Sample collection Kaesenbachtal, Tuebingen, Germany (Soil, Leaves, Fruits, Lichen and other)
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Unknown
SUBMITTER: 
Daniel Petras
PROVIDER: MSV000091687 | MassIVE | Wed Apr 12 01:52:00 BST 2023
REPOSITORIES: MassIVE
Similar Datasets
Project description:ObjectiveMulberry (Morus spp.) fruits and leaves have been proven to possess nutraceutical properties. Due to its fast and easy growing characteristics, mulberry fruits (MF) and leaves (ML) potentially emerge as a great source of functional foods. This study aims to enhance bioactivities (antioxidant, anti-inflammation, and hypoglycemic activity) of MF and ML via submerged fermentation using bacteria (Lactobacillus plantarum TAR 4), yeast (Baker's yeast and red yeast) and fungi (Tempeh and Tapai starter).MethodsIn this study, 25% (mass to volume ratio) of MF and ML were fermented (48 h) with 1% (mass to volume ratio) of different microbial cultures, respectively. Effects of different fermentations on MF and ML were determined based on the changes of total phenolics (TPC), flavonoids (TFC), anthocyanins, total sugar, DPPH activity, ferric reducing antioxidant power (FRAP), albumin denaturation inhibition activity (ADI), anti-lipoxygenase activity and α-amylase inhibition activity (AI).ResultsGenerally, ML had higher AI than MF. However, MF exhibited higher DPPH, FRAP and anti-lipoxygenase activity than ML. After all forms of fermentation, DPPH and AI activity of MF and ML were increased significantly (P < 0.05). However, the effects of fermentation on TPC, FRAP, ADI and anti-lipoxygenase activity of MF were in contrast with ML. TPC, FRAP and anti-lipoxygenase activity of ML were enhanced, but reduced in MF after fermentation. Although the effects exerted by different microorganisms in MF and ML fermentation were different, the bioactivities of MF and ML were generally improved after fermentation. Fermentation by Tempeh starter enhanced TPC (by 2-fold), FRAP (by 2.3-fold), AI (at 10% increment) and anti-lipoxygenase activity (by 5-fold) of ML, whereas Tapai fermentation effectively enhanced the DPPH (at 17% increment) and ADI (by 2-fold) activity of MF.ConclusionFindings of this study provide an insight into the future process design of MF and ML processing into novel functional foods.
| S-EPMC9476717 | biostudies-literature
Project description:Interactions between plants and leaf herbivores have long been implicated as the major driver of plant secondary metabolite diversity. However, other plant-animal interactions, such as those between fruits and frugivores, may also be involved in phytochemical diversification. Using 12 species of Piper, we conducted untargeted metabolomics and molecular networking with extracts of fruits and leaves. We evaluated organ-specific secondary metabolite composition and compared multiple dimensions of phytochemical diversity across organs, including richness, structural complexity, and variability across samples at multiple scales within and across species. Plant organ identity, species identity, and the interaction between the two all significantly influenced secondary metabolite composition. Leaves and fruit shared a majority of compounds, but fruits contained more unique compounds and had higher total estimated chemical richness. While the relative levels of chemical richness and structural complexity across organs varied substantially across species, fruit diversity exceeded leaf diversity in more species than the reverse. Furthermore, the variance in chemical composition across samples was higher for fruits than leaves. By documenting a broad pattern of high phytochemical diversity in fruits relative to leaves, this study lays groundwork for incorporating fruit into a comprehensive and integrative understanding of the ecological and evolutionary factors shaping secondary metabolite composition at the whole-plant level.
| S-EPMC8435686 | biostudies-literature
Project description:Oral lichen planus (OLP) is a poorly understood chronic inflammatory mucocutaneous disease and is associated with many systemic diseases, which may lead to the erosion of oral mucosa and bring physical and psychological disorders to patients. However, the pathogenesis and immune microenvironment of OLP with different clinical subtypes are unclear. therefore, this study established a clinical cohort of OLP with 1-year follow-up and obtained the clinical information and bulk RNA-seq files to explore the immune microenvironment and molecular mechanism of oral lichen planus with different clinical subtypes. Based on the erosion of oral mucosa in the biopsy, the participants of OLP were divided into two groups, non-erosive OLP (NEOLP) and erosive OLP (EOLP). According to whether erosion occurred in oral mucosa more than three times and a remission period of less than 3 months within a one-year follow-up, OLP was divided into two groups, recalcitrant erosive OLP (REOLP) and stable OLP (SOLP).
