Entire Organism Research Articles

Tissue Clearing and Its Application in Nanoparticle Development.

Nanoparticles are widely used in biomedical applications due to their small size, large surface area, and unique physicochemical properties. These characteristics make them ideal for drug delivery, diagnostic imaging, and therapeutic interventions. Their ability to interact with biological systems at the cellular and molecular levels enables targeted treatments. Understanding the biodistribution of nanoparticles at the cellular level within whole organisms is crucial for assessing their safety and effectiveness; however, proper technologies have been lacking to achieve this. For example, traditional imaging techniques like magnetic resonance imaging (MRI) and computed tomography (CT) often lack the resolution needed, while tissue-section-based methods miss the whole-body systemic view. Recent tissue clearing methods have emerged as a promising solution for 3D visualization of nanoparticles in entire organs, as they enable cellular-level imaging of whole organisms without the need for sectioning. This review explores advancements in diverse tissue clearing techniques and their application in studying nanoparticle biodistribution, providing insights crucial for the development of nanoparticle-based therapies.

Whole organism and tissue-specific analysis of pexophagy in Drosophila.

Peroxisomes are essential organelles involved in critical metabolic processes in animals such as fatty acid oxidation, ether phospholipid production and reactive oxygen species detoxification. We have generated transgenic Drosophila melanogaster models expressing fluorescent reporters for the selective autophagy of peroxisomes, a process known as pexophagy. We show that these reporters are colocalized with a peroxisomal marker and that they can reflect pexophagy induction by iron chelation and inhibition by depletion of the core autophagy protein Atg5. Using light sheet microscopy, we have been able to obtain a global overview of pexophagy levels across the entire organism at different stages of development. Tissue-specific control of pexophagy is exemplified by areas of peroxisome abundance but minimal pexophagy, observed in clusters of oenocytes surrounded by epithelial cells where pexophagy is much more evident. Enhancement of pexophagy was achieved by feeding flies with the iron chelator deferiprone, in line with past results using mammalian cells. Specific drivers were used to visualize pexophagy in neurons, and to demonstrate that specific depletion in the larval central nervous system of Hsc70-5, the Drosophila homologue of the chaperone HSPA9/mortalin, led to a substantial elevation in pexophagy.

Gene Therapy for Skin Aging.

Extrinsic and intrinsic factors contribute to skin aging; nonetheless, they are intertwined. Moreover, intrinsic skin aging mirrors age-related declines in the entire human body's internal organs. There is evidence that skin appearance is an indicator of the general health of somebody or a visual certificate of health. Earlier, it was apparent that the intrinsic factors are unalterable, but the sparkling of skin aging gene therapy on the horizon is changing this narrative. Skin aging gene therapy offers tools for skin rejuvenation, natural beauty restoration, and therapy for diseases affecting the entire skin. However, skin aging gene therapy is an arduous and sophisticated task relying on precise interim stimulation of telomerase to extend telomeres and wend back the biological clock in the hopes to find the fountain of youth, while preserving cells innate biological features. Finding the hidden fountain of youth will be a remarkable discovery for promoting aesthetics medicine, genecosmetics, and healthy aging. Caloric restriction offers ultimate health benefits and a reproducible way to promote longevity in mammals, while delaying age-related diseases. Moreover, exercise further enhances these health benefits. This article highlights the potential of skin aging gene therapy and foretells the emerging dawn of the genecosmetics era.

Mapping organism-wide single cell mRNA expression linked to extracellular vesicle biogenesis, secretion and cargo.

Extracellular vesicles (EVs) are functional lipid-bound nanoparticles trafficked between cells and found in every biofluid. It is widely claimed that EVs can be secreted by every cell, but the quantity and composition of these EVs can differ greatly among cell types and tissues. Defining this heterogeneity has broad implications for EV-based communication in health and disease. Recent discoveries have linked single-cell EV secretion to the expression of genes encoding EV machinery and cargo. To gain insight at single-cell resolution across an entire organism, we compared the abundance, variance and co-expression of 67 genes involved in EV biogenesis and secretion, or carried as cargo, across >44,000 cells obtained from 117 cell populations in the Tabula Muris.

