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Molecular Genetics & Diagnosis of Infectious Diseases
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Molecular Genetics & Diagnosis of Infectious Diseases

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (15 June 2023) | Viewed by 9748

Special Issue Editors

Prof. Dr. Abrar Hussain

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Guest Editor
Department of Biotechnology, Balochistan University of Information Technology and Management Sciences, Quetta, Balochistan, Pakistan
Interests: molecular techniques; infectious disease; prevalence; regional and global
Dr. Irshad ur Rehman

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Guest Editor
Centre for Biotechnology and Microbiology, University of Peshawar, Khyber Pakhtunkhwa, Pakistan
Interests: culture; viral; sequencing; disease

Special Issue Information

Dear Colleagues,

Infectious diseases pose a noteworthy public health risk, and infectious disease epidemics can have significant community, political, and economic costs. Historical outbreak conditions offer ways for designing an effective response to infectious disease events. In such circumstances, molecular diagnostics have important applications in screening and confirmation of asymptomatic infections, such as through syndromic therapy.

The first step to counter an infection is correct diagnosis, which depends upon important parameters such as assay sensitivity and specificity. These parameters can be used in the evaluation of a newly developed technique, after comparison with a reference gold standard method, to differentiate among the true positive and true negative.

In the last two decades, nucleic acid-based approaches have focused on the detection of either a single pathogen or multiple pathogens in a multiplex assay format, previously identified through culture, electron microscopy and immunological techniques. Now, the availability of bench-top sequencers, portable bench-top sequencers, rapid analytical software, on-chip RT-PCR, RT-LAMP, RT-qPCR, NASBA, fluorescence in situ hybridization (FISH), NGS and WGS has helped these methods become user friendly and less complex at a reduced cost, while also having increased sensitivity and specificity. In addition, they have the added benefit of detecting drug resistance genes, quantitative indications under therapy and the emergence of resistant strains.

Prof. Dr. Abrar Hussain
Dr. Irshad ur Rehman
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular techniques
  • microbes
  • infection
  • CRISPR
  • DNA
  • RNA
  • protein
  • PCR
  • LAMP
  • NGS
  • WGS
  • disease
  • culture
  • prevalence

Published Papers (5 papers)

