Urbanization mechanisms in bird species: population systems transformations or adaptations at the individual level?

The present research deals with urbanization of wild bird and mammal species. Forms and mechanisms of population steadiness in the urban landscape have been examined. The urbanization process turned out to be a directed change of the population system forming de novo in the urbolandscape leading to a sustainable organization peculiar for the particular environment. The population organization of different types in urbolandscape is found to provide its stability under conditions of directed and fast changes accompanied with instability and heterogenous structure of habitats. It is shown that the same type of population organization meets the corresponding demands among different species settling in the urban environment. Its features are "openness" and "flowage" of the groups, far order of settlement levels and other units of population system, constant movements of the individuals between the groups as a respond to the signals of urboenvironment significant changes. The "urban" variant of the population system organization turns out to be opposite to that of the same species in the non-urban habitats. After formation of the urban types by the species and successful developing of the town, the urban population becomes separated from the maternal local population and begins to exist independently in the urban landscape. The variety of adaptation aberrations in ecology, behavior, and mode of life of urban birds is the population system stability function in the urban landscape and is not a results of individual selection. It is shown that the urbanization process of the species goes firstly on the population level being the system structure transformation developed by the species towards the most stable state in the town (city) territory. Only after the appearance of stable urban population, the urban individuals show the rapid growth of different changes in ecology, behavior, mode of life that was traditionally described by naturalists as species adaptation to the city conditions. The key features of urban population stability/instability are described. Their application to closely related species allows us to distinguish potential urbanists from instable and vulnerable species that could be soon pushed out of the city. The application of corresponding criteria to the urban populations of such species constituting one guild allows us to predict if their developing in the given town would be successful or unsuccessful. The latter is very important since close species are, as a rule, ecologically indistinguishable in the urbanized landscapes. So one can not predict successful/unsuccessful urbanization taking into account the differences in the range of habitats, breeding success, and other external features.     

Chemical heterogeneity in cell death: combined synchrotron IR and fluorescence microscopy studies of single apoptotic and necrotic cells

The combination of synchrotron IR microspectroscopy and fluorescence microscopy has led to the identification of specific IR signatures of apoptosis and necrosis at a single cell level. Apoptosis was induced by treatment of Fas+ tumor cell lines with anti-Fas monoclonal antibodies. Detection of the early and late stages of apoptosis was performed using conjugated annexin V-fluorescein isothiocyanate (AV-FITC) and propidium iodide. Very early cellular changes were detected by IR before externalization of phosphatidylserine and AV-FITC labeling, and they were probably linked to DNA unwinding. The IR signals at 1044, 1177, and 1222 cm(-1), as well as an intensity variation in the CHx stretching region, are the main signature changes of early and late apoptosis, in line with the hypothesis of DNA fragmentation. The increased intensity of the CHx stretching bands of the lipids was observed only at an early stage of apoptosis. Changes in the relative intensity of CH3 and CH2 stretching accompany this increased intensity, suggesting changes in the relative amount and/or type of lipids concomitant with an increased lipid content. Finally, necrotic cells were characterized by marked changes in their chemical composition because several new vibrational features were observed.     

N-Glycosylation pattern of the zymogenic form of human matrix metalloproteinase-9

Glycosylation of proteins has profound consequences on the activities of macromolecules and their interactions with inhibitors/substrates. Matrix metalloproteinase-9 (MMP-9, also known as gelatinase B) is a member of the MMP family of zinc-dependent endopeptidases, with critical functions in both physiological and pathological processes. MMP-9, a glycosylated MMP, is implicated in inflammation, angiogenesis and tumor metastasis. We have determined by the use of mass spectrometry that of the three possible N-glycosylation sites in human MMP-9 only two are glycosylated. The N-glycosylation sites are at asparagines in positions 38 and 120, the first site within the propeptide domain of the zymogenic form (pro-MMP-9) of the enzyme and the second in the catalytic domain. The chemical nature of the sugar attachments to both these sites was determined by mass spectrometry. Both N-glycosylation sites have NeuAcalpha(1,2)-Galbeta(1,4)-GlcNAcbeta(1,2)-Manalpha(1,3)-[NeuAcalpha(1,2)-Galbeta(1,4)-GlcNAcbeta(1,2)-Manalpha(1,6)-]Manbeta(1,4)-GlcNAcbeta(1,4)-[Fucalpha(1,6)-]GlcNAcbeta oligosaccharide chains. A computational model of glycosylated pro-MMP-9 was generated and it was studied by dynamics simulations     

