Development of Malaysian Ethnobotanical Online Database

The existing Malaysian ethnobotanical database is not sufficiently comprehensive and may hindersharing of ethnobotanical knowledge. The lack of interest and documentation especially in digitalizing priorknowledge is a worrying trend since Malaysia possess high ethnicity and abundance of biodiversity. It is crucial topreserve and digitalize the comprehensive ethnobotanical database as it gives benefits worldwide. This study aimedto identify online database features and data type for an ethnobotanical database, to collect and populate existingdatabase via secondary data and to test the acceptance of the database by users by testing whether the databasefulfil the requirements of a good ethnobotanical database. Rapid Prototyping method has been used in this studyinvolving User Requirement Analysis and data acceptance test to construct and create the best ethnobotanicaldatabase. MYETHBO is the database created by using the Omeka Classic management system with Darwin Corestandard. There are 1,074 plants information are collected online and mostly referred GlobinMed and GBIF. In thisstudy, 30 plant species has been setup as exemplar pages. This study successfully developed a comprehensiveethnobotanical database (MYETHBO) by being able to identify the database features and data type needed via theRapid Prototyping method, collect and populate existing data via secondary data and test the acceptance of thedatabase by distributing the questionnaire to lecturers. MYETHBO will be beneficial to researchers, students andpublic people to gain knowledge of ethnobotany. It is available at https://cercom.uthm.edu.my/myethbo/

Development of Malaysian Mammal Online Database

Malaysia is one of 17 mega diverse countries in the world. Despite this fact, there is still no online standalone database that focuses on Malaysian mammals.  Creation of a mammalian database would allow researchers and conservationists to utilize the database for research, policy making and to answer broad scale of biodiversity questions.  Human development have contribute to the depleting of mammal population and species extinction rate is faster than the effort of cataloguing them. The aim of this study is to 1) identify online database features and the type of data required for mammal database, 2) collect and populate database from existing mammal data to assist the said database and 3) to test the acceptance of the database by user of this study. The secondary data from existing database was collected to determine the required features needed in the database. The database adhere to TDWG standard that facilitates exchange of biological information. Rapid Prototype Model was utilized as development method and Omeka Classic was used as platform of Content Management System. The mammal data was collected online and populate into the database. The acceptance testing in form of questionnaire were distributed to verify whether the database is function properly and meet the requirement of the study. We present MYMODS, a comprehensive mammal database with 361 mammal species in Malaysia deposited in the database. The development of this database will enable the researcher and conservationist to seek and identify mammal information based on species’ scientific name, description and IUCN Red List. We believe that MYMODS will contribute to the digital knowledge that provide tools for mammal research and contributes in management of biodiversity and conservation in Malaysia. MYMODS is available at https://cercom.uthm.edu.my/mymods

Review: DNA Barcoding and Chromatography Fingerprints for the Authentication of Botanicals in Herbal Medicinal Products

In the last two decades, there has been a tremendous increase in the global use of herbal medicinal products (HMPs) due to their claimed health benefits. This has led to increase in their demand and consequently, also, resulted in massive adulteration. This is due to the fact that most of the traditional methods cannot identify closely related species in a process product form. Therefore the urgent need for simple and rapid identification methods resulted in the discovery of a novel technique. DNA barcoding is a process that uses short DNA sequence from the standard genome for species identification. This technique is reliable and is not affected by external factors such as climates, age, or plant part. The difficulties in isolation of DNA of high quality in addition to other factors are among the challenges encountered using the DNA barcoding in the authentication of HMP. These limitations indicated that using DNA barcoding alone may ineffectively authenticate the HMP. Therefore, the combination of DNA barcoding with chromatographic fingerprint, a popular and generally accepted technique for the assessment and quality control of HMP, will offer an efficient solution to effectively evaluate the authenticity and quality consistency of HMP. Detailed and quality information about the main composition of the HMPs will help to ascertain their efficacy and safety as these are very important for quality control

Challenge in applying quantitative analysis on bull semen quality in Malaysia

There is a huge challenge in managing quality control (QC) for Malaysian semen production centres (MSPCs) supplying bull semen to breeders and State Department of Veterinary (SDV). MSPCs are moving away from subjective semen assessment that is largely uncorrelated to field fertility, to objective semen analyses that incorporate computer assisted sperm analysis (CASA) and flow cytometry. A quantitative analysis (QA) approach to semen analysis using a combination of CASA and flow cytometry can provide MSPCs with the highest QC for bull semen production. This paper will describe how this QA approach could be applied in MSPCs to establish QC procedures of bull semen production before the release of the product in the field

