Elucidating the protein cold-adaptation: Investigation of the parameters enhancing protein psychrophilicity

To investigate the role of the critical parameters in adaptation of proteins to low temperatures, a comparative systematic analysis was performed. Several parameters were proposed to have contribution to cold adaptation of proteins. Among proposed parameters, total values of residual structure states, secondary structure states and oligomeric states were alike in both psychrophilic and mesophilic proteins. In addition, our results provided new quantitative information about the trends in the substitution preference of Ile, Phe, Tyr, Lys, Arg, His, Glu and Leu with most of amino acids and substitution avoidance of Gly, Thr and Ala with most of amino acids. These findings would help future efforts propose a strategy for designing psychrophilic proteins.     

Dosing schedule-dependent change in the disruptive effects of interferon-alpha on the circadian clock function

Altered homeostatic regulation, including the disturbance of circadian rhythms, is often observed in patients undergoing interferon (IFN) therapy. We reported previously that IFN-alpha has the ability to modulate the circadian clock function at the molecular level and that the alteration of clock function could be overcome by changing the dosing schedule. In this study, we investigated the influence of IFN-alpha on the intrinsic biological rhythms in mice by comparing two dosing schedules, continuous administration and repetitive injection. Continuous administration of IFN-alpha to mice decreased the rhythm amplitude of locomotor activity, body temperature, leukocyte counts, and plasma corticosterone levels. The treatment also suppressed the oscillation in the expression of clock genes in the liver. On the other hand, modulation effects were scarcely observed in mice treated with repetitive injection of IFN-alpha. These results indicate that treatment with IFN-alpha does not always modulate the circadian clock function. This notion was also supported by in vitro findings that the inhibitory action of IFN-alpha on the expression of clock genes was dependent on its exposure time to cells. The alteration of clock function induced by IFN-alpha could be avoided by optimizing the dosing schedule.     

Apolipoprotein E polymorphism in Southern Iran: E4 allele in the lowest reported amounts

Background: Apolipoprotein E (apoE) with three major alleles E2, E3 and E4 is one of the critical genes in lipid metabolism. Common apoE alleles are in association with an increase in risk for central nervous and cardiovascular diseases such as Alzheimer’s disease, dementia, multiple sclerosis, atherosclerosis, coronary heart disease, hyperlipoproteinemia and stroke. ApoE3 is known as the most frequent allele in all populations, while association of apoE gene polymorphism with reported diseases have mostly been related to other two major alleles especially apoE4. Objective: To determine of apoE alleles frequencies in Southern Iran and comparison of those frequencies with other populations. Methods: DNA was extracted from the whole blood of 198 healthy unrelated candidates from population of Fars Province, Southern Iran, for apoE genotyping who were checked up by a physician. The frequencies of apoE alleles were compared with other populations by χ² test. Results: The frequencies of E2, E3 and E4 were 0.063, 0.886 and 0.051 respectively. These values were similar to those reported from populations of Kuwait, Oman, Lebanon, India, Turkey, Greece, Spain, Sardinia Islands of Italy and two Iranian populations but were different from South of Italy and Caucasians in other Europe regions, American, American-Indian, African, East Asian and Saudi populations (P < 0.05). Conclusion: The frequency of E4 allele as a genetic risk factor for some multifactorial diseases in the population of Southern Iran is in the lowest reported amounts in the world. Iranian population has Caucasoid origin but differs from some Caucasian populations in Europe and America. The results of present study are in agreement with the historical evidences which show admixture of Iranian population with other populations and some studies based on genetic polymorphisms in the population of Southern Iran.     

Using hydrothermal time concept to describe sesame (<Emphasis Type="Italic">Sesamum indicum</Emphasis> L.) seed germination response to temperature and water potential

