---
_id: '3023'
abstract:
- lang: eng
  text: 'Cytokinesis ensures proper partitioning of the nucleocytoplasmic contents
    into two daughter cells. It has generally been thought that cytokinesis is accomplished
    differently in animals and plants because of the differences in the preparatory
    phases, into the centrosomal or acentrosomal nature of the process, the presence
    or absence of rigid cell walls, and on the basis of ‘outside‐in’ or ‘inside‐out’
    mechanism. However, this long‐standing paradigm needs further reevaluation based
    on new findings. Recent advances reveal that plant cells, similarly to animal
    cells, possess astral microtubules that regulate the cell division plane. Furthermore,
    endocytosis has been found to be important for cytokinesis in animal and plant
    cells: vesicles containing endocytosed cargo provide material for the cell plate
    formation in plants and for closure of the midbody channel in animals. Thus, although
    the preparatory phases of the cell division process differ between plant and animal
    cells, the later phases show similarities. We unify these findings in a model
    that suggests a conserved mode of cytokinesis.'
author:
- first_name: Pankaj
  full_name: Dhonukshe, Pankaj
  last_name: Dhonukshe
- first_name: Jozef
  full_name: Šamaj, Jozef
  last_name: Šamaj
- first_name: František
  full_name: Baluška, František
  last_name: Baluška
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: 'Dhonukshe P, Šamaj J, Baluška F, Friml J. A unifying new model of cytokinesis
    for the dividing plant and animal cells. <i>Bioessays : News and Reviews in Molecular,
    Cellular and Developmental Biology</i>. 2007;29(4):371-381. doi:<a href="https://doi.org/10.1002/bies.20559">10.1002/bies.20559</a>'
  apa: 'Dhonukshe, P., Šamaj, J., Baluška, F., &#38; Friml, J. (2007). A unifying
    new model of cytokinesis for the dividing plant and animal cells. <i>Bioessays :
    News and Reviews in Molecular, Cellular and Developmental Biology</i>. Wiley-Blackwell.
    <a href="https://doi.org/10.1002/bies.20559">https://doi.org/10.1002/bies.20559</a>'
  chicago: 'Dhonukshe, Pankaj, Jozef Šamaj, František Baluška, and Jiří Friml. “A
    Unifying New Model of Cytokinesis for the Dividing Plant and Animal Cells.” <i>Bioessays :
    News and Reviews in Molecular, Cellular and Developmental Biology</i>. Wiley-Blackwell,
    2007. <a href="https://doi.org/10.1002/bies.20559">https://doi.org/10.1002/bies.20559</a>.'
  ieee: 'P. Dhonukshe, J. Šamaj, F. Baluška, and J. Friml, “A unifying new model of
    cytokinesis for the dividing plant and animal cells,” <i>Bioessays : News and
    Reviews in Molecular, Cellular and Developmental Biology</i>, vol. 29, no. 4.
    Wiley-Blackwell, pp. 371–381, 2007.'
  ista: 'Dhonukshe P, Šamaj J, Baluška F, Friml J. 2007. A unifying new model of cytokinesis
    for the dividing plant and animal cells. Bioessays : News and Reviews in Molecular,
    Cellular and Developmental Biology. 29(4), 371–381.'
  mla: 'Dhonukshe, Pankaj, et al. “A Unifying New Model of Cytokinesis for the Dividing
    Plant and Animal Cells.” <i>Bioessays : News and Reviews in Molecular, Cellular
    and Developmental Biology</i>, vol. 29, no. 4, Wiley-Blackwell, 2007, pp. 371–81,
    doi:<a href="https://doi.org/10.1002/bies.20559">10.1002/bies.20559</a>.'
  short: 'P. Dhonukshe, J. Šamaj, F. Baluška, J. Friml, Bioessays : News and Reviews
    in Molecular, Cellular and Developmental Biology 29 (2007) 371–381.'
date_created: 2018-12-11T12:00:55Z
date_published: 2007-04-01T00:00:00Z
date_updated: 2021-01-12T07:40:31Z
day: '01'
doi: 10.1002/bies.20559
extern: '1'
external_id:
  pmid:
  - '    17373659'
intvolume: '        29'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 371 - 381
pmid: 1
publication: 'Bioessays : News and Reviews in Molecular, Cellular and Developmental
  Biology'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3678'
quality_controlled: '1'
status: public
title: A unifying new model of cytokinesis for the dividing plant and animal cells
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2007'
...
---
_id: '3024'
abstract:
- lang: eng
  text: The plant hormone auxin is frequently observed to be asymmetrically distributed
    across adjacent cells during crucial stages of growth and development. These auxin
    gradients depend on polar transport and regulate a wide variety of processes,
    including embryogenesis, organogenesis, vascular tissue differentiation, root
    meristem maintenance and tropic growth. Auxin can mediate such a perplexing array
    of developmental processes by acting as a general trigger for the change in developmental
    program in cells where it accumulates and by providing vectorial information to
    the tissues by its polar intercellular flow. In recent years, a wealth of molecular
    data on the mechanism of auxin transport and its regulation has been generated,
    providing significant insights into the action of this versatile coordinative
    signal.
author:
- first_name: Anne
  full_name: Vieten, Anne
  last_name: Vieten
- first_name: Michael
  full_name: Sauer, Michael
  last_name: Sauer
- first_name: Philip
  full_name: Brewer, Philip
  last_name: Brewer
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Vieten A, Sauer M, Brewer P, Friml J. Molecular and cellular aspects of auxin-transport-mediated
    development. <i>Trends in Plant Science</i>. 2007;12(4):160-168. doi:<a href="https://doi.org/10.1016/j.tplants.2007.03.006">10.1016/j.tplants.2007.03.006</a>
  apa: Vieten, A., Sauer, M., Brewer, P., &#38; Friml, J. (2007). Molecular and cellular
    aspects of auxin-transport-mediated development. <i>Trends in Plant Science</i>.
    Cell Press. <a href="https://doi.org/10.1016/j.tplants.2007.03.006">https://doi.org/10.1016/j.tplants.2007.03.006</a>
  chicago: Vieten, Anne, Michael Sauer, Philip Brewer, and Jiří Friml. “Molecular
    and Cellular Aspects of Auxin-Transport-Mediated Development.” <i>Trends in Plant
    Science</i>. Cell Press, 2007. <a href="https://doi.org/10.1016/j.tplants.2007.03.006">https://doi.org/10.1016/j.tplants.2007.03.006</a>.
  ieee: A. Vieten, M. Sauer, P. Brewer, and J. Friml, “Molecular and cellular aspects
    of auxin-transport-mediated development,” <i>Trends in Plant Science</i>, vol.
    12, no. 4. Cell Press, pp. 160–168, 2007.
  ista: Vieten A, Sauer M, Brewer P, Friml J. 2007. Molecular and cellular aspects
    of auxin-transport-mediated development. Trends in Plant Science. 12(4), 160–168.
  mla: Vieten, Anne, et al. “Molecular and Cellular Aspects of Auxin-Transport-Mediated
    Development.” <i>Trends in Plant Science</i>, vol. 12, no. 4, Cell Press, 2007,
    pp. 160–68, doi:<a href="https://doi.org/10.1016/j.tplants.2007.03.006">10.1016/j.tplants.2007.03.006</a>.
  short: A. Vieten, M. Sauer, P. Brewer, J. Friml, Trends in Plant Science 12 (2007)
    160–168.
date_created: 2018-12-11T12:00:55Z
date_published: 2007-04-01T00:00:00Z
date_updated: 2021-01-12T07:40:31Z
day: '01'
doi: 10.1016/j.tplants.2007.03.006
extern: '1'
external_id:
  pmid:
  - '    17369077'
intvolume: '        12'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 160 - 168
pmid: 1
publication: Trends in Plant Science
publication_status: published
publisher: Cell Press
publist_id: '3679'
quality_controlled: '1'
status: public
title: Molecular and cellular aspects of auxin-transport-mediated development
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2007'
...
---
_id: '3026'
abstract:
- lang: eng
  text: In plants, each developmental process integrates a network of signaling events
    that are regulated by different phytohormones, and interactions among hormonal
    pathways are essential to modulate their effect. Continuous growth of roots results
    from the postembryonic activity of cells within the root meristem that is controlled
    by the coordinated action of several phytohormones, including auxin and ethylene.
    Although their interaction has been studied intensively, the molecular and cellular
    mechanisms underlying this interplay are unknown. We show that the effect of ethylene
    on root growth is largely mediated by the regulation of the auxin biosynthesis
    and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis
    and basipetal auxin transport toward the elongation zone, where it activates a
    local auxin response leading to inhibition of cell elongation. Consistently, in
    mutants affected in auxin perception or basipetal auxin transport, ethylene cannot
    activate the auxin response nor regulate the root growth. In addition, ethylene
    modulates the transcription of several components of the auxin transport machinery.
    Thus, ethylene achieves a local activation of the auxin signaling pathway and
    regulates root growth by both stimulating the auxin biosynthesis and by modulating
    the auxin transport machinery.
author:
- first_name: Kamil
  full_name: Růžička, Kamil
  last_name: Růžička
- first_name: Karin
  full_name: Ljung, Karin
  last_name: Ljung
- first_name: Steffen
  full_name: Vanneste, Steffen
  last_name: Vanneste
- first_name: Radka
  full_name: Podhorská, Radka
  last_name: Podhorská
- first_name: Tom
  full_name: Beeckman, Tom
  last_name: Beeckman
- first_name: Jirí
  full_name: Jirí Friml
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Eva
  full_name: Eva Benková
  id: 38F4F166-F248-11E8-B48F-1D18A9856A87
  last_name: Benková
  orcid: 0000-0002-8510-9739
citation:
  ama: Růžička K, Ljung K, Vanneste S, et al. Ethylene regulates root growth through
    effects on auxin biosynthesis and transport dependent auxin distribution. <i>Plant
    Cell</i>. 2007;19(7):2197-2212. doi:<a href="https://doi.org/10.1105/tpc.107.052126">10.1105/tpc.107.052126</a>
  apa: Růžička, K., Ljung, K., Vanneste, S., Podhorská, R., Beeckman, T., Friml, J.,
    &#38; Benková, E. (2007). Ethylene regulates root growth through effects on auxin
    biosynthesis and transport dependent auxin distribution. <i>Plant Cell</i>. American
    Society of Plant Biologists. <a href="https://doi.org/10.1105/tpc.107.052126">https://doi.org/10.1105/tpc.107.052126</a>
  chicago: Růžička, Kamil, Karin Ljung, Steffen Vanneste, Radka Podhorská, Tom Beeckman,
    Jiří Friml, and Eva Benková. “Ethylene Regulates Root Growth through Effects on
    Auxin Biosynthesis and Transport Dependent Auxin Distribution.” <i>Plant Cell</i>.
