- Open AccessArticle Galectin-9 as a Potential Modulator of Lymphocyte Adhesion to Endothelium via Binding to Blood Group H Glycan
Adhesion of leukocytes is a key stage in their trafficking into sites of inflammation. This process is mediated through the interaction of integrins, selectins or CD44, while the role of galectins is not completely clear. It is known that galectins are capable of interacting with oligolactosamines of endothelial cells, and also that in vitro tandem-type galectins (Gal-4, -8 and -9) bind with high affinity to glycans of the ABH blood group system. This work shows that in a cell lines system gal-9 mediates lymphocyte adhesion to endothelial cells through binding to their H-glycan, suggesting that lymphocyte adhesion to endothelium in the circulation occurs similarly and is regulated by the level of galectin-9 expression.
- Fractal droplets
Biological polymers (proteins, nucleic acids and their mixtures) are able to form macromolecular complexes in solution, which at a certain saturating concertation of a polymer grow in size and when crossing the diffraction limit (0.25 µm) become visible under the microscope. Such microscopically observed spherical liquid-like formations have various naming depending on a context such as: «coacervate droplets», biomolecular condensates, etc. Although these polymer droplets (especially proteinaceous) gained numerous attentions of scientist during the last century, e. g. as potential «protocells» in «the primordial soup» according to the life-origin hypothesis by Alexander Oparin, active studies of their functional roles in the living cells flourished in the recent decades.
- WINEGRET: а method for Wide-scale Identification of Novel and Eliminated Genes Responsible for Evolutionary Transformations
Scientists from the Laboratory of Molecular Bases of Embryogenesis at the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, in collaboration with researchers from the Kharkevich Institute for Problems of Information Transmission, Russian Academy of Sciences, have pioneered a method for wide-scale identification of genes whose loss or emergence during evolution correlates with the disappearance or emergence of distinct phenotypic or physiological traits.
- Hyperglycemia exacerbates ischemic stroke not through increased generation of hydrogen peroxide
Diabetes is one of the significant risk factors for ischemic stroke. Hyperglycemia exacerbates the pathogenesis of stroke, leading to more extensive cerebral damage. It is logical to assume that more extensive tissue damage during ischemia should somehow correlate with the severity of oxidative stress.
- New chaotropic mixtures simplify the genomic DNA preparation from fungi for PCR use
Researchers from the Laboratory of neuroreceptors and neuroregulators of IBCh RAS have improved the method of genomic DNA preparation from fungi for PCR diagnostics.
- Role of energy transfer in a nanoinitiator complex for upconversion-driven polymerization
The researchers from the Laboratory of Polymers for Biology, Institute of Bioorganic Chemistry RAS, together with colleagues from the Federal Scientific Research Center «Crystallography and Photonics» RAS and other institutes, have demonstrated an effective strategy for the polymerization of photocurable compositions (PCC) using a nanoinitiator based on upconversion nanoparticles (UCNPs), activated by near infrared (NIR) light.
- Classification of snake venoms using Raman spectroscopy
Scientists from the Department of Molecular Neuroimmune Signaling of the Institute of Bioorganic Chemistry RAS, together with colleagues from the Prokhorov General Physics Institute RAS conducted a study of various snake venoms using Raman spectroscopy and demonstrated the applicability of this method to the analysis of such complex biomolecular mixtures as venoms.
- Total synthesis of racemic thieno[3,2-f]thiochromene tricarboxylate, a luciferin from marine polychaete Odontosyllis undecimdonta
The researchers from the Laboratory of Chemistry of Metabolic Pathways in collaboration with colleagues from other department of IBCh RAS conducted the total synthesis of luciferin from marine polychaete Odontosyllis undecimdonta, a heterocyclic compound with a previously unknown skeleton. The research was published in Organic Letters.
- Effects of cobra cardiotoxins on intracellular calcium and the contracture of rat cardiomyocytes depend on their structural types
Scientists from the Department of Molecular Neuroimmune Signaling of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, together with colleagues from the Institute of Cell Biophysics and the Institute of Theoretical and Experimental Biophysics, studied the effect of cobra venom cardiotoxins on the intracellular concentration of calcium ions and the shape of rat cardiomyocytes.
- Intramolecular Hydrogen Bonding in N6-Substituted 2-Chloroadenosines: Evidence from NMR Spectroscopy
Two forms were found in the NMR spectra of N6-substituted 2-chloroadenosines. The proportion of the mini-form was 11–32% of the main form. It was characterized by a separate set of signals in NMR spectra. The team of scientists from IBCh RAS assumed that the mini-form arises due to an intramolecular hydrogen bond between the N6–CH proton of the substituent and the N7 atom of purine. The 15N-HMBC spectrum confirmed the presence of a hydrogen bond in the mini-form of the nucleoside and its absence in the main form. Compounds incapable of forming such a hydrogen bond were synthesized. In these compounds, either the N7 atom of the purine or the N6–CH proton of the substituent was absent. The mini-form was not found in the NMR spectra of these nucleosides, confirming the importance of the intramolecular hydrogen bond in its formation.
