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Automated inference of molecular mechanisms of disease from amino acid substitutions

B. Li, V. G. Krishnan, M. E. Mort, F. Xin, K. K. Kamati, D. N. Cooper, S. D. Mooney, P. Radivojac
2009 Bioinformatics  
Over the last decade, a number of computational methods have been developed to predict whether such amino acid substitutions result in an altered phenotype.  ...  Single nucleotide substitutions within protein coding regions are of particular importance owing to their potential to give rise to amino acid substitutions that affect protein structure and function which  ...  ACKNOWLEDGEMENTS The authors would like to thank Prateek Kumar and Pauline Ng from the J. Craig Venter Institute for their help with the SIFT tool.  ... 
doi:10.1093/bioinformatics/btp528 pmid:19734154 pmcid:PMC3140805 fatcat:46h4jv4sone2rc3qrl3z4yiq5u

Ethambutol resistance in Mycobacterium tuberculosis: critical role of embB mutations

S Sreevatsan, K E Stockbauer, X Pan, B N Kreiswirth, S L Moghazeh, W R Jacobs, A Telenti, J M Musser
1997 Antimicrobial Agents and Chemotherapy  
distinct IS6110 fingerprints confirmed the unique association of substitutions in amino acid residue 306 of EmbB with EMB resistance.  ...  Sixty-nine percent of epidemiologically unassociated EMB-resistant organisms had an amino acid substitution not found in susceptible strains, and most (89%) replacements occurred at amino acid residue  ...  The ongoing support of A. M. Ginsberg is gratefully appreciated.  ... 
doi:10.1128/aac.41.8.1677 fatcat:543naeyes5hgtll4si32np7s5i

Ethambutol resistance in Mycobacterium tuberculosis: critical role of embB mutations

S Sreevatsan, K E Stockbauer, X Pan, B N Kreiswirth, S L Moghazeh, W R Jacobs, A Telenti, J M Musser
1997 Antimicrobial Agents and Chemotherapy  
distinct IS6110 fingerprints confirmed the unique association of substitutions in amino acid residue 306 of EmbB with EMB resistance.  ...  Sixty-nine percent of epidemiologically unassociated EMB-resistant organisms had an amino acid substitution not found in susceptible strains, and most (89%) replacements occurred at amino acid residue  ...  ACKNOWLEDGMENTS The ongoing support of A. M. Ginsberg is gratefully appreciated.  ... 
pmid:9257740 pmcid:PMC163984 fatcat:bsoazlta4bdejalgrtfctgupxa

Antimicrobial agent resistance in mycobacteria: molecular genetic insights

J M Musser
1995 Clinical Microbiology Reviews  
A majority of fluoroquinolone-resistant M. tuberculosis isolates have amino acid substitutions in a region of the DNA gyrase A subunit homologous to a conserved fluoroquinolone resistance-determining region  ...  Mutations in the katG gene resulting in catalase-peroxidase amino acid alterations nad nucleotide substitutions in the presumed regulatory region of the inhA locus are repeatedly associated with isoniazid-resistant  ...  The four M. leprae strains each had a Ser3Leu substitution at amino acid residue 425.  ... 
doi:10.1128/cmr.8.4.496 fatcat:bau4hymemrdrvclwgvcp6ytck4

Antimicrobial agent resistance in mycobacteria: molecular genetic insights

J M Musser
1995 Clinical Microbiology Reviews  
A majority of fluoroquinolone-resistant M. tuberculosis isolates have amino acid substitutions in a region of the DNA gyrase A subunit homologous to a conserved fluoroquinolone resistance-determining region  ...  Mutations in the katG gene resulting in catalase-peroxidase amino acid alterations nad nucleotide substitutions in the presumed regulatory region of the inhA locus are repeatedly associated with isoniazid-resistant  ...  The four M. leprae strains each had a Ser3Leu substitution at amino acid residue 425.  ... 
pmid:8665467 pmcid:PMC172873 fatcat:5k4jmykio5e53eg6byqbi5ci7m

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

S. Kumar
2004 Briefings in Bioinformatics  
histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes.  ...  One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from  ...  MEGA software project has been supported by research grants from NIH, NSF and Burroughs-Wellcome Fund to S.K. and NIH and NSF to M.N.  ... 
doi:10.1093/bib/5.2.150 pmid:15260895 fatcat:nmi5opa5zzex5lwfq63q4zciyy

Characterization of group A Streptococcus strains recovered from Mexican children with pharyngitis by automated DNA sequencing of virulence-related genes: unexpectedly large variation in the gene (sic) encoding a complement-inhibiting protein

L M Mejia, K E Stockbauer, X Pan, A Cravioto, J M Musser
1997 Journal of Clinical Microbiology  
Sequence variation was studied in several target genes in 54 strains of group A Streptococcus (GAS) cultured from children with pharyngitis in Mexico City.  ...  The gene (sic) encoding an extracellular GAS protein that inhibits complement function was unusually variable among isolates with the emm1 family of alleles, with a total of seven variants identified.  ...  J.M.M. is an Established Investigator of the American Heart Association.  ... 
pmid:9399523 pmcid:PMC230151 fatcat:4ehzlyelyncaznaggv4my4w2ni

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources

R. Karchin, M. Diekhans, L. Kelly, D. J. Thomas, U. Pieper, N. Eswar, D. Haussler, A. Sali
2005 Bioinformatics  
It currently annotates 28 043 validated SNPs that produce amino acid residue substitutions in human proteins from the SwissProt/TrEMBL database.  ...  SNPs that result in amino acid residue changes (nsSNPs) are of critical importance in variation between individuals, including disease and drug sensitivity.  ...  Table 1 . 1 List of 13 features used to train an SVM to discriminate between monogenic disease-associated amino acid residue substitutions from OMIM and neutral/positive non-synonymous SNPs from dbSNP  ... 
doi:10.1093/bioinformatics/bti442 pmid:15827081 fatcat:vdfuvxosjjg25eljpouakufypm

