Topographic Distribution of miRNAs (miR-30a, miR-223, miR-let-7a, miR-let-7f, miR-451, and miR-486) in the Plasma Extracellular Vesicles

There are many articles on the quantitative analysis of miRNAs contained in a population of EVs of different sizes under various physiological and pathological conditions. For such analysis, it is important to correctly quantify the miRNA contents of EVs. It should be considered that quantification is skewed depending on the isolation protocol, and different miRNAs are degraded by nucleases with different efficiencies. In addition, it is important to consider the contribution of miRNAs coprecipitating with the EVs population, because the amount of miRNAs in the EVs population under study is skewed without appropriate enzymatic treatment. By studying a population of EVs from the blood plasma of healthy donors, we found that the absolute amount of miRNA inside the vesicles is commensurate with the amount of the same type of miRNA adhered to the outside of the EVs. The inside/outside ratio ranged from 1.02 to 2.64 for different investigated miRNAs. According to our results, we propose the hypothesis that high occupancy of miRNAs on the outer surface of EVs influence on the transporting RNA repertoire no less than the inner cargo received from the host cell.

Pun processing in advertising posters: evidence from eye tracking

This study examines the process of reading polycode advertising posters, focusing in particular on the effect of a pun in the headline. The pun, or a sequence of lexical items that can be perceived as ambiguous, is contained in the headline and different meanings of this sequence are supported by the picture and text. The results of the preliminary experiment showed that advertisements with puns are rated as more attractive, original, effective and positive compared to advertisements without puns. We hypothesized that puns in the headlines increase cognitive effort in processing posters, leading to higher evaluations. The main experiment tested this and examined differences in eye movement when reading posters with and without puns. Fifty-five Russian participants viewed advertisements while their eye movements were recorded. Our results showed no fundamental differences in the general pattern of viewing advertisement posters with and without puns. We found that readers start to perceive polycode advertisements from the text and spend more time reading the text than looking at an image. These findings shed light on how attention is distributed between verbal and non-verbal components of polycode texts, and which type of poster is more effective for information retrieval at different processing levels.

Predicting radon flux density from soil surface using machine learning and GIS data

Several machine learning algorithms including artificial neural networks (ANN), random forest (RF) and multivariate adaptive regression splines (MARS) were used to construct a radon flux density (RFD) map of Moscow for the purpose of finding which one of them would be the best for radon delineation. Predictors used included geological soil classes for quaternary and some pre-quaternary sediment types, elevations of quaternary and pre-quaternary layers, 226Ra content in soil, ambient dose equivalent rate (ADER), distances to geodynamically active zones and lineaments. Training of the models was performed using previously collected radon flux density data from approximately ten thousand of measurements over 756 sites. ANN and RF algorithms produced the best maps with high correlation coefficients and low mean squared error, while MARS failed to get a high correlation coefficient and low mean squared error. Predictions made using RF were found to be more conservative due to higher prediction values of RFD, while those made using ANN were likely more realistic in their prediction value distribution, leading to the conclusion that RF is better for the purposes of delineation, while ANN is better for predicting average RFD values. Based on the constructed maps, the main factors affecting the flow of radon in the city were determined.

Unveiling genetic diversity and forensic utility of SureID® human DNA identification kits: a comprehensive analysis of 44 autosomal STR loci in English and Irish populations

Background: Human identification and kinship testing in forensic science rely on Short Tandem Repeat (STR) multiplex kits, typically containing loci recommended by standard sets. However, complementary kits with additional STR loci can be valuable in complex cases. Allele frequency databases specific to the population are essential for accurate forensic analysis.Aim: This study aimed to generate allele frequencies and population genetic data for 44 autosomal STR loci from SureID® PanGlobal and 27comp kits in English and Irish populations for forensic casework, human identification, and kinship testing.Subjects and methods: Buccal swab samples from 645 White Caucasians (365 English, 280 Irish) were collected. DNA was extracted and amplified using the mentioned kits. Quality control, statistical analysis, and genetic distance calculations were performed.Results: Both kits demonstrated robustness with no significant deviations from Hardy-Weinberg Equilibrium (HWE). Variant alleles and minor discordances between kits were observed. Syntenic STR pairs were identified but showed no significant linkage. A close genetic relationship was found between English and Irish populations, allowing for combined databases.Conclusions: The SureID® PanGlobal and 27comp kits showed high discriminatory power and reliability in the English and Irish populations. Care is needed when handling variant alleles, discordances, and syntenic loci. Combining data from both populations is feasible for a comprehensive database. Further studies are required to explore their effectiveness in diverse populations.

