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Journal articles on the topic 'Assemblie'

Author: Grafiati

Published: 1 April 2023

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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

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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 ov

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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 a

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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 p

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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.

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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 referr

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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, an

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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

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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 indic

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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 d

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11

Pfeffer, Bubba, Chandler Lymbery, Brendan Booth, and Jessica L. Allen. "Chromosomal genome sequence assembly and mating-type (MAT) locus characterization of the leprose asexual lichenized fungus Lepraria neglecta (Nyl.) Erichsen." Lichenologist 55, no. 1 (2023): 41–50. http://dx.doi.org/10.1017/s002428292200041x.

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AbstractComplete chromosomal-level assemblies of fungal genomes are rare. The intimate ecological symbioses and complex reproduction strategies utilized by fungi make highly contiguous, gapless genome assemblies particularly difficult. Here, we use long-read sequencing on the Oxford Nanopore Technology MinION platform to sequence and assemble the genome of Lepraria neglecta (Ascomycota, Lecanorales). In addition to eight contigs ascribable to chromosomes, six of which are assembled telomere-to-telomere, we discovered the presence of a complete MAT locus with two conserved MAT1-2 genes and a pu

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Wick, Ryan R., and Kathryn E. Holt. "Benchmarking of long-read assemblers for prokaryote whole genome sequencing." F1000Research 8 (December 23, 2019): 2138. http://dx.doi.org/10.12688/f1000research.21782.1.

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Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of six long-read assemblers (Canu, Flye, Mi

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Erickson, Harold P., David E. Anderson, and Masaki Osawa. "FtsZ in Bacterial Cytokinesis: Cytoskeleton and Force Generator All in One." Microbiology and Molecular Biology Reviews 74, no. 4 (2010): 504–28. http://dx.doi.org/10.1128/mmbr.00021-10.

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SUMMARY FtsZ, a bacterial homolog of tubulin, is well established as forming the cytoskeletal framework for the cytokinetic ring. Recent work has shown that purified FtsZ, in the absence of any other division proteins, can assemble Z rings when incorporated inside tubular liposomes. Moreover, these artificial Z rings can generate a constriction force, demonstrating that FtsZ is its own force generator. Here we review light microscope observations of how Z rings assemble in bacteria. Assembly begins with long-pitch helices that condense into the Z ring. Once formed, the Z ring can transition to

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14

Lu, Lei, Mark S. Ladinsky, and Tomas Kirchhausen. "Formation of the postmitotic nuclear envelope from extended ER cisternae precedes nuclear pore assembly." Journal of Cell Biology 194, no. 3 (2011): 425–40. http://dx.doi.org/10.1083/jcb.201012063.

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During mitosis, the nuclear envelope merges with the endoplasmic reticulum (ER), and nuclear pore complexes are disassembled. In a current model for reassembly after mitosis, the nuclear envelope forms by a reshaping of ER tubules. For the assembly of pores, two major models have been proposed. In the insertion model, nuclear pore complexes are embedded in the nuclear envelope after their formation. In the prepore model, nucleoporins assemble on the chromatin as an intermediate nuclear pore complex before nuclear envelope formation. Using live-cell imaging and electron microscope tomography, w

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Linheiro, Raquel, and John Archer. "CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure." PLOS Computational Biology 17, no. 11 (2021): e1009631. http://dx.doi.org/10.1371/journal.pcbi.1009631.

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With the exponential growth of sequence information stored over the last decade, including that of de novo assembled contigs from RNA-Seq experiments, quantification of chimeric sequences has become essential when assembling read data. In transcriptomics, de novo assembled chimeras can closely resemble underlying transcripts, but patterns such as those seen between co-evolving sites, or mapped read counts, become obscured. We have created a de Bruijn based de novo assembler for RNA-Seq data that utilizes a classification system to describe the complexity of underlying graphs from which contigs

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Ghosh, Tarini Shankar, Varun Mehra, and Sharmila S. Mande. "Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly." Journal of Bioinformatics and Computational Biology 13, no. 03 (2015): 1541004. http://dx.doi.org/10.1142/s0219720015410048.

