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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 -
Plants (Basel, Switzerland) Jun 2024The use of rhizospheric SynComs can be a new and sustainable strategy in the agrobiotechnology sector. The objective of this study was to create the most appropriate...
The use of rhizospheric SynComs can be a new and sustainable strategy in the agrobiotechnology sector. The objective of this study was to create the most appropriate SynCom composition; examine the ability to dissolve natural rock phosphate (RP) from Morocco in liquid-modified NBRIP medium; determine organic acids, and phytohormones; and verify plant growth promoting and nutrition uptake effect in the pot experiments of winter wheat (). A total of nine different microorganisms were isolated, which belonged to three different genera: , , and . Out of the 21 treatments tested, four SynComs had the best phosphate-dissolving properties: IJAK-27+44+91 (129.17 mg L), IIBEI-32+40 (90.95 µg mL), IIIDEG-45+41 (122.78 mg L), and IIIDEG-45+41+72 (120.78 mg L). We demonstrate that these SynComs are capable of producing lactic, acetic, gluconic, malic, oxalic, citric acids, and phytohormones such as indole-3-acetic acid, zeatin, gibberellic acid, and abscisic acid. In pot experiments with winter wheat, we also demonstrated that the designed SynComs were able to effectively colonize the plant root rhizosphere and contributed to more abundant plant growth characteristics and nutrient uptake as uninoculated treatment or uninoculated treatment with superphosphate (NPK 0-19-0). The obtained results show that the SynCom compositions of IJAK-27+44+91, IIBEI-32+40, IIIDEG-45+41, and IIIDEG-45+41+72 can be considered as promising candidates for developing biofertilizers to facilitate P absorption and increase plant nutrition.
PubMed: 38931148
DOI: 10.3390/plants13121716 -
Plants (Basel, Switzerland) Jun 2024Motivated by the culinary and ethnopharmacological use of (L.) R.K. Jansen, this study aimed to unveil new chemical compounds from its essential oil (EO). , known for...
Motivated by the culinary and ethnopharmacological use of (L.) R.K. Jansen, this study aimed to unveil new chemical compounds from its essential oil (EO). , known for its anesthetic and spicy properties, has been used in traditional medicine and cuisine, particularly in Northern Brazil. Through a detailed GC-MS analysis, 180 constituents were identified, including 12 tentatively identified long-chain α-keto esters of various acids. Additionally, 18 new esters were synthesized for structural verification. This research expands the known chemical diversity of EO, providing a basis for potential pharmacological applications. The identification of new natural products, including homologs and analogs of acmellonate, underscores the EO's rich chemical profile and its potential for novel bioproduct development.
PubMed: 38931124
DOI: 10.3390/plants13121690 -
Plants (Basel, Switzerland) Jun 2024In this study, based on ethnobotanical data recorded in Transylvania, the polyphenolic compounds and the permeability of the aerial part's extract of were investigated....
In this study, based on ethnobotanical data recorded in Transylvania, the polyphenolic compounds and the permeability of the aerial part's extract of were investigated. Ultrahigh-performance liquid chromatography-tandem mass spectrometry was applied for the analysis of the extracts. Parallel artificial membrane permeability assay (PAMPA) for the gastrointestinal tract and the blood-brain barrier was conducted. In the ethanolic and aqueous extracts of the species traditionally used for wound, furuncle, and liver disorders, 92 polyphenols were characterized (e.g., flavonoid, hydroxycinnamic acid, catechin, dihydroxybenzoyl, lignan derivatives, and a monoterpene) including 54 compounds identified for the first time in the plant. In the PAMPA tests, eight components were shown to be capable of passive diffusion across the studied membranes. These include apigenin and seven methoxylated flavonoid derivatives. Based on these results, methoxylated flavonoids might promote the pharmacological potential of to be applied in the enhancement of novel remedies.
PubMed: 38931084
DOI: 10.3390/plants13121652 -
Plants (Basel, Switzerland) Jun 2024Michx. (common waterweed) and (Planch.) H. St. John (Nuttall's waterweed), two invasive aquatic plants from North America, have coexisted in European water bodies...
