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Abstract Evolutionary studies of plant groups which are distributed in vast geographical regions and face different ecological and environmental conditions are important as they through light on different mechanisms of local adaptation and species divergence through time. The genus Avicennia is one of these plant groups which inspire of few species show interesting geographical distribution with some degree of species-specific geographical isolations. In general, very limited molecular phylogenetic investigations have been carried out in the genus Avicennia, and therefore we conducted the present study with the following aims: 1. To estimate the species divergence time based on different nuclear and chloroplast DNA regions, separately. This will illustrate how different genetic regions evolved in this genus, 2. To identify the sequences with potential adaptive value against geographical variable by latent factor mixed models (LFMM) analysis, 3. To illustrate the phylogenetic signal of these DNA regions and their role in speciation within the genus and, 4. To introducing a new computational strategy for estimating adaptive time for the sequences. The results showed that different genetic regions may produce different species divergent time, both the nuclear ribosomal internal transcribed spacer (ITS) region and chloroplast DNA sequences, contained potentially adaptive single nucleotide polymorphisms (SNPs).We could present a suggestive time for these adaptive sequences for the first time. In conclusion both local adaptation and independent mutations seem to have played role in Avicennia speciation and evolution.

Evolutionary studies of plant groups which are distributed in vast geographical regions and face different ecological and environmental conditions are important as they through light on different mechanisms of local adaptation and species divergence through time. The genus Avicennia is one of these plant groups which inspire of few species show interesting geographical distribution with some degree of species-specific geographical isolations. In general, very limited molecular phylogenetic investigations have been carried out in the genus Avicennia, and therefore we conducted the present study with the following aims: To estimate the species divergence time based on different nuclear and chloroplast DNA regions, separately. This will illustrate how different genetic regions evolved in this genus, To identify the sequences with potential adaptive value against geographical variable by latent factor mixed models (LFMM) analysis, To illustrate the phylogenetic signal of these DNA regions and their role in speciation within the genus and, To introducing a new computational strategy for estimating adaptive time for the sequences. The results showed that different genetic regions may produce different species divergent time, both the nuclear ribosomal internal transcribed spacer (ITS) region and chloroplast DNA sequences, contained potentially adaptive single nucleotide polymorphisms (SNPs).We could present a suggestive time for these adaptive sequences for the first time. In conclusion both local adaptation and independent mutations seem to have played role in Avicennia speciation and evolution. [ABSTRACT FROM AUTHOR]

Abstract Background Male infertility is rapidly growing, and single nucleotide polymorphism (SNP) association studies are of critical importance. Tumor suppressor candidate 1 (TUSC1) gene is associated with azoospermia. We investigated association between rs1462218557 in TUSC1 with azoospermia. Methods We performed tetra-ARMS PCR analysis and sequencing on healthy and infertile individuals. Results Tetra-ARMS PCR results revealed that the allele frequency of the SNP for T alleles was 0.66, while the same value for C allele was 0.36. It was different from the previous reports of the other countries because they reported the allele C as the frequent allele and it was considered an ancestral allele. The genotype frequencies obtained showed that 67% of the samples were heterozygotes (T/C), while 33% were homozygotes (TT). SNP-STAT analysis showed a significant association (p = 0.04) with the studied SNP and azoospermia in Iranian samples. Conclusions The present study reports a new allele frequency of rs1462218557 in TUSC1 gene, which may be associated with azoospermia in Iranian people. Moreover, no association was observed between neighboring sequences/SNPs with male infertility.

Mandarins are one of the members of the genus Citrus L. which contain very important plant species that extensively contribute to humans. The classification of commercial mandarins is very complicated, which largely includes tangerine, satsuma, and clementine. Citrus hybrids are more diversified, and their taxonomy is somewhat inconsistent. A proper breeding and conservation plan for important plant species requires accurate genetic analysis and an evaluation of the available germplasm. The present study was conducted to produce data on genetic structure, gene flow, and admixture of the mandarin populations in Iran and also to identify the genetic regions associated with geographical and climatic variables. The start codon targeted molecular markers were used for this study. The results revealed some extent of gene flow and genetic admixture among mandarin populations and that some locally named cultivars are genetically alike and probably are homonyms. Mandarins comprise a complex genetic group of closely related individuals, but yet somewhat genetically differentiated probably due to local propagation practice and artificial selection by orchard management, as revealed by significant analysis of molecular variance. The accessions studied were grouped into three broad genetic groups which differ in their genetic content and may be used for the breeding program of mandarins. We also identified some genetic regions which are significantly associated with an environmental and climatic variable which can be used in the conservation program of mandarins in the country. Landscape genetic analyses revealed that both global and local spatial variables affect the genetic structuring of mandarins. [ABSTRACT FROM AUTHOR]

