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Spatial transcriptomics has revolutionized our understanding of cellular network dynamics in aging and disease by enabling the mapping of molecular and cellular organization across various anatomical locations. Despite these advances, current methods face significant challenges in throughput and cost, limiting their utility for comprehensive studies. To address these limitations, we introduce IRISeq (Imaging Reconstruction using Indexed Sequencing), a optics-free spatial transcriptomics platform that eliminates the need for predefined capture arrays or extensive imaging, allowing for the rapid and cost-effective processing of multiple tissue sections simultaneously. Its capacity to reconstruct images based solely on sequencing local DNA interactions allows for profiling of tissues without size constraints and across varied resolutions. Applying IRISeq, we examined gene expression and cellular dynamics in thirty brain regions of both adult and aged mice, uncovering region-specific changes in gene expression associated with aging. Further cell type-centric analysis further identified age-related cell subtypes and intricate changes in cell interactions that are distinct to certain spatial niches, emphasizing the unique aspects of aging in different brain regions. The affordability and simplicity of IRISeq position it as a versatile tool for mapping region-specific gene expression and cellular interactions across various biological systems.

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Goosecoid (GSC), translated from a homeobox gene, is a protein that participates in metastasis of various cancers. Pancreatic adenocarcinoma (PAAD) is one of the deadliest malignancies associated with a poor diagnosis and prognosis. To develop new treatment target or biomarker for PAAD, this study intended to assess the effects and the molecular mechanism of GSC on PAAD metastasis. The expressive discrepancy of GSC in PAAD and normal tissues/cells was compared by both the quantitative PCR and western blot. The effects of GSC silencing and GSC over-expression on PAAD cells and TGF-ß signaling were proved by wound-healing assay, cell counting kit-8, Transwell assay and western blot. From the results, GSC mRNA and protein levels were enriched in PAAD cancer tissues and cells. GSC silencing prohibited metastasis of PAAD cells including the ability to invade, migrate and epithelial-mesenchymal transition (EMT), whereas GSC upregulation stimulated these cells behaviors above. GSC silencing reversed the effects on cellular processes induced by activation of the TGF-ß pathway. Furthermore, silencing of GSC postponed tumor growth in xenograft model. In summary, GSC was abundantly expressed in PAAD, which activated the TGF-ß pathway to enhance cell metastasis and tumor development.

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To elucidate the aging-associated cellular population dynamics throughout the body, here we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissue samples, encompassing a range of organs across different life stages, sexes, and genotypes. This comprehensive dataset allowed us to identify more than 3,000 unique cellular states and catalog over 200 distinct aging-associated cell populations experiencing significant depletion or expansion. Our panoramic analysis uncovered temporally structured, organ- and lineage-specific shifts of cellular dynamics during lifespan progression. Moreover, we investigated aging-associated alterations in immune cell populations, revealing both widespread shifts and organ-specific changes. We further explored the regulatory roles of the immune system on aging and pinpointed specific age-related cell population expansions that are lymphocyte-dependent. The breadth and depth of our 'cell-omics' methodology not only enhance our comprehension of cellular aging but also lay the groundwork for exploring the complex regulatory networks among varied cell types in the context of aging and aging-associated diseases.

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Pancreatic cancer remains the common cancer with the worst prognosis because of its late diagnosis and extensive metastasis. This study aimed to investigate the effects of GABRP on pancreatic cancer metastasis and the molecular mechanism. The expression of GABRP was measured using the quantitative real-time PCR and western blot. The biological behaviors of cancer cells were assessed using the cell counting kit-8, Transwell assay, and western blot. The regulation of GABRP on the MEK/ERK pathway was detected by western blot. The results indicated that GABRP was overexpressed in pancreatic cancer tissues and cells. Knockdown of GABRP suppressed cell viability, invasion, migration, and epithelial-mesenchymal transition (EMT), whereas GABRP overexpression facilitated these biological behaviors. Inactivation of the MEK/ERK pathway reversed the effects on cellular processes induced by GABRP. Moreover, silencing of GABRP inhibited tumor growth. In conclusion, GABRP promoted the progression of pancreatic cancer by facilitating cell metastasis and tumor growth via activating the MEK/ERK pathway. The findings suggest that GABRP has the potential to be a therapeutic target for the metastatic pancreatic cancer.

