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Low SY, Lau SF, Ahmad NI, Sharma RSK, Rosli MZ, Mohd-Taib FS, Ajat MMM, Kamaludeen J, Syed Hussain SS, Wan KL, Salleh A, Aziz NAA. A cross-sectional study of Angiostrongylus malaysiensis in rats and gastropod hosts from recreational parks in Kuala Lumpur, Malaysia: Detection, risk factors and pathology. Zoonoses Public Health 2023; 70:636-646. [PMID: 37403513 DOI: 10.1111/zph.13072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/15/2023] [Accepted: 06/25/2023] [Indexed: 07/06/2023]
Abstract
Angiostrongylus malaysiensis is a potential zoonotic parasite, which reported to co-occur with A. cantonensis in human cerebrospinal fluid. It is a heteroxenous nematode that primarily develops through the early larval stages in gastropods and attains sexual maturity within rats. This study was conducted to determine the host species responsible for the reservoir of A. malaysiensis and investigate the risk factor for transmission among the hosts in Kuala Lumpur, Malaysia. Sampling was conducted in six recreational parks. The rats were trapped alive using steel wire traps with bait, while the gastropods were collected by active searching. The rats were euthanized and dissected to collect any adult worms observed. The molecular detection of A. malaysiensis was performed by PCR on gastropod tissue samples. Biotic and landscape factors were recorded for risk factor analysis. In total, 82 rats and 330 gastropods were collected throughout the study. Overall, 3.64% of gastropods and 32.9% of rats were infected with A. malaysiensis. Rattus tiomanicus (Malayan wood rat) and Parmarion martensi (Yellow-shelled semi-slug) were found as important hosts for A. malaysiensis. Host species, sampling site and macrohabitat type are risk factors associated with the prevalence of A. malaysiensis infection in rats. For gastropods, host species and sampling site are risk factors that correlate with the parasite detection. In total, 128 adult A. malaysiensis were recovered from the infected rats. The mean intensity of infection with adult A. malaysiensis was 4.65 for Rattus rattus complex and 4.90 for R. tiomanicus. Adult worms were found in the pulmonary artery or right ventricle, while eggs and first-stage larvae were found in capillaries of the caudal lung lobe. Infected lungs showed extravasated red blood cells in the alveolar spaces. The pulmonary arteries in the infected lung lobe were thickened. Kepong Metropolitan Park is the hotspot area for A. malaysiensis in Kuala Lumpur. These results provide essential information for public health officials to develop targeted interventions to reduce the transmission of A. malaysiensis in urban areas, particularly in recreational parks.
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Affiliation(s)
- Suey Yee Low
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Seng Fong Lau
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nur Indah Ahmad
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Reuben Sunil Kumar Sharma
- Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Muhammad Zahin Rosli
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Farah Shafawati Mohd-Taib
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Mohd Mokrish Md Ajat
- Department of Veterinary Pre-clinical Science, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Juriah Kamaludeen
- Department of Animal Science and Fishery, Faculty of Agriculture Science and Forestry, Universiti Putra Malaysia, Bintulu, Malaysia
| | - Sharifah Salmah Syed Hussain
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Kiew-Lian Wan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Annas Salleh
- Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nor Azlina Abdul Aziz
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
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Cao B, Fan XT, Wang RH, Luan XL, Qian CY, Yu JJ, Liu HC, Li MC, Li GL, Zhao XQ, Yuan XQ, Wan KL. [Preliminary evaluation of immunogenicity and protective effect of multicomponent recombinant protein vaccine EPRHP014 against tuberculosis]. Zhonghua Liu Xing Bing Xue Za Zhi 2023; 44:1653-1660. [PMID: 37875456 DOI: 10.3760/cma.j.cn112338-20230217-00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Objective: To evaluate the immunogenicity and protective effect of a multicomponent recombinant protein vaccine EPRHP014 constructed independently and provide a scientific basis for developing new tuberculosis (TB) vaccine and effective prevention and control of TB. Methods: Three full-length Mycobacterium (M.) tuberculosis protein antigens (EsxH, Rv2628, and HspX) and two epitope-predicted and optimized epitope-dominant protein antigens (nPPE18 and nPstS1) were selected, from which five protein antigens were used to construct a protein antigen composition EPRHP014, including a fusion expression multi-component protein antigen (EPRHP014f) and a multi-component mixed protein antigen (EPRHP014m) formed with the five single protein using clone, purification, and purification respectively. Multicomponent protein vaccines EPRHP014f and EPRHP014m were prepared with aluminum adjuvant, and the BCG vaccine was used as a control. ELISA detected the titer of serum-specific antibodies, the secretion of various cytokines was detected by ELISpot and Luminex, and immune protection was observed by the M. tuberculosis growth inhibition test in vitro. The results were statistically analyzed by t-test or rank sum test, and P<0.05 was considered a statistically significant difference. Results: Mice Immunized with EPRHP014m and EPRHP014f could produce highly effective IgG antibodies and their subtypes IgG1 and IgG2a, and the antibody titers were similar to those of mice immunized with BCG, with no statistical significance (P>0.05). The number of spot-forming cells (SFC) secreting IFN-γ and IL-4 induced by EPRHP014f group was significantly higher than those by EPRHP014m group and BCG group (P<0.05), but there was no significant difference in the number of SFC for IFN-γ and IL-4 induced between EPRHP014m group and BCG group (P>0.05). The secretion levels of GM-CSF and IL-12p70 induced by the EPRHP014m group were higher than those of the BCG group (P<0.05), but there was no significant difference in the levels of IL-6 and IL-10 induced between EPRHP014m group and BCG group (P>0.05). There was no significant difference in the secretions of IL-6, IL-10, IL-12, and GM-CSF between the EPRHP014f and BCG groups (P>0.05). EPRHP014m group, EPRHP014f group, and BCG group had obvious antibacterial effects in vitro, and the difference was insignificant (P>0.05). Conclusion: Both EPRHP014f and EPRHP014m can induce strong humoral and cellular immune responses in mice after immunization, and have a strong ability to inhibit the growth of M. tuberculosis in vitro, indicating that the antigen composition EPRHP014 has good potential in the development and application of TB vaccine.
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Affiliation(s)
- B Cao
- School of Public Health, University of South China, Hengyang 421001, China National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - X T Fan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - R H Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - X L Luan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - C Y Qian
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China School of Life Sciences, College of Laboratory Medicine, Wenzhou Medical University, Wenzhou 325035, China
| | - J J Yu
- School of Public Health, University of South China, Hengyang 421001, China National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - H C Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - M C Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - G L Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - X Q Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - X Q Yuan
- School of Public Health, University of South China, Hengyang 421001, China
| | - K L Wan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
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Mursyidah AK, Hafizzudin-Fedeli M, Nor Muhammad NA, Latiff A, Firdaus-Raih M, Wan KL. Dissecting the Biology of Rafflesia Species: Current Progress and Future Directions Made Possible with High-Throughput Sequencing Data. Plant Cell Physiol 2023; 64:368-377. [PMID: 36611267 DOI: 10.1093/pcp/pcad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 12/07/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
The angiosperm Rafflesia exhibits a unique biology, including a growth strategy that involves endophytic parasitism of a specific host, with only the gigantic flower externally visible. The Rafflesia possesses many unique evolutionary, developmental and morphological features that are rooted in yet-to-be-explained physiological processes. Although studies on the molecular biology of Rafflesia are limited by sampling difficulties due to its rarity in the wild and the short life span of its flower, current advances in high-throughput sequencing technology have allowed for the genome- and transcriptome-level dissection of the molecular mechanisms behind the unique characteristics of this parasitic plant. In this review, we summarize major findings on the cryptic biology of Rafflesia and provide insights into future research directions. The wealth of data obtained can improve our understanding of Rafflesia species and contribute toward the conservation strategy of this endangered plant.
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Affiliation(s)
- Anwarali-Khan Mursyidah
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor DE, Malaysia
| | - Mohamad Hafizzudin-Fedeli
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor DE, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor DE, Malaysia
| | - A Latiff
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor DE, Malaysia
| | - Mohd Firdaus-Raih
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor DE, Malaysia
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor DE, Malaysia
| | - Kiew-Lian Wan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor DE, Malaysia
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Loo SS, Mohamed M, Mohd-Taib FS, Khoo CK, Wan KL. Isolation and Establishment of eimeria tenella Populations from Local Broiler Chicken Farms. SAINS MALAYS 2022. [DOI: 10.17576/jsm-2022-5106-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Coccidiosis is a major intestinal disease in the chicken production industry that is caused by one or more of the seven Eimeria species known to infect chickens. Development of effective diagnostic methods and controls requires comprehensive knowledge on the Eimeria species in the local population, particularly the pathogenic E. tenella. In this study, 35 faecal samples were collected from local chicken farms, and through microscopic observation, nine samples (26%) were found to contain Eimeria oocysts. Subsequently, two positive samples, namely NSN6 and SGR6, were selected and propagated via passage in coccidian-free chickens. Species identification analyses based on oocyst morphological characterisation suggested the presence of small-sized oocysts (E. acervulina and/or E. mitis) and medium-sized oocysts (E. necatrix, E. tenella, and/or E. praecox) in NSN6 while in SGR6, the large-sized oocysts (E. brunetti and/or E. maxima) were also present in addition to the small and medium-sized oocysts. Subsequently, species identification with PCR using species-specific primers was successful in determining the presence of specific Eimeria species, which are E. acervulina and E. tenella in NSN6, and E. acervulina, E. tenella, and E. maxima in SGR6. The E. tenella populations of NSN6 and SGR6, namely EtNSN6 and EtSGR6, respectively, were established via passage in coccidian-free chickens and oocyst recovery from the caeca. The purity of EtNSN6 and EtSGR6 populations were confirmed based on oocyst morphological characterisation and PCR. The established EtNSN6 and EtSGR6 populations would be useful as research models for local strains in the development of more effective control methods.
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Runtuwene LR, Sathirapongsasuti N, Srisawat R, Komalamisra N, Tuda JSB, Mongan AE, Aboge GO, Shabardina V, Makalowski W, Nesti DR, Artama WT, Nguyen-Thi LA, Wan KL, Na BK, Hall W, Pain A, Eshita Y, Maeda R, Yamagishi J, Suzuki Y. Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing. BMC Res Notes 2022; 15:44. [PMID: 35151353 PMCID: PMC8840504 DOI: 10.1186/s13104-022-05927-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/26/2022] [Indexed: 11/25/2022] Open
Abstract
Objective To disseminate the portable sequencer MinION in developing countries for the main purpose of battling infectious diseases, we found a consortium called Global Research Alliance in Infectious Diseases (GRAID). By holding and inviting researchers both from developed and developing countries, we aim to train the participants with MinION’s operations and foster a collaboration in infectious diseases researches. As a real-life example in which resources are limited, we describe here a result from a training course, a metagenomics analysis from two blood samples collected from a routine cattle surveillance in Kulan Progo District, Yogyakarta Province, Indonesia in 2019. Results One of the samples was successfully sequenced with enough sequencing yield for further analysis. After depleting the reads mapped to host DNA, the remaining reads were shown to map to Theileria orientalis using BLAST and OneCodex. Although the reads were also mapped to Clostridium botulinum, those were found to be artifacts derived from the cow genome. An effort to construct a consensus sequence was successful using a reference-based approach with Pomoxis. Hence, we concluded that the asymptomatic cow might be infected with T. orientalis and showed the usefulness of sequencing technology, specifically the MinION platform, in a developing country. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-05927-2.
