Optogenetic cytosol acidification of mammalian cells using an inward proton-pumping rhodopsin

Ion gradients are a universal form of energy, information storage and conversion in living cells. Advances in optogenetics inspire the development of novel tools towards control of different cellular processes with light. Rhodopsins are perspective tools for optogenetic manipulation of ion gradients in cells and subcellular compartments, controlling pH of the cytosol and intracellular organelles. The key step of the development of new optogenetic tools is evaluation of their efficiency. Here, we used a high-throughput quantitative method for comparing efficiency of proton-pumping rhodopsins in Escherichia coli cells. This approach allowed us to show that an inward proton pump xenorhodopsin from Nanosalina sp. (NsXeR) is a powerful tool for optogenetic control of pH of mammalian subcellular compartments. Further, we demonstrate that NsXeR can be used for fast optogenetic acidification of the cytosol of mammalian cells. This is the first evidence of optogenetic cytosol acidification by an inward proton pump at physiological pH values. Our approach offers unique opportunities to study cellular metabolism at normal and pathological conditions and might help to understand the role of pH dysregulation in cellular dysfunctions.

Entrepreneurship Policy and SME Development during Pandemic Crisis in Russia

Small and medium-sized enterprises (SMEs) suffered from government restrictions and a drop in consumer demand in 2020–2021 and therefore became one of the main targets of anti-crisis support worldwide. We aimed to identify trends and factors influencing the SMEs’ dynamics in the Russian regions during the coronacrisis, including the impact of entrepreneurship policy. We have verified with the econometric analysis that the SMEs’ number reduction was more serious in regions with a large SME sector, with a high proportion of industries potentially affected by the crisis, with stricter anti-pandemic measures. The latter factor had an impact not only on the domestic market, but also on SMEs in neighboring regions, which proves the existence of close ties between enterprises of different regions. However, there are some factors that influenced the SMEs development positively: relatively higher income level, more favourable business climate and larger consumer market. The previously undertaken efforts of the regional authorities to improve the business climate had a positive effect on the SMEs survival during the crisis. Business digitalization turned out to be an effective way to adapt (online services and sales), and state support policies could be more efficient (targeted and accessible) in digitally advanced regions. The agrarian regions due to continued demand for food got through the crisis more easily, while the border regions, focused on foreign trade relations, suffered more. In general, the business performance reduction was smaller in the regions that significantly intensified support. In a group of proactive regions (Tyumen, Belgorod, Ulyanovsk oblast, Crimea,¹ etc.), where both general and specific support were increased above the national average, SMEs decrease rate was 1.6% lower. According to our calculations, during crises special attention should be paid to supporting business digitalization, improving regional business climate and increasing the accessibility of markets for SMEs (transport development, import substitution, etc.). These measures can become a significant factor in business development after the events of 2022.

[COMPREHENSIVE ASSESSMENT OF THE SPECIES COMPOSITION AND SENSITIVITY OF MICROFLORA IN PATIENTS WITH ODONTOGENIC MAXILLARY SINUSITIS]

Objective - to study the species composition of microflora and its sensitivity in patients with odontogenic maxillary sinusitis. The study included 230 patients of both sexes aged 18 to 70 years, who were treated at the Moscow Regional Scientifics Research and Clinical Institute named after M. F. Vladimirsky with a diagnosis of Odontogenic maxillary sinusitis. Of these, there were 155 patients with odontogenic sinusitis, complicated by perforation of the maxillary sinus and the presence of an oro-antral fistula, and 75 patients with maxillary aspergillosis. All patients underwent microbiological examination of smears and flushes from the maxillary sinus cavity with the determination of the species composition and antibiotic sensitivity. In the majority of the patients with perforative forms of odontogenic maxillary sinusitis, coccal flora (streptococci and various species) was detected, in a smaller number compared to it - facultative and obligate anaerobes, pathogenic fungi (Candida). A comparative analysis of the microflora, depending on the duration of the maxillary sinus perforation, showed that the rhinogenic microorganisms (Moraxella spp.) were found only in intraoperative perforations (up to 20% of cases). The presence of obligate anaerobes (Fusobacterium spp. Bacteroides spp.) was typical for long-existing perforations. In patients with maxillary aspergillosis facultative and obligate anaerobes were found less frequently and in a smaller variety than in patients with perforative maxillary sinusitis. There were no cases of sinus contamination by pathogenic fungi of the genus Candida in this group. At the same time, rhinogenic microgranisms (Moraxella spp.) were detected with a higher frequency (up to 27.3%) in this group of patients.

