Volume 31(1); 2023
| Molecular characterization and phylogenetic analysis of kaurene synthase protein in Stevia rebaudiana MS007 |
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| Nur Fathiah Rosilan, Muhammad Amirul Husni Samsulrizal, Nor Adilah A. Rani, Nurul Hidayah Samsulrizal, Zarina Zainuddin, Tamil Chelvan Meenakshi Sundram |
| APJMBB 31(1): 1-13 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.1.01 |
| Click here to download [PDF] |
| Stevia rebaudiana is a plant under the Asteraceae family and has been reported as a healthier alternative to sugar. Steviol glycosides (SGs) is the group of secondary metabolites responsible for the sweet taste. Among nine SGs synthesised by S. rebaudiana, stevioside and rebaudioside A are the sweetest. The biosynthetic pathway of SGs partly involves conversion of geranylgeranyl diphosphate (GGDP) into steviol, catalysed by ent- kaurene synthase (KS), ent-copalyl diphosphate synthase (CPPS), and kaurene oxidase (KO). This study focuses on in silico molecular characterization and phylogenetic analysis of KS from Malaysia’s S. rebaudiana MS007 variety (Stevia MS007). The transcriptomic dataset of S. rebaudiana accession MS007 was used in initial experiment toward analysing the KS. Through the blastx homology search using transcriptomic dataset query Cluster-31069.42907, the Stevia rebaudiana kaurene synthase (SrKS) sequence was identified with the highest similarity percentage identity (99.62%). The protein domain prediction using InterPro yields IPR005630 (terpene synthase metal-binding domain) at positions 490 to 755 and IPR001906 (terpene synthase-N-terminal-domain) at positions 258 to 477. Multiple sequence alignment was conducted using MUSCLE and MEGA-X as phylogenetic tree analysis tool for constructing the phylogenetic analysis tree. Based on the bootstrap value from the phylogenetic analysis, Cluster-31069.42907 represents relationships between the ancestors. Since both Helianthus annuusand S. rebaudiana are Asteraceae species, the bootstrap value for both species was 100%. In conclusion, this research contributes to a better understanding of Stevia MS007 KS via in silico analysis. |
| Production and functional characteristics of exopolysaccharide by Lactobacillus plantarum co-cultivation with Saccharomyces cerevisiae |
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| ‘Aina Nabilah Faizah Ahmad Bustamam, Nur Sazwani Daud, Zaheda Mohamad Azam, Mohamad Azzuan Rosli, Solleh Ramli, Noorazwani Zainol, Muhammad Helmi Nadri, Hong Yeng Leong, Nor Zalina Othman |
| APJMBB 31(1): 14-25 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.1.02 |
| Click here to download [PDF] |
| Exopolysaccharides (EPS) are well-known biopolymers secreted by several lactic acid bacteria with combination of various strains. The aim of this study is to increase EPS production by co-culturing Lactobacillus plantarum ATCC 8014 with Saccharomyces cerevisiae ICA-Y01 and study the changes in the functional characteristics of the EPS from both cultivations. In this study, the production and functional characteristics of EPS from co-cultivation culture of L. plantarumATCC 8014 with S. cerevisiae ICA-Y01 were evaluated. The co-cultivation of L. plantarum ATCC 8014 with S. cerevisiae ICA-Y01was markedly increased EPS production up to 55.84% with 6.8 g/l yield after 20 hours cultivation. The pH of the co-cultivation culture was remained constantly at 5.2 until the end of cultivation. Furthermore, co-cultivation under pH 6 in the 16L bioreactor showed a higher growth rate of 0.214 h-1 and EPS production increased up to 104.44% when compared with single cultivation of L. plantarum ATCC 8014. This result clearly indicates the importance of growing the cells in the controlled pH condition when cultivated with S. cerevisiae ICA-Y01 to enhance EPS production. The functional characteristics of EPS secreted from both cultivation strategies were also evaluated. FT-IR spectroscopy confirmed EPS presence from both cultivations, indicating functional group of the polysaccharide with D-glucose units bound by α-(1→6). The EPS production from single cultivation showed a higher DPPH radical scavenging activity (88.21%) and IC50 (19.57%) as compared to EPS produced from co-cultivation with DPPH scavenging exhibited 32.45% with no IC50 value detected. Furthermore, solubility and water uptake of EPS from single cultivation are higher in comparison to co-cultivation. In conclusion, higher efficiency in the bioactivity of EPS from the single cultivation of L. plantarum ATCC 8014 was confirmed even though the EPS yield is low as compared to EPS synthesis through inter-kingdom cultivation. |
| Characterisation of capsid polypeptide P1 and capsid protein VP1 of the Malaysia foot and mouth disease virus (FMDV) serotype O and A isolates |
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| Farah Najwa Abd-Halin, Zunita Zakaria, Saila Ismail, Sarah Othman |
| APJMBB 31(1): 26-38 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.1.03 |
| Click here to download [PDF] |
| Foot and mouth disease virus (FMDV) is the cause of foot and mouth disease (FMD) outbreaks in livestock worldwide, which affects domestic and international trade, resulting in significant economic losses and social consequences. For efficient monitoring and prevention of FMD outbreaks, the need for improved strategies to control FMDV and achieve FMD-free status with various control measures including vaccination can be established. In vaccinology, major advances and discoveries in vaccination variations including DNA and protein subunit vaccines proved to be more economical andsustainable. To develop a safe vaccine for animals, possible antigenic genes or antigens need to be identified andcharacterised. The FMDV is a single-stranded RNA virus consisting of a capsid precursor polypeptide, P1, which encodes for four structural proteins (VP4-1), leading to antigenic variation and VP1 potentially carrying the key epitope for vaccinedevelopment. This study aims to identify and characterise the capsid polypeptide, P1 and capsid protein, VP1 of theMalaysian FMDV serotype O and serotype A isolates. The nucleotide and protein sequences were identified based on the FMD outbreaks in Malaysia and the antigenicity of the P1 and VP1 was predicted by Kolaskar and Tongaonkar's semi-empirical method. Subsequently, the P1 and VP1 genes were inserted into pET-28a, respectively, and used for proteinexpression analysis. The P1 and VP1 were predicted to be antigenic via in silico analysis and successfully expressed and characterised through in vitro analysis. Hence, this study can be exploited as a tool to design a new novel vaccine for vaccine development against FMD in bovines. |
| Primer characterization of in-house real time PCR (RT-PCR) for BCL2 gene using saliva sample |
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| Indra Wahyu Nufroha, Adri Nora, Henny Saraswati |
| APJMBB 31(1): 39-44 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.1.04 |
| Click here to download [PDF] |
