Relevant bibliographies by topics / Assemblie

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  1. Journal articles

Academic literature on the topic 'Assemblie'

Author: Grafiati
Published: 1 April 2023

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Journal articles on the topic "Assemblie"

1

Colloms, Sean D., Christine A. Merrick, Femi J. Olorunniji, et al. "Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination." Nucleic Acids Research 42, no. 4 (2013): e23-e23. http://dx.doi.org/10.1093/nar/gkt1101.

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Abstract Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by ϕC31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. ϕC31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.
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2

MacGillivray, Leonard. "Hydrogen Bonds and Self-Assembly to Direct Reactivity in the Solid State." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C528. http://dx.doi.org/10.1107/s2053273314094716.

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In this presentation, we will describe our efforts to develop a general method to control chemical reactivity in the organic solid state. We use the method to provide access to complex organic molecules such as ladderanes and cyclophanes. In our method, we exploit hydrogen-bond-directed self-assembly with the use of small-molecule templates to assemble and preorganize olefins for intermolecular [2+2] photodimerizations. The templates assemble the olefins within discrete supramolecular assemblies for single and multiple photoreactions. By assembling the olefins within discrete assemblies, we overcome problems of long-range packing that have frustrated previous attempts to control the dimerization. We will also demonstrate how the approach provides a unique form of supamolecular catalysis that exploits fundamentals of mechanochemistry.
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3

Sciore, Aaron, Min Su, Philipp Koldewey, et al. "Flexible, symmetry-directed approach to assembling protein cages." Proceedings of the National Academy of Sciences 113, no. 31 (2016): 8681–86. http://dx.doi.org/10.1073/pnas.1606013113.

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The assembly of individual protein subunits into large-scale symmetrical structures is widespread in nature and confers new biological properties. Engineered protein assemblies have potential applications in nanotechnology and medicine; however, a major challenge in engineering assemblies de novo has been to design interactions between the protein subunits so that they specifically assemble into the desired structure. Here we demonstrate a simple, generalizable approach to assemble proteins into cage-like structures that uses short de novo designed coiled-coil domains to mediate assembly. We assembled eight copies of a C3-symmetric trimeric esterase into a well-defined octahedral protein cage by appending a C4-symmetric coiled-coil domain to the protein through a short, flexible linker sequence, with the approximate length of the linker sequence determined by computational modeling. The structure of the cage was verified using a combination of analytical ultracentrifugation, native electrospray mass spectrometry, and negative stain and cryoelectron microscopy. For the protein cage to assemble correctly, it was necessary to optimize the length of the linker sequence. This observation suggests that flexibility between the two protein domains is important to allow the protein subunits sufficient freedom to assemble into the geometry specified by the combination of C4 and C3 symmetry elements. Because this approach is inherently modular and places minimal requirements on the structural features of the protein building blocks, it could be extended to assemble a wide variety of proteins into structures with different symmetries.
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4

Wick, Ryan R., Louise M. Judd, and Kathryn E. Holt. "Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing." PLOS Computational Biology 19, no. 3 (2023): e1010905. http://dx.doi.org/10.1371/journal.pcbi.1010905.

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A perfect bacterial genome assembly is one where the assembled sequence is an exact match for the organism’s genome—each replicon sequence is complete and contains no errors. While this has been difficult to achieve in the past, improvements in long-read sequencing, assemblers, and polishers have brought perfect assemblies within reach. Here, we describe our recommended approach for assembling a bacterial genome to perfection using a combination of Oxford Nanopore Technologies long reads and Illumina short reads: Trycycler long-read assembly, Medaka long-read polishing, Polypolish short-read polishing, followed by other short-read polishing tools and manual curation. We also discuss potential pitfalls one might encounter when assembling challenging genomes, and we provide an online tutorial with sample data (github.com/rrwick/perfect-bacterial-genome-tutorial).
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5

Kleffe, Jürgen, Robert Weißmann, and Florian F. Schmitzberger. "Single Nucleotide Polymorphisms Caused by Assembly Errors." Genomics Insights 3 (January 2010): GEI.S3653. http://dx.doi.org/10.4137/gei.s3653.

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We compare the results of three different assembler programs, Celera, Phrap and Mira2, for the same set of about a hundred thousand Sanger reads derived from an unknown bacterial genome. In difference to previous assembly comparisons we do not focus on speed of computation and numbers of assembled contigs but on how the different sequence assemblies agree by content. Threefold consistently assembled genome regions are identified in order to estimate a lower bound of erroneously identified single nucleotide polymorphisms (SNP) caused by nothing but the process of mathematical sequence assembly. We identified 509 sequence triplets common to all three de-novo assemblies spanning only 34% (3.3 Mb) of the bacterial genome with 175 of these regions (~1.5 Mb) including erroneous SNPs and insertion/deletions. Within these triplets this on average leads to one error per 7,155 base pairs. Replacing the assembler Mira2 by the most recent version Mira3, the letter number even drops to 5,923. Our results therefore suggest that a considerably high number of erroneous SNPs may be present in current sequence data and mathematicians should urgently take up research on numerical stability of sequence assembly algorithms. Furthermore, even the latest versions of currently used assemblers produce erroneous SNPs that depend on the order reads are used as input. Such errors will severely hamper molecular diagnostics as well as relating genome variation and disease. This issue needs to be addressed urgently as the field is moving fast into clinical applications.
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6

Kuo, Chia Lung, and Jing Dae Huang. "Joint Design and Fabrication for Mechanical Elastic Self-deformation Micro-Assembly Technology." Materials Science Forum 505-507 (January 2006): 829–34. http://dx.doi.org/10.4028/www.scientific.net/msf.505-507.829.

