---
_id: '11119'
article_processing_charge: No
author:
- first_name: J. Robin
full_name: Harris, J. Robin
last_name: Harris
- first_name: Geneviève
full_name: Almouzni, Geneviève
last_name: Almouzni
- first_name: Doris
full_name: Kirschner, Doris
last_name: Kirschner
- first_name: Daniela
full_name: Dimitrova, Daniela
last_name: Dimitrova
- first_name: Jeffrey A.
full_name: Nickerson, Jeffrey A.
last_name: Nickerson
- first_name: Jean
full_name: Underwood, Jean
last_name: Underwood
- first_name: Stefan
full_name: Wagner, Stefan
last_name: Wagner
- first_name: Barbara
full_name: Korbei, Barbara
last_name: Korbei
- first_name: Roland
full_name: Foisner, Roland
last_name: Foisner
- first_name: Tobias C.
full_name: Walther, Tobias C.
last_name: Walther
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Reiner
full_name: Peters, Reiner
last_name: Peters
- first_name: Ivan
full_name: Walev, Ivan
last_name: Walev
- first_name: Anton I. P. M.
full_name: de Kroon, Anton I. P. M.
last_name: de Kroon
- first_name: Rutger W. H. M.
full_name: Staffhorst, Rutger W. H. M.
last_name: Staffhorst
- first_name: Ben
full_name: de Kruijff, Ben
last_name: de Kruijff
- first_name: Koert N. J.
full_name: Burger, Koert N. J.
last_name: Burger
- first_name: Luis Eduardo Soares
full_name: Netto, Luis Eduardo Soares
last_name: Netto
- first_name: Eric
full_name: Bertrand, Eric
last_name: Bertrand
- first_name: Judie B.
full_name: Alimonti, Judie B.
last_name: Alimonti
- first_name: Arnold H.
full_name: Greenberg, Arnold H.
last_name: Greenberg
- first_name: Jinnan
full_name: Xiao, Jinnan
last_name: Xiao
- first_name: Anuradha
full_name: Pradhan, Anuradha
last_name: Pradhan
- first_name: Yuechueng
full_name: Liu, Yuechueng
last_name: Liu
- first_name: Jacques
full_name: Paiement, Jacques
last_name: Paiement
- first_name: Robin
full_name: Young, Robin
last_name: Young
- first_name: Félix M.
full_name: Goñi, Félix M.
last_name: Goñi
- first_name: Ana-Victoria
full_name: Villar, Ana-Victoria
last_name: Villar
- first_name: F.-Xabier
full_name: Contreras, F.-Xabier
last_name: Contreras
- first_name: Alicia
full_name: Alonso, Alicia
last_name: Alonso
- first_name: Brian J.
full_name: Peter, Brian J.
last_name: Peter
- first_name: Ian G.
full_name: Mills, Ian G.
last_name: Mills
- first_name: Matthew K.
full_name: Higgins, Matthew K.
last_name: Higgins
- first_name: William J.
full_name: Brown, William J.
last_name: Brown
- first_name: K.
full_name: Chambers, K.
last_name: Chambers
- first_name: A.
full_name: Doody, A.
last_name: Doody
- first_name: C. Yan
full_name: Cheng, C. Yan
last_name: Cheng
- first_name: Dolores D.
full_name: Mruk, Dolores D.
last_name: Mruk
- first_name: Chunhong
full_name: Yang, Chunhong
last_name: Yang
- first_name: Helmut
full_name: Kirchhoff, Helmut
last_name: Kirchhoff
- first_name: Winfried
full_name: Haase, Winfried
last_name: Haase
- first_name: Stephanie
full_name: Boggasch, Stephanie
last_name: Boggasch
- first_name: Harald
full_name: Paulsen, Harald
last_name: Paulsen
- first_name: Julie
full_name: Benesova, Julie
last_name: Benesova
- first_name: Sven-T.
full_name: Liffers, Sven-T.
last_name: Liffers
- first_name: Matthias
full_name: Rögner, Matthias
last_name: Rögner
- first_name: Ya-sheng
full_name: Gao, Ya-sheng
last_name: Gao
- first_name: Elizabeth
full_name: Sztul, Elizabeth
last_name: Sztul
- first_name: Meinolf
full_name: Thiemann, Meinolf
last_name: Thiemann
- first_name: H. Dariush
full_name: Fahimi, H. Dariush
last_name: Fahimi
- first_name: Robert
full_name: Gniadecki, Robert
last_name: Gniadecki
- first_name: Barbara
full_name: Gajkowska, Barbara
last_name: Gajkowska
- first_name: Susan L.
full_name: Bane, Susan L.
last_name: Bane
- first_name: John F.
full_name: Hess, John F.
last_name: Hess
- first_name: John C.
full_name: Voss, John C.
last_name: Voss
- first_name: Paul G.
full_name: Fitzgerald, Paul G.
last_name: Fitzgerald
- first_name: Shin-ichi
full_name: Hisanaga, Shin-ichi
last_name: Hisanaga
- first_name: Takahiro
full_name: Sasaki, Takahiro
last_name: Sasaki
- first_name: Kenji
full_name: Uéda, Kenji
last_name: Uéda
- first_name: Terrence
full_name: Town, Terrence
last_name: Town
- first_name: Jun
full_name: Tan, Jun
last_name: Tan
- first_name: Nathaniel G. N.
full_name: Milton, Nathaniel G. N.
last_name: Milton
- first_name: Richard
full_name: Chi, Richard
last_name: Chi
- first_name: Thomas C. S.
full_name: Keller, Thomas C. S.
last_name: Keller
- first_name: Marina
full_name: Kriajevska, Marina
last_name: Kriajevska
- first_name: Igor
full_name: Bronstein, Igor
last_name: Bronstein
- first_name: Eugene
full_name: Lukanidin, Eugene
last_name: Lukanidin
- first_name: David F.
full_name: Holmes, David F.
last_name: Holmes
- first_name: Karl E.
full_name: Kadler, Karl E.
last_name: Kadler
citation:
ama: 'Harris JR, Almouzni G, Kirschner D, et al. In Vitro Techniques. In: Harris
R, Graham J, Rickwood D, eds. Cell Biology Protocols. Chichester, UK: Wiley;
2006:201-378. doi:10.1002/0470033487.ch6'
apa: 'Harris, J. R., Almouzni, G., Kirschner, D., Dimitrova, D., Nickerson, J. A.,
Underwood, J., … Kadler, K. E. (2006). In Vitro Techniques. In R. Harris, J. Graham,
& D. Rickwood (Eds.), Cell Biology Protocols (pp. 201–378). Chichester,
UK: Wiley. https://doi.org/10.1002/0470033487.ch6'
chicago: 'Harris, J. Robin, Geneviève Almouzni, Doris Kirschner, Daniela Dimitrova,
Jeffrey A. Nickerson, Jean Underwood, Stefan Wagner, et al. “In Vitro Techniques.”
In Cell Biology Protocols, edited by Robin Harris, John Graham, and David
Rickwood, 201–378. Chichester, UK: Wiley, 2006. https://doi.org/10.1002/0470033487.ch6.'
ieee: 'J. R. Harris et al., “In Vitro Techniques,” in Cell Biology Protocols,
R. Harris, J. Graham, and D. Rickwood, Eds. Chichester, UK: Wiley, 2006, pp. 201–378.'
ista: 'Harris JR, Almouzni G, Kirschner D, Dimitrova D, Nickerson JA, Underwood
J, Wagner S, Korbei B, Foisner R, Walther TC, Hetzer M, Peters R, Walev I, de
Kroon AIPM, Staffhorst RWHM, de Kruijff B, Burger KNJ, Netto LES, Bertrand E,
Alimonti JB, Greenberg AH, Xiao J, Pradhan A, Liu Y, Paiement J, Young R, Goñi
FM, Villar A-V, Contreras F-X, Alonso A, Peter BJ, Mills IG, Higgins MK, Brown
WJ, Chambers K, Doody A, Cheng CY, Mruk DD, Yang C, Kirchhoff H, Haase W, Boggasch
S, Paulsen H, Benesova J, Liffers S-T, Rögner M, Gao Y, Sztul E, Thiemann M, Fahimi
HD, Gniadecki R, Gajkowska B, Bane SL, Hess JF, Voss JC, Fitzgerald PG, Hisanaga
S, Sasaki T, Uéda K, Town T, Tan J, Milton NGN, Chi R, Keller TCS, Kriajevska
M, Bronstein I, Lukanidin E, Holmes DF, Kadler KE. 2006.In Vitro Techniques. In:
Cell Biology Protocols. , 201–378.'
mla: Harris, J. Robin, et al. “In Vitro Techniques.” Cell Biology Protocols,
edited by Robin Harris et al., Wiley, 2006, pp. 201–378, doi:10.1002/0470033487.ch6.
short: J.R. Harris, G. Almouzni, D. Kirschner, D. Dimitrova, J.A. Nickerson, J.
Underwood, S. Wagner, B. Korbei, R. Foisner, T.C. Walther, M. Hetzer, R. Peters,
I. Walev, A.I.P.M. de Kroon, R.W.H.M. Staffhorst, B. de Kruijff, K.N.J. Burger,
L.E.S. Netto, E. Bertrand, J.B. Alimonti, A.H. Greenberg, J. Xiao, A. Pradhan,
Y. Liu, J. Paiement, R. Young, F.M. Goñi, A.-V. Villar, F.-X. Contreras, A. Alonso,
B.J. Peter, I.G. Mills, M.K. Higgins, W.J. Brown, K. Chambers, A. Doody, C.Y.