Nurturing future leaders in research and innovation via knowledge sharing and exchange

Higher Education Institutions (HEIs) in Malaysia have experienced various transitions to cope with the accelerating pace of globalisation. With the increasing number of potential students within the country and beyond the national borders, HEIs must be visible. One way to gain visibility depends on the impactful research and development activities of that particular institution. Academics are the main drivers for these R&D activities, which will generate a certain amount of budget or income for the universities. Therefore, the university requires self-driven academics to act as institutions' representatives in developing their reputation at national and international levels

Molecular dynamics studies of human prion protein

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Model-guided in silico overexpression of adhe gene predicts increased ethanol production in escherichia coli from xylose

Escherichia coli systems metabolic engineering has progressed significantly in guiding future metabolic engineering targets for the production of bioethanol using different carbon sources. However, the use of xylose as substrate coupled with overexpression of E. coli native adhE using parsimonious enzyme usage (pFBA) algorithm with the OptFlux interface remained largely underexplored. Here, we show for the first time that in silico overexpression of the adhE and under expression of pflA lead to 2 fold increase in ethanol production from xylose using the E. coli GEM. The results indicate that 2 NADH molecules have been generated by under expression of pflA and ldhA. Furthermore, the triple overexpression of the native adhE/ b1241 using xylose as the substrate might have increased the consumption of NADH generated in the cell that lead to 2 fold increase in ethanol production with a growth rate that was 90.8% of the wild-type model. On the bases of these findings, we hypothesize that E. coli native adhE preferred xylose as substrate when overexpressed to achieve cellular redox balance by oxidizing NADH generated in increasing ethanol production. This study informs other studies that model-guided biological insight could be applied in identifying metabolic engineering targets, paving way for a comprehensive biological inquiry on the role of the E. coli native adhE overexpression in enhancing ethanol production using xylose as a solitary carbon source

Model-driven in silico glpC gene knockout predicts increased succinate production from glycerol in escherichia coli

Metabolic engineered targeting for increased succinate production in Escherichia coli using glycerol as a low cost carbon source has attracted global attention in recent years. Succinate production in engineered E. coli has progressed significantly using an experimental trial and error approach. The use of a model-guided, targeted metabolic gene knockout prediction for increased succinate production from glycerol under anaerobic conditions in E. coli still remains largely underexplored. In this study, we applied a model-driven, targeted glpC/b2243 in silico metabolic gene knockout using E. coli genome scale model iJO1366 under the OptFlux software platform with the aim of predicting high succinate flux. The results indicated that the mutant model lacking the glpC/b2243 gene will demonstrate increased succinate flux that is 30% higher than its wild-type control model. We can hypothesize that an additional NADH molecule was generated following the deletion of the gene and/or the alternatively preferred GldA-DhaKLM fermentative route for glycerol metabolism in E. coli may have been activated. Although the exact metabolic mechanism involved in increasing the succinate flux still remains obscure; the current study informs other studies that a model-driven, metabolic glpC/b2243 gene knockout could be applicable in filling our knowledge gap using a comprehensive experimental inquiry in the future; leading to a better understanding of the underlying metabolic function of this gene in relation to succinate production in E. coli from glycerol

Development and deployment of an ethnobotanical and phytochemical knowledge database of Malaysia

Currently, all the information regarding ethnobotanical, phytochemical and pharmaceutical information of South East Asia are scattered over many different publications, depositories and databases using various digital and analogue formats. Although there are taxonomic databases of medicinal plants, they are not linked to phytochemical and pharmaceutical information which are often resides in scientific literature. We present Phyknome; an ethnobotanical and phytochemical database with more than 22,000 species of ethnoflora of Asia. The creation of this database will enable a biotechnology researcher to seek and identify ethnobotanical information based on a species’ scientific name, description and phytochemical information. It is constructed using a digitization pipeline that allow high throughput digitization of archival data, an automated dataminer to mine for pharmaceutical compounds information and an online database to integrated these information. The main functions include an automated taxonomy, bibliography and API interface with primary databases such as Global Biodiversity Information Facility (GBIF). We believe that Phyknome will contribute to the digital knowledge ecosystem to elevate access and provide tools for ethnobotanical research and contributes to the management, assessment and stewardship of biodiversity. The database is available at http://mapping.fbb.utm.my/phyknome