Phylogenetic analysis of prevalent tuberculosis and non-Tuberculosis Mycobacteria in Isfahan, Iran, based on a 360 bp sequence of the rpoB gene

Background: Taxonomic and phylogenetic studies of Mycobacterium species have been based around the 16sRNA gene for many years. However, due to the high strain similarity between species in the Mycobacterium genus (94.3 - 100), defining a valid phylogenetic tree is difficult; consequently, its use in estimating the boundaries between species is limited. The sequence of the rpoB gene makes it an appropriate gene for phylogenetic analysis, especially in bacteria with limited variation. Objectives: In the present study, a 360bp sequence of rpoB was used for precise classification of Mycobacterium strains isolated in Isfahan, Iran. Materials and Methods: From February to October 2013, 57 clinical and environmental isolates were collected, subcultured, and identified by phenotypic methods. After DNA extraction, a 360bp fragment was PCR-amplified and sequenced. The phylogenetic tree was constructed based on consensus sequence data, using MEGA5 software. Results: Slow and fast-growing groups of the Mycobacterium strains were clearly differentiated based on the constructed tree of 56 common Mycobacterium isolates. Each species with a unique title in the tree was identified; in total, 13 nods with a bootstrap value of over 50 were supported. Among the slow-growing group was Mycobacterium kansasii, with M. tuberculosis in a cluster with a bootstrap value of 98 and M. gordonae in another cluster with a bootstrap value of 90. In the fast-growing group, one cluster with a bootstrap value of 89 was defined, including all fast-growing members present in this study. Conclusions: The results suggest that only the application of the rpoB gene sequence is sufficient for taxonomic categorization and definition of a new Mycobacterium species, due to its high resolution power and proper variation in its sequence (85 - 100); the resulting tree has high validity. � 2016, Ahvaz Jundishapur University of Medical Sciences

Human papilloma virus and breast cancer: The role of inflammation and viral expressed proteins

Background: Breast cancer is currently the most common neoplasm diagnosed in women globally. There is a growing body of evidence to suggest that human papillomavirus (HPV) infection may play a key role in invasiveness of breast cancer. The aim of this study was to determine the presence of HPV in patients with breast cancer and its possible association with cancer progression. Methods: Breast specimens were collected from 72 patients with breast cancer and 31 healthy controls. The presence of HPV was investigated by polymerase chain reaction (PCR) and genotyping was performed for positive cases. We also evaluated the viral factors such as E6, E2, and E7 in HPV positive cases. Enzyme-linked immunosorbent assay (ELISA (and Real-time PCR techniques were used to measure the expression level of anti-carcinogenic genes, such as p53, retinoblastoma (RB), breast and ovarian cancer susceptibility gene (BRCA1, BRCA2) and inflammatory cytokines, including tumor necrosis factor α (TNF-α), transforming growth factor β (TGF-β), nuclear factor-kB (NF-kB), and different interleukins ILs (IL-1,IL6, and IL-17). Results: The HPV DNA was detected in 48.6% of breast cancer samples, whereas only 16.1% of controls were positive for HPV. We observed statistically significant differences between breast cancer patients and HPV presence (P = 0.003). HPV type 18 was the most prevalent virus genotype in patients. The expression of P53, RB, BRCA1, and BRCA2 were decreased in patients with HPV-positive breast cancer as compared to HPV-negative breast cancer and healthy controls. (All P-values were less than 0.05). The presence of the HPV was associated with increased inflammatory cytokines (IL-1, IL-6, IL-17, TGF-β, TNF-α, and NF-kB) and tumor progression. Conclusion: The present study demonstrated that HPV infection may implicate in the development of some types of breast cancer. © 2019 The Author(s)

Human papilloma virus and breast cancer: The role of inflammation and viral expressed proteins

