---
_id: '3933'
abstract:
- lang: eng
text: Resident dendritic cells (DC) within the T cell area of the lymph node take
up soluble antigens that enter via the afferent lymphatics before antigen carrying
DC arrive from the periphery. The reticular network within the lymph node is a
conduit system forming the infrastructure for the fast delivery of soluble substances
from the afferent lymph to the lumen of high endothelial venules (HEVs). Using
high-resolution light microscopy and 3D reconstruction, we show here that these
conduits are unique basement membrane-like structures ensheathed by fibroblastic
reticular cells with occasional resident DC embedded within this cell layer. Conduit-associated
DC are capable of taking up and processing soluble antigens transported within
the conduits, whereas immigrated mature DC occur remote from the reticular fibers.
The conduit system is, therefore, not a closed compartment that shuttles substances
through the lymph node but represents the morphological equivalent to the filtering
function of the lymph node.
author:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Nobuo
full_name: Kanazawa, Nobuo
last_name: Kanazawa
- first_name: Manuel
full_name: Selg, Manuel
last_name: Selg
- first_name: Thomas
full_name: Samson, Thomas
last_name: Samson
- first_name: Gunnel
full_name: Roos, Gunnel
last_name: Roos
- first_name: Dieter
full_name: Reinhardt, Dieter
last_name: Reinhardt
- first_name: Reinhard
full_name: Pabst, Reinhard
last_name: Pabst
- first_name: Manfred
full_name: Lutz, Manfred
last_name: Lutz
- first_name: Lydia
full_name: Sorokin, Lydia
last_name: Sorokin
citation:
ama: Sixt MK, Kanazawa N, Selg M, et al. The conduit system transports soluble antigens
from the afferent lymph to resident dendritic cells in the T cell area of the
lymph node. Immunity. 2005;22(1):19-29. doi:10.1016/j.immuni.2004.11.013
apa: Sixt, M. K., Kanazawa, N., Selg, M., Samson, T., Roos, G., Reinhardt, D., …
Sorokin, L. (2005). The conduit system transports soluble antigens from the afferent
lymph to resident dendritic cells in the T cell area of the lymph node. Immunity.
Cell Press. https://doi.org/10.1016/j.immuni.2004.11.013
chicago: Sixt, Michael K, Nobuo Kanazawa, Manuel Selg, Thomas Samson, Gunnel Roos,
Dieter Reinhardt, Reinhard Pabst, Manfred Lutz, and Lydia Sorokin. “The Conduit
System Transports Soluble Antigens from the Afferent Lymph to Resident Dendritic
Cells in the T Cell Area of the Lymph Node.” Immunity. Cell Press, 2005.
https://doi.org/10.1016/j.immuni.2004.11.013.
ieee: M. K. Sixt et al., “The conduit system transports soluble antigens
from the afferent lymph to resident dendritic cells in the T cell area of the
lymph node,” Immunity, vol. 22, no. 1. Cell Press, pp. 19–29, 2005.
ista: Sixt MK, Kanazawa N, Selg M, Samson T, Roos G, Reinhardt D, Pabst R, Lutz
M, Sorokin L. 2005. The conduit system transports soluble antigens from the afferent
lymph to resident dendritic cells in the T cell area of the lymph node. Immunity.
22(1), 19–29.
mla: Sixt, Michael K., et al. “The Conduit System Transports Soluble Antigens from
the Afferent Lymph to Resident Dendritic Cells in the T Cell Area of the Lymph
Node.” Immunity, vol. 22, no. 1, Cell Press, 2005, pp. 19–29, doi:10.1016/j.immuni.2004.11.013.
short: M.K. Sixt, N. Kanazawa, M. Selg, T. Samson, G. Roos, D. Reinhardt, R. Pabst,
M. Lutz, L. Sorokin, Immunity 22 (2005) 19–29.
date_created: 2018-12-11T12:05:58Z
date_published: 2005-01-25T00:00:00Z
date_updated: 2021-01-12T07:53:18Z
day: '25'
doi: 10.1016/j.immuni.2004.11.013
extern: '1'
intvolume: ' 22'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 19 - 29
publication: Immunity
publication_status: published
publisher: Cell Press
publist_id: '2195'
status: public
title: The conduit system transports soluble antigens from the afferent lymph to resident
dendritic cells in the T cell area of the lymph node
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2005'
...
