Purification of RNA fragments from a complex mixture is a very common technique, and requires consideration of the time, cost, purity and yield of the purified RNA fragments. This study describes the fastest method of purifying small RNA with the lowest cost possible, without compromizing the yield and purity. The technique describes the purification of small RNA from polyacrylamide gel, resulting in a good yield of small RNA with minimum experimental steps in avoiding degradation of the RNA, obviating the use of ethidium bromide and phenol-chloroform extraction, as well as siliconized glass wools to remove the polyacrylamide gel particles. The purified small RNA is suitable for a wide variety of applications such as ligation, end labelling with radio isotope, RT-PCR (Reverse Transcriptase-PCR), Northern blotting, experimental RNomics study and also Systematic Evolution of Ligands by Exponential Enrichment (SELEX).
A locally isolated Acinetobacter sp. Strain AQ5NOL 1 was encapsulated in gellan gum and its ability to degrade phenol was compared with the free cells. Optimal phenol degradation was achieved at gellan gum concentration of 0.75% (w/v), bead size of 3 mm diameter (estimated surface area of 28.26 mm(2)) and bead number of 300 per 100 ml medium. At phenol concentration of 100 mg l(-1), both free and immobilized bacteria exhibited similar rates of phenol degradation but at higher phenol concentrations, the immobilized bacteria exhibited a higher rate of degradation of phenol. The immobilized cells completely degrade phenol within 108, 216 and 240 h at 1,100, 1,500 and 1,900 mg l(-1) phenol, respectively, whereas free cells took 240 h to completely degrade phenol at 1,100 mg l(-1). However, the free cells were unable to completely degrade phenol at higher concentrations. Overall, the rates of phenol degradation by both immobilized and free bacteria decreased gradually as the phenol concentration was increased. The immobilized cells showed no loss in phenol degrading activity after being used repeatedly for 45 cycles of 18 h cycle. However, phenol degrading activity of the immobilized bacteria experienced 10 and 38% losses after the 46 and 47th cycles, respectively. The study has shown an increased efficiency of phenol degradation when the cells are encapsulated in gellan gum.
This article presents the abilities and efficiencies of five different strains of Agrobacterium rhizogenes (strain ATCC 31798, ATCC 43057, AR12, A4 and A13) to induce hairy roots on Solanum mammosum through genetic transformation. There is significant difference in the transformation efficiency (average number of days of hairy root induction) and transformation frequency for all strains of A. rhizogenes (P < 0.05). Both A. rhizogenes strain AR12 and A13 were able to induce hairy root at 6 days of co-cultivation, which were the fastest among those tested. However, the transformation frequencies of all five strains were below 30 %, with A. rhizogenes strain A4 and A13 showing the highest, which were 21.41 ± 10.60 % and 21.43 ± 8.13 % respectively. Subsequently, the cultures for five different hairy root lines generated by five different strains of bacteria were established. However, different hairy root lines showed different growth index under the same culture condition, with the hairy root lines induced by A. rhizogenes strain ATCC 31798 exhibited largest increase in fresh biomass at 45 days of culture under 16 h light/8 h dark photoperiod in half-strength MS medium. The slowest growing hairy root line, which was previously induced by A. rhizogenes strain A13, when cultured in optimized half-strength MS medium containing 1.5 times the standard amount of ammonium nitrate and potassium nitrate and 5 % (w/v) sucrose, had exhibited improvement in growth index, that is, the fresh biomass was almost double as compared to its initial growth in unmodified half-strength MS medium.
The simultaneous production of hydrogen and ethanol by microorganisms from waste materials in a bioreactor system would establish cost-effective and time-saving biofuel production. This review aims to present the current status of fermentation processes producing hydrogen accompanied by ethanol as a co-product. We outlined the microbes used and their fundamental pathways for hydrogen and ethanol fermentation. Moreover, we discussed the exploitation of renewable and sustainable waste materials as promising feedstock and the limitations encountered. The low substrate bioconversion rate in hydrogen and ethanol co-production is regarded as the primary constraint towards the development of large scale applications. Thus, microbes with an enhanced capability have been generated via genetic manipulation to diminish the inefficiency of substrate consumption. In this review, other potential approaches to improve the performance of co-production through fermentation were also elaborated. This review will be a useful guide for the future development of hydrogen and ethanol co-production using waste materials.
