scholarly journals Evidence for Selection at the fused1 Locus of Drosophila americana

Genetics ◽  
2001 ◽  
Vol 158 (1) ◽  
pp. 279-290 ◽  
Author(s):  
Jorge Vieira ◽  
Bryant F McAllister ◽  
Brian Charlesworth
Keyword(s):  
Amino Acid ◽  
Sequence Variation ◽  
Amino Acid Replacement ◽  
Population Subdivision ◽  
Amino Acid Substitutions ◽  
Clinal Variation ◽  
Haplotype Structure ◽  
Common Amino Acid ◽  
Chromosome Arrangement ◽  
Dna Sequence Variation

Abstract We analyze genetic variation at fused1, a locus that is close to the centromere of the X chromosome-autosome (X/4) fusion in Drosophila americana. In contrast to other X-linked and autosomal genes, for which a lack of population subdivision in D. americana has been observed at the DNA level, we find strong haplotype structure associated with the alternative chromosomal arrangements. There are several derived fixed differences at fused1 (including one amino acid replacement) between two haplotype classes of this locus. From these results, we obtain an estimate of an age of ∼0.61 million years for the origin of the two haplotypes of the fused1 gene. Haplotypes associated with the X/4 fusion have less DNA sequence variation at fused1 than haplotypes associated with the ancestral chromosome arrangement. The X/4 haplotypes also exhibit clinal variation for the allele frequencies of the three most common amino acid replacement polymorphisms, but not for adjacent silent polymorphisms. These patterns of variation are best explained as a result of selection acting on amino acid substitutions, with geographic variation in selection pressures.

DNA Sequence Variation and Haplotype Structure of the ICAM1 and TNF Genes in 12 Ethnic Groups of India Reveal Patterns of Importance in Designing Association Studies

2004 ◽  
Vol 68 (6) ◽  
pp. 574-587 ◽  
Author(s):  
Sanghamitra Sengupta ◽  
Shabana Farheen ◽  
Neelanjana Mukherjee ◽  
Badal Dey ◽  
Barun Mukhopadhyay ◽  
...  
Keyword(s):  
Ethnic Groups ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Association Studies ◽  
Haplotype Structure ◽  
Dna Sequence Variation

DNA Sequence Variation in Domain a of the Acetolactate Synthase Genes of Herbicide-Resistant and -Susceptible Weed Biotypes

Weed Science ◽  
1992 ◽  
Vol 40 (4) ◽  
pp. 670-677 ◽  
Author(s):  
Mary J. Guttieri ◽  
Charlotte V. Eberlein ◽  
Carol A. Mallory-Smith ◽  
Donald C. Thill ◽  
David L. Hoffman
Keyword(s):  
Amino Acid ◽  
Point Mutation ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Polymerase Chain Reaction Amplification ◽  
Single Point ◽  
Acetolactate Synthase ◽  
Single Point Mutation ◽  
Dna Sequence Variation ◽  
Prickly Lettuce

The DNA sequence of a 196 base pair (bp) region of the acetolactate synthase (ALS) genes of three weed species, kochia, prickly lettuce, and Russian thistle, was determined. This region encompasses the coding sequence for Domain A, a region of the amino acid sequence previously demonstrated to play a pivotal role in conferring resistance to herbicides that inhibit ALS. The Domain A DNA sequence from a chlorsulfuron-resistant (R) prickly lettuce biotype from Idaho differed from that of a chlorsulfuron-susceptible (S) biotype by a single point mutation, which substituted a histidine for a proline. The Domain A DNA sequence from an R kochia biotype from Kansas also differed from that of an S biotype by a single point mutation in the same proline codon. This point mutation, however, conferred substitution of threonine for proline. Two different ALS-homologous sequences were isolated from an R biotype of Russian thistle. Neither sequence encoded amino acid substitutions in Domain A that differed from the consensus S sequence. The DNA sequence variation among the R and S kochia biotypes was used to characterize six Ada County, Idaho, kochia collections for correlation between phenotypic chlorsulfuron susceptibility and restriction digest patterns (RFLPs) of polymerase chain reaction amplification products. Most collections showed excellent correspondence between the RFLP patterns and the phenotypic response to chlorsulfuron application. However, one entirely R collection had the RFLP pattern of the S biotype, suggesting that resistance was not due to mutation in the proline codon.

Sequence variability of HCV 3a isolates based on core gene in patients from Lahore, Pakistan

2019 ◽  
Vol 14 (10) ◽  
pp. 641-653
Author(s):  
Muhammad Ajmal Khan ◽  
Sumera Afzal Khan ◽  
Muhammad Hamayun ◽  
Muhammad Ali ◽  
Muhammad Idrees
Keyword(s):  
Amino Acid ◽  
Treatment Response ◽  
Sequence Variation ◽  
Phylogenetic Analyses ◽  
Core Gene ◽  
Nucleotide Sequencing ◽  
Amino Acid Substitutions ◽  
Sequence Variability ◽  
Blood Samples ◽  
Core Sequence

