The cell organization underlying structural colour is involved in Flavobacterium IR1 predation

Flavobacterium IR1 is a gliding bacterium with a high degree of colonial organization as a 2D photonic crystal, resulting in vivid structural coloration when illuminated. Enterobacter cloacae B12, an unrelated bacterium, was isolated from the brown macroalga Fucus vesiculosus from the same location as IR1. IR1 was found to be a predator of B12. A process of surrounding, infiltration, undercutting and killing of B12 supported improved growth of IR1. A combination of motility and capillarity facilitated the engulfment of B12 colonies by IR1. Predation was independent of illumination. Mutants of IR1 that formed photonic crystals less effectively than the wild type were reduced in predation. Conversely, formation of a photonic crystal was not advantageous in resisting predation by Rhodococcus spp. PIR4. These observations suggest that the organization required to create structural colour has a biological function (facilitating predation) but one that is not directly related to the photonic properties of the colony. This work is the first experimental evidence supporting a role for this widespread type of cell organization in the Flavobacteriia.Subject terms: Water microbiology, Microbial ecology     

Design of a Single-Polarization Single-Mode Photonic Crystal Fiber Filter Based on Surface Plasmon Resonance

We design a single-polarization single-mode photonic crystal fiber filter based on surface plasmon resonance. The finite element method is employed to evaluate the characteristics of the filter. The proposed fiber is devised such that there is a great discrepant confinement loss between two polarizations of x and y by varying two air holes in the cladding region, which is composed of hexagonal structural air holes in pure silica selectively filling with gold wires. Numerical simulations show that single-polarization single-mode operation waveband can be tuned by adjusting the parameters of the photonic crystal fiber. The confinement losses of the unwanted polarization can reach to 126.10 and 326.30 dB/cm in the wavelengths of 1.31 and 1.55 μm, while the corresponding confinement losses of the wanted polarized mode are only 0.08 and 1.20 dB/cm, respectively. Furthermore, the crosstalk can come to a maximum of 120.34 and 310.41 dB in the two communication bands. The bandwidths of the fiber designed for 1.31 and 1.55 μm are, respectively, 20 and 60 nm, which may be found useful applications for fiber polarizer.     

Unique wing scale photonics of male Rajah Brooke’s birdwing butterflies

Background

Ultrastructures in butterfly wing scales can take many shapes, resulting in the often striking coloration of many butterflies due to interference of light. The plethora of coloration mechanisms is dazzling, but often only single mechanisms are described for specific animals.

Results

We have here investigated the male Rajah Brooke’s birdwing, Trogonoptera brookiana, a large butterfly from Malaysia, which is marked by striking, colorful wing patterns. The dorsal side is decorated with large, iridescent green patterning, while the ventral side of the wings is primarily brown-black with small white, blue and green patches on the hindwings. Dense arrays of red hairs, creating a distinct collar as well as contrasting areas ventrally around the thorax, enhance the butterfly’s beauty. The remarkable coloration is realized by a diverse number of intricate and complicated nanostructures in the hairs as well as the wing scales. The red collar hairs contain a broad-band absorbing pigment as well as UV-reflecting multilayers resembling the photonic structures of Morpho butterflies; the white wing patches consist of scales with prominent thin film reflectors; the blue patches have scales with ridge multilayers and these scales also have centrally concentrated melanin. The green wing areas consist of strongly curved scales, which possess a uniquely arranged photonic structure consisting of multilayers and melanin baffles that produces highly directional reflections.

Conclusion

Rajah Brooke’s birdwing employs a variety of structural and pigmentary coloration mechanisms to achieve its stunning optical appearance. The intriguing usage of order and disorder in related photonic structures in the butterfly wing scales may inspire novel optical materials as well as investigations into the development of these nanostructures in vivo.

     

Negative refraction angular characterization in one-dimensional photonic crystals

Background

Photonic crystals are artificial structures that have periodic dielectric components with different refractive indices. Under certain conditions, they abnormally refract the light, a phenomenon called negative refraction. Here we experimentally characterize negative refraction in a one dimensional photonic crystal structure; near the low frequency edge of the fourth photonic bandgap. We compare the experimental results with current theory and a theory based on the group velocity developed here. We also analytically derived the negative refraction correctness condition that gives the angular region where negative refraction occurs.

