Publications by authors named "Parviz Heidari"

14 Publications

  • Page 1 of 1

Comparative plastome analysis of , with implications for genome evolution and phylogeny of Asteroideae.

Ecol Evol 2021 Jun 6;11(12):7810-7826. Epub 2021 May 6.

Finnish Museum of Natural History University of Helsinki Helsinki Finland.

The genus (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three species . , , and and compared them with 26 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content, genome organization, and inverted repeat contraction and expansion comprising 113 genes, including 80 protein-coding, 29 transfer RNA, and 4 ribosomal RNA genes. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of . We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including 16-Q, 1, F-32, N-M, and 32-L, and they may be suitable for the development of robust, authentic, and cost-effective markers for barcoding and inference of the phylogeny of the genus . Among these highly polymorphic regions, five regions also co-occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between and within the tribe Inuleae. At tribe level, our phylogeny supports a sister relationship between Astereae and Anthemideae rooted as Gnaphalieae, Calenduleae, and Senecioneae. These results are contradictory to recent studies which reported a sister relationship between "Senecioneae and Anthemideae" and "Astereae and Gnaphalieae" or a sister relationship between Astereae and Gnaphalieae rooted as Calenduleae, Anthemideae, and then Senecioneae using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between plastidt and nuclear genome data require further investigation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ece3.7614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8216946PMC
June 2021

Genome-Wide Analysis of Genes in Rice: Expression of the and Genes under Salt Stress.

Genes (Basel) 2021 May 20;12(5). Epub 2021 May 20.

Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran.

Potassium (K+), as a vital element, is involved in regulating important cellular processes such as enzyme activity, cell turgor, and nutrient movement in plant cells, which affects plant growth and production. Potassium channels are involved in the transport and release of potassium in plant cells. In the current study, three genes and two genes, along with 11 nonredundant putative genes in the rice genome, were characterized based on their physiochemical properties, protein structure, evolution, duplication, in silico gene expression, and protein-protein interactions. In addition, the expression patterns of and were studied in root and shoot tissues under salt stress using real-time PCR in three rice cultivars. genes were found to have diverse functions and structures, and showed high genetic divergence from other genes. Furthermore, the Ka/Ks ratios of duplicated gene pairs from the gene family in rice suggested that these genes underwent purifying selection. Among the studied K+ channel proteins, OsKAT1 and OsAKT1 were identified as proteins with high potential N-glycosylation and phosphorylation sites, and LEU, VAL, SER, PRO, HIS, GLY, LYS, TYR, CYC, and ARG amino acids were predicted as the binding residues in the ligand-binding sites of K+ channel proteins. Regarding the coexpression network and KEGG ontology results, several metabolic pathways, including sugar metabolism, purine metabolism, carbon metabolism, glycerophospholipid metabolism, monoterpenoid biosynthesis, and folate biosynthesis, were recognized in the coexpression network of K+ channel proteins. Based on the available RNA-seq data, the genes showed differential expression levels in rice tissues in response to biotic and abiotic stresses. In addition, the real-time PCR results revealed that and are induced by salt stress in root and shoot tissues of rice cultivars, and was identified as a key gene involved in the rice response to salt stress. In the present study, we found that the repression of , , and in roots was related to salinity tolerance in rice. Our findings provide valuable insights for further structural and functional assays of genes in rice.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes12050784DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8160896PMC
May 2021

New Insights Into Structure and Function of Genes in and : A Genome-Wide Comprehensive Analysis.

Front Genet 2021 12;12:657970. Epub 2021 May 12.

Institute of Biological Sciences, University of Talca, Talca, Chile.

