EndoQuad: a comprehensive genome-wide experimentally validated endogenous G-quadruplex database

G-quadruplexes (G4s) are non-canonical four-stranded structures and are emerging as novel genetic regulatory elements. However, a comprehensive genomic annotation of endogenous G4s (eG4s) and systematic characterization of their regulatory network are still lacking, posing major challenges for eG4 research. Here, we present EndoQuad (https://EndoQuad.chenzxlab.cn/) to address these pressing issues by integrating high-throughput experimental data. First, based on high-quality genome-wide eG4s mapping datasets (human: 1181; mouse: 24; chicken: 2) generated by G4 ChIP-seq/CUT&Tag, we generate a reference set of genome-wide eG4s. Our multi-omics analyses show that most eG4s are identified in one or a few cell types. The eG4s with higher occurrences across samples are more structurally stable, evolutionarily conserved, enriched in promoter regions, mark highly expressed genes and associate with complex regulatory programs, demonstrating higher confidence level for further experiments. Finally, we integrate millions of functional genomic variants and prioritize eG4s with regulatory functions in disease and cancer contexts. These efforts have culminated in the comprehensive and interactive database of experimentally validated DNA eG4s. As such, EndoQuad enables users to easily access, download and repurpose these data for their own research. EndoQuad will become a one-stop resource for eG4 research and lay the foundation for future functional studies.

[Analysis of factors influencing the success rate of organoid culture in 1231 cases of colorectal cancer]

Objective: To investigate the risk factors for organoid culture failure in colorectal cancer. Methods: This was a retrospective observational study. Tumor specimens were obtained from 1130 patients with colorectal cancer who had undergone surgery or biopsy and had no other concurrent malignancies at Nanfang Hospital of Southern Medical University from December 2021 to November 2022. Organoid culture was performed on 1231 tumor tissue samples. Univariate analysis and multivariate logistic regression were used to analyze the factors that might have influenced the rate of successful organoid culture of colorectal cancer tissue samples. Results: The median (range) duration of organoid culture was 7 (3-12) days. The overall rate of successful culture was 76.3% (939/1231). The rate of successful organoid cultures varied according to the sampling site, malignant ascites having the highest success rate (96.4%, 27/28), followed by liver metastases (83.1%, 54/65), lung metastases (8/10), primary tumors (76.0%, 816/1074), omental metastases (10/14), peritoneal metastases (61.5%, 16/26), ovarian metastases (3/5), and lymph node metastases (5/9). The difference in rates of successful organoid culture between primary tumors and malignant ascites was statistically significant (P=0.012), whereas none of the other rates of successful organoid culture success differed significantly (all P>0.05). The rate of successful organoid culture was 96.4% (27/28) for malignant ascites obtained by abdominal puncture, 76.5% (864/1130) for surgical specimens, and 65.8% (48/73) for endoscopic biopsies; these differences are statistically significant (χ2=10.773, P=0.005). The rate of successful organoid culture was 62.5% (40/64) in the neoadjuvant chemoradiotherapy group, which is significantly lower than in the non-adjuvant (76.9%, 787/1023) and chemotherapy groups (77.8%, 112/144) (χ2=7.134, P=0.028). Multivariate logistic regression analysis revealed that endoscopic biopsy (OR=0.557, 95%CI: 0.335-0.924, P=0.024) and neoadjuvant chemoradiotherapy (OR=0.483, 95%CI: 0.285-0.820, P=0.007) were independent risk factors for failure of organoid culture of colorectal cancer samples. Malignant ascites (OR=8.537, 95%CI:1.154-63.131,P=0.036) and abdominal puncture (OR=8.294, 95% CI: 1.112-61.882, P=0.039) were identified as independent protective factors. Conclusions: The rate of successful organoid culture was influenced by the sampling site, sampling method, and chemoradiotherapy. The rate of successful organoid culture was lower for endoscopic biopsies and in patients receiving preoperative neoadjuvant chemoradiotherapy, and higher for malignant ascites. We consider that culture of malignant ascites is preferable when peritoneal metastases are suspected.

Integrating massive RNA-seq data to elucidate transcriptome dynamics in Drosophila melanogaster

The volume of ribonucleic acid (RNA)-seq data has increased exponentially, providing numerous new insights into various biological processes. However, due to significant practical challenges, such as data heterogeneity, it is still difficult to ensure the quality of these data when integrated. Although some quality control methods have been developed, sample consistency is rarely considered and these methods are susceptible to artificial factors. Here, we developed MassiveQC, an unsupervised machine learning-based approach, to automatically download and filter large-scale high-throughput data. In addition to the read quality used in other tools, MassiveQC also uses the alignment and expression quality as model features. Meanwhile, it is user-friendly since the cutoff is generated from self-reporting and is applicable to multimodal data. To explore its value, we applied MassiveQC to Drosophila RNA-seq data and generated a comprehensive transcriptome atlas across 28 tissues from embryogenesis to adulthood. We systematically characterized fly gene expression dynamics and found that genes with high expression dynamics were likely to be evolutionarily young and expressed at late developmental stages, exhibiting high nonsynonymous substitution rates and low phenotypic severity, and they were involved in simple regulatory programs. We also discovered that human and Drosophila had strong positive correlations in gene expression in orthologous organs, revealing the great potential of the Drosophila system for studying human development and disease.

In vivo dynamics and regulation of DNA G-quadruplex structures in mammals

G-quadruplex (G4) is a four-stranded helical DNA secondary structure formed by guanine-rich sequence folding, and G4 has been computationally predicted to exist in a wide range of species. Substantial evidence has supported the formation of endogenous G4 (eG4) in living cells and revealed its regulatory dynamics and critical roles in several important biological processes, making eG4 a regulator of gene expression perturbation and a promising therapeutic target in disease biology. Here, we reviewed the methods for prediction of potential G4 sequences (PQS) and detection of eG4s. We also highlighted the factors affecting the dynamics of eG4s and the effects of eG4 dynamics. Finally, we discussed the future applications of eG4 dynamics in disease therapy.

Dynamic Spatial-temporal Expression Ratio of X Chromosome to Autosomes but Stable Dosage Compensation in Mammals

In the evolutionary model of dosage compensation, per-allele expression level of the X chromosome has been proposed to have twofold up-regulation to compensate its dose reduction in males (XY) compared to females (XX). However, the expression regulation of X-linked genes is still controversial, and comprehensive evaluations are still lacking. By integrating multi-omics datasets in mammals, we investigated the expression ratios including X to autosomes (X:AA ratio) and X to orthologs (X:XX ratio) at the transcriptome, translatome, and proteome levels. We revealed a dynamic spatial-temporal X:AA ratio during development in humans and mice. Meanwhile, by tracing the evolution of orthologous gene expression in chickens, platypuses, and opossums, we found a stable expression ratio of X-linked genes in humans to their autosomal orthologs in other species (X:XX ≈ 1) across tissues and developmental stages, demonstrating stable dosage compensation in mammals. We also found that different epigenetic regulations contributed to the high tissue specificity and stage specificity of X-linked gene expression, thus affecting X:AA ratios. It could be concluded that the dynamics of X:AA ratios were attributed to the different gene contents and expression preferences of the X chromosome, rather than the stable dosage compensation.

Gut microbiome in tumorigenesis and therapy of colorectal cancer

Colorectal cancer (CRC) is the malignant tumor with the highest incidence in the digestive system, and the gut microbiome plays a crucial role in CRC tumorigenesis and therapy. The gastrointestinal tract is the organ harboring most of the microbiota in humans. Changes in the gut microbiome in CRC patients suggest possible host-microbe interactions, thereby hinting the potential tumorigenesis, which provides new perspective for preventing, diagnosing, or treating CRC. In this review, we discuss the effects of gut microbiome dysbiosis on CRC, and reveal the mechanisms by which gut microbiome dysbiosis leads to CRC. Gut microbiome modulation with the aim to reverse the established gut microbial dysbiosis is a novel strategy for the prevention and treatment of CRC. In addition, this review summarizes that probiotic antagonize CRC tumorigenesis by protecting intestinal barrier function, inhibiting cancer cell proliferation, resisting oxidative stress, and enhancing host immunity. Finally, we highlight clinical applications of the gut microbiome, such as gut microbiome analysis-based biomarker screening and prediction, and microbe modulation-based CRC prevention, treatment enhancement, and treatment side effect reduction. This review provides the reference for the clinical application of gut microbiome in the prevention and treatment of CRC.

