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Animal Models and Experimental Medicine Jul 2024Complementary medicine is an interesting field for extracting bioactive compounds from various plant and animal sources. The hepatoprotective effect of the methanolic...
BACKGROUND
Complementary medicine is an interesting field for extracting bioactive compounds from various plant and animal sources. The hepatoprotective effect of the methanolic extract of a species of sea cucumber called Holothuria leucospilota in an animal model of liver cancer caused by dimethyl nitrosamine (DMN) was studied.
METHODS
Wistar female rats were randomly divided into five groups (n = 12): control (intact), positive control (received 1% DMN [10 mg/kg/week, intraperitoneally] for 12 weeks), and three treatment groups (received 50, 100, and 200 mg/kg/day H. leucospilota extract orally for 12 weeks along with intraperitoneal administration of 1% DMN [10 mg/kg/week]). In all groups, ultrasound was performed on the liver every week to check its density. Blood sampling and liver isolation were performed on three occasions, at 4, 8, and 12 weeks, to check liver enzymes and the histopathological condition of the liver tissue (every week, four animals from each group were randomly selected).
RESULTS
Liver density changes were evident from the eighth week onward in the positive control group. Histopathological results indicated pathologic changes in the positive control group after 4 weeks. The increase in liver enzymes in the positive control group was significantly different from that in the treatment and control groups.
CONCLUSIONS
We demonstrated the hepatoprotective effect of H. leucospilota on DMN-induced liver damage in rats using biochemical and histological parameters and ultrasonography. More additional research (in silico or in vitro) is needed to find the exact mechanism and the main biological compound in H. leucospilota.
PubMed: 38949064
DOI: 10.1002/ame2.12451 -
Biochemistry Research International 2024The plant has been utilized in folk medicine. Analyzing phytochemical composition of dichloromethane/methanol (1 : 1) root part of gave oleic acid (), caffeic...
The plant has been utilized in folk medicine. Analyzing phytochemical composition of dichloromethane/methanol (1 : 1) root part of gave oleic acid (), caffeic acid-2-hydroxynonylester (), catechin (), and a pregnane derivative (). NMR spectroscopy was used to characterize compounds , while compound was identified through GC-MS analysis and literature comparison. The cytotoxicity of extracts from roots of was conducted against MCF-7 cell lines (human breast cancer) by MTT assay. According to the cytotoxicity study, -hexane extract exhibited a high level of toxicity with 28.9 ± 5.6% cell viability. Antibacterial activity was tested against , , , and The highest bacterial growth mean inhibition zone was measured for catechin (3) (13.72 ± 0.05 mm)) against at 0.25 mg/mL and acceptable related to standard. Antioxidant activity was studied by the DPPH assay. Based on the data from the antioxidant study, DCM/MeOH extract (70.32%) and catechin () showed good antioxidant activity (65.61%) (IC 0.25 g/mL) relative to that of the positive control (78.21%, IC 0.014 g/mL) at 12.5 g/mL. In each docking pose, catechin () scored higher binding affinity of -7.9, -7.2, and -6.4 kcal/mol towards PqsA, DNA gyraseB, and PK, respectively, compared to amoxicillin (-8.1, -6.1, and -6.4 kcal/mol). All five Lipinski rules were obeyed by compounds , which showed an acceptable drug resemblance. The lipophilicity was computed as less than five (1.47-4.01) indicating a lipophilic property. Catechin () obeys Veber's rule implying its good oral bioavailability. Binding affinity scores of catechin ()-protein interactions are in line with those from tests, indicating its potential antibacterial effect. The obtained cytotoxicity and antibacterial activity results support the utilization of in folk medicine.
PubMed: 38948887
DOI: 10.1155/2024/3713620 -
Evolutionary Applications Jul 2024Landscape genomic analyses associating genetic variation with environmental variables are powerful tools for studying molecular signatures of species' local adaptation...