Background: Breast cancer is currently the most common neoplasm diagnosed in women globally. There is a growing body of evidence to suggest that human papillomavirus (HPV) infection may play a key role in invasiveness of breast cancer. The aim of this study was to determine the presence of HPV in patients with breast cancer and its possible association with cancer progression. Methods: Breast specimens were collected from 72 patients with breast cancer and 31 healthy controls. The presence of HPV was investigated by polymerase chain reaction (PCR) and genotyping was performed for positive cases. We also evaluated the viral factors such as E6, E2, and E7 in HPV positive cases. Enzyme-linked immunosorbent assay (ELISA (and Real-time PCR techniques were used to measure the expression level of anti-carcinogenic genes, such as p53, retinoblastoma (RB), breast and ovarian cancer susceptibility gene (BRCA1, BRCA2) and inflammatory cytokines, including tumor necrosis factor α (TNF-α), transforming growth factor β (TGF-β), nuclear factor-kB (NF-kB), and different interleukins [ILs] (IL-1,IL6, and IL-17). Results: The HPV DNA was detected in 48.6% of breast cancer samples, whereas only 16.1% of controls were positive for HPV. We observed statistically significant differences between breast cancer patients and HPV presence (P = 0.003). HPV type 18 was the most prevalent virus genotype in patients. The expression of P53, RB, BRCA1, and BRCA2 were decreased in patients with HPV-positive breast cancer as compared to HPV-negative breast cancer and healthy controls. (All P-values were less than 0.05). The presence of the HPV was associated with increased inflammatory cytokines (IL-1, IL-6, IL-17, TGF-β, TNF-α, and NF-kB) and tumor progression. Conclusion: The present study demonstrated that HPV infection may implicate in the development of some types of breast cance

The role of viral and bacterial infections in the pathogenesis of IPF: a systematic review and meta-analysis

Background: Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease. Several risk factors such as smoking, air pollution, inhaled toxins, high body mass index and infectious agents are involved in the pathogenesis of IPF. In the present study, this meta-analysis study investigates the prevalence of viral and bacterial infections in the IPF patients and any possible association between these infections with pathogenesis of IPF. Methods: The authors carried out this systematic literature review from different reliable databases such as PubMed, ISI Web of Science, Scopus and Google Scholar to December 2020.Keywords used were the following �Idiopathic pulmonary fibrosis�, �Infection�, �Bacterial Infection� and �Viral Infection�, alone or combined together with the Boolean operators "OR�, �AND� and �NOT� in the Title/Abstract/Keywords field. Pooled proportion and its 95 CI were used to assess the prevalence of viral and bacterial infections in the IPF patients. Results: In this systematic review and meta-analyses, 32 studies were selected based on the exclusion/inclusion criteria. Geographical distribution of included studies was: eight studies in American people, 8; in European people, 15 in Asians, and one in Africans. The pooled prevalence for viral and bacterial infections w ere 53.72 (95 CI 38.1�69.1) and 31.21 (95 CI 19.9�43.7), respectively. The highest and lowest prevalence of viral infections was HSV (77.7 95 CI 38.48�99.32), EBV (72.02, 95 CI 44.65�90.79) and Influenza A (7.3, 95 CI 2.66�42.45), respectively. Whereas the highest and lowest prevalence in bacterial infections were related to Streptococcus sp. (99.49, 95 CI 96.44�99.9) and Raoultella (1.2, 95 CI 0.2�3.08), respectively. Conclusions: The results of this review were confirmed that the presence of viral and bacterial infections are the risk factors in the pathogenesis of IPF. In further analyses, which have never been shown in the previous studies, we revealed the geographic variations in the association strengths and emphasized other methodological parameters (e.g., detection method). Also, our study supports the hypothesis that respiratory infection could play a key role in the pathogenesis of IP. © 2021, The Author(s)

Multimeric recombinant M2e protein-based ELISA: A significant improvement in differentiating avian influenza infected chickens from vaccinated ones

