Journal articles on the topic 'Assemblie'
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1
Colloms, Sean D., Christine A. Merrick, Femi J. Olorunniji, W. Marshall Stark, Margaret C. M. Smith, Anne Osbourn, Jay D. Keasling, and Susan J. Rosser. "Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination." Nucleic Acids Research 42, no. 4 (November 12, 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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MacGillivray, Leonard. "Hydrogen Bonds and Self-Assembly to Direct Reactivity in the Solid State." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 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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Sciore, Aaron, Min Su, Philipp Koldewey, Joseph D. Eschweiler, Kelsey A. Diffley, Brian M. Linhares, Brandon T. Ruotolo, James C. A. Bardwell, Georgios Skiniotis, and E. Neil G. Marsh. "Flexible, symmetry-directed approach to assembling protein cages." Proceedings of the National Academy of Sciences 113, no. 31 (July 18, 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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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 (March 2, 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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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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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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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 (December 10, 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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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 (April 8, 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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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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Kobayashi, Risako, Hiroshi Inaba, and 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, no. 9 (April 30, 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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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 (January 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 putative MAT1-1 pseudogene. The full genome assembly of a widespread, common species presents an opportunity for new insights into lichen reproduction while the presence of the mating-type locus in the genome of an asexual lichen raises fundamental questions about reproductive biology in fungi generally.
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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, Miniasm/Minipolish, Raven, Redbean and Shasta) across a wide variety of genomes and read parameters. Assemblies were assessed on their structural accuracy/completeness, sequence identity, contig circularisation and computational resources used. Results: Canu v1.9 produced moderately reliable assemblies but had the longest runtimes of all assemblers tested. Flye v2.6 was more reliable and did particularly well with plasmid assembly. Miniasm/Minipolish v0.3 was the only assembler which consistently produced clean contig circularisation. Raven v0.0.5 was the most reliable for chromosome assembly, though it did not perform well on small plasmids and had circularisation issues. Redbean v2.5 and Shasta v0.3.0 were computationally efficient but more likely to produce incomplete assemblies. Conclusions: Of the assemblers tested, Flye, Miniasm/Minipolish and Raven performed best overall. However, no single tool performed well on all metrics, highlighting the need for continued development on long-read assembly algorithms.
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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 (December 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 short-pitch helices that are suggestive of its structure. FtsZ assembles in vitro into short protofilaments that are ∼30 subunits long. We present models for how these protofilaments might be further assembled into the Z ring. We discuss recent experiments on assembly dynamics of FtsZ in vitro, with particular attention to how two regulatory proteins, SulA and MinC, inhibit assembly. Recent efforts to develop antibacterial drugs that target FtsZ are reviewed. Finally, we discuss evidence of how FtsZ generates a constriction force: by protofilament bending into a curved conformation.
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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 (August 8, 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, we find that the mitotic assembly of the nuclear envelope primarily originates from ER cisternae. Moreover, the nuclear pore complexes assemble only on the already formed nuclear envelope. Indeed, all the chromatin-associated Nup107–160 complexes are in single units instead of assembled prepores. We therefore propose that the postmitotic nuclear envelope assembles directly from ER cisternae followed by membrane-dependent insertion of nuclear pore complexes.
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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 (November 23, 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 are created. Each contig is labelled with one of three levels, indicating whether or not ambiguous paths exist. A by-product of this is information on the range of complexity of the underlying gene families present. As a demonstration of CStones ability to assemble high-quality contigs, and to label them in this manner, both simulated and real data were used. For simulated data, ten million read pairs were generated from cDNA libraries representing four species, Drosophila melanogaster, Panthera pardus, Rattus norvegicus and Serinus canaria. These were assembled using CStone, Trinity and rnaSPAdes; the latter two being high-quality, well established, de novo assembers. For real data, two RNA-Seq datasets, each consisting of ≈30 million read pairs, representing two adult D. melanogaster whole-body samples were used. The contigs that CStone produced were comparable in quality to those of Trinity and rnaSPAdes in terms of length, sequence identity of aligned regions and the range of cDNA transcripts represented, whilst providing additional information on chimerism. Here we describe the details of CStones assembly and classification process, and propose that similar classification systems can be incorporated into other de novo assembly tools. Within a related side study, we explore the effects that chimera’s within reference sets have on the identification of differentially expression genes. CStone is available at: https://sourceforge.net/projects/cstone/.
