NEWSLETTER

FRESH FS RESEARCH HUB

E-ISSN: 2976-3436 https://science.utm.my/fresh-newsletter-fs/

SEPTEMBER 2022 . ISSUE 02/2022

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Faculty of Science, Universiti Teknologi Malaysia (UTM), 81310, Johor Bahru, Johor. Tel. Num.: +607-5534007 Fax Num.: +607-5566162

Website: https://science.utm.my/ First print: Volume 1 2021 e-ISSN: 2976-3436



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Published by: Faculty of Science, Universiti Teknologi Malaysia (UTM), 81310, Johor Bahru, Johor.

CONTENTS ARTICLES@FS

P01-P17

1. MICROBIAL SYNTHETIC BIOLOGY: THE PROMISING FUTURE 2. JOURNEY TO A HAPPY RESEARCH LIFE 3. VACCINES: A BRIEF HISTORY, DEVELOPMENT AND APPLICATION 4. POTENTIAL OF PETAI AS REDUCTION AGENT IN SYNTHESIS SILVER NANOPARTICLES 5. RAPID COVID-19 DIAGNOSIS VIA GOLD NANOPARTICLES SURFACE-ENHANCED RAMAN SCATTERING (SERS) 6. UNIVERSITI TEKNOLOGI MALAYSIA & DEPARTMENT OF STATISTICS MALAYSIA MOU SIGNING CEREMONY

ACHIEVEMENTS@FS P18-P22

1. GRANTS 2. PUBLICATIONS - BOOKS 3. PUBLICATIONS - ARTICLES 4. INNOVATIONS

MICROBIAL SYNTHETIC BIOLOGY: THE PROMISING FUTURE BY: DR. NUR IZZATI MOHD NOH (SYNBIO)

Synthetic Biology is a multidisciplinary research area that incorporates biology, chemistry, mathematics and engineering. In the past 20 decades, extensive developments and achievements have been seen in the field of Synthetic Biology. Different plant and microbial models have been used for different application purposes. Various research labs are collaborating in producing biological parts and devices for expression of transgenic proteins in new hosts.

The Concept of Synthetic Biology Synthetic biology approaches consist of several common steps: •Identify the biological/biosynthesis pathway for the target biological compounds • Identify the sources (eg. plants, animals, yeast) of gene(s) of interest encode for the biological/biosynthesis pathway • Amplify the gene(s) of interest and clone in suitable expression plasmid(s) • Transform the transgenic plasmid(s) into microbial hosts • Grow transgenic hosts for lab or largescale production of the targeted biological compounds • Perform algorithm/mathematical and computational modelling based on the laboratory results • Improve the experimental design to achieve optimal production of the targeted compounds by the host.

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Applications of Synthetic Biology

Synthetic Biology promises advancement of sustainable technology for renewable energy, environmental friendly compounds and treatment of infectious diseases. It has been reported that cloning and expressing plant genes involved in fatty acids biosynthesis in bacteria can enhance the production of internal lipid storage which can be harvested for esterification to produce biofuel. Remarkably, Eschericia coli (E. coli) has been vastly used in Synthetic Biology approaches. For example, genetic parts and devices are made available for expression of plant flavonoids pathway in E. coli in order to increase the yield of these biological compounds for industrial applications. Besides, engineered E. coli that produces anti-inducer molecules for anticholera treatment is a great milestone in applying Synthetic Biology into healthcare. Incorporating engineering design in construction of genetic circuit eases the development of new organisms that can produce valuable biological compounds or can show improved biological characteristics. Ultimately, Synthetic Biology ensures sustainable resources for valuable natural products.

Clean water, healthy air and fertile soil are what human needs to live a good life. Drastic changes to achieve modernization have a great impact to the earth. Two-years of lockdown during the pandemic Covid-19 was said to be the time of healing for the earth. Of which is true, despite the economy challenges faced by all nations. However, human should learn a good lesson from the pandemic Covid-19 situation that everyone plays a role in ensuring the clean water, healthy air and fertile soil are remained for the future generations. Therefore, Synthetic Biology approaches aim to achieve sustainable production of natural products that can be made available to public at cost effective.

