DNA,Flexibly Flexible

Investigators have constructed dsDNA molecules with several different base modifications and have characterized their bending and twisting flexibilities using atomic force microscopy, DNA ring closure, and single-molecule force spectroscopy with optical tweezers. The three methods provide persistence length measurements that agree semiquantitatively, and they show that the persistence length is surprisingly similar for all of the modified DNAs. The circular dichroism spectra of modified DNAs differ substantially. Simple explanations based on base stacking strength, polymer charge, or groove occupancy by functional groups cannot explain the results, which will guide further high-resolution theory and experiments.     

DNA,Flexibly Flexible

Investigators have constructed dsDNA molecules with several different base modifications and have characterized their bending and twisting flexibilities using atomic force microscopy, DNA ring closure, and single-molecule force spectroscopy with optical tweezers. The three methods provide persistence length measurements that agree semiquantitatively, and they show that the persistence length is surprisingly similar for all of the modified DNAs. The circular dichroism spectra of modified DNAs differ substantially. Simple explanations based on base stacking strength, polymer charge, or groove occupancy by functional groups cannot explain the results, which will guide further high-resolution theory and experiments.Real double-stranded DNA molecules differ from the idealized zero-Kelvin A, B, and Z forms. They can adopt deformed average conformations, as in bent A-tract DNA or protein-DNA complexes. The path of the DNA helix axis also varies due to thermal energy, so at very long lengths DNA behaves as a random coil. The term “long lengths” is relative to the persistence length P of the wormlike chain model. P is the average offset of the end of a chain along its initial direction, or alternatively the length over which the unit vectors μ1→ and μ2→ tangent to the helix axis lose colinearity according to〈μ1→⋅μ2→〉=〈cosθ〉=e−d12/P,where d₁₂ is the contour length from point 1 to point 2, as in Fig. 1. P can be measured by hydrodynamics (1), atomic force microscopy (AFM) (2), DNA ring closure (3) or protein-DNA looping (4), tethered particle microscopy (5), or single-molecule optical tweezers experiments (6). The long-range loss of memory of DNA direction grows out of local variations in the helix axis direction specified by roll, tilt, and twist angles that parameterize changes in the helix axis direction. For harmonic bending potentials, the bending persistence length is related to roll and tilt according toσroll2+σtilt2=2ℓ/P,where ℓ = 3.4 Å, so for P ∼ 50 nm (147 bp) the average standard deviations in the roll and tilt angles σ_roll and σ_tilt are ∼4.7°, although in real DNA, roll varies more than tilt. Similar relationships hold for twist flexibility (7).Open in a separate windowFigure 1The base modifications studied by Peters et al. (13,14) affect both Watson-Crick hydrogen bonding and groove occupancy. They used AFM, DNA ring closure, single-molecule force spectroscopy, and circular dichroism spectroscopy (not shown) to characterize the resulting changes in bending and twisting flexibility. DNA molecules are not shown to scale. To see this figure in color, go online.DNA flexibility can be studied at contour length scales from Ångstroms to microns. Flexibility at the atomic scale accessed by nuclear magnetic resonance, x-ray crystallography, cryo-electron microscopy, and molecular dynamics simulations (8) refers to many aspects of conformational variability. One active thread of research at this scale concerns interconversion among helical forms, base flipping, DNA kinking, changes in backbone torsion angles, and the sequence dependence of all of these local properties. Local fluctuations in the basepair roll, tilt, and twist angles do seem to predict the correct long-range behavior (9). A second thread asks whether the wormlike chain model holds at DNA lengths shorter than P (2,10); the active controversy concerning enhanced bendability at short lengths has recently been reviewed by Vologodskii and Frank-Kamenetskii (11). A third thread asks whether we can understand the underlying biophysical causes of long-range DNA flexibility. These presumably include base