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Synthetic genetics

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https://www.readbyqxmd.com/read/28229928/an-expanded-genetic-code-for-probing-the-role-of-electrostatics-in-enzyme-catalysis-by-vibrational-stark-spectroscopy
#1
REVIEW
Jan-Stefan Völler, Hernan Biava, Peter Hildebrandt, Nediljko Budisa
BACKGROUND: To find experimental validation for electrostatic interactions essential for catalytic reactions represents a challenge due to practical limitations in assessing electric fields within protein structures. SCOPE OF REVIEW: This review examines the applications of non-canonical amino acids (ncAAs) as genetically encoded probes for studying the role of electrostatic interactions in enzyme catalysis. MAJOR CONCLUSIONS: ncAAs constitute sensitive spectroscopic probes to detect local electric fields by exploiting the vibrational Stark effect (VSE) and thus have the potential to map the protein electrostatics...
February 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28228073/principal-physicochemical-methods-used-to-characterize-dendrimer-molecule-complexes-used-as-genetic-therapy-agents-nanovaccines-or-drug-carriers
#2
Rodríguez Fonseca Rolando Alberto, Rodrigues Joao, Muñoz-Fernández María de Los Angeles, Martínez Muñoz Alberto, Fragoso Vázquez Manuel Jonathan, Correa Basurto José
Nanomedicine is the application of nanotechnology to medicine. This field is related to the study of nanodevices and nanomaterials applied to various medical uses, such as in improving the pharmacological properties of different molecules. Dendrimers are synthetic nanoparticles whose physicochemical properties vary according to their chemical structure. These molecules have been extensively investigated as drug nanocarriers to improve drug solubility and as sustained-release systems. New therapies such as gene therapy and the development of nanovaccines can be improved by the use of dendrimers...
February 20, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28226781/host-aware-modelling-of-a-synthetic-genetic-oscillator
#3
Alexander Darlington, Declan G Bates, Alexander Darlington, Declan G Bates, Alexander Darlington, Declan G Bates
Synthetic genetic circuits sometimes exhibit unexpected functionality or even fail entirely when implemented in vivo, due to the effects of interactions with the host cell that were not accounted for in the circuit's design. In this paper, we consider the effects that limitations in cellular resources have on the dynamics of a synthetic cellular oscillator. We show that incorporating these effects into a host-aware model of the synthetic oscillator results in significant changes in its dynamics, highlighting the need to take account of host-circuit interactions in mathematical models that are to be used as CAD tools for synthetic circuitry...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226291/cell-free-synthetic-biology-for-environmental-sensing-and-remediation
#4
REVIEW
David K Karig
The fields of biosensing and bioremediation leverage the phenomenal array of sensing and metabolic capabilities offered by natural microbes. Synthetic biology provides tools for transforming these fields through complex integration of natural and novel biological components to achieve sophisticated sensing, regulation, and metabolic function. However, the majority of synthetic biology efforts are conducted in living cells, and concerns over releasing genetically modified organisms constitute a key barrier to environmental applications...
February 19, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28226217/sulfation-of-glycosaminoglycans-and-its-implications-in-human-health-and-disorders
#5
Diana Soares da Costa, Rui L Reis, Iva Pashkuleva
Sulfation is a dynamic and complex posttranslational modification process. It can occur at various positions within the glycosaminoglycan (GAG) backbone and modulates extracellular signals such as cell-cell and cell-matrix interactions; different sulfation patterns have been identified for the same organs and cells during their development. Because of their high specificity in relation to function,GAGsulfation patterns are referred to as the sulfation code. This review explores the role of GAG sulfation in different biological processes at the cell, tissue, and organism levels...
February 2, 2017: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/28224411/personalized-medicine-for-prevention-can-risk-stratified-screening-decrease-colorectal-cancer-mortality-at-an-acceptable-cost
#6
Sujha Subramanian, Georgiy Bobashev, Robert J Morris, Sonja Hoover
PURPOSE: Tailored health care interventions are expected to transform clinical practice. The objective of this study was to develop an innovative model to assess the effectiveness, cost, and harms of risk stratified colorectal cancer screening. METHODS: We updated a previously validated microsimulation model consisting of three interlinked components: risk assessment, natural history, and screening/treatment modules. We used data from representative national surveys and the literature to create a synthetic population that mimics the family history and genetic profile of the US population...
February 21, 2017: Cancer Causes & Control: CCC
https://www.readbyqxmd.com/read/28223907/comparative-bioavailability-and-utilization-of-particular-forms-of-b12-supplements-with-potential-to-mitigate-b12-related-genetic-polymorphisms
#7
REVIEW
Cristiana Paul, David M Brady
CONTEXT: Three natural forms of vitamin B12 are commercially available: methylcobalamin (MeCbl), adenosylcobalamin (AdCbl), and hydroxycobalamin (OHCbl), all of which have been shown in clinical studies to improve vitamin B12 status. They are bioidentical to the B12 forms occurring in human physiology and animal foods. In contrast, cyanocobalamin (CNCbl), a synthetic B12 compound used for food fortification and in some supplements, occurs only in trace amounts in human tissues as a result of cyanide intake from smoking or other sources...
