---
_id: '14770'
abstract:
- lang: eng
text: We developed LIONESS, a technology that leverages improvements to optical
super-resolution microscopy and prior information on sample structure via machine
learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio
and light exposure) of optical microscopy of living biological specimens. LIONESS
enables dense reconstruction of living brain tissue and morphodynamics visualization
at the nanoscale.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
citation:
ama: Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living
brain tissue. Nature Methods. 2023;20(8):1141-1142. doi:10.1038/s41592-023-01937-5
apa: Danzl, J. G., & Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction
of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01937-5
chicago: Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction
of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01937-5.
ieee: J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of
living brain tissue,” Nature Methods, vol. 20, no. 8. Springer Nature,
pp. 1141–1142, 2023.
ista: Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of
living brain tissue. Nature Methods. 20(8), 1141–1142.
mla: Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction
of Living Brain Tissue.” Nature Methods, vol. 20, no. 8, Springer Nature,
2023, pp. 1141–42, doi:10.1038/s41592-023-01937-5.
short: J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.
corr_author: '1'
date_created: 2024-01-10T08:07:15Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2026-04-14T08:34:34Z
day: '01'
department:
- _id: JoDa
doi: 10.1038/s41592-023-01937-5
external_id:
isi:
- '001025621500002'
fulldoi: https://doi.org/10.1038/s41592-023-01937-5
intvolume: ' 20'
isi: 1
issue: '8'
keyword:
- Cell Biology
- Molecular Biology
- Biochemistry
- Biotechnology
language:
- iso: eng
month: '08'
oa_version: None
page: 1141-1142
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13267'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: LIONESS enables 4D nanoscale reconstruction of living brain tissue
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2023'
...
---
_id: '15132'
abstract:
- lang: eng
text: Clustered regularly interspaced short palindromic repeats - CRISPR-associated
protein (CRISPR-Cas) systems are a critical component of the bacterial adaptive
immune response. Since the discovery that they can be reengineered as programmable
RNA-guided nucleases, there has been significant interest in using these systems
to perform diverse and precise genetic manipulations. Here, we outline recent
advances in the mechanistic understanding of CRISPR-Cas9, how these findings have
been leveraged in the rational redesign of Cas9 variants with altered activities,
and how these novel tools can be exploited for biotechnology and therapeutics.
We also discuss the potential of the ubiquitous, yet often-overlooked, multisubunit
CRISPR effector complexes for large-scale genomic deletions. Furthermore, we highlight
how future structural studies will bolster these technologies.
article_number: '102839'
article_processing_charge: No
article_type: review
author:
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Grace N
full_name: Hibshman, Grace N
last_name: Hibshman
- first_name: David W
full_name: Taylor, David W
last_name: Taylor
citation:
ama: Bravo JPK, Hibshman GN, Taylor DW. Constructing next-generation CRISPR–Cas
tools from structural blueprints. Current Opinion in Biotechnology. 2022;78.
doi:10.1016/j.copbio.2022.102839
apa: Bravo, J. P. K., Hibshman, G. N., & Taylor, D. W. (2022). Constructing
next-generation CRISPR–Cas tools from structural blueprints. Current Opinion
in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2022.102839
chicago: Bravo, Jack Peter Kelly, Grace N Hibshman, and David W Taylor. “Constructing
Next-Generation CRISPR–Cas Tools from Structural Blueprints.” Current Opinion
in Biotechnology. Elsevier, 2022. https://doi.org/10.1016/j.copbio.2022.102839.
ieee: J. P. K. Bravo, G. N. Hibshman, and D. W. Taylor, “Constructing next-generation
CRISPR–Cas tools from structural blueprints,” Current Opinion in Biotechnology,
vol. 78. Elsevier, 2022.
ista: Bravo JPK, Hibshman GN, Taylor DW. 2022. Constructing next-generation CRISPR–Cas
tools from structural blueprints. Current Opinion in Biotechnology. 78, 102839.
mla: Bravo, Jack Peter Kelly, et al. “Constructing Next-Generation CRISPR–Cas Tools
from Structural Blueprints.” Current Opinion in Biotechnology, vol. 78,
102839, Elsevier, 2022, doi:10.1016/j.copbio.2022.102839.
short: J.P.K. Bravo, G.N. Hibshman, D.W. Taylor, Current Opinion in Biotechnology
78 (2022).
date_created: 2024-03-20T10:41:53Z
date_published: 2022-12-01T00:00:00Z
date_updated: 2024-10-14T12:34:11Z
day: '01'
doi: 10.1016/j.copbio.2022.102839
extern: '1'
external_id:
pmid:
- '36371895'
fulldoi: https://doi.org/10.1016/j.copbio.2022.102839
intvolume: ' 78'
keyword:
- Biomedical Engineering
- Bioengineering
- Biotechnology
language:
- iso: eng
month: '12'
oa_version: None
pmid: 1
publication: Current Opinion in Biotechnology
publication_identifier:
issn:
- 0958-1669
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Constructing next-generation CRISPR–Cas tools from structural blueprints
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2022'
...
