Genetic Population Structure of Chum Salmon in the Pacific Rim Inferred from Mitochondrial DNA Sequence Variation

We examined the genetic population structure of chum salmon, Oncorhynchus keta, in the Pacific Rim using mitochondrial (mt) DNA analysis. Nucleotide sequence analysis of about 500 bp in the variable portion of the 5′ end of the mtDNA control region revealed 20 variable nucleotide sites, which defined 30 haplotypes of three genealogical clades (A, B, and C), in more than 2,100 individuals of 48 populations from Japan (16), Korea (1), Russia (10), and North America (21 from Alaska, British Columbia, and Washington). The observed haplotypes were mostly associated with geographic regions, in that clade A and C haplotypes characterized Asian populations and clade B haplotypes distinguished North American populations. The haplotype diversity was highest in the Japanese populations, suggesting a greater genetic variation in the populations of Japan than those of Russia and North America. The analysis of molecular variance and contingency χ² tests demonstrated strong structuring among the three geographic groups of populations and weak to moderate structuring within Japanese and North American populations. These results suggest that the observed geographic pattern might be influenced primarily by historic expansions or colonizations and secondarily by low or restricted gene flow between local groups within regions. In addition to the analysis of population structure, mtDNA data may be useful for constructing a baseline for stock identification of mixed populations of high seas chum salmon.     

Electron microscopic and radioautographic study of the wall of the large bronchi in chronic inflammatory processes in the lungs

Synthesis of DNA, RNA and protein in the structures of large bronchi in patients with chronic inflammatory processes was studied. It was shown, that nuclei of all cell types of the tegmental bronchial epithelium, capillary endotheliocytes and stromal cells actively included 3H-uridine. By the intensification of bronchial wall sclerosis index and hardness of label with 3H-uridine were reduced in epitheliocytes, endotheliocytes, pericytes, labrocytes, macrophages, but were increased in fibroblasts which also had a high level of 3H-proline inclusion. High index of label with 3H-thymidine was found in basal cells of epithelium and capillary endotheliocytes. In conditions of chronic inflammation of bronchial wall the greatest metabolic and proliferative activity was found in the capillary endotheliocytes and cells of a pericapillary zone. In sclerosis the proliferative activity of basal cells was changed, that predetermined the character of tegmental epithelium reorganization.     

Binding screen for cystic fibrosis transmembrane conductance regulator correctors finds new chemical matter and yields insights into cystic fibrosis therapeutic strategy

The most common mutation in cystic fibrosis (CF) patients is deletion of F508 (ΔF508) in the first nucleotide binding domain (NBD1) of the CF transmembrane conductance regulator (CFTR). ΔF508 causes a decrease in the trafficking of CFTR to the cell surface and reduces the thermal stability of isolated NBD1; it is well established that both of these effects can be rescued by additional revertant mutations in NBD1. The current paradigm in CF small molecule drug discovery is that, like revertant mutations, a path may exist to ΔF508 CFTR correction through a small molecule chaperone binding to NBD1. We, therefore, set out to find small molecule binders of NBD1 and test whether it is possible to develop these molecules into potent binders that increase CFTR trafficking in CF‐patient‐derived human bronchial epithelial cells. Several fragments were identified that bind NBD1 at either the CFFT‐001 site or the BIA site. However, repeated attempts to improve the affinity of these fragments resulted in only modest gains. Although these results cannot prove that there is no possibility of finding a high‐affinity small molecule binder of NBD1, they are discouraging and lead us to hypothesize that the nature of these two binding sites, and isolated NBD1 itself, may not contain the features needed to build high‐affinity interactions. Future work in this area may, therefore, require constructs including other domains of CFTR in addition to NBD1, if high‐affinity small molecule binding is to be achieved.     

Phosphorylation of the activation loop tyrosines is required for sustained Syk signaling and growth factor-independent B-cell proliferation

The Syk kinase is regarded as a promising target for the treatment of antigen-driven B-cell malignancies, considering its essential role in propagating antigenic stimuli through the B-cell receptor (BCR). In certain common B-cell malignancies Syk is activated even in the absence of BCR engagement, suggesting a wider role for this kinase in lymphomagenesis. In this paper, we have profiled molecular differences between BCR-induced and constitutive Syk activation in terms of phosphorylation of regulatory tyrosine residues, downstream signaling properties and capacity to sustain B-cell proliferation. Analysis of primary chronic lymphocytic leukemia B-cells and diffuse large B-cell lymphoma cell lines revealed that constitutive and BCR-induced Syk activation differ with respect to the phosphorylation status of the regulatory tyrosines at positions 352 and 525/526, with only the first site being phosphorylated in the case of constitutive and both sites in the case of BCR-induced Syk activation. Syk phosphorylated only on Y352 is capable of downstream signaling, as evidenced by experiments with a phosphomimetic mutant in which the activation loop tyrosines (YY525/526) were replaced with phenylalanines. However, phosphorylation at YY525/526 was shown to significantly increase the enzymatic activity of Syk and to be required for sustained PLCγ2, Akt and ERK signaling as well as B-cell transformation. These data demonstrate that constitutively active Syk and Syk activated by BCR crosslinking represent separate stages of Syk activation with distinct signaling properties and transforming capacities.     

