scholarly journals Analysis of Cadmium Root Retention for Two Contrasting Rice Accessions Suggests an Important Role for OsHMA2

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 806
Author(s):  
Moez Maghrebi ◽  
Elena Baldoni ◽  
Giorgio Lucchini ◽  
Gianpiero Vigani ◽  
Giampiero Valè ◽  
...  
Keyword(s):  
Transcript Abundance ◽  
Root Cells ◽  
Expression Levels ◽  
Cd Tolerance ◽  
Relative Contribution ◽  
Relative Transcript Abundance ◽  
Potential Capacity ◽  
Cd Distribution ◽  
Cd Exposure ◽  
Cd Availability

Two rice accessions, Capataz and Beirao, contrasting for cadmium (Cd) tolerance and root retention, were exposed to a broad range of Cd concentrations (0.01, 0.1, and 1 μM) and analyzed for their potential capacity to chelate, compartmentalize, and translocate Cd to gain information about the relative contribution of these processes in determining the different pathways of Cd distribution along the plants. In Capataz, Cd root retention increased with the external Cd concentration, while in Beirao it resulted independent of Cd availability and significantly higher than in Capataz at the lowest Cd concentrations analyzed. Analysis of thiol accumulation in the roots revealed that the different amounts of these compounds in Capataz and Beirao, as well as the expression levels of genes involved in phytochelatin biosynthesis and direct Cd sequestration into the vacuoles of the root cells, were not related to the capacity of the accessions to trap the metal into the roots. Interestingly, the relative transcript abundance of OsHMA2, a gene controlling root-to-shoot Cd/Zn translocation, was not influenced by Cd exposure in Capataz and progressively increased in Beirao with the external Cd concentration, suggesting that activity of the OsHMA2 transporter may differentially limit root-to-shoot Cd/Zn translocation in Capataz and Beirao.

Relative transcript abundance in porcine cumulus cells collected from different size follicles

2014 ◽  
Author(s):  
Carla Moros Nicolas ◽  
Maria Jose Izquierdo Rico ◽  
Y Li ◽  
Rakel Romar ◽  
H Funahashi
Keyword(s):  
Transcript Abundance ◽  
Cumulus Cells ◽  
Relative Transcript Abundance

Detection of abscisic acid and relative transcript abundance in Syntrichia caninervis Mitt.

2021 ◽  
pp. 1-8
Author(s):  
Yigong Zhang ◽  
Ayibaiheremu Mutailifu ◽  
Yi Zhang ◽  
Honglan Yang ◽  
Daoyuan Zhang
Keyword(s):  
Abscisic Acid ◽  
Transcript Abundance ◽  
Syntrichia Caninervis ◽  
Relative Transcript Abundance

scholarly journals Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its roles in salt resistance

2020 ◽  
Author(s):  
Cuiyu Liu ◽  
Yujie Zhao ◽  
Xueqing Zhao ◽  
Jianmei Dong ◽  
Zhaohe Yuan
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Nitrogen Deficiency ◽  
Punica Granatum ◽  
Salt Resistance ◽  
Specific Expression ◽  
Multiple Sequence ◽  
Root Cells ◽  
Expression Levels

