Food drugs as drivers of therapeutic knowledge and the role of chemosensory qualities.

ETHNOPHARMACOLOGICAL RELEVANCE: Chemosensory qualities of botanical drugs are important cues for anticipating physiologic consequences. Whether a botanical drug is used for both, food and medicine, or only as medicine depends on taste preferences, nutritional content, cultural background, and the individual and overall epidemiological context. MATERIAL AND METHODS: We subjected 540 botanical drugs described in De Materia Medica having at least one oral medical application to a tasting panel. The 540 drugs were grouped into those only used for medicine (388) and those also used for food (152). The associations with chemosensory qualities and therapeutic indications were compared across the two groups. We considered 22 experimentally assessed chemosensory qualities and 39 categories of therapeutic use groups. We wanted to know, 1): which chemosensory qualities increase the probability of an orally applied botanical drug to be also used for food ? 2): which chemosensory qualities augment the probability of an orally applied botanical drug to be only used for medicine? and 3): whether there are differences in therapeutic indications between orally applied botanical drugs also used for food (food drugs) and botanical drugs applied exclusively for medicinal purposes (non-food drugs) and, if yes, how the differences can be explained. RESULTS: Chemosensory qualities augmenting the probability of an orally applied botanical drug to be also used for food were sweet, starchy, salty, burning/hot, fruity, nutty, and cooling. Therapeutics used for diarrhoea, as libido modulators, purgatives, laxatives, for expelling parasites, breast and lactation and increasing diuresis, were preferentially sourced from food drugs while drugs used for liver and jaundice, vaginal discharge and humoral management showed significant negative associations with food dugs in ancient Greek-Roman materia medica. CONCLUSION: Therapeutics used for ailments of body organs involved in the digestion of food and the excretion of waste products showed a tendency to be sourced from food drugs. Arguably, the daily consumption of food offered the possibility for observing post-prandial physiologic and pharmacologic effects which led to a high therapeutic versatility of food drugs and the possibility to understand benefits of taste and flavour qualities. The difference in chemosensory qualities between food drugs and non-food drugs is demarcating the organoleptic requirements of food rather than that of medicine.

RND3 Potentiates Proinflammatory Activation through NOTCH Signaling in Activated Macrophages.

Macrophage activation is a complex process with multiple control elements that ensures an adequate response to the aggressor pathogens and, on the other hand, avoids an excess of inflammatory activity that could cause tissue damage. In this study, we have identified RND3, a small GTP-binding protein, as a new element in the complex signaling process that leads to macrophage activation. We show that RND3 expression is transiently induced in macrophages activated through Toll receptors and potentiated by IFN-γ. We also demonstrate that RND3 increases NOTCH signaling in macrophages by favoring NOTCH1 expression and its nuclear activity; however, Rnd3 expression seems to be inhibited by NOTCH signaling, setting up a negative regulatory feedback loop. Moreover, increased RND3 protein levels seem to potentiate NFκB and STAT1 transcriptional activity resulting in increased expression of proinflammatory genes, such as Tnf-α, Irf-1, or Cxcl-10. Altogether, our results indicate that RND3 seems to be a new regulatory element which could control the activation of macrophages, able to fine tune the inflammatory response through NOTCH.

Transfer Learning in Multiple Hypothesis Testing.

In this investigation, a synthesis of Convolutional Neural Networks (CNNs) and Bayesian inference is presented, leading to a novel approach to the problem of Multiple Hypothesis Testing (MHT). Diverging from traditional paradigms, this study introduces a sequence-based uncalibrated Bayes factor approach to test many hypotheses using the same family of sampling parametric models. A two-step methodology is employed: initially, a learning phase is conducted utilizing simulated datasets encompassing a wide spectrum of null and alternative hypotheses, followed by a transfer phase applying this fitted model to real-world experimental sequences. The outcome is a CNN model capable of navigating the complex domain of MHT with improved precision over traditional methods, also demonstrating robustness under varying conditions, including the number of true nulls and dependencies between tests. Although indications of empirical evaluations are presented and show that the methodology will prove useful, more work is required to provide a full evaluation from a theoretical perspective. The potential of this innovative approach is further illustrated within the critical domain of genomics. Although formal proof of the consistency of the model remains elusive due to the inherent complexity of the algorithms, this paper also provides some theoretical insights and advocates for continued exploration of this methodology.

