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Where sporting games may be said to epitomize our species' unique agential capacity for playful movement, sports played in nature differ from their equivalent played indoors in that they envelop the human agent within the living physical environment from which our agency originates. In this paper, we draw attention to how sporting sites differ according to origin by pursuing a biosemiotic line of reasoning. Here, the story of a meaningful human life begins with the eukaryotic cell, even though the human subject itself arises much later. As such, the story of nature in relation to our agency, here, in sports, changes too. We present key concepts from biosemiotics, including its continuum life-as-semiotic-agency view, Umwelt, metasemiosis, and semiotic scaffolding to advance our argument that naturogenic sporting sites provide continuity to the macro processes that have generated our semiotic ability to play. Meanwhile, secluded anthropogenic environments constitute yet another discontinuity for the modern sportsperson where the moving body steps into an anthroposemiotic loop and its restricted signscapes from centralized agency. We conclude on the primacy of naturogenic sporting sites as they preserve the quality and complexity of animal ludens' constitutive relations and therefrom semiotic freedom, on which current and future gameplaying depends. [ABSTRACT FROM AUTHOR]

Vegetables are crucial for a healthy human diet due to their abundance of essential macronutrients and micronutrients. However, there have been increased reports of antimicrobial-resistant Enterobacteriaceae isolated from vegetables. Enterobacteriaceae is a large group of Gram-negative bacteria that can act as commensals, intestinal pathogens, or opportunistic extraintestinal pathogens. Extraintestinal infections caused by Enterobacteriaceae are a clinical concern due to antimicrobial resistance (AMR). β-lactams have high efficacy against Gram-negative bacteria and low toxicity for eukaryotic cells. These antimicrobials are widely used in the treatment of Enterobacteriaceae extraintestinal infections. This review aimed to conduct a literature survey of the last five years (2018–2023) on the occurrence of β-lactam-resistant Enterobacteriaceae in vegetables. Research was carried out in PubMed, Web of Science, Scopus, ScienceDirect, and LILACS (Latin American and Caribbean Health Sciences Literature) databases. After a careful evaluation, thirty-seven articles were selected. β-lactam-resistant Enterobacteriaceae, including extended-spectrum β-lactamases (ESBLs)-producing, AmpC β-lactamases, and carbapenemases, have been isolated from a wide variety of vegetables. Vegetables are vectors of β-lactam-resistant Enterobacteriaceae, contributing to the dissemination of resistance mechanisms previously observed only in the hospital environment. [ABSTRACT FROM AUTHOR]

Microtubule and actin are the two major cytoskeletal polymers that form organized functional structures in the interior of eukaryotic cells. Although the structural mechanics of the cytoskeleton has been extensively studied by direct manipulations in in vitro reconstitution systems, such unambiguous characterizations inside the living cell are sparse. Here, we report a comprehensive analysis of how the microtubule and actin cytoskeletons structurally respond to direct intracellular load. Ferrofluid-based intracellular magnetic tweezers reveal rheological properties of the microtubule complex primarily determined by filamentous actin. The strain fields of the microtubule complex and actin meshwork follow the same scaling, suggesting that the two cytoskeletal systems behave as an integrated elastic body. The structural responses of single microtubules to contact and remote forces further evidence that the individual microtubules are enclosed by the elastic medium of actin. These results, directly characterizing the microtubule and actin cytoskeletons as an interacting continuum throughout the cytoplasm, serve as a cornerstone for the physical understanding of intracellular organization. [ABSTRACT FROM AUTHOR]

Actin is the most abundant protein in eukaryotic cells. They form filamentous polymers that are organized in different ways within the cell to perform various functions. For instance, prominent parallel bundles of F-actins mediate the formation and dynamics of filopodia that are long, finger-like protrusions of cell membrane occurring in certain cells, like growing neurons. Understanding actin organization dynamics and its regulation is a crucial problem for biologists that cannot be solved exclusively by biological methods, requiring the support of mathematical and computational modelling. In this work, grounded on a previous hypothesis of ours about the cytosol flow within filopodia, we address several modelling challenges posed by the growth of filopodia in neurons. We use alternative stochastic models and particle-centered numerical methods for transport and elongations, as well as an innovative object-oriented modelling-strategy to represent chemical transformations, polymerization, and their regulation. These modelling strategies allowed for simulating elongations 20 times longer than the typical ranges attained by commonly used filopodia diffusion models, and show that our hypothesis is feasible, acting as a proof-of-concept about the importance of considering organization as a key element in biological explanations. [ABSTRACT FROM AUTHOR]

Stalled ribosomes cause collisions, impair protein synthesis, and generate potentially harmful truncated polypeptides. Eukaryotic cells utilize the ribosome-associated quality control (RQC) and no-go mRNA decay (NGD) pathways to resolve these problems. In yeast, the E3 ubiquitin ligase Hel2 recognizes and polyubiquitinates disomes and trisomes at the 40S ribosomal protein Rps20/uS10, thereby priming ribosomes for further steps in the RQC/NGD pathways. Recent studies have revealed high concentrations of disomes and trisomes in unstressed cells, raising the question of whether and how Hel2 selects long-term stalled disomes and trisomes. This study presents quantitative analysis of in vivo-formed Hel2•ribosome complexes and the dynamics of Hel2-dependent Rps20 ubiquitination and Ubp2/Ubp3-dependent deubiquitination. Our findings show that Hel2 occupancy progressively increases from translating monosomes to disomes and trisomes. We demonstrate that disomes and trisomes with mono- or di-ubiquitinated Rps20 resolve independently of the RQC component Slh1, while those with tri- and tetra-ubiquitinated Rps20 do not. Based on the results, we propose a model in which Hel2 translates the duration of ribosome stalling into polyubiquitin chain length. This mechanism allows for the distinction between transient and long-term stalling, providing the RQC machinery with a means to select fatally stalled ribosomes over transiently stalled ones. The yeast E3 ligase Hel2 translates the duration of ribosome stalling into polyubiquitin chain length on Rps20, enabling the ribosome-associated quality control machinery to distinguish between transiently and fatally stalled ribosomes. [ABSTRACT FROM AUTHOR]

Lipophagy is a selective degradation of lipid droplets in lysosomes or vacuoles. Apart from its role in generating energy and free fatty acids for membrane repair, growth, and the formation of new membranes, lipophagy emerges as a key player in other cellular processes and disease pathogenesis. While fungal, plant, and algal cells use microlipophagy, the most prominent form of lipophagy in animal cells is macrolipophagy. However, recent studies showed that animal cells can also use microlipophagy to metabolize their lipid droplets. Therefore, to no surprise, microlipophagy is conserved from simple unicellular to the most complex multicellular eukaryotes, and many eukaryotic cells can operate both forms of lipophagy. Macrolipophagy is the most studied and better understood at the molecular level, while our understanding of microlipophagy is very sparse. This review will discuss microlipophagy from the perspective of its conservation in eukaryotes and its importance in diseases. To better appreciate the conserved nature of microlipophagy, different organisms and types of cells in which microlipophagy has been reported are also shown in a tabular form. We also point toward the gaps in our understanding of microlipophagy, including the signaling behind microlipophagy, especially in the cells of complex multicellular organisms. [ABSTRACT FROM AUTHOR]