Abstract Backgrounds: Pomegranate (Punica granatum L.) is an important commercial fruit tree, with moderate tolerance to salinity. The balance of Cl− and other anions in pomegranate tissues are affected by salinity, however, the accumulation patterns of anions are poorly understood. The chloride channel (CLC) gene family is involved in conducting Cl−, NO3−, HCO3− and I−, but its characteristics have not been reported on pomegranate.Results: In this study, we identified seven PgCLC genes, consisting of four antiporters and three channels, based on the presence of the gating glutamate (E) and the proton glutamate (E). Phylogenetic analysis revealed that seven PgCLCs were divided into two clades, with clade I containing the typical conserved regions GxGIPE (I), GKxGPxxH (II) and PxxGxLF (III), whereas clade II not. Multiple sequence alignment revealed that PgCLC-B had a P [proline, Pro] residue in region I, which was suspected to be a NO3–/H+ exchanger, while PgCLC-C1, PgCLC-C2, PgCLC-D and PgCLC-G contained a S [serine, Ser] residue, with a high affinity to Cl−. We determined the content of Cl−, NO3−, H2PO4−, and SO42− in pomegranate tissues after 18 days of salt treatments (0, 100, 200 and 300 mM NaCl). Compared with control, the Cl− content increased sharply in pomegranate tissues. Salinity inhibited the uptake of NO3− and SO42− , but accelerated H2PO4− uptake. The results of real-time reverse transcription PCR (qRT-PCR) revealed that PgCLC genes had tissue-specific expression patterns. The high expression levels of three antiporters PgCLC-C1, PgCLC-C2 and PgCLC-D in leaves might be contributed to sequestrating Cl− into the vacuoles. However, the low expression levels of PgCLCs in roots might be associated with the exclusion of Cl− from root cells. Also, the up-regulated PgCLC-B in leaves indicated that more NO3− was transported into leaves to mitigate the nitrogen deficiency.Conclusions: Our findings suggested that the PgCLC genes played important roles in balancing of Cl− and NO3− in pomegranate tissues under salt stress. This study establishes a theoretical foundation for the further functional characterization of CLC genes in pomegranate.

ISOFORM ABUNDANCE INFERENCE PROVIDES A MORE ACCURATE ESTIMATION OF GENE EXPRESSION LEVELS IN RNA-SEQ

2010 ◽  
Vol 08 (supp01) ◽  
pp. 177-192 ◽  
Author(s):  
XI WANG ◽  
ZHENGPENG WU ◽  
XUEGONG ZHANG
Keyword(s):  
Gene Expression ◽  
High Throughput Sequencing ◽  
Transcript Abundance ◽  
Accurate Estimation ◽  
Rna Seq ◽  
Estimation Errors ◽  
Expression Levels ◽  
Or Gene ◽  
Read Distribution ◽  
Gene Expression Levels

Due to its unprecedented high-resolution and detailed information, RNA-seq technology based on next-generation high-throughput sequencing significantly boosts the ability to study transcriptomes. The estimation of genes' transcript abundance levels or gene expression levels has always been an important question in research on the transcriptional regulation and gene functions. On the basis of the concept of Reads Per Kilo-base per Million reads (RPKM), taking the union-intersection genes (UI-based) and summing up inferred isoform abundance (isoform-based) are the two current strategies to estimate gene expression levels, but produce different estimations. In this paper, we made the first attempt to compare the two strategies' performances through a series of simulation studies. Our results showed that the isoform-based method gives not only more accurate estimation but also has less uncertainty than the UI-based strategy. If taking into account the non-uniformity of read distribution, the isoform-based method can further reduce estimation errors. We applied both strategies to real RNA-seq datasets of technical replicates, and found that the isoform-based strategy also displays a better performance. For a more accurate estimation of gene expression levels from RNA-seq data, even if the abundance levels of isoforms are not of interest, it is still better to first infer the isoform abundance and sum them up to get the expression level of a gene as a whole.

scholarly journals Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its roles in salt resistance

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Cuiyu Liu ◽  
Yujie Zhao ◽  
Xueqing Zhao ◽  
Jianmei Dong ◽  
Zhaohe Yuan
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Nitrogen Deficiency ◽  
Punica Granatum ◽  
Salt Resistance ◽  
Specific Expression ◽  
Multiple Sequence ◽  
Root Cells ◽  
Expression Levels