Cheng, D.D. Mruk, C. Yang, H. Kirchhoff, W. Haase, S. Boggasch, H. Paulsen, J.
Benesova, S.-T. Liffers, M. Rögner, Y. Gao, E. Sztul, M. Thiemann, H.D. Fahimi,
R. Gniadecki, B. Gajkowska, S.L. Bane, J.F. Hess, J.C. Voss, P.G. Fitzgerald,
S. Hisanaga, T. Sasaki, K. Uéda, T. Town, J. Tan, N.G.N. Milton, R. Chi, T.C.S.
Keller, M. Kriajevska, I. Bronstein, E. Lukanidin, D.F. Holmes, K.E. Kadler, in:,
R. Harris, J. Graham, D. Rickwood (Eds.), Cell Biology Protocols, Wiley, Chichester,
UK, 2006, pp. 201–378.
date_created: 2022-04-07T07:56:42Z
date_published: 2006-01-27T00:00:00Z
date_updated: 2022-07-18T08:57:08Z
day: '27'
doi: 10.1002/0470033487.ch6
editor:
- first_name: Robin
full_name: Harris, Robin
last_name: Harris
- first_name: John
full_name: Graham, John
last_name: Graham
- first_name: David
full_name: Rickwood, David
last_name: Rickwood
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 201-378
place: Chichester, UK
publication: Cell Biology Protocols
publication_identifier:
eisbn:
- '9780470033487 '
isbn:
- '9780470847589 '
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: In Vitro Techniques
type: book_chapter
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
year: '2006'
...
---
_id: '8488'
abstract:
- lang: eng
text: We demonstrate for different protein samples that three-dimensional HNCO and
HNCA correlation spectra may be recorded in a few minutes acquisition time using
the band-selective excitation short-transient sequences presented here. This opens
new perspectives for the NMR structural investigation of unstable protein samples
and real-time site-resolved studies of protein kinetics.
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: Hélène
full_name: Van Melckebeke, Hélène
last_name: Van Melckebeke
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Schanda P, Van Melckebeke H, Brutscher B. Speeding up three-dimensional protein
NMR experiments to a few minutes. Journal of the American Chemical Society.
2006;128(28):9042-9043. doi:10.1021/ja062025p
apa: Schanda, P., Van Melckebeke, H., & Brutscher, B. (2006). Speeding up three-dimensional
protein NMR experiments to a few minutes. Journal of the American Chemical
Society. American Chemical Society. https://doi.org/10.1021/ja062025p
chicago: Schanda, Paul, Hélène Van Melckebeke, and Bernhard Brutscher. “Speeding
up Three-Dimensional Protein NMR Experiments to a Few Minutes.” Journal of
the American Chemical Society. American Chemical Society, 2006. https://doi.org/10.1021/ja062025p.
ieee: P. Schanda, H. Van Melckebeke, and B. Brutscher, “Speeding up three-dimensional
protein NMR experiments to a few minutes,” Journal of the American Chemical
Society, vol. 128, no. 28. American Chemical Society, pp. 9042–9043, 2006.
ista: Schanda P, Van Melckebeke H, Brutscher B. 2006. Speeding up three-dimensional
protein NMR experiments to a few minutes. Journal of the American Chemical Society.
128(28), 9042–9043.
mla: Schanda, Paul, et al. “Speeding up Three-Dimensional Protein NMR Experiments
to a Few Minutes.” Journal of the American Chemical Society, vol. 128,
no. 28, American Chemical Society, 2006, pp. 9042–43, doi:10.1021/ja062025p.
short: P. Schanda, H. Van Melckebeke, B. Brutscher, Journal of the American Chemical
Society 128 (2006) 9042–9043.
date_created: 2020-09-18T10:13:36Z
date_published: 2006-06-21T00:00:00Z
date_updated: 2021-01-12T08:19:37Z
day: '21'
doi: 10.1021/ja062025p
extern: '1'
intvolume: ' 128'
issue: '28'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '06'
oa_version: None
page: 9042-9043
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Speeding up three-dimensional protein NMR experiments to a few minutes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2006'
...
---
_id: '8489'
abstract:
- lang: eng
text: Structure elucidation of proteins by either NMR or X‐ray crystallography often
requires the screening of a large number of samples for promising protein constructs
and optimum solution conditions. For large‐scale screening of protein samples
in solution, robust methods are needed that allow a rapid assessment of the folding
of a polypeptide under diverse sample conditions. Here we present HET‐SOFAST NMR,
a highly sensitive new method for semi‐quantitative characterization of the structural
compactness and heterogeneity of polypeptide chains in solution. On the basis
of one‐dimensional 1H HET‐SOFAST NMR data, obtained on well‐folded, molten globular,
partially‐ and completely unfolded proteins, we define empirical thresholds that
can be used as quantitative benchmarks for protein compactness. For 15N‐enriched
protein samples, two‐dimensional 1H‐15N HET‐SOFAST correlation spectra provide
site‐specific information about the structural heterogeneity along the polypeptide
chain.
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: Vincent
full_name: Forge, Vincent
last_name: Forge
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Schanda P, Forge V, Brutscher B. HET-SOFAST NMR for fast detection of structural
compactness and heterogeneity along polypeptide chains. Magnetic Resonance
in Chemistry. 2006;44(S1):S177-S184. doi:10.1002/mrc.1825
apa: Schanda, P., Forge, V., & Brutscher, B. (2006). HET-SOFAST NMR for fast
detection of structural compactness and heterogeneity along polypeptide chains.
Magnetic Resonance in Chemistry. Wiley. https://doi.org/10.1002/mrc.1825
chicago: Schanda, Paul, Vincent Forge, and Bernhard Brutscher. “HET-SOFAST NMR for
Fast Detection of Structural Compactness and Heterogeneity along Polypeptide Chains.”
Magnetic Resonance in Chemistry. Wiley, 2006. https://doi.org/10.1002/mrc.1825.
ieee: P. Schanda, V. Forge, and B. Brutscher, “HET-SOFAST NMR for fast detection
of structural compactness and heterogeneity along polypeptide chains,” Magnetic
Resonance in Chemistry, vol. 44, no. S1. Wiley, pp. S177–S184, 2006.
ista: Schanda P, Forge V, Brutscher B. 2006. HET-SOFAST NMR for fast detection of
structural compactness and heterogeneity along polypeptide chains. Magnetic Resonance
in Chemistry. 44(S1), S177–S184.
mla: Schanda, Paul, et al. “HET-SOFAST NMR for Fast Detection of Structural Compactness
and Heterogeneity along Polypeptide Chains.” Magnetic Resonance in Chemistry,
vol. 44, no. S1, Wiley, 2006, pp. S177–84, doi:10.1002/mrc.1825.
short: P. Schanda, V. Forge, B. Brutscher, Magnetic Resonance in Chemistry 44 (2006)
S177–S184.
date_created: 2020-09-18T10:13:42Z
date_published: 2006-07-06T00:00:00Z
date_updated: 2021-01-12T08:19:37Z
day: '06'
doi: 10.1002/mrc.1825
extern: '1'
intvolume: ' 44'
issue: S1
language:
- iso: eng
month: '07'
oa_version: None
page: S177-S184
publication: Magnetic Resonance in Chemistry
publication_identifier:
issn:
- 0749-1581
- 1097-458X
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: HET-SOFAST NMR for fast detection of structural compactness and heterogeneity
along polypeptide chains
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2006'
...
---
_id: '8490'
abstract:
- lang: eng
text: We demonstrate the feasibility of recording 1H–15N correlation spectra of
proteins in only one second of acquisition time. The experiment combines recently
proposed SOFAST-HMQC with Hadamard-type 15N frequency encoding. This allows site-resolved
real-time NMR studies of kinetic processes in proteins with an increased time
resolution. The sensitivity of the experiment is sufficient to be applicable to
a wide range of molecular systems available at millimolar concentration on a high
magnetic field spectrometer.
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
citation:
ama: Schanda P, Brutscher B. Hadamard frequency-encoded SOFAST-HMQC for ultrafast
two-dimensional protein NMR. Journal of Magnetic Resonance. 2006;178(2):334-339.
doi:10.1016/j.jmr.2005.10.007
apa: Schanda, P., & Brutscher, B. (2006). Hadamard frequency-encoded SOFAST-HMQC
for ultrafast two-dimensional protein NMR. Journal of Magnetic Resonance.
Elsevier. https://doi.org/10.1016/j.jmr.2005.10.007
chicago: Schanda, Paul, and Bernhard Brutscher. “Hadamard Frequency-Encoded SOFAST-HMQC
for Ultrafast Two-Dimensional Protein NMR.” Journal of Magnetic Resonance.
