The effect of alginate as an elicitor on transcription of steviol glycosides biosynthesis pathway related key genes and sweeteners content in in vitro cultured Stevia rebaudiana.

BACKGROUND: Stevia rebaudiana is a medicinal herb that accumulates non-caloric sweeteners called steviol glycosides (SGs) which are approximately 300 times sweeter than sucrose. This study used alginate (ALG) as an elicitor to increase steviol glycosides accumulation and elucidate gene transcription in the steviol glycosides biosynthesis pathway. METHODS AND RESULTS: To minimize the grassy taste associated with stevia sweeteners, plantlets were grown in complete darkness. ALG was applied to stevia plants grown in suspension culture with a Murashige and Skoog (MS) medium to determine its effect on SGs' content and the transcription profile of SG-related genes using the HPLC and RT-qPCR methods, respectively. Treatment with alginate did not significantly affect plantlet growth parameters such as shoot number, dry and fresh weight. Rebaudioside A (Reb A) content increased approximately sixfold in the presence of 1g L-1 alginate and KS, KAH, and UGT74G1 genes showed significant up-regulation. When the concentration was increased to 2g L-1, the transcription of KO and UGT76G1, responsible for the conversion of stevioside to Reb A, was increased about twofold. CONCLUSIONS: The current study proposes that adding alginate to the MS suspension medium can increase Reb A levels by altering the SG biosynthesize pathway's transcription profile. The present experiment provides new insights into the biochemical and transcriptional response mechanisms of suspension-cultured stevia plants to alginate.

Maize growth response to different Bacillus strains isolated from a salt-marshland area under salinity stress.

Maize (Zea mays) growth performance has been hindered due to the high soil salinity. Salinity is one of the most severe abiotic stresses that has led to growth imbalance and profitability of harvests in arid and semi-arid regions. Plants have taken advantage of salt-tolerant bacteria as plant growth-promoters to enhance growth and reduce the adverse effects of salinity through the regulation of some biochemical, physiological, and molecular features. Preferences for non-chemical, eco-friendly, and economical approaches have caused the inquiry of the Bacillus genus as a joint group of plant growth-promoting rhizobacteria known to alleviate salt-stress impacts. In the present study, halotolerant Bacillus strains were isolated from salt-marshland soil and characterized for their physiological, molecular, and biochemical properties. Twenty-four bacterial isolates collected from high saline fields of salt marshland were analyzed by MALDI-TOF MS proteome analysis, which confirmed the taxonomic affiliation with Bacillus cereus, Bacillus subtilis, Bacillus atrophaeus, and Bacillus thorngiensis. Applying the isolates on maize plants as bio-inoculant bacteria obviously increased the growth parameters (P < 0.01). Pot experiments showed that isolates 74 and 90 were the most prominent strains to minimize the harmful effects of salinity. Its effects are heightening the potassium/sodium ratio and K-Na selectivity in shoots and roots measured by flame atomic absorption photometry (AAS). Accordingly, Bacillus cereus isolate 74 showed a maximum increase in dry weights of the shoot (133.89%), root (237.08%), length of the shoot (125%), and root (119.44%) compared to the control condition. Our findings suggest that bacteria isolated from marshland may be an economical and simple means to increase plant growth and resistance to high salinity soil conditions.

Exploiting Differential Gene Expression to Discover Ionic and Osmotic-Associated Transcripts in the Halophyte Grass Aeluropus littoralis.

