Publications

publications 5

2017

Genome feautures of moderately halophilic polyhydroxyalkanoate-producing Yangia sp. CCB-MM3

Nyok-Sean Lau, Ka-Kei Sam, Abdullah Al-Ashraf Amirul. 2017. Standards in Genomic Sciences, doi:10.1186/s40793-017-0232-8


Mangrovimonas xylaniphaga sp. nov. isolated from estuarine mangrove sediment of matang mangrove forest, malaysia

Balachandra Dinesh, Go Furusawa, A. A. Amirul. 2017. Archives of Microbiology, 199-63-67


synthesis of high 4-hydroxybutyrate copolymer by Cupriavidus sp. transformants using one-stage cultivation and mixed precursor substrates strategy

Syafiq I.M., Bhubalan K., Huong K.-H., Vigneswari S., Amirul A.A., Shantini K., Aziz N.A. 2017. Enzyme and Microbial Technology,98,1-8


Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis
Yuko Makita, Kiaw Kiaw Ng, G. Veera Singham, Mika Kawashima, Hideki Hirakawa, Shushei Sato, Ahmad Sofiman Othman, Minami Matsui.2017. DNA Research, 1-11
 

Effects of Different Surfaces and Insecticide Carriers on Residual Insecticide Bioassays Againts Bed Bugs, Cimex spp. (Hemiptera: Cimicidae)
Kai Dang, G. Veera Singham, Stephen L. Doggett, David G. Lilly and Chow-Yang Lee.2017. Journal of Economic Entomology, 1-9
 
Complete genome sequences of three Cupriavidus strains isolated from various Malaysian environments

Shafie N.A.H., Lau N.-S., Amirul A.A., Ramachandran H.2017. Genome Announcements (2017), doi: 10.1128/genomeA.01498-16


Agarolytic bacterium Persicobacter sp. CCB-QB2 exhibited a diauxic growth involving galactose utilization pathway

Go Furusawa, Nyok-Sean Lau, Suganthi Appalasamy, Amirul Al-Ashraf Abdullah. Microbiology Open (2017), doi: 10.1002/mbo3.405


Crystallization and X-ray crystallographic analysis of recombinant TylP, a putative γ-butyrolactone receptor protein from Streptomyces fradiae

Mohd-Sharif N., Shaibullah S., Baharum S.N., Ng C.L., Givajothi V., Tan C.-S., Ho K.L., Teh A.-H., Waterman J. Acta Cryst. F (2017), 73,109-115


Microbial-based synthesis of highly elastomeric biodegradable poly(3-hydroxybutyrate-co-4-hydroxybutyrate) thermoplastic

Huong, K.-H.,Teh, C.-H., Amirul, A.A. International Journal of Biological Macromolecules (2017), doi:org/10.1016/j.ijbiomac.2017.03.179


Enhanced degradation of polyhydroxyalkanoates (PHAs) by newly isolated Burkholderia cepacia DP1 with high depolymerase activity

Azami, N.A., Wirjon, I.A., Kannusamy, S., Teh, A.-H., Abdullah, A.A.-A. 3 Biotech (2017), doi: 10.1007/s13205-017-0716-7


Enhanced production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) copolymer and antimicrobial yellow pigmentation from Cupriavidus sp. USMAHM13 with antibiofilm capability

Ismail, I., Gurusamy, T.P., Ramachandran, H., Al-Ashraf Amirul, A. Preparative Biochemistry and Biotechnology (2017), 47,388-396


Exploring the Potential of 1-Pentanol and Oleic Acid for Optimizing the Production of Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) Copolymer by Cupriavidus sp. USMAA1020

Huong K.-H., Amirul A.A., Shantini K., Sharmini R. Arabian Journal for Science and Engineering (2017), 42 (6), pp. 2313-2320


Combination of 4-Hydroxybutyrate Carbon Precursors as Substrate for Simultaneous Production of P(3HB-co-4HB) and Yellow Pigment by Cupriavidus sp. USMAHM13

I. Iszatty,O. Noor Aidda,R. Hema,A. A. Amirul. Arabian Journal for Science and Engineering (2017), 42 (6), pp. 2303–2311


Complete Genome Sequence of Proteus mirabilis Phage pPM_01 Isolated from Raw Sewage

Wirjon I.A.,Lau N.-S, Arip Y.M.. Intervirology (2017), 59:243-253


Pilot scale production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) biopolymers with high molecular weight and elastomeric properties

