Jing Lu

Guangdong Provincial Institute of Automation, Guangdongdi, Heilongjiang Sheng, China

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Publications (45)158.95 Total impact

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    ABSTRACT: Since early 2013, H7N9-subtype avian influenza virus (AIV) has caused human infection in eastern China. To evaluate AIV contamination and the public risk of infection, we systematically implemented environmental sampling from live poultry markets in Guangdong Province. Through real-time polymerase chain reaction assays and next-generation sequencing, we generated full nucleotide sequences of all 10 H6N6 AIVs isolated during sampling. Focusing on sequence analyses of hemagglutinin genes of the 10 H6N6 AIVs revealed that the viruses were low pathogenic AIVs with the typical hemagglutinin cleavage site of P-Q-I-E-T-R-G. The hemagglutinin, neuraminidase, and nucleocapsid genes of nine AIVs were of ST2853-like (H6-subtype) lineage, ST192-like (N6-subtype) lineage, and HN573-like (H6-subtype) lineage, respectively; whereas the other five genes were of ST339-like (H6-subtype) lineage. However, the polymerase PB2 and nucleocapsid genes of one strain (HZ057) were of GS/GD-like (H5N1-subtype) and ST339-like lineages. Phylogenic analysis revealed that all eight genes of the 10 viruses belonged to Eurasian avian lineage. Altogether, the 10 AIVs were reassortants of different genetic groups of exchanges with the same virus subtype, thus illustrating the genetic diversity and complexity of H6N6-subtype AIVs in Guangdong Province.
    No preview · Article · Feb 2016 · Frontiers in Microbiology
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    ABSTRACT: Lung cancer, characterized by uncontrolled cell growth in the lung tissue, is the leading cause of global cancer deaths. Until now, effective treatment of this disease is limited. Many synthetic compounds have emerged with the advancement of combinatorial chemistry. Identification of effective lung cancer candidate drug compounds among them is a great challenge. Thus, it is necessary to build effective computational methods that can assist us in selecting for potential lung cancer drug compounds. In this study, a computational method was proposed to tackle this problem. The chemical-chemical interactions and chemical-protein interactions were utilized to select candidate drug compounds that have close associations with approved lung cancer drugs and lung cancer-related genes. A permutation test and K-means clustering algorithm were employed to exclude candidate drugs with low possibilities to treat lung cancer. The final analysis suggests that the remaining drug compounds have potential anti-lung cancer activities and most of them have structural dissimilarity with approved drugs for lung cancer.
    Full-text · Article · Feb 2016 · Journal of biomolecular Structure & Dynamics
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    ABSTRACT: The development of biochemistry and molecular biology has revealed an increasingly important role of compounds in several biological processes. Like the aptamer-protein interaction, aptamer-compound interaction attracts increasing attention. However, it is time-consuming to select proper aptamers against compounds using traditional methods, such as exponential enrichment. Thus, there is an urgent need to design effective computational methods for searching effective aptamers against compounds. This study attempted to extract important features for aptamer-compound interactions using feature selection methods, such as Maximum Relevance Minimum Redundancy, as well as incremental feature selection. Each aptamer-compound pair was represented by properties derived from the aptamer and compound, including frequencies of single nucleotides and dinucleotides for the aptamer, as well as the constitutional, electrostatic, quantum-chemical, and space conformational descriptors of the compounds. As a result, some important features were obtained. To confirm the importance of the obtained features, we further discussed the associations between them and aptamer-compound interactions. Simultaneously, an optimal prediction model based on the nearest neighbor algorithm was built to identify aptamer-compound interactions, which has the potential to be a useful tool for the identification of novel aptamer-compound interactions. The program is available upon the request.
    No preview · Article · Feb 2016

  • No preview · Article · Dec 2015 · Clinical Infectious Diseases
  • Jing Lu · Pin Zhang · Yi Bi · Xiaomin Luo
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    ABSTRACT: Drug-target interaction is an important topic in drug discovery and drug repositioning. KEGG database offers a drug annotation and classification using a target-based classification system. In this study, we gave an investigation on five target-based classes: (I) G protein-coupled receptors; (II) Nuclear receptors; (III) Ion channels; (IV) Enzymes; (V) Pathogens, using molecular descriptors to represent each drug compounds. Two popular feature selection methods, maximum relevance minimum redundancy and incremental feature selection, were adopted to extract the important descriptors. Meanwhile, an optimal prediction model based on nearest neighbor algorithm was constructed, which got the best result in identifying drug target-based classes. Finally, some key descriptors were discussed to uncover their important roles in the identification of drug-target classes.
    No preview · Article · Nov 2015 · Combinatorial chemistry & high throughput screening