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Metagenomics approach involves extraction, sequencing and characterization of the genomic content of entire community of microbes present in a given environment. In contrast to genomic data, accurate assembly of metagenomic sequences is a challenging task. Given the huge volume and the diverse taxonomic origin of metagenomic sequences, direct application of single genome assembly methods on metagenomes are likely to not only lead to an immense increase in requirements of computational infrastructure, but also result in the formation of chimeric contigs. A strategy to address the above challeng

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Rey, Carine, Philippe Veber, Bastien Boussau, and Marie Sémon. "CAARS: comparative assembly and annotation of RNA-Seq data." Bioinformatics 35, no. 13 (2018): 2199–207. http://dx.doi.org/10.1093/bioinformatics/bty903.

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Abstract Motivation RNA sequencing (RNA-Seq) is a widely used approach to obtain transcript sequences in non-model organisms, notably for performing comparative analyses. However, current bioinformatic pipelines do not take full advantage of pre-existing reference data in related species for improving RNA-Seq assembly, annotation and gene family reconstruction. Results We built an automated pipeline named CAARS to combine novel data from RNA-Seq experiments with existing multi-species gene family alignments. RNA-Seq reads are assembled into transcripts by both de novo and assisted assemblies.

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Dognini, Paolo, Christopher R. Coxon, Wendel A. Alves, and Francesca Giuntini. "Peptide-Tetrapyrrole Supramolecular Self-Assemblies: State of the Art." Molecules 26, no. 3 (2021): 693. http://dx.doi.org/10.3390/molecules26030693.

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The covalent and noncovalent association of self-assembling peptides and tetrapyrroles was explored as a way to generate systems that mimic Nature’s functional supramolecular structures. Different types of peptides spontaneously assemble with porphyrins, phthalocyanines, or corroles to give long-range ordered architectures, whose structure is determined by the features of both components. The regular morphology and ordered molecular arrangement of these systems enhance the photochemical properties of embedded chromophores, allowing applications as photo-catalysts, antennas for dye-sensitized s

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Cunningham, Scott A., Nicholas Chia, Patricio R. Jeraldo, et al. "Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks." Journal of Clinical Microbiology 55, no. 6 (2017): 1946–53. http://dx.doi.org/10.1128/jcm.00029-17.

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ABSTRACT Whole-genome sequencing (WGS) can provide excellent resolution in global and local epidemiological investigations of Staphylococcus aureus outbreaks. A variety of sequencing approaches and analytical tools have been used; it is not clear which is ideal. We compared two WGS strategies and two analytical approaches to the standard method of SmaI restriction digestion pulsed-field gel electrophoresis (PFGE) for typing S. aureus . Forty-two S. aureus isolates from three outbreaks and 12 reference isolates were studied. Near-complete genomes, assembled de novo with paired-end and long-mate

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Goldberg, M., H. Jenkins, T. Allen, W. G. Whitfield, and C. J. Hutchison. "Xenopus lamin B3 has a direct role in the assembly of a replication competent nucleus: evidence from cell-free egg extracts." Journal of Cell Science 108, no. 11 (1995): 3451–61. http://dx.doi.org/10.1242/jcs.108.11.3451.

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Xenopus egg extracts which assemble replication competent nuclei in vitro were depleted of lamin B3 using monoclonal antibody L6 5D5 linked to paramagnetic beads. After depletion, the extracts were still capable of assembling nuclei around demembranated sperm heads. Using field emission in lens scanning electron microscopy (FEISEM) we show that most nuclei assembled in lamin B3-depleted extracts have continuous nuclear envelopes and well formed nuclear pores. However, several consistent differences were observed. Most nuclei were small and only attained diameters which were half the size of co

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Zuo, Guang Zhou, Qing Zhang, and Ming Liu. "Virtual Assembly of Equipment in Large Steel Structure." Advanced Materials Research 255-260 (May 2011): 4166–70. http://dx.doi.org/10.4028/www.scientific.net/amr.255-260.4166.

