Search results for: synthetic protein design

Authors: Ammar Said Ahmed, M. Reissmann, R. Bortfeldt, G. A. Brockmann

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Milk protein genetic variants are of interest for characterizing domesticated mammalian species and breeds, and for studying associations with economic traits. The aim of this work was to analyze milk protein genetic variation in the Sudanese native cattle breeds, which have been gradually declining in numbers over the last years due to the breed substitution, and indiscriminate crossbreeding. The genetic variation at three milk protein genes αS1-casein (CSN1S1), αS2-casein (CSN1S2) and ƙ-casein (CSN3) was investigated in 250 animals belonging to five Bos indicus cattle breeds of Sudan (Butana, Kenana, White-nile, Erashy and Elgash). Allele specific primers were designed for five SNPs determine the CSN1S1 variants B and C, the CSN1S2 variants A and B, the CSN3 variants A, B and H. Allele, haplotype frequencies and genetic distances (D) were calculated and the phylogenetic tree was constructed. All breeds were found to be polymorphic for the studied genes. The CSN1S1*C variant was found very frequently (>0.63) in all analyzed breeds with highest frequency (0.82) in White-nile cattle. The CSN1S2*A variant (0.77) and CSN3*A variant (0.79) had highest frequency in Kenana cattle. Eleven haplotypes in casein gene cluster were inferred. Six of all haplotypes occurred in all breeds with remarkably deferent frequencies. The estimated D ranged from 0.004 to 0.049. The most distant breeds were White-nile and Kenana (D 0.0479). The results presented contribute to the genetic knowledge of indigenous cattle and can be used for proper definition and classification of the Sudanese cattle breeds as well as breeding, utilization, and potential development of conservation strategies for local breeds.

Keywords: milk protein, genetic variation, casein haplotype, Bos indicus

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Authors: Conor Blunt, Mariluz del Pino-de Elias, Grace Cott, Saoirse Tracy, Rainer Melzer

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The European Green Deal announced in 2021 details agricultural chemical pesticide use and synthetic fertilizer application to be reduced by 50% and 20% by 2030. Increasing and maintaining expected yields under these ambitious goals has strained the agricultural sector. This intergovernmental plan has identified plant biostimulants as one potential input to facilitate this new phase of sustainable agriculture; these products are defined as microorganisms or substances that can stimulate soil and plant functioning to enhance crop nutrient use efficiency, quality and tolerance to abiotic stresses. Spring barley is Ireland’s most widely sown tillage crop, and grain destined for malting commands the most significant market price. Heavy erratic rainfall is forecasted in Ireland’s climate future, and barley is particularly susceptible to waterlogging. Recent findings suggest that plant receptivity to biostimulants may depend on the level of stress inflicted on crops to elicit an assisted plant response. In this study, three biostimulants of different genesis (seaweed, protein hydrolysate and bacteria) are applied to ‘RGT Planet’ malting barley fertilized at three different rates (0 kg/ha, 40 kg/ha, 75 kg/ha) of calcium ammonium nitrogen (27% N) under non-stressed and waterlogged conditions. This 4x3x2 factorial trial design was planted in a completed randomized block with one plant per experimental unit. Leaf gas exchange data and key agronomic and grain quality parameters were analyzed via ANOVA. No penalty on productivity was evident on plants receiving 40 kg/ha of N and bio stimulant compared to 75 kg/ha of N treatments. The main effects of nitrogen application and waterlogging provided the most significant variation in the dataset.

Keywords: biostimulant, Barley, malting, NUE, waterlogging

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Authors: Niharul Alam

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The development of energy efficient, economic and eco-friendly synthetic protocols for metal nanoparticles (NPs) with tailor-made structural properties and biocompatibility is a highly cherished goal for researchers working in the field of nanoscience and nanotechnology. In this context, green chemistry is highly relevant and the 12 principles of Green Chemistry can be explored to develop such synthetic protocols which are practically implementable. One of the most promising green chemical synthetic methods which can serve the purpose is biogenic synthetic protocol, which utilizes non-toxic multifunctional reactants derived from natural, biological sources ranging from unicellular organisms to higher plants that are often characterized as “medicinal plants”. Over the past few years, a plethora of medicinal plants have been explored as the source of this kind of multifunctional green chemical agents. In this presentation, we focus on the syntheses of stable monometallic Au and Ag NPs and also bimetallic Au/Ag alloy NPs with highly efficient catalytic property using aqueous extract of leaves of Indian Curry leaf plat (Murraya koenigii Spreng.; Fam. Rutaceae) as green multifunctional agents which is extensively used in Indian traditional medicine and cuisine. We have also studied the interaction between the synthesized metal NPs and surface-adsorbed fluorescent moieties, quercetin and quercetin glycoside which are its chemical constituents. This helped us to understand the surface property of the metal NPs synthesized by this plant based biogenic route and to predict a plausible mechanistic pathway which may help in fine-tuning green chemical methods for the controlled synthesis of various metal NPs in future. We observed that simple experimental parameters e.g. pH and temperature of the reaction medium, concentration of multifunctional agent and precursor metal ions play important role in the biogenic synthesis of Au NPs with finely tuned structures.

