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  1. Book ; Online ; E-Book: Oil crop genomics

    Tombuloglu, Huseyin

    2021  

    Author's details edited by Huseyin Tombuloglu [and three others]
    Keywords Oilseed plants/Genetics ; Oilseed plants/Genome mapping ; Plantes oleaginoses ; Genòmica ; Genètica vegetal ; Conreu
    Subject code 633.85
    Language English
    Size 1 online resource (444 pages)
    Publisher Springer
    Publishing place Cham, Switzerland
    Document type Book ; Online ; E-Book
    Note Includes index.
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 3-030-70420-3 ; 3-030-70419-X ; 978-3-030-70420-9 ; 978-3-030-70419-3
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

    Full text online

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  2. Book ; Online ; E-Book: Molecular Impacts of Nanoparticles on Plants and Algae

    Tombuloglu, Huseyin / Tombuloglu, Guzin / Al-Suhaimi, Ebtesam / Baykal, Abdulhadi / Hakeem, Khalid Rehman

    (Nanomaterial-Plant Interactions Series)

    2024  

    Series title Nanomaterial-Plant Interactions Series
    Subject code 581.7
    Language English
    Size 1 online resource (491 pages)
    Edition 1st ed.
    Publisher Elsevier Science & Technology
    Publishing place San Diego
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 0-323-95722-6 ; 0-323-95721-8 ; 978-0-323-95722-9 ; 978-0-323-95721-2
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  3. Article ; Online: Genome-wide identification and expression analysis of R2R3, 3R- and 4R-MYB transcription factors during lignin biosynthesis in flax (Linum usitatissimum).

    Tombuloglu, Huseyin

    Genomics

    2019  Volume 112, Issue 1, Page(s) 782–795

    Abstract: MYB transcription factors (TFs) have vital roles in regulating lignin or fiber development. Flax (Linum usitatissimum) is known as one of the plants with high fiber production capacity. However, no studies have been conducted to identify and characterize ...

    Abstract MYB transcription factors (TFs) have vital roles in regulating lignin or fiber development. Flax (Linum usitatissimum) is known as one of the plants with high fiber production capacity. However, no studies have been conducted to identify and characterize MYB TFs in the flax genome. Results showed that flax genome harbours 167 R2R3, seven 3R, and one 4R-type MYB TFs. 22 MYB genes (%13) were estimated to be tandem duplicated dated around 13.3-86.98 Mya. 130 flax MYB members have apparent orthologous with Arabidopsis, in which 17 R2R3 MYBs are associated with lignin biosynthesis. MYB062, MYB072, MYB096, MYB141, and MYB146 genes were up-regulated in tissues having higher lignin production capacity. In opposite, MYB012 and MYB113 genes were down-regulated which points out the involvement of those genes in the lignin biosynthesis mechanism. This comprehensive study can provide a basis for understanding the role of MYBs in fiber or lignin production in flax.
    MeSH term(s) Arabidopsis/genetics ; Flax/anatomy & histology ; Flax/genetics ; Flax/metabolism ; Gene Duplication ; Genome, Plant ; Lignin/biosynthesis ; Multigene Family ; Phylogeny ; Plant Proteins/chemistry ; Plant Proteins/classification ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plant Stems/anatomy & histology ; Protein Domains ; Transcription Factors/chemistry ; Transcription Factors/classification ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances Plant Proteins ; Transcription Factors ; Lignin (9005-53-2)
    Language English
    Publishing date 2019-05-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2019.05.017
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  4. Article ; Online: Effects of foliar iron oxide nanoparticles (Fe

    Tombuloglu, Guzin / Tombuloglu, Huseyin / Slimani, Yassine / Almessiere, Munirah A / Baykal, Abdulhadi / Bostancioglu, Safiye Merve / Kirat, Gokhan / Ercan, Ismail

    Plant physiology and biochemistry : PPB

    2024  Volume 210, Page(s) 108616

    Abstract: This study aims to examine the effect of foliar magnetic iron oxide ( ... ...

