Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana.

MOTIVATIONS: Gene regulatory networks (GRNs) are traditionally inferred from gene expression profiles monitoring a specific condition or treatment. In the last decade, integrative strategies have successfully emerged to guide GRN inference from gene expression with complementary prior data. However, datasets used as prior information and validation gold standards are often related and limited to a subset of genes. This lack of complete and independent evaluation calls for new criteria to robustly estimate the optimal intensity of prior data integration in the inference process. RESULTS: We address this issue for two regression-based GRN inference models, a weighted random forest (weigthedRF) and a generalized linear model estimated under a weighted LASSO penalty with stability selection (weightedLASSO). These approaches are applied to data from the root response to nitrate induction in Arabidopsis thaliana. For each gene, we measure how the integration of transcription factor binding motifs influences model prediction. We propose a new approach, DIOgene, that uses model prediction error and a simulated null hypothesis in order to optimize data integration strength in a hypothesis-driven, gene-specific manner. This integration scheme reveals a strong diversity of optimal integration intensities between genes, and offers good performance in minimizing prediction error as well as retrieving experimental interactions. Experimental results show that DIOgene compares favorably against state-of-the-art approaches and allows to recover master regulators of nitrate induction. AVAILABILITY AND IMPLEMENTATION: The R code and notebooks demonstrating the use of the proposed approaches are available in the repository https://github.com/OceaneCsn/integrative_GRN_N_induction.

Endoscopic Gastrointestinal Placement of Capsule Endoscopy to Investigate the Small Bowel: a Multicentric European Retrospective Series of 630 Procedures in Adult Patients.

BACKGROUND AND AIMS: Small bowel (SB) capsule endoscopy (CE) is a first line procedure for exploring the SB. Endoscopic GastroIntestinal PlacemenT (EGIPT) of SB CE is sometimes necessary. While the experience of EGIPT is large in pediatric populations, we aimed to describe the safety, efficacy and outcomes of EGIPT of SB CE in adult patients. METHODS: The international CApsule endoscopy REsearch (iCARE) group set up a retrospective multicenter study. Patients over 18 year-old who underwent EGIPT of SB CE before May 2022 were included. Data were collected from medical records and capsule recordings. The primary endpoint was the technical success rate of the EGIPT procedures. RESULTS: 630 patients were included (mean age 62.5 years old, 55.9% female) from 39,565 patients (1.6%) issued from 29 centers. EGIPT technical success was achieved in 610 procedures (96.8%). Anesthesia (moderate/deep sedation or general anesthesia) and centers with intermediate or high procedure loads were independent factors of technical success. Severe adverse events occurred in three (0.5%) patients. When technically successful, EGIPT was associated with a high SB CE completion rate (84.4%) and with a substantial diagnostic yield (61.1%). Completion rate was significantly higher when the capsule was delivered in the SB compared to when delivered in the stomach. CONCLUSION: EGIPT of SB CE is highly feasible, safe and comes with high completion rate and diagnostic yield. When indicated, it should rather be performed under anesthesia and the capsule should be delivered in the duodenum rather than in the stomach, for better SB examination outcomes.

Impact of Peripheral Hydrogen Bond on Electronic Properties of the Primary Acceptor Chlorophyll in the Reaction Center of Photosystem I.

Photosystem I (PS I) is a photosynthetic pigment-protein complex that absorbs light and uses the absorbed energy to initiate electron transfer. Electron transfer has been shown to occur concurrently along two (A- and B-) branches of reaction center (RC) cofactors. The electron transfer chain originates from a special pair of chlorophyll a molecules (P700), followed by two chlorophylls and one phylloquinone in each branch (denoted as A-1, A0, A1, respectively), converging in a single iron-sulfur complex Fx. While there is a consensus that the ultimate electron donor-acceptor pair is P700+A0-, the involvement of A-1 in electron transfer, as well as the mechanism of the very first step in the charge separation sequence, has been under debate. To resolve this question, multiple groups have targeted electron transfer cofactors by site-directed mutations. In this work, the peripheral hydrogen bonds to keto groups of A0 chlorophylls have been disrupted by mutagenesis. Four mutants were generated: PsaA-Y692F; PsaB-Y667F; PsaB-Y667A; and a double mutant PsaA-Y692F/PsaB-Y667F. Contrary to expectations, but in agreement with density functional theory modeling, the removal of the hydrogen bond by Tyr → Phe substitution was found to have a negligible effect on redox potentials and optical absorption spectra of respective chlorophylls. In contrast, Tyr → Ala substitution was shown to have a fatal effect on the PS I function. It is thus inferred that PsaA-Y692 and PsaB-Y667 residues have primarily structural significance, and their ability to coordinate respective chlorophylls in electron transfer via hydrogen bond plays a minor role.

