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https://www.readbyqxmd.com/read/29235352/systems-approaches-to-understanding-and-designing-allosteric-proteins
#1
Srivatsan Raman
The study of allostery has a central place in biology due to the myriad roles of allosteric proteins in cellular function. As technologies to probe spatiotemporal resolution of biomolecules have become increasingly sophisticated, so has our understanding of the diverse structural and molecular mechanisms of allosteric proteins. Studies have shown that allosteric signal is transmitted a through a network of residue-residue interactions connecting distal sites on a protein. Linking structural and dynamical changes to the functional role of individual residues will give a more complete molecular view of allostery...
December 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/29233745/retropath2-0-a-retrosynthesis-workflow-for-metabolic-engineers
#2
Baudoin Delépine, Thomas Duigou, Pablo Carbonell, Jean-Loup Faulon
Synthetic biology applied to industrial biotechnology is transforming the way we produce chemicals. However, despite advances in the scale and scope of metabolic engineering, the research and development process still remains costly. In order to expand the chemical repertoire for the production of next generation compounds, a major engineering biology effort is required in the development of novel design tools that target chemical diversity through rapid and predictable protocols. Addressing that goal involves retrosynthesis approaches that explore the chemical biosynthetic space...
December 9, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29231335/-review-on-skin-temperature-of-acupoints
#3
REVIEW
Ziyi Yang, Mengyuan Zhou, Xing Wang, Yunyun Zhao, Zhifeng Chen, Yi Lan, Tao Xu, Yu Zhao, Ling Zhao
We retrieve and analyze the articles on body surface temperature of acupoints in the recent 50 years. Surface temperatures have been compared between acupoints and nonacupoints, and among acupoints in different states. The impacts of interventions for acupoint temperature are explored, including acupuncture,moxibustion and cupping, etc. We summarize the features and the rules of acupoint skin temperature. It is considered that there exists distribution rule for healthy people's acupoint skin temperature. That means acupoints have higher surface temperature than nonacupoints...
January 12, 2017: Zhongguo Zhen Jiu, Chinese Acupuncture & Moxibustion
https://www.readbyqxmd.com/read/29228337/triplex-forming-oligonucleotides-a-third-strand-for-dna-nanotechnology
#4
Arun Richard Chandrasekaran, David A Rusling
DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical ('triplex') structure...
December 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29211649/hearing-shapes-event-related-potentials-reveal-the-time-course-of-auditory-visual-sensory-substitution
#5
Christian Graulty, Orestis Papaioannou, Phoebe Bauer, Michael A Pitts, Enriqueta Canseco-Gonzalez
In auditory-visual sensory substitution, visual information (e.g., shape) can be extracted through strictly auditory input (e.g., soundscapes). Previous studies have shown that image-to-sound conversions that follow simple rules [such as the Meijer algorithm; Meijer, P. B. L. An experimental system for auditory image representation. Transactions on Biomedical Engineering, 39, 111-121, 1992] are highly intuitive and rapidly learned by both blind and sighted individuals. A number of recent fMRI studies have begun to explore the neuroplastic changes that result from sensory substitution training...
December 6, 2017: Journal of Cognitive Neuroscience
https://www.readbyqxmd.com/read/29211336/diverse-effects-of-invasive-ecosystem-engineers-on-marine-biodiversity-and-ecosystem-functions-a-global-review-and-meta-analysis
#6
Tamar Guy-Haim, Devin A Lyons, Jonne Kotta, Henn Ojaveer, Ana M Queirós, Eva Chatzinikolaou, Christos Arvanitidis, Serena Como, Paolo Magni, Andrew J Blight, Helen Orav-Kotta, Paul J Somerfield, Tasman P Crowe, Gil Rilov
Invasive ecosystem engineers (IEE) are potentially one of the most influential types of biological invaders. They are expected to have extensive ecological impacts by altering the physical-chemical structure of ecosystems, thereby changing the rules of existence for a broad range of resident biota. To test the generality of this expectation, we used a global systematic review and meta-analysis to examine IEE effects on the abundance of individual species and communities, biodiversity (using several indices) and ecosystem functions, focusing on marine and estuarine environments...
December 6, 2017: Global Change Biology
https://www.readbyqxmd.com/read/29205536/energy-structure-function-maps-cartography-for-materials-discovery
#7
REVIEW
Graeme M Day, Andrew I Cooper
Some of the most successful approaches to structural design in materials chemistry have exploited strong directional bonds, whose geometric reliability lends predictability to solid-state assembly. For example, metal-organic frameworks are an important design platform in materials chemistry. By contrast, the structure of molecular crystals is defined by a balance of weaker intermolecular forces, and small changes to the molecular building blocks can lead to large changes in crystal packing. Hence, empirical rules are inherently less reliable for engineering the structures of molecular solids...