The gene family, a key plant-specific transcription factor (TF) family, is involved in diverse biological processes including plant defense and growth regulation. Despite TIFY proteins being reported in some plant species, a genome-wide comparative and comprehensive analysis of genes in plant species can reveal more details. In the current study, the members of the gene family were significantly increased by the identification of 18 and six new members using maize and tomato reference genomes, respectively. Thus, a genome-wide comparative analysis of the gene family between 48 tomato (, a dicot plant) genes and 26 maize (, a monocot plant) genes was performed in terms of sequence structure, phylogenetics, expression, regulatory systems, and protein interaction. The identified TIFYs were clustered into four subfamilies, namely, TIFY-S, JAZ, ZML, and PPD. The PPD subfamily was only detected in tomato. Within the context of the biological process, family genes in both studied plant species are predicted to be involved in various important processes, such as reproduction, metabolic processes, responses to stresses, and cell signaling. The Ka/Ks ratios of the duplicated paralogous gene pairs indicate that all of the duplicated pairs in the gene family of tomato have been influenced by an intense purifying selection, whereas in the maize genome, there are three duplicated blocks containing Ka/Ks > 1, which are implicated in evolution with positive selection. The amino acid residues present in the active site pocket of TIFY proteins partially differ in each subfamily, although the Mg or Ca ions exist heterogeneously in the centers of the active sites of all the predicted TIFY protein models. Based on the expression profiles of genes in both plant species, JAZ subfamily proteins are more associated with the response to abiotic and biotic stresses than other subfamilies. In conclusion, globally scrutinizing and comparing the maize and tomato genes showed that genes play a critical role in cell reproduction, plant growth, and responses to stress conditions, and the conserved regulatory mechanisms may control their expression.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2021.657970DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155530PMC
May 2021

Genome-wide comparative analysis of Mg transporter gene family between Triticum turgidum and Camelina sativa.

Biometals 2021 Jun 30;34(3):639-660. Epub 2021 Mar 30.

Faculty of Agriculture, Shahrood University of Technology, 3619995161, Shahrood, Iran.

Magnesium (Mg) as a bimetal plays critical roles in biochemical processes, membrane stability, and enzyme activity. Mg transporters (MGTs) are involving in maintaining Mg homeostasis in cells. Although the MGT family members have been identified in different plant species, there is no comprehensive analysis of the other plants' MGT genes. In the current study, 62 and 41 non-redundant putative MGT proteins were recognized into the genome of Camelina sativa, and Triticum turgidum and they were compared based on physicochemical properties, protein structure, expression, and interaction. All identified MGTs were classified into three subgroups, NIPA, CorA, and MRS2/MGT, based on conserved-motifs distribution. The results showed that the secondary structure pattern in NIPA and MRS2 subfamily members in both studied plant species were highly similar. Furthermore, MGTs encompass the conserved structures and the critical sites mainly in the metal ion and Mg binding centers as well as the catalytic sites were observed. The highest numbers of protein channels were predicted in CorA proteins in both C. sativa and T. turgidum with 24 and 17 channel numbers, respectively. The Ser, Pro, Gly, Lys, Tyr, and Arg amino acids were predicted as the binding residues in MGTs channel regions. The expression pattern of identified genes demonstrated that MGT genes have diverse tissue-specific expression and stress response expression patterns. Besides, 147 co-expressed genes with MGTs were clustered into the eight co-expression nodes involved in N-glycan biosynthesis, protein processing in the endoplasmic reticulum, carbon metabolism, biosynthesis of amino acids, and endocytosis. In the present study, all interpretations are based on in silico predictions, which can be used in further studies related to functional genomics of MGT genes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10534-021-00301-4DOI Listing
June 2021

Haplotype- and SNP-Based GWAS for Growth and Wood Quality Traits in Trees under Arid Conditions.

Plants (Basel) 2021 Jan 13;10(1). Epub 2021 Jan 13.

Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile.

The agricultural and forestry productivity of Mediterranean ecosystems is strongly threatened by the adverse effects of climate change, including an increase in severe droughts and changes in rainfall distribution. In the present study, we performed a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) and haplotype blocks associated with the growth and wood quality of , a tree species suitable for low-rainfall sites. The study was conducted in a progeny-provenance trial established in an arid site with Mediterranean patterns located in the southern Atacama Desert, Chile. A total of 87 SNPs and 3 haplotype blocks were significantly associated with the 6 traits under study (tree height, diameter at breast height, slenderness coefficient, first bifurcation height, stem straightness, and pilodyn penetration). In addition, 11 loci were identified as pleiotropic through Bayesian multivariate regression and were mainly associated with wood hardness, height, and diameter. In general, the GWAS revealed associations with genes related to primary metabolism and biosynthesis of cell wall components. Additionally, associations coinciding with stress response genes, such as and , were detected. The findings of this study provide valuable information regarding genetic control of morphological traits related to adaptation to arid environments.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/plants10010148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7828368PMC
January 2021

A genome-wide association study to identify candidate genes for erectile dysfunction.

