Bioactivities and in silico study of Pergularia tomentosa L. phytochemicals as potent antimicrobial agents targeting type IIA topoisomerase, TyrRS, and Sap1 virulence proteins

Pergularia tomentosa L. (P. tomentosa) has been largely used in Tunisian folk medicine as remedies against skin diseases, asthma, and bronchitis. The main objectives of this study were to identify phytochemical compounds that have antioxidant and antimicrobial properties from the stem, leaves, and fruit crude methanolic extracts of P. tomentosa, and to search for tyrosyl-tRNA synthetase (TyrRS), topoisomerase type IIA, and Candidapepsin-1 (SAP1) enzyme inhibitors through molecular docking study. Phytochemical quantification revealed that fruit and leaves extracts displayed the highest total flavonoids (582 mg QE/g Ex; 219 mg QE/g Ex) and tannins content (375 mg TAE/g Ex; 216 mg TAE/g Ex), also exhibiting significant scavenging activity to decrease free radicals for ABTS, DPPH, β-carotene, and FRAP assay with IC₅₀ values (> 1 mg/mL). Additionally, promising antimicrobial activities towards different organs have been observed against several bacteria and Candida strains. From the liquid chromatography-mass spectrometry (LC-MS) analysis, five polyphenolic compounds, namely digitoxigenin, digitonin glycoside and calactina in the leaves, kaempferol in the fruit, and calotropagenin in the stems, were identified. They were also analyzed for their drug likeliness, based on computational methods. Molecular docking study affirmed that the binding affinity of calactin and actodigin to the active site of TyrRS, topoisomerase type IIA, and SAP1 target virulence proteins was the highest among the examined dominant compounds. Therefore, this study indicated that P. tomentosa methanolic extracts displayed great potential to become a potent antimicrobial agent and might be a promising source for therapeutic and nutritional functions. These phytocompounds could be further promoted as a candidate for drug discovery and development.

Climate change influences on the potential distribution of Dianthus polylepis Bien. ex Boiss. (Caryophyllaceae), an endemic species in the Irano-Turanian region

Endemic and restricted-range species are considered to be particularly vulnerable to the effects of environmental change, which makes assessing likely climate change effects on geographic distributions of such species important to the development of integrated conservation strategies. Here, we determined distributional patterns for an endemic species of Dianthus (Dianthus polylepis) in the Irano-Turanian region using a maximum-entropy algorithm. In total, 70 occurrence points and 19 climatic variables were used to estimate the potential distributional area under current conditions and two future representative concentration pathway (RCP2.6 and RCP8.5) scenarios under seven general circulation models for 2050. Mean diurnal range, iso-thermality, minimum temperature of coldest quarter, and annual precipitation were major factors that appeared to structure the distribution of the species. Most current potential suitable areas were located in montane regions. Model transfers to future-climate scenarios displayed upward shifts in elevation and northward shifts geographically for the species. Our results can be used to define high-priority areas in the Irano-Turanian region for conservation management plans for this species and can offer a template for analyses of other endangered and threatened species in the region.

Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species

The complete plastome sequences of six species were sequenced to better understand the evolutionary relationships and mutation patterns in the chloroplast genome of the genus Colobanthus. The length of the chloroplast genome sequences of C. acicularis, C. affinis, C. lycopodioides, C. nivicola, C. pulvinatus and C. subulatus ranged from 151,050 to 151,462 bp. The quadripartite circular structure of these genome sequences has the same overall organization and gene content with 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames. A total of 153 repeat sequences were revealed. Forward repeats were dominant, whereas complementary repeats were found only in C. pulvinatus. The mononucleotide SSRs composed of A/T units were most common, and hexanucleotide SSRs were detected least often. Eleven highly variable regions which could be utilized as potential markers for phylogeny reconstruction, species identification or phylogeography were identified within Colobanthus chloroplast genomes. Seventy-three protein-coding genes were used in phylogenetic analyses. Reconstructed phylogeny was consistent with the systematic position of the studied species, and the representatives of the same genus were grouped in one clade. All studied Colobanthus species formed a single group and C. lycopodioides was least similar to the remaining species.