December 4, 2017: Advanced Materials
https://www.readbyqxmd.com/read/29170951/bacterial-genome-editing-strategy-for-control-of-transcription-and-protein-stability
#8
Ida Lauritsen, Virginia Martínez, Carlotta Ronda, Alex Toftgaard Nielsen, Morten H H Nørholm
In molecular biology and cell factory engineering, tools that enable control of protein production and stability are highly important. Here, we describe protocols for tagging genes in Escherichia coli allowing for inducible degradation and transcriptional control of any soluble protein of interest. The underlying molecular biology is based on the two cross-kingdom tools CRISPRi and the N-end rule for protein degradation. Genome editing is performed with the CRMAGE technology and randomization of the translational initiation region minimizes the polar effects of tag insertion...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29148087/an-agent-based-model-of-evolving-community-flood-risk
#9
Gina L Tonn, Seth D Guikema
Although individual behavior plays a major role in community flood risk, traditional flood risk models generally do not capture information on how community policies and individual decisions impact the evolution of flood risk over time. The purpose of this study is to improve the understanding of the temporal aspects of flood risk through a combined analysis of the behavioral, engineering, and physical hazard aspects of flood risk. Additionally, the study aims to develop a new modeling approach for integrating behavior, policy, flood hazards, and engineering interventions...
November 17, 2017: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/29134429/self-driving-cars-and-engineering-ethics-the-need-for-a-system-level-analysis
#10
Jason Borenstein, Joseph R Herkert, Keith W Miller
The literature on self-driving cars and ethics continues to grow. Yet much of it focuses on ethical complexities emerging from an individual vehicle. That is an important but insufficient step towards determining how the technology will impact human lives and society more generally. What must complement ongoing discussions is a broader, system level of analysis that engages with the interactions and effects that these cars will have on one another and on the socio-technical systems in which they are embedded...
November 13, 2017: Science and Engineering Ethics
https://www.readbyqxmd.com/read/29114106/designing-and-implementation-of-a-heart-failure-telemonitoring-system
#11
Reza Safdari, Maryam Jafarpour, Mehrshad Mokhtaran, Nasim Naderi
Introduction: The aim of this study was to identify patients at-risk, enhancing self-care management of HF patients at home and reduce the disease exacerbations and readmissions. Method: In this research according to standard heart failure guidelines and Semi-structured interviews with 10 heart failure Specialists, a draft heart failure rule set for alerts and patient instructions was developed. Eventually, the clinical champion of the project vetted the rule set...
September 2017: Acta Informatica Medica: AIM
https://www.readbyqxmd.com/read/29110490/ferroelectricity-in-ruddlesden-popper-chalcogenide-perovskites-for-photovoltaic-application-a-role-of-tolerance-factor
#12
Yajun Zhang, Takahiro Shimada, Takayuki Kitamura, Jie Wang
Chalcogenide perovskites with optimal bandgap and desirable light absorption are promising for photovoltaic devices, whereas the absence of ferroelectricity limits their potential in application. Based on first-principles calculations, we reveal the underlying mechanism of the paraelectric nature of Ba3Zr2S7 observed in experiments and demonstrate a general rule for the appearance of ferroelectricity in chalcogenide perovskites with Ruddlesden-Popper (RP) A3B2X7 structures. Group theoretical analysis shows that tolerance factor is the primary factor that dominates the ferroelectricity...
November 7, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29101046/structural-and-functional-insights-into-thermostable-and-organic-solvent-stable-variant-pro247-ser-of-bacillus-lipase
#13
Nisha Chopra, Arbind Kumar, Jagdeep Kaur
Thermostability of enzymes is an important issue in protein engineering and has been studied in detail. Still there is no hard and fast rule to define the conditions which will provide thermal stability. Understanding the various factors and mechanism responsible for thermal stability will add on new insights into our present knowledge in this area. Pro247-Ser variant was constructed based on homology modelling and rational design. It exhibited 60 fold increase in thermal stability at 60°C and+0.7M shift in C1/2 value for urea denaturation as compared to WT...
October 31, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29098147/synthetic-promoters-and-transcription-factors-for-heterologous-protein-expression-in-saccharomyces-cerevisiae
#14
Fabian Machens, Salma Balazadeh, Bernd Mueller-Roeber, Katrin Messerschmidt
Orthogonal systems for heterologous protein expression as well as for the engineering of synthetic gene regulatory circuits in hosts like Saccharomyces cerevisiae depend on synthetic transcription factors (synTFs) and corresponding cis-regulatory binding sites. We have constructed and characterized a set of synTFs based on either transcription activator-like effectors or CRISPR/Cas9, and corresponding small synthetic promoters (synPs) with minimal sequence identity to the host's endogenous promoters. The resulting collection of functional synTF/synP pairs confers very low background expression under uninduced conditions, while expression output upon induction of the various synTFs covers a wide range and reaches induction factors of up to 400...
