---
_id: '3225'
abstract:
- lang: eng
text: 'A robust multi-property combiner for a set of security properties merges
two hash functions such that the resulting function satisfies each of the properties
which at least one of the two starting functions has. Fischlin and Lehmann (TCC
2008) recently constructed a combiner which simultaneously preserves collision-resistance,
target collision-resistance, message authentication, pseudorandomness and indifferentiability
from a random oracle (IRO). Their combiner produces outputs of 5n bits, where
n denotes the output length of the underlying hash functions. In this paper we
propose improved combiners with shorter outputs. By sacrificing the indifferentiability
from random oracles we obtain a combiner which preserves all of the other aforementioned
properties but with output length 2n only. This matches a lower bound for black-box
combiners for collision-resistance as the only property, showing that the other
properties can be achieved without penalizing the length of the hash values. We
then propose a combiner which also preserves the IRO property, slightly increasing
the output length to 2n + ω(logn). Finally, we show that a twist on our combiners
also makes them robust for one-wayness (but at the price of a fixed input length). '
alternative_title:
- LNCS
author:
- first_name: Marc
full_name: Fischlin, Marc
last_name: Fischlin
- first_name: Anja
full_name: Lehmann, Anja
last_name: Lehmann
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Fischlin M, Lehmann A, Pietrzak KZ. Robust multi property combiners for hash
functions revisited. In: Vol 5126. Springer; 2008:655-666. doi:10.1007/978-3-540-70583-3_53'
apa: 'Fischlin, M., Lehmann, A., & Pietrzak, K. Z. (2008). Robust multi property
combiners for hash functions revisited (Vol. 5126, pp. 655–666). Presented at
the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-540-70583-3_53'
chicago: Fischlin, Marc, Anja Lehmann, and Krzysztof Z Pietrzak. “Robust Multi Property
Combiners for Hash Functions Revisited,” 5126:655–66. Springer, 2008. https://doi.org/10.1007/978-3-540-70583-3_53.
ieee: 'M. Fischlin, A. Lehmann, and K. Z. Pietrzak, “Robust multi property combiners
for hash functions revisited,” presented at the ICALP: Automata, Languages and
Programming, 2008, vol. 5126, no. PART 2, pp. 655–666.'
ista: 'Fischlin M, Lehmann A, Pietrzak KZ. 2008. Robust multi property combiners
for hash functions revisited. ICALP: Automata, Languages and Programming, LNCS,
vol. 5126, 655–666.'
mla: Fischlin, Marc, et al. Robust Multi Property Combiners for Hash Functions
Revisited. Vol. 5126, no. PART 2, Springer, 2008, pp. 655–66, doi:10.1007/978-3-540-70583-3_53.
short: M. Fischlin, A. Lehmann, K.Z. Pietrzak, in:, Springer, 2008, pp. 655–666.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:02:07Z
date_published: 2008-08-06T00:00:00Z
date_updated: 2023-02-23T11:01:10Z
day: '06'
doi: 10.1007/978-3-540-70583-3_53
extern: 1
intvolume: ' 5126'
issue: PART 2
month: '08'
page: 655 - 666
publication_status: published
publisher: Springer
publist_id: '3454'
quality_controlled: 0
related_material:
record:
- id: '2852'
relation: later_version
status: public
status: public
title: Robust multi property combiners for hash functions revisited
type: conference
volume: 5126
year: '2008'
...
---
_id: '3226'
abstract:
- lang: eng
text: 'A family of functions is weakly pseudorandom if a random member of the family
is indistinguishable from a uniform random function when queried on random inputs.
We point out a subtle ambiguity in the definition of weak PRFs: there are natural
weak PRFs whose security breaks down if the randomness used to sample the inputs
is revealed. To capture this ambiguity we distinguish between public-coin and
secret-coin weak PRFs. We show that the existence of a secret-coin weak PRF which
is not also a public-coin weak PRF implies the existence of two pass key-agreement
(i.e. public-key encryption). So in Minicrypt, i.e. under the assumption that
one-way functions exist but public-key cryptography does not, the notion of public-
and secret-coin weak PRFs coincide. Previous to this paper all positive cryptographic
statements known to hold exclusively in Minicrypt concerned the adaptive security
of constructions using non-adaptively secure components. Weak PRFs give rise to
a new set of statements having this property. As another example we consider the
problem of range extension for weak PRFs. We show that in Minicrypt one can beat
the best possible range expansion factor (using a fixed number of distinct keys)
for a very general class of constructions (in particular, this class contains
all constructions that are known today). '
acknowledgement: This work was partially supported by the Zurich Information Security
Center.
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Johan
full_name: Sjödin, Johan
last_name: Sjödin
citation:
ama: 'Pietrzak KZ, Sjödin J. Weak pseudorandom functions in minicrypt. In: Vol 5126.
Springer; 2008:423-436. doi:10.1007/978-3-540-70583-3_35'
apa: 'Pietrzak, K. Z., & Sjödin, J. (2008). Weak pseudorandom functions in minicrypt
(Vol. 5126, pp. 423–436). Presented at the ICALP: Automata, Languages and Programming,
Springer. https://doi.org/10.1007/978-3-540-70583-3_35'
chicago: Pietrzak, Krzysztof Z, and Johan Sjödin. “Weak Pseudorandom Functions in
Minicrypt,” 5126:423–36. Springer, 2008. https://doi.org/10.1007/978-3-540-70583-3_35.
ieee: 'K. Z. Pietrzak and J. Sjödin, “Weak pseudorandom functions in minicrypt,”
presented at the ICALP: Automata, Languages and Programming, 2008, vol. 5126,
no. PART 2, pp. 423–436.'
ista: 'Pietrzak KZ, Sjödin J. 2008. Weak pseudorandom functions in minicrypt. ICALP:
Automata, Languages and Programming, LNCS, vol. 5126, 423–436.'
mla: Pietrzak, Krzysztof Z., and Johan Sjödin. Weak Pseudorandom Functions in
Minicrypt. Vol. 5126, no. PART 2, Springer, 2008, pp. 423–36, doi:10.1007/978-3-540-70583-3_35.
short: K.Z. Pietrzak, J. Sjödin, in:, Springer, 2008, pp. 423–436.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:02:07Z
date_published: 2008-08-06T00:00:00Z
date_updated: 2021-01-12T07:41:56Z
day: '06'
doi: 10.1007/978-3-540-70583-3_35
extern: 1
intvolume: ' 5126'
issue: PART 2
month: '08'
page: 423 - 436
publication_status: published
publisher: Springer
publist_id: '3455'
quality_controlled: 0
status: public
title: Weak pseudorandom functions in minicrypt
type: conference
volume: 5126
year: '2008'
...
---
_id: '3227'
abstract:
- lang: eng
text: Large amount of data management can cause a lot of troubles which can be solved
by dedicated computer system. To facilitate management of measurement data which
are gathered in Institute of Power Engineering - Insulation Department a special
system called Elektrowiz® was developed. It allows storing measurement results
which concern partial discharges in insulation of turbo- and hydrogenerators in
power stations. Multilayer architecture of the system allows reaching gathered
data independently on user localization. There are possible different access methods
to the system and dependency on current requirements data exploration can be realized
with read-only or edit rights.
author:
- first_name: Piotr
full_name: Zubielik, Piotr
last_name: Zubielik
- first_name: Jerzy
full_name: Nadaczny, Jerzy
last_name: Nadaczny
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Marcin
full_name: Lawenda, Marcin
last_name: Lawenda
citation:
ama: Zubielik P, Nadaczny J, Pietrzak KZ, Lawenda M. Elektrowiz – system of measurement
data management. Przeglad Elektrotechniczny. 2008;84(10):239-242.
apa: Zubielik, P., Nadaczny, J., Pietrzak, K. Z., & Lawenda, M. (2008). Elektrowiz
– system of measurement data management. Przeglad Elektrotechniczny. SIGMA-NOT.
chicago: Zubielik, Piotr, Jerzy Nadaczny, Krzysztof Z Pietrzak, and Marcin Lawenda.
“Elektrowiz – System of Measurement Data Management.” Przeglad Elektrotechniczny.