Purpose: Poor response to ovarian stimulation (POR) typically is reflected as decreased follicular response and low estradiol (E2) levels following ovarian stimulation by FSH/HMG. Many genes are involved in oocyte maturation, and demographic features and lifestyle can affect the oocyte maturity and developmental competence. The present study was conducted to investigate the magnitude of gene expression and lifestyle habits in POR women as compared to healthy women, using different statistical and computational methods. Methods: Fifty women in the two groups were studied. The study groups included POR women (n = 25) with 1–9 released oocytes, and the control group (normal women, n = 25) with 9–15 released oocytes. Quantitative PCR was used to estimate the expression of FIGLA, ZAR1, WNT4, LHX8, APC, H1FOO, MOS, and DMC1 genes in granulosa cells. Results: The results showed no significant difference in the magnitude of the studied genes' expression and linear discriminant analysis did not differentiate the studied groups based on all the genes together. Redundancy analysis (RDA) and latent factor mixed model (LFMM) results produce no significant association between the genes' expression magnitude and the geographical variables of the patients' local habitat. Linear discriminant analysis (LDA) of the demographic features differentiated the two groups of women. Conclusion: Our results indicate that demographic features may have an effect on sample gene expression levels. [ABSTRACT FROM AUTHOR]

Forest trees growing in high altitude conditions offer a convenient model for studying adaptation processes. They are subject to a whole range of adverse factors that are likely to cause local adaptation and related genetic changes. Siberian larch (Larix sibirica Ledeb.), whose distribution covers different altitudes, makes it possible to directly compare lowland with highland populations. This paper presents for the first time the results of studying the genetic differentiation of Siberian larch populations, presumably associated with adaptation to the altitudinal gradient of climatic conditions, based on a joint analysis of altitude and six other bioclimatic variables, together with a large number of genetic markers, single nucleotide polymorphisms (SNPs), obtained from double digest restriction-site-associated DNA sequencing (ddRADseq). In total, 25,143 SNPs were genotyped in 231 trees. In addition, a dataset of 761 supposedly selectively neutral SNPs was assembled by selecting SNPs located outside coding regions in the Siberian larch genome and mapped to different contigs. The analysis using four different methods (PCAdapt, LFMM, BayeScEnv and RDA) revealed 550 outlier SNPs, including 207 SNPs whose variation was significantly correlated with the variation of some of environmental factors and presumably associated with local adaptation, including 67 SNPs that correlated with altitude based on either LFMM or BayeScEnv and 23 SNPs based on both of them. Twenty SNPs were found in the coding regions of genes, and 16 of them represented non-synonymous nucleotide substitutions. They are located in genes involved in the processes of macromolecular cell metabolism and organic biosynthesis associated with reproduction and development, as well as organismal response to stress. Among these 20 SNPs, nine were possibly associated with altitude, but only one of them was identified as associated with altitude by all four methods used in the study, a nonsynonymous SNP in scaffold_31130 in position 28092, a gene encoding a cell membrane protein with uncertain function. Among the studied populations, at least two main groups (clusters), the Altai populations and all others, were significantly genetically different according to the admixture analysis based on any of the three SNP datasets as follows: 761 supposedly selectively neutral SNPs, all 25,143 SNPs and 550 adaptive SNPs. In general, according to the AMOVA results, genetic differentiation between transects or regions or between population samples was relatively low, although statistically significant, based on 761 neutral SNPs (FST = 0.036) and all 25,143 SNPs (FST = 0.017). Meanwhile, the differentiation based on 550 adaptive SNPs was much higher (FST = 0.218). The data showed a relatively weak but highly significant linear correlation between genetic and geographic distances (r = 0.206, p = 0.001). [ABSTRACT FROM AUTHOR]

