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Sep 2023 DOI 10.14302/issn.2692-1537.ijcv-23-4660
SARS-CoV-2 real-time reverse-transcription PCR (rRT-PCR) is the most effective testing system available to combat COVID-19, given the absence of any specific treatment or vaccine. Moreover, numerous SARS-CoV-2 rRT-PCR kits have been approved under emergency-use-authorization (EUA) worldwide. In this article, we present a comparison of important performance features among five commercial RT-PCR assays. A total of consecutive nasopharyngeal (NPS) samples and oropharyngeal (OP) swabs were collected from 50 COVID-19 patients to analyze sensitivity and specificity. The results showed variations in sensitivity among all the RT-PCR kits examined. The Pishtaz teb assays demonstrated the highest positive percent agreement (PPA) of 95.2% (40/42), followed by Covitech (90.5% - 38/42), DaAn Gene (83.3% - 35/42), Sansure (66.66% - 28/42), and Power check of SARS- CoV-2 panel (64.3% - 27/42). Conversely, all five molecular assays demonstrated a negative percent agreement (NPA) of 100% (8/8). These findings provide a technical baseline for assessing the performance of five distinct commercial PCR assays for detecting SARS-CoV-2. They could prove practical and useful for laboratories seeking to purchase any of these assays for further clinical validation. Highlights ·Compared five COVID-19 RT-PCR kits approved and available by Iran Ministry of Health. ·Pishtaz teb's kit identified the highest number of positive clinical samples.
Mar 2024 DOI 10.14302/issn.2997-2108.jcc-23-4838
Among the reproductive cancers cervical cancer has special place, because the second most frequent cause of cancer-related death among women worldwide. The studies suggested that the PI3K/mTOR/AKT signaling pathway is associated with certain reproductive tumors. A lot of research is ongoing for understanding this pathway evidence of its role in promoting tumorigenesis and recent progress in the development of therapeutic agents that targeted PI3K/AKT. In this a single-arm study included 34 Azerbaijan population woman with HPV-negative cervical tumors. The core genes of PAM signaling pathway were analyzed using RT-PCR method. Our preliminary results suggested that tumorgenesis of HPV-negative cervical cancer patients approximately 25% associated with dysregulation of PAM signaling pathway reason which are core genes alteration. The overall survival times in the PAM-active and PAM-stable patients were not significantly varies. However, the main factor for overall survival times were treatment strategy: both PAM-active and PAM-stable patients who received radiation therapy alone had a shorter overall survival than patients who received radiation plus chemotherapy. The patients with alteration of ATK1 and mTOR genes in PAM signaling pathway had poor prognosis then patients with PIK3CA and PTEN mutation
Dec 2021 DOI 10.14302/issn.2692-1537.ijcv-21-4045
Introduction In December 2019, cases of serious illness causing pneumonia and death were first reported in Wuhan, China.2 The clinical features of Corona Virus Disease-19 (COVID-19) are ranging from asymptomatic to multi organ dysfunction. The disease can progress to pneumonia, respiratory failure and death.4 Thus, a tool is needed that can predict the severity and in-hospital mortality risk of a patient with COVID-19 Pneumonia. The PIRO (predisposition, insult, response, and organ dysfunction) scoring was developed for use in the emergency department to risk stratify sepsis cases.15 Eventually it was adapted in pneumonia cases to predict its severity. Objective To validate PIRO score as an assessment tool for COVID-19 mortality risk among patients with confirmed COVID-19 RT-PCR test among patients aged 19 and above admitted in World Citi Medical Center from March 2020 to August 2020 Methods This study included 93 patients aged 19 and above admitted in World Citi Medical Center with a primary diagnosis of COVID-19 Confirmed with pneumonia between March 2020 to August 2020. The patients’ charts were retrieved from the hospital medical records and case notes were reviewed. A severity assessment score was developed based on PIRO score (Predisposition comorbidities and age; Insult multilobar opacities and viremia; Response shock and hypoxemia; Organ Dysfunciton) were extracted. The patients were stratified in four levels of risk: a)Low,0-2 points; b)Mild,3 points; c)High,4 points; d)Very High,5-8 points. The PIRO score and the clinical outcome were compared. The discriminative ability of PIRO score to predict mortality risk was evaluated under receiver operating characteristic curve (AUC). Results The PIRO score had an excellent predictive ability for in-hospital mortality (AUC0.9197). Analysis of variance showed that higher levels of PIRO scores were significantly associated with higher mortality (p<0.001). Patients with Mild PIRO risk category were 98.65% less likely to expire (p<0.001, 95%CI 0.0015) and High PIRO risk category were 94.47% less likely to expire (p<0.001, 95%CI 0.0124), both compared to patients with Very high PIRO risk category. Finally, Very High PIRO risk category were more than 44 times likely to expire compared to patients with Low, Mild and High PIRO risk category (p<0.001, 95%CI 11.738). Conclusions The PIRO score is a valid risk model that can be used to predict in-hospital mortality, that can help clinicians provide timely and accurate assessment, and hence appropriate management to patients with COVID-19 Pneumonia.