BACKGROUND: Salinity as a most significant environmental challenges affects the growth and productivity of plants worldwide. In this study, the ionic and iso-osmotic effects of salt stress were investigated in Aeluropus littoralis L., a halophyte grass species from Poaceae family, by cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique. To dissect the two different effects (ionic and osmotic) exerted by salt stress, various ionic agents including 200 and 400 mM sodium chloride (NaCl), 200 and 400 mM potassium chloride (KCl) as well as 280 and 406 gl- 1 (- 0.9 and - 1.4 MPa) polyethylene glycol 6000 (PEG) as their iso-osmotic concentrations were applied. RESULTS: Application of KCl and PEG significantly reduced the fresh weight (FW) of A. littoralis seedlings compared to control while NaCl treatment markedly enhanced the FW. At the transcriptome level, different observations of changes in gene expression have been made in response of A. littoralis to ionic and osmotic stresses. Out of 69 transcript derived fragments (TDFs), 42 TDFs belong to 9 different groups of genes involved in metabolism (11.6%), transcription (10.2%), ribosomal protein (8.7%), protein binding (8.7%) transporter (5.8%), translation (5.8%), signal transduction (4.3%), nucleosome assembly protein (2.9%) and catabolism (2.9%). The 44 and 28 percent of transcripts were expressed under ionic stress (NaCl-specific and KCl-specific) and osmotic stress (common with NaCl, KCl and PEG), respectively which indicating a greater response of plants to ionic stress than osmotic stress. Expression pattern of eight candidate TDFs including; SYP81, CAND1, KATN, ISB1, SAMDC, GLY1, HAK18 and ZF30 was evaluated by RT-qPCR at high salinity levels and recovery condition. CONCLUSION: Differential regulation of these TDFs was observed in root and shoot which confirm their role in salt stress tolerance and provide initial insights into the transcriptome of A. littoralis. Expression pattern of ionic and osmotic-related TDFs at A. littoralis can be taken as an indication of their functional relevance at different salt and drought stresses.

Correction to: Plant growth promoting activity of an auxin and siderophore producing isolate of Streptomyces under saline soil conditions.

Unfortunately, one of the author's name had been published incorrectly as "Peyman Abaszadeh Dahaji". The correct name is " Payman Abbaszadeh Dahaji.

Discovery of novel potent imidazo[1,2-b]pyridazine PDE10a inhibitors.

Design and optimization of a novel series of imidazo[1,2-b]pyridazine PDE10a inhibitors are described. Compound 31 displays excellent pharmacokinetic properties and was also evaluated as an insulin secretagogue in vitro and in vivo.

Optimizing micropropagation of drought resistant Pyrus boissieriana Buhse.

The present study concentrated on introducing a micropropagation protocol for a drought resistant genotype from Pyrus boissieriana, which is the second most naturally widespread pear species in Iran with proper physiological and medicinal properties. Proliferating microshoot cultures were obtained by placing nodal segments on MS medium supplemented with BAP and IBA or NAA. The highest number of shoots (27 shoots per explant) were obtained with 1.5 mg l-1 BAP and 0.05 mg l-1 IBA, but this combination did not produce shoots of desirable length (>1.7 cm). Combination of 1.75 mg l-1 BAP and 0.07 mg l-1 IBA was the best for the shoot multiplication in P. boissieriana with a sufficient number of shoot production (22.33 shoots per explant) and relatively more appropriate shoot length. The larger and greenish leaves were obtained when PG was added to the best multiplication treatment. Microshoot elongation was carried out in 1/2 and 1/4 MS medium containing 50-100 mg l-1 PG with different concentrations of IBA or NAA at intervals of 30-60 days. Significant increase in shoot length was detected after 45-60 days of culture in the presence of PG. The highest shoot length (8 cm) was recorded on 1/2 MS medium supplemented with 0.5 mg l-1 IBA and 100 mg l-1 PG. GA3 negatively affected number and length of shoots and generally caused generation of red leaves. The highest percentage of root induction (100%) and root length (9 cm) were obtained on 1/6 strength MS medium supplemented with 0.005 mg l-1 IBA. All plantlets were hardened when transferred to ex vitro conditions through a period of 25-30 days. The results suggest axillary shoot proliferation of P. boissieriana could successfully be employed for propagation of candidate drought resistant seedling.

Proteomics study of silver nanoparticles toxicity on Bacillus thuringiensis.

