Shahir Shamsir

• Phd in Biological Sciences
• Professor at University of Technology Malaysia

DNA polymerase β, a member of the X-family of DNA polymerases, undergoes complex regulations both in vitro and in vivo through various posttranslational modifications, including phosphorylation and methylation. The impact of these modifications varies depending on the specific amino acid undergoing alterations. In vitro, methylation of DNA polymera...

Background The discovery of hepcidin, a peptide hormone primarily known for iron homeostasis regulation, has revealed promising anticancer properties. While extensively studied in mammals, fish-derived hepcidins represent an unexplored area in cancer therapeutics, offering unique structural and functional characteristics that may prove valuable in...

Historically, the trend in academia towards measurable measures has marginalised non-STEM, arts, and humanities subjects, often at the price of their inherent academic principles and capabilities. This review of the literature explores the shift in university policies and practises, emphasising the need for a more compassionate and inclusive approa...

Glucose-6-phosphate dehydrogenase deficiency (G6PDD) is a major enzymatic disease affecting human red blood cells (RBCs), causing hemolytic anemia due to the diminish of the nicotinamide adenine dinucleotide phosphate hydrogen (NADPH) synthesis and altered redox balance within erythrocytes. This study sought to correct the defect in G6PD Chatham (A...

Despite the average of 500 million tweets per day, little research has been conducted to categorize tweets and sentiment polarity so that tweets can be analysed based on user preferences. The objective of this paper is two-fold. The first is to perform comparative experiments for Tweet topic classification using six machine algorithms: Random Fores...

Despite the average of 500 million tweets per day, little research has been conducted to categorize tweets and sentiment polarity so that tweets can be analysed based on user preferences. The objective of this paper is two-fold. The first is to perform comparative experiments for Tweet topic classification using six machine algorithms: Random Fores...

This study addresses the underutilization of crowdsourcing, particularly involving citizen scientists, for biodiversity data collection in Malaysia. While high-income countries have embraced crowdsourcing to enhance scientific knowledge and inform conservation efforts, Malaysia lags behind due to the absence of a regulatory framework guiding govern...

Effective technology commercialization is critical for successful product delivery in the current environment of intense innovation competition. Although market acceptance is a crucial factor in the commercialization process, it is equally imperative to attain the suitable Technology Readiness Level (TRL). Given a lack of research on TRL of locally...

Grouper Iridovirus (GIV) infection induced cell death in grouper spleen cells and caused serious systemic diseases with more than 90% mortality. Therefore, effective strategies are critically needed to prevent economic losses and maintain the sustainability of grouper aquaculture. Using immuno-bioinformatics, this study aimed to create a multi-epit...

Background Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58–74 °...

Cancer is one of the leading causes of death worldwide and one of the greatest challenges in extending life expectancy. The paradigm of one-size-fits-all medicine has already given way to the stratification of patients by disease subtypes, clinical characteristics, and biomarkers (stratified medicine). The introduction of next-generation sequencing...

The spread of infectious illnesses has been a significant factor restricting aquaculture production. To maximise aquatic animal health, vaccination tactics are very successful and cost-efficient for protecting fish and aquaculture animals against many disease pathogens. However, due to the increasing number of immunological cases and their complexi...

The structural comparative analysis of β-Galactosidase in Sulfolobus acidocaldarius and Escherichia coli highlights its thermostable nature and potential industrial applications under extreme conditions. This study investigates the 3D structure of β-Galactosidase in the thermophilic archaeon Sulfolobus acidocaldarius and compares it with the mesoph...

G6PD deficiency (G6PDD) is associated with oxidative stress resulting from an imbalance between reactive oxygen species (ROS) production and the body's ability to counteract. In this review, we explore the adverse effects of G6PDD on diverse physiological processes and disease outcomes. Past studies have demonstrated the association between G6PDD a...

Drug repurposing is a methodology of identifying new therapeutic use for existing drugs. It is a highly efficient, time and cost-saving strategy that offers an alternative approach to the traditional drug discovery process. Past in-silico studies involving molecular docking have been successful in identifying potential repurposed drugs for the vari...

