Metabolic and Transcriptomic Approaches of Chitosan and Water Stress on Polyphenolic and Terpenoid Components and Gene Expression in Salvia abrotanoides (Karl.) and S. yangii.

In this research, a HPLC analysis, along with transcriptomics tools, was applied to evaluate chitosan and water stress for the prediction of phenolic flavonoids patterns and terpenoid components accumulation in Salvia abrotanoides Karel and S. yangii. The results indicated that the tanshinone contents under drought stress conditions increased 4.2-fold with increasing drought stress intensity in both species. The rosmarinic acid content in the leaves varied from 0.038 to 11.43 mg/g DW. In addition, the flavonoid content was increased (1.8 and 1.4-fold) under mild water deficit conditions with a moderate concentration of chitosan (100 mg L-1). The application of foliar chitosan at 100 and 200 mg L-1 under well-watered and mild stress conditions led to increases in hydroxyl cryptotanshinone (OH-CT) and cryptotanshinone (CT) contents as the major terpenoid components in both species. The expressions of the studied genes (DXS2, HMGR, KSL, 4CL, and TAT) were also noticeably induced by water deficit and variably modulated by the treatment with chitosan. According to our findings, both the drought stress and the application of foliar chitosan altered the expression levels of certain genes. Specifically, we observed changes in the expression levels of DXS and HMGR, which are upstream genes in the MEP and MVA pathways, respectively. Additionally, the expression level of KSL, a downstream gene involved in diterpenoid synthesis, was also affected. Finally, the present investigation confirmed that chitosan treatments and water stress were affected in both the methylerythritol phosphate pathway (MEP) and mevalonate (MVA) pathways, but their commitment to the production of other isoprenoids has to be considered and discussed.

The role of plant growth-promoting rhizobacteria (PGPR) in improving iron acquisition by altering physiological and molecular responses in quince seedlings.

Due to insoluble iron (Fe) sources in soil, limited Fe availability leads to the disruption of the photosynthetic apparatus; this affects the growth and productivity of plants such as quince (Cydonia oblonga) that are very sensitive to low Fe content. Plant growth-promoting rhizobacteria (PGPR) play an important role in the regulation of Fe uptake under its limited availability. Therefore, in this research, two PGPR (Pseudomonas fluorescens and Microccucuce yunnanensis), at two Fe levels [50 µM (Fe-sufficiency) or 5 µM (Fe-deficiency)], were used to investigate the impact of the given bacteria on improving the acquisition of Fe in quince seedlings. Upon Fe-deficiency, the highest shoot and root biomass (7.14 and 6.04 g plant-1 respectively), the greatest chlorophyll concentration (0.89 mg g-1FW), and the largest Fe concentrations in roots and shoots (30% and 48.7%, respectively) were shown in the quince treated with M. yunnanensis. Both PGPR increased the root citric acid and the phenolic compound concentration. Two days after Fe-deficiency and PGPR treatments, a 1.5- fold increase, was observed in the expression of HA7. The highest PAL1 gene expression and the greatest PAL activity (95.76 µmol cinnamic acid g-1FW) were obtained from the M. yunnanensis treatment. The expression of the FRO2 gene was also affected by Fe-deficiency and PGPR treatments, resulting in an increase in the FCR activity and a surge in the Fe concentrations of leaves and roots. It could, therefore, be concluded that the PGPR modulated Fe acquisition in the quince seedlings upon Fe-deficiency by influencing the physico-chemical and molecular responses.

Melatonin and calcium modulate the production of rosmarinic acid, luteolin, and apigenin in Dracocephalum kotschyi under salinity stress.