Elsevier, 2006. https://doi.org/10.1016/j.jmr.2005.10.007.
ieee: P. Schanda and B. Brutscher, “Hadamard frequency-encoded SOFAST-HMQC for ultrafast
two-dimensional protein NMR,” Journal of Magnetic Resonance, vol. 178,
no. 2. Elsevier, pp. 334–339, 2006.
ista: Schanda P, Brutscher B. 2006. Hadamard frequency-encoded SOFAST-HMQC for ultrafast
two-dimensional protein NMR. Journal of Magnetic Resonance. 178(2), 334–339.
mla: Schanda, Paul, and Bernhard Brutscher. “Hadamard Frequency-Encoded SOFAST-HMQC
for Ultrafast Two-Dimensional Protein NMR.” Journal of Magnetic Resonance,
vol. 178, no. 2, Elsevier, 2006, pp. 334–39, doi:10.1016/j.jmr.2005.10.007.
short: P. Schanda, B. Brutscher, Journal of Magnetic Resonance 178 (2006) 334–339.
date_created: 2020-09-18T10:13:51Z
date_published: 2006-02-01T00:00:00Z
date_updated: 2021-01-12T08:19:38Z
day: '01'
doi: 10.1016/j.jmr.2005.10.007
extern: '1'
intvolume: ' 178'
issue: '2'
keyword:
- Nuclear and High Energy Physics
- Biophysics
- Biochemistry
- Condensed Matter Physics
language:
- iso: eng
month: '02'
oa_version: None
page: 334-339
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
status: public
title: Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein
NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 178
year: '2006'
...
---
_id: '8513'
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: Maria
full_name: Saprykina, Maria
last_name: Saprykina
citation:
ama: Kaloshin V, Saprykina M. Generic 3-dimensional volume-preserving diffeomorphisms
with superexponential growth of number of periodic orbits. Discrete & Continuous
Dynamical Systems - A. 2006;15(2):611-640. doi:10.3934/dcds.2006.15.611
apa: Kaloshin, V., & Saprykina, M. (2006). Generic 3-dimensional volume-preserving
diffeomorphisms with superexponential growth of number of periodic orbits. Discrete
& Continuous Dynamical Systems - A. American Institute of Mathematical
Sciences (AIMS). https://doi.org/10.3934/dcds.2006.15.611
chicago: Kaloshin, Vadim, and Maria Saprykina. “Generic 3-Dimensional Volume-Preserving
Diffeomorphisms with Superexponential Growth of Number of Periodic Orbits.” Discrete
& Continuous Dynamical Systems - A. American Institute of Mathematical
Sciences (AIMS), 2006. https://doi.org/10.3934/dcds.2006.15.611.
ieee: V. Kaloshin and M. Saprykina, “Generic 3-dimensional volume-preserving diffeomorphisms
with superexponential growth of number of periodic orbits,” Discrete &
Continuous Dynamical Systems - A, vol. 15, no. 2. American Institute of Mathematical
Sciences (AIMS), pp. 611–640, 2006.
ista: Kaloshin V, Saprykina M. 2006. Generic 3-dimensional volume-preserving diffeomorphisms
with superexponential growth of number of periodic orbits. Discrete & Continuous
Dynamical Systems - A. 15(2), 611–640.
mla: Kaloshin, Vadim, and Maria Saprykina. “Generic 3-Dimensional Volume-Preserving
Diffeomorphisms with Superexponential Growth of Number of Periodic Orbits.” Discrete
& Continuous Dynamical Systems - A, vol. 15, no. 2, American Institute
of Mathematical Sciences (AIMS), 2006, pp. 611–40, doi:10.3934/dcds.2006.15.611.
short: V. Kaloshin, M. Saprykina, Discrete & Continuous Dynamical Systems -
A 15 (2006) 611–640.
date_created: 2020-09-18T10:48:43Z
date_published: 2006-05-01T00:00:00Z
date_updated: 2021-01-12T08:19:48Z
day: '01'
doi: 10.3934/dcds.2006.15.611
extern: '1'
intvolume: ' 15'
issue: '2'
language:
- iso: eng
month: '05'
oa_version: None
page: 611-640
publication: Discrete & Continuous Dynamical Systems - A
publication_identifier:
issn:
- 1553-5231
publication_status: published
publisher: American Institute of Mathematical Sciences (AIMS)
quality_controlled: '1'
status: public
title: Generic 3-dimensional volume-preserving diffeomorphisms with superexponential
growth of number of periodic orbits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2006'
...
---
_id: '8514'
abstract:
- lang: eng
text: We study the extent to which the Hausdorff dimension of a compact subset of
an infinite-dimensional Banach space is affected by a typical mapping into a finite-dimensional
space. It is possible that the dimension drops under all such mappings, but the
amount by which it typically drops is controlled by the ‘thickness exponent’ of
the set, which was defined by Hunt and Kaloshin (Nonlinearity12 (1999), 1263–1275).
More precisely, let $X$ be a compact subset of a Banach space $B$ with thickness
exponent $\tau$ and Hausdorff dimension $d$. Let $M$ be any subspace of the (locally)
Lipschitz functions from $B$ to $\mathbb{R}^{m}$ that contains the space of bounded
linear functions. We prove that for almost every (in the sense of prevalence)
function $f \in M$, the Hausdorff dimension of $f(X)$ is at least $\min\{ m, d
/ (1 + \tau) \}$. We also prove an analogous result for a certain part of the
dimension spectra of Borel probability measures supported on $X$. The factor $1
/ (1 + \tau)$ can be improved to $1 / (1 + \tau / 2)$ if $B$ is a Hilbert space.
Since dimension cannot increase under a (locally) Lipschitz function, these theorems
become dimension preservation results when $\tau = 0$. We conjecture that many
of the attractors associated with the evolution equations of mathematical physics
have thickness exponent zero. We also discuss the sharpness of our results in
the case $\tau > 0$.
article_processing_charge: No
article_type: original
author:
- first_name: WILLIAM
full_name: OTT, WILLIAM
last_name: OTT
- first_name: BRIAN
full_name: HUNT, BRIAN
last_name: HUNT
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: OTT W, HUNT B, Kaloshin V. The effect of projections on fractal sets and measures
in Banach spaces. Ergodic Theory and Dynamical Systems. 2006;26(3):869-891.
doi:10.1017/s0143385705000714
apa: OTT, W., HUNT, B., & Kaloshin, V. (2006). The effect of projections on
fractal sets and measures in Banach spaces. Ergodic Theory and Dynamical Systems.
Cambridge University Press. https://doi.org/10.1017/s0143385705000714
chicago: OTT, WILLIAM, BRIAN HUNT, and Vadim Kaloshin. “The Effect of Projections
on Fractal Sets and Measures in Banach Spaces.” Ergodic Theory and Dynamical
Systems. Cambridge University Press, 2006. https://doi.org/10.1017/s0143385705000714.
ieee: W. OTT, B. HUNT, and V. Kaloshin, “The effect of projections on fractal sets
and measures in Banach spaces,” Ergodic Theory and Dynamical Systems, vol.
26, no. 3. Cambridge University Press, pp. 869–891, 2006.
ista: OTT W, HUNT B, Kaloshin V. 2006. The effect of projections on fractal sets
and measures in Banach spaces. Ergodic Theory and Dynamical Systems. 26(3), 869–891.
mla: OTT, WILLIAM, et al. “The Effect of Projections on Fractal Sets and Measures
in Banach Spaces.” Ergodic Theory and Dynamical Systems, vol. 26, no. 3,
Cambridge University Press, 2006, pp. 869–91, doi:10.1017/s0143385705000714.
short: W. OTT, B. HUNT, V. Kaloshin, Ergodic Theory and Dynamical Systems 26 (2006)
869–891.
date_created: 2020-09-18T10:48:52Z
date_published: 2006-06-01T00:00:00Z
date_updated: 2021-01-12T08:19:48Z
day: '01'
doi: 10.1017/s0143385705000714
extern: '1'
intvolume: ' 26'
issue: '3'
language:
- iso: eng
month: '06'
oa_version: None
page: 869-891
publication: Ergodic Theory and Dynamical Systems
publication_identifier:
issn:
- 0143-3857
- 1469-4417
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
status: public
title: The effect of projections on fractal sets and measures in Banach spaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2006'
...
---
_id: '8515'
abstract:
- lang: eng
text: "We consider the evolution of a set carried by a space periodic incompressible
stochastic flow in a Euclidean space. We\r\nreport on three main results obtained
in [8, 9, 10] concerning long time behaviour for a typical realization of the
stochastic flow. First, at time t most of the particles are at a distance of order
√t away from the origin. Moreover, we prove a Central Limit Theorem for the evolution
of a measure carried by the flow, which holds for almost every realization of
the flow. Second, we show the existence of a zero measure full Hausdorff dimension
set of points, which\r\nescape to infinity at a linear rate. Third, in the 2-dimensional
case, we study the set of points visited by the original set by time t. Such a
set, when scaled down by the factor of t, has a limiting non random shape."
article_processing_charge: No
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: D.
full_name: DOLGOPYAT, D.
last_name: DOLGOPYAT
- first_name: L.
full_name: KORALOV, L.
last_name: KORALOV
citation:
ama: 'Kaloshin V, DOLGOPYAT D, KORALOV L. Long time behaviour of periodic stochastic
flows. In: XIVth International Congress on Mathematical Physics. World
Scientific; 2006:290-295. doi:10.1142/9789812704016_0026'
apa: 'Kaloshin, V., DOLGOPYAT, D., & KORALOV, L. (2006). Long time behaviour
of periodic stochastic flows. In XIVth International Congress on Mathematical
Physics (pp. 290–295). Lisbon, Portugal: World Scientific. https://doi.org/10.1142/9789812704016_0026'
chicago: Kaloshin, Vadim, D. DOLGOPYAT, and L. KORALOV. “Long Time Behaviour of
Periodic Stochastic Flows.” In XIVth International Congress on Mathematical
Physics, 290–95. World Scientific, 2006. https://doi.org/10.1142/9789812704016_0026.
ieee: V. Kaloshin, D. DOLGOPYAT, and L. KORALOV, “Long time behaviour of periodic
stochastic flows,” in XIVth International Congress on Mathematical Physics,
Lisbon, Portugal, 2006, pp. 290–295.
ista: Kaloshin V, DOLGOPYAT D, KORALOV L. 2006. Long time behaviour of periodic
stochastic flows. XIVth International Congress on Mathematical Physics. International
Congress on Mathematical Physics, 290–295.
mla: Kaloshin, Vadim, et al. “Long Time Behaviour of Periodic Stochastic Flows.”
