Orientalis Roots Research Articles

Full-Length Transcriptome Assembly of Platycladus orientalis Root Integrated with RNA-Seq to Identify Genes in Response to Root Pruning

Platycladus orientalis (P. orientalis) is a common tree used for vegetation restoration in northern China, and its large area propagation helps to improve site conditions. However, under harsh conditions such as poor land, the survival rate of P. orientalis is very low. Numerous studies have shown that root pruning can promote the formation of lateral roots in seedlings, enhancing the roots’ capacity to absorb soil nutrients and water, and thereby improving the survival rate of seedlings. In this study, a one-third root pruning treatment was applied to P. orientalis seedlings, and the whole transcriptome of seedlings subjected to both control (CK) and root pruning treatments was sequenced to analyze their gene expression profiles. This study investigated the regulatory mechanisms of lateral root development in response to root pruning damage at the molecular level. Using nine cells, 15.28 Gb of clean data were obtained, which yielded 101,688 high-quality full-length transcript sequences and 22,955 low-quality full-length transcript sequences after clustering. Redundancy was then removed using CD-HIT, and Illumina RNA-seq sequencing produced 139.26 Gb of clean data. A total of 2025 differentially expressed genes (DEGs) were identified at three time points following root pruning treatment. Enrichment analysis revealed that the peroxidase gene family plays a significant role in lateral root proliferation. Furthermore, the expression levels of the peroxidase gene family were notably upregulated in comparison to the control group. Pathway enrichment analysis identified 22 relevant genes, which appeared to be highly associated with root growth and resilience to stress. Through examining the expression patterns and correlations of these genes, five central genes emerged as key players. The findings of this research suggest that the peroxidase gene family plays a crucial role in the stress response and root development of P. orientalis, providing reference and guidance for root development in other plant species.

Clinical assessment of an ointment obtained from Alkanna orientalis root extract in the management of burn wounds: a pilot cross-sectional clinical trial

Clinical assessment of an ointment obtained from Alkanna orientalis root extract in the management of burn wounds: a pilot cross-sectional clinical trial

Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development.

Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.

Precursor genes of Bowman-Birk-type serine proteinase inhibitors comprise multiple inhibitory domains to promote diversity

BackgroundProteinase inhibitors are important for the regulation of the activity of enzymes essential for the survival and maintenance of all organisms, and they may hold medicinal and agricultural value. Hyacinthus orientalis L. serine protease inhibitors (HOSPIs), belonging to the Bowman–Birk type inhibitor (BBI) family, have strong inhibitory activities against mammalian serine proteinases. This study explored the relationship between gene structure and multiple isoinhibitor production of these diversified BBIs by analyzing sequences of HOSPI precursor genes. MethodsGenomic DNA of H. orientalis roots was obtained and fragmented using 13 specific restriction enzymes, which were amplified by inverse and nested polymerase chain reactions, cloned into the pBluescript II SK (+) vector, and directly sequenced using specific primers. HOSPI gene and protein expression were assessed by quantitative real-time PCR and western blot, respectively. Proteinase inhibitory activity of hyacinth bulb extracts was evaluated by fluorescein isothiocyanate-labeled casein. ResultsFour distinct HOSPI precursor genes were identified, encoding 2–4 different HOSPI domains that were surrounded by additional sequences (named head, linker, and tail sequences) and some introns. Moreover, 3′ splicing of the linker sequence may occur through introns inserted between linker sequences. HOSPI gene and protein expression was higher during the stem elongation and the flowering periods. ConclusionsThese results indicate that gene duplication of the HOSPI precursor as a single set, including tandem repeated HOSPI domains, leads to diversity and effective production of mature HOSPIs by posttranslational processing. General significanceThese findings shed light on the diversity of proteinase inhibitors.

Isolation and high-performance liquid chromatography analysis of chettaphanin I in extracts from Cladogynos orientalis roots

Isolation and high-performance liquid chromatography analysis of chettaphanin I in extracts from Cladogynos orientalis roots

Transcriptome analysis revealed cadmium accumulation mechanisms in hyperaccumulator Siegesbeckia orientalis L.

