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Enhancer-FACS-seq
Enhancer-FACS-seq (eFS), developed by the Bulyk lab at Brigham and Women’s Hospital and Harvard Medical School, is a highly parallel enhancer assay that aims for the identification of active, tissue-specific transcriptional enhancers, in the context of whole ''Drosophila melanogaster'' embryos. This technology replaces the use of microscopy to screen for tissue-specific enhancers with fluorescence activated cell sorting (Fluorescence-activated cell sorting, FACS) of dissociated cells from whole embryos, combined with identification by high-throughput Illumina (company), Illumina sequencing. Introduction Transcriptional regulation In metazoans, in order to respond to environmental stress, differentiate properly, and progress normally through the cell cycle, a eukaryotic cell needs a specific and coordinated gene expression program, which involves the highly regulated transcription of thousands of genes. This gene regulation is in large part controlled, in a tissue-specific ma ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Drosophila Melanogaster
''Drosophila melanogaster'' is a species of fly (an insect of the Order (biology), order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the "vinegar fly", "pomace fly", or "banana fly". In the wild, ''D. melanogaster'' are attracted to rotting fruit and fermenting beverages, and are often found in orchards, kitchens and pubs. Starting with Charles W. Woodworth's 1901 proposal of the use of this species as a model organism, ''D. melanogaster'' continues to be widely used for biological research in genetics, physiology, microbial pathogenesis, and Life history theory, life history evolution. ''D. melanogaster'' was the first animal to be Fruit flies in space, launched into space in 1947. As of 2017, six Nobel Prizes have been awarded to drosophilists for their work using the insect. ''Drosophila melanogaster'' is typically used in research owing to its rapid life cycle, relatively simple genetics with on ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Brigham And Women’s Hospital
Brigham and Women's Hospital (BWH or The Brigham) is a teaching hospital of Harvard Medical School and the largest hospital in the Longwood Medical Area in Boston, Massachusetts. Along with Massachusetts General Hospital, it is one of the two founding members of Mass General Brigham, the largest healthcare provider in Massachusetts. Giles Boland, MD, serves as the hospital's current president. Brigham and Women's Hospital conducts the second largest hospital-based research program in the world, with an annual research budget of more than $630 million. History File:Bwh-longwood.jpg, 221 Longwood Avenue, formerly the Boston Lying-In Hospital building, part of Brigham and Women's Hospital but separate from the main building at 15–75 Francis Street; view from Longwood Avenue File:Free Hospital for Women.jpg, Former site of the Free Hospital for Women across the street from Olmsted Park. This institution was absorbed into Brigham and Women's Hospital. File:Brigham Circle at du ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Silencer (DNA)
In genetics, a silencer is a DNA sequence capable of binding transcription factors, transcription regulation factors, called repressors. DNA contains genes and provides the template to produce messenger RNA (mRNA). That mRNA is then Translation (biology), translated into proteins. When a repressor protein binds to the silencer region of DNA, RNA polymerase is prevented from Transcription (genetics), transcribing the DNA sequence into RNA. With transcription blocked, the translation of RNA into proteins is impossible. Thus, silencers prevent genes from being Gene expression, expressed as proteins. RNA polymerase, a DNA-dependent enzyme, transcribes the DNA sequences, called nucleotides, in the directionality (molecular biology), 3' to 5' direction while the complementary RNA is synthesized in the 5' to 3' direction. RNA is similar to DNA, except that RNA contains uracil, instead of thymine, which forms a base pair with adenine. An important region for the activity of gene repress ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
H3K4me1
H3K4me1 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the mono-methylation at the 4th lysine residue of the histone H3 protein and often associated with gene enhancers. Nomenclature H3K4me1 indicates monomethylation of lysine 4 on histone H3 protein subunit: Lysine methylation : This diagram shows the progressive methylation of a lysine residue. The mono-methylation (second from left) denotes the methylation present in H3K4me1. Understanding histone modifications The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as histones. The complexes formed by the looping of the DNA are known as chromatin. The basic structural unit of chromatin is the nucleosome: this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The carboxyl (C) terminal end of these histon ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
H3K27ac
H3K27ac is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates acetylation of the lysine residue at N-terminal position 27 of the histone H3 protein. H3K27ac is associated with the higher activation of transcription and therefore defined as an ''active enhancer'' mark. H3K27ac is found at both proximal and distal regions of transcription start site (TSS). Lysine acetylation and deacetylation Proteins are typically acetylated on lysine residues, and the acetylation reaction relies on acetyl-coenzyme A as the acetyl group donor. In histone acetylation and deacetylation, histone proteins are acetylated and deacetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with ''histone acetyltransferase'' (HAT) or ''histone deacetylase'' (HDAC) activity, although HATs and HDACs can modify the acetylation status of non-histone proteins as well. The regulation of t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mesoderm
