• The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
  • Each transcription factor binds to one specific set of DNA sequences and activates or inhibits the transcription of genes that have these sequences near their promoters. (wikipedia.org)
  • Since 2012, mutations in genes encoding six proteins of the BAF complex were identified in both conditions. (nih.gov)
  • Genetic studies have clarified that most microcephaly genes encode ubiquitous proteins involved in mitosis and in maintenance of genomic stability, but the effects of their inactivation are particularly strong in neural progenitors. (cancerindex.org)
  • Transcription factors help to regulate gene expression-turning genes on or off and dialing up or down their level of activity-often in partnership with the proteins that they bind. (mit.edu)
  • When transcription factors had their ARMs mutated so they couldn't bind RNA, those transcription factors were less effective in finding their target sites, remaining at those sites and regulating genes. (mit.edu)
  • The study, published in the journal Nature Communications, shows that compared to flies and worms, there is an increase in tardigrades of genes responsible for the tolerance of stressful environments. (ibtimes.co.uk)
  • Changes in DNA methylation were especially prominent in genes that regulate the activity of neurons and the connectivity between them. (medscape.com)
  • Witt said it was also "fascinating that among those genes that showed the strongest changes in DNA methylation levels in our study, two genes were previously reported to regulate behavioral aspects of cocaine intake in rodent experiments. (medscape.com)
  • The absence of genomic resources renders the search for paralogous cuttlefish genes dependent upon the presence of highly conserved protein motifs within genes of interest, thus we used a degenerate primer strategy to isolate partial coding sequence from the conserved domains specific to these families. (europa.eu)
  • His research focuses on Kabuki syndrome, which is caused by mutations in one of two genes that govern proteins that DNA wrap around. (hopkinsmedicine.org)
  • Until now we've relied on studies in mice to understand human germ cell differentiation, but the reproductive genes are not the same. (sciencedaily.com)
  • Members of what's called the DAZ family, the genes are unusual in that they encode RNA-binding proteins rather than the DNA transcription factors more commonly known to regulate cellular events. (sciencedaily.com)
  • In the current study, the researchers treated human embryonic stem cells with proteins known to stimulate germ cell formation and isolated those that began to express germ-cell-specific genes -- about 5 percent of the total. (sciencedaily.com)
  • In addition to expressing key genes, these cells also began to remove modifications, or methyl groups, to their DNA that confer cell-specific traits that would interfere with their ability to function as germ cells. (sciencedaily.com)
  • After analyzing a set of genes involved in the cell's ability to dispose unneeded proteins in more than 2,500 patients who had come to the NIH with undiagnosed conditions, Dr. Kastner and his team discovered three middle-aged men who suffered from problems such as lung inflammation, skin lesions, and irritated cartilage in the nose and ears. (lupusresearch.org)
  • The IRF5 gene encodes the IRF5 protein that binds to specific regions of DNA and helps control the activity of certain genes. (lupusresearch.org)
  • Once the inhibitor enters cells, it keeps the IRF5 protein from traveling to the cell's nucleus, which houses DNA and activating genes that may encode proteins involved in an autoimmune attack. (lupusresearch.org)
  • Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. (cdc.gov)
  • These proteins organize the DNA into a compact structure called chromatin. (wikipedia.org)
  • Other non-specific DNA-binding proteins in chromatin include the high-mobility group (HMG) proteins, which bind to bent or distorted DNA. (wikipedia.org)
  • The laboratory is particularly interested in studying how specific DNA sequences, DNA binding proteins, and chromatin. (rochester.edu)
  • only by forming chromatin can several feet of DNA fit inside the tiny command centers of each cell. (hopkinsmedicine.org)
  • But in order for a cell to read the DNA and put it to use making new proteins of its own, the chromatin must temporarily open up. (hopkinsmedicine.org)
  • Specialized enzymes, often called "writers" and "erasers," add or subtract chemical groups to the packaging proteins to help induce the chromatin to open or close. (hopkinsmedicine.org)
  • One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
  • DSB sites are preferentially located within chromatin loops, while several proteins that are required for DSB formation (Rec114, Mei4, and Mer2) localize on the chromosome axis (Blat et al. (springer.com)
  • Protein-DNA interactions occur when a protein binds a molecule of DNA, often to regulate the biological function of DNA, usually the expression of a gene. (wikipedia.org)
  • In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). (rsc.org)
  • The technology actually uses the SOMAmers, which is a chemically modified single stranded DNA molecule. (dirjournal.com)
  • This DNA molecule is used to bind to target proteins resulting in the identification and quantifying biomarkers. (dirjournal.com)
  • Combining an optical tweezer technology called C-trap that manipulates a single molecule of DNA and a novel approach, researchers were able to receive a detailed view into how cells find and repair damaged DNA. (genengnews.com)
  • Their findings are described in an article titled, " Single-molecule analysis of DNA-binding proteins from nuclear extracts (SMADNE) ," published in Nucleic Acids Research . (genengnews.com)
