Some OpenMinTeD documents have missing species
Hi @maud.marty looks like some OpenMinTeD documents in DataDiscovery have the species field erroneous:
rflores@urgi131:~/local/git/data-discovery (data/udpate-gnpis-data-GNP-5564 *$%) $ zcat data/data-discovery/INRAE-URGI_Alvis_OMTD_* | jq '[.[] | select([.identifier?] |inside(["10.1038/hdy.1982.62","10.1094/PDIS-91-2-0185","10.1111/j.1601-5223.1990.tb00054.x","10.1111/jcmm.13419","10.1371/journal.pone.0032626","10.13
71/journal.pone.0081955","10.3389/fpls.2017.01022"]) )] '
[
{
"entryType": "Bibliography",
"databaseName": "OpenMinTeD@GnpIS",
"identifier": "10.1111/jcmm.13419",
"description": "Gallic acid attenuates calcium calmodulin-dependent kinase II-induced apoptosis in spontaneously hypertensive rats. 2018 Gallic acid attenuates calcium calmodulin-dependent kinase II-induced apoptosis in spontaneously hypertensive rats Hypertension causes cardiac hypertrophy and leads to heart fai
lure. Apoptotic cells are common in hypertensive hearts. Ca2+/calmodulin-dependent protein kinase II (CaMKII) is associated with apoptosis. We recently demonstrated that gallic acid reduces nitric oxide synthase inhibition-induced hypertension. Gallic acid is a trihydroxybenzoic acid and has been shown to have benefi
cial effects, such as anti-cancer, anti-calcification and anti-oxidant activity. The purpose of this study was to determine whether gallic acid regulates cardiac hypertrophy and apoptosis in essential hypertension. Gallic acid significantly lowered systolic and diastolic blood pressure in spontaneously hypertensive r
ats (SHRs). Wheat germ agglutinin (WGA) and H&E staining revealed that gallic acid reduced cardiac enlargement in SHRs. Gallic acid treatment decreased cardiac hypertrophy marker genes, including atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP), in SHRs. The four isoforms, alpha, beta, delta and g
amma, of CaMKII were increased in SHRs and were significantly reduced by gallic acid administration. Gallic acid reduced cleaved caspase-3 protein as well as bax, p53 and p300 mRNA levels in SHRs. CaMKII delta overexpression induced bax and p53 expression, which was attenuated by gallic acid treatment in H9c2 cells.
Gallic acid treatment reduced DNA fragmentation and the TUNEL positive cells induced by angiotensin II. Taken together, gallic acid could be a novel therapeutic for the treatment of hypertension through suppression of CaMKII delta-induced apoptosis. Jin, L et al. JOURNAL OF CELLULAR AND MOLECULAR MEDICINE",
"annotationId": [],
"annotationName": [],
"url": "https://doi.org/10.1111/jcmm.13419",
"species": "beta",
"name": "10.1111/jcmm.13419",
"node": "INRAE-URGI",
"ancestors": []
}
]
[
{
"entryType": "Bibliography",
"databaseName": "OpenMinTeD@GnpIS",
"identifier": "10.3389/fpls.2017.01022",
"description": "Bulked Segregant RNA-seq Reveals Differential Expression and SNPs of Candidate Genes Associated with Waterlogging Tolerance in Maize. 2017 Bulked Segregant RNA-seq Reveals Differential Expression and SNPs of Candidate Genes Associated with Waterlogging Tolerance in Maize Waterlogging has increasin
gly become one of the major constraints to maize productivity in some maize production zones because it causes serious yield loss. Bulked segregant RNA-seq (BSR-seq) has been widely applied to profile candidate genes and map associated Single Nucleotide Polymorphism (SNP) markers in many species. In this study, 10 wa
terlogging sensitive and eight tolerant inbred lines were selected from 60 maize inbred lines with waterlogging response determined and preselected by the International Maize and Wheat Improvement Center (CIMMYT) from over 400 tropical maize inbred lines. BSR-seq was performed to identify differentially expressed gen
es and SNPs associated with waterlogging tolerance. Upon waterlogging stress, 354 and 1094 genes were differentially expressed in the tolerant and sensitive pools, respectively, compared to untreated controls. When tolerant and sensitive pools were compared, 593 genes were differentially expressed under untreated and
431 genes under waterlogged conditions, of which 122 genes overlapped. To validate the BSR-seq results, the expression levels of six genes were determined by qRT-PCR. The qRT-PCR results were consistent with BSR-seq results. Comparison of allelic polymorphism in mRNA sequences between tolerant and sensitive pools re
vealed 165 (normal condition) and 128 (waterlogged condition) high-probability SNPs. We found 18 overlapping SNPs with genomic positions mapped. Eighteen SNPs were contained in 18 genes, and eight and nine of 18 genes were responsive to waterlogging stress in tolerant and sensitive lines, respectively. Six alleles of
