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Find video protocols related to scientific articles indexed in Pubmed.
Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.
J. Mol. Biol.
PUBLISHED: 08-08-2014
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Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged and six uncharged residues at the interface that play a dominant role in the compaction transition, and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations.
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Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes.
Nucleic Acids Res.
PUBLISHED: 08-06-2014
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Torsionally stressed DNA plays a critical role in genome organization and regulation. While the effects of torsional stresses on naked DNA have been well studied, little is known about how these stresses propagate within chromatin and affect its organization. Here we investigate the torsional behavior of nucleosome arrays by means of Brownian dynamics simulations of a coarse-grained model of chromatin. Our simulations reveal a strong dependence of the torsional response on the rotational phase angle ?0 between adjacent nucleosomes. Extreme values of ?0 lead to asymmetric, bell-shaped extension-rotation profiles with sharp maxima shifted toward positive or negative rotations, depending on the sign of ?0, and to fast, irregular propagation of DNA twist. In contrast, moderate ?0 yield more symmetric profiles with broad maxima and slow, uniform propagation of twist. The observed behavior is shown to arise from an interplay between nucleosomal transitions into states with crossed and open linker DNAs and global supercoiling of arrays into left- and right-handed coils, where ?0 serves to modulate the energy landscape of nucleosomal states. Our results also explain the torsional resilience of chromatin, reconcile differences between experimentally measured extension-rotation profiles, and suggest a role of torsional stresses in regulating chromatin assembly and organization.
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Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor.
Nat Commun
PUBLISHED: 05-20-2014
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How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by transitioning between extended and compact states, orchestrated by electrostatic interactions between complimentarily charged residues across the interface between the N- and C-terminal subdomains. Here we show that site-directed alterations in these residues cause force dependent impairments of motor function including lower translocation velocity, lower stall force and higher frequency of pauses and slips. We further show that the measured impairments correlate with computed changes in free-energy differences between the two states. These findings support the proposed structural mechanism and further suggest an energy landscape model of motor activity that couples the free-energy profile of motor conformational states with that of the ATP hydrolysis cycle.
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Evolutionary dynamics and information hierarchies in biological systems.
Ann. N. Y. Acad. Sci.
PUBLISHED: 05-20-2013
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The study of evolution has entered a revolutionary new era, where quantitative and predictive methods are transforming the traditionally qualitative and retrospective approaches of the past. Genomic sequencing and modern computational techniques are permitting quantitative comparisons between variation in the natural world and predictions rooted in neo-Darwinian theory, revealing the shortcomings of current evolutionary theory, particularly with regard to large-scale phenomena like macroevolution. Current research spanning and uniting diverse fields and exploring the physical and chemical nature of organisms across temporal, spatial, and organizational scales is replacing the model of evolution as a passive filter selecting for random changes at the nucleotide level with a paradigm in which evolution is a dynamic process both constrained and driven by the informational architecture of organisms across scales, from DNA and chromatin regulation to interactions within and between species and the environment.
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Maternal death inquiry and response in India--the impact of contextual factors on defining an optimal model to help meet critical maternal health policy objectives.
Health Res Policy Syst
PUBLISHED: 11-30-2011
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Maternal death reviews have been utilized in several countries as a means of identifying social and health care quality issues affecting maternal survival. From 2005 to 2009, a standardized community-based maternal death inquiry and response initiative was implemented in eight Indian states with the aim of addressing critical maternal health policy objectives. However, state-specific contextual factors strongly influenced the efforts success. This paper examines the impact and implications of the contextual factors.
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Bio-ecology of the louse, Upupicola upupae, infesting the Common Hoopoe, Upupa epops.
J. Insect Sci.
PUBLISHED: 08-25-2011
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Abstract The population characteristics of the louse, Upupicola upupae (Shrank) (Mallophaga: Philopteridae: Ishnocera), infesting the Common Hoopae, Upupa epops L. (Aves: Upupiformes), were recorded during 2007-08 in District Rampur, Uttar Pradesh India. The pattern of frequency distribution of the louse conformed to the negative binomial model. The lice and its nits were reared in vitro at 35 ± 1° C, 75-82 % RH, on a feather diet. The data obtained was used to construct the life table and to determine the intrinsic rate of natural increase (0.035 female/day), the net reproductive rate was 3.67 female eggs/female, the generation time was 37 days, and the doubling time of the population was 19 days. The chaetotaxy of the three nymphal instars has also been noted to record their diagnostic characteristics. Information on egg morphology and antennal sensilla is also presented.
