VOL 2 | December 2023 LEADING THE FUTURE “We don’t know enough to make informed efforts for their protection. We need to stop working in silos because time is running out for them.”
Table of Contents From The Dean ii From The Editor-In-Chief iii 1 What is Attacking My Mangoes? : The Case of the Mango Pulp Weevil 1 2 Environmental Health Risk Assessment : Leptospira Infections At Recreational Area 3 3 Mushrooms : Hidden Gems Of Penang Hill, Penang. 7 4 Insight into Plant-Microbe: Interaction and Soil Health – Pteris vittata L. 11 5 Exploring Halomonas sp. : Potential Therapeutic Agents 14 6 Leptospira interrogan ST238 : A Novel Leptospira Strain That Causes Severe Disease in Hamster Model 16 7 Rhamnolipid Biosurfactant : The Bacterial Antifungal Agent for Sustainable Agriculture 19 8 Mathematical Modelling : Illuminating Complex Systems Biology through Mathematical Modelling 22 9 Polyhydroxyalkanoates and Its Biodepolymerization 26 10 Konjac: A Mediocre Plant With Great Benefits and Potential 28 11 Geometric Morphometrics: Fisheries Resources Management and Conservation: The Strong Ties 31 12 Memorandum of Understanding (MoU) Signing Ceremony : Between SBS – Seberang Perai City Council (MBSP) 35 13 Research Collaboration : Tropical Rainforest Conservation Research Centre (TRCRC) and School of Biological Sciences (SBS) 39 14 VCRU : Soaring to Greater Height in 2023 41 15 Cat City doing Monkey Business: The IPS-MPS’23 Joint Meeting Draws Hundreds of Primatologists to Kuching, Sarawak 45 16 ERASMUS+ Mobility Programme : Keele University 49 17 ISP Academic Excellence Award 2022 55 18 Pioneering Visions: Biosociety’s Recollection of Academic Excellence and Social Innovation 59 19 SBS 3MT Competition 2023 65 20 Research Training : Keele University, United Kingdom 71 21 Understanding Metal Speciation and Its Importance in Environmental Science 77 22 Beneath the Surface : Exploring Blue Carbon Ecosystems 78 23 The Beauty of Peninsular Malaysia’s Peat Swamp Habitats : Closer Look at Its Fascinating Fish 80
Editorial Editor-In Chief Dr. Nik Ahmad Irwan Izzauddin Nik Him Editors Associate Prof. Dr. Amir Shah Rudin Md Sah Associate Prof Dr. Darlina Md Naim Dr. Kamarul Zaman Zarkasi Dr. Farah Alia Nordin Dr. Shuhaida Shuib Dr. Noraini Philip Dr. Hafizi Rosli Language Editor Dr. Shaidatul Akma Adi Kasuma Cover Design Husni Che Ngah Graphics & Layout Husni Che Ngah Frequency 2/2 2023 Bio-Bulletin December 2023 i
Copyright © 2023 School of Biological Sciences, Universti Sains Malaysia. Published under a Creative Commons Attribution license. You may copy and distribute this publication as long as credit is given to the original authors/ and Bio-Bulletin, School of Biological Sciences as the original source. Address all correspondence to: Dr. Nik Ahmad Irwan Izzauddin Nik him (Editor-in-Chief, Bio-Bulletin) School of Biological Sciences Universiti Sains Malaysia 11800 USM, Penang Fax: +604-656 5125 Tel: +604-653 3505 Email: [email protected] Published by: School of Biological Sciences Universiti Sains Malaysia 11800 USM Penang Email: [email protected] Tel : +604-653 3181 TITLE: BIO-BULLETIN - [ONLINE] eISSN : 3009-0229 ii Bio-Bulletin December 2023
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Praise be to Allah for His abundant grace and blessings. I am delighted to announce the successful publication of Bio-Bulletin Volume 2 of 2023. This edition showcases the outstanding achievements of the School of Biological Sciences (SBS), ranking as the top academic school at Universiti Sains Malaysia for both Myra 1.0 and Myra 2.0 in 2022. The remarkable achievement is the culmination of dedicated efforts by academic professionals and support staff working together to fulfil SBS’s vision and mission. In 2023, SBS welcomes five new contract lecturers who have also contributed articles to this publication. These pieces offer insight into their research and field of studies that will give a better understanding of their interest and expertise. It is hoped that with the influx of fresh perspectives of young minds, SBS will continue to excel and stand out in the years ahead. Bio-Bulletin Volume 2 publicises the events that were organised at SBS, as well as the activities lecturers and students undertook at the undergraduate and postgraduate levels. The undivided participation and commitment have holistically contributed to the growth of SBS. We also celebrate the success of two students who are recipients of the Academic Excellence Award 2022 sponsored by The Incorporated Society of Planters (ISP). Congratulations! This achievement will surely inspire and motivate other students at SBS. In October 2023, SBS welcomes new students for the Academic Session 2023/2024. I would like to warmly welcome all students and wish you the best experience at USM. Explore everything that USM has to offer, appreciate the learning experience, participate in extra-curricular activities, and make new friends. I pray that you will be successful in your endeavours and that you will become our driving force for continuous excellence. It is my sincerest hope that SBS will flourish and maintain its outstanding achievements and that the SBS community continues to thrive personally and professionally. May all our efforts benefit future generations. From The Dean Professor Dato’ Dr. Amirul Al-Ashraf Abdullah Dean. School of Biological Sciences “I would like to express my heartfelt thanks for the contributions and concerns of all parties at the School in ensuring the continuous excellence of this institution in research and academic achievements.” iv Bio-Bulletin December 2023
Firstly, I would like to extend a heartfelt gratitude to everyone who has contributed to the publication of Bio-Bulletin Volume 2, 2023. Without your cooperation and assistance, this publication would not have been realised. This publication holds more significance in light of our school’s, School of Biological Sciences (SBS), outstanding achievements in the 2022 Myra rankings. SBS has secured first place in both Myra 1.0 and Myra 2.0, establishing itself as the premier School at USM. Congratulations to all the SBS community! Volume 2 2023 also features articles written by our five new lecturers who are experts in various fields. I strongly believe that the diversity of research and skills is a uniqueness often associated with the excellence of a school. Therefore, as the Editor-in-Chief of BioBulletin, I would like to welcome you to SBS and hope that all of you will contribute to our shared success as well as excel in your respective fields. On behalf of SBS, I would also like to congratulate the recipients of the prestigious Academic Excellence Award for 2022, sponsored by the esteemed The Incorporated Society of Planters (ISP). This award shows that there is a wide opportunity for students to succeed at SBS and those who work hard will reap the benefits. May their accomplishments inspire and motivate us all. Finally, my best wishes to all lecturers and students at the School for the Academic Session 2023/2024. May it bring more valuable experiences that help us to progressively thrive in our endeavours. From The Editor-In-Chief Dr. Nik Ahmad Irwan Izzauddin Nik Him Editor-in-Chief “I would like to take this opportunity to thank each and every one of our contributors to this issues of the BioBulletin. I would like to express my heartfelt thanks to the dedicated team of editors who worked tirelessly to ensure the smooth running of this publication, and I am certain that this publication would not have been successful without them.” Bio-Bulletin December 2023 v
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1. What is Attacking My Mangoes? The Case of the Mango Pulp Weevil The mango, known by its scientific name Mangifera indica, is the most consumed fruit in Malaysia. A few selected mango cultivars planted in Malaysia are Sala (MA164), Harumanis (MA128), Chok Anan (MA224), Telur, Siku Raja, Siam, Epal, and Kuinin. Among the most popular cultivars are Harumanis (MA128), Masmuda (MA204), Siam Panjang (MA205), Nam Dokmai (MA223), Laris (MA154), Golek (MA162), Nang Klarngwun (MA125), Maha 65 (MA165) and Sala (MA164). Mangoes are grown in residential areas for personal consumption, and agricultural lands to be cultivated for sale. Many farmers in Kedah and Perlis rely on the mangoes as a secondary source of income. However, a range of factors, including mango variety, pest and disease management, and agronomic practices, have affected both the quantity and quality of mango production. The value of the mangoes produced significantly contributes to the Malaysian economy, as reflected in the high import values of Malaysian mangoes by other countries compared to the value of their exports (Suhana et al, 2022). Furthermore, mangoes are rich in vitamins, riboflavin, carotenoids, niacin, and minerals. Mangoes mature slowly, taking between 13 and 16 weeks after the fruit sets. Mango trees are particularly susceptible to pest and disease infections during the fruiting seasons. The pest and disease problem in this crop is significantly influenced by several factors, such as commercial mango production, changes in crop management, expansion into new plantation areas, increased chemical treatments, and variety replacement in the many mango-producing nations. Additionally, new pests may emerge due to climate change. Typical pests that commonly affect mango trees include the gold dust weevil, fruit fly, mango leaf cutting weevil, thrips, caterpillar, mango leaf hoppers, mango trunk borer, and mango shoot borer. Infested mango fruit with adult mango pulp weevil (in red circle). Presently, the mango pulp weevil (MPW), Sternochetus frigidus (Fabr.) (Coleoptera: Curculionidae) has become the most serious pest in mango plantations, surpassing fruit flies (Diptera: Tephtritidae), thrips (Thysanoptera) and mango stem borer (Coleoptera: Cerambycidae). Mangoes, both wild and cultivated are commonly infested with S. frigidus, which has also been found on M. odorata (kuinin) and M. foetida (bachang) in Malaysia. This weevil has been identified in Indonesia, northeast India, Myanmar, Singapore, Thailand, and Bangladesh. Sternochetus frigidus infestations are more severe than those of S. mangiferae, also known as the mango seed weevil. Adult S. mangiferae has an indistinct oblique pale stripe on the elytra (hard wing), whereas S. frigidus’s elytra are entirely black with brown patches. The Philippine Island of Palawan was the initial site of S. frigidus distribution. At that time, Palawan’s southern and central regions reported infestations of the mango pulp weevil, while the island’s northern region remained unaffected (De Jesus and Gabo, 2000). Due to the infestations that financially devastated the mango industry, quarantine restrictions were imposed on Philippine mangoes. The damage caused by S. frigidus in mango pulp results in unmarketable mangoes worldwide, making it a threatening international quarantine pest. Frass of the weevil on mango pulp. The S. frigidus infests only the mango pulp, leaving no visible signs of infestation on the fruit’s outer peel. The infestation becomes apparent only when a fruit’s skin is peeled off. Contaminated fruit symptoms can be detected after the adult weevils exit the mango. During the weevil’s mating season, the mango’s interior bears the weevil, and the fruit’s surface contains the weevil’s eggs. Mango weevil infestation is severe because it damages both the mango pulp and seed, contaminating the edible flesh without displaying any outward signs of damage. Mango pulp weevils excrete their granular faeces in the feeding holes. Mango pulp and flesh are the usual locations infested by this weevil, but the symptoms are not detectable when mango fruits are harvested before they ripen. Nur Aisyah Abdul Malek and Suhaila Ab Hamid Bio-Bulletin December 2023 1
Fig 3 Mango pulp weevil, Sternochetus frigidus (Coleoptera: Curculionidae). Sternochetus frigidus (Fig. 3) is a holometabolous insect, requiring four stages in its life cycle: egg; larva, pupa; and adult. The life cycle takes 182 to 190 days to complete. According to Lorenzana and Obra (2013), the life cycle begins and ends in the mango pulp, with the adult typically remaining inside the fruit for around 37 days before burrowing out by creating a hole. The mango pulp weevil prefers to move by crawling between trees rather than flying. It is a nocturnal insect, spending the day resting and becoming active at night. These weevils hide in the tree bark and feed on mango tree blossoms, particularly during the blooming season. They also prefer to complete their mating and egg-laying processes during the day. In addition, the volatile substances in mango fruits attract this weevil. Mushy flesh of mango due to feeding activity of mango pulp weevil. The most destructive stage of this pest is the larva, which feeds and develops within the mango pulp. The larva eventually matures into a new adult, remaining in the pupal cell within the mango pulp until the cell deteriorates and the pulp becomes mushy (Fig. 4). Female adults of S. frigidus lay 80 to 180 eggs on growing mangoes. If mangoes are placed in a bag or fully covered, weevils are unable to infest them (Fig.5). Pruning is an effective method for eliminating overlapping branches, unproductive branches, and branches affected by insects and diseases. To prevent the weevil from completing its life cycle, infected mango fruits that fall to the ground should be properly buried half a meter below the surface. If S. frigidus becomes a pest, some pesticides, such as carbaryl, dimethoate, and monocrotophos can be used as foliar sprays and spot applications on tree trunks during weevil oviposition. Dichlorvos, Deltamethrin, Endosulfan, and Malathion have also been proven to be highly effective in reducing S. frigidus infestations. Unbagged mangoes will be easily attacked by the mango pulp weevils. References De Jesus LRA, and Gabo RR. (2000). Life History and Host Range of The Mango Pulp Weevil, Sternochetus frigidus (Fabr.) In Palawan, Philippines. Philippines Agricultural Scientist. 83(2): 145-150. Lorenzana, L.R.J. and Obra, G.B. (2013). Mass rearing technique for mango pulp weevil, Sternochetus frigidus (Fabr.) (Coleoptera: Curculionidae). Journal of International Society for Southeast Asian Agricultural Sciences. 19(2):75-81. Suhana S, Rozhan AD, Nur Azlin R, and Wan Mahfuzah WI. (2022). Competitiveness of Malaysia’s Tropical Fruits in China Markets. FFTC Agricultural Policy Platform. Food and Fertilizer Technology Center for the Asian and Pacific Region. https:// https://ap.fftc.org.tw/article/3097 Nur Aisyah Abd Malek is a student at the School of Biological Sciences, USM. She conducted a study on mango pulp weevil infestation on various mango varieties for her final year project. Assoc. Prof. Dr. Suhaila Ab Hamid is a lecturer and researcher at the School of Biological Sciences, USM. Her research focuses on the taxonomy, biology, and biodiversity of insects and aquatic insects. She is currently investigating insects as biological indicators for environmental changes. 2 Bio-Bulletin December 2023
