Arrangement Of Strands Research Articles

Characterization and genetic diagnosis of centronuclear myopathies in seven Chinese patients.

Centronuclear myopathies (CNMs) are a group of clinically and genetically heterogeneous muscle disorders. Here, we report a cohort of seven CNM patients with their clinical, histological, and morphological features. In addition, using the next-generation sequencing (NGS) technique (5/7 patients), we identified small indels: intronic, exonic, and missense mutations in MTM1, DNM2, and RYR1 genes. Further genetic studies revealed skewed X-chromosome inactivation in two female patients carrying MTM1 mutations. Based on the results of genetic analysis, these seven patients were classified as (1) X-linked recessive myotubular myopathy (patients 1-3) with MTM1 mutations and mild phenotype, (2) the autosomal dominant CNM (patients 4-6) with DNM2 mutations, and (3) the autosomal recessive CNM (patient 7) with RYR1 mutations. In all patients, histological findings featured a high proportion of fibers with central nuclei. Radial arrangement of the sarcoplasmic strands was observed in DNM2-CNM and RYR1-CNM patients. Muscle magnetic resonance imaging (MRI) revealed a proximal pattern of involvement presented in both MTM1-CNM and RYR1-CNM patients. A distal pattern of involvement was present in DNM2-CNM patients. Our findings thereby identified a number of novel features that expand the reported clinicopathological phenotype of CNMs in China.

Branching morphology, vascular bundle arrangement and ontogenetic development in leaf insertion zones and ramifications of three arborescent Araliaceae species

Key messageA conspicuous ‘finger-like’ branching morphology is described for three arborescent Araliaceae species with a focus on the three-dimensional vascular bundle arrangement in leaf insertion and stem–branch attachment regions during ontogenetic development.The central aim of this study is to gain a deeper understanding of the structure and development in leaf insertions and stem–branch attachments of the arborescent Araliaceae species: Schefflera arboricola, Fatsia japonica and Polyscias balfouriana. Therefore, the vascular bundle arrangement in the leaf insertion zone and ontogenetic development of the stem–branch attachment after decapitation were analyzed, with a special focus on their conspicuous ‘finger-like’ branching morphology that, to our knowledge, is unique to the Araliaceae. Decortication of adult ramifications allows for a morphological analysis of the woody strands in the stem–branch attachment regions. Via high-resolution microscopy of serial thin-sections and 3D reconstructions, as well as cryotome sections, anatomical analysis was carried out of the course and arrangement of vascular bundles through leaf insertions and later developing ramifications, including a comparative analysis of the different ontogenetic stages. All three species investigated present a ‘finger-like’ branching morphology with variations in the number and arrangement of the woody strands. Thin-sectioning reveals a conspicuous pattern of leaf trace emergence from the main stem, proceeding into the leaf and the early developing ramifications. Vascular bundle derivatives contribute to the vascular integration of leaves and axillary buds. The described ‘finger-like’ branching morphology in the investigated Araliaceae species represents a sophisticated mode of vascular integration in leaf insertion zones and developing ramifications. In combination with forthcoming biomechanical experiments, this analysis shall serve as a basis for biomimetic translations into textile technology (fiber-reinforced branched composite materials) and civil engineering (optimization of branched building structures).

Bark anatomy ofAdansonia digitataL. (Malvaceae)

The bark structure of Adansonia digitata L. is described in detail. Characters of the bark that are shared with other Malvaceae include the presence of strongly dilating rays, mucilage cells and cavities, druses of calcium oxalate in the cells of cortical parenchyma and phloem rays, a storied arrangement of sieve tube members and axial parenchyma strands, the presence of secondary phloem fibers and their arrangement into tangential bands. The secondary phloem fibers are longer (2.8–8.6 mm) and more abundant than the libriform fibers (1.7–2.2 mm) in the wood of this species. The abundance of parenchyma in both axial and radial parts of the secondary phloem and in the pseudocortex is a noteworthy feature. Due to the complementarity of fibrous and parenchymatous tissues, the secondary phloem can provide substantial mechanical benefits and apparently play an important role in the biomechanical stability of the trunk. The meristematic capacity of dilated phloem rays and the pseudocortex allow for substantial bark dilatation with very limited abscission of the outer portions of the secondary phloem. Subsequent phellogen initiation in the outer part of the secondary phloem was not observed, not even in mature bark. Hence no rhytidome is present. The thin translucent phellem, formed by continuous phellogen arising in the subepidermal layer, allows for photosynthesis to potentially occur within the chloroplast-containing cells of phelloderm and pseudocortex, even when the plants are leafless, thus probably assisting them to survive harsh climatic conditions. The formation of sieve tube members by transverse anticlinal divisions from fusiform cambial initials in A. digitata is a first report for the Malvaceae sensu lato.

