scholarly journals Molecular Plasticity in Animal Pigmentation: Emerging Processes Underlying Color Changes

2020 ◽  
Vol 60 (6) ◽  
pp. 1531-1543 ◽  
Author(s):  
Sebastian G Alvarado
Keyword(s):  
Cell Biology ◽  
Molecular Mechanisms ◽  
Pigment Cell ◽  
Color Changes ◽  
Genome Wide ◽  
Full Picture ◽  
Dietary Cues ◽  
And Function ◽  
Molecular Plasticity ◽  
African Cichlids

Synopsis Animal coloration has been rigorously studied and has provided morphological implications for fitness with influences over social behavior, predator–prey interactions, and sexual selection. In vertebrates, its study has developed our understanding across diverse fields ranging from behavior to molecular biology. In the search for underlying molecular mechanisms, many have taken advantage of pedigree-based and genome-wide association screens to reveal the genetic architecture responsible for pattern variation that occurs in early development. However, genetic differences do not provide a full picture of the dynamic changes in coloration that are most prevalent across vertebrates at the molecular level. Changes in coloration that occur in adulthood via phenotypic plasticity rely on various social, visual, and dietary cues independent of genetic variation. Here, I will review the contributions of pigment cell biology to animal color changes and recent studies describing their molecular underpinnings and function. In this regard, conserved epigenetic processes such as DNA methylation play a role in lending plasticity to gene regulation as it relates to chromatophore function. Lastly, I will present African cichlids as emerging models for the study of pigmentation and molecular plasticity for animal color changes. I posit that these processes, in a dialog with environmental stimuli, are important regulators of variation and the selective advantages that accompany a change in coloration for vertebrate animals.

scholarly journals Multidimensional Mechanistic Spectrum of Long Non-coding RNAs in Heart Development and Disease

2021 ◽  
Vol 8 ◽  
Author(s):  
Lei Han ◽  
Lei Yang
Keyword(s):  
Heart Development ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Regulatory Mechanism ◽  
Mrna Translation ◽  
Genome Wide ◽  
Key Factor ◽  
Non Coding Rnas ◽  
And Function ◽  
Human Heart Disease

With the large-scale genome-wide sequencing, long non-coding RNAs (lncRNAs) have been found to compose of a large portion of the human transcriptome. Recent studies demonstrated the multidimensional functions of lncRNAs in heart development and disease. The subcellular localization of lncRNA is considered as a key factor that determines lncRNA function. Cytosolic lncRNAs mainly regulate mRNA stability, mRNA translation, miRNA processing and function, whereas nuclear lncRNAs epigenetically regulate chromatin remodeling, structure, and gene transcription. In this review, we summarize the molecular mechanisms of cytosolic and nuclear lncRNAs in heart development and disease separately, and emphasize the recent progress to dictate the crosstalk of cytosolic and nuclear lncRNAs in orchestrating the same biological process. Given the low evolutionary conservation of most lncRNAs, deeper understanding of human lncRNA will uncover a new layer of human regulatory mechanism underlying heart development and disease, and benefit the future clinical treatment for human heart disease.

scholarly journals Melanocyte differentiation and epidermal pigmentation is regulated by polarity proteins

2020 ◽  
Author(s):  
Sina K. Knapp ◽  
Sandra Iden
Keyword(s):  
Cell Biology ◽  
Kinase Inhibitor ◽  
Pigment Cell ◽  
Skin Pigmentation ◽  
Dendritic Morphology ◽  
Mouse Genetics ◽  
Melanin Production ◽  
Environmental Signals ◽  
Polarity Proteins ◽  
And Function

ABSTRACTPigmentation serves various purposes such as protection, camouflage, or attraction. In the skin epidermis, melanocytes react to certain environmental signals with melanin production and release, thereby ensuring photo-protection. For this, melanocytes acquire a highly polarized and dendritic architecture that facilitates interactions with surrounding keratinocytes and melanin transfer. How the morphology and function of these neural crest-derived cells is regulated remains poorly understood. Here, using mouse genetics and primary cell cultures, we show that conserved proteins of the mammalian Par3-aPKC polarity complex are required for epidermal pigmentation. Melanocyte-specific deletion of Par3 in mice caused skin hypopigmentation, reduced expression of components of the melanin synthesis pathway, and altered dendritic morphology. Mechanistically, Par3 was necessary downstream of α-melanocyte stimulating hormone (α-MSH) to elicit melanin production. Strikingly, pharmacologic activation of MITF using a salt-inducible kinase inhibitor was sufficient to restore melanocyte differentiation and skin pigmentation in the absence of Par3. This data reveals a central role of polarity proteins in transmitting external pigment-inducing signals through the α-MSH/Mc1R/MITF ‘tanning pathway’, exposing unexpected links between polarity signaling and melanogenesis with new insights for pigment cell biology.