Keywords: green multifunctional agent, metal nanoparticles, biogenic synthesis

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Authors: Yuexin Liu, Gordon B. Mills, Russell R. Broaddus, John N. Weinstein

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The lethality of endometrioid endometrial cancer (EEC) is primarily attributable to the high-stage diseases. However, there are no available biomarkers that predict EEC patient staging at the time of diagnosis. We aim to develop a predictive scheme to help in this regards. Using reverse-phase protein array expression profiles for 210 EEC cases from The Cancer Genome Atlas (TCGA), we constructed a Protein Scoring of EEC Staging (PSES) scheme for surgical stage prediction. We validated and evaluated its diagnostic potential in an independent cohort of 184 EEC cases obtained at MD Anderson Cancer Center (MDACC) using receiver operating characteristic curve analyses. Kaplan-Meier survival analysis was used to examine the association of PSES score with patient outcome, and Ingenuity pathway analysis was used to identify relevant signaling pathways. Two-sided statistical tests were used. PSES robustly distinguished high- from low-stage tumors in the TCGA cohort (area under the ROC curve [AUC]=0.74; 95% confidence interval [CI], 0.68 to 0.82) and in the validation cohort (AUC=0.67; 95% CI, 0.58 to 0.76). Even among grade 1 or 2 tumors, PSES was significantly higher in high- than in low-stage tumors in both the TCGA (P = 0.005) and MDACC (P = 0.006) cohorts. Patients with positive PSES score had significantly shorter progression-free survival than those with negative PSES in the TCGA (hazard ratio [HR], 2.033; 95% CI, 1.031 to 3.809; P = 0.04) and validation (HR, 3.306; 95% CI, 1.836 to 9.436; P = 0.0007) cohorts. The ErbB signaling pathway was most significantly enriched in the PSES proteins and downregulated in high-stage tumors. PSES may provide clinically useful prediction of high-risk tumors and offer new insights into tumor biology in EEC.

Keywords: endometrial carcinoma, protein, protein scoring of EEC staging (PSES), stage

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Authors: E. Oluwasola, E. Bamidele, E. Ogunbusola

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Enriched “aadun” was produced from maize with, supplemented with cray fish and beans. Sodium chloride (Nacl) was also added to the product which acts as preservatives. The produced enriched “aadun” was compared with commercial “aadun” organoleptically the result of the sensory evaluation carried out on the product showed that there is a statistical significant difference between the mouth feel of enriched and commercial “aadun” at 0.05 level of significance (t=5.499, P<0.05) Similarly, the mean difference between enriched and commercial “aadun” in terms of aroma (t=4.403, P<0.05), taste (t=4.592, P<0.05) colour (t=2.788, P<0.05) and general acceptability (t=3.894, P<0.05) is statistically significant at 95% confidence level in each case, therefore, it is clearly revealed that product 321 (Enriched “aadun”) is more acceptable and significant better than product 432 (commercial “aadun”) in all the attributes evaluated. The proximate analysis using standard methods of analysis was carried out which include the moisture content, ash and protein content for both the enriched aadun and commercial aadun the result showed moisture content 9%, ash 6.2%, protein 19.6% and 12.9% moisture content, 4%ash content, 8.75% protein for the commercial and improved aadun respectively.

Keywords: aadun, enriched, maize, supplemented

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Authors: Hae-Jun Lee, Ji-Sun Shin, Kyung-Tae Lee

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Potentilla species (Rosasease) have been used in traditional medicine to treat different ailment, disease or malady. In this study, we investigated the anti-inflammatory effects of ethanol extracts of NUTT (EPP) in lipopolysaccharide (LPS)-induced Raw 264.7 macrophages and septic mice. EPP suppressed LPS-induced nitric oxide (NO) and prostaglandin E2 (PGE2) production in LPS-induced Raw 264.7 macrophages. Consistent with these observations, EPP reduced the expressions of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) by downregulation of their promoter activities. EPP inhibited tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and interleukin-1β (IL-1β) at production and mRNA levels. Molecularly, EPP attenuated the LPS-induced transcriptional activity, and DNA-binding activity of nuclear factor-κB (NF-κB), and this was associated with a decrease of translocation and phosphorylation of p65 NF-κB by inhibiting the inhibitory κB-α (IκB-α) degradation and IκB kinase-α/β (IKK-α/β) phosphorylation. Furthermore, EPP suppressed the LPS-induced activation of activator protein-1 (AP-1) by reducing the expression of c-Fos and c-Jun in nuclear. EPP also reduced the phosphorylation of mitogen-activated protein kinase (MAPK), such as p38 MAPK and c-Jun N-terminal kinase/stress-activated protein kinase (JNK). In a sepsis model, pretreatment with EPP reduced the LPS-induced lethality. Collectively, these results suggest that the anti-inflammatory effects of EPP were associated with the suppression of NF-κB and AP-1 activation, and support its possible therapeutic role for the treatment of sepsis.

Keywords: anti-inflammation, activator protein-1, nuclear factor κB, Potentilla paradoxa Nutt

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Authors: A. O Amosu, A. M Hammed, G. W. Maneveldt, D. V. Robertson-Andersson

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In aquaculture, feed utilization is an important factor affecting growth of the target species, and thus the success of the aquaculture operation. Growth of C. gariepinus fingerlings (weight 1.60 ± 0.05 g; length 4.50 ± 0.07cm) was monitored in a closed door hatchery for a period of 21 days in an experiment consisting of 4 treatments stocked at 20 fish/10 litre tanks, fed in triplicate twice daily (08:30, 17:30) at 4% body weight with weight changes recorded every 3 days. Treatments were: 1) FeedX; 2) 35% crude protein diet + non enriched Ulva spp (11.18% crude protein) (CD + NEU); 3) 35% crude protein diet + enriched Ulva spp (11.98% crude protein)(CD +EU) and 4) control diet of 35% crude protein (CD). The production of Ulva spp. biomass was cultivated for a period of 3 months. The result shows that the fish fed macroalgal enriched diet had good growth, though no significant difference (p > 0.05) was recorded amongst the weight gain, %weight gain, specific growth rates and nitrogen metabolism of diets CD + NEU, CD + EU and CD. Significant differences (p < 0.05), were, however, found in the food conversion ratio (FCR) and gross food conversion ratio (gFCR) among the fingerlings across all the different experimental diets. The best FCRs were recorded for control diet (0.79 ± 2.39) and the Ulva enriched (1.75 ± 1.34) diets. The results suggest that the fingerlings were able to utilize Ulva supplemented with control diet better than the FeedX. We have shown that Ulva supplemented diets are good substitutes for formulated and commercial feeds, with potential to be successful fish feed in aquaculture systems.