Factors influencing radon transport in the soils of Moscow

This article delves into the factors that may influence radon flux, such as soil properties and weather conditions, on the example of two experimental locations with different soil compositions, composed primarily of clay and sand, respectively. The experimental location with sandy soil was previously observed to have anomalously high radon flux levels. Radon monitoring was performed routinely, approximately at the same time of day and in parallel on both of these locations to exclude the influence of diurnal variations. The results show that radon transport in these locations differs in mechanism: Location with clay soil has diffusive radon transport, with an average radon flux density of 37.4 ± 24.9 mBq m^-2 s^-1 and a range of 0.3-167.8 mBq m^-2 s^-1, while the location with sandy soil has convective radon transport with an average radon flux density of 93.6 ± 51.2 mBq m^-2 s^-1 and a range of 9.8-302.2 mBq m^-2 s^-1. This corresponds to about 8.3% of RFD measurements on site with clay soils exceeding the national reference level of 80 mBq m^-2 s^-1 and 45.6% exceeding them on the site with sandy soils. Average radon flux density values were then compared to meteorological variables using Pearson correlation analysis with Student's t-test. It was observed that radon flux density correlates the most with ambient air temperature both for diffusive and convective radon transport mechanisms, while a weaker inverse correlation is observed with atmospheric precipitation and wind speed for the diffusive mode of radon transport, but not for the convective. Radon activity concentration in soil air correlates with the radon flux density and air temperature in the case of convective radon transport, but does not correlate in the case of diffusive transport.

Improvement of the quality characteristics of semi-finished sponge cakes by using apple pomace powder

This study aims to assess the effect of powdered apple pomace on the technological characteristics of batter, and on the physicochemical and sensory quality characteristics of sponge cake. Apple pomace powder (10%, 25%, and 50 %) was introduced into the sponge cake formulation, where it replaced an equivalent amount of wheat flour. Assessment of the viscous properties of the composite flour has shown that the peak viscosity ranged from 330.00 to 731.00 Brabender units (BU) and its value decreased with an increase in the mass fraction of apple pomace powder. The gelatinisation temperature for the mixtures ranged 60.50–61.7°C and slightly decreased after adding by-products of apple processing. It has been found that the specific gravity of sponge cake batter increases when pomace powder is used (from 0.72±0.02c to 0.78±0.03d), which is due to the increase in the dietary fibre. The findings have shown that the volume of the cake samples containing apple pomace was smaller than that of the control sample (245.00±6.22 cm3), and the cake with 50% of apple pomace powder had the smallest volume (215.00±7.32cm3). The highest porosity was observed in the control cake sample (66.34±1.72%), while in the cake with 25 % of apple pomace powder, this parameter was 65.15±1.07%. The water absorption capacity of the control (312.60±3.15%) is the lowest compared with that of the cakes with apple pomace powder. Adding apple pomace resulted in a more intense brownish colour of the cakes and in the pleasant fresh apple taste. The semi-finished sponge cakes with 25% and 50% of apple pomace were characterised by an attractive brown colour, small-sized, properly distributed pores in the crumb, and high sensory characteristics. It can be concluded that powdered apple pomace can be successfully used as a functional and nutritionally valuable substitute for wheat flour, without a significant deterioration in the technological quality of products.

Effect of selected parameters on sectional expansion index and bulk density during the extrusion of chickpea instant semolina

A four-factor Response surface methodology central composite rotatable design was used to study the effect of moisture content, barrel temperature, screw speed, and feed screw speed on sectional expansion index and bulk density during extrusion of chickpea instant semolina for the purpose of instant product. The regression models for the investigated responses were highly significant (according to P-value) with satisfactory coefficients of determination (R2) 0.894 and 0.957. These results show that the predicted models for the investigated responses are adequate, indicating that the second-order polynomial model could be effectively used to represent the relationship between the selected parameters. The study showed that the expansion was influenced by moisture and temperature and it increased with increasing temperature for moisture content from 20 to 23% and after that decreased. Bulk density decreased with increasing feed moisture and barrel temperature in the extruder. The most important consequences for the science and practice resulting from the conducted research are that the resulting extrudates after grinding can be successfully used for the preparation of instant product with good characteristics, such as bulk density and sectional expansion index.

VARIATIONS OF INDOOR RADON CONCENTRATION IN TRADITIONAL RUSSIAN RURAL WOODEN HOUSES

Continuous indoor radon measurements were carried out in two traditional Russian rural houses located in different villages of the Moscow region in summer of 2017 and 2018. In additional, in the summer of 2017, continuous measurements of soil gas radon activity concentration at depth 0.8 m and radon exhalation rate from the ground surface near the house were performed simultaneously. It was found that the indoor radon concentration in rural houses is subject to strong daily variations, which are characterized by highs at night and lows during the day. Indoor radon concentration is directly proportional to indoor and outdoor temperature difference and inversely proportional to wind speed. While the radon exhalation rate from the ground surface, as well as the ventilation of premises (opening doors and windows) practically do not affect the concentration of radon in Russian rural wooden houses.

VARIATIONS IN SOIL RADON LEVELS DURING WINTER AND SPRING PERIODS

Radon poses significant health risk due to inhalation and subsequent α-decay of its progeny and is the second biggest cause of lung cancer worldwide. In Russian Federation, radon flux density (RFD) measurements are performed routinely to assess radon safety of land lots before construction takes place. This study aims to show possible 'weather'-influenced variations in RFD and radon activity concentration (RAC) that can occur during winter and spring periods in climatic conditions typical for territories with severe snowy winters. Results show that RFD correlates with weather, having a significant correlation with ambient air temperature in winter as well as spring periods and a weak inverse correlation with wind speed. In spring, RFD also responds to an increase in soil moisture, dropping severely because of rainfall. RAC, however, correlates very little with weather but has a weak inverse correlation with RFD.

