Shiraz University Press Molecular Biology Research Communications 2322-181X 9 4 2020 12 01 Association of two single nucleotide polymorphisms rs10407022 and rs3741664 with the risk of primary ovarian insufficiency in a sample of Iraqi women 141 144 5757 10.22099/mbrc.2020.36371.1477 EN Tamadher Abbas Rafaa University Headquarter, University of Anbar, Ramadi, Iraq Ahmed Abduljabar Suleiman College of Science, University of Anbar, Ramadi, Iraq Mustafa Falah Dawood College of Education for Pure Science, University of Anbar, Ramadi, Iraq Ali Mohammad Al-Rawi University Headquarter, University of Anbar, Ramadi, Iraq Journal Article 2020 02 08 Primary ovarian insufficiency (POI) can be a devastating disease impacting women below the age of forty. This involves a major decrease in the amount and quality of oocytes, or ovarian reserve in a woman. The distribution of single-nucleotide polymorphisms, rs10407022 and rs3741664, in Iraqi people and its association with primary ovarian insufficiency is the main objective of this study. The mean of FSH and LH levels of patients with POI was higher than control, while the mean of AMH levels of patients was lower compared to control. For rs10407022, the GT and TT genotypes were positively associated with the risk of POI. For the rs3741664, the AG genotype was negatively associated with the risk of POI. The results lead to the main conclusion that rs10407022 and rs3741664 polymorphisms may significantly affected the serum levels of AMH and FSH and thus affect POI etiology.

https://mbrc.shirazu.ac.ir/article_5757_2c295e3ef3dd8f353b8a1ce413a02c2a.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 9 4 2020 12 01 Platelet-rich plasma and platelet-derived lipid factors induce different and similar gene expression responses for selected genes related to wound healing in rat dermal wound environment 145 153 5760 10.22099/mbrc.2020.37181.1500 EN Fahri Akbas Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey Busra Ozdemir Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey Nurten Bahtiyar Department of Biophysics, Cerrahpasa Faculty of Medicine, Istanbul University- Cerrahpasa, Istanbul, Turkey Hulya Arkan Department of Medical Biology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey Ilhan Onaran Department of Medical Biology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey Journal Article 2020 05 06 Although platelet-rich plasma (PRP) is the plasma fraction that contains higher levels of platelet-sequestered proteins such as growth factors and chemokines, it is also abundant in bioactive lipids whose role in wound healing has not been well characterized. This study provides a preliminary evaluation for the effect of the lipid component of PRP on selected genes related to wound healing. Sprague-Dawley rats were classified into four groups after induction of full thickness excisional wounds: the lipid fraction (LF) (lipid extract from PRP) group, PRP group, dimethyl sulfoxide group, and sham group. Subsequently, relevant groups were topically treated with test preparations. Healing wounds were collected on 3rd, 7th and 14th days, and expression levels of 12 genes were determined using qPCR. LF treatment-induced gene expression signature distinct from that induced by PRP treatment, although there are some overlaps in LF- and PRP-responsive genes. Differentially expressed all eight genes (Cxcl5, Cxc11, Egfr, Tgfb1, IL10, Tgfa, Mmp1, and Mmp7) to LF response were significantly down-regulated at either 3rd, 7th, or 14th days. Also, the comparison between LF- and PRP-treatment groups showed that the LF significantly decreased expression of Cxcl11, Mmp7, and Tgfa mRNA on day 7 of healing. This study revealed that PRP and its LF induced different and similar gene expression responses of the skin during the repair of full thickness excisional wounds. Identifying mRNA response to LF treatment at whole transcriptome level can be beneficial for comprehensive understanding of the role of platelet-derived lipid factors in wound healing processes.

