QTL mapping for flowering time in a maize-teosinte population under well-watered and water-stressed conditions.

Maize grain yield can be greatly reduced when flowering time coincides with drought conditions, which delays silking and consequently increases the anthesis-silking interval. Although the genetic basis of delayed flowering time under water-stressed conditions has been elucidated in maize-maize populations, little is known in this regard about maize-teosinte populations. Here, 16 quantitative trait loci (QTL) for three flowering-time traits, namely days to anthesis, days to silk, and the anthesis-silking interval, were identified in a maize-teosinte introgression population under well-watered and water-stressed conditions; these QTL explained 3.98-32.61% of phenotypic variations. Six of these QTL were considered to be sensitive to drought stress, and the effect of any individual QTL was small, indicating the complex genetic nature of drought resistance in maize. To resolve which genes underlie the six QTL, 11 candidate genes were identified via colocalization analysis of known associations with flowering-time-related drought traits. Among the 11 candidate genes, five were found to be differentially expressed in response to drought stress or under selection during maize domestication, and thus represented the most likely candidates underlying the drought-sensitive QTL. The results lay a foundation for further studies of the genetic mechanisms of drought resistance and provide valuable information for improving drought resistance during maize breeding. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01413-0.

Large HBV Surface Protein-Induced Unfolded Protein Response Dynamically Regulates p27 Degradation in Hepatocellular Carcinoma Progression.

Up to 50% of hepatocellular carcinoma (HCC) is caused by hepatitis B virus (HBV) infection, and the surface protein of HBV is essential for the progression of HBV-related HCC. The expression of large HBV surface antigen (LHB) is presented in HBV-associated HCC tissues and is significantly associated with the development of HCC. Gene set enrichment analysis revealed that LHB overexpression regulates the cell cycle process. Excess LHB in HCC cells induced chronic endoplasmic reticulum (ER) stress and was significantly correlated with tumor growth in vivo. Cell cycle analysis showed that cell cycle progression from G1 to S phase was greatly enhanced in vitro. We identified intensive crosstalk between ER stress and cell cycle progression in HCC. As an important regulator of the G1/S checkpoint, p27 was transcriptionally upregulated by transcription factors ATF4 and XBP1s, downstream of the unfolded protein response pathway. Moreover, LHB-induced ER stress promoted internal ribosome-entry-site-mediated selective translation of p27, and E3 ubiquitin ligase HRD1-mediated p27 ubiquitination and degradation. Ultimately, the decrease in p27 protein levels reduced G1/S arrest and promoted the progress of HCC by regulating the cell cycle.

Population genomics of Zea species identifies selection signatures during maize domestication and adaptation.

BACKGROUND: Maize (Zea mays L. ssp. mays) was domesticated from teosinte (Zea mays ssp. parviglumis) about 9000 years ago in southwestern Mexico and adapted to a range of environments worldwide. Researchers have depicted the maize domestication and adaptation processes over the past two decades, but efforts have been limited either in sample size or genetic diversity. To better understand these processes, we conducted a genome-wide survey of 982 maize inbred lines and 190 teosinte accessions using over 40,000 single-nucleotide polymorphism markers. RESULTS: Population structure, principal component analysis, and phylogenetic trees all confirmed the evolutionary relationship between maize and teosinte, and determined the evolutionary lineage of all species within teosinte. Shared haplotype analysis showed similar levels of ancestral alleles from Zea mays ssp. parviglumis and Zea mays ssp. mexicana in maize. Scans for selection signatures identified 394 domestication sweeps by comparing wild and cultivated maize and 360 adaptation sweeps by comparing tropical and temperate maize. Permutation tests revealed that the public association signals for flowering time were highly enriched in the domestication and adaptation sweeps. Genome-wide association study identified 125 loci significantly associated with flowering-time traits, ten of which identified candidate genes that have undergone selection during maize adaptation. CONCLUSIONS: In this study, we characterized the history of maize domestication and adaptation at the population genomic level and identified hundreds of domestication and adaptation sweeps. This study extends the molecular mechanism of maize domestication and adaptation, and provides resources for basic research and genetic improvement in maize.

