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https://www.readbyqxmd.com/read/29243480/reshaping-the-energy-landscape-transforms-the-mechanism-and-binding-kinetics-of-dna-threading-intercalation
#1
Andrew G Clark, M Nabuan Naufer, Fredrik Westerlund, Per Lincoln, Ioulia Rouzina, Thayaparan Paramanathan, Mark C Williams
Molecules that bind DNA via threading intercalation show high binding affinity as well as slow dissociation kinetics, properties ideal for the development of anticancer drugs. To this end, it is critical to identify the specific molecular characteristics of threading intercalators that result in optimal DNA interactions. Using single molecule techniques, we quantify the binding of a small metalorganic ruthenium threading intercalator (Δ,Δ-B), and compare its binding characteristics to a similar molecule with significantly larger threading moieties (Δ,Δ-P)...
December 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/29243414/biomedical-device-innovation-methodology-applications-in-biophotonics
#2
Daniel M Beswick, Arjun Kaushik, Dylan Beinart, Sarah McGarry, Ming Khoon Yew, Brendan F Kennedy, Peter Luke Santa Maria
The process of medical device innovation involves an iterative method that focuses on designing innovative, device-oriented solutions that address unmet clinical needs. This process has been applied to the field of biophotonics with many notable successes. Device innovation begins with identifying an unmet clinical need and evaluating this need through a variety of lenses, including currently existing solutions for the need, stakeholders who are interested in the need, and the market that will support an innovative solution...
December 2017: Journal of Biomedical Optics
https://www.readbyqxmd.com/read/29242347/comprehensive-computational-design-of-ordered-peptide-macrocycles
#3
Parisa Hosseinzadeh, Gaurav Bhardwaj, Vikram Khipple Mulligan, Matthew D Shortridge, Timothy W Craven, Fátima Pardo-Avila, Stephen A Rettie, David E Kim, Daniel-Adriano Silva, Yehia M Ibrahim, Ian K Webb, John R Cort, Joshua N Adkins, Gabriele Varani, David Baker
Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with l-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of l- and d-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations...
December 15, 2017: Science
https://www.readbyqxmd.com/read/29238666/preoperative-counseling-and-expectation-management-for-inflatable-penile-prosthesis-implantation
#4
REVIEW
Gopal L Narang, Bradley D Figler, Robert M Coward
The inflatable penile prosthesis (IPP) is the gold standard surgical treatment for medical refractory erectile dysfunction (ED). While the modern IPP has enjoyed high satisfaction rates as a product of its continued innovation, reliability, and performance, patient dissatisfaction can still occur. IPP implantation restores physiologic function with cosmetic and psychological consequences, both of which place inherent emphasis on preoperative counseling and expectation management. This review aims to highlight the complex nature of such counseling and provide practitioners with a roadmap to navigate the landscape...
November 2017: Translational Andrology and Urology
https://www.readbyqxmd.com/read/29238550/plant-community-composition-and-species-richness-in-the-high-arctic-tundra-from-the-present-to-the-future
#5
Jacob Nabe-Nielsen, Signe Normand, Francis K C Hui, Lærke Stewart, Christian Bay, Louise I Nabe-Nielsen, Niels Martin Schmidt
Arctic plant communities are altered by climate changes. The magnitude of these alterations depends on whether species distributions are determined by macroclimatic conditions, by factors related to local topography, or by biotic interactions. Our current understanding of the relative importance of these conditions is limited due to the scarcity of studies, especially in the High Arctic. We investigated variations in vascular plant community composition and species richness based on 288 plots distributed on three sites along a coast-inland gradient in Northeast Greenland using a stratified random design...
December 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29237136/biomimetic-structural-materials-inspiration-from-design-and-assembly
#6
Nicholas A Yaraghi, David Kisailus
Nature assembles weak organic and inorganic constituents into sophisticated hierarchical structures, forming structural composites that demonstrate impressive combinations of strength and toughness. Two such composites are the nacre structure forming the inner layer of many mollusk shells, whose brick-and-mortar architecture has been the gold standard for biomimetic composites, and the cuticle forming the arthropod exoskeleton, whose helicoidal fiber-reinforced architecture has only recently attracted interest for structural biomimetics...
December 13, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/29232470/how-can-molecular-abnormalities-influence-our-clinical-approach
#7
W Wei, F Giulia, S Luffer, R Kumar, B Wu, M Tavallai, R T Bekele, M J Birrer
Background: Despite improvements in diagnostics and treatment, the clinical outcome of epithelial ovarian cancer remains poor over the last three decades. Recent high-throughput genomic studies have demonstrated ovarian cancer as a highly heterogeneous entity with distinctive molecular signatures among different or even within the same histotype. In this article, we review the molecular genetics of epithelial ovarian cancer and how they have been translated into modern clinical trials, as well as their implications in patient stratification for more targeted and personalized approaches...
