Profiling of REST-Dependent microRNAs Reveals Dynamic Modes of Expression

Multipotent neural stem cells (NSCs) possess the ability to self-renew and differentiate into both neurons and glia. However, the detailed mechanisms underlying NSC fate decisions are not well understood. Recent work suggests that the interaction between cell type specific transcription factors and microRNAs (miRNAs) is important as resident neural stem/progenitor cells give rise to functionally mature neurons. Recently, we demonstrated that the transcriptional repressor REST (RE1-silencing transcription factor) is essential to prevent precocious neuronal differentiation and maintain NSC self-renewal in the adult hippocampus. Here we show that REST is required for orchestrating the expression of distinct subsets of miRNAs in primary mouse NSC cultures, a physiologically relevant cell type. Using miRNA array profiling, we identified known REST-regulated miRNA genes, as well as previously uncharacterized REST-dependent miRNAs. Interestingly, in response to proliferation and differentiation stimuli, REST-regulated miRNAs formed distinct clusters and displayed variable expression dynamics. These results suggest that REST functions in a context-dependent manner through its target miRNAs for mediating neuronal production

Toll-like receptor 9 interaction with CpG ODN – An in silico analysis approach

BACKGROUND: Toll-like receptor 9 (TLR9) recognises unmethylated CpG DNA and activates a signalling cascade, leading to the production of inflammatory cytokines such as TNF-α, IL-1, IL-6 and IL-12 via the adaptor protein MyD88. However, the specific sequence and structural requirements of the CpG DNA for the recognition of and binding to TLR9 are unknown. Moreover, the 3D structures of TLR9 and the TLR9-ODN complex have not been determined. In this study, we propose a reliable model of the interaction of the TLR9 ECD with CpG ODN using bioinformatics tools. RESULTS: The three-dimensional structures of two TLR9 ECD-CpG ODN complexes were constructed using a homology modelling and docking strategy. Based on the models of these complexes, the TLR9 ECD-CpG ODN interaction patterns were calculated. The results showed that the interface between the human TLR9 and the CpG ODN molecule is geometrically complementary. The computed molecular interactions indicated that LRR11 is the main region of TLR9 that binds to CpG ODN and that five positively charged residues within LRR11 are involved in the binding of the TLR9 ECD to the CpG ODN. Observations in the close-up view of these interactions indicated that these five positively charged residues contribute differently to the binding region within the TLR9 ECD-CpG ODN complex. 337Arg and 338Lys reside in the binding sites of ODN, forming hydrogen bonds and direct contacts with the CpG ODN, whereas 347Lys, 348Arg, and 353His do not directly contact the CpG ODN. These results are in agreement with previously reported experimental data. CONCLUSION: In this study, we present two structural models for the human and mouse TLR9 ECD in a complex with CpG ODN. Some features predicted by this model are consistent with previously reported experimental data. This complex model may lead to a better understanding of the function of TLR9 and its interaction with CpG ODN and will improve our understanding of TLR9-ligand interaction in general

Multimodality of AI for Education: Towards Artificial General Intelligence

This paper presents a comprehensive examination of how multimodal artificial intelligence (AI) approaches are paving the way towards the realization of Artificial General Intelligence (AGI) in educational contexts. It scrutinizes the evolution and integration of AI in educational systems, emphasizing the crucial role of multimodality, which encompasses auditory, visual, kinesthetic, and linguistic modes of learning. This research delves deeply into the key facets of AGI, including cognitive frameworks, advanced knowledge representation, adaptive learning mechanisms, strategic planning, sophisticated language processing, and the integration of diverse multimodal data sources. It critically assesses AGI's transformative potential in reshaping educational paradigms, focusing on enhancing teaching and learning effectiveness, filling gaps in existing methodologies, and addressing ethical considerations and responsible usage of AGI in educational settings. The paper also discusses the implications of multimodal AI's role in education, offering insights into future directions and challenges in AGI development. This exploration aims to provide a nuanced understanding of the intersection between AI, multimodality, and education, setting a foundation for future research and development in AGI

Understanding LLMs: A Comprehensive Overview from Training to Inference

The introduction of ChatGPT has led to a significant increase in the utilization of Large Language Models (LLMs) for addressing downstream tasks. There's an increasing focus on cost-efficient training and deployment within this context. Low-cost training and deployment of LLMs represent the future development trend. This paper reviews the evolution of large language model training techniques and inference deployment technologies aligned with this emerging trend. The discussion on training includes various aspects, including data preprocessing, training architecture, pre-training tasks, parallel training, and relevant content related to model fine-tuning. On the inference side, the paper covers topics such as model compression, parallel computation, memory scheduling, and structural optimization. It also explores LLMs' utilization and provides insights into their future development.Comment: 30 pages,6 figure

Notch1 is required for maintenance of the reservoir of adult hippocampal stem cells

Notch1 regulates neural stem cell (NSC) number during development, but its role in adult neurogenesis is unclear. We generated nestin-CreER(T2)/R26R-YFP/Notch1(loxP/loxP) [Notch1inducible knock-out (iKO)] mice to allow tamoxifen (TAM)-inducible elimination of Notch1 and concomitant expression of yellow fluorescent protein (YFP) in nestin-expressing Type-1 NSCs and their progeny in the adult hippocampal subgranular zone (SGZ). Consistent with previous research, YFP+ cells in all stages of neurogenesis were evident in the subgranular zone (SGZ) of wild-type (WT) mice (nestin-CreER(T2)/R26R-YFP/Notch1(w/w)) after tamoxifen (post-TAM), producing adult-generated YFP+ dentate gyrus neurons. Compared with WT littermates, Notch1 iKO mice had similar numbers of total SGZ YFP+ cells 13 and 30 d post-TAM but had significantly fewer SGZ YFP+ cells 60 and 90 d post-TAM. Significantly fewer YFP+ Type-1 NSCs and transiently amplifying progenitors (TAPs) resulted in generation of fewer YFP+ granule neurons in Notch1 iKO mice. Strikingly, 30 d of running rescued this deficit, as the total YFP+ cell number in Notch iKO mice was equivalent to WT levels. This was even more notable given the persistent deficits in the Type-1 NSC and TAP reservoirs. Our data show that Notch1 signaling is required to maintain a reservoir of undifferentiated cells and ensure continuity of adult hippocampal neurogenesis, but that alternative Notch- and Type-1 NSC-independent pathways compensate in response to physical activity. These data shed light on the complex relationship between Type-1 NSCs, adult neurogenesis, the neurogenic niche, and environmental stimuli

