Cell Biology Research Articles

Supporting Instruction in Cell Biology Using No-Cost Open Educational Resources

To reduce the cost of educational materials needed by students, we generated a no-cost open educational resources (OER) textbook for an undergraduate level cell biology course. Cell biology is part of the curriculum in various undergraduate degrees for science, technology, engineering, and math majors, therefore generation of OER targets a large population of students. In addition to cost reduction, we unified the textbook content with course learning outcomes to ensure that the students have a clear understanding of course goals. To assess student perceptions of OER materials and their experiences related to learning outcomes, surveys were administered to students enrolled in sections of cell biology using a traditional textbook and those enrolled in sections using the OER. Data showed positive student attitudes about learning, accessibility, and cost of OER, supporting the use of no-cost OER in undergraduate classrooms and beyond.

Methods of miRNA delivery and possibilities of their application in neuro-oncology.

In the current phase of medical progress, practical neuro-oncology faces critical challenges. These include the quest for and development of innovative methodological approaches, as well as the enhancement of conventional therapies to boost their efficacy in treating brain tumors, especially the malignant varieties. Recent strides in molecular and cellular biology, molecular genetics, and immunology have charted the primary research pathways in the development of new anti-cancer medications, with a particular focus on microRNA (miRNA)-based therapy. MiRNAs possess the ability to function as suppressors of tumor growth while also having the potential to act as oncogenes. MiRNAs wield control over numerous processes within the human body, encompassing tumor growth, proliferation, invasion, metastasis, apoptosis, angiogenesis, and immune responses. A significant impediment to enhancing the efficacy of brain tumor treatment lies in the unresolved challenge of traversing the blood-brain barrier (BBB) and blood-tumor barrier (BTB) to deliver therapeutic agents directly to the tumor tissue. Presently, there is a worldwide effort to conduct intricate research and design endeavors aimed at creating miRNA-based dosage forms and delivery systems that can effectively target various structures within the central nervous system (CNS). MiRNA-based therapy stands out as one of the most promising domains in neuro-oncology. Hence, the development of efficient and safe methods for delivering miRNA agents to the specific target cells within brain tumors is of paramount importance. In this study, we will delve into recent findings regarding various methods for delivering miRNA agents to brain tumor cells. We will explore the advantages and disadvantages of different delivery systems and consider some clinical aspects of miRNA-based therapy for brain tumors.

Recent advances of exosomes in soft tissue injuries in sports medicine: A critical review on biological and biomaterial applications.

Sports medicine is generally associated with soft tissue injuries including muscle injuries, meniscus and ligament injuries, tendon ruptures, tendinopathy, rotator cuff tears, and tendon-bone healing during injuries. Tendon and ligament injuries are the most common sport injuries accounting for 30-40% of all injuries. Therapies for tendon injuries can be divided into surgical and non-surgical methods. Surgical methods mainly depend on the operative procedures, the surgeons and postoperative interventions. In non-surgical methods, cell therapy with stem cells and cell-free therapy with secretome of stem cell origin are current directions. Exosomes are the main paracrine factors of mesenchymal stem cells (MSCs) containing biological components such as proteins, nucleic acids and lipids. Compared with MSCs, MSC-exosomes (MSC-exos) possess the capacity to escape phagocytosis and achieve long-term circulation. In addition, the functions of exosomes from various cell sources in soft tissue injuries in sports medicine have been gradually revealed in recent years. Along with the biological and biomaterial advances in exosomes, exosomes can be designed as drug carriers with biomaterials and exosome research is providing promising contributions in cell biology. Exosomes with biomaterial have the potential of becoming one of the novel therapeutic modalities in regenerative researches. This review summarizes the derives of exosomes in soft tissue regeneration and focuses on the biological and biomaterial mechanism and advances in exosomal therapy in soft tissue injuries.

Biochemical and biophysical characterization of the RAS family small GTPase protein DiRAS3.

