Search results for: protein domains.

Authors: Aditi Shukla, Ambarish S. Vidyarthi, Subir Samanta

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The worldwide prevalence of H3N2 influenza virus and its increasing resistance to the existing drugs necessitates for the development of an improved/better targeting anti-influenza drug. H3N2 influenza neuraminidase is one of the two membrane-bound proteins belonging to group-2 neuraminidases. It acts as key player involved in viral pathogenicity and hence, is an important target of anti-influenza drugs. Oseltamivir is one of the potent drugs targeting this neuraminidase. In the present work, we have taken subtype N2 neuraminidase as the receptor and probable analogs of oseltamivir as drug molecules to study the protein-drug interaction in anticipation of finding efficient modified candidate compound. Oseltamivir analogs were made by modifying the functional groups using Marvin Sketch software and were docked using Schrodinger-s Glide. Oseltamivir analog 10 was detected to have significant energy value (16% less compared to Oseltamivir) and could be the probable lead molecule. It infers that some of the modified compounds can interact in a novel manner with increased hydrogen bonding at the active site of neuraminidase and it might be better than the original drug. Further work can be carried out such as enzymatic inhibition studies; synthesis and crystallizing the drug-target complex to analyze the interactions biologically.

Keywords: H3N2 Influenza, Neuraminidase, Oseltamiviranalogs, structure based drug designing

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Authors: Ghada Badr, Arwa Alturki

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The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures. Knowing the common functionalities between two RNA structures allows a better understanding and a discovery of other relationships between them. Besides, identifying non-coding RNAs -that is not translated into a protein- is a popular application in which RNA structural alignment is the first step A few methods for RNA structure-to-structure alignment have been developed. Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment. Less attention is given in the literature to the use of efficient RNA structure representation and the structure-to-structure alignment methods are lacking. In this paper, we introduce an O(N2) Component-based Pairwise RNA Structure Alignment (CompPSA) algorithm, where structures are given as a component-based representation and where N is the maximum number of components in the two structures. The proposed algorithm compares the two RNA secondary structures based on their weighted component features rather than on their base-pair details. Extensive experiments are conducted illustrating the efficiency of the CompPSA algorithm when compared to other approaches and on different real and simulated datasets. The CompPSA algorithm shows an accurate similarity measure between components. The algorithm gives the flexibility for the user to align the two RNA structures based on their weighted features (position, full length, and/or stem length). Moreover, the algorithm proves scalability and efficiency in time and memory performance.

Keywords: Alignment, RNA secondary structure, pairwise, component-based, data mining.

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Authors: Qiuyu Dai, Haochong Zhang, Xiangrong Liu

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Efficient matrix-vector multiplication with diagonal sparse matrices is pivotal in a multitude of computational domains, ranging from scientific simulations to machine learning workloads. When encoded in the conventional Diagonal (DIA) format, these matrices often induce computational overheads due to extensive zero-padding and non-linear memory accesses, which can hamper the computational throughput, and elevate the usage of precious compute and memory resources beyond necessity. The ’DIA-Adaptive’ approach, a methodological enhancement introduced in this paper, confronts these challenges head-on by leveraging the advanced parallel instruction sets embedded within Machine Learning Units (MLUs). This research presents a thorough analysis of the DIA-Adaptive scheme’s efficacy in optimizing Sparse Matrix-Vector Multiplication (SpMV) operations. The scope of the evaluation extends to a variety of hardware architectures, examining the repercussions of distinct thread allocation strategies and cluster configurations across multiple storage formats. A dedicated computational kernel, intrinsic to the DIA-Adaptive approach, has been meticulously developed to synchronize with the nuanced performance characteristics of MLUs. Empirical results, derived from rigorous experimentation, reveal that the DIA-Adaptive methodology not only diminishes the performance bottlenecks associated with the DIA format but also exhibits pronounced enhancements in execution speed and resource utilization. The analysis delineates a marked improvement in parallelism, showcasing the DIA-Adaptive scheme’s ability to adeptly manage the interplay between storage formats, hardware capabilities, and algorithmic design. The findings suggest that this approach could set a precedent for accelerating SpMV tasks, thereby contributing significantly to the broader domain of high-performance computing and data-intensive applications.

Keywords: Adaptive method, DIA, diagonal sparse matrices, MLU, sparse matrix-vector multiplication.