  • In collaboration with University of Kent researchers, the Van Houten group developed a new method called Single Molecule Analysis of DNA-binding proteins from Nuclear Extracts, or SMADNE. (genengnews.com)
  • It has long been a mystery how a bacterial cell is able to import a molecule as complex as DNA. (mpg.de)
  • In this process, the two strands of DNA making up the circular DNA molecule unwind and separate to become templates for generating new strands. (sciencedaily.com)
  • To ensure the process is well regulated, the bacterium has set a number of "roadblocks," or termination sites on the DNA, to ensure the permanent stoppage of replication forks, Y-shaped structures formed between the strands as the DNA molecule splits. (sciencedaily.com)
  • In lab and animal studies, Dr. Barnes developed a nontoxic inhibitor molecule that penetrates the cell membrane and enters into a variety of immune cells, including those called plasmacytoid dendritic cells, a rare type of immune cell known to secrete large quantities of type 1 interferons, which are the main disease drivers in lupus. (lupusresearch.org)
  • Overview of Genetics A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein) or a functional RNA molecule. (msdmanuals.com)
  • Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
  • An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. (nature.com)
  • Kornberg 7 has presented that the interactions between DNA and histones are involved in chromosome packaging in the cell nucleus. (nature.com)
  • Selective microfluidics-based ligand enrichment followed by sequencing, or SMiLE-seq, combines antibody arrays, mechanical trapping, and next-generation sequencing readouts to provide a new platform for characterizing DNA-protein interactions. (genomeweb.com)
  • That year, the two published a paper in Science describing a method to trap low-affinity DNA-protein interactions, specifically those of transcription factors. (genomeweb.com)
  • By physically restraining bound molecules against an antibody array, they capture both transient interactions, which yeast two-hybrid or tandem mass spectrometry methods don't, and weak interactions, which are usually obliterated by the wash in protein-DNA microarrays. (genomeweb.com)
  • The transcription factors bind to any number of DNA motifs in the library, those interactions are trapped, and then the readout matches up each motif with the transcription factor via the barcode. (genomeweb.com)
  • Deplancke also worked in advanced bioinformatics to derive predictive models for binding interactions. (genomeweb.com)
  • Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. (wikipedia.org)
  • These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence. (wikipedia.org)
  • The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to read the DNA sequence. (wikipedia.org)
  • Hydrophobicity was one of the most important physicochemical properties, due to the fact that it is involved in protein interactions, for example, by forming hydrophobic cores. (hindawi.com)
  • The clues have been there all along, but I think earlier work was so focused on the DNA and protein interactions that they didn't consider RNA. (mit.edu)
  • The laboratory is also interested in studying how those interactions are perturbed in disease states. (rochester.edu)
  • Protein analyses examine the primary structure (amino acids) as well as the secondary folded structure, more complex tertiary structures, and protein interactions. (jax.org)
  • Their results showed that efficiency of fork arrest is weakened by kinetic competition between the rate of strand separation by the helicase motor at the fork and the rate of rearrangement of Tus−Ter interactions that maintain Tus's strong grip on the DNA. (sciencedaily.com)
  • Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. (cdc.gov)
  • Studying interactions, we noted that all four Id proteins could dimerize with E47 or E2-2, but not with HASH-1 or dHAND. (lu.se)
  • Both predicted proteins are highly conserved with other known homologous sequences, with the exception of two small domains present only in the Sof-RXR. (europa.eu)
  • PURA encodes Pur-α, a highly conserved multifunctional protein that has an important role in normal postnatal brain development in animal models. (bmj.com)
  • Bullock and Fersht 8 have shown that mutations of DNA-binding residues, such as those on the tumor repressor protein P53, may predispose individuals to cancer. (nature.com)
  • Scope includes mutations and abnormal protein expression. (cancerindex.org)
  • [ 8 ] Both mutations created stop codons leading to truncation of the PAX3 protein. (medscape.com)
  • However, mutations in the gun-like structure cause the crown to disintegrate, so that the bacterial cell is no longer able to absorb DNA. (mpg.de)
  • Results Protein-altering de novo mutations in PURA were identified in four subjects. (bmj.com)
  • DNA microarrays are powerful tools that can be used to identify DNA mutations. (msdmanuals.com)
  • In contrast, other proteins have evolved to bind to specific DNA sequences. (wikipedia.org)
  • Protein design methods use trial and error or more sophisticated methods like directed evolution or inverse folding to generate novel scaffolds or to find novel protein sequences folding into a defined scaffold, respectively. (hindawi.com)
  • Given the intimate relationship between a protein's structure and function, a way to design proteins with targeted properties is to start from a desired structure and find sequences able to fold into it, imposing additional constraints in the process [ 1 ]. (hindawi.com)
  • They anchor themselves and their partner proteins to DNA at binding sites in genetic regulatory sequences, bringing together the components that are needed to make gene expression happen. (mit.edu)
