Catalytic FFPE Nucleic Acid Isolation for Best NGS Performance
... by fixation with formaldehyde, in formalin-fixed paraffin-embedded (FFPE) tissue block format. While formaldehyde stabilizes tissue for storage, it also forms extensive crosslinks and adducts with nucleic acids and other biomolecules in the sample. Such modifications strongly interfere with downstre ...
... by fixation with formaldehyde, in formalin-fixed paraffin-embedded (FFPE) tissue block format. While formaldehyde stabilizes tissue for storage, it also forms extensive crosslinks and adducts with nucleic acids and other biomolecules in the sample. Such modifications strongly interfere with downstre ...
The complete nucleotide sequence of apple mosaic virus (ApMV
... initially identified on the basis of sequences that were homologous to the 3h-NTR of RNA 3 but not to the rest of RNA 3, because the 3h-NTRs of the three RNAs of ApMV (and all other bromoviruses) are the only region which has sequence homology within the genome of each species. In addition to RNA 3, ...
... initially identified on the basis of sequences that were homologous to the 3h-NTR of RNA 3 but not to the rest of RNA 3, because the 3h-NTRs of the three RNAs of ApMV (and all other bromoviruses) are the only region which has sequence homology within the genome of each species. In addition to RNA 3, ...
Mitochondrial protein import: from transport pathways to an
... novel import components and three new import pathways have been identified. Moreover, several results indicate that preprotein translocases do not act as independent units but are linked to machineries involved in different tasks, from energy conversion to maintenance of mitochondrial morphology, in ...
... novel import components and three new import pathways have been identified. Moreover, several results indicate that preprotein translocases do not act as independent units but are linked to machineries involved in different tasks, from energy conversion to maintenance of mitochondrial morphology, in ...
Identification and expression of the first nonmammalian amyloid‐β
... during the evolution of the APP superfamily. Interestingly, APLP1, which has been identified only in mammals, is expressed exclusively in the brain and further displays a number of structural features not present in the other members of the APP superfamily, such as the absence of the exon encoding th ...
... during the evolution of the APP superfamily. Interestingly, APLP1, which has been identified only in mammals, is expressed exclusively in the brain and further displays a number of structural features not present in the other members of the APP superfamily, such as the absence of the exon encoding th ...
REVIEW - The Journal of Cell Biology
... membrane proteins, and it consists of at least two integral polypeptides (90) of similar molecular weights (cf. reference 4). Several peripheral membrane proteins including ferredoxin, ferredoxinNADP reductase (cf. reference 19), plastocyanin (53, 61), and probably two subunits of the chloroplast co ...
... membrane proteins, and it consists of at least two integral polypeptides (90) of similar molecular weights (cf. reference 4). Several peripheral membrane proteins including ferredoxin, ferredoxinNADP reductase (cf. reference 19), plastocyanin (53, 61), and probably two subunits of the chloroplast co ...
How to study proteins by circular dichroism
... haem groups strongly around 410 nm with other bands in the range from 350 nm to 650 nm (depending on spin state and coordination of the central Fe ion), and chlorophyll moieties in the visible and near IR regions. If a number of chromophores of the same type are in close proximity, they can behave a ...
... haem groups strongly around 410 nm with other bands in the range from 350 nm to 650 nm (depending on spin state and coordination of the central Fe ion), and chlorophyll moieties in the visible and near IR regions. If a number of chromophores of the same type are in close proximity, they can behave a ...
Full Text PDF - International Journal of Computational Bioinformatics
... and further analysed by multiple sequence alignment in Pan troglodytes, Nomascus leucogenys, Pongo abelii and Nomascus leucogenys. Phylogenetic results indicate that G8 protein of Homo sapiens is highly similar to G8 protein of Pan troglodytes, Nomascus leucogenys and closely related. Structure Mode ...
... and further analysed by multiple sequence alignment in Pan troglodytes, Nomascus leucogenys, Pongo abelii and Nomascus leucogenys. Phylogenetic results indicate that G8 protein of Homo sapiens is highly similar to G8 protein of Pan troglodytes, Nomascus leucogenys and closely related. Structure Mode ...
How to study proteins by circular dichroism
... haem groups strongly around 410 nm with other bands in the range from 350 nm to 650 nm (depending on spin state and coordination of the central Fe ion), and chlorophyll moieties in the visible and near IR regions. If a number of chromophores of the same type are in close proximity, they can behave a ...
... haem groups strongly around 410 nm with other bands in the range from 350 nm to 650 nm (depending on spin state and coordination of the central Fe ion), and chlorophyll moieties in the visible and near IR regions. If a number of chromophores of the same type are in close proximity, they can behave a ...
tRNA
... Initiation Factors: IF-2 ,control the initiator tRNA entry to the ribosome IF-1, bind 30S to complete initiation complex IF-3, need for 30S to bind initiation site ...
... Initiation Factors: IF-2 ,control the initiator tRNA entry to the ribosome IF-1, bind 30S to complete initiation complex IF-3, need for 30S to bind initiation site ...