2. Environmental Health Risk Assessment Leptospira Infections At Recreational Area Azlinda Abu Bakar INTRODUCTION In their effort to advance research in communicable disease prevention, the Disease Control Division, Ministry of Health Malaysia (MOH), Putrajaya organised a programme called Malaysia One Health University Network (MyOHUN). The School of Biological Sciences (SBS) was one of the invitees to this initiative. A briefing session by Dr. Rohani Jahis, Zoonosis Sector, MOH, with group members at PKDHS prior to the field activity. The event took place at the Hulu Selangor District Health Office Kuala Kubu Bharu, Selangor on August 14, 2023. Participants included Medical Officers from Health State Departments (Selangor, Negeri Sembilan, Johor, Pahang, Perak, Putrajaya, Melaka), Health Services from various MOH departments (Zoonosis Sector, Infectious Disease Control Division, Disease Control & Veterinary Biosecurity Division), State Perhilitan (Selangor, Negeri Sembilan) and public universities (USM, UKM, UPM). The primary aim of this event was to conduct a consensus assessment of risk factors associated with leptospirosis transmission in outdoor environments and explore indicators for its evaluation and mitigation. Upon arrival, we highlighted the essential components to observe. Leptospirosis is a zoonotic bacterial disease caused by spirochetes of the genus Leptospira. It is commonly associated with exposure to water contaminated with urine from infected animals. Leptospirosis is a significant global disease affecting both humans and animals, especially those engaged in outdoor activities with potential exposure to contaminated water sources. Outdoor enthusiasts, field researchers, adventurers, and agricultural workers are particularly vulnerable to contracting the disease due to their close interactions with nature. FIELD ASSESSMENT Background This programme was conducted simultaneously in two different states - Selangor and Negeri Sembilan. Each state was assigned to evaluate the risks at several natural waterfalls or man-made water recreational areas. The assessment occurred in the morning, and in the afternoon, each group gathered at the respective Health District Office (PKD) for discussion, report writing and presentation of findings. Our group was responsible for assessing the risk at Serendah Waterfall, Kuala Kubu Bharu, Selangor. Interestingly, the waterfall and its compound area are located at the village end of the ‘Orang Asli’- Temuan, the third-largest group tribe among the 19 Orang Asli groups living in Peninsular Malaysia. The place offers basic facilities, such as toilets, changing rooms, gazebos, and a musolla for Muslim visitors. There are also small stalls selling food, snacks, and drinks at the entrance. However, the stalls usually operate only on the weekends or during public holidays. In addition to picnics and swimming, visitors can enjoy hill hiking as well as jungle trekking. According to the staff of Hulu Selangor District Health Office, Leptospirae was present in the soil samples in this area for over six months. Discussion on the components grading - agree to disagree. Bio-Bulletin December 2023 3
Observation From Hulu Selangor District Health Office (PKDHS), the trip to Serendah Waterfall took 50-minute by car. It was drizzling, cloudy and windy throughout and we were concerned about the occurrence of ‘kepala air’ in the area, especially because Kuala Kubu Bharu was hit by a heavy rain the day before. Upon arrival, we received a standard leptospirosis risk assessment form for field evaluation. The guidelines and format of this form were developed by Health Officers from the District Health Office in Negeri Sembilan (1st Ed. 2019). The programme aimed to gain expert input in the improvement of the assessment forms used for leptospirosis indicators via discussions, knowledge sharing, and the exchange of ideas. Recreational hazard: Long-tail macaque was spotted in the area during assessment. Assessment A total of eight essential components were considered: solid waste management, runoff water surface management, recreational areas, facilities management, sewage management, weather conditions (monsoon), promotional activity and recreational hazard. Factors contributing to the risk of leptospirosis infections included the presence of wild animals in the area, water pH (7.2 - 7.6) and water temperature (25 - 35 °C), as these conditions favour Leptospirae survival. The waterfall area, however, was open and exposed to sunlight, with moderately rapid water movement. There was a lack of sufficient rubbish bins, with only one large bin (roro) located at the car park entrance. Visitors were encouraged to manage their waste properly, and sewage management was not a concern since no cooking activities occurred in the area; all foods were prepared and cooked at home. Recreational area: Water sampling pH 7.24 - 7.25 and temperature 25.6 °C. Water criteria met! Promotional: A warning poster of the communicable diseases risk. Weather condition: Southwest monsoon (April - October). 4 Bio-Bulletin December 2023
Finding and Conclusions Leptospirosis infection risk was assessed on a scale of low to high risk: low risk ≤ 35 %; medium risk 36% - 65%; and high risk 66% - 100%. The final grade was determined based on the collective marks in the assessment components. Each component has its own sets of maximum marks and weighted base values. Therefore, the final grade is the total marks obtained from each component, calculated using the formulation below: Markah diperolehi setiap komponen (A) Asas Wajaran (C) Markah maksimum setiap komponen (B) X From the findings and thorough discussions, all members agreed that the Serendah Waterfall recreational area scored 62.67% in the final grading and, thus, was categorised as a medium-risk area for Leptospirosis. However, we suggested a few improvements to the components assessed. The components were focused on the basic facilities, solid waste management, and water treatment supply resources. The responsible authorities were advised to increase surveillance and maintenance of facilities. Additionally, more rubbish bins were recommended, with at least one bin to be placed at each gazebo. Proper water treatment supply for visitors was also recommended as an area for improvement. These suggestions were presented during the programme and will be escalated to local authorities. The objectives of the programme were successfully achieved, and team members gained valuable experience working together in the field. Essentially, recommendations for improving the risk assessment form components were underlined. Serendah Waterfall team. Matrix calculation: Score for the risk of leptospirosis infections in Serendah waterfall on 14 August 2023. Dr. Azlinda Abu Bakar Entomology & Parasitology School of Biological Sciences, Universiti Sains Malaysia Vector Biology and Ecology (mosquito) Plant extracts in mosquito control Ectoparasites of arthropods Bio-Bulletin December 2023 5
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3. Mushrooms Hidden Gems of Penang Hill, Penang. Sofiya Nurainaa binti Muhamad Rushdi and Rosnida binti Tajuddin Penang Hill, often referred to as Bukit Bendera in Malay, is a well-known natural landmark on the Malaysian island of Penang. Both locals and international visitors enjoy visiting this lush, forested hill station, which provides a welcome respite from the hectic city life of Georgetown, Penang’s capital. The breathtaking natural splendour of Penang Hill is well-known. Offering a pleasant escape from the coastal heat, it is covered in deep tropical rainforests and offers a cool, refreshing climate. Situated approximately 830 meters (2,720 feet) above sea level, the hill’s summit provides sweeping views of the region and the Strait of Malacca. Numerous macrofungi species thrive in this unique climate, characterised by high humidity within a lush tropical setting. Bio-Bulletin December 2023 7
Macrofungi are often overlooked treasures of the natural world, revealing a realm of entrancing beauty. These wonderful organisms, sometimes referred to as mushrooms, are among nature’s most exquisite gems, displaying their attractiveness through their vibrant colours, unique shapes, and complicated ecological connections. These amazing organisms continue to engage our senses and inspire us, reminding us of the intricacies and beauty of our natural world, regardless of whether they are observed in the wild, enjoyed at the dinner table, or studied in the laboratories. Macrofungi possess an aesthetic appeal that extends beyond mere sight. Their complex mycelium networks connect with trees and plants below the earth, creating a web of life crucial for the stability of ecosystems. These inconspicuous woodland allies support the development and survival of numerous species of flora, making them the unsung heroes of the natural world. The well-being of the Penang Hill ecosystems depends on macrofungi. They play a vital role in breaking down organic materials, decomposing dead plant matter, and recycling nutrients back into the forest. This nutrient cycle contributes to the overall well-being and viability of the forest ecosystem. Penang Hill is home to a diverse range of macrofungi species, including those that are edible, species with special ecological functions, and medicinal mushrooms. Two special species found in the area are Laetiporus versisporus and Fistulina hepatica. Laetiporus versisporus The intriguing species of bracket fungus, L. versisporus, sometimes known as the “bitter bracket” or “bittersweet chicken of the woods,” belongs to the genus Laetiporus. This particular mushroom is well-known among mycologists and mushroom enthusiasts due to its peculiar traits, ecological significance, and culinary potential. Laetiporus versisporus was found growing on a dead stump in Penang Hill, Penang. A) Front view; and B) Back view of L. versisporus. Laetiporus versisporus is a highly-coloured and eyecatching mushroom (Figure 2). It often grows in a fan- or semi-circular configuration, with overlapping fruiting bodies resembling shelves (Petersen, 2013; Roberts & Evans, 2014). The upper surface of the brackets often has a velvety or suede-like texture and is brilliant orange or red-orange in colour, while the undersides are porous with tiny, closely spaced pores that are initially white to pale yellow but darken over time (Petersen, 2013; Roberts & Evans, 2014). The brackets, which can develop alone or in groups, are typically found attached to the trunks or branches of both living and dead hardwood trees. Ecological Role of Laetiporus versisporus: As a saprophyte, this fungus primarily consumes dead or decomposing wood and is commonly found on hardwood trees like oak and eucalyptus. Laetiporus versisporus plays a crucial ecological role in breaking down wood by dissolving cellulose and lignin, which are challenging for many other organisms to decompose. By colonising and decomposing wood, it contributes to the carbon and nutrient cycling in forest ecosystems (Petersen, 2013; Roberts & Evans, 2014). Culinary Use of Laetiporus versisporus: One of the most remarkable aspects of L. versisporus is its edibility. While L. versisporus is often considered inedible due to its extremely bitter flavour, some Laetiporus species are recognized for their culinary potential (Petersen, 2013; Roberts & Evans, 2014). The bitterness is attributed to certain molecules it contains, which can be unpleasant or even harmful to some individuals. However, it is worth noting that there have been reports of people successfully consuming L. versisporus after employing various preparation techniques to mitigate its bitterness, but caution is advised, and it is best to avoid this particular mushroom. Fistulina hepatica A fascinating and unique species of bracket fungi, Fistulina hepatica, sometimes known as the beefsteak fungus, is widespread around the world (Petersen, 2013; Roberts & Evans, 2014). The term ‘beefsteak fungus’ is derived from the fungus’ resemblance to a raw, bloodied steak (Petersen, 2013; Roberts & Evans, 2014). This fungus has a large, flat cap with a rough, meat-like surface that varies in colour from reddish-brown to maroon (Figure 3). The texture, sometimes described as slimy and moist, further enhances its steak-like appearance. As the fungus ages, the cap may become more wrinkled and asymmetrical. Fistulina hepatica was found growing on a dead log in Penang Hill, Penang. A) Front view; and B) Back view. Habitat of Fistulina hepatica: This unusual fungus is primarily found on the stumps and trunks of hardwood trees. Fistulina hepatica, a woodrotting fungus, colonises its host by breaking through the bark and generating a brown rot in the wood (Petersen, 2013; Roberts & Evans, 2014). It often feeds on dead logs as it is a saprophytic fungus. 8 Bio-Bulletin December 2023
