Search results for: dietary protein

Authors: Fabio Fabris, Alex A. Freitas

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Hierarchical classification is a special type of classification task where the class labels are organised into a hierarchy, with more generic class labels being ancestors of more specific ones. Meta-learning for classification-algorithm recommendation consists of recommending to the user a classification algorithm, from a pool of candidate algorithms, for a dataset, based on the past performance of the candidate algorithms in other datasets. Meta-learning is normally used in conventional, non-hierarchical classification. By contrast, this paper proposes a meta-learning approach for more challenging task of hierarchical classification, and evaluates it in a large number of bioinformatics datasets. Hierarchical classification is especially relevant for bioinformatics problems, as protein and gene functions tend to be organised into a hierarchy of class labels. This work proposes meta-learning approach for recommending the best hierarchical classification algorithm to a hierarchical classification dataset. This work’s contributions are: 1) proposing an algorithm for splitting hierarchical datasets into new datasets to increase the number of meta-instances, 2) proposing meta-features for hierarchical classification, and 3) interpreting decision-tree meta-models for hierarchical classification algorithm recommendation.

Keywords: algorithm recommendation, meta-learning, bioinformatics, hierarchical classification

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Authors: N. Othman, J. Ujang, M. N. Ismail, R. Noordin, B. H. Lim

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Amoebiasis is caused by the Entamoeba histolytica and still endemic in many parts of the tropical region, worldwide. Currently, there is no available vaccine against amoebiasis. Hence, there is an urgent need to develop a vaccine. The excretory secretory antigen (ESA) of E. histolytica is a suitable biomarker for the vaccine candidate since it can modulate the host immune response. Hence, the objective of this study is to identify the proteome of the ESA towards finding suitable biomarker for the vaccine candidate. The non-gel based and gel-based proteomics analyses were performed to identify proteins. Two kinds of mass spectrometry with different ionization systems were utilized i.e. LC-MS/MS (ESI) and MALDI-TOF/TOF. Then, the functional proteins classification analysis was performed using PANTHER software. Combination of the LC -MS/MS for the non-gel based and MALDI-TOF/TOF for the gel-based approaches identified a total of 273 proteins from the ESA. Both systems identified 29 similar proteins whereby 239 and 5 more proteins were identified by LC-MS/MS and MALDI-TOF/TOF, respectively. Functional classification analysis showed the majority of proteins involved in the metabolic process (24%), primary metabolic process (19%) and protein metabolic process (10%). Thus, this study has revealed the proteome the E. histolytica ESA and the identified proteins merit further investigations as a vaccine candidate.

Keywords: E. histolytica, ESA, proteomics, biomarker

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Authors: Saleh Gorji, Sahil Gulati, Ana Pakzad

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Continuous electron diffraction tomography, also known as microcrystal electron diffraction (MicroED) or three-dimensional electron diffraction (3DED), is a powerful technique, which in combination with cryo-electron microscopy (cryo-ED), can provide atomic-scale 3D information about the crystal structure and composition of different classes of crystalline materials such as proteins, peptides, and small molecules. Unlike the well-established X-ray crystallography method, 3DED does not require large single crystals and can collect accurate electron diffraction data from crystals as small as 50 – 100 nm. This is a critical advantage as growing larger crystals, as required by X-ray crystallography methods, is often very difficult, time-consuming, and expensive. In most cases, specimens studied via 3DED method are electron beam sensitive, which means there is a limitation on the maximum amount of electron dose one can use to collect the required data for a high-resolution structure determination. Therefore, collecting data using a conventional scintillator-based fiber coupled camera brings additional challenges. This is because of the inherent noise introduced during the electron-to-photon conversion in the scintillator and transfer of light via the fibers to the sensor, which results in a poor signal-to-noise ratio and requires a relatively higher and commonly specimen-damaging electron dose rates, especially for protein crystals. As in other cryo-EM techniques, damage to the specimen can be mitigated if a direct detection camera is used which provides a high signal-to-noise ratio at low electron doses. In this work, we have used two classes of such detectors from Gatan, namely the K3® camera (a monolithic active pixel sensor) and Stela™ (that utilizes DECTRIS hybrid-pixel technology), to address this problem. The K3 is an electron counting detector optimized for low-dose applications (like structural biology cryo-EM), and Stela is also a counting electron detector but optimized for diffraction applications with high speed and high dynamic range. Lastly, data collection workflows, including crystal screening, microscope optics setup (for imaging and diffraction), stage height adjustment at each crystal position, and tomogram acquisition, can be one of the other challenges of the 3DED technique. Traditionally this has been all done manually or in a partly automated fashion using open-source software and scripting, requiring long hours on the microscope (extra cost) and extensive user interaction with the system. We have recently introduced Latitude® D in DigitalMicrograph® software, which is compatible with all pre- and post-energy-filter Gatan cameras and enables 3DED data acquisition in an automated and optimized fashion. Higher quality 3DED data enables structure determination with higher confidence, while automated workflows allow these to be completed considerably faster than before. Using multiple examples, this work will demonstrate how to direct detection electron counting cameras enhance 3DED results (3 to better than 1 Angstrom) for protein and small molecule structure determination. We will also show how Latitude D software facilitates collecting such data in an integrated and fully automated user interface.

