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Synthetic biology

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https://www.readbyqxmd.com/read/27926854/structural-characterization-and-statistical-mechanical-model-of-epidermal-patterns
#1
Duyu Chen, Wen Yih Aw, Danelle Devenport, Salvatore Torquato
In proliferating epithelia of mammalian skin, cells of irregular polygon-like shapes pack into complex, nearly flat two-dimensional structures that are pliable to deformations. In this work, we employ various sensitive correlation functions to quantitatively characterize structural features of evolving packings of epithelial cells across length scales in mouse skin. We find that the pair statistics in direct space (correlation function) and Fourier space (structure factor) of the cell centroids in the early stages of embryonic development show structural directional dependence (statistical anisotropy), which is a reflection of the fact that cells are stretched, which promotes uniaxial growth along the epithelial plane...
December 6, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27925461/in-it-for-the-long-haul-the-cytocompatibility-of-aged-graphene-oxide-and-its-degradation-products
#2
Brian D Holt, Anne M Arnold, Stefanie A Sydlik
Synthetic biomaterials are poised to transform medicine; however, current synthetic options have yet to ideally recapitulate the desirable properties of native tissue. Thus, the development of new synthetic biomaterials remains an active challenge. Due to its excellent properties, including electrical conductivity, water dispersibility, and capacity for functionalization, graphene oxide (GO) holds potential for myriads of applications, including biological devices. While many studies have evaluated the compatibility of freshly prepared GO, understanding the compatibility of GO as it ages in an aqueous environment is crucial for its safe implementation in long-term biological applications...
December 2016: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/27925398/cell-based-biohybrid-drug-delivery-systems-the-best-of-the-synthetic-and-natural-worlds
#3
Samagya Banskota, Parisa Yousefpour, Ashutosh Chilkoti
The goal of drug delivery is to deliver therapeutics to the site of disease while reducing unwanted side effects. In recent years, a diverse variety of synthetic nano and microparticles have been developed as drug delivery systems. The success of these systems for drug delivery lies in their ability to overcome biological barriers such as the blood-brain barrier, to evade immune clearance and avoid nonspecific biodistribution. This Review provides an overview of recent advances in the design of biohybrid drug delivery systems, which combine cells with synthetic systems to overcome some of these biological hurdles...
December 7, 2016: Macromolecular Bioscience
https://www.readbyqxmd.com/read/27924940/the-metabolic-flux-regulation-of-klebsiella-pneumoniae-based-on-quorum-sensing-system
#4
Shujing Sun, Haiyang Zhang, Shuyi Lu, Chunfen Lai, Huijun Liu, Hu Zhu
Quorum-sensing (QS) systems exist universally in bacteria to regulate multiple biological functions. Klebsiella pneumoniae, an industrially important bacterium that produces bio-based chemicals such as 2,3-butanediol and acetoin, can secrete a furanosyl borate diester (AI-2) as the signalling molecule mediating a QS system, which plays a key regulatory role in the biosynthesis of secondary metabolites. In this study, the molecular regulation and metabolic functions of a QS system in K. pneumoniae were investigated...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924473/non-nucleotide-modification-of-anti-mirna-oligonucleotides
#5
Kim A Lennox, Christopher A Vakulskas, Mark A Behlke
MicroRNAs (miRNAs) are important modulators of gene expression. Synthetic anti-microRNA oligonucleotides (AMOs, or anti-miRs) are a form of steric-blocking antisense oligonucleotides (ASOs) that inhibit miRNA function through high-affinity binding and subsequent inactivation and/or degradation of the targeted miRNA. AMOs are a primary tool used to empirically determine the biological targets of a miRNA and can also be used therapeutically when overexpression of a miRNA contributes to a disease state. Chemical modification of synthetic AMOs enhance potency by protecting the oligonucleotide from nuclease degradation and by increasing binding affinity to the target miRNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924426/preditor-a-synthetic-biology-approach-to-removing-heterochromatin-from-cells
#6
Oscar Molina, Mar Carmena, Isabella E Maudlin, William C Earnshaw
It is widely accepted that heterochromatin is necessary to maintain genomic stability. However, direct experimental evidence supporting this is slim. Previous studies using either enzyme inhibitors, gene knockout or knockdown studies all are subject to the caveat that drugs may have off-target effects and enzymes that modify chromatin proteins to support heterochromatin formation may also have numerous other cellular targets as well. Here, we describe PREditOR (protein reading and editing of residues), a synthetic biology approach that allows us to directly remove heterochromatin from cells without either drugs or global interference with gene function...