Dec 2021 DOI 10.14302/issn.2575-1212.jvhc-21-4034
In bovine tuberculosis (bTB), cellular, humoral, or both types of immune responses have been observed. The purpose of this study was to examine the immune status of tuberculous cows based on the differential cytokine gene expression associated with Th1 (IFN-γ, IL-2), or Th2 (IL-4, IL-10) responses. Twenty-three (23) cows belonging to a dairy herd located in a rural region of the State of Hidalgo, México, were selected for the study. Single Intradermal Comparative Cervical Tuberculin (SICCT) Test, Interferon-Gamma (IFN-γ) Release Assay (BOVIGAM), and Enzyme-Linked Immunosorbent Assay (ELISA) were used for detection of cattle infected by M. bovis. Thirteen cows were positive to all the tests (Group 1); ten cows were positive only to ELISA (Group 2), and the remaining Group (Group 3, control) included cows negative to all the tests. Peripheral blood mononuclear cells (PBMC) from animals were in vitro stimulated by bovin purified protein derivative (PPD), avian PPD, and Concanavalin A (Con A) mitogen for 72h. Changes in the levels of expression of mRNA of the respective cytokines was measured by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) using β-actin gene as internal control. In group 1, PPD bovis and Con A-stimulated cells exhibited high production of IFN-γ, IL-2 and IL-4, but not IL-10. In contrast, PPD avium-stimulated cells displayed a low production of cytokine transcripts. In group 2, cells showed a significant production of IL-10 in response to bovine PPD (P< 0.001). In the control group, a high production of IFN-γ and IL-2 was observed only in Con A-stimulated cells. Post-mortem examinations in animals of group 1 showed slight and medium lesions in lymph nodes, whereas in group 2, the lesions were more extensive. Results indicate differences on gene expression levels of cytokines considered to determine balance in Th1/Th2 response among the evaluated groups. In addition, high levels of antibodies against M. bovis and high IL-10 expression in PBMC together are indicators of progressive bTB when both tuberculin test and IFN-γ assay are negative in tuberculous anergic cattle. Inclusion of serology and IL-10 cytokine expression in in the diagnosis checklist improves detection of infected cattle to help control bovine tuberculosis.
Aug 2021 DOI 10.14302/issn.2692-1537.ijcv-21-3924
This study measures the impact of chloroquine (CQ) therapy in reducing SARS-CoV-2 viral load in infected individuals and hence its transmissibility by describing changes in nasopharyngeal SARS-CoV-2 RNA kinetics in patients receiving standard of care (SOC) or CQ +/- ritonavir-boosted lopinavir (LPV/r). The nasopharyngeal (NP) samples were collected from mild COVID-19 patients admitted at Bamrasnaradura Infectious Diseases Institute between March and April of 2020. These patients either received SOC, or a high dose of CQ with loading dose, or high dose of CQ plus LPV/r. The samples were tested at AFRIMS using a quantitative RT-PCR assay. Levels of CQ in the plasma were measured 6 days post initiation of their treatment. In some instances, viral isolation was attempted to determine SARS-CoV-2 viability. Analyses of the clinical outcomes showed that CQ +/- lopinavir did not contribute significantly to decreasing the number of days with detected SARS-CoV-2 RNA. Viral NP GEs declined faster in the CQ group, but benefits diminished rapidly with delays in treatment initiation. Funding Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch (GEIS-AFHSB) for all research-related activities at the AFRIMS
May 2021 DOI 10.14302/issn.2690-4721.ijcm-21-3835
Objective Real-time surveillance of SARS-CoV-2 variants of concern (VOC) is of essential public health importance. Rapid Antigen Detection Tests (RAgDT) have become first-line COVID-19 diagnostic methods in many regions, but this strategy can hamper the surveillance of the virus variants due to their decentralized performance. The aim of this study was to assess the usefulness of the remaining sample of a widely used RAgDT (Panbio) for the surveillance of the B.1.1.7 VOC using molecular methods. Methods Symptomatic individuals and asymptomatic close contacts of confirmed cases were routinely screened for SARS-CoV-2 infection using the RAgDT in Primary Health Care Centers. After performing the test, the extraction tubes containing the remaining biological material of RAgDT-positive cases were sent to the clinical microbiology laboratory where RT-PCRs detecting key mutations of the VOC were conducted. Results A valid result was obtained in 1770/1812 (97.7%) RAgDT-positive cases. Variant B.1.1.7 was detected in 34.7% of the patients, increasing from 0% to 87.7% between the weeks beginning January 4 and March 15, 2021. Conclusion The sample remaining after performing the Panbio RAgDT allowed to monitor the emergence and circulation of the B.1.1.7, greatly improving the population screened for the molecular study of SARS-CoV-2 variants.