EYA2 suppresses the progression of hepatocellular carcinoma via SOCS3-mediated blockade of JAK/STAT signaling.

BACKGROUND: Somatic mutations are involved in hepatocellular carcinoma (HCC) progression, but the genetic mechanism associated to hepatocarcinogenesis remains poorly understood. We report that Eyes absent homolog 2 (EYA2) suppresses the HCC progression, while EYA2(A510E) mutation identified by exome sequencing attenuates the tumor-inhibiting effect of EYA2. METHODS: Whole-exome sequencing was performed on six pairs of human HCC primary tumors and matched adjacent tissues. Focusing on EYA2, expression level of EYA2 in human HCC samples was evaluated by quantitative real-time PCR, western blot and immunohistochemistry. Loss- and gain-of-function studies, hepatocyte-specific deletion of EYA2 (Eya2-/-) in mice and RNA sequencing analysis were used to explore the functional effect and mechanism of EYA2 on HCC cell growth and metastasis. EYA2 methylation status was evaluated using Sequenom MassARRAY and publicly available data analysis. RESULTS: A new somatic mutation p.Ala510Glu of EYA2 was identified in HCC tissues. The expression of EYA2 was down-regulated in HCC and associated with tumor size (P = 0.001), Barcelona Clinic Liver Cancer stage (P = 0.016) and tumor differentiation (P = 0.048). High level of EYA2 was correlated with a favorable prognosis in HCC patients (P = 0.003). Results from loss-of-function and gain-of-function experiments suggested that knockdown of EYA2 enhanced, while overexpression of EYA2 attenuated, the proliferation, clone formation, invasion, and migration of HCC cells in vitro. Delivery of EYA2 gene had a therapeutic effect on inhibition of orthotopic liver tumor in nude mice. However, EYA2(A510E) mutation led to protein degradation by unfolded protein response, thus weakening the inhibitory function of EYA2. Hepatocyte-specific deletion of EYA2 in mice dramatically promoted diethylnitrosamine-induced HCC development. EYA2 was also down-regulated in HCC by aberrant CpG methylation. Mechanically, EYA2 combined with DACH1 to transcriptionally regulate SOCS3 expression, thus suppressing the progression of HCC via SOCS3-mediated blockade of the JAK/STAT signaling pathway. CONCLUSIONS: In our study, we identified and validated EYA2 as a tumor suppressor gene in HCC, providing a new insight into HCC pathogenesis.

Gamma-secretase complex-dependent intramembrane proteolysis of CD147 regulates the Notch1 signaling pathway in hepatocellular carcinoma.

The γ-secretase complex is a presenilin-dependent aspartyl protease involved in the intramembranous cleavage of various type I transmembrane proteins. As a type I transmembrane protein, CD147 is highly expressed in hepatoma cells and promotes cell proliferation, migration, and invasion. However, the direct underlying mechanism of how CD147 promotes cancer cell proliferation is unknown. Here, we demonstrated that CD147 undergoes an intramembranous cleavage by the γ-secretase at lysine 231 to release its intracellular domains (ICDs). The nuclear translocation of the CD147ICD regulated Notch1 expression by directly binding to the NOTCH1 promoter and promoted the activation of the Notch signaling pathway. Simultaneously, overexpression of CD147ICD promoted cancer cell proliferation via Notch1 signaling. In 102 cases of human hepatocellular carcinoma (HCC) tissues, patients with a high positive rate of nuclear CD147ICD expression had a significantly poor overall survival compared with patients with a low positive rate of nuclear CD147ICD expression. We confirmed that nuclear CD147ICD predicted a poor prognosis in human HCC. The combined therapy of the γ-secretase complex inhibitor and CD147-directed antibody showed better efficacy than monotherapy in orthotopic transplantation HCC mouse models. In conclusion, CD147 is cleaved by the γ-secretase and releases CD147ICD to the cell nucleus, promoting Notch1 expression via direct binding to the NOTCH1 promoter. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Patterns of genomic variation in Chinese maize inbred lines and implications for genetic improvement.

