Displaying publications 61 - 80 of 106 in total

Abstract:
Sort:
  1. Fulltext Bamboo: an overview on its genetic diversity and characterization
    Yeasmin L, Ali MN, Gantait S, Chakraborty S
    3 Biotech, 2015 Feb;5(1):1-11.
    PMID: 28324361 DOI: 10.1007/s13205-014-0201-5
    Genetic diversity represents the heritable variation both within and among populations of organisms, and in the context of this paper, among bamboo species. Bamboo is an economically important member of the grass family Poaceae, under the subfamily Bambusoideae. India has the second largest bamboo reserve in Asia after China. It is commonly known as "poor man's timber", keeping in mind the variety of its end use from cradle to coffin. There is a wide genetic diversity of bamboo around the globe and this pool of genetic variation serves as the base for selection as well as for plant improvement. Thus, the identification, characterization and documentation of genetic diversity of bamboo are essential for this purpose. During recent years, multiple endeavors have been undertaken for characterization of bamboo species with the aid of molecular markers for sustainable utilization of genetic diversity, its conservation and future studies. Genetic diversity assessments among the identified bamboo species, carried out based on the DNA fingerprinting profiles, either independently or in combination with morphological traits by several researchers, are documented in the present review. This review will pave the way to prepare the database of prevalent bamboo species based on their molecular characterization.
  2. Fulltext Genotyping of Salmonella strains isolated from ducks, their rearing and processing environments in Penang, Malaysia, using RAPD
    Adzitey F, Ali GR, Huda N, Ahmad R
    3 Biotech, 2013 Dec;3(6):521-527.
    PMID: 28324423 DOI: 10.1007/s13205-013-0115-7
    Salmonella species are important foodborne pathogens that can cause illness and death in humans. The objective of this study was to determine the genetic relatedness of 115 Salmonella strains isolated from ducks and their environment using random amplified polymorphic deoxyribonucleic acid (RAPD). The analysis of Salmonella strains by RAPD produced DNA fingerprints of different sizes for differentiation purposes, and cluster analysis at a coefficient of 0.85 grouped the Salmonella strains into various clusters and singletons. S. Typhimurium were grouped into nine clusters and ten singletons, S. Hadar were grouped into seven clusters and nine singletons, S. Enteritidis were grouped into four clusters and five singletons, S. Braenderup were grouped into five clusters and four singletons, S. Albany were grouped into two clusters and seven singletons, and S. Derby were grouped into two clusters and four singletons at a coefficient of 0.85 with discriminatory index (D) ranging from 0.879 to 0.957. With the exception of S. Typhimurium strains which were grouped into three major groups (genotypes) by RAPD analysis, the rest were grouped into two major genotypes. RAPD was a useful genotyping tool for determining the genetic relatedness of the duck Salmonella strains. Comparison of the genetic relatedness among foodborne pathogens and their sources of isolation are important to trace their source and possibly the source of human infection.
  3. Fulltext Application of response surface methodology for optimization of decolorization and mineralization of triazo dye Direct Blue 71 by Pseudomonas aeruginosa
    Hafshejani MK, Ogugbue CJ, Morad N
    3 Biotech, 2014 Dec;4(6):605-619.
    PMID: 28324306 DOI: 10.1007/s13205-013-0192-7
    The decolorization and degradation of Direct Blue 71 were investigated using a mono culture of Pseudomonas aeruginosa. The bacterium was able to decolorize the dye medium to 70.43 % within 48 h under microaerophilic conditions. The medium was then aerated for 24 h to promote the biodegradation of the aromatic amines generated from azo bond cleavage. Reduction in total organic carbon in dye medium was 42.58 % in the microaerophilic stage and 78.39 % in the aerobic stage. The degradation metabolites formed were studied using UV-vis techniques, high performance liquid chromatography, Fourier transform infra red spectroscopy and nuclear magnetic resonance spectroscopy analysis. Data obtained provide evidence for the formation of aromatic amines and their subsequent oxidative biodegradation by a single strain of P. aeruginosa during successive microaerophilic/aerobic stages in the same flask. The influence of incubation temperature (20-45 °C), medium pH (5-10) and initial dye concentration (25-150 mg/L) on decolorization was evaluated to greatly influence decolorization extent. The optimal decolorization conditions were determined by response surface methodology based on three-variable central composite design to obtain maximum decolorization and to determine the significance and interaction effect of the variables on decolorization. The optimal conditions of response were found to be 35.15 °C, pH 8.01 and 49.95 mg/L dye concentration giving an experimental decolorization value of 84.80 %. Very high regression coefficient between the variables and the response (R(2) = 0.9624) indicated a good evaluation of experimental data by polynomial regression model.