Mutations associated with pyrazinamide resistance in pncA of Mycobacterium tuberculosis complex organisms

S Sreevatsan, X Pan, Y Zhang, B N Kreiswirth, J M Musser
1997 Antimicrobial Agents and Chemotherapy  
In striking contrast, 72% of the 67 resistant organisms had pncA mutations that altered the primary amino acid sequence of pyrazinamidase.  ...  with mutations associated with pyrazinamide resistance in Mycobacterium tuberculosis complex members was characterized in 67 pyrazinamide-resistant and 51 pyrazinamide-susceptible isolates recovered from  ...  We are grateful for the ongoing support of A. M. Ginsberg.  ... 
doi:10.1128/aac.41.3.636 fatcat:z3ayb2mxffbyhpghyliv7kx7qi

Mutations associated with pyrazinamide resistance in pncA of Mycobacterium tuberculosis complex organisms

S Sreevatsan, X Pan, Y Zhang, B N Kreiswirth, J M Musser
1997 Antimicrobial Agents and Chemotherapy  
In striking contrast, 72% of the 67 resistant organisms had pncA mutations that altered the primary amino acid sequence of pyrazinamidase.  ...  with mutations associated with pyrazinamide resistance in Mycobacterium tuberculosis complex members was characterized in 67 pyrazinamide-resistant and 51 pyrazinamide-susceptible isolates recovered from  ...  We are grateful for the ongoing support of A. M. Ginsberg.  ... 
pmid:9056006 pmcid:PMC163764 fatcat:peltutxyuvcd5je2yfejjyiv4m

Molecular genetic basis of antimicrobial agent resistance inMycobacterium tuberculosis: 1998 update

S. Ramaswamy, J.M. Musser
1998 Tubercle and Lung Disease  
It is reasonable to believe that development of new therapeutics based on knowledge obtained from the study of the molecular mechanisms of resistance will occur.  ...  Amino acid changes in the A subunit of deoxyribonucleic acid gyrase cause fluoroquinolone resistance in most organisms.  ...  ACKNOWLEDGEMENTS Research in the laboratory of JMM is supported by Public Health Services Grants AI-37004, DA-09238, AI-41168, and AI-33119, and a grant from the Texas Technology Development and Transfer  ... 
doi:10.1054/tuld.1998.0002 pmid:10645439 fatcat:x6kvp2wxqzb2ddg3mqhwozobwy

Missense Mutations of Human Hsp60: A Computational Analysis to Unveil Their Pathological Significance

Alessandra Maria Vitale, Everly Conway de Macario, Riccardo Alessandro, Francesco Cappello, Alberto J. L. Macario, Antonella Marino Gammazza
2020 Frontiers in Genetics  
inferred from crystal structures.  ...  of the amino acids in the human Hsp60 and/or in the highly similar bacterial ortholog GroEL; (c) the location of the mutant amino acids in the monomers and oligomers; and (d) structure-function relationships  ...  inferred from crystal structures.  ... 
doi:10.3389/fgene.2020.00969 pmid:33014020 pmcid:PMC7461820 fatcat:zu64a56tj5bglnersgw6cdodmy

Regulator of G-protein signaling 4 (RGS4)

2010 Science-Business eXchange  
Out of these 44 SNPs, 36% of amino acid substitutions were identified as deleterious by the SIFT program, 42% of amino acid substitutions were identified as damaging by PolyPhen-2 program, 57% and 47%  ...  A total of 44 variants were retrieved from dbSNP for the RGS4 gene in Homo sapiens.  ...  ACKNOWLEDGEMENTS The authors would like to thank School of Biosciences and Technology, VIT University for providing the facilities to carry out this work and for supporting in its timely completion.  ... 
doi:10.1038/scibx.2010.521 fatcat:i6z5eqo4ezbbpbmezlcwva4yce

Mutation analysis of CRYAA, CRYGC, and CRYGD associated with autosomal dominant congenital cataract in Brazilian families

Alessandro Santana, Mauro Waiswol, Enyr Saran Arcieri, José Paulo Cabral de Vasconcellos, Mônica Barbosa de Melo
2009 Molecular Vision  
Both tyrosine in amino acid 56 in CRYGD and arginine in amino acid 12 in CRYAA have been highly conserved throughout evolution in different species.  ...  Congenital cataracts are one of the most treatable causes of visual impairment and blindness during infancy. Approximately 50% of all congenital cataract cases may have a genetic cause.  ...  ACKNOWLEDGMENTS We thank all the members of the participating families. This study was supported by CAPES and FAP-SCSP (Santa Casa de São Paulo School of Medicine, São Paulo, Brazil).  ... 
pmid:19390652 pmcid:PMC2671581 fatcat:mze4imubzzd27k7mlxqbezwjea

Rapid Molecular Genetic Subtyping of Serotype M1 Group A Streptococcus Strains

Nancy Hoe, Kazumitsu Nakashima, Diana Grigsby, Xi Pan, Shu Jun Dou, Steven Naidich, Marianne Garcia, Emily Kahn, David Bergmire-Sweat, James M. Musser
1999 Emerging Infectious Diseases  
Alignment of inferred N-terminal amino acid sequences of 33 alleles of emm1. The region shown represents amino acids 27 through 110 (GenBank accession number X07860).  ...  Moreover, most of the amino acid changes were radical replacements, that is, those producing charge changes or polar-nonpolar substitutions.  ... 
doi:10.3201/eid0502.990210 pmid:10221878 pmcid:PMC2640708 fatcat:n6qcpmtumzgzxd5uwfaaeob6s4
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