- Liquid drop of DNA libraries reveals total genome information
Unlike the tightly controlled replication of DNA in living cells, PCR amplification, a “workhorse” of molecular biology, balances between simplicity and accuracy. Conventional “bulk” PCR often yields inefficient and nonuniform amplification of complex templates in DNA libraries, introducing unwanted biases.
- Discovery of the novel protein encoded in mammalian mitochondrial DNA polymerase gene POLG
Researchers from Laboratory of bioinformatics approaches in combinatorial chemistry and biology and Laboratory of high-performance screening of biological objects together with colleagues from Moscow State University and University College Cork (Ireland) discovered novel protein POLGARF, which is encoded in alternative reading frame of mitochondrial DNA polymerase POLG mRNA. The results of this study are published in PNAS.
- Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers
The scientists from the Laboratory of biocatalysis, the Laboratory of proteolytic enzyme chemistry, the Laboratory of bioinformatics approaches in combinatorial chemistry and biology and the Laboratory of hormonal regulation proteins, together with colleagues from EMBL-Hamburg, Moscow State University. M.V. Lomonosov, the Sheffield Institute and the Scripps Research Institute have developed a universal algorithm that makes it possible to create biological antidotes based on biocatalysts, directionally increasing their reactivity, and to predict stereoselectivity.
- The discovery of four genes of the Noggin family in lampreys is consistent with the hypothesis of two rounds of genomic duplications in vertebrate ancestors
Researchers from the Laboratory of Molecular Bases of Embryogenesis, together with a colleague from the Severtsov Institute of Ecology and Evolution, described for the first time four genes of the Noggin family in the oldest representatives of vertebrates - lampreys, and compared their structure, expression and some functional features with those of the known genes of this family in other vertebrates.
- A versatile platform for bioimaging based on colominic acid-decorated upconversion nanoparticles
Scientists from the IBCh RAS, Federal Scientific Research Centre “Crystallography and Photonics”, FSBSI “N.N. Blokhin Russian Cancer Research Center”, Lomonosov Moscow State University of Fine Chemical Technologies and Sechenov First Moscow State Medical University developed a method for the UCNP surface functionalization with endogenous colominic acid conferring “stealth” properties, which led to effective accumulation in the area of inflammation, as well as micro- and macro-blood vessels visualization.
- Toxin from black mamba venom inhibits growth of glioma cells selectively expressing ASIC1a channels
Gliomas are fast growing and highly invasive brain tumors, characterized by tumor microenvironment acidification that drives glioma cell growth and migration. Channels containing Acid-sensing Ion Channel 1a subunit (ASIC1a) mediate amiloride-sensitive cation influx in late stage glioma cells, but not in normal astrocytes. Thus, selective targeting of ASIC1a can be a perspective strategy for glioma treatment.
- Start codon context and occurrence of AUG codons in the beginning of protein coding open reading frames co-evolve
Researchers from IBCh RAS together with their international collаborators discovered an evolutionary link between efficiency of start codons and the probability of AUG codon occurrence in the 5'-end parts of protein-coding sequences. When start codons are inefficient the next AUG codon is more likely to be found in the same reading frame. At the same time in case of highly efficient start codons, the next AUG codon is more likely to be found in alternative frames. They also have shown that weak initiation at the first starts is associated with the synthesis of shortened proteoforms as a result of initiation at the second starts.
- New technology promises to revolutionize nanomedicine
A collaboration of scientists from the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, the Moscow Institute of Physics and Technology and Prokhorov General Physics Institute of the Russian Academy of Sciences have developed a breakthrough technology to resolve a key problem that has prevented the introduction of novel drugs into clinical practice for decades. The study was published in Nature Biomedical Engineering and featured in the journal’s News & Views section.
- A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding
Kinase-mediated phosphorylation represents one of the general strategies for the emergence of antibiotic resistance. A new subfamily of AmiN-like kinases, isolated from the Siberian bear microbiome, inactivates antibiotic amicoumacin by phosphorylation. The nanomolar substrate affinity defines AmiN as a phosphotransferase with a unique catalytic efficiency proximal to the diffusion limit. Crystallographic analysis and multiscale simulations revealed a catalytically perfect mechanism providing phosphorylation exclusively in the case of a closed active site that counteracts substrate promiscuity. AmiN kinase is a member of the previously unknown subfamily representing the first evidence of a specialized phosphotransferase bioscavenger.
- Transgenic aspen plants (Populus tremula) with the expression of recombinant xyloglucanase sp-Xeg show an increased growth rate, altered composition and properties of wood, and the phenotype of the plant as a whole
Scientists from the Group of Forest Biotechnology IBCh RAS obtained the transgenic aspen with acceletated growth, a modified carbohydrate composition and a slower rate of decomposition of wood.