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Affiliation(s)
- Lucky R Runtuwene
- Division 1, AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan. .,Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
| | - Nuankanya Sathirapongsasuti
- Section of Translational Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Raweewan Srisawat
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narumon Komalamisra
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Josef S B Tuda
- Faculty of Medicine, Sam Ratulangi University, Manado, Indonesia
| | - Arthur E Mongan
- Faculty of Medicine, Sam Ratulangi University, Manado, Indonesia
| | - Gabriel O Aboge
- Department of Public Health, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Victoria Shabardina
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Muenster, Germany
| | - Dela Ria Nesti
- Department of Bioresources Technology and Veterinary, Vocational College, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Wayan T Artama
- Department of Biochemistry, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Lan Anh Nguyen-Thi
- Center of Biomedical Research, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Kiew-Lian Wan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine, College of Medicine, Gyeongsang National University, Jinju, South Korea
| | - William Hall
- Centre for Research in Infectious Diseases, University College Dublin, Dublin, Ireland
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yuki Eshita
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryuichiro Maeda
- Division of Biomedical Science, Department of Basic Veterinary Medicine, Obihiro University of Agriculture and Veterinary, Obihiro, Japan
| | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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Chin Q, Mat-Isa MN, Abu-Bakar MF, Mohd-Assaad N, Wan KL. Pencirian Jujukan Genom Mitokondria Spesies Rafflesia (Rafflesiaceae) di Semenanjung Malaysia. SAINS MALAYS 2022. [DOI: 10.17576/jsm-2022-5101-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Rafflesia terkenal sebagai tumbuhan yang menghasilkan bunga tunggal yang terbesar di dunia. Namun, ia semakin jarang ditemui dan ialah spesies dalam bahaya. Sistem pengelasan spesies Rafflesia ialah komponen penting dalam usaha pemuliharaan lazimnya bergantung kepada pencirian morfologi bunga. Walau bagaimanapun, pendekatan molekul, termasuk yang berasaskan kepada jujukan genom mitokondria (mtDNA), berupaya menyediakan kaedah pengelasan yang lebih berkesan. Untuk meneroka kemungkinan ini, jujukan mtDNA empat spesies Rafflesia di Semenanjung Malaysia, iaitu R. cantleyi, R. azlanii, R. kerrii dan R. sharifah-hapsahiae telah dihimpun dan dicirikan dalam kajian ini. Bacaan jujukan mtDNA untuk setiap spesies kajian pada mulanya telah ditentukan masing-masing daripada set data genom keseluruhan menggunakan pendekatan pemetaan berbantukan rujukan. Proses penghimpunan secara de novo dan perancahan kemudiannya telah dijalankan ke atas bacaan jujukan yang telah dikenal pasti untuk menghasilkan jujukan mtDNA bagi R. cantleyi (441,992 pb), R. azlanii (472,723 pb), R. kerrii (500,932 pb) dan R. sharifah-hapsahiae (453,747 pb). Seterusnya, anotasi mtDNA bagi setiap spesies telah mengenal pasti sekurang-kurangnya 31 gen pengekodan protein, enam gen tRNA dan tiga rRNA. Perbandingan gen mitokondria mendapati bahawa beberapa gen seperti cob, rpl10, mttB dan ccmB mempamerkan orientasi yang berbeza dalam spesies Rafflesia yang tertentu manakala analisis penjajaran jujukan berganda menunjukkan jujukan gen nad1 adalah berbeza antara keempat-empat spesies Rafflesia yang dikaji. Analisis filogenetik dengan menggunakan jujukan bagi tujuh gen pengekodan protein yang terpelihara berupaya membezakan spesies Rafflesia yang dikaji. Kesimpulannya, hasil pencirian jujukan mtDNA menunjukkan bahawa jujukan gen mitokondria yang khusus berupaya membezakan spesies Rafflesia yang dikaji dan berpotensi untuk digunakan bagi tujuan pengenalpastian serta pengelasan spesies Rafflesia dalam usaha pemuliharaan organisma yang unik ini.
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Wan KL, Azlan MS, Syed-Azmi AS, Lattish R, Faisham WI. Three-year follow-up of a Traumatic Hemipelvectomy Survivor: A Case Report. Malays Orthop J 2021; 15:143-146. [PMID: 34966511 PMCID: PMC8667254 DOI: 10.5704/moj.2111.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/21/2021] [Indexed: 11/11/2022] Open
Abstract
The management of a patient with traumatic hemipelvectomy is complex. We report the acute management and rehabilitation of a 21-year-old patient as well as her prosthesis modification. She was able to return to society as a K3 level ambulator.
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Affiliation(s)
- K L Wan
- Department of Orthopaedics and Traumatology, Hospital Sungai Buloh, Sungai Buloh, Malaysia
| | - M S Azlan
- Department of Orthopaedics and Traumatology, Hospital Sungai Buloh, Sungai Buloh, Malaysia
| | - A S Syed-Azmi
- Department of Orthopaedics and Traumatology, Hospital Sungai Buloh, Sungai Buloh, Malaysia
| | - Rts Lattish
- Department of Rehabilitation Medicine, SOCSO Tun Razak Rehabilitation Centre, Melaka, Malaysia
| | - W I Faisham
- Department of Orthopaedics, Universiti Sains Malaysia, Kubang Kerian, Malaysia
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Adam JH, Aizat-Juhari MA, Nik Ariff NNF, Khamis S, Mohd. Yasin MH, Wan KL. Rafflesia tunku-azizahiae(Rafflesiaceae), a New Species from Pahang, Malaysia. SAINS MALAYS 2021. [DOI: 10.17576/jsm-2022-5111-27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A new species of Rafflesia (Rafflesiaceae) from Mt. Benom Forest Reserve, Ulu Dong, Raub, Pahang, Rafflesia tunku-azizahiae Adam, Aizat-Juhari & Wan is described and illustrated. Cluster analysis and principal component analysis showed that R. tunku-azizahiae and R. tuanku-halimii are closely related morphologically, characterized by perigone lobes covered by rows of very closely spaced coalesced white warts, and windows wholly covered by very closely rings of coalesced white warts. Score plot and bi-plot showed that R. tunku-azizahiae differs from R. tuanku-halimii by larger flower diameter, broader diaphragm and disc diameter, larger aperture diameter and longer ramenta.
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Dharmaputra RK, Wan KL, Samad N, Herath M, Wong J, Sarlos S, Holdsworth SR, Naderpoor N. A novel approach to a rare case of non-islet cell hypoglycaemia. Endocrinol Diabetes Metab Case Rep 2021; 2021:EDM210040. [PMID: 34236039 PMCID: PMC8284944 DOI: 10.1530/edm-21-0040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/14/2021] [Indexed: 12/24/2022] Open
Abstract
SUMMARY Insulin autoimmune syndrome (IAS) is a rare cause of non-islet cell hypoglycaemia. Treatment of this condition is complex and typically involves long-term use of glucocorticoids. Immunotherapy may provide an alternative in the management of this autoimmune condition through the suppression of antibodies production by B-lymphocyte depletion. We present a case of a 62-year-old male, with refractory hypoglycaemia initially presenting with hypoglycaemic seizure during an admission for acute psychosis. Biochemical testing revealed hypoglycaemia with an inappropriately elevated insulin and C-peptide level and no evidence of exogenous use of insulin or sulphonylurea. Polyethylene glycol precipitation demonstrated persistently elevated free insulin levels. This was accompanied by markedly elevated anti-insulin antibody (IA) titres. Imaging included CT with contrast, MRI, pancreatic endoscopic ultrasound and Ga 68-DOTATATE position emission tomography (DOTATATE PET) scan did not reveal islet cell aetiology for hyperinsulinaemia. Maintenance of euglycaemia was dependent on oral steroids and dextrose infusion. Complete resolution of hypoglycaemia and dependence on glucose and steroids was only achieved following treatment with plasma exchange and rituximab. LEARNING POINTS Insulin autoimmune syndrome (IAS) should be considered in patients with recurrent hyperinsulinaemic hypoglycaemia in whom exogenous insulin administration and islet cell pathologies have been excluded. Biochemical techniques play an essential role in establishing high insulin concentration, insulin antibody titres, and eliminating biochemical interference. High insulin antibody concentration can lead to inappropriately elevated serum insulin levels leading to hypoglycaemia. Plasma exchange and B-lymphocyte depletion with rituximab and immunosuppression with high dose glucocorticoids are effective in reducing serum insulin levels and hypoglycaemia in insulin autoimmune syndrome (IAS). Based on our observation, the reduction in serum insulin level may be a better indicator of treatment efficacy compared to anti-insulin antibody (IA) titre as it demonstrated greater correlation to the frequency of hypoglycaemia and to hypoglycaemia resolution.
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Affiliation(s)
- R K Dharmaputra
- Diabetes and Vascular Medicine Department, Monash Health, Victoria, Australia
| | - K L Wan
- Monash Health Pathology, Monash Health, Victoria, Australia
| | - N Samad
- Diabetes and Vascular Medicine Department, Monash Health, Victoria, Australia
| | - M Herath
- Diabetes and Vascular Medicine Department, Monash Health, Victoria, Australia
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Victoria, Australia
| | - J Wong
- Diabetes and Vascular Medicine Department, Monash Health, Victoria, Australia
- Department of Endocrinology, Monash Health, Victoria, Australia
| | - S Sarlos
- Diabetes and Vascular Medicine Department, Monash Health, Victoria, Australia
- Department of Endocrinology, Monash Health, Victoria, Australia
- Department of Medicine, School of Clinical Sciences, Monash University, Victoria, Australia
| | - S R Holdsworth
- Department of Immunology, Monash Health, Victoria, Australia
| | - N Naderpoor
- Diabetes and Vascular Medicine Department, Monash Health, Victoria, Australia
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Victoria, Australia
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Yip CH, Mahalingam S, Wan KL, Nathan S. Prodigiosin inhibits bacterial growth and virulence factors as a potential physiological response to interspecies competition. PLoS One 2021; 16:e0253445. [PMID: 34161391 PMCID: PMC8221495 DOI: 10.1371/journal.pone.0253445] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/06/2021] [Indexed: 11/19/2022] Open
Abstract
Prodigiosin, a red linear tripyrrole pigment, has long been recognised for its antimicrobial property. However, the physiological contribution of prodigiosin to the survival of its producing hosts still remains undefined. Hence, the aim of this study was to investigate the biological role of prodigiosin from Serratia marcescens, particularly in microbial competition through its antimicrobial activity, towards the growth and secreted virulence factors of four clinical pathogenic bacteria (methicillin-resistant Staphylococcus aureus (MRSA), Enterococcus faecalis, Salmonella enterica serovar Typhimurium and Pseudomonas aeruginosa) as well as Staphylococcus aureus and Escherichia coli. Prodigiosin was first extracted from S. marcescens and its purity confirmed by absorption spectrum, high performance liquid chromatography (HPLC) and liquid chromatography-tandem mass spectrophotometry (LC-MS/MS). The extracted prodigiosin was antagonistic towards all the tested bacteria. A disc-diffusion assay showed that prodigiosin is more selective towards Gram-positive bacteria and inhibited the growth of MRSA, S. aureus and E. faecalis and Gram-negative E. coli. A minimum inhibitory concentration of 10 μg/μL of prodigiosin was required to inhibit the growth of S. aureus, E. coli and E. faecalis whereas > 10 μg/μL was required to inhibit MRSA growth. We further assessed the effect of prodigiosin towards bacterial virulence factors such as haemolysin and production of protease as well as on biofilm formation. Prodigiosin did not inhibit haemolysis activity of clinically associated bacteria but was able to reduce protease activity for MRSA, E. coli and E. faecalis as well as decrease E. faecalis, Salmonella Typhimurium and E. coli biofilm formation. Results of this study show that in addition to its role in inhibiting bacterial growth, prodigiosin also inhibits the bacterial virulence factor protease production and biofilm formation, two strategies employed by bacteria in response to microbial competition. As clinical pathogens were more resistant to prodigiosin, we propose that prodigiosin is physiologically important for S. marcescens to compete against other bacteria in its natural soil and surface water environments.