Chemical and mechanical stability of an ion-exchanged lithium disilicate glass in artificial saliva

Multi-component lithium disilicate (LD) glasses were ion-exchanged in a pure or mixed nitrate salt bath. The surface morphologies, mechanical properties, chemical stability and ion leaching of ion-exchanged LD glasses before and after storage in artificial saliva for 21 days were investigated. It can be found that chemical stability of ion-exchanged LD glass was temperature-dependent. The residual compressive stress induced by ion-exchange increased the chemical potential of alkali ions in glass, and the ion-exchanged LD glass, especially 235 °C/64 h group, chemical stability in artificial saliva for 21 days were deteriorated. Back-exchange treatment could relax the stress on the outermost layer of the ion-exchanged LD glass without deteriorating its strengthening effect, and back-exchanged LD glass presented good chemical and mechanical stability in artificial saliva. The results might help to enhance the service stability of ion-exchanged LD glass-ceramics in the oral condition.

Evolution and function of developmentally dynamic pseudogenes in mammals

BACKGROUND

Pseudogenes are excellent markers for genome evolution, which are emerging as crucial regulators of development and disease, especially cancer. However, systematic functional characterization and evolution of pseudogenes remain largely unexplored.

RESULTS

To systematically characterize pseudogenes, we date the origin of human and mouse pseudogenes across vertebrates and observe a burst of pseudogene gain in these two lineages. Based on a hybrid sequencing dataset combining full-length PacBio sequencing, sample-matched Illumina sequencing, and public time-course transcriptome data, we observe that abundant mammalian pseudogenes could be transcribed, which contribute to the establishment of organ identity. Our analyses reveal that developmentally dynamic pseudogenes are evolutionarily conserved and show an increasing weight during development. Besides, they are involved in complex transcriptional and post-transcriptional modulation, exhibiting the signatures of functional enrichment. Coding potential evaluation suggests that 19% of human pseudogenes could be translated, thus serving as a new way for protein innovation. Moreover, pseudogenes carry disease-associated SNPs and conduce to cancer transcriptome perturbation.

CONCLUSIONS

Our discovery reveals an unexpectedly high abundance of mammalian pseudogenes that can be transcribed and translated, and these pseudogenes represent a novel regulatory layer. Our study also prioritizes developmentally dynamic pseudogenes with signatures of functional enrichment and provides a hybrid sequencing dataset for further unraveling their biological mechanisms in organ development and carcinogenesis in the future.

DSEATM: drug set enrichment analysis uncovering disease mechanisms by biomedical text mining

Disease pathogenesis is always a major topic in biomedical research. With the exponential growth of biomedical information, drug effect analysis for specific phenotypes has shown great promise in uncovering disease-associated pathways. However, this method has only been applied to a limited number of drugs. Here, we extracted the data of 4634 diseases, 3671 drugs, 112 809 disease-drug associations and 81 527 drug-gene associations by text mining of 29 168 919 publications. On this basis, we proposed a 'Drug Set Enrichment Analysis by Text Mining (DSEATM)' pipeline and applied it to 3250 diseases, which outperformed the state-of-the-art method. Furthermore, diseases pathways enriched by DSEATM were similar to those obtained using the TCGA cancer RNA-seq differentially expressed genes. In addition, the drug number, which showed a remarkable positive correlation of 0.73 with the AUC, plays a determining role in the performance of DSEATM. Taken together, DSEATM is an auspicious and accurate disease research tool that offers fresh insights.

Dynamic Chromatin States Coupling with Key Transcription Factors in Colitis-Associated Colorectal Cancer

Inflammation is one of the critical risk factors for colorectal cancer (CRC). However, the mechanisms for transition from colitis to CRC remain elusive. Recently, epigenetic changes have emerged as important regulatory factors for colitis-associated cancer. Here, a systematic epigenomic study of histone modifications is performed, including H3K4me1, H3K4me3, H3K27ac, H3K27me3 and H3K9me3, in an AOM-DSS-induced CRC mouse model. In combination with transcriptomic data, the authors generate a dataset of 105 deep sequencing files and illustrate the dynamic landscape of chromatin states at five time points during inflammation-cancer transition. Functional gene clusters are identified based on dynamic transcriptomic and epigenomic information, and key signaling pathways in the process are illustrated. This study's results reveal that enhancer state regions play important roles during inflammation-cancer transition. It predicts novel transcription factors based on enhancer information, and experimentally proves OTX2 as a critical tumor suppressive transcription factor. Taken together, this study provides comprehensive epigenomic data and reveals novel molecular mechanisms for colitis-associated cancer.

TDG is a pig-specific epigenetic regulator with insensitivity to H3K9 and H3K27 demethylation in nuclear transfer embryos

Pig cloning by somatic cell nuclear transfer (SCNT) frequently undergoes incomplete epigenetic remodeling during the maternal-to-zygotic transition, which leads to a significant embryonic loss before implantation. Here, we generated the first genome-wide landscapes of histone methylation in pig SCNT embryos. Excessive H3K9me3 and H3K27me3, but not H3K4me3, were observed in the genomic regions with unfaithful embryonic genome activation and donor-cell-specific gene silencing. A combination of H3K9 demethylase KDM4A and GSK126, an inhibitor of H3K27me3 writer, were able to remove these epigenetic barriers and restore the global transcriptome in SCNT embryos. More importantly, thymine DNA glycosylase (TDG) was defined as a pig-specific epigenetic regulator for nuclear reprogramming, which was not reactivated by H3K9me3 and H3K27me3 removal. Both combined treatment and transient TDG overexpression promoted DNA demethylation and enhanced the blastocyst-forming rates of SCNT embryos, thus offering valuable methods to increase the cloning efficiency of genome-edited pigs for agricultural and biomedical purposes.

•

Identification of reprogramming-resistant genes and regions in porcine SCNT embryos

•

H3K9me3 and H3K27me3 are enriched in reprogramming-resistant genes and regions

•

Removing H3K9me3 and H3K27me3 by KDM4A and GSK126 facilitates nuclear reprogramming

•

Transient TDG overexpression promotes DNA demethylation and improves reprogramming

G-quadruplexes in genomes of viruses infecting eukaryotes or prokaryotes are under different selection pressures from hosts

G-quadruplexes in viral genomes can be applied as the targets of antiviral therapies, which has attracted wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world is the result of natural selection for functionality. In this study, we identified putative quadruplex-forming sequences (PQSs) across the known viral genomes and analyzed the abundance, structural stability, and conservation of viral PQSs. A Viral Putative G-quadruplex Database (ViPGD,http://jsjds.hzau.edu.cn/MBPC/ViPGD/index.php/home/index) was constructed to collect the details of each viral PQS, which provides guidance for selecting the desirable PQS. The PQS with two putative G-tetrads (G₂-PQS) was significantly enriched in both eukaryotic viruses and prokaryotic viruses, while the PQSs with three putative G-tetrads (G₃-PQS) were only enriched in eukaryotic viruses and depleted in prokaryotic viruses. The structural stability of PQSs in prokaryotic viruses was significantly lower than that in eukaryotic viruses. Conservation analysis showed that the G₂-PQS, instead of G₃-PQS, was highly conserved within the genus. This suggested that the G₂-quadruplex might play an important role in viral biology, and the difference in the occurrence of G-quadruplex between eukaryotic viruses and prokaryotic viruses may result from the different selection pressures from hosts.

[Genotype and genetic characteristics of human respiratory syncytial virus circulating in Quanzhou, 2018-2019]

Objective: To study the prevalence and genetic characteristics of human respiratory syncytial virus (HRSV) in Quanzhou city, from 2018 to 2019. Methods: A total of 141 throat swabs were collected from children patients of lower respiratory tract infection in Quanzhou children Hospital, Fujian Province from November 2018 to May 2019. RT-PCR was used to amplify the 3 'end of G gene HRSV. Sequencer 5.0 and MEGA5.05 softwares were used for sequence editing, phylogenetic tree construction and genotyping analysis. Results: Twenty-five samples were positive for HRSV. Seventeen samples succeeded to obtain the target gene, including 13 of HRSVA and 4 of HRSVB. Two genotypes were identified: ON1 genotype (13 samples, HRSVA) and BA9 genotype (4 samples, HRSVB). Five strains of ON1 genotype sequences were clustered with the ON1 sequences prevalent in Beijing, Changchun and Zhejiang from 2012 to 2015 (cluster1); one strain (FJ19-02) was clustered with the sequences of ON1 genotype circulating in many regions of China from 2012 to 2015 (cluster2); Seven strains were clustered independently (cluster FJ). FJ18-02, FJ19-14 and FJ19-15 of HRSVB were clustered with the BA9 genotype sequences prevalent in Changchun, Jilin Province in 2015, while FJ19-13 was closely related to the BA9 genotype sequences prevalent in Guangzhou and Zhejiang Province in 2013. Both the ON1 and BA9 genotypes showed variations of nucleotide and amino acid in 72 and 60 insertion segments. Amino acid mutation (H266L) only occurred among the sequence of cluster-FJ, and the mutations of H261Q and Q265L only appeared in strain FJ19-13. Conclusion: BA9 and ON1 genotypes were prevalent in Quanzhou city, from 2018 to 2019. Cluster-FJ was a newly discovered independent transmission chain, which may continue to circulate in local Quanzhou area.