Brief Bioinform 2021 Jul;22(4)

Department of Information and Communication Technology (ICT) at the Mawlana Bhashani Science and Technology University, Tangail, Bangladesh.

Erectile dysfunction (ED) can be caused by different diseases and controlled by several genetic networks. In this study, to identify the genes related to ED, the expression profiles of normal and ED samples were investigated by the Gene Expression Omnibus (GEO) database. Seventeen genes were identified as associated genes with ED. The protein and nucleic acid sequences of selected genes were retrieved from the UCSC database. Selected genes were diverse according to their physicochemical properties and functions. Category function revealed that selected genes are involved in pathways related to humans some diseases. Furthermore, based on protein interactions, genes associated with the insulin pathway had the greatest interaction with the studied genes. To identify the common cis-regulatory elements, the promoter site of the selected genes was retrieved from the UCSC database. The Gapped Local Alignment of Motifs tool was used for finding common conserved motifs into the promoter site of selected genes. Besides, INSR protein as an insulin receptor precursor showed a high potential site for posttranslation modifications, including phosphorylation and N-glycosylation. Also, in this study, two Guanine-Cytosine (GC)-rich regions were identified as conserved motifs in the upstream of studied genes which can be involved in regulating the expression of genes associated with ED. Also, the conserved binding site of miR-29-3p that is involved in various cancers was observed in the 3' untranslated region of genes associated with ED. Our study introduced new genes associated with ED, which can be good candidates for further analyzing related to human ED.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/bib/bbaa338DOI Listing
July 2021

The Gene Family in : Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses.

Genes (Basel) 2020 12 7;11(12). Epub 2020 Dec 7.

Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran.

Members of the / transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify ss in the durum wheat ( ssp. ) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of ss. Furthermore, a duplication assay of ss demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with and subfamily genes. In addition, the results revealed that genes have tissue-specific expression patterns, and most genes were significantly induced in the root tissue. Additionally, 13 genes (six s, three s, two s, one , and one ) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes11121464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7762271PMC
December 2020

Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa.

J Genet Eng Biotechnol 2020 Oct 19;18(1):62. Epub 2020 Oct 19.

Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran.

Background: Ethylene is a gaseous plant hormone that acts as a requisite role in many aspects of the plant life cycle, and it is also a regulator of plant responses to abiotic and biotic stresses. In this study, we attempt to provide comprehensive information through analyses of existing data using bioinformatics tools to compare the identified ethylene biosynthesis genes between Arabidopsis (as dicotyledonous) and rice (as monocotyledonous).

Results: The results exposed that the Arabidopsis proteins of the ethylene biosynthesis pathway had more potential glycosylation sites than rice, and 1-aminocyclopropane-1-carboxylate oxidase proteins were less phosphorylated than 1-aminocyclopropane-1-carboxylate synthase and S-adenosylmethionine proteins. According to the gene expression patterns, S-adenosylmethionine genes were more involved in the rice-ripening stage while in Arabidopsis, ACS2, and 1-aminocyclopropane-1-carboxylate oxidase genes were contributed to seed maturity. Furthermore, the result of miRNA targeting the transcript sequences showed that ath-miR843 and osa-miR1858 play a key role to regulate the post-transcription modification of S-adenosylmethionine genes in Arabidopsis and rice, respectively. The discovered cis- motifs in the promoter site of all the ethylene biosynthesis genes of A. thaliana genes were engaged to light-induced response in the cotyledon and root genes, sulfur-responsive element, dehydration, cell cycle phase-independent activation, and salicylic acid. The ACS4 protein prediction demonstrated strong protein-protein interaction in Arabidopsis, as well as, SAM2, Os04T0578000, Os01T0192900, and Os03T0727600 predicted strong protein-protein interactions in rice.