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Affiliation(s)
- Chee-Hoo Yip
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Sobina Mahalingam
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Kiew-Lian Wan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Sheila Nathan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
- * E-mail:
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Yan YH, Li MC, Liu HC, Xiao TY, Li N, Lou YL, Wan KL. [Cellular immunity evaluation of five mycobacterium tuberculosis recombinant proteins and their compositions]. Zhonghua Yu Fang Yi Xue Za Zhi 2020; 54:539-545. [PMID: 32388956 DOI: 10.3760/cma.j.cn112150-20191119-00872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: The cellular immunity of 5 Mycobacterium tuberculosis recombinant proteins and their compositions was evaluated. Method: A total of 88 fresh venous blood from peripheral heparin anticoagulant population, 42 of which were from tuberculosis patients treated by The Tuberculosis Prevention and Treatment Center of Changping District, Beijing, and 46 of healthy volunteers were provided by the Infection Diseases of Chinese Center for Disease Control and Prevention. Healthy volunteers without a history of tuberculosis exposure and any clinical signs and symptoms. Using the Mycobacterium tuberculosis standard strain H37Rv DNA as a template, complete genes of the selected 5 recombinant proteins Rv3874, Rv3875, Rv2031c, Rv1411c and Rv3418c by PCR amplified; 5 recombinant proteins were cloned, expressed and purified as stimulants by genetic recombination and protein purification techniques, and the effector T cell enzyme-linked immunospot assay (ELISPOT) was used to detect cellular immunity in the population. Results: The recombinant proteins Rv3874, Rv3875, Rv2031c, Rv1411c and Rv3418c were successfully cloned, expressed and purified; And the sensitivities were 50.00%, 71.43%, 69.04%, 73.81% and 76.19%, and the specificities were 86.96%, 76.09%, 71.74%, 39.13% and 36.96%. In addition, the positive predictive value, negative predictive value, area under the curve and Youden index were 52.46% to 77.78%, 62.96% to 74.47%, 0.511 to 0.754 and 0.129 to 0.475, respectively. Except for Rv1411c and Rv3418c, the number of spot-forming cell (SFC) detected by Rv3874, Rv3875 and Rv2031c in tuberculosis patients was higher than healthy volunteers, and the differences were statistically significant (P<0.001). Among the 26 compositions composed of 5 recombinant proteins, the sensitivity was 80.95% to 95.24%, and the specificity was 68.89% to 24.44%. As the number of recombinant proteins in the composition increases, the sensitivity gradually increased, but the specificity decreased. Conclusion: The recombinant proteins of Mycobacterium tuberculosis Rv3874, Rv3875 and Rv2031c have strong ability to stimulate T cells to produce immune response, and have certain antigenicity. The efficacy of Rv1411c and Rv3418c alone as diagnostic antigens is not ideal, and the composition composed of multi-component antigens has certain application value. This article provides experimental evidence for the immune diagnosis of tuberculosis and the preparation of new anti-tuberculosis vaccines.
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Affiliation(s)
- Y H Yan
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - M C Li
- State Key Laboratory for Infection Diseases Prevention and Control/National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - H C Liu
- State Key Laboratory for Infection Diseases Prevention and Control/National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - T Y Xiao
- Guangdong Key Lab for Diagnosis & Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Guangzhou 518112, China
| | - N Li
- State Key Laboratory for Infection Diseases Prevention and Control/National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y L Lou
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - K L Wan
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
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Abstract
Gouty arthritis commonly affects peripheral joints and is associated with hyperuricaemia. Spinal manifestations of gouty arthritis are not common, and majority of published articles worldwide were case reports. This is a case report of spinal gouty arthritis that presented with spinal vertebrae destruction and cauda equina syndrome. The magnetic resonance imaging (MRI) showed destruction of L5/S1end plates with cystic collection mimicking infective changes. The tissue histological examination confirmed presence of urate crystal needles that displayed negative double refraction on light microscopy. Spinal gouty arthritis is part of the differential diagnoses in gouty arthritis patients.
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Affiliation(s)
- K Thuraikumar
- Department of Orthopaedics and Traumatology, Hospital Sungai Buloh, Sungai Buloh, Malaysia
| | - K L Wan
- Department of Orthopaedics and Traumatology, Hospital Sungai Buloh, Sungai Buloh, Malaysia
| | - K L Ong
- Department of Orthopaedics and Traumatology, Hospital Sungai Buloh, Sungai Buloh, Malaysia
| | - S W Lim
- Department of Orthopaedics and Traumatology, Hospital Sungai Buloh, Sungai Buloh, Malaysia
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Ho SK, Atar Singh MS, Nathan S, Wan KL. Pengimunan Protein Rekombinan SAG2 Eimeria tenella Melindungi Ayam terhadap Kesan Penyakit Koksidiosis. SAINS MALAYS 2020. [DOI: 10.17576/jsm-2020-4905-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Chen R, Li MC, Zhao LL, Zhao XQ, Liu HC, Liu ZG, Lu Y, Deng YL, Chen ZX, Wan KL, Yuan XQ. [Analysis on drug sensitivity spectrum of 167 multidrug-resistant Mycobacterium tuberculosis in China]. Zhonghua Liu Xing Bing Xue Za Zhi 2020; 41:764-769. [PMID: 32447922 DOI: 10.3760/cma.j.cn112338-20191121-00823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
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.
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Affiliation(s)
- R Chen
- School of Public Health, University of South China, Hengyang 421001, China; State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - M C Li
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - L L Zhao
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - X Q Zhao
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - H C Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Z G Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y Lu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Y L Deng
- School of Public Health, University of South China, Hengyang 421001, China; State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Z X Chen
- School of Public Health, University of South China, Hengyang 421001, China; State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - K L Wan
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - X Q Yuan
- School of Public Health, University of South China, Hengyang 421001, China
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Gao M, Yang TT, Li GL, Chen R, Liu HC, Gao Q, Wan KL, Feng SD. [Analysis on drug resistance-associated mutations of multi-drug resistant Mycobacterium tuberculosis based on whole-genome sequencing in China]. Zhonghua Liu Xing Bing Xue Za Zhi 2020; 41:770-775. [PMID: 32447923 DOI: 10.3760/cma.j.cn112338-20191111-00800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To analyze the resistance mutational profiles of multi-drug resistant Mycobacterium tuberculosis in China and the correlation between major mutation types and genotypes based on the whole-genome sequencing data. Methods: Search and download of the genome-wide sequencing data of M. tuberculosis published in China by August 2019 on NCBI database were conducted. Mutation frequency of drug resistance-related gene loci based on whole-genome sequencing was used to predict the molecular susceptibility of strains, and the correlation between mutation types and genotypes was analyzed. Results: According to the results of molecular resistance and susceptibility profiles, 1 024 MDR strains were identified from 2 019 M. tuberculosis strains. The major mutation types of resistance-related genes to common drugs were katG S315T (73.2%, isoniazid), rpoB S450L (63.1%, rifampicin), rpsL K43R (70.0%, streptomycin), embB M306V (37.4%, ethambutol), pncA_promoter T (-11)C (7.9%, pyrazinamide), gyrA A90V (32.3%, fluoroquinolones), rrs A1401G (67.7%, second-line injection drugs), fabG1_promoter C (-15) T (87.0%, Ethionamide), folC I43T (30.4%, P-aminosalicylic acid). Among them, the frequencies of katG S315T, embB M306V, rpsL K43R, gyrA A90V in lineage 2 were significantly higher than those in lineage 4, and folC I43T was only found in lineage 2. The proportion of katG S315T was significantly higher in the ancient Beijing genotype compared to the modern genotype, in contrast, the proportion of rpsL K43R was significantly higher in modern Beijing genotype, the differences were significant (all P<0.05). Conclusions: The results showed the main mutation types of resistance-related genes of MDR strains to many commonly used anti-tuberculosis drugs in China based on whole-genome sequencing, providing a basis for the development of sensitive and specific rapid molecular detection methods. At the same time, it was also found that the major mutation types of MDR-related genes were related to the genotype of the strains.
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Affiliation(s)
- M Gao
- School of Public Health, University of South China, Hengyang 421001, China
| | - T T Yang
- School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - G L Li
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - R Chen
- School of Public Health, University of South China, Hengyang 421001, China
| | - H C Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Q Gao
- School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - K L Wan
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - S D Feng
- School of Public Health, University of South China, Hengyang 421001, China
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Lee XW, Lam SD, Mohd Firdaus-Raih MFR, Wan KL. Molecular Characterisation of Eimeria tenella Porin, A Potential Anticoccidial Drug Target. SAINS MALAYS 2020. [DOI: 10.17576/jsm-2020-4904-04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Seah SW, Mohamad Jamil NSF, Lee YY, Kong C, Nathan S, Wan KL. Prodigiosin Serratia marcescens tidak Bersifat Toksik terhadap Caenorhabditis elegans. SAINS MALAYS 2020. [DOI: 10.17576/jsm-2020-4904-06] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Siti-Futri FF, Rosilawati R, Wan KL, Cheong YL, Nazni WA, Lee HL. Status of pyrethroid resistance in Aedes (Stegomyia) aegypti (Linneaus) from dengue hotspots in Klang Valley, Malaysia. Trop Biomed 2020; 37:201-209. [PMID: 33612731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The continued absence of an effective and safe tetravalent dengue vaccine and the lack of specific anti-viral treatment have made mosquito vector control using chemical insecticides as the mainstream for dengue prevention and control. However, the long-term use of chemical insecticides may induce resistance. Hence detection of insecticide resistance in dengue vectors is crucially important in ensuring the insecticide-based intervention in dengue control program is still effective and reliable. In this study, the susceptibility status of Aedes aegypti from five selected dengue hotspots in Klang Valley, Malaysia against pyrethroids was determined by employing the World Health Organization (WHO) protocol of adult bioassay. Four types of pyrethroids were tested against adult female Aedes aegypti to determine the knockdown rate, post 24-h adult mortality and resistance ratio. All field-collected Aedes aegypti strains were resistant to the four pyrethroids tested, except for the Taman Sungai Jelok (TSJ) strain. Permethrin exhibited the lowest knockdown rate against Aedes aegypti, followed by deltamethrin, cyfluthrin and lambda-cyhalothrin. This present study indicated the widespread of pyrethroid resistance in Aedes aegypti in Klang Valley, indicating the needs of implementing alternative measures in vector control program. The data in this study can be utilised as an input for insecticide resistance management of Aedes aegypti in Malaysia.
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Affiliation(s)
- F F Siti-Futri
- Medical Entomology Unit, and WHO Collaborating Centre for Vectors, Institute for Medical Research, Malaysia
- Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Malaysia
| | - R Rosilawati
- Medical Entomology Unit, and WHO Collaborating Centre for Vectors, Institute for Medical Research, Malaysia
| | - K L Wan
- Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Malaysia
| | - Y L Cheong
- Medical Entomology Unit, and WHO Collaborating Centre for Vectors, Institute for Medical Research, Malaysia
| | - W A Nazni
- Medical Entomology Unit, and WHO Collaborating Centre for Vectors, Institute for Medical Research, Malaysia
| | - H L Lee
- Medical Entomology Unit, and WHO Collaborating Centre for Vectors, Institute for Medical Research, Malaysia
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Amini S, Rosli K, Abu-Bakar MF, Alias H, Mat-Isa MN, Juhari MAA, Haji-Adam J, Goh HH, Wan KL. Transcriptome landscape of Rafflesia cantleyi floral buds reveals insights into the roles of transcription factors and phytohormones in flower development. PLoS One 2019; 14:e0226338. [PMID: 31851702 PMCID: PMC6919626 DOI: 10.1371/journal.pone.0226338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/25/2019] [Indexed: 11/19/2022] Open
Abstract
Rafflesia possesses unique biological features and known primarily for producing the world’s largest and existing as a single flower. However, to date, little is known about key regulators participating in Rafflesia flower development. In order to further understand the molecular mechanism that regulates Rafflesia cantleyi flower development, RNA-seq data from three developmental stages of floral bud, representing the floral organ primordia initiation, floral organ differentiation, and floral bud outgrowth, were analysed. A total of 89,890 transcripts were assembled of which up to 35% could be annotated based on homology search. Advanced transcriptome analysis using K-mean clustering on the differentially expressed genes (DEGs) was able to identify 12 expression clusters that reflect major trends and key transitional states, which correlate to specific developmental stages. Through this, comparative gene expression analysis of different floral bud stages identified various transcription factors related to flower development. The members of WRKY, NAC, bHLH, and MYB families are the most represented among the DEGs, suggesting their important function in flower development. Furthermore, pathway enrichment analysis also revealed DEGs that are involved in various phytohormone signal transduction events such as auxin and auxin transport, cytokinin and gibberellin biosynthesis. Results of this study imply that transcription factors and phytohormone signalling pathways play major role in Rafflesia floral bud development. This study provides an invaluable resource for molecular studies of the flower development process in Rafflesia and other plant species.
