scholarly journals Transcriptional Changes in Response to Arbuscular Mycorrhiza Development in the Model Plant Medicago truncatula

2003 ◽  
Vol 16 (4) ◽  
pp. 306-314 ◽  
Author(s):  
Anne Wulf ◽  
Katja Manthey ◽  
Jasmin Doll ◽  
Andreas M. Perlick ◽  
Burkhard Linke ◽  
...  
Keyword(s):  
Arbuscular Mycorrhiza ◽  
Medicago Truncatula ◽  
Expressed Sequence Tag ◽  
Gene Expression Pattern ◽  
Cdna Libraries ◽  
Suppressive Subtractive Hybridization ◽  
Specific Gene ◽  
Cdna Sequences ◽  
Wide Range ◽  
Transcriptional Changes

Significant changes in root morphology and physiology during arbuscular mycorrhiza (AM) development are likely to be controlled by specific gene expression pattern in the host plant. Until now, little was known about transcriptional changes which occur AM-exclusively; that is, they do not occur during other root-microbe associations, nor are they induced by improved phosphate nutrition. In order to identify such AM-exclusive gene inductions of Medicago truncatula, we used a pool of different RNA samples as subtractor population in a suppressive subtractive hybridization (SSH) experiment. This approach resulted in the identification of a number of new AM-regulated genes. None of these genes were expressed in nonmycorrhiza roots or leaves. Electronic data obtained by comparison of the cDNA sequences to expressed sequence tag (EST) sequences from a wide range of cDNA libraries in the M. truncatula EST database (Gene Index, MtGI) support the mycorrhiza specificity of the corresponding genes, because sequences in the MtGI that were found to match the identified SSH-cDNA sequences originated exclusively from AM cDNA libraries. The promoter of one of those genes, MtGst1, showing similarities to plant glutathione-S-transferase (GST) encoding genes, was cloned and used in reporter gene studies. In contrast to studies with the potato GST gene PRP, MtGst 1 promoter activity was detected in all zones of the root cortex colonized by Glomus intraradices, but nowhere else.

scholarly journals Biosynthesis of secondary metabolites in sugarcane

2001 ◽  
Vol 24 (1-4) ◽  
pp. 243-250 ◽  
Author(s):  
S.C. França ◽  
P.G. Roberto ◽  
M.A. Marins ◽  
R.D. Puga ◽  
A. Rodrigues ◽  
...  
Keyword(s):  
Secondary Metabolism ◽  
Environmental Changes ◽  
Expressed Sequence Tag ◽  
Gene Expression Pattern ◽  
Flavonoid Biosynthesis ◽  
Phenylpropanoid Metabolism ◽  
Supporting Evidence ◽  
Biotic And Abiotic Stress ◽  
Wide Range ◽  
Key Enzyme

A set of genes related to secondary metabolism was extracted from the sugarcane expressed sequence tag (SUCEST) database and was used to investigate both the gene expression pattern of key enzymes regulating the main biosynthetic secondary metabolism pathways and the major classes of metabolites involved in the response of sugarcane to environmental and developmental cues. The SUCEST database was constructed with tissues in different physiological conditions which had been collected under varied situation of environmental stress. This database allows researchers to identify and characterize the expressed genes of a wide range of putative enzymes able to catalyze steps in the phenylpropanoid, isoprenoid and other pathways of the special metabolic mechanisms involved in the response of sugarcane to environmental changes. Our results show that sugarcane cDNAs encoded putative ultra-violet induced sesquiterpene cyclases (SC); chalcone synthase (CHS), the first enzyme in the pathway branch for flavonoid biosynthesis; isoflavone synthase (IFS), involved in plant defense and root nodulation; isoflavone reductase (IFR), a key enzyme in phenylpropanoid phytoalexin biosynthesis; and caffeic acid-O-methyltransferase, a key enzyme in the biosynthesis of lignin cell wall precursors. High levels of CHS transcripts from plantlets infected with Herbaspirillum rubri or Gluconacetobacter diazotroficans suggests that agents of biotic stress can elicit flavonoid biosynthesis in sugarcane. From this data we have predicted the profile of isoprenoid and phenylpropanoid metabolism in sugarcane and pointed the branches of secondary metabolism activated during tissue-specific stages of development and the adaptive response of sugarcane to agents of biotic and abiotic stress, although our assignment of enzyme function should be confirmed by careful biochemical and genetic supporting evidence.

