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Synthetic biology

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https://www.readbyqxmd.com/read/28340309/analytical-techniques-in-lipidomics-state-of-the-art
#1
Kamil Jurowski, Kamila Kochan, Justyna Walczak, Małgorzata Barańska, Wojciech Piekoszewski, Bogusław Buszewski
Current studies related to lipid identification and determination, or lipidomics in biological samples, are one of the most important issues in modern bioanalytical chemistry. There are many articles dedicated to specific analytical strategies used in lipidomics in various kinds of biological samples. However, in such literature, there is lack of articles dedicated to a comprehensive review of the actual analytical methodologies used in lipidomics. The aim of this article is to characterize the lipidomics methods used in modern bioanalysis according to the methodological point of view: 1) chromatography/separation methods, 2) spectroscopic methods and 3) mass spectrometry and also hyphenated methods...
March 24, 2017: Critical Reviews in Analytical Chemistry
https://www.readbyqxmd.com/read/28340300/synthesis-of-3-o-sulfated-oligosaccharides-to-understand-the-relationship-between-structures-and-functions-of-heparan-sulfate
#2
Zhangjie Wang, Po-Hung Hsieh, Yongmei Xu, David Thieker, Evangeline Juan En Chai, Shaoshuai Xie, Brian Cooley, Robert Woods, Lianli Chi, Jian Liu
The sulfation at the 3-OH position of glucosamine is an important modification in forming structural domains for heparan sulfate to enable its biological functions. Seven 3-O-sulfotransferase isoforms in the human genome are involved in the biosynthesis of 3-O-sulfated heparan sulfate. As a rare modification present in heparan sulfate, the availability of 3-O-sulfated oligosaccharides is very limited. Here, we report the use of a chemoenzymatic synthetic approach to synthesize six 3-O-sulfated oligosaccharides, including three hexasaccharides and three octasaccharides...
March 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28335462/therapeutic-potentials-of-microalgae-in-the-treatment-of-alzheimer-s-disease
#3
REVIEW
Tosin A Olasehinde, Ademola O Olaniran, Anthony I Okoh
Current research is geared towards the discovery of new compounds with strong neuroprotective potential and few or no side effects compared to synthetic drugs. This review focuses on the potentials of extracts and biologically active compounds derived from microalgal biomass for the treatment and management of Alzheimer's disease (AD). Microalgal research has gained much attention recently due to its contribution to the production of renewable fuels and the ability of alga cells to produce several secondary metabolites such as carotenoids, polyphenols, sterols, polyunsaturated fatty acids and polysaccharides...
March 18, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335409/the-formyl-peptide-receptors-diversity-of-ligands-and-mechanism-for-recognition
#4
REVIEW
Hui-Qiong He, Richard D Ye
The formyl peptide receptors (FPRs) are G protein-coupled receptors that transduce chemotactic signals in phagocytes and mediate host-defense as well as inflammatory responses including cell adhesion, directed migration, granule release and superoxide production. In recent years, the cellular distribution and biological functions of FPRs have expanded to include additional roles in homeostasis of organ functions and modulation of inflammation. In a prototype, FPRs recognize peptides containing N-formylated methionine such as those produced in bacteria and mitochondria, thereby serving as pattern recognition receptors...
March 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335338/green-synthesis-of-iron-nanoparticles-and-their-environmental-applications-and-implications
#5
REVIEW
Sadia Saif, Arifa Tahir, Yongsheng Chen
Recent advances in nanoscience and nanotechnology have also led to the development of novel nanomaterials, which ultimately increase potential health and environmental hazards. Interest in developing environmentally benign procedures for the synthesis of metallic nanoparticles has been increased. The purpose is to minimize the negative impacts of synthetic procedures, their accompanying chemicals and derivative compounds. The exploitation of different biomaterials for the synthesis of nanoparticles is considered a valuable approach in green nanotechnology...
