Multi-contrast learning-guided lightweight few-shot learning scheme for predicting breast cancer molecular subtypes

Invasive gene expression profiling studies have exposed prognostically significant breast cancer subtypes: normal-like, luminal, HER-2 enriched, and basal-like, which is defined in large part by human epidermal growth factor receptor 2 (HER-2), progesterone receptor (PR), and estrogen receptor (ER). However, while dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) has been generally employed in the screening and therapy of breast cancer, there is a challenging problem to noninvasively predict breast cancer molecular subtypes, which have extremely low-data regimes. In this paper, a novel few-shot learning scheme, which combines lightweight contrastive convolutional neural network (LC-CNN) and multi-contrast learning strategy (MCLS), is worthwhile to be developed for predicting molecular subtype of breast cancer in DCE-MRI. Moreover, MCLS is designed to construct One-vs-Rest and One-vs-One classification tasks, which addresses inter-class similarity among normal-like, luminal, HER-2 enriched, and basal-like. Extensive experiments demonstrate the superiority of our proposed scheme over state-of-the-art methods. Furthermore, our scheme is able to achieve competitive results on few samples due to joint LC-CNN and MCLS for excavating contrastive correlations of a pair of DCE-MRI.

Uridine diphosphate glucosyltransferase is vital for fenpropathrin resistance in Bombyx mori (Lepidoptera)

The silkworm (Bombyx mori) is an important model lepidopteran insect and can be used to identify pesticide resistance-related genes of great significance for biological control of pests. Uridine diphosphate glucosyltransferases (UGTs), found in all organisms, are the main secondary enzymes involved in the metabolism of heterologous substances. However, it remains uncertain if silkworm resistance to fenpropathrin involves UGT. This study observes significant variations in BmUGT expression among B. mori strains with variable fenpropathrin resistance post-feeding, indicating BmUGT's role in fenpropathrin detoxification. Knockdown of BmUGT with RNA interference and overexpression of BmUGT significantly decreased and increased BmN cell activity, respectively, indicating that BmUGT plays an important role in the resistance of silkworms to fenpropathrin. In addition, fenpropathrin residues were significantly reduced after incubation for 12 h with different concentrations of a recombinant BmUGT fusion protein. Finally, we verified the conservation of UGT to detoxify fenpropathrin in Spodoptera exigua: Its resistance to fenpropathrin decreased significantly after knocking down SeUGT. In a word, UGT plays an important role in silkworm resistance to fenpropathrin by directly degrading the compound, a function seen across other insects. The results of this study are of great significance for breeding silkworm varieties with high resistance and for biological control of pests.

Composite Hydrogel Containing Collagen-Modified Polylactic Acid-Hydroxylactic Acid Copolymer Microspheres Loaded with Tetramethylpyrazine Promotes Articular Cartilage Repair

Articular cartilage defects pose a significant challenge due to the limited self-healing ability of cartilage. However, traditional techniques face limitations including autologous chondrocyte expansion issues. This study aims to investigate the effects of the polylactic acid-glycolic acid (PLGA) and collagen-surface modified polylactic acid-glycolic acid (CPLGA) microspheres loaded with tetramethylpyrazine (TMP) on two cell types and the regeneration potential of articular cartilage. CPLGA microspheres are prepared by Steglich reaction and characterized. They evaluated the effect of TMP-loaded microspheres on HUVECs (Human Umbilical Vein Endothelial Cells) and examined the compatibility of blank microspheres with BMSCs (Bone marrow mesenchymal stromal cells) and their potential to promote cartilage differentiation. Subcutaneous implant immune tests and cartilage defect treatment are conducted to assess biocompatibility and cartilage repair potential. The results highlight the efficacy of CPLGA microspheres in promoting tissue regeneration, attributed to improved hydrophilicity and collagen-induced mitigation of degradation. Under hypoxic conditions, both CPLGA and PLGA TMP-loaded microspheres exhibit inhibitory effects on HUVEC proliferation, migration, and angiogenesis. Notably, CPLGA microspheres show enhanced compatibility with BMSCs, facilitating chondrogenic differentiation. Moreover, the CPLGA microsphere-composite hydrogel exhibits potential for cartilage repair by modulating angiogenesis and promoting BMSC differentiation.

Combined volatile compounds and non-targeted metabolomics analysis reveals variation in flavour characteristics, metabolic profiles and bioactivity of mulberry leaves after Monascus purpureus fermentation

BACKGROUND

Mulberry leaves (MLs) are widely used in food because of their nutritional and functional characteristics. However, plant cell walls and natural bitterness influence nutrient release and the flavor properties of MLs. Liquid-state fermentation using Monascus purpureus (LFMP) is a common processing method used to improve food properties. The present study used headspace solid-phase micro extraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) and non-targeted metabolomics to examine changes in volatile and non-volatile metabolites in MLs. The transformation mechanism of LFMP was investigated by microscopic observation and dynamic analysis of enzyme activity, and changes in the biological activity of MLs were analyzed.

