• Pseudobase Recode Frameshifting,+Ribosomal at the U.S. National Library of Medicine Medical Subject Headings (MeSH) Wise2 - aligns a protein against a DNA sequence allowing frameshifts and introns FastY - compare a DNA sequence to a protein sequence database, allowing gaps and frameshifts Path - tool that compares two frameshift proteins (back-translation principle) Recode2 - Database of recoded genes, including those that require programmed Translational frameshift. (wikipedia.org)
  • Known as "destabilising motifs", these sequences attract the attention of a group of proteins called Ccr4-Not. (elifesciences.org)
  • The biological system is complex with many regulatory features such as DNA, mRNA, proteins, metabolites, and epigenetic features such as DNA methylation and histone post-translational modifications (PTMs). (rsc.org)
  • In addition to the host regulatory mechanisms response to disease, the microbiome can make changes to the expression of the host features such as their genes, proteins, and/or PTMs. (rsc.org)
  • Twenty eight (46.7%) of the proteins encoded by this virus exhibit sequence similarity to coliphage T7 proteins while 34 (81.0%) are similar to proteins of Pseudomonas phage gh-1. (biomedcentral.com)
  • but this includes many previously unknown effects at a variety of different levels, including post-translational changes in proteins and global cellular physiology. (biomedcentral.com)
  • Intriguingly, ZFP36L2 also decreased NanoLuc expression when bound within the coding sequence, revealing that ZFP36L2-and potentially many other mRNA regulatory proteins-can function when targeted to diverse locations within an mRNA. (bvsalud.org)
  • One such important family of regulatory RBPs is the Serine-Arginine (SR) family of proteins. (molcells.org)
  • This subfamily corresponds to the RRM1 of the CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. (nih.gov)
  • Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins have been classified into two subfamilies. (nih.gov)
  • The activation of the core promoter is done by the additional sequence of regulatory DNA sequence elements to which various proteins bind and subsequently interact with the transcription initiation complex to activate gene expression. (allindianpatents.com)
  • posttranslational modifications, amino acid variations, computational mutation analysis, protein PTM predictor, network biology Introduction Protein PTMs are biochemical alterations of amino acids that change the physicochemical properties of target proteins, leading to structural changes and therefore regulating protein-protein interactions and cellular signal transduction in developmental and cancer pathways [1]. (deepdyve.com)
  • 7] analyzed amino acid variations of 15 different PTMs and indicated that about 4.5% of amino acid variations may affect protein function through disruption of PTMs, and the mutation of 238 PTMs sites in human proteins was causative of disease. (deepdyve.com)
  • However, it often requires extensive laboratory work and considerable expense to make thousands of variant proteins and select amino acid variations that influence PTM sites. (deepdyve.com)
  • We determined the ribosome locations across six primary human cell types and five tissues and detected 7,767 smORFs with translational profiles matching those of known proteins. (biomed.news)
  • How do distinct transcriptional regulatory proteins coordinate their job with extrinsic factors and the microenvironment? (nih.gov)
  • IRVING, Texas and CAMBRIDGE, Massachusetts, June 1, 2023 - Caris Life Sciences ® (Caris), the leading molecular science, artificial intelligence (AI) and machine learning technology company actively developing and delivering innovative solutions to revolutionize healthcare, and ConcertAI , the leading oncology real-world evidence data and AI technology company, today announced an expanded translational sciences and clinical development solutions partnership. (carislifesciences.com)
  • Therapeutic oligonucleotides, such as antisense oligonucleotides or ribozymes, are short segments of DNA that have been designed to hybridize to a sequence on a specific mRNA. (justia.com)
  • The prevalence of this RNA structural feature and the conservation of RNA helicases across kingdoms suggest that mRNA structural remodelling is a general feature of translational reprogramming. (bvsalud.org)
  • It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. (nih.gov)
