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Article ; Online: Mapping CircRNA–miRNA–mRNA regulatory axis identifies hsa_circ_0080942 and hsa_circ_0080135 as a potential theranostic agents for SARS-CoV-2 infection

Hassan Ayaz / Nouman Aslam / Faryal Mehwish Awan / Rabea Basri / Bisma Rauff / Badr Alzahrani / Muhammad Arif / Aqsa Ikram / Ayesha Obaid / Anam Naz / Sadiq Noor Khan / Burton B. Yang / Azhar Nazir

PLoS ONE, Vol 18, Iss

2023 Volume 4

Abstract: Non-coding RNAs (ncRNAs) can control the flux of genetic information; affect RNA stability and play crucial roles in mediating epigenetic modifications. A number of studies have highlighted the potential roles of both virus-encoded and host-encoded ... ...

Abstract	Non-coding RNAs (ncRNAs) can control the flux of genetic information; affect RNA stability and play crucial roles in mediating epigenetic modifications. A number of studies have highlighted the potential roles of both virus-encoded and host-encoded ncRNAs in viral infections, transmission and therapeutics. However, the role of an emerging type of non-coding transcript, circular RNA (circRNA) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has not been fully elucidated so far. Moreover, the potential pathogenic role of circRNA-miRNA-mRNA regulatory axis has not been fully explored as yet. The current study aimed to holistically map the regulatory networks driven by SARS-CoV-2 related circRNAs, miRNAs and mRNAs to uncover plausible interactions and interplay amongst them in order to explore possible therapeutic options in SARS-CoV-2 infection. Patient datasets were analyzed systematically in a unified approach to explore circRNA, miRNA, and mRNA expression profiles. CircRNA-miRNA-mRNA network was constructed based on cytokine storm related circRNAs forming a total of 165 circRNA-miRNA-mRNA pairs. This study implies the potential regulatory role of the obtained circRNA-miRNA-mRNA network and proposes that two differentially expressed circRNAs hsa_circ_0080942 and hsa_circ_0080135 might serve as a potential theranostic agents for SARS-CoV-2 infection. Collectively, the results shed light on the functional role of circRNAs as ceRNAs to sponge miRNA and regulate mRNA expression during SARS-CoV-2 infection.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mapping CircRNA-miRNA-mRNA regulatory axis identifies hsa_circ_0080942 and hsa_circ_0080135 as a potential theranostic agents for SARS-CoV-2 infection.

Hassan Ayaz / Nouman Aslam / Faryal Mehwish Awan / Rabea Basri / Bisma Rauff / Badr Alzahrani / Muhammad Arif / Aqsa Ikram / Ayesha Obaid / Anam Naz / Sadiq Noor Khan / Burton B Yang / Azhar Nazir

PLoS ONE, Vol 18, Iss 4, p e

2023 Volume 0283589

Abstract	Non-coding RNAs (ncRNAs) can control the flux of genetic information; affect RNA stability and play crucial roles in mediating epigenetic modifications. A number of studies have highlighted the potential roles of both virus-encoded and host-encoded ncRNAs in viral infections, transmission and therapeutics. However, the role of an emerging type of non-coding transcript, circular RNA (circRNA) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has not been fully elucidated so far. Moreover, the potential pathogenic role of circRNA-miRNA-mRNA regulatory axis has not been fully explored as yet. The current study aimed to holistically map the regulatory networks driven by SARS-CoV-2 related circRNAs, miRNAs and mRNAs to uncover plausible interactions and interplay amongst them in order to explore possible therapeutic options in SARS-CoV-2 infection. Patient datasets were analyzed systematically in a unified approach to explore circRNA, miRNA, and mRNA expression profiles. CircRNA-miRNA-mRNA network was constructed based on cytokine storm related circRNAs forming a total of 165 circRNA-miRNA-mRNA pairs. This study implies the potential regulatory role of the obtained circRNA-miRNA-mRNA network and proposes that two differentially expressed circRNAs hsa_circ_0080942 and hsa_circ_0080135 might serve as a potential theranostic agents for SARS-CoV-2 infection. Collectively, the results shed light on the functional role of circRNAs as ceRNAs to sponge miRNA and regulate mRNA expression during SARS-CoV-2 infection.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Quantification of macro, micro and trace elements, and antimicrobial activity of medicinal herbs and their products

Naeem Khan / Nargis Jamila / Farhat Amin / Rehana Masood / Amir Atlas / Wajheeba Khan / Noor Ul Ain / Sadiq Noor Khan

Arabian Journal of Chemistry, Vol 14, Iss 4, Pp 103055- (2021)

2021

Abstract: The study describes the content of macro, micro, and trace essential and toxic elements in thirteen medicinal herbs and their products including Acorus calamus, Blepharis edulis, Caesalpinia bonducella, Curculigo orchioides, Helicteres isora, Holarrhena ... ...