Keywords: continuous electron diffraction tomography, direct detection, diffraction, Latitude D, Digitalmicrograph, proteins, small molecules

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Authors: Naiduwadura Ivon Upekala De Silva, Nathan Lehman, Talia Fargason, Trenton Paul, Zihan Zhang, Jun Zhang

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SRSF1 governs splicing of over 1,500 mRNA transcripts. SRSF1 contains two RNA-recognition motifs (RRMs) and a C-terminal Arg/Ser-rich region (RS). It has been thought that SRSF1 RRMs exclusively recognize single-stranded exonic splicing enhancers, while RS lacks RNA-binding specificity. With our success in solving the insolubility problem of SRSF1, we can explore the unknown RNA-binding landscape of SRSF1. We find that SRSF1 RS prefers purine over pyrimidine. Moreover, SRSF1 binds to the G-quadruplex (GQ) from the ARPC2 mRNA, with both RRMs and RS being crucial. Our binding assays show that the traditional RNA-binding sites on the RRM tandem and the Arg in RS are responsible for GQ binding. Interestingly, our FRET and circular dichroism data reveal that SRSF1 unfolds the ARPC2 GQ, with RS leading unfolding and RRMs aiding. Our saturation transfer difference NMR results discover that Arg residues in SRSF1 RS interact with the guanine base but with other nucleobases, underscoring the uniqueness of the Arg/guanine interaction. Our luciferase assays confirm that SRSF1 can alleviate the inhibitory effect of GQ on gene expression in the cell. Given the prevalence of RNA GQ and SR proteins, our findings unveil unexplored SR protein functions with broad implications in RNA splicing and translation.

Keywords: SR, SRSF!, RNA G-quadruplex, unfolding, RNA binding

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Authors: Jenan Shakoor

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Obesity prevalence is increasing worldwide. University life is a challenging period especially for students who have to leave their familiar surroundings and settle in a new environment. The current study aimed to assess the diet and exercise habits and their association with body mass index (BMI) among nursing college students living at Kirkuk University residence. This was a descriptive study. A non-probability (purposive) sample of 101 students living in Kirkuk University residence was recruited during the period from the 15^th November 2015 to the 5^th May 2016. A questionnaire was constructed for the purpose of the study which consisted of four parts: the demographic characteristics of the study sample, eating habits, eating at college and healthy habits. The data were collected by interviewing the study sample and the weight and height were measured by a trained researcher at the college. Descriptive statistical analysis was undertaken. Data were prepared, organized and entered into the computer file; the Statistical Package for Social Science (SPSS 20) was used for data analysis. A p value≤ 0.05 was accepted as statistical significant. A total of 63 (62.4%) of the sample were aged20-21with a mean age of 22.1 (SD±0.653). A third of the sample 38 (37.6%) were from level four at college, 67 (66.3%) were female and 46 45.5% of participants were from a middle socio-economic status. 14 (13.9%) of the study sample were overweight (BMI =25-29.9kg/m²) and 6 (5.9%) were obese (BMI≥30kg/m²) compared to 73 (72.3%) were of normal weight (BMI =18.5-24.9kg/m²). With regard to eating habits and exercise, 42 (41.6%) of the students rarely ate breakfast, 79 (78.2%) eat lunch at university residence, 77 (78.2%) of the students reported rarely doing exercise and 62 (61.4%) of them were sleeping for less than eight hours. No significant association was found between the variables age, sex, level of college and socio-economic status and BMI, while there was a significant association between eating lunch at university and BMI (p =0.03). No significant association was found between eating habits, healthy habits and BMI. The prevalence of overweight and obesity among the study sample was 19.8% with female students being more obese than males. Further studies are needed to identify BMI among residence students in other colleges and increasing the awareness of undergraduate students to healthy food habits.

Keywords: body mass index, diet, obesity, university residence

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Authors: Eman Alzahrani

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Efficient extraction of proteins by removing interfering materials is necessary in proteomics, since most instruments cannot handle such contaminated sample matrices directly. In this study, chitosan-coated magnetic nanoparticles (CS-MNPs) for purification of myoglobin were successfully fabricated. First, chitosan (CS) was prepared by a deacetylation reaction during its extraction from shrimp-shell waste. Second, magnetic nanoparticles (MNPs) were synthesised, using the coprecipitation method, from aqueous Fe2+ and Fe3+ salt solutions by the addition of a base under an inert atmosphere, followed by modification of the surface of MNPs with chitosan. The morphology of the formed nanoparticles, which were about 23 nm in average diameter, was observed by transmission electron microscopy (TEM). In addition, nanoparticles were characterised using X-ray diffraction patterns (XRD), which showed the naked magnetic nanoparticles have a spinel structure and the surface modification did not result in phase change of the Fe3O4. The coating of MNPs was also demonstrated by scanning electron microscopy (SEM) analysis, energy dispersive analysis of X-ray spectroscopy (EDAX), and Fourier transform infrared (FT-IR) spectroscopy. The adsorption behaviour of MNPs and CS-MNPs towards myoglobin was investigated. It was found that the difference in adsorption capacity between MNPs and CS-MNPs was larger for CS-MNPs. This result makes CS-MNPs good adsorbents and attractive for using in protein extraction from biological samples.

Keywords: chitosan, magnetic nanoparticles, coprecipitation, adsorption

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Authors: Keethadath Arshad, Kappalli Sudha

