BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers.

The early detection of cancer holds the key to combat and control the increasing global burden of cancer morbidity and mortality. Blood-based screenings using circulating DNAs (ctDNAs), circulating RNA (ctRNAs), circulating tumor cells (CTCs) and extracellular vesicles (EVs) have shown promising prospects in the early detection of cancer. Recent high-throughput gene expression profiling of blood samples from cancer patients has provided a valuable resource for developing new biomarkers for the early detection of cancer. However, a well-organized online repository for these blood-based high-throughput gene expression data is still not available. Here, we present BBCancer (http://bbcancer.renlab.org/), a web-accessible and comprehensive open resource for providing the expression landscape of six types of RNAs, including messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), microRNAs (miRNAs), circular RNAs (circRNAs), tRNA-derived fragments (tRFRNAs) and Piwi-interacting RNAs (piRNAs) in blood samples, including plasma, CTCs and EVs, from cancer patients with various cancer types. Currently, BBCancer contains expression data of the six RNA types from 5040 normal and tumor blood samples across 15 cancer types. We believe this database will serve as a powerful platform for developing blood biomarkers.

Expression, purification and molecular characterization of a novel endoglucanase protein from Bacillus subtilis SB13.

Bacillus subtilis strain SB13 which is isolated in our previous work was confirmed to produce endoglucanase. In this study, a novel endoglucanase gene (accession number: KX576676) was identified and cloned from SB13. Compared with other consensus sequence of reported endoglucanase genes in the GenBank database, this gene displays five differences (including T740C,A874G,A983G, T1210G and T1301C), which leading to five amino acid changes. Homology modeling has indicated that these five changes were located in the α-helix and random coil regions of the glycosyl hydrolase family 5 (GH5) domain, the random coil and ß-sandwich of the type 3 carbohydrate-binding module (CBM3) domain, and the random coil domain. Aprokaryotic expression vector pET30a-endoglucanase was constructed and the endoglucanase was induced to express. The expressed endoglucanase was confirmed by liquid chromatography-tandem mass spectrometry (LC-MSMS) and detected via reaction with carboxymethyl cellulose. In order to obtain the highest expression level of endoglucanase, the expression conditions including IPTG concentration, temperature and pH were optimized. The recombinant endoglucanase protein was purified using a Ni-NTA column, and the 6 × His-tag was removed with thrombin. The results showed that both the modified and unmodified purified endoglucanase had high activity (7.65 ± 0.35 U and 15.05 ± 1.81 U, respectively), thus demonstrating the potential use of this enzyme in various industrial applications. The substitutions of L247P,N292D, F404V and L434P might contribute to the activity of the endoglucanase, and the insertion of a 6 × His-tag at the N-terminal of the endoglucanase might also affect its activity.

Hydrothermal synthesis of ZnGa2O4 nanophosphors with high internal quantum efficiency for near-infrared pc-LEDs.

NIR luminescent materials have garnered widespread attention because of their exceptional properties, with high tissue penetration, low absorption and high signal-to-noise ratio in the field of optical imaging. However, producing nanophosphors with high quantum yields of emitting infrared light with wavelengths above 1000 nm remains a significant challenge. Here, we prepared a nanoscale ZnGa2O4:xCr3+,yNi2+ phosphor with good luminescence performance in near-infrared emission, which was synthesized via a hydrothermal method and subsequent calcination process. By co-doping with Cr3+ and Ni2+, the ZnGa2O4 phosphor shows a strong broadband emission of 1100-1600 nm in the second near-infrared (NIR-II) region, owing to the energy transfer from Cr3+ to Ni2+ with an efficiency up to 90%. Meanwhile, a near-infrared phosphor-conversion LED (NIR pc-LED) device is fabricated based on the ZnGa2O4:0.8%Cr3+,0.4%Ni2+ nanophosphor, which has under 100 mA input current, an output power of 23.99 mW, and a photoelectric conversion efficiency of 7.53%, and can be effectively applied in imaging and non-destructive testing. Additionally, the intensity ratio of INi/ICr of ZnGa2O4:0.8% Cr3+,0.4%Ni2+ with its high sensitivity value of 4.21% K-1 at 453 K under 410 nm excitation, indicates its potential for thermometry application.

RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database.

The antibody repertoire is a critical component of the adaptive immune system and is believed to reflect an individual's immune history and current immune status. Delineating the antibody repertoire has advanced our understanding of humoral immunity, facilitated antibody discovery, and showed great potential for improving the diagnosis and treatment of disease. However, no tool to date has effectively integrated big Rep-seq data and prior knowledge of functional antibodies to elucidate the remarkably diverse antibody repertoire. We developed a Rep-seq dataset Analysis Platform with an Integrated antibody Database (RAPID; https://rapid.zzhlab.org/), a free and web-based tool that allows researchers to process and analyse Rep-seq datasets. RAPID consolidates 521 WHO-recognized therapeutic antibodies, 88,059 antigen- or disease-specific antibodies, and 306 million clones extracted from 2,449 human IGH Rep-seq datasets generated from individuals with 29 different health conditions. RAPID also integrates a standardized Rep-seq dataset analysis pipeline to enable users to upload and analyse their datasets. In the process, users can also select set of existing repertoires for comparison. RAPID automatically annotates clones based on integrated therapeutic and known antibodies, and users can easily query antibodies or repertoires based on sequence or optional keywords. With its powerful analysis functions and rich set of antibody and antibody repertoire information, RAPID will benefit researchers in adaptive immune studies.

autoRPA: A web server for constructing cancer staging models by recursive partitioning analysis.

Cancer staging provides a common language that is used to describe the severity of an individual's cancer, which plays a critical role in optimizing cancer treatment. Recursive partitioning analysis (RPA) is the most widely accepted method for cancer staging. Despite its widespread use, to date, only limited tools have been developed to implement the RPA algorithm for cancer staging. Moreover, most of the available tools can be accessed only from command lines and also lack visualization, making them difficult for clinical investigators without programing skills to use. Therefore, we developed a web server called autoRPA that is dedicated to supporting the construction of prognostic staging models and performance comparisons among different staging models. Based on the RPA algorithm and log-rank test statistics, autoRPA can establish a decision-making tree from survival data and provide clinicians an intuitive method to further prune the decision tree. Moreover, autoRPA can evaluate the contribution of each submitted covariate that is involved in the grouping process and help identify factors that significantly contribute to cancer staging. Four indicators, including hazard consistency, hazard discrimination, percentage of variation explained, and sample size balance, are introduced to validate the performance of the designed staging models. In addition, autoRPA can also be used to compare the performance of different prognostic staging models using a standard bootstrap evaluation method. The web server of autoRPA is freely available at http://rpa.renlab.org.

lnCAR: A Comprehensive Resource for lncRNAs from Cancer Arrays.

Long noncoding RNAs (lncRNA) have emerged as promising biomarkers in cancer diagnosis, treatment, and prognosis. Recent studies suggest that a large number of coding gene expression microarray probes could be reannotated as lncRNAs. Microarray, once the most cutting-edge high-throughput gene expression technology, has been used for thousands of cancer studies and has brought invaluable resources for studying the functions of lncRNA in cancer development. However, a comprehensive lncRNA resource based on microarray data is still lacking. Here, we present lnCAR (lncRNAs from cancer arrays), a comprehensive open resource for providing expression profiles and prognostic landscape of lncRNAs derived from reannotation of public microarray data. Currently, lnCAR contains 52,300 samples for differential expression analysis and 12,883 samples for survival analysis from 10 cancer types. lnCAR allows users to interactively explore any annotated or novel lncRNAs. We believe lnCAR will serve as a valuable resource for the community focused on lncRNA research in cancer. SIGNIFICANCE: lnCAR, a new interactive tool of reannotated public cancer-related microarray data, provides expression profiles and prognostic landscapes of lncRNAs across thousands of samples and multiple cancer types.

In vitro fermentation of O­acetyl­arabinoxylan from bamboo shavings by human colonic microbiota.