Gypsophila bermejoi G. López: A possible case of speciation repressed by bioclimatic factors

Gypsophila bermejoi G. López is an allopolyploid species derived from the parental G. struthium L. subsp. struthium and G. tomentosa L. All these plants are gypsophytes endemic to the Iberian Peninsula of particular ecological, evolutionary and biochemical interest. In this study, we present evidence of a possible repression on the process of G. bermejoi speciation by climatic factors. We modelled the ecological niches of the three taxa considered here using a maximum entropy approach and employing a series of bioclimatic variables. Subsequently, we projected these models onto the geographical space of the Iberian Peninsula in the present age and at two past ages: the Last Glacial Maximum and the mid-Holocene period. Furthermore, we compared these niches using the statistical method devised by Warren to calculate their degree of overlap. We also evaluated the evolution of the bioclimatic habitat suitability at those sites were the soil favors the growth of these species. Both the maximum entropy model and the degree of overlap indicated that the ecological behavior of the hybrid differs notably from that of the parental species. During the Last Glacial Maximum, the two parental species appear to take refuge in the western coastal strip of the Peninsula, a region in which there are virtually no sites where G. bermejoi could potentially be found. However, in the mid-Holocene period the suitability of G. bermejoi to sites with favorable soils shifts from almost null to a strong adaptation, a clear change in this tendency. These results suggest that the ecological niches of hybrid allopolyploids can be considerably different to those of their parental species, which may have evolutionary and ecologically relevant consequences. The data obtained indicate that certain bioclimatic variables may possibly repress the processes by which new species are formed. The difference in the ecological niche of G. bermejoi with respect to its parental species prevented it from prospering during the Last Glacial Maximum. However, the climatic change in the mid-Holocene period released this block and as such, it permitted the new species to establish itself. Accordingly, we favor a recent origin of the current populations of G. bermejoi.

Simultaneous speciation in the European high mountain flowering plant genus Facchinia (Minuartia s.l., Caryophyllaceae) revealed by genotyping-by-sequencing

Understanding the relative importance of different mechanisms of speciation in a given lineage requires fully resolved interspecific relationships. Using Facchinia, a genus of seven species centred in the European Alps, we explore whether the polytomy found by Sanger sequencing analyses of standard nuclear (ITS) and plastid markers (trnQ-rps16) is a hard or soft polytomy by substantially increasing the amount of DNA sequence data, generated by genotyping-by-sequencing. In comparison to 142 phylogenetically informative sites in the Sanger sequences the GBS sequences yielded 3363 phylogenetically informative sites after exclusion of apparently oversaturated SNPs. Maximum parsimony, maximum likelihood, NeighborNet, SVDquartets and Astral-II analyses all resulted in phylogenetic trees (and networks) in which interspecific relationships were largely unresolved. After excluding incomplete lineage sorting, hybridisation and oversaturation of characters as possible causes for lack of phylogenetic resolution, we conclude that the polytomy obtained most likely represents a hard polytomy. We hypothesize that diversification of Facchinia is best interpreted as the result of multiple simultaneous vicariance in response to climatic changes during the Early Quaternary.

ECO-physiological response of S. vulgaris to CR(VI): Influence of concentration and genotype

The objective of this work is to study the response of Silene vulgaris to a range of environmentally relevant concentrations of Cr(VI) in order to evaluate its potential use in the phytomanagement of Cr polluted sites. Cuttings of six homogenous genotypes from Madrid (Spain) have been used as plant material. The eco-physiological response of S. vulgaris to Cr(VI) changed with the genotype. The yield dose-response curve was characterized by stimulation at low doses of Cr(VI). The effects of metal concentration were quantified on root dry weight, water content and chlorophyll content, determined by SPAD index. The response was not homogeneous for all studied genotypes. At high doses of Cr(VI), plants increased micronutrient concentration in dry tissues which suggested that nutrient balance could be implicated in the alleviation of Cr toxicity. This work highlights the importance of studying the eco-physiological response of metallophytes under a range of pollutant concentrations to determine the most favorable traits to be employed in the phytomanagement process.

Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula

Petrocoptis is a small genus of chasmophytic plants endemic to the Iberian Peninsula, with some localized populations in the French Pyrenees. Within the genus, a dozen species have been recognized based on morphological diversity, most of them with limited distribution area, in small populations and frequently with potential threats to their survival. To date, however, a molecular evaluation of the current systematic treatments has not been carried out. The aim of the present study is to infer phylogenetic relationships among its subordinate taxa by using plastidial rps16 intron and nuclear internal transcribed spacer (ITS) DNA sequences; and evaluate the phylogenetic placement of the genus Petrocoptis within the family Caryophyllaceae. The monophyly of Petrocoptis is supported by both ITS and rps16 intron sequence analyses. Furthermore, time estimates using BEAST analyses indicate a Middle to Late Miocene diversification (10.59 Myr, 6.44-15.26 Myr highest posterior densities [HPD], for ITS; 14.30 Myr, 8.61-21.00 Myr HPD, for rps16 intron).

One-seeded fruits in the core Caryophyllales: their origin and structural diversity

The core Caryophyllales consist of approximately 30 families (12 000 species) distributed worldwide. Many members evolved one-seeded or conjoined fruits, but their origin and structural diversity have not been investigated. A comparative anatomical investigation of the one-seeded fruits within the core Caryophyllales was conducted. The origin of the one-seeded fruits and the evolutionary reconstructions of some carpological characters were traced using a tree based on rbcl and matK data in order to understand the ancestral characters and their changes. The one-seeded fruit type is inferred to be an ancestral character state in core Caryophyllales, with a subsequent increase in the seed number seen in all major clades. Most representatives of the ‘Earlier Diverging’ clade are distinguished in various carpological traits. The organization of the pericarp is diverse in many groups, although fruits with a dry, many-layered pericarp, consisting of sclerenchyma as outer layers and a thin-walled parenchyma below, with seeds occupying a vertical embryo position, are likely ancestral character states in the core Caryophyllales clade. Several carpological peculiarities in fruit and seed structure were discovered in obligate one-seeded Achatocarpaceae, Chenopodiaceae, Nyctaginaceae, Seguieriaceae and Sarcobataceae. The horizontal embryo evolved in only certain groups of Chenopodiaceae. The bar-thickening of endotegmen cells appears to be an additional character typical of core Caryophyllales. The syncarpy-to-lysicarpy paradigm in Caryophyllaceae needs to be reinterpreted.

A split G-quadruplex and graphene oxide-based low-background platform for fluorescence authentication of Pseudostellaria heterophylla

A label-free split G-quadruplex and graphene oxide (GO)-based fluorescence platform has been designed to distinguish Pseudostellaria heterophylla (PH) from its adulterants based on the differences in their nrDNA ITS sequences. Herein, GO has been first introduced to capture G-rich probes with 2:2 split mode and then decrease the background signal. As T-DNA exists, the probes leave the GO surface to form double-stranded structures followed by the formation of the overhanging G-rich sequence into a G-quadruplex structure, which combines quinaldine red specifically to produce a strong fluorescence signal. In addition, this strategy allows detection of T-DNA in a wide range of concentrations from 1.0 × 10⁻⁸ to 2.0 × 10⁻⁶ mol·L⁻¹ with a detection limit of 7.8 × 10⁻⁹ mol·L⁻¹. We hope that the split G-quadruplex/GO platform can be utilized to further develop gene identification sensors in Traditional Chinese Medicine or other analysis areas.

[Rapid molecular identification of pseudostellariae radix]

To establish a convenient and rapid method for identification of Pseudostellariae Radix by molecular identification, the rDNA-ITS sequences of Pseudostella riaheterophylla and its adulterants had been aligned to find out specific fragment. The specific primers against the fragment were designed and the PCR amplification conditions were optimized. The fluorescence reaction of the PCR products colored by 100 x SYBR Green I was observed under UV. The concentration of reaction buffer included 5.5 μL DNA Taq polymerase premix, 10 pmol Tzs-2F and 10 pmol Tzs-2R, 20-80 ng template DNA, and plus double sterile distilled water to 25 μL. The PCR thermal profile was as follows: predenaturation at 95 degrees C for 1 min, followed by 30 cycles of denaturation at 95 degrees C for 5 seconds, primer annealing and extension at 56 degrees C for 15 seconds, then it was extension at 72 degrees C for 30 seconds. The fluorescence reaction of Pseudostellariae Radix showed green fluorescence, while adulterants had not. Extraction, amplification DNA and all steps of molecular identification could be completed successfully in 40 minutes. The approach could amplify DNA template of Pseudostellariae Radix specificity, and its product with 1 μL 100 x SYBR Green I could engender green fluorescence under UV. The method was simple and accurate, so it could be used for identification of Chinese traditional medicine.