Conclusion: In the current study, the complex between miRNAs with transcript sequences of ethylene biosynthesis genes in A. thaliana and O. sativa were identified, which could be helpful to understand the gene expression regulation after the transcription process. The binding sites of common transcription factors such as MYB, WRKY, and ABRE that control target genes in abiotic and biotic stresses were generally distributed in promoter sites of ethylene biosynthesis genes of A. thaliana. This was the first time to wide explore the ethylene biosynthesis pathway using bioinformatics tools that markedly showed the capability of the in silico study to integrate existing data and knowledge and furnish novel insights into the understanding of underlying ethylene biosynthesis pathway genes that will be helpful for more dissection.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s43141-020-00083-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7572930PMC
October 2020

Cell Signaling in Model Plants.

Int J Mol Sci 2020 Aug 23;21(17). Epub 2020 Aug 23.

Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran.

Plants as sessile organisms are not able to move and must cope with adverse environmental conditions and stresses such as extreme temperatures, drought, high soil salinity, oxidative stress, pathogen attack, and so on [...].
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms21176062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7503501PMC
August 2020

Sorption Mechanism and Optimization Study for the Bioremediation of Pb(II) and Cd(II) Contamination by Two Novel Isolated Strains Q3 and Q5 of sp.

Int J Environ Res Public Health 2020 06 6;17(11). Epub 2020 Jun 6.

Telematic University Pegaso, Piazza Trieste e Trento 48, 80132 Naples, Italy.

The use of bacterial strains as agents in bioremediation processes could reduce the harmfulness of potential toxic elements (PTEs) from water and soil with low or even no impact on the natural ecosystems. In this study, two new metal resistant-bacterial strains (Q3 and Q5) of sp. were isolated from a sulfurous spring and their potential (as pure cultures or mixed) to remove Pb(II) and Cd(II) from an aqueous matrix was evaluated and optimized using response surface methodology (RSM). The optimal conditions for Cd(II) removal from all tested strains combinations were observed at an initial pH 5, a temperature of 38 °C, and an initial Cd(II) concentration of 50 mg L, while the performance of bacterial strains on Pb(II) removal was strongly correlated to initial pH and temperature conditions. Moreover, the efficiency of bacterial strains in removing both PTEs, Pb(II) and Cd(II), from an aqueous matrix was considerably higher when they were used as a mixed culture rather than pure. According to field emission SEM (FESEM) and EDS analysis, the two bacterial strains showed different mechanisms in removing Cd(II): sp. Q5 bio-accumulated Cd(II) in its periplasmic space, whereas sp. Q3 bio-accumulated Cd(II) on its cell surface. On the other hand, Pb(II) is removed by chemical precipitation (lead sulfide) induced by both sp. Q3 and Q5. This study discloses new aspects of Pb(II) and Cd(II) bioremediation mechanisms in species that can be extremely useful for designing and operating novel PTEs bioremediation processes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijerph17114059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7312031PMC
June 2020

Insights into the SAM Synthetase Gene Family and Its Roles in Tomato Seedlings under Abiotic Stresses and Hormone Treatments.

Plants (Basel) 2020 May 4;9(5). Epub 2020 May 4.

Laboratory of Genomics for Breeding, DAFNAE, University of Padova, Campus of Agripolis, 35030 Legnaro, Italy.

S-Adenosyl-L-methionine (SAM) is a key enzyme involved in many important biological processes, such as ethylene and polyamine biosynthesis, transmethylation, and transsulfuration. Here, the SAM synthetase (SAMS) gene family was studied in ten different plants (Arabidopsis, tomato, eggplant, sunflower, , soybean, rice, barley, and sorghum) with respect to its physical structure, physicochemical characteristics, and post-transcriptional and post-translational modifications. Additionally, the expression patterns of SAMS genes in tomato were analyzed based on a real-time quantitative PCR assay and an analysis of a public expression dataset. SAMS genes of monocots were more conserved according to the results of a phylogenetic analysis and the prediction of phosphorylation and glycosylation patterns. SAMS genes showed differential expression in response to abiotic stresses and exogenous hormone treatments. Solyc01g101060 was especially expressed in fruit and root tissues, while Solyc09g008280 was expressed in leaves. Additionally, our results revealed that exogenous BR and ABA treatments strongly reduced the expression of tomato SAMS genes. Our research provides new insights and clues about the role of SAMS genes. In particular, these results can inform future functional analyses aimed at revealing the molecular mechanisms underlying the functions of SAMS genes in plants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/plants9050586DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7284622PMC
May 2020