QUALITY PARAMETERS OF SEMI-FINISHED SPONGE CAKE ENRICHED WITH PUMPKIN BY-PRODUCTS

Nowadays, there is growing demand for flour-based products that only contain natural ingredients and are highly nutritional. This tendency promotes further research to find new raw materials for their production. Using by-products of pumpkin processing is a promising way to solve this problem due to their chemical content. In this research, the physicochemical and sensory properties of sponge cake enriched with pumpkin seed powder in two different quantities (5% and 10%) have been studied. Sensory evaluation of sponge cakes with pumpkin seed powder has revealed very high consumer acceptance. It has been established that the semi-finished cake with 5% of pumpkin seed powder added decreased in volume (229.00±5.17cm3), compared with the control (255.00±5.07 cm3). Higher porosity was observed in the control sample (65.62±1.41%) and in the sample with 5% of pumpkin seed powder added (64.20±1.00%). The water-absorbing capacity of the control sample (312.60±3.15%) was the lowest, compared with that of the samples containing 5 and 10% of pumpkin by-products. The lowest values of the crust chroma were in the cake samples containing 10% of pumpkin seed powder. The colour of the crust and crumb in the control was similar to that in the cake with 5% of pumpkin seed powder. An increase in the proportion of pumpkin seed powder from 0 to 10% resulted in an increase in the protein content, fibre, and total carbohydrates. The cake samples with 10% of pumpkin seed powder were the highest in protein (14.77%), fibre (2.76%), and total carbohydrates (75.15%). The results of sensory evaluation have shown that the semi-finished sponge cake enriched with 10% of pumpkin seed powder had better sensory properties, a more acceptable shape, smell, texture of the crumb, colour, and taste, compared with other samples.

Expression of Prox1 in Medullary Thyroid Carcinoma Is Associated with Chromogranin A and Calcitonin Expression and with Ki67 Proliferative Index, but Not with Prognosis

Medullary thyroid carcinoma (MTC) has been shown to express Prospero homeobox protein 1 (Prox1), a transcription factor whose expression is altered in a variety of human cancers. We conducted a retrospective study on a series of 32 patients with MTC to test the correlation of Prox1 expression in MTC with clinicopathological features and to evaluate its prognostic significance. Correlation of Prox1 immunohistochemical expression with tumor size, proliferative index (Ki67), and calcitonin and CEA serum levels prior to surgery was tested for significant correlations. The difference in Prox1 and Ki67 immunohistochemical expression according to the immunohistochemical staining intensity of CEA, chromogranin A, and calcitonin was tested using the Kruskal-Wallis H test and linear regression analysis. The prognostic value of Prox1 and Ki67 for our patient cohort was assessed by Kaplan-Meier log rank survival analysis. We demonstrated a positive correlation between Prox1 expression and Ki67 index. Prox1 also showed significant difference in expression according to chromogranin A and calcitonin immunohistochemical expression, with higher Prox1 expression in tumors with stronger chromogranin A or calcitonin staining. Prox1 expression did not correlate with PFS or OS based on Kaplan-Meier log rank survival analysis. In conclusion, Prox1 expression in MTC is positively correlated with Ki67 and with the immunohistochemical expression of chromogranin A and calcitonin. However, the present study does not support a role for Prox1 in MTC prognosis.

Prediction of Occult Lymph Node Metastasis in Head and Neck Cancer with CD31 Vessel Quantification

Objective

The management of occult lymph node metastasis (LNM) in head and neck squamous cell carcinoma has been a matter of controversy for decades. The vascular density within the tumor microenvironment, as an indicator of ongoing angiogenesis, could constitute an attractive predictor of LNM. The use of the panvascular endothelial antibody CD31 as a marker of occult LNM has never been reported. The aim of this study was to assess the predictive value of CD31 microvascular density for the detection of occult LNM in squamous cell carcinoma of the oral cavity and oropharynx.

Study Design

Case series with chart review.

Setting

Tertiary university hospital.

Subjects and Methods

Intra- and peritumoral microvascular density values were determined in 56 cases of squamous cell carcinoma of the oral cavity (n = 50) and oropharynx (n = 6) with clinically negative necks using the CD31 marker. Statistical associations of CD31 microvascular densities with clinicopathologic data were then established.

Results

Peritumoral CD31 microvascular density was significantly associated with occult LNM in multivariate analysis ( P < .01). Recursive partitioning analysis for this parameter found a cutoff of 19.33, which identified occult LNM with a sensitivity of 91%, a specificity of 65%, a positive predictive value of 40%, a negative predictive value of 97%, and an overall diagnostic accuracy of 71%.

Conclusion

Peritumoral CD31 microvascular density in primary squamous cell carcinoma of the oral cavity and oropharynx allows accurate prediction of occult LNM.

