A Preparative Method for the Isolation of Calponin from Molluscan Catch Muscle

We describe the development of a preparative method to isolate molluscan catch muscle, calponin. This method is based on the ability of calponin to interact with actin in a temperature-dependent manner. After extracting thin filaments, as previously described, the extract was ultracentrifuged at 2 °C. While other surface proteins of thin filaments co-precipitated with actin, calponin, along with some minor contaminants, remained in the supernatant. Calponin was purified through cation-exchange chromatography. The yield of pure protein was four-fold higher than that achieved through high-temperature extraction. To evaluate functionally isolated proteins, we determined the effect of calponin on Mg²⁺-ATPase activity of hybrid and non-hybrid actomyosin. The degree of ATPase inhibition was consistent with previously published data but strongly dependent on the environmental conditions and source of actin and myosin used. Furthermore, at low concentrations, calponin could induce the ATPase activity of hybrid actomyosin. This result was consistent with data indicating that calponin can modulate actin conformation to increase the relative content of “switched on” actin monomers in thin filaments. We assume that calponin obtained by the isolation method proposed herein is a fully functional protein that can both inhibit and induce the ATPase activity.     

Novel A-Ring Chalcone Derivatives of Oleanolic and Ursolic Amides with Anti-Proliferative Effect Mediated through ROS-Triggered Apoptosis

A series of A-ring modified oleanolic and ursolic acid derivatives including C28 amides (3-oxo-C2-nicotinoylidene/furfurylidene, 3β-hydroxy-C2-nicotinoylidene, 3β-nicotinoyloxy-, 2-cyano-3,4-seco-4(23)-ene, indolo-, lactame and azepane) were synthesized and screened for their cytotoxic activity against the NCI-60 cancer cell line panel. The results of the first assay of thirty-two tested compounds showed that eleven derivatives exhibited cytotoxicity against cancer cells, and six of them were selected for complete dose–response studies. A systematic study of local SARs has been carried out by comparative analysis of potency distributions and similarity relationships among the synthesized compounds using network-like similarity graphs. Among the oleanane type triterpenoids, C2-[4-pyridinylidene]-oleanonic C28-morpholinyl amide exhibited sub-micromolar potencies against 15 different tumor cell lines and revealed particular selectivity for non-small cell lung cancer (HOP-92) with a GI₅₀ value of 0.0347 μM. On the other hand, superior results were observed for C2-[3-pyridinylidene]-ursonic N-methyl-piperazinyl amide 29, which exhibited a broad-spectrum inhibition activity with GI₅₀ < 1 μM against 33 tumor cell lines and <2 μM against all 60 cell lines. This compound has been further evaluated for cell cycle analysis to decipher the mechanism of action. The data indicate that compound 29 could exhibit both cytostatic and cytotoxic activity, depending on the cell line evaluated. The cytostatic activity appears to be determined by induction of the cell cycle arrest at the S (MCF-7, SH-SY5Y cells) or G₀/G₁ phases (A549 cells), whereas cytotoxicity of the compound against normal cells is nonspecific and arises from apoptosis without significant alterations in cell cycle distribution (HEK293 cells). Our results suggest that the antiproliferative effect of compound 29 is mediated through ROS-triggered apoptosis that involves mitochondrial membrane potential depolarization and caspase activation.     

Attaching Different Kinds of Proteinaceous Nanospheres to a Variety of Fabrics Using Ultrasound Radiation

The application of a rapid, non-destructive, cost-effective technique such as ultrasonic emulsification for the coating of different textiles was explored. The technical benefits for this research were the generation of multifunctional materials and their combinations through environmentally friendly processing technologies. We have shown for the first time that ultrasonic waves can be used to coat proteinaceous micro- and nanospheres (PM) of BSA (Bovine Serum Albumin) protein and casein on the surface of cotton and polyester (PE) fabrics. The creation and the anchoring of the microbubbles to the fabrics were performed by a one-step reaction, and the process is usually stopped after 3 min. The PM of bovine serum albumin (BSA) bonded to cotton and polyester fabrics has shown stability for ∼9 months. The PMs were shown to be attached more strongly to the polyester than to the cotton, and sustained stronger washing conditions on PE. The diameter of the BSA and the casein spheres on cotton was in the range of 0.8–1.0 μm, while on the PE it varied between 60 and 120 nm.     

