BACKGROUND

Chromosomal replication is the central event in the bacterial cell cycle. Identification of replication origins (oriCs) is necessary for almost all newly sequenced bacterial genomes. Given the increasing pace of genome sequencing, the current available software for predicting oriCs, however, still leaves much to be desired. Therefore, the increasing availability of genome sequences calls for improved software to identify oriCs in newly sequenced and unannotated bacterial genomes.

RESULTS

We have developed Ori-Finder, an online system for finding oriCs in bacterial genomes based on an integrated method comprising the analysis of base composition asymmetry using the Z-curve method, distribution of DnaA boxes, and the occurrence of genes frequently close to oriCs. The program can also deal with unannotated genome sequences by integrating the gene-finding program ZCURVE 1.02. Output of the predicted results is exported to an HTML report, which offers convenient views on the results in both graphical and tabular formats.

CONCLUSIONS

A web-based system to predict replication origins of bacterial genomes has been presented here. Based on this system, oriC regions have been predicted for the bacterial genomes available in GenBank currently. It is hoped that Ori-Finder will become a useful tool for the identification and analysis of oriCs in both bacterial and archaeal genomes.

The combination of high-density transposon-mediated mutagenesis and high-throughput sequencing has led to significant advancements in research on essential genes, resulting in a dramatic increase in the number of identified prokaryotic essential genes under diverse conditions and a revised essential-gene concept that includes all essential genomic elements, rather than focusing on protein-coding genes only. DEG 10, a new release of the Database of Essential Genes (available at http://www.essentialgene.org), has been developed to accommodate these quantitative and qualitative advancements. In addition to increasing the number of bacterial and archaeal essential genes determined by genome-wide gene essentiality screens, DEG 10 also harbors essential noncoding RNAs, promoters, regulatory sequences and replication origins. These essential genomic elements are determined not only in vitro, but also in vivo, under diverse conditions including those for survival, pathogenesis and antibiotic resistance. We have developed customizable BLAST tools that allow users to perform species- and experiment-specific BLAST searches for a single gene, a list of genes, annotated or unannotated genomes. Therefore, DEG 10 includes essential genomic elements under different conditions in three domains of life, with customizable BLAST tools.

The prediction of interresidue contacts and distances from coevolutionary data using deep learning has considerably advanced protein structure prediction. Here, we build on these advances by developing a deep residual network for predicting interresidue orientations, in addition to distances, and a Rosetta-constrained energy-minimization protocol for rapidly and accurately generating structure models guided by these restraints. In benchmark tests on 13th Community-Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP13)- and Continuous Automated Model Evaluation (CAMEO)-derived sets, the method outperforms all previously described structure-prediction methods. Although trained entirely on native proteins, the network consistently assigns higher probability to de novo-designed proteins, identifying the key fold-determining residues and providing an independent quantitative measure of the "ideality" of a protein structure. The method promises to be useful for a broad range of protein structure prediction and design problems.

Gold nanoparticles have been conceived as a radiosensitizer in cancer radiation therapy, but one of the important questions for primary drug screening is what size of gold nanoparticles can optimally enhance radiation effects. Herein, we perform in vitro and in vivo radiosensitization studies of 4.8, 12.1, 27.3, and 46.6 nm PEG-coated gold nanoparticles. In vitro results show that all sizes of the PEG-coated gold nanoparticles can cause a significant decrease in cancer cell survival after gamma radiation. 12.1 and 27.3 nm PEG-coated gold nanoparticles have dispersive distributions in the cells and stronger sensitization effects than 4.8 and 46.6 nm particles by both cell apoptosis and necrosis. Further, in vivo results also show all sizes of the PEG-coated gold nanoparticles can significantly decrease tumor volume and weight after 5 Gy radiations, and 12.1 and 27.3 nm PEG-coated gold nanoparticles have greater sensitization effects than 4.8 and 46.6 nm particles, which can lead to almost complete disappearance of the tumor. In vivo biodistribution confirms that 12.1 and 27.3 nm PEG-coated gold nanoparticles are accumulated in the tumor with high concentrations. The pathology, immune response, and blood biochemistry indicate that the PEG-coated gold nanoparticles have not caused spleen and kidney damages, but give rise to liver damage and gold accumulation. It can be concluded that 12.1 and 27.3 nm PEG-coated gold nanoparticles show high radiosensitivity, and these results have an important indication for possible radiotherapy and drug delivery.