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The equipment assembled in large steel structure is particular and complex, which must be assembled with a special process plan. Virtual assembly technology provides a feasible idea for equipment assembly. Assembly path planning is the key technology of Virtual assembly. We propose a method of assembly path planning based on the analysis of basic workflow in assembly path planning. Using our algorithm to assemble the equipment find encountered far fewer problems than previous.

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Liu, Yen-Yi, Bo-Han Chen, Chih-Chieh Chen, and Chien-Shun Chiou. "Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type." PeerJ 9 (August 19, 2021): e11842. http://dx.doi.org/10.7717/peerj.11842.

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With the reduction in the cost of next-generation sequencing, whole-genome sequencing (WGS)–based methods such as core-genome multilocus sequence type (cgMLST) have been widely used. However, gene-based methods are required to assemble raw reads to contigs, thus possibly introducing errors into assemblies. Because the robustness of cgMLST depends on the quality of assemblies, the results of WGS should be assessed (from sequencing to assembly). In this study, we investigated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. Differe

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Rice, Edward S., and Richard E. Green. "New Approaches for Genome Assembly and Scaffolding." Annual Review of Animal Biosciences 7, no. 1 (2019): 17–40. http://dx.doi.org/10.1146/annurev-animal-020518-115344.

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Affordable, high-throughput DNA sequencing has accelerated the pace of genome assembly over the past decade. Genome assemblies from high-throughput, short-read sequencing, however, are often not as contiguous as the first generation of genome assemblies. Whereas early genome assembly projects were often aided by clone maps or other mapping data, many current assembly projects forego these scaffolding data and only assemble genomes into smaller segments. Recently, new technologies have been invented that allow chromosome-scale assembly at a lower cost and faster speed than traditional methods.

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Villegas, José A., Nairiti J. Sinha, Naozumi Teramoto, Christopher D. Von Bargen, Darrin J. Pochan, and Jeffery G. Saven. "Computational Design of Single-Peptide Nanocages with Nanoparticle Templating." Molecules 27, no. 4 (2022): 1237. http://dx.doi.org/10.3390/molecules27041237.

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Protein complexes perform a diversity of functions in natural biological systems. While computational protein design has enabled the development of symmetric protein complexes with spherical shapes and hollow interiors, the individual subunits often comprise large proteins. Peptides have also been applied to self-assembly, and it is of interest to explore such short sequences as building blocks of large, designed complexes. Coiled-coil peptides are promising subunits as they have a symmetric structure that can undergo further assembly. Here, an α-helical 29-residue peptide that forms a tetrame

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Karunarathne, Kanchana, Nabila Bushra, Olivia Williams, et al. "Self-Assembly of Amyloid Fibrils Into 3D Gel Clusters Versus 2D Sheets." Biomolecules 13, no. 2 (2023): 230. http://dx.doi.org/10.3390/biom13020230.

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The deposition of dense fibril plaques represents the pathological hallmark for a multitude of human disorders, including many neurodegenerative diseases. Fibril plaques are predominately composed of amyloid fibrils, characterized by their underlying cross beta-sheet architecture. Research into the mechanisms of amyloid formation has mostly focused on characterizing and modeling the growth of individual fibrils and associated oligomers from their monomeric precursors. Much less is known about the mechanisms causing individual fibrils to assemble into ordered fibrillar suprastructures. Elucidat

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Kato, J. Y., M. Matsuoka, D. K. Strom, and C. J. Sherr. "Regulation of cyclin D-dependent kinase 4 (cdk4) by cdk4-activating kinase." Molecular and Cellular Biology 14, no. 4 (1994): 2713–21. http://dx.doi.org/10.1128/mcb.14.4.2713-2721.1994.

