Analysis of nucleic acid and protein. Medical search. Frequent questions

PAXgene Tissue reagents in prefilled containers and PAXgene Tissue Kits provide a complete preanalytical solution for collection, fixation, and stabilization of tissue, and purification of high-quality nucleic acids for molecular research analysis. (qiagen.com)
PAXgene Tissue Containers provide tissue fixation for histopathology studies and enable purification of high-quality nucleic acids from the same sample for molecular analysis. (qiagen.com)

This paper proposes a generative adversarial networks (GAN) model to create synthetic nucleic acid sequences of the cat genome tuned to exhibit specific desired properties. (mdpi.com)
Their amino acid sequences suggest that they are mainly cytosolic or nuclear proteins partly associating with membranes (Talbot et al. (springer.com)
2009 ). The designated dysbindin paralogs show very limited sequence homology which raised the question whether DBNDD1 and DBNDD2 are dysbindin-like proteins or proteins that share a less conserved domain with DTNBP1 in the context of otherwise unrelated sequences (Ghiani and Dell'Angelica 2011 ). (springer.com)
We performed a Basic Local Alignment Search Tool (BLAST) analysis to identify regions of local similarity between the human DBNDD1 and protein sequences from other species (Fig. 1 ). (springer.com)
2019 ) was used, https://www.ebi.ac.uk/Tools/msa/clustalo/ ] of human DBNDD1 and similar protein sequences found by a BLAST search in other selected species. (springer.com)
[8] Comparison between primates is especially similar, ranging from 92.9-99.6% similarity in amino acid sequences . (wikidoc.org)
Signal sequences in the amino - and carboxy - terminal ends are removed posttranslationally, resulting in a mature length of 208 amino acids. (wikidoc.org)
Known as "destabilising motifs", these sequences attract the attention of a group of proteins called Ccr4-Not. (elifesciences.org)
Genes are simply sequences of nucleic acid (DNA in humans) that code for a protein. (extremetech.com)
Sequences diagnostic for E. chaffeensis from three different loci (16S rRNA, 120-kDa protein, and a variable-length polymerase chain reaction [PCR] target, or VLPT) were targeted for amplification by the PCR. (google.com)
According to their differential sequences, SPRY proteins were divided into four subtypes (SPRY1, -2, -3 and -4). (spandidos-publications.com)
The DNA sequences of ospA , ospB , rrs-rrlA , and ospC ideal for deer and the small mammals that maintain the I. were determined for use in our phylogenetic analysis. (cdc.gov)

The immune-related DEOSGs and hub genes were identified by weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) analysis, respectively. (nature.com)
Enrichment analysis was performed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. (nature.com)
The diagnostic value of hub genes was assessed by receiver operating characteristic analysis and validated in GSE1297. (nature.com)
The mRNA expression of diagnostic genes was determined by qRT-PCR analysis. (nature.com)
We obtained 66 immune-related DEOSGs by intersecting turquoise module with the DEOSGs and identified 15 hub genes through PPI analysis. (nature.com)
Deletion of histidine-rich protein genes pfhrp2/3 in Plasmodium falciparum causes infections to go undetected by HRP2-based malaria rapid diagnostic tests. (cdc.gov)
Differential expression analyses revealed reprogramming of gene expression under anesthesia: 6,168 genes were upregulated, 6,310 genes were downregulated, while 9,914 genes were not affected in comparison with control plants. (frontiersin.org)
Our genome-wide analysis found 151 NAC transcription factor genes ( PgNAC s) in the pearl millet genome. (biomedcentral.com)
functional" genes encoding proteins such as late embryogenesis-associated proteins, detoxification enzymes, heat shock proteins and molecular chaperones, which directly protect plants from abiotic stress, and "regulatory" genes encoding proteins such as protein kinases and transcription factors (TFs), which have roles in the perception and transduction of stress signals. (biomedcentral.com)
Expression and estrogen sensitivity of target genes and nuclear receptor coregulators were altered at mRNA and protein levels in adult uterus, prostate and brain. (researchgate.net)
Subsequent genomic sequence analysis of multiple genes including elongation factor 3, a component of fungi protein synthesis not found in protozoa, further supported this notion. (medscape.com)
ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database. (cdc.gov)