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Affiliation(s)
- Safoora Amini
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Khadijah Rosli
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | | | - Halimah Alias
- Malaysia Genome Institute, Jalan Bangi, Kajang, Selangor, Malaysia
| | | | - Mohd-Afiq-Aizat Juhari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Jumaat Haji-Adam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- * E-mail:
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Loo SS, Lim LS, Efendi NA, Blake DP, Kawazu SI, Wan KL. Comparison of Molecular Methods for the Detection of Eimeria in Domestic Chickens in Malaysia. SAINS MALAYS 2019. [DOI: 10.17576/jsm-2019-4807-11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Yan CQ, Wang RB, Liu HC, Jiang Y, Li MC, Yin SP, Xiao TY, Wan KL, Rang WQ. [Application of ARIMA model in predicting the incidence of tuberculosis in China from 2018 to 2019]. Zhonghua Liu Xing Bing Xue Za Zhi 2019; 40:633-637. [PMID: 31238610 DOI: 10.3760/cma.j.issn.0254-6450.2019.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: Autoregressive integrated moving average (ARIMA) model was used to predict the incidence of tuberculosis in China from 2018 to 2019, providing references for the prevention and control of pulmonary tuberculosis. Methods: The monthly incidence data of tuberculosis in China were collected from January 2005 to December 2017. R 3.4.4 software was used to establish the ARIMA model, based on the monthly incidence data of tuberculosis from January 2005 to June 2017. Both predicted and actual data from July to December 2017 were compared to verify the effectiveness of this model, and the number of tuberculosis cases in 2018-2019 also predicted. Results: From 2005 to 2017, a total of 13 022 675 cases of tuberculosis were reported, the number of pulmonary tuberculosis patients in 2017 was 33.68% lower than that in 2005, and the seasonal character was obvious, with the incidence in winter and spring was higher than that in other seasons. According to the incidence data from 2005 to 2017, we established the model of ARIMA (0,1,2)(0,1,0)(12). The relative error between the predicted and actual values of July to December 2017 fitted by the model ranged from 1.67% to 6.80%, and the predicted number of patients in 2018 and 2019 were 789 509 and 760 165 respectively. Conclusion: The ARIMA (0, 1, 2)(0, 1, 0)(12) model well predicted the incidence of tuberculosis, thus can be used for short-term prediction and dynamic analysis of tuberculosis in China, with good application value.
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Affiliation(s)
- C Q Yan
- School of Public Health, University of South China, Hengyang 421001, China
| | - R B Wang
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - H C Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y Jiang
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - M C Li
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - S P Yin
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - T Y Xiao
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - K L Wan
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - W Q Rang
- School of Public Health, University of South China, Hengyang 421001, China
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Yip CH, Yarkoni O, Juhas M, Ajioka J, Wan KL, Nathan S. The Escherichia coli motA Flagellar Gene as a Potential Integration Site for Large Synthetic DNA. SAINS MALAYS 2019. [DOI: 10.17576/jsm-2019-4801-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Yip CH, Yarkoni O, Ajioka J, Wan KL, Nathan S. Recent advancements in high-level synthesis of the promising clinical drug, prodigiosin. Appl Microbiol Biotechnol 2019; 103:1667-1680. [PMID: 30637495 DOI: 10.1007/s00253-018-09611-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 12/19/2022]
Abstract
Prodigiosin, a red linear tripyrrole pigment and a member of the prodiginine family, is normally secreted by the human pathogen Serratia marcescens as a secondary metabolite. Studies on prodigiosin have received renewed attention as a result of reported immunosuppressive, antimicrobial and anticancer properties. High-level synthesis of prodigiosin and the bioengineering of strains to synthesise useful prodiginine derivatives have also been a subject of investigation. To exploit the potential use of prodigiosin as a clinical drug targeting bacteria or as a dye for textiles, high-level synthesis of prodigiosin is a prerequisite. This review presents an overview on the biosynthesis of prodigiosin from its natural host Serratia marcescens and through recombinant approaches as well as highlighting the beneficial properties of prodigiosin. We also discuss the prospect of adopting a synthetic biology approach for safe and cost-effective production of prodigiosin in a more industrially compliant surrogate host.
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Affiliation(s)
- Chee-Hoo Yip
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Orr Yarkoni
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - James Ajioka
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
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Ng SM, Lee XW, Mat-Isa MN, Aizat-Juhari MA, Adam JH, Mohamed R, Wan KL, Firdaus-Raih M. Comparative analysis of nucleus-encoded plastid-targeting proteins in Rafflesia cantleyi against photosynthetic and non-photosynthetic representatives reveals orthologous systems with potentially divergent functions. Sci Rep 2018; 8:17258. [PMID: 30467394 PMCID: PMC6250676 DOI: 10.1038/s41598-018-35173-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
Parasitic plants are known to discard photosynthesis thus leading to the deletion or loss of the plastid genes. Despite plastid genome reduction in non-photosynthetic plants, some nucleus-encoded proteins are transported back to the plastid to carry out specific functions. In this work, we study such proteins in Rafflesia cantleyi, a member of the holoparasitic genus well-known for producing the largest single flower in the world. Our analyses of three transcriptome datasets, two holoparasites (R. cantleyi and Phelipanche aegyptiaca) and one photosynthetic plant (Arabidopsis thaliana), suggest that holoparasites, such as R. cantleyi, retain some common plastid associated processes such as biosynthesis of amino acids and lipids, but are missing photosynthesis components that can be extensions of these pathways. The reconstruction of two selected biosynthetic pathways involving plastids correlates the trend of plastid retention to pathway complexity - transcriptome evidence for R. cantleyi suggests alternate mechanisms in regulating the plastidial heme and terpenoid backbone biosynthesis pathways. The evolution to holoparasitism from autotrophy trends towards devolving the plastid genes to the nuclear genome despite the functional sites remaining in the plastid, or maintaining non-photosynthetic processes in the plastid, before the eventual loss of the plastid and any site dependent functions.
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Affiliation(s)
- Siuk-Mun Ng
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- Codon Genomics SB, No 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Xin-Wei Lee
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Mohd-Noor Mat-Isa
- Malaysia Genome Institute, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohd Afiq Aizat-Juhari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Jumaat Haji Adam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Rahmah Mohamed
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| | - Mohd Firdaus-Raih
- Centre for Frontier Sciences, Faculty of Science and Technology and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
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Luo Q, Li SJ, Xiao TY, Li MC, Liu HC, Lou YL, Wan KL. [Cloning expression and serological evaluation on Mycobacterium tuberculosis four new antigens]. Zhonghua Liu Xing Bing Xue Za Zhi 2018; 39:514-518. [PMID: 29699049 DOI: 10.3760/cma.j.issn.0254-6450.2018.04.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To evaluate the serological diagnostic value of Mycobacterium (M.) tuberculosis four new antigens Rv0432, Rv0674, Rv1566c and Rv1547. Methods:Rv0432, Rv0674, Rv1566c and Rv1547 were amplified from M. tuberculosis strain H37Rv genomic DNA by using PCR, among which Rv1547 was divided into two segments for amplification (Rv1547-1 and Rv1547-2). The segments were cloned into expression vector PET-32a while the recombinant proteins were purified by affinity chromatography. Serums were incubated with BL21 (DE3) proteins. Antibodies IgG against M. tuberculosis were tested with 151 serum samples (41 healthy people and 110 TB patients) by using ELISA. The diagnostic efficiency of antigens was analyzed by means of receiver operating characteristic curve. Difference of the objective proteins in TB patients and healthy controls was compared by t-test. Results: Recombinant antigens Rv0432, Rv0674, Rv1566c, Rv1547-1 and Rv1547-2 were successfully expressed and purified. Results from ELISA showed that the sensitivity, specificity, positive predictive value, negative predictive value, Youden index and area under the curve of Rv0432, Rv0674, Rv1566c, Rv1547-1 and Rv1547-2, as 43.64%-92.73%, 80.49%-92.68%, 0.92-0.94, 0.38-0.80, 0.363-0.732 and 0.649-0.915. All the objective proteins showed significantly higher antibody levels in TB patients, when compared to the healthy controls (P<0.000 1). Conclusion: The newly identified antigens Rv0432, Rv0674, Rv1566c, Rv1547-1 and Rv1547-2 all performed well when being used for TB serological diagnosis, thus were expected to be new candidate antigens used for TB diagnosis.
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Affiliation(s)
- Q Luo
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - S J Li
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - T Y Xiao
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - M C Li
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - H C Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y L Lou
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - K L Wan
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China; State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Li WB, Ji LY, Xu DL, Liu HC, Zhao XQ, Wu YM, Wan KL. [Identification and drug susceptibility testing of Mycobacterium thermoresistibile and Mycobacterium elephantis isolated from a cow with mastitis]. Zhonghua Liu Xing Bing Xue Za Zhi 2018; 39:669-672. [PMID: 29860815 DOI: 10.3760/cma.j.issn.0254-6450.2018.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To understand the etiological characteristics and drug susceptibility of Mycobacterium thermoresistibile and Mycobacterium elephantis isolated from a cow with mastitis and provide evidence for the prevention and control of infectious mastitis in cows. Methods: The milk sample was collected from a cow with mastitis, which was pretreated with 4% NaOH and inoculated with L-J medium for Mycobacterium isolation. The positive cultures were initially identified by acid-fast staining and multi-loci PCR, then Mycobacterium species was identified by the multiple loci sequence analysis (MLSA) with 16S rRNA, hsp65, ITS and SodA genes. The drug sensitivity of the isolates to 27 antibiotics was tested by alamar blue assay. Results: Two anti-acid stain positive strains were isolated from the milk of a cow with mastitis, which were identified as non-tuberculosis mycobacterium by multi-loci PCR, and multi-loci nucleic acid sequence analysis indicated that one strain was Mycobacterium thermoresistibile and another one was Mycobacterium elephantis. The results of the drug susceptibility test showed that the two strains were resistant to most antibiotics, including rifampicin and isoniazid, but they were sensitive to amikacin, moxifloxacin, levofloxacin, ethambutol, streptomycin, tobramycin, ciprofloxacin and linezolid. Conclusions:Mycobacterium thermoresistibile and Mycobacterium elephantis were isolated in a cow with mastitis and the drug susceptibility spectrum of the pathogens were unique. The results of the study can be used as reference for the prevention and control the infection in cows.