Sep 2020 DOI 10.14302/issn.2379-7835.ijn-20-3369
Background Since swine flu has been declared pandemic in 2009 it has become a major challenging public-health problem associated with high morbidity and mortality. 25(OH)D deficiency is also pandemic and has been reported to be clinically correlated with decreased immunity and respiratory infections. The possible role of vitamin D in infections is implied from its impact on the innate and adaptive immune responses. This study is planned to evaluate clinical significance of 25(OH)D status on course and outcome in hospitalized cases of swine flu and to compare it with normal healthy subjects living in the same vicinity to evaluate if vitamin D is having any protective effect. Material & Methods Present prospective cross-sectional study was conducted on 79 RT-PCR confirmed cases of swine flu admitted during recent epidemic. All patients were evaluated thoroughly by clinical history physical examination and laboratory investigations as per Performa and followed-up during hospital stay. 25-hydroxyvitamin D (25(OH)D) estimation was done by electro-chemiluminescent Assay in all the cases and it was also done in 36 normal healthy family members of study patients living in the same vicinity (control group). Results High prevalence (70.9%) of low (≤30ng/ml) status of 25(OH)D was observed in cases of swine flu as compared to control group. 25(OH)D status was associated with severity of illness. Mean value of 25(OH)D in mechanically ventilated patients was 9.81±6.43 while it was 22.76±11.35 ng/ml in patients who do not required ventilation (p<0.05). Mean 25(OH)D level in patients who stayed in hospital for <5 days was 28.60±8.79 ng/ml, 24.18±11.67 for 6-10 days and 8.23±2.12 for >10 days (p<0.01). Mean value of 25(OH)D in patients who died was 9.59±5.90 ng/ml as compared to 23.13±11.62 ng/ml who survived (p<0.01). Conclusion Our study suggests that 25(OH)D may have preventive role for swine flu infection. Low level of 25(OH)D is associated with high morbidity in terms of increase requirement for mechanical ventilation, multiorgan dysfunction and long duration of hospital stay. 25(OH)D deficiency is associated with high mortality in swine flu. 25(OH)D status should be given due consideration in high risk patients especially during winter season.
Nov 2018
Pre-adipocytes are the precursors with the potential to make new fat cells during adipose tissue expansion. Nevertheless, the pre-adipocytes behaviors, and their possible roles in energy homeostasis have long been overlooked. Our previous study implicates that interleukin-4 (IL-4) plays a positive metabolic role by promoting insulin sensitivity and inhibiting lipid accumulation. Besides, abundant evidence shows the involvement of matrix metalloproteinase-2 (MMP-2) in the process of adipose tissue expansion. The present study aimed at examining the cross talk among glucose, insulin and IL-4 on regulating MMP-2 expression and activity in 3T3-L1 pre-adipocytes. Effects of insulin and/or IL-4 on MMP-2 expression and activity were examined in pre-adipocytes under euglycemic or hyperglycemic environment by RT-PCR and gelatin zymography, respectively. Our results revealed that glucose level is a pre-requisite for pre-adipocytes responding to insulin and/or IL-4 treatment. In high glucose-containing environment, short-term acute insulin treatment (AI) and long-term chronic insulin exposure (CI) showed opposite regulation to MMP-2 expression and activity. Interestingly, the dominant MMPs regulatory role of CI under euglycemic condition was attenuated in cells exposed to high glucose concentration. Our results suggest pre-adipocytes may participate in the process of increasing adiposity, diabetic onset and diabetic complications through ECM alterations resulted from the insulin- and/or glucose- mediated changes of MMP-2 activity. The present study uncovers novel observations regarding pre-adipocytes behaviors.
