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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.
  • 1.5K
  • 16 Jun 2022
Topic Review
Sodium Channels in Action Potentials Initiation
Living organisms react to external stimuli to adapt their activity to the environment for survival. Acquired information is encoded by neurons by action potentials (APs) in a series of discrete electrical events. Rapid initiation of the AP is critical for fast reactions and strongly relies on voltage-activated Na+-selective channels (NaVs), which are widely expressed by both invertebrate and vertebrate neurons.
  • 1.5K
  • 02 Sep 2022
Topic Review
Protein Binding of Benzofuran Derivatives
Benzofuran derivatives are synthetic compounds that are finding an increasing interest in the scientific community not only as building blocks for the realization of new materials, but also as potential drugs thanks to their ability to interact with nucleic acids, interfere with the amyloid peptide aggregation and cancer cell cycle. However, their ability to interact with proteins is a theme still in need of investigation for the therapeutic importance that benzofurans could have in the modulation of protein-driven processes, and for the possibility of making use of serum albumins as benzofurans delivery systems.
  • 1.5K
  • 29 Mar 2022
Topic Review
Applications of Molecular Dynamics Simulation in Protein Study
Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study protein function, protein stability, protein–protein interaction, enzymatic reactions and drug–protein interactions, and membrane proteins.
  • 1.5K
  • 08 Sep 2022
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. 
  • 1.5K
  • 13 Apr 2022
Topic Review
G-quadruplexes and ligands: Biophysical methods
Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized in structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and x-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In the last years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most used approaches to characterize the G4/ligand interactions, as well as the applications and type of information that can be obtained from the use of each technique.
  • 1.5K
  • 03 Dec 2021
Topic Review
Giant Unilamellar Vesicle Electroformation
Since its inception more than thirty years ago, electroformation has become the most commonly used method for growing giant unilamellar vesicles (GUVs). Although the method seems quite straightforward at first, researchers must consider the interplay of a large number of parameters, different lipid compositions, and internal solutions in order to avoid artifactual results or reproducibility problems.
  • 1.5K
  • 23 Nov 2021
Topic Review
Detection of Biological Molecules Using Nanopore Sensing Techniques
Usually, in the early stages of the disease, the number of specific biomarkers is very low and sometimes difficult to detect using classical diagnostic methods. Among detection methods, biosensors have advantages such as easy operation, speed, and portability, with additional benefits of low costs and repeated reliable results. Single-molecule sensors such as nanopores that can detect biomolecules at low concentrations have the potential to become clinically relevant. As such, several applications have been introduced in this field for the detection of blood markers, nucleic acids, or proteins. The use of nanopores has yet to reach maturity for standardization as diagnostic techniques, however, they promise enormous potential, as progress is made into stabilizing nanopore structures, enhancing chemistries, and improving data collection and bioinformatic analysis.
  • 1.5K
  • 19 Jun 2023
Topic Review
Probe for Single-Molecule Fluorescence Microscopy
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for this kind of advanced applications. The three typical groups of fluorophores are fluorescent proteins, organic dyes and quantum dots; here their advantages, drawbacks and use in single-molecule microscopy are discussed. Some requirements are common to all applications, such as high brightness and photostability, specific and efficient labeling, controlled stoichiometry, no perturbation on the system. Other requirements depend on the specific type of single-molecule technique; some of them are here described with their specific requirements for probe choice.
  • 1.4K
  • 13 Feb 2023
Topic Review
SARS-CoV-2 Nucleocapsid Protein
SARS-CoV-2 nucleocapsid protein (NCoV2) plays a key role in various processes related to the viral replication cycle such as the RNA genome packaging, interaction with other viral proteins. It has thus been a target for new drug development.
  • 1.4K
  • 27 May 2021
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. 