XIVth International Congress on Mathematical Physics, World Scientific,
2006, pp. 290–95, doi:10.1142/9789812704016_0026.
short: V. Kaloshin, D. DOLGOPYAT, L. KORALOV, in:, XIVth International Congress
on Mathematical Physics, World Scientific, 2006, pp. 290–295.
conference:
end_date: 2003-08-02
location: Lisbon, Portugal
name: International Congress on Mathematical Physics
start_date: 2003-07-28
date_created: 2020-09-18T10:48:59Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T08:19:49Z
day: '01'
doi: 10.1142/9789812704016_0026
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 290-295
publication: XIVth International Congress on Mathematical Physics
publication_identifier:
isbn:
- '9789812562012'
- '9789812704016'
publication_status: published
publisher: World Scientific
quality_controlled: '1'
status: public
title: Long time behaviour of periodic stochastic flows
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2006'
...
---
_id: '854'
abstract:
- lang: eng
text: Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius),
and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants
remain unresolved. Here, we report the sequence of the complete mitochondrial
genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved
remains from the Pleistocene epoch - the oldest mitochondrial genome sequence
determined to date. We demonstrate that well-preserved mitochondrial genome fragments,
as long as ∼1,600-1700 base pairs, can be retrieved from pre-Holocene remains
of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests
that M. primigenius and E. maximus are sister species that diverged soon after
their common ancestor split from the L. africana lineage. Low nucleotide diversity
found between independently determined mitochondrial genomic sequences of woolly
mammoths separated geographically and in time suggests that north-eastern Siberia
was occupied by a relatively homogeneous population of M. primigenius throughout
the late Pleistocene.
acknowledgement: |-
FAK is supported by the NSF Graduate Research Fellowship.
We thank the Natural History Museum, North-Eastern Research Center, Far Eastern Branch of the Russian Academy of Sciences for photographic material ofM. primigenius leg, V. A. Nikishina for artwork and technical support, Y.B. Yurov, G. Dvoryanchikov, N. Riazanskaya and T. Kolesnikova for technical support, K. Mehren and C. Gray for elephant specimens, and V. Y. Solovyev for help with artwork of animal images.
author:
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
- first_name: Yuri
full_name: Moliaka, Yuri K
last_name: Moliaka
- first_name: Boris
full_name: Malyarchuk, Boris A
last_name: Malyarchuk
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Miroslava
full_name: Derenko, Miroslava V
last_name: Derenko
- first_name: Ilya
full_name: Chumakov, Ilya M
last_name: Chumakov
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
citation:
ama: Rogaev E, Moliaka Y, Malyarchuk B, et al. Complete mitochondrial genome and
phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 2006;4(3):0403-0410.
doi:10.1371/journal.pbio.0040073
apa: Rogaev, E., Moliaka, Y., Malyarchuk, B., Kondrashov, F., Derenko, M., Chumakov,
I., & Grigorenko, A. (2006). Complete mitochondrial genome and phylogeny of
pleistocene mammoth Mammuthus primigenius. PLoS Biology. Public Library
of Science. https://doi.org/10.1371/journal.pbio.0040073
chicago: Rogaev, Evgeny, Yuri Moliaka, Boris Malyarchuk, Fyodor Kondrashov, Miroslava
Derenko, Ilya Chumakov, and Anastasia Grigorenko. “Complete Mitochondrial Genome
and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology.
Public Library of Science, 2006. https://doi.org/10.1371/journal.pbio.0040073.
ieee: E. Rogaev et al., “Complete mitochondrial genome and phylogeny of pleistocene
mammoth Mammuthus primigenius,” PLoS Biology, vol. 4, no. 3. Public Library
of Science, pp. 0403–0410, 2006.
ista: Rogaev E, Moliaka Y, Malyarchuk B, Kondrashov F, Derenko M, Chumakov I, Grigorenko
A. 2006. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus
primigenius. PLoS Biology. 4(3), 0403–0410.
mla: Rogaev, Evgeny, et al. “Complete Mitochondrial Genome and Phylogeny of Pleistocene
Mammoth Mammuthus Primigenius.” PLoS Biology, vol. 4, no. 3, Public Library
of Science, 2006, pp. 0403–10, doi:10.1371/journal.pbio.0040073.
short: E. Rogaev, Y. Moliaka, B. Malyarchuk, F. Kondrashov, M. Derenko, I. Chumakov,
A. Grigorenko, PLoS Biology 4 (2006) 0403–0410.
date_created: 2018-12-11T11:48:51Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T08:19:58Z
day: '01'
doi: 10.1371/journal.pbio.0040073
extern: 1
intvolume: ' 4'
issue: '3'
month: '03'
page: 0403 - 0410
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6794'
quality_controlled: 0
status: public
title: Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus
primigenius
type: journal_article
volume: 4
year: '2006'
...
---
_id: '868'
abstract:
- lang: eng
text: 'Background: The glyoxylate cycle is thought to be present in bacteria, protists,
plants, fungi, and nematodes, but not in other Metazoa. However, activity of the
glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in
animal tissues has been reported. In order to clarify the status of the MS and
ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic
study. Results: Using sequence similarity searches, we identified MS genes in
arthropods, echinoderms, and vertebrates, including platypus and opossum, but
not in the numerous sequenced genomes of placental mammals. The regions of the
placental mammals'' genomes expected to code for malate synthase, as determined
by comparison of the gene orders in vertebrate genomes, show clear similarity
to the opossum MS sequence but contain stop codons, indicating that the MS gene
became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable
in animals other than the nematodes that possess a bifunctional, fused ICL-MS
gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal
gene transfer events that probably went in both directions between several bacterial
and eukaryotic lineages. The strongest evidence was obtained for the acquisition
of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the
corresponding operonic organization by the common ancestor of the nematodes. Conclusion:
The distribution of the MS and ICL genes in animals suggests that either they
encode alternative enzymes of the glyoxylate cycle that are not orthologous to
the known MS and ICL or the animal MS acquired a new function that remains to
be characterized. Regardless of the ultimate solution to this conundrum, the genes
for the glyoxylate cycle enzymes present a remarkable variety of evolutionary
events including unusual horizontal gene transfer from bacteria to animals.'
acknowledgement: The authors thank Alexey Kondrashov for suggesting the possibility
of non- orthologous gene displacement in glyoxylate cycle specific enzymes and for
critical reading of this manuscript. FAK is a National Science Foundation Graduate
Fellow.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
- first_name: Igor
full_name: Morgunov, Igor G
last_name: Morgunov
- first_name: Tatiana
full_name: Finogenova, Tatiana V
last_name: Finogenova
- first_name: Marie
full_name: Kondrashova, Marie N
last_name: Kondrashova
citation:
ama: Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. Evolution
of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer
events and pseudogene formation. Biology Direct. 2006;1. doi:10.1186/1745-6150-1-31
apa: Kondrashov, F., Koonin, E., Morgunov, I., Finogenova, T., & Kondrashova,
M. (2006). Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple
horizontal transfer events and pseudogene formation. Biology Direct. BioMed
Central. https://doi.org/10.1186/1745-6150-1-31
chicago: Kondrashov, Fyodor, Eugene Koonin, Igor Morgunov, Tatiana Finogenova, and
Marie Kondrashova. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence
of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology Direct.
BioMed Central, 2006. https://doi.org/10.1186/1745-6150-1-31.
ieee: F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, and M. Kondrashova,
“Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal
transfer events and pseudogene formation,” Biology Direct, vol. 1. BioMed
Central, 2006.
ista: Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. 2006. Evolution
of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer
events and pseudogene formation. Biology Direct. 1.
mla: Kondrashov, Fyodor, et al. “Evolution of Glyoxylate Cycle Enzymes in Metazoa
Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology
Direct, vol. 1, BioMed Central, 2006, doi:10.1186/1745-6150-1-31.
short: F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, M. Kondrashova, Biology
Direct 1 (2006).
date_created: 2018-12-11T11:48:56Z
date_published: 2006-10-23T00:00:00Z
date_updated: 2021-01-12T08:20:31Z
day: '23'
doi: 10.1186/1745-6150-1-31
extern: 1
intvolume: ' 1'
license: https://creativecommons.org/licenses/by/4.0/
month: '10'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6778'
quality_controlled: 0
status: public
title: Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal
transfer events and pseudogene formation
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: 1
year: '2006'
...