DiRAS3, also called ARHI, is a RAS (sub)family small GTPase protein that shares 50-60% sequence identity with H-, K-, and N-RAS, with substitutions in key conserved G-box motifs and a unique 34 amino acid extension at its N-terminus. Unlike the RAS proto-oncogenes, DiRAS3 exhibits tumor suppressor properties. DiRAS3 function has been studied through genetics and cell biology, but there has been a lack of understanding of the biochemical and biophysical properties of the protein, likely due to its instability and poor solubility. To overcome this solubility issue, we engineered a DiRAS3 variant (C75S/C80S), which significantly improved soluble protein expression in E. coli. Recombinant DiRAS3 was purified by Ni-NTA and size exclusion chromatography (SEC). Concentration dependence of the SEC chromatogram indicated that DiRAS3 exists in monomer-dimer equilibrium. We then produced truncations of the N-terminal (ΔN) and both (ΔNC) extensions to the GTPase domain. Unlike full-length DiRAS3, the SEC profiles showed that ΔNC is monomeric while ΔN was monomeric with aggregation, suggesting that the N and/or C-terminal tail(s) contribute to dimerization and aggregation. The 1H-15N HSQC NMR spectrum of ΔNC construct displayed well-dispersed peaks similar to spectra of other GTPase domains, which enabled us to demonstrate that DiRAS3 has a GTPase domain that can bind GDP and GTP. Taken together, we conclude that, despite the substitutions in the G-box motifs, DiRAS3 can switch between nucleotide-bound states and that the N- and C-terminal extensions interact transiently with the GTPase domain in intra- and inter-molecular fashions, mediating weak multimerization of this unique small GTPase.

Novel STAT3 Inhibitor Exerts Anti-breast Cancer Effects Both In vitro and In vivo

Background: Breast cancer is one of the most common malignant tumors. Signal transduction and activators of transcription 3 (STAT3) have been demonstrated to play important roles in breast cancer. However, no direct inhibitor of STAT3 has been approved by the FDA for clinical use. Objective: LL1 is a newly designed STAT3 inhibitor that we identified. In this study, we investigated the cytotoxic effect of LL1 on breast cancer cells and its potential mechanisms. Methods: Colony formation and CCK-8 assay were used to detect the anti-proliferation of LL1. Flow cytometry was used to evaluate mitochondrial membrane potential and apoptosis in breast cancer cells following the treatment of LL1. The expression of proteins was analyzed using western blot, and the invasion and migration of cells were analyzed by wound healing assay and transwell assay. The xenograft model was used to evaluate the anti-cancer effect of LL1 in vivo. Results: LL1 selectively inhibited the expression of p-STAT3, but had no obvious effect on total STAT3. LL1 exhibited great potential in suppressing the proliferation of breast cancer in vitro. Moreover, LL1 induces apoptosis and the decrease of mitochondrial membrane potential in breast cancer cells. LL1 can also inhibit the invasion and migration of breast cancer cells. These cell biology changes may be induced via the regulation of Bcl-2, Bax, cleaved-caspase3, Survivn, Mmp-2, Mmp-9, N-cadherin, E-cadherin, vimentin, c-myc and cyclin D1 by LL1. In addition, LL1 exhibited great antitumor activity in vivo. Conclusion: Our study suggested that LL1 can be considered a promising candidate for the treatment of breast cancer.

Inhibition of chaetocin on retinoblastoma progression by modulating the miR-124/SBK1 axis

We conducted cellular and animal experiments to investigate the correlation between miR-124/SBK1 and retinoblastoma (RB) progression, as well as to elucidate the anti-cancer efficacy of chaetocin in RB. Initially, miR-124 levels showed a significant decrease in RB tissues and cells, which further declined with increasing tumor diameter and clinical stage. In cellular experiments, inhibiting miR-124 expression significantly enhanced the viability and invasiveness of Y79 cells, while up-regulating miR-124 suppressed the malignant biology of Y79 cells by targeting SBK1 levels, thereby reducing their viability and invasiveness. Subsequent animal experiments provided further evidence that SBK1 was the functional target of miR-124, and its up-regulation significantly facilitated RB progression. Additionally, chaetocin demonstrated anti-tumor effects through the upregulation of miR-124 and downregulation of SBK1. Therefore, chaetocin can effectively inhibit RB progression by targeting the upregulation of miR-124 and downregulation of SBK1.

Glucocorticoid Receptor Antagonism and Cardiomyocyte Regeneration Following Myocardial Infarction: A Systematic Review.