Nanoparticles prepared from porous silicon nanowires for bio-imaging and sonodynamic therapy

Evaluation of cytotoxicity, photoluminescence, bio-imaging, and sonosensitizing properties of silicon nanoparticles (SiNPs) prepared by ultrasound grinding of porous silicon nanowires (SiNWs) have been investigated. SiNWs were formed by metal (silver)-assisted wet chemical etching of heavily boron-doped (100)-oriented single crystalline silicon wafers. The prepared SiNWs and aqueous suspensions of SiNPs exhibit efficient room temperature photoluminescence (PL) in the spectral region of 600 to 1,000 nm that is explained by the radiative recombination of excitons confined in small silicon nanocrystals, from which SiNWs and SiNPs consist of. On the one hand, in vitro studies have demonstrated low cytotoxicity of SiNPs and possibilities of their bio-imaging applications. On the other hand, it has been found that SiNPs can act as efficient sensitizers of ultrasound-induced suppression of the viability of Hep-2 cancer cells.     

Reusable specification templates for defining dynamic semantics of DSLs

Software and Systems Modeling - In the context of model-driven engineering, the dynamic (execution) semantics of domain-specific languages (DSLs) is usually not specified explicitly and stays...     

Stabilizing RNA by the sonochemical formation of RNA nanospheres

Biological macromolecules, including DNA, RNA, and proteins, have intrinsic features that make them potential building blocks for the bottom-up fabrication of nanodevices. Unlike DNA, RNA is a more versatile molecule whose range in the cell is from 21 to thousands of nucleotides and is usually folded into stem and loop structures. RNA is unique in nanoscale fabrication due to its diversity in size, function, and structure. Because gene expression analysis is becoming a clinical reality and there is a need to collect RNA in minute amounts from clinical samples, keeping the RNA intact is a growing challenge. RNA samples are notoriously difficult to handle because of their highly labile nature and tendency to degrade even under controlled RNase-free conditions and maintenance in the cold. Silencing the RNA that induces the RNA interference is viewed as the next generation of therapeutics. The stabilization and delivery of RNA to cells are the major concerns in making siRNAs usable drugs. For the first time, ultrasonic waves are shown to convert native RNA molecules to RNA nanospheres. The creation of the nanobubbles is performed by a one-step reaction. The RNA nanospheres are stable at room temperature for at least one month. Additionally, the nanospheres can be inserted into mammalian cancer cells (U2OS). This research achieves: 1) a solution to RNA storage; and 2) a way to convert RNA molecules to RNA particles. RNA nanosphere formation is a reversible process, and by using denaturing conditions, the RNA can be refolded into intact molecules.     

Encapsulation of RNA Molecules in BSA Microspheres and Internalization into Trypanosoma Brucei Parasites and Human U2OS Cancer Cells

RNA was encapsulated in bovine serum albumin (BSA) microspheres using a one‐step sonochemical process from an water–oil solvent biphasic system. Confocal microcoscopy and fluorescence‐activated cell sorting indicate that a CY3‐RNA (RNA labeled with red fluorescent indocarbocyanine Cy3 dye) sphere is encapsulated in the BSA outer sphere. The diameter of the sphere depends on the number of nucleotides of the RNA, ranging from 0.63 to 2.74 μm. Total RNA (t‐RNA) was used as a prototype for the future small interfering RNA (siRNA) delivery. A very broad size distribution characterizes the RNA spheres and therefore, among the loaded BSA spheres, there were sufficiently small spheres to be successfully introduced into trypanosoma brucei parasites and human osteosarcoma U2OS cancer cells.     

