Expression of scFv-anti-CHIKV-E2 in Escherichia coli with chaperones Co-expression, and its functional assay by electrochemical immunosensor

Single Chain Variable Fragment (scFv), a small fragment of antibody can be used to substitute the monoclonal antibody for diagnostic purposes. Production of scFv in Escherichia coli host has been a challenge due to the potential miss-folding and formation of inclusion bodies. This study aimed to express anti-CHIKV E2 scFv which previously designed specifically for Asian strains by co-expression of three chaperones that play a role in increasing protein solubility; GroEL, GroES, and Trigger Factor. The scFv and chaperones were expressed in Origami B E. coli host under the control of the T7 promoter, and purified using a Ni-NTA column. Functional assay of anti-CHIKV-E2 scFv was examined by electrochemical immunosensor using gold modified Screen Printed Carbon Electrode (SPCE), and characterized by differential pulses voltammetry (DPV) using K3[Fe(CN)6] redox system and scanning microscope electron (SEM). The experimental condition was optimized using the Box-Behnken design. The results showed that co-expression of chaperone increased the soluble scFv yield from 54.405 μg/mL to 220.097 µg/mL (~5×). Furthermore, scFv can be used to detect CHIKV-E2 in immunosensor electrochemistry with a detection limit of 0.74048 ng/mL and a quantification limit of 2,24388 ng/mL. Thus, the scFv-anti-CHIKV-E2 can be applied as a bioreceptor in another immunoassay method.

Analyzing the Impact of Physicochemical Factors on Chlorella vulgaris Growth Through Design of Experiment (DoE) for Carbon Capture System

The CO2 emission is increasing every year and threatening both humans and the ecosystem. Carbon capture technological innovations have emerged as a potential solution to mitigate this emissions. Due to its high capacity of photosynthetic activity, CO2 sequestration by microalgae, such as Chlorella vulgaris has attracted much attention as a carbon capture system. The growth of this microalgae is influenced by various physicochemical factors. By designing the Design of Experiment (DoE) with Response Surface Methodology (RSM), the effect of several independent factor can be evaluated to optimize Chlorella vulgaris growth condition and CO2 conversion. This study aims to identify the most impact factors affecting C. vulgaris growth through investigating the variations in physicochemical factors of aeration, initial pH, dark light regime, saline, and substrates concentration using DoE. In this study, C. vulgaris was cultivated in batch culture for 10 days with 8 experiments that were designed under various conditions as per experimental run. Biomass growth was observed using optical density and analyzed by first order regression. The result shows that aeration parameters was statistically significant affect microalgae growth, evidence by p-value below 0.05 at all observation points. Runs with aeration treatment showed a prolonged exponential growth phase and delayed onset of the deceleration phase. Additionally, this study also found that the initial pH level also significantly affects growth at the last day of cultivation. Cultures with a higher initial pH reached the stationary phase earlier than those with a lower pH. Thus, the growth of C. vulgaris can be optimized by adding aeration treatment into culture media and regulating initial pH around 8 to enhancing carbon fixation and biomass yield.

Accelerated molecular dynamics study to compare the thermostability of Bacillus licheniformis and Aspergillus niger α-amylase

The thermostability of enzymes plays a significant role in the starch hydrolysis process in the industry. The structural difference between thermostable Bacillus licheniformis α-amylase (BLA) and thermolabile Aspergillus niger α-amylase (ANA) is interesting to be explored. This work aimed to study the thermostability-determining factor of BLA as compared to a non-thermostable enzyme, ANA, using molecular dynamics (MD) simulation at a high temperature. A 100 ns of classical MD, which was followed by 200 ns accelerated MD was conducted to explore the conformational changes of the enzyme. It is revealed that the intramolecular interactions through salt bridge interactions and the presence of calcium ions dominates the stability effect of BLA, despite the absence of a disulfide bond in the structure. These results should be useful in designing a thermostable enzyme that can be used in industrial processes.Communicated by Ramaswamy H. Sarma.

Effect of Lactic Acid and pH of Probiotic Yogurt on Peak Production of Laying Hens