November 12, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335213/biosynthesis-of-metal-nanoparticles-novel-efficient-heterogeneous-nanocatalysts
#6
REVIEW
Jose M Palomo, Marco Filice
This review compiles the most recent advances described in literature on the preparation of noble metal nanoparticles induced by biological entities. The use of different free or substituted carbohydrates, peptides, proteins, microorganisms or plants have been successfully applied as a new green concept in the development of innovative strategies to prepare these nanoparticles as different nanostructures with different forms and sizes. As a second part of this review, the application of their synthetic ability as new heterogonous catalysts has been described in C-C bond-forming reactions (as Suzuki, Heck, cycloaddition or multicomponent), oxidations and dynamic kinetic resolutions...
May 5, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334817/stability-of-synthetic-cannabinoids-in-biological-specimens-analysis-through-liquid-chromatography-tandem-mass-spectrometry
#7
Chelsea Fort, Thomas Jourdan, Jesse Kemp, Byron Curtis
The focus of this study was to determine the stability of four synthetic cannabinoids, XLR-11, UR-144, AB-Pinaca and AB-Fubinaca in biological specimens for the purpose of casework processing prioritization. The study used human whole blood spiked with the compounds of interest to mimic real forensic laboratory samples submitted for synthetic cannabinoid analysis. The spiked whole blood specimens were incubated under one of three temperature conditions: room or ambient (22°C), refrigerated (4°C) and frozen (-20°C) for a period of 12 weeks...
February 18, 2017: Journal of Analytical Toxicology
https://www.readbyqxmd.com/read/28334760/twin-primer-non-enzymatic-dna-assembly-an-efficient-and-accurate-multi-part-dna-assembly-method
#8
Jing Liang, Zihe Liu, Xi Z Low, Ee L Ang, Huimin Zhao
DNA assembly forms the cornerstone of modern synthetic biology. Despite the numerous available methods, scarless multi-fragment assembly of large plasmids remains challenging. Furthermore, the upcoming wave in molecular biological automation demands a rethinking of how we perform DNA assembly. To streamline automation workflow and minimize operator intervention, a non-enzymatic assembly method is highly desirable. Here, we report the optimization and operationalization of a process called Twin-Primer Assembly (TPA), which is a method to assemble polymerase chain reaction-amplified fragments into a plasmid without the use of enzymes...
February 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334756/measurements-of-translation-initiation-from-all-64-codons-in-e-coli
#9
Ariel Hecht, Jeff Glasgow, Paul R Jaschke, Lukmaan A Bawazer, Matthew S Munson, Jennifer R Cochran, Drew Endy, Marc Salit
Our understanding of translation underpins our capacity to engineer living systems. The canonical start codon (AUG) and a few near-cognates (GUG, UUG) are considered as the 'start codons' for translation initiation in Escherichia coli. Translation is typically not thought to initiate from the 61 remaining codons. Here, we quantified translation initiation of green fluorescent protein and nanoluciferase in E. coli from all 64 triplet codons and across a range of DNA copy number. We detected initiation of protein synthesis above measurement background for 47 codons...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334115/faster-a-user-friendly-tool-for-ultrafast-and-robust-cell-segmentation-in-large-scale-microscopy
#10
Oliver Hilsenbeck, Michael Schwarzfischer, Dirk Loeffler, Sotiris Dimopoulos, Simon Hastreiter, Carsten Marr, Fabian J Theis, Timm Schroeder
Motivation: Quantitative large-scale cell microscopy is widely used in biological and medical research. Such experiments produce huge amounts of image data and thus require automated analysis. However, automated detection of cell outlines (cell segmentation) is typically challenging due to, e.g., high cell densities, cell-to-cell variability and low signal-to-noise ratios. Results: Here, we evaluate accuracy and speed of various state-of-the-art approaches for cell segmentation in light microscopy images using challenging real and synthetic image data...
