---
OA_place: publisher
_id: '18766'
abstract:
- lang: eng
text: Poxviruses are large pleomorphic double-stranded DNA viruses that include
well known members such as variola virus, the causative agent of smallpox, Mpox
virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain
for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic
DNA viruses in general and poxviruses specifically, as many features, such as
core morphology and structural proteins, are well conserved within this family.
Despite decades of research, our understanding of the structural components and
proteins that comprise the poxvirus core in mature virions remains limited. Although
major core proteins were identified via indirect experimental evidence, the core's
complexity, with its large size, structure and number of involved proteins, has
hindered efforts to achieve high-resolution insights and to define the roles of
the individual proteins. The specific protein composition of the core's individual
layers, including the palisade layer and the inner core wall, has remained unclear.
In this study, we have merged multiple approaches, including single particle cryo
electron microscopy of purified virus cores, cryo-electron tomography and subtomogram
averaging of mature virions and molecular modeling to elucidate the structural
determinants of the VACV core. Due to the lack of experimentally derived structures,
either in situ or reconstituted in vitro, we used Alphafold to predict models
of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results
show that the VACV core is composed of several layers with varying local symmetries,
forming more intricate interactions than observed previously. This allowed us
to identify several molecular building blocks forming the viral core lattice.
In particular, we identified trimers of protein A10 as a major core structure
that forms the palisade layer of the viral core. Additionally, we revealed that
six petals of a flower shaped core pore within the core wall are composed of A10
trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that
could potentially accommodate an A3 dimer. Integrating descriptions of protein
interactions from previous studies enabled us to provide a detailed structural
model of the poxvirus core wall, and our findings indicate that the interactions
within A10 trimers are likely consistent across orthopox- and parapoxviruses.
This combined application of cryo-SPA and cryo-ET can help overcome obstacles
in studying complex virus structures in the future, including their key assembly
proteins, interactions, and the formation into a core lattice. Our work provides
important fundamental new insights into poxvirus core architecture, also considering
the recent re-emergence of poxviruses.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: "This work was funded by the Austrian Science Fund (FWF) grant P31445
and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units,
particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and
the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially
thank Alois for assisting me with the\r\ninstallation of countless new software
and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for
his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving
the process to ensure that I obtained the best possible\r\ndata from my sample."
alternative_title:
- ISTA thesis
article_processing_charge: No
author:
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
citation:
ama: Datler J. Elucidating the structural determinants of the poxvirus core using
multi-modal cryo-EM. 2024. doi:10.15479/at:ista:18766
apa: Datler, J. (2024). Elucidating the structural determinants of the poxvirus
core using multi-modal cryo-EM. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:18766
chicago: Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus
Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria,
2024. https://doi.org/10.15479/at:ista:18766.
ieee: J. Datler, “Elucidating the structural determinants of the poxvirus core using
multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024.
ista: Datler J. 2024. Elucidating the structural determinants of the poxvirus core
using multi-modal cryo-EM. Institute of Science and Technology Austria.
mla: Datler, Julia. Elucidating the Structural Determinants of the Poxvirus Core
Using Multi-Modal Cryo-EM. Institute of Science and Technology Austria, 2024,
doi:10.15479/at:ista:18766.
short: J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using
Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024.
