Reassembly Of Fragments Research Articles

Synthesis of Diarylpyrrole Pseudo-Natural Products: Cyanide-Mediated Nitrile-to-Nitrile Cyclocondensation and C–H Acidity-Guided Regioselectivity

AbstractPseudo-natural products (pseudo-NPs), the chemically reengineered molecular skeletons generated by the deconstruction of NPs into fragments and their subsequent recombination, have gained immense attention in recent times owing to their ability to occupy a significant portion of the medicinally relevant NP-based molecular space, their possession of novel bioactivities, and their ability to address chemical and biological challenges. In this study, the reassembly of fragments of combretastatin, steganacin, podophyllotoxin, colchicine, and other natural products and drug molecules by a cis-lock fusion-edge recombination led to the generation of diarylpyrrole pseudo-NP-functionalized skeletons, named combretapyrroles. These combretapyrroles were synthesized with excellent substrate scope in good yields by a new cyanide-mediated nitrile-to-nitrile cycloaddition reaction of a vic-dinitrile combined with 1,1,3,3-tetramethylguanidine-mediated desilylative cleavage of TMSCN and in situ generation of cyanide. The differential acidity of the benzylic C–H moieties of the vic-dinitrile intermediate was found to influence regioselectivity in the mechanistic pathway and to provide different products. A cheminformatic analysis showed that the combretapyrroles occupy a unique drug-relevant chemical space that is rarely covered by NPs. Combretapyrroles also were found to possess drug-like physicochemical properties.

Targeted therapies of inflammatory diseases with intracellularly gelated macrophages in mice and rats

Membrane-camouflaged nanomedicines often suffer from reduced efficacy caused by membrane protein disintegration and spatial disorder caused by separation and reassembly of membrane fragments during the coating process. Here we show that intracellularly gelated macrophages (GMs) preserve cell membrane structures, including protein content, integration and fluidity, as well as the membrane lipid order. Consequently, in our testing GMs act as cellular sponges to efficiently neutralize various inflammatory cytokines via receptor-ligand interactions, and serve as immune cell-like carriers to selectively bind inflammatory cells in culture medium, even under a flow condition. In a rat model of collagen-induced arthritis, GMs alleviate the joint injury, and suppress the overall arthritis severity. Upon intravenous injection, GMs efficiently accumulate in the inflammatory lungs of acute pneumonia mice for anti-inflammatory therapy. Conveniently, GMs are amenable to lyophilization and can be stored at ambient temperatures for at least 1 month without loss of integrity and bio-activity. This intracellular gelation technology provides a universal platform for targeted inflammation neutralization treatment.

3D-print as a template for reassembly of skull fragments in a homicide case

In this technical note we report a case where 3D-printing aided the reassembly of skull fragments in a homicide with severe tampering of the bones. A young male was shot, the body was incinerated and crushed with garden tools resulting in hundreds of brittle, calcine bone fragments from the skull. An antemortem computed tomography (CT)-scan of the skull was available from a previous assault of the victim. To aid the process of reassembly we used the antemortem CT-data to develop a 3D fixture-grid of the cranial cavity. The 3D grid was utilized as an anatomically correct template for bone reconstruction. This novel technique was based solely on open-source software including 3D Slicer and Blender and could have the potential to aid similar cases.

Ryugu’s Anhydrous Ingredients and Their Spectral Link to Primitive Dust from the Outer Solar System

Ryugu is a second-generation C-type asteroid formed by the reassembly of fragments of a previous larger body in the main asteroid belt. While the majority of Ryugu samples returned by Hayabusa2 are composed of a lithology dominated by aqueously altered minerals, clasts of pristine olivine and pyroxene remain in the least-altered lithologies. These clasts are objects of great interest for revealing the composition of the dust from which the original building blocks of Ryugu's parent asteroid formed. Here we show that some grains rich in olivine, pyroxene, and amorphous silicates discovered in one millimeter-sized stone of Ryugu have infrared spectra similar to the D-type asteroid Hektor (a Jupiter Trojan), to comet Hale–Bopp, and to some anhydrous interplanetary dust particles of probable cometary origin. This result indicates that Ryugu's primary parent body incorporated anhydrous ingredients similar to the building blocks of asteroids (and possibly some comets) formed in the outer solar system, and that Ryugu retained valuable information on the formation and evolution of planetesimals at different epochs of our solar system's history.