---
_id: '869'
abstract:
- lang: eng
text: The impact of synonymous nucleotide substitutions on fitness in mammals remains
controversial. Despite some indications of selective constraint, synonymous sites
are often assumed to be neutral, and the rate of their evolution is used as a
proxy for mutation rate. We subdivide all sites into four classes in terms of
the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold
synonymous sites and intron sites residing outside transposable elements. The
distribution of the rate of evolution across all synonymous sites is trimodal.
Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed
by G, is ∼10% below that at such intron sites. In contrast, rate of evolution
at postCpreG synonymous sites is ∼30% above that at such intron sites. Finally,
synonymous and intron postC and preG sites evolve at similar rates. The relationship
between the levels of polymorphism at the corresponding synonymous and intron
sites is very similar to that between their rates of evolution. Within every class,
synonymous sites are occupied by G or C much more often than intron sites, whose
nucleotide composition is consistent with neutral mutation-drift equilibrium.
These patterns suggest that synonymous sites are under weak selection in favor
of G and C, with the average coefficient s∼0.25/Ne∼10-5, where Ne is the effective
population size. Such selection decelerates evolution and reduces variability
at sites with symmetric mutation, but has the opposite effects at sites where
the favored nucleotides are more mutable. The amino-acid composition of proteins
dictates that many synonymous sites are CpGprone, which causes them, on average,
to evolve faster and to be more polymorphic than intron sites. An average genotype
carries ∼107 suboptimal nucleotides at synonymous sites, implying synergistic
epistasis in selection against them.
acknowledgement: This research was supported in part by the Intramural Research Program
of the NIH, National Library of Medicine.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Aleksey
full_name: Ogurtsov, Aleksey Yu
last_name: Ogurtsov
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Kondrashov F, Ogurtsov A, Kondrashov A. Selection in favor of nucleotides G
and C diversifies evolution rates and levels of polymorphism at mammalian synonymous
sites. Journal of Theoretical Biology. 2006;240(4):616-626. doi:10.1016/j.jtbi.2005.10.020
apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2006). Selection in favor
of nucleotides G and C diversifies evolution rates and levels of polymorphism
at mammalian synonymous sites. Journal of Theoretical Biology. Elsevier.
https://doi.org/10.1016/j.jtbi.2005.10.020
chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Selection
in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism
at Mammalian Synonymous Sites.” Journal of Theoretical Biology. Elsevier,
2006. https://doi.org/10.1016/j.jtbi.2005.10.020.
ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Selection in favor of nucleotides
G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous
sites,” Journal of Theoretical Biology, vol. 240, no. 4. Elsevier, pp.
616–626, 2006.
ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2006. Selection in favor of nucleotides
G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous
sites. Journal of Theoretical Biology. 240(4), 616–626.
mla: Kondrashov, Fyodor, et al. “Selection in Favor of Nucleotides G and C Diversifies
Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” Journal
of Theoretical Biology, vol. 240, no. 4, Elsevier, 2006, pp. 616–26, doi:10.1016/j.jtbi.2005.10.020.
short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Journal of Theoretical Biology
240 (2006) 616–626.
date_created: 2018-12-11T11:48:56Z
date_published: 2006-06-21T00:00:00Z
date_updated: 2021-01-12T08:20:33Z
day: '21'
doi: 10.1016/j.jtbi.2005.10.020
extern: 1
intvolume: ' 240'
issue: '4'
month: '06'
page: 616 - 626
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '6779'
quality_controlled: 0
status: public
title: Selection in favor of nucleotides G and C diversifies evolution rates and levels
of polymorphism at mammalian synonymous sites
type: journal_article
volume: 240
year: '2006'
...
---
_id: '873'
abstract:
- lang: eng
text: New genes commonly appear through complete or partial duplications of pre-existing
genes. Duplications of long DNA segments are constantly produced by rare mutations,
may become fixed in a population by selection or random drift, and are subject
to divergent evolution of the paralogous sequences after fixation, although gene
conversion can impede this process. New data shed some light on each of these
processes. Mutations which involve duplications can occur through at least two
different mechanisms, backward strand slippage during DNA replication and unequal
crossing-over. The background rate of duplication of a complete gene in humans
is 10-9-10-10 per generation, although many genes located within hot-spots of
large-scale mutation are duplicated much more often. Many gene duplications affect
fitness strongly, and are responsible, through gene dosage effects, for a number
of genetic diseases. However, high levels of intrapopulation polymorphism caused
by presence or absence of long, gene-containing DNA segments imply that some duplications
are not under strong selection. The polymorphism to fixation ratios appear to
be approximately the same for gene duplications and for presumably selectively
neutral nucleotide substitutions, which, according to the McDonald-Kreitman test,
is consistent with selective neutrality of duplications. However, this pattern
can also be due to negative selection against most of segregating duplications
and positive selection for at least some duplications which become fixed. Patterns
in post-fixation evolution of duplicated genes do not easily reveal the causes
of fixations. Many gene duplications which became fixed recently in a variety
of organisms were positively selected because the increased expression of the
corresponding genes was beneficial. The effects of gene dosage provide a unified
framework for studying all phases of the life history of a gene duplication. Application
of well-known methods of evolutionary genetics to accumulating data on new, polymorphic,
and fixed duplication will enhance our understanding of the role of natural selection
in the evolution by gene duplication.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Kondrashov F, Kondrashov A. Role of selection in fixation of gene duplications.
Journal of Theoretical Biology. 2006;239(2):141-151. doi:10.1016/j.jtbi.2005.08.033
apa: Kondrashov, F., & Kondrashov, A. (2006). Role of selection in fixation
of gene duplications. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.08.033
chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation
of Gene Duplications.” Journal of Theoretical Biology. Elsevier, 2006.
https://doi.org/10.1016/j.jtbi.2005.08.033.
ieee: F. Kondrashov and A. Kondrashov, “Role of selection in fixation of gene duplications,”
Journal of Theoretical Biology, vol. 239, no. 2. Elsevier, pp. 141–151,
2006.
ista: Kondrashov F, Kondrashov A. 2006. Role of selection in fixation of gene duplications.
Journal of Theoretical Biology. 239(2), 141–151.
mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of
Gene Duplications.” Journal of Theoretical Biology, vol. 239, no. 2, Elsevier,
2006, pp. 141–51, doi:10.1016/j.jtbi.2005.08.033.
short: F. Kondrashov, A. Kondrashov, Journal of Theoretical Biology 239 (2006) 141–151.
date_created: 2018-12-11T11:48:57Z
date_published: 2006-03-21T00:00:00Z
date_updated: 2021-01-12T08:20:47Z
day: '21'
doi: 10.1016/j.jtbi.2005.08.033
extern: 1
intvolume: ' 239'
issue: '2'
month: '03'
page: 141 - 151
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '6773'
quality_controlled: 0
status: public
title: Role of selection in fixation of gene duplications
type: journal_article
volume: 239
year: '2006'
...
---
_id: '1715'
abstract:
- lang: eng
text: 'Background: Cell-to-cell communication at the synapse involves synaptic transmission
as well as signaling mediated by growth factors, which provide developmental and
plasticity cues. There is evidence that a retrograde, presynaptic transforming
growth factor-β (TGF-β) signaling event regulates synapse development and function
in Drosophila. Results: Here we show that a postsynaptic TGF-β signaling event
occurs during larval development. The type I receptor Thick veins (Tkv) and the
R-Smad transcription factor Mothers-against-dpp (Mad) are localized postsynaptically
in the muscle. Furthermore, Mad phosphorylation occurs in regions facing the presynaptic
active zones of neurotransmitter release within the postsynaptic subsynaptic reticulum
(SSR). In order to monitor in real time the levels of TGF-β signaling in the synapse
during synaptic transmission, we have established a FRAP assay to measure Mad
nuclear import/export in the muscle. We show that Mad nuclear trafficking depends
on stimulation of the muscle. Conclusions: Our data suggest a mechanism linking
synaptic transmission and postsynaptic TGF-β signaling that may coordinate nerve-muscle
development and function.'
acknowledgement: This work was supported by the Max Planck Society, HFSP, and Deutsche
Forschungsgemeinschaft.
article_processing_charge: No
author:
- first_name: Veronika
full_name: Dudu, Veronika
last_name: Dudu
- first_name: Thomas
full_name: Bittig, Thomas
last_name: Bittig
- first_name: Eugeni
full_name: Entchev, Eugeni
last_name: Entchev
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Marcos
full_name: González Gaitán, Marcos
last_name: González Gaitán
citation:
ama: Dudu V, Bittig T, Entchev E, Kicheva A, Julicher F, González Gaitán M. Postsynaptic
mad signaling at the Drosophila neuromuscular junction. Current Biology.