To explore new approaches of phage-based bio-process of specifically pathogenic Escherichia coli bacteria in food products within a short period. One hundred and forty highly lytic designed coliphages were used. Escherichia coli naturally contaminated and Enterohemorrhagic Escherichia coli experimentally inoculated samples of lettuce, cabbage, meat, and egg were used. In addition, experimentally produced biofilms of E. coli were tested. A phage concentration of 10(3) PFU/ml was used for food products immersion, and for spraying of food products, 10(5) PFU/ml of a phage cocktail was used by applying a 20-s optimal dipping time in a phage cocktail. Food samples were cut into pieces and were either sprayed with or held in a bag immersed in lambda buffer containing a cocktail of 140 phages. Phage bio-processing was successful in eliminating completely E. coli in all processed samples after 48 h storage at 4°C. Partial elimination of E. coli was observed in earlier storage periods (7 and 18 h) at 24° and 37°C. Moreover, E. coli biofilms were reduced >3 log cycles upon using the current phage bio-processing. The use of a phage cocktail of 140 highly lytic designed phages proved highly effective in suppressing E. coli contaminating food products. Proper decontamination/prevention methods of pathogenic E. coli achieved in this study can replace the current chemically less effective decontamination methods.
This preliminary study aimed to identify a commercial gamat species, Stichopus horrens Selenka, 1867, and a timun laut species, Holothuria (Mertensiothuria) leucospilota (Brandt, 1835), from Pangkor Island, Perak, Malaysia, employing morphological techniques based on the shape of the ossicles and molecular techniques based on the cytochrome c oxidase I (COI) mitochondrial DNA (mtDNA) gene. In Malaysia, a gamat is defined as a sea cucumber species of the family Stichopodidae with medicinal value, and timun laut refers to non-gamat species. S. horrens is very popular on Pangkor Island as a main ingredient in the traditional production of air gamat and minyak gamat, while H. leucospilota is the most abundant species in Malaysia. In contrast to previous studies, internal body parts (the respiratory tree and gastrointestine) were examined in this study to obtain better inferences based on morphology. The results showed that there were no ossicles present in the gastrointestine of H. leucospilota, and this characteristic is suggested as a unique diagnostic marker for the timun laut species. In addition, the presence of Y-shaped rods in the respiratory tree of S. horrens subsequently supported the potential to use internal body parts to identify the gamat species. Phylogenetic analysis of the COI mtDNA gene of the sea cucumber specimens using the neighbour-joining method and maximum likelihood methods further confirmed the species status of H. leucospilota and S. horrens from Pangkor Island, Perak, Malaysia. The COI mtDNA gene sequences were registered with GenBank, National Center for Biotechnology Information (NCBI), US National Library of Medicine (GenBank accession no.: KC405565-KC405568). Although additional specimens from various localities will be required to produce more conclusive results, the current findings provide better insight into the importance of complementary approaches involving morphological and molecular techniques in the identification of the two Malaysian sea cucumber species.
Staphylococcus kloosii, an orange pigment-producing bacterium, was isolated from the respiratory tree of Holothuria (Mertensiothuria) leucospilota (Brandt 1835) from Teluk Nipah, Pangkor Island, Perak, Malaysia. This report is the first documentation of this Gram-positive strain, referred to as Strain 68 in Malaysia. A partial 16S ribosomal RNA gene sequence of the mesophilic strain has been registered with GenBank (National Center for Biotechnology Information, US National Library of Medicine) with accession number JX102547. Phylogenetic analysis using the neighbour-joining method further supported the identification of Strain 68 as S. kloosii. The circular strain produced orange pigments on tryptone glucose yeast extract agar (TGYEA) and in nutrient broth (NB) at approximately pH 7. The visible spectra of ethanolic and methanolic pigment extracts of the bacterial strain were considered identical with λmax at 426, 447 and 475 nm and λmax at 426, 445 and 473 nm, respectively. Both visible spectra resemble the visible spectra of lutein, which is a commercial carotenoid; however, further analyses are required to confirm the identity of this pigment. The methanolic extracts of the intracellular pigments comprised at least three pigment compounds: an orange pigment compound (major compound), a yellow pigment compound (the least polar) and a pink pigment compound (the most polar). These findings are the first documentation of the pigment composition of S. kloosii as no such record could be found to date.
