these organisms is crucial for understanding the evolution of multicellularity, and significant progress has been made in uncovering key aspects of the biology of the four microbial holozoans lineages: choanoflagellates, filastereans, ichthyosporeans and corallochytreans. However, reverse genetic tools are still lacking in corallochytreans, one of the earliest-branching holozoan lineages and the only known group with both coenocytic and binary fission development. Here, we present CRISPR-Cas9-mediated gene inactivation and point mutation methodologies in the corallochytrean Corallochytrium limacisporum. As a proof of concept, we inactivated the fkb12 gene, a component of the mTOR pathway, conferring rapamycin resistance, and introduced a point mutation in sdhB, encoding a subunit of succinate dehydrogenase, conferring carboxin resistance. Our results demonstrate the presence of both non-homologous end-joining and homology-directed repair pathways in C. limacisporum and shows an editing efficiency of approximately 2%. Furthermore, simultaneous gene targeting revealed a co-editing frequency of approximately 20%. Finally, this study establishes unequivocally that C. limacisporum is haploid, making it an ideal model for genetic studies and gene editing applications to unravel the molecular mechanisms involved in animal origins.

Orofacial clefts are the second-most prevalent congenital malformation. Risk factors are multifactorial and include genetic components, but also environmental factors. One environmental factor is hypoxia during pregnancy, caused for instance by tobacco smoking, medication or living at high altitudes. We here show that hypoxia has only modest effects on proliferating cranial neural crest cells (CNCC), but dramatically influences their differentiation potential. We detected massive perturbations in their differentiation to chondrocytes, osteoblasts and smooth muscle cells. The transcriptional induction of the majority of regulated genes during each of these processes was grossly impaired by hypoxic conditions, as evidenced by genome-wide transcriptomic analyses. These hypoxia-attenuated genes include several orofacial cleft risk genes. Among these, we bioinformatically identified the hedgehog co-receptor Boc and the cysteine dioxygenase Cdo1 as two central genes that display hypoxia-attenuated induction during all three differentiation pathways and that are relevant during craniofacial development. Moreover, several components of signalling pathways between undifferentiated CNCC and their derivatives, as well as components of signalling pathways from CNCC to epithelial cells, were affected by hypoxia. Our analyses reveal a drastic influence of hypoxia on the differentiation potential of CNCC as a possible cause for the occurrence of orofacial clefts.

The retinal determination genetic network controls the development of the visual system in all seeing animals through the molecular regulation of cells to adopt an eye tissue fate. The compound eye of the fruit fly, Drosophila melanogaster, is an excellent model system to study the complex mechanisms within the network that regulate specification of cellular identity during embryogenesis. In Drosophila, the two Pax6 paralogues, eyeless and twin of eyeless, sit at the very pinnacle of the network and their expression early in development activates critical downstream components of the retinal determination pathway. In this study, we investigate the expression of 21 known components of the network in two established embryonic cell lines, Kc167 and S2 cells, that show reciprocal expression patterns for the two Pax6 paralogues. Network mapping reveals that many of the components of the network demonstrate extensive interactions with additional factors. Integrating the transcriptional profile of the cell lines, interaction maps and embryonic expression patterns enables us to identify 16 potential novel components of the genetic network, 11 of which are transcription factors. We confirm the regulatory potential for a subset of the novel transcription factors through the identification of predicted binding sites in previously characterized enhancers for the core genes in the network.

The large membrane protein PIEZO1 assembles as trimers to form exceptional mechanical force-sensing ion channels of eukaryotes. When these channels are activated by force, cell membrane permeability to calcium ions and other ions increases rapidly, coupling force to cell function through ionic control. In humans and other species, PIEZO1 is both widely expressed and functional across major systems that include the cardiovascular, haematological and musculoskeletal systems, thereby serving diverse needs. In this narrative review of the scientific literature, we address what has been learned about PIEZO1 from associations of its gene variation with human characteristics. A particular physiological importance of PIEZO1 is emerging in lymphatics and thus in the control of tissue fluid homeostasis with relevance to the disease conditions of non-immune fetal hydrops and generalized lymphatic dysplasia. Other vascular relevance is seen in lower limb venous varicosities. PIEZO1 may be non-essential in red blood cells but the amplification of its function by gene variation quite selectively alters these cells, leading to haemolytic anaemia and other related disturbances that may be only mildly adverse and confer survival advantage. We speculate on what else might be learned in humans, guided by knowledge from PIEZO1 studies in mice, and describe how knowledge accumulated to date highlights new opportunities for PIEZO1 understanding and pathways to patient benefit.

Plasmids are pinnacle tools in synthetic biology and other biotechnological applications. They serve as the simplest approach to introduce recombinant DNA, which is then transcribed into RNA that functions as is or is translated into a protein of interest. Despite their widespread utility, the question 'how many plasmids can be used in this bacterium?' remains underexplored in the existing literature. In this article, I discuss the maintenance of multiple unique plasmids in bacteria through a microbial synthetic biology perspective, both in theoretical and practical aspects. I delve into the existing evidence of multi-plasmid systems, aiming to pinpoint the possible maximum number of unique plasmids a single microbe can carry. Finally, I highlight how the existing applications of multi-plasmid systems drive novel discovery and development in metabolic engineering, synthetic biology and other relevant areas in comparison to other non-plasmid strategies.