KEY MESSAGE: Genetic relationships among Chinese maize germplasms reveal historical trends in heterotic patterns from Chinese breeding programs and identify line Dan340 as a potential genome donor for elite inbred line Zheng58. The characterization of the genetic relationships, heterotic patterns and breeding history of lines in maize breeding programs allows breeders to efficiently use maize germplasm for line improvement over time. In this study, 269 temperate inbred lines, most of which have been widely used in Chinese maize breeding programs since the 1970s, were genotyped using the Illumina MaizeSNP50 BeadChip, which contains 56,110 single-nucleotide polymorphisms. The STRUCTURE analysis, cluster analysis and principal coordinate analysis results consistently revealed seven groups, of which five were consistent with known heterotic groups within the Chinese maize germplasm-Domestic Reid, Lancaster, Zi330, Tang SPT and Tem-tropic I (also known as "P"). These genetic relationships also allowed us to determine the historical trends in heterotic patterns during the three decades from 1970 to 2000, represented by Mo17 from Lancaster, HuangZaoSi (HZS) from Tang SPT, Ye478 from Domestic Reid and P178 from Tem-tropic I heterotic groups. Mo17-related commercial hybrids were widely used in the 1970s and 1980s, followed by the release of HZS- and Ye478-related commercial hybrids in the 1980s and 1990s, and the introduction of Tem-tropic I group in the 1990s and 2000s. Additionally, we identified inbred line Dan340 as a potential genome donor for Zheng58, which is the female parent of the most widely grown commercial hybrid ZhengDan958 in China. We also reconstructed the recombination events of elite line HZS and its 14 derived lines. These findings provide useful information to direct future maize breeding efforts.

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.

MOTIVATION: Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. METHOD: This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. RESULTS: Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact-assisted models also have much better quality than template-based models especially for membrane proteins. The 3D models built from our contact prediction have TMscore>0.5 for 208 of the 398 membrane proteins, while those from homology modeling have TMscore>0.5 for only 10 of them. Further, even if trained mostly by soluble proteins, our deep learning method works very well on membrane proteins. In the recent blind CAMEO benchmark, our fully-automated web server implementing this method successfully folded 6 targets with a new fold and only 0.3L-2.3L effective sequence homologs, including one ß protein of 182 residues, one α+ß protein of 125 residues, one α protein of 140 residues, one α protein of 217 residues, one α/ß of 260 residues and one α protein of 462 residues. Our method also achieved the highest F1 score on free-modeling targets in the latest CASP (Critical Assessment of Structure Prediction), although it was not fully implemented back then. AVAILABILITY: http://raptorx.uchicago.edu/ContactMap/.

CoinFold: a web server for protein contact prediction and contact-assisted protein folding.

CoinFold (http://raptorx2.uchicago.edu/ContactMap/) is a web server for protein contact prediction and contact-assisted de novo structure prediction. CoinFold predicts contacts by integrating joint multi-family evolutionary coupling (EC) analysis and supervised machine learning. This joint EC analysis is unique in that it not only uses residue coevolution information in the target protein family, but also that in the related families which may have divergent sequences but similar folds. The supervised learning further improves contact prediction accuracy by making use of sequence profile, contact (distance) potential and other information. Finally, this server predicts tertiary structure of a sequence by feeding its predicted contacts and secondary structure to the CNS suite. Tested on the CASP and CAMEO targets, this server shows significant advantages over existing ones of similar category in both contact and tertiary structure prediction.

Ginsenoside Rd Protects SH-SY5Y Cells against 1-Methyl-4-phenylpyridinium Induced Injury.

Ginsenoside Rd (GSRd), one of the main active monomer compounds from the medical plant Panax ginseng, has been shown to promote neuronal survival in models of ischemic cerebral damage. As an extending study, here we examined whether GSRd could exert a beneficial effect in an experimental Parkinson disease (PD) model in vitro, in which SH-SY5Y cells were injured by 1-methyl-4-phenylpyridinium (MPP+), an active metabolic product of the classical Parkinsonian toxin1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Our results, from the addition of different concentrations of GSRd (1, 10 and 50 µM), showed that GSRd at 1 and 10 µM could significantly attenuate MPP+-induced cell death. This protective effect may be ascribed to its ability to reduce intracellular reactive oxygen species levels, enhance antioxidant enzymatic activities, preserve the activity of respiratory complex I, stabilize the mitochondrial membrane potential and increase intracellular ATP levels. Additionally, the PI3K/Akt survival-signaling pathway was also involved in the protective effect of GSRd. Finally, using a mouse PD model in vivo, we also found that GSRd obviously reversed the loss of tyrosine hydroxylase-positive cells in substanitia nigra induced by MPTP. Thus, our findings demonstrated that GSRd showed a significant neuro-protective effect against experimental PD models, which may involve its antioxidant effects and mitochondrial function preservation.