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Affiliation(s)
- W B Li
- Institution of Pathogenic Biology, Medical College, University of South China, Hengyang 421001, China
| | - L Y Ji
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Department of Laboratory Medicine, Shanghai East Hospital, Tongji University, Shanghai 200123, China
| | - D L Xu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - H C Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - X Q Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y M Wu
- Institution of Pathogenic Biology, Medical College, University of South China, Hengyang 421001, China
| | - K L Wan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Wang XX, Chen X, Li YQ, Xiao TY, Jiang Y, Li MC, Liu HC, Wan KL. [Identification and evaluation of T cell epitopes of Rv0585c from Mycobacterium tuberculosis]. Zhonghua Liu Xing Bing Xue Za Zhi 2017. [PMID: 28651408 DOI: 10.3760/cma.j.issn.0254-6450.2017.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the human T cell epitopes of Mycobacterium (M.) tuberculosis Rv0585c protein antigen and their immunogenicity and provide evidence for the development of specific tuberculosis immune diagnostic techniques and tuberculosis vaccine. Methods: We synthesized peptides from M. tuberculosis Rv0585c protein antigen predicted by TE-predict and IEDB human T cell epitope prediction tool. The cellular immunoreactivity of the predicted peptides was evaluated through ELISpot assay with the peripheral blood monouclear cells (PBMC) of clinical tuberculosis patients. In animal experiments, BALB/c mice were respectively immunized with high dose (100 μg/mice) and low dose (50 μg/mice) of the peptides of Rv0585c, at the same time, high dose (50 μg/mice) and low dose (20 μg/mice) of Ag85B protein were used in positive control group. The levels of IFN-γ, IL-2, IL-4 and IL-10 were tested with ELISA kit respectively. Results: By means of bioinformatics technique, 66 human T cell epitopes of Rv0585c were predicted, from which9 peptides concentrated epitopes were synthesized for the animal immune experiments. Peptides P10110, P10112 and P10117 were confirmed to be antigenic. The sensitivity and specificity of P10110, P10112 and P10117 were 14.00%, 12.00%, 6.00% and 100.00%, 100.00%, 97.96% respectively when they were used as diagnostic reagents of tuberculosis. The sensitivity and specificity were 22.00% and 97.96% when the epitopes were combined together. The results of animal immunity test showed that high levels of cytokines IFN-γ, IL-2, IL-4 and IL-10 were induced by high and low dose of P10110, and high levels of IFN-γ、IL-2 and IL-10 were induced by high and low dose of P10112, which were much higher than that in negative controls, respectively (P<0.001). Conclusion: Rv0585c, including its human T cell epitopes, has good immunogenicity and immunoreactivity, stimulating the body to produce a stronger cellular immune response and has better potential application value in cellular diagnosis of tuberculosis and the development of new type of tuberculosis vaccine.
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Affiliation(s)
- X X Wang
- State Key Laboratory for Communicable Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - X Chen
- School of Public Health, University of South China, Hengyang 421001, China
| | - Y Q Li
- School of Public Health, University of South China, Hengyang 421001, China
| | - T Y Xiao
- State Key Laboratory for Communicable Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y Jiang
- State Key Laboratory for Communicable Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - M C Li
- State Key Laboratory for Communicable Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - H C Liu
- State Key Laboratory for Communicable Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - K L Wan
- State Key Laboratory for Communicable Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Amini S, Alias H, Aizat-Juhari MA, Mat-Isa MN, Adam JH, Goh HH, Wan KL. RNA-seq data from different developmental stages of Rafflesia cantleyi floral buds. Genom Data 2017; 14:5-6. [PMID: 28761813 PMCID: PMC5524293 DOI: 10.1016/j.gdata.2017.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/06/2017] [Accepted: 07/13/2017] [Indexed: 11/16/2022]
Abstract
Rafflesia cantleyi, known as one of the world's largest flowers, is a specialised holoparasite due to dramatic morphological modifications. It possesses highly reduced vegetative structure and only appears as a flower for sexual reproduction. Moreover, it has an unusual life cycle in that its floral bud development takes up to nine months. In order to fully understand the highly modified floral organ structure and long life cycle of R. cantleyi, we used Illumina sequencing technology (HiSeq) for sequence generation followed by de novo assembly of sequence reads. We obtained the RNA-seq data from three different stages of floral bud, representing the early, mid and advanced developmental stages. These data are available via BioProject accession number PRJNA378435. More than 10.3 Gb raw sequence data were generated, corresponding to 102,203,042 raw reads. Following removal of low-quality reads and trimming of adapter sequences, a total of 91,638,836 reads were obtained. De novo assembly of these sequences using Trinity resulted in 89,690 unique transcripts with an N50 of 1653 bp. The obtained transcriptomic data will be useful for further study to understand the molecular interactions that result in R. cantleyi floral development.
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Affiliation(s)
- Safoora Amini
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Halimah Alias
- Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Afiq Aizat-Juhari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Mohd-Noor Mat-Isa
- Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
| | - Jumaat Haji Adam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
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29
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Li C, Li GL, Luo Q, Li SJ, Wang RB, Lou YL, Lyu JX, Wan KL. [A preliminary study on the molecular characteristics of D-cycloserine resistance of Mycobacterium tuberculosis]. Zhonghua Liu Xing Bing Xue Za Zhi 2017; 38:240-243. [PMID: 28231674 DOI: 10.3760/cma.j.issn.0254-6450.2017.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the relationship between D-cycloserine resistance and the gene mutations of alrA, ddlA and cycA of Mycobacterium (M.) tuberculosis, as well as the association between D-cycloserine resistance and spoligotyping genotyping. Methods: A total of 145 M. tuberculosis strains were selected from the strain bank. D-cycloserine resistant phenotypes of the strains were determined by the proportion method and the minimal inhibitory concentration was determined by resazurin microtiter assay. PCR amplification and DNA direct sequencing methods were used for the analysis of gene mutations. Relationship between the resistance phenotype and genotype was analyzed by chi-square test. Results: Of the 145 clinically collected strains, 24 (16.6%) of them were D-cycloserine resistant and 121 (83.4%) were sensitive. There were only synonymous mutations noticed on alrA, ddlA and cycA in sensitive strains. Of the 24 D-cycloserine resistant strains, 3 (12.5%) isolates' cycA and 1 (4.2%) isolates' alrA happened to be non-synonymous mutations, in which the codes were 188, 318 and 508 of cycA, and 261 of alrA, respectively. Results on drug sensitivity tests confirmed the minimal inhibitory concentration of the mutant strains were all increased to some degrees. The D-cycloserine resistant rates of 88 Beijing genotype and 57 non-Beijing genotype strains were 20.5% and 10.5% , respectively, but with no statistically significant difference (χ(2) =2.47, P>0.05). Conclusions: The non-synonymous mutations of alrA and cycA might contribute to one of the mechanisms of M. tuberculosis D-cycloserine resistance. M. tuberculosis Beijing genotype or non-Beijing genotype was not considered to be associated with the D-cycloserine resistance.
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Affiliation(s)
- C Li
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - G L Li
- Tuberculosis Branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Q Luo
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - S J Li
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - R B Wang
- Tuberculosis Branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y L Lou
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - J X Lyu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - K L Wan
- Tuberculosis Branch, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
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Yao PP, Raih MF, Mohd Sidek H, Embi N, Wan KL. Pencirian Molekul Glikogen Sintase Kinase-3 daripada Eimeria tenella. SAINS MALAYS 2016. [DOI: 10.17576/jsm-2016-4512-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Xu YJ, Li MC, Chen SS, Xiao SQ, Liu HC, Zhao XQ, Wu YM, Wan KL. [Analysis on the polymorphisms of human B cell epitopes of 5 specificity antigens in Mycobacterium tuberculosis in China]. Zhonghua Jie He He Hu Xi Za Zhi 2016; 39:372-7. [PMID: 27180592 DOI: 10.3760/cma.j.issn.1001-0939.2016.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To study the diversities of human B cell epitopes of five proteins (Mpt83, Mpt70, LpqH, PstS3, GroES) in Mycobacterium tuberculosis isolates from China. METHODS We selected 179 strains isolated from patients with tuberculosis in different regions of China, and cultured these strains by L-J medium. The gene sequences of these 5 proteins were amplified and sequenced by PCR. The variations (single nucleotide polymorphisms, SNP) of the DNA sequences were compared and analyzed according to the immune epitope database (IEDB). The synonymous mutation rate (dS), non-synonymous mutation rate (dN) and dN/dS values were calculated with MEGA6 software. RESULTS Among the 179 clinical MTBC isolates, 7 SNP mutations were found in the mpt83gene. The dN/dS value of the whole mpt83 gene was 0.88. One SNP mutation was found in the mpt70 gene. The dN/dS values of the whole pstS3 gene and non-B epitopes areas were 1.74 and 1.40 respectively. But no mutation was found in the groES gene. CONCLUSION The mpt83, lpqH and pstS3 genes of 179 MTBC strains contain gene SNPs and human B cell epitopes diversities, while the coding gene and human B cell epitopes of protein mpt70 and groES were conservative.
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Affiliation(s)
- Y J Xu
- Institute of Pathogenic Biology, University of South China, Hunan, 421000, China
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Song BK, Pan MZ, Lau YL, Wan KL. Sequence analysis of the PIP5K locus in Eimeria maxima provides further evidence for eimerian genome plasticity and segmental organization. Genet Mol Res 2014; 13:5803-14. [PMID: 25117339 DOI: 10.4238/2014.july.29.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Commercial flocks infected by Eimeria species parasites, including Eimeria maxima, have an increased risk of developing clinical or subclinical coccidiosis; an intestinal enteritis associated with increased mortality rates in poultry. Currently, infection control is largely based on chemotherapy or live vaccines; however, drug resistance is common and vaccines are relatively expensive. The development of new cost-effective intervention measures will benefit from unraveling the complex genetic mechanisms that underlie host-parasite interactions, including the identification and characterization of genes encoding proteins such as phosphatidylinositol 4-phosphate 5-kinase (PIP5K). We previously identified a PIP5K coding sequence within the E. maxima genome. In this study, we analyzed two bacterial artificial chromosome clones presenting a ~145-kb E. maxima (Weybridge strain) genomic region spanning the PIP5K gene locus. Sequence analysis revealed that ~95% of the simple sequence repeats detected were located within regions comparable to the previously described feature-rich segments of the Eimeria tenella genome. Comparative sequence analysis with the orthologous E. maxima (Houghton strain) region revealed a moderate level of conserved synteny. Unique segmental organizations and telomere-like repeats were also observed in both genomes. A number of incomplete transposable elements were detected and further scrutiny of these elements in both orthologous segments revealed interesting nesting events, which may play a role in facilitating genome plasticity in E. maxima. The current analysis provides more detailed information about the genome organization of E. maxima and may help to reveal genotypic differences that are important for expression of traits related to pathogenicity and virulence.
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Affiliation(s)
- B K Song
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor DE, Malaysia
| | - M Z Pan
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor DE, Malaysia
| | - Y L Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - K L Wan
- Malaysia Genome Institute, Kajang, Selangor DE, Malaysia
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Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D, Malas TB, Mourier T, Naghra H, Nair M, Otto TD, Rawlings ND, Rivailler P, Sanchez-Flores A, Sanders M, Subramaniam C, Tay YL, Woo Y, Wu X, Barrell B, Dear PH, Doerig C, Gruber A, Ivens AC, Parkinson J, Rajandream MA, Shirley MW, Wan KL, Berriman M, Tomley FM, Pain A. Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Res 2014; 24:1676-85. [PMID: 25015382 PMCID: PMC4199364 DOI: 10.1101/gr.168955.113] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.