Mitotic clustering of pulverized chromosomes from micronuclei

Complex genome rearrangements can be generated by the catastrophic pulverization of missegregated chromosomes trapped within micronuclei through a process known as chromothripsis1–5. As each chromosome contains a single centromere, it remains unclear how acentric fragments derived from shattered chromosomes are inherited between daughter cells during mitosis6. Here we tracked micronucleated chromosomes with live-cell imaging and show that acentric fragments cluster in close spatial proximity throughout mitosis for asymmetric inheritance by a single daughter cell. Mechanistically, the CIP2A–TOPBP1 complex prematurely associates with DNA lesions within ruptured micronuclei during interphase, which poises pulverized chromosomes for clustering upon mitotic entry. Inactivation of CIP2A–TOPBP1 caused acentric fragments to disperse throughout the mitotic cytoplasm, stochastically partition into the nucleus of both daughter cells and aberrantly misaccumulate as cytoplasmic DNA. Mitotic clustering facilitates the reassembly of acentric fragments into rearranged chromosomes lacking the extensive DNA copy-number losses that are characteristic of canonical chromothripsis. Comprehensive analysis of pan-cancer genomes revealed clusters of DNA copy-number-neutral rearrangements—termed balanced chromothripsis—across diverse tumour types resulting in the acquisition of known cancer driver events. Thus, distinct patterns of chromothripsis can be explained by the spatial clustering of pulverized chromosomes from micronuclei.

An Automatic Chinaware Fragments Reassembly Method Framework Based on Linear Feature of Fracture Surface Contour

For Chinaware fragments, it is difficult to assemble them directly without considering the wonderful patterns painted on them. Given the simplicity of the Chinaware designs, each object contains similar textures and patterns. Compared to the oddly diverse appliance modeling, the difference between fragments of different Chinaware is small. The fragments are small and the fracture is flat, and there are many potential matching objects. For the Chinaware fragments’ reassembly, most of the work is still done manually. There is little available fully automatic reassembly work, and these approaches are for the reassembly of a single Chinaware. But what reality demands is the reassembly of the multi-Chinaware. Therefore, this article proposes an automatic method, whose strategy is analogous to the manual assembly, to accomplish this complex task. First, segment the contours of fracture surfaces of the fragments by the geometric feature of fracture edge; then, the contours are matched using our proposed multi-scale linear feature descriptor; given the massive fragments of multiple objects, we use the inaccurate matching strategy to build a matching set for each fracture surface contour and perform contour matching in this set. In this article, the fracture surface is segmented using the 2D slope information on the fragment edge. The descriptor proposed in the article uses distance triangle towers and chained angles to describe the “undulations” of the fracture surface. Moreover, the article uses a strict absolute-advantage-principle to reject false matching. In addition, after the initial reconstruction, we will iteratively adjust fragments according to the gap between the fragments to achieve better multi-fragment matching results. In this article, 18 porcelains, a total of 103 pieces, have been tested. Experiments are also carried out for special cases, including fragment reassembly with missing fragments and fragment reassembly with redundant fragments. The experimental results showed the effectiveness of method. However, the types of experimental data we currently have are relatively simple, and there is no way to reassemble the fragments in minutes. We hope to enable faster reassembly of more fragments in the future.

Small-Molecule-Mediated Split-Aptamer Assembly for Inducible CRISPR-dCas9 Transcription Activation.