  • No preview · Article · Sep 2015 · Letters in Drug Design & Discovery
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    ABSTRACT: Cancer is one of the leading causes of human death. Based on current knowledge, one of the causes of cancer is exposure to toxic chemical compounds, including radioactive compounds, dioxin, and arsenic. The identification of new carcinogenic chemicals may warn us of potential danger and help to identify new ways to prevent cancer. In this study, a computational method was proposed to identify potential carcinogenic chemicals, as well as non-carcinogenic chemicals. According to the current validated carcinogenic and non-carcinogenic chemicals from the CPDB (Carcinogenic Potency Database), the candidate chemicals were searched in a weighted chemical network constructed according to chemical-chemical interactions. Then, the obtained candidate chemicals were further selected by a randomization test and information on chemical interactions and structures. The analyses identified several candidate carcinogenic chemicals, while those candidates identified as non-carcinogenic were supported by a literature search. In addition, several candidate carcinogenic/non-carcinogenic chemicals present structural dissimilarity with validated carcinogenic/non-carcinogenic chemicals.
    Full-text · Article · Jul 2015 · Molecular BioSystems
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    ABSTRACT: In the past decade, the most prevalent norovirus genotype causing viral gastroenteritis outbreaks worldwide, including China, has been GII.4. In winter 2014-15, norovirus outbreaks in Guangdong, China, increased. Sequence analysis indicated that 82% of the outbreaks were caused by a norovirus GII.17 variant.
    Full-text · Article · Jul 2015 · Emerging infectious diseases
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    ABSTRACT: Nitric oxide (NO) and its auto-oxidation products are known to disrupt normal bacterial function and NO releasing molecules have the potential to be developed as antibacterial leads in drug discovery. We have designed and synthesized a series of novel nitrated compounds by combining NO releasing groups with ocotillol-type triterpenoids, which have previously demonstrated activity only against Gram-positive bacteria. The in vitro NO release capacity and antibacterial activity were sequentially evaluated and the data showed that most of the synthesized compounds could release nitric oxide. Compound 16a, 17a and 17c, with nitrated aliphatic esters at C-3 position, displayed higher NO release than other analogues, correlating to their good antibacterial activity, in which 17c demonstrated broad-spectrum activity against both Gram positive and -negative bacteria, as well as excellent synergism at sub-minimum inhibitory concentration when using with kanamycin and chloramphenicol. Furthermore, the epifluorescent microscopic study indicated that the ocotillol-type triterpenoid core may induce NO release on the bacterial membrane. Our results demonstrate that nitrated substitutions at C-3 of ocotillol-type derivatives could provide an approach to expand their antibacterial spectrum, and that ocotillol-type triterpenoids may also be developed as appropriate carriers for NO donors in antibacterial agent discovery with low cytotoxicity. Copyright © 2015 Elsevier Masson SAS. All rights reserved.
    No preview · Article · Jun 2015 · European Journal of Medicinal Chemistry
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    ABSTRACT: Enterovirus A71 (EVA71) and Coxsackievirus A16 (CVA16) are regarded as the two major causative pathogens in hand, foot and mouth disease (HFMD) epidemics. However, CVA6, previously largely ignored, became the predominant pathogen in China in 2013. In this study, we describe the epidemiological trendsofCVA6 during the annual HFMD outbreaks from 2008 to 2013 in Guangdong, China. The study results show that CVA6 has been one of three major causative agents of HFMD epidemics since 2009. The periodic rotation and dominance of the three pathogens, EVA71, CVA16 and CVA6, may have contributed to the continuously increasing HFMD epidemics. Moreover, phylogenetic analysis of the VP1 gene shows that major circulating CVA6 strains collected from 2009 to 2013 are distinct from the earlier strains collected before 2009. In conclusion, the discovery from this research investigating epidemiological trends of CVA6 from 2008 to 2013 explains the possible pattern of the continuous HFMD epidemic in China. The etiological change pattern also highlights the need for improvement for pathogen surveillance and vaccine strategies for HFMD control in China.
    Full-text · Article · May 2015 · Scientific Reports
