Spatial distribution characteristics and interaction effects of DOM and microbial communities in kelp cultivation areas.

The influence of macroalgae cultivation on aquaculture carbon sinks is significant, with microbial carbon (C) pumps contributing to a stable inert dissolved carbon pool in this context. Concurrently, dissolved organic matter (DOM) exchange at the marine sediment-water interface profoundly affects global ecosystem element cycling. However, the interactions between DOM and bacterial communities at the sediment-water interface in kelp cultivation areas, especially regarding microbial function prediction, have not been fully explored. This study analyzed the DOM characteristics, environmental factors, and bacterial community structure in the Tahewan kelp--Saccharina japonica cultivated area and compared them with those in non-cultivated areas. The results indicated significantly higher dissolved organic carbon (DOC) concentrations in the kelp culture area, particularly in surface seawater and overlying water. The dominant bacterial phyla in both regions included Pseudomonadota, Actinomycetota, and Bacteroidota in both regions, while Desulfobacterota was more prevalent in the sediment environment of the cultivated region. Parallel factor analysis (EEM-PARAFAC) was used to identify DOM components, among which component C2 (a microbial humic-like substance DOM) was highly resistant to microbial degradation. We infer that C2 has similar properties to recalcitrant dissolved organic matter (RDOM). Analysis of the predicted functional genes based on 16S rRNA gene data showed that methanol oxidation, methylotrophy, and methanotrophy were significant in the bottom seawater of the cultivation area. The carbon (C), nitrogen (N), and sulfur (S) cycle functional genes in the sediment environment of the kelp cultivation area were more active than those in other areas, especially in which sulfate reduction and denitrification were the two main processes. Furthermore, a DOM priming effect was identified in the cultivated sediment environment, where kelp-released labile dissolved organic matter (LDOM) stimulates rapid degradation of the original RDOM, potentially enhancing C sequestration.

Ultrasensitive Detection of miRNA via CRISPR/Cas12a Coupled with Strand Displacement Amplification Reaction.

MicroRNA (miRNA) is a promising biomarker for the diagnosis, monitoring, and prognostic evaluation of diseases, especially cancer. The existing miRNA detection methods usually need external instruments for quantitative signal output, limiting their practical applications in point-of-care (POC) settings. Here, we propose a distance-based biosensor through a responsive hydrogel, in combination with a CRISPR/Cas12a system and target-triggered strand displacement amplification (SDA) reaction for visual quantitative and sensitive measurement of miRNA. The target miRNA is first converted into plenty of double-stranded DNA (dsDNA) via target-triggered SDA reaction. Then, the dsDNA products trigger the collateral cleavage activity of CRISPR/Cas12a, leading to the release of trypsin from magnetic beads (MBs). The released trypsin can hydrolyze gelatin, and hence the permeability of gelatin-treated filter paper is increased, resulting in a visible distance signal on a cotton thread. Using this system, the concentration of the target miRNA can be quantified visually without any assistance of instruments, and a detection limit of 6.28 pM is obtained. In addition, the target miRNA in human serum samples and cell lysates can also be detected accurately. Owing to the characteristics of simplicity, sensitivity, specificity, and portability, the proposed biosensor provides a new tool for miRNA detection and holds great promise in POC applications.

Silencing the Catalase Gene with SiRNA for Enhanced Chemodynamic Therapy.

Chemodynamic therapy (CDT) has been emerging as a promising strategy for cancer treatment. But the CDT efficiency is restricted by the insufficient intracellular hydrogen peroxide (H2O2) level. Herein, we present a method for H2O2 accumulation in tumor cells by silencing the catalase (CAT) gene with siRNA to achieve enhanced CDT. Cu-siRNA nanocomposites are fabricated by self-assembly of Cu2+ and CAT siRNA and then modified with hyaluronic acid (HA) for active tumor targeting. After tumor cell uptake, the released Cu2+ is reduced by highly expressed glutathione (GSH) to Cu+, which then catalyzes H2O2 to produce toxic hydroxyl radicals (•OH) to kill tumor cells. CAT siRNA can efficiently silence the CAT mRNA to inhibit the consumption of H2O2, resulting in H2O2 accumulation. The Cu2+-mediated GSH elimination and siRNA-induced endogenous H2O2 enrichment both potentiate CDT. Cu-siRNA@HA exhibits good biocompatibility and therapeutic efficiency. This work thus paves a new way to supply H2O2 in CDT and may hold potential for clinical application.

An in situ exosomal miRNA sensing biochip based on multi-branched localized catalytic hairpin assembly and photonic crystals.