Landscape genomic analyses associating genetic variation with environmental variables are powerful tools for studying molecular signatures of species' local adaptation and for detecting candidate genes under selection. The development of landscape genomics over the past decade has been spurred by improvements in resolutions of genomic and environmental datasets, allegedly increasing the power to identify putative genes underlying local adaptation in non-model organisms. Although these associations have been successfully applied to numerous species across a diverse array of taxa, the spatial scale of environmental predictor variables has been largely overlooked, potentially limiting conclusions to be reached with these methods. To address this knowledge gap, we systematically evaluated performances of genotype-environment association (GEA) models using predictor variables at multiple spatial resolutions. Specifically, we used multivariate redundancy analyses to associate whole-genome sequence data from the plant L. collected across four neighboring valleys in the western Swiss Alps, with very high-resolution topographic variables derived from digital elevation models of grain sizes between 0.5 m and 16 m. These comparisons highlight the sensitivity of landscape genomic models to spatial resolution, where the optimal grain sizes were specific to variable type, terrain characteristics, and study extent. To assist in selecting variables at appropriate spatial resolutions, we demonstrate a practical approach to produce, select, and integrate multiscale variables into GEA models. After generalizing fine-grained variables to multiple spatial resolutions, a forward selection procedure is applied to retain only the most relevant variables for a particular context. Depending on the spatial resolution, the relevance for topographic variables in GEA studies calls for integrating multiple spatial scales into landscape genomic models. By carefully considering spatial resolutions, candidate genes under selection by a more realistic range of pressures can be detected for downstream analyses, with important applied implications for experimental research and conservation management of natural populations.
PubMed: 38948540
DOI: 10.1111/eva.13737 -
Mycobiology 2024Eritadenine from shiitake mushroom is a secondary metabolite with hypocholesterolemic, hypotensive and antiparasitic properties, thus promising for pharmaceutical and...
Enhancing Eritadenine Production in Submerged Cultures of Shiitake ( Berk. Pegler) Using Blue LED Light and Activated Charcoal. Revealing Eritadenine's Novel In Vitro Bioherbicidal Activity Against .
Eritadenine from shiitake mushroom is a secondary metabolite with hypocholesterolemic, hypotensive and antiparasitic properties, thus promising for pharmaceutical and agricultural applications. Eritadenine is obtained from submerged mycelial cultures of shiitake, but the actual yields remain unsatisfactory to explore potential applications or industrial-scale production. In this study, green and blue LED lights were tested to increase yields of eritadenine in submerged cultures of shiitake. Notably, blue LEDs increased yields by 13-14 times, reaching 165.7 mg/L, compared to darkness (11.2 mg/L) and green light (12.1 mg/L) ( < 0.05, Tukey test). Nitrogen sources yeast extract (YE) and peptone (at 2 g/L) increased eritadenine production. YE promoted 22.6 mg/L, while peptone 18.3 mg/L. The recovery of eritadenine was evaluated using amberlite and activated charcoal (AC) adsorption isotherms. AC demonstrated the highest adsorption rate, with 75 mg of eritadenine per gram of AC, according to the Freundlich isotherm. The desorption rate reached 93.95% at pH 10. The extract obtained from submerged cultures had eritadenine content of 63.31%, corresponding to 87.86% of recovery, according to HPLC analysis. Furthermore, the novel bioherbicidal potential of eritadenine was tested on plants. The cultures extract containing eritadenine had a detrimental impact on plant development, generating mortality of 100% at 3%, 0.5%, and 0.25%. Moreover, pure eritadenine exhibited a phytotoxic effect similar than glyphosate on leaves, stems and roots. These findings highlight the significant bioherbicidal properties of eritadenine. Further studies are needed to understand the biosynthetic pathway of eritadenine and its bioherbicidal properties on weeds and illicit crops.
PubMed: 38948450
DOI: 10.1080/12298093.2024.2350207 -
PeerJ 2024In the eastern coastal regions of Odisha, wilt caused by f. sp. is an extremely damaging disease in chilli. This disease is very difficult to manage with chemical...
In the eastern coastal regions of Odisha, wilt caused by f. sp. is an extremely damaging disease in chilli. This disease is very difficult to manage with chemical fungicides since it is soil-borne in nature. The natural rhizosphere soil of the chilli plant was used to isolate and test bacterial antagonists for their effectiveness and ability to promote plant growth. Out of the fifty-five isolates isolated from the rhizosphere of healthy chilli plants, five isolates, namely Iso 01, Iso 17, Iso 23, Iso 24, and Iso 32, showed their highly antagonistic activity against f. sp. under . In a dual culture, Iso 32 (73.3%) and Iso 24 (71.5%) caused the highest level of pathogen inhibition. In greenhouse trials, artificially inoculated chilli plants treated with Iso 32 (8.8%) and Iso 24 (10.2%) had decreased percent disease incidence (PDI), with percent disease reduction over control of 85.6% and 83.3%, respectively. Iso 32 and Iso 24 treated chilli seeds have shown higher seed vigor index of 973.7 and 948.8, respectively, as compared to untreated control 636.5. Furthermore, both the isolates significantly increased plant height as well as the fresh and dry weight of chilli plants under the rolled paper towel method. Morphological, biochemical, and molecular characterization identified (MH491049) as the key antagonist. This study demonstrates that rhizobacteria, specifically Iso 32 and Iso 24, can effectively protect chilli plants against Fusarium wilt while promoting overall plant development. These findings hold promise for sustainable and eco-friendly management of Fusarium wilt in chilli cultivation.
