Chen L et al. (2015) Curr Genomics "Circular RNAs in Eukaryotic Cells."

Shan G, Huang C, Chen L, Wang X

[Curr Genomics, 2015]

Circular RNAs (circRNAs) are now recognized as large species of transcripts in eukaryotic cells. From model organisms such as C. elegans, Drosophila, mice to human beings, thousands of circRNAs formed from back-splicing of exons have been identified. The known complexity of transcriptome has been greatly expanded upon the discovery of these RNAs. Studies about the biogenesis and physiological functions have yielded substantial knowledge for the circRNAs, and they are now more likely to be viewed as regulatory elements coded by the genome rather than unavoidable noise of gene expression. Certain human diseases may also relate to circRNAs. These circRNAs show diversifications in features such as sequence composition and cellular localization, and thus we propose that they may be divided into subtypes such as cytoplasmic circRNAs, nuclear circRNAs, and exon-intron circRNAs (EIciRNAs). Here we summarize and discuss knowns and unknowns for these RNAs, and we need to keep in mind that the whole field is still at the beginning of exciting explorations.

Chen L et al. (2020) J Nanosci Nanotechnol "Toxicological Evaluation of Graphene-Family Nanomaterials."

Gu Z, Yan L, Zhang A, Li J, Chen Z, Chen L, Zhao F

[J Nanosci Nanotechnol, 2020]

With the extending applications, graphene-family nanomaterials begin to enter people's life via various ways, largely increasing the exposure frequencies. In spite of the increasing toxicological studies, the biosafety of graphene-based nanomaterials still remains elusive. Graphene oxide (GO), an oxidation derivative of graphene, is considered as one of the recently-emerging nanomaterials attractive for biomedical applications. Accompanied with the prospect of applications are the great concerns about its biosafety for human and environment. Herein, this review intends to systematically summarize the research on GO toxicity both <i>in vitro</i> and <i>in vivo</i> followed by deep discussions about the toxicological mechanisms. The currently reported toxicity of GO mainly includes inhalation toxicity, ingestion toxicity, dermal toxicity and hemocompatibility depending on exposure routes. The toxicity evaluation of GO using non-rodent organisms (zebrafish, <i>Caenorhabditis elegans</i> and drosophila, etc.) is also summarized, supplementary to <i>in vivo</i> toxicity of GO. Based on the comprehensive summary of the reported GO-induced toxicity, our review suggests considerable emphasis being put on the balance of benefits and risks when employing the nanotechnology.

Chen L et al. (2022) Cell Rep "Escape steering by cholecystokinin peptidergic signaling."

Chen L, Liu Y, Zhang Y, Ge MH, Hung W, Chen LM, Su P, Gao S, Tao L, Zhen M, Li H, Wang Y, Wu ZX, Mao H, Yue Z, Fei P

[Cell Rep, 2022]

Escape is an evolutionarily conserved and essential avoidance response. Considered to be innate, most studies on escape responses focused on hard-wired circuits. We report here that a neuropeptide NLP-18 and its cholecystokinin receptor CKR-1 enable the escape circuit to execute a full omega (&#937;) turn. We demonstrate in vivo NLP-18 is mainly secreted by the gustatory sensory neuron (ASI) to activate CKR-1 in the head motor neuron (SMD) and the turn-initiating interneuron (AIB). Removal of NLP-18 or CKR-1 or specific knockdown of CKR-1 in SMD or AIB neurons leads to shallower turns, hence less robust escape steering. Consistently, elevation of head motor neuron (SMD)'s Ca2+ transients during escape steering is attenuated upon the removal of NLP-18 or CKR-1. In vitro, synthetic NLP-18 directly evokes CKR-1-dependent currents in oocytes and CKR-1-dependent Ca2+ transients in SMD. Thus, cholecystokinin peptidergic signaling modulates an escape circuit to generate robust escape steering.

Chen L et al. (2018) Genetics "Establishment of Signaling Interactions with Cellular Resolution for Every Cell Cycle of Embryogenesis."