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The accumulation of assembled holoenzymes composed of regulatory D-type cyclins and their catalytic partner, cyclin-dependent kinase 4 (cdk4), is rate limiting for progression through the G1 phase of the cell cycle in mammalian fibroblasts. Both the synthesis and assembly of D-type cyclins and cdk4 depend upon serum stimulation, but even when both subunits are ectopically overproduced, they do not assemble into complexes in serum-deprived cells. When coexpressed from baculoviral vectors in intact Sf9 insect cells, cdk4 assembles with D-type cyclins to form active protein kinases. In contrast,

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Kato, J. Y., M. Matsuoka, D. K. Strom, and C. J. Sherr. "Regulation of cyclin D-dependent kinase 4 (cdk4) by cdk4-activating kinase." Molecular and Cellular Biology 14, no. 4 (1994): 2713–21. http://dx.doi.org/10.1128/mcb.14.4.2713.

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The accumulation of assembled holoenzymes composed of regulatory D-type cyclins and their catalytic partner, cyclin-dependent kinase 4 (cdk4), is rate limiting for progression through the G1 phase of the cell cycle in mammalian fibroblasts. Both the synthesis and assembly of D-type cyclins and cdk4 depend upon serum stimulation, but even when both subunits are ectopically overproduced, they do not assemble into complexes in serum-deprived cells. When coexpressed from baculoviral vectors in intact Sf9 insect cells, cdk4 assembles with D-type cyclins to form active protein kinases. In contrast,

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ROGOJIN, VLADIMIR. "SUCCESSFUL ELEMENTARY GENE ASSEMBLY STRATEGIES." International Journal of Foundations of Computer Science 20, no. 03 (2009): 455–77. http://dx.doi.org/10.1142/s0129054109006681.

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We study elementary gene assembly in ciliates. During sexual reproduction, broken and shuffled gene segments in micronuclei get assembled into contiguous macronuclear genes. We consider here a restricted version of the intramolecular model (called elementary), where at most one gene segment is involved at a time (either inverted, or translocated). Not all gene patterns may be assembled by elementary operations, and not all assembly strategies are successful. For a given gene pattern, we characterize in this paper all successful translocation-only elementary assemblies. We also estimate the num

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Collins, Andrew. "The Challenge of Genome Sequence Assembly." Open Bioinformatics Journal 11, no. 1 (2018): 231–39. http://dx.doi.org/10.2174/1875036201811010231.

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Background: Although whole genome sequencing is enabling numerous advances in many fields achieving complete chromosome-level sequence assemblies for diverse species presents difficulties. The problems in part reflect the limitations of current sequencing technologies. Chromosome assembly from ‘short read’ sequence data is confounded by the presence of repetitive genome regions with numerous similar sequence tracts which cannot be accurately positioned in the assembled sequence. Longer sequence reads often have higher error rates and may still be too short to span the larger gaps between conti

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Ulbrich, Pavel, Sarka Haubova, Milan V. Nermut, Eric Hunter, Michaela Rumlova, and Tomas Ruml. "Distinct Roles for Nucleic Acid in In Vitro Assembly of Purified Mason-Pfizer Monkey Virus CANC Proteins." Journal of Virology 80, no. 14 (2006): 7089–99. http://dx.doi.org/10.1128/jvi.02694-05.

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ABSTRACT In contrast to other retroviruses, Mason-Pfizer monkey virus (M-PMV) assembles immature capsids in the cytoplasm. We have compared the ability of minimal assembly-competent domains from M-PMV and human immunodeficiency virus type 1 (HIV-1) to assemble in vitro into virus-like particles in the presence and absence of nucleic acids. A fusion protein comprised of the capsid and nucleocapsid domains of Gag (CANC) and its N-terminally modified mutant (ΔProCANC) were used to mimic the assembly of the viral core and immature particles, respectively. In contrast to HIV-1, where CANC assembled

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Ludgate, Laurie, Kuancheng Liu, Laurie Luckenbaugh, et al. "Cell-Free Hepatitis B Virus Capsid Assembly Dependent on the Core Protein C-Terminal Domain and Regulated by Phosphorylation." Journal of Virology 90, no. 12 (2016): 5830–44. http://dx.doi.org/10.1128/jvi.00394-16.