2006;16(7):625-635. doi:10.1016/j.cub.2006.02.061
apa: Dudu, V., Bittig, T., Entchev, E., Kicheva, A., Julicher, F., & González
Gaitán, M. (2006). Postsynaptic mad signaling at the Drosophila neuromuscular
junction. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2006.02.061
chicago: Dudu, Veronika, Thomas Bittig, Eugeni Entchev, Anna Kicheva, Frank Julicher,
and Marcos González Gaitán. “Postsynaptic Mad Signaling at the Drosophila Neuromuscular
Junction.” Current Biology. Cell Press, 2006. https://doi.org/10.1016/j.cub.2006.02.061.
ieee: V. Dudu, T. Bittig, E. Entchev, A. Kicheva, F. Julicher, and M. González Gaitán,
“Postsynaptic mad signaling at the Drosophila neuromuscular junction,” Current
Biology, vol. 16, no. 7. Cell Press, pp. 625–635, 2006.
ista: Dudu V, Bittig T, Entchev E, Kicheva A, Julicher F, González Gaitán M. 2006.
Postsynaptic mad signaling at the Drosophila neuromuscular junction. Current Biology.
16(7), 625–635.
mla: Dudu, Veronika, et al. “Postsynaptic Mad Signaling at the Drosophila Neuromuscular
Junction.” Current Biology, vol. 16, no. 7, Cell Press, 2006, pp. 625–35,
doi:10.1016/j.cub.2006.02.061.
short: V. Dudu, T. Bittig, E. Entchev, A. Kicheva, F. Julicher, M. González Gaitán,
Current Biology 16 (2006) 625–635.
date_created: 2018-12-11T11:53:37Z
date_published: 2006-04-04T00:00:00Z
date_updated: 2021-11-16T07:44:15Z
day: '04'
doi: 10.1016/j.cub.2006.02.061
extern: '1'
intvolume: ' 16'
issue: '7'
language:
- iso: eng
month: '04'
oa_version: None
page: 625 - 635
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5416'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1016/j.cub.2006.06.020
status: public
title: Postsynaptic mad signaling at the Drosophila neuromuscular junction
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 16
year: '2006'
...
---
_id: '1745'
abstract:
- lang: eng
text: SiGe islands grown by deposition of 10 monolayers of Ge on Si(0 0 1) at 740
°C were investigated by using a combination of selective wet chemical etching
and atomic force microscopy. The used etchant, a solution consisting of ammonium
hydroxide and hydrogen peroxide, shows a high selectivity of Ge over SixGe1-x
and is characterized by relatively slow etching rates for Si-rich alloys. By performing
successive etching experiments on the same sample area, we are able to gain a
deeper insight into the lateral displacement the islands undergo during post growth
annealing.
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Hans
full_name: Von Känel, Hans
last_name: Von Känel
- first_name: Alexander
full_name: Bittner, Alexander M
last_name: Bittner
- first_name: Jerry
full_name: Tersoff, Jerry
last_name: Tersoff
- first_name: Ulrich
full_name: Denker, Ulrich
last_name: Denker
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
citation:
ama: Katsaros G, Rastelli A, Stoffel M, et al. Investigating the lateral motion
of SiGe islands by selective chemical etching. Surface Science. 2006;600(12):2608-2613.
doi:10.1016/j.susc.2006.04.027
apa: Katsaros, G., Rastelli, A., Stoffel, M., Isella, G., Von Känel, H., Bittner,
A., … Kern, K. (2006). Investigating the lateral motion of SiGe islands by selective
chemical etching. Surface Science. Elsevier. https://doi.org/10.1016/j.susc.2006.04.027
chicago: Katsaros, Georgios, Armando Rastelli, Mathieu Stoffel, Giovanni Isella,
Hans Von Känel, Alexander Bittner, Jerry Tersoff, et al. “Investigating the Lateral
Motion of SiGe Islands by Selective Chemical Etching.” Surface Science.
Elsevier, 2006. https://doi.org/10.1016/j.susc.2006.04.027.
ieee: G. Katsaros et al., “Investigating the lateral motion of SiGe islands
by selective chemical etching,” Surface Science, vol. 600, no. 12. Elsevier,
pp. 2608–2613, 2006.
ista: Katsaros G, Rastelli A, Stoffel M, Isella G, Von Känel H, Bittner A, Tersoff
J, Denker U, Schmidt O, Costantini G, Kern K. 2006. Investigating the lateral
motion of SiGe islands by selective chemical etching. Surface Science. 600(12),
2608–2613.
mla: Katsaros, Georgios, et al. “Investigating the Lateral Motion of SiGe Islands
by Selective Chemical Etching.” Surface Science, vol. 600, no. 12, Elsevier,
2006, pp. 2608–13, doi:10.1016/j.susc.2006.04.027.
short: G. Katsaros, A. Rastelli, M. Stoffel, G. Isella, H. Von Känel, A. Bittner,
J. Tersoff, U. Denker, O. Schmidt, G. Costantini, K. Kern, Surface Science 600
(2006) 2608–2613.
date_created: 2018-12-11T11:53:47Z
date_published: 2006-06-15T00:00:00Z
date_updated: 2021-01-12T06:52:56Z
day: '15'
doi: 10.1016/j.susc.2006.04.027
extern: 1
intvolume: ' 600'
issue: '12'
month: '06'
page: 2608 - 2613
publication: Surface Science
publication_status: published
publisher: Elsevier
publist_id: '5379'
quality_controlled: 0
status: public
title: Investigating the lateral motion of SiGe islands by selective chemical etching
type: journal_article
volume: 600
year: '2006'
...
---
_id: '1746'
abstract:
- lang: eng
text: 'A microscopic picture for the GaAs overgrowth of self-organized InAs/GaAs(001)
quantum dots is developed. Scanning tunneling microscopy measurements reveal two
capping regimes: the first being characterized by a dot shrinking and a backward
pyramid-to-dome shape transition. This regime is governed by fast dynamics resulting
in island morphologies close to thermodynamic equilibrium. The second regime is
marked by a true overgrowth and is controlled by kinetically limited surface diffusion
processes. A simple model is developed to describe the observed structural changes
which are rationalized in terms of energetic minimization driven by lattice mismatch
and alloying.'
author:
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Carlos
full_name: Manzano, Carlos
last_name: Manzano
- first_name: P
full_name: Acosta-Diaz, P
last_name: Acosta Diaz
- first_name: Rudeeson
full_name: Songmuang, Rudeeson
last_name: Songmuang
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
citation:
ama: Costantini G, Rastelli A, Manzano C, et al. Interplay between thermodynamics
and kinetics in the capping of InAs/GaAs (001) quantum dots. Physical Review
Letters. 2006;96(22). doi:10.1103/PhysRevLett.96.226106
apa: Costantini, G., Rastelli, A., Manzano, C., Acosta Diaz, P., Songmuang, R.,
Katsaros, G., … Kern, K. (2006). Interplay between thermodynamics and kinetics
in the capping of InAs/GaAs (001) quantum dots. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.96.226106
chicago: Costantini, Giovanni, Armando Rastelli, Carlos Manzano, P Acosta Diaz,
Rudeeson Songmuang, Georgios Katsaros, Oliver Schmidt, and Klaus Kern. “Interplay
between Thermodynamics and Kinetics in the Capping of InAs/GaAs (001) Quantum
Dots.” Physical Review Letters. American Physical Society, 2006. https://doi.org/10.1103/PhysRevLett.96.226106.
ieee: G. Costantini et al., “Interplay between thermodynamics and kinetics
in the capping of InAs/GaAs (001) quantum dots,” Physical Review Letters,
vol. 96, no. 22. American Physical Society, 2006.
ista: Costantini G, Rastelli A, Manzano C, Acosta Diaz P, Songmuang R, Katsaros
G, Schmidt O, Kern K. 2006. Interplay between thermodynamics and kinetics in the
capping of InAs/GaAs (001) quantum dots. Physical Review Letters. 96(22).
mla: Costantini, Giovanni, et al. “Interplay between Thermodynamics and Kinetics
in the Capping of InAs/GaAs (001) Quantum Dots.” Physical Review Letters,
vol. 96, no. 22, American Physical Society, 2006, doi:10.1103/PhysRevLett.96.226106.
short: G. Costantini, A. Rastelli, C. Manzano, P. Acosta Diaz, R. Songmuang, G.
Katsaros, O. Schmidt, K. Kern, Physical Review Letters 96 (2006).
date_created: 2018-12-11T11:53:47Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:56Z
day: '01'
doi: 10.1103/PhysRevLett.96.226106
extern: 1
intvolume: ' 96'
issue: '22'
month: '01'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5378'
quality_controlled: 0
status: public
title: Interplay between thermodynamics and kinetics in the capping of InAs/GaAs (001)
quantum dots
type: journal_article
volume: 96
year: '2006'
...