---
_id: '3983'
abstract:
- lang: eng
text: Cdc25 phosphatases are key activators of the eukaryotic cell cycle and compelling
anticancer targets because their overexpression has been associated with numerous
cancers. However, drug discovery targeting these phosphatases has been hampered
by the lack of structural information about how Cdc25s interact with their native
protein substrates, the cyclin-dependent kinases. Herein, we predict a docked
orientation for Cdc25B with its Cdk2-pTpY-CycA protein substrate by a rigid-body
docking method and refine the docked models with full-scale molecular dynamics
simulations and minimization. We validate the stable ensemble structure experimentally
by a variety of in vitro and in vivo techniques. Specifically, we compare our
model with a crystal structure of the substrate-trapping mutant of Cdc25B. We
identify and validate in vivo a novel hot-spot residue on Cdc25B (Arg492) that
plays a central role in protein substrate recognition. We identify a hot-spot
residue on the Substrate Cdk2 (Asp206) and confirm its interaction with hot-spot
residues on Cdc25 using hot-spot swapping and double mutant cycles to derive interaction
energies. Our experimentally validated model is consistent with previous studies
of Cdk2 and its interaction partners and initiates the opportunity for drug discovery
of inhibitors that target the remote binding sites of this protein-protein interaction.
author:
- first_name: Jungsan
full_name: Sohn, Jungsan
last_name: Sohn
- first_name: Jerry
full_name: Parks, Jerry M
last_name: Parks
- first_name: Gregory
full_name: Buhrman, Gregory
last_name: Buhrman
- first_name: Paul
full_name: Brown, Paul
last_name: Brown
- first_name: Kolbrun
full_name: Kristjánsdóttir, Kolbrun
last_name: Kristjánsdóttir
- first_name: Alexias
full_name: Safi, Alexias
last_name: Safi
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Weitao
full_name: Yang, Weitao T
last_name: Yang
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: Sohn J, Parks J, Buhrman G, et al. Experimental validation of the docking orientation
of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry. 2005;44(50):16563-16573.
doi:10.1021/bi0516879
apa: Sohn, J., Parks, J., Buhrman, G., Brown, P., Kristjánsdóttir, K., Safi, A.,
… Rudolph, J. (2005). Experimental validation of the docking orientation of Cdc25
with its Cdk2-CycA protein substrate. Biochemistry. ACS. https://doi.org/10.1021/bi0516879
chicago: Sohn, Jungsan, Jerry Parks, Gregory Buhrman, Paul Brown, Kolbrun Kristjánsdóttir,
Alexias Safi, Herbert Edelsbrunner, Weitao Yang, and Johannes Rudolph. “Experimental
Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate.”
Biochemistry. ACS, 2005. https://doi.org/10.1021/bi0516879.
ieee: J. Sohn et al., “Experimental validation of the docking orientation
of Cdc25 with its Cdk2-CycA protein substrate,” Biochemistry, vol. 44,
no. 50. ACS, pp. 16563–16573, 2005.
ista: Sohn J, Parks J, Buhrman G, Brown P, Kristjánsdóttir K, Safi A, Edelsbrunner
H, Yang W, Rudolph J. 2005. Experimental validation of the docking orientation
of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry. 44(50), 16563–16573.
mla: Sohn, Jungsan, et al. “Experimental Validation of the Docking Orientation of
Cdc25 with Its Cdk2-CycA Protein Substrate.” Biochemistry, vol. 44, no.
50, ACS, 2005, pp. 16563–73, doi:10.1021/bi0516879.
short: J. Sohn, J. Parks, G. Buhrman, P. Brown, K. Kristjánsdóttir, A. Safi, H.
Edelsbrunner, W. Yang, J. Rudolph, Biochemistry 44 (2005) 16563–16573.
date_created: 2018-12-11T12:06:16Z
date_published: 2005-11-24T00:00:00Z
date_updated: 2021-01-12T07:53:39Z
day: '24'
doi: 10.1021/bi0516879
extern: 1
intvolume: ' 44'
issue: '50'
month: '11'
page: 16563 - 16573
publication: Biochemistry
publication_status: published
publisher: ACS
publist_id: '2144'
quality_controlled: 0
status: public
title: Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA
protein substrate
type: journal_article
volume: 44
year: '2005'
...
---
_id: '3982'
abstract:
- lang: eng
text: We present an efficient algorithm for generating a small set of coarse alignments
between interacting proteins using meaningful features on their surfaces. The
proteins are treated as rigid bodies, but the results are more generally useful
as the produced configurations can serve as input to local improvement algorithms
that allow for protein flexibility. We apply our algorithm to a diverse set of
protein complexes from the Protein Data Bank, demonstrating the effectivity of
our algorithm, both for bound and for unbound protein docking problems.
author:
- first_name: Yusu
full_name: Wang, Yusu
last_name: Wang
- first_name: Pankaj
full_name: Agarwal, Pankaj K
last_name: Agarwal
- first_name: Paul
full_name: Brown, Paul
last_name: Brown
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: 'Wang Y, Agarwal P, Brown P, Edelsbrunner H, Rudolph J. Coarse and reliable
geometric alignment for protein docking. In: World Scientific Publishing; 2005:64-75.
doi:10.1142/9789812702456_0007'
apa: 'Wang, Y., Agarwal, P., Brown, P., Edelsbrunner, H., & Rudolph, J. (2005).