February 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333079/marine-cyclic-guanidine-alkaloids-monanchomycalin-b-and-urupocidin-a-act-as-inhibitors-of-trpv1-trpv2-and-trpv3-but-not-trpa1-receptors
#11
Yuliya Korolkova, Tatyana Makarieva, Kseniya Tabakmakher, Larisa Shubina, Ekaterina Kudryashova, Yaroslav Andreev, Irina Mosharova, Hyi-Seung Lee, Yeon-Ju Lee, Sergey Kozlov
Marine sponges contain a variety of low-molecular-weight compounds including guanidine alkaloids possessing different biological activities. Monanchomycalin B and urupocidin A were isolated from the marine sponge Monanchora pulchra. We found that they act as inhibitors of the TRPV1, TRPV2, and TRPV3 channels, but are inactive against the TRPA1 receptor. Monanchomycalin B is the most active among all published marine alkaloids (EC50 6.02, 2.84, and 3.25 μM for TRPV1, TRPV2, and TRPV3, correspondingly). Moreover, monanchomycalin B and urupocidin A are the first samples of marine alkaloids affecting the TRPV2 receptor...
March 23, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28331815/measuring-e-coli-and-bacteriophage-dna-in-cell-sonicates-to-evaluate-the-cal1-reaction-as-a-synthetic-biology-standard-for-qpcr
#12
Alexander Templar, Desmond M Schofield, Darren N Nesbeth
We measured the impact of the presence of total Escherichia coli (E. coli) cellular material on the performance of the Linear Regression of Efficiency (LRE) method of absolute quantitative PCR (LRE qPCR), which features the putatively universal CAL1 calibration reaction, which we propose as a synthetic biology standard. We firstly used a qPCR reaction in which a sequence present in the lone genomic BirA locus is amplified. Amplification efficiency for this reaction, a key metric for many quantitative qPCR methods, was inhibited by cellular material from bioreactor cultivation to a greater extent than material from shake flask cultivation...
March 2017: Biomolecular Detection and Quantification
https://www.readbyqxmd.com/read/28330463/global-transcriptome-analysis-of-huperzia-serrata-and-identification-of-critical-genes-involved-in-the-biosynthesis-of-huperzine-a
#13
Mengquan Yang, Wenjing You, Shiwen Wu, Zhen Fan, Baofu Xu, Mulan Zhu, Xuan Li, Youli Xiao
BACKGROUND: Huperzia serrata (H. serrata) is an economically important traditional Chinese herb with the notably medicinal value. As a representative member of the Lycopodiaceae family, the H. serrata produces various types of effectively bioactive lycopodium alkaloids, especially the huperzine A (HupA) which is a promising drug for Alzheimer's disease. Despite their medicinal importance, the public genomic and transcriptomic resources are very limited and the biosynthesis of HupA is largely unknown...
March 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28330337/co-generating-synthetic-parts-toward-a-self-replicating-system
#14
Jun Li, Wilhelm Haas, Kirsten Jackson, Erkin Kuru, Michael C Jewett, Z Hugh Fan, Steven P Gygi, George M Church
To build replicating systems with new functions, the engineering of existing biological machineries requires a sensible strategy. Protein synthesis Using Recombinant Elements (PURE) system consists of the desired components for transcription, translation, aminoacylation and energy regeneration. PURE, might be the basis for a radically alterable, lifelike system after optimization. Here, we regenerated 54 E. coli ribosomal (r-) proteins individually from DNA templates in the PURE system. We show that using stable isotope labeling with amino acids, mass spectrometry based quantitative proteomics could detect 26 of the 33 50S and 20 of the 21 30S subunit r-proteins when co-expressed in batch format PURE system...