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Prevalence of Myrsidea salimalii (Amblycera: Phthiraptera) on striated babblers (Turdoides earlei) (Timaliidae: Passeriformes: Aves).
J Parasit Dis
PUBLISHED: 07-19-2011
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Survey of literature showed that the population characteristics of the phthirapterans parasitizing striated babblers deserved investigation. Hence, 30 birds were examined during 2007-2009 in district Rampur U.P. The prevalence of an amblyceran louse, Myrsidea salimalii on striated babblers was 40%. The mean intensity of infestation and the sample mean abundance were 33.5 and 13.4, respectively. The variance to mean ratio of the population exceeded unity (36.24). The frequency distribution pattern of the louse was aggregated but did not conform to the negative binomial model. Females outnumbered the males in natural condition (M:F-1:1.4) while the nymphal population had an edge over adult population (A:N-1:1.3).
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Engineering the cell-material interface for controlling stem cell adhesion, migration, and differentiation.
Biomaterials
PUBLISHED: 01-18-2011
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The effective utilization of stem cells in regenerative medicine critically relies upon our understanding of the intricate interactions between cells and their extracellular environment. While bulk mechanical and chemical properties of the matrix have been shown to influence various cellular functions, the role of matrix interfacial properties on stem cell behavior is unclear. Here, we report the striking effect of matrix interfacial hydrophobicity on stem cell adhesion, motility, cytoskeletal organization, and differentiation. This is achieved through the development of tunable, synthetic matrices with control over their hydrophobicity without altering the chemical and mechanical properties of the matrix. The observed cellular responses are explained in terms of hydrophobicity-driven conformational changes of the pendant side chains at the interface leading to differential binding of proteins. These results demonstrate that the hydrophobicity of the extracellular matrix could play a considerably larger role in dictating cellular behaviors than previously anticipated. Additionally, these tunable matrices, which introduce a new control feature for regulating various cellular functions offer a platform for studying proliferation and differentiation of stem cells in a controlled manner and would have applications in regenerative medicine.
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Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations.
BMC Biophys
PUBLISHED: 01-07-2011
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Eukaryotic genomes possess an elaborate and dynamic higher-order structure within the limiting confines of the cell nucleus. Knowledge of the physical principles and the molecular machinery that govern the 3D organization of this structure and its regulation are key to understanding the relationship between genome structure and function. Elegant microscopy and chromosome conformation capture techniques supported by analysis based on polymer models are important steps in this direction. Here, we review results from these efforts and provide some additional insights that elucidate the relationship between structure and function at different hierarchical levels of genome organization.
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Dynamic Electromechanical Hydrogel Matrices for Stem Cell Culture.
Adv Funct Mater
PUBLISHED: 01-07-2011
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Hydrogels have numerous biomedical applications including synthetic matrices for cell culture and tissue engineering. Here we report the development of hydrogel based multifunctional matrices that not only provide three-dimensional structural support to the embedded cells but also can simultaneously provide potentially beneficial dynamic mechanical and electrical cues to the cells. A unique aspect of these matrices is that they undergo reversible, anisotropic bending dynamics in an electric field. The direction and magnitude of this bending can be tuned through the hydrogel crosslink density while maintaining the same electric potential gradient, allowing control over the mechanical strain imparted to the cells in a three-dimensional environment. The conceptual design of these hydrogels was motivated through theoretical modeling of the osmotic pressure changes occurring at the gel-solution interfaces in an electric field. These electro-mechanical matrices support survival, proliferation, and differentiation of stem cells. Thus, these new three-dimensional in vitro synthetic matrices, which mimic multiple aspects of the native cellular environment, take us one step closer to in vivo systems.
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Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation.