Coarse and reliable geometric alignment for protein docking (pp. 64–75). Presented
at the PSB: Pacific Symposium on Biocomputing, World Scientific Publishing. https://doi.org/10.1142/9789812702456_0007'
chicago: Wang, Yusu, Pankaj Agarwal, Paul Brown, Herbert Edelsbrunner, and Johannes
Rudolph. “Coarse and Reliable Geometric Alignment for Protein Docking,” 64–75.
World Scientific Publishing, 2005. https://doi.org/10.1142/9789812702456_0007.
ieee: 'Y. Wang, P. Agarwal, P. Brown, H. Edelsbrunner, and J. Rudolph, “Coarse and
reliable geometric alignment for protein docking,” presented at the PSB: Pacific
Symposium on Biocomputing, 2005, pp. 64–75.'
ista: 'Wang Y, Agarwal P, Brown P, Edelsbrunner H, Rudolph J. 2005. Coarse and reliable
geometric alignment for protein docking. PSB: Pacific Symposium on Biocomputing,
64–75.'
mla: Wang, Yusu, et al. Coarse and Reliable Geometric Alignment for Protein Docking.
World Scientific Publishing, 2005, pp. 64–75, doi:10.1142/9789812702456_0007.
short: Y. Wang, P. Agarwal, P. Brown, H. Edelsbrunner, J. Rudolph, in:, World Scientific
Publishing, 2005, pp. 64–75.
conference:
name: 'PSB: Pacific Symposium on Biocomputing'
date_created: 2018-12-11T12:06:16Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:38Z
day: '01'
doi: 10.1142/9789812702456_0007
extern: 1
month: '01'
page: 64 - 75
publication_status: published
publisher: World Scientific Publishing
publist_id: '2143'
quality_controlled: 0
status: public
title: Coarse and reliable geometric alignment for protein docking
type: conference
year: '2005'
...
---
_id: '4144'
abstract:
- lang: eng
text: Wnt11 plays a central role in tissue morphogenesis during vertebrate gastrulation,
but the molecular and cellular mechanisms by which Wnt11 exerts its effects remain
poorly understood. Here, we show that Wnt11 functions during zebrafish gastrulation
by regulating the cohesion of mesodermal and endodermal (mesendodermal) progenitor
cells. Importantly, we demonstrate that Wnt11 activity in this process is mediated
by the GTPase Rab5, a key regulator of early endocytosis, as blocking Rab5c activity
in wild-type embryos phenocopies slb/wnt11 mutants, and enhancing Rab5c activity
in slb/wnt11 mutant embryos rescues the mutant phenotype. In addition, we find
that Wnt11 and Rab5c control the endocytosis of E-cadherin and are required in
mesendodermal cells for E-cadherin-mediated cell cohesion. Together, our results
suggest that Wnt11 controls tissue morphogenesis by modulating E-cadherin-mediated
cell cohesion through Rab5c, a novel mechanism of Wnt signaling in gastrulation.
article_processing_charge: No
author:
- first_name: Florian
full_name: Ulrich, Florian
last_name: Ulrich
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Eva
full_name: Schötz, Eva
last_name: Schötz
- first_name: Vinzenz
full_name: Link, Vinzenz
last_name: Link
- first_name: Irinka
full_name: Castanon, Irinka
last_name: Castanon
- first_name: Viktor
full_name: Schnabel, Viktor
last_name: Schnabel
- first_name: Anna
full_name: Taubenberger, Anna
last_name: Taubenberger
- first_name: Daniel
full_name: Müller, Daniel
last_name: Müller
- first_name: Pierre
full_name: Puech, Pierre
last_name: Puech
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Ulrich F, Krieg M, Schötz E, et al. Wnt11 functions in gastrulation by controlling
cell cohesion through Rab5c and E-cadherin. Developmental Cell. 2005;9(4):555-564.
doi:10.1016/j.devcel.2005.08.011
apa: Ulrich, F., Krieg, M., Schötz, E., Link, V., Castanon, I., Schnabel, V., …
Heisenberg, C.-P. J. (2005). Wnt11 functions in gastrulation by controlling cell
cohesion through Rab5c and E-cadherin. Developmental Cell. Cell Press.
https://doi.org/10.1016/j.devcel.2005.08.011
chicago: Ulrich, Florian, Michael Krieg, Eva Schötz, Vinzenz Link, Irinka Castanon,
Viktor Schnabel, Anna Taubenberger, Daniel Müller, Pierre Puech, and Carl-Philipp
J Heisenberg. “Wnt11 Functions in Gastrulation by Controlling Cell Cohesion through
Rab5c and E-Cadherin.” Developmental Cell. Cell Press, 2005. https://doi.org/10.1016/j.devcel.2005.08.011.
ieee: F. Ulrich et al., “Wnt11 functions in gastrulation by controlling cell
cohesion through Rab5c and E-cadherin,” Developmental Cell, vol. 9, no.