Structure of the yolk syncytial layer in the larvae of whitefishes: A histological study

The yolk syncytial layer (YSL) is a symplastic provisory system that forms at the early stages of embryogenesis of teleosts. The YSL serves morphogenetic, trophic, and immune functions. Despite its important role in development, data on the structure of YSL is scarce. In the present study, comparative histological research on the features of YSL structure in the development of larvae of four economically important species of Coregonidae (Salmoniformes)—Coregonus peled, Coregonus muksun, Coregonus nasus, and Stenodus leucichthys nelma—is presented. The YSL of the larvae of Coregonidae has a complex, differentiated structure. Functional regionalization of YSL cytoplasm, possibly determined by the specific features of nutrient assimilation, is typical for all aforementioned species. Cytoplasm that encircles a large oil globule appears striated. A division into an inner area, filled with yolk inclusions, and an outer, smoother homogeneous area, can be noted in the cytoplasm surrounding the yolk mass. The oil globule is retained after complete utilization of the yolk mass. The inequality of thickness of YSL along anteroposterior and dorsoventral axes also indicates the functional regionalization. The dorsomedial area of YSL, located under the intestine, is the least thick. Dorsolateral areas are strongly incrassated and envelop the intestine from two sides. Gigantic nuclei of exceptionally complex form are typical for YSL. Specific features apply to the form of YSL and its nuclei. Based on the obtained results, a fundamental similarity in organization of the YSL of larvae of the studied whitefishes can be concluded; however, its specific variations distinguishable on a histological level can be discussed.     

Bistability of cell adhesion in shear flow

Cell adhesion plays a central role in multicellular organisms helping to maintain their integrity and homeostasis. This complex process involves many different types of adhesion proteins, and synergetic behavior of these proteins during cell adhesion is frequently observed in experiments. A well-known example is the cooperation of rolling and stationary adhesion proteins during the leukocytes extravasation. Despite the fact that such cooperation is vital for proper functioning of the immune system, its origin is not fully understood. In this study we constructed a simple analytic model of the interaction between a leukocyte and the blood vessel wall in shear flow. The model predicts existence of cell adhesion bistability, which results from a tug-of-war between two kinetic processes taking place in the cell-wall contact area—bond formation and rupture. Based on the model results, we suggest an interpretation of several cytoadhesion experiments and propose a simple explanation of the existing synergy between rolling and stationary adhesion proteins, which is vital for effective cell adherence to the blood vessel walls in living organisms.     

Potassium channel blocker crafted by α-hairpinin scaffold engineering

The α-Hairpinins are a family of plant defense peptides with a common fold presenting two short α-helices stabilized by two invariant S–S-bridges. We have shown previously that substitution of just two amino acid residues in a wheat α-hairpinin Tk-AMP-X2 leads to Tk-hefu-2 that features specific affinity to voltage-gated potassium channels K_V1.3. Here, we utilize a combined molecular modeling approach based on molecular dynamics simulations and protein surface topography technique to improve the affinity of Tk-hefu-2 to K_V1.3 while preserving its specificity. An important advance of this work compared with our previous studies is transition from the analysis of various physicochemical properties of an isolated toxin molecule to its consideration in complex with its target, a membrane-bound ion channel. As a result, a panel of computationally designed Tk-hefu-2 derivatives was synthesized and tested against K_V1.3. The most active mutant Tk-hefu-10 showed a half-maximal inhibitory concentration of ～150 nM being >10 times more active than Tk-hefu-2 and >200 times more active than the original Tk-hefu. We conclude that α-hairpinins provide an attractive disulfide-stabilized scaffold for the rational design of ion channel inhibitors. Furthermore, the success rate can be considerably increased by the proposed “target-based” iterative strategy of molecular design.     

Molecular docking: The role of noncovalent interactions in the formation of protein-nucleotide and protein-peptide complexes

Knowledge of the spatial structure of complexes formed by cellular proteins and membrane receptors with their respective ligands is an important step towards understanding the mechanisms of their functioning. Rational drug design and the search for new therapeutically active compounds also require structural information on the interaction of prototypic drugs with the target protein. The present review briefly describes the main computational methods of molecular docking that are used to predict the conformation of a ligand bound to the active center of a protein. Approaches enabling an increase of the precision and efficiency of the currently used docking algorithms are exemplified by the recent projects of the Laboratory of Biomolecular Modeling of IBCh RAS. Special attention is paid to hydrophilic and hydrophobic interactions, as well as to the stacking phenomena that account for the molecular recognition of specific ligand fragments. These types of contacts are often inadequately described by the algorithms of the estimation of the intermolecular interaction energy of the existing docking programs (scoring functions), this ultimately leading to erroneous predictions of the three-dimensional structure of complexes. Therefore, a thorough consideration of these interactions is one of the most important tasks of molecular modeling.     

Formalized analysis of associativity of morphogenetic types and humus condition of ground litter in marsh birch forests

There are six morphogenetic types of forest ground litter in the gradient of big grass-sphagnous-dead litter marsh birch forest: deeply degraded litter, half degraded litter, rhizomatous litter (coarsely degraded), peaty litter, turfy-formed litter, and turfy litter. The specificity of their biochemical transformations is caused by the accumulation of humic acids (HA), especially of the first fraction (HA-1), alongside the relatively steady background formation of fulvic acids. The C/N value suggests that the intensity of HA-1 formation is closely associated with the biological activity of the substrate. However, the indistinct difference of these parameters in the forestry-morphological types of litters limits their diagnostic reliability. Grouped biochemical types of litters, such as “soft” (half- and deeply degraded), “intermediate” (rhizomatous, peaty and turfy-formed), and “coarse” (mossy), are considerably discriminated by both the C/N ratio (20, 30, 40) and the level of HA-1 (14, 10, and 6%) respectively.