Perfect Assembly Research Articles

Diverse new plasmid structures and antimicrobial resistance in strains isolated from perianal abscess patients.

Plasmids, the most important and versatile bacterial extrachromosomal DNA Molecules, has have been a center central topic for bacterial genetics and biology. However, the inability of short-read high-throughput sequencing methods to reliably assemble plasmids makes it difficult to investigate the diversity of plasmid structures and functions. In this work, we used the long-read Nanopore sequencing method to address this issue, by producing high quality whole genome sequences of 33 bacterial strains from 11 perianal abscess-suffering patients. Successful high quality assemblies were generated with this method, including 20 perfect assemblies out of 33 genomes. A total of 47 plasmids were identified from the bacterial strains, including 12 unique, newly identified, high quality circular plasmids. These plasmids were further subject to structural analysis, leading to the finding of significant diversification from previously known plasmids, suggesting the diversity of plasmid structure and function. Particularly, two mcr-10.1-harboring conjugative plasmids were found from Citrobacter portucalensis and Enterobacter kobei, which were not previously reported. This works shows the feasibility of using long-read sequencing to identify plasmids, and the high diversity of plasmid structure and function that awaits further surveillance.

Dark‐Bright Exciton Splitting Dominates Low‐Temperature Diffusion in Halide Perovskite Nanocrystal Assemblies

AbstractSemiconductor nanocrystals can replace conventional bulk materials completely in displays and light‐emitting diodes. Exciton transport dominates over charge carrier transport for materials with high exciton binding energies and long ligands, such as halide perovskite nanocrystal films. Here, how beneficial superlattices – nearly perfect 3D assemblies of nanocrystals ‐ are to exciton transport is investigated. Surprisingly, the high degree of order is not as crucial as the individual nanocrystal size, which strongly influences the splitting of the excitonic manifold into bright and dark states. At very low temperatures, the energetic splitting is larger for the smallest nanocrystals, and dark levels with low oscillator strength effectively trap excitons inside individual nanocrystals, suppressing diffusion. The effect is reversed at elevated temperatures, and the larger nanocrystal size becomes detrimental to exciton transport due to enhanced exciton trapping and dissociation. The results reveal that the nanocrystal size must be strongly accounted for in design strategies of future optoelectronic applications.

Complex TiC-Ni-based composites joined to steel support by thermal explosion under load: synthesis, microstructure and tribological behavior

ABSTRACT The combustion in thermal explosion mode of reactive mixtures of Ti–Ni–graphite(carbides, borides, oxides), under load, was used to produce complex composite materials, densified and joined to a C55 carbon steel support. The ignition of the exothermic reaction, carried out thanks to the rapid high-frequency heating of a green compact up to 1573 K, was followed by an isothermal holding at 1373 K for 360 s. This procedure ensured a perfect mechanical assembly between the composite material and the steel substrate. SEM analysis and concentration profiles carried out at the interface testified to the interdiffusion of iron and titanium atoms between the two materials. The maximum combustion temperature (Tmax.) exceeding 2200 K induced the appearance of a liquid phase that assisted densification and joining, and in which a part of the additions was dissolved before cooling. The starting chemical composition of reactive mixtures largely determined the microstructure, hardness and tribological behavior of the composites after the process. Thereby, the maximum hardness (1235 HV0.15) and the lowest wear rate (1.824 × 10−6 mm3.N−1.m−1) were obtained in the sample containing TiC, Al2O3 and TiB2 hard phases. The manufactured samples exhibit no deterioration of the composite by spalling, regardless of the starting composition.

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing.

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).