Myocardial regeneration has been a topic of interest in literature and research in recent years. An evolving approach reported is glucocorticoid (GC) receptor antagonism and its role in the regeneration of cardiomyocytes. The authors of this study aim to explore the reported literature on GC receptor antagonism and its effects on cardiomyocyte remodeling, hypertrophy, scar formation, and ongoing cardiomyocyte death following cardiac injury. This article overviews cellular biology, mechanisms of action, clinical implications, challenges, and future considerations. The authors of this study conducted a systematic review utilizing the Cochrane methodology and PRISMA guidelines. This study includes data collected and interpreted from 30 peer-reviewed articles from 3 databases with the topic of interest. The mammalian heart has regenerative potential during its embryonic and fetal phases which is lost during its developmental processes. The microenvironment, intrinsic molecular mechanisms, and systemic and external factors impact cardiac regeneration. GCs influence these aspects in some cases. Consequently, GC receptor antagonism is emerging as a promising potential target for stimulating endogenous cardiomyocyte proliferation, aiding in cardiomyocyte regeneration following a cardiac injury such as a myocardial infarction (MI). Experimental studies on neonatal mice and zebrafish have shown promising results with GC receptor ablation (or brief pharmacological antagonism) promoting the survival of myocardial cells, re-entry into the cell cycle, and cellular division, resulting in cardiac muscle regeneration and diminished scar formation. Transient GC receptor antagonism has the potential to stimulate cardiomyocyte regeneration and help prevent the dreaded complications of MI. More trials based on human populations are encouraged to justify their applications and weigh the risk-benefit ratio.

3DCNAS: A universal method for predicting the location of fluorescent organelles in living cells in three-dimensional space.

Cellular biology research relies on microscopic imaging techniques for studying the complex structures and dynamic processes within cells. Fluorescence microscopy provides high sensitivity and subcellular resolution but has limitations such as photobleaching and sample preparation challenges. Transmission light microscopy offers a label-free alternative but lacks contrast for detailed interpretation. Deep learning methods have shown promise in analyzing cell images and extracting meaningful information. However, accurately learning and simulating diverse subcellular structures remain challenging. In this study, we propose a method named three-dimensional cell neural architecture search (3DCNAS) to predict subcellular structures of fluorescence using unlabeled transmitted light microscope images. By leveraging the automated search capability of differentiable neural architecture search (NAS), our method partially mitigates the issues of overfitting and underfitting caused by the distinct details of various subcellular structures. Furthermore, we apply our method to analyze cell dynamics in genome-edited human induced pluripotent stem cells during mitotic events. This allows us to study the functional roles of organelles and their involvement in cellular processes, contributing to a comprehensive understanding of cell biology and offering insights into disease pathogenesis.

Protocol to dissociate epithelia from non-pregnant and pregnant mouse cervical tissue for single-cell RNA-sequencing.

A challenge in studying cervical epithelial cell biology at the single-cell level is that differentiated subtypes, in particular mucus-secreting goblet cells, are sensitive to disassociating enzymes making isolation of all epithelial subpopulations difficult. Here we present a protocol to dissociate epithelia from non-pregnant and pregnant mouse cervical tissue for single-cell RNA-sequencing. We describe steps for harvesting cervices, preparing cervical tissue, dissociation of cervical cells, and viability checks. We then detail library preparation, sequencing, and procedure for data analysis. For complete details on the use and execution of this protocol, please refer to Cooley etal. (2023).1.

Protein condensates as flexible platforms for membrane traffic.

With an essential role in nearly every physiological process and disease state, trafficking vesicles are fundamental to cell biology. Canonical understanding of membrane traffic has been driven by key achievements in structural biology. Nonetheless, discoveries over the past few years progressively point to the critical role of intrinsically disordered domains and proteins, which lack a well-defined secondary structure. From the initiation of endocytosis and the sequestration of synaptic vesicles to the stabilization of endoplasmic reticulum exit sites and the extension of the autophagic cup, flexible protein condensates, rich in intrinsic disorder, are increasingly implicated. While important debates about the physical nature and mechanistic interpretation of these findings remain, the significance of transient, multivalent protein assemblies in membrane traffic is increasingly clear.

A promising future in cancer immunotherapy: Oncolytic viruses.

Alongside the conventional methods, attention has been drawn to the use of immunotherapy-based methods for cancer treatment. Immunotherapy has developed as a therapeutic option that can be more specific with better outcomes in tumor treatment. It can boost or regulate the immune system behind the targeted virotherapy. Virotherapy is a kind of oncolytic immunotherapy that investigated broadly in cancer treatment in recent decades, due to its several advantages. According to recent advance in the field of understanding cancer cell biology and its occurrence, as well as increasing the knowledge about conditionally replicating oncolytic viruses and their destructive function in the tumor cells, nowadays, it is possible to apply this strategy in the treatment of malignancies. Relying on achievements in clinical trials of oncolytic viruses, we can certainly expect that this therapeutic perception can play a more central role in cancer treatment. In cancer treatment, combination therapy using oncolytic viruses alongside standard cancer treatment methods and other immunotherapy-based treatments can expect more promising results in the future.