Taxonomy and pollen morphology of Ankyropetalum Fenzl (Caryophyllaceae) species in Türkiye

There are 4 species belong to Ankyropetalum Fenzl (Caryophyllaceae) genus and three of them (A. reuteri Boiss. and Hausskn, A. arsusianum Kotschy ex Boiss. and A. gypsophiloides Fenzl) are distributed in Turkey. There are doubts about taxonomical studies depending on only morphological characteristics. This study has been made to put forth that palinological studies also contribute taxonomical studies. Pollen morphology of the three species belong to Ankyropetalum Fenzl (Caryophyllaceae) genus distributed in Turkey examined with ray microscope and electron microscope in this study. Results evaluated according to Duncan's multiple range test using SPSS statistic program. Pollen's polar and ecvatoral seeming photographs were taken in preparates. Morphology of pollens examined with 50 repetition for each taxon and morphological assessments were made. The common trait of pollens can be summarized as they are circular, oblate and prolate spheroidal, periporate (pore numbers ranged between 20-33), operculum is granulated, annulus is distinct, the form of pollens are tectat. Definition of pollens are given for each taxon, diagnostic specifications recognized as important are used for making diagnosis key. The difference between species are as below: A. arsusianum's pollen shape is oblate-spheroidal, type of pollen is periporate, pore numbers are between 23-33, form of pollen is tectat, ornamentation is perforate. A. reuteri's pollen shape is prolate-spheroidal, type of pollen is periporate, pore numbers are between 20-33, form of pollen is tectat, ornamentation is from perforate to eureticulate A. gypsophiloides pollen shape is oblate-spheroidal, type of pollen is periporate, pore numbers are between 21-30, form of pollen is tectat, ornamentation is perforate.

Measure for measure: comparing morphological and biomass traits for sex allocation in two gynodioecious species

PREMISE OF THE STUDY

Sex allocation models assume male and female traits are measured in a common currency, allocation traits show heritability, and tradeoffs between investment in the two sexual functions occur. The potential for model predictions and genetic parameters to depend on the currency used is not well understood, despite frequent use of measures not in a common currency. •

METHODS

We analyzed the relationship between common currency (biomass of carpels, seeds, and stamens) measures and morphological measures (numbers of ovules, seeds, and pollen) in Schiedea salicaria (12-13% females) and S. adamantis (39% females), two closely related gynodioecious species. Additionally, we compared heritabilities and genetic correlations for male and female allocation between these two types of measures. •

KEY RESULTS

Ovule, seed, and pollen number show greater sexual dimorphism in S. adamantis than in S. salicaria. Most but not all morphological traits and analogous biomass traits are highly correlated with a linear relationship. Narrow-sense heritabilities based on the two methods are often similar, but higher for ovule number than carpel mass and lower for anther number than stamen mass in S. adamantis. Neither trait type shows negative genetic correlations between male and female function. •

CONCLUSIONS

Both trait types show greater sexual dimorphism in S. adamantis, and significant heritabilities suggest that morphological traits will continue to evolve with breeding system changes. Although most relationships between morphological and biomass traits are linear, curvilinear relationships for two traits suggest that caution is warranted if morphological and common currency traits are used interchangeably in fitness gain curves.

Molecular adaptation during a rapid adaptive radiation

"Explosive" adaptive radiations on islands remain one of the most puzzling evolutionary phenomena and the evolutionary genetic processes behind such radiations remain unclear. Rapid morphological and ecological evolution during island radiations suggests that many genes may be under fairly strong selection, although this remains untested. Here, we report that during a rapid recent diversification in the Hawaiian endemic plant genus Schiedea (Caryophyllaceae), 5 in 36 studied genes evolved under positive selection. Positively selected genes are involved in defence mechanisms, photosynthesis, and reproduction. Comparison with eight mainland plant groups demonstrates both the relaxation of purifying selection and more widespread positive selection in Hawaiian Schiedea. This provides compelling evidence that adaptive evolution of protein-coding genes may play a significant role during island adaptive radiations.