Heat Transfer Process with Solid-solid Interface: Analytical and Numerical Solutions

This work is aimed at the study and analysis of the heat transport on a metal bar of length L with a solid-solid interface. The process is assumed to be developed along one direction, across two homogeneous and isotropic materials. Analytical and numerical solutions are obtained under continuity conditions at the interface, that is a perfect assembly. The lateral side is assumed to be isolated and a constant thermal source is located at the left-boundary while the right-end stays free allowing the heat to transfer to the surrounding fluid by a convective process. The differences between the analytic solution and temperature measurements at any point on the right would indicate the presence of discontinuities. The greater these differences, the greater the discontinuity in the interface due to thermal resistances, providing a measure of its propagation from the interface and they could be modeled as temperature perturbations. The problem of interest may be described by a parabolic equation with initial, interface and boundary conditions, where the thermal properties, the conductivity and diffusivity coefficients, are piecewise constant functions. The analytic solution is derived by using Fourier methods. Special attention is given to the Sturm-Liouville problem that arises when deriving the solution, since a complicated eigenvalue equation must to be solved. Numerical simulations are conducted by using finite difference schemes where its convergence and stability properties are discussed along with physical interpretations of the results.

Recyclable and Light-Adaptive Vitrimer-Based Nacre-Mimetic Nanocomposites.

Nacre's natural design consists of a perfect hierarchical assembly that resembles a brick-and-mortar structure with synergistic stiffness and toughness. The field of bioinspired materials often provides attractive architecture and engineering pathways which allow to explore outstanding property areas. However, the study of nacre-mimetic materials should not be limited to the design of its architecture but ought to include the understanding, operation, and improvement of internal interactions between their components. Here, we introduce a vitrimer prepolymer system that, once integrated into the nacre-mimetic nanocomposites, cures and cross-links with the presence of Lewis acid catalyst and further manifests associative dynamic exchange reactions. Bond exchanges are controllable by molecular composition and catalyst content and characterized by creep, shear-lag, and shape-locking tests. We exploit the vitrimer properties by laminating ca. 70 films into thick bulk materials, and characterize the flexural resistance and crack propagation. More importantly, we introduce recycling by grinding and hot-pressing. The recycling for highly reinforced nacre-mimetic nanocomposites is critically enabled by the vitrimer chemistry and improves the sustainability of bioinspired nanocomposites in cyclic economy. Finally, we integrate photothermal converters into the structures and use laser irradiation as external trigger to activate the vitrimer exchange reactions.

The ‘plebs contionalis’ – a perfect popular assembly participant?

The writings of Cicero refer in various ways, often critically, to citizens who participated in contiones. Contemporary researchers refer to them as plebs contionalis, coined by Christian Meier. Although this term does not occur in the sources, many historians have concluded that it perfectly describes the citizens who regularly attended popular gatherings. The problem, however, is that the issues raised during the contiones were so varied, and these assemblies were held so often that it is hard to imagine that the average citizen could afford to attend them regularly. The author of the article analyses various aspects of this issue and confronts them with the views of other researchers, in order to reach a more general conclusion about the participants in these contiones. W pismach Cycerona można znaleźć bardzo różne sformułowania, nierzadko krytyczne, odnoszące się do tych obywateli, którzy uczestniczą w contiones. Współcześni badacze określają ich mianem plebs contionalis, ukutym przez Christiana Meiera. Wprawdzie termin ten nie pojawia się w źródłach, ale wielu historyków uznało, że doskonale charakteryzuje on właśnie tych obywateli, którzy regularnie pojawiali się na zgromadzeniach ludowych. Problem polega jednak na tym, że sprawy poruszane podczas contiones były tak różne, a owe zgromadzenia odbywały sie tak często, że trudno wyobrazić sobie, by przeciętny obywatel mógł sobie pozwolić na regularne w nich uczestniczenie. Autorka artykułu analizuje różne aspekty tego zagadnienia i konfrontuje je z poglądami innych badaczy zmierzając do ogólniejszej konkluzji na temat uczestników owych contiones.