scholarly journals EST analysis of cDNA libraries from the entomopathogenic fungus Beauveria (Cordyceps) bassiana. I. Evidence for stage-specific gene expression in aerial conidia, in vitro blastospores and submerged conidia

Microbiology ◽  
2006 ◽  
Vol 152 (9) ◽  
pp. 2843-2854 ◽  
Author(s):  
Eun-Min Cho ◽  
Li Liu ◽  
William Farmerie ◽  
Nemat O. Keyhani
Keyword(s):  
Gene Expression ◽  
Entomopathogenic Fungus ◽  
Expressed Sequence Tag ◽  
Biological Control Agent ◽  
Expression Profiles ◽  
Cdna Libraries ◽  
Specific Gene ◽  
Cell Type ◽  
Aerial Conidia

The entomopathogenic fungus Beauveria (Cordyceps) bassiana holds much promise as a pest biological control agent. B. bassiana produces at least three in vitro single cell infectious propagules, including aerial conidia, vegetative cells termed blastospores and submerged conidia, that display different morphological, biochemical and virulence properties. Populations of aerial conidia, blastospores and submerged conidia were produced on agar plates, rich liquid broth cultures and under conditions of nutrient limitation in submerged cultures, respectively. cDNA libraries were generated from mRNA isolated from each B. bassiana cell type and ∼2500 5′ end sequences were determined from each library. Sequences derived from aerial conidia clustered into 284 contigs and 963 singlets, with those derived from blastospores and submerged conidia forming 327 contigs with 788 singlets, and 303 contigs and 1079 contigs, respectively. Almost half (40–45 %) of the sequences in each library displayed either no significant similarity (e value >10−4) or similarity to hypothetical proteins found in the NCBI database. The expressed sequence tag dataset also included sequences representing a significant portion of proteins in cellular metabolism, information storage and processing, transport and cell processes, including cell division and posttranslational modifications. Transcripts encoding a diverse array of pathogenicity-related genes, including proteases, lipases, esterases, phosphatases and enzymes producing toxic secondary metabolites, were also identified. Comparative analysis between the libraries identified 2416 unique sequences, of which 20–30 % were unique to each library, and only ∼6 % of the sequences were shared between all three libraries. The unique and divergent representation of the B. bassiana transcriptome in the cDNA libraries from each cell type suggests robust differential gene expression profiles in response to environmental conditions.

scholarly journals Fungal Elicitation of Signal Transduction-Related Plant Genes Precedes Mycorrhiza Establishment and Requires the dmi3 Gene in Medicago truncatula

2004 ◽  
Vol 17 (12) ◽  
pp. 1385-1393 ◽  
Author(s):  
Stéphanie Weidmann ◽  
Lisa Sanchez ◽  
Julie Descombin ◽  
Odile Chatagnier ◽  
Silvio Gianinazzi ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Medicago Truncatula ◽  
Sinorhizobium Meliloti ◽  
Expressed Sequence Tag ◽  
Signal Transduction Pathway ◽  
Suppressive Subtractive Hybridization ◽  
Cell Contact ◽  
Transduction Pathway ◽  
Transcript Accumulation ◽  
Plant Genes

Suppressive subtractive hybridization and expressed sequence tag sequencing identified 29 plant genes which are upregulated during the appressorium stage of mycorrhiza establishment between Medicago truncatula J5 (Myc+) and Glomus mosseae. Eleven genes coding plant proteins with predicted functions in signal transduction, transcription, and translation were investigated in more detail for their relation to early events of symbiotic interactions. Expression profiling showed that the genes are activated not only from the appressorium stage up to the fully established symbiosis in the Myc+ genotype of M. truncatula, but also when the symbionts are not in direct cell contact, suggesting that diffusible fungal molecules (Myc factors) play a role in the induction of a signal-transduction pathway. Transcript accumulation in roots of a mycorrhiza-defective Myc- dmi3 mutant of M. truncatula is not modified by appressorium formation or diffusible fungal molecules, indicating that the signal transduction pathway is required for a successful G. mosseae-M. truncatula interaction leading to symbiosis development. The symbiotic nodulating bacterium Sinorhizobium meliloti does not activate the 11 genes, which supposes early discrimination by plant roots between the microbial symbionts.