RESULTS

LFMP significantly increased total phenolics, total flavonoids, free amino acids and soluble sugars in MLs, at the same time as decreasing phytic acid levels. In total, 92 volatile organic compounds (VOCs) were identified and quantified. VOCs such as (2R,3R)-(-)-2,3-butanediol, terpineol and eugenol showed some improvement in the flavour characteristics of MLs. By using non-targeted metabolomics, 124 unique metabolites in total were examined. LFMP altered the metabolic profile of MLs, mainly in plant secondary metabolism, lipid metabolism and amino acid metabolism. Microscopic observation and dynamic analysis of enzyme activity indicated that LFMP promoted cell wall degradation and biotransformation of MLs. In addition, LFMP significantly increased the angiotensin I-converting enzyme and α-glucosidase inhibitory activity of MLs.

CONCLUSION

LFMP altered the flavour characteristics, metabolite profile and biological activity of MLs. These findings will provide ideas for the processing of MLs into functional foods. In addition, they also provide useful information for biochemical studies of fermented MLs. © 2023 Society of Chemical Industry.

Integrative analysis of metabolism subtypes and identification of prognostic metabolism-related genes for glioblastoma

Increasing evidence has demonstrated that cancer cell metabolism is a critical factor in tumor development and progression; however, its role in glioblastoma (GBM) remains limited. In the present study, we classified GBM into three metabolism subtypes (MC1, MC2, and MC3) through cluster analysis of 153 GBM samples from the RNA-sequencing data of The Cancer Genome Atlas (TCGA) based on 2752 metabolism-related genes (MRGs). We further explored the prognostic value, metabolic signatures, immune infiltration, and immunotherapy sensitivity of the three metabolism subtypes. Moreover, the metabolism scoring model was established to quantify the different metabolic characteristics of the patients. Results showed that MC3, which is associated with a favorable survival outcome, had higher proportions of isocitrate dehydrogenase (IDH) mutations and lower tumor purity and proliferation. The MC1 subtype, which is associated with the worst prognosis, shows a higher number of segments and homologous recombination defects and significantly lower mRNA expression-based stemness index (mRNAsi) and epigenetic-regulation-based mRNAsi. The MC2 subtype has the highest T-cell exclusion score, indicating a high likelihood of immune escape. The results were validated using an independent dataset. Five MRGs (ACSL1, NDUFA2, CYP1B1, SLC11A1, and COX6B1) correlated with survival outcomes were identified based on metabolism-related co-expression module analysis. Laboratory-based validation tests further showed the expression of these MRGs in GBM tissues and how their expression influences cell function. The results provide a reference for developing clinical management approaches and treatments for GBM.

TRIM5 as a promising diagnostic biomarker of hepatocellular carcinoma: integrated analysis and experimental validation

The TRIM family is associated with the membrane, and its involvement in the progression, growth, and development of various cancer types has been researched extensively. However, the role played by the TRIM5 gene within this family has yet to be explored to a great extent in terms of hepatocellular carcinoma (HCC). The data of patients relating to mRNA expression and the survival rate of individuals diagnosed with HCC were extracted from The Cancer Genome Atlas (TCGA) database. UALCAN was employed to examine the potential link between TRIM5 expression and clinicopathological characteristics. In addition, enrichment analysis of differentially expressed genes (DEGs) was conducted as a means of deciphering the function and mechanism of TRIM5 in HCC. The data in the TCGA and TIMER2.0 databases was utilized to explore the correlation between TRIM5 and immune infiltration in HCC. WGCNA was performed as a means of assessing TRIM5-related co-expressed genes. The "OncoPredict" R package was also used for investigating the association between TRIM5 and drug sensitivity. Finally, qRT-PCR, Western blotting (WB) and immunohistochemistry (IHC) were employed for exploring the differential expression of TRIM5 and its clinical relevance in HCC. According to the results that were obtained from the vitro experiments, mRNA and protein levels of TRIM5 demonstrated a significant upregulation in HCC tissues. It is notable that TRIM5 expression levels were found to have a strong association with the infiltration of diverse immune cells and displayed a positive correlation with several immune checkpoint inhibitors. The TRIM5 expression also displayed promising clinical prognostic value for HCC patients.

N6-methyladenosine-modified MIB1 promotes stemness properties and peritoneal metastasis of gastric cancer cells by ubiquitinating DDX3X

BACKGROUND

Peritoneal metastasis (PM), one of the most typical forms of metastasis in advanced gastric cancer (GC), indicates a poor prognosis. Exploring the potential molecular mechanism of PM is urgently necessary, as it has not been well studied. E3 ubiquitin ligase has been widely established to exert a biological function in various cancers, but its mechanism of action in GC with PM remains unknown.

METHODS

The effect of MIB1 on PM of GC was confirmed in vitro and in vivo. Co-immunoprecipitation (Co-IP) and mass spectrometry demonstrated the association between MIB1 and DDX3X. Western blot, flow cytometry and immunofluorescence determined that DDX3X was ubiquitylated by MIB1 and promoted stemness. We further confirmed that METTL3 promoted the up-regulation of MIB1 by RNA immunoprecipitation (RIP), luciferase reporter assay and other experiments.

