Entire Organism Research Articles

INSP-13. Malignant networks in brain tumors: from basic discoveries to clinical implications

Abstract Integration into communicating tumor cell networks is a way how the entire brain tumor organism can progress in the brain, and resist therapies. It started with our discovery of ultra-long membrane protrusions, tumor microtube (TM), in tumor cells from glioblastomas and other incurable adult and pediatric glioma entities (Osswald et al., Nature 2015). These TMs are used for early brain invasion, and later interconnect single tumor cells to communicating and resistant multicellular networks, but also glioma cells to neurons in the brain, with neuron-glioma synapses stimulating glioma progression (Venkataramani et al., Nature 2019). Increasing formation of these homotypic and heterotypic networks is seen with increasing glioma malignancy: lowest in low-grade oligodendrogliomas, and highest in glioblastomas and K27M mutated gliomas. The genetic reduction of GAP-43, a crucial neurodevelopmental factor that drives TM formation and function, not only deprived glioblastoma cells from the ability to form functional tumor networks, but also made radiotherapy much more effective, by and large eradicating experimental tumors from the mouse brain, which is typically not possible with radiotherapy alone. Consistent with the concept of tumor cell resilience by network integration, radiotherapy and also chemotherapy (Weil et al., Neuro-Oncology 2017) preferentially killed the unconnected glioblastoma cells, leaving the tumor cell networks largely intact. Damage to the tumor network by surgical measures induced a self-healing response. Taken together, integration into multicellular, highly functional, communicating and resilient networks is not only a feature of the nervous system, but also of incurable, most aggressive brain tumors. In this talk, clinical concepts that originate from these discoveries are presented, including a network disconnection strategy currently tested in the German MecMeth trial (EudraCT2021-000708-39), and the AMPAR inhibitor perampanel as a potential inhibitor of neuron-glioma synapses. Furthermore, new basic and translational developments in the field of brain tumor networks are presented and discussed.

Melatonin as an Anti-Aging Therapy for Age-Related Cardiovascular and Neurodegenerative Diseases.

The concept of “aging” is defined as the set of gradual and progressive changes in an organism that leads to an increased risk of weakness, disease, and death. This process may occur at the cellular and organ level, as well as in the entire organism of any living being. During aging, there is a decrease in biological functions and in the ability to adapt to metabolic stress. General effects of aging include mitochondrial, cellular, and organic dysfunction, immune impairment or inflammaging, oxidative stress, cognitive and cardiovascular alterations, among others. Therefore, one of the main harmful consequences of aging is the development and progression of multiple diseases related to these processes, especially at the cardiovascular and central nervous system levels. Both cardiovascular and neurodegenerative pathologies are highly disabling and, in many cases, lethal. In this context, melatonin, an endogenous compound naturally synthesized not only by the pineal gland but also by many cell types, may have a key role in the modulation of multiple mechanisms associated with aging. Additionally, this indoleamine is also a therapeutic agent, which may be administered exogenously with a high degree of safety. For this reason, melatonin could become an attractive and low-cost alternative for slowing the processes of aging and its associated diseases, including cardiovascular and neurodegenerative disorders.

THE PRESENCE OF ANTIOXIDANTS IN THE HAIR INFUNDIBULUM IMPLICATIONS IN HAIR DISEASES SUCH AS ALOPECIA

Anatomically, as a rule the hairs in mammals consists of an unseen follicle or root anchored into the skin with a shaft or visible hair exiting exteriorly. As a note of interest, the hair follicle has been described as a miniorgan having its own cells division, metabolism and aging stages (1). As previously stated “metabolism entails electron transfers in both plants (photosynthesis) and animals (cellular respiration) involving movement of electrons from donor to acceptor along the electron transfer chain thus inducing a current within each cell and from cell to cell” (2,3). This continuity of energy transfer in living organisms is at the very essence of life; and is ubiquitously present in all living matter and the generator of Bioelectricity (a.k.a. electromagnetic radiation), the protein enzyme catalase having an essential pivotal role in energy production in the breakdown of toxic materials such as H2O2 into H2O and O2 molecules. During the breakdown of O2 molecules energy is generated. When catalase is depleted life ends and regional death occurs (4,5). We could then theorize that if cell respiration ceases throughout the entire organism (organs) death ensues (6). Only in living tissue is that elimination of toxic material such as H2O2 has any relevance.