Application of the Innovative and Non-Invasive Technique, Molecular Music Therapy (MMT), Bio-Frequency Therapy, for the Treatment of a Wide Range of Disorders and Pathologies, with Consequent Verification of Molecular Parameters by Using Bi-Digital O-Ring Test (BDORT)

2020 ◽  
Vol 44 (3) ◽  
pp. 177-189
Author(s):  
Momir Dunjic ◽  
Stefano Turini ◽  
Dejan Krstic ◽  
Katarina Dunjic ◽  
Marija Dunjic ◽  
...  
Keyword(s):  
Amino Acid ◽  
Music Therapy ◽  
Amino Acid Sequences ◽  
Sirtuin 1 ◽  
Ring Test ◽  
Invasive Technique ◽  
Specific Gene ◽  
Radiofrequency Therapy ◽  
Wide Range ◽  
Clinical Pictures

Radiofrequency therapy is an unconventional method, already applied for some time, with numerous results in numerous clinical pictures. Our group has developed a software, later called SONGENPROT-SOLARIS, capable of directly converting nucleotide sequences (DNA and/or RNA) and amino acid sequences (polypeptides and proteins) into musical sequences, based on mathematic matrices, designed by the French physicist and musician Joel Sternheimer, which allows to associate a musical note with a nucleotide or an amino acid. Innovation in our software is that, in the algorithm that defines it, a variant is directly implemented that allows the reproduction of sounds, phase-shifted by 30 Hz, between one ear and another reproducing the phenomenon of Binaural Tones, capable of induce a specific brain activity and also the release of particles called solitons. Thanks to this software we have developed a technique called MMT (Molecular Music Therapy) and currently, we are in the phase of applying the technique on a cohort of 91 patients, with a high spectrum of clinical pictures, examining the same, using the technique Bi-Digital-ORing-Test (BDORT), before and after treatment with MMT. Aim of project is to stimulate the expression of a specific gene (the same genetic sequence that the patient listens to, translated into music), only through the use of sound sequences. We have concentrated our attention on three main molecules: Sirtuin-1, Telomers and TP-53. The results obtained with BDORT, after treatment with MMT, showed a significant increase in the values of the three molecules, on all the examined patients, demonstrating the operative efficacy of the technique and the its applicability to numerous diseases. In order to confirm the data obtained by BDORT, we propose, with the help of an accredited laboratory, to perform epigenetic tests on the three parameters listed above, paving the way to understanding how frequencies can influence gene expression.

scholarly journals Verticillium wilt resistant and susceptible olive cultivars express a very different basal set of genes in roots

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jorge A. Ramírez-Tejero ◽  
Jaime Jiménez-Ruiz ◽  
Alicia Serrano ◽  
Angjelina Belaj ◽  
Lorenzo León ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Growth And Development ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Expression Level ◽  
Resistant Cultivars ◽  
Pathogen Invasion ◽  
Wide Range ◽  
Olive Cultivars

