scholarly journals Single nucleotide polymorphisms of the c-MYC gene’s relationship with formation of Burkitt’s lymphoma using bioinformatics analysis

2018 ◽  
Author(s):  
Anfal Osama Mohamed Sati ◽  
Weaam Anwer Osman ◽  
Enas Abdalla Mohammed Ahmedon ◽  
Safa Hamed Elneel Yousif ◽  
Enas Dawoud Khairi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Homo Sapiens ◽  
Burkitt’S Lymphoma ◽  
Burkitt's Lymphoma ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Single Nucleotide ◽  
Myc Gene

AbstractBurkitt’s lymphoma (BL) is an aggressive form of non-Hodgkin lymphoma, originates from germinal center B cells, MYC gene (MIM ID 190080) is an important proto-oncogene transcriptional factor encoding a nuclear phosphoprotein for central cellular processes. Dysregulated expression or function of c-MYC is one of the most common abnormalities in BL. This study focused on the investigation of the possible role of single nucleotide polymorphisms (SNPs) in MYC gene associated with formation of BL.MYC SNPs were obtained from NCBI database. SNPs in the coding region that are non-synonymous (nsSNPs) were analysed by multiple programs such as SIFT, Polyphen2, SNPs&GO, PHD-SNP and I-mutant. In this study, a total of 286 Homo sapiens SNPs were found. Roughly, forty-eight of them were deleterious and were furtherly investigated.Eight SNPs were considered most disease causing [rs4645959 (N26S), rs4645959 (N25S), rs141095253 (P396L), rs141095253 (P397L), rs150308400 (C233Y), rs150308400 (C147Y), rs150308400 (C147Y), rs150308400 (C148Y)] according to the four softwares used. Two of which have not been reported previously [rs4645959 (N25S), rs141095253 (P396L)]. SNPs analysis helps is a diagnostic marker which helps in diagnosing and consequently, finding therapeutics for clinical diseases. This is through SNPs genotyping arrays and other techniques. Thus, it is highly recommended to confirm the findings in this study in vivo and in vitro.

scholarly journals The CT-Element of The C-Myc Gene Does Not Predispose to Chromosomal Breakpoints in Burkitt'S Lymphoma

2006 ◽  
Vol 28 (1-2) ◽  
pp. 31-35
Author(s):  
Achim Weber ◽  
Marina I. Gutierrez ◽  
David Levens
Keyword(s):  
Fragile Site ◽  
Burkitt’S Lymphoma ◽  
Burkitt's Lymphoma ◽  
Chromosomal Translocations ◽  
Wild Type ◽  
Chromosomal Breakpoints ◽  
Myc Gene

Background: Chromosomal translocations are causally related to the development of many tumors. In Burkitt's lymphoma, abnormalities involving the c-myc gene are essential. The CT-element of the c-myc promoter adopts non-B-conformation in vivo and in vitro, and therefore provides a potential fragile site. Methods: We have developed a LM-PCR-based approach to test if chromosomal breakpoints indeed cluster in this region. Results: Amplifying both, wild-type as well as the translocated c-myc gene by LM-PCR, it was shown that chromosomal breakpoints did not cluster within the CT-element. Conclusions: Therefore, the CT-element is not especially susceptible to the formation of breakpoints leading to chromosomal translocations in Burkitt's lymphoma.

scholarly journals Resistência anti-helmíntica em nematoides gastrintestinais de pequenos ruminantes: avanços e limitações para seu diagnóstico

2013 ◽  
Vol 33 (12) ◽  
pp. 1391-1402 ◽  
Author(s):  
Fernanda S. Fortes ◽  
Marcelo B. Molento
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

A seleção e a crescente disseminação de nematoides resistentes aos anti-helmínticos mais comumente utilizados, benzimidazóis (BZs), imidazotiazóis e lactonas macrocíclicas (LMs), constituem um sério entrave na produção de pequenos ruminantes em todo o mundo. O uso de métodos eficientes e sensíveis para a detecção e o monitoramento da resistência anti-helmíntica no campo torna-se urgente, especialmente para os grupos de BZs e LMs, devido aos constantes relatos de resistência. A obtenção de um diagnóstico preciso e precoce da resistência é extremamente importante para auxiliar a tomada de decisão em programas de controle parasitário, com o objetivo de preservar a vida útil dos produtos e limitar o desenvolvimento da resistência nas populações de nematoides. Os testes in vivo e, mais recentemente, os testes in vitro têm sido desenvolvidos para a detecção de nematoides resistentes aos principais grupos de anti-helmínticos. No entanto, a disponibilidade de testes in vitro validados e o seu uso prático ainda são muito limitados. Embora o teste de redução na contagem de ovos nas fezes (TRCOF, in vivo - indireto) seja o principal método de escolha para a detecção de resistência no campo, vem recebendo críticas quanto à validade dos resultados, e passa por significativas modificações. Além disso, o desenvolvimento de técnicas moleculares a partir de alterações genômicas gerou avanços consideráveis nessa área de investigação, com o uso de mutações nos códons 167, 198 e 200 do gene da β-tubulina como principais SNPs (polimorfismos de nucleotídeo único; do inglês Single Nucleotide Polymorphisms) associados à resistência aos BZs. A presente revisão tem o objetivo de discutir os métodos de diagnóstico disponíveis para a detecção de resistência anti-helmíntica em nematoides de pequenos ruminantes, destacando progressos e obstáculos para seu uso na rotina laboratorial e no campo.