  • It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. (nih.gov)
  • Whole genome sequencing analysis for 100~ liver cancers reveals whole genome landscape of various phenotypes of liver cancers with multiple etiological backgrounds (virus and non-virus) for point mutations, CNVs, SVs, and virus integrations. (selectbiosciences.com)
  • We find that whole genome sequencing-derived telomere content estimates strongly correlate with telomere qPCR measurements (r = 0.94). (biomedcentral.com)
  • For the first time, we determine the correlation of in silico telomere content quantification from whole genome sequencing and whole genome bisulfite sequencing data derived from the same tumor sample (r = 0.78). (biomedcentral.com)
  • An analogous comparison of whole exome sequencing data and whole genome sequencing data measured slightly lower correlation (r = 0.79). (biomedcentral.com)
  • Besides whole genome sequencing, whole exome sequencing and whole genome bisulfite sequencing are suited for in silico telomere content quantification, especially if matched control samples are available. (biomedcentral.com)
  • All these phages, most of which have members of the Enterobacteriaceae as their host, present a highly conserved genome organization and mainly differ at sequence level through the presence or absence of nonessential genes [ 8 ]. (biomedcentral.com)
  • The human genome was found to contain highly cell-type- and tissue-specific smORFs and a subset that encodes highly conserved amino acid sequences. (biomed.news)
  • The mRNAs can carry short sequences of genetic letters that can trigger their own destruction. (elifesciences.org)
  • We introduced an RNA hairpin recognition site for the MS2 coat protein into the untranslated regions or coding sequence of mRNAs expressing a luminescent reporter protein, NanoLuc. (bvsalud.org)
  • We formulated the hypothesis that the amounts of NSP1 and VP6 were regulated by the translational efficiencies of the respective mRNAs. (microbiologyresearch.org)
  • These data define a regulatory mechanism for the difference in amounts of VP6 and NSP1 and provide evidence for post-transcriptional control of rotavirus gene expression mediated by the translational efficiency of individual viral mRNAs. (microbiologyresearch.org)
  • A four-nucleotide translation enhancer in the 3′-terminal consensus sequence of the nonpolyadenylated mRNAs of rotavirus. (microbiologyresearch.org)
  • Translational control of cellular and viral mRNAs. (microbiologyresearch.org)
  • The role of the 3′-untranslated region of non-polyadenylated plant viral mRNAs in regulating translational efficiency. (microbiologyresearch.org)
  • Translational specificity in reovirus-infected mouse fibroblasts. (microbiologyresearch.org)
  • Non-natural oligonucleotides are valuable probes of biological systems, as they can convey synthetic control of endogenous nucleic acids with high sequence specificity. (cdc.gov)
  • With the advancement of next-generation sequencing and mass spectrometry, there is a growing need for the ability to merge biological features in order to study a system as a whole. (rsc.org)
  • The scope of studies ranges from those focused-on sequencing, mass spectrometry, bioimaging and other high-through-put techniques in data to medicine, pharmacology, and populational studies. (nih.gov)
  • Antisense Uchl1 activity depends on the presence of a 5′ overlapping sequence and an embedded inverted SINEB2 element. (nature.com)
  • These features are shared by other natural antisense transcripts and can confer regulatory activity to an artificial antisense to green fluorescent protein. (nature.com)
  • PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element. (nature.com)
  • Hastings, M. L., Ingle, H. A., Lazar, M. A. & Munroe, S. H. Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA. (nature.com)
  • According to the methods, a mixture of lipids containing a protonatable or deprotonatable lipid, for example an amino lipid and a lipid such as a PEG- or Polyamide oligomer-modified lipid is combined with a buffered aqueous solution of a charged therapeutic agent, for example polyanionic nucleic acids, to produce particles in which the therapeutic agent is encapsulated in a lipid vesicle. (justia.com)
  • A slippery sequence is a small section of codon nucleotide sequences (usually UUUAAAC) that controls the rate and chance of ribosomal frameshifting. (wikipedia.org)