DNA replication, a fundamental process in all living organisms, proceeds with continuous synthesis of the leading strand by DNA polymerase ε (Pol ε) and discontinuous synthesis of the lagging strand by polymerase δ (Pol δ). This inherent asymmetry at each replication fork necessitates the development of methods to distinguish between these two nascent strands in vivo. Over the past decade, strand-specific sequencing strategies, such as enrichment and sequencing of protein-associated nascent DNA (eSPAN) and Okazaki fragment sequencing (OK-seq), have become essential tools for studying chromatin replication in eukaryotic cells. In this review, we outline the foundational principles underlying these methodologies and summarize key mechanistic insights into DNA replication, parental histone transfer, epigenetic inheritance, and beyond, gained through their applications. Finally, we discuss the limitations and challenges of current techniques, highlighting the need for further technological innovations to better understand the dynamics and regulation of chromatin replication in eukaryotic cells. Strand-specific sequencing methods are essential tools to dissect the molecular mechanisms of chromatin replication in eukaryotic cells. Li and Zhang review the recent technological advancements and mechanistic insights gained through their applications in epigenetic inheritance and beyond. [ABSTRACT FROM AUTHOR]

Autophagy is a conserved physiological phenomenon commonly found in all eukaryotic cells, which promotes cell survival by degrading intracellular proteins and organelles during starvation or nutrient deficiency. Dysfunction autophagy is closely related to various diseases. Soluble N-elthylmaleimide-sensitive factor attachment protein receptor (SNARE) complex is a protein complex that mediates membrane fusion and plays a key role in the fusion process of autophagosomes and lysosomes. The aberrant assembly of the SNARE complex results in the arrest of autophagic flow, thereby leading to cellular dysfunction and the occurrence of diseases. In this review, we summarized the roles of SNARE proteins in the autophagosome-lysosome fusion and the latest research in related diseases, providing a reference for studying the mechanism of autophagy and diseases targeting the SNARE complex. [ABSTRACT FROM AUTHOR]

Dynamic disassembly and reconstruction of the nuclear lamina during entry and exit of mitosis, respectively, are pivotal steps in the proliferation of higher eukaryotic cells. Although numerous post-translational modifications of lamin proteins have been identified, key factors driving the nuclear lamina dynamics remain elusive. Here we identified CDK1-elicited phosphorylation sites on endogenous Lamin A/C and characterized their functions in regulation of the nuclear lamina. Specifically, mass spectrometry revealed CDK1-mediated phosphorylation of Lamin A/C at the N-terminal Thr19/Ser22 and the C-terminal Ser390/Ser392 during mitosis. Importantly, the phospho-mimicking 4D mutant T19D/S22D/S390D/S392D completely disrupted Lamin A filamentous structure in interphase cells. Conversely, the nonphosphorylatable mutant T19A/S22A and especially the 4A mutant T19A/S22A/S390A/S392A protected Lamin A from depolymerization during mitosis. These results suggest that phosphorylation and dephosphorylation of both N-and Cterminal sites regulate the nuclear lamina dynamics. Engineering the non-phosphorylatable mutant T19A/S22A into the endogenous LMNA gene resulted in nuclear abnormalities and micronucleus formation during telophase. Perturbation of the Lamin A phosphorylation is shown to prevent proper nuclear envelope dynamics and impair nuclear integrity. These findings reveal a previously undefined link between the CDK1-elicited Lamin A phosphorylation dynamics, nuclear envelope plasticity, and genomic stability during the cell cycle. [ABSTRACT FROM AUTHOR]

The human body is an intricate ensemble of prokaryotic and eukaryotic cells, and this coexistence relies on the interplay of many biotic and abiotic factors. The inhabiting microbial population has to maintain its physiological homeostasis under highly dynamic and often hostile host environments. While bacterial colonization primarily relies on the metabolic suitability for the niche, there are reports of active remodeling of niche microenvironments to create favorable habitats, especially in the context of pathogenic settlement. Such physiological plasticity requires a robust metabolic system, often dependent on an adaptable energy metabolism. This review focuses on the respiratory electron transport system and its adaptive consequences within the host environment. We provide an overview of respiratory chain plasticity, which allows pathogenic bacteria to niche-specify, niche-diversify, mitigate inflammatory stress, and outcompete the resident microbiota. We have reviewed existing and emerging knowledge about the role of respiratory chain components responsible for the entry and exit of electrons in influencing the pathogenic outcomes. [ABSTRACT FROM AUTHOR]

The exocyst complex in eukaryotic cells modulates secretory vesicle transportation to promote exocytosis. The exocyst is also required for the hyphal growth and pathogenic development of several filamentous phytopathogens. Obligate biotrophic powdery mildew fungi cause considerable damage to many cash crops; however, the exocyst's roles in this group of fungi is not well studied. To verify the functions of the exocyst in powdery mildew fungus, we identified two exocyst subunits, EqSec5 and EqSec6, from Erysiphe quercicola, a powdery mildew fungus that infects the rubber tree Hevea brasiliensis. When GFP-fused EqSec5 and EqSec6 were introduced into E. quercicola and another phytopathogenic fungus, Magnaporthe oryzae, they primarily localized to the hyphal tip region. Inducing gene silencing of EqSec5 or EqSec6 caused growth and infection defects, and those defects could not be fully restored under the NADPH oxidase inhibitor treatment to the plant. The silenced strains also induced the host defense response including reactive oxygen species accumulation and callose deposition. The silencing of EqSec5 or EqSec6 also inhibited the secretion of the effector protein EqIsc1, interrupting plant salicylic acid biosynthesis. Yeast two-hybrid and gene overexpression assays suggested that EqSec5 and EqSec6 interact with each other and can complement each other's function during host infection. Overall, our study provides evidence that the exocyst in this powdery mildew fungus facilitates effector secretion, hyphal growth, and infection. [ABSTRACT FROM AUTHOR]

The DNA replication machinery is highly conserved from bacteria to eukaryotic cells. Faithful DNA replication is vital for cells to transmit accurate genetic information to the next generation. However, both internal and external DNA damages threaten the intricate DNA replication process, leading to the activation of the DNA damage response (DDR) system. Dysfunctional DNA replication and DDR are a source of genomic instability, causing heritable mutations that drive cancer evolutions. The family of minichromosome maintenance (MCM) proteins plays an important role not only in DNA replication but also in DDR. Here, we will review the current strides of MCM proteins in these integrated processes as well as the acetylation/deacetylation of MCM proteins and the value of MCMs as biomarkers in cancer. [ABSTRACT FROM AUTHOR]

Simple Summary: Autophagy is a "self-eating" process that is important for cells to dispose of and/or recycle any component. Beclin 1 is the crucial member of the autophagic process in cells. It acts as the key regulator as it interacts with different binding partners to modify the activity of autophagy. This article explores how FE65, a protein mainly found in the brain, enhances autophagy by interacting with Beclin 1. Autophagy is a vital cellular pathway in eukaryotic cells, including neurons, where it plays significant roles in neurodevelopment and maintenance. A crucial step in autophagy is the formation of the class III phosphatidylinositol 3-kinase complex 1 (PI3KC3-C1), which is essential for initiating autophagosome biogenesis. Beclin 1 is the key component of PI3KC3-C1, and its interactors have been reported to affect autophagy. The brain-enriched adaptor protein FE65 has been shown to interact with Alzheimer's disease amyloid precursor protein (APP) to alter the processing of APP. Additionally, FE65 has been implicated in various cellular pathways, including autophagy. We demonstrate here that FE65 positively regulates autophagy. FE65, through its C-terminus, has been shown to interact with Beclin 1. Notably, the overexpression of FE65 enhances Beclin 1-mediated autophagy, whereas this process is attenuated in FE65 knockout cells. Moreover, the stimulatory effect of FE65 on Beclin 1-mediated autophagy is diminished by an FE65 C-terminus deletion mutant that disrupts the FE65–Beclin 1 interaction. Lastly, we have found that the FE65-Beclin 1 interaction modulates the kinase activity of the PI3KC3-C1 complex. Together, we have identified FE65 as a novel Beclin 1 interactor, and this interaction potentiates autophagy. [ABSTRACT FROM AUTHOR]

