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Article ; Online: Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans.

Artan, Murat / Hartl, Markus / Chen, Weiqiang / de Bono, Mario

2022 Volume 298, Issue 9, Page(s) 102343

Abstract: Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase ... ...

Abstract	Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His
MeSH term(s)	Acetyl-CoA Carboxylase/metabolism ; Animals ; Biotinylation/methods ; Caenorhabditis elegans/enzymology ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Carboxy-Lyases/genetics ; Carboxy-Lyases/metabolism ; Carrier Proteins/metabolism ; Intercellular Signaling Peptides and Proteins/metabolism ; Methylmalonyl-CoA Decarboxylase/metabolism ; Pyruvate Carboxylase/metabolism ; Streptavidin
Chemical Substances	Caenorhabditis elegans Proteins ; Carrier Proteins ; Intercellular Signaling Peptides and Proteins ; SYD-2 protein, C elegans ; unc-10 protein, C elegans ; Streptavidin (9013-20-1) ; Carboxy-Lyases (EC 4.1.1.-) ; Pyruvate Carboxylase (EC 6.4.1.1) ; Acetyl-CoA Carboxylase (EC 6.4.1.2) ; Methylmalonyl-CoA Decarboxylase (EC 7.2.4.3)
Language	English
Publishing date	2022-08-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.102343
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Article ; Online: Artificial Neural Network (ANN) Validation Research

Murat Çelik / Emircan Gündoğdu / Emin Emre Özdilek / Erol Demirkan / Reha Artan

Applied Sciences, Vol 14, Iss 1, p

Free Vibration Analysis of Functionally Graded Beam via Higher-Order Shear Deformation Theory and Artificial Neural Network Method

2023 Volume 217

Abstract: Presented herein is the free vibration analysis of functionally graded beams (FGMs) via higher-order shear deformation theory and an artificial neural network method (ANN). The transverse displacement (w) is expressed as bending (w b ) and shear (w s ) ... ...

Abstract	Presented herein is the free vibration analysis of functionally graded beams (FGMs) via higher-order shear deformation theory and an artificial neural network method (ANN). The transverse displacement (w) is expressed as bending (w b ) and shear (w s ) components to define the deformation of the beam. The higher-order variation of the transverse shear strains is accounted for through the thickness direction of the FGM beam, and satisfies boundary conditions. The governing equations are derived with the help of Hamilton’s principle. Non-dimensional frequencies are obtained using Navier’s solution. To validate and enrich the proposed research, an artificial neural network method (ANN) was developed in order to predict the dimensionless frequencies. Material properties and previous studies were used to generate the ANN dataset. The obtained frequency values from the analytical solution and ANN method were compared and discussed with respect to the mean error. In conclusion, the solutions were demonstrated for various deformation theories, and all of the results were thereupon tabularized and visualized using 2D and 3D plots.
Keywords	functionally graded material ; composite beam ; artificial neural network ; free vibration ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	690
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications.

Artan, Murat / Sohn, Jooyeon / Lee, Cheolju / Park, Seung-Yeol / Lee, Seung-Jae V

Autophagy

2022 Volume 18, Issue 5, Page(s) 1208–1210

Abstract: The Golgi apparatus regulates the process of modification and subcellular localization of macromolecules, including proteins and lipids. Aberrant protein sorting caused by defects in the Golgi leads to various diseases in mammals. However, the role of ... ...

Abstract	The Golgi apparatus regulates the process of modification and subcellular localization of macromolecules, including proteins and lipids. Aberrant protein sorting caused by defects in the Golgi leads to various diseases in mammals. However, the role of the Golgi apparatus in organismal longevity remained largely unknown. By employing a quantitative proteomic approach, we demonstrated that MON-2, an evolutionarily conserved Arf-GEF protein implicated in Golgi-to-endosome trafficking, promotes longevity via upregulating macroautophagy/autophagy in
MeSH term(s)	Animals ; Autophagy/physiology ; Caenorhabditis elegans ; Endosomes/metabolism ; Golgi Apparatus/metabolism ; Longevity ; Mammals ; Proteomics
Language	English
Publishing date	2022-02-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2022.2039523
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Article ; Online: Correction: Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling.

Artan, Murat / Barratt, Stephen / Flynn, Sean M / Begum, Farida / Skehel, Mark / Nicolas, Armel / de Bono, Mario

The Journal of biological chemistry

2022 Volume 298, Issue 6, Page(s) 102081

Language	English
Publishing date	2022-06-01
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.102081
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Article ; Online: Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling.

