The separation of DNA-based processes from cytoplasmic protein synthesis demands precise and effective nuclear import of histones and chromatin regulators. Because histones are highly basic and aggregation-prone, their proper folding, sequestration, and deposition into chromatin depend on coordinated action of histone chaperones and nuclear import receptors. This review summarizes recent advances in understanding the mechanisms of core and linker histone import and chaperoning. Structural and biochemical studies have elucidated how Importin-4/Kap123 mediates nuclear import of H3-H4 heterodimers in concert with ASF1, revealing Importin-4's dual role as both transporter and histone chaperone. Likewise, Importin-9/Kap114 recognizes and imports H2A-H2B heterodimers through a mechanism unusually insensitive to RanGTP, which cooperates with Nap1 for histone release. Finally, new structural analyses of the Importin-β-Importin-7 heterodimer clarify its mode of linker histone H1 import. Together, these studies establish importins as multifunctional factors that couple histone stabilization, protection from aberrant interactions, nuclear import, and targeted delivery for nucleosome assembly. Outstanding questions include how secondary importins, histone modifications, and compartment-specific chaperone dynamics regulate histone trafficking, and whether importins themselves function in nucleosome assembly. Addressing these questions will define how nuclear import integrates with chromatin homeostasis.
Fluorescence microscopy is essential in modern cell biology but remains constrained by photobleaching, autofluorescence, and the intrinsic quantum yields of emitters. Metal-enhanced fluorescence (MEF) is a photophysical phenomenon in which interactions between luminescent species and metal nanostructures markedly increase emission, enabling a route to brighter, high-contrast, noninvasive bioimaging by reshaping photophysical pathways without modifying fluorophore chemistry. This review translates MEF fundamentals into an experimental playbook for biologists, distinguishing MEF mechanisms and explaining how distance, spectral overlap, and nanoparticle morphology govern whether emission is boosted or quenched. We synthesize recent live-cell applications-using gold and silver nanoparticles-to illustrate gains in signal-to-noise at lower excitation power, improved photostability, and opportunities where small-molecule dyes often suffer low quantum yield, and provide practical guidelines for pairing dyes with metal nanostructures to lower the barrier to adopting MEF in cellular imaging.
Intracellular cargo transport relies on a microtubule (MT) network and its molecular motors, dynein and kinesin. While conventional models emphasize motor-driven cargo movement along stationary MT tracks, emerging evidence suggests that dynamic movements of MTs also contribute to directional transport. We propose a model of cargo co-migration with moving MTs, exemplified by nuclear migration in developing neurons. This transport mode may operate across cell types, provided that cargo-MT tethering and directional MT movements are present. We hypothesize multiple complementary mechanisms, including motor catch-bond formation and clustering, as well as MT-associated protein-mediated anchorage. We further discuss how directional MT movements can be generated through motor-driven sliding, cortical gliding, actin-MT crosslinking, and dynamic MT instability. This coupled transport mechanism provides an additional layer of directional control that supplements motor-stepping-dependent transport. Potential experimental approaches to validate this hypothesis are discussed. Understanding MT-mediated cargo delivery could refine our current models of intracellular transport and reveal new insights into neurodevelopmental and neurodegenerative disorders.
Research in molecular cell biology has typically been focused on identifying specific genes and proteins responsible for cellular phenomena. However, it is increasingly recognized that the function of many biomolecules is variable and context dependent, raising the question if specific components can adequately explain cellular mechanisms. Philosophers of biology have proposed an alternative perspective known as process ontology, posing that not objects or molecules, but processes are the fundamental units of living systems. Process ontology is gaining popularity in biological theory, but remains challenging to integrate into scientific practice. Here, we assess the applicability of the process perspective in the context of a concrete biological system, namely polarization in budding yeast. We identify relevant processes in yeast polarization at different timescales and examine how these processes affect our understanding of polarity. Using this case study, we demonstrate how the processual perspective evokes new kinds of scientific questions and provide concrete pointers for incorporating processual thought into cell biological research.
Diseases due to mutations in essential molecules can involve tissues functioning in very different environments, with some in mechanically active environments. Diseases arising from mutations in a single molecule, such as the CFTR in cystic fibrosis exhibit varied clinical phenotypes. The lung cells expressing mutations in CFTR are functioning in the mechanically active environment of the lung, but these mutations may also play an adverse role in the cardiovascular system. Similarly, Marfan syndrome arises from mutations in an extracellular matrix (ECM) molecule, fibrillin-1 and this molecule is also involved in tissues operating in very mechanically active environments. Thus, there is the potential for genetic variants with or without clinical symptoms individually to interact in the same individual to exhibit a unique interdependent phenotype involving disruption of the "Cell-ECM" relationship. Although the clinical phenotypes for the CFTR and fibrillin-1 individually are rare, both molecules are known to each have >500 mutations. This may be one example of a molecular pair that could uniquely interact, influencing cell function. This article will discuss this premise and address the potential basis for complementarity using CFTR and fibrillin-1 as examples.