Dr Rosnida Tajuddin’s research interests include the identification of mycorrhizal fungi, understanding ectomycorrhizal fungi communities and their distribution in Malaysian rainforests, as well as studying nutrient transportation in ectomycorrhizal and arbuscular mycorrhizal symbioses. Additionally, her research encompasses the diversity of macrofungi in Malaysian forests. The macrofungi diversity project in Penang Hill is sponsored by The Habitat Foundation Research Grant under research grant number: THF2019/ RT/RG-111219/18 and 304 /PBIOLOGI /6501070 /T146. Email: [email protected] Ecological Significance of Fistulina hepatica: As a decomposer, F. hepatica is essential to the functioning of forest ecosystems. It aids in the recycling of nutrients and the development of soil by the lignin and cellulose present in trees. It is intriguing how this fungus can exude brilliant crimson liquid droplets, creating the impression of “bleeding” (Petersen, 2013; Roberts & Evans, 2014). Quinone-containing pigments found in this crimson liquid may function as a defense mechanism against parasites or potential herbivores. Conclusion In conclusion, the macrofungi of Penang Hill are an integral part of its unique ecosystem, enhancing biodiversity, nutrient cycling, and human well-being. To ensure the long-term preservation of Penang’s distinctive natural history, it is crucial to preserve and study these macrofungi. The conservation of these macrofungi should be an integral component of broader regional conservation initiatives. References: Petersen, J. H. (2013). The kingdom of fungi. Princeton University Press. Roberts, P., & Evans, S. (2014). The book of fungi: a life-size guide to six hundred species from around the world. University of Chicago Press. Sofiya Nurainaa binti Muhamad Rushdi was a former student at the School of Biological Sciences, Universiti Sains Malaysia, majoring in Microbiology during the academic year 2022/2023. She is currently awaiting her graduation ceremony scheduled for November 2023. Email: [email protected]. Bio-Bulletin December 2023 9
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4. Insight into Plant-Microbe Interaction and Soil Health Pteris vittata L. Nuur Athirah Bakar, Hazwani Sofia Hazizal, Aminu Salisu Mu’azu and Amir Hamzah Ghazali Soil is a thin layer (ca. 1 meter deep) covering the earth’s surface, essential for continuing human existence and balancing the natural ecosystem. Though vital for survival and civilisation, these non-renewable resources are often disregarded and taken for granted by humans, as historically proven. Humans mainly focus on the potential of soils for biomass production (e.g., food, fibre, and energy production) through the implementation of intensive agricultural activities. This has resulted in rapid deterioration and degradation of soil quality, which include loss of soil organic matter, erosion, salinisation, and heavy metal pollution. The phenomenon of soil degradation is detrimental since the soil takes millions of years to naturally form. Soil health is compromised, affecting planetary well-being and the survival of future human generations. The concept of soil health centres on the role and importance of soil for the future existence of human generations and its functions in balancing the natural ecosystem. Among the main factors that contribute to soil degradation are mining activities and industrial processing, which cause heavy metal contamination in soils (e.g., arsenic contamination). The handling and disposal of mine tailings, which contain high concentrations of arsenic, is a significant problem in the mining industry. The presence of arsenic in the environment, even at relatively low doses, may cause detrimental effects on the ecosystem, especially human health. Inorganic arsenic was confirmed as a class I human carcinogen by the International Agency for Research on Cancer (IARC). The fate of arsenic in contaminated soil is driven by the redox reactions, which greatly influence the metal’s toxicity, bioavailability, and mobility. Oxidised arsenic forms can be found naturally in the environment, including elemental arsenic, arsine (As3-), arsenite (As3+), and arsenate (As5+). However, the inorganic forms As3+ and As5+ are both the most toxic forms of arsenic, although it was concerned that As3+ is about five to ten times more toxic than As5+. Therefore, remediation of arsenic from the environment is necessary to minimise significant impacts on planetary well-being. Pteris vittata. A selected group of plants which can remove arsenic from contaminated soils and accumulate it in its tissues (via phytoremediation process) is known as Pteris vittata L. (Voucher specimen [USM. Herbarium 11872] was deposited in the Universiti Sains Malaysia herbarium). P. vittata belongs to the Family Pteridaceae, commonly known as the Chinese brake fern. It is widely distributed in the tropics and subtropics and has been known as a good hyperaccumulator plant in arsenic phytoremediation. It was first discovered in 2001 and became a research interest due to its potential to remediate arseniccontaminated soil. Sampling of rhizosphere soils of Pteris vittata. P. vittata holds a tolerance towards arsenic concentration in soil up to 1500 mg/kg besides having the ability to accumulate arsenic in a short time. The fronds could hold about 25 times more arsenic concentrations than the roots. It exhibited a more efficient reduction of arsenic concentration compared to other hyperaccumulator plants. The contribution of arsenic-resistant microbes is also crucial in arsenic transformation to control the influx of toxic elements in the environment. Mutualistic interactions between the plant (e.g., P. vittata) and its arsenic-resistant rhizobacteria play a significant role in enhancing the uptake of arsenic from the soil by promoting the bioavailability of arsenic for plants. Documentation of the function of rhizobacteria, e.g., Pseudomonas and Cupriavidus isolated from P. vittata to catalyse arsenic phytoextraction, was reported in several studies. The transformation of As (III) to As (V) may subsequently facilitate the element accumulation by plant roots in higher concentrations due to reduced toxicity. Bio-Bulletin December 2023 11
Pteris vittata. P. vittata grown in arsenic-contaminated sites can harbour bacterial populations coping with arsenic toxicity due to arsenic resistance (ars) genes. There are three characteristics of bacteria residing in heavy metal-contaminated areas: i) metal resistance, ii) ability to bioaccumulate metals into cells, and iii) ability to transform the toxic metal species into non-toxic species. In addition, the bacteria can also indirectly promote phytoremediation by enhancing plant growth. These unique properties held by the bacteria can be utilised to facilitate the process of arsenic phytoremediation. The inoculation of arsenic-resistant bacteria (ARB) increased the concentration of arsenic in P. vittata compared to noninoculated plants. It was also found that with bacterial inoculation, the translocation of arsenic from root to frond was significantly higher than that without bacterial inoculation. The inoculation also enhances the defence mechanism of P. vittata against oxidative damage due to arsenic-stressed conditions and promotes the growth of the host plants. Scanning Electron Microscopy (SEM) images of arsenic-tolerant Bacillus sp. 3P20. The cells exhibit a Gram-positive rod-shaped morphology. Additionally, the rhizospheric bacteria also benefit its host by providing essential vitamins, improving the solubilisation of nutrients, and promoting and improving the physiological functions of plants. Furthermore, bacteria also promote stomatal regulation, modification of osmosis, and adaptation of root morphology. The bacteria also possess the ability to promote the growth of P. vittata through the production of phytohormones, e.g., Indole-3- Acetic acid and nitrogen fixation, which then enhances the phytoremediation efficiency of arsenic by P. vittata. Therefore, bacteria improve plant growth in metalloidcontaminated soil and facilitate phytoremediation. The bacteria also tolerated high levels of arsenic metal, promoted plant growth, and played a significant role in arsenic biotransformation, its hyperaccumulation by P. vittata, in the contaminated soils. Hence, the interactions between arsenic-tolerant microbes and Pteris vittata play essential roles in the phytoremediation process of soils contaminated with arsenic, contributing to boosting soil health and planetary well-being. Scanning Electron Microscopy (SEM) images of arsenic-tolerant Enterobacter sp. 3U4. The cells exhibit a Gram-negative rod-shaped morphology. 12 Bio-Bulletin December 2023
Mr. Aminu Salisu Mu’azu is a PhD student in environmental microbiology at the School of Biological Sciences, Universiti Sains Malaysia. His study focuses on understanding the bacterial population of the rhizosphere soils of Pteris vittata (arsenic hyperaccumulator plants) of arsenic-rich (ex-tin mining area) and natural mineral soils. The plant-microbes interactions promote bioremediation of soils enriched in arsenic. Table 1: Top ten bacterial phyla with percentage (%) occurrence in the rhizosphere soils of P. vittata from arsenicrich sites (ARS) and non-arsenic-rich sites (NARS). Phyla Occurrence of bacterial phyla (%) ARS 1 ARS 2 ARS 3 NARS 1 NARS 2 NARS 3 Actinobacteria 59.4 30.4 55.3 37.3 39.5 45.4 Proteobacteria 17.0 26.0 15.0 22.1 19.2 22.0 Chloroflexi 10.3 17.0 9.0 7.0 10.0 8.1 Acidobacteria 3.1 9.0 5.0 11.0 9.0 8.0 Planctomycetes 2.0 3.4 2.0 6.0 3.9 4.0 Verrucomicrobia 1.0 1.2 1.3 7.4 6.5 2.9 Bacteroidetes 0.5 2.4 1.1 1.9 3.1 2.3 Myxococcota 1.3 2.2 1.3 2.4 3.0 1.9 Gemmatimonadetes 2.3 2.9 3.3 3.2 1.0 1.4 Firmicutes 0.5 0.6 3.9 1.1 2.3 1.1 Nuur Athirah Bakar is an undergraduate student in microbiology at the School of Biological Sciences, Universiti Sains Malaysia. Her study focuses on the plant-microbes interactions of arsenic-tolerant microbes and Pteris vittata in promoting the bioremediation of soils enriched in arsenic. Dr. Amir Hamzah Ghazali is an Associate Professor at the School of Biological Sciences, USM and researches plant-microbial interactions, emphasising plant growth and development, and soil health. The research focuses on genomic analysis, bioremediation, biological controls, and beneficial plant growth-promoting microbes. Hazwani Sofia Hazizal is an undergraduate student in microbiology at the School of Biological Sciences, Universiti Sains Malaysia. Her study investigates the role of arsenic-resistant bacteria in the reduction of As (V) and oxidation of As (III). The study also demonstrated the ability of the isolates to produce superoxide dismutase (SOD) under oxidative stress conditions. Bio-Bulletin December 2023 13
5. Exploring Halomonas sp. Potential Therapeutic Agents Wan Siti Nur Atirah Wan Mohd Azemin and Mohd Shahir Shamsir Omar In recent years, the study of marine metabolites and natural products has attracted growing attention from both biologists and chemists due to their remarkable potential in various research areas. Numerous metabolites sourced from marine environments have exhibited substantial biological activities, rendering them valuable commodities in the pharmaceutical and cosmeceutical industries. Of fascination is the biosynthesis of bioactive molecules by symbiotic marine organisms. The pathways for nutrient exchange between symbiotic partners raise intriguing questions about the origin and production of metabolites within these associations. In the context of this review, we delve into the realm of epibiotic bacteria, a distinctive category of organisms that inhabit the surfaces of other organisms. They exist in a biologically competitive milieu, often demonstrating unique biological activities to inhibit the settlement of potential competitors. Their biological prowess is largely attributed to antimicrobial peptide (AMP) compounds, frequently found on fish skin mucous membranes, and bacteriocins, produced by bacterial species in their ecological niches. The EPS-producing of isolate cream colony (CC) from Halomonas sp. Strain M3. Bacteriocins, a class of biologically active compounds, are typically produced by Gram-positive bacteria, and in some cases, Gram-negative bacteria. Distinguished by their relatively short peptides (30 to 60 amino acids), bacteriocins differ from antibiotics in terms of molecular weight, biochemical properties, amphiphilic helices, and their spectrum of activity and mode of action. These compounds are categorized into four classes based on host producer, intrinsic role, physicochemical properties, molecular mass, and amino acid sequences. Class I includes ribosomally synthesized post-translationally modified peptides that are heat-stable, typically containing peptides of less than 5-kDa. They function by binding to a docking molecule, which can inhibit RNA or cell wall synthesis or form pores in the cell membrane. Class II comprises unmodified peptides, also heat-stable and with peptides smaller than 10-kDa. These peptides attack invaders by disrupting the proton motive force through pore formation. Class III refers to large proteins, heat-sensitive, containing hydrophilic peptides of more than 10-kDa, which catalyze cell wall hydrolysis and induce cell lysis. Finally, Class IV consists of circular proteins with hydrophobic lipid- or carbohydrate-conjugated complexes, ranging in size from 5.5 to 7.5-kDa, and they are heatstable. These bacteriocins insert into the cell membrane of the target, causing membrane permeabilization. Scanning Electron Microscope (SEM) image of Halomonas sp. strain M3 at 5,000 x magnification at bars, 5 µm. The Halomonas species strain M3, as a halophile microorganism, was initially isolated and identified from Malaysian Crimson snapper (Lutjanus erythropterus) in the aquaculture industry within the Straits of Johor. This bacterium, known as epibiotic bacterium, adheres to solid surfaces of fish through exopolysaccharides (EPS) in both marine and freshwater environments. Halomonas sp. Strain M3 has been found to produce potent antimicrobial compound namely bacteriocin Cream Colony (CC) within its EPS. Characterization of this bacterium revealed that optimal growth and bacteriocin production occur at ambient temperature, pH of 8-8.5 in nutrient broth medium supplemented with 2.9% w/v NaCI to mimic saltwater conditions. The stability studies indicated that bacteriocin CC is heat-labile (35°C-50°C) and was stable over 2 years when stored in 0.02M TrisHCI with 30-60% glycerol at 4°C. A loss of activity was detected after proteolytic enzyme treatment, showing the proteinaceous nature of the antimicrobial compound. This fact elucidated that there was a relationship between bacteriocin and exopolysaccharides (EPS) in Halomonas sp. They may interact and influence each other in various ways such as EPS as a bacteriocin carrier, biofilm formation, microbial competition, quorum sensing, and environmental adaptation. 14 Bio-Bulletin December 2023