This study is focused towards developing a global consensus sequence of nonstructural protein 2 (NSP2), a protease of Chikungunya Virus (CHIKV) and predict immunogenic promiscuous T-cell epitopes based on various bioinformatics tools. To date, no epitope data is available for the Chikungunya virus in the IEDB database. In this study, 100 available nucleotide sequences of NSP2-CHIKV belonging to different strains were downloaded from the National Centre for Biotechnology Information (NCBI) database. The nucleotide sequences were subjected to translated sequencing using the EXPASY tool followed by protein alignment using the CLC workbench and a global consensus sequence for the respective protein was developed. IEDB tool was used to predict HLA-I and HLA-II binding promiscuous epitopes from the consensus sequence of NSP2-CHIKV. Thirty-four B-cell based epitopes are predicted and the promiscuous epitope is VVDTTGSTKPDPGD at position 341-354. Twenty-six MHC-I short peptide epitopes are predicted to bind with HLA-A. The promiscuous epitopes predicted to bind with HLA-A*01:01 are VTAIVSSLHY, SLSESATMVY, FSKPLVYY, QPTDHVVGEY at positions 317-326, 84-93, 535-544 and 15-24 with percentile ranks 0.17, 0.39, 0.51 and 0.81, respectively. Twenty-four MHC-II short peptide epitopes are predicted for HLA-DRB. The promiscuous epitope predicted to bind with HLA-DRB*01:01 is VVGEYLVLSPQTVLRS from 20-35 with a lowest percentile rank of 0.01. These predicted epitopes can be effective targets towards development of vaccine against CHIKV. Epitopes predicted in this study displayed good binding affinity, antigenicity and promiscuity for the HLA classes. These predicted epitopes can prove to be translationally important towards the development of CHIKV.
Given their advantages of high photosynthetic efficiency and non-competition with land-based crops, algae, that are carbon-hungry and sunlight-driven microbial factories, are a promising solution to resolve energy crisis, food security, and pollution problems. The ability to recycle nutrient and CO2 fixation from waste sources makes algae a valuable feedstock for biofuels, food and feeds, biochemicals, and biomaterials. Innovative technologies such as the bicarbonate-based integrated carbon capture and algae production system (BICCAPS), integrated algal bioenergy carbon capture and storage (BECCS), as well as ocean macroalgal afforestation (OMA), can be used to realize a low-carbon algal bioeconomy. We review how algae can be applied in the framework of integrated low-carbon circular bioeconomy models, focusing on sustainable biofuels, low-carbon feedstocks, carbon capture, and advances in algal biotechnology.
Excessive carbon dioxide (CO2) emissions into the atmosphere have become a dire threat to the human race and environmental sustainability. The ultimate goal of net zero emissions requires combined efforts on CO2 sequestration (natural sinks, biomass fixation, engineered approaches) and reduction in CO2 emissions while delivering economic growth (CO2 valorization for a circular carbon bioeconomy, CCE). We discuss microalgae-based CO2 biosequestration, including flue gas cultivation, biotechnological approaches for enhanced CO2 biosequestration, technological innovations for microalgal cultivation, and CO2 valorization/biofuel productions. We highlight challenges to current practices and future perspectives with the goal of contributing to environmental sustainability, net zero emissions, and the CCE.
In this study, the methanolysis process of sunflower oil was investigated to get high methyl esters (biodiesel) content using sodium methoxide. To reach to the best process conditions, central composite design (CCD) through response surface methodology (RSM) was employed. The optimal conditions predicted were the reaction time of 60 min, an excess stoichiometric amount of alcohol to oil ratio of 25%w/w and the catalyst content of 0.5%w/w, which lead to the highest methyl ester content (100%w/w). The methyl ester content of the mixture from gas chromatography analysis (GC) was compared to that of optimum point. Results, confirmed that there was no significant difference between the fatty acid methyl ester content of sunflower oil produced under the optimized condition and the experimental value (P ≥ 0.05). Furthermore, some fuel specifications of the resultant biodiesel were tested according to American standards for testing of materials (ASTM) methods. The outcome showed that the methyl ester mixture produced from the optimized condition met nearly most of the important biodiesel specifications recommended in ASTM D 6751 requirements. Thus, the sunflower oil methyl esters resulted from this study could be a suitable alternative for petrol diesels.
Biotechnological tools are being used in malaria, filariasis and dengue research. The main emphasis has been on the production of reagents for immunodiagnosis and research. In this respect monoclonal antibodies (McAbs) against various species and stages of the above pathogens have been produced. It is hoped that these McAbs will be useful not only in immunodiagnosis but also for seroepidemiological applications. A DNA probe against Brugia malayi has been tested in Malaysia and was found to be sensitive and specific.
