A hybrid discriminative/generative approach to protein fold recognition

There are two standard approaches to the classification task: generative, which use training data to estimate a probability model for each class, and discriminative, which try to construct flexible decision boundaries between the classes. An ideal classifier should combine these two approaches. In this paper a classifier combining the well-known support vector machine (SVM) classifier with regularized discriminant analysis (RDA) classifier is presented. The hybrid classifier is used for protein structure prediction which is one of the most important goals pursued by bioinformatics. The obtained results are promising, the hybrid classifier achieves better result than the SVM or RDA classifiers alone. The proposed method achieves higher recognition ratio than other methods described in the literature.     

Chemical and enzymatic interesterification of a beef tallow and rapeseed oil equal‐weight blend

A mixture of beef tallow and rapeseed oil (1:1, wt/wt) was interesterified using sodium methoxide or immobilized lipases from Rhizomucor miehei (Lipozyme IM) and Candida antarctica (Novozym 435) as catalysts. Chemical interesterifications were carried out at 60 and 90 °C for 0.5 and 1.5 h using 0.4, 0.6 and 1.0 wt‐% CH₃ONa. Enzymatic interesterifications were carried out at 60 °C for 8 h with Lipozyme IM or at 80 °C for 4 h with Novozym 435. The biocatalyst doses were kept constant (8 wt‐%), but the water content was varied from 2 to 10 wt‐%. The starting mixture and the interesterified products were separated by column chromatography into a pure triacylglycerol fraction and a nontriacylglycerol fraction, which contained free fatty acids, mono‐, and diacylglycerols. It was found that the concentration of free fatty acids and partial acylglycerols increased after interesterification. The slip melting points and solid fat contents of the triacylglycerol fractions isolated from interesterified fats were lower compared with the nonesterified blends. The sn‐2 and sn‐1,3 distribution of fatty acids in the TAG fractions before and after interesterification were determined. These distributions were random after chemical interesterification and near random when Novozym 435 was used. When Lipozyme IM was used, the fatty acid composition at the sn‐2 position remained practically unchanged, compared with the starting blend. The interesterified fats and isolated triacylglycerols had reduced oxidative stabilities, as assessed by Rancimat induction times. Addition of 0.02% BHA and BHT to the interesterified fats improved their stabilities.     

An important step towards a prevascularized islet macroencapsulation device—effect of micropatterned membranes on development of endothelial cell network

The development of immune protective islet encapsulation devices could allow for islet transplantation in the absence of immunosuppression. However, the immune protective membrane / barrier introduced there could also impose limitations in transport of oxygen and nutrients to the encapsulated cells resulting to limited islet viability. In the last years, it is well understood that achieving prevascularization of the device in vitro could facilitate its connection to the host vasculature after implantation, and therefore could provide sufficient blood supply and oxygenation to the encapsulated islets. However, the microvascular networks created in vitro need to mimic well the highly organized vasculature of the native tissue. In earlier study, we developed a functional macroencapsulation device consisting of two polyethersulfone/polyvinylpyrrolidone (PES/PVP) membranes, where a bottom microwell membrane provides good separation of encapsulated islets and the top flat membrane acts as a lid. In this work, we investigate the possibility of creating early microvascular networks on the lid of this device by combining novel membrane microfabrication with co-culture of human umbilical vein endothelial cell (HUVEC) and fibroblasts. We create thin porous microstructured PES/PVP membranes with solid and intermittent line-patterns and investigate the effect of cell alignment and cell interconnectivity as a first step towards the development of a stable prevascularized layer in vitro. Our results show that, in contrast to non-patterned membranes where HUVECs form unorganized HUVEC branch-like structures, for the micropatterned membranes, we can achieve cell alignment and the co-culture of HUVECs on a monolayer of fibroblasts attached on the membranes with intermittent line-pattern allows for the creation of HUVEC branch-like structures over the membrane surface. This important step towards creating early microvascular networks was achieved without the addition of hydrogels, often used in angiogenesis assays, as gels could block the pores of the membrane and limit the transport properties of the islet encapsulation device.

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An important step towards a prevascularized islet microencapsulation device: in vivo prevascularization by combination of mesenchymal stem cells on micropatterned membranes

Extrahepatic transplantation of islets of Langerhans could aid in better survival of islets after transplantation. When islets are transfused into the liver 60-70% of them are lost immediately after transplantation. An important factor for a successful extrahepatic transplantation is a well-vascularized tissue surrounding the implant. There are many strategies known for enhancing vessel formation such as adding cells with endothelial potential, the combination with angiogenic factors and / or applying surface topography at the exposed surface of the device. Previously we developed porous, micropatterned membranes which can be applied as a lid for an islet encapsulation device and we showed that the surface topography induces human umbilical vein endothelial cell (HUVEC) alignment and interconnection. This was achieved without the addition of hydrogels, often used in angiogenesis assays. In this work, we went one step further towards clinical implementation of the device by combining this micropatterned lid with Mesenchymal Stem Cells (MSCs) to facilitate prevascularization in vivo. As for HUVECs, the micropatterned membranes induced MSC alignment and organization in vitro, an important contributor to vessel formation, whereas in vivo (subcutaneous rat model) they contributed to improved implant prevascularization. In fact, the combination of MSCs seeded on the micropatterned membrane induced the highest vessel formation score in 80% of the sections.

