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Topic Review
Mechanisms of α-Syn Aggregation In Vitro
The aggregation of proteins into amyloid fibers is linked to more than forty still incurable cellular and neurodegenerative diseases such as Parkinson’s disease (PD), multiple system atrophy, Alzheimer’s disease and type 2 diabetes, among others. The process of amyloid formation is a main feature of cell degeneration and disease pathogenesis. Despite being methodologically challenging, a complete understanding of the molecular mechanism of aggregation, especially in the early stages, is essential to find new biological targets for innovative therapies. Here, chemical and biophysical methodologies that provided insights on Alpha-synuclein aggregation that would help to investigate other less-known aggregation-prone peptides and proteins were presented.
  • 834
  • 03 Jan 2023
Topic Review
Biological Effects of Non-Ionising UVR and Ionising Radiation
Non-ionising ultraviolet radiation (UVR) and ionising radiation differ in their interactions with biomolecules, resulting in varied consequences. Here describing the underlying molecular interactions of radiation in the context of biological systems and their outcomes from exposure. 
  • 827
  • 24 Nov 2021
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.
  • 816
  • 02 Feb 2021
Topic Review
Reasoning for Symmetry in Biological Systems
Physical roots, exemplifications and consequences of periodic and aperiodic ordering (represented by Fibonacci series) in biological systems are discussed. The physical and biological roots and role of symmetry and asymmetry appearing in biological patterns are addressed. A generalization of the Curie–Neumann principle as applied to biological objects is presented, briefly summarized as: “asymmetry is what creates a biological phenomenon”. The “top-down” and “bottom-up” approaches to the explanation of symmetry in organisms are presented and discussed in detail. The “top-down” approach implies that the symmetry of the biological structure follows the symmetry of the media in which this structure is functioning; the “bottom-up” approach, in turn, accepts that the symmetry of biological structures emerges from the symmetry of molecules constituting the structure. Informational reasoning for symmetry in biological systems is discussed. 
  • 814
  • 30 Sep 2022
Topic Review
Collagen D-Band Periodicity
The molecules follow a quarter-staggered fashion packing, which leads to the formation of the so call D-band periodicity. This D-band periodicity is a repeating banding pattern of about 67 nm (depending on the different tissue) and includes gap and overlap regions. Collagen fibrils form bundles and fibers by appropriate alignment.
  • 812
  • 06 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.
  • 803
  • 02 Jul 2021
Topic Review
Application of Monolayer Graphene
Cryo-electron microscopy (Cryo-EM) has become a routine technology for resolving the structure of biological macromolecules due to the resolution revolution in recent years. The specimens are typically prepared in a very thin layer of vitrified ice suspending in the holes of the perforated amorphous carbon film. However, the samples prepared by directly applying to the conventional support membranes may suffer from partial or complete denaturation caused by sticking to the air-water-interface (AWI). With the application in materials, graphene has also been used recently to improve frozen sample preparation instead of a suspended conventional amorphous thin carbon. It has been proved that graphene or graphene oxide and various chemical modifications on its surface can effectively prevent particles from adsorbing to the AWI, which improves the dispersion, adsorbed number, and orientation preference of frozen particles in the ice layer. Their excellent properties and thinner thickness can significantly reduce the background noise, allowing high-resolution three-dimensional reconstructions using a minimum data set.
  • 801
  • 16 Sep 2021
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.
  • 799
  • 06 Nov 2020
Topic Review
Molecular Hydrogen as Radioprotective Agent
Molecular hydrogen (H2) has the potential to be a radioprotective agent because it can selectively scavenge •OH, a reactive oxygen species with strong oxidizing power. Animal experiments and clinical trials have reported that H2 exhibits a highly safe radioprotective effect.
  • 789
  • 23 Jun 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.
  • 780
  • 14 Jul 2021
Topic Review
Signal Peptide Interactions during ER Translocation
Cleavable endoplasmic reticulum (ER) signal peptides (SPs) and other non-cleavable signal sequences target roughly a quarter of the human proteome to the ER. These short peptides, mostly located at the N-termini of proteins, are highly diverse. For most proteins targeted to the ER, it is the interactions between the signal sequences and the various ER targeting and translocation machineries such as the signal recognition particle (SRP), the protein-conducting channel Sec61, and the signal peptidase complex (SPC) that determine the proteins’ target location and provide translocation fidelity. 
  • 768
  • 16 Dec 2021
Topic Review
Non-equilibrium Thermodynamic Foundations of the Origin of Life
There is little doubt that life’s origin followed from the known physical and chemical laws of Nature. The most general scientific framework incorporating the laws of Nature and applicable to most known processes to good approximation, is that of thermodynamics and its extensions to treat out-of-equilibrium phenomena. The event of the origin of life should therefore also be amenable to such an analysis. The Thermodynamic Dissipation Theory of the Origin and Evolution of Life postulates that the first molecules of life (the fundamental molecules) were, at their origin, pigments dissipatively structured through photochemical and chemical reactions on the surface of the oceans from simpler and more common precursor molecules in water under the solar long-wavelength UVC (205–285 nm) light of the Archean. They were “designed” by Nature to carry out this thermodynamic imperative of absorbing light in this UVC region and then to dissipate it into heat (longer wavelength photons) released into the environment. 
  • 759
  • 13 Apr 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 .
