UPLIFT Plastic Upcycling project

This repository will collect the datasets, public deliverables and published articles of the UPLIFT project, funded European Union’s Horizon 2020 research and innovation programme under grant agreement Nº 953073

Figure 3 from: Cannon P, Buddie A, Bridge P, de Neergaard E, Lübeck M, Askar M (2012) Lectera, a new genus of the Plectosphaerellaceae for the legume pathogen Volutella colletotrichoides. MycoKeys 3: 23-36. https://doi.org/10.3897/mycokeys.3.3065

Figure 3 - ML tree of GAPDH sequences, of a subset of the strains used for the ITS sequence set

Figure 1 from: Cannon P, Buddie A, Bridge P, de Neergaard E, Lübeck M, Askar M (2012) Lectera, a new genus of the Plectosphaerellaceae for the legume pathogen Volutella colletotrichoides. MycoKeys 3: 23-36. https://doi.org/10.3897/mycokeys.3.3065

Figure 1 - ML ITS phyogram showing the phylogenetic position of Lectera species

Figure 2 from: Cannon P, Buddie A, Bridge P, de Neergaard E, Lübeck M, Askar M (2012) Lectera, a new genus of the Plectosphaerellaceae for the legume pathogen Volutella colletotrichoides. MycoKeys 3: 23-36. https://doi.org/10.3897/mycokeys.3.3065

Figure 2 - Lectera species. A–L Lectera colletotrichoides A–C IMI 166394 D–F, IMI 265740 G–I IMI 303685 J–L IMI 368065 M–O Lectera longa (IMI 181698) A, D, G, J, M colonies on PCA agar after 7 d B, E, H, K, N colonies on PDA agar after 7 d C, F, I, L, O: conidia mounted in lactic acid: bar = 10 µm

Metabolic engineering of Aspergillus niger via ribonucleoprotein-based CRISPR–Cas9 system for succinic acid production from renewable biomass

Abstract Background Succinic acid has great potential to be a new bio-based building block for deriving a number of value-added chemicals in industry. Bio-based succinic acid production from renewable biomass can provide a feasible approach to partially alleviate the dependence of global manufacturing on petroleum refinery. To improve the economics of biological processes, we attempted to explore possible solutions with a fungal cell platform. In this study, Aspergillus niger, a well-known industrial production organism for bio-based organic acids, was exploited for its potential for succinic acid production. Results With a ribonucleoprotein (RNP)-based CRISPR–Cas9 system, consecutive genetic manipulations were realized in engineering of the citric acid-producing strain A. niger ATCC 1015. Two genes involved in production of two byproducts, gluconic acid and oxalic acid, were disrupted. In addition, an efficient C4-dicarboxylate transporter and a soluble NADH-dependent fumarate reductase were overexpressed. The resulting strain SAP-3 produced 17 g/L succinic acid while there was no succinic acid detected at a measurable level in the wild-type strain using a synthetic substrate. Furthermore, two cultivation parameters, temperature and pH, were investigated for their effects on succinic acid production. The highest amount of succinic acid was obtained at 35 °C after 3 days, and low culture pH had inhibitory effects on succinic acid production. Two types of renewable biomass were explored as substrates for succinic acid production. After 6 days, the SAP-3 strain was capable of producing 23 g/L and 9 g/L succinic acid from sugar beet molasses and wheat straw hydrolysate, respectively. Conclusions In this study, we have successfully applied the RNP-based CRISPR–Cas9 system in genetic engineering of A. niger and significantly improved the succinic acid production in the engineered strain. The studies on cultivation parameters revealed the impacts of pH and temperature on succinic acid production and the future challenges in strain development. The feasibility of using renewable biomass for succinic acid production by A. niger has been demonstrated with molasses and wheat straw hydrolysate

Disruption of a putative mitochondrial oxaloacetate shuttle protein in Aspergillus carbonarius results in secretion of malic acid at the expense of citric acid production

