Department of Biological Sciences

Department of Biological Sciences
Science Building, Block A (SA)
Xi'an Jiaotong-Liverpool University
111 Ren'ai Road Suzhou Dushu Lake Science and Education Innovation District , Suzhou Industrial Park
Suzhou,Jiangsu Province,P. R. China,215123
1. Detection of human IgM and IgG antibodies by means of galactofuranose-coated and rhamnose-coated gold nanoparticles

Author:Wang, Xinyue; Chen, Huaiyong; Chiodo, Fabrizio; Tefsen, Boris


Abstract:Many infectious diseases lack cheap, fast, and reliable serodiagnostic tools. Recently, glycans coupled to gold nanoparticles (GNPs) have shown potential to fill this void by utilizing them as a coating in ELISA experiments. In this study, we used GNPs functionalized either with galactofuranose (Galf), rhamnose (Rhap) or a mixture of these monosaccharides to detect the presence of IgM and IgG antibodies against these non-human carbohydrates in sera obtained from tuberculosis patients and control groups. Our findings confirm the wide abundance of anti-Rhap antibodies in humans and show for the first time the presence of anti-Galf antibodies in human sera. This study supports further investigation of using GNP-ELISA with microbe-specific carbohydrates for serodiagnosis of infectious diseases.
2. Production of "biobetter" variants of glucarpidase with enhanced enzyme activity

Author:Al-Qahtani, AD;Bashraheel, SS;Rashidi, FB;O'Connor, CD;Romero, AR;Domling, A;Goda, SK


Abstract:Glucarpidase, also known as carboxypeptidase G(2), is a Food and Drug Administration-approved enzyme used in targeted cancer strategies such as antibody-directed enzyme prodrug therapy (ADEPT). It is also used in drug detoxification when cancer patients have excessive levels of the anti-cancer agent methotrexate. The application of glucarpidase is limited by its potential immunogenicity and limited catalytic efficiency. To overcome these pitfalls, mutagenesis was applied to the glucarpidase gene of Pseudomonas sp. strain RS-16 to isolate three novels "biobetter" variants with higher specific enzyme activity. DNA sequence analysis of the genes for the variants showed that each had a single point mutation, resulting in the amino acid substitutions: I100 T, G123S and T239 A. K-m, V-max and K-cat measurements confirmed that each variant had increased catalytic efficiency relative to wild type glucarpidase. Additionally, circular dichroism studies indicated that they had a higher alpha-helical content relative to the wild type enzyme. However, three different software packages predicted that they had reduced protein stability, which is consistent with having higher activities as a tradeoff. The novel glucarpidase variants presented in this work could pave the way for more efficient drug detoxification and might allow dose escalation during chemotherapy. They also have the potential to increase the efficiency of ADEPT and to reduce the number of treatment cycles, thereby reducing the risk that patients will develop antibodies to glucarpidase.
3. Clinical features and outcomes of adult COVID-19 patients co-infected with Mycoplasma pneumoniae

Author:Zha, L;Shen, J;Tefsen, B;Wang, YJ;Lu, WH;Xu, QC


4. Tethering tissue inhibitors of metalloproteinase (TIMP) to the cell surface for enhanced activity against cervical cancer cell (HeLa) progression

Author:Lee, MH;Jiang, BJ;Tsigkou, A


5. Neutralizing and non-neutralizing antibody responses in HIV-1 subtype C chronically infected patients with divergent rates of disease progression

Author:Archary, D;Rong, R;Gordon, ML;Boliar, S;Gray, ES;Dugast, A;Hermanus, T;Goulder, PJ;Coovadia, HM;Morris, L;Alter, G;Derdeyn, CA;Ndung'u, T