Phys Chem Chem Phys
PUBLISHED: 12-15-2010
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The H4 histone tail plays a critical role in chromatin folding and regulation--it mediates strong interactions with the acidic patch of proximal nucleosomes and its acetylation at lysine 16 (K16) leads to partial unfolding of chromatin. The molecular mechanism associated with the H4 tail/acidic patch interactions and its modulation via K16 acetylation remains unknown. Here we employ a combination of molecular dynamics simulations, molecular docking calculations, and free energy computations to investigate the structure of the H4 tail in solution, the binding of the H4 tail with the acidic patch, and the effects of K16 acetylation. The H4 tail exhibits a disordered configuration except in the region Ala15-Lys20, where it exhibits a strong propensity for an ?-helical structure. This ?-helical region is found to dock very favorably into the acidic patch groove of a nucleosome with a binding free energy of approximately -7 kcal mol(-1). We have identified the specific interactions that stabilize this binding as well as the associated energetics. The acetylation of K16 is found to reduce the ?-helix forming propensity of the H4 tail and K16s accessibility for mediating external interactions. More importantly, K16 acetylation destabilizes the binding of the H4 tail at the acidic patch by mitigating specific salt bridges and longer-ranged electrostatic interactions mediated by K16. Our study thus provides new microscopic insights into the compaction of chromatin and its regulation via posttranslational modifications of histone tails, which could be of interest to chromatin biology, cancer, epigenetics, and drug design.
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Population characteristics and the nature of egg shells of two Phthirapteran species parasitizing Indian cattle egrets.
J. Insect Sci.
PUBLISHED: 11-12-2010
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The prevalence, intensities of infestation, range of infestation and population composition of two phthirapteran species, Ardeicola expallidus Blagoveshtchensky (Phthiraptera: Philopteridae) and Ciconiphilus decimfasciatus Boisduval and Lacordaire (Menoponidae) on seventy cattle egrets were recorded during August 2004 to March 2005, in India. The frequency distribution patterns of both the species were skewed but did not correspond to the negative binomial model. The oviposition sites, egg laying patterns and the nature of the eggs of the two species were markedly different.
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Chain stiffness and attachment-dependent attraction between polyelectrolyte-grafted colloids.
J Phys Chem B
PUBLISHED: 11-11-2010
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We report here the effects of chain stiffness and surface attachment on the effective interactions between polyelectrolyte-grafted colloidal particles in monovalent salt obtained using Monte Carlo simulations. Our approach involves computation of the distance-dependent potential of mean force between two polyelectrolyte-grafted colloidal particles treated at a coarse-grained resolution. Two chain stiffnesses, flexible and stiff, and two surface attachment modes, free and constrained, at low grafting densities are examined. PMF calculations across a range of surface and polyelectrolyte charge allows us to map out the strength and extent of the attractive and repulsive regime in the two-dimensional charge space. We observe striking differences in the effects of chain stiffness between the two modes of attachment. When the chains are freely attached, the stiff-chains colloids exhibit a marginal reduction in the attraction compared to their flexible-chain counterparts. In contrast, when the chains are attached in a constrained manner, the colloids with stiff chains exhibit a significantly stronger attraction and a broader attractive regime compared to flexible-chain colloids. These differences in the effects of stiffness between the two attachment modes are explained in terms of differences in the energetic and entropic forces balancing adsorption of chains at their own surface versus chain extension to mediate bridging interactions across two particles. Our results thus underscore the importance of surface attachment of chains and its proper accounting in computational and experimental studies and suggests the mode of chain attachment as an additional control parameter for modulating intercolloid interactions for applications such as stabilization of colloidal systems and bottom-up self-assembly of nanostructures.
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Heparin mimicking polymer promotes myogenic differentiation of muscle progenitor cells.
Biomacromolecules
PUBLISHED: 11-08-2010
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Heparin and heparan sulfate mediated basic fibroblast growth factor (bFGF) signaling plays an important role in skeletal muscle homeostasis by maintaining a balance between proliferation and differentiation of muscle progenitor cells. In this study we investigate the role of a synthetic mimic of heparin, poly(sodium-4-styrenesulfonate) (PSS), on myogenic differentiation of C2C12 cells. Exogenous supplementation of PSS increased the differentiation of C2C12 cells in a dose-dependent manner, while the formation of multinucleated myotubes exhibited a nonmonotonic dependence with the concentration of PSS. Our results further suggest that one possible mechanism by which PSS promotes myogenic differentiation is by downregulating the mitogen activated extracellular regulated signaling kinase (MAPK/ERK) pathway. The binding ability of PSS to bFGF was found to be comparable to heparin through molecular docking calculations and by native PAGE. Such synthetic heparin mimics could offer a cost-effective alternative to heparin and also reduce the risk associated with batch-to-batch variation and contamination of heparin.