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    ABSTRACT: Drug-target interaction (DTI) is a key aspect in pharmaceutical research. With the ever-increasing new drug data resources, computational approaches have emerged as powerful and labor-saving tools in predicting new DTIs. However, so far, most of these predictions have been based on structural similarities rather than biological relevance. In this study, we proposed for the first time a " GO and KEGG enrichment score " method to represent a certain category of drug molecules by further classification and interpretation of the DTI database. A benchmark dataset consisting of 2,015 drugs that are assigned to nine categories ((1) G protein-coupled receptors, (2) cytokine receptors, (3) nuclear receptors, (4) ion channels , (5) transporters, (6) enzymes, (7) protein kinases, (8) cellular antigens and (9) pathogens) was constructed by collecting data from KEGG. We analyzed each category and each drug for its contribution in GO terms and KEGG pathways using the popular feature selection " minimum redundancy maximum relevance (mRMR) " method, and key GO terms and KEGG pathways were extracted. Our analysis revealed the top enriched GO terms and KEGG pathways of each drug category, which were highly enriched in the literature and clinical trials. Our results provide for the first time the biological relevance among drugs, targets and biological functions, which serves as a new basis for future DTI predictions.
    Full-text · Article · May 2015 · PLoS ONE
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    ABSTRACT: A series of novel ocotillol-type furoxan derivatives was synthesized by coupling various furoxans to 3-OH of 6-deoxy ocotillol, and their in vitro nitric oxide (NO) releasing capability was studied. The discharge of NO was examined after 30 min at two different concentrations, the results showed that all of the compounds tested could release NO in a dose-dependent manner. All of the synthesized compounds released similar amounts of NO at 100 μM, whereas at 500 μM these compounds showed more difference, in which compound II1, II3, II4, III2 displayed higher potency in releasing NO at this concentration. Analysis of the in vitro data showed that the derivatives bearing the same furoxan group on different ocotillol cores possessed various NO releasing capacity, suggesting that the structure of carrier of NO releasing groups may affect the NO release. Indeed, except compound II2, 24(S)-6-deoxy ocotillol derivatives from compound 6 with different furoxan substitutions at 3-OH and III2 displayed enhanced NO releasing capacity, compared to other compounds derived from compounds 5 and 9. The results illustrated that the functional group and the stereochemistry on the ocotillol structure may affect the NO release of furoxans.
    No preview · Article · Apr 2015 · Pharmazie
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    ABSTRACT: Classification for enzymes is essential for understanding the functions of organisms because it is directly related to the knowledge about which specific target it acts on, as well as to its catalytic process. Hence, it is crucial to use an accurate and robust approach to correctly map the enzyme in specific enzyme family class that it is belong to. In this research, a protein-protein interaction (PPI) network-based method was developed for predicting the families of enzyme. As a demonstration, the overall success rate by the jackknife test in identifying enzyme’s family class was 62.86%. The promising results imply that the predictor as presented in this paper may become a useful tool for studying enzymes.
    No preview · Article · Feb 2015 · Current Bioinformatics
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    ABSTRACT: An aseptic meningitis outbreak occurred in Luoding City of Guangdong, China in 2012, and Echovirus type 30 (ECHO30) was identified as the major causative pathogen. Environmental surveillance indicated that ECHO30 was detected in the sewage of a neighboring city, Guangzhou, from 2010-2012 and also occurred in Luoding City sewage samples (6/43, 14%) collected after the outbreak. In order to track the potential origin of the outbreak viral strains, we sequenced VP1 of 29 viral strains from clinical patients and environmental samples. Sequences alignments and phylogenetic analyses based on VP1 gene sequences revealed that virus strains isolated from the sewage of Guangzhou and Luoding cities match well the clinical strains from the outbreak with high nucleotide sequence similarity (98.5%-100%) and similar cluster distribution. Five ECHO30 clinical strains were clustered with the Guangdong environmental strains but separated from strains from other regions suggesting this sub-cluster of virus most likely originated from the circulating virus in Guangdong rather than being more recently imported from other regions. These findings underscore the importance of long-term, continuous environmental surveillance and genetic analysis to monitor circulating enteroviruses. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Full-text · Article · Jan 2015 · Applied and Environmental Microbiology
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    ABSTRACT: Triterpenoid saponins are involved in plant defense systems to inhibit bacterial invasion. A new series of hydrophilic ocotillol-type triterpenoid derivatives 5-26 have been synthesized with antibacterial activity against Gram-positive bacteria, including a community associated methicillin-resistant Staphylococcus aureus (CA-MRSA; strain USA300). From this series, compounds 6 and 15 were found to be the most active, both with MIC values of 2 μg/mL against B. subtilis 168 and 8 μg/mL against S. aureus USA300, respectively. Furthermore, subsequent assays showed that compounds 6 and 15 displayed strong synergistic effects at sub-MIC levels against both S. aureus USA300 and B. subtilis 168 when combined with two commercial antibiotics, kanamycin and chloramphenicol. Preliminary structure-activity relationship studies were also performed.
    No preview · Article · Jan 2015 · Records of Natural Products