A gene regulatory network in Arabidopsis roots reveals features and regulators of the plant response to elevated CO2.

The elevation of CO2 in the atmosphere increases plant biomass but decreases their mineral content. The genetic and molecular bases of these effects remain mostly unknown, in particular in the root system, which is responsible for plant nutrient uptake. To gain knowledge about the effect of elevated CO2 on plant growth and physiology, and to identify its regulatory in the roots, we analyzed genome expression in Arabidopsis roots through a combinatorial design with contrasted levels of CO2 , nitrate, and iron. We demonstrated that elevated CO2 has a modest effect on root genome expression under nutrient sufficiency, but by contrast leads to massive expression changes under nitrate or iron deficiencies. We demonstrated that elevated CO2 negatively targets nitrate and iron starvation modules at the transcriptional level, associated with a reduction in high-affinity nitrate uptake. Finally, we inferred a gene regulatory network governing the root response to elevated CO2 . This network allowed us to identify candidate transcription factors including MYB15, WOX11, and EDF3 which we experimentally validated for their role in the stimulation of growth by elevated CO2 . Our approach identified key features and regulators of the plant response to elevated CO2 , with the objective of developing crops resilient to climate change.

Characterization of the signalling pathways involved in the repression of root nitrate uptake by nitrate in Arabidopsis thaliana.

In Arabidopsis thaliana, root high-affinity nitrate (NO3-) uptake depends mainly on NRT2.1, 2.4, and 2.5, which are repressed by high NO3- supply at the transcript level. For NRT2.1, this regulation is due to the action of (i) feedback down-regulation by N metabolites and (ii) repression by NO3- itself mediated by the transceptor NRT1.1(NPF6.3). However, for NRT2.4 and NRT2.5, the signalling pathway(s) remain unknown as do the molecular elements involved. Here we show that unlike NRT2.1, NRT2.4 and NRT2.5 are not induced in an NO3- reductase mutant but are up-regulated following replacement of NO3- by ammonium (NH4+) as the N source. Moreover, increasing the NO3- concentration in a mixed nutrient solution with constant NH4+ concentration results in a gradual repression of NRT2.4 and NRT2.5, which is suppressed in an nrt1.1 mutant. This indicates that NRT2.4 and NRT2.5 are subjected to repression by NRT1.1-mediated NO3- sensing, and not to feedback repression by reduced N metabolites. We further show that key regulators of NRT2 transporters, such as HHO1, HRS1, PP2C, LBD39, BT1, and BT2, are also regulated by NRT1.1-mediated NO3- sensing, and that several of them are involved in NO3- repression of NRT2.1, NRT2.4, and NRT2.5. Finally, we provide evidence that it is the phosphorylated form of NRT1.1 at the T101 residue, which is most active in triggering the NRT1.1-mediated NO3- regulation of all these genes. Altogether, these data led us to propose a regulatory model for high-affinity NO3- uptake in Arabidopsis, highlighting several NO3- transduction cascades downstream of the phosphorylated form of the NRT1.1 transceptor.

WallFlex® and Evolution® Duodenal Stents Have Similar Efficacy but Different Safety for Malignant Gastric Outlet Obstruction.

