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https://www.readbyqxmd.com/read/27914366/rapid-and-low-cost-biosensor-for-the-detection-of-staphylococcus-aureus
#1
Ghadeer A R Y Suaifan, Sahar Alhogail, Mohammed Zourob
Staphylococcus aureus (S. aureus) is one of the most common etiological agents in hospital-acquired infections and food-borne illness. S. aureus toxins and virulence proteases often circulate in host blood vessels leading to life-threatening diseases. Standard identification approaches include bacterial culturing method, which takes several days. Other nucleic acid-based methods were expensive and required trained personnel. To surmount these limitations, a paper-based biosensor was developed. The sensing mechanism was based on the proteolytic activity of S...
November 21, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27914358/defining-the-role-of-perioperative-statin-treatment-in-patients-after-cardiac-surgery-a-meta-analysis-and-systematic-review-of-20-randomized-controlled-trials
#2
Xin Yuan, Jianlin Du, Qi Liu, Ling Zhang
BACKGROUND: Although statin use has been indicated to prevent atrial fibrillation in previous observational and experimental trials, the issue remains inadequately and insufficiently explored. We therefore performed this meta-analysis to evaluate the effects of perioperative statin therapy on complications and short-term prognosis following cardiac surgery. METHODS: A search of the PubMed, EMBASE and the Cochrane database of controlled trials was performed from inception to June 2016 to identify relevant randomized controlled trials (RCTs)...
November 9, 2016: International Journal of Cardiology
https://www.readbyqxmd.com/read/27914346/tuning-particle-geometry-of-chemically-anisotropic-dumbbell-shaped-colloids
#3
Bas G P van Ravensteijn, Willem K Kegel
Chemically anisotropic dumbbell-shaped colloids are prepared starting from cross-linked polymer seed particles coated with a chlorinated outer layer. These chlorinated seeds are swollen with monomer. Subsequently, a liquid protrusion is formed on the surface of the seed particle by phase separation between the monomer and the swollen polymer network. Solidification of these liquid lobes by polymerization leads to the desired dumbbell-shaped colloids. The chlorine groups remain confined on the seed lobe of the particles, ensuring chemical anisotropy of the resulting particles...
November 15, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27914306/a-contactless-ultrasonic-surface-wave-approach-to-characterize-distributed-cracking-damage-in-concrete
#4
Suyun Ham, Homin Song, Michael L Oelze, John S Popovics
We describe an approach that utilizes ultrasonic surface wave backscatter measurements to characterize the volume content of relatively small distributed defects (microcrack networks) in concrete. A simplified weak scattering model is used to demonstrate that the scattered wave field projected in the direction of the surface wave propagation is relatively insensitive to scatterers that are smaller than the propagating wavelength, while the scattered field projected in the opposite direction is more sensitive to sub-wavelength scatterers...
November 9, 2016: Ultrasonics
https://www.readbyqxmd.com/read/27914302/progressive-multi-atlas-label-fusion-by-dictionary-evolution
#5
Yantao Song, Guorong Wu, Khosro Bahrami, Quansen Sun, Dinggang Shen
Accurate segmentation of anatomical structures in medical images is important in recent imaging based studies. In the past years, multi-atlas patch-based label fusion methods have achieved a great success in medical image segmentation. In these methods, the appearance of each input image patch is first represented by an atlas patch dictionary (in the image domain), and then the latent label of the input image patch is predicted by applying the estimated representation coefficients to the corresponding anatomical labels of the atlas patches in the atlas label dictionary (in the label domain)...
November 24, 2016: Medical Image Analysis
https://www.readbyqxmd.com/read/27914294/selective-agonism-of-mglu8-receptors-by-s-3-4-dicarboxyphenylglycine-does-not-affect-sleep-stages-in-the-rat
#6
María Cavas, Gianluigi Scesa, Mercedes Martín-López, José Francisco Navarro
BACKGROUND: Metabotropic glutamate receptors (mGlu) play a role in a number of physiological processes and behaviors, as well as in certain pathological conditions and diseases. New drugs targetting mGlu receptors are being developed with treatment purposes. Recent data indicates that glutamate is involved in sleep, and pharmacological manipulation of distinct subtypes of mGlu receptors affect sleep. Here the consequences of selective pharmacological agonism of mGlu8 receptor upon sleep and wakefulness are explored for the first time...