DIFFERENTIATED APPROACH TO THE DEVELOPMENT OF SPECIAL PHYSICAL QUALITIES IN SAMBO WRESTLERS

Aim. The article deals with developing the scheme of differentiating means for the development of special physical qualities in sambo wrestlers. Materials and Methods. We studied a differentiated development of special physical qualities in sambo wrestlers. During the study, we used the following methods: the analysis of scientific and methodical literature, generalization of practical experience, pedagogical monitoring, pedagogical experiment, somatotyping, pedagogical control tests, statistical processing of the results obtained. We conducted a series of searching experiments with 48 (16 – microsomal, 16 – mesosomal, 16 – macrosomal) sambo wrestlers from the youth team of the Perm regional Federation of sports and combat Sambo. Results. The analysis of the data obtained proves the necessity of developing an experimental scheme for differentiating means for the development of special physical qualities in sambo wrestlers depending on their somatotype. Conclusion. High-performance results require constant improvement of the training system for sambo wrestlers. Taking into account morphological features while differentiating means for the development of special physical qualities in sambo wrestlers positively influences their performance.

Preventive chemotherapy to control soil-transmitted helminthiasis averted more than 500 000 DALYs in 2015

Background

Preventive chemotherapy (PC), the large-scale administration of anthelminthics, is recommended by the World Health Organization (WHO) for the control of soil-transmitted helminthiasis (STH). Since 2010, donated anthelminthics for STH have boosted the implementation of PC programmes in children, achieving global coverage of more than 60% in 2015. The WHO Global Health Estimates attribute an annual loss of over 3.3 million disability-adjusted life-years (DALYs) to STH. The aim of this study is to estimate the impact of PC programmes on child morbidity.

Method

We used data from the WHO Global Health Estimates, national coverage data on PC and the results of an evaluation of the impact of PC in 17 countries on morbidity previously conducted by our group.

Results

We estimated that the implementation of PC averted in 2015 over 44% of the DALYs that would have been caused in children by STH without the control intervention. A reduction in morbidity of over 75% is expected, if the global target is reached in 2020. If the programme is subsequently maintained, morbidity from STH will be almost totally removed by 2025.

Conclusions

In endemic areas, preventive chemotherapy provides a significant health benefit. We consider this estimation potentially useful to evaluate the cost utility of the investment made by several endemic countries on PC to control STH.

High-accuracy reference standards for two-photon absorption in the 680-1050 nm wavelength range

Degenerate two-photon absorption (2PA) of a series of organic fluorophores is measured using femtosecond fluorescence excitation method in the wavelength range, λ_2PA = 680-1050 nm, and ~100 MHz pulse repetition rate. The function of relative 2PA spectral shape is obtained with estimated accuracy 5%, and the absolute 2PA cross section is measured at selected wavelengths with the accuracy 8%. Significant improvement of the accuracy is achieved by means of rigorous evaluation of the quadratic dependence of the fluorescence signal on the incident photon flux in the whole wavelength range, by comparing results obtained from two independent experiments, as well as due to meticulous evaluation of critical experimental parameters, including the excitation spatial- and temporal pulse shape, laser power and sample geometry. Application of the reference standards in nonlinear transmittance measurements is discussed.

A MicroRNA-Transcription Factor Blueprint for Early Atrial Arrhythmogenic Remodeling

Spontaneous self-terminating atrial fibrillation (AF) is one of the most common heart rhythm disorders, yet the regulatory molecular mechanisms underlying this syndrome are rather unclear. MicroRNA (miRNA) transcriptome and expression of candidate transcription factors (TFs) with potential roles in arrhythmogenesis, such as Pitx2, Tbx5, and myocardin (Myocd), were analyzed by microarray, qRT-PCR, and Western blotting in left atrial (LA) samples from pigs with transitory AF established by right atrial tachypacing. Induced ectopic tachyarrhythmia caused rapid and substantial miRNA remodeling associated with a marked downregulation of Pitx2, Tbx5, and Myocd expression in atrial myocardium. The downregulation of Pitx2, Tbx5, and Myocd was inversely correlated with upregulation of the corresponding targeting miRNAs (miR-21, miR-10a/10b, and miR-1, resp.) in the LA of paced animals. Through in vitro transient transfections of HL-1 atrial myocytes, we further showed that upregulation of miR-21 did result in downregulation of Pitx2 in cardiomyocyte background. The results suggest that immediate-early miRNA remodeling coupled with deregulation of TF expression underlies the onset of AF.