[Application of cell transfer technique in the diagnosis of fine needle aspiration cytology]

Objective: To study the application of cell transfer technology to solve the problem of the limited number of fine needle aspiration cytology (FNAC) smears for various immunocytochemistry (ICC) staining and other auxiliary tests, and to enhance accurate cytological diagnosis. Methods: Thirty-four cases of FNAC smears from January 2020 to April 2020 in the Department of Pathology of Beijing Hospital were collected for investigation of the cell transfer technique. The materials in the most cell smear were divided and transferred to several glass slides. After de-staining, the recipient slides were stained with EnVision ICC. The technique was validated by comparing the consistency of the ICC of transferred cell smears and the corresponding immunohistochemical (IHC) staining on biopsies. Results: There were a total of 180 cell transfer slides from 34 cases, of which 174 had the same cell morphology, size and structure as the original smears, with the success rate of cell transfer of 96.7% (174/180). Totally 174 ICC stains were performed on the successfully transferred cell smears, of which 153 smears had available corresponding IHC staining of histologic specimens. Of these, 148 showed concordance between ICC staining and the IHC staining. Cells were successfully transferred in 96.7 % (148/153) of the cell sheets, keeping the same morphology and structure as compared to their original smears. The diagnosis of all 34 FNAC cases was the same to that of their corresponding pathology on biopsies with 100 % concordance. Conclusions: The cell transfer technique is a simple and effective way to make full use of diagnostic cells on a cell smear, and is valuable for accurate cytological diagnosis.

[Occurrence and related factors of preterm birth in Guangxi Zhuang Autonomous Region during 2017-2019]

Objective: To investigate the incidence of preterm birth in Guangxi Zhuang Autonomous Region and explore the related factors and their combined effects. Methods: The study subjects were women giving birth to live babies at the monitoring points of critical maternal hospital monitoring system in Guangxi Zhuang Autonomous Region from January 1, 2017 to December 31, 2019. The data of general characteristics (age and marital status), pregnancies (parity, number of previous cesarean delivery, the number of prenatal check and number of fetuses in this pregnancy) and disease conditions (placenta previa, placental abruption, hypertension, diabetes, anemia, and heart disease) were collected, and the incidence of preterm birth were calculated according to the definition of preterm birth set by WHO and China, respectively. Logistic regression model was used to explore the factors associated with premature birth and their combined effects. Results: According to definitions of WHO and China, the cumulative incidence of preterm birth in Guangxi from 2017 to 2019 was 7.45% (16 819/225 727) and 7.34% (16 559/225 727), respectively. Advanced age [≤34 years old as reference, OR (95%CI) of 35-39 and ≥40 years old were 1.36 (1.30-1.42) and 1.61 (1.50-1.74), respectively], unmarried (including divorced or widowed) [OR (95%CI): 1.28 (1.17-1.40)], primiparae [OR (95%CI): 1.34 (1.29-1.40)], previous cesarean section [no previous cesarean section as reference, OR (95%CI) of 1 and ≥2 times of previous cesarean section were 1.30 (1.24-1.36) and 1.85 (1.65-2.08), respectively], antenatal examination<8 [OR (95%CI): 2.72 (2.62-2.81)], multiple pregnancies [OR (95%CI): 15.00 (14.01-16.06)], placenta previa [OR (95%CI): 6.90 (6.35-7.50)], placental abruption [OR (95%CI): 8.18 (7.36-9.10)], gestational hypertension [OR (95%CI): 2.29 (2.17-2.42)], gestational diabetes mellitus [OR (95%CI): 1.43 (1.37-1.49)], anemia [OR (95%CI): 1.10 (1.07-1.14)], and heart diseases [OR (95%CI): 2.98(2.43-3.65)] were all positively correlated with preterm birth. The risk of preterm birth in pregnant women exposed to 1, 2, 3, 4, 5, 6 and ≥7 preterm birth related factors was 1.51, 2.29, 4.49, 9.69, 20.87, 46.88 and 192.11 times that of non-exposed women, respectively (all P values<0.001). Conclusion: Preterm birth is associated with maternal general characteristics, pregnancy and disease status, and the combined effect of preterm birth related factors significantly increases the risk of preterm birth.

Improved reliability of mechanical behavior for a thermal tempered lithium disilicate glass-ceramic by regulating the cooling rate

Traditional thermal tempering was applied to lithium disilicate (LD) glass-ceramic specimens with bar-like and disc-like shapes. The tempering process was conducted by heating the specimens to a temperature below the dynamic softening point, and then rapid cooling in silicone oil with different temperatures ranging from room-temperature to 300 °C to regulate the cooling rate. Effect of the oil-temperature on mechanical behavior of the tempered glass-ceramic was investigated. For the tempering at the lower oil-temperature (e.g., at room-temperature), it was found that the LD glass-ceramic specimens with both the bar-like and disc-like shapes could be remarkably strengthen and toughen, however, obvious anisotropy in fracture toughness was displayed by the specimens with the bar-like shape. With increasing the oil-temperature up to 250 °C, the mechanical anisotropy of the bar-like specimens could be significantly alleviated without much loss of the strengthening effect. The results can provide references for improving reliability of mechanical behavior for the tempered LD glass-ceramic by regulating the cooling condition according to specimen geometry.

[Investigation on the awareness of snoring hazard and prevalence of obstructive sleep apnea among civil servants]

Objective: To investigate the awareness of snoring hazard and prevalence of obstructive sleep apnea (OSA) among civil servants. Methods: A cross-sectional survey was conducted to investigate the awareness of snoring hazards among in-service civil servants who had annual medical examination in a Guangdong provincial institution from September to November 2017. The high-risk group for OSA was screened and diagnosed by sleep monitoring. Results: 1 036 of 1 241 civil servants were enrolled in the study for integral data. 60.1% (623/1 036) of the subjects realized that snoring was harmful to health. The most common source to develop OSA awareness was network (59.6%, 371/623), followed by television (48.0%), relatives and friends (46.6%), newspaper (44.5%) and radio (18.9%). The awareness rate of snoring consequences was as follows: decreased sleep quality (71.9%, 448/623), sudden death (52.2%), daytime sleepiness (44.3%), cardiovascular and cerebrovascular diseases (42.9%), hypertension (24.4%) and sexual dysfunction (16.7%). 22.0% (228 / 1 036) of the cases were classified into high-risk OSA. The prevalence of OSA among high-risk group was 46.05%(105/228)and only 0.9% (2/228) of them had been diagnosed with OSA. Conclusion: Civil servants had awareness of snoring hazard to a certain extent. Among civil servants classified into high-risk OSA, the OSA perveance was high but the rate of diagnosis and treatment was very low.

pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms

Background

Many disease causing genes have been identified through different methods, but there have been no uniform annotations of biomedical named entity (bio-NE) of the disease phenotypes of these genes yet. Furthermore, semantic similarity comparison between two bio-NE annotations has become important for data integration or system genetics analysis.

Results

The package pyMeSHSim recognizes bio-NEs by using MetaMap which produces Unified Medical Language System (UMLS) concepts in natural language process. To map the UMLS concepts to Medical Subject Headings (MeSH), pyMeSHSim is embedded with a house-made dataset containing the main headings (MHs), supplementary concept records (SCRs), and their relations in MeSH. Based on the dataset, pyMeSHSim implemented four information content (IC)-based algorithms and one graph-based algorithm to measure the semantic similarity between two MeSH terms. To evaluate its performance, we used pyMeSHSim to parse OMIM and GWAS phenotypes. The pyMeSHSim introduced SCRs and the curation strategy of non-MeSH-synonymous UMLS concepts, which improved the performance of pyMeSHSim in the recognition of OMIM phenotypes. In the curation of 461 GWAS phenotypes, pyMeSHSim showed recall > 0.94, precision > 0.56, and F1 > 0.70, demonstrating better performance than the state-of-the-art tools DNorm and TaggerOne in recognizing MeSH terms from short biomedical phrases. The semantic similarity in MeSH terms recognized by pyMeSHSim and the previous manual work was calculated by pyMeSHSim and another semantic analysis tool meshes, respectively. The result indicated that the correlation of semantic similarity analysed by two tools reached as high as 0.89–0.99.

