Artem Blagodatski

Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis.

A large number of cDNA inserts were sequenced from a high-quality library of chicken bursal lymphocyte cDNAs. Comparisons to public gene databases indicate that the cDNA collection represents more than 2,000 new, full-length transcripts. This resource defines the structure and the coding potential of a large fraction of B-cell specific and housekeeping genes whose function can be analyzed by disruption in the chicken DT40 B-cell line.

A cis-Acting Diversification Activator Both Necessary and Sufficient for AID-Mediated Hypermutation

Hypermutation of the immunoglobulin (Ig) genes requires Activation Induced cytidine Deaminase (AID) and transcription, but it remains unclear why other transcribed genes of B cells do not mutate. We describe a reporter transgene crippled by hypermutation when inserted into or near the Ig light chain (IgL) locus of the DT40 B cell line yet stably expressed when inserted into other chromosomal positions. Step-wise deletions of the IgL locus revealed that a sequence extending for 9.8 kilobases downstream of the IgL transcription start site confers the hypermutation activity. This sequence, named DIVAC for diversification activator, efficiently activates hypermutation when inserted at non-Ig loci. The results significantly extend previously reported findings on AID-mediated gene diversification. They show by both deletion and insertion analyses that cis-acting sequences predispose neighboring transcription units to hypermutation.

Targeting the Wnt pathways for therapies

The Wnt/β-catenin signaling pathway is crucial in animal development from sponges to humans. Its activity in the adulthood is less general, with exceptions having huge medical importance. Namely, improper activation of this pathway is carcinogenic in many tissues, most notably in the colon, liver and the breast. On the other hand, the Wnt/β-catenin signaling must be re-activated in cases of tissue damage, and insufficient activation results in regeneration failure and degeneration. These both medically important implications are unified by the emerging importance of this signaling pathway in the control of proliferation of various types of stem cells, crucial for tissue regeneration and, in case of cancer stem cells – cancer progression and relapse. This article aims at briefly reviewing the current state of knowledge in the field of Wnt signaling, followed by a detailed discussion of current medical developments targeting distinct branches of the Wnt pathway for anti-cancer and pro-regeneration therapies.

Diverse set of Turing nanopatterns coat corneae across insect lineages

Significance Corneal surfaces of some insects are coated with nipple-like nanostructures reducing the light reflection. Here we provide an extensive analysis of corneae across insect groups. Using atomic force microscopy, we discover a striking diversity of corneal nanocoatings, omnipresent in arthropods. These fascinating bionanostructures replicate the complete set of the Turing patterns—shapes resulting from the reaction−diffusion modeling underlying many examples of patterning in biological and physicochemical systems. Our work, verging on the interface of nanotechnology and zoology, evolution and biophysics, and ecology and genetics, sheds light on the molecular origin and evolutionary diversification of a beautiful diversity of insect corneal nanostructures. It also describes, to our knowledge, the first-ever biological example of Turing nanopatterns. Nipple-like nanostructures covering the corneal surfaces of moths, butterflies, and Drosophila have been studied by electron and atomic force microscopy, and their antireflective properties have been described. In contrast, corneal nanostructures of the majority of other insect orders have either been unexamined or examined by methods that did not allow precise morphological characterization. Here we provide a comprehensive analysis of corneal surfaces in 23 insect orders, revealing a rich diversity of insect corneal nanocoatings. These nanocoatings are categorized into four major morphological patterns and various transitions between them, many, to our knowledge, never described before. Remarkably, this unexpectedly diverse range of the corneal nanostructures replicates the complete set of Turing patterns, thus likely being a result of processes similar to those modeled by Alan Turing in his famous reaction−diffusion system. These findings reveal a beautiful diversity of insect corneal nanostructures and shed light on their molecular origin and evolutionary diversification. They may also be the first-ever biological example of Turing nanopatterns.

Under- and over-water halves of Gyrinidae beetle eyes harbor different corneal nanocoatings providing adaptation to the water and air environments

Whirligig beetles (Gyrinidae) inhabit water surfaces and possess unique eyes which are split into the overwater and underwater parts. In this study we analyze the micro- and nanostructure of the split eyes of two Gyrinidae beetles genera, Gyrinus and Orectochilus. We find that corneae of the overwater ommatidia are covered with maze-like nanostructures, while the corneal surface of the underwater eyes is smooth. We further show that the overwater nanostructures possess no anti-wetting, but the anti-reflective properties with the spectral preference in the range of 450–600 nm. These findings illustrate the adaptation of the corneal nanocoating of the two halves of an insects eye to two different environments. The novel natural anti-reflective nanocoating we describe may find future technological applications.

