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Article ; Online: Questioning whether there was a short-term interaction between the 6 February 2023 earthquakes and air quality parameters in Türkiye.

Alver Şahin, Ülkü / Kaynak, Burçak

2023 Volume 347, Page(s) 140616

Abstract: On 6 February 2023, Türkiye was hit by two earthquakes with 7.5 (Eq2) and 7.8 (Eq1) magnitudes. In this study, the hourly ground-level air pollutant concentrations measured in the earthquake areas were examined in detail. In addition, the remote sensing ... ...

Abstract	On 6 February 2023, Türkiye was hit by two earthquakes with 7.5 (Eq2) and 7.8 (Eq1) magnitudes. In this study, the hourly ground-level air pollutant concentrations measured in the earthquake areas were examined in detail. In addition, the remote sensing retrievals of CO, NO
MeSH term(s)	Earthquakes ; Nitrogen Dioxide/analysis ; Air Pollution/analysis ; Air Pollutants/analysis ; Particulate Matter/analysis
Chemical Substances	Nitrogen Dioxide (S7G510RUBH) ; Air Pollutants ; Particulate Matter
Language	English
Publishing date	2023-11-09
Publishing country	England
Document type	Journal Article
ZDB-ID	120089-6
ISSN	1879-1298 ; 0045-6535 ; 0366-7111
ISSN (online)	1879-1298
ISSN	0045-6535 ; 0366-7111
DOI	10.1016/j.chemosphere.2023.140616
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Article ; Online: Use of dispersion model and satellite SO

Akyuz, Ezgi / Kaynak, Burcak

The Science of the total environment

2019 Volume 689, Page(s) 808–819

Abstract: The aim of this study is to investigate the impact of ten proposed plants along with three operating plants in Çanakkale province of Turkey where the proposed plants are within very close proximity. The province has the highest capacity of the planned ... ...

Abstract	The aim of this study is to investigate the impact of ten proposed plants along with three operating plants in Çanakkale province of Turkey where the proposed plants are within very close proximity. The province has the highest capacity of the planned plants and the region is also of interest due to its history, tourism and agriculture potential. Current SO
MeSH term(s)	Air Pollutants/analysis ; Coal ; Environmental Monitoring/methods ; Models, Theoretical ; Power Plants ; Remote Sensing Technology ; Spacecraft ; Sulfur Dioxide/analysis
Chemical Substances	Air Pollutants ; Coal ; Sulfur Dioxide (0UZA3422Q4)
Language	English
Publishing date	2019-06-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2019.06.464
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Article ; Online: Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions.

Cheng, Mary Hongying / Krieger, James M / Banerjee, Anupam / Xiang, Yufei / Kaynak, Burak / Shi, Yi / Arditi, Moshe / Bahar, Ivet

iScience

2022 Volume 25, Issue 3, Page(s) 103939

Abstract: The emergence of SARS-CoV-2 variants necessitates rational assessment of their impact on the recognition and neutralization of the virus by the host cell. We present a comparative analysis of the interactions of Alpha, Beta, Gamma, and Delta variants ... ...

Abstract	The emergence of SARS-CoV-2 variants necessitates rational assessment of their impact on the recognition and neutralization of the virus by the host cell. We present a comparative analysis of the interactions of Alpha, Beta, Gamma, and Delta variants with cognate molecules (ACE2 and/or furin), neutralizing nanobodies (Nbs), and monoclonal antibodies (mAbs) using
Language	English
Publishing date	2022-02-17
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.103939
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Article ; Online: ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python.

Zhang, She / Krieger, James M / Zhang, Yan / Kaya, Cihan / Kaynak, Burak / Mikulska-Ruminska, Karolina / Doruker, Pemra / Li, Hongchun / Bahar, Ivet

Bioinformatics (Oxford, England)

2021 Volume 37, Issue 20, Page(s) 3657–3659

Abstract: Summary: ProDy, an integrated application programming interface developed for modelling and analysing protein dynamics, has significantly evolved in recent years in response to the growing data and needs of the computational biology community. We ... ...

Abstract	Summary: ProDy, an integrated application programming interface developed for modelling and analysing protein dynamics, has significantly evolved in recent years in response to the growing data and needs of the computational biology community. We present major developments that led to ProDy 2.0: (i) improved interfacing with databases and parsing new file formats, (ii) SignDy for signature dynamics of protein families, (iii) CryoDy for collective dynamics of supramolecular systems using cryo-EM density maps and (iv) essential site scanning analysis for identifying sites essential to modulating global dynamics. Availability and implementation: ProDy is open-source and freely available under MIT License from https://github.com/prody/ProDy. Supplementary information: Supplementary data are available at Bioinformatics online.
Language	English
Publishing date	2021-03-30
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btab187
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Zs.A 2374: Show issues

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Article ; Online: Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.