Siegesbeckia orientalis L. was identified as a novel Cd-hyperaccumulator and valuable phytoremediation material. However, the molecular mechanisms underlying Cd accumulation in S. orientalis are largely unknown. In this study, RNA-Seq analysis was performed to study the Cd-accumulating mechanisms in its roots with or without Cd treatment. The RNA-seq analysis generated 312 million pairs of clean reads and 78G sequencing data. De novo transcriptome assembly produced 355,070 transcripts with an average length of 823.59 bp and 194,207 unigenes with an average length of 605.68 bp. Comparative transcriptome analyses identified a large number of differentially expressed genes in roots under Cd stress, and functional annotation suggested that S. orientalis utilizes various biological pathways involving many gene networks working simultaneously to cope with the stress. This study revealed that four biological pathways were mainly involved in S. orientalis tolerance to Cd stress, including reactive oxygen species scavenging, phenylpropanoid biosynthesis pathway, Cd absorption and transport, and ABA signaling pathway. The genes related to photosynthesis and heavy metal transport are likely the potential candidates and could be further investigated to determine their roles in Cd tolerance in S. orientalis roots. These findings will be useful to understand the Cd accumulation mechanisms in S. orientalis and facilitate the study of phytoremediation at the molecular level in plants.

Mechanical Characteristics of the Fine Roots of Two Broadleaved Tree Species from the Temperate Caspian Hyrcanian Ecoregion

In view of the important role played by roots against shallow landslides, root tensile force was evaluated for two widespread temperate tree species within the Caspian Hyrcanian Ecoregion, i.e., Fagus orientalis L. and Carpinus betulus L. Fine roots (0.02 to 7.99 mm) were collected from five trees of each species at three different elevations (400, 950, and 1350 m a.s.l.), across three diameter at breast height (DBH) classes (small = 7.5–32.5 cm, medium = 32.6–57.5 cm, and large =57.6–82.5 cm), and at two slope positions relative to the tree stem (up- and down-slope). In the laboratory, maximum tensile force (N) required to break the root was determined for 2016 roots (56 roots per each of two species x three sites x three DBH classes x two slope positions). ANCOVA was used to test the effects of slope position, DBH, and study site on root tensile force. To obtain the power-law regression coefficients, a nonlinear least square method was used. We found that: 1) root tensile force strongly depends on root size, 2) F. orientalis roots are stronger than C. betulus ones in the large DBH class, although they are weaker in the medium and small DBH classes, 3) root mechanical resistance is higher upslope than downslope, 4) roots of the trees with larger DBH were the most resistant roots in tension in compare with roots of the medium or small DBH classes, and 5) the root tensile force for both species is notably different from one site to another site. Overall, our findings provide a fundamental contribution to the quantification of the protective effects of forests in the temperate region.

Transcriptome -wide modulation combined with morpho-physiological analyses of Typha orientalis roots in response to lead challenge

Lead (Pb) is a common pollutant in many environments, including in the soil, water, and/or air. Typha orientalis Presl, a large emergent aquatic plant, has been reported to function as a Pb-tolerant and Pb-accumulating plant; however, very little molecular information regarding the tolerance of T. orientalis towards Pb is known. In this study, Pb accumulation and key factors involved in the Pb stress response at different Pb concentrations were investigated. Pb was primarily accumulated in the roots and was mainly located in the cell wall and membrane systems. Differentially expressed genes (DEGs) were identified in T. orientalis roots after Pb exposure via RNA-seq analyses. In the 0.10 mM and 0.25 mM Pb2+-treated groups, a total of 3275 DEGs were detected relative to the control. Many of these genes were associated with oxidation-reduction processes, metal transport, protein kinase/phosphorylation, and DNA binding transcription factors, which were shown to be Pb-responsive DEGs. Mapping Kyoto Encyclopedia of Genes and Genomes (KEGG) database, “phenylpropanoid biosynthesis” was analyzed as the major pathway of the important modules of overlapping DEGs of 0.10 mM and 0.25 mM Pb2+ treatments. Furthermore, a lead response gene named ToLR1 with unknown function was of particular interest. The full-length of ToLR1 sequence was cloned using rapid amplification of cDNA ends (RACE) and overexpressed in Arabidopsis thaliana, which resulted in enhanced resistance to Pb stress. This is the first report providing genomic information detailing Pb responsive genes in T. orientalis. Moreover, this study provides novel insights into the molecular mechanisms underlying the response of T. orientalis and other accumulators towards Pb stress. The key genes identified in this study may serve as potential targets for genetic engineering targeting phytoremediation.

