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Methods in Molecular Biology (Clifton,... 2024The proteomic approach plays a key role to characterize a biological system at any given time. In recent years, advances in proteomics have led to an increasing...
The proteomic approach plays a key role to characterize a biological system at any given time. In recent years, advances in proteomics have led to an increasing application in all biological fields, including plant matrices and associated microbiome studies. However, extracting adequate protein samples remains the most critical step for any plant proteomics study. The protein extraction protocols proposed for the phyllosphere involve an initial leaf washing step; however, this is an approach only applicable if interest is restricted to epiphytes. A metaproteomic approach is required to obtain an overall picture and consequently an extraction that considers proteins derived from the plant, epiphytic and endophytic microorganisms. The most commonly used extractions for plant tissue involve the use of phenol or TCA-acetone. However, for efficient protein recovery is essential to remove interfering components abundant in plant tissues, such as polysaccharides, lipids, and phenolic compounds. A well-proven protocol on the basis of a combination of TCA-acetone and phenol extraction is presented here, obtaining some cleaned protein pellets, suitable for electrophoresis and subsequent proteomics studies. Important points for the success of this protocol are (i) a proper sampling and sample preparation, (ii) maintaining samples at a low temperature during extraction and using protease inhibitors, (iii) an initial step in TCA-acetone to remove part of the interfering substances, and (iv) careful recovery of the phenolic phase. Furthermore, the protocol is timesaving and can be completed in one working day.
Topics: Plant Proteins; Proteomics; Plant Leaves; Acetone; Phenol; Plants; Trichloroacetic Acid
PubMed: 38941013
DOI: 10.1007/978-1-0716-3910-8_5 -
Frontiers in Bioscience (Elite Edition) May 2024Flaxseed mucilage (FSM) is one of the healthy components of flaxseed. FSM is an example of a material that can be used in the food, cosmetic, and pharmaceutical...
BACKGROUND
Flaxseed mucilage (FSM) is one of the healthy components of flaxseed. FSM is an example of a material that can be used in the food, cosmetic, and pharmaceutical industries due to its rheological properties. FSM consists mainly of two polysaccharides, arabinoxylan, and rhamnogalacturonan I, and it also contains protein components and minerals. The prospect of using FSM in food is due to its gelling, water binding, emulsifying, and foaming properties. In addition, valuable natural sources of phenolic compounds such as lignans, phenolic acids, flavonoids, phenylpropanoids, and tannins are partially extracted from flaxseed in FSM. These antioxidant components have pharmacological properties, including anti-diabetic, anti-hypertensive, immunomodulatory, anti-inflammatory and neuroprotective properties. A combination of FSM and lactobacilli in dairy foods can improve their functional properties. This study aimed to develop dairy products by adding of FSM and using two lactic acid bacteria (LAB). FSM (0.2%) was used as an ingredient to improve both the texture and antioxidant properties of the product.
METHODS
Skim milk was fermented with 0.2% flaxseed mucilage using and the probiotic AG9. The finished fermented milk products were stored at 4 °C for 14 days. Quantitative chemical, textural, and antioxidant analyses were carried out.
RESULTS
Adding 0.2% FSM to the dairy product stimulated the synthesis of lactic acid. FSM increased the viscosity and water-holding capacity of or AG9 fermented milk products. Combining these starter strains with FSM promoted the formation of a hard, elastic, resilient casein matrix in the product. When only AG9 was used for the fermentation, the dairy product had a high syneresis and a low viscosity and firmness; such a product is inferior in textural characteristics to the variant with commercial . The addition of FSM improved the textural properties of this variant. The use of AG9 and FSM makes it possible to obtain a fermented milk product with the highest content of polyphenolic compounds, which have the highest antioxidant properties and stimulate lipase and α-glucosidase inhibitor synthesis. Combining of and AG9 in the starter (20% of the total mass of the starter) and adding of 0.2% FSM is the optimal combination for obtaining a dairy product with high textural and antioxidant properties.
