---
_id: '12188'
abstract:
- lang: eng
text: Molecular mechanisms enabling the switching and maintenance of epigenetic
states are not fully understood. Distinct histone modifications are often associated
with ON/OFF epigenetic states, but how these states are stably maintained through
DNA replication, yet in certain situations switch from one to another remains
unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11
(ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated
in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER
1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS
(TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated
with histone demethylation in other organisms, and mutant plants show defects
in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular
function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target
and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying
vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during
the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This
was coincident with an attenuation of H3K27me3 at the internal nucleation site
in FLC, and reduction in H3K27me3 levels across the body of the gene after plants
were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic
switching between the mutually exclusive chromatin states at FLC, from the active
H3K36me3 state to the silenced H3K27me3 state. These data support the importance
of physical coupling of histone modification activities to promote epigenetic
switching between opposing chromatin states.
acknowledgement: We would like to thank Scott Berry for help with ICU-GFP nuclear
localization microscopy, Hao Yu and Lisha Shen for assistance with 6mA DNA methylation
analysis, Donna Gibson for graphic design assistance, and members of the C.D. and
Howard laboratories for helpful discussions. This work was funded by the European
Research Council grants to “MEXTIM” (to C.D.) and “SexMeth” (to X. Feng), by the
Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic
Programmes GRO (BB/J004588/1), GEN (BB/P013511/1), BBSRC grant (to X. Feng) (BB/S009620/1),
and the Marie Sklodowska–Curie Postdoctoral Fellowships “UNRAVEL” (to R.H.B.) and
"WISDOM" (to X. Fang). Additional funding via the Wellcome Trust through a Senior
Research Fellowship (to J.R.) (103139) and a multiuser equipment grant (108504).
The Wellcome Centre for Cell Biology is supported by core funding from the Wellcome
Trust (203149).
article_processing_charge: No
article_type: original
author:
- first_name: Rebecca H.
full_name: Bloomer, Rebecca H.
last_name: Bloomer
- first_name: Claire E.
full_name: Hutchison, Claire E.
last_name: Hutchison
- first_name: Isabel
full_name: Bäurle, Isabel
last_name: Bäurle
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Xiaofeng
full_name: Fang, Xiaofeng
last_name: Fang
- first_name: Pumi
full_name: Perera, Pumi
last_name: Perera
- first_name: Christos N.
full_name: Velanis, Christos N.
last_name: Velanis
- first_name: Serin
full_name: Gümüs, Serin
last_name: Gümüs
- first_name: Christos
full_name: Spanos, Christos
last_name: Spanos
- first_name: Juri
full_name: Rappsilber, Juri
last_name: Rappsilber
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Justin
full_name: Goodrich, Justin
last_name: Goodrich
- first_name: Caroline
full_name: Dean, Caroline
last_name: Dean
citation:
ama: Bloomer RH, Hutchison CE, Bäurle I, et al. The Arabidopsis epigenetic regulator
ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings
of the National Academy of Sciences. 2020;117(28):16660-16666. doi:10.1073/pnas.1920621117
apa: Bloomer, R. H., Hutchison, C. E., Bäurle, I., Walker, J., Fang, X., Perera,
P., … Dean, C. (2020). The Arabidopsis epigenetic regulator ICU11 as an accessory
protein of polycomb repressive complex 2. Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1920621117
chicago: Bloomer, Rebecca H., Claire E. Hutchison, Isabel Bäurle, James Walker,
Xiaofeng Fang, Pumi Perera, Christos N. Velanis, et al. “The Arabidopsis Epigenetic
Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences, 2020. https://doi.org/10.1073/pnas.1920621117.
ieee: R. H. Bloomer et al., “The Arabidopsis epigenetic regulator ICU11
as an accessory protein of polycomb repressive complex 2,” Proceedings of the
National Academy of Sciences, vol. 117, no. 28. Proceedings of the National
Academy of Sciences, pp. 16660–16666, 2020.
ista: Bloomer RH, Hutchison CE, Bäurle I, Walker J, Fang X, Perera P, Velanis CN,
Gümüs S, Spanos C, Rappsilber J, Feng X, Goodrich J, Dean C. 2020. The Arabidopsis
epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex
2. Proceedings of the National Academy of Sciences. 117(28), 16660–16666.
mla: Bloomer, Rebecca H., et al. “The Arabidopsis Epigenetic Regulator ICU11 as
an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the
National Academy of Sciences, vol. 117, no. 28, Proceedings of the National
Academy of Sciences, 2020, pp. 16660–66, doi:10.1073/pnas.1920621117.
short: R.H. Bloomer, C.E. Hutchison, I. Bäurle, J. Walker, X. Fang, P. Perera, C.N.
Velanis, S. Gümüs, C. Spanos, J. Rappsilber, X. Feng, J. Goodrich, C. Dean, Proceedings
of the National Academy of Sciences 117 (2020) 16660–16666.
date_created: 2023-01-16T09:15:44Z
date_published: 2020-05-22T00:00:00Z
date_updated: 2023-05-08T10:53:55Z
day: '22'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1073/pnas.1920621117
extern: '1'
external_id:
pmid:
- '32601198'
file:
- access_level: open_access
checksum: cedee184cb12f454f2fba4158ff47db9
content_type: application/pdf
creator: alisjak
date_created: 2023-02-07T11:29:55Z
date_updated: 2023-02-07T11:29:55Z
file_id: '12526'
file_name: 2020_PNAS_Bloomer.pdf
file_size: 1105414
relation: main_file
success: 1
file_date_updated: 2023-02-07T11:29:55Z
has_accepted_license: '1'
intvolume: ' 117'
issue: '28'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/
month: '05'
oa: 1
oa_version: Published Version
page: 16660-16666
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb
repressive complex 2
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2020'
...