Kinetics of Ordering and Deformation in Photosensitive Azobenzene LC Networks

Azobenzene-containing polymer networks are unique compounds that are able to change their shape in response to light, which makes them prospective materials for photocontrollable nano-templates, sensors, microrobots, artificial muscles, etc. In present work, we study the kinetics of light-induced ordering and deformation in two-component polymer networks containing optically inert liquid crystalline (LC) mesogens and azobenzene chromophores. By this, we generalize our previous theory [J. Phys. Chem. Lett. 2017, 8, 1094⁻1098] devoted to the kinetics of photoizomerization in one-component azo-polymers without mesogenic inclusions. The kinetic equations of photoisomerization are used, taking into account the angular selectivity of the photoisomerization with respect to the polarization direction of the light E. After multiple trans-cis-trans photoisomerization cycles, the azobenzenes are reoriented preferably perpendicular to the vector E. This changes the ordering of the mesogens due to the orientational LC interactions between the components. The light-induced reordering is accompanied by network deformation. Time evolution of ordering and deformation is found as a function of the intensity of light and structural parameters of the LC azo-networks, which define the viscosity, the strength of the LC interactions between the components, the volume fraction of the azobenzene moieties, and the angular distribution of azobenzenes in polymer chains. Established structure-property relationships are in agreement with a number of experimental data.

Kinetics of light-induced ordering and deformation in LC azobenzene-containing materials

Azobenzene-containing smart materials are able to transform the energy of light into directional mechanical stress. We develop a theory of time-dependent light-induced ordering and deformation in azobenzene materials starting from the kinetic equations of photoisomerization. The liquid crystalline (LC) interactions between rod-like trans-isomers are taken into account. Angular selectivity of the photoisomerization known as an "angular hole burning" or the Weigert effect leads to the light-induced ordering and deformation of the azobenzene materials. The time evolution of ordering and deformation is found as a function of intensity of light depending on the opto-mechanical characteristics of the materials, such as probabilities of the optical excitation of trans- and cis-isomers, angular jump during the single isomerization event, viscosity of the materials, strength of the LC interactions in both the isotropic and LC materials, and the angular distribution of chromophores in polymer chains. Established structural-property relationships are in agreement with a number of experiments and can be used for the construction of light-controllable smart materials for practical applications.

pH-Sensitive Hydrogels Composed of Chitosan and Polyacrylamide: Enzymatic Degradation

The enzymatic degradation of three types of pH-sensitive hydrogels, composed of the natural polyaminosaccharide chitosan and polyacrylamide, was studied. The weight of the films that were made with net-PAAm- i-chitosan, net-chitosan- i-PAAm and net-chitosan- net-PAAm decreased in the presence of the Trichoderma viride enzyme complex ; thus, the chitosan in the composite retained its degradability after crosslinking. The rate of enzymatic degradation depended on the structure of the network, on the amount of crosslinking agents, on the pH of the medium and on the temperature. Crosslinked chitosan alone degraded slower than net-chitosan- i-PAAm; this was attributed to the facilitated penetration of enzyme by the water-soluble PAAm in the semi-IPNs. T. viride embedded in chitosan/PAAm films or beads developed and reproduced normally. However, T. viride embedded in net-chitosani-PAAm developed considerably slower, and development was not detected in the case of net-PAAm- i-chitosan. All of the networks proved to be appropriate carriers of Bacillus subtilis.

High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP-oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution

Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader's quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H⋯H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface.

Heat-induced conformational changes of TET peptidase from crenarchaeon Desulfurococcus kamchatkensis

The effects of heating on the structure and stability of multimeric TET aminopeptidase (APDkam589) were studied by differential scanning calorimetry, tryptophan fluorescence quenching, and dynamic light scattering. Thermally induced structural changes in APDkam589 were found to occur in two phases: local conformational changes, which occur below 70 °C and are not associated with thermal denaturation of the protein, and global structural changes (above 70 °C) induced by irreversible thermal unfolding of the protein accompanied by its spontaneous aggregation. These results may explain the bell-shaped temperature dependence with a maximum at ~70 °C previously observed for enzymatic activity of APDkam589. Interestingly, the thermal unfolding of APDkam589 at about 81.2 °C is accompanied by a so-called blue-shift of about 10 nm-a shift of the Trp fluorescence spectrum toward shorter wavelength. From this point of view, APDkam589 is quite different from most proteins, which are characterized by a long wavelength shift of the spectrum ("red-shift") upon denaturation. The blue-shift of the Trp fluorescence spectrum reflects the changes in the environment of Trp residues, which becomes more hydrophobic upon denaturation. The molecular structure of APDkam589 was determined by X-ray diffraction. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. Therefore, the blue-shift of the Trp fluorescence spectrum can be explained, at least partly, by aggregation of APDkam589, which occurs simultaneously with its thermal denaturation and probably makes the environment of these Trp residues more hydrophobic.