BSH-1 is an O­acetyl-arabinoxylan obtained from bamboo shavings. This study investigated its fermentation behavior by human colonic microbiota in vitro. Results showed that BSH-1 remarkably modulated the composition of human colonic microbiota, mainly by increasing the growth of potential beneficial genera (i.e. Bifidobacterium, Lactobacillus, Bacteroides, Prevotella_7, Parabacteroides) and by decreasing the growth of potential harmful genera (i.e. Fusobacterium, Lachnospiraceae_UCG-008, Bilophila and Desulfovibrio). BSH-1 significantly promoted the production of short-chain fatty acids, especially acetic, propionic and n-butyric acids. After 48 h fermentation, the concentration of n-butyric acid in BSH-1 fermentation culture was increased by 2.41 times compared to the blank. During fermentation, the activity of acetyl xylan esterase, arabinofuranosidase, xylanase and xylosidase was enhanced. Moreover, free arabinose, xylose, xylobiose, xylotriose, xylotetraose, xylopentaose and xylohexaose were detected. These results suggest that BSH-1 could potentially be a functional ingredient to improve gut health.

Screening and characterization of lactic acid bacterial strains that produce fermented milk and reduce cholesterol levels.

OBJECTIVE: To screen for and characterize lactic acid bacteria strains with the ability to produce fermented milk and reduce cholesterol levels. METHODS: The strains were isolated from traditional fermented milk in China. In vitro and in vivo evaluation of cholesterol-reduction were used to identify and verify strains of interest. Characteristics were analyzed using spectrophotometry and plate counting assays. RESULTS: The isolate HLX37 consistently produced fermented milk with strong cholesterol-reducing properties was identified as Lactobacillus plantarum (accession number: KR105940) and was thus selected for further study. The cholesterol reduction by strain HLX37 was 45.84%. The isolates were acid-tolerant at pH 2.5 and bile-tolerant at 0.5% (w/v) in simulated gastric juice (pH 2.5) for 2h and in simulated intestinal fluid (pH 8.0) for 3h. The auto-aggregation rate increased to 87.74% after 24h, while the co-aggregation with Escherichia coli DH5 was 27.76%. Strain HLX37 was intrinsically resistant to antibiotics such as penicillin, tobramycin, kanamycin, streptomycin, vancomycin and amikacin. Compared with rats in the model hyperlipidemia group, the total cholesterol content in the serum and the liver as well as the atherogenic index of rats in the viable fermented milk group significantly decreased by 23.33%, 32.37% and 40.23%, respectively. Fewer fat vacuoles and other lesions in liver tissue were present in both the inactivated and viable fermented milk groups compared to the model group. CONCLUSION: These studies indicate that strain HLX37 of L. plantarum demonstrates probiotic potential, potential for use as a candidate for commercial use for promoting health.

Screening and characterization of lactic acid bacterial strains that produce fermented milk and reduce cholesterol levels

ABSTRACT Objective To screen for and characterize lactic acid bacteria strains with the ability to produce fermented milk and reduce cholesterol levels. Methods The strains were isolated from traditional fermented milk in China. In vitro and in vivo evaluation of cholesterol-reduction were used to identify and verify strains of interest. Characteristics were analyzed using spectrophotometry and plate counting assays. Results The isolate HLX37 consistently produced fermented milk with strong cholesterol-reducing properties was identified as Lactobacillus plantarum (accession number: KR105940) and was thus selected for further study. The cholesterol reduction by strain HLX37 was 45.84%. The isolates were acid-tolerant at pH 2.5 and bile-tolerant at 0.5% (w/v) in simulated gastric juice (pH 2.5) for 2 h and in simulated intestinal fluid (pH 8.0) for 3 h. The auto-aggregation rate increased to 87.74% after 24 h, while the co-aggregation with Escherichia coli DH5 was 27.76%. Strain HLX37 was intrinsically resistant to antibiotics such as penicillin, tobramycin, kanamycin, streptomycin, vancomycin and amikacin. Compared with rats in the model hyperlipidemia group, the total cholesterol content in the serum and the liver as well as the atherogenic index of rats in the viable fermented milk group significantly decreased by 23.33%, 32.37% and 40.23%, respectively. Fewer fat vacuoles and other lesions in liver tissue were present in both the inactivated and viable fermented milk groups compared to the model group. Conclusion These studies indicate that strain HLX37 of L. plantarum demonstrates probiotic potential, potential for use as a candidate for commercial use for promoting health.