Kaplan, Oktay İsmail

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Profile URL
https://hdl.handle.net/20.500.12573/2664
Name Variants
Kaplan, O. I.
Kaplan, Oktay I.
Kaplan, Oktay Ismail
Kaplan, Oktay, I
Oktay I Kaplan
Job Title
Doç. Dr.
Email Address
oktay.kaplan@agu.edu.tr
Main Affiliation
04.01. Biyomühendislik
Status
Current Staff
Website
ORCID ID
0000-0002-8733-0920
Scopus Author ID
23472963100
Turkish CoHE Profile ID
134882
Google Scholar ID
YFzvQQUAAAAJ
WoS Researcher ID
F-8531-2015
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5252_Oktayİsmail_Kaplan.jpg (23.19 KB)

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LIFE ON LAND
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DECENT WORK AND ECONOMIC GROWTH
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REDUCED INEQUALITIES
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LIFE BELOW WATER
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SUSTAINABLE CITIES AND COMMUNITIES
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PEACE, JUSTICE AND STRONG INSTITUTIONS
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INDUSTRY, INNOVATION AND INFRASTRUCTURE
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Documents

21

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664

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Scholarly Output

25

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Supervised MSc Theses

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WoS Citation Count

59

Scopus Citation Count

60

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4

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2

WoS Citations per Publication

2.36

Scopus Citations per Publication

2.40

Open Access Source

16

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4

JournalCount
European Journal of Human Genetics5
58th Conference of the European-Society-of-Human-Genetics (ESHG) -- MAY 24-27, 2025 -- Milan, ITALY3
Nucleic ACIds Research2
Current Protocols1
Database-The Journal of Biological Databases and Curation1
Current Page: 1 / 3

