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https://www.readbyqxmd.com/read/27914090/measuring-antibody-orientation-at-the-bacterial-surface
#1
Oonagh Shannon, Pontus Nordenfelt
Many bacteria have the ability to interact with antibodies as a means to circumvent the immune response. This includes binding to the Fc portion of antibodies, effectively reversing the antibody orientation and thus decreasing the Fc-mediated immune signaling. Since antibody orientation at the bacterial surface has been shown to be important in human disease, it is valuable to be able to assess how antibodies are interacting with bacterial pathogens. Here, we describe a method to measure the proportion of human IgG that are bound via their Fc or Fabs to a bacterial surface...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914084/the-zebrafish-as-a-model-for-human-bacterial-infections
#2
Melody N Neely
The development of the zebrafish (Danio rerio) infectious disease model has provided new insights and information into pathogenesis. Many of these new discoveries would not have been possible using a typical mammalian model. The advantages of using this model are many and in the last 15 years the model has been exploited for the analysis of many different pathogens. Here, we describe in detail how to perform a bacterial infection using either the adult zebrafish or zebrafish larvae using microinjection. Multiple methods of analysis are described that can be used to address specific questions pertaining to disease progression and the interactions with the immune system...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914081/negative-staining-and-transmission-electron-microscopy-of-bacterial-surface-structures
#3
Matthias Mörgelin
Negative staining is an essential and versatile staining technique in transmission electron microscopy that can be employed for visualizing bacterial cell morphology, size, and surface architecture at high resolution. Bacteria are usually transferred by passive electrostatic adsorption from suspensions in physiological saline onto suitable hydrophilic support films on electron microscopic grids. There they are contrasted, or "stained," by heavy metal ions in solution such as tungsten, uranyl, molybdate, or vanadate compounds...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914077/making-fluorescent-streptococci-and-enterococci-for-live-imaging
#4
Sarah Shabayek, Barbara Spellerberg
Since the discovery of the green fluorescent protein (GFP) from the jellyfish Aequorea victoria, outstanding fluorescent labeling tools with numerous applications in vastly different areas of life sciences have been developed. To optimize GFP for diverse life science applications, a large variety of GFP derivatives with different environmental characteristics have been generated by mutagenesis. The enhanced green fluorescent protein (EGFP) is a well-known GFP derivative with highly increased fluorescence intensity compared to the GFP wild-type molecule...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914074/common-challenges-in-studying-the-structure-and-function-of-bacterial-proteins-case-studies-from-helicobacter-pylori
#5
Daniel A Bonsor, Eric J Sundberg
Employing biophysical and structural methods is a powerful way to elucidate mechanisms of molecular recognition in bacterial pathogenesis. Such studies invariably depend on the production of pure, folded and stable proteins. Many proteins that can be expressed recombinantly ultimately fail to meet one or more of these criteria. The cag proteins from Helicobacter pylori form a secretion system that delivers the oncoprotein, CagA, into human gastric epithelial cells through an interaction between CagL and host cell integrins, where it can cause gastric adenocarcinoma...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914065/computational-design-of-membrane-curvature-sensing-peptides
#6
Armando Jerome de Jesus, Hang Yin
Computer simulations have become an indispensable tool in studying molecular biological systems. The unmatched spatial and temporal resolution that it offers enables for microscopic-level views into the dynamics and mechanics of biological systems. Recent advances in hardware resources have also opened up to computer simulations the investigation of longer timescale biological processes and larger systems. The study of membrane proteins or peptides especially benefits from simulations due to difficulties related to crystallization of such proteins in a membrane environment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914064/computational-tools-for-aiding-rational-antibody-design
#7
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/27914058/osprey-predicts-resistance-mutations-using-positive-and-negative-computational-protein-design
#8
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
#9
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/27914052/applications-of-normal-mode-analysis-methods-in-computational-protein-design
#10
Vincent Frappier, Matthieu Chartier, Rafael Najmanovich
Recent advances in coarse-grained normal mode analysis methods make possible the large-scale prediction of the effect of mutations on protein stability and dynamics as well as the generation of biologically relevant conformational ensembles. Given the interplay between flexibility and enzymatic activity, the combined analysis of stability and dynamics using the Elastic Network Contact Model (ENCoM) method has ample applications in protein engineering in industrial and medical applications such as in computational antibody design...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914051/integration-of-molecular-dynamics-based-predictions-into-the-optimization-of-de-novo-protein-designs-limitations-and-benefits
#11
Henrique F Carvalho, Arménio J M Barbosa, Ana C A Roque, Olga Iranzo, Ricardo J F Branco
Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#12
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/27914000/from-transformation-to-metastasis-deconstructing-the-extracellular-matrix-in-breast-cancer
#13
Shelly Kaushik, Michael W Pickup, Valerie M Weaver
The extracellular matrix (ECM) is a guiding force that regulates various developmental stages of the breast. In addition to providing structural support for the cells, it mediates epithelial-stromal communication and provides cues for cell survival, proliferation, and differentiation. Perturbations in ECM architecture profoundly influence breast tumor progression and metastasis. Understanding how a dysregulated ECM can facilitate malignant transformation is crucial to designing treatments to effectively target the tumor microenvironment...
