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Article: The Atlas of Bacterial & Archaeal Cell Structure

Oikonomou, Catherine M / Jensen, Grant J

Journal of microbiology & biology education

2021 Volume 22, Issue 2

Abstract: Here, we describe a new open-access digital textbook for microbiology, ...

Abstract	Here, we describe a new open-access digital textbook for microbiology,
Language	English
Publishing date	2021-08-31
Publishing country	United States
Document type	Journal Article
ISSN	1935-7877
ISSN	1935-7877
DOI	10.1128/jmbe.00128-21
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Article ; Online: Diagnostic performance of quantitative flow ratio in non-ST elevation acute coronary syndromes in comparison to non-hyperemic pressure ratios: a prospective study.

Liontou, Catherine / Kalogera, Vasiliki / Oikonomou, Dimitrios / Stalikas, Dimitrios / Pappas, Loukas / Triantafyllou, Konstantinos

The international journal of cardiovascular imaging

2023 Volume 39, Issue 12, Page(s) 2567–2574

Abstract: Quantitative flow ratio (QFR) is a new angiography-based coronary physiology tool aimed to evaluate functional relevance of intermediate coronary lesions. Aim of the study is to assess diagnostic performance of QFR in patients with non-ST-elevation acute ...

Abstract	Quantitative flow ratio (QFR) is a new angiography-based coronary physiology tool aimed to evaluate functional relevance of intermediate coronary lesions. Aim of the study is to assess diagnostic performance of QFR in patients with non-ST-elevation acute coronary syndrome (NSTE-ACS) in comparison to currently used non-hyperaemic pressure ratios (NHPRs). In this prospective, single-centre study, coronary physiology of intermediate coronary stenoses of non-culprit vessels in patients presenting with NSTE-ACS was evaluated using NHPRs (iFR, DFR or RFR). Subsequently, QFR was computed offline by a QFR analyst blinded to the NHPR results. Diagnostic performance of QFR was assessed in comparison to NHPRs as reference standard. A total of 60 vessels with intermediate coronary stenoses was investigated. The NHPRs were used as follows: RFR 38%, DFR 47% and iFR 15% of the cases. The NHPR result was positive, showing significant lesion, in 19 cases. A significant correlation was found between NHPR and QFR (r = 0.84, p < 0.001). Classification agreement of the two methods (95%) and diagnostic performance of QFR in comparison to NHPR (AUC: 0.962 [0.914-1.00]) were both high. Sensitivity, specificity, positive and negative predictive value of QFR in comparison to NHPR were 84.2%, 100%, 100% and 93.2% respectively. QFR has high diagnostic performance in detecting functionally significant lesions of non-culprit arteries in patients with NSTE-ACS and multivessel disease. Due to its high negative predictive value, it can be used to safely avoid unnecessary invasive physiological assessment of these lesions.
MeSH term(s)	Humans ; Prospective Studies ; Acute Coronary Syndrome/diagnostic imaging ; Acute Coronary Syndrome/therapy ; Coronary Angiography/methods ; Fractional Flow Reserve, Myocardial/physiology ; Coronary Vessels/diagnostic imaging ; Predictive Value of Tests ; Coronary Stenosis/diagnostic imaging ; Coronary Stenosis/therapy ; Severity of Illness Index ; Coronary Artery Disease
Language	English
Publishing date	2023-10-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2055311-0
ISSN	1875-8312 ; 1573-0743 ; 1569-5794 ; 0167-9899
ISSN (online)	1875-8312 ; 1573-0743
ISSN	1569-5794 ; 0167-9899
DOI	10.1007/s10554-023-02967-y
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Article ; Online: Simulations of Proposed Mechanisms of FtsZ-Driven Cell Constriction.

Nguyen, Lam T / Oikonomou, Catherine M / Jensen, Grant J

Journal of bacteriology

2021 Volume 203, Issue 3

Abstract: To divide, bacteria must constrict their membranes against significant force from turgor pressure. A tubulin homolog, FtsZ, is thought to drive constriction, but how FtsZ filaments might generate constrictive force in the absence of motor proteins is not ...

