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Topic Review
Remodeler Catalyzed Nucleosome Repositioning
The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell's DNA metabolism machinery.  Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified.  One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes.  Here we review recent work on the nucleosome mobilization activity of this essential family of molecular machines.
  • 1.3K
  • 08 Jan 2021
Topic Review
FT-IR Spectroscopy Studies of Sphingolipids in Human Cells
Sphingolipids have attracted significant attention due to their pivotal role in cellular functions and physiological diseases. A valuable tool for investigating the characteristics of sphingolipids can be represented via Fourier-transform infrared (FT-IR) spectroscopy, generally recognized as a very powerful technique that provides detailed biochemical information on the examined sample with the unique properties of sensitivity and accuracy.
  • 1.3K
  • 06 Apr 2023
Topic Review
Uses of Magnetic Fields for Health Applications
Early life on Earth evolved in the contexts of temperature, available elements, and molecules (including water), as well as the biophysical boundary conditions of the planet. The latter include gravity (1 g), exogenous and endogenous radiation from particles from beyond Earth and radioactive elements on Earth, and magnetic fields due to the planet’s magnetic field and local concentrations of molecules such as iron. Humans and other animals, plants, and microorganisms have been exposed to a variety of magnetic fields other than the geomagnetic field of Earth and deposits of ferro materials. Magnetic fields, static or electromagnetic, have been used in attempts to improve outcomes for the repair of a variety of tissues.
  • 1.2K
  • 19 Jun 2024
Topic Review
Non-Equilibrium Thermodynamics and Psychology in Biological Aging
In humans, biological aging (age-associated degrading changes), widely observed in molecular and cellular processes, underly the time-dependent decline in spatial navigation, time perception, cognitive and psychological abilities, and memory. Cross-talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, genome, proteome, and lipidome instability are widely recognized as the primary causal factors in aging. Through stress response systems (SRS), the environmental and psychological stressors contribute to the age-associated “collapse” of protein homochirality. The role of prevalent protein chirality and entropy of protein folding in biological aging is mainly overlooked. In a more generalized context, the time-dependent shift from enzymatic to the nonenzymatic transformation of biochirality might represent an important and yet underappreciated hallmark of aging. We provide the experimental arguments in support of the racemization theory of aging.
  • 1.2K
  • 17 Jan 2022
Topic Review
Protein One-Dimensional Sliding
One-dimensional (1D) sliding of DNA-binding proteins has been observed by numerous kinetic studies. It appears that many of these sliding events play important roles in a wide range of biological processes. However, one challenge is to determine the physiological relevance of these motions in the context of the protein’s biological function. Here, we discuss methods of measuring protein 1D sliding by highlighting the single-molecule approaches that are capable of visualizing particle movement in real time. We also present recent fifindings that show how protein sliding contributes to function. 
  • 1.2K
  • 12 Nov 2021
Topic Review
LOCs/OOCs for Biomedical Applications
Lab-on-a-chip (LOC) and organ-on-a-chip (OOC) devices are highly versatile platforms that enable miniaturization and advanced controlled laboratory functions (i.e., microfluidics, advanced optical or electrical recordings, high-throughput screening). The manufacturing advancements of LOCs/OOCs for biomedical applications and their current limitations are briefly discussed. Multiple studies have exploited the advantages of mimicking organs or tissues on a chip. Among these, we focused our attention on the brain-on-a-chip, blood–brain barrier (BBB)-on-a-chip, and neurovascular unit (NVU)-on-a-chip applications.
  • 1.2K
  • 14 Jul 2021
Topic Review
Tumor Microenvironment in Osteosarcoma Cells
Osteosarcoma (OS) is a malignancy that is becoming increasingly common in adolescents. OS stem cells (OSCs) form a dynamic subset of OS cells that are responsible for malignant progression and chemoradiotherapy resistance. The unique properties of OSCs, including self-renewal, multilineage differentiation and metastatic potential, 149 depend closely on their tumor microenvironment.
  • 1.2K
  • 30 Dec 2022
Topic Review
Vibrational Imaging Techniques and Hard Dental Tissues
Raman Microspectroscopy (RMS) represents an innovative tool to in vitro situation hard dental tissues. In fact, this vibrational technique has the advantage of providing, at the same time and on the same sample, a morpho-chemical correlation between the microscopic information from the visual analysis of the sample and its chemical and macromolecular composition. Moreover, thanks to the light scattering, it is possible to simultaneously perform the imaging analysis of both the inorganic and organic components of teeth, at a high spatial resolution level and in a confocal mode. The identification of specific Raman markers representative of sound and pathological hard dental tissues is crucial to improve the diagnosis of several dental pathologies and to detect dental lesions at an early stage when they are not visually detectable .
  • 1.2K
  • 25 Apr 2022
Topic Review
Commonalities in Amyloid Prefibrillar Oligomers
It has been proposed that a “common core” of pathologic pathways exists for the large family of amyloid-associated neurodegenerations, including Alzheimer’s, Parkinson’s, type II diabetes and Creutzfeldt–Jacob’s Disease. Aggregates of the involved proteins, independently from their primary sequence, induced neuron membrane permeabilization able to trigger an abnormal Ca2+ influx leading to synaptotoxicity, resulting in reduced expression of synaptic proteins and impaired synaptic transmission. Emerging evidence is now focusing on low-molecular-weight prefibrillar oligomers (PFOs), which mimic bacterial pore-forming toxins that form well-ordered oligomeric membrane-spanning pores. At the same time, the neuron membrane composition and its chemical microenvironment seem to play a pivotal role. However, up to now the existence of a specific “common structure” of the toxic aggregate, and a “common mechanism” by which it induces neuronal damage, synaptotoxicity and impaired synaptic transmission, is still an open hypothesis. In this review, we gathered information concerning this hypothesis, focusing on the proteins linked to several amyloid diseases. We noted commonalities in their structure and membrane activity, and their ability to induce Ca2+ influx, neurotoxicity, synaptotoxicity and impaired synaptic transmission.