Keywords: aquaculture, clarias gariepinus, growth, macroalgae, nutrient, ulva

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Authors: Alireza Mohadesi, Ashraf Salmanipour

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A chemically modified glassy carbon electrode for electrocatalytic determination of sulfide was developed using multiwalled carbon nanotubes (MWCNTs) covalently immobilized with 2,6-dichlorophenolindophenol (DPIP). The immobilization of 2,6-dichlorophenolindophenol with MWCNTs was performed with a new synthetic strategy and characterized by UV–visible absorption spectroscopy, Fourier transform infrared spectroscopy and cyclic voltammetry. The cyclic voltammetric response of DPIP grafted onto MWCNTs indicated that it promotes the low potential, sensitive and stable determination of sulfide. The dependence of response currents on the concentration of sulfide was examined and was linear in the range of 10 - 1100 µM. The detection limit of sulfide was 5 µM and RSD for 100 and 500 µM sulfides were 1.8 and 1.3 %. Many interfering species had little or no effect on the determination of sulfide. The procedure was applied to determination of sulfide in waters samples.

Keywords: functionalized carbon nanotubes, sulfide, biological samples, 2, 6-dichlorophenolindophenol

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Authors: Rojean Ghafariasar, Leili Nosrati

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The article introduces the categories and characteristics of cross-design, respectively, between industry and industry designers, artists, brands and brands, science, technology, and fashion. It focuses on the combination of technology and fashion cross-design methods, corresponding case studies on the combination of new technology fabrics, fashion design, smart devices, and also 3D printing technology, emphasizing the integration and application value of technology and fashion. The document also introduces design elements into fashion design through scientific and technological intelligence, promoting fashion innovation as well as research and development of new materials and functions, and incubates an ecosystem for the fashion industry through science and technology.

Keywords: fashion, design, industrial design, crossover design

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Authors: Demiraw Bikila, Tadesse Lejisa, Yosef Tolcha, Chala Bashea, Mehari Meles Tigist Getahun Genet Ashebir, Wossene Habtu, Feyissa Challa, Ousman Mohammed, Melkitu Kassaw, Adisu Kebede, Letebrhan G. Egzeabher, Endalkachew Befekadu, Mistire Wolde, Aster Tsegaye

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Background: Even though several factors affect reference intervals (RIs), the company-derived values are currently in use in many laboratories worldwide. However, little or no data is available regarding serum protein RIs, mainly in resource-limited setting countries like Ethiopia. Objective: To establish a reference interval for serum protein electrophoresis of apparently healthy adults in Addis Ababa, Ethiopia. Method: A cross-sectional study was conducted on a total of 297 apparently healthy adults from April-October 2019 in four selected sub-cities (Akaki, Kirkos, Arada, Yeka) of Addis Ababa, Ethiopia. Laboratory analysis of collected samples was performed using Capillarys 2 Flex Piercing analyzer, while statistical analysis was done using SPSS version 23 and med-cal software. Mann-Whitney test was used to check Partitions. Non-parametric method of reference range establishment was performed as per CLSI guideline EP28A3C. Result: The established RIs were: Albumin 53.83-64.59%, 52.24-63.55%; Alpha-1 globulin 3.04-5.40%, 3.44-5.60%; Alpha-2 globulin 8.0-12.67%, 8.44-12.87%; and Beta-1 globulin 5.01-7.38%, 5.14-7.86%. Moreover, Albumin to globulin ratio was 1.16-1.8, 1.09-1.74 for males and females, respectively. The combined RIs for Beta-2 globulin and Gamma globulin were 2.54-4.90% and 12.40-21.66%, respectively. Conclusion: The established reference interval for serum protein fractions revealed gender-specific differences except for Beta-2 globulin and Gamma globulin.

Keywords: serum protein electrophoresis, reference interval, Addis Ababa, Ethiopia

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Authors: Sundara Subramanian Karuppasamy, Che Hua Yang

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In this work, the laser ultrasound technique has been used for analyzing and imaging the inner defects in metal blocks. To detect the defects in blocks, traditionally the researchers used piezoelectric transducers for the generation and reception of ultrasonic signals. These transducers can be configured into the sparse and phased array. But these two configurations have their drawbacks including the requirement of many transducers, time-consuming calculations, limited bandwidth, and provide confined image resolution. Here, we focus on the non-contact method for generating and receiving the ultrasound to examine the inner defects in aluminum blocks. A Q-switched pulsed laser has been used for the generation and the reception is done by using Laser Doppler Vibrometer (LDV). Based on the Doppler effect, LDV provides a rapid and high spatial resolution way for sensing ultrasonic waves. From the LDV, a series of scanning points are selected which serves as the phased array elements. The side-drilled hole of 10 mm diameter with a depth of 25 mm has been introduced and the defect is interrogated by the linear array of scanning points obtained from the LDV. With the aid of the Synthetic Aperture Focusing Technique (SAFT) algorithm, based on the time-shifting principle the inspected images are generated from the A-scan data acquired from the 1-D linear phased array elements. Thus the defect can be precisely detected with good resolution.