Inducible CRISPR-dCas9 transcription system has become a powerful tool for transcription regulation and sensing. Here, we develop a new concept of small-molecule-mediated split-aptamer assembly for inducible CRISPR-dCas9 transcription activation, allowing quantitative detection and imaging of S-adenosyl methionine (SAM) in live cells. This inducible transcription system is designed by integrating one fragment of a split SAM aptamer to guide RNA (gRNA) and the other to MS2 arrays. SAM-mediated reassembly of the split fragments recruits an MCP-fused transcription activator to the gRNA-dCas9 complex, activating the expression of a near-infrared fluorescent protein for imaging. We demonstrate that this inducible transcription system achieves quantitative detection of SAM with high sensitivity in live cells. Our system shows that methionine adenosyltransferase 1A (MAT1A) and MAT2A can both catalyze SAM production in live cells and the SAM levels in cancer cells can be increased via upregulation of MAT1A mRNA by epigenetic inhibitors. This split-aptamer assembly strategy could afford a new approach for controlling the CRISPR-dCas9 system, enabling conditional transcription regulation in response to endogenous metabolites in live cells.

Combining cytogenetic and genomic technologies for deciphering challenging complex chromosomal rearrangements.

Complex chromosomal rearrangements (CCRs), a class of structural variants (SVs) involving more than two chromosome breaks, were classically thought to be extremely rare. As advanced technologies become more available, it has become apparent that CCRs are more common than formerly thought, and are a substantial cause of genetic disorders. We attempted a novel approach for solving the mechanism of challenging CCRs, which involve repetitive sequences, by precisely identifying sequence-level changes and their order. Chromosomal microarray (CMA) and FISH analyses were used for interpretation of SVs detected by whole exome sequencing (WES). Breakpoint junctions were analyzed by Nanopore sequencing, a novel long-read whole genome sequencing tool. A large deletion identified by WES, encompassing the FOXF1 enhancer, was the cause of alveolar capillary dysplasia and respiratory insufficiency, resulting in perinatal death. CMA analysis of the newborn's mother revealed two duplications encompassing the deleted region in theproband, raising our hypothesis that the deletion resulted from themother's CCR. Breakpoint junctions of complex SVs were determined at thenucleotide level using Nanopore long-read sequencing. According to sequencing results of breakpoint junctions, the CCR in the newborn was considered the consequence of at least one double-strand break during meiosis, and reassembly of DNA fragments by intra-chromosomal homologous recombination. Our comprehensive approach, combining cytogenetics and long-read sequencing, enabled delineation of the exact breakpoints in a challenging CCR, and proposal of a mechanism in which it arises. We suggest applying our integrative approach combining technologies for deciphering future challenging CCRs, enabling risk assessment in families.

RestArt method: innovative high-precision mechatronic-based procedure for fragmented stone statues restoration

Abstract The RestArt method is an innovative mechatronic-based procedure for high-precision reassembly of stone fragments intended to improve the restoration of ancient statues and architectural elements. The procedure comprises high-accuracy 3D laser scanning of two fragments positioned on the RestArt machine. After software simulated best-fitting of the two homologous fractured faces, the calculated roto-translation matrix is sent to the machine control system that moves one fragment to match the other one. The machine integrates a numeric-controlled moving drilling device for high-precision boring of the fractured surfaces at selected points for optimal rods insertion. This permits a very effective fixing of the fragments and allows multi-point fixing, which is practically impossible with conventional methods. Several stone specimens were experimentally recomposed through the RestArt and the traditional method. Then, they were compared in terms of mechanical resistance by shaking table tests, reproducing extreme strong-motion vibrations. The specimens recomposed through the RestArt method resulted less time-consuming and much more resistant to vibration excitation than the ones by traditional reassembly method. The RestArt method was applied to reassemble some original ancient statues currently exhibited at several Italian museums.