Conclusions

The integrative MeSH tool pyMeSHSim embedded with the MeSH MHs and SCRs realized the bio-NE recognition, normalization, and comparison in biomedical text-mining.

[Analysis on drug sensitivity spectrum of 167 multidrug-resistant Mycobacterium tuberculosis in China]

Objective: To investigate the drugs-sensitivity spectrum of multidrug-resistant tuberculosis (MDR-TB) in China and provide a scientific evidence for the drug selection in clinical therapy and the control of MDR-TB. Methods: A total of 167 strains of MDR-TB were included in this study. Every strain was genotyped by lysX gene sequencing and their sensitivity to 13 different anti-TB drugs was tested by using MicroDST(TM) and BACTEC(TM) MGIT 960(TM) liquid-culturing method. The association between drug resistance and genotypes as well as cross drug resistance was also analyzed. The results were analyzed by means of the comparison of enumeration data between two groups with χ(2) test. Results: The overall resistance rate of 167 MDR-TB strains to 11 anti-TB drugs, except isoniazide and rifampicin, was 95.81%, the rates of pre-extensive drug-resistance (pre-XDR) and extensive drug-resistance were 31.14%(52/167) and 6.59% (11/167), respectively. The streptomycin resistance rate of Beijing genotypes was significantly higher than that of the non-Beijing genotypes ( χ(2)=30.682, P<0.05), while the pre-XDR proportion in Beijing genotypes was lower than that in non-Beijing genotypes (χ(2)=5.332, P<0.05). The resistance rates of Ofloxacin and Pyrazinamide in the modern Beijing genotype were significantly higher than those in classical ones (χ(2)=4.105 and χ(2)=3.912, P<0.05). In addition, the cross-resistance rate to rifampicin and rifabutin was 86.23%. A significant difference in drug-resistance rate to rifabutin was seen among groups with different levels of rifampicin resistance (χ(2)=45.912, P<0.05). There was positive correlation not only between ofloxac resistance and moxifloxac resistance, but also between amikacin resistance and kanamycin resistance, with the coefficient of 0.87 and 0.91, respectively. Conclusions: In this study, we observed that there were high incidences of the resistance to 11 anti-TB drugs in 167 clinical MDR-TB strains and the cross resistance phenomena between drugs of the same type were quite serious. The majority of MDR-TB strains belonged to Beijing genotype, which was highly associated with streptomycin resistance.

SAGD: a comprehensive sex-associated gene database from transcriptomes

Many animal species present sex differences. Sex-associated genes (SAGs), which have female-biased or male-biased expression, have major influences on the remarkable sex differences in important traits such as growth, reproduction, disease resistance and behaviors. However, the SAGs resulting in the vast majority of phenotypic sex differences are still unknown. To provide a useful resource for the functional study of SAGs, we manually curated public RNA-seq datasets with paired female and male biological replicates from the same condition and systematically re-analyzed the datasets using standardized methods. We identified 27,793 female-biased SAGs and 64,043 male-biased SAGs from 2,828 samples of 21 species, including human, chimpanzee, macaque, mouse, rat, cow, horse, chicken, zebrafish, seven fly species and five worm species. All these data were cataloged into SAGD, a user-friendly database of SAGs (http://bioinfo.life.hust.edu.cn/SAGD) where users can browse SAGs by gene, species, drug and dataset. In SAGD, the expression, annotation, targeting drugs, homologs, ontology and related RNA-seq datasets of SAGs are provided to help researchers to explore their functions and potential applications in agriculture and human health.

[Effect of standardized surgical treatment and multidisciplinary treatment strategy on the prognosis of gastric cancer patients: report of a single-center cohort study]

Objective: To explore the effect of standardized surgical treatment and multidisciplinary treatment strategy on the treatment outcomes of gastric cancer patients. Methods: A single-center cohort study was carried out. Clinicopathological and long-term follow up data of primary gastric cancer patients were retrieved from the database of Surgical Gastric Cancer Patient Registry (SGCPR) in West China Hospital of Sichuan University. Finally, 4516 gastric cancer patients were included and were divided into three groups according to time periods (period 1 group: exploration stage of standardized surgical treatment, 2000 to 2006, 967 cases; period 2 group: application stage of standardized surgical treatment, 2007 to 2012, 1962 cases; period 3 group: optimization stage of standardized surgical treatment and application stage of multidisciplinary treatment strategy, 2013 to 2016, 1587 cases). Differences in clinical data, pathologic features, and prognosis were compared among 3 period groups. Follow-up information was updated to January 1, 2020. The overall follow-up rate was 88.9% (4016/4516) and median follow-up duration was 51.58 months. Survival curve was drawn by Kaplan-Meire method and compared with log-rank test. Univariate and multivariate analyses were performed by Cox proportional hazards model. Results: There were significant differences among period 1, period 2 and period 3 groups in the rates of D2/D2+ lymphadenectomy [14.4%(139/967) vs. 47.2%(927/1962) vs. 75.4%(1197/1587), χ(2)=907.210, P<0.001], in the ratio of proximal gastrectomy [19.8%(191/967) vs. 16.6%(325/1962) vs. 8.2%(130/1587), χ(2)=100.020, P<0.001], and in the median intraoperative blood loss (300 ml vs. 100 ml vs. 100 ml, H=1126.500, P<0.001). Besides, the increasing trend and significant difference were also observed in the median number of examined lymph nodes among period 1, period 2 and period 3 groups (14 vs. 26 vs. 30, H=987.100, P<0.001). Survival analysis showed that the 5-year overall survival rate was 55.3% in period 1, 55.2% in period 2 and 62.8% in period 3, and significant difference existed between period 3 and period 1 (P=0.004). The Cox proportional hazards model analysis showed that treatment period (period 3, HR=0.820, 95%CI: 0.708 to 0.950, P=0.008), postoperative chemotherapy (HR=0.696, 95%CI: 0.631 to 0.768, P<0.001) and mid-low gastric cancer (HR=0.884, 95%CI: 0.804 to 0.973, P=0.011) were good prognostic factors. Whereas old age (≥65 years, HR=1.189, 95%CI: 1.084 to 1.303, P<0.001), palliative resection (R1/R2, HR=1.538,95%CI: 1.333 to 1.776, P<0.001), large tumor size (≥5 cm, HR=1.377, 95%CI: 1.239 to 1.529, P<0.001), macroscopic type III to IV (HR=1.165, 95%CI: 1.063 to 1.277, P<0.001) and TNM stage II to IV(II/I:HR=1.801,95%CI:1.500~2.162,P<0.001;III/I:HR=3.588, 95%CI: 3.028~4.251, P<0.001; IV/I: HR=6.114, 95%CI: 4.973~7.516, P<0.001) were independent prognostic risk factors. Conclusion: Through the implementation of standardized surgical treatment technology and multidisciplinary treatment model, the quality of surgery treatment and overall survival increase, and prognosis of gastric cancer patients has been improved.

The epigenetic landscapes of histone modifications on HSV-1 genome in human THP-1 cells

Histone positioning and modifications on viral genomes are important factors regulating virus replication. To investigate the dynamics of modified histones on the viral genome and their potential roles in antiviral response, we studied the dynamic changes of histone modifications across the HSV-1 genome in THP-1 cells. Histone modifications were detected on the HSV-1 genome soon after infection, including H3K9me3, H3K27me3, H3K4me3 and H3K27ac. These modifications emerged on the viral genome soon after infection and changed rapidly along with virus life cycle progression. The transcription repression marks, H3K9me3 and H3K27me3, decreased on the viral genome during the infection process; the transcription activation mark H3K27ac increased. Treatment with C646, an inhibitor of H3K27ac transferase p300, significantly repressed virus replication and viral gene expression. Our study reveals the relationship between histone modifications and viral gene expression and provides potential novel strategies for antiviral treatment.