Keywords: laser ultrasonics, linear phased array, nondestructive testing, synthetic aperture focusing technique, ultrasonic imaging

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Authors: Dong Tran, Thanh Dac Van, Ly Le

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Hemagglutinin (HA) and Neuraminidase (NA) play an important role in host immune evasion across influenza virus evolution process. The correlation between HA and NA evolution in respect to epitopic evolution and drug interaction has yet to be investigated. In this study, combining of sequence to structure evolution and statistical analysis on epitopic/binding site specificity, we identified potential therapeutic features of HA and NA that show specific antibody binding site of HA and specific binding distribution within NA active site of current inhibitors. Our approach introduces the use of sequence variation and molecular interaction to provide an effective strategy in establishing experimental based distributed representations of protein-protein/ligand complexes. The most important advantage of our method is that it does not require complete dataset of complexes but rather directly inferring feature interaction from sequence variation and molecular interaction. Using correlated sequence analysis, we additionally identified co-evolved mutations associated with maintaining HA/NA structural and functional variability toward immunity and therapeutic treatment. Our investigation on the HA binding specificity revealed unique conserved stalk domain interacts with unique loop domain of universal antibodies (CR9114, CT149, CR8043, CR8020, F16v3, CR6261, F10). On the other hand, NA inhibitors (Oseltamivir, Zaninamivir, Laninamivir) showed specific conserved residue contribution and similar to that of NA substrate (sialic acid) which can be exploited for drug design. Our study provides an important insight into rational design and identification of novel therapeutics targeting universally recognized feature of influenza HA/NA.

Keywords: influenza virus, hemagglutinin (HA), neuraminidase (NA), sequence evolution

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Authors: Ghada A. Alfattni

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Analysing unbalanced datasets is one of the challenges that practitioners in machine learning field face. However, many researches have been carried out to determine the effectiveness of the use of the synthetic minority over-sampling technique (SMOTE) to address this issue. The aim of this study was therefore to compare the effectiveness of the SMOTE over different models on unbalanced datasets. Three classification models (Logistic Regression, Support Vector Machine and Nearest Neighbour) were tested with multiple datasets, then the same datasets were oversampled by using SMOTE and applied again to the three models to compare the differences in the performances. Results of experiments show that the highest number of nearest neighbours gives lower values of error rates. 

Keywords: imbalanced datasets, SMOTE, machine learning, logistic regression, support vector machine, nearest neighbour

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Authors: Umairah Natasya Binti Mohd Omeershffudin, Suresh Kumar

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Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. Particular concern is the global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae. Characterization of antibiotic resistance determinants at the genomic level plays a critical role in understanding, and potentially controlling, the spread of multidrug-resistant (MDR) pathogens. In this study, drug-resistant Klebsiella pneumoniae strain 825795-1 was investigated with extensive computational approaches aimed at identifying novel drug targets among hypothetical proteins. We have analyzed 1099 hypothetical proteins available in genome. We have used in-silico genome subtraction methodology to design potential and pathogen-specific drug targets against Klebsiella pneumoniae. We employed bioinformatics tools to subtract the strain-specific paralogous and host-specific homologous sequences from the bacterial proteome. The sorted 645 proteins were further refined to identify the essential genes in the pathogenic bacterium using the database of essential genes (DEG). We found 135 unique essential proteins in the target proteome that could be utilized as novel targets to design newer drugs. Further, we identified 49 cytoplasmic protein as potential drug targets through sub-cellular localization prediction. Further, we investigated these proteins in the DrugBank databases, and 11 of the unique essential proteins showed druggability according to the FDA approved drug bank databases with diverse broad-spectrum property. The results of this study will facilitate discovery of new drugs against Klebsiella pneumoniae.

Keywords: pneumonia, drug target, hypothetical protein, subtractive genomics

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Authors: Mark Bezner, Shani Deri, Tom Trigano, Kfir Ben-Harush

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Intermediate filament (IF) proteins-based fibers are among the toughest fibers in nature, as was shown by native hagfish slime threads and by synthetic fibers that are based on type V IF-proteins, the nuclear lamins. It is assumed that their mechanical performance stems from two major factors: (1) the transition from elastic -helices to stiff-sheets during tensile load; and (2) the specific organization of the coiled-coil proteins into a hierarchical network of nano-filaments. Here, we investigated the interrelationship between these two factors by using wet-spun fibers based on C. elegans (Ce) lamin. We found that Ce-lamin fibers, whether assembled in aqueous or alcoholic solutions, had the same nonlinear mechanical behavior, with the elastic region ending at ~5%. The pattern of the transition was, however, different: the ratio between -helices and -sheets/random coils was relatively constant until a 20% strain for fibers assembled in an aqueous solution, whereas for fibers assembled in 70% ethanol, the transition ended at a 6% strain. This structural phenomenon in alcoholic solution probably occurred through the transition between compacted and extended conformation of the random coil, and not between -helix and -sheets, as cycle analyses had suggested. The different transition pattern can also be explained by the different higher order organization of Ce-lamins in aqueous or alcoholic solutions, as demonstrated by introducing a point mutation in conserved residue in Ce-lamin gene that alter the structure of the Ce-lamins’ nano-fibrils. In addition, biomimicking the layered structure of silk and hair fibers by coating the Ce-lamin fiber with a hydrophobic layer enhanced fiber toughness and lead to a reversible transition between -helix and the extended conformation. This work suggests that different hierarchical structures, which are formed by specific assembly conditions, lead to diverse secondary structure transitions patterns, which in turn affect the fibers’ mechanical properties.