Emerging technologies in functional genomics and proteomics provide a way of achieving high-throughput analyses, understanding effects on protein populations and sub-populations and follow up environmental stresses. To accomplish these, the action of homemade spherical Silver nanoparticles colloidal suspension (AgNPs) against Bacillus thuringiensis (isolate from Oryza sativa L. rhizosphere) was investigated by a proteomic approach (2-DE and NanoLC/FT-ICR MS identification). Thirty four responsive (up/down regulated) proteins were identified. Proteomic results revealed that an exposure of B. thuringiensis cells with different concentrations of AgNPs resulted in an accumulation of envelope protein precursors, indicative of the dissipation of a proton motive force. Identified proteins are involved in oxidative stress tolerance, metal detoxification, transcription and elongation processes, protein degradation, cytoskeleton remodeling and cell division. The expression pattern of these proteins and their possible involvement in the nontoxicity mechanisms were discussed.

Proteomics study of silver nanoparticles toxicity on Oryza sativa L.

The increasing use of silver nanoparticles, (AgNPs), will inevitably result in their release into the environment and thereby cause the exposure to plants. It was claimed that using AgNPs is a safe and efficient method to preserve and treat agents of disease in agriculture. This study tries to understand the protein populations and sub-populations and follow up environmental AgNPs stresses. To accomplish these, the action of homemade spherical AgNPs colloidal suspension against Oryza sativa L. was investigated by a proteomic approach (2-DE and NanoLC/FT-ICR MS identification). Twenty-eight responsive (decrement/increment in abundance) proteins were identified. Proteomic results revealed that an exposure of O. sativa L., root with different concentrations of AgNPs resulted in an accumulation of protein precursors, indicative of the dissipation of a proton motive force. The identified proteins are involved in oxidative stress tolerance, Ca(2+) regulation and signaling, transcription and protein degradation, cell wall and DNA/RNA/protein direct damage, cell division and apoptosis. The expression pattern of these proteins and their possible involvement in the nontoxicity mechanisms were discussed.

Effect of silver nanoparticles on Oryza sativa L. and its rhizosphere bacteria.

Silver nanoparticles (AgNPs) are widely used as antibacterial and antifungal agents in agriculture. Nevertheless, these nanoparticles with newborn properties pose a potential risk to the environment, Due to contact with crops and bacteria that are beneficial to the soil. This study is based on the examination of the phytotoxic effects of AgNPs on Oryza sativa L. and some of its rhizosphere bacteria, by physiological and biochemical assays. In order to study the complex interaction of the AgNPs life expectancy that are mixed with culture medium, the incubation time for the fresh mixture, 7, 14 and 21 days old of AgNPs, on the seedlings growth was investigated. Results indicated that plant's response to the treatment with AgNPs affected on the cell wall, and that with an increase in its concentration (up to 60 µg/mL). The obtained results of transmission electron microscopy (TEM) exhibited that those particles not only penetrated the cell wall, but they could also damage the cell morphology and its structural features. AgNPs treatment up to 30 µg/mL accelerated root growth and at 60 µg/mL was able to restrict a root's ability to grow. The 30 µg/mL treatment had significant effect on root branching and dry weight. In contrast, shoot growth was more susceptible to the effects of AgNPs treatment. The root content for total soluble carbohydrates and starch demonstrated that despite stable starch content, total soluble carbohydrates showed the tendency to significantly decline in response to AgNPs. However, induction of root branching and photosynthetic pigments can attributed to AgNPs stress based on evidence from the production of the reactive oxygen species (ROS) and local root tissue death. Nine isolates of the genus Bacillus selected and identified according to morphological and chemotaxonomic methods. The AgNPs treatment revolutionized the populations of bacteria as Bacillus thuringiensis SBURR1 was totally eliminated, and Bacillus amyloliquefaciens SBURR5 became the most populated one. Images from an electron microscope and the leakage of reducing sugars and protein through the bacterial membrane, similarly confirmed the "pit" formation mechanism of the AgNPs. Moreover the hypothesis from the growth curve study demonstrated that AgNPs may damage bacterium cell wall and transform them to protoplasts.

Isolation, Identification, and Characterization of the Native Yeast Strains from Homemade Cheese to Assess their Eliminating Impact on the Aflatoxin B1 and M1 of the Simulated Gastrointestinal Fluid.

