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Biology subjects

Chen, D. F.

Publications and source records attributed to Chen, D. F..

5 recordsLinked to original sources

Assessment of Visual Function in Mice Using Light/Dark Box and Multi-Feature Machine Learning

The light/dark box test can be used to assess visual function in rodents based on their spontaneous behavior in response to light. Commonly used assay relies on a single behavioral metric, dwell time in the light or dark compartment, which may be influenced by factors other than vision, leading to unreliable assessment results. To overcome this, we developed a multi-feature machine learning paradigm by extracting multiple mouse behavioral metrics, standardizing them as features to train machine learning models, thereby achieving reliable and automated vision assessment. We systematically compared the classification performance of single-metric versus multi-feature machine learning approaches in sighted and blind mice, using wild-type and rhodopsin-deficient mice, with a subset further subjected to double optic nerve crush. We found that the multi-feature method can improve classification performance and exhibit great robustness to different experimental settings. Additionally, we further improved model performance by applying feature importance analysis and constructing an optimized feature subset. These findings suggest that the reliability of commonly used single dwell time measure for vision assessment could become unreliable, as shown in our experiment, probably because in addition to vision other factors also impact dwell time. Our study demonstrated an improved assessment method based on a combination of multiple behavior features through machine learning. Author SummaryAssessing visual function in mice is essential for studying eye diseases and drug development. The light/dark box test evaluates visual function by measuring the spontaneous behavioral response of mice to light, providing a training-free behavioral approach that helps simplify the assessment process and improve research efficiency. However, traditional light/dark box tests rely on a single behavioral metric, dwell time in the light or dark compartment, to assess visual function, which may be influenced by factors other than vision, such as anxiety and exploratory behavior, leading to limited reliability of assessment results. Here, we demonstrate that integrating multiple behavioral features through machine learning can improve the reliability and stability of vision assessment. By automatically tracking and analyzing various behavioral metrics of mice, such as movement patterns, speed, and spatial preferences, the proposed method can more reliably distinguish between sighted and blind mice. Furthermore, the method demonstrates stable performance across different experimental settings, showing good applicability. This automated, reliable, and easily generalizable method can provide a convenient and efficient means for visual assessment in preclinical research, facilitating vision disease research and drug development.

animal behavior and cognition↗

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

Phage-encoded anti-CRISPR (Acr) proteins inhibit CRISPR-Cas systems to allow phage replication and lysogeny maintenance. Most of the Acrs characterized to date are stable stoichiometric inhibitors. While enzymatic Acrs have been characterized biochemically, little is known about their potency, specificity, and reversibility. Here, we examine AcrIF11, a widespread phage and plasmid-encoded ADP-ribosyltransferase (ART) that inhibits the Type I-F CRISPR-Cas system. We present an NMR structure of an AcrIF11 homolog that reveals chemical shift perturbations consistent with NAD (cofactor) binding. In experiments that model both lytic phage replication and MGE/lysogen stability under high targeting pressure, AcrIF11 is a highly potent CRISPR-Cas inhibitor and more robust to Cas protein level fluctuations than stoichiometric inhibitors. Furthermore, we demonstrate that AcrIF11 is remarkably specific, predominantly ADP-ribosylating Csy1 when expressed in P. aeruginosa. Given the reversible nature of ADP-ribosylation, we hypothesized that ADPr eraser enzymes (macrodomains) could remove ADPr from Csy1, a potential limitation of PTM-based CRISPR inhibition. We demonstrate that diverse macrodomains can indeed remove the modification from Csy1 in P. aeruginosa lysate. Together, these experiments connect the in vitro observations of AcrIF11s enzymatic activity to its potent and specific effects in vivo, clarifying the advantages and drawbacks of enzymatic Acrs in the evolutionary arms race between phages and bacteria.

microbiology↗

Suppressing DNMT3a Alleviates the Intrinsic Epigenetic Barrier for Optic Nerve Regeneration and Restores Vision in Adult Mice