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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 (May 15, 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 challenge would be to partition metagenomic sequence datasets into clusters and assemble separately the sequences in individual clusters using any single-genome assembly method. The current study presents such an approach that uses tetranucleotide usage patterns to first represent sequences as points in a three dimensional (3D) space. The 3D space is subsequently partitioned into "Grids". Sequences within overlapping grids are then progressively assembled using any available assembler. We demonstrate the applicability of the current Grid-Assembly method using various categories of assemblers as well as different simulated metagenomic datasets. Validation results indicate that the Grid-Assembly approach helps in improving the overall quality of assembly, in terms of the purity and volume of the assembled contigs.
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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 (November 19, 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. Then, CAARS incorporates transcripts into gene families, builds gene alignments and trees and uses phylogenetic information to classify the genes as orthologs and paralogs of existing genes. We used CAARS to assemble and annotate RNA-Seq data in rodents and fishes using distantly related genomes as reference, a difficult case for this kind of analysis. We showed CAARS assemblies are more complete and accurate than those assembled by a standard pipeline consisting of de novo assembly coupled with annotation by sequence similarity on a guide species. In addition to annotated transcripts, CAARS provides gene family alignments and trees, annotated with orthology relationships, directly usable for downstream comparative analyses. Availability and implementation CAARS is implemented in Python and Ocaml and is freely available at https://github.com/carinerey/caars. Supplementary information Supplementary data are available at Bioinformatics online.
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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 (January 28, 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 solar cells, biosensors, and agents for light-triggered therapies. Chemical modifications of peptide and tetrapyrrole structures and control over the assembly process can steer the organization and influence the properties of the resulting system. Here we provide a review of the field, focusing on the assemblies obtained from different classes of self-assembling peptides with tetrapyrroles, their morphologies and their applications as innovative functional materials.
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Cunningham, Scott A., Nicholas Chia, Patricio R. Jeraldo, Daniel J. Quest, Julie A. Johnson, Dave J. Boxrud, Angela J. Taylor, et al. "Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks." Journal of Clinical Microbiology 55, no. 6 (April 12, 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-pair (8 kb) libraries were first assembled and analyzed utilizing an in-house assembly and analytical informatics pipeline. In addition, paired-end data were assembled and analyzed using a commercial software package. Single nucleotide variant (SNP) analysis was performed using the in-house pipeline. Two assembly strategies were used to generate core genome multilocus sequence typing (cgMLST) data. First, the near-complete genome data generated with the in-house pipeline were imported into the commercial software and used to perform cgMLST analysis. Second, the commercial software was used to assemble paired-end data, and resolved assemblies were used to perform cgMLST. Similar isolate clustering was observed using SNP calling and cgMLST, regardless of data assembly strategy. All methods provided more discrimination between outbreaks than did PFGE. Overall, all of the evaluated WGS strategies yielded statistically similar results for S. aureus typing.
