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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. 
  • 1.4K
  • 30 Sep 2022
Topic Review
DNA Manipulation and Single-Molecule Imaging
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. 
  • 1.4K
  • 01 Apr 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.
  • 1.3K
  • 16 Sep 2021
Topic Review
The Coupling in Biological Membranes
Cell membrane structure is proposed as a lipid matrix with embedded proteins, and thus, their emerging mechanical and electrostatic properties are commanded by lipid behavior and their interconnection with the included and absorbed proteins, cytoskeleton, extracellular matrix and ionic media. Structures formed by lipids are soft, dynamic and viscoelastic, and their properties depend on the lipid composition and on the general conditions, such as temperature, pH, ionic strength and electrostatic potentials. The dielectric constant of the apolar region of the lipid bilayer contrasts with that of the polar region, which also differs from the aqueous milieu, and these changes happen in the nanometer scale. Besides, an important percentage of the lipids are anionic, and the rest are dipoles or higher multipoles, and the polar regions are highly hydrated, with these water molecules forming an active part of the membrane. Therefore, electric fields (both, internal and external) affects membrane thickness, density, tension and curvature, and conversely, mechanical deformations modify membrane electrostatics. As a consequence, interfacial electrostatics appears as a highly important parameter, affecting the membrane properties in general and mechanical features in particular.
  • 1.3K
  • 12 Jul 2021
Topic Review
The Magnetoencephalogram
In 1968, biomagnetism pioneer David Cohen performed the first measurement of the magnetic field of the brain: the magnetoencephalogram (MEG). He detected the brain’s largest signal: the alpha rhythm. This nearly sinusoidal oscillation at a frequency of about 10 Hz is turned on or off by closing or opening your eyes.
  • 1.3K
  • 04 May 2023
Topic Review
Candida albicans Cells
In the absence of proper immunity, such as in the case of acquired immune deficiency syndrome (AIDS) patients, Candida albicans, the most common human fungal pathogen, may cause mucosal and even life-threatening systemic infections. P-113 (AKRHHGYKRKFH), an antimicrobial peptide (AMP) derived from the human salivary protein histatin 5, shows good safety and efficacy profiles in gingivitis and human immunodeficiency virus (HIV) patients with oral candidiasis. However, little is known about how P-113 interacts with Candida albicans or its degradation by Candida-secreted proteases that contribute to the fungi’s resistance. Here, we use solution nuclear magnetic resonance (NMR) methods to elucidate the molecular mechanism of interactions between P-113 and living Candida albicans cells. Furthermore, we found that proteolytic cleavage of the C-terminus prevents the entry of P-113 into cells and that increasing the hydrophobicity of the peptide can significantly increase its antifungal activity.
  • 1.3K
  • 29 Oct 2020
Topic Review
Francisella FupA and FupB Proteins
Responsible for tularemia, Francisella tularensis bacteria are highly infectious Gram-negative, category A bioterrorism agents. The molecular mechanisms for their virulence and resistance to antibiotics remain largely unknown. FupA (Fer Utilization Protein), a protein mediating high-affinity transport of ferrous iron across the outer membrane, is associated with both. Recent studies demonstrated that fupA deletion contributed to lower F. tularensis susceptibility towards fluoroquinolones, by increasing the production of outer membrane vesicles. Although the paralogous FupB protein lacks such activity, iron transport capacity and a role in membrane stability were reported for the FupA/B chimera, a protein found in some F. tularensis strains, including the live vaccine strain (LVS). To investigate the mode of action of these proteins, we purified recombinant FupA, FupB and FupA/B proteins expressed in Escherichia coli and incorporated them into mixed lipid bilayers. We examined the porin-forming activity of the FupA/B proteoliposomes using a fluorescent 8-aminonaphthalene-1,3,6-trisulfonic acid, disodium salt (ANTS) probe. Using electrophysiology on tethered bilayer lipid membranes, we confirmed that the FupA/B fusion protein exhibits pore-forming activity with large ionic conductance, a property shared with both FupA and FupB. This demonstration opens up new avenues for identifying functional genes, and novel therapeutic strategies against F. tularensis infections.
  • 1.3K
  • 27 Oct 2020
Topic Review
Allosteric Drug Discovery
Understanding molecular mechanisms underlying the complexity of allosteric regulation in proteins has attracted considerable attention in drug discovery due to the benefits and versatility of allosteric modulators in providing desirable selectivity against protein targets while minimizing toxicity and other side effects. The proliferation of novel computational approaches for predicting ligand–protein interactions and binding using dynamic and network-centric perspectives has led to new insights into allosteric mechanisms and facilitated computer-based discovery of allosteric drugs. Although no absolute method of experimental and in silico allosteric drug/site discovery exists, current methods are still being improved. As such, the critical analysis and integration of established approaches into robust, reproducible, and customizable computational pipelines with experimental feedback could make allosteric drug discovery more efficient and reliable. In this article, we review computational approaches for allosteric drug discovery and discuss how these tools can be utilized to develop consensus workflows for in silico identification of allosteric sites and modulators with some applications to pathogen resistance and precision medicine. The emerging realization that allosteric modulators can exploit distinct regulatory mechanisms and can provide access to targeted modulation of protein activities could open opportunities for probing biological processes and in silico design of drug combinations with improved therapeutic indices and a broad range of activities.