  • 759
  • 25 Apr 2022
Topic Review
Pod Photosynthetic
Increasing photosynthetic ability as a whole is essential for acquiring higher crop yields. Nonleaf green organs (NLGOs) make important contributions to photosynthate formation, especially under stress conditions.In the present study, the experiment is designed for alfalfa (Medicago sativa) under drought stress to explore the photosynthetic responses of pod walls after 5, 10, 15, and 20 days of pollination (DAP5, DAP10, DAP15, and DAP20) based on ultrastructural, physiological and proteomic analyses. Stomata were evidently observed on the outer epidermis of the pod wall. Chloroplasts had intact structures arranged alongside the cell wall, which on DAP5 were already capable of producing photosynthate. The pod wall at the late stage (DAP20) still had photosynthetic ability under well-watered (WW) treatments, while under water-stress (WS), the structure of the chloroplast membrane was damaged and the grana lamella of thylakoids were blurry. The chlorophyll a and chlorophyll b concentrations both decreased with the development of pod walls, and drought stress impeded the synthesis of photosynthetic pigments. Although the activity of ribulose-1,5-bisphosphate carboxylase (RuBisCo) decreased in the pod wall under drought stress, the activity of phosphoenolpyruvate carboxylase (PEPC) increased higher than that of RuBisCo. The proteomic analysis showed that the absorption of light is limited due to the suppression of the synthesis of chlorophyll a/b binding proteins by drought stress. Moreover, proteins involved in photosystem I and photosystem II were downregulated under WW compared with WS. Although the expression of some proteins participating in the regeneration period of RuBisCo was suppressed in the pod wall subjected to drought stress, the synthesis of PEPC was induced. In addition, some proteins, which were involved in the reduction period of RuBisCo, carbohydrate metabolism, and energy metabolism, and related to resistance, including chitinase, heat shock protein 81-2 (Hsp81-2), and lipoxygenases (LOXs), were highly expressed for the protective response to drought stress. It could be suggested that the pod wall in alfalfa is capable of operating photosynthesis and reducing the photosynthetic loss from drought stress through the promotion of the C4 pathway, ATP synthesis, and resistance ability.
  • 758
  • 27 Oct 2020
Topic Review
Nanomaterials in Cancer Therapy
This entry analyzed the different roles of nanomaterials, such as contrast agent and dose enhancer, in biomedical imaging and cancer therapy. Moreover, the review discussed the underlying mechanisms of nanomaterials including physical, chemical, and biological mechanisms. Some new applications of nanomaterials as theranostic agents are explored. Through a thorough understanding of the recent advances in nanomaterial application in biomedical imaging and cancer therapy, we identified new directions for the optimization and clinical transformation of nanomaterials.
  • 758
  • 08 Feb 2021
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. 
  • 756
  • 12 Nov 2021
Topic Review
Two phytochrome A Types in Plants
The phytochrome (phy) system of plants with the main phyA and phyB controls their development beginning from seed germination to fruiting and senescence. The regulation reactions are categorized into three modes—the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is unique among the other phytochromes; it is major in etiolated seedlings and light-labile, and mediates all the three photoresponse modes. The phyB is light-stable, dominates in deetiolated plants, and performs the LFR. The phyA is itself heterogeneous which may explain its functional complexity. It comprises two native types, phyA′ and phyA″, the products of post-translational modification of the molecule at the N-terminus, possibly, via serine phosphorylation. This alters chromophore-apoprotein interactions resulting in the different photochemical, phenomenological, and functional properties of the two phyA pools. The phyA′ is major, water-soluble, and light-labile; the phyA″ is minor, amphiphilic, and relatively light-stable. The phyA′ mediates the VLFR whereas the water-soluble fraction of phyA″ is responsible for the HIR and LFR, the processes taking place in the nucleus. The membrane- (protein-) associated fraction of phyA” is likely to participate in the cytoplasmic photoregulation processes. The phyA pools' functions—their mode, intensity and sign—depend on plant's species, genotype and organ/tissue. The evidence of the existence of the two distinct phyA types in a plant, and their physicochemical properties and their role in the phyA functioning are discussed.
  • 756
  • 17 May 2023
Topic Review
Nanosecond Pulsed Electric Field Applications
Nanosecond Pulsed Electric Field (nsPEF) is an electrostimulation technique first developed in 1995; nsPEF requires the delivery of a series of pulses of high electric fields in the order of nanoseconds into biological tissues or cells. They primary effects in cells is the formation of membrane nanopores and the activation of ionic channels, leading to an incremental increase in cytoplasmic Ca2+ concentration, which triggers a signaling cascade producing a variety of effects: from apoptosis up to cell differentiation and proliferation. Further, nsPEF may affect organelles, making nsPEF a unique tool to manipulate and study cells. This technique is exploited in a broad spectrum of applications, such as: sterilization in the food industry, seed germination, anti-parasitic effects, wound healing, increased immune response, activation of neurons and myocites, cell proliferation, cellular phenotype manipulation, modulation of gene expression, and as a novel cancer treatment.
  • 751
  • 16 Jun 2022
Topic Review
Xenopus Oocytes to Study Fully-Processed Membrane Proteins
The use of Xenopus oocytes in electrophysiological and biophysical research constitutes a long and successful story, providing major advances to the knowledge of the function and modulation of membrane proteins, mostly receptors, ion channels, and transporters. These cells are capable of correctly expressing heterologous proteins after injecting the corresponding mRNA or cDNA. The Xenopus oocyte has become an outstanding host–cell model to carry out detailed studies on the function of fully-processed foreign membrane proteins after their microtransplantation to the oocyte. 
  • 747
  • 24 Oct 2022
Topic Review
Phase Separation of Intrinsically Disordered Nucleolar Proteins
The process of phase separation allows for the establishment and formation of subcompartmentalized structures, thus enabling cells to perform simultaneous processes with precise organization and low energy requirements. Chemical modifications of proteins, RNA, and lipids alter the molecular environment facilitating enzymatic reactions at higher concentrations in particular regions of the cell. 
  • 743
  • 14 Dec 2021
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