Browsing by Author "Mehmet Cengiz BALOĞLU"

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Antibacterial Effects of Phlomoides molucelloides (Bunge) Salmaki
(2022-12-15) Anfal Izaldeen Mutar AL KATEEB; Enis Fuat TÜFEKCI; Mehmet Cengiz BALOĞLU; Gokhan ZENGIN; Evren YILDIZTUGAY
The insufficiency of existing antibiotics in the combat against antibiotics-resistant bacteria has necessitated the discovery of new and effective antibacterial drugs. The discovery that bacteria synthesize various virulence factors by the quorum sensing system has suggested that quorum sensing inhibitors may be used in the fight against infectious diseases. This study aimed to determine the antibacterial and anti-quorum sensing activities of methanol and water extracts of aerial and root parts of Phlomoides molucelloides (Bunge) Salmaki. The minimal inhibitory concentration (MIC) values of the extracts were investigated against reference bacterial strains using the broth microdilution method. Anti-quorum sensing activities were examined by violacein and pyocyanin pigments inhibition and swarming motility inhibition assays against Chromobacterium violaceum ATCC 12472 and Pseudomonas aeruginosa PAO1 bioreporter strains. The antibiofilm activities of the extracts were tested against P. aeruginosa PAO1 using the crystal violet staining method. The MIC value (> 2000 µg/mL) of all extracts against the tested bacteria could not be determined at the concentrations studied. All extracts partially inhibited the swarming motility of P. aeruginosa. Methanol extract of the aerial part inhibited pyocyanin production by 81.7% without interfering with P. aeruginosa growth. The extracts had no significant inhibitory activity on biofilm formation and violacein pigment production. These results showed that the extracts of P. molucelloides may be good anti-quorum sensing agents. Further research can be done to elucidate the mechanisms underlying these biological activities.
Antimicrobial and anti-quorum sensing activities of giant fennel (Ferula elaeochytris Korovin) from the Hatay region
(2020-03-01) Sarah AKAR; Nilay ÇÖPLÜ; Mehmet Cengiz BALOĞLU; Anfal Izaldeen ALKATEEB; Enis Fuat TÜFEKCI; Muammer KİRAZ; Orhan CORUM; Yasemin Celik ALTUNOĞLU
Aim: Today, increasing antibiotic resistance has focused the science world onthe discovery of new antimicrobial molecules or the development of alternative methods of struggle. One of the alternative methods is thought to be inhibition of bacterial quorum sensing (QS). Because the QS system performs acrucial part in the synthesis of virulence factors in bacteria. Numerous medicinal plants are known to have promising antimicrobial and anti-QS activities.One of these plants may be giant fennel (Ferula elaeochytris Korovin), whichhas been extensively used in Anatolia for years. Therefore, it was aimed to investigate the antimicrobial and anti-QS activities of the root extract of F. elaeochytris Korovin in this study. .Materials and Methods: The antimicrobial activity of the extract was screened by disc diffusion assay against various microorganisms. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) ofthe extract against sensitive strain(s) were determined using broth microdilution assay. Anti-QS activity investigated on inhibition of violacein and pyocyanin production in Chromobacterium violaceum and Pseudomonas aeruginosabioreporter strains, respectively.Results: The extract exhibited the antimicrobial activity against only Staphylococcus aureus (zone of inhibition (ZOI) = 9.3±0.6 mm). The MIC and theMBC values were determined as 4.4±1.9 mg/mL and >105 mg/mL, respectively. No inhibition of violacein production was detected. Pyocyanin productionwas reduced by 60% and 82% at sub-MIC concentrations (at 1.64 mg/mL and3.28 mg/mL, respectively) as against the control (p<0.05) without suppressing bacterial growth.Conclusion: This study shows that the root extract of F. elaeochytris Korovinmay be a good candidate to develop antistaphylococcal and anti-QS agents.