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Progenitor cells are critical in preserving organismal homeostasis, yet their diversity and dynamics in the aged brain remain underexplored. We introduced TrackerSci, a single-cell genomic method that combines newborn cell labeling and combinatorial indexing to characterize the transcriptome and chromatin landscape of proliferating progenitor cells in vivo. Using TrackerSci, we investigated the dynamics of newborn cells in mouse brains across various ages and in a mouse model of Alzheimer's disease. Our dataset revealed diverse progenitor cell types in the brain and their epigenetic signatures. We further quantified aging-associated shifts in cell-type-specific proliferation and differentiation and deciphered the associated molecular programs. Extending our study to the progenitor cells in the aged human brain, we identified conserved genetic signatures across species and pinpointed region-specific cellular dynamics, such as the reduced oligodendrogenesis in the cerebellum. We anticipate that TrackerSci will be broadly applicable to unveil cell-type-specific temporal dynamics in diverse systems.

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BACKGROUNDS: To compare the clinical effectiveness of different mesh fixation techniques in Lichtenstein tension-free repair using network meta-analysis. METHODS: Cochrane Library, Medline, EMBASE, and Web of Science databases were searched until 1 December 2020, and randomized controlled trials (RCTs) comparing outcomes between different mesh fixation techniques were included. The primary endpoints were chronic postoperative inguinal pain (CPIP) and hernia recurrence. The second endpoint was seroma and infection. Data were processed using Stata MP16.0, and R x64 3.6.1. RESULTS: The results demonstrated that 32 RCTs (n = 6362) were eligible for pooling. Six types of mesh fixation techniques were used: non-absorbable suture, absorbable suture, chemical glue, fibrin glue, self-gripping mesh, and staple fixation. Network meta-analysis indicated that the incidence of CPIP with fibrin glue was lower than that with non-absorbable sutures (relative risk [RR] = 0.23, 95% credibility interval [95%CrI] [0.09, 0.50]), absorbable sutures (RR = 0.24, 95%CrI [0.08, 0.60]), chemical glue (RR = 0.36, 95%CrI [0.13, 0.87]), and self-gripping mesh (RR = 0.27 95%CrI [0.09, 0.62]). Self-gripping mesh was superior to non-absorbable sutures (RR = 0.44, 95%CrI [0.23, 0.74]) in reducing postoperative infection. CONCLUSION: This network meta-analysis suggests that fibrin glue might be best for reducing CPIP and recurrence. However, a large-scale RCT is warranted to confirm the results.

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Hedgehog (Hh) signalling plays conserved roles in controlling embryonic development; its dysregulation causes many diseases including cancers. The G protein-coupled receptor Smoothened (Smo) is the key signal transducer of the Hh pathway, whose posttranslational regulation has been shown to be critical for its accumulation and activation. Ubiquitination has been reported an essential posttranslational regulation of Smo. Here, we identify a novel E3 ligase of Smo, Herc4, which binds to Smo, and regulates Hh signalling by controlling Smo ubiquitination and degradation. Interestingly, our data suggest that Herc4-mediated Smo degradation is regulated by Hh in PKA-primed phosphorylation-dependent and independent manners.

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The Hedgehog (Hh) signaling pathway plays important roles in developmental processes including pattern formation and tissue homeostasis. The seven-pass transmembrane receptor Smoothened (Smo) is the pivotal transducer in the pathway; it, and thus the pathway overall, is regulated by ubiquitin-mediated degradation, which occurs in the absence of Hh. In the presence of Hh, the ubiquitination levels of Smo are decreased, but the molecular basis for this outcome is not well understood. Here, we identify the deubiquitinase UCHL5 as a positive regulator of the Hh pathway. We provide both genetic and biochemical evidence that UCHL5 interacts with and deubiquitinates Smo, increasing stability and promoting accumulation at the cell membrane. Strikingly, we find that Hh enhances the interaction between UCHL5 and Smo, thereby stabilizing Smo. We also find that proteasome subunit RPN13, an activator of UCHL5, could enhance the effect of UCHL5 on Smo protein level. More importantly, we find that the mammalian counterpart of UCHL5, UCH37, plays the same role in the regulation of Hh signaling by modulating hSmo ubiquitination and stability. Our findings thus identify UCHL5/UCH37 as a critical regulator of Hh signaling and potential therapeutic target for cancers.