  4. Fulltext Characterization of detergent compatible protease from halophilic Virgibacillus sp. CD6
    Lam MQ, Nik Mut NN, Thevarajoo S, Chen SJ, Selvaratnam C, Hussin H, et al.
    3 Biotech, 2018 Feb;8(2):104.
    PMID: 29404232 DOI: 10.1007/s13205-018-1133-2
    A halophilic bacterium, Virgibacillus sp. strain CD6, was isolated from salted fish and its extracellular protease was characterized. Protease production was found to be highest when yeast extract was used as nitrogen source for growth. The protease exhibited stability at wide range of salt concentration (0-12.5%, w/v), temperatures (20-60 °C), and pH (4-10) with maximum activity at 10.0% (w/v) NaCl, 60 °C, pH 7 and 10, indicating its polyextremophilicity. The protease activity was enhanced in the presence of Mg2+, Mn2+, Cd2+, and Al3+ (107-122% relative activity), and with retention of activity > 80% for all of other metal ions examined (K+, Ca2+, Cu2+, Co2+, Ni2+, Zn2+, and Fe3+). Both PMSF and EDTA inhibited protease activity, denoting serine protease and metalloprotease properties, respectively. High stability (> 70%) was demonstrated in the presence of organic solvents and detergent constituents, and the extracellular protease from strain CD6 was also found to be compatible in commercial detergents. Proteinaceous stain removal efficacy revealed that crude protease of strain CD6 could significantly enhance the performance of commercial detergent. The protease from Virgibacillus sp. strain CD6 could serve as a promising alternative for various applications, especially in detergent industry.
  5. Optimisation of culture composition for glyphosate degradation byBurkholderia vietnamiensisstrain AQ5-12
    Manogaran M, Shukor MY, Yasid NA, Khalil KA, Ahmad SA
    3 Biotech, 2018 Feb;8(2):108.
    PMID: 29430369 DOI: 10.1007/s13205-018-1123-4
    The herbicide glyphosate is often used to control weeds in agricultural lands. However, despite its ability to effectively kill weeds at low cost, health problems are still reported due to its toxicity level. The removal of glyphosate from the environment is usually done by microbiological process since chemical process of degradation is ineffective due to the presence of highly stable bonds. Therefore, finding glyphosate-degrading microorganisms in the soil of interest is crucial to remediate this glyphosate.Burkholderia vietnamiensisstrain AQ5-12 was found to have glyphosate-degrading ability. Optimisation of biodegradation condition was carried out utilising one factor at a time (OFAT) and response surface methodology (RSM). Five parameters including carbon and nitrogen source, pH, temperature and glyphosate concentration were optimised. Based on OFAT result, glyphosate degradation was observed to be optimum at fructose concentration of 6, 0.5 g/L ammonia sulphate, pH 6.5, temperature of 32 °C and glyphosate concentration at 100 ppm. Meanwhile, RSM resulted in a better degradation with 92.32% of 100 ppm glyphosate compared to OFAT. The bacterium was seen to tolerate up to 500 ppm glyphosate while increasing concentration results in reduced degradation and bacterial growth rate.
  6. Characterisation of the simultaneous molybdenum reduction and glyphosate degradation byBurkholderia vietnamiensisAQ5-12 andBurkholderiasp. AQ5-13