Malaysian Crimson snapper (Lutjanus erythropterus). (Photo credit; https://fishider.org/en). Importantly, many bacteriocins have been isolated from mucosal surfaces, serving as the first line of innate defence for aquatic animals, which are in constant contact with a diverse array of opportunistic pathogens. Recent studies have unveiled the significant biological activities of EPS-secreted Halomonas sp. strains. For instance, Halomonas sp. BS4, isolated from the Thamaraikulam solar salt works in India, has demonstrated effective protection against human pathogenic bacteria, fungi, and the aquaculturally significant virus, WSSV. Furthermore, it has exhibited the inhibition of mammary epithelial carcinoma cell growth. Halomonas sp. NASH has also been reported to produce EPS and actively inhibits the growth of Pseudomonas aeruginosa and Candida albicans. Additionally, it boasts strong antioxidant and anti-inflammatory properties. Beyond antimicrobial activity, Halomonas species exhibit potential in cancer cell treatment. For instance, El-Garawani and co-workers (2020) reported that a new strain of Halomonas sp. HA1 induced apoptosis and arrested the cell cycle of hepatocellular carcinoma cells at the G2/M phase. Furthermore, research has highlighted Halomonas sp. Exo1’s ability to accumulate high levels of arsenic within its cell biomass through EPS-mediated absorption, transforming the metals into degradable compounds. These findings underscore the pivotal role that bacteriocins play in inhibiting the growth or metabolism of other organisms. Their discovery holds tremendous promise for the development of antimicrobial compounds with applications in various sectors, including food, health, veterinary, and high-value products for drug development. While promising, it is important to note that the specific proteins responsible for the observed therapeutic effects have yet to be definitively identified, highlighting an area ripe for further investigation. Investigating the protein-protein interaction (PPI) networks associated with Halomonas sp. or bacteriocins is a crucial preliminary step before identifying the specific proteins involved in various fields. This planned strategy establishes the foundation for extensive research and discovery across numerous fields. PPI networks provide a holistic view of how proteins in Halomonas sp. interact with one another and with proteins from other organisms. This allows researchers to identify the key players (central or highly connected proteins) within the network and explain how the bacterium interacts with host proteins. It helps elucidate pathways and functional modules within the bacterium. This information is critical for deciphering the roles of proteins in various cellular processes, such as metabolism, signal transduction, or stress responses. Understanding the mechanisms underlying their bioactivity against cancer cells and other potential health benefits can open new avenues for drug development and biotechnological applications. Future research efforts should focus on unravelling the molecular basis of these interactions, which could lead to the discovery of novel anticancer agents and other bioactive compounds. By delving deeper into the biotechnological potential of Halomonas sp., we may unlock valuable solutions for healthcare and environmental challenges alike. Dr. Wan Siti Nur Atirah Wan Mohd Azemin is a Senior lecturer at the School of Biological Sciences, Universiti Sains Malaysia. Her research interests are in microbiology, cell stress signalling in cancer biology, bioinformatics, as well as computational protein biology. Prof. Dr. Mohd Shahir Shamsir Omar is a Professor at the Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia (UTM), Johor with expertise in bioinformatics. He is also the founder of the Bioinformatics Research Group (BIRG) at UTM, where he led various projects on molecular dynamics, prion disease, and geographic information systems. Bio-Bulletin December 2023 15
6. Leptospira interrogan ST238 A Novel Leptospira Strain That Causes Severe Disease in Hamster Model Noraini Philip and Vasantha Kumari Neela Leptospirosis, also known as rat urine disease, is a zoonotic infection that causes more than 500,000 cases each year globally. It is endemic in countries with humid subtropical and tropical climates. Leptospirosis is transmitted by rodents, but other wild animals such as Orang Utan and bats, as well as domestic animals (cattle, dogs, cats), can also be sources of infection. The clinical presentations of leptospirosis are wide, ranging from mild to severe diseases. It affects vital organs such as the lungs, liver, and kidneys. In a few cases, Leptospira also affects the brain. The bacteria that cause leptospirosis is known as Leptospira. Currently, there are more than sixty-six species of Leptospira including pathogenic and non-pathogenic species. The species of Leptospira contributes to the broad clinical presentation of leptospirosis with some of the pathogenic Leptospira species causing severe diseases. Hamster infected with L. interrogans ST238. The hamster became inactive after three days of infection with L. interrogans ST238. In Malaysia, several Leptospira species including novel species have been isolated from animals especially rodents and the environment (water and soil). It is well known that the virulence of Leptospira species/strains differed geographically, hence it is important to assess the virulence potential of the local Leptospira species/ strains. The virulence potential of three pathogenic Leptospira species (L. interrogans ST238 (strain HP358), L. borgpetersenii ST143 (strain HP364) and L. weilii ST242 (strain SC295)) isolated from rats captured from the human leptospirosis suspected areas in Selangor state, Malaysia was investigated and showed different capacity to cause disease in animal model. These three Leptospira strains were injected into golden hamsters (Mesocricetus auratus) and caused different levels of clinical presentations. Hamsters infected with L. borgpetersenii ST143 showed no signs and symptoms while hamsters infected with L. weilii ST242 became inactive and had less appetite but recovered and survived. Not only did the hamsters infected with L. interrogans ST238 become inactive, but they also died. The vital organs of the hamsters infected with L. interrogans ST238 were damaged with bleeding observed in the lungs and kidneys, while only the kidneys were damaged with no bleeding in hamsters infected with L. weilii ST242. Arrows show bleeding (petechial haemorrhage) in the lungs of hamsters infected with L. interrogans ST238 (strain HP358). The kidney and liver of hamsters infected with L. interrogans ST238 became pale and congested, respectively. It was observed that although L. interrogans ST238 infected all three vital organs in hamsters, bleeding first occurred in the lung, on the first day of infection. Damage in the liver and kidneys occurred on the third day of infections accompanied by clinical manifestations such as inactivity, breathing difficulty, and loss of appetite. Some of the hamsters died on day five of infections. Severe form of leptospirosis is challenging as it affects vital organs and the rapid transition from mild to severe contributes to the difficulty not only in diagnosis but also in giving appropriate treatment. As the bleeding in the lungs was first observed in severe leptospirosis, it is suggested that medical practitioners observe the lung signs and symptoms of patients with leptospirosis to monitor the disease progression from mild to severe. The changes in organs of hamsters after infected with L. interrogans ST238. Bleeding was observed in the lungs from day 1 post infection and became severe from day 3 post infection onwards. Kidneys became progressively pale from day 6 post infection onwards. No notable changes were observed in the liver. C: Control; D1-D7: Day 1 to Day 7. The arrow shows bleeding. Several Leptospira species isolated from rodents in Malaysia are highly virulent, hence it is essential to practice preventive measures when involved with activities exposed to leptospirosis infections. The bacteria can enter the human body through the eyes, nose, mouth, or broken skin (cut or scratch). Wearing protective clothing and taking antibiotics before being involved with water and soil-related activities can reduce the likelihood of infection. 16 Bio-Bulletin December 2023
Papers associated with this article: 1. Azhari NN, Ramli SN, Joseph N, Philip N, Mustapha NF, Ishak SN, et al. Molecular characterization of pathogenic Leptospira sp. in small mammals captured from the human leptospirosis suspected areas of Selangor state, Malaysia. Acta Trop. 2018; 188:68–77. 2. Philip N, Jani J, Azhari NN, Sekawi Z, Neela VK. In vivo and in silico virulence analysis of Leptospira species isolated from environments and rodents in leptospirosis outbreak areas in Malaysia. Front Microbiol. 2021; 12:753328. 3. Philip N, Priya SP, Jumah Badawi AH, Mohd Izhar MH, Mohtarrudin N, Tengku Ibrahim TA, Sekawi Z, Neela VK. Pulmonary haemorrhage as the earliest sign of severe leptospirosis in hamster model challenged with Leptospira interrogans strain HP358. PLoS Negl Trop Dis. 2022; 16: e0010409. Dr. Noraini Philip is a lecturer at the School of Biological Sciences, USM. Her main research interest is leptospirosis epidemiology and pathogenicity. Assoc. Prof. Dr. Vasantha Kumari Neela is a lecturer at the Faculty of Medicine and Health Sciences, UPM. Her main research interest is medical microbiology focusing on diagnosis and epidemiology. Bio-Bulletin December 2023 17
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7. Rhamnolipid Biosurfactant The Bacterial Antifungal Agent for Sustainable Agriculture Izah Adlina Mohamad Shukri, Ahmad Ramli Mohd Yahya, Masratul Hawa Mohd and Nur Asshifa Md Noh Rhamnolipid – a multifunctional biocompound Biosurfactants are a structurally diverse group of surfaceactive metabolites synthesized by living cells, primarily bacteria and yeasts. They possess hydrophilic lipophilic balance which specifies the portion of hydrophilic and hydrophobic constituents of the molecule. They are excellent emulsifiers, foaming, and dispersing agents. Their special properties, namely low or non-toxicity, high biodegradability, stability, and environmental compatibility, have attracted substantial interest in these surface-active biomolecules for various applications. Based on their chemical composition, biosurfactants can be glycolipids, lipopeptides and lipoproteins, phospholipids, and polymeric surfactants. Glycolipids and lipopeptides are among the promising biosurfactants that were successfully produced from local bacterial isolates. Some examples of microbes capable of producing biosurfactants include Pseudomonas, Bacillus, Acinetobacter, Rhodococcus, and Thiobacillus. Rhamnolipid is a glycolipid biosurfactant produced predominantly by Pseudomonas aeruginosa. It offers many advantages in a wide range of industrial applications due to its structural diversity, versatile biochemical properties, and stability at extreme temperatures, pH, and salinity. This ‘green’ surfactant is also well-known for its strong emulsification activities towards hydrophobic compounds, high surface activities, and antimicrobial activities, which augurs well in environmental bioremediation and agriculture. The favourable results of rhamnolipid as an antifungal agent against plant pathogenic fungi causing diseases on crops led to the interest in exploring rhamnolipid applications in agriculture. Pseudomonas aeruginosa – the prime producer of rhamnolipid Pseudomonas aeruginosa, a Gram-negative rod-shaped bacterium, can survive in various environmental conditions, especially in oil-contaminated sites. It is an opportunistic pathogen, which exists in a pearl-like or grape-like form, growing best at 25 °C to 37 °C. Additionally, this species can be differentiated from other Pseudomonas species due to its ability to grow at 42 °C. Specifically, P. aeruginosa USM-AR2 was isolated from a crude oil sample and has been found to naturally produce an appreciable amount of rhamnolipid. Rhamnolipid is a secondary metabolite produced by the bacterial culture at the end of the exponential phase and the onset of the stationary phase of microbial growth. Thus far, rhamnolipid production is carried out by batch and fed-batch submerged fermentation process. In adhering to sustainable agricultural practices, renewable raw materials such as agricultural wastes can be used as feedstock for rhamnolipid production. Currently, waste cooking oil has been proven viable in producing good yields of rhamnolipid in P. aeruginosa USM-AR2 fermentation. The fermentation is conducted in a stirred tank bioreactor, equipped with an integrated foam fractionation system. Rhamnolipid is collected from the fermentation broth and recovered using solvent extraction. The dried crude rhamnolipid extract is used for antifungal activity evaluation. Rhamnolipid production in a benchtop stirred tank bioreactor. Rhamnolipid as a promising antifungal agent in agriculture The demand for safer food crops leads to the investigation of rhamnolipid as a biofungicide in sustainable agricultural practices. Having a good natural producer of rhamnolipid, together with the motivation to address food security through agriculture, our current focus of research is the application of rhamnolipid to control the spread of Pyricularia oryzae causing blast diseases on rice (Oryza sativa). According to the Muda Agricultural Development Authority (MADA) and Malaysian Agricultural Research and Development Institute (MARDI), rice blast is a major rice disease affecting rice crop productivity in Malaysia. Rhamnolipid antifungal activity against a wide range of phytopathogenic fungi, consequentially offering a sustainable alternative to chemical fungicides, has become a prevalent topic of research in recent years. The role of rhamnolipid as a biocontrol agent against pathogenic microbes to treat various plant diseases has also emerged through the years. Its application is anticipated to alleviate the occurrence of resistant target Bio-Bulletin December 2023 19
