e gene
Recently Published Documents


TOTAL DOCUMENTS

735
(FIVE YEARS 109)

H-INDEX

53
(FIVE YEARS 5)

2022 ◽  
Vol 23 (2) ◽  
pp. 906
Author(s):  
Tao Li ◽  
Nianzhi Ning ◽  
Angelo Iacobino ◽  
Liangyan Zhang ◽  
Hui Wang ◽  
...  

Previously, a whole-genome comparison of three Clostridium butyricum type E strains from Italy and the United States with different C. botulinum type E strains indicated that the bont/e gene might be transferred between the two clostridia species through transposition. However, transposable elements (TEs) have never been identified close to the bont/e gene. Herein, we report the whole genome sequences for four neurotoxigenic C. butyricum type E strains that originated in China. An analysis of the obtained genome sequences revealed the presence of a novel putative TE upstream of the bont/e gene in the genome of all four strains. Two strains of environmental origin possessed an additional copy of the putative TE in their megaplasmid. Similar putative TEs were found in the megaplasmids and, less frequently, in the chromosomes of several C. butyricum strains, of which two were neurotoxigenic C. butyricum type E strains, and in the chromosome of a single C. botulinum type E strain. We speculate that the putative TE might potentially transpose the bont/e gene at the intracellular and inter-cellular levels. However, the occasional TE occurrence in the clostridia genomes might reflect rare transposition events.


Diagnostics ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 147
Author(s):  
Sergei A. Kiryanov ◽  
Tatiana A. Levina ◽  
Maria V. Konopleva ◽  
Anatoly P. Suslov

Sensitive and reliable diagnostic test systems based on real-time PCR are of great importance in the fight against the ongoing SARS-CoV-2 pandemic. The genetic variability of the SARS-CoV-2 virus leads to the accumulation of mutations, some of which may affect the sensitivity of modern PCR assays. The aim of this study was to search in Russian clinical samples for new mutations in SARS-CoV-2 gene N that can affect the detection by RT-PCR. In this study, the polymorphisms in the regions of the target gene N causing failed or poor detection of the target N in the RT-PCR assay on 12 selected samples were detected. Sequencing the entire N and E genes in these samples along with other 195 samples that were positive for both target regions was performed. Here, we identified a number of nonsynonymous mutations and one novel deletion in the N gene that affected the ability to detect a target in the N gene as well a few mutations in the E gene of SARS-CoV-2 that did not affect detection. Sequencing revealed that majority of the mutations in the N gene were located in the variable region between positions 193 and 235 aa, inside and nearby the phosphorylated serine-rich region of the protein N. This study highlights the importance of the further characterization of the genetic variability and evolution of gene N, the most common target for detecting SARS-CoV-2. The use of at least two targets for detecting SARS-CoV-2, including one for the E gene, will be necessary for reliable diagnostics.


Vaccines ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 51
Author(s):  
Svetlana V. Dentovskaya ◽  
Anastasia S. Vagaiskaya ◽  
Mikhail E. Platonov ◽  
Alexandra S. Trunyakova ◽  
Sergei A. Kotov ◽  
...  

To develop a modern plague vaccine, we used hypo-endotoxic Yersinia pestis bacterial ghosts (BGs) with combinations of genes encoding the bacteriophage ɸX174 lysis-mediating protein E and/or holin-endolysin systems from λ or L-413C phages. Expression of the protein E gene resulted in the BGs that retained the shape of the original bacterium. Co-expression of this gene with genes coding for holin-endolysin system of the phage L-413C caused formation of structures resembling collapsed sacs. Such structures, which have lost their rigidity, were also formed as a result of the expression of only the L-413C holin-endolysin genes. A similar holin-endolysin system from phage λ containing mutated holin gene S and intact genes R-Rz coding for the endolysins caused generation of mixtures of BGs that had (i) practically preserved and (ii) completely lost their original rigidity. The addition of protein E to the work of this system shifted the equilibrium in the mixture towards the collapsed sacs. The collapse of the structure of BGs can be explained by endolysis of peptidoglycan sacculi. Immunizations of laboratory animals with the variants of BGs followed by infection with a wild-type Y. pestis strain showed that bacterial envelopes protected only cavies. BGs with maximally hydrolyzed peptidoglycan had a greater protectivity compared to BGs with a preserved peptidoglycan skeleton.