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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 (November 1, 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 controls. In a small number of nuclei, nuclear pore baskets, normally present on the inner aspect of the nuclear envelope, appeared on its outer surface. Finally, the assembly of nuclear pores was slower in lamin B3-depleted extracts, indicating a slower overall rate of nuclear envelope assembly. The results of FEISEM were confirmed using conventional TEM thin sections, where again the majority of nuclei assembled in lamin B3-depleted extracts had well formed double unit membranes containing a high density of nuclear pores. Since nuclear envelope assembly was mostly normal but slow in these nuclei, the lamin content of ‘depleted’ extracts was investigated. While lamin B3 was recovered efficiently from cytosolic and membrane fractions by our procedure, a second minor lamin isoform, which has characteristics similar to those of the somatic lamin B2, remained in the extract. Thus it is likely that this lamin is necessary for nuclear envelope assembly. However, while lamin B2 did not co-precipitate with lamin B3 during immunodepletion experiments, several protein species did specifically associate with lamin B3 on paramagnetic immunobeads. The major protein species associated with lamin B3 migrated with molecular masses of 102 kDa and 57 kDa, respectively, on one-dimensional polyacrylamide gels. On two-dimensional O'Farrell gels the mobility of the 102 kDa protein was identical to the mobility of a major nuclear matrix protein, indicating a specific association between lamin B3 and other nuclear matrix proteins. Nuclei assembled in lamin B3-depleted extracts did not assemble a lamina, judged by indirect immunofluorescence, and failed to initiate semi-conservative DNA replication. However, by reinoculating depleted extracts with purified lamin B3, nuclear lamina assembly and DNA replication could both be rescued. Thus it seems likely that the inability of lamin-depleted extracts to assemble a replication competent nucleus is a direct consequence of a failure to assemble a lamina.
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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. Different combinations of read lengths and read depths were simulated from the complete genomes of three common food-borne pathogens: Escherichia coli, Listeria monocytogenes, and Salmonella enterica. We found that the quality of assemblies was mainly affected by read depth, irrespective of the assembler used. In addition, we suggest several cutoff values for future cgMLST experiments. Furthermore, we recommend the combinations of read lengths, read depths, and assemblers that can result in a higher cost/performance ratio for cgMLST.
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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 (February 15, 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. Here, we give an overview of the problem of chromosome-scale assembly and traditional methods for tackling this problem. We then review new technologies for chromosome-scale assembly and recent genome projects that used these technologies to create highly contiguous genome assemblies at low cost.
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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 (February 12, 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 tetrameric coiled coil was computationally designed to assemble into a spherical cage that is approximately 9 nm in diameter and presents an interior cavity. The assembly comprises 48 copies of the designed peptide sequence. The design strategy allowed breaking the side chain conformational symmetry within the peptide dimer that formed the building block (asymmetric unit) of the cage. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) techniques showed that one of the seven designed peptide candidates assembled into individual nanocages of the size and shape. The stability of assembled nanocages was found to be sensitive to the assembly pathway and final solution conditions (pH and ionic strength). The nanocages templated the growth of size-specific Au nanoparticles. The computational design serves to illustrate the possibility of designing target assemblies with pre-determined specific dimensions using short, modular coiled-coil forming peptide sequences.
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Karunarathne, Kanchana, Nabila Bushra, Olivia Williams, Imad Raza, Laura Tirado, Diane Fakhre, Fadia Fakhre, and Martin Muschol. "Self-Assembly of Amyloid Fibrils Into 3D Gel Clusters Versus 2D Sheets." Biomolecules 13, no. 2 (January 24, 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. Elucidating the mechanisms regulating this “secondary” self-assembly into distinct suprastructures is important for understanding how individual protein fibrils form the prominent macroscopic plaques observed in disease. Whether and how amyloid fibrils assemble into either 2D or 3D supramolecular structures also relates to ongoing efforts on using amyloid fibrils as substrates or scaffolds for self-assembling functional biomaterials. Here, we investigated the conditions under which preformed amyloid fibrils of a lysozyme assemble into larger superstructures as a function of charge screening or pH. Fibrils either assembled into three-dimensional gel clusters or two-dimensional fibril sheets. The latter displayed optical birefringence, diagnostic of amyloid plaques. We presume that pH and salt modulate fibril charge repulsion, which allows anisotropic fibril–fibril attraction to emerge and drive the transition from 3D to 2D fibril self-assembly.
