Browsing by Author "Wang, X."
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Item Cytotoxic isoprenylated flavonoids from the roots of sophora flavescens.(Helvetica Chimica Acta, 2004) Ding, P.; Chen, D.; Bastow, K.F.; Nyarko, A.K.; Wang, X.; Lee, K.Three new flavonoids, which are isoprenylated by fused 2,2-dimethyl-3,4-dihydro-2H-pyran moieties, were isolated from the roots of Sophora flavescens and named flavenochromanes A–C (1–3). Their structures were elucidated by spectroscopic methods, including 2D-NMR techniques. Flavenochromane C (3) showed strong cytotoxic activity against A549 (lung carcinoma), 1A9 (ovarian carcinoma), KB (epidermoid carcinoma of the nasopharynx), and KB-Vin (drug-resistant variant KB) cell lines with IC50 values ≤1.7 μM, and significant activity against the MCF-7 (breast adenocarcinoma) cell line with an IC50 value of 3.6 μM. Flavenochromane B (2) displayed slightly lower inhibitory effects (IC50 3.2–6.9 μM) as compared with 3.Item Draft genome sequence of Streptomyces sp. strain CT34, isolated from a Ghanaian soil sample(Genome Announcements, 2015-02) Zhai, Y.; Cheng, B.; Hu, J.; Kyeremeh, K.; Wang, X.; Jaspars, M.; Deng, H.; Deng, Z.-X.; Hong, K.Presented here is a draft genome sequence of Streptomyces sp. strain CT34, which produces a novel ribosomally synthesized and posttranslationally modified peptide (RiPP). Analysis of the deduced open reading frame set identified the putative RiPP biosynthesis gene cluster, as well as other secondary metabolite gene clusters. © 2015 Zhai et al.Item Legonaridin, a new member of linaridin RiPP from a Ghanaian Streptomyces isolate(Organic and Biomolecular Chemistry, 2015-10) Rateb, M.E.; Zhai, Y.; Ehrner, E.; Rath, C.M.; Wang, X.; Tabudravu, J.; Ebel, R.; Bibb, M.; Kyeremeh, K.; Dorrestein, P.C.; Hong, K.; Jaspars, M.; Deng, H.Linaridins are rare linear ribosomally-synthesized and post-translationally modified peptides (RiPPs) and only two, cypemycin and SGR-1832, in this family have been identified so far. Legonaridin 1 has been discovered as a new member of linaridins through chemical isolation, peptidogenomics, comprehensive 1- and 2-D NMR and advanced Marfey's analyses from the soil bacterium Streptomyces sp. CT34, an isolate collected from Legon, Ghana. Bioinformatics analysis of the gene cluster suggested that the biosynthesis of legonaridin 1 is different from those of cypemycin and SGR-1832. Consistent with bioinformatics and peptidogenomics analyses, 1 has a total of nine post-modifications, 8 dehydrobutyrine residues and a N,N-dimethylated N-terminus with a carboxylic acid at the C-terminus. Legonaridin 1 is structurally different from the two known linaridins comprising a new subfamily. This is the first time that NMR spectroscopy is used to establish the 2-D structure of a linaridin RiPP.Item Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa(BioMed Central Ltd., 2018-05) Zhong, D.; Lo, E.; Wang, X.; Yewhalaw, D.; Zhou, G.; Atieli, H.E.; Githeko, A.; Hemming-Schroeder, E.; Lee, M.-C.; Afrane, Y.; Yan, G.Background: Parasite genetic diversity and multiplicity of infection (MOI) affect clinical outcomes, response to drug treatment and naturally-acquired or vaccine-induced immunity. Traditional methods often underestimate the frequency and diversity of multiclonal infections due to technical sensitivity and specificity. Next-generation sequencing techniques provide a novel opportunity to study complexity of parasite populations and molecular epidemiology. Methods: Symptomatic and asymptomatic Plasmodium vivax samples were collected from health centres/hospitals and schools, respectively, from 2011 to 2015 in Ethiopia. Similarly, both symptomatic and asymptomatic Plasmodium falciparum samples were collected, respectively, from hospitals and schools in 2005 and 2015 in Kenya. Finger-pricked blood samples were collected and dried on filter paper. Long amplicon (> 400 bp) deep sequencing of merozoite surface protein 1 (msp1) gene was conducted to determine multiplicity and molecular epidemiology of P. vivax and P. falciparum infections. The results were compared with those based on short amplicon (117 bp) deep sequencing. Results: A total of 139 P. vivax and 222 P. falciparum samples were pyro-sequenced for pvmsp1 and pfmsp1, yielding a total of 21 P. vivax and 99 P. falciparum predominant haplotypes. The average MOI for P. vivax and P. falciparum were 2.16 and 2.68, respectively, which were