The long non-coding RNA Hox transcript antisense intergenic RNA (HOTAIR) was recently implicated in breast cancer metastasis and is predictive of poor prognosis in colorectal and pancreatic cancers. We recently discovered that HOTAIR is a cell cycle-related lncRNA in human glioma, and its expression is closely associated with glioma staging and poor prognosis. Although lysine specific demethylase 1 (LSD1) and polycomb repressive complex 2 (PRC2) have been demonstrated to be functional targets of HOTAIR, how HOTAIR regulates glioma cell cycle progression remains largely unknown. In this study, we found that EZH2 (predominant PRC2 complex component) inhibition blocked cell cycle progression in glioma cells, consistent with the effects elicited by HOTAIR siRNA. However, the inhibition of LSD1 did not affect cell cycle progression in glioma cells. These results suggest that HOTAIR might regulate cell cycle progression through EZH2. Our intracranial mice model also revealed delayed tumor growth in HOTAIR siRNA- and EZH2 inhibitor-treated groups. Moreover, in HOTAIR knock-down cell lines, the expression of the PRC2-binding domain of HOTAIR (5' domain) but not of the LSD1-binding domain of HOTAIR (3' domain) resulted in accelerated cell cycle progression. In conclusion, HOTAIR promotes cell cycle progression in glioma as a result of the binding of its 5' domain to the PRC2 complex.

A new system, ZCURVE 1.0, for finding protein- coding genes in bacterial and archaeal genomes has been proposed. The current algorithm, which is based on the Z curve representation of the DNA sequences, lays stress on the global statistical features of protein-coding genes by taking the frequencies of bases at three codon positions into account. In ZCURVE 1.0, since only 33 parameters are used to characterize the coding sequences, it gives better consideration to both typical and atypical cases, whereas in Markov-model-based methods, e.g. Glimmer 2.02, thousands of parameters are trained, which may result in less adaptability. To compare the performance of the new system with that of Glimmer 2.02, both systems were run, respectively, for 18 genomes not annotated by the Glimmer system. Comparisons were also performed for predicting some function-known genes by both systems. Consequently, the average accuracy of both systems is well matched; however, ZCURVE 1.0 has more accurate gene start prediction, lower additional prediction rate and higher accuracy for the prediction of horizontally transferred genes. It is shown that the joint applications of both systems greatly improve gene-finding results. For a typical genome, e.g. Escherichia coli, the system ZCURVE 1.0 takes approximately 2 min on a Pentium III 866 PC without any human intervention. The system ZCURVE 1.0 is freely available at: http://tubic. tju.edu.cn/Zcurve_B/.

In order to understand the evolution, structure and function of genomes, it is important to know the general compositional features of DNA sequences. Based on the quadratic divergence, a new segmentation algorithm to partition a given genome or DNA sequence into compositionally distinct domains has been put forward. With the aid of the technique of cumulative GC profile, the distribution of segmentation points can be displayed intuitively. We have therefore developed them into GC-Profile, an interactive web-based software system, which can be used to segment prokaryotic and eukaryotic genomes. GC-Profile provides a quantitative and qualitative view of genome organization. Based on the obtained results, the relationships between the G+C content and other genomic features, such as distributions of genes and CpG islands, can be analyzed in a perceivable manner. It shows that GC-Profile would be an appropriate starting point for analyzing the isochore structure of higher eukaryotic genomes, and an intuitive tool for identifying genomic islands in prokaryotic genomes. GC-Profile is freely available at the website http://tubic.tju.edu.cn/GC-Profile/. In addition, precompiled binaries, together with examples and documentation, can also be freely downloaded for a local execution.