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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 (April 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, recombinant D-type cyclin and cdk4 subunits produced in insect cells or in bacteria do not assemble as efficiently into functional holoenzymes when combined in vitro but can be activated in the presence of lysates obtained from proliferating mammalian cells. Assembly of cyclin D-cdk4 complexes in coinfected Sf9 cells facilitates phosphorylation of cdk4 on threonine 172 by a cdk-activating kinase (CAK). Assembly can proceed in the absence of this modification, but cdk4 mutants which cannot be phosphorylated by CAK remain catalytically inactive. Therefore, formation of the cyclin D-cdk4 complex and phosphorylation of the bound catalytic subunit are independently regulated, and in addition to the requirement for CAK activity, serum stimulation is required to promote assembly of the complexes in mammalian cells.
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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 (April 1994): 2713–21. http://dx.doi.org/10.1128/mcb.14.4.2713.
Full textAbstract:
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, recombinant D-type cyclin and cdk4 subunits produced in insect cells or in bacteria do not assemble as efficiently into functional holoenzymes when combined in vitro but can be activated in the presence of lysates obtained from proliferating mammalian cells. Assembly of cyclin D-cdk4 complexes in coinfected Sf9 cells facilitates phosphorylation of cdk4 on threonine 172 by a cdk-activating kinase (CAK). Assembly can proceed in the absence of this modification, but cdk4 mutants which cannot be phosphorylated by CAK remain catalytically inactive. Therefore, formation of the cyclin D-cdk4 complex and phosphorylation of the bound catalytic subunit are independently regulated, and in addition to the requirement for CAK activity, serum stimulation is required to promote assembly of the complexes in mammalian cells.
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ROGOJIN, VLADIMIR. "SUCCESSFUL ELEMENTARY GENE ASSEMBLY STRATEGIES." International Journal of Foundations of Computer Science 20, no. 03 (June 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 number of such assemblies. We solve the problem in terms of graphs and permutations.
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Collins, Andrew. "The Challenge of Genome Sequence Assembly." Open Bioinformatics Journal 11, no. 1 (October 17, 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 contigs. Objective: Given the emergence of exciting new applications using sequencing technology, such as the Earth BioGenome Project, it is necessary to further develop and apply a range of strategies to achieve robust chromosome-level sequence assembly. Reviewed here are a range of methods to enhance assembly which include the use of cross-species synteny to understand relationships between sequence contigs, the development of independent genetic and/or physical scaffold maps as frameworks for assembly (for example, radiation hybrid, optical motif and chromatin interaction maps) and the use of patterns of linkage disequilibrium to help position, orient and locate contigs. Results and Conclusion: A range of methods exist which might be further developed to facilitate cost-effective large-scale sequence assembly for diverse species. A combination of strategies is required to best assemble sequence data into chromosome-level assemblies. There are a number of routes towards the development of maps which span chromosomes (including physical, genetic and linkage disequilibrium maps) and construction of these whole chromosome maps greatly facilitates the ordering and orientation of sequence contigs.
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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 (July 15, 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 efficiently into cylindrical structures, the same domains of M-PMV were assembly incompetent. The addition of RNA or oligonucleotides did not complement this defect. In contrast, the M-PMV ΔProCANC molecule was able to assemble into spherical particles, while that of HIV-1 formed both spheres and cylinders. For M-PMV, the addition of purified RNA increased the efficiency with which ΔProCANC formed spherical particles both in terms of the overall amount and the numbers of completed spheres. The amount of RNA incorporated was determined, and for both rRNA and MS2-RNA, quantities similar to that of genomic RNA were encapsidated. Oligonucleotides also stimulated assembly; however, they were incorporated into ΔProCANC spherical particles in trace amounts that could not serve as a stoichiometric structural component for assembly. Thus, oligonucleotides may, through a transient interaction, induce conformational changes that facilitate assembly, while longer RNAs appear to facilitate the complete assembly of spherical particles.
