Rambod Abiri

Towards understanding pre-mRNA splicing mechanisms and the role of SR proteins

Alternative pre-mRNA splicing provides a source of vast protein diversity by removing non-coding sequences (introns) and accurately linking different exonic regions in the correct reading frame. The regulation of alternative splicing is essential for various cellular functions in both pathological and physiological conditions. In eukaryotic cells, this process is commonly used to increase proteomic diversity and to control gene expression either co- or post-transcriptionally. Alternative splicing occurs within a megadalton-sized, multi-component machine consisting of RNA and proteins; during the splicing process, this complex undergoes dynamic changes via RNA-RNA, protein-protein and RNA-protein interactions. Co-transcriptional splicing functionally integrates the transcriptional machinery, thereby enabling the two processes to influence one another, whereas post-transcriptional splicing facilitates the coupling of RNA splicing with post-splicing events. This review addresses the structural aspects of spliceosomes and the mechanistic implications of their stepwise assembly on the regulation of pre-mRNA splicing. Moreover, the role of phosphorylation-based, signal-induced changes in the regulation of the splicing process is demonstrated.

Conjugated linoleic acid: A potent fatty acid linked to animal and human health

ABSTRACT Conjugated linoleic acid (CLA) is a mixture of isomers of linoleic acid (C18:2 n-6), which is mostly found in the ruminant meat and dairy products. The CLA is known to have many potential health benefits, and considered a potent powerful fatty acid, which is linked to animal and human health. The present work aims to discuss the source and production, mechanism of action, and effects of CLA on humans, poultry, and ruminants by reviewing the recent studies carried out on CLA. Despite most of the recent studies indicating beneficial effects of CLA on improving body weight control parameters, its effects on reducing risk factors of cardiovascular diseases (CVD), inflammation, blood glucose, and insulin are still controversial, and need to be further studied in different hosts.

Ornamental Exterior versus Therapeutic Interior of Madagascar Periwinkle (Catharanthus roseus): The Two Faces of a Versatile Herb

Catharanthus roseus (L.) known as Madagascar periwinkle (MP) is a legendary medicinal plant mostly because of possessing two invaluable antitumor terpenoid indole alkaloids (TIAs), vincristine and vinblastine. The plant has also high aesthetic value as an evergreen ornamental that yields prolific blooms of splendid colors. The plant possesses yet another unique characteristic as an amiable experimental host for the maintenance of the smallest bacteria found on earth, the phytoplasmas and spiroplasmas, and serves as a model for their study. Botanical information with respect to synonyms, vernacular names, cultivars, floral morphology, and reproduction adds to understanding of the plant while the geography and ecology of periwinkle illustrate the organisms ubiquity. Good agronomic practices ensure generous propagation of healthy plants that serve as a source of bioactive compounds and multitudinous horticultural applications. The correlation between genetic diversity, variants, and TIA production exists. MP is afflicted with a whole range of diseases that have to be properly managed. The ethnobotanical significance of MP is exemplified by its international usage as a traditional remedy for abundant ailments and not only for cancer. TIAs are present only in micro quantities in the plant and are highly poisonous per se rendering a challenge for researchers to increase yield and reduce toxicity.

Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives.

Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.

Genoproteomics-assisted improvement of Andrographis paniculata: toward a promising molecular and conventional breeding platform for autogamous plants affecting the pharmaceutical industry

