Sub-cellular biochemistry最新文献

The definitive diagnosis of human prion diseases can only be obtained postmortem by combining clinical symptoms, neuropathology and PrP immunohistochemistry, Western blotting of PrP types, zygosity of codon 129, and genetic study of PRNP. Premortem diagnosis is strongly sustained by one positive prion-specific assay, commonly protein misfolded cyclic amplification (PMCA) or real-time quaking-induced conversion (RT-QuIC), principally in CSF samples. Surrogate biomarkers 14-3-3, t-tau, P-tau, βA4, and total-PrP levels in the CSF help discriminate other neurodegenerative diseases, but their sensitivity and specificity are variable depending on the prion disease. Other altered proteins in the CSF, such as neurofilament light chain (NfL), calcium-binding protein S100β, neuron-specific enolase, α-synuclein and β-synuclein, neurogranin and SNAP-25, triggering receptor expressed on myeloid cells 2 (TREM2), cytokines, astroglial markers, and microRNAs, need further validation. Total-tau and NfL levels in the blood may serve to monitor disease progression, whereas the value of total-PrP, synuclein, S100β, TREM2, and peripheral inflammatory markers in the blood is limited. Since the products of positive PMCA and PrP^Sc are present in several tissues in CJD, special care and biosafety conditions must be applied in managing and processing human biological samples of suspected prion disease. Regarding RT-QuIC products, further experimental studies are needed to elucidate their seeding capacity.

Lamins are essential for maintaining the mechanical stability of the nucleus and organizing chromatin. B-type lamins are expressed early in embryogenesis, particularly in the central nervous system, where they are crucial for development. In contrast, A-type lamins are predominantly expressed in differentiated cells and are vital for maintaining nuclear stability and chromatin organization. These differences likely account for the distinct clinical characteristics of B-type and A-type laminopathies: B-type laminopathies primarily affect the central nervous system, whereas A-type laminopathies are mainly associated with metabolic dysfunction, cardiopathies, and premature aging.In this chapter, we explore the broad and heterogeneous group of diseases caused by lamin alterations, detailing the genetic basis of laminopathies, their clinical manifestations, and the current state of research. We also discuss clinical management strategies and the role of chromatin organization in the pathophysiology of these diseases. Finally, we examine the variations in A- and B-type lamin expression in cancer.

Lamin proteins, predominantly located near the nuclear lamina, are known to play an important role in maintaining large-scale genome organisation. Disruptions in lamin assembly have been implicated in various diseases exhibiting altered chromatin organisation, nuclear stiffness and chromosome dynamics. Theoretical and computational modelling is essential for understanding these diverse observations through the lens of physical forces and interactions. This review focuses on modelling efforts aimed at elucidating the multifaceted role of lamins in genome organisation and how disruptions in these interactions contribute to the pathologies observed in different cell types, disease conditions and lamin mutants. We categorise the major modelling approaches used to study lamin-mediated chromatin organisation, summarise key findings within each category and highlight future directions in developing a comprehensive understanding of the role of lamins in the spatial organisation of the genome.

Macromolecular crowding affects many areas, including protein folding, binding of small molecules, enzymatic activity, interaction with nucleic acids, protein aggregation, and protein-protein interactions. While the common belief has been that the primary impact of crowded environments on the function, structure, thermodynamics, and aggregation of a protein can be described in terms of excluded volume effects, it has now become clear that other factors, which originate from high concentrations of "inert" macromolecules in crowded solution, must be considered in order to get a clearer understanding a protein's behavior in a crowded environment. This review will highlight several important factors that arise in a crowded environment, including perturbed diffusion, viscosity, soft interactions, direct physical interactions between the crowding agents and proteins, and, most importantly, the effects of crowders on solvent properties.

Dynamic and thermodynamic properties of RNA molecules vary across different cellular locations through multiple environmental factors, such as excluded volume interactions of cellular substances, alteration of the physical properties of the surrounding medium, and binding interactions with cellular substances. These environmental factors modulate the energy landscape of RNA transitions, thereby consideration of the effects of the intracellular environment on molecular interactions contributing to RNA folding and RNA-protein complexation is important for understanding RNA structures and their interactions in living cells. This chapter describes the dynamics and interactions of several RNA structures, including functional RNAs such as aptamers and ribozymes, in the environment of molecular crowding, revealed by in-cell, in silico, and in vitro studies. Specifically, in vitro model studies that have used cell-mimicking solutions comprising cellular substances or artificial molecular crowding agents have enhanced our understanding of RNA interactions and their molecular functions under molecular crowding conditions and increased our ability to predict RNA structures in cells. This chapter also provides an overview of the comparison between RNA and DNA interactions because the effects of the environmental factors on DNA are similar to those on RNA.

