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Topic Review
DGKα
Cancer immunotherapy has revolutionized the oncology field. Despite the success, new molecular targets are needed to increase the percentage of patients that benefits from this therapy. Diacylglycerol kinase α (DGKα) has gathered great attention as a potential molecular target in immunotherapy because of its role in cancer proliferation and immunosuppression. DGKα catalyzes the ATP-dependent phosphorylation of diacylglycerol (DAG) to produce phosphatidic acid (PA). Since both lipids are potent signaling messengers, DGKα acts as a switch between different signaling pathways. Its role in cancer and immunosuppression has long been ascribed to the regulation of DAG/PA levels. However, this paradigm has been challenged with the identification of DGKα substrate acyl chain specificity, which suggests its role in signaling could be specific to DAG/PA molecular species. In several biological processes where DGKα plays a role, large membrane morphological changes take place. DGKα substrate specificity depends on the shape of the membrane that the enzyme binds to. 
  • 512
  • 15 Nov 2022
Topic Review
Molecular Phase Separation in Chromosomes
Biomolecular phase separation denotes the demixing of a specific set of intracellular components without membrane encapsulation.
  • 507
  • 19 Oct 2021
Topic Review
Protein-DNA Interactions
Protein-DNA interactions are the core of the cell’s molecular machinery. Conventional biochemical methods served as a powerful investigatory basis of protein-DNA interactions and target search mechanisms. Single-molecule (SM) techniques have emerged as a complementary tool for studying these interactions and have revealed plenty of previously obscured mechanistic details.
  • 505
  • 09 Feb 2022
Topic Review
Metal-Based Nanoparticle-Mediated Biological Effects in Arabidopsis thaliana
The widespread application of metal-based nanoparticles (MNPs) has prompted great interest in nano-biosafety. Consequently, as more and more MNPs are released into the environment and eventually sink into the soil, plants, as an essential component of the ecosystem, are at greater risk of exposure and response to these MNPs. Therefore, to understand the potential impact of nanoparticles on the environment, their effects should be thoroughly investigated. Arabidopsis (Arabidopsis thaliana L.) is an ideal model plant for studying the impact of environmental stress on plants’ growth and development because the ways in which Arabidopsis adapt to these stresses resemble those of many plants, and therefore, conclusions obtained from these scientific studies have often been used as the universal reference for other plants.
  • 503
  • 11 Jul 2022
Topic Review
Circulating Tumour Cells
Cancer is one of the dreaded diseases to which a sizeable proportion of the population succumbs every year. Circulating tumour cells (CTCs) have grabbed the attention of researchers in the detection of metastasis and there has been a huge surge in the surrounding research activities. Acting as a biomarker, CTCs prove beneficial in a variety of aspects. Nanomaterial-based strategies have been devised to have a tremendous impact on the early and rapid examination of tumor cells.
  • 497
  • 01 Feb 2023
Topic Review
Quantitative Super-Resolution Imaging and GPCR Oligomerization Analysis
G-protein coupled receptors (GPCRs) are the largest family of cell surface receptors in eukaryotic cells. These seven-transmembrane receptors have influence in physiological events such as cell to cell communication, immune responses, nerve transmission and even hunger and sleep regulation. The role of GPCRs in diseases such as rheumatoid arthritis, heart disease, cancer, obesity, and neurodegenerative disorders accentuates the need to investigate this family of receptors further. More than a third of all drugs approved by the FDA target GPCRs but often such drugs have a variety of poorly understood mechanisms, as a recent example surrounding opioid receptor agonists illustrates.
  • 490
  • 15 Nov 2021
Topic Review
Membrane Structure Obtained in an Experimental Evolution Process
The functionalized vesicle membrane is a product of the evolution process and is connected to several survival mechanisms. An octapeptide (KSPFPFAA) is identified which rapidly integrated into the vesicle membrane and is obviously connected to a particular advantage of the corresponding functionalized vesicle according to its significant accumulation.
  • 483
  • 09 Feb 2022
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.
  • 479
  • 19 Jun 2023
Topic Review
Statistical Genetic Physics of COVID-19 Spread
Researchers propose a computational framework for quantitatively coalescing transmitter–recipient–virus interactions, pertaining to the genetic system into a hypergraph. Subsequent transmissions of the virus to other individuals lead to the formation of a new genetic system.
  • 476
  • 06 Jan 2022
Topic Review
N-Tailed Monomeric Proto-Type-like Galectin
Galectins are multi-purpose effectors acting via interactions with distinct counterreceptors based on protein-glycan/protein recognition. These processes are emerging to involve several regions on the protein so that the availability of a detailed structural characterization of a full-length galectin is essential.
  • 474
  • 23 Dec 2021
Topic Review
Genetically Encoded Biosensors for O2 and ROS Detection
The intracellular concentrations of oxygen and reactive oxygen species (ROS) in living cells represent critical information for investigating physiological and pathological conditions. Real-time measurement often relies on genetically encoded proteins that are responsive to fluctuations in either oxygen or ROS concentrations. The direct binding or chemical reactions that occur in their presence either directly alter the fluorescence properties of the binding protein or alter the fluorescence properties of fusion partners, mostly consisting of variants of the green fluorescent protein. Oxygen sensing takes advantage of several mechanisms, including (i) the oxygen-dependent hydroxylation of a domain of the hypoxia-inducible factor-1, which, in turn, promotes its cellular degradation along with fluorescent fusion partners; (ii) the naturally oxygen-dependent maturation of the fluorophore of green fluorescent protein variants; and (iii) direct oxygen binding by proteins, including heme proteins, expressed in fusion with fluorescent partners, resulting in changes in fluorescence due to conformational alterations or fluorescence resonance energy transfer. 