Background: The occurrence of aflatoxins in food products is a silent threat to human health worldwide. A range of strategies has been introduced to address the bioavailability of aflatoxins, which are considered microbial tools to provide a low-cost and promising approach. Objectives: The present study focused on the separation of yeast strains from the homemade cheese rind layer to investigate the ability of native yeasts to eliminate AB1 and AM1 from simulated gastrointestinal fluids. Material and Methods: Homemade cheese samples were prepared from different locations in Tehran provinces and yeast strains were isolated and identified through the biochemical methods and molecular analysis of internal transcribed spacer and D1/D2 domain of 26S rDNA regions. Isolated strains were screened using simulated gastrointestinal fluids, and the ability of yeast strains to absorb aflatoxin was evaluated. Results: Out of 13 strains, 7 yeast strains were not affected by 5 ppm AFM1 while 11 strains did not show any significant response to 5 mg.L-1 (ppm) of AFB1. On the other hand, 5 strains were able to successfully tolerate 20 ppm AFB1. Candidate yeasts showed different abilities to remove aflatoxins B1 and M1. In addition, C. lusitaniae, G. geotrichum, G. candidum, and C. sanyaensis exhibited a significant ability to detoxify aflatoxins from the gastrointestinal fluid, respectively. Conclusion: Our data suggest that yeast communities with essential effects on the quality of homemade cheese appear to be precise candidates for the potential elimination of aflatoxins from the gastrointestinal fluid.

Natural variation in photosynthesis and water use efficiency of locally adapted Persian walnut populations under drought stress and recovery.

Persian walnut is a drought-sensitive species with considerable genetic variation in the photosynthesis and water use efficiency of its populations, which is largely unexplored. Here, we aimed to elucidate changes in the efficiency of photosynthesis and water content using a diverse panel of 60 walnut families which were submitted to a progressive drought for 24 days, followed by two weeks of re-watering. Severe water-withholding reduced leaf relative water content (RWC) by 20%, net photosynthetic rate (Pn) by 50%, stomatal conductance (gs) by 60%, intercellular CO2 concentration (Ci) by 30%, and transpiration rate (Tr) by 50%, but improved water use efficiency (WUE) by 25%. Severe water-withholding also inhibited photosystem II functionality as indicated by reduced quantum yield of intersystem electron transport (φEo) and transfer of electrons per reaction center (ET0/RC), also enhanced accumulation of QA (VJ) resulted in the reduction of the photosynthetic performance (PIABS) and maximal quantum yield of PSII (FV/FM); while elevated quantum yield of energy dissipation (φDo), energy fluxes for absorption (ABS/RC) and dissipated energy flux (DI0/RC) in walnut families. Cluster analysis classified families into three main groups (tolerant, moderately tolerant, and sensitive), with the tolerant group from dry climates exhibiting lesser alterations in assessed parameters than the other groups. Multivariate analysis of phenotypic data demonstrated that RWC and biophysical parameters related to the chlorophyll fluorescence such as FV/FM, φEo, φDo, PIABS, ABS/RC, ET0/RC, and DI0/RC represent fast, robust and non-destructive biomarkers for walnut performance under drought stress. Finally, phenotype-environment association analysis showed significant correlation of some photosynthetic traits with geoclimatic factors, suggesting a key role of climate and geography in the adaptation of walnut to its habitat conditions.

The use of stable isotope-labeled glycerol and oleic acid to differentiate the hepatic functions of DGAT1 and -2.