Three-dimensional structure of entire hydrated murine hearts at histological resolution

Imaging the entire cardiomyocyte network in entire small animal hearts at single cell resolution is a formidable challenge. Optical microscopy provides sufficient contrast and resolution in 2d, however fails to deliver non-destructive 3d reconstructions with isotropic resolution. It requires several invasive preparation steps, which introduce structural artefacts, namely dehydration, physical slicing and staining, or for the case of light sheet microscopy also clearing of the tissue. Our goal is to provide 3d reconstructions of the cardiomyocyte network in entire hydrated murine hearts, and to develop a methodology for quantitative analysis of heart pathologies based on X-ray phase contrast computed tomography (XPCT). We have used XPCT at two beamlines of the extremely brilliant source (EBS) at the European Synchrotron Radiation Facility (ESRF) to scan wild-type murine hearts at high resolution, as well as a series of murine hearts of different pathological models, at reduced resolution and higher throughput. All hearts were obtained from the small animal facility of the university medical center in Göttingen. The hearts were fixed in formalin, stored and measured non-destructively in phosphate buffer solution. The high resolution dataset allows to discern individual cardiomyocytes in the tissue. All datasets have been analyzed using semi-automated image segmentation of the ventricles, rotation into a common coordinate system, classification into different anatomical compartments, and finally the structure tensor approach. A 3d streamline representation of the cardiomyocyte orientation vector field is provided. The different cardiovascular disease models are analysed based on metrics derived from the 3d structure tensor. An entire hydrated murine heart has been covered at an isotropic voxel size of 1.6μm (distributed over several volumes). A binned and fused dataset of this heart is available at 3.2μm, and has been analyzed by the structure tensor approach to yield the ventricular cardiomyocyte network or mesh, i.e. the aggregation of the cardiomyocyte chains in particular in the ventricular wall. Semi-automatic determination of structural metrics is already achieved and the corresponding tools and resulting data are made publically available. XPCT using extremely brilliant undulator radiation is close to achieve single cell reconstruction in an entire small animal organ.

Tissue optical clearing and expanding solution for improved nuclear segmentation

AbstractOver the recent years, fluorescence microscopy has seen substantial progress, transitioning from primarily qualitative analysis to a profoundly quantitative methodology, yet limitations in imaging depth and data quality persist due to tissue opacity. Tissue optical clearing (TOC) methodologies were implemented to overcome this hurdle, enabling the imaging and quantitative analysis of large tissue samples such as entire murine organs. Further improvements, including expansion microscopy merge TOC benefits with improved imaging resolution, converting cells and tissues into tissue‒gel hybrids. Yet, its intricate protocols lead to a remarkable, ∼10‒20× tissue volume expansion, making the acquisition of even thin sections exceedingly challenging in terms of time, labor, and data handling. Here, we present a novel solution, Improved Segmentation by gEntle Expansion (ISEE), for both TOC and gentle (1.6‒1.7×) tissue expansion for significantly improved precision of fluorescent signal segmentation, while maintaining tolerable increase during data acquisition in everyday laboratory practice. When applied to thick ∼40‒200 µm tissue slices, ISEE renders them transparent and ultimately expanded within minutes, in a simple, one‐step process compatible with immunohistochemistry as well as with all major murine organs.

3D multiscale characterization of the human placenta: Bridging anatomy and histology by X-ray phase-contrast tomography.

The human placenta exhibits a complex three-dimensional (3D) structure with a interpenetrating vascular tree and large internal interfacial area. In a unique and yet insufficiently explored way, this parenchymal structure enables its multiple functions as a respiratory, renal, and gastrointestinal multiorgan. The histopathological states are highly correlated with complications and health issues of mother, and fetus or newborn. Macroscopic and microscopic examination has so far been challenging to reconcile on the entire organ. Here we show that anatomical and histological scales can be bridged with the advent of hierarchical phase-contrast tomography and highly brilliant synchrotron radiation. To this end, we are exploiting the new capabilities offered by the BM18 beamline at ESRF, Grenoble for whole organ as well as the coherence beamline P10 at DESY, Hamburg for high-resolution, creating unique multiscale datasets. We also show that within certain limits, translation to μCT instrumentation for 3D placenta examination becomes possible based on advanced preparation and CT protocols, while segmentation of the datasets by machine learning now remains the biggest challenge.