    Abstract This study aims to examine the effect of foliar magnetic iron oxide (Fe
    MeSH term(s) Solanum lycopersicum/genetics ; Solanum lycopersicum/drug effects ; Solanum lycopersicum/metabolism ; Photosynthesis/drug effects ; Plant Leaves/metabolism ; Plant Leaves/drug effects ; Magnetic Iron Oxide Nanoparticles ; Chlorophyll/metabolism ; Minerals/metabolism ; Carotenoids/metabolism ; Gene Expression Regulation, Plant/drug effects ; Ferric Compounds
    Chemical Substances Chlorophyll (1406-65-1) ; Minerals ; Carotenoids (36-88-4) ; ferric oxide (1K09F3G675) ; Ferric Compounds
    Language English
    Publishing date 2024-04-08
    Publishing country France
    Document type Journal Article
    ZDB-ID 742978-2
    ISSN 1873-2690 ; 0981-9428
    ISSN (online) 1873-2690
    ISSN 0981-9428
    DOI 10.1016/j.plaphy.2024.108616
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 2696: Show issues
    Z 2005/727: Show issues

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  5. Article ; Online: Development of loop-mediated isothermal amplification (LAMP) assays using five primers reduces the false-positive rate in COVID-19 diagnosis.

    Alhamid, Galyah / Tombuloglu, Huseyin / Al-Suhaimi, Ebtesam

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 5066

    Abstract: The reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a cheaper and faster testing alternative for detecting SARS-CoV-2. However, a high false-positive rate due to misamplification is one of the major limitations. To overcome ... ...

    Abstract The reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a cheaper and faster testing alternative for detecting SARS-CoV-2. However, a high false-positive rate due to misamplification is one of the major limitations. To overcome misamplifications, we developed colorimetric and fluorometric RT-LAMP assays using five LAMP primers, instead of six. The gold-standard RT-PCR technique verified the assays' performance. Compared to other primer sets with six primers (N, S, and RdRp), the E-ID1 primer set, including five primers, performed superbly on both colorimetric and fluorometric assays. The sensitivity of colorimetric and fluorometric assays was 89.5% and 92.2%, respectively, with a limit of detection of 20 copies/µL. The colorimetric RT-LAMP had a specificity of 97.2% and an accuracy of 94.5%, while the fluorometric RT-LAMP obtained 99% and 96.7%, respectively. No misamplification was evident even after 120 min, which is crucial for the success of this technique. These findings are important to support the use of RT-LAMP in the healthcare systems in fighting COVID-19.
    MeSH term(s) Humans ; COVID-19/diagnosis ; SARS-CoV-2/genetics ; COVID-19 Testing ; Molecular Diagnostic Techniques/methods ; Nucleic Acid Amplification Techniques/methods ; Sensitivity and Specificity ; RNA, Viral
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2023-03-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-31760-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Ultrasensitive and fast detection of SARS-CoV-2 using RT-LAMP without pH-dependent dye.

    Alsaeed, Moneerah / Alhamid, Galyah / Tombuloglu, Huseyin / Kabanja, Juma H / Karagoz, Aysel / Tombuloglu, Guzin / Rabaan, Ali A / Al-Suhaimi, Ebtesam / Unver, Turgay

    Functional & integrative genomics

    2024  Volume 24, Issue 1, Page(s) 16

    Abstract: This study investigates the performance of reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the colorimetric detection of SARS-CoV-2 using fluorometric dye, namely, calcein. The detection limit (LoD) with the N-ID1 primer ... ...

