Chromatic Information Research Articles

Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle.

MyoD, a myogenic differentiation protein, has been studied for its critical role in skeletal muscle differentiation. MyoD-expressing myoblasts have a potency to be differentiated with proliferation of ectopic cells. However, little is known about the effect on chromatin structure of MyoD binding in proliferative myoblasts. In this study, we evaluated the chromatin structure around MyoD-bound genome regions during the cell cycle by chromatin immunoprecipitation sequencing. Genome-wide analysis of histone modifications was performed in proliferative mouse C2C12 myoblasts during three phases (G1, S, G2/M) of the cell cycle. We found that MyoD-bound genome regions had elevated levels of active histone modifications, such as H3K4me1/2/3 and H3K27ac, compared with MyoD-unbound genome regions during the cell cycle. We also demonstrated that the elevated H3K4me2/3 modification level was maintained during the cell cycle, whereas the H3K27ac and H3K4me1 modification levels decreased to the same level as MyoD-unbound genome regions during the later phases. Immunoblot analysis revealed that MyoD abundance was high in the G1 phase then decreased in the S and G2/M phases. Our results suggest that MyoD binding formed selective epigenetic memories with H3K4me2/3 during the cell cycle in addition to myogenic gene induction via active chromatin formation coupled with transcription.

MeCP2: latest insights fundamentally change our understanding of its interactions with chromatin and its functional attributes.

Methyl CpG binding protein 2 (MeCP2) was initially isolated as an exclusive reader of DNA methylated at CpG. This recognition site, was subsequently extended to other DNA methylated residues and it has been the persisting dogma that binding to methylated DNA constitutes its physiologically relevant role. As we review here, two very recent papers fundamentally change our understanding of the interactions of this protein with chromatin, as well as its functional attributes. In the first one, the protein has been shown to bind to tri-methylated histone H3 (H3K27me3), providing a hint for what might turn out to be the first described chromodomain-containing protein reader in the animal kingdom, and unequivocally demonstrates the ability of MeCP2 to bind to nonmethylated CpG regions of the genome. The second paper reports how the protein dynamically participates in the formation of constitutive heterochromatin condensates. Histone H3K27me3 is a critical component of this form of chromatin.

DBP-PSSM: Combination of Evolutionary Profiles with the XGBoost Algorithm to Improve the Identification of DNA-binding Proteins.

DNA-binding proteins play important roles in a variety of biological processes, such as gene transcription and regulation, DNA replication and repair, DNA recombination and packaging, and the formation of chromatin and ribosomes. Therefore, it is urgent to develop a computational method to improve the recognition efficiency of DNA-binding proteins. We proposed a novel method, DBP-PSSM, which constructed the features from amino acid composition and evolutionary information of protein sequences. The maximum relevance, minimum redundancy (mRMR) was employed to select the optimal features for establishing the XGBoost classifier, therefore, the novel model of prediction DNA-binding proteins, DBP-PSSM, was established with 5-fold cross-validation on the training dataset. DBP-PSSM achieved an accuracy of 81.18% and MCC of 0.657 in a test dataset, which outperformed the many existing methods. These results demonstrated that our method can effectively predict DNA-binding proteins. The data and source code are provided at https://github.com/784221489/DNA-binding.

A Sparse Representation Based Joint Demosaicing Method for Single-Chip Polarized Color Sensor.

The emergence of the single-chip polarized color sensor now allows for simultaneously capturing chromatic and polarimetric information of the scene on a monochromatic image plane. However, unlike the usual camera with an embedded demosaicing method, the latest polarized color camera is not delivered with an in-built demosaicing tool. For demosaicing, the users have to down-sample the captured images or to use traditional interpolation techniques. Neither of them can perform well since the polarization and color are interdependent. Therefore, joint chromatic and polarimetric demosaicing is the key to obtaining high-quality polarized color images. In this paper, we propose a joint chromatic and polarimetric demosaicing model to address this challenging problem. Instead of mechanically demosaicing for the multi-channel polarized color image, we further present a sparse representation-based optimization strategy that utilizes chromatic information and polarimetric information to jointly optimize the model. To avoid the interaction between color and polarization during demosaicing, we separately construct the corresponding dictionaries. We also build an optical data acquisition system to collect a dataset, which contains various sources of polarization, such as illumination, reflectance and birefringence. Results of both qualitative and quantitative experiments have shown that our method is capable of faithfully recovering full RGB information of four polarization angles for each pixel from a single mosaic input image. Moreover, the proposed method can perform well not only on the synthetic data but the real captured data.