Artan, Murat / Barratt, Stephen / Flynn, Sean M / Begum, Farida / Skehel, Mark / Nicolas, Armel / de Bono, Mario

The Journal of biological chemistry

2021 Volume 297, Issue 3, Page(s) 101094

Abstract: Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering ... ...

Abstract	Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.
MeSH term(s)	Animals ; Biotin/chemistry ; Biotinylation ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans Proteins/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; Protein Interaction Mapping/methods ; Proteome/metabolism ; Proteomics/methods ; Staining and Labeling/methods ; Synapses/metabolism
Chemical Substances	Caenorhabditis elegans Proteins ; Intracellular Signaling Peptides and Proteins ; Proteome ; Biotin (6SO6U10H04)
Language	English
Publishing date	2021-08-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2021.101094
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Article ; Online: Heat FLiPs a Hormonal Switch for Longevity.

Artan, Murat / An, Seon Woo A / Lee, Seung-Jae V

Developmental cell

2016 Volume 39, Issue 2, Page(s) 133–134

Abstract: Temperature-sensing neurons in C. elegans reduce the life-shortening effects of high temperatures via steroid signaling. In this issue of Developmental Cell, Chen et al. (2016) elucidate the underlying mechanisms by which the transcription factor CREB ... ...

Abstract	Temperature-sensing neurons in C. elegans reduce the life-shortening effects of high temperatures via steroid signaling. In this issue of Developmental Cell, Chen et al. (2016) elucidate the underlying mechanisms by which the transcription factor CREB induces the neuropeptide FLP-6 in the temperature-sensing neurons to counteract the life-shortening effects of high temperature.
MeSH term(s)	Animals ; Caenorhabditis elegans ; Caenorhabditis elegans Proteins ; Hot Temperature ; Longevity ; Transcription Factors
Chemical Substances	Caenorhabditis elegans Proteins ; Transcription Factors
Language	English
Publishing date	2016--24
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2016.10.004
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Zs.A 5742: 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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Article ; Online: Long-term follow-up of 89 patients with giant cell arteritis: a retrospective observational study on disease characteristics, flares and organ damage.

Ince, Burak / Artan, Selay / Yalcinkaya, Yasemin / Artim-Esen, Bahar / Gul, Ahmet / Ocal, Lale / Inanc, Murat

Rheumatology international

2020 Volume 41, Issue 2, Page(s) 439–448

Abstract: The objective of the study is to investigate the clinical characteristics and long-term prognosis including flares and organ damage in patients with giant cell arteritis (GCA) from a tertiary referral centre and compare these features in different ... ...

Abstract	The objective of the study is to investigate the clinical characteristics and long-term prognosis including flares and organ damage in patients with giant cell arteritis (GCA) from a tertiary referral centre and compare these features in different subgroups. In this retrospective observational study, patients with GCA who were followed up in our vasculitis clinic between 1998 and 2018 were evaluated by a predefined protocol. Patients with and without cranial symptoms were compared for clinical and laboratory features, flares and permanent damage findings. Vasculitis Damage Index and Large Vessel Vasculitis Index of Damage were used for damage assessment. Records of 89 patients (median follow-up time 46 months) were analysed; mean time to diagnosis after initial symptom was longer in patients with acute vision loss (11 ± 4 vs. 4.8 ± 1.1 months p = 0.002). EGG (n = 19) was younger (63 ± 2 vs. 69 ± 1 years old p = 0.01); had higher mean CRP (141.8 ± 107.3 vs. 76.6 ± 67.9 mg/dL p = 0.023) and ESR (120.8 ± 25.1 vs. 99.3 ± 24.3 mm/h p = 0.004) at diagnosis. PET-CT detected large vessel vasculitis in 42/48 (87.5%) cases of the entire cohort. Thirty-one patients had flares and proportion of flared patients was significantly higher in patients with cranial symptoms. At least one damage item (DI) was present in 54 (60.7%) patients. The development of damage was found to be associated with flares. Evaluation of our cohort revealed the importance of early diagnosis for prevention of vision loss in GCA. Patients without cranial symptoms were younger, present with higher inflammatory response and for these, PET-CT was the main diagnostic tool. Relapse rate was higher in patients with cranial symptoms. Flares and accompanying corticosteroid treatment may contribute to organ damage in GCA.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Disease Progression ; Female ; Follow-Up Studies ; Giant Cell Arteritis/complications ; Giant Cell Arteritis/diagnosis ; Giant Cell Arteritis/physiopathology ; Humans ; Male ; Middle Aged ; Positron Emission Tomography Computed Tomography ; Recurrence ; Retrospective Studies ; Vision Disorders/diagnostic imaging ; Vision Disorders/etiology
Language	English
Publishing date	2020-10-28
Publishing country	Germany
Document type	Journal Article ; Observational Study
ZDB-ID	8286-7
ISSN	1437-160X ; 0172-8172
ISSN (online)	1437-160X
ISSN	0172-8172
DOI	10.1007/s00296-020-04730-1
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Article ; Online: VRK-1 extends life span by activation of AMPK via phosphorylation.