September 22, 2016: Pharmacological Reports: PR
https://www.readbyqxmd.com/read/27914256/the-effect-of-sambucus-nigra-l-extract-and-phytosinthesized-gold-nanoparticles-on-diabetic-rats
#7
Razvan Opris, Corina Tatomir, Diana Olteanu, Remus Moldovan, Bianca Moldovan, Luminita David, Andras Nagy, Nicoleta Decea, Mihai Ludovic Kiss, Gabriela Adriana Filip
Nanomaterials such as gold nanoparticles (NPs) conjugated with natural products have shown good results in lowering the glycated hemoglobin and have an anti-inflamatory effect. The aim of our study is to evaluate the antidiabetic effect of NPs functionalized with Sambucus nigra L. (SN) extract on experimental model of diabetes in rats. Diabetes was induced to 18 Wistar male rats (n=6) by a single intramuscular injection of streptozotocin (30mg/kg body weight - b.w.). SN extract (15mg/kg b.w.), NPs (0.3mg/kg b...
November 27, 2016: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/27914209/methodological-flaws-introduce-strong-bias-into-molecular-analysis-of-microbial-populations
#8
Niclas Krakat, Reshma Anjum, Burak Demirel, Patrick Schröder
AIMS: Here we report how different cell disruption methods, PCR primers and in-silico analyses can seriously bias results from microbial population studies, with consequences for the credibility and reproducibility of the findings. Our results emphasize the pitfalls of commonly used experimental methods that can seriously weaken the interpretation of results. METHODS AND RESULTS: Four different cell lysis methods, three commonly used primer pairs and various computer-based analyses were applied to investigate the microbial diversity of a fermentation sample composed of chicken dung...
December 3, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27914200/assembling-the-tat-protein-translocase
#9
Felicity Alcock, Phillip J Stansfeld, Hajra Basit, Johann Habersetzer, Matthew Ab Baker, Tracy Palmer, Mark I Wallace, Ben C Berks
The twin-arginine protein translocation system (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membranes of plant chloroplasts. The Tat transporter is assembled from multiple copies of the membrane proteins TatA, TatB, and TatC. We combine sequence co-evolution analysis, molecular simulations, and experimentation to define the interactions between the Tat proteins of Escherichia coli at molecular-level resolution. In the TatBC receptor complex the transmembrane helix of each TatB molecule is sandwiched between two TatC molecules, with one of the inter-subunit interfaces incorporating a functionally important cluster of interacting polar residues...
December 3, 2016: ELife
https://www.readbyqxmd.com/read/27914171/clinical-feasibility-of-brain-computer-interface-based-on-steady-state-visual-evoked-potential-in-patients-with-locked-in-syndrome-case-studies
#10
Han-Jeong Hwang, Chang-Hee Han, Jeong-Hwan Lim, Yong-Wook Kim, Soo-In Choi, Kwang-Ok An, Jun-Hak Lee, Ho-Seung Cha, Seung Hyun Kim, Chang-Hwan Im
Although the feasibility of brain-computer interface (BCI) systems based on steady-state visual evoked potential (SSVEP) has been extensively investigated, only a few studies have evaluated its clinical feasibility in patients with locked-in syndrome (LIS), who are the main targets of BCI technology. The main objective of this case report was to share our experiences of SSVEP-based BCI experiments involving five patients with LIS, thereby providing researchers with useful information that can potentially help them to design BCI experiments for patients with LIS...
