---
_id: '6467'
abstract:
- lang: eng
text: Fitness interactions between mutations can influence a population’s evolution
in many different ways. While epistatic effects are difficult to measure precisely,
important information is captured by the mean and variance of log fitnesses for
individuals carrying different numbers of mutations. We derive predictions for
these quantities from a class of simple fitness landscapes, based on models of
optimizing selection on quantitative traits. We also explore extensions to the
models, including modular pleiotropy, variable effect sizes, mutational bias and
maladaptation of the wild type. We illustrate our approach by reanalysing a large
dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized
by some large epistatic effects, these data give a good overall fit to the non-epistatic
null model, suggesting that epistasis might have limited influence on the evolutionary
dynamics in this system. We also show how the amount of epistasis depends on both
the underlying fitness landscape and the distribution of mutations, and so is
expected to vary in consistent ways between new mutations, standing variation
and fixed mutations.
article_number: '0881'
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: John J.
full_name: Welch, John J.
last_name: Welch
citation:
ama: Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes.
Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881
apa: Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple
fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881
chicago: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis
on Simple Fitness Landscapes.” Biology Letters. Royal Society of London,
2019. https://doi.org/10.1098/rsbl.2018.0881.
ieee: C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness
landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London,
2019.
ista: Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness
landscapes. Biology Letters. 15(4), 0881.
mla: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple
Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society
of London, 2019, doi:10.1098/rsbl.2018.0881.
short: C. Fraisse, J.J. Welch, Biology Letters 15 (2019).
date_created: 2019-05-19T21:59:15Z
date_published: 2019-04-03T00:00:00Z
date_updated: 2023-08-25T10:34:41Z
day: '03'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1098/rsbl.2018.0881
ec_funded: 1
external_id:
isi:
- '000465405300010'
pmid:
- '31014191'
intvolume: ' 15'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rsbl.2018.0881
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Biology Letters
publication_identifier:
eissn:
- 1744957X
issn:
- '17449561'
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://dx.doi.org/10.6084/m9.figshare.c.4461008
record:
- id: '9798'
relation: research_data
status: public
- id: '9799'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The distribution of epistasis on simple fitness landscapes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '6470'
abstract:
- lang: eng
text: 'Investigating neuronal activity using genetically encoded Ca2+ indicators
in behaving animals is hampered by inaccuracies in spike inference from fluorescent
tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings,
followed by post hoc determination of the expression level of GCaMP6f, to explore
how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+]
transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary
[Ca2+] transients (evoked by a single action potential) negatively correlates
with GCaMP6f expression, but displays large variability even among PCs with similarly
low expression levels. The summation of fluorescence signals is frequency‐dependent,
supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental
data‐based simulations and found that spike inference error rates using MLspike
depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide
simple methods for estimating the unitary [Ca2+] transients in individual weakly
GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. '
article_processing_charge: No
article_type: original
author:
- first_name: Tímea
full_name: Éltes, Tímea
last_name: Éltes
- first_name: Miklos
full_name: Szoboszlay, Miklos
last_name: Szoboszlay
- first_name: Margit Katalin
full_name: Szigeti, Margit Katalin
id: 44F4BDC0-F248-11E8-B48F-1D18A9856A87
last_name: Szigeti
orcid: 0000-0001-9500-8758
- first_name: Zoltan
full_name: Nusser, Zoltan
last_name: Nusser
citation:
ama: Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy
by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing
hippocampal pyramidal cells. Journal of Physiology. 2019;597(11):2925–2947.
doi:10.1113/JP277681
apa: Éltes, T., Szoboszlay, M., Szigeti, M. K., & Nusser, Z. (2019). Improved
spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients
in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology.
Wiley. https://doi.org/10.1113/JP277681
chicago: Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser.
“Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary
[Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal
of Physiology. Wiley, 2019. https://doi.org/10.1113/JP277681.
ieee: T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference
accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly
GCaMP6f-expressing hippocampal pyramidal cells,” Journal of Physiology,
vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.
ista: Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference
accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly
GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11),
2925–2947.
mla: Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak
Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal
Pyramidal Cells.” Journal of Physiology, vol. 597, no. 11, Wiley, 2019,
pp. 2925–2947, doi:10.1113/JP277681.
short: T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597
(2019) 2925–2947.
date_created: 2019-05-19T21:59:17Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-25T10:34:15Z
day: '01'
department:
- _id: GaNo
doi: 10.1113/JP277681
external_id:
isi:
- '000470780400013'
pmid:
- '31006863'
intvolume: ' 597'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1113/JP277681
month: '06'
oa: 1
oa_version: Published Version
page: 2925–2947
pmid: 1
publication: Journal of Physiology
publication_identifier:
eissn:
- '14697793'
issn:
- '00223751'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improved spike inference accuracy by estimating the peak amplitude of unitary
[Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 597
year: '2019'
...
---
_id: '6493'
abstract:
- lang: eng
text: We present two algorithmic approaches for synthesizing linear hybrid automata
from experimental data. Unlike previous approaches, our algorithms work without
a template and generate an automaton with nondeterministic guards and invariants,
and with an arbitrary number and topology of modes. They thus construct a succinct
model from the data and provide formal guarantees. In particular, (1) the generated
automaton can reproduce the data up to a specified tolerance and (2) the automaton
is tight, given the first guarantee. Our first approach encodes the synthesis
problem as a logical formula in the theory of linear arithmetic, which can then
be solved by an SMT solver. This approach minimizes the number of modes in the
resulting model but is only feasible for limited data sets. To address scalability,
we propose a second approach that does not enforce to find a minimal model. The
algorithm constructs an initial automaton and then iteratively extends the automaton
based on processing new data. Therefore the algorithm is well-suited for online
and synthesis-in-the-loop applications. The core of the algorithm is a membership
query that checks whether, within the specified tolerance, a given data set can
result from the execution of a given automaton. We solve this membership problem
for linear hybrid automata by repeated reachability computations. We demonstrate
the effectiveness of the algorithm on synthetic data sets and on cardiac-cell
measurements.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Miriam
full_name: Garcia Soto, Miriam
id: 4B3207F6-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Soto
orcid: 0000−0003−2936−5719
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Luka
full_name: Zeleznik, Luka
id: 3ADCA2E4-F248-11E8-B48F-1D18A9856A87
last_name: Zeleznik
citation:
ama: 'Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis
of linear hybrid automata. In: 31st International Conference on Computer-Aided
Verification. Vol 11561. Springer; 2019:297-314. doi:10.1007/978-3-030-25540-4_16'
apa: 'Garcia Soto, M., Henzinger, T. A., Schilling, C., & Zeleznik, L. (2019).
Membership-based synthesis of linear hybrid automata. In 31st International
Conference on Computer-Aided Verification (Vol. 11561, pp. 297–314). New York
City, NY, USA: Springer. https://doi.org/10.1007/978-3-030-25540-4_16'
chicago: Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka
Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In 31st International
Conference on Computer-Aided Verification, 11561:297–314. Springer, 2019.
https://doi.org/10.1007/978-3-030-25540-4_16.
ieee: M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based
synthesis of linear hybrid automata,” in 31st International Conference on Computer-Aided
Verification, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.
ista: 'Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based
synthesis of linear hybrid automata. 31st International Conference on Computer-Aided
Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314.'
mla: Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.”
31st International Conference on Computer-Aided Verification, vol. 11561,
Springer, 2019, pp. 297–314, doi:10.1007/978-3-030-25540-4_16.
short: M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International
Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314.
conference:
end_date: 2019-07-18
location: New York City, NY, USA
name: 'CAV: Computer-Aided Verification'
start_date: 2019-07-15
date_created: 2019-05-27T07:09:53Z
date_published: 2019-07-12T00:00:00Z
date_updated: 2023-08-25T10:40:41Z
day: '12'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-25540-4_16
ec_funded: 1
external_id:
isi:
- '000491468000016'
file:
- access_level: open_access
checksum: 1f1d61b83a151031745ef70a501da3d6
content_type: application/pdf
creator: dernst
date_created: 2019-08-14T11:05:30Z
date_updated: 2020-07-14T12:47:32Z
file_id: '6817'
file_name: 2019_CAV_GarciaSoto.pdf
file_size: 674795
relation: main_file
file_date_updated: 2020-07-14T12:47:32Z
has_accepted_license: '1'
intvolume: ' 11561'
isi: 1
keyword:
- Synthesis
- Linear hybrid automaton
- Membership
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 297-314
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 31st International Conference on Computer-Aided Verification
publication_identifier:
isbn:
- '9783030255398'
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Membership-based synthesis of linear hybrid automata
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: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11561
year: '2019'
...
