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“PCD”

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Method / resourceobservedoriginal resultpositivemeasured

Claim · model-written summary

Flow cytometry distinguished living, early PCD and late PCD cells.

Taxon: poplarPopuluse1
Outcome: living cellse0
Comparator: early PCD cellse0

Verbatim

e0
“living cells (annexin V-FITC negative/PI negative), early PCD cells (annexin V-FITC positive/PI negative), and late PCD cells (annexin V-FITC positive/PI positive) could be finely distinguished through this method and then subjected for quantitative analysis”
✓ located verbatim in the source · abstract, characters 655–913

e1
“xylem cell protoplasts from poplar stem”
✓ located verbatim in the source · abstract, characters 479–518

Title

A method for analyzing programmed cell death in xylem development by flow cytometry

Ying-Li Liu; Ying-Hua Guo; Xue-Qin Song; et al. Frontiers in Plant Science 2023. doi:10.3389/fpls.2023.1196618

Other claims from this paper (2)

Method / resource Marker gene expression agreed with cell morphology.
Method / resource The FACS method can be used to study programmed cell death in woody plants.

Method / resourceobservedoriginal resultmeasured

Claim · model-written summary

An array of specific promoter reporter lines for developmental PCD was established.

Taxon: ArabidopsisArabidopsise0
Outcome: promoter-reporter lines for developmental PCDe0
Value: an arraye0

Verbatim

e0
“we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis”
✓ located verbatim in the source · abstract, characters 1184–1280

Title

A conserved core of PCD indicator genes discriminates developmentally and environmentally induced programmed cell death in plants

Yadira Olvera-Carrillo; Michiel Van Bel; Tom Van Hautegem; et al. PLANT PHYSIOLOGY 2015. doi:10.1104/pp.15.00769

Other claims from this paper (3)

Observation Developmental and environmental cell death had largely distinct transcriptional signatures.
Observation Different developmental cell death cases shared a gene set.
Observation Most shared genes were conserved in the green plant lineage.

Method / resourceobservedoriginal resultmeasured

Claim · model-written summary

The analysis identified putative PCD transcriptional regulators.

Taxon: ArabidopsisArabidopsist0
Outcome: putative transcriptional regulators of PCDe0

Not reportedValue

Verbatim

e0
“identification of putative transcriptional regulators of PCD in plants”
✓ located verbatim in the source · abstract, characters 918–988

t0
“Arabidopsis”
✓ located verbatim in the source · title, characters 0–11

Title

Arabidopsis cell suspension culture and RNA sequencing reveal regulatory networks underlying plant‐programmed cell death

Rory Burke; Aideen McCabe; Neetu Ramesh Sonawane; et al. The Plant Journal 2023. doi:10.1111/tpj.16407

Other claims from this paper (6)

Method / resource The treatment and modulator design enabled isolation of candidate core and stimulus-specific PCD genes.
Method / resource The analysis inferred regulatory networks underlying programmed cell death.
Observation Cell-cycle disturbance was a key feature of the PCD transcriptional signature.
Observation Mitochondrial retrograde signaling was implicated in the PCD transcriptional signature.
Observation Pro-survival stress responses were repressed in the PCD signature.
Method / resource Phenotyping insertion mutants validated the resource for identifying PCD and stress-tolerance genes.

Method / resourceobservedoriginal resultpositivemeasured

Claim · model-written summary

Third stalk internodes supplied more reliable PCD data than other internodes.

Taxon: cornZea mays subsp. mayse1
Outcome: PCD datae0
Direction: more reliablee0
Comparator: the otherse0

Verbatim

e0
“the third internodes provided more reliable PCD data than the others”
✓ located verbatim in the source · abstract, characters 1464–1532

e1
“corn ( Zea mays L.)”
✓ located verbatim in the source · abstract, characters 58–77

Title

Genetics of Parenchyma Cell Death in Corn Stalk Internodes and Leaf Midribs

S. Dronavalli; Manjit S. Kang; D. P. Gorman Crop Science 1992. doi:10.2135/cropsci1992.0011183x003200060037x

Other claims from this paper (9)

Observation Specific combining ability exceeded general combining ability for stalk pith cell death.
Association A632, B73, and Mo17 synthetics had significant negative GCA effects on PCD.
Association Three named crosses had significant positive SCA effects for PCD.
Association Pith cell death was significantly lower in leafy plants.
Association Midrib and stalk cell death were uncorrelated genetically and phenotypically.
Observation Both GCA and SCA were important for midrib cell death.
Association A632 and B73 had negative GCA effects on both LMCD and PCD.
Association The 914 synthetic had positive GCA effects on both LMCD and PCD.
Association Leafy plants had significantly lower mean midrib cell death in two of three environments.