Isolation of phenylpropanoid sucrose esters from the roots of Persicaria orientalis and their potential as inhibitors of melanogenesis

Cosmetically, hyperpigmentation is an important issue and the most prominent target for inhibiting hyperpigmentation is, tyrosinase, the rate-limiting enzyme in melanogenesis. Therefore, in this research, we have screened several medicinal plants collected from Bangladesh for their anti-tyrosinase activity and found that roots of Persicaria orientalis have potent inhibitory activity. Nine compounds, including five phenylpropanoid sucrose esters (1–5), were isolated from the EtOH extract of P. orientalis roots. The chemical structures were determined based on spectroscopic methods. All the tested compounds (1–5), significantly reduced extracellular melanin formation in B16 melanoma cells and inhibited tyrosinase monophenolase and diphenolase activity in a dose dependent manner. Compound 4 was twice as effective as kojic acid, when l-DOPA was used as the substrate. Compound 1 and 4 showed better inhibitory activity (>59%) on melanin synthesis at a treated concentration of 50 µM compare with arbutin (730 µM). At 6.25 µM concentration, compounds 2 and 5, inhibited extracellular melanin production by 53.1% and 40.2%, respectively. Structure-activity-relationship suggested that both the feruloyl (C-6′) and acetyl (C-2′/ C-4′) groups in sucrose moiety is essential for cytotoxicity. Our finding indicated the roots of P. orientalis is a potential source of natural compounds that could be used in dermatological and cosmetological research. To the best of our knowledge, this is the first study to report the potential melanogenesis inhibitory activity of phenylpropanoid sucrose esters.

Response to cadmium and phytostabilization potential of Platycladus orientalis in contaminated soil

The tolerance characteristics and phytostabilization potential of Platycladus orientalis grown in soil contaminated by cadmium (Cd) were studied using a greenhouse experiment. The results showed that the ornamental plant P. orientalis had high tolerance for Cd in contaminated soil at 24.6 mg·kg−1 and its physiological activities were slightly affected after 203 days (d) of cultivation. Moreover, Cd in soil at 9.6 mg·kg−1 was beneficial for P. orientalis growth, and the total biomass after 203 d cultivation was significantly (p < 0.05) increased by 35.03%, while the contents of chlorophyl a, chlorophyl b and carotenoid in leaves also increased by 20.84%, 44.06% and 28.25% compared to the control, respectively. Meanwhile, the Cd content in the tissues of P. orientalis was increased with both plant growth and the Cd content in the soil. The uptake of Cd in P. orientalis roots was greater than in shoots, with the Cd content in roots reaching 41.45 mg·kg−1. P. orientalis, an ornamental plant, that accumulates Cd predominantly in its roots, can be suggested as a promising plant for phytostabilization in Cd-contaminated soil.

Responses of Typha orientalis Roots to Pb2+ Stress

To investigate phytoremediation potential of Typha orientalis Presl in removing Pb2+ from polluted water, relevant experiments were conducted to evaluate responses activated by Pb2+ (0.25–2 mM) in T. orientalis roots over a period of ten days. Pb contents in subcellular fractions decreased in the following order: cell wall > organelle > soluble fraction. Most of Pb was located in cell wall and membrane system. Contents of K and Ca declined in T. orientalis roots under Pb2+ stress, but an opposite effect was noted for some mineral elements (Mg, Cu, Zn, and Fe). H2O2 level increased in a concentration-dependent manner, which induced oxidative stress. However, significant reduction in levels of O 2 ·− and malondialdehyde (MDA) were observed in all Pb2+ treatment groups. Findings indicated toxicity of Pb2+ to T. orientalis in terms of inducing oxidative stress and causing imbalance in mineral elements. However, T. orientalis also resisted Pb2+-induced damage through isolation mechanism, which involves cell wall and membrane systems.