Various experimental approaches exist for the study of nucleic acid-protein interactions in vitro and in vivo , but the detection of such interactions at the subcellular level remains challenging. (nature.com)
Here we describe how to detect nucleic acid-protein interactions in plant leaves by using a fluorescence resonance energy transfer (FRET) approach coupled to fluorescence lifetime imaging microscopy (FLIM). (nature.com)
Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. (wikipedia.org)
Melting is the process by which the interactions between the strands of the double helix are broken, separating the two nucleic acid strands. (wikipedia.org)
The database enables the analysis of these data in the context of signaling pathways, protein-protein interactions, gene ontology terms, protein domains, and post-translational modifications," they add. (genomeweb.com)
Nanoscale imaging enables the analysis of biological systems, such as cells and tissues, at the fundamental length scales of biomolecules and biomolecular interactions, but classically has required expensive equipment and advanced skillsets to perform, e . g ., via super-resolution microscopy [ 1 ]. (plos.org)
Knowledge of the three-dimensional structures of the carbo-hydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein-carbohydrate interactions. (iucr.org)
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)

The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein-carbohydrate complexes. (iucr.org)
Functional and structural characterization of human adrenoleukodystrophy protein (ALDP). (elifesciences.org)
Antibody-based analysis of surface proteins revealed no significant structural damage due to LEEI. (bvsalud.org)

Fixatives that contain formaldehyde crosslink biomolecules and modify nucleic acids and proteins. (qiagen.com)

In a non-biological context, secondary structure is a vital consideration in the nucleic acid design of nucleic acid structures for DNA nanotechnology and DNA computing, since the pattern of basepairing ultimately determines the overall structure of the molecules. (wikipedia.org)
Importantly, pairing is the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA during protein translation. (wikipedia.org)
The double helix is an important tertiary structure in nucleic acid molecules which is intimately connected with the molecule's secondary structure. (wikipedia.org)
Together these proteins shorten the end of the mRNAs, preparing the molecules for degradation. (elifesciences.org)
The energy transferred from the activated photosensitizer to available oxygen results in the formation of highly reactive oxygen species, which may eliminate microorganisms by damaging their essential cellular molecules, including proteins, nucleic acids and lipid membranes (10). (bvsalud.org)

The highly basic 55 amino acid nucleocapsid protein (NC) that coats the HIV-1 genome has two zinc fingers that differ by five amino acids (strain pNL4-3). (umd.edu)
Motion, G.B., Howden, A.J.M., Huitema, E. & Jones, S. DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool. (nature.com)
SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence. (cdc.gov)

Most PTMs are catalyzed by highly specific protein modifying enzymes, which have some specific recognition motif. (deepdyve.com)
Laboratory methodologies include analysis of proteins, including enzymes in clinical samples, and manipulation of microbial nucleic acids. (cuny.edu)
Functional analysis of chromatin modifying enzymes in vitro and in vivo. (uni-regensburg.de)

In the 1980s, biochemical analysis of the nucleic acid composition of Pneumocystis rRNA and mitochondrial DNA identified the organism as a unicellular fungus rather than a protozoan. (medscape.com)

We compared the S protein structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 viruses and identified the residues like C526, C383, and N468 located in equivalent positions of these viruses have effects on S protein structure. (frontiersin.org)
This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures. (iucr.org)
Submissions are encouraged to report on advances in algorithm development and optimization , data structures , data visualization, artificial intelligence/machine learning , text mining , statistical inference, database and ontology development , image analysis , citizen and open science, etc . to analyze all types of biological data. (iscb.org)
Guanine quadruplexes are nucleic acid structures built ions in slow exchange with bulk ions. (lu.se)

To understand these processes through comprehensive analyses of microbial ecology, evolution and metabolism, sequenced reference genomes of representative native prokaryotes are crucial. (biomedcentral.com)

A key component in the virulence of MERS-CoV is the Spike (S) protein, which binds with the host membrane receptor dipeptidyl peptidase 4 (DPP4). (frontiersin.org)
Adrenoleukodystrophy protein (ALDP) is responsible for the transport of very-long-chain fatty acids (VLCFAs) and corresponding CoA-esters across the peroxisomal membrane. (elifesciences.org)
The adrenoleukodystrophy protein (ALDP) or ABCD1 is an ABC transporter that participates in the transport of free very long-chain fatty acids and their CoA esters across the peroxisomal membrane. (elifesciences.org)
For example, the gene MARCH1 codes for a protein called Membrane Associated Ring-CH-Type Finger 1. (extremetech.com)
CASC4 was named as a CAncer Susceptibility Candidate 4 , and now it's GOLM2 (golgi membrane protein 2). (extremetech.com)
Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (− 073, − 29, and − 151) were found to be membrane-associated transcription factors. (biomedcentral.com)