---
_id: '15144'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
citation:
ama: Bravo JPK. SuperFi-Cas9 exceeds fidelity, matches speed of original Cas9. Genetic
Engineering & Biotechnology News. 2022;42(4):12. doi:10.1089/gen.42.04.03
apa: Bravo, J. P. K. (2022). SuperFi-Cas9 exceeds fidelity, matches speed of original
Cas9. Genetic Engineering & Biotechnology News. Mary Ann Liebert. https://doi.org/10.1089/gen.42.04.03
chicago: Bravo, Jack Peter Kelly. “SuperFi-Cas9 Exceeds Fidelity, Matches Speed
of Original Cas9.” Genetic Engineering & Biotechnology News. Mary Ann
Liebert, 2022. https://doi.org/10.1089/gen.42.04.03.
ieee: J. P. K. Bravo, “SuperFi-Cas9 exceeds fidelity, matches speed of original
Cas9,” Genetic Engineering & Biotechnology News, vol. 42, no. 4. Mary
Ann Liebert, p. 12, 2022.
ista: Bravo JPK. 2022. SuperFi-Cas9 exceeds fidelity, matches speed of original
Cas9. Genetic Engineering & Biotechnology News. 42(4), 12.
mla: Bravo, Jack Peter Kelly. “SuperFi-Cas9 Exceeds Fidelity, Matches Speed of Original
Cas9.” Genetic Engineering & Biotechnology News, vol. 42, no. 4, Mary
Ann Liebert, 2022, p. 12, doi:10.1089/gen.42.04.03.
short: J.P.K. Bravo, Genetic Engineering & Biotechnology News 42 (2022) 12.
date_created: 2024-03-20T10:43:19Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2024-10-14T12:32:14Z
day: '01'
doi: 10.1089/gen.42.04.03
extern: '1'
fulldoi: https://doi.org/10.1089/gen.42.04.03
intvolume: ' 42'
issue: '4'
keyword:
- Management of Technology and Innovation
- Biomedical Engineering
- Bioengineering
- Biotechnology
language:
- iso: eng
month: '04'
oa_version: None
page: '12'
publication: Genetic Engineering & Biotechnology News
publication_identifier:
eissn:
- 1937-8661
issn:
- 1935-472X
publication_status: published
publisher: Mary Ann Liebert
quality_controlled: '1'
scopus_import: '1'
status: public
title: SuperFi-Cas9 exceeds fidelity, matches speed of original Cas9
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2022'
...
---
_id: '13363'
abstract:
- lang: eng
text: Temporal activation of biological processes by visible light and subsequent
return to an inactive state in the absence of light is an essential characteristic
of photoreceptor cells. Inspired by these phenomena, light-responsive materials
are very attractive due to the high spatiotemporal control of light irradiation,
with light being able to precisely orchestrate processes repeatedly over many
cycles. Herein, it is reported that light-driven proton transfer triggered by
a merocyanine-based photoacid can be used to modulate the permeability of pH-responsive
polymersomes through cyclic, temporally controlled protonation and deprotonation
of the polymersome membrane. The membranes can undergo repeated light-driven swelling–contraction
cycles without losing functional effectiveness. When applied to enzyme loaded-nanoreactors,
this membrane responsiveness is used for the reversible control of enzymatic reactions.
This combination of the merocyanine-based photoacid and pH-switchable nanoreactors
results in rapidly responding and versatile supramolecular systems successfully
used to switch enzymatic reactions ON and OFF on demand.