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Hedgehog (Hh) signaling plays a pivotal role in animal development and its deregulation in humans causes birth defects and several types of cancer. Protein Kinase A (PKA) modulates Hh signaling activity through phosphorylating the transcription factor Cubitus interruptus (Ci) and G protein coupled receptor (GPCR) family protein Smoothened (Smo) in Drosophila, but how PKA activity is regulated remains elusive. Here, we identify a novel regulator of the Hh pathway, the capping-enzyme mRNA-cap, which positively regulates Hh signaling activity through modulating PKA activity. We provide genetic and biochemical evidence that mRNA-cap inhibits PKA kinase activity to promote Hh signaling. Interestingly, regulation of Hh signaling by mRNA-cap depends on its cytoplasmic capping-enzyme activity. In addition, we show that the mammalian homolog of mRNA-cap, RNGTT, can replace mRNA-cap to play the same function in the Drosophila Hh pathway and that knockdown of Rngtt in cultured mammalian cells compromised Shh pathway activity, suggesting that RNGTT is functionally conserved. Our study makes an unexpected link between the mRNA capping machinery and the Hh signaling pathway, unveils a new facet of Hh signaling regulation, and reveals a potential drug target for modulating Hh signaling activity.

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Organic thiols have received extensive attention recently because of their relative stability and ease of examination compared to other potential molecular electronic materials. In this work, scanning probe microscopy (SPM) is used to study (i) the structural properties of self-assembled monolayers (SAMs) containing conjugated dithiols and (ii) the formation of the upper molecule-metal interface on dithiol SAMs. The top gold film is deposited either by thermal evaporation or by nano-transfer printing (nTP). Generally, the utility of thermal evaporation is limited because of Au diffusion through the SAMs. However, several dithiol SAMs are identified in this work that bond well to Au overlayers and act as satisfactory diffusion barriers. Coassembly of conjugated dithiols and alkanemonothiols is suggested as a route to obtain dithiols that are denser packed and more vertical (than is obtained from pure dithiol routes). High-yield nTP is demonstrated on coassembled SAMs. Advantages and limitations of different Au deposition and transfer techniques are compared on a variety of length scales.

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The use of surface-initiated ring-opening metathesis polymerization (SI-ROMP) for producing polymer dielectric layers is reported. Surface tethering of the catalyst to Au or Si/SiO2 surfaces is accomplished via self-assembled monolayers of thiols or silanes containing reactive olefins. Subsequent SI-ROMP of norbornene can be conducted under mild conditions. Pentacene semiconducting layers and gold drain/source electrodes are deposited over these polymer dielectric films. The resulting field effect transistors display promising device characteristics, demonstrating for the first time that SI-ROMP can be used in the construction of organic thin-film electronic devices.

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We present grazing-incidence Fourier transform infrared and AFM data of Au, Al, and Ti vapor-deposited onto self-assembled monolayers (SAMs) of conjugated mono- and dithiols. SAMs of 4,4'''-dimercapto-p-quaterphenyl, 4,4"-dimercapto-p-terphenyl, and 4,4'-dimercapto-p-biphenyl have reactive thiols at the SAM/vacuum interface that interact with vapor-deposited Au or Al atoms, preventing metal penetration. Conjugated monothiols lack such metal blocking groups, and metals (Au, Al) can penetrate into their SAMs. Vapor deposition of Ti onto conjugated mono- and dithiol SAMs and onto hexadecanethiol SAMs destroys the monolayers.