Keywords: protein-based fibers, intermediate filaments (IF) assembly, toughness, structure-property relationships

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Authors: Atul K. Desai, Hemal J. Shah

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The tall windmill towers are designed as monopole tower or lattice tower. In the present research, a 125-meter high hybrid tower which is a combination of lattice and monopole type is proposed. The response of hybrid tower is compared with conventional monopole tower. The towers were analyzed in finite element method software considering nonlinear seismic time history load. The synthetic seismic time history for different soil is derived using the SeismoARTIF software. From the present research, it is concluded that, in the hybrid tower, we are not getting resonance condition. The base shear is less in hybrid tower compared to monopole tower for different soil conditions.

Keywords: dynamic analysis, hybrid wind mill tower, resonance condition, synthetic time history

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Authors: Kshitij Bhardwaj, R.K. Trivedi, Shipra Dixit

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We used biological detoxification method that converts toxic residue waste of Jatropha curcas oil seeds (non edible oil seed) into industrial bio-products and animal feed material. Present study describes the complete degradation of phorbol esters by Aspergillus Niger strain during solid state fermentation (SSF) of deoiled Jatropha curcas seed cake. Phorbol esters were completely degraded in 15 days under the optimized SSF conditions viz deoiled cake 5.0 gm moistened with 5.0 ml distilled water; inoculum 2 ml of overnight grown Aspergillus niger; incubated at 30◦ C, pH 7.0. This method simultaneously induces the production of Protease enzyme by Aspergillus Niger which has high potential to be used in feedstuffs .The maximum Protease activities obtained were 709.16 mg/ml in Jatropha curcas oil seed cake. The protein isolate had small amounts of phorbol esters, phytic acid, and saponin without any lectin. Its minimum and maximum solubility were at pH 4.0&12.0. Water and oil binding capacities were 3.22 g water/g protein and 1.86 ml oil/g protein respectively.Emulsion activity showed high values in a range of basic pH. We concluded that Jatropha Curcas seed cake has a potential to be used as a novel source of functional protein for food or feed applications.

Keywords: solid state fermentation, Jatropha curcas, oil seed cake, phorbol ester

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Authors: W. P. Hu, J. V. Kumar, Jeffrey J. P. Tsai

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The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.

Keywords: nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation

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Authors: Mateen A Khan, Taj Mohammad, Md. Imtaiyaz Hassan

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Alzheimer’s disease is characterized by the accumulation of the processing products of the amyloid beta peptide cleaved by amyloid precursor protein (APP). Iron increases the synthesis of amyloid beta peptides, which is why iron is present in Alzheimer's disease patients' amyloid plaques. Iron misregulation in the brain is linked to the overexpression of APP protein, which is directly related to amyloid-β aggregation in Alzheimer’s disease. The APP 5'-UTR region encodes a functional iron-responsive element (IRE) stem-loop that represents a potential target for modulating amyloid production. Targeted regulation of APP gene expression through the modulation of 5’-UTR sequence function represents a novel approach for the potential treatment of AD because altering APP translation can be used to improve both the protective brain iron balance and provide anti-amyloid efficacy. The molecular docking analysis of APP IRE RNA with eukaryotic translation initiation factors yields several models exhibiting substantial binding affinity. The finding revealed that the interaction involved a set of functionally active residues within the binding sites of eIF4F. Notably, APP IRE RNA and eIF4F interaction were stabilized by multiple hydrogen bonds with residues of APP IRE RNA and eIF4F. It was evident that APP IRE RNA exhibited a structural complementarity that tightly fit within binding pockets of eIF4F. The simulation studies further revealed the stability of the complexes formed between RNA and eIF4F, which is crucial for assessing the strength of these interactions and subsequent roles in the pathophysiology of Alzheimer’s disease. In addition, MD simulations would capture conformational changes in the IRE RNA and protein molecules during their interactions, illustrating the mechanism of interaction, conformational change, and unbinding events and how it may affect aggregation propensity and subsequent therapeutic implications. Our binding studies correlated well with the translation efficiency of APP mRNA. Overall, the outcome of this study suggests that the genomic modification and/or inhibiting the expression of amyloid protein by targeting APP IRE RNA can be a viable strategy to identify potential therapeutic targets for AD and subsequently be exploited for developing novel therapeutic approaches.

Keywords: Alzheimer's disease, Protein-RNA interaction analysis, molecular docking simulations, conformational dynamics, binding stability, binding kinetics, protein synthesis.

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin 1), whose disruption leads to increased drought stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1 is regulated in response to drought stress by alternative splicing.

Keywords: alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance

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Authors: Pawan Kumar Sharma, J. Stephan Sampath Kumar, S. Anand, Chandana B. L.

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Protein is the major component for the success in culture of shrimp and fishes. Apparently, excess dietary protein is undesirable, as it not only enhances the production cost but also leads to water quality deterioration. A field survey was conducted with aqua farmers of Kerala, India, a leading state in coastal aquaculture, to assess the role of protein component in feed that can be efficiently and effectively managed for sustainable aquaculture. The study showed an average feed amount of 13.55 ± 2.16 tonnes per hectare was being used by the farmers of Kerala. The average feed cost percentage of Rs. 57.76 ± 13.46 /kg was invested for an average protein level of 36.26 % ± 0.082 in the feed and Rs.78.95 ± 3.086 per kilogram of feed was being paid by the farmers. Study revealed that replacement of fish meal and fish oil within shrimp aquafeeds with alternative protein, and lipid sources can only be achieved if changes are made in the basic shrimp culturing practices, such as closed farming system through water recycling or zero-water exchange, and by maximizing in-situ, floc and natural food production within the culture system. The upshot of such production systems is that imports of high-quality feed ingredients and aqua feeds can eventually be eliminated, and the utilization of locally available feed ingredients from agricultural by-products can be greatly improved and maximized. The promotion of closed shrimp production systems would also greatly reduce water use and increase shrimp production per unit area but would necessitate the continuous provision of electricity for aeration during production. Alternative energy sources such as solar power might be used, and resource poor farming communities should also explore wind energy for use. The study concluded that farm made feed and closed farming systems are essential for the sustainability and profitability of the aquaculture industry.