Formation of Regular Surface-Supported Mesostructures with Periodicity Controlled by Chemical Reaction Rate

We report a LEEM and XPEEM study of the formation of a variety of stationary two-dimensional metallic and oxygen structures in Au and Au + Pd adlayers on Rh(110) during water formation reaction. They result from chemically frozen spinodal decomposition and are created, preserved, or reversibly modified by tuning the reaction conditions. The wavelength of lamellar structures obtained at intermediate metal coverage is found to obey a power scaling law with respect to the reaction rate.

Front explosion in a periodically forced surface reaction

Resonantly forced oscillatory reaction-diffusion systems can exhibit fronts with complicated interfacial structure separating phase-locked homogeneous states. For values of the forcing amplitude below a critical value the front "explodes" and the width of the interfacial zone grows without bound. Such front explosion phenomena are investigated for a realistic model of catalytic CO oxidation on a Pt(110) surface in the 2:1 and 3:1 resonantly forced regimes. In the 2:1 regime, the fronts are stationary and the front explosion leads to a defect-mediated turbulent state. In the 3:1 resonantly forced system, the fronts propagate. The front velocity tends to zero as the front explosion point is reached and the final asymptotic state is a 2:1 resonantly locked labyrinthine pattern. The front dynamics described here should be observable in experiment since the model has been shown to capture essential features of the CO oxidation reaction.

Crystallisation under microgravity of mistletoe lectin I from Viscum album with adenine monophosphate and the crystal structure at 1.9 A resolution

The crystal structure of the ribosome-inactivating protein (RIP) mistletoe lectin I (ML-I) from Viscum album in complex with adenine has been refined to 1.9 A resolution. High quality crystals of the ML-I complex were obtained by the method of vapour diffusion using the high density protein crystal growth system (HDPCG) on the international space station, mission ISS 6A. Hexagonal crystals were grown during three months under microgravity conditions. Diffraction data to 1.9A were collected applying synchrotron radiation and cryo- techniques. The structure was refined subsequently to analyse the structure of ML-I and particularly the active site conformation, complexed by adenine that mimics the RNA substrate binding.

Production and specificity of monoclonal antibodies against nodularin conjugated through N-methyldehydrobutyrine

Nodularin (Nod) is a cyclic pentapeptide hepatotoxin produced by the cyanobacterial genus Nodularia living in brackish waters and coastal lagoons. The toxicity of Nod is due to specific inhibition of the type-1 and type-2A intracellular protein phosphatases (PP1 and PP2A, respectively). We have developed a monoclonal antibody against Nod using chemical modification (aminoethylation) of one of its core amino acids, N-methyldehydrobutyrine. The developed antibody is highly specific for Nod, with negligible reactivity to the closely related cyanobacterial toxin microcystin (MC). The monoclonal antibody was employed for quantitative competitive ELISA assay. The analytical sensitivity of the assay was up to 0.2 ng/ml. Comparison of the developed ELISA test with HPLC-based measurements of Nod, with both laboratory and field samples, showed a good correspondence between the results yielded by these two methods. The antibodies developed by this technique provide means for developing extremely sensitive and specific analytical assays for direct measurement of nodularin and related toxins in cyanobacterial or water samples.