BACKGROUND: The WallFlex® and Evolution® stents are the most widely used duodenal stents, but no study has compared them. AIMS: We aimed to compare the efficacy and safety of WallFlex® and Evolution® stents for malignant gastric outlet obstruction. METHODS: We included all consecutive patients who were treated for malignant gastric outlet obstruction with WallFlex® or Evolution® self-expandable metal uncovered duodenal stents between 2013 and 2020. Multivariable Cox models were performed to assess duodenal stent failure, as defined by gastric outlet obstruction necessitating another duodenal stent. RESULTS: We included 129 patients: 74 received a WallFlex® stent and 55 received an Evolution® stent. The non-failure rate was of 68% (95%CI 55-84) and 65% (95%CI 50-84) at 6 months and of 48% (95%CI 32-73) and 45% (95%CI 27-74) at 1 year, with the WallFlex® and Evolution® stents, respectively. The median time to duodenal stent failure was 10.5 months in the WallFlex® group and 9.3 months in the Evolution® group. The type of duodenal stent was not associated with duodenal stent failure (p logrank = 0.43, adjusted hazard ratio 1.55; 95%CI 0.77-3.14). The overall survival was similar between the two groups (p logrank = 0.92). Three patients had complications due to Evolution® stents; it consisted in dismantled stents that led to hemorrhage in one patient. CONCLUSIONS: WallFlex® and Evolution® duodenal stents had similar efficacy for malignant gastric outlet obstruction. There were more adverse events with Evolution® stents.

Dilatation of the main pancreatic duct of unknown origin: causes and risk factors of pre-malignancy or malignancy.

INTRODUCTION: A dilatation of the main pancreatic duct (MPD) is mainly due to obstructive causes (pancreatic tumor, chronic pancreatitis) or intraductal papillary mucinous neoplasm (IPMN). This study aims to assess the risk of pre-malignancy or malignancy in case of MPD dilatation with no visible mass nor obstructive calcification on computed tomography scan (CT-scan) in a population operated for it. PATIENTS AND METHODS: All patients operated on from November 2015 to December 2019 in our center for a significant dilatation of the MPD without visible obstructive cause on CT-scan were included. Preoperative work-up included at least CT-scan, magnetic resonance imaging (MRI), and endoscopic ultrasonography (EUS). Primary endpoint was the final pathological diagnosis. Secondary endpoints were predictive factors of malignancy. RESULTS: 101 patients were included, mean age 68 years-old. Final pathological data were pancreatic adenocarcinoma (n = 2), IPMN with high-grade dysplasia (n = 37), high-grade Pancreatic Intraepithelial Neoplasia (PanIN) (n = 2) (total of pre-malignant or malignant lesions: n = 41), neuroendocrine tumor (n = 6), IPMN with low-grade dysplasia (n = 45), low-grade PanIN (n = 5), chronic pancreatitis (n = 3), and benign stenosis (n = 1). On preoperative explorations, the median diameter of MPD was 7 mm [3-35]. MRI and/or EUS showed intraductal material, nodule, or cyst in 22, 32, and 52 patients, respectively; 22 patients without nodule visible on MRI or EUS had still a pre-malignant or malignant lesion. In multivariate analysis, predictive factors for pre-malignancy or malignancy were symptoms before surgery (p = 0.01), MPD dilatation without downstream stenosis (p = 0.046), and the presence of nodule (p = 0.009). CONCLUSION: A dilatation of the MPD without detectable mass or obstructive calcification on CT-scan was associated with a pre-malignant or malignant lesion in 41 patients. Symptoms before surgery, MPD dilatation without duct narrowing, and the presence of nodules on MRI/EUS were associated with the risk of  pre-malignancy or malignancy.

Loss of Polycomb proteins CLF and LHP1 leads to excessive RNA degradation in Arabidopsis.

Polycomb-group (PcG) proteins are major chromatin complexes that regulate gene expression, mainly described as repressors keeping genes in a transcriptionally silent state during development. Recent studies have nonetheless suggested that PcG proteins might have additional functions, including targeting active genes or acting independently of gene expression regulation. However, the reasons for the implication of PcG proteins and their associated chromatin marks on active genes are still largely unknown. Here, we report that combining mutations for CURLY LEAF (CLF) and LIKE HETEROCHROMATIN PROTEIN1 (LHP1), two Arabidopsis PcG proteins, results in deregulation of expression of active genes that are targeted by PcG proteins or enriched in associated chromatin marks. We show that this deregulation is associated with accumulation of small RNAs corresponding to massive degradation of active gene transcripts. We demonstrate that transcriptionally active genes and especially those targeted by PcG proteins are prone to RNA degradation, even though deregulation of RNA degradation following the loss of function of PcG proteins is not likely to be mediated by a PcG protein-mediated chromatin environment. Therefore, we conclude that PcG protein function is essential to maintain an accurate level of RNA degradation to ensure accurate gene expression.