Relationship Between Long-Term Variability of Facial Hue Information in Physiological and Psychological ROIs and Health Condition

In this study, we evaluate the relationship between long-term variability of facial hue information in physiological and psychological regions of interests (ROIs) and health condition. Long-term facial hue information, RGB, and L*a*b* color space, were obtained from 13 physiological and psychological ROIs in visible facial images measured for approximately six months. In this study, the evaluation was performed based on four conditions (absolute value of RGB, absolute value of L*a*b*, relative value of RGB, and relative value of L*a*b*). These four long-term variabilities of facial hue information were applied to principal component analysis to clarify the relationship between facial hue information and health condition. The results suggested that long-term variability of chromaticity information around the periorbital region may be related to health conditions. Furthermore, physiological and psychological states related to health condition were estimated with the accuracy of approximately 80% using relative chromaticity information around the periorbital region.

Quality Assessment of Multimodal Medical Image Fusion Images Using Chromaticity Similarity and Information Similarity

Quality Assessment of Multimodal Medical Image Fusion Images Using Chromaticity Similarity and Information Similarity

A content‐dependent Daltonization algorithm for colour vision deficiencies based on lightness and chroma information

To help CVD (colour vision deficiency) observers distinguish among different colours in digital images, this study proposes a content-dependent Daltonization algorithm based on lightness and chroma information. This improves the trade-offs in contrast, naturalness, and colour consistency deficiencies found in existing methods. Chroma remapping and brightness adjustments on image content are utilized to increase contrast and maximize the preservation of the original hue. In a quantitative study, the proposed method proved more useful for dichromats than did existing methods. The evaluation by research subjects showed that the method was superior to the current methods in balancing contrast, naturalness, and colour consistency.

Anagallis arvensis Induces Apoptosis in HL-60 Cells Through ROS-Mediated Mitochondrial Pathway

The present study was taken up to evaluate the apoptosis inducing ability of alcoholic extract of whole plant of Anagallis arvensis (AAE) in HL-60 cells. We observed time and concentration dependent decrease in cell viability after treatment with AAE. Fluorescent staining and scanning electron micrographs of treated HL-60 cells demonstrated chromatin condensation, nuclear fragmentation and formation of apoptotic blebs. There was a marked increase in hypodiploid population of cells as observed by cell cycle analysis. Annexin V-FITC/PI also depicted the presence of apoptotic cells. Anti-apoptotic protein Bcl-2 was observed to be decreased by 62% at 20 µg/ml concentration and a significant increase in ROS production up to 6.9-fold was observed in time dependent manner. In addition, alteration in mitochondrial membrane potential was observed, which was followed by cytochrome c release to cytoplasm. Activated levels of mitochondrial downstream pathway protein namely Caspase-3 and 9, were detected in treated HL-60 cells by colorimetric analysis. DNA ladder formation, a biochemical hallmark of apoptosis was also observed in treated HL-60 cells. The results of the present study support the apoptotic potential of AAE and probability of its promising role in development as effective anticancer agent against leukemia cells.

Colored visual stimuli evoke spectrally tuned neuronal responses across the central nervous system of zebrafish larvae

BackgroundVisually guided behaviors such as optomotor and optokinetic responses, phototaxis, and prey capture are crucial for survival in zebrafish and become apparent after just a few days of development. Color vision, which in zebrafish is based on a spatially anisotropic tetrachromatic retina, provides an additional important component of world representation driving fundamental larval behaviors. However, little is known about the central nervous system (CNS) circuitry underlying color vision processing downstream of the retina, and its activity correlates with behavior. Here, we used the transparent larva of zebrafish to image CNS neurons and their activity in response to colored visual stimuli.ResultsTo investigate the processing of chromatic information in the zebrafish larva brain, we mapped with cellular resolution, spectrally responsive neurons in the larva encephalon and spinal cord. We employed the genetically encoded calcium indicator GCaMP6s and two-photon microscopy to image the neuronal activity while performing visual stimulation with spectrally distinct stimuli at wavelengths matching the absorption peaks of the four zebrafish cone types. We observed the presence of a high number of wavelength-selective neurons not only in the optic tectum, but also in all other regions of the CNS, demonstrating that the circuitry involved in processing spectral information and producing color-selective responses extends to the whole CNS.ConclusionsOur measurements provide a map of neurons involved in color-driven responses, revealing that spectral information spreads in all regions of the CNS. This suggests the underlying complexity of the circuits involved and opens the way to their detailed future investigation.

Quantification of the effect of site-specific histone acetylation on chromatin transcription rate.