    American Society of Plant Biologists, 2007. <a href="https://doi.org/10.1105/tpc.107.052126">https://doi.org/10.1105/tpc.107.052126</a>.
  ieee: K. Růžička <i>et al.</i>, “Ethylene regulates root growth through effects
    on auxin biosynthesis and transport dependent auxin distribution,” <i>Plant Cell</i>,
    vol. 19, no. 7. American Society of Plant Biologists, pp. 2197–2212, 2007.
  ista: Růžička K, Ljung K, Vanneste S, Podhorská R, Beeckman T, Friml J, Benková
    E. 2007. Ethylene regulates root growth through effects on auxin biosynthesis
    and transport dependent auxin distribution. Plant Cell. 19(7), 2197–2212.
  mla: Růžička, Kamil, et al. “Ethylene Regulates Root Growth through Effects on Auxin
    Biosynthesis and Transport Dependent Auxin Distribution.” <i>Plant Cell</i>, vol.
    19, no. 7, American Society of Plant Biologists, 2007, pp. 2197–212, doi:<a href="https://doi.org/10.1105/tpc.107.052126">10.1105/tpc.107.052126</a>.
  short: K. Růžička, K. Ljung, S. Vanneste, R. Podhorská, T. Beeckman, J. Friml, E.
    Benková, Plant Cell 19 (2007) 2197–2212.
date_created: 2018-12-11T12:00:56Z
date_published: 2007-07-01T00:00:00Z
date_updated: 2021-01-12T07:40:32Z
day: '01'
doi: 10.1105/tpc.107.052126
extern: 1
intvolume: '        19'
issue: '7'
month: '07'
page: 2197 - 2212
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3676'
quality_controlled: 0
status: public
title: Ethylene regulates root growth through effects on auxin biosynthesis and transport
  dependent auxin distribution
type: journal_article
volume: 19
year: '2007'
...
---
_id: '3027'
abstract:
- lang: eng
  text: Polar transport of the phytohormone auxin controls numerous growth responses
    in plants. Molecular characterization of auxin transport in Arabidopsis thaliana
    has provided important insights into the mechanisms underlying the regulation
    of auxin distribution. In particular, the control of subcellular localization
    and expression of PIN-type auxin efflux components appears to be fundamental for
    orchestrated distribution of the growth regulator throughout the entire plant
    body. Here we describe the identification of two Arabidopsis loci, MOP2 and MOP3
    (for MODULATOR OF PIN), that are involved in control of the steady-state levels
    of PIN protein. Mutations in both loci result in defects in auxin distribution
    and polar auxin transport, and cause phenotypes consistent with a reduction of
    PIN protein levels. Genetic interaction between PIN2 and both MOP loci is suggestive
    of functional cross-talk, which is further substantiated by findings demonstrating
    that ectopic PIN up-regulation is compensated in the mop background. Thus, in
    addition to pathways that control PIN localization and transcription, MOP2 and
    MOP3 appear to be involved in fine-tuning of auxin distribution via post-transcriptional
    regulation of PIN expression.
author:
- first_name: Nenad
  full_name: Malenica, Nenad
  last_name: Malenica
- first_name: Lindy
  full_name: Abas, Lindy
  last_name: Abas
- first_name: René
  full_name: Benjamins, René
  last_name: Benjamins
- first_name: Saeko
  full_name: Kitakura, Saeko
  last_name: Kitakura
- first_name: Harald
  full_name: Sigmund, Harald F
  last_name: Sigmund
- first_name: Kim
  full_name: Jun, Kim S
  last_name: Jun
- first_name: Marie
  full_name: Hauser, Marie-Theres
  last_name: Hauser
- first_name: Jirí
  full_name: Jirí Friml
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Christian
  full_name: Luschnig, Christian
  last_name: Luschnig
citation:
  ama: Malenica N, Abas L, Benjamins R, et al. MODULATOR of PIN genes control steady
    state levels of Arabidopsis PIN proteins. <i>Plant Journal</i>. 2007;51(4):537-550.
    doi:<a href="https://doi.org/10.1111/j.1365-313X.2007.03158.x">10.1111/j.1365-313X.2007.03158.x</a>
  apa: Malenica, N., Abas, L., Benjamins, R., Kitakura, S., Sigmund, H., Jun, K.,
    … Luschnig, C. (2007). MODULATOR of PIN genes control steady state levels of Arabidopsis
    PIN proteins. <i>Plant Journal</i>. Wiley-Blackwell. <a href="https://doi.org/10.1111/j.1365-313X.2007.03158.x">https://doi.org/10.1111/j.1365-313X.2007.03158.x</a>
  chicago: Malenica, Nenad, Lindy Abas, René Benjamins, Saeko Kitakura, Harald Sigmund,
    Kim Jun, Marie Hauser, Jiří Friml, and Christian Luschnig. “MODULATOR of PIN Genes
    Control Steady State Levels of Arabidopsis PIN Proteins.” <i>Plant Journal</i>.
    Wiley-Blackwell, 2007. <a href="https://doi.org/10.1111/j.1365-313X.2007.03158.x">https://doi.org/10.1111/j.1365-313X.2007.03158.x</a>.
  ieee: N. Malenica <i>et al.</i>, “MODULATOR of PIN genes control steady state levels
    of Arabidopsis PIN proteins,” <i>Plant Journal</i>, vol. 51, no. 4. Wiley-Blackwell,
    pp. 537–550, 2007.
  ista: Malenica N, Abas L, Benjamins R, Kitakura S, Sigmund H, Jun K, Hauser M, Friml
    J, Luschnig C. 2007. MODULATOR of PIN genes control steady state levels of Arabidopsis
    PIN proteins. Plant Journal. 51(4), 537–550.
  mla: Malenica, Nenad, et al. “MODULATOR of PIN Genes Control Steady State Levels
    of Arabidopsis PIN Proteins.” <i>Plant Journal</i>, vol. 51, no. 4, Wiley-Blackwell,
    2007, pp. 537–50, doi:<a href="https://doi.org/10.1111/j.1365-313X.2007.03158.x">10.1111/j.1365-313X.2007.03158.x</a>.
  short: N. Malenica, L. Abas, R. Benjamins, S. Kitakura, H. Sigmund, K. Jun, M. Hauser,
    J. Friml, C. Luschnig, Plant Journal 51 (2007) 537–550.
date_created: 2018-12-11T12:00:56Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2021-01-12T07:40:32Z
day: '01'
doi: 10.1111/j.1365-313X.2007.03158.x
extern: 1
intvolume: '        51'
issue: '4'
month: '08'
page: 537 - 550
publication: Plant Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3675'
quality_controlled: 0
status: public
title: MODULATOR of PIN genes control steady state levels of Arabidopsis PIN proteins
type: journal_article
volume: 51
year: '2007'
...
---
_id: '3028'
abstract:
- lang: eng
  text: In plants, cell polarity and tissue patterning are connected by intercellular
    flow of the phytohormone auxin, whose directional signaling depends on polar subcellular
    localization of PIN auxin transport proteins. The mechanism of polar targeting
    of PINs or other cargos in plants is largely unidentified, with the PINOID kinase
    being the only known molecular component. Here, we identify PP2A phosphatase as
    an important regulator of PIN apical-basal targeting and auxin distribution. Genetic
    analysis, localization, and phosphorylation studies demonstrate that PP2A and
    PINOID both partially colocalize with PINs and act antagonistically on the phosphorylation
    state of their central hydrophilic loop, hence mediating PIN apical-basal polar
    targeting. Thus, in plants, polar sorting by the reversible phosphorylation of
    cargos allows for their conditional delivery to specific intracellular destinations.
    In the case of PIN proteins, this mechanism enables switches in the direction
    of intercellular auxin fluxes, which mediate differential growth, tissue patterning,
    and organogenesis.
author:
- first_name: Marta
  full_name: Michniewicz, Marta
  last_name: Michniewicz
- first_name: Marcelo
  full_name: Zago, Marcelo K
  last_name: Zago
- first_name: Lindy
  full_name: Abas, Lindy
  last_name: Abas
- first_name: Dolf
  full_name: Weijers, Dolf
  last_name: Weijers
- first_name: Alois
  full_name: Schweighofer, Alois
  last_name: Schweighofer
- first_name: Irute
  full_name: Meskiene, Irute
  last_name: Meskiene
- first_name: Marcus
  full_name: Heisler, Marcus G
  last_name: Heisler
- first_name: Carolyn
  full_name: Ohno, Carolyn
  last_name: Ohno
- first_name: Jing
  full_name: Zhang, Jing
  last_name: Zhang
- first_name: Fang
  full_name: Huang, Fang
  last_name: Huang
- first_name: Rebecca
  full_name: Schwab, Rebecca
  last_name: Schwab
- first_name: Detlef
  full_name: Weigel, Detlef
  last_name: Weigel
- first_name: Elliot
  full_name: Meyerowitz, Elliot M
  last_name: Meyerowitz
- first_name: Christian
  full_name: Luschnig, Christian
  last_name: Luschnig
- first_name: Remko
  full_name: Offringa, Remko
  last_name: Offringa
- first_name: Jirí
  full_name: Jirí Friml
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Michniewicz M, Zago M, Abas L, et al. Antagonistic regulation of PIN phosphorylation
    by PP2A and PINOID directs auxin flux. <i>Cell</i>. 2007;130(6):1044-1056. doi:<a
    href="https://doi.org/10.1016/j.cell.2007.07.033">10.1016/j.cell.2007.07.033</a>
  apa: Michniewicz, M., Zago, M., Abas, L., Weijers, D., Schweighofer, A., Meskiene,
    I., … Friml, J. (2007). Antagonistic regulation of PIN phosphorylation by PP2A
    and PINOID directs auxin flux. <i>Cell</i>. Cell Press. <a href="https://doi.org/10.1016/j.cell.2007.07.033">https://doi.org/10.1016/j.cell.2007.07.033</a>
  chicago: Michniewicz, Marta, Marcelo Zago, Lindy Abas, Dolf Weijers, Alois Schweighofer,
    Irute Meskiene, Marcus Heisler, et al. “Antagonistic Regulation of PIN Phosphorylation
    by PP2A and PINOID Directs Auxin Flux.” <i>Cell</i>. Cell Press, 2007. <a href="https://doi.org/10.1016/j.cell.2007.07.033">https://doi.org/10.1016/j.cell.2007.07.033</a>.