CONCLUSIONS
The physicochemical properties (viscosity, syneresis, water holding capacity, texture) and antioxidant properties of fermented milk were improved. In the future, as part of the work to investigate the functional properties of dairy products with FSM, studies will be conducted using in models.
Topics: Flax; Lactobacillus delbrueckii; Plant Mucilage; Lactobacillus plantarum; Antioxidants; Cultured Milk Products; Animals; Milk; Fermentation
PubMed: 38939910
DOI: 10.31083/j.fbe1602011 -
Przeglad Gastroenterologiczny 2024is a common medicinal plant widely cultivated in tropical regions of the world. The outer seed coat of , obtained by cleaning the seeds, contains soluble and insoluble... (Review)
Review
The role and therapeutic effectiveness of seed husk (psyllium husk) in the prevention and non-pharmacological treatment of gastrointestinal diseases. Part 1. Clinical use of psyllium husk in the treatment of irritable bowel syndrome, ulcerative colitis, and colorectal cancer.
is a common medicinal plant widely cultivated in tropical regions of the world. The outer seed coat of , obtained by cleaning the seeds, contains soluble and insoluble fibre in a ratio of 7:3, making products containing husk an ideal source of health-beneficial fibre. The results of clinical trials demonstrate the therapeutic efficacy of psyllium husk for various gastrointestinal disorders. It has also been documented that psyllium ingestion exhibits antioxidant, immunomodulatory, antiproliferative, anticancer, and antiviral effects. Such pleiotropic effects of husk are related to the presence in its composition of arabinoxylan, which forms a gel in an aqueous environment, as well as bioactive compounds and their metabolites. This article presents the evidence available in the literature on the therapeutic potential and possible mechanisms of action of psyllium in the treatment of irritable bowel syndrome and ulcerative colitis, and prevention of colorectal cancer.
PubMed: 38939069
DOI: 10.5114/pg.2024.139209 -
Frontiers in Plant Science 2024Common object detection and image segmentation methods are unable to accurately estimate the shape of the occluded fruit. Monitoring the growth status of shaded crops in...
Common object detection and image segmentation methods are unable to accurately estimate the shape of the occluded fruit. Monitoring the growth status of shaded crops in a specific environment is challenging, and certain studies related to crop harvesting and pest detection are constrained by the natural shadow conditions. Amodal segmentation can focus on the occluded part of the fruit and complete the overall shape of the fruit. We proposed a Transformer-based amodal segmentation algorithm to infer the amodal shape of occluded tomatoes. Considering the high cost of amodal annotation, we only needed modal dataset to train the model. The dataset was taken from two greenhouses on the farm and contains rich occlusion information. We introduced boundary estimation in the hourglass structured network to provide information about the completion of the amodal shapes, and reconstructed the occluded objects using a GAN network (with discriminator) and GAN loss. The model in this study showed accuracy, with average pairwise accuracy of 96.07%, mean intersection-over-union (mIoU) of 94.13% and invisible mIoU of 57.79%. We also examined the quality of pseudo-amodal annotations generated by our proposed model using Mask R-CNN. Its average precision (AP) and average precision with intersection over union (IoU) 0.5 (AP50) reached 63.91%,86.91% respectively. This method accurately and rationally achieves the shape of occluded tomatoes, saving the cost of manual annotation, and is able to deal with the boundary information of occlusion while decoupling the relationship of occluded objects from each other. Future work considers how to complete the amodal segmentation task without overly relying on the occlusion order and the quality of the modal mask, thus promising applications to provide technical support for the advancement of ecological monitoring techniques and ecological cultivation.
PubMed: 38938637
DOI: 10.3389/fpls.2024.1376138 -
Journal of Plant Research Jun 2024Most studies of terrestrial bryophytes as natural substrates for photosynthetic microorganisms have been performed in the polar regions, where bryophytes are an...