The mesoderm is the middle layer of the three germ layers that develops during gastrulation in the very early development of the embryo of most animals. The outer layer is the ectoderm, and the inner layer is the endoderm.Langman's Medical Embryology, 11th edition. 2010. The mesoderm forms mesenchyme, mesothelium and coelomocytes. Mesothelium lines coeloms. Mesoderm forms the muscles in a process known as myogenesis, septa (cross-wise partitions) and mesenteries (length-wise partitions); and forms part of the gonads (the rest being the gametes). Myogenesis is specifically a function of mesenchyme. The mesoderm differentiates from the rest of the embryo through intercellular signaling, after which the mesoderm is polarized by an organizing center. The position of the organizing center is in turn determined by the regions in which beta-catenin is protected from degradation by GSK-3. Beta-catenin acts as a co-factor that alters the activity of the transcription facto ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNase I Hypersensitive Site
In genetics, DNase I hypersensitive sites (DHSs) are regions of chromatin that are sensitive to cleavage by the DNase I enzyme. In these specific regions of the genome, chromatin has lost its condensed structure, exposing the DNA and making it accessible. This raises the availability of DNA to degradation by enzymes, such as DNase I. These accessible chromatin zones are functionally related to transcriptional activity, since this remodeled state is necessary for the binding of proteins such as transcription factors. Since the discovery of DHSs 30 years ago, they have been used as markers of regulatory DNA regions. These regions have been shown to map many types of cis-regulatory elements including promoters, enhancers, insulators, silencers and locus control regions. A high-throughput measure of these regions is available through DNase-Seq. Massive analysis The ENCODE project proposes to map all of the DHSs in the human genome with the intention of cataloging human regulatory D ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polymerase Chain Reaction
The polymerase chain reaction (PCR) is a method widely used to make millions to billions of copies of a specific DNA sample rapidly, allowing scientists to amplify a very small sample of DNA (or a part of it) sufficiently to enable detailed study. PCR was invented in 1983 by American biochemist Kary Mullis at Cetus Corporation. Mullis and biochemist Michael Smith (chemist), Michael Smith, who had developed other essential ways of manipulating DNA, were jointly awarded the Nobel Prize in Chemistry in 1993. PCR is fundamental to many of the procedures used in genetic testing and research, including analysis of Ancient DNA, ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory research for a broad variety of applications including biomedical research and forensic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fluorescence
Fluorescence is one of two kinds of photoluminescence, the emission of light by a substance that has absorbed light or other electromagnetic radiation. When exposed to ultraviolet radiation, many substances will glow (fluoresce) with colored visible light. The color of the light emitted depends on the chemical composition of the substance. Fluorescent materials generally cease to glow nearly immediately when the radiation source stops. This distinguishes them from the other type of light emission, phosphorescence. Phosphorescent materials continue to emit light for some time after the radiation stops. This difference in duration is a result of quantum spin effects. Fluorescence occurs when a photon from incoming radiation is absorbed by a molecule, exciting it to a higher energy level, followed by the emission of light as the molecule returns to a lower energy state. The emitted light may have a longer wavelength and, therefore, a lower photon energy than the absorbed radi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Green Fluorescent Protein
The green fluorescent protein (GFP) is a protein that exhibits green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish ''Aequorea victoria'' and is sometimes called ''avGFP''. However, GFPs have been found in other organisms including corals, sea anemones, zoanithids, copepods and lancelets. The GFP from ''A. victoria'' has a major excitation peak at a wavelength of 395 nm and a minor one at 475 nm. Its emission peak is at 509 nm, which is in the lower green portion of the visible spectrum. The fluorescence quantum yield (QY) of GFP is 0.79. The GFP from the sea pansy ('' Renilla reniformis'') has a single major excitation peak at 498 nm. GFP makes for an excellent tool in many forms of biology due to its ability to form an internal chromophore without requiring any accessory cofactors, gene products, or enzymes / substrates other than molecular ox ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reporter Gene
Reporter genes are molecular tools widely used in molecular biology, genetics, and biotechnology to study gene function, expression patterns, and regulatory mechanisms. These genes encode proteins that produce easily detectable signals, such as fluorescence, luminescence, or enzymatic activity, allowing researchers to monitor cellular processes in real-time. Reporter genes are often fused to regulatory sequences of genes of interest, enabling scientists to analyze promoter activity, transcriptional regulation, and signal transduction pathways. Common reporter gene systems include green fluorescent protein (GFP), β-galactosidase (lacZ), luciferase, and chloramphenicol acetyltransferase (CAT), each offering distinct advantages depending on the experimental application. Their versatility makes reporter genes invaluable in fields such as drug discovery, gene therapy, and synthetic biology. Common Reporter Genes To introduce a reporter gene into an organism, scientists place the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cell Types
A cell type is a classification used to identify cells that share morphological or phenotypical features. A multicellular organism may contain cells of a number of widely differing and specialized cell types, such as muscle cells and skin cells, that differ both in appearance and function yet have identical genomic sequences. Cells may have the same genotype, but belong to different cell types due to the differential regulation of the genes they contain. Classification of a specific cell type is often done through the use of microscopy (such as those from the cluster of differentiation family that are commonly used for this purpose in immunology). Recent developments in single cell RNA sequencing facilitated classification of cell types based on shared gene expression patterns. This has led to the discovery of many new cell types in e.g. mouse cortex, hippocampus, dorsal root ganglion and spinal cord. Animals have evolved a greater diversity of cell types in a multicellular b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