  ieee: M. Michniewicz <i>et al.</i>, “Antagonistic regulation of PIN phosphorylation
    by PP2A and PINOID directs auxin flux,” <i>Cell</i>, vol. 130, no. 6. Cell Press,
    pp. 1044–1056, 2007.
  ista: Michniewicz M, Zago M, Abas L, Weijers D, Schweighofer A, Meskiene I, Heisler
    M, Ohno C, Zhang J, Huang F, Schwab R, Weigel D, Meyerowitz E, Luschnig C, Offringa
    R, Friml J. 2007. Antagonistic regulation of PIN phosphorylation by PP2A and PINOID
    directs auxin flux. Cell. 130(6), 1044–1056.
  mla: Michniewicz, Marta, et al. “Antagonistic Regulation of PIN Phosphorylation
    by PP2A and PINOID Directs Auxin Flux.” <i>Cell</i>, vol. 130, no. 6, Cell Press,
    2007, pp. 1044–56, doi:<a href="https://doi.org/10.1016/j.cell.2007.07.033">10.1016/j.cell.2007.07.033</a>.
  short: M. Michniewicz, M. Zago, L. Abas, D. Weijers, A. Schweighofer, I. Meskiene,
    M. Heisler, C. Ohno, J. Zhang, F. Huang, R. Schwab, D. Weigel, E. Meyerowitz,
    C. Luschnig, R. Offringa, J. Friml, Cell 130 (2007) 1044–1056.
date_created: 2018-12-11T12:00:57Z
date_published: 2007-09-21T00:00:00Z
date_updated: 2021-01-12T07:40:33Z
day: '21'
doi: 10.1016/j.cell.2007.07.033
extern: 1
intvolume: '       130'
issue: '6'
month: '09'
page: 1044 - 1056
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3674'
quality_controlled: 0
status: public
title: Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin
  flux
type: journal_article
volume: 130
year: '2007'
...
---
_id: '3029'
abstract:
- lang: eng
  text: In Arabidopsis thaliana, lateral roots are formed from root pericycle cells
    adjacent to the xylem poles. Lateral root development is regulated antagonistically
    by the plant hormones auxin and cytokinin. While a great deal is known about how
    auxin promotes lateral root development, the mechanism of cytokinin repression
    is still unclear. Elevating cytokinin levels was observed to disrupt lateral root
    initiation and the regular pattern of divisions that characterizes lateral root
    development in Arabidopsis. To identify the stage of lateral root development
    that is sensitive to cytokinins, we targeted the expression of the Agrobacterium
    tumefaciens cytokinin biosynthesis enzyme isopentenyltransferase to either xylem-pole
    pericycle cells or young lateral root primordia using GAL4-GFP enhancer trap lines.
    Transactivation experiments revealed that xylem-pole pericycle cells are sensitive
    to cytokinins, whereas young lateral root primordia are not. This effect is physiologically
    significant because transactivation of the Arabidopsis cytokinin degrading enzyme
    cytokinin oxidase 1 in lateral root founder cells results in increased lateral
    root formation. We observed that cytokinins perturb the expression of PIN genes
    in lateral root founder cells and prevent the formation of an auxin gradient that
    is required to pattern lateral root primordia.
author:
- first_name: Laurent
  full_name: Laplaze, Laurent
  last_name: Laplaze
- first_name: Eva
  full_name: Eva Benková
  id: 38F4F166-F248-11E8-B48F-1D18A9856A87
  last_name: Benková
  orcid: 0000-0002-8510-9739
- first_name: Ilda
  full_name: Casimiro, Ilda
  last_name: Casimiro
- first_name: Lies
  full_name: Maes, Lies
  last_name: Maes
- first_name: Steffen
  full_name: Vanneste, Steffen
  last_name: Vanneste
- first_name: Ranjan
  full_name: Swarup, Ranjan
  last_name: Swarup
- first_name: Dolf
  full_name: Weijers, Dolf
  last_name: Weijers
- first_name: Vanessa
  full_name: Calvo, Vanessa
  last_name: Calvo
- first_name: Boris
  full_name: Parizot, Boris
  last_name: Parizot
- first_name: Maria
  full_name: Herrera-Rodriguez, Maria Begoña
  last_name: Herrera Rodriguez
- first_name: Remko
  full_name: Offringa, Remko
  last_name: Offringa
- first_name: Neil
  full_name: Graham, Neil
  last_name: Graham
- first_name: Patrick
  full_name: Doumas, Patrick
  last_name: Doumas
- first_name: Jirí
  full_name: Jirí Friml
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Didier
  full_name: Bogusz, Didier
  last_name: Bogusz
- first_name: Tom
  full_name: Beeckman, Tom
  last_name: Beeckman
- first_name: Malcolm
  full_name: Bennett, Malcolm
  last_name: Bennett
citation:
  ama: Laplaze L, Benková E, Casimiro I, et al. Cytokinins act directly on lateral
    root founder cells to inhibit root initiation. <i>Plant Cell</i>. 2007;19(12):3889-3900.
    doi:<a href="https://doi.org/10.1105/tpc.107.055863">10.1105/tpc.107.055863</a>
  apa: Laplaze, L., Benková, E., Casimiro, I., Maes, L., Vanneste, S., Swarup, R.,
    … Bennett, M. (2007). Cytokinins act directly on lateral root founder cells to
    inhibit root initiation. <i>Plant Cell</i>. American Society of Plant Biologists.
    <a href="https://doi.org/10.1105/tpc.107.055863">https://doi.org/10.1105/tpc.107.055863</a>
  chicago: Laplaze, Laurent, Eva Benková, Ilda Casimiro, Lies Maes, Steffen Vanneste,
    Ranjan Swarup, Dolf Weijers, et al. “Cytokinins Act Directly on Lateral Root Founder
    Cells to Inhibit Root Initiation.” <i>Plant Cell</i>. American Society of Plant
    Biologists, 2007. <a href="https://doi.org/10.1105/tpc.107.055863">https://doi.org/10.1105/tpc.107.055863</a>.
  ieee: L. Laplaze <i>et al.</i>, “Cytokinins act directly on lateral root founder
    cells to inhibit root initiation,” <i>Plant Cell</i>, vol. 19, no. 12. American
    Society of Plant Biologists, pp. 3889–3900, 2007.
  ista: Laplaze L, Benková E, Casimiro I, Maes L, Vanneste S, Swarup R, Weijers D,
    Calvo V, Parizot B, Herrera Rodriguez M, Offringa R, Graham N, Doumas P, Friml
    J, Bogusz D, Beeckman T, Bennett M. 2007. Cytokinins act directly on lateral root
    founder cells to inhibit root initiation. Plant Cell. 19(12), 3889–3900.
  mla: Laplaze, Laurent, et al. “Cytokinins Act Directly on Lateral Root Founder Cells
    to Inhibit Root Initiation.” <i>Plant Cell</i>, vol. 19, no. 12, American Society
    of Plant Biologists, 2007, pp. 3889–900, doi:<a href="https://doi.org/10.1105/tpc.107.055863">10.1105/tpc.107.055863</a>.
  short: L. Laplaze, E. Benková, I. Casimiro, L. Maes, S. Vanneste, R. Swarup, D.
    Weijers, V. Calvo, B. Parizot, M. Herrera Rodriguez, R. Offringa, N. Graham, P.
    Doumas, J. Friml, D. Bogusz, T. Beeckman, M. Bennett, Plant Cell 19 (2007) 3889–3900.
date_created: 2018-12-11T12:00:57Z
date_published: 2007-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:33Z
day: '01'
doi: 10.1105/tpc.107.055863
extern: 1
intvolume: '        19'
issue: '12'
month: '12'
page: 3889 - 3900
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3673'
quality_controlled: 0
status: public
title: Cytokinins act directly on lateral root founder cells to inhibit root initiation
type: journal_article
volume: 19
year: '2007'
...
---
_id: '3144'
abstract:
- lang: eng
  text: Accumulation of specific proteins at synaptic structures is essential for
    synapse assembly and function, but mechanisms regulating local protein enrichment
    remain poorly understood. At the neuromuscular junction (NMJ), subsynaptic nuclei
    underlie motor axon terminals within extrafusal muscle fibers and are transcriptionally
    distinct from neighboring nuclei. In this study, we show that expression of the
    ETS transcription factor Erm is highly concentrated at subsynaptic nuclei, and
    its mutation in mice leads to severe downregulation of many genes with normally
    enriched subsynaptic expression. Erm mutant mice display an expansion of the muscle
    central domain in which acetylcholine receptor (AChR) clusters accumulate, show
    gradual fragmentation of AChR clusters, and exhibit symptoms of muscle weakness
    mimicking congenital myasthenic syndrome (CMS). Together, our findings define
    Erm as an upstream regulator of a transcriptional program selective to subsynaptic
    nuclei at the NMJ and underscore the importance of transcriptional control of
    local synaptic protein accumulation.
author:
- first_name: Simon
  full_name: Simon Hippenmeyer
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
- first_name: Roland
  full_name: Huber, Roland M
  last_name: Huber
- first_name: David
  full_name: Ladle, David R
  last_name: Ladle
- first_name: Kenneth
  full_name: Murphy, Kenneth
  last_name: Murphy
- first_name: Silvia
  full_name: Arber, Silvia
  last_name: Arber
citation:
  ama: Hippenmeyer S, Huber R, Ladle D, Murphy K, Arber S. ETS transcription factor
    Erm controls subsynaptic gene expression in skeletal muscles. <i>Neuron</i>. 2007;55(5):726-740.
    doi:<a href="https://doi.org/10.1016/j.neuron.2007.07.028">10.1016/j.neuron.2007.07.028</a>
  apa: Hippenmeyer, S., Huber, R., Ladle, D., Murphy, K., &#38; Arber, S. (2007).