Huong K-H, Azuraini M.J., Aziz N.A., Amirul A.-A.A.Journal of Bioscience and Bioengineering (2017), 124:76-83


Microbial-based synthesis of highly elastomeric biodegradable poly(3-hydroxybutyrate-co-4-hydroxybutyrate) thermoplastic

Huong K-H, Teh C.-H, Amirul A.-A.A.International Journal of Biological Macromolecules (2017), 101:983-995


Insecticide resistance and resistance mechanisms in bed bugs, Cimex spp. (Hemiptera: Cimicidae)

Dang, K., Doggett, S.L. , Veera Singham, G., Lee, C.-Y.Parasites and Vectors (2017), doi:10.1186/s13071-017-2232-3


Effect of dietary lipid source on expression of lipid metabolism genes and tissue lipid profile in juvenile spiny lobster Sagmariasus verreauxi

Shu-Chien A.C., Han W.-Y., Carter C.G., Fitzgibbon Q.P., Simon C.J., Battaglene S.C., Codabaccus B.M., Kuah M.-K., Ventura T.Aquaculture (2017), 479:342-351


Functional and Structural Studies of a Multidomain Alginate Lyase from Persicobacter sp. CCB-QB2

Sim, P.-F., Furusawa, G., Teh, A.-H.Scientific Reports (2017), 7(1),13656


Cupriavidus malaysiensis sp. nov., a novel poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment

Hema Ramachandran,Nur Asilla Hani Shafie, Kumar Sudesh, Mohamad Noor Azizan, Mohamad Isa Abdul Majid, Al-Ashraf Abdullah Amirul.Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology (2017), pp. 1-12


Biodegradation of Natural Rubber and Natural Rubber Products by Streptomyces sp. Strain CFMR 7

Nanthini, J., Sudesh, K.Journal of Polymers and the Environment (2017), 25(3), pp. 606-616


Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia.

Moh, T.H., Lau, N.-S., Furusawa, G., Amirul, A.-A.A..Standards in Genomic Sciences (2017), 12(1),36


Draft genome sequence of halophilic Hahella sp. strain CCB-MM4, isolated from Matang Mangrove Forest in Perak, Malaysia

Nanthini, J., Ong, S.Y., Sudesh, K..Genome Announcements. (2017), 5(42),e01147-17


Identification of three homologous latex-clearing protein (lcp) genes from the genome of Streptomyces sp. strain CFMR 7

Nanthini, J., Ong, S.Y., Sudesh, K..Gene (2017), 628, pp. 146-155


Microbulbifer aggregans sp. nov., isolated from estuarine sediment from a mangrove forest

Moh, T.H., Furusawa, G., Amirul, A.A.-A.International Journal of Systematic and Evolutionary Microbiology (2017), 67(10),002258, pp. 4089-4094.


2016

The rubber tree genome shows expansion of gene family associated with rubber biosynthesis

Nyok-Sean Lau,Yuko Makita, Mika Kawashima, Todd D. Taylor, Shinji Kondo, Ahmad Sofiman Othman,Alexander Chong Shu-Chien & Minami Matsui. 2016. Scientific Reports 6, Article number: 28594.


 Comparative genome analyses of novel Mangrovimonas-like strains isolated from estuarine mangrove sediments reveal xylan and arabinan utilization genes

Balachandra Dinesh, Nyok-Sean Lau, Go Furusawa, Seok-Won Kim, Todd D. Taylor, Swee Yeok Foong, Alexander Chong Shu-Chien. 2016. Marine Genomics, 25 (2016), 115-121.


Discovery Of a new polyhydroxyalkanoate synthase from limestone soil through metagenomic approach

Yen Teng Tai, Choon Pin Foong, Nazalan Najimudin, Kumar Sudesh. 2016. Journal of Bioscience and Bioengineering, 121, 355-364.


Crystal Structure Of Anoxybacillus α-amylase Provides Insights Into Maltose Binding Of A New Glycosyl Hydrolase Subclass
Kian Piaw Chai, Noor Farhan Binti Othman. Aik-Hong Teh, Kok Lian Ho, Kok-Gan Chan, Mohd Shahir Shamsir, Kian Mau Goh & Chyan Leong Ng.    2016. Scientific Report, 6, Article number:23126.

