Ali Niazi

Ali Niazi
Shiraz University

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209
Publications
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Introduction
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Publications

Publications (209)
Article
Saccharomyces cerevisiae is known for its outstanding ability to produce ethanol in industry. Underlying the dynamics of gene expression in S . cerevisiae in response to fermentation could provide informative results, required for the establishment of any ethanol production improvement program. Thus, representing a new approach, this study was cond...
Article
Full-text available
The cholecystokinin-2 receptor (CCK 2 R) is a G protein-coupled receptor (GPCR) that is expressed in peripheral tissues and the central nervous system and constitutes a promising target for drug development in several diseases, such as gastrointestinal cancer. The search for ligands of this receptor over the past years mainly resulted in the discov...
Article
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Natural compounds are proper tools for inhibiting cancer cell proliferation. Hence, the search for these ligands of overexpressed receptors in breast cancer has been a competitive challenge recently and opens new avenues for drug discovery. In this research, we have investigated molecular interactions between natural products and overexpressed rece...
Article
Among the various treatments, GLP-1 receptor agonists (incretin mimics) such as liraglutide and exenatide have been well received in treating type 2 diabetes mellitus (T2DM) and obesity. In this study, an exenatide analogue, in which methionine at position 14 substituted with leucine, was ligated to human α-crystallin (α-Cry) and then expressed in...
Preprint
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Nitrogen (N) and phosphorus (P) are two essential plant macronutrients that can limit plant growth by different mechanisms. We aimed to shed light on how soybean respond to low nitrogen (LN), low phosphorus (LP) and their combined deficiency (LNP). Generally, these conditions triggered changes in gene expression of the same processes, including cel...
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of the coronavirus disease (COVID-19) pandemic, has infected millions of people globally. Genetic variation and selective pressures lead to the accumulation of single nucleotide polymorphism (SNP) within the viral genome that may affect virulence, transmission rate, vira...
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Leaf rust caused by Puccinia triticina Eriks. is the most prevalent wheat rust worldwide and occurs annually wherever wheat is grown. The most economical and environmentally friendly method to control this fungal disease is genetic resistance, which is achieved through deploying effective resistance genes. Tightly-linked molecular markers facilitat...
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Full-text available
Since potato is the fourth most important crop, the development of a practical and simple transformation method for cultivars recalcitrant in tissue culture is absolutely vital. When the potato is fried at temperatures higher than 120 °C, acrylamide that is probably carcinogenic in humans is formed in French fries and potato chips during the Mailla...
Preprint
Leaf rust caused by Puccinia triticina Eriks. is the most prevalent wheat rust worldwide and occurs annually wherever wheat is grown. The most economical and environmentally friendly method to control this fungal disease is genetic resistance, which is achieved through deploying effective resistance genes. Tightly-linked molecular markers facilitat...
Article
Full-text available
Background SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes. Results We analyzed SPX gene family evolution in legumes and in a number of key speci...
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Full-text available
Background Hypoxia refers to the condition of low oxygen pressure in the atmosphere and characterization of response to hypoxia as a biological complex puzzle, is challenging. Previously, we carried out a comparative genomic study by whole genome resequencing of highland and lowland Iranian native chickens to identify genomic variants associated wi...
Article
Catharanthus roseus as an exclusive producer of rare terpenoid indole alkaloids (TIA) is considered as one of the main sources for the production of anticancer agents like vinblastine through the TIA pathway. It also produces some other important metabolites such as ajmalicine with anti-hypertension activity. According to low yield of important ind...
Preprint
Saccharomyces cerevisiae is known for its outstanding ability to produce ethanol in industry. Identifying the dynamic of gene expression in S. cerevisiae in response to fermentation is required for the establishment of any ethanol production improvement program. The goal of this study was to identify the discriminative genes between improved and re...
Article
Full-text available
BackgroundDNA methylation is one of the most important epigenetic event that regulates gene expression. In addition to DNA methylation, transgene copy number may induce gene silencing. Therefore, the study of these cases is useful for understanding of gene silencing regulation.Methods and resultsIn this study, the methylation pattern of 35S promote...