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Authors: Permphan Dharmasaroja

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Acute disseminated encephalomyelitis (ADEM) has been reported to develop after a hymenoptera sting, but its pathogenesis is not known in detail. Myelin basic protein (MBP)- specific T cells have been detected in the blood of patients with ADEM, and a proportion of these patients develop multiple sclerosis (MS). In an attempt to understand the mechanisms underlying ADEM, molecular mimicry between hymenoptera venom peptides and the human immunodominant MBP peptide was scrutinized, based on the sequence and structural similarities, whether it was the root of the disease. The results suggest that the three wasp venom peptides have low sequence homology with the human immunodominant MBP residues 85-99. Structural similarity analysis among the three venom peptides and the MS-related HLA-DR2b (DRA, DRB1*1501)-associated immunodominant MHC binding/TCR contact residues 88-93, VVHFFK showed that hyaluronidase residues 7-12, phospholipase A1 residues 98-103, and antigen 5 residues 109-114 showed a high degree of similarity 83.3%, 100%, and 83.3% respectively. In conclusion, some wasp venom peptides, particularly phospholipase A1, may potentially act as the molecular motifs of the human 3HLA-DR2b-associated immunodominant MBP88-93, and possibly present a mechanism for induction of wasp sting-associated ADEM.

Keywords: central nervous system, Hymenoptera, myelin basicprotein, molecular mimicry.

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Authors: Hai Xu, Yiwei Wang, Xi Bao, Bihua Deng, Pengcheng Li, Yu Lu

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T7 phage could be used as a perfect vector for peptides expression and haptens presentation. T7-3GnRH recombinant phage was constructed by inserting three copies of Gonadotrophin Releasing Hormone (GnRH) gene into the multiple cloning site of T7 Select 415-1b phage genome. The positive T7-3GnRH phage was selected by using polymerase chain reaction amplification, and the p10B-3GnRH fusion protein was verified by SDS-PAGE and Western-blotting assay. T7-3GnRH vaccine was made and immunized with 10¹⁰ pfu in 0.2 ml per dose in mice. Blood samples were collected at an interval in weeks, and anti-GnRH antibody and testosterone concentrations were detected by ELISA and radioimmunoassay, respectively. The results show that T7-3GnRH phage particles confer a high immunogenicity to the GnRH-derived epitope. Moreover, the T7-3GnRH vaccine induced higher level of anti-GnRH antibody than ImproVac^®. However, the testosterone concentrations in both immunized groups were at a similar level, and the testis developments were significantly inhibited compared to controls. These findings demonstrated that the anti-GnRH antibody could neutralize the endogenous GnRH to down regulate testosterone level and limit testis development, highlighting the potential value of T7-3GnRH in the immunocastration vaccine research.

Keywords: Gonadotrophin releasing hormone, GnRH, immunocastration, T7 phage, phage vaccine.

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Authors: W. I. Wan Rosli, M. A. Solihah., N. A. Nik Fakurudin, M. S. Aishah, S. S. J. Mohsin

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The nutrient composition and sensory properties of poultry-based patties (PBPs) incorporated with various levels of grey oyster mushroom (Pleurotus sajor-caju, PSC) were studied. The PBPs were formulated with either 0%, 25% or 50% of fresh ground PSC. Results show poultry patty formulated with 25% PSC had protein content of 17.46% lower than the control patty which had 18.13% but it was not significant. Meanwhile, both cooked poultry patties containing 25% and 50% PSC significantly recorded lower concentration of fat at 10.67% and 7.15%, respectively. On the other hand, poultry patty added with 50% ground PSC shows the highest concentration of total dietary fibre (TDF) of 4.90 g/100g compared to poultry patty containing 25% of mushroom (3.40 g/100g) and to the control (1.90g/100g). In addition, patty incorporated with 25% PSC had moisture content of 57.91% which is significantly lower than patty formulated with 50% which had moisture of 61.80%. In the sensory evaluation, there were no differences recorded in all sensory attributes of PSC-based patties judged by untrained panelists. In conclusion, the addition of PSC to replace poultry meat can be recommended for the purpose of lowering production cost, enhancing nutritional composition and maintaining the acceptability of poultry patties.

Keywords: oyster mushroom (PSC), poultry patty, nutrient composition, sensory evaluation

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Authors: N. Cetinkaya, Y. S. Kuleyin

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The aim of this study was to estimate the digestibility of the fruit internal skin of different varieties of hazelnuts to propose hazelnut fruit skin as an alternative feed source as roughage in ruminant nutrition. In 2015, the fruit internal skins of three different varieties of round hazelnuts (RH), pointed hazelnuts (PH) and almond hazelnuts (AH) were obtained from hazelnut processing factory then their crude nutrients analysis were carried out. Organic matter digestibility (OMD) and metabolisable energy (ME) values of hazelnut fruit skins were estimated from gas measured by in vitro gas production method. Their antioxidant activities were determined by spectrophotometric method. Crude nutrient values of three different varieties were; organic matter (OM): 87.83, 87.81 and 87.78%), crude protein (CP): 5.97, 5.93 and 5.89%, neutral detergent fiber (NDF): 30.30, 30.29 and 30.29%, acid detergent fiber (ADF): 48.68, 48.67 and 48.66% and acid detergent lignin (ADL): 25.43, 25.43 and 25.39% respectively. OMD from 24 h incubation time of RH, PH and AH were 22.04, 22.46 and 22.74%; ME_GP values were 3.69, 3.75 and 3.79 MJ/kg DM; and antioxidant activity values were 94.60, 94.54 and 94.52 IC 50 mg/mL respectively. The fruit internal skin of different varieties of hazelnuts may be considered as an alternative roughage for ruminant nutrition regarding to their crude and digestible nutritive values. Moreover, hazelnut fruit skin has a rich antioxidant content so it may be used as a feed additive for both ruminant and non-ruminant animals.