- Conjugated dienoic acid peroxides as substrates in Chaetopterus bioluminescence system
Marine polychaete worm Chaetopterus variopedatus bioluminescence mechanism investigations date back several decades. Researchers from the Laboratory of Chemistry of Metabolic Pathways, the Laboratory of Biomolecular NMR-Spectroscopy and other subdivisions of the Institute of Bioorganic Chemistry RAS, in collaboration with scientists from the Laboratory of Photobiology of the IBP SB RAS, Moscow Institute of Physics and Technology, Pacific State Medical University, and Yeshiva University (USA) have established the structures of three substrates of the Chaetopterus luciferase bioluminescence reaction. The work was published in the International Journal of Molecular Sciences.
- New structural data made it possible to decipher the mechanism of human oncochannel TRPV6 inhibition by the natural phytoestrogen genistein
Calcium-selective oncochannel TRPV6 is the major driver of cell proliferation in human body and its overexpression was found in some of the most severe human cancers, including leukemia, breast, prostate, colon, ovarian, thyroid, and endometrial cancers. While significant effort has been invested in the development of synthetic TRPV6 inhibitors, natural channel blockers have been largely neglected despite of their pharmacological value.
- Enzymatic synthesis of 2-chloropurine arabinonucleosides with chiral amino acid amides at the c6 position and an evaluation of antiproliferative activity in vitro
A number of purine arabinosides containing chiral amino acid amides at the C6 position of the purine were synthesized using a transglycosylation reaction with recombinant E. coli nucleoside phosphorylases.
- Doxorubicin-Loaded Polyelectrolyte Multilayer Capsules Modified with Antitumor DR5-Specific TRAIL Variant
Carriers providing active targeted delivery of anticancer drugs to tumor cells are promising for cancer chemotherapy. A team of scientists from the Laboratory of protein engineering and the Laboratory of Biomedical Materials IBCh RAS in collaboration with collegues from other Russian Institutes have developed biodegradable polyelectrolyte microcapsules which have been modified with the DR5-B ligand.
- Diversity of structural, dynamic, and environmental effects explain a distinctive functional role of transmembrane domains in the insulin receptor subfamily
Human InsR, IGF1R, and IRR receptor tyrosine kinases of the insulin receptor subfamily play an important role in signaling pathways for a wide range of physiological processes. Sharing high sequence and structure homology, the receptors differ dramatically in their localization, expression, and functions. A team of scientists from IBСH RAS in cooperation with colleagues from other institutions using the high-peroscopy of high resolution and computer modeling established that the conformational variability of transmembrane domains and their interaction with surrounding lipids differ significantly among representatives of the subfamily.
- Assessment of core-shell nanoparticles surface structure heterogeneity by SAXS contrast variation and ab initio modeling
A group of scientists from the Laboratory of Molecular Biophysics and the Laboratory of Carbohydrates of the IBH RAS in collaboration with colleagues from the A.V. Shubnikov Institute of Crystallography of the Russian Academy of Sciences and the European Molecular Biology Laboratory (Hamburg) has developed a new approach to the study of the structure of nanoparticles, combining the methods of SAXS and molecular dynamics.
- Bet v 1-independent sensitization to major allergens in Fagales pollen: Evidence at the T-cell level
A collaboration of scientists from the Science-Educational center of the IBCh RAS and the Center for Pathophysiology, Infectology and Immunology of the Medical University of Vienna proved that the main allergens from the pollen from trees of the order Fagales, including alder Aln g 1, have the ability to cause Bet v 1-independent sensitization of the immune system in patients living in birch-dominated areas.
- Lectin-Modified Magnetic Nano-PLGA for Photodynamic Therapy In Vivo
The extreme aggressiveness and lethality of many cancer types appeal to the problem of the development of new-generation treatment strategies based on smart materials. The targeted delivery of nanoparticles to specific cancer cell receptors is believed to be such a strategy; however, there are no targeted nano-drugs that have successfully completed clinical trials to date. To meet the challenge, the team of the Laboratory of Molecular Immunology of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, the Laboratory for Biochemical Research of Carcinogenesis of the Moscow Institute of Physics and Technology, and the Department of Nanobiomedicine of the Sirius University, have developed an alternative method of oncotherapy.
- RALF peptides modulate immune response in the moss Physcomitrium patens
Plants utilize small secreted peptides as important mediators of many processes, from growth and development to response to stress conditions. One of such regulators is the conservative 5 kDa cysteine-rich RALF (Rapid Alkalinization Factor) peptide family, which is widely present in terrestrial plants. RAPID ALKALINIZATION FACTOR (RALFs) are peptides that regulate multiple physiological processes in plants. This peptide family has considerably expanded during land plant evolution, but the role of ancient RALFs in modulating stress responses is unknown
- Antibody fragment-drug conjugates selectively eliminate GD2-expressing tumor cells
Employing antibody fragments instead of full-length antibodies in antibody-drug conjugates can facilitate accumulation of the therapeutics in the tumor and reduce their side effects. Scientists from the Laboratory of molecular immunology together with colleagues from the Laboratory of cell interactions, the Laboratory of molecular diagnostics at IBCh RAS, and other Russian Institutes have for the first time developed GD2-specific antibody fragment-drug conjugates. Minibody and scFv fragment conjugates with the tubulin-inhibiting drugs MMAE and MMAF manifested strong cytotoxic and cytostatic effects in GD2-positive neuroblastoma and melanoma cell lines.