November 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29230060/natural-erosion-of-sandstone-as-shape-optimisation
#8
Igor Ostanin, Alexander Safonov, Ivan Oseledets
Natural arches, pillars and other exotic sandstone formations have always been attracting attention for their unusual shapes and amazing mechanical balance that leave a strong impression of intelligent design rather than the result of a stochastic process. It has been recently demonstrated that these shapes could have been the result of the negative feedback between stress and erosion that originates in fundamental laws of friction between the rock's constituent particles. Here we present a deeper analysis of this idea and bridge it with the approaches utilized in shape and topology optimisation...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229974/ensemble-modeling-approach-targeting-heterogeneous-rna-seq-data-application-to-melanoma-pseudogenes
#9
Enrico Capobianco, Camilo Valdes, Samanta Sarti, Zhijie Jiang, Laura Poliseno, Nicolas F Tsinoremas
We studied the transcriptome landscape of skin cutaneous melanoma (SKCM) using 103 primary tumor samples from TCGA, and measured the expression levels of both protein coding genes and non-coding RNAs (ncRNAs). In particular, we emphasized pseudogenes potentially relevant to this cancer. While cataloguing the profiles based on the known biotypes, all the employed RNA-Seq methods generated just a small consensus of significant biotypes. We thus designed an approach to reconcile the profiles from all methods following a simple strategy: we selected genes that were confirmed as differentially expressed by the ensemble predictions obtained in a regression model...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229813/human-genetic-variation-alters-crispr-cas9-on-and-off-targeting-specificity-at-therapeutically-implicated-loci
#10
Samuel Lessard, Laurent Francioli, Jessica Alfoldi, Jean-Claude Tardif, Patrick T Ellinor, Daniel G MacArthur, Guillaume Lettre, Stuart H Orkin, Matthew C Canver
The CRISPR-Cas9 nuclease system holds enormous potential for therapeutic genome editing of a wide spectrum of diseases. Large efforts have been made to further understanding of on- and off-target activity to assist the design of CRISPR-based therapies with optimized efficacy and safety. However, current efforts have largely focused on the reference genome or the genome of cell lines to evaluate guide RNA (gRNA) efficiency, safety, and toxicity. Here, we examine the effect of human genetic variation on both on- and off-target specificity...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29226011/role-of-conformational-dynamics-in-the-evolution-of-retro-aldolase-activity
#11
Adrian Romero-Rivera, Marc Garcia-Borràs, Sílvia Osuna
Enzymes exist as ensembles of conformations that are important for function. Tuning these populations of conformational states through mutation enables evolution toward additional activities. Here we computationally evaluate the population shifts induced by distal and active site mutations in a family of computationally designed and experimentally optimized retro-aldolases. The conformational landscape of these enzymes was significantly altered during evolution, as pre-existing catalytically active conformational substates became major states in the most evolved variants...
December 1, 2017: ACS Catalysis
https://www.readbyqxmd.com/read/29217218/nature-based-solutions-for-resilient-landscapes-and-cities
#12
Raffaele Lafortezza, Jiquan Chen, Cecil Konijnendijk van den Bosch, Thomas B Randrup
Nature-based solutions (NBS) are increasingly applied to guide the design of resilient landscapes and cities to enable them to reach economic development goals with beneficial outcomes for the environment and society. The NBS concept is closely related to other concepts including sustainability, resilience, ecosystem services, coupled human and environment, and green (blue) infrastructure; however, NBS represent a more efficient and cost-effective approach to development than traditional approaches. The European Commission is actively engaged in investing in NBS as a driver in developing ecosystem services-based approaches throughout Europe and the world...
December 4, 2017: Environmental Research
https://www.readbyqxmd.com/read/29216860/-the-end-of-sitting-in-a-public-space-observations-of-spontaneous-visitors
#13
Lidewij R Renaud, Maaike A Huysmans, Erwin M Speklé, Allard J van der Beek, Hidde P van der Ploeg
BACKGROUND: Sitting too much has been associated with negative health outcomes. 'The End of Sitting' is a newly developed office landscape that moves away from the traditional chair-desk setup. The landscape aims to reduce sitting time by offering a variety of (supported) standing positions. The aim of this study was to determine the usage of the landscape after being placed in the main entrance hall of the VU University in Amsterdam. METHODS: We observed the number of spontaneous visitors as well as the duration of visits, changes to another location within the landscape, and adopted postures...
December 8, 2017: BMC Public Health
https://www.readbyqxmd.com/read/29212614/clinical-trials-in-gynecologic-oncology-past-present-and-future
#14
REVIEW
Christina M Annunziata, Elise C Kohn
The Gynecologic Oncology Group has historically performed ground-breaking, practice-changing clinical trials in women's cancers. The current standard of care for initial treatment of ovarian, endometrial, cervical, and trophoblastic cancers was determined by clinical trials completed within this cooperative group structure. For example, trial GOG-0111 set the standard for combining platinum and taxane chemotherapy in ovarian cancer, and more recently GOG-0240 provided evidence for adding bevacizumab to chemotherapy for women with advanced cervical cancer...
