De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress.

The study of salt tolerance mechanisms in halophyte plants can provide valuable information for crop breeding and plant engineering programs. The aim of the present study was to investigate whole transcriptome analysis of Aeluropus littoralis in response to salinity stress (200 and 400 mM NaCl) by de novo RNA-sequencing. To assemble the transcriptome, Trinity v2.4.0 and Bridger tools, were comparatively used with two k-mer sizes (25 and 32 bp). The de novo assembled transcriptome by Bridger (k-mer 32) was chosen as final assembly for subsequent analysis. In general, 103290 transcripts were obtained. The differential expression analysis (log2FC > 1 and FDR < 0.01) showed that 1861 transcripts expressed differentially, including169 up and 316 down-regulated transcripts in 200 mM NaCl treatment and 1035 up and 430 down-regulated transcripts in 400 mM NaCl treatment compared to control. In addition, 89 transcripts were common in both treatments. The most important over-represented terms in the GO analysis of differentially expressed genes (FDR < 0.05) were chitin response, response to abscisic acid, and regulation of jasmonic acid mediated signaling pathway under 400 mM NaCl treatment and cell cycle, cell division, and mitotic cell cycle process under 200 mM treatment. In addition, the phosphatidylcholine biosynthetic process term was common in both salt treatments. Interestingly, under 400 mM salt treatment, the PRC1 complex that contributes to chromatin remodeling was also enriched along with vacuole as a general salinity stress responsive cell component. Among enriched pathways, the MAPK signaling pathway (ko04016) and phytohormone signal transduction (ko04075) were significantly enriched in 400 mM NaCl treatment, whereas DNA replication (ko03032) was the only pathway that significantly enriched in 200 mM NaCl treatment. Finally, our findings indicate the salt-concentration depended responses of A. littoralis, which well-known salinity stress-related pathways are induced in 400 mM NaCl, while less considered pathways, e.g. cell cycle and DNA replication, are highlighted under 200 mM NaCl treatment.

A study on the antioxidant and antimicrobial activities in the chloroformic and methanolic extracts of 6 important medicinal plants collected from North of Iran.

BACKGROUND: As possible sources of natural bioactive molecules, the plant essential oils and extracts have been used globally in new antimicrobial compounds, food preservatives, and alternatives to treat infectious disease. METHODS: In this research, the antimicrobial activities of chloroformic and methanolic extracts of Sophora flavescens, Rhaponticum repens, Alhagi maurorum, Melia azedarach, Peganum harmala, and Juncus conglomeratus were evaluated against 8 bacteria (S. aureus, B. subtilis, R. toxicus, P. aeruginosa, E. coli, P. syringae, X. campestris, P. viridiflava) and 3 fungi (Pyricularia oryzae, Fusarium oxysporum and Botrytis cinerea), through disc diffusion method. Furthermore, the essential oils of plants with the highest antibacterial activity were analyzed utilizing GC/MS. Moreover, the tested plants were exposed to screening for possible antioxidant effect utilizing DPPH test, guaiacol peroxidas, and catalase enzymes. Besides, the amount of total phenol and flavonoid of these plants was measured. RESULTS: Among the tested plants, methanolic and chloroformic extracts of P. harmala fruits showed the highest antibacterial activity against the tested bacteria. Besides, the investigation of free radical scavenging effects of the tested plants indicated the highest DPPH, protein, guaiacol peroxidase, and catalase in P. harmala, M. azedarach, J. conglomeratus fruits, and J. conglomeratus fruits, respectively. In addition, the phytochemical analysis demonstrated the greatest amounts of total phenolic and flavonoid compositions in J. conglomeratus and P. harmala, respectively. CONCLUSION: The results indicated that these plants could act as a promising antimicrobial agent, due to their short killing time.

Effect of light/dark cycle on nitrate and phosphate removal from synthetic wastewater based on BG11 medium by Scenedesmus sp.

In this study, microalgae growth in the synthetic wastewater and their ability to remove nutrients under different light levels was investigated. For this purpose, a comparative study was conducted on freshwater microalgae Scenedesmus sp. to evaluate their performance to remove nitrate and phosphate from both slaughterhouse and dairy synthetic treated wastewaters, under different light/dark cycles (12/12, 16/8 and 24/0 h), in Erlenmeyer flasks. The best light/dark cycles in Erlenmeyer flasks for nitrate and phosphate removal and growth were obtained at 24/0 h. Moreover, nitrate and phosphate removal under light conditions at 24/0 h light/dark cycles were tested in a designed open raceway pond. The maximum nitrate removal in slaughterhouse and dairy synthetic wastewater was 78% and 99.7%, and the phosphate removal was 31% and 68%, respectively. Furthermore, the highest biomass productivity in dairy and slaughterhouse synthetic wastewater during 9 days was 0.65 g L-1 and 1.5 g L-1, respectively. Thus, Scenedesmus sp. could be potential candidates by showing their intrinsic merit, for the reduction of nitrate and phosphate residue levels from dairy and slaughterhouse synthetic wastewaters in open raceway ponds.

