Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis

<p>Abstract</p> <p>Background</p> <p>Holistic profiling and systems biology studies of nutrient availability are providing more and more insight into the mechanisms by which gene expression responds to diverse nutrients and metabolites. Less is known about the mechanisms by which gene expression is affected by endogenous metabolites, which can change dramatically during development. Multivariate statistics and correlation network analysis approaches were applied to non-targeted profiling data to investigate transcriptional and metabolic states and to identify metabolites potentially influencing gene expression during the heterotrophic to autotrophic transition of seedling establishment.</p> <p>Results</p> <p>Microarray-based transcript profiles were obtained from extracts of Arabidopsis seeds or seedlings harvested from imbibition to eight days-old. ¹H-NMR metabolite profiles were obtained for corresponding samples. Analysis of transcript data revealed high differential gene expression through seedling emergence followed by a period of less change. Differential gene expression increased gradually to day 8, and showed two days, 5 and 7, with a very high proportion of up-regulated genes, including transcription factor/signaling genes. Network cartography using spring embedding revealed two primary clusters of highly correlated metabolites, which appear to reflect temporally distinct metabolic states. Principle Component Analyses of both sets of profiling data produced a chronological spread of time points, which would be expected of a developmental series. The network cartography of the transcript data produced two distinct clusters comprising days 0 to 2 and days 3 to 8, whereas the corresponding analysis of metabolite data revealed a shift of day 2 into the day 3 to 8 group. A metabolite and transcript pair-wise correlation analysis encompassing all time points gave a set of 237 highly significant correlations. Of 129 genes correlated to sucrose, 44 of them were known to be sucrose responsive including a number of transcription factors.</p> <p>Conclusions</p> <p>Microarray analysis during germination and establishment revealed major transitions in transcriptional activity at time points potentially associated with developmental transitions. Network cartography using spring-embedding indicate that a shift in the state of nutritionally important metabolites precedes a major shift in the transcriptional state going from germination to seedling emergence. Pair-wise linear correlations of transcript and metabolite levels identified many genes known to be influenced by metabolites, and provided other targets to investigate metabolite regulation of gene expression during seedling establishment.</p

Polyhydroxybutyrate (PHB) produced from red grape pomace: Effect of purification processes on structural, thermal and antioxidant properties.

Red grape pomace was used as a source for poly(3-hydroxybutyrate) (PHB) production, which was then subject to a range of purification processes. The different PHB biopolymers were characterized for chemical structure, crystallinity, thermal properties, colour, release of compounds into different food simulants and antioxidant inhibition, and comparisons were made with a commercially available PHB. An increase in purification steps did not have a significant effect on the high thermal stability of the extracted biopolymer, but it decreased the degree of crystallinity and the presence of amino acids and aromatic compounds. With additional purification, the PHB powders also whitened and the number of components released from the biopolymer into food simulants decreased. The released compounds presented antioxidant inhibition, which has not been previously reported in the literature or with commercially available polyhydroxyalkanoates. This is of great interest for food packaging and biomedical industries where the addition of antioxidant additives to improve PHB functional properties may not be necessary and could be avoided.The authors would like to thank the Ministry of Business, Innovation and Employment of New Zealand (MBIE, Biocide Toolbox programme), the Basque Government (KK-2021/00131 and IT1658-22) and PID2021-124294OB-C22 project funded by MCIN/AEI/10.13039/501100011033/FEDER, UE. A.E. thanks the State Research Agency of Spain within the Juan de la Cierva - Incorporation action (IJC2019-039697I)

Disruption of the potassium channel regulatory subunit Kcne2 causes iron-deficient anemia

Iron homeostasis is a dynamic process that is tightly controlled to balance iron uptake, storage, and export. Reduction of dietary iron from the ferric to the ferrous form is required for uptake by solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2 (Slc11a2) into the enterocytes. Both processes are proton dependent and have led to the suggestion of the importance of acidic gastric pH for the absorption of dietary iron. Potassium voltage-gated channel subfamily E, member 2 (KCNE2), in combination with potassium voltage-gated channel, KQT-like subfamily, member 1 (KCNQ1), form a gastric potassium channel essential for gastric acidification. Deficiency of either Kcne2 or Kcnq1 results in achlorhydia, gastric hyperplasia, and neoplasia, but the impact on iron absorption has not, to our knowledge, been investigated. Here we report that Kcne2-deficient mice, in addition to the previously reported phenotypes, also present with iron-deficient anemia. Interestingly, impaired function of KCNQ1 results in iron-deficient anemia in Jervell and Lange-Nielsen syndrome patients. We speculate that impaired function of KCNE2 could result in the same clinical phenotype

