Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method.

Eukaryotic transcription is tightly regulated by transcriptional regulatory elements, even though these elements may be located far away from their target genes. It is now widely recognized that these regulatory elements can be brought in close proximity through the formation of chromatin loops, and that these loops are crucial for transcriptional regulation of their target genes. The chromosome conformation capture (3C) technique presents a snapshot of long-range interactions, by fixing physically interacting elements with formaldehyde, digestion of the DNA, and ligation to obtain a library of unique ligation products. Recently, several large-scale modifications to the 3C technique have been presented. Here, we describe chromosome conformation capture sequencing (4C-seq), a high-throughput version of the 3C technique that combines the 3C-on-chip (4C) protocol with next-generation Illumina sequencing. The method is presented for use in mammalian cell lines, but can be adapted to use in mammalian tissues and any other eukaryotic genome.

Negative antagonists promote an inactive conformation of the beta 2-adrenergic receptor.

The beta 2-adrenergic receptor undergoes isomerization between an inactive conformation (R) and an active conformation (R*). The formation of the active conformation of the receptor molecule can be promoted by adrenergic agonists or by mutations in the third cytoplasmic domain that constitutively activate the receptor. Here we show that, of several beta-adrenergic receptor-blocking drugs tested, only two, ICI 118551 and betaxolol, inhibit the basal signaling activity of the beta 2-adrenergic receptor, thus acting as negative antagonists. We document the molecular properties of the more efficacious ICI 118551; (i) it shows higher affinity for the inactive form of the receptor and (ii) it inhibits the spontaneous formation of a beta-adrenergic receptor kinase substrate by the receptor. These properties are opposite those of adrenergic agonists, indicating that, in a fashion reciprocal to that of agonists, negative antagonists promote the formation of an inactive conformation of the receptor.

Color of smoked loin from animals fed with bioactive compounds added to forage

The objective of this work was to evaluate the influence of the breed and of the addition of bioactive substances to forage on the color of smoked pork loin. Two pig breeds (Polish Landrace and the crossbreed Polish Landrace x Duroc), three types of bioactive components (organic selenium; 2% of canola oil and 1% of flaxseed oil; and 2% of flaxseed oil and 1% of canola oil), and a control treatment were evaluated. Computer image analysis included the color assessment of muscle, fat, connective tissues, and smoked loin surface. For Polish Landrace, selenium supplementation caused higher values of red, green, and blue color components of the muscle tissue, which were lower for the crossbreed. However, there was no difference in the color components of loin fat tissue of the Polish Landrace breed due to selenium supplementation. In the case of oil supplementation, values of the color components of the muscle tissue for the Polish Landrace x Duroc crossbreed were also lower. The color components of muscle, fat, connective tissues, and smoked loin surface depend on the pig breed and on the bioactive compounds added to the forage.

Protein homology reveals new targets for bioactive small molecules.

MOTIVATION: The functional impact of small molecules is increasingly being assessed in different eukaryotic species through large-scale phenotypic screening initiatives. Identifying the targets of these molecules is crucial to mechanistically understand their function and uncover new therapeutically relevant modes of action. However, despite extensive work carried out in model organisms and human, it is still unclear to what extent one can use information obtained in one species to make predictions in other species. RESULTS: Here, for the first time, we explore and validate at a large scale the use of protein homology relationships to predict the targets of small molecules across different species. Our results show that exploiting target homology can significantly improve the predictions, especially for molecules experimentally tested in other species. Interestingly, when considering separately orthology and paralogy relationships, we observe that mapping small molecule interactions among orthologs improves prediction accuracy, while including paralogs does not improve and even sometimes worsens the prediction accuracy. Overall, our results provide a novel approach to integrate chemical screening results across multiple species and highlight the promises and remaining challenges of using protein homology for small molecule target identification. AVAILABILITY AND IMPLEMENTATION: Homology-based predictions can be tested on our website http://www.swisstargetprediction.ch. CONTACT: david.gfeller@unil.ch or vincent.zoete@isb-sib.ch. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Fiber-reinforced Composite as Oral Implant Material. Experimental studies of glass fiber and bioactive glass in vitro and in vivo

