Molecular phylogeny and structure prediction of rice RFT1 protein

Rice is one of the most important species in the family of Poaceae. As one of the major crop that is consumed by world population, it is cultivated commercially in many parts of the world. Hence, the phylogeny study of this crop is crucial as a step for improvement of its breeding programs. Phylogenetic relationship among 12 rice cultivars that originated from two common sub-species; Indica and Japonica were inferred by comparing protein sequence data sets derived from its flowering time gene, namely RFT1 and analyzed using maximum parsimony (MP) method. The predicted structure of RFT1 protein was generated by I-TASSER server and analyzed using YASARA software. The result showed that the cultivars were classified into two major groups, where the first group (Japonica) evolved first followed by the second group (Indica). The findings suggested that some cultivars had a close relationship with each other even it is originates from different varieties. The relationships among these cultivars provide useful information for better understanding of molecular evolution process and designing good breeding program in order to generate new cultivar

Substrate and cofactor binding interaction studies of galactitol -1- Phosphate 5- Dehydrogenase from Peptoclostridium difficile

Tagatose is a high value low calorie sweetener that is used as a sugar substitute in the food and pharmaceutical industry. The production of tagatose requires the conversion of galactitol-1-phosphate to tagatose-6-phosphate by galactitol-1-phosphate 5-dehydrogenase (PdGPDH). Theobjective of this work is to study the protein-ligand interaction between PdGPDH and its ligands; galactitol-1-phosphate, Zn2+ and NAD+. Understanding of this mechanism will provide an insight into the possible catalytic events in these domains, thus providing information for potential protein engineering to improve the tagatose production. A 3D model of PdGPDH was constructed to identify the catalytic and coenzyme binding domains. In order to understand the interaction of PdGPDH with its ligands, a docking analysis of PdGPDH-substrate, PdGPDH-Zn2+ and PdGPDH-NAD+ complex was performed using CDOCKER in Discovery Studio 4.0 (DS 4.0). A series of docking events were performed to find the most stable binding interaction for the enzyme and its ligands. This study found that Cys 37, His 58, Glu 59, Glu 142 residues from PdGPDH form an active site pocket similar to known GPDH. A catalytic Zn2+ binding domain and a cofactor NAD+binding domain with strong hydrogen bonding contacts with the substrate and the cofactor were identified. The binding pockets of the enzyme for galactitol-1-phosphate, NAD+ and Zn2+has been defined. The stability of PdGPDH with its ligand was verified by utilizing the molecular dynamic simulation of docked complex. The results from this study will assist future mutagenesis study and enzyme modification work to improve the tagatose production

Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges

The published articles in PLoS Computational Biology on the development of computational biology research in Mexico, Brazil, Cuba, Costa Rica, and Thailand have inspired us to report on the development of bioinformatics activities in Malaysia. Rapid progress in molecular biology research and biotechnology in Malaysia has created sufficient demand for bioinformatics in Malaysia. Although bioinformatics in Malaysia started in the early 1990s, the initial focus on the development of the biotechnology industry has curtailed the early gains and overshadowed the systematic development of bioinformatics in Malaysia, which currently lacks in human capital development, research, and commercialization. However, government initiatives have been devised to develop the necessary national bioinformatics network and human resource development programs and to provide the necessary infrastructure, connectivity, and resources for bioinformatics. Stakeholders are experiencing reorientation and consolidating existing strengths to align with the global trends in bioinformatics. This exercise is expected to reinvigorate the bioinformatics industry in Malaysia. Tapping into niche expertise and resources such as biodiversity and coupling it with the existing biotechnology infrastructure will help to create sustainable development momentum for the future. An initiative arose from several senior scientists across local universities in Malaysia to promote this new scientific discipline in the country

The first complete mitochondrial genome data of hippocampus kuda originating from Malaysia

The spotted seahorse, Hippocampus kuda population is exponentially decreasing globally due to habitat loss contributed by massive coastal urbanization as well as its large exploitation for Chinese herbal medicine. Genomic data would be highly useful to improve biomonitoring of seahorse populations in Malaysia via the usage of non-invasive approaches such as water environmental DNA. Here we report the first complete mitogenome of two H. kuda individuals originating from Malaysia, generated using BGISEQ-500RS sequencer. The lengths of both mitogenomes are 16,529bp, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. The overall base composition was 32.46% for A, 29.40% for T, 14.73% for G and 23.41% for C with AT rich features (61.86%). The gene organization of Malaysian H. kuda were similar to that of most teleost species. A phylogenetic analysis of the genome against mtDNA data from other Hippocampus species showed that Malaysian H. kuda samples clustered with H. capensis, H. reidi and H. kuda. Notably however, analysis of the data using BLASTn revealed they had 99.18% similarity to H. capensis, and only 97.66% to H. kuda and H. reidi, which are all part of the unresolved H. kuda complex. The mitogenomes are deposited in Genbank under the accession number MT221436 (HK1) and MT221436 (HK2)