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Mud crab, Scylla Serrata, a commercially important shellfish with high global demand appears to be the rich source of dietary fatty acids. Its increased production through aquaculture and highly perishable nature would necessitate improved techniques for their proper preservation. Optimized irradiation has been identified as an effective method to facilitate safety and extended shelf life for a broad range of the perishable food items including finfishes and shellfishes. The present study analyzed the effects of dose-dependent gamma irradiation on the fatty acid profile of the muscle derived from the candidate species (S. serrata) at both qualitative and quantitative levels. Wild grown, average sized, intermolt male S. Serrata were gamma irradiated (^60C, 3.8kGy/ hour) at the dosage of 0.5kGy, 1.0kGy and 2.0kGy using gamma chamber. Total lipid extracted by Folch method, after methylation, were analyzed for the presence fatty acids adopting Gas Chromatograph equipped with flame ionization detector by comparing with the authentic FAME reference standards. The tissue from non-irradiated S. serrata showed the presence of 12 SFA, 6 MUFA, 8PUFA and 2 TF; PUFA includes medicinally important ω-3 FA such as C18:3, C20:5 and C22:6 and ω-6 FA such as γ- C18:3 and C20:2. Dose-dependent gamma irradiation reduced the number of detectable fatty acids (10, 8 and 8 SFA, 6, 6 and 5MUFA, 7, 7, and 6 PUFA and 1, 1, and 0 TF in 0.5kGy, 1.0kGy and 2kGy irradiated samples respectively). Major fatty acids detected in both irradiated and non-irradiated samples were as follows: SFA- C16:0, C18:0, C22:0 and C14:0; MUFA - C18:1 and C16:1and PUFA- C18:2, C20:5, C20:2 and C22:6. Irradiation doses ranging from 1-2kGy substantially reduced the ω-6 C18:3 and ω-3 C18:3. However, the omega fatty acids such as C20:5, C22:6 and C20:2 could survive even after 2kGy irradiation. Significantly, trans fat like C18:2T and C18:1T were completely disappeared upon 2kGy irradiation. From the overall observations made from the present study, it is suggested that irradiation dose up to 1kGy is optimum to maintain the fatty acid profile and eradicate the trans fat of the muscle derived from S. serrata.

Keywords: fatty acid profile, food preservation, gamma irradiation, scylla serrata

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Authors: Izdihar Ismail, Alona C. Linatoc, Maryati Mohamed

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The tropical rainforest of Malaysia is known for its rich biological diversity and high endemicity. The potential for these forests to hold the cure for many diseases and illnesses is high and much is yet to be discovered. This study explores the richness of the tropical rainforest of Endau-Rompin National Park in Johor, Malaysia in search of plants traditionally used by the indigenous people in the treatment of malaria and malaria-like symptoms. Seven species of plants were evaluated and tested for antiplasmodial activities. Different plant parts were subjected to methanolic and aqueous extractions. A total of 24 extracts were evaluated by histidine-rich protein II (HRP2) assay against K1 strain of Plasmodium falciparum chloroquine-resistant. Ten extracts showed significant inhibition of the growth of P. falciparum. Phytochemical screening of the same extracts revealed the presence of alkaloids, flavonoids, terpenoids and anthraquinones. This study affirms that tropical rainforests may still hold undiscovered cures for many diseases and illnesses that have inflicted millions of people worldwide. The species studied herein have not known to have been studied elsewhere before.

Keywords: Endau-Rompin, malaria, Malaysia, tropical rainforest, traditional knowledge

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Authors: Muhammad Asif Rasheed

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Newcastle disease virus (NDV), an avian orthoavulavirus, is a causative agent of Newcastle disease named (NDV) and can cause even the epidemics when the disease is not treated. Previously several vaccines based on attenuated and inactivated viruses have been reported, which are rendered useless with the passage of time due to versatile changes in viral genome. Therefore, we aimed to develop an effective multi-epitope vaccine against the haemagglutinin neuraminidase (HN) protein of 26 NDV strains from Pakistan through a modern immunoinformatic approaches. As a result, a vaccine chimaera was constructed by combining T-cell and B-cell epitopes with the appropriate linkers and adjuvant. The designed vaccine was highly immunogenic, non-allergen, and antigenic; therefore, the potential 3D-structureof multi epitope vaccine was constructed, refined, and validated. A molecular docking study of a multiepitope vaccine candidate with the chicken Toll-like receptor-4 indicated successful binding. An In silico immunological simulation was used to evaluate the candidate vaccine's ability to elicit an effective immune response. According to the computational studies, the proposed multiepitope vaccine is physically stable and may induce immune responses, whichsuggested it a strong candidate against 26 Newcastle disease virus strains from Pakistan. A wet lab study is under process to confirm the results.

Keywords: epitopes, newcastle disease virus, paramyxovirus virus, vaccine

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Authors: Weili Shao, Qian Wang, Jianxin He

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Recently, the applications of graphene oxide in fabricating scaffolds for bone tissue engineering have been received extensive concern. In this work, poly l-lactic/graphene oxide composite nanofibers were successfully fabricated by electrospinning. The morphology structure, porosity and mechanical properties of the composite nanofibers were characterized using different techniques. And mouse mesenchymal stem cells were cultured on the composite nanofiber scaffolds to assess their suitability for bone tissue engineering. The results indicated that the composite nanofiber scaffolds had finer fiber diameter and higher porosity as compared with pure poly l-lactic nanofibers. Furthermore, incorporation of graphene oxide into the poly l-lactic nanofibers increased protein adsorptivity, boosted the Young’s modulus and tensile strength by nearly 4.2-fold and 3.5-fold, respectively, and significantly enhanced adhesion, proliferation, and osteogenesis in mouse mesenchymal stem cells. The results indicate that composite nanofibers could be excellent and versatile scaffolds for bone tissue engineering.

Keywords: poly l-lactic, graphene oxide, osteogenesis, bone tissue engineering

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Authors: Hammed Tanimowo Aiyelabegan, Oluchukwu Franklin Aladi, Mutiu Adewumi Alabi, Raliat Abimbola Aladodo, Emmanuel Oladipupo Ajani, Abdulganiyu Giwa, Esther Owolabi

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The study aimed to evaluate the inhibitory activities of ligands from Enantia chlorantha stem bark on α-amylase and α-glucosidase. In silico pharmacokinetic properties and docking scores were employed to analyse the inhibition using SwissADME and Autodock4.2, respectively. Results revealed that drug-likeness, pharmacokinetics and bioavailability radar of all the ligands except jatrorrhizine and acarbose falls within the radar according to the Lipinski rule of 5. The binding energies of the protein-ligand interactions also show that the ligand fits into the active site. The results obtained from this study show that the chemical constituents from Enantia chlorantha stem bark may bring about positive physiological changes in a patient suffering from diabetes mellitus. Further in vitro studies on diabetes cell lines and in vivo studies on the animal may validate these compounds for diabetes treatment. These phytoconstituents could help in the development of novel anti-diabetic molecules.