    ETS transcription factor Erm controls subsynaptic gene expression in skeletal
    muscles. <i>Neuron</i>. Elsevier. <a href="https://doi.org/10.1016/j.neuron.2007.07.028">https://doi.org/10.1016/j.neuron.2007.07.028</a>
  chicago: Hippenmeyer, Simon, Roland Huber, David Ladle, Kenneth Murphy, and Silvia
    Arber. “ETS Transcription Factor Erm Controls Subsynaptic Gene Expression in Skeletal
    Muscles.” <i>Neuron</i>. Elsevier, 2007. <a href="https://doi.org/10.1016/j.neuron.2007.07.028">https://doi.org/10.1016/j.neuron.2007.07.028</a>.
  ieee: S. Hippenmeyer, R. Huber, D. Ladle, K. Murphy, and S. Arber, “ETS transcription
    factor Erm controls subsynaptic gene expression in skeletal muscles,” <i>Neuron</i>,
    vol. 55, no. 5. Elsevier, pp. 726–740, 2007.
  ista: Hippenmeyer S, Huber R, Ladle D, Murphy K, Arber S. 2007. ETS transcription
    factor Erm controls subsynaptic gene expression in skeletal muscles. Neuron. 55(5),
    726–740.
  mla: Hippenmeyer, Simon, et al. “ETS Transcription Factor Erm Controls Subsynaptic
    Gene Expression in Skeletal Muscles.” <i>Neuron</i>, vol. 55, no. 5, Elsevier,
    2007, pp. 726–40, doi:<a href="https://doi.org/10.1016/j.neuron.2007.07.028">10.1016/j.neuron.2007.07.028</a>.
  short: S. Hippenmeyer, R. Huber, D. Ladle, K. Murphy, S. Arber, Neuron 55 (2007)
    726–740.
date_created: 2018-12-11T12:01:39Z
date_published: 2007-09-06T00:00:00Z
date_updated: 2021-01-12T07:41:22Z
day: '06'
doi: 10.1016/j.neuron.2007.07.028
extern: 1
intvolume: '        55'
issue: '5'
month: '09'
page: 726 - 740
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '3551'
quality_controlled: 0
status: public
title: ETS transcription factor Erm controls subsynaptic gene expression in skeletal
  muscles
type: journal_article
volume: 55
year: '2007'
...
---
_id: '3187'
abstract:
- lang: eng
  text: Stereo vision has numerous applications in robotics, graphics, inspection
    and other areas. A prime application, one which has driven work on stereo in our
    laboratory, is teleconferencing in which the use of a stereo webcam already makes
    possible various transformations of the video stream. These include digital camera
    control, insertion of virtual objects, background substitution, and eye-gaze correction
    [9, 8].
author:
- first_name: Andrew
  full_name: Blake, Andrew
  last_name: Blake
- first_name: Antonio
  full_name: Criminisi, Antonio
  last_name: Criminisi
- first_name: Geoffrey
  full_name: Cross, Geoffrey
  last_name: Cross
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Carsten
  full_name: Rother, Carsten
  last_name: Rother
citation:
  ama: Blake A, Criminisi A, Cross G, Kolmogorov V, Rother C. Fusion of stereo colour
    and contrast. <i>Springer Tracts in Advanced Robotics</i>. 2007;28:295-304. doi:<a
    href="https://doi.org/10.1007/978-3-540-48113-3_27">10.1007/978-3-540-48113-3_27</a>
  apa: Blake, A., Criminisi, A., Cross, G., Kolmogorov, V., &#38; Rother, C. (2007).
    Fusion of stereo colour and contrast. <i>Springer Tracts in Advanced Robotics</i>.
    Springer. <a href="https://doi.org/10.1007/978-3-540-48113-3_27">https://doi.org/10.1007/978-3-540-48113-3_27</a>
  chicago: Blake, Andrew, Antonio Criminisi, Geoffrey Cross, Vladimir Kolmogorov,
    and Carsten Rother. “Fusion of Stereo Colour and Contrast.” <i>Springer Tracts
    in Advanced Robotics</i>. Springer, 2007. <a href="https://doi.org/10.1007/978-3-540-48113-3_27">https://doi.org/10.1007/978-3-540-48113-3_27</a>.
  ieee: A. Blake, A. Criminisi, G. Cross, V. Kolmogorov, and C. Rother, “Fusion of
    stereo colour and contrast,” <i>Springer Tracts in Advanced Robotics</i>, vol.
    28. Springer, pp. 295–304, 2007.
  ista: Blake A, Criminisi A, Cross G, Kolmogorov V, Rother C. 2007. Fusion of stereo
    colour and contrast. Springer Tracts in Advanced Robotics. 28, 295–304.
  mla: Blake, Andrew, et al. “Fusion of Stereo Colour and Contrast.” <i>Springer Tracts
    in Advanced Robotics</i>, vol. 28, Springer, 2007, pp. 295–304, doi:<a href="https://doi.org/10.1007/978-3-540-48113-3_27">10.1007/978-3-540-48113-3_27</a>.
  short: A. Blake, A. Criminisi, G. Cross, V. Kolmogorov, C. Rother, Springer Tracts
    in Advanced Robotics 28 (2007) 295–304.
date_created: 2018-12-11T12:01:54Z
date_published: 2007-02-05T00:00:00Z
date_updated: 2021-01-12T07:41:40Z
day: '05'
doi: 10.1007/978-3-540-48113-3_27
extern: 1
intvolume: '        28'
main_file_link:
- open_access: '0'
  url: http://research.microsoft.com/pubs/67417/criminisi_isrr2005.pdf
month: '02'
page: 295 - 304
publication: Springer Tracts in Advanced Robotics
publication_status: published
publisher: Springer
publist_id: '3492'
quality_controlled: 0
status: public
title: Fusion of stereo colour and contrast
type: journal_article
volume: 28
year: '2007'
...
---
_id: '3191'
abstract:
- lang: eng
  text: 'The maximum flow algorithm for minimizing energy functions of binary variables
    has become a standard tool in computer vision. In many cases, unary costs of the
    energy depend linearly on parameter lambda. In this paper we study vision applications
    for which it is important to solve the maxflow problem for different lambda''s.
    An example is a weighting between data and regularization terms in image segmentation
    or stereo: it is desirable to vary it both during training (to learn lambda from
    ground truth data) and testing (to select best lambda using high-knowledge constraints,
    e.g. user input). We review algorithmic aspects of this parametric maximum flow
    problem previously unknown in vision, such as the ability to compute all breakpoints
    of lambda and corresponding optimal configurations infinite time. These results
    allow, in particular, to minimize the ratio of some geometric functional, such
    as flux of a vector field over length (or area). Previously, such functional were
    tackled with shortest path techniques applicable only in 2D. We give theoretical
    improvements for &quot;PDE cuts&quot; [5]. We present experimental results for
    image segmentation, 3D reconstruction, and the cosegmentation problem.'
author:
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Yuri
  full_name: Boykov, Yuri
  last_name: Boykov
- first_name: Carsten
  full_name: Rother, Carsten
  last_name: Rother
citation:
  ama: 'Kolmogorov V, Boykov Y, Rother C. Applications of parametric maxflow in computer
    vision. In: IEEE; 2007. doi:<a href="https://doi.org/10.1109/ICCV.2007.4408910">10.1109/ICCV.2007.4408910</a>'
  apa: 'Kolmogorov, V., Boykov, Y., &#38; Rother, C. (2007). Applications of parametric
    maxflow in computer vision. Presented at the ICCV: International Conference on
    Computer Vision, IEEE. <a href="https://doi.org/10.1109/ICCV.2007.4408910">https://doi.org/10.1109/ICCV.2007.4408910</a>'
  chicago: Kolmogorov, Vladimir, Yuri Boykov, and Carsten Rother. “Applications of
    Parametric Maxflow in Computer Vision.” IEEE, 2007. <a href="https://doi.org/10.1109/ICCV.2007.4408910">https://doi.org/10.1109/ICCV.2007.4408910</a>.
  ieee: 'V. Kolmogorov, Y. Boykov, and C. Rother, “Applications of parametric maxflow
    in computer vision,” presented at the ICCV: International Conference on Computer
    Vision, 2007.'
  ista: 'Kolmogorov V, Boykov Y, Rother C. 2007. Applications of parametric maxflow
    in computer vision. ICCV: International Conference on Computer Vision.'
  mla: Kolmogorov, Vladimir, et al. <i>Applications of Parametric Maxflow in Computer
    Vision</i>. IEEE, 2007, doi:<a href="https://doi.org/10.1109/ICCV.2007.4408910">10.1109/ICCV.2007.4408910</a>.
  short: V. Kolmogorov, Y. Boykov, C. Rother, in:, IEEE, 2007.
conference:
  name: 'ICCV: International Conference on Computer Vision'
date_created: 2018-12-11T12:01:55Z
date_published: 2007-12-26T00:00:00Z
date_updated: 2021-01-12T07:41:41Z
day: '26'
doi: 10.1109/ICCV.2007.4408910
extern: 1
main_file_link:
- open_access: '0'
  url: http://research.microsoft.com/pubs/70474/iccv07-paramaxflow.pdf
month: '12'
publication_status: published
publisher: IEEE
publist_id: '3489'
quality_controlled: 0
status: public
title: Applications of parametric maxflow in computer vision
type: conference
year: '2007'
...