organisms, due to the repeated and indiscriminate use of synthetic fungicides. The wide use of synthetic fungicides in controlling plant diseases often leads to several concerning implications from their adverse effects on the environment, causing secondary pollution, disturbing the ecological balance of natural soil microbes, leading to the emergence of resistant pathogenic strains, groundwater contamination, and increased health risks to humans. Generally, rhamnolipid owes its broad applications in agriculture due to its excellent solubility and wetting properties which are favourable in enhancing soil quality, boosting plant immunity, and improving plant growth against pathogens. It also serves as an enhancer of existing pesticides, boosting wettability and coverage, and increasing the potency of pesticides, which reduces the amount of pesticides that are required. In addition, rhamnolipid is used for soil remediation to boost soil fertility. Several studies have reported rhamnolipid to exhibit good antimicrobial and antifungal properties. Within the last decade, rhamnolipid produced by P. aeruginosa has been reported to show antifungal activity towards Colletotrichum falcatum, Alternaria alternata, Phytophthora capsici, P. sojae, Verticillium dahliae, Mucor sp., Aspergillus sp., and many other reported microbes. Thus far, the main mechanisms of action are via the destruction of the cell membranes and the reduction of spore movement that may lead to spore collapse. The inhibition effect of rhamnolipid against Pyricularia oryzae USM-PD1 on PDA plates. (a) Positive control (Amistartop®). (b) Negative control. (c) Treated with rhamnolipid. Pyricularia oryzae – the primary plant pathogen causing rice blast Symptom of rice blast observed in the rice field. Rice blast disease, known as ‘karah padi’ caused by Pyricularia oryzae (telemorph: Magnaporthe grisea) is one of the key restrictions causing significant harm to rice production in Malaysia. The blast fungus, P. oryzae, attacks the rice plants at all stages of growth, causing diamondshaped or spindle-shaped lesions with greyish centres, brown margins on the leaves and panicle neck rot at the culm. A complete cycle of blast diseases begins when spores infect the host, followed by germ tube growth, appressorium creation, production penetration peg, and invasive hyphae in the host. The hyphae extend, causing symptoms such as lesions or spots on the rice plant, and subsequently, the fungus begins sporulation and releases new spores into the air. Rice blast outbreaks are a major and recurring concern not only in Malaysia but in all rice growing countries around the world. To date, various managing strategies have been taken to control rice blast, such as breeding rice with improved resistance, chemical control, cultural practices, and nutrient management. However, one of the major challenges in producing a new variety of rice is the need to increase resistance towards P. oryzae. Several studies on biocontrol management have reported P. fluorescens, Bacillus sp., Streptomyces sp., and Trichoderma sp. as showing good potential to inhibit mycelial and spore germination of P. oryzae. Rhamnolipid use in agriculture. In line with this management strategy, rhamnolipid produced by P. aeruginosa USM-AR2 has been explored as an antifungal agent against P. oryzae causing rice blast. Rhamnolipid has been shown to inhibit the mycelial growth of P. oryzae USM-PD1, isolated from a paddy field in Alor Setar, Kedah. The mycelia were retarded and unhealthy when compared to controls, although treated with a lower concentration of rhamnolipid compared to the chemical fungicide used. These results encourage further investigation of rhamnolipid as an antifungal agent. It is anticipated that more favourable results will emerge, securing rhamnolipid as part of an efficient strategy in stopping the spread of plant diseases for better crop management and protection. 20 Bio-Bulletin December 2023
This is just the tip of the iceberg for applications of rhamnolipid in agriculture. Recent literature is replete with reports of rhamnolipid applications. The table shows that even within the limited scope of agriculture, rhamnolipid can be used in many ways, spanning from assisting plant nutrition uptake by way of soil conditioning to biological control which is the focus of this article. Undoubtedly, rhamnolipid is poised to be an important compound in the near future. Dr. Nur Asshifa Md Noh is an academic staff at the School of Biological Sciences, Universiti Sains Malaysia. Her work is related to microbial fermentation and applied microbiology. Her research involves the production of microbial biosurfactant, specifically rhamnolipid production and its applications, with a current focus on the application of rhamnolipid in agriculture. Ms. Izah Adlina Mohamad Shukri is a Master’s degree student in Industrial Microbiology at the School of Biological Sciences, Universiti Sains Malaysia. Her study focuses on rhamnolipid application as an antifungal agent against blast and sheath blight diseases on rice (Oryza sativa). Associate Professor Dr. Ahmad Ramli Mohd Yahya believes that solutions for real world problems often lie in simple but practical solutions that transcend multiple disciplines, despite having innovative solutions that are always impractical, associated with prohibitive costs. He is currently an academic staff working on bioprocessing, bridging biology and engineering innovation. Dr. Masratul Hawa Mohd currently holds the position of senior lecturer at the School of Biological Sciences, Universiti Sains Malaysia. Her research expertise extends across Plant Pathology and Mycology, with specific interests in plant disease diagnosis, fungal systematics, plant disease management, and mycotoxicology. She is presently dedicated to researching fungal diseases across various host plants and is actively involved in the investigation of fungal and mycotoxin contamination in agricultural crop products. Bio-Bulletin December 2023 21
8. Mathematical Modelling Illuminating Complex Systems Biology through Mathematical Modelling Nurul Izza Ismail The complexity of the cell’s intracellular signalling pathways makes it difficult to study, both in vitro and in vivo. Moreover, difficulties in obtaining human samples create limitations for experimental work. For these reasons, mathematical modelling can be employed to investigate intracellular cell signalling pathways in a biologically realistic manner. Mathematical models have been widely used to complement biological studies of cellular and subcellular signalling pathways and gene regulatory networks and are used widely in systems biology to predict responses of systems under different conditions. This write-up describes the overall process of mathematical model development and an overview of the natural killer (NK) cell model, introduces the concepts and software used for model implementation, and discusses the possible challenges associated with developing a mathematical model for this complexity. Model construction Biological pathways are comprised of ligands (L), receptors (R), kinases (K) and substrates (S). One can draw a pathway diagram based on the current understanding of the signalling pathways to get a clear picture of how ligands, receptors and kinases interact within reaction networks. This diagram can include every reaction that occurs in a system or can ’bundle’ multiple reactions together. The diagram is used to explain how the system works. Each of the biomolecules can exist as a complex or alone as illustrated in the pathway diagram. Steps in physicochemical modelling. Using ordinary differential equations to model signalling pathways There are several ways in which a mathematical model of cell signalling behaviours can be constructed. The most employed method is to translate a signalling pathway into a system of ordinary differential equations (ODEs), with each ligand, receptor, kinase, or substrate’s concentration being defined by an ODE representing an increase or decrease in concentration as reactions occur. Other methods that are typically employed include delay differential equations (DDE), partial differential equation (PDE), and stochastic differential equation (SDE). Advantages, disadvantages, and examples of each modelling approach: ODEs, DDEs, PDE and SDEs. 22 Bio-Bulletin December 2023
When information is unavailable to be associated with delayed feedback, spatial dynamics, probabilistic events or stochastic effects, an ODE model is a suitable approach. An ODE model can be employed to capture a large signalling pathway, with significant interconnectivity; this provides a simple to generate and readily interpretable model of the system. In addition, information on the spatial distribution of components of the pathway and data to parameterise a stochastic model is limited. To create an ODE model of the system, a list of biochemical reactions is generated from the pathway diagram, which includes forward and backward reactions. Open-source software, i.e., CellML and OpenCOR (www.opencor.ws) can be used as a platform to run the code with appropriate initial values and parameters. ODEs are generated using reaction kinetics. The essential features of an ODE model include the variables, parameters, and constants. There are two types of variables for the ODE model: independent (time) and dependent (substrate (S), product (P) and enzyme (E)). The ODE approach describes the concentration changes of a compound at a time. For example, a concentration of component A, [A] evolved over time. An ODE calculates the sum of association reaction rates consuming A and the sum of dissociation reaction rates forming A as the following equation: ODEs describing the signalling pathways of interest were generated using the law of mass action kinetic and Michaelis-Menten approximation. The simulation of the ODE model requires information on the initial conditions of the state variables, i.e., the initial condition of the substrates and the kinetic rates that describe the reaction. For a reaction defined using the law of mass action kinetic, the change of concentration over time of ligand, receptor, and ligand-receptor complex can be defined by the following ODE: For a reaction that is catalysed by an enzyme and defined using Michaelis-Menten kinetics, the reaction rate can be defined using the following ODE: For dimeric and tetrameric receptors that are defined by the Hill equation, the reaction rate can be defined using the following ODE: Model reusability, modularity, and documentation A reproducible model in system biology can be resimulated at various stages of its development process, from equation generation to data fitting, parameter optimization, and validation. This approach enables the model to adapt to different experimental conditions, such as varying cell types, species, or temperatures. Modular and reproducible modelling has gained importance among researchers, as it enhances model robustness and prevents failures from affecting the entire model. Modular construction involves breaking down the model into smaller, interconnected components or modules, allowing researchers to focus on specific pathways while reusing well-studied models. Modularity enhances a model’s robustness and encourages the reuse of sub-modules. It often involves organizing models into hierarchical structures with layers, where smaller sub-modules form the bottom layer, and the complete model, assembled from these sub-modules, constitutes the top layer. The CellML modelling approach for example employs modularity through componentbased model development, enabling the composition of meaningful molecular reactions or functional units. Reusing existing models is strongly recommended during model development to save time and costs, reduce errors, and encourage focus on developing new models. Connecting these models is facilitated through component-based approaches, which enables the creation of more complex models by combining existing components. Proper documentation, along with a simulation protocol like Simulation Experiment Description Markup Language (SED-ML), is crucial for ensuring model reproducibility. SED-ML records simulation conditions and output, making it easier for users to understand a model’s mathematical equations, parameters, solver algorithms, simulation times, and time steps. This protocol also aids in referencing and accurately reproducing a model’s results in research publications. Modelling research increasingly relies on curated databases and public repositories. Essential principles that lead to sharing databases are becoming essential. Models that have been built or are going to be built are expected to use the FAIR Guiding Principles (https:// www.force11.org/node/6062). FAIR refers to Findable, Accessible, Interoperable and Reusable. These principles are important in ensuring the reliability, reproducibility, and re-usability of a model. Bio-Bulletin December 2023 23
Case in point: A modular approach to understanding natural killer (NK) cell function A comprehensive qualitative description of the intracellular signalling pathways leading to chemokine and cytotoxin release from peripheral NKs is available from the KEGG database (https://www.genome.jp/keggbin/show_pathway?hsa04650) and databases such as PMR (https://models.physiomeproject.org/welcome) and BioModels (https://www.ebi.ac.uk/biomodels-main/). Using this approach, the key pathways relevant to NK cell signalling from cell surface receptor to cytokine release were identified. Complete NK cell signalling pathway created based on KEGG database and literature survey. Mathematical models enable complex signalling pathways to be interpreted by physical laws governing reaction kinetics. Curated models of numerous pathways exist, including several components of NK cell intracellular signalling. To manage the complexity of NK cell intracellular signalling, and to allow reuse of existing models from the literature, we simplify the system into smaller modules that can be solved and validated against biological data alone or within a larger system. With modularisation, components of curated models can easily be combined to represent larger systems. Models were modularised, and compiled to be tested against published results, before the reuse of modules. Here the model of Dupont and Erneux (1997) is shown. 24 Bio-Bulletin December 2023