A Fragment Fracture Surface Segmentation Method Based on Learning of Local Geometric Features on Margins Used for Automatic Utensil Reassembly

To achieve the automatic reassembly (piecing) of utensil fragments, a fracture surface extraction method based on the learning of local geometric features (core focus) and a utensil reassembly method (secondary focus) are presented in this paper. The steps of the methodological framework are as follows. First, based on obtained 3D models of utensil fragments, a triangle cell descriptor is proposed to describe the geometric features of spatial neighborhoods. Second, a set of feature mapping images (FMIs) is established as a training dataset. Third, after labeling of the ground-truth data, a convolutional neural network (CNN) is trained using the FMIs. Fourth, based on processing to eliminate mislabeled triangle cells, skeletons of the fracture surface margins can be generated. Fifth, a shortcut-based strategy is proposed to eliminate residual triangle cells to extract the fracture surfaces. Sixth, a control-point- and vector-based strategy is proposed to achieve the matching and prealignment of the fracture surfaces. Finally, a cyclic error iteration strategy is designed to assemble the fragments into a holonomic utensil. This learning-based framework is more effective at extracting the key geometric data (fracture surfaces) of utensil fragments than several classical methods. It may also enable a new strategy for 3D graph processing.

3D object reassembly using region-pair-relation and balanced cluster tree

Background and ObjectiveObject reassembly is a key technology in scenarios such as surgical planning and broken object restoration. Based on previous research, this work intends to explore the general tasks of 3D object reassembly, including conventional object reconstruction and bone fracture reduction. MethodsWe introduce an efficient and robust region-pair-relation descriptor, which incorporates strong geometric constraints and remains invariant to rotation and translation. We segment the fractured objects using balanced cluster tree, and develop a coarse-to-fine method for object reassembly. The matching quality of potential region contact pairs at different depths is estimated recursively from the root of the tree. Once the best contact pairs are determined, the least squares method is implemented to obtain the matching results. In addition, we also provide a semi-interactive manipulation to deal with the complex objects. ResultsFor most types of broken objects, our approach can generate high accuracy matching results within 10 s, with the cluster tree depth equals to 11. It allows the automatic reassembly of different-sized fragments. For bone fracture blocks with cancellous structures, a semi-interactive operation is integrated so that the precise matching can also be achieved in 30 s. ConclusionThe proposed framework can be expanded to various object reassembly tasks in either automated or semi-automated manner, including the fracture reduction problem which used to be an intensive manual process. Therefore, our work shows significant advantages in medical applications.

Vimentin S-glutathionylation at Cys328 inhibits filament elongation and induces severing of mature filaments invitro.

Vimentin intermediate filaments are a significant component of the cytoskeleton in cells of mesenchymal origin. In vivo, filaments assemble and disassemble and thus participate in the dynamic processes of the cell. Post‐translational modifications (PTMs) such as protein phosphorylation regulate the multiphasic association of vimentin from soluble complexes to insoluble filaments and the reverse processes. The thiol side chain of the single vimentin cysteine at position 328 (Cys328) is a direct target of oxidative modifications inside cells. Here, we used atomic force microscopy, electron microscopy and a novel hydrogen–deuterium exchange mass spectrometry (HDex‐MS) procedure to investigate the structural consequences of S‐nitrosylation and S‐glutathionylation of Cys328 for in vitro oligomerisation of human vimentin. Neither modification affects the lateral association of tetramers to unit‐length filaments (ULF). However, S‐glutathionylation of Cys328 blocks the longitudinal assembly of ULF into extended filaments. S‐nitrosylation of Cys328 does not hinder but slows down the elongation. Likewise, S‐glutathionylation of preformed vimentin filaments causes their extensive fragmentation to smaller oligomeric species. Chemical reduction of the S‐glutathionylated Cys328 thiols induces reassembly of the small fragments into extended filaments. In conclusion, our in vitro results suggest S‐glutathionylation as a candidate PTM for an efficient molecular switch in the dynamic rearrangements of vimentin intermediate filaments, observed in vivo, in response to changes in cellular redox status. Finally, we demonstrate that HDex‐MS is a powerful method for probing the kinetics of vimentin filament formation and filament disassembly induced by PTMs.

