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Article ; Online: Spatial proteomic alterations detected

Karayel-Basar, Merve / Uras, Irep / Kiris, Irem / Sahin, Betul / Akgun, Emel / Baykal, Ahmet Tarik

Molecular omics

2022 Volume 18, Issue 4, Page(s) 336–347

Abstract: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that occurs with the increase of CAG trinucleotide repeats in ... ...

Abstract	Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that occurs with the increase of CAG trinucleotide repeats in the
MeSH term(s)	Animals ; Brain/metabolism ; Chromatography, Liquid ; Huntington Disease/diagnostic imaging ; Huntington Disease/genetics ; Huntington Disease/metabolism ; Mice ; Proteomics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Tandem Mass Spectrometry
Language	English
Publishing date	2022-05-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2515-4184
ISSN (online)	2515-4184
DOI	10.1039/d1mo00440a
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Article ; Online: Evaluation of the Efficacy of Different Cleaning Methods for Orthodontic Thermoplastic Retainers in terms of Bacterial Colonization.

Akgün, Filiz Aydoğan / Şenışık, Neslihan Ebru / Çetin, Emel Sesli

Turkish journal of orthodontics

2019 Volume 32, Issue 4, Page(s) 219–228

Abstract: Objective: This study investigated the antimicrobial efficacy of three different cleaning methods on : Methods: In this prospective, cross-over study, a total of 21 volunteers were included. All VFRs used by the volunteers were cleaned using three ... ...

Abstract	Objective: This study investigated the antimicrobial efficacy of three different cleaning methods on Methods: In this prospective, cross-over study, a total of 21 volunteers were included. All VFRs used by the volunteers were cleaned using three different cleaning methods in a sequence. These methods were peroxide-based cleanser tablets (PBCTs) plus brushing, control (only brushing), and vinegar plus brushing, respectively. The obtained salivary, VFR material, and periodontal data were statistically compared by factorial design repeated measures analysis of variance. Results: The SM and LB bacteria counts on VFRs after using both PBCTs and vinegar were statistically similar (p>0.05), but bacteria counts were statistically lower than the control method (p<0.01). There were no statistically significant differences between the SM and LB bacteria counts in saliva samples taken before and after the application of the cleaning methods (p>0.05). Similarly, there were no significant differences between periodontal data obtained from plaque and bleeding indices at all study times. The periodontal pocket depth gradually decreased in the successively performed cleaning applications (p<0.05). Conclusion: The application of PBCTs and vinegar to VFRs at sequential time intervals resulted in similar bacteria counts. The higher LB counts and similarly higher SM counts on the VFR samples indicate that mechanical cleaning only (control method) is not adequate to obtain hygiene. Salivary flora was not correlated with bacteria counts of VFRs.
Language	English
Publishing date	2019-12-01
Publishing country	Turkey
Document type	Journal Article
ISSN	2148-9505
ISSN (online)	2148-9505
DOI	10.5152/TurkJOrthod.2019.19061
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Article ; Online: Altered expression of MZB1 in periodontitis: A possible link to disease pathogenesis.

Sunnetci-Akkoyunlu, Deniz / Guzeldemir-Akcakanat, Esra / Alkan, Begum / Gurel, Busra / Balta-Uysal, V Merve / Akgun, Emel / Baykal, Ahmet Tarik / Olgac, Vakur

Journal of periodontology

2023 Volume 94, Issue 11, Page(s) 1285–1294

Abstract: Background: Our previous study explored the molecular signatures of generalized aggressive periodontitis (GAgP) using gingival tissues through omics-based-whole-genome transcriptomic analysis. This continuation study aimed to investigate the whole ... ...