  • 1.3K
  • 26 Sep 2021
Topic Review
Chondrocyte De-Differentiation for Nuclear Alterations
Autologous chondrocyte implantation (ACI) is a cell therapy to repair cartilage defects. In ACI a biopsy is taken from a non-load bearing area of the knee and expanded in-vitro. The expansion process provides the benefit of generating a large number of cells required for implantation; however, during the expansion these cells de-differentiate and lose their chondrocyte phenotype.
  • 1.3K
  • 06 Mar 2023
Topic Review
Factors Affecting Protein Cysteine Reactivity
Protein cysteines are involved in many critical structural and functional roles that can be performed thanks to the peculiar properties of their sulfhydryl group, which, in its deprotonated form, becomes an active nucleophile. Due to the physiological importance of this residue, it represents an attractive and emerging target for the development and design of covalent ligands, which are able to modulate the function of specific proteins and enzymes.
  • 1.3K
  • 01 Oct 2020
Topic Review
Single-Molecule Labeling and Imaging Strategies
Single-molecule imaging is emerging as a revolutionary approach to studying fundamental questions in plants. However, compared with its use in animals, the application of single-molecule imaging in plants is still underexplored. 
  • 1.3K
  • 31 May 2021
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.
  • 1.3K
  • 03 Jan 2023
Topic Review
G Protein-Coupled Receptor (GPCR) Dimers
G protein-coupled receptor (GPCR) oligomerization, while contentious, continues to attract the attention of researchers. Numerous experimental investigations have validated the presence of GPCR dimers, and the relevance of dimerization in the effectuation of physiological functions intensifies the attractiveness of this concept as a potential therapeutic target. GPCRs, as a single entity, have been the main source of scrutiny for drug design objectives for multiple diseases such as cancer, inflammation, cardiac, and respiratory diseases. The existence of dimers broadens the research scope of GPCR functions, revealing new signaling pathways that can be targeted for disease pathogenesis that have not previously been reported when GPCRs were only viewed in their monomeric form. This review will highlight several aspects of GPCR dimerization, which include a summary of the structural elucidation of the allosteric modulation of class C GPCR activation offered through recent solutions to the three-dimensional, full-length structures of metabotropic glutamate receptor and γ-aminobutyric acid B receptor as well as the role of dimerization in the modification of GPCR function and allostery. 
  • 1.3K
  • 30 Apr 2021
Topic Review
IR/Raman Spectroscopy in Biological and Environmental Studies
Various types of vibrational spectroscopy (generally, it includes various variants of Raman and infrared spectroscopy) have been used for a long time to evaluate a variety of biological objects. Moreover, using vibrational spectroscopy, it is possible to evaluate individual compounds, cells, tissues, multicellular organisms (both living and fixed), and the products of their vital activity. These techniques are used for the assessment of the qualitative and quantitative composition of substances in studied biological objects and the conformations of compounds composing them. Among the advantages of these methods, one can mention their relative non-invasiveness, their significant experience in the subsequent analysis of results, and the possibility to perform in situ and in vivo measurements. 
  • 1.3K
  • 27 Apr 2023
Topic Review
COVID 19 MATHEMATICS AND STATISTICS
In this approach we will summarise the the last three publications highlighting the key mathematical approach like Exponential F ( x ) to further exponential –Gaussian F ( x ) and finally the Linear Combination of Atomic Orbital ( LCAO ) ie a hybridised SP orbital overlapping to Remdesivir ( Drug ) –Covid19 approach. .Sigmoid Statistics or Logistics regression is a method to applied to Infection fatality rate ( IFR ) the most important epidemological parameters is also under consideration .
  • 1.3K
  • 29 Oct 2020
Topic Review
Technologies Enabling Single-Molecule Super-Resolution Imaging of mRNA
The transient nature of RNA has rendered it one of the more difficult biological targets for imaging. This difficulty stems both from the physical properties of RNA as well as the temporal constraints associated therewith. These concerns are further complicated by the difficulty in imaging endogenous RNA within a cell that has been transfected with a target sequence. These concerns, combined with traditional concerns associated with super-resolution light microscopy has made the imaging of this critical target difficult. 
  • 1.3K
  • 08 Oct 2022
Topic Review
3D Live Cell Imaging Challenges
Relevant samples are described and various problems and challenges—including 3D Challenges of 3D imaging by optical sectioning, light scattering and phototoxicity—are addressed. Furthermore, enhanced methods of wide-field or laser scanning microscopy together with some relevant examples and applications are summarized. In the future one may profit from a continuous increase in microscopic resolution, but also from molecular sensing techniques in the nanometer range using e.g., non-radiative energy transfer (FRET).
  • 1.3K
  • 23 Aug 2021
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. 
  • 1.3K
  • 24 Nov 2021
Topic Review
HDX-MS Applications on Membrane Proteins
Understanding the higher-order structure of membrane proteins (MPs), which are vital for numerous biological processes, is crucial for comprehending their function. Although several biophysical approaches have been used to study the structure of MPs, limitations exist owing to the proteins’ dynamic nature and heterogeneity. Mass spectrometry (MS) is emerging as a powerful tool for investigating membrane protein structure and dynamics.
  • 1.3K
  • 19 May 2023
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.
  • 1.3K
  • 23 Jun 2021
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