SIGMA-NOT, 2008.
ieee: P. Zubielik, J. Nadaczny, K. Z. Pietrzak, and M. Lawenda, “Elektrowiz – system
of measurement data management,” Przeglad Elektrotechniczny, vol. 84, no.
10. SIGMA-NOT, pp. 239–242, 2008.
ista: Zubielik P, Nadaczny J, Pietrzak KZ, Lawenda M. 2008. Elektrowiz – system
of measurement data management. Przeglad Elektrotechniczny. 84(10), 239–242.
mla: Zubielik, Piotr, et al. “Elektrowiz – System of Measurement Data Management.”
Przeglad Elektrotechniczny, vol. 84, no. 10, SIGMA-NOT, 2008, pp. 239–42.
short: P. Zubielik, J. Nadaczny, K.Z. Pietrzak, M. Lawenda, Przeglad Elektrotechniczny
84 (2008) 239–242.
date_created: 2018-12-11T12:02:08Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2021-01-12T07:41:56Z
day: '01'
extern: 1
intvolume: ' 84'
issue: '10'
main_file_link:
- open_access: '0'
url: http://pe.org.pl/abstract_pl.php?nid=1917
month: '10'
page: 239 - 242
publication: Przeglad Elektrotechniczny
publication_status: published
publisher: SIGMA-NOT
publist_id: '3452'
quality_controlled: 0
status: public
title: Elektrowiz – system of measurement data management
type: journal_article
volume: 84
year: '2008'
...
---
_id: '3228'
abstract:
- lang: eng
text: |2-
A black-box combiner for collision resistant hash functions (CRHF) is a construction which given black-box access to two hash functions is collision resistant if at least one of the components is collision resistant. In this paper we prove a lower bound on the output length of black-box combiners for CRHFs. The bound we prove is basically tight as it is achieved by a recent construction of Canetti et al [Crypto'07]. The best previously known lower bounds only ruled out a very restricted class of combiners having a very strong security reduction: the reduction was required to output collisions for both underlying candidate hash-functions given a single collision for the combiner (Canetti et al [Crypto'07] building on Boneh and Boyen [Crypto'06] and Pietrzak [Eurocrypt'07]). Our proof uses a lemma similar to the elegant "reconstruction lemma" of Gennaro and Trevisan [FOCS'00], which states that any function which is not one-way is compressible (and thus uniformly random function must be one-way). In a similar vein we show that a function which is not collision resistant is compressible. We also borrow ideas from recent work by Haitner et al. [FOCS'07], who show that one can prove the reconstruction lemma even relative to some very powerful oracles (in our case this will be an exponential time collision-finding oracle). © 2008 Springer-Verlag Berlin Heidelberg.
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. Compression from collisions or why CRHF combiners have a long
output. In: Vol 5157. Springer; 2008:413-432. doi:10.1007/978-3-540-85174-5_23'
apa: 'Pietrzak, K. Z. (2008). Compression from collisions or why CRHF combiners
have a long output (Vol. 5157, pp. 413–432). Presented at the CRYPTO: International
Cryptology Conference, Springer. https://doi.org/10.1007/978-3-540-85174-5_23'
chicago: Pietrzak, Krzysztof Z. “Compression from Collisions or Why CRHF Combiners
Have a Long Output,” 5157:413–32. Springer, 2008. https://doi.org/10.1007/978-3-540-85174-5_23.
ieee: 'K. Z. Pietrzak, “Compression from collisions or why CRHF combiners have a
long output,” presented at the CRYPTO: International Cryptology Conference, 2008,
vol. 5157, pp. 413–432.'
ista: 'Pietrzak KZ. 2008. Compression from collisions or why CRHF combiners have
a long output. CRYPTO: International Cryptology Conference, LNCS, vol. 5157, 413–432.'
mla: Pietrzak, Krzysztof Z. Compression from Collisions or Why CRHF Combiners
Have a Long Output. Vol. 5157, Springer, 2008, pp. 413–32, doi:10.1007/978-3-540-85174-5_23.
short: K.Z. Pietrzak, in:, Springer, 2008, pp. 413–432.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:08Z
date_published: 2008-09-11T00:00:00Z
date_updated: 2021-01-12T07:41:57Z
day: '11'
doi: 10.1007/978-3-540-85174-5_23
extern: 1
intvolume: ' 5157'
month: '09'
page: 413 - 432
publication_status: published
publisher: Springer
publist_id: '3453'
quality_controlled: 0
status: public
title: Compression from collisions or why CRHF combiners have a long output
type: conference
volume: 5157
year: '2008'
...
---
_id: '3229'
abstract:
- lang: eng
text: 'We construct a stream-cipher S whose implementation is secure even if a bounded
amount of arbitrary (adversarially chosen) information on the internal state ofS
is leaked during computation. This captures all possible side-channel attacks
on S where the amount of information leaked in a given period is bounded, but
overall can be arbitrary large. The only other assumption we make on the implementation
of S is that only data that is accessed during computation leaks information.
The stream-cipher S generates its output in chunks K1, K2, . . . and arbitrary
but bounded information leakage is modeled by allowing the adversary to adaptively
chose a function fl : {0,1}* rarr {0, 1}lambda before Kl is computed, she then
gets fl(taul) where taul is the internal state ofS that is accessed during the
computation of Kg. One notion of security we prove for S is that Kg is indistinguishable
from random when given K1,..., K1-1,f1(tau1 ),..., fl-1(taul-1) and also the complete
internal state of S after Kg has been computed (i.e. S is forward-secure). The
construction is based on alternating extraction (used in the intrusion-resilient
secret-sharing scheme from FOCS''07). We move this concept to the computational
setting by proving a lemma that states that the output of any PRG has high HILLpseudoentropy
(i.e. is indistinguishable from some distribution with high min-entropy) even
if arbitrary information about the seed is leaked. The amount of leakage lambda
that we can tolerate in each step depends on the strength of the underlying PRG,
it is at least logarithmic, but can be as large as a constant fraction of the
internal state of S if the PRG is exponentially hard.'
author:
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Dziembowski S, Pietrzak KZ. Leakage resilient cryptography. In: IEEE; 2008:293-302.
doi:10.1109/FOCS.2008.56'
apa: 'Dziembowski, S., & Pietrzak, K. Z. (2008). Leakage resilient cryptography
(pp. 293–302). Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2008.56'
chicago: Dziembowski, Stefan, and Krzysztof Z Pietrzak. “Leakage Resilient Cryptography,”
293–302. IEEE, 2008. https://doi.org/10.1109/FOCS.2008.56.
ieee: 'S. Dziembowski and K. Z. Pietrzak, “Leakage resilient cryptography,” presented
at the FOCS: Foundations of Computer Science, 2008, pp. 293–302.'
ista: 'Dziembowski S, Pietrzak KZ. 2008. Leakage resilient cryptography. FOCS: Foundations
of Computer Science, 293–302.'
mla: Dziembowski, Stefan, and Krzysztof Z. Pietrzak. Leakage Resilient Cryptography.
IEEE, 2008, pp. 293–302, doi:10.1109/FOCS.2008.56.
short: S. Dziembowski, K.Z. Pietrzak, in:, IEEE, 2008, pp. 293–302.
conference:
name: 'FOCS: Foundations of Computer Science'
date_created: 2018-12-11T12:02:08Z
date_published: 2008-10-28T00:00:00Z
date_updated: 2021-01-12T07:41:57Z
day: '28'
doi: 10.1109/FOCS.2008.56
extern: 1
month: '10'
page: 293 - 302
publication_status: published
publisher: IEEE
publist_id: '3451'
quality_controlled: 0
status: public
title: Leakage resilient cryptography
type: conference
year: '2008'
...
---
_id: '3291'
abstract:
- lang: eng
text: 'The filamentous fungus Aspergillus fumigatus is responsible for a lethal
disease called Invasive Aspergillosis that affects immunocompromised patients.