Novel modules are created from models of components of the NK cell signalling pathways that already exist in the literature. These are parameterised and tested against experimental data, and thus, need to be implemented and curated to work within the more complete model of the NK cell pathways. Unknown parameters in new modules (or combination of modules representing components of the NK cell intracellular signalling pathway) were fitted to literature data, where available. For example, a model was compiled to represent the biology of FCεRIγ interaction with Syk and Grb2. This model was compared to published experimental data. We now have a full model of NK intracellular signalling pathways. Steps have been made toward a quantitative model of the NK cell intracellular signalling pathway. The model has been fitted to experimental data so that it responds in a physiologically reasonable manner regarding NK cytokines secretion. The model developed was used to assess the parametrisation of the kinetic parameters and hypothesise the kinetic mechanisms that allow multiple receptors to activate signalling pathways in NK cells. Dr. Nurul Izza Ismail is a senior lecturer at School of Biological Sciences, USM. Her research interests focus on implementing efficient and reliable computational methods for biological study. Izza’s expertise lies in the modelling of cell signalling processes and employing in silico methods to anticipate binding modes of biological molecules. Bio-Bulletin December 2023 25
Siti Nor Syairah Binti Anis Polyhydroxyalkanoates (PHAs) are a class of natural materials that have been present in the environment. PHAs have been discovered by Maurice Lemoigne since the early 1920s. These materials are bio-based and biodegradable, like other natural materials such as proteins, starch, and cellulose. PHAs are synthesized by a wide variety of microorganisms through bacterial fermentation. During fermentation, bacteria transform different types of feedstocks into a product. In this case, the microbes produce PHA, a biodegradable plastics that has drawn interest as a promising alternative for conventional plastics derived from petroleum. The feedstocks used in the synthesis of PHAs have evolved over time, reflecting efforts to make the production of these biopolymers more sustainable and economically viable. Ten years ago, the main feedstock sources were corn, sugar, and vegetable oils. Presently, utilizing waste materials as feedstocks for PHA-producing start-ups are a promising strategy to enhance the sustainability of PHA production. For example, by utilizing wastewater streams, plastic waste, palm oil waste, food processing waste, and so forth. PHA exhibits a range of properties that make them attractive for various applications due to their biodegradability, biocompatibility, renewability, and versatility in terms of physical and mechanical properties. Depending on the different properties, PHAs can be used as packaging materials, agricultural films, disposable bottles and containers, medical devices, textiles, 3D printing filaments, and electronics and consumer goods. Biopolymer PHA inside the bacterial cell under Transmission Electron Microscope. Furthermore, PHA also can be reused and recycled to polymer for different applications. First, PHA can be recycled to raw materials to be used as renewable feedstock. Second, it can be recycled to the environment through industrial or home composting. Third, it can be recycled through incineration to create renewable energy. Finally, it can be recycled into nutrients for living organisms through full biodegradation. Consequently, it can be concluded that, the potential of PHA is not limited to the versatility and flexibility of the neat polymer but also its biodepolymerization products such as monomers, dimers, and oligomers. Currently, there is a strong demand in the chemical industries for chiral molecules from renewable resources. Depolymerization of PHA to produce chiral molecules in the form of monomers, dimers and oligomers is envisaged as a potential environmentally friendly route to platform chemicals with high yield and productivity, at a relatively low cost. (R)-3-hydroxyalkanoic acids ((R)-3HAs)) produced by the hydrolysis of PHAs can be used as chiral starting materials in fine chemicals, pharmaceuticals, and medical industries. PHA biosynthesis in the fermenter. Therefore, studies on the biopolymerization of PHA are also important and and has to distinguish between extracellular and intracellular PHA depolymerizations. Intracellular depolymerization is the hydrolysis of an endogenous carbon reservoir or PHA by the accumulating bacteria themselves, while extracellular depolymerization is the utilization of PHA as an exogenous carbon source not necessarily by the accumulating microorganisms alone but also by other organisms. Extracellular depolymerization of PHA occurs after the polymer is released from the cell (e.g., after cell lysis, death or by solvent extraction), and the polymer becomes more or less crystalline. In this case, PHA is utilised for a variety of purposes, as previously stated above. Crystalline PHA can be prepared by extraction and digestion of biopolymer from bacteria cells through solvent extraction and chemical digestion. Studies about extracellular depolymerization of PHA are wider, more extensive, and very well understood compared to intracellular depolymerization of PHA. Studies on depolymerization of extracellular PHA can be divided into three viz. in the environment, in vivo, and in vitro. 9. Polyhydroxyalkanoates and Its Biodepolymerization 26 Bio-Bulletin December 2023
General biosynthesis and biodegradation process of PHA in a natural environment (Numata et al, 2009). The significance of environmental depolymerization of extracellular PHA is to evaluate the population of polymerdepolymerizing microorganisms in the environment and to prove that neat PHA can be degraded upon disposal of end usage. The in vitro depolymerization of extracellular PHA studies carried out are usually aimed to investigate the stability of the polymers in model systems that mimic in vivo conditions by varying values of several factors. Furthermore, the production of (R)-3HB is also made possible via enzymatic depolymerization of extracellular PHA. Besides, the use of PHA in in vivo applications as biodegradable material for sutures, microcapsules, bone plates, scaffolds, and gauzes require serious attention in the study of in vivo depolymerization of extracellular PHA. The unique properties of these PHA are their biodegradability and excellent biocompatibility because the rate of depolymerization of the material should equal the regenerative rate of tissue, which makes them attractive and effectively utilized as a scaffold in tissue engineering applications. Nevertheless, intracellular PHA depolymerization could occur as in vivo and in vitro processes. In vivo depolymerization of intracellular PHA occurs on the PHA granule itself, where intracellular PHA depolymerases (iPHA depolymerase) is also located, and the activity is associated with the protein complex encompassing the native PHA inclusion bodies inside the bacterial cells. While in vitro depolymerization of intracellular PHA occurs when the polymer granules are isolated from intact bacterial cells, with their protein coat intact, without losing their amorphous and elastomeric nature characteristic, and the iPHA depolymerase remains active on the isolated PHA inclusion bodies. This is also called a cell-free system. Both PHA intracellular depolymerization can be a strategic approach in the production of monomers, dimers, or oligomers as end of depolymerization products for various applications. From previous study, in vivo and in vitro depolymerizations of intracellular medium chain length PHA (mcl-PHA) could be a potential biological route for the production of various types of mcl (R)-3HAs as platform chemicals. The monomer liberation rate reflected the mol% distribution of the initial polymer subunit composition, and the resulting direct individual products of depolymerization were identical for both in vivo and in vitro processes. It points to exo-type reactions for both processes. Its primary advantage is the absence of complicated and often nonenvironmentally friendly multistep upstream processes. Dr. Siti Nor Syairah Binti Anis is a new lecturer at the School of Biological Sciences, Universiti Sains Malaysia. Her research focuses on microbial biotechnology, specifically Polyhydroxyalkanoates (PHA), a biopolymer produced from bacterial cells, which includes several fields such as biosynthesis, recovery, depolymerization and applications of the biopolymer. Bio-Bulletin December 2023 27
10. Konjac A Mediocre Plant With Great Benefits and Potential Dahlia binti Shahbuddin Erra Fazira as Captain Dolphin brand ambassador for the Konjac jelly product. As you drive along the North-South highway, you will notice a huge billboard showing a versatile Malaysian celebrity, Erra Fazira, who is promoting a food product called ‘Konjac Jeli’. This advertisement has received much attention from the public who were curious about Konjac and its properties. Konjac is popular among the Chinese, Japanese and Korean. It is derived from a well-known plant-based ingredient with high dietary fibre and comes from the same family as yam, known as Araceae. Konjac is widely consumed among the East Asian community, but it is mostly found in Southeast Asia, mainly Malaysia and Indonesia. Konjac glucomannan (KGM) is a refined powder extracted from the corm of Amorphophallus spp. It has the unique ability to hold two hundred times more water than its mass to form a gel-like substance. Those who consume it will easily feel sated, thus reducing their food intake. This property is, therefore, immensely helpful for consumers who wish to reduce weight. It can usually be found in the forms of noodles, rice, snacks, fruit jellies, and as a substitute for gelatin in cakes and thickener in soup (Figure 2). It is considered GRAS (Generally Recognized as Safe) by the USFDA (United States Food and Drug Administration) and European Standard (E-45). Konjac has low calorific value and provides greater health benefits, especially in regulating blood sugar levels among diabetic patients as it may slow down the absorption of sugar. Konjac also contains substances that are friendly to guts with micro and macroflora to aid in digestion. Low molecular weight glucomannan in konjac is a prebiotic that strengthens the immune system of those with Gerd and Crone diseases. The benefits and uses of konjac are endless, especially in biomedical devices and in chemical processes and industries. It is used as hydrogel to aid the injuries associated with burns and accidents. Its water-holding capacity helps to absorb exudates and pus from wounds and helps to accelerate healing. Konjac is also used in regenerative medicine and tissue engineering applications, especially in targeted drug delivery systems. Low molecular weight konjac is used as nanoparticles for cancer targeting and drug formulations such as Tamiflu that are used for the treatment of SARS influenza. As hydrogels, konjac is widely used in cosmetic formulations as a filler and emulsifier because of its unique physicochemical properties that can stimulate skin cells to produce metabolites and cytokines, while keeping the skin moist and protect it from harmful UV rays to give users youthful looks and feel after several applications. It is also made into facial masks that are widely sold in drug stores such as Watson and Guardian alongside other natural products made from honey, collagen, and chitosan. Konjac sponge is an eco-tool make-up remover that effectively cleans the face from traces of foundation and impurities. Regular usage of the sponge unclogs the skin pores and removes whiteheads and blackheads easily through gentle exfoliation. Unlike plastic sponge, which is non-recyclable, konjac sponge can be replaced regularly without the guilt of contaminating. In the textile manufacturing industry, the versatile and malleable konjac polymeric chain is incorporated to enhance the strength, improve ink absorption and promote smoothness. The same benefit applies in the manufacturing of papers and boxes, whereby, instead of using chemicals this green and eco-friendly method of using konjac produces material that is long-lasting and has minimal impact on the environment. 28 Bio-Bulletin December 2023
Konjac in various food products. Konjac as a potential valuable crop in Malaysia Climate change is changing the way we grow food and feed the population. As the global population is now crossing eight billion today, there is an urgent need for sustainable supplies that address food and nutrition security concerns for Malaysians. Cultivation and production of food are in line with the Sustainable Development Goals (SDGs) by the United Nations, which is an urgent call to all nations to protect the earth, end poverty and hunger and ensure livelihood in prosperity and peace by 2030. Konjac is native to Malaysia and mostly found everywhere in the country, especially in secondary forests and widely grown in palm oil and rubber plantations. By tapping into the versatility of konjac, Malaysia could very well propose a new, lucrative economy segment and market. Variations in the konjac species. From left to right, A. titanium (largest flower in the world), A. konjac, A. muellerii, A. paeoniifolius, A. prainii Amorphophallus paeoniifolius is the most common species in Malaysia. Locally known as ‘lekir’ or ‘sarek,’ people in Kelantan and Pahang have used it since long ago in their cuisines and desserts. There are about twelve species of Amorphophallus in Malaysia with differences in glucomannan content, glucose-to-mannose ratios, and average molecular weight distribution. Each species is unique in geographical sites, soil profile, and characteristics. Amorphophallus muellerii which is commonly grown in the northern Peninsular of Malaysia has the highest glucomannan content of fiftyeight percent (58%); thus, poses a high potential for commercialization and new bioeconomy in the region. Cultivation of konjac into rice could solve issues with food insecurity and health. We are currently producing only 60% of our rice supply and rely on imports for the rest. With Indonesia, India, and Thailand now restricting their rice export, there is a need for Malaysians to switch to new crop cultivation that addresses national food security and tackle health issues altogether. The integration of the corm into palm oil and rubber plantations by symbiotically providing nutrients to the soil and surrounding plants could be part of agro-forestry Bio-Bulletin December 2023 29
initiatives to tackle climate change. It absorbs carbon dioxide and provides habitats for insects and animals. Exploiting the large reservoir of minor and underutilized crop plants would provide diversity in the ecosystem as it would easily integrate as intercrop. It can grow easily under the canopy of other crops on the plantation. The plant does not require strict supervision as it is noninvasive and does not affect the yield and development of other crops, which complements the tagline of 3T: Tanam, Tinggal and Tuai (i.e., sow, leave and harvest). The konjac plant grows naturally and propagates easily on corm, seeds, and bulbil (bulb that forms at the angle between leaves and stem). The Amorphophallus plant. Dr. Dahlia Shahbuddin is a lecturer at the School of Biological Sciences, USM, Penang with expertise in Botany and Plant Physiology. 30 Bio-Bulletin December 2023