Aug 2018 DOI 10.14302/issn.2641-9181.ijnr-18-2195
Objectives: An association between the measles virus and Hodgkin lymphoma has been disclosed by our laboratory in Beer-Sheva, starting in 2003. We question the refutation of our study and the absence of interest among experts. Methodology: It was based on immunohistochemistry with commercial, as well as experimental anti-measles antibodies. It relied also on RT-PCR and in situ hybridization evidence of measles virus RNA. Key Results: At this stage (2004), the link between the virus and the lymphoma was essentially descriptive. The first and last response to our challenge appeared in 2007, in the form of doublet articles, in the same issue of a major cancer journal. The two European research groups responding, rejected categorically our findings by proposing different arguments. Major Conclusion: As reservations to these reactions became soon apparent, a series of papers from our laboratory were published. These articles concerned the evidence of a relationship between the measles virus and additional categories of cancers. Different malignancies in which this virus was not expressed at all, were also described. A further study suggested a mechanism by which the measles virus may activate lymphomagenesis in classic Hodgkin lymphoma. To our dismay, and in spite of repeated calls to verify the various results, no further response was obtained from international experts.
Nov 2017 DOI 10.14302/issn.2638-4469.japb-17-1838
Strawberry powdery mildew, caused by Podosphaeraaphanis is a major fungal disease that affects strawberry yield and quality. In the model plant species Arabidopsis and the crop plants barley, tomato and pea, the Mildew resistance locus O (MLO) proteins have been found to be required for powdery mildew susceptibility. The present study, based on the sequence of a wild plum (Prunus americana) MLO protein, identified 16 MLO genes within the genome of woodland strawberry, Fragaria vesca and examined their expression pattern in response to powdery mildew infection in three diploid strawberry cultivars. Phylogenetic analysis showed that the FvMLO genes can be classified into six clades. Four FvMLO genes were grouped into clade III, which comprises MLO genes from Arabidopsis, tomato and grapevine that mediate powdery mildew susceptibility. A RNA-seq analysis of two diploid strawberry cultivars, F. vescassp. vesca accession Hawaii 4 (HW) and F. vesca f. semperflorens line “Yellow Wonder 5AF7” (YW) at 1 d (1 DAI) and 8 d (8 DAI) after infection showed the expression of 12 out of the 16 FvMLO genes. The comparison of Fragments Per Kilobase of transcript per Million mapped reads (FPKM values) detected by RNA-seq and expression values of qRT-PCR for FvMLO genes showed substantial agreement. The FvMLO3 gene, which was grouped in clade III and orthologous to the Arabidopsis,tomato and grapevine genes, was highly expressed in YW compared to other FvMLO genes across varieties. The results showed that FvMLO genes can be used as potential candidates to engineer powdery mildew resistance in strawberry based on MLO suppression or genome editing.
Nov 2017 DOI 10.14302/issn.2576-6694.jbbs-17-1744
Aim: Colorectal cancer is one of the most commonly diagnosed cancers in the world. Cell adhesion molecules play an important role in the progression of various cancers. It has been shown that the high level expression of some Cell adhesion molecule could be a new diagnostic factor for several cancers. Vascular cell adhesion molecule 1(VCAM1) is a cell surface glycoprotein that is expressed in the endothelium activated by cytokine. Generally, VCAM-1 expression level is very poor in normal adult tissue endothelial cells. According to the above explanation, this study was conducted to investigate the expression of VCAM-1 in tumoral tissues and adjacent normal tissues in Iranian colorectal cancer patients to its relation with clinicopathological Features in patients with cancer. Methods: In this study, 60 tumoral tissues and 39 adjacent normal tumor tissues were evaluated using reverse transcription-polymerase chain reaction (RT-PCR) technique. Conclusion: A significant correlation was found between VCAM-1 expression level and the stage, lymph nodes involvement, tumor progression factor of cancer and sex. Interestingly, VCAM-1 expression not observed in tumors with stage0. No association was seen between VCAM-1 expression and other clinical features such as age, size of the tumor, metastasis and the number of lymph nodes. These findings suggest that VCAM-1 expression level may reflected disease progression and elevation in VCAM-1 has prognostic significance in patients with colorectal carcinoma.