2017: Frontiers in Bioengineering and Biotechnology
https://www.readbyqxmd.com/read/29081959/1d-vs-2d-shape-selectivity-in-the-crystallization-driven-self-assembly-of-polylactide-block-copolymers
#15
Maria Inam, Graeme Cambridge, Anaïs Pitto-Barry, Zachary P L Laker, Neil R Wilson, Robert T Mathers, Andrew P Dove, Rachel K O'Reilly
2D materials such as graphene, LAPONITE® clays or molybdenum disulfide nanosheets are of extremely high interest to the materials community as a result of their high surface area and controllable surface properties. While several methods to access 2D inorganic materials are known, the investigation of 2D organic nanomaterials is less well developed on account of the lack of ready synthetic accessibility. Crystallization-driven self-assembly (CDSA) has become a powerful method to access a wide range of complex but precisely-defined nanostructures...
June 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29081050/design-principles-of-peptide-based-self-assembled-nanomaterials
#16
Rania S Seoudi, Adam Mechler
The ability to design functionalized peptide nanostructures for specific applications is tied to the ability of controlling the morphologies of the self-assembled superstructures. That, in turn, is based on a thorough understanding of the structural and environmental factors affecting self-assembly. The aim of designing self-assembling nanostructures of controlled geometries is achieved via a combination of directional and non-directional second order interactions. If the interactions are distributed in a geometrically defined way, a specific and selective supramolecular self-assembly motif is the result...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29077104/polydopamine-based-concentric-nanoshells-with-programmable-architectures-and-plasmonic-properties
#17
Chun Kit K Choi, Xiaolu Zhuo, Yee Ting Elaine Chiu, Hongrong Yang, Jianfang Wang, Chung Hang Jonathan Choi
Nanoshells, classically comprising gold as the metallic component and silica as the dielectric material, are important for fundamental studies in nanoplasmonics. They also empower a myriad of applications, including sensing, energy harvesting, and cancer therapy. Yet, laborious preparation precludes the development of next-generation nanoshells with structural complexity, compositional diversity, and tailorable plasmonic behaviors. This work presents an efficient approach to the bottom-up assembly of concentric nanoshells...
November 9, 2017: Nanoscale
https://www.readbyqxmd.com/read/29071327/engineering-of-inorganic-nanoparticles-as-magnetic-resonance-imaging-contrast-agents
#18
REVIEW
Dalong Ni, Wenbo Bu, Emily B Ehlerding, Weibo Cai, Jianlin Shi
Magnetic resonance imaging (MRI) is a highly valuable non-invasive imaging tool owing to its exquisite soft tissue contrast, high spatial resolution, lack of ionizing radiation, and wide clinical applicability. Contrast agents (CAs) can be used to further enhance the sensitivity of MRI to obtain information-rich images. Recently, extensive research efforts have been focused on the design and synthesis of high-performance inorganic nanoparticle-based CAs to improve the quality and specificity of MRI. Herein, the basic rules, including the choice of metal ions, effect of electron motion on water relaxation, and involved mechanisms, of CAs for MRI have been elucidated in detail...
October 26, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/29065633/the-research-of-clinical-decision-support-system-based-on-three-layer-knowledge-base-model
#19
Yicheng Jiang, Bensheng Qiu, Chunsheng Xu, Chuanfu Li
In many clinical decision support systems, a two-layer knowledge base model (disease-symptom) of rule reasoning is used. This model often does not express knowledge very well since it simply infers disease from the presence of certain symptoms. In this study, we propose a three-layer knowledge base model (disease-symptom-property) to utilize more useful information in inference. The system iteratively calculates the probability of patients who may suffer from diseases based on a multisymptom naive Bayes algorithm, in which the specificity of these disease symptoms is weighted by the estimation of the degree of contribution to diagnose the disease...
2017: Journal of Healthcare Engineering
https://www.readbyqxmd.com/read/29053936/evaluation-of-an-improved-prototype-mini-baghouse-to-control-the-release-of-respirable-crystalline-silica-from-sand-movers
#20
Barbara M Alexander, Eric J Esswein, Michael G Gressel, Jerry L Kratzer, H Amy Feng, Arthur L Miller, Emanuele Cauda, Graeham Heil
The OSHA final rule on respirable crystalline silica (RCS) will require hydraulic fracturing companies to implement engineering controls to limit workers' exposure to RCS. RCS is generated by pneumatic transfer of quartz-containing sand during hydraulic fracturing operations. Chronic inhalation of RCS can lead to serious disease, including silicosis and lung cancer. NIOSH research identified at least seven sources where RCS aerosols were generated at hydraulic fracturing sites. NIOSH researchers developed an engineering control to address one of the largest sources of RCS aerosol generation, RCS escaping from thief hatches on the top of sand movers...
October 20, 2017: Journal of Occupational and Environmental Hygiene
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