---
_id: '7724'
abstract:
- lang: eng
text: Modern molecular genetic datasets, primarily collected to study the biology
of human health and disease, can be used to directly measure the action of natural
selection and reveal important features of contemporary human evolution. Here
we leverage the UK Biobank data to test for the presence of linear and nonlinear
natural selection in a contemporary population of the United Kingdom. We obtain
phenotypic and genetic evidence consistent with the action of linear/directional
selection. Phenotypic evidence suggests that stabilizing selection, which acts
to reduce variance in the population without necessarily modifying the population
mean, is widespread and relatively weak in comparison with estimates from other
species.
article_processing_charge: No
article_type: original
author:
- first_name: Jaleal S.
full_name: Sanjak, Jaleal S.
last_name: Sanjak
- first_name: Julia
full_name: Sidorenko, Julia
last_name: Sidorenko
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Kevin R.
full_name: Thornton, Kevin R.
last_name: Thornton
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
citation:
ama: Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. Evidence of
directional and stabilizing selection in contemporary humans. Proceedings of
the National Academy of Sciences. 2018;115(1):151-156. doi:10.1073/pnas.1707227114
apa: Sanjak, J. S., Sidorenko, J., Robinson, M. R., Thornton, K. R., & Visscher,
P. M. (2018). Evidence of directional and stabilizing selection in contemporary
humans. Proceedings of the National Academy of Sciences. Proceedings of
the National Academy of Sciences. https://doi.org/10.1073/pnas.1707227114
chicago: Sanjak, Jaleal S., Julia Sidorenko, Matthew Richard Robinson, Kevin R.
Thornton, and Peter M. Visscher. “Evidence of Directional and Stabilizing Selection
in Contemporary Humans.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1707227114.
ieee: J. S. Sanjak, J. Sidorenko, M. R. Robinson, K. R. Thornton, and P. M. Visscher,
“Evidence of directional and stabilizing selection in contemporary humans,” Proceedings
of the National Academy of Sciences, vol. 115, no. 1. Proceedings of the National
Academy of Sciences, pp. 151–156, 2018.
ista: Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. 2018. Evidence
of directional and stabilizing selection in contemporary humans. Proceedings of
the National Academy of Sciences. 115(1), 151–156.
mla: Sanjak, Jaleal S., et al. “Evidence of Directional and Stabilizing Selection
in Contemporary Humans.” Proceedings of the National Academy of Sciences,
vol. 115, no. 1, Proceedings of the National Academy of Sciences, 2018, pp. 151–56,
doi:10.1073/pnas.1707227114.
short: J.S. Sanjak, J. Sidorenko, M.R. Robinson, K.R. Thornton, P.M. Visscher, Proceedings
of the National Academy of Sciences 115 (2018) 151–156.
date_created: 2020-04-30T10:45:43Z
date_published: 2018-01-02T00:00:00Z
date_updated: 2021-01-12T08:15:07Z
day: '02'
doi: 10.1073/pnas.1707227114
extern: '1'
intvolume: ' 115'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 151-156
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1073/pnas.1806837115
status: public
title: Evidence of directional and stabilizing selection in contemporary humans
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2018'
...
---
_id: '6109'
abstract:
- lang: eng
text: Neuropeptides are ubiquitous modulators of behavior and physiology. They are
packaged in specialized secretory organelles called dense core vesicles (DCVs)
that are released upon neural stimulation. Unlike synaptic vesicles, which can
be recycled and refilled close to release sites, DCVs must be replenished by de
novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in
a Caenorhabditis elegans sensory neuron whose tonic activity we can control using
a natural stimulus. We express fluorescently tagged neuropeptides in the neuron
and define parameters that describe their subcellular distribution. We measure
these parameters at high and low neural activity in 187 mutants defective in proteins
implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic
activity. Using unsupervised hierarchical clustering methods, we analyze these
data and identify 62 groups of genes with similar mutant phenotypes. We explore
the function of a subset of these groups. We recapitulate many previous findings,
validating our paradigm. We uncover a large battery of proteins involved in recycling
DCV membrane proteins, something hitherto poorly explored. We show that the unfolded
protein response promotes DCV production, which may contribute to intertissue
communication of stress. We also find evidence that different mechanisms of priming
and exocytosis may operate at high and low neural activity. Our work provides
a defined framework to study DCV biology at different neural activity levels.
author:
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
- first_name: QueeLim
full_name: Ch’ng, QueeLim
last_name: Ch’ng
- first_name: Maëlle
full_name: Jospin, Maëlle
last_name: Jospin
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Ramiro
full_name: Lorenzo, Ramiro
last_name: Lorenzo
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. Genetic dissection
of neuropeptide cell biology at high and low activity in a defined sensory neuron.
Proceedings of the National Academy of Sciences. 2018;115(29):E6890-E6899.
doi:10.1073/pnas.1714610115
apa: Laurent, P., Ch’ng, Q., Jospin, M., Chen, C., Lorenzo, R., & de Bono, M.
(2018). Genetic dissection of neuropeptide cell biology at high and low activity
in a defined sensory neuron. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.1714610115
chicago: Laurent, Patrick, QueeLim Ch’ng, Maëlle Jospin, Changchun Chen, Ramiro
Lorenzo, and Mario de Bono. “Genetic Dissection of Neuropeptide Cell Biology at
High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National
Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1714610115.
ieee: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, and M. de Bono, “Genetic
dissection of neuropeptide cell biology at high and low activity in a defined
sensory neuron,” Proceedings of the National Academy of Sciences, vol.
115, no. 29. National Academy of Sciences, pp. E6890–E6899, 2018.
ista: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. 2018. Genetic
dissection of neuropeptide cell biology at high and low activity in a defined
sensory neuron. Proceedings of the National Academy of Sciences. 115(29), E6890–E6899.
mla: Laurent, Patrick, et al. “Genetic Dissection of Neuropeptide Cell Biology at
High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National
Academy of Sciences, vol. 115, no. 29, National Academy of Sciences, 2018,
pp. E6890–99, doi:10.1073/pnas.1714610115.
short: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, M. de Bono, Proceedings
of the National Academy of Sciences 115 (2018) E6890–E6899.
date_created: 2019-03-19T12:41:33Z
date_published: 2018-07-17T00:00:00Z
date_updated: 2021-01-12T08:06:09Z
day: '17'
ddc:
- '570'
doi: 10.1073/pnas.1714610115
extern: '1'
external_id:
pmid:
- '29959203'
file:
- access_level: open_access
checksum: 5e81665377441cdd8d99ab952c534319
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T13:01:58Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6110'
file_name: 2018_PNAS_Laurent.pdf
file_size: 1567765
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 115'
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: E6890-E6899
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Genetic dissection of neuropeptide cell biology at high and low activity in
a defined sensory neuron
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: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2018'
...
