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Molecular & Cellular Proteomics : MCP Jun 2024At the molecular scale, adaptive advantages during plant growth and development rely on modulation of gene expression, primarily provided by epigenetic machinery. One...
At the molecular scale, adaptive advantages during plant growth and development rely on modulation of gene expression, primarily provided by epigenetic machinery. One crucial part of this machinery is histone post-translational modifications (PTMs), which form a flexible system, driving transient changes in chromatin and defining particular epigenetic states. PTMs work in concert with replication-independent histone variants further adapted for transcriptional regulation and chromatin repair. However, little is known about how such complex regulatory pathways are orchestrated and interconnected in cells. In this work, we demonstrate the utility of mass spectrometry-based approaches to explore how different epigenetic layers interact in Arabidopsis mutants lacking certain histone chaperones. We show that defects in histone chaperone function (e.g., CAF-1 or NAP1 mutations) translate into an altered epigenetic landscape, which aids the plant in mitigating internal instability. We observe changes in both the levels and distribution of H2A.W.7, altogether with partial repurposing of H3.3 and changes in the key repressive (H3K27me1/2) or euchromatic marks (H3K36me1/2). These shifts in the epigenetic profile serve as a compensatory mechanism in response to impaired integration of the H3.1 histone in the fas1 mutants. Altogether, our findings suggest that maintaining genome stability involves a two-tiered approach. The first relies on flexible adjustments in histone marks, while the second level requires the assistance of chaperones for histone variant replacement.
PubMed: 38848995
DOI: 10.1016/j.mcpro.2024.100795 -
Open Research Europe 2023The Bulgarian research landscape, presented mainly by the research institutes that are part of the Bulgarian Academy of Sciences and the Agricultural Academy, needs...
The Bulgarian research landscape, presented mainly by the research institutes that are part of the Bulgarian Academy of Sciences and the Agricultural Academy, needs diversification to match the research and innovation potential of the other European Union (EU) countries. This article describes the establishment of the Center of Plant Systems Biology and Biotechnology (CPSBB), a new innovative type of independent research organization that is changing the research landscape in Bulgaria. Supported by the EU Commission, Bulgarian Government, and Plovdiv Municipality, CPSBB has quickly become the leading plant science institute in Bulgaria, creating knowledge in diverse fields such as bioinformatics, biotechnology, genetics and genomics, metabolomics, and systems biology. We outline the organizational structure of CPSBB, the development of its infrastructure, and its scientific productivity. Finally, we compare CPSBB with other similar research establishments in Europe and we conclude that such new types of institutes have a bright future in Bulgaria due to their operational flexibility, productivity, and connections with academia and industry.
PubMed: 38846177
DOI: 10.12688/openreseurope.16514.2 -
BMC Plant Biology Jun 2024The invasion of Mikania micrantha by climbing and covering trees has rapidly caused the death of many shrubs and trees, seriously endangering forest biodiversity. In...
The invasion of Mikania micrantha by climbing and covering trees has rapidly caused the death of many shrubs and trees, seriously endangering forest biodiversity. In this study, M. micrantha seedlings were planted together with local tree species (Cryptocarya concinna) to simulate the process of M. micrantha climbing under the forest. We found that the upper part of the M. micrantha stem lost its support after climbing to the top of the tree, grew in a turning and creeping manner, and then grew branches rapidly to cover the tree canopy. Then, we simulated the branching process through turning treatment. We found that a large number of branches had been formed near the turning part of the M. micrantha stem (TP). Compared with the upper part of the main stem (UP), the contents of plant hormones (auxin, cytokinin, gibberellin), soluble sugars (sucrose, glucose, fructose) and trehalose-6-phosphate (T6P) were significantly accumulated at TP. Further combining the transcriptome data of different parts of the main stem under erect or turning treatment, a hypothetical regulation model to illustrate how M. micrantha can quickly cover trees was proposed based on the regulation of sugars and hormones on plant branching; that is, the lack of support after ascending the top of the tree led to turning growth of the main stem, and the enhancement of sugars and T6P levels in the TP may first drive the release of nearby dormant buds. Plant hormone accumulation may regulate the entrance of buds into sustained growth and maintain the elongation of branches together with sugars to successfully covering trees.