  • Furthermore, nucleotide sequences related to the cluster vanHAX are present in this DNA, suggesting that the prolonged use of avoparcin in agriculture led to the uptake of glycopeptide resistance genes by animal commensal bacteria, which were subsequently transferred to humans. (cdc.gov)
  • the invention also provides non-human animals and cells comprising a transgene encoding an APP comprising the Swedish mutation and further comprising functionally disrupted endogenous APP gene loci, transgenes and targeting constructs used to produce such transgenic cells and animals, transgenes encoding human Swedish mutation APP polypeptide sequences, and methods for using the transgenic animals in pharmaceutical screening and as commercial research animals for modeling neurodegenerative diseases (e.g. (justia.com)
  • Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes. (nih.gov)
  • Here, by integrating transcriptome-wide translational and structural analyses during pattern-triggered immunity in Arabidopsis, we found that transcripts with immune-induced translation are enriched with upstream open reading frames (uORFs). (bvsalud.org)
  • The CaMV promoter is a sequence of about 350 basepairs upstream of the 35S transcript (-343 to +8, with Cap site at +1), about 250 basepairs of which overlap with the 3' end of gene Vl, the last of the six large open reading frames. (i-sis.org.uk)
  • These short regulatory elements are located at a varying distance from transcription start point, some regulatory elements (called proximal elements) are adjacent to core promoter while other elements can be positioned several kilobases upstream or downstream of the promoter (enhancers). (allindianpatents.com)
  • Changes in the translational efficiency of upstream-encoded smORFs (uORFs) and the corresponding main ORFs predominantly occur in the same direction. (biomed.news)
  • Recovery of Five Complete Influenza A(H1N1)pdm09 Genome Sequences from the 2015 Influenza Outbreak in India by Metagenomic Sequencing. (ncbs.res.in)
  • Concept of gene, Prokaryotes as genetic system, Prokaryotic and eukaryotic chromosomes, methods of gene isolation and identification, Split genes, overlapping genes and pseudo genes, Organization of prokaryotic and eukaryotic genes and genomes including operan, exon, intron, enhancer promoter sequences and other regulatory elements. (nipaers.com)
  • 2019. Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum. . (ncbs.res.in)
  • Compared to the genome of gh-1, the sequence of ϕIBB-PF7A is longer and contains more genes with unassigned function and lacks a few potentially essential and non-essential T7 genes, such as gene1.1, 3.8, and 7. (biomedcentral.com)
  • Today, phage genome sequencing is commonly performed for classification and characterization purposes and is based on the arrangement of conserved genes and the nucleotide and protein sequence identity [ 5 , 6 ]. (biomedcentral.com)
  • Only two of the 147 genes contain a TTA codon, but some effects of bldA could be traced to TTA codons in regulatory genes or polycistronic operons. (biomedcentral.com)
  • Some researchers have proposed that the vanH , vanA , and vanX genes of hospital enterococci may have been acquired en bloc from the actinomycetes ( 8 ). (cdc.gov)
  • The initiation of transcription and modulation of gene expression in eukaryotic genes is directed by a variety of DNA sequence elements collectively arranged in a larger sequence called promoter. (allindianpatents.com)
  • The minimal promoter or core promoter is a minimal stretch of contiguous DNA sequence that is sufficient to direct accurate initiation of transcription by RNA [Pol II machinery, Smale, S. T, genes dev 15, 2503-2508 2001]. (allindianpatents.com)
  • The physiological conditions experienced by a microbial community can thus be inferred using meta-transcriptomic sequencing by comparing transcription levels of specifically chosen genes. (osti.gov)
  • NRL interacts with homeodomain protein CRX and numerous other regulatory factors to control expression of most rod-expressed genes. (nih.gov)
  • There is significant and sex-specific natural genetic variation in the transcriptional response to developmental exposure to ethanol in Drosophila that comprises networks of genes affecting nervous system development and ethanol metabolism as well as networks of regulatory non-coding RNAs. (biomedcentral.com)