Comparative study of fiber trapping by filaments in conventional and diagonal sirofil systems

In this study, geometrical and theoretical analyses were conducted comparatively for fiber trappings by filaments in the left diagonal, conventional and right diagonal sirofil with right strand and left filament arrangement (denoted as LDS-RS-LF, CS-RS-LF and RDS-RS-LF, respectively)and left diagonal, conventional and right diagonal sirofil with right filament and left strand arrangement (LDS-RF-LS, CS-RF-LS and RDS-RF-LS, respectively). White filaments and blue rovings were used to produce conventional and diagonal sirofil yarns to validate the analysis. Online and offline fiber trapping capacity comparisons indicated that CS-RS-LF and CS-RF-LS had higher capacities of trapping fibers than LDS-RS-LF and RDS-RF-LS, respectively, and lower capacities than RDS-RS-LF and LDS-RF-LS, respectively. Yarn appearance and tensile properties results revealed that diagonal sirofils with improved fiber trappings increased yarn hairiness and tensile properties, while the ones with deteriorated fiber trappings decreased yarn hairiness and tensile properties. Sirofil yarn unevenness CVm decreased as the fiber trapping enhanced by RDS-RS-LF and LDS-RF-LS and increased as the fiber trapping weakened by LDS-RS -LF and RDS-RF-LS. This corresponded well to our theoretical hypotheses on fiber trappings by filaments in conventional and diagonal sirofil systems.

Critical current retention of potted and unpotted REBCO Roebel cables under transverse pressure and thermal cycling

Coated conductor Roebel cables are an effective way to create a high current density, fully transposed cable. However, despite REBCO tapes being robust against transverse stress, the Roebel architecture can concentrate transverse stress in non-trivial and random patterns depending on the exact arrangement of strands. If stands are embedded in a solid media which consolidates all strands then a transverse stress concentration will not occur. We tested this idea through mechanical and thermo-cycling tests on 5 strand Roebel cables. For non-impregnated cable irreversible degradation in critical currents is initiated at transverse pressures in a range of 4–34 MPa. Optical examination of the cables shows stress concentration patterns beyond those predicted by thickness variations. For cables impregnated with epoxy filled with SiO2 nanopowder, which has a similar thermal expansion coefficient to the metallic substrate of the strands, the irreversibility point is increased above our highest experimentally available pressure of 270 MPa. Thermo-cycling experiments confirmed a closely matched thermal expansion coefficient between the embedding media and metallic substrate is critical to avoid wire failures.

Automated Quantification of the Impact of Defects on the Mechanical Behavior of Deoxyribonucleic acid Origami Nanoplates.

Deoxyribonucleic acid (DNA) origami is a method for the bottom-up self-assembly of complex nanostructures for applications, such as biosensing, drug delivery, nanopore technologies, and nanomechanical devices. Effective design of such nanostructures requires a good understanding of their mechanical behavior. While a number of studies have focused on the mechanical properties of DNA origami structures, considering defects arising from molecular self-assembly is largely unexplored. In this paper, we present an automated computational framework to analyze the impact of such defects on the structural integrity of a model DNA origami nanoplate. The proposed computational approach relies on a noniterative conforming to interface-structured adaptive mesh refinement (CISAMR) algorithm, which enables the automated transformation of a binary image of the nanoplate into a high fidelity finite element model. We implement this technique to quantify the impact of defects on the mechanical behavior of the nanoplate by performing multiple simulations taking into account varying numbers and spatial arrangements of missing DNA strands. The analyses are carried out for two types of loading: uniform tensile displacement applied on all the DNA strands and asymmetric tensile displacement applied to strands at diagonal corners of the nanoplate.