Anti-masculinization induced by aromatase inhibitors in adult female zebrafish

Background

Early sex differentiation genes of zebrafish remain an unsolved mystery due to the difficulty to distinguish the sex of juvenile zebrafish. However, aromatase inhibitors (AIs) could direct juvenile zebrafish sex differentiation to male and even induce ovary-to-testis reversal in adult zebrafish.

Results

In order to determine the transcriptomic changes of sex differentiation in juvenile zebrafish and early sex-reversal in adult zebrafish, we sequenced the transcriptomes of juvenile and adult zebrafish treated with AI exemestane (EM) for 32 days, when juvenile zebrafish sex differentiation finished. EM treatment in females up-regulated the expression of genes involved in estrogen metabolic process, female gamete generation and oogenesis, including gsdf, macf1a and paqr5a, while down-regulated the expression of vitellogenin (vtg) genes, including vtg6, vtg2, vtg4, and vtg7 due to the lower level of Estradiol (E2). Furthermore, EM-juveniles showed up-regulation in genes related to cell death and apoptosis, such as bcl2l16 and anax1c, while the control-juveniles exhibited up-regulation of genes involved in positive regulation of reproductive process and oocyte differentiation such as zar1 and zpcx. Moreover, EM-females showed higher enrichment than control females in genes involved in VEGF signaling pathway, glycosaminoglycan degradation, hedgehog signaling pathway, GnRH signaling pathway and steroid hormone biosynthesis.

Conclusions

Our study shows anti-masculinization in EM-treated adult females but not in EM-treated juveniles. This may be responsible for the lower sex plasticity in adults than juveniles.

[Genome survey and characteristic analysis of SSR in Callicarpa nudiflora]

Callicarpa nudiflora,which is a big brand of Li nationality medicine with Hainan characteristics,has the effects of dissolving stasis,hemostasis,anti-inflammatory and antibacterial. At present,there is a lack of information about the reference genome of C. nudiflora. The study of the genome size,heterozygosity rate and characteristics of SSR of C. nudiflora,can provide an effective basis for the formulation of the whole genome de novo sequencing strategy and development of SSR molecular markers of C. nudiflora. To realize this purpose,high throughput sequencing platform Illumina Hiseq was used to sequence the genome structure of C. nudiflora and K-mer analysis was applied to estimate genome size,repeat sequences and heterozygosity rate. Simple-sequence repeat( SSR) loci that are suitable as markers were identified by MISA software. The results showed the estimated genome size of C. nudiflora was 822. 43 Mb,with a 0. 85% heterozygosity rate and 71. 67% repeats,and the GC content of genome was about 49. 20%. Therefore,C. nudiflora belongs to a complex genome with high heterozygosity and repetition. SSR molecular genetic markers were analyzed in the genome sequence,and a total of 206 049 SSRs were identified,among which mono-nucleotide,di-nucleotide and tri-nucleotide repetitive motifs summed up to 198 993,accounting for 96. 57% of the total SSRs. Among the 2-6 nucleotide repeats,AT/AT,AAT/ATT,AGCC/CTGG,AAAAT/ATTTT and AGATAT/ATATCT have the largest number,respectively. This report represents the first genome-wide characterization of C. nudiflora,and provides a reference for the construction of the library for the fine sequencing of the genome,and a molecular basis for the development of SSR molecular markers as well as for the protection and utilization of gene resources.

[Long non-coding RNA RAB11B-AS1 prevents osteosarcoma proliferation via its sense gene RAB11B]

Objective: To detect the expression of lncRNA RAB11B-AS1 in osteosarcoma and investigate its role in osteosarcoma cells proliferation and the responsible mechanisms. Methods: Osteosarcoma and corresponding adjacent normal tissues were collected from 24 patients subjected to operations from October 2015 to October 2017 in the Third Affiliated Hospital of Southern Medical University.RAB11B-AS1 expression was detected in osteosarcoma specimens by quantitative real-time polymerase chain reaction (qRT-PCR). Lentiviral vectors that stably over-expressing RAB11B-AS1 were constructed and transfected into U2OS osteosarcoma cell line.The effect of RAB11B-AS1 on osteosarcoma cell proliferation and apoptosis was investigated by cell counting kit (CCK-8) assay and flow cytometry.U2OS osteosarcoma xenograft model of nude mice was established to observe the effect of RAB11B-AS1 on xenograft growth in mice, and the role of RAB11B-AS1 in proliferation and apoptosis of osteosarcoma cells was investigated by immunohistochemistry and TUNEL staining of osteosarcoma slices.The relationship between RAB11B-AS1 and RAB11B was explored using luciferase reporter assay.The data were compared with t test between the two groups. Results: Expression of RAB11B-AS1 was significantly down-regulated in osteosarcoma (0.010±0.015) versus their paired non-neoplastic tissues (0.022±0.030) (t=2.117, P=0.045). Up-regulation of RAB11B-AS1 resulted in decreased proliferative rate of U2OS cells (F=15.659, P<0.001). The ratios of cells in G0-G1 phase, S phase, G2-M phase were 62.6%±6.3%, 21.4%±2.2%, 16.3%±1.6% respectively in RAB11B-AS1 up-regulated group versus 59.4%±5.9%, 25.9%±2.6%, 15.5%±1.1% respectively in control group, and cell ratio in G0-G1 and S phase were increased significantly by RAB11B-AS1 up-regulation (t=17.124, 17.321, both P<0.05). Apoptosis rate was significantly elevated in RAB11B-AS1 over-expressed cells (12.7%±1.3%) when compared with that in control (10.3%±1.0%)(t=17.321, P=0.003). Mice transplanted with osteosarcoma cells that overexpressed RAB11B-AS1 exhibited lower growth rate of tumor (F=8.798, P=0.009). Mechanistically, RAB11B-AS1 expression correlated negatively with RAB11B expression (r=-0.356, P=0.044). Conclusions: lncRNA RAB11B-AS1 expression is down-regulated significantly in osteosarcoma tissues.RAB11B-AS1 may suppress the progression of osteosarcoma via down-regulating RAB11B.

[Determination of iodine content in the left ventricular myocardium of healthy subjects using dual-source dual-energy CT myocardial first perfusion imaging: a preliminary study]

Objective: To analyze the normal value of the iodine content in the left ventricular myocardium of healthy subjects and to observe if there is a segmental differences on iodine distribution by using the second generation dual-source dual-energy computed tomography myocardial first perfusion imaging. Methods: In this retrospective study, 42 healthy subjects, who admitted to our department between January to June 2016, with normal second generation dual-source dual-energy computed tomography and coronary CT angioghphy (CTA), electrocardiogram (ECG) results, normal cardiac, hepatic, renal function, normal myocardial enzymes results were enrolled, data from 38 out of 42 subjects with satisfactory image quality were analyzed using Siemens Dual Energy-Heart PBV image processing software.In accordance with the standards of the American Heart Association myocardial 17 fractionation method, content of iodine was measured at different segmental left ventricular myocardium and aorta (left coronary artery from the opening level). The standardized containing iodine value (nIC) was calculated. Results: The iodine content of left ventricular myocardium in normal subjects was 3.1-7.8 mg/ml.The nIC of myocardium from 1st to 17th segments was 0.28±0.06, 0.31±0.07, 0.30±0.07, 0.30±0.04, 0.28±0.04, 0.29±0.05, 0.29±0.01, 0.30±0.07, 0.31±0.07, 0.27±0.06, 0.28±0.08, 0.28±0.07, 0.29±0.08, 0.31±0.07, 0.27±0.06, 0.29±0.06 and 0.21±0.07, respectively.The nIC of the 17th segment was the lowest and was significantly lower than in other segments (all P<0.05), the nIC was similar among the rest 16 segments (all P>0.05). Conclusion: The normal iodine content range in left ventricle myocardium is 3.1-7.8 mg/ml, and the lowest iodine content is detected in the apex and which is significantly lower than the other left ventricular segments.

Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements

Inverted duplicates are a type of repetitive DNA motifs consist of two copies of reverse complementary sequences separated by a spacer sequence. They can lead to genome instability and many may have no function, but some functional small RNAs are processed from hairpins transcribed from these elements. It is not clear whether the pervasive numbers of such elements in genomes, especially those of mammals, is the result of high generation rates of neutral or slightly deleterious duplication events or positive selection for functionality. To test the functionality of intergenic inverted duplicates without known functions, we used mirror duplicates, a type of repetitive DNA motifs with few reported functions and little potential to form hairpins when transcribed, as a nonfunctional control. We identified large numbers of inverted duplicates within intergenic regions of human and mouse genomes, as well as 19 other vertebrate genomes. Structure characterization of these inverted duplicates revealed higher proportion to form stable hairpins compared with converted mirror duplicates, suggesting that inverted duplicates may produce hairpin RNAs. Expression profiling across tissues demonstrated that 7.8% of human and 5.7% of mouse inverted duplicates were expressed even under strict criteria. We found that expressed inverted duplicates were more likely to be structurally stable than both unexpressed inverted duplicates and expressed converted mirror duplicates. By dating inverted duplicates in the vertebrate phylogenetic tree, we observed higher conservation of inverted duplicates than mirror duplicates. These observations support the notion that expressed inverted duplicates may be functional through forming hairpin RNAs.

[Road-side observational survey on 4 unlawful acts among electric bicycle riders in Zhejiang]

OBJECTIVE

To investigate the prevalence of key unlawful acts among electric bicycle riders and provide evidence for the development of specific interventions.

METHODS

A 4-day road-side survey was conducted in Jinhua, Zhejiang province, in 2013. The speed of electric bicycle was measured by speed measuring instrument and the unlawful acts of riders, such as reverse riding, running the red-light and carrying passengers, were observed with non-participatory way.

RESULTS

A total of 3 448 running electric bicycles were observed and the average speed was 26 km/h, the proportion of electric bicycle at the speed of ≥15 km/h was 87.06%. The average speed was highest during 10 am-11 am(30 km/h). the number of observed electric bicycle riders with unlawful acts of ' running the red-light','reverse riding' and ' carrying passengers' were 1 315, 656 and 1 877 respectively, and the estimated rate was 10.01%, 4.99% and 15.22%, respectively. More ' running the red-light','reverse riding' and ' carrying passengers' occurred during 7 am-8 am(14.59%)and 13 pm-14 pm(15.25%), 13 pm-14 pm(7.33%)and 17 pm-18 pm(7.63%), 6 am-7 am(32.44%)and 12 pm-13 pm(27.90%), respectively.

CONCLUSION

Overspeeding, carrying passengers, running the red-light, reverse riding were the key unlawful acts among electric bicycle riders. Targeted intervention should be carried out to reduce the prevalence of unlawful riding acts and the incidence of electric bicycle related injuries and deaths.

Evaluation of paeonol-loaded transethosomes as transdermal delivery carriers

Paeonol shows effective anti-allergic, anti-inflammatory and analgesic activities. However, because of its poor solubility in water and high volatility at room temperature, the application of this drug is restricted in the clinic. The objective of this research was to develop a biocompatible paeonol formulation with improved stability, skin delivery and pharmacokinetic efficiency. In this paper, paeonol-loaded vesicles were prepared using an ethanol injection method. Nano-vesicles were characterized for their physical properties and encapsulation efficiency (EE). Drug permeation behavior in vitro and deposition quantity in porcine ear skin were measured with a Valia-Chien (V-C) diffusion device. Additionally, a validated and sensitive high performance liquid chromatography (HPLC) method was developed to analyze paeonol concentrations in rat plasma after transdermal administration. The results showed that the particle-size order of the nano-vesicles was the following: transethosomes (122.5±7.5nm)<transfersomes (256.5±8.9nm). Compared to the paeonol transfersomes, the transethosomes had a higher EE (85.5±5.2%), and they showed a spherical morphology with a smooth surface when viewed under a transmission electron microscope (TEM). In an in vitro permeation study, the paeonol transethosomes showed an enhanced transdermal flux of 95.7±8.8μg/cm²/h and a higher deposition quantity in porcine ear skin compared to the transfersomes. A one-compartment first-order absorption model could be used to describe the pharmacokinetics of paeonol in rats after transdermal administration. The AUC of the paeonol transethosomes was approximately 1.57- and 3.52-fold higher than those of the transfersomes and a saturated solution of paeonol in 35% ethanol, respectively. The results demonstrated that the paeonol transethosomes had a narrow size distribution, high encapsulation efficiency, and long residence in the plasma. This formulation remarkably enhanced the bioavailability of paeonol.

[Critical roles of matrix metalloproteinases secreted by leukemic cells in the pathogenesis of central nervous system leukemia]

目的

观察白血病细胞分泌的基质金属蛋白酶（MMP）-2和MMP-9对脑微血管内皮细胞（BMVEC）紧密连接蛋白ZO-1、claudin-5、occludin表达及对血脑屏障（BBB）通透性的影响，探讨MMP-2和MMP-9在中枢神经系统白血病（CNSL）发病机制中的作用。

方法

①实时定量PCR检测SHI-1、HL-60、U937细胞MMP-2、MMP-9基因的转录水平；明胶酶谱法检测细胞培养上清中MMP-2和MMP-9蛋白表达；体外穿膜实验观察各白血病细胞株的侵袭能力。②将原代人BMVEC接种于铺有Matrigel胶和纤维黏连蛋白包被的Transwell小室系统中，建立体外BBB模型。将蛋白酶抑制剂GM6001处理或未处理的SHI-1、HL-60、U937细胞或MMP-2/MMP-9基因沉默的SHI-1细胞接种于BBB模型的Transwell小室上层与BMVEC共培养，倒置相差显微镜观察BMVEC的形态变化，激光共聚焦显微镜观察紧密连接蛋白ZO-1、claudin-5和occludin的表达，计算白血病细胞的穿膜率。

结果

①SHI-1细胞表达较高转录水平的MMP-2和MMP-9及酶活性，且侵袭能力强于HL-60、U937细胞（P< 0.01）。②与HL-60、SHI-1和U937细胞共培养后，融合致密的BMVEC之间出现间隙、细胞呈单个生长，紧密连接蛋白ZO-1、claudin-5和occludin的表达明显下调，各白血病细胞均不同程度地穿过体外BBB进入Transwell小室下层。其中SHI-1细胞对BMVEC的形态改变及3种紧密连接蛋白的下调最为明显，穿膜率最高。GM6001明显抑制白血病细胞分泌MMP-2和MMP-9，使BMVEC的形态有所恢复，同时上调ZO-1、claudin-5和occludin的表达，降低了BBB的通透性。③用siRNA分别沉默MMP-2和MMP-9基因后，SHI-1细胞分泌MMP-2和MMP-9被抑制，SHI-1细胞穿膜率较沉默前分别下降43.64％和57.30%（P<0.01），ZO-1、claudin-5和occludin表达上调。

结论

白血病细胞株分泌的MMP-2和MMP-9能通过降解BMVEC紧密连接蛋白ZO-1、claudin-5和occludin而破坏BBB。

[Study of the correlation between the expression of angiotensin Ⅱ and its receptors and collagen deposition in human keloid]

Objective: To study the correlation between the expression of angiotensin Ⅱ, angiotensin Ⅱ type 1 receptor (AT1R), angiotensin Ⅱ type 2 receptor (AT2R) and collagen deposition in human keloid. Methods: The keloid from 19 keloid patients and normal skin from 13 patients performed with free skin transplantation hospitalized in our unit from May 2014 to January 2015 were obtained. The expressions of angiotensin Ⅱ, AT1R, and AT2R were detected by immunohistochemical staining, and the results were semi-quantitatively analyzed by immunohistochemical scoring. The expression of collagen in keloid was detected by picrosirius-red staining, and the percentage of total collagen was calculated. Data were processed with t test. The expressions of angiotensin Ⅱ, AT1R, AT2R and the total content of collagen of 13 keloid patients were analyzed by Pearson correlation analysis. Results: (1) There was negative or probably positive expression of angiotensin Ⅱ in normal skin tissue, mainly distributed in the epidermal basal layer. The expression of angiotensin Ⅱ was strong in keloid, most distributed in spinous layer and basal layer of epidermis and most region of dermis, and was strongly positive in most cells, and most cells were fibroblasts. The expressions of AT1R and AT2R were similar to angiotensin Ⅱ in two types of tissue. The expressions of angiotensin Ⅱ, AT1R, and AT2R in keloid scored (305±34), (281±32), and (285±25) points, respectively, which were significantly higher than those in normal tissue [respectively (54±17), (89±47), and (97±32) points, with t values from 12.03 to 23.21, P values below 0.01]. (2) The total content of collagen in keloid was (88±4)%. There was a lot of thick and dense type Ⅰcollagen in keloid, with massive structure and distributed like bamboo segment and arranged in disorder. The expression of type Ⅲ collagen was increased, which was distributed scatteredly around type Ⅰcollagen. (3) There were positive correlations between the expressions of angiotensin Ⅱ, AT1R, AT2R and the total content of collagen in keloid (with r values from 0.452 to 0.720, P values below 0.05). Conclusions: The expressions of angiotensin Ⅱ, AT1R, and AT2R were abnormally increased in human keloid, which may play an important role in the collagen deposition of keloid.

