scholarly journals Characterization of the human properdin gene

1992 ◽  
Vol 287 (1) ◽  
pp. 291-297 ◽  
Author(s):  
K F Nolan ◽  
S Kaluz ◽  
J M G Higgins ◽  
D Goundis ◽  
K B M Reid
Keyword(s):  
Amino Acids ◽  
Tandem Repeats ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Phase 1 ◽  
Repeat Sequence ◽  
Sequence Motif ◽  
Type I ◽  
Alignment Analysis

A cosmid clone containing the complete coding sequence of the human properdin gene has been characterized. The gene is located at one end of the approximately 40 kb cosmid insert and approximately 8.2 kb of the sequence data have been obtained from this region. Two discrepancies with the published cDNA sequence [Nolan, Schwaeble, Kaluz, Dierich & Reid (1991) Eur. J. Immunol. 21, 771-776] have been resolved. Properdin has previously been described as a modular protein, with the majority of its sequence composed of six tandem repeats of a sequence motif of approximately 60 amino acids which is related to the type-I repeat sequence (TSR), initially described in thrombospondin [Lawler & Hynes (1986) J. Cell Biol. 103, 1635-1648; Goundis & Reid (1988), Nature (London) 335, 82-85]. Analysis of the genomic sequence data indicates that the human properdin gene is organized into ten exons which span approximately 6 kb of the genome. TSRs 2-5 are coded for by discrete, symmetrical exons (phase 1-1), which supports the hypothesis that modular proteins evolved by a process involving exon shuffling. TSR1 is also coded for by a discrete exon, but the boundaries are asymmetrical (phase 2-1). The sequence coding for the sixth TSR is split across the final two exons of the gene with the first 38 amino acids of the repeat coded for by an asymmetric exon (phase 1-2). This split at the genomic level has been shown, by alignment analysis, to be reflected at the protein level with the division of repeat 6 into TSR-like and TSR-unlike sequences.

Molecular Basis of Antithrombin Type I Deficiency: The First Large In-frame Deletion and Two Novel Mutations in Exon 6

1994 ◽  
Vol 72 (04) ◽  
pp. 534-539 ◽  
Author(s):  
J Emmerich ◽  
G Chadeuf ◽  
M Alhenc-Gelas ◽  
M Gouault-Heilman ◽  
P Toulon ◽  
...  
Keyword(s):  
Amino Acids ◽  
Stop Codon ◽  
Direct Sequencing ◽  
Gene Mutations ◽  
Repeat Sequence ◽  
Type I ◽  
Novel Mutations ◽  
Flanking Sequences ◽  
At Deficiency ◽  
Exon 4

SummaryWe report three novel mutations accounting for cases of inherited type I antithrombin (AT) deficiency. Using the polymerase chain reaction (PCR) and direct sequencing of the coding sequences of the AT gene, we found one mutation in exon 4 and two in exon 6. A deletion of 105 bp causing an in-frame deletion of 35 amino acids between Tyr 240 and Gly 276 was found in exon 4. In a second kindred, deletion of two adenines in codon 412-413 introduced a frameshift and a stop codon at position 431. The last mutation was an insertion of ACCG in codon 387, generating a frameshift with a stop codon located at the normal position.The finding of a sequence repeat of nine residues located at the 5’and 3’ ends of the deleted fragment might explain the 105 bp deletion by slippage and mispairing at the replication fork during DNA synthesis. The second mutation is the fourth described within a region of six amino acids (between Phe 408 and Arg 413), which seems to be a cluster of mutations. In this case, the presence of a double repeat sequence - TTCCT and AACA - flanking this region could be particularly favorable for slipped mispairing.These results confirm that human gene mutations are not random events but are strongly influenced by DNA flanking sequences.

scholarly journals The chemistry of the collagen cross-links. Purification and characterization of cross-linked polymeric peptide material from mature collagen containing unknown amino acids

1980 ◽  
Vol 185 (2) ◽  
pp. 373-381 ◽  
Author(s):  
N D Light ◽  
A J Bailey
Keyword(s):  
Amino Acids ◽  
Type I Collagen ◽  
Gel Filtration ◽  
Amino Acid Content ◽  
Exchange Chromatography ◽  
Type I ◽  
Polymeric Form ◽  
Cross Links ◽  
Helical Region

