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Pence S, Caykara B, Pence HH, Tekin S, Keskin BC, Uncu AT, Uncu AO, Ozturk E. Transcriptomic analysis of asymptomatic and symptomatic severe Turkish patients in SARS-CoV-2 infection. North Clin Istanb 2022; 9:122-130. [PMID: 35582503 PMCID: PMC9039630 DOI: 10.14744/nci.2022.28000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/22/2022] [Indexed: 11/20/2022] Open
Abstract
Objective Coronavirus disease 2019 (COVID-19), leading to mild infection (MI), acute respiratory distress syndrome or death in different persons. Although the basis of these variabilities has not been fully elucidated, some possible findings have been encountered. In the present study, we aimed to reveal genes with different expression profiles by next-generation sequencing of RNA isolated from blood taken from infected patients to reveal molecular causes of different response. Methods Two healthy, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-negative control individuals (NCI), two SARS-CoV-2-positive patients who have MI, and two patients who have critical infection (CI) were included in the study. Total RNA was extracted from blood samples and sequenced. Raw RNA-Seq data were analyzed on Galaxy platform for the identification of differentially expressed genes and their pathway involvements. Results We found that 199 and 521 genes were downregulated in whole blood of COVID-19-positive CI patients compared to NCI and MI patients, respectively. We identified 21 gene ontology pathways commonly downregulated in CI patients compared to both NCI and MI, mostly associated with innate and adaptive immune responses. Three hundred and fifty-four and 600 genes were found to be upregulated compared to NCI and MI, respectively. Upregulated six pathways included genes that function in inflammatory response and inflammatory cytokine release. Conclusion The transcriptional profile of CI patients deviates more significantly from that of MI in terms of the number of differentially expressed genes, implying that genotypic differences may account for the severity of SARS-CoV-2 infection and inflammatory responses through differential regulation of gene expression. Therefore, further studies that involve whole genome analysis coupled with differential expression analysis are required in order to determine the dynamics of genotype - gene expression profile associations.
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Affiliation(s)
- Sadrettin Pence
- Department of Physiology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - Burcu Caykara
- Department of Physiology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - Halime Hanim Pence
- Department of Biochemistry, Health Sciences University Faculty of Medicine, Istanbul, Turkey
| | - Saban Tekin
- Department of Medical Biology, Health Sciences University, Faculty of Medicine, Istanbul, Turkey
- TUBITAK, Marmara Research Center, Gene Engineering and Biotechnology Institute, Kocaeli, Turkey
| | - Birsen Cevher Keskin
- TUBITAK, Marmara Research Center, Gene Engineering and Biotechnology Institute, Kocaeli, Turkey
| | - Ali Tevfik Uncu
- Department of Molecular Biology and Genetics, Necmettin Erbakan University Faculty of Science, Konya, Turkey
| | - Ayse Ozgur Uncu
- Department of Biotechnology, Necmettin Erbakan University Faculty of Science, Konya, Turkey
| | - Erman Ozturk
- Division of Hematology, Department of Internal Diseases, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
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Aksoy E, Uncu AT, Filiz E, Orman Ş, Çetin D, Akbudak MA. Genes involved in mRNA surveillance are induced in Brachypodium distachyon under cadmium toxicity. Mol Biol Rep 2021; 49:5303-5313. [PMID: 34812999 DOI: 10.1007/s11033-021-06952-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/10/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Cd accumulation in plant cells results in dramatic problems including oxidative stress and inhibition of vital enzymes. It also affects mineral uptakes by disrupting membrane permeability. Interaction among Cd and other plant nutrient elements changes the nutritional contents of crops and reduces their yield. METHODS AND RESULTS In the present study, Cd stress in Brachypodium distachyon led to the upregulation of some heavy metal transport genes (influx or efflux) encoding cation-efflux proteins, heavy metal-associated proteins and NRAMP proteins. The Arabidopsis orthologs of the differentially expressed B. distachyon genes (DEGs) under Cd toxicity were identified, which exhibited Bradi4g26905 was an ortholog of AtALY1-2. Detailed co-expression network and gene ontology analyses found the potential involvement of the mRNA surveillance pathway in Cd tolerance in B. distachyon. These genes were shown to be downregulated by sulfur (S) deficiency. CONCLUSIONS This is the first transcriptomic study investigating the effect of Cd toxicity in B. distachyon, a model plant for genomic studies in Poaceae (Gramineae) species. The results are expected to provide valuable information for more comprehensive research related to heavy metal toxicity in plants.