HIGHLIGHTS  Structural characterization of luciferase-like monooxygenase in P. meliae.  Bioluminescence can be used to evaluate antimicrobial efficacy by releasing light emissions.  Luciferase-like monooxygenase: a potential therapeutic candidate for clinical applications. ABSTRACT Keywords: Bioluminescence Luciferase Luciferase-like monooxygena...

Ischyja marapok is a moth species from the genus Ischyja, a member of the Lepidoptera family, Erebidae. Due to their wide variation, this family constitutes the largest described species, however, the mitogenome dataset on the genus Ischyja is scarce. Hence, the mitochondrial genome dataset of Ischyja marapok from Malaysia was completely sequenced...

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect that affects more than 500 million people worldwide. Individuals affected with G6PD deficiency may occasionally suffer mild-to-severe chronic hemolytic anemia. Chronic non-spherocytic hemolytic anemia (CNSHA) is a potential result of the Class I G6PD variants...

Background Luciferase is a well-known oxidative enzyme that produces bioluminescence. The Pseudomonas meliae is a plant pathogen that causes wood rot on nectarine and peach and possesses a luciferase-like monooxygenase. After activation, it produces bioluminescence, and the pathogen’s bioluminescence is a visual indicator of diseased plants. Metho...

In the present study, the nearly complete mitochondrial genome of Euphaea ochracea was described and its phylogenetic position in the family Euphaeidae was analyzed. Here, we recovered 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and a partial control region, resulting in a mitogenome length of 15,545bp. All protein-coding genes were...

The Great Marquis or Bassarona dunya is a butterfly species commonly found in the tropical regions of Asia, America, and Africa. This butterfly is a member of the subfamily Limenitidinae and the classification within this subfamily has been unstable. Here, we report the first complete mitochondrial genome (mitogenome) of B. dunya sampled from Malay...

Worldwide, breast cancer is the leading type of cancer among women. Overexpression of various prognostic indicators, including nuclear receptors, is linked to breast cancer features. To date, no effective drug has been discovered to block the proliferation of breast cancer cells. This study has been designed to discover target-based small molecular...

Glucose-6-phosphate dehydrogenase (G6PD) is a housekeeping enzyme expressed in all cells of the body, where it catalyzes the first step of the pentose phosphate pathway (PPP) in the red blood cells. Deficiency of this enzyme causes hemolytic attacks as well as anemia that can be, fatal in certain cases. G6PD enzyme occurs in an active form in the c...

The existing Malaysian ethnobotanical database is not sufficiently comprehensive and may hinder sharing of ethnobotanical knowledge. The lack of interest and documentation especially in digitalizing prior knowledge is a worrying trend since Malaysia possess high ethnicity and abundance of biodiversity. It is crucial to preserve and digitalize the c...

Malaysia is one of 17 mega diverse countries in the world. Despite this fact, there is still no online standalone database that focuses on Malaysian mammals. Creation of a mammalian database would allow researchers and conservationists to utilize the database for research, policy making and to answer broad scale of biodiversity questions. Human dev...

Glucose-6-phosphate dehydrogenase deficiency is by far the most prevalent human enzymopathy and is generated by a series of point mutations in the X-linked gene encoding G6PD. The severity of the deficiency relies on the various mutational sites in the gene, affecting the protein structure and function in at least two ways: by disrupting the entire...

Fluorescent protein has been applied in various diagnostic and biotechnology application. However, in these applications, the temperature conditions are simulated at higher temperatures of 289K and 300K compared to natural sea anemone Cribrinopsis japonica fluorescent protein. This study evaluates the predictive structure and the molecular dynamic...

The SKY hot spring is a unique site filled with a thick layer of plant litter. With the advancement of next-generation sequencing, it is now possible to mine many new biocatalyst sequences. In this study, we aimed to (i) identify the metataxonomic of prokaryotes and eukaryotes in microbial mats using 16S and 18S rRNA markers, (ii) and explore carbo...

Many studies reported that the activation of tumour suppressor protein, p53 induced the human hepcidin expression. However, its expression decreased when p53 was silenced in human hepatoma cells. Contrary to Tilapia hepcidin TH1-5, HepTH1-5 was previously reported to trigger the p53 activation through the molecular docking approach. The INhibitor o...