Supramolecular Structure of Temperature‐Dependent Polymeric Hydrogels Modulated by Drug Incorporation

AbstractPoloxamers or Pluronics® (PL) have been described as promising pharmaceutical and cosmetics matrices. Herein, we have explored the structural organization of hydrogel formulations composed of PL F‐127 and PL L‐81, considering their different hydrophilic‐lipophilic balances and interactions with an antimigraine drug, sumatriptan succinate (SMT). Hydrogels phase organizations were investigated by X‐ray diffraction (XRD) and Small Angle Neutron Scattering (SANS) to establish the relationship between structural features and drug release modulation. XRD analysis revealed very low intensity peaks for hydrogels containing SMT due to the presence of small amounts of SMT as crystalline form, which is an evidence of drug incorporation into hydrogels. At physiological temperature, a structural transition from lamellar to hexagonal was observed after SMT incorporation. In addition, SANS patterns displayed a distorted hexagonal structure, (calculated >experimental ), indicating the presence of a comprised structure compared to a perfect hexagonal assembly. This structural shift however have no influence on the drug release mechanism, allowing the SMT molecules to access the micellar and intermicellar hydrophilic spaces, with release mechanism dependent on the drug diffusion (R2=0.998 ≥ 0.986) from the hydrogel to the medium and release constant (Krel) values from 9.8 to 14.7 %.h−1; 31.5 to 39.1 %.h−1/2; 0.84 to 1.2 %.h−n for Zero‐order, Higuchi and Korsmeyer‐Peppas models, respectively. Using SMT as a drug model, it could be concluded that the drug access to the micellar/intermicellar hydrophilic spaces can be modulated by interplaying the polarity of binary PL‐based hydrogels. Therefore, drug release constants and mechanisms will be then dependent on the hydrogels physico‐chemical and structural properties, which determine the drug diffusion from the hydrogel to the release medium.

Influence of surface design on performance of MnO‐decorated nanocatalyst for olefin production from methanol: ZSM‐5@MnO core–shellversusMnO/ZSM‐5 dispersed nanocatalysts

AbstractBACKGROUNDIn the assembly of nanoparticles (NPs) onto zeolites, the surface design of NPs has a great influence on various catalytic properties. Herein, ZSM‐5 was hydrothermally synthesized and its external surface was decorated by MnO NPs in two different surface designs: distributed MnO NPs and MnO shell.RESULTSThe synthesized MnO‐decorated samples, MnO/ZSM‐5 and ZSM‐5@MnO, were analyzed using various techniques. The results of these analyses reveal the formation of desired crystal phases without any impurities and confirm the perfect assembly of uniform MnO NPs on the surface of ZSM‐5. Also, it was found that the surface design of MnO NPs has a great impact on the physicochemical properties of the nanocatalyst. Basically, ZSM‐5 is highly selective toward propylene, but the shape selectivity of MnO NPs increases the selectivity of MnO‐decorated nanocatalysts toward ethylene. Moreover, this study delves deeply into differences in catalytic behaviors of the nanocatalysts during the methanol‐to‐olefin process and explains how they are attributed to the applied surface designs.CONCLUSIONSThe catalytic performance studies at optimum temperature show that the ZSM‐5@MnO nanocatalyst is more selective toward ethylene, and it has a nearly 20% higher methanol conversion rate compared to the MnO/ZSM‐5 nanostructured catalyst. Due to the surface acidity adjustment of MnO shell as well as high control of core–shell structure over the location of coke formation, the ZSM‐5@MnO nanocatalyst shows longer stability and its activity remains constant with time on stream. © 2020 Society of Chemical Industry

Defect Annihilation in the Directed Self-Assembly of Block Copolymers in Films with Increasing Thickness

We investigate directed self-assembly (DSA), with 3× density multiplication, of symmetric polystyrene-block-poly(methyl methacrylate) (L0 = 28 nm) with increasing film thicknesses and reveal a thickness limit above which the defect annihilation mechanism is different than in thinner films. Block copolymer films of increasing thickness underwent DSA on a macroscopic chemical pattern under optimum geometrical and chemical conditions. Scanning electron microscopy and grazing-incidence small-angle X-ray scattering (GISAXS) were used to characterize the long-range ordering and buried structures as a function of film thickness and thermal annealing time. Rotational GISAXS measurements revealed a critical thickness of ∼3L0, below which defect annihilation is cooperative across the film depth and above which it is faster at the free surface than in the film’s interior. In the latter case, defects can persist in the film’s interior despite perfect assembly and registration at the free surface of the film.