Diacylglycerol acyltransferase (DGAT) catalyzes the final step in triglyceride (TG) synthesis. There are two isoforms, DGAT1 and DGAT2, with distinct protein sequences and potentially different physiological functions. To date, the ability to determine clear functional differences between DGAT1 and DGAT2, especially with respect to hepatic TG synthesis, has been elusive. To dissect the roles of these two key enzymes, we pretreated HepG2 hepatoma cells with (13)C(3)-D(5)-glycerol or (13)C(18)-oleic acid, and profiled the major isotope-labeled TG species by liquid chromatography tandem mass spectrometry. Selective DGAT1 and DGAT2 inhibitors demonstrated that (13)C(3)-D(5)-glycerol-incorporated TG synthesis was mediated by DGAT2, not DGAT1. Conversely, (13)C(18)-oleoyl-incorporated TG synthesis was predominantly mediated by DGAT1. To trace hepatic TG synthesis and VLDL triglyceride (VLDL-TG) secretion in vivo, we administered D(5)-glycerol to mice and measured plasma levels of D(5)-glycerol-incorporated TG. Treatment with an antisense oligonucleotide (ASO) to DGAT2 led to a significant reduction in D(5)-glycerol incorporation into VLDL-TG. In contrast, the DGAT2 ASO had no effect on the incorporation of exogenously administered (13)C(18)-oleic acid into VLDL-TG. Thus, our results indicate that DGAT1 and DGAT2 mediate distinct hepatic functions: DGAT2 is primarily responsible for incorporating endogenously synthesized FAs into TG, whereas DGAT1 plays a greater role in esterifying exogenous FAs to glycerol.

Plant growth promoting activity of an auxin and siderophore producing isolate of Streptomyces under saline soil conditions.

A biocontrol Streptomyces isolate (C) was tested for its plant growth promoting qualities under saline conditions. Exposure to elevated osmotic strengths up to 300 mM NaCl increased dry weight and cfu/ml significantly. The isolate C produced indolyl-3-acetic acid (IAA) into the medium in the amount of 2.4 µg/ml. The amount of auxin increased after adding salt and reached to 4.7 µg/ml in 300 mM NaCl. Biosynthesis of siderophore was detectable and increased in presence of NaCl. Streptomyces isolate C showed good solubilization of tricalcium phosphate in culture medium with 92 mg/l. Solubilization decreased in presence of NaCl. Soil treatment with isolate C increased the growth and development of wheat plant in normal and saline conditions. In this treatment there were significant increases in germination rate, percentage and uniformity, shoot length and dry weight compared to the control. Applying the bacterial inocula increased the concentration of N, P, Fe and Mn in wheat shoots grown in normal and saline soil, but had non-significant effect on other micro and macronutrients concentrations. Results of this study show that Streptomyces isolate C has potential to be utilized as biofertilizer in saline soils.

Characterization of bacterial diversity between two coastal regions with heterogeneous soil texture.

Studying microbial diversity and the effects of external factors on the microbiome could expand our understanding of environmental alterations. Silt and sand are mineral particles that form soil texture and even though most of the soils on earth contain a fraction of them and some other soils form almost by them, their effects on the microbiome remained to elucidate. In this study, the bacterial biodiversity of sand and silt clay soils was investigated. Furthermore, their effects on plant growth have been determined. Our data showed that biodiversity and biomass of microbiome are higher in silt-based soil. It is interesting that the pseudomonas genera only exist in silt-based soil while it is in the absence of sand-based soil. In contrast, B. thuringiensis could be found in sand-based soil while it is not found in silt texture. Our data also demonstrated that there are no significant changes in stress response between the two groups however, differential physiological changes in plants inoculated with silt and sand based bacterial isolates have been observed. This data could indicate that smaller size particles could contain more bacteria with higher biodiversity due to providing more surfaces for bacteria to grow.

Bacterial diversity changes in response to an altitudinal gradient in arid and semi-arid regions and their effects on crops growth.

The microbiome of soil has a fundamental role in maintaining the health of soil and plants. While the diversity of microbes is one of the most important factors in the environment, little is known about the effects of elevation on the microbiome and the impact of the affected microbiome on plants. The main goal of this study is to expand our knowledge of what happens to the soil bacterial community along an altitudinal gradient and investigate their possibly different impacts on plant growth. Bacteria from soils at various altitudes have been isolated, characterized, and identified by Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) to determine the effects of an elevational gradient on the microbiome and plant growth. Furthermore, their effects have been investigated by isolates assessment on maize, wheat, and canola. Based on our results, higher altitude results in a higher diversity of the microbiome and lower bacteria biomass. Bacillus cereus is found in abundance in arid and semi-arid samples. Interestingly, enhanced diversity in higher altitudes shows similarity in response to environmental stress and tolerates these factors well. Furthermore, the inoculation of these bacteria could enhance the overall growth of plants. We prove that bacterial communities could change their biomass and diversity in response to altitude changes. These indicate evolutionary pressure as these bacteria could tolerate stress factors well and have a better relationship with plants.