Exosomal microRNAs (miRNAs) are emerging as attractive non-invasive and reliable biomarkers for disease diagnosis. In situ exosomal miRNA detection can avoid laborious and time-consuming exosome lysis, RNA extraction and effectively improve the accuracy. However, in situ exosomal miRNA detection is hampered by the low abundance of the targets and low permeability of the probes. Herein, an in situ exosomal miRNA sensing biochip based on multi-branched localized catalytic hairpin assembly (MLCHA) and photonic crystals (PCs) was proposed. The MLCHA probes could penetrate into the exosomes nondestructively due to its rigidity and generate amplified fluorescence signal upon recognizing the target miRNA. And then, the fluorescence signal was further enhanced by PCs to improve the sensitivity. The developed biosensor can not only detect exosomal miRNA in a concentration-dependent manner but also distinguish samples from cancer state and healthy state, which is potential for non-invasive clinical diagnostics.

Cotton thread-based multi-channel photothermal biosensor for simultaneous detection of multiple microRNAs.

The abnormal expression of microRNAs (miRNAs) is associated with various diseases. Developing simple and portable methods for sensitive, rapid and simultaneous detection of multiple miRNAs is critical to achieve accurate and timely diagnosis. Herein, a cotton thread-based multi-channel photothermal biosensor was proposed for simultaneous detection of three breast cancer-related miRNAs including miRNA-10b, miRNA-27a and miRNA-let-7a. Three cotton thread-based channels with one input were designed and the capture probes for detecting different miRNAs were immobilized on the test zones of the corresponding channels. Cu2-xS nanostrings prepared on the basis of hybridization chain reaction (HCR) were taken as the photothermal agents for signal transduction and amplification. The formation of a sandwich structure among the capture probe, target miRNA, and Cu2-xS nanostrings led to the accumulation of the Cu2-xS nanostrings on the test zones and transformed the concentration of miRNA into temperature signal under 808 nm laser irradiation. The temperature changes were quantified by a portable thermal camera and directly reflected the concentration of miRNAs. Under the optimal conditions, the developed multi-channel photothermal biosensor showed excellent specificity and sensitivity with the detection limits of 37 pM, 38 pM and 38 pM for miRNA-10b, miRNA-27a and miRNA-let-7a, respectively. Furthermore, a simultaneous detection of the three miRNAs in cell lysates were achieved and the results were in accordance with that obtained by the quantitative reverse transcription polymerase chain reaction (qRT-PCR), indicating its excellent capacity for practical applications. The developed biosensor provided an important tool for analysis of multiple targets and showed great potential in clinical diagnosis.

Integrated Profiling Identifies CCNA2 as a Potential Biomarker of Immunotherapy in Breast Cancer.

INTRODUCTION: Breast cancer is the main reason for cancer-related deaths in women and the most common malignant cancer among women. In recent years, immunosuppressive factors have become a new type of treatment for cancer. However, there are no effective biomarkers for breast cancer immunotherapy. Therefore, exploring immune-related biomarkers is presently an important topic in breast cancer. METHODS: Gene expression profile data of breast cancer from The Cancer Genome Atlas (TCGA) was downloaded. Scale-free gene co-expression networks were built with weighted gene co-expression network analysis. The correlation of genes was performed with Pearson's correlation values. The potential associations between clinical features and gene sets were studied, and the hub genes were screened out. Gene Ontology and gene set enrichment analysis were used to reveal the function of hub gene in breast cancer. The gene expression profiles of GSE15852, downloaded from the Gene Expression Omnibus database, were used for hub gene verification. In addition, candidate biomarkers expression in breast cancer was studied. Survival analysis was performed using Log rank test and Kaplan-Meier. Immunohistochemistry was used to analyze the expression of CCNA2. RESULTS: A total of 6 modules related to immune cell infiltration were identified via the average linkage hierarchical clustering. According to the threshold criteria (module membership >0.9 and gene significance >0.35), a significant module consisting of 13 genes associated with immune cells infiltration were identified as candidate hub genes after performed with the human protein interaction network. And 3 genes with high correlation to clinical traits were identified as hub genes, which were negatively associated with the overall survival. Among them, the expression of CCNA2 was increased in metastatic breast cancer compare with non-metastatic breast cancer, who underwent immunotherapy. Immunohistochemistry results showed that CCNA2 expression in carcinoma tissues was elevated compared with normal control. DISCUSSION: CCNA2 identified as a potential immune therapy marker in breast cancer, which were first reported here and deserved further research.