Article
Full-text available
Hyaluronic acid (HA), a unique polysaccharide with excellent Physico-chemical properties, is broadly used in pharmaceutical, biomedical, and cosmetic fields. It is widely present in all vertebrates, certain bacterial strains, and even viruses while it is not found in plants, fungi, and insects. HA is naturally synthesized by a class of integral mem...
Preprint
Full-text available
Background SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes. Results We analyzed SPX gene family evolution in legumes and in a number of key speci...
Article
Full-text available
Drought stress affects a range of plant processes. It is still not well-known how C3 and C4 plants respond to drought. Here, we used a combination of meta-analysis and network analysis to compare the transcriptional responses of Oryza sativa (rice), a C3 plant, and Zea mays (maize), a C4 plant, to drought stress. The findings showed that drought st...
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In human αB-crystallin or HspB5, the substitution of arginine residue at position 157 with histidine has been reported to cause cardiomyopathy. In this study, the impact of R157H mutation on the structure, stability and functional properties of human αB-crystallin was investigated using a variety of spectroscopic techniques and microscopic analyses...
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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) together with CRISPR-associated (Cas) proteins have catalysed a revolution in genetic engineering. Native CRISPR-Cas systems exist in many bacteria and archaea where they provide an adaptive immune response through sequence-specific degradation of an invading pathogen’s genome. Thi...
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Breast cancer is one of the most widespread diseases with high incidence and mortality rate in females. The accurate biomarker discovery for the early detection of patients prone to breast cancer is crucial in the treatment and diagnosis of breast cancer. The current study employed a comprehensive approach to detect an epigenomic data pattern of br...
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Full-text available
Coronavirus disease 2019 has developed into a dramatic pandemic with tremendous global impact. The receptor-binding motif (RBM) region of the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), binds to host angiotensin-converting enzyme 2 (ACE2) receptors for infection. As ACE2 receptors are highly conserved within verte...
Article
Valeriana officinalis is a medicinal plant, a source of bioactive chemical compounds and secondary metabolites which are applied in pharmaceutical industries. The advent of ethnomedicine has provided alternatives for disease treatment and has increased demands for natural products and bioactive compounds. A set of preliminary steps to answers for s...
Article
Cecropin A, as an antimicrobial peptide (AMP), is possible to use in medical and agricultural fields as a new and safe bio‐control agent. Therefore, it is highly necessary to find a cost‐effective and scalable approach to generate a large scale of it. In this research, the Agrobacterium rhizogenes strain ATCC 15834 was used to transfer the Cecropin...
Article
Full-text available
Drought stress causes changes in morphology, physiology and gene expression profile in the plants. One of the ways to respond to this stress is to change the synthesis of specific polypeptides such as LTP (Lipid transfer proteins). For this purpose, LTp expression level was investigated under three osmotic potentials of -2, -4 and -6 bar in combina...
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Full-text available
The application of high throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent o...
Article
Despite the limitations of current methods in cancer treatment, the use of bioactive peptides can be as an alternative to treat today. Therefore, isolation and relative purification of bioactive peptides was carried out form Achillea eriophora using a Sep-Pak C18 SPE cartridge and Amicon® Ultra Centrifugal Filters. The presence of desired peptides...
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Full-text available
Virus-like particles (VLPs) are a class of structures formed by the self-assembly of viral capsid protein subunits and contain no infective viral genetic material. The Hepatitis B core (HBc) antigen is capable of assembling into VLPs that can elicit strong immune responses and has been licensed as a commercial vaccine against Hepatitis B. The HBc V...
Preprint
Full-text available
Hyaluronic acid (HA), a unique polysaccharide with excellent physicochemical properties, is broadly used in pharmaceutical, biomedical, and cosmetic fields. It is widely present in all vertebrates, certain bacterial strains, and even viruses while it is not found in plants, fungi, and insects. HA is naturally synthesized by a class of integral memb...
Article
Cadmium (Cd) is a toxic metal, which seems to be crucial during the prepubertal period. Cd can destroy the structural integrity of the blood-brain barrier (BBB) and enters into the brain. Although the brain is susceptible to neurotoxicity induced by Cd, the effects of Cd on the brain, particularly hypothalamic transcriptome, are still relatively po...