Abstract Background In filamentous fungi, transport of organic acids across the mitochondrial membrane is facilitated by active transport via shuttle proteins. These transporters may transfer different organic acids across the membrane while taking others the opposite direction. In Aspergillus niger, accumulation of malate in the cytosol can trigger production of citric acid via the exchange of malate and citrate across the mitochondrial membrane. Several mitochondrial organic acid transporters were recently studied in A. niger showing their effects on organic acid production. Results In this work, we studied another citric acid producing fungus, Aspergillus carbonarius, and identified by genome-mining a putative mitochondrial transporter MtpA, which was not previously studied, that might be involved in production of citric acid. This gene named mtpA encoding a putative oxaloacetate transport protein was expressed constitutively in A. carbonarius based on transcription analysis. To study its role in organic acid production, we disrupted the gene and analyzed its effects on production of citric acid and other organic acids, such as malic acid. In total, 6 transformants with gene mtpA disrupted were obtained and they showed secretion of malic acid at the expense of citric acid production. Conclusion A putative oxaloacetate transporter gene which is potentially involved in organic acid production by A. carbonarius was identified and further investigated on its effects on production of citric acid and malic acid. The mtpA knockout strains obtained produced less citric acid and more malic acid than the wild type, in agreement with our original hypothesis. More extensive studies should be conducted in order to further reveal the mechanism of organic acid transport as mediated by the MtpA transporter

Disruption of a putative mitochondrial oxaloacetate shuttle protein in Aspergillus carbonarius results in secretion of malic acid at the expense of citric acid production

Abstract Background In filamentous fungi, transport of organic acids across the mitochondrial membrane is facilitated by active transport via shuttle proteins. These transporters may transfer different organic acids across the membrane while taking others the opposite direction. In Aspergillus niger, accumulation of malate in the cytosol can trigger production of citric acid via the exchange of malate and citrate across the mitochondrial membrane. Several mitochondrial organic acid transporters were recently studied in A. niger showing their effects on organic acid production. Results In this work, we studied another citric acid producing fungus, Aspergillus carbonarius, and identified by genome-mining a putative mitochondrial transporter MtpA, which was not previously studied, that might be involved in production of citric acid. This gene named mtpA encoding a putative oxaloacetate transport protein was expressed constitutively in A. carbonarius based on transcription analysis. To study its role in organic acid production, we disrupted the gene and analyzed its effects on production of citric acid and other organic acids, such as malic acid. In total, 6 transformants with gene mtpA disrupted were obtained and they showed secretion of malic acid at the expense of citric acid production. Conclusion A putative oxaloacetate transporter gene which is potentially involved in organic acid production by A. carbonarius was identified and further investigated on its effects on production of citric acid and malic acid. The mtpA knockout strains obtained produced less citric acid and more malic acid than the wild type, in agreement with our original hypothesis. More extensive studies should be conducted in order to further reveal the mechanism of organic acid transport as mediated by the MtpA transporter

Gene expression profile of L428 cell line with inhibited expression of miR-9

An Hodgkin Lymphoma cell line have been treated with an LNA inhibitor for miR-9 or with a scramble LNA to identify miR-9 regulated pathways that could be important for Hodgkin Lymphoma pathogenesis. L428 cells were transfected with a miR-9 LNA inhibitor or a scrambled LNA. Total RNA was harvested 9 hours post-transfection and analyzed on Affymetrix HG-U133 Plus 2.0 human arrays. A total of six arrays were analyzed. For filtering, uninformative genes with the same expression level across all arrays (including non-expressed genes) were removed and the differentially expressed genes, their corresponding p-values and false discovery rates were calculated using limma

Additional file 1 of Metabolic engineering of Aspergillus niger via ribonucleoprotein-based CRISPR–Cas9 system for succinic acid production from renewable biomass

Additional file 1: Table S1. Strain morphology in succinic acid production. Table S2. The initial and final pH value in the cultures at different cultivation temperatures. Table S3. Genes manipulated in this study using corresponding gRNAs. Table S4. Primers used in this study. Figure S1. Plasmids used in this study

Transcription profiling by array of liver from chimpanzees with chronic hepatitis C virus infection after treatment with SPC3649

Chimpanzees with chronic Hepatitis C infection treated with LNA-antimiR-122