Hierarchical Assembly Process Research Articles

Cross-catenation between position-isomeric metallacages

The study of cross-catenated metallacages, which are complex self-assembly systems arising from multiple supramolecular interactions and hierarchical assembly processes, is currently lacking but could provide facile insights into achieving more precise control over low-symmetry/high-complexity hierarchical assembly systems. Here, we report a cross-catenane formed between two position-isomeric Pt(II) metallacages in the solid state. These two metallacages formed [2]catenanes in solution, whereas a 1:1 mixture selectively formed a cross-catenane in crystals. Varied temperature nuclear magnetic resonance experiments and time-of-flight mass spectra are employed to characterize the cross-catenation in solutions, and the dynamic library of [2]catenanes are shown. Additionally, we searched for the global-minimum structures of three [2]catenanes and re-optimized the low-lying structures using density functional theory calculations. Our results suggest that the binding energy of cross-catenanes is significantly larger than that of self-catenanes within the dynamic library, and the selectivity in crystallization of cross-catenanes is thermodynamic. This study presents a cross-catenated assembly from different metallacages, which may provide a facile insight for the development of low-symmetry/high-complexity self-assemble systems.

Monitoring Hierarchical Assembly of Ring-in-Ring and Russian Doll Complexes Based on Carbon Nanoring by Förster Resonance Energy Transfer.

We presented the construction of the ring-in-ring and Russian doll complexes on the basis of triptycene-derived carbon nanoring (TP-[12]CPP), which not only acts as a host for pillar[5]arene (P5A) but also serves as an energy donor for building Förster resonance energy transfer (FRET) systems. We also demonstrated that their hierarchical assembly processes could be efficiently monitored in real time using FRET. NMR, UV-vis and fluorescence, and mass spectroscopy analyses confirmed the successful encapsulation of the guests P5A/P5A-An by TP-[12]CPP, facilitated by C-H···π and ···π interactions, resulting in the formation of a distinct ring-in-ring complex with a binding constant of Ka = 2.23 × 104 M-1. The encapsulated P5A/P5A-An can further reverse its role to be a host for binding energy acceptors to form Russian doll complexes, as evidenced by the occurrence of FRET and mass spectroscopy analyses. The apparent binding constant of the Russian doll complexes was up to 3.6 × 104 M-1, thereby suggesting an enhanced synergistic effect. Importantly, the Russian doll complexes exhibited both intriguing one-step and sequential FRET dependent on the subcomponent P5A/P5A-An during hierarchical assembly, reminiscent of the structure and energy transfer of the light-harvesting system presented in purple bacteria.

Effect of low-mass galaxy interactions on their star formation

According to the Λ cold dark matter model of galaxy formation, the hierarchical assembly process is scale-free and interactions between galaxies in all mass ranges are expected. The effects of interactions between dwarf galaxies on their evolution are not well understood. In this study, we aim to understand the effect of low-mass galaxy interactions on their star formation rate (SFR). We estimated the SFR of 22 interacting and 36 single gas-rich dwarf galaxies in the Lynx-Cancer void region using their far-ultraviolet (FUV) images from the GALEX mission. We find an enhancement in SFR by a factor of 3.4 ± 1.2 for interacting systems compared to single dwarf galaxies in the stellar mass range of 107–108 M⊙. Our results indicate that dwarf–dwarf galaxy interactions can lead to an enhancement in their SFR. These observations are similar to the predictions based on the simulations of dwarf galaxies at lower redshifts. Future deeper and higher-spatial-resolution UV studies will help us to understand the effect of dwarf galaxy interactions on the spatial distribution of star forming clumps and to identify star formation in tidal tails.

Whole-Genome Sequence and Pathogenicity Analysis of Providencia Heimbachae Causing Diarrhea in Weaned Piglets.