Acylation of exenatide by glycolic acid and its anti-diabetic activities in db/db mice.

PURPOSE: To prepare acylated exenatide analogues and investigate their biological properties for guiding the development of PLGA formulations of exenatide. METHODS: The acylated exenatide analogues were prepared by reaction with glycolic acid (GA), one constitutional unit of PLGA, and characterized by HPLC-MS/MS and Circular Dichroism (CD). The pharmacokinetic properties and anti-diabetic activities were studied in SD rats and db/db mice, respectively. RESULTS: Structural characterizations of the acylated products showed that one to four glycolic acids (GAs) were connected to the primary amine groups of exenatide, and there was a conversion of α-helix to ß-sheet to some extent. Pharmacokinetic studies in SD rats revealed that acylated exenatides had a similar Tmax with that of the prototype drug, whereas the Cmax and the AUC values of the adducts were significantly decreased. Biological activity tests demonstrated that exenatide and acylated exenatide analogues had similar in vivo antidiabetic activities in terms of controlling blood glucose concentration, HbA1c level, body weight and food intake. CONCLUSIONS: These findings suggest that GA conjugated exenatide had no influence on the peptide efficacy, therefore it's not necessary to inhibit exenatide acylation in PLGA formulations during the peptide release process.

UBE2S promotes glycolysis in hepatocellular carcinoma by enhancing E3 enzyme-independent polyubiquitination of VHL.

Background/Aims: Ubiquitination is widely involved in the progression of hepatocellular carcinoma (HCC) by regulating various cellular processes. However, systematic strategies for screening core ubiquitin-related genes, clarifying their functions and mechanisms, and ultimately developing potential therapeutics for patients with HCC are still lacking. Methods: Cox and LASSO regression analyses were performed to construct a ubiquitin-related gene prediction model for HCC. Loss- and gain-of-function studies, transcriptomic and metabolomics analysis were used to explore the function and mechanism of UBE2S on HCC cell glycolysis and growth. Results: Based on 1423 ubiquitin-related genes, a four-gene signature was successfully constructed to evaluate the prognosis of patients with HCC. UBE2S was identified in this signature with the potential to predict the survival of patients with HCC. E2F2 transcriptionally upregulated UBE2S expression by directly binding to its promoter. UBE2S positively regulated glycolysis in a HIF-1α-dependent manner, thus promoting the proliferation of HCC cells. Mechanistically, UBE2S enhanced K11-linkage polyubiquitination at lysine residues 171 and 196 of VHL independent of E3 ligase, thereby indirectly stabilizing HIF-1α protein levels by mediating the degradation of VHL by the proteasome. In particular, the combination of cephalomannine, a small molecule compound that inhibits the expression of UBE2S, and PX-478, an inhibitor of HIF-1α, significantly improved the anti-tumor efficacy. Conclusions: UBE2S is identified as a key biomarker in HCC among the thousands of ubiquitin-related genes and promotes glycolysis by E3 enzyme-independent ubiquitination, thus serving as a therapeutic target for the treatment of HCC.

Effects of sex, sire and in-bag dry-ageing on the physicochemical and microbial properties, colour and fatty acids stability of lamb.

Forty legs from twenty lamb of different sexes and sires (colour stable and labile) were aged using in-bag dry- (BD) and wet-ageing (W) for 21 days. BD resulted in significantly lower moisture content, cook loss, colour (L*, a*, b* and chroma) and % polyunsaturated fatty acids (FAs), higher levels of microbial growth and saturated FAs compared to W. Similar NADH content was observed regardless of sex, sire and ageing. Samples from ram and labile sire had significantly higher pH and saturated FAs and reduced monounsaturated FAs composition compared to those from ewe and stable sire. Lamb from labile sire had significantly higher fat melting point than the stable. Thus, the superior stability of stabile sire was observed only in ram and was not impaired by BD. The sex × sire interaction on oxidative stability demonstrated potential to tailor the quality of dry-aged lamb through altering sex and sire of animals.