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Ludgate, Laurie, Kuancheng Liu, Laurie Luckenbaugh, Nicholas Streck, Stacey Eng, Christian Voitenleitner, William E. Delaney, and Jianming Hu. "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 (April 13, 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 (low-nanomolar) HBc concentrations mimicked those achieved under conditions of viral replicationin vivoand were far below those used previously for capsid assemblyin vitro. Furthermore, at physiologically low HBc concentrations in RRL, the NTD was insufficient for capsid assembly and the CTD was also required. The CTD likely facilitated assembly under these conditions via RNA binding and protein-protein interactions. Moreover, the CTD underwent phosphorylation and dephosphorylation events in RRL similar to those seenin vivowhich regulated capsid assembly. Importantly, the NTD alone also failed to accumulate in mammalian cells, likely resulting from its failure to assemble efficiently. Coexpression of the full-length HBc rescued NTD assembly in RRL as well as NTD expression and assembly in mammalian cells, resulting in the formation of mosaic capsids containing both full-length HBc and the NTD. These results have important implications for HBV assembly during replication and provide a facile cell-free system to study capsid assembly under physiologically relevant conditions, including its modulation by host factors.IMPORTANCEHepatitis B virus (HBV) is an important global human pathogen and the main cause of liver cancer worldwide. An essential component of HBV is the spherical capsid composed of multiple copies of a single protein, the core protein (HBc). We have developed a mammalian cell-free system in which HBc is expressed at physiological (low) concentrations and assembles into capsids under near-physiological conditions. In this cell-free system, as in mammalian cells, capsid assembly depends on the C-terminal domain (CTD) of HBc, in contrast to other assembly systems in which HBc assembles into capsids independently of the CTD under conditions of nonphysiological protein and salt concentrations. Furthermore, the phosphorylation state of the CTD regulates capsid assembly and RNA encapsidation in the cell-free system in a manner similar to that seen in mammalian cells. This system will facilitate detailed studies on capsid assembly and RNA encapsidation under physiological conditions and identification of antiviral agents that target HBc.
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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 (December 13, 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 system is based on pick-to-light (PTL) modules, used primarily in logistics as an additional aid in the order picking process, and Computer Vision technology. The designed system includes a personal computer (PC), several custom-developed PTL modules and a USB camera. The PC with a touchscreen visualizes the assembly process and allows the assembler to interact with the system. The developed PC application guides the operator through the assembly process by showing all the necessary assembly steps and parts. Two-step verification is used to ensure that the correct part is picked out of the bin, first by checking that the correct pushbutton on the PTL module has been pressed and second by using a camera with a Computer Vision algorithm. The paper is supported by a use case demonstrating that the proposed system reduces the assembly time of the used product. The presented solution is scalable and flexible as it can be easily adapted to show the assembly steps of another product.
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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 (PS) theory. According to the two models, the systems of location relation equations and interference relation equations are established. Then, using methods of topologically related surfaces (TTRS) theory and variational geometric constraints (VGC) theory, three VGC reasoning matrices are constructed. According to corresponding relations between VGCs and assembly tolerance types, the reasoning matrices of tolerance types are also established by using contour matrices of PS. Finally, an exemplary product is used to construct its assembly tolerance networks and meanwhile to verify the feasibility and effectiveness of the proposed method.
