Studies on genetic diversity, gene flow and landscape genetic in Avicennia marina: Spatial PCA, Random Forest, and phylogeography approaches.

Mangrove forests grow in coastal areas, lagoons, estuaries, and deltas and form the main vegetation in tidal and saline wetlands. Due to the mankind activities and also changes in climate, these forests face degradations and probably extinction in some areas. Avicennia marina is one of the most distributed mangrove species throughout the world. The populations of A. marina occur in a limited region in southern parts of Iran. Very few genetic and spatial analyses are available on these plants from our country. Therefore, the present study was planned to provide detailed information on Avicennia marina populations with regard to genetic diversity, gene flow versus genetic isolation, effects of spatial variables on connectivity and structuring the genetic content of trees populations and also identifying adaptive genetic regions in respond too spatial variables. We used SCoT molecular markers for genetic analyses and utilized different computational approaches for population genetics and landscapes analyses. The results of present study showed a low to moderate genetic diversity in the studied populations and presence of significant Fst values among them. Genetic fragmentation was also observed within each province studied. A limited gene flow was noticed among neighboring populations within a particular province. One population was almost completely isolated from the gene flow with other populations and had peculiar genetic content.Spatial PCA analysis revealed both significant global and local genetic structuring in the studied populations. Spatial variables like humidity, longitude and altitude were the most important spatial features affecting genetic structure in these populations.

Putative Local Adaptive SNPs in the Genus Avicennia.

The genus Avicennia with eight species grow in intertidal zones of tropical and temperate regions, ranging in distribution from West Asia, to Australia, and Latin America. These mangroves have several medicinal applications for mankind. Many genetic and phylogenetic studies have been carried out on mangroves, but none is concerned with geographical adaptation of SNPs. We therefore, used ITS sequences of about 120 Avicennia taxa growing in different parts of the world and undertook computational analyses to identify discriminating SNPs among these species and to study their association with geographical variables. A combination of multivariate and Bayesian approaches such as CCA, RDA, and LFMM were conducted to identify the SNPs with potential adaptation to geographical and ecological variables. Manhattan plot revealed that many of these SNPs are significantly associated with these variables. The genetic changes accompanied by local and geographical adaptation were illustrated by skyline plot. These genetic changes occurred not under a molecular clock model of evolution and probably under a positive selection pressure imposed in different geographical regions in which these plants grow.

Molecular barcoding of Melissa officinalis L. (badranjboye) in Iran and identification of adulteration in its medicinal services.

Medicinal plants are an important source for treatment of diseases in many countries. Today, controlling the quality of the products of medicinal plants is an important task. Customer health may be in danger due to the fraud and misconduct by the sales associates in the sales centers. Melissa officinalis L. (Lamiaceae) is an important medicinal plant used for treatment of several diseases. In Iran, the species of Dracocephalum, Hymencrater, Nepeta and Stachys are mistakenly sold under the name of Badranjboye that have different pharmaceutical properties. For avoiding this mistake, this investigation was performed with the following aims: 1) Checking for the cheating and identifying the Badranjboye in the Iran's market of medicinal plants, 2) Providing the molecular barcode for the medicinal species of Melissa. For this purpose, Market-sold plant samples (leaves) and original reference plant species were compared by morphology, odor as well as Internal transcribed spacer (ITS) and chloroplast DNA ((psbA-trnH) and (trnL-trnF)) sequences. Various molecular analyses, such as sequencing, determination of genetic distance, and construction of phylogenetic tree were performed. These reports have shown that internal transcribed spacer (ITS) and chloroplast DNA (psbA-trnH) sequences are an efficient molecular marker to produce barcode gap and differentiating Melissa officinalis from other species.

A new insight on genetic diversity of sweet oranges: CAPs-SSR and SSR markers.

BACKGROUND: Citrus species are among the most important and widely consumed fruit trees in the world and are subjected to increasing global cultivation. Sweet orange (Citrus sinensis L. Osbeck) is one of 30 species of citrus which is cultivated in different regions of Iran. In this study, 80 trees of 13 sweet orange cultivars of Mazandaran province were studied for genetic diversity and fingerprinting by five short simple repeat (SSR) marker. RESULTS: The studied cultivars showed a high degree of genetic variability with an average genetic polymorphism of 98.46%. Behshahr and Jadeh Ghadim2 genotypes had the highest and lowest values in Nei genetic diversity, number of effective alleles, and Shannon index, respectively. Based on k-means clustering, the studied genotypes were divided into two main different groups. The high magnitude of genetic similarity between replicates of different cultivars indicated a potential case of homonymy or synonymy. DAPC analysis showed genetic admixture among some of the cultivars. The heatmap plot illustrated the alleles involved in cultivar differentiation. The CAPs analysis of monomorphic alleles of SSR loci indicated that these alleles differ in their sequences which add up to the genetic variability of citrus germplasm. CONCLUSION: In general, SSR markers, due to their codominant nature and abundance in genome, are a good indicator for cultivar fingerprinting and hybrid prediction in orange cultivars. The present results showed the high diversity of sweet orange trees in different cultivars in the north of the country.