article_number: '2002135'
article_processing_charge: No
article_type: original
author:
- first_name: Silvia
full_name: Moreno, Silvia
last_name: Moreno
- first_name: Priyanka
full_name: Sharan, Priyanka
last_name: Sharan
- first_name: Johanna
full_name: Engelke, Johanna
last_name: Engelke
- first_name: Hannes
full_name: Gumz, Hannes
last_name: Gumz
- first_name: Susanne
full_name: Boye, Susanne
last_name: Boye
- first_name: Ulrich
full_name: Oertel, Ulrich
last_name: Oertel
- first_name: Peng
full_name: Wang, Peng
last_name: Wang
- first_name: Susanta
full_name: Banerjee, Susanta
last_name: Banerjee
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Brigitte
full_name: Voit, Brigitte
last_name: Voit
- first_name: Albena
full_name: Lederer, Albena
last_name: Lederer
- first_name: Dietmar
full_name: Appelhans, Dietmar
last_name: Appelhans
citation:
ama: Moreno S, Sharan P, Engelke J, et al. Light‐driven proton transfer for cyclic
and temporal switching of enzymatic nanoreactors. Small. 2020;16(37). doi:10.1002/smll.202002135
apa: Moreno, S., Sharan, P., Engelke, J., Gumz, H., Boye, S., Oertel, U., … Appelhans,
D. (2020). Light‐driven proton transfer for cyclic and temporal switching of enzymatic
nanoreactors. Small. Wiley. https://doi.org/10.1002/smll.202002135
chicago: Moreno, Silvia, Priyanka Sharan, Johanna Engelke, Hannes Gumz, Susanne
Boye, Ulrich Oertel, Peng Wang, et al. “Light‐driven Proton Transfer for Cyclic
and Temporal Switching of Enzymatic Nanoreactors.” Small. Wiley, 2020.
https://doi.org/10.1002/smll.202002135.
ieee: S. Moreno et al., “Light‐driven proton transfer for cyclic and temporal
switching of enzymatic nanoreactors,” Small, vol. 16, no. 37. Wiley, 2020.
ista: Moreno S, Sharan P, Engelke J, Gumz H, Boye S, Oertel U, Wang P, Banerjee
S, Klajn R, Voit B, Lederer A, Appelhans D. 2020. Light‐driven proton transfer
for cyclic and temporal switching of enzymatic nanoreactors. Small. 16(37), 2002135.
mla: Moreno, Silvia, et al. “Light‐driven Proton Transfer for Cyclic and Temporal
Switching of Enzymatic Nanoreactors.” Small, vol. 16, no. 37, 2002135,
Wiley, 2020, doi:10.1002/smll.202002135.
short: S. Moreno, P. Sharan, J. Engelke, H. Gumz, S. Boye, U. Oertel, P. Wang, S.
Banerjee, R. Klajn, B. Voit, A. Lederer, D. Appelhans, Small 16 (2020).
date_created: 2023-08-01T09:36:48Z
date_published: 2020-08-11T00:00:00Z
date_updated: 2023-08-07T10:11:41Z
day: '11'
doi: 10.1002/smll.202002135
extern: '1'
external_id:
pmid:
- '32783385'
fulldoi: https://doi.org/10.1002/smll.202002135
intvolume: ' 16'
issue: '37'
keyword:
- Biomaterials
- Biotechnology
- General Materials Science
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/smll.202002135
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Small
publication_identifier:
eissn:
- 1613-6829
issn:
- 1613-6810
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light‐driven proton transfer for cyclic and temporal switching of enzymatic
nanoreactors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '8402'
abstract:
- lang: eng
text: "Background: The mitochondrial pyruvate carrier (MPC) plays a central role
in energy metabolism by transporting pyruvate across the inner mitochondrial membrane.
Its heterodimeric composition and homology to SWEET and semiSWEET transporters
set the MPC apart from the canonical mitochondrial carrier family (named MCF or
SLC25). The import of the canonical carriers is mediated by the carrier translocase
of the inner membrane (TIM22) pathway and is dependent on their structure, which
features an even number of transmembrane segments and both termini in the intermembrane
space. The import pathway of MPC proteins has not been elucidated. The odd number
of transmembrane segments and positioning of the N-terminus in the matrix argues
against an import via the TIM22 carrier pathway but favors an import via the flexible
presequence pathway.\r\nResults: Here, we systematically analyzed the import pathways
of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible
presequence pathway, yeast MPC proteins with an odd number of transmembrane segments
and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor
Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones
MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic
motifs that are also required for the interaction with canonical carrier proteins.\r\nConclusions:
The carrier pathway can import paired and non-paired transmembrane helices and
translocate N-termini to either side of the mitochondrial inner membrane, revealing
an unexpected versatility of the mitochondrial import pathway for non-cleavable
inner membrane proteins."