Abstract Backgrounds Pomegranate (Punica granatum L.) is an important commercial fruit tree, with moderate tolerance to salinity. The balance of Cl− and other anions in pomegranate tissues are affected by salinity, however, the accumulation patterns of anions are poorly understood. The chloride channel (CLC) gene family is involved in conducting Cl−, NO3−, HCO3− and I−, but its characteristics have not been reported on pomegranate. Results In this study, we identified seven PgCLC genes, consisting of four antiporters and three channels, based on the presence of the gating glutamate (E) and the proton glutamate (E). Phylogenetic analysis revealed that seven PgCLCs were divided into two clades, with clade I containing the typical conserved regions GxGIPE (I), GKxGPxxH (II) and PxxGxLF (III), whereas clade II not. Multiple sequence alignment revealed that PgCLC-B had a P [proline, Pro] residue in region I, which was suspected to be a NO3−/H+ exchanger, while PgCLC-C1, PgCLC-C2, PgCLC-D and PgCLC-G contained a S [serine, Ser] residue, with a high affinity to Cl−. We determined the content of Cl−, NO3−, H2PO4−, and SO42− in pomegranate tissues after 18 days of salt treatments (0, 100, 200 and 300 mM NaCl). Compared with control, the Cl− content increased sharply in pomegranate tissues. Salinity inhibited the uptake of NO3− and SO42−, but accelerated H2PO4− uptake. The results of real-time reverse transcription PCR (qRT-PCR) revealed that PgCLC genes had tissue-specific expression patterns. The high expression levels of three antiporters PgCLC-C1, PgCLC-C2 and PgCLC-D in leaves might be contributed to sequestrating Cl− into the vacuoles. However, the low expression levels of PgCLCs in roots might be associated with the exclusion of Cl− from root cells. Also, the up-regulated PgCLC-B in leaves indicated that more NO3− was transported into leaves to mitigate the nitrogen deficiency. Conclusions Our findings suggested that the PgCLC genes played important roles in balancing of Cl− and NO3− in pomegranate tissues under salt stress. This study established a theoretical foundation for the further functional characterization of the CLC genes in pomegranate.

scholarly journals Maternal nutrition affects the composition of follicular fluid and transcript content in gilt oocytes

2011 ◽  
Vol 56 (No. 4) ◽  
pp. 156-167 ◽  
Author(s):  
E. Warzych ◽  
A. Cieslak ◽  
P. Pawlak ◽  
N. Renska ◽  
E. Pers-Kamczyc ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Fatty Acid Profile ◽  
Follicular Fluid ◽  
Diet Composition ◽  
Transcript Abundance ◽  
Marker Genes ◽  
Fluid Composition ◽  
Experimental Diet ◽  
Relative Transcript Abundance

Metabolomics focused on reproduction have been the subject of special interest in the past decade. Metabolite profiling provides detailed information on the status of follicular fluid and follicular cells which accompany the growing oocyte. Although nutrients present in the diet reach oocytes via the follicular fluid, it is not evident whether oocyte/embryo quality can be predicted based on the follicular fluid composition. Since this phenomenon has not yet been investigated in the pig, the aim of the present study was to investigate associations between diet composition and (1) selected markers related to developmental potential of oocytes (brilliant cresyl blue &ndash; BCB test, relative transcript abundance of EEF1A1 and ATP5A1 marker genes) and (2) fatty acid profile in the follicular fluid. Gilts were fed control and experimental diets which differed in composition and fatty acid profiles. The experimental diet used in this study comprised mainly locally grown grains (barley and rye) traditionally used for fattening pigs in Poland. Cumulus-oocyte complexes were aspirated from individual pairs of ovaries after animal slaughter, evaluated morphologically and subjected to the BCB test. Relative transcript abundance for the two marker genes was monitored by real-time PCR in oocytes of both categories (BCB+ and BCB&ndash;). Fatty acid profile in follicular fluid was analyzed by gas chromatography. We show that the experimental diet rich in n-3 fatty acid significantly influences fatty acid composition of the follicular fluid. The fatty acid profile of the follicular fluid of gilts fed the experimental diet differed from that of the control females. The content of saturated fatty acids was higher in the experimental group, whereas unsaturated and polyunsaturated fatty acids were more abundant in the control group (P &lt; 0.05). With regard to individual fatty acids, only C16:0 (palmitic acid), C18:2n-6 (linoleic acid) and C22:6 (docosahexaenoic acid) differed significantly. The abundance of ATP5A1 mRNA was influenced neither by diet composition nor by oocyte category (BCB<sup>+</sup>/BCB<sup>&ndash;</sup>) whereas that of the EEF1A1 was affected by both factors. Since higher mRNA level of the EEF1A1 gene was noted in BCB+ oocytes this may be considered as a marker of oocyte quality in the pig.