    Abstract This study investigates the performance of reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the colorimetric detection of SARS-CoV-2 using fluorometric dye, namely, calcein. The detection limit (LoD) with the N-ID1 primer set resulted in superior performance, corresponding to ~ 2 copies/reaction or ~ 0.1 copies/μL of the RNA sample. The color development can be observed by the naked eye, using an ultraviolet (UV) transilluminator or a hand-UV light without the requirement of expensive devices. The average time-to-reaction (TTR) value was 26.2 min in high-copy number samples, while it was about 50 min in rRT-PCR. A mobile application was proposed to quantify the positive and negative results based on the three-color spaces (RGB, Lab, and HSB). Compared to rRT-PCR (n = 67), this assay allows fast and sensitive visual detection of SARS-CoV-2, with high sensitivity (90.9%), selectivity (100%), and accuracy (94.03%). Besides, the assay was sensitive regardless of variants. Since this assay uses a fluorescent dye for visual observation, it can be easily adapted in RT-LAMP assays with high sensitivity. Thus, it can be utilized in low-source centers and field testing such as conferences, sports meetings, refugee camps, companies, and schools.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; Sensitivity and Specificity ; Hydrogen-Ion Concentration ; RNA, Viral/genetics ; Nucleic Acid Amplification Techniques ; Molecular Diagnostic Techniques
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2024-01-20
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2014670-X
    ISSN 1438-7948 ; 1438-793X
    ISSN (online) 1438-7948
    ISSN 1438-793X
    DOI 10.1007/s10142-024-01297-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5230: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  7. Article: Genome-wide identification and expression analysis of R2R3, 3R- and 4R-MYB transcription factors during lignin biosynthesis in flax (Linum usitatissimum)

    Tombuloglu, Huseyin

    Genomics. 2019 May 20,

    2019  

    Abstract: MYB transcription factors (TFs) have vital roles in regulating lignin or fiber development. Flax (Linum usitatissimum) is known as one of the plants with high fiber production capacity. However, no studies have been conducted to identify and characterize ...

    Abstract MYB transcription factors (TFs) have vital roles in regulating lignin or fiber development. Flax (Linum usitatissimum) is known as one of the plants with high fiber production capacity. However, no studies have been conducted to identify and characterize MYB TFs in the flax genome. Results showed that flax genome harbours 167 R2R3, seven 3R, and one 4R-type MYB TFs. 22 MYB genes (%13) were estimated to be tandem duplicated dated around 13.3–86.98 Mya. 130 flax MYB members have apparent orthologous with Arabidopsis, in which 17 R2R3 MYBs are associated with lignin biosynthesis. MYB062, MYB072, MYB096, MYB141, and MYB146 genes were up-regulated in tissues having higher lignin production capacity. In opposite, MYB012 and MYB113 genes were down-regulated which points out the involvement of those genes in the lignin biosynthesis mechanism. This comprehensive study can provide a basis for understanding the role of MYBs in fiber or lignin production in flax.
    Keywords Arabidopsis ; Linum usitatissimum ; biosynthesis ; flax ; gene expression regulation ; genes ; lignin ; tissues ; transcription factors
    Language English
    Dates of publication 2019-0520
    Publishing place Elsevier Inc.
    Document type Article
    Note Pre-press version
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2019.05.017
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2367: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  8. Article ; Online: Development of loop-mediated isothermal amplification (LAMP) assays using five primers reduces the false-positive rate in COVID-19 diagnosis

    Galyah Alhamid / Huseyin Tombuloglu / Ebtesam Al-Suhaimi

    Scientific Reports, Vol 13, Iss 1, Pp 1-

    2023  Volume 13

    Abstract: Abstract The reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a cheaper and faster testing alternative for detecting SARS-CoV-2. However, a high false-positive rate due to misamplification is one of the major limitations. To ... ...

    Abstract Abstract The reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a cheaper and faster testing alternative for detecting SARS-CoV-2. However, a high false-positive rate due to misamplification is one of the major limitations. To overcome misamplifications, we developed colorimetric and fluorometric RT-LAMP assays using five LAMP primers, instead of six. The gold-standard RT-PCR technique verified the assays' performance. Compared to other primer sets with six primers (N, S, and RdRp), the E-ID1 primer set, including five primers, performed superbly on both colorimetric and fluorometric assays. The sensitivity of colorimetric and fluorometric assays was 89.5% and 92.2%, respectively, with a limit of detection of 20 copies/µL. The colorimetric RT-LAMP had a specificity of 97.2% and an accuracy of 94.5%, while the fluorometric RT-LAMP obtained 99% and 96.7%, respectively. No misamplification was evident even after 120 min, which is crucial for the success of this technique. These findings are important to support the use of RT-LAMP in the healthcare systems in fighting COVID-19.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  9. Article ; Online: Comparative transcriptome analysis of resistant and cultivated tomato lines in response to Clavibacter michiganensis subsp. michiganensis.