Topics: Mikania; Introduced Species; Trees; Plant Growth Regulators
PubMed: 38844870
DOI: 10.1186/s12870-024-05210-5 -
Frontiers in Pharmacology 2024There is a limited number of studies focusing on ethnomedical practices in children, particularly in Eastern Europe. Romania has a rich history of using medicinal plants...
There is a limited number of studies focusing on ethnomedical practices in children, particularly in Eastern Europe. Romania has a rich history of using medicinal plants in ethnopediatric care, and our objective was to identify the medicinal plants currently employed in treating childhood illnesses in the southern region of the country. Our investigation used structured interviews, focusing on respondent demographics, local names of therapeutically employed herbs, the specific plant part(s) utilized, methods of preparation and administration, and local folk indications of taxa. A total of 326 mothers with children aged 0 to 18, hospitalized in the "Grigore Alexandrescu" Children Emergency Hospital Bucharest and residing in Southern Romania, were enrolled in the study. Use Value Citation Index (UV), Informant Consensus Factor (Fic), and Fidelity Level (FL) were calculated. Twenty-five plants were identified for treating children's diseases in Southern Romania. The majority of informants resided in urban areas, and mothers primarily acquired knowledge from family members and healthcare professionals. The herbs most frequently employed were spp. (UV = 0.509) for diarrhea, . (UV = 0.301) for skin infections (Fic = 0.99) and digestive diseases (Fic = 0.98), and L. (UV = 0.365) for skin diseases (Fic = 0.99). Less utilized were (L.) Domin in respiratory diseases, (L.) L. stalks in urinary tract ailments, L. in ear infections, L. in intestinal parasitosis, L. in hives, L. in dermatitis and L. as a tonic. In 184 cases herbal treatment was used in conjunction with conventional medications. Education level correlated with the number of employed plants and the variety of treated ailments, while residency (rural vs. urban) did not. Both residency and education influenced plant procurement methods: rural background and, surprisingly, higher education were linked to a preference for harvesting rather than purchasing plants. Botanical remedies are still commonly used in the treatment of pediatric diseases in Southern Romania, although the variety of taxa seems reduced compared to the past. Further exploration is essential to unlock the maximum benefits of ethnopediatric practices.
PubMed: 38841372
DOI: 10.3389/fphar.2024.1377341 -
Bioinformatics Advances 2024Identifying -regulatory elements (CREs) is crucial for analyzing gene regulatory networks. Next generation sequencing methods were developed to identify CREs but...
MOTIVATION
Identifying -regulatory elements (CREs) is crucial for analyzing gene regulatory networks. Next generation sequencing methods were developed to identify CREs but represent a considerable expenditure for targeted analysis of few genomic loci. Thus, predicting the outputs of these methods would significantly cut costs and time investment.
RESULTS
We present Predmoter, a deep neural network that predicts base-wise Assay for Transposase Accessible Chromatin using sequencing (ATAC-seq) and histone Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) read coverage for plant genomes. Predmoter uses only the DNA sequence as input. We trained our final model on 21 species for 13 of which ATAC-seq data and for 17 of which ChIP-seq data was publicly available. We evaluated our models on and . Our best models showed accurate predictions in peak position and pattern for ATAC- and histone ChIP-seq. Annotating putatively accessible chromatin regions provides valuable input for the identification of CREs. In conjunction with other data, this can significantly reduce the search space for experimentally verifiable DNA-protein interaction pairs.
AVAILABILITY AND IMPLEMENTATION
The source code for Predmoter is available at: https://github.com/weberlab-hhu/Predmoter. Predmoter takes a fasta file as input and outputs h5, and optionally bigWig and bedGraph files.
PubMed: 38841126
DOI: 10.1093/bioadv/vbae074 -
Appetite Jun 2024The market for new plant protein-based meat substitutes is expanding, although their consumption remains limited compared to animal-based protein sources. Further...