Strategies for quantifying the enzymatic activities of glycoside hydrolases within cells and invivo.

Within their native milieu of the cell, the activities of enzymes are controlled by a range of factors including protein interactions and post-translational modifications. The involvement of these factors in fundamental cell biology and the etiology of diseases is stimulating interest in monitoring enzyme activities within tissues. The creation of synthetic substrates, and their use with different imaging modalities, to detect and quantify enzyme activities has great potential to propel these areas of research. Here we describe the latest developments relating to the creation of substrates for imaging and quantifying the activities of glycoside hydrolases, focusing on mammalian systems. The limitations of current tools and the difficulties within the field are summarised, as are prospects for overcoming these challenges.

IL-17A Orchestrates Reactive Oxygen Species/HIF1α-Mediated Metabolic Reprogramming in Psoriasis.

Immune cell-derived IL-17A is one of the key pathogenic cytokines in psoriasis, an immunometabolic disorder. Although IL-17A is an established regulator of cutaneous immune cell biology, its functional and metabolic effects on nonimmune cells of the skin, particularly keratinocytes, have not been comprehensively explored. Using multiomics profiling and systems biology-based approaches, we systematically uncover significant roles for IL-17A in the metabolic reprogramming of human primary keratinocytes (HPKs). High-throughput liquid chromatography-tandem mass spectrometry and nuclear magnetic resonance spectroscopy revealed IL-17A-dependent regulation of multiple HPK proteins and metabolites of carbohydrate and lipid metabolism. Systems-level MitoCore modeling using flux-balance analysis identified IL-17A-mediated increases in HPK glycolysis, glutaminolysis, and lipid uptake, which were validated using biochemical cell-based assays and stable isotope-resolved metabolomics. IL-17A treatment triggered downstream mitochondrial reactive oxygen species and HIF1α expression and resultant HPK proliferation, consistent with the observed elevation of these downstream effectors in the epidermis of patients with psoriasis. Pharmacological inhibition of HIF1α or reactive oxygen species reversed IL-17A-mediated glycolysis, glutaminolysis, lipid uptake, and HPK hyperproliferation. These results identify keratinocytes as important target cells of IL-17A and reveal its involvement in multiple downstream metabolic reprogramming pathways in human skin.

On the origin of the nucleus: a hypothesis.

SUMMARYIn this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions-emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.

Filamentous actin destabilization by H2O2 favors DnmA aggregation, with crucial roles of cysteines 450 and 776 in mitochondrial and peroxisomal division in Aspergillus nidulans.

Mitochondria constitute major sources of H2O2 and other reactive oxygen species in eukaryotic cells. The division of these organelles is crucial for multiple processes in cell biology and relies on highly regulated mechano-GTPases that are oligomerization dependent and belong to the dynamin-related protein family, like A. nidulans DnmA. Our previous work demonstrated that H2O2 induces mitochondrial constriction, division, and remodeling of the outer membrane. Here, we show that H2O2 also induces a DnmA aggregation consistent with higher-order oligomerization and its recruitment to mitochondria. The study of this response uncovered that H2O2 induces the depolymerization and reorganization of actin as well as the critical role that cysteines 450 and 776 play in DnmA function. Our results provide new insights into the mechanisms of reactive oxygen species cell signaling and how they can regulate the dynamics of the actin cytoskeleton and the division of mitochondria and peroxisomes.

K+ and pH homeostasis in plant cells is controlled by a synchronized K+ /H+ antiport at the plasma and vacuolar membrane.