Oxygen management during kombucha production: Roles of the matrix, microbial activity, and process parameters.

Oxygen plays a key role in kombucha production, since the production of main organic acids, acetic and gluconic acids, is performed through acetic acid bacteria's oxidative metabolism. Oxygen consumption during traditional kombucha production was investigated by comparing kombucha to mono and cocultures in sugared tea of microorganisms isolated from kombucha. Two yeasts, Brettanomyces bruxellensis and Hanseniaspora valbyensis and one acetic acid bacterium Acetobacter indonesiensis were used. Results showed that tea compounds alone were mainly responsible for oxygen depletion during the first 24 h following inoculation. During the first 7 days phase of production in open vessel, the liquid surface was therefore the only access to oxygen for microorganisms, as anaerobic conditions were sustained below this area. During the 5 days second phase of production after bottling, comparison of cultures with different microbial compositions showed that oxygen was efficiently depleted in the head space of the bottles in 3-6 h if the acetic acid bacterium was present. Lower access to oxygen after bottling stimulated ethanol production in B. bruxellensis and H. valbyensis cocultures with or without A. indonesiensis. This study provides insights into the management of oxygen and the roles of the tea and the biofilm during kombucha production.

Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suite.

BACKGROUND: High-throughput transcriptomic datasets are often examined to discover new actors and regulators of a biological response. To this end, graphical interfaces have been developed and allow a broad range of users to conduct standard analyses from RNA-seq data, even with little programming experience. Although existing solutions usually provide adequate procedures for normalization, exploration or differential expression, more advanced features, such as gene clustering or regulatory network inference, often miss or do not reflect current state of the art methodologies. RESULTS: We developed here a user interface called DIANE (Dashboard for the Inference and Analysis of Networks from Expression data) designed to harness the potential of multi-factorial expression datasets from any organisms through a precise set of methods. DIANE interactive workflow provides normalization, dimensionality reduction, differential expression and ontology enrichment. Gene clustering can be performed and explored via configurable Mixture Models, and Random Forests are used to infer gene regulatory networks. DIANE also includes a novel procedure to assess the statistical significance of regulator-target influence measures based on permutations for Random Forest importance metrics. All along the pipeline, session reports and results can be downloaded to ensure clear and reproducible analyses. CONCLUSIONS: We demonstrate the value and the benefits of DIANE using a recently published data set describing the transcriptional response of Arabidopsis thaliana under the combination of temperature, drought and salinity perturbations. We show that DIANE can intuitively carry out informative exploration and statistical procedures with RNA-Seq data, perform model based gene expression profiles clustering and go further into gene network reconstruction, providing relevant candidate genes or signalling pathways to explore. DIANE is available as a web service ( https://diane.bpmp.inrae.fr ), or can be installed and locally launched as a complete R package.

Conserved residue PsaB-Trp673 is essential for high-efficiency electron transfer between the phylloquinones and the iron-sulfur clusters in Photosystem I.

Despite the high level of symmetry between the PsaA and PsaB polypeptides in Photosystem I, some amino acids pairs are strikingly different, such as PsaA-Gly693 and PsaB-Trp673, which are located near a cluster of 11 water molecules between the A1A and A1B quinones and the FX iron-sulfur cluster. In this work, we changed PsaB-Trp673 to PsaB-Phe673 in Synechocystis sp. PCC 6803. The variant contains ~ 85% of wild-type (WT) levels of Photosystem I but is unable to grow photoautotrophically. Both time-resolved and steady-state optical measurements show that in the PsaB-W673F variant less than 50% of the electrons reach the terminal iron-sulfur clusters FA and FB; the majority of the electrons recombine from A1A- and A1B-. However, in those reaction centers which pass electrons forward the transfer is heterogeneous: a minor population shows electron transfer rates from A1A- and A1B- to FX slightly slower than that of the WT, whereas a major population shows forward electron transfer rates to FX slowed to the ~ 10 µs time range. Competition between relatively similar forward and backward rates of electron transfer from the quinones to the FX cluster account for the relatively low yield of long-lived charge separation in the PsaB-W673F variant. A higher water content and its increased mobility observed in MD simulations in the interquinone cavity of the PsaB-W673F variant shifts the pK of PsaB-Asp575 and allows its deprotonation in situ. The heterogeneity found may be rooted in protonation state of PsaB-Asp575, which controls whether electron transfer can proceed beyond the phylloquinone cofactors.

