scholarly journals Software tools for visualizing Hi-C data

2016 ◽  
Author(s):  
Galip Gürkan Yardımcı ◽  
William Stafford Noble
Keyword(s):  
High Throughput ◽  
Three Dimensional ◽  
Software Tools ◽  
Genome Browser ◽  
Visualization Tool ◽  
3D Genome ◽  
Accurate Interpretation ◽  
Three Dimensional Configuration ◽  
And Function ◽  
The Relationship

AbstractRecently developed, high-throughput assays for measuring the three-dimensional configuration of DNA in the nucleus have provided unprecedented insights into the relationship between DNA 3D configuration and function. However, accurate interpretation of data from assays such as ChIA-PET and Hi-C is challenging because the data is large and cannot be easily rendered using a standard genome browser. In particular, an effective Hi-C visualization tool must provide a variety of visualization modes and be capable of viewing the data in conjunction with existing, complementary data. We review a number of such software tools that have been described recently in the literature, focusing on tools that do not require programming expertise on the part of the user. In particular, we describe HiBrowse, Juicebox, my5C, the 3D Genome Browser, and the Epigenome Browser, outlining their complementary functionalities and highlighting which types of visualization tasks each tool is best designed to handle.

Structure and function of voltage-dependent sodium channels: comparison of brain II and cardiac isoforms

1996 ◽  
Vol 76 (3) ◽  
pp. 887-926 ◽  
Author(s):  
H. A. Fozzard ◽  
D. A. Hanck
Keyword(s):  
Amino Acid ◽  
Three Dimensional ◽  
Point Mutations ◽  
Amino Acid Sequences ◽  
Na Channel ◽  
Na Channels ◽  
Voltage Dependent ◽  
And Function ◽  
Relationship Of ◽  
The Relationship

Cardiac and nerve Na channels have broadly similar functional properties and amino acid sequences, but they demonstrate specific differences in gating, permeation, ionic block, modulation, and pharmacology. Resolution of three-dimensional structures of Na channels is unlikely in the near future, but a number of amino acid sequences from a variety of species and isoforms are known so that channel differences can be exploited to gain insight into the relationship of structure to function. The combination of molecular biology to create chimeras and channels with point mutations and high-resolution electrophysiological techniques to study function encourage the idea that predictions of structure from function are possible. With the goal of understanding the special properties of the cardiac Na channel, this review examines the structural (sequence) similarities between the cardiac and nerve channels and considers what is known about the relationship of structure to function for voltage-dependent Na channels in general and for the cardiac Na channels in particular.

Dysregulation of chromatin organization in pediatric and adult brain tumors: oncoepigenomic contributions to tumorigenesis and cancer stem cell properties

Genome ◽  
2020 ◽  
pp. 1-11
Author(s):  
Seungil Paik ◽  
Francesca Maule ◽  
Marco Gallo
Keyword(s):  
Brain Tumors ◽  
Cell Fate ◽  
Three Dimensional ◽  
Genetic Alterations ◽  
Adult Brain ◽  
Post Translational Modifications ◽  
3D Genome ◽  
Differentiated Cells ◽  
Aberrant Dna Methylation ◽  
And Function

The three-dimensional (3D) organization of the genome is a crucial enabler of cell fate, identity, and function. In this review, we will focus on the emerging role of altered 3D genome organization in the etiology of disease, with a special emphasis on brain cancers. We discuss how different genetic alterations can converge to disrupt the epigenome in childhood and adult brain tumors, by causing aberrant DNA methylation and by affecting the amounts and genomic distribution of histone post-translational modifications. We also highlight examples that illustrate how epigenomic alterations have the potential to affect 3D genome architecture in brain tumors. Finally, we will propose the concept of “epigenomic erosion” to explain the transition from stem-like cells to differentiated cells in hierarchically organized brain cancers.

scholarly journals Under pressure: the relationship between cranial shape and burrowing force in caecilians (Gymnophiona)