Light-induced deformation of polymer networks containing azobenzene chromophores and liquid crystalline mesogens

Two-component polymer networks containing liquid crystalline (LC) mesogens and azobenzene chromophores belong to a class of smart materials which combine uniquely the orientation order of liquid crystals and light-induced deformation of photosensitive polymers. In the present study we develop a theory of light-induced deformation of azobenzene-containing LC networks. It is shown that preferential reorientation of chromophores perpendicular to the polarization direction of the light E leads to the reorientation of the mesogens due to LC interactions between the components. Reorientation of the chromophores and mesogens results in the light-induced deformation of the polymer network. The sign of deformation (expansion/contraction with respect to the vector E) depends on the orientation distribution of the mesogens and chromophores inside the network strands. The magnitude of deformation increases with increase of the volume fraction of chromophores and the strength of LC interactions between the components. The influence of the dilution of azobenzene-containing networks by the bent cis-isomers of the chromophores on the light-induced deformation is discussed.

Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography

The 1.8 Å resolution neutron structure of deuterated type III antifreeze protein in which the methyl groups of leucine and valine residues are selectively protonated is presented. Comparison between this and the 1.85 Å resolution neutron structure of perdeuterated type III antifreeze protein indicates that perdeuteration improves the visibility of solvent molecules located in close vicinity to hydrophobic residues, as cancellation effects between H atoms of the methyl groups and nearby heavy-water molecules (D2O) are avoided.

UHR PX and NPC studies of H-FABP water network with tiny perdeuterated crystals

We have obtained very detailed information about the internal water molecules in the large internal cavity inside fatty acid binding (FABP) proteins , in the presence of bound fatty acids (FA), by Ultra High Resolution X-Ray Crystallography (UHR) to 0.7 Å and Neutron Protein Crystallography (NPC) to 1.9 Å using a "radically small" (V=0.05 mm3) crystal. These waters form a very well ordered dense cluster of 12 molecules, positioned between the hydrophilic internal wall of the cavity and the fatty acid molecule. This information has been used for a detailed electrostatic analysis based on the charge distribution description modeled in the multipole formalism and on the Atoms in Molecules theory. This information is also being used in molecular dynamics simulations of H-FABP and its complex with FA in order to quantify the energetic contribution of these internal waters to the binding energy. The experiment has been done with oleic acid, coming with the protein expressed in E. Coli. The results have been analyzed in order to understand the interactions between the FA, the internal water and the protein, and in particular the role played by the water molecules in determining the potency and specificity of FA binding to FABPs. The major tool for visualizing the water molecules inside the H-FABP cavity is UHR X-Ray Crystallography combined with NPC. UHR crystallographic structures give the positions of hydrogen and oxygen atoms for well-ordered water molecules. NPC determines hydrogen atom positions, particularly of water molecules which have multiple conformations, leading to the best possible crystallographic model. This model was then complemented by a transferred charge distribution to accurately determine the electrostatic and topological properties in the binding pocket, providing a description of the way water molecules in hydration layer contribute to the binding of ligand, which is essential to understand and model ligand binding.

ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain

DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential for maintaining genome integrity in the replication, recombination and repair of DNA. High flexibility is important for the function of DNA ligase molecules. Two types of overall conformations of archaeal DNA ligase that depend on the relative position of the OB-fold domain have previously been revealed: closed and open extended conformations. The structure of ATP-dependent DNA ligase from Thermococcus sp. 1519 (LigTh1519) in the crystalline state determined at a resolution of 3.02 Å shows a new relative arrangement of the OB-fold domain which is intermediate between the positions of this domain in the closed and the open extended conformations of previously determined archaeal DNA ligases. However, small-angle X-ray scattering (SAXS) measurements indicate that in solution the LigTh1519 molecule adopts either an open extended conformation or both an intermediate and an open extended conformation with the open extended conformation being dominant.

Structural and functional studies of ReP1-NCXSQ, a protein regulating the squid nerve Na+/Ca2+ exchanger

The protein ReP1-NCXSQ was isolated from the cytosol of squid nerves and has been shown to be required for MgATP stimulation of the squid nerve Na(+)/Ca(2+) exchanger NCXSQ1. In order to determine its mode of action and the corresponding biologically active ligand, sequence analysis, crystal structures and mass-spectrometric studies of this protein and its Tyr128Phe mutant are reported. Sequence analysis suggests that it belongs to the CRABP family in the FABP superfamily. The X-ray structure at 1.28 Å resolution shows the FABP β-barrel fold, with a fatty acid inside the barrel that makes a relatively short hydrogen bond to Tyr128 and shows a double bond between C9 and C10 but that is disordered beyond C12. Mass-spectrometric studies identified this fatty acid as palmitoleic acid, confirming the double bond between C9 and C10 and establishing a length of 16 C atoms in the aliphatic chain. This acid was caught inside during the culture in Escherichia coli and therefore is not necessarily linked to the biological activity. The Tyr128Phe mutant was unable to activate the Na(+)/Ca(2+) exchanger and the corresponding crystal structure showed that without the hydrogen bond to Tyr128 the palmitoleic acid inside the barrel becomes disordered. Native mass-spectrometric analysis confirmed a lower occupancy of the fatty acid in the Tyr128Phe mutant. The correlation between (i) the lack of activity of the Tyr128Phe mutant, (ii) the lower occupancy/disorder of the bound palmitoleic acid and (iii) the mass-spectrometric studies of ReP1-NCXSQ suggests that the transport of a fatty acid is involved in regulation of the NCXSQ1 exchanger, providing a novel insight into the mechanism of its regulation. In order to identify the biologically active ligand, additional high-resolution mass-spectrometric studies of the ligands bound to ReP1-NCXSQ were performed after incubation with squid nerve vesicles both with and without MgATP. These studies clearly identified palmitic acid as the fatty acid involved in regulation of the Na(+)/Ca(2+) exchanger from squid nerve.