BAZI KAVAK (POPULUS L.) TAKSONLARININ KADMIYUMA KARŞI FITOEKSTRAKSIYON ROLLERI
(2021-04-01) Sezgin AYAN; Mehmet Cengiz BALOĞLU; Esra Nurten YER ÇELİK
Kadmiyum (Cd) ile kontamine olmuş toprakların ıslah başarısı; dokularına Cd birikmesine izin veren bitkilerin seçimine ve kullanımına bağlıdır. Kavak taksonlarının hızlı büyüme, derin kök sistemlerine sahip olma ve kısa rotasyonla işletilebilme özellikleri yeşil ıslah için kullanılmalarına olanak sağlamaktadır. Bu araştırmada; altı kavak taksonu/klonu araştırmaya obje olmuştur. Bunlar; Populus alba L. (Akkavak), P. tremula L. (Titrek kavak), P. nigra L. (Karakavak) klon: Geyve ve N03.368A ve melez kavak klonları P. euramericana Dode. Guinier I-214 ve P. deltoides Bartr / Samsun (I-77/51). Kavak taksonlarının yaprak, kök ve dal aksamlarında Cd birikme miktarları Atomik Absorpsiyon Spektrometresi (AAS) cihazı ile belirlenmiştir. Araştırmacılar Cd birikimi yapan bitki dokularını; en çok biriken aksamdan en az birikim yapan doku kısmına doğru; kök> gövde> yapraklar> meyve> tohum olarak sıralamaktadır. Çalışma kapsamında; yaprak örneklerinin analizi sonucunda; P. tremula'da 12,45 ppm miktarında en yüksek Cd miktarı tespit edilirken, minimum kadmiyum birikimi, 0,84 ppm ile P. alba türlerinde tespit edilmiştir. Kök örneklerinin analizinde; en yüksek kadmiyum miktarı 34 ppm miktarıyla P. euramericana I-214'te, en düşük birikim miktarı ise P. alba türünde 4.6 ppm olarak saptanmıştır. Dal örneklerinde ise; en yüksek kadmiyum miktarı 5,54 ppm ile P. deltoides Samsun (I-77/51) klonunda bulunmuştur. Minimum kadmiyum birikimi ise, P. nigra Geyve klonunda 0.44 ppm seviyesinde belirlenmiştir. Ayrıca araştırma sonucuna göre; Kavak taksonlarında sırasıyla en yüksek Cd birikimi yapan dokuların kök, dal ve yaprak olduğu tespit edilmiştir.
Determination of PER-1 and OXA-10-like ExtendedSpectrum Beta-Lactamases Frequency in CeftazidimeResistant Pseudomonas aeruginosa Strains Isolated in Kastamonu Training and Research Hospital, Turkey
(2022-03-01) Sarah AKAR; Mehmet Cengiz BALOĞLU; Nilay ÇÖPLÜ; Yasemin ÇELİK ALTUNOĞLU; Enis Fuat TÜFEKCİ; Çetin KILINÇ
Introduction: Detecting Pseudomonas aeruginosa strains producing extended-spectrum beta-lactamase (ESBL) in the hospital setting and taking necessary precautions against them is important for infection control and public health. This study aimed to investigate PER-1 and OXA-10-like ESBLs production frequency in ceftazidime-resistant P. aeruginosa obtained from Kastamonu Training and Research Hospital. Materials and Methods: Forty-two ceftazidime-resistant P. aeruginosa strains from different patients between April 2018 and March 2020 were included in the study. Identification of the strains and antibiotic susceptibility tests were studied according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria by VITEK 2 Compact automated system (BioMerieux, France). ESBL production of the strains was studied by combined disk test, phenotypically. The presence of PER-1 and OXA-10-like genes was investigated by polymerase chain reaction (PCR). Confirmation of the PCR product was done using DNA sequencing on an ABI PRISM 3130XL Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). Results: The resistance rates of the strains were: 19%, 81%, 88%, 88%, 91%, 95%, and 95% for amikacin, gentamicin, meropenem, cefepime, imipenem, piperacillin-tazobactam, and ciprofloxacin, respectively. Twenty-seven (64%) strains had the ESBL phenotype. Only one strain had PER-1 gene. OXA-10-like gene was not found in any strains. PER-1 sequence was identical and corresponded to the published sequences for PER-1 gene in GenBank at the National Center for Biotechnology Information. Conclusion: These results showed that PER-1 and OXA-10-like genes were not common among ceftazidime-resistant P. aeruginosa strains obtained from our hospital. ESBL production can be determined phenotypically in ceftazidime-resistant P. aeruginosa strains. However, confirming the results with molecular tests is significant for epidemiological studies.