article_number: '2'
article_processing_charge: No
article_type: original
author:
- first_name: Heike
full_name: Rampelt, Heike
last_name: Rampelt
- first_name: Iva
full_name: Sucec, Iva
last_name: Sucec
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Patrick
full_name: Horten, Patrick
last_name: Horten
- first_name: Inge
full_name: Perschil, Inge
last_name: Perschil
- first_name: Jean-Claude
full_name: Martinou, Jean-Claude
last_name: Martinou
- first_name: Martin
full_name: van der Laan, Martin
last_name: van der Laan
- first_name: Nils
full_name: Wiedemann, Nils
last_name: Wiedemann
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Nikolaus
full_name: Pfanner, Nikolaus
last_name: Pfanner
citation:
ama: Rampelt H, Sucec I, Bersch B, et al. The mitochondrial carrier pathway transports
non-canonical substrates with an odd number of transmembrane segments. BMC
Biology. 2020;18. doi:10.1186/s12915-019-0733-6
apa: Rampelt, H., Sucec, I., Bersch, B., Horten, P., Perschil, I., Martinou, J.-C.,
… Pfanner, N. (2020). The mitochondrial carrier pathway transports non-canonical
substrates with an odd number of transmembrane segments. BMC Biology. Springer
Nature. https://doi.org/10.1186/s12915-019-0733-6
chicago: Rampelt, Heike, Iva Sucec, Beate Bersch, Patrick Horten, Inge Perschil,
Jean-Claude Martinou, Martin van der Laan, Nils Wiedemann, Paul Schanda, and Nikolaus
Pfanner. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates
with an Odd Number of Transmembrane Segments.” BMC Biology. Springer Nature,
2020. https://doi.org/10.1186/s12915-019-0733-6.
ieee: H. Rampelt et al., “The mitochondrial carrier pathway transports non-canonical
substrates with an odd number of transmembrane segments,” BMC Biology,
vol. 18. Springer Nature, 2020.
ista: Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der
Laan M, Wiedemann N, Schanda P, Pfanner N. 2020. The mitochondrial carrier pathway
transports non-canonical substrates with an odd number of transmembrane segments.
BMC Biology. 18, 2.
mla: Rampelt, Heike, et al. “The Mitochondrial Carrier Pathway Transports Non-Canonical
Substrates with an Odd Number of Transmembrane Segments.” BMC Biology,
vol. 18, 2, Springer Nature, 2020, doi:10.1186/s12915-019-0733-6.
short: H. Rampelt, I. Sucec, B. Bersch, P. Horten, I. Perschil, J.-C. Martinou,
M. van der Laan, N. Wiedemann, P. Schanda, N. Pfanner, BMC Biology 18 (2020).
date_created: 2020-09-17T10:26:53Z
date_published: 2020-01-06T00:00:00Z
date_updated: 2024-10-15T13:23:11Z
day: '06'
doi: 10.1186/s12915-019-0733-6
extern: '1'
external_id:
pmid:
- '31907035'
fulldoi: https://doi.org/10.1186/s12915-019-0733-6
intvolume: ' 18'
keyword:
- Biotechnology
- Plant Science
- General Biochemistry
- Genetics and Molecular Biology
- Developmental Biology
- Cell Biology
- Physiology
- Ecology
- Evolution
- Behavior and Systematics
- Structural Biology
- General Agricultural and Biological Sciences
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s12915-019-0733-6
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: BMC Biology
publication_identifier:
issn:
- 1741-7007
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: The mitochondrial carrier pathway transports non-canonical substrates with
an odd number of transmembrane segments
type: journal_article
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
volume: 18
year: '2020'
...
---
_id: '14286'
abstract:
- lang: eng
text: 'The bacteriophage M13 has found frequent applications in nanobiotechnology
due to its chemically and genetically tunable protein surface and its ability
to self-assemble into colloidal membranes. Additionally, its single-stranded (ss)
genome is commonly used as scaffold for DNA origami. Despite the manifold uses
of M13, upstream production methods for phage and scaffold ssDNA are underexamined
with respect to future industrial usage. Here, the high-cell-density phage production
with Escherichia coli as host organism was studied in respect of medium composition,
infection time, multiplicity of infection, and specific growth rate. The specific
growth rate and the multiplicity of infection were identified as the crucial state
variables that influence phage amplification rate on one hand and the concentration
of produced ssDNA on the other hand. Using a growth rate of 0.15 h−1 and a multiplicity
of infection of 0.05 pfu cfu−1 in the fed-batch production process, the concentration
of pure isolated M13 ssDNA usable for scaffolded DNA origami could be enhanced
by 54% to 590 mg L−1. Thus, our results help enabling M13 production for industrial
uses in nanobiotechnology. Biotechnol. Bioeng. 2017;114: 777–784.'
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin
full_name: Kick, Benjamin
last_name: Kick
- first_name: Samantha
full_name: Hensler, Samantha
last_name: Hensler
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
- first_name: Dirk
full_name: Weuster-Botz, Dirk
last_name: Weuster-Botz
citation:
ama: Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. Specific growth
rate and multiplicity of infection affect high-cell-density fermentation with
bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering.
2017;114(4):777-784. doi:10.1002/bit.26200
apa: Kick, B., Hensler, S., Praetorius, F. M., Dietz, H., & Weuster-Botz, D.
