Plant cells have the capacity to generate a new plant without egg fertilization by a process known as somatic embryogenesis (SE), in which differentiated somatic cells can form somatic embryos able ...to generate a functional plant. Although there have been advances in understanding the genetic basis of SE, the epigenetic mechanism that regulates this process is still unknown. Here, we show that the embryogenic development of Coffea canephora proceeds through a crosstalk between DNA methylation and histone modifications during the earliest embryogenic stages of SE. We found that low levels of DNA methylation, histone H3 lysine 9 dimethylation (H3K9me2) and H3K27me3 change according to embryo development. Moreover, the expression of LEAFY cotyledon1 (LEC1) and BABY BOOM1 (BBM1) are only observed after SE induction, whereas WUSCHEL-related homeobox4 (WOX4) decreases its expression during embryo maturation. Using a pharmacological approach, it was found that 5-Azacytidine strongly inhibits the embryogenic response by decreasing both DNA methylation and gene expression of LEC1 and BBM1. Therefore, in order to know whether these genes were epigenetically regulated, we used Chromatin Immunoprecipitation (ChIP) assays. It was found that WOX4 is regulated by the repressive mark H3K9me2, while LEC1 and BBM1 are epigenetically regulated by H3K27me3. We conclude that epigenetic regulation plays an important role during somatic embryogenic development, and a molecular mechanism for SE is proposed.
Microbes and plants have evolved biochemical mechanisms to communicate with each other. The molecules responsible for such communication are secreted during beneficial or harmful interactions. ...Hundreds of these molecules secreted into the rhizosphere have been identified, and their functions are being studied in order to understand the mechanisms of interaction and communication among the different members of the rhizosphere community. The importance of root and microbe secretion to the underground habitat in improving crop productivity is increasingly recognized, with the discovery and characterization of new secreting compounds found in the rhizosphere. Different omic approaches, such as genomics, transcriptomics, proteomics, and metabolomics, have expanded our understanding of the first signals between microbes and plants. In this review, we highlight the more recent discoveries related to molecules secreted into the rhizosphere and how they affect plant productivity, either negatively or positively. In addition, we include a survey of novel approaches to studying the rhizosphere and emerging opportunities to direct future studies.
Signaling Overview of Plant Somatic Embryogenesis Méndez-Hernández, Hugo A; Ledezma-Rodríguez, Maharshi; Avilez-Montalvo, Randy N ...
Frontiers in plant science,
02/2019, Letnik:
10
Journal Article
Recenzirano
Odprti dostop
Somatic embryogenesis (SE) is a means by which plants can regenerate bipolar structures from a somatic cell. During the process of cell differentiation, the explant responds to endogenous stimuli, ...which trigger the induction of a signaling response and, consequently, modify the gene program of the cell. SE is probably the most studied plant regeneration model, but to date it is the least understood due to the unclear mechanisms that occur at a cellular level. In this review, the authors seek to emphasize the importance of signaling on plant SE, highlighting the interactions between the different plant growth regulators (PGR), mainly auxins, cytokinins (CKs), ethylene and abscisic acid (ABA), during the induction of SE. The role of signaling is examined from the start of cell differentiation through the early steps on the embryogenic pathway, as well as its relation to a plant's tolerance of different types of stress. Furthermore, the role of genes encoded to transcription factors (TFs) during the embryogenic process such as the
,
,
and
) genes, Arabinogalactan-proteins (AGPs),
and epigenetic factors is discussed.