6. Predict Epitranscriptome Targets and Regulatory Functions of N-6-Methyladenosine (m(6)A) Writers and Erasers

Author:Song, YY;Xu, QR;Wei, Z;Zhen, D;Su, JL;Chen, KQ;Meng, J


Abstract:Currently, although many successful bioinformatics efforts have been reported in the epitranscriptomics field for N-6-methyladenosine (m(6)A) site identification, none is focused on the substrate specificity of different m(6)A-related enzymes, ie, the methyltransferases (writers) and demethylases (erasers). In this work, to untangle the target specificity and the regulatory functions of different RNA m6A writers (METTL3-METT14 and METTL16) and erasers (ALKBH5 and FTO), we extracted 49 genomic features along with the conventional sequence features and used the machine learning approach of random forest to predict their epitranscriptome substrates. Our method achieved reasonable performance on both the writer target prediction (as high as 0.918) and the eraser target prediction (as high as 0.888) in a 5-fold crossvalidation, and results of the gene ontology analysis of their preferential targets further revealed the functional relevance of different RNA methylation writers and erasers.
7. Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia

Author:Nash, HC;Wirdateti;Low, GW;Choo, SW;Chong, JL;Semiadi, G;Hari, R;Sulaiman, MH;Turvey, ST;Evans, TA;Rheindt, FE


Abstract:The use of genome-wide genetic markers is an emerging approach for informing evidence-based management decisions for highly threatened species. Pangolins are the most heavily trafficked mammals across illegal wildlife trade globally, but critically endangered Sunda pangolins (Manis javanica) have not been widely studied in insular Southeast Asia. We used > 12,000 single nucleotide polymorphic markers (SNPs) to assign pangolin seizures from illegal trade of unknown origin to possible geographic sources via genetic clustering with pangolins of known origin. Our SNPs reveal three previously unrecognized genetic lineages of Sunda pangolins, possibly from Borneo, Java and Singapore/Sumatra. The seizure assignments suggest the majority of pangolins were traded from Borneo to Java. Using mitochondrial markers did not provide the same resolution of pangolin lineages, and to explore if admixture might explain these differences, we applied sophisticated tests of introgression using > 2000 SNPs to investigate secondary gene flow between each of the three Sunda pangolin lineages. It is possible the admixture which we discovered is due to human-mediated movements of pangolins. Our findings impact a range of conservation actions, including tracing patterns of trade, repatriation of rescue animals, and conservation breeding. In order to conserve genetic diversity, we suggest that, pending further research, each pangolin lineage should as a precaution be protected and managed as an evolutionarily distinct conservation unit.
8. P2X7 receptor regulates CSD and CSD-induced TNF-alpha induction

Author:Ma, DQ;Bu, F;Jiang, LW;Quinn, JP;Wang, MY


9. Combined effects of seasonality and stagnation on tap water quality: Changes in chemical parameters, metabolic activity and co-existence in bacterial community

Author:Zhang, HH;Xu, L;Huang, TL;Yan, MM;Liu, KW;Miao, YT;He, HY;Li, SL;Sekar, R


Abstract:In drinking water distribution pipeline systems, the tap water quality is regulated by several biotic and abiotic factors, which can threaten the health of consumers. Stagnation is inevitable in the water distribution pipeline however, the combined effects of seasonal changes and stagnation on tap water quality are not well understood. Here, we investigated the seasonal variations in the chemical and biological quality of water after overnight stagnation for a period of one year. The results showed that the tap water quality deteriorated after overnight stagnation, with up to a 2.7-fold increase in the total iron concentrations. The total bacterial cell concentrations increased by 59-231%% after overnight stagnation. The total cell and cell-bound adenosine triphosphate (ATP) of the stagnant water samples peaked in summer. In addition, Biolog analysis showed that the metabolic activities of microbes were higher in spring. The bacterial community based on Illumina Miseq DNA sequence analysis found that Proteobacteria dominated the drinking water bacterial community. The bacterial community structure varied significantly among different seasons, where the diversity and richness of the community were much higher in spring. Structural equation modeling (SEM) was constructed to determine the correlations between bacterial metabolic functions and the community structure. The redundancy analysis (RDA) indicated that the residual chlorine played a critical role in the construction of the bacterial community. Altogether, the overall findings from the present work provide novel insights into how the quality of tap water quality impacted by the seasonal changes and overnight stagnation.
10. Plant-Derived Tick Repellents Activate the Honey Bee Ectoparasitic Mite TRPA1

