News

GENOME OF MICROBULBIFER sp. CCB-MM1

PUBLICATION

Moh Tsu Horng , a MSc student alongside Dr. Lau Nyok Sean, Dr. Go Furusawa and Prof. Dr. Amirul Al-Ashraf Abdullah have published a research article titled “Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia” in Standards in Genomic Sciences. The strain CCB-MM1 was isolated from an estuarine sediment sample taken from Matang Mangrove Forest, Malaysia. 16s rRNA shows the strain only shares 98.1% similarity to Microbulbifer rhizosphaerae Cs16bT. The one of unique features found of Microbulbifer sp. CCB-MM1 is that the bacteria has the ability to alter its shape depending on its growth cycle, cocci-shaped in growth phase upon reaching exponential phase the shape of the bacterium changes to a rod-shaped. This strain is also known to produce a secondary metabolite, ectoine, which has cell protectant and protein stabilizing properties. https://doi.org/10.1186/s40793-017-0248-0

VISIT BY DR. PRIYADARSHAN

Dr.Priya

Friday, 28th July 2017 – The Centre for Chemical Biology (CCB) hosted a visit by Dr. P. M. Priyadarshan, formerly deputy director of Rubber Research Institute of India, who had a one-day official visit to Universiti Sains Malaysia. The much anticipated book Biology of Hevea Rubber, recently released at the Singapore Botanic Gardens on 4th August commemorating 140 years of the arrival of first rubber seeds at Singapore was authored by Dr. Priyadarshan. CCB has greatly benefited from the immense knowledge and ideas shared by Dr. Priyadarshan during his visit especially on the direction and future of rubber research at CCB. CCB has formerly published the first draft genome of Hevea rubber in 2013 and subsequently a second draft of the rubber genome in 2016. The director of CCB, Professor Dr. Alexander Chong Shu Chien, led a tour of the centre and explained research projects that CCB currently focusing. Dr. Priyadarshan then proceeded with a visit to School of Biological Sciences which was led by Professor Dr. Sudesh Kumar to explore research projects conducted at the newly established rubber tissue culture laboratory.

NEXT GENERATION SEQUENCING (NGS) - BACTERIA WHOLE GENOME SEQUENCING TRAINING

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CCB has organised a private NGS Training on Bacteria Whole Genome session for Dr. Sofia Bashir from National University Research Institute, Sudan commencing on 17th April 2017 to 5th May 2017. This training was led by CCB NGS specialist Dr. Lau Nyok Sean with assistance of CCB NGS team. These 19 days training covered the theoretical and hands on session using her own bacterial sample for Library Preparation, Quality Control (QC) Analysis, Sequencing, and Bioinformatics Analysis. In library preparation session, Dr. Sofia was able to learn on how to prepare her sample's DNA library for her sample, how to troubleshoot the problems encountered throughout the library preparation session. She was also taught on how to perform Qubit Quantification and Bioanalyser Analysis as quality control check up pre- and post library preparation session. As for sequencing part, Dr. Sofia is able to learn on the principle of the sequencing of different platforms, and able to closely observe on how the sequencer works. Subsequently, for bioinformatics part, she was taught by Dr. Lau on how to analyse the data. CCB are looking forward for future research collaboration with NURI soon.

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LARGE-SCALE COLLECTION OF FULL-LENGTH cDNA AND TRANSCRIPTOME ANALYSIS IN HEVEA BRASILIENSIS

Paper Dr. Veera

Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer. With these data, we updated around 5,500 gene structures and newly annotated around 9,500 transcription start sites. Second, to elucidate the rubber biosynthetic pathways and their transcriptional regulation, we carried out tissue- and cultivar-specific RNA-Seq analysis. By using our recently published genome sequence, we confirmed the expression patterns of the rubber biosynthetic genes. Our data suggest that the cytoplasmic mevalonate (MVA) pathway is the main route for isoprenoid biosynthesis in latex production. In addition to the well-studied polymerization factors, we suggest that rubber elongation factor 8 (REF8) is a candidate factor in cis-polyisoprene biosynthesis. We have also identified 39 transcription factors that may be key regulators in latex production. Expression profile analysis using two additional cultivars, RRIM 901 and PB 350, via an RNA-Seq approach revealed possible expression differences between a high latex-yielding cultivar and a disease-resistant cultivar.

DOI: https://doi.org/10.1093/dnares/dsw056

IDENTIFICATION OF NEW SPECIES OF GENUS MANGROVIMONAS


Dr. Go paper

Balachandra Dinesh, a MSc. student, Dr Go Furusawa from CCB and Prof. Dr. Amirul Al-Ashraf Abdullah have published a research article entitled “Mangrovimonas xylaniphaga sp. nov. isolated from estuarine mangrove sediment of Matang Mangrove Forest, Malaysia” in Archives of Microbiology. In this study, strain ST2L12T was isolated from estuarine mangrove sediment of Matang Mangrove Forest, Malaysia. 16S rRNA sequences of the strain exhibited 95.3% similarity to the genus Mangrovimonas, which is a closest relative. The fatty acid profile of strain ST2 ST2L12T was slightly different from that of Mangrovimonas yunxiaonensis LYYY01T. Interestingly, strain ST2L12T showed capability of xylan degradation which was not observed in the strain LYYY01T. These data indicate that strain ST2L12T represents a novel species of the genus Mangrovimonas, for which the name Mangrovimonas xylaniphaga sp. nov. is proposed.

http://link.springer.com/article/10.1007%2Fs00203-016-1275-8