A polymeric form of the alpha 1-chain C-terminal peptide alpha 1 CB6 (poly-alpha 1 CB6) was purified from CNBr digests of insoluble bovine tendon type-I-collagen by gel filtration and ion-exchage chromatography. The purified material had a molecular weight of 1.5 × 10(6)-5 × 10(6) on gel filtration and an amino acid content virtually identical with that of monomeric peptide alpha 1 CB6. The material could be adsorbed on affinity gels containing immobilized anti-(alpha 1 CB6-peptide non-helical region) antibodies and was an inhibitor of haemagglutination by the same antibodies of alpha 1 CB6-peptide-coated sheep erythrocytes. Periodate treatment of the material had no effect. Alkali hydrolysates were shown to contain two unknown amino acids, which were purified by gel filtration and ion-exchange chromatography in volatile buffers and are believed to be components of the mature cross-link of collagen.

scholarly journals Fine-mapping of genes determining extrafusal fiber properties in murine soleus muscle

2017 ◽  
Vol 49 (3) ◽  
pp. 141-150 ◽  
Author(s):  
A. M. Carroll ◽  
R. Cheng ◽  
E. S. R. Collie-Duguid ◽  
C. Meharg ◽  
M. E. Scholz ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Muscle Fiber ◽  
Soleus Muscle ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Mouse Strains ◽  
Sequence Information ◽  
Type I ◽  
Fiber Types ◽  
Genome Wide

Muscle fiber cross-sectional area (CSA) and proportion of different fiber types are important determinants of muscle function and overall metabolism. Genetic variation plays a substantial role in phenotypic variation of these traits; however, the underlying genes remain poorly understood. This study aimed to map quantitative trait loci (QTL) affecting differences in soleus muscle fiber traits between the LG/J and SM/J mouse strains. Fiber number, CSA, and proportion of oxidative type I fibers were assessed in the soleus of 334 genotyped female and male mice of the F34generation of advanced intercross lines (AIL) derived from the LG/J and SM/J strains. To increase the QTL detection power, these data were combined with 94 soleus samples from the F2intercross of the same strains. Transcriptome of the soleus muscle of LG/J and SM/J females was analyzed by microarray. Genome-wide association analysis mapped four QTL (genome-wide P < 0.05) affecting the properties of muscle fibers to chromosome 2, 3, 4, and 11. A 1.5-LOD QTL support interval ranged between 2.36 and 4.67 Mb. On the basis of the genomic sequence information and functional and transcriptome data, we identified candidate genes for each of these QTL. The combination of analyses in F2and F34AIL populations with transcriptome and genomic sequence data in the parental strains is an effective strategy for refining QTL and nomination of the candidate genes.

scholarly journals Functional significance of lysine 1423 of neurofibromin and characterization of a second site suppressor which rescues mutations at this residue and suppresses RAS2Val-19-activated phenotypes.

1994 ◽  
Vol 14 (1) ◽  
pp. 815-821 ◽  
Author(s):  
P Poullet ◽  
B Lin ◽  
K Esson ◽  
F Tamanoi
Keyword(s):  
Amino Acids ◽  
Neurofibromatosis Type ◽  
Type I ◽  
Ras Proteins ◽  
Wild Type ◽  
Conserved Residues ◽  
Mutant Proteins ◽  
Quantitative Analyses ◽  
Intrinsic Gtpase Activity

Lysine 1423 of neurofibromin (neurofibromatosis type I gene product [NF1]) plays a crucial role in the function of NF1. Mutations of this lysine were detected in samples from a neurofibromatosis patient as well as from cancer patients. To further understand the significance of this residue, we have mutated it to all possible amino acids. Functional assays using yeast ira complementation have revealed that lysine is the only amino acid that produced functional NF1. Quantitative analyses of different mutant proteins have suggested that their GTPase-activating protein (GAP) activity is drastically reduced as a result of a decrease in their Ras affinity. Such a requirement for a specific residue is not observed in the case of other conserved residues within the GAP-related domain. We also report that another residue, phenylalanine 1434, plays an important role in NF1 function. This was first indicated by the finding that defective NF1s due to an alteration of lysine 1423 to other amino acids can be rescued by a second site intragenic mutation at residue 1434. The mutation partially restored GAP activity in the lysine mutant. When the mutation phenylalanine 1434 to serine was introduced into a wild-type NF1 protein, the resulting protein acquired the ability to suppress activated phenotypes of RAS2Val-19 cells. This suppression, however, does not involve Ras interaction, since the phenylalanine mutant does not stimulate the intrinsic GTPase activity of RAS2Val-19 protein and does not have an increased affinity for Ras proteins.