---
_id: '3192'
abstract:
- lang: eng
  text: Many computer vision applications rely on the efficient optimization of challenging,
    so-called non-submodular, binary pairwise MRFs. A promising graph cut based approach
    for optimizing such MRFs known as &quot;roof duality&quot; was recently introduced
    into computer vision. We study two methods which extend this approach. First,
    we discuss an efficient implementation of the &quot;probing&quot; technique introduced
    recently by Boros et al. [5]. It simplifies the MRF while preserving the global
    optimum. Our code is 400-700 faster on some graphs than the implementation of
    [5]. Second, we present a new technique which takes an arbitrary input labeling
    and tries to improve its energy. We give theoretical characterizations of local
    minima of this procedure. We applied both techniques to many applications, including
    image segmentation, new view synthesis, superresolution, diagram recognition,
    parameter learning, texture restoration, and image deconvolution. For several
    applications we see that we are able to find the global minimum very efficiently,
    and considerably outperform the original roof duality approach. In comparison
    to existing techniques, such as graph cut, TRW, BP, ICM, and simulated annealing,
    we nearly always find a lower energy.
author:
- first_name: Carsten
  full_name: Rother, Carsten
  last_name: Rother
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Victor
  full_name: Lempitsky, Victor
  last_name: Lempitsky
- first_name: Martin
  full_name: Szummer, Martin
  last_name: Szummer
citation:
  ama: 'Rother C, Kolmogorov V, Lempitsky V, Szummer M. Optimizing binary MRFs via
    extended roof duality. In: IEEE; 2007. doi:<a href="https://doi.org/10.1109/CVPR.2007.383203">10.1109/CVPR.2007.383203</a>'
  apa: 'Rother, C., Kolmogorov, V., Lempitsky, V., &#38; Szummer, M. (2007). Optimizing
    binary MRFs via extended roof duality. Presented at the CVPR: Computer Vision
    and Pattern Recognition, IEEE. <a href="https://doi.org/10.1109/CVPR.2007.383203">https://doi.org/10.1109/CVPR.2007.383203</a>'
  chicago: Rother, Carsten, Vladimir Kolmogorov, Victor Lempitsky, and Martin Szummer.
    “Optimizing Binary MRFs via Extended Roof Duality.” IEEE, 2007. <a href="https://doi.org/10.1109/CVPR.2007.383203">https://doi.org/10.1109/CVPR.2007.383203</a>.
  ieee: 'C. Rother, V. Kolmogorov, V. Lempitsky, and M. Szummer, “Optimizing binary
    MRFs via extended roof duality,” presented at the CVPR: Computer Vision and Pattern
    Recognition, 2007.'
  ista: 'Rother C, Kolmogorov V, Lempitsky V, Szummer M. 2007. Optimizing binary MRFs
    via extended roof duality. CVPR: Computer Vision and Pattern Recognition.'
  mla: Rother, Carsten, et al. <i>Optimizing Binary MRFs via Extended Roof Duality</i>.
    IEEE, 2007, doi:<a href="https://doi.org/10.1109/CVPR.2007.383203">10.1109/CVPR.2007.383203</a>.
  short: C. Rother, V. Kolmogorov, V. Lempitsky, M. Szummer, in:, IEEE, 2007.
conference:
  name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:55Z
date_published: 2007-07-16T00:00:00Z
date_updated: 2021-01-12T07:41:42Z
day: '16'
doi: 10.1109/CVPR.2007.383203
extern: 1
main_file_link:
- open_access: '0'
  url: http://www.robots.ox.ac.uk/~vilem/QPBOPI.pdf
month: '07'
publication_status: published
publisher: IEEE
publist_id: '3490'
quality_controlled: 0
status: public
title: Optimizing binary MRFs via extended roof duality
type: conference
year: '2007'
...
---
_id: '3193'
abstract:
- lang: eng
  text: 'Optimization techniques based on graph cuts have become a standard tool for
    many vision applications. These techniques allow to minimize efficiently certain
    energy functions corresponding to pairwise Markov Random Fields (MRFs). Currently,
    there is an accepted view within the computer vision community that graph cuts
    can only be used for optimizing a limited class of MRF energies (e.g., submodular
    functions). In this survey, we review some results that show that graph cuts can
    be applied to a much larger class of energy functions (in particular, nonsubmodular
    functions). While these results are well-known in the optimization community,
    to our knowledge they were not used in the context of computer vision and MRF
    optimization. We demonstrate the relevance of these results to vision on the problem
    of binary texture restoration. '
author:
- first_name: Vladimir
  full_name: Vladimir Kolmogorov
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
- first_name: Carsten
  full_name: Rother, Carsten
  last_name: Rother
citation:
  ama: Kolmogorov V, Rother C. Minimizing nonsubmodular functions with graph cuts
    - A review. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>.
    2007;29(7):1274-1279. doi:<a href="https://doi.org/10.1109/TPAMI.2007.1031">10.1109/TPAMI.2007.1031</a>
  apa: Kolmogorov, V., &#38; Rother, C. (2007). Minimizing nonsubmodular functions
    with graph cuts - A review. <i>IEEE Transactions on Pattern Analysis and Machine
    Intelligence</i>. IEEE. <a href="https://doi.org/10.1109/TPAMI.2007.1031">https://doi.org/10.1109/TPAMI.2007.1031</a>
  chicago: Kolmogorov, Vladimir, and Carsten Rother. “Minimizing Nonsubmodular Functions
    with Graph Cuts - A Review.” <i>IEEE Transactions on Pattern Analysis and Machine
    Intelligence</i>. IEEE, 2007. <a href="https://doi.org/10.1109/TPAMI.2007.1031">https://doi.org/10.1109/TPAMI.2007.1031</a>.
  ieee: V. Kolmogorov and C. Rother, “Minimizing nonsubmodular functions with graph
    cuts - A review,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>,
    vol. 29, no. 7. IEEE, pp. 1274–1279, 2007.
  ista: Kolmogorov V, Rother C. 2007. Minimizing nonsubmodular functions with graph
    cuts - A review. IEEE Transactions on Pattern Analysis and Machine Intelligence.
    29(7), 1274–1279.
  mla: Kolmogorov, Vladimir, and Carsten Rother. “Minimizing Nonsubmodular Functions
    with Graph Cuts - A Review.” <i>IEEE Transactions on Pattern Analysis and Machine
    Intelligence</i>, vol. 29, no. 7, IEEE, 2007, pp. 1274–79, doi:<a href="https://doi.org/10.1109/TPAMI.2007.1031">10.1109/TPAMI.2007.1031</a>.
  short: V. Kolmogorov, C. Rother, IEEE Transactions on Pattern Analysis and Machine
    Intelligence 29 (2007) 1274–1279.
date_created: 2018-12-11T12:01:56Z
date_published: 2007-07-01T00:00:00Z
date_updated: 2021-01-12T07:41:42Z
day: '01'
doi: 10.1109/TPAMI.2007.1031
extern: 1
intvolume: '        29'
issue: '7'
month: '07'
page: 1274 - 1279
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3491'
quality_controlled: 0
status: public
title: Minimizing nonsubmodular functions with graph cuts - A review
type: journal_article
volume: 29
year: '2007'
...
---
_id: '3218'
abstract:
- lang: eng
  text: 'A (k, ℓ)-robust combiner for collision-resistant hash-functions is a construction
    which from ℓ hash-functions constructs a hash-function which is collision-resistant
    if at least k of the components are collision-resistant. One trivially gets a
    (k, ℓ)-robust combiner by concatenating the output of any ℓ - k + 1 of the components,
    unfortunately this is not very practical as the length of the output of the combiner
    is quite large. We show that this is unavoidable as no black-box (k, ℓ)-robust
    combiner whose output is significantly shorter than what can be achieved by concatenation
    exists. This answers a question of Boneh and Boyen (Crypto''06). '
acknowledgement: Supported by DIAMANT, the Dutch national mathematics cluster for
  discrete interactive and algorithmic algebra and number theory.
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. Non-trivial black-box combiners for collision-resistant hash-functions
    don’t exist. In: Vol 4515. Springer; 2007:23-33. doi:<a href="https://doi.org/10.1007/978-3-540-72540-4_2">10.1007/978-3-540-72540-4_2</a>'
  apa: 'Pietrzak, K. Z. (2007). Non-trivial black-box combiners for collision-resistant
    hash-functions don’t exist (Vol. 4515, pp. 23–33). Presented at the EUROCRYPT:
    Theory and Applications of Cryptographic Techniques, Springer. <a href="https://doi.org/10.1007/978-3-540-72540-4_2">https://doi.org/10.1007/978-3-540-72540-4_2</a>'
  chicago: Pietrzak, Krzysztof Z. “Non-Trivial Black-Box Combiners for Collision-Resistant
    Hash-Functions Don’t Exist,” 4515:23–33. Springer, 2007. <a href="https://doi.org/10.1007/978-3-540-72540-4_2">https://doi.org/10.1007/978-3-540-72540-4_2</a>.
  ieee: 'K. Z. Pietrzak, “Non-trivial black-box combiners for collision-resistant
    hash-functions don’t exist,” presented at the EUROCRYPT: Theory and Applications
    of Cryptographic Techniques, 2007, vol. 4515, pp. 23–33.'
  ista: 'Pietrzak KZ. 2007. Non-trivial black-box combiners for collision-resistant
    hash-functions don’t exist. EUROCRYPT: Theory and Applications of Cryptographic
    Techniques, LNCS, vol. 4515, 23–33.'
  mla: Pietrzak, Krzysztof Z. <i>Non-Trivial Black-Box Combiners for Collision-Resistant
    Hash-Functions Don’t Exist</i>. Vol. 4515, Springer, 2007, pp. 23–33, doi:<a href="https://doi.org/10.1007/978-3-540-72540-4_2">10.1007/978-3-540-72540-4_2</a>.
  short: K.Z. Pietrzak, in:, Springer, 2007, pp. 23–33.
conference:
  name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:05Z
date_published: 2007-06-12T00:00:00Z
date_updated: 2021-01-12T07:41:52Z
day: '12'
doi: 10.1007/978-3-540-72540-4_2
extern: 1
intvolume: '      4515'
month: '06'
page: 23 - 33
publication_status: published
publisher: Springer
publist_id: '3461'
quality_controlled: 0
status: public
title: Non-trivial black-box combiners for collision-resistant hash-functions don't
  exist
type: conference
volume: 4515
year: '2007'
...
---
_id: '3219'
abstract:
- lang: eng
  text: 'Many aspects of cryptographic security proofs can be seen as the proof that
    a certain system (e.g. a block cipher) is indistinguishable from an ideal system
    (e.g. a random permutation), for different types of distinguishers. This paper
    presents a new generic approach to proving upper bounds on the information-theoretic
    distinguishing advantage (from an ideal system) for a combined system, assuming
    upper bounds of certain types for the component systems. For a general type of
    combination operation of systems, including the XOR of functions or the cascade
    of permutations, we prove two amplification theorems. The first is a product theorem,
    in the spirit of XOR-lemmas: The distinguishing advantage of the combination of
    two systems is at most twice the product of the individual distinguishing advantages.