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Advancement in Synthetic Biology technology might assist Malaysia to achieve the socio-economic drivers in: i) energy, ii) medical and healthcare, iii) agriculture, water and food, iv) environment and biodiversity.

This is because, through Synthetic Biology, i) renewable energy can be harnessed from microbes and algae, ii) clean water can be produced using bioremediation and biofiltration methods, iii) alternative ingredients, bioactive compounds and biomaterials can be explored from new natural resources, iv) conservation of flora, fauna, indigenous species and plants can be implemented due to effective natural resources management.

With continuous efforts from researchers and graduates, hopefully Synthetic Biology can be applied vastly in Malaysia in the very near future.

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JOURNEY TO A HAPPY RESEARCH LIFE BY: DR. NURHAFIZAH HASIM (AOMRG)

Identify the big picture, then delve into the specifics.

Identify the quality sources.

Multiple sources should be used to verify the information.

Keep an open mind when it comes to surprising answers.

Be organized.

Use library resources as your advantage.

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Vaccines: A Brief History, Development and Application BY: DR. ABDUL FATAH A. SAMAD (NATPRO)

The word "vaccine" may be familiar to most of us as the implication of the COVID-19 pandemic over the last two years. Vaccine refers to a diseasecausing antigen that can stimulate the immune system to produce antibodies against a specific disease. By boosting the natural defenses of the body, vaccine reduces the chances of getting a disease. It was Edward Jenner who described the term "vaccine" for the first time in the 18th century. The term is derived from a Latin word for cow, Vacca. In 1796, Jenner inoculated cowpox lesions from the hands of milkmaids onto an eight-years-old boy, which resulted in immunity against smallpox [1]. About eight decades later, Louis Pasteur was successful in developing a live attenuated vaccine for rabies, which was considered as a novel platform during that era. Currently, at least 20 vaccines have been developed that help people live longer by preventing death from fatal diseases such as tetanus, influenza, diphtheria, and measles.

Vaccines can be developed through different platforms. However, the purpose is the same, which is to trigger immunity. The traditional way to produce a vaccine is by weakening or inactivating the virus. Weakening (attenuating) the virus is often carried out by introducing it into a species/medium in which it does not replicate well (Figure 1(A)). Meanwhile, for the inactivating virus approach, the virus will be killed by heat or chemicals (Figure 1 (B)) [2]. Both the weakened and inactivated (killed) virus approaches are recognized by the immune system to trigger a response with a minimal or no illness. Oral polio and rabies vaccines are examples of vaccines that are produced through an attenuated viral platform. Meanwhile, the influenza vaccine was developed via an inactivated approach. Besides, instead of using the whole part of the virus, a vaccine can be developed by using only a part of the virus component (Figure 1 (C)). The human papillomavirus (HPV) and hepatitis B are made through this approach.

(A) Attenuating the virus

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(B) Inactivating the virus

(C) Using a part of the virus

Figure 1: (A) Attenuating the virus by culturing it in the different media. (B) Inactivating the virus through chemical or heat. (C) A part of the vaccine is used to develop the vaccine.

Another vaccine manufacturing platform is via the genetic materials of the virus such as DNA and RNA (Figure 2 (A) and (B)). In this approach, the vaccine will contain a segment of the genetic material of the particular virus that codes for a specific protein. When introduced into the cells, the genetic codes will be translated into a protein recognized by the immune system to trigger a response. DNA vaccine-mediated immunity was first documented in the 1990s, when the plasmid DNA encoding influenza A nucleoprotein was used to generate protective T lymphocytes (CTLs) [3]. A major advantage of DNA vaccinations is that they are simple to make and easy to store [4]. However, it is possible for DNA vaccines to integrate into host genomes, which can lead to insertional mutations. This mutation can result in the dysfunction of another gene [5].