<b>Background and Objective:</b> Probiotic yogurt is beneficial for laying hens because it can improve the animal's hematological status which will improve livestock health, therefore it is hoped that probiotic yogurt can increase the production of laying hens. This research was conducted to determine the lactic acid levels and pH of probiotic yogurt, probiotic yogurt's effect on feed conversion ratio and total production of laying hens. <b>Materials and Methods:</b> The research was carried out using experimental methods using a Completely Randomized Design (CRD) with 5 treatments and 8 replications so the total sample was 40. The treatment consisted of P0: Basal ration; P1: Basal diet+2% probiotic powder B1 (<i>Bifidobacterium</i> spp. and <i>L. acidophilus</i>), P2: Basal ration+3% probiotic powder B1, P3: Basal diet+2% probiotic powder B2 (<i>L. bulgaricus</i>, <i>S. thermophilus</i>, <i>L. acidophilus</i> and <i>B. bifidum</i>) and P4: Basal ration+3% probiotic powder B2. The data were analyzed using Analysis of Variance (ANOVA) and followed by Duncan's Multiple Range Test. <b>Results:</b> Lactic acid content in probiotic yogurts B1 is 0.945% and B2 is 0.638%. Based on the results of statistical analysis using the variance test, show that giving probiotic powder to laying hens has a significant effect on the feed conversion ratio and has no significant effect on the production of laying hens. <b>Conclusion:</b> Based on the results of statistical analysis using the variance test, it shows that giving probiotic powder to laying hens has no significant effect on the production of laying hens during the peak period.

Theoretical and Experimental Studies on the Evidence of 1,3-β-Glucan in Marennine of Haslea ostrearia

Marennine, a blue pigment produced by the blue diatom Haslea ostrearia, is known to have some biological activities. This pigment is responsible for the greening of oysters on the West Coast of France. Other new species of blue diatom, H. karadagensis, H. silbo sp. inedit., H. provincialis sp. inedit, and H. nusantara, also produce marennine-like pigments with similar biological activities. Aside from being a potential source of natural blue pigments, H. ostrearia-like diatoms present a commercial potential for the aquaculture, food, cosmetics, and health industries. Unfortunately, for a hundred years, the exact molecular structure of this bioactive compound has remained a mystery. A lot of hypotheses regarding the chemical structure of marennine have been proposed. The recent discovery of this structure revealed that it is a macromolecule, mainly carbohydrates, with a complex composition. In this study, some glycoside hydrolases were used to digest marennine, and the products were further analyzed using nuclear magnetic resonance (NMR) and mass spectroscopy (MS). The reducing sugar assay showed that marennine was hydrolyzed only by endo-1,3-β-glucanase. Further insight into the structure of marennine was provided by the spectrum of 1H NMR, MS, a colorimetric assay, and a computational study, which suggest that the chemical structure of marennine contains 1,3-β-glucan.

Potential of Syzygnium polyanthum as Natural Food Preservative: A Review

Food preservation is one of the strategies taken to maintain the level of public health. Oxidation activity and microbial contamination are the primary causes of food spoilage. For health reasons, people prefer natural preservatives over synthetic ones. Syzygnium polyanthum is widely spread throughout Asia and is utilized as a spice by the community. S. polyanthum has been found to be rich in phenols, hydroquinones, tannins, and flavonoids, which are potential antioxidants and antimicrobial agents. Consequently, S. polyanthum presents a tremendous opportunity as a natural preservative. This paper reviews recent articles about S. polyanthum dating back to the year 2000. This review summarizes the findings of natural compounds presented in S. polyanthum and their functional properties as antioxidants, antimicrobial agents, and natural preservatives in various types of food.

Enhancement Methods of Antioxidant Capacity in Rice Bran: A Review

Rice (Oryza sativa L.) is a primary food that is widely consumed throughout the world, especially in Asian countries. The two main subspecies of rice are japonica and indica which are different in physical characteristics. In general, both indica and japonica rice consist of three types of grain colors, namely white, red, and black. Furthermore, rice and rice by-products contain secondary metabolites such as phenolic compounds, flavonoids, and tocopherols that have bioactivities such as antioxidants, antimicrobial, cancer chemopreventive, antidiabetic, and hypolipidemic agents. The existence of health benefits in rice bran, especially as antioxidants, gives rice bran the opportunity to be used as a functional food. Most of the bioactive compounds in plants are found in bound form with cell wall components such as cellulose and lignin. The process of releasing bonds between bioactive components and cell wall components in rice bran can increase the antioxidant capacity. Fermentation and treatment with enzymes were able to increase the total phenolic content, total flavonoids, tocotrienols, tocopherols, and γ-oryzanol in rice bran.

Resistance of Nilaparvata lugens to Fenobucarb and Imidacloprid and Susceptibility to Neem Oil Insecticides

This study aims to monitor and determine the level of resistance of N. lugens to fenobucarb and imidacloprid, to analyse of the specific activities of asetylcholinesterase, Glutation S-Transferase, esterase, and to determine sensitivity of resistant N. lugens to the neem oil. Resistance tests were conducted on a field population from Cipunagara, Subang, West Java, Indonesia, and a standard population originating from Banyuwangi, East Java, that was obtained from the Indonesian Center for Rice Research. Synthetic and neem Insecticides were applied using the leaf-stem dipping method. The resistance ratio obtained by comparing the LC50 value of the field population with the standard. The test insects were considered to be resistant to synthetic insecticide if they had a resistance ratio (RR) of more than 4, indicated resistance if RR ≥1, and susceptible to neem if has RR <1. The results of the research showed that the N. lugens population of Cipunagara indicated resistance to fenobucarb (RR = 2.43), while it was clearly resistance to imidacloprid (RR = 13.95). Specific activities of the acetylcholinesterase and Glutathione S-Transferase of the N. lugens Cipunagara populations were higher than the standard, while the esterase specific activity was lower. These two enzymes are responsible for the resistance of N. lugens to fenobucarb and imidacloprid. Nevertheless, the N. lugens population of Cipunagara was susceptible to neem (RR <1) that never been reported before. Therefore, it is important to know the change in the sensitivity of the target and the metabolic pathway of the insecticide used to manage insect resistance.