---
_id: '6485'
abstract:
- lang: eng
text: Traditional concurrent programming involves manipulating shared mutable state.
Alternatives to this programming style are communicating sequential processes
(CSP) [1] and actor [2] models, which share data via explicit communication. Rendezvous
channelis the common abstraction for communication between several processes,
where senders and receivers perform a rendezvous handshake as a part of their
protocol (senders wait for receivers and vice versa). Additionally to this, channels
support the select expression. In this work, we present the first efficient lock-free
channel algorithm, and compare it against Go [3] and Kotlin [4] baseline implementations.
article_processing_charge: No
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Roman
full_name: Elizarov, Roman
last_name: Elizarov
citation:
ama: Koval N, Alistarh D-A, Elizarov R. Lock-Free Channels for Programming via
Communicating Sequential Processes. ACM Press; 2019:417-418. doi:10.1145/3293883.3297000
apa: 'Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Lock-free channels
for programming via communicating sequential processes. Proceedings of
the 24th Symposium on Principles and Practice of Parallel Programming (pp.
417–418). Washington, NY, United States: ACM Press. https://doi.org/10.1145/3293883.3297000'
chicago: Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. Lock-Free Channels
for Programming via Communicating Sequential Processes. Proceedings of
the 24th Symposium on Principles and Practice of Parallel Programming. ACM
Press, 2019. https://doi.org/10.1145/3293883.3297000.
ieee: N. Koval, D.-A. Alistarh, and R. Elizarov, Lock-free channels for programming
via communicating sequential processes. ACM Press, 2019, pp. 417–418.
ista: Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming
via communicating sequential processes, ACM Press,p.
mla: Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating
Sequential Processes.” Proceedings of the 24th Symposium on Principles and
Practice of Parallel Programming, ACM Press, 2019, pp. 417–18, doi:10.1145/3293883.3297000.
short: N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming
via Communicating Sequential Processes, ACM Press, 2019.
conference:
end_date: 2019-02-20
location: Washington, NY, United States
name: 'PPoPP: Principles and Practice of Parallel Programming'
start_date: 2019-02-16
date_created: 2019-05-24T10:09:12Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-08-25T10:41:20Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3293883.3297000
external_id:
isi:
- '000587604600044'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 417-418
publication: Proceedings of the 24th Symposium on Principles and Practice of Parallel
Programming
publication_identifier:
isbn:
- '9781450362252'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
status: public
title: Lock-free channels for programming via communicating sequential processes
type: conference_poster
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '6504'
abstract:
- lang: eng
text: "Root gravitropism is one of the most important processes allowing plant adaptation
to the land environment. Auxin plays a central role in mediating root gravitropism,
but how auxin contributes to gravitational perception and the subsequent response
is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient
within the root apex, which is generated by the PIN directional auxin transporters,
regulates the expression of three key starch granule synthesis genes, SS4, PGM
and ADG1, which in turn influence the accumulation of starch granules that serve
as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system,
we also showed that TIR1‐mediated auxin signaling is required for starch granule
formation and gravitropic response within root tips. In addition, axr3 mutants
showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism
within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith
production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary,
we propose a dual role for auxin in gravitropism: the regulation of both gravity
perception and response."
article_processing_charge: No
article_type: original
author:
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: P
full_name: He, P
last_name: He
- first_name: X
full_name: Ma, X
last_name: Ma
- first_name: Z
full_name: Yang, Z
last_name: Yang
- first_name: C
full_name: Pang, C
last_name: Pang
- first_name: J
full_name: Yu, J
last_name: Yu
- first_name: G
full_name: Wang, G
last_name: Wang
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: G
full_name: Xiao, G
last_name: Xiao
citation:
ama: Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism.
New Phytologist. 2019;224(2):761-774. doi:10.1111/nph.15932
apa: Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated
statolith production for root gravitropism. New Phytologist. Wiley. https://doi.org/10.1111/nph.15932
chicago: Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and
G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist.