On the other hand, global efforts to end the COVID-19 pandemic have led to the development of the world's first mRNA vaccine. The first Covid-19 vaccine was made by Pfizer/BioNTech, while the second was developed by Moderna – marking the first time this vaccine technology has been approved for use. Similar to DNA vaccine, mRNA-based vaccine is easy to manufacture. However, they need to be stored at an ultra-low temperature. In terms of effectiveness, mRNA is proven to be superior as it can effectively induce neutralizing antibody responses in low-dose immunized individuals. In addition, the mRNA vaccine has less risk of integrating with the host genome, therefore preventing insertional mutagenesis [6].

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In another approach, a viral vector is utilized to deliver the genetic materials of the viruses instead of introducing them directly to the cells (Figure 2 (C)). While inside the cells, the viruses will release the genetic materials, to be converted into proteins that trigger the immune response. This approach could trigger a strong immune response and enhance the specificity of gene delivery [7]. In contrast, the procedure is a little bit complex as the viral candidates have to be engineered before they can be used to eliminate the disease-causing agents. Among the virus candidates that are commonly used as vectors is the adenovirus. The E-bola and COVID19 vaccines are among the vaccines that have been developed through a viral vector approach.

(A)

DNA-Based

(C)

(B)

mRNA-Based

Viral Vector

Figure 2: (A) Genetic code (DNA) is used to make the vaccine. (B) Blueprint of a protein (mRNA) is used to make the vaccine. (C) Utilizing a virus to deliver genetic materials. 7

In conclusion, the burdens of infectious disease have been reduced significantly by vaccines. Since the invention of the first vaccine, knowledge about vaccine development has continued to grow, and improvements in laboratory techniques have saved millions of lives. The development of each vaccine is unique, and studying it can contribute to much-needed wisdom that could be useful in the event of a pandemic in the future.

References: 1. Saleh A, Qamar S, Tekin A, Singh R, Kashyap R: Vaccine Development Throughout History. Cureus 2021, 13(7):e16635. 2. Sanders B, Koldijk M, Schuitemaker H: Inactivated Viral Vaccines: Vaccine Analysis: Strategies, Principles, and Control. 2014 Nov 28:45-80. doi: 10.1007/978-3-662-45024-6_2. 3. Yankauckas MA, Morrow JE, Parker SE, Abai A, Rhodes GH, Dwarki VJ, Gromkowski SH: Long-term anti-nucleoprotein cellular and humoral immunity is induced by intramuscular injection of plasmid DNA containing NP gene. DNA Cell Biol 1993, 12(9):771-776. 4. Silveira MM, Moreira G, Mendonça M: DNA vaccines against COVID-19: Perspectives and challenges. Life Sci 2021, 267:118919. 5. Li L, Petrovsky N: Molecular mechanisms for enhanced DNA vaccine immunogenicity. Expert Rev Vaccines 2016, 15(3):313-329. 6. Qin F, Xia F, Chen H, Cui B, Feng Y, Zhang P, Chen J, Luo M: A Guide to Nucleic Acid Vaccines in the Prevention and Treatment of Infectious Diseases and Cancers: From Basic Principles to Current Applications. Frontiers in Cell and Developmental Biology 2021, 9. 7. Travieso T, Li J, Mahesh S, Mello JDFRE, Blasi M: The use of viral vectors in vaccine development. npj Vaccines 2022, 7(1):75.

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Potential of Petai as Reduction Agent in the Synthesis of Silver Nanoparticles BY: DR. SITI SALWA ALIAS (AOMRG) Imagine you are sitting around the table enjoying your favorite local food nasi lemak served with sambal petai udang with your beloved family. Suddenly, one of your family member says “Do you know, nowadays, our local scientist use petai to treat the wastewater?” Suddenly, you may be startled as you squint and verified if it was true. Parkia speciosa (P. speciosa) generally known as stink bean, it is known locally as petai in Malaysia, commonly used in Malaysian local cuisine. Although it has a pungent smell, it tastes so good when eaten. On the other hand, the greeninspired production of silver nanoparticles is a process that involves the reduction of silver ions using a biological mass/extract as a source of reductant. Various kind of local plants have been used as reduction agent. P. speciosa contains phenolic (50-85 wt. %), flavonoids (5-6 wt.%), saponins and tannins. These compounds play an important role in the reduction of silver ions and followed by the capping of green-silver nanoparticles according to the reaction (Ag^+) + (NO^3−) (ions from silver nitrate) + Plant molecule (OH, C H, etc.) Ag^0 (silver nanoparticles).