Multimaterial 3D-Printed Water Electrolyzer with Earth-Abundant Electrodeposited Catalysts

Additive manufacturing (AM) is reaching a stage of development that enables high throughput fabrication of end products/devices. An important contribution to the advancement of this technology is given by the possibility to combine different materials into a single printing process or integrate diverse technologies for the fabrication of different components. Here we show how a prototype water electrolyzer can be fabricated using two different AM technologies, named selective laser melting and fused deposition modeling to produce the metallic components (electrodes) and the liquid/gas handling components (cells) of the electrolyzer, respectively. Both components are produced following a precise design which enables their perfect integration and assembly. The electrodes are produced in stainless steel which can be directly used for both the cathodic hydrogen evolution reaction (HER) and the anodic oxygen evolution reaction. However, we propose to introduce a simple and rapid electrochemical surface modific...

Fundamental Limits of Genome Assembly Under an Adversarial Erasure Model

In contrast to second-generation DNA sequencing technologies, emerging third-generation technologies are capable of delivering reads that are long enough to enable perfect genome assembly. Unfortunately, the benefits of long reads are accompanied by higher rates of read errors. This motivates a question of fundamental import: what read-length and error-rate combinations allow for perfect assembly of the genome? Formal investigation of this tradeoff is complicated by the fact that tractable probabilistic models for the genome sequence and error process fail to capture key features of the problem: real genomes contain long repetitive patterns, and read errors are often bursty and sequence-dependent. In order to circumvent these modeling barriers and take a first step toward the study of this question, we consider a simple setting: the genome sequence is arbitrary, and the read errors are erasures that can occur at adversarially chosen positions, up to a limit in the number of erasures per read and per genome position. In this context, we show that a natural error-correction scheme is optimal in the sense that it recovers the error-free ${k}$ - spectrum of the genome for the largest possible ${k}$ . The worst-case nature of our analysis ensures that the proposed error-correction method is robust and allows us to study its performance under stochastic error models. As a result, we show that, for several real genomes, the impact of read errors on the information-theoretic requirements for perfect assembly is relatively mild.

Multiplex pairwise assembly of array-derived DNA oligonucleotides

While the cost of DNA sequencing has dropped by five orders of magnitude in the past decade, DNA synthesis remains expensive for many applications. Although DNA microarrays have decreased the cost of oligonucleotide synthesis, the use of array-synthesized oligos in practice is limited by short synthesis lengths, high synthesis error rates, low yield and the challenges of assembling long constructs from complex pools. Toward addressing these issues, we developed a protocol for multiplex pairwise assembly of oligos from array-synthesized oligonucleotide pools. To evaluate the method, we attempted to assemble up to 2271 targets ranging in length from 192–252 bases using pairs of array-synthesized oligos. Within sets of complexity ranging from 131–250 targets, we observed error-free assemblies for 90.5% of all targets. When all 2271 targets were assembled in one reaction, we observed error-free constructs for 70.6%. While the assembly method intrinsically increased accuracy to a small degree, we further increased accuracy by using a high throughput ‘Dial-Out PCR’ protocol, which combines Illumina sequencing with an in-house set of unique PCR tags to selectively amplify perfect assemblies from complex synthetic pools. This approach has broad applicability to DNA assembly and high-throughput functional screens.

Organometallic assemblies: π-electron delocalization, μ-bridging spacers, flexibility, lipophilic nature, bio-accessibility, bioavailability, intracellular trafficking pathways and antimicrobial assimilation