Collective cell migration is fundamental to developmental processes and disease progression. Despite extensive study, the field lacks a unifying framework for how collective cells initiate and terminate their migration. While these processes have traditionally been explained for individual cell migration by epithelial‒mesenchymal transition (EMT) and mesenchymal‒epithelial transition (MET), these models do not fully recapitulate the complex features of collective cell migration. In this review, I explore the distinct mechanisms by which groups of cells initiate and terminate collective migration, highlighting in vivo examples such as gastrulation and neural crest formation in vertebrates, lateral line migration in zebrafish, and tracheal branch and border cell migration in Drosophila. I also discuss collective cell migration in cancer metastasis. I focus on how the initiation and termination of collective migration are regulated, emphasizing the regulatory pathways and unique features. Clarifying these mechanisms will guide hypothesis-driven discovery and inform strategies to modulate collective cell behaviors in development, regeneration, and metastasis.
Most vertebrate genes are split up into exons and introns, with exons being spliced together to make mRNA. Many of the proteins involved in splicing, called splicing factors, exert concentration-dependent effects on gene expression through post-transcriptional modification of mRNAs. These include the serine/arginine-enriched (SR) proteins that have essential roles in normal development and physiology. All SR proteins (and many other splicing factors) regulate their own expression levels, often using negative feedback pathways involving alternative splicing of "poison exons" (PEs), which lead to mRNA degradation. The PEs within SR protein genes are encoded by ultra-conserved genome sequences, suggesting they have been under extreme selective pressure despite not encoding protein sequences. Here, we discuss the hypothesis that PEs enable rapid switches in SR protein concentrations, yet prevent these splicing regulators from increasing to toxic levels that cause cell death or interfere with cell function. This hypothesis is based on analysis of an ultra-conserved PE in the TRA2B gene during male meiosis. Distinct roles for this TRA2B PE in different tissues further predict cell type-specific effects on development and physiology that will need to be experimentally detected using animal models.
Flow cytometry is a versatile analytical technology for measuring physical and molecular characteristics of individual cells or particles in suspension. The technology has had its greatest impact in immunology, enabling the identification and quantification of rare cell populations within complex mixtures, but applications span diverse biological systems including hematopoietic cells, microorganisms, cultured cells, plant cells, gametes, and disaggregated tissues. Target molecules are typically identified using fluorophore-conjugated antibodies, though alternative labeling strategies exist. A key advantage of flow cytometry is the ability to physically isolate cells of interest for downstream applications such as culture, genomic analysis, or functional studies. The field has undergone substantial evolution from conventional filter-based polychromatic systems to spectral cytometry platforms that capture full emission spectra, enabling higher-parameter analyses and more flexible panel design. This review examines current capabilities and limitations of flow cytometry technology, with emphasis on recent advances in spectral detection, quantitative standardization, and computational analysis. We discuss remaining technical challenges and explore emerging opportunities for innovation in excitation systems, detector technology, and integration with artificial intelligence-based analysis platforms. Addressing these challenges will be essential for cytometry to continue driving biological discovery and clinical applications in the coming decades.
Mitochondria are vital not only for energy production but also for regulating signaling pathways that influence aging. While mitochondrial dysfunction contributes to age-related decline, emerging evidence shows that mild, regulated mitochondrial stress can paradoxically promote longevity. This review highlights recent advances in mitochondrial biology and aging across species. We explore the dual role of reactive oxygen species (ROS) as both damaging agents and signaling molecules that activate adaptive stress responses. Key pathways such as the mitochondrial unfolded protein response (UPRMT) and integrated stress response (ISR) are discussed, including their tissue-specific as well as non-cell-autonomous effects on aging. Additionally, we examine the impact of mitochondrial protein import/export, dynamics (fission, fusion, mitophagy, biogenesis), and quality control in aging. Finally, we address challenges in understanding context-dependent mitochondrial responses and mitonuclear communication. Together, these insights position mitochondria as central regulators of aging and highlight their potential as therapeutic targets to enhance health span and longevity.
T cell receptor (TCR) recognition of peptide/MHC complexes is fundamental for adaptive immunity. Many studies have described the importance of peptide/MHC motion or dynamics in TCR recognition. A role for dynamics in recognition intersects with the concept of dynamic allostery, which describes how alterations to a protein's energy landscape and thus motions influence function, often in the absence of conformational changes. Tuning of MHC protein energy landscapes by different peptides has clearly been shown. Evidence is mounting, however, that MHC polymorphisms also alter the protein's energy landscape. Here, we address this concept, summarizing findings that suggest that, in addition to dictating peptide binding and selection, naturally occurring variations within MHC proteins promote differential peptide and protein dynamics, altering TCR recognition in an MHC allele-dependent manner. We hypothesize that MHC polymorphisms have been selected evolutionarily in part to tune the protein's dynamic response, altering immune specificity and further diversifying immune responses across populations.