Eukaryotic transcription is epigenetically regulated by chromatin structure and post-translational modifications (PTMs). For example, lysine acetylation in histone H4 is correlated with activation of RNA polymerase I-, II- and III-driven transcription from chromatin templates, which requires prior chromatin remodeling. However, quantitative understanding of the contribution of particular PTM states to the sequential steps of eukaryotic transcription has been hampered partially because reconstitution of a chromatin template with designed PTMs is difficult. In this study, we reconstituted a di-nucleosome with site-specifically acetylated or unmodified histone H4, which contained two copies of the Xenopus somatic 5S rRNA gene with addition of a unique sequence detectable by hybridization-assisted fluorescence correlation spectroscopy. Using a Xenopus oocyte nuclear extract, we analyzed the time course of accumulation of nascent 5S rRNA-derived transcripts generated on chromatin templates in vitro. Our mathematically described kinetic model and fitting analysis revealed that tetra-acetylation of histone H4 at K5/K8/K12/K16 increases the rate of transcriptionally competent chromatin formation ∼3-fold in comparison with the absence of acetylation. We provide a kinetic model for quantitative evaluation of the contribution of epigenetic modifications to chromatin transcription.

Color enhancement algorithm based on Daltonization and image fusion for improving the color visibility to color vision deficiencies and normal trichromats

In recent years, helping individuals with color vision deficiency to distinguish confusing colors in digital images, which is called Daltonization, is a hot topic. However, a number of Daltonization methods have a color reduction problem that causes unnatural image colors for normal color vision observers and those with anomalous trichromatic color vision deficiencies. A color-enhancing algorithm is proposed to make up for the shortage in color naturalness. Based on the conclusion in previous studies that colors confused in the same type of color blindness are approximately straight lines (called confusion lines) on the u ′ v ′ chromaticity plane and all of the confusion lines intersect at the same point (called the confusion point), we propose a polar coordinate transformation based on intersection points of confusion lines, which can transform chromaticity information into perceptually sensitive and perceptually insensitive color blindness information. From the two color-blind sensitive information of the Daltonized image and the one color-blind insensitive information of the original image, the three-dimensional information can be combined to obtain an enhanced image. The enhanced image has a similar color appearance of the Daltonized image under the perspective of dichromats and has a more natural and colorful color appearance under the perspective of anomalous and normal trichromats. In addition, we propose a lightness modification to reduce lightness errors between the enhanced images and the Daltonized images. The quantitative evaluation shows that the method proposed is effective but sacrificing a small amount of color contrast of the Daltonized images.

The normalized segment classification model: A new tool to compare spectral reflectance curves.

Color patterns are complex traits under selective pressures from conspecifics, mutualists, and antagonists. To evaluate the salience of a pattern or the similarity between colors, several visual models are available. Color discrimination models estimate the perceptual difference between any two colors. Their application to a diversity of taxonomic groups has become common in the literature to answer behavioral, ecological, and evolutionary questions. To use these models, we need information about the visual system of our beholder species. However, many color patterns are simultaneously subject to selective pressures from different species, often from different taxonomic groups, with different visual systems. Furthermore, we lack information about the visual system of many species, leading ecologists to use surrogate values or theoretical estimates for model parameters.Here, we present a modification of the segment classification method proposed by Endler (Biological Journal of the Linnean Society, 1990 41, 315–352): the normalized segment classification model (NSC). We explain its logic and use, exploring how NSC differs from other visual models. We also compare its predictions with available experimental data.Even though the NSC model includes no information about the visual system of the receiver species, it performed better than traditional color discrimination models when predicting the output of some behavioral tasks. Although vision scientists define color as independent of stimulus brightness, a likely explanation for the goodness of fit of the NSC model is that its distance measure depends on brightness differences, and achromatic information can influence the decision‐making process of animals when chromatic information is missing.Species‐specific models may be insufficient for the study of color patterns in a community context. The NSC model offers a species‐independent solution for color analyses, allowing us to calculate color differences when we ignore the intended viewer of a signal or when different species impose selective pressures on the signal.

Computer Vision-based Early Fire Detection Using Enhanced Chromatic Segmentation and Optical Flow Analysis Technique

Recent advances in video processing technologies have led to a wave of research on computer vision-based fire detection systems. This paper presents a multi-level framework for fire detection that analyses patterns in chromatic information, shape transmutation, and optical flow estimation of fire. First, the decision function of fire pixels based on chromatic information uses majority voting among state-of-the-art fire color detection rules to extract the regions of interest. The extracted pixels are then verified for authenticity by examining the dynamics of shape. Finally, a measure of turbulence is assessed by an enhanced optical flow analysis algorithm to confirm the presence of fire. To evaluate the performance of the proposed model, we utilize videos from the Mivia and Zenodo datasets, which have a diverse set of scenarios including indoor, outdoor, and forest fires, along with videos containing no fire. The proposed model exhibits an average accuracy of 97.2% for our tested dataset. In addition, the experimental results demonstrate that the proposed model significantly reduces the rate of false alarms compared to the other existing models

Tinospora cordifolia and arabinogalactan exert chemopreventive action during benzo(a)pyrene-induced pulmonary carcinogenesis: studies on ultrastructural, molecular, and biochemical alterations.