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The next questions you might raise are as follows (i) which part of P. speciosa is suitable to be extracted? What are the best green silver nanoparticle properties that can be used in treating wastewater? Based on the collaborative research done by Advanced Optical Materials Research Group (AOMRG), Physics Department, Faculty of Science, UTM and Advanced Manufacturing and Materials Centre (AMMC), Institute Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia (UTHM), the green-silver nanoparticles can be produced from P. speciosa beans, pods and leaves. The average of particle size is around 34.65 nm. Later, this green-silver nanoparticles will be mixed in polysulfone to form a hybrid porous membrane. The P. speciosa pods and leaves have better properties when mixed in porous polysulfone hybrid membrane based on its ability to remove humic acid from wastewater up to 99 % and it is antifouling. In fact, the antibacterial properties of green-silver nanoparticles against E.coli enhanced the dual-function of hybrid ultrafiltration membrane as a water separator for wastewater treatment. 9

Recently, researchers from the Centre for Sustainable Nanomaterials (CSNano) and several research groups from the Faculty of Science, UTM (Green Chemistry (GChem), Environmental Chemistry (EnviroChem) and AOMRG) have collaborated with Platinum Coating Malaysia Sdn. Bhd. for the production of a large scale fine colloidal silver nanoparticles solution. Interestingly, under this Memorandum of Understanding (MoU), a few chemistry and biology techniques have been explored to obtain the silver nanoparticles with optimum properties. Petai! Green Silver Nanoparticles! Clean Water for Better Future! Looks interesting doesn't it? Find out more on green-inspired production of silver nanoparticles based on P. speciosa in the research articles entitled “A study of different concentrations of bio-silver nanoparticles in polysulfone mixed matrix membranes in water separation performance”, “Enhancing the performance of a hybrid porous polysulfone membrane impregnated with green Ag/AgO additives derived from the Parkia speciosa” and “Parkia speciosa as Reduction Agent in Green Synthesis Silver Nanoparticles”.

Properties and performance of green-inspired silver nanoparticles based on P. speciosa in polysulfone mixed matrix membranes for water separation (Reprint with permission, License Number 5090811108133)

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Rapid COVID-19 Diagnosis via Gold Nanoparticles Surface-Enhanced Raman Scattering (SERS) BY: LIYANA BINTI SHATAR & TS. DR. FARIZA HANIM BINTI SUHAILIN (NURP)

The pandemic of the novel coronavirus disease 2019 (COVID-19) has caused significant global disruption due to shortage of testing facilities and equipment [1]. The gold standard for COVID-19 diagnosis is via real time-polymerase chain reaction (RT-PCR). The RT-PCR involves multi-step procedures such as purification, nucleic acid amplification and fluorescence detection, of which requires trained operators, expensive high-end facilities and it may take hours to perform [2]. To speed up the diagnosis process and to reduce the cost for detection, numerous rapid test kits for immune-diagnosis utilizing antigen– antibody reactions have been made available for purchase. However, due to their poor accuracy and low limit of detection (LoD), they have not yet become the high standard diagnostic method [3].

Recently, alternative, and supplementary diagnostic method based on surfaceenhanced Raman scattering (SERS) receives attention for its ability to detect viral envelope of SARS-CoV-2 virus. Continuous advancement in term of sensitivity, specificity and LoD are amongst the promising capabilities of SERS. In theory, SERS is a molecular vibrational spectroscopy technique that produce highly distinctive molecule fingerprint with minimal sample preparation. The SERS leverage the noble characteristics of metal nanoparticles (NPs) such as gold (Au), silver (Ag), or copper (Cu), to confined the electromagnetic (EM) field originated from localize surface plasmon resonance (LSPR) when the NPs are place in close proximate distance, as show in Figure 1 [4-5]. Despite its promising capabilities, the feasibility of mass and cheap productions of SERS-active substrate containing precious NPs like Au is still a challenge.

