Development of a high-throughput technology capable of detecting in situ DNA-RNA interactions and transcriptomes in single cells

While methods for detecting single cell transcriptome and genome architecture have been established, there are currently no technologies for detecting single-cell DNA-RNA interactions. Thus, while a regulatory role for chromatin and RNA organization has been hypothesized, we still lack a comprehensive understanding of where and how chromatin and RNA interact, as well as the consequences for gene regulation.In this thesis, I describe a breakthrough technology called single cell in situ Mapping of RNA-Genome Interactome (sciMARGI). Through integrating two promising technologies, combinatorial indexing and microdroplet methods, we can decode single-cell single-complex information by labeling interacting DNA and RNA molecules with unique cell and cluster barcodes. Currently, a DNA library based on human brain tissue has been successfully generated and shown to have a proper single cell cluster distribution and DNA-DNA interaction map. While the RNA library still needs additional adjustments, the libraries as a whole demonstrated promising results. When fully developed, the sciMARGI technology will not only detect three-way in situ interactions between DNA and DNA, DNA and RNA, and RNA and RNA, but also quantify RNA within the single nucleus, establishing a direct link between chromatin-RNA organization and gene expression. Due to its exceptional versatility, sciMARGI can be applied to not only cell lines but also complex tissues, allowing us to resolve some of the most critical obstacles regarding gene expression regulatory processes

Innovation Ability Training Mode of Postgraduates in the Mechanical Discipline Based on Simulation Technology

The innovation ability of mechanical discipline graduate students in China is trained mainly through classroom teaching and scientific research. Theoretical knowledge is traditionally passed on to students in class by “spoon-feeding,” which makes the learning process boring. Scientific research combines theoretical knowledge with experiment. However, its experimental condition and experimental equipment requirements are high. The experimental resources in many universities can hardly satisfy the requirements, seriously hindering the cultivation of the innovation ability of postgraduates. Therefore, this study proposes a new approach to enhancing the innovation ability of postgraduates in the mechanical discipline based on simulation technology, describes the positive role of simulation technology in the training process, and takes the wavy lip seal as an example to illustrate the application of simulation technology in enhancing innovation ability in detail. The comparison of the traditional and new training modes shows that the innovation ability of postgraduates in the mechanical discipline improves considerably when the new training mode is adopted. Furthermore, the new training mode is recognized by graduate students and enterprises

More Features in Bound Representations Does Not Require Extra Object-based Attention in Working Memory

PURPOSE: Feature binding is a core concept in many research fields, including the study of working memory (WM).We recently proposed that binding in WM is not passive, but requires more object-based attention to actively bind distinct single features into a coherent unit (Gao et al., Attention, Perception, &amp; Psychophysics, 2017; Shen, Huang, &amp; Gao, Journal of Experimental Psychology: Human Perception and Performance, 2015). However, a hallmark of object-based attention&mdash;the amount of attention is not modulated by the number features contained in an object&mdash;has not been examined. In the current study, we closed this gap by examining whether this hallmark of object-based attention still holds in WM. METHODS: In two experiments, we required the participants to memorize three bound representations, and manipulated the number of features (2 vs. 3 features) contained in each binding. To examine the role of object-based attention in retaining bindings in WM, we also manipulated whether a secondary task consuming object-based attention was interpolated into the maintenance phase of WM (with vs. without secondary task). If more object-based attention was required after an extra feature was added into the bound representation, then the secondary task would result in worse performance for 3-featured binding than 2-featured binding. RESULTS: In two experiments, we consistently found that the added secondary task significantly impaired the binding performance. However, the added secondary task impaired the 2-featured and 3-featured bindings to the same extent. CONCLUSION: The number of features contained in binding does not modulate the required object-based attention for binding in WM, suggesting that WM and perception share the same hallmark of object-based attention.</p

Retaining Bindings of Integral Features in Working Memory: The Role of Object-based Attention