Chromosomal instability reducing effect of paclitaxel and lapatinib in mouse embryonic stem cells with chromosomal abnormality.

Chromosomal abnormalities, as a frequent phenomenon in cultured embryonic stem cells (ESCs), is a major obstacle in the ESC application in regenerative medicine. Recent studies showed that aneuploid embryonic stem cells of humans and mice are more vulnerable to anticancer drugs, compared with normal cells. The aim of the current study was to evaluate effects of three anticancer drugs, paclitaxel, lapatinib and bortezomib, on mouse embryonic stem cells (mESCs) as a suitable and available model. To assess in vitro cell toxicity, two mESC lines were treated with the aforementioned drugs. Using G-band karyotyping and micronucleus assay, the effect of anticancer drugs in terms of reduction of chromosomal instability in the mESCs was evaluated in control and treatment groups. Also, apoptosis rate of both groups was estimated by FITC-Annexin V/Propidium Iodide (PI) double staining. In addition, the effect of these three drugs in maintaining the pluripotency was assessed through alkaline phosphatase assay and quantification of the expression of three key pluripotency genes, Nanog, Pou5f1 and Sox-2 was performed using Real Time PCR. The rate of numerical abnormalities after treatment with paclitaxel and lapatinib was lower than the control group. The expression level of pluripotency genes exhibited no significant difference between control and treatment groups. Administration of paclitaxel and lapatinib to the mESCs culture at an appropriate dose and in a timely manner could decrease chromosome stability without affecting pluripotency.

Taxol Improves Pre-Implantation Development Potential of Mouse Embryos.

AIM: The objective of the present study was to investigate the development of mouse embryos and the chromosomal status after the pre-implantation treatment with paclitaxel (Taxol) based on the reports that indicate Taxol improves the developmental potential of vitrified human and mouse oocytes. METHODS: Outbred female mice were superovulated and in vitro fertilization (IVF) was carried out using sperms from the same strain. Two-cell stage mouse embryos were cultured in the presence of Taxol for 24 h. After the determination of a non-toxic dose of Taxol, embryo development in control and Taxol-treated groups was compared during 3.5 days post-IVF. The aneuploidy rate of embryos was assessed by fluorescence in situ hybridization for chromosomes 2 and 11. RESULTS: Development to morula and blastocyst stages was considerably enhanced following the addition of Taxol 0.01 µM compared to a similar situation in controls (p < 0.0001). Moreover, the degeneration rate was decreased following treatment with this concentration of Taxol (p < 0.01). The rate of aneuploidy in embryos and individual blastomeres did not vary between groups (p = 0.518 and 0.810 respectively). CONCLUSION: Pre-implantation treatment with Taxol 0.01 µM had a positive effect on the development to morula/blastocyst stages and decreased the degeneration rate without affecting the aneuploidy rate of chromosomes 2 and 11.

The Potential Role of TNF-α (rs361525 and rs1800629) in Hepatocellular Carcinoma: Multivariate Analysis (Meta-Analysis).

PURPOSE: Tumor necrosis factor-α has been suggested to play a crucial role in the development andprogression of hepatocellular carcinoma (HCC). Previous reports have indicated that rs361525 and rs1800629 might be risk factors for various cancers. Increasing studies have been conducted on the association of these two SNPs with HCC risk but the results remain inconclusive. METHODS: In order to detect association between TNF- α and HCC, a meta-analysis was performed. Five studies with 541 cases and 795 controls were used for rs361525, while six studies including 925 cases and 1307 controls were collected for investigating rs1800629. The grouping of countries from data were obtained was done by Principal Coordinate Analysis plot (PCA). Moreover, association between geographical area and grouping of genotypes was determined by Canonical Correspondence Analysis (CCA). RESULTS: Our meta-analysis showed that rs361525 and rs1800629 were not significantly associated with the risk of HCC. CCA analysis illustrated that there was not any correlation between genotype distribution and geographical distance for rs1800629 but there was significant correlation between genotype distribution and geographical features for rs361525. PCA analysis for both SNPs showed India and Korea were placed near each other and also China and Brazil were in same part of PCA plot. CONCLUSION: To sum up, this meta-analysis suggests that the rs361525 and rs1800629 are not associated with HCC development while geographical distance effect on rs361525 genetic inheritance but not effect on rs1800629. However, it is necessary to conduct further studies with larger sample. Moreover, gene-gene and gene-environment interactions should also be considered.

