An automated digital colony picker monitors growth and metabolite production, eliminating the need for culturing cells

https://www.nature.com/articles/s41467-025-63929-7

http://english.cas.cn/newsroom/research_news/life/202510/t20251014_1089412.shtml

The group around Jian XU from the CAS Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT) has developed a fully automated “Digital Colony Picker” (DCP). This device identifies and retrieves high-performance microbial clones by simultaneously monitoring their growth and metabolite production—eliminating the need for culture plates, sampling needles, or manual picking.

Designed for the “design-build-test-learn” framework widely adopted in synthetic biology, the DCP streamlines the traditionally slow, labor-intensive “test” phase into a fast, parallel workflow with little hands-on time. It has a microfluidic chip containing 16,000 addressable microchambers that isolate single cells and track their expansion into micro-colonies. An integrated AI engine conducts time-lapse analysis of both brightfield and biosensor signals to quantify growth kinetics and metabolite production in real time. Once target colonies are identified, a laser-induced bubble technique exports them as droplets directly into standard culture plates. This contact-free transfer minimizes cross-contamination and preserves cell viability.

The equipment which was tested for identifying high-yield or lactate-tolerant Zymomonas mobilis mutants is broadly applicable to adaptive evolution studies, functional gene discovery, and phenotype screening across diverse microbial species.

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Epigenetic modifications help algae to adapt to low CO2 environments

http://english.cas.cn/newsroom/research_news/life/202510/t20251010_1089023.shtml

https://www.cell.com/plant-communications/pdf/S2590-3462(25)00296-2.pdf?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2590346225002962%3Fshowall%3Dtrue

A research team from the Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT) of the Chinese Academy of Sciences has identified a specific histone modification as the key regulator governing microalgae’s adaptation to low-CO₂environments.

The study focused on Nannochloropsis oceanica, tracking its epigenomic dynamics as it transitioned from an environment with 5% CO₂ to one with just 0.01% CO₂. Using multi-dimensional epigenomic sequencing techniques, the researchers discovered that global DNA methylation in the alga remained stable at 0.13%, effectively ruling out DNA methylation as a major driver of its low-CO₂response. By contrast, H3K4me2 methylationwas found to be closely associated with 43.1% of the genes that respond to low-CO₂ conditions. These genes include those critical to photosynthesis and ribosome biogenesis, two processes essential for the alga’s survival under carbon-limited stress. Further analysis revealed that H3K4me2 appears to regulate gene transcription by altering chromatin accessibility, a mechanism that aligns with its role as a central regulator of low-CO₂ adaptation.

To validate their findings, the team used CRISPR/Cas9 gene-editing technology. They knocked out NO24G02310—a gene that encodes an H3K4 methyltransferase, the enzyme responsible for adding methyl groups to H3K4. The modified algae showed a roughly 22% reduction in growth rate and a 15% decrease in biomass. Additionally, the levels of another histone modification (H3K4me1) dropped, and the genome-wide localization of H3K4me2 shifted—providing direct evidence of H3K4me2’s role in low-CO₂ adaptation. Further experiments uncovered that H3K4 modification may act via two pathways: by regulating enzyme networks and by modulating chloroplast transmembrane pH gradients. Both mechanisms work to optimize the alga’s use of available CO₂, enhancing its survival under low-carbon conditions.

Sorting cells by Raman fingerprint

Nachrichten aus der Chemie (2025) 73, p. 37 – 39 (in English)

Raman article

Trans-aconitic acid from Aspergillus terreus – a new biopesticide and bio-based plasticizer

https://doi.org/10.1016/j.ymben.2023.06.007

https://doi.org/10.1016/j.greenca.2023.08.001

https://www.guanhai.com.cn/p/39 4312.html

Trans-aconitic acid TAA (CAS RN 4023-65-8) is an unsaturated tricarboxylic acid that occurs in various plants. Although it exhibits broad application potential in agriculture, food, biomaterials, and green chemistry, its practical use remains limited. This is primarily because the traditional production processes of plant extraction (from sugar cane)and chemical synthesis (complex and inefficient) cannot achieve large-scale production at a low cost.

Researchers around LU Xuefeng, director of the Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT) under the Chinese Academy of Sciences, have now established a cell factory for the production of TAA based on a genome-edited industrial strain of Aspergillus terreus. Several rounds of metabolic engineering resulted in strains which produced 57 g/L TAA in shake flask cultures. Scale-up to tank fermentations up to 120 kL – in cooperation with Shandong Lukang Pharmaceutical Co., Ltd.– then led to yields of 88 g/L after 100 hours. A simple recovery procedure combining membrane concentration and crystallization provided TAA crystals with a purity of 98.4%. Given its superior nematicidal properties, QIBEBT and Lukang Pharmaceutical are now in the process of registering TAA as a new nematicide biopesticide.

The QIBEBT team has further found that TAA esters (trans-Aconitates) can be used as plasticizers and could replace the ambiguous phthalates widely used in plastic products. Haier Blood Technology Co., a Qingdao-based company, plans to use TAA esters as plasticizers in its PVC-based blood bags and other products.

TAA ester’s wide temperature stability, from -46°C to 120°C, might also find applications in automotive cable materials as they exhibit excellent resistance to high-temperature volatilization and low-temperature brittle cracking.

In summary, biomanufacturing based on smart cells of A. terreus has provided a new material, TAA and TAA esters, which offer exciting application potentials as a biopesticide and a non-toxic bioplasticizer.

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