    This bound is optimal. The second theorem states that the combination of systems
    is secure against some strong class of distinguishers, assuming only that the
    components are secure against some weaker class of distinguishers. A key technical
    tool of the paper is the proof of a tight two-way correspondence, previously only
    known to hold in one direction, between the distinguishing advantage of two systems
    and the probability of winning an appropriately defined game. © International
    Association for Cryptologic Research 2007.'
alternative_title:
- LNCS
author:
- first_name: Ueli
  full_name: Maurer, Ueli M
  last_name: Maurer
- first_name: Krzysztof Z
  full_name: Krzysztof Pietrzak
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
- first_name: Renato
  full_name: Renner, Renato
  last_name: Renner
citation:
  ama: 'Maurer U, Pietrzak KZ, Renner R. Indistinguishability amplification. In: Vol
    4622. Springer; 2007:130-149. doi:<a href="https://doi.org/10.1007/978-3-540-74143-5_8">10.1007/978-3-540-74143-5_8</a>'
  apa: 'Maurer, U., Pietrzak, K. Z., &#38; Renner, R. (2007). Indistinguishability
    amplification (Vol. 4622, pp. 130–149). Presented at the CRYPTO: International
    Cryptology Conference, Springer. <a href="https://doi.org/10.1007/978-3-540-74143-5_8">https://doi.org/10.1007/978-3-540-74143-5_8</a>'
  chicago: Maurer, Ueli, Krzysztof Z Pietrzak, and Renato Renner. “Indistinguishability
    Amplification,” 4622:130–49. Springer, 2007. <a href="https://doi.org/10.1007/978-3-540-74143-5_8">https://doi.org/10.1007/978-3-540-74143-5_8</a>.
  ieee: 'U. Maurer, K. Z. Pietrzak, and R. Renner, “Indistinguishability amplification,”
    presented at the CRYPTO: International Cryptology Conference, 2007, vol. 4622,
    pp. 130–149.'
  ista: 'Maurer U, Pietrzak KZ, Renner R. 2007. Indistinguishability amplification.
    CRYPTO: International Cryptology Conference, LNCS, vol. 4622, 130–149.'
  mla: Maurer, Ueli, et al. <i>Indistinguishability Amplification</i>. Vol. 4622,
    Springer, 2007, pp. 130–49, doi:<a href="https://doi.org/10.1007/978-3-540-74143-5_8">10.1007/978-3-540-74143-5_8</a>.
  short: U. Maurer, K.Z. Pietrzak, R. Renner, in:, Springer, 2007, pp. 130–149.
conference:
  name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:05Z
date_published: 2007-10-03T00:00:00Z
date_updated: 2021-01-12T07:41:53Z
day: '03'
doi: 10.1007/978-3-540-74143-5_8
extern: 1
intvolume: '      4622'
month: '10'
page: 130 - 149
publication_status: published
publisher: Springer
publist_id: '3462'
quality_controlled: 0
status: public
title: Indistinguishability amplification
type: conference
volume: 4622
year: '2007'
...
---
_id: '3220'
abstract:
- lang: eng
  text: We introduce a new primitive called intrusion-resilient secret sharing (IRSS),
    whose security proof exploits the fact that there exist functions which can be
    efficiently computed interactively using low communication complexity in k, but
    not in k-1 rounds. IRSS is a means of sharing a secret message amongst a set of
    players which comes with a very strong security guarantee. The shares in an IRSS
    are made artificially large so that it is hard to retrieve them completely, and
    the reconstruction procedure is interactive requiring the players to exchange
    k short messages. The adversaries considered can attack the scheme in rounds,
    where in each round the adversary chooses some player to corrupt and some function,
    and retrieves the output of that function applied to the share of the corrupted
    player. This model captures for example computers connected to a network which
    can occasionally he infected by malicious software like viruses, which can compute
    any function on the infected machine, but cannot sent out a huge amount of data.
    Using methods from the bounded-retrieval model, we construct an IRSS scheme which
    is secure against any computationally unbounded adversary as long as the total
    amount of information retrieved by the adversary is somewhat less than the length
    of the shares, and the adversary makes at most k-1 corruption rounds (as described
    above, where k rounds are necessary for reconstruction). We extend our basic scheme
    in several ways in order to allow the shares sent by the dealer to be short (the
    players then blow them up locally) and to handle even stronger adversaries who
    can learn some of the shares completely. As mentioned, there is an obvious connection
    between IRSS schemes and the fact that there exist functions with an exponential
    gap in their communication complexity for k and k-1 rounds. Our scheme implies
    such a separation which is in several aspects stronger than the previously known
    ones.
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. Intrusion resilient secret sharing. In: IEEE;
    2007:227-237. doi:<a href="https://doi.org/10.1109/FOCS.2007.63">10.1109/FOCS.2007.63</a>'
  apa: 'Dziembowski, S., &#38; Pietrzak, K. Z. (2007). Intrusion resilient secret
    sharing (pp. 227–237). Presented at the FOCS: Foundations of Computer Science,
    IEEE. <a href="https://doi.org/10.1109/FOCS.2007.63">https://doi.org/10.1109/FOCS.2007.63</a>'
  chicago: Dziembowski, Stefan, and Krzysztof Z Pietrzak. “Intrusion Resilient Secret
    Sharing,” 227–37. IEEE, 2007. <a href="https://doi.org/10.1109/FOCS.2007.63">https://doi.org/10.1109/FOCS.2007.63</a>.
  ieee: 'S. Dziembowski and K. Z. Pietrzak, “Intrusion resilient secret sharing,”
    presented at the FOCS: Foundations of Computer Science, 2007, pp. 227–237.'
  ista: 'Dziembowski S, Pietrzak KZ. 2007. Intrusion resilient secret sharing. FOCS:
    Foundations of Computer Science, 227–237.'
  mla: Dziembowski, Stefan, and Krzysztof Z. Pietrzak. <i>Intrusion Resilient Secret
    Sharing</i>. IEEE, 2007, pp. 227–37, doi:<a href="https://doi.org/10.1109/FOCS.2007.63">10.1109/FOCS.2007.63</a>.
  short: S. Dziembowski, K.Z. Pietrzak, in:, IEEE, 2007, pp. 227–237.
conference:
  name: 'FOCS: Foundations of Computer Science'
date_created: 2018-12-11T12:02:05Z
date_published: 2007-10-23T00:00:00Z
date_updated: 2021-01-12T07:41:54Z
day: '23'
doi: 10.1109/FOCS.2007.63
extern: 1
month: '10'
page: 227 - 237
publication_status: published
publisher: IEEE
publist_id: '3459'
quality_controlled: 0
status: public
title: Intrusion resilient secret sharing
type: conference
year: '2007'
...
---
_id: '3221'
abstract:
- lang: eng
  text: |-
    We investigate a general class of (black-box) constructions for range extension of weak pseudorandom functions: a construction based on m independent functions F 1,...,F m is given by a set of strings over {1,...,m}*, where for example {〈2〉, 〈1,2〉} corresponds to the function X ↦[F 2(X),F 2(F 1(X))]. All efficient constructions for range expansion of weak pseudorandom functions that we are aware of are of this form.
    We completely classify such constructions as good, bad or ugly, where the good constructions are those whose security can be proven via a black-box reduction, the bad constructions are those whose insecurity can be proven via a black-box reduction, and the ugly constructions are those which are neither good nor bad.
    Our classification shows that the range expansion from [10] is optimal, in the sense that it achieves the best possible expansion (2 m  − 1 when using m keys).
    Along the way we show that for weak quasirandom functions (i.e. in the information theoretic setting), all constructions which are not bad – in particular all the ugly ones – are secure.
acknowledgement: This work was partially supported by the Zurich Information Security
  Center. It represents the views of the authors.
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. Range extension for weak PRFs the good the bad and
    the ugly. In: Vol 4515. Springer; 2007:517-533. doi:<a href="https://doi.org/10.1007/978-3-540-72540-4_30">10.1007/978-3-540-72540-4_30</a>'
  apa: 'Pietrzak, K. Z., &#38; Sjödin, J. (2007). Range extension for weak PRFs the
    good the bad and the ugly (Vol. 4515, pp. 517–533). Presented at the EUROCRYPT:
    Theory and Applications of Cryptographic Techniques, Springer. <a href="https://doi.org/10.1007/978-3-540-72540-4_30">https://doi.org/10.1007/978-3-540-72540-4_30</a>'
  chicago: Pietrzak, Krzysztof Z, and Johan Sjödin. “Range Extension for Weak PRFs
    the Good the Bad and the Ugly,” 4515:517–33. Springer, 2007. <a href="https://doi.org/10.1007/978-3-540-72540-4_30">https://doi.org/10.1007/978-3-540-72540-4_30</a>.
  ieee: 'K. Z. Pietrzak and J. Sjödin, “Range extension for weak PRFs the good the
    bad and the ugly,” presented at the EUROCRYPT: Theory and Applications of Cryptographic
    Techniques, 2007, vol. 4515, pp. 517–533.'
  ista: 'Pietrzak KZ, Sjödin J. 2007. Range extension for weak PRFs the good the bad
    and the ugly. EUROCRYPT: Theory and Applications of Cryptographic Techniques,
    LNCS, vol. 4515, 517–533.'
  mla: Pietrzak, Krzysztof Z., and Johan Sjödin. <i>Range Extension for Weak PRFs
    the Good the Bad and the Ugly</i>. Vol. 4515, Springer, 2007, pp. 517–33, doi:<a
    href="https://doi.org/10.1007/978-3-540-72540-4_30">10.1007/978-3-540-72540-4_30</a>.
  short: K.Z. Pietrzak, J. Sjödin, in:, Springer, 2007, pp. 517–533.
conference:
  name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
date_created: 2018-12-11T12:02:06Z
date_published: 2007-06-12T00:00:00Z
date_updated: 2021-01-12T07:41:54Z
day: '12'
doi: 10.1007/978-3-540-72540-4_30
extern: 1
intvolume: '      4515'
month: '06'
page: 517 - 533
publication_status: published
publisher: Springer
publist_id: '3460'
quality_controlled: 0
status: public
title: Range extension for weak PRFs the good the bad and the ugly
type: conference
volume: 4515
year: '2007'
...