---
_id: '9135'
abstract:
- lang: eng
text: Idealized simulations of tropical moist convection have revealed that clouds
can spontaneously clump together in a process called self-aggregation. This results
in a state where a moist cloudy region with intense deep convection is surrounded
by extremely dry subsiding air devoid of deep convection. Because of the idealized
settings of the simulations where it was discovered, the relevance of self-aggregation
to the real world is still debated. Here, we show that self-aggregation feedbacks
play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving
simulations. Those feedbacks accelerate the cyclogenesis process by a factor of
2, and the feedbacks contributing to the cyclone formation show qualitative and
quantitative agreement with the self-aggregation process. Once the cyclone is
formed, wind-induced surface heat exchange (WISHE) effects dominate, although
we find that self-aggregation feedbacks have a small but nonnegligible contribution
to the maintenance of the mature cyclone. Our results suggest that self-aggregation,
and the framework developed for its study, can help shed more light into the physical
processes leading to cyclogenesis and cyclone intensification. In particular,
our results point out the importance of the longwave radiative cooling outside
the cyclone.
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: David M.
full_name: Romps, David M.
last_name: Romps
citation:
ama: Muller CJ, Romps DM. Acceleration of tropical cyclogenesis by self-aggregation
feedbacks. Proceedings of the National Academy of Sciences. 2018;115(12):2930-2935.
doi:10.1073/pnas.1719967115
apa: Muller, C. J., & Romps, D. M. (2018). Acceleration of tropical cyclogenesis
by self-aggregation feedbacks. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1719967115
chicago: Muller, Caroline J, and David M. Romps. “Acceleration of Tropical Cyclogenesis
by Self-Aggregation Feedbacks.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1719967115.
ieee: C. J. Muller and D. M. Romps, “Acceleration of tropical cyclogenesis by self-aggregation
feedbacks,” Proceedings of the National Academy of Sciences, vol. 115,
no. 12. Proceedings of the National Academy of Sciences, pp. 2930–2935, 2018.
ista: Muller CJ, Romps DM. 2018. Acceleration of tropical cyclogenesis by self-aggregation
feedbacks. Proceedings of the National Academy of Sciences. 115(12), 2930–2935.
mla: Muller, Caroline J., and David M. Romps. “Acceleration of Tropical Cyclogenesis
by Self-Aggregation Feedbacks.” Proceedings of the National Academy of Sciences,
vol. 115, no. 12, Proceedings of the National Academy of Sciences, 2018, pp. 2930–35,
doi:10.1073/pnas.1719967115.
short: C.J. Muller, D.M. Romps, Proceedings of the National Academy of Sciences
115 (2018) 2930–2935.
date_created: 2021-02-15T14:18:16Z
date_published: 2018-03-20T00:00:00Z
date_updated: 2022-01-24T12:39:49Z
day: '20'
doi: 10.1073/pnas.1719967115
extern: '1'
intvolume: ' 115'
issue: '12'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1719967115
month: '03'
oa: 1
oa_version: Published Version
page: 2930-2935
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Acceleration of tropical cyclogenesis by self-aggregation feedbacks
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 115
year: '2018'
...
---
_id: '7729'
abstract:
- lang: eng
text: Quantifying the effects of inbreeding is critical to characterizing the genetic
architecture of complex traits. This study highlights through theory and simulations
the strengths and shortcomings of three SNP-based inbreeding measures commonly
used to estimate inbreeding depression (ID). We demonstrate that heterogeneity
in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates,
and we develop an approach to correct this bias using LD and minor allele frequency
stratified inference (LDMS). We quantified ID in 25 traits measured in ∼140,000
participants of the UK Biobank, using LDMS, and confirmed previously published
ID for 4 traits. We find unique evidence of ID for handgrip strength, waist/hip
ratio, and visual and auditory acuity (ID between −2.3 and −5.2 phenotypic SDs
for complete inbreeding; P<0.001). Our results illustrate that a careful choice
of the measure of inbreeding combined with LDMS stratification improves both detection
and quantification of ID using SNP data.
article_processing_charge: No
article_type: original
author:
- first_name: Loic
full_name: Yengo, Loic
last_name: Yengo
- first_name: Zhihong
full_name: Zhu, Zhihong
last_name: Zhu
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Bruce S.
full_name: Weir, Bruce S.
last_name: Weir
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
citation:
ama: Yengo L, Zhu Z, Wray NR, et al. Detection and quantification of inbreeding
depression for complex traits from SNP data. Proceedings of the National Academy
of Sciences. 2017;114(32):8602-8607. doi:10.1073/pnas.1621096114
apa: Yengo, L., Zhu, Z., Wray, N. R., Weir, B. S., Yang, J., Robinson, M. R., &
Visscher, P. M. (2017). Detection and quantification of inbreeding depression
for complex traits from SNP data. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1621096114
chicago: Yengo, Loic, Zhihong Zhu, Naomi R. Wray, Bruce S. Weir, Jian Yang, Matthew
Richard Robinson, and Peter M. Visscher. “Detection and Quantification of Inbreeding
Depression for Complex Traits from SNP Data.” Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621096114.
ieee: L. Yengo et al., “Detection and quantification of inbreeding depression
for complex traits from SNP data,” Proceedings of the National Academy of Sciences,
vol. 114, no. 32. Proceedings of the National Academy of Sciences, pp. 8602–8607,
2017.
ista: Yengo L, Zhu Z, Wray NR, Weir BS, Yang J, Robinson MR, Visscher PM. 2017.
Detection and quantification of inbreeding depression for complex traits from
SNP data. Proceedings of the National Academy of Sciences. 114(32), 8602–8607.
mla: Yengo, Loic, et al. “Detection and Quantification of Inbreeding Depression
for Complex Traits from SNP Data.” Proceedings of the National Academy of Sciences,
vol. 114, no. 32, Proceedings of the National Academy of Sciences, 2017, pp. 8602–07,
doi:10.1073/pnas.1621096114.
short: L. Yengo, Z. Zhu, N.R. Wray, B.S. Weir, J. Yang, M.R. Robinson, P.M. Visscher,
Proceedings of the National Academy of Sciences 114 (2017) 8602–8607.
date_created: 2020-04-30T10:47:19Z
date_published: 2017-08-08T00:00:00Z
date_updated: 2021-01-12T08:15:09Z
day: '08'
doi: 10.1073/pnas.1621096114
extern: '1'
intvolume: ' 114'
issue: '32'
language:
- iso: eng
month: '08'
oa_version: None
page: 8602-8607
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: other
url: https://doi.org/10.1073/pnas.1718598115
status: public
title: Detection and quantification of inbreeding depression for complex traits from
SNP data
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '7757'
abstract:
- lang: eng
text: Recent advances in designing metamaterials have demonstrated that global mechanical
properties of disordered spring networks can be tuned by selectively modifying
only a small subset of bonds. Here, using a computationally efficient approach,
we extend this idea to tune more general properties of networks. With nearly complete
success, we are able to produce a strain between any two target nodes in a network
in response to an applied source strain on any other pair of nodes by removing
only ∼1% of the bonds. We are also able to control multiple pairs of target nodes,
each with a different individual response, from a single source, and to tune multiple
independent source/target responses simultaneously into a network. We have fabricated
physical networks in macroscopic 2D and 3D systems that exhibit these responses.