Genome-wide association analysis and pathway enrichment provide insights into the genetic basis of photosynthetic responses to drought stress in Persian walnut.

Uncovering the genetic basis of photosynthetic trait variation under drought stress is essential for breeding climate-resilient walnut cultivars. To this end, we examined photosynthetic capacity in a diverse panel of 150 walnut families (1500 seedlings) from various agro-climatic zones in their habitats and grown in a common garden experiment. Photosynthetic traits were measured under well-watered (WW), water-stressed (WS) and recovery (WR) conditions. We performed genome-wide association studies (GWAS) using three genomic datasets: genotyping by sequencing data (∼43 K SNPs) on both mother trees (MGBS) and progeny (PGBS) and the Axiom™ Juglans regia 700 K SNP array data (∼295 K SNPs) on mother trees (MArray). We identified 578 unique genomic regions linked with at least one trait in a specific treatment, 874 predicted genes that fell within 20 kb of a significant or suggestive SNP in at least two of the three GWAS datasets (MArray, MGBS, and PGBS), and 67 genes that fell within 20 kb of a significant SNP in all three GWAS datasets. Functional annotation identified several candidate pathways and genes that play crucial roles in photosynthesis, amino acid and carbohydrate metabolism, and signal transduction. Further network analysis identified 15 hub genes under WW, WS and WR conditions including GAPB, PSAN, CRR1, NTRC, DGD1, CYP38, and PETC which are involved in the photosynthetic responses. These findings shed light on possible strategies for improving walnut productivity under drought stress.

Transcriptional responses of wheat roots inoculated with Arthrobacter nitroguajacolicus to salt stress.

It is commonly accepted that bacteria actively interact with plant host and have beneficial effects on growth and adaptation and grant tolerance to various biotic and abiotic stresses. However, the mechanisms of plant growth promoting bacteria to communicate and adapt to the plant environment are not well characterized. Among the examined bacteria isolates from different saline soils, Arthrobacter nitroguajacolicus was selected as the best plant growth-promoting bacteria under salt stress. To study the effect of bacteria on wheat tolerance to salinity stress, bread wheat seeds were inoculated with A. nitroguajacolicus and grown under salt stress condition. Comparative transcriptome analysis of inoculated and un-inoculated wheat roots under salt stress showed up-regulation of 152 genes whereas 5 genes were significantly down-regulated. Many genes from phenylpropanoid, flavonoid and terpenoid porphyrin and chlorophyll metabolism, stilbenoid, diarylheptanoid metabolism pathways were differentially expressed within inoculated roots under salt stress. Also, a considerable number of genes encoding secondary metabolites such as phenylpropanoids was detected. They are known to take part in lignin biosynthesis of the cell wall as well as antioxidants.

Energy Flow from Root to Shoot: A Comprehensive In silico Analysis.