RESULTS

We observed that the E3 ubiquitin ligase Mind bomb 1 (MIB1) was highly expressed in PMs, and patients with PM with high MIB1 expression showed a worse prognosis than those with low MIB1 expression. Mechanistically, our study demonstrated that the E3 ubiquitin ligase MIB1 promoted epithelial-mesenchymal transition (EMT) progression and stemness in GC cells by degrading DDX3X. In addition, METTL3 mediated m6A modification to stabilize MIB1, which required the m6A reader IGF2BP2.

CONCLUSIONS

Our study elucidated the specific molecular mechanism by which MIB1 promotes PM of GC, and suggested that targeting the METTL3-MIB1-DDX3X axis may be a promising therapeutic strategy for GC with PM.

The Dynamical Biomarkers in Functional Connectivity of Autism Spectrum Disorder Based on Dynamic Graph Embedding

Autism spectrum disorder (ASD) is a neurological and developmental disorder and its early diagnosis is a challenging task. The dynamic brain network (DBN) offers a wealth of information for the diagnosis and treatment of ASD. Mining the spatio-temporal characteristics of DBN is critical for finding dynamic communication across brain regions and, ultimately, identifying the ASD diagnostic biomarker. We proposed the dgEmbed-KNN and the Aggregation-SVM diagnostic models, which use the spatio-temporal information from DBN and interactive information among brain regions represented by dynamic graph embedding. The classification accuracies show that dgEmbed-KNN model performs slightly better than traditional machine learning and deep learning methods, while the Aggregation-SVM model has a very good capacity to diagnose ASD using aggregation brain network connections as features. We discovered over- and under-connections in ASD at the level of dynamic connections, involving brain regions of the postcentral gyrus, the insula, the cerebellum, the caudate nucleus, and the temporal pole. We also found abnormal dynamic interactions associated with ASD within/between the functional subnetworks, including default mode network, visual network, auditory network and saliency network. These can provide potential DBN biomarkers for ASD identification.

Application Prospect of Induced Pluripotent Stem Cells in Organoids and Cell Therapy

Since its inception, induced pluripotent stem cell (iPSC) technology has been hailed as a powerful tool for comprehending disease etiology and advancing drug screening across various domains. While earlier iPSC-based disease modeling and drug assessment primarily operated at the cellular level, recent years have witnessed a significant shift towards organoid-based investigations. Organoids derived from iPSCs offer distinct advantages, particularly in enabling the observation of disease progression and drug metabolism in an in vivo-like environment, surpassing the capabilities of iPSC-derived cells. Furthermore, iPSC-based cell therapy has emerged as a focal point of clinical interest. In this review, we provide an extensive overview of non-integrative reprogramming methods that have evolved since the inception of iPSC technology. We also deliver a comprehensive examination of iPSC-derived organoids, spanning the realms of the nervous system, cardiovascular system, and oncology, as well as systematically elucidate recent advancements in iPSC-related cell therapies.

Food Waste and Lunar Phases: Evidence from a Randomized Controlled Trial

To examine a potential correlation between food waste and lunar phases, we have devised a randomized controlled trial. The experiment spanned from 31 March to 10 July 2022, during which we employed the direct weighing method to collect 1903 valid data points on food waste. Utilizing propensity score matching, we meticulously controlled for various factors, including dining dates, the number of diners, dining times, spending levels, and store activities. The study revealed a close relationship between lunar phases and food waste. During the new moon phase, there was an increase in both orders and waste generated by consumers. Specifically, individuals, on average, squandered an additional 6.27% of animal protein (0.79 g), 24.5% of plant protein (1.26 g), 60.95% of starchy foods (3.86 g), and 61.09% of vegetables (5.12 g), resulting in an aggregate food waste of 32.14% (10.79 g). Conversely, during the full moon phase, consumers decreased their orders and subsequently decreased food waste. On average, individuals wasted 44.65% less animal protein (5.76 g), 43.36% less plant protein (2.5 g), 85.39% less seafood (0.73 g), and 8.43% less vegetables (0.93 g), resulting in a 20.52% (7.81 g) reduction in food waste. Furthermore, we validated our conclusions through various validation methods, including model replacement, to ensure robustness and reliability.

Peroxin MoPex22 Regulates the Import of Peroxisomal Matrix Proteins and Appressorium-Mediated Plant Infection in Magnaporthe oryzae

Magnaporthe oryzae, the pathogen responsible for rice blast disease, utilizes specialized infection structures known as appressoria to breach the leaf cuticle and establish intracellular, infectious hyphae. Our study demonstrates that the peroxin MoPex22 is crucial for appressorium function, specifically for the development of primary penetration hyphae. The ∆Mopex22 mutant exhibited slow growth, reduced aerial hyphae, and almost complete loss of virulence. Specifically, despite the mutant's capability to form appressoria, it showed abnormalities during appressorium development, including reduced turgor, increased permeability of the appressorium wall, failure to form septin rings, and significantly decreased ability to penetrate host cells. Additionally, there was a delay in the degradation of lipid droplets during conidial germination and appressorium development. Consistent with these findings, the ΔMopex22 mutant showed an inefficient utilization of long-chain fatty acids and defects in cell wall integrity. Moreover, our findings indicate that MoPex22 acts as an anchor for MoPex4, facilitating the localization of MoPex4 to peroxisomes. Together with MoPex4, it affects the function of MoPex5, thus regulating the import of peroxisomal matrix proteins. Overall, these results highlight the essential role of MoPex22 in regulating the transport of peroxisomal matrix proteins, which affect fatty acid metabolism, glycerol accumulation, cell wall integrity, growth, appressorium development, and the pathogenicity of M. oryzae. This study provides valuable insights into the significance of peroxin functions in fungal biology and appressorium-mediated plant infection.