  • the majority of human transcription factors contain an ARM-like region between their DNA and protein binding regions, and these sequences were conserved across animal species. (mit.edu)
  • We then extended these sequences in both directions using rapid-amplification of complementary deoxyribonucleic acid (c-DNA) ends (RACE) to obtain full length transcripts, all of which will be deposited in the public database GenBank. (europa.eu)
  • In terms of predicting where in the genome the transcription factors bind, the models we're able to derive seem to be, in general, actually better than the other assays. (genomeweb.com)
  • These DNA targets can occur throughout an organism's genome. (wikipedia.org)
  • Tat increases the transcription of HIV's RNA genome by binding to the virus' RNA and then recruiting cellular machinery to it. (mit.edu)
  • Voxelwise genome-wide association study (vGWAS). (nih.gov)
  • We are using genome technology such as gene-editing and data science method/analysis to study immunological and neurological diseases. (stanford.edu)
  • molecular studies are difficult due to the absence of genome sequence data for any cephalopod. (europa.eu)
  • The archaeal DNA folding , reported August 10 in Science , hints at the evolutionary origins of genome folding, a process that involves bending DNA and one that is remarkably conserved across all eukaryotes (organisms that have a defined nucleus surrounded by a membrane). (newswise.com)
  • Along with 5-carboxyl-cytosine (5caC) both modifications are present at low levels in the genome and are widely considered to be intermediates en route from methylated to unmethylated cytosine. (genomeweb.com)
  • DNA microarrays can be used in genome-wide association studies (GWAS) to compare patient and control populations to identify DNA variants that can contribute to disease risk. (msdmanuals.com)
  • Array comparative genomic hybridization (aCGH) is a type of microarray now routinely used to identify deleted or duplicated regions of DNA sequence in specific chromosomes on a genome-wide basis. (msdmanuals.com)
  • DNA from a patient is compared to a reference genome using many oligonucleotide probes. (msdmanuals.com)
  • Computational methods to identify the DNA binding sequence specificity have been proposed to make a good use of the abundant sequence data in the post-genomic era. (wikipedia.org)
  • Because my protein is a DNA binding protein, I think that I lost some proteins fixed on genomic DNA that are found in the pellet during the step of clarification just after breaking cells. (bio.net)
  • Genomic testing is moving beyond DNA testing. (jax.org)
  • We conducted detailed functional, genomic, and structural studies of BEND3. (bvsalud.org)
  • Extractions of genomic DNA were made from the dental root after exposure to high temperatures (600ºC, 800ºC and 1000ºC), during 10, 30 and 60 minutes. (bvsalud.org)
  • In a paper published in Nature Methods this week, a Switzerland-based team of researchers, led by bioengineer Bart Deplancke of the École Polytechnique Fédérale de Lausanne (EPFL), showcased the assay's ability to determine DNA-binding specificities for transcription factors. (genomeweb.com)
  • A mounting number of researchers are studying the mechanism and detection methods. (biomedcentral.com)
  • The researchers found that RNA binding keeps transcription factors near their DNA binding sites for longer, helping to fine tune gene expression. (mit.edu)
  • A few papers, including one from Young's lab, had previously identified individual transcription factors as being able to bind RNA, but researchers thought that this was a quirk of the specific transcription factors. (mit.edu)
  • The reason that researchers had not recognized transcription factors' RNA binding region as such is because it is not a typical RNA binding domain. (mit.edu)
  • Typical RNA binding domains form stable structures that researchers can detect or predict with current technologies. (mit.edu)
  • Young, Oksuz and Henninger got their biggest clue that researchers might be overlooking something from the human immunodeficiency virus (HIV), which produces a transcription factor-like protein called Tat. (mit.edu)
  • Next, the researchers tested to see if RNA binding affected the transcription factors' function. (mit.edu)
  • The researchers found out that it had the potential to protect DNA in the cells from damage caused by radiation. (ibtimes.co.uk)
  • Recently, researchers at NYU Langone Medical Center have come up with a unique protein test which they claim can help detect early stage pulmonary cancer which is asbestos related. (dirjournal.com)
  • By studying the 3-D structure of proteins bound to DNA in microbes called archaea, researchers have turned up surprising similarities to DNA packing in more complicated organisms. (newswise.com)
  • The researchers revealed that despite using a single type of histone (and not four as do eukaryotes), the archaea were folding DNA in a very familiar way, creating the same sort of bends as those found in eukaryotic nucleosomes. (newswise.com)
  • Next, researchers used a strong laser, which they knew would damage the DNA and cause DSBs, to see if healthy alpha-synuclein are recruited there to help seal the breaks. (parkinson.org)
  • In the new study, the researchers used the C-trap to investigate how different DNA repair proteins identify and bind to their respective forms of damage. (genengnews.com)
  • Using SMADNE, the researchers extracted DNA repair proteins from the nucleus of the cell. (genengnews.com)
  • The researchers found that when DDB1 and DDB2 were working together at the damage site, they usually arrived at the DNA together and departed together, as expected. (genengnews.com)