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Affiliation(s)
- Adam J Reid
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Damer P Blake
- Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom
| | - Hifzur R Ansari
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Karen Billington
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom
| | - Hilary P Browne
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Josephine Bryant
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Matt Dunn
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Stacy S Hung
- Program in Molecular Structure and Function, Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - Fumiya Kawahara
- Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan
| | - Diego Miranda-Saavedra
- Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Tareq B Malas
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Hardeep Naghra
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Mridul Nair
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Thomas D Otto
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Neil D Rawlings
- European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Pierre Rivailler
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Apoyo Bioinformático, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Chandra Subramaniam
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom
| | - Yea-Ling Tay
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia; Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Yong Woo
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Xikun Wu
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Amgen Limited, Uxbridge UB8 1DH, United Kingdom
| | - Bart Barrell
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Paul H Dear
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Christian Doerig
- Department of Microbiology, Monash University, Clayton VIC 3800, Australia
| | - Arthur Gruber
- Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Alasdair C Ivens
- Centre for Immunity, Infection and Evolution, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - John Parkinson
- Program in Molecular Structure and Function, Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - Marie-Adèle Rajandream
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Martin W Shirley
- The Pirbright Institute, Pirbright Laboratory, Pirbright, Surrey GU24 0NF, United Kingdom
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia; Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Fiona M Tomley
- Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;
| | - Arnab Pain
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia;
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Lim LS, Tay YL, Alias H, Wan KL, Dear PH. Insights into the genome structure and copy-number variation of Eimeria tenella. BMC Genomics 2012; 13:389. [PMID: 22889016 PMCID: PMC3505466 DOI: 10.1186/1471-2164-13-389] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 08/01/2012] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Eimeria is a genus of parasites in the same phylum (Apicomplexa) as human parasites such as Toxoplasma, Cryptosporidium and the malaria parasite Plasmodium. As an apicomplexan whose life-cycle involves a single host, Eimeria is a convenient model for understanding this group of organisms. Although the genomes of the Apicomplexa are diverse, that of Eimeria is unique in being composed of large alternating blocks of sequence with very different characteristics - an arrangement seen in no other organism. This arrangement has impeded efforts to fully sequence the genome of Eimeria, which remains the last of the major apicomplexans to be fully analyzed. In order to increase the value of the genome sequence data and aid in the effort to gain a better understanding of the Eimeria tenella genome, we constructed a whole genome map for the parasite. RESULTS A total of 1245 contigs representing 70.0% of the whole genome assembly sequences (Wellcome Trust Sanger Institute) were selected and subjected to marker selection. Subsequently, 2482 HAPPY markers were developed and typed. Of these, 795 were considered as usable markers, and utilized in the construction of a HAPPY map. Markers developed from chromosomally-assigned genes were then integrated into the HAPPY map and this aided the assignment of a number of linkage groups to their respective chromosomes. BAC-end sequences and contigs from whole genome sequencing were also integrated to improve and validate the HAPPY map. This resulted in an integrated HAPPY map consisting of 60 linkage groups that covers approximately half of the estimated 60 Mb genome. Further analysis suggests that the segmental organization first seen in Chromosome 1 is present throughout the genome, with repeat-poor (P) regions alternating with repeat-rich (R) regions. Evidence of copy-number variation between strains was also uncovered. CONCLUSIONS This paper describes the application of a whole genome mapping method to improve the assembly of the genome of E. tenella from shotgun data, and to help reveal its overall structure. A preliminary assessment of copy-number variation (extra or missing copies of genomic segments) between strains of E. tenella was also carried out. The emerging picture is of a very unusual genome architecture displaying inter-strain copy-number variation. We suggest that these features may be related to the known ability of this parasite to rapidly develop drug resistance.
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Affiliation(s)
- Lik-Sin Lim
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
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Chow KS, Mat-Isa MN, Bahari A, Ghazali AK, Alias H, Mohd.-Zainuddin Z, Hoh CC, Wan KL. Metabolic routes affecting rubber biosynthesis in Hevea brasiliensis latex. J Exp Bot 2012; 63:1863-71. [PMID: 22162870 PMCID: PMC3295384 DOI: 10.1093/jxb/err363] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/12/2011] [Accepted: 10/17/2011] [Indexed: 05/05/2023]
Abstract
The cytosolic mevalonate (MVA) pathway in Hevea brasiliensis latex is the conventionally accepted pathway which provides isopentenyl diphosphate (IPP) for cis-polyisoprene (rubber) biosynthesis. However, the plastidic 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway may be an alternative source of IPP since its more recent discovery in plants. Quantitative RT-PCR (qRT-PCR) expression profiles of genes from both pathways in latex showed that subcellular compartmentalization of IPP for cis-polyisoprene synthesis is related to the degree of plastidic carotenoid synthesis. From this, the occurrence of two schemes of IPP partitioning and utilization within one species is proposed whereby the supply of IPP for cis-polyisoprene from the MEP pathway is related to carotenoid production in latex. Subsequently, a set of latex unique gene transcripts was sequenced and assembled and they were then mapped to IPP-requiring pathways. Up to eight such pathways, including cis-polyisoprene biosynthesis, were identified. Our findings on pre- and post-IPP metabolic routes form an important aspect of a pathway knowledge-driven approach to enhancing cis-polyisoprene biosynthesis in transgenic rubber trees.
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Affiliation(s)
- Keng-See Chow
- Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, 47000 Sungai Buloh, Selangor, Malaysia
| | - Mohd.-Noor Mat-Isa
- Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
| | - Azlina Bahari
- Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, 47000 Sungai Buloh, Selangor, Malaysia
| | - Ahmad-Kamal Ghazali
- Science Vision SB, Setia Avenue, 33A-4 Jalan Setia Prima S, U13/S, Setia Alam, Seksyen U13, 40170 Shah Alam, Selangor, Malaysia
| | - Halimah Alias
- Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
| | - Zainorlina Mohd.-Zainuddin
- Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, 47000 Sungai Buloh, Selangor, Malaysia
| | - Chee-Choong Hoh
- Science Vision SB, Setia Avenue, 33A-4 Jalan Setia Prima S, U13/S, Setia Alam, Seksyen U13, 40170 Shah Alam, Selangor, Malaysia
| | - Kiew-Lian Wan
- Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
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Amiruddin N, Lee XW, Blake DP, Suzuki Y, Tay YL, Lim LS, Tomley FM, Watanabe J, Sugimoto C, Wan KL. Characterisation of full-length cDNA sequences provides insights into the Eimeria tenella transcriptome. BMC Genomics 2012; 13:21. [PMID: 22244352 PMCID: PMC3315734 DOI: 10.1186/1471-2164-13-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 01/13/2012] [Indexed: 11/12/2022] Open
Abstract
Background Eimeria tenella is an apicomplexan parasite that causes coccidiosis in the domestic fowl. Infection with this parasite is diagnosed frequently in intensively reared poultry and its control is usually accorded a high priority, especially in chickens raised for meat. Prophylactic chemotherapy has been the primary method used for the control of coccidiosis. However, drug efficacy can be compromised by drug-resistant parasites and the lack of new drugs highlights demands for alternative control strategies including vaccination. In the long term, sustainable control of coccidiosis will most likely be achieved through integrated drug and vaccination programmes. Characterisation of the E. tenella transcriptome may provide a better understanding of the biology of the parasite and aid in the development of a more effective control for coccidiosis. Results More than 15,000 partial sequences were generated from the 5' and 3' ends of clones randomly selected from an E. tenella second generation merozoite full-length cDNA library. Clustering of these sequences produced 1,529 unique transcripts (UTs). Based on the transcript assembly and subsequently primer walking, 433 full-length cDNA sequences were successfully generated. These sequences varied in length, ranging from 441 bp to 3,083 bp, with an average size of 1,647 bp. Simple sequence repeat (SSR) analysis identified CAG as the most abundant trinucleotide motif, while codon usage analysis revealed that the ten most infrequently used codons in E. tenella are UAU, UGU, GUA, CAU, AUA, CGA, UUA, CUA, CGU and AGU. Subsequent analysis of the E. tenella complete coding sequences identified 25 putative secretory and 60 putative surface proteins, all of which are now rational candidates for development as recombinant vaccines or drug targets in the effort to control avian coccidiosis. Conclusions This paper describes the generation and characterisation of full-length cDNA sequences from E. tenella second generation merozoites and provides new insights into the E. tenella transcriptome. The data generated will be useful for the development and validation of diagnostic and control strategies for coccidiosis and will be of value in annotation of the E. tenella genome sequence.
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Affiliation(s)
- Nadzirah Amiruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
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Abstract
Mycobacterium abscessus (M. abscessus) is a non-tuberculous mycobacterium and an important emerging pathogen causing skin, soft tissue and pulmonary infections. The case of a 59-year-old man with a history of pulmonary tuberculosis (TB) and current pulmonary infection due to M. abscessus, complicated with pneumocardial disease and bronchiectasis, is described. Zhiel-Neelsen stain and acid Lowenstein-Jensen culture were both positive for acid-fast bacillus. The patient was initially misdiagnosed and ineffectively treated for pulmonary TB. Antimycobacterial susceptibility tests found the isolate to be resistant to four first-line and seven second-line antituberculosis drugs. The isolate was finally identified as M. abscessus using 16S ribosomal RNA and hsp65 and rpoB gene sequence analysis. Species of mycobacterium should be included in the differential diagnosis when patients do not respond to standard antituberculosis therapy. Molecular methods are useful for rapid and species-specific identification.
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Affiliation(s)
- P Zhao
- Chaoyang Centre for Disease Control and Prevention, Beijing, China
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Chow YP, Wan KL, Blake DP, Tomley F, Nathan S. Immunogenic Eimeria tenella glycosylphosphatidylinositol-anchored surface antigens (SAGs) induce inflammatory responses in avian macrophages. PLoS One 2011; 6:e25233. [PMID: 21980402 PMCID: PMC3182191 DOI: 10.1371/journal.pone.0025233] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 08/30/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND At least 19 glycosylphosphatidylinositol (GPI)-anchored surface antigens (SAGs) are expressed specifically by second-generation merozoites of Eimeria tenella, but the ability of these proteins to stimulate immune responses in the chicken is unknown. METHODOLOGY/PRINCIPAL FINDINGS Ten SAGs, belonging to two previously defined multigene families (A and B), were expressed as soluble recombinant (r) fusion proteins in E. coli. Chicken macrophages were treated with purified rSAGs and changes in macrophage nitrite production, and in mRNA expression profiles of inducible nitric oxide synthase (iNOS) and of a panel of cytokines were measured. Treatment with rSAGs 4, 5, and 12 induced high levels of macrophage nitric oxide production and IL-1β mRNA transcription that may contribute to the inflammatory response observed during E. tenella infection. Concomitantly, treatment with rSAGs 4, 5 and 12 suppressed the expression of IL-12 and IFN-γ and elevated that of IL-10, suggesting that during infection these molecules may specifically impair the development of cellular mediated immunity. CONCLUSIONS/SIGNIFICANCE In summary, some E. tenella SAGs appear to differentially modulate chicken innate and humoral immune responses and those derived from multigene family A (especially rSAG 12) may be more strongly linked with E. tenella pathogenicity associated with the endogenous second generation stages.