scholarly journals The Palade Symposium: Celebrating Cell Biology at Its Best

2010 ◽  
Vol 21 (14) ◽  
pp. 2367-2370 ◽  
Author(s):  
Sandra L. Schmid ◽  
Marilyn G. Farquhar
Keyword(s):  
Human Disease ◽  
Cell Biology ◽  
Secretory Pathway ◽  
Molecular Mechanisms ◽  
Nobel Laureate ◽  
Structure And Function ◽  
Nuclear Pore ◽  
Rab Gtpases ◽  
Membrane Composition ◽  
And Function

A symposium was held at the University of California, San Diego, to honor the contributions of Nobel Laureate, George Palade, to cell biology. The speakers included Günter Blobel, on the structure and function of nuclear pore complexes; Peter Walter, on the unfolded protein response in health and disease; Randy Schekman, on human disease-linked mutations in the COPII machinery; Scott Emr, on the regulation of plasma membrane composition by selective endocytosis; Roger Kornberg, on the structure and function of the transcription machinery; Peter Novick, on the regulation of rab GTPases along the secretory pathway; Jim Spudich, on the mechanism of the enigmatic myosin VI motor; and Joe Goldstein, on the function of the Niemann-Pick C (NPC)-linked gene products, NPC1 and NPC2, in cholesterol transport. Their work showcased the multidisciplinary nature, diversity, and vitality of cell biology. In the words of George Palade, their talks also illustrated “how cell biology could be used to understand disease and how disease could be used to discover normal cell biology.” An integrated understanding of the cellular machinery will be essential in tackling the plethora of questions and challenges posed by completion of the human genome and for understanding the molecular mechanisms underlying human disease.

scholarly journals G Protein-Coupled Receptor 83 Is Dispensable for the Development and Function of Regulatory T Cells

2007 ◽  
Vol 27 (23) ◽  
pp. 8065-8072 ◽  
Author(s):  
Li-Fan Lu ◽  
Marc A. Gavin ◽  
Jeffrey P. Rasmussen ◽  
Alexander Y. Rudensky
Keyword(s):  
T Cells ◽  
G Protein ◽  
Treg Cell ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Foxp3 Expression ◽  
Treg Cells ◽  
G Protein Coupled Receptor ◽  
And Function ◽  
G Protein Coupled

ABSTRACT Global analyses of gene expression in regulatory T (Treg) cells, whose development is critically dependent upon the transcription factor Foxp3, have provided many clues as to the molecular mechanisms these cells employ to control immune responses and establish immune tolerance. Through these studies, G protein-coupled receptor 83 (GPR83) was found to be expressed at high levels in Treg-cell populations. However, its function remained unclear. Recently, it has been suggested that GPR83 is involved in the induction of Foxp3 expression in the peripheral nonregulatory Foxp3− CD4 T cells. To examine a role for GPR83 in Treg-cell biology, we generated and characterized GPR83-deficient mice. We have shown that GPR83 abolition does not result in measurable pathology or changes in the numbers or function of Foxp3+ Treg cells. Furthermore, while in vitro analysis suggested a potential involvement of GPR83 in transforming growth factor β-dependent Foxp3 induction, there was no difference in the ability of nonregulatory GPR83-deficient and nondeficient Foxp3− T cells to acquire Foxp3 expression in vivo. Collectively, our results demonstrate that GPR83 is dispensable for Treg-cell development and function.

scholarly journals Role of SNPs in the biogenesis of mature miRNAs

2020 ◽  
Author(s):  
Ying Wang ◽  
Jidong Ru ◽  
Meng Xianglian
Keyword(s):  
Molecular Mechanisms ◽  
Mature Mirnas ◽  
Mirna Biogenesis ◽  
Sequencing Data ◽  
Whole Genome Analysis ◽  
Association Analyses ◽  
Genome Wide ◽  
Mirna Sequencing ◽  
And Function