Melatonin (Mel) and calcium (Ca2+) have a regulatory role in the induction of specialized metabolites production and defensive responses against stresses. Therefore, in this study, the effects of Mel and Ca2+ and the possible relationship between them in the increase of the production of phenolic compounds in Dracocephalum kotschyi Boiss. under both control and salinity stress conditions were investigated. The results showed that 75 mM NaCl reduced shoot dry biomass but elevated H2O2 content, electrolyte leakage (EL) level, total phenolic and flavonoid contents (TPC and TFC), and DPPH scavenging capacity. Salinity stress also upregulated gene expression of phenylalanine ammonia-lyase (PAL) and rosmarinic acid synthase (RAS), as well as the activities of PAL and tyrosine ammonia-lyase (TAL) enzymes. Pre-treatment of the plants with CaCl2 and Mel affected these attributes in a dose-dependent manner. Application of 5 mM Ca2+ and 100 µM Mel improved shoot dry biomass and reduced the level of EL and H2O2 content but enhanced TPC and TFC, DPPH scavenging capacity, PAL and TAL activities, PAL and RAS transcripts, and content of rosmarinic acid (RA), luteolin flavone (LF) and apigenin flavone (AF) under salinity stress. Pre-treatment of D. kotschyi with lanthanum chloride (LaCl3) as a plasma membrane channel blocker, ethylene glycol tetra-acetic acid (EGTA) as a Ca2+ chelator and trifluoperazine (TFP) as a calmodulin (CaM) antagonist, impaired Mel effects on the above attributes under salinity stress. In contrast, pre-treatment with p-chlorophenylalanine (p-CPA), as an inhibitor of Mel biosynthesis, did not impair the impacts of Ca2+ on the production of phenolic compounds in salt-exposed plants. These results suggested that the effect of Mel on the induction of phenolic compounds production requires the influx of extracellular Ca2+ into the cells and is dependent on Ca2+/CaM signaling.

A flowering inhibitor of the temperature-dependent pathway in Crocus sativus L.

Saffron is the world highest-priced spice because its production requires intensive hand labour. Reduce saffron production costs require containerised plant production under controlled conditions and expand the flowering period. Controlling the flowering process and identify the factors involved in saffron flowering is crucial to introduce technical improvements. The research carried out so far in saffron has allowed an extensive knowledge of the influence of temperature on the flower induction, but the molecular mechanisms controlling flowering induction processes are largely unknown. The present study is the first conducted to isolate and characterize a regulator gene of saffron floral induction the Short Vegetative Phase (SVP) gene, which represses the floral initiation genes in the temperature response pathway, which involved in saffron flower induction. The results obtained from both phylogenetic analysis and T-coffee alignment confirms that the isolated sequence belongs to the SVP gene clades of MADS-box gene family. Gene expression analysis in different developmental stages revealed the highest expression of SVP transcript (CsSVP) during the dormancy and the vegetative stages, but decrease when flower development initiated and it was the least in late September when flower primordia are developed. Furthermore, its expression increased in the apical bud when corms are storage at 9-10 ºC, thus inhibiting flower induction. Additionally, comparison of the CsSVP transcript in apical buds from big and small corms, differing in their flowering capacity, indicates that the CsSVP transcript is present only in vegetative buds. Taken together, these results suggested inhibitory role of the SVP gene.

Molecular evolution and selection pressure analysis of infectious hematopoietic necrosis virus (IHNV) revealed the origin and phylogenetic relationship of Iranian isolates in recent epidemics in Iran.

Infectious hematopoietic necrosis virus (IHNV) is the causative agent for a lethal salmonid disease. In this study, we surveyed the IHNV's epidemiology, diversity and the origin of infection in Iran. Phylogenetic analysis revealed that Iranian isolates belonged to one of the two lineages of E genogroup. Subsequently, a combination of phylogenetic, antigenic and structural analysis was performed to investigate the evolution of E genogroup lineages. Site-specific analysis of the viral glycoprotein showed different co-evolving and positively selected sites in each lineage. Most of these sites were mapped to the predicted antigenic patches of the glycoprotein. Further characterization revealed E lineages can be differentiated, in part, by specific mutations at positions 91 and 130, which are located in the structurally flexible regions of the glycoprotein, suggesting a key adaptative role for these sites. These data may assist in better monitoring the emerging isolates in regions infected to IHNV from E genogroup.

Hyperaccumulation of Cu, Zn, Ni, and Cd in Azolla species inducing expression of methallothionein and phytochelatin synthase genes.