(2017). Specific growth rate and multiplicity of infection affect high-cell-density
fermentation with bacteriophage M13 for ssDNA production. Biotechnology and
Bioengineering. Wiley. https://doi.org/10.1002/bit.26200
chicago: Kick, Benjamin, Samantha Hensler, Florian M Praetorius, Hendrik Dietz,
and Dirk Weuster-Botz. “Specific Growth Rate and Multiplicity of Infection Affect
High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” Biotechnology
and Bioengineering. Wiley, 2017. https://doi.org/10.1002/bit.26200.
ieee: B. Kick, S. Hensler, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Specific
growth rate and multiplicity of infection affect high-cell-density fermentation
with bacteriophage M13 for ssDNA production,” Biotechnology and Bioengineering,
vol. 114, no. 4. Wiley, pp. 777–784, 2017.
ista: Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. 2017. Specific
growth rate and multiplicity of infection affect high-cell-density fermentation
with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering.
114(4), 777–784.
mla: Kick, Benjamin, et al. “Specific Growth Rate and Multiplicity of Infection
Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.”
Biotechnology and Bioengineering, vol. 114, no. 4, Wiley, 2017, pp. 777–84,
doi:10.1002/bit.26200.
short: B. Kick, S. Hensler, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Biotechnology
and Bioengineering 114 (2017) 777–784.
date_created: 2023-09-06T12:08:29Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-11-07T12:36:20Z
day: '01'
doi: 10.1002/bit.26200
extern: '1'
external_id:
pmid:
- '27748519'
fulldoi: https://doi.org/10.1002/bit.26200
intvolume: ' 114'
issue: '4'
keyword:
- Applied Microbiology and Biotechnology
- Bioengineering
- Biotechnology
language:
- iso: eng
month: '04'
oa_version: None
page: 777-784
pmid: 1
publication: Biotechnology and Bioengineering
publication_identifier:
issn:
- 0006-3592
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Specific growth rate and multiplicity of infection affect high-cell-density
fermentation with bacteriophage M13 for ssDNA production
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '15162'
abstract:
- lang: eng
text: Cytological profiling (CP) is an unbiased image-based screening technique
that uses automated microscopy and image analysis to profile compounds based on
numerous quantifiable phenotypic features. We used CP to evaluate a library of
nearly 500 compounds with documented mechanisms of action (MOAs) spanning a wide
range of biological pathways. We developed informatics techniques for generating
dosage-independent phenotypic “fingerprints” for each compound, and for quantifying
the likelihood that a compound's CP fingerprint corresponds to its annotated MOA.
We identified groups of features that distinguish classes with closely related
phenotypes, such as microtubule poisons vs. HSP90 inhibitors, and DNA synthesis
vs. proteasome inhibitors. We tested several cases in which cytological profiles
indicated novel mechanisms, including a tyrphostin kinase inhibitor involved in
mitochondrial uncoupling, novel microtubule poisons, and a nominal PPAR-gamma
ligand that acts as a proteasome inhibitor, using independent biochemical assays
to confirm the MOAs predicted by the CP signatures. We also applied maximal-information
statistics to identify correlations between cytological features and kinase inhibitory
activities by combining the CP fingerprints of 24 kinase inhibitors with published
data on their specificities against a diverse panel of kinases. The resulting
analysis suggests a strategy for probing the biological functions of specific
kinases by compiling cytological data from inhibitors of varying specificities.
article_number: '2604'
article_processing_charge: No
article_type: original
author:
- first_name: Marcos H.
full_name: Woehrmann, Marcos H.
last_name: Woehrmann
- first_name: Walter M.
full_name: Bray, Walter M.
last_name: Bray
- first_name: James K.
full_name: Durbin, James K.
last_name: Durbin
- first_name: Sean C.
full_name: Nisam, Sean C.
last_name: Nisam
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Emerson
full_name: Glassey, Emerson
last_name: Glassey
- first_name: Joshua M.
full_name: Stuart, Joshua M.
last_name: Stuart
- first_name: R. Scott
full_name: Lokey, R. Scott
last_name: Lokey
citation:
ama: Woehrmann MH, Bray WM, Durbin JK, et al. Large-scale cytological profiling
for functional analysis of bioactive compounds. Molecular BioSystems. 2013;9(11).
doi:10.1039/c3mb70245f
apa: Woehrmann, M. H., Bray, W. M., Durbin, J. K., Nisam, S. C., Michael, A. K.,
Glassey, E., … Lokey, R. S. (2013). Large-scale cytological profiling for functional
analysis of bioactive compounds. Molecular BioSystems. Royal Society of
Chemistry. https://doi.org/10.1039/c3mb70245f
chicago: Woehrmann, Marcos H., Walter M. Bray, James K. Durbin, Sean C. Nisam, Alicia
K. Michael, Emerson Glassey, Joshua M. Stuart, and R. Scott Lokey. “Large-Scale
Cytological Profiling for Functional Analysis of Bioactive Compounds.” Molecular
BioSystems. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3mb70245f.
ieee: M. H. Woehrmann et al., “Large-scale cytological profiling for functional
analysis of bioactive compounds,” Molecular BioSystems, vol. 9, no. 11.