February 2017: Integrative Medicine
https://www.readbyqxmd.com/read/28223667/-molecular-diagnosis-and-treatment-of-hboc-syndrome
#8
Yoshio Miki
Hereditary breast and ovarian cancer(HBOC)is an inherited cancer caused by mutations of the BRCA1 or BRCA2 genes. BRCA genetic testing is used for HBOC diagnosis and continues to progress such as the annotation of VUS. In HBOC clinical practice, surveillance methods have been established through collaboration between genetic medicine and cancer medicine, and treatment, including options based on genetic diagnosis, has advanced significantly. Furthermore, the analysis of BRCA1 and BRCA2 function has progressed, and a novel therapeutic method based on synthetic lethality, such as a PARP inhibitor use, has been developed...
February 2017: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/28218791/development-and-validation-of-the-first-ssr-markers-for-mimosa-scabrella-benth
#9
F A Saiki, A P Bernardi, M S Reis, H Faoro, E M Souza, F O Pedrosa, A Mantovani, A F Guidolin
Mimosa scabrella Benth., popularly known as ''bracatinga'', is a pioneer and endemic species of Brazil, occurring in Mixed Ombrophilous Forest associated with Brazilian Atlantic Rainforest biomes. It is a fast-growing tree of the Fabaceae family that facilitates the dynamics of ecological succession. SSR development, when there is no genome sequence, is time and labor intensive and there are no molecular markers for M. scabrella. We developed and validated the first microsatellite markers for this tetraploid species, evaluating mother trees and progenies...
February 16, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28215088/mechanistic-modeling-of-genetic-circuits-for-arsr-arsenic-regulation
#10
Yves Berset, Davide Merulla, Aurélie Joublin, Vassily Hatzimanikatis, Jan Roelof van der Meer
Bioreporters are living cells that generate an easily measurable signal in the presence of a chemical compound. They acquire their functionality from synthetic gene circuits, whose configuration defines the response signal and signal-to-noise ratio. Bioreporters based on the Escherichia coli ArsR system have raised significant interest for quantifying arsenic pollution, but they need to be carefully optimized to accurately work in the required low concentration range (1-10 µg arsenite L-1). In order to better understand the general functioning of ArsR-based genetic circuits, we developed a comprehensive mechanistic model that was empirically tested and validated in E...
February 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28213833/molecular-imaging-in-synthetic-biology-and-synthetic-biology-in-molecular-imaging
#11
REVIEW
Assaf A Gilad, Mikhail G Shapiro
Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies...
February 17, 2017: Molecular Imaging and Biology: MIB: the Official Publication of the Academy of Molecular Imaging
https://www.readbyqxmd.com/read/28212797/ca-2-calmodulin-dependent-protein-kinase-ii-in-vascular-smooth-muscle
#12
F Z Saddouk, R Ginnan, H A Singer
Ca(2+)-dependent signaling pathways are central regulators of differentiated vascular smooth muscle (VSM) contractile function. In addition, Ca(2+) signals regulate VSM gene transcription, proliferation, and migration of dedifferentiated or "synthetic" phenotype VSM cells. Synthetic phenotype VSM growth and hyperplasia are hallmarks of pervasive vascular diseases including hypertension, atherosclerosis, postangioplasty/in-stent restenosis, and vein graft failure. The serine/threonine protein kinase Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) is a ubiquitous mediator of intracellular Ca(2+) signals...
2017: Advances in Pharmacology
https://www.readbyqxmd.com/read/28207991/high-yield-secretion-of-recombinant-proteins-from-the-microalga-chlamydomonas-reinhardtii
#13
E M Ramos-Martinez, L Fimognari, Y Sakuragi
Microalga-based biomanufacturing of recombinant proteins is attracting growing attention due to its advantages in safety, metabolic diversity, scalability, and sustainability. Secretion of recombinant proteins can accelerate the use of microalgal platforms by allowing post-translational modifications and easy recovery of products from the culture media. However, currently, the yields of secreted recombinant proteins are low, which hampers the commercial application of this strategy. This study aimed at expanding the genetic tools for enhancing secretion of recombinant proteins in Chlamydomonas reinhardtii, a widely used green microalga as a model organism and a potential industrial biotechnology platform...