Recording Lineage History with Cellular Barcodes in the Mammary Epithelium and in Breast Cancer.

Lineage tracing methods have extensively advanced our understanding of physiological cell behaviour in vivo and in situ and have vastly contributed to decipher the phylogeny and cellular hierarchies during normal and tumour development. In recent years, increasingly complex systems have been developed to track thousands of cells within a given tissue or even entire organisms. Cellular barcoding comprises all techniques designed to genetically label single cells with unique DNA sequences or with a combination of fluorescent proteins, in order to trace their history and lineage production in space and time. We distinguish these two types of cellular barcoding as genetic or optical barcodes. Furthermore, transcribed cellular barcodes can integrate the lineage information with single-cell profiling of each barcoded cell. This enables the potential identification of specific markers or signalling pathways defining distinct stem cell states during development, but also signals promoting tumour growth and metastasis or conferring therapy resistance.In this chapter, we describe recent advances in cellular barcoding technologies and outline experimental and computational challenges. We discuss the biological questions that can be addressed using single-cell dynamic lineage tracing, with a focus on the study of cellular hierarchies in the mammary epithelium and in breast cancer.

Structural biology inside multicellular specimens using electron cryotomography.

The electron cryomicroscopy (cryo-EM) resolution revolution has shifted structural biology into a new era, enabling the routine structure determination of macromolecular complexes at an unprecedented rate. Building on this, electron cryotomography (cryo-ET) offers the potential to visualise the native three-dimensional organisation of biological specimens, from cells to tissues and even entire organisms. Despite this huge potential, the study of tissue-like multicellular specimens via cryo-ET still presents numerous challenges, wherein many steps in the workflow are being developed or in urgent need of improvement. In this review, we outline the latest techniques currently utilised for in situ imaging of multicellular specimens, while clearly enumerating their associated limitations. We consider every step in typical workflows employed by various laboratories, including sample preparation, data collection and image analysis, to highlight recent progress and showcase prominent success stories. By considering the entire structural biology workflow for multicellular specimens, we identify which future exciting developments in hardware and software could enable comprehensive in situ structural biology investigations, bringing forth a new age of discovery in molecular structural and cell biology.

Ultrasmall metal nanoclusters as efficient luminescent probes for bioimaging.

Ultrasmall metal nanoclusters (NCs, <2 nm) have emerged as a novel class of luminescent probes due to their atomically precise size and tailored physicochemical properties. The rapid advancements in the design and utilization of metal NC-based luminescent probes are facilitated by the atomic-level manipulation of metal NCs. This review article explores (i) the engineering of metal NCs' functions for bioimaging applications, and (ii) the diverse uses of metal NCs in bioimaging. We begin by presenting an overview of the engineering functions of metal NCs as luminescent probes for bioimaging applications, highlighting key strategies for enhancing NCs' luminescence, biocompatibility and targeting capabilities towards biological specimens. Our discussion then centers on the bioimaging applications of metal NCs in subcellular organelles, individual cells, tissues, and entire organs. Finally, we offer a perspective on the challenges and potential developments in the future use of metal NCs for bioimaging applications.

Navigating the complex role of senescence in liver disease.

Cellular senescence, an irreversible state of cell cycle arrest characterized by phenotypic changes and a specific secretory profile, plays a dual role in liver health and disease. Under physiological conditions, senescence aids organ repair and regeneration, but its accumulation due to aging or pathological stress significantly contributes to chronic liver diseases, including alcoholic liver disease, metabolic dysfunction-associated steatohepatitis, liver fibrosis, and hepatocellular carcinoma. Senescence is identified by a range of cellular and molecular changes, such as morphological alterations, expression of cell cycle inhibitors, senescence-associated β-galactosidase activity, and nuclear membrane changes. The onset of senescence in organ cells can affect the entire organism, primarily through the senescence-associated secretory phenotype, which has autocrine, paracrine, and endocrine effects on tissue microenvironments. The objective of this review is to offer a contemporary overview of the pathophysiological events involving hepatic senescent cells and to elucidate their role in the onset and progression of liver diseases, particularly through mechanisms like telomere shortening, genomic and mitochondrial DNA damage, and inflammation. Additionally, this review discusses the emerging senolytic therapies aimed at targeting senescent cells to delay or mitigate liver disease progression. The therapeutic potential of these interventions, alongside their safety and effectiveness, highlights the need for further research to refine these approaches and address unresolved problems in the field of hepatic cellular senescence.