Royal Society of Chemistry, 2013.
ista: Woehrmann MH, Bray WM, Durbin JK, Nisam SC, Michael AK, Glassey E, Stuart
JM, Lokey RS. 2013. Large-scale cytological profiling for functional analysis
of bioactive compounds. Molecular BioSystems. 9(11), 2604.
mla: Woehrmann, Marcos H., et al. “Large-Scale Cytological Profiling for Functional
Analysis of Bioactive Compounds.” Molecular BioSystems, vol. 9, no. 11,
2604, Royal Society of Chemistry, 2013, doi:10.1039/c3mb70245f.
short: M.H. Woehrmann, W.M. Bray, J.K. Durbin, S.C. Nisam, A.K. Michael, E. Glassey,
J.M. Stuart, R.S. Lokey, Molecular BioSystems 9 (2013).
date_created: 2024-03-21T07:58:57Z
date_published: 2013-08-20T00:00:00Z
date_updated: 2024-03-25T11:45:46Z
day: '20'
doi: 10.1039/c3mb70245f
extern: '1'
fulldoi: https://doi.org/10.1039/c3mb70245f
intvolume: ' 9'
issue: '11'
keyword:
- Molecular Biology
- Biotechnology
language:
- iso: eng
month: '08'
oa_version: None
publication: Molecular BioSystems
publication_identifier:
eissn:
- 1742-2051
issn:
- 1742-206X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Large-scale cytological profiling for functional analysis of bioactive compounds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '13408'
abstract:
- lang: eng
text: Well-defined metallic nanobowls can be prepared by extending the concept of
a protecting group to colloidal synthesis. Magnetic nanoparticles are employed
as “protecting groups” during the galvanic replacement of silver with gold. The
replacement reaction is accompanied by spontantous dissociation of the protecting
groups, leaving behind metallic nanobowls.
article_processing_charge: No
article_type: original
author:
- first_name: Yonatan
full_name: Ridelman, Yonatan
last_name: Ridelman
- first_name: Gurvinder
full_name: Singh, Gurvinder
last_name: Singh
- first_name: Ronit
full_name: Popovitz-Biro, Ronit
last_name: Popovitz-Biro
- first_name: Sharon G.
full_name: Wolf, Sharon G.
last_name: Wolf
- first_name: Sanjib
full_name: Das, Sanjib
last_name: Das
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. Metallic nanobowls
by galvanic replacement reaction on heterodimeric nanoparticles. Small.
2012;8(5):654-660. doi:10.1002/smll.201101882
apa: Ridelman, Y., Singh, G., Popovitz-Biro, R., Wolf, S. G., Das, S., & Klajn,
R. (2012). Metallic nanobowls by galvanic replacement reaction on heterodimeric
nanoparticles. Small. Wiley. https://doi.org/10.1002/smll.201101882
chicago: Ridelman, Yonatan, Gurvinder Singh, Ronit Popovitz-Biro, Sharon G. Wolf,
Sanjib Das, and Rafal Klajn. “Metallic Nanobowls by Galvanic Replacement Reaction
on Heterodimeric Nanoparticles.” Small. Wiley, 2012. https://doi.org/10.1002/smll.201101882.
ieee: Y. Ridelman, G. Singh, R. Popovitz-Biro, S. G. Wolf, S. Das, and R. Klajn,
“Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles,”
Small, vol. 8, no. 5. Wiley, pp. 654–660, 2012.
ista: Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. 2012. Metallic
nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small.
8(5), 654–660.
mla: Ridelman, Yonatan, et al. “Metallic Nanobowls by Galvanic Replacement Reaction
on Heterodimeric Nanoparticles.” Small, vol. 8, no. 5, Wiley, 2012, pp.
654–60, doi:10.1002/smll.201101882.
short: Y. Ridelman, G. Singh, R. Popovitz-Biro, S.G. Wolf, S. Das, R. Klajn, Small
8 (2012) 654–660.
date_created: 2023-08-01T09:47:55Z
date_published: 2012-03-12T00:00:00Z
date_updated: 2024-10-14T12:21:38Z
day: '12'
doi: 10.1002/smll.201101882
extern: '1'
external_id:
pmid:
- '22392681'
fulldoi: https://doi.org/10.1002/smll.201101882
intvolume: ' 8'
issue: '5'
keyword:
- Biomaterials
- Biotechnology
- General Materials Science
- General Chemistry
language:
- iso: eng
month: '03'
oa_version: None
page: 654-660
pmid: 1
publication: Small
publication_identifier:
eissn:
- 1613-6829
issn:
- 1613-6810
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2012'
...