Article
The effects of different levels of fish oil on productive and reproductive performance as well as serum biochemical indices in female Chukar partridges were evaluated. Thirty-six 1.5-yearold laying Chukar partridges and 12 age-matched males (female: male ratio of 3:1) were divided to four experimental groups (three replicates of three birds each) i...
Article
Full-text available
The application of high throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent o...
Article
Full-text available
The plant Citrullus colocynthis, a member of the squash (Cucurbitaceae) family, has a long history in traditional medicine. Based on the ancient knowledge about the healing properties of herbal preparations, plant-derived small molecules, e.g., salicylic acid, or quinine, have been integral to modern drug discovery. Additionally, many plant familie...
Article
Functional evaluation of encrypted bioactive peptides in protein structure helps to better understand those for using in pharmacy and food sciences. For this purpose, the total protein was extracted from Matricaria chamomilla, Ziziphora clinopodioides, and Cressa cretica, and partially purified with ammonium sulfate. Protein hydrolysates were obtai...
Article
Fars native chicken (FNC) is utilized as a food source, and plays a critical role in earning money in rural areas. However, little attention has been paid to FNC at molecular level and its genetic background is unknown for organizing the breeding programs. For the first time, herein, the effect of Ovocalyxin-32 (OCX-32) variant on egg production tr...
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Full-text available
Cataract is the major reason for human blindness worldwide. α-Crystallin, as a key chaperone of eye lenses, keeps the lenticular tissues in its transparent state over time. In this study, cataract-causing familial mutations, P20R and A171T, were introduced in CRYАB gene. After successful expression in Escherichia coli and subsequent purification, t...
Article
Nowadays, transgenic plants are considered as an expression system for therapeutic recombinant proteins. One of the approaches to recombinant protein production is the introduction of the relevant genes to plant cells and produce hairy roots from these cells using the plant tissue culture methods. L-asparaginase II is one of the important therapeut...
Article
Root-knot nematodes (Meloidogyne spp.) are among the most dangerous herbal parasites which destroy 8.8 to 14.6 percent of agricultural products annually. This study examined inducing resistance to tomato against Meloidogyne javanica, as well as time-dependent changes in the expression of PR1 gene, after applying salicylic acid (SA) and Pseudomonas...
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Full-text available
Understanding how plants respond to salinity stress is essential for developing tolerant genotypes, to keep human food secure since it is threaten by climate changes and increasing population worldwide. Barley (Hordeum vulgare) is a crop that possesses various salinity tolerance mechanisms that remain to be explored. In this study, data from an RNA...
Article
The lack of an efficient protocol for the transformation of Catharanthus roseus, as an important medicinal plant, causes obstacles in the genetic engineering programmes of this plant. Therefore, the present study was conducted to examine a convenient and reliable system for generating stable transgenic lines based on the in planta method. To do so,...
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Full-text available
Native chickens are endangered genetic resources that are kept by farmers for different purposes. Native chickens distributed in a wide range of altitudes, have developed adaptive mechanisms to deal with hypoxia. For the first time, we report variants associated with high-altitude adaptation in Iranian native chickens by whole genome sequencing of...
Article
Full-text available
WRKY transcription factors play important roles in regulation of various plant biological processes, including response to ab iotic stresses. WRKY genes might be potential targets for transgenic breeding to enhance stress tolerance in rapeseed (Brassica napus). The present study aimed to clone and characterize WRKY57 (BnWRKY57) gene derived from B....
Article
WRKY transcription factors play important roles in regulation of various plant biological processes, including response to abiotic stresses. WRKY genes might be potential targets for transgenic breeding to enhance stress tolerance in rapeseed (Brassica napus). The present study aimed to clone and characterize WRKY57 (BnWRKY57) gene derived from B....
Article
Full-text available
The successful introduction of isopentenyl transferase (IPT) gene into perennial ryegrass, cultivars Numan and Grassland using Agrobacterium tumefaciens via three explants (callus, seed and meristem tip) under three individual experiment was evaluated. In the first experiment, the calli were inoculated with LBA4404 Agrobacterium strain under vacuum...
Article
Phytoremediation is an appropriate technology used to remove pollutants from environment components. A greenhouse trial was conducted to test the hypothesis that application of surfactant levels and inoculation with Pseudomonas fluorescens bacterium and/or Piriformospora indica fungus enhances the phytoremediation of cadmium (Cd). Maize seeds were...