  • 469
  • 06 Nov 2023
Topic Review
Repair of HSGc-C5 Carcinoma Cell Using Geant4-DNA
To evaluate the repair performance of HSGc-C5 carcinoma cell against radiation-induced DNA damage, a Geant4-DNA application for radiobiological research was extended by using newly measured experimental data acquired.
  • 464
  • 17 Jan 2022
Topic Review
The DNA Alkyltransferase Family of DNA Repair Proteins
DNA alkyltransferase and alkyltransferase-like family proteins are responsible for the repair of highly mutagenic and cytotoxic O6-alkylguanine and O4-alkylthymine bases in DNA. Their mechanism involves binding to the damaged DNA and flipping the base out of the DNA helix into the active site pocket in the protein. Alkyltransferases then directly and irreversibly transfer the alkyl group from the base to the active site cysteine residue. In contrast, alkyltransferase-like proteins recruit nucleotide excision repair components for O6-alkylguanine elimination. One or more of these proteins are found in all kingdoms of life, and where this has been determined, their overall DNA repair mechanism is strictly conserved between organisms.
  • 463
  • 19 Jan 2024
Topic Review
Arabidopsis thaliana Plant Natriuretic Peptide Active Domain
Plant natriuretic peptides (PNPs) are hormones that have been extracted from many different species, with the Arabidopsis thaliana PNP (AtPNP-A) being the most studied among them. AtPNP-A is a signaling molecule that consists of 130 residues and is secreted into the apoplast, under conditions of biotic or abiotic stress. AtPNP-A has distant sequence homology with human ANP, a protein that forms amyloid fibrils in vivo.
  • 461
  • 23 Dec 2021
Topic Review
Advanced Microscopy Techniques for Molecular Biophysics
Though microscopy is most often intended as a technique for providing qualitative assessment of cellular and subcellular properties, when coupled with other instruments such as wavelength selectors, lasers, photoelectric devices and computers, it can perform a wide variety of quantitative measurements, which are demanding in establishing relationships between the properties and structures of biological material in all their spatial and temporal complexities. These combinations of instruments are a powerful approach to improve non-destructive investigations of cellular and subcellular properties (both physical and chemical) at a macromolecular scale resolution.
  • 454
  • 20 Jun 2023
Topic Review
Site-Search Process for Synaptic Protein-DNA Complexes
The assembly of synaptic protein-DNA complexes by specialized proteins is critical for bringing together two distant sites within a DNA molecule or bridging two DNA molecules. The assembly of such synaptosomes is needed in numerous genetic processes requiring the interactions of two or more sites. The molecular mechanisms by which proteins bring the sites together, enabling the assembly of synaptosomes, remain unknown. Such proteins can utilize sliding, jumping, and segmental transfer pathways for the single-site search process, but none of these pathways explains how the synaptosome assembles. Here we used restriction enzyme SfiI, that requires the assembly of synaptosome for DNA cleavage, as our experimental system and applied time-lapse high-speed AFM (HS-AFM) to directly visualize the site search process accomplished by the SfiI enzyme.
  • 451
  • 17 Jan 2022
Topic Review
Mechanisms of Low-Dose Effects on Bacterial Cells
Mechanisms of low-dose responses of bacteria can be considered at the biochemical, chemical, and physico-chemical levels. 
  • 443
  • 01 Feb 2023
Topic Review
Biological Activity of C60,70 Fullerenols
The simplest bioassay based on a bioluminescent system of coupled enzyme reactions was used to study toxic and antioxidant effects of a water-soluble fullerene derivative, fullerenol, with 10-12 oxygen groups (F10-12) at the enzymatic level. Toxic and antioxidant characteristics of F10-12 were compared to those of homologous fullerenols with a higher number of oxygen groups: F24-28 and F40-42. An active role of reactive oxygen species (ROS) in the bioeffects of F10-12 was demonstrated.
  • 438
  • 11 Aug 2021
Topic Review
Elucidating Selenoprotein M Function from Structure
Selenocysteine (Sec), the 21st amino acid, is structurally similar to cysteine but with a sulfur to selenium replacement. This single change retains many of the chemical properties of cysteine but often with enhanced catalytic and redox activity. Incorporation of Sec into proteins is unique, requiring additional translation factors and multiple steps to insert Sec at stop (UGA) codons. These Sec-containing proteins (selenoproteins) are found in all three domains of life where they often are involved in cellular homeostasis (e.g., reducing reactive oxygen species). The essential role of selenoproteins in humans requires us to maintain appropriate levels of selenium, the precursor for Sec, in our diet. Too much selenium is also problematic due to its toxic effects. Deciphering the role of Sec in selenoproteins is challenging for many reasons, one of which is due to their complicated biosynthesis pathway. However, clever strategies are surfacing to overcome this and facilitate production of selenoproteins.
  • 430
  • 01 Nov 2023
Topic Review
The Cell Nucleus as a Multiscale Porous Medium
Chromatin regulatory processes physically take place in the environment of the cell nucleus, which is filled with the chromosomes and a plethora of smaller biomolecules. The nucleus contains macromolecular assemblies of different sizes, from nanometer-sized protein complexes to micrometer-sized biomolecular condensates, chromosome territories, and nuclear bodies. This multiscale organization impacts the transport processes within the nuclear interior, the global mechanical properties of the nucleus, and the way the nucleus senses and reacts to mechanical stimuli. 
  • 429
  • 10 Aug 2023
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