As Data Flows Surge Data Infrastructure Groans

As Data Flows Surge Data Infrastructure Groans

New clearing protocol for tannic roots optical imaging.

The understanding of plant physiological complexity requires 3D imaging of the entire organ with subcellular resolution. However, most plant organs are highly opaque to light and their study under optical sectioning microscopes is difficult. By gathering the latest developments in the field of optical clearing of pigmented plant tissues, it was found that the clearing tannic roots (CTR) protocol drastically reduces light absorption by a depigmentation step and light scattering by the homogenisation of refractive indices through entire grapevine roots.

On genome editing in embryos and cells of the freshwater prawn Macrobrachium rosenbergii

The clustered regularly interspaced short palindromic repeats (CRISPR) technology provides the means for accurate genomic editing. It has been applied in many kinds of cells and animals for functional genomic studies and for precise selective breeding. Nonetheless, this method has not yet been applied in one of the most important – and well studied – decapod crustacean aquaculture species, the giant freshwater prawn Macrobrachium rosenbergii. We thus established two CRISPR platforms for M. rosenbergii—the first through direct injection into early-stage embryos (entire organism genome editing) and the second by electroporation of a primary embryonic cell culture. The systems were calibrated by optimizing Cas9 concentrations, delivery methods and editing efficiencies. Editing patterns utilizing multiple guides were examined through next generation sequencing. Our results showed a wide range of editing efficiencies in embryos, in some cases reaching as high as 100%. In contrast, in primary embryonic cell cultures, the highest editing efficiency obtained reached a maximum of 64%. In addition, there was a striking difference between the two platforms in terms of the pattern of deletions around the Cas9 cut site. This finding suggests distinct repair mechanisms in the two systems, which calls for further clarification. A phenotypic proof of concept was provided through the investigation of an early acting paired box protein 6 (Pax6) transcription factor, which showed clear effects on eye development in edited embryos and larvae. The current study lays down the foundations for precise functional genomic research and applications of genome editing in crustacean species for both aquaculture and sustainable biocontrol, opening opportunities for the creation of selected crustacean lines with distinct attributes.

Hepatic Hedgehog Signaling Participates in the Crosstalk between Liver and Adipose Tissue in Mice by Regulating FGF21.

The Hedgehog signaling pathway regulates many processes during embryogenesis and the homeostasis of adult organs. Recent data suggest that central metabolic processes and signaling cascades in the liver are controlled by the Hedgehog pathway and that changes in hepatic Hedgehog activity also affect peripheral tissues, such as the reproductive organs in females. Here, we show that hepatocyte-specific deletion of the Hedgehog pathway is associated with the dramatic expansion of adipose tissue in mice, the overall phenotype of which does not correspond to the classical outcome of insulin resistance-associated diabetes type 2 obesity. Rather, we show that alterations in the Hedgehog signaling pathway in the liver lead to a metabolic phenotype that is resembling metabolically healthy obesity. Mechanistically, we identified an indirect influence on the hepatic secretion of the fibroblast growth factor 21, which is regulated by a series of signaling cascades that are directly transcriptionally linked to the activity of the Hedgehog transcription factor GLI1. The results of this study impressively show that the metabolic balance of the entire organism is maintained via the activity of morphogenic signaling pathways, such as the Hedgehog cascade. Obviously, several pathways are orchestrated to facilitate liver metabolic status to peripheral organs, such as adipose tissue.

FIRM: Flexible integration of single-cell RNA-sequencing data for large-scale multi-tissue cell atlas datasets.

Single-cell RNA-sequencing (scRNA-seq) is being used extensively to measure the mRNA expression of individual cells from deconstructed tissues, organs and even entire organisms to generate cell atlas references, leading to discoveries of novel cell types and deeper insight into biological trajectories. These massive datasets are usually collected from many samples using different scRNA-seq technology platforms, including the popular SMART-Seq2 (SS2) and 10X platforms. Inherent heterogeneities between platforms, tissues and other batch effects make scRNA-seq data difficult to compare and integrate, especially in large-scale cell atlas efforts; yet, accurate integration is essential for gaining deeper insights into cell biology. We present FIRM, a re-scaling algorithm which accounts for the effects of cell type compositions, and achieve accurate integration of scRNA-seq datasets across multiple tissue types, platforms and experimental batches. Compared with existing state-of-the-art integration methods, FIRM provides accurate mixing of shared cell type identities and superior preservation of original structure without overcorrection, generating robust integrated datasets for downstream exploration and analysis. FIRM is also a facile way to transfer cell type labels and annotations from one dataset to another, making it a reliable and versatile tool for scRNA-seq analysis, especially for cell atlas data integration.