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A new insight into in vitro behaviour of poly(ε-caprolactone)/bioactive glass composites in biologically related fluids

In the present work, the role of content, size and chemical composition of gel-derived bioactive glass particles from the SiO₂–CaO–P₂O₅ system in modulating the in vitro bioactivity, osteoinductive properties and long-term (up to 15 months) degradation behaviour of poly(ε-caprolactone)-based composite films was investigated. Bioactivity was assessed in simulated body fluid (SBF) and HEPES-free Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% foetal bovine serum (FBS), while hydrolytic degradation tests were performed in phosphate buffer saline. Obtained composite films showed excellent calcium phosphate (CaP) layer forming ability in both SBF and DMEM-10% FBS. However, kinetics of bioactivity process strongly depended on the type of medium used. The layer of amino acids and proteins, derived from cell culture medium, on the surfaces of composites created barrier that inhibited release of the ions on the one hand, while increasing nucleation density of calcium phosphates, affecting the morphology of formed CaP layers on the other. The presence of bioactive glass fillers was shown to impart osteoinductive properties to obtained films, supporting osteoblast attachment and proliferation, as well as stimulating cell differentiation and also matrix mineralization process in vitro. We showed that kinetics of bioactivity process and also osteoinductive properties of composite films could be easily modulated with the use of different contents and chemical compositions of fillers. The results showed that modification of PCL matrix with bioactive glass particles accelerated its degradation. We proved that the degradation rate of composites could be controlled and optimized for bone regeneration, in particular by using bioactive fillers causing different calcium phosphate layer forming ability on the surfaces of composites, depending on particle size and chemical composition. We have presented new opportunities to design and obtain multifunctional composites with tunable degradation and bioactivity kinetics, as well as biological properties that can meet complex requirements of bone tissue engineering.     

Bacterial cell killing properties of silver-loaded polysiloxane microspheres

Cross-linked polysiloxane microspheres containing a large number of SiOH groups were modified by introduction of organic thiol groups, which were further used for the functionalization of the microspheres with silver thiolate groups. The microspheres were characterized by ²⁹Si MAS NMR, ¹³C MAS NMR, SEM, XPS and elemental analysis. They were tested as biocides against selected Gram-positive and Gram-negative bacteria strains and exhibited high bactericidal activity. Separately, linear polysiloxane polymers equipped with organothiol groups and loaded with silver were synthesized. Their antibacterial activity was compared with that of silver thiolate-functionalized microspheres. Different shape of particles and a different form of silver explained somewhat lower activity of polymers.     

Synthesis of silver nanoparticles by Bacillus subtilis T‐1 growing on agro‐industrial wastes and producing biosurfactant

In this study, culture supernatnats of Bacillus subtilis T‐1 growing on brewery effluents and molasses was used for silver nanoparticles (Ag‐NPs) synthesis. The biosurfactant production of B. subtilis T‐1 was confirmed by the detection of genes in the genome and by the identification of the product in the supernatants. The genes for synthesis of surfactin (sfp, srfAA) and iturin (ituC) were noted by PCR reactions. Also, in examined culture supernatants the presence of C₁₃, C₁₄ and C₁₅ surfactin homologues with the sodiated molecules [M + Na]⁺ at m /z 1030, 1044 and 1058 was confirmed using LC/MS/MS analysis. The formation of NPs in the culture supernatants was confirmed by UV–vis spectroscopy. The dynamic light scattering measurements and transmission electron microscopy images showed the nanometric sizes of the biosynthesised Ag‐NPs which ranged from several nm to several tens of nm depending on the used culture supernatant. Biological properties of Ag‐NPs were evaluated by binding of Ag‐NPs with DNA isolated from the Escherichia coli ATCC 25922 and B. subtilis ATCC 6633. Biogenic Ag‐NPs were actively bound to DNA in increased concentration which could be the one important mode of antibacterial action of the Ag‐NPs.Inspec keywords: silver, nanoparticles, nanofabrication, materials preparation, microorganisms, antibacterial activity, industrial waste, agrochemicals, surfactants, breweries, genomics, genetics, chromatography, mass spectroscopic chemical analysis, ultraviolet spectroscopy, visible spectroscopy, spectrochemical analysis, light scattering, transmission electron microscopy, DNA, bonds (chemical), biochemistry, molecular biophysics, nanobiotechnology, biological techniques, particle size, enzymesOther keywords: silver nanoparticle synthesis, Bacillus subtilis T‐1 growth, agro‐industrial waste, biosurfactant production, brewery effluent, molasses, Ag‐NP synthesis, B. subtilis T‐1, gene detection, genome, supernatant product identification, surfactin synthesis, sfp, srfAA, iturin synthesis, ituC, PCR reaction, C₁₃ surfactin homologue, C₁₄ surfactin homologue, C₁₅ surfactin homologue, sodiated molecules, LC‐MS‐MS analysis, UV‐vis spectroscopy, dynamic light scattering measurement, transmission electron microscopy image, Ag‐NP nanometric size range, Ag‐NP biosynthesis, used culture supernatant dependence, biological properties, DNA isolation, Escherichia coli ATCC 25922, B. subtilis ATCC 6633, biogenic Ag‐NP‐DNA binding, Ag‐NP antibacterial action, Ag     