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Affiliation(s)
- Yock-Ping Chow
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor D.E., Malaysia
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor D.E., Malaysia
- Malaysia Genome Institute, Kajang, Selangor D.E., Malaysia
| | - Damer P. Blake
- Pathology and Infectious Diseases, Royal Veterinary College, University of London, North Mymms, United Kingdom
| | - Fiona Tomley
- Pathology and Infectious Diseases, Royal Veterinary College, University of London, North Mymms, United Kingdom
| | - Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor D.E., Malaysia
- Malaysia Genome Institute, Kajang, Selangor D.E., Malaysia
- * E-mail:
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Goh MY, Pan MZ, Blake DP, Wan KL, Song BK. Eimeria maxima phosphatidylinositol 4-phosphate 5-kinase: locus sequencing, characterization, and cross-phylum comparison. Parasitol Res 2011; 108:611-20. [PMID: 20938684 DOI: 10.1007/s00436-010-2104-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2010] [Accepted: 09/23/2010] [Indexed: 10/19/2022]
Abstract
Phosphatidylinositol 4-phosphate 5-kinase (PIP5K) may play an important role in host-cell invasion by the Eimeria species, protozoan parasites which can cause severe intestinal disease in livestock. Here, we report the structural organization of the PIP5K gene in Eimeria maxima (Weybridge strain). Two E. maxima BAC clones carrying the E. maxima PIP5K (EmPIP5K) coding sequences were selected for shotgun sequencing, yielding a 9.1-kb genomic segment. The EmPIP5K coding region was initially identified using in silico gene-prediction approaches and subsequently confirmed by mapping rapid amplification of cDNA ends and RT-PCR-generated cDNA sequence to its genomic segment. The putative EmPIP5K gene was located at position 710-8036 nt on the complimentary strand and comprised of 23 exons. Alignment of the 1147 amino acid sequence with previously annotated PIP5K proteins from other Apicomplexa species detected three conserved motifs encompassing the kinase core domain, which has been shown by previous protein deletion studies to be necessary for PIP5K protein function. Phylogenetic analysis provided further evidence that the putative EmPIP5K protein is orthologous to that of other Apicomplexa. Subsequent comparative gene structure characterization revealed events of intron loss/gain throughout the evolution of the apicomplexan PIP5K gene. Further scrutiny of the genomic structure revealed a possible trend towards "intron gain" between two of the motif regions. Our findings offer preliminary insights into the structural variations that have occurred during the evolution of the PIP5K locus and may aid in understanding the functional role of this gene in the cellular biology of apicomplexan parasites.
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Affiliation(s)
- Mei-Yen Goh
- School of Science, Monash University Sunway Campus, Jalan Lagoon Selatan, 46150 Bandar Sunway, Selangor, DE, Malaysia
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Blake DP, Billington KJ, Copestake SL, Oakes RD, Quail MA, Wan KL, Shirley MW, Smith AL. Genetic mapping identifies novel highly protective antigens for an apicomplexan parasite. PLoS Pathog 2011; 7:e1001279. [PMID: 21347348 PMCID: PMC3037358 DOI: 10.1371/journal.ppat.1001279] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 01/07/2011] [Indexed: 11/19/2022] Open
Abstract
Apicomplexan parasites are responsible for a myriad of diseases in humans and livestock; yet despite intensive effort, development of effective sub-unit vaccines remains a long-term goal. Antigenic complexity and our inability to identify protective antigens from the pool that induce response are serious challenges in the development of new vaccines. Using a combination of parasite genetics and selective barriers with population-based genetic fingerprinting, we have identified that immunity against the most important apicomplexan parasite of livestock (Eimeria spp.) was targeted against a few discrete regions of the genome. Herein we report the identification of six genomic regions and, within two of those loci, the identification of true protective antigens that confer immunity as sub-unit vaccines. The first of these is an Eimeria maxima homologue of apical membrane antigen-1 (AMA-1) and the second is a previously uncharacterised gene that we have termed ‘immune mapped protein-1’ (IMP-1). Significantly, homologues of the AMA-1 antigen are protective with a range of apicomplexan parasites including Plasmodium spp., which suggest that there may be some characteristic(s) of protective antigens shared across this diverse group of parasites. Interestingly, homologues of the IMP-1 antigen, which is protective against E. maxima infection, can be identified in Toxoplasma gondii and Neospora caninum. Overall, this study documents the discovery of novel protective antigens using a population-based genetic mapping approach allied with a protection-based screen of candidate genes. The identification of AMA-1 and IMP-1 represents a substantial step towards development of an effective anti-eimerian sub-unit vaccine and raises the possibility of identification of novel antigens for other apicomplexan parasites. Moreover, validation of the parasite genetics approach to identify effective antigens supports its adoption in other parasite systems where legitimate protective antigen identification is difficult. Protozoan parasites are responsible for serious diseases in humans and livestock species. Vaccination is a declared intervention of choice with these infections, but even after many years of effort few effective vaccines are available. Identification of the right antigens for inclusion in sub-unit vaccines is a particular problem with complex pathogens. Moreover, the host response does not discriminate between protective and non-protective antigens, confounding development of effective screening systems. This study represents the culmination of work using parasite genetics and immunity as a selective barrier to find parts of the parasite genome targeted by immunity. The pathogen used in these studies (Eimeria maxima) is very important in livestock and related to a number of human pathogens including those responsible for malaria. Our studies indicate that just six regions in the genome were targeted by immunity and two of these have now been interrogated to determine the protective antigen encoding gene. Interestingly, one of these (called AMA-1) has homologues known to be protective with other apicomplexan parasites. This raises the intriguing possibility that a set of homologous antigens may be protective across the apicomplexan parasites and that protective antigen discovery in one parasite may generate new leads in other vaccine programmes.
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Affiliation(s)
- Damer P. Blake
- Institute for Animal Health, Compton, Berkshire, United Kingdom
- Pathology and Infectious Diseases, Royal Veterinary College, University of London, North Mymms, United Kingdom
- * E-mail: (DPB); (ALS)
| | | | | | | | - Michael A. Quail
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Kiew-Lian Wan
- Malaysia Genome Institute, UKM-MTDC Technology Centre, Selangor, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | | | - Adrian L. Smith
- Institute for Animal Health, Compton, Berkshire, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (DPB); (ALS)
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Su YC, Wan KL, Mohamed R, Nathan S. Immunization with the recombinant Burkholderia pseudomallei outer membrane protein Omp85 induces protective immunity in mice. Vaccine 2010; 28:5005-11. [PMID: 20546831 DOI: 10.1016/j.vaccine.2010.05.022] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Revised: 05/06/2010] [Accepted: 05/07/2010] [Indexed: 11/16/2022]
Abstract
Burkholderia pseudomallei is resistant to a wide range of antibiotics, leading to relapse and recrudescence of melioidosis after cessation of antibiotic therapy. More effective immunotherapies are needed for better management of melioidosis. We evaluated the prophylactic potential of the immunogenic outer membrane protein Omp85 as a vaccine against murine melioidosis. Immunization of BALB/c mice with recombinant Omp85 (rOmp85) triggered a Th2-type immune response. Up to 70% of the immunized animals were protected against infectious challenge of B. pseudomallei with reduced bacterial load in extrapulmonary organs. Mouse anti-rOmp85 promoted complement-mediated killing and opsonophagocytosis of B. pseudomallei by human polymorphonuclear cells. In conclusion, we demonstrated that B. pseudomallei Omp85 is potentially able to induce protective immunity against melioidosis.
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Affiliation(s)
- Yu-Ching Su
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia
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Lokanathan Y, Mohd-Adnan A, Wan KL, Nathan S. Transcriptome analysis of the Cryptocaryon irritans tomont stage identifies potential genes for the detection and control of cryptocaryonosis. BMC Genomics 2010; 11:76. [PMID: 20113487 PMCID: PMC2828411 DOI: 10.1186/1471-2164-11-76] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 01/29/2010] [Indexed: 01/26/2023] Open
Abstract
Background Cryptocaryon irritans is a parasitic ciliate that causes cryptocaryonosis (white spot disease) in marine fish. Diagnosis of cryptocaryonosis often depends on the appearance of white spots on the surface of the fish, which are usually visible only during later stages of the disease. Identifying suitable biomarkers of this parasite would aid the development of diagnostic tools and control strategies for C. irritans. The C. irritans genome is virtually unexplored; therefore, we generated and analyzed expressed sequence tags (ESTs) of the parasite to identify genes that encode for surface proteins, excretory/secretory proteins and repeat-containing proteins. Results ESTs were generated from a cDNA library of C. irritans tomonts isolated from infected Asian sea bass, Lates calcarifer. Clustering of the 5356 ESTs produced 2659 unique transcripts (UTs) containing 1989 singletons and 670 consensi. BLAST analysis showed that 74% of the UTs had significant similarity (E-value < 10-5) to sequences that are currently available in the GenBank database, with more than 15% of the significant hits showing unknown function. Forty percent of the UTs had significant similarity to ciliates from the genera Tetrahymena and Paramecium. Comparative gene family analysis with related taxa showed that many protein families are conserved among the protozoans. Based on gene ontology annotation, functional groups were successfully assigned to 790 UTs. Genes encoding excretory/secretory proteins and membrane and membrane-associated proteins were identified because these proteins often function as antigens and are good antibody targets. A total of 481 UTs were classified as encoding membrane proteins, 54 were classified as encoding for membrane-bound proteins, and 155 were found to contain excretory/secretory protein-coding sequences. Amino acid repeat-containing proteins and GPI-anchored proteins were also identified as potential candidates for the development of diagnostic and control strategies for C. irritans. Conclusions We successfully discovered and examined a large portion of the previously unexplored C. irritans transcriptome and identified potential genes for the development and validation of diagnostic and control strategies for cryptocaryonosis.
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Affiliation(s)
- Yogeswaran Lokanathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
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Su YC, Wan KL, Mohamed R, Nathan S. A genome level survey of Burkholderia pseudomallei immunome expressed during human infection. Microbes Infect 2008; 10:1335-45. [PMID: 18761419 DOI: 10.1016/j.micinf.2008.07.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 07/22/2008] [Accepted: 07/30/2008] [Indexed: 11/26/2022]
Abstract
Burkholderia pseudomallei is the etiological agent of melioidosis, a severe infectious disease of humans and animals. The role of the bacterium's proteins expressed in vivo during human melioidosis continues to remain an enigma. This study's aim was to identify B. pseudomallei target proteins that elicit the humoral immune response in infected humans. A small insert genomic expression library was constructed and immunoscreened to identify peptides that reacted exclusively with melioidosis patients' sera. Sero-positive clones expressing immunogenic peptides were sequenced and annotated, and shown to represent 109 proteins involved in bacterial cell envelope biogenesis, cell motility and secretion, transcription, amino acid, ion and protein metabolism, energy production, DNA repair and unknown hypothetical proteins. Western blot analysis of three randomly selected full-length immunogenic polypeptides with patients' sera verified the findings of the immunome screening. The patients' humoral immune response to the 109 proteins suggests the induction or significant upregulation of these proteins in vivo during human infection and thus may play a role in the pathogenesis of B. pseudomallei. Identification of B. pseudomallei immunogens has shed new light on the elucidation of the bacterium's pathogenesis mechanism and disease severity. These immunogens can be further evaluated as prophylactic and serodiagnostic candidates as well as drug targets.
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Affiliation(s)
- Yu-Ching Su
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia
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Low ETL, Alias H, Boon SH, Shariff EM, Tan CYA, Ooi LCL, Cheah SC, Raha AR, Wan KL, Singh R. Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: identifying genes associated with callogenesis and embryogenesis. BMC Plant Biol 2008; 8:62. [PMID: 18507865 PMCID: PMC2442076 DOI: 10.1186/1471-2229-8-62] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 05/29/2008] [Indexed: 05/21/2023]
Abstract
BACKGROUND Oil palm (Elaeis guineensis Jacq.) is one of the most important oil bearing crops in the world. However, genetic improvement of oil palm through conventional breeding is extremely slow and costly, as the breeding cycle can take up to 10 years. This has brought about interest in vegetative propagation of oil palm. Since the introduction of oil palm tissue culture in the 1970s, clonal propagation has proven to be useful, not only in producing uniform planting materials, but also in the development of the genetic engineering programme. Despite considerable progress in improving the tissue culture techniques, the callusing and embryogenesis rates from proliferating callus cultures remain very low. Thus, understanding the gene diversity and expression profiles in oil palm tissue culture is critical in increasing the efficiency of these processes. RESULTS A total of 12 standard cDNA libraries, representing three main developmental stages in oil palm tissue culture, were generated in this study. Random sequencing of clones from these cDNA libraries generated 17,599 expressed sequence tags (ESTs). The ESTs were analysed, annotated and assembled to generate 9,584 putative unigenes distributed in 3,268 consensi and 6,316 singletons. These unigenes were assigned putative functions based on similarity and gene ontology annotations. Cluster analysis, which surveyed the relatedness of each library based on the abundance of ESTs in each consensus, revealed that lipid transfer proteins were highly expressed in embryogenic tissues. A glutathione S-transferase was found to be highly expressed in non-embryogenic callus. Further analysis of the unigenes identified 648 non-redundant simple sequence repeats and 211 putative full-length open reading frames. CONCLUSION This study has provided an overview of genes expressed during oil palm tissue culture. Candidate genes with expression that are modulated during tissue culture were identified. However, in order to confirm whether these genes are suitable as early markers for embryogenesis, the genes need to be tested on earlier stages of tissue culture and a wider range of genotypes. This collection of ESTs is an important resource for genetic and genome analyses of the oil palm, particularly during tissue culture development.