Replication of chromosomes is one of the central events in the cell cycle. Chromosome replication begins at specific sites, called origins of replication (oriCs), for all three domains of life. However, the origins of replication still remain unknown in a considerably large number of bacterial and archaeal genomes completely sequenced so far. The availability of increasing complete bacterial and archaeal genomes has created challenges and opportunities for identification of their oriCs in silico, as well as in vivo. Based on the Z-curve theory, we have developed a web-based system Ori-Finder to predict oriCs in bacterial genomes with high accuracy and reliability by taking advantage of comparative genomics, and the predicted oriC regions have been organized into an online database DoriC, which is publicly available at http://tubic.tju.edu.cn/doric/ since 2007. Five years after we constructed DoriC, the database has significant advances over the number of bacterial genomes, increasing about 4-fold. Additionally, oriC regions in archaeal genomes identified by in vivo experiments, as well as in silico analyses, have also been added to the database. Consequently, the latest release of DoriC contains oriCs for >1500 bacterial genomes and 81 archaeal genomes, respectively.

OBJECTIVE

The purpose of this study was to assess the effects of qili qiangxin capsules in patients with chronic heart failure (CHF).

BACKGROUND

Qili qiangxin capsules are a traditional Chinese medicine that has been approved in China for the treatment of CHF, but the evidence supporting its efficacy remains unclear.

METHODS

A total of 512 patients with CHF were enrolled and randomly assigned to receive the placebo or qili qiangxin capsules in addition to their standard medications for the treatment of CHF. The primary endpoint was the reduction or percent change in the plasma N-terminal pro-B-type natriuretic peptide (NT-proBNP) level during 12 weeks of treatment.

RESULTS

At the 12-week follow-up, a significant reduction in the NT-proBNP level from baseline was observed in both groups, but the qili qiangxin capsule group demonstrated a significantly greater reduction than the placebo group (p = 0.002); 47.95% of patients in the qili qiangxin capsule group demonstrated reductions in NT-proBNP levels of at least 30% compared with 31.98% of patients in the placebo group (p < 0.001). Treatment with qili qiangxin capsules also demonstrated superior performance in comparison to the placebo with respect to New York Heart Association functional classification, left ventricular ejection fraction, 6-min walking distance, and quality of life.

CONCLUSIONS

On a background of standard treatment, qili qiangxin capsules further reduced the levels of NT-proBNP. Together, our data suggest that qili qiangxin capsules could be used in combination therapy for CHF.

Cell therapy is emerging as a viable therapy to restore neurological function after stroke. Many types of stem/progenitor cells from different sources have been explored for their feasibility and efficacy for the treatment of stroke. Transplanted cells not only have the potential to replace the lost circuitry, but also produce growth and trophic factors, or stimulate the release of such factors from host brain cells, thereby enhancing endogenous brain repair processes. Although stem/progenitor cells have shown a promising role in ischemic stroke in experimental studies as well as initial clinical pilot studies, cellular therapy is still at an early stage in humans. Many critical issues need to be addressed including the therapeutic time window, cell type selection, delivery route, and in vivo monitoring of their migration pattern. This review attempts to provide a comprehensive synopsis of preclinical evidence and clinical experience of various donor cell types, their restorative mechanisms, delivery routes, imaging strategies, future prospects and challenges for translating cell therapies as a neurorestorative regimen in clinical applications.

Panax ginseng C.A. Meyer is a well-known medicinal herb native to China and Korea, and has been used as a herbal remedy in eastern Asia for thousands of years. However, there is different evidence of ginseng efficacy between traditional Chinese medicine (TCM), modern pharmacological experiments and clinical trials. In TCM, ginseng is a highly valued herb and has been applied to a variety of pathological conditions and illnesses such as hypodynamia, anorexia, shortness of breath, palpitation, insomnia, impotence, hemorrhage and diabetes. Modern pharmacological experiments have proved that ginseng possesses multiple constituents (ginsenosides, polysaccharides, peptides, polyacetylenic alcohols, etc.) and actions (central nervous system effects, neuroprotective effect, immunomodulation, anticancer, etc.), ginsenosides as the active ingredients, especially, having antioxidant, antiinflammatory, antiapoptotic and immunostimulant properties. Recently, ginseng has been studied in a number of randomized controlled trials investigating its effect mainly on physical and psychomotor performance, cognitive function, immunomodulation, diabetes mellitus, cardiovascular risk factors, quality of life, as well as adverse effects. Equivocal results have been demonstrated for many of these indications. Because of the poor quality of most clinical trials on ginseng, reliable clinical data in humans are still lacking. Therefore, a broader understanding of medical knowledge and reasoning on ginseng is necessary.