2023-08-01 | GSE213346 | GEO
Project description:BackgroundInferior quality of biological material compromises data, slows discovery, and wastes research funds. The gut microbiome plays a critical role in human health and disease, yet little attention has been given to optimizing collection and processing methods of human stool.MethodsWe collected the entire bowel movement from 2 healthy volunteers: one to examine stool sample heterogeneity and one to test stool sample handling parameters. Sequencing and bioinformatic analyses were used to examine the microbiome composition.ResultsThe microbiome profile varied depending on where the subsample was obtained from the stool. The exterior cortex of the stool was rich in specific phyla and deficient in others while the interior core of the stool revealed opposite microbiome profiles. Sample processing also resulted in varying microbiome profiles. Homogenization and stabilization at 4°C gave superior microbial diversity profiles compared to the fresh or frozen subsamples of the same stool sample. Bacterial proliferation continued in the fresh subsample when processed at ambient temperature. Bacteroidetes proliferated and Firmicutes diminished during the 30-minute processing of fresh sample. The frozen sample had good overall diversity but Proteobacteria diminished likely because of the freeze/thaw.ConclusionThe microbiome profile is specific to the section of the stool being sampled. Stool sample collection, homogenization and stabilization at 4°C for 24 hours provides a neat, high-quality sample of sufficient quantity that can be banked into aliquots with nearly identical microbial diversity profiles. This collection pipeline is essential to accelerate our understanding of the gut microbiome in health and disease.
| S-EPMC10308701 | biostudies-literature
Project description:BackgroundThe hawthorn has recently been used as a popular herbal medicine in food applications and phytotherapy, especially for the cardiovascular system.MethodsIn this study, phytochemicals were evaluated by LC-ESI-MS, GC-MS, and biological activity, including antioxidant (DPPH test) and antibacterial (broth dilution assay), in different extracts of Crataegus pentagyna fruit, leaf, and root.ResultsGlobally, 49 phenolics were tentatively identified using HPLC-ESI-MS/MS in the hydro-methanolic extract of the fruit (major apigenin, caffeoylquinic acid derivative, and 4-O-(3'-O-glucopyranosyl)-caffeoyl quinic acid), 42 in the leaf (major salicylic acid, naringenin-6-C-glucoside, and naringin), and 33 in the root (major naringenin-7-O-neohesperidoside, isovitexin-2″-O-rhamnoside, and 4-O-(3'-O-glucopyranosyl)-caffeoyl quinic acid). The major group compounds analyzed by GC-MS in petroleum ether extracts were hydrocarbons (63.80%) and fatty acids and their derivatives (11.77%) in fruit, hydrocarbons (49.20%) and fatty acids and their derivatives (13.85%) in leaf, and hydrocarbons (53.96%) and terpenes (13.06%) in root. All samples exhibited promising phytochemical profile (total phenol, flavonoid, phenolic acid, and anthocyanin), antioxidant and antibacterial capacities, especially in hydro-methanolic extract of fruit (210.22 ± 0.44 mg GAE/g DE; 79.93 ± 0.54 mg QE/g DE; 194.64 ± 0.32 mg CAE/g DE; 85.37 ± 0.13 mg cyanidin 3-glucoside/100 g FW; DPPH: 15.43 ± 0.65 µg/mL; MIC: 0.15-0.62 µg/mL; and MBC: 0.62-1.25 mg/mL), followed by the leaf and root extracts, respectively. The PCA and heatmap analysis results distinguished metabolite profile differences for samples.ConclusionThe results of the present work provide scientific support for C. pentagyna as antimicrobial agents and natural antioxidants in human health and food preservation.
| S-EPMC10949799 | biostudies-literature
Project description:Circular RNAs (circRNAs) are covalently closed non-coding RNAs that play pivotal roles in various biological processes. However, circRNAs' roles in different tissues of apple are currently unknown. A total of 6495 unique circRNAs were identified from roots, phloem, leaves, flowers and fruits; 65.99% of them were intergenic circRNAs. Similar to other plants, tissue-specific expression was also observed for apple circRNAs; only 175 (2.69%) circRNAs were prevalently expressed in all five different tissues, while 1256, 1064, 912, 904 and 1080 circRNAs were expressed only in roots, phloem, leaves, flowers and fruit, respectively. The hosting-genes of circRNAs showed significant differences enriched in COG, GO terms or KEGG pathways in five tissues, suggesting the special functions of circRNAs in different tissues. Potential binding interactions between circRNAs and miRNAs were investigated using TargetFinder; 2989 interactions between 647 circRNAs and 192 miRNA were predicated in the present study. It also predicted that Chr00:18744403|18744580-mdm-miR160 might play an important role in the formation of flowers or in regulating the coloration of flowers, Chr10:6857496|6858910-mdm-miR168 might be involved in response to drought stress in roots, and Chr03:1226434|1277176 may absorb mdm-miR482a-3p and play a major role in disease resistance. Two circRNAs were experimentally analyzed by qRT-PCR with divergent primers, the expression levels were consistent with RNA-seq, which indicates that the RNA-seq datasets were reliable.