---
_id: '13411'
abstract:
- lang: eng
text: Photoresponsive gold nanoparticles dispersed in a solid/frozen matrix provide
a basis for sensors that “remember” whether the sample has ever exceeded the melting
temperature of the matrix. The operation of these sensors rests on the ability
to photoinduce metastable electric dipoles on NP surfaces – upon melting, these
dipoles drive NP aggregation, precipitation, and crosslinking. These events are
manifested by a pronounced color change.
article_processing_charge: No
article_type: original
author:
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Kevin P.
full_name: Browne, Kevin P.
last_name: Browne
- first_name: Siowling
full_name: Soh, Siowling
last_name: Soh
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Klajn R, Browne KP, Soh S, Grzybowski BA. Nanoparticles that “remember” temperature.
Small. 2010;6(13):1385-1387. doi:10.1002/smll.200902272
apa: Klajn, R., Browne, K. P., Soh, S., & Grzybowski, B. A. (2010). Nanoparticles
that “remember” temperature. Small. Wiley. https://doi.org/10.1002/smll.200902272
chicago: Klajn, Rafal, Kevin P. Browne, Siowling Soh, and Bartosz A. Grzybowski.
“Nanoparticles That ‘Remember’ Temperature.” Small. Wiley, 2010. https://doi.org/10.1002/smll.200902272.
ieee: R. Klajn, K. P. Browne, S. Soh, and B. A. Grzybowski, “Nanoparticles that
‘remember’ temperature,” Small, vol. 6, no. 13. Wiley, pp. 1385–1387, 2010.
ista: Klajn R, Browne KP, Soh S, Grzybowski BA. 2010. Nanoparticles that “remember”
temperature. Small. 6(13), 1385–1387.
mla: Klajn, Rafal, et al. “Nanoparticles That ‘Remember’ Temperature.” Small,
vol. 6, no. 13, Wiley, 2010, pp. 1385–87, doi:10.1002/smll.200902272.
short: R. Klajn, K.P. Browne, S. Soh, B.A. Grzybowski, Small 6 (2010) 1385–1387.
date_created: 2023-08-01T09:48:38Z
date_published: 2010-07-05T00:00:00Z
date_updated: 2023-08-08T08:15:25Z
day: '05'
doi: 10.1002/smll.200902272
extern: '1'
external_id:
pmid:
- '20521264'
fulldoi: https://doi.org/10.1002/smll.200902272
intvolume: ' 6'
issue: '13'
keyword:
- Biomaterials
- Biotechnology
- General Materials Science
- General Chemistry
language:
- iso: eng
month: '07'
oa_version: None
page: 1385-1387
pmid: 1
publication: Small
publication_identifier:
eissn:
- 1613-6829
issn:
- 1613-6810
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nanoparticles that “remember” temperature
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2010'
...
---
_id: '13414'
abstract:
- lang: eng
text: Supraspherical aggregates of crosslinked metal nanoparticles are transformed
into pancakes and nanorods by mechanical stresses and shears imparted by macroscopic
objects (see image). The dimensions of both types of nanostructures can be controlled
by the pressures applied.
article_processing_charge: No
article_type: original
author:
- first_name: Kevin P.
full_name: Browne, Kevin P.
last_name: Browne
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: JulieAnn
full_name: Villa, JulieAnn
last_name: Villa
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Browne KP, Klajn R, Villa J, Grzybowski BA. Mechanofabrication of pancake and
rodlike nanostructures from deformable nanoparticle aggregates. Small.
2009;5(23):2656-2658. doi:10.1002/smll.200900902
apa: Browne, K. P., Klajn, R., Villa, J., & Grzybowski, B. A. (2009). Mechanofabrication
of pancake and rodlike nanostructures from deformable nanoparticle aggregates.
Small. Wiley. https://doi.org/10.1002/smll.200900902
chicago: Browne, Kevin P., Rafal Klajn, JulieAnn Villa, and Bartosz A. Grzybowski.