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Influence of pulling handles and device stiffness in single-molecule force spectroscopy.
Phys Chem Chem Phys
PUBLISHED: 10-11-2010
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In single-molecule force spectroscopy, individual molecules and complexes are often stretched by pulling devices via intervening molecular handles. Accurate interpretation of measurements from such experiments in terms of the underlying energy landscape, defined by activation barriers and intrinsic rates of transition, relies on our understanding, and proper theoretical treatment, of the effects of the pulling device and handle. Here, we present a framework based on Kramers theory that elucidates the dependence of measured rupture forces and rates on the pulling device stiffness and attributes of the handle, contour length and persistence length. We also introduce a simple analytic model that improves prediction of activation barriers and intrinsic rates for all device stiffnesses and handle properties, thus allowing for a more reliable interpretation of experiments. Our analyses also suggests intuitive ways of displaying the measured force spectra for proper prognosis of device and handle effects and provides the range of device and handle attributes over which these effects can be neglected.
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Twist propagation in dinucleosome arrays.
Biophys. J.
PUBLISHED: 07-13-2010
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We present a Monte Carlo simulation study of the distribution and propagation of twist from one DNA linker to another for a two-nucleosome array subjected to externally applied twist. A mesoscopic model of the array that incorporates nucleosome geometry along with the bending and twisting mechanics of the linkers is employed and external twist is applied in stepwise increments to mimic quasistatic twisting of chromatin fibers. Simulation results reveal that the magnitude and sign of the imposed and induced twist on contiguous linkers depend strongly on their relative orientation. Remarkably, the relative direction of the induced and applied twist can become inverted for a subset of linker orientations-a phenomenon we refer to as "twist inversion". We characterize the twist inversion, as a function of relative linker orientation, in a phase diagram and explain its key features using a simple model based on the geometry of the nucleosome/linker complex. In addition to twist inversion, our simulations reveal "nucleosome flipping", whereby nucleosomes may undergo sudden flipping in response to applied twist, causing a rapid bending of the linker and a significant change in the overall twist and writhe of the array. Our findings shed light on the underlying mechanisms by which torsional stresses impact chromatin organization.
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A structural perspective on the where, how, why, and what of nucleosome positioning.
J. Biomol. Struct. Dyn.
PUBLISHED: 03-18-2010
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The DNA in eukaryotic chromatin is packed by histones into arrays of repeating units called nucleosomes. Each nucleosome contains a nucleosome core, where the DNA is wrapped around a histone octamer, and a stretch of relatively unconstrained DNA called the linker DNA. Since nucleosome cores occlude the DNA from many DNA-binding factors, their positions provide important clues for understanding chromatin packing and gene regulation. Here we review the recent advances in the genome-wide mapping of nucleosome positions, the molecular and structural determinants of nucleosome positioning, and the importance of nucleosome positioning in chromatin higher order folding and transcriptional regulation.
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Model accounting for the effects of pulling-device stiffness in the analyses of single-molecule force measurements.
Phys. Rev. Lett.
PUBLISHED: 03-12-2010
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Single-molecule force spectroscopy provides a powerful approach for investigating molecular transitions along specific reaction coordinates. Here, we present a general analytical model for extracting the intrinsic rates and activation free energies from force measurements on single molecules that is applicable to a broad range of pulling speeds and device stiffnesses. This model relaxes existing limitations to perform force measurements with soft pulling devices for proper theoretical analyses and, in fact, allows experiments to specifically exploit device stiffness as a control parameter in addition to pulling speed for a reliable estimation of energetic and kinetic parameters.
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Biophysics of knotting.
Annu Rev Biophys
PUBLISHED: 03-03-2010
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Knots appear in a wide variety of biophysical systems, ranging from biopolymers, such as DNA and proteins, to macroscopic objects, such as umbilical cords and catheters. Although significant advancements have been made in the mathematical theory of knots and some progress has been made in the statistical mechanics of knots in idealized chains, the mechanisms and dynamics of knotting in biophysical systems remain far from fully understood. We report on recent progress in the biophysics of knotting-the formation, characterization, and dynamics of knots in various biophysical contexts.
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Energetic and entropic forces governing the attraction between polyelectrolyte-grafted colloids.