  • Typical applications of design include novel therapeutic strategies, control principles for existing biological systems, or sensors for the presence of small molecules [3], but designed sequences can also provide an objective experimental assessment of functional hypotheses, where designs are synthesized and their effect on the cellular context can be tested in vitro and, in turn, in vivo. (dagstuhl.de)
  • vi)a nucleic acid sequence according to any of (i) and (ii) which is degenerate as a result of the genetic code. (allindianpatents.com)
  • In this regard, comprehensive studies of the impact of amino acid variation on protein PTMs will be helpful for further understanding of how genetic polymorphisms are involved in regulating biological and pathological processes and providing instructive information for drug development of various related diseases. (deepdyve.com)
  • This research holds great potential for elucidating how genetic variation and regulatory elements lead to diverse visual phenotypes. (nih.gov)
  • We used 96 sequenced, wild-derived inbred lines from the Drosophila melanogaster Genetic Reference Panel (DGRP) to profile genome-wide transcript abundances in young adult flies that developed on ethanol-supplemented medium or standard culture medium. (biomedcentral.com)
  • As shown for the Macrophage Inflammatory Protein 1α, de novo RNA synthesis correlates with the number of CpG dinucleotides, whereas RNA splicing, stability, nuclear export and translation are not affected by the sequence modification. (nih.gov)
  • Features such as the transcriptome, methylome, proteome, histone post-translational modifications and the microbiome all influence the host response to various diseases and cancers. (rsc.org)
  • Combining the deep clinical data at ConcertAI with the whole exome and whole transcriptome sequencing and other data at Caris enables researchers to discover new associations and information to improve patient care, versus datasets with smaller panels that inherently cover only what is known," said David Spetzler , M.S., Ph.D., MBA, Caris President. (carislifesciences.com)
  • With landmark mutation studies for each cancer type completed and the reduced cost in high throughput sequencing, the pace toward personalized oncology is gaining momentum. (selectbiosciences.com)
  • The process of agent-induced mu- the mutation - either through faulty not a mutation and general y does tagenesis consists of three parts: the DNA repair of the mutagen-induced not alter the linear sequence of nu- induction of DNA damage, the sen- or spontaneous DNA damage, or cleotides. (who.int)
  • A mutation is defined as a sing of the DNA damage by the cel by replicating past the unrepaired change in the sequence or number (the DNA damage response), and DNA damage, thereby introducing a of nucleotides in the DNA. (who.int)
  • Leverage the strength of Thermo Fisher's nucleic acid extraction, PCR, qPCR, Capillary Electrophoresis, microarray and Next Generation Sequencing platforms. (triconference.com)
  • For example, phosphorylation mainly occurs on a subset of three types of amino acids, including serine (S), threonine (T) and tyrosine (Y). Methylation is predominantly found on lysine (K) and arginine (R) residues. (deepdyve.com)
  • The graphene surface of the CRISPR-Chip is functionalized with nuclease-deactivated CRISPR RNA-guided ribonucleoproteins (dRNPs) which scan the genomic sample, bind to their target sequence, and produce a detectable change in the gFET signal output. (triconference.com)
  • Although genomic and transcriptomic studies of S. pneumoniae have provided detailed perspectives on gene content and expression programs, they have lacked information pertaining to the translational landscape, particularly at a resolution that identifies commonly overlooked small open reading frames (sORFs), whose importance is increasingly realized in metabolism, regulation, and virulence. (biomed.news)
  • The process of transcription is the most important regulatory step in the process of gene expression and its regulation. (allindianpatents.com)
  • These findings identify miR-27a* as a functional star sequence that exhibits novel coordinated regulation of the EGFR pathway in solid tumors and potentially represents a novel therapeutic option. (oncotarget.com)
  • Due to high sequence similarity, members in this subfamily may share similar expression patterns and functions. (nih.gov)