Design and Fabrication of Complex Scaffolds for Bone Defect Healing: Combined 3D Plotting of a Calcium Phosphate Cement and a Growth Factor-Loaded Hydrogel

Additive manufacturing enables the fabrication of scaffolds with defined architecture. Versatile printing technologies such as extrusion-based 3D plotting allow in addition the incorporation of biological components increasing the capability to restore functional tissues. We have recently described the fabrication of calcium phosphate cement (CPC) scaffolds by 3D plotting of an oil-based CPC paste under mild conditions. In the present study, we have developed a strategy for growth factor loading based on multichannel plotting: a biphasic scaffold design was realised combining CPC with VEGF-laden, highly concentrated hydrogel strands. As hydrogel component, alginate and an alginate-gellan gum blend were evaluated; the blend exhibited a more favourable VEGF release profile and was chosen for biphasic scaffold fabrication. After plotting, two-step post-processing was performed for both, hydrogel crosslinking and CPC setting, which was shown to be compatible with both materials. Finally, a scaffold was designed and fabricated which can be applied for testing in a rat critical size femur defect. Optimization of CPC plotting enabled the fabrication of highly resolved structures with strand diameters of only 200µm. Micro-computed tomography revealed a precise strand arrangement and an interconnected pore space within the biphasic scaffold even in swollen state of the hydrogel strands.

Structural stability of DNA origami nanostructures in the presence of chaotropic agents.

DNA origami represent powerful platforms for single-molecule investigations of biomolecular processes. The required structural integrity of the DNA origami may, however, pose significant limitations regarding their applicability, for instance in protein folding studies that require strongly denaturing conditions. Here, we therefore report a detailed study on the stability of 2D DNA origami triangles in the presence of the strong chaotropic denaturing agents urea and guanidinium chloride (GdmCl) and its dependence on concentration and temperature. At room temperature, the DNA origami triangles are stable up to at least 24 h in both denaturants at concentrations as high as 6 M. At elevated temperatures, however, structural stability is governed by variations in the melting temperature of the individual staple strands. Therefore, the global melting temperature of the DNA origami does not represent an accurate measure of their structural stability. Although GdmCl has a stronger effect on the global melting temperature, its attack results in less structural damage than observed for urea under equivalent conditions. This enhanced structural stability most likely originates from the ionic nature of GdmCl. By rational design of the arrangement and lengths of the individual staple strands used for the folding of a particular shape, however, the structural stability of DNA origami may be enhanced even further to meet individual experimental requirements. Overall, their high stability renders DNA origami promising platforms for biomolecular studies in the presence of chaotropic agents, including single-molecule protein folding or structural switching.

Development of Leaf Lobing and Vein Pattern Architecture in the GenusIpomoea(Morning Glory)

Premise of research. Formation of leaf shape and establishment of vascular pattern are intrinsically tied during development. While vein formation resists major changes in patterning, leaf shape is more liable to change. We investigated the pattern of major vascular strands among species with varying leaf shapes within the genus Ipomoea (Convolvulaceae). Our study was conducted to identify structural similarities in vascular architecture despite differences in leaf morphology.Methodology. We used SEM to observe the initiation and formation of leaf lobes, while vascular strand development was examined in cleared leaves. A generalized Procrustes analysis was used to analyze branching patterns of the major secondary veins.Pivotal results. Analysis of vascular strands in the five Ipomoea species revealed that the two most proximal major secondary veins emerging from the petiole-blade junction are highly conserved, and the shapes defined by the trajectories of those veins through the leaf blade show significant overlap among the divergent leaf forms.Conclusions. The longitudinal arrangement of vascular strands is highly reproducible, while leaf morphology is amenable to changes within species. Our data show that a common vascular architecture exists and that significant consistencies can be seen in the basic shape described by this architecture across species.

Polar Phase of Superfluid (3)He in Anisotropic Aerogel.

We report the first observation of the polar phase of superfluid (3)He. This phase appears in (3)He confined in a new type of aerogel with a nearly parallel arrangement of strands which play the role of ordered impurities. Our experiments qualitatively agree with theoretical predictions and suggest that in other systems with unconventional Cooper pairing (e.g., in unconventional superconductors) similar phenomena may be found in the presence of anisotropic impurities.