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

Heterogeneity in gene expression and epigenetic states exists across individual cells. Here, the authors develop scCAT-seq, a technique for simultaneously performing ATAC-seq and RNA-seq within the same single cell

Functional analysis of Hic-5/ARA55 isoforms in C2C12 myogenesis

Hic-5 is a focal adhesion protein of paxillin superfamily that was initially cloned from mouse osteoblasts as a TGF-β or H2O2 inducible cDNA. As well, Hic-5 was independently identified as an Androgen receptor activator (ARA55). Conflicting data have implicated Hic-5 in opposing processes. With two Hic-5 isoforms documented, I hypothesized that multiple Hic-5 isoforms may exist that have both overlapping and isoform-specific functions, which may explain those discrepancies. To test this hypothesis, I have utilized C2C12 myoblasts and analyzed the roles of Hic-5 isoforms in development and homeostasis. 1. I have confirmed the presence of the two previous reported Hic-5 isoforms (α and β) and uncovered 10 additional novel Hic-5 transcripts. Conceptually translated proteins from these transcripts significantly differ at the N-terminal region and likely have distinct binding properties and functions. Hic-5 isoforms have distinct tissue distribution and are developmentally regulated in the mouse mammary gland in vivo (Chapter two). 2. I found that: (a) myoblasts express multiple Hic-5 isoforms; (b) the two predominant isoforms, Hic-5α and Hic-5β, are differentially expressed during myogenesis; (c) any experimentally-induced change in Hic-5 expression results in a substantial increase in apoptosis during differentiation; (d) ectopic expression of Hic-5α is permissive to differentiation while expression of either Hic-5β or antisense Hic-5 reduces myoblast chemo-differentiation and blocks fusion; (e) Hic-5 localizes to focal adhesion in C2C12 myoblasts and perturbation of Hic-5 leads to defects in cell spreading; (f) perturbations of Hic-5 expression interfere with the normal expression dynamics of laminin; and (g) the rescue of myoblast survival and differentiation by laminin but not fibronectin suggests that Hic-5 isoforms differentially regulate myogenesis due to their different impacts on cell-ECM interaction, focal adhesion dynamics and integrin signaling (Chapter Three). In summary, the roles Hic-5 may assume in development and homeostasis are complex and the different Hic-5 isoforms may mediate distinct physiological and/or pathological responses in cells. Therefore, a more precise analysis of Hic-5 isoforms is required to more fully understand the roles of not only Hic-5, but also integrin signaling in normal and diseased cells ( Chapter four and five)

TEMPO/NaBr/NaClO-Mediated Surface Oxidation of Nanocrystalline Cellulose and Its Microparticulate Retention System with Cationic Polyacrylamide

TEMPO/NaBr/NaClO-mediated surface oxidation of NCC, acid-extracted from aspen kraft pulp, was studied, and the properties of nanocellulose whiskers before and after oxidation were characterized by conductimetry, Fourier transform infrared spectroscopy, X-ray diffraction, and atomic force microscopy. The resulting products with varied oxidation degrees were then applied in the deinked pulp to evaluate the improvements of fines retention and pulp drainage. It was found that TEMPO-oxidized NCC maintained its crystalline form of cellulose I, while it showed better dispersibility and smaller dimension due to the high level of carboxyl content and degree of oxidation. By adding NCC and TONCC to the deinked pulp, the retention was improved while the drainage rate was decreased to some extent. When TONCC samples were applied together with cationic polyacrylamide to constitute a microparticulate retention system, both fines retention and pulp drainage were apparently improved. Further study showed that the retention and drainage rate were significantly influenced by the degree of oxidation. TONCC sample with the highest DO (0.134) gave the highest retention and drainage rate, 89.6% and 9.41 mL/s, respectively

Postnatal Vitamin D Intake Modulates Hippocampal Learning and Memory in Adult Mice

Vitamin D (VD) is a neuroactive steroid crucial for brain development, function and homeostasis. Its deficiency is associated with numerous brain conditions. As such, VD and its variants are routinely taken by a broad of groups with/without known VD deficiency. In contrast, the harmful effects of VD overdose have been poorly studied. Similarly, the developmental stage-specific VD deficiency and overdose have been rarely explored. In the present work, we showed that postnatal VD supplementation enhanced the motor function transiently in the young adult, but not in the older one. Postnatal VD intake abnormality did not impact the anxiety and depressive behavior but was detrimental to spatial learning and hippocampus-dependent memory. At the molecular level we failed to observe an obvious and constant change with the neural development and activity-related genes examined. However, disrupted developmental expression dynamics were observed for most of the genes, suggesting that the altered neural development dynamics and therefore aberrant adult plasticity might underlie the functional deficits. Our work highlights the essence of VD homeostasis in neural development and adult brain function. Further studies are needed to determine the short- and long-term effects VD intake status may have on brain development, homeostasis, and diseases