To quantify both temperature (T) and water potential (ψ) effects on sesame (Sesamum indicum L.) seed germination (SG) and also to determine the cardinal T _s for this plant, a laboratory experiment was carried out using hydrothermal time model (HTT). For this purpose, four sesame cultivars (‘Asbomahalleh’, ‘Darab’, ‘Dashtestan’ and ‘Yellowhite’) were germinated at seven constant T _s (20, 25, 30, 35, 37, 39 and 43 °C) at each of the following ψ _s (0, ? 0.12, ? 0.24 and ? 0.36 MPa; provided by PEG 8000). Germination rate (GR) and germination percentage (GP) significantly influenced by ψ, T and their interactions in all cultivars (P ≤ 0.01). There was no significant difference, based on the confidence intervals of the model coefficients, between cultivars, so an average of cardinal T _s was 14.7, 35.4 and 47.2 °C for the minimum (T _b), optimum (T _o) and maximum (T _c) T _s, respectively, in the control condition (0 MPa). Hydrotime values in all cultivars decreased when T was increased to T _o and then remained constant at T _s > T _o (15 MPa h^?1). An average value of ψ _b(50) was estimated to be ? 1.23 MPa at T _s ≤ T _o and then increased linearly (0.1041 MPa°Ch^?1, the slope of the relationship between ψ _b(50) and supra-optimal T _s) with T when T _s increased above T _o and finally reached to zero at T _c. The T _b and T _o values were not influenced by ψ, but T _c value decreased (from 47.2 for zero to 43.5 °C for ? 0.36 MPa) at supra-optimal T _s as a result of the effect of ψ on GR. Based on our findings, this model (as a predictive tool) and or the estimated parameter values in this study can easily be used in sesame SG simulation models to quantitatively characterize the physiological status of sesame seed populations at different T _s and ψ _s.     

Nutritional status,essential oil changes and water-use efficiency of rose geranium in response to arbuscular mycorrhizal fungi and water deficiency stress

Stress induced by water deficit is considered to be a global problem and one of the most important factors limiting crop production in arid and semi-arid regions of the world. Application of certain microorganisms, including arbuscular mycorrhizal fungi (AMF), is considered to be an effective and sustainable strategy to mitigate the problem. A pot experiment was conducted in the field (from Feb. to Sep. in 2013–2014 in Isfahan, Iran) to assess the effectiveness of AMF inoculation on changes in biomass, essential oils, nutrient uptake and water-use efficiency of rose geranium (Pelargonium graveolens L.) experiencing stress induced by a deficit of water. The experiment was planned as a factorial experiment, using a completely randomized design, with two factors, including four AMF inoculation (non-mycorrhizal, Rhizophagus intraradices and Funneliformis mosseae inoculated, and the combination of both species) and three irrigation levels including well-watered (WW), moderate water deficiency (MWD) and severe water deficiency (SWD). The results indicated the occurrence of an adverse effect of water deficit on plant total biomass; however, AMF inoculation positively increased plant biomass compared to the non-inoculated ones under three irrigation levels. MWD condition resulted in higher essential oil (EO) content (12.4 %), water-use efficiency (WUE) (29.5 %) and glomalin-related soil proteins (GRSP) (19.1 %) in the plants compared to WW condition. Furthermore, all AMF inoculation improved EO content by at least 12 k%. The results also showed that severe water deficiency adversely affected the uptake of most nutrients by plants especially in non-inoculated plants. The results also revealed that, although EO production was under the control of irrigation regime, nutrient uptake was critically dependent on an association with mycorrhizae. Notwithstanding the fact that rose geranium can tolerate moderate drought stress, the high responsiveness of rose geranium to AMF under water deficiency stress confirms the key role of AMF in facilitating the production of this valuable crop in harsh environments. Dual infection of rose geranium with two AMF species could also synergistically affect biomass, essential oil content and mineral elements absorption.     

Reconstructing subsistence practices: taphonomic constraints and the interpretation of wild plant remains at aceramic Neolithic Chogha Golan,Iran

In this paper we discuss the plant-based subsistence economy during the formation of archaeological horizons (AH) II and I at the aceramic Neolithic site of Chogha Golan, Iran. The deposits date to between 9,800 and 9,600 cal bp. In order to reconstruct subsistence practices and their development reliably, we conducted a taphonomic analysis to identify factors that influenced the composition of the archaeobotanical assemblage. The flotation samples derive from two excavation areas in the centre of the tell, the deep sounding and area A. Using correspondence analysis, we link the biased composition of the plant remains from AH I to their relatively poor preservation. Two different sampling strategies applied in excavation area A also affected the composition of the samples. In contrast, we did not find compositional differences among the samples from AH II of both excavation areas. Our results emphasize the need for taphonomic analyses prior to interpreting the taxonomic composition of charred archaeobotanical assemblages. Considering these results, we discuss the subsistence economy of Chogha Golan. Domestic emmer wheat was cultivated from AH II onwards. Wild barley, Aegilops sp., lentils, peas and various vetches may have been cultivated as well. This spectrum of typical Neolithic food plants was supplemented by a high diversity of other potential wild food resources, including medium and small-seeded grasses, Pistacia, Bolboschoenus glaucus, Malva and Brassicaceae. A compilation of ethnobotanical data, mainly from the Near and Middle East, represents the basis for assessing the potential uses of the wild plants.     