Spider mites (Acari: Trombidiformes; Tetranychidae) are globally important herbivore pests of crops. They have also become powerful genetic models for understanding chelicerate biology and the evolution of xenobiotic (i.e., pesticide) resistance and host plant adaptation. The first spider mite genome, that of Tetranychus urticae, uncovered dramatic expansions of gene families and horizontally acquired genes that associate with this species' very broad host plant range. While in its infancy, comparative genomics with other Tetranychidae species with more restricted host plant ranges is already uncovering relationships between gene content and host plant breadth. Further, quantitative genetic methods adapted to spider mites' life history now enable the identification of loci underlying adaptive traits, and functional studies are possible with RNAi and a recent breakthrough in high-efficiency gene editing. This review combines a primer in spider mite biology and experimental tractability with recent genome-enabled findings to highlight the potential of spider mites to inform Acari and chelicerate biology, as well as mechanisms of genetic adaptation and evolution more broadly.
The interactions between human viruses and human stem cells may differ from those with differentiated cells. These differences may arise through heterogeneous intercellular mechanisms and responses to specific infectious agents, resulting in different phenotypes that affect human pathophysiology. Understanding and exploiting such differences could have clinical and translational potential. Here, we discuss the various mechanistic interactions between stem cells and viruses related to entry mechanisms, replication dynamics, and immunomodulation. In doing so, we critically assess proposed models and hypotheses about how viruses manipulate stem cell biology, while also providing new paradigms for stem cell biology and therapeutic interventions. We highlight recent discoveries on the dual role of viruses in oncogenesis and oncolysis. In parallel, we explore similarities between stem cells and complex viruses-such as giant viruses and jumbo phages-to propose novel perspectives on viral adaptability and pathogenesis. We examine both established mechanisms and emerging viral phenomena to encourage further research and debate on the clinical implications of viral interactions with stem cells.
Stem cell populations employ cell-intrinsic and niche-mediated mechanisms to preserve long-term self-renewal and regenerative potential. We propose that tumor-initiating cells (TICs) hijack this developmental circuitry to sustain their growth and establish an early immunosuppressive microenvironment during malignant progression. Recent work implicates CXCR4+ tissue-resident macrophages (TRMs) in the mammary gland as a central orchestrator of this process. Conserved CXCL12/CXCR4-AKT-β-catenin signaling links CXCR4+ TRM support of normal mammary stem cells to TIC maintenance, underscoring how developmental niches are exploited in malignancy. During tumorigenesis, aberrant CXCL12 production from tumor-associated fibroblasts promotes the expansion of CXCR4+ TRMs, while CXCR4 signaling enhances ALDH1A2-dependent retinoic acid production, which induces regulatory T cells and thereby suppresses anti-tumor immunity at the earliest stages of tumor development. From this perspective, early immune evasion is not only a hallmark of cancer but also a therapeutic window. Targeting TRMs early in cancer development could delay, or even prevent, malignant initiation. More broadly, we propose that TIC-niche crosstalk constitutes a tractable vulnerability, and that incorporating TRM-directed interventions alongside conventional and immune-based therapies may shift the balance toward durable tumor control.
Autoimmune diseases such as multiple sclerosis (MS) and rheumatoid arthritis (RA) involve complex interactions between local tissues and the immune system. Here, we highlight the immunological parallels between the central nervous system (CNS) meninges and the synovial joint, two sites traditionally considered immune-privileged. Both harbor resident immune cells and lymphatic vessels and support the formation of tertiary lymphoid organs (TLO) during chronic inflammation. In MS, meningeal TLO contributes to cortical grey matter damage, while in RA, synovial TLO drives joint destruction. T peripheral helper (Tph) cells, a subset of CD4+ T cells, are key players in both conditions by supporting B cell activation and autoantibody production. Epstein-Barr virus (EBV) infection, particularly in B cells within TLO, is implicated in the pathogenesis of both diseases. Targeting EBV-infected B cells, depleting Tph cells, or disrupting TLO represent promising therapeutic strategies for controlling disease progression and severity in MS and RA.
In eukaryotic cells, genomic DNA is packaged into chromatin, restricting the access of regulatory proteins and thus regulating key processes such as transcription, replication, recombination, and the repair of DNA. Barrier-to-autointegration factor (BAF) plays key roles in organizing chromatin architecture and nuclear functions. BAF bridges DNA segments and connects them to Lamin A/C and inner nuclear membrane proteins containing the LEM domain, ensuring proper chromatin organization and nuclear envelope assembly and repair. Over the last three decades, multiple structural studies have revealed that BAF dimerizes to bind DNA and shapes higher-order chromatin structure. In this review, we summarize the structural features of BAF in complexes with its binding partners and explore how these interactions contribute to maintaining nuclear integrity and regulating genome function.