---
_id: '3222'
abstract:
- lang: eng
  text: |-
    Parallel repetition is well known to reduce the error probability at an exponential rate for single- and multi-prover interactive proofs.
    Bellare, Impagliazzo and Naor (1997) show that this is also true for protocols where the soundness only holds against computationally bounded provers (e.g. interactive arguments) if the protocol has at most three rounds.
    On the other hand, for four rounds they give a protocol where this is no longer the case: the error probability does not decrease below some constant even if the protocol is repeated a polynomial number of times. Unfortunately, this protocol is not very convincing as the communication complexity of each instance of the protocol grows linearly with the number of repetitions, and for such protocols the error does not even decrease for some types of interactive proofs. Noticing this, Bellare et al. construct (a quite artificial) oracle relative to which a four round protocol exists whose communication complexity does not depend on the number of parallel repetitions. This shows that there is no “black-box” error reduction theorem for four round protocols.
    In this paper we give the first computationally sound protocol where k-fold parallel repetition does not decrease the error probability below some constant for any polynomial k (and where the communication complexity does not depend on k). The protocol has eight rounds and uses the universal arguments of Barak and Goldreich (2001). We also give another four round protocol relative to an oracle, unlike the artificial oracle of Bellare et al., we just need a generic group. This group can then potentially be instantiated with some real group satisfying some well defined hardness assumptions (we do not know of any candidate for such a group at the moment).
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: Douglas
  full_name: Wikström, Douglas
  last_name: Wikström
citation:
  ama: 'Pietrzak KZ, Wikström D. Parallel repetition of computationally sound protocols
    revisited. In: Vol 4392. Springer; 2007:86-102. doi:<a href="https://doi.org/10.1007/978-3-540-70936-7_5">10.1007/978-3-540-70936-7_5</a>'
  apa: 'Pietrzak, K. Z., &#38; Wikström, D. (2007). Parallel repetition of computationally
    sound protocols revisited (Vol. 4392, pp. 86–102). Presented at the TCC: Theory
    of Cryptography Conference, Springer. <a href="https://doi.org/10.1007/978-3-540-70936-7_5">https://doi.org/10.1007/978-3-540-70936-7_5</a>'
  chicago: Pietrzak, Krzysztof Z, and Douglas Wikström. “Parallel Repetition of Computationally
    Sound Protocols Revisited,” 4392:86–102. Springer, 2007. <a href="https://doi.org/10.1007/978-3-540-70936-7_5">https://doi.org/10.1007/978-3-540-70936-7_5</a>.
  ieee: 'K. Z. Pietrzak and D. Wikström, “Parallel repetition of computationally sound
    protocols revisited,” presented at the TCC: Theory of Cryptography Conference,
    2007, vol. 4392, pp. 86–102.'
  ista: 'Pietrzak KZ, Wikström D. 2007. Parallel repetition of computationally sound
    protocols revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 4392,
    86–102.'
  mla: Pietrzak, Krzysztof Z., and Douglas Wikström. <i>Parallel Repetition of Computationally
    Sound Protocols Revisited</i>. Vol. 4392, Springer, 2007, pp. 86–102, doi:<a href="https://doi.org/10.1007/978-3-540-70936-7_5">10.1007/978-3-540-70936-7_5</a>.
  short: K.Z. Pietrzak, D. Wikström, in:, Springer, 2007, pp. 86–102.
conference:
  name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:06Z
date_published: 2007-03-22T00:00:00Z
date_updated: 2021-01-12T07:41:54Z
day: '22'
doi: 10.1007/978-3-540-70936-7_5
extern: 1
intvolume: '      4392'
month: '03'
page: 86 - 102
publication_status: published
publisher: Springer
publist_id: '3457'
quality_controlled: 0
status: public
title: Parallel repetition of computationally sound protocols revisited
type: conference
volume: 4392
year: '2007'
...
---
_id: '3223'
abstract:
- lang: eng
  text: |-
    “Hash then encrypt” is an approach to message authentication, where first the message is hashed down using an ε-universal hash function, and then the resulting k-bit value is encrypted, say with a block-cipher. The security of this scheme is proportional to εq2, where q is the number of MACs the adversary can request. As ε is at least 2−k, the best one can hope for is O(q2/2k) security. Unfortunately, such small ε is not achieved by simple hash functions used in practice, such as the polynomial evaluation or the Merkle-Damg ̊ard construction, where ε grows with the message length L.
    The main insight of this work comes from the fact that, by using ran- domized message preprocessing via a short random salt p (which must then be sent as part of the authentication tag), we can use the “hash then encrypt” paradigm with suboptimal “practical” ε-universal hash func- tions, and still improve its exact security to optimal O(q2/2k). Specif- ically, by using at most an O(logL)-bit salt p, one can always regain the optimal exact security O(q2/2k), even in situations where ε grows polynomially with L. We also give very simple preprocessing maps for popular “suboptimal” hash functions, namely polynomial evaluation and the Merkle-Damg ̊ard construction.
    Our results come from a general extension of the classical Carter- Wegman paradigm, which we believe is of independent interest. On a high level, it shows that public randomization allows one to use the potentially much smaller “average-case” collision probability in place of the “worst-case” collision probability ε.
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
  full_name: Dodis, Yevgeniy
  last_name: Dodis
- first_name: Krzysztof Z
  full_name: Krzysztof Pietrzak
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
citation:
  ama: 'Dodis Y, Pietrzak KZ. Improving the security of MACs via randomized message
    preprocessing. In: Vol 4593. Springer; 2007:414-433. doi:<a href="https://doi.org/10.1007/978-3-540-74619-5_26">10.1007/978-3-540-74619-5_26</a>'
  apa: 'Dodis, Y., &#38; Pietrzak, K. Z. (2007). Improving the security of MACs via
    randomized message preprocessing (Vol. 4593, pp. 414–433). Presented at the FSE:
    Fast Software Encryption, Springer. <a href="https://doi.org/10.1007/978-3-540-74619-5_26">https://doi.org/10.1007/978-3-540-74619-5_26</a>'
  chicago: Dodis, Yevgeniy, and Krzysztof Z Pietrzak. “Improving the Security of MACs
    via Randomized Message Preprocessing,” 4593:414–33. Springer, 2007. <a href="https://doi.org/10.1007/978-3-540-74619-5_26">https://doi.org/10.1007/978-3-540-74619-5_26</a>.
  ieee: 'Y. Dodis and K. Z. Pietrzak, “Improving the security of MACs via randomized
    message preprocessing,” presented at the FSE: Fast Software Encryption, 2007,
    vol. 4593, pp. 414–433.'
  ista: 'Dodis Y, Pietrzak KZ. 2007. Improving the security of MACs via randomized
    message preprocessing. FSE: Fast Software Encryption, LNCS, vol. 4593, 414–433.'
  mla: Dodis, Yevgeniy, and Krzysztof Z. Pietrzak. <i>Improving the Security of MACs
    via Randomized Message Preprocessing</i>. Vol. 4593, Springer, 2007, pp. 414–33,
    doi:<a href="https://doi.org/10.1007/978-3-540-74619-5_26">10.1007/978-3-540-74619-5_26</a>.
  short: Y. Dodis, K.Z. Pietrzak, in:, Springer, 2007, pp. 414–433.
conference:
  name: 'FSE: Fast Software Encryption'
date_created: 2018-12-11T12:02:06Z
date_published: 2007-10-11T00:00:00Z
date_updated: 2021-01-12T07:41:55Z
day: '11'
doi: 10.1007/978-3-540-74619-5_26
extern: 1
intvolume: '      4593'
month: '10'
page: 414 - 433
publication_status: published
publisher: Springer
publist_id: '3458'
quality_controlled: 0
status: public
title: Improving the security of MACs via randomized message preprocessing
type: conference
volume: 4593
year: '2007'
...
---
_id: '3305'
abstract:
- lang: eng
  text: The accumulation of deleterious mutations plays a major role in evolution,
    and key to this are the interactions between their fitness effects, known as epistasis.
    Whether mutations tend to interact synergistically (with multiple mutations being
    more deleterious than would be expected from their individual fitness effects)
    or antagonistically is important for a variety of evolutionary questions, particularly
    the evolution of sex. Unfortunately, the experimental evidence on the prevalence
    and strength of epistasis is mixed and inconclusive. Here we study theoretically
    whether synergistic or antagonistic epistasis is likely to be favored by evolution
    and by how much. We find that in the presence of recombination, evolution favors
    less synergistic or more antagonistic epistasis whenever mutations that change
    the epistasis in this direction are possible. This is because evolution favors
    increased buffering against the effects of deleterious mutations. This suggests
    that we should not expect synergistic epistasis to be widespread in nature and
    hence that the mutational deterministic hypothesis for the advantage of sex may
    not apply widely.
author:
- first_name: Michael
  full_name: Desai, Michael M
  last_name: Desai
- first_name: Daniel
  full_name: Daniel Weissman
  id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
  last_name: Weissman
- first_name: Marcus
  full_name: Feldman, Marcus W
  last_name: Feldman
citation:
  ama: Desai M, Weissman D, Feldman M. Evolution can favor antagonistic epistasis.
    <i>Genetics</i>. 2007;177(2):1001-1010. doi:<a href="https://doi.org/10.1534/genetics.107.075812">10.1534/genetics.107.075812</a>
  apa: Desai, M., Weissman, D., &#38; Feldman, M. (2007). Evolution can favor antagonistic
    epistasis. <i>Genetics</i>. Genetics Society of America. <a href="https://doi.org/10.1534/genetics.107.075812">https://doi.org/10.1534/genetics.107.075812</a>
  chicago: Desai, Michael, Daniel Weissman, and Marcus Feldman. “Evolution Can Favor
    Antagonistic Epistasis.” <i>Genetics</i>. Genetics Society of America, 2007. <a
    href="https://doi.org/10.1534/genetics.107.075812">https://doi.org/10.1534/genetics.107.075812</a>.
  ieee: M. Desai, D. Weissman, and M. Feldman, “Evolution can favor antagonistic epistasis,”
    <i>Genetics</i>, vol. 177, no. 2. Genetics Society of America, pp. 1001–10, 2007.
  ista: Desai M, Weissman D, Feldman M. 2007. Evolution can favor antagonistic epistasis.