Most studies of terrestrial bryophytes as natural substrates for photosynthetic microorganisms have been performed in the polar regions, where bryophytes are an important part of the ecosystem. As they remain green throughout the year, bryophytes may also be an ideal substrate for epiphytic organisms in temperate regions. The present study investigated the colonization potential and diversity of microalgae on selected plant species in riparian forest and spruce monoculture in a temperate region. It examines whether the presence of algae is related to substrate humidity, the micromorphology of gametophyte or the seasonal availability of substrate. The taxonomic diversity of algae was studied. Cyanobacteria and green algae were cultured on BG-11 agar medium, while diatoms were identified in permanent diatomaceous slides. The alpha- and beta-diversity indices were calculated, and the communities were compared using Bray-Curtis distances and multidimensional correspondence analyses. Our findings indicate that the largest number of alga species were diatoms; however, their presence was only observed in riparian forest and was associated with high humidity. Both aerophilic and freshwater taxa were noted, the latter carried by water from nearby aquatic ecosystem. Green algae were present in both phytocoenoses and humidity appears to have no substantial effect on the degree of colonization; their diversity was low and the group consisted of terrestrial taxa. In two bryophytes growing at the highest humidity, cyanobacteria were only identified in culture. The key factor influencing the degree of microalgae colonization was the humidity of the substrate, which was related to the distance from water.
PubMed: 38935314
DOI: 10.1007/s10265-024-01551-2 -
The Journal of Animal Ecology Jun 2024Unravelling the intricate mechanisms that govern community coexistence remains a daunting challenge, particularly amidst ongoing environmental change. Individual...
Unravelling the intricate mechanisms that govern community coexistence remains a daunting challenge, particularly amidst ongoing environmental change. Individual physiology and metabolism are often studied to understand the response of individual animals to environmental change. However, this perspective is currently largely lacking in community ecology. We argue that the integration of individual metabolism into community theory can offer new insights into coexistence. We present the first individual-based metabolic community model for a terrestrial mammal community to simulate energy dynamics and home range behaviour in different environments. Using this model, we investigate how ecologically similar species coexist and maintain their energy balance under food competition. Only if individuals of different species are able to balance their incoming and outgoing energy over the long-term will they be able to coexist. After thoroughly testing and validating the model against real-world patterns such as of home range dynamics and field metabolic rates, we applied it as a case study to scenarios of habitat fragmentation - a widely discussed topic in biodiversity research. First, comparing single-species simulations with community simulations, we find that the effect of habitat fragmentation on populations is strongly context-dependent. While populations of species living alone in the landscape were mostly positively affected by fragmentation, the diversity of a community of species was highest under medium fragmentation scenarios. Under medium fragmentation, energy balance and reproductive investment were also most similar among species. We therefore suggest that similarity in energy balance among species promotes coexistence. We argue that energetics should be part of community ecology theory, as the relative energetic status and reproductive investment can reveal why and under what environmental conditions coexistence is likely to occur. As a result, landscapes can potentially be protected and designed to maximize coexistence. The metabolic community model presented here can be a promising tool to investigate other scenarios of environmental change or other species communities to further disentangle global change effects and preserve biodiversity.
PubMed: 38932441
DOI: 10.1111/1365-2656.14134 -
Viruses Jun 2024Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various...
BACKGROUND
Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited.
METHODS
Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization.
RESULTS
Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed.
CONCLUSION
By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.
Topics: Humans; Metagenomics; Virome; Genome, Viral; Respiratory System; Viruses; Metagenome; Computer Simulation; Phylogeny; Computational Biology; Microbiota; Bacteriophages
PubMed: 38932245
DOI: 10.3390/v16060953 -
Viruses May 2024Viral diseases pose a significant threat to tomato crops ( L.), one of the world's most economically important vegetable crops. The limited genetic diversity of...