Изменчивость анатомических характеристик древесины рябины обыкновенной (Sorbus aucuparia L.) в условиях Северного Кавказа

The article presents the results of a study of the structure of the wood of mountain ash (Sorbus aucuparia L.) in the mountains of the North Caucasus. The direction of adaptive changes occurring in the elements of the secondary xylem of the plant at various heights, including extreme ones, is shown. The conclusions of a number of studies have been confirmed that the basic reaction of mountain ash with an increase in altitude and a decrease in growing capacity, as well as an increasе in the intensity of transpiration, is a decrease in plant size and a narrowing of the annual growth of the stem in diameter. At the same time, a number of quantitative changes occur in the wood itself, mainly aimed at optimizing the water-transporting function. With increasing altitude, as water supply conditions become more stringent, maintaining normal water balance is achieved by narrowing the diameters of vessels and increasing their number per unit area. The increase in the total area of the pores occurs due to an increase in the number of narrow, single vessels. The quantitative anatomical changes established during the study are adaptive in nature. In the storage parenchyma of wood, there is an increase in the density and linear dimensions of the rays. The volume of the radial parenchyma at a relatively constant average ply value occurs due to an increase in the height of the cells composing the ray. It is noted that sufficient water balance and enrichment of Sorbus aucuparia wood with living cells of the axial and radial parenchyma increases the viability and plasticity of the entire organism, covers the energy costs for reparation processes, and also stimulates the possibility of vegetative reproduction in conditions unfavorable for seed renewal. A significant range of fluctuations in the quantitative characteristics of mountain ash wood elements increases its adaptive capabilities, helping it to occupy a variety of ecological niches in nature, as evidenced by the wide range of this species.

“Rotting Away Into A Woman”: Castration, Gender and Biological Sex in Late Imperial Fiction

In the aftermath of the Ming-Qing transition, philosopher Tang Zhen 唐甄 (1630–1704) wrote of eunuchs: “If a castrated individual can become a female, then [the eunuch] is acceptable, but if they cannot do this, then they remain a male” 奄若化為女子則可，不然，固男也. Here, Tang suggests the topical question: without sexual potency, does a castrated male become female? And if not, what is to be made of an emasculated male? Due to their perceived part in the dynastic fall of the Ming, eunuchs were a subject of curiosity and unease among Qing scholars like Tang, who began to question the effects of castration upon the male body. Castration, beginning with its earliest usage as a commutation for the death sentence, signaled not only social death but an entrance into the yin 陰, the cosmological force associated with the feminine and counteracted by the masculine yang 陽. Through the removal of the entire sexual organ, the castrated male was removed from Confucian society and sexually neutered in a way that was thought to render him more female than male. Eunuchs, who were also often illiterate, possessed neither sexual or social determiners of masculinity. As my following analysis of fictional Ming-Qing castration narratives will show, the presence of literally or metaphorically castrated men threatened masculine identity. A masculinity that is defined by its opposition to a constructed femininity is necessarily a fragile existence, at all times endangered by a fall into the feminine. Narratives of castration, whether of eunuchs, transformation into the female or male-male relationships, offer a compelling glimpse into late imperial definitions of gender, by illustrating when and how a male body was no longer considered that of a man.

Organ-on-a-Chip Models-New Possibilities in Experimental Science and Disease Modeling.

'Organ-on-a-chip' technology is a promising and rapidly evolving model in biological research. This innovative microfluidic cell culture device was created using a microchip with continuously perfused chambers, populated by living cells arranged to replicate physiological processes at the tissue and organ levels. By consolidating multicellular structures, tissue-tissue interfaces, and physicochemical microenvironments, these microchips can replicate key organ functions. They also enable the high-resolution, real-time imaging and analysis of the biochemical, genetic, and metabolic activities of living cells in the functional tissue and organ contexts. This technology can accelerate research into tissue development, organ physiology and disease etiology, therapeutic approaches, and drug testing. It enables the replication of entire organ functions (e.g., liver-on-a-chip, hypothalamus-pituitary-on-a-chip) or the creation of disease models (e.g., amyotrophic lateral sclerosis-on-a-chip, Parkinson's disease-on-a-chip) using specialized microchips and combining them into an integrated functional system. This technology allows for a significant reduction in the number of animals used in experiments, high reproducibility of results, and the possibility of simultaneous use of multiple cell types in a single model. However, its application requires specialized equipment, advanced expertise, and currently incurs high costs. Additionally, achieving the level of standardization needed for commercialization remains a challenge at this stage of development.