Providencia heimbachae was previously identified in piglets with post-weaned diarrhea and associated with hindlimb paralysis. However, the pathogenic mechanisms and virulence factors of P. heimbachae are not fully known. Whole-genome sequence analysis will be helpful to extend our understanding of the characterization of P. heimbachae at a genomic level. In this study, we sequenced the whole genome of P. heimbachae for the first time using PacBio RS II sequencers and assembled de novo through hierarchical genome assembly process (HGAP). Furthermore, we performed further genome annotation. The genome of P. heimbachae 99101 consists of a circular chromosome (4,262,828bp) and a circular plasmid (231,957bp) with G + C contents of 40.43 and 47.16%, respectively. Genome-wide sequence analysis yielded a total of 286 predicted virulence factors, 178 resistance genes, 17 chaperone protein manipulators of fimbriae, 47 genes involved in the encoding of flagellin, 12 cell membrane-associated virulence genes, 18 Enterobacteriaceae common antigens, etc. Based on genome analysis, we preliminarily confirmed through animal experiments that the capsule was the virulence factor of P. heimbachae causing hindlimb paralysis in animals. Our study provides a genetic basis for further elucidation of the characteristics and functional mechanisms of P. heimbachae as a conditionally pathogenic bacterium, as well as a direction for research into the mechanism of action of P. heimbachae infecting humans, extending knowledge of P. heimbachae as an important zoonotic pathogen.

GreenGate 2.0: Backwards compatible addons for assembly of complex transcriptional units and their stacking with GreenGate.

Molecular cloning is a crucial technique in genetic engineering that enables the precise design of synthetic transcriptional units (TUs) and the manipulation of genomes. GreenGate and several other modular molecular cloning systems were developed about ten years ago and are widely used in plant research. All these systems define grammars for assembling transcriptional units from building blocks, cloned as Level 0 modules flanked by four-base pair overhangs and recognition sites for a particular Type IIs endonuclease. Modules are efficiently assembled into Level 1 TUs in a hierarchical assembly process, and Level 2 multigene constructs are assembled by stacking Level 1 TUs. GreenGate is highly popular but has three main limitations. First, using ad-hoc overhangs added by PCR and classical restriction/ligation prevents the efficient use of a one-pot, one-step reaction to generate entry clones and domesticate internal sites; second, a Level 1 TU is assembled from a maximum of six modules, which may be limiting for applications such as multiplex genome editing; third, the generation of Level 2 assemblies is sequential and inefficient. GreenGate 2.0 (GG2.0) expands GreenGate features. It introduces additional overhangs, allowing for the combination of up to 12 Level 0 modules in a Level 1 TU. It includes a Universal Entry Generator plasmid (pUEG) to streamline the generation of Level 0 modules. GG2.0 introduces GreenBraid, a convenient method for stacking transcriptional units iteratively for multigene assemblies. Importantly, GG2.0 is backwards compatible with most existing GreenGate modules. Additionally, GG2.0 includes Level 0 modules for multiplex expression of guide RNAs for CRISPR/Cas9 genome editing and pre-assembled Level 1 vectors for dexamethasone-inducible gene expression and ubiquitous expression of plasma membrane and nuclear fluorescent markers. GG2.0 streamlines and increases the versatility of assembling complex transcriptional units and their combination.

Draft genome sequence and probiotic functional property analysis of Lactobacillus gasseri LM1065 for food industry applications

Probiotics are defined as live organisms in the host that contribute to health benefits. Lactobacillus gasseri LM1065, isolated from human breast milk, was investigated for its probiotic properties based on its genome. Draft genome map and de novo assembly were performed using the PacBio RS II system and hierarchical genome assembly process (HGAP). Probiotic properties were determined by the resistance to gastric conditions, adherence ability, enzyme production, safety assessment and mobile genetic elements. The fungistatic effect and inhibition of hyphae transition were studied using the cell-free supernatant (CFS). L. gasseri LM1065 showed high gastric pepsin tolerance and mild tolerance to bile salts. Auto-aggregation and hydrophobicity were measured to be 61.21% and 61.55%, respectively. The adherence to the human intestinal epithelial cells was measured to be 2.02%. Antibiotic-resistance genes and putative virulence genes were not predicted in the genomic analysis, and antibiotic susceptibility was satisfied by the criteria of the European Food Safety Authority. CFS showed a fungistatic effect and suppressed the tricarboxylic acid cycle in Candida albicans (29.02%). CFS also inhibited the transition to true hyphae and damaged the blastoconidia. This study demonstrates the essential properties of this novel probiotic, L. gasseri LM1065, and potential to inhibit vaginal C. albicans infection.