the 18 originated from tolerant pool were significantly up-regulated under waterlogging, but not those from sensitive pool. Importantly, one allele (GRMZM2G055704) of the six genes was mapped between umc1619 and umc1948 on chromosome 1 where a QTL associated with waterlogging tolerance was identified in a previous r
esearch, strongly indicating that GRMZM2G055704 is a candidate gene responsive to waterlogging. Our research contributes to the knowledge of the molecular mechanism for waterlogging tolerance in maize. Du, HW et al. FRONTIERS IN PLANT SCIENCE",
"annotationId": [],
"annotationName": [],
"url": "https://doi.org/10.3389/fpls.2017.01022",
"species": null,
"name": "10.3389/fpls.2017.01022",
"node": "INRAE-URGI",
"ancestors": []
}
]
[
{
"entryType": "Bibliography",
"databaseName": "OpenMinTeD@GnpIS",
"identifier": "10.1371/journal.pone.0081955",
"description": "Reticulated Origin of Domesticated Emmer Wheat Supports a Dynamic Model for the Emergence of Agriculture in the Fertile Crescent. 2013 Reticulated Origin of Domesticated Emmer Wheat Supports a Dynamic Model for the Emergence of Agriculture in the Fertile Crescent We used supernetworks with dataset
s of nuclear gene sequences and novel markers detecting retrotransposon insertions in ribosomal DNA loci to reassess the evolutionary relationships among tetraploid wheats. We show that domesticated emmer has a reticulated genetic ancestry, sharing phylogenetic signals with wild populations from all parts of the wild
range. The extent of the genetic reticulation cannot be explained by post-domestication gene flow between cultivated emmer and wild plants, and the phylogenetic relationships among tetraploid wheats are incompatible with simple linear descent of the domesticates from a single wild population. A more parsimonious exp
lanation of the data is that domesticated emmer originates from a hybridized population of different wild lineages. The observed diversity and reticulation patterns indicate that wild emmer evolved in the southern Levant, and that the wild emmer populations in south-eastern Turkey and the Zagros Mountains are relativ
ely recent reticulate descendants of a subset of the Levantine wild populations. Based on our results we propose a new model for the emergence of domesticated emmer. During a pre-domestication period, diverse wild populations were collected from a large area west of the Euphrates and cultivated in mixed stands. Withi
n these cultivated stands, hybridization gave rise to lineages displaying reticulated genealogical relationships with their ancestral populations. Gradual movement of early farmers out of the Levant introduced the pre-domesticated reticulated lineages to the northern and eastern parts of the Fertile Crescent, giving
rise to the local wild populations but also facilitating fixation of domestication traits. Our model is consistent with the protracted and dispersed transition to agriculture indicated by the archaeobotanical evidence, and also with previous genetic data affiliating domesticated emmer with the wild populations in sou
theast Turkey. Unlike other protracted models, we assume that humans played an intuitive role throughout the process. Civan, P et al. PLOS ONE",
"annotationId": [],
"annotationName": [],
"url": "https://doi.org/10.1371/journal.pone.0081955",
"species": null,
"name": "10.1371/journal.pone.0081955",
"node": "INRAE-URGI",
"ancestors": []
},
{
"entryType": "Bibliography",
"databaseName": "OpenMinTeD@GnpIS",
"identifier": "10.1371/journal.pone.0032626",
"description": "Genetic Characterization of a Core Set of a Tropical Maize Race Tuxpeno for Further Use in Maize Improvement. 2012 Genetic Characterization of a Core Set of a Tropical Maize Race Tuxpeno for Further Use in Maize Improvement The tropical maize race Tuxpeno is a well-known race of Mexican dent germp
lasm which has greatly contributed to the development of tropical and subtropical maize gene pools. In order to investigate how it could be exploited in future maize improvement, a panel of maize germplasm accessions was assembled and characterized using genome-wide Single Nucleotide Polymorphism (SNP) markers. This
panel included 321 core accessions of Tuxpeno race from the International Maize and Wheat Improvement Center (CIMMYT) germplasm bank collection, 94 CIMMYT maize lines (CMLs) and 54 U.S. Germplasm Enhancement of Maize (GEM) lines. The panel also included other diverse sources of reference germplasm: 14 U.S. maize land