Effect of organic solvents on stability and activity of two related alcohol dehydrogenases: a comparative study.

A comparative study was performed regarding the catalytic activity and stability of two related enzymes (thermophilic alcohol dehydrogenase from Thermoanaerobacter brockii and its mesophilic counterpart from yeast) in the presence of a number of miscible and immiscible organic solvents. The study was performed in view of the practical usefulness of organic solvents for alcohol dehydrogenases which have been shown to catalyse a variety of industrially-important dehydrogenation reactions. A number of organic solvents of different physicochemical characteristics were used and substantial stabilization was achieved. The non-polar solvents utilized showed the ability to enhance thermal stability of both proteins. Protection against thermal denaturation was especially pronounced by n-dodecane, the solvent with the highest logP used in the present study. Dimethylformamide and dioxane, employed as two miscible organic solvents, showed the ability to cause substrate inhibition and changes in protein conformation as indicated by kinetic and fluorescence studies. A higher resistance of the thermophilic protein to the deleterious effect of pyridine and thermostabilization of the mesophilic enzyme by non-polar solvents are especially emphasized. Combined differences in protein structure and nature of organic solvents are suggested to explain the differences in stability and catalytic activity observed in the present investigation.     

Effect of endophytic fungi on cadmium tolerance and bioaccumulation by Festuca arundinacea and Festuca pratensis

Endophytic fungi are a group of fungi that live asymptomatically inside plant tissue. These fungi may increase host plant tolerance to biotic and abiotic stresses. The effect of Neotyphodium endophytes in two grass species (Festuca arundinacea and Festuca pratensis) on cadmium (Cd) tolerance, accumulation and translocation has been our main objective. The plants were grown in a hydroponic system under different Cd concentrations (0, 5, 10, and 20 mg L(-1)) for 6 weeks. They were also grown in soil spiked with different concentrations of Cd (0, 10, 20, and 40 mg kg(-1)) for 2 months. The results from all Cd treatments showed higher biomass production (12-24%) and higher potential to accumulate Cd in roots (6-16%) and shoots (6-20%) of endophyte-infected plants than endophyte-free plants. Cadmium accumulation by plants indicated that the grasses were capable of Cd hyperaccumulation, a property that was augmented after endophyte infection. Maximum photochemical efficiency of photosystem II (Fv/Fm) revealed that Cd stress was significantly reduced in endophyte-infected plants compared to non-infected ones.     

Genetic diversity and structure among Iranian tall fescue populations based on genomic-SSR and EST-SSR marker analysis

Tall fescue (Festuca arundinacea Schreb. subsp. arundinacea) is one of the most economically important forage grasses in cold and temperate regions of the world. In this study, we have assessed the genetic diversity and structure of wild Iranian tall fescue populations. Thirty-seven individuals from nine natural populations from northern, western, and southern Iranian mountain ranges were analyzed using six genomic-SSRs and five EST-SSRs primer pairs. Our analysis has demonstrated that transcribed EST-SSR regions showed levels of polymorphism similar to genomic-SSR regions. UPGMA, repeated bisection, and model-based Bayesian STRUCTURE clustering methods coupled with neighbor-net network were used to establish six divergent groups of individuals. F _ST estimates among clusters showed moderate to low genetic structure. Within-group genetic diversity estimate H and partial correlations between genetic and geographic distances among populations suggested that western Zagros population was related to the rest of the Iranian individuals. The isolation-by-distance hypothesis was not supported by SSR data and the present geographical sampling.     

Effect of Epichloë fungal endophyte symbiosis on tall fescue to cope with flooding-derived oxygen-limited conditions depends on the host genotype

Plant and Soil - There is little information about the role of fungal endophytes on plant performance under oxygen-limited conditions. This study aimed to investigate the effect of Epichloë...