Keywords: diabetes mellitus, ?-amylase, ?-glucosidase, in silico, Enantia chlorantha stem bark

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Authors: M. G. Shehata, S. A. El Sohaimy, Marwa M. Abu-Serie, Nourhan M. Abd El-Aziz

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Probiotic strains can potentially be used as bio-preservatives and functional food supplement. Eight lactic acid bacteria strains (LAB) Lactobacillus brevis NRRL B-4527; Streptococcus thermophilus BLM 58; Pediococcusacidilactici ATCC 8042; Lactobacillus rhamnosus CCUG 1452; Lactobacillus curvatus ATCC 51436; Lactococcuslactis sub sp. lactisDSM 20481; Lactobacillus plantarum DMSZ 20079 and Lactobacillus plantarumTF103 were selected to screen the antioxidant, anticancer potential and probiotic properties. LAB strains exhibited good probiotic, antioxidant properties and showed antagonistic activity against food-borne pathogenic (Bacillus subtilis DB 100 host; Candida albicans ATCCMYA-2876; Clostridium botulinum ATCC 3584; Escherichia coli BA 12296; Klebsiellapneumoniae ATCC12296; Salmonella senftenberg ATCC 8400 and Staphylococcus aureus NCTC 10788). Further, in vitro probiotic properties of eight strains displayed excellent acid tolerance, bile tolerance, simulated gastrointestinal juice tolerance, in vitro adhesion ability for HT-29 cell line. The antioxidant effect of intracellular and cell-free extract of lactic acid bacteria strains was evaluated by various antioxidant assays, namely, resistance to hydrogen peroxide, DPPH radical scavenging, ABTS radical scavenging, and hydroxyl radical scavenging (HRS). The results showed that intracellular and cell-free supernatant of S. Thermophilus BLM 58, L. lactissubsp.lactis DSM 20481, P. acidilactici ATCC 8042, L. brevis NRRL B-4527 strains possess excellent antioxidant capacity. The intracellular of S. Thermophilus BLM 58 and P. acidilactici ATCC 8042 also showed excellent anticancer activity against Caco-2, MCF-7, HepG-2, and PC-3. Antioxidative property of selected lactic acid bacteria strains would be useful in the functional food manufacturing industry. They could beneficially affect the consumer by providing dietary source of antioxidants.

Keywords: anticancer activity, antioxidant activity, functional food, lactic acid bacteria, probiotic

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Authors: Nnennaya Samuel Okoro

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An experiment was conducted to determine the growth performance, blood parameters and reproductive characteristics of 8-week old male weaner rabbits fed 20% boiled pigeon pea seed meal (PPSM). The study lasted for 16 weeks. Results showed that haematological parameters of the two groups of rabbit bucks were not significantly affected (P>0.05) by the treatment, meaning that the PPSM was adequate for maintaining the blood parameters at the normal levels. The 20% boiled PPSM significantly affected (P<0.05) serum Alanine Aminotransferase (ALT) (67.72±2.5 I.U/I) more than the ALT (57.50±2.02 I.U/I) of the control, which is an indication of liver problem. The globulin level (3.00 ± 0.23 g/d) of the 20% boiled PPSM group was significantly higher than that of the control (2.60±0.06 g/dl), indicating that the test diet did not alter protein metabolism in the rabbits. Boiled pigeon pea seed meal supported organ weight and testicular development in rabbit bucks, suggesting that boiling reduced the level of the anti-nutritional factors in pigeon pea seed meal. Thus, 20% boiled pigeon pea can be included in diets of rabbits without adverse effect on blood parameters and internal organs characteristics.

Keywords: haematology, internal organs, pigeon pea, rabbits, serum biochemistry

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Authors: Chin-Yuan Hsieh, Wei-Chun Lu, Yu-Hong Zeng

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The situation of a group of fish die is frequently found due to the fish disease caused by the deterioration of aquaculture water quality. The toxic ammonia is produced by animals as a byproduct of protein. The system is designed by the smart sensor technology and developed by the mathematical model to monitor the water parameters 24 hours a day and predict the relationship among twelve water quality parameters for monitoring the water quality in aquaculture. All data measured are stored in cloud server. In productive ponds, the daytime pH may be high enough to be lethal to the fish. The sudden change of the aquaculture conditions often results in the increase of PH value of water, lack of oxygen dissolving content, water quality deterioration and yield reduction. From the real measurement, the system can send the message to user’s smartphone successfully on the bad conditions of water quality. From the data comparisons between measurement and model simulation in fish aquaculture site, the difference of parameters is less than 2% and the correlation coefficient is at least 98.34%. The solubility rate of oxygen decreases exponentially with the elevation of water temperature. The correlation coefficient is 98.98%.

