Ontology highlight
ABSTRACT:
PROVIDER: PRJNA646686 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12235435_1.fastq.gz | Fastqsanger.gz | |||
| SRR12235435_2.fastq.gz | Fastqsanger.gz | |||
| SRR12235436_1.fastq.gz | Fastqsanger.gz | |||
| SRR12235436_2.fastq.gz | Fastqsanger.gz | |||
| SRR12235437_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 54 |
Similar Datasets
Project description:This model is from the article:
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ.
Proc Natl Acad Sci U S A.2012 Mar 20;109(12):4668-73
22393022,
Abstract:
Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.
This model corresponds to the simplified model described in the article. It is assumed that, on the timescale of DII-VENUS degradation, the concentrations of auxin, TIR1/AFB, and their complexes can be approximated by quasi-steady-state expressions. This reduced the full model to a single ODE that describes how the DII-VENUS dynamics depend on the auxin influx and four parameter groupings.
2024-09-02 | BIOMD0000000414 | BioModels
Project description:This model is from the article:
The auxin signalling network translates dynamic input into robust patterning at the shoot apex.
Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J. Mol Syst Biol.
2011 Jul 5;7:508. 21734647
,
Abstract:
The plant hormone auxin is thought to provide positional information for patterning during development. It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is sensed in space and time. The control of gene expression in response to auxin involves a complex network of over 50 potentially interacting transcriptional activators and repressors, the auxin response factors (ARFs) and Aux/IAAs. Here, we perform a large-scale analysis of the Aux/IAA-ARF pathway in the shoot apex of Arabidopsis, where dynamic auxin-based patterning controls organogenesis. A comprehensive expression map and full interactome uncovered an unexpectedly simple distribution and structure of this pathway in the shoot apex. A mathematical model of the Aux/IAA-ARF network predicted a strong buffering capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predictions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunction with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin signalling network is essential to create robust patterns at the shoot apex. Note:
Figure 4 of the supplementary material of the reference article has been reproduced here. In this model, the fluctuations of auxin level is represented using sinux function. Time evolution of the variables AUX/IAA (I) and mRNA (R) are plotted, under the influence of fluctuations of auxin level. pi_A is varied between 0 and 2 by steps of 0.1.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use
.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000352 | BioModels
Project description:This model is from the article:
The auxin signalling network translates dynamic input into robust patterning at the shoo
t apex.
Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D
, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M
, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J. Mol Syst Biol.
2011 Jul 5;7:508. 21734647
,
Abstract:
The plant hormone auxin is thought to provide positional information for patterning during development.
It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is
sensed in space and time. The control of gene expression in response to auxin involves a complex netwo
rk of over 50 potentially interacting transcriptional activators and repressors, the auxin response fac
tors (ARFs) and Aux/IAAs. Here, we perform a large-scale analysis of the Aux/IAA-ARF pathway in the sho
ot apex of Arabidopsis, where dynamic auxin-based patterning controls organogenesis. A comprehensive ex
pression map and full interactome uncovered an unexpectedly simple distribution and structure of this p
athway in the shoot apex. A mathematical model of the Aux/IAA-ARF network predicted a strong buffering
capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predic
tions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunct
ion with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin
signalling network is essential to create robust patterns at the shoot apex. Note:
Figure 3 of the supplementary material of the reference article has been reproduced here. Time evolution of all the variables in the model are plotted, under the influence of a step input of auxin level (auxin=5, when time>1000; 0.11, otherwise). pi_A is varied between 0 and 2 by steps of 0.1.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use
.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000351 | BioModels
Project description:This model is from the article:
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ.
Proc Natl Acad Sci U S A.2012 Mar 20;109(12):4668-73
22393022,
Abstract:
Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.
This model corresponds to the full model described in the article.
2024-09-02 | BIOMD0000000413 | BioModels
Project description:We provide an atlas of gene and protein expression in Arabidopsis root hair cells, generated by paired-end RNA-seq and LC/MS-MS analysis from protoplasts that carry the root hair-specific pEXP7-GFP reporter construct. In total, transcripts from 23,234 genes were detected in root hairs; those related to cell wall biosynthesis and translation differed most dramatically in abundance when compared to non-GFP root protoplasts.
2012-12-04 | E-MTAB-4375 | biostudies-arrayexpress
Project description:In maize, nitrate regulates root development thanks to the coordinated action of many players. In this study, the involvement of SLs and auxin as putative downstream components of the nitrate regulation of lateral root development was investigated. To this aim, the endogenous SL content of maize root in response to nitrate availability was assessed by means of LC-MS/MS and measurements of lateral root density in the presence of analogues or inhibitors of auxin and strigolactones were performed. Furthermore, un untargeted RNA-seq based approach was used to better characterize the participation of auxin and strigolacotones to the transcriptional signature of maize root response to nitrate. Our results suggested that N deprivation toughly induces zealactone and carlactonoic acid biosynthesis in maize root, to a higher extent if compared to P-deprived roots. Moreover, data on lateral root density led to hypothesise the existence of both auxin-dependent and auxin-independent effects of nitrate on LR development. In addition, the inhibition of SL biosynthesis seems to participate to the auxin-dependent induction of LR, but the involvement of further downstream unknown components cannot be ruled out.
2021-04-11 | GSE162411 | GEO
Project description:A human organoid culture system was set up to grow enteroendocrine cells with a venus labeled on the glucagon gene promoter sequence. This enabled the sorting of glucagon gene positive cells from negative cells, thereby enabling the enrichment of glucagon producing cells for study. Both Venus positive and venus negative cell populations were collected and their peptidome was assessed using nano LC-MS/MS
2020-07-01 | PXD017825 | Pride
Project description:ES derived Flk-1+ cells were separated by sorting into Hoxb6 positive and negative populations by Venus reporter. Gene expression was compared between these two groups. Duplicate analysis of Hoxb6-Venus positive and negative Flk-1+ cells.
2013-04-16 | E-GEOD-45191 | biostudies-arrayexpress