Keywords: aqua feeds, floc, fish meal, protein, zero-water exchange

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Authors: Jyh-Cheng Chen, Tai-Jing Wang, Yun-Wei Lin

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Astaxanthin has been demonstrated to exhibit a wide range of beneficial effects including anti-inflammatory and anti-cancer properties. However, the molecular mechanism of astaxanthin-induced cytotoxicity in non-small cell lung cancer (NSCLC) cells has not been identified. Rad51 plays a central role in homologous recombination and high levels of Rad51 expression are observed in chemo- or radioresistant carcinomas. In this study, astaxanthin treatment inhibited cell viability and proliferation of two NSCLC cells, A549 and H1703. Treatment with astaxanthin decreased Rad51 expression and phospho-AKT protein level in a time and dose-dependent manner. Furthermore, expression of constitutively active AKT (AKT-CA) vector significantly rescued the decreased Rad51 protein and mRNA levels in astaxanthin-treated NSCLC cells. Combined treatment with PI3K inhibitors (LY294002 or wortmannin) and astaxanthin further decreased the Rad51 expression in NSCLC cells. Knockdown of Rad51 enhanced astaxanthin-induced cytotoxicity and growth inhibition in NSCLC cells. These findings may have implications for the rational design of future drug regimens incorporating astaxanthin for the treatment of NSCLC.

Keywords: astaxanthin, cytotoxicity, AKT, non-small cell lung cancer, PI3K

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Authors: Natalia Caldeira De Carvalho, Tassia Batista Pessato, Luis Gustavo R. Fernandes, Ricardo L. Zollner, Flavia Maria Netto

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Protein hydrolysates are ingredients of enteral diets and hypoallergenic formulas. Enzymatic hydrolysis is the most commonly used method for reducing the antigenicity of milk protein. The antigenicity and physicochemical characteristics of the protein hydrolysates depend on the reaction parameters. Among them, pH has been pointed out as of the major importance. Hydrolysis reaction in laboratory scale is commonly carried out under controlled pH (pH-stat). However, from the industrial point of view, controlling pH during hydrolysis reaction may be infeasible. This study evaluated the impact of pH control on the physicochemical properties and antigenicity of the hydrolysates of whey proteins with Alcalase. Whey protein isolate (WPI) solutions containing 3 and 7 % protein (w/v) were hydrolyzed with Alcalase 50 and 100 U g-1 protein at 60°C for 180 min. The reactions were carried out under controlled and uncontrolled pH conditions. Hydrolyses performed under controlled pH (pH-stat) were initially adjusted and maintained at pH 8.5. Hydrolyses carried out without pH control were initially adjusted to pH 8.5. Degree of hydrolysis (DH) was determined by OPA method, peptides profile was evaluated by HPLC-RP, and molecular mass distribution by SDS-PAGE/Tricine. The residual α-lactalbumin (α-La) and β-lactoglobulin (β-Lg) concentrations were determined using commercial ELISA kits. The specific IgE and IgG binding capacity of hydrolysates was evaluated by ELISA technique, using polyclonal antibodies obtained by immunization of female BALB/c mice with α-La, β-Lg and BSA. In hydrolysis under uncontrolled pH, the pH dropped from 8.5 to 7.0 during the first 15 min, remaining constant throughout the process. No significant difference was observed between the DH of the hydrolysates obtained under controlled and uncontrolled pH conditions. Although all hydrolysates showed hydrophilic character and low molecular mass peptides, hydrolysates obtained with and without pH control exhibited different chromatographic profiles. Hydrolysis under uncontrolled pH released, predominantly, peptides between 3.5 and 6.5 kDa, while hydrolysis under controlled pH released peptides smaller than 3.5 kDa. Hydrolysis with Alcalase under all conditions studied decreased by 99.9% the α-La and β-Lg concentrations in the hydrolysates detected by commercial kits. In general, β-Lg concentrations detected in the hydrolysates obtained under uncontrolled pH were significantly higher (p<0.05) than those detected in hydrolysates produced with pH control. The anti-α-La and anti-β-Lg IgE and IgG responses to all hydrolysates decreased significantly compared to WPI. Levels of specific IgE and IgG to the hydrolysates were below 25 and 12 ng ml-1, respectively. Despite the differences in peptide composition and α-La and β-Lg concentrations, no significant difference was found between IgE and IgG binding capacity of hydrolysates obtained with or without pH control. These results highlight the impact of pH on the hydrolysates characteristics and their concentrations of antigenic protein. Divergence between the antigen detection by commercial ELISA kits and specific IgE and IgG binding response was found in this study. This result shows that lower protein detection does not imply in lower protein antigenicity. Thus, the use of commercial kits for allergen contamination analysis should be cautious.

Keywords: allergy, enzymatic hydrolysis, milk protein, pH conditions, physicochemical characteristics

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Authors: I. Sani, A. Abdulhamid, F. Bello, Isah M. Fakai

Abstract:

This research has focused on the application of green fluorescent protein (GFP) as a new technique for direct monitoring of fermentation processes involving cultured bacteria. To use GFP as a sensor for pH and oxygen, percentage ratio of red fluorescence to green (% R/G) was evaluated. Assessing the magnitude of the % R/G ratio in relation to low or high pH and oxygen concentration, the bacterial strains were cultivated under aerobic and anaerobic conditions. SCC1 strains of E. coli were grown in a 5 L laboratory fermenter, and during the fermentation, the pH and temperature were controlled at 7.0 and 370C respectively. Dissolved oxygen tension (DOT) was controlled between 15-100% by changing the agitation speed between 20-500 rpm respectively. Effect of reducing the DOT level from 100% to 15% was observed after 4.5 h fermentation. There was a growth arrest as indicated by the decrease in the OD650 at this time (4.5-5 h). The relative fluorescence (green) intensity was decreased from about 460 to 420 RFU. However, %R/G ratio was significantly increased from about 0.1% to about 0.25% when the DOT level was decreased to 15%. But when the DOT was changed to 100%, a little increase in the RF and decrease in the %R/G ratio were observed. Therefore, GFP can effectively detect and indicate any change in pH and oxygen level during fermentation processes.