Optimisation of Zinc Oxide Nanoparticle Biosynthesis Using Saccharomyces Cerevisiae with Box-Behnken Design

Zinc oxide nanoparticles have wide applications as catalysts, antimicrobial agents, drug delivery agents, etc. because of their intrinsic properties. Various methods can be applied to synthesise nanoparticles, one of which is the biosynthesis process. Biosynthesis is more eco-friendly than chemical and physical methods. In the present study, the optimisation of zinc oxide nanoparticle biosynthesis using the yeast Saccharomyces cerevisiae was performed by applying a response surface method called the Box�Behnken design (BBD). Three factors were optimised in the present study, namely the concentration of zinc acetate as the precursor (X1), concentration of the S. cerevisiae fermentation broth (X2), and the incubation time (X3). The mass of zinc oxide nanoparticles (Y) was recorded as the response of the experiment. The product was then characterised by fourier transform infrared spectroscopy (FTIR), X-Ray diffraction (XRD), scanning electron microscopy/energy dispersive spectroscopy (SEM/EDS), and particle size analyser (PSA). The optimum conditions for the preparation of zinc oxide nanoparticles were found to be 0.3 M, 100% (v/v), and 24 h as the zinc acetate concentration, medium concentration, and incubation time, respectively. The FTIR analysis showed peaks at ~600 cm−1, which is characteristic for ZnO stretching. From the XRD result, the ZnO nanoparticles with hexagonal structure was confirm. The SEM/EDS analysis confirmed that the morphology was spherical and showed the major energy emission for zinc and oxygen. Moreover, the PSA analysis revealed that the smallest size was 218.6 nm (12%) when the synthesis was performed at the optimum conditions, while when the incubation time was prolonged for 120 h, the size decreased to 134.2 nm.

Optimization of Voltammetric Determination of Dysprosium (III) Using Plackett-Burman and RSM-CCD Experimental Designs

This study was aimed to develop an optimized Dy determination method using differential pulse voltammetry (DPV). The Plackett-Burman (PB) experimental design was used to select significant factors that affect the electrical current response, which were further optimized using the response surface method-central composite design (RSM-CCD). The type of electrolyte solution and amplitude modulation were found as two most significant factors, among the nine factors tested, which enhance the current response based on PB design. Further optimization using RSM-CCD shows that the optimum values for the two factors were 0.1046 M and 0.1082 V respectively. When the optimum conditions were applied for Dy determination good recovery and precision were achieved with values of 91.58%, and 99.80%, respectively. The detection limit and quantification limit of the method were 1.4322 mg/L and of 4.7741 mg/L, respectively.

Molecular dynamics study to improve the substrate adsorption of Saccharomycopsis fibuligera R64 alpha-amylase by designing a new surface binding site

Background: Carbohydrate binding module (CBM) and surface binding site (SBS) are two important parts of amylase which respond to the raw starch digestion. They are related to the enzyme ability to adsorb and to catalyze the starch hydrolysis. However, starch processing is still expensive due to the high temperature in the gelatinization step. Therefore, direct starch digestion is more favorable. One of the solutions is to use α-amylase with high starch adsorptivity, which is expected to be capable of digesting starch below the gelatinization temperature. In Indonesia, Saccharomycopsis fibuligera R64 α-amylase (Sfamy R64) is one of the enzymes with the highest activity on starch. However, its raw starch adsorptivity was low. The aim of this study was to propose an in-silico model of Sfamy R64 mutant by introducing a new SBS using molecular dynamics (MD) simulation.

Methods: The structural behavior of Sfamy R64 and positive control were studied using MD simulation. Furthermore, the mutants of Sfamy R64 were designed to have a stable SBS which mimics the positive control. The substrate affinity in all systems was evaluated using the molecular mechanics generalized Born surface area (MM/GBSA) method.

Results: The stability of a new SBS constructed by seven substitutions and a loop insertion was improved throughout MD simulation. The substrate was consistently bound to the SBS over 55 ns of simulation, as compared to 14 ns in wild-type. The structural behavior of SBS in mutant and positive control was similar. The interaction energies of the positive control, wild-type, and mutant were −17.6, −5.2, and −8.2 kcal/mol, respectively.