11. Geometric Morphometrics Fisheries Resources Management and Conservation: The Strong Ties Jolly Babangida Kachi and Darlina Md Naim Geometric morphometrics is a subfield of morphometrics that quantitatively analyses shape and form in biological organisms using geometric techniques to record, examine, and compare structures like bones, shells, and organs. Traditional morphometrics uses measurements and ratios of various features to assess an organism’s size and shape. These measurements may include the lengths, widths, areas, and ratios of various body parts. Although this method can offer useful information, it frequently ignores the full complexity of shape variation. However, geometric morphometrics overcomes the limitations of traditional morphometrics by representing the shape of biological structures with landmarks or points in a coordinate system. These landmarks are points determined anatomically and arranged to perfectly express the shape. Since the landmarks consider the relative positions and relationships between various features, they provide a more thorough and accurate description of shape. Geometric morphometrics aims to investigate and understand shape variation within and among groups of organisms. To investigate morphological diversity, adaptability, and evolutionary trends, geometric morphometrics has been widely utilised in fields like evolutionary biology, ecology, anthropology, palaeontology, and medical research. With geometric morphometrics’ strong mathematical and statistical foundations, researchers can conduct extensive shape studies and draw insightful conclusions from the resulting data. Generating landmarks for geometric morphometric analysis practically involves creating landmarks (points) on the organisms of interest, which are then used to measure and analyse variations in shapes using coordinates. Generating these landmarks follows a step-by-step guide that includes: a. Determining the study object or organism: The organisms or objects to be analysed are determined. They could be biological specimens (fish, scales, bones, skulls, flowers, etc.), archaeological artefacts, or any other structures with shape variations. b. Selection of landmarks: A set of landmarks accurately captures the pertinent features of the shape variation under study. Landmarks constitute anatomical points, curves, intersections, or any other clearly defined features that are congruent across all specimens. The landmarks should be easily recognisable and biologically significant. c. Standardisation: This is a crucial step that ensures similar orientation and scale for accurate comparison and analysis of specimens. d. Placement of landmarks: This is achieved using specialised software or image processing tools (e.g., tpsUtil and tpsDig2) to place the selected landmarks on each specimen. Identifying the selected anatomical features or points and noting their (x, y) coordinates are crucial in this procedure. e. Annotation of landmarks: This ensures that every landmark is accurately labelled to account for accurate identification and statistical analysis. f. Replication of landmarks: This involves replicating landmarks’ placement on different specimens multiple times, by the same and separate observers to help quantify measurement inaccuracy. g. Data Formatting: An appropriate data matrix is created using the landmark coordinates. The (x, y) coordinates of a particular landmark are represented by each column, while each row represents the sample/specimen. h. Analyses: At this stage, the landmark data are now ready for the geometric morphometric analysis. Multivariate analyses often employed are Principal component analysis (PCA), Canonical variate analysis (CVA), and Discriminant function analysis (DFA). Procrustes superimposition and shape deformation analysis are other examples of the common techniques used. i. Statistical Tests: This entails the application of proper statistical tests to investigate patterns of variation in shape, differences between groups, or correlations with other variables. The choice of the appropriate statistical test is often determined by the specific research questions and the type of data. j. Visualisation: The data is visualised using scatter plots, shape deformation grids, heatmaps, or other graphical techniques for a clear understanding and presentation. Bio-Bulletin December 2023 31
General Application of Geometric Morphometrics As an essential field within related disciplines such as biology, palaeontology, and anthropology, the biological application of geometric morphometrics stands out in the following aspects: 1. Biodiversity and Taxonomy: Taxonomy and classification require the understanding of species diversity and morphological variations. Geometric morphometrics aids in identifying distinctive traits, that lead to species delineation and identification. It contributes to biodiversity and taxonomy by; objective identification of species, discrimination of populations, delimiting species boundaries, rapid species assessment, reconstruction of fossil species, species discovery and validation, and integration with molecular data to create robust phylogenetic studies and species delimitation which ultimately provides a multidimensional approach to understanding relations among species. Combining geometric morphometric analysis with taxonomy allows researchers to gain objective, consistent, and data-driven knowledge of species diversity and evolution. This leads to better conservation plans, evolutionary understanding, and improved biodiversity management. 2. Fisheries and Wildlife Management: Geometric morphometrics can help study morphological variations among fish species or animal populations in fisheries and wildlife management, making it crucial for conservation initiatives, population control strategies, and understanding the impact of changes in natural habitats. This is achieved by: a. Species identification: This may facilitate the differentiation of closely related species that exhibit comparable outward characteristics. Accurate identification plays a crucial role in the management and conservation of endangered or vulnerable species, making it particularly significant. b. Population differentiation is the alteration of physical characteristics in distinct species’ populations, particularly in terms of form. This process provides valuable insights into how different animal groups have adapted to their habitats, aiding in understanding genetic diversity and the phenomenon of local adaptations. c. Assessing environmental changes: The evaluation of environmental changes may be conducted using geometric morphometrics, which enables the monitoring of animal populations as they respond to modifications in their habitat, climatic variations, or other environmental influences. This phenomenon has the potential to serve as an indicator of population decreases or changes in geographical dispersion. d. Conservation planning: Understanding shape differences within and across species populations can aid in developing conservation measures, such as identifying priority conservation areas, guiding captive breeding initiatives, and formulating strategies for habitat restoration, providing valuable insights for conservation efforts. e . F i s h e r i e s m a n a ge m e nt : G e o m et r i c morphometrics can be used in fisheries management to assess fish population age and overall well-being. By examining anatomical elements like fish scales and otoliths, scholars can estimate growth rates, age, and overall fish population health. This information is crucial for sustainable fisheries management practices and aids in the effective implementation of sustainable practices. f. Monitoring of invasive species: Geometric morphometrics helps detect and monitor invasive species by comparing their morphological shape to native ones, enabling timely identification and effective control, thus mitigating their potential harm to indigenous ecosystems. g. Biodiversity assessment: Geometric morphometrics can quantitatively analyse form variations among species within a specific geographical region, aiding in understanding species diversity patterns and potentially guiding conservation prioritisation efforts. 3. Conservation Biology: Conservation efforts are well aided when there is a proper understanding of the form variations in vulnerable, threatened, or endangered species. Geometric morphometrics can provide valuable data on population structure and adaptation to certain habitats which can be helpful guides for conservationists’ strategic planning. It can contribute to conservation efforts in specific ways as follows: a. Monitoring and assessment: This is where geometric morphometrics can serve as a noninvasive technique for monitoring the stability and health of populations. As environmental stresses are found to induce variations in shape changes over time, conservationists can take preventive measures before a population’s loss becomes permanent; 32 Bio-Bulletin December 2023
Jolly Babangida Kachi A Ph.D. candidate at the School of Biological Sciences (SBS), USM, whose research focuses on the geometric morphometrics and molecular characterisation of commercially important Sciaenid fishes in Malaysia and Nigeria. The sole aim is to understand their systematics, population structure to help their conservation and management. b. Conservation prioritisation: Here, it helps conservationists prioritise the populations or areas that require conservation efforts and efficient devotion of resources to facilitate the survival of vulnerable species; c. Invasive species management: This happens when geometric morphometrics assists in identifying morphological variations that give invaders competitive advantages over native species and furnishes information to prevent invasive species spread and preserve local biodiversity; d. Hybridization and introgression: It can help in the detection of hybridisation events between populations or species that are closely related to prevent the loss of distinct morphological traits or adaptations; hence, the identification of these events is essential in maintaining the integrity of separate species; e. Genetic and Morphological diversity: Populations with less genetic variety are more susceptible to illnesses and environmental changes. Geometric morphometrics provides insights into morphological variation, assisting conservationists in identifying and managing populations with increased vulnerability. This information complements genetic investigations and aids in addressing potential threats. Malaysia boasts a robust biodiversity in both marine and freshwater ecosystems. The conservation of these abundant fisheries resources has been central to the activities of various stakeholders saddled with the responsibilities of fisheries management. To corroborate the efforts of the stakeholders in achieving the 14th Sustainable Development Goal (SDG 14) of “Life Underwater”, recent studies have focused on the use of geometric morphometric techniques to study morphological variations in different categories of fish and invertebrates such as jellyfish and shrimps, to understand their classification, morphological uniqueness, and population structures for conservation purposes. Notable among fish families that have been studied within Peninsular Malaysia using geometric morphometrics are Nemipteridae, Scombridae (tuna), and Sciaenidae (croakers/drums), among others. Without a doubt, the strong ties that exist between geometric morphometrics techniques, fisheries resource management, and conservation cannot be over-emphasized. Employing the use of these veritable and proven techniques will improve comprehension of aquatic resources’ distinctiveness for better conservation management policies in Malaysia. Assoc. Prof. Dr. Darlina Binti Md Naim A senior lecturer at the School of Biological Sciences, Universiti Sains Malaysia. She is currently the Program Manager for the Animal Biology and Plant Biology program and Animal and Plant Biodiversity program. Her research interests are systematics, biodiversity, conservation, and molecular ecology of marine and coastal fishes. Bio-Bulletin December 2023 33
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12. Memorandum of Understanding (MoU) Signing Ceremony Between SBS – Seberang Perai City Council (MBSP) Farah Haizqah Meor Termizi, Siti Nasuha Hamzah and Izzat Azmeer Ahmad On 19 September 2023, the School of Biological Sciences (SBS), USM, successfully signed two Memorandums of Understanding (MoUs) with the Seberang Perai City Council (MBSP) at the Kenanga Hall of MBSP City Tower. Representatives from both organisations were present for the signing. Prof. Dato’ Dr. Amirul Al-Ashraf Abdullah, the Dean of SBS, witnessed the signing, and Prof. Dr. Azlan Amran, the Deputy Vice-Chancellor (Industry, Community Network, and Institutional Sustainability) signed on behalf of SBS. The MBSP was represented by the Mayor of Seberang Perai, YBhg. Dato’ Azhar Hj Arshad, who signed the MoUs. Tuan Hj. Baderul Amin Abdul Hamid, the City Secretary of Seberang Perai bore witness. These MoUs are focused on strengthening the strategic partnership for urban pest management, particularly in dealing with crows and rodents. The MOU signing was officiated by the the Mayor of Seberang Perai, YBhg. Dato’ Azhar Hj Arshad and Professor Dr. Azlan Amran, the Deputy Vice-Chancellor (Industry, Community Network, and Institutional Sustainability) USM. Part of project members as well as the admin representative from USM and MBSP. 1. INTEGRATED URBAN PEST BIRD MANAGEMENT AND ITS BASELINE STUDY The rapid urbanisation driven by Earth’s high human populations has a significant global impact on ecosystems. It alters the interaction between birds and urban communities. This urban growth, accompanied by increased human activities, leads to a rise in pest bird populations, worrying many local authorities, especially those with (Bandaraya) status. The Seberang Perai City Council (MBSP) is no exception and has experienced an increase in complaints and negative effects from pest birds, especially crows. These pest bird infestations worsen each year. The goal of this project is to establish an ecological baseline through the study of house crows, integrating the most effective pest bird control strategy in Seberang Perai. Additionally, this project also aims to enhance community interaction and engagement in raising awareness of their responsibility in pest bird control. Pest bird management in the urban environment is not the sole responsibility of the authorities; community cooperation is crucial for a sustainable city. The Memorandum of Understanding is important as it involves research collaboration, expertise exchange, and sharing of facilities and skills in urban pest management, particularly in controlling pest bird populations. The collaboration between USM and MBSP began in 2022, primarily through SBS and the Department of Health Services, led by Ts. Dr. Siti Nasuha Hamzah and Dr. Izzat Azmeer Ahmad. Successful activities have taken place, such as the three series of the Mega Crow Sharpshooter (CroSS) Operation organised by MBSP, to provide crow samples for bird parasite analysis. On July 11, 2023, a discussion involving researchers from USM and representatives from MBSP and Paramit Malaysia Sdn. Bhd. was conducted, focusing on Research Collaboration regarding the Growing Crow Issues in Seberang Perai. Bio-Bulletin December 2023 35