Aim: To investigate the HCV 3a core sequence variation and amino acid substitutions of patients from Lahore, Pakistan. Materials & methods: Blood samples from HCV positive patients (n = 232) were collected for viral genotypes. Moreover, the nucleotide sequencing was performed for core gene of 20 samples. Results: Viral genotyping showed that 69.82% (n = 162) belonged to 3a genotype, 9.05% (1a; n = 21), 2.15% (3b; n = 5) and 18.98% were untypable (n = 44). Phylogenetic analyses suggest majority of our isolates clustered with previously reported reference isolates from Pakistan. The remaining isolates clustered with HCV-core sequences reported from Vietnam, Japan, Thailand, Iran, USA, Bangladesh, Malaysia and Morocco. Conclusion: We report HCV-core substitutions (G60E, R70Q, C91A, A94Q and Q63E/D) that could be associated with treatment response in Pakistani patients.

scholarly journals Mutation Spectra and the Neutrality of Mutations

1974 ◽  
Vol 27 (3) ◽  
pp. 309 ◽  
Author(s):  
J Langridge
Keyword(s):  
Amino Acid ◽  
Catalytic Efficiency ◽  
Amino Acid Replacement ◽  
Enzyme Function ◽  
Substrate Affinity ◽  
Amino Acid Substitutions ◽  
Galactosidase Activity ◽  
Immunological Tests ◽  
Normal Enzyme ◽  
Mutation Spectra

The effect of amino acid replacements on enzyme function was studied in the tJ-galactosidase of Escherichia coli. Mutants possessing 50% or less of normal enzyme activity were isolated and examined. Of 733 amino acid substitutions calculated to have occurred, only 11 reduced tJ-galactosidase activity below 50 %. These mutations were expressed because they greatly impaired the substrate affinity or catalytic efficiency of the enzyme. The inertness of the enzyme to amino acid replacement was confirmed by immunological tests of tJ-galactosidase molecules changed in amino acid sequence by suppression.

Evolutionary relationships and sequence variation of alpha-amylase variants encoded by duplicated genes in the Amy locus of Drosophila melanogaster.

Genetics ◽  
1995 ◽  
Vol 141 (1) ◽  
pp. 237-244
Author(s):  
N Inomata ◽  
H Shibata ◽  
E Okuyama ◽  
T Yamazaki
Keyword(s):  
Drosophila Melanogaster ◽  
Amino Acid ◽  
Sequence Variation ◽  
Alpha Amylase ◽  
Single Amino Acid ◽  
Amino Acid Substitutions ◽  
Duplicated Genes ◽  
Synonymous Sites ◽  
Or Gene ◽  
Amy Genes

Abstract To infer the genealogical relationships of alpha-amylase electromorphs of Drosophila melanogaster, we determined the nucleotide sequences of a collection of electromorphs sampled throughout the world. On average there were 1.0 amino acid substitutions between identical electromorphs and 3.9 between different electromorphs, respectively. We found that the evolution of AMY1 through AMY6 electromorphs occurred by sequential accumulation of single amino acid substitutions each causing one charge difference. The nucleotide diversities at synonymous sites within Amy1,Amy2,Amy3,Amy4 and Amy6 were 0.0321, 0.0000, 0.0355, 0.0059 and 0.0030, respectively. We also obtained evidence of genetic exchanges, such as intrachromosomal recombination, interchromosomal recombination or gene conversion, between the two duplicated Amy genes as well as among the alleles.

scholarly journals In Vitro Antiviral Activity and Resistance Profile of the Next-Generation Hepatitis C Virus NS5A Inhibitor Pibrentasvir

2017 ◽  
Vol 61 (5) ◽  
Author(s):  
Teresa I. Ng ◽  
Preethi Krishnan ◽  
Tami Pilot-Matias ◽  
Warren Kati ◽  
Gretja Schnell ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Amino Acid ◽  
Clinical Samples ◽  
Amino Acid Substitutions ◽  
Next Generation ◽  
Common Amino Acid ◽  
Hcv Genotypes ◽  
Ns5a Inhibitor ◽  
Genotype 1A

ABSTRACT Pibrentasvir (ABT-530) is a novel and pan-genotypic hepatitis C virus (HCV) NS5A inhibitor with 50% effective concentration (EC50) values ranging from 1.4 to 5.0 pM against HCV replicons containing NS5A from genotypes 1 to 6. Pibrentasvir demonstrated similar activity against a panel of chimeric replicons containing HCV NS5A of genotypes 1 to 6 from clinical samples. Resistance selection studies were conducted using HCV replicon cells with NS5A from genotype 1a, 1b, 2a, 2b, 3a, 4a, 5a, or 6a at a concentration of pibrentasvir that was 10- or 100-fold over its EC50 for the respective replicon. With pibrentasvir at 10-fold over the respective EC50, only a small number of colonies (0.00015 to 0.0065% of input cells) with resistance-associated amino acid substitutions were selected in replicons containing genotype 1a, 2a, or 3a NS5A, and no viable colonies were selected in replicons containing NS5A from other genotypes. With pibrentasvir at 100-fold over the respective EC50, very few colonies (0.0002% of input cells) were selected by pibrentasvir in genotype 1a replicon cells while no colonies were selected in other replicons. Pibrentasvir is active against common resistance-conferring substitutions in HCV genotypes 1 to 6 that were identified for other NS5A inhibitors, including those at key amino acid positions 28, 30, 31, or 93. The combination of pibrentasvir with HCV inhibitors of other classes produced synergistic inhibition of HCV replication. In summary, pibrentasvir is a next-generation HCV NS5A inhibitor with potent and pan-genotypic activity, and it maintains activity against common amino acid substitutions of HCV genotypes 1 to 6 that are known to confer resistance to currently approved NS5A inhibitors.

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