Investigation of Dyeing Properties of Different Fabric Species with Alkanna Orientalis Root Extract

Investigation of Dyeing Properties of Different Fabric Species with Alkanna Orientalis Root Extract

Root transcriptome sequencing and differentially expressed drought-responsive genes in the Platycladus orientalis (L.)

Platycladus orientalis (L.) is used extensively for afforestation and is a common medicinal ingredient. Because of its drought tolerance, P. orientalis is widely used for afforestation in arid and semi-arid areas. To better understand the mechanisms involved in drought-stress tolerance in this important tree, the transcriptome profiles of drought-treated P. orientalis seedlings were analyzed using Illumina technology, and differentially expressed genes (DEGs) between drought-treated and well-watered trees were identified. We performed transcriptome sequencing of P. orientalis roots using the Illumina 4000 paired-end sequencing technique. More than 53 million 151-bp paired-end clean reads were obtained from each of the cDNA libraries and biological replicates, and de novo assembly generated 148,392 unigenes with an average length of 927.77 bp. After removing contaminating sequences, we found that 29.9 % (34,845) of the unigenes exhibited significant similarity to known sequences in the GenBank non-redundant protein database. A total of 3930 unigenes were found to be significantly differentially expressed between drought-treated and well-watered trees. Among them, 881 (22.42 %) were up-regulated and 3049 (77.58 %) were down-regulated in roots. Several DEGs had known functions in categories related to the biosynthesis of secondary metabolites, phenylalanine metabolism, starch and sucrose metabolism, and arginine and proline metabolism. A total of 194 genes that were found to be differentially regulated in response to drought stress were categorized as transcription factors. The transcriptome profiles obtained provide a valuable resource for future research to understand the molecular adaptation of Cupressaceae plants under drought condition and facilitate the exploration of drought-tolerant candidate genes.

Response characteristics of soil water use patterns by different plants to precipitation in rocky mountainou areas.

Water-use characteristics of plants are important for vegetation restoration in shallow earth-rock mountain area. In this study, soil and plant samples of Platycladus orientalis and corn were collected after rainfall events in Yingwugou watershed of Dan River to analyze the signatures of oxygen isotopes and the response of water use patterns to precipitation using stable isotope technology. The results showed that there were different response characteristics of the soil water utilization to precipitation between P. orientalis and corn. The root of P. orientalis mainly used the soil moisture from 10-30 cm layer, while corn mainly used that in the depth of 0-20 cm. The water absorption depth (WAP) of P. orientalis root decreased from 20-30 cm to 10-20 cm, while that of corn altered from 10-20 cm to 0-20 cm, when precipitation decreased from 29 mm to 8 mm. The WAP of P. orientalis gradually changed from deep to shallow soil, while the main WAP of corn increased from 10-20 cm to 0-20 cm, whenprecipitation decreased. The response of P. orientalis and corn to precipitation was very obvious.

The structure of fungal population from Galega orientalis root system formed as the result of fertilization

The composition of the fungal population colonizing the rhizosphere, the rhizoplane and the roots of &lt;i&gt;Galega orientalis&lt;/i&gt; Lam. plants was studied. The following factors had an influence on the quantity and the composition of the species: fertilization, the analysed root zone and the date of the completed analyses.

Antibacterial and anti-inflammatory effects of Jeju medicinal plants against acne-inducing bacteria

Propionibacterium acnes and Staphylococcus epidermidis are pus-forming bacteria that trigger inflammation in acne. The present study was conducted to evaluate the antimicrobial activities of Jeju medicinal plants against these etiologic agents of acne vulgaris. Ethanol extracts of Jeju plants were tested for antimicrobial activities by disc diffusion and broth dilution methods. The results from the disc diffusion assays revealed that four medicinal plants, Mollugo pentaphylla, Angelica anomala, Matteuccia orientalis, and Orixa japonica inhibited the growth of both pathogens. Among these, A. anomala had strong inhibitory effects. Its MIC values were 15.6 microg/ml and 125 microg/ml against P. acnes and S. epidermidis, respectively. The cytotoxic effects of the four extracts were determined by colorimetric MTT assays using two animal cell lines: human dermal fibroblasts and HaCaT cells. Although the M. orientalis root extract had moderate cytotoxicity in HaCaT cells at 200 microg/ml, most extracts exhibited low cytotoxicity at 200 microg/ml in both cell lines. In addition, the extracts reduced the P. acnes-induced secretion of interleukin-8 and tumor necrosis factor-alpha (TNF-alpha) in THP-1 cells, an indication of their anti-inflammatory effects. Based on these results, we suggest that M. pentaphylla, A. anomala, M. orientalis, and O. japonica are attractive acne-mitigating candidates for topical application.