Supramolecular architectures of triphenylSn(IV)-A(lII)-μ-oxoisopropoxide (organometallic assemblies i.e. Ph3SnOAl(OPri)L and Ph3SnOAl(L)2) were yielded by the reaction of triphenyltin acetate, aluminiumisopropoxide and different ligands (L1 to L5) having different backbones (NOONO and OONO) in presence of xylene. Spectral analysis (IR, 1H NMR, 13C NMR, 27Al NMR, 119Sn NMR and MS) and molecular modeling revealed coordination modes between metals and donor atoms entirely within supramolecular architectures. Ph3SnOAl(OPri)L and Ph3SnOAl(L)2 showed tetra- and penta-coordination of metals center with distorted tetrahedral and distorted trigonal-bipyramidal geometries for Sn(IV) and Al(III) respectively. Organometallic assemblies went through self-organization of atoms through μ-bridging, hydrophobic, hydrophilic and electrostatic effects. Antimicrobial assimilation was dependent on good adsorptive ability, generated by the interaction between microbial and organometallic assemblies. Finally, organometallic assemblies were screened extensively in-vitro against a number of pathogens. The toxicity of metal ion(s) was reduced or eliminated by changing donor backbone of ligands. Computational models and molecular mechanics were employed to reveal architectural features. The donating nature of substituent of ligands affected antimicrobial assimilation. Because of this, desired modifications were done through computational calculations to achieve perfect organometallic assemblies with HOMO for ligands(L1 to L5).

Fabrication and magnetic properties of FePt nanoparticle assemblies embedded in MgO-matrix systems

Hydrophilic FePt nanoparticles (NPs) have been embedded into the MgO-matrix systems via a sol–gel process to prevent FePt NPs from aggregating and sintering during the heat-treatment process required for the L10 ordering. The chemically ordered L10-phase FePt can be obtained after annealing at 700 °C for 60 min in atmosphere containing H2. The effect of the pH value of MgO collosol and FePt nanocrystal loading amount on the structure, morphology, and magnetic properties of FePt/MgO nanocomposites has been investigated. The neutral pH value of 7 in MgO sol is beneficial to stabilize FePt NPs and obtain higher chemical ordering parameter S for the face-centered tetragonal -FePt/MgO nanocomposites with larger coercivity. The FePt NPs loading amount also plays a key role in tuning the microstructure and magnetic properties of the nanocomposites. The relatively higher FePt NPs loading with FePt/MgO molar ratio (RFM) of 1:2 leads to relatively perfect hexagonal assembly and pure L10 phase. When the RFM is 1:5 and 1:10, the MgO-matrix in nanocomposites causes the Fe element loss in FePt NPs along with formation of secondary phases such as magnesioferrite or Pt3Fe during the annealing process. Under optimal processing of neutral pH value of 7 and RFM of 1:2, the presence of MgO matrix produces more homogeneous microstructures and better magnetic properties with higher room-temperature coercivity (H C = 4.65 kOe).

Assessing De Novo transcriptome assembly metrics for consistency and utility

BackgroundTranscriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality.ResultsWe simulated sequencing transcripts of Drosophila melanogaster. By assembling these simulated reads using both a “perfect” and a modern transcriptome assembler while varying read length and sequencing depth, we evaluated quality metrics to determine whether they 1) revealed perfect assemblies to be of higher quality, and 2) revealed perfect assemblies to be more complete as data quantity increased.Several commonly used metrics were not consistent with these expectations, including average contig coverage and length, though they became consistent when singletons were included in the analysis. We found several annotation-based metrics to be consistent and informative, including contig reciprocal best hit count and contig unique annotation count. Finally, we evaluated a number of novel metrics such as reverse annotation count, contig collapse factor, and the ortholog hit ratio, discovering that each assess assembly quality in unique ways.ConclusionsAlthough much attention has been given to transcriptome assembly, little research has focused on determining how best to evaluate assemblies, particularly in light of the variety of options available for read length and sequencing depth. Our results provide an important review of these metrics and give researchers tools to produce the highest quality transcriptome assemblies.