Owing to the increasing emissions of carbon dioxide (CO(2)), human life and the ecological environment have been affected by global warming and climate changes. To mitigate the concentration of CO(2) in the atmosphere various strategies have been implemented such as separation, storage, and utilization of CO(2). Although it has been explored for many years, hydrogenation reaction, an important representative among chemical conversions of CO(2), offers challenging opportunities for sustainable development in energy and the environment. Indeed, the hydrogenation of CO(2) not only reduces the increasing CO(2) buildup but also produces fuels and chemicals. In this critical review we discuss recent developments in this area, with emphases on catalytic reactivity, reactor innovation, and reaction mechanism. We also provide an overview regarding the challenges and opportunities for future research in the field (319 references).

Exosomes are a class of naturally occurring nanoparticles that are secreted endogenously by mammalian cells. Clinical applications for exosomes remain a challenge because of their unsuitable donors, low scalability, and insufficient targeting ability. In this study, we developed a dual-functional exosome-based superparamagnetic nanoparticle cluster as a targeted drug delivery vehicle for cancer therapy. The resulting exosome-based drug delivery vehicle exhibits superparamagnetic behavior at room temperature, with a stronger response to an external magnetic field than individual superparamagnetic nanoparticles. These properties enable exosomes to be separated from the blood and to target diseased cells. In vivo studies using murine hepatoma 22 subcutaneous cancer cells showed that drug-loaded exosome-based vehicle delivery enhanced cancer targeting under an external magnetic field and suppressed tumor growth. Our developments overcome major barriers to the utility of exosomes for cancer application.

Recently reported metamaterial analogues of electromagnetically induced transparency enable a unique route to endow classical optical structures with aspects of quantum optical systems. This method opens up many fascinating prospects on novel optical components, such as slow light units, highly sensitive sensors and nonlinear devices. In particular, optical control of electromagnetically induced transparency in metamaterials promises essential application opportunities in optical networks and terahertz communications. Here we present active optical control of metamaterial-induced transparency through active tuning of the dark mode. By integrating photoconductive silicon into the metamaterial unit cell, a giant switching of the transparency window occurs under excitation of ultrafast optical pulses, allowing for an optically tunable group delay of the terahertz light. This work opens up the possibility for designing novel chip-scale ultrafast devices that would find utility in optical buffering and terahertz active filtering.

Quercetin is a bioactive compound that is widely used in botanical medicine and traditional Chinese medicine due to its potent antioxidant activity. In recent years, antioxidant activities of quercetin have been studied extensively, including its effects on glutathione (GSH), enzymatic activity, signal transduction pathways, and reactive oxygen species (ROS) caused by environmental and toxicological factors. Chemical studies on quercetin have mainly focused on the antioxidant activity of its metal ion complexes and complex ions. In this review, we highlight the recent advances in the antioxidant activities, chemical research, and medicinal application of quercetin.

The pseudo-amino acid composition has been widely used to convert complicated protein sequences with various lengths to fixed length digital feature vectors while keeping considerable sequence order information. However, so far the only software available to the public is the web server PseAAC (http://www.csbio.sjtu.edu.cn/bioinf/PseAAC), which has some limitations in dealing with large-scale datasets. Here, we propose a new cross-platform stand-alone software program, called PseAAC-Builder (http://www.pseb.sf.net), which can be used to generate various modes of Chou's pseudo-amino acid composition in a much more efficient and flexible way. It is anticipated that PseAAC-Builder may become a useful tool for studying various protein attributes.

Uncovering complex oil-water flow structure represents a challenge in diverse scientific disciplines. This challenge stimulates us to develop a new distributed conductance sensor for measuring local flow signals at different positions and then propose a novel approach based on multi-frequency complex network to uncover the flow structures from experimental multivariate measurements. In particular, based on the Fast Fourier transform, we demonstrate how to derive multi-frequency complex network from multivariate time series. We construct complex networks at different frequencies and then detect community structures. Our results indicate that the community structures faithfully represent the structural features of oil-water flow patterns. Furthermore, we investigate the network statistic at different frequencies for each derived network and find that the frequency clustering coefficient enables to uncover the evolution of flow patterns and yield deep insights into the formation of flow structures. Current results present a first step towards a network visualization of complex flow patterns from a community structure perspective.