Primary structure, isoforms, and molecular modeling of a chitin-binding mistletoe lectin

From mistletoe Viscum album L. extracts three chitin-binding lectin isoforms, cbML1, cbML2, and cbML3, were isolated and their primary structure determined. All three cbML isoforms are composed of two protein chains of 48 or 49 amino acid residues, linked by an intermolecular disulfide bond. The sequence of each single cbML chain is characterized by a relatively high number of cysteine and glycine residues, 9 and 6, respectively, and contains four intramolecular disulfide bridges. On the basis of the combined interpretation of sequencing and MALDI MS data, the following results for the three cbML isoforms were obtained: the first one consists of two identical truncated polypeptide chains (1--48), the second is a heterodimer, containing one truncated (1--48) and one full-length chain (1--49), and the third is composed of two full length chains (1--49). The cbML sequence shows 55% identity to hevein, a single-chain chitin-binding protein of 43 amino acids, one of the most predominant proteins in natural rubber latex. On the basis of the NMR data on hevein from Hevea brasiliensis the three-dimensional structure of cbML3 was modelled. The 26 sequence changes between cbML3 and hevein were accommodated with only little perturbation in the main chain folding. A comparison of the primary structures of cbML3 and hevein is shown and the effects of the sequence changes are discussed. Differences have been identified in the loop region of the molecule and the potential interface region of cbML3 supporting the dimer formation. The high-affinity chitin-binding site seems to be highly conserved.

A time-resolved fluoroimmunometric assay for the detection of microcystins, cyanobacterial peptide hepatotoxins

An immunoassay based on the time-resolved fluorometry (TR-FIA) was developed for microcystins, cyanobacterial peptide hepatotoxins. The assay was performed in a competitive mode and it utilised the monoclonal antibodies raised against microcystin-LR, and a europium chelate of microcystin-LR as a competitive antigen. The sensitivity of the assay was 0.1microg/l. The detection method of TR-FIA was compared to a commercially available kit based on the enzyme-linked immunosorbent assay (ELISA). The same level of sensitivity could be obtained with TR-FIA (in a non-optimised system). The simplified method of TR-FIA leads to a shorter analysis time.

Mitotic reorganization of the intermediate filament protein nestin involves phosphorylation by cdc2 kinase

The intermediate filament protein nestin is expressed during early stages of development in the central nervous system and in muscle tissues. Nestin expression is associated with morphologically dynamic cells, such as dividing and migrating cells. However, little is known about regulation of nestin during these cellular processes. We have characterized the phosphorylation-based regulation of nestin during different stages of the cell cycle in a neuronal progenitor cell line, ST15A. Confocal microscopy of nestin organization and (32)P in vivo labeling studies show that the mitotic reorganization of nestin is accompanied by elevated phosphorylation of nestin. The phosphorylation-induced alterations in nestin organization during mitosis in ST15A cells are associated with partial disassembly of nestin filaments. Comparative in vitro and in vivo phosphorylation studies identified cdc2 as the primary mitotic kinase and Thr(316) as a cdc2-specific phosphorylation site on nestin. We generated a phosphospecific nestin antibody recognizing the phosphorylated form of this site. By using this antibody we observed that nestin shows constitutive phosphorylation at Thr(316), which is increased during mitosis. This study shows that nestin is reorganized during mitosis and that cdc2-mediated phosphorylation is an important regulator of nestin organization and dynamics during mitosis.

Production and specificity of mono and polyclonal antibodies against microcystins conjugated through N-methyldehydroalanine

Microcystins (MCs) are a group of closely related toxic cyclic heptapeptides produced by common cyanobacteria (blue-green algae). Their toxicity is associated with specific inhibition of intracellular protein phosphatases type-1 and type-2A (PP1 and PP2A, respectively). We have developed a battery of antibodies to microcystins using chemical modification (aminoethylation) of one of its core amino acids, N-methyl-dehydroalanine. The developed antibodies displayed different reactivities to closely related MCs. Selected monoclonal antibodies were used for quantitative competitive ELISA assays. The analytical sensitivity of these assays was up to 1 ng/ml. Comparison of the developed ELISA tests with HPLC-based measurements of MCs in laboratory and field samples showed a good correspondence between the results yielded by these two methods. The antibodies developed by this technique provide the means for developing extremely sensitive and specific analytical assays for direct measurement of toxins in cyanobacterial or water samples.