  • Studying mice with a genetic change similar to what is found in Kabuki syndrome, an inherited disease of humans, Johns Hopkins researchers report they have used an anticancer drug to "open up" DNA and improve mental function. (hopkinsmedicine.org)
  • Studying the brains of the treated mice, the researchers saw that compared to untreated peers, they had more newly formed neurons in a part of the hippocampus called the dentate gyrus. (hopkinsmedicine.org)
  • Overexpressing the three proteins together allowed the researchers to generate haploid cells -- those with only one copy of each chromosome -- expressing proteins found in mature sperm. (sciencedaily.com)
  • Together, the methods enhance researchers' toolkit for studying epigenetic modifications, which also include cytosine methylation and hydroxymethylation, allowing them to elucidate their potential biological role in mammalian cells. (genomeweb.com)
  • Researchers at the Max Planck Institute of Biophysics and Goethe University in Frankfurt have now gained new insights into exactly how bacteria import DNA. (mpg.de)
  • The researchers now want to identify the protein that makes up the crown. (mpg.de)
  • A key mystery of the DNA replication process has been unraveled by researchers, resolving a long-standing mystery that has clouded our understanding of DNA replication, and also has important implications for all domains of life. (sciencedaily.com)
  • A key mystery of the DNA replication process has been unraveled by researchers from King Abdullah University of Science and Technology (KAUST). (sciencedaily.com)
  • The assay could help accelerate efforts to map where transcription factors bind the genomes of humans and model organisms, Deplancke said. (genomeweb.com)
  • In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair. (wikipedia.org)
  • Scientists have identified a unique protein in tardigrades that could protect humans against DNA damage. (ibtimes.co.uk)
  • With an ability to trick death worthy of the best sci-fi stories, scientists believe that the miniature aquatic creatures could provide clues to protect humans against DNA damage. (ibtimes.co.uk)
  • The results from this study suggest that tardigrades have evolved unique strategies to cope with stressful conditions and that there is an avenue for future research, in order to better protect humans from environmental stressors. (ibtimes.co.uk)
  • Newswise - In the cells of palm trees, humans, and some single-celled microorganisms, DNA gets bent the same way. (newswise.com)
  • In humans and mice, hotspots are specified by PRDM9, a meiosis-specific PRDM family protein (Baudat et al. (springer.com)
  • Studies in experimental incidence and multiplicity of tumours to Wilms tumour in humans - in the animals increase and the latency period de adult rat after perinatal exposure to a creases with increasing dose. (who.int)
  • Wang and his coworkers 12 investigated the discriminative power of three sequence features from protein sequence, including the side chain pKa value, the hydrophobicity index and the molecular mass of an amino acid. (nature.com)
  • However, molecular weight is also important due to potential steric incompatibilities within protein cores. (hindawi.com)
  • In a paper published in Molecular Cell on July 3 , Young and postdocs Ozgur Oksuz and Jonathan Henninger reveal that along with DNA and protein, many transcription factors can also bind RNA. (mit.edu)
  • The Steiner laboratory utilizes genomics techniques to study the molecular mechanisms underlying erythroid maturation and development. (rochester.edu)
  • Some of these methods, such as family studies, have been going on in the background at molecular genetics labs for many years. (jax.org)
  • Tris buffer solutions are widely used in cell and molecular biology for processes such as protein and nucleic acid extraction and purification. (sigmaaldrich.com)
  • The communication between molecular motors and double-stranded DNA binding proteins is a common feature in DNA replication, repair, recombination and transcription and also in instances where conflict occurs between these processes. (sciencedaily.com)
  • Molecular chaperones are known to play a role in stabilizing protein structure and function during events of cellular stress. (bioone.org)
  • Although questions remain concerning the relationship between protein adduct levels and disease risk, measurement of protein adducts has been, and will continue to be, a valuable tool in molecular epidemiology studies. (cdc.gov)
  • Results: We present ZEAL, an interactive tool to superpose global and local protein structures based on their shape resemblance using 3D (Zernike-Canterakis) functions to represent the molecular surface. (lu.se)
  • After molecular analysis through PCR technique, it was verified that DNA amplification of the samples was not possible at any of the periods and temperatures analyzed. (bvsalud.org)
  • The MATR3 gene mutation associated with distal myopathy 2 changes a single protein building block (amino acid) in the matrin 3 protein. (medlineplus.gov)
  • This mutation, known as Ser85Cys (or S85C), replaces the amino acid serine with the amino acid cysteine at position 85 of the protein. (medlineplus.gov)
  • The effect of the S85C mutation on the function of the matrin 3 protein is unknown, although one study indicates that the mutation may change the location of the protein in the nucleus. (medlineplus.gov)
  • A novel PAX3 heterozygous mutation of c.372-373delGA (p.N125fs) was found that gave rise to a frameshift and truncation of the PAX3 protein. (medscape.com)
  • DNA testing did not identify a pathogenic variant (mutation) using a multi-gene neurology panel. (jax.org)