stacking, electrostatic repulsion along the backbone, changes in the counterion atmosphere (12), occupancy of the major and minor grooves by functional groups, conformational entropy, the strength of Watson-Crick hydrogen bonding, and water structure. Helical polymorphisms and the junctions between polymorphs presumably affect the sequence dependence of the persistence length.Peters et al. (13,14) have attempted to understand bending and twisting flexibility by characterizing a variety of modified nucleic acids using DNA ring closure, AFM, and optical tweezer methods, sketched in Fig. 1. In previous work (13), they used ring closure to show that major groove substituents that alter the charge on the polymer do not have substantial effects on the bending persistence length, and that the effects were not correlated in an obvious way to the stacking propensity of the modified bases. The work described in this issue of the Biophysical Journal (14) uses all three methods to demonstrate that DNA with 2-amino-adenosine (a.k.a., 2,6-diaminopurine) substituted for adenosine has an increased persistence length, whereas inosine substitution for guanosine reduces the persistence length, as would be expected if groove occupancy (or the number of Watson-Crick hydrogen bonds) affects flexibility. However, the authors did one experiment too many—when they measured the effects of the earlier major groove substituents (13) using AFM, the correlation with groove occupancy disappeared. This could be because changes in helical geometry, as evidenced by the circular dichroism spectroscopy also reported in the article, alter the grooves sufficiently to prevent a straightforward connection to flexibility.The magnitude of the effect of base modifications on P is the largest for the optical tweezers and the smallest for DNA ring closure, showing that no more than one of the experiments is perfect. The Supporting Material for both articles (13,14) offers valuable resources for the careful evaluation of experimental results and possible sources of error within and between experiments. For example, the DNA lengths and the ionic conditions required by the different methods differ. Ring closure results depend critically on the purity of the DNA and appropriate ligation conditions. Analysis of AFM results averaged several different statistical measures of decaying angular correlations and end-to-end distance, which did not individually always agree. In force spectroscopy there are variations in the bead attachment for each molecule, errors in the stretch modulus can affect the measured persistence length, force can induce DNA melting, and very few molecules can be observed. Rare kinking events proposed to explain enhanced bendability should affect the cyclization experiment most markedly; no evidence for enhanced flexibility was seen. Finally, Peters et al. (14) have observed that DNA twist and twisting flexibility seem to be more sensitive than the persistence length to base modifications.Taken as a whole, this extremely thorough series of experiments shows that we still do not understand the fundamental origins of the remarkable stiffness of double-stranded DNA. There may be compensating effects that make the dissection difficult. For example, changing the charge on the polymer may induce a corresponding adjustment in the counterion condensation atmosphere, leading to a relatively constant residual charge. Groove substituents that enhance basepair stability could enhance bendability for steric reasons. Stacking thermodynamics may not change very much for the very small bend angles at any individual basepair. Locally stiff regions may introduce nearby junctions that are flexible.The stiffness of DNA relative to other biopolymers inspired the development of DNA nanotechnology (although that field has adopted bridged synthetic constructs that are even more rigid). Further research on the biophysics, and specifically the long-range mechanical properties of DNA, will be essential as we build better models of DNA in the cell, which has evolved many proteins that act to increase apparent flexibility. The various aspects of DNA flexibility influence the protein-DNA complexes that mediate DNA’s informational role, the induction of and responses to supercoiling used for long-range communication among sites (15), and chromosome structure and genome organization.     