Abstract Background Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased tolerance to the pathogen. Disease resistance not only depends on detection of pathogen invasion and induction of responses by the plant, but also on barriers to avoid the invasion and active resistance mechanisms constitutively expressed in the absence of the pathogen. In a previous work we found that two healthy non-infected plants from cultivars that differ in V. dahliae resistance such as ‘Frantoio’ (resistant) and ‘Picual’ (susceptible) had a different root morphology and gene expression pattern. In this work, we have addressed the issue of basal differences in the roots between Resistant and Susceptible cultivars. Results The gene expression pattern of roots from 29 olive cultivars with different degree of resistance/susceptibility to V. dahliae was analyzed by RNA-Seq. However, only the Highly Resistant and Extremely Susceptible cultivars showed significant differences in gene expression among various groups of cultivars. A set of 421 genes showing an inverse differential expression level between the Highly Resistant to Extremely Susceptible cultivars was found and analyzed. The main differences involved higher expression of a series of transcription factors and genes involved in processes of molecules importation to nucleus, plant defense genes and lower expression of root growth and development genes in Highly Resistant cultivars, while a reverse pattern in Moderately Susceptible and more pronounced in Extremely Susceptible cultivars were observed. Conclusion According to the different gene expression patterns, it seems that the roots of the Extremely Susceptible cultivars focus more on growth and development, while some other functions, such as defense against pathogens, have a higher expression level in roots of Highly Resistant cultivars. Therefore, it seems that there are constitutive differences in the roots between Resistant and Susceptible cultivars, and that susceptible roots seem to provide a more suitable environment for the pathogen than the resistant ones.

scholarly journals Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

Biology ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 36
Author(s):  
Te-Hua Hsu ◽  
Yu-Ting Chiu ◽  
Hung-Tai Lee ◽  
Hong-Yi Gong ◽  
Chang-Wen Huang
Keyword(s):  
Molecular Markers ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Growth Traits ◽  
Gene Diversity ◽  
Snp Markers ◽  
Cdna Libraries ◽  
Functional Markers ◽  
Genetic Management ◽  
Ssr And Snp Markers

The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.

scholarly journals Role of CxxC-finger protein 1 in establishing mouse oocyte epigenetic landscapes

2021 ◽  
Author(s):  
Qian-Qian Sha ◽  
Ye-Zhang Zhu ◽  
Yunlong Xiang ◽  
Jia-Li Yu ◽  
Xiao-Ying Fan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Histone H3 ◽  
Finger Protein ◽  
Maternal Genome ◽  
Wide Range ◽  
Transcriptional Changes ◽  
Nuclear Events ◽  
Genomic Regions ◽  
Cxxc Finger Protein 1

Abstract During oogenesis, oocytes gain competence and subsequently undergo meiotic maturation and prepare for embryonic development; trimethylated histone H3 on lysine-4 (H3K4me3) mediates a wide range of nuclear events during these processes. Oocyte-specific knockout of CxxC-finger protein 1 (CXXC1, also known as CFP1) impairs H3K4me3 accumulation and causes changes in chromatin configurations. This study investigated the changes in genomic H3K4me3 landscapes in oocytes with Cxxc1 knockout and the effects on other epigenetic factors such as the DNA methylation, H3K27me3, H2AK119ub1 and H3K36me3. H3K4me3 is overall decreased after knocking out Cxxc1, including both the promoter region and the gene body. CXXC1 and MLL2, which is another histone H3 methyltransferase, have nonoverlapping roles in mediating H3K4 trimethylation during oogenesis. Cxxc1 deletion caused a decrease in DNA methylation levels and affected H3K27me3 and H2AK119ub1 distributions, particularly at regions with high DNA methylation levels. The changes in epigenetic networks implicated by Cxxc1 deletion were correlated with the transcriptional changes in genes in the corresponding genomic regions. This study elucidates the epigenetic changes underlying the phenotypes and molecular defects in oocytes with deleted Cxxc1 and highlights the role of CXXC1 in orchestrating multiple factors that are involved in establishing the appropriate epigenetic states of maternal genome.

scholarly journals Dissecting the sugarcane expressed sequence tag (SUCEST) database: unraveling flower-specific genes

2001 ◽  
Vol 24 (1-4) ◽  
pp. 77-84 ◽  
Author(s):  
R.C. Figueiredo ◽  
M.S. Brito ◽  
L.H.M. Figueiredo ◽  
A.C. Quiapin ◽  
P.M. Vitorelli ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Tissue Expression ◽  
Reproductive Organs ◽  
Cdna Libraries ◽  
Computer Assisted ◽  
Transcript Accumulation ◽  
Gene Encoding ◽  
Assisted Analysis ◽  
Expressed Sequence ◽  
Different Tissues