Viral diseases pose a significant threat to tomato crops ( L.), one of the world's most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and confirmation with PCR and RT-PCR were used. Single and mixed infections with tomato mosaic virus (ToMV), tomato golden mosaic virus (ToGMoV), and pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3' UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the , , and genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3' UTR, as well as amino acid mutations in the ORFs encoding 126 KDa, 183 KDa, and MP of Mexican ToMV isolates, suggest that it is necessary to evaluate the capacity of these variants to overcome , , and resistance genes. This evaluation, along with the characterization of advanced lines using molecular markers linked to these resistant genes, will be addressed in future studies as part of the breeding strategy. This study emphasizes the importance of using HTS for accurate identification and characterization of plant viruses that naturally infect tomato germplasm based on the consensus genome sequences. This study provides crucial insights to select appropriate disease management strategies and resistance genes and guide breeding efforts toward the development of virus-resistant tomato varieties.
Topics: Plant Diseases; Solanum lycopersicum; High-Throughput Nucleotide Sequencing; Plant Breeding; Plant Viruses; Genome, Viral; Phylogeny; Disease Resistance; RNA, Viral
PubMed: 38932180
DOI: 10.3390/v16060888 -
Pharmaceuticals (Basel, Switzerland) May 2024We recently reported that extract prepared from the aerial part of L. (CE) possesses hepatoprotective, hypolipidemic, and hypoglycemic properties. This paper focuses on...
BACKGROUND
We recently reported that extract prepared from the aerial part of L. (CE) possesses hepatoprotective, hypolipidemic, and hypoglycemic properties. This paper focuses on the effects of CE on the male rat reproductive system and the effects of this treatment on pregnancy and offspring development.
METHODS
The experimental male rats received 100 mg/kg bw/day, 500 mg/kg bw/day, and 1000 mg/kg bw/day of CE orally for 60 consecutive days. Rats that received tap water were used as controls. After treatment, we evaluated the effects of CE on the male reproductive system, fertility, and offspring development.
RESULTS
For CE-treated male rats, there was a significant increase in the (1) diameter of seminiferous tubules, (2) spermatogenic index, (3) number of total and motile spermatozoa, and (4) testosterone levels. Additionally, there was a decrease in the pre- and post-implantation death of the embryos in the CE-treated group. All pups born from CE-treated males demonstrated normal development.
CONCLUSIONS
CE treatment significantly improved male reproductive functions. No adverse effects on pregnancy and offspring development were observed when males were treated with CE. Further clinical evaluation of CE should lead to the development of a safe and effective phytodrug for treating male infertility.
PubMed: 38931367
DOI: 10.3390/ph17060700 -
Nutrients Jun 2024Pulses, as an important part of the human diet, can act as a source of high-quality plant proteins. Pulse proteins and their hydrolysates have shown promising results in... (Review)
Review
Pulses, as an important part of the human diet, can act as a source of high-quality plant proteins. Pulse proteins and their hydrolysates have shown promising results in alleviating metabolic syndrome and modulating the gut microbiome. Their bioactivities have become a focus of research, with many new findings added in recent studies. This paper comprehensively reviews the anti-hypertension, anti-hyperglycemia, anti-dyslipidemia and anti-obesity bioactivities of pulse proteins and their hydrolysates in recent in vitro and in vivo studies, which show great potential for the prevention and treatment of metabolic syndrome. In addition, pulse proteins and their hydrolysates can regulate the gut microbiome, which in turn can have a positive impact on the treatment of metabolic syndrome. Furthermore, the beneficial effects of some pulse proteins and their hydrolysates on metabolic syndrome have been supported by clinical studies. This review might provide a reference for the application of pulse proteins and their hydrolysates in functional foods or nutritional supplements for people with metabolic syndrome.
Topics: Metabolic Syndrome; Humans; Gastrointestinal Microbiome; Protein Hydrolysates; Animals; Plant Proteins
PubMed: 38931200
DOI: 10.3390/nu16121845