Fiber-reinforced composite as oral implant material: Experimental studies of glass fiber and bioactive glass in vitro and in vivo Department of Prosthetic Dentistry and Biomaterials Science, Institute of Dentistry, University of Turku, Turku, Finland 2008. Biocompatibility and mechanical properties are important variables that need to be determined when new materials are considered for medical implants. Special emphasis was placed on these characteristics in the present work, which aimed to investigate the potential of fiber-reinforced composite (FRC) material as an oral implant. Furthermore, the purpose of this study was to explore the effect of bioactive glass (BAG) on osseointegration of FRC implants. The biocompatibility and mechanical properties of FRC implants were studied both in vitro and in vivo. The mechanical properties of the bulk FRC implant were tested with a cantilever bending test, torsional test and push-out test. The biocompatibility was first evaluated with osteoblast cells cultured on FRC substrates. Bone bonding was determined with the mechanical push-out test and histological as well as histomorplanimetric evaluation. Implant surface was characterized with SEM and EDS analysis. The results of these studies showed that FRC implants can withstand the static load values comparably to titanium. Threaded FRC implants had significantly higher push-out strength than the threaded titanium implants. Cell culture study revealed no cytotoxic effect of FRC materials on the osteoblast-like-cells. Addition of BAG particles enhanced cell proliferation and mineralization of the FRC substrates The in vivo study showed that FRC implants can withstand static loading until failure without fracture. The results also suggest that the FRC implant is biocompatible in bone. The biological behavior of FRC was comparable to that of titanium after 4 and 12 weeks of implantation. Furthermore, addition of BAG to FRC implant increases peri-implant osteogenesis and bone maturation.

Reversal of a full-length mutant huntingtin neuronal cell phenotypeby chemical inhibitors of polyglutamine-mediated aggregation

Background: Huntington's disease (HD) is an inherited neurodegenerative disorder triggered by an expanded polyglutamine tract in huntingtin that is thought to confer a new conformational property on this large protein. The propensity of small amino-terminal fragments with mutant, but not wild-type, glutamine tracts to self-aggregate is consistent with an altered conformation but such fragments occur relatively late in the disease process in human patients and mouse models expressing full-length mutant protein. This suggests that the altered conformational property may act within the full-length mutant huntingtin to initially trigger pathogenesis. Indeed, genotypephenotype studies in HD have defined genetic criteria for the disease initiating mechanism, and these are all fulfilled by phenotypes associated with expression of full-length mutant huntingtin, but not amino-terminal fragment, in mouse models. As the in vitro aggregation of amino-terminal mutant huntingtin fragment offers a ready assay to identify small compounds that interfere with the conformation of the polyglutamine tract, we have identified a number of aggregation inhibitors, and tested whether these are also capable of reversing a phenotype caused by endogenous expressionof mutant huntingtin in a striatal cell line from the HdhQ111/Q111 knock-in mouse. Results: We screened the NINDS Custom Collection of 1,040 FDA approved drugs and bioactive compounds for their ability to prevent in vitro aggregation of Q58-htn 1¿171 amino terminal fragment. Ten compounds were identified that inhibited aggregation with IC50 < 15 ¿M, including gossypol, gambogic acid, juglone, celastrol, sanguinarine and anthralin. Of these, both juglone and celastrol were effective in reversing the abnormal cellular localization of full-length mutant huntingtin observed in mutant HdhQ111/Q111 striatal cells. Conclusions: At least some compounds identified as aggregation inhibitors also prevent a neuronal cellular phenotype caused by full-length mutant huntingtin, suggesting that in vitro fragment aggregation can act as a proxy for monitoring the disease-producing conformational property in HD. Thus, identification and testing of compounds that alter in vitro aggregation is a viable approach for defining potential therapeutic compounds that may act on the deleterious conformational property of full-length mutant huntingtin.