| In organisms, cells perform apoptosis to remove damaged or mutated cells from the body. The Bcl-2 family protein encoded by the BCL2 gene plays a role in regulating apoptosis. Abnormalities in the function and expression level of the Bcl-2 protein are associated with several cancers. Saliva is a body fluid that can be used for biomedical research because it contains essential biomarkers of the body and genetic material derived from free cells in the oral cavity. This study aims to get primer characterization for the RT-PCR method for the BCL2 gene. We used RNA samples isolated from saliva to optimize the primers' annealing temperature, concentration, and combination pairs. Previous studies produced three primer candidates, i.e., primers A, B, and C, used in this research. The optimization results showed that primer C was the best primer to be used in the real-time PCR of this study. The optimal annealing temperature used was 60.3°C with a primer concentration of 400 nM. This study also shows the potential of saliva as a material for biomedical studies on the BCL2 gene. The results of the primer characterization resulting from this research are the first step in establishing the in-house RT-PCR method. The validation research will use a larger sample to validate this method. |
| Simple approach for expression and rapid purification of Taq DNA polymerase in three Escherichia coli strains |
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| Xue Chi Teng, See Yin Ang, Marimuthu Citartan, Thean Hock Tang, Siti Aminah Ahmed |
| APJMBB 31(1): 45-52 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.1.05 |
| Click here to download [PDF] |
| Background and objectives: One of the most commonly employed bacterial hosts for the synthesis of recombinant proteins is Escherichia coli (E. coli). Choosing an ideal host for the production of the protein of interest is an important step in the large-scale production process. Due to its thermostable characteristic, Taq Pol I, which was first isolated from the bacterium Thermus aquaticus (Taq), is now a typical enzyme found in many laboratories. This study aimed to identify the ideal host for large-scale production of Taq Pol I and purify the enzyme under a simple and rapid purification method. Methods: Taq Pol I gene in pSE420 plasmid was overexpressed in E. coli strains DH5α, TOP10 and BL21(DE3) pLysS. The enzyme was purified using Pluthero’s method and dialyzed using Amicon® Ultra-4 Centrifugal Filter. Results: The host strain E. coli TOP10 produced the highest amounts of Taq Pol I, followed by DH5α and BL21(DE3) pLysS. An estimated 4.5 U/μL of Taq Pol I was produced from a 200 mL culture of TOP10 host. Conclusion: This study provides data on the capacity of the E. coli strains used for Taq Pol I protein production. This information can be used to accelerate future targeted strain selection for the production of a specific protein of interest. |
| Validation of endophytic bacteria colonisation in tissue culture-derived oil palm plantlets via green fluorescent visualization |
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| Salwa Abdullah Sirajuddin, Intan Nur Ainni Mohamed Azni, Nur Diyana Roslan, Shamala Sundram |
| APJMBB 31(1): 53-63 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.1.06 |
| Click here to download [PDF] |
| This study aimed to validate the colonisation capability of endophytic bacteria (EB) isolates, Bacillus cereus EB2 and Pseudomonas aeruginosa EB35, that previously exhibited their potentials as biological control agents (BCAs) against the Ganoderma spp., a pathogen for Ganoderma disease in oil palm. Here, we demonstrated a rapid method to determine the colonisation capacity of the selected EB using oil palm tissue culture plantlets and a green fluorescent protein (GFP) visual marker. Wounded plantlet roots were inoculated with GFP-tagged B. cereus EB2 and P. aeruginosa EB35 while the plantlets without EB inoculation served as controls. The GFP signals appeared as bright green spots or lines in the inoculated GFP-tagged EB cells in root and leaf plantlet tissues, respectively, under the confocal laser scanning microscopy (CLSM) 5 days post-inoculation. In contrast, there was no intense GFP spots in neither the control root nor leaf tissues. The cracks in the roots by wounding facilitated the entry of the GFP-tagged EB cells into root tissues, allowing for endophytically colonisation of the root and above-ground tissues. Subsequent result of polymerase chain reaction (PCR)-GFP analysis further displayed the endophytic nature and early chronological colonisation of the tested EB. This is a preliminary report on root colonisation by a Gram-positive endophyte, B. cereus EB2 and leaf tissues colonisation by both EB isolates as internal colonisers, demonstrating their potential as BCAs to protect oil palm against Ganoderma spp. for a sustainable disease management. |
| Influence of IL-28B serum level and gene polymorphism in a sample of Iraqi patients with ankylosing spondylitis |
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| Hadeel Waleed Abdulmalek, Reema Mohammed Abed, Laith Ahmad Yaaqoob, Maha Fakhry Altaee, Zaid Kadim Kamona |
| APJMBB 31(1): 64-73 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.1.07 |
| Click here to download [PDF] |
| Ankylosing spondylitis (AS) represents one kind of advanced arthritis formed via inflammatory stimuli long-term in the spin‘s joints. Interleukin (IL)-29 (interferon- lambda1(IFN- λ1)), interleukin (IL)-28A (interferon- lambda 2 (IFN- λ2)) and interleukin (IL)-28B (interferon- lambda 3(IFN-λ3)) are three interferon lambda (IFN- λs) molecules that have recently been identified as new members of the IFN family. IL-28B expression in ankylosing spondylitis (AS) is not well understood. 150 male healthy controls ((HC) and 160 males with AS as patients group participated in this study. Serum level and gene polymorphism were assessed using an enzyme-linked immunosorbent assay and Sanger sequencing for IL-28B, respectively. The results showed significantly lower serum IL-28B concentrations in the AS groups in comparison to the HC groups (both p values equal to 0.003). There was a large difference in IL-28B genotype and allele frequency between the two individuals. IL-28B heterozygote genotype CT of rs12979860 SNP exhibits a substantial correlation with AS (P = 0.008). While the genotypes of rs12980275 SNP were not shown any significant correlation with AS. The findings suggest that serum concentration of IL-28B is a potential diagnostic biomarker in patients with AS, and that the heterozygote CT of rs12979860 SNP serves as a potential risk factor for the onset of AS in the Iraqi population. |
| The effect of HIV protease gene mutations to protease inhibitor drugs resistance in Papua patients: In silico analysis |
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| Mirna Widiyanti, Yustinus Maladan, Setyo Adiningsih |
| APJMBB 31(1): 74-80 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.1.08 |
| Click here to download [PDF] |
| The use of phenotypic assay requires laborious work to culture HIV isolates to observe the phenotypic change of the virus in the presence of antiretroviral drugs. The genotypic approach may rely on the secondary data of documented mutations that are responsible for phenotypic alterations to antiretroviral-resistant HIV. HIV genomes were extracted from patients’ plasma, which was subsequently subjected to RT-PCR and Sanger sequencing. The obtained HIV genome sequencing data were analyzed for mutation detection. Three-dimensional (3D) structures of mutant HIV protease were constructed using FoldX software. The binding affinity of the mutant HIV protease with protease inhibitor drugs (Saquinavir, Ritonavir, Nelfinavir, Indinavir, and Lopinavir) was analyzed using AutoDock Vina. There were 90 patients involved in this study. The patients attended the Voluntary Counseling Test (VCT) of Mitra Masyarakat Hospital in Mimika, Papua, Indonesia. Among recruited subjects, the HIV genomes corresponding to the protease-encoded gene of 30 patients were successfully sequenced. There was only one patient (RSMM_70) infected with HIV harboring minor mutations (L10V, I15V, M36I, and R41K) in the protease-encoded gene that was not a new finding mutation. The 3D structure showed that the hydrophobicity and stability of mutant HIV protease were different from the wild genotype. Docking analysis showed decreasing binding affinity of the mutant HIV protease to the protease inhibitor drugs, which may lead to the alteration of inhibitory effectiveness. In silico docking, the analysis may provide an alternative approach to predict the effect of minor mutations in the HIV protease gene on the effectiveness of protease inhibitor drugs. |
