Clustal W and Clustal X version 2.0 Larkin, M.A.; Blackshields, G.; Brown, N.P. ...
Bioinformatics,
11/2007, Letnik:
23, Številka:
21
Journal Article
Recenzirano
Odprti dostop
The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has ...allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/ Contact: clustalw@ucd.ie
Aliment Pharmacol Ther 31, 548–552
Summary
Background Confocal laser endomicroscopy (CLE) is rapidly emerging as a valuable tool for gastrointestinal endoscopic imaging. Fluorescent contrast agents ...are used to optimize imaging with CLE, and intravenous fluorescein is the most widely used contrast agent. Fluorescein is FDA‐cleared for diagnostic angiography of the retina. For these indications, the safety profile of fluorescein has been well‐documented; however, to date, fluorescein is not cleared for use with CLE.
Aims To estimate the rate of serious and total adverse events attributable to intravenous fluorescein when used for gastrointestinal CLE.
Methods We performed a cross sectional survey of 16 International Academic Medical Centres with active research protocols in CLE that involved intravenous fluorescein. Centres using i.v. fluorescein for CLE who were actively monitored for adverse events were included.
Results Sixteen centres performed 2272 gastrointestinal CLE procedures. The most common dose of contrast agent was 2.5–5 mL of 10% sodium fluorescein. No serious adverse events were reported. Mild adverse events occurred in 1.4% of individuals, including nausea/vomiting, transient hypotension without shock, injection site erythema, diffuse rash and mild epigastric pain. The limitation is that only immediate post procedure events were actively monitored.
Conclusions Use of intravenous fluorescein for gastrointestinal CLE appears to be safe with few acute complications.
Quartz crystal microbalance with dissipation monitoring (QCM-D) was employed to characterize the adsorption of the model proteins, bovine serum albumin (BSA) and fibronectin (FN), to polypyrrole ...doped with dextran sulfate (PPy–DS) as a function of DS loading and surface roughness. BSA adsorption was greater on surfaces of increased roughness and was above what could be explained by the increase in surface area alone. Furthermore, the additional mass adsorbed on the rough films was concomitant with an increase in the rigidity of the protein layer. Analysis of the dynamic viscoelastic properties of the protein adlayer reveal BSA adsorption on the rough films occurs in two phases: (1) arrival and initial adsorption of protein to the polymer surface and (2) postadsorption molecular rearrangement to a more dehydrated and compact conformation that facilitates further recruitment of protein to the polymer interface, likely forming a multilayer. In contrast, FN adsorption was independent of surface roughness. However, films prepared from solutions containing the highest concentration of DS (20 mg/mL) demonstrated both an increase in adsorbed mass and adlayer viscoelasticity. This is attributed to the higher DS loading in the conducting polymer film resulting in presentation of a more hydrated molecular structure indicative of a more unfolded and bioactive conformation. Modulating the redox state of the PPy–DS polymers was shown to modify both the adsorbed mass and viscoelastic nature of FN adlayers. An oxidizing potential increased both the total adsorbed mass and the adlayer viscoelasticity. Our findings demonstrate that modification of polymer physicochemical and redox condition alters the nature of protein–polymer interaction, a process that may be exploited to tailor the bioactivity of protein through which interactions with cells and tissues may be controlled.
Single-stranded DNA or RNA sequences rich in guanine (G) can adopt non-canonical structures known as G-quadruplexes (G4). Mitochondrial DNA (mtDNA) sequences that are predicted to form G4 are ...enriched on the heavy-strand and have been associated with formation of deletion breakpoints. Increasing evidence supports the ability of mtDNA to form G4 in cancer cells; however, the functional roles of G4 structures in regulating mitochondrial nucleic acid homeostasis in non-cancerous cells remain unclear. Here, we demonstrate by live cell imaging that the G4-ligand RHPS4 localizes primarily to mitochondria at low doses. We find that low doses of RHPS4 do not induce a nuclear DNA damage response but do cause an acute inhibition of mitochondrial transcript elongation, leading to respiratory complex depletion. We also observe that RHPS4 interferes with mtDNA levels or synthesis both in cells and isolated mitochondria. Importantly, a mtDNA variant that increases G4 stability and anti-parallel G4-forming character shows a stronger respiratory defect in response to RHPS4, supporting the conclusion that mitochondrial sensitivity to RHPS4 is G4-mediated. Taken together, our results indicate a direct role for G4 perturbation in mitochondrial genome replication, transcription processivity, and respiratory function in normal cells.