Wiley, 2019. https://doi.org/10.1111/nph.15932.
ieee: Y. Zhang et al., “Auxin-mediated statolith production for root gravitropism,”
New Phytologist, vol. 224, no. 2. Wiley, pp. 761–774, 2019.
ista: Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019.
Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2),
761–774.
mla: Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.”
New Phytologist, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:10.1111/nph.15932.
short: Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao,
New Phytologist 224 (2019) 761–774.
date_created: 2019-05-28T14:33:26Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-28T08:40:13Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.15932
external_id:
isi:
- '000487184200024'
pmid:
- '31111487'
file:
- access_level: open_access
checksum: 6488243334538f5c39099a701cbf76b9
content_type: application/pdf
creator: dernst
date_created: 2020-10-14T08:59:33Z
date_updated: 2020-10-14T08:59:33Z
file_id: '8661'
file_name: 2019_NewPhytologist_Zhang_accepted.pdf
file_size: 1099061
relation: main_file
success: 1
file_date_updated: 2020-10-14T08:59:33Z
has_accepted_license: '1'
intvolume: ' 224'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 761-774
pmid: 1
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646x
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin-mediated statolith production for root gravitropism
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 224
year: '2019'
...
---
_id: '6506'
abstract:
- lang: eng
text: How does environmental complexity affect the evolution of single genes? Here,
we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase
mutants across 19 different environments—from phenotypically homogeneous single-cell
populations in liquid media to heterogeneous biofilms, plant roots and soil populations.
The effects of individual gene mutations on organismal fitness were highly reproducible
in liquid cultures. However, 84% of the tested alleles showed opposing fitness
effects under different growth conditions (sign environmental pleiotropy). In
colony biofilms and soil samples, different alleles dominated in parallel replica
experiments. Accordingly, we found that in these heterogeneous cell populations
the fate of mutations was dictated by a combination of selection and drift. The
latter relates to programmed prophage excisions that occurred during biofilm development.
Overall, for each condition, a wide range of glutamate dehydrogenase mutations
persisted and sometimes fixated as a result of the combined action of selection,
pleiotropy and chance. However, over longer periods and in multiple environments,
nearly all of this diversity would be lost—across all the environments and conditions
that we tested, the wild type was the fittest allele.
article_processing_charge: No
article_type: original
author:
- first_name: Lianet
full_name: Noda-García, Lianet
last_name: Noda-García
- first_name: Dan
full_name: Davidi, Dan
last_name: Davidi
- first_name: Elisa
full_name: Korenblum, Elisa
last_name: Korenblum
- first_name: Assaf
full_name: Elazar, Assaf
last_name: Elazar
- first_name: Ekaterina
full_name: Putintseva, Ekaterina
id: 2EF67C84-F248-11E8-B48F-1D18A9856A87
last_name: Putintseva
- first_name: Asaph
full_name: Aharoni, Asaph
last_name: Aharoni
- first_name: Dan S.
full_name: Tawfik, Dan S.
last_name: Tawfik
citation:
ama: Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate
genetic diversity in complex bacterial environments. Nature Microbiology.
2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y
apa: Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni,
A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity
in complex bacterial environments. Nature Microbiology. Springer Nature.
https://doi.org/10.1038/s41564-019-0412-y
chicago: Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina
Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate
Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology.
Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y.
ieee: L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity
in complex bacterial environments,” Nature Microbiology, vol. 4, no. 7.
Springer Nature, pp. 1221–1230, 2019.
ista: Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik
DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial
environments. Nature Microbiology. 4(7), 1221–1230.
mla: Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity
in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7,
Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y.
short: L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni,
D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.
date_created: 2019-05-29T13:03:30Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-28T08:39:47Z
day: '01'
department:
- _id: FyKo
doi: 10.1038/s41564-019-0412-y
external_id:
isi:
- '000480348200017'
intvolume: ' 4'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/340828v2
month: '07'
oa: 1
oa_version: Preprint
page: 1221–1230
publication: Nature Microbiology
publication_identifier:
issn:
- 2058-5276
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chance and pleiotropy dominate genetic diversity in complex bacterial environments
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2019'
...
---
_id: '6521'
abstract:
- lang: eng
text: Microglia have emerged as a critical component of neurodegenerative diseases.
Genetic manipulation of microglia can elucidate their functional impact in disease.