Cancer-induced systemic pre-conditioning of distant organs: building a niche for metastatic cells.

From their early genesis, tumour cells integrate with the surrounding normal cells to form an abnormal structure that is tightly integrated with the host organism via blood and lymphatic vessels and even neural associations. Using these connections, emerging cancers send a plethora of mediators that efficiently perturb the entire organism and induce changes in distant tissues. These perturbations serendipitously favour early metastatic establishment by promoting a more favourable tissue environment (niche) that supports the persistence of disseminated tumour cells within a foreign tissue. Because the establishment of early metastatic niches represents a key limiting step for metastasis, the creation of a more suitable pre-conditioned tissue strongly enhances metastatic success. In this Review, we provide an updated view of the mechanisms and mediators of primary tumours described so far that induce a pro-metastatic conditioning of distant organs, which favours early metastatic niche formation. We reflect on the nature of cancer-induced systemic conditioning, considering that non-cancer-dependent perturbations of tissue homeostasis are also able to trigger pro-metastatic conditioning. We argue that a more holistic view of the processes catalysing metastatic progression is needed to identify preventive or therapeutic opportunities.

Light-Modulated Circadian Synaptic Plasticity in the Somatosensory Cortex: Link to Locomotor Activity.

The circadian clock controls various physiological processes, including synaptic function and neuronal activity, affecting the functioning of the entire organism. Light is an important external factor regulating the day-night cycle. This study examined the effects of the circadian clock and light on synaptic plasticity, and explored how locomotor activity contributes to these processes. We analyzed synaptic protein expression and excitatory synapse density in the somatosensory cortex of mice from four groups exposed to different lighting conditions (LD 12:12, DD, LD 16:8, and LL). Locomotor activity was assessed through individual wheel-running monitoring. To explore daily and circadian changes in synaptic proteins, we performed double-immunofluorescence labeling and laser scanning confocal microscopy imaging, targeting three pairs of presynaptic and postsynaptic proteins (Synaptophysin 1/PSD95, Piccolo/Homer 1, Neurexins/PICK1). Excitatory synapse density was evaluated by co-labeling presynaptic and postsynaptic markers. Our results demonstrated that all the analyzed synaptic proteins exhibited circadian regulation modulated by light. Under constant light conditions, only Piccolo and Homer 1 showed rhythmicity. Locomotor activity was also associated with the circadian clock's effects on synaptic proteins, showing a stronger connection to changes in postsynaptic protein levels. Excitatory synapse density peaked during the day/subjective day and exhibited an inverse relationship with locomotor activity. Continued light exposure disrupted cyclic changes in synapse density but kept it consistently elevated. These findings underscore the crucial roles of light and locomotor activity in regulating synaptic plasticity.

Systemic coordination of whole-body tissue remodeling during local regeneration in sea anemones.

The complexity of regeneration extends beyond local wound responses, eliciting systemic processes across the entire organism. However, the functional relevance and coordination of distant molecular processes remain unclear. In the cnidarian Nematostella vectensis, we show that local regeneration triggers a systemic homeostatic response, leading to coordinated whole-body remodeling. Leveraging spatial transcriptomics, endogenous protein tagging, and live imaging, we comprehensively dissect this systemic response at the organismal scale. We identify proteolysis as a critical process driven by both local and systemic upregulation of metalloproteases. We show that metalloproteinase expression levels and activity scale with the extent of tissue loss. This proportional response drives long-range tissue and extracellular matrix movement. Our findings demonstrate the adaptive nature of the systematic response in regeneration, enabling the organism to maintain shape homeostasis while coping with a wide range of injuries.

Individual Pharmacotherapy Management (IPM-II) for Patient and Drug Safety in Polypharmacy via Clinical Electronic Health Record Is Associated with Significant Fall Prevention.