Effects of Metabolites, Sex, Sire, and Muscle Type on Chilled Lamb Meat Colour.

Meat is an important source of high-value protein providing sustainable nutrition for human health. The discolouration of meat results in significant waste, which threatens the sustainability of meat production in terms of availability, affordability, and utilisation. Advancing the knowledge of factors and underlying mechanisms for meat discolouration supports the sustainability transformation of meat production practices. Previous studies found that colour stability may be associated with signature changes in certain metabolites, including NADH, glutamate, methionine, and testosterone. This study aimed to confirm the effect of these metabolites and sex, sire, and muscle type on lamb meat colour. NADH and glutamate improved colour stability as evidenced by the increased metmyoglobin reductase activity, while methionine and testosterone had detrimental effects. Overall, lamb meat was discoloured with retail display for up to 10 days at 4 °C. The semitendinosus muscle had higher L*, b*, and hue angle and lower a* (p < 0.05) than other muscles, especially in ewes. Lamb meat from rams had a higher L* and hue angle and lower a* than the ewes (p < 0.05), especially in the colour-labile group, suggesting an interaction between sex and sire. The outcomes of this study will help make the production of meat more sustainable by assisting the meat industry in improving the selection of animals for meat production and processing practices to reduce meat waste due to discolouration.

Challenges and processing strategies to produce high quality frozen meat.

Freezing is an effective means to extend the shelf-life of meat products. However, freezing and thawing processes lead to physical (e.g., ice crystals formation and freezer burn) and biochemical changes (e.g., protein denaturation and lipid oxidation) in meat resulting in loss of quality. Over the last two decades, several attempts have been made to produce thawed meat with qualities similar to that of fresh meat to no avail. This is due to the fact that no single technique exists to date that can mitigate all the quality challenges caused by freezing and thawing. This is further confounded by the consumer perception of frozen meat as lower quality compared to equivalent fresh-never-frozen meat cuts. Therefore, it remains challenging for the meat industry to produce high quality frozen meat and increase consumer acceptability of frozen products. This review aimed to provide an overview of the applications of novel freezing and thawing technologies that could improve the quality of thawed meat including deep freezing, high pressure, radiofrequency, electro-magnetic resonance, electrostatic field, immersion solution, microwave, ohmic heating, and ultrasound. This review will also discuss the development in processing strategies such as optimising the ageing of meat pre- or post-freezing, and the integration of freezing and thawing in one process/regime to collapse the difference in quality between thawed meat and fresh-never-frozen equivalents.

Rapid Evaporative Ionisation Mass Spectrometry fingerprinting can discriminate lamb meat due to different ageing methods and levels of dehydration.

Dry-ageing is a technique for developing characteristic dry-aged flavour through the interplay of dehydration, lipid oxidation and microbial activities. In this study, we tested the hypothesis that the extent of drying influences the metabolite profile and the final flavour of lamb using an "Age-and-Dry" regime; and that Rapid Evaporative Ionisation Mass Spectrometry (REIMS) fingerprinting can be used to discriminate the metabolic fingerprints of lambs due to ageing methods and dehydration levels. Lamb loins (n = 60) were dehydrated with low (12%), medium (17%) and high (22%) weight losses and compared with the wet-aged equivalents using REIMS and evaluated by 12-member sensory panel. Orthogonal projection to latent structures-discriminant analysis (OPLS-DA) models based on 1400 tentatively identified m/z features were obtained for ageing methods (Q2 > 0.95) and dehydration levels (Q2 > 0.82) with high discrimination accuracy. Increased concentrations of dipeptides and metabolites associated with energy metabolism were observed in aged-and-dried lamb meat which supports the umami and savoury taste perceived by the sensory panel. A reduced concentration of polyunsaturated fatty acids with more aldehydes was observed in aged-and-dried lamb meat contributing to the nutty, roasted, and fatty flavour notes detected by the sensory panellists in these samples compared to the wet-aged. SIGNIFICANCE: Outcomes of this study demonstrated that REIMS can be used to accurately discriminate between different ageing methods and dehydration levels of meat, and the compounds that are associated with lamb flavour. The implications of this finding include: (1) the metabolite concentrating effect of dehydration and the associated effect on aged lamb flavour determined in this study could be used to tailor the processing of dry-aged lamb to deliver specific flavour outcomes in an industrial setting; (2) the ability of REIMS to rapidly detect differences in the aged lamb flavour due to dehydration effect would improve the quality of dry-aged meat and the efficiency with which it can be industrially produced. Thus, REIMS can be used as a rapid authentication and quality prediction tool for different ageing regimes and flavour for the meat industry.