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of recombinant human c1ORF123 protein
Rahaman, S.N.A, Yusop, J.M., Mohamed-Hussein, Z.-A, Ho, K.L., Teh, A.-H, Waterman, J., Ng, C.L.. 2016. Acta Cryst. F, 72, 207-213.
 

simultaneous dual syringe electrospinning system using benign solvent to fabricate nanofibrous P(3HB-co-4HB)/ collagen peptides construct as potential leave-on wound dressing
S. Vigneswari, V. Murugaiyah, G. Kaur, H.P.S. Abdul Khalil, A.A. Amirul. 2016. Materials Science and Engineering C, 66, 147-155.
 

Identification of a new polyhydroxyalkanoate (PHA) producer Aquitalea sp. USM4 (JCM 19919) and characterization of its PHA synthase
Lee-Mei Ng, Kumar Sudesh.2016. Journal of Bioscience and Bioengineering (2016). doi:10.1016/j.jbiosc.2016.03.024
 
Identification of differentially expressed genes and signalling pathways in bark of Hevea brasiliensis seedlings associated with secondary laticifer differentiation using gene expression microarray
Swee Cheng Loh,  Gincy P. Thottathil, Ahmad Sofiman Othman.2016. Plant Physiology and Biochemistry,107, 45-55
 

A fatty acyl desaturase (fads2) with dual ∆6 and ∆5 activities from the freshwater carnivorous striped snakehead Channa striata
Kuah M.-K., Shu-Chien A.C., Jaya-Ram A.2016. Comparative Biochemistry and Physiology -Part A, 201,146-155
 

Effects of polyhydroxyalkanoate degradation on soil microbial community
Ong S.Y., Sudesh K..2016. Polymer Degradation and Stability, 131,9-19
 

Biodegradation of Natural Rubber and Natural Rubber Products by Streptomyces sp. Strain CFMR 7
Nanthini J., Sudesh K..2016. Journal of Polymers and the Environment, 1-11
 

Synthesis, structures and antibacterial studies of non-functionalized and nitrile-functionalized bis-benzimidazolium salts and respective dinuclear silver(I)-N-heterocyclic carbene complexes
Haziz U.F.M., Haque R.A., Razali M.R., Amirul A.A., Shaheeda N..2016. Polyhedron, 117,628-636
 

New non-functionalized and nitrile-functionalized benzimidazolium salts and their silver(I) complexes: Synthesis, crystal structures and antibacterial studies
Haque R.A., Haziz U.F.M., Razali M.R., Abdullah A.A.-A., Shaheeda N..2016. Polyhedron, 109,208-217
 

Mangrovimonas xylaniphaga sp. nov. isolated from estuarine mangrove sediment of Matang Mangrove Forest, Malaysia
Dinesh B., Furusawa G., Amirul A.A..2016. Archives of Microbiology, 1-5
 
Biomacromolecule immobilization: grafting of fish-scale collagen peptides onto aminolyzed P(3HB-co-4HB) scaffolds as a potential wound dressing
S Vigneswari, V Murugaiyah, G Kaur, H P S Abdul Khalil, and A A Amirul.2016. Biomedical Materials, 11,5
 

Synthesis of a palladium(II) complex of a N-heterocyclic carbene via transmetalation: crsytal structure and antibacterial studies
S Vigneswari, V Murugaiyah, G Kaur, H P S Abdul Khalil, and A A Amirul.2016. Transition Metal Chemistry, 41,715-781
 

Sequencing crop genomes: A gateway to improve tropical agriculture
Thottathil G.P., Jayasekaran K., Othman A.S..2016. Tropical Life Sciences Research, 1,93-114
 

Pilot scale production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) biopolymers with high molecular weight and elastomeric properties

Huong, K.-H., Azuraini, M.J., Aziz, N.A.,Amirul, A.A.A. Journal of Bioscience and Bioengineering (2017), doi:org/10.1016/j.jbiosc.2017.02.003

 


 

2015

 
Cloning, expression, purification, characterization, crystallization and X-ray crystallographic analysis of recombinant Der f 21 (rDer f 21) from Dermatophagoides farinae
S. L. Pang, K. L. Ho, J. Waterman, A.-H. Teh, F. T. Chew and C. L. Ng. 2015. Acta Crystallographica Section F: Structural Biology Communications 71, 1396–1400 (2015).

Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia.
Beng Soon Teh, Nyok-Sean Lau, Fui Ling Ng, Ahmad Yamin Abdul Rahman, Xuehua Wan, Jennifer A. Saito, Shaobin Hou, Aik-Hong Teh, Nazalan Najimudin, and Maqsudul Alam. 2015. Standards in Genomic Sciences, , 10(2015), 76

Calcium is required for ixotrophy of Aureispira sp. CCB-QB1.
Furusawa, G., Hartzell, P. L., & Navaratnam, V. 2015. Microbiology , 161(10), 1933-1941

Complete genome sequence of Streptomyces sp. strain CFMR 7, a natural rubber degrading actinomycete isolated from Penang, Malaysia
Jayaram Nanthini, Kim-Hou Chia, Gincy P. Thottathil, Todd D. Taylor, Shinji Kondo, Nazalan Najimudin, Primo Baybayan, Siddharth Singh, Kumar Sudesh. 2015. Journal of Biotechnology , 214(2015), 47-48

Cyanobacteria: Photoautotrophic Microbial Factories for the Sustainable Synthesis of Industrial Products
Nyok-Sean Lau, Minami Matsui, Amirul Al-Ashraf Abdullah. 2015. BioMed Research International  Volume 2015 (2015), Article ID 754934, 9 pages

Open and Lys–His hexacoordinated closed structures of a globin with swapped proximal and distal sites
Teh AH, Saito JA, Najimudin N, Alam M. 2015. Scientific Reports 5, 11407 (2015).

Structure of the RsbX phosphatase involved in the general stress response of Bacillus subtilis
Teh AH, Makino M, Hoshino T, Baba S, Shimizu N, Yamamoto M, Kumasaka T. 2015. Acta Crystallographica Section D: Biological Crystallography 71, 1392–1399 (2015).

Identification of polyunsaturated fatty acid and diterpenoid biosynthesis pathways from draft genome of Aureispira sp. CCB-QB1
Furusawa G, Lau NS, Shu-Chien AC, Jaya-Ram A, Al-Ashraf AA. 2015. Marine Genomics, 19 (2015), 39-44.
 
Genetic relatedness of Candida albicans bloodstream infection clinical isolates in Malaysia
Saranpal C.-S., Lim C.S.Y., Chong P.P., Ng K.P. 2015. Malaysian Journal of Microbiology,11,294-299
 
Characteristics of limestone soil collected from Gunung Lang, Perak and metagenomic analysis of the soil microbial community
Shantini K., Yahya A.R.M., Amirul A.A.. 2015. Applied Biochemistry and Biotechnology,11,373-382
 

Influence of feeding and controlled dissolved oxygen level on the production of poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) Copolymer by Cupriavidus sp. USMAA2-4 and its characterization
Tai Y.T., Najimudin N., Sudesh K. 2015. Malaysian Journal of Microbiology,5,doi:10.1038/srep11407
 

Complete genome sequence of Streptomyces sp. strain CFMR 7, a natural rubber degrading actinomycete isolated from Penang, Malaysia
Nanthini J., Chia K.-H., Najimudin N., Sudesh K., Thottathil G.P., Taylor T.D., Kondo S., Baybayan P., Singh S. 2015. Journal of Biotechnology,214,47-48
 

2014

Identification of new rubber-degrading bacterial strains from aged latex
Chia, K.-H., Nanthini, J., Thottathil, G.P., Najimudin, N., Hakim Mas Haris, M.R., Sudesh, K. 2014. Polymer Degradation and Stability, 109 (2014), 354-361.

Chemopreventive effects of standardized papaya leaf fraction on oxidatively stressed human liver cells
S.-A. Tan, L. Goya, S. Ramanathan, S.F. Sulaiman, M. Alam, V. Navaratnam. 2014. Food Research International, 64 (2014) 387-395.

Allosteric pocket of the dengue virus (serotype 2) NS2B/NS3 protease: In silico ligand screening and molecular dynamics studies of inhibition
A. Mukhametov, E.I. Newhouse, N.A. Aziz, J.A. Saito, M. Alam. 2014. Journal of Molecular Graphics and Modelling, 52 (2014) 103-113.