Method / resourceobservedoriginal resultno effectnot significant (as stated)measured

Claim · model-written summary

PCD from airborne imagery had no significant correlation with berry quality attributes.

Taxon: Vitis vinifera L. ‘Chardonnay’Vitis viniferae0
Outcome: correlation against berry quality attributese1
Comparator: PCD derived from airborne imagerye1

Not reportedDirection

Verbatim

e0
“Vitis vinifera L. ‘Chardonnay’”
✓ located verbatim in the source · abstract, characters 671–701

e1
“PCD derived from airborne imagery, as well as the SR, did not show significant correlation against berry quality attributes”
✓ located verbatim in the source · abstract, characters 1453–1576

Title

IS PCD A RELIABLE INDICATOR OF BERRY QUALITY ATTRIBUTES IN WATER STRESSED VINEYARDS?

J.M. Pons; L. Serrano; C. Gonzales-Flor; et al. Acta Horticulturae 2013. doi:10.17660/actahortic.2013.978.8

Other claims from this paper (8)

Observation Predawn water potential ranged from -0.85±0.06 MPa to -0.50±0.07 MPa.
Association Berry quality attributes had no significant relationship with fIPAR.
Association Berry quality attributes were variably related to midday canopy-to-air temperature difference.
Method / resource SR had no significant correlation with berry quality attributes.
Association WI correlated significantly with midday canopy-to-air temperature difference at r = -0.82.
Method / resource WI estimated titratable acidity at r = 0.70.
Method / resource WI estimated maturation index at r = 0.70.
Recommendation WI may be more appropriate than SR or PCD for characterizing berry composition in water-deficit vineyards.

Method / resourceobservedoriginal resultpositivemeasured

Claim · model-written summary

Wheat PCD differences under heat were greatest at 35 °C.

Taxon: wheatTriticum aestivume0
Treatment: heate0
Outcome: PCD inflection pointse0
Value: 35 °Ce0

Verbatim

e0
“response of eight wheat varieties to heat and salt stress allowed identification of their PCD inflection points (35 °C and 150 mM NaCl), where the largest differences in PCD levels arise”
✓ located verbatim in the source · abstract, characters 739–925

Title

Sorting the Wheat From the Chaff: Programmed Cell Death as a Marker of Stress Tolerance in Agriculturally Important Cereals

Alysha Chua; Laurence Fitzhenry; Cara T. Daly Frontiers in Plant Science 2019. doi:10.3389/fpls.2019.01539

Other claims from this paper (8)

Method / resource PCD susceptibility separated winter and spring barley varieties after heat shock.
Method / resource Wheat PCD differences under salt were greatest at 150 mM NaCl.
Association Heat-susceptible wheat varieties were similarly vulnerable to salt stress.
Method / resource Stress-induced PCD supported assessment of basal, induced, and cross-stress wheat tolerance.
Observation Two susceptible wheat varieties had high PCD under single and combined stress exposure.
Observation PCD declined later in both susceptible varieties, indicating rapid adaptation.
Method / resource The root hair assay supported high-throughput cereal analysis in about four days.
Recommendation The authors propose using laboratory PCD screening to target later field trials.

Method / resourceobservedoriginal resultmeasured

Claim · model-written summary

The treatment and modulator design enabled isolation of candidate core and stimulus-specific PCD genes.

Taxon: ArabidopsisArabidopsist0
Outcome: isolation of candidate core- and stimuli-specific PCD genese0

Not reportedValue

Verbatim

e0
“enabled isolation of candidate core- and stimuli-specific PCD genes”
✓ located verbatim in the source · abstract, characters 801–868

t0
“Arabidopsis”
✓ located verbatim in the source · title, characters 0–11

Title

Arabidopsis cell suspension culture and RNA sequencing reveal regulatory networks underlying plant‐programmed cell death

Rory Burke; Aideen McCabe; Neetu Ramesh Sonawane; et al. The Plant Journal 2023. doi:10.1111/tpj.16407

Other claims from this paper (6)

Method / resource The analysis inferred regulatory networks underlying programmed cell death.
Method / resource The analysis identified putative PCD transcriptional regulators.
Observation Cell-cycle disturbance was a key feature of the PCD transcriptional signature.
Observation Mitochondrial retrograde signaling was implicated in the PCD transcriptional signature.
Observation Pro-survival stress responses were repressed in the PCD signature.
Method / resource Phenotyping insertion mutants validated the resource for identifying PCD and stress-tolerance genes.

