Effect of stored oil palm trunk sap towards methyl ester synthesis / Nurnuha Shamsir... [et al.]

Oil palm trunk (OPT) has highest content of sap, 80% of the overall weight. OPT sap contains free sugars which can be converted into valuable compounds such as ester. The objective of this study is to determine the changes of free sugars at different storage time and the effect on methyl ester synthesis. The sap was extracted and stored at different durations time (1, 7, 14, 21 and 28 days). 10ml of dried sap was added with 100mg Fe2(SO4)3 EFB and 15ml of methanol. The mixture was put into the autoclave to be heated at 160 oC for 150 minutes. Free sugars found in OPT sap were glucose, fructose and sucrose. The free sugars vary upon the storage time and highest concentration of glucose and fructose achieved at day 21. This is due to hydrolysis of sucrose. The GC-MS analysis identified and quantified several methyl ester such as methyl pyruvate, methyl levulinate, methyl-9- oxononanoate and methyl palmitate. These findings confirmed that the free sugars from OPT sap were possible to be an alternative carbon in ester synthesi

Fenazin sebagai potensi antibiotik baru daripada Streptomyces kebangsaanensis

Fenazin merupakan metabolit sekunder yang biasanya disintesis secara semula jadi oleh Pseudomonas dan Streptomyces. Ia merupakan sebatian heterosiklik yang mempunyai sebatian bernitrogen pada struktur teras cecincin. Kajian mengenai antibiotik ini telah bermula seawal abad ke-19 lagi dan ternyata menjadi calon dadah yang berpotensi tinggi dalam dunia perubatan. Sehingga kini, lebih daripada 100 jenis fenazin telah diterokai daripada sumber semula jadi dan boleh bertindak sebagai antibakteria, antikanser, antivirus, antitumor serta antiparasit. Setakat ini, kajian biosintesis fenazin yang telah dijalankan terhadap Pseudomonas dan Streptomyces telah mendedahkan gen yang bertanggungjawab dalam tapak jalan biosintesis fenazin, namun begitu, gen khusus yang terlibat dalam penghasilan terbitan fenazin yang kompleks masih dalam hipotesis. Dalam ulasan ini, kami membincangkan kepentingan fenazin serta pemahaman terkini tentang tapak jalan biosintesis fenazin yang berjaya diterokai di dalam Streptomyces kebangsaanensis

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Genomic characterization of a new endophytic Streptomyces kebangsaanensis identifies biosynthetic pathway gene clusters for novel phenazine antibiotic production

Background Streptomyces are well known for their capability to produce many bioactive secondary metabolites with medical and industrial importance. Here we report a novel bioactive phenazine compound, 6-((2-hydroxy-4-methoxyphenoxy) carbonyl) phenazine-1-carboxylic acid (HCPCA) extracted from Streptomyces kebangsaanensis, an endophyte isolated from the ethnomedicinal Portulaca oleracea. Methods The HCPCA chemical structure was determined using nuclear magnetic resonance spectroscopy. We conducted whole genome sequencing for the identification of the gene cluster(s) believed to be responsible for phenazine biosynthesis in order to map its corresponding pathway, in addition to bioinformatics analysis to assess the potential of S. kebangsaanensis in producing other useful secondary metabolites. Results The S. kebangsaanensis genome comprises an 8,328,719 bp linear chromosome with high GC content (71.35%) consisting of 12 rRNA operons, 81 tRNA, and 7,558 protein coding genes. We identified 24 gene clusters involved in polyketide, nonribosomal peptide, terpene, bacteriocin, and siderophore biosynthesis, as well as a gene cluster predicted to be responsible for phenazine biosynthesis. Discussion The HCPCA phenazine structure was hypothesized to derive from the combination of two biosynthetic pathways, phenazine-1,6-dicarboxylic acid and 4-methoxybenzene-1,2-diol, originated from the shikimic acid pathway. The identification of a biosynthesis pathway gene cluster for phenazine antibiotics might facilitate future genetic engineering design of new synthetic phenazine antibiotics. Additionally, these findings confirm the potential of S. kebangsaanensis for producing various antibiotics and secondary metabolites

Adaptation of coastal defence structure as a mechanism to alleviate coastal erosion in monsoon dominated coast of Peninsular Malaysia

The complexity of the coastal environment and the advent of climate change cause coastal erosion, which is incontrovertibly a significant concern worldwide, including Peninsular Malaysia, where, the coast is threatened by severe erosion linked to anthropogenic factors and monsoonal wind-driven waves. Consequently, the Malaysian government implemented a mitigation plan using several coastal defence systems to overcome the coastal erosion problem. This study assesses coastal erosion management strategies along a monsoon-dominated coasts by evaluating the efficacy of coastal protection structures against the coast. To this end, we analysed 244 km of the coastline of Terengganu, a federal state located on the east coast of Peninsular Malaysia. Due to a higher frequency of storms and the ensuing inception of high wave energy environments during the northeast monsoon (relative to southwest monsoon), the study area is the most impacted region in Malaysia with regard to coastal erosion. Fifty-five (55) coastal defence structures were detected along the Terengganu coastline. The Digital Shoreline Analysis System (DSAS) was utilised to compute changes in the rate statistics for various historical shoreline positions along the Terengganu coast to assess the efficacy of the defence structures. Additionally, this study acquired the perception of the existing coastal management strategies through an interview session with the concerned stakeholders. The rate statistics revealed the effectiveness and impact of the coastal defence structure on the coastline. Assessing the functionality of the coastal defence structures shed light on the present scenario of coastal erosion management. Greater efficacy and lower impact of coastal defence structures are prescribed for coastal erosion management strategies across the monsoon-dominated coast