2021 ◽  
Author(s):  
Noah Toppings ◽  
Lisa Oberding ◽  
Yi-Chan Lin ◽  
David Evans ◽  
Dylan R Pillai

Reverse transcription-PCR (RT-PCR) is the standard method of diagnosing COVID-19. An inconclusive test result occurs when one RT-PCR target is positive for SARS-CoV-2 and one RT-PCR target is negative within the same sample. An inconclusive result generally requires retesting. One reason why a sample may yield an inconclusive result is that one target is at a higher concentration than another target. It was hypothesized that concentration differences across targets may be due to the transcription of sub-genomic RNA, as this would result in an increase in the concentration of gene targets near the 3’ end of the SARS-CoV-2 genome.  A panel of six digital droplet (dd)PCR assays was designed to quantitate the ORF1, E-gene, and N-gene of SARS-CoV-2. This panel was used to quantify viral cultures of SARS-CoV-2 that were harvested during the eclipse phase and at peak infectivity in such a way as to maximize gene-to-gene copy ratios. Eleven clinical nasopharyngeal swabs were also tested with this panel. In culture, infected cells showed higher N-gene/ORF1 copy ratios than culture supernatants. Both the highest specific infectivity (copies/pfu) and the highest differences between gene targets were observed at 6 hours post-infection (eclipse phase) in infected cells. The same trends in the relative abundance of copies across different targets observed in infected cells was observed in clinical samples, though trends were more pronounced in infected cells. This study showed that a greater copy number of N-gene relative to E-gene and ORF1 transcripts could potentially explain inconclusive results for some RT-PCR tests on low viral load samples. The use of N-gene RT-PCR target(s) as opposed to ORF1 targets for routine testing is supported by this data.


2021 ◽  
Vol 12 ◽  
Author(s):  
Jianxin Zhou ◽  
Li Jiang ◽  
Sangui Yuan ◽  
Jiashang Huang ◽  
Quanhong Shi ◽  
...  

Objective: This study investigates the correlation between Apolipoprotein E gene (APOE) polymorphism and the incidence and delayed resolution of hemifacial spasms.Methods: The APOE genotypes of 151 patients with hemifacial spasm and 73 control cases were determined by cleaved amplification polymorphism sequence-tagged sites. The distribution of three APOE alleles (ε2, ε3, and ε4) in two groups and the delayed resolution rate in 6 genotypes were calculated and statistically analyzed.Results: The proportion of patients with APOE ε3/ε4 genotype in the hemifacial spasm group (25.17%) was significantly higher than that in the control group (12.33%) (P = 0.027). In terms of allele frequency, the proportion of the APOE ε4 allele in the hemifacial spasm group (15.56%) was significantly higher than that in the control group (6.85%) (P = 0.009). Meanwhile, the proportion of APOE ε4 allele carriers in the hemifacial spasm group (29.80%) was significantly higher than that in the control group (13.7%) (P = 0.009). Logistic regression analysis showed that the ε4 allele significantly increased the incidence of hemifacial spasm (OR 2.675, 95%CI 1.260-5.678, P = 0.010). Among the 32 patients with a delayed resolution, the ε3/ε3 and ε3/ε4 had the highest proportion in 6 genotypes. The delayed resolution rate of APOE ε3/ε4 (34.21%) was significantly higher than APOE ε3/ε3 (17.78%) (P < 0.05). The delayed resolution rate of APOE ε4 carriers was the highest (33.33%) in the 3 allele carriers, but there was no significant difference among the 3 allele carriers (P = 0.065).Conclusion: The polymorphism of APOE is relevant to the incidence rate of hemifacial spasms. APOE ε4 allele increases the incidence of hemifacial spasm. The APOE ε4 allele may promote the occurrence of delayed resolution.


2021 ◽  
Vol 16 (2) ◽  
pp. 209-236
Author(s):  
Larissa Nunes Durigan ◽  
Lilian Al-Chueyr Pereira Martins

O presente artigo se refere ao período da chamada genética clássica. Seu objetivo é discutir sobre as concepções e terminologia aplicadas ao material hereditário entre 1900 (“redescoberta” do trabalho de Mendel) e a publicação do livro The theory of the gene (1926) de Thomas Hunt Morgan (1866-1945), procurando averiguar se houve mudanças em relação a esses aspectos durante o período. O foco de nossa análise são as contribuições de dois grupos: o grupo britânico liderado por William Bateson (1861-1926) e o grupo norte-americano, liderado por Morgan. No período estudado, a terminologia foi mudando de “fator”, “caracteres”, “caracteres-unitários” e “gene”, que foi adotado a partir de 1926. Apesar de Bateson e Morgan considerarem que os agentes hereditários estivessem nas células germinativas, desconheciam sua composição. Esta pesquisa mostrou que durante o estabelecimento de uma nova área de estudo vão ocorrendo modificações em relação à terminologia empregada bem como à conotação dos termos, até que haja um consenso por parte da comunidade científica que os adote.