race accessions, 4 temperate inbred lines from the U. S. and China, and 11 CIMMYT populations (a total of 498 entries with 795 plants). Clustering analyses (CA) based on Modified Rogers Distance (MRD) clearly partitioned all 498 entries into their corresponding groups. No sub clusters were observed within the Tuxpeno
core set. Various breeding strategies for using the Tuxpeno core set, based on grouping of the studied germplasm and genetic distance among them, were discussed. In order to facilitate sampling diversity within the Tuxpeno core, a minicore subset of 64 Tuxpeno accessions (20% of its usual size) representing the dive
rsity of the core set was developed, using an approach combining phenotypic and molecular data. Untapped diversity represents further use of the Tuxpeno landrace for maize improvement through the core and/or minicore subset available to the maize community. Wen, WW et al. PLOS ONE",
"annotationId": [],
"annotationName": [],
"url": "https://doi.org/10.1371/journal.pone.0032626",
"species": null,
"name": "10.1371/journal.pone.0032626",
"node": "INRAE-URGI",
"ancestors": []
},
{
"entryType": "Bibliography",
"databaseName": "OpenMinTeD@GnpIS",
"identifier": "10.1094/PDIS-91-2-0185",
"description": "The Mdm1 locus and maize resistance to Maize dwarf mosaic virus. 2007 The Mdm1 locus and maize resistance to Maize dwarf mosaic virus Previously, Mdm1, a gene controlling resistance to Maize dwarf mosaic virus (MDMV), was identified in the inbred line Pa405. The gene was tightly linked to the rest
riction fragment length polymorphism marker umc85 on the short arm of chromosome 6. This chromosomal region is also the location of resistance genes to two other viruses in the family Potyviridae, Sugarcane mosaic virus (SCMV) and Wheat streak mosaic virus (WSMV). A diverse collection of 115 maize inbred lines was ev
aluated for resistance to MDMV and SCMV, and for MDMV resistance loci on chromosome 6S. Forty-six resistant inbred lines were crossed to three MDMV-susceptible inbred lines to develop F-2 populations. The F-2 populations were inoculated with MDMV and scored for infection and symptom type. Environmental factors influe
nced both the rate and type of symptom development. Bulked segregant analysis of each F-2 population indicated that, in 42 of 43 MDMV-resistant lines, chromosome 6S markers found in the resistant parent also were present in the bulked resistant but not the susceptible tissue. Markers previously associated with resist
ance to both SCMV and WSMV on chromosome 3 and to WSMV on chromosome 10 were associated with resistance in nine and seven of the F-2 populations, respectively. These data suggest that Mdm1 or closely linked genes on chromosome 6S are associated with MDMV resistance in most germplasm, but that other loci also may affe
ct resistance. Jones, MW et al. PLANT DISEASE",
"annotationId": [],
"annotationName": [],
"url": "https://doi.org/10.1094/PDIS-91-2-0185",
"species": null,
"name": "10.1094/PDIS-91-2-0185",
"node": "INRAE-URGI",
"ancestors": []
}
]
[
{
"entryType": "Bibliography",
"databaseName": "OpenMinTeD@GnpIS",
"identifier": "10.1111/j.1601-5223.1990.tb00054.x",
"description": "GENETIC-CONTROL OF RECOMBINATION IN BARLEY .2. VARIATION IN LINKAGE BETWEEN MARKER GENES. 1990 GENETIC-CONTROL OF RECOMBINATION IN BARLEY .2. VARIATION IN LINKAGE BETWEEN MARKER GENES SALL, T HEREDITAS",
"annotationId": [],
"annotationName": [],
"url": "https://doi.org/10.1111/j.1601-5223.1990.tb00054.x",
"species": null,
"name": "10.1111/j.1601-5223.1990.tb00054.x",
"node": "INRAE-URGI",
"ancestors": []
},
{
"entryType": "Bibliography",
"databaseName": "OpenMinTeD@GnpIS",
"identifier": "10.1038/hdy.1982.62",
"description": "LINKAGE MAP OF THE LONG ARM OF BARLEY CHROMOSOME-3 USING C-BANDS AND MARKER GENES. 1982 LINKAGE MAP OF THE LONG ARM OF BARLEY CHROMOSOME-3 USING C-BANDS AND MARKER GENES LINDELAURSEN, I HEREDITY",
"annotationId": [],
"annotationName": [],
"url": "https://doi.org/10.1038/hdy.1982.62",
"species": null,
"name": "10.1038/hdy.1982.62",
"node": "INRAE-URGI",
"ancestors": []
}
]
Species is either null
or beta
. That makes them unavailable with the new species restriction which relies on the species field at indexing step instead of wheat dedicated data files.
We could fix that by updating the files directly, but it looks there is a fix to do in the Alvis pipeline itself, I believe.
Should we have a look at that soon?
Ping @cyril.pommier for opinion.