Keywords: Escherichia coli SCC1, fermentation process, green fluorescent protein, red fluorescence

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Authors: Mohammed Alasel, Michael Keusgen

Abstract:

Gold is a noble metal; in its nano-scale level (e.g. spherical nanoparticles), the conduction electrons are triggered to collectively oscillate with a resonant frequency when certain wavelengths of electromagnetic radiation interact with its surface; this phenomenon is known as surface plasmon resonance (SPR). SPR is responsible for giving the gold nanoparticles its intense red color depending mainly on its size, shape and distance between nanoparticles. A decreased distance between gold nanoparticles results in aggregation of them causing a change in color from red to blue. This aggregation enables gold nanoparticles to serve as a sensitive biosensoric indicator. In the proposed work, gold nanoparticles were modified with two proteins: i) Borrelia antigen, variable lipoprotein surface-exposed protein (VlsE), and ii) protein A. VlsE antigen induces a strong antibody response against Lyme disease and can be detected from early to late phase during the disease in humans infected with Borrelia. In addition, it shows low cross-reaction with the other non-pathogenic Borrelia strains. The high specificity of VlsE antigen to anti-Borrelia antibodies, combined simultaneously with the high specificity of protein A to the Fc region of all IgG human antibodies, was utilized to develop a rapid test for serological point of care diagnosis of borreliosis in human serum. Only in the presence of anti-Borrelia antibodies in the serum probe, an aggregation of gold nanoparticles can be observed, which is visible by a concentration-dependent colour shift from red (low IgG) to blue (high IgG). Experiments showed it is clearly possible to distinguish between positive and negative sera samples using a simple suspension of the two-protein modified gold nanoparticles in a very short time (30 minutes). The proposed work showed the potential of using such modified gold nanoparticles generally for serological diagnosis. Improved specificity and reduced assay time can be archived in applying increased salt concentrations combined with decreased pH values (pH 5).

Keywords: gold nanoparticles, gold aggregation, serological diagnosis, protein A, lyme borreliosis

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Authors: Kübra Aktaş, Nihat Akin

Abstract:

Tarhana is a traditional Turkish fermented food. It is widely consumed as soup and includes many different ingredients such as wheat flour, various vegetables, and spices, yoghurt, bakery yeast. It can also be enriched by adding other ingredients. Thus, its nutritional properties can be enhanced. In this study, tarhana was supplemented with two different types of brans (rice bran and corn bran) and WPC (whey protein concentrate powder) to improve its nutritional and functional properties. Some chemical properties of tarhana containing two different brans and their levels (0, 5, 10 and 15%) and WPC (0, 5, 10%) were investigated. The results indicated that addition of WPC increased ash content in tarhanas which were fortified with rice and corn bran. The highest antioxidant and phenolic content values were obtained with addition of rice bran in tarhana formulation. Compared to tarhana with corn bran, rice bran addition gave higher oil content values. The cellulose content of tarhana samples was determined between 0.75% and 2.74% and corn bran showed an improving effect on cellulose contents of samples. In terms of protein content, addition of WPC into the tarhana raised protein content for the samples.

Keywords: corn, rice, tarhana, whey

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Authors: Katerina H. Takova, Ivan N. Minkov, Gergana G. Zahmanova

Abstract:

Molecular farming is the production of recombinant proteins in plants with the aim to use the protein as a purified product, crude extract or directly in the planta. Plants gain more attention as expression systems compared to other ones due to the cost effective production of pharmaceutically important proteins, appropriate post-translational modifications, assembly of complex proteins, absence of human pathogens to name a few. In addition, transient expression in plant leaves enables production of recombinant proteins within few weeks. Hepatitis E virus (HEV) is a causative agent of acute hepatitis. HEV causes epidemics in developing countries and is primarily transmitted through the fecal-oral route. Presently, all efforts for development of Hepatitis E vaccine are focused on the Open Read Frame 2 (ORF2) capsid protein as it contains epitopes that can induce neutralizing antibodies. For our purpose, we used the CMPV-based vector-pEAQ-HT for transient expression of HEV ORF2 in Nicotiana benthamina. Different molecular analysis (Western blot and ELISA) showed that HEV ORF2 capsid protein was expressed in plant tissue in high-yield up to 1g/kg of fresh leaf tissue. Electron microscopy showed that the capsid protein spontaneously assembled in low abundance virus-like particles (VLPs), which are highly immunogenic structures and suitable for vaccine development. The expressed protein was recognized by both human and swine HEV positive sera and can be used as a diagnostic reagent for the detection of HEV infection. Production of HEV capsid protein in plants is a promising technology for further HEV vaccine investigations. Here, we reported for a rapid high-yield transient expression of a recombinant protein in plants suitable for vaccine production as well as a diagnostic reagent. Acknowledgments -The authors’ research on HEV is supported with grants from the Project PlantaSYST under the Widening Program, H2020 as well as under the UK Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programme Grant ‘Understanding and Exploiting Plant and Microbial Secondary Metabolism’ (BB/J004596/1). The authors want to thank Prof. George Lomonossoff (JIC, Norwich, UK) for his contribution.