PURPOSE: Over the past decade, it has been debated whether retaining bindings in working memory (WM) requires more attention than retaining constituent features, focusing on domain-general attention and space-based attention. Recently we proposed that retaining bindings in WM needs more object-based attention than retaining constituent features (Gao et al., 2017; Shen, Huang, &amp; Gao, 2015). However, the composed features in the tested bindings all belong to separable feature dimensions. It has been suggested that there are two types of feature relations: Separable features (e.g., color and shape in a colored shape) and integral features (e.g., width and height of a rectangle). While our brain encodes separable features independently, it is difficult to encode the integral features separately. Consequently, the object-based attention hypothesis of retaining bindings in WM may be constrained to separable features, and retaining bindings of integral features does not require more object-based attention than the constitute single features. METHODS: In the current study we addressed this issue by requiring the participants to memorize both width and height of three rectangles or the binding between the two feature dimensions. In the critical condition, we added a secondary transparent motion task during the delay interval of the change-detection task, such that the secondary task competed for object-based attention with the to-be-memorized stimuli. If more object-based attention is required for retaining bindings than for retaining constituent features, the secondary task should impair the binding performance to a larger degree relative to the performance of constituent features. RESULTS: In contrast to the prediction of object-based attention hypothesis, the added secondary task equally impaired the performance of single features and binding. CONCLUSION: Retaining bindings of integral features in WM does not require more object-based attention than the constitute single features, providing a key constraint to the object-based attention hypothesis.</p

Mechanism of intestinal microbiota disturbance promoting the occurrence and development of esophageal squamous cell carcinoma——based on microbiomics and metabolomics

Abstract Esophageal squamous cell carcinoma (ESCC) is a high-risk malignant tumor that has been reported in China. Some studies indicate that gut microbiota disorders can affect the occurrence and development of ESCC, but the underlying mechanism remains unclear. In this study, we aimed to explore the possible underlying mechanisms using microbiomics and metabolomics. Fifty ESCC patients and fifty healthy controls were selected as the study subjects according to sex and age, and fecal samples were collected. 16S rDNA sequencing and LC‒MS were used for microbiomics and nontargeted metabolomics analyses. We found significant differences in the composition of the gut microbiota and metabolites between the ESCC patients and control individuals (P < 0.05). ESCC patients exhibited increased abundances of Fusobacteriaceae and Lactobacillus, increased levels of GibberellinA34 and decreased levels of 12-hydroxydodecanoic acid; these metabolites could be diagnostic and predictive markers of ESCC. An increase in the abundance of Enterobacteriaceae and Lactobacillus significantly reduced the content of L-aspartate and pantothenic acid, which may be involved in the occurrence and development of ESCC by downregulating the expression of proteins in the pantothenate and coenzyme A biosynthesis pathways. An imbalance in the intestinal flora may decrease the number of eosinophils in peripheral blood, resulting in the activation of an inflammatory response and immune dysfunction, leading to ESCC deterioration. We hypothesize that this imbalance in the gut microbiota can cause an imbalance in intestinal metabolites, which can activate carcinogenic metabolic pathways, affect inflammation and immune function, and play a role in the occurrence and development of ESCC

Single-cell multiplex chromatin and RNA interactions in ageing human brain.

Dynamically organized chromatin complexes often involve multiplex chromatin interactions and sometimes chromatin-associated RNA1-3. Chromatin complex compositions change during cellular differentiation and ageing, and are expected to be highly heterogeneous among terminally differentiated single cells4-7. Here we introduce the multinucleic acid interaction mapping in single cells (MUSIC) technique for concurrent profiling of multiplex chromatin interactions, gene expression and RNA-chromatin associations within individual nuclei. When applied to 14 human frontal cortex samples from&nbsp;older donors, MUSIC delineated diverse cortical cell types and states. We observed that nuclei exhibiting fewer short-range chromatin interactions were correlated with both an older transcriptomic signature and Alzheimers disease pathology. Furthermore, the cell type exhibiting chromatin contacts between cis expression quantitative trait loci and a promoter tends to be that in which these cis expression quantitative trait loci specifically affect the expression of their target gene. In addition, female cortical cells exhibit highly heterogeneous interactions between XIST non-coding RNA and chromosome X, along with diverse spatial organizations of the X chromosomes. MUSIC presents a potent tool for exploration of chromatin architecture and transcription at cellular resolution in complex tissues