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Project description:Telomere length (TL) is a biomarker of aging and age-related decline. Although venous blood is considered the "gold standard" for TL measurement, its collection is often not feasible or desired in nonclinical settings. Saliva and dried blood spots (DBS) have been used as alternatives when venipuncture cannot be performed. However, it is not known whether these sample types yield TL measurements comparable to those obtained from venous blood. We sought to determine whether different samples from the same individual yield comparable TL measurements.We extracted DNA from matched buffy coat, saliva (Oragene and Oasis), and DBS (venous and capillary) samples from 40 women aged 18-77 years. We used the monochrome multiplex qPCR (MMQPCR) assay to measure TL in all sample types for each participant and applied quality control measures to retain only high-quality samples for analysis. We then compared TL from buffy coat and saliva to examine how these measurements differ and to test if TL is correlated across sample types.TL differed significantly across buffy coat, Oragene saliva, and Oasis saliva samples. TL from buffy coat and Oragene saliva was moderately correlated (??=?0.48, P = .002) and the most similar in size. Oasis saliva TL was not correlated with buffy coat or Oragene saliva TL, and was the shortest. DBS DNA yields were inadequate for TL measurement using the MMQPCR assay.Using a matched dataset we demonstrate that sample type significantly influences the TL measurement obtained using the MMQPCR assay.
| S-EPMC5785450 | biostudies-other
Project description:Enzyme biosensors are useful tools that can monitor rapid changes in metabolite levels in real-time. However, current approaches are largely constrained to metabolites within a limited chemical space. With the rising development of artificial metalloenzymes (ArM), a unique opportunity exists to design biosensors from the ground-up for metabolites that are difficult to detect using current technologies. Here we present the design and development of the ArM ethylene probe (AEP), where an albumin scaffold is used to solubilize and protect a quenched ruthenium catalyst. In the presence of the phytohormone ethylene, cross metathesis can occur to produce fluorescence. The probe can be used to detect both exogenous- and endogenous-induced changes to ethylene biosynthesis in fruits and leaves. Overall, this work represents an example of an ArM biosensor, designed specifically for the spatial and temporal detection of a biological metabolite previously not accessible using enzyme biosensors.
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Project description:Fully ripe fruits and mature leaves of Elaeagnus angustifolia were harvested and analyzed by means of analytical and biological tests to better comprehend the chemical composition and therapeutic/nutraceutical potential of this plant. Fruits and leaves were dried and the obtained powders were analyzed to study their color character and (via headspace gas chromatography) describe the chemical profile. Subsequently, they were submitted to a chloroform-methanol extraction, to a hydroalcoholic extraction procedure assisted or not by microwaves, and to an extraction with supercritical CO2, assisted or not by ethanol as the co-solvent, to detect the polyphenolic and the volatile content. The resulting extracts were evaluated in terms of chlorophyll and carotenoid content, polyphenolic content, volatile fraction, total phenolic content, total flavonoid content, antioxidant activity, radical scavenging activity, and enzymatic inhibition activity. The results confirmed the correlation between the chemical composition and the high antioxidant potential of leaf extracts compared to the fruit extracts in terms of the phenolic and pigment content. A promising effect against tyrosinase emerged for all the extracts, suggesting a therapeutic/nutraceutical use for this plant. Conversely, the volatile content from both natural matrices was similar.
| S-EPMC7248930 | biostudies-literature
Project description:This study was carried out to determine the possible heavy metal accumulation in fruits and leaves of Zivzik pomegranate (Punica granatum L.) grown in two different roadside orchards located in Pirinçli and Kapılı villages of Siirt province, Turkey. Leaf and fruit samples were collected from trees located at 0, 50, 100 m distances from the main roads. Plant samples were analyzed for cobalt (Co), nickel (Ni), cadmium (Cd), lead (Pb) and chromium (Cr) concentrations. The Co, Ni, Cd, Pb and Cr concentrations of fruit samples collected from Pirinçli village were ranged from 0.082 to 0.238 mg kg-1, from 1.160 to 1.559 mg kg-1, from 0.087 to 0.179 mg kg-1, 0.326 to 0.449 mg kg-1 and 0.606 to 1.054 mg kg-1, respectively. The Co, Ni, Cd, Pb and Cr concentrations of fruit samples from Kapılı village were between 0.085 and 0.137 mg kg-1, 1.042 and 1.123 mg kg-1, 0.037 and 0.076 mg kg-1, 0.277 and 0.520 mg kg-1 and 0.762 and 0.932 mg kg-1, respectively. Heavy metal concentrations of leaf samples from Pirinçli village varied from 0.191 to 0.227 mg Co kg-1, 2.201 to 3.547 mg Ni kg-1, 0.051 to 0.098 mg Cd kg-1, 0.535 to 0.749 mg Pb kg-1 and from 1.444 to 2.017 mg Cr kg-1. Similarly, the heavy metal concentration of leaf samples from Kapılı villages were between 0.213 and 0.217 mg Co kg-1, 2.160 and 2.511 mg Ni kg-1, 0.058 and 0.114 mg Cd kg-1, 0.579 and 0.676 mg Pb kg-1 and 1.688 and 1.518 mg Cr kg-1. The Co, Ni and Cr concentrations in fruit samples collected from 0, 50 and 100 meters to the main road in Pirinçli village were at statistically significant level, while only Ni concentration in leaf samples collected from 0, 50 and 100 meters to the main road was at significant level. In contrast, heavy metal concentrations in fruit and leaf samples collected from 0, 50 and 100 m to the main road in Kapılı village were not statistically significant level.
| S-EPMC7164423 | biostudies-literature