Flexible Fiberoptic Bronchoscopy: Anesthesia,Technique and Results

During a period of three years, 256 diagnostic bronchoscopies were done with flexible fiberoptic bronchoscopes at a Veterans Administration hospital. In all of these procedures, topical cocaine hydrochloride anesthesia was used, and it proved satisfactory and free of any undesirable side effects.The peroral route using an endotracheal tube is preferred for flexible bronchofiberscopy. Fluoroscopic guidance is essential in examining peripheral lung lesions. A 70 percent positive yield was obtained for patients with peripheral carcinoma of the lung as contrasted to a 47 percent yield when the tissue specimens were obtained blindly.     

A Simple,Flexible Failure Model

A new failure model is introduced in the form of a four-parameter nonlinear differential equation, with failure probability as the dependent variable and failure time as the independent variable. The first parameter characterizes the location, the second the scale, and the other two the shape of the model. The type of the accompanying hazard function is immediately read off the shape parameters. The new model approximates the classical failure models with rather high precision, but also models cases where the failure density is skewed to the left. It can be used to analyze survival data objectively, based on the shape of the failure distribution. The computation of quantiles and moments is easy and fast. Nonlinear regression methods are used to estimate parameter values.     

GranatumX: A Community-engaging,Modularized, and Flexible Webtool for Single-cell Data Analysis

We present GranatumX, a next-generation software environment for single-cell RNA sequencing (scRNA-seq) data analysis. GranatumX is inspired by the interactive webtool Granatum. GranatumX enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical environment. It also offers software developers the opportunity to rapidly promote their own tools with others in customizable pipelines. The architecture of GranatumX allows for easy inclusion of plugin modules, named Gboxes, which wrap around bioinformatics tools written in various programming languages and on various platforms. GranatumX can be run on the cloud or private servers and generate reproducible results. It is a community-engaging, flexible, and evolving software ecosystem for scRNA-seq analysis, connecting developers with bench scientists. GranatumX is freely accessible at http://garmiregroup.org/granatumx/app.     

Flexible ligand docking using conformational ensembles.

Molecular docking algorithms suggest possible structures for molecular complexes. They are used to model biological function and to discover potential ligands. A present challenge for docking algorithms is the treatment of molecular flexibility. Here, the rigid body program, DOCK, is modified to allow it to rapidly fit multiple conformations of ligands. Conformations of a given molecule are pre-calculated in the same frame of reference, so that each conformer shares a common rigid fragment with all other conformations. The ligand conformers are then docked together, as an ensemble, into a receptor binding site. This takes advantage of the redundancy present in differing conformers of the same molecule. The algorithm was tested using three organic ligand protein systems and two protein-protein systems. Both the bound and unbound conformations of the receptors were used. The ligand ensemble method found conformations that resembled those determined in X-ray crystal structures (RMS values typically less than 1.5 A). To test the method's usefulness for inhibitor discovery, multi-compound and multi-conformer databases were screened for compounds known to bind to dihydrofolate reductase and compounds known to bind to thymidylate synthase. In both cases, known inhibitors and substrates were identified in conformations resembling those observed experimentally. The ligand ensemble method was 100-fold faster than docking a single conformation at a time and was able to screen a database of over 34 million conformations from 117,000 molecules in one to four CPU days on a workstation.     

Tracking Changing Environments: Innovators Are Fast,but Not Flexible Learners

Behavioural innovations are increasingly thought to provide a rich source of phenotypic plasticity and evolutionary change. Innovation propensity shows substantial variation across avian taxa and provides an adaptive mechanism by which behaviour is flexibly adjusted to changing environmental conditions. Here, we tested for the first time the prediction that inter-individual variation in innovation propensity is equally a measure of behavioural flexibility. We used Indian mynas, Sturnus tristis, a highly successful worldwide invader. Results revealed that mynas that solved an extractive foraging task more quickly learnt to discriminate between a cue that predicted food, and one that did not more quickly. However, fast innovators were slower to change their behaviour when the significance of the food cues changed. This unexpected finding appears at odds with the well-established view that avian taxa with larger brains relative to their body size, and therefore greater neural processing power, are both faster, and more flexible learners. We speculate that the existence of this relationship across taxa can be reconciled with its absence within species by assuming that fast, innovative learners and non innovative, slow, flexible learners constitute two separate individual strategies, which are both underpinned by enhanced neural processing power. This idea is consistent with the recent proposal that individuals may differ consistently in ‘cognitive style’, differentially trading off speed against accuracy in cognitive tasks.     