Abstract	The study describes the content of macro, micro, and trace essential and toxic elements in thirteen medicinal herbs and their products including Acorus calamus, Blepharis edulis, Caesalpinia bonducella, Curculigo orchioides, Helicteres isora, Holarrhena pubescens, Pastinaca sativa, Pistacia integerrima, Quercus infectoria, Rauwolfia serpentina, Saussurea lappa, Teucrium stocksianum, and Xanthium strumarium available in the local markets of Pakistan. The elemental content were analyzed with the techniques of inductively coupled plasma (ICP) optical emission spectroscopy (OES) and ICP-mass spectrometry (MS). Furthermore, their antibacterial and antifungal activities were evaluated against the selected microbial pathogens including Staphylococcus aureus, Pseudomonas aeruginosa, Bacillus subtilis and Escherichia coli, Candida albicans, Candida krusei, Aspergillus flavus, and Trichophyton mentagrophytes. Among macro elements, K and Ca showed the highest content, micro elements were in the order of Rb85/ Sr87 > Zn64/Cu63 > Ni60, and among essential trace elements, the content of Cr52/Cr53 and Co59 were high. The content of the analyzed toxic elements were lower than the permissible standard values. The antimicrobial activities against the subject strains were significant with inhibition zones of 7.0-19.0 mm in disc diffusion procedure, and 62.5–1000 µg/mL in minimum inhibitory concentration method. Hence, the presence of nutritional elements at appreciable concentrations, toxic elements within permissible ranges, and significant antimicrobial potential assume the subject herbs as promising nutritional and therapeutic remedies.
Keywords	Herbs ; Pakistan ; Trace elements ; Inductively coupled plasma-optical emission spectroscopy ; Antimicrobial ; Chemistry ; QD1-999
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Schiff base stabilized silver nanoparticles as potential sensor for Hg(II) detection, and anticancer and antibacterial agent

Aaliya Minhaz / Naeem Khan / Nargis Jamila / Fatima Javed / Muhammad Imran / Shaukat Shujah / Sadiq Noor Khan / Amir Atlas / Muhammad Raza Shah

Arabian Journal of Chemistry, Vol 13, Iss 12, Pp 8898-

2020 Volume 8908

Abstract: This study reports a facile synthesis of silver nanoparticles (C3-AgNPs) by chemical route, using C3; 2,2′-((1E,1′E)-(propane-1,3-diylbis(azanylylidene))bis(methanylylidene))diphenol (3) and silver nitrate. The formation of nanoparticles was monitored ... ...

Abstract	This study reports a facile synthesis of silver nanoparticles (C3-AgNPs) by chemical route, using C3; 2,2′-((1E,1′E)-(propane-1,3-diylbis(azanylylidene))bis(methanylylidene))diphenol (3) and silver nitrate. The formation of nanoparticles was monitored using UV–Vis spectroscopy by the appearance of typical surface plasmon absorption maxima. The synthesized C3-AgNPs were characterized using Fourier-Transform-infrared (FTIR) and atomic force microscopy (AFM) techniques. In addition, the effect of concentration, temperature, time, pH, and stability in salts solution on C3-AgNPs was determined. From AFM, C3-AgNPs were found polydispersed with average size of 29.93 nm. Furthermore, the study reports C3-AgNPs as sensitive protocol for the detection of toxic metal; Hg(II) in tap water. From ten salts tested, C3-AgNPs demonstrated a sensitive and selective spectrophotometric signal and aggregation induced decrease of surface plasmon resonance (SPR) band. The nanosensor probe displayed a sensitive response to Hg(II) in a wide range of concentrations and pH. In addition, the decrease in SPR band of C3-AgNPs due to Hg(II) was not affected by tap water samples. C3-AgNPs also exhibited a redox catalytic potential in dyes degradation. In biological application, C3-AgNPs exhibited significant anticancer and antibacterial potential of 65 to 94% at 24–72 h, and inhibition zone of 7–18 mm, respectively. Hence, the synthesized C3-AgNPs could have promising application in environmental and pharmacological remediation.
Keywords	Silver nanoparticles ; Hg(II) sensor ; Tap water ; Redox ; Anticancer ; Chemistry ; QD1-999
Subject code	500
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Piper longum catkin extract mediated synthesis of Ag, Cu, and Ni nanoparticles and their applications as biological and environmental remediation agents

Nargis Jamila / Naeem Khan / Amina Bibi / Adnan Haider / Sadiq Noor Khan / Amir Atlas / Umar Nishan / Aaliya Minhaz / Fatima Javed / Ahtaram Bibi

Arabian Journal of Chemistry, Vol 13, Iss 8, Pp 6425-

2020 Volume 6436

Abstract: Piper longum (long pepper) in dried form is used in several traditional medicines and as a spice. The present study highlights nutritional and toxic elements content, synthesis, and characterization of silver, copper oxide, and nickel nanoparticles using ...