Azolla is a floating aquatic fern, having amazing capacity for concentrating toxic heavy metals. Metallothioneins (MTs) and phytochelatins (PCs) are well-defined heavy metal-binding ligands in plants. Bioaccumulation potential of different Azolla species varies according to their heavy metal ions. Therefore, the accumulation of Ni, Zn, Cu, and Cd was studied in A. pinnata, A. filiculoides, and a sample taken from Anzali wetland. Moreover, the expression of metallothionein and phytochelatin synthase encoding genes was examined at different metal concentrations. The highest level of Cu and Cd absorption was detected in A. pinnata, while the maximum amount of Ni and Zn absorption was observed in A. filiculoides and the sample taken from Anzali, respectively. The MT2 and PCS1 gene expression patterns were significantly induced by the heavy metal treatments, confirming their roles in phytoremediation potential of Azolla. However, as the results concerning heavy metal accumulation and gene expression vary in different species, only specific species of Azolla can be used for special purposes. It can be concluded that the Azolla is a good candidate for phytoremediation purposes, and the formation of phytochelatin-heavy metal complexes and their sequestration in vacuole are the main processes influencing susceptibility of Azolla to heavy metals.

The effect of drought stress on polyphenolic compounds and expression of flavonoid biosynthesis related genes in Achillea pachycephala Rech.f.

This study investigated the effect of drought stress on the amount of phenolic and flavonoid compounds as well as H2O2 and malondialdehyde (MDA) in Achillea pachycephala. The expression patterns of the key genes and their molecular mechanisms in the phenylpropanoid pathway (PAL, CHS, CHI, F3H, F3'H, F3'5'H, FLS) were also assessed during drought stress using quantitative real-time polymerase chain reaction (qRT-PCR). The samples were harvested at 0, 7, 14, 21 and 28 days after exposure to drought stress. High-performance liquid chromatography (HPLC) analysis was performed to determine the changes of phenolic and flavonoid compounds - chlorogenic acid, caffeic acid, rutin, luteolin-7-O-glycoside, 1,3-dicaffeoylquinic acid, apigenin-7-O-glycoside, luteolin, apigenin and kaempferol - during stress conditions. Concentrations of most of the compounds increased with increasing drought stress duration. Most of the phenolic acids continued to accumulate with increasing duration of stress, while flavonoids dramatically decreased at day 28 of stress. Chlorogenic acid was the most abundant phenolic acid (4.97 mg/100 g dry weight [DW]) at the beginning of the experiment, while it decreased at day 7 and increased again at day 21. However, different trends were observed for some flavonoids, such as luteolin and apigenin. At the beginning of stress treatment, high accumulation of free radicals (H2O2) and lipid peroxidation (MDA) led to elevated expression of most of the flavonoid genes. MDA increased from 22.66 to 43.28 µmol g-1 DW at day 28. CHS gene expression was elevated at day 7, while chi gene expression remained unchanged. At the end of the stress period, most of the flavonoid concentrations and expression of the relevant genes also increased. The results can facilitate selection of appropriate drought conditions to obtain the highest levels of flavonoids such as luteolin and apigenin and phenolic compounds such as chlorogenic acid for improved health benefits.

Isolation and Characterization of Pb-Solubilizing Bacteria and Their Effects on Pb Uptake by Brassica juncea: Implications for Microbe-Assisted Phytoremediation.