Bacteriophages, as ubiquitous bacterial viruses in various natural ecosystems, play an important role in maintaining the homeostasis of the natural microbiota. For many years, bacteriophages were not believed to act on eukaryotic cells; however, recent studies have confirmed their ability to affect eukaryotic cells and interact with the host immune system. Due to their complex protein structure, phages can also directly or indirectly modulate immune processes, including innate immunity, by modulating phagocytosis and cytokine reactions, as well as acquired immunity, by producing antibodies and activating effector cells. They can therefore have a profound impact on the course of bacterial infections by stimulating and at the same time inhibiting the systemic pro-inflammatory response. This review article presents a characterization of the processes by which bacteriophages affect selected immune mechanisms in selected animal species. The results of our own experiments using calves are also presented as examples. The paper contains many new examples of potential uses of bacteriophages and their effects on eukaryotic cells, especially in the course of bacterial infections, which are extremely important in experimental treatments exploiting phages as alternatives to antibiotics. The positive results of the effects of bacteriophages on eukaryotic cells during infections open up promising new prospects for their use as natural tools in the treatment of bacterial, fungal, and viral diseases in animals and humans. [ABSTRACT FROM AUTHOR]

Autophagy is a conservative lysosome-dependent material catabolic pathway, and exists in all eukaryotic cells. Autophagy controls cell quality and survival by eliminating intracellular dysfunction substances, and plays an important role in various pathophysiology processes. Erectile dysfunction (ED) is a common male disease. It is resulted from a variety of causes and pathologies, such as diabetes, hypertension, hyperlipidemia, aging, spinal cord injury, or cavernous nerve injury caused by radical prostatectomy, and others. In the past decade, autophagy has begun to be investigated in ED. Subsequently, an increasing number of studies have revealed the regulation of autophagy contributes to the recovery of ED, and which is mainly involved in improving endothelial function, smooth muscle cell apoptosis, penile fibrosis, and corpus cavernosum nerve injury. Therefore, in this review, we aim to summarize the possible role of autophagy in ED from a cellular perspective, and we look forward to providing a new idea for the pathogenesis investigation and clinical treatment of ED in the future. [ABSTRACT FROM AUTHOR]

Recombinant protein production in prokaryotic and eukaryotic cells is a fundamental technology for both research and industry. Achieving efficient protein synthesis is key to accelerating the discovery, characterization, and practical application of proteins. This review focuses on recent advances in recombinant protein production and strategies for more efficient protein production, especially using Escherichia coli and Saccharomyces cerevisiae. Additionally, this review summarizes the development of various functional peptide tags that can be employed for protein production, modification, and purification, including translation-enhancing peptide tags developed by our research group. [ABSTRACT FROM AUTHOR]

• We revealed a common flow using single cell database to disclose biomarker for cancer. • Proteasome markers are indispensable for cancer progression. • PSMD11 is identified to play significant roles in the development of breast cancer. Single cell sequencing and related databases have been widely used in the exploration of cancer occurrence and development, but there is still no in-depth explanation of specific and complicated cellular protein modification processes. Ubiquitin-Proteasome System (UPS), as a specific and precise protein modification and degradation process, plays an important role in the biological functions of cancer cell proliferation and apoptosis. Proteasomes, vital multi-catalytic proteinases in eukaryotic cells, play a crucial role in protein degradation and contribute to tumor regulation. The 26S proteasome, part of the ubiquitin–proteasome system. In this study, we have enrolled a common SITP process including analysis of single cell sequencing to elucidate a flow that can capture typical proteasome markers in the oncogenesis and progression of breast cancer. PSMD11, a key component of the 26S proteasome regulatory particle, has been identified as a critical survival factor in cancer cells. Results suggest that PSMD11's rapid degradation is linked to acute apoptosis in cancer cells, making it a potential target for cancer treatment. Our study explored the potential mechanisms of PSMD11 in breast cancer development. The findings revealed the feasibility of disclosing ubiquitinating biomarkers from public database, as well as presented new evidence supporting PSMD11 as a potential therapeutic biomarker for breast cancer. [ABSTRACT FROM AUTHOR]

Bisphenol A, an endocrine-disrupting compound, is widely used in the industrial production of plastic products. Despite increasing concerns about its harmful effects on human health, animals, and the environment, the use of BPA has been banned only in infant products, and its effects on cellular processes are not fully understood. To investigate the impact of BPA on eukaryotic cells, we analyzed the proteome changes of wild-type and PDR5-deleted S. cerevisiae strains exposed to different doses of BPA using sample multiplexing-based proteomics. We found that the ABC multidrug transporter Pdr5 plays an important role in protecting yeast cells from BPA toxicity, with its absence significantly sensitizing cells to BPA. BPA inhibited yeast growth in a dose-dependent manner, with a more pronounced effect in PDR5-deleted cells. Proteomic analysis revealed that BPA induces widespread dose-dependent changes in protein abundance, including the upregulation of metabolic pathways such as arginine biosynthesis and the downregulation of mitochondrial proteins. Additionally, we observed markers of cellular stress induced by BPA by identifying multiple stress-induced proteins that were upregulated by this compound. As cellular processes affected by BPA have been shown to be evolutionarily conserved, these insights can advance our understanding of BPA's cellular impact and its broader effects on human health. [ABSTRACT FROM AUTHOR]

Spontaneous tumor regression is a recognized phenomenon across various cancer types. Recent research emphasizes the alterations in autoantibodies against carbonic anhydrase I (CA I) (anti‐CA I) levels as potential prognostic markers for various malignancies. Particularly, autoantibodies targeting CA I and II appear to induce cellular damage by inhibiting their respective protein's catalytic functions. Our study illuminates the profound impact of anti‐CA I autoantibodies from patient serum on the esterase activity of human CA I, exhibiting inhibitory effects akin to the acetazolamide inhibitor. Concurrently, our newly synthesized mouse monoclonal IgG antibody, mAb 2B8, against human CA I showcased a potent inhibitory action. An in‐depth exploration into mAb 2B8′s binding dynamics with its target enzyme was undertaken. Leveraging epitope extraction and phage display library techniques, we identified the amino acid sequence DFWTYP (positions 191–196 of CA I) as crucial for mAb 2B8′s interaction. In 3‐D structural analysis, this sequence is spatially adjacent to a previously identified epitope (DFWTYP) that interacts with patient‐derived autoantibodies. Critically, mAb 2B8 demonstrated an ability to infiltrate eukaryotic cells, engaging specifically with its intracytoplasmic target. This positions mAb 2B8 as a promising model for future studies aimed at tumor cell eradication. [ABSTRACT FROM AUTHOR]