December 6, 2016: Chromosome Research
https://www.readbyqxmd.com/read/27924262/mass-spectrometric-analysis-of-protein-ligand-interactions
#7
Kentaro Ishii, Masanori Noda, Susumu Uchiyama
The interactions of small molecules with proteins (protein-ligand interactions) mediate various biological phenomena including signal transduction and protein transcription and translation. Synthetic compounds such as drugs can also bind to target proteins, leading to the inhibition of protein-ligand interactions. These interactions typically accompany association-dissociation equilibrium according to the free energy difference between free and bound states; therefore, the quantitative biophysical analysis of the interactions, which uncovers the stoichiometry and dissociation constant, is important for understanding biological reactions as well as for rational drug development...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27923493/in%C3%A2-vivo-effect-of-innate-immune-response-modulating-impurities-on-the-skin-milieu-using-a-macaque-model-impact-on-product-immunogenicity
#8
Lydia A Haile, Montserrat Puig, Swamy K Polumuri, Jill Ascher, Daniela Verthelyi
Unwanted immune responses to therapeutic proteins can severely impact their safety and efficacy. Studies show that the presence of trace amounts of host cells and process-related impurities that stimulate pattern recognition receptors (PRR) can cause local inflammation and enhance product immunogenicity. Here we used purified PRR agonists as model impurities to assess the minimal level of individual innate immune response modulating impurities (IIRMIs) that could activate a local immune response. We show that levels of endotoxin as low as 10 pg (0...
December 3, 2016: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27923064/sparse-regression-based-structure-learning-of-stochastic-reaction-networks-from-single-cell-snapshot-time-series
#9
Anna Klimovskaia, Stefan Ganscha, Manfred Claassen
Stochastic chemical reaction networks constitute a model class to quantitatively describe dynamics and cell-to-cell variability in biological systems. The topology of these networks typically is only partially characterized due to experimental limitations. Current approaches for refining network topology are based on the explicit enumeration of alternative topologies and are therefore restricted to small problem instances with almost complete knowledge. We propose the reactionet lasso, a computational procedure that derives a stepwise sparse regression approach on the basis of the Chemical Master Equation, enabling large-scale structure learning for reaction networks by implicitly accounting for billions of topology variants...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27922613/elements-of-biological-oscillations-in-time-and-space
#10
Yangxiaolu Cao, Allison Lopatkin, Lingchong You
Oscillations in time and space are ubiquitous in nature and play critical roles in dynamic cellular processes. Although the molecular mechanisms underlying the generation of the dynamics are diverse, several distinct regulatory elements have been recognized as being critical in producing and modulating oscillatory dynamics. These include negative and positive feedback, time delay, nonlinearity in regulation, and random fluctuations ('noise'). Here we discuss the specific roles of these five elements in promoting or attenuating oscillatory dynamics, by drawing on insights from quantitative analyses of natural or synthetic biological networks...