Author:Peng, GD;Kashio, M;Morimoto, T;Li, TB;Zhu, JT;Tominaga, M;Kadowaki, T

Source:CELL REPORTS,2015,Vol.12

Abstract:We have identified and characterized the TRPA1 channel of Varroa destructor (VdTRPA1), a major ectoparasitic mite of honey bee. One of the two VdTRPA1 isoforms, VdTRPA1L, was activated by a variety of plant-derived compounds, including electrophilic compounds, suggesting that chemical activation profiles are mostly shared between arthropod TRPA1 channels. Nevertheless, carvacrol and alpha-terpineol activated VdTRPA1L but not a honey bee noxious-stimuli-sensitive TRPA, AmHsTRPA, and Drosophila melanogaster TRPA1. Activation of VdTRPA1L in D. melanogaster taste neurons by the above compounds was sufficient to modify the gustatory behaviors. Carvacrol and a-terpineol repelled V. destructor in a laboratory assay, and a-terpineol repressed V. destructor entry for reproduction into the brood cells in hives. Understanding the functions of parasite TRP channels not only gives clues about the evolving molecular and cellular mechanisms of parasitism but also helps in the development of control methods.
11. Topological Characterization of Human and Mouse m(5)C Epitranscriptome Revealed by Bisulfite Sequencing

Author:Wei, Z;Panneerdoss, S;Timilsina, S;Zhu, JT;Mohammad, TA;Lu, ZL;de Magalhaes, JP;Chen, YD;Rong, R;Huang, YF;Rao, MK;Meng, J


Abstract:Background. Compared with the well-studied 5-methylcytosine (m(5)C) in DNA, the role and topology of epitranscriptome m(5)C remain insufficiently characterized. Results. Through analyzing transcriptome-wide m(5)C distribution in human and mouse, we show that the m(5)C modification is significantly enriched at 5' untranslated regions (5' UTRs) of mRNA in human and mouse. With a comparative analysis of the mRNA and DNA methylome, we demonstrate that, like DNA methylation, transcriptome m(5)C methylation exhibits a strong clustering effect. Surprisingly, an inverse correlation between mRNA and DNA m(5)C methylation is observed at CpG sites. Further analysis reveals that RNA m(5)C methylation level is positively correlated with both RNA expression and RNA half-life. We also observed that the methylation level of mitochondrial RNAs is significantly higher than RNAs transcribed from the nuclear genome. Conclusions. This study provides an in-depth topological characterization of transcriptome-wide m(5)C modification by associating RNA m(5)C methylation patterns with transcriptional expression, DNA methylations, RNA stabilities, and mitochondrial genome.
12. Src Family Kinases in the Central Nervous System: Their Emerging Role in Pathophysiology of Migraine and Neuropathic Pain

Author:Nie, LD;Ye, WR;Chen, SB;Chirchiglia, D;Wang, MY


Abstract:Src family kinases (SFK) are a group of non-receptor tyrosine kinases which play a pivotal role in cellular responses and oncogenesis. Accumulating evidence suggest that SFK also act as a key component in signalling pathways of the central nervous system (CNS) in both physiological and pathological conditions. Despite the crucial role of SFK in signal transduction of the CNS, the relationship between SFK and molecules implicated in pain has been relatively unexplored. This article briefly reviews the recent advances uncovering the interplay of SFK with diverse membrane proteins and intracellular proteins in the CNS and the importance of SFK in the pathophysiology of migraine and neuropathic pain. Mechanisms underlying the role of SFK in these conditions and potential clinical applications of SFK inhibitors in neurological diseases are also summarised. We propose that SFK are the convergent point of signalling pathways in migraine and neuropathic pain and may constitute a promising therapeutic target for these diseases.
13. Identification and functional analysis of two Golgi-localized UDP-galactofuranose transporters with overlapping functions in Aspergillus niger

Author:Park, J;Tefsen, B;Heemskerk, MJ;Lagendijk, EL;van den Hondel, CAMJJ;van Die, I;Ram, AFJ