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Research

13 pages, 2230 KiB  
Article
Expression of Chitinase and shRNA Gene Exhibits Resistance to Fungi and Virus
by Samia Parveen, Anwar Khan, Nusrat Jahan, Khadija Aaliya, Adnan Muzaffar, Bushra Tabassum, Syed Inayatullah, Syed Moeezullah, Muhammad Tariq, Zainia Rehmat, Niaz Ali and Abrar Hussain
Genes 2023, 14(5), 1090; https://doi.org/10.3390/genes14051090 - 15 May 2023
Cited by 2 | Viewed by 1534
Abstract
With the increasing global population, saving crops from diseases caused by different kinds of bacteria, fungi, viruses, and nematodes is essential. Potato is affected by various diseases, destroying many crops in the field and storage. In this study, we developed potato lines resistant [...] Read more.
With the increasing global population, saving crops from diseases caused by different kinds of bacteria, fungi, viruses, and nematodes is essential. Potato is affected by various diseases, destroying many crops in the field and storage. In this study, we developed potato lines resistant to fungi and viruses, Potato Virus X (PVX) and Potato Virus Y (PVY), by inoculating chitinase for fungi and shRNA designed against the mRNA of the coat protein of PVX and PVY, respectively. The construct was developed using the pCAMBIA2301 vector and transformed into AGB-R (red skin) potato cultivar using Agrobacterium tumefaciens. The crude protein extract of the transgenic potato plant inhibited the growth of Fusarium oxysporum from ~13 to 63%. The detached leaf assay of the transgenic line (SP-21) showed decreased necrotic spots compared to the non-transgenic control when challenged with Fusarium oxysporum. The transgenic line, SP-21, showed maximum knockdown when challenged with PVX and PVY, i.e., 89 and 86%, while transgenic line SP-148 showed 68 and 70% knockdown in the PVX- and PVY-challenged conditions, respectively. It is concluded from this study that the developed transgenic potato cultivar AGB-R showed resistance against fungi and viruses (PVX and PVY). Full article
(This article belongs to the Special Issue Molecular Genetics & Diagnosis of Infectious Diseases)
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11 pages, 2583 KiB  
Article
Histological and Microscopic Analysis of Fats in Heart, Liver Tissue, and Blood Parameters in Experimental Mice
by Sehrish Basheer, Imran Riaz Malik, Fazli Rabbi Awan, Kalsoom Sughra, Sadia Roshan, Adila Khalil, Muhammad Javed Iqbal and Zahida Parveen
Genes 2023, 14(2), 515; https://doi.org/10.3390/genes14020515 - 17 Feb 2023
Viewed by 1472
Abstract
The intake of various types and amounts of dietary fats influences metabolic and cardiovascular health. Hence, this study evaluated the impact of routinely consumed Pakistani dietary fats on their cardiometabolic impact. For this, we made four groups of mice, each comprising 5 animals: [...] Read more.
The intake of various types and amounts of dietary fats influences metabolic and cardiovascular health. Hence, this study evaluated the impact of routinely consumed Pakistani dietary fats on their cardiometabolic impact. For this, we made four groups of mice, each comprising 5 animals: (1) C-ND: Control mice on a normal diet, (2) HFD-DG: High-fat diet mice on a normal diet plus 10% (w/w) desi ghee, (3) HFD-O: Mice on normal diet plus 10% (w/w) plant oil (4) HFD-BG: Mice on normal diet plus 10% (w/w) banaspati ghee. Mice were fed for 16 weeks, and blood, liver, and heart samples were collected for biochemical, histological, and electron microscopic analysis. The physical factors indicated that mice fed on HFD gained more body weight than the C-ND group. Blood parameters do not show significant differences, but overall, the glucose and cholesterol concentrations were raised in the mice fed with a fat-rich diet, with the highest concentrations in the HFD-BG group. The mice fed with HFD-BG and HFD-O had more lipid droplets in the liver, compared to HFD-DG and C-ND. Full article
(This article belongs to the Special Issue Molecular Genetics & Diagnosis of Infectious Diseases)
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12 pages, 969 KiB  
Article
Serum MicroRNAs as Predictors for HCV Progression and Response to Treatment in Pakistani Patients
by Sadia Manzoor, Imran Riaz Malik, Shah Jahan, Muhammad Bilal Sarwar, Asma Bashir, Sulaiman Shams and Abrar Hussain
Genes 2023, 14(2), 441; https://doi.org/10.3390/genes14020441 - 09 Feb 2023
Viewed by 1881
Abstract
Hepatitis is one of the common liver diseases, imposing a heavy health burden worldwide. Acute hepatitis may develop into chronic hepatitis, progressing to cirrhosis and hepatocellular carcinoma. In the present study, the expression of miRNAs was quantified by real-time PCR, such as miRNA-182, [...] Read more.
Hepatitis is one of the common liver diseases, imposing a heavy health burden worldwide. Acute hepatitis may develop into chronic hepatitis, progressing to cirrhosis and hepatocellular carcinoma. In the present study, the expression of miRNAs was quantified by real-time PCR, such as miRNA-182, 122, 21, 150, 199, and 222. Along with the control group, HCV was divided into chronic, cirrhosis, and HCC groups. The treated group was also included after the successful treatment of HCV. Biochemical parameters, such as ALT, AST, ALP, bilirubin, viral load, and AFP (HCC), were also evaluated in all of the study groups. We compared the control and diseased groups; these parameters showed significant results (p = 0.000). The viral load was high in HCV but was not detected after treatment. miRNA-182 and miRNA-21 were overexpressed with disease progression, while the expression of miRNA-122 and miRNA-199 was increased compared with the control, but decreased in the cirrhosis stage compared with chronic and HCC. The expression of miRNA-150 was increased in all of the diseased groups compared with the control, but decreased compared with the chronic group. We compared the chronic and treated groups and then all of these miRNAs were down-regulated after treatment. These microRNAs could be used as potential biomarkers for diagnosing different stages of HCV. Full article