The market for new plant protein-based meat substitutes is expanding, although their consumption remains limited compared to animal-based protein sources. Further research is necessary to comprehend the perceptions of diets in which animal-based protein sources are partially replaced with plant proteins. This qualitative study is part of an intervention trial, during which participants adhered to one of the three intervention diets for 12 weeks: the ANIMAL diet (70% animal-based protein/30% plant-based protein), the 50/50 diet (50% animal/50% plant) or the PLANT diet (30% animal/70% plant). The dataset comprises 79 experience diaries from healthy participants aged 23 to 69. The study investigated perceptions of intervention diets, the meat protein (MPPs) and the plant protein products (PPPs) included in the intervention and self-reported changes in perceptions during the intervention period. These perceptions were categorized into eight themes: body-related experiences, practicalities and everyday life, sensory properties, social situations and special occasions, familiarity and novelty, health, ethical aspects, and non-specific liking. Across the diets, body-related experiences were the most frequently mentioned theme. The ANIMAL diet received more negative than positive comments. In contrast, comments on the 50/50 diet were relatively balanced between positive and negative, and the PLANT diet received more positive comments than negative ones. The PPPs were commented on in a positive way more often than the MPPs were. With consistent exposure, participants reported more positive than negative changes in perceptions. However, there is still room for improvement in enhancing the sensory quality and ease of food preparation of PPPs.
PubMed: 38838916
DOI: 10.1016/j.appet.2024.107538 -
Frontiers in Plant Science 2024Fusarium crown rot (FCR) is an important and devastating disease of wheat () caused by the fungus and related pathogens. Using two distinct susceptible cultivars, we...
Fusarium crown rot (FCR) is an important and devastating disease of wheat () caused by the fungus and related pathogens. Using two distinct susceptible cultivars, we investigated the isolation frequencies of and quantified its biomass accumulation and the levels of the associated toxins deoxynivalenol (DON) and DON-3-glucoside (D3G) in inoculated field-grown wheat plants. We detected in stem, peduncle, rachis, and husk tissues, but not in grains, whereas DON and D3G accumulated in stem, rachis, husk, and grain tissues. Disease severity was positively correlated with the frequency of pathogen isolation, biomass, and mycotoxin levels. The amount of biomass and mycotoxin contents in asymptomatic tissue of diseased plants were associated with the distance of the tissue from the diseased internode and the disease severity of the plant. Thus, apparently healthy tissue may harbor and contain associated mycotoxins. This research helps clarify the relationship between occurrence, biomass, and mycotoxin accumulation in tissues of susceptible wheat cultivars with or without disease symptoms, providing information that can lead to more effective control measures.
PubMed: 38835863
DOI: 10.3389/fpls.2024.1356723 -
Frontiers in Plant Science 2024Currently, the control of rhizosphere selection on farms has been applied to achieve enhancements in phenotype, extending from improvements in single root... (Review)
Review
Currently, the control of rhizosphere selection on farms has been applied to achieve enhancements in phenotype, extending from improvements in single root characteristics to the dynamic nature of entire crop systems. Several specific signals, regulatory elements, and mechanisms that regulate the initiation, morphogenesis, and growth of new lateral or adventitious root species have been identified, but much more work remains. Today, phenotyping technology drives the development of root traits. Available models for simulation can support all phenotyping decisions (root trait improvement). The detection and use of markers for quantitative trait loci (QTLs) are effective for enhancing selection efficiency and increasing reproductive genetic gains. Furthermore, QTLs may help wheat breeders select the appropriate roots for efficient nutrient acquisition. Single-nucleotide polymorphisms (SNPs) or alignment of sequences can only be helpful when they are associated with phenotypic variation for root development and elongation. Here, we focus on major root development processes and detail important new insights recently generated regarding the wheat genome. The first part of this review paper discusses the root morphology, apical meristem, transcriptional control, auxin distribution, phenotyping of the root system, and simulation models. In the second part, the molecular genetics of the wheat root system, SNPs, TFs, and QTLs related to root development as well as genome editing (GE) techniques for the improvement of root traits in wheat are discussed. Finally, we address the effect of omics strategies on root biomass production and summarize existing knowledge of the main molecular mechanisms involved in wheat root development and elongation.
PubMed: 38835859
DOI: 10.3389/fpls.2024.1397337 -
Frontiers in Pharmacology 2024Chronic hyperglycemia-induced oxidative stress plays a crucial role in the development of diabetic nephropathy (DN). Moreover, adverse extracellular matrix (ECM)...