corr_author: '1'
das_tickbox: '1'
date_created: 2025-01-07T10:23:12Z
date_published: 2024-12-30T00:00:00Z
date_updated: 2026-10-02T11:21:19Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: FlSc
doi: 10.15479/at:ista:18766
doi_confirm: '1'
file:
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checksum: 3e51cab327c754045c3d29c1a50cc9a9
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: jstanger
date_created: 2025-01-07T12:15:11Z
date_updated: 2025-01-07T12:15:11Z
file_id: '18769'
file_name: PhD_thesis_Julia_Datler.docx
file_size: 38814932
relation: source_file
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checksum: 22fabe5b97950bf852212f6edb555173
content_type: application/pdf
creator: jstanger
date_created: 2025-01-07T12:15:14Z
date_updated: 2025-01-07T12:15:14Z
file_id: '18770'
file_name: PhD_thesis_Julia_Datler.pdf
file_size: 12044865
relation: main_file
success: 1
file_date_updated: 2025-01-07T12:15:14Z
fulldoi: https://doi.org/10.15479/at:ista:18766
has_accepted_license: '1'
keyword:
- cryo-EM
- cryo-ET
- cryo-SPA
- Structural Virology
- Poxvirus
- Vaccinia Virus
- Structural Biology
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '106'
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication_identifier:
isbn:
- 978-3-99078-049-7
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12334'
relation: part_of_dissertation
status: public
- id: '14979'
relation: part_of_dissertation
status: public
researchdata_availability: yes
status: public
supervisor:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
supplementarymaterial: no
title: Elucidating the structural determinants of the poxvirus core using multi-modal
cryo-EM
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: free access
_id: '18443'
abstract:
- lang: eng
text: "In [KW06] Kapustin and Witten conjectured that there is a mirror symmetry
relation between\r\nthe hyperkähler structures on certain Higgs bundle moduli
spaces. As a consequence, they\r\nconjecture an equivalence between categories
of BBB and BAA-branes. At the classical\r\nlevel, this mirror symmetry is given
by T-duality between semi-flat hyperkähler structures on\r\nalgebraic integrable
systems.\r\nIn this thesis, we investigate the T-duality relation between hyperkähler
structures and the\r\ncorresponding branes on affine torus bundles. We use the
techniques of generalized geometry\r\nto show that semi-flat hyperkähler structures
are T-dual on algebraic integrable systems.\r\nWe also describe T-duality for
generalized branes. Motivated by Fourier-Mukai transform\r\nwe upgrade the T-duality
between generalized branes to T-duality of submanifolds endowed\r\nwith U(1)-bundles
and connections. This T-duality in the appropriate context specializes to\r\nT-duality
between BBB and BAA-branes.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maria A
full_name: Sisak, Maria A
id: 44A03D04-AEA4-11E9-B225-EA2DE6697425
last_name: Sisak
citation:
ama: Sisak MA. T-dual branes on hyperkähler manifolds. 2024. doi:10.15479/at:ista:18443
apa: Sisak, M. A. (2024). T-dual branes on hyperkähler manifolds. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:18443
chicago: Sisak, Maria A. “T-Dual Branes on Hyperkähler Manifolds.” Institute of
Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18443.
ieee: M. A. Sisak, “T-dual branes on hyperkähler manifolds,” Institute of Science
and Technology Austria, 2024.
ista: Sisak MA. 2024. T-dual branes on hyperkähler manifolds. Institute of Science
and Technology Austria.
mla: Sisak, Maria A. T-Dual Branes on Hyperkähler Manifolds. Institute of
Science and Technology Austria, 2024, doi:10.15479/at:ista:18443.
short: M.A. Sisak, T-Dual Branes on Hyperkähler Manifolds, Institute of Science
and Technology Austria, 2024.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-10-19T12:00:37Z
date_published: 2024-10-24T00:00:00Z
date_updated: 2026-10-02T11:43:57Z
day: '24'
ddc:
- '516'
degree_awarded: PhD
department:
- _id: GradSch
- _id: TaHa
doi: 10.15479/at:ista:18443
doi_confirm: '1'
file:
- access_level: open_access
checksum: 8c4893e726aaa4b3efb82758da9b6851
content_type: application/pdf
creator: msisak
date_created: 2024-10-23T14:42:45Z
date_updated: 2024-10-23T14:42:45Z
file_id: '18467'
file_name: MASisak_dissertation.pdf
file_size: 1672547
relation: main_file
success: 1
- access_level: closed
checksum: 1831b072e861a1e5481024ca9d02b036
content_type: application/x-zip-compressed
creator: msisak
date_created: 2024-10-23T14:43:56Z
date_updated: 2024-10-24T08:09:13Z
file_id: '18468'
file_name: MASisak_source.zip
file_size: 617913
relation: source_file
file_date_updated: 2024-10-24T08:09:13Z
fulldoi: https://doi.org/10.15479/at:ista:18443
has_accepted_license: '1'
keyword:
- hyperkaehler geometry
- branes
- mirror symmetry
- T-duality
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '178'
project:
- _id: 6286e8c4-2b32-11ec-9570-f5297902f67f
grant_number: '26069'
name: Branes on hyperkähler manifolds
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
researchdata_availability: no
status: public
supervisor:
- first_name: Tamás
full_name: Hausel, Tamás
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
orcid: 0000-0002-9582-2634
supplementarymaterial: no
title: T-dual branes on hyperkähler manifolds
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
_id: '12491'
abstract:
- lang: eng
text: "The extracellular matrix (ECM) is a hydrated and complex three-dimensional
network consisting of proteins, polysaccharides, and water. It provides structural
scaffolding for the cells embedded within it and is essential in regulating numerous
physiological processes, including cell migration and proliferation, wound healing,
and stem cell fate. \r\nDespite extensive study, detailed structural knowledge
of ECM components in physiologically relevant conditions is still rudimentary.