Abstract\nHIGHLIGHTSWith numerous advantages over conventional techniques, ultrasound-assisted extraction (UAE) has become a viable method for the effective extraction of biomolecules from prokaryotic and eukaryotic cells. The fundamentals and workings of UAE are examined in this review, focusing on current developments, including how these impact the extraction of proteins, lipids, enzymes, and other bioactive compounds. UAE not only enhances cell disruption and mass transfer, leading to improved extraction yields, but also preserves the integrity of the extracted bioactive molecules under optimized conditions, making it a preferred choice in Biochemistry and Biotechnology. Additionally, this review explores recent innovative approaches that combine ultrasound with other techniques like enzymatic digestion, supercritical CO2, deep eutectic solvents, and Three-Phase Partitioning (UA-TPP) etc, to further enhance extraction efficiency. The differences in extraction effectiveness between prokaryotic and eukaryotic cells are attributed to cellular structure and ultrasonic conditions. Overall, this review highlights UAE’s promise as a viable and efficient substitute for biomolecule extraction concerning prokaryotic and eukaryotic cells while bringing up areas that need additional research and development.Illustrates recent advances in Ultrasound-assisted extraction (UAE) methods of biomolecules from prokaryotic and eukaryotic cellsExamined the fundamental processes by which ultrasound affects prokaryotic and eukaryotic cells.The paper underlines the sustainability aspect of ultrasound-assisted techniques.Highlights UAE relevance across multiple disciplines, connecting industrial processing, chemistry, and biotechnology.Illustrates recent advances in Ultrasound-assisted extraction (UAE) methods of biomolecules from prokaryotic and eukaryotic cellsExamined the fundamental processes by which ultrasound affects prokaryotic and eukaryotic cells.The paper underlines the sustainability aspect of ultrasound-assisted techniques.Highlights UAE relevance across multiple disciplines, connecting industrial processing, chemistry, and biotechnology. [ABSTRACT FROM AUTHOR]

Images taken by transmission electron microscopes are usually affected by lens aberrations and image defocus, among other factors. These distortions can be modeled in reciprocal space using the contrast transfer function (CTF). Accurate estimation and correction of the CTF is essential for restoring the high-resolution signal in cryogenic electron microscopy (cryoEM). Previously, we described the implementation of algorithms for this task in the cisTEM software package (Grant et al., 2018). Here we show that taking sample characteristics, such as thickness and tilt, into account can improve CTF estimation. This is particularly important when imaging cellular samples, where measurement of sample thickness and geometry derived from accurate modeling of the Thon ring pattern helps judging the quality of the sample. This improved CTF estimation has been implemented in CTFFIND5, a new version of the cisTEM program CTFFIND. We evaluated the accuracy of these estimates using images of tilted aquaporin crystals and eukaryotic cells thinned by focused ion beam milling. We estimate that with micrographs of sufficient quality CTFFIND5 can measure sample tilt with an accuracy of 3° and sample thickness with an accuracy of 5 nm. [ABSTRACT FROM AUTHOR]

Ionic liquids (ILs) are structurally tunable salts with applications ranging from chemical synthesis to batteries, novel materials and medicine. Despite their potential, the toxicity of ILs poses significant environmental and biological challenges. This study introduces a comprehensive dataset of cytotoxicity of 1227 ILs, compiled from 151 research papers and encompassing 3837 data entries. For each entry, the following information is provided: substance name, empirical formula, CAS, SMILES, molecular weight, cytotoxicity value, details on the experimental setup (incubation time, cell line, assay used, etc.), and reference to the original publication. This dataset can be used for deriving structure‒activity relationships and establishing the major structural elements that govern the cytotoxic effects of ILs on eukaryotic cells. The dataset is available freely to all researchers. [ABSTRACT FROM AUTHOR]

Autophagy is a fundamental process in eukaryotic cells, essential for maintaining cellular homeostasis and promoting survival. This process involves the formation of a structure known as the autophagosome, which sequesters damaged cellular components such as misfolded proteins and dysfunctional organelles. These components are subsequently transported to lysosomes for degradation. Autophagy allows cells to withstand various stress conditions, including nutrient deprivation, hypoxia, and microbial infections. There are three primary types of autophagy: macroautophagy, microautophagy, and chaperone-mediated autophagy, each characterized by distinct mechanisms and features. The autophagy process is tightly regulated by autophagy-related genes (ATG) and consists of several stages: induction, autophagosome formation, fusion with lysosomes, and cargo degradation. Dysfunctional autophagy has been implicated in the development of various diseases, including cancer, neurodegenerative disorders, metabolic diseases, and bacterial or viral infections. Recent studies have highlighted the dual role of autophagy in cancer: while it can act as a tumor suppressor in early stages, it may also support tumor cell survival in advanced stages. In the nervous system, autophagy helps prevent the accumulation of harmful proteins and supports neuronal function. Additionally, autophagy plays a significant role in combating invasive pathogens, serving as a defensive mechanism against bacteria and viruses. Research indicates that autophagy is a promising target for developing new therapeutic strategies for a wide range of diseases. In-depth investigations into the molecular pathways regulating autophagy, particularly the mTOR and AMPK pathways, offer potential avenues for innovative treatments. This review provides a comprehensive analysis of the mechanisms and functions of autophagy, exploring its association with various human diseases. It presents a novel perspective on the potential clinical applications of autophagy, highlighting its role in the development of therapeutic strategies and deepening our understanding of this essential cellular process. [ABSTRACT FROM AUTHOR]

Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multisubunit enzymes consist of a soluble catalytic V1 subcomplex and a membrane-embedded proton-translocating VO subcomplex. The V1 and VO subcomplexes can undergo reversible dissociation to regulate proton pumping, with reassociation of V1 and VO requiring the protein complex known as RAVE (regulator of the ATPase of vacuoles and endosomes). In the yeast Saccharomyces cerevisiae, RAVE consists of subunits Rav1p, Rav2p, and Skp1p. We used electron cryomicroscopy (cryo-EM) to determine a structure of yeast RAVE bound to V1. In the structure, RAVE is an L-shaped complex with Rav2p pointing toward the membrane and Skp1p distant from both the membrane and V1. Only Rav1p interacts with V1, binding to a region of subunit A not found in the corresponding ATP synthase subunit. When bound to RAVE, V1 is in a rotational state suitable for binding the free VO complex, but in the structure, it is partially disrupted, missing five of its 16 subunits. Other than these missing subunits and the conformation of the inhibitory subunit H, the V1 complex with RAVE appears poised for reassembly with VO. [ABSTRACT FROM AUTHOR]

Autophagy is a ubiquitous process of organelle interaction in eukaryotic cells, in which various organelles or proteins are recycled and operated through the autophagy pathway to ensure nutrient and energy homeostasis. Although numerous fluorescent probes have been developed to image autophagy, these environment‐responsive probes suffer from inherent deficiencies such as inaccuracy and limited versatility. Here, we present a modular macrocyclic amphiphile Förster Resonance Energy Transfer (FRET) platform (SC6A12C/NCM, SN), constructed through the amphiphilic assembly of sulfonatocalix[6]arene (SC6A12C) with N‐cetylmorpholine (NCM) for lysosome targeting. The hydrophobic fluorophore BPEA (FRET donor) was entrapped within the inner hydrophobic phase and showed strong fluorescence emission. Attributed to the broad‐spectrum encapsulation of SC6A12C, three commercially available organelle probes (Mito‐Tracker Red, ER Tracker Red, and RhoNox‐1) were selected as SC6A12C guests (FRET acceptors). During autophagy process, the formation of intracellular host–guest complexes leads to strong FRET signal, allowing us to visualize the fusion of mitochondria, endoplasmic reticulum, and Golgi apparatus with lysosomes, respectively. This study provides a versatile and accessible platform for imaging organelle autophagy. [ABSTRACT FROM AUTHOR]