Keywords: Antioxidant activity, hazelnut fruit skin, metabolizable energy, organic matter digestibility.

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Authors: A. L. Ho, N. Ab. Aziz, F. S. Taip, M. N. Ibrahim

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The study of the fouling deposition of pink guava juice (PGJ) is relatively new research compared to milk fouling deposit. In this work, a new experimental set-up was developed to imitate the fouling formation in heat exchanger, namely a continuous flow experimental set-up heat exchanger. The new experimental setup was operated under industrial pasteurization temperature of PGJ, which was at 93°C. While the flow rate and pasteurization period were based on the experimental capacity, which were 0.5 and 1 liter/min for the flow rate and the pasteurization period was set for 1 hour. Characterization of the fouling deposit was determined by using various methods. Microstructure of the deposits was carried out using ESEM. Proximate analyses were performed to determine the composition of moisture, fat, protein, fiber, ash and carbohydrate content. A study on the hardness and stickiness of the fouling deposit was done using a texture analyzer. The presence of seedstone in pink guava juice was also analyzed using a particle analyzer. The findings shown that seedstone from pink guava juice ranging from 168 to 200μm and carbohydrate was found to be a major composition (47.7% of fouling deposit consists of carbohydrate). Comparison between the hardness and stickiness of the deposits at two different flow rates showed that fouling deposits were harder and denser at higher flow rate. Findings from this work provide basis knowledge for further study on fouling and cleaning of PGJ.

Keywords: Pink guava juice, fouling deposit, heat exchanger.

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Authors: Hritwik Ghosh, Irfan Sadiq Rahat, Sachi Nandan Mohanty, J. V. R. Ravindra, Abdus Sobur

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In the rapidly evolving landscape of medical diagnostics, the early detection and accurate classification of skin cancer remain paramount for effective treatment outcomes. This research delves into the transformative potential of artificial intelligence (AI), specifically deep learning (DL), as a tool for discerning and categorizing various skin conditions. Utilizing a diverse dataset of 3,000 images, representing nine distinct skin conditions, we confront the inherent challenge of class imbalance. This imbalance, where conditions like melanomas are over-represented, is addressed by incorporating class weights during the model training phase, ensuring an equitable representation of all conditions in the learning process. Our approach presents a hybrid model, amalgamating the strengths of two renowned convolutional neural networks (CNNs), VGG16 and ResNet50. These networks, pre-trained on the ImageNet dataset, are adept at extracting intricate features from images. By synergizing these models, our research aims to capture a holistic set of features, thereby bolstering classification performance. Preliminary findings underscore the hybrid model's superiority over individual models, showcasing its prowess in feature extraction and classification. Moreover, the research emphasizes the significance of rigorous data pre-processing, including image resizing, color normalization, and segmentation, in ensuring data quality and model reliability. In essence, this study illuminates the promising role of AI and DL in revolutionizing skin cancer diagnostics, offering insights into its potential applications in broader medical domains.

Keywords: Artificial intelligence, machine learning, deep learning, skin cancer, dermatology, convolutional neural networks, image classification, computer vision, healthcare technology, cancer detection, medical imaging.

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Authors: Solvita Kalnina, Tatjana Rakcejeva, Daiga Kunkulberga, Anda Linina

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Triticale is a manmade hybrid of wheat and rye that carries the A and B genome of durum wheat and the R genome of rye. In the scientific literature information about in Latvia harvested organic and conventional triticale grain physically-chemical composition was not found in general. Therefore, the main purpose of the current research was to investigate physically-chemical parameters of in Latvia harvested organic and convectional triticale grains. The research was accomplished on in Year 2012 from State Priekuli Plant Breeding Institute (Latvia) harvested organic and conventional triticale grains: “Dinaro”, “9403-97”, “9405-23” and “9402-3”. In the present research significant differences in chemical composition between organic and conventional triticale grains harvested in Latvia was found. It is necessary to mention that higher 1000 grain weight, bulk density and gluten index was obtained for conventional and organic triticale grain variety “9403-97”. However higher falling number, gluten and protein content was obtained for triticale grain variety “9405-23”.

Keywords: Physically-chemical parameters, technological properties, triticale grains.