Variations in Essential Oil Yield, Composition, and Antioxidant Activity of Different Plant Organs from Blumea balsamifera (L.) DC. at Different Growth Times

Blumea balsamifera, also named Ainaxiang, is widely used as an ancient medicinal herb in tropical and subtropical Asia. It is rich in essential oils. In this work the essential oils of B. balsamifera from different plant organs and in different months were extracted, and then analyzed by gas chromatography-mass spectrometry. The results showed that essential oil yield of young leaves was the highest (0.65 mL/100 g), followed by mature leaves (0.57 mL/100 g), and the oil yield was higher in October (0.47 mL/100 g) than other months. A total of 44 compounds were identified, representing 92.64%–96.71% of the oil. Eighteen common chemical components were found among the six plant organs, representing >80% of the oil constituents. l-borneol was the main ingredient in leaves, and its content was the highest in senescent leaves and in December. In the essential oils of young shoots and young stems, the main component was dimethoxydurene. Antioxidant activity was also determined using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and β-carotene bleaching (BCB) assays. The results indicated that the β-carotene bleaching activity was far stronger than the DPPH radical-scavenging capacity, and the young leaves and young shoots showed stronger antioxidant activity. Dimethoxydurene, β-caryophyllene, and α-caryophyllene play a positive role in good antioxidant activity, while β-eudesmol, phytol, and tetradecanal play a negative role. The antioxidant activity revealed in this study might help in developing this promising bioresource for use in the medicinal and cosmetic industries.

Overexpression of OsOSM1 Enhances Resistance to Rice Sheath Blight

Sheath blight (SB), caused by Rhizoctonia solani, is one of the most destructive rice diseases worldwide. It has been difficult to generate SB-resistant varieties through conventional breeding because of the quantitative nature of rice resistance to SB. In this study, we found that overexpression of the OsOSM1 gene, encoding an osmotin protein belonging to the pathogenesis-related protein 5 family, is able to improve rice resistance to SB in field tests. Although there are two osmotin genes in rice, OsOSM1 is the one mainly expressed in leaf sheath at the booting stage, coinciding with the critical stage of SB development in the field. In addition, OsOSM1 expression is strongly induced by R. solani in SB-resistant rice variety YSBR1 but not in susceptible varieties, suggesting its involvement in SB resistance. Overexpression of OsOSM1 (OsOSM1ox) in susceptible variety Xudao 3 significantly increases resistance to SB in transgenic rice. The OsOSM1 mRNA levels in different transgenic lines are found to be positively correlated with their SB resistance levels. Intriguingly, although extremely high levels of OsOSM1 were detrimental to rice development, appropriately elevated levels of OsSOM1 were obtained that enhanced rice SB resistance without affecting rice development or grain yield. The OsSOM1 protein is localized on plasma membrane. OsOSM1 is upregulated by jasmonic acid (JA); furthermore, JA-responsive marker genes are induced in OsOSM1ox lines. These results suggest that the activation of JA signaling pathway may account for the increased resistance in transgenic OsOSM1ox lines. Taken together, our results demonstrate that OsOSM1 plays an important role in defense against rice SB disease and provides a new target for engineering resistance to SB.

Development of expressed sequence tag-simple sequence repeat markers for genetic characterization and population structure analysis of Praxelis clematidea (Asteraceae)

Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37.6%) were trinucleotide repeat motifs. Of the 24 primer pairs designed from these 133 ESTs, 7 (29.2%) resulted in significant polymorphisms. The number of alleles per locus ranged from 5 to 9. The relatively high genetic diversity (H = 0.2667, I = 0.4212, and P = 100%) of P. clematidea was related to high gene flow (Nm = 1.4996) among populations. The coefficient of population differentiation (GST = 0.2500) indicated that most genetic variation occurred within populations. A Mantel test suggested that there was significant correlation between genetic distance and geographical distribution (r = 0.3192, P = 0.012). These results further support the transferability of EST-SSR markers between closely related genera of the same family.

Overexpression of OsPGIP1 Enhances Rice Resistance to Sheath Blight

Rice sheath blight (SB), caused by necrotrophic pathogen Rhizoctonia solani, is one of the most destructive rice diseases, and no major resistance genes are available. Polygalacturonase-inhibiting proteins (PGIP) are extracellular leucine-rich repeat proteins and play important roles in plant defense against different pathogenic fungi by counteracting secreted fungal polygalacturonases (PG). However, the role of PGIP in conferring resistance to rice SB remains to be thoroughly investigated. Here, we showed that OsPGIP1 is capable of inhibiting PG derived from R. solani. Our real-time reverse-transcription polymerase chain reaction results indicated that resistant rice 'YSBR1' and 'Jasmine 85' express significantly higher levels of OsPGIP1 than susceptible 'Lemont'. Our results also show that OsPGIP1 is most highly expressed at the late tillering stage in the sheath of YSBR1, coinciding with the critical stage of SB development in field. More importantly, the OsPGIP1 level is highly elevated by inoculation with R. solani in resistant cultivars but not in susceptible Lemont. Overexpression of OsPGIP1 significantly increased rice resistance to SB and inhibited tissue degradation caused by R. solani-secreted PG. Furthermore, OsPGIP1 overexpression did not affect rice agronomic traits or yield components. Together, our results not only demonstrate the important role of OsPGIP1 in combatting the rice SB disease but also provide a new avenue to the improvement of rice SB resistance by manipulating an endogenous gene.

Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster

Background

A generally accepted approach to the analysis of RNA-Seq read count data does not yet exist. We sequenced the mRNA of 726 individuals from the Drosophila Genetic Reference Panel in order to quantify differences in gene expression among single flies. One of our experimental goals was to identify the optimal analysis approach for the detection of differential gene expression among the factors we varied in the experiment: genotype, environment, sex, and their interactions. Here we evaluate three different filtering strategies, eight normalization methods, and two statistical approaches using our data set. We assessed differential gene expression among factors and performed a statistical power analysis using the eight biological replicates per genotype, environment, and sex in our data set.

Results

We found that the most critical considerations for the analysis of RNA-Seq read count data were the normalization method, underlying data distribution assumption, and numbers of biological replicates, an observation consistent with previous RNA-Seq and microarray analysis comparisons. Some common normalization methods, such as Total Count, Quantile, and RPKM normalization, did not align the data across samples. Furthermore, analyses using the Median, Quantile, and Trimmed Mean of M-values normalization methods were sensitive to the removal of low-expressed genes from the data set. Although it is robust in many types of analysis, the normal data distribution assumption produced results vastly different than the negative binomial distribution. In addition, at least three biological replicates per condition were required in order to have sufficient statistical power to detect expression differences among the three-way interaction of genotype, environment, and sex.

Conclusions

The best analysis approach to our data was to normalize the read counts using the DESeq method and apply a generalized linear model assuming a negative binomial distribution using either edgeR or DESeq software. Genes having very low read counts were removed after normalizing the data and fitting it to the negative binomial distribution. We describe the results of this evaluation and include recommended analysis strategies for RNA-Seq read count data.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2353-z) contains supplementary material, which is available to authorized users.

Drought-tolerant rice germplasm developed from an Oryza officinalis transformation-competent artificial chromosome clone

Oryza officinalis has proven to be a natural gene reservoir for the improvement of domesticated rice as it carries many desirable traits; however, the transfer of elite genes to cultivated rice by conventional hybridization has been a challenge for rice breeders. In this study, the conserved sequence of plant stress-related NAC transcription factors was selected as a probe to screen the O. officinalis genomic transformation-competent artificial chromosome library by Southern blot; 11 positive transformation-competent artificial chromosome clones were subsequently detected. By Agrobacterium-mediated transformation, an indica rice variety, Huajingxian 74 (HJX74), was transformed with a TAC clone harboring a NAC gene-positive genomic fragment from O. officinalis. Molecular analysis revealed that the O. officinalis genomic fragment was integrated into the genome of HJX74. The transgenic lines exhibited high tolerance to drought stress. Our results demonstrate that the introduction of stress-related transformation-competent artificial chromosome clones, coupled with a transgenic validation approach, is an effective method of transferring agronomically important genes from O. officinalis to cultivated rice.