2021 ◽  
Author(s):  
Aurélien Lowie ◽  
Barbara De Kegel ◽  
Mark Wilkinson ◽  
John Measey ◽  
James C. O'Reilly ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Three Dimensional ◽  
Form And Function ◽  
Biomechanical Models ◽  
Cranial Osteology ◽  
Head Morphology ◽  
And Function ◽  
The Relationship ◽  
Cranial Shape

Caecilians are elongate, limbless, and annulated amphibians that, with the exception of one aquatic family, all have an at least partly fossorial lifestyle. It has been suggested that caecilian evolution resulted in sturdy and compact skulls with fused bones and tight sutures, as an adaptation to their head-first burrowing habits. However, although their cranial osteology is well described, relationships between form and function remain poorly understood. In the present study, we explored the relationship between cranial shape and in vivo burrowing forces. Using µCT-data, we performed three-dimensional geometric morphometrics to explore whether cranial and mandibular shapes reflected patterns that might be associated with maximal push forces. The results highlight important differences in maximal push forces, with the aquatic Typhlonectes producing a lower force for a given size compared to other species. Despite substantial differences in head morphology across species, no relation between overall skull shape and push force could be detected. Although a strong phylogenetic signal may partly obscure the results, our conclusions confirm previous studies using biomechanical models and suggest that differences in the degree of fossoriality do not appear to be driving the evolution of head shape.

scholarly journals A határérték bal kamrai ejekciós frakció együtt jár a mitralis anulus méretének és funkciójának eltéréseivel. Eredmények a MAGYAR-Healthy Tanulmányból

2018 ◽  
Vol 159 (50) ◽  
pp. 2129-2135
Author(s):  
Zsolt Kovács ◽  
Árpád Kormányos ◽  
Péter Domsik ◽  
Anita Kalapos ◽  
Csaba Lengyel ◽  
...  
Keyword(s):  
Speckle Tracking Echocardiography ◽  
Three Dimensional ◽  
Mitral Annulus ◽  
Left Ventricular ◽  
Functional Parameters ◽  
Area And Perimeter ◽  
Lv Volumes ◽  
Lv Ejection Fraction ◽  
And Function ◽  
The Relationship

Abstract: Introduction: Morphology and function of the mitral annulus (MA) shows alterations in different valvular (for instance in mitral regurgitation) and non-valvular disorders (for instance in certain cardiomyopathies, cardiac amyloidosis). Aim: The aim of the present study was to examine the relationship between MA morphologic and functional properties and three-dimensional speckle-tracking echocardiography- (3DSTE) derived left ventricular (LV) ejection fraction (EF) in subjects with normal versus borderline LV-EF. Method: The present study comprised 146 volunteers (mean age: 32.0 ± 11.4 years; 74 males) in whom complete two-dimensional Doppler echocardiography was performed with a negative result extended with 3DSTE. The population was further divided into two groups according to their 3DSTE-derived LV-EF (borderline 50–54% versus ≥55%). Results: In cases with borderline LV-EF, higher LV end-systolic LV volumes and lower LV longitudinal strain could be measured. All end-systolic and end-diastolic MA diameter, area and perimeter data proved to be higher in cases with borderline LV-EF. In these subjects, MA functional parameters proved to be lower as well. In contrast, LV-EF showed correlations neither with end-systolic and end-diastolic MA dimensions nor with MA functional parameters. Conclusions: 3DSTE-derived borderline LV-EF is associated with MA dilatation and functional impairment. Orv Hetil. 2018; 159(50): 2129–2135.

scholarly journals Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

2017 ◽  
Author(s):  
Wenxiu Ma ◽  
Ferhat Ay ◽  
Choli Lee ◽  
Gunhan Gulsoy ◽  
Xinxian Deng ◽  
...  
Keyword(s):  
High Resolution ◽  
High Throughput ◽  
Three Dimensional ◽  
Dnase I ◽  
Genome Architecture ◽  
Whole Genome ◽  
Fine Scale ◽  
3D Genome ◽  
Dna Capture ◽  
Global And Local