Hepcidin is a principal regulator of iron homeostasis and its dysregulation has been recognised as a causative factor in cancers and iron disorders. The strategy of manipulating the presence of hepcidin peptide has been used for cancer treatment. However, this has demonstrated poor efficiency and has been short-lived in patients. Many studies repor...

Here, we present the complete mitochondrial genome of Pachliopta aristolochiae, a Common Rose butterfly from Malaysia. The sequence was generated using Illumina NovaSeq 6000 sequencing platform. The mitogenome is 15,235bp long, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two D-loop regions. The total base compos...

β-amylase is a hydrolytic enzyme that is involved in breaking down starch and producing energy. Since the discovery of β-amylase, it has been applied in various applications especially in the food industry. In this study, a novel β-amylase from Clostridium thermosuluregen, a thermophilic anaerobic bacterium that ferments its extracellular emulsion...

Batu Caves is an isolated limestone massif surrounded by urban areas located 11km north of Kuala Lumpur and making it a “habitat island” and sanctuary for wildlife. Urban habitat islands are known as biodiversity hotspots and assist conservation in fragmented city landscapes for animals. The Batu Caves complex offer a unique condition as it houses...

The wide use of whole-genome sequencing approach in the modern genomic era has opened a great opportunity to reveal the prospective applications of halophilic bacteria. Robertkochia marina CC-AMO-30DT is one of the halophilic bacteria that was previously taxonomically identified without any inspection on its biotechnological potential from a genomi...

The point mutations in the gene coding of prion protein (PrP) originate human familial prion protein (HuPrP) diseases. Such diseases are caused by several amino acid mutations of HuPrP including V176G, I215V, and E196A located at the second, third native helix and in their loop, respectively. Determining the transition from cellular prion protein (...

Psychrophiles are cold-living microorganisms synthesizing enzymes that are permanently active at almost near-zero temperatures. Psychrozymes are supposed to be structurally more flexible than their homologous proteins. This structural flexibility enables these proteins to undergo conformational changes during catalysis and improve catalytic efficie...

Two mitogenomes of long-tailed giant rat, Leopoldamys sabanus (Thomas, 1887), which belongs to the family Muridae were sequenced and assembled in this study. Both mitogenomes have a length of 15,973 bp and encode 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and one control region. The circular molecule of L. sabanu...

Managing education and research during pandemics has increased in importance since the onset of epidemics such as avian flu, SARS and now CoViD-19. Successful management in times of crisis ensures business continuity and institutional survival, making preparedness preceding an impending pandemic essential. Institutions of higher education (IHEs) mu...

We assembled the complete mitogenome of Cynopterus sphinx (Vahl, 1797) of the family Pteropodidae originating from Malaysia. The total mitogenome size was 16,710bp which consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region). A phylogenetic and BLASTn result showed the mitogenome sequen...

The speed at which COVID-19 has altered global education systems is unprecedented. In an effort to enhance support systems during the prolonged crisis period, and to better prepare Higher Learning Institutions (HLIs) for similar future events, this survey was conducted to capture the state of Universiti Tun Hussein Onn Malaysia (UTHM) students' wel...

The purpose of this paper is to highlight the potential impact of the outbreak on students learning in one of the public universities in Malaysia, providing greater clarity on what kinds of technological and psychosocial support are needed to address their students' needs. A set of online questionnaires was distributed to students through social me...

The main objectives of this paper were to identify the perceived severity of COVID-19 on students' well-being and learning readiness, and to better understand how students are coping with the present crisis, both in general and in regard to their daily learning activities. Despite the difficulties experienced, the students were optimistic about the...

Structural conformation of XPDH enzymes in the substrate binding pocket. The structural comparison and MD simulations displayed a significant difference in the conformational dynamics of the catalytic and coenzyme loops between Apo and XPDH-complexes and highlight the contribution of newly found triad residues.

The mitogenome of a plantain squirrel, Callosciurus notatus, collected from Bukit Tarek Forest Reserve (Extension), Selangor, Malaysia was sequenced using BGISEQ-500RS technology. The 16,582 bp mitogenome consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. A phylogenetic and BLASTn analysis again...