Abstract	To divide, bacteria must constrict their membranes against significant force from turgor pressure. A tubulin homolog, FtsZ, is thought to drive constriction, but how FtsZ filaments might generate constrictive force in the absence of motor proteins is not well understood. There are two predominant models in the field. In one, FtsZ filaments overlap to form complete rings around the circumference of the cell, and attractive forces cause filaments to slide past each other to maximize lateral contact. In the other, filaments exert force on the membrane by a GTP-hydrolysis-induced switch in conformation from straight to bent. Here, we developed software, ZCONSTRICT, for quantitative three-dimensional (3D) simulations of Gram-negative bacterial cell division to test these two models and identify critical conditions required for them to work. We find that the avidity of any kind of lateral interactions quickly halts the sliding of filaments, so a mechanism such as depolymerization or treadmilling is required to sustain constriction by filament sliding. For filament bending, we find that a mechanism such as the presence of a rigid linker is required to constrain bending to within the division plane and maintain the distance observed
MeSH term(s)	Bacteria/metabolism ; Bacterial Proteins/metabolism ; Cell Division/physiology ; Cell Wall ; Cytoskeletal Proteins/metabolism ; Cytoskeleton/metabolism ; Hydrolysis
Chemical Substances	Bacterial Proteins ; Cytoskeletal Proteins ; FtsZ protein, Bacteria
Language	English
Publishing date	2021-01-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00576-20
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Article ; Online: Electron Cryotomography of Bacterial Secretion Systems.

Oikonomou, Catherine M / Jensen, Grant J

Microbiology spectrum

2019 Volume 7, Issue 2

Abstract: In biology, function arises from form. For bacterial secretion systems, which often span two membranes, avidly bind to the cell wall, and contain hundreds of individual proteins, studying form is a daunting task, made possible by electron cryotomography ( ...

Abstract	In biology, function arises from form. For bacterial secretion systems, which often span two membranes, avidly bind to the cell wall, and contain hundreds of individual proteins, studying form is a daunting task, made possible by electron cryotomography (ECT). ECT is the highest-resolution imaging technique currently available to visualize unique objects inside cells, providing a three-dimensional view of the shapes and locations of large macromolecular complexes in their native environment. Over the past 15 years, ECT has contributed to the study of bacterial secretion systems in two main ways: by revealing intact forms for the first time and by mapping components into these forms. Here we highlight some of these contributions, revealing structural convergence in type II secretion systems, structural divergence in type III secretion systems, unexpected structures in type IV secretion systems, and unexpected mechanisms in types V and VI secretion systems. Together, they offer a glimpse into a world of fantastic forms-nanoscale rotors, needles, pumps, and dart guns-much of which remains to be explored.
MeSH term(s)	Bacteria/metabolism ; Bacterial Proteins ; Bacterial Secretion Systems/chemistry ; Bacterial Secretion Systems/classification ; Electron Microscope Tomography/methods ; Electrons ; Type II Secretion Systems ; Type III Secretion Systems ; Type IV Secretion Systems ; Type V Secretion Systems ; Type VI Secretion Systems
Chemical Substances	Bacterial Proteins ; Bacterial Secretion Systems ; Type II Secretion Systems ; Type III Secretion Systems ; Type IV Secretion Systems ; Type V Secretion Systems ; Type VI Secretion Systems
Language	English
Publishing date	2019-04-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/microbiolspec.PSIB-0019-2018
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Article ; Online: The Atlas of Bacterial & Archaeal Cell Structure

Catherine M. Oikonomou / Grant J. Jensen

Journal of Microbiology & Biology Education, Vol 22, Iss

an Interactive Open-Access Microbiology Textbook

2021 Volume 2

Abstract: ABSTRACT Here, we describe a new open-access digital textbook for microbiology, The Atlas of Bacterial & Archaeal Cell Structure (available at cellstructureatlas.org). The book addresses a fundamental gap in existing textbooks, namely, what bacterial and ...

