Project description:To investigate gene expression differences of different tylosin high-producing strains, transcriptomes of three tylosin high-producing engineered strains (TLPH08-2, TLPH11 and TLPH17) and the vector control strain TLSET152 were analyzed by RNA-Seq. Different strains (TLSET152, TLPH08-2, TLPH11 and TLPH17) were harvested at 96 h of fermentationat and then RNA isolation, transcriptome sequencing and data analysis were conducted.
Project description:High throughput sequencing was used to investigate the production of small RNAs from in Chlamydomonas in different strains and different stages of the life cycle. The association between these and methylation was assessed using genomic sequencing, comparing a sequenced genome with one enriched for methylated DNA sequence by immuno-precipitation. Examination of small RNA production in several strains and of the methylation of regions producing these small RNAs.
Project description:Strains: non-producing refernece strain pXMJ19 (CR099 pXMJ19; Goldbeck et al., 2021) and Pediocin-producer pxMJ19 ped (CR099 pXMJ19 Ptac pedACDCg, Goldbeck et al., 2021) Pediocin-producing and non-producing strains of Corynebacterium glutamicum were compared in a whole genome microarray analysis setup in order to identify potential strain optimization targets
Project description:RNA-seq of three different Yarrowia lipolytica strains: OKYL029 (control, W29 derived), OKYL049 (high-lipid producing strain), JFYL007 (or Q4, no-lipid producing strain). The strains were grown on DELFT media containing either ammonium sulphate or urea as nitrogen sources. DELFT media had two different carbon-to-nitrogen (C/N) ratios: a nitrogen limiting ratio of 116 and a carbon limiting ratio of 3. The experiments were performed in chemostats, with two different dilution rates of 0,06 and 0,1. Every condition was performed in quadruplicate, and triplicates were selected for RNA-seq.
Project description:We investigated miRNA expression in Holstein dairy cow of mammary gland with different producing quality milk using high-throughput sequence and qRT-PCR techniques. miRNA libraries were constructed from mammary gland tissues taken from a high producing quality milk and a low producing quality milk Holstein dairy cow, the small RNA digitalization analysis based on HiSeq high-throughput sequencing takes the SBS-sequencing by synthesis.The libraries included 4732 miRNAs. A total of 124 miRNAs in the high producing quality milk mammary gland showed significant differences in expression compared to low producing quality milk mammary gland (P<0.05). Conclusion: Our study provides a broad view of the bovine mammary gland small RNA expression profile characteristics. Differences in types and expression levels of miRNAs were observed between high producing quality milk and a low producing quality milk Holstein dairy cow
Project description:In studies on beta-lactam production by Penicillium chrysogenum, addition and omission of a side-chain precursor is commonly used to generate producing and non-producing scenarios. To dissect effects of penicillin-G production and of its side-chain precursor phenylacetic acid (PAA), a derivative of a penicillin-G high-producing strain without a functional penicillin-biosynthesis gene cluster (pcbAB-pcbC-penDE) was constructed. The copy number of this cluster was first reduced to one via spontaneous recombination. The remaining copy was removed by targeted deletion, thereby completely abolishing beta-lactam biosynthesis. In glucose-limited chemostat cultures of the high-producing and cluster-free strains, PAA addition caused a small reduction of the biomass yield, consistent with PAA acting as a weak-organic-acid uncoupler. A low rate of penicillin-G-independent PAA consumption indicated activity of a PAA-degrading pathway. Microarray-based analysis on chemostat cultures of the high-producing and cluster-free strains, grown in the presence and absence of PAA, showed that: (i) Absence of a penicillin gene cluster resulted in transcriptional upregulation of a gene cluster putatively involved in production of the secondary metabolite aristolochene and its derivatives, (ii) The homogentisate pathway for PAA catabolism is strongly transcriptionally upregulated in PAA-supplemented cultures (iii) Several genes involved in nitrogen and sulfur metabolism were transcriptionally upregulated under penicillin-G producing conditions only, suggesting a drain of amino-acid precursor pools. Furthermore, the number of candidate genes for penicillin transporters was strongly reduced, thus enabling a focusing of functional analysis studies. This study demonstrates the usefulness of combinatorial transcriptome analysis in chemostat cultures to dissect effects of biological and process parameters on transcriptional regulation.
Project description:Deep-sequencing of the engineered production genes in five E coli production chassis strains (BL21(DE3), MG1655, TOP10, W and W3110) producing two case metabolic products, 2,3-butanediol and mevalonic acid