  • In these disorders, a genetic mutation causes errors in the way proteins and chemicals bind to DNA, which in turn affects the rate at which DNA make proteins. (hopkinsmedicine.org)
  • Biophysical studies show that these architectural HMG proteins bind, bend and loop DNA to perform its biological functions. (wikipedia.org)
  • Glass or quartz nanopipettes have found increasing use as tools for studying the biophysical properties of DNA and proteins, and as sensor devices. (imperial.ac.uk)
  • DNA-binding proteins include transcription factors which modulate the process of transcription, various polymerases, nucleases which cleave DNA molecules, and histones which are involved in chromosome packaging and transcription in the cell nucleus. (wikipedia.org)
  • A critical function of telomeres is to prevent the ligation of chromosome ends by DNA repair enzymes. (ens-lyon.fr)
  • However, Drosophila capping proteins can bind chromosome extremities in a DNA sequence-independent manner. (ens-lyon.fr)
  • This epigenetic protection of fly telomeres has been essentially studied in somatic cells where capping proteins such as HOAP or HP1 are essential in preventing chromosome end-to-end fusions. (ens-lyon.fr)
  • This gene encodes a large protein that functions as a GDP to GTP exchange factor. (cancerindex.org)
  • More recently, his group invented tools for cleavage-free large gene insertion via mining microbial recombination protein, and developed single-cell tracking approach for studying cancer biology and cancer immunology. (stanford.edu)
  • PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. (springer.com)
  • Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs), generated by SPO11 and accessory proteins (de Massy 2013 ). (springer.com)
  • In both human cells in a dish (in vitro) and living mouse brains (in vivo) alpha-synuclein was present in the exact same location as the DNA repair proteins, suggesting alpha-synuclein binds directly to DSBs, and helps repair those breaks. (parkinson.org)
  • Van Houten's lab is interested in repair proteins that mend DNA lesions caused by environmental factors, such as ultraviolet (UV) radiation from the sun and environmental pollutants. (genengnews.com)
  • Van Houten thinks about DNA repair proteins like people socializing at a bar. (genengnews.com)
  • In addition to DDB1 and DDB2, Van Houten's team used the C-trap and SMADNE to investigate the activities of DNA repair proteins from several different repair pathways to better understand these repair systems. (genengnews.com)
  • In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)
  • Superposition of proteins based on surface shape can enable comparison of highly divergent proteins, identify convergent evolution and enable detailed comparison of surface features and binding sites. (lu.se)
  • Some studies indicate that matrin 3 binds and stabilizes a type of RNA called messenger RNA (mRNA), which provides the genetic blueprint for proteins. (medlineplus.gov)
  • If your clinical and family history assessment make you suspicious of a genetic condition, DNA testing is currently still the first step to investigate this possibility. (jax.org)
  • Kabuki syndrome is a genetic disease that affects proteins that help control the compaction of DNA. (hopkinsmedicine.org)
  • Mendelian disorders of the epigenetic machinery affect how cells 'package' and use DNA, so they tend to have complicated and far-reaching effects," says Hans Bjornsson, M.D., Ph.D., an assistant professor of pediatrics and genetics in the Johns Hopkins University School of Medicine's McKusick-Nathans Institute of Genetic Medicine. (hopkinsmedicine.org)
  • Genetic studies have shown that the crown is not formed by the secretin protein itself. (mpg.de)
  • Before a bacterium can divide, it must make a copy of its genetic material, the circular DNA molecules that resemble bunched rubber bands, through a process called DNA replication. (sciencedaily.com)
  • Within chromosomes, DNA is held in complexes with structural proteins. (wikipedia.org)
  • However, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)
  • hi, I try to purify a protein from yeast to assay some structural studies. (bio.net)
  • This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. (rsc.org)
  • The nuclear matrix is a network of proteins that provides structural support for the nucleus and aids in several important nuclear functions. (medlineplus.gov)
  • RNA testing looks for changes in gene expression, and protein analysis assesses structural changes in the protein product of the gene. (jax.org)
  • In the crown we may have discovered a crucial switch for the recognition and binding of DNA," says Edoardo D'Imprima of the Department of Structural Biology at the Max Planck Institute in Frankfurt. (mpg.de)
  • Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins. (bvsalud.org)
  • Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins . (bvsalud.org)
  • Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins . (bvsalud.org)
  • DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. (wikipedia.org)
  • The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface. (wikipedia.org)
  • Recently, we have demonstrated high-bandwidth detection of double-stranded (ds) DNA with microsecond time resolution in nanopipettes, using custom-designed electronics. (imperial.ac.uk)
  • DNA-Binding Proteins (DBP) plays a pivotal role in biological system. (biomedcentral.com)
  • Antifreeze proteins (AFPs) are a group of proteins that inhibit body fluids from growing to ice crystals and thus improve biological antifreeze ability. (biomedcentral.com)