December 2, 2016: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/27913986/establishing-clinical-meaning-and-defining-important-differences-for-patient-reported-outcomes-measurement-information-system-promis-%C3%A2-measures-in-juvenile-idiopathic-arthritis-using-standard-setting-with-patients-parents-and-providers
#14
Esi M Morgan, Constance A Mara, Bin Huang, Kimberly Barnett, Adam C Carle, Jennifer E Farrell, Karon F Cook
BACKGROUND: Patient-Reported Outcomes Measurement Information System (PROMIS) measures are used increasingly in clinical care. However, for juvenile idiopathic arthritis (JIA), scores lack a framework for interpretation of clinical severity, and minimally important differences (MID) have not been established, which are necessary to evaluate the importance of change. METHODS: We identified clinical severity thresholds for pediatric PROMIS measures of mobility, upper extremity function (UE), fatigue, and pain interference working with adolescents with JIA, parents of JIA patients, and clinicians, using a standard setting methodology modified from educational testing...
December 2, 2016: Quality of Life Research
https://www.readbyqxmd.com/read/27913981/the-challenges-of-anaesthesia-and-pain-relief-in-hip-fracture-care
#15
Rachel Cowan, Jun Hao Lim, Terence Ong, Ashok Kumar, Opinder Sahota
The care of the older person with hip fracture is complicated by their comorbid condition, limited physiological reserve, cognitive impairment and frailty. Two aspects of hip fracture management that have received considerable attention are how best to manage the pain associated with it and the ideal mode of anaesthesia. Existing literature has reported on the suboptimal treatment of pain in this orthogeriatric cohort. With recent advancements in medical care, a number of options have emerged as alternatives to conservative systemic analgesia...
December 3, 2016: Drugs & Aging
https://www.readbyqxmd.com/read/27913958/the-effect-of-mass-transfer-parameterization-and-ice-retention-on-the-scavenging-and-redistribution-of-so2-by-a-deep-convective-cloud
#16
Vladan Vučković, Dragana Vujović
A chemistry module with the aqueous chemistry coupled with the complex 3D nonhydrostatic atmospheric model is used to investigate how the representation of gas-aqueous mass transfer and ice retention affect the SO2 redistribution in the presence of a convective cloud. Gas uptake to the liquid water is calculated using both Henry's law equilibrium (HE) and kinetic mass transport (KMT). The constant retention coefficients for SO2 (k ret = 0.46) and for H2O2 (k ret = 0.64) are used. It is shown that the amount of SO2 in the air at higher altitudes (10-12 km) is greater when partial retention (PR) is included...
December 2, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27913950/mechanics-reveals-the-biological-trigger-in-wrinkly-fingers
#17
P Sáez, A M Zöllner
Fingertips wrinkle due to long exposure to water. The biological reason for this morphological change is unclear and still not fully understood. There are two main hypotheses for the underlying mechanism of fingertip wrinkling: the 'shrink' model (in which the wrinkling is driven by the contraction of the lower layers of skin, associated with the shrinking of the underlying vasculature), and the 'swell' model (in which the wrinkling is driven by the swelling of the upper layers of the skin, associated with osmosis)...
December 2, 2016: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/27913910/a-randomized-trial-of-displaying-paid-price-information-on-imaging-study-and-procedure-ordering-rates
#18
Alyna T Chien, Lisa Soleymani Lehmann, Laura A Hatfield, Kate E Koplan, Carter R Petty, Anna D Sinaiko, Meredith B Rosenthal, Thomas D Sequist
BACKGROUND: Prior studies have demonstrated how price transparency lowers the test-ordering rates of trainees in hospitals, and physician-targeted price transparency efforts have been viewed as a promising cost-controlling strategy. OBJECTIVE: To examine the effect of displaying paid-price information on test-ordering rates for common imaging studies and procedures within an accountable care organization (ACO). DESIGN: Block randomized controlled trial for 1 year...
December 2, 2016: Journal of General Internal Medicine
https://www.readbyqxmd.com/read/27913855/what-can-the-microstructure-of-stones-tell-us
#19
REVIEW
James C Williams, Elaine Worcester, James E Lingeman
How stones are retained within the kidney while small in size is still not fully understood. In this paper, we show two examples of how stones are retained during early growth: one is growth on Randall's (interstitial) plaque, and the other is growth on mineral that has formed as a luminal plug in a terminal collecting duct. These two mechanisms of stone retention during early growth have distinctive morphologic features that can be seen by methods that show the microscopic structure of the stones. Stones growing on Randall's plaque display an apatite region that is typically not large in size (<0...
December 2, 2016: Urolithiasis
https://www.readbyqxmd.com/read/27913822/more-than-just-scanning-the-importance-of-cap-independent-mrna-translation-initiation-for-cellular-stress-response-and-cancer
#20
REVIEW
Rafaela Lacerda, Juliane Menezes, Luísa Romão
The scanning model for eukaryotic mRNA translation initiation states that the small ribosomal subunit, along with initiation factors, binds at the cap structure at the 5' end of the mRNA and scans the 5' untranslated region (5'UTR) until an initiation codon is found. However, under conditions that impair canonical cap-dependent translation, the synthesis of some proteins is kept by alternative mechanisms that are required for cell survival and stress recovery. Alternative modes of translation initiation include cap- and/or scanning-independent mechanisms of ribosomal recruitment...
December 2, 2016: Cellular and Molecular Life Sciences: CMLS
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