Abstract	Background: Our previous study explored the molecular signatures of generalized aggressive periodontitis (GAgP) using gingival tissues through omics-based-whole-genome transcriptomic analysis. This continuation study aimed to investigate the whole protein profiling of these gingival samples through liquid chromatography-mass spectroscopy/mass spectroscopy (LC-MS/MS) analysis and to validate the identified proteins through immunohistochemistry to provide further evidence for the quality of the results. Methods: In previous study, gene expression patterns were identified in gingival tissues from 23 GAgP and 25 control individuals. In the current study, comparative proteomic analysis was performed on isolated proteins from the same study groups using LC-MS/MS analysis. The data from the transcriptomics study published before and the proteomics data were integrated to reveal any common genes and proteins. Additionally, immunohistochemical analysis was conducted to further investigate the findings. Results: The most upregulated proteins in patients compared to controls were ITGAM, AZU1, MMP9, BPI, UGGG1, MZB1, TRFL, PDIA6, PRDX4, and PLG. The top six pathways associated with these proteins were involved in innate immune system, post-translational protein phosphorylation, interleukin-4 and -13 signaling, toll-like receptors cascades, and extracellular matrix organization. Based on the integration and validation analysis of transcriptomics and proteomics data, as well as immunohistochemical analysis, MZB1 was identified as a shared gene and protein that were upregulated in the patients. Conclusions: MZB1 is a protein that is involved in the development of B cells and the production of antibodies. Its upregulation in periodontitis suggests that there may be a dysregulation of the immune response in this condition, and MZB1 may be a potent biomarker for periodontitis.
MeSH term(s)	Humans ; Chromatography, Liquid ; Proteomics ; Tandem Mass Spectrometry ; Aggressive Periodontitis/genetics ; Aggressive Periodontitis/metabolism ; Gingiva/metabolism
Language	English
Publishing date	2023-06-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	390921-9
ISSN	1943-3670 ; 0022-3492 ; 1049-8885 ; 0095-960X
ISSN (online)	1943-3670
ISSN	0022-3492 ; 1049-8885 ; 0095-960X
DOI	10.1002/JPER.23-0224
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Article: Transcriptomics and Proteomics Analyses Reveal JAK Signaling and Inflammatory Phenotypes during Cellular Senescence in Blind Mole Rats: The Reflections of Superior Biology.

Inci, Nurcan / Akyildiz, Erdogan Oguzhan / Bulbul, Abdullah Alper / Turanli, Eda Tahir / Akgun, Emel / Baykal, Ahmet Tarik / Colak, Faruk / Bozaykut, Perinur

Biology

2022 Volume 11, Issue 9

Abstract: The blind mole rat (BMR), a long-living subterranean rodent, is an exceptional model for both aging and cancer research since they do not display age-related phenotypes or tumor formation. The Janus kinase-signal transducer and activator of transcription ...

Abstract	The blind mole rat (BMR), a long-living subterranean rodent, is an exceptional model for both aging and cancer research since they do not display age-related phenotypes or tumor formation. The Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling is a cytokine-stimulated pathway that has a crucial role in immune regulation, proliferation, and cytokine production. Therefore, the pathway has recently attracted interest in cellular senescence studies. Here, by using publicly available data, we report that JAK-STAT signaling was suppressed in the BMR in comparison to the mouse. Interestingly, our experimental results showed upregulated
Language	English
Publishing date	2022-08-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology11091253
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Article: Antibiotic Stewardship Program Experience in a Training and Research Hospital.

Alp, Emel Eksi / Oncul, Ahsen / Dalgic, Nazan / Akgun, Cem / Aktas, Elif / Bayraktar, Banu

Sisli Etfal Hastanesi tip bulteni

2021 Volume 55, Issue 2, Page(s) 253–261

Abstract: Objectives: Antibiotic Stewardship Programs (ASP) have been developed for the spread of rational antibiotic use. Our hospital is one of the first centers where ASP applications were launched in Turkey. In this study, we aimed to share our experience ... ...

