Variant analysis

The research project deals with two different types of data for two separate analysis. The first analysis deals with normalised RNA-seq breast cancer data where machine learning techniques are used to classify and identify the biomarker of cancer. Second analysis deals with raw DNA methylated leukemia samples to determine the mutations.

102p runthenight04 02-02-2023 8 4   Download

Research objective: Establish the genetic variants database of 04 genes CYP2C9, CYP2C19, CYP2D6 and CYP3A5 in Kinh Vietnamese. Identification of genotype and allele frequencies of 04 genes CYP2C9, CYP2C19, CYP2D6 and CYP3A5 in Kinh Vietnamese. Perform in silico functional analysis of novel variants.

27p extraenglish 24-05-2021 27 4   Download

Establish the genetic variants database of 04 genes CYP2C9, CYP2C19, CYP2D6 and CYP3A5 in Kinh Vietnamese. Identification of genotype and allele frequencies of 04 genes CYP2C9, CYP2C19, CYP2D6 and CYP3A5 in Kinh Vietnamese. Perform in silico functional analysis of novel variants.

27p capheviahe27 23-02-2021 5 3   Download

To examine the role of the distal His42 residue in the catalytic mechanism of pea cytosolic ascorbate peroxidase, two site-directed variants were prepared in which His42 was replaced with alanine (H42A) or glutamic acid (H42E). Electronic spectra of the ferric derivatives of H42A and H42E (pH 7.0, l ¼ 0.10 M, 25.0 °C) revealed wavelength maxima [kmax (nm): 397, 509, % 540sh, 644 (H42A); 404, 516, % 538sh, 639 (H42E)] consistent with a predominantly fiveco-ordinate high-spin iron. The specific activity of H42E for oxidation of L-ascorbate (8.2 ± 0.

11p system191 01-06-2013 39 4   Download

The centromere–kinetochore complex is a highly specialized chromatin domain that both mediates and monitors chromosome–spindle interactions responsible for accurate partitioning of sister chromatids to daughter cells. Centromeres are distinguished from adjacent chromatin by specific patterns of histone modification and the presence of a centromere-specific histone H3 variant (e.g. CENP-A). Centromere-proximal regions usually correspond to sites of avid and persistent sister chromatid cohesion mediated by the conserved cohesin complex.

15p research12 01-06-2013 50 4   Download

The as1-casein (as1-Cas) locus in the goat is characterized by a polymorphism, the main feature of which is to be qualitative as well as quantitative. A systematic analysis performed in an autochthon southern Italy breed identified a new rare allele (M), which was characterized at both the protein and genomic level. The M protein displays the slowest electrophoretic mobility of the as1-Cas variants described so far.

11p research12 01-06-2013 40 5   Download

Caseins are highly phosphorylated milk proteins assembled in large colloidal structures termed micelles. In the milk of ruminants, as1-casein has been shown to be extensively phosphorylated. In this report we have determined the phosphorylation pattern of humanas1 -casein by a combi-nationofmatrix-assisted laserdesorptionmass spectrometry and amino acid sequence analysis. Three phosphorylation variants were identified. A nonphosphorylated form, a variant phosphorylated at Ser18 and a variant phosphory-lated at Ser18 and Ser26.

5p tumor12 20-04-2013 34 4   Download

A100-kDa proteinwith endoglucanase activitywas purified from Triton X-100 extract of cells of the thermoacidophilic Gram-positive bacterium Alicyclobacillus acidocaldarius. The enzyme exhibited activity towards carboxy methyl cel-lulose and oat spelt xylan with pH and temperature optima of 4 and 80
C, respectively. Cloning and nucleotide sequence analysis of the corresponding gene (celB) revealed an ORF encoding a preprotein of 959 amino acids which is consistent with an extracellular localization.

10p tumor12 20-04-2013 34 2   Download

The Tat system catalyzes the transport of folded globular proteins across the bacterial plasma membrane and the chloroplast thylakoid. It recognizes cleavable signal peptides containingacritical twin-argininemotif but little isknownof the overall structure of these peptides. In this report, we have analyzed the secondary structure of the SufI signal peptide, together with those of two nonfunctional variants in which the region around the twin-arginine, RRQFI, is replaced by KKQFI or RRQAA.

8p tumor12 20-04-2013 47 3   Download

The availability of a system for the functional expression of genes coding formolybdenumhydroxylases is a prerequisite for the construction of enzyme variants bymutagenesis. For the expression cloning of quinoline 2-oxidoreductase (Qor) fromPseudomonas putida86 – that contains the molybdo-pterin cytosine dinucleotide molybdenum cofactor (Mo-MCD), two distinct [2Fe)2S] clusters and FAD – the qorMSLgenes were inserted into the broad host range vector, pJB653, generating pUF1.P. putidaKT2440 and P. putida86-1Dqor were used as recipients for pUF1....

