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Biology subjects

Chen, K.-N.

Publications and source records attributed to Chen, K.-N..

3 recordsLinked to original sources

OptoCRISPRi-HD: engineering a green-light activated CRISPRi system with high dynamic range

The ability to modulate gene expression is crucial for studying gene function and programming cell behaviors. Combining the reliability of CRISPRi and the precision of optogenetics, the opto-CRISPRi technique is emerging as an advanced tool for live-cell gene regulation. Since previous versions of opto-CRISPRi often exhibit a no more than 10 folds dynamic range due to the leakage activity, they are not suitable for targets that are sensitive to such leakage or critical for cell growth. Here, we describe a green-light activated CRISPRi system with high dynamic range (40-fold) and the flexibility of changing targets in Escherichia coli. Our optoCRISPRi-HD system can efficiently repress essential genes, non-essential genes or inhibit the initiation of DNA replication. Providing a regulative system with high resolution over space-time and extensive targets, our study would facilitate further researches involving complex gene networks, metabolic flux redirection or bioprinting.

synthetic biology↗

Lapatinib protects against epileptic seizures via halting glutathione peroxidase 4-dependent ferroptosis

Background and PurposeRepetitive epileptic seizures trigger massive neuronal death. Therefore, neuroprotection plays a role in preventing neuronal death and inversely suppresses seizure generation. Additionally, some studies have shown ferroptosis, featured by lipid peroxidation (a dominant form of oxidative stress in the brain), is of paramount importance in epileptic seizures. Lapatinib can play a first-line anti-tumor role by targeting oxidative stress and a recent work illustrates the improvement of encephalomyelitis in rodent models after lapatinib treatment. We hypothesize whether lapatinib can protect against ferroptosis in epileptic seizures via regulating lipid peroxidation. Experimental ApproachThe epileptic behavior of the mice was recorded after intracranial injection of KA. Western blot and RT-qPCR were used to detect the protein expression of 4-hydroxynonenal (4-HNE) and glutathione peroxidase 4 (GPX4) and the mRNA expression of prostaglandin endoperoxide synthase 2 (PTGS2) in vivo and in vitro. The level of lipid reactive oxygen species (lipid ROS) in cells pretreated with lapatinib was analyzed by flow cytometry. Key ResultsLapatinib remarkably prevented KA-induced epileptic seizures in mice and ferroptosis was involved in the neuroprotection of lapatinib. Compared with the model group, western blot showed that lapatinib significantly upregulated the levels of GPX4. In the ferroptotic cell death model, lapatinib exerted neuroprotection via up-regulating GPX4. Treatment with Ras-selective lethal small molecule 3 (RSL3), a selective GPX4 inhibitor abrogated its anti-ferroptotic potential. Conclusions and ImplicationsThese results illustrated that lapatinib has neuroprotective potential against KA-triggered epileptic seizures via suppressing GPX4-dependent ferroptosis. What is already knownO_LIActivation of ferroptosis occurs in epileptic seizures. C_LI What this study addsO_LILapatinib protects brain against epileptic seizures via blocking ferroptosis. C_LIO_LIGPX4-dependent ferroptosis is involved in the neuroprotection of lapatinib. C_LI What is the clinical significanceO_LIInhibition of ferroptosis by lapatinib represents a potential neuroprotective strategy for epileptic patients. C_LI

neuroscience↗

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

The high computational cost of current assembly methods for the long, noisy single molecular sequencing (SMS) reads has prevented them from assembling large genomes. We introduce an ultra-fast alignment method based on a novel global alignment score. For large human SMS data, our method is 7X faster than MHAP for pairwise alignment and 15X faster than BLASR for reference mapping. We develop a Mapping, Error Correction and de novo Assembly Tool (MECAT) by integrating our new alignment and error correction methods, with the Celera Assembler. MECAT is capable of producing high quality de novo assembly of large genome from SMS reads with low computational cost. MECAT produces reference-quality assemblies of Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster and reconstructs the human CHM1 genome with 15% longer NG50 in only 7600 CPU core hours using 54X SMS reads and a Chinese Han genome in 19200 CPU core hours using 102X SMS reads.

bioinformatics↗