Long-read RNA sequencing has transformed transcriptome analysis by enabling comprehensive mapping of full-length transcripts, providing an unprecedented resolution of transcript diversity, alternative splicing and transcript-specific regulation. In this study, we employed nanopore long-read RNA sequencing to profile the transcriptomes of three cell types commonly used to model brain disorders, human fibroblasts, induced pluripotent stem cells and stem cell-derived cortical neurons, identifying extensive transcript diversity with 15 072 transcripts in stem cell-derived cortical neurons, 13 048 in fibroblasts and 12 759 in induced pluripotent stem cells. Our analyses uncovered 35 519 differential transcript expression events and 5135 differential transcript usage events, underscoring the complexity of transcriptomic regulation across these cell types. Importantly, by integrating differential transcript expression and usage analyses, we gained deeper insights into transcript dynamics that are not captured by gene-level expression analysis alone. Differential transcript usage analysis highlighted transcript-specific changes in disease-relevant genes such as APP, KIF2A and BSCL2, associated with Alzheimer's disease, neuronal migration disorders and degenerative axonopathies, respectively. This added resolution emphasizes the significance of transcript-level variations that often remain hidden in traditional differential gene expression analyses. Overall, our work provides a framework for understanding transcript diversity in both pluripotent and specialized cell types, which can be used to investigate transcriptomic changes in disease states in future work. Additionally, this study underscores the utility of differential transcript usage analysis in advancing our understanding of neurodevelopmental and neurodegenerative diseases, paving the way for identifying transcript-specific therapeutic targets.

During nervous system development, growing axons find their targets with the help of guidance cues. These cues, which can be secreted molecules provided by neighbouring cells or transmembrane proteins mediating cell-cell contacts with the growing axons, act as either chemoattractants or chemorepellents. Over the last decades, several axon guidance molecules have been identified. One of the classical guidance cues is the Slit protein. Slit is a secreted protein, initially identified in a genetic screen in the fruit fly Drosophila melanogaster but later shown to be present in other organisms including vertebrates. Slit was originally classified as a repellent guidance cue, but nowadays it is recognized as a promoter of axonal growth in some contexts. Slit action is mediated mainly by the Roundabout (Robo) family of single pass transmembrane proteins, although it has been shown more recently that other proteins can also function as Slit receptors. In this review, we describe the main aspects of Slit-Robo signalling during development of the nervous system. We start with a historical view of the discovery of these proteins, followed by a description of their main molecular characteristics. We then explore specific examples that describe the functions and signal transduction mechanisms of this signalling pathway.

Circadian rhythm, as a homeostatic tool of biological life, plays a vital role in regulating human physiology, metabolism, endocrinology, and emotional and cognitive behaviour. A disrupted circadian rhythm, marked by age-related alterations such as decreased variation in sleep-wake patterns and instability in the timing of these patterns, can worsen age-related problems such as increased oxidative stress and inflammation. Advancing age is associated with anomalies in the redox balance, gradual alterations in physiological functions and deregulation of various metabolic pathways. The mutual interaction between circadian rhythm and ageing may potentially contribute to the development of neurodegenerative disorders. Consistent alterations in circadian rhythms could lead to various degenerative disorders and aggravate age-related ailments. Therefore, understanding and unravelling the intricate interplay between circadian rhythm and ageing holds immense potential for developing therapeutic interventions and promoting healthy ageing strategies. In this review article, we discuss the role of circadian rhythms in physiology and their age-related changes that impact health. We focus on how disruptions in circadian rhythms, common with ageing, may increase risks for neurodegenerative disorders. Understanding this interaction holds promise for developing therapeutic approaches to support healthy ageing.

Macrophage extracellular traps (METs) represent a recently discovered complex defence mechanism that is distinct from phagocytosis and involves the release of DNA and antibacterial proteins. They play an important role in pathogen removal, and calcium ions (Ca²⁺) have also been reported to be involved. In the present study, we identified METotic cells using digitonin as an alternative to Triton X-100, coupled with immunofluorescence staining using lamin antibodies. The limited permeability of digitonin ensures exclusive intranuclear antibody labelling of MET cells, therefore providing a straightforward and intuitive differentiation method. We found that under lipopolysaccharide stimulation, macrophages undergo store-operated Ca²⁺ entry (SOCE) to facilitate Ca²⁺ influx. Elevation of cytoplasmic Ca²⁺ levels by SOCE promotes the generation of superoxide anions by NADPH oxidase (NOX), ultimately leading to METosis. In summary, our study strengthens the role of Ca²⁺ in NOX-dependent METosis, which differs from previous studies focusing on Ca²⁺ in the NOX-independent pathway. Our research reveals that Ca²⁺-mediated regulation of NOX plays a crucial role in METosis, especially in SOCE, and provides novel ideas for future research.