Technologies of directed protein evolution in vivo

Directed evolution of proteins for improved or modified functionality is an important branch of modern biotechnology. It has traditionally been performed using various in vitro methods, but more recently, methods of in vivo artificial evolution come into play. In this review, we discuss and compare prokaryotic and eukaryotic-based systems of directed protein evolution in vivo, highlighting their benefits and current limitations and focusing on the biotechnological potential of vertebrate immune cells for the generation of protein diversity by means of the immunoglobulin diversification machinery.

Origin of order in bionanostructures

Nanoscale nipple arrays covering the corneal surface of many insects provide antireflection properties and have inspired industrial applications. Based on visual inspection, the dense packing of these nanostructures was initially described to adopt a regular hexagonal order. However, Fourier analysis revealed lack of order over larger distances of the lens cornea, with only patches of hexagonally organized nanostructures. Here we developed a formal mathematical analysis of nippled nanocoatings read by atomic-force microscopy (AFM). This analysis permits automatic assessment of the degree of order in nanostructural packings and its correlation with various characteristics of the nanoscale objects. We applied this analysis to corneae of 17 insect species from 6 orders. We find no correlation between the degree of order and the overall size of the lens. Instead, a strong correlation of the order and the density of the nipple packing exists. Surprisingly, we also see that order correlates with the height of the nanostructures. We discuss these findings in the context of the origin of order in the bio-nanoworld, where order may result largely from the dense packing of the nanostructures, rather than from specialized patterning mechanisms. Our findings uncover mechanisms of order formation, which may also apply to micro- and macro-structures.

Alternative moth-eye nanostructures: antireflective properties and composition of dimpled corneal nanocoatings in silk-moth ancestors

Moth-eye nanostructures are a well-known example of biological antireflective surfaces formed by pseudoregular arrays of nipples and are often used as a template for biomimetic materials. Here, we provide morphological characterization of corneal nanostructures of moths from the Bombycidae family, including strains of domesticated Bombyx mori silk-moth, its wild ancestor Bombyx mandarina, and a more distantly related Apatelodes torrefacta. We find high diversification of the nanostructures and strong antireflective properties they provide. Curiously, the nano-dimple pattern of B. mandarina is found to reduce reflectance as efficiently as the nanopillars of A. torrefacta. Access to genome sequence of Bombyx further permitted us to pinpoint corneal proteins, likely contributing to formation of the antireflective nanocoatings. These findings open the door to bioengineering of nanostructures with novel properties, as well as invite industry to expand traditional moth-eye nanocoatings with the alternative ones described here.

Arthropod Corneal Nanocoatings: Diversity, Mechanisms, and Functions

Corneal surfaces of terrestrial insects and other arthropods are covered with elaborate nanocoatings. Initially described as moth-eye nanostructures – paraboloid nipple-like evaginations regularly assembled on the lenses of some Lepidopterans – they were in recent years discovered to be omnipresent across insect lineages. In addition to the nipple-type morphology, corneal nanocoatings can be built as ridge-, maze-, or dimple-type nanopatterns, with various transitions among these morphologies seen in different species or even within the same specimen. Varying in the height of dozens to hundreds nanometers, and in the diameter being thinner than the wavelength of the visible light, these nanostructures provide the antireflective function to the surfaces they coat. Additional functionalities, such as water-repelling, antifouling, or antibacterial, could also be attributed to them. Turing reaction-diffusion and the block copolymerization mechanisms of molecular self-assembly have been proposed to guide the formation of corneal nanostructures during insect eye development. Both mechanisms envision interactions of two types of molecular agents with different diffusion and/or hydrophobicity properties as the underlying principle of building of the nanostructures. Using model insect organisms, the molecular identities of these agents can be revealed. These studies will elucidate the mechanism of formation and diversity of the corneal nanostructures in arthropods. Further, they will lay the ground for bioengineering, in vivo and in vitro, of novel nanocoatings with desired properties.

Medicinal mushrooms as an attractive new source of natural compounds for future cancer therapy

Medicinal mushrooms have been used throughout the history of mankind for treatment of various diseases including cancer. Nowadays they have been intensively studied in order to reveal the chemical nature and mechanisms of action of their biomedical capacity. Targeted treatment of cancer, non-harmful for healthy tissues, has become a desired goal in recent decades and compounds of fungal origin provide a vast reservoir of potential innovational drugs. Here, on example of four mushrooms common for use in Asian and Far Eastern folk medicine we demonstrate the complex and multilevel nature of their anticancer potential, basing upon different groups of compounds that can simultaneously target diverse biological processes relevant for cancer treatment, focusing on targeted approaches specific to malignant tissues. We show that some aspects of fungotherapy of tumors are studied relatively well, while others are still waiting to be fully unraveled. We also pay attention to the cancer types that are especially susceptible to the fungal treatments.