Feasibility and diagnostic yield of small-bowel capsule endoscopy in patients with surgically altered gastric anatomy: the SAGA study.

BACKGROUND AND AIMS: Little is known about small-bowel (SB) capsule endoscopy (CE) in patients with a history of gastric surgery. This study aims to evaluate the feasibility and diagnostic yield (DY) of orally ingested SB-CE in patients with surgically altered gastric anatomy. METHODS: Twenty-four European centers retrospectively identified patients who had SB-CE after total or subtotal gastrectomy. The primary outcome was the DY of SB-CE (intermediate P1 to highly P2 relevant findings). Secondary outcomes were gastric and SB transit times, completion, cleanliness, and adverse event rates. RESULTS: Studied were 248 procedures from 243 patients (mean age, 62 years) with a history of partial gastrectomy (Billroth I, 13.1%; Billroth II, 34.6%), total gastrectomy (7.4%), Whipple procedure (12.8%), sleeve gastrectomy (7.2%), or gastric bypass surgery (24.7%). Obscure GI bleeding was the most frequent indication (85.1%). SB completion rate was 84.3%. One capsule retention in the SB was noted (adverse event rate, .4%). Median SB transit time was 286 minutes (interquartile range [235; 387]). Cleanliness was rated as adequate in 92.1% of procedures. After exclusion of abnormalities found at the upper anastomotic site, the DY was 43.6%, with inflammatory/ulcerated lesions observed more frequently (23.4%) than vascular lesions (21.0%). CONCLUSIONS: SB-CE seems to be feasible and safe in selected patients with a history of major gastric surgery and comes with a high DY. The spectrum of abnormal SB findings in these patients may be different from what is known from the literature in nonoperated patients.

[Epidemiology and risk factors of nosocomial COVID infections in the Service of internal medicine at CHUV]. / Épidémiologie et facteurs de risque des infections Covid nosocomiales dans le Service de médecine interne du CHUV.

Nosocomial COVID-19 infections are a challenge for hospitals. In order to assess possible demographic, personal, environmental or medical care related risk factors, data of nosocomial cases occurring in the Service of internal medicine at CHUV between February and March 2021 were retrospectively analyzed. Neither personal nor medical care related factors were identified as risk factor for a nosocomial infection. However, a significant number of patients with hospital-acquired COVID infection stayed in a 5-bed ward (versus 1-2 beds) and shared toilets in these rooms. Patient distancing measures and weekly screening led to a subsequent significant reduction of nosocomial SARS-CoV-2 infections.

Les infections Covid-19 nosocomiales sont un défi pour les hôpitaux. Afin d'identifier d'éventuels facteurs de risque démographiques, personnels, environnementaux ou de prise charge, nous avons analysé rétrospectivement les cas nosocomiaux survenus dans le Service de médecine interne du CHUV en février-mars 2021. Aucun facteur personnel ou de prise en charge n'a été mis en évidence. Par contre, un plus grand nombre de patients avec infection nosocomiale avait séjourné dans une chambre à 5 lits (versus 1-2 lits) et utilisé les toilettes communes de ces chambres. La limitation de l'occupation des chambres multiples et des dépistages hebdomadaires ont permis de contrôler la transmission nosocomiale du SARS-CoV-2.

Sequential mutational evaluation of CALR -mutated myeloproliferative neoplasms with thrombocytosis reveals an association between CALR allele burden evolution and disease progression.