2021 ◽  
Author(s):  
Pragya D. Yadav ◽  
Gunjan Kumar ◽  
Aparna Mukherjee ◽  
Dimpal A. Nyayanit ◽  
Anita M. Shete ◽  
...  

AbstractThe aim of this study was to identify the SARS-CoV-2 lineages circulating in the pediatric population of India during the second wave of the pandemic. Clinical and demographic details linked with the nasopharyngeal/oropharyngeal swabs (NPS/OPS) collected from SARS-CoV-2 cases (n=583) aged 0-18 year and tested positive by real-time RT-PCR were retrieved from March to June 2021.Symptoms were reported among 37.2% of patients and 14.8% reported to be hospitalized. The E gene CT value had significant statistical difference at the point of sample collection when compared to that observed in the sequencing laboratory. Out of these 512 sequences 372 were VOCs, 51 were VOIs. Most common lineages observed were Delta, followed by Kappa, Alpha and B.1.36, seen in 65.82%, 9.96%, 6.83% and 4.68%, respectively in the study population. Overall, it was observed that Delta strain was the leading cause of SARS-CoV-2 infection in Indian children during the second wave of the pandemic. We emphasize on the need of continuous genomic surveillance in SARS-CoV-2 infection even amongst children.


Diagnostics ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2286
Author(s):  
Paolo Giuseppe Bonacci ◽  
Dalida Angela Bivona ◽  
Dafne Bongiorno ◽  
Stefano Stracquadanio ◽  
Mariacristina Massimino ◽  
...  

Starting in 2019, the COVID-19 pandemic is a global threat that is difficult to monitor. SARS-CoV-2 is known to undergo frequent mutations, including SNPs and deletions, which seem to be transmitted together, forming clusters that define specific lineages. Reverse-Transcription quantitative PCR (RT-qPCR) has been used for SARS-CoV-2 diagnosis and is still considered the gold standard method. Our Eukaryotic Host Pathogens Interaction (EHPI) laboratory received six SARS-CoV-2-positive samples from a Sicilian private analysis laboratory, four of which showed a dropout of the E gene. Our sequencing data revealed the presence of a synonymous mutation (c.26415 C > T, TAC > TAT) in the E gene of all four samples showing the dropout in RT-qPCR. Interestingly, these samples also harbored three other mutations (S137L—Orf1ab; N439K—S gene; A156S—N gene), which had a very low diffusion rate worldwide. This combination suggested that these mutations may be linked to each other and more common in a specific area than in the rest of the world. Thus, we decided to analyze the 103 sequences in our internal database in order to confirm or disprove our “mutation cluster hypothesis”. Within our database, one sample showed the synonymous mutation (c.26415 C > T, TAC > TAT) in the E gene. This work underlines the importance of territorial epidemiological surveillance by means of NGS and the sequencing of samples with clinical and or technical particularities, e.g., post-vaccine infections or RT-qPCR amplification failures, to allow for the early identification of these SNPs. This approach may be an effective method to detect new mutational clusters and thus to predict new emerging SARS-CoV-2 lineages before they spread globally.


2021 ◽  
Vol 26 (1) ◽  
Author(s):  
Yushen Jiang ◽  
Shanming Zhang ◽  
Hong Qin ◽  
Shuai Meng ◽  
Xuyi Deng ◽  
...  

Abstract Background The outbreak of novel coronavirus disease 2019 (COVID-19) has become a public health emergency of international concern. Quantitative testing of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus is demanded in evaluating the efficacy of antiviral drugs and vaccines and RT-PCR can be widely deployed in the clinical assay of viral loads. Here, we developed a quantitative RT-PCR method for SARS-CoV-2 virus detection in this study. Methods RT-PCR kits targeting E (envelope) gene, N (nucleocapsid) gene and RdRP (RNA-dependent RNA polymerase) gene of SARS-CoV-2 from Roche Diagnostics were evaluated and E gene kit was employed for quantitative detection of COVID-19 virus using Cobas Z480. Viral load was calculated according to the standard curve established by series dilution of an E-gene RNA standard provided by Tib-Molbiol (a division of Roche Diagnostics). Assay performance was evaluated. Results The performance of the assay is acceptable with limit of detection (LOD) below 10E1 copies/μL and lower limit of quantification (LLOQ) as 10E2 copies/μL. Conclusion A quantitative detection of the COVID-19 virus based on RT-PCR was established.


Sign in / Sign up

Export Citation Format

Share Document