(This article belongs to the Special Issue Molecular Genetics & Diagnosis of Infectious Diseases)
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10 pages, 261 KiB  
Article
Clinical Evaluation of BioFire COVID-19 Test, BioFire Respiratory Panel 2.1, and Cepheid Xpert Xpress SARS-CoV-2 Assays for Sample-to-Answer Detection of SARS-CoV-2
by Joonhong Park, So Yeon Kim, Jaehyeon Lee and Ki Ho Hong
Genes 2023, 14(1), 233; https://doi.org/10.3390/genes14010233 - 16 Jan 2023
Cited by 2 | Viewed by 2138
Abstract
Background: Due to the extreme infectivity of SARS-CoV-2, sample-to-answer SARS-CoV-2 reverse transcription (RT) polymerase chain reaction (PCR) assays are urgently needed in order to facilitate infectious disease surveillance and control. The purpose of this study was to evaluate three sample-to-answer SARS-CoV-2 RT-PCR assays—BioFire [...] Read more.
Background: Due to the extreme infectivity of SARS-CoV-2, sample-to-answer SARS-CoV-2 reverse transcription (RT) polymerase chain reaction (PCR) assays are urgently needed in order to facilitate infectious disease surveillance and control. The purpose of this study was to evaluate three sample-to-answer SARS-CoV-2 RT-PCR assays—BioFire COVID-19 Test, BioFire RP 2.1, and Cepheid Xpert Xpress SARS-CoV-2—using clinical samples. Methods: A total of 77 leftover nasopharyngeal swab (NP) swabs (36 positives and 41 negatives) confirmed by reference SARS-CoV-2 RT real-time (q) PCR assay were collected. The clinical sample concordance, as specified by their respective emergency use authorizations (EUAs), in comparison to the reference SARS-CoV-2 RT-qPCR assay, was assessed. Results: The results showed that all three sample-to-answer SARS-CoV-2 RT-PCR assays provided perfectly concordant results consistent with the reference SARS-CoV-2 RT-qPCR assay. The BioFire COVID-19 Test exhibited the best turnaround time (TAT) compared to the other assays, regardless of the test results, using one-way analysis of variance followed by Scheffe’s post hoc test (p < 0.001). The Xpert Xpress SARS-CoV-2 showed a shorter average TAT (mean ± standard deviation, 49.9 ± 3.1 min) in the positive samples compared to that (55.7 ± 2.5 min) of the negative samples. Conclusions: Our evaluation demonstrates that the BioFire COVID-19 Test, BioFire RP 2.1, and Cepheid Xpert Xpress SARS-CoV-2 assays compare favorably to the reference SARS-CoV-2 RT-qPCR assay, along with a 100% concordance in assay results for clinical samples and an acceptable analytical performance at their guaranteed limits of detection. The addition of a widely used simultaneous sample-to-answer SARS-CoV-2 RT-PCR assay will contribute to the number of medical laboratories able to test for COVID-19. Full article
(This article belongs to the Special Issue Molecular Genetics & Diagnosis of Infectious Diseases)
21 pages, 5195 KiB  
Article
Molecular Characterization, Purification, and Mode of Action of Enterocin KAE01 from Lactic Acid Bacteria and Its In Silico Analysis against MDR/ESBL Pseudomonas aeruginosa
by Asma Bashir, Kashif Ali, Khair Bux, Neha Farid, Mitra Khaireabadi, Khwaja Ali Hassan, Abrar Hussain, Kiran Fatima, Shahab Mehmood, Syed Ali Haider and Ralf Herwig
Genes 2022, 13(12), 2333; https://doi.org/10.3390/genes13122333 - 10 Dec 2022
Cited by 3 | Viewed by 2147
Abstract
Bacteriocins are gaining immense importance in therapeutics since they show significant antibacterial potential. This study reports the bacteriocin KAE01 from Enterococcus faecium, along with its characterization, molecular modeling, and antibacterial potency, by targeting the matrix protein of Pseudomonas aeruginosa. The bacteriocin was [...] Read more.
Bacteriocins are gaining immense importance in therapeutics since they show significant antibacterial potential. This study reports the bacteriocin KAE01 from Enterococcus faecium, along with its characterization, molecular modeling, and antibacterial potency, by targeting the matrix protein of Pseudomonas aeruginosa. The bacteriocin was purified by using ammonium sulfate precipitation and fast protein liquid chromatography (FPLC), and its molecular weight was estimated as 55 kDa by means of SDS-PAGE. The bacteriocin was found to show stability in a wide range of pH values (2.0–10.0) and temperatures (100 °C for 1 h and 121 °C for 15 min). Antimicrobial screening of the purified peptide against different strains of P. aeruginosa showed its significant antibacterial potential. Scanning electron microscopy of bacteriocin-induced bacterial cultures revealed significant changes in the cellular morphology of the pathogens. In silico molecular modeling of KAE01, followed by molecular docking of the matrix protein (qSA) of P. aeruginosa and KAE01, supported the antibacterial potency and SEM findings of this study. Full article
(This article belongs to the Special Issue Molecular Genetics & Diagnosis of Infectious Diseases)
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