A Cleavage‐Modification‐Reassembly Process Catalyzed by Rhodium and Brønsted Acid for the Synthesis of Multi‐Substituted Anilines

AbstractA synergistic rhodium‐ and Brønsted acid‐ catalyzed reaction of quinone imine ketals with diazo compounds to access multi‐substituted anilines is presented here. This reaction takes place through a process involving C−O bond cleavage, modification of the leaving alcoholic fragment, and selective reassembly of the reactive fragments. Moderate enantioselectivities are achieved when a chiral 1,1’‐bi(2‐naphthol)‐based phosphoric acid is used.magnified image

Establishment of a tTA-dependent photoactivatable Cre recombinase knock-in mouse model for optogenetic genome engineering

The Cre-loxP recombination system is widely used to generate genetically modified mice for biomedical research. Recently, a highly efficient photoactivatable Cre (PA-Cre) based on reassembly of split Cre fragments has been established. This technology enables efficient DNA recombination that is activated upon blue light illumination with spatiotemporal precision. In this study, we generated a tTA-dependent photoactivatable Cre-loxP recombinase knock-in mouse model (TRE-PA-Cre mice) using a CRISPR/Cas9 system. These mice were crossed with ROSA26-tdTomato mice (Cre reporter mouse) to visualize DNA recombination as marked by tdTomato expression. We demonstrated that external noninvasive LED blue light illumination allows efficient DNA recombination in the liver of TRE-PA-Cre:ROSA26-tdTomato mice transfected with tTA expression vectors using hydrodynamic tail vein injection. The TRE-PA-Cre mouse established here promises to be useful for optogenetic genome engineering in a noninvasive, spatiotemporal, and cell-type specific manner in vivo.

Chromothripsis and DNA Repair Disorders.

Chromothripsis is a mutational mechanism leading to complex and relatively clustered chromosomal rearrangements, resulting in diverse phenotypic outcomes depending on the involved genomic landscapes. It may occur both in the germ and the somatic cells, resulting in congenital and developmental disorders and cancer, respectively. Asymptomatic individuals may be carriers of chromotriptic rearrangements and experience recurrent reproductive failures when two or more chromosomes are involved. Several mechanisms are postulated to underlie chromothripsis. The most attractive hypothesis involves chromosome pulverization in micronuclei, followed by the incorrect reassembly of fragments through DNA repair to explain the clustered nature of the observed complex rearrangements. Moreover, exogenous or endogenous DNA damage induction and dicentric bridge formation may be involved. Chromosome instability is commonly observed in the cells of patients with DNA repair disorders, such as ataxia telangiectasia, Nijmegen breakage syndrome, and Bloom syndrome. In addition, germline variations of TP53 have been associated with chromothripsis in sonic hedgehog medulloblastoma and acute myeloid leukemia. In the present review, we focus on the underlying mechanisms of chromothripsis and the involvement of defective DNA repair genes, resulting in chromosome instability and chromothripsis-like rearrangements.

Macrophages promote network formation and maturation of transplanted adipose tissue–derived microvascular fragments

Adipose tissue–derived microvascular fragments rapidly reassemble into microvascular networks within implanted scaffolds. Herein, we analyzed the contribution of macrophages to this process. C57BL/6 mice received clodronate (clo)-containing liposomes for macrophage depletion, whereas animals treated with phosphate-buffered-saline-containing liposomes served as controls. Microvascular fragments were isolated from clo- and phosphate-buffered-saline-treated donor mice and seeded onto collagen–glycosaminoglycan matrices, which were implanted into dorsal skinfold chambers of clo- and phosphate-buffered-saline-treated recipient mice. The implants’ vascularization and incorporation were analyzed by stereomicroscopy, intravital fluorescence microscopy, histology, and immunohistochemistry. Compared to controls, matrices within clo-treated animals exhibited a significantly reduced functional microvessel density. Moreover, they contained a lower fraction of microvessels with an α-smooth muscle actin (SMA)+ cell layer, indicating impaired vessel maturation. This was associated with a deteriorated implant incorporation. These findings demonstrate that macrophages not only promote the reassembly of microvascular fragments into microvascular networks, but also improve their maturation during this process.