Abstract	Piper longum (long pepper) in dried form is used in several traditional medicines and as a spice. The present study highlights nutritional and toxic elements content, synthesis, and characterization of silver, copper oxide, and nickel nanoparticles using P. longum catkin extract. The study also determined anticancer, antioxidant, antimicrobial, and redox catalytic activities of the synthesized NPs. The P. longum extract mediated nanoparticles (PLNPs) synthesized at different pH and ratios were characterized by UV–Vis (ultra-violet-visible), FT-IR (Fourier-Transform infrared), and scanning electron and atomic force microscopic (SEM, AFM) techniques. Elemental content of P. longum catkin determined by inductively coupled plasma-optical emission spectroscopy (ICP-OES) and ICP-mass spectrometry (ICP-MS) indicated appreciable concentrations of nutritional elements, and well below permissible ranges of toxic elements. Well-defined and stable silver nanoparticles (PLAgNPs) were formed in 1:4 to 1:6 ratios, while copper oxide and nickel NPs (PLCuONPs and PLNiNPs) were found prominent in 1:6 ratio. In determining the effect of pH on synthesized PLNPs, sharp intense absorption peaks were obtained under slightly neutral to highly basic conditions (pH 6 to 13) for PLAgNPs, whereas for PLCuONPs and PLNiNPs, pH 7–8 was optimum. In biological activities, PLNPs exhibited significant anticancer efficacy against DU-145 (prostate cancer) cell line in the range from 92.7% (PLCuONPs) to 100% (PLAgNPs, PLNiNPs). Fuurthermore, the sythesized NPs exhibited significant antioxidant, antimicrobial, and redox catalytic properties. This study concluded the promising nutritional, biological and environmental remediation applications, and hence, further exploration of the synthesized NPs in biological and clinical applications is currently under investigation.
Keywords	P. longum ; Elemental content ; Nickel nanoparticles ; Inductively coupled plasma-optical emission spectroscopy ; Atomic force microscopy ; Anticancer ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Phytochemicals from the Bark of Garcinia hombroniana and Their Biological Activities

Nargis Jamila / Melati Khairuddean / Sadiq Noor Khan / Naeem Khan / Hasnah Osman

Records of Natural Products, Vol 8, Iss 3, Pp 312-

2014 Volume 316

Abstract: The dichloromethane and ethyl acetate extracts from the bark of Garcinia hombroniana yielded lupeol (1), lupeol acetate (2), 3β-acetoxy- lup-12,20(29)-diene (3), β-sitosterol (4), 22-dehydroclerosterol (5), mangiferolic acid (6), ursolic acid (7), ... ...

Abstract	The dichloromethane and ethyl acetate extracts from the bark of Garcinia hombroniana yielded lupeol (1), lupeol acetate (2), 3β-acetoxy- lup-12,20(29)-diene (3), β-sitosterol (4), 22-dehydroclerosterol (5), mangiferolic acid (6), ursolic acid (7), betulin (8), betulinic acid (9), 1,3,6-trihydroxy-7-methoxy-2,8-(3-methyl-2-butenyl)xanthone (10), leucodin (11), p-hydroxycinnamate (12), p-hydroxybenzoic acid (13) and stearic acid (14). Compounds 10, 12 and 13 exhibited significant antioxidant activities by DPPH (2,2-diphenyl-1-picrylhydrazyl), ABTS (2,2-azinobis-3-ethylbenzothiazoline-6-sulfonic acid) and FRAP (ferric ion reducing antioxidant power) assays. Antibacterial studies showed strong inhibitory effects for compound 11 while other compounds (1-9 and 14) were either inactive or moderately active for the bacterial strains investigated. This study presents the first report on the isolation and biological activities of the chemical constituents from the bark of G. hombroniana. The compounds 3, 5-12 and 14 are reported for the first time from this source.
Keywords	Garcinia hombroniana ; bark ; triterpenoids ; antioxidant activities ; antibacterial activities ; Chemistry ; QD1-999 ; Organic chemistry ; QD241-441 ; Botany ; QK1-989
Subject code	540
Language	English
Publishing date	2014-05-01T00:00:00Z
Publisher	ACG Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan

Abdul Jabbar / Jody E. Phelan / Paola Florez de Sessions / Taj Ali Khan / Hazir Rahman / Sadiq Noor Khan / Daire M. Cantillon / Leticia Muraro Wildner / Sajid Ali / Susana Campino / Simon J. Waddell / Taane G. Clark

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 9

Abstract: Abstract Tuberculosis (TB), caused by Mycobacterium tuberculosis bacteria, is a leading infectious cause of mortality worldwide, including in Pakistan. Drug resistant M. tuberculosis is an emerging threat for TB control, making it important to detect the ...