There are essentially no reports on the use of modern biotechnological methods on the study of cestode parasites in the Philippines, Indonesia or Malaysia. The only recent reports of cestode studies in these countries have been on reports of new species in animals and on prevalence rates of cestode parasites in humans; Taenia solium and cysticercosis, Taenia saginata and Hymenolepis nana, etc. Reports on the use of biotechnology has emanated from outside the area on cestodes of humans and animals, and some of these methods could be used to study cestodes in this part of the world.
Red seaweeds (Rhodophyta) produce a variety of sulfated galactans in their cell wall matrix and intercellular space, contributing up to 50-60 % of their total dry weight. These sulfated polysaccharides are made up of galactose disaccharides substituted with sulfate, methoxyl, pyruvic acid, or non-galactose monosaccharides (e.g. xylose, glucose and mannose). They are required by the Rhodophytes for protection against pathogen, desiccation, tidal waves and extreme changes in pH, temperature and salinity. Since ancient times, sulfated galactans from red seaweeds, such as agar and carrageenan, have been consumed as human foods and later being used in traditional medicine. Nowadays, some red seaweeds are cultivated and exploited for commercial uses in various fields. In this review, different types of sulfated galactans found in red seaweeds and their current and potential uses in food, biotechnology, medical and pharmaceutical industries are discussed.
The coronavirus disease 2019 (COVID-19) pandemic is severe and has not shown any signs of warning up to today. Biotech companies around the world have raced to come up with an acceptable vaccine and recently two mRNA vaccines have received emergency usage authorisation from regulatory bodies in several countries. mRNA vaccines, which consist of a new and revolutionary technology have not been previously tested widely on humans. Medium- and long-term safety data are not available. While many experts seem to support the start of a mass vaccination campaign, others feel there are too many unknowns to embark on a mass vaccination campaign. Concerns include uncertainties about the long-term effects of foreign mRNA on human cellular physiology and the possibility of vaccine-enhanced disease severity, which may not be unlikely with the current disease presentation of COVID-19.
A biosurfactant-producing and hydrocarbon-utilizing bacterium, Pseudomonas aeruginosa USM-AR2, was used to assist conventional distillation. Batch cultivation in a bioreactor gave a biomass of 9.4 g L(-1) and rhamnolipid concentration of 2.4 g L(-1) achieved after 72 h. Biosurfactant activity (rhamnolipid) was detected by the orcinol assay, emulsification index and drop collapse test. Pretreatment of crude oil TK-1 and AG-2 with a culture of P. aeruginosa USM-AR2 that contains rhamnolipid was proven to facilitate the distillation process by reducing the duration without reducing the quality of petroleum distillate. It showed a potential in reducing the duration of the distillation process, with at least 2- to 3-fold decreases in distillation time. This is supported by GC-MS analysis of the distillate where there was no difference between compounds detected in distillate obtained from treated or untreated crude oil. Calorimetric tests showed the calorie value of the distillate remained the same with or without treatment. These two factors confirmed that the quality of the distillate was not compromised and the incubation process by the microbial culture did not over-degrade the oil. The rhamnolipid produced by this culture was the main factor that enhanced the distillation performance, which is related to the emulsification of hydrocarbon chains in the crude oil. This biotreatment may play an important role to improve the existing conventional refinery and distillation process. Reducing the distillation times by pretreating the crude oil with a natural biosynthetic product translates to energy and cost savings in producing petroleum products.