Methodology/Principal Findings

By using standard photonic techniques we experimentally determined the relationship between incidence and negative refraction angles and found the negative refraction range by applying the correctness condition. In order to compare both theories with experimental results an output refraction correction was utilized. The correction uses Snell''s law and an effective refractive index based on two effective dielectric constants. We found good agreement between experiment and both theories in the negative refraction zone.

Conclusions/Significance

Since both theories and the experimental observations agreed well in the negative refraction region, we can use both negative refraction theories plus the output correction to predict negative refraction angles. This can be very useful from a practical point of view for space filtering applications such as a photonic demultiplexer or for sensing applications.     

Using Microwave and Macroscopic Samples of Dielectric Solids to Study the Photonic Properties of Disordered Photonic Bandgap Materials

Recently, disordered photonic materials have been suggested as an alternative to periodic crystals for the formation of a complete photonic bandgap (PBG). In this article we will describe the methods for constructing and characterizing macroscopic disordered photonic structures using microwaves. The microwave regime offers the most convenient experimental sample size to build and test PBG media. Easily manipulated dielectric lattice components extend flexibility in building various 2D structures on top of pre-printed plastic templates. Once built, the structures could be quickly modified with point and line defects to make freeform waveguides and filters. Testing is done using a widely available Vector Network Analyzer and pairs of microwave horn antennas. Due to the scale invariance property of electromagnetic fields, the results we obtained in the microwave region can be directly applied to infrared and optical regions. Our approach is simple but delivers exciting new insight into the nature of light and disordered matter interaction.Our representative results include the first experimental demonstration of the existence of a complete and isotropic PBG in a two-dimensional (2D) hyperuniform disordered dielectric structure. Additionally we demonstrate experimentally the ability of this novel photonic structure to guide electromagnetic waves (EM) through freeform waveguides of arbitrary shape.     

Tunable Plasmon-Induced Transparency Effect in MIM Side-Coupled Isosceles Trapezoid Cavities System

We propose a plasmonic structure based on the metal-insulator-metal waveguide with the side-coupled isosceles trapezoid cavities. Both of the structures based on the side-coupled trapezoid cavities separated or connected with waveguides can realize the plasmon-induced transparency (PIT). By adjusting the structure parameters, the off-to-on PIT response can be tunably achieved. The coupled mode theory (CMT) method is used to study the PIT phenomenon and explain the transmission characteristics. This work may provide a potential way for designing highly integrated photonic devices.

     

Multicellular Stalk-Like Structures in Saccharomyces cerevisiae

Stalk formation is a novel pattern of multicellular organization. Yeast cells which survive UV irradiation form colonies that grow vertically to form very long (0.5 to 3.0 cm) and thin (0.5 to 4 mm in diameter) multicellular structures. We describe the conditions required to obtain these stalk-like structures reproducibly in large numbers. Yeast mutants, mutated for control of cell polarity, developmental processes, UV response, and signal transduction cascades were tested and found capable of forming stalk-like structures. We suggest a model that explains the mechanism of stalk formation by mechanical environmental forces. We show that other microorganisms (Candida albicans, Schizosaccharomyces pombe, and Escherichia coli) also form stalks, suggesting that the ability to produce stalks may be a general property of microorganisms. Diploid yeast stalks sporulate at an elevated frequency, raising the possibility that the physiological role of stalks might be disseminating spores.     

A Polarization Filter Based on Photonic Crystal Fiber with Symmetry Around Gold-Coated Holes

We propose a modified design for a photonic crystal fiber (PCF) polarization filter based on surface plasmon resonance (SPR). The air holes are arrayed in diamond lattices, and the diameter of the holes around the gold-coated holes are different that can separate the refractive index of the x-polarization and y-polarization second order surface plasmon polariton (SPP) modes. The influences of structural parameters of the photonic crystal fiber (PCF) on the filter characteristics are studied using the finite element method (FEM). Great changes have taken place in the results of numerical simulation by changing the thickness of the gold film and air hole diameter. Simulation results show that the resonance wavelength is communication wavelength 1550 mm, the loss of the y-polarization mode is 43,126.7 dB/m. When the length of the fiber is 500 μm, extinction ratio is more than 20 dB at the communication wavelength, and bandwidth achieve to 190 nm. It is an important property of PCF polarization filter in production.     

Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc,k-Ras and c-Kit promoter sequences

We report on higher-order G-quadruplex structures adopted by long promoter sequences obtained by an iterative integrated structural biology approach. Our approach uses quantitative biophysical tools (analytical ultracentrifugation, small-angle X-ray scattering, and circular dichroism spectroscopy) combined with modeling and molecular dynamics simulations, to derive self-consistent structural models. The formal resolution of our approach is 18 angstroms, but in some cases structural features of only a few nucleotides can be discerned. We report here five structures of long (34–70 nt) wild-type sequences selected from three cancer-related promoters: c-Myc, c-Kit and k-Ras. Each sequence studied has a unique structure. Three sequences form structures with two contiguous, stacked, G-quadruplex units. One longer sequence from c-Myc forms a structure with three contiguous stacked quadruplexes. A longer c-Kit sequence forms a quadruplex-hairpin structure. Each structure exhibits interfacial regions between stacked quadruplexes or novel loop geometries that are possible druggable targets. We also report methodological advances in our integrated structural biology approach, which now includes quantitative CD for counting stacked G-tetrads, DNaseI cleavage for hairpin detection and SAXS model refinement. Our results suggest that higher-order quadruplex assemblies may be a common feature within the genome, rather than simple single quadruplex structures.     

In vitro selections with RNAs of variable length converge on a robust catalytic core

In vitro selection is a powerful tool that can be used to understand basic principles of molecular evolution. We used in vitro selection to understand how changes in length and the accumulation of point mutations enable the evolution of functional RNAs. Using RNA populations of various lengths, we performed a series of in vitro experiments to select for ribozymes with RNA ligase activity. We identified a core ribozyme structure that was robust to changes in RNA length, high levels of mutagenesis, and increased selection pressure. Elaboration on this core structure resulted in improved activity which we show is consistent with a larger trend among functional RNAs in which increasing motif size can lead to an exponential improvement in fitness. We conclude that elaboration on conserved core structures is a preferred mechanism in RNA evolution. This conclusion, drawn from selections of RNAs from random sequences, is consistent with proposed evolutionary histories of specific biological RNAs. More generally, our results indicate that modern RNA structures can be used to infer ancestral structures. Our observations also suggest a mechanism by which structural outcomes of early RNA evolution would be largely reproducible even though RNA fitness landscapes consist of disconnected clusters of functional sequences.     

Identification of putative G-quadruplex DNA structures in S. pombe genome by quantitative PCR stop assay

In order to understand in which biological processes the four-stranded G-quadruplex (G4) DNA structures play a role, it is important to determine which predicted regions can actually adopt a G4 structure. Here, to identify DNA regions in Schizosaccharomyces pombe that fold into G4 structures, we first optimized a quantitative PCR (qPCR) assay using the G4 stabilizer, PhenDC3. We call this method the qPCR stop assay, and used it to screen for G4 structures in genomic DNA. The presence of G4 stabilizers inhibited DNA amplification in 14/15 unexplored genomic regions in S. pombe that encompassed predicted G4 structures, suggesting that at these sites the stabilized G4 structure formed an obstacle for the DNA polymerase. Furthermore, the formation of G4 structures was confirmed by complementary in vitro assays. In vivo, the S. pombe G4 unwinder Pif1 helicase, Pfh1, was associated with tested G4 sites, suggesting that the G4 structures also formed in vivo. Thus, we propose that the confirmed G4 structures in S. pombe form an obstacle for replication in vivo, and that the qPCR stop assay is a method that can be used to identify G4 structures. Finally, we suggest that the qPCR stop assay can also be used for identifying G4 structures in other organisms, as well as being adapted to screen for novel G4 stabilizers.     

Mycobacterium tuberculosis DinG Is a Structure-specific Helicase That Unwinds G4 DNA: IMPLICATIONS FOR TARGETING G4 DNA AS A NOVEL THERAPEUTIC APPROACH*