3D molecular phenotyping of cleared human brain tissues with light-sheet fluorescence microscopy

The combination of optical tissue transparency with immunofluorescence allows the molecular characterization of biological tissues in 3D. However, adult human organs are particularly challenging to become transparent because of the autofluorescence contributions of aged tissues. To meet this challenge, we optimized SHORT (SWITCH—H2O2—antigen Retrieval—TDE), a procedure based on standard histological treatments in combination with a refined clearing procedure to clear and label portions of the human brain. 3D histological characterization with multiple molecules is performed on cleared samples with a combination of multi-colors and multi-rounds labeling. By performing fast 3D imaging of the samples with a custom-made inverted light-sheet fluorescence microscope (LSFM), we reveal fine details of intact human brain slabs at subcellular resolution. Overall, we proposed a scalable and versatile technology that in combination with LSFM allows mapping the cellular and molecular architecture of the human brain, paving the way to reconstruct the entire organ.

The response of geophytes to continuous human foraging on the Cape south coast, South Africa and its implications for early hunter-gatherer mobility patterns.

Current ecological understanding of plants with underground storage organs (USOs) suggests they have, in general, low rates of recruitment and thus as a resource it should be rapidly exhausted, which likely had implications for hunter-gatherer mobility patterns. We focus on the resilience (defined here as the ability of species to persist after being harvested) of USOs to human foraging. Human foragers harvested all visible USO material from 19 plots spread across six Cape south coast (South Africa) vegetation types for three consecutive years (2015–2017) during the period of peak USO apparency (September–October). We expected the plots to be depleted after the first year of harvesting since the entire storage organ of the USO is removed during foraging, i.e. immediate and substantial declines from the first to the second harvest. However, over 50% of the total weight harvested in 2015 was harvested in 2016 and 2017; only after two consecutive years of harvesting, was there evidence of significantly lower yield (p = 0.034) than the first (2015) harvest. Novel emergence of new species and new individuals in year two and three buffered the decline of harvested USOs. We use our findings to make predictions on hunter-gatherer mobility patterns in this region compared to the Hadza in East Africa and the Alyawara in North Australia.

Tissue Engineering for the Diaphragm and its Various Therapeutic Possibilities – A Systematic Review

AbstractDiaphragmatic impairments exhibit high morbidity as well as mortality while current treatment options remain unsatisfactory. Tissue engineering (TE) approaches have explored the generation of an optimal biocompatible scaffold for diaphragmatic repair through tissue decellularization or de novo construction, with or without the addition of cells. The authors conducted a systematic review on the current state of the art in diaphragmatic tissue engineering (DTE) and found 24 articles eligible for final synthesis. The included approaches studied decellularization‐based graft generation (9) and de novo bioscaffold construction (9). Three studies focused on in vitro host‐scaffold interaction with synthesized, recellularized grafts (2) and decellularized extracellular matrix scaffolds (1). Another three studies investigated evaluation tools for decellularization efficacy. Among all studies, recellularization is performed in both decellularization‐based (4) and de novo generated scaffolds (4). De novo constructed biocomposites as well as decellularized and recellularized scaffolds induced pro‐regenerative remodeling and recovery of diaphragmatic function in all examined animal models. Potential therapeutic applications comprise substance defects requiring patch repair, such as congenital diaphragmatic hernia, and functional diseases demanding an entire organ transplant, like muscular dystrophies or dysfunction after prolonged artificial respiration.

Ayurvedic Management of Cholelithiasis - A Case Study

Cholelithiasis (gallstone formation) is a common Gastrointestinal disorder. The disease Cholelithiasis has not been described directly in Ayurvedic classics. The word Ashmari is described only in the context of Ashmari (urinary calculi). Surgery is the most common form of treatment for gall stones, however the fact that surgically removing gallstones requires the removal of an entire organ has led to a growing interest in non-surgical treatment. But so far as the medical management of gall stone is concerned, it is not up to the mark in allopathic system. Hence our article is a step in the direction of making an availability of a safe and effective non-surgical management of Cholelithiasis. A 35-year-old female patient reported to OPD Bangalore, with the complaints of severe pain abdomen, anorexia, distension of abdomen and vomiting. The patient was diagnosed as cholelithiasis with physical symptoms and with the help of all investigation. Oral medications like Arogyavardini vati, Varunadi Kashaya, Yavakshara and Katuki Churna was administered to the patient for 1 month and follow up was done after 3 months of treatment, a significant response was observed over clinical symptoms and USG reports