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A microstructure assembled into another part using the mechanical elastic self-deformation assembly technology is proposed in the paper. To attain the self-deformation during assembling, the assembly joint on the microstructure is analytically designed as the feature with an appropriate taper and cross clearance. Take account of the accuracy, the whole process from micro-fabrication to micro-assembly is carefully planned and practiced under a micro-EDM machining center system which consists of vertical micro-EDM with dividing mechanism, and horizontal micro-machining mechanism, which is referred to as on-process micro-assembly. To illustrate the micro-assembly strategies and procedures, a micro-rotor production including assemble a tungsten carbide four-phase micro-rotor into an alumina base has been provided and discussed.
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7

Khezri, Abdolrahman, Ekaterina Avershina, and Rafi Ahmad. "Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates." Microorganisms 9, no. 12 (2021): 2560. http://dx.doi.org/10.3390/microorganisms9122560.

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Emerging new sequencing technologies have provided researchers with a unique opportunity to study factors related to microbial pathogenicity, such as antimicrobial resistance (AMR) genes and virulence factors. However, the use of whole-genome sequence (WGS) data requires good knowledge of the bioinformatics involved, as well as the necessary techniques. In this study, a total of nine Escherichia coli and Klebsiella pneumoniae isolates from Norwegian clinical samples were sequenced using both MinION and Illumina platforms. Three out of nine samples were sequenced directly from blood culture, and one sample was sequenced from a mixed-blood culture. For genome assembly, several long-read, (Canu, Flye, Unicycler, and Miniasm), short-read (ABySS, Unicycler and SPAdes) and hybrid assemblers (Unicycler, hybridSPAdes, and MaSurCa) were tested. Assembled genomes from the best-performing assemblers (according to quality checks using QUAST and BUSCO) were subjected to downstream analyses. Flye and Unicycler assemblers performed best for the assembly of long and short reads, respectively. For hybrid assembly, Unicycler was the top-performing assembler and produced more circularized and complete genome assemblies. Hybrid assembled genomes performed substantially better in downstream analyses to predict putative plasmids, AMR genes and β-lactamase gene variants, compared to MinION and Illumina assemblies. Thus, hybrid assembly has the potential to reveal factors related to microbial pathogenicity in clinical and mixed samples.
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8

Kim, Boyoung, Minyong Choi, Seung-Woo Son, Deokwon Yun, and Sukjune Yoon. "Vision-force guided precise robotic assembly for 2.5D components in a semistructured environment." Assembly Automation 41, no. 2 (2021): 200–207. http://dx.doi.org/10.1108/aa-03-2020-0039.

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Purpose Many manufacturing sites require precision assembly. Particularly, similar to cell phones, assembly at the sub-mm scale is not easy, even for humans. In addition, the system should assemble each part with adequate force and avoid breaking the circuits with excessive force. The purpose of this study is to assemble high precision components with relatively reasonable vision devices compared to previous studies. Design/methodology/approach This paper presents a vision-force guided precise assembly system using a force sensor and two charge coupled device (CCD) cameras without an expensive 3-dimensional (3D) sensor or computer-aided design model. The system accurately estimates 6 degrees-of-freedom (DOF) poses from a 2D image in real time and assembles parts with the proper force. Findings In this experiment, three connectors are assembled on a printed circuit board. This system obtains high accuracy under 1 mm and 1 degree error, which shows that this system is effective. Originality/value This is a new method for sub-mm assembly using only two CCD cameras and one force sensor.
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9

Hu, Xiao Guang, Jing Bo Yang, and Zi Fu Zhang. "Construction Methods on Mechanical and Material's Deformation Control during Assembling and Erecting Cup Type Transmission Tower." Applied Mechanics and Materials 540 (April 2014): 205–8. http://dx.doi.org/10.4028/www.scientific.net/amm.540.205.

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Take a 1000kV Cup-Type tubular steel test tower as research object, and it is the first one of this type used in heavy ice area. Research on the assembly load’s affect to tower structure was made. The process of assembling tower using suspend guyed pole was analyzed with Finite Element Method. Structures overhanging the tower body, such as cross arms and bracket of earth wire, could be assembled in different ways. The different affect to the built structure corresponding to different assembly method was researched. The objective is to make the deformation of the structure minimum. It was indicated that, reinforce the K-joint by cable and the deformation of structure reduced obviously. The reinforce method is simple and efficient, and ensure the cross arm assembling smoothly. It is avail to improve the assemble quality of the whole structure.
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10

Kobayashi, Risako, Hiroshi Inaba та Kazunori Matsuura. "Fluorescence Correlation Spectroscopy Analysis of Effect of Molecular Crowding on Self-Assembly of β-Annulus Peptide into Artificial Viral Capsid". International Journal of Molecular Sciences 22, № 9 (2021): 4754. http://dx.doi.org/10.3390/ijms22094754.

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Recent progress in the de novo design of self-assembling peptides has enabled the construction of peptide-based viral capsids. Previously, we demonstrated that 24-mer β-annulus peptides from tomato bushy stunt virus spontaneously self-assemble into an artificial viral capsid. Here we propose to use the artificial viral capsid through the self-assembly of β-annulus peptide as a simple model to analyze the effect of molecular crowding environment on the formation process of viral capsid. Artificial viral capsids formed by co-assembly of fluorescent-labelled and unmodified β-annulus peptides in dilute aqueous solutions and under molecular crowding conditions were analyzed using fluorescence correlation spectroscopy (FCS). The apparent particle size and the dissociation constant (Kd) of the assemblies decreased with increasing concentration of the molecular crowding agent, i.e., polyethylene glycol (PEG). This is the first successful in situ analysis of self-assembling process of artificial viral capsid under molecular crowding conditions.
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