Sex determination of date palm seedlings is the challengeable effort for breeders. Different studies based on molecular markers and genome sequencing have provided some insight in to the genetic regions related to sex determination in date palms in general. But due to differences in cultivar population structure and also cost of whole genome sequencing, we may need a more suitable approach in developing countries for this task. Therefore, we suggest using a combination of different available molecular markers and a computational approach to identify the genetic regions involved in sex differentiation in date palm cultivars. In this study we used twenty-three cultivars including 7 male and 16 female cultivars that were examined by 30 different dominant and co-dominant molecular markers which deal with different genomic regions. Grouping of the tree samples based on 178 loci resulted in genetic differentiation of the studied male and female palm trees. Multiple correspondence analysis (MCA) bi-plot also showed genetic difference within male and female trees. Heatmap plot specified those markers which differentiate date palm trees. SSR (simple sequence repeats) and IRAP (inter retrotransposon amplified polymorphism) markers provided sex linked markers for male cultivars. In present study, we introduced sex specific alleles for Iranian male date palm cultivars as a fast track in seedlings. Different association studies performed identified the candidate genetic regions which are significantly associated with sex differentiation in date palm cultivars.

The pomegranate fruit is one of the most important horticultural products due to the presence of polyphenols, anti-oxidant and anti-fungal compounds. In the present study, we report the genetic fingerprinting, as well as genetic diversity in some Iranian commercial pomegranate cultivars by using simple sequence repeats (SSRs). In total 188 pomegranate trees of 47 presumed genotypes were used in genetic analyses. Based on multivariate and Bayesian statistical analyses, different genetic groups as well as clonal genotypes were identified. AMOVA, G'Nei as well as Jost D revealed significant genetic differentiation of the studied genotypes. LFMM analysis identified two potentially adaptive SSR alleles which differentiated pomegranate genotypes based on environmental conditions. Mantel test did not show correlation between genetic distance and geographical distances of the studied genotypes. Some of the hybrid plants obtained had new alleles which were not present in parental genotypes. These findings may be utilized in future selection and breeding pomegranate in the country. [ABSTRACT FROM AUTHOR]

The P-APC ligands (EDTA-like aminopolycarboxylate ligands comprising 1,3-propanediamine backbone) H 4 pdta, H 4 pd3ap, H 4 pddadp and H 4 pdtp (H 4 pdta = 1,3-propanediamine- N , N , N ′, N ′-tetraacetatic acid; H 4 pd3ap = 1,3-propanediamine- N , N , N ′-triacetic- N ′-3-propionic acid; H 4 pddadp = 1,3-propanediamine- N , N ′-diacetatic- N , N ′-di-3-propionic acid; H 4 pdtp = 1,3-propanediaminetetra-3-propionic acid) were investigated. The chelating ligands coordinate to copper(II) via five or six donor atoms affording distorted trigonal-bipyramid and octahedral structures that were verified by X-ray analysis for Ba[Cu(pd3ap)]·6H 2 O ( 1 ) and trans (O 6 )-Ba[Cu(pddadp)]·8H 2 O ( 2 ) complexes respectively. The impact of counter-ions on the P-APC complexes is shown in detail together with the analysis of another strain parameters. EPR spectral results confirm the penta-coordination of 1 and hexa-coordination of 2 in aqueous solution, even if several Cu(II) species with different protonation degree exist as a function of pH, and indicate that a hexa-coordinated structure is favored when the two axial COO − donors close five-membered chelate rings. We also present here the results of molecular mechanics (LFMM) calculations based on our previously-developed force field along with results of DFT (Density Functional Theory). On the basis of extensive DFT and TD-DFT calculations the B1LYP/6-311++G(d,p) level has been seen as an accurate theory for calculating and predicting the UV–Vis spectra in case of copper–P-APC compounds. [ABSTRACT FROM AUTHOR]

Flexible metal–organic Frameworks (MOFs) are an interesting class of materials due to their diverse properties. One representative of this class is the layered‐pillar MOF DUT‐8(Ni). This MOF consists of Ni2 paddle wheels interconnected by naphthalene dicarboxylate linkers and dabco pillars (Ni2(ndc)2(dabco), ndc = 2,6‐naphthalene–dicarboxylate, dabco = 1,4‐diazabicyclo‐[2.2.2]‐octane). DUT‐8(Ni) undergoes a volume change of over 140% upon adsorption of guest molecules. Herein, a ligand field molecular mechanics (LFMM) study of the CO2‐induced flexibility of DUT‐8(Ni) is presented. LFMM is able to reproduce experimental and DFT structural features as well as properties that require large simulation cells. It is shown that the transformation energy from a closed to open state of the MOF is overcompensated fivefold by the host–guest interactions. Structural characteristics of the MOF explain the shape of the energy profile at different loading states and provide useful insights to the interpretation of previous experimental results. [ABSTRACT FROM AUTHOR]