This work is inspired by the long-range coupled conformational changes that constitute
allosteric function in proteins. The fact that allostery is a common means for
regulation in biological molecules suggests that it is a relatively easy property
to develop through evolution. In analogy, our results show that long-range coupled
mechanical responses are similarly easy to achieve in disordered networks.
article_processing_charge: No
article_type: original
author:
- first_name: Jason W.
full_name: Rocks, Jason W.
last_name: Rocks
- first_name: Nidhi
full_name: Pashine, Nidhi
last_name: Pashine
- first_name: Irmgard
full_name: Bischofberger, Irmgard
last_name: Bischofberger
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. Designing
allostery-inspired response in mechanical networks. Proceedings of the National
Academy of Sciences. 2017;114(10):2520-2525. doi:10.1073/pnas.1612139114
apa: Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J.,
& Nagel, S. R. (2017). Designing allostery-inspired response in mechanical
networks. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1612139114
chicago: Rocks, Jason W., Nidhi Pashine, Irmgard Bischofberger, Carl Peter Goodrich,
Andrea J. Liu, and Sidney R. Nagel. “Designing Allostery-Inspired Response in
Mechanical Networks.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1612139114.
ieee: J. W. Rocks, N. Pashine, I. Bischofberger, C. P. Goodrich, A. J. Liu, and
S. R. Nagel, “Designing allostery-inspired response in mechanical networks,” Proceedings
of the National Academy of Sciences, vol. 114, no. 10. Proceedings of the
National Academy of Sciences, pp. 2520–2525, 2017.
ista: Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. 2017.
Designing allostery-inspired response in mechanical networks. Proceedings of the
National Academy of Sciences. 114(10), 2520–2525.
mla: Rocks, Jason W., et al. “Designing Allostery-Inspired Response in Mechanical
Networks.” Proceedings of the National Academy of Sciences, vol. 114, no.
10, Proceedings of the National Academy of Sciences, 2017, pp. 2520–25, doi:10.1073/pnas.1612139114.
short: J.W. Rocks, N. Pashine, I. Bischofberger, C.P. Goodrich, A.J. Liu, S.R. Nagel,
Proceedings of the National Academy of Sciences 114 (2017) 2520–2525.
date_created: 2020-04-30T11:38:53Z
date_published: 2017-03-07T00:00:00Z
date_updated: 2021-01-12T08:15:19Z
day: '07'
doi: 10.1073/pnas.1612139114
extern: '1'
intvolume: ' 114'
issue: '10'
language:
- iso: eng
month: '03'
oa_version: None
page: 2520-2525
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Designing allostery-inspired response in mechanical networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '7758'
abstract:
- lang: eng
text: Controlling motion at the microscopic scale is a fundamental goal in the development
of biologically inspired systems. We show that the motion of active, self-propelled
colloids can be sufficiently controlled for use as a tool to assemble complex
structures such as braids and weaves out of microscopic filaments. Unlike typical
self-assembly paradigms, these structures are held together by geometric constraints
rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves
precisely controlling the 2D motion of active colloids so that their path has
a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics
simulations that, when the colloids are attached to long semiflexible filaments,
this motion causes the filaments to braid. The ability of the active particles
to provide sufficient force necessary to bend the filaments into a braid depends
on a number of factors, including the self-propulsion mechanism, the properties
of the filament, and the maximum curvature in the braid. Our work demonstrates
that nonequilibrium assembly pathways can be designed using active particles.
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
citation:
ama: Goodrich CP, Brenner MP. Using active colloids as machines to weave and braid
on the micrometer scale. Proceedings of the National Academy of Sciences.
2017;114(2):257-262. doi:10.1073/pnas.1608838114
apa: Goodrich, C. P., & Brenner, M. P. (2017). Using active colloids as machines
to weave and braid on the micrometer scale. Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1608838114
chicago: Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as
Machines to Weave and Braid on the Micrometer Scale.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1608838114.
ieee: C. P. Goodrich and M. P. Brenner, “Using active colloids as machines to weave
and braid on the micrometer scale,” Proceedings of the National Academy of
Sciences, vol. 114, no. 2. Proceedings of the National Academy of Sciences,
pp. 257–262, 2017.
ista: Goodrich CP, Brenner MP. 2017. Using active colloids as machines to weave
and braid on the micrometer scale. Proceedings of the National Academy of Sciences.
114(2), 257–262.
mla: Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines
to Weave and Braid on the Micrometer Scale.” Proceedings of the National Academy
of Sciences, vol. 114, no. 2, Proceedings of the National Academy of Sciences,
2017, pp. 257–62, doi:10.1073/pnas.1608838114.
short: C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences
114 (2017) 257–262.
date_created: 2020-04-30T11:39:09Z
date_published: 2017-01-10T00:00:00Z
date_updated: 2021-01-12T08:15:20Z
day: '10'
doi: 10.1073/pnas.1608838114
extern: '1'
intvolume: ' 114'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 257-262
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Using active colloids as machines to weave and braid on the micrometer scale
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '6113'
author:
- first_name: Shigekazu
full_name: Oda, Shigekazu
last_name: Oda
- first_name: Yu
full_name: Toyoshima, Yu
last_name: Toyoshima
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Oda S, Toyoshima Y, de Bono M. Modulation of sensory information processing
by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy
of Sciences. 2017;114(23):E4658-E4665. doi:10.1073/pnas.1614596114
apa: Oda, S., Toyoshima, Y., & de Bono, M. (2017). Modulation of sensory information
processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1614596114
chicago: Oda, Shigekazu, Yu Toyoshima, and Mario de Bono. “Modulation of Sensory
Information Processing by a Neuroglobin in Caenorhabditis Elegans.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1614596114.
ieee: S. Oda, Y. Toyoshima, and M. de Bono, “Modulation of sensory information processing
by a neuroglobin in Caenorhabditis elegans,” Proceedings of the National Academy
of Sciences, vol. 114, no. 23. National Academy of Sciences, pp. E4658–E4665,
2017.
ista: Oda S, Toyoshima Y, de Bono M. 2017. Modulation of sensory information processing
by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy
of Sciences. 114(23), E4658–E4665.
mla: Oda, Shigekazu, et al. “Modulation of Sensory Information Processing by a Neuroglobin
in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences,
vol. 114, no. 23, National Academy of Sciences, 2017, pp. E4658–65, doi:10.1073/pnas.1614596114.