  • In a novel study of postmortem brain tissue, "we detected a trend towards stronger biological aging of the brain in individuals with cocaine use disorder compared to individuals without cocaine use disorder," lead investigator Stephanie Witt, PhD, Central Institute of Mental Health, Mannheim, Germany, said in a news release. (medscape.com)
  • Using patterns of DNA methylation as a measure of the biological age of cells, a total of 20 differentially methylated regions were significantly associated with CUD status after multiple testing correction. (medscape.com)
  • However, she cautioned that because biological age estimation is "a very recent concept in addiction research and is influenced by many factors, further studies are required to investigate this phenomenon, with larger sample sizes than were possible here. (medscape.com)
  • Previous efforts to study infertility have been hampered by the fact that -- unlike many other biological processes -- the human reproductive cycle cannot be adequately studied in animal models. (sciencedaily.com)
  • Due to this resilience against environmental changes (incineration, immersion, traumas, mutilation and decomposition), teeth represent an excellent source of DNA, when the other biological sources have been lost 20,29,30 . (bvsalud.org)
  • Time scales of water dynamics at biological interfaces: peptides, proteins and cells. (lu.se)
  • Luger says she'd like to look for the missing link - a nucleosome-like structure that bridges the gap between the simple archaeal fold and the elaborate nucleosome found in eukaryotes, which can pack a huge amount of DNA into a small space and regulate gene behavior in many ways. (newswise.com)
  • The knowledge about DNA-binding residues, binding specificity and binding affinity helps to not only understand the recognition mechanism of protein-DNA complex, but also give clues for protein function annotation. (nature.com)
  • Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
  • VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
  • DNA-binding hot spots are dominant and fundamental residues that contribute most of the binding free energy yet accounting for a small portion of protein-DNA interfaces. (biomedcentral.com)
  • However, removing RbmA led to visually similar biofilms, despite the absence of the cross-linked protein complexes. (elifesciences.org)
  • In particular, X-ray structures of BEN domain DNA complexes are only known for Drosophila factors bearing a single BEN domain, which lack direct vertebrate orthologs. (bvsalud.org)
  • It is assumed that the Id helix-loop-helix (HLH) proteins act by associating with ubiquitously expressed basic HLH (bHLH) transcription factors, such as E47 and E2-2, which prevents these factors from forming functional hetero- or homodimeric DNA binding complexes. (lu.se)
  • In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. (nature.com)
  • They are typically trained from a set of input features, which can be generally divided into three categories: protein sequence information, protein structure information and a combination of the two categories. (nature.com)
  • Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair. (wikipedia.org)
  • Mathematical descriptions of protein-DNA binding taking into account sequence-specificity, and competitive and cooperative binding of proteins of different types are usually performed with the help of the lattice models. (wikipedia.org)
  • A termination site comprises a 23-base pair termination sequence (Ter) bound to the protein terminus utilization substance (Tus). (sciencedaily.com)
  • Dr. Kastner and his team implemented a "gene-first" strategy to define new illnesses based on a permanent change in the DNA sequence - the blueprint for building our body's cells - that makes up a gene shared among patients who display distinct clinical features. (lupusresearch.org)
  • In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. (bvsalud.org)
  • For comparisons of proteins with limited sequence and backbone-fold similarity, where coordinate-based methods typically fail, ZEAL can often find alignments with substantial surface-shape correspondence. (lu.se)
  • PCR (polymerase chain reaction) technique has achieved increased importance for post-mortem DNA analysis in forensic cases 8 because of the millions of copies amplified from one specific sequence of DNA. (bvsalud.org)
  • Different types of probes may investigate a broad range of sizes of DNA sequence. (msdmanuals.com)
  • Very interestingly, a vital insight of neuroinflammation research in ALS was generated by the evidence that both the mRNA and protein levels of the pro-inflammatory enzyme cyclooxygenase-2 (COX-2) are upregulated in both transgenic mouse models and in human postmortem brain and spinal cord. (nature.com)
  • Challenge of rGMCs with 1 or 10 μM HgCl 2 or Pb 2 acetate increased HSPA5 mRNA and protein levels. (bioone.org)
  • High water mobility on the ice-binding surface of a hyperactive antifreeze protein. (lu.se)
  • As DNA methylation is an important regulatory mechanism for gene expression, the identified DNA methylation alterations might contribute to functional changes in the human brain and thereby to the associated behavioral aspects of addiction," first author Eric Poisel, a PhD student at the Central Institute of Mental Health in Mannheim, said in the release. (medscape.com)
  • Bacteria often can't support over-expression needed to get workable quantities of protein for an assay, and in vitro expression often can't synthesize a fully functional transcription factor. (genomeweb.com)
  • However, for a discrete number of patients whose results are uninformative, it may be possible to get a more definitive answer about the consequences of a variant using additional methods like RNA sequencing, protein analysis and predictive or functional studies. (jax.org)