4. Cell Press, pp. 555–564, 2005.
ista: Ulrich F, Krieg M, Schötz E, Link V, Castanon I, Schnabel V, Taubenberger
A, Müller D, Puech P, Heisenberg C-PJ. 2005. Wnt11 functions in gastrulation by
controlling cell cohesion through Rab5c and E-cadherin. Developmental Cell. 9(4),
555–564.
mla: Ulrich, Florian, et al. “Wnt11 Functions in Gastrulation by Controlling Cell
Cohesion through Rab5c and E-Cadherin.” Developmental Cell, vol. 9, no.
4, Cell Press, 2005, pp. 555–64, doi:10.1016/j.devcel.2005.08.011.
short: F. Ulrich, M. Krieg, E. Schötz, V. Link, I. Castanon, V. Schnabel, A. Taubenberger,
D. Müller, P. Puech, C.-P.J. Heisenberg, Developmental Cell 9 (2005) 555–564.
date_created: 2018-12-11T12:07:12Z
date_published: 2005-10-01T00:00:00Z
date_updated: 2021-01-12T07:54:50Z
day: '01'
doi: 10.1016/j.devcel.2005.08.011
extern: '1'
intvolume: ' 9'
issue: '4'
language:
- iso: eng
month: '10'
oa_version: None
page: 555 - 564
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '1977'
status: public
title: Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c
and E-cadherin
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2005'
...
---
_id: '4138'
abstract:
- lang: eng
text: |-
Adaptive dynamics describes the evolution of an asexual population through the successive substitution of mutations of small effect. Waxman & Gavrilets (2005) give an excellent overview of the method and its applications. In this note, we focus on the plausibility of the key assumption that mutations have small effects, and the consequences of relaxing that assumption. We argue that: (i) successful mutations often have large effects; (ii) such mutations generate a qualitatively different evolutionary pattern, which is inherently stochastic; and (iii) in models of competition for a continuous resource, selection becomes very weak once several phenotypes are established. This makes the effects of introducing new mutations unpredictable using the methods of adaptive dynamics.
We should make clear at the outset that our criticism is of methods that rely on local analysis of fitness gradients (eqn 2 of Waxman & Gavrilets, 2005), and not of the broader idea that evolution can be understood by examining the invasion of successive mutations. We use the term ‘adaptive dynamics’ to refer to the former technique, and contrast it with a more general population genetic analysis of probabilities of invasion.
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jitka
full_name: Jitka Polechova
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
citation:
ama: Barton NH, Polechova J. The limitations of adaptive dynamics as a model of
evolution. Journal of Evolutionary Biology. 2005;18(5):1186-1190. doi:10.1111/j.1420-9101.2005.00943.x
apa: Barton, N. H., & Polechova, J. (2005). The limitations of adaptive dynamics
as a model of evolution. Journal of Evolutionary Biology. Wiley-Blackwell.
https://doi.org/10.1111/j.1420-9101.2005.00943.x
chicago: Barton, Nicholas H, and Jitka Polechova. “The Limitations of Adaptive Dynamics
as a Model of Evolution.” Journal of Evolutionary Biology. Wiley-Blackwell,
2005. https://doi.org/10.1111/j.1420-9101.2005.00943.x.
ieee: N. H. Barton and J. Polechova, “The limitations of adaptive dynamics as a
model of evolution,” Journal of Evolutionary Biology, vol. 18, no. 5. Wiley-Blackwell,
pp. 1186–1190, 2005.
ista: Barton NH, Polechova J. 2005. The limitations of adaptive dynamics as a model
of evolution. Journal of Evolutionary Biology. 18(5), 1186–1190.
mla: Barton, Nicholas H., and Jitka Polechova. “The Limitations of Adaptive Dynamics
as a Model of Evolution.” Journal of Evolutionary Biology, vol. 18, no.
5, Wiley-Blackwell, 2005, pp. 1186–90, doi:10.1111/j.1420-9101.2005.00943.x.
short: N.H. Barton, J. Polechova, Journal of Evolutionary Biology 18 (2005) 1186–1190.
date_created: 2018-12-11T12:07:10Z
date_published: 2005-09-01T00:00:00Z
date_updated: 2021-01-12T07:54:47Z
day: '01'
doi: 10.1111/j.1420-9101.2005.00943.x
extern: 1
intvolume: ' 18'
issue: '5'
month: '09'
page: 1186 - 1190
publication: Journal of Evolutionary Biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1982'
quality_controlled: 0
status: public
title: The limitations of adaptive dynamics as a model of evolution
type: journal_article
volume: 18
year: '2005'
...