Progress in Biological Sciences
Volume:5 Issue: 1, Winter and Spring 2015

Living organisms can sense and respond to external and internal stimuli. Response is demonstrated in many forms including modulation of gene expression profiles, motility, secretion, cell death, etc. Nevertheless, all forms share a basic property: they depend on sensing small changes in the concentration of an effector molecule or subtle conformational changes in a protein and invoking the appropriate molecular response by the relevant signaling pathways. Sensing, transduction, and response to signals may be directly carried out by controlled changes in the conformation or the assembly of pre-existing components(1,2)or may involve changes in gene expression patterns (as in cell differentiation and development), which in turn is carried out by protein-nucleic acid interactions and complex formation. Hence, understanding conformational changes in proteins and nucleic acids, ligand binding, and complex formation play acentral role in advancing our knowledge of cellular dynamics. Large-scale interaction mapping projects continue to provide detailed (though approximate) interaction networks between pairs of proteins (3–6), but fall short of capturing the stability or dynamics of the interactions. Integration of these maps with thermodynamic and kinetic information about conformational changes and binding events in proteins and nucleic acids holds the promise of discovering simple universal mechanisms that explain and relate seemingly disparate biological phenomena at many levels of complexity. In this article, I will explore ‘cooperativity’, one of the most ubiquitous features in molecular biology and discuss how it impacts macromolecular folding, complex assembly, formation of biological networks, and eventually cellular function and pathology.

One of the most efficient mechanisms by which plants protect themselves from invading viruses is the specific RNA-dependent silencing pathway termed post-transcriptional gene silencing (PTGS). In this mechanism, resistance to a virus is engineered through the expression of a segment of the virus genomein transgenic plants. Potato VirusY (PVY) is one of the most damaging viruses of potato, infecting most cultivars and causing significant yield losses throughout the world. The present study was performed to compare the efficiency of three construct containing different regions of 3′UTR (UR) and coat protein (CP) against PVY infection. Expression of homologous hairpin RNA to PVY in potato plant was carried out by transient gene expression of constructs with agro-infiltration followed by mechanical viral infection. Results showed that successful production of siRNAs confer resistance to two PVY strain. Comparison between transiently expressed constructs indicated that applying CP+UR PVY hairpin RNA was the most efficient RNAi construct to confer resistance. Resistance was found to have taken the form of immunity, since no viral particle could be detected in the upper leaves as shown by ELISA assay and Northern hybridizations. To the best of our knowledge, this is the first report on the application of 3'non-coding region of PVY in conferring complete resistance against virus in potato.

Endophytes are important resources of bioactive compounds and due to their potential in the production of secondary metabolites, they are regarded as a potential reservoir of biotechnological applications. In this study, the bioactivity of bacteria and yeasts endophytes residing in Thymus sp. was evaluated. During April to October 2011, symptomless and healthy tissues of Thymus sp. were collected. A total of 23 strains of endophytic bacteria and 6 yeasts were isolated. The bio-effects of the endophytes were studied on Botrytis cinerea and plant pathogenic bacteria Xanthomonas arboricola pv. juglandis and Streptomyces scabies and human pathogens Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC. Growth inhibition mechanisms of the endophytes against B. cinerea were evaluated and it seems that the antimicrobial effects of bacterial endophytes are related to the production of protease enzyme, hydrogen cyanide and volatile compounds. Bacterial strains were identified as Bacillus, Pseudomonas and Xanthomonas of which Bacillus was the predominant isolate. For the first time, Bacillus is reported from Thymus eriocalyx, T. lancifolius, T. fallax, T. kotschyanus and T. vulgaris and Pseudomonas and Xanthomonas as endophytic bacteria from Thymus.

Endophytes are considered as an important source of bioactive natural products because these microorganisms are able to occupy unique biological niches and grow in non-ordinary environments. Therefore, endophytic fungi of medicinal plants can be developed for medicinal applications. On the other hand, medicinal properties of plant can be ascribed to its endophytic fungi. Thymus sp. is widely used as a medicinal plant. In this research, the endophytic microflora of the plant was studied. In order to isolate endophytic fungi, 800 segments of 6 Thymus species were collected from its natural habitats in Hamedan province (Iran) and medicinal plants garden during the seasons of spring, summer and fall 2011. Finally, 95 isolates consisting of 11 different fungal genera, 6 yeast isolates and 19 infertile mycelium were obtained. Among the identified isolates, the most abundant genera were Alternaria, Phoma, and Fusarium. The above mentioned genera and the genera of Cladosporium and Colletorichum were first reported from Thymus in Iran. The genera Curvularia, Cylindrocarpon, Drecheslra, Aspergillus, Stemphylium and Ulocladium were also, first reported from Thymus in the world.