- 5-(Perylen-3-ylethynyl)uracil as an antiviral scaffold: Potent suppression of enveloped virus reproduction by 3-methyl derivatives in vitro
A group of scientists from the Laboratory of Molecular Design and Synthesis, the Protein Growth and Differentiation Factor Expression Group of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, the Institute of Poliomyelitis and other institutes synthesized a series of compounds based on 5-(perylene-3-ylethynyl)uracil and studied their antiviral properties and mechanism of action. Previous studies of this class of compounds have suggested controversial types of mechanisms of action. Nonetheless providing comparable high activity. The present study showed that, upon irradiation with light, amphiphilic compounds accumulated in cell and viral membranes inhibit the entry of enveloped viruses into the cell.
- Prophage-derived regions in Curtobacterium genomes: good things, small packages
Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods.
- Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of Duplodnaviria Viruses
One of the challenging tasks of Duplodnaviria taxonomy is the classification of high-ranked taxa, including families and orders. In this study, the team of scientists from the Laboratory of molecular bioengineering IBCh RAS in collaboration with the colleagues from the Limnological Institute analized the evolutionary relationships of conserved viral proteins, representing different viruses, including all classified Duplodnaviria families, using AlphaFold modelling.
- Chemogenetic emulation of intraneuronal oxidative stress affects synaptic plasticity
The members of the redox biology group and the Laboratory of molecular technologies from the Department of Metabolism and Redox Biology, IBCH RAS, in the collaboration with colleagues from Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, and Pirogov Russian National Research Medical University, using a well-established model of long-term potentiation, revealed that neuronal oxidative stress affects synaptic plasticity.
- Study of aging of contrast nanoparticles for MRI
December 22, 2022
A group of scientists from the Laboratory of Molecular Immunology of the IBCh RAS, GPI RAS and a several other scientific Institutes investigated biotransformation of magnetic nanoparticles in the body and the effect of this process both on the metabolism of the iron and on reducing the contrast properties of nanoparticles during imaging. For a long time, it remained unclear what happens in the long term with nanoparticle contrasts for MRI after their distribution in tissues. In addition, magnetic particle biodegradation is accompanied by abundant release of iron ions, which can cause toxic effects. A recent study published in the high-ranking Journal of Nanobiotechnology clarified these issues.
- New Type of Interaction of Snake Three-Finger α-Neurotoxins with Nicotinic Acetylcholine Receptors
December 14, 2022
Nicotinic acetylcholine receptor of α7 type (α7-nAChR) presented in the nervous and immune systems and epithelium is a promising therapeutic target for cognitive disfunctions and cancer treatment. Weak toxin from venom of cobra Naja kaouthia (WTX) is a non-conventional three-finger α-neurotoxin from Naja kaouthia venom, targeting α7-nAChR with weak affinity. There were no data on interaction mode of non-conventional neurotoxins with α7-nAChR.
- Identification of HLA-B*27-bound peptides recognized by TCRs associated with ankylosing spondylitis
December 13, 2022
Ankylosing spondylitis is an autoimmune rheumatological disease, where aberrant immune response against self-antigens is considered as a main trigger of the pathology. Up to date identification of antigen epitopes recognized by specific T cell receptors (TCRs), especially self-epitopes, remains tricky challenge and there is the very limited list of TCRs with characterized antigen specificity.
- Relationship between phenolic compounds and antioxidant activity in berries and leaves of raspberry genotypes and their genotyping using SSR markers
November 21, 2022
In recent years, the enrichment of fruits and berries with biologically active substances, in particular, antioxidants has received increased development in breeding (the creation of functional food). Researchers from the Forest Biotechnology Group of the FIBCh, together with colleagues from other institutes, studied the content of total phenols, flavonoids and anthocyanins, their relationship with the antioxidant activity of berries and leaves of various raspberry cultivars of Russian and foreign origin, as well as new breeding lines.
- A Single Fluorescent Protein-Based Indicator with a Time-Resolved Fluorescence Readout for Precise pH Measurements in the Alkaline Range
November 17, 2022
The real-time monitoring of the intracellular pH in live cells with high precision represents an important methodological challenge. Although genetically encoded fluorescent indicators can be considered as a probe of choice for such measurements, they are hindered mostly by the inability to determine an absolute pH value and/or a narrow dynamic range of the signal, making them inefficient for recording the small pH changes that typically occur within cellular organelles.
- Longitudinal profiling of human peripheral blood B cell clonal repertoire: memory B cell persistence and signs of negative and positive selection at the BCR repertoire level
October 12, 2022
Persistence of B cell clones and fine-tuning of their BCRs allow them to respond effectively to repeated immune challenges. Researchers from the Genomics of adaptive immunity department of IBCH in collaboration with colleagues from IITP and Skoltech, performed long-term study of structure and dynamics of BCR repertoire of memory B cells and antibody-secreting cells from peripheral blood of healthy donors.