Thermoplastic bioactive composite – with special reference to dissolution behaviour and tissue response

Bioactive glasses are surface-active ceramic materials which support and accelerate bone growth in the body. During the healing of a bone fracture or a large bone defect, fixation is often needed. The aim of this thesis was to determine the dissolution behaviour and biocompatibility of a composite consisting of poly(ε-caprolactone-co-DL-lactide) and bioactive glass (S53P4). In addition the applicability as an injectable material straight to a bone defect was assessed. In in vitro tests the dissolution behaviour of plain copolymer and composites containing bioactive glass granules was evaluated, as well as surface reactivity and the material’s capability to form apatite in simulated body fluid (SBF). The human fibroblast proliferation was tested on materials in cell culture. In in vivo experiments, toxicological tests, material degradation and tissue reactions were tested both in subcutaneous space and in experimental bone defects. The composites containing bioactive glass formed a unified layer of apatite on their surface in SBF. The size and amount of glass granules affected the degradation of polymer matrix, as well the material’s surface reactivity. In cell culture on the test materials the human gingival fibroblasts proliferated and matured faster compared with control materials. In in vitro tests a connective tissue capsule was formed around the specimens, and became thinner in the course of time. Foreign body cell reactions in toxicological tests were mild. In experimental bone defects the specimens with a high concentration of small bioactive glass granules (<45 μm) formed a dense apatite surface layer that restricted the bone ingrowth to material. The range of large glass granules (90-315 μm) with high concentrations formed the best bonding with bone, but slow degradation on the copolymer restricted the bone growth only in the superficial layers. In these studies, the handling properties of the material proved to be good and tissue reactions were mild. The reactivity of bioactive glass was retained inside the copolymer matrix, thus enabling bone conductivity with composites. However, the copolymer was noticed to degradate too slowly compared with the bone healing. Therefore, the porosity of the material should be increased in order to improve tissue healing.

Atropoisomerismo: o efeito da quiralidade axial em substâncias bioativas

Atropisomerism is a special kind of stereoisomeric relationship that arises from the freezing of a certain conformation of an organic molecule, associated with a high rotational barrier about a single covalent bond. Atropisomerism has been originally described in orto-functionalyzed biphenyl derivatives, but a lot of other organic functionalities can present this structural phenomenon, characterized by the presence of chiral properties in compounds that don't present classical stereogenic centers. Atropisomeric compounds, intermediates and catalysts have well-know importance in organic synthesis, but the influence of the axial chirality in substances able to modulate biological systems is still not very exploited in drug design and development. In this context, the present account describes the importance of this structural property in the medicinal chemistry of different classes of bioactive compounds or therapeutic agents, emphasizing how atropisomerism could affect the molecular recognition of a ligand or a prototype by the target bioreceptor.

UVA I-protection effectiveness of bioactive compound and organic UV filters: an in vitro assessment

This research work aimed at determining the UVA effectiveness (UVA I/UV ratio), by diffuse transmittance analysis, of sunscreens developed with a bioactive substance, the rutin, associating or not with organic UVB-UVA filters incorporated at a phosphate-base O/W emulsion. Sunscreens provided conflicting and unpredictable results concerning the anti-UVA protection, specially, at the UVA I region. Possible interactions among the organic UV filters and the polyphenolic bioactive substance may have accounted with improvement or reduction of UV protection by a complex and not yet elucidated mechanism, probably regarding wavelength delocalization to superior or inferior values, by resonant molecule stabilization or destabilization.

Flavonoids and other bioactive phenolics isolated from Cenostigma macrophyllum (Leguminosae)

This work describes the phytochemical study of stem bark and leaves of Cenostigma macrophyllum Tul. (Leguminosae). Through usual chromatographic techniques were isolated bergenin as the primary compound of the stem bark of and from the leaves gallic acid, methyl gallate, ellagic acid, quercetin, quercetin-3-O-β-D-glucopyranoside, quercetin-3-O-(6"-O-galloyl)-β-D-glucopyranoside (tellimoside), quercetin-3-O-(6"-O-E-p-coumaroyl)-β-D-glucopyranoside (helichrysroside), agathisflavone and vitexin were obtained. The isolates were identified by spectroscopic data analysis, and bergenin showed dose-related antinociception when assessed in acetic acid-induced writhing in mice.

Bioactive triterpenes and phenolics of leaves of Eugenia brasiliensis

A chemical investigation of Eugenia brasiliensis Lam. (Myrtaceae) leaves led to the isolation of α-amyrin and β-amyrin (in a mixture), betulin, 29-hydroxy-oleanolic acid, quercetin, catechin and gallocatechin. Herein, the identification of 29-hydroxy-oleanolic acid is reported for the first time in the Myrtaceae family. Moreover, in this study, the extract, fractions and six of the seven compounds were monitored for toxicity toward Artemia salina, antibacterial and acetylcholinesterase inhibitory activity. The crude ethanol extract of the leaves and fractions were found be active on A. salina toxicity bioassay.

Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single-crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer.

Flavonoides de Lonchocarpus araripensis (Leguminoseae) - isolamento, atribuição inequívoca dos sinais de RMN ¹H e 13C e análise conformacional

In a continuing investigation for potentially bioactive natural products, flavonoids were isolated from Lonchocarpus araripensis (Leguminoseae) and identified as 3-methoxy-6-O-prenyl-6'',6''-dimethylchromene-[7,8,2'',3'']-flavone (1), 3,6-dimethoxy-6'',6''-dimethylchromene-[7,8,2'',3'']-flavone (2) and 3,5,8-trimethoxy-[6,7,2",3"]-furanoflavone (3). This is the first time compound 3 has been described. Compound 2 has been previously isolated from roots while this is the first time 1 is reported in this species. Complete NMR assignments are given for1 ,2 and 3 together with the determination of conformation for 1.

Catalyzed and non-catalyzed synthesis of bioactive monastrol

The bioactive 3,4-dihydropyrimidin-2(1H)-thione derivative known as Monastrol was synthesized under catalyzed and non-catalyzed conditions through the Biginelli multicomponent reaction under solvent-free conditions. The use of two Lewis acids (FeCl3 and CuCl2) and two Brønsted acids (HCl and CF3COOH) as catalysts improved the reaction yields of the transformation compared with the non-catalyzed reaction. The experiments investigated catalysis and its role, the importance of multicomponent reactions and their green features, and the application of these concepts to the synthesis of a biologically important structure.

Crystallization characteristics of bioactive glasses

Bioactive glasses are excellent candidates for implant materials, because they can form a chemical bond to bone or guide bone growth, depending on the glass composition. Some compositions have even shown soft tissue attachment and antimicrobial effects. So far, most clinical applications are based on monoliths, plates and particulates of different grain sizes. There is a growing interest in special products such as porous implants sintered from microspheres and fibers drawn from preforms or glass melts. The viscosity range at which these are formed coincides with the crystallization temperature range for most bioactive glasses, thus complicating the manufacturing process. In this work, the crystallization tendency and its kinetics for a series of glasses with their compositions within the range of bioactivity were investigated. The factors affecting crystallization and how it is related to composition were studied by means of thermal analysis and hot stage microscopy. The crystal compositions formed during isothermal and non-isothermal heat treatments were analyzed with SEM-EDXA and X-ray diffraction analysis. The temperatures at which sintering and fiber drawing can take place without interfering with crystallization were determined and glass compositions which are suitable for these purposes were established. The bioactivity of glass fibers and partly crystallized glass plates was studied by soaking them in simulated body fluid (SBF). The thickness of silica, calcium and phosphate rich reaction layers on the glass surface after soaking was used as an indication of the bioactivity. The results indicated that the crystallization tendencies of the experimental glasses are strongly dependent on composition. The main factor affecting the crystallization was found to be the alkali oxide content: the higher the alkali oxide content the lower the crystallization temperature. The primary crystalline phase formed at low temperatures in these glasses was sodium calcium silicate. The crystals were found to form through internal nucleation, leading to bulk crystallization. These glasses had high bioactivity in vitro. Even when partially crystalline, they formed typical reaction layers, indicating bioactivity. In fact, sodium calcium silicate crystals were shown to transform in vitro into hydroxyapatite during soaking. However, crystallization should be avoided because it was shown to retard dissolution, bioactivity reactions and complicate fiber drawing process. Glass compositions having low alkali oxide content showed formation of wollastonite crystals on the surface, at about 300°C above the glass transition temperature. The wide range between glass transition and crystallization allowed viscous flow sintering of these compositions. These glasses also withstood the thermal treatments required for fiber drawing processing. Precipitation of calcium and phosphate on fibers of these glasses in SBF suggested that they were osteoconductive. Glasses showing bioactivity crystallize easily, making their hot working challenging. Undesired crystallization can be avoided by choosing suitable compositions and heat treatment parameters, allowing desired product forms to be attained. Small changes in the oxide composition of the glass can have large effects and therefore a thorough understanding of glass crystallization behavior is a necessity for a successful outcome, when designing and manufacturing implants containing bioactive glasses.