The aim of this study was to isolate and characterize lead (Pb)-solubilizing bacteria from heavy metal-contaminated mine soils and to evaluate their inoculation effects on the growth and Pb absorption of Brassica juncea. The isolates were also evaluated for their plant growth-promoting characteristics as well as heavy metal and salt tolerance. A total of 171 Pb-tolerant isolates were identified, of which only 15 bacterial strains were able to produce clear haloes in solid medium containing PbO or PbCO3, indicating Pb solubilization. All of these 15 strains were also able to dissolve the Pb minerals in a liquid medium, which was accompanied by significant decreases in pH values of the medium. Based on 16S rRNA gene sequence analysis, the Pb-solubilizing strains belonged to genera Bacillus, Paenibacillus, Brevibacterium, and Staphylococcus. A majority of the Pb-solubilizing strains were able to produce indole acetic acid and siderophores to different extents. Two of the Pb-solubilizing isolates were able to solubilize inorganic phosphate as well. Some of the strains displayed tolerance to different heavy metals and to salt stress and were able to grow in a wide pH range. Inoculation with two selected Pb-solubilizing and plant growth-promoting strains, (i.e., Brevibacterium frigoritolerans YSP40 and Bacillus paralicheniformis YSP151) and their consortium enhanced the growth and Pb uptake of B. juncea plants grown in a metal-contaminated soil. The bacterial strains isolated in this study are promising candidates to develop novel microbe-assisted phytoremediation strategies for metal-contaminated soils.

Genetic diversity among and within Ferula asafoetida H. Karst. populations using molecular and phytochemical markers.

Ferula asafoetida is an herbaceous, perennial and monocarpic species of the Apiaceae family with medicinal properties. In this study, the genetic diversity of F. asafetida populations was assessed using SCoT and SRAP molecular markers. Nine SCoT and nine SRAP primer combinations amplified 211 and 194 bands, showing 96.07% and 92.87% of polymorphism, respectively. The dendrograms generated from Jaccard's similarity matrix and the UPGMA method revealed that genetic relationships among the F. asafoetida genotypes were not related to their geographical regions. The analysis also revealed a relatively acceptable differentiation in allele frequencies, illustrating the high genetic diversity and gene flows among the populations. The high percent of diversity among the populations indicated a rich resource of germplasm for breeding programs. Moreover, STRUCTURE analysis showed the high admixture of the studied accessions. According to AMOVA analysis, higher genetic variation occurred within the populations. Total phenolic content was also assessed using the folin-ciocalteu method, observing a relatively extent variety (0.163-0.938 mg TA/g DW) among the populations. In addition, HPLC analysis defined eleven compounds in which p-coumaric and 1,3- caffeoylquinic acids were the most abundant phenolic acids. Finally, Feragheh population possessed the highest TPC (total phenolic content) and gene diversity. Karaj population also exhibited the highest amount of flavonoids and phenolic acids such as kaempferol and p-coumaric acids.

Correlation between Vitamin D3 level and extrahepatic manifestation in chronic hepatitis type-C virus patients.

BACKGROUND: Chronic hepatitis type-C virus (HCV) infection is one of the most common worldwide viral disorders, which leads to various clinical complications as well as extrahepatic manifestations. Furthermore, Vitamin D3 has also been reported to have relationship with the mentioned complications. The aim is to evaluate the correlation between Vitamin D3 level and extrahepatic manifestation in chronic HCV patients. MATERIALS AND METHODS: This cross-sectional study has been carried out on 90 patients with chronic hepatitis C. The level of Vitamin D3 was assessed in plasma of 90 patients with chronic HCV. Genotyping was done and clinical and sign and symptoms of recruited patients were gathered. Extrahepatic manifestations were evaluated and the correlation of blood, hepatic, and immunological factors and the level of Vitamin D3 were assessed. RESULTS: Most of our patients were male (92% vs. 8%). Twenty-nine percent had the insufficient amount of Vitamin D3 (21-30 ng/ml), and the remains had the Vitamin D3 level between 13-20 ng/ml. Furthermore, our assessment demonstrated that deficiency of Vitamin D3 was associated with the extrahepatic manifestations such as purpura (odds radio [OR] [95% confidence interval (CI) 95%] = 8.80 [1.74-44.47], P = 0.004), vasculitis (OR [95% CI] = 11.70 [3.01-45.41], P < 0.001), arthralgia (OR [95% CI] = 20.26 [4.21-97.47], P < 0.001), myalgia (OR [95% CI] = 4.00 [1.01-17.27], P = 0.048), and glomerulonephritis (P = 0.021). CONCLUSION: According to our results, the extrahepatic manifestation in the patients with sufficient levels of Vitamin D3 would be less possible. In fact, it could be stated that deficiency in the Vitamin D3 can have a significant relationship with these manifestations.