Conclusion: The enhanced substrate binding in the mutant, due to the existence of a new SBS, suggests the potential of improving starch adsorptivity of Sfamy R64. This result should be useful in developing an enzyme with better substrate adsorption based on the rational computer-aided molecular design approach.

Computational Model of the Effect of a Surface-Binding Site on the Saccharomycopsis fibuligera R64 α-Amylase to the Substrate Adsorption

α-Amylase is one of the important enzymes in the starch-processing industry. However, starch processing requires high temperature, thus resulting in high cost. The high adsorptivity of α-amylase to the substrate allows this enzyme to digest the starch at a lower temperature. α-Amylase from Saccharomycopsis fibuligera R64 (Sfamy R64), a locally sourced enzyme from Indonesia, has a high amylolytic activity but low starch adsorptivity. The objective of this study was to design a computational model of Sfamy R64 with increased starch adsorptivity using bioinformatics method. The model structure of Sfamy R64 was compared with the positive control, ie, Aspergillus niger α-amylase. The structural comparison showed that Sfamy R64 lacks the surface-binding site (SBS). An SBS was introduced to the structure of Sfamy R64 by S383Y/S386W mutations. The dynamics and binding affinity of the SBS of mutant to the substrate were also improved and comparable with that of the positive control.

Expression of Recombinant Antibody Fragment, Anti BNP-SCFV on the Periplasm of Escherichia Coli for the Detection of Heart Failure

Basic natriuretic peptide (BNP) is a polypeptide hormone consist of 32 amino acids that secreted by the heart ventricle to respond the excessive stretching of heart muscle cells. BNP can be used as prognostic marker for patients with heart failure. The presence of BNP in blood can be detected by BNP antibody, which is anti BNP-single chain variable fragment (Anti BNP-SCFV). The antibody is a combination of polypeptides between varying region on the heavy chain (VH) and the light chain (VL) of immunoglobulin. Anti BNP-SCFV will bind to BNP through the antigen-antibody interaction. Concentration of BNP in a patient’s blood can be detected through the interaction of BNP with Anti BNP-SCFV using immunosensor method. Production of recombinant Anti BNP-SCFV in Escherichia coli as host is reported in the present study. Anti BNP-SCFV was expressed in fusion form with OmpC signal peptide that direct the protein to a periplasmic space. Expression was performed under RhaBad promoter as control using L-rhamnose as inducer. SDS-PAGE characterization showed consistent band at 28 kDa, which was assumed as Anti BNP-SCFV. The optimum expression was found at four hours after induction with 4 mM inducer. Anti BNP-SCFV was secreted from the cell as characterized by the presence of the protein on periplasmic membrane and extracellular fraction.

EVALUASI PENGGUNAAN METILEN BIRU SEBAGAI MEDIATOR ELEKTRON PADA MICROBIAL FUEL CELL DENGAN BIOKATALIS ACETOBACTER ACETI

Microbial fuel cell (MFC) merupakan salah satu teknologi sel bahan bakar alternatif yang dapat diperbarui. MFC memanfaatkan proses oksidasi senyawa kimia oleh biokatalis untuk menghasilkan energi listrik daya rendah. Tujuan dari penelitian ini adalah mengetahui kinerja MFC dengan dan tanpa mediator elektron metilen biru (MB) menggunakan biokatalis Acetobacter aceti dan substrat glukosa agar diperoleh energi listrik. Metode yang dilakukan adalah peremajaan kultur A. aceti, persiapan inokulum, persiapan reaktor MFC, persiapan media MFC dengan substrat glukosa 2% dengan dan tanpa mediator MB, pencuplikan secara periodik, penentuan kurva pertumbuhan, arus, potensial, kerapatan daya, energi, kadar glukosa dan tingkat keasaman (pH). Hasil penelitian menunjukkan bahwa MFC dengan mediator menghasilkan kuat arus sebesar 0,040 mA, potensial 878 mV, kerapatan daya 0,395 mW/cm2, energi maksimum 3,685 kJ, pemanfaatan glukosa 93,02% dan pH akhir 3,33, sedangkan MFC tanpa mediator menghasilkan kuat arus 0,035 mA, potensial 773 mV, kerapatan daya 0,290 mW/cm2, energi maksimum 2,434 kJ, pemanfaatan glukosa 90,16% dan pH akhir 3,24. Perolehan kerapatan daya pada kedua jenis MFC masih tergolong kecil dan tidak berbeda secara signifikan. Berdasarkan hasil penelitian dapat disimpulkan bahwa penggunaan mediator MB hanya berpengaruh terhadap perolehan potensial pada MFC dengan kondisi perlakuan yang diterapkan dalam penelitian ini.