Normal Macroscopic, Morphological, and Morphometric Parameters of the Esophagus of Whiterats

Histological methods of analysis of the morphofunctional status of the esophagus are widely used in the diagnosis and differential diagnosis of diseases of the gastrointestinal tract of various etiologies. However, their results do not always reflect the disruption of the entire organ structure. All this together increases the interest of researchers in the application of new methods of assessing esophageal pathology, which may be associated with microscopic evaluation of criteria for changes in esophageal pathomorphological structures, several anti-inflammatory agents, i.e. help detect changes in polypragmasic state. Therefore, macroscopic and microscopic studies of white esophageal rat esophagus were aimed at studying the normal data of esophageal tissue and comparing them with pathological processes, and 12 white non-white rat esophageal macroscopic and microscopic studies were performed.

Neuron quantum computers and a way to unification of science: A compendium of Efim Liberman's scientific work

In 1972, Efim Liberman, a Soviet biophysicist, pioneered a brand-new approach to studying the operation of the brain, the live cell and the human mind by publishing a paper titled “Cell as a molecular computer” (1972). In this paper, Liberman posited that a consecutive/parallel stochastic molecular computer (MCC) controls a living cell. An MCC operates with molecule-words (DNA, RNA, proteins) according to the program recorded in DNA and RNA. Computational operations are implemented by molecular operators acting as enzymes. An MCC is present in each live cell. A neuron cell MCC can be involved in solving tasks for the entire organism. Neuron MCC investigation was started with studying an impact of an intracellular injection of cyclic AMP on electric activity of a neuron. Cyclic nucleotides were considered as input words for an MCC, which are generated inside a neuron as a result of synaptic activity. This led Efim Liberman to the idea that, in order to solve complex physical problems, which are encountered by a neuron and require rapid solutions, the molecular computer adjusts the operation of the quantum molecular regulator, which uses the “computational environment” of the cytoskeleton and quantum properties of the elementary hypersound quasiparticles for completing mathematical operations for the minimum price of action. Efim Liberman suggested that the human self-consciousness is a quantum computer of even a higher level and designated it as an extreme quantum regulator. In order to describe such systems, he suggested to join biology, physics and mathematics into a unified science, and formulated its four fundamental principles. Results of Efim Liberman’s theoretical and experimental studies on the topic of biological computation are summarized in this review.

Influence of B vitamins on the development of lesions typical of rosacea

Rosacea is a chronic inflammatory disease characterized by erythema and inflammatory maculopapular lesions. Its cause may be a number of endogenous factors, such as improper functioning of the immune system, genetic predisposition, or vascular disorders, but also external stimuli, such as medications, and dietary supplements, including vitamins. The aim of the article is to describe the effect of B vitamins on the skin and the entire organism, as well as their possible negative impact on the development of lesions typical of rosacea.

Dermatokinetics: Advances and Experimental Models, Focus on Skin Metabolism

Numerous dermal contact products, such as drugs or cosmetics, are applied on the skin, the first protective barrier to their entrance into the organism. These products contain various xenobiotic molecules that can penetrate the viable epidermis. Many studies have shown that keratinocyte metabolism could affect their behavior by biotransformation. While aiming for detoxification, toxic metabolites can be produced. These metabolites may react with biological macromolecules often leading to sensitization reactions. After passing through the epidermis, xenobiotics can reach the vascularized dermis and therefore, be bioavailable and distributed into the entire organism. To highlight these mechanisms, dermatokinetics, based on the concept of pharmacokinetics, has been developed recently. It provides information on the action of xenobiotics that penetrate the organism through the dermal route. The purpose of this review is first to describe and synthesize the dermatokinetics mechanisms to consider when assessing the absorption of a xenobiotic through the skin. We focus on skin absorption and specifically on skin metabolism, the two main processes involved in dermatokinetics. In addition, experimental models and methods to assess dermatokinetics are described and discussed to select the most relevant method when evaluating, in a specific context, dermatokinetics parameters of a xenobiotic. We also discuss the limits of this approach as it is notably used for risk assessment in the industry where scenario studies generally focus only on one xenobiotic and do not consider interactions with the rest of the exposome. The hypothesis of adverse effects due to the combination of chemical substances in contact with individuals and not to a single molecule, is being increasingly studied and embraced in the scientific community.