Crystal structure of truncated hemoglobin from an extremely thermophilic and acidophilic bacterium
Farrukh Jamil,*, Aik-Hong Teh, Ermin Schadich, Jennifer A. Saito, Nazalan Najimudin, and Maqsudul Alam. 2014. J Biochem (2014) doi: 10.1093/jb/mvu023

Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater

Foong C.P., Lau N.-S., Matsui M., Sudesh K., Deguchi S., Toyofuku T., Taylor T.D. 2014. BMC Microbiology  doi:10.1186/s12866-014-0318-z

2013

Draft genome sequence of the rubber tree Hevea brasiliensis
Ahmad Yamin Abdul Rahman, Abhilash O. Usharraj, Biswapriya B. Misra, Gincy P. Thottathil, Kandakumar Jayasekaran, Yun Feng, Shaobin Hou, Su Yean Ong, Fui Ling Ng, Ling Sze Lee, Hock Siew Tan, Muhd Khairul Luqman Muhd Sakaff, Beng Soon Teh, Bee Feong Khoo, Siti Suriawati Badai, Nurohaida Ab Aziz, Anton Yuryev, Bjarne Knudsen, Alexandre Dionne-Laporte, Nokuthula P. Mchunu, Qingyi Yu, Brennick J. Langston, Tracey Allen K. Freitas, Aaron G. Young, Rui Chen, Lei Wang, Nazalan Najimudin, Jennifer A. Saito, and Maqsudul Alam. 2013. BMC Genomics, 14:75. (http://www.biomedcentral.com/1471-2164/14/75/abstract) Rubber Tree Genome Browser (http://bioinfo-ccb.usm.my/cgi-bin/gb2/gbrowse/Rubber/)
 

Xylanase superproducer: Genome sequence of a compost-loving thermophilic fungus, Thermomyces lanuginosus strain SSBP
Mchunu N.P., Permaul K., Singh S., Saito J.A., Alam M., Abdul Rahman A.Y. 2013. Genome Announcements, 3,doi: 10.1128/genomeA.00388-13
 

The genomic Blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12

Ong S.Y., Rahman A.Y.A., Saito J.A., Pratap C.B., Nath G., Wan X., Hou S., Alam M. 2013. Standards in Genomic Sciences, 7,483-496


Crystal structure of a compact α-amylase from Geobacillus thermoleovorans

Mok S.-C., Teh A.-H., Saito J.A., Najimudin N., Alam M. 2013. Enzyme and Microbial Technology, 53,46-54

2012

Complete genome sequence of the thermophilic bacterium Geobacillus thermoleovorans CCB_US3_UF5
Muhd Khairul Luqman Muhd Sakaff, Ahmad Yamin Abdul Rahman, Jennifer A. Saito, Shaobin Hou, and Maqsudul Alam. 2012. Journal of Bacteriology. 194(5):1239.

Complete genome sequence of the thermophilic bacterium Thermus sp. strain CCB_US3_UF1
Beng Soon Teh, Ahmad Yamin Abdul Rahman, Jennifer A. Saito, Shaobin Hou, and Maqsudul Alam. 2012. Journal of Bacteriology. 194(5):1240.

Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium
Jimmy H. W. Saw, Anton Yuryev, Masaomi Kanbe, Shaobin Hou, Aaron G. Young, Shin-Ichi Aizawa, and Maqsudul Alam. 2012. Standards in Genomic Sciences, 6(1):84-93.

Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12
Su Yean Ong, Chandra Bhan Pratap, Xuehua Wan, Shaobin Hou, Ahmad Yamin Abdul Rahman, Jennifer A. Saito, Gopal Nath, and Maqsudul Alam. 2012. Journal of Bacteriology, 194(8):2115-2116.

Protective effects of papaya extracts on tert-butyl hydroperoxide mediated oxidative injury to human liver cells (an in-vitro study)
Sheri-Ann Tan, Sonia Ramos, Maria Angeles Martin, Raquel Mateos, Michael Harvey, Surash Ramanathan, Nazalan Najimudin, Maqsudul Alam, Laura Bravo, and Luis Goya. 2012. Free Radicals and Antioxidants, 2(3):10-19.

Tools to kill: Genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina
Md. Shahidul Islam, Md. Samiul Haque, Mohammad Moinul Islam, Emdadul Mannan Emdad, Abdul Halim, Quazi Md. Mosaddeque Hossen, Md. Zakir Hossain, Borhan Ahmed, Sifatur Rahim, Md. Sharifur Rahman, Md. Monjurul Alam, Shaobin Hou, Xuehua Wan, Jennifer A. Saito, and Maqsudul Alam. 2012. BMC Genomics, 13,493
 

 Co-expressed peJK genes of lobster (Jasus edwardsii)

Schadich E., Mason D., Sin F. 2012. Australian Journal of Zoology, 60,10-17