AbstractThe folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods.HighlightsDNase Hi-C, a method for comprehensive mapping of chromatin contacts on a whole-genome scale, is based on random chromatin fragmentation by DNase I digestion instead of sequence-specific restriction enzyme (RE) digestion.Targeted DNase Hi-C, which combines DNase Hi-C with DNA capture technology, is a high-throughput method for mapping fine-scale chromatin architecture of genomic loci of interest at a resolution comparable to that of genomic annotations of functional elements.DNase Hi-C and targeted DNase Hi-C provide the first high-throughput way to overcome the RE-digestion-associated resolution limit of 3C-based methods.Step-by-step whole-genome and targeted DNase Hi-C protocols for mapping global and local 3D genome architecture, respectively, are described.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

Structural Role of rRNAs on the Ribosomal Subunits from E. Coli by Scanning Transmission Electron Microscopy

1981 ◽  
Vol 39 ◽  
pp. 424-425
Author(s):  
M. Boublik ◽  
N. Robakis ◽  
J.S. Wall
Keyword(s):  
Three Dimensional ◽  
Uranyl Acetate ◽  
Dimensional Structure ◽  
Electron Microscopic ◽  
Ribosomal Subunits ◽  
E Coli ◽  
Freeze Dried ◽  
16S Rna ◽  
Scanning Transmission ◽  
And Function

The three-dimensional structure and function of biological supramolecular complexes are, in general, determined and stabilized by conformation and interactions of their macromolecular components. In the case of ribosomes, it has been suggested that one of the functions of ribosomal RNAs is to act as a scaffold maintaining the shape of the ribosomal subunits. In order to investigate this question, we have conducted a comparative TEM and STEM study of the structure of the small 30S subunit of E. coli and its 16S RNA.The conventional electron microscopic imaging of nucleic acids is performed by spreading them in the presence of protein or detergent; the particles are contrasted by electron dense solution (uranyl acetate) or by shadowing with metal (tungsten). By using the STEM on freeze-dried specimens we have avoided the shearing forces of the spreading, and minimized both the collapse of rRNA due to air drying and the loss of resolution due to staining or shadowing. Figure 1, is a conventional (TEM) electron micrograph of 30S E. coli subunits contrasted with uranyl acetate.

Predicting spatial activity patterns in a neural map from a probabilistic atlas of 3-D reconstructed neurons

1995 ◽  
Vol 53 ◽  
pp. 812-813
Author(s):  
G. Jacobs ◽  
F. Theunissen
Keyword(s):  
Activity Patterns ◽  
Three Dimensional ◽  
Sensory System ◽  
Neural System ◽  
Probabilistic Atlas ◽  
Uniform Sample ◽  
Dimensional Reconstruction ◽  
The Time Domain ◽  
And Function ◽  
Visualization Techniques

In order to understand how the algorithms underlying neural computation are implemented within any neural system, it is necessary to understand details of the anatomy, physiology and global organization of the neurons from which the system is constructed. Information is represented in neural systems by patterns of activity that vary in both their spatial extent and in the time domain. One of the great challenges to microscopists is to devise methods for imaging these patterns of activity and to correlate them with the underlying neuroanatomy and physiology. We have addressed this problem by using a combination of three dimensional reconstruction techniques, quantitative analysis and computer visualization techniques to build a probabilistic atlas of a neural map in an insect sensory system. The principal goal of this study was to derive a quantitative representation of the map, based on a uniform sample of afferents that was of sufficient size to allow statistically meaningful analyses of the relationships between structure and function.

Scanning tunneling microscopy (STM) of DNA and RNA

1989 ◽  
Vol 47 ◽  
pp. 34-35
Author(s):  
Patricia G. Arscott ◽  
Gil Lee ◽  
Victor A. Bloomfield ◽  
D. Fennell Evans
Keyword(s):  
Molecular Structures ◽  
Inorganic Materials ◽  
Resolving Power ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Form And Function ◽  
Dna And Rna ◽  
Calf Thymus ◽  
And Function ◽  
The Relationship

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).

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