Single cell–inductively coupled plasma–mass spectrometry (SC-ICP-MS) offers an attractive option for rapidly measuring trace metal heterogeneity at the single cell level. Chemical fixation has been previously applied to mammalian cells prior to sample introduction so that they can be resuspended in a solution suitable for SC-ICP-MS. However, the effect of fixation on the elemental composition of suspended cells is unknown, and robust methodologies are urgently needed so that the community can measure the effects of intracellular pathogens on elemental composition of their host cells. We demonstrate that different fixatives impact measured cell elemental composition. We have compared suspensions treated using different fixatives (methanol 60–100% in H2O and 4% paraformaldehyde in phosphate-buffered saline solution), and the number of distinguishable single cell events, keeping a constant particle number concentration. Significantly more single cell events (n = 3, P ≤ 0.05) were observed for Ca and Mg when cells were fixed in 4% paraformaldehyde than for the methanol-based fixatives, confirming the hypothesis that methanol fixatives cause leaching of these elements from the cells. The impact of fixation on Mn and Zn was less pronounced. Microbial and viral infection of eukaryotic cells can have profound effects on their elemental composition, but chemical fixation is necessary to render infected cells safe before analysis. We have successfully applied our methodology to a macrophage model of tuberculosis demonstrating utility in understanding metal homeostasis during microbial infection of mammalian cells. [ABSTRACT FROM AUTHOR]

Gpn2 is a highly conserved protein essential for the assembly of RNA polymerase II (RNAPII) in eukaryotic cells. Mutations in Gpn2, specifically Phe105Tyr and Leu164Pro, confer temperature sensitivity and significantly impair RNAPII assembly. Despite its crucial role, the complete range of Gpn2 functions remains to be elucidated. To further explore these functions, we conducted large-scale multicopy suppressor screening in budding yeast, aiming to identify genes whose overexpression could mitigate the growth defects of a temperature-sensitive gpn2 mutant (gpn2ts) at restrictive temperatures. We screened over 30,000 colonies harboring plasmids from a multicopy genetic library and identified 31 genes that rescued the growth defects of gpn2ts to various extents. Notably, we found that PAB1, CDC5, and RGS2 reduced the drug sensitivity of gpn2ts mutants. These findings lay a theoretical foundation for future studies on the function of Gpn2 in RNAPII assembly. [ABSTRACT FROM AUTHOR]

Lipids, which are highly diverse, are finely distributed between organelle membranes and the plasma membrane (PM) of eukaryotic cells. As a result, each compartment has its own lipid composition and molecular identity, which is essential for the functional fate of many proteins. This distribution of lipids depends on two main processes: lipid synthesis, which takes place in different subcellular regions, and the transfer of these lipids between and across membranes. This review will discuss the proteins that carry lipids throughout the cytosol, called LTPs (Lipid Transfer Proteins). More than the modes of action or biological roles of these proteins, we will focus on the in vitro strategies employed during the last 60 years to address a critical question: What are the lipid ligands of these LTPs? We will describe the extent to which these strategies, combined with structural data and investigations in cells, have made it possible to discover proteins, namely ORPs, Sec14, PITPs, STARDs, Ups/PRELIs, START-like, SMP-domain containing proteins, and bridge-like LTPs, which compose some of the main eukaryotic LTP families, and their lipid ligands. We will see how these approaches have played a central role in cell biology, showing that LTPs can connect distant metabolic branches, modulate the composition of cell membranes, and even create new subcellular compartments. • Overview of the principal families of eukaryotic lipid transfer proteins (LTPs). • Story on the discovery of LTPs in the last six decades. • Listing of the in vitro approaches to define how LTPs select and transfer lipids. • Crosstalk between in vitro and in-cell investigations to define LTPs' functions. [ABSTRACT FROM AUTHOR]

Bacteria use the type VI secretion system (T6SS) to secrete toxins into pro- and eukaryotic cells via machinery consisting of a contractile sheath and a rigid tube. Rearrangement hotspot (Rhs) proteins represent one of the most common T6SS effectors. The Rhs C-terminal toxin domain displays great functional diversity, while the Rhs core is characterized by YD repeats. We elucidate the Rhs core structures of PAAR- and VgrG-linked Rhs proteins from Salmonella bongori and Advenella mimigardefordensis , respectively. The Rhs core forms a large shell of β-sheets with a negatively charged interior and encloses a large volume. The S. bongori Rhs toxin does not lead to ordered density in the Rhs shell, suggesting the toxin is unfolded. Together with bioinformatics analysis showing that Rhs toxins predominantly act intracellularly, this suggests that the Rhs core functions two-fold, as a safety feature for the producer cell and as delivery mechanism for the toxin. [Display omitted] • PAAR- and VgrG-linked Rhs form large, negatively charged shells • Rhs toxins function predominantly intracellularly, in contrast to non-Rhs toxins • TMDs, prePAAR motifs, and VIRs are not consistently present in Rhs effectors Kielkopf et al. elucidate the structures of two bacterial T6SS-associated Rhs proteins. Rhs cores form large, negatively charged shells that encapsulate unfolded or molten globule toxin domains. Their bioinformatic analyses show that Rhs toxins predominantly act intracellularly and that TMDs, prePAAR motifs, and VIRs are not consistently present in Rhs effectors. [ABSTRACT FROM AUTHOR]

Thymus vulgaris is considered one of the herbal plants rich in active compounds that have attracted the attention of many scientists and researchers. However, the genetic safety of these compounds must be investigated, as food safety is one of the topics that has recently topped the field of scientific research. The study objectives included obtaining Thyme Essential Oil (TEO) by hydrodistillation extraction, and then analysing by Gas Chromatography technic (GC), all tests were done on the A1 (Wa1) strain of Aspergillus amstelodami. Thyme was collected from local nurseries. The mutagenic effect of four sub-lethal concentrations (0.01 -0.016 - 0.02 - 0.05) ml/ml of thyme oil was evaluated by using mutagenesis methods. The results showed that the highest phenolic compounds in (TEO) were Thymol and Carvacrol, with a percentage of 58.89% and 4.11%, respectively. The study also included investigating the ability of thyme oil to cause genetic effects on eukaryotic cells by testing the ability of this oil to induce genetic mutations in the conidia of fungus A. amstelodami by using the mutagenesis methods of pretreatment, plate incorporation and growth-mediated, as the study did not record the presence of any mutagenic effect for the four sub-toxic concentrations (Sub lethal) (0.01 -0.016 - 0.02 - 0.05) ml/ml of thyme oil, this confirms its safety genetically and can be used as a herbal food and medicinal plant. [ABSTRACT FROM AUTHOR]