The significance of G-quadruplexes and the helicases that resolve G4 structures in prokaryotes is poorly understood. The Mycobacterium tuberculosis genome is GC-rich and contains >10,000 sequences that have the potential to form G4 structures. In Escherichia coli, RecQ helicase unwinds G4 structures. However, RecQ is absent in M. tuberculosis, and the helicase that participates in G4 resolution in M. tuberculosis is obscure. Here, we show that M. tuberculosis DinG (MtDinG) exhibits high affinity for ssDNA and ssDNA translocation with a 5′ → 3′ polarity. Interestingly, MtDinG unwinds overhangs, flap structures, and forked duplexes but fails to unwind linear duplex DNA. Our data with DNase I footprinting provide mechanistic insights and suggest that MtDinG is a 5′ → 3′ polarity helicase. Notably, in contrast to E. coli DinG, MtDinG catalyzes unwinding of replication fork and Holliday junction structures. Strikingly, we find that MtDinG resolves intermolecular G4 structures. These data suggest that MtDinG is a multifunctional structure-specific helicase that unwinds model structures of DNA replication, repair, and recombination as well as G4 structures. We finally demonstrate that promoter sequences of M. tuberculosis PE_PGRS2, mce1R, and moeB1 genes contain G4 structures, implying that G4 structures may regulate gene expression in M. tuberculosis. We discuss these data and implicate targeting G4 structures and DinG helicase in M. tuberculosis could be a novel therapeutic strategy for culminating the infection with this pathogen.     

A study of the interactions that stabilize DNA frayed wires

Oligodeoxyribonucleotides (ODNs) with long, terminal runs of consecutive guanines, and either a dA or dT tract at the other end form higher-order structures called DNA frayed wires. These aggregates self-assemble into species consisting of 2, 3, 4, 5, … associated strands. Some of the remarkable features of these structures are their extreme thermostability and resistance to chemical denaturants and nucleases. However, the nature of the molecular interactions that stabilize these structures remains unclear. Based on dimethyl sulfate (DMS) methylation results, our group previously proposed DNA frayed wires to be a unique set of nucleic-acid assemblies in which the N7 of guanine does not participate in the guanine–guanine interactions. To probe the hydrogen bonding involved in the stabilization of d(A₁₅G₁₅) frayed wires, we used Raman spectroscopy in which the DNA sample is held in photonic crystal fibers. This technique significantly enhances the signals thus allowing the use of very low laser power. Based on our results for d(A₁₅G₁₅) and those of incorporating the isoelectronic guanine analog pyrazolo[3,4,-d]pyrimidine or PPG, into a frayed wire-forming sequence, we provide evidence that these structures are based on the G-quadruplex model. Furthermore, from the Raman spectrum, we observed markers that are consistent with the presence of deoxyguanosine residues in the syn conformation, this suggests the presence of anti-parallel G-quadruplexes. To identify the species that contain syn guanine residues, we used circular dichroism and gel electrophoresis to study an ODN in which all of the guanine residues were brominated, d(A₁₅^8-BrG₁₅). In the presence of potassium, d(A₁₅^8-BrG₁₅) forms what appears to be an anti-parallel dimeric G-quadruplex. To our knowledge, this is the first report of a DNA sequence having all its guanine residues replaced by 8-bromo-guanine and maintaining its ability to form a G-quadruplex structure.     

Structural Colour in Butterfly Apatura Ilia Scales and the Microstructure Simulation of Photonic Crystal

The butterfly Apatura ilia is a species in the Northeast of China. There are billions of tiny scales on its wings, which overlap like roof tiles and completely cover the membrane, appearing as dust to people naked eye. The scales produce brilliant structural colour through their multilayer microstructure. In this paper, the microstructure and geometrical dimension of the scales were observed using a Scanning Electron Microscope (SEM). The cross section micro-configuration of the purple scales was achieved using a Transmission Electron Microscope (TEM). The reflectivity of the wing was measured by a spectrometer. The 3D multilayer microstructure of the ridges was optimized to 1D photonic crystal structure. The spectrometer experimental graph is in accord with the 1D photonic crystal simulation curves basically. In the end, the phenomenon of the purple structural colour was explained through the Snell equation.     

Modeling the Structure of RNA Molecules with Small-Angle X-Ray Scattering Data

We propose a novel fragment assembly method for low-resolution modeling of RNA and show how it may be used along with small-angle X-ray solution scattering (SAXS) data to model low-resolution structures of particles having as many as 12 independent secondary structure elements. We assessed this model-building procedure by using both artificial data on a previously proposed benchmark and publicly available data. With the artificial data, SAXS-guided models show better similarity to native structures than ROSETTA decoys. The publicly available data showed that SAXS-guided models can be used to reinterpret RNA structures previously deposited in the Protein Data Bank. Our approach allows for fast and efficient building of de novo models of RNA using approximate secondary structures that can be readily obtained from existing bioinformatic approaches. We also offer a rigorous assessment of the resolving power of SAXS in the case of small RNA structures, along with a small multimetric benchmark of the proposed method.     