Adaptation and Protein Quality Control Under Metalloid
... Several human degenerative diseases are linked to misfolding and aggregation of specific proteins. I have shown that many of these proteins have yeast homologs that are particularly prone to misfolding and aggregation during arsenite exposure. The yeast proteins are highly dependent on chaperones fo ...
... Several human degenerative diseases are linked to misfolding and aggregation of specific proteins. I have shown that many of these proteins have yeast homologs that are particularly prone to misfolding and aggregation during arsenite exposure. The yeast proteins are highly dependent on chaperones fo ...
The YidC/Oxa1/Alb3 protein family Saller, Manfred J.
... 2005; van Bloois et al., 2005, 2007). However, specific differences can also be observed. For example, the depletion of the E. coli YidC and yeast Oxa1 results in reduced amounts of assembled F1F0 ATP synthase and cytochrome o oxidase (Hell et al., 2001; Stuart, 2002), whereas the human Oxa1 is invo ...
... 2005; van Bloois et al., 2005, 2007). However, specific differences can also be observed. For example, the depletion of the E. coli YidC and yeast Oxa1 results in reduced amounts of assembled F1F0 ATP synthase and cytochrome o oxidase (Hell et al., 2001; Stuart, 2002), whereas the human Oxa1 is invo ...
Systematic Characterisation of Cellular Localisation and
... Methodology/Principal Finding: In the present large-scale study, we used a large data set of proteins containing experimentally identified MHC class I or II ligands and examined the proteins according to their expression profiles at the mRNA level and their Gene Ontology (GO) classification within t ...
... Methodology/Principal Finding: In the present large-scale study, we used a large data set of proteins containing experimentally identified MHC class I or II ligands and examined the proteins according to their expression profiles at the mRNA level and their Gene Ontology (GO) classification within t ...
Alterations in oxidative phosphorylation complex proteins in the
... divide the full MS scan into four smaller sections covering a total range of 400 –1,800 mass-to-charge ratio. Each of the smaller MS scans was followed by 5 MS/MS scans of the most intense ions from the preceding MS scan. The raw data were then extracted and searched using the SEQUEST program, as pr ...
... divide the full MS scan into four smaller sections covering a total range of 400 –1,800 mass-to-charge ratio. Each of the smaller MS scans was followed by 5 MS/MS scans of the most intense ions from the preceding MS scan. The raw data were then extracted and searched using the SEQUEST program, as pr ...
Article
... Conditions such as environmental stress, viral infection and the absence of required partner proteins can result in the accumulation of aberrantly folded proteins in the rough endoplasmic reticulum (RER). The RER has a “quality control” system that targets these misfolded proteins for degradation. T ...
... Conditions such as environmental stress, viral infection and the absence of required partner proteins can result in the accumulation of aberrantly folded proteins in the rough endoplasmic reticulum (RER). The RER has a “quality control” system that targets these misfolded proteins for degradation. T ...
The Ribosome, rRNA and mRNA (3.1)
... The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotid ...
... The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotid ...
The Binding Site for the @r Subunits of Heterotrimeric G Proteins on
... stimuli (1-3). For several years interest has focused on the of numerous GTP-binding a subunits and their activation effector molecules which include enzymes and ion channels. The tightly associated @ysubunits were initially believed to play only a supporting role, in which they served merely as reg ...
... stimuli (1-3). For several years interest has focused on the of numerous GTP-binding a subunits and their activation effector molecules which include enzymes and ion channels. The tightly associated @ysubunits were initially believed to play only a supporting role, in which they served merely as reg ...
Amino Acids and Proteins - Gadarif University Repository
... The helix is stabilized by hydrogen bonding between the backbone carbonyl of one amino acid and the backbone NH of the amino acid four residues away. All main chain amino and carboxyl groups are hydrogen bonded, and the R groups stick out from the structure in a ...
... The helix is stabilized by hydrogen bonding between the backbone carbonyl of one amino acid and the backbone NH of the amino acid four residues away. All main chain amino and carboxyl groups are hydrogen bonded, and the R groups stick out from the structure in a ...
JNK1 plays an important part in this process provides an
... The bracket (Nop10) Nop10, a protein of 60 amino acids, lines the oblong catalytic domain of Cbf5 with a random coil central segment that separates its own N-terminal Zn2C-binding and C-terminal a-helical domains (Figure 1, red). Although Nop10 seems to be intrinsically disordered on its own [13], i ...
... The bracket (Nop10) Nop10, a protein of 60 amino acids, lines the oblong catalytic domain of Cbf5 with a random coil central segment that separates its own N-terminal Zn2C-binding and C-terminal a-helical domains (Figure 1, red). Although Nop10 seems to be intrinsically disordered on its own [13], i ...
Auxin Action in a Cell
... weakly with SCFTIR1 (data not shown). These results are not consistent with a model in which auxin regulation of Aux/IAA proteins is directly dependent on proline hydroxylation. The importance of the prolines in domain II led us to consider the possibility that a peptidyl prolyl cis/trans isomerase ...