Stitching time: artisanal collaboration and slow fashion in post-disaster Haiti

The promotion of the textile and garment industries as a development strategy following the 2010 earthquake in Haiti and a US-backed return to garment assembly lines has prompted an interrogation of some of the local impacts of transnational manufacturing practices in this context. This essay seeks to evaluate alternative fashion practices and social enterprises in Haiti that are currently challenging and disassembling the contemporary forms of slavery predominant in offshore low-wage garment manufacturing. These slower “ethical fashion” cooperatives integrate traditional Haitian skills and cultural konesans (knowledge) with international design languages and market savoir-faire to produce unique handcrafted pieces for the global fashion market. Yet, as this paper argues, these collaborations reveal ongoing neo-colonial inequalities that side-line Haitian agency. Their uneven modes of production and marketing strategies often involve short-term interventions by Western fashion designers that undermine Haitian expertise. This examination of artisan “development” therefore seeks to situate these enterprises in a longer history of sustainability in Haiti, and considers how stitching cloth in response to disaster can retrace the stories of loss and survival of communities and mediate cultural knowledge

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care

Modelling the peroxisomal carbon leak during lipid mobilization in Arabidopsis

Abstract Mutation of the ACN1 (acetate non-utilizing 1) locus of Arabidopsis results in altered acetate assimilation into gluconeogenic sugars and anapleurotic amino acids and leads to an overall depression in primary metabolite levels by approx. 50% during seedling development. Levels of acetyl-CoA were higher in acn1 compared with wild-type, which is counterintuitive to the activity of ACN1 as a peroxisomal acetyl-CoA synthetase. We hypothesize that ACN1 recycles free acetate to acetyl-CoA within peroxisomes in order that carbon remains fed into the glyoxylate cycle. When ACN1 is not present, carbon in the form of acetate can leak out of peroxisomes and is reactivated to acetyl-CoA within the cytosol. Kinetic models incorporating estimates of carbon input and pathway dynamics from a variety of literature sources have proven useful in explaining how ACN1 may prevent the carbon leak and even contribute to the control of peroxisomal carbon metabolism. Lipid mobilization in oilseeds The processes by which a seed starts to germinate and quickly establishes itself as a fully self-nourishing organism, as well as the mechanisms that prevent these processes when growth conditions prove unfavourable, are truly remarkable. For seed to become seedling, the seed must imbibe, experience favourable environmental signals to germinate and then produce a set of machinery for the breakdown of reserves. In a few days after germination this machinery is degraded and the photosynthetic machinery takes over to make a self-sufficient plant. The processes that govern dormancy and germination have been studied extensively both physiologically and molecularly The control of lipid mobilization The efficient degradation of lipid stores requires the coordinate use of fatty acids by β-oxidation and the subsequent assimilation of acetyl-CoA. The induction of enzyme activities in both pathways matches the profile of TAG (triacylglycerol) degradation Overall, very few studies have been directed toward standard metabolic control processes regulating lipid mobilization in plants. One study attempted to investigate the regulation of the glyoxylate cycle using castor bean endosperm Creating models and fitting parameters We chose a relatively simple kinetic model in which metabolite concentrations are governed by mass flow and enzymatic rate constants E-MEXP-2493). A number of assumptions had to be made to form the model and assign rate constants. A major assumption of the model was a potential efflux of acetate from peroxisomes (k T ). Tobacco plants expressing a yeast acetyl-CoA hydrolase in mitochondria had elevated acetyl-CoA levels, which probably was due to acetate export and reactivation in the cytosol Output from the model The goal of the modelling was to produce realistic values for rate constants that would explain the observations that acetylCoA levels and metabolites were lower in acn1 than wild-type at day 3. By HPLC In conclusion, the model has allowed us to hypothesize that ACN1 prevents a leak of carbon as acetate from peroxisomes. We can extend this hypothesis to ACN1 serving a role to help regulate the flow of acetyl-CoA between β-oxidation and the glyoxylate cycle as part of a synthetase/thioesterase substrate cycle. Further refinement of the model will be possible by studying the fate of isotopically labelled fatty acids, acetate and other substrates in acn1 and other mutants, and obtaining metabolite levels in experiments conducted over the developmental time course