Abstract	ABSTRACT Here, we describe a new open-access digital textbook for microbiology, The Atlas of Bacterial & Archaeal Cell Structure (available at cellstructureatlas.org). The book addresses a fundamental gap in existing textbooks, namely, what bacterial and archaeal cells look like and how the macromolecular structures they contain give rise to their diverse and complex functions. The interactive, multimedia resource features real data from more than 150 cells belonging to approximately 70 different species, imaged by cutting-edge cryogenic electron microscopy (cryo-EM). Complementary animations show the cellular machinery in action. Only a basic familiarity with fundamental biology concepts is required to understand the material, which targets a wide range of students in courses from general biology for nonmajors to specialized graduate-level microbiology. The content can be digested in several hours, making it well suited to be assigned as a supplemental resource for a course covering either more diverse topics in cell biology or a more specialized topic such as medical microbiology. By making this resource freely available online, we hope it will serve students in diverse educational settings, including self-directed learners.
Keywords	bacteria ; archaea ; cryo-EM ; cryo-electron tomography ; microbiology ; educational resource ; Special aspects of education ; LC8-6691 ; Biology (General) ; QH301-705.5
Subject code	028
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	American Society for Microbiology
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The development of cryo-EM and how it has advanced microbiology.

Oikonomou, Catherine M / Jensen, Grant J

Nature microbiology

2017 Volume 2, Issue 12, Page(s) 1577–1579

MeSH term(s)	Cryoelectron Microscopy/history ; Cryoelectron Microscopy/methods ; History, 20th Century ; History, 21st Century ; Microbiology/trends ; Nobel Prize
Language	English
Publishing date	2017-11-14
Publishing country	England
Document type	Historical Article ; Journal Article
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-017-0073-7
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Article ; Online: ZnO NPs immobilized by Alizarin as in vitro predictive and imaging biomarkers for protein amyloidosis.

Giannousi, Kleoniki / Karageorgou, Maria-Eleni / Oikonomou, Ilias M / Komninou, Philomela / Dendrinou-Samara, Catherine

Journal of inorganic biochemistry

2022 Volume 236, Page(s) 111971

Abstract: Protein amyloidosis represents the main pathological hallmark of many incurable neurodegenerative disorders and protein misfolding diseases. Nanomaterials-based approaches give rise to diagnosis and/or prediction of these proteinopathies, with regards to ...

Abstract	Protein amyloidosis represents the main pathological hallmark of many incurable neurodegenerative disorders and protein misfolding diseases. Nanomaterials-based approaches give rise to diagnosis and/or prediction of these proteinopathies, with regards to the multifactorial nature of their pathogenesis. Herein, crystalline truncated hexagonal shaped naked ZnO nanoparticles (mean value 47.4 nm) have been solvothermally prepared and immobilized further with alizarin (Alzn) molecules (54%) to stand up to amyloidosis acting both as inhibitors and imaging agents, as well as antioxidants. Thioflavin-T (ThT) assay revealed that the resulted zinc oxide nanoparticles immobilized with alizarin (ZnO@Alzn NPs) inhibited in vitro insulin amyloids formation in a dose-dependent manner, while the kinetic mechanism of the phenomenon was recorded. In parallel, amyloid oligomers and plaques have been visualized by conventional optical microscopy upon protein co-incubation with ZnO@Alzn NPs, highlighting the imaging ability of the immobilized NPs. The antioxidant activity was monitored by 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay, through which it was shown that alizarin incorporation onto the inorganic core leads to the reduction of IC
MeSH term(s)	Amyloid ; Amyloidosis/diagnostic imaging ; Anthraquinones ; Anti-Bacterial Agents/pharmacology ; Antioxidants/chemistry ; Antioxidants/pharmacology ; Biomarkers ; Free Radicals ; Humans ; Insulins ; Metal Nanoparticles/chemistry ; Microbial Sensitivity Tests ; Zinc Oxide/chemistry ; Zinc Oxide/pharmacology
Chemical Substances	Amyloid ; Anthraquinones ; Anti-Bacterial Agents ; Antioxidants ; Biomarkers ; Free Radicals ; Insulins ; alizarin (60MEW57T9G) ; Zinc Oxide (SOI2LOH54Z)
Language	English
Publishing date	2022-08-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	162843-4
ISSN	1873-3344 ; 0162-0134
ISSN (online)	1873-3344
ISSN	0162-0134
DOI	10.1016/j.jinorgbio.2022.111971
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Article ; Online: A new view into prokaryotic cell biology from electron cryotomography.

