The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using ...short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.
The northern bay scallop Argopecten irradians irradians (Lamarck) and the southern bay scallop Argopecten irradians concentricus (Say) were introduced into China in the 1980s and 1990s, and are now ...major aquaculture molluscs in China. Here, we report the transcriptome sequencing of the two subspecies and the subsequent association analysis on candidate gene on the trait of heat tolerance. In total, RNA from six tissues of 67 and 42 individuals of northern and southern bay scallops, respectively, were used and 55.5 and 34.9 million raw reads were generated, respectively. There were 82,267 unigenes produced in total, of which 32,595 were annotated. Altogether, 32,206 and 23,312 high-quality SNPs were identified for northern and southern bay scallops, respectively. For case-control analysis, two intercrossed populations were heat stress treated, and both heat-susceptible and heat-resistant individuals were collected. According to annotation and SNP allele frequency analysis, 476 unigenes were selected, and 399 pairs of primers were designed. Genotyping was conducted using the high-resolution melting method, and Fisher's exact test was performed for allele frequency comparison between the heat-susceptible and heat-resistant groups. SNP all-53308-760 T/C showed a significant difference in allele frequency between the heat-susceptible and heat-resistant groups. Notably, considerable difference in allele frequency at this locus was also observed between the sequenced natural populations. These results suggest that SNP all-53308-760 T/C may be related to the heat tolerance of the bay scallop. Moreover, quantitative expression analysis revealed that the expression level of all-53308 was negatively correlated with heat tolerance of the bay scallop.
The human insulin-like growth factor 2 mRNA binding proteins 1-3 (IGF2BP1-3, also called IMP1-3) play essential roles in mRNA regulation, including its splicing, translocation, stability, and ...translation. However, knowledge regarding the involvement of IGF2BPs in tumor immunity and stemness across cancer types is still lacking.
In this study, we comprehensively analyzed pan-cancer multi-omic data to determine the correlation of IGF2BPs mRNA and protein expression with various cancer parameters such as mutation frequency, prognostic value, the tumor microenvironment (TME), checkpoint blockade, tumor immune infiltration, stemness and drug sensitivity. Validation of the expression of IGF2BPs in cancer samples and glioma cells were performed by quantitative real-time (qRT)-PCR, and immunofluorescence staining. Investigation of the functional role of IGF2BP3 in glioma stem cells(GSCs) were performed by sphere formation, cytotoxicity, transwell, and wound healing assays.
We found that IGF2BP1 and 3 are either absent or expressed at very low levels in most normal tissues. However, IGF2BP1-3 can be re-expressed in a broad range of cancer types and diverse cancer cell lines, where their expression often correlates with poor prognosis. Immunofluorescence staining and qRT-PCR analyses also showed that the expression of IGF2BP2 and IGF2BP3 were higher in cancer tissues than that in adjacent normal tissues. Moreover, IGF2BPs are associated with TME and stemness in human pan-cancer. Remarkably, IGF2BP3 participated in the maintenance and self-renewal of glioma stem cell (GSCs). Knockdown of IGF2BP3 attenuated GSC and glioma cell proliferation, invasion, and migration.
Our systematic pan-cancer study confirmed the identification of IGF2BPs as therapeutic targets and highlighted the need to study their association with stemness, and the TME, which contribute to the cancer drug-discovery research. Especially, preliminary studies demonstrate the IGF2BP3 as a potential negative regulator of glioma tumorigenesis by modulating stemness.
The interplay between divergence and phenotypic plasticity is critical to our understanding of a species' adaptive potential under rapid climate changes. We investigated divergence and plasticity in ...natural populations of the Pacific oyster Crassostrea gigas with a congeneric oyster Crassostrea angulata from southern China used as an outgroup. Genome re-sequencing of 371 oysters revealed unexpected genetic divergence in a small area that coincided with phenotypic divergence in growth, physiology, heat tolerance and gene expression across environmental gradients. These findings suggest that selection and local adaptation are pervasive and, together with limited gene flow, influence population structure. Genes showing sequence differentiation between populations also diverged in transcriptional response to heat stress. Plasticity in gene expression is positively correlated with evolved divergence, indicating that plasticity is adaptive and favoured by organisms under dynamic environments. Divergence in heat tolerance-partly through acetylation-mediated energy depression-implies differentiation in adaptive potential. Trade-offs between growth and survival may play an important role in local adaptation of oysters and other marine invertebrates.