    Manogaran M, Ahmad SA, Yasid NA, Yakasai HM, Shukor MY
    3 Biotech, 2018 Feb;8(2):117.
    PMID: 29430378 DOI: 10.1007/s13205-018-1141-2
    In this novel study, we report on the use of two molybdenum-reducing bacteria with the ability to utilise the herbicide glyphosate as the phosphorus source. The bacteria reduced sodium molybdate to molybdenum blue (Mo-blue), a colloidal and insoluble product, which is less toxic. The characterisation of the molybdenum-reducing bacteria was carried out using resting cells immersed in low-phosphate molybdenum media. Two glyphosate-degrading bacteria, namelyBurkholderia vietnamiensisAQ5-12 andBurkholderiasp. AQ5-13, were able to use glyphosate as a phosphorous source to support molybdenum reduction to Mo-blue. The bacteria optimally reduced molybdenum between the pHs of 6.25 and 8. The optimum concentrations of molybdate for strainBurkholderia vietnamiensis strainAQ5-12 was observed to be between 40 and 60 mM, while forBurkholderiasp. AQ5-13, the optimum molybdate concentration occurred between 40 and 50 mM. Furthermore, 5 mM of phosphate was seen as the optimum concentration supporting molybdenum reduction for both bacteria. The optimum temperature aiding Mo-blue formation ranged from 30 to 40 °C forBurkholderia vietnamiensis strainAQ5-12, whereas forBurkholderiasp. AQ5-13, the range was from 35 to 40 °C. Glucose was the best electron donor for supporting molybdate reduction, followed by sucrose, fructose and galactose for both strains. Ammonium sulphate was the best nitrogen source in supporting molybdenum reduction. Interestingly, increasing the glyphosate concentrations beyond 100 and 300 ppm forBurkholderia vietnamiensis strainAQ5-12 andBurkholderiasp. AQ5-13, respectively, significantly inhibited molybdenum reduction. The ability of these bacteria to reduce molybdenum while degrading glyphosate is a useful process for the bioremediation of both toxicants.
  7. Fulltext Genetic variability in selected date palm (Phoenix dactylifera L.) cultivars of United Arab Emirates using ISSR and DAMD markers
    Purayil FT, Robert GA, Gothandam KM, Kurup SS, Subramaniam S, Cheruth AJ
    3 Biotech, 2018 Feb;8(2):109.
    PMID: 29430370 DOI: 10.1007/s13205-018-1108-3
    Nine (9) different date palm (Phoenix dactylifera L.) cultivars from UAE, which differ in their flower timings were selected to determine the polymorphism and genetic relationship between these cultivars. Hereditary differences and interrelationships were assessed utilizing inter-simple sequence repeat (ISSR) and directed amplification of minisatellite DNA region (DAMD) primers. Analysis on eight DAMD and five ISSR markers produced total of 113 amplicon including 99 polymorphic and 14 monomorphic alleles with a polymorphic percentage of 85.45. The average polymorphic information content for the two-marker system was almost similar (DAMD, 0.445 and ISSR, 0.459). UPGMA based clustering of DAMD and ISSR revealed that mid-season cultivars, Mkh (Khlas) and MB (Barhee) grouped together to form a subcluster in both the marker systems. The genetic similarity analysis followed by clustering of the cumulative data from the DAMD and ISSR resulted in two major clusters with two early-season cultivars (ENg and Ekn), two mid-season cultivars (MKh and MB) and one late-season cultivar (Lkhs) in cluster 1, cluster 2 includes two late-season cultivars, one early-season cultivar and one mid-season cultivar. The cluster analysis of both DAMD and ISSR marker revealed that, the patterns of variation between some of the tested cultivars were similar in both DNA marker systems. Hence, the present study signifies the applicability of DAMD and ISSR marker system in detecting genetic diversity of date palm cultivars flowering at different seasons. This may facilitate the conservation and improvement of date palm cultivars in the future.
  8. Characterization of Thiomonas delicata arsenite oxidase expressed in Escherichia coli
    Teoh WK, Salleh FM, Shahir S
    3 Biotech, 2017 Jun;7(2):97.
    PMID: 28560637 DOI: 10.1007/s13205-017-0740-7
    Microbial arsenite oxidation is an essential biogeochemical process whereby more toxic arsenite is oxidized to the less toxic arsenate. Thiomonas strains represent an important arsenite oxidizer found ubiquitous in acid mine drainage. In the present study, the arsenite oxidase gene (aioBA) was cloned from Thiomonas delicata DSM 16361, expressed heterologously in E. coli and purified to homogeneity. The purified recombinant Aio consisted of two subunits with the respective molecular weights of 91 and 21 kDa according to SDS-PAGE. Aio catalysis was optimum at pH 5.5 and 50-55 °C. Aio exhibited stability under acidic conditions (pH 2.5-6). The V max and K m values of the enzyme were found to be 4 µmol min(-1) mg(-1) and 14.2 µM, respectively. SDS and Triton X-100 were found to inhibit the enzyme activity. The homology model of Aio showed correlation with the acidophilic adaptation of the enzyme. This is the first characterization studies of Aio from a species belonging to the Thiomonas genus. The arsenite oxidase was found to be among the acid-tolerant Aio reported to date and has the potential to be used for biosensor and bioremediation applications in acidic environments.