Effects of organic carbon and subsurface dams on saltwater intrusion and nitrate pollution in sandy coastal aquifers

This study explores the impact of a novel approach on the levels of SWI (saltwater intrusion) and NO3- (nitrate) contamination. Some numerical simulations were conducted utilizing a coupled model that incorporates variably saturation and density, as well as convection diffusion reaction within a sandy coastal aquifer. We verified the reliability of the model for SWI based on comparison lab experiments and for chemical reactions based on a comparison of previous in situ observations. Cutoff walls and subsurface dams cannot simultaneously control SWI and reduce NO3- contamination. A novel approach that combines subsurface dams and permeable CH2O (organic carbon) walls (PC-Wall) is proposed. Subsurface dams are utilized to prevent SWI, while PC-Walls are employed to mitigate NO3- pollution. Results demonstrate that the construction of a PC-Wall with a concentration of 1.0 mM facilitated a transition from nitrification (Ni)-dominated to denitrification (Dn)-dominated. An increase in CH2O concentration to 1.0 mM caused a significant 1942.5 % rise in mDn (the mass of NO3- removed through Dn). Increment of the distance between the PC-Wall and the ocean from 35 to 45 m could result in a 103.7 % mDn increase and reduce mN (the compound mass of NO3- remaining in the aquifer) by 11.7 %. The study offers a detailed comprehension of the intricate hydrodynamics of SWI and NO3- pollution. In addition, it provides design guidance for engineering to mitigate contamination by NO3- and controlling SWI, thus fostering the management of groundwater quality.

A design approach of panel size for the cooperative development of cropland protection and coal mining in a coal-cropland overlapping area

Cropland is the foundation of food security. Coal is the guarantee of energy security. As China's demand for coal and grain continues to increase, so does the overlap area of their production bases. Unrestrained underground mining can cause serious damage to cropland, leading to increasing conflicts between coal mining and food production. Thus, this paper used a partial backfilling mining technology to control surface subsidence and thus protect cropland. The key to successfully implementing the technology is how to design the panel size. However, the design efficiency of the conventional enumeration method is low. Therefore, this paper proposed a design approach based on improved particle swarm optimization. The results indicated that the approach could quickly find the optimal size of the panel compared with the enumeration method and particle swarm optimization. Moreover, if the longwall panel is mined according to the size designed by the approach, the cropland will be protected, and the cost will be reduced. This study can provide technical support for the cooperative development of cropland protection and coal mining in a coal-cropland overlapping area.

Reticulate evolution of the tertiary relict Osmanthus

When interspecific gene flow is common, species relationships are more accurately represented by a phylogenetic network than by a bifurcating tree. This study aimed to uncover the role of introgression in the evolution of Osmanthus, the only genus of the subtribe Oleinae (Oleaceae) with its distribution center in East Asia. We built species trees, detected introgression, and constructed networks using multiple kinds of sequencing data (whole genome resequencing, transcriptome sequencing, and Sanger sequencing of nrDNA) combined with concatenation and coalescence approaches. Then, based on well-understood species relationships, historical biogeographic analyses and diversification rate estimates were employed to reveal the history of Osmanthus. Osmanthus originated in mid-Miocene Europe and dispersed to the eastern Tibetan Plateau in the late Miocene. Thereafter, it continued to spread eastwards. Phylogenetic conflict is common within the 'Core Osmanthus' clade and is seen at both early and late stages of diversification, leading to hypotheses of net-like species relationships. Incomplete lineage sorting proved ineffective in explaining phylogenetic conflicts and thus supported introgression as the main cause of conflicts. This study elucidates the diversification history of a relict genus in the subtropical regions of eastern Asia and reveals that introgression had profound effects on its evolutionary history.

SOX18 Promotes the Proliferation of Dermal Papilla Cells via the Wnt/β-Catenin Signaling Pathway

SRY-box transcription factor 18 (SOX18) is known to play a crucial role in the growth and development of hair follicles (HF) in both humans and mice. However, the specific effect of SOX18 on sheep hair follicles remains largely unknown. In our previous study, we observed that SOX18 was specifically expressed within dermal papilla cells (DPCs) in ovine hair follicles, leading us to investigate its potential role in the growth of hair follicles in sheep. In the present study, we aimed to examine the effect of SOX18 in DPCs and preliminarily study its regulatory mechanism through RNA-seq. We initially found that the overexpression of SOX18 promoted the proliferation of DPCs compared to the negative control group, while the interference of SOX18 had the opposite effect. To gain further insight into the regulatory mechanism of SOX18, we conducted RNA-seq analysis after knocking down SOX18 in Hu sheep DPCs. The result showed that the Wnt/β-Catenin signaling pathway was involved in the growth process of DPC after SOX18 knockdown. Subsequently, we investigated the effect of SOX18 on the Wnt/β-Catenin signaling pathway in DPCs using TOP/FOP-flash, qRT-PCR, and Western blot (WB) analysis. Our data demonstrated that SOX18 could activate the Wnt/β-Catenin signaling pathway in DPCs. Additionally, we observed that SOX18 could rescue the proliferation of DPCs after inhibiting the Wnt/β-Catenin signaling pathway. These findings underscore the essential role of SOX18 as a functional molecule governing the proliferation of DPCs. Additionally, these findings also greatly enhance our understanding of the role of SOX18 in the proliferation of DPCs and the growth of wool in Hu sheep.