Cell division presents a challenge for eukaryotic cells: how can chromosomes effectively segregate within the confines of a membranous nuclear compartment? Different organisms have evolved diverse solutions by modulating the degree of nuclear compartmentalization, ranging from complete nuclear envelope breakdown to complete maintenance of nuclear compartmentalization via nuclear envelope expansion. Many intermediate forms exist between these extremes, suggesting that nuclear dynamics during cell division are surprisingly plastic. In this review, we highlight the evolutionary diversity of nuclear divisions, focusing on two defining characteristics: (1) chromosome compartmentalization and (2) nucleocytoplasmic transport. Further, we highlight recent evidence that nuclear behavior during division can vary within different cellular contexts in the same organism. The variation observed within and between organisms underscores the dynamic evolution of nuclear divisions tailored to specific contexts and cellular requirements. In-depth investigation of diverse nuclear divisions will enhance our understanding of the nucleus, both in physiological and pathological states. [ABSTRACT FROM AUTHOR]

In eukaryotic cells, the nuclear envelope (NE) is a membrane partition between the nucleus and the cytoplasm to compartmentalize nuclear contents. It plays an important role in facilitating nuclear functions including transcription, DNA replication and repair. In mammalian cells, the NE breaks down and then reforms during cell division, and in interphase it is restored shortly after the NE rupture induced by mechanical force. In this way, the partitioning effect is regulated through dynamic processes throughout the cell cycle. A failure in rebuilding the NE structure triggers the mixing of nuclear and cytoplasmic contents, leading to catastrophic consequences for the nuclear functions. Whereas the precise details of molecular mechanisms for NE reformation during cell division and NE restoration in interphase are still being investigated, here, we mostly focus on mammalian cells to describe key aspects that have been identified and to discuss the crosstalk between them. [ABSTRACT FROM AUTHOR]

Mitochondria, known as the "energy factory" of cells, are essential organelles with a double membrane structure and genetic material found in most eukaryotic cells. They play a crucial role in tumorigenesis and development, with alterations in mitochondrial structure and function in tumor cells leading to characteristics such as rapid proliferation, invasion, and drug resistance. Glioma, the most common brain tumor with a high recurrence rate and limited treatment options, has been linked to changes in mitochondrial structure and function. This review focuses on the bioenergetics, dynamics, metastasis, and autophagy of mitochondria in relation to glioma proliferation, as well as the potential use of mitochondria‐targeting drugs in glioma treatment. [ABSTRACT FROM AUTHOR]

Antibiotic susceptibility testing (AST) by agar diffusion has been repeatedly standardized and, in most cases, gives results which predict clinical success when antibiotic treatment is based on such results. The formation of the inhibition zone is due to a transition from planktonic to biofilm mode of growth. The kinetics of the interaction of antibiotics with bacteria is similar during AST by agar diffusion and during administration of antibiotics to the patients. However, the Mueller‐Hinton agar (MHA) recommended for AST agar diffusion test is fundamentally different from the composition of the interstitial fluid in the human body where the infections take place and human cells do not thrive in MH media. Use of RPMI 1640 medium designed for growth of eucaryotic cells for AST of Pseudomonas aeruginosa against azithromycin results in lower minimal inhibitory concentration, compared to results obtained by MHA. The reason is that the RPMI 1640 medium increases uptake and reduces efflux of azithromycin compared to MHA. During treatment of cystic fibrosis patients with azithromycin, mutational resistance occur which is not detected by AST with MHA. Whether this is the case with other antibiotics and bacteria is not known but it is of clinical importance to be studied. [ABSTRACT FROM AUTHOR]

Lipid droplets (LDs) are the major sites of lipid and energy homeostasis. However, few LD biogenesis proteins have been identified. Using model microalga Chlamydomonas , we show that ABHD1, an α/β-hydrolase domain-containing protein, is localized to the LD surface and stimulates LD formation through two actions: one enzymatic and one structural. The knockout mutants contained similar amounts of triacylglycerols (TAG) but their LDs showed a higher content of lyso-derivatives of betaine lipid diacylglyceryl- N,N,N -trimethylhomoserine (DGTS). Over-expression of ABHD1 increased LD abundance and boosted TAG content. Purified recombinant ABHD1 hydrolyzed lyso-DGTS, producing a free fatty acid and a glyceryltrimethylhomoserine. In vitro droplet-embedded vesicles showed that ABHD1 promoted LD emergence. Taken together, these results identify ABHD1 as a new player in LD formation by its lipase activity on lyso-DGTS and by its distinct biophysical property. This study further suggests that lipases targeted to LDs and able to act on their polar lipid coat may be interesting tools to promote LD assembly in eukaryotic cells. [ABSTRACT FROM AUTHOR]

Simple Summary: Many cellular processes in eukaryotic cells are regulated by vacuolar (H+)-ATPases (V-ATPases), energy-driven proton pumps that primarily function to acidify intracellular organelles across all eukaryotes. These enzymes are densely packed on both the plasma membrane and the endomembrane in specific cell types of insects and vertebrates. Significant prior studies have demonstrated the presence of V-ATPases in insect olfactory sensilla, highlighting their role in olfaction. In our research, we used bioinformatics and immunohistochemistry to investigate the expression and localization of V-ATPase in the Drosophila melanogaster antenna. Our findings show that genes encoding V-ATPase are highly expressed in the Drosophila antenna, as demonstrated by bulk and single-cell antennal transcriptome analyses. The results from immunohistochemistry further confirm that V-ATPase is restricted to non-neuronal support cells within the antenna. We therefore propose that V-ATPase activity in support cells plays a specific and important role in odor processing. V-ATPases are ubiquitous and evolutionarily conserved rotatory proton pumps, which are crucial for maintaining various biological functions. Previous investigations have shown that a V-ATPase is present in the support cells of moth trichoid sensilla and influences their olfactory sensory neuron performance. Generally, V-ATPases are thought to regulate the pH value within the sensillum lymph, and aid K+ homeostasis within the sensillum. This, in turn, could influence various mechanisms involved within the support cells, like maintaining the receptor membrane potential (receptor current), nutrient and ion transport, odorant solubility, and various signaling mechanisms. In this study, we identify V-ATPase expression and localization in the Drosophila melanogaster antenna using bioinformatics and immunohistochemistry. Elucidating an olfactory V-ATPase function will improve our current understanding of how support cells contribute to Drosophila's sense of smell. [ABSTRACT FROM AUTHOR]

Bacteria were once thought to be simple organisms, lacking the membrane‐bound organelles found in eukaryotic cells. However, recent advancements in microscopy have changed this view, revealing a diverse array of organelles within bacterial cells. These organelles, surrounded by lipid bilayers, protein‐lipid monolayers, or proteinaceous shells, play crucial roles in facilitating biochemical reactions and protecting cells from harmful byproducts. Unlike eukaryotic organelles, which are universally present, bacterial organelles are species‐specific and induced only under certain conditions. This review focuses on the bacterial organelles that contain iron, an essential micronutrient for all life forms but potentially toxic when present in excess. To date, three types of iron‐related bacterial organelles have been identified: two membrane‐bound organelles, magnetosomes and ferrosomes, and one protein‐enclosed organelle, the encapsulated ferritin‐like proteins. This article provides an updated overview of the genetics, biogenesis, and physiological functions of these organelles. Furthermore, we discuss how bacteria utilize these specialized structures to adapt, grow, and survive under various environmental conditions. [ABSTRACT FROM AUTHOR]