| Invasive non-typhoidal Salmonella in adult patients: A three-year review in a Malaysian General Hospital |
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| Karshini Jeya Pirathaba, Maria Kahar Bador Abdul Kahar, Nurzam Suhaila Che Hussin |
| APJMBB 31(1): 81-88 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.1.09 |
| Click here to download [PDF] |
| Invasive non-typhoidal Salmonella (iNTS) are recognized as an important cause of infection among immunocompromised patients with high morbidity and mortality. This study focused on the epidemiology, risk factors, antibiotic susceptibility, and clinical outcome of iNTS in Hospital Kuala Lumpur over 3 years period (2017-2019). Methods: A retrospective study was conducted on 43 adult patient who had NTS isolated from a sterile sample. The patient’s microbiology worksheets and medical notes were reviewed and analyzed. Results: The overall incidence rate for iNTS was 2.4 per 10,000 admissions. The patients median age was 57 years, with majority of them being above ≥ 55 years old (n=24, 55.8%). The most prevalent diseases are hypertension (28%), human immunodeficiency virus (20.9%), diabetes mellitus (18.6%) and heart disease (6.3%). Primary bacteraemia (95.3%) was the most frequent cause of iNTS, followed by tubo-ovarian abscess (2.3%) and urinary tract infections (2.3%). The overall mortality rate was 30%. The mortality rate was greater in patient presenting with shock on admission (p=0.04). Most of the invasive diseases were caused by Salmonella enterica serovar Enteritidis (95.3%). Overall, most isolates were susceptible to ceftriaxone (97.7%). Five isolates were intermediately resistant to ciprofloxacin (11.6%). Only one isolate (2.3%) was multidrug resistant. Conclusions: The comorbidities of iNTS varies even within the same country. Mortality rates are higher in those with primary bacteraemia and shock during admission. By understanding the epidemiology of iNTS in Malaysia, it will provide valuable information about the vulnerable population at risk of iNTS and improve the treatment and management of this patients. |
| Role of type IV pilin biosynthesis genes in biofilm formation of Aeromonas hydrophila |
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| Nancy Garg, Geetika Sharma, Daad Saffarini, Shivani Sharda, Rachana Sahney, Sheetal Shirodkar |
| APJMBB 31(1): 89-96 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.1.10 |
| Click here to download [PDF] [Supplementary Data] |
| Aeromonads resides in aquatic environments and infect humans and fish among other animals. This opportunistic pathogen is predicted to have several pili and fimbriae genes which may promote biofilm formation and attachment affecting the infection process. The present study compares biofilm formation and subsequent infection on MDCK cell lines using wildtype Aeromonas hydrophila and putative type IV pilin biosynthesis gene mutant generated by standard protocol. The results indicate the involvement of putative pilus biosynthesis operon AHA0686-AHA0696 in biofilm formation of Aeromonas hydrophila and infection of MDCK cells. In silico analysis of the operon predicts to contain putative type IV pili and pilin biosynthetic genes. Detailed analysis of these genes is required to evaluate the applicability of these mutant strains as potential vaccine candidates. |
Volume 31(2); 2023
| Escherichia coli phages isolated from broiler chickens showed ideal characteristics in gut modulation |
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| Mohd Asrore Mohd Shaufi, Chin Chin Sieo |
| APJMBB 31(2): 1-25 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.2.01 |
| Click here to download [PDF] |
| Phage has gained interest as an alternative antibiotic growth promoter (AGPs) in poultry production. Most phage studies only focus on phages that target pathogens. In this study, we isolated and characterised phages that target non-pathogens from chicken intestines. This study aimed to isolate and characterise phages that target non-pathogenic Escherichia coli for gut modulation study in broiler chickens. Based on a morphological study, the C1 phage belonged to the Podoviridae family, whereas C2, C3, and C4 phages belonged to the Siphoviridae family. The C1, C2, C3, and C4 phages appeared to be unique based on restriction fragment length polymorphisms (RFLPs), amplification of phage signature genes, and protein profiling (SDS-PAGE). The C1 phage had an ideal multiplicity of infection (MOI) of 0.001, followed by 0.1 for the C2, C3, and C4 phages. C1 had the highest adsorption rate of 99.7% in 1 min, followed by C2 (98%), C3 (98.7%), and C4 (98.2%), all of which were within 2 min. C1 also exhibited the largest burst size (72 PFU/infected cell) and the shortest latent period (5 min). The latent period of the C2, C3, and C4 phages was longer, lasting 10 minutes, and their burst sizes were 70, 77, and 46 PFU/infected cells, respectively. All phages had optimum lytic activity at pH 7 and 37°C. Each phage was unique and possessed favourable lytic characteristics, making all of them suitable for gut modulation study in chickens. |
| Structural complexity and physical mechanism of self-assembled lipid as nanocarriers: A review |
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| Nazhan Ilias, Rocky Vester Richmond, Gayathri Thevi Selvarajah, Intan Diana Mat Azmi, Mokrish Ajat |
| APJMBB 31(2): 26-35 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.2.02 |
| Click here to download [PDF] |
| Lipids such as glyceryl monooleate, phosphatidylcholine, and monoglyceride (CITREM) possess an amphipathic property that allows them to self-assemble into a complex internal structure when interacting with an aqueous solution. Since amphiphilic molecules possess hydrophilic heads and lipophilic tails, hydrophobic effects cause the spontaneous activity of the molecular rearrangement. The self-organization of the molecules often results in the phases of lipid polymorphism, for example microemulsion, inverse bicontinuous cubic (Q2), discontinuous hexagonal (H2), and micellar cubic (I2) Fd3m. Interestingly, these lamellar and non-lamellar phases have been applied in the development of nanocarriers for drug delivery due to their ability to provide a sustained drug release system, better drug bioavailability, and improved overall treatment. However, the attention that they are receiving from their application is not comparable to our understanding of the mechanisms involved in their synthesis. Elucidation of the spontaneous process helps in predicting and tuning the internal structure of an amphiphilic molecule to suit its application. Therefore, this review discusses the formation of lipid polymorphism from the thermodynamic point of view, critical packing parameter, and modified stalk theory. |
| Long non-coding RNA in glioblastoma invasion: Angiogenesis and mesenchymal transition via PI3K and Wnt signalling |
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| Dexter Hoi Long Leung |
| APJMBB 31(2): 36-52 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.2.03 |
