PMC

The core and flexible Pacific Ocean viromes. (a) Euler diagram depicting shared and exclusive PCs that are core to the photic and aphotic zone viromes. (b) Core and flexible PCs as a function of the number of viromes in the analysis. Core PCs (squares) are present in all viromes considered, whereas flexible PCs (triangles) are present in only a subset of viromes. Symbols represent the average number of PCs for all combinations of a given number of metagenomes, and error bars represent the range.

Sensor sensitivity for applications inside steel cord conveyor belts: (a) Response curve of wire rope core conveyor belt to pressure and resistance change of internal flexible sensor. (b) Response curve of the change in resistance of the internal flexible sensor and the amount of pulling force on the conveyor belt rope.

a) The structure of a monomeric HBc VLP with one HBcAg dimer shown in a surface representation coloured yellow and green. b) Two HBcAg sequences fused together via a flexible linker makes a tandem core construct, with either full-length (hetero-tandem) or truncated (homo-tandem) C-terminus, and two modifiable major insertion regions (MIRs). c) Structure of a tandem core protein: N-terminal core 1 (in green) is fused via a flexible linker (red) to C-terminal core 2 (yellow). The two views are related by a 90° rotation.

(a) The flexible and rigid piezoelectric sensitive core sample. (b) The FPCHT and RPCHT sample.

Functional categorization of ORFs in core and flexible BvgAS regulons. Bvg-regulated genes (red, Bvg activated; green, Bvg repressed) were grouped by functional categories (, ). Data are expressed as the percentage that is regulated by BvgAS among all annotated ORFs in each class. (A) B. bronchiseptica. ORFs in the core regulon were Bvg regulated by strains RB50, Bbr77, and Bbr81. Those in the flexible regulon were Bvg regulated in either one or two of the three strains. (B) B. pertussis. ORFs in the core regulon were Bvg regulated by strains GMT-1 and Tohama I. Those in the flexible regulon were Bvg regulated in only one of the two strains.

Outline of the construction of double-bend tRNA–A₅ bulge constructs. (A) Construction of the tRNA core and A₅ bulge. The phasing bases are indicated as N. The additional extensions are indicated as (dotted line). (B) Schematic representation of the phase constructs for a rigid tRNA core, and (C) for a flexible tRNA core.

—The P. aeruginosa pan-genome (A) a pan-genome is constituted by three types of genes: core, flexible, and unique. Core genes are present in all isolates of a given bacterial species, flexible genes are present in more than one isolates but not all of them, unique genes are present in one single isolate. (B) Pie chart showing the proportions of core, flexible and unique genes determined by SaturnV (https://github.com/ejfresch/saturnV; last accessed May 18, 2017). Unique genes constitute 51% of the P. aeruginosa pan-genome, whereas flexible genes constitute 48% of it. Core genes constitute only 1% of the pan-genome.

Gene necessity analysis and COG functional enrichment of HEG. All coding-sequence genes were searched on the Database of Essential Genes (DEG8.0 []) using BLASTx (E-value = 1 × 10^-4). (a) Comparison of the DEG-hit genes in the core and flexible genomes. (b) Comparisons of gene expression subclasses between DEG-hit and DEG-miss genes. (c) COG functional enrichment of HEG in the core genome. Statistic significance was performed by Fisher’s exact test (one-tailed). P-value ≤ 0.05 was indicated in figure. COG, clusters of orthologous groups; Core, the core genome; DEG-hit, genes with homologs identified in the database; DEG-miss, genes without any known homologs; Flexible, the flexible genome; Unk, unknown function.

Comparison of simulated core stability (R_g data as of ) with experimentally obtained DLS data, providing R_h. (a) Comparison with experimentally available mutants without flexible domains (CD). For these, experimental R_h is defined accurately because (almost) no flexible regions disturb the measurement. PCC = 0.986. (b) Comparison with mutants with flexible domains. The variable conformation of flexible domains in these cases blurs the experimental results. The PCC decreases to 0.857. All the experimental data from Guo et al. were rearranged for this comparison study.

(a) Schematic diagram of the TB-OFDI distal end. (b) Photograph of the polished ball-lens optical core. (c) Photograph of the flexible OFDI catheter insert. The inner optical core, which is encased in a nitinol driveshaft, is located within the sealed, optically transparent polyimide sheath.