Somatic embryogenesis (SE) is a cell differentiation process by which a somatic cell changes its genetic program and develops into an embryonic cell. Investigating this process with various explant ...sources
has allowed us to trace somatic embryo development from germination to plantlets and has led to the generation of new technologies, including genetic transformation, endangered species conservation, and synthetic seed production. A transcriptome data comparison from different stages of the developing somatic embryo has revealed a complex network controlling the somatic cell's fate, suggesting that an interconnected network acts at the protein level. Here, we discuss the current progress on SE using proteomic-based data, focusing on changing patterns of proteins during the establishment of the somatic embryo. Despite the advanced proteomic approaches available so far, deciphering how the somatic embryo is induced is still in its infancy. The new proteomics techniques that lead to the quantification of proteins with different abundances during the induction of SE are opening this area of study for the first time. These quantitative differences can elucidate the different pathways involved in SE induction. We envisage that the application of these proteomic technologies can be pivotal to identifying proteins critical to the process of SE, demonstrating the cellular localization, posttranslational modifications, and turnover protein events required to switch from a somatic cell to a somatic embryo cell and providing new insights into the molecular mechanisms underlying SE. This work will help to develop biotechnological strategies for mass production of quality crop material.
Auxin is involved in almost every aspect of plant growth and development, from embryogenesis to senescence. Indole‐3‐acetic acid (IAA) is the main known natural auxin that is synthesized by enzymes ...tryptophan aminotransferase of arabidopsis (TAA) and YUCCA (YUC) of the flavin‐containing monooxygenases family (FMO) from one of the tryptophan‐dependent pathways. Genome‐wide identification and comprehensive analysis of the YUC‐protein family have been conducted in Coffea canephora in the present study. A total of 10 members CcYUC gene family were identified in C. canephora. Phylogenetic analysis revealed that the CcYUC protein family is evolutionarily conserved, and they consist of four groups. In contrast, bioinformatic analysis predicted a hydrophobic transmembrane helix (TMH) for one CcYUC (YUC10) member only. Isoelectric point (pI), molecular mass (Ms), signal peptide, subcellular localization, and phosphorylation sites were predicted for CcYUC proteins. YUC enzymes require the prosthetic group flavin adenine dinucleotide (FAD) and the cofactor nicotinamide adenine dinucleotide phosphate (NADPH) for their enzymatic activity. Therefore, we include the molecular docking for CcYUC2‐FAD‐NADPH‐IPyA and yucasin, which is a specific inhibitor for YUC activity. The docking results showed FAD and NADPH binding at the big and small domain sites, respectively, in CcYUC2. IPyA binds very close to FAD along the big domain, and yucasin competes for the same site as IPA, blocking IAA production. Furthermore, in silico point mutations affect the stability of the CcYUC2‐4 proteins.
Somatic embryogenesis is a powerful biotechnological tool for the mass production of economically important cultivars. Due to the cellular totipotency of plants, somatic cells under appropriate ...conditions are able to develop a complete functional embryo. During the induction of somatic embryogenesis, there are different factors involved in the success or failure of the somatic embryogenesis response. Among these factors, the origin of the explant, the culture medium and the in vitro environmental conditions have been the most studied. However, the secretion of molecules into the media has not been fully addressed. We found that the somatic embryogenesis of Coffea canephora, a highly direct embryogenic species, is disrupted by the metabolites secreted from C. arabica, a poorly direct embryogenic species. These metabolites also affect DNA methylation. Our results show that the abundance of two major phenolic compounds, caffeine and chlorogenic acid, are responsible for inhibiting somatic embryogenesis in C. canephora.
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•Liver stiffness improves after antiviral therapy in most patients.•Hepatocellular carcinoma can still occur after antiviral therapy in patients with cACLD.•Non-invasive tests at ...follow-up can stratify the risk of hepatocellular carcinoma.•Portal hypertension-related decompensation is rare after treatment in patients with cACLD.
It is important to know which patients with hepatitis C are likely to develop liver-related complications after achieving a sustained virological response (SVR) to direct-acting antiviral (DAA) therapy. We aimed to describe the incidence of liver-related events in a population of patients with HCV-associated compensated advanced chronic liver disease (cACLD) who achieved SVR and to identify non-invasive parameters that predict the occurrence of liver-related events.