11p tumor12 20-04-2013 56 5   Download

We have previously cloned, expressedand characterized two variants of the major allergen Lep d 2 from culturedLepi-doglyphus destructor mites. These variants, Lep d 2.0101 and Lep d 2.0201, differ at 13 amino acid positions. In this study we investigated Lep d 2 sequence diversity between wild and cultured mites. PCR, Southern blot and DNA sequence analysis revealed the presence of two different Lep d 2 genes, one with and one without an intron.

8p tumor12 20-04-2013 49 3   Download

Recent research suggests that minor changes in the primary sequence of the conserved histones may become major determinants for the chromatin structure regulating gene expression and other DNA-related processes. An analysis of the involvement of different core histone variants in different nuclear processes and the structure of different variant nucleosome cores shows that this may indeed be so. Histone variants may also be involved in demarcating functional regions of the chromatin.

20p fptmusic 12-04-2013 38 4   Download

To examine the interaction of human arginase II (EC 3.5.3.1) with sub-strate and manganese ions, the His120Asn, His145Asn and Asn149Asp mutations were introduced separately. About 53% and 95% of wild-type arginase activity were expressed by fully manganese activated species of the His120Asn and His145Asn variants, respectively. TheKmfor arginine (1.4– 1.6 mm) was not altered and the wild-type and mutant enzymes were essen-tially inactive on agmatine.

9p fptmusic 12-04-2013 31 2   Download

TheRel/NF-jBfamilyof transcription factorsplaykey roles in morphogenesis and immune responses. We reported previously that As-rel1 and As-rel2 of the ascidianHalo-cynthia roretziare involved in notochord formation. The As-rel1 protein is a typical Rel/NF-jB family member, whereas the As-rel2 protein is a novel truncated product of As-rel1 that lacks a nuclear localization signal and the unique C-terminal region. Here, we present conclusive evi-dence that As-rel1 and As-rel2 are generated from a single gene by alternative splicing....

10p fptmusic 12-04-2013 41 2   Download

To learn about the correlation between allostery and ligand binding of the Tet repressor (TetR) we analyzed the effect of mutations in the DNA read-ing head–core interface on the effector specific TetR i2 variant. The same mutations in these subdomains can lead to completely different activities, e.g. the V99G exchange in the wild-type leads to corepression by 4-ddma-atc without altering DNA binding. However, in TetR i2 it leads to 4-ddma-atc dependent repression in combination with reduced DNA binding in the absence of effector. ...

10p fptmusic 11-04-2013 38 3   Download

Multiple ankyrin repeat motif-containing proteins play an important role in protein–protein interactions. ANKHD1 proteins are known to possess multiple ankyrin repeat domains and a single KH domain with no known function. Using yeast two-hybrid system analysis, we identified a novel splice variant of ANKHD1. This splice variant of ANKHD1, which we designated as HIV-1 Vpr-binding ankyrin repeat protein (VBARP), does not contain the signature KH domain, and codes for only a single ankyrin repeat motif. ...

12p fptmusic 11-04-2013 45 3   Download

Hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) are the most common hereditary cardiac conditions. Both are frequent causes of sudden death and are often associated with an adverse disease course.Alpha-cardiac actinis one of the disease genes where different mis-sense mutations have been found to cause either HCM or DCM. We have tested the hypothesis that the protein-folding pathway plays a role in dis-ease development for two actin variants associated with DCM and six asso-ciated with HCM....

13p awards 06-04-2013 46 3   Download

In Picrophilus torridus, a euryarchaeon that grows optimally at 60
C and pH 0.7 and thus represents the most acidophilic thermophile known, glu-cose oxidation is the first proposed step of glucose catabolism via a non-phosphorylated variant of the Entner–Doudoroff pathway, as deduced from the recently completed genome sequence of this organism. The P. torridusgene for a glucose dehydrogenase was cloned and expressed in Escherichia coli, and the recombinant enzyme, GdhA, was purified and characterized....

9p awards 05-04-2013 54 3   Download

To address questions of protein stability, researchers have increasingly turned to combinatorial approaches that permit the rapid analysis of libraries of protein variants. Phage-displayhasprovedtobeapowerful tool foranalyzingprotein stabilitydue to the large library sizeand the robustnessof the phageparticle toavarietyofdenaturingconditions.

7p dell39 03-04-2013 35 5   Download

Why do proteins adopt the conformations that they do, and what determines their stabilities? While we have come to some understandingof the forces that underlie protein architecture, a precise, predictive, physicochemical explanation is still elusive. Two obstacles to addressing these questions are the unfathomable vastness of protein sequence space, and the difficulty in makingdirect phy-sical measurements on large numbers of protein variants. Here, we review combinatorial methods that have been applied to problems in protein biophysics over the last 15 years.

14p dell39 03-04-2013 62 3   Download