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Horvath, David P., Sagar Patel, Münevver Doğramaci, Wun S. Chao, James V. Anderson, Michael E. Foley, Brian Scheffler, 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 (February 28, 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 development and responses to environmental stress and provide a better understanding of genetic factors impacting weediness traits, evolution, and herbicide resistance. A comprehensive transcriptome database would also assist in analyzing future RNA-seq studies and is needed to annotate and assess genomic sequence assemblies. Here, we assembled and annotated 56,234 unigenes from an assembly of 589,235 RNA-seq-derived contigs and a previously published Sanger-sequenced expressed sequence tag collection. The resulting data indicate that we now have sequence for >90% of the expressedE. esulaprotein-coding genes. We also assembled the gene space ofE. esulaby using a limited coverage (18X) genomic sequence database. In this study, the programs Velvet and Trinity produced the best gene-space assemblies based on representation of expressed and conserved eukaryotic genes. The results indicate thatE. esulacontains as much as 23% repetitive sequences, of which 11% are unique. Our sequence data were also sufficient for assembling a full chloroplast and partial mitochondrial genome. Further, marker analysis identified more than 150,000 high-quality variants in ourE. esulaL-RNA–scaffolded, whole-genome, Trinity-assembled genome. Based on these results,E. esulaappears to have limited heterozygosity. This study provides a blueprint for low-cost genomic assemblies in weed species and new resources for identifying conserved and novel promoter regions among coordinately expressed genes ofE. esula.
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Tian, Yunsheng, Jie Xu, Yichen Li, Jieliang Luo, Shinjiro Sueda, Hui Li, Karl D. D. Willis, and Wojciech Matusik. "Assemble Them All." ACM Transactions on Graphics 41, no. 6 (November 30, 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-disassembly principle and physics-based simulation to efficiently explore a reduced search space. To evaluate the generality of our method, we define a large-scale dataset consisting of thousands of physically valid industrial assemblies with a variety of assembly motions required. Our experiments on this new benchmark demonstrate we achieve a state-of-the-art success rate and the highest computational efficiency compared to other baseline algorithms. Our method also generalizes to rotational assemblies (e.g., screws and puzzles) and solves 80-part assemblies within several minutes.
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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 (February 20, 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 based on the primitive information from CAD is designed. Thirdly, according to the pixel value calibration and the graphics algorithm, the projection pictures are shown on the control interface. Lastly, the control method of micro parts is proposed to assemble them with given space angle. And we accomplished an assembly experiment of micro-tube and micro-column in this way, whose assembly deviation is 0.12[Formula: see text]. Experiment results indicate that the angle between two micro parts assembled can be controlled within the given deviation.
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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, Ludmila P. Kudryavtseva, Alexander A. Zhuchenko, Roman O. Novakovskiy, Daiana A. Zhernova, et al. "Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data." Journal of Fungi 9, no. 3 (February 26, 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) and received different volumes of sequencing data: 1.7 Gb, 3.9 Gb, and 11.1 Gb, respectively. To obtain the optimal genome sequences, we studied the effect of input data quality and genome coverage on assembly statistics and tested the performance of different assembling and polishing software. For C. lini, the most contiguous and complete assembly was obtained by the Flye assembler and the Homopolish polisher. The genome coverage had more effect than data quality on assembly statistics, likely due to the relatively low amount of sequencing data obtained for C. lini. The final assembly was 53.4 Mb long and 96.4% complete (according to the glomerellales_odb10 BUSCO dataset), consisted of 42 contigs, and had an N50 of 4.4 Mb. For A. pullulans and F. verticillioides (F. moniliforme), the best assemblies were produced by Canu–Medaka and Canu–Homopolish, respectively. The final assembly of A. pullulans had a length of 29.5 Mb, 99.4% completeness (dothideomycetes_odb10), an N50 of 2.4 Mb and consisted of 32 contigs. F. verticillioides (F. moniliforme) assembly was 44.1 Mb long, 97.8% complete (hypocreales_odb10), consisted of 54 contigs, and had an N50 of 4.4 Mb. The obtained results can serve as a guideline for assembling a de novo genome of a fungus. In addition, our data can be used in genomic studies of fungal pathogens or plant–pathogen interactions and assist in the management of flax diseases.