Carbohydrates differ from proteins in two important features. (iucr.org)

Fixation is comparable to formalin fixation, but without the destructive nucleic acid crosslinking and degradation. (qiagen.com)
Such crosslinks lead to nucleic acid degradation during tissue fixation, storage, and processing. (qiagen.com)
During tissue fixation, storage, and processing, cross-links lead to degradation of nucleic acids. (qiagen.com)
The fixation and stabilization method preserves tissue morphology and the integrity of nucleic acids without destructive cross-linking and degradation found in formalin-fixed tissues. (qiagen.com)

In contrast, isoform 3 (UniProtKB: Q9H9R9-3) carries a 100 amino acids long N-terminal sequence extension. (springer.com)
The primary sequence of PrP is 253 amino acids long before post-translational modification . (wikidoc.org)

To determine at an amino acid level the reason for the apparent distinction between the fingers, five point mutants were designed with amino acid residues in finger one incrementally replaced by those at corresponding locations in finger two. (umd.edu)
PTMs are specific to types of amino acid residues. (deepdyve.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)
Consequently, amino acid variations through changing the type of residues of the target sites or key flanking residues could directly or indirectly influence PTM of protein and bring about a detrimental effect on protein function. (deepdyve.com)
The SPRY2 protein contains 315 human amino acid residues (35 kDa), with the C-terminal residues 178-282 being rich in cysteine. (spandidos-publications.com)

The most significantly upregulated process was the response to heat stress (mainly heat shock proteins, HSPs). (frontiersin.org)

The mechanism and function of heterochromatin disruption in FSHD muscular dystrophy is another area of research, in which we perform single cell/nucleus analyses to isolate and characterize a small number of disease-driving cells and are developing 3D and tissue on a chip to measure intrinsic defects of FSHD and CRISPR-engineered mutant myocytes. (uci.edu)
NC also exhibits a strong affinity for both nucleic acids (DNA and RNA) and proteins (antigens and antibodies) and is, therefore, used extensively in research and clinical settings for the immobilization of nucleic acids and/or proteins for analysis. (cdc.gov)

We further identified top 5 compounds including cynarine, stigmasterin, kushenol, β -sitosterol, and (24S)-24-propylcholesta-5-ene-3 β -ol as putative key active compounds on the basis of their molecular docking scores with identified hub target proteins. (hindawi.com)

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)

Real‑time quantitative polymerase chain reaction (PCR) and western blot analyses were used to detect SPRY2 expression and miR‑21 protein expression levels. (spandidos-publications.com)

A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (nih.gov)
The amino acid variation S326C of human OGG1 disrupts Ser-326 phosphorylation site and affects susceptibility to a variety of cancers [9]. (deepdyve.com)

Predicted to enable protein serine/threonine phosphatase inhibitor activity. (nih.gov)

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)
Biosynthesis, structure and biological activities of envelope protein gp65 of murine coronavirus. (uci.edu)
At our microscopy platform in Lund, you meet personnel with expertise and long experience working with biological material and microscopy, imaging, and analysis. (lu.se)

The BLM protein helps to prevent excess sister chromatid exchanges and is also involved in other processes that help maintain the stability of the DNA during the copying process. (medlineplus.gov)
Histidine-rich protein 2 (HRP2)-based RDTs are largely preferred for detecting P. falciparum malaria because of their superior sensitivity and heat-stability profile over Plasmodium lactate dehydrogenase (pLDH) or aldolase ( 6 ). (cdc.gov)
The goal of the present investigation is to examine the effects of missense mutations in the MERS-CoV S protein on protein stability and binding affinity with DPP4 to provide insight that is useful in developing vaccines to prevent coronavirus infection. (frontiersin.org)
We investigated the effects of MERS-CoV S protein viral mutations on protein stability and binding affinity. (frontiersin.org)
In addition, we studied all DPP4 mutations and found the functional substitution R336T weakens both DPP4 protein stability and S-DPP4 binding affinity. (frontiersin.org)
NMR spectroscopy or X-ray crystallography, but important width measurements at a single resonance frequency (or questions remain concerning the energetics, stability, and magnetic field strength), making it difficult to separate dynamics of this structurally diverse nucleic acid class. (lu.se)