The increasing interest in understanding the evolutionary relationship between members of the Pteropodidae family has been greatly aided by genomic data from the Old World fruit bats. Here we present the complete mitogenome of Geoffroy’s rousette, Rousettus amplexicaudatus found in Peninsular Malaysia . The mitogenome constructed is 16,511bp in len...

To date, the genus Parvularcula consists of 6 species and no potential application of this genus was reported. Current study presents the genome sequence of Parvularcula flava strain NH6-79 T and its cellulolytic enzyme analysis. The assembled draft genome of strain NH6-79 T consists of 9 contigs and 7 scaffolds with 3.68 Mbp in size and GC content...

The majority of the members in order Rhodothermales are underexplored prokaryotic extremophiles. Roseithermus, a new genus within Rhodothermales, was first described in 2019. Roseithermus sacchariphilus is the only species in this genus. The current report aims to evaluate the transcriptomic responses of R. sacchariphilus strain RA when cultivated...

Mangrovimonas sp. strain CR14 is a halophilic bacterium affiliated with family Flavobacteriaceae which was successfully isolated from mangrove soil samples obtained from Tanjung Piai National Park, Johor. The whole genome of strain CR14 was sequenced on an Illumina HiSeq 2500 platform (2 × 150 bp paired end). Herein, we report the genome sequence o...

The spotted seahorse, Hippocampus kuda population is exponentially decreasing globally due to habitat loss contributed by massive coastal urbanization as well as its large exploitation for Chinese herbal medicine. Genomic data would be highly useful to improve biomonitoring of seahorse populations in Malaysia via the usage of non-invasive approache...

The concept of the "middle innovation trap" has been proposed as a phenomenon of a "failed transformation from implementation based to concept design based capability" (Lee et al., 2019). It has trapped nations from evolving from middle income to high-income status. Over the past two decades, many countries have been caught in the middle-income tra...

Xylitol is a high-value low-calorie sweetener used as sugar substitute in food and pharmaceutical industry. Xylitol phosphate dehydrogenase (XPDH) catalyses the conversion of d-xylulose 5-phosphate (XU5P) and d-ribulose 5-phosphate (RU5P) to xylitol and ribitol respectively in the presence of nicotinamide adenine dinucleotide hydride (NADH). Althou...

Longimonas halophila and Longibacter salinarum are type strains of underexplored genera affiliated with Salisaetaceae . Herein, we report the draft genome sequences of two strains of these bacteria, L. halophila KCTC 42399 and L. salinarum KCTC 52045, with the intent of broadening knowledge of this family. Genome annotation and gene mining revealed...

This paper presents the on-going work of MyDNAmark crowdsourcing biodiversity mobile application which enable the researchers and public alike to collaboratively record the species information and observation. The MyDNAmark application utilizes the Cordova API and various other APIs such as RESTful and Google Map to provide a means to display the c...

Xylanases (EC 3.2.1.8) are essential enzymes due to their applications in various industries such as textile, animal feed, paper and pulp, and biofuel industries. Halo-thermophilic Rhodothermaceae bacterium RA was previously isolated from a hot spring in Malaysia. Genomic analysis revealed that this bacterium is likely to be a new genus of the fami...

Proteins can interact in various ways, ranging from direct physical relationships to indirect interactions in a formation of protein-protein interaction network. Diagnosis of the protein connections is critical to identify various cellular pathways. Today constructing and analyzing the protein interaction network is being developed as a powerful ap...

Dehalogenases continue to garner interest of the scientific community due to their potential applications in bioremediation of halogen-contaminated environment and in synthesis of various industrially relevant products. Example of such enzymes is DehL, an L-2-haloacid dehalogenase (EC 3.8.1.2) from Rhizobium sp. RC1 that catalyses the specific clea...

A halo-thermophilic bacterium, Roseithermus sacchariphilus strain RA (previously known as Rhodothermaceae bacterium RA), was isolated from a hot spring in Langkawi, Malaysia. A complete genome analysis showed that the bacterium harbors 57 glycoside hydrolases (GHs), including a multi-domain xylanase (XynRA2). The full-length XynRA2 of 813 amino aci...