Keto-form directed hierarchical chiral self-assembly of Schiff base derivatives with amplified circularly polarized luminescence

While enol-keto tautomerism has attracted great interest in Schiff bases and related compounds in solution and crystal states, the self-assembly of energy-unfavored keto form were scarcely investigated. Here, we report a keto-form directed self-assembly of a naphthalene-attached enantiomeric N-salicylideneanil analog L/DGG-Nap accompanied with a significantly amplified circularly polarized luminescence (CPL). It was found that LGG-Nap exists as a mixture of enol and keto form in monomer at a diluted toluene solution. The increment of the concentrations leads to the formation of predominated keto form, which subsequently triggers the self-assembly. Cryo-transmission electron microscopy (Cryo-TEM) revealed that a hierarchical assembly process happened upon increasing the concentration of LGG-Nap in toluene. Individual nanofibers formed at 1 × 10−4 mol/L and transferred into helical nanofiber bundles in 5 × 10−3 mol/L. Interestingly, while these is nearly no circular dichroism (CD) or CPL in the monomeric solution, the assembly showed strong CD and CPL. Remarkably, the dissymmetry factor (glum) was significantly amplified from zero in solution through the 0.005 in individual nanofiber to 0.1 in nanofiber bundles. This work demonstrates that the enol-keto tautomerism can be broken and trigger the self-assembly upon increasing the concentration, which can subsequently direct the chiral self-assembly and significantly amplify the dissymmetry factor of assembled CPL materials.

Self-Assembly of the Tetraphenylethylene-Capped Diserine through a Hierarchical Assembly Process.

We report a new peptide-based urchin-shaped structure prepared through two-step self-assembly of tetraphenylethylene-diserine (TPE-SS). Hydrogelation generated nanobelts through the first stage of self-assembly of TPE-SS; these nanobelts further transformed on silicon wafers into urchin-like microstructures featuring nanosized spines. The presence of the TPE moiety in the hydrogelator resulted in aggregation-induced emission characteristics both in the solution and in the gel phases. TPE-SS has the lowest molecular weight of any TPE-capped hydrogelator with β-sheet-like structures under physiological pH. This new design strategy appears to be useful for generating three-dimensional self-assembled microstructures and multifunctional biomaterials. We found that TPE-SS is biocompatible with human mesenchymal stem cells and breast cancer cells, making them potential applications in tissue engineering and biomedical research.

Liquid to solid transition of elastin condensates

Liquid-liquid phase separation of tropoelastin has long been considered to be an important early step in the complex process of elastin fiber assembly in the body and has inspired the development of elastin-like peptides with a wide range of industrial and biomedical applications. Despite decades of study, the material state of the condensed liquid phase of elastin and its subsequent maturation remain poorly understood. Here, using a model minielastin that mimics the alternating domain structure of full-length tropoelastin, we examine the elastin liquid phase. We combine differential interference contrast (DIC), fluorescence, and scanning electron microscopy with particle-tracking microrheology to resolve the material transition occurring within elastin liquids over time in the absence of exogenous cross-linking. We find that this transition is accompanied by an intermediate stage marked by the coexistence of insoluble solid and dynamic liquid phases giving rise to significant spatial heterogeneities in material properties. We further demonstrate that varying the length of the terminal hydrophobic domains of minielastins can tune the maturation process. This work not only resolves an important step in the hierarchical assembly process of elastogenesis but further contributes mechanistic insight into the diverse repertoire of protein condensate maturation pathways with emerging importance across biology.

Complete Genome Sequence of Vibrio maritimus BH16, a Siderophore-Producing Mutualistic Bacterium Isolated from Diatom Skeletonema costatum.

Complete Genome Sequence of Vibrio maritimus BH16, a Siderophore-Producing Mutualistic Bacterium Isolated from Diatom Skeletonema costatum.