Keywords: aquaculture, sensor, ammonia, dissolved oxygen

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Authors: Wen-Yu Lin, Yi-Ching Chung, Tzyy-Rong Jinn

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It is well known that enterovirus 71 (EV71) causes recurring outbreaks of hand, foot and mouth disease (HFMD) and encephalitis leading to complications or death in young children. And, several HFMD of EV71 with high mortalities occurred in Asia countries, such as Malaysia (1997), Taiwan (1998) and China (2008). Thus, more effective antiviral drugs are needed to prevent or reduce EV71-related complications. As reported, interferon-α protects mice from lethal EV71 challenge by the modulation of innate immunity and then degrade enterovirus protease 3Cᵖʳᵒ. On the other side, pleconaril by targeting enterovirus VP1 protein and then block virus entry and attachment. Thus, the aim of this study was to evaluate the synergistic antiviral activity of interferon-α and pleconaril against enterovirus 71 infection. In a preliminary study showed that pleconaril at concentrations of 50, 100 and 300 µg/mL reduced EV71-induced CPE to 52.0 ± 2.5%, 40.2 ± 3.5% and 26.5 ± 1.5%, respectively, of that of the EV71-infected RD control cells (taken as 100%). Notably, 1000 IU/mL of interferon-α in combination with pleconaril at concentrations of 50, 100 and 300µg/mL suppressed EV71-induced CPE by 30.2 ± 3.8%, 16.5 ± 1.3% and 2.8 ± 2.0%, respectively, of that of the pleconaril alone treated with the infected RD cells. These results indicated that interferon-α 1000 IU/mL combination with pleconaril (50, 100 and 300µg/mL) inhibited EV71-induced CPE more effectively than treated with pleconaril alone in the infected RD cells.

Keywords: enterovirus 71, interferon-α, pleconaril, RD cells

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Authors: Ramandeep Kaur, Kamaljit Kaur, Preeti Ahluwalia, Poonam A. Sachdev

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Bread is an ideal vehicle to impart bioactive compounds to the consumers in a convenient manner. This study evaluated bread enriched with red sweet pepper powder (RSP) at 2, 4, 6, 8, 10% and compared to control bread (without RSP). The bread crumbs were assayed for bioactive, physical, nutritional, textural, color, and sensory properties. Bread supplemented with RSP improved its color, nutritional, and bioactive properties. The low moisture content and increased hardness were observed at higher levels of RSP. Color intensity (expressed as L*, a*, b* values) of bread with 2 and 4% RSP were lower than those of high levels, and the same trend was observed for protein, fibre and ash content of bread. Significant (p < 0.05) increases were recorded for bioactive compounds such as total phenols (0.145 to 235 mg GAE/g), antioxidant activity (56% to 78%) and flavonoids (0.112 to 0.379 mg/g) as the level of powder increased. Bread enriched with 8% RSP showed improved sensory profile as compared to control, whereas a further increase in RSP decreased the sensory and textural properties. Thus, RSP act as a natural colorant and functional food that enhanced the functional and nutritional properties of bread and can be used to customize bread for specific health needs.

Keywords: breads, bioactive compounds, red sweet pepper powder, sensory scores

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Authors: Muhammad Ali Syed, Arshad Saleem Bhatti, Chen-zhong Li, Habib Ali Bokhari

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Surface plasmon resonance (SPR) biosensors have emerged as a promising technique for bioanalysis as well as microbial detection and identification. Real time, sensitive, cost effective, and label free detection of biomolecules from complex samples is required for early and accurate diagnosis of infectious diseases. Like many other types of optical techniques, SPR biosensors may also be successfully utilized for microbial detection for accurate, point of care, and rapid results. In the present study, we have utilized a commercially available automated SPR biosensor of BI company to study the microbial detection form water samples spiked with different concentration of Staphylococcus aureus bacterial cells. The gold thin film sensor surface was functionalized to react with proteins such as protein G, which was used for directed immobilization of monoclonal antibodies against Staphylococcus aureus. The results of our work reveal that this immunosensor can be used to detect very small number of bacterial cells with higher sensitivity and specificity. In our case 10^3 cells/ml of water have been successfully detected. Therefore, it may be concluded that this technique has a strong potential to be used in microbial detection and identification.

Keywords: surface plasmon resonance (SPR), Staphylococcus aureus, biosensors, microbial detection

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Authors: Jae Woong Sull, Sun Ha Jee

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High-density lipoprotein (HDL) cholesterol levels are associated with decreased risk of coronary artery disease. Several genome-wide association studies (GWAS) for HDL cholesterol levels have implicated cholesterol ester transfer protein (CETP) as possibly causal. We tested for the association between single nucleotide polymorphisms (SNPs) in CETP gene and HDL cholesterol levels in Korean population. Subjects were selected from the Korean Metabolic Syndrome Research Initiative study in the Bundang-Gu area. A total of 2,304 individuals from Bundang-Gu were recruited in 2008. Other subjects were selected from the Severance Hospital (N=4,294). SNP rs6499861 in the CETP gene was associated with mean HDL cholesterol levels (effect per allele -2.044 mg/dL, p=7.23×10-7). Subjects with the CG/GG genotype had a 1.46 -fold (range 1.24–1.72-fold) higher risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. When analyzed by gender, the association of CETP was stronger in women than in men. When analyzed by physical activity behavior, the association with CETP was much stronger in male subjects with low physical activity (OR=1.54, 95% CI: 1.23-1.92, P=0.0001) than in male subjects with high physical activity. This study clearly demonstrates that genetic variants in CETP influence HDL cholesterol levels in Korean adults.

Keywords: CETP, HDL cholesterol, physical activity, polymorphisms

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Authors: Manal M. Shehata, Kawther M. Abdel-Hamid, Nashwa A. Mohamed, Marwa H. Bakr, Maged S. Mahmoud, Hala M. Elbadre

