scholarly journals Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling.

2016 ◽  
Author(s):  
François Serra ◽  
Davide Baù ◽  
Guillaume Filion ◽  
Marc A. Marti-Renom

The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three- dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, now permit to investigate the spatial organization of genomes. However, inferring structures from raw contact data is a tedious process for shortage of available tools. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions. To illustrate the use of TADbit, we automatically modeled 50 genomic domains from the fly genome revealing differential structural features of the previously defined chromatin colors, establishing a link between the conformation of the genome and the local chromatin composition. More generally, TADbit allows to obtain three-dimensional models ready for visualization from 3C-based experiments and to characterize their relation to gene expression and epigenetic states. TADbit is open-source and available for download from http://www.3DGenomes.org.

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Emre Sefer

AbstractChromosome conformation capture experiments such as Hi–C map the three-dimensional spatial organization of genomes in a genome-wide scale. Even though Hi–C interactions are not biased towards any of the histone modifications, previous analysis has revealed denser interactions around many histone modifications. Nevertheless, simultaneous effects of these modifications in Hi–C interaction graph have not been fully characterized yet, limiting our understanding of genome shape. Here, we propose ChromatinCoverage and its extension TemporalPrizeCoverage methods to decompose Hi–C interaction graph in terms of known histone modifications. Both methods are based on set multicover with pairs, where each Hi–C interaction is tried to be covered by histone modification pairs. We find 4 histone modifications H3K4me1, H3K4me3, H3K9me3, H3K27ac to be significantly predictive of most Hi–C interactions across species, cell types and cell cycles. The proposed methods are quite effective in predicting Hi–C interactions and topologically-associated domains in one species, given it is trained on another species or cell types. Overall, our findings reveal the impact of subset of histone modifications in chromatin shape via Hi–C interaction graph.


2021 ◽  
Vol 12 ◽  
Author(s):  
Maria Marti-Marimon ◽  
Nathalie Vialaneix ◽  
Yvette Lahbib-Mansais ◽  
Matthias Zytnicki ◽  
Sylvie Camut ◽  
...  

The spatial organization of the genome in the nucleus plays a crucial role in eukaryotic cell functions, yet little is known about chromatin structure variations during late fetal development in mammals. We performed in situ high-throughput chromosome conformation capture (Hi-C) sequencing of DNA from muscle samples of pig fetuses at two late stages of gestation. Comparative analysis of the resulting Hi-C interaction matrices between both groups showed widespread differences of different types. First, we discovered a complex landscape of stable and group-specific Topologically Associating Domains (TADs). Investigating the nuclear partition of the chromatin into transcriptionally active and inactive compartments, we observed a genome-wide fragmentation of these compartments between 90 and 110 days of gestation. Also, we identified and characterized the distribution of differential cis- and trans-pairwise interactions. In particular, trans-interactions at chromosome extremities revealed a mechanism of telomere clustering further confirmed by 3D Fluorescence in situ Hybridization (FISH). Altogether, we report major variations of the three-dimensional genome conformation during muscle development in pig, involving several levels of chromatin remodeling and structural regulation.


1986 ◽  
Vol 102 (1) ◽  
pp. 112-123 ◽  
Author(s):  
M Hochstrasser ◽  
D Mathog ◽  
Y Gruenbaum ◽  
H Saumweber ◽  
J W Sedat

Using a computer-based system for model building and analysis, three-dimensional models of 24 Drosophila melanogaster salivary gland nuclei have been constructed from optically or physically sectioned glands, allowing several generalizations about chromosome folding and packaging in these nuclei. First and most surprising, the prominent coiling of the chromosomes is strongly chiral, with right-handed gyres predominating. Second, high frequency appositions between certain loci and the nuclear envelope appear almost exclusively at positions of intercalary heterochromatin; in addition, the chromocenter is always apposed to the envelope. Third, chromosomes are invariably separated into mutually exclusive spatial domains while usually extending across the nucleus in a polarized (Rabl) orientation. Fourth, the arms of each autosome are almost always juxtaposed, but no other relative arm positions are strongly favored. Finally, despite these nonrandom structural features, each chromosome is found to fold into a wide variety of different configurations. In addition, a set of nuclei has been analyzed in which the normally aggregrated centromeric regions of the chromosomes are located far apart from one another. These nuclei have the same architectural motifs seen in normal nuclei. This implies that such characteristics as separate chromosome domains and specific chromosome-nuclear envelope contacts are largely independent of the relative placement of the different chromosomes within the nucleus.