Student navigation through a PhD Program is marked by intellectual challenges, emotional fluctuations, and personal growth. Students develop excellence by absorbing and adjusting, recovering, and improving in response to challenges. The ability to bounce back is termed elasticity, an engineering principle where systems are designed to withstand stress, recover from disruptions, and maintain functionality. Students can proceed from elasticity (resilience) to then develop antifragility, the ability to become better from an experience. It occurred to the first author (a PhD graduate student in biomedical sciences) that developing antifragility is conceptually easier to understand by applying basic engineering concepts. We examine five thematic categories that connect engineering concepts with practical realities of graduate study: (1) load and stress management; (2) redundancy and backup systems; (3) setback modes and recovery; (4) adaptive capacity and flexibility; and (5) sustainability and long-term performance. By understanding how to gain antifragility, one can navigate demands more effectively.
This paper proposes an extension of the traditional Central Dogma of molecular biology to a more dynamic model termed the Central Dogma cycle (CDC) and a broader network called the Central Dogma cyclic network (CDCN). While the Central Dogma is necessary for genetic information flow, it is insufficient to fully explain cellular memory, decision-making, and information management. The CDC incorporates additional well-established steps such as protein folding and networking, highlighting the cyclical nature of biological information flow. I propose that this cyclic architecture functions as a key mechanism for cellular memory, drawing analogies to memory functions in computers, such as input, read, write, execute, and erase. Within the CDCN, interconnected metabolic and signaling pathways act as logic-enabled processors that bridge DNA mutations to phenotypes. This model reframes heredity beyond nucleic acid sequences and evolution as the optimization of memory-bearing networks. It is extensible to broader biological systems such as physiological feedback loops. Understanding cellular memory through this cyclic network model offers a unified perspective on heredity, adaptation to the environment, cell processes, and the disruptions of information flow in disease pathology.
Accurate and timely genome replication is a universal feature of living organisms and a prerequisite for cell proliferation. In eukaryotes, genomic DNA replication initiates in two steps, origin licensing and origin firing, reflecting the loading and activation of the MCM replicative helicase motor on origin DNA. Biochemical reconstitution of these steps in the budding yeast model system signified a major advance towards understanding the molecular and structural details of eukaryotic replication initiation events. With recent successes in reconstituting origin licensing with purified human proteins, a mechanistic picture is beginning to emerge on how DNA replication initiates in higher eukaryotes and how it deviates from the paradigms established in budding yeast. In this review, we highlight similarities and differences in licensing mechanisms between yeast and metazoa.
We propose a novel hypothesis that artificial food colors (AFCs) may act as sleep disruptors in children by interfering with neurochemical pathways involved in circadian regulation and behavioral stability. Although widely used in ultra-processed foods (UPFs) to enhance visual appeal, especially targeting children, emerging evidence suggests that frequent exposure to AFCs is linked to behavioral disturbances such as hyperactivity, irritability, and attention deficits, as well as sleep-related problems. Recent updates from the Food and Drug Administration (FDA) highlight growing regulatory concern about the health risks of petroleum-based colorants in pediatric populations. Despite these concerns, the current body of knowledge on the specific mechanisms through which artificial colorants may impact sleep remains limited and superficial. This paper proposes that AFCs may negatively affect sleep quality through disruptions in neurophysiological signaling, and it calls for rigorous investigation via double-blind, placebo-controlled, cross-over clinical trials, which may contribute to a better understanding of the neurobehavioral effects of AFCs and provide a scientific basis for future regulatory decisions and public health strategies.
In well-perfused tissues, interstitial composition resembles capillary plasma. Solid tumors break this norm because cancer cell proliferation outpaces vascular expansion, leading to a diffusion-limited tumor microenvironment (TME) that is notably depleted of oxygen and enriched in acids. The magnitude of tumor acidosis; its chemical composition in terms of [CO2] and [HCO3 -] (components of the major extracellular buffer); and its relationship with hypoxia are not intuitive to predict but important to know for designing experiments and contextualising results. We address these timely questions using mathematical models of a monolayer, spheroid, and poorly-perfused tissue. Our simulations suggest a physiologically realistic TME pH range of 6.7-7.4, reveal a prominence of hypercapnia, and indicate varying levels of HCO3 - depletion or accumulation arising from fermentation and respiration, respectively. The trajectories of tumor hypoxia and acidosis depend on the balance between aerobic and anaerobic pathways, with important consequences on hypoxic signaling where many responses are pH-sensitive.