Background
It is now understood that APOBEC3 family proteins (A3s) are essential in tumor progression, yet their involvement in tumor immunity and stemness across diverse cancer types remains poorly ...understood.
Methods
In the present study, comprehensive genome-wide statistical and bioinformatic analyses were conducted to elucidate A3 family expression patterns, establishing clinically relevant correlations with prognosis, the tumor microenvironment(TME), immune infiltration, checkpoint blockade, and stemness across cancers. Different experimental techniques were applied, including RT–qPCR, immunohistochemistry, sphere formation assays, Transwell migration assays, and wound-healing assays, to investigate the impact of A3C on low-grade glioma (LGG) and glioblastoma multiforme (GBM), as well as its function in glioma stem cells(GSCs).
Results
Dysregulated expression of A3s was observed in various human cancer tissues. The prognostic value of A3 expression differed across cancer types, with a link to particularly unfavorable outcomes in gliomas. A3s are associated with the the TME and stemness in multiple cancers. Additionally, we developed an independent prognostic model based on A3s expression, which may be an independent prognostic factor for OS in patients with glioma. Subsequent validation underscored a strong association between elevated A3C expression and adverse prognostic outcomes, higher tumor grades, and unfavorable histology in glioma. A potential connection between A3C and glioma progression was established. Notably, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses implicated A3C in immune system-related diseases, with heightened A3C levels contributing to an immunosuppressive tumor microenvironment (TME) in glioma. Furthermore,
in vitro
experiments substantiated the role of A3C in sustaining and renewing glioma stem cells, as A3C deletion led to diminished proliferation, invasion, and migration of glioma cells.
Conclusion
The A3 family exhibits heterogeneous expression across various cancer types, with its expression profile serving as a predictive marker for overall survival in glioma patients. A3C emerges as a regulator of glioma progression, exerting its influence through modulation of the tumor microenvironment and regulation of stemness.
Phenol red (PR) is a standard acid-base indicator in cell and tissue culture media, as well as multiple detection protocols. Meanwhile, catalytic nanomaterials such as nanozymes demonstrate great ...potential in biomedical applications, but there were few studies about the direct impact of nanozymes on the ubiquitous pH indicators. We demonstrate for the first time the degradation of phenol red by highly active nanoceria. The results provide evidence that phenol red is a redox active molecule and it may be oxidized quickly by nanoceria so that its pH-indicating functionality may be lost. Investigators need to be cautious in their routine use of phenol red, particularly when it is exposed to active nanozymes. Herein, we construct a PR-hydrogel as a protective strategy for phenol red against oxidation. Results show that the PR-hydrogel maintained the quantitative acid-base indicating capability while resisting the degradation by nanoceria. The hydrogel exhibits high stability, good pH sensitivity and recyclability, negligible cytotoxicity and dye leaching, which provides a strong practical resolution to the application of phenol red in future challenges of nanomedicines.
This study describes the complete diaUel hybridization between newly introduced bay scallop stock （W） from Canada and local commercial stock （D） grown under laboratory conditions, in China. Larval ...survival and growth during all life stages （larvae, spat, and adult） were compared among hybrid （DW, WD） and purebred （DD, WW） populations. Significant heterosis was detected for survival during the larval stage （〉 1% of the mid-parent values）. The mean heterosis （Hm） varied in growth throughout the life span. More than 50% of the Hm values were positive and negative in the DW and WD groups, respectively. The influence of maternal effects and mating types （intrapopulation vs. interpopulation crosses） on growth for all life stages was not consistent. Larval survival did not differ significantly （P〉0.05） with maternal effect or mating type. In the harvest stage, shell length （SL）, shell height （SH）, shell width （SW）, and total weight （TW） were larger in the hybrid compared with the inbred groups. Positive Hm values were observed in SL （1.5%）, SW （5.8%）, and TW （12.3%）, and were more significant in the DW groups （6.1%, 4.5%, 6.8%, and 27.2%）. These results suggest that hybridization between two geographic populations is a good tool for improving bay scallop growth. However, unstable heterosis between the two populations requires further study.