  9. Fulltext Bioremediation of palm industry wastes using vermicomposting technology: its environmental application as green fertilizer
    Rupani PF, Embrandiri A, Ibrahim MH, Shahadat M, Hansen SB, Mansor NNA
    3 Biotech, 2017 Jul;7(3):155.
    PMID: 28623493 DOI: 10.1007/s13205-017-0770-1
    Several technologies are being applied for treatment of palm oil mill wastes. Among them, the biological treatments (vermicomposting) have widely been recognized as one of the most efficient and eco-friendly methods for converting organic waste materials into valuable products. The present study focuses on vermicomposting of acidic palm oil mill effluent (POME) mixed with the palm pressed fibre (PPF) which are found difficult to decompose in the environment. The industrial waste (POME) was vermicomposted using Lumbricus rubellus under laboratory conditions for a period of 45 days. A significant improvement in nitrogen, phosphorus, and potassium content was monitored during vermicomposting process. In addition, the decline in C:N ratio of vermicompost (up to 17.20 ± 0.60) reflects the degree of stabilization of POME-PPF mixture. Different percentages of the vermicompost extract obtained from POME-PPF mixture were also examined for the germination of mung bean (Vigna radiata) seed. The results showed that 75% vermicompost extract demonstrated better performance for the seed germination. On the basis of significant findings, POME-PPF mixture can be successfully used as a feeding material for the earthworms, while on the other hand, it can also be used as a cost-effective fertilizer for the germination and the proper growth of mung bean.
  10. Fulltext Characterization, drug loading and antibacterial activity of nanohydroxyapatite/polycaprolactone (nHA/PCL) electrospun membrane
    Hassan MI, Sultana N
    3 Biotech, 2017 Aug;7(4):249.
    PMID: 28714045 DOI: 10.1007/s13205-017-0889-0
    Considering the important factor of bioactive nanohydoxyapatite (nHA) to enhance osteoconductivity or bone-bonding capacity, nHA was incorporated into an electrospun polycaprolactone (PCL) membrane using electrospinning techniques. The viscosity of the PCL and nHA/PCL with different concentrations of nHA was measured and the morphology of the electrospun membranes was compared using a field emission scanning electron microscopy. The water contact angle of the nanofiber determined the wettability of the membranes of different concentrations. The surface roughness of the electrospun nanofibers fabricated from pure PCL and nHA/PCL was determined and compared using atomic force microscopy. Attenuated total reflectance Fourier transform infrared spectroscopy was used to study the chemical bonding of the composite electrospun nanofibers. Beadless nanofibers were achieved after the incorporation of nHA with a diameter of 200-700 nm. Results showed that the fiber diameter and the surface roughness of electrospun nanofibers were significantly increased after the incorporation of nHA. In contrast, the water contact angle (132° ± 3.5°) was reduced for PCL membrane after addition of 10% (w/w) nHA (112° ± 3.0°). Ultimate tensile strengths of PCL membrane and 10% (w/w) nHA/PCL membrane were 25.02 ± 2.3 and 18.5 ± 4.4 MPa. A model drug tetracycline hydrochloride was successfully loaded in the membrane and the membrane demonstrated good antibacterial effects against the growth of bacteria by showing inhibition zone for E. coli (2.53 ± 0.06 cm) and B. cereus (2.87 ± 0.06 cm).