| Click here to download [PDF] |
| Glioblastoma (GBM) is the deadliest type of primary brain tumours with a high mortality rate, attributing to high post-surgical tumour recurrence. This unfavourable prognosis is due to the highly invasive phenotype observed in GBM cells, especially within the mesenchymal (MES) subtype of GBM. In recent years, the involvement of non-coding RNA (ncRNA) such as long non-coding RNA (lncRNA) and microRNA (miRNA) have been extensively deliberated in cancers and GBM. They were reported to be involved in the regulation of multiple biological pathways and cellular processes, which leads to increased cell invasion observed in tumours. This review focuses on two cellular processes; angiogenesis and MES transition, which can stimulate the invasive nature of GBM cells. Additionally, the extracellular matrix (ECM) and the hypoxic environment of GBM microenvironment which are central factors regulating both cellular processes will be discussed. Both cellular processes affiliated with cell invasion are downstream of signalling pathways such as PI3K/Akt or Wnt/β-catenin signalling, which will also be elaborated. Finally, recent studies characterising novel lncRNAs in the regulation of cell-invasion in GBM, specifically via the biological processes and signalling pathways discussed previously will be compiled and reviewed. |
| Bacteria as promising biofactory for pigment production: A prospective insights into production strategies and industrial applications |
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| Priya Sundararajan, Shanmuga Priya Ramasamy |
| APJMBB 31(2): 53-61 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.2.04 |
| Click here to download [PDF] |
| The pigments are the coloured substances obtained from various organic and inorganic sources. Due to the negative impact of chemically synthesized dyes and pigments, there is a significant demand for microbially derived natural colourants. Microorganisms secrete pigments as their secondary metabolites. Microbial pigments are found as an alternative to synthetic pigments as they are produced significantly in higher quantities through biotechnological processes. Microbial pigments replaced by artificial colourants are easily decomposable and do not cause hazardous effects on the ecosystem. Different microbes like bacteria, fungi and actinomycetes could be exploited in pigment production. Despite varied groups of microorganisms acting as a source of pigment, bacteria are predominant source for pigment production because of their genetic simplicity. Moreover, bacterial pigments are recognized for their biological activities which accomplish their usage as colourants and therapeutics in various industries. Regarding bacterial pigment production, fermentation strategies are essential to overcome the market demand, which is applied in the pharmaceutical, chemical and food industries. The importance of bacterial pigments over synthetic pigments in various industrial applications and their production strategies is well narrated in this review. |
| The biosensor application in cancer detections: A review |
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| Norhaniza Emrizal, Zaini Haryati Mohd Zain, Khor Goot Heah |
| APJMBB 31(2): 62-70 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.2.05 |
| Click here to download [PDF] |
| Cancer has a higher possibility to be cured if the cancer can be detected earlier. However, many malignancies are currently diagnosed only after they have spread throughout the body due to late diagnosis. Current devices have limitations to detect early cancer cells as the huge variations in the signal and limiting repeatability and sensitivity. Thus, more specific, and sensitive device of biosensor is required urgently for early cancer cells detection. The design and advancement of biosensor technology has become a focal point in recent years due to a broad variety of biosensor applications of cancer detections. These devices convert the genomic materials into an electric signal that can be identified by recognizing a specific biological analyte. In addition, the recent application of biosensors together with nanomaterials has constituted an excellent strategy in cancer monitoring and detection. This review recaps the latest literature search insights the biosensors development and application on their biological recognitions. Finally, the up-to-date approaches applied in biosensors using the nanomaterials and micro-technologies as advancement in detecting various cancers are highlighted in this review paper. |
| Utilizing waste mango and avocado seeds for highly effective dye removal with activated carbon |
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| Rawa Ghassan Yousuf, Huda Adil Sabbar, Zainab Yaqoub Atiyah |
| APJMBB 31(2): 71-79 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.2.06 |
| Click here to download [PDF] |
| Activated carbon (AC) is a highly important adsorbent material, as it is a solid form of pure carbon that boasts a porous structure and a large surface area, making it effective for capturing pollutants. Thanks to its exceptional features, AC is widely used for purifying water that is contaminated with odors and removing dyes in a cost-effective manner. A variety of carbonic materials have been employed to prepare AC, and this study aimed to evaluate the suitability of utilizing waste mango and avocado seeds for this purpose, followed by testing their efficacy in removing dye from aqueous solutions. The results indicate that using waste mango and avocado as AC is technically feasible, achieving dye removal percentages of 98% and 93%, respectively. Equilibrium isotherms were explained using Langmuir and Freundlich adsorption models, with the former proving to be the best fit for the experimental data (R2=0.99). Additionally, adsorption kinetics were analyzed and found to be well represented by the pseudo-2nd kinetic model. |
| The first DNA barcode of medically important cockroaches in Bangladesh |
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| Faria Farhana Rain, Abu Faiz Md. Aslam |
| APJMBB 31(2): 80-90 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.2.07 |
| Click here to download [PDF] |
| Cockroaches can spread various pathogenic agents which are accountable for food adulteration and the dispersing of foodborne pathogens. Pest management depends on proper identification. Nowadays, the COI gene of mitochondrial DNA has been anticipated as a recent systematic method functional in taxonomy and evolutionary study on species identification. The present research work is an initiative to identify the medically important cockroaches based on mitochondrial COI gene sequences. Eight (8) cockroach species (Periplaneta americana, Periplaneta brunnea, Periplaneta australasiae, Blatella germanica, Hebardina concinna, Pycnoscleus surinamensis, Blaberidae sp. and Balta notulata) were identified. Among them, four cockroach species (Balta notulata, Blaberidae sp., Hebardina Concinna and Pycnoscelus surinamensis) were the new record from Bangladesh. AT base content in DNA fragments of cockroaches was higher than GC base content. The highest AT content was 70% and the lowest GC content was 30%. The interspecific genetic divergence range of medically important cockroach species was 0.01-0.25. According to mutational steps, Pycnoscelus surinamensis was mostly diverged from its common ancestor by 88 mutational steps. Phylogenetic analysis revealed that species belonging to the same family were in the same major clade. This research is the first molecular approach to identify the medically important cockroach species based on MT-COI gene sequences in Bangladesh. |