BACKGROUND: Root to shoot connection and transfer of information seems to be taken place mostly via the transmissions of signal molecules, secondary metabolites, amino acids, hormones and proteins, through xylem sap. Examination of earlier reports is indicative of relatively high levels of conservation in xylem sap protein compositions. Apparently these protein molecules are being synthesized in roots in response to environmental changes and get transported to aerial plant parts after secretion into xylem sap. OBJECTIVES: In order to comprehend this so-called passive signaling, some questions need to be answered: 1) Do these proteins have the capability to act as signals? 2) How much energy does root spend for the biosynthesis of the secreted proteins? How similar is the amount of energy that root cells spent for the biosynthesis of intra- and extra-cellular proteins? MATERIALS AND METHODS: Reported xylem sap proteins curated from Arabidopsis, maize and soybean. Their sequences were put under scrutiny in terms of considering their mobility, and physical and chemical properties. Metabolic energy required for their biosynthesis along with the energy hidden in their peptide bonds were calculated and compared with random non-xylem sap proteins as control. RESULTS: Xylem sap proteins were significantly smaller than the root proteins, while they were bigger in size when compared to the leaf group. Xylem protein pIs were significantly higher than the control proteins in different plants. Similarly, the protein stability was higher for xylem sap proteins in comparison with roots and leaves in all analyzed plants, except for soybean that the stability was indifferent between xylem and root. The data were suggestive a significantly lower energy consumption for the synthesis of xylem sap proteins. CONCLUSIONS: Lower energy consumption may suggest an economical route of communication between roots and shoots in plants that mainly rely on symplastic signaling.

Genome-wide patterns of population structure and association mapping of nut-related traits in Persian walnut populations from Iran using the Axiom J. regia 700K SNP array.

Persian plateau (including Iran) is considered as one of the primary centers of origin of walnut. Sampling walnut trees originating from this arena and exploiting the capabilities of next-generation sequencing (NGS) can provide new insights into the degree of genetic variation across the walnut genome. The present study aimed to explore the population structure and genomic variation of an Iranian collection of Persian walnut (Juglans regia L.) and identify loci underlying the variation in nut and kernel related traits using the new Axiom J. regia 700K SNP genotyping array. We genotyped a diversity panel including 95 walnut genotypes from eight Iranian provinces with a variety of climate zones. A majority of the SNPs (323,273, 53.03%) fell into the "Poly High Resolution" class of polymorphisms, which includes the highest quality variants. Genetic structure assessment, using several approaches, divided the Iranian walnut panel into four principal clusters, reflecting their geographic partitioning. We observed high genetic variation across all of the populations (HO = 0.34 and HE = 0.38). The overall level of genetic differentiation among populations was moderate (FST = 0.07). However, the Semnan population showed high divergence from the other Iranian populations (on average FST = 0.12), most likely due to its geographical isolation. Based on parentage analysis, the level of relatedness was very low among the Iranian walnuts examined, reflecting the geographical distance between the Iranian provinces considered in our study. Finally, we performed a genome-wide association study (GWAS), identifying 55 SNPs significantly associated with nut and kernel-related traits. In conclusion, by applying the novel Axiom J. regia 700K SNP array we uncovered new unexplored genetic diversity and identified significant marker-trait associations for nut-related traits in Persian walnut that will be useful for future breeding programs in Iran and other countries.

Structural determination of estrogen-related receptor gamma in the presence of phenol derivative compounds.

We screened the ligand-binding domain of estrogen-related receptor (ERR) gamma in ThermoFluor, in an effort to develop chemical tools and decipher the biology of this orphan nuclear receptor. Several ligands were found to stabilize thermodynamically the protein. Amongst the ligands were bisphenol A (BPA) and 4-chloro-3-methyl phenol (ClCH3Ph). These ligands were further characterized and found to be competitive for 4-hydroxytamoxifen (4OHT) binding, a known reported antagonist ligand for ERRgamma, but functionally they did not enhance or disrupt affinity of the receptor for co-activator peptides. The preservation of the constitutive active conformation of the receptor in the presence of these two ligands was confirmed upon the determination of the co-crystal structures. The structures of BPA and ClCH3Ph were determined to a resolution of 2.1 and 2.3A, respectively, and the antagonist 4OHT was refined to 2.5A resolution. In the presence of BPA and ClCH3Ph the receptor maintained the transcriptional active conformation as reported previously for the apo-protein in the presence of a co-activator peptide fragment. In addition the ERRgamma-BPA structure identifies an interaction between the phenolic-OH and the side chain of N346. The preservation of the constitutive active conformation of the receptor in the presence of the small phenol compounds suggest that the biological activity of the receptor might be regulated by a natural occurring ligand.