Abstract	Abstract Tuberculosis (TB), caused by Mycobacterium tuberculosis bacteria, is a leading infectious cause of mortality worldwide, including in Pakistan. Drug resistant M. tuberculosis is an emerging threat for TB control, making it important to detect the underlying genetic mutations, and thereby inform treatment decision making and prevent transmission. Whole genome sequencing has emerged as the new diagnostic to reliably predict drug resistance within a clinically relevant time frame, and its deployment will have the greatest impact on TB control in highly endemic regions. To evaluate the mutations leading to drug resistance and to assess for evidence of the transmission of resistant strains, 81 M. tuberculosis samples from Khyber Pakhtunkhwa province (North West Pakistan) were subjected to whole genome sequencing and standard drug susceptibility testing for eleven anti-TB drugs. We found the majority of M. tuberculosis isolates were the CAS/Delhi strain-type (lineage 3; n = 57; 70.4%) and multi-drug resistant (MDR; n = 62; 76.5%). The most frequent resistance mutations were observed in the katG and rpoB genes, conferring resistance to isoniazid and rifampicin respectively. Mutations were also observed in genes conferring resistance to other first and second-line drugs, including in pncA (pyrazinamide), embB (ethambutol), gyrA (fluoroquinolones), rrs (aminoglycosides), rpsL, rrs and giB (streptomycin) loci. Whilst the majority of mutations have been reported in global datasets, we describe unreported putative resistance markers in katG, ethA (ethionamide), gyrA and gyrB (fluoroquinolones), and pncA. Analysis of the mutations revealed that acquisition of rifampicin resistance often preceded isoniazid in our isolates. We also observed a high proportion (17.6%) of pre-MDR isolates with fluoroquinolone resistance markers, potentially due to unregulated anti-TB drug use. Our isolates were compared to previously sequenced strains from Pakistan in a combined phylogenetic tree analysis. The presence of lineage 2 was only observed in our isolates. Using a cut-off of less than ten genome-wide mutation differences between isolates, a transmission analysis revealed 18 M. tuberculosis isolates clustering within eight networks, thereby providing evidence of drug-resistant TB transmission in the Khyber Pakhtunkhwa province. Overall, we have demonstrated that drug-resistant TB isolates are circulating and transmitted in North West Pakistan. Further, we have shown the usefulness of whole genome sequencing as a diagnostic tool for characterizing M. tuberculosis isolates, which will assist future epidemiological studies and disease control activities in Pakistan.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2019-10-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Frequency of typhoid fever and its association with seasonal variations in Taxila, Pakistan

Naeem Bukhari / Afshan Saleem / Abdul Jabbar / Sadiq Noor Khan / Bilal Ahmad / Nasir Habib / Abdul Haseeb / Azhar Khan / Muhammad Zahid Ali / Mohammad Adeeb khan / Aftab Ahmad Khan

Asian Pacific Journal of Tropical Disease, Vol 6, Iss 8, Pp 608-

2016 Volume 610

Abstract: Objective: To analyse seropositivity rates of salmonella with seasonal variations in the population of Taxila and the surrounding rural areas. Methods: The study was conducted among 760 suspected patients with symptoms of fever, headache, nausea and ... ...

Abstract	Objective: To analyse seropositivity rates of salmonella with seasonal variations in the population of Taxila and the surrounding rural areas. Methods: The study was conducted among 760 suspected patients with symptoms of fever, headache, nausea and decreased white blood cells count screened for the typhoid fever. Blood samples collected from the suspected patients were tested for seropositivity by slide agglutination (Widal test) and Immunochromatographic test, i.e. Typhidot. Results: From overall 760 suspected patients of typhoid fever only 192 (25.26%) samples were positive for Widal and Typhidot test. The peak seropositivity rates were identified during the months of April–June, while decreased cases were observed from January to March. Age wise distribution of typhoid fever reflected that age groups of 10–15 years and 25–35 years were at higher risks of developing enteric fever with respect to age groups of 5–10 years and 61–70 years, respectively. On gender basis evaluation, females (24.49%) were slightly at low risks of developing typhoid fever than males (25.9%). Conclusions: The present study highlights a higher burden of typhoid fever in Taxila and the surrounding areas population that directly reflects the poor hygienic condition and contamination of drinking water. The frequency of typhoid fever fluctuates with seasonal variations as higher rates found during the summer as compared to winter season.
Keywords	Typhoid ; Seasonal variations ; Taxila ; Pakistan ; Medicine ; R ; Arctic medicine. Tropical medicine ; RC955-962
Language	English
Publishing date	2016-08-01T00:00:00Z
Publisher	Asian Pacific Journal of Tropical Disease Editorial Office
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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