MicroRNA-200c Inhibits the Metastasis of Triple-Negative Breast Cancer by Targeting ZEB2, an Epithelial-Mesenchymal Transition Regulator.

OBJECTIVE: Triple-negative breast cancer (TNBC) is one of the most common malignant, highly heterogeneous tumors in women. MicroRNAs (miRNAs), such as miR-200c, play an important role in various types of malignant cancer, including TNBC. However, the biological role of miRNA-200c in TNBC is not well understood. In this study, we investigated the mechanism of miR-200c in the growth of TNBC. METHODS: Reverse transcription quantitative polymerase chain reaction was used to detect the expression of miR-200c in TNBC tissues and TNBC cells. Cell Counting Kit-8 (CCK-8) assays, wound healing, and transwell assays were used to observe the effects of miR-200c on TNBC cell proliferation, migration, and invasion, respectively. The expression of epithelial-mesenchymal transition (EMT) markers were detected by Western blotting. Dual luciferase reporter assays were used to test whether ZEB2 is a novel target of miR-200c. RESULT: Our results show that ZEB2 is a novel target of miR-200c and that ZEB2 mediates the metastasis of triple-negative breast cancer via EMT. CONCLUSION: miR-200c attenuates TNBC cell invasion and EMT by targeting ZEB2. Our data therefore suggest that miR-200c may be used to develop novel early-stage diagnostic and therapeutic strategies for TNBC.

lncRNA TCL6 correlates with immune cell infiltration and indicates worse survival in breast cancer.

BACKGROUND: Long non-coding RNA (lncRNA) T-cell leukemia/lymphoma 6 (TCL6) has been reported as a potential tumor suppressor. However, its expression and function in breast cancer remain unknown. This study was performed to investigate the expression of lncRNA TCL6 in breast cancer and its clinical significance. METHODS: The survival and clinical molecular roles of TCL6 in breast cancer were analyzed. The underlying mechanism modulated by TCL6 and its correlation with immune-infiltrating cells were investigated. Gene Expression Omnibus (GEO) datasets were further used to confirm the prognostic role of TCL6. RESULTS: TCL6 low expression was not correlated with age, clinical stage, T stage, lymph node metastasis, distant metastasis, human epidermal growth factor 2 status, but was associated with estrogen receptor and progesterone receptor (PR) status and was an independent factor for worse survival (HR 1.876, P = 0.016). Specifically, low TCL6 expression correlated with worse prognosis in PR-negative patients. TCL6 could predict worse survival in luminal B breast cancer based on intrinsic subtypes. Immune-related pathways such as Janus kinase-signal transducer of activators of transcription were regulated by TCL6. Further finding revealed that TCL6 correlated with immune infiltrating cells such as B cells (r = 0.25, P < 0.001), CD8+ T cells (r = 0.23, P < 0.001), CD4+ T cells (r = 0.25, P < 0.001), neutrophils (r = 0.21, P < 0.001), and dendritic cells (r = 0.27, P < 0.001). TCL6 was also positively correlated with tumor-infiltrating lymphocytes infiltration and PD-1, PD-L1, PD-L2, and CTLA-4 immune checkpoint molecules (P < 0.001). CONCLUSION: Our findings suggest that lncRNA TCL6 correlates with immune infiltration and may act as a useful prognostic molecular marker in breast cancer.

Identification of a New Eight-Long Noncoding RNA Molecular Signature for Breast Cancer Survival Prediction.

Because of the phenotypic and molecular diversity, it is still difficult to predict breast cancer prognosis. This study aimed to develop and validate a multi-lncRNA (long noncoding RNA) signature to improve the survival prediction for breast cancer. Three hundred twenty-seven breast cancer patients from GSE20685 were used as a training set. GSE88770 including 117 patients and The Cancer Genome Atlas datasets including 1077 patients were used as 2 validation sets. Kaplan-Meier curve, the LASSO (least absolute shrinkage and selection operator) method, univariate and multivariate Cox analyses were applied to build a molecular model for predicting survival. Function analysis of this lncRNA signature was investigated. A novel eight-lncRNA molecular signature was first identified from multiple datasets. This signature classified patients into the high-risk and low-risk groups. Breast cancer in the high-risk group showed significantly worse survival than that in the low-risk group. Further multivariate Cox analysis revealed that this molecular signature was an independent prognostic factor for breast cancer in the training and validation sets. Furthermore, stratification analyses showed that this molecular signature was also used to classify patients into the low- and high-risk groups in patients with low or high T-stage, patients with or without lymph node metastasis, older or younger, estrogen receptor-positive or -negative, and progesterone receptor-positive or -negative patients. Our eight-lncRNA signature was a powerful tool in predicting prognosis in Luminal B breast cancer based on molecular subtype. This lncRNA signature involved in cell adhesion, apoptosis, cell differentiation, and immune regulation. Our study provided a reliable eight-lncRNA molecular signature for survival prediction of breast cancer, and this signature can stratify patients into the high- and low-risk groups. This molecular signature may help the selection of the suitable treatment strategies.