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Introduction: The worldwide rapid increase in diabetes poses a significant challenge to current therapeutic approaches. Therapeutic utility of bone marrow transplantation in diabetes is an attractive approach. However, the oxidative stress generated by hyperglycemia may hinder β-cell regeneration. Curcumin, is a dietary spice with antioxidant activity. Aim of work: The present study was undertaken to investigate the therapeutic potential of curcumin, bone marrow transplantation, and their combined effects in the reversal of experimental diabetes. Material and Methods: Fifty adult male healthy albino rats were included in the present study.They were divided into two groups: Group І: (control group) included 10 rats. Group П: (diabetic group): included 40 rats. Diabetes was induced by single intraperitoneal injection of streptozotocin (STZ). Group II will be further subdivided into four groups (10 rats for each): Group II-a (diabetic control). Group II-b: rats were received single intraperitoneal injection of bone marrow suspension (un-fractionated bone marrow cells) prepared from rats of the same family. Group II-c: rats were treated with curcumin orally by gastric intubation for 6 weeks. Group II-d: rats were received a combination of single bone marrow transplantation and curcumin for 6 weeks. After 6 weeks, blood glucose, insulin levels were measured and the pancreas from all rats were processed for Histological, Immunohistochemical and morphometric examination. Results: Diabetic group, showed progressive histological changes in the pancreatic islets. Treatment with either curcumin or bone marrow transplantation improved the structure of the islets and reversed streptozotocin-induced hyperglycemia and hypoinsulinemia. Combination of curcumin and bone marrow transplantation elicited more profound alleviation of streptozotocin-induced changes including islet regeneration and insulin secretion. Conclusion: The use of natural antioxidants combined with bone marrow transplantation to induce pancreatic regeneration is a promising strategy in the management of diabetes.

Keywords: diabtes, panceatic islets, bone marrow transplantation, curcumin

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Authors: H. J. T. Kevin Mozes, Dyah Purnamasari

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Background: Lung cancer accounted for the fourth most common cancer in Indonesia. 85% of all lung cancer cases are the Non-Small Cell Lung Cancer (NSCLC). The indistinct signs and symptoms of NSCLC sometimes lead to misdiagnosis. The gold standard assessment for the diagnosis of NSCLC is the histopathological biopsy, which is invasive. Cyfra 21-1 is a tumor marker, which can be found in the intermediate protein structure in the epitel. The accuracy of Cyfra 21-1 in diagnosing NSCLC is not yet known, so this report is made to seek the answer for the question above. Methods: Literature searching is done using online databases. Proquest and Pubmed are online databases being used in this report. Then, literature selection is done by excluding and including based on inclusion criterias and exclusion criterias. The selected literature is then being appraised using the criteria of validity, importance, and validity. Results: From six journals appraised, five of them are valid. Sensitivity value acquired from all five literature is ranging from 50-84.5 %, meanwhile the specificity is 87.8 %-94.4 %. Likelihood the ratio of all appraised literature is ranging from 5.09 -10.54, which categorized to Intermediate High. Conclusion: Serum Cyfra 21-1 is a sensitive and very specific tumor marker for diagnosis of non-small cell lung cancer (NSCLC).

Keywords: cyfra 21-1, diagnosis, nonsmall cell lung cancer, NSCLC, tumor marker

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Authors: Nicolas Lopez-Villalobos, Dorian J. Garrick, Hugh T. Blair

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Many dairy goat farmers of New Zealand milk herds of mixed breed does. Simultaneous evaluation of sires and does across breed is required to select the best animals for breeding on a common basis. Across-breed estimated breeding values (EBV) and estimated producing values for 208-day lactation yields of milk (MY), fat (FY), protein (PY) and somatic cell score (SCS; LOG2(SCC) of Saanen, Nubian, Alpine, Toggenburg and crossbred dairy goats from 75 herds were estimated using a test day model. Evaluations were based on 248,734 herd-test records representing 125,374 lactations from 65,514 does sired by 930 sires over 9 generations. Averages of MY, FY and PY were 642 kg, 21.6 kg and 19.8 kg, respectively. Average SCC and SCS were 936,518 cells/ml milk and 9.12. Pure-bred Saanen does out-produced other breeds in MY, FY and PY. Average EBV for MY, FY and PY compared to a Saanen base were Nubian -98 kg, 0.1 kg and -1.2 kg; Alpine -64 kg, -1.0 kg and -1.7 kg; and Toggenburg -42 kg, -1.0 kg and -0.5 kg. First-cross heterosis estimates were 29 kg MY, 1.1 kg FY and 1.2 kg PY. Average EBV for SCS compared to a Saanen base were Nubian 0.041, Alpine -0.083 and Toggenburg 0.094. Heterosis for SCS was 0.03. Breeding values are combined with respective economic values to calculate an economic index used for ranking sires and does to reflect farm profit.

Keywords: breed effects, dairy goats, milk traits, test-day model

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Authors: Wenxiao Liu, Kun Zhang, Yongqing Li

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Bovine herpesvirus 1, a member of the genus Variellovirus of the subfamily Alphaherpesvirinae, has caused severe economic cost to the bovine industry. In this study, BoHV-1 glycerol protein gD was expressed in insect cells, and the purified gD was immunized in the Balb/C mice to generate monoclonal antibodies. Based on hybridoma cell fusion techniques, 20 monoclonal antibodies against Bovine herpesvirus 1 have been obtained. Further, mAb 3F8 with neutralizing activity and gD were applied to develop a blocking enzyme-linked immunosorbent assay (Elisa) for detecting neutralizing antibodies against BoHV-1, which shows a significant correlation between the blocking Elisa and VNT. The sensitivity and specificity of the test were estimated to be 94.59% and 93.42%, respectively. Furthermore, antibody pairing tests revealed that mAb 1B6 conjugated to fluorescence microspheres was used as the capture antibody, and mAb 3F9 was used as the detectable antibody to establish the immunochromatographic assay (ICS). The ICS was conducted to detect BoHV-1 in bovine samples with high sensitivity, specificity, and good stability. Clinical sample testing revealed that the results of ICS and real-time PCR have a coincidence rate of 95.42%. Our research confirmed that the ICS is a rapid and reliable method for the diagnosis of BoHV-1. In conclusion, our results lay a solid foundation for the prevention and control of BoHV-1 infection.