Method / resourceobservedoriginal resultpositivemeasured

Claim · model-written summary

Wheat PCD differences under salt were greatest at 150 mM NaCl.

Taxon: wheatTriticum aestivume0
Treatment: salt stresse0
Outcome: PCD inflection pointse0
Value: 150 mM NaCle0

Verbatim

e0
“response of eight wheat varieties to heat and salt stress allowed identification of their PCD inflection points (35 °C and 150 mM NaCl), where the largest differences in PCD levels arise”
✓ located verbatim in the source · abstract, characters 739–925

Title

Sorting the Wheat From the Chaff: Programmed Cell Death as a Marker of Stress Tolerance in Agriculturally Important Cereals

Alysha Chua; Laurence Fitzhenry; Cara T. Daly Frontiers in Plant Science 2019. doi:10.3389/fpls.2019.01539

Other claims from this paper (8)

Method / resource PCD susceptibility separated winter and spring barley varieties after heat shock.
Method / resource Wheat PCD differences under heat were greatest at 35 °C.
Association Heat-susceptible wheat varieties were similarly vulnerable to salt stress.
Method / resource Stress-induced PCD supported assessment of basal, induced, and cross-stress wheat tolerance.
Observation Two susceptible wheat varieties had high PCD under single and combined stress exposure.
Observation PCD declined later in both susceptible varieties, indicating rapid adaptation.
Method / resource The root hair assay supported high-throughput cereal analysis in about four days.
Recommendation The authors propose using laboratory PCD screening to target later field trials.

Method / resourceobservedoriginal resultmeasured

Claim · model-written summary

RFP fusion permits visualization of changing subcellular localization during PCD.

Taxon: plantt0
Outcome: changes of sub-cellular localisatione0

Not reportedComparatorValue

Verbatim

e0
“changes of sub-cellular localisation can be visualised during PCD using the protein of interest fused to RFP”
✓ located verbatim in the source · abstract, characters 873–981

t0
“The acidification that occurs in the cytosol during plant PCD was monitored”
✓ located verbatim in the source · abstract, characters 434–509

Title

pH-sensitivity of YFP provides an intracellular indicator of programmed cell death

Bennett Young; Raymond Wightman; Robert Blanvillain; et al. Plant Methods 2010. doi:10.1186/1746-4811-6-27

Other claims from this paper (5)

Method / resource YFP fluorescence was extinguished by cytosolic acidification during plant PCD.
Intervention effect YFP fluorescence recovered when intracellular pH returned to 7, indicating no YFP degradation.
Method / resource The YFP assay allows non destructive time lapse studies without interfering with PCD.
Mechanism In onion epidermal cells, the pH shift occurred downstream of AtBI-1 suppression of PCD.
Method / resource YFP extinction occurred during Arabidopsis xylogenesis.

Method / resourceobservedoriginal resultmeasured

Claim · model-written summary

The YFP assay allows non destructive time lapse studies without interfering with PCD.

Taxon: plantt0
Outcome: allows time-lapse studiese0

Not reportedComparatorValue

Verbatim

e0
“the assay is none-destructive, does not interfere with the PCD process and allows time-lapse studies to be carried out”
✓ located verbatim in the source · abstract, characters 740–858

t0
“The acidification that occurs in the cytosol during plant PCD was monitored”
✓ located verbatim in the source · abstract, characters 434–509

Title

pH-sensitivity of YFP provides an intracellular indicator of programmed cell death

Bennett Young; Raymond Wightman; Robert Blanvillain; et al. Plant Methods 2010. doi:10.1186/1746-4811-6-27

Other claims from this paper (5)

Method / resource YFP fluorescence was extinguished by cytosolic acidification during plant PCD.
Intervention effect YFP fluorescence recovered when intracellular pH returned to 7, indicating no YFP degradation.
Method / resource RFP fusion permits visualization of changing subcellular localization during PCD.
Mechanism In onion epidermal cells, the pH shift occurred downstream of AtBI-1 suppression of PCD.
Method / resource YFP extinction occurred during Arabidopsis xylogenesis.

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“PCD”

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