scholarly journals Characterization of the genomic sequence data around common cutworm resistance genes in soybean (Glycine max) using short- and long-read sequencing methods

Data in Brief ◽  
2021 ◽  
Vol 34 ◽  
pp. 106577
Author(s):  
Eri Ogiso-Tanaka ◽  
Nobuhiko Oki ◽  
Tsuyoshi Tanaka ◽  
Takehiko Shimizu ◽  
Masao Ishimoto ◽  
...  
Keyword(s):  
Glycine Max ◽  
Resistance Genes ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Common Cutworm ◽  
Long Read

scholarly journals GrigoraSNPs: Optimized HTS DNA Forensic SNP Analysis

2017 ◽  
Author(s):  
Darrell O. Ricke ◽  
Anna Shcherbina ◽  
Adam Michaleas ◽  
Philip Fremont-Smith
Keyword(s):  
High Throughput ◽  
Tandem Repeats ◽  
High Throughput Sequencing ◽  
Dna Analysis ◽  
Sequence Data ◽  
Snp Analysis ◽  
Analysis Pipeline ◽  
Sequencing Technologies ◽  
High Throughput Dna Sequencing

AbstractHigh throughput DNA sequencing technologies enable improved characterization of forensic DNA samples enabling greater insights into DNA contributor(s). Current DNA forensics techniques rely upon allele sizing of short tandem repeats by capillary electrophoresis. High throughput sequencing enables forensic sample characterizations for large numbers of single nucleotide polymorphism loci. The slowest computational component of the DNA forensics analysis pipeline is the characterization of raw sequence data. This paper optimizes the SNP calling module of the DNA analysis pipeline with runtime results that scale linearly with the number of HTS sequences (patent pending)[1]. GrigoraSNPs can analyze 100 million reads in less than 5 minutes using 3 threads on a 4.0 GHz Intel i7-6700K laptop CPU.

Functional significance of lysine 1423 of neurofibromin and characterization of a second site suppressor which rescues mutations at this residue and suppresses RAS2Val-19-activated phenotypes

1994 ◽  
Vol 14 (1) ◽  
pp. 815-821
Author(s):  
P Poullet ◽  
B Lin ◽  
K Esson ◽  
F Tamanoi
Keyword(s):  
Amino Acids ◽  
Neurofibromatosis Type ◽  
Type I ◽  
Ras Proteins ◽  
Wild Type ◽  
Conserved Residues ◽  
Mutant Proteins ◽  
Quantitative Analyses ◽  
Intrinsic Gtpase Activity

Lysine 1423 of neurofibromin (neurofibromatosis type I gene product [NF1]) plays a crucial role in the function of NF1. Mutations of this lysine were detected in samples from a neurofibromatosis patient as well as from cancer patients. To further understand the significance of this residue, we have mutated it to all possible amino acids. Functional assays using yeast ira complementation have revealed that lysine is the only amino acid that produced functional NF1. Quantitative analyses of different mutant proteins have suggested that their GTPase-activating protein (GAP) activity is drastically reduced as a result of a decrease in their Ras affinity. Such a requirement for a specific residue is not observed in the case of other conserved residues within the GAP-related domain. We also report that another residue, phenylalanine 1434, plays an important role in NF1 function. This was first indicated by the finding that defective NF1s due to an alteration of lysine 1423 to other amino acids can be rescued by a second site intragenic mutation at residue 1434. The mutation partially restored GAP activity in the lysine mutant. When the mutation phenylalanine 1434 to serine was introduced into a wild-type NF1 protein, the resulting protein acquired the ability to suppress activated phenotypes of RAS2Val-19 cells. This suppression, however, does not involve Ras interaction, since the phenylalanine mutant does not stimulate the intrinsic GTPase activity of RAS2Val-19 protein and does not have an increased affinity for Ras proteins.

scholarly journals Isolation and characterization of a 15-kilobase genomic sequence coding for part of the Pro alpha 2 chain of sheep type I collagen.

1980 ◽  
Vol 255 (7) ◽  
pp. 3212-3220
Author(s):  
C.D. Boyd ◽  
P. Tolstoshev ◽  
M.P. Schafer ◽  
B.C. Trapnell ◽  
H.C. Coon ◽  
...  
Keyword(s):  
Type I Collagen ◽  
Genomic Sequence ◽  
Type I ◽  
Isolation And Characterization
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