TNF-α, IL-4Rα AND IL-4 Polymorphisms in Mild to Severe Asthma from Italian Caucasians

Asthma is a chronic airway inflammatory disease associated with airway hyperresponsiveness which affects subjects with genetic predisposition. An association has been reported between some polymorphisms in various cytokine genes and asthma. Most of them are single nucleotide polymorphisms (SNPs). These polymorphisms are detected in the protein coding sequence or in the promoter region thus influencing cytokine production. We investigated the involvement of SNP mapping in 5 cytokine genes in mild to severe asthmatics of Italian Caucasians. The frequency of alleles and genotypes, relatively to 10 allelic specificities of the cytokine genes, was defined in 57 asthmatics and in 124 control subjects by a Polymerase Chain Reaction-Sequence Specific Primer method. TNF-α -308A and TNF-α -238A allele frequencies were higher in asthmatics than in controls (p<0.001). Significant differences in the frequency of IL-4 -590T allele and of IL-4Rα + 1902A allele were also detected in asthmatics in comparison with controls (p<0.001 and p=0.005, respectively). Similarly, IL-1α -889C allele was present in 84.1% of asthmatics and in 70.2% of controls (p=0.013). Furthermore, the IL-4Rα + 1902A/A and IL-1α -889C/C homozygous conditions and the TNF-α -308G/A, TNF-α -238G/A, IL-4 -590T/C and IL-10 -1082G/A heterozygous conditions were significantly associated with asthma (p<0.05). ACA haplotype of IL-10 was observed only in asthmatic patients. This study reports, for the first time, the frequency of 10 different single nucleotide polymorphisms in 5 cytokine genes in the Italian Caucasians. Furthermore, we also indicate that in our population some single nucleotide polymorphisms are associated with mild to severe bronchial asthma.

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IMPACT OF DELETERIOUS NON-SYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISMS OF CYTOKINE GENES ON NON-CLASSICAL HYDROGEN BONDS PREDISPOSING TO CARDIOVASCULAR DISEASE: AN IN SILICO APPROACH

Asian Journal of Pharmaceutical and Clinical Research ◽

10.22159/ajpcr.2017.v10i11.19531 ◽

2017 ◽

Vol 10 (11) ◽

pp. 214

Author(s):

Sai Ramesh A ◽

Rao Sethumadhavan ◽

Padma Thiagarajan

Keyword(s):

Cardiovascular Disease ◽

Single Nucleotide Polymorphisms ◽

In Silico ◽

Point Mutations ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Cytokine Genes ◽

Sorting Intolerant From Tolerant ◽

Tnf Α ◽

Factor Α

Objective: Cardiovascular disease (CVD) is a leading cause of death worldwide. Malfunctioning of genes that are responsible for several inflammatory processes is the major cause for its initiation. Cytokine genes are one such group of genes that are involved in the development of CVD. Hence, the prediction of potential point mutations in these genes is important for diagnostic purposes. Such mutations result in altered protein structure and function when compared to neutral ones.Methods: In this study, interleukin factor 6 (IL6), tumor necrosis factor α (TNF-α), interleukin factor 4 (IL4), and interferon gamma have been analyzed using sorting intolerant from tolerant and PolyPhen 2.0 tools.Results: Several single nucleotide polymorphisms (SNPs), in IL6, TNF-α, and IL4, are found to be potentially deleterious. In addition, bond analysis has also been performed on these SNPs. It has been predicted that L119P and R196H of IL6 as well as K87T and T181N of TNF-α are potential ns-SNP’s that may cause structural and functional variations in the corresponding proteins. The hydrogen and Cation-Pi bond analysis performed in this study provides molecular-based evidence that support the predicted deleterious potential of such SNPs for these CVD candidate genes along with other conventional in silico tools.Conclusion: The study testifies the importance of adopting a computational approach to narrow down potential point mutants for disease predictions.

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Genotyping single nucleotide polymorphisms using intact polymerase chain reaction products by electrospray quadrupole mass spectrometry

Rapid Communications in Mass Spectrometry ◽

10.1002/rcm.435 ◽

2001 ◽

Vol 15 (18) ◽

pp. 1752-1759 ◽

Cited By ~ 22

Author(s):

James J. Walters ◽

Warees Muhammad ◽

Karen F. Fox ◽

Alvin Fox ◽

Dawen Xie ◽

...