In myeloproliferative neoplasms (MPN), JAK2V617F allele burden measurement has an impact on prognosis that helps in patient monitoring. Less is known about its usefulness in CALR-mutated cases. Additional mutations found by next-generation sequencing have also shown an impact on prognosis that may drive therapeutic choices, especially in myelofibrosis, but few studies focused on CALR-mutated patients. We performed a molecular evaluation combining next-generation sequencing with a myeloid panel and CALR allele burden measurement at diagnosis and during follow-up in a cohort of 45 patients with CALR-mutated essential thrombocythaemia. The bone marrow histology was also blindly reviewed in order to apply the WHO2016 classification. The most frequently mutated gene was TET2 (11/21 mutations). CALR type 1-like patients appear to have a more complex molecular landscape. We found an association between disease progression and CALR allele burden increase during follow-up, independently of additional mutations and WHO2016-reviewed diagnosis. Patients with disease progression at the time of follow-up showed a significant increase in CALR allele burden (+16·7%, P = 0·005) whereas patients without disease progression had a stable allele burden (+3·7%, P = 0·194). This result argues for clinical interest in CALR allele burden monitoring.

NRT2.1 C-terminus phosphorylation prevents root high affinity nitrate uptake activity in Arabidopsis thaliana.

In Arabidopsis thaliana, NRT2.1 codes for a main component of the root nitrate high-affinity transport system. Previous studies revealed that post-translational regulation of NRT2.1 plays an important role in the control of root nitrate uptake and that one mechanism could correspond to NRT2.1 C-terminus processing. To further investigate this hypothesis, we produced transgenic plants with truncated forms of NRT2.1. This revealed an essential sequence for NRT2.1 activity, located between the residues 494 and 513. Using a phospho-proteomic approach, we found that this sequence contains one phosphorylation site, at serine 501, which can inactivate NRT2.1 function when mimicking the constitutive phosphorylation of this residue in transgenic plants. This phenotype could neither be explained by changes in abundance of NRT2.1 and NAR2.1, a partner protein of NRT2.1, nor by a lack of interaction between these two proteins. Finally, the relative level of serine 501 phosphorylation was found to be increased by ammonium nitrate in wild-type plants, leading to the inactivation of NRT2.1 and to a decrease in high affinity nitrate transport into roots. Altogether, these observations reveal a new and essential mechanism for the regulation of NRT2.1 activity.

The Chromatin Factor HNI9 and ELONGATED HYPOCOTYL5 Maintain ROS Homeostasis under High Nitrogen Provision.

Reactive oxygen species (ROS) can accumulate in cells at excessive levels, leading to unbalanced redox states and to potential oxidative stress, which can have damaging effects on the molecular components of plant cells. Several environmental conditions have been described as causing an elevation of ROS production in plants. Consequently, activation of detoxification responses is necessary to maintain ROS homeostasis at physiological levels. Misregulation of detoxification systems during oxidative stress can ultimately cause growth retardation and developmental defects. Here, we demonstrate that Arabidopsis (Arabidopsis thaliana) plants grown in a high nitrogen (N) environment express a set of genes involved in detoxification of ROS that maintain ROS at physiological levels. We show that the chromatin factor HIGH NITROGEN INSENSITIVE9 (HNI9) is an important mediator of this response and is required for the expression of detoxification genes. Mutation in HNI9 leads to elevated ROS levels and ROS-dependent phenotypic defects under high but not low N provision. In addition, we identify ELONGATED HYPOCOTYL5 as a major transcription factor required for activation of the detoxification program under high N. Our results demonstrate the requirement of a balance between N metabolism and ROS production, and our work establishes major regulators required to control ROS homeostasis under conditions of excess N.

Redox metabolism: the hidden player in carbon and nitrogen signaling?