    Basim, Huseyin / Basim, Esin / Tombuloglu, Huseyin / Unver, Turgay

    Genomics

    2021  Volume 113, Issue 4, Page(s) 2455–2467

    Abstract: Clavibacter michiganensis subsp. michiganensis (Cmm) is a gram-positive bacterium causing destructive bacterial wilt and canker disease in tomato. Herein, a comparative transcriptome analysis was performed on Cmm-resistant and -susceptible tomato lines. ... ...

    Abstract Clavibacter michiganensis subsp. michiganensis (Cmm) is a gram-positive bacterium causing destructive bacterial wilt and canker disease in tomato. Herein, a comparative transcriptome analysis was performed on Cmm-resistant and -susceptible tomato lines. Tomato seedlings were inoculated with Cmm and harvested for transcriptome analysis after 4 and 8 day time-points. Twenty-four transcriptome libraries were profiled by RNA sequencing approach. Total of 545 million clean reads was generated. 1642 and 2715 differentially expressed genes (DEG) were identified in susceptible lines within 4 and 8 days after inoculation (DAI), respectively. In resistant lines, 1731 and 1281 DEGs were found following 4 and 8 DAI, respectively. Gene Ontology analysis resulted in a higher number of genes involved in biological processes and molecular functions in susceptible lines. On the other hand, such biological processes, "defense response", and "response to stress" were distinctly indicated in resistant lines which were not found in susceptible ones upon inoculation, according to the gene set enrichment analyses. Upon Cmm-inoculation, several defense responsive genes were found to be differentially expressed. Of which 26 genes were in the resistant line and three were in the susceptible line. This study helps to understand the transcriptome response of Cmm-resistant and -susceptible tomato lines. The results provide comprehensive data for molecular breeding studies, for the purpose to control of the pathogen in tomato.
    MeSH term(s) Clavibacter ; Gene Expression Profiling ; Lycopersicon esculentum/genetics ; Plant Diseases/genetics ; Plant Diseases/microbiology ; Transcriptome
    Language English
    Publishing date 2021-05-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2021.05.033
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Uptake and bioaccumulation of iron oxide nanoparticles (Fe

    Tombuloglu, Guzin / Aldahnem, Anwar / Tombuloglu, Huseyin / Slimani, Yassine / Akhtar, Sultan / Hakeem, Khalid Rehman / Almessiere, Munirah A / Baykal, Abdulhadi / Ercan, Ismail / Manikandan, Ayyar

    Environmental science and pollution research international

    2024  Volume 31, Issue 14, Page(s) 22171–22186

    Abstract: Root-to-shoot translocation of nanoparticles (NPs) is a matter of interest due to their possible unprecedented effects on biota. Properties of NPs, such as structure, surface charge or coating, and size, determine their uptake by cells. This study ... ...

    Abstract Root-to-shoot translocation of nanoparticles (NPs) is a matter of interest due to their possible unprecedented effects on biota. Properties of NPs, such as structure, surface charge or coating, and size, determine their uptake by cells. This study investigates the size effect of iron oxide (Fe
    MeSH term(s) Hordeum/metabolism ; Particle Size ; Bioaccumulation ; Hydrogen Peroxide/metabolism ; Seedlings ; Magnetic Iron Oxide Nanoparticles
    Chemical Substances Hydrogen Peroxide (BBX060AN9V)
    Language English
    Publishing date 2024-02-26
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1178791-0
    ISSN 1614-7499 ; 0944-1344
    ISSN (online) 1614-7499
    ISSN 0944-1344
    DOI 10.1007/s11356-024-32378-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 5915: Show issues

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