Inhibitory action of dicyclomine on lipase activity, kinetics and molecular study.

Lipase is one of the most important groups of enzymes for industry and medicine. It breaks down triacylglycerol to glycerol and fatty acids. Some bacteria use lipase to degrade the extracellular matrix of the host cells to penetrate into the tissues. Dicyclomine is a muscarinic antagonist receptor that relieves the smooth muscle spasm of the gastrointestinal tract and affects the cardiovascular system. In this research, the effect of a dicyclomine on the lipase activity of Pseudomonas aeruginosa was studied. Hanes-Woolf plot showed that the drug inhibited the enzyme by competitive inhibition. The IC50 value (60uM) and Ki (30uM) of the drug revealed that the drug bound to enzyme with high affinity. Determination of enzyme activity in various temperature showed that the maximum activity of lipase was at 60°C both in the presence and absence of the drug. Arrhenius plot determined that the activation energy of the enzyme reaction was increased in the presence of the drug. The model of binding demonstrated that the drug entered a pocket containing 10 amino acids and interacted by hydrogen bond and hydrophobic interaction and the conformational change of the enzyme after binding of the drug was confirmed by fluorescence measurement.

Plasmid DNA purification by zirconia magnetic nanocomposite.

A zirconia magnetic nanocomposite was prepared by a co-precipitation method in one step. The synthesized nanocomposite was characterized by scanning electron microscopy, energy-dispersive X-ray and Fourier transform infrared spectroscopy. The nanocomposite was applied for the adsorption/desorption of tobacco plant DNA (as a model). Experimental parameters controlling adsorption efficiency, including pH of binding solution, extraction time, the amount of nanocomposite and ionic strength, were optimized. To obtain high desorption efficiency, the effects of pH, the ionic strength of elution buffer and desorption time were investigated. The nanocomposite provided the adsorption capacity of 53.5 mg g-1 for DNA. The adsorption and desorption efficiency of the sorbent was found to be greater than 98 and 81%, respectively. The zirconia magnetic nanocomposite was used for the purification of plasmid DNA (pDNA) from Escherichia coli cell culture. The yield and purity of pDNA obtained by the method were compared to those obtained by the phenol-chloroform solvent extraction and a commercial kit.

A novel diagnostic biosensor for distinguishing immunoglobulin mutated and unmutated types of chronic lymphocytic leukemia.

In chronic lymphocytic leukemia (CLL), the immunoglobulin heavy-chain variable (IgVH) region may be mutated (Ig-mutated CLL) or unmutated (Ig-unmutated CLL); and the presence or absence of mutations in this region of CLL cells distinguishes two clinically distinct forms. It is important for physicians to distinguish between patients with Ig-unmutated CLL, where typically have more indolent disease with median survivals close to 25 years, and Ig-mutated CLL, where have more aggressive disease with median survivals around eight years. In this work, a biosensor capable of diagnosis and distinguishing between these two types of CLL was reported. The biosensor was fabricated by modifying a gold electrode with gold nanoparticles (AuNPS) followed by coating of ZAP70 oligonucleotide probe on the surface to detect specific sequence of ZAP70 gene. ZAP70 could predict the IgVH mutation status and is a good marker for differentiating Ig-mutated and Ig-unmutated CLL and serve as prognostic marker. First, we focused on achieving hybridization between probe and its complementary sequence. Hybridization between probe and target was determined with electrochemical impedance spectroscopy (EIS). Then, our efforts turned to optimize the conditions for the detection of any point mutation and also to maximize the selectivity. Under optimal conditions, the biosensor has a good calibration range between 2.0 × 10(-14) and 1.0 × 10(-9)molL(-1), with ZAP70 DNA sequence detection limit of 4.0 × 10(-15)molL(-1). We successfully detect hybridization first in synthetic samples, and ultimately in blood samples from patients. Experimental results illustrated that the nanostructured biosensor clearly discriminates between mutated and non-mutated CLL and predict the IgVH mutation status, which it has been considered as the single most informative stage independent prognostic factor in CLL.