  • 1.4K
  • 24 Oct 2022
Topic Review
Magnetic nanoparticles: coating and applications
Magnetic nanoparticles (MNPs) have great potential in material science, drug delivery, magnetic resonance imaging, and therapeutic applications. Indeed, a number of iron oxide nanoparticles have been withdrawn due to their poor clinical performance and/or toxicity issues. MNPs have successfully been converted into water-soluble, stable, bio-accessible systems using the proprietary various coating strategy. Herein, we summarize the data of applications and coating strategies of MNPs.
  • 1.4K
  • 11 Jan 2022
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.
  • 1.4K
  • 17 May 2023
Topic Review
Single-Stranded DNA Binding Protein in DNA Metabolism
Single-stranded DNA-binding proteins (SSBs) play vital roles in DNA metabolism. Proteins of the SSB family exclusively and transiently bind to ssDNA, preventing the DNA double helix from re-annealing and maintaining genome integrity. In the meantime, they interact and coordinate with various proteins vital for DNA replication, recombination, and repair. Although SSB is essential for DNA metabolism, proteins of the SSB family have been long described as accessory players, primarily due to their unclear dynamics and mechanistic interaction with DNA and its partners. Recently-developed single-molecule tools, together with biochemical ensemble techniques and structural methods, have enhanced our understanding of the different coordination roles that SSB plays during DNA metabolism. 
  • 1.4K
  • 15 Feb 2023
Topic Review
Complex Nonlinear Biophysical Brain Dynamics
The human brain is a complex network whose ensemble time evolution is directed by the cumulative interactions of its cellular components, such as neurons and glia cells. Coupled through chemical neurotransmission and receptor activation, these individuals interact with one another to varying degrees by triggering a variety of cellular activity from internal biological reconfigurations to external interactions with other network agents. Consequently, such local dynamic connections mediating the magnitude and direction of influence cells have on one another are highly nonlinear and facilitate, respectively, nonlinear and potentially chaotic multicellular higher-order collaborations. Thus, as a statistical physical system, the nonlinear culmination of local interactions produces complex global emergent network behaviors, enabling the highly dynamical, adaptive, and efficient response of a macroscopic brain network.
  • 1.4K
  • 07 Jun 2022
Topic Review
Colorectal Cancer Treatment Based on Nanomaterials
Colorectal cancer (CRC) is a global health problem responsible for 10% of all cancer incidences and 9.4% of all cancer deaths worldwide. The number of new cases increases per annum, whereas the lack of effective therapies highlights the need for novel therapeutic approaches. Conventional treatment methods, such as surgery, chemotherapy and radiotherapy, are widely applied in oncology practice. Their therapeutic success is little, and therefore, the search for novel technologies is ongoing. Many efforts have focused recently on the development of safe and efficient cancer nanomedicines. Nanoparticles are among them. They are unique with their properties on a nanoscale and hold the potential to exploit intrinsic metabolic differences between cancer and healthy cells. This feature allows them to induce high levels of toxicity in cancer cells with little damage to the surrounding healthy tissues.
  • 1.4K
  • 21 Jul 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. 
  • 1.4K
  • 14 Dec 2021
Topic Review
β-Amyloid Vaccination
β-amyloid (Aβ) is a peptide, 38 to 43 amino acids long, that derives from the proteolytic processing of amyloid precursor protein (APP) by the γ-secretase; Aβ40 and Aβ42 are the most studied Aβ peptide species.
  • 1.4K
  • 20 Apr 2021
Topic Review
Replication-Coupled Chromatin Remodeling
The doubling of genomic DNA during the S-phase of the cell cycle involves the global remodeling of chromatin at replication forks.
  • 1.4K
  • 09 Mar 2021
Topic Review
Autonomous Molecular Design: Machine Intelligence
The workflow for computational autonomous molecular design (CAMD) must be an integrated and closed-loop system with (i) efficient data generation and extraction tools, (ii) robust data representation techniques, (iii) physics-informed predictive machine learning (ML) models, and (iv) tools to generate new molecules using the knowledge learned from steps i–iii.
  • 1.4K
  • 29 Mar 2022
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