  • The predicted effects of a variant on functional areas of the protein such as binding sites for DNA or other proteins can also be analyzed. (jax.org)
  • 2010 ). PRDM9 includes several functional domains, such as a DNA-binding zinc finger array, a histone lysine methyltransferase PR/SET (PRDI-BF1 and RIZ1 homology) domain, and a Krüppel-associated box (KRAB)-related domain. (springer.com)
  • This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT. (cdc.gov)
  • 2012 ), generalizing the observation that hotspot localization is determined by the DNA-binding specificity of the zinc finger array (Grey et al. (springer.com)
  • This resolves a long-standing mystery that has clouded our understanding of DNA replication, and also has important implications for all domains of life. (sciencedaily.com)
  • thus, requiring replication in additional studies. (cdc.gov)
  • It shares homology with the mating-type protein, Mc, from the fission yeast Schizosaccharomyces pombe and a conserved DNA-binding motif present in the nuclear high-mobility-group proteins HMG1 and HMG2. (nih.gov)
  • instead, it binds RNA from a region called an arginine-rich motif (ARM) that is unstructured but has a high affinity for RNA. (mit.edu)
  • OBJECTIVE High-mobility group package-1 (HMGB1) proteins is a nuclear DNA-binding proteins released from necrotic cells, inducing inflammatory reactions and promoting cells restoration and angiogenesis. (exposed-skin-care.net)
  • High-mobility group package-1 (HMGB1) is usually a nuclear proteins that functions as a cytokine when released in to the extracellular milieu by necrotic and inflammatory cells, and it is involved with inflammatory reactions and tissue restoration (4). (exposed-skin-care.net)
  • The 1st identified mobile receptor because of this nuclear proteins was the receptor for advanced glycation end items (Trend), which mediates the relationships between advanced glycation end item (Age group)Cmodified proteins as well as the endothelium and additional cell types (7). (exposed-skin-care.net)
  • The MATR3 gene provides instructions for making a protein called matrin 3, which is found in the nucleus of the cell as part of the nuclear matrix. (medlineplus.gov)
  • and amphoterin, a nuclear protein sometimes found in the ECM (Table 1 ). (jci.org)
  • According to Dr. Pass, the test measures 19 protein biomarkers for malignant pleural mesothelioma and can find and quantify the small amount of proteins secreted by the tumor cells. (dirjournal.com)
  • We found that the three Id proteins expressed in neuroblastoma cells (Id1, Id2, and Id3) were down-regulated during induced differentiation, indicating that Id proteins help keep the tumor cells in an undifferentiated state. (lu.se)
  • Methods The Deciphering Developmental Disorders study is using whole exome sequencing in family trios to investigate children with severe, sporadic, undiagnosed developmental delay. (bmj.com)
  • This study reports the function of CmNAC1, a stress-responsive pumpkin NAC domain protein. (frontiersin.org)
  • HipHop and K81 are two recently identified paralogous capping proteins with complementary expression patterns. (ens-lyon.fr)
  • The tagged DNA binds to its complementary DNA segment and can be detected by measuring the amount and type of fluorescence. (msdmanuals.com)
  • Several tissue-specific bHLH proteins, including HASH-1, dHAND, and HES-1, are important for development of the nervous system. (lu.se)
  • Cephalopods offer enormous opportunities for studies of the developmental genetics of complex organ systems within an invertebrate model. (europa.eu)
  • Bjornsson led the study in collaboration with Harry "Hal" Dietz, M.D., the Victor A. McKusick Professor of Medicine and Genetics and director of the William S. Smilow Center for Marfan Syndrome Research. (hopkinsmedicine.org)
  • The idea of redBS-seq and fCAB-seq is similar − reducing 5fC to 5hmC prior to sequencing − but He and his colleagues used EtONH 2 instead of borohydride, which they found to result in lower background, according to Peng Jin, a professor of human genetics at Emory University School of Medicine and the co-senior author of last year's study. (genomeweb.com)
  • Most evidence of cocaine-associated epigenetic changes derives from rodent studies, while only a few studies have been performed using human tissue. (medscape.com)
  • As a largest plant-specific transcription factor family, NAC domain proteins play an important role in plant development and regulation of abiotic stress tolerance. (frontiersin.org)
  • We thus propose that the maintenance of capping proteins at Drosophila sperm telomeres is crucial for the transmission of telomere identity to the diploid zygote. (ens-lyon.fr)
  • 2019), wondered if healthy alpha-synuclein help repair DNA damage caused by double-strand breaks (DSBs). (parkinson.org)
  • They also found that the healthy human cells repaired DSBs more rapidly compared to the knock-out cells, again supporting the role of alpha-synuclein in aiding DNA repair. (parkinson.org)
  • In both healthy human cells and living mouse brains, the laser-induced DSBs, triggered alpha-synuclein to move to the site of DNA damage. (parkinson.org)
  • In diseased human cells and mice carrying the abnormal form of alpha-synuclein, the laser-induced DSBs, impaired alpha-synuclein from moving to the site of DNA damage. (parkinson.org)
  • These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that form chromosomes. (wikipedia.org)
  • Specifically, these methods were used to ascertain how the presence of bound Ni2+ ions affects the stability of the known open, cis, and trans forms observed in the crystal structures of this protein as well as their interconversion capability. (sissa.it)
  • Transcription factors do not contain such structures, and so standard searches for RNA binding domains had not identified them in transcription factors. (mit.edu)