Self‐assembly in additive manufacturing: opportunities and obstacles

PurposeAdditive manufacturing (AM) offers substantial flexibility in shape, but much less flexibility in materials and functionality – particularly at small size scales. A system for automatically incorporating microscale components would enable the fabrication of objects with more functionality. The purpose of this paper is to consider the potential of self‐assembly to serve as an automated programmable integration method. In particular, it addresses the ability of random self‐assembly processes to successfully assemble objects with high performance despite the possibility of assembly errors.Design/methodology/approachA self‐assembled thermoelectric system is taken as a sample system. The performance expectations for these systems are then predicted using modified one‐dimensional models that incorporate the effects of random errors. Monte‐Carlo simulation is used to predict the likely performance of self‐assembled thermoelectric systems and evaluate the impact of key process and system design parameters.FindingsWhile assembly yield can drop quickly with increasing numbers of assembled parts, large functional assemblies can be constructed by arranging components in parallel to provide redundancy. In some cases, the performance losses are minimal. Alternatively, sensing can be incorporated to identify perfect assemblies. For small assemblies, the probability of perfection may be high enough to achieve an acceptable assembly rate. Small assemblies could then be combined into larger functional systems.Originality/valueThe paper identifies two strategies that can guide the development of AM processes that incorporate miniature components to increase the system functionality. The analysis shows that this may be possible despite significant errors in the self‐assembly process because systems may be tolerant of significant assembly errors.

Complete genomic sequence analysis of the temperate bacteriophage phiSASD1 of Streptomyces avermitilis

The bacteriophage phiSASD1, isolated from a failed industrial avermectin fermentation, belongs to the Siphoviridae family. Its four predominant structural proteins, which include the major capsid, portal and two tail-related proteins, were separated and identified by SDS-PAGE and N-terminal sequence analysis. The entire double-stranded DNA genome of phiSASD1 consists of 37,068 bp, with 3'-protruding cohesive ends of nine nucleotides. Putative biological functions have been assigned to 24 of the 43 potential open reading frames. Comparative analysis shows perfect assembly of three "core" gene modules: the morphogenesis and head module, the tail module and the right arm gene module, which displays obvious similarity to the right arm genes of Streptomyces phage phiC31 in function and arrangement. Meanwhile, structural module flexibility within phiSASD1 suggests that assignment of phage taxonomy based on comparative genomics of structural genes will be more complex than expected due to the exchangeability of functional genetic elements.

A MATHEMATICAL MODEL FOR A PSEUDO-PLASTIC WELDING JOINT

An elementary situation in welding involves the perfect assembly of two adherents and a strong adhesive occupying a thin layer. The bulk energy density of the hyperelastic adherents grows superlinearly while that of the pseudo-plastic adhesive grows linearly with a stiffness of the order of the inverse of its thickness ε. We propose a simplified but accurate model by studying the asymptotic behavior, when ε goes to zero, through variational convergence methods: at the limit, the intermediate layer is replaced by a pseudo-plastic interface which allows cracks to appear.

Growing applications of "click chemistry" for bioconjugation in contemporary biomedical research.

This update summarizes the growing application of "click" chemistry in diverse areas such as bioconjugation, drug discovery, materials science, and radiochemistry. This update also discusses click chemistry reactions that proceed rapidly with high selectivity, specificity, and yield. Two important characteristics make click chemistry so attractive for assembling compounds, reagents, and biomolecules for preclinical and clinical applications. First, click reactions are bio-orthogonal; neither the reactants nor their product's functional groups interact with functionalized biomolecules. Second, the reactions proceed with ease under mild nontoxic conditions, such as at room temperature and, usually, in water. The copper-catalyzed Huisgen cycloaddition, azide-alkyne [3 + 2] dipolar cycloaddition, Staudinger ligation, and azide-phosphine ligation each possess these unique qualities. These reactions can be used to modify one cellular component while leaving others unharmed or untouched. Click chemistry has found increasing applications in all aspects of drug discovery in medicinal chemistry, such as for generating lead compounds through combinatorial methods. Bioconjugation via click chemistry is rigorously employed in proteomics and nucleic research. In radiochemistry, selective radiolabeling of biomolecules in cells and living organisms for imaging and therapy has been realized by this technology. Bifunctional chelating agents for several radionuclides useful for positron emission tomography and single-photon emission computed tomography imaging have also been prepared by using click chemistry. This review concludes that click chemistry is not the perfect conjugation and assembly technology for all applications, but provides a powerful, attractive alternative to conventional chemistry. This chemistry has proven itself to be superior in satisfying many criteria (e.g., biocompatibility, selectivity, yield, stereospecificity, and so forth); thus, one can expect it will consequently become a more routine strategy in the near future for a wide range of applications.