Crystal packing modifies ligand binding affinity: the case of aldose reductase

The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question, simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; K(d) = 6.5 nM) and IDD594 (594; K(d) = 61 nM), which bind to h-aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the Loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used.

Neutron structure of type-III antifreeze protein allows the reconstruction of AFP-ice interface

Antifreeze proteins (AFPs) inhibit ice growth at sub-zero temperatures. The prototypical type-III AFPs have been extensively studied, notably by X-ray crystallography, solid-state and solution NMR, and mutagenesis, leading to the identification of a compound ice-binding surface (IBS) composed of two adjacent ice-binding sections, each which binds to particular lattice planes of ice crystals, poisoning their growth. This surface, including many hydrophobic and some hydrophilic residues, has been extensively used to model the interaction of AFP with ice. Experimentally observed water molecules facing the IBS have been used in an attempt to validate these models. However, these trials have been hindered by the limited capability of X-ray crystallography to reliably identify all water molecules of the hydration layer. Due to the strong diffraction signal from both the oxygen and deuterium atoms, neutron diffraction provides a more effective way to determine the water molecule positions (as D(2) O). Here we report the successful structure determination at 293 K of fully perdeuterated type-III AFP by joint X-ray and neutron diffraction providing a very detailed description of the protein and its solvent structure. X-ray data were collected to a resolution of 1.05 Å, and neutron Laue data to a resolution of 1.85 Å with a "radically small" crystal volume of 0.13 mm(3). The identification of a tetrahedral water cluster in nuclear scattering density maps has allowed the reconstruction of the IBS-bound ice crystal primary prismatic face. Analysis of the interactions between the IBS and the bound ice crystal primary prismatic face indicates the role of the hydrophobic residues, which are found to bind inside the holes of the ice surface, thus explaining the specificity of AFPs for ice versus water.

X-ray-induced deterioration of disulfide bridges at atomic resolution

Overall and site-specific X-ray-induced damage to porcine pancreatic elastase was studied at atomic resolution at temperatures of 100 and 15 K. The experiments confirmed that irradiation causes small movements of protein domains and bound water molecules in protein crystals. These structural changes occur not only at 100 K but also at temperatures as low as 15 K. An investigation of the deterioration of disulfide bridges demonstrated the following. (i) A decrease in the occupancy of S(γ) atoms and the appearance of new cysteine rotamers occur simultaneously. (ii) The occupancy decrease is observed for all S(γ) atoms, while new rotamers arise for some of the cysteine residues; the appearance of new conformations correlates with the accessibility to solvent. (iii) The sum of the occupancies of the initial and new conformations of a cysteine residue is approximately equal to the occupancy of the second cysteine residue in the bridge. (iv) The most pronounced changes occur at doses below 1.4 × 10(7) Gy, with only small changes occurring at higher doses. Comparison of the radiation-induced changes in an elastase crystal at 100 and 15 K suggested that the dose needed to induce a similar level of deterioration of the disulfide bonds and atomic displacements at 15 K to those seen at 100 K is more than two times higher.

X-ray-radiation-induced cooperative atomic movements in protein

X-rays interact with biological matter and cause damage. Proteins and other macromolecules are damaged primarily by ionizing X-ray photons and secondarily by reactive radiolytic chemical species. In particular, protein molecules are damaged during X-ray diffraction experiments with protein crystals, which is, in many cases, a serious hindrance to structure solution. The local X-ray-induced structural changes of the protein molecule have been studied using a number of model systems. However, it is still not well understood whether these local chemical changes lead to global structural changes in protein and what the mechanism is. We present experimental evidence at atomic resolution indicating the movement of large parts of the protein globule together with bound water molecules in the early stages of radiation damage to the protein crystal. The data were obtained from a crystal cryocooled to approximately 100 K and diffracting to 1 A. The movement of the protein structural elements occurs simultaneously with the decarboxylation of several glutamate and aspartate residues that mediate contacts between moving protein structural elements and with the rearrangement of the water network. The analysis of the anisotropy of atomic displacement parameters reveals that the observed atomic movements occur at different rates in different unit cells of the crystal. Thus, the examination of the cooperative atomic movement enables us to better understand how radiation-induced local chemical and structural changes of the protein molecule eventually lead to disorder in protein crystals.

