Identification of putative drug targets for human sperm-egg interaction defect using protein network approach

Background: Sperm-egg interaction defect is a significant cause of in-vitro fertilization failure for infertile cases. Numerous molecular interactions in the form of protein-protein interactions mediate the sperm-egg membrane interaction process. Recent studies have demonstrated that in addition to experimental techniques, computational methods, namely protein interaction network approach, can address protein-protein interactions between human sperm and egg. Up to now, no drugs have been detected to treat sperm-egg interaction disorder, and the initial step in drug discovery research is finding out essential proteins or drug targets for a biological process. The main purpose of this study is to identify putative drug targets for human sperm-egg interaction deficiency and consider if the detected essential proteins are targets for any known drugs using protein-protein interaction network and ingenuity pathway analysis. Results: We have created human sperm-egg protein interaction networks with high confidence, including 106 nodes and 415 interactions. Through topological analysis of the network with calculation of some metrics, such as connectivity and betweenness centrality, we have identified 13 essential proteins as putative drug targets. The potential drug targets are from integrins, fibronectins, epidermal growth factor receptors, collagens and tetraspanins protein families. We evaluated these targets by ingenuity pathway analysis, and the known drugs for the targets have been detected, and the possible effective role of the drugs on sperm-egg interaction defect has been considered. These results showed that the drugs ocriplasmin (Jetrea (c)), gefitinib (Iressa (c)), erlotinib hydrochloride (Tarceva (c)), clingitide, cetuximab (Erbitux (c)) and panitumumab (Vectibix (c)) are possible candidates for efficacy testing for the treatment of sperm-egg interaction deficiency. Further experimental validation can be carried out to confirm these results. Conclusion: We have identified the first potential list of drug targets for human sperm-egg interaction defect using the protein interaction network approach. The essential proteins or potential drug targets were found using topological analysis of the protein network. These putative targets are promising for further experimental validation. These study results, if validated, may develop drug discovery techniques for sperm-egg interaction defect and also improve assisted reproductive technologies to avoid in-vitro fertilization failure

Educating the educators: Incorporating bioinformatics into biological science education in Malaysia

Bioinformatics can be defined as a fusion of computational and biological sciences. The urgency to process and analyse the deluge of data created by proteomics and genomics studies has caused bioinformatics to gain prominence and importance. However, its multidisciplinary nature has created a unique demand for specialist trained in both biology and computing. In this review, we described the components that constitute the bioinformatics field and distinctive education criteria that are required to produce individuals with bioinformatics training. This paper will also provide an introduction and overview of bioinformatics in Malaysia. The existing bioinformatics scenario in Malaysia was surveyed to gauge its advancement and to plan for future bioinformatics education strategies. For comparison, we surveyed methods and strategies used in education by other countries so that lessons can be learnt to further improve the implementation of bioinformatics in Malaysia. It is believed that accurate and sufficient steerage from the academia and industry will enable Malaysia to produce quality bioinformaticians in the future

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/

birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics

Summary: birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in parallel by simply booting the birgHPC CD or flash drive from the head node, which immediately positions the rest of the PCs on the network as computing nodes. Thus, a temporary, affordable, scalable and high-performance computing environment can be built by non-computing-based researchers using low-cost commodity hardware

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

MyRice: pangkalan data pengetahuan padi Malaysia

Pada masa ini, semua maklumat mengenai penyelidikan padi di Malaysia bertaburan di penerbitan yang berbeza, depositori dan pangkalan data dengan menggunakan pelbagai format digital dan analog. Walaupun terdapat pangkalan data antarabangsa mengenai penyelidikan padi, data tersebut tidak dipautkan dengan dengan geolokasi dan maklumat arkib asas lain yang diperlukan penyelidik untuk membawa penyelidikan ke peringkat yang lebih tinggi. Kami mempersembahkan MyRice, sebuah pangkalan data atas talian Malaysia untuk kegunaan penyelidik dan orang awam. Pembangunan pangkalan data ini akan membolehkan penyelidik saintifik untuk mengesan kembali maklumat penyelidikan padi dan lokasi ia ditanam. Ia dibina menggunakan saluran pendigitalan yang membolehkan pendigitalan pemprosesan berkelajuan tinggi data arkib dan dihubungkan terus dengan enjin carian penerbitan seperti Google Scholar. Fungsi utama termasuk bibliografi, pemetaan dan pemuat naik media untuk penyelidik berkongsi video dan imej. Kami percaya MyRice yang akan menyumbang kepada ekosistem pengetahuan digital di kalangan penyelidik padi tempatan untuk meningkatkan akses kepada pengetahuan dan menjadi tumpuan utama untuk memacu penyelidikan padi Malaysia ke arah sebuah negara berstatus sara diri dalam keterjaminan makanan. Pangkalan data dapat dilayari di http://biodiversity.fbb.utm.my/myrice/