To date, the "top-down" and "bottom-up" techniques are the two main strategies employed for the synthesis of Au NPs. In the top-down strategy, the process will start with bulk metal target, i.e., few millimeters thick. The phenomenon of lightmatter interaction will result in strong energy absorption to fracture the bulk Au into NPs in techniques such as laser ablation, ion sputtering, and ultraviolet (UV)and infrared (IR)-irradiations. In contrast, the bottom-up method will start with the synthesis of NPs at the atomic level by reducing Au ions (Au^3+) to produce Au atoms (Au^0) in a method known as the Turkevich-Frens. 11

Figure 1: Schematic diagram for the SERS detection of analyte [6]

In our lab, we established efficient and simple fabrication steps for various Au NPs size via the latter method to enable mass and cheap productions of SERSactive substrate. The inset in Figure 2 is an image of the fabricated Au NPs solutions. In solution form, the Au NPs come in wide range of colors (light pink, pink, red, orange, brown, blue and purple) depending on the size of the particles. The plasmonic absorption peak can be tuned to specific band required by the application via regulating the NPs size. Figure 2 is the plasmonic absorption bands of the synthesized Au NPs at different concentrations as measured via the ultraviolet-visible (UV-Vis) spectrometer.

Figure 2: UV-Vis absorption spectra of ~40 nm (top line) and ~20 nm (bottom line) Au NPs synthesized at via Turkevich-Frens method 12

Figure 3 is the scanning electron microscopy (SEM) image from our progressing work in developing active SERS substrate based on Au NPs for COVID-19 detection. The Au NPs cluster are well decorated on the SERS substrate. The energy dispersive X-ray (EDX) analysis confirmed the presence of Au on the functionalized single-crystalline silicon chip. We optimized the substrate for strong Raman vibrational signal and we are moving to the next steps of detection. A way forward after the completion of the project is to use the developed SERS substrate for actual clinical diagnosis with strong support from university collaborators; Institute for Research in Molecular Medicine, Universiti Sains Malaysia (USM) Health Campus, Kubang Kerian, and Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, and industrial collaborator; Biogenes Technologies Sdn. Bhd.

Figure 3: (a) The SEM image of the fabricated Au embedded SERS substrate, together with their (b) EDX analysis. Top insert is the percentage of elemental compositions, bottom insert is the image of the 10 mm x 10 mm SERS substrate. 13

Acknowledgement: Authors wish to thanks UTM for supporting this work. This work was supported by the Ministry of Higher Education under Fundamental Research Grant Scheme (FRGS/1/2021/STG07/UTM/02/4).

References: [1] Yüce, M., Filiztekin, E., & Özkaya, K. G. (2021). COVID-19 diagnosis -A review of current methods. Biosensors & bioelectronics, 172, 112752. [2] Taha, B. A., Al Mashhadany, Y., Bachok, N. N., Ashrif A Bakar, A., Hafiz Mokhtar, M. H., Dzulkefly Bin Zan, M. S., & Arsad, N. (2021). Detection of COVID-19 virus on surfaces using photonics: challenges and perspectives. Diagnostics, 11(6), 1119. [3] Ghodake, G. S., Shinde, S. K., Kadam, A. A., Saratale, R. G., Saratale, G. D., Syed, A., & Kim, D. Y. (2021). Biological characteristics and biomarkers of novel SARSCoV-2 facilitated rapid development and implementation of diagnostic tools and surveillance measures. Biosensors and Bioelectronics, 177, 112969. [4] Demirel, G., Usta, H., Yilmaz, M., Celik, M., Alidagi, H. A., & Buyukserin, F. (2018). Surface-enhanced Raman spectroscopy (SERS): An adventure from plasmonic metals to organic semiconductors as SERS platforms. Journal of Materials Chemistry C, 6(20), 5314-5335. [5] Payne, T. D., Klawa, S. J., Jian, T., Kim, S. H., Papanikolas, M. J., Freeman, R., & Schultz, Z. D. (2021). Catching COVID: Engineering peptide-modified surfaceenhanced Raman spectroscopy sensors for SARS-CoV-2. ACS sensors, 6(9), 34363444. [6] Mousavi, S. M., Hashemi, S. A., Rahmanian, V., Kalashgrani, M. Y., Gholami, A., Omidifar, N., & Chiang, W. H. (2022). Highly sensitive flexible SERS-based sensing platform for detection of COVID-19. Biosensors, 12(7), 466.