December 3, 2016: Psychophysiology
https://www.readbyqxmd.com/read/27914086/killing-bacteria-with-cytotoxic-effector-proteins-of-human-killer-immune-cells-granzymes-granulysin-and-perforin
#11
Diego López León, Isabelle Fellay, Pierre-Yves Mantel, Michael Walch
Bacterial pathogens represent a constant threat to human health that was exacerbated in recent years by a dramatic increase of strains resistant to last resort antibiotics. The immune system of higher vertebrates generally evolved several efficient innate and adaptive mechanisms to fight ubiquitous bacterial pathogens. Among those mechanisms, immune proteases were recognized to contribute essentially to antibacterial immune defense. The effector serine proteases of the adaptive immune system, the granzymes, exert potent antimicrobial activity when they are delivered into the bacterial cytosol by prokaryotic membrane disrupting proteins, such as granulysin...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914070/analysis-of-bacterial-surface-interactions-with-mass-spectrometry-based-proteomics
#12
Christofer Karlsson, Johan Teleman, Johan Malmström
Host-pathogen protein-protein interaction networks are highly complex and dynamic. In this experimental protocol we describe a method to isolate host proteins attached to the bacterial surface followed by quantitative mass spectrometry based proteomics analysis. This technique provides an overview of the host-pathogen interaction network, which can be used to guide directed perturbations of the system, and to select target of specific interest for further studies.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914064/computational-tools-for-aiding-rational-antibody-design
#13
Konrad Krawczyk, James Dunbar, Charlotte M Deane
Antibodies are a group of proteins responsible for mediating immune reactions in vertebrates. They are able to bind a variety of structural motifs on noxious molecules tagging them for elimination from the organism. As a result of their versatile binding properties, antibodies are currently one of the most important classes of biopharmaceuticals. In this chapter, we discuss how knowledge-based computational methods can aid experimentalists in the development of potent antibodies. When using common experimental methods for antibody development, we often know the sequence of an antibody that binds to our molecule, antigen, of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914063/episweep-computationally-driven-reengineering-of-therapeutic-proteins-to-reduce-immunogenicity-while-maintaining-function
#14
Yoonjoo Choi, Deeptak Verma, Karl E Griswold, Chris Bailey-Kellogg
Therapeutic proteins are yielding ever more advanced and efficacious new drugs, but the biological origins of these highly effective therapeutics render them subject to immune surveillance within the patient's body. When recognized by the immune system as a foreign agent, protein drugs elicit a coordinated response that can manifest a range of clinical complications including rapid drug clearance, loss of functionality and efficacy, delayed infusion-like allergic reactions, more serious anaphylactic shock, and even induced auto-immunity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#15
Christine E Tinberg, Sagar D Khare
The ability to design novel small-molecule binding sites in proteins is a stringent test of our understanding of the principles of molecular recognition, and would have many practical applications, in synthetic biology and medicine. Here, we describe a computational method in the context of the macromolecular modeling suite Rosetta to designing proteins with sites featuring predetermined interactions to ligands of choice. The required inputs for the method are a model of the small molecule and the desired interactions (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914058/osprey-predicts-resistance-mutations-using-positive-and-negative-computational-protein-design
#16
Adegoke Ojewole, Anna Lowegard, Pablo Gainza, Stephanie M Reeve, Ivelin Georgiev, Amy C Anderson, Bruce R Donald
Drug resistance in protein targets is an increasingly common phenomenon that reduces the efficacy of both existing and new antibiotics. However, knowledge of future resistance mutations during pre-clinical phases of drug development would enable the design of novel antibiotics that are robust against not only known resistant mutants, but also against those that have not yet been clinically observed. Computational structure-based protein design (CSPD) is a transformative field that enables the prediction of protein sequences with desired biochemical properties such as binding affinity and specificity to a target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914055/an-evolution-based-approach-to-de-novo-protein-design
#17
Jeffrey R Brender, David Shultis, Naureen Aslam Khattak, Yang Zhang
EvoDesign is a computational algorithm that allows the rapid creation of new protein sequences that are compatible with specific protein structures. As such, it can be used to optimize protein stability, to resculpt the protein surface to eliminate undesired protein-protein interactions, and to optimize protein-protein binding. A major distinguishing feature of EvoDesign in comparison to other protein design programs is the use of evolutionary information in the design process to guide the sequence search toward native-like sequences known to adopt structurally similar folds as the target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914049/modeling-binding-affinity-of-pathological-mutations-for-computational-protein-design
#18
Miguel Romero-Durana, Chiara Pallara, Fabian Glaser, Juan Fernández-Recio
An important aspect of protein functionality is the formation of specific complexes with other proteins, which are involved in the majority of biological processes. The functional characterization of such interactions at molecular level is necessary, not only to understand biological and pathological phenomena but also to design improved, or even new interfaces, or to develop new therapeutic approaches. X-ray crystallography and NMR spectroscopy have increased the number of 3D protein complex structures deposited in the Protein Data Bank (PDB)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#19
Ilan Samish
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914040/formulation-optimization-and-ex-vivo-and-in-vivo-evaluation-of-celecoxib-microemulsion-based-gel-for-transdermal-delivery
#20
Mengyuan Cao, Lili Ren, Guoguang Chen
Celecoxib (CXB) is a poorly aqueous solubility sulfonamide non-steroidal anti-inflammatory drug (NSAID). Hence, the formulation of CXB was selected for solubilization and bioavailability. To find out suitable formulation for microemulsion, the solubility of CXB in triacetin (oil phase), Tween 80 (surfactant), and Transcutol-P (co-surfactant) was screened respectively and optimized by using orthogonal experimental design. The Km value and concentration of oil, Smix, and water were confirmed by pseudo-ternary phase diagram studies and central composite design...
December 2, 2016: AAPS PharmSciTech
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