BLM gene mutations result in the absence of functional BLM protein. (medlineplus.gov)
These findings provide further information on how mutations in coronavirus S proteins effect protein function. (frontiersin.org)
Based on the structure, we performed integrative analysis of the cellular trafficking, protein thermostability, ATP hydrolysis, and the transport activity of representative mutations. (elifesciences.org)
All recognized mutations for AD are associated with increased deposition of amyloid-beta (Abeta), a peptide fragment comprising 39-43 amino acids that derive from the catabolism of the amyloid precursor protein (APP) molecule. (medscape.com)

We first identified 51 active compounds from SZT and their 81 potential molecular targets by high-throughput computational analysis, from which we identified 4 major pathways including Th17 cell differentiation, metabolic pathways, pathways in cancer, and the PI3K-Akt signaling pathway. (hindawi.com)
Through network analysis of the compound-target pathway, we identified hub molecular targets within these pathways including carbonic anhydrase II (CA2), peroxisome proliferator activated receptor γ (PPAR γ ), retinoid X receptor α (RXRA), and vitamin D receptor (VDR). (hindawi.com)

Overview of Viral Infections A virus is composed of nucleic acid, either DNA or RNA, surrounded by a protein coat. (msdmanuals.com)

Now, researchers to want to analyze a single cell's proteins too. (acs.org)
Researchers have long had tools to look at nucleic acids at the single-cell level, but studying single cells' proteins hasn't been as easy. (acs.org)
To detect low levels of nucleic acids, researchers can use long-standing methods for boosting even the faintest of genetic signals by making copies. (acs.org)
Single-Molecule Techniques: A Laboratory Manual fills this requirement it is the first to take researchers who know nothing about single molecule analyses to the point where they can successfully design and execute appropriate experiments. (cshlpress.com)

Here we present a multifunctional anchor, an acrylate epoxide, that enables proteins and RNAs to be equipped with anchors in a single experimental step. (plos.org)

Here, using a combination of RNA-seq and proteomic LC-MS/MS analyses, we investigated the effect of anesthetic diethyl ether on gene expression and downstream consequences in plant Arabidopsis thaliana . (frontiersin.org)

As an outcome human DBNDD1 revealed a high sequence identity to dysbindin domain-containing proteins from other Hominidae (e.g. (springer.com)
Proteins with high sequence identity to human DBNDD1 can also be found in evolutionarily more distant species (e.g. (springer.com)
Prion protein contains 5 amino-terminal octapeptide repeats with sequence PHGGGWGQ. (wikidoc.org)

The development of better methods for mutation analysis-related protein PTMs will help to facilitate the development of personalized precision medicine. (deepdyve.com)
Now single-cell proteomics is possible too, thanks to new methods in sample processing and analysis. (acs.org)
People have been able to detect a handful of proteins in individual cells using fluorescence- or antibody-based methods. (acs.org)
The methods for tissue fixation currently used in traditional histology are of limited use for molecular analysis. (qiagen.com)
Current tissue fixation methods used in traditional histology are of limited use for molecular analysis. (qiagen.com)
Methods for UV filter analysis followed the principles of European standardized methods for pesticide residue analysis (EN 15289). (researchgate.net)

Pathologic features of AD are characterized by persistent deposition of the intercellular amyloid β-peptide (Aβ) plaques and intracellular tau protein and impairment of the neuron-to-neuron synaptic communication and nutrient transportation inside neuron 3 . (nature.com)

Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. (biomedcentral.com)

Nucleic acid sequencing expresses the evolutionary changes among organisms and revolutionizes disease diagnosis in animals. (mdpi.com)

Nucleic acid secondary structure is generally divided into helices (contiguous base pairs), and various kinds of loops (unpaired nucleotides surrounded by helices). (wikipedia.org)
Our chemical-shift based secondary structure analysis reveals the human DBNDD1 as an intrinsically disordered protein. (springer.com)

2021 ). The human DBNDD1 isoforms 1 (UniProtKB: Q9H9R9-1) and 2 (UniProtKB: Q9H9R9-2) differ only in the N-terminal region where 20 amino acids are additional in isoform 2. (springer.com)
Unlike other dysbindin family proteins, DBNDD1 isoforms are probably non-classical secretory proteins (Talbot et al. (springer.com)
The protein can exist in multiple isoforms , the normal PrP C , and as Protease resistant PrP Res like the disease-causing PrP Sc(scrapie) and an isoform located in mitochondria . (wikidoc.org)