Comparative Study of Unbonded Carbon Fiber and Steel Strands in Posttensioned Pier Caps

AbstractCarbon fiber strands offer a viable alternative to corrosion-prone steel strands in posttensioning applications. This study focused on a side-by-side comparison of two types of carbon fiber strands with different elastic moduli against steel strands in a 5½∶1 scaled model of a typical interior hammerhead pier of the San Antonio Downtown Y project with two identical cantilever overhangs. Two different strand arrangements were used for posttensioning, with eight and six strands, respectively representing an overdesign and a slight underdesign relative to the factored demand. The model was tested under service and factored flexure and shear loads. The study confirmed the feasibility of using carbon fiber strands in unbonded posttensioning of pier caps. Given the strength-based design of the pier cap, the elastic moduli of different carbon fiber strands did not seem to have affected the serviceability performance with respect to either cracking or deflection. Considering both serviceability and overlo...

Structural constraints and dynamics of bacterial cell wall architecture.

The peptidoglycan wall (PG) is a unique structure which confers physical strength and defined shape to bacteria. It consists of a net-like macromolecule of peptide interlinked glycan chains overlying the cell membrane. The structure and layout of the PG dictates that the wall has to be continuously modified as bacteria go through division, morphological differentiation, and adaptive responses. The PG is poorly known in structural terms. However, to understand morphogenesis a precise knowledge of glycan strand arrangement and of local effects of the different kinds of subunits is essential. The scarcity of data led to a conception of the PG as a regular, highly ordered structure which strongly influenced growth models. Here, we review the structure of the PG to define a more realistic conceptual framework. We discuss the consequences of the plasticity of murein architecture in morphogenesis and try to define a set of minimal structural constraints that must be fulfilled by any model to be compatible with present day information.

Construction of DNA hemicatenanes from two small circular DNA molecules.

DNA hemicatenanes, one of the simplest possible junctions between two double stranded DNA molecules, have frequently been mentioned in the literature for their possible function in DNA replication, recombination, repair, and organization in chromosomes. They have been little studied experimentally, however, due to the lack of an appropriate method for their preparation. Here we have designed a method to build hemicatenanes from two small circular DNA molecules. The method involves, first, the assembly of two linear single strands and their circularization to form a catenane of two single stranded circles, and, second, the addition and base-pairing of the two single stranded circles complementary to the first ones, followed by their annealing using DNA topoisomerase I. The product was purified by gel electrophoresis and characterized. The arrangement of strands was as expected for a hemicatenane and clearly distinct from a full catenane. In addition, each circle was unwound by an average of half a double helical turn, also in excellent agreement with the structure of a hemicatenane. It was also observed that hemicatenanes are quickly destabilized by a single cut on either of the two strands passing inside the junction, strongly suggesting that DNA strands are able to slide easily inside the hemicatenane. This method should make it possible to study the biochemical properties of hemicatenanes and to test some of the hypotheses that have been proposed about their function, including a possible role for this structure in the organization of complex genomes in loops and chromosomal domains.

G-quadruplex formation between G-rich PNA and homologous sequences in oligonucleotides and supercoiled plasmid DNA.

Guanine (G)-rich DNA sequences can adopt four-stranded quadruplex conformations that may play a role in the regulation of genetic processes. To explore the possibility of targeted molecular recognition of DNA sequences with short G-rich peptide nucleic acids (PNA) and to assess the strand arrangement in such complexes, we used PNA and DNA with the Oxytricha nova telomeric sequence d(G4T4G4) as a model. PNA probes were complexed with DNA targets in the following forms: single-stranded oligonucleotides, a loop of DNA in a hairpin conformation, and as supercoiled plasmid with the (G4T4G4)/(C4A4C4) insert. Gel-shift mobility assays demonstrated formation of stable hybrid complexes between the homologous G4T4G4 PNA and DNA with multiple modes of binding. Chemical and enzymatic probing revealed sequence-specific and G-quadruplex dependent binding of G4T4G4 PNA to dsDNA. Spectroscopic and electrophoretic analysis of the complex formed between PNA and the synthetic DNA hairpin containing the G4T4G4 loop showed that the stoichiometry of a prevailing complex is three PNA strands per one DNA strand. We speculate how this new PNA-DNA complex architecture can help to design more selective, quadruplex-specific PNA probes.