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Affiliation(s)
- Emre Aksoy
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ali Tevfik Uncu
- Department of Molecular Biology and Genetics, Necmettin Erbakan University, Konya, Turkey
| | - Ertugrul Filiz
- Department of Agricultural Production, Duzce University, Cilimli Vocational School, Duzce, Turkey
| | - Şule Orman
- Department of Soil Science and Plant Nutrition, Akdeniz University, Antalya, Turkey
| | - Durmuş Çetin
- Department of Agricultural Biotechnology, Akdeniz University, Antalya, Turkey
| | - M Aydın Akbudak
- Department of Agricultural Biotechnology, Akdeniz University, Antalya, Turkey.
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Uncu AO, Uncu AT. A barcode-DNA analysis method for the identification of plant oil adulteration in milk and dairy products. Food Chem 2020; 326:126986. [PMID: 32407998 DOI: 10.1016/j.foodchem.2020.126986] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/02/2020] [Accepted: 05/03/2020] [Indexed: 11/19/2022]
Abstract
In the present work, a barcode-DNA analysis method is described for the detection of plant oil adulteration in milk and dairy products. The method relies on the fact that plant DNA should not be present in readily detectable amounts in a dairy product unless it contains undeclared plant material. Thus, a universal plant barcode is chosen as the target to be amplified from dairy samples. Accordingly, barcode PCR-CE (PCR-capillary electrophoresis) assays are described, which do not require preliminary information on the species source of the adulterant oil type. Two PCR-CE assays, one operating on the plastid trnL (UAA) intron and the other targeting its inner P6 loop in nested format, were shown to detect corn, soybean, rapeseed and sunflower oils in clarified butter, milk and yogurt. Both barcodes are robustly amplified with extremely conserved primers. While the intron provides the species discrimination ability, the P6 loop provides superior detection sensitivity.
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Affiliation(s)
- Ayse Ozgur Uncu
- Necmettin Erbakan University, Department of Biotechnology, Meram, Konya 42090, Turkey.
| | - Ali Tevfik Uncu
- Necmettin Erbakan University, Department of Molecular Biology & Genetics, Meram, Konya 42090, Turkey.
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Sen F, Uncu AO, Uncu AT, Erdeger SN. The trnL (UAA)-trnF (GAA) intergenic spacer is a robust marker of green pea (Pisum sativum L.) adulteration in economically valuable pistachio nuts (Pistacia vera L.). J Sci Food Agric 2020; 100:3056-3061. [PMID: 32077485 DOI: 10.1002/jsfa.10336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Pistachio (Pistacia vera L.) is an expensive culinary nut species; it is therefore susceptible to adulteration for economic profit. Green pea (Pisum sativum L.) kernels constitute the most common material used for adulterating chopped / ground pistachio nuts and pistachio paste. Food genomics enables the species composition of a food sample to be ascertained through DNA analysis. Accordingly, a barcode DNA genotyping approach was used to standardize a test method to identify green pea adulteration in pistachio nuts. RESULTS The trnL (UAA)-trnF (GAA) intergenic spacer in the plastid genome was the target analyte in the present study. The barcode locus displayed a significant, discriminatory size difference between pistachio and pea, with amplicon sizes of 449 and 179 bp, respectively. Polymerase chain reaction-capillary electrophoresis (PCR-CE) analysis of the intergenic spacer resulted in the successful identification of species composition in the in-house admixtures, which contained 5% to 30% of green pea. CONCLUSION The present work describes a fast and straightforward DNA test that identifies green pea adulteration in pistachio nuts without requiring a statistical data interpretation process. The plastid trnL (UAA)-trnF (GAA) intergenic spacer length widely varies among plant taxa, so the PCR-CE protocol that operates on the intergenic spacer holds the potential to reveal adulteration with a plethora of adulterants. The PCR-CE assay described in the present work can be adopted readily by food-quality laboratories in the public sector or the food industry as an easy and reliable method to analyze pistachio authenticity. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Fatima Sen
- Department of Biotechnology, Faculty of Science, Necmettin Erbakan University, Konya, Turkey
| | - Ayse Ozgur Uncu
- Department of Biotechnology, Faculty of Science, Necmettin Erbakan University, Konya, Turkey
| | - Ali Tevfik Uncu
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Konya, Turkey
| | - Seyma Nur Erdeger
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Konya, Turkey
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Uncu AO, Uncu AT. High-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markers. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1701551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Ayse Ozgur Uncu
- Department of Biotechnology, Faculty of Science, Necmettin Erbakan University, Meram, Turkey
| | - Ali Tevfik Uncu
- Department of Molecular Biology & Genetics, Faculty of Science, Necmettin Erbakan University, Meram, Turkey