Keyword(s):

Mass Spectrometry ◽

Polymerase Chain Reaction ◽

Single Nucleotide Polymorphisms ◽

Nucleotide Polymorphisms ◽

Reaction Products ◽

Quadrupole Mass ◽

Chain Reaction ◽

Single Nucleotide ◽

Quadrupole Mass Spectrometry ◽

Polymerase Chain

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Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome

GigaScience ◽

10.1093/gigascience/giz115 ◽

2019 ◽

Vol 8 (10) ◽

Cited By ~ 3

Author(s):

Bo Song ◽

Yue Song ◽

Yuan Fu ◽

Elizabeth Balyejusa Kizito ◽

Sandra Ndagire Kamenya ◽

...

Keyword(s):

Disease Resistance ◽

Single Nucleotide Polymorphisms ◽

Drought Tolerance ◽

Resistance Genes ◽

Draft Genome ◽

Disease Resistance Genes ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Protein Coding ◽

Protein Coding Genes

Abstract Background The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops. Results We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome. Conclusions The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.

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Heterozygous Ile453Val codon mutation in exon 7, homozygous single nucleotide polymorphisms in intron 2 and 5 of cathepsin C are associated with Haim-Munk syndrome

European Journal of Dentistry ◽

10.4103/1305-7456.126250 ◽

2014 ◽

Vol 08 (01) ◽

pp. 079-084 ◽

Cited By ~ 6

Author(s):

Nalini Aswath ◽

Bhuminathan Swamikannu ◽

Sankar Narayanan Ramakrishnan ◽

Rajendran Shanmugam ◽

Jayakar Thomas ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Direct Sequencing ◽

Sequencing Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Heterozygous Condition ◽

South Indian ◽

The Subject ◽

First Time ◽

Intron 2

ABSTRACT Objective: In the present study, we have investigated the genetic status of CTSC gene in a HMS subject, who along with her parents belonged to non-Jewish South Indian Dravidian community. Materials and Methods: Genomic deoxyribonucleic acid isolated from the peripheral blood of the subject was amplified with CTSC exon specific primers and were analyzed by direct sequencing. Results: Sequencing analysis identified Ile453Val mutation within exon 7 of CTSC gene in heterozygous condition, and two single nucleotide polymorphisms (SNPs) within intron 2 and 5 in homozygous condition. Conclusion: The present study has identified for the first time the association of Ile453Val mutation within exon 7 and the two SNPs in a subject with HMS.

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In-Depth Study of a Nosocomial Outbreak Caused by Extensively Drug-Resistant Pseudomonas aeruginosa Using Whole Genome Sequencing Coupled With a Polymerase Chain Reaction Targeting Strain-Specific Single Nucleotide Polymorphisms

American Journal of Epidemiology ◽

10.1093/aje/kwaa025 ◽

2020 ◽

Vol 189 (8) ◽

pp. 841-849

Author(s):

Fermín Acosta ◽

Ana Fernández-Cruz ◽

Sandra R Maus ◽

Pedro J Sola-Campoy ◽

Mercedes Marín ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Outbreak Strain ◽

Single Nucleotide ◽

Specific Pcr ◽

Extensively Drug Resistant ◽

Polymerase Chain

Abstract In 2013–2014, an outbreak involving 14 patients infected by an extensively drug-resistant strain of Pseudomonas aeruginosa was detected in a hospital in Madrid, Spain. Our objective was to evaluate an alternative strategy for investigating the outbreak in depth by means of molecular and genomic approaches. Pulsed-field gel electrophoresis (PFGE) was applied as a first-line approach, followed by a more refined whole genome sequencing analysis. Single nucleotide polymorphisms identified by whole genome sequencing were used to design a specific polymerase chain reaction (PCR) for screening unsuspected cases infected by the outbreak strain. Whole genome sequencing alerted us to the existence of greater genetic diversity than was initially assumed, splitting the PFGE-associated outbreak isolates into 4 groups, 2 of which represented coincidental transmission unrelated to the outbreak. A multiplex allele-specific PCR targeting outbreak-specific single nucleotide polymorphisms was applied to 290 isolates, which allowed us to identify 25 additional cases related to the outbreak during 2011–2017. Whole genome sequencing coupled with an outbreak-strain-specific PCR enabled us to markedly redefine the initial picture of the outbreak by 1) ruling out initially suspected cases, 2) defining likely independent coincidental transmission events, 3) predating the starting point of the outbreak, 4) capturing new unsuspected cases, and 5) revealing that the outbreak was still active.