Abstract Andrographis paniculata (Burm. f.) Wall. ex Nees. (AP) is a hermaphroditic, self-compatible, and habitual inbreeding plant. Its main bioactive component is andrographolide, which is capable of inducing autophagic cell death in some human cancer cells and helps fight HIV/AIDS. Increasing the andrographolide content by investigating the genetic mechanisms controlling its biosynthesis in order to improve and develop high-yielding cultivars are the main breeding targets for AP. However, there might exist some limitations or barriers for crossability within AP accessions. Recently, this problem was addressed in AP by using a combination of crossbreeding and biotechnology-aided genetic methods. This review emphasizes that development of a breeding platform in a hard-to-breed plant, such as AP, requires the involvement of a broad range of methods from classical genetics to molecular breeding. To this end, a phenological stage (for example, flowering and stigma development) can be simplified to a quantitative morphological trait (for example, bud or stigma length) to be used as an index to express the highest level of receptivity in order to manage outcrossing. The outcomes of the basic crossability research can be then employed in diallel mating and crossbreeding. This review explains how genomic data could produce useful information regarding genetic distance and its influence on the crossability of AP accessions. Our review indicates that co-dominant DNA markers, such as microsatellites, are also capable of resolving the evolutionary pathway and cryptic features of plant populations and such information can be used to select the best breeding strategy. This review also highlights the importance of proteomic analysis as a breeding tool. In this regard, protein diversification, as well as the impact of normal and stress-responsive proteins on morphometric and physiological behaviors, could be used in breeding programs. These findings have immense potential for improving plant production and, therefore, can be regarded as prospective breeding platforms for medicinal plants that have an autogamous mode of reproduction. Finally, this review suggests that novel site-directed genome editing approaches such as TALENs (Transcription Activator-Like Effector Nucleases) and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein-9 nuclease) systems together with other new plant breeding technologies (NPBT) should simultaneously be taken into consideration for improvement of pharmaceutical plants.

Highly efficient protocol for callogenesis, somagenesis and regeneration of Indica rice plants

In the present study, we have reported a simple, fast and efficient regeneration protocol using mature embryos as explants, and discovered its effective applicability to a range of Indica rice genotypes. We have considered the response of six varieties in the steps of the regeneration procedure. The results showed that calli were variably developed from the scutellar region of seeds and visible within 6-20 days. The highest and lowest calli induction frequency (70% and 51.66%) and number of induced calli from seeds (14 and 10.33) were observed in MR269 and MRQ74, respectively. The maximum and minimum number (7.66 and 4) and frequency of embryogenic calli (38.33% and 20%) were recorded in MR219 and MRQ74, respectively. However, the highest browning rate was observed in MR84 (87%) and the lowest rate in MRQ50 (46%). The majority of plants regenerated from embryogenic calli were obtained from MRQ50 (54%) and the minimum number of plants from MR84. In this study, the maximum numbers of plantlets were regenerated from the varieties with highest rate of embryogenic calli. Also, various varieties, including MRQ50, MR269, MR276 and MR219, were satisfactorily responding, while MRQ74 and MR84 weakly responded to the procedure. Such a simple, successful and generalized method possesses the potential to become an important tool for crop improvement and functional studies of genes in rice as a model monocot plant.

Salt stress-induced protein pattern associated with photosynthetic parameters and andrographolide content in Andrographis paniculata Nees

Andrographis paniculata is a multifunctional medicinal plant and a potent source of bioactive compounds. Impact of environmental stresses such as salinity on protein diversification, as well as the consequent changes in the photosynthetic parameters and andrographolide content (AG) of the herb, has not yet been thoroughly investigated. The present study showed that the salinity affects the protein pattern, and subsequently, it decreased the photosynthetic parameters, protein content, total dry weight, and total crude extract. Exceptionally, the AG content was increased (p ≤ 0.01). Moreover, it was noticed that the salinity at 12 dS m−1 led to the maximum increase in AG content in all accessions. Interestingly, the leaf protein analysis revealed that the two polymorphic protein bands as low- and medium-sized of 17 and 45 kDa acted as the activator agents for the photosynthetic parameters and AG content. Protein sequencing and proteomic analysis can be conducted based on the present findings in the future. Graphical Abstract Impact of salinity on the protein pattern, photosynthetic parameters and andrographolide content in Andrographis paniculata Nees.

Towards a better understanding of Artemisia vulgaris : Botany, phytochemistry, pharmacological and biotechnological potential