2021 ◽  
pp. 6-14
Author(s):  
N.P. KARPENKO ◽  
◽  
M.A. SHIRYAEVA

The method of three-dimensional model in the system of computer modeling MathCad and Autodesk 3ds Max by categories of total soil pollution is developed. A visualization block and an analytical block have been developed which are based on calculated mathematical models for analyzing and evaluating the environmental situation, risks, and environmental safety of the territory. Three-dimensional models of relief mapping of the Pekhorka river fl oodplain are constructed by integrating them with the help of a programming environment and optimized 3D modeling programs. Three-dimensional models with total soil contamination for water body sections are constructed. On the example of some sections of the catchment area of the Pekhorka river in the Balashikha region, models with soil contamination by the total ZC indicator were created. The development of 3D modeling techniques allows you to create predictive scenarios more accurately with a high degree of detail, as well as quickly approach the solution of environmental problems. Optimization of three-dimensional modeling in the fi eld of problems related to the catchment area contributes to the further operational solution of problems of rational land use and improvement of the environmental situation.


1987 ◽  
Vol 58 (4) ◽  
pp. 832-849 ◽  
Author(s):  
D. Tweed ◽  
T. Vilis

1. This paper develops three-dimensional models for the vestibuloocular reflex (VOR) and the internal feedback loop of the saccadic system. The models differ qualitatively from previous, one-dimensional versions, because the commutative algebra used in previous models does not apply to the three-dimensional rotations of the eye. 2. The hypothesis that eye position signals are generated by an eye velocity integrator in the indirect path of the VOR must be rejected because in three dimensions the integral of angular velocity does not specify angular position. Computer simulations using eye velocity integrators show large, cumulative gaze errors and post-VOR drift. We describe a simple velocity to position transformation that works in three dimensions. 3. In the feedback control of saccades, eye position error is not the vector difference between actual and desired eye positions. Subtractive feedback models must continuously adjust the axis of rotation throughout a saccade, and they generate meandering, dysmetric gaze saccades. We describe a multiplicative feedback system that solves these problems and generates fixed-axis saccades that accord with Listing's law. 4. We show that Listing's law requires that most saccades have their axes out of Listing's plane. A corollary is that if three pools of short-lead burst neurons code the eye velocity command during saccades, the three pools are not yoked, but function independently during visually triggered saccades. 5. In our three-dimensional models, we represent eye position using four-component rotational operators called quaternions. This is not the only algebraic system for describing rotations, but it is the one that best fits the needs of the oculomotor system, and it yields much simpler models than do rotation matrix or other representations. 6. Quaternion models predict that eye position is represented on four channels in the oculomotor system: three for the vector components of eye position and one inversely related to gaze eccentricity and torsion. 7. Many testable predictions made by quaternion models also turn up in models based on other mathematics. These predictions are therefore more fundamental than the specific models that generate them. Among these predictions are 1) to compute eye position in the indirect path of the VOR, eye or head velocity signals are multiplied by eye position feedback and then integrated; consequently 2) eye position signals and eye or head velocity signals converge on vestibular neurons, and their interaction is multiplicative.(ABSTRACT TRUNCATED AT 400 WORDS)


2021 ◽  
Vol 20 (7) ◽  
pp. 48-61
Author(s):  
Pavel V. Chistyakov ◽  
Ekaterina N. Bocharova ◽  
Ksenia A. Kolobova