Oikonomou, Catherine M / Jensen, Grant J

Nature reviews. Microbiology

2016 Volume 15, Issue 2, Page(s) 128

Language	English
Publishing date	2016-12-28
Publishing country	England
Document type	Journal Article ; Published Erratum
ZDB-ID	2139054-X
ISSN	1740-1534 ; 1740-1526
ISSN (online)	1740-1534
ISSN	1740-1526
DOI	10.1038/nrmicro.2016.195
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Zs.A 5865: 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: Cellular Electron Cryotomography: Toward Structural Biology In Situ.

Oikonomou, Catherine M / Jensen, Grant J

Annual review of biochemistry

2017 Volume 86, Page(s) 873–896

Abstract: Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also ... ...

Abstract	Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.
MeSH term(s)	Archaea/metabolism ; Archaea/ultrastructure ; Bacteria/metabolism ; Bacteria/ultrastructure ; Bacterial Secretion Systems/metabolism ; Bacterial Secretion Systems/ultrastructure ; Cryoelectron Microscopy/history ; Cryoelectron Microscopy/instrumentation ; Cryoelectron Microscopy/methods ; Electron Microscope Tomography/history ; Electron Microscope Tomography/instrumentation ; Electron Microscope Tomography/methods ; Fimbriae, Bacterial/metabolism ; Fimbriae, Bacterial/ultrastructure ; Flagella/metabolism ; Flagella/ultrastructure ; History, 20th Century ; History, 21st Century ; Models, Molecular ; Nuclear Pore/chemistry ; Nuclear Pore/metabolism ; Nuclear Pore/ultrastructure ; Optical Imaging/history ; Optical Imaging/instrumentation ; Optical Imaging/methods ; Prokaryotic Cells/metabolism ; Prokaryotic Cells/ultrastructure ; Protein Domains ; Protein Structure, Secondary
Chemical Substances	Bacterial Secretion Systems
Language	English
Publishing date	2017-06-20
Publishing country	United States
Document type	Historical Article ; Journal Article ; Review
ZDB-ID	207924-0
ISSN	1545-4509 ; 0066-4154
ISSN (online)	1545-4509
ISSN	0066-4154
DOI	10.1146/annurev-biochem-061516-044741
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Article ; Online: A new view into prokaryotic cell biology from electron cryotomography.

Oikonomou, Catherine M / Jensen, Grant J

Nature reviews. Microbiology

2016 Volume 14, Issue 4, Page(s) 205–220

Abstract: Electron cryotomography (ECT) enables intact cells to be visualized in 3D in an essentially native state to 'macromolecular' (∼4 nm) resolution, revealing the basic architectures of complete nanomachines and their arrangements in situ. Since its ... ...

Abstract	Electron cryotomography (ECT) enables intact cells to be visualized in 3D in an essentially native state to 'macromolecular' (∼4 nm) resolution, revealing the basic architectures of complete nanomachines and their arrangements in situ. Since its inception, ECT has advanced our understanding of many aspects of prokaryotic cell biology, from morphogenesis to subcellular compartmentalization and from metabolism to complex interspecies interactions. In this Review, we highlight how ECT has provided structural and mechanistic insights into the physiology of bacteria and archaea and discuss prospects for the future.
MeSH term(s)	Archaea/physiology ; Archaea/ultrastructure ; Bacteria/ultrastructure ; Bacterial Physiological Phenomena ; Cryoelectron Microscopy/methods ; Cytoskeleton/metabolism ; Image Processing, Computer-Assisted
Language	English
Publishing date	2016-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2139054-X
ISSN	1740-1534 ; 1740-1526
ISSN (online)	1740-1534
ISSN	1740-1526
DOI	10.1038/nrmicro.2016.7
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Zs.A 5865: 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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