Relationship between microtubule dynamics and lamellipodium formation revealed by direct imaging of microtubules in cells treated with nocodazole or taxol

Microtubules (MTs) contribute to the directional locomotion of many cell types through an unknown mechanism. Previously, we showed that low concentrations (<200 nM) of nocodazole or taxol reduced the rate of locomotion of NRK fibroblasts over 60% without altering MT polymer level [Liao et al., 1995: J. Cell Sci. 108:3473-3483]. In this paper, we directly measured the dynamics of MTs in migrating NRK cells injected with rhodamine tubulin and treated with low concentrations of nocodazole or taxol. Both drug treatments caused statistically significant reductions (approx. twofold) in growth and shortening rates and less dramatic effects on rescue and catastrophe transition frequencies. The percent time MTs were inactive (i.e., paused) increased greater than twofold in nocodazole- and taxol-treated cells, while the percent time growing was substantially reduced. Three parameters of MT dynamics were linearly related to the rates of locomotion determined previously: rate of shortening, percent time pausing and percent time growing. The number of MTs that came within 1 microm of the leading edge was reduced in drug-treated cells, suggesting that reduced MT dynamics may affect actin arrays necessary for cell locomotion. We examined two such structures, lamellipodium and adhesion plaques, and found that lamellipodia area was coordinately reduced with MT dynamics. No effect was detected on adhesion plaque density or distribution. In time-lapse recordings, MTs did not penetrate into the lamellipodium of untreated cells, suggesting that MTs affect lamellipodia either through their interaction with factors at the base of the lamellipodium or by releasing factors that diffuse into the lamellipodia. In support of the latter hypothesis, when all MTs were rapidly depolymerized by 20 microM nocodazole, we detected the rapid formation of exaggerated protrusions from the leading edge of the cell. Our results show for the first time a linear relationship between MT dynamics and the formation of the lamellipodium and support the idea that MT dynamics may contribute to cell locomotion by regulating the size of the lamellipodium, perhaps through diffusable factors.

Microcystin-LR toxicodynamics, induced pathology, and immunohistochemical localization in livers of blue-green algae exposed rainbow trout (oncorhynchus mykiss)

With this retrospective study, we investigated the temporal pattern of toxin exposure and pathology, as well as the topical relationship between hepatotoxic injury and localization of microcystin-LR, a potent hepatotoxin, tumor promoter, and inhibitor of protein phosphatases-1 and -2A (PP), in livers of MC-gavaged rainbow trout (Oncorhynchus mykiss) yearlings, using an immunohistochemical detection method and MC-specific antibodies. H&E stains of liver sections were used to determine pathological changes. Nuclear morphology of hepatocytes and ISEL analysis were employed as endpoints to detect the advent of apoptotic cell death in hepatocytes. Trout had been gavaged with lyophilized cyanobacteria (Microcystis aeruginosa, strain PCC 7806) at acutely toxic doses of 5700 microg microcystin (MC) per kg of body weight (bw), as described previously (Tencalla and Dietrich, 1997). Briefly, 3 control and 3 test animal were killed 1, 3, 12, 24, 48, and 72 h after bolus dosing, and livers were fixed and paraffin embedded for histological analysis and later retrospective histochemical analyses. The results of the immunohistochemistry reported here revealed a time dependent, discernible increase in MC-positive staining intensity throughout the liver, clearly not concurring with the kinetics of hepatic PP inhibition observed in the same fish and reported in an earlier publication by Tencalla and Dietrich (1997). After 3 h, marked and increasing MC-immunopositivity was observed in the cytoplasm, as well as the nuclei of hepatocytes. Apoptotic cell death could be detected after 48 h, at the very earliest. These data suggest that accumulation of MC and subsequent changes in cellular morphology, PP inhibition, and hepatocyte necrosis represent the primary events in microcystin induced hepatotoxicity and appear to be associated with the reversible interaction of MC with the PP. In contrast, apoptotic cell death, as demonstrated here, seems to be of only secondary nature and presumably results from the covalent interaction of MC with cellular and nuclear PP as well as other thiol containing cellular proteins.

Manipulation of cells through elastic films

Manipulation of cells in open dishes is often incompatible withpreservation of sterility. A dish covered with an elastic orstretchable latex or plastic film allows manipulation of cellsthrough the film with preservation of sterility of the cultureand the integrity of the film. The latter forms a ;microglove'for the instrument tip. The idea of manipulation through a thintransparent film is also applicable to general surgery, so thatthe surgeon's hand operates through a film and without a glove.