Amino acid distribution rules predict protein fold: protein grammar for beta-strand sandwich-like structures.

We present an alternative approach to protein 3D folding prediction based on determination of rules that specify distribution of “favorable” residues, that are mainly responsible for a given fold formation, and “unfavorable” residues, that are incompatible with that fold, in polypeptide sequences. The process of determining favorable and unfavorable residues is iterative. The starting assumptions are based on the general principles of protein structure formation as well as structural features peculiar to a protein fold under investigation. The initial assumptions are tested one-by-one for a set of all known proteins with a given structure. The assumption is accepted as a “rule of amino acid distribution” for the protein fold if it holds true for all, or near all, structures. If the assumption is not accepted as a rule, it can be modified to better fit the data and then tested again in the next step of the iterative search algorithm, or rejected. We determined the set of amino acid distribution rules for a large group of beta sandwich-like proteins characterized by a specific arrangement of strands in two beta sheets. It was shown that this set of rules is highly sensitive (~90%) and very specific (~99%) for identifying sequences of proteins with specified beta sandwich fold structure. The advantage of the proposed approach is that it does not require that query proteins have a high degree of homology to proteins with known structure. So long as the query protein satisfies residue distribution rules, it can be confidently assigned to its respective protein fold. Another advantage of our approach is that it allows for a better understanding of which residues play an essential role in protein fold formation. It may, therefore, facilitate rational protein engineering design.

Near-infrared silver cluster optically signaling oligonucleotide hybridization and assembling two DNA hosts.

Silver clusters with ∼10 atoms form within DNA strands, and the conjugates are chemical sensors. The DNA host hybridizes with short oligonucleotides, and the cluster moieties optically respond to these analytes. Our studies focus on how the cluster adducts perturb the structure of their DNA hosts. Our sensor is comprised of an oligonucleotide with two components: a 5′-cluster domain that complexes silver clusters and a 3′-recognition site that hybridizes with a target oligonucleotide. The single-stranded sensor encapsulates an ∼11 silver atom cluster with violet absorption at 400 nm and with minimal emission. The recognition site hybridizes with complementary oligonucleotides, and the violet cluster converts to an emissive near-infrared cluster with absorption at 730 nm. Our key finding is that the near-infrared cluster coordinates two of its hybridized hosts. The resulting tertiary structure was investigated using intermolecular and intramolecular variants of the same dimer. The intermolecular dimer assembles in concentrated (∼5 μM) DNA solutions. Strand stoichiometries and orientations were chromatographically determined using thymine-modified complements that increase the overall conjugate size. The intramolecular dimer develops within a DNA scaffold that is founded on three linked duplexes. The high local cluster concentrations and relative strand arrangements again favor the antiparallel dimer for the near-infrared cluster. When the two monomeric DNA/violet cluster conjugates transform to one dimeric DNA/near-infrared conjugate, the DNA strands accumulate silver. We propose that these correlated changes in DNA structure and silver stoichiometry underlie the violet to near-infrared cluster transformation.

Asymmetric triplex metallohelices with high and selective activity against cancer cells.

Small cationic amphiphilic α-helical peptides are emerging as agents for the treatment of cancer and infection, but they are costly and display unfavourable pharmacokinetics. Helical coordination complexes may offer a three-dimensional scaffold for the synthesis of mimetic architectures. However, the high symmetry and modest functionality of current systems offer little scope to tailor the structure to interact with specific biomolecular targets, or to create libraries for phenotypic screens. Here, we report the highly stereoselective asymmetric self-assembly of very stable, functionalized metallohelices. Their anti-parallel head-to-head-to-tail 'triplex' strand arrangement creates an amphipathic functional topology akin to that of the active sub-units of, for example, host-defence peptides and p53. The metallohelices display high, structure-dependent toxicity to the human colon carcinoma cell-line HCT116 p53(++), causing dramatic changes in the cell cycle without DNA damage. They have lower toxicity to human breast adenocarcinoma cells (MDA-MB-468) and, most remarkably, they show no significant toxicity to the bacteria methicillin-resistant Staphylococcus aureus and Escherichia coli.

Uncovering the self-assembly of DNA nanostructures by thermodynamics and kinetics.