December 3, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29209596/aflp-reveals-low-genetic-diversity-of-the-bryozoan-pectinatella-magnifica-leidy-1851-in-the-czech-republic
#15
Vendula Moravcová, Jana Moravcová, Vladislav Čurn, Zuzana Balounová, Josef Rajchard, Lenka Havlíčková
Background: Non-native species have aroused scientific interest because of their ability to successfully colonise areas to which they have been introduced, despite their sometimes limited genetic variation compared to their native range. These species establish themselves with the aid of some pre-existing features favouring them in the new environment. Pectinatella magnifica (Leidy, 1851), the freshwater magnificent bryozoan, is non-native in Europe and Asia. This study was designed to determine the genetic diversity and population structure of P...
December 2017: Journal of Biological Research
https://www.readbyqxmd.com/read/29208897/network-dynamics-based-cancer-panel-stratification-for-systemic-prediction-of-anticancer-drug-response
#16
Minsoo Choi, Jue Shi, Yanting Zhu, Ruizhen Yang, Kwang-Hyun Cho
Cancer is a complex disease involving multiple genomic alterations that disrupt the dynamic response of signaling networks. The heterogeneous nature of cancer, which results in highly variable drug response, is a major obstacle to developing effective cancer therapy. Previous studies of cancer therapeutic response mostly focus on static analysis of genome-wide alterations, thus they are unable to unravel the dynamic, network-specific origin of variation. Here we present a network dynamics-based approach to integrate cancer genomics with dynamics of biological network for drug response prediction and design of drug combination...
December 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/29205815/advocating-a-need-for-suitable-breeding-approaches-to-boost-integrated-pest-management-a-european-perspective
#17
Jay Ram Lamichhane, Edward Arseniuk, Piet Boonekamp, Jerzy Czembor, Veronique Decroocq, Jérome Enjalbert, Maria R Finckh, Małgorzata Korbin, Mati Koppel, Per Kudsk, Akos Mesterhazy, Danuta Sosnowska, Ewa Zimnoch-Guzowska, Antoine Messéan
Currently, European farmers do not have access to a sufficient number and diversity of crop species/varieties. This prevents them from designing more resilient cropping systems to abiotic and biotic stresses. Crop diversification is a key lever to reduce pest (pathogens, animal pests and weeds) pressures at all spatial levels from fields to landscapes. In this context, plant breeding should consist of: i) increased efforts in the development of new or minor crop varieties to foster diversity of cropping systems, and ii) focus on more resilient varieties showing local adaptation...
December 4, 2017: Pest Management Science
https://www.readbyqxmd.com/read/29195207/spatial-diversification-of-agroecosystems-to-enhance-biological-control-and-other-regulating-services-an-agroecological-perspective
#18
Séverin Hatt, Fanny Boeraeve, Sidonie Artru, Marc Dufrêne, Frédéric Francis
Spatial diversification of crop and non-crop habitats in farming systems is promising for enhancing natural regulation of insect pests. Nevertheless, results from recent syntheses show variable effects. One explanation is that the abundance and diversity of pests and natural enemies are affected by the composition, design and management of crop and non-crop habitats. Moreover, interactions between both local and landscape elements and practices carried out at different spatial scales may affect the regulation of insect pests...
November 28, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29194330/accelerating-innovation-through-coopetition-the-innovation-learning-network-experience
#19
Chris McCarthy, Penny Ford Carleton, Elizabeth Krumpholz, Marilyn P Chow
Coopetition, the simultaneous pursuit of cooperation and competition, is a growing force in the innovation landscape. For some organizations, the primary mode of innovation continues to be deeply secretive and highly competitive, but for others, a new style of shared challenges, shared purpose, and shared development has become a superior, more efficient way of working to accelerate innovation capabilities and capacity. Over the last 2 decades, the literature base devoted to coopetition has gradually expanded...
January 2018: Nursing Administration Quarterly
https://www.readbyqxmd.com/read/29193992/tlrs-nlrs-shaping-the-landscape-of-host-immunity
#20
Komal Dolasia, Manoj K Bisht, Gourango Pradhan, Atul Udgata, Sangita Mukhopadhyay
Innate immune system provides the first line of defense against pathogenic organisms. It has a varied and large collection of molecules known as pattern recognition receptors (PRRs) which can tackle the pathogens promptly and effectively. Toll-like receptors (TLRs) and NOD-like receptors (NLRs) are members of the PRR family that recognize pathogen associated molecular patterns (PAMPs) and play pivotal roles to mediate defense against infections from bacteria, fungi, virus and various other pathogens. In this review, we discuss the critical roles of TLRs and NLRs in the regulation of host immune-effector functions such as cytokine production, phagosome-lysosome fusion, inflammasome activation, autophagy, antigen presentation, and B and T cell immune responses that are known to be essential for mounting a protective immune response against the pathogens...
December 1, 2017: International Reviews of Immunology
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