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ABSTRACTMultiple subunits of the hepatitis B virus (HBV) core protein (HBc) assemble into an icosahedral capsid that packages the viral pregenomic RNA (pgRNA). The N-terminal domain (NTD) of HBc is sufficient for capsid assembly, in the absence of pgRNA or any other viral or host factors, under conditions of high HBc and/or salt concentrations. The C-terminal domain (CTD) is deemed dispensable for capsid assembly although it is essential for pgRNA packaging. We report here that HBc expressed in a mammalian cell lysate, rabbit reticulocyte lysate (RRL), was able to assemble into capsids when (l

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Hercog, Darko, Primož Bencak, Uroš Vincetič, and Tone Lerher. "Product Assembly Assistance System Based on Pick-To-Light and Computer Vision Technology." Sensors 22, no. 24 (2022): 9769. http://dx.doi.org/10.3390/s22249769.

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Product assembly is often one of the last steps in the production process. Product assembly is often carried out by workers (assemblers) rather than robots, as it is generally challenging to adapt automation to any product. When assembling complex products, it can take a long time before the assembler masters all the steps and can assemble the product independently. Training time has no added value; therefore, it should be reduced as much as possible. This paper presents a custom-developed system that enables the guided assembly of complex and diverse products using modern technologies. The sy

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Zhang, Yi, Zongbin Li, Jianmin Gao, Jun Hong, Francesco Villecco, and Yunlong Li. "A Method for Designing Assembly Tolerance Networks of Mechanical Assemblies." Mathematical Problems in Engineering 2012 (2012): 1–26. http://dx.doi.org/10.1155/2012/513958.

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When designing mechanical assemblies, assembly tolerance design is an important issue which must be seriously considered by designers. Assembly tolerances reflect functional requirements of assembling, which can be used to control assembling qualities and production costs. This paper proposes a new method for designing assembly tolerance networks of mechanical assemblies. The method establishes the assembly structure tree model of an assembly based on its product structure tree model. On this basis, assembly information model and assembly relation model are set up based on polychromatic sets (

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Horvath, David P., Sagar Patel, Münevver Doğramaci, et al. "Gene Space and Transcriptome Assemblies of Leafy Spurge (Euphorbia esula) Identify Promoter Sequences, Repetitive Elements, High-Quality Markers, and a Full-Length Chloroplast Genome." Weed Science 66, no. 3 (2018): 355–67. http://dx.doi.org/10.1017/wsc.2018.2.

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AbstractLeafy spurge (Euphorbia esulaL.) is an invasive perennial weed infesting range and recreational lands of North America. Previous research and omics projects withE. esulahave helped develop it as a model for studying many aspects of perennial plant development and response to abiotic stress. However, the lack of an assembled genome forE. esulahas limited the power of previous transcriptomics studies to identify functional promoter elements and transcription factor binding sites. An assembled genome forE. esulawould enhance our understanding of signaling processes controlling plant devel

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Tian, Yunsheng, Jie Xu, Yichen Li, et al. "Assemble Them All." ACM Transactions on Graphics 41, no. 6 (2022): 1–11. http://dx.doi.org/10.1145/3550454.3555525.

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Assembly planning is the core of automating product assembly, maintenance, and recycling for modern industrial manufacturing. Despite its importance and long history of research, planning for mechanical assemblies when given the final assembled state remains a challenging problem. This is due to the complexity of dealing with arbitrary 3D shapes and the highly constrained motion required for real-world assemblies. In this work, we propose a novel method to efficiently plan physically plausible assembly motion and sequences for real-world assemblies. Our method leverages the assembly-by-disasse

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Bi, Lie, Wenrong Wu, Juan Zhang, and Honggang Yang. "An assembly method for micro parts jointing with given space angle based on projection matching." Modern Physics Letters B 31, no. 05 (2017): 1750041. http://dx.doi.org/10.1142/s0217984917500415.