https://mbrc.shirazu.ac.ir/article_5760_f352fc6a0420e5fd543014c4bf3edc8f.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 9 4 2020 12 01 Computational insights into fluconazole resistance by the suspected mutations in lanosterol 14α-demethylase (Erg11p) of Candida albicans 155 167 5762 10.22099/mbrc.2020.36298.1476 EN Sagunthala Murugesan Udaya Prakash Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut 673601, Kerala, India Yasin Nazeer Regional Medical Research Centre, Indian Council of Medical Research (ICMR), Belagavi -590010, Karnataka, India Sivaraman Jayanthi Computational Drug Design Lab, School of BioSciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India Mohammad Anaul Kabir Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut 673601, Kerala, India Journal Article 2020 02 01 Mutations in the ergosterol biosynthesis gene 11 (ERG11) of Candida albicans have been frequently reported in fluconazole-resistant clinical isolates. Exploring the mutations and their effect could provide new insights into the underlying mechanism of fluconazole resistance. Erg11p_Threonine285Alanine (Erg11p_THR285ALA), Erg11p_Leucine321Phenylalanine (Erg11p_LEU321PHE) and Erg11p_Serine457Proline (Erg11p_SER457PRO) are three fluconazole-resistant suspected mutations reported in clinical isolates of C. albicans. Therefore, our study aims to investigate the role of these suspected mutations in fluconazole resistance using in-silico methods. Molecular dynamics simulation (MDS) analysis of apo-protein for 25ns (nanosecond) showed that suspected mutant proteins underwent slight conformational changes in the tertiary structure. Molecular docking with fluconazole followed by binding free energy analysis showed reduced non-bonded interactions with loss of heme interaction and the least binding affinity for Erg11p_SER457PRO mutation. MDS of suspected mutant proteins-fluconazole complexes for 50ns revealed that Erg11p_SER457PRO and Erg11p_LEU321PHE have clear differences in the interaction pattern and loss or reduced heme interaction compared to wild type Erg11p-fluconazole complex. MDS and binding free energy analysis of Erg11p_SER457PRO-fluconazole complex showed the least binding similar to verified mutation Erg11p_TYR447HIS-fluconazole complex. Taken together, our study concludes that suspected mutation Erg11p_THR285ALA may not have any role whereas Erg11p_LEU321PHE could have a moderate role. However, Erg11p_SER457PRO mutation has a strong possibility to play an active role in fluconazole resistance of C. albicans.

https://mbrc.shirazu.ac.ir/article_5762_cdcb5187db8f26bb286a16b3a4b1db07.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 9 4 2020 12 01 Differential expression of inflammatory responsive genes between chronic periodontitis and periodontally affected bronchiectasis patients 169 172 5800 10.22099/mbrc.2020.37397.1508 EN Abhaya Gupta Department of Periodontology, Faculty of Dental Sciences, King George’s Medical University, Uttar Pradesh, Lucknow, India Neetu Singh Department of Molecular Biology, Center for Advanced Research, King George’s Medical University, Uttar Pradesh, Lucknow, India Anil Kumar Department of Molecular Biology, Center for Advanced Research, King George’s Medical University, Uttar Pradesh, Lucknow, India Umesh Pratap Verma Department of Periodontology, Faculty of Dental Sciences, King George’s Medical University, Uttar Pradesh, Lucknow, India Ajay Kumar Verma Department of Respiratory Medicine, King George’s Medical University, Uttar Pradesh, Lucknow, India Hari Shyam Department of Molecular Biology, Center for Advanced Research, King George’s Medical University, Uttar Pradesh, Lucknow, India Nand Lal Department of Periodontology, Faculty of Dental Sciences, King George’s Medical University, Uttar Pradesh, Lucknow, India Surya Kant Department of Respiratory Medicine, King George’s Medical University, Uttar Pradesh, Lucknow, India Ankur Kumari Department of Periodontology, Faculty of Dental Sciences, King George’s Medical University, Uttar Pradesh, Lucknow, India Journal Article 2020 05 29 The study aimed to investigate differential expression of targeted inflammatory-immune responsive genes [LTA, LTB, TNFSF4, TNFSF11/RANKL, TNFSF13, TNFSF13B, TNFRSF11B/ Osteoprotegerin; OPG and GFPT1/GFA ] in gingival tissues of bronchiectasis patients having chronic periodontitis in North central Indian population. Gingival tissues were collected from 30 systemically healthy chronic periodontitis patients (CP), 30 bronchiectasis patients with chronic periodontitis (B+CP), 3 systemically healthy with healthy gingiva (healthy control; HC) and 3 bronchiectasis with healthy gingiva (bronchiectasis control; BC). Statistical analysis revealed 7 genes to be significantly upregulated on comparing CP with B+CP i.e LTA (p <0.0001) in B+CP while LTB (p <0.0001), TNFSF4 (P=0.0003), TNFSF11 (p <0.0001), TNFSF13 (P=0.0003), TNFSF13B (p <0.0001) and TNFRSF11B (P=0.0004) in CP group. LTA (Lymphotoxin A) gene could be a potential genetic marker in bronchiectasis patients with chronic periodontitis.