Dynamics of gap junctions observed in living cells with connexin43-GFP chimeric protein

To study the aggregation of cell-to-cell channels into gap junctions at individual cell-cell contacts, we transfected cells with an expression vector for a chimeric protein composed of the cell-to-cell channel protein connexin43 and a green fluorescent protein. The chimeric channel protein was visualized in the fluorescence microscope and was found to form gap junctions at the cell-cell contacts just like wild-type connexin43. Cells expressing the chimeric protein had functional cell-to-cell channels. Using timelapse videomicroscopy on live cells we observed individual gap junctions over long periods and recorded the time course of aggregation of the chimeric channel protein into gap junctions at newly formed cell-cell contacts. We found that individual small gap junctions were very dynamic, moving about or becoming assembled and disassembled in the course of minutes. Larger gap junctions were more stable than small punctate ones. In control condition, stable new gap junctions were not formed during observation times of 30 min or longer. But at elevated levels of cyclic adenosine monophosphate, the chimeric channel protein began aggregating at new junctions 5-10 minutes after cell-cell contact and continued to concentrate there for at least one hour. Also already established junctions grew in size. The fluorescent chimeric channel protein will be an excellent tool to investigate the regulation of trafficking of connexin from and to the membrane and the mechanism of connexin channel aggregation into gap junctions.

Focal adhesion motility revealed in stationary fibroblasts

Focal adhesions (FAs) are clustered integrins and associated proteins that mediate cell adhesion and signaling. A green fluorescent protein-beta1 integrin chimera was used to label FAs in living cells. In stationary cells, FAs were highly motile, moving linearly for several plaque lengths toward the cell center. FA motility was independent of cell density and resulted from contraction of associated actin fibers. In migrating cells, FAs were stationary and only moved in the tail. FA motility in stationary cells suggests that cell movement may be regulated by a clutch-like mechanism by which the affinity of integrins to substrate may be altered in response to migratory cues.

Structure of ribosomal protein L30 from Thermus thermophilus at 1.9 A resolution: conformational flexibility of the molecule

The crystal structure of ribosomal protein L30 from the extreme thermophilic bacterium Thermus thermophilus has been determined at 1. 9 A resolution. The crystals are trigonal and belong to space group P3(2)21, with unit-cell parameters a = b = 63.5, c = 77.8 A, alpha = beta = 90, gamma = 120 degrees and two molecules per asymmetric unit. The structure was solved by the molecular-replacement method with AMoRe and refined with X-PLOR to an R value of 20.3% and an R(free) of 25.3% in the resolution range 8-1.9 A. Detailed analyses of the structures of the two molecules in the asymmetric unit and comparison of T. thermophilus L30 structure with the structure of homologous L30 from Bacillus stearothermophilus reveal two flexible regions at opposite ends of the rather elongated molecule. Such flexibility could be important for the protein fitting in the ribosome. A comparison with B. stearothermophilus L30 shows a higher number of salt bridges and unbound positively charged residues and an increased accessible hydrophobic area on the surface of T. thermophilus L30. This could contribute to the stability of both the extreme thermophile protein and the ribosome as a whole.

Self-organizing molecular networks

Strong diffusional mixing and short delivery times typical for micrometer and sub-micrometer reaction volumes lead to a special situation where the turnover times of individual enzyme molecules become the largest characteristic time scale of the chemical kinetics. Under these conditions, populations of cross-regulating allosteric enzymes form molecular networks that exhibit various kinds of self-organized coherent collective dynamics.

Crystal structure of mistletoe lectin I from Viscum album

The crystal structure of the ribosome-inactivating protein (RIP) mistletoe lectin I (ML-I) from Viscum album has been solved by molecular replacement techniques. The structure has been refined to a crystallographic R-factor of 24.5% using X-ray diffraction data to 2.8 A resolution. The heterodimeric 63-kDa protein consists of a toxic A subunit which exhibits RNA-glycosidase activity and a galactose-specific lectin B subunit. The overall protein fold is similar to that of ricin from Ricinus communis; however, unlike ricin, ML-I is already medically applied as a component of a commercially available misteltoe extract with immunostimulating potency and for the treatment of human cancer. The three-dimensional structure reported here revealed structural details of this pharmaceutically important protein. The comparison to the structure of ricin gives more insights into the functional mechanism of this protein, provides structural details for further protein engineering studies, and may lead to the development of more effective therapeutic RIPs.