Dissecting molecular mechanisms underlying salt tolerance in rice: a comparative transcriptional profiling of the contrasting genotypes.

BACKGROUND: Salinity expansion in arable land is a threat to crop plants. Rice is the staple food crop across several countries worldwide; however, its salt sensitive nature severely affects its growth under excessive salinity. FL478 is a salt tolerant indica recombinant inbred line, which can be a good source of salt tolerance at the seedling stage in rice. To learn about the genetic basis of its tolerance to salinity, we compared transcriptome profiles of FL478 and its sensitive parent (IR29) using RNA-seq technique. RESULTS: A total of 1714 and 2670 genes were found differentially expressed (DEGs) under salt stress compared to normal conditions in FL478 and IR29, respectively. Gene ontology analysis revealed the enrichment of transcripts involved in salinity response, regulation of gene expression, and transport in both genotypes. Comparative transcriptome analysis revealed that 1063 DEGs were co-expressed, while 338/252 and 572/908 DEGs were exclusively up/down-regulated in FL478 and IR29, respectively. Further, some biological processes (e.g. iron ion transport, response to abiotic stimulus, and oxidative stress) and molecular function terms (e.g. zinc ion binding and cation transmembrane transporter activity) were specifically enriched in FL478 up-regulated transcripts. Based on the metabolic pathways analysis, genes encoding transport and major intrinsic proteins transporter superfamily comprising aquaporin subfamilies and genes involved in MAPK signaling and signaling receptor kinases were specifically enriched in FL478. A total of 1135 and 1894 alternative splicing events were identified in transcripts of FL478 and IR29, respectively. Transcripts encoding two potassium transporters and two major facilitator family transporters were specifically up-regulated in FL478 under salt stress but not in the salt sensitive genotype. Remarkably, 11 DEGs were conversely regulated in the studied genotypes; for example, OsZIFL, OsNAAT, OsGDSL, and OsELIP genes were up-regulated in FL478, while they were down-regulated in IR29. CONCLUSIONS: The achieved results suggest that FL478 employs more efficient mechanisms (especially in signal transduction of salt stress, influx and transport of k+, ionic and osmotic homeostasis, as well as ROS inhibition) to respond to the salt stress compared to its susceptible parent.

Magnetic nano fluids for isolation of genomic DNA and total RNA from various prokaryote and eukaryote cells.

The correct isolation of nucleic acid from various cells is an important preliminary step before many biochemical and diagnostic processes such as cloning, sequencing, replication, hybridization, and complementary DNA (cDNA) synthesis. In this study, the coated magnetic nanoparticles (MNFs) with Tween 20 and oleic acid because of paramagnetic and bio-compatibility properties used in the extractions of genomic DNA (gDNA) and total RNA from prokaryote and eukaryote cells. The amount and accuracy of gDNA and total RNA extracted were proved via agarose gel electrophoresis, digestion and polymerase chain reaction (PCR) techniques. According to UV-Vis spectrophotometry data and gDNA and ribosomal RNA (rRNA) bands observed on the agarose gel, the results showed that extraction of this nano-kit can be comparable with the existing methods used to purifying nucleic acids such as purification based on the use of Cetyltrimethylammonium bromide (CTAB) and phenol-chloroform methods. Characterization of the particles defines them to be ~34.85 nm in diameter and exhibiting high saturation magnetization (28 emu/g). Elimination of hazardous reagents such as phenol and chloroform from extraction solutions, the replacement for inorganic coating such as silica with organic oil, and reduction of reaction time are some advantages of this method. Therefore, according to the challenges in the nucleic acid purification pathway, the use of these kits can be remarkable.

Chemical Composition, Antioxidant and Biological Activities of the Essential Oil and Extract of the Seeds of Glycine max (Soybean) from North Iran.

Glycine max (L.) Merrill (soybean) is a major leguminous crop, cultivated globally as well as in Iran. This study examines the chemical composition of soybean essential oil, and evaluates the antioxidant and antimicrobial activities of seeds on various plant pathogens that commonly cause irreparable damages to agricultural crops. The essential oil of soybean seeds was analyzed by gas chromatography coupled to mass spectrometry. Antimicrobial activity was tested against 14 microorganisms, including three gram-positive, five gram-negative bacteria, and six fungi, using disk diffusion method and the Minimum Inhibitory Concentration technique. The soybean seeds were also subjected to screening for possible antioxidant activity by using catalase, peroxidase, superoxide dismutase, and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. Forty components were identified, representing 96.68% of the total oil. The major constituents of the oil were carvacrol (13.44%), (E,E)-2,4-decadienal (9.15%), p-allylanisole (5.65%), p-cymene (4.87%), and limonene (4.75%). The oil showed significant activity against Pseudomonas syringae subsp. syringae, Rathayibacter toxicus with MIC = 25 µg/mL, and Pyricularia oryzae with MIC = 12.5 µg/mL. In addition, the free radical scavenging capacity of the essential oil was determined with an IC50 value of 162.35 µg/mL. Our results suggest that this plant may be a potential source of biocide, for economical and environmentally friendly disease control strategies. It may also be a good candidate for further biological and pharmacological investigations.