Semantic-based automated reassembly of heritage fragments

L'intelligence artificielle apporte des solutions à de nombreux problèmes de conservation du patrimoine. Parmi ceux-ci, la reconstruction d'artefacts pourrait être facilitée grâce à l’automatisation. Après la diffusion des techniques de réassemblage basées sur la continuité des motifs ou des fractures, la dernière décennie a vu l'essor des algorithmes basés sur la sémantique. Ceux-ci permettent d'effectuer des tâches visuelles en utilisant le sens de ce qui est représenté sur les images. Nous présumons que ces méthodes aideront à résoudre les problèmes patrimoniaux ne pouvant être solutionnés par les méthodes classiques, par exemple lorsque les fragments sont trop érodés pour utiliser les continuités.

Remontage sémantique de fragments grâce à l’intelligence artificielle

Le remontage de sites archéologiques permet d’en améliorer la compréhension et la conservation. Parfois, le grand nombre de fragments décourage toute tentative d’assemblage. Les archéologues se tournent alors vers des solutions informatisées, permettant l’analyse de l’aspect visuel des blocs. Les dernières avancées de l’intelligence artificielle ont permis de concevoir des méthodes de remontage utilisant la sémantique. Cet article présente les balbutiements de cette recherche : nous détaillons comment un algorithme peut donner du sens à des fragments, puis nous présentons quelques résultats préliminaires.

Spinup and Disruption of Interstellar Asteroids by Mechanical Torques, and Implications for 1I/2017 U1 (‘Oumuamua)

Abstract The discovery of the first interstellar asteroid, 1I/2017 U1 (‘Oumuamua), has opened a new era for research on interstellar objects. In this paper, we study the rotational dynamics of interstellar asteroids (ISAs) of irregular shapes moving through the interstellar gas. We find that regular mechanical torques resulting from the bombardment of gas flow on the irregular body could be important for the dynamics and destruction of ISAs. Mechanical torques can spin up the ISA, resulting in the breakup of the original ISA into small binary asteroids when the rotation rate exceeds the critical frequency. We find that the breakup timescale is short for ISAs of highly irregular shapes and low tensile strength. We apply our results to the first observed ISA, ‘Oumuamua, and suggest that its extreme elongated shape may originate from a reassembly of the binary fragments, due to gravity along its journey in the interstellar medium. The tumbling of ‘Oumuamua could have been induced by rotational disruption due to mechanical torques. Finally, we discuss the survival possibility of high-velocity asteroids presumably formed by tidal disruption of planetary systems by the black hole at the Galactic center.

A lightweight signcryption scheme for defense against fragment duplication attack in the 6LoWPAN networks

The Internet of Things (IoT) presents a new paradigm of the future Internet that intends to provide interactive communication between various processing objects via heterogeneous networks. The IPv6 over Low power Wireless Personal Area Networks (6LoWPAN) is an IPv6 adaptation sub-layer and provides the requirements of IP connectivity between resource-constrained devices in lossy, low power networks. Since the size of a packet in the IPv6 is larger than the size of a frame in the IEEE 802.15.4, the 6LoWPAN adaptation layer performs packet fragmentation. In this paper, first, the 6LoWPAN fragmentation mechanism in terms of security issues is analyzed and then, fragment duplication attack which an attacker can selectively disrupt the reassembly of fragments of a particular packet at a receiver node is identified. Next, signcryption, which is a high performance cryptographic primitive, is discussed. Finally, a lightweight Offline-Online SignCryption (OOSC) scheme is proposed to counter fragment duplication attack. The evaluation shows that the proposed scheme is secure in the random oracle model and in terms of computational cost, and energy consumption efficiently counters with this attack.