Magnetic Anomaly Detection Based on a Compound Tri-Stable Stochastic Resonance System

In the case of strong background noise, a tri-stable stochastic resonance model has higher noise utilization than a bi-stable stochastic resonance (BSR) model for weak signal detection. However, the problem of severe system parameter coupling in a conventional tri-stable stochastic resonance model leads to difficulty in potential function regulation. In this paper, a new compound tri-stable stochastic resonance (CTSR) model is proposed to address this problem by combining a Gaussian Potential model and the mixed bi-stable model. The weak magnetic anomaly signal detection system consists of the CTSR system and judgment system based on statistical analysis. The system parameters are adjusted by using a quantum genetic algorithm (QGA) to optimize the output signal-to-noise ratio (SNR). The experimental results show that the CTSR system performs better than the traditional tri-stable stochastic resonance (TTSR) system and BSR system. When the input SNR is -8 dB, the detection probability of the CTSR system approaches 80%. Moreover, this detection system not only detects the magnetic anomaly signal but also retains information on the relative motion (heading) of the ferromagnetic target and the magnetic detection device.

Visible-Light-Irradiated Multicomponent Reactions of Aliphatic Amines, Propiolate Acid Esters, and CF3 SO2 Na for Accessing β-CF3 Enamines

A novel one-pot two-step multicomponent reaction has been achieved for the preparation of β-CF3 enamines by using different aliphatic amines, propiolates, and CF3 SO2 Na as starting material. In this protocol, various aliphatic amines including primary amines, cyclic or acyclic secondary amines were demonstrated to be good coupling partners, and different β-CF3 enamines were obtained in moderate to good yields. Among them, the primary aliphatic amines only gave pure (E)-β-CF3 enamines as products. The synthetic utility of the MCRs strategy was further demonstrated by mild conditions, gram-scale synthesis and natural sunlight-induced protocol. Preliminary mechanistic studies suggest that this trifluoromethylation of C(sp2 )-H involves radical process.

A Trojan-Horse-Like Biomimetic Nano-NK to Elicit an Immunostimulatory Tumor Microenvironment for Enhanced GBM Chemo-Immunotherapy

Although the chemo- and immuno-therapies have obtained good responses for several solid tumors, including those with brain metastasis, their clinical efficacy in glioblastoma (GBM) is disappointing. The lack of safe and effective delivery systems across the blood-brain barrier (BBB) and the immunosuppressive tumor microenvironment (TME) are two main hurdles for GBM therapy. Herein, a Trojan-horse-like nanoparticle system is designed, which encapsulates biocompatible PLGA-coated temozolomide (TMZ) and IL-15 nanoparticles (NPs) with cRGD-decorated NK cell membrane (R-NKm@NP), to elicit the immunostimulatory TME for GBM chemo-immunotherapy. Taking advantage of the outer NK cell membrane cooperating with cRGD, the R-NKm@NPs effectively traversed across the BBB and targeted GBM. In addition, the R-NKm@NPs exhibited good antitumor ability and prolonged the median survival of GBM-bearing mice. Notably, after R-NKm@NPs treatment, the locally released TMZ and IL-15 synergistically stimulated the proliferation and activation of NK cells, leading to the maturation of dendritic cells and infiltration of CD8+ cytotoxic T cells, eliciting an immunostimulatory TME. Lastly, the R-NKm@NPs not only effectively prolonged the metabolic cycling time of the drugs in vivo, but also has no noticeable side effects. This study may offer valuable insights for developing biomimetic nanoparticles to potentiate GBM chemo- and immuno-therapies in the future.

Study on mechanical properties of coal gangue and fly ash mixture as backfill material based on fractal characteristics

Backfill mining can effectively alleviate the problems of surface collapse and ecological water pollution, in which the mechanical properties of backfill materials, including coal gangue and coal fly ash, have a decisive role in the effect of filling mining. In this study, we analyze the permeability characteristics of coal gangue filler through a set of homemade percolation test systems and introduce fractal characteristics to investigate the key factors affecting percolation in complex pores of broken coal gangue. The results indicate that the fractal dimensions of crushed coal gangue particles show an increasing trend with increasing axial loading and that the variation range is from 2.15647 to 2.58933. The coal fly ash concentration has a positive relationship with the acceleration factor. The permeability of crushed coal gangue follows a hierarchical distribution law and the permeability changes in the magnitude range of 10-11 ~ 10-9 m2. The fractal dimension is inversely related to the permeability of crushed coal gangue. The experimental results show that the coal gangue will be further crushed and that adding a certain concentration of coal fly ash can achieve a better water barrier, which provides theoretical support and engineering significance for the stability analysis of geological engineering and backfill mining technology.