Effects of physiochemical factors on prokaryotic Biodiversity in Malaysian circumneutral hot springs

Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3-V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334-26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity.Centro de Investigación y Desarrollo en Fermentaciones Industriale

Collaborative curation in marine biodiversity informatics

Biodiversity data is complex with different levels of data standard and quality. It also exists in non discrete data boundaries over a wide spectrum, from variation in genes to diversity of species within an ecosystem. Data sources and collections are also very diverse as it is a mix of analogous legacy data and mostly digitized real time observations. Making biodiversity data visible, accessible and usable has always been a challenge, ever more now as the increasing awareness of the importance of biodiversity has widened the audience to non specialist stakeholders. Hence, this motivated us to develop a marine biodiversity management system (MBMS) to enable collaborative curation of marine biodiversity data. It is available as an easy Web based intuitive interface that is suited to collaborative real time curation by multiple researchers from different ecological and biodiversity research groups typified in Malaysian research community. The MBMS has an interactive visualization interface designed for marine data variables such as depth and current flow that provides an effective way of presenting large amounts of complex information to a wide audience using visual cues that are more intuitive than those of a conventional map. It is also designed to incorporate different layers of knowledge to allow selective viewing to protect sensitive indigenous biodiversity data

Pembangunan pengkalan maklumat dan pemetaan spesis digital biodiversiti Terengganu

Sebuah pengkalan maklumat dan sistem pemetaan spesis telah dibangunkan untuk membantu penyelidik-penyelidik kepelbagaian biologi di negeri Terengganu. Memandangkan, peta-peta berkaitan kepelbagaian biologi secara lazimnya berbentuk analog, sistem ini juga telah mendigitalkan peta analog untuk memudahkan rujukan para pengkaji seperti maklumat alam sekitar seperti kontor, kecerunan, sistem saliran (sungai, tasik, empangan) dan kawasan hutan. Maklumat – maklumat kadaster dan tematik juga dimuatnaik seperti data terperinci sempadan seperti mukim, daerah, rangkaian jalanraya dan maklumat gunatanah negeri. Maklumat kepelbagaian biologi yang menunjukkan taburan spesis dari sumber arkib juga telah diambil dari Global Biodiversity Information Facility (GBIF) untuk peringkat skala perintis. Pengkalan ini juga mempunyai keupayaan untuk memetakan maklumat spesis yang di jumpai di negeri Terengganu. Pengkalan maklumat ini dibuka kepada semua penyelidik yang berminat secara percuma

Digitising Mersing: a web based biodiversity analysis tool for the East Coast of Johor

Biodiversity informatics is a currently developing bioinformatics field that contributes to the management of the biodiversity and ecosystem by providing decision making cues to researchers, environmental managers and policymakers. It brings together ecologist, environmentalist and computer scientists to solve real-world conservation challenges while developing the underlying ecological, bioinformatics, and information sciences. However, biodiversity information are currently presented in text databases located in dispersed locations even within the same research institution. The data itself are usually difficult or even inaccessible, flat file formatted and with existing geospatial information in numbered coordinates that is almost meaningless in first instance. Availability of an easy Web based intuitive interface will facilitate and accelerate analysis of biodiversity data. Hence, this motivated us to develop a web based biodiversity and ecosystem informatics database suited for the numerous scattered ecological and biodiversity data typically found in Malaysian research community. The paper presents an online biodiversity database system integrated with GIS with a centralized enterprise repository. Interactive visualization provides an effective way of presenting large amounts of complex information to a wide audience, especially those with no experience of GIS or mapping, as it provides the user with visual cues that are more intuitive than those of a conventional map. It is a scalable database that provides variable and adaptable feature modification for its users. It is also designed to incorporate different layers of knowledge to allow selective viewing to protect sensitive indigenous biodiversity data. The use of spatial information will enable researcher to analyze ecological trends and behavior. The database is also accessible via the web for easy data population and curation

β-sheet containment by flanking prolines: Molecular Dynamic Simulations of the inhibition of β-sheet elongation by proline residues in human prion protein.

Previous molecular dynamic simulations have reported elongation of the existing β-sheet in prion proteins. Detailed examination has shown that these elongations do not extend beyond the proline residues flanking these β-sheets. In addition, proline has also been suggested to possess a possible structural role in preserving protein interaction sites by preventing invasion of neighbouring secondary structures. In this paper, we have studied the possible structural role of the flanling proline residues by simulating mutant structures with alternate substitution of the proline residues with valine. Simulations showed a directional inhibition of elongation with the elongation progressing in the direction of valine including evident inhibition of elongation by existing proline residues. This suggests that the flanking proline residues in prion proteins may have a containment role and would confine the β-sheet within a specific length