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Study of the association of seventeen single nucleotide polymorphisms and their haplotypes in the TNF-α, IL-2, IL-4 and IL-10 genes with the antibody response to inactivated Japanese encephalitis vaccine

Human Vaccines & Immunotherapeutics ◽

10.1080/21645515.2020.1724743 ◽

2020 ◽

Vol 16 (10) ◽

pp. 2449-2455

Author(s):

Yufeng Yao ◽

Xiuwen Xu ◽

Yaheng Li ◽

Xiaona Wang ◽

Huijuan Yang ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Antibody Response ◽

Japanese Encephalitis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Japanese Encephalitis Vaccine ◽

Tnf Α

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Polymorphisms of LHβ and GnRHR genes and their association with the number of embryos recovered in goats

Animal Production Science ◽

10.1071/an13076 ◽

2014 ◽

Vol 54 (8) ◽

pp. 987 ◽

Cited By ~ 1

Author(s):

M. Z. Fu ◽

G. Li ◽

Z. Q. Zhou

Keyword(s):

Polymerase Chain Reaction ◽

Single Nucleotide Polymorphisms ◽

Gene Polymorphism ◽

Corpus Luteum ◽

Nucleotide Polymorphisms ◽

Chain Reaction ◽

Single Strand Conformational Polymorphism ◽

Single Nucleotide ◽

Exon 2 ◽

Polymerase Chain

The objective of the present study was to explore a predictor of superovulation response on the basis of associations between the number of embryos recovered and gene polymorphism. Variation in the goat LHβ and GnRHR genes was investigated using polymerase chain reaction–single-strand conformational polymorphism and DNA sequencing. Two single nucleotide polymorphisms (SNPs) were identified in the 5′-UTR of LHβ gene (A59C, P1 locus) and in the Exon 2 of GnRHR gene (T177A, P6 locus). At the P1 locus in both breeds, the frequencies of one allele were 0.46 and 0.51, respectively. At the P6 locus, the minor allele frequency was 0.23. Associations of both SNPs with the number of embryos recovered and the corpus luteum number were evaluated in Boer and Shaanbei goat breeds. Association analysis showed that both SNPs had significant (P < 0.05) effects on the number of embryos recovered and corpus luteum number. These results indicate that LHβ and GnRHR genes are potential markers for the number of embryos recovered.

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Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen

Journal of Bacteriology ◽

10.1128/jb.00124-06 ◽

2006 ◽

Vol 188 (12) ◽

pp. 4453-4463 ◽

Cited By ~ 114

Author(s):

Patrick S. G. Chain ◽

Ping Hu ◽

Stephanie A. Malfatti ◽

Lyndsay Radnedge ◽

Frank Larimer ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Yersinia Pestis ◽

Yersinia Pseudotuberculosis ◽

Open Reading Frames ◽

Genomic Diversity ◽

Avirulent Strain ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Protein Coding ◽

Definition Of

ABSTRACT Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has undergone detailed study at the molecular level. To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the “classical” antiqua biovar, strains Antiqua and Nepal516. The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. Though both strains belong to one of the three classical biovars, they represent separate lineages defined by recent phylogenetic studies. We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis. There are strain-specific rearrangements, insertions, deletions, single nucleotide polymorphisms, and a unique distribution of insertion sequences. We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. The results presented here clearly demonstrate the differences between the two biovar antiqua lineages and support the notion that grouping Y. pestis strains based strictly on the classical definition of biovars (predicated upon two biochemical assays) does not accurately reflect the phylogenetic relationships within this species. A comparison of four virulent Y. pestis strains with the human-avirulent strain 91001 provides further insight into the genetic basis of virulence to humans.

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