Flexible chitin films: structural studies

Chitin gels were transformed into thin, flexible chitin films with minimal dimensional shrinkage and maximum flexibility and thickness in the range of 25-80 microm by a cold-press process. Solvent residue was removed by heating the films at 50 degrees C for 12 h, followed by rinsing in 95% ethanol. The crystallinity and mechanical properties of the flexible chitin films were found to be a function of the amount of shrinkage from the gel to the final film that was obtained. For 28-microm thick films with 30% shrinkage, transparency of up to 90% was found. X-ray diffractometry (XRD) showed that the number of diffraction peaks appearing at 2theta;=23 degrees and 2theta;=27 degrees became increasingly sharper with shrinkage. Topographical information obtained from scanning electron microscopy (SEM) and atomic force microscopy (AFM) attributed the structural morphology of the films to the formation of sub-microscopic micelles. Scanning transmission electron microscopy (STEM) showed that shrinkage resulted in coarser microstructure, affecting tensile properties, where the ductility and toughness were proportional to the amount of shrinkage. These flexible chitin films have potential as wound dressing materials.     

Recent Progress in Flexible Electrochemical Capacitors: Electrode Materials,Device Configuration,and Functions

With increasing demand for portable, flexible, and even wearable electronic devices, flexible energy storage systems have received increasing attention as a key component in this emerging field. Among the options, supercapacitors, commonly referred to as ultracapacitors or electrochemical capacitors, are widely recognized as a potential energy storage system due to their high power, fast charge/discharge rate, long cycling life‐time, and low cost. To date, considerable effort has been dedicated to developing high‐performance flexible supercapacitors based on various electrode materials; including carbon nanomaterials (e.g., carbon nanotubes, graphene, porous carbon materials, carbon paper, and textile), conducting polymers (e.g., polyaniline, polypyrrole, polythiophene), and hybrid materials. A brief introduction to the field is provided and the state‐of‐the‐art is reviewed with special emphasis on electrode materials and device configurations.     

Production Capacity Modeling of Alternative, Nonidentical, Flexible Machines

Analyzing the production capacity of a flexible manufacturing system consisting of a number of alternative, nonidentical, flexible machines, where each machine is capable of producing several different part types simultaneously (by flexibly allocating its production capacity among these part types), is not a trivial task. The production capacity set of such a system is naturally expressed in terms of the machine-specific production rates of all part types. In this paper we also express it in terms of the total production rates of all part types over all machines. More specifically, we express the capacity set as the convex hull of a set of points corresponding to all possible assignments of machines to part types, where in each assignment each machine allocates all its capacity to only one part type. First, we show that within each subset of assignments having a given number of machines assigned to each part type, there is a unique assignment that corresponds to an extreme point of the capacity set. Then, we propose a procedure for generating all the extreme points and facets of the capacity set. Numerical experience shows that when the number of part types is less than four, the size of the capacity set (measured in terms of the number of variables times the number of constraints) is smaller, if the capacity set is expressed in terms of the total production rates of all part types over all machines than if it is expressed in terms of the machine-specific production rates of all part types. When the number of part types is four or more, however, the opposite is true.     

Flexible social structure of a desert rodent, Rhombomys opimus: philopatry, kinship, and ecological constraints

We tested hypotheses based on philopatry, kinship, and ecologicalconstraints to explain sociality in a semifossorial desert rodent,the great gerbil, Rhombomys opimus. Data were collected in thefield in Uzbekistan in the spring and fall of 1996 and 1998–2004.Population densities fluctuated dramatically with high turnoverin both males and females to reveal that dispersal and socialstructure were density dependent. Fewer gerbils dispersed athigher densities and members of family groups dispersed together.A majority of females lived in groups at high densities, butas population densities declined, proportionally more femaleswere solitary. DNA analysis revealed that group-living femaleswere genetically similar, whereas solitary females visited bythe same male, as well as adult males and females in the samefamily group, were usually not genetically similar. Reproductivesuccess as measured by the number of emergent pups and survivalof juveniles during the summer drought was not related to groupsize or whether females were philopatric. A majority of femalesin family groups reproduced, and all females engaged in cooperativebehaviors. We accepted three hypotheses to explain fluctuationsin group formation in the great gerbil: variation in food abundanceand distribution, habitat saturation, and kinship. We concludethat great gerbils are facultatively social. Flexible socialbehavior may be adaptive in unpredictable desert conditions.Females live solitarily under conditions of limited food andhigh mortality that disrupt social behavior and group formationand share territories with female kin under favorable conditionsfor survival and reproduction when kin groups can be maintained.Males adjust to the distribution of females.     