Killed avian influenza virus (AIV) vaccines have been used to control H5N1 infections in countries where the virus is endemic. Distinguishing vaccinated from naturally infected birds (DIVA) in such situations however, has become a major challenge. Recently, we introduced the recombinant ectodomain of the M2 protein (M2e) of H5N1 subtype as a novel tool for an ELISA based DIVA test. Despite being antigenic in natural infection the monomer form of the M2e used in ELISA had limited antigenicity and consequently poor diagnostic capability. To address this shortcoming, we evaluated the use of four tandem copies of M2e (tM2e) for increased efficiency of M2e antibody detection. The tM2e gene of H5N1 strain from Indonesia (A/Indonesia/CDC540/2006) was cloned into a pMAL- p4x expression vector and expressed in E.coli as a recombinant tM2e-MBP or M2e-MBP proteins. Both of these, M2e and tM2e antigens reacted with sera obtained from chickens following live H5N1 infection but not with sera from vaccinated birds. A significantly stronger M2e antibody reaction was observed with the tM2e compared to M2e antigen. Western blotting also supported the superiority of tM2e over M2e in detection of specific M2e antibodies against live H5N1 infection. Results from this study demonstrate that M2e tetramer is a better antigen than single M2e and could be more suitable for an ELISA based DIVA test.Farshid Hadifar, Jagoda Ignjatovic, Simson Tarigan, Risa Indriani, Esmaeil Ebrahimie, Noor Haliza Hasan, Andrea McWhorter, Sophie Putland, Abdulghaffar Ownagh, Farhid Hemmatzade

Prevalence of influenza A infection in the Middle-East: A systematic review and meta-analysis

Objective: This systematic review and meta-analysis was performed to determine the prevalence rate of influenza virus from different parts of Middle East region, and present an overall relative frequency (RF) for this region. Methods: The authors performed a systematic literature review from several reliable databases such as PubMed, ISI Web of Science and Scopus during 2000�2016. Furthermore, the keywords of this research were �Influenza�, �Subtype�, �Seroprevalence�, �Incidence�, �Seroepidemiology�, �H1N1�, �H3N2�, �H5N1�, �H9N2�, �Middle-East� and �Meta-analysis�. The reported data were selected according to inclusion and exclusion criteria. Results: The authors selected 71 studies out of 1147 for the present review. The overall estimation of the prevalence of influenza virus was 10.2 95% confidence interval (CI): 10.1%�10.3%. However, based on our records, the evident heterogeneity of influenza virus was observed among the studies (Cochran Q test, P value <.001 and I-squared = 100%). It should be noted that influenza virus infection's RF varied from 0.5% in Qatar to 70% in Syria. Conclusions: The results of this review are remarkable, they show that influenza infection RF is variable due to several factors. Thus, further researches should be taken to minimize the emergence and transmission of influenza virus. © 2018 John Wiley & Sons Lt

Prevalence of influenza A infection in the Middle-East: A systematic review and meta-analysis

Objective: This systematic review and meta-analysis was performed to determine the prevalence rate of influenza virus from different parts of Middle East region, and present an overall relative frequency (RF) for this region. Methods: The authors performed a systematic literature review from several reliable databases such as PubMed, ISI Web of Science and Scopus during 2000�2016. Furthermore, the keywords of this research were �Influenza�, �Subtype�, �Seroprevalence�, �Incidence�, �Seroepidemiology�, �H1N1�, �H3N2�, �H5N1�, �H9N2�, �Middle-East� and �Meta-analysis�. The reported data were selected according to inclusion and exclusion criteria. Results: The authors selected 71 studies out of 1147 for the present review. The overall estimation of the prevalence of influenza virus was 10.2 95% confidence interval (CI): 10.1%�10.3%. However, based on our records, the evident heterogeneity of influenza virus was observed among the studies (Cochran Q test, P value <.001 and I-squared = 100%). It should be noted that influenza virus infection's RF varied from 0.5% in Qatar to 70% in Syria. Conclusions: The results of this review are remarkable, they show that influenza infection RF is variable due to several factors. Thus, further researches should be taken to minimize the emergence and transmission of influenza virus. © 2018 John Wiley & Sons Lt

