Biomedical subjects

Wenrui Li

Publications and source records attributed to Wenrui Li.

4 recordsLinked to original sources

PubMed2025

soFusion: facilitating tissue structure identification via spatial multi-omics data fusion.

The rapid advancement of spatial multi-omics technologies has opened new avenues for dissecting tissue architecture with unprecedented resolution. However, inherent disparities across omics modalities, such as differences in biological hierarchy and resolution, pose significant challenges for integrative analysis. To address this, we present soFusion, a method for representation learning on spatial multi-omics data that enables automated identification of tissue compartmentalization. soFusion employs a graph convolutional network (GCN) to extract latent embeddings from spatial omics profiles. To simultaneously capture both cross-modality relationships and modality-specific features, we introduce a novel strategy for intra- and inter-omics feature learning. Moreover, modality-specific decoders are designed to preserve the unique information embedded in each omics type. We evaluated soFusion on multiple datasets including gene expression, protein expression, and epigenetic features. Across all benchmarks, soFusion consistently outperformed existing methods in delineating anatomical structures and identifying spatial domains with improved continuity and reduced noise. Collectively, soFusion offers an effective solution for spatial multi-omics integration, substantially enhancing the robustness of spatial domain identification.

Humans↗

PubMed2006

JNK1 phosphorylation of SCG10 determines microtubule dynamics and axodendritic length.

c-Jun NH(2)-terminal kinases (JNKs) are essential during brain development, when they regulate morphogenic changes involving cell movement and migration. In the adult, JNK determines neuronal cytoarchitecture. To help uncover the molecular effectors for JNKs in these events, we affinity purified JNK-interacting proteins from brain. This revealed that the stathmin family microtubule-destabilizing proteins SCG10, SCLIP, RB3, and RB3' interact tightly with JNK. Furthermore, SCG10 is also phosphorylated by JNK in vivo on sites that regulate its microtubule depolymerizing activity, serines 62 and 73. SCG10-S73 phosphorylation is significantly decreased in JNK1-/- cortex, indicating that JNK1 phosphorylates SCG10 in developing forebrain. JNK phosphorylation of SCG10 determines axodendritic length in cerebrocortical cultures, and JNK site-phosphorylated SCG10 colocalizes with active JNK in embryonic brain regions undergoing neurite elongation and migration. We demonstrate that inhibition of cytoplasmic JNK and expression of SCG10-62A/73A both inhibited fluorescent tubulin recovery after photobleaching. These data suggest that JNK1 is responsible for regulation of SCG10 depolymerizing activity and neurite elongation during brain development.

Animals↗

PubMed2006

Sample preparation project for the subcellular proteome of mouse liver.

Organelle proteome has become one of the most important fields of proteomics, and the subcellular fractionation with high purity and yield has always been a challenge for cell biologists and also for the Human Liver Proteome Project (HLPP). The liver of a C57BL/6J mouse was chosen as the model to find the optimum method for subcellular preparation. The method we selected could obtain the multiple fractions including plasma membrane, mitochondria, nucleus, ER, and cytosol from a single homogenate. With the same procedure, it is for the first time that the preparation method of frozen homogenized livers was compared with that of the fresh livers and frozen livers. We systematically evaluated the purity, efficiency, and integrity by protein yield, immunoblotting, and transmission electron microscopy. Taken together, the method of multiple fractions from a single tissue is effective enough for subcellular fractionation of mouse liver. We give a selective sample preparation method for frozen homogenized livers, for rare clinical samples, which cannot easily be used for subcellular separation immediately. But the frozen livers are not recommended for organelles isolation. This result is especially useful for sample preparation of human liver for subcellular fractionation of HLPP.

Animals↗

PubMed2005

The effect of perceived spatial separation on informational masking of Chinese speech.

The effect of perceived spatial separation, induced by the precedence effect, on release from noise or speech masking was investigated. Listeners were asked to orally repeat Chinese nonsense sentences, which were spoken by a female talker and presented by both the left (-45 degrees) and right (+45 degrees) loudspeakers, when maskers, which were either speech-spectrum noise sounds or Chinese nonsense sentences spoken by two other female talkers, were presented by the same two loudspeakers. Delays between identical sounds presented over the two loudspeakers were used to control the perceived locations of the target (right only) and masker (right, center, or left). The results show that perceived 45 degrees and 90 degrees separations of target speech from masking speech led to equivalently marked improvement in speech recognition, even though the degree of improvement was smaller than that reported in [J. Acoust. Soc. Am. 106 (1999) 3578 (using English nonsense speech)]. When the masker was noise, however, perceived separation only marginally improved speech recognition. These results indicate that release from informational masking, due to perceived target/masker spatial separation induced by the precedence effect, also occurs for tonal Chinese speech. Compared to the 45 degrees perceived within-hemifield separation, the 90 degrees perceived cross-hemifield separation does not produce further unmasking.

Acoustic Stimulation↗