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    ABSTRACT: Influenza A(H7N9) virus emerged in eastern China in February 2013 and continues to circulate in this region, but its ecology is poorly understood. In April 2013, the Guangdong Provincial Center for Disease Control and Prevention (CDC) implemented environmental and human syndromic surveillance for the virus. Environmental samples from poultry markets in 21 city CDCs (n = 8,942) and respiratory samples from persons with influenza-like illness or pneumonia (n = 32,342) were tested; viruses isolated from 6 environmental samples and 16 patients were sequenced. Sequence analysis showed co-circulation of 4 influenza A(H7N9) virus strains that evolved by reassortment with avian influenza A(H9N2) viruses circulating in this region. In addition, an increase in human cases starting in late 2013 coincided with an increase in influenza A H7 virus isolates detected by environmental surveillance. Co-circulation of multiple avian influenza viruses that can infect humans highlights the need for increased surveillance of poultry and potential environmental sources.
    Full-text · Article · Dec 2014 · Emerging infectious diseases
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    ABSTRACT: Since its first identification, the epizootic avian influenza A H7N9 virus has continued to cause infections in China. Two waves were observed during this outbreak. No cases were reported from Guangdong Province during the first wave, but this province became one of the prime outbreak sites during the second wave. In order to identify the transmission potential of this continuously evolving infectious virus, our research group monitored all clusters of H7N9 infections during the second wave of the epidemic in Guangdong Province. Epidemiological, clinical, and virological data on these patients were collected and analyzed. Three family clusters including six cases of H7N9 infection were recorded. The virus caused severe disease in two adult patients but only mild symptoms for all four pediatric patients. All patients reported direct poultry or poultry market exposure history. Relevant environment samples collected according to their reported exposures tested H7N9 positive. Virus isolates from patients in the same cluster shared high sequence similarities. In conclusion, although continually evolving, the currently circulating H7N9 viruses in Guangdong Province have not yet demonstrated the capacity for efficient and sustained person-to-person transmission.
    Full-text · Article · Oct 2014 · Journal of Clinical Microbiology
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    Lei Chen · Jing Lu · Tao Huang · Jun Yin · Lai Wei · Yu-Dong Cai
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    ABSTRACT: Hepatitis C virus (HCV) is an infectious virus that can cause serious illnesses. Only a few drugs have been reported to effectively treat hepatitis C. To have greater diversity in drug choice and better treatment options, it is necessary to develop more drugs to treat the infection. However, it is time-consuming and expensive to discover candidate drugs using experimental methods, and computational methods may complement experimental approaches as a preliminary filtering process. This type of approach was proposed by using known chemical-chemical interactions to extract interactive compounds with three known drug compounds of HCV, and the probabilities of these drug compounds being able to treat hepatitis C were calculated using chemical-protein interactions between the interactive compounds and HCV target genes. Moreover, the randomization test and expectation-maximization (EM) algorithm were both employed to exclude false discoveries. Analysis of the selected compounds, including acyclovir and ganciclovir, indicated that some of these compounds had potential to treat the HCV. Hopefully, this proposed method could provide new insights into the discovery of candidate drugs for the treatment of HCV and other diseases.
    Full-text · Article · Sep 2014 · PLoS ONE
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    Preview · Article · Sep 2014 · Emerging infectious diseases
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    ABSTRACT: We describe the clinical and epidemiologic characteristics of 7 children infected with A/H7N9 in Guangdong Province during the winter of 2013-2014. Our results indicate that the mild or asymptomatic characteristics common in H7N9-infected children could pose challenges to our surveillance system becoming a hidden threat to the public health of China and the world.
    Full-text · Article · Jul 2014 · The Pediatric Infectious Disease Journal

Publication Stats

296 Citations
158.95 Total Impact Points

Institutions

  • 2015
    • Guangdong Provincial Institute of Automation
      Guangdongdi, Heilongjiang Sheng, China
  • 2014-2015
    • Yantai University
      • School of Pharmacy
      Chifu, Shandong Sheng, China
  • 2013-2015
    • Shanghai Research Institute of Materials
      Shanghai, Shanghai Shi, China
  • 2013-2014
    • Guangdong Center for Disease Control and Prevention
      Shengcheng, Guangdong, China
  • 2011-2014
    • Chinese Academy of Sciences
      • • Drug Discovery and Design Center
      • • State Key Laboratory of Drug Research
      Peping, Beijing, China
  • 2011-2012
    • The Chinese University of Hong Kong
      • Department of Medicine and Therapeutics
      Hong Kong, Hong Kong