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Uncu AT, Uncu AO. Plastid trnH-psbA intergenic spacer serves as a PCR-based marker to detect common grain adulterants of coffee ( Coffea arabica L.). Food Control 2018. [DOI: 10.1016/j.foodcont.2018.03.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Uncu AO, Torlak E, Uncu AT. A Cost-Efficient and Simple Plant Oil DNA Extraction Protocol Optimized for DNA-Based Assessment of Product Authenticity. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-1070-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Celik I, Gurbuz N, Uncu AT, Frary A, Doganlar S. Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing. BMC Genomics 2017; 18:1. [PMID: 28049423 PMCID: PMC5209891 DOI: 10.1186/s12864-016-3406-7] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 12/09/2016] [Indexed: 11/10/2022] Open
Abstract
Background Solanum pimpinellifolium has high breeding potential for fruit quality traits and has been used as a donor in tomato breeding programs. Unlocking the genetic potential of S. pimpinellifolium requires high-throughput polymorphism identification protocols for QTL mapping and introgression of favourable alleles into cultivated tomato by both positive and background selection. Results In this study we identified SNP loci using a genotyping by sequencing (GBS) approach in an IBL mapping population derived from the cross between a high yielding fresh market tomato and S. pimpinellifolium (LA1589) as the recurrent and donor parents, respectively. A total of 120,983,088 reads were generated by the Illumina HiSeq next-generation sequencing platform. From these reads 448,539 sequence tags were generated. A majority of the sequence tags (84.4%) were uniquely aligned to the tomato genome. A total of 3.125 unique SNP loci were identified as a result of tag alignment to the genome assembly and were used in QTL analysis of 11 fruit quality traits. As a result, 37 QTLs were identified. S. pimpinellifolium contributed favourable alleles for 16 QTLs (43.2%), thus confirming the high breeding potential of this wild species. Conclusions The present work introduced a set of SNPs at sufficiently high density for QTL mapping in populations derived from S. pimpinellifolium (LA1589). Moreover, this study demonstrated the high efficiency of the GBS approach for SNP identification, genotyping and QTL mapping in an interspecific tomato population. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3406-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ibrahim Celik
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Nergiz Gurbuz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Ali Tevfik Uncu
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey.,Pressent Address: Department of Molecular Biology and Genetics, Necmettin Erbakan University, Konya, Turkey
| | - Anne Frary
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Sami Doganlar
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey.
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Uncu AT, Uncu AO, Frary A, Doganlar S. Authentication of Botanical Origin in Herbal Teas by Plastid Noncoding DNA Length Polymorphisms. J Agric Food Chem 2015; 63:5920-5929. [PMID: 26054647 DOI: 10.1021/acs.jafc.5b01255] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The aim of this study was to develop a DNA barcode assay to authenticate the botanical origin of herbal teas. To reach this aim, we tested the efficiency of a PCR-capillary electrophoresis (PCR-CE) approach on commercial herbal tea samples using two noncoding plastid barcodes, the trnL intron and the intergenic spacer between trnL and trnF. Barcode DNA length polymorphisms proved successful in authenticating the species origin of herbal teas. We verified the validity of our approach by sequencing species-specific barcode amplicons from herbal tea samples. Moreover, we displayed the utility of PCR-CE assays coupled with sequencing to identify the origin of undeclared plant material in herbal tea samples. The PCR-CE assays proposed in this work can be applied as routine tests for the verification of botanical origin in herbal teas and can be extended to authenticate all types of herbal foodstuffs.
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Abstract
The aim of this study was to establish a DNA-based identification key to ascertain the cultivar origin of Turkish monovarietal olive oils. To reach this aim, we sequenced short fragments from five olive genes for SNP (single nucleotide polymorphism) identification and developed CAPS (cleaved amplified polymorphic DNA) assays for SNPs that alter restriction enzyme recognition motifs. When applied on the oils of 17 olive cultivars, a maximum of five CAPS assays were necessary to discriminate the varietal origin of the samples. We also tested the efficiency and limit of our approach for detecting olive oil admixtures. As a result of the analysis, we were able to detect admixing down to a limit of 20%. The SNP-based CAPS assays developed in this work can be used for testing and verification of the authenticity of Turkish monovarietal olive oils, for olive tree certification, and in germplasm characterization and preservation studies.
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Affiliation(s)
- Ali Tevfik Uncu
- Department of Molecular Biology & Genetics, Izmir Institute of Technology , Urla, Izmir 35430, Turkey
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Bazakos C, Dulger AO, Uncu AT, Spaniolas S, Spano T, Kalaitzis P. A SNP-based PCR–RFLP capillary electrophoresis analysis for the identification of the varietal origin of olive oils. Food Chem 2012; 134:2411-8. [DOI: 10.1016/j.foodchem.2012.04.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 11/09/2011] [Accepted: 04/07/2012] [Indexed: 11/29/2022]
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