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Affiliation(s)
- Eng-Ti L Low
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Halimah Alias
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
- Malaysia Genome Institute, Heliks Emas Block, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Soo-Heong Boon
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
- Asiatic Centre for Genome Technology Sdn Bhd (ACGT), Lot L3-I-1, Enterprise 4, Technology Park Malaysia, 57000 Kuala Lumpur, Malaysia
| | - Elyana M Shariff
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
- Myagri Associates Sdn. Bhd., 25-2, Jalan Seri Putra 1/2, Bandar Seri Putra Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Chi-Yee A Tan
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
- Thermo Fisher Scientific, 3, Jalan Sepadu 25/123, Taman Perindustrian Axis, Seksyen 25, 40400 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Leslie CL Ooi
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Suan-Choo Cheah
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
- Asiatic Centre for Genome Technology Sdn Bhd (ACGT), Lot L3-I-1, Enterprise 4, Technology Park Malaysia, 57000 Kuala Lumpur, Malaysia
| | - Abdul-Rahim Raha
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43300 UPM Serdang, Selangor DE, Malaysia
| | - Kiew-Lian Wan
- Malaysia Genome Institute, Heliks Emas Block, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
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Tan SL, Mohd-Adnan A, Mohd-Yusof NY, Forstner MRJ, Wan KL. Identification and analysis of a prepro-chicken gonadotropin releasing hormone II (preprocGnRH-II) precursor in the Asian seabass, Lates calcarifer, based on an EST-based assessment of its brain transcriptome. Gene 2008; 411:77-86. [PMID: 18280674 DOI: 10.1016/j.gene.2008.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 01/13/2008] [Accepted: 01/16/2008] [Indexed: 11/27/2022]
Abstract
Using a novel library of 5637 expressed sequence tags (ESTs) from the brain tissue of the Asian seabass (Lates calcarifer), we first characterized the brain transcriptome for this economically important species. The ESTs generated from the brain of L. calcarifer yielded 2410 unique transcripts (UTs) which comprise of 982 consensi and 1428 singletons. Based on database similarity, 1005 UTs (41.7%) can be assigned putative functions and were grouped into 12 functional categories related to the brain function. Amongst others, we have identified genes that are putatively involved in energy metabolism, ion pumps and channels, synapse related genes, neurotransmitter and its receptors, stress induced genes and hormone related genes. Subsequently we selected a putative preprocGnRH-II precursor for further characterization. The complete cDNA sequence of the gene obtained was found to code for an 85-amino acid polypeptide that significantly matched preprocGnRH-II precursor sequences from other vertebrates, and possesses structural characteristics that are similar to that of other species, consisting of a signal peptide (23 residues), a GnRH decapeptide (10 residues), an amidation/proteolytic-processing signal (glycine-lysine-argine) and a GnRH associated peptide (GAP) (49 residues). Phylogenetic analysis showed that this putative L. calcarifer preprocGnRH-II sequence is a member of the subcohort Euteleostei and divergent from the sequences of the subcohort Otocephalan. These findings provide compelling evidence that the putative L. calcarifer preprocGnRH-II precursor obtained in this study is orthologous to that of other vertebrates. The functional prediction of this preprocGnRH-II precursor sequence through in silico analyses emphasizes the effectiveness of the EST approach in gene identification in L. calcarifer.
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Affiliation(s)
- Sik-Loo Tan
- Malaysia Genome Institute, Heliks Emas Block, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
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Latifah I, Teoh KY, Wan KL, Normaznah Y, Rahmah M. A study on PCR-RFLP of Giardia duodenalis in Malaysia. Malays J Pathol 2007; 29:25-31. [PMID: 19105325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Giardia duodenalis causes diarrhoea and malabsorption. The objectives of the study were to detect local isolates of G. doudenalis by polymerase chain reaction (PCR) and to determine their restriction fragment length polymorphisms (RFLP). G. doudenalis isolated from stools of patients from Hospital Orang Asli Gombak were cultured axenically using TYI-S-33 medium with 10% foetal calf serum. The commercially designed primer-pair 432/433 was used to amplify a 0.52 kb segment known to encode the homologous cysteine-rich trophozoite surface antigen (tsp11 and tsa417). Results showed that the primer-pair 432/433 could amplify the target region of the local isolates. RFLP study on the identical isolates showed that all the restriction enzymes tested ( HindIII, ClaI, PstI and Kpn) gave a banding pattern similar to that of the WB strain a reference pathogenic strain from human. The reference pathogenic strain were commercially obtained from the American Type Culture Collection (ATCC).
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Affiliation(s)
- I Latifah
- Biotechnology Unit, Institute for Medical Research, Kuala Lumpur, Malaysia.
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Ling KH, Rajandream MA, Rivailler P, Ivens A, Yap SJ, Madeira AM, Mungall K, Billington K, Yee WY, Bankier AT, Carroll F, Durham AM, Peters N, Loo SS, Mat Isa MN, Novaes J, Quail M, Rosli R, Nor Shamsudin M, Sobreira TJ, Tivey AR, Wai SF, White S, Wu X, Kerhornou A, Blake D, Mohamed R, Shirley M, Gruber A, Berriman M, Tomley F, Dear PH, Wan KL. Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization. Genome Res 2007; 17:311-9. [PMID: 17284678 PMCID: PMC1800922 DOI: 10.1101/gr.5823007] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Eimeria tenella is an intracellular protozoan parasite that infects the intestinal tracts of domestic fowl and causes coccidiosis, a serious and sometimes lethal enteritis. Eimeria falls in the same phylum (Apicomplexa) as several human and animal parasites such as Cryptosporidium, Toxoplasma, and the malaria parasite, Plasmodium. Here we report the sequencing and analysis of the first chromosome of E. tenella, a chromosome believed to carry loci associated with drug resistance and known to differ between virulent and attenuated strains of the parasite. The chromosome--which appears to be representative of the genome--is gene-dense and rich in simple-sequence repeats, many of which appear to give rise to repetitive amino acid tracts in the predicted proteins. Most striking is the segmentation of the chromosome into repeat-rich regions peppered with transposon-like elements and telomere-like repeats, alternating with repeat-free regions. Predicted genes differ in character between the two types of segment, and the repeat-rich regions appear to be associated with strain-to-strain variation.
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Affiliation(s)
- King-Hwa Ling
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- Molecular Genetics Laboratory, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Marie-Adele Rajandream
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Pierre Rivailler
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Alasdair Ivens
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Soon-Joo Yap
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Alda M.B.N. Madeira
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil
| | - Karen Mungall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Karen Billington
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Wai-Yan Yee
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Alan T. Bankier
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
| | - Fionnadh Carroll
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Alan M. Durham
- Departamento de Ciências da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil
| | - Nicholas Peters
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Shu-San Loo
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Jeniffer Novaes
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil
| | - Michael Quail
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Rozita Rosli
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- Molecular Genetics Laboratory, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Mariana Nor Shamsudin
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Tiago J.P. Sobreira
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil
| | - Adrian R. Tivey
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Siew-Fun Wai
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Sarah White
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Xikun Wu
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Arnaud Kerhornou
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Damer Blake
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Rahmah Mohamed
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Martin Shirley
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Arthur Gruber
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil
| | - Matthew Berriman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Fiona Tomley
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Paul H. Dear
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
- Corresponding author.E-mail ; fax 44-1-223-412-178
| | - Kiew-Lian Wan
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- Corresponding author.E-mail ; fax 44-1-223-412-178
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Chow KS, Wan KL, Isa MNM, Bahari A, Tan SH, Harikrishna K, Yeang HY. Insights into rubber biosynthesis from transcriptome analysis of Hevea brasiliensis latex. J Exp Bot 2007; 58:2429-40. [PMID: 17545224 DOI: 10.1093/jxb/erm093] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Hevea brasiliensis is the most widely cultivated species for commercial production of natural rubber (cis-polyisoprene). In this study, 10,040 expressed sequence tags (ESTs) were generated from the latex of the rubber tree, which represents the cytoplasmic content of a single cell type, in order to analyse the latex transcription profile with emphasis on rubber biosynthesis-related genes. A total of 3,441 unique transcripts (UTs) were obtained after quality editing and assembly of EST sequences. Functional classification of UTs according to the Gene Ontology convention showed that 73.8% were related to genes of unknown function. Among highly expressed ESTs, a significant proportion encoded proteins related to rubber biosynthesis and stress or defence responses. Sequences encoding rubber particle membrane proteins (RPMPs) belonging to three protein families accounted for 12% of the ESTs. Characterization of these ESTs revealed nine RPMP variants (7.9-27 kDa) including the 14 kDa REF (rubber elongation factor) and 22 kDa SRPP (small rubber particle protein). The expression of multiple RPMP isoforms in latex was shown using antibodies against REF and SRPP. Both EST and quantitative reverse transcription-PCR (QRT-PCR) analyses demonstrated REF and SRPP to be the most abundant transcripts in latex. Besides rubber biosynthesis, comparative sequence analysis showed that the RPMPs are highly similar to sequences in the plant kingdom having stress-related functions. Implications of the RPMP function in cis-polyisoprene biosynthesis in the context of transcript abundance and differential gene expression are discussed.
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Affiliation(s)
- Keng-See Chow
- Biotechnology Unit, Rubber Research Institute of Malaysia, Malaysian Rubber Board, RRIM Experiment Station, 47000 Sungai Buloh, Selangor, Malaysia.
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Ling KH, Loo SS, Rosli R, Shamsudin MN, Mohamed R, Wan KL. In silico identification and characterization of a putative phosphatidylinositol 4-phosphate 5-kinase (PIP5K) gene in Eimeria tenella. In Silico Biol 2007; 7:115-21. [PMID: 17688436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks) play diverse roles in the cellular biology of many organisms, including signal transduction, secretion and vesicular trafficking, and regulation of cytoskeleton assembly. Discovery of the PIP5K gene in Eimeria tenella may shed light on its role in the biology of this avian protozoan, and afford further understanding of the cell-host interaction, particularly during the invasion process. In this study, we report the identification of the PIP5K coding region in the genome sequence of Eimeria tenella using in silico gene prediction approaches. Prediction of the PIP5K coding sequence was confirmed by mapping the full-length cDNA sequence, generated via the Rapid Amplification of cDNA Ends (RACE) method, to the genomic sequence. The putative PIP5K gene of Eimeria tenella is located on the complementary strand of the E1080B12.b1 contig, and comprises 12 exons. Further analysis showed that the coding region spans from exon 1 to exon 7, with all exons obeying the adopted 'gt...ag' splicing rule of intronic sequences. Consensus of the hexameric 5' donor-splice site was deduced as GTRDBB... and the consensus for the 3' acceptor-splice sites as ...BHDYAG. The gene encodes a 252-amino acid residue protein. Domain search and protein fold recognition analyses provide compelling evidences that the deduced protein is a PIP5K.
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Affiliation(s)
- King-Hwa Ling
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, Selangor DE, Malaysia.
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