---
_id: '1747'
abstract:
- lang: eng
text: 'We report on recent advances in the understanding of surface processes occurring
during growth and post-growth annealing of strained islands which may find application
as self-assembled quantum dots. We investigate the model system SiGe/Si(0 0 1)
by a new approach based on "reading the footprints" which islands leave
on the substrate during their growth and evolution. Such footprints consist of
trenches carved in the Si substrate. We distinguish between surface footprints
and footprints buried below the islands. The former allow us to discriminate islands
which are in the process of growing from those which are shrinking. Islands with
steep morphologies grow at the expense of smaller and shallower islands, consistent
with the kinetics of anomalous coarsening. While shrinking, islands change their
shape according to thermodynamic predictions. Buried footprints are investigated
by removing the SiGe epilayer by means of selective wet chemical etching. Their
reading shows that: (i) during post-growth annealing islands move laterally because
of surface-mediated Si-Ge intermixing; (ii) a tree-ring structure of trenches
is created by dislocated islands during their "cyclic" growth. This
allows us to distinguish coherent from dislocated islands and to establish whether
the latter are the result of island coalescence.'
acknowledgement: This work was supported by the BMBF (03N8711)
author:
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Jerry
full_name: Tersoff, Jerry
last_name: Tersoff
- first_name: Ulrich
full_name: Denker, Ulrich
last_name: Denker
- first_name: Tsvetelina
full_name: Merdzhanova, Tsvetelina
last_name: Merdzhanova
- first_name: Gouranga
full_name: Kar, Gouranga S
last_name: Kar
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
- first_name: Hans
full_name: Von Känel, Hans
last_name: Von Känel
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
citation:
ama: Rastelli A, Stoffel M, Katsaros G, et al. Reading the footprints of strained
islands. Microelectronics Journal. 2006;37(12):1471-1476. doi:10.1016/j.mejo.2006.05.029
apa: Rastelli, A., Stoffel, M., Katsaros, G., Tersoff, J., Denker, U., Merdzhanova,
T., … Schmidt, O. (2006). Reading the footprints of strained islands. Microelectronics
Journal. Elsevier. https://doi.org/10.1016/j.mejo.2006.05.029
chicago: Rastelli, Armando, Mathieu Stoffel, Georgios Katsaros, Jerry Tersoff, Ulrich
Denker, Tsvetelina Merdzhanova, Gouranga Kar, et al. “Reading the Footprints of
Strained Islands.” Microelectronics Journal. Elsevier, 2006. https://doi.org/10.1016/j.mejo.2006.05.029.
ieee: A. Rastelli et al., “Reading the footprints of strained islands,” Microelectronics
Journal, vol. 37, no. 12. Elsevier, pp. 1471–1476, 2006.
ista: Rastelli A, Stoffel M, Katsaros G, Tersoff J, Denker U, Merdzhanova T, Kar
G, Costantini G, Kern K, Von Känel H, Schmidt O. 2006. Reading the footprints
of strained islands. Microelectronics Journal. 37(12), 1471–1476.
mla: Rastelli, Armando, et al. “Reading the Footprints of Strained Islands.” Microelectronics
Journal, vol. 37, no. 12, Elsevier, 2006, pp. 1471–76, doi:10.1016/j.mejo.2006.05.029.
short: A. Rastelli, M. Stoffel, G. Katsaros, J. Tersoff, U. Denker, T. Merdzhanova,
G. Kar, G. Costantini, K. Kern, H. Von Känel, O. Schmidt, Microelectronics Journal
37 (2006) 1471–1476.
date_created: 2018-12-11T11:53:47Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T06:52:57Z
day: '01'
doi: 10.1016/j.mejo.2006.05.029
extern: 1
intvolume: ' 37'
issue: '12'
month: '12'
page: 1471 - 1476
publication: Microelectronics Journal
publication_status: published
publisher: Elsevier
publist_id: '5377'
quality_controlled: 0
status: public
title: Reading the footprints of strained islands
type: journal_article
volume: 37
year: '2006'
...
---
_id: '1748'
abstract:
- lang: eng
text: The authors apply selective wet chemical etching and atomic force microscopy
to reveal the three-dimensional shape of SiGeSi (001) islands after capping with
Si. Although the "self-assembled quantum dots" remain practically unaffected
by capping in the temperature range of 300-450 °C, significant morphological changes
take place on the Si surface. At 450 °C, the morphology of the capping layer (Si
matrix) evolves toward an intriguing semifacetted structure, which we call a "ziggurat,"
giving the misleading impression of a stepped SiGe island shape.
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
- first_name: Jerry
full_name: Tersoff, Jerry
last_name: Tersoff
- first_name: Elisabeth
full_name: Müller, Elisabeth
last_name: Müller
- first_name: Hans
full_name: Von Känel, Hans
last_name: Von Känel
citation:
ama: Katsaros G, Rastelli A, Stoffel M, et al. Evolution of buried semiconductor
nanostructures and origin of stepped surface mounds during capping. Applied
Physics Letters. 2006;89(25). doi:10.1063/1.2405876
apa: Katsaros, G., Rastelli, A., Stoffel, M., Costantini, G., Schmidt, O., Kern,
K., … Von Känel, H. (2006). Evolution of buried semiconductor nanostructures and
origin of stepped surface mounds during capping. Applied Physics Letters.
American Institute of Physics. https://doi.org/10.1063/1.2405876
chicago: Katsaros, Georgios, Armando Rastelli, Mathieu Stoffel, Giovanni Costantini,
Oliver Schmidt, Klaus Kern, Jerry Tersoff, Elisabeth Müller, and Hans Von Känel.
“Evolution of Buried Semiconductor Nanostructures and Origin of Stepped Surface
Mounds during Capping.” Applied Physics Letters. American Institute of
Physics, 2006. https://doi.org/10.1063/1.2405876.
ieee: G. Katsaros et al., “Evolution of buried semiconductor nanostructures
and origin of stepped surface mounds during capping,” Applied Physics Letters,
vol. 89, no. 25. American Institute of Physics, 2006.
ista: Katsaros G, Rastelli A, Stoffel M, Costantini G, Schmidt O, Kern K, Tersoff
J, Müller E, Von Känel H. 2006. Evolution of buried semiconductor nanostructures
and origin of stepped surface mounds during capping. Applied Physics Letters.
89(25).
mla: Katsaros, Georgios, et al. “Evolution of Buried Semiconductor Nanostructures
and Origin of Stepped Surface Mounds during Capping.” Applied Physics Letters,
vol. 89, no. 25, American Institute of Physics, 2006, doi:10.1063/1.2405876.
short: G. Katsaros, A. Rastelli, M. Stoffel, G. Costantini, O. Schmidt, K. Kern,
J. Tersoff, E. Müller, H. Von Känel, Applied Physics Letters 89 (2006).
date_created: 2018-12-11T11:53:48Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:57Z
day: '01'
doi: 10.1063/1.2405876
extern: 1
intvolume: ' 89'
issue: '25'
month: '01'
publication: Applied Physics Letters
publication_status: published
publisher: American Institute of Physics
publist_id: '5376'
quality_controlled: 0
status: public
title: Evolution of buried semiconductor nanostructures and origin of stepped surface
mounds during capping
type: journal_article
volume: 89
year: '2006'
...
---
_id: '1796'
abstract:
- lang: eng
text: Drugs that block the entry of human immunodeficiency virus type 1 (HIV-1)
into host cells abrogate the establishment of a productive infection and should
ideally diminish the chances of HIV-1 developing resistance. This review will
give an overview of the mechanism by which the envelope glycoprotein mediates
HIV-1 entry and will summarize current drug developments.
author:
- first_name: Sandra
full_name: Sandra Siegert
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Peter
full_name: Schnierle, Peter
last_name: Schnierle
- first_name: Barbara
full_name: Schnierle, Barbara S
last_name: Schnierle
citation:
ama: 'Siegert S, Schnierle P, Schnierle B. Novel anti-viral therapy: Drugs that
block HIV entry at different target sites. Mini-Reviews in Medicinal Chemistry.
2006;6(5):557-562. doi:10.2174/138955706776876267'
apa: 'Siegert, S., Schnierle, P., & Schnierle, B. (2006). Novel anti-viral therapy:
Drugs that block HIV entry at different target sites. Mini-Reviews in Medicinal
Chemistry. Bentham Science Publishers. https://doi.org/10.2174/138955706776876267'
chicago: 'Siegert, Sandra, Peter Schnierle, and Barbara Schnierle. “Novel Anti-Viral
Therapy: Drugs That Block HIV Entry at Different Target Sites.” Mini-Reviews
in Medicinal Chemistry. Bentham Science Publishers, 2006. https://doi.org/10.2174/138955706776876267.'
ieee: 'S. Siegert, P. Schnierle, and B. Schnierle, “Novel anti-viral therapy: Drugs
that block HIV entry at different target sites,” Mini-Reviews in Medicinal
Chemistry, vol. 6, no. 5. Bentham Science Publishers, pp. 557–562, 2006.'
ista: 'Siegert S, Schnierle P, Schnierle B. 2006. Novel anti-viral therapy: Drugs
that block HIV entry at different target sites. Mini-Reviews in Medicinal Chemistry.
6(5), 557–562.'
mla: 'Siegert, Sandra, et al. “Novel Anti-Viral Therapy: Drugs That Block HIV Entry
at Different Target Sites.” Mini-Reviews in Medicinal Chemistry, vol. 6,
no. 5, Bentham Science Publishers, 2006, pp. 557–62, doi:10.2174/138955706776876267.'
short: S. Siegert, P. Schnierle, B. Schnierle, Mini-Reviews in Medicinal Chemistry
6 (2006) 557–562.
date_created: 2018-12-11T11:54:03Z
date_published: 2006-05-01T00:00:00Z
date_updated: 2021-01-12T06:53:15Z
day: '01'
doi: 10.2174/138955706776876267
extern: 1
intvolume: ' 6'
issue: '5'
month: '05'
page: 557 - 562
publication: Mini-Reviews in Medicinal Chemistry
publication_status: published
publisher: Bentham Science Publishers
publist_id: '5314'
quality_controlled: 0
status: public
title: 'Novel anti-viral therapy: Drugs that block HIV entry at different target sites'
type: journal_article
volume: 6
year: '2006'
...