  11. Fulltext Assessment of three plastid DNA barcode markers for identification of Clinacanthus nutans (Acanthaceae)
    Ismail NZ, Arsad H, Samian MR, Hamdan MR, Othman AS
    3 Biotech, 2018 Jan;8(1):62.
    PMID: 29354373 DOI: 10.1007/s13205-018-1092-7
    This study was conducted to determine the feasibility of using three plastid DNA regions (matK, trnH-psbA, and rbcL) as DNA barcodes to identify the medicinal plant Clinacanthus nutans. In this study, C. nutans was collected at several different locations. Total genomic DNA was extracted, amplified by polymerase chain reaction (PCR), and sequenced using matK, trnH-psbA, and rbcL, primers. DNA sequences generated from PCR were submitted to the National Center for Biotechnology Information's (NCBI) GenBank. Identification of C. nutans was carried out using NCBI's Basic Local Alignment Search Tool (BLAST). The rbcL and trnH-psbA regions successfully identified C. nutans with sequencing rates of 100% through BLAST identification. Molecular Evolutionary Genetics Analysis (MEGA) 6.0 was used to analyze interspecific and intraspecific divergence of plastid DNA sequences. rbcL and matK exhibited the lowest average interspecific distance (0.0487 and 0.0963, respectively), whereas trnH-psbA exhibited the highest average interspecific distance (0.2029). The R package Spider revealed that trnH-psbA correctly identified Barcode of Life Data System (BOLD) 96%, best close match 79%, and near neighbor 100% of the species, compared to matK (BOLD 72%; best close match 64%; near neighbor 78%) and rbcL (BOLD 77%; best close match 62%; near neighbor 88%). These results indicate that trnH-psbA is very effective at identifying C. nutans, as it performed well in discriminating species in Acanthaceae.
  12. The antioxidant, wound healing properties and proteomic analysis of water extracts from the tropical cyanobacteria, Nostoc NIES-2111_MUM004
    Foo SC, Lee ZS, Yap MKK, Tan JW
    3 Biotech, 2023 Feb;13(2):71.
    PMID: 36742448 DOI: 10.1007/s13205-022-03448-0
    Cyanobacteria bioactive compounds are chemical treasure troves for product discovery and development. The wound healing effects and antioxidant capacities of water extracts from Nostoc NIES-2111_MUM004 were evaluated via in vitro wound scratch assay and three antioxidant assays respectively. Results showed that the water extracts were protein-rich and exhibited good antioxidant properties in ABTS radical scavenging (11.27 ± 0.205 mg TAE g-1 extract), Ferric reducing antioxidant power (1652.71 ± 110.71 mg TAE g-1 extract) and β-carotene bleaching assay (354.90 ± 31.80 mg TAE g-1 extract). Also, extracts were non-cytotoxic in concentrations up to 250 µg/mL as reflected in cytotoxicity assay. Importantly, water extracts showed considerable proliferation and migration activity at 125 µg/mL with wound closure rate as high as 42.67%. Statistical correlation revealed no significant relationship (p > 0.05) between protein fraction and the wound healing properties, confirming that phycobiliproteins were not solely responsible for wound healing activities. Subsequent Q-TOF-LCMS analysis identified six protein families involved in enhancing the proliferation and migration of epithelial cells. These findings are antecedent in the uncovering of continuous supplies of bioactive compounds from new and sustainable sources. Ultimately, enriching the microalgae menu for applications in pharmaceutical, nutraceutical and cosmeceuticals.
  13. Investigating the potential of mono-chalcone compounds in targeting breast cancer receptors through network pharmacology, molecular docking, molecular dynamics simulation, antiproliferative effects, and gene expressions
    Ismail NZ, Khairuddean M, Alidmat MM, Abubakar S, Arsad H
    3 Biotech, 2024 Jun;14(6):151.
    PMID: 38737798 DOI: 10.1007/s13205-024-03991-y
    The study aims to investigate various aspects of synthesized mono-chalcone compounds 5 and 8 concerning breast cancer, including network pharmacology, molecular docking, molecular dynamics (MD) simulations, antiproliferative effects, and gene expressions. Initially, the compounds underwent a network pharmacology analysis targeting breast cancer-related targets, with MalaCards, SwissTargetPrediction, and PharmMapper identifying 70 breast cancer target receptors. Subsequently, protein-protein interaction (PPI) network analysis revealed two distinct target gene clusters. Survival analysis identified seven significant target genes following Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and Gene Ontology (GO) evaluation. Molecular docking and MD simulations were conducted on these seven target genes (AKT2, BRAF, ESR1, FGFR1, IGF1, IGF1R, and KIT), revealing that compound 8 exhibited the highest binding affinities, as well as better stability and compactness when interacting with the targeted proteins. Next, the compounds underwent cell viability assay and gene expression analysis to validate the in silico findings. Both compounds demonstrated the ability to suppress breast cancer proliferation, with compound 8 showing increased selectivity in targeting breast cancer cells while causing minimal harm to normal breast cells. The suppression of breast cancer cell proliferation was attributed to decreased expression levels of AKT2, BRAF, FGFR1, IGF1, IGF1R, KIT, and ESR1. Hence, the results provide insights into the molecular interaction responsible for the anti-breast cancer capabilities of mono-chalcone compounds.

    SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-024-03991-y.

  14. Prevention of aspirin-mediated secondary toxicity by combined treatment of carotenoids in macrophages
    Vijay K, Ambedkar R, Sowmya PR, Ramaiah S, Ranga Rao A, Gundamaraju R, et al.
    3 Biotech, 2023 Jul;13(7):223.
    PMID: 37292139 DOI: 10.1007/s13205-023-03632-w
    Upon understanding the boosting role of carotenoids on the endogenous anti-inflammatory system, it is vital to explore their role in reducing the use of high doses of non-steroidal anti-inflammatory drug (NSAIDs), and their mediated secondary toxicity during the treatment of chronic diseases. The current study investigates the carotenoids potential on inhibition of secondary complications induced by NSAIDs, aspirin (ASA) against lipopolysaccharide (LPS) stimulated inflammation. Initially, this study evaluated a minimal cytotoxic dose of ASA and carotenoids (β-carotene, BC/lutein, LUT/astaxanthin, AST/fucoxanthin FUCO) in Raw 264.7, U937, and peripheral blood mononuclear cells (PBMCs). In all three cells, carotenoids + ASA treatment reduced the LDH release, NO, and PGE2 efficiently than an equivalent dose of carotenoid or ASA treated alone. Based on cytotoxicity and sensitivity results, RAW 264.7 cells were selected for further cell-based assay. Among carotenoids, FUCO + ASA exhibited an efficient reduction of LDH release, NO, and PGE2 than the other carotenoids (BC + ASA, LUT + ASA, and AST + ASA) treatment. FUCO + ASA combination decreased LPS/ASA induced oxidative stress, pro-inflammatory mediators (iNOS, COX-2, and NF-κB), and cytokines (IL-6, TNF-α, and IL-1β) efficiently. Further, apoptosis was inhibited by 69.2% in FUCO + ASA, and 46.7% in ASA than LPS treated cells. A drastic decrease in intracellular ROS generation with the increase in GSH was observed in FUCO + ASA compared to LPS/ASA groups. The results documented on the low dose of ASA with a relative physiological concentration of FUCO suggested greater importance for alleviating secondary complications and optimize prolonged chronic disease treatments with NSAID's associated side effects.

    SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03632-w.

  15. A streamlined strategy for self-production of a commercial positive selection vector, the pJET1.2/blunt cloning vector, using common laboratory E. coli strains
    Nawawi O, Abdullah MP, Yusuf CYL
    3 Biotech, 2023 Jul;13(7):224.
    PMID: 37292140 DOI: 10.1007/s13205-023-03647-3
    Positive selection vectors carry a lethal gene encoding a toxic product that is harmful to most laboratory E. coli strains. Previously, we reported a strategy for in-house production of a commercial positive selection vector, the pJET1.2/blunt cloning vector, using common laboratory E. coli strains. However, the strategy involves lengthy gel electrophoresis and extraction procedures to purify the linearized vector after digestion. Here, we streamlined the strategy to eliminate the gel-purification step. A uniquely designed short fragment called the Nawawi fragment was inserted into the coding sequence of the lethal gene of the pJET1.2 plasmid, resulting in the pJET1.2N plasmid that can be propagated in the E. coli strain DH5α. Digestion of the pJET1.2N plasmid with EcoRV released the Nawawi fragment, and the resulting blunt-ended pJET1.2/blunt cloning vector can be used directly for DNA cloning without prior purification. Cloning of a DNA fragment was not hindered by the Nawawi fragments carried over from the digestion step. After transformation, the pJET1.2N-derived pJET1.2/blunt cloning vector produced > 98% positive clones. The streamlined strategy accelerates the in-house production of the pJET1.2/blunt cloning vector and enables DNA cloning at a lower cost.

    SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03647-3.