NOTCH4 potentiates the IL-13 induced genetic program in M2 alternative macrophages through the AP1 and IRF4-JMJD3 axis.

IL-13 signaling polarizes macrophages to an M2 alternatively activated phenotype, which regulates tissue repair and anti-inflammatory responses. However, an excessive activation of this pathway leads to severe pathologies, such as allergic airway inflammation and asthma. In this work, we identified NOTCH4 receptor as an important modulator of M2 macrophage activation. We show that the expression of NOTCH4 is induced by IL-13, mediated by Janus kinases and AP1 activity, probably mediated by the IL-13Rα1 and IL-13Rα2 signaling pathway. Furthermore, we demonstrate an important role for NOTCH4 signaling in the IL-13 induced gene expression program in macrophages, including various genes that contribute to pathogenesis of the airways in asthma, such as ARG1, YM1, CCL24, IL-10, or CD-163. We also demonstrate that NOTCH4 signaling modulates IL-13-induced gene expression by increasing IRF4 activity, mediated, at least in part, by the expression of the histone H3K27me3 demethylase JMJD3, and by increasing AP1-dependent transcription. In summary, our results provide evidence for an important role of NOTCH4 signaling in alternative activation of macrophages by IL-13 and suggest that NOTCH4 may contribute to the increased severity of lesions in M2 inflammatory responses, such as allergic asthma, which points to NOTCH4 as a potential new target for the treatment of these pathologies.

LPDA: A new classification method based on linear programming.

The search of separation hyperplanes is an efficient way to find rules with classification purposes. This paper presents an alternative mathematical programming formulation to existing methods to find a discriminant hyperplane. The hyperplane H is found by minimizing the sum of all the distances to the area assigned to the group each individual belongs to. It results in a convex optimization problem for which we find an equivalent linear programming problem. We demonstrate that H exists when the centroids of the two groups are not equal. The method is effective dealing with low and high dimensional data where reduction of the dimension is proposed to avoid overfitting problems. We show the performance of this approach with different data sets and comparisons with other classifications methods. The method is called LPDA and it is implemented in a R package available in https://github.com/mjnueda/lpda.

Mammalian NOTCH Receptor Activation and Signaling Protocols.

The NOTCH signaling pathway is one of the highly conserved key pathways involved in most cell differentiation and proliferation processes during both developmental and adult stages in most animals. The NOTCH signaling pathway appears to be very simple but the existence of several receptors and ligands, their posttranslational modifications, their activation in the cell surface and its migration to the cell nucleus, as well as their interaction with multiple signaling pathways in the cytoplasm and the nucleus of cells, make the study of its function very complex.To determine the activation of NOTCH signaling in animal cells, several complementary approaches can be performed. One of them is the analysis of the transcription of NOTCH receptor target genes HES/HEY by qRT-PCR and Western blot. This approach would give us an idea of the global NOTCH activation and signaling. We can also analyze the NOTCH transcriptional activity by luciferase assays to determine the global or specific activation of NOTCH receptors under a given treatment or in response to the modification of gene expression. On the other hand, we can determine the specific activation of each NOTCH receptor by Western blot with antibodies that recognize the active forms of each NOTCH receptor. For this assay will be very important to collect the cells to be analyzed under the appropriate conditions. Finally, we can detect the intracellular domain of each NOTCH receptor into the cell nucleus by confocal microscopy using the appropriate antibodies that recognize the intracellular domain of the receptors.

MultiBaC: an R package to remove batch effects in multi-omic experiments.