Molecular crowding plays a crucial role in biological and medicinal systems, impacting the structure, behavior, and function of biomolecules within the densely packed environments of cells. This chapter provides an overview of the implications of molecular crowding, exploring how the high concentration of macromolecules such as proteins, nucleic acids, and other biological entities impacts biochemical reactions and cellular processes. The discussion highlights the challenges associated with experimental studies of molecular crowding, including challenges in creating accurate in vitro models, controlling concentrations, and isolating crowding effects from other interactions. To address these challenges, the chapter emphasizes the importance of computational techniques. Various computational approaches, including molecular dynamics simulations, Monte Carlo simulations, Brownian dynamics, lattice-models, finite element analysis, coarse-grained modeling, quantum mechanics/molecular mechanics simulations, and multi-scale modeling, are discussed in detail. Each of these techniques contributes unique insights into the molecular-level impacts of crowding, enhancing our understanding of biophysical processes critical for therapeutic development and biological function. The chapter discusses also quantum computing, machine learning and classical simulations hybrid approaches for future directions around molecular crowding studies.

To study macromolecular crowding (MC) in living cells, one needs a method to measure it. Several existing approaches to quantify MC address slightly different aspects of crowding. If we define MC through protein concentration, it can be measured by quantitative phase imaging coupled with volume determination; both can be realized on a standard bright-field microscope. Osmotic cell theory can help identify the essential factors that control MC. Nevertheless, there are still many gaps in our understanding of MC regulation and, in particular, of the interrelationship between MC and cell stress or damage. Experiments show that MC is subject to homeostatic control and returns to its resting values following various disturbances. Severe cell damage causes an accumulation of water and a decrease in MC; however, based on limited data, water accumulation is restricted to one area of the cell (necrotic bleb), while the rest of the cell remains at normal density. Similar heterogeneous water distribution is observed in vacuolated mammalian cells. Intermediate degrees of stress tend to produce dehydration and an increase in MC. Apoptotic shrinkage is one common example of stress-induced dehydration, but the effect may be more general. A hypothesis on its mechanism is proposed.

Epigenetic mechanisms are key processes that constantly reshape genome activity carrying out physiological responses to environmental stimuli. Such mechanisms regulate gene activity without modifying the DNA sequence, providing real-time adaptation to changing environmental conditions. Both favorable and unfavorable lifestyles have been shown to influence body and brain by means of epigenetics, leaving marks on the genome that can either be rapidly reversed or persist in time and even be transmitted trans-generationally. Among virtuous habits, meditation seemingly represents a valuable way of activating inner resources to cope with adverse experiences. While unhealthy habits, stress, and traumatic early-life events may favor the onset of diseases linked to inflammation, neuroinflammation, and neuroendocrine dysregulation, the practice of mindfulness-based techniques was associated with the alleviation of many of the above symptoms, underlying the importance of lifestyles for health and well-being. Meditation influences brain and body systemwide, eliciting structural/morphological changes as well as modulating the levels of circulating factors and the expression of genes linked to the HPA axis and the immune and neuroimmune systems. The current chapter intends to give an overview of pioneering research showing how meditation can promote health through epigenetics, by reshaping the profiles of the three main epigenetic markers, namely DNA methylation, histone modifications, and non-coding RNAs.

Urea transporters (UTs) are a group of membrane channel proteins that specifically facilitate the permeation of urea, from bacteria to mammals, playing an essential role in urea reabsorption and water conservation. In mammals, there are two subfamilies of UT: the UT-A group originally isolated from the kidney inner medulla, and UT-B originally isolated from erythrocytes. The human UT-B gene (Slc14a1) arises from a single locus located on chromosome 18q12.1-q21.1, which is close to the UT-A gene (Slc14a2). The human Slc14a1 gene includes 11 exons, with the coding region extending from exon 4 to exon 11, and is approximately 30 kb in length. The rat Slc14a2 gene is very large, containing 24 exons, approximately 300 kb in length, and encodes 6 different isoforms. The Slc14a2 gene has two promoter elements: promoter I, located upstream of exon 1, drives the transcription of UT-A1, UT-A1b, UT-A3, UT-A3b, and UT-A4; promoter II, located within intron 12, drives the transcription of UT-A2 and UT-A2b. This chapter will summarize the evolution and genetic characteristics of UTs.

Rapid urea permeation mediated by urea transporters (UTs) is crucial for maintaining normal physiological processes in organisms. UTs not only facilitate urea transport but also water transport, further underscoring their role in maintaining fluid balance. Advances in structural biology have led to the elucidation of high-resolution three-dimensional structures of various UTs, offering critical insights into the molecular mechanisms underlying their efficiency in transporting urea and water. UT-B displays high permeability to urea analogs, which can competitively inhibit urea permeation by obstructing the channel. However, whether UT-A is capable of transporting urea analogs remains contentious. Additionally, further investigation is required to determine if UTs can facilitate ammonia transport. Urea permeability (P_urea) in erythrocytes differs between different mammals. Carnivores exhibit high P_urea. In contrast, herbivores show much lower P_urea. Erythrocyte P_urea in omnivores was intermediate. Rodents and lagomorphs have P_urea intermediate between carnivores and omnivores. This chapter provides information about the transporter characteristics of UTs.