Atomic Force Microscopy to Study the Physical Properties of Epidermal Cells of Live Arabidopsis Roots.

A method is described here to characterize the physical properties of the cell wall of epidermal cells of living Arabidopsis roots through nanoindentations with an atomic force microscope (AFM) coupled with an optical inverted fluorescence microscope. The method consists of applying controlled forces to the sample while measuring its deformation, allowing quantifying parameters such as the apparent Young's modulus of cell walls at subcellular resolutions. It requires a careful mechanical immobilization of the sample and correct selection of indenters and indentation depths. Although it can be used only in external tissues, this method allows characterizing mechanical changes in plant cell walls during development and enables the correlation of these microscopic changes with the growth of an entire organ.

In silico designed Staphylococcus aureus B-cell multi-epitope vaccine did not elicit antibodies against target antigens suggesting multi-domain approach

The vaccine development strategies have evolved from using an entire organism as an immunogen to a single antigen and further towards an epitope. Since an epitope is a relatively tiny and immunologically relevant part of an antigen, it has the potential to stimulate more robust and specific immune responses while causing minimal adverse effects. As a result, the recent focus of vaccine development has been to develop multi-epitope vaccines that can target multiple virulence mechanisms. Accordingly, we designed multi-epitope vaccine candidates B (multi-B-cell epitope immunogen) and CTB-B (an adjuvant – cholera toxin subunit B (CTB) – attached to immunogen B) against S. aureus by employing immunoinformatics approaches. The designed vaccines are composed of B-cell epitope segments (20-mer) of the eight well-characterized S. aureus virulence factors, namely ClfB, FnbpA, Hla, IsdA, IsdB, LukE, SdrD, and SdrE connected in series. The designed vaccines were expressed, purified, and administered to C57BL/6 mice with Freund adjuvant to evaluate the immunogenicity and protective efficacy. The results revealed that the immunized mice showed high IgG titers for the immunogen, and the antibody titers increased significantly following the second immunization. However, the generated antibodies did not protect the mice from infection. The interaction of anti-B antibodies with source virulence factors showed that the generated antibodies have no binding affinity with any of the corresponding virulence factors. Our results demonstrate the limitation of the in silico designed B-cell multi-epitope vaccine and suggest that a protein domain carrying both linear and conformational B-cell epitopes might be a better choice for developing an effective multi-epitope vaccine against S. aureus.

Unraveling the sorghum domestication

Sorghum, the fifth major cereal crop, was domesticated in Africa and expanded globally. As with many other crops, this process can be generally separated into two stages: the first stage from wild ancestors to landraces, and the second stage from landraces to improved cultivars. Through domestication and crop improvement, sorghum has been selected to meet various human needs. Domesticated sorghum is typically classified into five races: bicolor, guinea, durra, caudatum, and kafir. It can be also classified by end uses: grain sorghum for seeds from panicles, sweet sorghum for sugar from stems, forage sorghum for biomass from entire above-ground organs, and broom sorghum for long and stiff primary branches from panicles (Council, 1996; Smith and Frederiksen, 2000) (Figure 1).

Single-cell genomics revolutionizes plant development studies across scales.

Understanding the development of tissues, organs and entire organisms through the lens of single-cell genomics has revolutionized developmental biology. Although single-cell transcriptomics has been pioneered in animal systems, from an experimental perspective, plant development holds some distinct advantages: cells do not migrate in relation to one another, and new organ formation (of leaves, roots, flowers, etc.) continues post-embryonically from persistent stem cell populations known as meristems. For a time, plant studies lagged behind animal or cell culture-based, single-cell approaches, largely owing to the difficulty in dissociating plant cells from their rigid cell walls. Recent intensive development of single-cell and single-nucleus isolation techniques across plant species has opened up a wide range of experimental approaches. This has produced a rapidly expanding diversity of information across tissue types and species, concomitant with the creative development of methods. In this brief Spotlight, we highlight some of the technical developments and how they have led to profiling single-cell genomics in various plant organs. We also emphasize the contribution of single-cell genomics in revealing developmental trajectories among different cell types within plant organs. Furthermore, we present efforts toward comparative analysis of tissues and organs at a single-cell level. Single-cell genomics is beginning to generate comprehensive information relating to how plant organs emerge from stem cell populations.