Project description:Modelo_mod3_032020.m is a Matlab code used for the simulation of the growth curve of Antarctic thraustochytrid Oblongichytrium sp. RT2316-13.
The model is based on the genome scale model adapted for the strain that is found in the Excel file ExcelAurant_28102019.xlsx.
Flux balance analysis is used to predict the specific growth rate of the biomass, specific synthesis of neutral lipids and specific consumption rate of the nutrients.
The code crea_modelo.m transform the excel file into the array model_T.mat used in by Modelo_mod3_032020.m
This model was used to generate data presented in the manuscript Dynamic flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium sp. RT2316-13, 2020,
Carolina Shene, Paris Paredes, Liset Flores, Allison Leyton, Juan A. Asenjo, Yusuf Chisti, Biotechnology and Bioengineering, DOI: 10.1002/bit.27463.
Project description:The transcript profiles of Nesterenkonia sp. AN1 grown at 5 ºC (Cold) and 21 ºC (Topt) were acccessed to evaluate the cold reposnse of this Antarctic Nesterenkonia strain. The strain was grown in triplicates at the optimum growth temperature of 21 ºC and a test temperature of 5 ºC. Total RNA was extracted from two replicate samples for each treatment condition and the total RNA was enriched for mRNA. RNA-seq was done using Illumina Miseq platform at Inqaba Biotech, South Africa. The reads were mapped against the genome sequence of Nesterenkonia sp. AN1 (obtained from NCBI database) and assesed for differeential gene expression using CLC Genomics Workbench 7.5.
Project description:Proteogenomics analysis was employed to refine the genome annotation and provide new insights into nitrogen metabolism of Nostoc sp. PCC 7120.
Project description:Chlorella sp. HS2 is a halotolerant microalga exhibiting relatively high biomass productivity and substantially high lipid accumulation in marine growth media, which suggests this alga as an important crop for industrial algal cultivation systems. To determine pathways leading to HS2's acclimation responses to salt stress, we performed RNA-seq analysis with triplicated cultures grown in freshwater and marine media at both exponential and stationary growth phases. We then run de novo assembly to obtain HS2 transcriptome, which in turn was annotated and processed to extract dysregulated pathways. Results showed a large proportion of down-regulated genes, for instance photosynthesis and TCA pathways. Photosynthesis appeared, however, to recover at the stationary phase, while the general down-regulation pattern was maintained.
Project description:The transcript profiles of Nesterenkonia sp. AN1 grown at 5 ºC (Cold) and 21 ºC (Topt) were acccessed to evaluate the cold reposnse of this Antarctic Nesterenkonia strain. The strain was grown in triplicates at the optimum growth temperature of 21 ºC and a test temperature of 5 ºC. Total RNA was extracted from two replicate samples for each treatment condition and the total RNA was enriched for mRNA. RNA-seq was done using Illumina Miseq platform at Inqaba Biotech, South Africa. The reads were mapped against the genome sequence of Nesterenkonia sp. AN1 (obtained from NCBI database) and assesed for differeential gene expression using CLC Genomics Workbench 7.5. Evaluation of RNA-seq data for Nesterenkonia sp. AN1 at 5 ºC (Cold) and 21 ºC (Topt) in two biological replicates
Project description:Proteomic analysis of an Antarctic bacterium Pseudomonas sp. Lz4W by tandem mass spectrometry to unveil the process of cold adaptation. Comparative whole proteome analysis was performed at Low and optimum temperature.