An efficient qPCR assay for the quantification of human cells in preclinical animal models by targeting human specific DNA in the intron of BRCA1

BACKGROUND

Precise quantification of grafted human cells in preclinical animal models such as non-human primates, rodents and rabbits is needed for the evaluations of the safety and efficacy of cell therapy. Quantitative PCR (qPCR) as a swift, sensitive and powerful assay is suitable for human cell quantification. However, it is a formidable challenge due to that the genome of non-human primates share more than 95% of similarity as human.

METHODS

In the present study, we developed a probe-based quantitative PCR (qPCR) assay for the quantification of human cells in preclinical animal models via targeting human specific DNA in the intron of BRCA1 (termed BRCA1-qPCR). The 5' and 3' end of BRCA1-qPCR probe was conjugated with FAM and non-fluorescent quencher-minor groove binder (NFQ-MGB), respectively. 1 µg of genomic DNA from human and preclinical animal models including rhesus monkeys, cynomolgus monkeys, New Zealand white rabbits, SD rats, C57BL/6 and BALB/c mice were used for determining the specificity and sensitivity of the BRCA1-qPCR assay. A calibration curve was generated by BRCA1-qPCR analysis of linearized plasmid containing targeted human specific DNA in BRCA1. The BRCA1-qPCR assay was validated by analysis of 0.003%, 0.03% and 0.3% of human leukocytes mixed within murine leukocytes.

RESULTS

The BRCA1-qPCR assay detected human DNA rather than DNA from tested species. The amplification efficiency of the BRCA1-qPCR assay was 95.4% and the linearity of the calibration curve was R2 = 0.9997. The BRCA1-qPCR assay detected as low as 5 copies of human specific DNA and is efficient to specially amplify 30 pg human DNA in the presence of 1 µg of genomic DNA from tested species, respectively. The BRCA1-qPCR assay was able to quantify as low as 0.003% of human cells within murine leukocytes.

CONCLUSION

The BRCA1-qPCR assay is efficient for the quantification of human cells in preclinical animal models.

Structural plasticity of the contralesional hippocampus and its subfields in patients with glioma

OBJECTIVES

To characterize the structural plasticity of the contralesional hippocampus and its subfields in patients with unilateral glioma.

METHODS

3D T1-weighted MRI images were collected from 55 patients with tumors infiltrating the left (HipL, n = 27) or right (HipR, n = 28) hippocampus, along with 30 age- and sex-matched healthy controls (HC). Gray matter volume differences of the contralesional hippocampal regions and three control regions (superior frontal gyrus, caudate nucleus, and superior occipital gyrus) were evaluated using voxel-based morphometry (VBM) analyses. Volumetric differences in the hippocampus and its subregional volume were measured using the FreeSurfer software.

RESULTS

Compared with HC, patients with unilateral hippocampal glioma exhibited significantly larger gray matter volume in the contralesional hippocampus and parahippocampal regions (cluster = 571 voxels for HipL; cluster 1 = 538 voxels and cluster 2 = 88 voxels for HipR; family-wise error corrected p < 0.05). No significant alterations were found in control regions. Volumetric analyses showed the same trend in the contralesional hippocampal subregions for both patient groups, including the CA1 head, CA3 head, hippocampus amygdala transition area (HATA), fimbria, and the granule cell molecular layer of the dentate gyrus head (GC-ML-DG head). Notably, the differences of the contralesional HATA (HipL: η2 = 0.418, corrected p = 0.002; HipR: η2 = 0.313, corrected p = 0.052) and fimbria (HipL: η2 = 0.450, corrected p < 0.001; HipR: η2 = 0.358, corrected p = 0.012) still held after the Bonferroni correction.

CONCLUSIONS

Our findings provide evidence for macrostructural plasticity of the contralateral hippocampus in patients with unilateral hippocampal glioma. Specifically, HATA and fimbria exhibit great potential in this process.

KEY POINTS

• Glioma infiltration of the hippocampal regions induces a significant increase in gray matter volume on the contralateral side. • Specifically, the HATA and fimbria regions exhibit favorable plastic potential in the process of lesion-induced structural remolding.

Integrated assessment and critical obstacle diagnosis of rural resource and environmental carrying capacity with a social-ecological framework: a case study of Liyang county, Jiangsu Province