Zhang, Yan / Doruker, Pemra / Kaynak, Burak / Zhang, She / Krieger, James / Li, Hongchun / Bahar, Ivet

Current opinion in structural biology

2019 Volume 62, Page(s) 14–21

Abstract: Allosteric behavior is central to the function of many proteins, enabling molecular machinery, metabolism, signaling and regulation. Recent years have shown that the intrinsic dynamics of allosteric proteins defined by their 3-dimensional architecture or ...

Abstract	Allosteric behavior is central to the function of many proteins, enabling molecular machinery, metabolism, signaling and regulation. Recent years have shown that the intrinsic dynamics of allosteric proteins defined by their 3-dimensional architecture or by the topology of inter-residue contacts favors cooperative motions that bear close similarity to structural changes they undergo during their allosteric actions. These conformational motions are usually driven by energetically favorable or soft modes at the low frequency end of the mode spectrum, and they are evolutionarily conserved among orthologs. These observations brought into light evolutionary adaptation mechanisms that help maintain, optimize or regulate allosteric behavior as the evolution from bacterial to higher organisms introduces sequential heterogeneities and structural complexities.
MeSH term(s)	Allosteric Regulation ; Bacteria/metabolism ; Eukaryota/metabolism ; Evolution, Molecular ; Protein Binding ; Protein Conformation ; Proteins/chemistry ; Signal Transduction
Chemical Substances	Proteins
Language	English
Publishing date	2019-11-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2019.11.002
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Article ; Online: Impact of South African 501.V2 Variant on SARS-CoV-2 Spike Infectivity and Neutralization: A Structure-based Computational Assessment

Cheng, Mary Hongying / Krieger, James M / Kaynak, Burak / Arditi, Moshe A / Bahar, Ivet

bioRxiv

Abstract: Motivation: The SARS-CoV-2 variants emerging from South Africa (501.V2) and the UK (B.1.1.7) necessitate rapid assessment of the effects of the corresponding amino acid substitutions in the spike (S) receptor-binding domain (RBD) of the variants on the ... ...

Abstract	Motivation: The SARS-CoV-2 variants emerging from South Africa (501.V2) and the UK (B.1.1.7) necessitate rapid assessment of the effects of the corresponding amino acid substitutions in the spike (S) receptor-binding domain (RBD) of the variants on the interactions with the human ACE2 receptor and monoclonal antibodies (mAbs) reported earlier to neutralize the spike. Results: Molecular modeling and simulations reveal that N501Y, shared by both variants, increases ACE2 binding affinity, and may impact the collective dynamics of the ACE2-RBD complex, occupying a central hinge site that modulates the overall dynamics of the complex. In contrast, the substitutions K417N and E484K in the South African variant 501.V2 would reduce the ACE2-binding affinity by abolishing two interfacial salt bridges that facilitate RBD binding to ACE2, K417(S)-D30(ACE2) and E484 (S)-K31(ACE2). These two mutations may thus be more than compensating the attractive effect induced by N501Y, overall resulting in an ACE2-binding affinity comparable to that of the wildtype RBD. Further analysis of the impact of these mutations on the interactions with mAbs targeting the spike indicate that the substitutions K417N and E484K may also abolish the salt bridges between the spike and selected mAbs, such as REGN10933, BD23, H11_H4, and C105, thus reducing the binding affinity and effectiveness of these mAbs.
Keywords	covid19
Language	English
Publishing date	2021-01-11
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.01.10.426143
Database	COVID19

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Article ; Online: State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.

Zhang, Yan / Krieger, James / Mikulska-Ruminska, Karolina / Kaynak, Burak / Sorzano, Carlos Oscar S / Carazo, José-María / Xing, Jianhua / Bahar, Ivet

Progress in biophysics and molecular biology

2020 Volume 160, Page(s) 104–120

Abstract: The eukaryotic chaperonin TRiC/CCT plays a major role in assisting the folding of many proteins through an ATP-driven allosteric cycle. Recent structures elucidated by cryo-electron microscopy provide a broad view of the conformations visited at various ... ...