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Authors: M. Hetmańczyk, R. Polaniak, K. Brukało, E. Grochowska-Niedworok

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Eating behaviours of people are determined by knowledge gained at different stages of life. Children’s diet is especially important. They have to eat meals regularly. Meals should consist of protein, carbohydrates and fat, and drinking the right amount of water. Mistakes in children’s diets affect their health and may lead to health issues such as diabetes, overweight, obesity or malnutrition. The aim of the study was to assess the eating habits among 10-15-year-old children. To achieve this aim, the study included children aged 10-15 years living in Silesia Province, Poland; the participants consisted of 52.08% girls and 47.92% boys. Authorial questionnaire contains 28 questions about eating habits. The results of 192 students were subjected to analysis. The results show that half of the surveyed students participated in physical activity every day. Most children ate 4-5 meals every day, but the breaks between them were too long (four and more hours). Children generally ate cooked meals. Most children ate first breakfast every day, but only one third of studied children ate a second breakfast daily, while 93.75% ate vegetables at least once a day, 94.79% ate fruit at least once a day, and 79.17% drink a daily glass of milk or more. The study found that the eating behaviours of the surveyed children were unsatisfying. While the children did not participate in physical activity often enough, girls took part slightly more often. Children eat second breakfast not often enough. Younger children (10-12 years old) are doing it more often than the older children (13-15 years old). Gender is not a determinant of the frequency of second breakfast consumption.

Keywords: Eating habits, children, diet, nutrition status.

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Authors: Yose Rizal, Maria Endo Mahata, Mira Andriani, Guoyao Wu

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An experiment was conducted with 80 unsexed broilers of the Arbor Acress strain to determine the capability of a carrot and fruit juice wastes mixture (carrot, apple, manggo, avocado, orange, melon and Dutch egg plant) in the same proportion for replacing corn in broiler diet. This study involved a completely randomized design (CRD) with 5 treatments (0, 5, 10, 15, and 20% of juice wastes mixture in diets) and 4 replicates per treatment. Diets were isonitrogenous (22% crude protein) and isocaloric (3000 kcal/kg diet). Measured variables were feed consumption, average daily gain, feed conversion, as well as percentages of abdominal fat pad, carcass, digestive organs (liver, pancreas and gizzard), and heart. Data were analyzed by analysis of variance for CRD. Increasing juice wastes mixture levels in diets increased feed consumption (P<0.05) and average daily gain (P<0.01), while improving feed utilization efficiency (P<0.05). These treatments also affected (P<0.05) abdominal fat pad percentage but had no effect (P>0.05) on carcass, liver, pancreas, gizzard or heart percentages. In conclusion, up to 20% of juice wastes mixture could be included for the broiler diet to effectively replace up to 40% corn in the diet.

Keywords: average daily gain, feed consumption, feedconversion, juice waste mixture

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Authors: Khaddouja Boujenfa, Nadia Essoussi, Mohamed Limam

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Multiple sequence alignment is a fundamental part in many bioinformatics applications such as phylogenetic analysis. Many alignment methods have been proposed. Each method gives a different result for the same data set, and consequently generates a different phylogenetic tree. Hence, the chosen alignment method affects the resulting tree. However in the literature, there is no evaluation of multiple alignment methods based on the comparison of their phylogenetic trees. This work evaluates the following eight aligners: ClustalX, T-Coffee, SAGA, MUSCLE, MAFFT, DIALIGN, ProbCons and Align-m, based on their phylogenetic trees (test trees) produced on a given data set. The Neighbor-Joining method is used to estimate trees. Three criteria, namely, the dNNI, the dRF and the Id_Tree are established to test the ability of different alignment methods to produce closer test tree compared to the reference one (true tree). Results show that the method which produces the most accurate alignment gives the nearest test tree to the reference tree. MUSCLE outperforms all aligners with respect to the three criteria and for all datasets, performing particularly better when sequence identities are within 10-20%. It is followed by T-Coffee at lower sequence identity (<10%), Align-m at 20-30% identity, and ClustalX and ProbCons at 30-50% identity. Also, it is noticed that when sequence identities are higher (>30%), trees scores of all methods become similar.

Keywords: Multiple alignment methods, phylogenetic trees, Neighbor-Joining method, Robinson-Foulds distance.

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Authors: Ekesa B. Nakhauka, De Lange M., Macharia I., Garming H., Ouma E., Birachi E., Van Asten P., Van-Lauwe B., Blomme G.

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Impact of adopting products promoted by the Consortium for Improving Agriculture-based livelihoods in Central Africa (CIALCA) on food and nutrition security was tested. Multi-stage sampling was used to select 7 project mandate areas, 5 villages/mandate area (stratified into action, satellite and control sites) and 913 households. Structured questionnaires were administered; analysis of impact based on comparison between stratums, differences in means tested by ANOVA and significance of difference obtained by Tukey's HSD multiple rank tests. Perception of adequate food sufficiency received a higher rating in action and satellite sites compared to control sites reason being improved agricultural technologies. For >60% of households, worsened food security was due to climatic conditions. Although a higher proportion of households in action and satellite was meeting calorie RDIs in DRC and Burundi the difference was insignificant from control sites. 53% of respondents in control sites indicated a decrease in intake of protein rich foods, this was significantly higher than the proportion in the action (46%) and satellite (41%) sites.