Abstract	Objectives: Antibiotic Stewardship Programs (ASP) have been developed for the spread of rational antibiotic use. Our hospital is one of the first centers where ASP applications were launched in Turkey. In this study, we aimed to share our experience with ASP which has been applied in our hospital since 2013. Methods: We adapted ASP to our hospital program from Centers for Disease Control and Prevention's ASP checklist. Revisions on surgical prophylaxis guidelines and practices were performed. Surgical prophylaxis was evaluated from hospital infection surveillance and antibiotic usage by point prevalence surveys. Antibiotic consumption indexes (ACI) were calculated from hospital pharmacy records. Rapid antigen detection test (RADT) for Group A beta-hemolytic streptococcus and influenza rapid antigen test were started to be used. Cumulative antibiotic susceptibility results were prepared annually. Results: Surgical prophylaxis was started to be administered in the operating room within 60 min of incision. Third-generation cephalosporin usage for surgical prophylaxis could be restricted in all clinics but the duration could only be shortened in neurosurgery and general surgery. There was no statistically significant change in antibiotic usage rates and appropriateness between 2014 and 2018. ACI for the class J01 in adult wards was 80.5 daily defined doses (DDD) per 100 patient days in 2014 and reduced to 64.8 DDD per 100 patient days in 2018. 22.445 pediatric patients presenting with complaints of the upper respiratory tract were evaluated with RADT and 75.1% were treated without antibiotics. Conclusion: In this global antimicrobial resistance era, all hospitals should have motivated antimicrobial stewardship teams. Each hospital should establish its own stewardship program and often revise it. Improvement in rational antibiotic use is hard to achieve without multidisciplinary involvement.
Language	English
Publishing date	2021-07-02
Publishing country	Turkey
Document type	Journal Article
ZDB-ID	3026862-X
ISSN	1308-5123 ; 1302-7123
ISSN (online)	1308-5123
ISSN	1302-7123
DOI	10.14744/SEMB.2020.96337
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Article: Serum Proteomic Changes in Dogs with Different Stages of Chronic Heart Failure.

Saril, Ahmet / Kocaturk, Meric / Shimada, Kazumi / Uemura, Akiko / Akgün, Emel / Levent, Pinar / Baykal, Ahmet Tarik / Prieto, Alberto Muñoz / Agudelo, Carlos Fernando / Tanaka, Ryou / Ceron, Jose Joaquin / Koch, Jorgen / Yilmaz, Zeki

Animals : an open access journal from MDPI

2022 Volume 12, Issue 4

Abstract: MMVD, the most common cause of CHF in dogs, is a chronic disease with variable clinical signs, with some patients remaining asymptomatic while others develop CHF. Here, we aimed to evaluate serum proteins by proteomic analysis in dogs at different stages ...

Abstract	MMVD, the most common cause of CHF in dogs, is a chronic disease with variable clinical signs, with some patients remaining asymptomatic while others develop CHF. Here, we aimed to evaluate serum proteins by proteomic analysis in dogs at different stages of CHF due to MMVD, and proteome behaviors after conventional treatment. A total of 32 dogs were divided equally into four groups-stage A (healthy/controls), stage B2 (asymptomatic), stage C and stage D (symptomatic)-according to the ACVIM consensus. Serum proteomes were evaluated using LC/MS-based label-free differential proteome analysis. The study revealed 157 different proteins; 11 were up- and 21 down-regulated in dogs with CHF compared to controls. In stage B2 dogs, angiotensinogen (AGT) was up-regulated, but immunoglobulin iota chain-like, lipopolysaccharide-binding protein, and carboxypeptidase (CPN) were down-regulated. In stage C dogs, complement C3 (C3) and inter-alpha-trypsin inhibitor heavy chain were up-regulated, but hemopexin, and actin-cytoplasmic-1 (ACT-1) were down-regulated. In stage D dogs, AGT was up-regulated, whereas tetranectin, paraoxonase-1, adiponectin and ACT-1 were down-regulated. A decrease in CPN, C3 and AGT and an increase in ACT-1 were observed after treatment of dogs in stage C. This pilot study identified that dogs at different stages of CHF show different serum protein composition which has potential to be biomarker for diagnose and treatment monitorization.
Language	English
Publishing date	2022-02-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606558-7
ISSN	2076-2615
ISSN	2076-2615
DOI	10.3390/ani12040490
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Article ; Online: Serum Proteomic Changes in Dogs with Different Stages of Chronic Heart Failure

Ahmet Saril / Meric Kocaturk / Kazumi Shimada / Akiko Uemura / Emel Akgün / Pinar Levent / Ahmet Tarik Baykal / Alberto Muñoz Prieto / Carlos Fernando Agudelo / Ryou Tanaka / Jose Joaquin Ceron / Jorgen Koch / Zeki Yilmaz