scholarly journals Imidazopyridine Compounds Inhibit Mycobacterial Growth by Depleting ATP Levels

2018 ◽  
Vol 62 (6) ◽  
Author(s):  
Theresa O'Malley ◽  
Torey Alling ◽  
Julie V. Early ◽  
Heather A. Wescott ◽  
Anuradha Kumar ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Bacterial Species ◽  
Cross Resistance ◽  
Nucleotide Polymorphisms ◽  
Ph Homeostasis ◽  
Single Nucleotide ◽  
Atp Generation ◽  
Resistant Mutants

ABSTRACT The imidazopyridines are a promising new class of antitubercular agents with potent activity in vitro and in vivo . We isolated mutants of Mycobacterium tuberculosis resistant to a representative imidazopyridine; the mutants had large shifts (>20-fold) in MIC. Whole-genome sequencing revealed mutations in Rv1339, a hypothetical protein of unknown function. We isolated mutants resistant to three further compounds from the series; resistant mutants isolated from two of the compounds had single nucleotide polymorphisms in Rv1339 and resistant mutants isolated from the third compound had single nucleotide polymorphisms in QcrB, the proposed target for the series. All the strains were resistant to two compounds, regardless of the mutation, and a strain carrying the QcrB T313I mutation was resistant to all of the imidazopyridine derivatives tested, confirming cross-resistance. By monitoring pH homeostasis and ATP generation, we confirmed that compounds from the series were targeting QcrB; imidazopyridines disrupted pH homeostasis and depleted ATP, providing further evidence of an effect on the electron transport chain. A representative compound was bacteriostatic against replicating bacteria, consistent with a mode of action against QcrB. The series had a narrow inhibitory spectrum, with no activity against other bacterial species. No synergy or antagonism was seen with other antituberculosis drugs under development. In conclusion, our data support the hypothesis that the imidazopyridine series functions by reducing ATP generation via inhibition of QcrB.

scholarly journals Somatic variants for seed and fruit set in grapevine

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Laura Costantini ◽  
Paula Moreno-Sanz ◽  
Chinedu Charles Nwafor ◽  
Silvia Lorenzi ◽  
Annarita Marrano ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Fruit Set ◽  
Climatic Factors ◽  
Embryo Sac ◽  
Wine Industry ◽  
Nucleotide Polymorphisms ◽  
Wine Quality ◽  
Single Nucleotide ◽  
Germplasm Collections

Abstract Background Grapevine reproductive development has direct implications on yield. It also impacts on berry and wine quality by affecting traits like seedlessness, berry and bunch size, cluster compactness and berry skin to pulp ratio. Seasonal fluctuations in yield, fruit composition and wine attributes, which are largely driven by climatic factors, are major challenges for worldwide table grape and wine industry. Accordingly, a better understanding of reproductive processes such as gamete development, fertilization, seed and fruit set is of paramount relevance for managing yield and quality. With the aim of providing new insights into this field, we searched for clones with contrasting seed content in two germplasm collections. Results We identified eight variant pairs that seemingly differ only in seed-related characteristics while showing identical genotype when tested with the GrapeReSeq_Illumina_20K_SNP_chip and several microsatellites. We performed multi-year observations on seed and fruit set deriving from different pollination treatments, with special emphasis on the pair composed by Sangiovese and its seedless variant locally named Corinto Nero. The pollen of Corinto Nero failed to germinate in vitro and gave poor berry set when used to pollinate other varieties. Most berries from both open- and cross-pollinated Corinto Nero inflorescences did not contain seeds. The genetic analysis of seedlings derived from occasional Corinto Nero normal seeds revealed that the few Corinto Nero functional gametes are mostly unreduced. Moreover, three genotypes, including Sangiovese and Corinto Nero, were unexpectedly found to develop fruits without pollen contribution and occasionally showed normal-like seeds. Five missense single nucleotide polymorphisms were identified between Corinto Nero and Sangiovese from transcriptomic data. Conclusions Our observations allowed us to attribute a seedlessness type to some variants for which it was not documented in the literature. Interestingly, the VvAGL11 mutation responsible for Sultanina stenospermocarpy was also discovered in a seedless mutant of Gouais Blanc. We suggest that Corinto Nero parthenocarpy is driven by pollen and/or embryo sac defects, and both events likely arise from meiotic anomalies. The single nucleotide polymorphisms identified between Sangiovese and Corinto Nero are suitable for testing as traceability markers for propagated material and as functional candidates for the seedless phenotype.