(Left) Schematic illustration of the flexible core, flexible helix model. The coordinates ϕ₁,ϕ₂ () are decomposed into the contribution from the flexible junction core (ϕ_J1,ϕ_J2) and from the flexible helix (ϕ_H1,ϕ_H2): ϕ₁ = ϕ_J1 + ϕ_H1, ϕ₂ = ϕ_J2 + ϕ_H2. (Panels) Fitting of the isotropic flexible core, flexible helix model. The contour length is the distance along H76 from its base pair closest to the core to the middle of the segment chosen in H76. The bending angle variation is defined by . The model predicts a linear relation between the contour length and the bending angle variation []. The simulated data (blue crosses) satisfy the linear relation very well. The model stiffness parameters are inferred from the fitted linear functions (red lines). The intersection of the line with the y-axis determines the stiffness of the junction core a_J, the line slope determines the stiffness of the helix expressed by persistence length L_p [ and ]. The stiffness parameters inferred from the data are shown. The complete list of the inferred parameters is in , analogous plots for the remaining systems are in Supplementary Figure S3.

(Color online) (a) Flexible optitrode; inset shows the cross-sectional view: tetrode (T), inner cladding (IC), core (C), and outer cladding (OC); (b) optitrode snaked through a tetrode micro-drive for studying free-moving rats.

a, Cartoon representation of the in vitro VACV core based on visual analysis of tomograms, depicting a slice through the center of the core (top) and details of the three layers from the side and top view (bottom). The red structures, displayed as circles in the top view, represent the ring-like structures. b, Digital slices of a representative tomogram with side (left) and top (right) views of the in vitro core. The top view reveals a palisade made of tube-like structures, the stakes, that have an irregular arrangement. The side view of the core reveals three layers, that is, the palisade, the core wall and the innermost layer, and sparse densities in the inner part of the core. Insets indicate the rough positions of the respective tomogram slices with respect to the core. c–f, Details of the three different layers surrounding the inner part of the core from the side (S) and the top (T) views. c, Detail of the organization from the side view (left) and its corresponding annotation (right). The dark blobs depict the strong density occasionally observed on top of the palisade stakes. d, Detail of the palisade layer at the surface of the core from the top view (top) and its corresponding annotation (bottom): the palisade stakes in blue with connections between them in violet and the ring-like structures in red. e, Detail of the core wall layer from the top view (top) and its corresponding annotation showing the stripe-like pattern in orange (bottom). f, Detail of the innermost layer of the core wall from the top view (top) and its corresponding annotation in green (bottom). Scale bars, 30 nm.

Mediator-Tail and SAGA sensitivity depend on a combination of UAS localization and flexible core promoter elements. TFIID sensitivity is dependent on the core promoter sequence and independent of UAS identity.

A representative snapshot of the hydrophilic core of the ligase from Molecular Dynamics simulations. The point of view is that of the flexible termini. Protein residues in the core are colored yellow, zinc ions atoms are grey balls, and water molecules within 5 Å of zinc ions are red.

Relative abundance and distribution of selected COG categories within SAR11 core and flexible genomes (A) or SAR11 shared non-core and unique genes (B).

a) Schematic of a flexible core/cladding step-index optical fiber and the chemical structures of the core (POMC) and cladding (POC) materials. b) FTIR spectra of POMC and POC. c) Refractive indices and d) material attenuations of POMC and POC.

-values obtained from three independent fits to Equation (7) as a function of the solute diameter for drugs housed in the core of rigid and flexible nanogels (square and circles, respectively). The predictions obtained from Equations (5) and (8) (rigid nanogel, open black squares) and Equations (6) and (8) (flexible nanogel, open red circles) are also plotted.

Small-molecule cores of SMDH₃ comonomers with three DNA arms. Cores 1 and 2 are both pyramidal but 1 is flexible and 2 is more rigid. Cores 3 and 4 are both trigonal planar and rigid. For the remainder of this paper, we will use the notation fSMDH₃, pyrSMDH₃, tpSMDH₃, and rSMDH₃ to denote SMDHs with 3 arms based on cores 1, 2, 3, and 4, respectively. When there is a T_n spacer between the core and the DNA arm, the notation T_n will be inserted in between the core notations and the SMDH₃ notation. For example, pyr-T₃-SMDH₃ indicates a three-arm SMDH based on the pyramidal core 2, with a T₃ spacer between the core and each of the DNA arms. In addition, we will use the notation 9-fSMDH₃ to indicate a three-arm SMDH based on the flexible core 1 and 9 bases on each of the DNA arms.

Fraction of drug released at 100 ns as a function of the solute size for rigid and flexible nanogels (square and circles, respectively). Drug molecules are housed in the core of the nanogel.