  • 1.2K
  • 02 Jul 2021
Topic Review
Intramolecular Dynamics of Membrane Proteins
Membrane proteins play important roles in biological functions, with accompanying allosteric structure changes. Understanding intramolecular dynamics helps elucidate catalytic mechanisms and develop new drugs. In contrast to the various technologies for structural analysis, methods for analyzing intramolecular dynamics are limited. Single-molecule measurements using optical microscopy have been widely used for kinetic analysis.
  • 1.2K
  • 09 Dec 2022
Topic Review
DispHred
DispHred is the first disorder predictor that includes the effect of the solution pH in its calculations. The DispHred key feature is profiling the pH-dependence disorder of a protein sequence across a pH interval, identifying pH-induced order/disorder protein transitions. DispHred is freely available for academic users at https://ppmclab.pythonanywhere.com/DispHred.
  • 1.2K
  • 02 Feb 2021
Topic Review
Activity and Affinity of Pin1 Variants
Pin1, or Protein interacting with Never-in-Mitosis (NIMA) 1, is a peptidyl-prolyl isomerase responsible for isomerizing phosphorylated S/T-P motifs. Pin1 has two domains that each have a distinct ligand binding site, but only its PPIase domain has catalytic activity. Vast evidence supports interdomain allostery of Pin1, with binding of a ligand to its regulatory WW domain impacting activity in the PPIase domain. 
  • 1.2K
  • 22 Feb 2022
Topic Review
3-D structures of Potent Antimicrobial Peptides
Global rise of infections and deaths caused by drug-resistant bacterial pathogens are among the unmet medical needs. In an age of drying pipeline of novel antibiotics to treat bacterial infections, antimicrobial peptides (AMPs) are proven to be valid therapeutics modalities.  Direct in vivo applications of many AMPs could be challenging; however, works are demonstrating encouraging results for some of them.
  • 1.2K
  • 05 May 2022
Topic Review
Membrane Fusion Description Approaches
From the very beginning at the stage of fertilization, through the tissue growth, hormone secretion and synaptic transmission, and sometimes morbid events of carcinogenesis and viral infections, membrane fusion regulates the whole life of high organisms. Despite that, a lot of fusion processes still lack the well-established model of the process and even a list of main actors. Merger of membranes requires their topological rearrangements controlled by elastic properties of the lipid bilayer. That is why continuum models of fusion based on theories of membrane elasticity are actively applied for the construction of physical models of membrane fusion. Started from the view on the membrane as a structureless film with postulated geometry of fusion intermediates, they developed along with experimental and calculation techniques to the powerful tool for prediction of the whole process with molecular accuracy. Modern approaches in this field allow continuum models of membrane fusion to stand shoulder to shoulder with molecular dynamics simulations to provide the deepest understanding of this process in multiple biological systems.
  • 1.2K
  • 06 Nov 2020
Topic Review
Aquaporin-1 Facilitates Transmesothelial Water Permeability
Mesothelial cells in human peritoneum express the water channel aquaporin 1 (AQP1) at the plasma membrane, suggesting that, although in a non-physiological context, it may facilitate osmotic water exchange during peritoneal dialysis (PD).
  • 1.2K
  • 08 Dec 2021
Topic Review
Amyloid Beta Oligomers
Amyloid beta (Aβ) oligomers are the most neurotoxic aggregates causing neuronal death and cognitive damage. A detailed elucidation of the aggregation pathways from oligomers to fibril formation is crucial to develop therapeutic strategies for Alzheimer’s disease (AD). This review mainly focused on future perspective of Aβ peptide research using computer simulations.
  • 1.1K
  • 27 Oct 2021
Topic Review
RNA Structure and RNA–RNA Interactions
Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation. By contrast, the nature of these interactions and characteristics of their interfaces, especially those that involve partially or wholly structured RNAs, remain elusive. This entry describes different modalities of RNA–RNA interactions with an emphasis on those that depend on secondary, tertiary, or quaternary structure, and highlight a two-way relationship between RNA structure and interactions.
  • 1.1K
  • 12 Jan 2022
Topic Review
Polymorphism in α-Synuclein
The synucleinopathies exhibit differences in their clinical and pathological representations, reminiscent of prion disorders. Emerging evidence suggests that α-Syn self-assembles and polymerizes into conformationally diverse polymorphs in vitro and in vivo, similar to prions. These α-Syn polymorphs arising from the same precursor protein may exhibit strain-specific biochemical properties and the ability to induce distinct pathological phenotypes upon their inoculation in animal models.
  • 1.1K
  • 20 Oct 2021
Topic Review
Bioelectricity in Developmental Patterning and Size Control
Developmental patterning is essential for regulating cellular events such as axial patterning, segmentation, tissue formation, and organ size determination during embryogenesis. Understanding the patterning mechanisms remains a central challenge and fundamental interest in developmental biology. Ion-channel-regulated bioelectric signals have emerged as a player of the patterning mechanism, which may interact with morphogens.
  • 1.1K
  • 03 Jul 2023
Topic Review
GSL-Enriched Microdomains in Immune Functions
Glycosphingolipids (GSLs), together with cholesterol, sphingomyelin (SM), and glycosylphosphatidylinositol (GPI)-anchored and membrane-associated signal transduction molecules, form GSL-enriched microdomains. These specialized microdomains interact in a cis manner with various immune receptors, affecting immune receptor-mediated signaling.
  • 1.1K
  • 22 Sep 2021
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