This article provides a detailed account of the process of scanning, post-processing and further manipulation of three-dimensional models obtained with structured light scanners. Purpose. The purpose of the study is determined by the need for national archaeologists to learn the methods of three-dimensional modeling for the implementation of scientific research corresponding to international standards. Unfortunately, this direction in national archaeology began to develop in a relatively recent time and there is a lag in the application of three-dimensional modeling of national archaeology compared to the world level. Results. Any archaeological, experimental or ethnographic artifact can be used for three-dimensional scanning. To perform post-processing of three-dimensional models it is necessary to carry out primary scanning of an artifact by one of the existing algorithms. The algorithm for creating models, their positioning, simplification, saving in various formats and export is described. The main sequence of 3D models post-processing includes: processing of groups of scanned projections (their cleaning and alignment), creation of artifact model and processing/rectification of the resulting model using special software. Conclusion. As a result of correct implementation of the algorithm, the researcher receives a scaled model completely corresponding to the original artifact. Obtaining a scalable, texture-free three-dimensional model of the artifact, which fully corresponds to the original and exceeds a photograph in the quality of detail transfer, allows a scientist to conduct precise metric measurements and any procedures of non-invasive manipulation of the models. The ability to access a database of three-dimensional models of archaeological collections greatly simplifies the work of archaeologists, especially in situations when country borders are closed.


2012 ◽  
Vol 488-489 ◽  
pp. 1001-1005 ◽  
Author(s):  
Jamal Kashani ◽  
Zohreh Arabshahi ◽  
Mohammed Rafiq Abdul Kadir ◽  
Abbas Azari

Despite efficiency of modern implantology, unplanned perforation and drill deviation could be happened during freehand placement. The aim of this study was to provide a methodology for fabricating dental surgical drill guide for fully edentulous patients while it was flexible in term of changing drill diameter. The data of patient consisted of bone anatomy and radio-opaque template obtained from computed tomography. Jawbone and radio-opaque template three dimensional models converted into a three dimensional modeling software by means of an image processing package. Based on jawbone anatomy and radio-opaque template, implantation plan and design of surgical guides were carried out in three dimensional software. Rapid prototyping technique was used to manufacture several surgical guides to be used in different drilling sequences. Finally stainless steel tubes were accommodated passage of drill. Sequential surgical guides were different only in terms of the metal tubes internal diameter. This provides the ability of changing diameter of the implant or drill after fabricating surgical guide.


2016 ◽  
Vol 27 (21) ◽  
pp. 3357-3368 ◽  
Author(s):  
Chen Chen ◽  
Hong Hwa Lim ◽  
Jian Shi ◽  
Sachiko Tamura ◽  
Kazuhiro Maeshima ◽  
...  

Chromatin organization has an important role in the regulation of eukaryotic systems. Although recent studies have refined the three-dimensional models of chromatin organization with high resolution at the genome sequence level, little is known about how the most fundamental units of chromatin—nucleosomes—are positioned in three dimensions in vivo. Here we use electron cryotomography to study chromatin organization in the budding yeast Saccharomyces cerevisiae. Direct visualization of yeast nuclear densities shows no evidence of 30-nm fibers. Aside from preribosomes and spindle microtubules, few nuclear structures are larger than a tetranucleosome. Yeast chromatin does not form compact structures in interphase or mitosis and is consistent with being in an “open” configuration that is conducive to high levels of transcription. From our study and those of others, we propose that yeast can regulate its transcription using local nucleosome–nucleosome associations.


2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Jackson Nowotny ◽  
Sharif Ahmed ◽  
Lingfei Xu ◽  
Oluwatosin Oluwadare ◽  
Hannah Chen ◽  
...  

Author(s):  
Dominik Scholz ◽  
Alexander Du¨ster ◽  
Ernst Rank

Our approach is to use fully three-dimensional models for both the fluid and the structure. For thin-walled structures, which are typically sensitive to loads resulting from the surrounding fluid, it will be shown that the use of high-order hexahedral elements with high aspect ratios is feasible. Furthermore, it will be demonstrated that three-dimensional elements of high order can be used very efficiently by choosing a high polynomial degree in in-plane direction and a low polynomial degree in thickness direction. By varying the polynomial degrees in the local directions of the elements, the choice of an appropriate structural model can be achieved in an adaptive way. This will be demonstrated by means of a numerical example.


Sign in / Sign up

Export Citation Format

Share Document