In neuroscience, recombinant viruses such as lentiviruses and adeno-associated
viruses (AAVs) have been successfully used to target various cell types in the
brain, although effective transduction of microglia is rare. In this review, we
provide a short background of lentiviruses and AAVs, and strategies for designing
recombinant viral vectors. Then, we will summarize recent literature on successful
microglial transductions in vitro and in vivo, and discuss the current challenges.
Finally, we provide guidelines for reporting the efficiency and specificity of
viral targeting in microglia, which will enable the microglial research community
to assess and improve methodologies for future studies.
article_number: '134310'
article_processing_charge: No
article_type: original
author:
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: 'Maes ME, Colombo G, Schulz R, Siegert S. Targeting microglia with lentivirus
and AAV: Recent advances and remaining challenges. Neuroscience Letters.
2019;707. doi:10.1016/j.neulet.2019.134310'
apa: 'Maes, M. E., Colombo, G., Schulz, R., & Siegert, S. (2019). Targeting
microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience
Letters. Elsevier. https://doi.org/10.1016/j.neulet.2019.134310'
chicago: 'Maes, Margaret E, Gloria Colombo, Rouven Schulz, and Sandra Siegert. “Targeting
Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.”
Neuroscience Letters. Elsevier, 2019. https://doi.org/10.1016/j.neulet.2019.134310.'
ieee: 'M. E. Maes, G. Colombo, R. Schulz, and S. Siegert, “Targeting microglia with
lentivirus and AAV: Recent advances and remaining challenges,” Neuroscience
Letters, vol. 707. Elsevier, 2019.'
ista: 'Maes ME, Colombo G, Schulz R, Siegert S. 2019. Targeting microglia with lentivirus
and AAV: Recent advances and remaining challenges. Neuroscience Letters. 707,
134310.'
mla: 'Maes, Margaret E., et al. “Targeting Microglia with Lentivirus and AAV: Recent
Advances and Remaining Challenges.” Neuroscience Letters, vol. 707, 134310,
Elsevier, 2019, doi:10.1016/j.neulet.2019.134310.'
short: M.E. Maes, G. Colombo, R. Schulz, S. Siegert, Neuroscience Letters 707 (2019).
date_created: 2019-06-05T13:16:24Z
date_published: 2019-08-10T00:00:00Z
date_updated: 2023-08-28T09:30:57Z
day: '10'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.neulet.2019.134310
ec_funded: 1
external_id:
isi:
- '000486094600037'
pmid:
- '31158432'
file:
- access_level: open_access
checksum: 553c9dbd39727fbed55ee991c51ca4d1
content_type: application/pdf
creator: dernst
date_created: 2019-06-08T11:44:20Z
date_updated: 2020-07-14T12:47:33Z
file_id: '6551'
file_name: 2019_Neuroscience_Maes.pdf
file_size: 1779287
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 707'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
- _id: 267F75D8-B435-11E9-9278-68D0E5697425
name: Modulating microglia through G protein-coupled receptor (GPCR) signaling
publication: Neuroscience Letters
publication_identifier:
issn:
- 0304-3940
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Targeting microglia with lentivirus and AAV: Recent advances and remaining
challenges'
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: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 707
year: '2019'
...
---
_id: '6513'
abstract:
- lang: eng
text: Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn,
where they express markers such as LGR5 1,2 and fuel the constant replenishment
of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise
to adult intestinal stem cells3,4, it remains unclear whether this population
in the patterned epithelium represents unique intestinal stem-cell precursors.
Here we show, using unbiased quantitative lineage-tracing approaches, biophysical
modelling and intestinal transplantation, that all cells of the mouse intestinal
epithelium—irrespective of their location and pattern of LGR5 expression in the
fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using
3D imaging, we find that during fetal development the villus undergoes gross remodelling
and fission. This brings epithelial cells from the non-proliferative villus into
the proliferative intervillus region, which enables them to contribute to the
adult stem-cell niche. Our results demonstrate that large-scale remodelling of
the intestinal wall and cell-fate specification are closely linked. Moreover,
these findings provide a direct link between the observed plasticity and cellular
reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9,
revealing that stem-cell identity is an induced rather than a hardwired property.
