Analytical Application of Lectins.

This review is devoted to the analytical application of carbohydrate-binding proteins called lectins. The nature of lectins and the regularities of their specificity with respect to simple sugars and complex carbohydrate-containing biomolecules are discussed. The main areas of the modern analytical application of lectins are described.

Search of tandem repeats with insertion and deletions in the A. thaliana genome.

A new mathematical method was used for the first time to search for tandem repeats with insertions and deletions in the full-length sequence of the A. thaliana genome. The method is based on a new algorithm for multiple alignment of sequences of certain periods without using paired comparisons of sequences.

Binding of thioflavin T by albumins: An underestimated role of protein oligomeric heterogeneity.

Amyloid fibrils formation is the well-known hallmark of various neurodegenerative diseases. Thioflavin T (ThT)-based fluorescence assays are widely used to detect and characterize fibrils, however, if performed in bioliquids, the analysis can be biased due to the presence of other, especially abundant, proteins. Particularly, it is known that albumin may bind ThT, although the binding mechanism remains debatable.

Key Roles of Size and Crystallinity of Nanosized Iron Hydr(oxides) Stabilized by Humic Substances in Iron Bioavailability to Plants.

Availability of Fe in soil to plants is closely related to the presence of humic substances (HS). Still, the systematic data on applicability of iron-based nanomaterials stabilized with HS as a source for plant nutrition are missing. The goal of our study was to establish a connection between properties of iron-based materials stabilized by HS and their bioavailability to plants.

Association of Multiple Phosphorylated Proteins with the 14-3-3 Regulatory Hubs: Problems and Perspectives.

14-3-3 proteins are well-known universal regulators binding a vast number of partners by recognizing their phosphorylated motifs, typically located within the intrinsically disordered regions. The abundance of such phosphomotifs ensures the involvement of 14-3-3 proteins in sophisticated protein-protein interaction networks that govern vital cellular processes. Thousands of 14-3-3 partners have been either experimentally identified or predicted, but the spatiotemporal hierarchy of the processes based on 14-3-3 interactions is not clearly understood.

Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome.

Background: The multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear.

Improvement of a yeast self-excising integrative vector by prevention of expression leakage of the intronated Cre recombinase gene during plasmid maintenance in Escherichia coli.

The use of plasmids possessing a regulatable gene coding for a site-specific recombinase together with its recognition sequences significantly facilitates genome manipulations since it allows self-excision of the portion of the genetic construct integrated into the host genome. Stable maintenance of such plasmids in Escherichia coli, which is used for plasmid preparation, requires prevention of recombinase synthesis in this host, which can be achieved by interrupting the recombinase gene with an intron. Based on this approach, Saccharomyces cerevisiae and Hansenula polymorpha self-excising vectors possessing intronated gene for Cre recombinase and its recognition sites (LoxP) were previously constructed.

Chimeric 14-3-3 proteins for unraveling interactions with intrinsically disordered partners.

In eukaryotes, several "hub" proteins integrate signals from different interacting partners that bind through intrinsically disordered regions. The 14-3-3 protein hub, which plays wide-ranging roles in cellular processes, has been linked to numerous human disorders and is a promising target for therapeutic intervention. Partner proteins usually bind via insertion of a phosphopeptide into an amphipathic groove of 14-3-3.

Erratum to: Interaction of the signaling state analog and the apoprotein form of the orange carotenoid protein with the fluorescence recovery protein.

In Fig. 1a in the original article, the amino acid side chains were incorrectly labeled in the structure representation of the orange carotenoid protein (OCP). The corrected figure is printed in this erratum.

[Hsp70 Genes of the Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae) Parasitic Wasp].

Miniaturization is an evolutionary process that is widely represented in both invertebrates and vertebrates. Miniaturization frequently affects not only the size of the organism and its constituent cells, but also changes the genome structure and functioning. The structure of the main heat shock genes (hsp70 and hsp83) was studied in one of the smallest insects, the Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae) parasitic wasp, which is comparable in size with unicellular organisms.

Influence of dicarbonyls on kinetic characteristics of glutathione peroxidase.

Se-containing glutathione peroxidase (GSH-Px) is one of the key enzymes of the body's antioxidant system. The kinetic characteristics of GSH-Px (substrate is tert-butyl hydroperoxide) after modification of the enzyme by various concentrations of natural dicarbonyls (glyoxal, methylglyoxal, malonic dialdehyde) were studied. It was shown that dicarbonyls affected both K and V for GSH-Px.

Whole-Genome Sequence and Methylome Analysis of the Freshwater Colorless Sulfur Bacterium D3.

In this report, we announce the availability of a whole-genome sequence and methylome analysis of strain D3.

Wheat germ agglutinin and Lens culinaris agglutinin sensitized anisotropic silver nanoparticles in detection of bacteria: A simple photometric assay.

Efficacy of anisotropic silver nanoparticles sensitized with wheat germ agglutinin (WGA) and Lens culinaris agglutinin (LCA) was studied for detection of Staphylococcus aureus and Escherichia coli. It was demonstrated that interaction of these nanoparticles with bacteria stabilizes them and prevents their aggregation upon addition of sodium chloride; such stabilization depends on bacteria concentration. High concentration of bacteria results in higher stabilization whereas low concentration leads to aggregation of nanoparticles.

Recent biotechnology developments and trends in the Russian Federation.

This paper addresses recent government initiatives in biotechnology and various federal and regional initiatives. It presents an overview of the most visible industrial biotechnology projects under implementation and highlights changes in legislation affecting development of the bioeconomy in the Russian Federation.