Abstract BackgroundSNPs within pre-miRNA regions play a significant role in miRNA generation, processing and function by different molecular mechanisms and are thought to be major contributors to the variations in phenotypes and diseases. Therefore, whole-genome analysis of how SNPs affect mature miRNA biogenesis is important for precision medicine. ResultsIn this study, aiming to analyze the role of SNPs in mature miRNA biogenesis genome-wide, we constructed a SNP-pre-miRNA database, named miRSNPBase, consisting of 886 pre-miRNAs and 2640 SNPs based on the latest data. Then, we identified 10574 SNP-pre-miRNAs based on 886 pre-miRNAs and their associated 2640 SNPs, and we performed genome-wide association analyses to identify isoform miRNAs (isomiRs) based on miRFind that are associated with the mechanism of SNPs affecting miRNA maturation. A total of 4235 nor-SNP-pre-miRNAs based on 480 nor-pre-miRNAs and 1250 nor-SNPs were identified. We analyzed the effects of SNP type, SNP location and SNP-mediated free energy change during mature miRNA biogenesis and found that they are closely related to mature miRNA biogenesis. In addition, the MAF distribution of the iso-pre-miRNAs and nor-SNPs was analyzed based on the 1000 Genomes Project. The results demonstrated that individuals who contained the iso-SNPs were in the minority, and those who contained the nor-SNPs were in the majority. Notably, to verify our method and identify important biomarkers, we identified isomiRs and iso-SNPs in 18 GBR individuals of European origin. In the results, 209 iso-pre-miRNA candidates and 71 verified iso-pre-miRNAs of the 18 GBR samples were identified, and 2667 isomiRs of 209 pre-miRNAs were verified by miRNA sequencing data.ConclusionsOur results clearly indicated that SNPs that altered the mature miRNA splicing mechanism and led to the production of isomiRs, were closely related to and affected normal life processes, and led to epigenetic changes and diseases.

A Mucin-Specific Protease Enables Molecular and Functional Analysis of Human Cancer-Associated Mucins

2018 ◽  
Author(s):  
Stacy A. Malaker ◽  
Kayvon Pedram ◽  
Michael J. Ferracane ◽  
Elliot C. Woods ◽  
Jessica Kramer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Mechanisms ◽  
Cultured Cells ◽  
High Resolution Mass Spectrometry ◽  
Human Cancer ◽  
Glycosylation Sites ◽  
Bacterial Protease ◽  
Specific Protease ◽  
To Come ◽  
And Function

<div> <div> <div> <p>Mucins are a class of highly O-glycosylated proteins that are ubiquitously expressed on cellular surfaces and are important for human health, especially in the context of carcinomas. However, the molecular mechanisms by which aberrant mucin structures lead to tumor progression and immune evasion have been slow to come to light, in part because methods for selective mucin degradation are lacking. Here we employ high resolution mass spectrometry, polymer synthesis, and computational peptide docking to demonstrate that a bacterial protease, called StcE, cleaves mucin domains by recognizing a discrete peptide-, glycan-, and secondary structure- based motif. We exploited StcE’s unique properties to map glycosylation sites and structures of purified and recombinant human mucins by mass spectrometry. As well, we found that StcE will digest cancer-associated mucins from cultured cells and from ovarian cancer patient-derived ascites fluid. Finally, using StcE we discovered that Siglec-7, a glyco-immune checkpoint receptor, specifically binds sialomucins as biological ligands, whereas the related Siglec-9 receptor does not. Mucin-specific proteolysis, as exemplified by StcE, is therefore a powerful tool for the study of glycoprotein structure and function and for deorphanizing mucin-binding receptors. </p> </div> </div> </div>

Artificial Intelligence for epigenetics: towards personalized medicine

2020 ◽  
Vol 27 ◽  
Author(s):  
Giulia De Riso ◽  
Sergio Cocozza
Keyword(s):  
Biological Sciences ◽  
Artificial Intelligence ◽  
Personalized Medicine ◽  
Molecular Mechanisms ◽  
Genomic Sequence ◽  
Health Care Interventions ◽  
Genome Wide ◽  
Genetic And Environmental Factors ◽  
Opening Up ◽  
Omic Data

: Epigenetics is a field of biological sciences focused on the study of reversible, heritable changes in gene function not due to modifications of the genomic sequence. These changes are the result of a complex cross-talk between several molecular mechanisms, that is in turn orchestrated by genetic and environmental factors. The epigenetic profile captures the unique regulatory landscape and the exposure to environmental stimuli of an individual. It thus constitutes a valuable reservoir of information for personalized medicine, which is aimed at customizing health-care interventions based on the unique characteristics of each individual. Nowadays, the complex milieu of epigenomic marks can be studied at the genome-wide level thanks to massive, highthroughput technologies. This new experimental approach is opening up new and interesting knowledge perspectives. However, the analysis of these complex omic data requires to face important analytic issues. Artificial Intelligence, and in particular Machine Learning, are emerging as powerful resources to decipher epigenomic data. In this review, we will first describe the most used ML approaches in epigenomics. We then will recapitulate some of the recent applications of ML to epigenomic analysis. Finally, we will provide some examples of how the ML approach to epigenetic data can be useful for personalized medicine.

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