short: S. Oda, Y. Toyoshima, M. de Bono, Proceedings of the National Academy of
Sciences 114 (2017) E4658–E4665.
date_created: 2019-03-19T13:29:51Z
date_published: 2017-06-06T00:00:00Z
date_updated: 2021-01-12T08:06:11Z
day: '06'
ddc:
- '570'
doi: 10.1073/pnas.1614596114
extern: '1'
external_id:
pmid:
- '28536200'
file:
- access_level: open_access
checksum: 9e42ce47090ecdad7d76f2dbdebb924e
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T13:42:58Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6114'
file_name: 2017_PNAS_Oda.pdf
file_size: 1469622
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 114'
issue: '23'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: E4658-E4665
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Modulation of sensory information processing by a neuroglobin in Caenorhabditis
elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '6115'
abstract:
- lang: eng
text: Animals adjust their behavioral priorities according to momentary needs and
prior experience. We show that Caenorhabditis elegans changes how it processes
sensory information according to the oxygen environment it experienced recently.
C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that
attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged
activity differences in a circuit that continuously signals O2 levels. A sustained
change in the activity of O2-sensing neurons reprograms the properties of their
postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled
to the ASK and ADL pheromone sensors that respectively drive pheromone attraction
and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness
of these neurons. These circuit changes provide a physiological correlate of altered
pheromone valence. Our results suggest C. elegans stores a memory of recent O2
experience in the RMG circuit and illustrate how a circuit is flexibly sculpted
to guide behavioral decisions in a context-dependent manner.
author:
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Fenk LA, de Bono M. Memory of recent oxygen experience switches pheromone valence
inCaenorhabditis elegans. Proceedings of the National Academy of Sciences.
2017;114(16):4195-4200. doi:10.1073/pnas.1618934114
apa: Fenk, L. A., & de Bono, M. (2017). Memory of recent oxygen experience switches
pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1618934114
chicago: Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience
Switches Pheromone Valence InCaenorhabditis Elegans.” Proceedings of the National
Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1618934114.
ieee: L. A. Fenk and M. de Bono, “Memory of recent oxygen experience switches pheromone
valence inCaenorhabditis elegans,” Proceedings of the National Academy of Sciences,
vol. 114, no. 16. National Academy of Sciences, pp. 4195–4200, 2017.
ista: Fenk LA, de Bono M. 2017. Memory of recent oxygen experience switches pheromone
valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences.
114(16), 4195–4200.
mla: Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches
Pheromone Valence InCaenorhabditis Elegans.” Proceedings of the National Academy
of Sciences, vol. 114, no. 16, National Academy of Sciences, 2017, pp. 4195–200,
doi:10.1073/pnas.1618934114.
short: L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 114
(2017) 4195–4200.
date_created: 2019-03-19T13:46:36Z
date_published: 2017-04-18T00:00:00Z
date_updated: 2021-01-12T08:06:11Z
day: '18'
ddc:
- '570'
doi: 10.1073/pnas.1618934114
extern: '1'
external_id:
pmid:
- '28373553'
file:
- access_level: open_access
checksum: 1801bc8319b752fa17598004ec375279
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:00:42Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6116'
file_name: 2017_PNAS_Fenk.pdf
file_size: 1217696
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 114'
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 4195-4200
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Memory of recent oxygen experience switches pheromone valence inCaenorhabditis
elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '8452'
abstract:
- lang: eng
text: During spore formation in Bacillus subtilis a transenvelope complex is assembled
across the double membrane that separates the mother cell and forespore. This
complex (called the “A–Q complex”) is required to maintain forespore development
and is composed of proteins with remote homology to components of type II, III,
and IV secretion systems found in Gram-negative bacteria. Here, we show that one
of these proteins, SpoIIIAG, which has remote homology to ring-forming proteins
found in type III secretion systems, assembles into an oligomeric ring in the
periplasmic-like space between the two membranes. Three-dimensional reconstruction
of images generated by cryo-electron microscopy indicates that the SpoIIIAG ring
has a cup-and-saucer architecture with a 6-nm central pore. Structural modeling
of SpoIIIAG generated a 24-member ring with dimensions similar to those of the
EM-derived saucer. Point mutations in the predicted oligomeric interface disrupted
ring formation in vitro and impaired forespore gene expression and efficient spore
formation in vivo. Taken together, our data provide strong support for the model
in which the A–Q transenvelope complex contains a conduit that connects the mother
cell and forespore. We propose that a set of stacked rings spans the intermembrane
space, as has been found for type III secretion systems.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher D. A.
full_name: Rodrigues, Christopher D. A.
last_name: Rodrigues
- first_name: Xavier
full_name: Henry, Xavier
last_name: Henry
- first_name: Emmanuelle
full_name: Neumann, Emmanuelle
last_name: Neumann
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Laure
full_name: Bellard, Laure
last_name: Bellard
- first_name: Yann
full_name: Fichou, Yann
last_name: Fichou
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Guy
full_name: Schoehn, Guy
last_name: Schoehn
- first_name: David Z.
full_name: Rudner, David Z.
last_name: Rudner
- first_name: Cecile
full_name: Morlot, Cecile
last_name: Morlot
citation:
ama: Rodrigues CDA, Henry X, Neumann E, et al. A ring-shaped conduit connects the
mother cell and forespore during sporulation in Bacillus subtilis. Proceedings
of the National Academy of Sciences. 2016;113(41):11585-11590. doi:10.1073/pnas.1609604113
apa: Rodrigues, C. D. A., Henry, X., Neumann, E., Kurauskas, V., Bellard, L., Fichou,
Y., … Morlot, C. (2016). A ring-shaped conduit connects the mother cell and forespore
during sporulation in Bacillus subtilis. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1609604113
chicago: Rodrigues, Christopher D. A., Xavier Henry, Emmanuelle Neumann, Vilius
Kurauskas, Laure Bellard, Yann Fichou, Paul Schanda, Guy Schoehn, David Z. Rudner,
and Cecile Morlot. “A Ring-Shaped Conduit Connects the Mother Cell and Forespore
during Sporulation in Bacillus Subtilis.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1609604113.
ieee: C. D. A. Rodrigues et al., “A ring-shaped conduit connects the mother
cell and forespore during sporulation in Bacillus subtilis,” Proceedings of
the National Academy of Sciences, vol. 113, no. 41. National Academy of Sciences,
pp. 11585–11590, 2016.