This disease, like other human fungal diseases, is generally treated by compounds
targeting the primary fungal cell membrane sterol. Recently, glucan synthesis
inhibitors were added to the limited antifungal arsenal and encouraged the search
for novel targets in cell wall biosynthesis. Although galactomannan is a major
component of the A. fumigatus cell wall and extracellular matrix, the biosynthesis
and role of galactomannan are currently unknown. By a targeted gene deletion approach,
we demonstrate that UDP-galactopyranose mutase, a key enzyme of galactofuranose
metabolism, controls the biosynthesis of galactomannan and galactofuranose containing
glycoconjugates. The glfA deletion mutant generated in this study is devoid of
galactofuranose and displays attenuated virulence in a low-dose mouse model of
invasive aspergillosis that likely reflects the impaired growth of the mutant
at mammalian body temperature. Furthermore, the absence of galactofuranose results
in a thinner cell wall that correlates with an increased susceptibility to several
antifungal agents. The UDP-galactopyranose mutase thus appears to be an appealing
adjunct therapeutic target in combination with other drugs against A. fumigatus.
Its absence from mammalian cells indeed offers a considerable advantage to achieve
therapeutic selectivity. '
author:
- first_name: Philipp S
full_name: Philipp Schmalhorst
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Sven
full_name: Krappmann, Sven
last_name: Krappmann
- first_name: Wouter
full_name: Vervecken, Wouter
last_name: Vervecken
- first_name: Manfred
full_name: Rohde, Manfred
last_name: Rohde
- first_name: Meike
full_name: Müller, Meike
last_name: Müller
- first_name: Gerhard
full_name: Braus, Gerhard H.
last_name: Braus
- first_name: Roland
full_name: Contreras, Roland
last_name: Contreras
- first_name: Armin
full_name: Braun, Armin
last_name: Braun
- first_name: Hans
full_name: Bakker, Hans
last_name: Bakker
- first_name: Françoise
full_name: Routier, Françoise H
last_name: Routier
citation:
ama: Schmalhorst PS, Krappmann S, Vervecken W, et al. Contribution of galactofuranose
to the virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic
Cell. 2008;7(8):1268-1277. doi:10.1128/EC.00065-08
apa: Schmalhorst, P. S., Krappmann, S., Vervecken, W., Rohde, M., Müller, M., Braus,
G., … Routier, F. (2008). Contribution of galactofuranose to the virulence of
the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell. American
Society for Microbiology. https://doi.org/10.1128/EC.00065-08
chicago: Schmalhorst, Philipp S, Sven Krappmann, Wouter Vervecken, Manfred Rohde,
Meike Müller, Gerhard Braus, Roland Contreras, Armin Braun, Hans Bakker, and Françoise
Routier. “Contribution of Galactofuranose to the Virulence of the Opportunistic
Pathogen Aspergillus Fumigatus.” Eukaryotic Cell. American Society for
Microbiology, 2008. https://doi.org/10.1128/EC.00065-08.
ieee: P. S. Schmalhorst et al., “Contribution of galactofuranose to the virulence
of the opportunistic pathogen Aspergillus fumigatus,” Eukaryotic Cell,
vol. 7, no. 8. American Society for Microbiology, pp. 1268–1277, 2008.
ista: Schmalhorst PS, Krappmann S, Vervecken W, Rohde M, Müller M, Braus G, Contreras
R, Braun A, Bakker H, Routier F. 2008. Contribution of galactofuranose to the
virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell.
7(8), 1268–1277.
mla: Schmalhorst, Philipp S., et al. “Contribution of Galactofuranose to the Virulence
of the Opportunistic Pathogen Aspergillus Fumigatus.” Eukaryotic Cell,
vol. 7, no. 8, American Society for Microbiology, 2008, pp. 1268–77, doi:10.1128/EC.00065-08.
short: P.S. Schmalhorst, S. Krappmann, W. Vervecken, M. Rohde, M. Müller, G. Braus,
R. Contreras, A. Braun, H. Bakker, F. Routier, Eukaryotic Cell 7 (2008) 1268–1277.
date_created: 2018-12-11T12:02:29Z
date_published: 2008-06-13T00:00:00Z
date_updated: 2021-01-12T07:42:26Z
day: '13'
doi: 10.1128/EC.00065-08
extern: 1
intvolume: ' 7'
issue: '8'
month: '06'
page: 1268 - 1277
publication: Eukaryotic Cell
publication_status: published
publisher: American Society for Microbiology
publist_id: '3354'
quality_controlled: 0
status: public
title: Contribution of galactofuranose to the virulence of the opportunistic pathogen
Aspergillus fumigatus
type: journal_article
volume: 7
year: '2008'
...
---
_id: '3307'
abstract:
- lang: eng
text: A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000
year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8
Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally
establishes that the Neandertal mtDNA falls outside the variation of extant human
mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages
of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2
of cytochrome c oxidase of the mitochondrial electron transport chain has experienced
the largest number of amino acid substitutions in human ancestors since the separation
from Neandertals. There is evidence that purifying selection in the Neandertal
mtDNA was reduced compared with other primate lineages, suggesting that the effective
population size of Neandertals was small.
author:
- first_name: Richard
full_name: Green, Richard E
last_name: Green
- first_name: Anna
full_name: 'Malaspinas, Anna-Sapfo '
last_name: Malaspinas
- first_name: Johannes
full_name: Krause, Johannes
last_name: Krause
- first_name: Adrian
full_name: Briggs, Adrian W
last_name: Briggs
- first_name: Philip
full_name: Johnson, Philip L
last_name: Johnson
- first_name: Caroline
full_name: Caroline Uhler
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Matthias
full_name: Meyer, Matthias
last_name: Meyer
- first_name: Jeffrey
full_name: Good, Jeffrey M
last_name: Good
- first_name: Tomislav
full_name: Maricic, Tomislav
last_name: Maricic
- first_name: Udo
full_name: Stenzel, Udo
last_name: Stenzel
- first_name: Kay
full_name: Prüfer, Kay
last_name: Prüfer
- first_name: Michael
full_name: Siebauer, Michael F
last_name: Siebauer
- first_name: Hernän
full_name: Burbano, Hernän A
last_name: Burbano
- first_name: Michael
full_name: Ronan, Michael T
last_name: Ronan
- first_name: Jonathan
full_name: Rothberg, Jonathan M
last_name: Rothberg
- first_name: Michael
full_name: Egholm, Michael
last_name: Egholm
- first_name: Pavao
full_name: Rudan, Pavao
last_name: Rudan
- first_name: Dejana
full_name: Brajković, Dejana
last_name: Brajković
- first_name: Željko
full_name: Kućan, Željko
last_name: Kućan
- first_name: Ivan
full_name: Gušić, Ivan
last_name: Gušić
- first_name: Mårten
full_name: Wikström, Mårten K
last_name: Wikström
- first_name: Liisa
full_name: Laakkonen, Liisa J
last_name: Laakkonen
- first_name: Janet
full_name: Kelso, Janet F
last_name: Kelso
- first_name: Montgomery
full_name: Slatkin, Montgomery
last_name: Slatkin
- first_name: Svante
full_name: Pääbo, Svante H
last_name: Pääbo
citation:
ama: Green R, Malaspinas A, Krause J, et al. A complete neandertal mitochondrial
genome sequence determined by highhhroughput sequencing. Cell. 2008;134:416-426.
doi:10.1016/j.cell.2008.06.021
apa: Green, R., Malaspinas, A., Krause, J., Briggs, A., Johnson, P., Uhler, C.,
… Pääbo, S. (2008). A complete neandertal mitochondrial genome sequence determined
by highhhroughput sequencing. Cell. Cell Press. https://doi.org/10.1016/j.cell.2008.06.021
chicago: Green, Richard, Anna Malaspinas, Johannes Krause, Adrian Briggs, Philip
Johnson, Caroline Uhler, Matthias Meyer, et al. “A Complete Neandertal Mitochondrial
Genome Sequence Determined by Highhhroughput Sequencing.” Cell. Cell Press,
2008. https://doi.org/10.1016/j.cell.2008.06.021.
ieee: R. Green et al., “A complete neandertal mitochondrial genome sequence
determined by highhhroughput sequencing,” Cell, vol. 134. Cell Press, pp.