  • This project seeks to elucidate transcriptional and post-transcriptional regulatory networks that determine cell fate and guide the development of photoreceptors from retinal progenitor cells. (nih.gov)
  • This invention relates to compositions comprising a combination of a lipid and a therapeutic agent, particularly to lipid-nucleic acid compositions, for in vivo therapeutic use. (justia.com)
  • CpG dinucleotides are known to play a crucial role in regulatory domains, affecting gene expression in their natural context. (nih.gov)
  • 2017. Oestrogen Receptor-α binds the FOXP3 promoter and modulates regulatory T-cell function in human cervical cancer. . (ncbs.res.in)
  • These studies show that the loss of up to 40 amino acids from the 3' end of gene Vl (which overlaps with the 35S promoter) had no effect on pathogenesis whereas further truncation into a putative zinc finger region was fatal to the virus. (i-sis.org.uk)
  • Promoter is the portion of DNA sequence on 5' side, i.e. before beginning of the coding region of a gene. (allindianpatents.com)
  • Since the complex bldA phenotype is likely to involve elements of both transcriptional and translational control, it is particularly suitable for an integrated functional genomics approach. (biomedcentral.com)
  • This generates a vast repertoire of transcripts that includes protein-coding messenger RNAs, long non-coding RNAs (lncRNAs) and repetitive sequences, such as SINEs (short interspersed nuclear elements). (nature.com)
  • This suggests that important sequence elements are at the interfaces of the subdomains, or that the combination of subdomains is not simply additive but results in qualitatively novel specificities. (i-sis.org.uk)
  • We envisioned that enzyme-activatable cMOs could overcome these limitations, as the triggering enzymes could be expressed in individual cell populations using cis regulatory elements. (cdc.gov)
  • The recent Encyclopedia of studies in the 1950s and 1960s in Escherichia coli and then by DNA Elements (ENCODE) project showed binding of carcinogens to nu- Szybalski (1958) , who tested more indicates that at least 80% of the cleic acids ( Wiest and Heidelberger, than 400 compounds in E. coli . (who.int)
  • For many functional RNA families [11], decades of research have produced a deep understanding of the sequence and structural basis underlying their biological function(s). (dagstuhl.de)
  • Owing to the discrete nature of RNA sequence and popular structural representations (e.g. secondary structure), RNA design has inspired the contribution of a large number of diverse algorithms [9, 20, 14, 4] for the inverse folding problem, i.e. the design of an RNA sequence which preferentially and effectively folds into a predefined (secondary) structure. (dagstuhl.de)
  • This enzyme is detected in all tissues, especially in embryonic tissues and immune cells ( https://www.proteinatlas.org/ ) ( Figures 1B,C ). The full-length human RNase T2 has 256 amino acids (AA) and a predicted size of 29 kD ( Table 1 ). (frontiersin.org)
  • Here, we identified the coding sequence of the EZH2 gene and characterized its expression pattern in fetal tissues of Duroc pigs at 65- and 90-day postcoitus (dpc). (hindawi.com)
  • In this study, we identified a transcript variant of EZH2 in porcine fetal tissues by cloning and sequencing. (hindawi.com)
  • To build a foundation necessary to engineer robust ethanol-producing cyanobacterial hosts, in this study we applied a quantitative transcriptomics approach with a next-generation sequencing technology, combined with quantitative reverse-transcript PCR (RT-PCR) analysis, to reveal the global metabolic responses to ethanol in model cyanobacterial Synechocystis sp. (biomedcentral.com)
  • In this talk, I will introduce Chromatin Interaction Analysis with Paired-End Tag sequencing (ChIA-PET), a next-generation sequencing-based method for identifying chromatin interactions between transcription factor binding sites on a genome-wide scale which was part of the ENCODE consortium. (selectbiosciences.com)
  • Next generation sequencing (NGS) promises much to clinical diagnostics with its digital output, speed, and depth and breadth of coverage. (selectbiosciences.com)
  • We are using state-of-the-art next generation sequencing combined with bioinformatic strategies, and developing stem cell-based approaches for gene therapy and drug discovery. (nih.gov)
  • Nucleic Acids Research. (wikipedia.org)