    Genetics. 177(2), 1001–10.
  mla: Desai, Michael, et al. “Evolution Can Favor Antagonistic Epistasis.” <i>Genetics</i>,
    vol. 177, no. 2, Genetics Society of America, 2007, pp. 1001–10, doi:<a href="https://doi.org/10.1534/genetics.107.075812">10.1534/genetics.107.075812</a>.
  short: M. Desai, D. Weissman, M. Feldman, Genetics 177 (2007) 1001–10.
date_created: 2018-12-11T12:02:34Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:32Z
day: '01'
doi: 10.1534/genetics.107.075812
extern: 1
intvolume: '       177'
issue: '2'
month: '01'
page: 1001 - 10
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3335'
quality_controlled: 0
status: public
title: Evolution can favor antagonistic epistasis
type: journal_article
volume: 177
year: '2007'
...
---
_id: '3411'
abstract:
- lang: eng
  text: Mechanical single-molecule techniques offer exciting possibilities to investigate
    protein folding and stability in native environments at submolecular resolution.
    By applying a free-energy reconstruction procedure developed by Hummer and Szabo,
    which is based on a statistical theorem introduced by Jarzynski, we determined
    the unfolding free energy of the membrane proteins bacteriorhodopsin (BR), halorhodopsin,
    and the sodium-proton antiporter NhaA. The calculated energies ranged from 290.5kcal/mol
    for BR to 485.5kcal/mol for NhaA. For the remarkably stable BR, the equilibrium
    unfolding free energy was independent of pulling rate and temperature ranging
    between 18 and 42°C. Our experiments also revealed heterogeneous energetic properties
    in individual transmembrane helices. In halorhodopsin, the stabilization of a
    short helical segment yielded a characteristic signature in the energy profile.
    In NhaA, a pronounced peak was observed at a functionally important site in the
    protein. Since a large variety of single- and multispan membrane proteins can
    be tackled in mechanical unfolding experiments, our approach provides a basis
    for systematically elucidating energetic properties of membrane proteins with
    the resolution of individual secondary-structure elements.
author:
- first_name: Johannes
  full_name: Preiner, Johannes
  last_name: Preiner
- first_name: Harald L
  full_name: Harald Janovjak
  id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
  last_name: Janovjak
  orcid: 0000-0002-8023-9315
- first_name: Christian
  full_name: Rankl, Christian
  last_name: Rankl
- first_name: Helene
  full_name: Knaus, Helene
  last_name: Knaus
- first_name: David
  full_name: Cisneros, David A
  last_name: Cisneros
- first_name: Alexej
  full_name: Kedrov, Alexej
  last_name: Kedrov
- first_name: Ferry
  full_name: Kienberger, Ferry
  last_name: Kienberger
- first_name: Daniel
  full_name: Mueller, Daniel J
  last_name: Mueller
- first_name: Peter
  full_name: Hinterdorfer, Peter
  last_name: Hinterdorfer
citation:
  ama: Preiner J, Janovjak HL, Rankl C, et al. Free energy of membrane protein unfolding
    derived from single-molecule force measurements. <i>Biophysical Journal</i>. 2007;93(3):930-937.
    doi:<a href="https://doi.org/10.1529/biophysj.106.096982">10.1529/biophysj.106.096982</a>
  apa: Preiner, J., Janovjak, H. L., Rankl, C., Knaus, H., Cisneros, D., Kedrov, A.,
    … Hinterdorfer, P. (2007). Free energy of membrane protein unfolding derived from
    single-molecule force measurements. <i>Biophysical Journal</i>. Biophysical Society.
    <a href="https://doi.org/10.1529/biophysj.106.096982">https://doi.org/10.1529/biophysj.106.096982</a>
  chicago: Preiner, Johannes, Harald L Janovjak, Christian Rankl, Helene Knaus, David
    Cisneros, Alexej Kedrov, Ferry Kienberger, Daniel Mueller, and Peter Hinterdorfer.
    “Free Energy of Membrane Protein Unfolding Derived from Single-Molecule Force
    Measurements.” <i>Biophysical Journal</i>. Biophysical Society, 2007. <a href="https://doi.org/10.1529/biophysj.106.096982">https://doi.org/10.1529/biophysj.106.096982</a>.
  ieee: J. Preiner <i>et al.</i>, “Free energy of membrane protein unfolding derived
    from single-molecule force measurements,” <i>Biophysical Journal</i>, vol. 93,
    no. 3. Biophysical Society, pp. 930–937, 2007.
  ista: Preiner J, Janovjak HL, Rankl C, Knaus H, Cisneros D, Kedrov A, Kienberger
    F, Mueller D, Hinterdorfer P. 2007. Free energy of membrane protein unfolding
    derived from single-molecule force measurements. Biophysical Journal. 93(3), 930–937.
  mla: Preiner, Johannes, et al. “Free Energy of Membrane Protein Unfolding Derived
    from Single-Molecule Force Measurements.” <i>Biophysical Journal</i>, vol. 93,
    no. 3, Biophysical Society, 2007, pp. 930–37, doi:<a href="https://doi.org/10.1529/biophysj.106.096982">10.1529/biophysj.106.096982</a>.
  short: J. Preiner, H.L. Janovjak, C. Rankl, H. Knaus, D. Cisneros, A. Kedrov, F.
    Kienberger, D. Mueller, P. Hinterdorfer, Biophysical Journal 93 (2007) 930–937.
date_created: 2018-12-11T12:03:11Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2021-01-12T07:43:18Z
day: '01'
doi: 10.1529/biophysj.106.096982
extern: 1
intvolume: '        93'
issue: '3'
main_file_link:
- open_access: '1'
  url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913163/
month: '08'
oa: 1
page: 930 - 937
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '2990'
quality_controlled: 0
status: public
title: Free energy of membrane protein unfolding derived from single-molecule force
  measurements
type: journal_article
volume: 93
year: '2007'
...
---
_id: '3412'
abstract:
- lang: eng
  text: |-
    Molecular interactions are the basic language of biological processes.
    They establish the forces interacting between the building blocks of
    proteins and other macromolecules, thus determining their functional
    roles. Because molecular interactions trigger virtually every
    biological process, approaches to decipher their language are needed.
    Single-molecule force spectroscopy (SMFS) has been used to detect
    and characterize different types of molecular interactions that occur
    between and within native membrane proteins. The first experiments
    detected and localized molecular interactions that stabilized
    membrane proteins, including how these interactions were established
    during folding of α-helical secondary structure elements into
    the native protein and how they changed with oligomerization, temperature,
    and mutations. SMFS also enables investigators to detect
    and locate molecular interactions established during ligand and inhibitor
    binding. These exciting applications provide opportunities
    for studying the molecular forces of life. Further developments will
    elucidate the origins of molecular interactions encoded in their lifetimes,
    interaction ranges, interplay, and dynamics characteristic of biological systems.
author:
- first_name: Alexej
  full_name: Kedrov, Alexej
  last_name: Kedrov
- first_name: Harald L
  full_name: Harald Janovjak
  id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
  last_name: Janovjak
  orcid: 0000-0002-8023-9315
- first_name: Tanuj
  full_name: Sapra, Tanuj K
  last_name: Sapra
- first_name: Daniel
  full_name: Mueller, Daniel J
  last_name: Mueller
citation:
  ama: Kedrov A, Janovjak HL, Sapra T, Mueller D. Deciphering molecular interactions
    of native membrane proteins by single-molecule force spectroscopy. <i>Annual Review
    of Biophysics</i>. 2007;36:233-260. doi:<a href="https://doi.org/10.1146/annurev.biophys.36.040306.132640">10.1146/annurev.biophys.36.040306.132640</a>
  apa: Kedrov, A., Janovjak, H. L., Sapra, T., &#38; Mueller, D. (2007). Deciphering
    molecular interactions of native membrane proteins by single-molecule force spectroscopy.
    <i>Annual Review of Biophysics</i>. Annual Reviews. <a href="https://doi.org/10.1146/annurev.biophys.36.040306.132640">https://doi.org/10.1146/annurev.biophys.36.040306.132640</a>
  chicago: Kedrov, Alexej, Harald L Janovjak, Tanuj Sapra, and Daniel Mueller. “Deciphering
    Molecular Interactions of Native Membrane Proteins by Single-Molecule Force Spectroscopy.”
    <i>Annual Review of Biophysics</i>. Annual Reviews, 2007. <a href="https://doi.org/10.1146/annurev.biophys.36.040306.132640">https://doi.org/10.1146/annurev.biophys.36.040306.132640</a>.
  ieee: A. Kedrov, H. L. Janovjak, T. Sapra, and D. Mueller, “Deciphering molecular
    interactions of native membrane proteins by single-molecule force spectroscopy,”
    <i>Annual Review of Biophysics</i>, vol. 36. Annual Reviews, pp. 233–260, 2007.
  ista: Kedrov A, Janovjak HL, Sapra T, Mueller D. 2007. Deciphering molecular interactions
    of native membrane proteins by single-molecule force spectroscopy. Annual Review
    of Biophysics. 36, 233–260.
  mla: Kedrov, Alexej, et al. “Deciphering Molecular Interactions of Native Membrane
    Proteins by Single-Molecule Force Spectroscopy.” <i>Annual Review of Biophysics</i>,
    vol. 36, Annual Reviews, 2007, pp. 233–60, doi:<a href="https://doi.org/10.1146/annurev.biophys.36.040306.132640">10.1146/annurev.biophys.36.040306.132640</a>.
  short: A. Kedrov, H.L. Janovjak, T. Sapra, D. Mueller, Annual Review of Biophysics
    36 (2007) 233–260.
date_created: 2018-12-11T12:03:11Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2019-04-26T07:22:27Z
day: '01'
doi: 10.1146/annurev.biophys.36.040306.132640
extern: 1
intvolume: '        36'
month: '06'
page: 233 - 260
publication: Annual Review of Biophysics
publication_status: published
publisher: Annual Reviews
publist_id: '2989'
quality_controlled: 0
status: public
title: Deciphering molecular interactions of native membrane proteins by single-molecule
  force spectroscopy
type: review
volume: 36
year: '2007'
...