Sensitivity of mesenchymal stem cells and their progeny to medicines used for the treatment of hematoproliferative diseases

BACKGROUND/AIMS

The influence of cytostatic medicines on mesenchymal stem cells (MSC) and their progeny, fibroblastic colony-forming units (CFU-F), was investigated.

METHODS

Mice were treated with busulfan, cyclophosphamide, cytarabine, methotrexate and bortezomib, as used in clinical practice. MSC and CFU-F were analyzed 3 days and 6 weeks after the treatment termination. To estimate MSC numbers, the ectopic foci formation method was used. Briefly, a donor bone marrow plug was transplanted under the renal capsule of a syngeneic animal, leading to ectopic foci formation. The systemic response of the hematopoietic microenvironment to these drugs was studied using the same method applied to recipients pretreated with the medicines.

RESULTS

CFU-F concentration was halved in the bone marrow of mice treated with busulfan, methotrexate and cyclophosphamide, and was not restored for the next 6 weeks. Proliferative potential and differentiation abilities of MSC were not affected by these medicines. The enlargement of foci size in mice treated with cytostatic agents was not conditioned by MSC, but by more mature stromal precursor cells.

CONCLUSIONS

Cytostatic medicines affect stromal precursors in 2 ways: they decrease CFU-F concentration in the 'steady-state' bone marrow, while stimulating growth of the stromal microenvironment during its de novo formation. MSC are not sensitive to the cytostatic agents used.

Novel hexamerization motif is discovered in a conserved cytoplasmic protein from Salmonella typhimurium

The cytoplasmic protein Stm3548 of unknown function obtained from a strain of Salmonella typhimurium was determined by X-ray crystallography at a resolution of 2.25 A. The asymmetric unit contains a hexamer of structurally identical monomers. The monomer is a globular domain with a long beta-hairpin protrusion that distinguishes this structure. This beta-hairpin occupies a central position in the hexamer, and its residues participate in the majority of interactions between subunits of the hexamer. We suggest that the structure of Stm3548 presents a new hexamerization motif. Because the residues participating in interdomain interactions are highly conserved among close members of protein family DUF1355 and buried solvent accessible area for the hexamer is significant, the hexamer is most likely conserved as well. A light scattering experiment confirmed the presence of hexamer in solution.

Ultrahigh-resolution study of protein atomic displacement parameters at cryotemperatures obtained with a helium cryostat

Two X-ray data sets for a complex of human aldose reductase (h-AR) with the inhibitor IDD 594 and the cofactor NADP(+) were collected from two different parts of the same crystal to a resolution of 0.81 A at 15 and 60 K using cold helium gas as cryogen. The contribution of temperature to the atomic B values was estimated by comparison of the independently refined models. It was found that although being slightly different for different kinds of atoms, the differences (deltaB) in the isotropic equivalents B of atomic displacement parameters (ADPs) were approximately constant (about 1.7 A(2)) for well ordered atoms as the temperature was increased from 15 to 60 K. The mean value of this difference varied according to the number of non-H atoms covalently bound to the parent atom. Atoms having a B value of higher than 8 A(2) at 15 K showed much larger deviations of deltaB from the average value, which might reflect partial occupancy of atomic sites. An analysis of the anisotropy of ADPs for individual atoms revealed an increase in the isotropy of ADPs with the increase of the temperature from 15 to 60 K. In a separate experiment, a 0.93 A resolution data set was collected from a different crystal of the same complex at 100 K using cold nitrogen as a cryogen. The effects of various errors on the atomic B values were estimated by comparison of the refined models and the temperature-dependent component was inferred. It was found that both decreasing the data redundancy and increasing the resolution cutoff led to an approximately constant increase in atomic B values for well ordered atoms.

Early Lymph Vessel Development From Embryonic Stem Cells

Objective— The purpose of this study was to establish a model system for lymph vessel development based on directed differentiation of murine embryonic stem cells.

Methods and Results— Stem cells were aggregated to form embryoid bodies, and subsequently cultured in 3-dimensional collagen matrix for up to 18 days. Treatment with vascular endothelial growth factor (VEGF)-C and VEGF-A individually enhanced formation of lymphatic vessel structures, although combined treatment with VEGF-C and VEGF-A was most potent and gave rise to a network of LYVE-1, podoplanin, Prox1, and VEGF receptor-3 positive lymphatic vessel structures running parallel to and apparently emanating from, capillaries. In contrast, fibroblast growth factor-2, hepatocyte growth factor, or hypoxia had little or no effect on the development of the early lymphatics. Further, cells of hematopoietic origin were shown to express lymphatic markers. In summary, different subpopulations of lymphatic endothelial cells were identified on the basis of differential expression of several lymphatic and blood vessel markers, indicating vascular heterogeneity.

Conclusions— We conclude that the present model closely mimics the early steps of lymph vessel development in mouse embryos.