Keywords: Food security, Farmer-households, Nutrition security

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Authors: Ferial M. Abu-Salem, Rasha K. Mohamed, Ahmed Y. Gibriel, Nagwa M. H. Rasmy

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Three legumes i.e. soybean, kidney bean and mung bean, and jojoba seed as an oil seed were processed into tempeh, a fermented food. Changes in phytic acid, total phenols and trypsin inhibitor were monitored during the pretreatments (soaking, soaking– dehulling, washing and cooking) and fermentation with Rhizopus oligosporus. Soaking was found to reduce total phenol and trypsin inhibitor levels in soybean, kidney bean and mung bean. However, phytic acid was reduced by soaking in kidney bean and mung bean. Cooking was the most effective in reducing the activity of trypsin inhibitor. During fermentation, a slight increase in the level of trypsin inhibitor was noticed in soybean. Phytic acid and total phenols were decreased during fermentation in soybean, kidney bean but mung bean faild to form tempeh because the antifungal activity of herein a protein in mung bean, which exerts both chitinase activity and antifungal activity against a variety of fungal species. On the other hand, solid- state fermentation of jojoba seeds was not effective in reducing their content from cyanogenic glycosides (simmondsin).

Keywords: Antinutritional factors, cyanogenic glycosides (Simmondsin), tempeh.

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Authors: Amina M. Bishr, Ahmed B. Magdub, Abdul-Baset R. Abuzweda

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A major challenge in camel productivity is the high mortality rate of camel calves in the early stage due to the lack of colostrums. This study investigates the time required for the calves to obtain the optimum amount of the immunoglobulin (IgG). Eleven pregnant female camels (Camelus Dromedarus) were selected randomly and variant in age and gestation. After delivery, 7 calves were obtained and used for this investigation. Colostrum samples were collected from mothers immediately after parturition. Blood samples were obtained from the calves as follow: 0 day (before suckling), 24, 48, 72, 96, 120 and 144 hours, 2nd, 3rd, and 4th weeks post suckling. Blood serum and colostrums whey were separated and used to determine IgG concentration, total protein and concentration of Cortisol and Thyroxin. The results showed high levels of IgG in camel colostrums (328.8 ± 4.5 mg / ml). The IgG concentration in serum of calves was the highest within 1st 24 h after suckling (140.75 mg /ml), and then declined gradually reached lower level at 144 h (41.97 mg / ml). The average turnover rate (t 1/2) of serum IgG in the all cases was 3.22 days. The turnover of ranged from 2.56 days for calves have values of IgG more than average and 7.7 days for those with values below average. In spite of very high levels of thyroxin in sera of new born the results showed no correlation between cortisol and thyroxin with IgG levels.

Keywords: Camel, cortisol, IgG, thyroxin, turn-over rate.

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Authors: Ratnakar Tripathi, Rajnikant Mishra

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The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.

Keywords: Interacting Proteins, Pax6, PIP, STRING

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Authors: Nneka N. Uchegbu, Charles N. Ishiwu

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The nutritional composition and hypoglycaemic effect of crackers produced from blend of sprouted pigeon pea, unripe plantain and brewers’ spent grain and fed to Alloxan induced diabetic rat was investigated. Crackers were produced from different blends of sprouted pigeon pea, unripe plantain and brewers’ spent grain. The crackers were evaluated for proximate composition, amino acid profile and antinutritional factors. Blood glucose levels of normal and diabetic rats fed with the control sample and different formulations of cracker were measured. The protein content of the samples were significantly different (p<0.05) from each other with sample A having the lowest value and sample B with the highest value. The values obtained showed that the samples contained most of the amino acids that are found in plant proteins. The levels of antinutritional factor determined were generally low. Administration of the formulated cracker meals led to a significant reduction in the fasting blood glucose level in the diabetic rats. The present study concluded that consumption of crackers produced from this composite flour could be recommended for the diabetics and those who are sceptical about the disease.

Keywords: Crackers, diabetics rat, sprouted pigeon pea, unripe plantain and brewers’ spent grain.