Recent Development of Macrocyclic Compounds as Potential Tool for Cancer Therapy and Diagnosis: A Mini-Review

Macrocyclic compounds can be easily sustained into varied functionality, which has recently famed them as an individual supramolecular entity. Owing to their tenable non-covalent interactions or dynamic covalent bonding, these macrocyclic formulations have contemporaneously inhibited and controlled the progression of infectious diseases and cancers. Macrocyclic supramolecular assemblies have been fabricated for staging the medicinal accuracy of different therapies as well as diagnostic pathways. This mini-review, therefore, focuses on the design of a hierarchical assembly process at the molecular level of chemical composition and presents interesting illustrations of supramolecular assembled structural motifs as new cancer diagnostic and therapeutic options.

Morphology Control of Multicompartment Micelles in Water through Hierarchical Self-Assembly of Amphiphilic Terpolymers

Multicompartment micelles (MCMs) allow the simultaneous storage of multiple cargoes such as dyes, catalysts, or drugs, and have therefore gained attention in catalysis, nanotechnology, and nanomedicine. In the present work, we describe design rules to control the morphology of MCMs in water including spheres, cylinders, sheets, and vesicles. For that, we synthesized a series of poly(ethylene oxide) (PEO)-b-polystyrene (PS)-b-poly(methyl acrylate) (PMA) triblock terpolymers and systematically varied the length of the PS and PMA block. Using a stepwise hierarchical assembly process, we first form patchy precursor micelles in organic solvent with PS core and mixed PEO/PMA corona. In the second step, these micelles act as subunits, which assemble (or cluster) in water into MCMs, where PEO forms the stabilizing corona, PS the compartment, and PMA the inner core. We find that the shape of the final MCM can be predicted by ascribing a Janus balance to precursor micelles as the molar ratio of PEO to PMA, which provides a synthetic handle to target specific MCM morphologies.

Co-assembly of a multicomponent network of nanofiber-wrapped nanotubes.

Strategies to create organized multicomponent nanostructures composed of discrete, self-sorted domains are important for developing materials that mimic the complexity and multifunctionality found in biological systems. These structures can be challenging to achieve due to the required balance of molecular self-recognition and supramolecular attraction needed between the components. Herein, we report a strategy to construct a two-component nanostructure via a hierarchical assembly process whereby two monomeric building blocks undergo self-sorting assembly at the molecular level followed by a supramolecular association to form a nanofiber-wrapped nanotube. The two molecules self-sorted into respective nanofiber and nanotube assemblies, yet assembly of the nanofibers in the presence of the nanotube template allowed for directed integration into a hierarchical multilayer structure via electrostatic interactions. The fiber-wrapped nanotube co-assembly was characterized using transmission electron microscopy (TEM), atomic force microscopy (AFM) and Förster resonance energy transfer (FRET) between the components. Strategies to co-assemble multicomponent nanostructures composed of discrete, spatially sorted domains with controllable higher level interactions will be critical for the development of novel, functionally competent nanomaterials.

Revealing the formation mechanism and band gap tuning of Sb2S3 nanoparticles.

Sb2S3 is a promising nanomaterial for application in solar cells and in the fields of electronics and optoelectronics. Herein, Sb2S3 nanoparticles were prepared via the hot-injection approach. In contrast to earlier work, the reaction temperature was decreased to 150 °C so that the reaction was slowed down and could be stopped at defined reaction stages. Thereby, the formation mechanism of the nanomaterial and the associated kinetics could be revealed. Based on morphological and structural analyses, it is suggested that seed particles (type 0) formed immediately after injecting the antimony precursor into the sulfur precursor. These seeds fused to form amorphous nanoparticles (type I) that contained a lower percentage of sulfur than that corresponding to the expected stoichiometric ratio of Sb2S3. The reason for this possibly lies in the formation of an oxygen- or carbon-containing intermediate during the seeding process. Afterward, the type I nanoparticles aggregated into larger amorphous nanoparticles (type II) in a second hierarchical assembly process and formed superordinate structures (type III). This process was followed by the crystallization of these particles and a layer-like growth of the crystalline particles by an Ostwald ripening process at the expense of the amorphous particles. It was demonstrated that the kinetic control of the reaction allowed tuning of the optical band gap of the amorphous nanoparticles in the range of 2.2–2.0 eV. On the contrary, the optical band gap of the crystalline particles decreased to a value of 1.7 eV and remained constant when the reaction progressed. Based on the proposed formation mechanism, future syntheses for Sb2S3 particles can be developed, allowing tuning of the particle properties in a broad range. In this way, the selective use of this material in a wide range of applications will become possible.