The innate immune system, present in various species, functions as the primary barrier against pathogens, preventing infection and maintaining homeostasis. It consists of mechanical, chemical, and cellular elements across eukaryotic organisms, including physical barriers, physiological processes, pattern recognition molecules, proteins, and cytokines. Despite significant taxonomic differences, both bacteria and complex multicellular organisms exhibit strikingly analogous immune system attributes. Specifically, conserved features in their anti-phage defense mechanisms include the regulation of cellular responses to cytosolic double-stranded DNA and the presence of functional nucleases for viral nucleic acid degradation. Both bacteria and eukaryotes also employ pattern recognition receptors (PRRs) with central nucleoside triphosphatases domains for phage identification and targeting, alongside shared strategies such as gasdermins and pore-forming proteins that confer protection against phages and induce cellular apoptosis. These evolutionary parallels suggest that innate immunity has deep, ancient roots and may reflect the progression of complex life forms from simpler ancestors. Understanding these similarities could inspire new therapeutic strategies and provide deeper insight into the diverse evolutionary pathways of immunity across species. The current article examines these evolutionary connections by comparing innate immune systems in bacteria and eukaryotes, focusing on shared components and molecular insights. Future research should aim to identify and bridge knowledge gaps, further elucidating the evolutionary origins and functional diversity of innate immunity across species. [Display omitted] • The innate immune system preventing infection and maintaining homeostasis. • Bacteria & complex multicellular organisms exhibit strikingly analogous immune system attributes. • We examine the evolutionary connections between innate immunity in bacteria and eukaryotes. [ABSTRACT FROM AUTHOR]

The evolution of complex life forms, exemplified by multicellular organisms, can be traced through a series of evolutionary transitions in individuality, beginning with the origin of life, followed by the emergence of the eukaryotic cell, and, among other transitions, culminating in the shift from unicellularity to multicellularity. Several attempts have been made to explain the origins of such transitions, many of which have been internalist (i.e., based largely on internal properties of ancestral entities). Here, we show how externalist perspectives can shed new light on questions pertaining to evolutionary transitions in individuality. We do this by presenting the ecological scaffolding framework in which properties of complex life forms arise from an external scaffold. Ultimately, we anticipate that progress will come from recognition of the importance of both the internalist and externalist modes of explanation. We illustrate this by considering an extension of the ecological scaffolding model in which cells modify the environment that later becomes the scaffold giving rise to multicellular individuality. [ABSTRACT FROM AUTHOR]

Various DNA damage checkpoint control mechanisms in eukaryotic cells help maintain genomic integrity. Among these, NBS1, a key component of the MRE11-RAD50-NBS1 (MRN) complex, is an essential protein involved in the DNA damage response (DDR). In this study, we discovered that DNA damage-binding protein 1 (DDB1) interacts with NBS1. DDB1 is a DDR sensor protein found in UV-induced DNA replication blocks. Through pull-down and immunoprecipitation assays conducted in Xenopus egg extracts and human cell lines, we demonstrated a specific interaction between NBS1 and DDB1. DDB1 was also found to associate with several proteins that interact with NBS1, including DNA topoisomerase 2-binding protein 1 (TopBP1) and Mediator of DNA damage checkpoint protein 1 (MDC1). Notably, the interaction between DDB1 and NBS1 is disrupted in MDC1-depleted egg extracts, indicating that MDC1 is necessary for this interaction. Furthermore, the depletion of DDB1 leads to increased Chk1 activation upon DNA damage. These novel findings regarding the interaction between NBS1 and DDB1 provide new insights into how DDB1 regulates DNA damage pathways. [ABSTRACT FROM AUTHOR]

Cell division cycle 6 (CDC6) is essential for the initiation of DNA replication in eukaryotic cells and contributes to the development of various human tumors. Polycystic ovarian syndrome (PCOS) is a reproductive endocrine disease in women of childbearing age, with a significant risk of endometrial cancer (EC). However, the role of CDC6 in the progression of PCOS to EC is unclear. Therefore, we examined CDC6 expression in patients with PCOS and EC. We evaluated the relationship between CDC6 expression and its prognostic value, potential biological functions, and immune infiltrates in patients with EC. In vitro analyses were performed to investigate the effects of CDC6 knockdown on EC proliferation, migration, invasion, and apoptosis. CDC6 expression was significantly upregulated in patients with PCOS and EC. Moreover, this protein caused EC by promoting the aberrant infiltration of macrophages into the immune microenvironment in patients with PCOS. A functional enrichment analysis revealed that CDC6 exerted its pro-cancer and pro-immune cell infiltration functions via the PI3K-AKT pathway. Moreover, it promoted EC proliferation, migration, and invasion but inhibited apoptosis. This protein significantly reduced EC survival when mutated. These findings demonstrate that CDC6 regulates the progression of PCOS to EC and promotes immune infiltration. [ABSTRACT FROM AUTHOR]

Normally, and under low-dose mutagen exposure, a key mechanism to tolerate DNA lesions in bacterial and eukaryotic cells is the DNA damage tolerance (DDT) system. Two distinct pathways of DDT, the error-prone (translesion synthesis, TLS) and error-free (recombination) ones, function in all eukaryotic organisms. TLS involves the polymerase zeta (Polζ) protein complex (encoded by the REV1, REV3, and REV7 genes) and polymerase eta (Polη) (encoded by the RAD30 gene); these polymerases are evolutionarily conserved from yeast to humans. It was demonstrated that at low doses of UV radiation, high Polη activity plays a key role in mutagenesis, bypassing most of the DNA lesions encountered by the replication machinery. In both high and low doses of UV irradiation, the important role in induced mutagenesis is played by the DNA damage checkpoint. However, the functions of genes involved in the regulation of UV-induced mutagenesis at low and high doses of irradiation often differ. At low doses, the RAD30 gene inactivation resulted in the elevated level of induced mutagenesis, while at high doses, the mutagenesis level was virtually identical to that in wild-type strain. Deletions of the HIM1, HSM3, and HIF1 genes, on the contrary, reduced the high level of mutagenesis characteristic of high doses to wild-type strain level at low doses. These differences apparently characterize local and global checkpoint. [ABSTRACT FROM AUTHOR]

The 2-micron plasmid residing within the host budding yeast Saccharomyces cerevisiae nucleus serves as a model system for understanding the mechanism of segregation and stable maintenance of circular endogenously present extrachromosomal DNA in eukaryotic cells. The plasmid is maintained at a high average copy number (40-60 copies per yeast cell) through generations despite there is no apparent benefit to the host. Notably, the segregation mechanism of 2-micron plasmid shares significant similarities with those of bacterial low-copy-number plasmids and episomal forms of viral genomes in mammalian cells. These similarities include formation of a complex where the plasmid- or viral encoded proteins bind to a plasmid- or viral genome-borne locus, respectively and interaction of the complex with the host proteins. These together form a partitioning system that ensures stable symmetric inheritance of both these genomes from mother to daughter cells. Recent studies with substantial evidence showed that the 2-micron plasmid, like episomes of viruses such as Epstein--Barr virus, relies on tethering itself to the host chromosomes in a non-random fashion for equal segregation. This review delves into the probable chromosome hitchhiking mechanisms of 2-micron plasmid during its segregation, highlighting the roles of specific plasmid-encoded proteins and their interactions with host proteins and the chromosomes. Understanding these mechanisms provides broader insights into the genetic stability and inheritance of extrachromosomal genetic elements across diverse biological systems. [ABSTRACT FROM AUTHOR]