[Accurate identification of Psammosilene tunicoides and its confused species by systematic identification method]

OBJECTIVE

To develop an effective identification method for accurately discriminating Psammosilene tunicoides and its confused species by the combined method of microscopic identification and molecular identification, so-called systematic identification of Chinese materia medica (SICMM).

METHOD

P. tunicoides and its confused species were accurately discriminated by SICMM method, which was established by comprehensively use of microscopic identification and DNA identification method. The DNA identification included the following analysis: the BLAST alignment, specific bases and N-J phylogenetic tree analysis.

RESULT

The cluster crystals were not observed in P. tunicoides, but great deals of them were found in Silene viscidula. Further more, big differences of ITS sequence were observed and analyzed between P. tunicoides and its confused specie of S. viscidula.

CONCLUSION

The system method is a scientific and accurate method for the identification of P. tunicoides and its counterfeit species.

[Ribosomal DNA ITS sequence of analysis of Psammosilene tunicoides from different populations]

OBJECTIVE

To analyze the ribosomal ITS sequence variation of Psammosilene tuncolides W. C. Wu et C. Y. Wu from different populations, for identifying different local populations.

METHODS

A pair of primers of 18SP1 and 26SP2 with PCR technique had been applied to study the ITS sequences.

RESULTS

The sequences of ITS1, ITS2 and 5.8S are 225-229 bp, 166-170 bp and 261-264 bp. Among 12 local populations, the sequence of Kunming, Lijiang, Gejiu, Heqing of Yunnan and Yanyuan of Sichuan showed no variation, there were 1-4 variable sites (including 5.8S coding region) in pairwise comparison of the other 7 local populations, including Xuanwei, Huize, Zhongdian, Baoshan of Yunnan, Muli of Sichuan and Linzhi of Tibet.

CONCLUSION

Comparative analysis shows that the ITS sequences of different local populations in the middle of Yunnan, southwest of Sichuan and west, northwest of Yunnan, southeast of Tibet, southwest of Sichuan have different fingerprint character, so the ITS sequences can be used to identify different local populations. The variation of ITS sequence of Psammosilene tunicoides is related to its geographical distribution.

Molecular adaptation during adaptive radiation in the Hawaiian endemic genus Schiedea

BACKGROUND

"Explosive" adaptive radiations on islands remain one of the most puzzling evolutionary phenomena. The rate of phenotypic and ecological adaptations is extremely fast during such events, suggesting that many genes may be under fairly strong selection. However, no evidence for adaptation at the level of protein coding genes was found, so it has been suggested that selection may work mainly on regulatory elements. Here we report the first evidence that positive selection does operate at the level of protein coding genes during rapid adaptive radiations. We studied molecular adaptation in Hawaiian endemic plant genus Schiedea (Caryophyllaceae), which includes closely related species with a striking range of morphological and ecological forms, varying from rainforest vines to woody shrubs growing in desert-like conditions on cliffs. Given the remarkable difference in photosynthetic performance between Schiedea species from different habitats, we focused on the "photosynthetic" Rubisco enzyme, the efficiency of which is known to be a limiting step in plant photosynthesis.

RESULTS

We demonstrate that the chloroplast rbcL gene, encoding the large subunit of Rubisco enzyme, evolved under strong positive selection in Schiedea. Adaptive amino acid changes occurred in functionally important regions of Rubisco that interact with Rubisco activase, a chaperone which promotes and maintains the catalytic activity of Rubisco. Interestingly, positive selection acting on the rbcL might have caused favorable cytotypes to spread across several Schiedea species.

SIGNIFICANCE

We report the first evidence for adaptive changes at the DNA and protein sequence level that may have been associated with the evolution of photosynthetic performance and colonization of new habitats during a recent adaptive radiation in an island plant genus. This illustrates how small changes at the molecular level may change ecological species performance and helps us to understand the molecular bases of extremely fast rate of adaptation during island adaptive radiations.