J Phys Chem B
PUBLISHED: 10-22-2009
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The energetic and entropic interactions governing the attraction between like-charged colloidal particles grafted with oppositely charged polyelectrolyte chains in a monovalent electrolyte are investigated computationally. We employ coarse-grained models of the colloids with varying surface and polyelectrolyte charges and Monte Carlo simulations to compute the potential of mean force between two colloidal particles as a function of their separation distance. By categorizing the potentials as attractive or purely repulsive, we obtain the extent and location of the attractive-force regime within the two-dimensional parameter space comprised of the colloid surface and polyelectrolyte charge. The attractive regime is found to occupy the inside of a hyperbola in this charge space, whose shape and size is determined by a complex interplay between energetic and entropic interactions. In particular, we find that the strength of attraction at short distances is governed by a balance between favorable energetic and entropic terms arising from polymer-bridging interactions, unfavorable energies arising from the mutual repulsion of the colloid surfaces and polyelectrolyte chains, and unfavorable entropies arising from the overlap and crowding effects of chains confined between the colloid surfaces. A phenomenological model is proposed to explain the hyperbolic shape of the attractive regime and make useful predictions about changes in its shape and location for conditions not investigated in this study.
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Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 07-27-2009
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The architecture of the chromatin fiber, which determines DNA accessibility for transcription and other template-directed biological processes, remains unknown. Here we investigate the internal organization of the 30-nm chromatin fiber, combining Monte Carlo simulations of nucleosome chain folding with EM-assisted nucleosome interaction capture (EMANIC). We show that at physiological concentrations of monovalent ions, linker histones lead to a tight 2-start zigzag dominated by interactions between alternate nucleosomes (i +/- 2) and sealed by histone N-tails. Divalent ions further compact the fiber by promoting bending in some linker DNAs and hence raising sequential nucleosome interactions (i +/- 1). Remarkably, both straight and bent linker DNA conformations are retained in the fully compact chromatin fiber as inferred from both EMANIC and modeling. This conformational variability is energetically favorable as it helps accommodate DNA crossings within the fiber axis. Our results thus show that the 2-start zigzag topology and the type of linker DNA bending that defines solenoid models may be simultaneously present in a structurally heteromorphic chromatin fiber with uniform 30 nm diameter. Our data also suggest that dynamic linker DNA bending by linker histones and divalent cations in vivo may mediate the transition between tight nucleosome packing within discrete 30-nm fibers and self-associated higher-order chromosomal forms.
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A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments.
J Phys Chem A
PUBLISHED: 03-21-2009
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To elucidate the role of the histone tails in chromatin compaction and in higher-order folding of chromatin under physiological conditions, we extend a mesoscale model of chromatin (Arya, Zhang, and Schlick. Biophys. J. 2006, 91, 133; Arya and Schlick. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 16236) to account for divalent cations (Mg(2+)) and linker histones. Configurations of 24-nucleosome oligonucleosomes in different salt environments and in the presence and absence of linker histones are sampled by a mixture of local and global Monte Carlo methods. Analyses of the resulting ensembles reveal a dynamic synergism between the histone tails, linker histones, and ions in forming compact higher-order structures of chromatin. In the presence of monovalent salt alone, oligonucleosomes remain relatively unfolded, and the histone tails do not mediate many internucleosomal interactions. Upon the addition of linker histones and divalent cations, the oligonucleosomes undergo a significant compaction triggered by a dramatic increase in the internucleosomal interactions mediated by the histone tails, formation of a rigid linker DNA "stem" around the linker histones C-terminal domains, and reduction in the electrostatic repulsion between linker DNAs via sharp bending in some linker DNAs caused by the divalent cations. Among all histone tails, the H4 tails mediate the most internucleosomal interactions, consistent with experimental observations, followed by the H3, H2A, and H2B tails in decreasing order. Apart from mediating internucleosomal interactions, the H3 tails also contribute to chromatin compaction by attaching to the entering and exiting linker DNA to screen electrotatic repulsion among the linker DNAs. This tendency of the H3 tails to attach to linker DNA, however, decreases significantly upon the addition of linker histones due to competition effects. The H2A and H2B tails do not mediate significant internucleosomal interactions but are important for mediating fiber/fiber intractions, especially in relatively unfolded chromatin in monovalent salt environments.
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Menacanthus palmai, a new species of chewing louse (Menoponidae: Amblycera: Phthiraptera) from the Coturnix coromandelica.