An Overview of Hazardous Impacts of Soil Salinity in Crops, Tolerance Mechanisms, and Amelioration through Selenium Supplementation.

Int J Mol Sci 2019 Dec 24;21(1). Epub 2019 Dec 24.

Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.

Soil salinization is one of the major environmental stressors hampering the growth and yield of crops all over the world. A wide spectrum of physiological and biochemical alterations of plants are induced by salinity, which causes lowered water potential in the soil solution, ionic disequilibrium, specific ion effects, and a higher accumulation of reactive oxygen species (ROS). For many years, numerous investigations have been made into salinity stresses and attempts to minimize the losses of plant productivity, including the effects of phytohormones, osmoprotectants, antioxidants, polyamines, and trace elements. One of the protectants, selenium (Se), has been found to be effective in improving growth and inducing tolerance against excessive soil salinity. However, the in-depth mechanisms of Se-induced salinity tolerance are still unclear. This review refines the knowledge involved in Se-mediated improvements of plant growth when subjected to salinity and suggests future perspectives as well as several research limitations in this field.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms21010148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981449PMC
December 2019

Effects of clozapine and sulpiride on morphine state-dependent memory in the step-down passive avoidance test.

Pharmacology 2007 21;79(3):149-53. Epub 2006 Dec 21.

Department of Pharmacology, School of Medicine and Iranian National Center for Addiction Studies, Tehran University of Medical Sciences, Tehran, Iran.

The effects of antipsychotic drugs sulpiride and clozapine on morphine state-dependent memory of passive avoidance task were examined in mice. Post-training administration of morphine (5 mg/kg) led to state-dependent learning with impaired memory retrieval on the test day which was reversed by pre-test administration of the same dose of the opioid (5 mg/kg). In animals where memory was impaired by post-training morphine, the administration of either sulpiride or clozapine before pre-test morphine reduced the improvement of memory produced by the opioid. Co-administration of sulpiride with clozapine did not potentiate their antagonistic response. In conclusion, the inhibition of improvement of memory retrieval by morphine treatment on the test day by the two dopamine receptor antagonists seems to be induced through two different receptor mechanisms.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1159/000098151DOI Listing
July 2007

Influence of morphine and dopamine receptor sensitization on locomotor activity in mice.

Pharmacology 2006 23;78(4):185-92. Epub 2006 Oct 23.

Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.

In the present study, the influence of morphine- and dopamine receptor antagonists-induced sensitization on morphine-induced locomotion in mice was investigated. Morphine (30, 40 and 50 mg/kg) increased, while lower doses of the opioid (10 and 20 mg/kg) decreased locomotor activity of mice. Subchronic repeated pretreatment of animals with morphine showed an increase in locomotion induced by the opioid. Clozapine reduced locomotor activity induced by morphine in both the naïve and subchronic morphine-treated animals. Subchronic pretreatment of clozapine also caused an increase in the locomotion induced by morphine. Sulpiride also decreased locomotion induced by morphine and its subchronic administration of the drug caused an increase in morphine- or apomorphine-induced locomotion. Co-administration of clozapine with sulpiride did not elicit potentiation in inhibiting the morphine effect. The D2 receptor mRNA expression was also increased by repeated morphine administration. It may be concluded that morphine-induced sensitization may be due to increase in D2 receptor mRNA expression. Sulpiride and clozapine may induce sensitization and also inhibit morphine-induced locomotion through their dopamine receptor blocking properties.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1159/000096428DOI Listing
February 2007
-->