This is due to methodological limitations in specimen preparation protocols which
are incompatible with keeping large samples, such as the ECM, in their native
state for subsequent imaging. Conventional electron microscopy (EM) techniques
rely on fixation, dehydration, contrasting, and sectioning. This results in the
alteration of a highly hydrated environment and the potential introduction of
artifacts. Other structural biology techniques, such as nuclear magnetic resonance
(NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of
protein structures but only work on homogenous and purified samples, hence lacking
contextual information. Currently, no approach exists for the ultrastructural
and structural study of extracellular components under native conditions in a
physiological, 3D environment. \r\nIn this thesis, I have developed a workflow
that allows for the ultrastructural analysis of the ECM in near-native conditions
at molecular resolution. The developments I introduced include implementing a
novel specimen preparation workflow for cell-derived matrices (CDMs) to render
them compatible with ion-beam milling and subsequent high-resolution cryo-electron
tomography (ET). \r\nTo this end, I have established protocols to generate CDMs
grown over several weeks on EM grids that are compatible with downstream cryo-EM
sample preparation and imaging techniques. Characterization of these ECMs confirmed
that they contain essential ECM components such as collagen I, collagen VI, and
fibronectin I in high abundance and hence represent a bona fide biologically-relevant
sample. I successfully optimized vitrification of these specimens by testing various
vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution
molecular insights into the ultrastructure and organization of CDMs, I established
cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging
and complex specimens. I explored different approaches for the creation of thin
cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique,
resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution
Cryo-ET of these lamellae revealed for the first time the architecture of native
CDM in the context of matrix-secreting cells. This allowed for the in situ visualization
of fibrillar matrix proteins such as collagen, laying the foundation for future
structural and ultrastructural characterization of these proteins in their near-native
environment. \r\nIn summary, in this thesis, I present a novel workflow that combines
state-of-the-art cryo-EM specimen preparation and imaging technologies to permit
characterization of the ECM, an important tissue component in higher organisms.
This innovative and highly versatile workflow will enable addressing far-reaching
questions on ECM architecture, composition, and reciprocal ECM-cell interactions."
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
citation:
ama: Zens B. Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491
apa: Zens, B. (2023). Ultrastructural characterization of natively preserved
extracellular matrix by cryo-electron tomography. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:12491
chicago: Zens, Bettina. “Ultrastructural Characterization of Natively Preserved
Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12491.
ieee: B. Zens, “Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography,” Institute of Science and Technology Austria,
2023.
ista: Zens B. 2023. Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography. Institute of Science and Technology Austria.
mla: Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular
Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12491.
short: B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular
Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria,
2023.
corr_author: '1'
date_created: 2023-02-02T14:50:20Z
date_published: 2023-02-02T00:00:00Z
date_updated: 2026-04-07T13:49:23Z
day: '02'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: FlSc
doi: 10.15479/at:ista:12491
file:
- access_level: open_access
checksum: 069d87f025e0799bf9e3c375664264f2
content_type: application/pdf
creator: bzens
date_created: 2023-02-07T13:07:38Z
date_updated: 2024-02-08T23:30:04Z
embargo: 2024-02-07
file_id: '12527'
file_name: PhDThesis_BettinaZens_2023_final.pdf
file_size: 23082464
relation: main_file
- access_level: closed
checksum: 8c66ed203495d6e078ed1002a866520c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: bzens
date_created: 2023-02-07T13:09:05Z
date_updated: 2024-02-08T23:30:04Z
embargo_to: open_access
file_id: '12528'
file_name: PhDThesis_BettinaZens_2023_final.docx
file_size: 106169509
relation: source_file
file_date_updated: 2024-02-08T23:30:04Z
fulldoi: https://doi.org/10.15479/at:ista:12491
has_accepted_license: '1'
keyword:
- cryo-EM
- cryo-ET
- FIB milling
- method development
- FIBSEM
- extracellular matrix
- ECM
- cell-derived matrices
- CDMs
- cell culture
- high pressure freezing
- HPF
- structural biology
- tomography
- collagen
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '187'
project:
- _id: eba3b5f6-77a9-11ec-83b8-cf0905748aa3
name: Integrated visual proteomics of reciprocal cell-extracellular matrix interactions
- _id: 059B463C-7A3F-11EA-A408-12923DDC885E
name: "NÃ\x96-Fonds Preis für die Jungforscherin des Jahres am IST Austria"
publication_identifier:
isbn:
- 978-3-99078-027-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8586'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
title: Ultrastructural characterization of natively preserved extracellular matrix
by cryo-electron tomography
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22540'
abstract:
- lang: eng
text: The reliable partitioning of the terrestrial latent heat flux into evaporation
(E) and transpiration (T) is important for linking carbon and water cycles and
for better understanding ecosystem functioning at local, regional and global scales.