significantly higher than that of microsatellite markers and short amplicon (117 bp) deep sequencing. Multiclonal infections were detected in 62.2% of the samples for P. vivax and 74.8% of the samples for P. falciparum. Four out of the five subjects with recurrent P. vivax malaria were found to be a relapse 44-65 days after clearance of parasites. No difference was observed in MOI among P. vivax patients of different symptoms, ages and genders. Similar patterns were also observed in P. falciparum except for one study site in Kenyan lowland areas with significantly higher MOI. Conclusions: The study used a novel method to evaluate Plasmodium MOI and molecular epidemiological patterns by long amplicon ultra-deep sequencing. The complexity of infections were similar among age groups, symptoms, genders, transmission settings (spatial heterogeneity), as well as over years (pre- vs. post-scale-up interventions). This study demonstrated that long amplicon deep sequencing is a useful tool to investigate multiplicity and molecular epidemiology of Plasmodium parasite infections. © 2018 The Author(s).Item QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica(Frontiers in Plant Science, 2018-07) Odonkor, S.; Choi, S.; Chakraborty, D.; Martinez-Bello, L.; Wang, X.; Bahri, B.A.; Tenaillon, M.I.; Panaud, O.; Devos, K.M.Setaria (L.) P. Beauv is a genus of grasses that belongs to the Poaceae (grass) family, subfamily Panicoideae. Two members of the Setaria genus, Setaria italica (foxtail millet) and S. viridis (green foxtail), have been studied extensively over the past few years as model species for C4-photosynthesis and to facilitate genome studies in complex Panicoid bioenergy grasses. We exploited the available genetic and genomic resources for S. italica and its wild progenitor, S. viridis, to study the genetic basis of seed shattering. Reduced shattering is a key trait that underwent positive selection during domestication. Phenotyping of F2:3 and recombinant inbred line (RIL) populations generated from a cross between S. italica accession B100 and S. viridis accession A10 identified the presence of additive main effect quantitative trait loci (QTL) on chromosomes V and IX. As expected, enhanced seed shattering was contributed by the wild S. viridis. Comparative analyses pinpointed Sh1 and qSH1, two shattering genes previously identified in sorghum and rice, as potentially underlying the QTL on Setaria chromosomes IX and V, respectively. The Sh1 allele in S. italica was shown to carry a PIF/Harbinger MITE in exon 2, which gave rise to an alternatively spliced transcript that lacked exon 2. This MITE was universally present in S. italica accessions around the world and absent from the S. viridis germplasm tested, strongly suggesting a single origin of foxtail millet domestication. The qSH1 gene carried two MITEs in the 5'UTR. Presence of one or both MITEs was strongly associated with cultivated germplasm. If the MITE insertion(s) in qSH1 played a role in reducing shattering in S. italica accessions, selection for the variants likely occurred after the domestication of foxtail millet.Item Worldwide Universities Network (WUN) Web Observatory Applying Lessons from the Web to Transform the Research Data Ecosystem(26th International World Wide Web Conference 2017, WWW 2017 Companion, 2019-01) Price, S.; Boateng, R.; Loader, B.; Suleman, H.; Hall, W.; Earl, G.; Tiropanis, T.; Tinati, R.; Wang, X.; Gandolfi, E.et.al.The ongoing growth in research data publication supports global intra-disciplinary and inter-disciplinary research col- laboration but the current generation of archive-centric re- search data repositories do not address some of the key prac- tical obstacles to research data sharing and re-use, specifi- cally: discovering relevant data on a global scale is time- consuming; sharing ‘live’ and streaming data is non-trivial; managing secure access to sensitive data is overly compli- cated; and, researchers are not guaranteed attribution for re-use of their own research data. These issues are keenly felt in an international network like the Worldwide Univer- sities Network (WUN) as it seeks to address major global challenges. In this paper we outline the WUN Web Obser- vatory project’s plan to overcome these obstacles and, given that these obstacles are not unique to WUN, we also pro- pose an ambitious, longer-term route to their solution at Web-scale by applying lessons from the Web itself.