ista: Rodrigues CDA, Henry X, Neumann E, Kurauskas V, Bellard L, Fichou Y, Schanda
P, Schoehn G, Rudner DZ, Morlot C. 2016. A ring-shaped conduit connects the mother
cell and forespore during sporulation in Bacillus subtilis. Proceedings of the
National Academy of Sciences. 113(41), 11585–11590.
mla: Rodrigues, Christopher D. A., et al. “A Ring-Shaped Conduit Connects the Mother
Cell and Forespore during Sporulation in Bacillus Subtilis.” Proceedings of
the National Academy of Sciences, vol. 113, no. 41, National Academy of Sciences,
2016, pp. 11585–90, doi:10.1073/pnas.1609604113.
short: C.D.A. Rodrigues, X. Henry, E. Neumann, V. Kurauskas, L. Bellard, Y. Fichou,
P. Schanda, G. Schoehn, D.Z. Rudner, C. Morlot, Proceedings of the National Academy
of Sciences 113 (2016) 11585–11590.
date_created: 2020-09-18T10:06:58Z
date_published: 2016-09-28T00:00:00Z
date_updated: 2021-01-12T08:19:22Z
day: '28'
doi: 10.1073/pnas.1609604113
extern: '1'
intvolume: ' 113'
issue: '41'
language:
- iso: eng
month: '09'
oa_version: None
page: 11585-11590
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: A ring-shaped conduit connects the mother cell and forespore during sporulation
in Bacillus subtilis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '7760'
abstract:
- lang: eng
text: We propose a Widom-like scaling ansatz for the critical jamming transition.
Our ansatz for the elastic energy shows that the scaling of the energy, compressive
strain, shear strain, system size, pressure, shear stress, bulk modulus, and shear
modulus are all related to each other via scaling relations, with only three independent
scaling exponents. We extract the values of these exponents from already known
numerical or theoretical results, and we numerically verify the resulting predictions
of the scaling theory for the energy and residual shear stress. We also derive
a scaling relation between pressure and residual shear stress that yields insight
into why the shear and bulk moduli scale differently. Our theory shows that the
jamming transition exhibits an emergent scale invariance, setting the stage for
the potential development of a renormalization group theory for jamming.
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: James P.
full_name: Sethna, James P.
last_name: Sethna
citation:
ama: Goodrich CP, Liu AJ, Sethna JP. Scaling ansatz for the jamming transition.
Proceedings of the National Academy of Sciences. 2016;113(35):9745-9750.
doi:10.1073/pnas.1601858113
apa: Goodrich, C. P., Liu, A. J., & Sethna, J. P. (2016). Scaling ansatz for
the jamming transition. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1601858113
chicago: Goodrich, Carl Peter, Andrea J. Liu, and James P. Sethna. “Scaling Ansatz
for the Jamming Transition.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1601858113.
ieee: C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Scaling ansatz for the jamming
transition,” Proceedings of the National Academy of Sciences, vol. 113,
no. 35. Proceedings of the National Academy of Sciences, pp. 9745–9750, 2016.
ista: Goodrich CP, Liu AJ, Sethna JP. 2016. Scaling ansatz for the jamming transition.
Proceedings of the National Academy of Sciences. 113(35), 9745–9750.
mla: Goodrich, Carl Peter, et al. “Scaling Ansatz for the Jamming Transition.” Proceedings
of the National Academy of Sciences, vol. 113, no. 35, Proceedings of the
National Academy of Sciences, 2016, pp. 9745–50, doi:10.1073/pnas.1601858113.
short: C.P. Goodrich, A.J. Liu, J.P. Sethna, Proceedings of the National Academy
of Sciences 113 (2016) 9745–9750.
date_created: 2020-04-30T11:39:53Z
date_published: 2016-08-30T00:00:00Z
date_updated: 2021-01-12T08:15:21Z
day: '30'
doi: 10.1073/pnas.1601858113
extern: '1'
intvolume: ' 113'
issue: '35'
language:
- iso: eng
month: '08'
oa_version: None
page: 9745-9750
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Scaling ansatz for the jamming transition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '6118'
abstract:
- lang: eng
text: 'Carbon dioxide (CO2) gradients are ubiquitous and provide animals with information
about their environment, such as the potential presence of prey or predators.
The nematode Caenorhabditis elegans avoids elevated CO2, and previous work identified
three neuron pairs called “BAG,” “AFD,” and “ASE” that respond to CO2 stimuli.
Using in vivo Ca2+ imaging and behavioral analysis, we show that C. elegans can
detect CO2 independently of these sensory pathways. Many of the C. elegans sensory
neurons we examined, including the AWC olfactory neurons, the ASJ and ASK gustatory
neurons, and the ASH and ADL nociceptors, respond to a rise in CO2 with a rise
in Ca2+. In contrast, glial sheath cells harboring the sensory endings of C. elegans’
major chemosensory neurons exhibit strong and sustained decreases in Ca2+ in response
to high CO2. Some of these CO2 responses appear to be cell intrinsic. Worms therefore
may couple detection of CO2 to that of other cues at the earliest stages of sensory
processing. We show that C. elegans persistently suppresses oviposition at high
CO2. Hermaphrodite-specific neurons (HSNs), the executive neurons driving egg-laying,
are tonically inhibited when CO2 is elevated. CO2 modulates the egg-laying system
partly through the AWC olfactory neurons: High CO2 tonically activates AWC by
a cGMP-dependent mechanism, and AWC output inhibits the HSNs. Our work shows that
CO2 is a more complex sensory cue for C. elegans than previously thought, both
in terms of behavior and neural circuitry.'
author:
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Fenk LA, de Bono M. Environmental CO2 inhibits Caenorhabditis elegans egg-laying
by modulating olfactory neurons and evokes widespread changes in neural activity.
Proceedings of the National Academy of Sciences. 2015;112(27):E3525-E3534.
doi:10.1073/pnas.1423808112
apa: Fenk, L. A., & de Bono, M. (2015). Environmental CO2 inhibits Caenorhabditis
elegans egg-laying by modulating olfactory neurons and evokes widespread changes
in neural activity. Proceedings of the National Academy of Sciences. National
Academy of Sciences. https://doi.org/10.1073/pnas.1423808112
chicago: Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis
Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes
in Neural Activity.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423808112.
ieee: L. A. Fenk and M. de Bono, “Environmental CO2 inhibits Caenorhabditis elegans
egg-laying by modulating olfactory neurons and evokes widespread changes in neural
activity,” Proceedings of the National Academy of Sciences, vol. 112, no.