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Coropceanu, Igor, Eric M. Janke, Joshua Portner, Danny Haubold, Trung Dac Nguyen, Avishek Das, Christian P. N. Tanner, et al. "Self-assembly of nanocrystals into strongly electronically coupled all-inorganic supercrystals." Science 375, no. 6587 (March 25, 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 behavior of charge-stabilized nanocrystals can be rationalized and navigated with phase diagrams computed for particles interacting through short-range attractive potentials. By finely tuning interparticle interactions, the assembly was directed either through one-step nucleation or nonclassical two-step nucleation pathways. In the latter case, the nucleation was preceded by the formation of two metastable colloidal fluids.
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Cheignon, Clémence, Fabrice Collin, Laurent Sabater, and Christelle Hureau. "Oxidative Damages on the Alzheimer’s Related-Aβ Peptide Alters Its Ability to Assemble." Antioxidants 12, no. 2 (February 13, 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. oxAβ was still able to assemble but displayed ill-defined and small oligomeric assemblies compared to the long and thick β-sheet rich fibrils from the non-oxidized counterpart. In addition, oxAβ does affect the assembly of the parent Aβ peptide. In a mixture of the two peptides, oxAβ has a mainly kinetic effect on the assembly of the Aβ peptide and was able to slow down the formation of Aβ fibril in a wide pH range [6.0–7.4]. However, oxAβ does not change the quantity and morphology of the Aβ fibrils formed to a significant extent. In the presence of copper or zinc di-cations, oxAβ assembled into weakly-structured aggregates rather than short, untangled Cu-Aβ fibrils and long untangled Zn-Aβ fibrils. The delaying effect of oxAβ on metal altered Aβ assembly was also observed. Hence, our results obtained here bring new insights regarding the tight interconnection between (i) ROS production leading to Aβ oxidation and (ii) Aβ assembly, in particular via the modulation of the Aβ assembly by oxAβ. It is the first time that co-assembly of oxAβ and Aβ under various environmental conditions (pH, metal ions …) are reported.
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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 (October 16, 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, but the new long-read methods (PacBio and Nanopore) tended to result in longer assembled satellites. Important differences exist between the assemblies resulting from the two long-read technologies, such as the sizes of long satellites. Our results also suggest that the lengths of some annotated genes with internal repeats which were assembled using Sanger sequencing are likely to be incorrect.
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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 (February 20, 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 β -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 β-sheet structures, short helical peptides have been recently discovered to possess a diverse set of functionalities with the potential to fabricate artificial self-assembling materials. Here, we outline the functional roles of self-assembled nanostructures formed by short helical peptides and their potential as artificial materials. We focus on the association between self-assembled mesoscale structures and their material function and demonstrate the way by which this class of building blocks bears the potential for diverse applications, such as the future fabrication of smart devices.
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Ryadnov, M. G. "Peptide α-helices for synthetic nanostructures." Biochemical Society Transactions 35, no. 3 (May 22, 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 here is the extraction of reliable rules that link the chemistry of biopolymers to the mechanisms of their assembly. Once established these can be further harnessed in designing supramolecular objects de novo. Different biopolymer classes compile a rich repertoire of assembly motifs to facilitate the synthesis of otherwise inaccessible nanostructures. Among those are peptide α-helices, ubiquitous folding elements of natural protein assemblies. These are particularly appealing candidates for prescriptive supramolecular engineering, as their well-established and conservative design rules give unmatched predictability and rationale. Recent developments of self-assembling systems based on helical peptides, including fibrous systems, nanoscale linkers and reactors will be highlighted herein.
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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 (October 13, 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 (UHV) conditions at the UHV–solid interface. The outcome of the molecular self-assembly process depends on a variety of factors such as the nature of functional groups present on assembling molecules, the type of solvent, the temperature at which the molecules assemble and the concentration of the building blocks. The objective of this review is to provide a brief account of the progress in understanding various parameters affecting two-dimensional molecular self-assembly through illustration of some key examples from contemporary literature.