Abstract	The eukaryotic chaperonin TRiC/CCT plays a major role in assisting the folding of many proteins through an ATP-driven allosteric cycle. Recent structures elucidated by cryo-electron microscopy provide a broad view of the conformations visited at various stages of the chaperonin cycle, including a sequential activation of its subunits in response to nucleotide binding. But we lack a thorough mechanistic understanding of the structure-based dynamics and communication properties that underlie the TRiC/CCT machinery. In this study, we present a computational methodology based on elastic network models adapted to cryo-EM density maps to gain a deeper understanding of the structure-encoded allosteric dynamics of this hexadecameric machine. We have analysed several structures of the chaperonin resolved in different states toward mapping its conformational landscape. Our study indicates that the overall architecture intrinsically favours cooperative movements that comply with the structural variabilities observed in experiments. Furthermore, the individual subunits CCT1-CCT8 exhibit state-dependent sequential events at different states of the allosteric cycle. For example, in the ATP-bound state, subunits CCT5 and CCT4 selectively initiate the lid closure motions favoured by the overall architecture; whereas in the apo form of the heteromer, the subunit CCT7 exhibits the highest predisposition to structural change. The changes then propagate through parallel fluxes of allosteric signals to neighbours on both rings. The predicted state-dependent mechanisms of sequential activation provide new insights into TRiC/CCT intra- and inter-ring signal transduction events.
MeSH term(s)	Allosteric Regulation ; Chaperonin Containing TCP-1/chemistry ; Cryoelectron Microscopy/methods ; Eukaryotic Cells/enzymology ; Eukaryotic Cells/metabolism ; Models, Molecular ; Protein Conformation ; Protein Subunits/chemistry ; Protein Subunits/metabolism ; Structure-Activity Relationship
Chemical Substances	Protein Subunits ; Chaperonin Containing TCP-1 (EC 3.6.1.-)
Language	English
Publishing date	2020-08-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209302-9
ISSN	1873-1732 ; 0079-6107
ISSN (online)	1873-1732
ISSN	0079-6107
DOI	10.1016/j.pbiomolbio.2020.08.006
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Article ; Online: Toxicity evaluation and source apportionment of Polycyclic Aromatic Hydrocarbons (PAHs) at three stations in Istanbul, Turkey.

Hanedar, Asude / Alp, Kadir / Kaynak, Burçak / Avşar, Edip

The Science of the total environment

2014 Volume 488-489, Page(s) 437–446

Abstract: This paper focuses on the toxicity evaluation and source apportionment of Polycyclic Aromatic Hydrocarbons (PAHs) in three monitoring stations in Istanbul, Turkey. A total of 326 airborne samples were collected and analyzed for 16 PAHs and Total ... ...

Abstract	This paper focuses on the toxicity evaluation and source apportionment of Polycyclic Aromatic Hydrocarbons (PAHs) in three monitoring stations in Istanbul, Turkey. A total of 326 airborne samples were collected and analyzed for 16 PAHs and Total Suspended Particles (TSP) for the period of September 2006-December 2007. The total average PAH concentrations were 100.7±61.3, 84.6±46.7 and 25.1±13.3 ng m(-3) and the TSP concentrations were 101.2±53.2, 152.3±99.1, 49.8±18.6 μg m(-3) for URB1, URB2 and RUR stations, respectively. Benzo(a)Pyren (BaP) toxic equivalency factors to PAH concentration values were calculated indicating that the health risk of BaP and DiBenz(a,h)Anthracene (markers of traffic emissions) have the highest contribution compared to all of the other species measured at the sampling sites. In order to determine PAH sources, two different source apportionment techniques were applied to the measurements; diagnostic ratios (DR) and Positive Matrix Factorization (PMF). The results of the two applications were compatible indicating the vehicle emissions - especially diesel engines - as the major source for urban stations.
MeSH term(s)	Air Pollutants/analysis ; Air Pollutants/toxicity ; Air Pollution/statistics & numerical data ; Environmental Monitoring ; Particulate Matter/analysis ; Particulate Matter/toxicity ; Polycyclic Aromatic Hydrocarbons/analysis ; Polycyclic Aromatic Hydrocarbons/toxicity ; Turkey
Chemical Substances	Air Pollutants ; Particulate Matter ; Polycyclic Aromatic Hydrocarbons
Language	English
Publishing date	2014-08-01
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2013.11.123
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Article: Self-gripping Covidien™ ProGrip™ mesh versus polypropylene mesh in open inguinal hernia repair: multicenter short term results.

Yilmaz, A / Yener, O / Kaynak, B / Yiğitbaşi, R / Demir, M / Burcu, B / Aksoy, F

Prague medical report

2013 Volume 114, Issue 4, Page(s) 231–238

Abstract: The purpose of this study was to compare clinical outcomes following sutureless ProGrip™ mesh repair to traditional Lichtenstein repair with polypropylene mesh secured with sutures. Data were collected prospectively and were analyzed for 57 male and 3 ... ...