Three-dimensional (3D) bioprinting is driving major innovations in the area of cartilage tissue engineering. Extrusion-based 3D bioprinting necessitates a phase change from a liquid bioink to a ...semi-solid crosslinked network achieved by a photo-initiated free radical polymerization reaction that is known to be cytotoxic. Therefore, the choice of the photocuring conditions has to be carefully addressed to generate a structure stiff enough to withstand the forces phisiologically applied on articular cartilage, while ensuring adequate cell survival for functional chondral repair. We recently developed a handheld 3D printer called "Biopen". To progress towards translating this freeform biofabrication tool into clinical practice, we aimed to define the ideal bioprinting conditions that would deliver a scaffold with high cell viability and structural stiffness relevant for chondral repair. To fulfill those criteria, free radical cytotoxicity was confined by a co-axial Core/Shell separation. This system allowed the generation of Core/Shell GelMa/HAMa bioscaffolds with stiffness of 200KPa, achieved after only 10 seconds of exposure to 700 mW/cm
of 365 nm UV-A, containing >90% viable stem cells that retained proliferative capacity. Overall, the Core/Shell handheld 3D bioprinting strategy enabled rapid generation of high modulus bioscaffolds with high cell viability, with potential for in situ surgical cartilage engineering.
We introduce M-Coffee, a meta-method for assembling multiple sequence alignments (MSA) by combining the output of several individual methods into one single MSA. M-Coffee is an extension of T-Coffee ...and uses consistency to estimate a consensus alignment. We show that the procedure is robust to variations in the choice of constituent methods and reasonably tolerant to duplicate MSAs. We also show that performances can be improved by carefully selecting the constituent methods. M-Coffee outperforms all the individual methods on three major reference datasets: HOMSTRAD, Prefab and Balibase. We also show that on a case-by-case basis, M-Coffee is twice as likely to deliver the best alignment than any individual method. Given a collection of pre-computed MSAs, M-Coffee has similar CPU requirements to the original T-Coffee. M-Coffee is a freeware open-source package available from http://www.tcoffee.org/.
Conductive polymers (CPs) are organic materials that hold great promise for biomedicine. Potential applications include in vitro or implantable electrodes for excitable cell recording and stimulation ...and conductive scaffolds for cell support and tissue engineering. In this study, we demonstrate the utility of electroactive CP polypyrrole (PPy) containing the anionic dopant dodecylbenzenesulfonate (DBS) to differentiate novel clinically relevant human neural stem cells (hNSCs). Electrical stimulation of PPy(DBS) induced hNSCs to predominantly β-III Tubulin (Tuj1) expressing neurons, with lower induction of glial fibrillary acidic protein (GFAP) expressing glial cells. In addition, stimulated cultures comprised nodes or clusters of neurons with longer neurites and greater branching than unstimulated cultures. Cell clusters showed a similar spatial distribution to regions of higher conductivity on the film surface. Our findings support the use of electrical stimulation to promote neuronal induction and the biocompatibility of PPy(DBS) with hNSCs and opens up the possibility of identifying novel mechanisms of fate determination of differentiating human stem cells for advanced in vitro modeling, translational drug discovery, and regenerative medicine.
Using phase-separated droplet interface bilayers, we observe membrane binding and pore formation of a eukaryotic cytolysin, Equinatoxin II (EqtII). EqtII activity is known to depend on the presence ...of sphingomyelin in the target membrane and is enhanced by lipid phase separation. By imaging the ionic flux through individual pores in vitro, we observe that EqtII pores form predominantly within the liquid-disordered phase. We observe preferential binding of labeled EqtII at liquid-ordered/liquid-disordered domain boundaries before it accumulates in the liquid-disordered phase.
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