J Parasit Dis
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The new species Menacanthus palmai collected from Coturnix coromandelica (Gmelin), in Rampur district (UP), India, is described and illustrated. Morphologically the new species is close to M. abdominalis from Coturnix coturnix but differs in having long pointed ventral processes on the postero-medial angles of the second to fifth pleurites. Furthermore, these two species also differ in the number of tergal and sternal abdominal setae, and the morphology of the male genitalia. Another species, Menacanthus pallipes from C. chinensis, does not have ventral processes on the postero-medial angles of pleurites.
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Egg laying site and oviposition pattern of two Phthirapteran species parasitizing red whiskered Bulbul (Pycnonotus jocosus).
Turkiye Parazitol Derg
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Present study was performed to record the oviposition and egg laying pattern of two phthirapteran species infesting red whiskered Bulbul.
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Recovering ensembles of chromatin conformations from contact probabilities.
Nucleic Acids Res.
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The 3D higher order organization of chromatin within the nucleus of eukaryotic cells has so far remained elusive. A wealth of relevant information, however, is increasingly becoming available from chromosome conformation capture (3C) and related experimental techniques, which measure the probabilities of contact between large numbers of genomic sites in fixed cells. Such contact probabilities (CPs) can in principle be used to deduce the 3D spatial organization of chromatin. Here, we propose a computational method to recover an ensemble of chromatin conformations consistent with a set of given CPs. Compared with existing alternatives, this method does not require conversion of CPs to mean spatial distances. Instead, we estimate CPs by simulating a physically realistic, bead-chain polymer model of the 30-nm chromatin fiber. We then use an approach from adaptive filter theory to iteratively adjust the parameters of this polymer model until the estimated CPs match the given CPs. We have validated this method against reference data sets obtained from simulations of test systems with up to 45 beads and 4 loops. With additional testing against experiments and with further algorithmic refinements, our approach could become a valuable tool for researchers examining the higher order organization of chromatin.
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Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions.
Biophys. J.
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A coarse-grained model of the nucleosome is introduced to investigate the dynamics of force-induced unwrapping of DNA from histone octamers. In this model, the DNA is treated as a charged, discrete worm-like chain, and the octamer is treated as a rigid cylinder carrying a positively charged superhelical groove that accommodates 1.7 turns of DNA. The groove charges are parameterized to reproduce the nonuniform histone/DNA interaction free energy profile and the loading rate-dependent unwrapping forces, both obtained from single-molecule experiments. Brownian dynamics simulations of the model under constant loading conditions reveal that nucleosome unraveling occurs in three distinct stages. At small extensions, the flanking DNA exhibits rapid unwrapping-rewrapping (breathing) dynamics and the octamer flips ?180° and moves toward the pulling axis. At intermediate extensions, the outer turn of DNA unwraps gradually and the octamer swivels about the taut linkers and flips a further ?90° to orient its superhelical axis almost parallel to the pulling axis. At large extensions, a portion of the inner turn unwraps abruptly with a notable rip in the force-extension plot and a >90° flip of the octamer. The remaining inner turn unwraps reversibly to leave a small portion of DNA attached to the octamer despite extended pulling. Our simulations further reveal that the nonuniform histone/DNA interactions in canonical nucleosomes serve to: stabilize the inner turn against unraveling while enhancing the breathing dynamics of the nucleosome and prevent dissociation of the octamer from the DNA while facilitating its mobility along the DNA. Thus, the modulation of the histone/DNA interactions could constitute one possible mechanism for regulating the accessibility of the nucleosome-wound DNA sequences.
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Lattice animal model of chromosome organization.
Phys Rev E Stat Nonlin Soft Matter Phys
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Polymer models tied together by constraints of looping and confinement have been used to explain many of the observed organizational characteristics of interphase chromosomes. Here we introduce a simple lattice animal representation of interphase chromosomes that combines the features of looping and confinement constraints into a single framework. We show through Monte Carlo simulations that this model qualitatively captures both the leveling off in the spatial distance between genomic markers observed in fluorescent in situ hybridization experiments and the inverse decay in the looping probability as a function of genomic separation observed in chromosome conformation capture experiments. The model also suggests that the collapsed state of chromosomes and their segregation into territories with distinct looping activities might be a natural consequence of confinement.
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Self-orienting nanocubes for the assembly of plasmonic nanojunctions.