Synthesis and Anticancer Activity of Mitotic-Specific 3,4-Dihydropyridine-2(1H)-thiones

Most anticancer drugs target mitosis as the most crucial and fragile period of rapidly dividing cancer cells. However the limitations of classical chemotherapeutics drive the search for new more effective and selective compounds. For this purpose structural modifications of the previously characterized pyridine analogue (S1) were incorporated aiming to obtain an antimitotic inhibitor of satisfactory and specific anticancer activity. Structure-activity relationship analysis of the compounds against a panel of cancer cell lines allowed to select a compound with a thiophene ring at C5 of a 3,4-dihydropyridine-2(1H)-thione (S22) with promising antiproliferative activity (IC₅₀ equal 1.71 ± 0.58 µM) and selectivity (SI = 21.09) against melanoma A375 cells. Moreover, all three of the most active compounds from the antiproliferative study, namely S1, S19 and S22 showed better selectivity against A375 cells than reference drug, suggesting their possible lower toxicity and wider therapeutic index. As further study revealed, selected compounds inhibited tubulin polymerization via colchicine binding site in dose dependent manner, leading to aberrant mitotic spindle formation, cell cycle arrest and apoptosis. Summarizing, the current study showed that among obtained mitotic-specific inhibitors analogue with thiophene ring showed the highest antiproliferative activity and selectivity against cancer cells.     

Functionalized Peptide Fibrils as a Scaffold for Active Substances in Wound Healing

Technological developments in the field of biologically active peptide applications in medicine have increased the need for new methods for peptide delivery. The disadvantage of peptides as drugs is their low biological stability. Recently, great attention has been paid to self-assembling peptides that can form fibrils. Such a formulation makes bioactive peptides more resistant to enzymatic degradation and druggable. Peptide fibrils can be carriers for peptides with interesting biological activities. These features open up prospects for using the peptide fibrils as long-acting drugs and are a valid alternative to conventional peptidic therapies. In our study, we designed new peptide scaffolds that are a hybrid of three interconnected amino acid sequences and are: pro-regenerative, cleavable by neutrophilic elastase, and fibril-forming. We intended to obtain peptides that are stable in the wound environment and that, when applied, would release a biologically active sequence. Our studies showed that the designed hybrid peptides show a high tendency toward regular fibril formation and are able to release the pro-regenerative sequence. Cytotoxicity studies showed that all the designed peptides were safe, did not cause cytotoxic effects and revealed a pro-regenerative potential in human fibroblast and keratinocyte cell lines. In vivo experiments in a dorsal skin injury model in mice indicated that two tested peptides moderately promote tissue repair in their free form. Our research proves that peptide fibrils can be a druggable form and a scaffold for active peptides.     

The CD200 Regulates Inflammation in Mice Independently of TNF-α Production

Inflammatory bowel disease is characterized by the infiltration of immune cells and chronic inflammation. The immune inhibitory receptor, CD200R, is involved in the downregulation of the activation of immune cells to prevent excessive inflammation. We aimed to define the role of CD200R ligand-CD200 in the experimental model of intestinal inflammation in conventionally-reared mice. Mice were given a dextran sodium sulfate solution in drinking water. Bodyweight loss was monitored daily and the disease activity index was calculated, and a histological evaluation of the colon was performed. TNF-α production was measured in the culture of small fragments of the distal colon or bone marrow-derived macrophages (BMDMs) cocultured with CD200⁺ cells. We found that Cd200^−/− mice displayed diminished severity of colitis when compared to WT mice. Inflammation significantly diminished CD200 expression in WT mice, particularly on vascular endothelial cells and immune cells. The co-culture of BMDMs with CD200⁺ cells inhibited TNF-α secretion. In vivo, acute colitis induced by DSS significantly increased TNF-α secretion in colon tissue in comparison to untreated controls. However, Cd200^−/− mice secreted a similar level of TNF-α to WT mice in vivo. CD200 regulates the severity of DSS-induced colitis in conventionally-reared mice. The presence of CD200⁺ cells decreases TNF-α production by macrophages in vitro. However, during DDS-induced intestinal inflammation secretion of TNF-α is independent of CD200 expression.