Monoraphidium neglectum strain:SAG 48.87
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA275987 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR5798952_1.fastq.gz | Fastqsanger.gz | |||
| SRR5798952_2.fastq.gz | Fastqsanger.gz | |||
| SRR5798953_1.fastq.gz | Fastqsanger.gz | |||
| SRR5798953_2.fastq.gz | Fastqsanger.gz |
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Project description:Monoraphidium neglectum strain:SAG 48.87 Genome sequencing and assembly
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Project description:Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source.
2023-03-09 | GSE193998 | GEO
Project description:Chemostat experiments: Predator-prey dynamics were followed in four replicate chemostats (continuous-flow aquatic culture vessels) supplied with nitrogen-limited sterile medium that was otherwise sufficient in all nutrient constituents (Yoshida et al. 2003; Becks et al. 2010). Three chemostats contained 380 mL of medium, while the fourth, used for our algal gene expression study, contained 3000 mL so as to provide sufficient material for genetic analysis. Brachionus calyciflorus was isolated originally from Milwaukee harbor, Wisconsin, and provided by M. Boraas. Chlamydomonas reinhardtii was obtained from the University of Texas algal culture collection (UTEX 89). Both species reproduced asexually in our chemostat system. Though B. calyciflorus is naturally cyclically parthenogenetic, the rotifers in our stock culture have evolved not to produce males because the bubbling in our chemostats prevents mating; we used only one mating type of Chlamydomonas. Absence of sexual reproduction does not preclude the processes of microevolution (Bell 2009) that we study, and it is commonly accepted that asexual species can evolve (Lenski et al. 1991; Barrett et al. 2005). We used a Chlamydomonas lineage, founded from our original Chlamydomonas stock and then exposed continuously to Brachionus predation for six months in chemostat culture prior to this study during which Chlamydomonas evolved to form clumps (the 'grazed Chlamydomonas' lineage in Becks et al. 2010). We tracked changes in Chlamydomonas gene expression throughout two complete cycles of algal and rotifer abundance and concurrent cycles in algal defense. Algal samples were taken from one chemostat at intervals of approximately every ten days (8 dates total), chosen to capture critical transitions in cell clumping. A sample taken at the start of the experiment from the culture that was used to inoculate the chemostat was the standard against which algae from later samples were compared (i.e., the M-^Sgrazed ChlamydomonasM-^T). To obtain sufficient material for microarray analysis, ca. 1 - 1.5 L algal samples were collected and filtered through a 10-um mesh to exclude rotifers and rotifer eggs. The algal samples of ca. 100 ml of chemostat medium were concentrated by centrifugation and frozen. Samples were shock frozen in liquid nitrogen and transferred to -80C.
2012-03-20 | E-MEXP-3562 | biostudies-arrayexpress
Project description:Microalgae remain an important feedstock for the production of biofuels and bioproducts. Discovery of new species drives innovation for biotransformation, where bioengineering and other technological advances can significantly optimize performance. Production is predicated on deep knowledge of algal behavior predicted from genomic and phenotypic studies. However, prediction and manipulation of behavior, particularly for scale up, remains a challenge. Understanding the contribution of epigenetic processes to algal function provides another piece of this complex puzzle for achieving bioeconomy goals. Utilizing Nannochloropsis species as a model, we provide a methodological framework for investigating epigenetic processes, specifically DNA methylation, in new species and demonstrate best practices for discerning novel epigenetic modifications. We demonstrate specific forms of DNA methylation can be overlooked by traditional epigenetic analysis strategies. Using high-throughput, lower cost techniques, we provide evidence demonstrating Nannochloropsis gaditana and N. salina lack the most ubiquitous forms of eukaryotic DNA methylation (5mC and 5hmC) and instead employ N6-adenine methylation (6mA), commonly found in bacteria, in their genomes.
2024-12-15 | GSE264626 | GEO
Project description:Short Description: Oleaginous microalgae are capable of producing large quantities of fatty acids and triacylglycerides. As such, they are promising feedstocks for the production of biofuels and bioproducts. Genetic strain-engineering strategies offer a means to accelerate the commercialization of algal biofuels by improving the rate and total accumulation of microalgal lipids. However, the industrial potential of these organisms remains to be met, largely due to the incomplete knowledgebase surrounding the mechanisms governing the induction of algal lipid biosynthesis. Such strategies require further elucidation of genes and gene products controlling algal lipid accumulation. In this study, we have set out to examine these mechanisms and identify novel strain-engineering targets in the oleaginous microalga, Chlorella vulgaris. Comparative shotgun proteomic analyses have identified a number of novel targets, including previously unidentified transcription factors and proteins involved in cell signaling and cell cycle regulation. These results lay the foundation for strain-improvement strategies and demonstrate the power of translational proteomic analysis. Experimental: Lysates were diluted 1:300 for quantitation in order to abate interference due to the chlorophyll content of the samples. Quantitation was performed by Qubit fluorometry (Invitrogen) and 20 ug of each sample was solubilized in LDS buffer, heated at 85 C for 5 min and separated on a 4-12% Bis-Tris Novex mini-gel (Invitrogen) using the MOPS buffer system. The gel was stained with coomassie and each lane was excised into 40 equally sized segments. The gel bands were processed using a robot (ProGest, DigiLab) with the following protocol: - Washed with 25mM ammonium bicarbonate followed by acetonitrile. - Reduced with 10mM dithiothreitol at 60 C followed by alkylation with 50mM iodoacetamide at RT. - Digested with trypsin (Promega) at 37 C for 4h. - Quenched with formic acid and the supernatant was analyzed directly without further processing. The gel digests were analyzed by nano LC/MS/MS with a Waters NanoAcquity HPLC system interfaced to a ThermoFisher Orbitrap Velos Pro. Peptides were loaded on a trapping column and eluted over a 75um analytical column at 350 nL/min; both columns were packed with Jupiter Proteo resin (Phenomenex).The mass spectrometer was operated in data-dependent mode, with MS performed in the Orbitrap at 60,000 FWHM resolution and MS/MS performed in the LTQ. The fifteen most abundant ions were selected for MS/MS. Mascot DAT files were parsed into the Scaffold software for validation, filtering and to create a non-redundant list per sample. Data were filtered using a minimum protein value of 99%, a minimum peptide value of 50% (Prophet scores) and requiring at least two unique peptides per protein.
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Project description:In this study transcriptomic data of three life history stages of Orciraptor agilis was generated: 1) Gliding cells in absence of food ('gliding'), 2) Cells attached to the cell wall of its algal prey during perforation ('fattacking'), 3) Cells after acquisition of the algal plastid material ('digesting'). Furthermore, RNA-seq of the algal prey Mougeotia sp. was also performed. A de novo transcriptome assembly of the algal reads was performed in order to identify and substract algal reads of the Orciraptor samples by mapping the Orciraptor reads to the algal transcriptome. After this filtering step the remaining Orciraptor reads from all libraries were pooled for a de novo transcriptome assembly of Orciraptor agilis. This transcriptome was the basis for a comparative transcriptomic study in which transcript expression was compared between the three life history stages.
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