416–426, 2008.
ista: Green R, Malaspinas A, Krause J, Briggs A, Johnson P, Uhler C, Meyer M, Good
J, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano H, Ronan M, Rothberg J,
Egholm M, Rudan P, Brajković D, Kućan Ž, Gušić I, Wikström M, Laakkonen L, Kelso
J, Slatkin M, Pääbo S. 2008. A complete neandertal mitochondrial genome sequence
determined by highhhroughput sequencing. Cell. 134, 416–426.
mla: Green, Richard, et al. “A Complete Neandertal Mitochondrial Genome Sequence
Determined by Highhhroughput Sequencing.” Cell, vol. 134, Cell Press, 2008,
pp. 416–26, doi:10.1016/j.cell.2008.06.021.
short: R. Green, A. Malaspinas, J. Krause, A. Briggs, P. Johnson, C. Uhler, M. Meyer,
J. Good, T. Maricic, U. Stenzel, K. Prüfer, M. Siebauer, H. Burbano, M. Ronan,
J. Rothberg, M. Egholm, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, M. Wikström,
L. Laakkonen, J. Kelso, M. Slatkin, S. Pääbo, Cell 134 (2008) 416–426.
date_created: 2018-12-11T12:02:35Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2021-01-12T07:42:32Z
day: '01'
doi: 10.1016/j.cell.2008.06.021
extern: 1
intvolume: ' 134'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602844/
month: '08'
oa: 1
page: 416 - 426
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3333'
quality_controlled: 0
status: public
title: A complete neandertal mitochondrial genome sequence determined by highhhroughput
sequencing
type: journal_article
volume: 134
year: '2008'
...
---
_id: '11109'
abstract:
- lang: eng
text: The nuclear envelope (NE) provides a selective barrier between the nuclear
interior and the cytoplasm and constitutes a central component of intracellular
architecture. During mitosis in metazoa, the NE breaks down leading to the complete
mixing of the nuclear content with the cytosol. Interestingly, many NE components
actively participate in mitotic progression. After chromosome segregation, the
NE is reassembled around decondensing chromatin and the nuclear compartment is
reestablished in the daughter cells. Here, we summarize recent progress in deciphering
the molecular mechanisms underlying NE dynamics during cell division.
article_processing_charge: No
article_type: original
author:
- first_name: Ulrike
full_name: Kutay, Ulrike
last_name: Kutay
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Kutay U, Hetzer M. Reorganization of the nuclear envelope during open mitosis.
Current Opinion in Cell Biology. 2008;20(6):669-677. doi:10.1016/j.ceb.2008.09.010
apa: Kutay, U., & Hetzer, M. (2008). Reorganization of the nuclear envelope
during open mitosis. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2008.09.010
chicago: Kutay, Ulrike, and Martin Hetzer. “Reorganization of the Nuclear Envelope
during Open Mitosis.” Current Opinion in Cell Biology. Elsevier, 2008.
https://doi.org/10.1016/j.ceb.2008.09.010.
ieee: U. Kutay and M. Hetzer, “Reorganization of the nuclear envelope during open
mitosis,” Current Opinion in Cell Biology, vol. 20, no. 6. Elsevier, pp.
669–677, 2008.
ista: Kutay U, Hetzer M. 2008. Reorganization of the nuclear envelope during open
mitosis. Current Opinion in Cell Biology. 20(6), 669–677.
mla: Kutay, Ulrike, and Martin Hetzer. “Reorganization of the Nuclear Envelope during
Open Mitosis.” Current Opinion in Cell Biology, vol. 20, no. 6, Elsevier,
2008, pp. 669–77, doi:10.1016/j.ceb.2008.09.010.
short: U. Kutay, M. Hetzer, Current Opinion in Cell Biology 20 (2008) 669–677.
date_created: 2022-04-07T07:55:00Z
date_published: 2008-12-01T00:00:00Z
date_updated: 2022-07-18T08:55:32Z
day: '01'
doi: 10.1016/j.ceb.2008.09.010
extern: '1'
external_id:
pmid:
- '18938243'
intvolume: ' 20'
issue: '6'
keyword:
- Cell Biology
language:
- iso: eng
month: '12'
oa_version: None
page: 669-677
pmid: 1
publication: Current Opinion in Cell Biology
publication_identifier:
issn:
- 0955-0674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reorganization of the nuclear envelope during open mitosis
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 20
year: '2008'
...
---
_id: '11110'
abstract:
- lang: eng
text: Nuclear pore complexes are large aqueous channels that penetrate the nuclear
envelope, thereby connecting the nuclear interior with the cytoplasm. Until recently,
these macromolecular complexes were viewed as static structures, the only function
of which was to control the molecular trafficking between the two compartments.
It has now become evident that this simplistic scenario is inaccurate and that
nuclear pore complexes are highly dynamic multiprotein assemblies involved in
diverse cellular processes ranging from the organization of the cytoskeleton to
gene expression. In this review, we discuss the most recent developments in the
nuclear-pore-complex field, focusing on the assembly, disassembly, maintenance
and function of this macromolecular structure.
article_processing_charge: No
article_type: review
author:
- first_name: Maximiliano A.
full_name: D’Angelo, Maximiliano A.
last_name: D’Angelo
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: D’Angelo MA, Hetzer M. Structure, dynamics and function of nuclear pore complexes.
Trends in Cell Biology. 2008;18(10):456-466. doi:10.1016/j.tcb.2008.07.009
apa: D’Angelo, M. A., & Hetzer, M. (2008). Structure, dynamics and function
of nuclear pore complexes. Trends in Cell Biology. Elsevier. https://doi.org/10.1016/j.tcb.2008.07.009
chicago: D’Angelo, Maximiliano A., and Martin Hetzer. “Structure, Dynamics and Function
of Nuclear Pore Complexes.” Trends in Cell Biology. Elsevier, 2008. https://doi.org/10.1016/j.tcb.2008.07.009.
ieee: M. A. D’Angelo and M. Hetzer, “Structure, dynamics and function of nuclear
pore complexes,” Trends in Cell Biology, vol. 18, no. 10. Elsevier, pp.
456–466, 2008.
ista: D’Angelo MA, Hetzer M. 2008. Structure, dynamics and function of nuclear pore
complexes. Trends in Cell Biology. 18(10), 456–466.
mla: D’Angelo, Maximiliano A., and Martin Hetzer. “Structure, Dynamics and Function
of Nuclear Pore Complexes.” Trends in Cell Biology, vol. 18, no. 10, Elsevier,
2008, pp. 456–66, doi:10.1016/j.tcb.2008.07.009.
short: M.A. D’Angelo, M. Hetzer, Trends in Cell Biology 18 (2008) 456–466.
date_created: 2022-04-07T07:55:10Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2022-07-18T08:55:33Z
day: '01'
doi: 10.1016/j.tcb.2008.07.009
extern: '1'
external_id:
pmid:
- '18786826'
intvolume: ' 18'
issue: '10'
keyword:
- Cell Biology
language:
- iso: eng
month: '10'
oa_version: None
page: 456-466
pmid: 1
publication: Trends in Cell Biology
publication_identifier:
issn:
- 0962-8924
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure, dynamics and function of nuclear pore complexes
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 18
year: '2008'
...
---
_id: '11111'
abstract:
- lang: eng
text: During mitosis in metazoans, segregated chromosomes become enclosed by the
nuclear envelope (NE), a double membrane that is continuous with the endoplasmic
reticulum (ER). Recent in vitro data suggest that NE formation occurs by chromatin-mediated
reorganization of the tubular ER; however, the basic principles of such a membrane-reshaping
process remain uncharacterized. Here, we present a quantitative analysis of nuclear
membrane assembly in mammalian cells using time-lapse microscopy. From the initial
recruitment of ER tubules to chromatin, the formation of a membrane-enclosed,
transport-competent nucleus occurs within ∼12 min. Overexpression of the ER tubule-forming
proteins reticulon 3, reticulon 4, and DP1 inhibits NE formation and nuclear expansion,
whereas their knockdown accelerates nuclear assembly. This suggests that the transition
from membrane tubules to sheets is rate-limiting for nuclear assembly. Our results
provide evidence that ER-shaping proteins are directly involved in the reconstruction
of the nuclear compartment and that morphological restructuring of the ER is the
principal mechanism of NE formation in vivo.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel J.
full_name: Anderson, Daniel J.
last_name: Anderson
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Anderson DJ, Hetzer M. Reshaping of the endoplasmic reticulum limits the rate
for nuclear envelope formation. Journal of Cell Biology. 2008;182(5):911-924.
doi:10.1083/jcb.200805140
apa: Anderson, D. J., & Hetzer, M. (2008). Reshaping of the endoplasmic reticulum
limits the rate for nuclear envelope formation. Journal of Cell Biology.