  16. Microalgae for freshwater arsenic bioremediation: examining cellular toxicity, bioconcentration factor and eluding an alternative arsenic detoxification pathway
    Tang WW, Foo SC
    3 Biotech, 2024 May;14(5):130.
    PMID: 38605865 DOI: 10.1007/s13205-024-03977-w
    Microalgae are photoautotrophic organisms in freshwater systems known to uptake and bioremediate arsenic, a heavy metal. In this study, we compared the growth and arsenic uptake of two microalgae strains, Nostoc and Chlorella, to determine their suitability for arsenic bioremediation. As compared to the control, our results showed that treatment with As (III) enhanced the Nostoc growth by approximately 15% when grown in the absence of phosphate. The highest bioconcentration factor of Nostoc at this treatment was 1463.6, whereas 0.10 mg L-1 As (V) treatment improved the Chlorella growth by 25%, in the presence of phosphate. However, arsenic uptake reduced from 175.7 to 32.3 throughout the cultivation period for Chlorella. This suggests that Nostoc has an upper advantage in the bioremediation of arsenic as compared to the Chlorella strain. To gain insights into the potential of Nostoc in arsenic bioremediation, we further conducted SEM analysis on the vegetative cell surface. The SEM results showed that As (III) disrupted the Nostoc vegetative cell surface and structure. Further to this, pathway analysis and polymerase chain reaction (PCR) were conducted to identify the potential arsenic pathway regulated by Nostoc. The primary As (III)-related pathways elucidated include the arsA transporter and arsD complex that require ATP and As (III) methylation to S-adenosylmethionine. The phosphate deficiency condition resulting in the inability to generate ATP caused As (III) could not be excreted from the Nostoc cells, potentially contributing to the high arsenic concentration accumulated under phosphate-depleted conditions. These insights contribute to understanding the efficacy of microalgae strains in freshwater arsenic bioremediation.
  17. Colorimetric detection of mercury (Hg2+) using UV-vis spectroscopy and digital image analysis based on gold nanoparticles functionalized with bromelain enzyme
    Suhaidi NA, Halmi MIE, Rashidi AA, Anuar MFM, Mahmud K, Kusnin N, et al.
    3 Biotech, 2023 May;13(5):121.
    PMID: 37033387 DOI: 10.1007/s13205-023-03532-z
    A very sensitive and selective colorimetric biosensor for the measurement of mercury ion (Hg2+) in environmental samples has been developed using functionalized gold nanoparticles with bromelain enzyme (brn-AuNPs). This work has shown that Hg2+ measurement based on spectrophotometer and digital image analysis is a very innovative and successful method for providing an effective preliminary system and has promise for the future of water quality biomonitoring. Response Surface Methodology (RSM), a Box-Behnken design-based technique, was used to identify the optimum levels of functionalization of bromelain to AuNPs. The created model's validity was confirmed, and statistical analysis revealed that the ideal functionalize conditions were 1 mM of AuNPs, functionalize with 0.59 mM bromelain concentration on 14 ℃ temperature and 72 h incubation time. The lowest colorimetric detection concentration (LOD) of brn-AuNPs of Hg2+ was 0.0092 ppm and 0.011 ppm for spectrophotometer and digital image analysis. As shown, digital image analysis had advantages based on the LOD result comparable to UV-VIS spectrophotometer. The practical application of the brn-AuNPs sensing was proven with mercury determination in water samples. The present study developed a robust sensor, which successfully implemented in a compact portable sensor kit, turning this sensor into a very potent tool for the development water quality biomonitoring system of Hg2+ application.
  18. X-ray crystallography of mutant GDSL esterase S12A of Photobacterium marinum J15
    Rahman NNA, Sharif FM, Kamarudin NHA, Ali MSM, Aris SNAM, Jonet MA, et al.
    3 Biotech, 2023 May;13(5):128.
    PMID: 37064003 DOI: 10.1007/s13205-023-03534-x
    GDSL esterase is designated as a member of Family II of lipolytic enzymes known to catalyse the synthesis and hydrolysis of ester bonds. The enzyme possesses a highly conserved motif Ser-Gly-Asn-His in the four conserved blocks I, II, III and V respectively. The enzyme characteristics, such as region-, chemo-, and enantioselectivity, help in resolving the racemic mixture of single-isomer chiral drugs. Recently, crystal structure of GDSL esterase from Photobacterium J15 has been reported (PDB ID: 5XTU) but not in complex with substrate. Therefore, GDSL in complex with substrate could provide insights into the binding mode of substrate towards inactive form of GDSL esterase (S12A) and identify the hot spot residues for the designing of a better binding pocket. Insight into molecular mechanisms is limited due to the lack of crystal structure of GDSL esterase-substrate complex. In this paper, the crystallization of mutant GDSL esterase (S12A) (PDB ID: 8HWO) and its complex with butyric acid (PDB ID: 8HWP) are reported. The optimized structure would be vital in determining hot spot residue for GDSL esterase. This preliminary study provides an understanding of the interactions between enzymes and hydrolysed p-nitro-phenyl butyrate. The information could guide in the rational design of GDSL esterase in overcoming the medical limitations associated with racemic mixture.