It is recommended to simultaneously attend the practical module BIO-M-PM-PBE Protein Biochemistry and Enzymology. (uni-regensburg.de)

When a cell needs to make a particular protein, it first copies the instructions from the matching gene into a molecule known as a messenger RNA (or an mRNA for short). (elifesciences.org)
The more mRNA copies it makes, the more protein it can produce. (elifesciences.org)
A simple way to control protein production is to raise or lower the number of these mRNA messages, and living cells have lots of ways to make this happen. (elifesciences.org)

Analysis with the both the 120-kDa protein primers and the VLPT primers showed that genetic variance exists. (google.com)
Structure and function of nucleic acids and proteins and the genetic basis of human disease. (cuny.edu)

Identification of proteins that interact with alpha A-crystallin using a human proteome microarray. (nih.gov)

Used with the containers, the kit provides a complete preanalytical solution for collection, fixation, and stabilization through to purification of high-quality miRNA and total RNA for molecular analysis. (qiagen.com)
Human evidence of this is provided by molecular analysis of Pneumocystis isolates obtained from groups of patients involved in hospital outbreaks. (medscape.com)

This protein is 1,353 amino acids in length, and the monomers assemble to form a homotrimer. (frontiersin.org)

Computational mutation analysis can greatly narrow down the efforts on experimental work. (deepdyve.com)

To illustrate our approach, we provide experimental procedures to detect the interaction between plant DNA and two proteins (the AeCRN13 effector from the oomycete Aphanomyces euteiches and the AtWRKY22 defensive transcription factor from Arabidopsis ). (nature.com)
The NAC domain was deduced from three previously characterized proteins, petunia NAM (no apical meristem), Arabidopsis thaliana ATAF1/2 ( Arabidopsis thaliana activation factor 1/2) and CUC2 (cup-shaped cotyledon) [ 13 , 14 ]. (biomedcentral.com)

Figure 3: GFP fluorescence observed in Nicotiana leaves that express GFP-tagged proteins. (nature.com)

The site, dubbed BloodSpot, currently houses almost two dozen curated gene expression datasets generated for normal and malignant human and mouse hematopoietic cells that were sorted using FACS analysis. (genomeweb.com)
Here, we present the backbone and side chain nuclear magnetic resonance assignments for the human DBNDD1 protein. (springer.com)
Human dysbindin domain-containing protein 1 (DBNDD1) is encoded by the gene DBNDD1 at chromosome locus 16q24.3. (springer.com)
PRNP ( PR io N P rotein) is the human gene encoding for the major prion protein PrP (for pr ion p rotein), also known as CD230 ( cluster of differentiation 230). (wikidoc.org)
The human protein structure consists of a globular domain with three α-helices and a two-strand antiparallel β-sheet , an NH 2 -terminal tail, and a short COOH -terminal tail. (wikidoc.org)
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)
For instance, the SwissVariant database (http://swissvar.expasy.org/) contained 76 613 variants in 20 244 human proteins on 10 January 2018. (deepdyve.com)

Hudson, W.H. & Ortlund, E.A. The structure, function and evolution of proteins that bind DNA and RNA. (nature.com)
The dysbindin domain-containing protein 1 (DBNDD1) is a conserved protein among higher eukaryotes whose structure and function are poorly investigated so far. (springer.com)
PrP messenger RNA contains a pseudoknot structure ( prion pseudoknot ), which is thought to be involved in regulation of PrP protein translation . (wikidoc.org)

In our laboratories, you can use both standard microscope techniques, like scanning electron microscopy (SEM), transmission electron microscopy (TEM) and confocal laser scanning microscopy (CLSM), as well as infra-red based analysis techniques and micro-computed tomography (micro-CT). (lu.se)

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)
Updated with more coverage of nuclear magnetic resonance spectroscopy, expanded with new end-of-chapter mechanism problems and Practice Your Scientific Reasoning and Analysis questions, and enhanced with OWLv2, the latest version of the leading online homework and learning system for chemistry, John McMurry's Organic Chemistry continues to set the standard for the course. (nhbs.com)

Super absorbent polymers utilized in agriculture are typically arranged from acrylic acids and a cross-connecting agent like potassium by solution or suspension polymerization. (prlog.org)

The MERS-CoV S protein has 21 N-linked glycosylation sites (Wang et al. (frontiersin.org)
Glycosylation is classified by the way the carbohydrate chain is linked to the protein. (iucr.org)
Protein glycosylation fulfils a variety of roles. (iucr.org)

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