Study of single nucleotide polymorphism (rs28368082) in SPO11 gene and its association with male infertility.

PURPOSE: The present study is a case-control analysis of a SNP (rs28368082) in exon 7 of the SPO11 gene and its possible association with male infertility in three provinces of Iran. We also searched for genetic differences among populations. METHODS: Using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis, we genotyped 113 infertile men and 50 fertile controls. Then, samples consisting SNP, as determined by PCR-RFLP, were genotyped by sequencing. The differences in genotype distributions between cases and fertile controls were examined using Chi-squared analysis. The genetic difference between individuals with mutated nucleotide was investigated by phylogenetic trees. Genetic difference among populations (provinces) was analyzed through ANOVA test, and homogeneity was investigated using STRUCTURE and K-means clustering analysis. RESULTS: According to the statistical analysis, the SNP was significantly associated with male infertility in all populations except oligozoospermic cases of the Center region. The phylogenetic trees showed partial genetic variation among the individuals, although ANOVA test showed no significant genetic difference between populations (provinces) for both azoospermic, and oligozoospermic cases. Eventually, we affirmed that individuals in the inclusive populations had genetic difference, but it was not statistically significant for dividing underlying populations to separate groups, so each population was homogenous. CONCLUSION: Our study indicates that the mentioned polymorphism in SPO11 gene may be linked to the susceptibility of azoospermia and oligozoospermia male infertility in three provinces of Iran. Further studies are required to support obtained results. It finally should be noted that the possible association between a particular SNP and a specific disease completely depends on the underlying population.

Intragenic DNA polymorphism analysis of DMD/BMD dystrophy gene for carrier and prenatal diagnosis in 60 Iranian healthy individuals.

Duchenne and Becker muscular dystrophies (DMD/BMD) are allelic, x-linked neuromuscular disease resulting from mutations in dystrophin gene. DMD is the most severe and frequent inherited but still incurable disease in males. About two-third of such patients have large deletions or duplications that can be identified by multiplex polymerase chain reaction (PCR). In one-third of remaining cases, a linkage analysis that involves DNA markers of intragenic dystrophic gene is considered a rapid and simple method for carrier detection and prenatal diagnosis. In the present study, we investigated frequency and heterozygosity of three polymorphic restriction sites and also four highly polymorphic (CA)(n) repeat microsatellites loci within hot spots region of human dystrophin gene in 60 healthy Iranian populations. Our findings indicated that the allele frequencies of pERT87-8/TaqI, pERT87-15/BamHI, and pERT87-15/XmnI were 0.23/0.77, 0.221/0.779, and 0.239/0.761, respectively. Among these three polymorphic sites, pERT78-15/XmnI locus had the highest heterozygosity with frequency of 47.17%. We also found that STR49 had the highest heterozygosity among four polymorphic microsatellites. These findings are useful in linkage analysis of Iranian DMD families in both carrier detection and prenatal diagnosis.

Numerical taxonomy of Stipa (Poaceae) species in Iran.

Numerical taxonomic studies were performed on 57 populations of 15 Stipa species belonging to 5 different sections, concerning intra-population and inter-populations variations as well as inter-specific relationships. The most variable morphological characters useful in the species delimitation were also determined. The species studied also differed significantly in most of the quantitative characters studied and the mean of such characters may be of use in the species delimitation. The clustering showed distinctness of the species studied as the populations of each species are placed close to each other and separate from the other species.

Cytogenetic study of the genus Cousinia ( Asteraceae, section Serratuloideae ) in Iran

Meiotic studies of ploidy level, chromosome paring and chiasma frequency were performed on 11 Cousinia (Asteraceae) species of the section Serratuloideae. The diploid number of the species studied was 2n = 2x = 24 and 26 so these species possess two different basic numbers (x = 12 or 13), a phenomenon common to other sections of the genus. The chromosome numbers of 9 species are reported here for the first time. When the 2n = 24 and 2n = 26 species were subjected to cluster analysis based on relative meiotic characters two different clusters were formed indicating their distinctness. Our data support the results obtained from morphometry, anatomy, pollen morphology and molecular studies of the genus Cousinia.