[Growth comparison among Psammosilene tunicoides populations in tissue culture]

The comparison between the growth of eight populations from Psammosilene tunicoides at Yunnan Province was made by the tissue culture. The initial results showed out two populations from Yunshanping (Lijiang) and Xiaomoyu (Kunming) was dominant than orthers. It would be regard as one of fine germplasm resources for the culture of Psammosilence tunicoides.

Distribution of phytoecdysteroids in the Caryophyllaceae

Certain genera within the Caryophyllaceae (especially Silene and Lychnis) have received a significant amount of attention with regard to the isolation and identification of ecdysteroids. However, the taxonomy of this family is difficult. Hence, the occurrence of phytoecdysteroids in members of the Caryophyllaceae is presented, and combined with new data on ecdysteroid agonist (phytoecdysteroid) and antagonist activities, in order to survey the distribution of phytoecdysteroid-containing species within this large family, and to assess the utility of phytoecdysteroids as chemotaxonomic markers. The new data presented (representing ca. 110 species) have been obtained by the application of sensitive biological/biochemical methods for the detection of ecdysteroid agonists and antagonists, using Drosophila melanogaster B(II) bioassay and ecdysteroid-specific immunoassays. In the antagonist version of the B(II) bioassay, only weak ecdysteroid antagonist activities were detected in a few of the extracts. From both new and previously available data, it was found that phytoecdysteroids were present predominantly in the Genera Lychnis, Petrocoptis, Sagina and Silene. Comparison of ecdysteroid occurrence with a molecular phylogeny for the tribe Sileneae [Taxon 44 (1995) 525] revealed close association of ecdysteroid occurrence with certain groups of this tribe. In 14 species of Silene examined, there is a reasonable, but not absolute, relationship between the presence of ecdysteroids in the seeds and in other plant parts. Where ecdysteroids are present in the plant, highest concentrations are generally present in the roots.

[A revision of species and distribution of medicinal plants in Guizhou Province]

OBJECTIVE

To reconfirm the medicinal plants of Aristolochiaceae, Caryophyllaceae, Menispermaceae, Illiciaceae and Magnoliaceae found in Guizhou Province.

METHODS

Making a textual research on the Latin names and geographical distribution of medicinal plants recorded in <<Medicinal Material Resources of Guizhou>>.

RESULT

Of the above-cited medicinal plants 27 species are absent in Guizhou Province, 21 species and 2 varieties misnamed in Latin, and 8 species newly supplemented.

CONCLUSION

At present in Guizhou Province there are 22 species and 2 varieties of Aristolochiaceae, 29 species, 1 variety and 1 subspecies of Caryophyllaceae, 23 species and 2 varieties of Menispermaceae, 7 species of Illiciaceae, and 24 species and 1 subspecies of Magnoliaceae.

[Studies on identification of yinchaihu by UV and IR]

OBJECTIVE

To study the identification of nine species of Yinchaihu derived from four genera of Caryophyllaceae, namely, Stellaria dichotoma var. lanceolata, St. dichotoma var. dichotoma, Arenaria juncea, A. capillaris var. glandulifera, Silene fortunei, Si. jenisseensis, Gypsophila pacifica, G. oldhamiana and G. licentiana.

METHOD

UV and IR of alcohol extraction.

RESULTS

The UV and IR spectra of these 9 plant roots have some difference.

CONCLUSION

St. dichotoma var. lanceolata specified in the Chinese Pharmacopoeia can be distinguished from the other plants and all these 4 genera can be differentiated from one another by both UV and first derivative spectra. The genus Stellaria can be identified from the other 3 genera by IR.

[Ultra-morphological study on the surface of the stem and leaf of the original plant of herba Dianthi in Shandong]

Ultra-morphology of 4 spieces and 2 varities of the original plant of Herba Dianthi grown in Shandong was identified with SEM. The result showed that they were aparently divided into the Shizhu group and the Qumai group, and the Dianthus shandongensis was between the two groups, on the basis of the cutin-grain type of the epidermis of the stem and leaf as well as the surface of the guard cell of the stoma.