The Siberian sturgeon (Acipenser baerii) is an economically important species. Sturgeon stock assessment during fingerling production is considered to be one of the most difficult phases of hatchery rearing. The present study investigated the expression of growth hormone (GH) mRNA in unfertilized eggs, fertilized eggs, eyed eggs (2 day before hatching), non-viable eggs and newly-hatched Siberian sturgeon. Knowledge about the expression of GH during egg and embryo development can help determine the quality of the eggs. This can help predict larval viability and, to some extent, directly determine the growth and survival of young fish. Little is known about the effect of this hormone on egg quality in sturgeon. The present study analyzed relative GH mRNA expression using the 2-ΔΔCT method. Ribosomal protein L6 (RPL6) transcripts were used as the housekeeping gene for normalization of GH mRNA transcription. The highest levels of GH mRNA were found in eyed eggs and the lowest levels were detected in non-viable eggs (P< 0.05). These findings suggest GH mRNA as a potential marker for egg quality in Siberian sturgeon.

Microbial phytases were applied mainly to animal and human foodstuffs in order to improve mineral bioavailability and food processing. In addition, phytases have potential biotechnological application in various other fields, such as environmental protection, aquaculture and agriculture. Bacillus sp. DM12, an isolate from a hot spring, produces phytase, which catalyzes the hydrolysis of phytic acid into myo-inositol and inorganic phosphates. Phytase from Bacillus sp. DM12 was purified using ammonium sulfate precipitation and dialysis, followed by anion exchange and gel filtration chromatography. Molecular weight of the purified phytase was estimated to be 28 kDa by SDS-PAGE. Km and Vmax values for sodium phytate were 0.177 mM and 1.126 μmol/min, respectively. The optimum temperature for phytase activity was found to be 50°C. The enzyme retained over 75% of its activity over a temperature range of 30 to 80°C. The highest phytase activity was observed at pH 4.5 and a decline of enzyme activity was observed on both sides of pH optimum. The enzyme was stable over the pH range of 3.0 to 6.0. The enzyme retained over 80% of its activity in the presence of 5 mM metal ions except CaCl2. It is also indicated that the enzyme retained over 65% of its activity over a 5 mM metal ions. These properties suggest that this phytase is a suitable enzyme for the hydrolysis of phytic acid and phytates in food and feed processing industries.

The rhizosphere is the area around the root of a plant occupied by a unique population of useful bacteria known as plant growth promoting rhizobacteria (PGPR). In this study, the isolation and identification of rhizobacteria from orange (Citrus sinensis) orchards using 16S rRNA gene, as well as biological and biochemical assays is reported. Analysis of 16S rRNA gene was confirmed bybiological and biochemical assays and showed that the isolated bacteria belong to the genera Bacilli,Enterobacter and Pseudomonas. Accordingly, Enterobacterkobei MR-R2, Pseudomonas putida MRR5, Bacillus cereus MR-R, Bacillus thuringiensis MR-R1 and Bacillus mycoides MR-R4 were identified and registered in GenBank. The results of phosphate solubilization testing revealed that the maximum rate of phosphate solubilization was observed for B. thuringiensis, and E. kobei; however, B. cereus, B. mycoides, and P. putida indicated the least activity. It can be concluded that the isolated strains (especially B. thuringiensis) are newly identified phosphate solubilizing bacterial strains, among which B. thuringiensis can be used for growth promotion of orange trees.

Francoeuria undulata (L.) LACK is often synonymous with two species of the genus Pulicaria, i.e. Pulicaria undulata (L.) C.A. Mey and Pulicaria crispa (Forssk.) olive, which are often included under the genus Francoeuria. The essential oil yield and compositions in the five natural populations of Francoeuria undulata from Fars Province in southern Iran were determined by GC and GC/MS analysis. The essential oil yields ranged between 0.34 and 0.52% (w/w) with a mean of 0.42%, in the five populations studied. Fifty-six compounds were identified in the oil samples, representing 92.9% of the total oil. Eighteen major compounds detected in the oil samples at an average concentration of about 1% of the total oil in the five populations have been considered for statistical analyses. The main components included 1,8- cineol (21.1%), alloaromadendrene epoxide (16.9%), eudesma-4(15),7-dien-1-ß-ol (15.7%), α- terpineol (8.1%), α-pinene (5.0%) and terpinen-4-ol (5.0%). By evaluating the changes in the essential oil components, we have concluded the existence of a high intraspecific genetic variation among the Francoeuria undulata populations. Based on the canonical discriminant functions the analysis enabled the identification of four chemotypes. Moreover, the presence of trans-methyl dihydrojasmonate and high levels of oxygenated mono- and sesquiterpenes in the essential oils of the plant, indicate the high chemical defensive ability of Francoeuria undulata.