Epitope mapping of avian influenza m2e protein: different species recognise various epitopes

Published: June 30, 2016A common approach for developing diagnostic tests for influenza virus detection is the use of mouse or rabbit monoclonal and/or polyclonal antibodies against a target antigen of the virus. However, comparative mapping of the target antigen using antibodies from different animal sources has not been evaluated before. This is important because identification of antigenic determinants of the target antigen in different species plays a central role to ensure the efficiency of a diagnostic test, such as competitive ELISA or immunohistochemistry-based tests. Interest in the matrix 2 ectodomain (M2e) protein of avian influenza virus (AIV) as a candidate for a universal vaccine and also as a marker for detection of virus infection in vaccinated animals (DIVA) is the rationale for the selection of this protein for comparative mapping evaluation. This study aimed to map the epitopes of the M2e protein of avian influenza virus H5N1 using chicken, mouse and rabbit monoclonal or monospecific antibodies. Our findings revealed that rabbit antibodies (rAbs) recognized epitope 6EVETPTRN13 of the M2e, located at the N-terminal of the protein, while mouse (mAb) and chicken antibodies (cAbs) recognized epitope 10PTRNEWECK18, located at the centre region of the protein. The findings highlighted the difference between the M2e antigenic determinants recognized by different species that emphasized the importance of comparative mapping of antibody reactivity from different animals to the same antigen, especially in the case of multi-host infectious agents such as influenza. The findings are of importance for antigenic mapping, as well as diagnostic test and vaccine development.Noor Haliza Hasan, Esmaeil Ebrahimie, Jagoda Ignjatovic, Simson Tarigan, Anne Peaston, Farhid Hemmatzade

An emotional journey: Detecting emotion trajectories in dutch customer service dialogues

The ability to track fine-grained emotions in customer service dialogues has many real-world applications, but has not been studied extensively. This paper measures the potential of prediction models on that task, based on a real-world dataset of Dutch Twitter conversations in the domain of customer service. We find that modeling emotion trajectories has a small, but measurable benefit compared to predictions based on isolated turns. The models used in our study are shown to generalize well to different companies and economic sectors

Genetic diversity of Mycobacterium tuberculosis isolates causing pulmonary and extrapulmonary tuberculosis in the capital of Iran

Objectives: Evaluation of the genetic diversity of Mycobacterium tuberculosis (M.tb) and determining if the association between a specific genotype and the site of infection is crucial. Accordingly, the current study aimed at comparing predominant M.tb genotypes in pulmonary (PTB) and extrapulmonary tuberculosis (EPTB) isolates circulating in the capital of Iran. Methods: The genetic diversity of culture-confirmed PTB and EPTB isolates were evaluated by Spoligotyping and MIRU-VNTR (mycobacterial interspersed repetitive-unit�variable-number tandem-repeat) typing methods. Genotyping data were analyzed with SITVIT, MIRU-VNTRplus, and TBminer databases. To assess adjusted associations, chi-square/the Fisher exact test and multiple logistic regression model were applied. Results: URAL2 (NEW-1) (28/88; 31.8) and CAS1-DELHI (25/84; 29.8) genotypes were predominant in EPTB and PTB strains, respectively. Based on MIRU-VNTR typing, 158 different MIRU-VNTR patterns were identified. Clustering rate and minimum estimate of the proportion of TB caused by recent transmission was 4.1 and 8.1, respectively. Conclusions: The current study provided new insight into circulating genotypes of M.tb in PTB and EPTB patients in Tehran, Iran. This low percentage of TB transmission rate, demonstrated that mode of TB transmission was mainly associated with reactivation of latent TB rather than recently transmitted infection in this region. There was no significant difference in the association between the genotypes of M.tb strains and the site of the disease. © 2018 Elsevier Inc