Keywords: bovine disease, BoHV-1, ELISA, ICS assay

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Authors: Pedro Maldonado-Alvarado

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An important cassava quality production was detected in Ecuador. However, in this country, few products with low adding-value are produced from the tuber and none from cassava by-products. To our best knowledge, lactic acid was produced from Ecuadorian cassava bagasse starch in a biotechnological way. The objective of this contribution was to study the influence of the fermentation variables (pH and agitation) on the lactic acid production of Ecuadorian cassava varieties from bagasse starch. Enzymatic hydrolysis of cassava bagasse starch for INIAP 650 and INIAP 651 varieties spread in Ecuador was performed using α-amylase and amyloglucosidase. Then, glucose was fermented by Lactobacillus leichmannii strains in different conditions of agitation (0 and 150 rpm) and pH (4.5, 5.0, and 5.5). Significant differences in ash, fibre, protein, lipids, and amylose were found in cassava bagasse starch of INIAP 650 and INIAP 651 with 1.4 and 1.3%, 4.3 and 6%, 1.2 and 2.1%, 1.9 and 1.5%, and 24.3 and 26.5%, respectively. The determination of lactic acid was performed by potentiometric and FTIR analysis. Conversions of cassava bagasse to reduced sugars were 71.7 and 85.1% for INIAP 650 and INIAP 651, respectively. The best lactic acid concentrations were 27.6 and 33.5 g/L, obtained at agitation 150 rpm and pH 5.5 for INIAP 650 and INIAP 651. Qualitative analysis conducted by FTIR spectrophotometry confirmed the presence of lactic acid in the reacted products. This investigation could contribute to the valorisation of residues from promising cassava varieties in Ecuador and hence to increase the development of this country.

Keywords: bagasse starch, cassava, Ecuador, fermentation, lactic acid

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Authors: Sonam Agarwal, Renu Bist

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Current study emphasizes the toxic effects of dichlorvos on serum in terms of oxidative stress. Meanwhile, a protective action of bacoside A and bromelain was investigated against the biochemical alterations in serum. The experimental design included six groups of mice: saline was given as a vehicle to the control mice (group I). Mice belonging to groups II, III and IV, were administered with dichlorvos (40 mg/kg b.w.), bromelain and bacoside A, respectively. The fifth group received a combination of bromelain and bacoside A. In group VI, Bacoside A, and bromelain were administered 20 minutes prior to exposure of dichlorvos. Thiobarbituric acid reactive substances (TBARS), protein carbonyl content (PCC), catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx) and reduced glutathione (GSH) level were used as biochemical test of toxic action for dichlorvos intoxication. Significantly increased TBARS and PCC level in second group suggests that dichlorvos enhances the production of free radicals in serum of mice (p< 0.05). Antioxidants treatment significantly decreased the levels of TBARS and PCC (p< 0.05). Dichlorvos administration causes a significant reduction in the level of CAT, SOD, GPx and GSH (p< 0.05) which was restored significantly by co-administration of bromelain and Bacoside A in dichlorvos exposed mice (p< 0.05). Treatment of bromelain and Bacoside A in combination served as better scavengers of toxicity induced by dichlorvos.

Keywords: bacoside A, bromelain, dichlorvos, serum

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Authors: Pradeep Lamichhane, Nima Pourali, E. V. Rebrov, Volker Hessel

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Nitrogen fixation is critical for plants for the biosynthesis of protein and nucleic acid. Most of our atmosphere is nitrogen, yet plants cannot directly absorb it from the air, and natural nitrogen fixation is insufficient to meet the demands. This experiment used a fast-modulated surface-confined atmospheric pressure plasma created by a 6 kV (peak-peak) sinusoidal power source with a repetition frequency of 68 kHz to fix nitrogen. Plasmas have been proposed for excitation of nitrogen gas, which quickly oxidised to NOX. With different N2/O2 input ratios, the rate of NOX generation was investigated. The rate of NOX production was shown to be optimal for mixtures of 60–70% O2 with N2. To boost NOX production in plasma, metal oxide catalysts based on TiO2 were coated over the dielectric layer of a reactor. These results demonstrate that nitrogen activation was more advantageous in surface-confined plasma sources because micro-discharges formed on the sharp edges of the electrodes, which is a primary function attributed to NOX synthesis and is further enhanced by metal oxide catalysts. The energy-efficient and sustainable NOX synthesis described in this study will offer a fresh perspective for ongoing research on green nitrogen fixation techniques.

Keywords: nitrogen fixation, fast-modulated, surface-confined, sustainable

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Authors: K. Tesfamariam, S. Gebreyesus, C. Lachat, P. Kolsteren, S. De Saeger, M. De Boevre, A. Argaw

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Aflatoxins are toxic secondary metabolites produced by Aspergillus fungi, which are ubiquitously present in the food supplies of low- and middle-income countries. Studies of maternal aflatoxin exposure and fetal outcomes are mainly focused on size at birth and the effect on intrauterine fetal growth has not been assessed using repeated longitudinal fetal biometry across gestation. Therefore, this study intends to assess the association between chronic aflatoxin exposure during pregnancy and fetal growth trajectories in a rural Ethiopian setting. In a prospective cohort study, we enrolled 492 pregnant women. A phlebotomist collected 5 mL of a venous blood sample from eligible women before 28 completed weeks of gestation and aflatoxin B1-lysine concentration was determined using liquid chromatography-tandem mass spectrometry. The mean (±SD) gestational age was 19.1 (3.71) weeks at enrollment, and 28.5 (3.51) and 34.5 (2.44) weeks of gestation at the second and third rounds of ultrasound measurements, respectively. Estimated fetal weight was expressed in centiles using the INTERGROWTH-21st reference. We fitted a multivariable linear mixed-effects model to estimate the rate of fetal growth between aflatoxin-exposed (i.e., aflatoxin B1-lysine concentration above or equal to the limit of detection) and non-exposed mothers in the study. Mothers had a mean (±SD) age of 26.0 (4.58) years. The median (P25, P75) serum AFB1-lysine concentration was 12.6 (0.93, 96.9) pg/mg albumin, and aflatoxin exposure was observed in 86.6% of maternal blood samples. Eighty-five percent of the women enrolled provided at least two ultrasound measurements for analysis. On average, the aflatoxin-exposed group had a significantly lower change over time in fetal weight-for-gestational age centile than the unexposed group (ß = -1.01 centiles/week, 95% CI: -1.87, -0.15, p = 0.02). Chronic maternal AF exposure is associated with lower fetal weight gain over time. Our findings emphasize the importance of nutrition-sensitive strategies to mitigate dietary aflatoxin exposure as well as adopting food safety measures in low-income settings, particularly during the fetal period of development.