article_processing_charge: No
article_type: original
author:
- first_name: Jordi
full_name: Guiu, Jordi
last_name: Guiu
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Shiro
full_name: Yui, Shiro
last_name: Yui
- first_name: Samuel
full_name: Demharter, Samuel
last_name: Demharter
- first_name: Svetlana
full_name: Ulyanchenko, Svetlana
last_name: Ulyanchenko
- first_name: Martti
full_name: Maimets, Martti
last_name: Maimets
- first_name: Anne
full_name: Jørgensen, Anne
last_name: Jørgensen
- first_name: Signe
full_name: Perlman, Signe
last_name: Perlman
- first_name: Lene
full_name: Lundvall, Lene
last_name: Lundvall
- first_name: Linn Salto
full_name: Mamsen, Linn Salto
last_name: Mamsen
- first_name: Agnete
full_name: Larsen, Agnete
last_name: Larsen
- first_name: Rasmus H.
full_name: Olesen, Rasmus H.
last_name: Olesen
- first_name: Claus Yding
full_name: Andersen, Claus Yding
last_name: Andersen
- first_name: Lea Langhoff
full_name: Thuesen, Lea Langhoff
last_name: Thuesen
- first_name: Kristine Juul
full_name: Hare, Kristine Juul
last_name: Hare
- first_name: Tune H.
full_name: Pers, Tune H.
last_name: Pers
- first_name: Konstantin
full_name: Khodosevich, Konstantin
last_name: Khodosevich
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Kim B.
full_name: Jensen, Kim B.
last_name: Jensen
citation:
ama: Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem
cells. Nature. 2019;570:107-111. doi:10.1038/s41586-019-1212-5
apa: Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets,
M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells.
Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1212-5
chicago: Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko,
Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal
Stem Cells.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1212-5.
ieee: J. Guiu et al., “Tracing the origin of adult intestinal stem cells,”
Nature, vol. 570. Springer Nature, pp. 107–111, 2019.
ista: Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen
A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen
LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin
of adult intestinal stem cells. Nature. 570, 107–111.
mla: Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature,
vol. 570, Springer Nature, 2019, pp. 107–11, doi:10.1038/s41586-019-1212-5.
short: J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets,
A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y.
Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B.
Jensen, Nature 570 (2019) 107–111.
date_created: 2019-06-02T21:59:14Z
date_published: 2019-06-06T00:00:00Z
date_updated: 2023-08-28T09:30:23Z
day: '06'
department:
- _id: EdHa
doi: 10.1038/s41586-019-1212-5
external_id:
isi:
- '000470149000048'
pmid:
- '31092921'
intvolume: ' 570'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928
month: '06'
oa: 1
oa_version: Submitted Version
page: 107-111
pmid: 1
publication: Nature
publication_identifier:
eissn:
- '14764687'
issn:
- '00280836'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tracing the origin of adult intestinal stem cells
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 570
year: '2019'
...
---
_id: '6564'
abstract:
- lang: eng
text: Optogenetics enables the spatio-temporally precise control of cell and animal
behavior. Many optogenetic tools are driven by light-controlled protein–protein
interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs).
Applying light-controlled PPIs to new target proteins is challenging because it
is difficult to predict which of the many available LSDs, if any, will yield robust
light regulation. As a consequence, fusion protein libraries need to be prepared
and tested, but methods and platforms to facilitate this process are currently
not available. Here, we developed a genetic engineering strategy and vector library
for the rapid generation of light-controlled PPIs. The strategy permits fusing
a target protein to multiple LSDs efficiently and in two orientations. The public
and expandable library contains 29 vectors with blue, green or red light-responsive
LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate
the versatility of the approach and the necessity for sampling LSDs by generating
light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a
new resource for optical regulation of a broad range of target proteins in cell
and developmental biology.
article_processing_charge: No
article_type: original
author:
- first_name: Alexandra-Madelaine
full_name: Tichy, Alexandra-Madelaine
id: 29D8BB2C-F248-11E8-B48F-1D18A9856A87
last_name: Tichy
- first_name: Elliot J.
full_name: Gerrard, Elliot J.
last_name: Gerrard
- first_name: Julien M.D.
full_name: Legrand, Julien M.D.
last_name: Legrand
- first_name: Robin M.
full_name: Hobbs, Robin M.
last_name: Hobbs
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy
and vector library for the rapid generation of modular light-controlled protein–protein
interactions. Journal of Molecular Biology. 2019;431(17):3046-3055. doi:10.1016/j.jmb.2019.05.033
apa: Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., & Janovjak,
H. L. (2019). Engineering strategy and vector library for the rapid generation
of modular light-controlled protein–protein interactions. Journal of Molecular
Biology. Elsevier. https://doi.org/10.1016/j.jmb.2019.05.033
chicago: Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin
M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for
the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.”