The contradiction among human being, resources, and environment has become a significant obstacle to achieving sustainable development, especially in rural areas subject to the spillover of urban development elements. With the immense strain of resources and environment, it is critical to assess whether human activities fall within the carrying capacity range of a natural ecosystem in a rural system. Taking the rural areas of Liyang county as an example, this study aims to assess the rural resource and environmental carrying capacity (RRECC) and diagnose its critical obstacles. Firstly, a social-ecological framework focusing on human-environment interaction was employed to construct the RRECC indicator system. Subsequently, the entropy-TOPSIS method was introduced to assess the performance of the RRECC. Finally, the obstacle diagnosis method was applied to identify the critical obstacles of RRECC. Our results show that the distribution of RRECC presents a spatial heterogeneity, with high- and medium-high-level villages primarily concentrated in the south of the study area, where there are abundant hills and ecological lakes. Medium-level villages are scattered throughout each town, and low and medium-low level villages are concentrated across all the towns. Moreover, the resource subsystem of RRECC (RRECC_RS) exhibits a similar spatial distribution to RRECC, while the outcome subsystem of RRECC (RRECC_OS) has a comparable quantity proportion of different levels to RRECC. Furthermore, the diagnosis results of critical obstacle vary between the town scale divided by administrative units and the regional scale divided by RRECC values. In detail, arable land occupied by construction is the main critical obstacle at the town scale, while the poor people in villages, people left-behind, and arable land occupied by construction are the main critical obstacles at the regional scale. Targeted differentiated improvement strategies for RRECC at regional scale from various perspectives of global, local, and single are proposed. This research can serve as a theoretical foundation for assessing RRECC and developing differentiated sustainable development strategies for the path forward to rural revitalization.

Efficient Autonomous Exploration and Mapping in Unknown Environments

Autonomous exploration and mapping in unknown environments is a critical capability for robots. Existing exploration techniques (e.g., heuristic-based and learning-based methods) do not consider the regional legacy issues, i.e., the great impact of smaller unexplored regions on the whole exploration process, which results in a dramatic reduction in their later exploration efficiency. To this end, this paper proposes a Local-and-Global Strategy (LAGS) algorithm that combines a local exploration strategy with a global perception strategy, which considers and solves the regional legacy issues in the autonomous exploration process to improve exploration efficiency. Additionally, we further integrate Gaussian process regression (GPR), Bayesian optimization (BO) sampling, and deep reinforcement learning (DRL) models to efficiently explore unknown environments while ensuring the robot's safety. Extensive experiments show that the proposed method could explore unknown environments with shorter paths, higher efficiencies, and stronger adaptability on different unknown maps with different layouts and sizes.

Crosstalk between miR-144/451 and Nrf2 during Recovery from Acute Hemolytic Anemia

miR-144/451 and nuclear factor (erythroid-derived 2)-like 2 (Nrf2) regulate two antioxidative systems that have been identified to maintain redox homeostasis in erythroid cells by removing excess reactive oxygen species (ROS). Whether these two genes coordinate to affect ROS scavenging and the anemic phenotype, or which gene is more important for recovery from acute anemia, has not been explored. To address these questions, we crossed miR-144/451 knockout (KO) and Nrf2 KO mice and examined the phenotype change in the animals as well as the ROS levels in erythroid cells either at baseline or under stress condition. Several discoveries were made in this study. First, Nrf2/miR-144/451 double-KO mice unexpectedly exhibit similar anemic phenotypes as miR-144/451 single-KO mice during stable erythropoiesis, although compound mutations of miR-144/451 and Nrf2 lead to higher ROS levels in erythrocytes than single gene mutations. Second, Nrf2/miR-144/451 double-mutant mice exhibit more dramatic reticulocytosis than miR-144/451 or Nrf2 single-KO mice during days 3 to 7 after inducing acute hemolytic anemia using phenylhydrazine (PHZ), indicating a synergistic effect of miR-144/451 and Nrf2 on PHZ-induced stress erythropoiesis. However, the coordination does not persist during the whole recovery stage of PHZ-induced anemia; instead, Nrf2/miR-144/451 double-KO mice follow a recovery pattern similar to miR-144/451 single-KO mice during the remaining period of erythropoiesis. Third, the complete recovery from PHZ-induced acute anemia in miR-144/451 KO mice takes longer than in Nrf2 KO mice. Our findings demonstrate that complicated crosstalk between miR-144/451 and Nrf2 does exist and the crosstalk of these two antioxidant systems is development-stage-dependent. Our findings also demonstrate that miRNA deficiency could result in a more profound defect of erythropoiesis than dysfunctional transcription factors.

Construction of the genetic switches in response to mannitol based on artificial MtlR box

Synthetic biology has rapidly advanced from the setup of native genetic devices to the design of artificial elements able to provide organisms with highly controllable functions. In particular, genetic switches are crucial for deploying new layers of regulation into the engineered organisms. While the assembly and mutagenesis of native elements have been extensively studied, limited progress has been made in rational design of genetic switches due to a lack of understanding of the molecular mechanism by which a specific transcription factor interacts with its target gene. Here, a reliable workflow is presented for designing two categories of genetic elements, one is the switch element-MtlR box and the other is the transcriptional regulatory element- catabolite control protein A (CcpA) box. The MtlR box was designed for ON/OFF-state selection and is controlled by mannitol. The rational design of MtlR box-based molecular structures can flexibly tuned the selection of both ON and OFF states with different output switchability in response to varied kind effectors. Different types of CcpA boxes made the switches with more markedly inducer sensitivities. Ultimately, the OFF-state value was reduced by 90.69%, and the maximum change range in the presence of two boxes was 15.31-fold. This study presents a specific design of the switch, in a plug-and-play manner, which has great potential for controlling the flow of the metabolic pathway in synthetic biology.

