A new method to quantify atmospheric Poaceae pollen DNA based on the trnT-F cpDNA region

Background: Pollen, mold spores, bacteria and viruses are the main biological substances in the atmosphere causing allergic symptoms and disease. Distinguishing pollen and spores is quite time consuming and requires a trained expert. There is a different approach to identification of these substances such as microscopic analysis. However, DNA based identification of these is becoming popular recently. Objective: We evaluated the correlation between the quantity of DNA, which was amplified using trnT-F cpDNA specific primers in samples obtained from a high volume air sampler (HVAS), and concentration of Poaceae pollen collected with a Burkard trap. Materials and methods: Here, we present a method for identifying and quantifying airborne Poaceae pollen using a single step polymerase chain reaction (PCR) technique. Forty daily air samples were collected by HVAS. The method was optimised using two different methods (M1 and M2) and the trnT-F cpDNA region was amplified using a Poaceae specific primer pair. The correlation between the quantity of DNA and pollen concentration was tested using R statistical programming language. Results: Although a significant correlation was obtained between the M1 and M2 methods (R2 = 0.655, p < 0.01), the M2 method was more correlated with pollen concentration. The correlation between pollen and DNA content changed due to episodes that were observed during the pollen season. DNA concentrations from the PCR data were significantly correlated with pollen concentrations determined by light microscopy (R2 = 0.767, p < 0.01) in episode II using the M2 method and during the entire season (R2 = 0.469, p < 0.01) using M2. Conclusions: The M2 method correctly identified Poaceae pollen in mixed air samples from Zonguldak Province. The non-coding trnT-F cpDNA region was used for the first time in aerobiological samples to identify Poaceae pollen. Use of this method that does not require DNA extraction may be a crucial step for real-time pollen monitoring devices to be developed in the future. The correlation strength between pollen and amplified DNA content could be improved using a sampler that has a lower absorption rate, and a more sensitive technique, such as qPCR. © 2019 De Gruyter. All rights reserved.

Yazar Alan Ş.
Sarışahin T.
Şahin A.A.
Kaplan A.
Erdoğan İ.
Pınar N.M.
Yayın Türü Article
Tek Biçim Adres https://hdl.handle.net/20.500.12628/3979
Tek Biçim Adres 10.1515/tjb-2018-0020
Konu Başlıkları DNA quantity
PCR
Poaceae
Pollen identification
TrnT-F region
Koleksiyonlar Araştırma Çıktıları | WoS | Scopus | TR-Dizin | PubMed | SOBİAD
Scopus İndeksli Yayınlar Koleksiyonu
WoS İndeksli Yayınlar Koleksiyonu
Dergi Adı Turkish Journal of Biochemistry
Dergi Cilt Bilgisi 44
Dergi Sayısı 3
Sayfalar 248 - 253
Yayın Yılı 2019
Eser Adı
[dc.title]
A new method to quantify atmospheric Poaceae pollen DNA based on the trnT-F cpDNA region
Yazar
[dc.contributor.author]
Alan Ş.
Yazar
[dc.contributor.author]
Sarışahin T.
Yazar
[dc.contributor.author]
Şahin A.A.
Yazar
[dc.contributor.author]
Kaplan A.
Yazar
[dc.contributor.author]
Erdoğan İ.
Yazar
[dc.contributor.author]
Pınar N.M.
Yayın Yılı
[dc.date.issued]
2019
Yayıncı
[dc.publisher]
De Gruyter
Yayın Türü
[dc.type]
article
Özet
[dc.description.abstract]
Background: Pollen, mold spores, bacteria and viruses are the main biological substances in the atmosphere causing allergic symptoms and disease. Distinguishing pollen and spores is quite time consuming and requires a trained expert. There is a different approach to identification of these substances such as microscopic analysis. However, DNA based identification of these is becoming popular recently. Objective: We evaluated the correlation between the quantity of DNA, which was amplified using trnT-F cpDNA specific primers in samples obtained from a high volume air sampler (HVAS), and concentration of Poaceae pollen collected with a Burkard trap. Materials and methods: Here, we present a method for identifying and quantifying airborne Poaceae pollen using a single step polymerase chain reaction (PCR) technique. Forty daily air samples were collected by HVAS. The method was optimised using two different methods (M1 and M2) and the trnT-F cpDNA region was amplified using a Poaceae specific primer pair. The correlation between the quantity of DNA and pollen concentration was tested using R statistical programming language. Results: Although a significant correlation was obtained between the M1 and M2 methods (R2 = 0.655, p < 0.01), the M2 method was more correlated with pollen concentration. The correlation between pollen and DNA content changed due to episodes that were observed during the pollen season. DNA concentrations from the PCR data were significantly correlated with pollen concentrations determined by light microscopy (R2 = 0.767, p < 0.01) in episode II using the M2 method and during the entire season (R2 = 0.469, p < 0.01) using M2. Conclusions: The M2 method correctly identified Poaceae pollen in mixed air samples from Zonguldak Province. The non-coding trnT-F cpDNA region was used for the first time in aerobiological samples to identify Poaceae pollen. Use of this method that does not require DNA extraction may be a crucial step for real-time pollen monitoring devices to be developed in the future. The correlation strength between pollen and amplified DNA content could be improved using a sampler that has a lower absorption rate, and a more sensitive technique, such as qPCR. © 2019 De Gruyter. All rights reserved.
Kayıt Giriş Tarihi
[dc.date.accessioned]
2019-12-23
Açık Erişim Tarihi
[dc.date.available]
2019-12-23
Yayın Dili
[dc.language.iso]
eng
Konu Başlıkları
[dc.subject]
DNA quantity
Konu Başlıkları
[dc.subject]
PCR
Konu Başlıkları
[dc.subject]
Poaceae
Konu Başlıkları
[dc.subject]
Pollen identification
Konu Başlıkları
[dc.subject]
TrnT-F region
Haklar
[dc.rights]
info:eu-repo/semantics/closedAccess
ISSN
[dc.identifier.issn]
0250-4685
Sponsor YAYINCI
[dc.description.sponsorship]
KBAG-113Z762 Türkiye Bilimsel ve Teknolojik Araştirma Kurumu
Sponsor YAYINCI
[dc.description.sponsorship]
Acknowledgements: This research was partly supported by the Scientific and Technological Research Council of Turkey (TÜBİTAK), Grant No: KBAG-113Z762.
İlk Sayfa Sayısı
[dc.identifier.startpage]
248
Son Sayfa Sayısı
[dc.identifier.endpage]
253
Dergi Adı
[dc.relation.journal]
Turkish Journal of Biochemistry
Dergi Sayısı
[dc.identifier.issue]
3
Dergi Cilt Bilgisi
[dc.identifier.volume]
44
Tek Biçim Adres
[dc.identifier.uri]
https://dx.doi.org/10.1515/tjb-2018-0020
Tek Biçim Adres
[dc.identifier.uri]
https://hdl.handle.net/20.500.12628/3979
Görüntülenme Sayısı ( Şehir )
Görüntülenme Sayısı ( Ülke )
Görüntülenme Sayısı ( Zaman Dağılımı )
Görüntülenme
17
09.12.2022 tarihinden bu yana
İndirme
1
09.12.2022 tarihinden bu yana
Son Erişim Tarihi
09 Şubat 2024 08:29
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pollen method between Poaceae correlation samples concentration trnT-F amplified methods correlated content obtained region technique during season sampler concentrations collected specific quantity substances different identification spores determined significantly reserved improved absorption sensitive rights microscopy observed
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