Advances of development and application amino acid biosensors / 生物工程学报

Amino acids are the basic building blocks of protein that are very important to the nutrition and health of humans and animals, and widely used in feed, food, medicine and daily chemicals. At present, amino acids are mainly produced from renewable raw materials by microbial fermentation, forming one of the important pillar industries of biomanufacturing in China. Amino acid-producing strains are mostly developed through random mutagenesis- and metabolic engineering-enabled strain breeding combined with strain screening. One of the key limitations to further improvement of production level is the lack of efficient, rapid, and accurate strain screening methods. Therefore, the development of high-throughput screening methods for amino acid strains is very important for the mining of key functional elements and the creation and screening of hyper-producing strains. This paper reviews the design of amino acid biosensors and their applications in the high-throughput evolution and screening of functional elements and hyper-producing strains, and the dynamic regulation of metabolic pathways. The challenges of existing amino acid biosensors and strategies for biosensor optimization are discussed. Finally, the importance of developing biosensors for amino acid derivatives is prospected.

New opportunities and challenges for hybrid data and model driven bioprocess optimization and scale-up / 生物工程学报

Currently, biomanufacturing technology and industry are receiving worldwide attention. However, there are still great challenges on bioprocess optimization and scale-up, including: lacing the process detection methods, which makes it difficult to meet the requirement of monitoring of key indicators and parameters; poor understanding of cell metabolism, which arouses problems to rationally achieve process optimization and regulation; the reactor environment is very different across the scales, resulting in low efficiency of stepwise scale-up. Considering the above key issues that need to be resolved, here we summarize the key technological innovations of the whole chain of fermentation process, i.e., real-time detection-dynamic regulation-rational scale-up, through case analysis. In the future, bioprocess design will be guided by a full lifecycle in-silico model integrating cellular physiology (spatiotemporal multiscale metabolic models) and fluid dynamics (CFD models). This will promote computer-aided design and development, accelerate the realization of large-scale intelligent production and serve to open a new era of green biomanufacturing.

Dynamic Regulation of Histone Acetylase on Cardiac Development Gene NKX2.5 During Cardio-genesis in Fetal Mice / 中国循环杂志

Objective: To explore the dynamic regulation of histone acetylases p300 and p300/CBP associated factor (PCAF) on cardiac development gene NKX2.5 during cardio-genesis and to provide the new theoretical basis to clarify the regulatory mechanism for cardio-genesis in fetal mice. Methods: Our research included 4 groups of cardiac tissues: Embryo (EB) 14.5 days group,n=10, EB 16.5 days group, n=10 and Neonatal 0.5 day group,n=5, Neonatal 7 days group,n=3. Immunoprecipitation was performed in myocardial tissues using anti-p300, anti-PCAF and anti-H3K9ac antibodies to retrieve p300, PCAF and H3K9ac binding DNA, the speciifc DNA sequences were ampliifed by real-time PCR to detect and the binding levels of p300, PCAF and the acetylation level of H3K9ac in NKX2.5 promoter sequence. In addition, the mRNA expression of NKX2.5 was examined by RT-PCR. Results: The binding levels of p300 and PCAF had the timing consequence at different stage of cardio-genesis. The binding level of p300 in EB 16.5 days group (0.063 ± 0.021), Neonatal 0.5 day group (0.019 ± 0.008), Neonatal 7 days group (0.011 ± 0.003) were all lower than that in EB 14.5 days group (0.231 ± 0.033), and in Neonatal 0.5 day group and Neonatal 7 days group were lower than EB 16.5 days group, allP Conclusion: Histone acetylases p300 and PCAF may dynamically regulate H3K9ac acetylation in NKX2.5 promoter sequence, and the mRNA of NKX2.5 was dynamically expressed during cardio-genesis in experimental fetal mice.

Statistical Analysis of Gene Expression in Innate Immune Responses: Dynamic Interactions between MicroRNA and Signaling Molecules

MicroRNAs (miRNAs) are known to negatively control protein-coding genes by binding to messenger RNA (mRNA) in the cytoplasm. In innate immunity, the role of miRNA gene silencing is largely unknown. In this study, we performed microarray-based experiments using lipopolysaccharide (LPS)-stimulated macrophages derived from wild-type, MyD88 knockout (KO), TRIF KO, and MyD88/TRIF double KO mice. We employed a statistical approach to determine the importance of the commonality and specificity of miRNA binding sites among groups of temporally co-regulated genes. We demonstrate that both commonality and specificity are irrelevant to define a priori groups of co-downregulated genes. In addition, analyzing the various experimental conditions, we suggest that miRNA regulation may not only be a late-phase process (after transcription) but can also occur even early (1h) after stimulation in knockout conditions. This further indicates the existence of dynamic interactions between miRNA and signaling molecules/ transcription factor regulation; this is another proof for the need of shifting from a 'hard-wired' paradigm of gene regulation to a dynamical one in which the gene co-regulation is established on a case-by-case basis.