Phytochemical screening and antimicrobial activities of the constituents isolated from Koelreuteria paniculata leaves.

Methanolic extract of Golden rain leaves was fractionated by column chromatography on silica gel and 18 fractions were obtained. Antimicrobial activities of fractions were investigated against Bacillus subtilis, Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa as quality control bacteria and fungus Pyricularia grisea which causes Blast disease in rice. Fractions showed more antibacterial activity at 0.04 g/mL concentration only on B. subtilis and S. aureus as gram positive bacteria. Also, three fractions indicated excellent antifungal effect on fungus P. grisea. Moreover, in the present study, fractions that showed very good effect on microorganisms were used for gas chromatography-mass spectrometry analysis to identify different phytochemicals.

Quantitative gene expression analysis of some sodium ion transporters under salinity stress in Aeluropus littoralis.

Plant sodium transporters activity is one of the most important salt tolerance mechanisms to keep normal status of cytosolic sodium content. In the present study, expression pattern of genes encoding Na(+)/H(+) antiporters in the plasma membrane (SOS1 gene), vacuolar membrane (NHX1 gene) and H(+)-ATPase pump (VHA gene) in Aeluropus littoralis under different treatments of NaCl was measured by the semi-quantitative RT-PCR method. Our results indicated that root and shoot sodium contents were increased along with increasing salinity pressure. In response to 200 and 400 mM NaCl, mRNA level of SOS1 and NHX1 was increased in the shoot and root tissues, while VHA transcripts were increased only under 400 mM of NaCl. Transcripts of VHA-c and NHX1 in root were higher than shoot in all treatments. In general, our results indicated that transcriptional level of SOS1, and NHX1 genes induced in parallel with VHA expression may be involved in controlling cytosolic Na(+) concentration in A. littoralis.

Phosphate solubilization potential and modeling of stress tolerance of rhizobacteria from rice paddy soil in northern Iran.

The purposes of this study were to evaluate the phosphate solubilization activity of bacteria isolated from the rhizosphere of rice paddy soil in northern Iran, and to study the effect of temperature, NaCl and pH on the growth of these isolates by modeling. Three of the most effective strains from a total of 300 isolates were identified and a phylogenetic analysis was carried out by 16S rDNA sequencing. The isolates were identified as Pantoea ananatis (M36), Rahnella aquatilis (M100) and Enterobacter sp. (M183). These isolates showed multiple plant growth-promoting attributes such as phosphate solubilization activity and indole-3-acetic acid (IAA) production. The M36, M100 and M183 isolates were able to solubilize 172, 263 and 254 µg ml(-1) of Ca3(PO4)2 after 5 days of growth at 28 °C and pH 7.5, and to produce 8.0, 2.0 and 3.0 µg ml(-1) of IAA when supplemented with L-tryptophan (1 mg ml(-1)) for 72 h, at 28 °C and pH 7.0, respectively. The solubilization of insoluble phosphate was associated with a drop in the pH of the culture medium and there was an inverse relationship between pH and solubilized P (r = -0.98, P < 0.0952). There were no significant differences among isolates in terms of acidity tolerance based on their confidence limits as assessed by segmented model analysis and all isolates were able to grow at pH 4.3-11 (with optimum at 7.0-7.5). Based on a sigmoidal trend of a three-parameter logistic model, the salt concentration required for 50 % inhibition was 8.15, 6.30 and 8.23 % NaCl for M36, M100 and M183 isolates, respectively. Moreover, the minimum and maximum growth temperatures estimated by the segmented model were 5.0 and 42.75 °C for M36, 12.76 and 40.32 °C for M100, and 10.63 and 43.66 °C for M183. The three selected isolates could be deployed as inoculants to promote plant growth in an agricultural environment.

Evaluation of Bt (Bacillus thuringiensis) rice varieties against stem borer (Chilo suppressalis).

Three transgenic rice varieties namely Khazar, Neda and Nemat, all containing a cry1Ab gene, were evaluated through PCR analysis and field examinations for their resistance at natural infestation of insect pests during 2007. The results showed that all transgenic varieties produced 1.2 kb PCR product derived from application of cry1Ab gene. In field conditions, transgenic varieties exhibited high levels of resistance against natural infestation of stem borer and the damaged plants based on dead heart or white heat for them were less than 1%. Moreover, in stem-cut bioassay 100% of released larvae died within four days after infestation. These results demonstrate that expression of cry1Ab gene in the genome of transgenic varieties provided season-long protection from the natural infestation of lepidopteran insects.

Agronomic and quality characteristics of high-yielding rice lines.

This study is a part of rice cultivar development program in north of Iran with the aim of yield potential increase and attention to eating quality. Thirteen lines developed from the crosses between high yielding cultivars with aromatic low yield ones based on pedigree breeding method. These lines along with two controls (Neda and Sang-e-Tarom) were evaluated for agronomic and quality traits in a randomized complete block design during 2005. Farm and laboratory tests showed that lines 33-DN-1, 33-DN-18 and 32-DN-6 were superior in yield (more than 5.5 t ha(-1)) and had suitable eating quality in comparison with Sang-e-tarom as a local control.