Effect of drought stress on oxidative damage and antioxidant enzyme activity in melon seedlings
(2013-11-01) Mehmet Cengiz BALOĞLU; Musa KAVAS; Fatma Selin KÖSE; Derya GÖKÇAY; Oya AKÇA
Drought stress is one of the most serious environmental limitations affecting the growth and productivity of plants. In the current study, oxidative damage and antioxidant responses under polyethylene glycol (PEG)-induced osmotic stress were compared in 2 melon cultivars, Kırkağac and Galia. Melon seedlings were subjected to PEG-6000 solutions of 2 different osmotic potentials, 0.2 MPa and 0.4 MPa. Various physiological parameters, malondialdehyde (MDA), proline content, and antioxidant enzymes including catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR) were measured. A reduction in fresh and dry weights of shoot and root tissues was observed. Significant proline accumulation was detected with increasing osmotic potential for both cultivars. A significant rise in MDA was detected in Kırkağac at 0.4 MPa osmotic potential. In Galia hydrogen peroxide ($H_{2}O_{2}$) content increased significantly as PEG concentration increased. CAT showed significantly increased activity only at 0.4 MPa osmotic potential in both cultivars. PEG-induced osmotic stress altered GR activity in both cultivars. These results suggest that (i) Galia is more tolerant than Kırkağac, and (ii) drought tolerance in both cultivars might be closely related to an increase in capacity for antioxidant enzyme activity and the osmoprotective function of proline. Comparing these responses will help to identify drought tolerance mechanisms in melon cultivars.
Enhanced salt tolerance of transgenic tobacco expressing a wheat salt tolerance gene
(2016-02-01) Musa KAVAS; Ayşe Meral YÜCEL; Hüseyin Avni ÖRTEM; Mehmet Cengiz BALOĞLU
Soil salinity is one of the most important limiting factors of agricultural productivity in the world. The Triticum aestivum salt tolerance-related gene (TaSTRG) possesses a functional response to salt and drought stress conditions. A variety of stress factors, such as salt, drought, abscisic acid, and cold, may induce the expression of TaSTRG in wheat. In this study, the TaSTRG gene was transferred to tobacco via Agrobacterium-mediated transformation. Overexpression of TaSTRG in transgenic tobacco plants indicated higher salt tolerance and mediated more vigorous growth than in wild-type plants. Under salt stress conditions, the transgenic tobacco plants had higher germination and survival rates and longer root length than the control plants. Under salt treatments (200-250 mM), TaSTRG-overexpressing tobacco plants accumulated a higher amount of proline and had significantly lower malondialdehyde content than wild-type plants. Furthermore, transgene inheritance followed Mendelian laws, indicating the stability of TaSTRG in transgenic tobacco plants. These results indicated that the wheat TaSTRG gene plays an important role in responding to salt stress.
Evaluation of genotoxic and cytologic effects of environmental stressin wheat species with different ploidy levels
(2016-02-01) Mehmet Cengiz BALOĞLU; Yasemin ALTUNOĞLU ÇELİK; Sefa PEKOL
Drought and salinity induce biochemical, physiological, morphological, and genetic responses in plants. To understand the damage to different wheat species caused by these stresses, we investigated root-shoot growth, cell division, chromosomal aberrations, and nucleolus organizer regions (AgNORs) in root tip cells. Inhibition of root and shoot growth were observed in diploid, tetraploid, and hexaploid wheat genotypes after salt and drought stresses. Both stresses had adverse effects on dividing cells in root tips of all wheat species and caused a decrease in mitotic index values. Salt and drought lead to the induction of chromosome aberrations and repression of interphase AgNOR parameters. Both treatments produced different mitotic abnormalities including chromosomal stickiness, c-mitosis, and micronuclei formation, which indicated their action on the mitotic spindle. Reduction in AgNOR parameters showed that salt and drought may decrease the level of ribosomal biogenesis and reduce the length of the cell cycle. Because of the toxicity of Na ions, salinity inhibited all parameters at a higher degree than drought in all Triticum species. Cytotoxic effects of salinity and drought were mainly observed in meristematic cells in all wheat species. This comprehensive analysis may provide valuable information for understanding the effects of salt and drought stresses on cytogenetics of wheat species.