The aim of the present study was to unveil the chemopreventive potentials of aqueous Tinospora cordifolia stem extract and its active component viz. Arabinogalactan against Benzo(a)pyrene-induced pulmonary carcinogenesis. Animals were divided into six groups: (I) Control, (II) aqueous Tinospora cordifolia (200 mg/kg b.wt, p.o.), (III) arabinogalactan (7.5 mg/kg b.wt, p.o.), (IV) benzo(a)pyrene (50 mg/kg b.wt, i.p.) at second and fourth week of study, (V) benzo(a)pyrene + aqueous Tinospora cordifolia, and (VI) benzo(a)pyrene + arabinogalactan. The benzo(a)pyrene treatment resulted in severe alterations in the cellular arrangement and morphology of the alveolar tissue in benzo(a)pyrene group. However, benzo(a)pyrene + aqueous Tinospora cordifolia and benzo(a)pyrene + arabinogalactan groups revealed classical features of apoptosis including chromatin condensation and formation of apoptotic bodies. Furthermore, Fourier transform Infrared spectroscopy analysis showed disturbed phospholipid saturation and protein secondary structures in benzo(a)pyrene treated animals. Depletion in relative glycogen and enhancement in total nucleic acid content was observed in benzo(a)pyrene treated animals, and the same was found to be restored upon arabinogalactan and aqueous Tinospora cordifolia supplementation. Benzo(a)pyrene insult also upregulated the phase I carcinogen metabolizing enzymes and differentially modulated the phase II metabolizing enzymes during pulmonary carcinogenesis. Also, depleted (reduced glutathione) and increased lipid peroxidation levels were observed in benzo(a)pyrene treated animals, which was found to be normalized upon aqueous Tinospora cordifolia and arabinogalactan administration. Clastogenic damage inflicted by benzo(a)pyrene was also reversed in benzo(a)pyrene + aqueous Tinospora cordifolia and benzo(a)pyrene + arabinogalactan group. Thus, the present study infers that aqueous Tinospora cordifolia and arabinogalactan showed promising anticancer activity against lung tumorigenesis in terms of ultrastructural, biochemical, and biomolecular aspects.

Nucleosomes and Epigenetics from a Chemical Perspective.

Nucleosomes, which are the fundamental building blocks of chromatin, are highly dynamic, they play vital roles in the formation of higher-order chromatin structures and orchestrate gene regulation. Nucleosome structures, histone modifications, nucleosome-binding proteins, and their functions are being gradually unravelled with the development of epigenetics. With the continuous development of research approaches such as cryo-EM, FRET and next-generation sequencing for genome-wide analysis of nucleosomes, the understanding of nucleosomes is getting wider and deeper. Herein, we review recent progress in research on nucleosomes and epigenetics, from nucleosome structure to chromatin formation, with a focus on chemical aspects. Basic knowledge of the nucleosome (nucleosome structure, nucleosome position sequence, nucleosome assembly and remodeling), epigenetic modifications, chromatin structure, chemical biology methods and nucleosome, observation nucleosome by AFM, phase separation and nucleosomes are described in this review.

PML nuclear bodies and chromatin dynamics: catch me if you can!

Eukaryotic cells compartmentalize their internal milieu in order to achieve specific reactions in time and space. This organization in distinct compartments is essential to allow subcellular processing of regulatory signals and generate specific cellular responses. In the nucleus, genetic information is packaged in the form of chromatin, an organized and repeated nucleoprotein structure that is a source of epigenetic information. In addition, cells organize the distribution of macromolecules via various membrane-less nuclear organelles, which have gathered considerable attention in the last few years. The macromolecular multiprotein complexes known as Promyelocytic Leukemia Nuclear Bodies (PML NBs) are an archetype for nuclear membrane-less organelles. Chromatin interactions with nuclear bodies are important to regulate genome function. In this review, we will focus on the dynamic interplay between PML NBs and chromatin. We report how the structure and formation of PML NBs, which may involve phase separation mechanisms, might impact their functions in the regulation of chromatin dynamics. In particular, we will discuss how PML NBs participate in the chromatinization of viral genomes, as well as in the control of specific cellular chromatin assembly pathways which govern physiological mechanisms such as senescence or telomere maintenance.