Molecular insights into quality and authentication of sheep meat from proteomics and metabolomics.

Sheep meat (encompassing lamb, hogget and mutton) is an important source of animal protein in many countries, with a unique flavour and sensory profile compared to other red meats. Flavour, colour and texture are the key quality attributes contributing to consumer liking of sheep meat. Over the last decades, various factors from 'farm to fork', including production system (e.g., age, breed, feeding regimes, sex, pre-slaughter stress, and carcass suspension), post-mortem manipulation and processing (e.g., electrical stimulation, ageing, packaging types, and chilled and frozen storage) have been identified as influencing different aspects of sheep meat quality. However conventional meat-quality assessment tools are not able to elucidate the underlying mechanisms and pathways for quality variations. Advances in broad-based analytical techniques have offered opportunities to obtain deeper insights into the molecular changes of sheep meat which may become biomarkers for specific variations in quality traits and meat authenticity. This review provides an overview on how omics techniques, especially proteomics (including peptidomics) and metabolomics (including lipidomics and volatilomics) are applied to elucidate the variations in sheep meat quality, mainly in loin muscles, focusing on colour, texture and flavour, and as tools for authentication. SIGNIFICANCE: From this review, we observed that attempts have been made to utilise proteomics and metabolomics techniques on sheep meat products for elucidating pathways of quality variations due to various factors. For instance, the improvement of colour stability and tenderness could be associated with the changes to glycolysis, energy metabolism and endogenous antioxidant capacity. Several studies identify proteolysis as being important, but potentially conflicting for quality as the enhanced proteolysis improves tenderness and flavour, while reducing colour stability. The use of multiple analytical methods e.g., lipidomics, metabolomics, and volatilomics, detects a wider range of flavour precursors (including both water and lipid soluble compounds) that underlie the possible pathways for sheep meat flavour evolution. The technological advancement in omics (e.g., direct analysis-mass spectrometry) could make analysis of the proteins, lipids and metabolites in sheep meat routine, as well as enhance the confidence in quality determination and molecular-based assurance of meat authenticity.

ATAT: Automated Tissue Alignment and Traversal in Spatial Transcriptomics with Self-Supervised Learning.

Spatial transcriptomics (ST) has enhanced RNA analysis in tissue biopsies, but interpreting these data is challenging without expert input. We present Automated Tissue Alignment and Traversal (ATAT), a novel computational framework designed to enhance ST analysis in the context of multiple and complex tissue architectures and morphologies, such as those found in biopsies of the gastrointestinal tract. ATAT utilizes self-supervised contrastive learning on hematoxylin and eosin (H&E) stained images to automate the alignment and traversal of ST data. This approach addresses a critical gap in current ST analysis methodologies, which rely heavily on manual annotation and pathologist expertise to delineate regions of interest for accurate gene expression modeling. Our framework not only streamlines the alignment of multiple ST samples, but also demonstrates robustness in modeling gene expression transitions across specific regions. Additionally, we highlight the ability of ATAT to traverse complex tissue topologies in real-world cases from various individuals and conditions. Our method successfully elucidates differences in immune infiltration patterns across the intestinal wall, enabling the modeling of transcriptional changes across histological layers. We show that ATAT achieves comparable performance to the state-of-the-art method, while alleviating the burden of manual annotation and enabling alignment of tissue samples with complex morphologies.

HMMR alleviates endoplasmic reticulum stress by promoting autophagolysosomal activity during endoplasmic reticulum stress-driven hepatocellular carcinoma progression.