Feb 2016 DOI 10.14302/issn.2575-7881.jdrr-15-849
Reverse Transcription Polymerase Chain Reaction (RT-PCR) using new designed primers pair for Heat Shock Protein70 homologue (HSP70h) of Olive leaf yellowing-associated virus revealed 667 amplified product of 10 olive accessions collected from various olive-growing regions in Tunisia. Amplicons were cloned and sequenced. The sequences were deposited in the international databases. Pairwise sequence comparisons among 10 Tunisian isolates along with a reference sequence (AJ440010) extracted from GenBank revealed a nucleotide identity of 86.06-99.40 and an amino acid similarity of 91.89-99.55. Sequence multiple alignments were searched for evidence of recombination using three methods, ie. Differences of Sums of Squares (DSS) implemented in TOPALi v2.5 software and Single Breakpoint (SBP) along with GARD, a genetic algorithm, both incorporated in HyPhy package. All used methods pointed out the presence of putative breaking points in partially sequenced HSP70h-coding gene. Since failing to account for recombination can mislead the phylogeny inference and can elevate the false positive error rate in positive selection assessment, the use of GARD resulted in the reconstruction of different phylogenies on the left as well as on the right sides of putative recombination breaking points, and the 11 accessions were distributed into at least three clusters compared to MEGA6 software which delineated only two clades. Nonetheless, by dividing the aligned sequences at breakpoints into separate sequence sets, MEGA6 delineated a clustering pattern different from the former two. As a result, recombination reshuffled the affiliation of the different accessions to the clusters. Analysis of selection pressures exerted on HSP70h encoded protein using different models (SLAC, IFEL, FEL, REL, PARRIS, FUBAR, MEME, GA Branch, and PRIME) taking into account recombination, and implemented in HyPhy package, revealed that it underwent predominantly purifying selection as confirmed by Tajima’s D, Fu and Li’s D and F tests, and SNAP algorithm. However, a few sites were also under positive selection as assessed by various models such as FEL, IFEL, REL, MEME, and PRIME.
May 2015 DOI 10.14302/issn.2471-7061.jcrc-14-574
Colon cancer has a five-year survival of 64.7%, and about 50,000 people are expected to die from colon cancer this year. Patients with metastatic colorectal cancer have a significantly worse prognosis, a 12.9% five-year survival. This emphasizes the need for strategies to inhibit the growth and metastases of colorectal cancer. Prostate apoptosis response protein 4 (Par-4) is a pro-apoptotic protein that has been shown to mediate apoptosis in response to stimuli, such as chemotherapeutics and radiation. Recombinant Par-4 protein has been shown to reduce the occurrence of Lewis lung carcinoma metastases in-vivo; however, the mechanism by which Par-4 can inhibit metastasis has not been elucidated. In this study, human colon cancer cell lines - SW480 and SW620 - were transfected with Par-4 plasmid or anti-Par-4 shRNA, and the effect on metastasis was examined. Par-4 overexpression inhibited cell migration and invasion, while Par-4 knockdown promoted it. Moreover, the morphology of SW620 cells was altered when Par-4 levels were increased. The change was characteristic of a mesenchymal-to-epithelial transition (MET) in these cells. MET can be induced by upregulation of E-cadherin expression, and RT-PCR and Western blot analyses showed that E-cadherin mRNA and protein levels, respectively, were increased in the Par-4 overexpressing cells concomitant with a decrease in vimentin. The results of this study demonstrate the potential of Par-4 in colon cancer therapy, not only in primary tumors but also in metastatic cells.
Feb 2014 DOI 10.14302/issn.2372-6601.jhor-13-358
Acute lymphoblastic leukemia (ALL) is a rapid form of leukemia characterized by clonal proliferation and accumulation of immature hematopoietic stem cells of the lymphoid lineage in the bone marrow as well as peripheral blood. Chromosomal aberrations identified in childhood ALL have an important role in disease diagnosis, prognosis and management. We present the results of hematologic, immunophenotypic, cytogenetic, FISH and Multiplex RT-PCR analysis of a 6-year-old boy diagnosed with B-cell precursor Acute Lymphoblastic Leukemia (BCP- ALL). In this study, we identified a novel chromosomal translocation t(10;15)(q22;q22) by cytogenetic and FISH analysis. To the best of our knowledge, this is the first report of this novel chromosomal translocation in this subset of ALL and has not yet been reported elsewhere. This rearrangement may include certain cancer associated tumor suppressor gene(s) or genes involved in apoptosis and transcription regulation, which on loss of normal function may lead to leukaemogenesis.
Jan 2014 DOI 10.14302/issn.2326-0793.jpgr-13-355
FIP-2 is a multifunctional protein which is involved in various cellular processes. Using different approaches we investigated its regulatory activity. The microarray analysis has shown that FIP-2 substantially altered the expression of 75 genes (35+/40-) from different functional groups with maximal presentation in “Signal transduction” and “Transcription regulation”. Real time RT-PCR indicated significant elevation in the transcription of chemokines, particularly IL-8 (CXCL8). Production of IL-8 in HEK293 cells dramatically increased with FIP-2 overexpression. We also demonstrated that FIP-2 induced activation of IL-8 promoter activity through NF-kB binding site. Additionally, we showed that FIP-2 could interact with PAK3 and increase its kinase activity. Overall, we demonstrated the role of FIP-2 in the regulation of chemokines (IL-8, MPIF-1, MCP-1) and kinases (PAK3, ALK).