SAMHD1 is a dGTP-activated deoxynucleoside triphosphate triphosphohydrolase (dNTPase) whose dNTPase activity has been linked to HIV/SIV restriction. The mechanism of its dGTP-activated dNTPase function remains unclear. Recent data also indicate that SAMHD1 regulates retrotransposition of LINE-1 elements. Here we report the 1.8-Å crystal structure of homotetrameric SAMHD1 in complex with the allosteric activator and substrate dGTP/dATP. The structure indicates the mechanism of dGTP-dependent tetramer formation, which requires the cooperation of three subunits and two dGTP/dATP molecules at each allosteric site. Allosteric dGTP binding induces conformational changes at the active site, allowing a more stable interaction with the substrate and explaining the dGTP-induced SAMHD1 dNTPase activity. Mutations of dGTP binding residues in the allosteric site affect tetramer formation, dNTPase activity and HIV-1 restriction. dGTP-triggered tetramer formation is also important for SAMHD1-mediated LINE-1 regulation. The structural and functional information provided here should facilitate future investigation of SAMHD1 function, including dNTPase activity, LINE-1 modulation and HIV-1 restriction.

MicroRNAs have been demonstrated to be deregulated in different types of cancer. miR-21 is a key player in the majority of cancers. Down-regulation of miR-21 in glioblastoma cells leads to repression of cell growth, increased cellular apoptosis and cell-cycle arrest, which can theoretically enhance the chemotherapeutic effect in cancer therapy. In this study, the poly(amidoamine) (PAMAM) dendrimer was employed as a carrier to co-deliver antisense-miR-21 oligonucleotide (as-miR-21) and 5-fluorouracil (5-FU) to achieve delivery of as-miR-21 to human glioblastoma cells and enhance the cytotoxicity of 5-FU antisense therapy. The inhibitory effect toward brain tumors was evaluated by MTT assay, and measurements of cell apoptosis and invasion using the human brain glioma cell line U251. PAMAM could be simultaneously loaded with 5-FU and as-miR-21, forming a complex smaller than 100 nm in diameter. Both the chemotherapeutant and as-miR-21 could be efficiently introduced into tumor cells. The co-delivery of as-miR-21 significantly improved the cytotoxicity of 5-FU and dramatically increased the apoptosis of U251 cells, while the migration ability of the tumor cells was decreased. These results suggest that our co-delivery system may have important clinical applications in the treatment of miR-21-overexpressing glioblastoma.

Circular RNA (circRNA) is mainly generated by the splice donor of a downstream exon joining to an upstream splice acceptor, a phenomenon known as backsplicing. It has been reported that circRNA can function as microRNA (miRNA) sponges, transcriptional regulators, or potential biomarkers. The availability of massive non-polyadenylated transcriptomes data has facilitated the genome-wide identification of thousands of circRNAs. Several circRNA detection tools or pipelines have recently been developed, and it is essential to provide useful guidelines on these pipelines for users, including a comprehensive and unbiased comparison. Here, we provide an improved and easy-to-use circRNA read simulator that can produce mimicking backsplicing reads supporting circRNAs deposited in CircBase. Moreover, we compared the performance of 11 circRNA detection tools on both simulated and real datasets. We assessed their performance regarding metrics such as precision, sensitivity, F1 score, and Area under Curve. It is concluded that no single method dominated on all of these metrics. Among all of the state-of-the-art tools, CIRI, CIRCexplorer, and KNIFE, which achieved better balanced performance between their precision and sensitivity, compared favorably to the other methods.

Replication origins (oriCs) of bacterial genomes currently available in GenBank have been predicted by using a systematic method comprising the Z-curve analysis for nucleotide distribution asymmetry, DnaA box distribution, genes adjacent to candidate oriCs and phylogenetic relationships. These oriCs are organized into a MySQL database, DoriC, which provides extensive information and graphical views of the oriC regions. In addition, users can Blast a query sequence or even a whole genome against DoriC to find a homologous one. DoriC will be updated timely and the latest version is DoriC 1.8, in which oriCs of 425 genomes (468 chromosomes) are identified.