Abstract	The purpose of this study was to compare clinical outcomes following sutureless ProGrip™ mesh repair to traditional Lichtenstein repair with polypropylene mesh secured with sutures. Data were collected prospectively and were analyzed for 57 male and 3 female patients with 60 inguinal hernias. All patients included underwent open surgical repair for inguinal hernia with polypropylene mesh or ProGrip mesh. In our two centres study sixty patients were operated; 30 were treated with Lichtenstein repair with polypropylene mesh (L group) and 30 with ProGrip mesh (P group) with or without fixation. The primary parameter measured was intensity of postoperative pain using visual analogue scale (VAS); other outcomes included assessment of early and late complication. VAS was assessed in 7 days and 4 months of the postoperative period. Our results show that VAS scored at the 7th postoperative day was 1.5 for the ProGrip mesh versus 4.4 in Lichtenstein repair group. The difference between groups was statistically significant (P=0.001). Surgery duration was significantly shorter in the P group (24.9 vs. 58.3 min; P=0.001). No recurrence was observed at 3 months in both groups. The 3-months follow-up has shown that time necessary to return to daily routine activity was significantly lower in the P group during the (P=0.001). Surgery duration, early and late postoperative, pain and return to daily routine activity rates were significantly reduced with self-gripping ProGrip mesh compared to Lichtenstein repair with polypropylene mesh.
MeSH term(s)	Adult ; Equipment Design ; Female ; Follow-Up Studies ; Hernia, Inguinal/psychology ; Hernia, Inguinal/surgery ; Humans ; Male ; Middle Aged ; Polypropylenes ; Prospective Studies ; Quality of Life ; Secondary Prevention ; Surgical Mesh ; Treatment Outcome
Chemical Substances	Polypropylenes
Keywords	covid19
Language	English
Publishing date	2013
Publishing country	Czech Republic
Document type	Comparative Study ; Journal Article ; Multicenter Study
ZDB-ID	2148569-0
ISSN	1214-6994
ISSN	1214-6994
DOI	10.14712/23362936.2014.12
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Article: Analysis of NO, NO₂, and O ₃ Between Model Simulations and Ground-Based, Aircraft, and Satellite Observations

Kaynak, Burcak / Hu, Yongtao / Russell, Armistead G

Water, air and soil pollution. 2013 Sept., v. 224, no. 9

2013

Abstract: Regional air quality model simulations with Community Multiscale Air Quality Modeling System (CMAQ) were evaluated using multiple platforms for a 2-month summer period. In this context, inter-comparisons of the model with available satellite-based ... ...

Abstract	Regional air quality model simulations with Community Multiscale Air Quality Modeling System (CMAQ) were evaluated using multiple platforms for a 2-month summer period. In this context, inter-comparisons of the model with available satellite-based observations of NO₂, ground- and aircraft-based observations of NO, NO₂, NO ₓ , NO y , and O₃ were performed. NO₂ comparisons found low biases in CMAQ results when using both ground- and satellite-based observations. Aircraft-based observations, on the other hand, indicated a higher positive bias and error, but the overall NO₂ vertical profile was captured well by the model. The highest correlation was observed with satellite-based NO₂ observations indicating that the model and satellite found similar spatial gradients. NO concentrations were underestimated in comparison with both ground- and aircraft-based observations, especially near the surface, indicating the limitations of the model to simulate primary pollutant concentrations at point observations when there are sources nearby. NO y comparisons found positive biases in the model when using both ground- and aircraft-based observations. The main reason for this overestimation was the consistent overestimation of peroxyacyl nitrates (PANs) in CMAQ results. Modeled O₃ concentrations compared well with lowest biases and errors when compared to aircraft- and ground-based observations. The O₃ vertical profile indicated a small positive bias in the model results near the surface similar to the comparison with ground-based observations. However, a negative bias in the model was observed above 2� km. Comparison with aircraft-based observations revealed significant overestimations in PAN and OH concentrations. Overestimation of the modeled OH concentrations is particularly important considering the effect of OH in atmospheric reactions.
Keywords	air quality ; aircraft ; nitrates ; simulation models ; summer
Language	English
Dates of publication	2013-09
Size	p. 1674.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	120499-3
ISSN	1573-2932 ; 0049-6979 ; 0043-1168
ISSN (online)	1573-2932
ISSN	0049-6979 ; 0043-1168
DOI	10.1007/s11270-013-1674-2
Database	NAL-Catalogue (AGRICOLA)

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