March 23, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28330230/isolation-and-biological-evaluation-of-n-4-aminocyclooctyl-3-5-dinitrobenzamide-a-new-semisynthetic-derivative-from-the-mangrove-associated-actinomycete-pseudonocardia-endophytica-vuk-10
#15
Usha Kiranmayi Mangamuri, Muvva Vijayalakshmi, Sudhakar Poda, Bramanandam Manavathi, Bhujangarao Chitturi, Venkateswarlu Yenamandra
The present study was aimed to isolate novel bioactive compounds from actinomycetes species isolated from mangrove habitats. With this connection, Pseudonocardia endophytica (VUK-10) was isolated using dilution plate technique and was examined for its secondary metabolite profiling. After successive purification and spectroscopic characterization viz., FTIR, mass, NMR, DEPT, HMQC, HMBC, and COSY spectroscopy, two compounds were identified including a semi synthetic derivative N-(4-aminocyclooctyl)-3, 5-dinitrobenzamide (1), obtained from the precursor of novel natural product cyclooctane-1,4-diamine (3), along with a known compound 3-((1H-indol-6-yl) methyl) hexahydropyrrolo [1, 2-a] pyrazine-1, 4-dione (2)...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329028/non-equilibrium-assembly-of-microtubules-from-molecules-to-autonomous-chemical-robots
#16
REVIEW
H Hess, Jennifer L Ross
Biological systems have evolved to harness non-equilibrium processes from the molecular to the macro scale. It is currently a grand challenge of chemistry, materials science, and engineering to understand and mimic biological systems that have the ability to autonomously sense stimuli, process these inputs, and respond by performing mechanical work. New chemical systems are responding to the challenge and form the basis for future responsive, adaptive, and active materials. In this article, we describe a particular biochemical-biomechanical network based on the microtubule cytoskeletal filament - itself a non-equilibrium chemical system...
March 22, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28328998/combinatorial-selection-for-replicable-rna-by-q%C3%AE-replicase-while-maintaining-encoded-gene-function
#17
Mio Yumura, Natsuko Yamamoto, Katsushi Yokoyama, Hirotada Mori, Tetsuya Yomo, Norikazu Ichihashi
Construction of a complex artificial self-replication system is challenging in the field of in vitro synthetic biology. Recently, we developed a translation-coupled RNA replication system, wherein an artificial genomic RNA replicates with the Qβ RNA replicase gene encoded on itself. The challenge is to introduce additional genes into the RNA to develop a complex system that mimics natural living systems. However, most RNA sequence encoding genes are not replicable by the Qβ replicase owing to its requirement for strong secondary structures throughout the RNA sequence that are absent in most genes...
2017: PloS One
https://www.readbyqxmd.com/read/28328315/analysis-of-protein-target-interactions-of-synthetic-mixtures-by-affinity-lc-ms
#18
Prachi Singh, Kalaipriya Madhaiyan, Minh-Dao Duong-Thi, Brian W Dymock, Sten Ohlson
Analysis of interactions between molecules is of fundamental importance in life science research. In this study, we applied weak affinity chromatography, based on high-performance liquid chromatography and mass spectrometry, as a powerful tool for direct analysis of the components of a chemical reaction mixture for their binding to a target protein. As a demonstration of the potential of this method, we analyzed the binding of the compounds of the reaction mixture to the chaperone heat shock protein 90 (Hsp90)...
April 2017: SLAS Discov
https://www.readbyqxmd.com/read/28328298/the-synthetic-progestin-gestodene-affects-functional-biomarkers-in-neonatal-rat-osteoblasts-through-an-estrogen-receptor-related-mechanism-of-action
#19
Juana Enríquez, Gustavo García, Bertha Herrero, Fernando Larrea
BACKGROUND: Clinical studies have shown that gestodene (GDN), a potent third-generation synthetic progestin, affects bone resorption. However, its mode of action in bone cells is not fully understood. The aim of this study was to establish whether GDN affects bone directly or through its bioconversion to other metabolites with different biological activities. METHODS: In this study, we investigated the effects of GDN and its A-ring reduced metabolites on proliferation, differentiation, and mineralization of calvarial osteoblasts isolated from neonatal rat and their capacity to displace [(3)H]-E2 at ER binding sites...
March 22, 2017: Endocrine Research
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#20
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
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