CONSPECTUS: DNA nanotechnology is one of the most flourishing interdisciplinary research fields. DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales. They can be used as scaffolds for organizing other nanoparticles, proteins, and chemical groups, leveraging their functions for creating complex bioinspired materials that may serve as smart drug delivery systems, in vitro or in vivo biomolecular computing platforms, and diagnostic devices. Achieving optimal structural features, efficient assembly protocols, and precise functional group positioning and modification requires a thorough understanding of the thermodynamics and kinetics of the DNA nanostructure self-assembly process. The most common real-time measurement strategies include monitoring changes in UV absorbance based on the hyperchromic effect of DNA, and the emission signal changes of DNA intercalating dyes or covalently conjugated fluorescent dyes/pairs that accompany temperature dependent structural changes. Thermodynamic studies of a variety of DNA nanostructures have been performed, from simple double stranded DNA formation to more complex origami assembly. The key parameters that have been evaluated in terms of stability and cooperativity include the overall dimensions, the folding path of the scaffold, crossover and nick point arrangement, length and sequence of single strands, and salt and ion concentrations. DNA tile-tile interactions through sticky end hybridization have also been analyzed, and the steric inhibition and rigidity of tiles turn out to be important factors. Many kinetic studies have also been reported, and most are based on double stranded DNA formation. A two-state assumption and the hypothesis of several intermediate states have been applied to determine the rate constant and activation energy of the DNA hybridization process. A few simulated models were proposed to represent the structural, mechanical, and kinetic properties of DNA hybridization. The kinetics of strand displacement reactions has also been studied as a special case of DNA hybridization. The thermodynamic and kinetic characteristics of DNA nanostructures have been exploited to develop rapid and isothermal annealing protocols. It is conceivable that a more thorough understanding of the DNA assembly process could be used to guide the structural design process and optimize the conditions for assembly, manipulation, and functionalization, thus benefiting both upstream design and downstream applications.

An Efficient Electrochemical Biosensor for Silver Ion Detection Using Hydrogen Peroxide as a Redox Indicator

The strong and specific binding of two DNA cytosine bases by silver ion (C-Ag+-C) was applied to develop an efficient electrochemical biosensor for the detection of silver ion in aqueous solution. As a redox indicator, the hydrogen peroxide worked to generate a readable electrochemical signal. Thiolated short oligonucleotide strands containing 5 cytosine bases served as probe and self-assembled via AuS bonding on gold electrode. In the presence of Ag+, the specific coordination between Ag+ and cytosine bases resulted in more stable and porous arrangement of oligonucleotide strands. Hydrogen peroxide could adsorb onto the surface of gold electrode and produce an electrochemical signal. The cyclic voltammetry shows a linear correlation between the signal and the concentration of Ag+ over the range 0-0.2 μM (R2 = 0.9955) with a detection limit of 30 nM. The length of probe DNA has no significant impact on the sensor performance. This biosensor is simple, economical and reusable with good sensitivity and selectivity. We also validated the practicality for the determination of Ag+ in real water samples.

Alkoxy-benzoic acids: Some lacking structures and rationalization of the molecular features governing their crystalline architectures

The crystalline structure of four alkoxy-substituted benzoic acids, namely 3-(methoxy)benzoic acid (I), (with two independent molecules in the asymmetric unit); 3,4-di(ethoxy)benzoic acid (II), 3,5-di(ethoxy)benzoic acid (III) and 3,4,5-tri(ethoxy)benzoic acid (IV) are presented, and the details of their packing arrangements discussed. In all cases the synthon is a H-bonded head-to-head dimer. C–H⋯π interactions involving C atoms at the 4-positions of neighbouring molecules organize the dimeric synthons in a perpendicular orientation in the case of I. These interactions being blocked for II, Van der Waals interchain interactions organise synthons therein in parallel orientation. In the case of III, although C–H⋯π interactions at the 4-positions are possible in principle, interchain interactions prevail, giving rise to a parallel arrangement of linear strands. Finally, compound IV with all three 3,4,5 substituted sites reduces its interaction scheme to stacking contacts, and the columns thus formed are essentially non interacting. An attempt to rationalize the molecular factors influencing the structures of the whole set of 3-, 4- and/or 5-methoxy- and ethoxy-substituted benzoic acids reported so far in the literature is performed.