Antibiotic Biosynthesis Pathways from Endophytic Streptomyces SUK 48 through Metabolomics and Genomics Approaches.

Streptomyces sp. has been known to be a major antibiotic producer since the 1940s. As the number of cases related to resistance pathogens infection increases yearly, discovering the biosynthesis pathways of antibiotic has become important. In this study, we present the streamline of a project report summary; the genome data and metabolome data of newly isolated Streptomyces SUK 48 strain are also analyzed. The antibacterial activity of its crude extract is also determined. To obtain genome data, the genomic DNA of SUK 48 was extracted using a commercial kit (Promega) and sent for sequencing (Pac Biosciences technology platform, Menlo Park, CA, USA). The raw data were assembled and polished using Hierarchical Genome Assembly Process 4.0 (HGAP 4.0). The assembled data were structurally predicted using tRNAscan-SE and rnammer. Then, the data were analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG) database and antiSMASH analysis. Meanwhile, the metabolite profile of SUK 48 was determined using liquid chromatography-mass spectrophotometry (LC-MS) for both negative and positive modes. The results showed that the presence of kanamycin and gentamicin, as well as the other 11 antibiotics. Nevertheless, the biosynthesis pathways of aurantioclavine were also found. The cytotoxicity activity showed IC50 value was at 0.35 ± 1.35 mg/mL on the cell viability of HEK 293. In conclusion, Streptomyces sp. SUK 48 has proven to be a non-toxic antibiotic producer such as auranticlavine and gentamicin.

Genome based phylogeny and virulence factor analysis of mastitis causing Escherichia coli isolated from Indian cattle

Mastitis is a highly infectious disease prevalent in dairy cattle and it is majorly caused by Escherichia coli (E. coli). The objective of present study is to investigate the occurrence of virulence genes, antimicrobial susceptibility and comparative analysis of E. coli (IVRI KOL CP4 and CM IVRI KOL-1) isolates from mastitis infected animal. Whole-genome sequencing (WGS) was performed using a PacBio RS II system and de novo assembled using Hierarchical Genome Assembly Process (HGAP3). Bacterial Pan Genome Analysis Pipeline (BPGA) was used for pangenome analysis. A set of 50 E. coli isolates were used for comparative analysis (48 collected from the database and 2 reference sequences). Core genes were further concatenated for phylogenetic analyses. In silico analysis was performed for antibiotic resistance and virulence gene identification. Both of the E. coli isolates carried many resistance genes including, b-lactamase, quinolones, rifampicin, macrolide, aminoglycoside and phenicols resistance. We detected 39 virulence genes in IVRI KOL CP4 and 52 in CM IVRI KOL-1 which include toxins, adhesions, invasins, secretion machineries or iron acquisition system. High prevalence of mastitis strains belongs to phylogroups A, although few isolates were also assigned to phylogenetic groups B1 and B2. In conclusion, the present study reported the presence of genes involved in Adherence, Iron acquisition, secretion system and toxins which shown to be crucial in MPEC pathogenicity. This is the first whole genome analysis of MPEC strains to be carried out in Indian isolate to highlights the spread of resistance and virulence genes in food animals.

Genomic insights into a complete deletion of the mgrB locus in colistin-resistant Klebsiella pneumoniae ST2268 isolated from a human infection

The emergence of colistin-resistant Klebsiella pneumoniae (CoRKp) is a serious public-health issue as colistin is the last line of defence against infections caused by multidrug-resistant Gram-negative bacteria. In this study, we generated a draft genome sequence for CoRKp strain P094-1 isolated from a sputum sample of an infected patient. Whole genomic DNA of strain P094-1 was sequenced using a PacBio sequencing platform. Generated reads were de novo assembled using Hierarchical Genome Assembly Process (HGAP) v.3.0. Colistin resistance-related genes were predicted from the genome sequence and were validated experimentally. The genome of strain P094-1 lacked a 20.3-kb region, including complete deletion of the mgrB gene. Molecular and genome sequencing-based analyses revealed that the observed colistin resistance of P094-1 could not be attributed to plasmid-borne genes mcr-1 to mcr-9 or to alteration of the pmr and pho operons (deletions, insertions or substitutions), but was conferred by an insertion sequence 1 (IS1)-induced total deletion of mgrB. This is the first reported whole-genome sequence of an unusual CoRKp isolate containing an IS1-induced deletion of mgrB.