The latest draft of the action plan, titled “PELAN TINDAKAN PENCEGAHAN KAWALAN KACAU GANGGU BURUNG GAGAK” (PETEGAK), has been successfully prepared by the Department of Health Services, MBSP. The team was led by Mr. Mohd Ibrahim and Dr. Izzat Azmeer in collaboration with Ts. Dr. Siti Nasuha from SBS. This marks the first initiative of its kind in Malaysia for crow control. The plan was officially launched on September 19, 2023, by the Mayor of Seberang Perai, YBhg. Dato’ Azhar Hj Arshad, witnessed by Professor Dr. Azlan Amran, the Deputy Vice-Chancellor of USM, along with members of the Seberang Perai Municipal Council and the Dean of the School of Biological Sciences, USM. The 2023-2030 action plan focuses on a databasedriven intervention strategy and will require collaborative research efforts and intervention management support from both USM and MBSP. It constitutes one of the key components of this Memorandum of Understanding (MOU). The action plan PETEGAK launch by the Mayor of Seberang Perai, YBhg. Dato’ Azhar Hj Arshad, witnessed by Professor Dr. Azlan Amran, the Deputy Vice-Chancellor of USM, along with members of the Seberang Perai Municipal Council, the Dean of the School of Biological Sciences, USM and the project members. 2. STRATEGIC PARTNERSHIP IN ZERO RODENT PROJECT (Project ZoRo MBSPxUSM) For centuries, rodents have been a threat to public health. This project aims to promote, develop, and The representative from USM, MBSP and Paramit Malaysia Sdn. Bhd. for the University-Local AuthoritiesIndustry discussion on Research Collaboration on Growing Crow Issues in Seberang Perai. The shooters before flag-off session of the MBSP, CroSS Event. This event provides crow samples for the parasite analysis activity. The parasite sampling performed by students and researchers from School of Biological Sciences during the CroSS Events. 36 Bio-Bulletin December 2023
establish research, education, and training programs in cooperation with community campaigns, focusing on wild rat awareness programs in selected areas and premises in Seberang Perai. These campaigns emphasise community interaction and engagement, specifically creating awareness of potential zoonotic diseases related to rodents, such as rat bite fever, plague, hantavirus, leptospirosis, salmonellosis, yersiniosis, pathogenic E. coli infections, giardiasis, and Lyme disease. Encouraging public participation in such projects or awareness campaigns will significantly impact society’s understanding of rodent control. Part of the Zero Rodent Project team members. Our first rodent awareness campaign was conducted at Kompleks Penjaja Mak Mandin, Butterworth, and Taman Haji Mohd Amin, Permatang Pauh. To examine the feasibility of the project and implement the collaborations between USM and MBSP, the Zero Rodent Project will be led by Dr. Farah Haziqah Meor Termizi (SBS) and Dr. Izzat Azmeer Ahmad (MBSP). The latest community project, “Kempen Basmi Tikus Bersama Komuniti,” was conducted in early October 2023 at a wet market in Butterworth and a residential area in Permatang Pauh. The main objective of this project is to share knowledge with the public about zoonotic diseases carried by wild rats. Additionally, a program called “Rat to Cash” was introduced, offering money in exchange for live rodents. Given that a female rat can potentially produce three to six litters of six to ten offspring per year, this program aims to reduce rodent populations in rural settings with the participation of the public and the city council. MBSP provides rat traps to the community to encourage them to control the rodent population in the area. Through this Memorandum of Understanding, USM, represented by the School of Biological Sciences (SBS), will assist MBSP in enhancing the outcomes of crow and rodent intervention activities through highquality scientific research. This collaboration ensures more sustainable urban pest management in the future. Comprehensive scientific research will undoubtedly add value to existing intervention efforts, and collaborative activities with the community and industry raise awareness about collective involvement that leads to more efficient and successful problem management. These efforts pave the way for environmental sustainability and global well-being, which is one of the core tenets of USM’s APEX agenda. Ts. Dr. Siti Nasuha Hamzah is a Senior Lecturer at the School of Biological Sciences, USM. Her expertise is in Proteomic, Toxicology and Pest Management Studies. Dr. Izzat Azmeer Ahmad is a Deputy Director, at the Department of Health Services, Seberang Perai City Council, MBSP and is an expert in Public Health. Dr. Farah Haziqah Meor Termizi is a Senior Lecturer at the School of Biological Sciences, USM, with expertise in zoonotic parasitology in animals. Bio-Bulletin December 2023 37
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13. Research Collaboration Tropical Rainforest Conservation Research Centre (TRCRC) and School of Biological Sciences (SBS) Asyraf Mansor The restoration effort of degraded forests in Malaysia is a critical initiative aimed at addressing not only various environmental and ecological impacts but also the socioeconomic challenges of the community affected by the loss of a functioning forest ecosystem. Malaysia, known for its rich biodiversity and lush rainforests, has been grappling with deforestation, illegal logging, and habitat degradation, which have led to adverse impacts on wildlife, climate change, and local communities. Malaysia has a history of rapid deforestation, primarily driven by agricultural expansion, palm oil plantations, and timber extraction. This deforestation has resulted in habitat loss for many endangered species, such as orangutans and tigers. Thus, the Malaysian government recognizes the need for forest restoration and introduces various policies and programs to address deforestation. These include the National Forestry Policy, the Heart of Borneo initiative, the Malaysian Timber Certification Scheme and other key strategies that focus on reforestation and afforestation. The strategy involves planting native tree species in degraded areas to restore ecosystems and increase forest cover. The government and NGOs have launched numerous tree-planting campaigns to achieve these goals. This is where the TROPICAL RAINFOREST CONSERVATION RESEARCH CENTRE (TRCRC) plays its role in restoring tropical rainforests and addressing the crucial aspect of biodiversity loss in Malaysia. By establishing a protected zone within a logged-over forest in Perak, TRCRC manages this area by establishing a living seed-seedlings collection in its Tropical Rainforest Living Collection (TLRC), Banun, Perak. An example of living plant collections in TLRC. An example of living plant collections in TLRC. Tapping into academic expertise, TRCRC in collaboration with the School of Biological Sciences (SBS) to enhance its restoration effort through research and technology (Figure 2). This includes the use of satellite imagery, GIS, and remote sensing to monitor deforestation and plan restoration projects effectively. Apart from focusing on the restoration activities, both SBS and TRCRC are in strong agreement that the involvement of local communities in forest restoration projects is essential for its lifelong success. These initiatives provide employment opportunities and promote the conservation of natural resources for the benefit of local communities. Dr Zarul Hazrin visiting the TLRC Banun as a representative from the SBS research group. Bio-Bulletin December 2023 39
Despite making satisfactory progress, Malaysia faces challenges in achieving comprehensive forest restoration. These challenges include illegal logging, encroachment on protected areas, and the need for financial resources to sustain restoration efforts. Therefore, SBS and TRCRC actively and continuously search for collaboration opportunities with international organizations, such as the United Nations Development Programme (UNDP) and the World Wide Fund for Nature (WWF), to access expertise and funding for forest restoration projects. Other than that, the researchers also apply for research grants like the Fundamental Research Grants (FRGS), Research University grants (RU), as well as other potential sources of funding to sustain the projects. Forest restoration in Malaysia plays a crucial role in mitigating climate change by sequestering carbon dioxide and maintaining ecological balance. Forest restoration efforts are vital for conserving its rich biodiversity, mitigating climate change, and promoting sustainable development. While progress has been made, ongoing commitment, funding, and effective enforcement of conservation policies are necessary to ensure the longterm success of these initiatives. Assoc. Prof. Dr. Asyraf Mansor is a botanist interested in the study of plants in Malaysia. His research focuses on the biodiversity of rattan and plants in tropical forests. 40 Bio-Bulletin December 2023
14. VCRU Soaring to Greater Height in 2023 Zary Shariman Yahaya Introduction Established in 1991, VCRU was founded with the mission of consolidating and enhancing research capabilities in vector control. The unit boasts a wide array of research facilities, including those dedicated to insecticide resistance, toxicology and analysis, space spray applications, and studies related to insecticide formulations for household and public health. VCRU has earned recognition as a leading research facility in the Asia-Pacific region for studies on vector and urban pest control. In addition to its research endeavours, VCRU is known for manufacturing insecticide resistance monitoring test kits and insecticide-impregnated papers that adhere to the technical specifications and guidance of the World Health Organization (WHO) in Geneva. Furthermore, VCRU serves as a top-notch rearing facility for various species and strains of vector mosquitoes, cockroaches, and flies. VCRU takes pride in its accreditation for OECD Good Laboratory Practice (GLP) and ISO17025:2017 certification, affirming its status as a bio-efficacy testing facility and field research expert. Notably, VCRU actively publishes scientific articles and is a preferred choice for postgraduate students conducting research in vector and urban control studies. VCRU Named as the Recipient of Hadiah Sanjungan Kualiti Award 2020 In 2023, VCRU achieved a significant milestone when it was awarded the prestigious Hadiah Sanjungan Kualiti Award for the year 2020. This award indicates USM’s recognition of VCRU’s exceptional dedication and commitment, transforming it into one of the institution’s primary service centres. VCRU extends heartfelt congratulations to its communities who played pivotal roles in realising this remarkable accolade. VCRU Consultation Service with ECO World Developer Batu Kawan The VCRU team was privileged to be invited by ECO World Developer Batu Kawan’s CEO, Dato’ Chan, to visit their brand-new ECO World Club House in Batu Kawan on September 7, 2023. The purpose of the visit was to engage in fruitful discussions regarding effective control methods of large mosquito and biting midge populations in the surrounding area. The VCRU team provided valuable suggestions, and Dato’ Chan enthusiastically embraced these recommendations, by swiftly acting on them. Furthermore, he generously extended his development areas in Batu Kawan, Penang for the VCRU team to utilize as future research sites. Bio-Bulletin December 2023 41
C o m m u n i t y E n g a g e m e n t Work with Sekolah Menengah Kebangsaan Agama Al-Irshad, Penang In a recent school project conducted at SMK(A) Al-Irshad, six secondary students, accompanied by their teacher, embarked on a research endeavour to explore the potential of mugwort plant extract as a mosquito repellent. Mugwort, historically valued in traditional medicine across the globe, emerged as a noteworthy candidate for mosquito control. Under the supervision of Dr. Manorenjitha, the team utilized the facilities at the VCRU lab, adhering to the Malaysia Standard (MS 1497:2007) procedure for bio efficacy testing, potentially paving the way for an innovative mosquito control method. Working Visit from Syngenta, Malaysia to VCRU, SBS, USM VCRU received an official visit from Syngenta, Malaysia, represented by Dr. Hui Sang, a USM and School of Biological Sciences (SBS) alumnus, on July 5, 2023, to discuss the company’s latest projects in collaboration with VCRU. Several new bio efficacy testing projects were discussed and are scheduled to commence in 2023. Visitors from Jabatan Kesihatan Negeri (JKN) (Unit Kawalan Penyakit Bawaan Vektor), N. Sembilan A group of 10 visitors (6 students & 4 IMR staff) from the Diploma of Applied Parasitology and Entomology sponsored by SEAMEO-TROPMED, IMR had a study tour to VCRU, SBS, USM on 10 August 2023. The half-day visit was aimed at allowing the DAP&E 2023 IMR students to delve deeper into the practices of pesticide testing in the laboratory and insectarium at VCRU, USM Penang. 42 Bio-Bulletin December 2023