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  • Thumbnail Image
    Master Thesis
    Yeni Bir Silya Geni Olan TMEM145'in Karakterizasyonu
    (Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2020) Pir, Mustafa Samet; Kaplan, Oktay İsmail
    Silya ve flagella çoğu organizmada bulunan, mikrotübül yapılı, yüksek korunumlu hücresel bir yapıdır. Bunlar, protozoalarda hareket sağlamadan, çok hücreli canlılarda sinyal iletimine kadar bir çok fonksiyona sahiptir. Silyanın yapısında veya fonksiyonunda meydana gelen bozulmalar insanlarda silyopati denilen çeşitli hastalıklara sebep olur. Silyada meydana gelen bu bozukluklar silya genlerinde veya silya fonksiyonunu etkileyen silya geni olmayan genlerde meydana gelen mutasyonlardan kaynaklanır. Bu yüzden silyopatilerin moleküler temelini ortaya çıkarmaya yardımcı olacak yeni silya genleri keşfetmeye ihtiyaç vardır. GPCR proteini olan, insan TMEM145 geninin ortoloğu olan ve Caenorhabditis elegans'ta bulunan C15A7.2 genini silya geni olarak tanımladık. C15A7.2 geni tarafından kodlanan TMEM-145 proteinin fonksiyonunu araştırdık ve C15A7.2 mutantlarda intraflagellar transport sisteminin hızının yavaşladığını bulduk. Ne tekli, ne de çeşitli çiftli mutantlarda herhangi bir yapısal bozukluk gözlemlemedik. Bu da TMEM-145'in silya yapımında görev almadığını gösteriyor. Silyada bulunan bu genin tam fonksiyonunu öğrenmek için ilave analizler yapılmalıdır.
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    Conference Object
    ConVarT: A New Search Engine for Orthologous Variants for Functional Inference of Human Genetic Variants
    (Springernature, 2022) Pir, Mustafa S.; Bilgin, Halil I.; Sayici, Ahmet; Coskun, Fatih; Torun, Furkan M.; Zhao, Pei; Kaplan, Oktay I.
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    Article
    Citation - WoS: 1
    Citation - Scopus: 1
    ConVarT: Search Engine for Missense Variants Between Humans and Other Organisms
    (Wiley, 2022) Pir, Mustafa S.; Cevik, Sebiha; Kaplan, Oktay I.
    ConVarT (https://convart.org/) is a search engine for searching for conjugate variants between humans and other species. The search engine is based on matching conjugate variants called MatchVars between species. Matching equivalent variants requires correct alignment of orthologous proteins with the use of multiple sequence alignments (MSA). Indeed, the ConVarT pipeline has performed over a million MSAs and integrated variants and variant-specific annotations (pathogenicity, phenotypic variants; etc.) into the corresponding positions on MSAs. When a clinically relevant variant is discovered whose functional relevance is unknown, ConVarT offers clinician scientists the possibility to search for a MatchVar in other species and to look for functional data on that variant. Fortunately, ConVarT enables users to paste a protein sequence in FASTA format to search for human orthologous proteins. A pairwise sequence alignment (PSA) is then performed between the provided protein sequence and the human orthologous protein, allowing users to visualize human variants on the PSA. Here, we describe the step-by-step usage of ConVarT.
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    Article
    Citation - WoS: 3
    Citation - Scopus: 3
    MSABrowser: Dynamic and Fast Visualization of Sequence Alignments, Variations and Annotations
    (Oxford Univ Press, 2021) Torun, Furkan M.; Bilgin, Halil, I; Kaplan, Oktay, I
    Sequence alignment is an excellent way to visualize the similarities and differences between DNA, RNA or protein sequences, yet it is currently difficult to jointly view sequence alignment data with genetic variations, modifications such as post-translational modifications and annotations (i.e. protein domains). Here, we present the MSABrowser tool that makes it easy to co-visualize genetic variations, modifications and annotations on the respective positions of amino acids or nucleotides in pairwise or multiple sequence alignments. MSABrowser is developed entirely in JavaScript and works on any modern web browser at any platform, including Linux, Mac OS X and Windows systems without any installation. MSABrowser is also freely available for the benefit of the scientific community.
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    Master Thesis
    Hastalık Geni Karakterizasyonu
    (2025) Yetgin, Fatma Nihal; Kaplan, Oktay İsmail
    Hasta olmak insan yaşamının bir parçasıdır. Bazı hastalıklara sık rastlanırken bazı hastalıklar nadirdir. Günümüzde 7000den fazla nadir hastalık vardır ve sayısı artmaktadır. Silyopatiler de nadir hastalıklardan biridir. Silyopatiler, silyanın fonksiyonunu ya da yapısını etkileyen mutasyonlar sonucu oluşan hastalıklardır. Silya birçok kompartmandan oluşan, hücreden dışarıya doğru uzanan bir organeldir ve Hedgehog sinyal yolağı gibi bazı önemli sinyal yolaklarını etkiler. 2014 yılında EFCAB7'in EVC ve EVC2 proteinleri ile ilişkisi bulunmuştur. EVC ve EVC2 genlerindeki mutasyonlar Ellis van Creveld hastalığına sebep olmaktadır. 2023'de ise sendromik olmayan postaksial polidaktiliye sebep olduğu keşfedilmiştir. Ancak EFCAB7 ile silya arasındaki ilişki yeterince aydınlatılamamıştır. Bu çalışmada, mikroskobik yöntemler ve fonksiyonel deneylerle EFCAB7 ile cilia arasındaki ilişki incelenmiştir. Sonuçlarımız, efcab-7 mutantlarının silialarının vahşi tipe kıyasla önemli ölçüde daha kısa olduğunu, buna karşın IFT (intraflagellar transport) hızı ve partikül sayısında belirgin bir değişiklik olmadığını göstermiştir. Ayrıca, normal koşullarda silyaya girmeyen ELMOD-3 proteini, efcab-7 mutantlarında da silyaya giriş yapmamış ve bu durum silial geçidin sağlam olduğunu ortaya koymuştur. Beklenmedik bir şekilde, efcab-7 mutantlarının hareket kabiliyetinin azaldığı ve akson sayısının da azaldığı gözlemlenmiştir, bu da EFCAB7'nin nöronal veya kas fonksiyonunda ek bir rolü olabileceğini düşündürmektedir. Bu bulgular, EFCAB7'nin silya ve nöronal bütünlüğün korunmasındaki fonksiyonlarını genişletmekte ve ilişkili nadir hastalıkların patogenezi hakkında yeni bilgiler sağlamaktadır.