Anti-inflammatory and antinociceptive activity assessment of plants used as remedy in Turkish folk medicine

Ethanolic and aqueous extracts from seven plant species used in Turkish traditional medicine were evaluated for in vivo anti-inflammatory and antinociceptive activities; Helleborus orientalis Lam. roots and herbs, Juglans regia L. leaves, Laurocerasus officinalis Roemer leaves, Nerium oleander L. dried and fresh flowers and leaves, Rhododendron ponticum L. leaves, Rubus hirtus Walds. et Kit aerial parts and Rubus sanctus Schreber aerial parts and roots. All the plant extracts, except the aqueous extract of Rubus hirtus, were shown to possess significant antinociceptive activity in varying degrees against p-benzoquinone-induced abdominal contractions in mice. However, only the ethanolic extracts of Helleborus orientalis roots, Juglans regia leaves, Laurocerasus officinalis leaves, Nerium oleander dried and fresh flowers, and Rhododendron ponticum leaves exhibited potent anti-inflammatory activity against carrageenan-induced hind paw edema model in mice without inducing any gastric damage. Results of the present study confirmed the folkloric claim that all the selected materials to possess potent antinociceptive and anti-inflammatory activity.

Activation of the nodA promoter by the nodD genes of Rhizobium galegae induced by synthetic flavonoids or Galega orientalis root exudate

Rhizobial nodD genes produce transcriptional regulators that, together with appropriate inducer compounds, activate the other symbiotic nodulation ( nod) genes and initiate the nodule formation process. Two nodD homologues, nodD1 and nodD2, are present in the Rhizobium galegae strain HAMBI 1174. In this work we analysed their ability to induce the nodA promoter with synthetic inducers known to activate nod genes in other rhizobia. According to phylogenetic analysis, the inducer-specific carboxy-terminal part of the R. galegae nodD protein sequence groups together with those of Rhizobium leguminosarum and Sinorhizobium meliloti. However, the respective inducer compounds for their NodD proteins are not highly effective with R. galegae nodD products. The best inducer discovered with R. galegae nodD1 was the root exudate of the host plant of R. galegae, Galega orientalis. HPLC analyses revealed the presence of many divergent flavonoid compounds in the G. orientalis root exudate. The most effective HPLC fractions induced R. galegae nodD1 up to the level obtained by intact G. orientalis root exudate while apigenin and luteolin, which were also present in the root exudate, were only moderate inducers. A UV-Vis diode array spectrum of the most active peak indicated that the main inducer present in the G. orientalis root exudate is an unidentified chalcone-type compound. In the Galega– R. galegae interaction the first recognition between the NodD protein and the flavonoid inducer secreted from the roots of Galega is specific for these organisms, and thus partly responsible of the strict host specificity of this symbiosis.

Inhibitory effects of Turkish folk remedies on inflammatory cytokines: interleukin-1 α, interleukin-1 β and tumor necrosis factor α

In this study, in vitro inhibitory effects of 55 extracts or fractions obtained from 10 plant species on interleukin-1 (IL-1 α, IL-1 β) and tumor necrosis factor (TNF- α) biosynthesis were studied. The following plant materials from Turkish folk medicine for the treatment of various diseases which are thought to be inflammatory in nature e.g. rheumatism, fever, infections, edemas or related inflammatory diseases were selected as the subject of this study: Cistus laurifolius leaves, Clematis flammna flowering herbs, Crataegus orientalis roots, Daphne oleoides ssp. oleoides whole plant, Ecbalium elaterium roots, Rosa canina roots, Rubus discolor roots, Rubus hirtus roots, Sambucus ebulus flowers and leaves, Sambucus nigra flowers and leaves. All plants showed inhibitory activity against at least one of these models in various percentages depending upon the concentration, thus supporting the folkloric utilization. Daphne oleoides was found to be the most active plant against the test models.