MOTIVATION: Batch effects in omics datasets are usually a source of technical noise that masks the biological signal and hampers data analysis. Batch effect removal has been widely addressed for individual omics technologies. However, multi-omic datasets may combine data obtained in different batches where omics type and batch are often confounded. Moreover, systematic biases may be introduced without notice during data acquisition, which creates a hidden batch effect. Current methods fail to address batch effect correction in these cases. RESULTS: In this article, we introduce the MultiBaC R package, a tool for batch effect removal in multi-omics and hidden batch effect scenarios. The package includes a diversity of graphical outputs for model validation and assessment of the batch effect correction. AVAILABILITY AND IMPLEMENTATION: MultiBaC package is available on Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/MultiBaC.html) and GitHub (https://github.com/ConesaLab/MultiBaC.git). The data underlying this article are available in Gene Expression Omnibus repository (accession numbers GSE11521, GSE1002, GSE56622 and GSE43747). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Different Expression Levels of DLK2 Inhibit NOTCH Signaling and Inversely Modulate MDA-MB-231 Breast Cancer Tumor Growth In Vivo.

NOTCH signaling is implicated in the development of breast cancer tumors. DLK2, a non-canonical inhibitor of NOTCH signaling, was previously shown to be involved in skin and breast cancer. In this work, we studied whether different levels of DLK2 expression influenced the breast cancer characteristics of MDA-MB-231 cells. We found that DLK2 overexpression inhibited NOTCH activation in a dose-dependent manner. Moreover, depending on the level of inhibition of NOTCH1 activation generated by different levels of DLK2 expression, cell proliferation, cell cycle dynamics, cell apoptosis, cell migration, and tumor growth in vivo were affected in opposite directions. Low levels of DLK2 expression produced a slight inhibition of NOTCH1 activation, and enhanced MDA-MB-231 cell invasion in vitro and cell proliferation both in vitro and in vivo. In contrast, MDA-MB-231 cells expressing elevated levels of DLK2 showed a strong inhibition of NOTCH1 activation, decreased cell proliferation, increased cell apoptosis, and were unable to generate tumors in vivo. In addition, DLK2 expression levels also affected some members of other cell signaling pathways implicated in cancer, such as ERK1/2 MAPK, AKT, and rpS6 kinases. Our data support an important role of DLK2 as a protein that can finely regulate NOTCH signaling and affect the tumor properties and growth dynamics of MDA-MB-231 breast cancer cells.

NOTCH4 Exhibits Anti-Inflammatory Activity in Activated Macrophages by Interfering With Interferon-γ and TLR4 Signaling.

NOTCH4 is a member of the NOTCH family of receptors whose expression is intensively induced in macrophages after their activation by Toll-like receptors (TLR) and/or interferon-γ (IFN-γ). In this work, we show that this receptor acts as a negative regulator of macrophage activation by diminishing the expression of proinflammatory cytokines, such as IL-6 and IL-12, and costimulatory proteins, such as CD80 and CD86. We have observed that NOTCH4 inhibits IFN-γ signaling by interfering with STAT1-dependent transcription. Our results show that NOTCH4 reprograms the macrophage response to IFN-γ by favoring STAT3 versus STAT1 phosphorylation without affecting their expression levels. This lower activation of STAT1 results in diminished transcriptional activity and expression of STAT1-dependent genes, including IRF1, SOCS1 and CXCL10. In macrophages, NOTCH4 inhibits the canonical NOTCH signaling pathway induced by LPS; however, it can reverse the inhibition exerted by IFN-γ on NOTCH signaling, favoring the expression of NOTCH-target genes, such as Hes1. Indeed, HES1 seems to mediate, at least in part, the enhancement of STAT3 activation by NOTCH4. NOTCH4 also affects TLR signaling by interfering with NF-κB transcriptional activity. This effect could be mediated by the diminished activation of STAT1. These results provide new insights into the mechanisms by which NOTCH, TLR and IFN-γ signal pathways are integrated to modulate macrophage-specific effector functions and reveal NOTCH4 acting as a new regulatory element in the control of macrophage activation that could be used as a target for the treatment of pathologies caused by an excess of inflammation.

Chitosan modulates Pochonia chlamydosporia gene expression during nematode egg parasitism.