Assessment of the spatial variability of intertidal benthic communities by axial tomodensitometry: importance of fine-scale heterogeneity

At the water-sediment interface of aquatic ecosystems, the presence of biogenic structures produced by benthic invertebrates strongly affects biogeochemical processes. The quantification of these structures and the assessment of the vertical distribution of fauna are essential for determining the impact of communities in sediments. In the present study, computer axial tomodensitometry (CAT-scan) was used to measure the space occupied by an intertidal community of the St. Lawrence estuary. Three cores were sampled at a site that was considered homogeneous according to surface sediments. The vertical distribution of biogenic structures and gravel were measured in the three cores using CAT-scan; the vertical distribution of fauna was also analysed for each core. The biogenic structures were highest at the water-sediment interface and decreased with depth in the three cores. The number of invertebrates also decreased with depth. We observed similar distributions of biogenic structures in cores 1 and 2. However, fewer biogenic structures were observed below 90 mm in core 3. This result was correlated with a high quantity of gravel from 90 to 140 mm in core 3 whereas the other cores had lower quantities of coarse material. We found relationships among the distributions of biogenic structures, fauna, and sediment characteristics (gravel quantity) that can affect species distribution. The vertical distributions of Macoma balthica, Mya arenaria, Nereis virens, and small-sized gallery-producing species (nematodes and oligochaetes) could also be recorded with the CAT-scan method. Thus, CAT-scan is an excellent tool to determine the fine-scale heterogeneity in the space occupied by benthic invertebrates in sediments.     

Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins

Clathrin-coated structures must assemble on cell membranes to internalize receptors, with the clathrin protein only linked to the membrane via adaptor proteins. These structures can grow surprisingly large, containing over 20 clathrin, yet they often fail to form productive vesicles, instead aborting and disassembling. We show that clathrin structures of this size can both form and disassemble spontaneously when adaptor protein availability is low, despite high abundance of clathrin. Here, we combine recent in vitro kinetic measurements with microscopic reaction-diffusion simulations and theory to differentiate mechanisms of stable vs unstable clathrin assembly on membranes. While in vitro conditions drive assembly of robust, stable lattices, we show that concentrations, geometry, and dimensional reduction in physiologic-like conditions do not support nucleation if only the key adaptor AP-2 is included, due to its insufficient abundance. Nucleation requires a stoichiometry of adaptor to clathrin that exceeds 1:1, meaning additional adaptor types are necessary to form lattices successfully and efficiently. We show that the critical nucleus contains ~25 clathrin, remarkably similar to sizes of the transient and abortive structures observed in vivo. Lastly, we quantify the cost of bending the membrane under our curved clathrin lattices using a continuum membrane model. We find that the cost of bending the membrane could be largely offset by the energetic benefit of forming curved rather than flat structures, with numbers comparable to experiments. Our model predicts how adaptor density can tune clathrin-coated structures from the transient to the stable, showing that active energy consumption is therefore not required for lattice disassembly or remodeling during growth, which is a critical advance towards predicting productive vesicle formation.     

A Structural Portrait of the PDZ Domain Family

PDZ (PSD-95/Discs-large/ZO1) domains are interaction modules that typically bind to specific C-terminal sequences of partner proteins and assemble signaling complexes in multicellular organisms. We have analyzed the existing database of PDZ domain structures in the context of a specificity tree based on binding specificities defined by peptide-phage binding selections. We have identified 16 structures of PDZ domains in complex with high-affinity ligands and have elucidated four additional structures to assemble a structural database that covers most of the branches of the PDZ specificity tree. A detailed comparison of the structures reveals features that are responsible for the diverse specificities across the PDZ domain family. Specificity differences can be explained by differences in PDZ residues that are in contact with the peptide ligands, but these contacts involve both side-chain and main-chain interactions. Most PDZ domains bind peptides in a canonical conformation in which the ligand main chain adopts an extended β-strand conformation by interacting in an antiparallel fashion with a PDZ β-strand. However, a subset of PDZ domains bind peptides with a bent main-chain conformation and the specificities of these non-canonical domains could not be explained based on canonical structures. Our analysis provides a structural portrait of the PDZ domain family, which serves as a guide in understanding the structural basis for the diverse specificities across the family.     

Nucleic acid helix structure determination from NMR proton chemical shifts

We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.