Journal of Molecular Biology. Elsevier, 2019. https://doi.org/10.1016/j.jmb.2019.05.033.
ieee: A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak,
“Engineering strategy and vector library for the rapid generation of modular light-controlled
protein–protein interactions,” Journal of Molecular Biology, vol. 431,
no. 17. Elsevier, pp. 3046–3055, 2019.
ista: Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering
strategy and vector library for the rapid generation of modular light-controlled
protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055.
mla: Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library
for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.”
Journal of Molecular Biology, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55,
doi:10.1016/j.jmb.2019.05.033.
short: A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal
of Molecular Biology 431 (2019) 3046–3055.
date_created: 2019-06-16T21:59:14Z
date_published: 2019-08-09T00:00:00Z
date_updated: 2023-08-28T09:39:22Z
day: '09'
department:
- _id: HaJa
doi: 10.1016/j.jmb.2019.05.033
external_id:
isi:
- '000482872100002'
intvolume: ' 431'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.biorxiv.org/content/10.1101/583369v1
month: '08'
oa: 1
oa_version: Preprint
page: 3046-3055
publication: Journal of Molecular Biology
publication_identifier:
eissn:
- '10898638'
issn:
- '00222836'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Engineering strategy and vector library for the rapid generation of modular
light-controlled protein–protein interactions
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 431
year: '2019'
...
---
_id: '6552'
abstract:
- lang: eng
text: 'When animals become sick, infected cells and an armada of activated immune
cells attempt to eliminate the pathogen from the body. Once infectious particles
have breached the body''s physical barriers of the skin or gut lining, an initially
local response quickly escalates into a systemic response, attracting mobile immune
cells to the site of infection. These cells complement the initial, unspecific
defense with a more specialized, targeted response. This can also provide long-term
immune memory and protection against future infection. The cell-autonomous defenses
of the infected cells are thus aided by the actions of recruited immune cells.
These specialized cells are the most mobile cells in the body, constantly patrolling
through the otherwise static tissue to detect incoming pathogens. Such constant
immune surveillance means infections are noticed immediately and can be rapidly
cleared from the body. Some immune cells also remove infected cells that have
succumbed to infection. All this prevents pathogen replication and spread to healthy
tissues. Although this may involve the sacrifice of some somatic tissue, this
is typically replaced quickly. Particular care is, however, given to the reproductive
organs, which should always remain disease free (immune privilege). '
article_processing_charge: No
article_type: original
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Cremer S. Social immunity in insects. Current Biology. 2019;29(11):R458-R463.
doi:10.1016/j.cub.2019.03.035
apa: Cremer, S. (2019). Social immunity in insects. Current Biology. Elsevier.
https://doi.org/10.1016/j.cub.2019.03.035
chicago: Cremer, Sylvia. “Social Immunity in Insects.” Current Biology. Elsevier,
2019. https://doi.org/10.1016/j.cub.2019.03.035.
ieee: S. Cremer, “Social immunity in insects,” Current Biology, vol. 29,
no. 11. Elsevier, pp. R458–R463, 2019.
ista: Cremer S. 2019. Social immunity in insects. Current Biology. 29(11), R458–R463.
mla: Cremer, Sylvia. “Social Immunity in Insects.” Current Biology, vol.
29, no. 11, Elsevier, 2019, pp. R458–63, doi:10.1016/j.cub.2019.03.035.
short: S. Cremer, Current Biology 29 (2019) R458–R463.
date_created: 2019-06-09T21:59:10Z
date_published: 2019-06-03T00:00:00Z
date_updated: 2023-08-28T09:38:00Z
day: '03'
department:
- _id: SyCr
doi: 10.1016/j.cub.2019.03.035
external_id:
isi:
- '000470902000023'
pmid:
- '31163158'
intvolume: ' 29'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2019.03.035
month: '06'
oa: 1
oa_version: Published Version
page: R458-R463
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- '09609822'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Social immunity in insects
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2019'
...