The ZmbZIP22 Transcription Factor Regulates 27-kD γ-Zein Gene Transcription during Maize Endosperm Development.

Zeins are the most abundant storage proteins in maize (Zea mays) kernels, thereby affecting the nutritional quality and texture of this crop. 27-kD γ-zein is highly expressed and plays a crucial role in protein body formation. Several transcription factors (TFs) (O2, PBF1, OHP1, and OHP2) regulate the expression of the 27-kD γ-zein gene, but the complexity of its transcriptional regulation is not fully understood. Here, using probe affinity purification and mass spectrometry analysis, we identified ZmbZIP22, a TF that binds to the 27-kD γ-zein promoter. ZmbZIP22 is a bZIP-type TF that is specifically expressed in endosperm. ZmbZIP22 bound directly to the ACAGCTCA box in the 27-kD γ-zein promoter and activated its expression in wild tobacco (Nicotiana benthamiana) cells. 27-kD γ-zein gene expression was significantly reduced in CRISPR/Cas9-generated zmbzip22 mutants. ChIP-seq (chromatin immunoprecipitation coupled to high-throughput sequencing) confirmed that ZmbZIP22 binds to the 27-kD γ-zein promoter in vivo and identified additional direct targets of ZmbZIP22. ZmbZIP22 can interact with PBF1, OHP1, and OHP2, but not O2. Transactivation assays using various combinations of these TFs revealed multiple interaction modes for the transcriptional activity of the 27-kD γ-zein promoter. Therefore, ZmbZIP22 regulates 27-kD γ-zein gene expression together with other known TFs.

[Chemical constituents of Pileostegia viburnoides var. glabrescens].

OBJECTIVE: To study the chemical constituents of Pileostegia viburnoides var. glabrescens. METHODS: The compounds were isolated and purified by various techniques. Their structures were determined by physicochemical properties and spectral analysis. RESULTS: Five compounds were isolated and identified as friedelin (1), beta-sitosterol (2), umbelliferone (3), daucosterol (4) and skimmin (5). CONCLUSION: All the compounds were isolated from this genus for the first time.

[Study on chemical constituents of volatile oil from rhizomes and leaves of Pileostegia viburnoides var. glabrescens by GC-MS].

OBJECTIVE: To analyze the chemical constituents of volatile oil from the rhizomes and leaves of Pileostegia viburnoides var. glabrescens by GC-MS. METHODS: The volatile oil was extracted from the rhizomes and leaves of Pileostegia viburnoides var. glabrescens by steam distillation. The constituents of volatile oil were identified by GC-MS technology. RESULTS: 37 compounds were identified from the oil of rhizomes. 36 compounds were identified from the oil of leaves. The rhizomes and leaves volatile oil had 18 compounds in common. CONCLUSION: This study is the first one to report the volatile components of Pileostegia viburnoides var. glabrescens. It can provide a scientific basis for rational use of the rhizomes and leaves of Pileostegia viburnoides var. glabrescens.

Expressional profiling study revealed unique expressional patterns and dramatic expressional divergence of maize alpha-zein super gene family.

The alpha-zein super gene family encodes the most predominant storage protein in maize (Zea mays) endosperm. In maize inbred line B73, it consists of four gene families with 41 member genes. In this study, we combined quantitative real-time PCR and random clone sequencing to successfully profile the expression of alpha-zein super gene family during endosperm development. We found that only 18 of the 41 member genes were expressed, and their expression levels diverge greatly. At the gene family level, all families had characteristic "up-and-down" oscillating expressional patterns that diverged into two major groups. At the individual gene level, member genes showed dramatic divergence of expression patterns, indicating fast differentiation of their expression regulation. A comparison study among different inbred lines revealed significantly different expressed gene sets, indicating the existence of highly diverged haplotypes. Large gene families containing long gene clusters, e.g. z1A or z1C, mainly contributed the highly divergent haplotypes. In addition, allelic genes also showed significant divergence in their expressional levels. These results indicated a highly dynamic and fast evolving nature to the maize alpha-zein super gene family, which might be a common feature for other large gene families.