Nat Nanotechnol
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Plasmonic hot spots are formed when metal surfaces with high curvature are separated by nanoscale gaps and an electromagnetic field is localized within the gaps. These hot spots are responsible for phenomena such as subwavelength focusing, surface-enhanced Raman spectroscopy and electromagnetic transparency, and depend on the geometry of the nanojunctions between the metal surfaces. Direct-write techniques such as electron-beam lithography can create complex nanostructures with impressive spatial control but struggle to fabricate gaps on the order of a few nanometres or manufacture arrays of nanojunctions in a scalable manner. Self-assembly methods, in contrast, can be carried out on a massively parallel scale using metal nanoparticle building blocks of specific shape. Here, we show that polymer-grafted metal nanocubes can be self-assembled into arrays of one-dimensional strings that have well-defined interparticle orientations and tunable electromagnetic properties. The nanocubes are assembled within a polymer thin film and we observe unique superstructures derived from edge-edge or face-face interactions between the nanocubes. The assembly process is strongly dependent on parameters such as polymer chain length, rigidity or grafting density, and can be predicted by free energy calculations.
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Oro-dental findings in Bardet-Biedl syndrome.
BMJ Case Rep
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The Bardet-Biedl syndrome (BBS) is a human genetic disorder with an array of clinical features affecting many body systems. BBS is a pleiotropic disorder with mostly monogenic causes. It is also considered a primary ciliopathy syndrome. It is characterised by obesity, pigmentary retinopathy, polydactyly, mental deficiency and hypogonadism and recently a sixth feature, renal disease, has also been described. Since none of the diverse symptoms of BBS by itself is diagnostic of the disorder and many of the symptoms only become apparent over time, diagnosis of the BBS is often delayed until about 9 years of age when visual problems first appear.
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Rapid self-healing hydrogels.
Proc. Natl. Acad. Sci. U.S.A.
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Synthetic materials that are capable of autonomous healing upon damage are being developed at a rapid pace because of their many potential applications. Despite these advancements, achieving self-healing in permanently cross-linked hydrogels has remained elusive because of the presence of water and irreversible cross-links. Here, we demonstrate that permanently cross-linked hydrogels can be engineered to exhibit self-healing in an aqueous environment. We achieve this feature by arming the hydrogel network with flexible-pendant side chains carrying an optimal balance of hydrophilic and hydrophobic moieties that allows the side chains to mediate hydrogen bonds across the hydrogel interfaces with minimal steric hindrance and hydrophobic collapse. The self-healing reported here is rapid, occurring within seconds of the insertion of a crack into the hydrogel or juxtaposition of two separate hydrogel pieces. The healing is reversible and can be switched on and off via changes in pH, allowing external control over the healing process. Moreover, the hydrogels can sustain multiple cycles of healing and separation without compromising their mechanical properties and healing kinetics. Beyond revealing how secondary interactions could be harnessed to introduce new functions to chemically cross-linked polymeric systems, we also demonstrate various potential applications of such easy-to-synthesize, smart, self-healing hydrogels.
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Computational prediction of efficient splice sites for trans-splicing ribozymes.
RNA
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Group I introns have been engineered into trans-splicing ribozymes capable of replacing the 3-terminal portion of an external mRNA with their own 3-exon. Although this design makes trans-splicing ribozymes potentially useful for therapeutic application, their trans-splicing efficiency is usually too low for medical use. One factor that strongly influences trans-splicing efficiency is the position of the target splice site on the mRNA substrate. Viable splice sites are currently determined using a biochemical trans-tagging assay. Here, we propose a rapid and inexpensive alternative approach to identify efficient splice sites. This approach involves the computation of the binding free energies between ribozyme and mRNA substrate. We found that the computed binding free energies correlate well with the trans-splicing efficiency experimentally determined at 18 different splice sites on the mRNA of chloramphenicol acetyl transferase. In contrast, our results from the trans-tagging assay correlate less well with measured trans-splicing efficiency. The computed free energy components suggest that splice site efficiency depends on the following secondary structure rearrangements: hybridization of the ribozymes internal guide sequence (IGS) with mRNA substrate (most important), unfolding of substrate proximal to the splice site, and release of the IGS from the 3-exon (least important). The proposed computational approach can also be extended to fulfill additional design requirements of efficient trans-splicing ribozymes, such as the optimization of 3-exon and extended guide sequences.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.