Cardiac steroids induce changes in recycling of the plasma membrane in human NT2 cells

Cardiac steroids (CSs) are specific inhibitors of Na+, K(+)-ATPase activity. Although the presence of CS-like compounds in animal tissues has been established, their physiological role is not evident. In the present study, treatment of human NT2 cells with physiological concentrations (nanomolar) of CSs caused the accumulation of large vesicles adjacent to the nucleus. Experiments using N-(3-triethylammonium propyl)-4-(dibutilamino)styryl-pyrodinum dibromide, transferrin, low-density lipoprotein, and selected anti-transferrin receptor and Rab protein antibodies revealed that CSs induced changes in endocytosis-dependent membrane traffic. Our data indicate that the CS-induced accumulation of cytoplasmic membrane components is a result of inhibited recycling within the late endocytic pathway. Furthermore, our results support the notion that the CS-induced changes in membrane traffic is mediated by the Na+, K(+)-ATPase. These phenomena were apparent in NT2 cells at nanomolar concentrations of CSs and were observed also in other human cell lines, pointing to the generality of this phenomenon. Based on these observations, we propose that the endogenous CS-like compounds are physiological regulators of recycling of endocytosed membrane proteins and cargo.     

Structural basis for potent slow binding inhibition of human matrix metalloproteinase-2 (MMP-2)

The zinc-dependent gelatinases belong to the family of matrix metalloproteinases (MMPs), enzymes that have been shown to play a key role in angiogenesis and tumor metastasis. These enzymes are capable of hydrolyzing extracellular matrix (ECM) components under physiological conditions. Specific and selective inhibitors aimed at blocking their activity are highly sought for use as potential therapeutic agents. We report herein on a novel mode of inhibition of gelatinase A (MMP-2) by the recently characterized inhibitors 4-(4-phenoxphenylsulfonyl)butane-1,2-dithiol (inhibitor 1) and 5-(4-phenoxphenylsulfonyl) pentane-1,2-dithiol (inhibitor 2). These synthetic inhibitors are selective for MMP-2 and MMP-9. We show that the dithiolate moiety of these inhibitors chelates the catalytic zinc ion of MMP-2 via two sulfur atoms. This mode of binding results in alternation of the coordination number of the metal ion and the induction of conformational changes at the microenvironment of the catalytic zinc ion; a set of events that is likely to be at the root of the potent slow binding inhibition behavior exhibited by these inhibitors. This study demonstrates a distinct approach for the understanding of the structural mechanism governing the molecular interactions between potent inhibitors and catalytic sites of MMPs, which may aid in the design of effective inhibitors.     

c-Raf-1 RBD associates with a subset of active v-H-Ras

Mutational analysis of the cRaf-1 Ras binding domain (RBD) identified several point mutants with elevated Ras binding. Detailed examination of the binding kinetics of one mutant (A85K) suggests that it associates with a greater range of isomeric conformers of v-H-Ras than wt-RBD. At limiting v-H-Ras concentrations, saturation binding to A85K-RBD is higher than to wt-RBD. Notably, in assay systems where the RBD concentration is limiting, no difference exists between wt-RBD and A85K-RBD saturation levels in the presence of a sufficiently large molar excess of Ras. The inability of wt-RBD to saturate all bindable Ras/GTP (defined by its binding to A85K-RBD) suggests that Ras/GTP exists as several isoforms and that only a minority of these isoforms are capable of associating with wt-RBD. These findings provide the first experimental evidence in support of functionally distinct Ras/GTP isoforms. We also describe a novel analysis of such isoforms.     

Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations

To dissect common human diseases such as obesity and diabetes, a systematic approach is needed to study how genes interact with one another, and with genetic and environmental factors, to determine clinical end points or disease phenotypes. Bayesian networks provide a convenient framework for extracting relationships from noisy data and are frequently applied to large-scale data to derive causal relationships among variables of interest. Given the complexity of molecular networks underlying common human disease traits, and the fact that biological networks can change depending on environmental conditions and genetic factors, large datasets, generally involving multiple perturbations (experiments), are required to reconstruct and reliably extract information from these networks. With limited resources, the balance of coverage of multiple perturbations and multiple subjects in a single perturbation needs to be considered in the experimental design. Increasing the number of experiments, or the number of subjects in an experiment, is an expensive and time-consuming way to improve network reconstruction. Integrating multiple types of data from existing subjects might be more efficient. For example, it has recently been demonstrated that combining genotypic and gene expression data in a segregating population leads to improved network reconstruction, which in turn may lead to better predictions of the effects of experimental perturbations on any given gene. Here we simulate data based on networks reconstructed from biological data collected in a segregating mouse population and quantify the improvement in network reconstruction achieved using genotypic and gene expression data, compared with reconstruction using gene expression data alone. We demonstrate that networks reconstructed using the combined genotypic and gene expression data achieve a level of reconstruction accuracy that exceeds networks reconstructed from expression data alone, and that fewer subjects may be required to achieve this superior reconstruction accuracy. We conclude that this integrative genomics approach to reconstructing networks not only leads to more predictive network models, but also may save time and money by decreasing the amount of data that must be generated under any given condition of interest to construct predictive network models.     

Cell-mediate cytotoxicity in vitro of human lymphocytes against a tissue culture melanoma cell line (igr3).

Purified peripheral blood lymphocytes from 13 healthy donors, 6 melanoma patients and 1 halo nevus patient were tested for cytotoxic activity against an allogeneic melanoma cell line (IGR3) in, at least, one of the following assays: cell-mediated cytotoxicity (ADCC) and microcytotoxicity assays (ma). The lymphocytes were isolated by Ficoll-Triosil gradient centrifugation (fraction F) followed by removal of iron-phagocytosing and adherent cells (fraction FFF) and by subsequent passage through anti-IgG columns (fraction FFF-C). Leukocytes of each fraction were identified by different methods including morphology, rosette-formation, phagocytic activity, and membrane fluorescence. CMC activity paralled ADCC activity at a log lower level of sensitivity. In both assays lymphocytes of fractions F and FFF had the highest activity, whereas in fraction FFF-C cytotoxicity was strongly reduced. In all three lymphocyte fractions CMC and ADCC activity could be blocked by preincubation of the effector cells in aggregated IgG. Furthermore, depletion of E rosette-forming lymphocytes slightly increased ADCC and CMC activity, whereas depletion of EA and EAC rosette-forming lymphocytes strongly decreased it. Our results therefore indicate that in both CMC and ADCC assays, non-adherent, non-phagocytic Fc receptor-bearing lymphocytes ("K" cells) were the active cytotoxic cells. In MA, on the other hand, mononuclear phagocytes seemed to be the most active cell population. So far no significant difference was observed in CMC, ADCC, and MA between control persons and melanoma patients     

Soluble CD16 inhibits CR3 (CD11b/CD18)-mediated infection of monocytes/macrophages by opsonized primary R5 HIV-1

We demonstrate that soluble CD16 (sCD16; soluble Fc gamma RIII), a natural ligand of CR3, inhibits the infection of monocytes by primary R5 HIV-1 strain opsonized with serum of seronegative individuals. Inhibition of monocyte infection by sCD16 was similar to that observed with anti-CR3 mAbs, indicating that opsonized HIV may use a CR3-dependent pathway for entry in monocytic cells. Cultured human monocytes express both CR3 (CD11b/CD18) and CCR5 receptors. RANTES, the natural ligand of CCR5, inhibited infection of monocytes with unopsonized HIV particles and partially that of monocytes infected with HIV particles opsonized with complement-derived fragments. Although HIV-infected monocytes from homozygous CCR5 Delta 32/Delta 32 (CCR5(-/-)) individuals produce low levels of p24, cells infected with opsonized particles produced higher levels of p24 than cells infected with unopsonized particles. Our results thus suggest that CR3 may represent an alternative coreceptor to CCR5 of opsonized primary R5 virus entry into monocytes/macrophages. We also observed that the concentration of sCD16 is greatly decreased in sera of HIV-infected patients with low lymphocyte CD4(+) counts. Taken together, our findings suggest that sCD16, present in plasma, may play an important role in controlling HIV-1 spread.     

Synthesis and immunomodulating activity of new diglycopeptides of of glycyrrhizinic acid and it's 30-methyl ester

New amino acid derivatives of glycyrrhizic acid and its methyl ester were selectively synthesized using active N-succinimide esters. The compounds with residues of glycine ethyl ester and alanine methyl and butyl esters increased the level of agglutinins and hemolysins in blood serum of mice two- to threefold in comparison with the control upon parenteral administration at a dose of 2 mg/kg for 14 days. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 2; see also http://www.maik.ru.