  • Our research seeks to answer both basic and translational questions related to the retina and especially focuses on photoreceptors which initiate the visual process. (nih.gov)
  • Vanderbilt's CTSA program, the Vanderbilt Institute for Clinical and Translational Research (VICTR), was discussed. (biomedcentral.com)
  • StarBRITE offers clinical researchers a number of tools for conducting patient-based research, including regulatory support, patient recruitment support, data management, and clinical systems integration for electronic medical record (EMR) support. (biomedcentral.com)
  • No clinical assessment currently employs the basic phosphodiester chemistry found in natural nucleic acids, because of these and other known problems. (justia.com)
  • The combined Caris and ConcertAI initiative will now enable multi-year programs around specific cancers, programs and molecular targets spanning translational sciences, clinical development and post-approval evidence generation, including increased regulatory application of real-world molecular data and direct support for clinical trials. (carislifesciences.com)
  • Dr Masys, along with Paul Harris of Vanderbilt, presented an overview of the Clinical and Translational Science Awards (CTSA) program at NIH. (biomedcentral.com)
  • Methods for the preparation of a lipid-nucleic acid composition are provided. (justia.com)
  • The described procedures and data sets provide a model for microbiologists seeking to explore the translational landscape of bacteria. (biomed.news)
  • gene that contains a sequence that hybridizes with an oligonucleotide probe specific for M. tuberculosis complex bacteria. (cdc.gov)
  • I will also discuss their emerging regulatory roles in mediating and connecting post-transcriptional processes from the nucleus to the cytoplasm. (molcells.org)
  • Proteomic analysis and prediction of amino acid variations that influence protein. (deepdyve.com)
  • To increase the utilization of current computational resources, we 﫿rst provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis. (deepdyve.com)
  • RiboNucleic Acids (RNAs) are ubiquitous macromolecules within biological systems, capable of performing a wide range of regulatory and catalytic functions. (dagstuhl.de)
  • More generally, RNA design addresses the generation of sequences of nucleotides targeting a given biological function. (dagstuhl.de)
  • Otherwise, it may function as a translational inhibitor when dephosphorylated and bind to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. (nih.gov)
  • Mechanism of translation and its control, post translational modifications. (nipaers.com)
  • The amino acid variation S326C of human OGG1 disrupts Ser-326 phosphorylation site and affects susceptibility to a variety of cancers [9]. (deepdyve.com)
  • Immune response monoclonal and polyclonal antibodies and ELISA, DNA sequencing. (nipaers.com)
  • 2022. Immune profile and responses of a novel Dengue DNA vaccine encoding EDIII-NS1 consensus design based on Indo-African sequences. . (ncbs.res.in)
  • To retrieve these telomere characteristics from high-throughput sequencing data the available computational approaches need to be extended and optimized to fully exploit the information provided by large scale cancer genome data sets. (biomedcentral.com)
  • 2 − 6 These nuclease-resistant polymers persist in live organisms for days and are typically designed to recognize 25-base sequences that span intron-exon junctions or translational start sites. (cdc.gov)
  • DNA Sequencing Validation: After DNA sequencing, gel electrophoresis can confirm the size of sequenced fragments, verifying the sequence data. (excedr.com)
  • En 1990, il est recruté par le Salk Institute de San Diego pour lancer un centre de recherche sur le SIDA. (epfl.ch)
  • Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. (nih.gov)
  • We find that the fission yeast homologues of Tristetraprolin/TTP and Pumilio/Puf (Zfs1 and Puf3) interact with Ccr4-Not via multiple regions within low-complexity sequences, suggestive of a multipartite interface that extends beyond previously defined interactions. (elifesciences.org)
  • Didier Trono s'est beaucoup intéressé aux interactions entre les virus et leurs hôtes, ce qui l'a conduit à étudier la biologie de pathogènes comme le VIH et le virus de l''hépatite B, et à créer des outils de transfert génétique dérivés du VIH aujourd'hui utilisés avec succès en thérapie génique. (epfl.ch)