---
_id: '1961'
abstract:
- lang: eng
text: |
Respiratory complex I plays a central role in cellular energy production in bacteria and mitochondria. Its dysfunction is implicated in many human neurodegenerative diseases, as well as in aging. The crystal structure of the hydrophilic domain (peripheral arm) of complex I from Thermus thermophilus has been solved at 3.3 angstrom resolution. This subcomplex consists of eight subunits and contains all the redox centers of the enzyme, including nine iron-sulfur clusters. The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway, and of the distal cluster Nia, a possible antioxidant. The structure reveals new aspects of the mechanism and evolution of the enzyme. The terminal cluster N2 is coordinated, uniquely, by two consecutive cysteines. The novel subunit Nqo15 has a similar fold to the mitochondrial iron chaperone frataxin, and it may be involved in iron-sulfur cluster regeneration in the complex.
acknowledgement: This work was funded by the Medical Research Council.
author:
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Philip
full_name: 'Hinchliffe, Philip '
last_name: Hinchliffe
citation:
ama: Sazanov LA, Hinchliffe P. Structure of the hydrophilic domain of respiratory
complex I from Thermus thermophilus. Science. 2006;311(5766):1430-1436.
doi:10.1126/science.1123809
apa: Sazanov, L. A., & Hinchliffe, P. (2006). Structure of the hydrophilic domain
of respiratory complex I from Thermus thermophilus. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1123809
chicago: Sazanov, Leonid A, and Philip Hinchliffe. “Structure of the Hydrophilic
Domain of Respiratory Complex I from Thermus Thermophilus.” Science. American
Association for the Advancement of Science, 2006. https://doi.org/10.1126/science.1123809.
ieee: L. A. Sazanov and P. Hinchliffe, “Structure of the hydrophilic domain of respiratory
complex I from Thermus thermophilus,” Science, vol. 311, no. 5766. American
Association for the Advancement of Science, pp. 1430–1436, 2006.
ista: Sazanov LA, Hinchliffe P. 2006. Structure of the hydrophilic domain of respiratory
complex I from Thermus thermophilus. Science. 311(5766), 1430–1436.
mla: Sazanov, Leonid A., and Philip Hinchliffe. “Structure of the Hydrophilic Domain
of Respiratory Complex I from Thermus Thermophilus.” Science, vol. 311,
no. 5766, American Association for the Advancement of Science, 2006, pp. 1430–36,
doi:10.1126/science.1123809.
short: L.A. Sazanov, P. Hinchliffe, Science 311 (2006) 1430–1436.
date_created: 2018-12-11T11:54:56Z
date_published: 2006-03-10T00:00:00Z
date_updated: 2021-01-12T06:54:22Z
day: '10'
doi: 10.1126/science.1123809
extern: 1
intvolume: ' 311'
issue: '5766'
month: '03'
page: 1430 - 1436
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5121'
quality_controlled: 0
status: public
title: Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus
type: journal_article
volume: 311
year: '2006'
...
---
_id: '1966'
abstract:
- lang: eng
text: The hydrophilic domain (peripheral arm) of the proton-translocating NADH:quinone
oxidoreductase (complex I) from the thermophilic organism Thermus thermophilus
HB8 has been purified and characterized. The subcomplex is stable in sodium dodecyl
sulfate up to 80 °C. Of nine iron-sulfur clusters, four to five (one or two binuclear
and three tetranuclear) could be detected by EPR in the NADH-reduced enzyme. The
preparation consists of eight different polypeptides. Seven of them have been
positively identified by peptide mass mapping and N-terminal sequencing as known
hydrophilic subunits of T. thermophilus complex I. The eighth polypeptide copurified
with the subcomplex at all stages, is strongly associated with the other subunits,
and is present in crystals of the subcomplex, used for X-ray data collection.
Therefore, it has been identified as a novel complex I subunit and named Nqo15.
It is encoded in a locus separate from the nqo operon, containing the 14 other
known complex I genes. ORFs encoding Nqo15 homologues are present in the genomes
of the closest relatives of T. thermophilus. Our data show that, contrary to previous
assumptions, bacterial complex I can contain proteins in addition to a "core"
complement of 14 subunits.
author:
- first_name: Philip
full_name: 'Hinchliffe, Philip '
last_name: Hinchliffe
- first_name: Joe
full_name: Carroll, Joe D
last_name: Carroll
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Hinchliffe P, Carroll J, Sazanov LA. Identification of a novel subunit of respiratory
complex I from Thermus thermophilus. Biochemistry. 2006;45(14):4413-4420.
doi:10.1021/bi0600998
apa: Hinchliffe, P., Carroll, J., & Sazanov, L. A. (2006). Identification of
a novel subunit of respiratory complex I from Thermus thermophilus. Biochemistry.
ACS. https://doi.org/10.1021/bi0600998
chicago: Hinchliffe, Philip, Joe Carroll, and Leonid A Sazanov. “Identification
of a Novel Subunit of Respiratory Complex I from Thermus Thermophilus.” Biochemistry.
ACS, 2006. https://doi.org/10.1021/bi0600998.
ieee: P. Hinchliffe, J. Carroll, and L. A. Sazanov, “Identification of a novel subunit
of respiratory complex I from Thermus thermophilus,” Biochemistry, vol.
45, no. 14. ACS, pp. 4413–4420, 2006.
ista: Hinchliffe P, Carroll J, Sazanov LA. 2006. Identification of a novel subunit
of respiratory complex I from Thermus thermophilus. Biochemistry. 45(14), 4413–4420.
mla: Hinchliffe, Philip, et al. “Identification of a Novel Subunit of Respiratory
Complex I from Thermus Thermophilus.” Biochemistry, vol. 45, no. 14, ACS,
2006, pp. 4413–20, doi:10.1021/bi0600998.
short: P. Hinchliffe, J. Carroll, L.A. Sazanov, Biochemistry 45 (2006) 4413–4420.
date_created: 2018-12-11T11:54:57Z
date_published: 2006-04-11T00:00:00Z
date_updated: 2021-01-12T06:54:23Z
day: '11'
doi: 10.1021/bi0600998
extern: 1
intvolume: ' 45'
issue: '14'
month: '04'
page: 4413 - 4420
publication: Biochemistry
publication_status: published
publisher: ACS
publist_id: '5120'
quality_controlled: 0
status: public
title: Identification of a novel subunit of respiratory complex I from Thermus thermophilus
type: journal_article
volume: 45
year: '2006'
...
---
_id: '2066'
abstract:
- lang: eng
text: Although the X chromosome is usually similar to the autosomes in size and
cytogenetic appearance, theoretical models predict that its hemizygosity in males
may cause unusual patterns of evolution. The sequencing of several genomes has
indeed revealed differences between the X chromosome and the autosomes in the
rates of gene divergence, patterns of gene expression and rates of gene movement
between chromosomes. A better understanding of these patterns should provide valuable
information on the evolution of genes located on the X chromosome. It could also
suggest solutions to more general problems in molecular evolution, such as detecting
selection and estimating mutational effects on fitness
acknowledgement: B.V. is supported by a postgraduate fellowship from the Fundação
de Ciência e Tecnologia of Portugal, and B.C. by the Royal Society (UK)
author:
- first_name: Beatriz
full_name: Beatriz Vicoso
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
citation:
ama: 'Vicoso B, Charlesworth B. Evolution on the X chromosome: Unusual patterns
and processes. Nature Reviews Genetics. 2006;7(8):645-653. doi:10.1038/nrg1914'
apa: 'Vicoso, B., & Charlesworth, B. (2006). Evolution on the X chromosome:
Unusual patterns and processes. Nature Reviews Genetics. Nature Publishing
Group. https://doi.org/10.1038/nrg1914'
chicago: 'Vicoso, Beatriz, and Brian Charlesworth. “Evolution on the X Chromosome:
Unusual Patterns and Processes.” Nature Reviews Genetics. Nature Publishing
Group, 2006. https://doi.org/10.1038/nrg1914.'
ieee: 'B. Vicoso and B. Charlesworth, “Evolution on the X chromosome: Unusual patterns
and processes,” Nature Reviews Genetics, vol. 7, no. 8. Nature Publishing
Group, pp. 645–653, 2006.'
ista: 'Vicoso B, Charlesworth B. 2006. Evolution on the X chromosome: Unusual patterns
and processes. Nature Reviews Genetics. 7(8), 645–653.'
mla: 'Vicoso, Beatriz, and Brian Charlesworth. “Evolution on the X Chromosome: Unusual
Patterns and Processes.” Nature Reviews Genetics, vol. 7, no. 8, Nature
Publishing Group, 2006, pp. 645–53, doi:10.1038/nrg1914.'
short: B. Vicoso, B. Charlesworth, Nature Reviews Genetics 7 (2006) 645–653.
date_created: 2018-12-11T11:55:31Z
date_published: 2006-08-01T00:00:00Z
date_updated: 2021-01-12T06:55:05Z
day: '01'
doi: 10.1038/nrg1914
extern: 1
intvolume: ' 7'
issue: '8'
month: '08'
page: 645 - 653
publication: Nature Reviews Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '4973'
quality_controlled: 0
status: public
title: 'Evolution on the X chromosome: Unusual patterns and processes'
type: journal_article
volume: 7
year: '2006'
...