| Phytochemical, anti-microbial activity, and anti-proliferation tests against human cancer-origin cell lines using water and ethanolic extracts of Momordica cochinchinensis (Gac fruit) |
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| Priscilla Jayanthi Thavamany, Ming Thong Ong, Sreeramanan Subramaniam, Vikneswaran Murugaiyah |
| APJMBB 31(2): 91-108 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.2.08 |
| Click here to download [PDF] |
| Momordica cochinchinensis (Gac fruit) is a perennial tropical fruit which nutritional benefits have drawn significant attention in Southeast Asian countries but are not completely explored in this region. In addition to aril extracts, pulp and seed extracts were the focus of this study in terms of their phytochemical composition, antioxidant, antimicrobial, antiproliferative, and wound healing properties. The extracts obtained were aril water extract (AW), pulp water extract (PW) and seed extracts (SW), and its ethanolic counterpart, namely aril extract (AE), pulp extract (PE) and seed extract (SE). Both water and ethanolic extracts of the aril, pulp and seed contain alkaloids, flavonoids, saponins, volatile oil and reducing sugars. However, glycosides were only present in water extracts (AW, PW, SW), meanwhile tannins were detected only in SW. The PW exhibited an increased level of total phenolic content (TPC); 0.0215 ± 0.00060 mg GAE/g whereas, total flavonoid content (TFC) was quantitated at 0.083 ± 0.022 mg QE/g FW (TFC), respectively. Apart from that, the PW extract also exhibited potent antibacterial activity, with MIC values between 5 and 20 mg/ml and MBC values between 10 and 20 mg/ml against E. coli, P. aeruginosa, S. flexneri, and B. cereus. Cancer- origin cell lines MCF7, HepG2, A549, HCT116 and HT29 have been discovered to be most susceptible to AW and PW at 72 hours (h) post-treatment. The concentrations ranged between 1 µg/ml and 10 µg/ml of PE and SW extracts showed positive effects in the wound healing experiment. |
| Dissolved oxygen on xylanase production by Trichoderma reesei using Reutalis trisperma press cake as an additional substrate |
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| Lieke Riadi, Yuana Elly Agustin, Ruth Chrisnasari, Tjie Kok, Meyta Sanoe |
| APJMBB 31(2): 109-118 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.2.09 |
| Click here to download [PDF] |
| Dissolved oxygen (DO) level in media plays a big role in the succession of the fermentation process by a microorganism. In this project, Trichoderma reesei was cultivated in two types of media, media A and B, both in 250 mL shake flask and 1.5 L fermenter at varying DO level. Media A and B contained the same carbon source and mineral salts, the difference between both media was the presence of press cake in Media B as urea and ammonium sulfate replacement, whereas the nitrogen sources in media A consists of urea and ammonium sulfate. The batch fermentation process was conducted in a 7.8 C/N ratio with an initial pH of 6. The purified enzyme was shown to convert xylan to xylose. Media B that contained Reutealis trisperma press cake gives a higher xylanase activity than media A without press cake, for both shake flask and fermenter cultivations. A xylanase activity of 101.07±1.65 U/mL and 39.30±0.64 U/mL was produced in a shake flask under 140 rpm for 96 hours of fermentation with ratio of 0.6 media B/flask volume and 0.6 media A/flask volume, respectively. A xylanase activity of 205.90±0.84 U/mL and 88.87±1.45 U/mL was produced in 72 hours at 0.8 L/min of aeration rate in a 1.5 L fermenter with media A and media B, respectively. Thus, this study identified the Reutealis trisperma cake can be used as a beneficial additional substrate and nitrogen sources. The increase in DO level, which indicated by increasing aeration rate, can generate a higher xylanase activity for both media in shake flask and fermenter. |
| Homeopathic interventions against Salmonella typhi: A narrative review |
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| Chitram Umashankar, Bipinraj Nirichan Kunchirman, Chetan H. Shinde |
| APJMBB 31(2): 119-128 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.2.10 |
| Click here to download [PDF] |
| This review discusses the importance of the antimicrobial action of homoeopathic medicine in the general management of typhoid. The main aim is to provide individualized homoeopathic treatment with symptomatic improvement, minimizing complications, and promoting early recovery. Justifying homoeopathy as preventive and curative in epidemic diseases. To review the effectiveness of homoeopathic medicine against Salmonella typhi by agar well diffusion and MIC value methods. Google scholar and PubMed databases were searched for this study to analyse the effects of homoeopathic medicine against Salmonella typhi. After scrutiny, shortlisted studies were reviewed for the study. The Google scholar search yielded 41 studies, a bibliography from 13 different sources books, and the Selection of 6 clinical rubrics from Radar 10-Synthesis Repertories after analysis of abstracts of 60 studies, 27 were shortlisted including five in-vitro and two in-vivo studies. Most of the studies showed the significance of minimum inhibitory concentration (MIC) for homoeopathic medicine exhibited antibacterial potential against the related miniature organisms. The studies regarding antimicrobial action and other mechanisms of activity were heterogeneous. Homoeopathic remedies will allow the vital force immediately to deal with any exposure agents viz. various antigenic variants of salmonella. It appears to actuate resistant framework by initiating both T and B cells by the arrangement of antibodies. Further expansion of experimental studies is needed to know the exact action mechanism of homoeopathic medicines against Salmonella typhi. |
| Volume 31(2) Supplementary June 2023 |
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| Click here to download [PDF] |
Volume 31(3); 2023
| Microbial synthesis of silver nanoparticles and their effect of wheat seeds’ germination |
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| Lyudmila Ibrahimovna Zaynitdinova, Rokhila Nazarovna Juraeva, Javlon Jamondinovich Tashpulatov, Nikolay Anatol’evich Lazutin, Aziza Madjidovna Mavjudova, Tat’yana Bronislavovna Khegay |
| APJMBB 31(3): 1-9 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.3.01 |
| Click here to download [PDF] |
| One of the little-studied and promising ways to increase the yield of crops is the use of nanoparticles, especially of the biological origin. Recently, research has been carried out in this direction, however, there is still very little information and it is unambiguous. In this regard, the purpose of this study was to obtain silver nanoparticles (AgNPs) with use of Pseudomonas stutzeri and Bacillus sp. bacteria, which expressed high biosynthetic activity, and to determine their effect on the germination of wheat seeds. The culture liquids containing AgNPs were used to treat wheat seeds (Unumli bugdoy variety). The treated seeds were placed in Petri dishes with moistened filter paper to germinate during 7 days. The received AgNPs were characterized by UV spectroscopy and AFM. It was determined that strains of Pseudomonas stutzeri and Bacillus sp. possess the ability to synthesize oval and spherical AgNPs ranging in size from 5 to 100 nm. It was revealed that the treatment of wheat seeds with a cultural liquid containing biogenic AgNPs stimulated seeds’ germination, and also had a stimulating effect on the growth of roots and stems of plants, the accumulation of the dry matter mass of the roots and the aerial part of the seedlings. |