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It is difficult to assemble micro parts jointing with given space angle as the parts assembled are not on the same flat and the visual depth of microscopic vision is small, which can cause the images gathered by the microscopic vision unintelligible and feature extraction difficult. For the problem, this paper presents an assembly method of micro parts based on projection matching. It can assemble micro parts jointing with given space angle accurately. Firstly, an ideal assembly model is established as the size of the micro parts through the drawing software. Secondly, a graphics algorithm bas

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Li, Kun Shan, and Yang Li. "The Assembly Design of Non-Ball Mills." Advanced Materials Research 605-607 (December 2012): 65–68. http://dx.doi.org/10.4028/www.scientific.net/amr.605-607.65.

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The purposes of assembly design (DFA) are aimed to rapidly fit certain machine parts together with the final assemble quality guaranteed. This indicates certain measurements are taken in the very initiative stages to achieve the lowest assembly cost, include quantitative analysis of products; products design optimizations and compression of assembly time. To both aspects of products assemblage capabilities and cost reductions, the DFA usually acquires the least numbers of parts also ensures the ease manufacture and assemble of the parts.

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Sigova, Elizaveta A., Elena N. Pushkova, Tatiana A. Rozhmina, et al. "Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data." Journal of Fungi 9, no. 3 (2023): 301. http://dx.doi.org/10.3390/jof9030301.

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Flax (Linum usitatissimum L.) is attacked by numerous devastating fungal pathogens, including Colletotrichum lini, Aureobasidium pullulans, and Fusarium verticillioides (Fusarium moniliforme). The effective control of flax diseases follows the paradigm of extensive molecular research on pathogenicity. However, such studies require quality genome sequences of the studied organisms. This article reports on the approaches to assembling a high-quality fungal genome from the Oxford Nanopore Technologies data. We sequenced the genomes of C. lini, A. pullulans, and F. verticillioides (F. moniliforme)

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Coropceanu, Igor, Eric M. Janke, Joshua Portner, et al. "Self-assembly of nanocrystals into strongly electronically coupled all-inorganic supercrystals." Science 375, no. 6587 (2022): 1422–26. http://dx.doi.org/10.1126/science.abm6753.

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Colloidal nanocrystals of metals, semiconductors, and other functional materials can self-assemble into long-range ordered crystalline and quasicrystalline phases, but insulating organic surface ligands prevent the development of collective electronic states in ordered nanocrystal assemblies. We reversibly self-assembled colloidal nanocrystals of gold, platinum, nickel, lead sulfide, and lead selenide with conductive inorganic ligands into supercrystals exhibiting optical and electronic properties consistent with strong electronic coupling between the constituent nanocrystals. The phase behavi

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Cheignon, Clémence, Fabrice Collin, Laurent Sabater та Christelle Hureau. "Oxidative Damages on the Alzheimer’s Related-Aβ Peptide Alters Its Ability to Assemble". Antioxidants 12, № 2 (2023): 472. http://dx.doi.org/10.3390/antiox12020472.

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Oxidative stress that can lead to oxidation of the amyloid-β (Aβ) peptide is considered a key feature in Alzheimer’s disease (AD), influencing the ability of Aβ to assemble into β-sheet rich fibrils that are commonly found in senile plaques of AD patients. The present study aims at investigating the fallouts of Aβ oxidation on the assembly properties of the Aβ peptide. To accomplish this, we performed kinetics and analysis on an oxidized Aβ (oxAβ) peptide, resulting from the attack of reactive oxygen species (ROS) that are formed by the biologically relevant Cu/Aβ/dioxygen/ascorbate system. ox

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Subirana, Juan A., and Xavier Messeguer. "How Long Are Long Tandem Repeats? A Challenge for Current Methods of Whole-Genome Sequence Assembly: The Case of Satellites in Caenorhabditis elegans." Genes 9, no. 10 (2018): 500. http://dx.doi.org/10.3390/genes9100500.