Artemisia vulgaris is one of the important medicinal plant species of the genus Artemisia, which is usually known for its volatile oils. The genus Artemisia has become the subject of great interest due to its chemical and biological diversity as well as the discovery and isolation of promising anti-malarial drug artemisinin. A. vulgaris has a long history in treatment of human ailments by medicinal plants in various parts of the world. This medicinal plant possesses a broad spectrum of therapeutic properties including: anti-malarial, anti-inflammatory, anti-hypertensive, anti-oxidant, anti-tumoral, immunomodulatory, hepatoprotective, anti-spasmodic and anti-septic. These activities are mainly attributed to the presence of various classes of secondary metabolites, including flavonoids, sesquiterpene lactones, coumarins, acetylenes, phenolic acids, organic acids, mono- and sesquiterpenes. Studies related to A. vulgaris morphology, anatomy and phytochemistry has gained a significant interest for better understanding of production and accumulation of therapeutic compounds in this species. Recently, phytochemical and pharmacological investigations have corroborated the therapeutic potential of bioactive compounds of A. vulgaris. These findings provided further evidence for gaining deeper insight into the identification and isolation of novel compounds, which act as alternative sources of anti-malarial drugs in a cost-effective manner. Considering the rising demand and various medical applications of A. vulgaris, this review highlights the recent reports on the chemistry, biological activities and biotechnological interventions for controlled and continuous production of bioactive compounds from this plant species.

Selection, Characterizations and Somatic Embryogenesis of Malaysian Salt-tolerant Rice (Oryza sativa cv. MR219) through Callogenesis

Salt-tolerant lines of MR219 were produced through somatic embryogenesis from salt-tolerant callus of Oryza sativa L. cv.MR219 using in vitro selection procedure. Callus was developed aseptically from seeds on MS media supplemented with 2 mg/L 2, 4-D. Then, callus directly was sub-cultured on MS media with different concentrations of NaCl (0, 50, 100, 200, and 300 mM) to produce salt-tolerant callus. Based on the callus characteristics which are morphological, physiological and biochemical cascades such as proline content, total protein, total soluble sugar, lipid peroxidation, activity of ascorbate peroxidase and catalase, salt-tolerant callus was screened and selected. After 4 months, callus cultured in 50 and 100 mM NaCl showed yellow color, soft, friable and nodular proliferating. However, callus cultured in 200 and 300 mM NaCl turn blackish-brown and stiff and acutely-necrotic. The selected salt-tolerant callus was sub-cultured on MS media for somatic embryogenesis. The salt-tolerant plantlets were transferred into pots individually for acclimatization purpose. Salt stress caused significant reduction in water content, fresh and dry weight of callus. The level of total soluble sugar, proline, lipid peroxidation and ascorbate peroxidase significantly increased under salt stress. Salt-tolerant callus indicated high activity of catalase that determined more protection against production of reactive oxygen species. According to growth performance and antioxidant capacity, the plantlets from 50 and 100 mM NaCl, selected as salt-tolerant line. This study suggests the methodology to produce salt-tolerant cultivar of rice which could be a step forward to commercialization.

Quantitative assessment of indica rice germination to hydropriming, hormonal priming and polyethylene glycol priming

2 CHILEAN JOURNAL OF AGRICULTURAL RESEARCH 76(1) JANUARY-MARCH 2016 4 OCTOBER DECEMBER 2016 Seed priming is a useful technique which improves seed germination parameters. The present investigation was conducted to evaluate some of the most important germination parameters such as total germination, germination rate, mean germination time, average speed, germination percentage (GP), germination vigor index (GVI), relative frequency, plumule fresh and dry weight, radical fresh and dry weight, plumule and radical length, leaf and root proline content of six indica rice (Oryza sativa L.) varieties, including MR219, MR219-4, MR219-9, MR220, MR159, and MR 211 under hydro-, hormonaland polyethylen glycol (PEG)priming conditions. The highest germination parameters were achieved under the hydro-priming treatment, at 18 h (100%), 6 h (100%), 18 h (90.3%), 12 h (91.6%), 18 h (86.6%), and 18 h (78.3%) for the genotypes MR219, MR219-4, MR2199, MR220, MR159, and MR211, respectively. The best germination feedback of the rice varieties under the hormonal priming were observed in 50 mg L abscisic acid (ABA), 10 mg L gibberellic acid-3 (GA3), 50 mg L indole-3-acetic acid (IAA), 50 mg L GA3, 100 mg L ABA, and 10 mg L GA3 for the genotypes MR219, MR219-4, MR219-9, MR220, MR159 and MR211, respectively. The rice varieties showed different responses to various levels of PEG in which MR219, MR219-4 and MR219-9 responded positively to higher PEG levels, while MR220, MR159 and MR211 showed better feedback under lower PEG concentrations. These outcomes comply with the higher tolerance of MR219, MR219-9 and MR219-4 varieties to drought stress.