Animals, Vol 12, Iss 490, p

2022 Volume 490

Abstract	MMVD, the most common cause of CHF in dogs, is a chronic disease with variable clinical signs, with some patients remaining asymptomatic while others develop CHF. Here, we aimed to evaluate serum proteins by proteomic analysis in dogs at different stages of CHF due to MMVD, and proteome behaviors after conventional treatment. A total of 32 dogs were divided equally into four groups—stage A (healthy/controls), stage B2 (asymptomatic), stage C and stage D (symptomatic)—according to the ACVIM consensus. Serum proteomes were evaluated using LC/MS-based label-free differential proteome analysis. The study revealed 157 different proteins; 11 were up- and 21 down-regulated in dogs with CHF compared to controls. In stage B2 dogs, angiotensinogen (AGT) was up-regulated, but immunoglobulin iota chain-like, lipopolysaccharide-binding protein, and carboxypeptidase (CPN) were down-regulated. In stage C dogs, complement C3 (C3) and inter-alpha-trypsin inhibitor heavy chain were up-regulated, but hemopexin, and actin-cytoplasmic-1 (ACT-1) were down-regulated. In stage D dogs, AGT was up-regulated, whereas tetranectin, paraoxonase-1, adiponectin and ACT-1 were down-regulated. A decrease in CPN, C3 and AGT and an increase in ACT-1 were observed after treatment of dogs in stage C. This pilot study identified that dogs at different stages of CHF show different serum protein composition which has potential to be biomarker for diagnose and treatment monitorization.
Keywords	proteomic ; mitral valve disease ; heart disease ; ACVIM ; dogs ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Kappa/Lambda light-chain typing in Alzheimer's Disease.

Kaya, Zelal Zuhal / Tuzuner, Mete Bora / Sahin, Betul / Akgun, Emel / Aksungar, Fehime / Koca, Sebile / Serdar, Muhittin / Sahin, Sevki / Cinar, Nilgun / Karsidag, Sibel / Hanagasi, Hasmet Ayhan / Kilercik, Meltem / Serteser, Mustafa / K Baykal, Ahmet Tari

Current Alzheimer research

2022 Volume 19, Issue 1, Page(s) 84–93

Abstract: Background: Alzheimer's disease is a progressive neurodegenerative disorder characterized by memory loss and cognitive impairment. The diagnosis of Alzheimer's disease according to symptomatic events is still a puzzling task. Developing a biomarker- ... ...

Abstract	Background: Alzheimer's disease is a progressive neurodegenerative disorder characterized by memory loss and cognitive impairment. The diagnosis of Alzheimer's disease according to symptomatic events is still a puzzling task. Developing a biomarker-based, low-cost, and high-throughput test, readily applicable in clinical laboratories, dramatically impacts the rapid and reliable detection of the disease. Objective: This study aimed to develop an accurate, sensitive, and reliable screening tool for diagnosing Alzheimer's disease, which can significantly reduce the cost and time of existing methods. Methods: We have employed a MALDI-TOF-MS-based methodology combined with a microaffinity chromatography enrichment approach using affinity capture resins to determine serum kappa (κ) and lambda (λ) light chain levels in control and patients with AD. Results: We observed a statistically significant difference in the kappa light chain over lambda light chain (κLC/λLC) ratios between patients with AD and controls (mean difference -0,409; % 95 CI:- 0.547 to -0.269; p<0.001). Our method demonstrated higher sensitivity (100.00%) and specificity (71.43%) for discrimination between AD and controls. Conclusion: We have developed a high-throughput screening test with a novel sample enrichment method for determining κLC/λLC ratios associated with AD diagnosis. Following further validation, we believe our test has the potential for clinical laboratories.
MeSH term(s)	Alzheimer Disease/complications ; Biomarkers ; Cognitive Dysfunction/diagnosis ; Humans ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Chemical Substances	Biomarkers
Language	English
Publishing date	2022-02-01
Publishing country	United Arab Emirates
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205170-3
ISSN	1875-5828 ; 1567-2050
ISSN (online)	1875-5828
ISSN	1567-2050
DOI	10.2174/1567205019666220131101334
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Article: Transcriptomics and Proteomics Analyses Reveal JAK Signaling and Inflammatory Phenotypes during Cellular Senescence in Blind Mole Rats: The Reflections of Superior Biology

Inci, Nurcan / Akyildiz, Erdogan Oguzhan / Bulbul, Abdullah Alper / Turanli, Eda Tahir / Akgun, Emel / Baykal, Ahmet Tarik / Colak, Faruk / Bozaykut, Perinur

Biology. 2022 Aug. 23, v. 11, no. 9

2022

Abstract: The blind mole rat (BMR), a long-living subterranean rodent, is an exceptional model for both aging and cancer research since they do not display age-related phenotypes or tumor formation. The Janus kinase–signal transducer and activator of transcription ...