INTRODUCTION
Chronic hyperglycemia-induced oxidative stress plays a crucial role in the development of diabetic nephropathy (DN). Moreover, adverse extracellular matrix (ECM) accumulation elevates renal resistive index leading to progressive worsening of the pathology in DN. Nimbidiol is an alpha-glucosidase inhibitor, isolated from the medicinal plant, 'neem' () and reported as a promising anti-diabetic compound. Previously, a myriad of studies demonstrated an anti-oxidative property of a broad-spectrum neem-extracts in various diseases including diabetes. Our recent study has shown that Nimbidiol protects diabetic mice from fibrotic renal dysfunction in part by mitigating adverse ECM accumulation. However, the precise mechanism remains poorly understood.
METHODS
The present study aimed to investigate whether Nimbidiol ameliorates renal injury by reducing oxidative stress in type-1 diabetes. To test the hypothesis, wild-type (C57BL/6J) and diabetic Akita (C57BL/6-/J) mice aged 10-14 weeks were used to treat with saline or Nimbidiol (400 μg kg day) for 8 weeks.
RESULTS
Diabetic mice showed elevated blood pressure, increased renal resistive index, and decreased renal vasculature compared to wild-type control. In diabetic kidney, reactive oxygen species and the expression levels of 4HNE, p22phox, Nox4, and ROMO1 were increased while GSH: GSSG, and the expression levels of SOD-1, SOD-2, and catalase were decreased. Further, eNOS, ACE2, Sirt1 and IL-10 were found to be downregulated while iNOS and IL-17 were upregulated in diabetic kidney. The changes were accompanied by elevated expression of the renal injury markers viz., lipocalin-2 and KIM-1 in diabetic kidney. Moreover, an upregulation of p-NF-κB and a downregulation of IkBα were observed in diabetic kidney compared to the control. Nimbidiol ameliorated these pathological changes in diabetic mice.
CONCLUSION
Altogether, the data of our study suggest that oxidative stress largely contributes to the diabetic renal injury, and Nimbidiol mitigates redox imbalance and thereby protects kidney in part by inhibiting NF-κB signaling pathway in type-1 diabetes.
PubMed: 38835661
DOI: 10.3389/fphar.2024.1369408 -
Frontiers in Microbiology 2024Fungi are an integral part of the nitrogen and phosphorus cycling in trophic networks, as they participate in biomass decomposition and facilitate plant nutrition...
Fungi are an integral part of the nitrogen and phosphorus cycling in trophic networks, as they participate in biomass decomposition and facilitate plant nutrition through root symbioses. Nutrient content varies considerably between the main fungal habitats, such as soil, plant litter or decomposing dead wood, but there are also large differences within habitats. While some soils are heavily loaded with N, others are limited by N or P. One way in which nutrient availability can be reflected in fungi is their content in biomass. In this study, we determined the C, N, and P content (in dry mass) of fruiting bodies of 214 fungal species to inspect how phylogeny and membership in ecological guilds (soil saprotrophs, wood saprotrophs, and ectomycorrhizal fungi) affect the nutrient content of fungal biomass. The C content of fruiting bodies (415 ± 25 mg g) showed little variation (324-494 mg g), while the range of N (46 ± 20 mg g) and P (5.5 ± 3.0 mg g) contents was within one order of magnitude (8-103 mg g and 1.0-18.9 mg g, respectively). Importantly, the N and P contents were significantly higher in the biomass of soil saprotrophic fungi compared to wood saprotrophic and ectomycorrhizal fungi. While the average C/N ratio in fungal biomass was 11.2, values exceeding 40 were recorded for some fungi living on dead wood, typically characterized by low N content. The N and P content of fungal mycelium also showed a significant phylogenetic signal, with differences in nutrient content being relatively low within species and genera of fungi. A strong correlation was found between N and P content in fungal biomass, while the correlation of N content and the N-containing fungal cell wall biopolymer-chitin showed only weak significance. The content of macronutrients in fungal biomass is influenced by the fungal life style and nutrient availability and is also limited by phylogeny.
PubMed: 38835487
DOI: 10.3389/fmicb.2024.1379825