Climate change makes plant-parasitic nematodes (PPN) an increasing threat to commercial crops. PPN can be managed sustainably by the biocontrol fungus Pochonia chlamydosporia (Pc). Chitosan generated from chitin deacetylation enhances PPN parasitism by Pc. In this work, we investigate the molecular mechanisms of Pc for chitosan resistance and root-knot nematode (RKN) parasitism, using transcriptomics. Chitosan and RKN modify the expression of Pc genes, mainly those involved in oxidation-reduction processes. Both agents significantly modify the expression of genes associated to 113 GO terms and 180 Pc genes. Genes encoding putative glycoproteins (Pc adhesives) to nematode eggshell, as well as genes involved in redox, carbohydrate and lipid metabolism trigger the response to chitosan. We identify genes expressed in both the parasitic and endophytic phases of the Pc lifecycle; these include proteases, chitosanases and transcription factors. Using the Pathogen-Host Interaction database (PHI-base), our previous RNA-seq data and RT-PCR of Pc colonizing banana we have investigated genes expressed both in the parasitic and endophytic phases of Pc lifecycle.

Chitosan Induces Plant Hormones and Defenses in Tomato Root Exudates.

In this work, we use electrophysiological and metabolomic tools to determine the role of chitosan as plant defense elicitor in soil for preventing or manage root pests and diseases sustainably. Root exudates include a wide variety of molecules that plants and root microbiota use to communicate in the rhizosphere. Tomato plants were treated with chitosan. Root exudates from tomato plants were analyzed at 3, 10, 20, and 30 days after planting (dap). We found, using high performance liquid chromatography (HPLC) and excitation emission matrix (EEM) fluorescence, that chitosan induces plant hormones, lipid signaling and defense compounds in tomato root exudates, including phenolics. High doses of chitosan induce membrane depolarization and affect membrane integrity. 1H-NMR showed the dynamic of exudation, detecting the largest number of signals in 20 dap root exudates. Root exudates from plants irrigated with chitosan inhibit ca. twofold growth kinetics of the tomato root parasitic fungus Fusarium oxysporum f. sp. radicis-lycopersici. and reduced ca. 1.5-fold egg hatching of the root-knot nematode Meloidogyne javanica.

NOTCH Receptors and DLK Proteins Enhance Brown Adipogenesis in Mesenchymal C3H10T1/2 Cells.

The NOTCH family of receptors and ligands is involved in numerous cell differentiation processes, including adipogenesis. We recently showed that overexpression of each of the four NOTCH receptors in 3T3-L1 preadipocytes enhances adipogenesis and modulates the acquisition of the mature adipocyte phenotype. We also revealed that DLK proteins modulate the adipogenesis of 3T3-L1 preadipocytes and mesenchymal C3H10T1/2 cells in an opposite way, despite their function as non-canonical inhibitory ligands of NOTCH receptors. In this work, we used multipotent C3H10T1/2 cells as an adipogenic model. We used standard adipogenic procedures and analyzed different parameters by using quantitative-polymerase chain reaction (qPCR), quantitative reverse transcription-polymerase chain reaction (qRT-PCR), luciferase, Western blot, and metabolic assays. We revealed that C3H10T1/2 multipotent cells show higher levels of NOTCH receptors expression and activity and lower Dlk gene expression levels than 3T3-L1 preadipocytes. We found that the overexpression of NOTCH receptors enhanced C3H10T1/2 adipogenesis levels, and the overexpression of NOTCH receptors and DLK (DELTA-like homolog) proteins modulated the conversion of cells towards a brown-like adipocyte phenotype. These and our prior results with 3T3-L1 preadipocytes strengthen the idea that, depending on the cellular context, a precise and highly regulated level of global NOTCH signaling is necessary to allow adipogenesis and determine the mature adipocyte phenotype.

NOTCH3 signaling is essential for NF-κB activation in TLR-activated macrophages.