Spectroscopic Constraints on the Buildup of Intracluster Light in the Coma Cluster

Abstract The stellar content of the intracluster light (ICL) provides unique insight into the hierarchical assembly process of galaxy clusters. We present optical spectra of three ICL regions (μ g ≈ 25.3–26.2 mag arcsec−2) in the Coma cluster, located between 100 and 180 kpc from their nearest brightest cluster galaxies (BCGs): NGC 4889 and NGC 4874. Integral-field unit (IFU) spectroscopy with 13.5 hr on-source integration was acquired in an ancillary program within the Sloan Digital Sky Survey-IV MaNGA survey. We stacked the 127 individual fiber spectra in each IFU to achieve a 1σ limiting surface brightness of 27.9 mag arcsec−2, corresponding to a mean signal-to-noise ratio in the optical of 21.7, 9.0, and 11.7 Å−1, for each ICL region. We apply stellar population models to the stacked spectra. Our results show that the velocity dispersions of ICL regions are very high (σ ∼ 630 km s−1), indicating the stars in these regions are tracing the gravitational potential of the cluster, instead of any individual galaxy. The line-of-sight velocities are different from each other by ∼700 km s−1, while the velocity of each region is similar to the closest BCG. This suggests that the ICL regions are associated with two distinct subclusters centered on NGC 4889 and NGC 4874. The stellar populations of these regions are old and metal-poor, with ages of , , and Gyr, and [Fe/H] of , , and . From the derived age and metallicity, the buildup of ICL in Coma is likely to be through the accretion of low-mass galaxies or the tidal stripping of the outskirts of massive galaxies that have ended their star formation early on, instead of directly from major mergers of massive galaxies.

Supramolecular Organic Frameworks with Controllable Shape and Aggregation‐Induced Emission for Tunable Luminescent Materials through Aqueous Host–Guest Complexation

AbstractHere, a series of shape‐controllable and fluorescent supramolecular organic frameworks (SOFs) exhibiting aggregation‐induced emission (AIE) are reported as a new kind of tunable luminescent material, constructed hierarchically from fluorescent guests (1–5) and cucurbit[8]uril (CB[8]) through homo/hetero host–guest complexation in water. These SOFs can further form regular supramolecular cuboids via a hierarchical assembly process in the solid state. Interestingly, the emission of hetero‐SOFs systems exhibiting AIE, which are a combination of two or three SOFs with two complementary colors (i.e., yellow and blue) or three primary RGB colors (red, green, and blue) through the hetero host–guest complexation between CB[8] and two pyridinium rings of different guests, can be easily tuned by adjusting the excitation wavelength and guests ratios, thereby achieving a wide‐color tunability (≈64% sRGB area) and white‐light emission (0.31, 0.34) in the solution state. This study therefore provides insight into the fabrication of tunable luminescent materials based on SOFs with controllable shapes and AIE properties as fluorescent platforms, and may facilitate the further design and synthesis of tunable luminescent materials and other fluorescent supramolecular systems based on host–guest complexation both in the solution and solid states.

Cell-Based Interaction Analysis of ADAMTS Proteases and ADAMTS-Like Proteins with Fibrillin Microfibrils.

The extracellular matrix (ECM) is a composite biomaterial that serves as an anchor for cells and provides guidance cues for cell migration, proliferation, and differentiation. However, many details of the hierarchical ECM assembly process and the role of individual protein-protein interactions are not well understood. Here, I describe a cell-culture-based method that allows for determination of the ECM localization of recombinant ADAMTS proteases and ADAMTS-like (L) proteins in relationship to fibrillin microfibrils deposited by human dermal fibroblasts. The method can be readily adapted to study the localization of ECM components other than ADAMTS and ADAMTSL proteins to fibrillin microfibrils and other ECM networks.