Bacterial co-expression of human Tau protein with protein kinase A and 14-3-3 for studies of 14-3-3/phospho-Tau interaction.

Abundant regulatory 14-3-3 proteins have an extremely wide interactome and coordinate multiple cellular events via interaction with specifically phosphorylated partner proteins. Notwithstanding the key role of 14-3-3/phosphotarget interactions in many physiological and pathological processes, they are dramatically underexplored. Here, we focused on the 14-3-3 interaction with human Tau protein associated with the development of several neurodegenerative disorders, including Alzheimer's and Parkinson's diseases.

Ribosome-bound Pub1 modulates stop codon decoding during translation termination in yeast.

In eukaryotes, termination of translation is controlled by polypeptide chain release factors eRF1 and eRF3, of which the former recognizes nonsense codons, while the latter interacts with eRF1 and stimulates polypeptide release from the ribosome in a GTP- dependent manner, and ABCE1, which facilitates ribosome recycling. In this work, we demonstrate that Pub1, a yeast protein known to be involved in stress granule formation, regulation of gene expression, and organization of the tubulin cytoskeleton, also plays a role in translation termination. Pub1 was shown to bind to ribosomes independent of eRF1 and eRF3 and to interact with the N-terminal glutamine-/asparagine-rich prion domain of eRF3 via its short C-terminal glutamine-rich tract.

Alkaline pH induces IRR-mediated phosphorylation of IRS-1 and actin cytoskeleton remodeling in a pancreatic beta cell line.

Secretion of mildly alkaline (pH 8.0-8.5) juice to intestines is one of the key functions of the pancreas.

New yeast models for studying mitochondrial morphology as affected by oxidative stress and other factors.

The overwhelming majority of investigations on mitochondrial morphology were performed using S. cerevisiae. In this study we showed the benefits of applying new model organisms including petite-negative D.

Rpf Proteins Are the Factors of Reactivation of the Dormant Forms of Actinobacteria.

As the response to unfavorable growth conditions, nonsporulating mycobacteria transform into the dormant state with the concomitant formation of the specialized dormant forms characterized by low metabolic activity and resistance to antibiotics. Such dormant cells can be reactivated under the influence of several factors including proteins of Rpf (Resuscitation promoting factor) family, which possess peptidoglycan hydrolase activity and were considered to belong to the group of the autocrine growth factors of the bacteria. Remarkable interest toward Rpf family is determined by its participation in resuscitation of the dormant forms of Mycobacterium tuberculosis, what in turn is the key element in resuscitation of the latent tuberculosis - an infectious disease that affects one third of the World's population.

Genomics and Biochemistry of Saccharomyces cerevisiae Wine Yeast Strains.

Saccharomyces yeasts have been used for millennia for the production of beer, wine, bread, and other fermented products. Long-term "unconscious" selection and domestication led to the selection of hundreds of strains with desired production traits having significant phenotypic and genetic differences from their wild ancestors. This review summarizes the results of recent research in deciphering the genomes of wine Saccharomyces strains, the use of comparative genomics methods to study the mechanisms of yeast genome evolution under conditions of artificial selection, and the use of genomic and postgenomic approaches to identify the molecular nature of the important characteristics of commercial wine strains of Saccharomyces.

Interaction of the signaling state analog and the apoprotein form of the orange carotenoid protein with the fluorescence recovery protein.

Photoprotection in cyanobacteria relies on the interplay between the orange carotenoid protein (OCP) and the fluorescence recovery protein (FRP) in a process termed non-photochemical quenching, NPQ. Illumination with blue-green light converts OCP from the basic orange state (OCP) into the red-shifted, active state (OCP) that quenches phycobilisome (PBs) fluorescence to avoid excessive energy flow to the photosynthetic reaction centers. Upon binding of FRP, OCP is converted to OCP and dissociates from PBs; however, the mode and site of OCP/FRP interactions remain elusive.

Assembly of photoactive orange carotenoid protein from its domains unravels a carotenoid shuttle mechanism.

The photoswitchable orange carotenoid protein (OCP) is indispensable for cyanobacterial photoprotection by quenching phycobilisome fluorescence upon photoconversion from the orange OCP to the red OCP form. Cyanobacterial genomes frequently harbor, besides genes for orange carotenoid proteins (OCPs), several genes encoding homologs of OCP's N- or C-terminal domains (NTD, CTD). Unlike the well-studied NTD homologs, called Red Carotenoid Proteins (RCPs), the role of CTD homologs remains elusive.

Structural Basis for the Interaction of a Human Small Heat Shock Protein with the 14-3-3 Universal Signaling Regulator.

By interacting with hundreds of protein partners, 14-3-3 proteins coordinate vital cellular processes. Phosphorylation of the small heat shock protein, HSPB6, within its intrinsically disordered N-terminal domain activates its interaction with 14-3-3, ultimately triggering smooth muscle relaxation. After analyzing the binding of an HSPB6-derived phosphopeptide to 14-3-3 using isothermal calorimetry and X-ray crystallography, we have determined the crystal structure of the complete assembly consisting of the 14-3-3 dimer and full-length HSPB6 dimer and further characterized this complex in solution using fluorescence spectroscopy, small-angle X-ray scattering, and limited proteolysis.

Structure-activity relationship for branched oxyquinoline HIF activators: Effect of modifications to phenylacetamide "tail".

HIF prolyl hydroxylase is a major regulator of HIF stability. Branched tail oxyquinolines have been identified as specific inhibitors of HIF prolyl hydroxylase and recently demonstrated clear benefits in various scenarios of neuronal failure. The structural optimization for branched tail oxyquinolines containing an acetamide bond has been performed in the present study using HIF1 ODD-luc reporter assay.