Macrophage activation by Toll receptors is an essential event in the development of the response against pathogens. NOTCH signaling pathway is involved in the control of macrophage activation and the inflammatory processes. In this work, we have characterized NOTCH signaling in macrophages activated by Toll-like receptor (TLR) triggering and determined that DLL1 and DLL4 are the main ligands responsible for NOTCH signaling. We have identified ADAM10 as the main protease implicated in NOTCH processing and activation. We have also observed that furin, which processes NOTCH receptors, is induced by TLR signaling in a NOTCH-dependent manner. NOTCH3 is the only NOTCH receptor expressed in resting macrophages. Its expression increased rapidly in the first hours after TLR4 activation, followed by a gradual decrease, which was coincident with an elevation of the expression of the other NOTCH receptors. All NOTCH1, 2 and 3 contribute to the increased NOTCH signaling detected in activated macrophages. We also observed a crosstalk between NOTCH3 and NOTCH1 during macrophage activation. Finally, our results highlight the relevance of NOTCH3 in the activation of NF-κB, increasing p65 phosphorylation by p38 MAP kinase. Our data identify, for the first time, NOTCH3 as a relevant player in the control of inflammation.

Functionalized CdSe/ZnS Quantum Dots for Intracellular pH Measurements by Fluorescence Lifetime Imaging Microscopy.

pH is an important biomarker for many human diseases and great efforts are being made to develop new pH probes for bioimaging and biomedical applications. Here, the use of three different CdSe/ZnS QDs, functionalized with d-penicillamine and small peptides, as pH probes for fluorescence lifetime imaging microscopy (FLIM) is investigated. The fluorescence pH sensitivity of the nanoparticles is analyzed in different experimental media: aqueous solution, synthetic intracellular medium, and mesenchymal C3H10T1/2 and tumoral SK-MEL-2 cell lines. Different experiments along with theoretical calculations are conducted to unravel the mechanisms causing pH sensitivity of the nanoparticles and the effect of the length and composition of the peripheral branches on their photophysical properties. Absolute intracellular pH values measured in live cells with FLIM using a fluorescent probe based on a QD are reported here for the first time (intracellular pH values of 7.0 and 7.1 for C3H10T1/2 and SK-MEL-2 cells, respectively). These fluorescent nanoprobes can also be used to distinguish between different types of cells in cocultures on the basis of their different fluorescence lifetimes in dissimilar intracellular environments.

Author Correction: DLK proteins modulate NOTCH signaling to influence a brown or white 3T3-L1 adipocyte fate.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

DLK proteins modulate NOTCH signaling to influence a brown or white 3T3-L1 adipocyte fate.

The role of NOTCH signaling in adipogenesis is highly controversial, with data indicating null, positive or negative effects on this differentiation process. We hypothesize that these contradictory results could be due to the different global NOTCH signaling levels obtained in different experimental settings, because of a specific modulation of NOTCH receptors' activity by their ligands. We have previously demonstrated that DLK1 and DLK2, two non-canonical NOTCH1 ligands that inhibit NOTCH1 signaling in a dose-dependent manner, modulate the adipogenesis process of 3T3-L1 preadipocytes. In this work, we show that over-expression of any of the four NOTCH receptors enhanced adipogenesis of 3T3-L1 preadipocytes. We also determine that DLK proteins inhibit not only the activity of NOTCH1, but also the activity of NOTCH2, 3 and 4 receptors to different degrees. Interestingly, we have observed, by different approaches, that NOTCH1 over-expression seems to stimulate the differentiation of 3T3-L1 cells towards a brown-like adipocyte phenotype, whereas cells over-expressing NOTCH2, 3 or 4 receptors or DLK proteins would rather differentiate towards a white-like adipocyte phenotype. Finally, our data also demonstrate a complex feed-back mechanism involving Notch and Dlk genes in the regulation of their expression, which suggest that a precise level of global NOTCH expression and NOTCH-dependent transcriptional activity of specific targets could be necessary to determine the final phenotype of 3T3-L1 adipocytes.

Identification and visualization of differential isoform expression in RNA-seq time series.