- Structure of Supramers Formed by the Amphiphile Biotin‐CMG‐DOPE
Scientists from the Department of Chemical Biology of Glycans and Lipids, the Department of structural biology and the Department of Biomaterials and Bionanotechnology IBCh RAS in collaboration with Russian and foreign colleges published a paper in ChemistryOpen on the study of conjugate of a biotin with DOPE (dioleoylphosphatidyl ethanolamine) and on its interaction with streptavidin.
- Soluble Variant of Human Lynx1 Positively Modulates Synaptic Plasticity and Ameliorates Cognitive Impairment Associated with α7-nAChR Dysfunction
Scientists from the Laboratory of bioengineering of neuromodulators and neuroreceptors, the Laboratory of structural biology of ion channels and the Laboratory of neuroreceptors and neuroregulators Shemyakin-Ovchnnikov Institute together with colleagues from the Faculty of biology of Moscow State University and other russian scientific institutes, found that the intranasal administration of the water-soluble analogue of the human neuromodulator Lynx1 can prevent cognitive impairment associated with dysfunction of the α7 type nicotinic acetylcholine receptor.
- Pyrophosphate pharmacophore model: How nisin captures lipid II
Researchers from the Group of in silico analysis of membrane proteins structure and the Laboratory of biomolecular modeling of IBCh RAS have predicted the structure of the complex between lantibiotic nisin with the bacterial cell wall precursor — lipid II — on the membrane surface.
- How the fluorescent nanoclusters look like
Our new article “Albumin-stabilized fluorescent metal nanoclusters: fabrication, physico-chemical properties and cytotoxicity” was recently published in Materials and Design journal. The work was performed by a team of authors from the Scientific Clinical Center for Physico-Chemical Medicine, Moscow Institute of Physics and Technology and IBCh RAS. The researchers of the Electron microscopy group of our institute carried out an important part of the work on direct visualization of the obtained structures, as well as on the measurement of energy dispersive X-ray spectra.
- The role of chloroplast protein remodeling in stress responses and shaping of the plant peptidome
Researchers of the Laboratory of plant functional genomics and proteomics, IBCh RAS, in collaboration with Laboratory of molecular basis of plant stress resistance, IBCh RAS, and James Hutton Institute (United Kingdom) published a review article in the international peer-reviewed scientific journal New Phytologist (IF = 7.29). This review “The role of chloroplast protein remodeling in stress responses and shaping of the plant peptidome” is focused on processes of reorganization of the chloroplast proteome under stress conditions and on the roles of bioactive peptides generated from chloroplast proteins.
- Sustainable Light Achieved in Living Plants
The movie Avatar evoked an imaginary world of lush bioluminescent jungles. Now the popular fascination for sustainably glowing foliage is being realized through advances in designer genetics. This week in Nature Biotechnology, scientists have announced the feasibility of creating plants that produce their own visible luminescence.
- A new direction of synthetic chemistry was developed in the Institute of Bioorganic Chemistry RAS
Small molecules play a critical role in many biological processes and are used as drugs and other research tools.
- Why acupuncture increases pain threshold of the rodent?
Scientists from the Laboratory of neuroreceptors and neuroregulators helped colleagues from Chengdu University (China) to conduct a series of in vivo experiments on wild-type and knockout by pain sensing receptors TRPV1 and P2X7 animals. It was shown that a stimulation of ST36 acupuncture point leads to an analgesic effect in the model of inflammation from the introduction of a slightly acidic solution into the paw, similar to the effects of selective TRPV1 and ASIC3 ion channel inhibitors. In the model of inflammation from the administration of α, β-meATP (a P2X1,3 purinergic receptor agonist) the ST36 point stimulation also reduced pain sensitivity, but not so effective as the P2X3 antagonist A-317491 or different ASIC3 channel blockers. The results are published in the British Journal of Pharmacology.
- Deciphering Ribosomes’ Actions in Living Cells
December 30, 2019
Researchers from the Laboratory of Bioinformatics Approaches in Combinatorial Chemistry and Biology IBCH RAS, in collaboration with Irish colleagues, recently published a review in WIRES RNA that compiles the computational approaches, software tools, and data resources that have been developed over the last ten years for ribosome profiling data processing and analysis.
- The new method for T-cell receptor alpha chain clonality assessment can be used for minimal disease monitoring in leukemia
December 27, 2019
Monitoring of minimum residual disease (MRD) is one of the most important diagnostic tests in the treatment of acute and chronic lymphoblastic leukemia. Currently, several methods for MRD are used, the most sensitive of which is the assessment and monitoring of clonal rearrangements in the immunoglobulin genes characteristic of tumor cells. High sensitivity, up to 1 tumor cell per million, is achieved by using next generation highthroughput sequencing technology (Illumina).