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Repetitive genome regions have been difficult to sequence, mainly because of the comparatively small size of the fragments used in assembly. Satellites or tandem repeats are very abundant in nematodes and offer an excellent playground to evaluate different assembly methods. Here, we compare the structure of satellites found in three different assemblies of the Caenorhabditis elegans genome: the original sequence obtained by Sanger sequencing, an assembly based on PacBio technology, and an assembly using Nanopore sequencing reads. In general, satellites were found in equivalent genomic regions,

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Lohse, Konrad, Alex Hayward, and Sam Ebdon. "The genome sequences of the male and female green-veined white, Pieris napi (Linnaeus, 1758)." Wellcome Open Research 6 (October 26, 2021): 288. http://dx.doi.org/10.12688/wellcomeopenres.17277.1.

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We present genome assemblies from a male and female Pieris napi (the green-veined white; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequences of the male and female are 320 and 319 megabases in span, respectively. The majority of the assembly (99.79% of the male assembly, 99.88% of the female) is scaffolded into 24 autosomal pseudomolecules, with the Z sex chromosome assembled for the male and Z and W chromosomes assembled for the female. Gene annotation of the male assembly on Ensembl has identified 13,221 protein coding genes.

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Bera, Santu, and Ehud Gazit. "Self-assembly of Functional Nanostructures by Short Helical Peptide Building Blocks." Protein & Peptide Letters 26, no. 2 (2019): 88–97. http://dx.doi.org/10.2174/0929866525666180917163142.

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The self-assembly of short peptide building blocks into well-ordered nanostructures is a key direction in bionanotechnology. The formation of &#946; -sheet organizations by short peptides is well explored, leading to the development of a wide range of functional assemblies. Likewise, many natural proteinaceous materials, such as silk and amyloid fibrils, are based on β-sheet structures. In contrast, collagen, the most abundant protein in mammals, is based on helical arrangement. Similar to &#946;-sheet structures, short helical peptides have been recently discovered to possess a divers

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Ryadnov, M. G. "Peptide α-helices for synthetic nanostructures". Biochemical Society Transactions 35, № 3 (2007): 487–91. http://dx.doi.org/10.1042/bst0350487.

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Supramolecular structures arising from a broad range of chemical archetypes are of great technological promise. Defining such structures at the nanoscale is crucial to access principally new types of functional materials for applications in bionanotechnology. In this vein, biomolecular self-assembly has emerged as an efficient approach for building synthetic nanostructures from the bottom up. The approach predominantly employs the spontaneous folding of biopolymers to monodisperse three-dimensional shapes that assemble into hierarchically defined mesoscale composites. An immediate interest her

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Mali, Kunal S., and Steven De Feyter. "Principles of molecular assemblies leading to molecular nanostructures." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 371, no. 2000 (2013): 20120304. http://dx.doi.org/10.1098/rsta.2012.0304.

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Self-assembled physisorbed monolayers consist of regular two-dimensional arrays of molecules. Two-dimensional self-assembly of organic and metal–organic building blocks is a widely used strategy for nanoscale functionalization of surfaces. These supramolecular nanostructures are typically sustained by weak non-covalent forces such as van der Waals, electrostatic, metal–ligand, dipole–dipole and hydrogen bonding interactions. A wide variety of structurally very diverse monolayers have been fabricated under ambient conditions at the liquid–solid and air–solid interface or under ultra-high-vacuum

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Zoued, Abdelrahim, Eric Durand, Cecilia Bebeacua, et al. "TssK Is a Trimeric Cytoplasmic Protein Interacting with Components of Both Phage-like and Membrane Anchoring Complexes of the Type VI Secretion System." Journal of Biological Chemistry 288, no. 38 (2013): 27031–41. http://dx.doi.org/10.1074/jbc.m113.499772.