Topics: Fusarium; Plant Diseases; Soil Microbiology; Rhizosphere; Capsicum; Antibiosis; Plant Development
PubMed: 38948222
DOI: 10.7717/peerj.17578 -
PeerJ 2024Plasmodesmata are transmembrane channels embedded within the cell wall that can facilitate the intercellular communication in plants. Plasmodesmata callose-binding...
Plasmodesmata are transmembrane channels embedded within the cell wall that can facilitate the intercellular communication in plants. Plasmodesmata callose-binding (PDCB) protein that associates with the plasmodesmata contributes to cell wall extension. Given that the elongation of cotton fiber cells correlates with the dynamics of the cell wall, this protein can be related to the cotton fiber elongation. This study sought to identify PDCB family members within the genome and to elucidate their expression profiles. A total of 45 distinct family members were observed through the identification and screening processes. The analysis of their physicochemical properties revealed the similarity in the amino acid composition and molecular weight across most members. The phylogenetic analysis facilitated the construction of an evolutionary tree, categorizing these members into five groups mainly distributed on 20 chromosomes. The fine mapping results facilitated a tissue-specific examination of group V, revealing that the expression level of peaked five days after flowering. The VIGS experiments resulted in a marked decrease in the gene expression level and a significant reduction in the mature fiber length, averaging a shortening of 1.43-4.77 mm. The results indicated that played a pivotal role in the cotton fiber development and served as a candidate for enhancing cotton yield.
Topics: Gossypium; Plasmodesmata; Cotton Fiber; Plant Proteins; Phylogeny; Gene Expression Regulation, Plant; Glucans; Multigene Family; Cell Wall; Carrier Proteins
PubMed: 38948221
DOI: 10.7717/peerj.17625 -
PeerJ 2024Leaf inclination angle (LIA) and tillering impact the winter wheat ( L.) population canopy structure. Understanding their effects on water use (WU) parameters and yield...
Leaf inclination angle (LIA) and tillering impact the winter wheat ( L.) population canopy structure. Understanding their effects on water use (WU) parameters and yield can guide water-saving strategies through population control. In this study, six near-isogenic lines (NILs) and their parents were selected as materials. These special materials were characterized by varying tillering at the current sowing density, a similar genetic background, and, particularly, a gradient in mean flag leaf LIA. The investigation focused on the jointing to early grain-filling stage, the peak water requirement period of wheat crops. Population-scale transpiration (PT) and evaporation from the soil surface (E) were partitioned from total evapotranspiration (ET) by the means of micro-lysimeters. The results showed decreased PT, E, and ET with increased population density (PD) within a narrow density range derived from varying tillering across genotypes. Significant correlations existed between PD and ET, E, and PT, especially in the wettest 2017-2018 growing season. Within such narrow PD range, all the correlations between WU parameters and PD were negative, although some correlations were not statistically significant, thereby suggesting the population structure's predominant impact. No significant correlation existed between LIA and both ET and PT within the LIA range of 35°-65°. However, significant correlations occurred between LIA and E in two growing seasons. Genotypes with similar LIA but different PD produced varied ET; while with similar PD, the four pairs of genotypes with different LIA each consumed similar ET, thus highlighting PD's more crucial role in regulating ET. The yield increased with higher LIA, and showed a significant correlation, emphasizing the LIA's significant effect on yield. However, no correlation was observed with PD, indicating the minor effect of tillering at the current sowing density. Therefore these results might offer valuable insights for breeding water-saving cultivars and optimizing population structures for effective field water conservation.
Topics: Triticum; Plant Leaves; Plant Transpiration; Soil; Seasons; Water; Genotype
PubMed: 38948218
DOI: 10.7717/peerj.17618 -
PeerJ 2024crown rot (FCR), caused by spp., is a devastating disease in wheat growing areas. Previous studies have shown that FCR is caused by co-infection of and in Hubei...
crown rot (FCR), caused by spp., is a devastating disease in wheat growing areas. Previous studies have shown that FCR is caused by co-infection of and in Hubei Province, China. In this study, a method was developed to simultaneously detected DNAs of and that can efficiently differentiate them. Whole genome sequence comparison of these four spp. was performed and a 20 bp sequence was designed as an universal upstream primer. Specific downstream primers of each pathogen was also designed, which resulted in a 206, 482, 680, and 963 bp amplicon for each pathogen, respectively. Multiplex PCR specifically identified and but not from other 46 pathogens, and the detection limit of target pathogens is about 100 pg/μl. Moreover, we accurately determined the FCR pathogen species in wheat samples using the optimized multiplex PCR method. These results demonstrate that the multiplex PCR method established in this study can efficiently and rapidly identify , , , and , which should provide technical support for timely and targeted prevention and control of FCR.