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

A flowing liquid lithium limiter for the Experimental Advanced Superconducting Tokamak

A program involving the extensive and systematic use of lithium (Li) as a "first," or plasma-facing, surface in Tokamak fusion research devices located at Institute of Plasma Physics, Chinese Academy of Sciences, was started in 2009. Many remarkable results have been obtained by the application of Li coatings in Experimental Advanced Superconducting Tokamak (EAST) and liquid Li limiters in the HT-7 Tokamak-both located at the institute. In furtherance of the lithium program, a flowing liquid lithium (FLiLi) limiter system has been designed and manufactured for EAST. The design of the FLiLi limiter is based on the concept of a thin flowing film which was previously tested in HT-7. Exploiting the capabilities of the existing material and plasma evaluation system on EAST, the limiter will be pre-wetted with Li and mechanically translated to the edge of EAST during plasma discharges. The limiter will employ a novel electro-magnetic pump which is designed to drive liquid Li flow from a collector at the bottom of limiter into a distributor at its top, and thus supply a continuously flowing liquid Li film to the wetted plasma-facing surface. This paper focuses on the major design elements of the FLiLi limiter. In addition, a simulation of incoming heat flux has shown that the distribution of heat flux on the limiter surface is acceptable for a future test of power extraction on EAST.

Cloning and sequence analysis of the Blumea balsamifera DC farnesyl diphosphate synthase gene

Blumea balsamifera DC is a member of the Compositae family and is frequently used as traditional Chinese medicine. Blumea balsamifera is rich in monoterpenes, which possess a variety of pharmacological activities, such as antioxidant, anti-bacteria, and anti-viral activities. Farnesyl diphosphate synthase (FPS) is a key enzyme in the biosynthetic pathway of terpenes, playing an important regulatory role in plant growth, such as resistance and secondary metabolism. Based on the conserved oligo amino acid residues of published FPS genes from other higher plant species, a cDNA sequence, designated BbFPS, was isolated from B. balsamifera DC using polymerase chain reaction. The clones were an average of 1.6 kb and contained an open reading frame that predicted a polypeptide of 342 amino acids with 89.07% identity to FPS from other plants. The deduced amino acid sequence was dominated by hydrophobic regions and contained 2 highly conserved DDxxD motifs that are essential for proper functioning of FPS. Phylogenetic analysis indicated that FPS grouped with other composite families. Prediction of secondary structure and subcellular localization suggested that alpha helices made up 70% of the amino acids of the sequence.

Comparison and Confirmation of Quantitative Trait Loci Conferring Partial Resistance to Rice Sheath Blight on Chromosome 9

Sheath blight (SB), caused by Rhizoctonia solani, is one of the worst rice (Orzya sativa) diseases worldwide. Resistance to the SB disease in rice is a complex trait controlled by quantitative trait loci (QTLs). Through map integration, we found several previously identified SB resistance (SBR) QTLs reported in inconsistent regions on the long arm of chromosome 9. Five of them were detected on 'Jasmine 85' (J85), 'Minghui 63' (MH63), and 'Lemont' (LMNT) rice and were designated qSB-9^J85-1, qSB-9^J85-2, qSB-9^MH63-1, qSB-9^MH63-2, and qSB-9^LMNT, respectively, in the present study. To further verify and physically map the five potential SBR QTLs, we introduced these SBR QTLs into a common susceptible variety (LMNT) and developed a few chromosomal segment substitution lines through marker-assisted selection. After artificial inoculation with the SB fungus, we were able to validate qSB-9^J85-2 but not the other four SBR QTLs; whereas, on MH63, an SBR QTL designated qSB-9^MH63-3 was confirmed in the region defined by markers Y83 and Y91.8 that included qSB-9^J85-2, covering approximately 1,235 kb. Both qSB-9^J85-2 and qSB-9^MH63-3 appeared to be dominant resistance genes and contributed to similar levels to SB resistance, reducing SB disease severity by approximately 1.0 on a 0-to-9 SB disease rating system. After comparing with another confirmed SBR QTL (qSB-9^TQ) from 'Teqing' rice (TQ), we conclude that qSB-9^J85-2, qSB-9^MH63-3, and qSB-9^TQ are probably controlled by the same allelic resistance genes. These results will accelerate the utilization of this major SBR QTL and its map-based cloning.

Transcriptional effects of gene dose reduction

Large-scale gene dose reductions usually lead to abnormal phenotypes or death. However, male mammals, Drosophila, and Caenorhabditis elegans have only one X chromosome and thus can be considered as monosomic for a major chromosome. Despite the deleterious effects brought about by such gene dose reduction in the case of an autosome, X chromosome monosomy in males is natural and innocuous. This is because of the nearly full transcriptional compensation for X chromosome genes in males, as opposed to no or partial transcriptional compensation for autosomal one-dose genes arising due to deletions. Buffering, the passive absorption of disturbance due to enzyme kinetics, and feedback responses triggered by expression change contribute to partial compensation. Feed-forward mechanisms, which are active responses to genes being located on the X, rather than actual gene dose are important contributors to full X chromosome compensation. In the last decade, high-throughput techniques have provided us with the tools to effectively and quantitatively measure the small-fold transcriptional effects of dose reduction. This is leading to a better understanding of compensatory mechanisms.

Low-density lipoprotein receptor-related protein 2 gene is associated with egg-quality traits in dwarf layers

Some members of the low-density lipoprotein receptor (LDLR) family play important roles in the regulation of lipoprotein metabolism and egg quality traits. Low-density lipoprotein receptor-related protein 2 (LRP2) gene belongs to the LDLR super family, and widely expresses in many tissues. This work identified and genotyped 1 single-nucleotide polymorphism (SNP), T14347C, at 3'-UTR of the LRP2 using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS), and analyzed the effects of the SNP (T14347C) on egg-quality traits in 544 dwarf hens from 44 sire families. Frequencies of this SNP in the studied population did not agree with the Hardy-Weinberg equilibrium (P < 0.0001). Egg weight, albumen weight, albumen height, and albumen ratio of the TT genotype were significantly higher than those of the CC genotype (P < 0.05), whereas eggshell ratio of the TT genotype was significantly lower than that of the CC genotype (P < 0.05). The relative expression level of the LRP2 gene in the magnum was determined by real-time quantitative PCR. The gene expression of genotype CC individuals was significantly higher than that of TT and CT birds (P < 0.05). By combining both genetic effects and expression analyses results, we propose that the LRP2 gene is a good candidate gene, exhibiting a key role in albumen formation processes.

Preparation of mononuclear, homodinuclear, and heterotrinuclear complexes by salicylaldiminato-functionalized imidazolium salt: approach to multifunctional catalysts

A salicylaldiminato imidazolium salt that bears both a Schiff base and imidazolium salt moiety was used to synthesize heterometallic compounds that could serve as multifunctional catalysts in certain reactions. The successful preparation of seven mononuclear compounds with a variety of transition metals (Pd, Ir, Ru, Zn, Ni) illustrated the high versatility of this class of ligands, which is crucial for the design of catalysts. Synthesis of homodinuclear compounds and heterotrinuclear compounds provided practical methods to connect multiple metal fragments through these ligands. The heterotrinuclear complex (Ni/Ir) was employed as a catalyst in the reaction of dehalogenation/transfer hydrogenation of halo-acetophenones. The preliminary catalytic study showed that this heterometallic species is more active than a combination of the corresponding monometallic species.

Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome

Inverted duplicates (IDs) are pervasive in genomes and have been reported to play functional roles in various biological processes. However, the general underlying evolutionary forces that maintain IDs in genomes remain largely elusive. Through a systematic screening of the Drosophila melanogaster genome, 20,223 IDs were detected in nonrepetitive intergenic regions, far more than expectation under the neutrality model. 3,846 of these IDs were identified to have stable hairpin structure (i.e., the structural IDs). Based on whole-genome transcriptome profiling data, we found 628 unannotated expressed structural IDs, which had significantly different genomic distributions and structural properties from the unexpressed IDs. Among the expressed structural IDs, 130 exhibited higher expression in males than in females (i.e., male-biased expression). Compared with sex-unbiased ones, these male-biased IDs were significantly underrepresented on the X chromosome, similar to previously reported pattern of male-biased protein-coding genes. These analyses suggest that a selection-driven process, rather than a purely neutral mutation-driven mechanism, contributes to the maintenance of IDs in the Drosophila genome.