Identification of Amyloidogenic Regions in Pseudomonas aeruginosa Ribosomal S1 Protein

Bacterial S1 protein is a functionally important ribosomal protein. It is a part of the 30S ribosomal subunit and is also able to interact with mRNA and tmRNA. An important feature of the S1 protein family is a strong tendency towards aggregation. To study the amyloidogenic properties of S1, we isolated and purified the recombinant ribosomal S1 protein of Pseudomonas aeruginosa. Using the FoldAmyloid, Waltz, Pasta 2.0, and AGGRESCAN programs, amyloidogenic regions of the protein were predicted, which play a key role in its aggregation. The method of limited proteolysis in combination with high performance liquid chromatography and mass spectrometric analysis of the products, made it possible to identify regions of the S1 protein from P. aeruginosa that are protected from the action of proteinase K, trypsin, and chymotrypsin. Sequences of theoretically predicted and experimentally identified amyloidogenic regions were used to synthesize four peptides, three of which demonstrated the ability to form amyloid-like fibrils, as shown by electron microscopy and fluorescence spectroscopy. The identified amyloidogenic sites can further serve as a basis for the development of new antibacterial peptides against the pathogenic microorganism P. aeruginosa.     

Impact of Autophagy Impairment on Experience- and Diet-Related Synaptic Plasticity

The beneficial effects of diet and exercise on brain function are traditionally attributed to the enhancement of autophagy, which plays a key role in neuroprotection via the degradation of potentially harmful intracellular structures. The molecular machinery of autophagy has also been suggested to influence synaptic signaling via interaction with trafficking and endocytosis of synaptic vesicles and proteins. Still, the role of autophagy in the regulation of synaptic plasticity remains elusive, especially in the mammalian brain. We explored the impact of autophagy on synaptic transmission and homeostatic and acute synaptic plasticity using transgenic mice with induced deletion of the Beclin1 protein. We observed down-regulation of glutamatergic and up-regulation of GABAergic synaptic currents and impairment of long-term plasticity in the neocortex and hippocampus of Beclin1-deficient mice. Beclin1 deficiency also significantly reduced the effects of environmental enrichment, caloric restriction and its pharmacological mimetics (metformin and resveratrol) on synaptic transmission and plasticity. Taken together, our data strongly support the importance of autophagy in the regulation of excitatory and inhibitory synaptic transmission and synaptic plasticity in the neocortex and hippocampus. Our results also strongly suggest that the positive modulatory actions of metformin and resveratrol in acute and homeostatic synaptic plasticity, and therefore their beneficial effects on brain function, occur via the modulation of autophagy.     

Genomic Determinants Potentially Associated with Clinical Manifestations of Human-Pathogenic Tick-Borne Flaviviruses

The tick-borne flavivirus group contains at least five species that are pathogenic to humans, three of which induce encephalitis (tick-borne encephalitis virus, louping-ill virus, Powassan virus) and another two species induce hemorrhagic fever (Omsk hemorrhagic fever virus, Kyasanur Forest disease virus). To date, the molecular mechanisms responsible for these strikingly different clinical forms are not completely understood. Using a bioinformatic approach, we performed the analysis of each amino acid (aa) position in the alignment of 323 polyprotein sequences to calculate the fixation index (F_st) per site and find the regions (determinants) where sequences belonging to two designated groups were most different. Our algorithm revealed 36 potential determinants (F_st ranges from 0.91 to 1.0) located in all viral proteins except a capsid protein. In an envelope (E) protein, most of the determinants were located on the virion surface regions (domains II and III) and one (absolutely specific site 457) was located in the transmembrane region. Another 100% specific determinant site (E63D) with F_st = 1.0 was located in the central hydrophilic domain of the NS2b, which mediates NS3 protease activity. The NS5 protein contains the largest number of determinants (14) and two of them are absolutely specific (T226S, E290D) and are located near the RNA binding site 219 (methyltransferase domain) and the extension structure. We assume that even if not absolutely, highly specific sites, together with absolutely specific ones (F_st = 1.0) can play a supporting role in cell and tissue tropism determination.