Abstract	The blind mole rat (BMR), a long-living subterranean rodent, is an exceptional model for both aging and cancer research since they do not display age-related phenotypes or tumor formation. The Janus kinase–signal transducer and activator of transcription (JAK–STAT) signaling is a cytokine-stimulated pathway that has a crucial role in immune regulation, proliferation, and cytokine production. Therefore, the pathway has recently attracted interest in cellular senescence studies. Here, by using publicly available data, we report that JAK–STAT signaling was suppressed in the BMR in comparison to the mouse. Interestingly, our experimental results showed upregulated Jak1/2 expressions in BMR fibroblasts during the replicative senescence process. The transcriptomic analysis using publicly available data also demonstrated that various cytokines related to JAK–STAT signaling were upregulated in the late passage cells, while some other cytokines such as MMPs and SERPINs were downregulated, representing a possible balance of senescence-associated secretory phenotypes (SASPs) in the BMR. Finally, our proteomics data also confirmed cytokine-mediated signaling activation in senescent BMR fibroblasts. Together, our findings suggest the critical role of JAK–STAT and cytokine-mediated signaling pathways during cellular senescence, pointing to the possible contribution of divergent inflammatory factors to the superior resistance of aging and cancer in BMRs.
Keywords	cell senescence ; cytokines ; fibroblasts ; mice ; models ; mole rats ; moles ; neoplasms ; proteomics ; serpins ; transactivators ; transcriptomics
Language	English
Dates of publication	2022-0823
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology11091253
Database	NAL-Catalogue (AGRICOLA)

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Article: Serum Proteomic Changes in Dogs with Different Stages of Chronic Heart Failure

Animals. 2022 Feb. 16, v. 12, no. 4

2022

Abstract	MMVD, the most common cause of CHF in dogs, is a chronic disease with variable clinical signs, with some patients remaining asymptomatic while others develop CHF. Here, we aimed to evaluate serum proteins by proteomic analysis in dogs at different stages of CHF due to MMVD, and proteome behaviors after conventional treatment. A total of 32 dogs were divided equally into four groups—stage A (healthy/controls), stage B2 (asymptomatic), stage C and stage D (symptomatic)—according to the ACVIM consensus. Serum proteomes were evaluated using LC/MS-based label-free differential proteome analysis. The study revealed 157 different proteins; 11 were up- and 21 down-regulated in dogs with CHF compared to controls. In stage B2 dogs, angiotensinogen (AGT) was up-regulated, but immunoglobulin iota chain-like, lipopolysaccharide-binding protein, and carboxypeptidase (CPN) were down-regulated. In stage C dogs, complement C3 (C3) and inter-alpha-trypsin inhibitor heavy chain were up-regulated, but hemopexin, and actin-cytoplasmic-1 (ACT-1) were down-regulated. In stage D dogs, AGT was up-regulated, whereas tetranectin, paraoxonase-1, adiponectin and ACT-1 were down-regulated. A decrease in CPN, C3 and AGT and an increase in ACT-1 were observed after treatment of dogs in stage C. This pilot study identified that dogs at different stages of CHF show different serum protein composition which has potential to be biomarker for diagnose and treatment monitorization.
Keywords	adiponectin ; angiotensinogen ; biomarkers ; blood serum ; chronic diseases ; complement ; heart failure ; immunoglobulins ; protein composition ; proteome ; proteomics
Language	English
Dates of publication	2022-0216
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2606558-7
ISSN	2076-2615
ISSN	2076-2615
DOI	10.3390/ani12040490
Database	NAL-Catalogue (AGRICOLA)

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