Source:BMC MICROBIOLOGY,2015,Vol.15

Abstract:Background: Galactofuranose (Galf)-containing glycoconjugates are present in numerous microbes, including filamentous fungi where they are important for morphology, virulence and maintaining cell wall integrity. The incorporation of Galf-residues into galactomannan, galactomannoproteins and glycolipids is carried out by Golgi-localized Galf transferases. The nucleotide sugar donor used by these transferases (UDP-Galf) is produced in the cytoplasm and has to be transported to the lumen of the Golgi by a dedicated nucleotide sugar transporter. Methods: Based on homology with recently identified UDP-Galf-transporters in A. fumigatus and A. nidulans, two putative UDP-Galf-transporters in A. niger were found. Their function and localization was determined by gene deletions and GFP-tagging studies, respectively. Results: The two putative UDP-Galf-transporters in A. niger are homologous to each other and are predicted to contain eleven transmembrane domains (UgtA) or ten transmembrane domains (UgtB) due to a reduced length of the C-terminal part of the UgtB protein. The presence of two putative UDP-Galf-transporters in the genome was not unique for A. niger. From the twenty Aspergillus species analysed, nine species contained two additional putative UDP-Galf-transporters. Three of the nine species were outside the Aspergillus section nigri, indication an early duplication of UDP-Galf-transporters and subsequent loss of the UgtB copy in several aspergilli. Deletion analysis of the single and double mutants in A. niger indicated that the two putative UDP-Galf-transporters (named UgtA and UgtB) have a redundant function in UDP-Galf-transport as only the double mutant displayed a Galf-negative phenotype. The Galf-negative phenotype of the double mutant could be complemented by expressing either CFP-UgtA or CFP-UgtB fusion proteins from their endogenous promoters, indicating that both CFP-tagged proteins are functional. Both Ugt proteins co-localize with each other as well as with the GDP-mannose nucleotide transporter, as was demonstrated by fluorescence microscopy, thereby confirming their predicted localization in the Golgi. Conclusion: A. niger contains two genes encoding UDP-Galf-transporters. Deletion and localization studies indicate that UgtA and UgtB have redundant functions in the biosynthesis of Galf-containing glycoconjugates.
14. Molecular Identification of Chronic Bee Paralysis Virus Infection in Apis mellifera Colonies in Japan

Author:Morimoto, T;Kojima, Y;Yoshiyama, M;Kimura, K;Yang, B;Kadowaki, T


Abstract:Chronic bee paralysis virus (CBPV) infection causes chronic paralysis and loss of workers in honey bee colonies around the world. Although CBPV shows a worldwide distribution, it had not been molecularly detected in Japan. Our investigation of Apis mellifera and Apis cerana japonica colonies with RT-PCR has revealed CBPV infection in A. mellifera but not A. c. japonica colonies in Japan. The prevalence of CBPV is low compared with that of other viruses: deformed wing virus (DWV), black queen cell virus (BQCV), Israel acute paralysis virus (IAPV), and sac brood virus (SBV), previously reported in Japan. Because of its low prevalence (5.6%%) in A. mellifera colonies, the incidence of colony losses by CBPV infection must be sporadic in Japan. The presence of the (-) strand RNA in dying workers suggests that CBPV infection and replication may contribute to their symptoms. Phylogenetic analysis demonstrates a geographic separation of Japanese isolates from European, Uruguayan, and mainland US isolates. The lack of major exchange of honey bees between Europe/mainland US and Japan for the recent 26 years (1985-2010) may have resulted in the geographic separation of Japanese CBPV isolates.
15. Mapping the T cell response to COVID-19

Author:Li Junwei;Wang Junhua;Kang Angray S;Sacitharan Pradeep Kumar

Source:Signal Transduction and Targeted Therapy,2020,Vol.5

Abstract:A recent article by Grifoni et al. elegantly demonstrated the ability to measure and understand the human CD4+ and CD8+ T cell responses to SARS-CoV-2 infection. These findings highlighted below gave new insights into the immunopathogenesis of COVID-19, the crossreactivity of the SARS-CoV-2 infections, the potential targets of T cells, and for vaccine design.
16. Goji Berries as a Potential Natural Antioxidant Medicine: An Insight into Their Molecular Mechanisms of Action

Author:Ma, ZF;Zhang, HX;Teh, SS;Wang, CW;Zhang, YT;Hayford, F;Wang, LY;Ma, T;Dong, ZH;Zhang, Y;Zhu, YF