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Authors: Mpho A. Mbeo, Patient Rambe

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The 13th year of the Central University of Technology, Free State’s (CUT) transition from a vocational and professional training orientation institution (i.e. a technikon) into a university with a strong research focus has neither been a smooth nor an easy one. At the heart of this transition was the need to transform the psychological faculties of academic and research staffs compliment who were accustomed to training graduates for industrial placement. The lack of a research culture that fully embraces the strong solid ethos of conducting cutting-edge research needs to be addressed. The induction and socialisation of academic staff into the development and execution of cutting-edge research also required the provision of research support and the creation of a conducive academic environment for research, both for emerging and non-research active academics. Drawing on ten cases, consisting of four heads of departments, three seasoned researchers, and three novice researchers, this study explores the challenges faced in establishing a strong research culture at the university. Furthermore, it gives an account of the extent to which the current research interventions have addressed the perceivably “missing research culture”, and the implications of these interventions for knowledge management. Evidence suggests that the capability of an ideal institutional research environment, consisting of mentorship of novice researchers by seasoned researchers, balanced effort into teaching and research responsibilities, should be supported by strong research-oriented leadership. Furthermore, recruitment of research passionate staff, adoption of a salary structure that encourages the retention of excellent scholars should be matched by a coherent research incentive culture to growth research publication outputs. This is critical for building new knowledge and entrenching knowledge management founded on communities of practice and scholarly networking through the documentation and communication of research findings. The study concludes that the multiple policy documents set for the different domains of research may be creating pressure on researchers to engage research activities and increase output at the expense of research quality.

Keywords: Central University of Technology, performance, publication, research culture, university.

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Authors: Laila Ozola, Evita Straumite

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Celiac disease is a permanent enteropathy caused by the ingestion of gluten, a protein occurring in wheat, rye and barley. The only way of the effective daily treatment is a strict gluten-free diet. From the investigation of products available in the local market, it was found that Latvian producers do not offer gluten-free products. The aim of this research was to study and analyze changes of celiac patient’s attitude to gluten-free product quality and availability in the Latvian market and purchasing habits. The survey was designed using website www.visidati.lv, and a questionnaire was sent to people suffering from celiac disease. The first time the respondents were asked to fill in the questionnaire in 2011, but now repeatedly from the beginning of September 2013 till the end of January 2014. The questionnaire was performed with 75 celiac patients, respondents were from all Latvian regions and they answered 16 questions. One of the most important questions was aimed to find out consumers’ opinion about quality of gluten-free products, consumption patterns of gluten-free products, and, moreover, their interest in products made in Latvia. Respondents were asked to name gluten-free products they mainly buy and give specific purchase locations, evaluate the quality of products and necessity for products produced in Latvia. The results of questionnaire show that the consumers are satisfied with the quality of gluten-free flour, flour blends, sweets and pasta, but are not satisfied with the quality of bread and confectionery available in the Latvian markets.

Keywords: Consumers, gluten-free products, quality, survey.

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Authors: Sarkar M. A. Kawsar, Sarkar M. A. Mamun, Md S. Rahman, Hidetaro Yasumitsu, Yasuhiro Ozeki

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Lectins have a good scope in current clinical microbiology research. In the present study evaluated the antimicrobial activities of a D-galactose binding lectin (PnL) was purified from the annelid, Perinereis nuntia (polychaeta) by affinity chromatography. The molecular mass of the lectin was determined to be 32 kDa as a single polypeptide by SDS-PAGE under both reducing and non-reducing conditions. The hemagglutinating activity of the PnL showed against trypsinized and glutaraldehyde-fixed human erythrocytes was specifically inhibited by D-Gal, GalNAc, Galβ1-4Glc and Galα1-6Glc. PnL was evaluated for in vitro antibacterial screening studies against 11 gram-positive and gram-negative microorganisms. From the screening results, it was revealed that PnL exhibited significant antibacterial activity against gram-positive bacteria. Bacillus megaterium showed the highest growth inhibition by the lectin (250 μg/disc). However, PnL did not inhibit the growth of gram-negative bacteria such as Vibrio cholerae and Pseudomonas sp. PnL was also examined for in vitro antifungal activity against six fungal phytopathogens. PnL (100 μg/mL) inhibited the mycelial growth of Alternaria alternata (24.4%). These results indicate that future findings of lectin applications obtained from annelids may be of importance to life sciences.

Keywords: Perinereis nuntia, Lectin, Inhibition zone, Mycelial growth.

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Authors: Teti Estiasih, Harijono, Weny Bekti Sunarharum, Atina Rahmawati

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This research studied the hypoglycemic effect of water soluble polysaccharide (WSP) extracted from yam (Dioscorea hispida) tuber by three different methods: aqueous extraction, papain assisted extraction, and tempeh inoculums assisted extraction. The two later extraction methods were aimed to remove WSP binding protein to have more pure WSP. The hypoglycemic activities were evaluated by means in vivo test on alloxan induced hyperglycemic rats, glucose response test (GRT), in situ glucose absorption test using everted sac, and short chain fatty acids (SCFAs) analysis. All yam WSP extracts exhibited ability to decrease blood glucose level in hyperglycemia condition as well as inhibited glucose absorption and SCFA formation. The order of hypoglycemic activity was tempeh inoculums assisted- >papain assisted- >aqueous WSP extracts. GRT and in situ glucose absorption test showed that order of inhibition was papain assisted- >tempeh inoculums assisted- >aqueous WSP extracts. Digesta of caecum of yam WSP extracts oral fed rats had more SCFA than control. Tempeh inoculums assisted WSP extract exhibited the most significant hypoglycemic activity.