“Mechanofabrication of Pancake and Rodlike Nanostructures from Deformable Nanoparticle
Aggregates.” Small. Wiley, 2009. https://doi.org/10.1002/smll.200900902.
ieee: K. P. Browne, R. Klajn, J. Villa, and B. A. Grzybowski, “Mechanofabrication
of pancake and rodlike nanostructures from deformable nanoparticle aggregates,”
Small, vol. 5, no. 23. Wiley, pp. 2656–2658, 2009.
ista: Browne KP, Klajn R, Villa J, Grzybowski BA. 2009. Mechanofabrication of pancake
and rodlike nanostructures from deformable nanoparticle aggregates. Small. 5(23),
2656–2658.
mla: Browne, Kevin P., et al. “Mechanofabrication of Pancake and Rodlike Nanostructures
from Deformable Nanoparticle Aggregates.” Small, vol. 5, no. 23, Wiley,
2009, pp. 2656–58, doi:10.1002/smll.200900902.
short: K.P. Browne, R. Klajn, J. Villa, B.A. Grzybowski, Small 5 (2009) 2656–2658.
date_created: 2023-08-01T09:50:12Z
date_published: 2009-12-01T00:00:00Z
date_updated: 2023-08-08T08:49:22Z
day: '01'
doi: 10.1002/smll.200900902
extern: '1'
external_id:
pmid:
- '19771567'
fulldoi: https://doi.org/10.1002/smll.200900902
intvolume: ' 5'
issue: '23'
keyword:
- Biomaterials
- Biotechnology
- General Materials Science
- General Chemistry
language:
- iso: eng
month: '12'
oa_version: None
page: 2656-2658
pmid: 1
publication: Small
publication_identifier:
eissn:
- 1613-6829
issn:
- 1613-6810
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanofabrication of pancake and rodlike nanostructures from deformable nanoparticle
aggregates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2009'
...
---
_id: '13422'
abstract:
- lang: eng
text: 'Make like a leaf: The synthesis and characterization of a family of “flowerlike”
Au/Fe3O4 nanoparticles is described, whereby Fe3O4 “leaves” adhere to a gold core
(see image). The size and numbers of iron oxide domains can be adjusted flexibly
by changing the proportion of the starting materials and the reaction time.'
article_processing_charge: No
article_type: original
author:
- first_name: Yanhu
full_name: Wei, Yanhu
last_name: Wei
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Anatoliy O.
full_name: Pinchuk, Anatoliy O.
last_name: Pinchuk
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Wei Y, Klajn R, Pinchuk AO, Grzybowski BA. Synthesis, shape control, and optical
properties of hybrid Au/Fe3O4 “nanoflowers.” Small. 2008;4(10):1635-1639.
doi:10.1002/smll.200800511
apa: Wei, Y., Klajn, R., Pinchuk, A. O., & Grzybowski, B. A. (2008). Synthesis,
shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers.” Small.
Wiley. https://doi.org/10.1002/smll.200800511
chicago: Wei, Yanhu, Rafal Klajn, Anatoliy O. Pinchuk, and Bartosz A. Grzybowski.
“Synthesis, Shape Control, and Optical Properties of Hybrid Au/Fe3O4 ‘Nanoflowers.’”
Small. Wiley, 2008. https://doi.org/10.1002/smll.200800511.
ieee: Y. Wei, R. Klajn, A. O. Pinchuk, and B. A. Grzybowski, “Synthesis, shape control,
and optical properties of hybrid Au/Fe3O4 ‘nanoflowers,’” Small, vol. 4,
no. 10. Wiley, pp. 1635–1639, 2008.
ista: Wei Y, Klajn R, Pinchuk AO, Grzybowski BA. 2008. Synthesis, shape control,
and optical properties of hybrid Au/Fe3O4 “nanoflowers”. Small. 4(10), 1635–1639.
mla: Wei, Yanhu, et al. “Synthesis, Shape Control, and Optical Properties of Hybrid
Au/Fe3O4 ‘Nanoflowers.’” Small, vol. 4, no. 10, Wiley, 2008, pp. 1635–39,
doi:10.1002/smll.200800511.
short: Y. Wei, R. Klajn, A.O. Pinchuk, B.A. Grzybowski, Small 4 (2008) 1635–1639.
date_created: 2023-08-01T10:30:42Z
date_published: 2008-10-09T00:00:00Z
date_updated: 2023-08-08T11:14:50Z
day: '09'
doi: 10.1002/smll.200800511
extern: '1'
external_id:
pmid:
- '18636405'
fulldoi: https://doi.org/10.1002/smll.200800511
intvolume: ' 4'
issue: '10'
keyword:
- Biomaterials
- Biotechnology
- General Materials Science
- General Chemistry
language:
- iso: eng
month: '10'
oa_version: None
page: 1635-1639
pmid: 1
publication: Small
publication_identifier:
eissn:
- 1613-6829
issn:
- 1613-6810
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers”
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2008'
...