  19. Encapsulation of in vitro Plectranthus amboinicus (Lour.) Spreng. shoot apices for propagation and conservation
    Arumugam G, Sinniah UR, Swamy MK, Lynch PT
    3 Biotech, 2019 Aug;9(8):298.
    PMID: 31328080 DOI: 10.1007/s13205-019-1831-4
    This investigation demonstrates an efficient method of propagation, short-term conservation, and germplasm exchange for Plectranthus amboinicus (Lour.) Spreng. encapsulated propagules. In vitro-derived shoot apices (shoot tips and nodal segments) which showed 100% survival on MS medium supplemented with 0.4 mg/L 6-benzylaminopurine were selected for encapsulation studies. Shoot apices measuring about 3-5 mm in size showed the ability to break the beads and exhibited 100% survival and regrowth. The combination of 3% (w/v) sodium alginate and 100 mM CaCl2 was found to be ideal for forming uniformally spherical beads, and successive preservation of encapsulated shoot apices into plantlets. The encapsulated shoot tips were relatively more effective than the nodal segments in terms of shoot growth and multiplication. Encapsulated shoot tips retained the ability to regrow (63.3%) for up to 40 days when maintained at 4 °C. Encapsulated shoot tips effectively converted into plantlets on agar medium (78%) and peat moss (58%) under in vitro conditions. Encapsulated shoot tips on agar medium showed a higher shoot regeneration (9.91 ± 0.15 shoots per explant) ability than the peat moss (5.71 ± 0.34 shoots per explant), while the highest rooting (12.16 ± 0.23 roots per explant) was observed on peat moss. Thus, calcium alginate encapsulation holds latent qualities that could be explored to develop a future alternative method of propagation, short-term storage and germplasm distribution for elite genotypes of Plectranthus sp.
  20. In vitro and in silico cholinesterase inhibitory potential of metabolites from Laurencia snackeyi (Weber-van Bosse) M. Masuda
    Palaniveloo K, Ong KH, Satriawan H, Abdul Razak S, Suciati S, Hung HY, et al.
    3 Biotech, 2023 Oct;13(10):337.
    PMID: 37701628 DOI: 10.1007/s13205-023-03725-6
    Alzheimer's disease (AD) is a neurodegenerative disease that causes deterioration in intelligence and psychological activities. Yet, till today, no cure is available for AD. The marine environment is an important sink of bioactive compounds with neuroprotective potential with reduced adverse effects. Recently, we collected the red algae Laurencia snackeyi from Terumbu Island, Malaysia which is known to be rich in halogenated metabolites making it the most sought-after red algae for pharmaceutical studies. The red alga was identified based on basic morphological characteristics, microscopic observation and chemical data from literature. The purplish-brown algae was confirmed a new record. In Malaysia, this species is poorly documented in Peninsular Malaysia as compared to its eastern continent Borneo. Thus, this study intended to investigate the diversity of secondary metabolites present in the alga and its cholinesterase inhibiting potential for AD. The extract inhibited both acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) with IC50 values of  14.45 ± 0.34 μg mL-1 and 39.59 ± 0.24 μg mL-1, respectively. Subsequently, we isolated the synderanes, palisadin A (1), aplysistatin (2) and 5-acetoxypalisadin B (3) that was not exhibit potential. Mass spectrometry analysis detected at total of 33 additional metabolites. The computational aided molecular docking using the AChE and BChE receptors on all metabolites shortlisted 5,8,11,14-eicosatetraynoic acid (31) and 15-hydroxy-1-[2-(hydroxymethyl)-1-piperidinyl]prost-13-ene-1,9-dione (42) with best inhibitory properties, respectively with the lowest optimal combination of S-score and RMSD values. This study shows the unexplored potential of marine natural resources, however, obtaining sufficient biomass for detailed investigation is an uphill task. Regardless, there is a lot of potential for future prospects with a wide range of marine natural resources to study and the incorporation of synthetic chemistry, in vivo studies in experimental design.

    SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03725-6.

Related Terms
Filters
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links