| Osteoinductive effect β-TCP and vitamin D3 on RUNX2 mRNA expression |
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| Noor Abdulkareem Razouki, Ban A. Ghani |
| APJMBB 31(3): 10-16 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.3.02 |
| Click here to download [PDF] |
| Although the autograft is regarded as the gold standard bone graft, β-TCP artificial alloplastic is widely used in bone defect healing and has been accepted in human and animal studies to be resorbed and interchanged by vital bone. The active form of vitamin D3 is calcitriol, on mesenchymal stem cells (MSCs) it has a direct influence on encouraging their osteogenic differentiation which is identified as osteoinductive. The need for osteoinductive ability is a demanding issue regarding medical and dental care. RUNX2 regards an essential transcriptional factor for osteoblast differentiation. Adult male New Zealand rabbits (Twenty-four) with an average weight of (1.5-2 kg) were elected in this study. Four holes were made intra-bone in both tibias of each animal. The experimental groups divide as follows: Group C: Bone defect will be left to heal naturally as control; Group TCP: Bone defect will be occupied with β-TCP. Group vitamin D3: Bone defect will be filled with vitamin D3; Group TCPD: Bone defect will be filled with a combination of β-TCP and vitamin D3. Animals sacrificed at (1 and 3 weeks). Purification of total RNA from formalin fixed paraffin embedded (FFPE), The cDNA of RUNX2 and VDR amplify in RT-PCR and detected with sybr green. One-way Analysis of Variance (ANOVA) and least significant difference (LSD) was used as a tool for statistical analysis. Results at 7 days highest mean value of mRNA RUNX2 gene expression Fold Change estimated in TCP followed by TCPD experimental group while at 21 days, the highest mean value in TCPD. All measured parameters showed highly significant differences in the course of healing periods from 7 days to 21 days. In mRNA VDR gene expression parameters showed a highly significant difference in 7days and 21 days durations among experimental groups and the highest mean value of mRNA VDR gene expression Fold Change is recorded in TCPD followed by vitamin D3 groups in both durations. These findings suggest positive inductive effects of local application of vitamin D3 combined with β-TCP as well as vitamin D3 on osteoblast cells and induced bone defect healing. |
| In silico analysis of xylanase in Bacillus coagulans ST-6 |
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| Ainu Husna M S Suhaimi, Rabiatul Adawiah Zainal Abidin, Fairuz Mohd Yusof, Abdullah Munir Roslan, Abdullah Sipat, Khatijah Yusoff |
| APJMBB 31(3): 17-27 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.3.03 |
| Click here to download [PDF] |
| Bacillus coagulans ST-6 is a thermophile isolated from a local hot spring in Malaysia. It expresses xylanase activity and has potential industrial applications. In silico structure prediction and modeling of a 210 amino acid sequence (XYNBC) translated from 872 bp Bacillus coagulans ST-6 xylanase gene was performed. The predicted molecular weight of the translated amino acid sequence is 20 kDa with theoretical isoelectric point value at 9.10 predicting that the xylanase belongs to the GH11 xylanase family. The protein is predicted to be hydrophilic with Grand average of hydropathicity (GRAVY) value of -0.6555 and possibly has better interaction with water. Predicted motif for XYNBC was revealed to be from Glycosyl hydrolases family 11(IPR00137) with signature motif 1 and 2 and only one known activity, xylanase. A three-dimensional (3D) model was constructed using PDB ID 2DCZ|A (http://www.rcsb. org) as the template as it has the highest similarity with XYNBC protein sequence. The 2DCZ|A xylanase sequence is from Bacillus Subtilis family-11 and is 185 amino acid long. The predicted 3D model consists of eleven beta sheets and one alpha helix. The stereochemical quality of protein structure revealed by Ramachandran Plot showed acceptable model with 99.4% residues fall in the most favored regions. Ten residues were predicted to be involved in active sites where residues Tyr7, Val15 and Asn16 are located at beta sheet while Asp118, Gly119, Thr120 are located at the loop. The catalytic residues E78 and E172 common to other G1H1 xylanases were also revealed. |
| Phytochemical and cytotoxic properties of Solanum aethiopicum fruit extracts against HeLa human cervical cancer cell line |
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| Lim Yee Thing, Lejaniya Abdul Kalam Saleena, Crystale Lim Siew Ying, Rhun Yian Koh, Pui Liew Phing |
| APJMBB 31(3): 28-38 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.3.04 |
| Click here to download [PDF] |
| Eggplant, also known as Solanum aethiopicum (S. aethiopicum), is a highly favoured vegetable globally and belongs to the Solanaceae family. Various research studies have provided evidence of African eggplant's biological properties, such as antioxidant potential, anti-inflammatory, anti-cancer, anti-diabetic, liver-protective, and renal-protective effects. Therefore, our investigation focused on examining the impact of S. aethiopicum on the cytotoxicity of HeLa cells, which are derived from human cervical cancer. Fruits were freeze-dried or oven-dried before being subjected to aqueous infusion or hot aqueous extraction. Hot aqueous extracted (oven-dried) samples contained the highest concentration of total phenol and flavonoids. After that, HeLa cells were treated with hot aqueous extracts. After a 24-hour incubation period, the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) test was conducted. According to the cytotoxicity analysis, neither oven-dried nor freeze-dried induced significant inhibitory effects towards HeLa cell proliferation. These findings suggest that both extracts demonstrated weak cytotoxic effects on cervical cancer cells. |
| Preliminary molecular identification of proteolytic and lipolytic-enzyme producing bacteria isolated from sediment of Litopenaeus vannamei pond |
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| Diah Ayuningrum, Diva Triza Novitasari, Aninditia Sabdaningsih, Oktavianto Eko Jati |
| APJMBB 31(3): 39-49 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.3.05 |
| Click here to download [PDF] |
| The enzyme is a catalyst that serves as an accelerator in a biochemical process. A hydrolytic enzyme is among the existing enzymes useful for environmental organic waste degradation. This research aimed to (1) investigate the ability of bacteria isolated from Litopenaeus vannamei pond sediment to produce proteolytic and lipolytic enzymes, (2) identify the isolates with 16S rRNA gene amplification, and (3) construct a phylogenetic tree according to the 16S rRNA genes. The preliminary proteolytic assay consisted of a skim milk agar medium and the lipolytic assay consisted of a Tween 20/80 medium or so-called precipitation test. Among 28 bacterial isolates, 4 of them showed potential for proteolytic activity and 6 of them showed lipolytic activity as well. Further, the amplification of 16S rRNA gene showed that 5 out of the 28 isolates were closely related to Bacillus infantis SA 3.2 (IM8), Marinobacter koreensis SB 1.1 (IM6), Vibrio algynolyticus SA 4.2 (IM6), Streptomyces euryhalinus SB 1.2 (IM6), and Cytobacillus kochii SC 3.4 (IM6). Amongst the most active isolate, one of the was included in Actinobacteria phylum. Many Bacilli strains shows enzymatic activity such as amylase, protease and lypase. The genus Marinobacter also found to be able to produce hydrolytic enzyme such as amylase and protease. Furthermore, the genus Vibrio such as V. algynoliticus produce several enzymes i.e., gelatinase, lecithinase, caseinase, amylase and lipase. In summary, the bacteria from L. vannamei pond sediment exhibit a potential as proteolytic and lipolytic enzyme producers. |