Antibiotic resistance of fecal carriage of Escherichia coli from pig farms in China: a meta-analysis

Fecal carriage of bacteria is a major source of antibiotic resistance genes (ARGs) and a public health risk, but the antibiotic resistance of Escherichia coli (E. coli) in Chinese pig farms remains a major gap in the available literature. Our goal was to conduct a meta-analysis of studies reporting antibiotic resistance of fecal carriage of E. coli from pig farms in China, calculating the pooled resistance rates and summarizing factors associated with it. We searched PubMed and Web of Science for studies published in English up to February 28, 2021. We also searched bibliographic indices and corresponded with the authors. We chose ciprofloxacin, gentamicin, tetracycline, ampicillin, and florfenicol from five major types of antibiotics to comprehensively evaluate the resistance rate of E. coli. We used a random-effects model and Freeman-Tukey double arcsine transformation to calculate the resistance rate and 95% confidence interval. Among the 120 retrieved manuscripts, 16 studies (1985 E. coli isolates) were deemed eligible for our analysis. The combined resistance rate of E. coli from feces was 58.8% (95% CI: 45.3-71.7%) to ciprofloxacin, 54.3% (95% CI: 35.3-72.6%) to gentamicin, 91.0% (95% CI: 83.1-96.7%) to tetracycline, 81.4% (95% CI: 62.0-95.1%) to ampicillin, and 65.4% (95% CI: 33.9-90.9%) to florfenicol. In conclusion, fecal carriage of E. coli in Chinese pig farms shows high resistance to ciprofloxacin, gentamicin, tetracycline, ampicillin, and florfenicol. Subgroup analysis showed that the resistance of E. coli to antibiotics was closely related to the sample size and the health condition of the pigs. Specifically, ESBL-producing E. coli has a higher ratio of resistance to other antibiotics. Future collection of antibiotic resistance and other information in pig farms should be more precise and depend on local surveys.

YAP promotes autophagy and progression of gliomas via upregulating HMGB1

BACKGROUND

Due to the hypoxia and nutrient deficiency microenvironment, glioblastoma (GBM) exhibits high autophagy activity and autophagy plays an important role in the progression of GBM. However, the molecular mechanism of autophagy in GBM progression remains unclear. The aim of this study is to delve out the role and mechanism of yes-associated protein (YAP) in GBM autophagy and progression.

METHODS

The level of autophagy or autophagy flux were assessed by using western blotting, GFP-LC3 puncta (Live) imaging, transmission electron microscopy and GFP-RFP-LC3 assay. The GBM progression was detected by using CCK8, EdU, nude mouse xenograft and Ki67 staining. Isobaric tags for relative and absolute quantification (iTraq) quantitative proteomics was used to find out the mediator of YAP in autophagy. Expression levels of YAP and HMGB1 in tissue samples from GBM patients were examined by Western blotting, tissue microarray and immunohistochemistry.

RESULTS

YAP over-expression enhanced glioma cell autophagy under basal and induced conditions. In addition, blocking autophagy by chloroquine abolished the promoting effect of YAP on glioma growth. Mechanistically, YAP over-expression promoted the transcription and translocation of high mobility group box 1(HMGB1), a well-known regulator of autophagy, from nucleus to cytoplasm. Down-regulation of HMGB1 abolished the promoting effect of YAP on autophagy and glioma growth. Furthermore, the expression of YAP and HMGB1 were positively associated with each other and suggested poor prognosis for clinical GBM.

CONCLUSION

YAP promoted glioma progression by enhancing HMGB1-mediated autophagy, indicating that YAP-HMGB1 axis was a feasible therapeutic target for GBM. Our study revealed a clinical opportunity involving the combination of chemo-radiotherapy with pharmacological autophagy inhibition for treating GBM patients with YAP high expression.

Transcriptional profiling of long noncoding RNAs associated with leaf-color mutation in Ginkgo biloba L

BACKGROUND

Long noncoding RNAs (lncRNAs) play an important role in diverse biological processes and have been widely studied in recent years. However, the roles of lncRNAs in leaf pigment formation in ginkgo (Ginkgo biloba L.) remain poorly understood.

RESULTS

In this study, lncRNA libraries for mutant yellow-leaf and normal green-leaf ginkgo trees were constructed via high-throughput sequencing. A total of 2044 lncRNAs were obtained with an average length of 702 nt and typically harbored 2 exons. We identified 238 differentially expressed lncRNAs (DELs), 32 DELs and 49 differentially expressed mRNAs (DEGs) that constituted coexpression networks. We also found that 48 cis-acting DELs regulated 72 target genes, and 31 trans-acting DELs regulated 31 different target genes, which provides a new perspective for the regulation of the leaf-color mutation. Due to the crucial regulatory roles of lncRNAs in a wide range of biological processes, we conducted in-depth studies on the DELs and their targets and found that the chloroplast thylakoid membrane subcategory and the photosynthesis pathways (ko00195) were most enriched, suggesting their potential roles in leaf coloration mechanisms. In addition, our correlation analysis indicates that eight DELs and 68 transcription factors (TFs) might be involved in interaction networks.

CONCLUSIONS

This study has enriched the knowledge concerning lncRNAs and provides new insights into the function of lncRNAs in leaf-color mutations, which will benefit future selective breeding of ginkgo.