Pathologically relevant behaviors of Vibrio, such as the expression of virulence factors, biofilm production, and swarming motility, have been shown to be controlled by quorum sensing. The autoinducer-2 quorum sensing receptor protein LuxP is one of the target proteins for drug development to suppress the virulence of Vibrio. Here, we reported the...

The research in water cycle management is an important endeavour in any nation’s environmental management practices. Bibliometric examination the breadth and scope of research is one way to study past research focus. This will allow establishment of prior research trends, output and performance in order to reorient future resources, improve researc...

Background: Orthosiphon stamineus is a traditional medicinal plant in Southeast Asia countries with various well-known pharmacological activities such as antidiabetic, diuretics and antitumor activities. Transketolase is one of the proteins identified in the leaves of the plant and transketolase is believed able to lower blood sugar level in human...

Rhodothermaceae bacterium RA is a halo-thermophile isolated from a saline hot spring. Previously, the genome of this bacterium was sequenced using a HiSeq 2500 platform culminating in 91 contigs. In this report, we report on the resequencing of its complete genome using a PacBio RSII platform. The genome has a GC content of 68.3%, is 4,653,222 bp i...

Context: Eurycoma longifolia Jack (Simaroubaceae) commonly known as Tongkat Ali is one of the most important plants in Malaysia. The plant extracts (particularly roots) are widely used for the treatment of cough and fever besides having antimalarial, antidiabetic, anticancer and aphrodisiac activities. Objectives: This study assesses the extent of...

The present paper reports structure prediction and analysis of a psychrophilic β-mannanase from Glaciozyma antarctica PI12 yeast. A threading method was used for 3D structure prediction of the enzyme using the MODELLER 9v12 program regarding its low sequence identity (<30%). The constructed model has been used in a comparative study to analyse its...

Beta-glucosidase (BGL) is an important industrial enzyme for food, waste and biofuel processing. Jeotgalibacillus is an understudied halophilic genus, and no beta-glucosidase from this genus has been reported. A novel beta-glucosidase gene (1344 bp) from J. malaysiensis DSM 28777T was cloned and expressed in E. coli. The recombinant protein, referr...

Congenital myopathy is a broad category of muscular diseases with symptoms appearing at the time of birth. One type of congenital myopathy is Congenital Fiber Type Disproportion (CFTD), a severely debilitating disease. The G48D and G48C mutations in the D-loop and the actin-myosin interface are the two causes of CFTD. These mutations have been show...

Mathematical modelling is fundamental to understand the dynamic behavior and regulation of the biochemical metabolisms and pathways that are found in biological systems. Pathways are used to describe complex processes that involve many parameters. It is important to have an accurate and complete set of parameters that describe the characteristics o...

Background: Southeast (SE) Asia is one of the most biodiverse regions in the world and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic diversity is still poorly characterised. The growing interest in using environmental DNA (eDNA) to assess and monitor SE Asian species, in particular threatened mamm...

Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six...

Library building protocol for archival samples with single 8-nt adapters for Illumina platforms.

This protocol allows for adequate DNA extraction from archival samples.

This protocol allows for adequate DNA extraction from fresh blood samples.

Gen-IALFirst All-tissue DNA extraction kit -This protocol provides an efficient DNA extraction and purification of historic sample (tissue material)

This protocol allows for adequate DNA extraction from fresh tissue samples.

Southeast (SE) Asia is one of the most biodiverse regions in the world and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia’s genetic diversity is still poorly characterized. The growing interest in using environmental DNA (eDNA) to assess and monitor SE Asian species, in particular, threatened mammals - has c...

This protocol provides an efficient DNA extraction and purification of historical museum hides, which potentially have been chemically tanned.

Gen-IALFirst All-tissue DNA extraction kit -This protocol provides an efficient DNA extraction and purification of fresh sample (tissue material)

Conventionally, bat roost counts and roost size estimation are potentially a disruptive, repetitive method and are time consuming. Introduction of the Light Detection and Ranging (LiDAR) scanning system, an optical remote sensing technology, for scientific purposes have open many research possibilities especially on cave wildlife surveys. Scanned i...