Assessment of the Genetic Diversity Among Potato Cultivars from Different Geographical Areas Using the Genomic and EST Microsatellites.

BACKGROUND: Potato has a narrow genetic base which is due to its development, as it takes its genetic root from a few genotypes originated from South America. OBJECTIVES: The objective of this study was to assess the genetic relationships among potato (Solanum tuberosum L.) genotypes originated from different geographical regions. MATERIALS AND METHODS: This study has rendered 25 useful SSRs and EST-SSRs that were located in pre-existing genetic maps, fingerprinted in a collection of the 47 potato genotypes from America, Europe and Iran. RESULTS: The number of alleles per locus ranged from 2 to 9 with an average of 6.22 alleles per locus. UPGMA dendrogram, constructed from microsatellite data based on Jaccard similarity coefficient slightly clustered the American and European potatoes according to their geographical distribution. Iranian genotype, "Istanbuli", joined to a group with American genotype. The results indicated that American genotypes show the highest expected heterozygosity compared to the European genotype. This result was expected due to the narrow genetic base of European potatoes considering their origin from a limited number of introductions. CONCLUSIONS: It could be concluded that SSR is an appropriate marker for evaluating genetic diversity within and among potatoes from different geographical regions.

Molecular polymorphism in Pistacia vera L. using non-coding regions of chloroplast DNA.

The present study describes plastid DNA polymorphism and reports a comparative analysis of two non-coding cpDNA regions (trnC-trnD and atpB-rbcL) in pistachio. Seventeen different genotypes of domestic and wild pistachio from Iran, Syria, Turkey and America were sampled. Total genomic DNA was extracted and amplified with trnC-trnD and atpB-rbcL specific primers and then were sequenced. Phylogenetic relationships and depiction of phylogenetic trees were conducted. Cultivated genotypes of Pistacia vera were classified in a group regardless of their geographic location. P. vera was isolated from Sarakhs but they placed in the two close groups. Among cultivated genotypes, Jalab was separated from other cultivated genotypes. Pistacia Khinjuk was classified with Pistacia atlantica subsp. mutica. The findings confirm the common splitting hypothesis for commercial pistachio genotypes of the P. vera wild-type and also indicated the direct impact of Iranian genotypes in the evolutionary process of cultivated pistachios in other parts of the world. In conclusion it can be inferred that cultivated varieties of pistachio and P. vera var. sarakhs have the same origin, moreover genomic chloroplast could appropriately identify the interspecies relationships of pistachios.

Statin efficacy in the treatment of hepatitis C genotype I.

BACKGROUND: Lipid metabolism is one of the hepatitis C virus (HCV) life cycle steps. Statins can reduce cholesterol level and finally can decrease HCV replication. Thus, we assessed the effect of Statins in combination with standard antiviral treatment on hyperlipidemic genotype I HCV infected patients. MATERIALS AND METHODS: This study was a prospective clinical trial. 40 patients were selected from those referred to educational and Therapeutic Centers of Isfahan University of Medical Sciences from 2009 to 2010 with confirmed HCV viremia. All patients received Peg-interferon-a2a and ribavirin. 20 hyperlipidemic Patients received 20 mg atorvastatin nightly for 3 months and placebo was prescribed for 20 normolipidemic HCV infected patients as a control group. Liver enzymes and complete blood count were checked monthly and thyroid stimulating hormone was checked every 3 months. We also performed quantitative HCV-ribonucleic acid (RNA) test in 12(th) week of therapy, at the end of treatment and 6 months after therapy for all samples. RESULTS: We didn't find any significant differences in the mean of HCV-RNA numbers between statin and placebo groups in 12(th) week of treatment, in the end of treatment and 6 months after treatment (P > 0.05). CONCLUSION: Atorvastatin has no effect on the mean of HCV viral load when we added it to standard treatment for hepatitis C infection. Further studies are necessary to examine the possible antiviral properties of statins and their potential role as adjuncts to standard HCV therapy.