Motivation: As sequencing technologies improve their capacity to detect distinct transcripts of the same gene and to address complex experimental designs such as longitudinal studies, there is a need to develop statistical methods for the analysis of isoform expression changes in time series data. Results: Iso-maSigPro is a new functionality of the R package maSigPro for transcriptomics time series data analysis. Iso-maSigPro identifies genes with a differential isoform usage across time. The package also includes new clustering and visualization functions that allow grouping of genes with similar expression patterns at the isoform level, as well as those genes with a shift in major expressed isoform. Availability and implementation: The package is freely available under the LGPL license from the Bioconductor web site. Contact: mj.nueda@ua.es or aconesa@ufl.edu. Supplementary information: Supplementary data are available at Bioinformatics online.

Different expression levels of DLK1 inversely modulate the oncogenic potential of human MDA-MB-231 breast cancer cells through inhibition of NOTCH1 signaling.

NOTCH receptors participate in cancer cell proliferation and survival. Accumulated evidence indicates that, depending on the cellular context, these receptors can function as oncogenes or as tumor-suppressor genes. The epidermal growth factor-like protein delta-like homolog (DLK)1 acts as a NOTCH inhibitor and is involved in the regulation of normal and tumoral growth. In this work, we focused on the role of DLK1 in the control of breast cancer cell growth, a tumor type in which NOTCH receptors have been shown to play both opposite roles. We found that human DLK1 inhibits NOTCH signaling in MDA-MB-231 breast cancer cells. The proliferation rate and invasion capabilities of these cells depended on the level of NOTCH activation and signaling, as regulated by DLK1. High levels of DLK1 expression led to a significant decrease in NOTCH signaling, which was associated with a decrease in breast cancer cell proliferation and invasion. On the contrary, lower levels of NOTCH inhibition, caused by lower levels of DLK1 overexpression, led to enhanced in vitro MDA-MB-231 cell invasion, and to both in vitro and in vivo increased cell proliferation. The data presented in this work suggest that a fine regulation of NOTCH signaling plays an important role in the control of breast cancer cell proliferation and invasion.-Nueda, M.-L., Naranjo, A.-I., Baladrón V., Laborda, J. Different expression levels of DLK1 inversely modulate the oncogenic potential of human MDA-MB-231 breast cancer cells through inhibition of NOTCH1 signaling.

Neurospora crassa transcriptomics reveals oxidative stress and plasma membrane homeostasis biology genes as key targets in response to chitosan.

Chitosan is a natural polymer with antimicrobial activity. Chitosan causes plasma membrane permeabilization and induction of intracellular reactive oxygen species (ROS) in Neurospora crassa. We have determined the transcriptional profile of N. crassa to chitosan and identified the main gene targets involved in the cellular response to this compound. Global network analyses showed membrane, transport and oxidoreductase activity as key nodes affected by chitosan. Activation of oxidative metabolism indicates the importance of ROS and cell energy together with plasma membrane homeostasis in N. crassa response to chitosan. Deletion strain analysis of chitosan susceptibility pointed NCU03639 encoding a class 3 lipase, involved in plasma membrane repair by lipid replacement, and NCU04537 a MFS monosaccharide transporter related to assimilation of simple sugars, as main gene targets of chitosan. NCU10521, a glutathione S-transferase-4 involved in the generation of reducing power for scavenging intracellular ROS is also a determinant chitosan gene target. Ca(2+) increased tolerance to chitosan in N. crassa. Growth of NCU10610 (fig 1 domain) and SYT1 (a synaptotagmin) deletion strains was significantly increased by Ca(2+) in the presence of chitosan. Both genes play a determinant role in N. crassa membrane homeostasis. Our results are of paramount importance for developing chitosan as an antifungal.

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package.

As the use of RNA-seq has popularized, there is an increasing consciousness of the importance of experimental design, bias removal, accurate quantification and control of false positives for proper data analysis. We introduce the NOISeq R-package for quality control and analysis of count data. We show how the available diagnostic tools can be used to monitor quality issues, make pre-processing decisions and improve analysis. We demonstrate that the non-parametric NOISeqBIO efficiently controls false discoveries in experiments with biological replication and outperforms state-of-the-art methods. NOISeq is a comprehensive resource that meets current needs for robust data-aware analysis of RNA-seq differential expression.