  • Data derived from cephalopod studies can be used to compare and contrast known mechanisms underlying the development of analogous vertebrate structures. (europa.eu)
  • But growing the crystals was tricky (the histones would stick to any given stretch of DNA, making it hard to create consistent histone-DNA structures), and making sense of the data they could get was no easy feat. "It was a very gnarly crystallographic problem," says Luger. (newswise.com)
  • But, of course, we also want to identify target structures that could inhibit DNA transfer and, for example, stem the spread of antibiotic resistance," D'Imprima says. (mpg.de)
  • He also performs unique dermatologic research studying the three-dimensional structures of skin-related proteins using x-ray crystallography and cryo-electron microscopy. (yale.edu)
  • His PhD research studied the three-dimensional structures of calcium-binding proteins and proteins involved in DNA repair processes (e.g. the skin disease xeroderma pigmentosum). (yale.edu)
  • In a benchmark study of structures with the same fold, we show that ZEAL outperforms two. (lu.se)
  • DNA strands are wound around a "hockey puck" composed of eight histone proteins, forming what's called a nucleosome. (newswise.com)
  • Instead of individual beads on a string, the archaeal DNA formed a long superhelix, a single, large curve of already twisty DNA strands. (newswise.com)
  • A ) Vibrio cholera e (white) secretes four main matrix proteins: RbmA (blue), RbmC (orange), Bap1 (green) and VPS (red strands). (elifesciences.org)
  • C ) An RbmA dimer can bind to several strands of VPS to create a stable mesh across the matrix. (elifesciences.org)
  • The machine pulls DNA through the outer cell layers, separates it into two single strands and assimilates one of them," Beate Averhoff explains. (mpg.de)
  • In eukaryotes, this structure involves DNA binding to a complex of small basic proteins called histones. (wikipedia.org)
  • These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription. (wikipedia.org)
  • Alternatively, transcription factors can bind enzymes that modify the histones at the promoter. (wikipedia.org)
  • By examining the detailed structure of a crystal that contained DNA bound to archaeal histones, the new study reveals exactly how DNA packing works. (newswise.com)
  • RNA sequencing is beginning to show promise for understanding how a DNA variant may disrupt the normal transcription to RNA, post-transcriptional modifications, or the subsequent protein structure. (jax.org)
  • In differentiating neuroblastoma cells, HASH-1 is down-regulated, and there is coincident up-regulation of the transcriptional repressor HES-1, which is known to bind the HASH-1 promoter. (lu.se)
  • Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
  • Earlier work by Reeve had turned up histone proteins in archaeal cells. (newswise.com)
  • But, archaea are prokaryotes (microgorganisms without a defined nucleus), so it wasn't clear just what those histone proteins were doing. (newswise.com)
  • Luger and her colleagues wanted to make crystals of the histone-DNA complex in Methanothermus fervidus , a heat-loving archaeal species. (newswise.com)
  • This role involves its DNA-binding domain, which is composed of a tandem array of zinc fingers, and PRDM9-dependent trimethylation of histone H3 at lysine 4. (springer.com)
  • Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)
  • Associate Professor of Biology Dr. Jason Kuehner was awarded a three-year, $372,026 grant from the National Science Foundation (NSF) Research in Undergraduate Institutions (RUI) to examine control of DNA traffic and regulation of gene expression. (emmanuel.edu)
  • The ability of Id proteins to affect HES-1 activity is of particular interest in neuronal cells, where regulation of HES-1 is essential for the timing of neuronal differentiation. (lu.se)
  • However, it is still unclear how these matrix proteins interact to simultaneously remain a connected and flexible multicellular structure. (elifesciences.org)
  • In addition, we identified proteins that interact with the KRAB domain of PRDM9 in yeast two-hybrid assay screens, particularly CXXC1, a member of the COMPASS complex. (springer.com)
  • Gene probes can be used to locate specific segments of normal or mutated DNA. (msdmanuals.com)
  • The CmNAC1-GFP fusion protein was transiently expressed in tobacco leaves for subcellular localization analysis, and we found that CmNAC1 is localized in the nucleus. (frontiersin.org)
  • As poly adenosine diphosphate (ADP)-ribose polymerase 1 (PARP-1) is overexpressed in various cancer types, and is localized to the nucleus, PARP-1 can be safely targeted with Auger emitters to induce DNA damage in tumors. (osti.gov)
  • DNA-binding proteins can incorporate such domains as the zinc finger, the helix-turn-helix, and the leucine zipper (among many others) that facilitate binding to nucleic acid. (wikipedia.org)
  • In most eukaryotes, telomeric DNA consists in large arrays of G-rich tandem repeats that are recognized by DNA binding capping proteins. (ens-lyon.fr)
  • Scientists have long known that cells in all eukaryotes, from fish to trees to people, pack DNA in exactly the same way. (newswise.com)
  • If all eukaryotes have the same DNA bending style, "then it must have evolved in a common ancestor," says study coauthor John Reeve, a microbiologist at Ohio State University. (newswise.com)
  • In classification studies, amino acids are often represented by so called descriptors, mapping each amino acid to a numerical value. (hindawi.com)
  • In this work, we generated and optimized a new synthetic fusion protein using an evolutionary approach. (hindawi.com)