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    Conference Object
    Understanding the Role of FAM120A Gene in a Neurodevelopmental Disorder
    (Springernature, 2024) Sezer, Abdullah; Pucak, Damla; Cevik, Sebiha; Kaplan, Oktay I.
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    Conference Object
    PATL1: A Novel Candidate Gene for Neurodevelopmental Disorders with Motor Impairment
    (Springer Nature, 2025) Alders, Marielle; Maas, Saskia; Sezer, Abdullah; Percin, Ferda Emriye; Kayhan, Gulsum; Kaplan, Oktay Ismail; Yenisert, Ferhan
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    Article
    The Joubert syndrome protein CEP41 is excluded from the distal segment of cilia in C. elegans
    (2021) Sebiha Cevik; Oktay I Kaplan
    Rare diseases are a fundamental issue in today's world, affecting more than 300 million individuals worldwide. According to data from Orphanet and OMIM, about 50-60 new conditions are added to the list of over 6,000 clinically distinct diseases each year, rendering disease diagnosis and treatment even more challenging. Ciliopathies comprise a heterogeneous category of rare diseases made up of over 35 distinct diseases, including Joubert syndrome (JBTS; OMIM 213300), that are caused by functional and structural defects in cilia. JBTS is an autosomal recessive condition characterized by a range of symptoms, including cerebellar vermis hypoplasia and poor muscle tone. There are now a total of 38 genes that cause JBTS, almost all of which encode protein products that are found in cilia and cilia-associated compartments, such as the basal body and transition zone. CEP41 is a JBTS-associated protein that is found in cilia and the basal body of mammals, but its localization in other ciliary organisms remains elusive. C. elegans is an excellent model organism for studying the molecular mechanisms of rare diseases like JBTS. We, therefore, decided to use C. elegans to identify the localization of CEP41. Our microscopy analysis revealed that CEPH-41(CEntrosomal Protein Homolog 41) not only localizes to cilia but is excluded from the distal segment of the amphid and phasmid cilia in C. elegans. Furthermore, we discovered a putative X-box motif located in the promoter of ceph-41 and the expression of ceph-41 is regulated by DAF-19, a sole Regulatory Factor X (RFX) transcription factor.
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    Article
    Investigating the Impact of Birt–hogg–dubé Syndrome Associated Folliculin (Flcn) and Retinitis Pigmentosa 2 (Rp2) Loss on Cilia Function and Morphology
    (2024) Kaplan, Oktay Ismail
    Folliculin (FLCN), a GTPase-activating protein (GAP), has been linked to Birt–Hogg–Dubé syndrome, the mTORC1 signaling pathway and cilia. Disruptions in cilia structure and function lead to a group of diseases known as ciliopathies. Birt-Hogg-Dubé syndrome is one of 35 different ciliopathy diseases and there are more than 250 genes that cause ciliopathy diseases. FLCN interacts with kinesin-2 along cilia. The specific role of FLCN in regulating Kinesin-IFT trafficking has, however, remained unclear. In the current study, we investigated the effects of flcn-1 loss (the human ortholog of FLCN) on kinesin and IFT trafficking in C. elegans. The loss of flcn-1 alone did not result in any apparent alterations to kinesin or IFT trafficking within the cilia. However, when we combined the deletion of flcn-1 with the deletion of Retinitis Pigmentosa 2 (RP2), another GAP protein, the ciliary entry of a non-ciliary membrane protein TRAM-1 (Translocation Associated Membrane Protein 1) occured. Additionally, although cilia length was unaltered, our analysis of double mutants revealed the extra branch in wing AWB cilia morphology but not the single rod-like PHA/PHB cilia. In summary, our study reveals the previously unknown functions of FLCN in ciliary gating and cilia morphology in C. elegans
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    Article
    Citation - WoS: 3
    Citation - Scopus: 4
    Matching Variants for Functional Characterization of Genetic Variants
    (Oxford Univ Press inc, 2023) Cevik, Sebiha; Zhao, Pei; Zorluer, Atiyye; Pir, Mustafa S.; Bian, Wenyin; Kaplan, Oktay, I
    Rapid and low-cost sequencing, as well as computer analysis, have facilitated the diagnosis of many genetic diseases, resulting in a substantial rise in the number of disease-associated genes. However, genetic diagnosis of many disorders remains problematic due to the lack of interpretation for many genetic variants, especially missenses, the infeasibility of high-throughput experiments on mammals, and the shortcomings of computational prediction technologies. Additionally, the available mutant databases are not well-utilized. Toward this end, we used Caenorhabditis elegans mutant resources to delineate the functions of eight missense variants (V444I, V517D, E610K, L732F, E817K, H873P, R1105K, and G1205E) and two stop codons (W937stop and Q1434stop), including several matching variants (MatchVar) with human in ciliopathy associated IFT-140 (also called CHE-11)//IFT140 (intraflagellar transport protein 140). Moreover, MatchVars carrying C. elegans mutants, including IFT-140(G680S) and IFT-140(P702A) for the human (G704S) (dbSNP: rs150745099) and P726A (dbSNP: rs1057518064 and a conflicting variation) were created using CRISPR/Cas9. IFT140 is a key component of IFT complex A (IFT-A), which is involved in the retrograde transport of IFT along cilia and the entrance of G protein-coupled receptors into cilia. Functional analysis of all 10 variants revealed that P702A and W937stop, but not others phenocopied the ciliary phenotypes (short cilia, IFT accumulations, mislocalization of membrane proteins, and cilia entry of nonciliary proteins) of the IFT-140 null mutant, indicating that both P702A and W937stop are phenotypic in C. elegans. Our functional data offered experimental support for interpreting human variants, by using ready-to-use mutants carrying MatchVars and generating MatchVars with CRISPR/Cas9.