December 6, 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27922059/protein-self-assembly-onto-nanodots-leads-to-formation-of-conductive-bio-based-hybrids
#11
Xiao Hu, Chenbo Dong, Rigu Su, Quan Xu, Cerasela Zoica Dinu
The next generation of nanowires that could advance the integration of functional nanosystems into synthetic applications from photocatalysis to optical devices need to demonstrate increased ability to promote electron transfer at their interfaces while ensuring optimum quantum confinement. Herein we used the biological recognition and the self-assembly properties of tubulin, a protein involved in building the filaments of cellular microtubules, to create stable, free standing and conductive sulfur-doped carbon nanodots-based conductive bio-hybrids...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921334/synacton-and-individual-activity-of-synthetic-and-natural-corticotropins
#12
T V Vyunova, L A Andreeva, K V Shevchenko, N F Myasoedov
Short endogenous peptides represent one of the most important constituents of the mammalian body's general regulatory system. Some synthesized analogs and modified natural peptides (eg, corticotropins) also show high biological activity. Nevertheless, the mechanism of action of regulatory peptides remains unclear. To explain the effects of peptides of intermolecular processes, the hypothesis that a synactonal mechanism underlies the action of regulatory peptides, exemplified by the heptapeptide Semax, has been proposed...
December 6, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27921179/activation-of-dioxygen-by-copper-metalloproteins-and-insights-from-model-complexes
#13
REVIEW
David A Quist, Daniel E Diaz, Jeffrey J Liu, Kenneth D Karlin
Nature uses dioxygen as a key oxidant in the transformation of biomolecules. Among the enzymes that are utilized for these reactions are copper-containing metalloenzymes, which are responsible for important biological functions such as the regulation of neurotransmitters, dioxygen transport, and cellular respiration. Enzymatic and model system studies work in tandem in order to gain an understanding of the fundamental reductive activation of dioxygen by copper complexes. This review covers the most recent advancements in the structures, spectroscopy, and reaction mechanisms for dioxygen-activating copper proteins and relevant synthetic models thereof...
December 5, 2016: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/27920698/a-case-of-en-bloc-excision-of-a-chest-wall-leiomyosarcoma-and-closure-of-the-defect-with-non-cross-linked-collagen-matrix-egis-%C3%A2
#14
Marco Rastrelli, Saveria Tropea, Romina Spina, Alessandra Costa, Roberto Stramare, Simone Mocellin, Maria Giuseppina Bonavina, Carlo Riccardo Rossi
Sarcomas arising from the chest wall account for less than 20% of all soft tissue sarcomas, and at this site, primitive tumors are the most frequent to occur. Leiomyosarcoma is a malignant smooth muscle tumor and the best outcomes are achieved with wide surgical excision. Although advancements have been made in treatment protocols, leiomyosarcoma remains one of the more difficult soft tissue sarcoma to treat. Currently, general local control is obtained with surgical treatment with wide negative margins. We describe the case of a 50-year-old man who underwent a chest wall resection involving a wide portion of the pectoralis major and minor muscle, the serratus and part of the second, third and fourth ribs of the left side...
September 2016: Case Reports in Oncology
https://www.readbyqxmd.com/read/27919613/cellular-uptake-of-glucoheptoamidated-poly-amidoamine-pamam-g3-dendrimer-with-amide-conjugated-biotin-a-potential-carrier-of-anticancer-drugs
#15
Łukasz Uram, Magdalena Szuster, Aleksandra Filipowicz, Magdalena Zaręba, Elżbieta Wałajtys-Rode, Stanisław Wołowiec
In search for soluble derivatives of PAMAM dendrimers as potential carriers for hydrophobic drugs, the conjugates of PAMAM G3 with biotin, further converted into glycodendrimer with d-glucoheptono-1,4-lactone, were prepared. Polyamidoamine dendrimer (PAMAM) of third generation, G3 was functionalized with four biotin equivalents covalently attached to terminal amine nitrogens via amide bond G3(4B). The remaining 28 amine groups were blocked by glucoheptoamide substituents (gh) to give G3(4B28gh) or with one fluorescein equivalent (attached by reaction of G3(4B) with fluorescein isothiocyanate, FITC) via thiourea bond as FITC followed by exhaustive glucoheptoamidation to get G3(4B27gh1F)...