Large-scale identification of genes implicated in kidney glomerulus development and function

To advance our understanding of development, function and diseases in the kidney glomerulus, we have established and large-scale sequenced cDNA libraries from mouse glomeruli at different stages of development, resulting in a catalogue of 6053 different genes. The glomerular cDNA clones were arrayed and hybridized against a series of labeled targets from isolated glomeruli, non-glomerular kidney tissue, FACS-sorted podocytes and brain capillaries, which identified over 300 glomerular cell-enriched transcripts, some of which were further sublocalized to podocytes, mesangial cells and juxtaglomerular cells by in situ hybridization. For the earliest podocyte marker identified, Foxc2, knockout mice were used to analyze the role of this protein during glomerular development. We show that Foxc2 controls the expression of a distinct set of podocyte genes involved in podocyte differentiation and glomerular basement membrane maturation. The primary podocyte defects also cause abnormal differentiation and organization of the glomerular vascular cells. We surmise that studies on the other novel glomerulus-enriched transcripts identified in this study will provide new insight into glomerular development and pathomechanisms of disease.

Factorizing Selectivity Determinants of Inhibitor Binding toward Aldose and Aldehyde Reductases: Structural and Thermodynamic Properties of the Aldose Reductase Mutant Leu300Pro−Fidarestat Complex

Structure of the Leu300Pro mutant of human aldose reductase (ALR2) in complex with the inhibitor fidarestat is determined. Comparison with the hALR2-fidarestat complex and the porcine aldehyde reductase (ALR1)-fidarestat complex indicates that the hydrogen bond between the Leu300 amino group of the wild-type and the exocyclic amide group of the inhibitor is the key determinant for the specificity of fidarestat for ALR2 over ALR1. Thermodynamic data also suggest an enthalpic contribution as the predominant difference in the binding energy between the aldose reductase mutant and the wild-type. An additional selectivity-determining feature is the difference in the interaction between the inhibitor and the side chain of Trp219, ordered in the present structure but disordered (corresponding Trp220) in the ALR1-fidarestat complex. Thus, the hydrogen bond ( approximately 7 kJ/mol) corresponds to a 23-fold difference in inhibitor potency while the differences in the interactions between Trp219(ALR2) and fidarestat and between Trp220(ALR1) and fidarestat can account for an additional 10-fold difference in potency.

Discovery of 3-[(4,5,7-trifluorobenzothiazol-2-yl)methyl]indole-N-acetic acid (lidorestat) and congeners as highly potent and selective inhibitors of aldose reductase for treatment of chronic diabetic complications

Recent efforts to identify treatments for chronic diabetic complications have resulted in the discovery of a novel series of highly potent and selective 3-[(benzothiazol-2-yl)methyl]indole-N-alkanoic acid aldose reductase inhibitors. The lead candidate, 3-[(4,5,7-trifluorobenzothiazol-2-yl)methyl]indole-N-acetic acid (lidorestat, 9) inhibits aldose reductase with an IC(50) of 5 nM, while being 5400 times less active against aldehyde reductase, a related enzyme involved in the detoxification of reactive aldehydes. It lowers nerve and lens sorbitol levels with ED(50)'s of 1.9 and 4.5 mg/kg/d po, respectively, in the 5-day STZ-induced diabetic rat model. In a 3-month diabetic intervention model (1 month of diabetes followed by 2 months of drug treatment at 5 mg/kg/d po), it normalizes polyols and reduces the motor nerve conduction velocity deficit by 59% relative to diabetic controls. It has a favorable pharmacokinetic profile (F, 82%; t(1/2), 5.6 h; Vd, 0.694 L/kg) with good drug penetration in target tissues (C(max) in sciatic nerve and eye are 2.36 and 1.45 mug equiv/g, respectively, when dosed with [(14)C]lidorestat at 10 mg/kg po).

Lymphatic Neoangiogenesis in Human Kidney Transplants Is Associated with Immunologically Active Lymphocytic Infiltrates

Renal transplant rejection is caused by a lymphocyte-rich inflammatory infiltrate that attacks cortical tubules and endothelial cells. Immunosuppressive therapy reduces the number of infiltrating cells; however, their exit routes are not known. Here a >50-fold increase of lymphatic vessel density over normal kidneys in grafts with nodular mononuclear infiltrates is demonstrated by immunohistochemistry on human renal transplant biopsies using antibodies to the lymphatic endothelial marker protein podoplanin. Nodular infiltrates are constantly associated with newly formed, Ki-67-expressing lymphatic vessels and contain the entire repertoire of T and B lymphocytes to provide specific cellular and humoral alloantigenic immune responses, including Ki-67(+) CD4(+) and CD8(+) T lymphocytes, S100(+) dendritic cells, and Ki-67(+)CD20(+) B lymphocytes and lambda- and kappa-chain-expressing plasmacytoid cells. Numerous chemokine receptor CCR7(+) cells within the nodular infiltrates seemed to be attracted by secondary lymphatic chemokine (SLC/CCL21) that is produced and released by lymphatic endothelial cells in a complex with podoplanin. From these results, it is speculated that lymphatic neoangiogenesis not only contributes to the export of the rejection infiltrate but also is involved in the maintenance of a potentially detrimental alloreactive immune response in renal transplants and provides a novel therapeutic target.