Previous research revealed that the transpiration-to-evapotranspiration ratio
(T/ET) is well constrained across ecosystems and is nearly independent of vegetation
characteristics and climate. Here we investigated the reasons for such a global
constancy in present-day T/ET by jointly analysing observations and process-based
model simulations. Using this framework, we also quantified how the ratio T/ET
could be influenced by changing climate. For present conditions, we found that
the various components of land surface evaporation (bare soil evaporation, below
canopy soil evaporation, evaporation from interception), and their respective
ratios to plant transpiration, depend largely on local climate and equilibrium
vegetation properties. The systematic covariation between local vegetation characteristics
and climate, resulted in a globally constrained value of T/ET = ∼70 ± 9% for undisturbed
ecosystems, nearly independent of specific climate and vegetation attributes.
Moreover, changes in precipitation amounts and patterns, increasing air temperatures,
atmospheric CO2 concentration, and specific leaf area (the ratio of leaf area
per leaf mass) was found to affect T/ET in various manners. However, even extreme
changes in the aforementioned factors did not significantly modify T/ET.
article_number: '104012'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Athanasios
full_name: Paschalis, Athanasios
last_name: Paschalis
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Christoforos
full_name: Pappas, Christoforos
last_name: Pappas
- first_name: Dani
full_name: Or, Dani
last_name: Or
citation:
ama: Paschalis A, Fatichi S, Pappas C, Or D. Covariation of vegetation and climate
constrains present and future T/ET variability. Environmental Research Letters.
2018;13(10). doi:10.1088/1748-9326/aae267
apa: Paschalis, A., Fatichi, S., Pappas, C., & Or, D. (2018). Covariation of
vegetation and climate constrains present and future T/ET variability. Environmental
Research Letters. IOP Publishing . https://doi.org/10.1088/1748-9326/aae267
chicago: Paschalis, Athanasios, Simone Fatichi, Christoforos Pappas, and Dani Or.
“Covariation of Vegetation and Climate Constrains Present and Future T/ET Variability.”
Environmental Research Letters. IOP Publishing , 2018. https://doi.org/10.1088/1748-9326/aae267.
ieee: A. Paschalis, S. Fatichi, C. Pappas, and D. Or, “Covariation of vegetation
and climate constrains present and future T/ET variability,” Environmental
Research Letters, vol. 13, no. 10. IOP Publishing , 2018.
ista: Paschalis A, Fatichi S, Pappas C, Or D. 2018. Covariation of vegetation and
climate constrains present and future T/ET variability. Environmental Research
Letters. 13(10), 104012.
mla: Paschalis, Athanasios, et al. “Covariation of Vegetation and Climate Constrains
Present and Future T/ET Variability.” Environmental Research Letters, vol.
13, no. 10, 104012, IOP Publishing , 2018, doi:10.1088/1748-9326/aae267.
short: A. Paschalis, S. Fatichi, C. Pappas, D. Or, Environmental Research Letters
13 (2018).
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2018-10-05T00:00:00Z
date_updated: 2026-08-06T07:46:04Z
day: '05'
ddc:
- '550'
doi: 10.1088/1748-9326/aae267
extern: '1'
fulldoi: https://doi.org/10.1088/1748-9326/aae267
has_accepted_license: '1'
intvolume: ' 13'
issue: '10'
keyword:
- T/ET
- Evapotranspiration partitioning
- Ecohydrology
- Modelling
- Climate change
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/1748-9326/aae267
month: '10'
oa: 1
oa_version: Published Version
publication: Environmental Research Letters
publication_identifier:
eissn:
- 1748-9326
publication_status: published
publisher: 'IOP Publishing '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Covariation of vegetation and climate constrains present and future T/ET variability
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2018'
...