The development of molecularly imprinted polymer nanoparticles (MIP-NPs), which specifically bind biomolecules, is of great interest in the area of biosensors, sample purification, therapeutic agents and biotechnology. Polymerisation techniques such as precipitation polymerisation, solid phase synthesis and core shell surface imprinting have allowed for significant improvements to be made in developing MIP-NPs which specifically recognise proteins. However, the development of MIP-NPs for protein templates (targets) still require lengthy optimisation and characterisation using different ratios of monomers in order to control their size, binding affinity and specificity. In this work we successfully demonstrated that differential scanning fluorimetry (DSF) can be used to rapidly determine the optimum imprinting conditions and monomer composition required for MIP-NP design and polymerisation. This is based on the stability of the protein template and shift in apparent melting points (Tm) upon interaction with different functional acrylic monomers. The method allows for the characterisation of molecularly imprinted nanoparticles (MIP-NPs) due to the observed differences in melting point profiles between, protein-MIP-NPs complexes, pre-polymerisation mixtures and non-imprinted nanoparticles (NIP-NPs) without the need for prior purification. The technique is simple, rapid and can be carried out on most quantitative polymerase chain reaction (qPCR) thermal cyclers which have the required filters for SYPRO
Conference abstracts: Malaysia in affiliation
(1). PO-211. AGE-SPECIFIC STRESS-MODULATED
CHANGES OF SPLENIC IMMUNOARCHITECTURE
IN THE GROWING BODY. Marina Yurievna Kapitonova, Syed Baharom Syed Ahmad Fuad, Flossie Jayakaran; Faculty of Medicine, Universiti Teknologi MARA, Shah Alam, Malaysia
syedbaharom@salam.uitm.edu.my
(2). PO-213. A DETAILED OSTEOLOGICAL STUDY OF THE ANOMALOUS GROOVES NEAR THE
MASTOID NOTCH OF THE SKULL. ISrijit Das, 2Normadiah Kassim, lAzian Latiff, IFarihah Suhaimi, INorzana Ghafar, lKhin Pa Pa Hlaing, lIsraa Maatoq, IFaizah Othman; I Department of Anatomy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia; 2 Department of Anatomy, Universiti Malaya, Kuala Lumpur, Malaysia. das_sri jit23@rediffmail.com
(3). PO-21S. FIRST LUMBRICAL MUSCLE OF THE
PALM: A DETAILED ANATOMICAL STUDY WITH
CLINICAL IMPLICATIONS. Srijit Das, Azian Latiff, Parihah Suhaimi, Norzana Ghafar, Khin Pa Pa Hlaing, Israa Maatoq, Paizah Othman; Department of Anatomy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia. das_srijit23@rediffmail.com
(4). PO-336. IMPROVEMENT IN EXPERIMENTALLY
INDUCED INFRACTED CARDIAC FUNCTION
FOLLOWING TRANSPLANTATION OF HUMAN
UMBILICAL CORD MATRIX-DERIVED
MESENCHYMAL CELLS. lSeyed Noureddin Nematollahi-Mahani, lMastafa Latifpour, 2Masood Deilami, 3Behzad Soroure-Azimzadeh, lSeyed
Hasan Eftekharvaghefi, 4Fatemeh Nabipour, 5Hamid
Najafipour, 6Nouzar Nakhaee, 7Mohammad Yaghoobi, 8Rana Eftekharvaghefi, 9Parvin Salehinejad, IOHasan Azizi; 1 Department of Anatomy, Kerman University of Medical Sciences, Kerman, Iran; 2 Department of Cardiosurgery, Hazrat-e Zahra Hospital, Kerman, Iran; 3 Department of Cardiology, Kerman University of Medical Sciences, Kerman, Iran; 4 Department of Pathology, Kerman University of Medical Sciences, Kerman, Iran; 5 Department of Physiology, Kerman University of Medical Sciences, Kerman, Iran; 6 Department of Neuroscience Research Center, Kerman University of Medical Sciences, Kerman, Iran; 7 Department
of Biotechnology, Research Institute of Environmental Science, International Center for Science, High Technology & Environmental Science, Kerman, Iran; 8 Students Research Center, Kerman University of Medical Sciences, Kerman, Iran; 9 Institute of Bioscience, University Putra Malaysia,
Kuala Lumpur, Malaysia; 10 Department of Stem Cell, Cell Science Research Center, Royan Institute, ACECR, Tehran, Iran. nnematollahi@kmu.ac.ir
(5).
Simultaneous saccharification and fermentation (SSF) with delayed yeast extract feeding (DYEF) was conducted in a 2-L bioreactor equipped with in-situ recovery using a gas stripping in order to enhance biobutanol production from lignocellulosic biomass of oil palm empty fruit bunch (OPEFB). This study showed that 2.88 g/L of biobutanol has been produced from SSF with a similar yield of 0.23 g/g as compared to separate hydrolysis and fermentation (SHF). An increase of 42% of biobutanol concentration was observed when DYEF was introduced in the SSF at 39 h of fermentation operation. Biobutanol production was further enhanced up to 11% with a total improvement of 72% when in-situ recovery using a gas stripping was implemented to reduce the solvents inhibition in the bioreactor. In overall, DYEF and in-situ recovery were able to enhance biobutanol production in SSF.