Keywords: aflatoxin, fetal growth, low-income setting, mycotoxins

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Authors: Ozcan Baris Citil

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The aim of the present study is the determination of the effects of variations in the proximate analysis, cholesterol content and fatty acid compositions of Helix aspersa. Garden snails (Helix aspersa) were picked up by hand from the Central Anatolia Region of Turkey, in autumn (November) in 2015. Fatty acid methyl esters (FAMEs) and cholesterol analysis were analyzed by gas chromatography (GC). The protein contents of snail muscle were determined with Kjeldahl distillation units. Statistical comparisons were made by using SPSS Software (version 16.0). Thirty different fatty acids of different saturation levels were detected. As the predominant fatty acids, stearic acid (C18:0), oleic acid (C18:1ω9), linoleic acid (C18:2ω6), palmitic acid (C16:0), arachidonic acid (C20:4ω6), eicosadienoic acid (C20:2) and linolenic acid (C18:3ω3) were found in Helix aspersa. Palmitic acid (C16:0) was identified as the major SFA in autumn. Linoleic acid (C18:2ω6), eicosadienoic acid (C20:2) and arachidonic acid (C20:4ω6) have the highest levels among the PUFAs. In the present study, ω3 were found 5.48% in autumn. Linolenic acid and omega-3 fatty acid amounts in the autumn decreased significantly but cholesterol content was not affected in Helix aspersa in autumn (November) in 2015.

Keywords: Helix aspersa, fatty acid, SFA, PUFA, cholesterol

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Authors: Amir Hosseinvand

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Probiotics have health-giving effects on the human body, so by stimulating the immune system, they prevent many occurrences they are diseases and food allergies in humans. There are various bacteria in the human digestive system; some are useful, some are harmless, and other groups of bacteria are harmful to human health. These bacteria should be in balance in the body of people in a normal state. In certain conditions, such as a person's high stress, aging, continuous use of antibiotics, or improper diet, the intestinal microbial flora has changed, and these changes cause some diseases in people. Probiotics have health benefits for the human body and are often found in the digestive system of healthy people. Nevertheless, fermented foods such as fermented dairy products such as yogurt, cheese, buttermilk or fermented pickles contain some species of these bacteria that are useful. But the important point that should be noted is that due to modern and industrial life, high fat and high protein diets, and excessive use of antibiotics, the number of these bacteria in people's bodies has decreased, and it is necessary to consume probiotics either in the form of probiotic foods or in the form of supplements. Probiotics with mild stimulation of the immune system increase the immunity level of the body and prevent the occurrence of food allergies in people.

Keywords: human health, dairy products, food allergies, probiotic

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Authors: Nahid Banihashemi

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An emerging important area of the life sciences is systems biology, which involves understanding the integrated behavior of large numbers of components interacting via non-linear reaction terms. A centrally important problem in this area is an understanding of the co-metabolism of protein and carbohydrate, as it has been clearly demonstrated that the ratio of these metabolites in diet is a major determinant of obesity and related chronic disease. In this regard, we have considered a systems biology model for the co-metabolism of carbon and nitrogen in colonies of the fungus Mucor mucedo. Oscillations are an important diagnostic of underlying dynamical processes of this model. The maintenance of specific patterns of oscillation and its relation to the robustness of this system are the important issues which have been targeted in this paper. In this regard, parametric sensitivity approach as a theoretical approach has been considered for the analysis of the robustness of this model. As a result, the parameters of the model which produce the largest sensitivities have been identified. Furthermore, the largest changes that can be made in each parameter of the model without losing the oscillations in biomass production have been computed. The results are obtained from the implementation of parametric sensitivity analysis in Matlab.

Keywords: system biology, parametric sensitivity analysis, robustness, carbon and nitrogen co-metabolism, Mucor mucedo

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Authors: A. Morina, S. Ö. Muti, M. Öztürk

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Celiac disease is a chronic intestinal disease observed in individuals with gluten intolerance. In this study, our aim was to create a protein matrix to mimic the functional properties of gluten. For this purpose, rennet casein and four emulsifying salts (disodium phosphate (DSP), tetrasodium pyrophosphate (TSPP), sodium acid pyrophosphate (SAPP), and sodium hexametaphosphate (SHMP)) were investigated in gluten-free bread manufacture. Compositional, textural, and visual properties of the gluten-free bread dough and gluten-free breads were investigated by a two–level factorial experimental design with two-star points (α = 1.414) and two replicates of the center point. Manufacturing gluten-free bread with rennet casein and SHMP significantly increased the bread volume (P < 0.0001, R² = 97.8). In general, utilization of rennet casein with DSP and SAPP increased bread hardness while no difference was observed in samples manufactured with TSPP and SHMP. Except for TSPP, bread color was improved by the utilization of rennet casein and DSP, SAPP, and SHMP combinations. In conclusion, it is possible to manufacture gluten-free bread with acceptable texture and color by rennet casein and SHMP.

Keywords: celiac disease, gluten-free bread, emulsified salts, rennet casein, rice flour

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