Rockefeller University Press. https://doi.org/10.1083/jcb.200805140
chicago: Anderson, Daniel J., and Martin Hetzer. “Reshaping of the Endoplasmic Reticulum
Limits the Rate for Nuclear Envelope Formation.” Journal of Cell Biology.
Rockefeller University Press, 2008. https://doi.org/10.1083/jcb.200805140.
ieee: D. J. Anderson and M. Hetzer, “Reshaping of the endoplasmic reticulum limits
the rate for nuclear envelope formation,” Journal of Cell Biology, vol.
182, no. 5. Rockefeller University Press, pp. 911–924, 2008.
ista: Anderson DJ, Hetzer M. 2008. Reshaping of the endoplasmic reticulum limits
the rate for nuclear envelope formation. Journal of Cell Biology. 182(5), 911–924.
mla: Anderson, Daniel J., and Martin Hetzer. “Reshaping of the Endoplasmic Reticulum
Limits the Rate for Nuclear Envelope Formation.” Journal of Cell Biology,
vol. 182, no. 5, Rockefeller University Press, 2008, pp. 911–24, doi:10.1083/jcb.200805140.
short: D.J. Anderson, M. Hetzer, Journal of Cell Biology 182 (2008) 911–924.
date_created: 2022-04-07T07:55:23Z
date_published: 2008-09-08T00:00:00Z
date_updated: 2022-07-18T08:56:02Z
day: '08'
doi: 10.1083/jcb.200805140
extern: '1'
external_id:
pmid:
- '18779370'
intvolume: ' 182'
issue: '5'
keyword:
- Cell Biology
language:
- iso: eng
month: '09'
oa_version: None
page: 911-924
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reshaping of the endoplasmic reticulum limits the rate for nuclear envelope
formation
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 182
year: '2008'
...
---
_id: '11112'
abstract:
- lang: eng
text: The nuclear envelope is a double-layered membrane that encloses the nuclear
genome and transcriptional machinery. In dividing cells of metazoa, the nucleus
completely disassembles during mitosis, creating the need to re-establish the
nuclear compartment at the end of each cell division. Given the crucial role of
the nuclear envelope in gene regulation and cellular organization, it is not surprising
that its biogenesis and organization have become active research areas. We will
review recent insights into nuclear membrane dynamics during the cell cycle.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel J
full_name: Anderson, Daniel J
last_name: Anderson
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Anderson DJ, Hetzer M. The life cycle of the metazoan nuclear envelope. Current
Opinion in Cell Biology. 2008;20(4):386-392. doi:10.1016/j.ceb.2008.03.016
apa: Anderson, D. J., & Hetzer, M. (2008). The life cycle of the metazoan nuclear
envelope. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2008.03.016
chicago: Anderson, Daniel J, and Martin Hetzer. “The Life Cycle of the Metazoan
Nuclear Envelope.” Current Opinion in Cell Biology. Elsevier, 2008. https://doi.org/10.1016/j.ceb.2008.03.016.
ieee: D. J. Anderson and M. Hetzer, “The life cycle of the metazoan nuclear envelope,”
Current Opinion in Cell Biology, vol. 20, no. 4. Elsevier, pp. 386–392,
2008.
ista: Anderson DJ, Hetzer M. 2008. The life cycle of the metazoan nuclear envelope.
Current Opinion in Cell Biology. 20(4), 386–392.
mla: Anderson, Daniel J., and Martin Hetzer. “The Life Cycle of the Metazoan Nuclear
Envelope.” Current Opinion in Cell Biology, vol. 20, no. 4, Elsevier, 2008,
pp. 386–92, doi:10.1016/j.ceb.2008.03.016.
short: D.J. Anderson, M. Hetzer, Current Opinion in Cell Biology 20 (2008) 386–392.
date_created: 2022-04-07T07:55:34Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2022-07-18T08:56:07Z
day: '01'
doi: 10.1016/j.ceb.2008.03.016
extern: '1'
external_id:
pmid:
- '18495454'
intvolume: ' 20'
issue: '4'
keyword:
- Cell Biology
language:
- iso: eng
month: '08'
oa_version: None
page: 386-392
pmid: 1
publication: Current Opinion in Cell Biology
publication_identifier:
issn:
- 0955-0674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The life cycle of the metazoan nuclear envelope
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 20
year: '2008'
...
---
_id: '11113'
abstract:
- lang: eng
text: The nuclear envelope (NE), a double membrane enclosing the nucleus of eukaryotic
cells, controls the flow of information between the nucleoplasm and the cytoplasm
and provides a scaffold for the organization of chromatin and the cytoskeleton.
In dividing metazoan cells, the NE breaks down at the onset of mitosis and then
reforms around segregated chromosomes to generate the daughter nuclei. Recent
data from intact cells and cell-free nuclear assembly systems suggest that the
endoplasmic reticulum (ER) is the source of membrane for NE assembly. At the end
of mitosis, ER membrane tubules are targeted to chromatin via tubule ends and
reorganized into flat nuclear membrane sheets by specific DNA-binding membrane
proteins. In contrast to previous models, which proposed vesicle fusion to be
the principal mechanism of NE formation, these new studies suggest that the nuclear
membrane forms by the chromatin-mediated reshaping of the ER.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Daniel J.
full_name: Anderson, Daniel J.
last_name: Anderson
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Anderson DJ, Hetzer M. Shaping the endoplasmic reticulum into the nuclear envelope.
Journal of Cell Science. 2008;121(2):137-142. doi:10.1242/jcs.005777
apa: Anderson, D. J., & Hetzer, M. (2008). Shaping the endoplasmic reticulum
into the nuclear envelope. Journal of Cell Science. The Company of Biologists.
https://doi.org/10.1242/jcs.005777
chicago: Anderson, Daniel J., and Martin Hetzer. “Shaping the Endoplasmic Reticulum
into the Nuclear Envelope.” Journal of Cell Science. The Company of Biologists,
2008. https://doi.org/10.1242/jcs.005777.
ieee: D. J. Anderson and M. Hetzer, “Shaping the endoplasmic reticulum into the
nuclear envelope,” Journal of Cell Science, vol. 121, no. 2. The Company
of Biologists, pp. 137–142, 2008.
ista: Anderson DJ, Hetzer M. 2008. Shaping the endoplasmic reticulum into the nuclear
envelope. Journal of Cell Science. 121(2), 137–142.
mla: Anderson, Daniel J., and Martin Hetzer. “Shaping the Endoplasmic Reticulum
into the Nuclear Envelope.” Journal of Cell Science, vol. 121, no. 2, The
Company of Biologists, 2008, pp. 137–42, doi:10.1242/jcs.005777.
short: D.J. Anderson, M. Hetzer, Journal of Cell Science 121 (2008) 137–142.
date_created: 2022-04-07T07:55:46Z
date_published: 2008-01-15T00:00:00Z
date_updated: 2022-07-18T08:56:10Z
day: '15'
doi: 10.1242/jcs.005777
extern: '1'
external_id:
pmid:
- '18187447'
intvolume: ' 121'
issue: '2'
keyword:
- Cell Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/jcs.005777
month: '01'
oa: 1
oa_version: Published Version
page: 137-142
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Shaping the endoplasmic reticulum into the nuclear envelope
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 121
year: '2008'
...