This 2-center prospective study included 572 patients with cACLD who had been treated with DAAs and had achieved SVR. Patients had liver stiffness measurement (LSM) ≥10 kPa at baseline and had never decompensated (Child-Pugh class A). Laboratory work-up and LSM were performed at baseline and at 1 year of follow-up.
The median follow-up was 2.8 years during which 32 patients (5.6%) presented with a liver-related event. The incidence rate (IR) of portal hypertension-related decompensation was 0.34/100 patient-years. These patients all had baseline LSM >20 kPa, and LSM did not improve during follow-up in 4 out of 5 of them. Hepatocellular carcinoma (HCC) occurred in 25 patients (IR 1.5/100 patient-years). Albumin levels at follow-up (hazard ratio HR 0.08; 95% CI 0.02–0.25) and LSM <10 kPa at follow-up (HR 0.33; 95% CI 0.11–0.96) were independently associated with the risk of HCC. Combining both predictors identified 2 groups with differing risk of HCC occurrence: those with LSM ≥20 kPa at follow-up or those with LSM between 10–20 kPa and albumin levels <4.4 g/dl were at the highest risk (IR ≥1.9/100 patient-years). Visual nomograms predicting HCC risk based on LSM and albumin at 1 year of follow-up were constructed.
In patients with HCV-related cACLD who have achieved SVR with DAAs, HCC is the most frequent liver-related event. Both albumin levels and LSM are useful for stratifying patients based on their risk of developing HCC during follow-up.
New oral antivirals can cure chronic hepatitis C infection, however patients with advanced chronic liver disease are still at risk of presenting with liver-related complications. The most frequent complication after oral antiviral therapy in asymptomatic patients with advanced chronic liver disease was liver cancer. The use of simple parameters such liver stiffness and albumin levels after treatment can help to identify patients at higher or lower risk of liver cancer.
•Unimodal regularisation for cross-entropy loss using the beta distribution.•Comparison with other regularisation methods based on other distributions.•Ordinal output scheme based on the ...stick-breaking process.•Application to convolutional neural networks and several benchmark datasets.
Currently, the use of deep learning for solving ordinal classification problems, where categories follow a natural order, has not received much attention. In this paper, we propose an unimodal regularisation based on the beta distribution applied to the cross-entropy loss. This regularisation encourages the distribution of the labels to be a soft unimodal distribution, more appropriate for ordinal problems. Given that the beta distribution has two parameters that must be adjusted, a method to automatically determine them is proposed. The regularised loss function is used to train a deep neural network model with an ordinal scheme in the output layer. The results obtained are statistically analysed and show that the combination of these methods increases the performance in ordinal problems. Moreover, the proposed beta distribution performs better than other distributions proposed in previous works, achieving also a reduced computational cost.
•Urban ecosystems near cities offer key services, facing urbanisation threats.•Acoustic monitoring assesses habitat status, yet produces vast data.•Neural networks and acoustic indices proposed to ...refine data analysis.•Short-time acoustic indices boost sound event detection accuracy.•Methodology validates with F1-score of 0.614 for habitat conservation.
Urban-natural environments, proximal to rapidly urbanizing cities, provide essential ecosystem functions that benefit both city residents and ecological communities. With escalating urbanization, the resilience of these ecosystems is being progressively challenged, highlighting the need for robust monitoring mechanisms. Acoustic monitoring has emerged as an unobtrusive method to evaluate the status of these environments, capitalizing on indicators that reflect both landscape features and specific acoustic events. Despite potentially offering significant insights, this approach generates a large volume of acoustic data, introducing complexities in subsequent analyses. To mitigate this, we propose integrating artificial neural networks with acoustic indices to enhance data analysis. Our approach emphasizes the usefulness of short-time acoustic indices, computed over finite-duration analysis windows, to enhance polyphonic sound event detection accuracy. Empirical results support the performance of our approach, registering both an F1-Score and an error rate of 0.614. Overall, this study delineates a novel paradigm geared towards enhancing or preserving the biological diversity of urban-natural environments in areas with population growth and urban development.
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