Low-contrast image enhancement using spatial contextual similarity histogram computation and color reconstruction

This paper presents an adaptive enhancement framework for low contrast images to improve the deteriorated details and color information. The proposed algorithm is composed of two adaptive steps: Contrast enhancement and Color restoration. Firstly, according to the luminance map separated from the RGB image, a new spatial contextual similarity histogram (SCSH) is developed. The new SCSH considers the gray-level similarities among the adjacent pixels, following the standard deviation value of the luminance image. The contrast-enhanced image is obtained by applying the intensity transformation function derived from the cumulative distribution function obtained from the normalized values of SCSH. An adaptive weighted fusion is carried out between the luminance enhanced channel and original luminance channel with the weights computed from the enhanced luminance channel. Secondly, an adaptive color restoration technique is designed to reconstruct the more consistent color image using original chromatic information and modified luminance. The results are analyzed using the statistical paired t-test. Both objective and subjective experimentation prove the supremacy of the proposed algorithm with conventional and state-of-the-art algorithms.

An improved algorithm of multi-exposure image fusion by detail enhancement

Multi-exposure image fusion is an effective method for depicting high dynamic range of the target scene in a single image. However, there are still some problems remaining: the preserving of global contrast, the preserving of the local details in saturated regions, and the existence of halo artifacts. To solve these problems, this paper proposes a new multi-exposure image fusion algorithm with detail enhancement. Firstly, the well-exposedness evaluation function, the chromatic information evaluation function and the local detail preserved function are used to measure weight maps. Then, an improved multi-exposure fusion framework based on pyramid decomposition is proposed to further enhance the details. The experimental results demonstrate that the proposed algorithm can preserve more details than the state-of-the-art. In the view of appreciation, our approach could produce a more realistic brightness distribution of target scene as well as avoid halo artifacts.

LSD1 prevents aberrant heterochromatin formation in Neurospora crassa.

Heterochromatin is a specialized form of chromatin that restricts access to DNA and inhibits genetic processes, including transcription and recombination. In Neurospora crassa, constitutive heterochromatin is characterized by trimethylation of lysine 9 on histone H3, hypoacetylation of histones, and DNA methylation. We explored whether the conserved histone demethylase, lysine-specific demethylase 1 (LSD1), regulates heterochromatin in Neurospora, and if so, how. Though LSD1 is implicated in heterochromatin regulation, its function is inconsistent across different systems; orthologs of LSD1 have been shown to either promote or antagonize heterochromatin expansion by removing H3K4me or H3K9me respectively. We identify three members of the Neurospora LSD complex (LSDC): LSD1, PHF1, and BDP-1. Strains deficient for any of these proteins exhibit variable spreading of heterochromatin and establishment of new heterochromatin domains throughout the genome. Although establishment of H3K9me3 is typically independent of DNA methylation in Neurospora, instances of DNA methylation-dependent H3K9me3 have been found outside regions of canonical heterochromatin. Consistent with this, the hyper-H3K9me3 phenotype of Δlsd1 strains is dependent on the presence of DNA methylation, as well as HCHC-mediated histone deacetylation, suggesting that spreading is dependent on some feedback mechanism. Altogether, our results suggest LSD1 works in opposition to HCHC to maintain proper heterochromatin boundaries.

Organization of the Pluripotent Genome.

In the past several decades, the establishment of in vitro models of pluripotency has ushered in a golden era for developmental and stem cell biology. Research in this arena has led to profound insights into the regulatory features that shape early embryonic development. Nevertheless, an integrative theory of the epigenetic principles that govern the pluripotent nucleus remains elusive. Here, we summarize the epigenetic characteristics that define the pluripotent state. We cover what is currently known about the epigenome of pluripotent stem cells and reflect on the use of embryonic stem cells as an experimental system. In addition, we highlight insights from super-resolution microscopy, which have advanced our understanding of the form and function of chromatin, particularly its role in establishing the characteristically "open chromatin" of pluripotent nuclei. Further, we discuss the rapid improvements in 3C-based methods, which have given us a means to investigate the 3D spatial organization of the pluripotent genome. This has aided the adaptation of prior notions of a "pluripotent molecular circuitry" into a more holistic model, where hotspots of co-interacting domains correspond with the accumulation of pluripotency-associated factors. Finally, we relate these earlier hypotheses to an emerging model of phase separation, which posits that a biophysical mechanism may presuppose the formation of a pluripotent-state-defining transcriptional program.