BACKGROUND

DoriC can be accessed from http://tubic.tju.edu.cn/doric/.

BACKGROUND

Supplementary data are available at http://tubic.tju.edu.cn/doric/supplementary.htm.

Danshensu (3-(3,4-dihydroxyphenyl) lactic acid) and salvianolic acid B, two natural phenolic acids of caffeic acid derivatives isolated from Salvia miltiorrhiza root of the most widely used traditional Chinese medicine for the treatment of various cardiovascular diseases, have been reported to have potential protective effects from oxidative injury. To better understand their biological functions, the in vitro radical scavenging and antioxidant activities of danshensu and salvianolic acid B were evaluated along with vitamin C. Both danshensu and salvianolic acid B exhibited higher scavenging activities against free hydroxyl radicals (HO()), superoxide anion radicals (O(2)(-)), 1,1-diphenyl-2-picryl-hydrazyl (DPPH) radicals and 2-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radicals than vitamin C. In contrary, danshensu and salvianolic acid B showed weaker iron chelating and hydrogen peroxide (H(2)O(2)) scavenging activities than vitamin C. As expressed as vitamin C equivalent capacity (VCEAC), the relative VCEAC values (mg/100ml) were in the order of salvianolic acid B (18.59)>> danshensu (12.89)>> vitamin C (10.00) by ABTS radical assay. The protective efficiencies against hydrogen peroxide induced human vein vascular endothelial cell damage were correlated with their antioxidant activities. Analysis of structure-activity relationship of these two compounds showed that the condensation and conjugation of danshensu and caffeic acid appears important for antioxidant activity. These results indicated that danshensu and salvianolic acid B are efficient radical scavengers and antioxidants, and salvianolic acid B is superior to danshensu. Their radical scavenging and antioxidant properties might have potential applications in food and healthcare industry.

Traditional radiomics models mainly rely on explicitly-designed handcrafted features from medical images. This paper aimed to investigate if deep features extracted via transfer learning can generate radiomics signatures for prediction of overall survival (OS) in patients with Glioblastoma Multiforme (GBM). This study comprised a discovery data set of 75 patients and an independent validation data set of 37 patients. A total of 1403 handcrafted features and 98304 deep features were extracted from preoperative multi-modality MR images. After feature selection, a six-deep-feature signature was constructed by using the least absolute shrinkage and selection operator (LASSO) Cox regression model. A radiomics nomogram was further presented by combining the signature and clinical risk factors such as age and Karnofsky Performance Score. Compared with traditional risk factors, the proposed signature achieved better performance for prediction of OS (C-index = 0.710, 95% CI: 0.588, 0.932) and significant stratification of patients into prognostically distinct groups (P < 0.001, HR = 5.128, 95% CI: 2.029, 12.960). The combined model achieved improved predictive performance (C-index = 0.739). Our study demonstrates that transfer learning-based deep features are able to generate prognostic imaging signature for OS prediction and patient stratification for GBM, indicating the potential of deep imaging feature-based biomarker in preoperative care of GBM patients.

MicroRNAs (miRNAs) are often deregulated in cancer and are thought to play an important role in cancer development. Large amount of differentially expressed miRNAs have been identified in various cancers by using high-throughput methods. It is therefore quite important to make a comprehensive collection of these miRNAs and to decipher their roles in oncogenesis and tumor progression. In 2010, we presented the first release of dbDEMC, representing a database for collection of differentially expressed miRNAs in human cancers obtained from microarray data. Here we describe an update of the database. dbDEMC 2.0 documents 209 expression profiling data sets across 36 cancer types and 73 subtypes, and a total of 2224 differentially expressed miRNAs were identified. An easy-to-use web interface was constructed that allows users to make a quick search of the differentially expressed miRNAs in certain cancer types. In addition, a new function of 'meta-profiling' was added to view differential expression events according to user-defined miRNAs and cancer types. We expect this database to continue to serve as a valuable source for cancer investigation and potential clinical application related to miRNAs. dbDEMC 2.0 is freely available at http://www.picb.ac.cn/dbDEMC.