---
_id: '11114'
abstract:
- lang: eng
text: We present a miniaturized pull-down method for the detection of protein-protein
interactions using standard affinity chromatography reagents. Binding events between
different proteins, which are color-coded with quantum dots (QDs), are visualized
on single affinity chromatography beads by fluorescence microscopy. The use of
QDs for single molecule detection allows the simultaneous analysis of multiple
protein-protein binding events and reduces the amount of time and material needed
to perform a pull-down experiment.
article_number: e2061
article_processing_charge: No
article_type: original
author:
- first_name: Roberta
full_name: Schulte, Roberta
last_name: Schulte
- first_name: Jessica
full_name: Talamas, Jessica
last_name: Talamas
- first_name: Christine
full_name: Doucet, Christine
last_name: Doucet
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Schulte R, Talamas J, Doucet C, Hetzer M. Single bead affinity detection (SINBAD)
for the analysis of protein-protein interactions. PLoS ONE. 2008;3(4).
doi:10.1371/journal.pone.0002061
apa: Schulte, R., Talamas, J., Doucet, C., & Hetzer, M. (2008). Single bead
affinity detection (SINBAD) for the analysis of protein-protein interactions.
PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0002061
chicago: Schulte, Roberta, Jessica Talamas, Christine Doucet, and Martin Hetzer.
“Single Bead Affinity Detection (SINBAD) for the Analysis of Protein-Protein Interactions.”
PLoS ONE. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002061.
ieee: R. Schulte, J. Talamas, C. Doucet, and M. Hetzer, “Single bead affinity detection
(SINBAD) for the analysis of protein-protein interactions,” PLoS ONE, vol.
3, no. 4. Public Library of Science, 2008.
ista: Schulte R, Talamas J, Doucet C, Hetzer M. 2008. Single bead affinity detection
(SINBAD) for the analysis of protein-protein interactions. PLoS ONE. 3(4), e2061.
mla: Schulte, Roberta, et al. “Single Bead Affinity Detection (SINBAD) for the Analysis
of Protein-Protein Interactions.” PLoS ONE, vol. 3, no. 4, e2061, Public
Library of Science, 2008, doi:10.1371/journal.pone.0002061.
short: R. Schulte, J. Talamas, C. Doucet, M. Hetzer, PLoS ONE 3 (2008).
date_created: 2022-04-07T07:55:57Z
date_published: 2008-04-30T00:00:00Z
date_updated: 2022-07-18T08:56:36Z
day: '30'
doi: 10.1371/journal.pone.0002061
extern: '1'
external_id:
pmid:
- '18446240'
intvolume: ' 3'
issue: '4'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1371/journal.pone.0002061'
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
issn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single bead affinity detection (SINBAD) for the analysis of protein-protein
interactions
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 3
year: '2008'
...
---
_id: '844'
abstract:
- lang: eng
text: Mutation rate varies greatly between nucleotide sites of the human genome
and depends both on the global genomic location and the local sequence context
of a site. In particular, CpG context elevates the mutation rate by an order of
magnitude. Mutations also vary widely in their effect on the molecular function,
phenotype, and fitness. Independence of the probability of occurrence of a new
mutation's effect has been a fundamental premise in genetics. However, highly
mutable contexts may be preserved by negative selection at important sites but
destroyed by mutation at sites under no selection. Thus, there may be a positive
correlation between the rate of mutations at a nucleotide site and the magnitude
of their effect on fitness. We studied the impact of CpG context on the rate of
human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous
coding sites. We compared nucleotides that occupy identical positions within codons
of identical amino acids and only differ by being within versus outside CpG context.
Nucleotides within CpG context are under a stronger negative selection, as revealed
by their lower, proportionally to the mutation rate, rate of evolution and nucleotide
diversity. In particular, the probability of fixation of a non-synonymous transition
at a CpG site is two times lower than at a CpG site. Thus, sites with different
mutation rates are not necessarily selectively equivalent. This suggests that
the mutation rate may complement sequence conservation as a characteristic predictive
of functional importance of nucleotide sites.
acknowledgement: This work was supported in part by NIH grants R01 GM078598 and U54
LM008748.
author:
- first_name: Steffen
full_name: Schmidt, Steffen
last_name: Schmidt
- first_name: Anna
full_name: Gerasimova, Anna
last_name: Gerasimova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ivan
full_name: Adzuhbei, Ivan A
last_name: Adzuhbei
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
citation:
ama: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S.
Hypermutable non-synonymous sites are under stronger negative selection. PLoS
Genetics. 2008;4(11). doi:10.1371/journal.pgen.1000281
apa: Schmidt, S., Gerasimova, A., Kondrashov, F., Adzuhbei, I., Kondrashov, A.,
& Sunyaev, S. (2008). Hypermutable non-synonymous sites are under stronger
negative selection. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000281
chicago: Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey
Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger
Negative Selection.” PLoS Genetics. Public Library of Science, 2008. https://doi.org/10.1371/journal.pgen.1000281.
ieee: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and
S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,”
PLoS Genetics, vol. 4, no. 11. Public Library of Science, 2008.
ista: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S.
2008. Hypermutable non-synonymous sites are under stronger negative selection.
PLoS Genetics. 4(11).
mla: Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger
Negative Selection.” PLoS Genetics, vol. 4, no. 11, Public Library of Science,
2008, doi:10.1371/journal.pgen.1000281.
short: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S.
Sunyaev, PLoS Genetics 4 (2008).
date_created: 2018-12-11T11:48:48Z
date_published: 2008-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:16Z
day: '01'
doi: 10.1371/journal.pgen.1000281
extern: 1
intvolume: ' 4'
issue: '11'
month: '11'
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '6800'
quality_controlled: 0
status: public
title: Hypermutable non-synonymous sites are under stronger negative selection
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
volume: 4
year: '2008'
...
---
_id: '8480'
abstract:
- lang: eng
text: The KIX domain of the transcription co-activator CBP is a three-helix bundle
protein that folds via rapid accumulation of an intermediate state, followed by
a slower folding phase. Recent NMR relaxation dispersion studies revealed the
presence of a low-populated (excited) state of KIX that exists in equilibrium
with the natively folded form under non-denaturing conditions, and likely represents
the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium
exchange measurements using rapid NMR data acquisition techniques with backbone
15N and 13C relaxation dispersion experiments to further investigate the equilibrium
folding of the KIX domain. Residual structure within the folding intermediate
is detected by both methods, and their combination enables reliable quantification
of the amount of persistent residual structure. Three well-defined folding subunits
are found, which display variable stability and correspond closely to the individual
helices in the native state. While two of the three helices (α2 and α3) are partially
formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C),
the third helix is disordered. The observed helical content within the excited
state exceeds the helical propensities predicted for the corresponding peptide
regions, suggesting that the two helices are weakly mutually stabilized, while
methyl 13C relaxation dispersion data indicate that a defined packing arrangement
is unlikely. Temperature-dependent experiments reveal that the largest enthalpy
and entropy changes along the folding reaction occur during the final transition
from the intermediate to the native state. Our experimental data are consistent
with a folding mechanism where helices α2 and α3 form rapidly, although to different
extents, while helix α1 consolidates only as folding proceeds to complete the
native state-structure.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
citation:
ama: 'Schanda P, Brutscher B, Konrat R, Tollinger M. Folding of the KIX domain:
Characterization of the equilibrium analog of a folding intermediate using 15N/13C
relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal
of Molecular Biology. 2008;380(4):726-741. doi:10.1016/j.jmb.2008.05.040'
apa: 'Schanda, P., Brutscher, B., Konrat, R., & Tollinger, M. (2008). Folding
of the KIX domain: Characterization of the equilibrium analog of a folding intermediate
using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy.
Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2008.05.040'
chicago: 'Schanda, Paul, Bernhard Brutscher, Robert Konrat, and Martin Tollinger.
“Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding
Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange
NMR Spectroscopy.” Journal of Molecular Biology. Elsevier, 2008. https://doi.org/10.1016/j.jmb.2008.05.040.'
ieee: 'P. Schanda, B. Brutscher, R. Konrat, and M. Tollinger, “Folding of the KIX
domain: Characterization of the equilibrium analog of a folding intermediate using
15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy,”
Journal of Molecular Biology, vol. 380, no. 4. Elsevier, pp. 726–741, 2008.'
ista: 'Schanda P, Brutscher B, Konrat R, Tollinger M. 2008. Folding of the KIX domain:
Characterization of the equilibrium analog of a folding intermediate using 15N/13C
relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal
of Molecular Biology. 380(4), 726–741.'
mla: 'Schanda, Paul, et al. “Folding of the KIX Domain: Characterization of the
Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion
and Fast 1H/2H Amide Exchange NMR Spectroscopy.” Journal of Molecular Biology,
vol. 380, no. 4, Elsevier, 2008, pp. 726–41, doi:10.1016/j.jmb.2008.05.040.'
short: P. Schanda, B. Brutscher, R. Konrat, M. Tollinger, Journal of Molecular Biology
380 (2008) 726–741.
date_created: 2020-09-18T10:12:29Z
date_published: 2008-07-18T00:00:00Z
date_updated: 2021-01-12T08:19:34Z
day: '18'
doi: 10.1016/j.jmb.2008.05.040
extern: '1'
intvolume: ' 380'
issue: '4'
keyword:
- Molecular Biology
language:
- iso: eng
month: '07'
oa_version: None
page: 726-741
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Folding of the KIX domain: Characterization of the equilibrium analog of a
folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange
NMR spectroscopy'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2008'
...