Falls and fractures are emerging as a near-pandemic and major global health concern, placing an enormous burden on ageing patients and public health economies. Despite the high risk of polypharmacy in the elderly patients, falls are usually attributed to age-related changes. For the "Individual Pharmacotherapy Management (IPM)" established at the University Hospital Halle, the IPM medication adjustments and their association with in-hospital fall prevention were analysed. On the basis of the most updated digital overall patient view via his inpatient electronic health record (EHR), IPM adapts each drug's Summary of Product Characteristics to the patient's condition. A retrospective pre-post intervention study in geriatric traumatology on ≥70 years old patients compared 200 patients before IPM implementation (CG) with 204 patients from the IPM intervention period (IG) for the entire medication list, organ, cardiovascular and vital functions and fall risk parameters. Statistically similar baseline data allowed a comparison of the average 80-year-old patient with a mean of 11.1 ± 4.9 (CG) versus 10.4 ± 3.6 (IG) medications. The IPM adjusted for drug-drug interactions, drug-disease interactions, overdoses, anticholinergic burden, adverse drug reactions, esp. from opioids inducing increased intrasynaptic serotonin, psychotropic drugs, benzodiazepines, contraindications and missing prescriptions. IPM was associated with a significant reduction in in-hospital falls from 18 (9%) in CG to 3 (1.5%) in IG, a number needed to treat of 14, relative risk reduction 83%, OR 0.17 [95% CI 0.04; 0.76], p = 0.021 in multivariable regression analysis. Factors associated with falls were antipsychotics, digitoxin, corticosteroids, Würzburg pain drip (combination of tramadol, metamizole, metoclopramide), head injury, cognitive impairment and aspects of the Huhn Fall Risk Scale including urinary catheter. The results indicate medication risks constitute a major iatrogenic cause of falls in this population and support the use of EHR-based IPM in standard care for the prevention of falls in the elderly and for patient and drug safety. In terms of global efforts, IPM contributes to the running WHO and United Nations Decade of Healthy Ageing (2021-2030).

Lament ‘With’ Dear Earth: The Complexity of Hope in the Dynamics of Interemptying and Intergiving1

This study examines the role of religious education in fostering commitments to the health and responsibility of the entire Earth organism, especially in the context of inhabiting a damaged land. It delves into the concept of sympoiesis and the Korean concept of yeomul as a life attitude to respond to Earth’s suffering. This research advocates for lament as an empathetic and epistemological performance that not only emotionally connects with all Earth’s suffering but also fosters a community of mutual engagement. As a part of religious education, preaching is considered a potential catalyst and platform for the practical lament to share knowledge and nurture response-ability.

INFLUENCE OF FLUORIDE ON PUBLIC HEALTH AND WORKER’S HEALTH – LITERATURE REVIEW

Dental caries is a multifactorial disease that affects a large part of the world's population. Can be prevented by various means and methods, including the use of fluoridated mouthwashes, topical fluoride, fluoridated toothpaste and fluoridation of public water supplies for human consumption. Fluoride has been shown to be a therapeutic agent that modulates dental caries. Frequent contact between patients and small concentrations of fluoride hinders demineralization and activates remineralization, in addition to inhibiting cariogenic microorganisms. The oral health of workers is directly related to the health of the population, since they are part of this context and suffer from the same problems that occur in the environment in which they live. Since workers are the agents who convert work activity into profits for the employer, a detailed and complete vision addressing prevention is extremely important, as this is a way to reduce absenteeism and keep workers in their jobs, achieving better performance of their activities. This bibliographic review aims to analyze fluoride in its various forms and evaluate its anti-cariogenic power for workers, with the aim of preventing cavities and providing well-being, quality of life and greater productivity to them. Based on the data analyzed, it is concluded that fluoride is an effective and inexpensive measure to prevent the appearance of cavities and that due to the large size of Brazil and its socioeconomic difficulties, fluoridated toothpaste associated with assisted brushing, with topical fluoride applications, prove to be the best measures to prevent cavities and absenteeism, consequently improving public health indices. This is one of the most relevant public policies, which is in fact underestimated and which can change the reality of Brazil, reducing high government costs and promoting the quality of life of the population, which suffers from oral problems, which can affect the entire organism, causing a series of other ailments, which should be avoided by adopting preventive measures on a permanent basis.