Topics: Fusarium; Triticum; Plant Diseases; Multiplex Polymerase Chain Reaction; China; DNA, Fungal
PubMed: 38948216
DOI: 10.7717/peerj.17656 -
Heliyon Jun 2024Microbes are a worthwhile organism of the earth that could be formulated as consortium which can be utilized as biofertilizers. Consortium-based bioinoculants or...
Microbes are a worthwhile organism of the earth that could be formulated as consortium which can be utilized as biofertilizers. Consortium-based bioinoculants or biofertilizers are superior to single strain-based inoculants for sustainable agricultural productivity and increased micronutrient content in yield. The aim of present study was to evaluate the effect of different combinations of beneficial bacteria that are more effective than single-based bioinoculants. The current work focuses on the isolation of rhizospheric microorganisms from various cereals and pseudocereal crops and the development of a single inoculum as well as a bacterial consortium which were evaluated on wheat crop. A total 214 rhizospheric bacteria were sorted out and, screened for mineral solubilizing attributes i.e., phosphorus, potassium, zinc and selenium solubilization. Among all the bacterial isolates, four potential strains exhibiting P, K, Zn and Se-solubilizing attributes were identified with the help of 16S rRNA gene sequencing as EU-A3Rb1, EU-A2RNL1, EU-C3SK2, and EU-WRSe4, respectively. The identified strains formulated as a consortium which were found to improve the plant growth and physiological parameters in comparison to single culture inoculants and control. To the best of our knowledge, the present investigation is the first report that has developed the consortium from bacterial strains EU-A3Rb1, EU-A2RNL1, EU-C3SK2, and EU-WRSe4. A combination of bacterial strains could be used as liquid inoculants for cereal crops growing in mountainous regions.
PubMed: 38948031
DOI: 10.1016/j.heliyon.2024.e33167 -
ACS Omega Jun 2024Glycosylation represents a major chemical challenge; while it is one of the most common reactions in Nature, conventional chemistry struggles with stereochemistry,...
GASP: A Pan-Specific Predictor of Family 1 Glycosyltransferase Acceptor Specificity Enabled by a Pipeline for Substrate Feature Generation and Large-Scale Experimental Screening.
Glycosylation represents a major chemical challenge; while it is one of the most common reactions in Nature, conventional chemistry struggles with stereochemistry, regioselectivity, and solubility issues. In contrast, family 1 glycosyltransferase (GT1) enzymes can glycosylate virtually any given nucleophilic group with perfect control over stereochemistry and regioselectivity. However, the appropriate catalyst for a given reaction needs to be identified among the tens of thousands of available sequences. Here, we present the glycosyltransferase acceptor specificity predictor (GASP) model, a data-driven approach to the identification of reactive GT1:acceptor pairs. We trained a random forest-based acceptor predictor on literature data and validated it on independent in-house generated data on 1001 GT1:acceptor pairs, obtaining an AUROC of 0.79 and a balanced accuracy of 72%. The performance was stable even in the case of completely new GT1s and acceptors not present in the training data set, highlighting the pan-specificity of GASP. Moreover, the model is capable of parsing all known GT1 sequences, as well as all chemicals, the latter through a pipeline for the generation of 153 chemical features for a given molecule taking the CID or SMILES as input (freely available at https://github.com/degnbol/GASP). To investigate the power of GASP, the model prediction probability scores were compared to GT1 substrate conversion yields from a newly published data set, with the top 50% of GASP predictions corresponding to reactions with >50% synthetic yields. The model was also tested in two comparative case studies: glycosylation of the antihelminth drug niclosamide and the plant defensive compound DIBOA. In the first study, the model achieved an 83% hit rate, outperforming a hit rate of 53% from a random selection assay. In the second case study, the hit rate of GASP was 50%, and while being lower than the hit rate of 83% using expert-selected enzymes, it provides a reasonable performance for the cases when an expert opinion is unavailable. The hierarchal importance of the generated chemical features was investigated by negative feature selection, revealing properties related to cyclization and atom hybridization status to be the most important characteristics for accurate prediction. Our study provides a GT1:acceptor predictor which can be trained on other data sets enabled by the automated feature generation pipelines. We also release the new in-house generated data set used for testing of GASP to facilitate the future development of GT1 activity predictors and their robust benchmarking.
PubMed: 38947828
DOI: 10.1021/acsomega.4c01583