February 16, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28207544/tser-polymorphism-is-not-associated-with-risk-of-pediatric-acute-lymphoblastic-leukemia-a-meta-analysis
#14
Zhaohua Qiao, Dan Lou, Li Ruan
BACKGROUND: Accumulating studies have explored the effect of thymidylate synthase enhancer region (TSER) variation on risk of pediatric acute lymphoblastic leukemia (ALL) with controversial results. Therefore, this quantitative meta-analysis was performed to assess synthetically the association of TSER variation with susceptibility to develop pediatric ALL. METHODS: The PubMed, ScienceDirect, Google Scholar, Wanfang Database, and China National Knowledge Infrastructure were systematically retrieved to obtain the published case-control studies about the relationship between TSER variation and pediatric ALL risk...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28207402/reconstructing-the-temporal-progression-of-biological-data-using-cluster-spanning-trees
#15
Ryan Eshleman, Rahul Singh
Identifying the temporal progression of a set of biological samples is crucial for comprehending the dynamics of the underlying molecular interactions. It is often also a basic step in data denoising and synchronization. Finally, identifying the progression order is crucial for problems like cell lineage identification, disease progression, tumor classification, and epidemiology and thus impacts the spectrum of disciplines spanning basic biology, drug discovery, and public health. Current methods that attempt solving this problem face difficulty when it is necessary to factor-in complex relationships within the data such as grouping, partial ordering or bifurcating or multifurcating progressions...
February 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28202725/stretchable-living-materials-and-devices-with-hydrogel-elastomer-hybrids-hosting-programmed-cells
#16
Xinyue Liu, Tzu-Chieh Tang, Eléonore Tham, Hyunwoo Yuk, Shaoting Lin, Timothy K Lu, Xuanhe Zhao
Living systems, such as bacteria, yeasts, and mammalian cells, can be genetically programmed with synthetic circuits that execute sensing, computing, memory, and response functions. Integrating these functional living components into materials and devices will provide powerful tools for scientific research and enable new technological applications. However, it has been a grand challenge to maintain the viability, functionality, and safety of living components in freestanding materials and devices, which frequently undergo deformations during applications...
February 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28197701/-innovative-forms-of-specific-immunotherapy
#17
REVIEW
P Zieglmayer
The clinical efficacy of allergen-specific immunotherapy depends on tolerance induction. Treatment success is currently limited by treatment-related adverse reactions. Novel approaches mainly target improvement of tolerability in addition to optimized immunogenicity. For epicutaneous immunotherapy (EPIT), commercially available treatment extracts are applied to skin via a patch. The route exhibits excellent tolerability and good clinical efficacy. The first encouraging data on a peanut EPIT were published in 2016...
February 14, 2017: Der Hautarzt; Zeitschrift Für Dermatologie, Venerologie, und Verwandte Gebiete
https://www.readbyqxmd.com/read/28196402/pimelic-acid-the-first-precursor-of-the-bacillus-subtilis-biotin-synthesis-pathway-exists-as-the-free-acid-and-is-assembled-by-fatty-acid-synthesis
#18
Miglena Manandhar, John E Cronan
Biotin synthetic pathways are readily separated into two stages, synthesis of the seven carbon α, ω-dicarboxylic acid pimelate moiety and assembly of the fused heterocyclic rings. The biotin pathway genes responsible for pimelate moiety synthesis vary widely among bacteria whereas the ring synthesis genes are highly conserved. Bacillus subtilis seems to have redundant genes, bioI and bioW, for generation of the pimelate intermediate. Largely consistent with previous genetic studies we found that deletion of bioW caused a biotin auxotrophic phenotype whereas deletion of bioI did not...
February 14, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28195039/speed-and-segmentation-control-mechanisms-characterized-in-rhythmically-active-circuits-created-from-spinal-neurons-produced-from-genetically-tagged-embryonic-stem-cells
#19
Matthew J Sternfeld, Christopher A Hinckley, Niall J Moore, Matthew T Pankratz, Kathryn L Hilde, Shawn P Driscoll, Marito Hayashi, Neal D Amin, Dario Bonanomi, Wesley D Gifford, Kamal Sharma, Martyn Goulding, Samuel L Pfaff
Flexible neural networks, such as the interconnected spinal neurons that control distinct motor actions, can switch their activity to produce different behaviors. Both excitatory (E) and inhibitory (I) spinal neurons are necessary for motor behavior, but the influence of recruiting different ratios of E-to-I cells remains unclear. We constructed synthetic microphysical neural networks, called circuitoids, using precise combinations of spinal neuron subtypes derived from mouse stem cells. Circuitoids of purified excitatory interneurons were sufficient to generate oscillatory bursts with properties similar to in vivo central pattern generators...
February 14, 2017: ELife
https://www.readbyqxmd.com/read/28192413/evolution-of-a-split-rna-polymerase-as-a-versatile-biosensor-platform
#20
Jinyue Pu, Julia Zinkus-Boltz, Bryan C Dickinson
Biosensors that transduce target chemical and biochemical inputs into genetic outputs are essential for bioengineering and synthetic biology. Current biosensor design strategies are often limited by a low signal-to-noise ratio, the extensive optimization required for each new input, and poor performance in mammalian cells. Here we report the development of a proximity-dependent split RNA polymerase (RNAP) as a general platform for biosensor engineering. After discovering that interactions between fused proteins modulate the assembly of a split T7 RNAP, we optimized the split RNAP components for protein-protein interaction detection by phage-assisted continuous evolution (PACE)...
February 13, 2017: Nature Chemical Biology
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