scholarly journals Mycobacterium chimaera genomics with regard to epidemiological and clinical investigations conducted for the open-chest post-surgical Mycobacterium chimaera infections outbreak

2021 ◽  
Author(s):  
Emmanuel Lecorche ◽  
Côme Daniau ◽  
Kevin La ◽  
Faiza Mougari ◽  
Hanaa Benmansour ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Healthcare Facilities ◽  
Open Chest

Abstract Background Post-surgical infections due to Mycobacterium chimaera appeared as a novel nosocomial threat in 2015, with a worldwide outbreak due to contaminated heater-cooler units used in open chest surgery. We report the results of investigations conducted in France including whole genome sequencing comparison of patient and HCU isolates. Methods We sought M. chimaera infection cases from 2010 onwards through national epidemiological investigations in healthcare facilities performing cardiopulmonary bypass together with a survey on good practices and systematic heater-cooler unit microbial analyses. Clinical and HCU isolates were subjected to whole genome sequencing analyzed with regards to the reference outbreak strain Zuerich-1. Results Only two clinical cases were shown to be related to the outbreak, although 23% (41/175) heater-cooler units were declared positive for M. avium complex. Specific measures to prevent infection were applied in 89% (50/56) healthcare facilities although only 14% (8/56) of them followed the manufacturer maintenance recommendations. Whole genome sequencing comparison showed that the clinical isolates and 72% (26/36) of heater-cooler unit isolates belonged to the epidemic cluster. Within clinical isolates, 5 to 9 non-synonymous single nucleotide polymorphisms were observed, among which an in vivo mutation in a putative efflux pump gene observed in a clinical isolate obtained for one patient under antimicrobial treatment. Conclusions Cases of post-surgical M. chimaera infections were declared to be rare in France, although heater-cooler units were contaminated as in other countries. Genomic analyses confirmed the connection to the outbreak and identified specific single nucleotide polymorphisms, including one suggesting fitness evolution in vivo.

The Implications of CaMK2A And MeCP2 Signalings In The Cognitive Ability of Adolescents

2021 ◽  
Author(s):  
Li-Ching Lee ◽  
Ming-Tsan Su ◽  
Hsing-Ying Huang ◽  
Ying-Chun Cho ◽  
Ting-Kuang Yeh ◽  
...  
Keyword(s):  
High School Students ◽  
Single Nucleotide Polymorphisms ◽  
Cognitive Ability ◽  
Signaling Pathway ◽  
Collective Effects ◽  
Nucleotide Polymorphisms ◽  
School Students ◽  
Single Nucleotide ◽  
Glutamatergic Signaling

Abstract The glutamatergic signaling pathway is involved in molecular learning and human cognitive ability. Specific single nucleotide polymorphisms (SNPs) in the genes encoding NMDA receptor subunits have been associated with neuropsychiatric disorders by altering glutamate transmission. But how these polymorphisms associated with cognition and brain psychological activities were rarely been explored in healthy adolescents. In this study, we screened SNPs of the glutamatergic signaling pathway to identify genetic variants associated with cognitive ability. We found that single nucleotide polymorphisms (SNPs) in subunits of ionotropic glutamate receptors, including GRIA1, GRINN1, GRIN2B, GRIN2C, GRIN3A, GRIN3B, and Calcium/ Calmodulin-dependent protein kinase II α (CaMK2A) associated with the cognitive function of students. Importantly, the plasma CaMK2A levels correlated positively with the cognitive ability of senior high school students in Taiwan. We demonstrated that the elevated CaMK2A increased its autophosphorylation at T286 and increased the expression of its downstream targets, including GRIA1 and phosphor GRIA1 in vivo. Additionally, the Methyl CpG binding protein 2 (MeCP2), a downstream target of CaMK2A, can activate the expression of CaMK2A, suggesting that MeCP2 and CaMK2A could form a positive feedback loop. In summary, we concluded that members of the glutamatergic signaling, CaMK2A, and MeCP2 were implicated in the cognitive ability of adolescents, and alternating in the CaMK2A expressing may have collective effects on the cognitive ability of youths.

scholarly journals ABCG2 regulatory single-nucleotide polymorphisms alter in vivo enhancer activity and expression

2017 ◽  
Vol 27 (12) ◽  
pp. 454-463 ◽  
Author(s):  
Rachel J. Eclov ◽  
Mee J. Kim ◽  
Aparna Chhibber ◽  
Robin P. Smith ◽  
Nadav Ahituv ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Enhancer Activity ◽  
Single Nucleotide
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