Ho VWS, Ng HCK, Zhao Z, Ren X, Yan H, Chan LY, Huang X, Wong MK, Chen L

[Genetics, 2018]

Intercellular signaling interaction plays a key role in breaking fate symmetry during animal development. Identification of the signaling interaction at cellular resolution is technically challenging, especially in a developing embryo. Here we develop a platform that allows automated inference and validation of signaling interaction for every cell cycle of<i>C. elegans</i>embryogenesis. This is achieved by generation of a systems-level cell contact map that consists of 1,114 highly confident intercellular contacts by modeling analysis and is validated through cell membrane labeling coupled with cell lineage analysis. We apply the map to identify cell pairs between which a Notch signaling interaction takes place. By generating expression patterns for two ligands and two receptors of Notch signaling pathway with cellular resolution using automated expression profiling technique, we are able to refine existing and identify novel Notch interactions during<i>C. elegans</i>embryogenesis. Targeted cell ablation followed by cell lineage analysis demonstrates the roles of signaling interactions over cell division in breaking fate symmetry. We finally develop a website that allows online access to the cell-cell contact map for mapping of other signaling interaction in the community. The platform can be adapted to establish cellular interaction from any other signaling pathways.

Chen L et al. (2016) PLoS One "rBmTX14 Increases the Life Span and Promotes the Locomotion of Caenorhabditis Elegans."

Huang Z, Chen L, Xu J, Li W, Liu X, Liu Y, Wan L, Zhang J, Xiang J, Zhang R, Teng K

[PLoS One, 2016]

The scorpion has been extensively used in various pharmacological profiles or as food supplies. The exploration of scorpion venom has been reported due to the presence of recombinant peptides. rBmTX14 is an alpha-neurotoxin extracted from the venom gland of the East Asian scorpion Buthus martensii Karsch and can affect ion channel conductance. Here, we investigated the functions of rBmTX14 using the Caenorhabditis elegans model. Using western blot analysis, rBmTX14 was shown to be expressed both in the cytoplasm and inclusion bodies in the E.coli Rosetta (DE3) strain. Circular dichroism spectroscopy analysis demonstrated that purified rBmTX14 retained its biological structures. Next, feeding nematodes with E.coli Rosetta (DE3) expressing rBmTX14 caused extension of the life span and promoted the locomotion of the nematodes. In addition, we identified several genes that play various roles in the life span and locomotion of C. elegans through microarray analysis and quantitative real-time PCR. Furthermore, if the amino acid site H15 of rBmTX14 was mutated, rBmTX14 no longer promoted the C. elegans life span. In conclusion, the results not only demonstrated the functions and mechanism of rBmTX14 in C. elegans, but also provided the new sight in the utility of recombinant peptides from scorpion venom.

Chen L et al. (2016) Worm "A joint graph inference case study: the C. elegans chemical and electrical connectomes."

Vogelstein JT, Priebe CE, Chen L, Lyzinski V

[Worm, 2016]

We investigate joint graph inference for the chemical and electrical connectomes of the Caenorhabditis elegans roundworm. The C. elegans connectomes consist of [Formula: see text] non-isolated neurons with known functional attributes, and there are two types of synaptic connectomes, resulting in a pair of graphs. We formulate our joint graph inference from the perspectives of seeded graph matching and joint vertex classification. Our results suggest that connectomic inference should proceed in the joint space of the two connectomes, which has significant neuroscientific implications.

Chen L et al. (2011) Neuron "Axon regeneration pathways identified by systematic genetic screening in C. elegans."

Wu Z, Chen L, Wang Z, Yan D, Hubert T, Jin Y, Chisholm AD, Ghosh-Roy A, Bowerman B, O'Rourke S

[Neuron, 2011]

The mechanisms underlying the ability of axons to regrow after injury remain poorly explored at the molecular genetic level. We used a laser injury model in Caenorhabditis elegans mechanosensory neurons to screen 654 conserved genes for regulators of axonal regrowth. We uncover several functional clusters of genes that promote or repress regrowth, including genes classically known to affect axon guidance, membrane excitability, neurotransmission, and synaptic vesicle endocytosis. The conserved Arf Guanine nucleotide Exchange Factor (GEF), EFA-6, acts as an intrinsic inhibitor of regrowth. By combining genetics and invivo imaging, we show that EFA-6 inhibits regrowth via microtubule dynamics, independent of its Arf GEF activity. Among newly identified regrowth inhibitors, only loss of function in EFA-6 partially bypasses the requirement for DLK-1 kinase. Identification of these pathways significantly expands our understanding of the genetic basis of axonal injury responses and repair.

Chen L et al. (2015) Sci Rep "Enhanced nematicidal potential of the chitinase pachi from Pseudomonas aeruginosa in association with Cry21Aa."