Keywords: hypoglycemic activity, papain, tempeh inoculums, water soluble polysaccharides, yam (Discorea hispida)

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Authors: Reihaneh Ahmadzadeh Ghavidel, Mehdi Ghiafeh Davoodi

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The usefulness of weaning foods to meet the nutrient needs of children is well recognized, and most of them are precooked roller dried mixtures of cereal and/or legume flours which posses a high viscosity and bulk when reconstituted. The objective of this study was to formulate composite weaning foods using cereals, malted legumes and vegetable powders and analyze them for nutrients, functional properties and sensory attributes. Selected legumes (green gram and lentil) were germinated, dried and dehulled. Roasted wheat, rice, carrot powder and skim milk powder also were used. All the ingredients were mixed in different proportions to get four formulations, made into 30% slurry and dried in roller drier. The products were analyzed for proximate principles, mineral content, functional and sensory qualities. The results of analysis showed following range of constituents per 100g of formulations on dry weight basis, protein, 18.1-18.9 g ; fat, 0.78-1.36 g ; iron, 5.09-6.53 mg; calcium, 265-310 mg. The lowest water absorption capacity was in case of wheat green gram based and the highest was in rice lentil based sample. Overall sensory qualities of all foods were graded as “good" and “very good" with no significant differences. The results confirm that formulated weaning foods were nutritionally superior, functionally appropriate and organoleptically acceptable.

Keywords: malted legumes, weaning foods, nutrition, functional properties

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Authors: Je-Hoon Michael Oh

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The major source of allergy in home is the house dust mite (Dematophagoides farina, Dermatophagoides pteronyssinus) causing allergic symptom include atopic dermatitis, asthma, perennial rhinitis and even infant death syndrome. Control of this mite species is dependent on the use of chemical methods such as fumigation treatments with methylene bromide, spraying with organophosphates such as pirimiphos-methyl, or treatments with repellents such as DEET and benzyl benzoate. Although effective, their repeated use for decades has sometimes resulted in development of resistance and fostered environmental and human health concerns. Both decomposing animal parts and the protein that surrounds mite fecal pellets cause mite allergy. So it is more effective to repel than to kill them because allergen is not living house dust mite but dead body or fecal particles of house dust mite. It is important to find out natural repellent material against house dust mite to control them and reduce the allergic reactions. Plants may be an alternative source for dust mite control because they contain a range of bioactive chemicals. The research objectives of this paper were to verify the acaricidal and repellent effects of cinnamon essential oil and to find out it-s most effective concentrations. We could find that cinnamon bark essential oil was very effective material to control the house dust mite. Furthermore, it could reduce chemical resistance and danger for human health.

Keywords: house dust mite, cinnamon, repellent effect

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Authors: Aminat. O Adelekan, Olawale T. Gbadebo

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Biscuit is one of the most consumed cereal foods in Nigeria and research has shown that locally available tropical crops like cassava, sweet potato can be made into flour and used in the production of biscuits and other pastries. This study investigates some quality parameters in biscuits made from blends of wheat, cassava and carrot flour. The values of result of samples increased with increasing percentage substitution of cassava and carrot flour in some quality parameter like fiber, ash, gluten content, and carbohydrate. The protein content reduced significantly (P < 0.05) with increasing percentage substitution of cassava and carrot flour which ranged from 14.80% to 11.80% compared with the control sample which had 15.60%. There was a recorded significant increase (P < 0.05) in some mineral composition such as calcium, magnesium, sodium, iron, phosphorus, and vitamin A and C composition as the percentage substitution of cassava and carrot flour increased. During storage stability test, samples stored in the fridge and freezer were found to be the best storage location to preserve the sensory attributes and inhibit microbial growth when compared with storage under the sun and on the shelf. Biscuit made with blends of wheat, cassava and carrot flour can therefore serve as an alternative to biscuits made from 100% wheat flour, as they are richer in vitamin A, vitamin C, carbohydrate, dietary fiber and some essential minerals.

Keywords: Biscuit, carrot, flour blends, storage.

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Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

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Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p>0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: Kidney cancer, molecular biomarker, expression analysis, mutation screening.

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Authors: Rosa Buxeda, Lorenzo Saliceti-Piazza, Rodolfo J. Romañach, Luis Ríos, Sandra L. Maldonado-Ramírez

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Biopharmaceuticals manufacturing is one of the major economic activities worldwide. Ninety-three percent of the workforce in a biomanufacturing environment concentrates in production-related areas. As a result, strategic collaborations between industry and academia are crucial to ensure the availability of knowledgeable workforce needed in an economic region to become competitive in biomanufacturing. In the past decade, our institution has been a key strategic partner with multinational biotechnology companies in supplying science and engineering graduates in the field of industrial biotechnology. Initiatives addressing all levels of the educational pipeline, from K-12 to college to continued education for company employees have been established along a ten-year span. The Amgen BioTalents Program was designed to provide undergraduate science and engineering students with training in biomanufacturing. The areas targeted by this educational program enhance their academic development, since these topics are not part of their traditional science and engineering curricula. The educational curriculum involved the process of producing a biomolecule from the genetic engineering of cells to the production of an especially targeted polypeptide, protein expression and purification, to quality control, and validation. This paper will report and describe the implementation details and outcomes of the first sessions of the program.