Erythromycin production is clearly enhanced by the addition of vegetable oils. However, whether this positive effect is brought about by the triglyceride or non-triglyceride fraction, is not clear. The non-triglyceride portions of the oils accumulate in the waste during the refining process leaving mainly triglycerides in the refined oil. In this research, sub-fractions of soybean oil, including lecithin, soap stock, free fatty acid, deodorizer distillate and unsaponifiable matter were supplemented by batch and fed-batch to chemically defined and complex fermentation media. The fermentation flasks were incubated at 30°C for 8 days at 220 rpm. It resulted in the production of low concentrations of oil by-products (1-5 g/l) at the beginning of fermentation, increased antibiotic production and had a greater enhancing effect than using crude oil. However, some fractions of oil such as free fatty acids considerably reduced antibiotic production. The results of this study highlight the advantages of substitution of vegetable oil with its refining by-products in the fermentation media.

The response of Clarias gariepinus to Paraquat dichloride, a herbicide that is in high demand in the fragile Niger Delta ecological zone was investigated. The herbicide had been detected in most of the water bodies in the region. The fishes were exposed to the range of concentrations observed in the field (0, 2, 4, 6 and 8) µg/L for 28 days, conducted under the Organization for Economic Co-operation and Development (OECD) test guidelines. Signs of stress were monitored and blood samples were taken from the caudal vein located behind the backbone for biochemical study. Biochemical parameters were measured spectrophotometrically. There were moderate changes in cortisol secretion, glucose levels and fluctuation in protein levels. No mortalities occurred during the test. These findings indicate that Paraquat dichloride can be tolerated by the tropical fish. Nevertheless, it should be used with care as incessant usage can increase its concentrations in the environment. The herbicide binds rapidly and tightly to clay materials and can easily leach into water, which could be lethal to aquatic and terrestrial flora and fauna. It can also magnify along the trophic level, which could be detrimental to humans.

Green olive cultivars “Manzanila” and “Mission” were harvested at the mature green stage. They were either treated with 1-methylcyclopropane (1-MCP) at a concentration of 1.8 µL/L for 24 h at 20°C or kept untreated as a control. Both treated and untreated fruits were then immersed in water containing CaCl2 of 0 (control), 50 and 100 mM for 2 h under 1.2 bar pressure. Fruits were then surface dried, put into plastic basket and stored at 6°C with relative humidity of 80% in a refrigerator for 12 weeks. The non-1-MCP treated fruits softened within 6 weeks after harvest. In contrast, the 1-MCP treatment inhibited fruit softening and color changes. Treatment with CaCl2 delayed fruit softening, but had little effect on fruit color. The rate of ethylene production and respiration were also significantly (P<0.05) lower in fruits treated separately by 1-MCP and CaCl2, compared to the control. However, the effect of 1-MCP in combination with CaCl2 was more effective in the case of color change and softening during cold storage. It could be concluded that the fruits treated with a combination of 1-MCP and CaCl2, were superior in preventing fruit softening and green color loss, and suffered minimum damage for 12 weeks at 6°C.

Plant lipid transfer proteins (LTPs) are members of the pathogenesis-related proteins (PR-14) and some of them exhibit activity against phytopathogenic fungi. To investigate whether rice LTP2 plays a role in antifungal activity, the coding region of an Iranian rice Ltp2 gene was cloned into expression vector pET24-d(+) and then expressed in Escherichia coli Rosetta strain (DE3). The potential antifungal activity of the purified LTP2 was tested on mycelial growth of some important phytopathogenic fungi. The results showed that the rice LTP2 inhibit the growth of Rhizoctonia solani, Botrytis cinerea,Sclerotinia sclerotiorum, Fusarium sporotrichioides and F. oxysporum. Also, the purified LTP2 protein was shown to strongly inhibit spore germination and consequential mycelia of Alternaria brassicola.