Michx. (common waterweed) and (Planch.) H. St. John (Nuttall's waterweed), two invasive aquatic plants from North America, have coexisted in European water bodies since the early 20th century. New localities for both species in Croatia continued to be discovered during a study that ran from 2016 to 2023 as a part of the annual implementation of Water Framework Directive monitoring that covered the entire territory of Croatia (786 sampling points in total). Based on these data, the distribution and ecology of both species were analysed. was found at 30 sampling points, mostly in rivers, and at 15 sampling points, mostly in artificial canals. Nearly three-quarters (72.5%) of all elodea sampling points were in the Pannonian Ecoregion. was discovered for the first time in the Continental-Dinaric and Mediterranean-Dinaric Subecoregions. To study the ecology of the species, for each sampling point, vegetation relevés were performed and monthly measurements of physico-chemical parameters were collected. The most common accompanying species for both elodeas are presented, and the difference in species assemblages between the sites with and was confirmed with the ANOSIM test. Furthermore, Indicator Species Analysis revealed eight species characteristic of sites and eleven species characteristic of sites. Fitting multivariate models (CCA and NPMR) to species abundance revealed the ecological reaction of and to environmental descriptors. The most strongly contributing environmental descriptors that influence the distribution of both species are biochemical oxygen demand, electrical conductivity and total phosphorus. In Croatia, the replacement of with was observed in several water bodies with high nutrient loads.
PubMed: 38931056
DOI: 10.3390/plants13121624 -
Plants (Basel, Switzerland) Jun 2024Lateral roots (LRs) receive signals from the inter-root environment and absorb water and nutrients from the soil. Auxin regulates LR formation, but the mechanism in...
Lateral roots (LRs) receive signals from the inter-root environment and absorb water and nutrients from the soil. Auxin regulates LR formation, but the mechanism in tomato remains largely unknown. In this study, 'Ailsa Craig' tomato LRs appeared on the third day and were unevenly distributed in primary roots. According to the location of LR occurrence, roots were divided into three equal parts: the shootward part of the root (RB), the middle part of the root (RM), and the tip part of the root (RT). Transverse sections of roots from days 1 to 6 revealed that the number of RB cells and the root diameter were significantly increased compared with RM and RT. Using roots from days 1 to 3, we carried out transcriptome sequencing analysis. Identified genes were classified into 16 co-expression clusters based on K-means, and genes in four associated clusters were highly expressed in RB. These four clusters (3, 5, 8, and 16) were enriched in cellulose metabolism, microtubule, and peptide metabolism pathways, all closely related to LR development. The four clusters contain numerous transcription factors linked to LR development including transcription factors of () and families. Additionally, auxin-related genes , , , , , , , , , and were highly expressed in RB tissue. Free IAA content in 3 d RB was notably higher, reaching 3.3-5.5 ng/g, relative to RB in 1 d and 2 d. The LR number was promoted by 0.1 μM of exogenous IAA and inhibited by exogenous NPA. We analyzed the root cell state and auxin signaling module during LR formation. At a certain stage of pericycle cell development, LR initiation is regulated by auxin signaling modules IAA14-ARF7/ARF19-LBD16-CDKA1 and IAA14-ARF7/ARF19-MUS/MUL-XTR6/EXP. Furthermore, as a key regulatory factor, auxin regulates the process of LR initiation and LR primordia (LRP) through different auxin signaling pathway modules.
PubMed: 38931052
DOI: 10.3390/plants13121620 -
Plants (Basel, Switzerland) Jun 2024This study aimed to analyze the effects of salt stress on the growth physiology and plant-cell ultrastructure of Fort. () to evaluate its adaptability under salt...
This study aimed to analyze the effects of salt stress on the growth physiology and plant-cell ultrastructure of Fort. () to evaluate its adaptability under salt stress. The effects of different concentrations of salt (NaCl; 0, 25, and 300 mmol·L) on the agronomic traits, activities of related enzymes, ion balance, and mesophyll-cell ultrastructure of were studied in a controlled pot experiment. Results showed that compared with those of the control group, the aerial-part fresh weight, underground fresh weight, tiller number, root length, root diameter, plant height, and leaf area of salt-stressed increased at 25 mmol·L and then decreased at 300 mmol·L. The changes in levels of superoxide dismutase, peroxidase, ascorbate peroxidase, and catalase showed a similar trend, with significant differences compared with control group. Salt stress altered the ion balance of , resulting in a significant increase in Na content and a significant decrease in K content. The contents of Ca and Mg changed to varying degrees. The analysis of the microstructure of the root showed that under salt treatment, the epidermal cells of the root significantly thickened and the diameter of the xylem decreased. The results of ultrastructural analysis of mesophylls showed that salt stress can cause cell-membrane contraction, cell-gap enlargement, disorder in the structures of chloroplasts and mitochondria, and an increase in the number of osmiophilic particles. These changes were aggravated by the increase in NaCl concentration. This study reveals the response of to salt stress and provides a basis for further study on the salt-tolerance mechanism of .
PubMed: 38931025
DOI: 10.3390/plants13121593