November 25, 2016: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/27919539/nanostructured-fusiform-hydroxyapatite-particles-precipitated-from-aquaculture-wastewater
#16
Covadonga Correas, Michael L Gerardo, Alexander M Lord, Michael B Ward, Enrico Andreoli, Andrew R Barron
The present work represents a new approach for the isolation of uniform nano particulate hydroxyapatite (HAp). The chemical characterization of a calcium phosphate product obtained from industrial trout farm aquaculture wastewater by two different routes, washing either with a basic aqueous medium (washNaOH) or followed by a further washing with ethanol (washEtOH), is explored. Characterization of the isolated materials includes morphology studies (SEM and TEM), structural (XRD, electron diffraction), compositional (EDX) and thermogravimetric analysis (TGA)...
December 2, 2016: Chemosphere
https://www.readbyqxmd.com/read/27919066/designed-proteins-induce-the-formation-of-nanocage-containing-extracellular-vesicles
#17
Jörg Votteler, Cassandra Ogohara, Sue Yi, Yang Hsia, Una Nattermann, David M Belnap, Neil P King, Wesley I Sundquist
Complex biological processes are often performed by self-organizing nanostructures comprising multiple classes of macromolecules, such as ribosomes (proteins and RNA) or enveloped viruses (proteins, nucleic acids and lipids). Approaches have been developed for designing self-assembling structures consisting of either nucleic acids or proteins, but strategies for engineering hybrid biological materials are only beginning to emerge. Here we describe the design of self-assembling protein nanocages that direct their own release from human cells inside small vesicles in a manner that resembles some viruses...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27918838/quality-of-governance-and-effectiveness-of-protected-areas-crucial-concepts-for-conservation-planning
#18
Johanna Eklund, Mar Cabeza
Protected areas (PAs) are a key tool for biodiversity conservation and play a central role in the Convention on Biological Diversity. Recently, the effectiveness of PAs has been questioned, and assessing how effective they are in enabling the future persistence of biodiversity is not trivial. Here, we focus on terrestrial PAs and clarify the terminology related to PA effectiveness, distinguishing between management and ecological aspects. We suggest that the quality of governance affects both aspects of effectiveness but recognize a lack of synthetic understanding of the topic...
December 5, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27918765/development-of-a-biochemical-diagnosis-of-parkinson-disease-by-detection-of-%C3%AE-synuclein-misfolded-aggregates-in-cerebrospinal-fluid
#19
Mohammad Shahnawaz, Takahiko Tokuda, Masaaki Waragai, Nicolas Mendez, Ryotaro Ishii, Claudia Trenkwalder, Brit Mollenhauer, Claudio Soto
Importance: Parkinson disease (PD) is a highly prevalent and incurable neurodegenerative disease associated with the accumulation of misfolded α-synuclein (αSyn) aggregates. An important problem in this disease is the lack of a sensitive, specific, and noninvasive biochemical diagnosis to help in clinical evaluation, monitoring of disease progression, and early differential diagnosis from related neurodegenerative diseases. Objective: To develop a novel assay with high sensitivity and specificity to detect small quantities of αSyn aggregates circulating in cerebrospinal fluid (CSF) of patients affected by PD and related synucleinopathies...
December 5, 2016: JAMA Neurology
https://www.readbyqxmd.com/read/27918296/crystal-structures-of-deprotonated-nucleobases-from-an-expanded-dna-alphabet
#20
Mariko F Matsuura, Hyo Joong Kim, Daisuke Takahashi, Khalil A Abboud, Steven A Benner
Reported here is the crystal structure of a heterocycle that implements a donor-donor-acceptor hydrogen-bonding pattern, as found in the Z component [6-amino-5-nitropyridin-2(1H)-one] of an artificially expanded genetic information system (AEGIS). AEGIS is a new form of DNA from synthetic biology that has six replicable nucleotides, rather than the four found in natural DNA. Remarkably, Z crystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine-pyrimidine pair in this structure...
December 1, 2016: Acta Crystallographica. Section C, Structural Chemistry
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