The limited regenerative potential of the optic nerve in adult mammals presents a major challenge for restoring vision after optic nerve trauma or disease. The mechanisms of this regenerative failure are not fully understood1,2. Here, through small-molecule and genetic screening for epigenetic modulators3, we identify DNA methyltransferase 3a (DNMT3a) as a potent inhibitor of axon regeneration in mouse and human retinal explants. Selective suppression of DNMT3a in retinal ganglion cells (RGCs) by gene targeting or delivery of shRNA leads to robust, full-length regeneration of RGC axons through the optic nerve and restoration of vision in adult mice after nerve crush injury. Genome-wide bisulfite and transcriptome profiling in combination with single nucleus RNA-sequencing of RGCs revealed selective DNA demethylation and reactivation of genetic programs supporting neuronal survival and axonal growth/regeneration by DNMT3a deficiency. This was accompanied by the suppression of gene networks associated with apoptosis and inflammation. Our results identify DNMT3a as the central orchestrator of an RGC-intrinsic mechanism that limits optic nerve regeneration. Suppressing DNMT3a expression in RGCs unlocks the epigenetic switch for optic nerve regeneration and presents a promising therapeutic avenue for effectively reversing vision loss resulted from optic nerve trauma or diseases.

neuroscience↗

Nanopore-based genome-wide DNA methylation sequencing data of Nosema ceranae-inoculated and un-inoculated eastern honeybee workers' midguts

Apis cerana cerana is an excellent subspecies of Apis cerana, playing a vital role in pollination for wild flowers and crops as well as ecological balance. Nosema ceranae, an emergent fungal parasite infecting various bee species, originates from eastern honeybee. In this article, midguts of N. ceranae-inoculated A. c. cerana workers at 7 days post inoculation (dpi) and 10 dpi (AcT1 and AcT2) and un-inoculated workers midguts (AcCK1, AcCK2) were subjected to Nanopore-based genome-wide DNA methylation sequencing. Totally, 1773258, 2151476, 1927874 and 2109961 clean reads were generated from AcCK1, AcCK2, AcT1, and AcT2 groups, with the N50 lengths of 7548, 7936, 7678, and 7291 and the average quality value of 8.97, 8.95, 9.24, and 8.98, respectively. Among these, 93.85%, 94.49%, 88.69%, and 81.27% clean reads could be mapped to the reference genome of A. c. cerana. In the aforementioned four groups, 2149685, 2614513, 1637018 and 2726985 CHG sites were identified; the numbers of CHH sites were 9581990, 11801082, 7178559, and 12342423, whereas those of CpG sites were 14325356, 15703508, 14856284 and 13956849, respectively. Additionally, there were 36114, 118867, 30249, and 82984 6mA methylation sites respectively discovered. These data can be used for identifying differential 5mC methylation and 6mA methylation engaged in response of eastern honeybee workers to N. ceranae infestation, and for investigating the 5mC or 6mA methylation-mediated mechanism underlying host response. Value of the dataO_LIThe data provide enrichment for information about 5mC and 6mA methylation in eastern honeybees. C_LIO_LIOur data contributes to clarification of the epigenetic mechanism underlying eastern honeybee workers response to microsporidian infestation. C_LIO_LIThis presented data offer novel insights into interaction between Apis cerana and Nosema ceranae. C_LI

molecular biology↗

Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy

As the general population ages and the incidence of diabetes increases epidemically, more people are affected by eye diseases, such as retinopathies. It is therefore critical to improve imaging of eye disease mouse models. Here, we demonstrate that 1) rapid, quantitative 3D and 4D (time lapse) imaging of cellular and subcellular processes in the murine eye is feasible, with and without tissue clearing, using light-sheet fluorescent microscopy (LSFM) and 2) LSFM readily reveals new features of even well studied eye disease mouse models, such as the Oxygen-Induced Retinopathy (OIR) model. Through correlative LSFM-Confocal imaging we find that flat-mounting retinas for confocal microscopy significantly distorts tissue morphology. The minimized distortion with LSFM dramatically improved analysis of pathological vascular tufts in the OIR model revealing \"knotted\" morphologies, leading to a proposed new tuft nomenclature. Furthermore, live-imaging of OIR tuft formation revealed abnormal cell motility and altered filopodia dynamics. We conclude that quantitative 3D/4D LSFM imaging and analysis has the potential to advance our understanding of pathological processes in the eye, in particular neuro-vascular degenerative processes.

developmental biology↗