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The Type VI secretion system (T6SS) is a macromolecular machine that mediates bacteria-host or bacteria-bacteria interactions. The T6SS core apparatus assembles from 13 proteins that form two sub-assemblies: a phage-like complex and a trans-envelope complex. The Hcp, VgrG, TssE, and TssB/C subunits are structurally and functionally related to components of the tail of contractile bacteriophages. This phage-like structure is thought to be anchored to the membrane by a trans-envelope complex composed of the TssJ, TssL, and TssM proteins. However, how the two sub-complexes are connected remains u

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Zhang, Huixi Violet, Frank Polzer, Michael J. Haider, et al. "Computationally designed peptides for self-assembly of nanostructured lattices." Science Advances 2, no. 9 (2016): e1600307. http://dx.doi.org/10.1126/sciadv.1600307.

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Folded peptides present complex exterior surfaces specified by their amino acid sequences, and the control of these surfaces offers high-precision routes to self-assembling materials. The complexity of peptide structure and the subtlety of noncovalent interactions make the design of predetermined nanostructures difficult. Computational methods can facilitate this design and are used here to determine 29-residue peptides that form tetrahelical bundles that, in turn, serve as building blocks for lattice-forming materials. Four distinct assemblies were engineered. Peptide bundle exterior amino ac

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Qin, Zhaoqiong. "The Strategic Use of a Wholesale-Price Contract in a Decentralized Assembly System." International Journal of Operations Research and Information Systems 3, no. 4 (2012): 74–87. http://dx.doi.org/10.4018/joris.2012100105.

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Increasing global competition provides the opportunity for companies to pursue cost reduction. Therefore, a decentralized assembly channel structure has been widely adopted by many manufacturing firms. The author studies an assembling system where one party needs to pay the wholesale price to order one component from the other party and assembles the final product. They assume that there is enough capacity for the two parties to provide the components and assemble the final product. Based on each party pursuing its own maximized profit, the author develops a model and analyzes different mechan

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Zhang, Peng, Fenghuan Wang, Yuxuan Wang, Shuangyang Li, and Sai Wen. "Self-Assembling Behavior of pH-Responsive Peptide A6K without End-Capping." Molecules 25, no. 9 (2020): 2017. http://dx.doi.org/10.3390/molecules25092017.

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A short self-assembly peptide A6K (H2N−AAAAAAK−OH) with unmodified N− and C−terminus was designed, and the charge distribution model of this short peptide at different pH was established by computer simulation. The pH of the solution was adjusted according to the model and the corresponding self-assembled structure was observed using a transmission electron microscope (TEM). As the pH changes, the peptide will assemble into blocks or nanoribbons, which indicates that the A6K peptide is a pH-responsive peptide. Circular dichroism (CD) and molecular dynamics (MD) simulation showed that the block

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Salinas-Restrepo, Cristian, Elizabeth Misas, Sebastian Estrada-Gómez, et al. "Improving the Annotation of the Venom Gland Transcriptome of Pamphobeteus verdolaga, Prospecting Novel Bioactive Peptides." Toxins 14, no. 6 (2022): 408. http://dx.doi.org/10.3390/toxins14060408.

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Spider venoms constitute a trove of novel peptides with biotechnological interest. Paucity of next-generation-sequencing (NGS) data generation has led to a description of less than 1% of these peptides. Increasing evidence supports the underestimation of the assembled genes a single transcriptome assembler can predict. Here, the transcriptome of the venom gland of the spider Pamphobeteus verdolaga was re-assembled, using three free access algorithms, Trinity, SOAPdenovo-Trans, and SPAdes, to obtain a more complete annotation. Assembler’s performance was evaluated by contig number, N50, read re

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