... weakly with SCFTIR1 (data not shown). These results are not consistent with a model in which auxin regulation of Aux/IAA proteins is directly dependent on proline hydroxylation. The importance of the prolines in domain II led us to consider the possibility that a peptidyl prolyl cis/trans isomerase ...
Protein Composition of a High-Protein Barley Flour and Barley Grain
... proportions of histidine, arginine, and tryptophan could not be determined. Tryptophan decomposes during HCl hydrolysis, whereas pentafluoropropionyl-2-propyl derivatives of arginine and histidine were not formed. There were also other restrictions due to the chromatographic method. Valine and threo ...
... proportions of histidine, arginine, and tryptophan could not be determined. Tryptophan decomposes during HCl hydrolysis, whereas pentafluoropropionyl-2-propyl derivatives of arginine and histidine were not formed. There were also other restrictions due to the chromatographic method. Valine and threo ...
Pharmacophore screening of the Protein Data Bank for specific
... required residue types, but also the relative geometry. The number of unique sites selected using various radius (Qm/n) and direction (Qv) b-factors is shown in Fig. 3 (results from the individual pharmacophore queries were merged and redundant hits were clustered). Ultimately, the objective is not ...
... required residue types, but also the relative geometry. The number of unique sites selected using various radius (Qm/n) and direction (Qv) b-factors is shown in Fig. 3 (results from the individual pharmacophore queries were merged and redundant hits were clustered). Ultimately, the objective is not ...
Predicting protein folding rates from geometric contact and amino
... residues that form geometric contacts. The correlation coefficients are 0.86, 0.86, and 0.83 for two-state proteins, multistate proteins, and all proteins combined, respectively. Using a reduced alphabet of only two types of amino acids which are weighted differently, these correlation coefficien ...
... residues that form geometric contacts. The correlation coefficients are 0.86, 0.86, and 0.83 for two-state proteins, multistate proteins, and all proteins combined, respectively. Using a reduced alphabet of only two types of amino acids which are weighted differently, these correlation coefficien ...
Logistic regression models to predict solvent accessible residues
... least-squares fit corresponds to the NACCESS RSA values regressed on E6 and amino acid type (AA). For illustrative purposes only two amino acid types are shown. Valine (top) and aspartate (bottom) include 177 and 172 residues, respectively. Both least-squares fits have a slope (E6) of 10.56, but the ...
... least-squares fit corresponds to the NACCESS RSA values regressed on E6 and amino acid type (AA). For illustrative purposes only two amino acid types are shown. Valine (top) and aspartate (bottom) include 177 and 172 residues, respectively. Both least-squares fits have a slope (E6) of 10.56, but the ...
Characterisation and functional properties of watermelon (Citrullus
... The successive extraction of defatted watermelon seed meal with different solvents yielded albumin, globulin, prolamin and glutelin in varying proportions (data not shown). Globulin was the major protein, accounting for 549.7 and 575.0 g kg−1 of the crude protein (CP) in Mateera and Sugar Baby respe ...
... The successive extraction of defatted watermelon seed meal with different solvents yielded albumin, globulin, prolamin and glutelin in varying proportions (data not shown). Globulin was the major protein, accounting for 549.7 and 575.0 g kg−1 of the crude protein (CP) in Mateera and Sugar Baby respe ...
SR protein
SR proteins are a conserved family of proteins involved in RNA splicing. SR proteins are named because they contain a protein domain with long repeats of serine and arginine amino acid residues, whose standard abbreviations are ""S"" and ""R"" respectively. SR proteins are 50-300 amino acids in length and composed of two domains, the RNA recognition motif (RRM) region and the RS binding domain. SR proteins are more commonly found in the nucleus than the cytoplasm, but several SR proteins are known to shuttle between the nucleus and the cytoplasm.SR proteins were discovered in the 1990s in Drosophila and in amphibian oocytes, and later in humans. In general, metazoans appear to have SR proteins and unicellular organisms lack SR proteins.SR proteins are important in constitutive and alternative pre-mRNA splicing, mRNA export, genome stabilization, nonsense-mediated decay, and translation. SR proteins alternatively splice pre-mRNA by preferentially selecting different splice sites on the pre-mRNA strands to create multiple mRNA transcripts from one pre-mRNA transcript. Once splicing is complete the SR protein may or may not remain attached to help shuttle the mRNA strand out of the nucleus. As RNA Polymerase II is transcribing DNA into RNA, SR proteins attach to newly made pre-mRNA to prevent the pre-mRNA from binding to the coding DNA strand to increase genome stabilization. Topoisomerase I and SR proteins also interact to increase genome stabilization. SR proteins can control the concentrations of specific mRNA that is successfully translated into protein by selecting for nonsense-mediated decay codons during alternative splicing. SR proteins can alternatively splice NMD codons into its own mRNA transcript to auto-regulate the concentration of SR proteins. Through the mTOR pathway and interactions with polyribosomes, SR proteins can increase translation of mRNA.Ataxia telangiectasia, neurofibromatosis type 1, several cancers, HIV-1, and spinal muscular atrophy have all been linked to alternative splicing by SR proteins.