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Zoued, Abdelrahim, Eric Durand, Cecilia Bebeacua, Yannick R. Brunet, Badreddine Douzi, Christian Cambillau, Eric Cascales, and Laure Journet. "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 (August 6, 2013): 27031–41. http://dx.doi.org/10.1074/jbc.m113.499772.
Full textAbstract:
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 unknown. Here we identify TssK, a protein that establishes contacts with the two T6SS sub-complexes through direct interactions with TssL, Hcp, and TssC. TssK is a cytoplasmic protein assembling trimers that display a three-armed shape, as revealed by TEM and SAXS analyses. Fluorescence microscopy experiments further demonstrate the requirement of TssK for sheath assembly. Our results suggest a central role for TssK by linking both complexes during T6SS assembly.
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Zhang, Huixi Violet, Frank Polzer, Michael J. Haider, Yu Tian, Jose A. Villegas, Kristi L. Kiick, Darrin J. Pochan, and Jeffery G. Saven. "Computationally designed peptides for self-assembly of nanostructured lattices." Science Advances 2, no. 9 (September 2016): e1600307. http://dx.doi.org/10.1126/sciadv.1600307.
Full textAbstract:
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 acids were designed in the context of three different interbundle lattices in addition to one design to produce bundles isolated in solution. Solution assembly produced three different types of lattice-forming materials that exhibited varying degrees of agreement with the chosen lattices used in the design of each sequence. Transmission electron microscopy revealed the nanostructure of the sheetlike nanomaterials. In contrast, the peptide sequence designed to form isolated, soluble, tetrameric bundles remained dispersed and did not form any higher-order assembled nanostructure. Small-angle neutron scattering confirmed the formation of soluble bundles with the designed size. In the lattice-forming nanostructures, the solution assembly process is robust with respect to variation of solution conditions (pH and temperature) and covalent modification of the computationally designed peptides. Solution conditions can be used to control micrometer-scale morphology of the assemblies. The findings illustrate that, with careful control of molecular structure and solution conditions, a single peptide motif can be versatile enough to yield a wide range of self-assembled lattice morphologies across many length scales (1 to 1000 nm).
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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 (October 2012): 74–87. http://dx.doi.org/10.4018/joris.2012100105.
Full textAbstract:
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 mechanisms of deciding the wholesale price of the component. The author’s objective is to optimize the whole supply chain for improving the customer service level. Results are derived for the author to recommend the optimal mechanism.
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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 (April 26, 2020): 2017. http://dx.doi.org/10.3390/molecules25092017.
Full textAbstract:
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 structure was formed by random coils, while the increase in β-turn content contributes to the formation of intact nanoribbons. A reasonable explanation of the self-assembling structure was made according to the electrostatic distribution model and the effect of electrostatic interaction on self-assembly was investigated. This study laid the foundation for further design of nanomaterials based on pH-responsive peptides.
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Salinas-Restrepo, Cristian, Elizabeth Misas, Sebastian Estrada-Gómez, Juan Carlos Quintana-Castillo, Fanny Guzman, Juan C. Calderón, Marco A. Giraldo, and Cesar Segura. "Improving the Annotation of the Venom Gland Transcriptome of Pamphobeteus verdolaga, Prospecting Novel Bioactive Peptides." Toxins 14, no. 6 (June 15, 2022): 408. http://dx.doi.org/10.3390/toxins14060408.
Full textAbstract:
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 representation on the assembly, and BUSCO’s terms retrieval against the arthropod dataset. Out of all the assembled sequences with all software, 39.26% were common between the three assemblers, and 27.88% were uniquely assembled by Trinity, while 27.65% were uniquely assembled by SPAdes. The non-redundant merging of all three assemblies’ output permitted the annotation of 9232 sequences, which was 23% more when compared to each software and 28% more when compared to the previous P. verdolaga annotation; moreover, the description of 65 novel theraphotoxins was possible. In the generation of data for non-model organisms, as well as in the search for novel peptides with biotechnological interest, it is highly recommended to employ at least two different transcriptome assemblers.