Abstract:Goji berries (Lycium fruits) are usually found in Asia, particularly in northwest regions of China. Traditionally, dried goji berries are cooked before they are consumed. They are commonly used in Chinese soups and as herbal tea. Moreover, goji berries are used for the production of tincture, wine, and juice. Goji berries are high antioxidant potential fruits which alleviate oxidative stress to confer many health protective benefits such as preventing free radicals from damaging DNA, lipids, and proteins. Therefore, the aim of the review was to focus on the bioactive compounds and pharmacological properties of goji berries including their molecular mechanisms of action. The health benefits of goji berries include enhancing hemopoiesis, antiradiation, antiaging, anticancer, improvement of immunity, and antioxidation. There is a better protection through synergistic and additive effects in fruits and herbal products from a complex mixture of phytochemicals when compared to one single phytochemical.

Author:Dong, XF;Chaisiri, K;Donnelly, MJ;McGarry, JW;Kadowaki, T;Darby, AC;Makepeace, BL


18. Comparative genome analyses of mycobacteria give better insights into their evolution

Author:Wee, WY;Dutta, A;Choo, SW

Source:PLOS ONE,2017,Vol.12

Abstract:Mycobacteria a genus of Actinobacteria are widespread in nature ranging from soil-dwelling saprophytes to human and animal pathogens. The rate of growth has been a classifying factor for the Mycobacterium spp., dividing them into the rapid growers and the slow growers. Here we have performed a comparative genome study of mycobacterial species in order to get better understanding of their evolution, particularly to understand the distinction between the rapid and slow growers. Our study shows that the slow growers had generally gained and lost more genes compared to the rapid growers. The slow growers might haved eventually lost genes (LivFGMH operon, shaACDEFG genes and MspA porin) that could contribute to the slow growth rate of the slow growers. The genes gained and lost in mycobacteria had eventually helped these bacteria to adapt to different environments and have led to the evolution of the present day rapid and slow growers. Our results also show high number of Mycobacterium abscessus specific genes (811 genes) and some of them are associated with the known bacterial quorum sensing genes that might be important for Mycobacterium abscessus to adapt and survive in variety of unfavorable environments. Mycobacterium abscessus also does not contains genes involved in the bacterial defense system and together with the quorum sensing genes may have contributed to the high gene gain rate of Mycobacterium abscessus.
19. Methodological approaches for studying the microbial ecology of drinking water distribution systems

Author:Douterelo, I;Boxall, JB;Deines, P;Sekar, R;Fish, KE;Biggs, CA

Source:WATER RESEARCH,2014,Vol.65

Abstract:The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects. (C) 2014 The Authors. Published by Elsevier Ltd.
20. Assessing the wellbeing of Chinese university students: validation of a Chinese version of the college student subjective wellbeing questionnaire

Author:Zhang, Y;Carciofo, R

Source:BMC PSYCHOLOGY,2021,Vol.9

Abstract:Background In response to the rising concern with promoting the wellbeing of university students and relative lack of domain-specific wellbeing measurement instruments in China, the current study aimed to validate a Chinese version of the College Student Subjective Wellbeing Questionnaire (CSSWQ), a 16-item self-report English-language rating scale assessing four aspects of wellbeing (academic satisfaction, academic efficacy, school connectedness, and college gratitude). Methods The Chinese translation of the CSSWQ, the Students' Life Satisfaction Scale, the Positive and Negative Affect Schedule, the 10-Item Big Five Personality Inventory, and demographic questions were completed by 252 Chinese students at a university in Suzhou, China. Results Exploratory factor analysis found four factors each with the same four items as in the original English scale. Each subscale showed good internal consistency. Test-retest for a one-month interval showed generally moderate reliability. As predicted, Pearson correlational analysis found positive correlations between the Chinese CSSWQ and life satisfaction, positive affect, extraversion, and GPA, and negative correlations with neuroticism and negative affect. Monthly income had small negative correlations with academic satisfaction and academic efficacy, smoking had a small positive correlation with school connectedness, and exercise had a small positive correlation with academic efficacy. Conclusion Data for the Chinese CSSWQ in the current study showed validity and reliability, supporting the use of this instrument as a measurement of college student wellbeing in China.
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