Fagaceae familyasında ısı şoku protein 70 gen ailesinin (Hsp70) tanımlanması ve biyoinformatik analizleri
(2016-04-01) Sezgin AYAN; Mehmet Cengiz BALOĞLU; Esra Nurten YER; Yasemin ÇELİK ALTUNOĞLU
Isı şoku proteinleri (Hsps: Heat Shock Proteins), canlı organizmalarda bulunan bir grup protein ailesidir. Isı şoku protein genleri stres anında örneğin tuzluluk, kuraklık ve ekstrem sıcaklık değişimlerinin düzenlenmesinde anahtar bir rol üstlenmektedirler. Bu proteinler hücresel şaperonlar gibi fonksiyon görürler, protein sentezinde proteinlerin doğru katlanmasında ve taşınmasında rol oynarlar. Hsp70 gen ailesinin moleküler işlevlerine ait bazı çalışmalar yapılmıştır. Fakat Fagaceae familyası (Amerikan kayını, Amerikan kestanesi, Çin kestanesi, Avrupa kestanesi, Japon kestanesi, Meşe, Kırmızı meşe ve Ak meşe) Hsp70 gen ailesinin genom analizi ve gen karakterizasyonuna ait sınırlı çalışma mevcuttur. Bu çalışmada Tanımlanan Hsp70 gen ailesi dizilerinin genomdaki dağılımları, korunmuş motiflerinin tanımlanması ve tahmini üç boyutlu protein yapılarının belirlenmesi hedeflenmiştir. Hsp70 gen ailesine ait Kayın, Meşe ve Kestane'de sırasıyla 13, 17 ve 15 gen tanımlanmıştır. Filogenetik analiz sonucuna göre Hsp70 genleri 3 farklı grup oluşturmuştur. Yapılan motif analizine göre Hsp70 proteinlerinin genom içerisinde (kayın, meşe ve kestanede) nispeten korunduğu görülmüştür. Proteinlerin üç boyutlu modellemesi yapıldığında toplam Fagaceae familyasına ait 13 Hsp70 geni >90% güven düzeyinde test edilmiştir. Bu on üç protein "(FagHsp70-03(%68) / FagHsp70-08(%65) / FagHsp70-09(%71) / FagHsp70-13(%80) / QuerHsp70-03(%65) / QuerHsp70-04(%68) / QuerHsp70-09(%71) / QuerHsp70-14(%77) / CasHsp70-03(%65)/ CasHsp70-04(%67) / CasHsp70-11(%65) / CasHsp70-14(%65) / CasHsp70-15(%61)" data bankta bulunan proteinlerle yaklaşık %65-%80 arasında üç boyutlu homoloji modellemesi göstermiştir. Bu sonuçlar Fagaceae familyasında Hsp70 gen ailesinin karakterizasyonu ve fonksiyonel işlevleri hakkında bilgi sağlamaktadır. Bu çalışma ile bitkilerde stres toleransının geliştirilmesine ait birçok araştırma için yeni bir perspektif sağlanacaktır
Gene expression profiles of Hsp family members in different poplar taxa under cadmium stress
(2021-02-01) Mehmet Cengiz BALOĞLU; Sezgin AYAN; Esra Nurten YER ÇELİK
Heat shock proteins (Hsps), also known as stress proteins, are expressed by living organisms. Hsp genes play key roles in the regulation of change in response to various abiotic stresses (e.g., salinity, drought, heavy metal, and extreme temperatures). In our previous studies, all Hsp family gene members were determined and named using bioinformatics approaches. We also examined their expression profiles under different stress conditions. In this study, the aim was to indicate the expression pattern of Hsp family genes under cadmium (Cd) stress in different poplar taxa which are resistant to various stresses. Firstly, transcriptome data including RNA-seq and microarray were evaluated to select Hsp gene members that were suitable targets for the cadmium stress response. Then, the expression analysis of selected genes was studied with qRT-PCR (real-time quantitative reverse transcription PCR) in different poplar taxa. Under cadmium stress conditions, the expression profiles of genes including PtsHsp-44, PtsHsp-54, PtHsp40-117, PtHsp60-06, PtHsp60-12, PtHsp70-21, PtHsp70-28, PtHsp90-02, PtHsp90-10, PtHsp90-12, PtHsp100-22, and PtHsp100-71 were observed. In the future, N.03.368A and I-214 taxa may be used for plantation in Cd-contaminated areas and studied under subsequent long-term observation. This study yielded preliminary information about Cd-stress-related molecular mechanisms that will be utilized for future projects. In addition, the genes responsive against Cd stress can be used for gene cloning and functional analyses, which could open new perspectives for improving Cd-tolerant plants or trees.
Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods
(2021-03-01) Kevser Betül CEYLAN; Mehmet Cengiz BALOĞLU; Yasemin ÇELĠK ALTUNOĞLU; Yusuf CEYLAN
Aim of study: It was aimed to identify and characterize Hsp genes in jujube genome using genomics methods. Material and method: Protein sequences of jujube Hsp genes were obtained from NCBI databases. GSDS program was used to detect of exon-intron sites. To define the conserved motifs and estimated 3D-structures, Hsp proteins were used in the MEME-SUITE and PHYRE2 program, respectively. miRNAs targeting ZjuHsp transcripts were identified using the psRNATarget Server database. The gene annotations of Hsp proteins were presented by Blast2GO program. Sequence alignment was performed with ClustalW software, and then the phylogenetic tree was drawn using MEGAX program. Main results: A total of 474 genes were defined in the jujube genome. The amino acid length of the Hsp proteins changes from 75 aa to 2577 aa. The estimated 3-D structure of the ZjuHsp proteins revealed the dominance of the αhelix structure. Phylogenetic tree was constructed to detect evolutionary relationships revealed the eight major groups of the ZjuHsp100 and ZjuHsp60. ZjuHsp proteins could be mainly found in cell parts, membranes, and organelles. It was determined that the ZjuHsp100 genes was targeted by 313 miRNAs. Highlights: This study helps the researchers who would like to comparative and functional genomic studies.
Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses
(2019-02-01) Merve KELEŞ; Mehmet Cengiz BALOĞLU; Yasemin ÇELİK ALTUNOĞLU; Tevfik Hasan CAN
Heat shock protein (Hsp) gene family members in the watermelon genome were identified and characterized by bioinformaticsanalysis. In addition, expression profiles of genes under combined drought and heat stress conditions were experimentally analyzed.In the watermelon genome, 39 genes belonging to the sHsp family, 101 genes belonging to the Hsp40 family, 23 genes belonging to theHsp60 family, 12 genes belonging to the Hsp70 family, 6 genes belonging to the Hsp90 family, and 102 genes belonging to the Hsp100family were found. It was also observed that the proteins in the same cluster in the phylogenetic trees had similar motif patterns. Whenthe estimated 3-dimensional structures of the Hsp proteins were examined, it was determined that the α-helical structure was dominantin almost all families. The most orthologous relationship appeared to be between watermelon, soybean, and poplar in the ClaHsp genefamilies. For tissue-specific gene expression analysis under combined stress conditions, expression analysis of one representative Hspgene each from root, stem, leaf, and shoot tissues was performed by real-time PCR. A significant increase was detected usually at 30min in almost all tissues. This study provides extensive information for watermelon Hsps, and can enhance our knowledge about therelationships between Hsp genes and combined stresses.
Investigation of Metallo-Beta-Lactamase Production in Carbapenem-resistant Clinical Acinetobacter baumannii Isolates
(2022-12-09) Enis Fuat TÜFEKCİ; Anfal ALKATEEB; Çetin KILINÇ; Melike YAŞAR DUMAN; Mehmet Cengiz BALOĞLU; Yasemin ÇELİK ALTUNOĞLU; Nilay ÇÖPLÜ
Introduction: Carbapenem resistance generally emerges from carbapenemase production in Acinetobacter baumannii isolates. It is known that prognosis is adversely affected, and mortality rate increases in infections caused by Metallo-beta-lactamase (MBL) type carbapenemase-producing isolates. This study aimed to investigate MBL production in carbapenem-resistant A. baumannii isolated from inpatients in Kastamonu Training and Research Hospital (TRH), Türkiye. Materials and Methods: A total of 110 non-duplicated carbapenems (imipenem and meropenem) resistant A. baumannii isolates between July 2020 and July 2021 were included in the study. Identification of the isolates was performed by conventional methods, VITEK 2 Compact automated system, and amplification of the OXA-51-like gene region. Antibiotic susceptibility tests were conducted and evaluated with EUCAST criteria using VITEK 2. Carbapenemase production of the isolates was tested using the modified Hodge test. MBL production was screened using imipenem-EDTA double-disc synergy test. The presence of blaIMP, blaVIM, blaGIM, and blaNDM genes was investigated using polymerase chain reaction (PCR) to confirm the MBL production. Results: All isolates were confirmed to be A. baumannii. All isolates were resistant to imipenem, meropenem, ciprofloxacin, and levofloxacin. The susceptibilities to trimethoprim-sulfamethoxazole, tobramycin, amikacin, and gentamicin were 0.9% (n= 1), 1.8% (n= 2), 2.7% (n= 3), and 2.7% (n= 3), respectively. All isolates had carbapenemase activity. However, the MBL phenotype was present in none of the strains. Also, MBL genes were not detected in the isolates. Conclusion: MBL production was not detected in carbapenem-resistant A. baumannii isolates obtained from Kastamonu TRH. Carbapenem resistance in these isolates may be due to the production of non-MBL carbapenemases such as OXA-type carbapenemases.