Effects of vitrification on the expression of pluripotency, apoptotic and stress genes in in vitro-produced porcine blastocysts

2015 ◽  
Vol 27 (7) ◽  
pp. 1072 ◽  
Author(s):  
Miriam Castillo-Martín ◽  
Marc Yeste ◽  
Eva Pericuesta ◽  
Roser Morató ◽  
Alfonso Gutiérrez-Adán ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
Dna Fragmentation ◽  
Transcript Abundance ◽  
Cell Number ◽  
Total Cell ◽  
Total Cell Number ◽  
Altered Expression ◽  
Stress Genes ◽  
Relative Transcript Abundance

The aims of the present study were to: (1) evaluate the effect of vitrification and warming on quality parameters and expression levels of pluripotency, apoptotic and stress genes in in vitro-produced (IVP) porcine blastocysts; and (ii) determine the correlation between these parameters. To this end, total cell number, DNA fragmentation, peroxide levels and the relative transcript abundance of BCL-2 associated X protein (BAX), BCL2-like 1 (BCL2L1), heat shock protein 70 (HSPA1A), POU class 5 homeobox 1 (POU5F1), superoxide dismutase 1 (SOD1) and superoxide dismutase 2 (SOD2) were analysed in fresh and vitrified IVP blastocysts. The results suggest that vitrification procedures have no effect on total cell number and gene expression of BAX, BCL2L1, SOD1 and SOD2 or the BAX : BCL2L1 ratio. Nevertheless, a significant increase in DNA fragmentation (2.9 ± 0.4% vs 11.9 ± 2.0%) and peroxide levels (80.4 ± 2.6 vs 97.2 ± 3.1) were seen in vitrified compared with Day 7 fresh blastocysts. In addition, after blastocyst vitrification, relative transcript abundance was downregulated for POU5F1 and upregulated for HSPA1A. Finally, there was a significant correlation of POU5F1 and HSPA1A with DNA fragmentation (POU5F1, r = –0.561; HSPA1A, r = 0.604) and peroxide levels (POU5F1, r = –0.590; HSPA1A, r = 0.621). In conclusion, under the conditions of the present study, vitrification and warming of IVP porcine blastocysts resulted in altered expression of POU5F1 and HSPA1A, but had no effect on BAX, BCL2L1, SOD1 and SOD2 expression.

Folliculogenesis-related genes are differently expressed in secondary and tertiary ovarian follicles

Zygote ◽  
2021 ◽  
pp. 1-4
Author(s):  
L.B.S. Moura ◽  
D.M. Magalhães-Padilha ◽  
A.N.P. Morais ◽  
F.L.N. Aguiar ◽  
J. Geisler–Lee ◽  
...  
Keyword(s):  
Transcript Abundance ◽  
Ovarian Follicles ◽  
Mrna Abundance ◽  
Qpcr Data ◽  
Relative Transcript Abundance ◽  
Six Genes

Summary The relative mRNA abundance of 10 genes associated with folliculogenesis was compared between late preantral (secondary) and early antral (tertiary) ovarian follicles in goats. In total, 100 follicles in each category were mechanically isolated. The relative transcript abundance of the mRNAs were determined by qPCR. Data were analyzed using unpaired Student’s t-test. Of the 10 tested genes, ABLIM mRNA was not detected in either follicle category, six genes (SLIT3, TYMS, GTPBP1, AKR1C4, PIK3R6, and MAOB) were upregulated in secondary follicles compared with tertiary follicles, and three genes (ARHGEF12, CLEC6A, and CYTL1) showed similar mRNA abundances in both secondary and tertiary follicles. In conclusion, SLIT3, GTPBP1, AKR1C4, and PIK3R6 mRNA abundance was upregulated in secondary follicles (preantral phase) compared with in tertiary follicles (antral phase) in goats.

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