Trimethylphenol is an organic toxic byproduct of industrial process, which is difficult to be eliminated through conventional degradation without harsh conditions. In this work, a sulfite-based ...oxidation process activated by ZnO-embedded hydrogel was studied for the degradation of 2,4,6-trimethylphenols in the ambient conditions. The ZnO/Na
2
SO
3
oxidative system can effectively degrade trimethylphenol via the generation of radicals such as
SO
4
.
−
, OH
·
, and
SO
3
.
−
. The presence of hydrogel matrix facilitates the distribution and recyclability of ZnO catalysts while maintaining high degradation kinetics and little leaching of metal ions. Results suggest the promising potential of ZnO-hydrogel in wastewater treatment with good performance in terms of pH sensitivity, anion interference, recyclability, etc. The combination of ZnO catalysts, hydrogel, and sulfite-based advanced oxidation process may provide essential support for the current treatment of alkylated phenols with strong potential in the commercial scale-ups.
Pacific oysters, Crassostrea gigas, are the most abundantly harvested shellfish in the world and are ecologically significant. The content of nutrients, including protein, glycogen, lipid, zinc (Zn), ...and selenium (Se), is important for oyster meat quality, but heritability estimates of such traits have rarely been reported. In this study, 64 full‐sib families were generated using a nested mating design. Finally, 18 full‐sib families, of which there were nine half‐sib families, with each containing 2 full‐sib families, were sampled for heritability estimates. The narrow‐sense heritabilities of glycogen, protein, lipid, Zn, and Se contents were 0.29 ± 0.02, 0.38 ± 0.02, 0.58 ± 0.08, 0.02 ± 0.02, and 0, respectively. Negative genetic correlations existed between both glycogen and protein content (−0.95 ± 0.004) and between lipid and protein content (−0.59 ± 0.05), whereas a positive correlation was observed between lipid and glycogen content (0.16 ± 0.06). Weak genetic and phenotypical correlations (r = 0–0.2) were observed between shell height and nutritional quality traits. These data demonstrated that glycogen, protein, and lipid content can be chosen in a selective breeding program, but glycogen and lipids cannot be selected together with protein. Furthermore, performing indirect selective breeding for quality traits by selecting traits related to growth is impossible. This study provides information for the development of breeding strategies for oyster quality traits.
Atrial fibrillation (AF) is a major risk factor for ischemic stroke. We aimed to identify novel potential biomarkers with diagnostic value in patients with atrial fibrillation-related cardioembolic ...stroke (AF-CE).Publicly available gene expression profiles related to AF, cardioembolic stroke (CE), and large artery atherosclerosis (LAA) were downloaded from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were identified and then functionally annotated. The support vector machine recursive feature elimination (SVM-RFE) and least absolute shrinkage and selection operator (LASSO) regression analysis were conducted to identify potential diagnostic AF-CE biomarkers. Furthermore, the results were validated by using external data sets, and discriminability was measured by the area under the ROC curve (AUC). In order to verify the predictive results, the blood samples of 13 healthy controls, 20 patients with CE, and 20 patients with LAA stroke were acquired for RT-qPCR, and the correlation between biomarkers and clinical features was further explored. Lastly, a nomogram and the companion website were developed to predict the CE-risk rate. Three feature genes (C1QC, VSIG4, and CFD) were selected and validated in the training and the external datasets. The qRT-PCR evaluation showed that the levels of blood biomarkers (C1QC, VSIG4, and CFD) in patients with AF-CE can be used to differentiate patients with AF-CE from normal controls (P<0.05) and can effectively discriminate AF-CE from LAA stroke (P<0.05). Immune cell infiltration analysis revealed that three feature genes were correlated with immune system such as neutrophils. Clinical impact curve, calibration curves, ROC, and DCAs of the nomogram indicate that the nomogram had good performance. Our findings showed that C1QC, VSIG4, and CFD can potentially serve as diagnostic blood biomarkers of AF-CE; novel nomogram and the companion website can help clinicians to identify high-risk individuals, thus helping to guide treatment decisions for stroke patients.
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