Objective: The development of systems for targeted delivery of nucleic acids (NAs) is necessary to ensure their selective transport to the site of therapeutic action. The aim of this work was to synthesize carbohydrate-modified amphiphiles containing a spermine residue, required for compaction and binding to NAs, as well as a diglyceride residue for forming lipid aggregates and a carbohydrate residue (lactose or D-mannose) for improving the hydrophilic–lipophilic balance of the molecule. The lactose residue can serve as a targeting ligand for NA delivery into liver hepatocytes, and the D-mannose residue can perform specific NA transport into dendritic cells and macrophages. Methods: New carbohydrate-modified cationic amphiphiles were obtained by organic synthesis, and their aqueous dispersions or cationic liposomes were prepared. Cytotoxicity of the cationic amphiphiles and liposomes was performed using the MTT assay on HEK 293 and BHK cell lines in the absence of fetal bovine serum (FBS). Complexes of the cationic amphiphiles or liposomes with NAs (FITC-ODN, pDNA, and siRNA) were formed at various component ratios (N/P), and the efficiency of transfection in HEK 293 and BHK IR-780 cells was assessed by flow cytometry. Results and Discussion: New cationic amphiphiles containing lactose or D-mannose residues were synthesized. The cationic amphiphiles, whatever the structure of their carbohydrate residue, effectively deliver a short FITC-ODN into HEK293 cells in the presence of FBS, and are nontoxic. The cationic liposome formed by the lactose-containing amphiphile and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) successfully delivers short NAs (FITC-ODN and siRNA) both in the absence and in the presence of serum in the culture media. Conclusions: The obtained carbohydrate-modified cationic amphiphiles, both individually and as component of cationic liposomes, hold promise to be used as systems for the delivery of short nucleic acids in further development of drugs for gene therapy. [ABSTRACT FROM AUTHOR]

Flavonoids are known to be effective biomodulators of various processes in eukaryotic cells. As these compounds are present in wine and beer raw materials, they can influence the qualitative characteristics of the ethanol content in wine-making and brewing products, including directly through the mechanisms of regulation of gene expression and the activity of ATP-binding cassette (ABC) proteins. The main function of ABC transporters in yeast cells is to transport various substrates, including ethanol. This process ensures the survival of yeast cells under conditions of ethanol stress. It has been found that flavonoids, as well as their Schiff base derivatives, are effective stimulators and inhibitors of mRNA expression and activity of ABC proteins both in logarithmic and stationary phases of growth, which has a direct impact on bioethanol production by yeast. [ABSTRACT FROM AUTHOR]

The budding yeast Saccharomyces cerevisiae is commonly used as an expression platform for the production of valuable compounds. Yeast‐based genetic research can uniquely utilize auxotrophy in transformant selection: auxotrophic complementation by an auxotrophic marker gene on exogenous DNA (such as plasmids). However, the number of required auxotrophic nutrients restricts the number of plasmids maintained by the cells. We, therefore, developed novel Δ10 strains that are auxotrophic for 10 different nutrients and new plasmids with two multiple cloning sites and auxotrophic markers for use in Δ10 strains. We confirmed that Δ10 strains were able to maintain 10 types of plasmids. Using plasmids encoding model proteins, we detected the co‐expression of 17 different genes in Δ10 cell lines. We also constructed Δ9 strains that exhibited auxotrophy for nine nutrients and increased growth compared to Δ10. This study opens a new avenue for the co‐expression of a large number of genes in eukaryotic cells. [ABSTRACT FROM AUTHOR]

BACKGROUND: Aldosterone and the MR (mineralocorticoid receptor) are important therapeutic targets for hypertension and cardiovascular diseases. However, biomarkers of tissue MR signaling are not fully established. Extracellular vesicles released from eukaryotic cells can provide information on tissue signaling. Using samples from patients with primary aldosteronism (PA), we explored the potential of urinary extracellular vesicles (uEVs) as a noninvasive indicator of MR signaling to guide treatment. METHODS: We analyzed proteins contained in PA uEVs by liquid chromatography tandem mass spectrometry. We narrowed down candidate biomarkers by referring to an existing database of urinary exosomes. The results were validated through Western blot analysis involving 63 patients with PA and 11 healthy volunteers. RESULTS: We identified a total of 1940 proteins in PA uEVs. Comparative analysis with the existing database narrowed down the pathways enriched in PA uEVs, which were related to diabetic complications, Rac1 signaling, and aldosterone-regulated sodium reabsorption. A closer look at the identified proteins revealed ENaCγ (epithelial Na+ channel γ) peptides near the proteolytic cleavage sites, and Western blot analysis confirmed the predominant presence of cleaved ENaCγ, a marker of aldosterone signaling in renal tubules. In PA uEVs, cleaved ENaCγ showed a 4.8-fold increase compared with healthy volunteers and was significantly correlated with the aldosterone-to-renin ratio, aldosterone levels, and fractional excretion of K+. Targeted treatment in PA reduced the abundance of cleaved ENaCγ, suggesting a causal role for MR in its induction. CONCLUSIONS: This study provides a list of proteins contained in PA uEVs and suggests that ENaCγ in uEVs is a promising biomarker for renal MR signaling. [ABSTRACT FROM AUTHOR]

In this study, the cytotoxic effects of brake wear particles (≥250 nm ceramic/ceramic wear particles (CCWPs) and ≤100 nm ceramic/steel wear particles (CSWPs)) and 100 nm iron (III) oxide ultrafine particles (IOUFPs) on human lung carcinoma (A549) and Chinese hamster ovary (CHO) cells were investigated. Cell viability was determined using the MTT and Calcein AM methods. Oxidative stress was assessed by measuring reactive oxygen species (ROS), intracellular reduced glutathione (GSH), and malondialdehyde (MDA) concentrations under exposure to the above particles in the concentration range of 10–80 µg/mL. The initial assessments of CCWPs and CSWPs on the cell viability were performed after a 4-h exposure but later extended to 24 h to investigate the time-dependent of the cell viability and oxidative stress. MTT and Calcein AM assays indicated that the A549 cells are less susceptible to CCWPs and CSWPs than the CHO cells when exposed for both 4 h and 24 h. This study highlights that oxidative stress induced by CCWPs, CSWPs, and IOUFPs is cell-specific. While CCWPs did not affect glutathione (GSH) levels in the CHO cells, it significantly reduced GSH levels in A549 cells, with the exception of 80 µg/mL. Both CCWPs and CSWPs increased the lipid peroxidation in both cell types; however, the A549 cells demonstrated lower sensitivity to these treatments. [ABSTRACT FROM AUTHOR]

Rpd3L is a highly conserved histone deacetylase complex in eukaryotic cells and participates in various cellular processes. However, the roles of the Rpd3L component in filamentous fungi remain to be delineated ultimately. In this study, we constructed two knockout mutants of Rpd3L's Rxt3 subunit and characterized their biological functions in A. oryzae. Phenotypic analysis showed that AoRxt3 played a positive role in hyphal growth and conidia formation. Deletion of Aorxt3 resulted in augmented tolerance to multiple stresses, including cell wall stress, cell membrane stress, endoplasmic reticulum stress, osmotic stress and oxidative stress. Noteworthily, we found that Aorxt3-deleting mutants showed a higher kojic acid production than the control strain. However, the loss of Aorxt3 led to a significant decrease in amylase synthesis. Our findings lay the foundation for further exploring the role of other Rpd3L subunits and provide a new strategy to improve kojic acid production in A. oryzae. [ABSTRACT FROM AUTHOR]