BACKGROUND: The mechanism of hepatitis B virus (HBV)-induced carcinogenesis remains an area of interest. The accumulation of hepatitis B surface antigen in the endoplasmic reticulum (ER) of hepatocytes stimulates persistent ER stress. Activity of the unfolded protein response (UPR) pathway of ER stress may play an important role in inflammatory cancer transformation. How the protective UPR pathway is hijacked by cells as a tool for malignant transformation in HBV-related hepatocellular carcinoma (HCC) is still unclear. Here, we aimed to define the key molecule hyaluronan-mediated motility receptor (HMMR) in this process and explore its role under ER stress in HCC development. METHODS: An HBV-transgenic mouse model was used to characterize the pathological changes during the tumor progression. Proteomics and transcriptomics analyses were performed to identify the potential key molecule, screen the E3 ligase, and define the activation pathway. Quantitative real-time PCR and Western blotting were conducted to detect the expression of genes in tissues and cell lines. Luciferase reporter assay, chromatin immunoprecipitation, coimmunoprecipitation, immunoprecipitation, and immunofluorescence were employed to investigate the molecular mechanisms of HMMR under ER stress. Immunohistochemistry was used to clarify the expression patterns of HMMR and related molecules in human tissues. RESULTS: We found sustained activation of ER stress in the HBV-transgenic mouse model of hepatitis-fibrosis-HCC. HMMR was transcribed by c/EBP homologous protein (CHOP) and degraded by tripartite motif containing 29 (TRIM29) after ubiquitination under ER stress, which caused the inconsistent expression of mRNA and protein. Dynamic expression of TRIM29 in the HCC progression regulated the dynamic expression of HMMR. HMMR could alleviate ER stress by increasing autophagic lysosome activity. The negative correlation between HMMR and ER stress, positive correlation between HMMR and autophagy, and negative correlation between ER stress and autophagy were verified in human tissues. CONCLUSIONS: This study identified the complicated role of HMMR in autophagy and ER stress, that HMMR controls the intensity of ER stress by regulating autophagy in HCC progression, which could be a novel explanation for HBV-related carcinogenesis.

How Do Mobile Social Apps Matter for College Students' Satisfaction in Group-Based Learning? The Mediation of Collaborative Learning.

Recently, many universities apply mobile tools to teaching practices. For instance, some teachers may set up groups on mobile social apps and assign course tasks and advise college students to submit papers online. Nevertheless, how these mobile social apps affect teaching practices, especially the process of students' satisfaction needs to be further explored. To fill this research gap, we build a theoretical model of how mobile social apps' functions affect course satisfaction from the perspective of Media Richness theory and the Uses and Gratifications (U and G) theory. A total of 186 valid questionnaires from college students in China were collected, and a structural equation model was built to test our research model. The results show that as: (1) only the communication function has positive impacts on knowledge sharing, while the impact of the information storing function and information distribution function on knowledge sharing is not significant; (2) knowledge sharing does not affect course satisfaction in a direct way, but it can act indirectly through promoting collaborative learning, which shows the mediating role of collaborative learning. The theoretical implications and practical implications of the study are discussed.

Metabolic fingerprinting using Rapid evaporative ionisation mass spectrometry can discriminate meat quality and composition of lambs from different sexes, breeds and forage systems.

Assurance of food quality and allied farming systems is increasingly sought by consumers and food processors. Yet, there are no validated analytical approaches for food-based verification of farming systems. Rapid evaporative ionisation mass spectrometry (REIMS) is an emerging analytical tool that can provide sufficient details to meet this need. M. Longissimus lumborum of 10 groups of lambs (n = 140) from 3 farms, varying by breed, sex, and forage type, were measured using REIMS fingerprinting. Modelling of features detected by REIMS could discriminate for most comparisons of sex (including castration status), breed, and diet. Tentative identification suggested that lipids, hormone-related compounds, amino acids and dipeptides were the main discriminatory features. Several REIMS features were correlated with pH and shear force in Merino lambs. REIMS was able to detect features related to breed, sex and feed in lamb meat, suggesting that these characteristics can be independently measured using rapid metabolic fingerprinting.