The Art of Being Flexible: How to Escape from Shade,Salt, and Drought

Environmental stresses, such as shading of the shoot, drought, and soil salinity, threaten plant growth, yield, and survival. Plants can alleviate the impact of these stresses through various modes of phenotypic plasticity, such as shade avoidance and halotropism. Here, we review the current state of knowledge regarding the mechanisms that control plant developmental responses to shade, salt, and drought stress. We discuss plant hormones and cellular signaling pathways that control shoot branching and elongation responses to shade and root architecture modulation in response to drought and salinity. Because belowground stresses also result in aboveground changes and vice versa, we then outline how a wider palette of plant phenotypic traits is affected by the individual stresses. Consequently, we argue for a research agenda that integrates multiple plant organs, responses, and stresses. This will generate the scientific understanding needed for future crop improvement programs aiming at crops that can maintain yields under variable and suboptimal conditions.A fundamental difference between plant and animal development is the plasticity in organ formation after germination. Whereas animals are born with a complete set of organs, a germinating seedling has just one embryonic root and one or two embryonic leaves, the cotyledons. All other organs are formed postembryonically, by the interplay of developmental programs and environmental conditions. So, although each plant has a basic body plan, its final size and shape are largely determined by the specific conditions that the plant experiences, and its growth can be adjusted to suit those conditions. This interplay is crucial in both natural and agricultural settings where plants forage for resources and often avoid/escape from stress.Examples of how plants adjust to environmental conditions include phototropism (Darwin, 1880) to bring the photosynthesizing leaves into well-lit microsites such as canopy gaps and root proliferation toward moisture- or nutrient-rich areas to enhance water uptake and nutrient acquisition (Comas et al., 2013). Examples of stress escape include shoot elongation away from the shade of neighbor plants (shade avoidance; Pierik and de Wit, 2014), escape from submerged conditions to reach the air (Bailey-Serres and Voesenek, 2008), and root growth away from saline soil microsites (halotropism; Galvan-Ampudia et al., 2013). Although some of these responses are termed escape from stress (e.g. shade avoidance), others are considered as attraction to more favorable conditions (e.g. hydrotropism). In the case of directional growth responses, the most unifying way is probably to consider these as responses to gradients of stresses (e.g. salt) or resources (e.g. water).The molecular, biochemical, and physiological pathways that underlie these responses have been intensively researched, and this has provided substantial knowledge on the regulatory mechanisms. However, relatively little research has been devoted to studying these modes of plasticity in combination. For example, dense plantings of crops growing on irrigated soils in arid conditions likely need to deal with drought, soil salinity, and shading by neighbor crops and weeds simultaneously. Above ground, plants use light cues, particularly enrichment of far-red light (FR) through reflection by nearby vegetation, to detect neighboring vegetation and respond with shade avoidance responses (Casal, 2013; Pierik and de Wit, 2014). Below ground, plants can sense neighbors and their abiotic environment through a variety of putative cues. Some of these result from selective changes made to the rhizospheres by root absorption of minerals and water and excretion of organic compounds. Plants respond to these cues in various ways, including growth toward or away from neighbors, nutrient hotspots, water, and more (Fang et al., 2013; Pierik et al., 2013).Importantly, the global crop production chain is anticipating intensification of various abiotic stresses: increased temperatures, progressive salinization of highly water-limited production grounds, and more extreme situations of drought and flood (Tubiello et al., 2007; Bailey-Serres and Voesenek, 2008; Munns and Tester, 2008). At the same time, agricultural productivity must be increased to feed the ever-expanding global population, calling for high-density cropping systems with potentially severe mutual shading among plants. Therefore, it is of great importance to understand how plants respond to high-density and abiotic stress(es) simultaneously.Here, we will review the current molecular and physiological understanding of both shoot developmental plasticity in response to high plant density-derived light signals (shade avoidance) and root developmental plasticity in response to the widely occurring abiotic stresses salt and drought. We will then implement this mechanistic knowledge to generate ideas about (1) how these different modes of plasticity may interact to modulate the known stress response phenotypes and (2) how responses to one stress may affect responses to a second. Addressing these ideas experimentally will generate the knowledge needed to guide crop improvement programs under suboptimal agricultural conditions.     