| Effect of salinity and biopesticide on Arthrospira platensis mass culture growth, metabolites, and bacterial diversity |
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| Irma Rohmawati, Basith Kuncoro Adji, Dea Putri Andeska, Eko Agus Suyono |
| APJMBB 31(3): 50-60 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.3.06 |
| Click here to download [PDF] |
| Arthrospira platensis mass culture contamination is a recurring concern. Salinity alteration appears to be a promising approach, given that A. platensis can withstand various salinities. In addition, biopesticide is also expected to eliminate the bacteria. Therefore, it is critical to investigate the effects of salinity and biopesticide on the growth, nutritional value, and bacterial diversity of A. platensis mass culture. A completely randomized design was used, with five salinity treatment levels: 5 ppt (S5B), 10 ppt (S10B), 15 ppt (S15B), 20 ppt (S20B), and 25 ppt (S25B), with 0.5 ml/L of biopesticide Azadirachta indica applied on days 2 and 4. The growth rate was calculated using daily density and biomass, and on day 7, carbohydrates, proteins, lipids, and pigments were determined. Furthermore, the contamination test and bacterial diversity were determined using Total Plate Count and Next-Generation Sequencing, respectively. The results showed that the S15B had the fastest growth rate and the largest carbohydrate content. However, S5B produced the best results in terms of protein, chlorophyll, and phycocyanin content, while S25B produced the most carotene and lipids. Proteobacteria were the most abundant in all NGS samples. The number of OTU treatments obtained for A (NCD7), B (NCD0), and C (S15BD7) were 646, 636, and 286, respectively. Moreover, C (S15BD7) was the most effective treatment to reduce bacterial diversity contamination, in which several bacterial diversity, including Acidobacteriota, Chloroflexi, Gemmatimonadota, Myxococcota, and Desulfobacterota, were eliminated completely. As a result of the salinity adjustment and the use of biopesticides, the mass culture of A. platensis was able to grow more quickly and contain more nutrients while having less bacterial diversity. |
| Characterization of fumarate reduction by Klebsiella pneumoniae isolated from patients with chronic periodontitis |
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| Geetika Sharma, Nancy Garg, Shamimul Hasan, Daad Saffarini, Sheetal Shirodkar |
| APJMBB 31(3): 61-70 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.3.07 |
| Click here to download [PDF] [Supplementary Data] |
| Chronic periodontitis is oral inflammatory gum disease which affects the tissues that support the teeth. It is caused by formation of bacterial plaque consisting of bacterial species that produces various virulence factors. Oral bacterial species from the periodontitis patients include species of Fusobacterium, Porphyromonas, Prevotella, Tannerella, etc. In the present study, we isolated the Klebsiella pneumoniae strain 9A from the pockets of patients suffering from chronic periodontitis. The strain was isolated on enriched tryptic soya media containing 10 mM fumarate and identified based on Gram staining, 16S rRNA gene sequencing, biochemical tests and ability to reduce fumarate. Our study is the first report of anaerobic fumarate reduction capabilities of Klebsiella spp. isolated from chronic periodontitis patients, which may help in growth and survival of species in periodontal pockets leading to progression of the disease. In addition, experimental evidence is provided through reduction, growth, and inhibitor assays for the presence of fumarate reductase (Frd) activities. Furthermore, we detected a 400 bp frdA gene fragment in Klebsiella pneumoniae strain 9A using degenerate PCR. This fragment show similarity to fumarate reductases flavoprotein subunit (FrdA). Our findings suggest that the FrdA subunit is responsible for anaerobic fumarate respiration in Klebsiella spp. to be important in the survival of bacteria in oxygen-deprived environments in humans such as periodontal pockets, thus contributing to its pathogenicity. |
| Effects of nitrogen starvation on TAG biosynthesis genes expression in Chlorella vulgaris |
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| Jesreen Tega, Cha Thye San, Malinna Jusoh |
| APJMBB 31(3): 71-83 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.3.08 |
| Click here to download [PDF] [Supplementary Data] |
| Microalgal oils and lipids are the potential sources of sustainable industrial products for pharmaceuticals, nutraceuticals, and cosmeceuticals. However, the production cost of microalgal-based products is still expensive and hinders their marketability. Therefore, research has been focusing on increasing microalgae's oil and lipids content to be economically reasonable. Nutrient stresses were often used to enhance oils and lipids production in microalgae. In this study, the microalga Chlorella vulgaris was exposed to nitrogen starvation for 21 days to examine the effect of nitrogen removal on cell density, total oil content, fatty acids composition, and the expression of two triacylglycerols (TAG) biosynthetic genes, glycerol-3-phosphate acyltransferase (GPAT) and diacylglycerol acyltransferase (DGAT). The results showed that the C. vulgaris cells grew extremely slowly (p<0.05) under nitrogen starvation conditions. However, despite the growth outcome, the nitrogen starvation increased (p<0.05) total oil contents on days 3, 11 and 14 relatives to control. Nitrogen starvation also stimulated (p<0.05) the production of saturated fatty acids (SFA). The primary fatty acids detected were C16:0, C18:0, C18:1, C18:2, C18:3 and C20:0. The effect of nitrogen starvation on the expression of TAG biosynthetic genes, GPAT and DGAT genes were enumerated using real-time PCR. Both GPAT and DGAT were downregulated in this study. Interestingly, the buildup of C18:2 and C18:3 was positively linked with GPAT expression, demonstrating that GPAT affected the synthesis of polyunsaturated fatty acids (PUFA) in nitrogen-starved circumstances. This suggests that the GPAT gene may be altered to increase PUFA in microalgae, notably C18:2 and C18:3. |
| Review of bioactive components property of Malaysian propolis: A review |
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| Khor Goot Heah, Eleena Mohd Yusof, Sharvitha Dhamotharan, Ikmal Hisham Ismail |
| APJMBB 31(3): 84-105 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.3.09 |
| Click here to download [PDF] |
| Over the past few decades, traditional medicinal products have grown in popularity. It is estimated that 80% of patients worldwide use them for basic health treatment. Due to its extraordinary bioactive properties, propolis is a bee product commonly utilised in alternative medicines. Propolis is a complicated mixture of substances, procured by bees from diverse vegetations and mix them with beeswax and bee saliva enzymes. Propolis bioactivities have been examined and reported in the treatments of numerous chronic diseases. Given the differences in pharmacological activity and compound markup of propolis, huge variation exists due to numerous hive localities. This study intends to define and explore the bioactive qualities of propolis in Malaysia. Information on the antibacterial, antioxidant, anti-inflammatory, and other bioactivity properties from studies conducted on Malaysian propolis have been consolidated in this review. This research would result in an enhanced understanding of the safe consumption of Malaysian propolis and may spur the development of novel and more affordable treatments for various infections. |