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Universiti Teknologi Malaysia & Department of Statistics Malaysia MoU Signing Ceremony

BY: DR. SITI ROHANI MOHD NOR, DR. NORHAIZA AHMAD, CHM. DR. MOHD FIRDAUS ABDUL WAHAB

On August 3, 2022, UTM and Department of Statistics Malaysia (DOSM) signed a memorandum of understanding at UTM, Johor Bahru, to foster data-driven academic and research collaboration. Vice-Chancellor Prof. Datuk Ts Dr. Ahmad Fauzi Ismail represented UTM at the signing ceremony, while Chief Statistician Dato' Sri Dr. Mohd Uzir Mahidin represented DOSM. The MoU was also witnessed by Prof. ChM. Dr. Zaiton Abdul Majid, Dean of the Faculty of Science, UTM, and Puan Hajah Nazaria Baharudin, Deputy Chief Statistician (Technical Development & Social), DOSM.

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The MoU builds upon an existing collaboration between staff at the Department of Mathematical Sciences, Faculty of Science, UTM, and DOSM through internships, conferences, doctoral supervision, and research grants. Since DOSM is the premier government agency responsible for producing the official national statistics to monitor the national economic performance and social development, this MoU will have a broader impact on UTM and DOSM, especially on data science and the development of advanced statistical techniques to make better-informed decisions on issues of national interest. In addition to the MoU, Dato’ Sri. Dr. Mohd Uzir Mahidin is also appointed as UTM’s Adjunct Professor, from August 3, 2022 to August 2, 2023. With his vast experience and expertise in data and statistical knowledge, the appointment of Dato’ Sri. Dr. Mohd Uzir Mahidin will be a part of the efforts to achieve the key indicators outlined in UTM’s enVision 2025 strategic plan.

"Collaboration is Multiplication." John C. Maxwell

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"No great achievement is possible without persistent work." Bertrand Russell

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International Grant

International Grant

International Grant

University Grant

National Grant

University Grant

Industry Grant

National Grant

University Grant

"If you want to change the world, pick up your pen and write." Martin Luther

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"The road to publication is like a churro - long & bumpy, but sweet." Jay Asher

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"The only way to DISCOVER the limits of the POSSIBLE is to go beyond them into the IMPOSSIBLE." Arthur C. Clarke

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ADVISOR

Prof. Dr. Suhairul Hashim

EDITOR-IN-CHIEF

Dr. Nurhafizah Binti Hasim (AOMRG)

EDITOR-ON-DUTY

Dr. Khairil Juhanni Abd. Karim (SepsTec) Dr. Mohd Farizal Ahmad Kamaroddin (EnvBio) Ts. Dr. Fariza Hanim Suhailin (NurP) Dr. Ang Tau Keong (DSM) Dr. Mark Lee Wun Fui (Gchem)

EDITORIAL TEAM MEMBER

PM. Dr. Nor Muhainiah Mohd Ali (AAAG) PM. ChM. Dr. Bakri Bakar (NatPro) Dr. Adina Najwa Kamarudin (STAM) PM. Dr. Raja Kamarulzaman Raja Ibrahim (AORG) Dr. Nur Izzati Mohd Noh (SynBio) Dr. Mohammad Izat Emir Zulkifly (ISC)

CONTRIBUTORS

Dr. Nur Izzati Bt Mohd Noh, Dr. Nurhafizah Binti Hasim, Dr. Abdul Fatah Bin A. Samad, Dr. Siti Salwa Alias, Liyana Binti Shatar, Ts. Dr. Fariza Hanim Binti Suhailin, Dr. Siti Rohani Mohd Nor, Dr. Norhaiza Ahmad, Chm. Dr. Mohd Firdaus Abdul Wahab

SPECIAL TASK FORCE

Pn. Hamidah Mat Arif