---
_id: '8481'
abstract:
- lang: eng
text: 'The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans
CH34 within the complex cop cluster of genes, for which 21 genes have been identified.
The expression of the corresponding periplasmic CopK protein is strongly upregulated
in the presence of copper, leading to a high periplasmic accumulation. The structure
and metal-binding properties of CopK were investigated by NMR and mass spectrometry.
The protein is dimeric in the apo state with a dissociation constant in the range
of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed
that CopK has two high-affinity Cu(I)-binding sites per monomer with different
Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific.
The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets
in perpendicular orientation with an unstructured C-terminal tail. The dimer interface
is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion
induces a major structural modification involving dissociation of the dimeric
apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm
the conservation of the N-terminal β-sheet, while the last strand of the C-terminal
sheet appears in slow conformational exchange. We hypothesize that the partial
disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange
data acquired on the apo-protein are consistent with a lower thermodynamic stability
of the C-terminal sheet. CopK contains seven methionine residues, five of which
appear highly conserved. Chemical shift data suggest implication of two or three
methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second
Cu(I) ion further increases protein plasticity. Comparison of the structural and
metal-binding properties of CopK with other periplasmic copper-binding proteins
reveals two conserved features within these functionally related proteins: the
all-β fold and the methionine-rich Cu(I)-binding site.'
article_processing_charge: No
article_type: original
author:
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Sébastien
full_name: van Aelst, Sébastien
last_name: van Aelst
- first_name: Tatiana
full_name: Vallaeys, Tatiana
last_name: Vallaeys
- first_name: Jacques
full_name: Covès, Jacques
last_name: Covès
- first_name: Max
full_name: Mergeay, Max
last_name: Mergeay
- first_name: Ruddy
full_name: Wattiez, Ruddy
last_name: Wattiez
citation:
ama: Bersch B, Favier A, Schanda P, et al. Molecular structure and metal-binding
properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans
CH34 during copper challenge. Journal of Molecular Biology. 2008;380(2):386-403.
doi:10.1016/j.jmb.2008.05.017
apa: Bersch, B., Favier, A., Schanda, P., van Aelst, S., Vallaeys, T., Covès, J.,
… Wattiez, R. (2008). Molecular structure and metal-binding properties of the
periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper
challenge. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2008.05.017
chicago: Bersch, Beate, Adrien Favier, Paul Schanda, Sébastien van Aelst, Tatiana
Vallaeys, Jacques Covès, Max Mergeay, and Ruddy Wattiez. “Molecular Structure
and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus
Metallidurans CH34 during Copper Challenge.” Journal of Molecular Biology.
Elsevier, 2008. https://doi.org/10.1016/j.jmb.2008.05.017.
ieee: B. Bersch et al., “Molecular structure and metal-binding properties
of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during
copper challenge,” Journal of Molecular Biology, vol. 380, no. 2. Elsevier,
pp. 386–403, 2008.
ista: Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M,
Wattiez R. 2008. Molecular structure and metal-binding properties of the periplasmic
CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge.
Journal of Molecular Biology. 380(2), 386–403.
mla: Bersch, Beate, et al. “Molecular Structure and Metal-Binding Properties of
the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during
Copper Challenge.” Journal of Molecular Biology, vol. 380, no. 2, Elsevier,
2008, pp. 386–403, doi:10.1016/j.jmb.2008.05.017.
short: B. Bersch, A. Favier, P. Schanda, S. van Aelst, T. Vallaeys, J. Covès, M.
Mergeay, R. Wattiez, Journal of Molecular Biology 380 (2008) 386–403.
date_created: 2020-09-18T10:12:37Z
date_published: 2008-07-04T00:00:00Z
date_updated: 2021-01-12T08:19:34Z
day: '04'
doi: 10.1016/j.jmb.2008.05.017
extern: '1'
intvolume: ' 380'
issue: '2'
keyword:
- Molecular Biology
language:
- iso: eng
month: '07'
oa_version: None
page: 386-403
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Molecular structure and metal-binding properties of the periplasmic CopK protein
expressed in Cupriavidus metallidurans CH34 during copper challenge
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2008'
...
---
_id: '8482'
abstract:
- lang: eng
text: The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional
NMR spectroscopy for real-time investigation of dynamic events in proteins on
the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording
two-dimensional correlation spectra of macromolecules such as proteins in only
a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC
experiments are preferably performed on high-field NMR spectrometers equipped
with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC
experiments, however, may cause problems when using a cryogenic probe. Here we
introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity
to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection,
and thus significantly reducing the radiofrequency load of the probe during the
experiment. The experiment is also attractive for fast and sensitive measurement
of heteronuclear one-bond spin coupling constants.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Thomas
full_name: Kern, Thomas
last_name: Kern
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Kern T, Schanda P, Brutscher B. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing
2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance.
2008;190(2):333-338. doi:10.1016/j.jmr.2007.11.015
apa: Kern, T., Schanda, P., & Brutscher, B. (2008). Sensitivity-enhanced IPAP-SOFAST-HMQC
for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic
Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2007.11.015
chicago: Kern, Thomas, Paul Schanda, and Bernhard Brutscher. “Sensitivity-Enhanced
IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” Journal
of Magnetic Resonance. Elsevier, 2008. https://doi.org/10.1016/j.jmr.2007.11.015.
ieee: T. Kern, P. Schanda, and B. Brutscher, “Sensitivity-enhanced IPAP-SOFAST-HMQC
for fast-pulsing 2D NMR with reduced radiofrequency load,” Journal of Magnetic
Resonance, vol. 190, no. 2. Elsevier, pp. 333–338, 2008.
ista: Kern T, Schanda P, Brutscher B. 2008. Sensitivity-enhanced IPAP-SOFAST-HMQC
for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic
Resonance. 190(2), 333–338.
mla: Kern, Thomas, et al. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing
2D NMR with Reduced Radiofrequency Load.” Journal of Magnetic Resonance,
vol. 190, no. 2, Elsevier, 2008, pp. 333–38, doi:10.1016/j.jmr.2007.11.015.
short: T. Kern, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 190 (2008)
333–338.
date_created: 2020-09-18T10:12:46Z
date_published: 2008-02-01T00:00:00Z
date_updated: 2021-01-12T08:19:35Z
day: '01'
doi: 10.1016/j.jmr.2007.11.015
extern: '1'
intvolume: ' 190'
issue: '2'
keyword:
- Nuclear and High Energy Physics
- Biophysics
- Biochemistry
- Condensed Matter Physics
language:
- iso: eng
month: '02'
oa_version: None
page: 333-338
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced
radiofrequency load
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 190
year: '2008'
...
---
_id: '8509'
abstract:
- lang: eng
text: The goal of this paper is to present to nonspecialists what is perhaps the
simplest possible geometrical picture explaining the mechanism of Arnold diffusion.