| In silico expression profiling and function prediction of transcribed small open reading frames from Cucumis sativus var. hardwickii PI183967 in C. sativus var. sativus |
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| Gabrielle Shiao Wei Chieng, Boon Chin Tan, Chee How Teo |
| APJMBB 31(3): 106-121 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.3.10 |
| Click here to download [PDF] |
| Cucumis sativus is one of the most cultivated and consumed plants worldwide. To meet the demanding requirements following the rise in population, it is important to maintain and enhance the growth and development of this crop. Recent findings suggest that small open reading frames (sORFs) are associated not only with plant growth but with plant stress responses, especially in the case of drought and salt stress conditions. Hence, in this present study, we aim to determine the function and expression profile reflected in Cucumis sativus var. hardwickii PI183967 sORFs in the variety C. sativus var. sativus through transcriptomic analyses of publicly available RNA-seq datasets of var. sativus. We managed to obtain 14,799 transcribed sORF from the transcriptome datasets of var. sativus. Among these, only 689 (4.66%) transcribed sORF have translational potential. We were able to unveil the roles of transcribed sORFs associated with biological processes (reproductive process, immune response, and multicellular organism reproduction), molecular functions (transferase activity, catalytic activity, acting on a protein, hydrolase activity, and oxidoreductase activity), and cellular component (cytoplasm). KEGG pathway analysis revealed that the transcribed sORFs were significantly enriched in two of the KEGG Ontology (KO) terms, namely, plant-pathogen interaction and plant hormone signal transduction. Results from this study aid the understanding of sORF roles in Cucumis sativus and pave the way for future attempts to utilize these sORFs involved in stress responses to enhance the quality of the crop. |
Volume 31(4); 2023
| Novel single nucleotide polymorphism (rs1600485907) of IL-41 gene associated with systemic lupus erythematous |
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| Reema Mohammed Abed, Laith Ahmed Yaaqoob |
| APJMBB 31(4): 1-8 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.4.01 |
| Click here to download [PDF] |
| This study evaluated the serum concentrations of IL-41 and the detection of specific single nucleotide polymorphisms (SNPs) (rs1600485907, rs762398841, and rs575275512) within the IL-41 gene in female subjects diagnosed with systemic lupus erythematosus (SLE). The study sample comprised 124 female patients who had been diagnosed with SLE, with an equivalent number of healthy control volunteers. The levels of serum were determined using the application of an enzyme-linked immunosorbent assay (ELISA) technology, while SNPs were determined by conventional polymerase chain reaction (PCR), and subsequent Sanger sequencing. The results revealed that the mean age of the healthy control group was 31.64 years, whereas the mean age of the group diagnosed with SLE was 33.66 years. The findings of the present investigation indicate that the individuals under examination demonstrated an average disease duration of 9.0 years, whereas the average SLEDAI-2k score for those diagnosed with SLE was 11.0. The concentrations of ESR, CRP, urea, creatinine, C3, and C4 in individuals diagnosed with SLE showed a statistically significant elevation in comparison to the control cohort. The analysis of patients’ anti-nuclear antibodies (ANA) revealed that 89% of individuals have ANA, whereas 95.61% display anti-dsDNA. Significantly elevated levels of serum IL-41 were seen in patients diagnosed with SLE in comparison to healthy controls. A receiver operating characteristic (ROC) analysis was performed on a cohort of patients diagnosed with SLE to assess the diagnostic efficacy of IL-41 in discriminating between SLE patients and non-afflicted persons. The study determined that the specificity of IL-41 was 82.26%, representing the percentage of accurate negative outcomes. In contrast, the sensitivity of IL-41 was found to be 84.68%, indicating the percentage of accurate positive outcomes. The computed value for the area under the curve (AUC) was found to be 0.937. The statistical analysis revealed a significant connection between the existence of both heterozygote and homozygote mutant genotypes of IL-41 (rs1600485907) and an increased vulnerability to the formation of SLE. In conclusion, it has been shown that individuals diagnosed with SLE demonstrate heightened concentrations of IL-41in their circulating blood plasma. Furthermore, a particular genetic variation, specifically a single nucleotide polymorphism (SNP) denoted as rs1600485907 located within the IL-41 gene, has been recognized as a potential susceptibility factor for the onset of this disorder. |
| Genetic diversity of multidrug resistant Salmonella enterica subsp. enterica serovar Brancaster isolated from chicken in Malaysia |
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| Evie Khoo, Roseliza Roslee, Zunita Zakaria, Nur Indah Ahmad |
| APJMBB 31(4): 9-20 |
| Article DOI: https://doi.org/10.35118/apjmbb.2023.031.4.02 |
| Click here to download [PDF] |
| Salmonella enterica subsp. enterica serovar Brancaster is a chicken-associated serovar that is increasingly reported in the Asian region, including Malaysia. The shortfall of conventional serovar identification for nomenclature alone is insufficient for studying the genetic and clonal relationships of Salmonella of the same serovar. Whereas DNA sequence-based typing method is useful to study the genetic diversity and relatedness of the highly diverse Salmonella. In this study, the genetic diversity, phenotypic antimicrobial resistance (AMR) profiles, and detection of selected AMR genes from ten representative Salmonella Brancaster isolates from chicken cloacal swabs and raw chicken meat were carried out. Based on multilocus sequence typing (MLST), all Salmonella Brancaster belonged to sequence type ST2133. Further analysis of the MLST sequencing data using concatenated nucleotide sequences of the seven housekeeping genes divided them into nine clusters, revealed heterogeneity and genetic diversity among the isolates. All isolates were multidrug-resistant (MDR), which confers resistance to three or more classes of antibiotics. Seven Salmonella Brancaster isolates exhibited phenotypic ACSSuT-type MDR profile, and two of them were also resistant towards ciprofloxacin. Salmonella Brancaster in the present study possessed at least one and up to six resistance genes, with the most prevalent being the ampicillin (blaTEM), tetracycline (tetA), chloramphenicol (floR), gentamicin (ant(3”)-Ia), streptomycin (strA), and sulfonamides (sul-2). Chickens are common reservoir for serovar Brancaster and the emergence, persistence, and dissemination of MDR Salmonella Brancaster possessed a public health risk. The authorities need to strengthen salmonellosis control management programme in poultry farms, abattoirs, and processing facilities. |