Studying genetic variability of pomegranate (Punica granatum L.) based on chloroplast DNA and barcode genes.

Chloroplast DNA has been used extensively to analyze plant phylogenies at different taxonomic levels because of its size, organization and sequence conservation. In the present research, two chloroplastic regions, petA­psaJ, trnC­trnD and four DNA barcodes (trnH­psbA, ITS, rbcL, matK), were used to introduce suitable regions for the assessment of genetic diversity among P. granatum L. genotypes. Analysis of psbE­petL in petA­psaJ region revealed 1,300 nucleotides with 4.29 % genetic diversity among genotypes, while trnC­petN in trnC­trnD region showed 1.8 % genetic diversity. Therefore, despite the results obtained from the study of other plants, the trnC­trnD region had a low potential for the evaluation of diversity among pomegranate genotypes. Analysis of DNA barcodes in pomegranate showed that trnH­psbA (genetic diversity 2.91 %) provides the highest intra-species variation, followed by ITS (genetic diversity 0.44 %). Eighteen genotypes from different geographical origins of Iran were used to investigate psbE­petL and trnH­psbA potential as novel barcodes to determine genetic polymorphism and characterize pomegranate genotypes. The results suggested that two regions, psbE­petL and trnH­psbA, were more suitable for determining intra-species relationships of pomegranate.

An improved heuristic for haplotype inference.

Haplotypes include essential SNP information used for a variety of purposes such as investigating potential links between certain diseases and genetic variations. Given a set of genotypes, the haplotype inference problem based on pure parsimony is the problem of finding a minimum set of haplotypes that explains all the given genotypes. The problem is especially important because, while it is fairly inexpensive to obtain genotypes, other approaches to obtaining haplotypes are significantly expensive. There are two types of methods proposed for the problem, namely exact and inexact methods. Existing exact methods guarantee obtaining purely parsimonious solutions but have exponential time-complexities and are not practical for large number or length of genotypes. However, inexact methods are relatively fast but do not always obtain optimum solutions. In this paper, an improved heuristic is proposed, based on which new inexact and exact methods are provided. Experimental results indicate that the proposed methods replace the state-of-the-art inexact and exact methods for the problem.

Assessment of genetic diversity of Bermudagrass (Cynodon dactylon) using ISSR markers.

Bermudagrass (Cynodon spp.) is a major turfgrass for home lawns, public parks, golf courses and sport fields and is known to have originated in the Middle East. Morphological and physiological characteristics are not sufficient to differentiate some bermudagrass genotypes because the differences between them are often subtle and subjected to environmental influences. In this study, twenty seven bermudagrass accessions and introductions, mostly from different parts of Iran, were assayed by inter-simple sequence repeat (ISSR) markers to differentiate and explore their genetic relationships. Fourteen ISSR primers amplified 389 fragments of which 313 (80.5%) were polymorphic. The average polymorphism information content (PIC) was 0.328, which shows that the majority of primers are informative. Cluster analysis using the un-weighted paired group method with arithmetic average (UPGMA) method and Jaccard's similarity coefficient (r = 0.828) grouped the accessions into six main clusters according to some degree to geographical origin, their chromosome number and some morphological characteristics. It can be concluded that there exists a wide genetic base of bermudograss in Iran and that ISSR markers are effective in determining genetic diversity and relationships among them.

Effective haplotype assembly via maximum Boolean satisfiability.

The haplotype assembly problem seeks the haplotypes of an individual from which a set of aligned SNP fragments are available. The problem is important as the haplotypes contain all the SNP information, which is essential to such studies as the analysis of the association between specific diseases and their potential genetic causes. Using Minimum Error Correction as the objective function, the problem is NP-hard, which raises the demand for effective yet affordable solutions. In this paper, we propose a new method to solve the problem by providing a novel Max-2-SAT formulation for the problem. The proposed method is compared with several well-known algorithms proposed for the problem in the literature on a recent extensive benchmark, outperforming them all by achieving solutions of higher average quality.