We choose to speak of a specific model—that of geometric rays in a periodic optical
medium. This model is equivalent to that of a particle in a periodic potential
in ${\mathbb R}^{n}$ with energy prescribed and to the geodesic flow in a Riemannian
metric on ${\mathbb R}^{n} $.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
citation:
ama: Kaloshin V, Levi M. Geometry of Arnold diffusion. SIAM Review. 2008;50(4):702-720.
doi:10.1137/070703235
apa: Kaloshin, V., & Levi, M. (2008). Geometry of Arnold diffusion. SIAM
Review. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/070703235
chicago: Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM
Review. Society for Industrial & Applied Mathematics, 2008. https://doi.org/10.1137/070703235.
ieee: V. Kaloshin and M. Levi, “Geometry of Arnold diffusion,” SIAM Review,
vol. 50, no. 4. Society for Industrial & Applied Mathematics, pp. 702–720,
2008.
ista: Kaloshin V, Levi M. 2008. Geometry of Arnold diffusion. SIAM Review. 50(4),
702–720.
mla: Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM Review,
vol. 50, no. 4, Society for Industrial & Applied Mathematics, 2008, pp. 702–20,
doi:10.1137/070703235.
short: V. Kaloshin, M. Levi, SIAM Review 50 (2008) 702–720.
date_created: 2020-09-18T10:48:12Z
date_published: 2008-11-05T00:00:00Z
date_updated: 2021-01-12T08:19:46Z
day: '05'
doi: 10.1137/070703235
extern: '1'
intvolume: ' 50'
issue: '4'
keyword:
- Theoretical Computer Science
- Applied Mathematics
- Computational Mathematics
language:
- iso: eng
month: '11'
oa_version: None
page: 702-720
publication: SIAM Review
publication_identifier:
issn:
- 0036-1445
- 1095-7200
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
status: public
title: Geometry of Arnold diffusion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2008'
...
---
_id: '8510'
abstract:
- lang: eng
text: In this paper, using the ideas of Bessi and Mather, we present a simple mechanical
system exhibiting Arnold diffusion. This system of a particle in a small periodic
potential can be also interpreted as ray propagation in a periodic optical medium
with a near-constant index of refraction. Arnold diffusion in this context manifests
itself as an arbitrary finite change of direction for nearly constant index of
refraction.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
citation:
ama: Kaloshin V, Levi M. An example of Arnold diffusion for near-integrable Hamiltonians.
Bulletin of the American Mathematical Society. 2008;45(3):409-427. doi:10.1090/s0273-0979-08-01211-1
apa: Kaloshin, V., & Levi, M. (2008). An example of Arnold diffusion for near-integrable
Hamiltonians. Bulletin of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/s0273-0979-08-01211-1
chicago: Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable
Hamiltonians.” Bulletin of the American Mathematical Society. American
Mathematical Society, 2008. https://doi.org/10.1090/s0273-0979-08-01211-1.
ieee: V. Kaloshin and M. Levi, “An example of Arnold diffusion for near-integrable
Hamiltonians,” Bulletin of the American Mathematical Society, vol. 45,
no. 3. American Mathematical Society, pp. 409–427, 2008.
ista: Kaloshin V, Levi M. 2008. An example of Arnold diffusion for near-integrable
Hamiltonians. Bulletin of the American Mathematical Society. 45(3), 409–427.
mla: Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable
Hamiltonians.” Bulletin of the American Mathematical Society, vol. 45,
no. 3, American Mathematical Society, 2008, pp. 409–27, doi:10.1090/s0273-0979-08-01211-1.
short: V. Kaloshin, M. Levi, Bulletin of the American Mathematical Society 45 (2008)
409–427.
date_created: 2020-09-18T10:48:20Z
date_published: 2008-07-01T00:00:00Z
date_updated: 2021-01-12T08:19:47Z
day: '01'
doi: 10.1090/s0273-0979-08-01211-1
extern: '1'
intvolume: ' 45'
issue: '3'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '07'
oa_version: None
page: 409-427
publication: Bulletin of the American Mathematical Society
publication_identifier:
issn:
- 0273-0979
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: An example of Arnold diffusion for near-integrable Hamiltonians
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2008'
...
---
_id: '895'
abstract:
- lang: eng
text: Background. The arginine vasopressin V1a receptor (V1aR) modulates social
cognition and behavior in a wide variety of species. Variation in a repetitive
microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in
rodents has been associated with variation in brain V1aR expression and in social
behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication
of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb
upstream of the transcription start site. The first block, referred to as DupA,
contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex
(CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3
have been associated with variation in sociobehavioral traits in humans, including
autism spectrum disorders. Thus, evolution of these regions may have contributed
to variation in social behavior in primates. We examined the structure of these
regions in six ape, six monkey, and one prosimian species. Results. Both tandem
repeat blocks are present upstream of the AVPR1A coding region in five of the
ape species we investigated, while monkeys have only one copy of this region.
As in humans, the microsatellites within DupA and DupB are polymorphic in many
primate species. Furthermore, both single (lacking DupB) and duplicated alleles
(containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations
with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles,
respectively, based on the analysis of 47 wild-caught individuals. Finally, a
phylogenetic reconstruction suggests two alternate evolutionary histories for
this locus. Conclusion. There is no obvious relationship between the presence
of the RS3 duplication and social organization in primates. However, polymorphisms
identified in some species may be useful in future genetic association studies.
In particular, the presence of both single and duplicated alleles in chimpanzees
provides a unique opportunity to assess the functional role of this duplication
in contributing to variation in social behavior in primates. While our initial
studies show no signs of directional selection on this locus in chimps, pharmacological
and genetic association studies support a potential role for this region in influencing
V1aR expression and social behavior.
acknowledgement: |
We thank the caretakers at Zoo Atlanta and Yerkes National Primate Center for help with procuring specimens. Additional DNA samples were supplied by Bill Hopkins, Emory University (chimpanzee), Allyson Bennet, Wake Forest University (chimpanzee, rhesus macaque, bonnet macaque), Mar Sanchez, Emory University (rhesus macaque), and Anne Yoder, Duke University (galago). Susan Lambeth, M.D. Anderson Cancer Center, and Katie Chace, Yerkes National Primate Center, helped provide records regarding the origins of wild born chimps at these centers. We would like to thank Dr Lisa McGraw and two anonymous reviewers for their com- ments on this manuscript. This work was supported by NSF IBN-9876754, NIH RR00165, NIMH56897 (LJY), MH64692 (LJY) and a Howard Hughes Predoctoral Fellowship (ZRD).
author:
- first_name: Zoe
full_name: Donaldson, Zoe R
last_name: Donaldson
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Andrea
full_name: Putnam, Andrea S
last_name: Putnam
- first_name: Yaohui
full_name: Bai, Yaohui
last_name: Bai
- first_name: Tara
full_name: Stoinski, Tara S
last_name: Stoinski
- first_name: Elizabeth
full_name: Hammock, Elizabeth A
last_name: Hammock
- first_name: Larry
full_name: Young, Larry
last_name: Young
citation:
ama: Donaldson Z, Kondrashov F, Putnam A, et al. Evolution of a behavior-linked
microsatellite-containing element in the 5′ flanking region of the primate AVPR1A
gene. BMC Evolutionary Biology. 2008;8(1). doi:10.1186/1471-2148-8-180
apa: Donaldson, Z., Kondrashov, F., Putnam, A., Bai, Y., Stoinski, T., Hammock,
E., & Young, L. (2008). Evolution of a behavior-linked microsatellite-containing
element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary
Biology. BioMed Central. https://doi.org/10.1186/1471-2148-8-180
chicago: Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski,
Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing
Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary
Biology. BioMed Central, 2008. https://doi.org/10.1186/1471-2148-8-180.
ieee: Z. Donaldson et al., “Evolution of a behavior-linked microsatellite-containing
element in the 5′ flanking region of the primate AVPR1A gene,” BMC Evolutionary
Biology, vol. 8, no. 1. BioMed Central, 2008.
ista: Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L.
2008. Evolution of a behavior-linked microsatellite-containing element in the
5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1).
mla: Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing
Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary
Biology, vol. 8, no. 1, BioMed Central, 2008, doi:10.1186/1471-2148-8-180.
short: Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock,
L. Young, BMC Evolutionary Biology 8 (2008).
date_created: 2018-12-11T11:49:04Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:29Z
day: '01'
doi: 10.1186/1471-2148-8-180
extern: 1
intvolume: ' 8'
issue: '1'
month: '01'
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '6753'
quality_controlled: 0
status: public
title: Evolution of a behavior-linked microsatellite-containing element in the 5′
flanking region of the primate AVPR1A gene
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
volume: 8
year: '2008'
...