27. National Academy of Sciences, pp. E3525–E3534, 2015.
ista: Fenk LA, de Bono M. 2015. Environmental CO2 inhibits Caenorhabditis elegans
egg-laying by modulating olfactory neurons and evokes widespread changes in neural
activity. Proceedings of the National Academy of Sciences. 112(27), E3525–E3534.
mla: Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis
Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes
in Neural Activity.” Proceedings of the National Academy of Sciences, vol.
112, no. 27, National Academy of Sciences, 2015, pp. E3525–34, doi:10.1073/pnas.1423808112.
short: L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 112
(2015) E3525–E3534.
date_created: 2019-03-19T14:15:50Z
date_published: 2015-07-07T00:00:00Z
date_updated: 2021-01-12T08:06:12Z
day: '07'
ddc:
- '570'
doi: 10.1073/pnas.1423808112
extern: '1'
external_id:
pmid:
- '26100886'
file:
- access_level: open_access
checksum: 3d2da5af8d72467e382a565abc2e003d
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:21:07Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6119'
file_name: 2015_PNAS_Fenk.pdf
file_size: 2822681
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 112'
issue: '27'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: E3525-E3534
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating
olfactory neurons and evokes widespread changes in neural activity
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '6133'
abstract:
- lang: eng
text: cGMP signaling is widespread in the nervous system. However, it has proved
difficult to visualize and genetically probe endogenously evoked cGMP dynamics
in neurons in vivo. Here, we combine cGMP and Ca2+ biosensors to image and dissect
a cGMP signaling network in a Caenorhabditis elegans oxygen-sensing neuron. We
show that a rise in O2 can evoke a tonic increase in cGMP that requires an atypical
O2-binding soluble guanylate cyclase and that is sustained until oxygen levels
fall. Increased cGMP leads to a sustained Ca2+ response in the neuron that depends
on cGMP-gated ion channels. Elevated levels of cGMP and Ca2+ stimulate competing
negative feedback loops that shape cGMP dynamics. Ca2+-dependent negative feedback
loops, including activation of phosphodiesterase-1 (PDE-1), dampen the rise of
cGMP. A different negative feedback loop, mediated by phosphodiesterase-2 (PDE-2)
and stimulated by cGMP-dependent kinase (PKG), unexpectedly promotes cGMP accumulation
following a rise in O2, apparently by keeping in check gating of cGMP channels
and limiting activation of Ca2+-dependent negative feedback loops. Simultaneous
imaging of Ca2+ and cGMP suggests that cGMP levels can rise close to cGMP channels
while falling elsewhere. O2-evoked cGMP and Ca2+ responses are highly reproducible
when the same neuron in an individual animal is stimulated repeatedly, suggesting
that cGMP transduction has high intrinsic reliability. However, responses vary
substantially across individuals, despite animals being genetically identical
and similarly reared. This variability may reflect stochastic differences in expression
of cGMP signaling components. Our work provides in vivo insights into the architecture
of neuronal cGMP signaling.
author:
- first_name: A.
full_name: Couto, A.
last_name: Couto
- first_name: S.
full_name: Oda, S.
last_name: Oda
- first_name: V. O.
full_name: Nikolaev, V. O.
last_name: Nikolaev
- first_name: Z.
full_name: Soltesz, Z.
last_name: Soltesz
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. In vivo genetic dissection
of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings
of the National Academy of Sciences. 2013;110(35):E3301-E3310. doi:10.1073/pnas.1217428110
apa: Couto, A., Oda, S., Nikolaev, V. O., Soltesz, Z., & de Bono, M. (2013).
In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans
gas sensor. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1217428110
chicago: Couto, A., S. Oda, V. O. Nikolaev, Z. Soltesz, and Mario de Bono. “In Vivo
Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas
Sensor.” Proceedings of the National Academy of Sciences. Proceedings of
the National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1217428110.
ieee: A. Couto, S. Oda, V. O. Nikolaev, Z. Soltesz, and M. de Bono, “In vivo genetic
dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor,”
Proceedings of the National Academy of Sciences, vol. 110, no. 35. Proceedings
of the National Academy of Sciences, pp. E3301–E3310, 2013.
ista: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. 2013. In vivo genetic dissection
of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings
of the National Academy of Sciences. 110(35), E3301–E3310.
mla: Couto, A., et al. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in
a Caenorhabditis Elegans Gas Sensor.” Proceedings of the National Academy of
Sciences, vol. 110, no. 35, Proceedings of the National Academy of Sciences,
2013, pp. E3301–10, doi:10.1073/pnas.1217428110.
short: A. Couto, S. Oda, V.O. Nikolaev, Z. Soltesz, M. de Bono, Proceedings of the
National Academy of Sciences 110 (2013) E3301–E3310.
date_created: 2019-03-20T14:05:06Z
date_published: 2013-08-27T00:00:00Z
date_updated: 2021-01-12T08:06:16Z
day: '27'
ddc:
- '570'
doi: 10.1073/pnas.1217428110
extern: '1'
external_id:
pmid:
- '23940325'
file:
- access_level: open_access
checksum: 3ee28a694f74a49f0d098970ae391a91
content_type: application/pdf
creator: kschuh
date_created: 2019-03-20T14:07:53Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6134'
file_name: 2013_PNAS_Couto.pdf
file_size: 2198763
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 110'
issue: '35'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: E3301-E3310
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans
gas sensor
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '6137'
abstract:
- lang: eng
text: Variation in food quality and abundance requires animals to decide whether
to stay on a poor food patch or leave in search of better food. An important question
in behavioral ecology asks when is it optimal for an animal to leave a food patch
it is depleting. Although optimal foraging is central to evolutionary success,
the neural and molecular mechanisms underlying it are poorly understood. Here
we investigate the neuronal basis for adaptive food-leaving behavior in response
to resource depletion in Caenorhabditis elegans, and identify several of the signaling
pathways involved. The ASE neurons, previously implicated in salt chemoattraction,
promote food-leaving behavior via a cGMP pathway as food becomes limited. High
ambient O2 promotes food-leaving via the O2-sensing neurons AQR, PQR, and URX.