Novel features of intermediate filament dynamics revealed by green fluorescent protein chimeras

In order to study the dynamic behavior of intermediate filament networks in living cells, we have prepared constructs fusing green fluorescent protein to intermediate filament proteins. Vimentin fused to green fluorescent protein labeled the endogenous intermediate filament network. We generated stable SW13 and NIH3T3 cell lines that express an enhanced green fluorescent protein fused to the N-terminus of full-length vimentin. We were able to observe the dynamic behavior of the intermediate filament network in these cells for periods as long as 4 hours (images acquired every 2 minutes). In both cell lines, the vimentin network constantly moves in a wavy manner. In the NIH3T3 cells, we observed extension of individual vimentin filaments at the edge of the cell. This movement is dependent on microtubules, since the addition of nocodazole stopped the extension of the intermediate filaments. Injection of anti-IFA causes the redistribution or ‘collapse’ of intermediate filaments. We injected anti-IFA antibodies into NIH3T3 cells stably expressing green fluorescent protein fused to vimentin and found that individual intermediate filaments move slowly towards the perinuclear area without obvious disassembly. These results demonstrate that individual intermediate filaments are translocated during the collapse, rather than undergoing disassembly-induced redistribution. Injections of tubulin antibodies disrupt the interactions between intermediate filaments and stable microtubules and cause the collapse of the vimentin network showing that these interactions play an important role in keeping the intermediate filament network extended. The nocodazole inhibition of intermediate filament extension and the anti-IFA microinjection experiments are consistent with a model in which intermediate filaments exhibit an extended distribution when tethered to microtubules, but are translocated to the perinuclear area when these connections are severed.

Primary structure and molecular modeling of mistletoe lectin I from Viscum album

The first three-dimensional structure of the ribosome inactivating protein mistletoe lectin I (ML-I) from Viscum album has been modeled on the basis of the X-ray structure of castor bean ricin from Ricinus communis. The relative high sequence homology and conserved secondary structure enabled accurate modeling. The 196 sequence changes between ML-I and ricin could be accomodated with only little pertubation in the main chain folding. A close comparison of the primary structures of ML-I and ricin is given and the effects of the sequence changes are elucidated on the basis of the modeled three-dimensional structure. Differences have been identified in the vicinity of the active site, in the high affinity galactose binding site and in the interface between the A and B chains, which might account for the reduced cytotoxicity of ML-I.

Self-organizing molecular networks

Strong diffusional mixing and short delivery times typical for micrometer and sub-micrometer reaction volumes lead to a special situation where the turnover times of individual enzyme molecules become the largest characteristic time scale of the chemical kinetics. Under these conditions, populations of cross-regulating allosteric enzymes form molecular networks that exhibit various kinds of self-organized coherent collective dynamics.

Transition from molecular chaos to coherent spiking of enzymic reactions in small spatial volumes

Theoretical study of an irreversible enzymic reaction with allosteric product activation reveals that, in small spatial volumes, it can undergo a transition to coherent spiking regime characterized by the presence of strong correlations between reaction events and the states of individual enzyme molecules.

Microscopic self-organization in living cells: a study of time matching

Biochemical subsystems of a living cell may operate with only a few thousand enzyme molecules and their response can be triggered by the entrance of individual molecules of a certain species. This mode of operation is not described by classical chemical kinetics, which deals with large numbers of reacting molecules. Theoretical estimates for the characteristic times of enzymic reactions in small cells and cellular compartments show that any two macromolecules within a micrometer-size volume meet each other each second and that the transit time, required for a mediator molecule to meet a target enzyme, is comparable to the duration of a catalytic round for a single enzyme molecule. When these conditions are satisfied, an enzymic subsystem represents a coherent molecular network with persistent strong temporal correlations between the catalytic events of individual enzyme molecules.

Fluctuations in living cells and intracellular traffic

Theoretical estimates reveal the presence of strong thermal hydrodynamic fluctuations in the cytoplasm of living cells. It is suggested here that these intensive fluctuations may be utilized by biological vesicles inside the cells to produce their directed drift to the targets. A possible mechanism of partial rectification of thermal fluctuations is based on the effect of active navigation: i.e. on the controlled response of vesicles to velocity fluctuations.