Flexible structural comparison allowing hinge-bending, swiveling motions

We present an efficient method for flexible comparison of protein structures, allowing swiveling motions. In all currently available methodologies developed and applied to the comparisons of protein structures, the molecules are considered to be rigid objects. The method described here extends and generalizes current approaches to searches for structural similarity between molecules by viewing proteins as objects consisting of rigid parts connected by rotary joints. During the matching, the rigid subparts are allowed to be rotated with respect to each other around swiveling points in one of the molecules. This technique straightforwardly detects structural motifs having hinge(s) between their domains. Whereas other existing methods detect hinge-bent motifs by initially finding the matching rigid parts and subsequently merging these together, our method automatically detects recurring substructures, allowing full 3 dimensional rotations about their swiveling points. Yet the method is extremely fast, avoiding the time-consuming full conformational space search. Comparison of two protein structures, without a predefinition of the motif, takes only seconds to one minute on a workstation per hinge. Hence, the molecule can be scanned for many potential hinge sites, allowing practically all C(alpha) atoms to be tried as swiveling points. This algorithm provides a highly efficient, fully automated tool. Its complexity is only O(n2), where n is the number of C(alpha) atoms in the compared molecules. As in our previous methodologies, the matching is independent of the order of the amino acids in the polypeptide chain. Here we illustrate the performance of this highly powerful tool on a large number of proteins exhibiting hinge-bending domain movements. Despite the motions, known hinge-bent domains/motifs which have been assembled and classified, are correctly identified. Additional matches are detected as well. This approach has been motivated by a technique for model based recognition of articulated objects originating in computer vision and robotics.     

Ribozymes: Flexible molecular devices at work

The discovery of ribozymes, RNAs with catalytic activity, revealed the extraordinary characteristic of this molecule, and corroborated the idea that RNA was the first informative polymer. The “RNA world” hypothesis asserts that the DNA/RNA/PROTEIN world arose from an earlier RNA world in which were present only RNA molecules able to perform both of the two functions performed separately by DNA and proteins in the present-day cells: the ability to transfer genetic information and to carry out catalytic activity.The catalytic properties of ribozymes are exclusively due to the capacity of RNA molecules to assume particular structures. Moreover, the structural versatility of RNA can allow to a single RNA sequence to fold in more than one structure, able to perform more than one function. In the first part of this work we will discuss the RNA plasticity, focusing on “bifunctional” ribozymes isolated by in vitro selection experiments, and on the consequences of this plasticity in the prospective of the emergence of new specific functions.The possibility that one sequence could have more than one structure/function, greatly increase the evolutionary potential of RNA, and the capacity of RNA to switch from a structure/function to another is probably one of the reasons of the evolutionary success also in modern-day cells. Naturally occurring ribozymes discovered in contemporary cells, demonstrate the crucial role that ribozymes still have in the modern protein world. In the second part of this paper we will discuss the capacity of natural ribozymes to modulate gene expression making use of their exclusive catalytic properties. Moreover, we will consider the possibility of their ancient origin.