Ectopic activation of these neurons using channelrhodopsin is sufficient to induce
high food-leaving behavior. In contrast, the neuropeptide receptor NPR-1, which
regulates social behavior on food, acts in the ASE neurons, the nociceptive ASH
neurons, and in the RMG interneuron to repress food-leaving. Finally, we show
that neuroendocrine signaling by TGF-β/DAF-7 and neuronal insulin signaling are
necessary for adaptive food-leaving behavior. We suggest that animals integrate
information about their nutritional state with ambient oxygen and gustatory stimuli
to formulate optimal foraging strategies.
author:
- first_name: K.
full_name: Milward, K.
last_name: Milward
- first_name: K. E.
full_name: Busch, K. E.
last_name: Busch
- first_name: R. J.
full_name: Murphy, R. J.
last_name: Murphy
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: B.
full_name: Olofsson, B.
last_name: Olofsson
citation:
ama: Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. Neuronal and molecular
substrates for optimal foraging in Caenorhabditis elegans. Proceedings of the
National Academy of Sciences. 2011;108(51):20672-20677. doi:10.1073/pnas.1106134109
apa: Milward, K., Busch, K. E., Murphy, R. J., de Bono, M., & Olofsson, B. (2011).
Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1106134109
chicago: Milward, K., K. E. Busch, R. J. Murphy, Mario de Bono, and B. Olofsson.
“Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2011. https://doi.org/10.1073/pnas.1106134109.
ieee: K. Milward, K. E. Busch, R. J. Murphy, M. de Bono, and B. Olofsson, “Neuronal
and molecular substrates for optimal foraging in Caenorhabditis elegans,” Proceedings
of the National Academy of Sciences, vol. 108, no. 51. National Academy of
Sciences, pp. 20672–20677, 2011.
ista: Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. 2011. Neuronal and
molecular substrates for optimal foraging in Caenorhabditis elegans. Proceedings
of the National Academy of Sciences. 108(51), 20672–20677.
mla: Milward, K., et al. “Neuronal and Molecular Substrates for Optimal Foraging
in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences,
vol. 108, no. 51, National Academy of Sciences, 2011, pp. 20672–77, doi:10.1073/pnas.1106134109.
short: K. Milward, K.E. Busch, R.J. Murphy, M. de Bono, B. Olofsson, Proceedings
of the National Academy of Sciences 108 (2011) 20672–20677.
date_created: 2019-03-20T14:30:06Z
date_published: 2011-12-20T00:00:00Z
date_updated: 2021-01-12T08:06:18Z
day: '20'
doi: 10.1073/pnas.1106134109
extern: '1'
external_id:
pmid:
- '22135454'
intvolume: ' 108'
issue: '51'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251049/
month: '12'
oa: 1
oa_version: Submitted Version
page: 20672-20677
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2011'
...
---
_id: '6146'
abstract:
- lang: eng
text: Homeostasis of internal carbon dioxide (CO2) and oxygen (O2) levels is fundamental
to all animals. Here we examine the CO2 response of the nematode Caenorhabditis
elegans. This species inhabits rotting material, which typically has a broad CO2
concentration range. We show that well fed C. elegans avoid CO2 levels above 0.5%.
Animals can respond to both absolute CO2 concentrations and changes in CO2 levels
within seconds. Responses to CO2 do not reflect avoidance of acid pH but appear
to define a new sensory response. Sensation of CO2 is promoted by the cGMP-gated
ion channel subunits TAX-2 and TAX-4, but other pathways are also important. Robust
CO2 avoidance in well fed animals requires inhibition of the DAF-16 forkhead transcription
factor by the insulin-like receptor DAF-2. Starvation, which activates DAF-16,
strongly suppresses CO2 avoidance. Exposure to hypoxia (<1% O2) also suppresses
CO2 avoidance via activation of the hypoxia-inducible transcription factor HIF-1.
The npr-1 215V allele of the naturally polymorphic neuropeptide receptor npr-1,
besides inhibiting avoidance of high ambient O2 in feeding C. elegans, also promotes
avoidance of high CO2. C. elegans integrates competing O2 and CO2 sensory inputs
so that one response dominates. Food and allelic variation at NPR-1 regulate which
response prevails. Our results suggest that multiple sensory inputs are coordinated
by C. elegans to generate different coherent foraging strategies.
author:
- first_name: A. J.
full_name: Bretscher, A. J.
last_name: Bretscher
- first_name: K. E.
full_name: Busch, K. E.
last_name: Busch
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Bretscher AJ, Busch KE, de Bono M. A carbon dioxide avoidance behavior is integrated
with responses to ambient oxygen and food in Caenorhabditis elegans. Proceedings
of the National Academy of Sciences. 2008;105(23):8044-8049. doi:10.1073/pnas.0707607105
apa: Bretscher, A. J., Busch, K. E., & de Bono, M. (2008). A carbon dioxide
avoidance behavior is integrated with responses to ambient oxygen and food in
Caenorhabditis elegans. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0707607105
chicago: Bretscher, A. J., K. E. Busch, and Mario de Bono. “A Carbon Dioxide Avoidance
Behavior Is Integrated with Responses to Ambient Oxygen and Food in Caenorhabditis
Elegans.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0707607105.
ieee: A. J. Bretscher, K. E. Busch, and M. de Bono, “A carbon dioxide avoidance
behavior is integrated with responses to ambient oxygen and food in Caenorhabditis
elegans,” Proceedings of the National Academy of Sciences, vol. 105, no.
23. Proceedings of the National Academy of Sciences, pp. 8044–8049, 2008.
ista: Bretscher AJ, Busch KE, de Bono M. 2008. A carbon dioxide avoidance behavior
is integrated with responses to ambient oxygen and food in Caenorhabditis elegans.
Proceedings of the National Academy of Sciences. 105(23), 8044–8049.
mla: Bretscher, A. J., et al. “A Carbon Dioxide Avoidance Behavior Is Integrated
with Responses to Ambient Oxygen and Food in Caenorhabditis Elegans.” Proceedings
of the National Academy of Sciences, vol. 105, no. 23, Proceedings of the
National Academy of Sciences, 2008, pp. 8044–49, doi:10.1073/pnas.0707607105.
short: A.J. Bretscher, K.E. Busch, M. de Bono, Proceedings of the National Academy
of Sciences 105 (2008) 8044–8049.
date_created: 2019-03-21T08:10:15Z
date_published: 2008-06-10T00:00:00Z
date_updated: 2021-01-12T08:06:21Z
day: '10'
ddc:
- '570'
doi: 10.1073/pnas.0707607105
extern: '1'
external_id:
pmid:
- '18524954'
file:
- access_level: open_access
checksum: eac0413064b022c1489f7b6719e7228c
content_type: application/pdf
creator: kschuh
date_created: 2019-03-21T08:14:54Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6147'
file_name: 2008_PNAS_Bretscher.pdf
file_size: 501506
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 105'
issue: '23'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 8044-8049
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: A carbon dioxide avoidance behavior is integrated with responses to ambient
oxygen and food in Caenorhabditis elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 105
year: '2008'
...