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Full-text available
Plant root symbiosis with Arbuscular mycorrhizal (AM) fungi improves uptake of water and mineral nutrients, improving plant development under stressful conditions. Unraveling the unified transcriptomic signature of a successful colonization provides a better understanding of symbiosis. We developed a framework for finding the transcriptomic signatu...
Data
Mining transcriptome profile of Medicago roots to achieve transcriptomic signature of Arbuscular mycorrhiza (AM) inoculation. Seven feature selection models including RELIEF, UNCERTAINTY, GINI INDEX, CHI SQUARED, RULE, INFO GAIN, and INFO GAIN RATIO evaluated the relevance of 33685 genes as well as Study ID and AM type in discriminating AM inoculat...
Data
Transcription factors matrix families that have enriched binding sites on promoter regions of the top 20 upregulated genes during successful Arbuscular mycorrhiza (AM) colonization according to common TFs analysis of MatInspector tool. Transcription factor Matrix similarity was set to >0.95.
Data
Available expression data on Arbuscular mycorrhiza at NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/) database.
Data
Gene ontology classification of transcriptomic signature of Arbuscular mycorrhiza (AM) inoculation. GO approach in terms of Molecular Function, Biological Process, and Cellular Component was used for functional annotation of 73 unregulated genes in AM inoculation that were announced important by most of feature selection models with Z-value differe...
Data
Genes discriminating Arbuscular mycorrhiza (AM) inoculated roots from non-inoculated ones according to UNCERTAINTY, GINI INDEX, CHI SQUARED, RULE, INFO GAIN, and INFO GAIN RATIO feature selection models (weight higher than 0.95)and also Z-value difference of > 0.5 or < −0.5. The resulting weights of each feature selection model were normalized into...
Data
The top 20 highly upregulated meta-genes of successful Arbuscular mycorrhiza (AM) colonization transcriptomic signature on roots of Medicago truncatula, obtained by integration of meta-analysis and machine learning, were used for promoter analysis and common regulator discovery.
Data
RNA-seq based differential expression analysis of Medicago truncatula response of Arbuscular mycorrhiza (AM) inoculation compared to non-AM inoculation.
Data
Pseudo codes for scaling and quartiling normalization approaches, employed in this study. (A) Scaling approach. (B) Quartiling approach.
Data
High correspondence between independent RNA-seq data of Arbuscular mycorrhiza (AM) colonization in Medicago truncatula and the identified AM colonization signature in this study, derived by integration of meta-analysis and supervised attribute weighting models.
Article
Full-text available
Fast free of acrylamide clearing tissue (FACT) is a modified sodium dodecyl sulfate‐based clearing protocol for the chemical clearing of lipids that completely preserves fluorescent signals in the cleared tissues. The FACT protocol was optimized to image translucent immunostained brain and non‐nervous tissues. For this purpose adult male Chukar par...
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Full-text available
Tulip (Tulipa L.) is one of the most important ornamental geophytes in the world. Analysis of molecular variability of tulips is of great importance in conservation and parental lines selection in breeding programs. Of the 70 genic microsatellites, 15 highly polymorphic and reproducible markers were used to assess the genetic diversity, structure,...
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Full-text available
Many studies have been performed to identify regulatory circuit underlying plant stress tolerance. However, the reliability of some findings has been criticized because of exclusive use of stress sensitive plant species such as Arabidopsis thaliana. Sensitive plant species often harbor narrow defensive mechanisms and have relatively low capacity fo...
Article
Assisted phytoremediation has been widely used for decontamination of potentially toxic elements contaminated soils. A greenhouse experiment was conducted to evaluate the effectiveness of different microbial inoculations and surfactant levels on the phytoremediation of a Pb-polluted calcareous soil by maize. The results showed that application of s...
Article
Full-text available
One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydroc...
Article
Salvia mirzayanii is a medicinal and aromatic plant with many pharmaceutical properties. The aims of this study were to isolate and characterise a specific gene involved in biosynthesis of major terpenoids produced by S. mirzayanii under increasing salinity stress, followed by investigation of photosynthetic responses under which yield of these ter...