Keywords: Biomanufacturing curriculum, interdisciplinary learning, workforce development, industry-academia partnering.

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Authors: D. C. Soares, J. T. S. Santos, D. G. Costa, A. K. S. Abud, T. P. Nunes, A. V. D. Figueiredo, A. M. de Oliveira Junior

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Mangabeira (Hancornia speciosa Gomes), a native plant in Brazil, is found growing spontaneously in various regions of the country. The high perishability of tropical fruits such as mangaba, causes it to be necessary to use technologies that promote conservation, aiming to increase the shelf life of this fruit and add value. The objective of this study was to compare the mangabas lyophilization curves behaviors with different sizes and maturation stages. The fruits were freeze-dried for a period of approximately 45 hours at lyophilizer Liotop brand, model L -108. It has been considered large the fruits between 38 and 58 mm diameter and small, between 23 and 28 mm diameter and the two states of maturation, intermediate and mature. Large size mangabas drying curves in both states of maturation were linear behavior at all process, while the kinetic drying curves related to small fruits, independent of maturation state, had a typical behavior of drying, with all the well-defined steps. With these results it was noted that the time of lyophilization was suitable for small mangabas, a fact that did not happen with the larger one. This may indicate that the large mangabas require a longer time to freeze until reaches the equilibrium level, as it happens with the small fruits, going to have constant moisture at the end of the process. For both types of fruit were analyzed water activity, acidity, protein, lipid, and vitamin C before and after the process.

Keywords: Freeze dryer, mangaba, conservation, chemical characteristics.

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Authors: Wenjun Zhang, Yunqing Du, Steven W. Cranford, Ming L. Wang

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The beginning of 21st century has witnessed new advancements in the design and use of new materials for biosensing applications, from nano to macro, protein to tissue. Traditional analytical methods lack a complete toolset to describe the complexities introduced by living systems, pathological relations, discrete hierarchical materials, cross-phase interactions, and structure-property dependencies. Materiomics – via systematic molecular dynamics (MD) simulation – can provide structureprocess- property relations by using a materials science approach linking mechanisms across scales and enables oriented biosensor design. With this approach, DNA biosensors can be utilized to detect disease biomarkers present in individuals’ breath such as acetone for diabetes. Our wireless sensor array based on single-stranded DNA (ssDNA)-decorated single-walled carbon nanotubes (SWNT) has successfully detected trace amount of various chemicals in vapor differentiated by pattern recognition. Here, we present how MD simulation can revolutionize the way of design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. It demonstrates great potential to be utilized to build a library of DNDA sequences for reliable detection of several biomarkers of one specific disease, and as well provides a new methodology of creating, designing, and applying of biosensors.

Keywords: Biosensor, design, DNA, molecular dynamics simulation.

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Authors: A. Zonouzi, M. Auli, M. Javanmard Dakheli, M. A. Hejazi

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Microalgae are tiny photosynthetic plants. Nowadays, microalgae are being used as nutrient-dense foods and sources of fine chemicals. They have significant amounts of lipid, carotenoids, vitamins, protein, minerals, chlorophyll, and pigments. Oil extraction from algae is a hotly debated topic currently because introducing an efficient method could decrease the process cost. This can determine the sustainability of algae-based foods. Scientific research works show that solvent extraction using chloroform/methanol (2:1) mixture is one of the efficient methods for oil extraction from algal cells, but both methanol and chloroform are toxic solvents, and therefore, the extracted oil will not be suitable for food application. In this paper, the effect of two food grade solvents (hexane and hexane/ isopropanol) on oil extraction yield from microalgae Dunaliella sp. was investigated and the results were compared with chloroform/methanol (2:1) extraction yield. It was observed that the oil extraction yield using hexane, hexane/isopropanol (3:2) and chloroform/methanol (2:1) mixture were 5.4, 13.93, and 17.5 (% w/w, dry basis), respectively. The fatty acid profile derived from GC illustrated that the palmitic (36.62%), oleic (18.62%), and stearic acids (19.08%) form the main portion of fatty acid composition of microalgae Dunalliela sp. oil. It was concluded that, the addition of isopropanol as polar solvent could increase the extraction yield significantly. Isopropanol solves cell wall phospholipids and enhances the release of intercellular lipids, which improves accessing of hexane to fatty acids.

Keywords: Fatty acid profile, Microalgae, Oil extraction, Polar solvent.

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