While decades of research have considered redox metabolism as purely defensive, recent results show that reactive oxygen species (ROS) are necessary for growth and development. Close relationships have been found between the regulation of nitrogen metabolism and ROS in response to both carbon and nitrogen availability. Root nitrate uptake and nitrogen metabolism have been shown to be regulated by a signal from the oxidative pentose phosphate pathway (OPPP) in response to carbon signaling. As a major source of NADP(H), the OPPP is critical to maintaining redox balance under stress situations. Furthermore, recent results suggest that at least part of the regulation of the root nitrate transporter by nitrogen signaling is also linked to the redox status of the plant. This leads to the question of whether there is a more general role of redox metabolism in the regulation of nitrogen metabolism by carbon and nitrogen. This review highlights the role of the OPPP in carbon signaling and redox metabolism, and the interaction between redox and nitrogen metabolism. We discuss how redox metabolism could be an important player in the regulation of nitrogen metabolism in response to carbon/nitrogen interaction and the implications for plant adaptation to extreme environments and future crop development.

Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects.

There is renewed interest in whether environmentally induced changes in phenotypes can be heritable. In plants, heritable trait variation can occur without DNA sequence mutations through epigenetic mechanisms involving DNA methylation. However, it remains unknown whether this alternative system of inheritance responds to environmental changes and if it can provide a rapid way for plants to generate adaptive heritable phenotypic variation. To assess potential transgenerational effects induced by the environment, we subjected four natural accessions of Arabidopsis thaliana together with the reference accession Col-0 to mild drought in a multi-generational experiment. As expected, plastic responses to drought were observed in each accession, as well as a number of intergenerational effects of the parental environments. However, after an intervening generation without stress, except for a very few trait-based parental effects, descendants of stressed and non-stressed plants were phenotypically indistinguishable irrespective of whether they were grown in control conditions or under water deficit. In addition, genome-wide analysis of DNA methylation and gene expression in Col-0 demonstrated that, while mild drought induced changes in the DNA methylome of exposed plants, these variants were not inherited. We conclude that mild drought stress does not induce transgenerational epigenetic effects.

Microbiological and technological parameters impacting the chemical composition and sensory quality of kombucha.

Kombucha is a beverage made from sugared tea transformed by yeasts and acetic acid bacteria. Being originally homemade, it has become an industrially produced soft drink whose quality standards are poorly defined and whose production process is still not fully controlled. Based on current knowledge in beverages, links between kombucha's chemical composition and sensorial compounds are drawn. Macromolecules create turbidity, whereas uncharacterized tea pigments derivatives participate in the color. Residual sugars bring sweetness and organic acids produced by acetic acid bacteria form its characteristic sour taste. Acetic acid is also part of its aroma profile, although little data are available on the smell of kombucha. Carbon dioxide, potentially polyphenols, and residual ethanol are involved in the mouthfeel. In this review, after defining the key compounds that shape the characteristic sensory properties of kombucha, the impact of different production parameters is discussed. Water composition is determinant in the extraction of tea compounds along with the tea type and infusion duration and temperature. The type and amount of sweeteners play a role in the sweetness and influences the production kinetics. Similarly, the amount of inoculum and its microbial composition have an effect on the production, but the role of the vessels' geometry and temperature are also essential parameters that can be used to adjust the acidification phase's duration. Despite the amount of research carried out, further investigations of kombucha's sensory characteristics are needed. Such research could lead to a better definition of kombucha's quality and to an improved control over its production process.

Transcriptional integration of the responses to iron availability in Arabidopsis by the bHLH factor ILR3.

Iron (Fe) homeostasis is crucial for all living organisms. In mammals, an integrated posttranscriptional mechanism couples the regulation of both Fe deficiency and Fe excess responses. Whether in plants an integrated control mechanism involving common players regulates responses both to deficiency and to excess is still to be determined. In this study, molecular, genetic and biochemical approaches were used to investigate transcriptional responses to both Fe deficiency and excess. A transcriptional activator of responses to Fe shortage in Arabidopsis, called bHLH105/ILR3, was found to also negatively regulate the expression of ferritin genes, which are markers of the plant's response to Fe excess. Further investigations revealed that ILR3 repressed the expression of several structural genes that function in the control of Fe homeostasis. ILR3 interacts directly with the promoter of its target genes, and repressive activity was conferred by its dimerisation with bHLH47/PYE. Last, this study highlighted that important facets of plant growth in response to Fe deficiency or excess rely on ILR3 activity. Altogether, the data presented herein support that ILR3 is at the centre of the transcriptional regulatory network that controls Fe homeostasis in Arabidopsis, in which it acts as both transcriptional activator and repressor.