Chen L, Sun M, Cheng Q, Kumar A, Chen J, Liu Z, Wu G, Jiang H

[Sci Rep, 2015]

Nematodes are known to be harmful to various crops, vegetables, plants and insects. The present study reports that, chitin upregulates the activity of chitinase (20%) and nematicidal potential (15%) of Pseudomonas aeruginosa. The chitinase gene (pachi) from P. aeruginosa was cloned, and its nematicidal activity of pachi protein against Caenorhabditis elegans was studied. The mortality rate induced by pachi increased by 6.3-fold when in association with Cry21Aa from Bacillus thuringiensis. Pachi efficiently killed C. elegans in its native state (LC50 = 387.3 +/- 31.7 g/ml), as well as in association with Cry21Aa (LC50 = 30.9 +/- 4.1 g/ml), by degrading the cuticle, egg shell and intestine in a relatively short time period of 24 h. To explore the nematidal potential of chitinase, six fusion proteins were constructed using gene engineering techniques. The CHACry showed higher activity against C. elegans than others owing to its high solubility. Notably, the CHACry showed a synergistic factor of 4.1 versus 3.5 a mixture [1:1] of pachi and Cry21Aa. The present study has identified eco-friendly biological routes (e.g., mixed proteins, fusion proteins) with potent nematicidal activity, which not only can help to prevent major crop losses but also strengthen the agro-economy and increase gross crop yield.

Chen L et al. (2013) BMC Bioinformatics "A novel cell nuclei segmentation method for 3D C. elegans embryonic time-lapse images."

Chen L, Chan LL, Yan H, Zhao Z

[BMC Bioinformatics, 2013]

BACKGROUND: Recently a series of algorithms have been developed, providing automatic tools for tracing C. elegans embryonic cell lineage. In these algorithms, 3D images collected from a confocal laser scanning microscope were processed, the output of which is cell lineage with cell division history and cell positions with time. However, current image segmentation algorithms suffer from high error rate especially after 350-cell stage because of low signal-noise ratio as well as low resolution along the Z axis (0.5-1 microns). As a result, correction of the errors becomes a huge burden. These errors are mainly produced in the segmentation of nuclei. Thus development of a more accurate image segmentation algorithm will alleviate the hurdle for automated analysis of cell lineage. RESULTS: This paper presents a new type of nuclei segmentation method embracing an bi-directional prediction procedure, which can greatly reduce the number of false negative errors, the most common errors in the previous segmentation. In this method, we first use a 2D region growing technique together with the level-set method to generate accurate 2D slices. Then a modified gradient method instead of the existing 3D local maximum method is adopted to detect all the 2D slices located in the nuclei center, each of which corresponds to one nucleus. Finally, the bi-directional prediction method based on the images before and after the current time point is introduced into the system to predict the nuclei in low quality parts of the images. The result of our method shows a notable improvement in the accuracy rate. For each nucleus, its precise location, volume and gene expression value (gray value) is also obtained, all of which will be useful in further downstream analyses. CONCLUSIONS: The result of this research demonstrates the advantages of the bi-directional prediction method in the nuclei segmentation over that of StarryNite/MatLab StarryNite. Several other modifications adopted in our nuclei segmentation system are also discussed.

Chen L et al. (2015) Elife "Axon injury triggers EFA-6 mediated destabilization of axonal microtubules via TACC and doublecortin like kinase."

Chisholm AD, Chuang M, Boxem M, Chen L, Jin Y, Koorman T

[Elife, 2015]

Axon injury triggers a series of changes in the axonal cytoskeleton that are prerequisites for effective axon regeneration. In Caenorhabditis elegans the signaling protein Exchange Factor for ARF-6 (EFA-6) is a potent intrinsic inhibitor of axon regrowth. Here we show that axon injury triggers rapid EFA-6-dependent inhibition of axonal microtubule (MT) dynamics, concomitant with relocalization of EFA-6. EFA-6 relocalization and axon regrowth inhibition require a conserved 18-aa motif in its otherwise intrinsically disordered N-terminal domain. The EFA-6 N-terminus binds the MT-associated proteins TAC-1/Transforming-Acidic-Coiled-Coil, and ZYG-8/Doublecortin-Like-Kinase, both of which are required for regenerative growth cone formation, and which act downstream of EFA-6. After injury TAC-1 and EFA-6 transiently relocalize to sites marked by the MT minus end binding protein PTRN-1/Patronin. We propose that EFA-6 acts as a bifunctional injury-responsive regulator of axonal MT dynamics, acting at the cell cortex in the steady state and at MT minus ends after injury.