Stomatal movement involves ion transport across the plasma membrane (PM) and vacuolar membrane (VM) of guard cells. However, the coupling mechanisms of ion transporters in both membranes and their interplay with Ca2+ and pH changes are largely unclear. Here, we investigated transporter networks in tobacco guard cells and mesophyll cells using multiparametric live-cell ion imaging and computational simulations. K+ and anion fluxes at both, PM and VM, affected H+ and Ca2+ , as changes in extracellular KCl or KNO3 concentrations were accompanied by cytosolic and vacuolar pH shifts and changes in [Ca2+ ]cyt and the membrane potential. At both membranes, the K+ transporter networks mediated an antiport of K+ and H+ . By contrast, net transport of anions was accompanied by parallel H+ transport, with differences in transport capacity for chloride and nitrate. Guard and mesophyll cells exhibited similarities in K+ /H+ transport but cell type-specific differences in [H+ ]cyt and pH-dependent [Ca2+ ]cyt signals. Computational cell biology models explained mechanistically the properties of transporter networks and the coupling of transport across the PM and VM. Our integrated approach indicates fundamental principles of coupled ion transport at membrane sandwiches to control H+ /K+ homeostasis and points to transceptor-like Ca2+ /H+ -based ion signaling in plant cells.

Lipid metabolism in B cell biology.

In recent years, the field of immunometabolism has solidified its position as a prominent area of investigation within the realm of immunological research. An expanding body of scientific literature has unveiled the intricate interplay between energy homeostasis, signaling molecules, and metabolites in relation to fundamental aspects of our immune cells. It is now widely accepted that disruptions in metabolic equilibrium can give rise to a myriad of pathological conditions, ranging from autoimmune disorders to cancer. Emerging evidence, although sometimes fragmented and anecdotal, has highlighted the indispensable role of lipids in modulating the behavior of immune cells, including B cells. In light of these findings, this review aims to provide a comprehensive overview of the current state of knowledge regarding lipid metabolism in the context of B cell biology.

The role of extended synaptotagmin at membrane contact sites in cancer research

Membrane contact sites (MCSs) are adjacent locations between the membranes of two different organelles and play important roles in various physiological processes, including cellular calcium and lipid signaling. In cancer research, MCSs have been proposed to regulate tumor metabolism and fate, contributing to tumor progression, and this function could be exploited for tumor therapy. However, there is little evidence on how MCSs are involved in cancer progression. In this review, we use extended synaptotagmins (E-Syts) as an entry point to describe how MCSs affect cancer progression and may be used as new diagnostic biomarkers. We then introduced the role of E-Syt and its related pathways in calcium and lipid signaling, aiming to explain how MCSs affect tumor proliferation, progression, metastasis, apoptosis, drug resistance, and treatment through calcium and lipid signaling. Generally, this review will facilitate the understanding of the complex contact biology of cancer cells.

Flow Cytometry: Aspects and Application in Plant and Biological Science.

Flow cytometry is a potent method that enables the quick and concurrent investigation of several characteristics of single cells in solution. Photodiodes or photomultiplier tubes are employed to detect the dispersed and fluorescent light signals that are produced by the laser beam as it passes through the cells. Photodetectors transform the light signals produced by the laser into electrical impulses. A computer then analyses these electrical impulses to identify and measure the various cell populations depending on their fluorescence or light scattering characteristics. Based on their fluorescence or light scattering properties, cell populations can be examined and/or isolated. This review covers the basic principle, components, working and specific biological applications of flow cytometry, including studies on plant, cell and molecular biology and methods employed for data processing and interpretation as well as the potential future relevance of this methodology in light of retrospective analysis and recent advancements in flow cytometry. This article is protected by copyright. All rights reserved.

Lipid-laden foam cells in the pathology of atherosclerosis: shedding light on new therapeutic targets.

Lipid-laden foam cells within atherosclerotic plaques are key players in all phases of lesion development including its progression, necrotic core formation, fibrous cap thinning, and eventually plaque rupture. Manipulating foam cell biology is thus an attractive therapeutic strategy at early, middle, and even late stages of atherosclerosis. Traditional therapies have focused on prevention, especially lowering plasma lipid levels. Despite these interventions, atherosclerosis remains a major cause of cardiovascular disease, responsible for the largest numbers of death worldwide. Foam cells within atherosclerotic plaques are comprised of macrophages, vascular smooth muscle cells, and other cell types which are exposed to high concentrations of lipoproteins accumulating within the subendothelial intimal layer. Macrophage-derived foam cells are particularly well studied and have provided important insights into lipid metabolism and atherogenesis. The contributions of foam cell-based processes are discussed with an emphasis on areas of therapeutic potential and directions for drug development. As key players in atherosclerosis, foam cells are attractive targets for developing more specific, targeted therapies aimed at resolving atherosclerotic plaques. Recent advances in our understanding of lipid handling within these cells provide insights into how they might be manipulated and clinically translated to better treat atherosclerosis.