https://mbrc.shirazu.ac.ir/article_5800_48d915ce3f3d4b87f5082e5f803c39b4.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 9 4 2020 12 01 Differential genes expression analysis of invasive aspergillosis: a bioinformatics study based on mRNA/microRNA 173 180 5807 10.22099/mbrc.2020.37432.1509 EN Maryam Hosseinipour Department of Medical Mycology, Faculty of Medical Science, Tarbiat Modares University, Tehran Iran Shirin Shahbazi Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, ‎Tehran, Iran Shahla Roudbar-Mohammadi Department of Medical Mycology, Faculty of Medical Science, Tarbiat Modares University, Tehran Iran Maryam Khorasani Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran Majid Marjani Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran Journal Article 2020 05 30 Invasive aspergillosis is a severe opportunistic infection with high mortality in immunocompromised patients. Recently, the roles of microRNAs have been taken into consideration in the immune system and inflammatory responses. Using bioinformatics approaches, we aimed to study the microRNAs related to invasive aspergillosis to understand the molecular pathways involved in the disease pathogenesis. Data were extracted from the gene expression omnibus (GEO) database. We proposed 3 differentially expressed genes; S100B, TDRD9 and TMTC1 related to pathogenesis of invasive aspergillosis. Using miRWalk 2.0 predictive tool, microRNAs that targeted the selected genes were identified. The roles of microRNAs were investigated by microRNA target prediction and molecular pathways analysis. The significance of combined expression changes in selected genes was analyzed by ROC curves study. Thirty-three microRNAs were identified as the common regulator of S100B, TDRD9 and TMTC1 genes. Several of them were previously reported in the pathogenesis of fungal infections including miR-132. Predicted microRNAs were involved in innate immune response as well as toll-like receptor signaling. Most of the microRNAs were also linked to platelet activation. The ROC chart in the combination mode of S100B/TMTC1, showed the sensitivity of 95.65 percent and the specificity of 69.23 percent. New approaches are needed for rapid and accurate detection of invasive aspergillosis. Given the pivotal signaling pathways involved, predicted microRNAs can be considered as the potential candidates of the disease diagnosis. Further investigation of the microRNAs expression changes and related pathways would lead to identifying the effective biomarkers for IA detection.

https://mbrc.shirazu.ac.ir/article_5807_e629a5ebd6e6232968eb8b0e9ef55b45.pdf

Shiraz University Press Molecular Biology Research Communications 2322-181X 9 4 2020 12 01 Nucleotide mutation analyses of isolated lentogenic newcastle disease virus in live bird market 181 188 5867 10.22099/mbrc.2020.38061.1530 EN Jola Rahmahani Laboratory of Virology and Immunology, Department of Microbiology, Faculty of Veterinary Medicine, Airlangga University, Indonesia, 60115 Aisyah Nikmatuz Zahro Bachelor of Veterinary Science, Faculty of Veterinary Medicine, Airlangga University, Indonesia, 60115 Indah Laili Rahmawati Master of Vaccinology, Faculty of Veterinary Medicine, Airlangga University, Indonesia, 60115 Nurvita Putih Master of Vaccinology, Faculty of Veterinary Medicine, Airlangga University, Indonesia, 60115 Innah Wulandari Master of Vaccinology, Faculty of Veterinary Medicine, Airlangga University, Indonesia, 60115 Fedik Abdul- Rantam Laboratory of Virology and Immunology, Department of Microbiology, Faculty of Veterinary Medicine, Airlangga University, Indonesia, 60115 Stem Cell Research and Development Center, Airlangga University, Indonesia, 60115 Journal Article 2020 08 07 Newcastle Disease (ND) is a major viral disease in Indonesia. It is an RNA virus belongs to Paramyxovirinae. It is well known that RNA virus is easily to mutate. In some cases, this mutation could generate virulence alteration. It is noted that mutation of NDV which has avirulent amino acid sequence on the cleavage site, could mutate to be virulent Newcastle Disease Virus (NDV). It is needed to analyze the nucleotide and amino acid mutations and the effect of those to its virulence. The aim of this study was to analyze nucleotide and amino acid mutations of original isolated Lentogenic Newcastle Disease Virus (NDV). Samples were collected from cloacal swab of native chicken (Gallus gallus domesticus) suspected to be infected by Lentogenic NDV from live bird markets. They were inoculated into embryonated eggs, to isolate the virus. HA and HI assays were conducted to confirm that they were NDV. Positive samples were processed into serial passages in embryonated egg to observe their death time. Samples caused mortality of the embryonated eggs more than 90 hours post infection were suspected as Lentogenic NDV. They were processed to RT-PCR then sequenced. Lentogenic NDV confirmation was done by comparing amino acid at Fusion protein cleavage site of the samples to Lasota/JF950510. Nucleotide and amino acid mutations were analyzed. The result showed that some nucleotide mutations were capable to change sequences of amino acid but the virulence of the samples remained the same to the reference sequence.

https://mbrc.shirazu.ac.ir/article_5867_0653df2858605dea2f1d41c050b41b03.pdf