Park, Sangsoon / Artan, Murat / Han, Seung Hyun / Park, Hae-Eun H / Jung, Yoonji / Hwang, Ara B / Shin, Won Sik / Kim, Kyong-Tai / Lee, Seung-Jae V

Science advances

2020 Volume 6, Issue 27

Abstract: Vaccinia virus-related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the ... ...

Abstract	Vaccinia virus-related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the single
Keywords	covid19
Language	English
Publishing date	2020-07-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.aaw7824
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Article ; Online: Meeting Report: International Symposium on the Genetics of Aging and Life History II.

Artan, Murat / Hwang, Ara B / Lee, Seung V / Nam, Hong Gil

Aging

2015 Volume 7, Issue 6, Page(s) 362–369

Abstract: The second International Symposium on the Genetics of Aging and Life History was held at the campus of Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea, from May 14 to 16, 2014. Many leading scientists in the field of aging ...

Abstract	The second International Symposium on the Genetics of Aging and Life History was held at the campus of Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea, from May 14 to 16, 2014. Many leading scientists in the field of aging research from all over the world contributed to the symposium by attending and presenting their recent work and thoughts. The aim of the symposium was to stimulate international collaborations and interactions among scientists who work on the biology of aging. In the symposium, the most recent and exciting work on aging research was presented, covering a wide range of topics, including the genetics of aging, age-associated diseases, and cellular senescence. The work was conducted in various organisms, includingC. elegans, mice, plants, and humans. Topics covered in the symposium stimulated discussion of novel directions for future research on aging. The meeting ended with a commitment for the third International Symposium on the Genetics of Aging and Life History, which will be held in 2016.
MeSH term(s)	Aged ; Aged, 80 and over ; Aging/physiology ; Animals ; Biomedical Research ; Cellular Senescence/physiology ; Geriatrics ; Humans ; Internationality
Language	English
Publishing date	2015-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1945-4589
ISSN (online)	1945-4589
DOI	10.18632/aging.100762
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Article ; Online: Diacetyl odor shortens longevity conferred by food deprivation in C. elegans via downregulation of DAF-16/FOXO.

Park, Sangsoon / Artan, Murat / Jeong, Dae-Eun / Park, Hae-Eun H / Son, Heehwa G / Kim, Sieun S / Jung, Yoonji / Choi, Yunji / Lee, Jin I / Kim, Kyuhyung / Lee, Seung-Jae V

Aging cell

2020 Volume 20, Issue 1, Page(s) e13300

Abstract: Dietary restriction extends lifespan in various organisms by reducing the levels of both nutrients and non-nutritional food-derived cues. However, the identity of specific food-derived chemical cues that alter lifespan remains unclear. Here, we ... ...

Abstract	Dietary restriction extends lifespan in various organisms by reducing the levels of both nutrients and non-nutritional food-derived cues. However, the identity of specific food-derived chemical cues that alter lifespan remains unclear. Here, we identified several volatile attractants that decreased the longevity on food deprivation, a dietary restriction regimen in Caenorhabditis elegans. In particular, we found that the odor of diacetyl decreased the activity of DAF-16/FOXO, a life-extending transcription factor acting downstream of insulin/IGF-1 signaling. We then demonstrated that the odor of lactic acid bacteria, which produce diacetyl, reduced the nuclear accumulation of DAF-16/FOXO. Unexpectedly, we showed that the odor of diacetyl decreased longevity independently of two established diacetyl receptors, ODR-10 and SRI-14, in sensory neurons. Thus, diacetyl, a food-derived odorant, may shorten food deprivation-induced longevity via decreasing the activity of DAF-16/FOXO through binding to unidentified receptors.
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans Proteins/metabolism ; Diacetyl/adverse effects ; Diet Therapy ; Down-Regulation ; Forkhead Transcription Factors/metabolism ; Longevity ; Odorants/analysis
Chemical Substances	Caenorhabditis elegans Proteins ; Forkhead Transcription Factors ; daf-16 protein, C elegans ; Diacetyl (K324J5K4HM)
Language	English
Publishing date	2020-12-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2113083-8
ISSN	1474-9726 ; 1474-9718
ISSN (online)	1474-9726
ISSN	1474-9718
DOI	10.1111/acel.13300
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