Keywords: hepatitis E virus, plant molecular farming, transient expression, vaccines

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Authors: Muhammad Arifur Rahman, Talukdar M. Waliullah, Takashi Ushimaru

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Nucleophagy selectively degrades nuclear materials, especially nucleolus after nutrient starvation or inactivation of TORC1 kinase in budding yeast. Budding yeast phosphatidate (PA) phosphatase Pah1 that converts PA to diacylglycerol is essential for partitioning of lipid precursors between membrane and storage that is crucial for many aspects of cell growth and development. Pah1 is required for nuclear/ER membrane biogenesis and vacuole function, but whether Pah1 and its activator Nem1/Spo7 protein phosphatase complex are involved in autophagy is largely unknown. Loss of Pah1 causes expansion of the nucleus and fragmentation of the vacuole. Here we show that Pah1 is required for bulk autophagy and nucleophagy after TORC1 inactivation. Loss of Pah1 impaired nucleophagy severely and bulk autophagy to a lesser extent. Loss of the Pah1 activator Nem1-Spo7 protein phosphatase exhibited similar features.

Keywords: autophagy, Nem1/Spo7 phosphatase, Pah1, nucleophagy, TORC1

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Authors: Nijole Savickiene, Antonella Di Sotto, Gabriela Mazzanti, Rasa Starselskyte, Silvia Di Giacomo, Annabella Vitalone

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Plant lectins are non-enzymic and non-immune origin proteins that specifically recognize and bind to various sugar structures and possess the activity to agglutinate cells and/or precipitate polysaccharides and glycoconjugates. The emerging evidences showed that plant lectins contribute not only to tumour cell recognition but also to cell adhesion and localization, to signal transduction, to mitogenic cytotoxicity and apoptosis. Among chitin-binding lectins, the Urtica dioica agglutinin (UDA), which is a complex of different isoforms, has been poorly studied for its biological activity. In this context and according to the increasing interest for lectins as novel antitumor drugs, present paper aimed at evaluating the potential antimutagenic activity of a lectin-like glycoprotein-enriched fraction from aerial part of Urtica dioica L. Aim: to evaluate the potential chemopreventive properties of a protein - lectin fraction from the aerial part of Urtica dioica. Materials and methods: Protein – lectin fraction has been tested for the antimutagenic activity in bacteria (50–800 mg/plate; Ames test by the preincubation method) and for the cytotoxicity on human hepatoma HepG2 cells (0.06–2 mg/mL; 24 and 48 h incubation). Results: Protein – lectin fraction from stinging nettle was not cytotoxic on HepG2 cells up to 2 mg/mL; conversely, it exhibited a strong antimutagenic activity against the mutagen 2-aminoanthracene (2AA) in all strains tested (maximum inhibition of 56.78 and 61% in TA98, TA100, and WP2uvrA strains, respectively, at 800 mg/plate). Discussion and conclusions: Protein – lectin fraction from Urtica dioica L. possesses antimutagenic and radical scavenging properties. Being 2AA a pro-carcinogenic agent, we hypothesize that the antimutagenicity of it can be due to the inhibition of CYP450-isoenzymes, involved in the mutagen bioactivation.

Keywords: lectins, antimutagenicity, chemoprevention, Urtica dioica

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Authors: Babak Forouraghi

Abstract:

A genetic circuit is a collection of interacting genes and proteins that enable individual cells to implement and perform vital biological functions such as cell division, growth, death, and signaling. In cell engineering, synthetic gene circuits are engineered networks of genes specifically designed to implement functionalities that are not evolved by nature. These engineered networks enable scientists to tackle complex problems such as engineering cells to produce therapeutics within the patient's body, altering T cells to target cancer-related antigens for treatment, improving antibody production using engineered cells, tissue engineering, and production of genetically modified plants and livestock. Construction of computational models to realize genetic circuits is an especially challenging task since it requires the discovery of flow of genetic information in complex biological systems. Building synthetic biological models is also a time-consuming process with relatively low prediction accuracy for highly complex genetic circuits. The primary goal of this study was to investigate the utility of a pre-trained bidirectional encoder transformer that can accurately predict gene expressions in genetic circuit designs. The main reason behind using transformers is their innate ability (attention mechanism) to take account of the semantic context present in long DNA chains that are heavily dependent on spatial representation of their constituent genes. Previous approaches to gene circuit design, such as CNN and RNN architectures, are unable to capture semantic dependencies in long contexts as required in most real-world applications of synthetic biology. For instance, RNN models (LSTM, GRU), although able to learn long-term dependencies, greatly suffer from vanishing gradient and low-efficiency problem when they sequentially process past states and compresses contextual information into a bottleneck with long input sequences. In other words, these architectures are not equipped with the necessary attention mechanisms to follow a long chain of genes with thousands of tokens. To address the above-mentioned limitations of previous approaches, a transformer model was built in this work as a variation to the existing DNA Bidirectional Encoder Representations from Transformers (DNABERT) model. It is shown that the proposed transformer is capable of capturing contextual information from long input sequences with attention mechanism. In a previous work on genetic circuit design, the traditional approaches to classification and regression, such as Random Forrest, Support Vector Machine, and Artificial Neural Networks, were able to achieve reasonably high R2 accuracy levels of 0.95 to 0.97. However, the transformer model utilized in this work with its attention-based mechanism, was able to achieve a perfect accuracy level of 100%. Further, it is demonstrated that the efficiency of the transformer-based gene expression classifier is not dependent on presence of large amounts of training examples, which may be difficult to compile in many real-world gene circuit designs.

Keywords: transformers, generative ai, gene expression design, classification

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