There are almost 260,000 independent clones sequenced from the 5’ end in the Sugarcane Expressed Sequence Tag (SUCEST) database, which have been obtained from 37 cDNA libraries prepared from different tissues. This large number of expressed sequence tags (ESTs) provides an opportunity, unprecedented in plants, to perform ‘digital differential screening’ on selected cDNA libraries. In general, the frequency of a particular EST correlates with transcript accumulation in the tissues from which the cDNA libraries were constructed, so it is possible to compare the whole transcriptome from different tissues using computer-assisted analysis of an EST database. In our research we analyzed sugarcane ESTs according to tissue expression and identified more than 1,000 putative flower-specific genes. The fact that using this technique we were able to identify sugarcane homologues of several genes previously described as pollen-specific justifies this method of assessing tissue specificity. In addition, ESTs similar to genes specific to reproductive organs were detected e.g. a sugarcane gene encoding a meiotic protein essential for assembly of the synaptonemal complex and normal synapsis. This approach also allowed the identification of many flower-specific anonymous sequences that are good candidates for being novel genes involved in plant reproduction. This paper describes the analysis of the gene expression levels of 24 EST clusters during flower development using a ‘digital northern blot’ constructed from direct EST counts made on the non-normalized sugarcane cDNA libraries.

scholarly journals Separation of important new platelet glycoproteins (GPIa, GPIc, GPIc*, GPIIa and GMP-140) by f.p.l.c. Characterization by monoclonal antibodies and gas-phase sequencing

1991 ◽  
Vol 279 (2) ◽  
pp. 419-425 ◽  
Author(s):  
B Catimel ◽  
S Parmentier ◽  
L L K Leung ◽  
J L McGregor
Keyword(s):  
Gas Phase ◽  
Polyclonal Antibodies ◽  
Umbilical Vein ◽  
Blood Platelets ◽  
Cdna Libraries ◽  
Membrane Glycoproteins ◽  
Terminal Sequence ◽  
Cdna Sequences ◽  
Functional Studies ◽  
Vinylidene Difluoride

A large number of membrane glycoproteins (around 40) are present on the surface of human blood platelets. Some of these glycoproteins are expressed in relatively small amounts, and their functions, as well as their structure, remain to be elucidated. The aim of the present study was to separate rapidly, under non-denaturing conditions, and characterize minor glycoproteins such as Very Late Antigens (VLA) (GPIa, GPIc, GPIc* and GPIIa) and GMP-140 (also known as PADGEM). VLAs and GMP-140 are respectively members of the integrin and selectin families. Platelet membrane glycoproteins were separated by wheat-germ agglutinin lectin affinity and Mono Q anion-exchange f.p.l.c. Peaks bearing isolated glycoproteins were electrophoresed on one- or two-dimensional SDS/polyacrylamide gels, Western blotted on to Immobilon poly(vinylidene difluoride) membranes and gas-phase-sequenced. The identity of isolated glycoproteins was also obtained by the use of monoclonal or polyclonal antibodies and tryptic peptide maps. Five minor [GPIa, GPIc, GPIc*, GPIIa and GMP 140 (PADGEM)], as well as a major (GPIIIb) glycoprotein, were eluted at low salt concentrations. GPIIb-IIIa and GPIb were eluted at high salt concentrations. The N-terminal sequence of platelet GPIa was identical with that obtained by Takada & Hemler [(1989) J. Cell Biol. 109, 397-407]. However, the N-terminal sequence of platelet GPIc + Ic* and GPIIa were found to differ from those deduced from cDNA sequences isolated from human placenta or umbilical-vein endothelial-cell cDNA libraries. The combined use of f.p.l.c. and gas-phase sequencing techniques provides a very powerful tool to separate and characterize rapidly platelet or other cellular proteins for structural, immunological and functional studies.

Sign in / Sign up

Export Citation Format

Share Document