Search results for: vegetable protein (VP)

Authors: Harika Atmaca, Emir Bozkurt, Latife Merve Oktay, Selim Uzunoglu, Ruchan Uslu, Burçak Karaca

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Microarrays have been developed for highly parallel enzyme-linked immunosorbent assay (ELISA) applications. The most common protein arrays are produced by using multiple monoclonal antibodies, since they are robust molecules which can be easily handled and immobilized by standard procedures without loss of activity. Protein expression profiling with protein array technology allows simultaneous analysis of the protein expression pattern of a large number of proteins. Trabectedin, a tetrahydroisoquinoline alkaloid derived from a Caribbean tunicate, Ecteinascidia turbinata, has been shown to have antitumor effects. Here, we used a novel proteomic approach to explore the mechanism of action of trabectedin in prostate cancer cell line PC-3 by apoptosis antibody microarray. XTT cell proliferation kit and Cell Death Detection Elisa Plus Kit (Roche) was used for measuring cytotoxicity and apoptosis. Human Apoptosis Protein Array (R&D Systems) which consists of 35 apoptosis related proteins was used to assess the omic protein expression pattern. Trabectedin induced cytotoxicity and apoptosis in prostate cancer cells in a time and concentration-dependent manner. The expression levels of the death receptor pathway molecules, TRAIL-R1/DR4, TRAIL R2/DR5, TNF R1/TNFRSF1A, FADD were significantly increased by 4.0-, 21.0-, 4.20- and 11.5-fold by trabectedin treatment in PC-3 cells. Moreover, mitochondrial pathway related pro-apoptotic proteins Bax, Bad, Cytochrome c, and Cleaved Caspase-3 expressions were induced by 2.68-, 2.07-, 2.8-, and 4.5-fold and the expression levels of anti-apoptotic proteins Bcl-2 and Bcl-XL were reduced by 3.5- and 5.2-fold in PC-3 cells. Proteomic (antibody microarray) analysis suggests that the mechanism of action of trabectedin may be exerted via the induction of both intrinsic and extrinsic apoptotic pathways. The antibody microarray platform can be utilised to explore the molecular mechanism of action of novel anticancer agents.

Keywords: trabectedin, prostate cancer, omic protein expression profile, apoptosis

Procedia PDF Downloads 442

Authors: S. Mowafi, A. Abou El-Kheir, M. Abou Taleb, H. El-Sayed

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Two proteinic biopolymers; namely keratin and sericin, were extracted from their respective natural resources by simple appropriate methods. The said proteins were dissolved in the appropriate solvents followed by regeneration in a form of film polyvinyl alcohol. Protein-starch-potassium iodide (PSPI) composite was prepared by anchoring starch and potassium iodide mixture onto the film surface using appropriate polymeric material. The possibility of using PSPI composite for determination of the concentration of chlorine ions in domestic as well as industrial water was examined. The concentration of chlorine in water was determined spectrophotometrically by measuring the intensity of blue colour of formed between starch and the released iodine obtained by interaction of potassium iodide chlorine in the tested water sample.

Keywords: chlorine, protein, potassium iodide, water

Procedia PDF Downloads 377

Authors: M. Kouyate, M. Sangare, S. Samake, S. Keita, H. G. Kim, D. H. Geschwind

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Background & Objectives: Human genetic studies can be expensive, even unaffordable, in developing countries, partly due to the sequencing costs. Our aim is to pilot the use of bioinformatics tools to guide scientifically valid, locally relevant, and economically sound autism genetic research in Mali. Methods: The following databases, NCBI, HGMD, and LSDB, were used to identify hot point mutations. Phenotype, transmission pattern, theoretical protein expression in the brain, the impact of the mutation on the 3D structure of the protein) were used to prioritize selected autism genes. We used the protein database, Modeller, and clustal W. Results: We found Mef2c (Gly27Ala/Leu38Gln), Pten (Thr131IIle), Prodh (Leu289Met), Nme1 (Ser120Gly), and Dhcr7 (Pro227Thr/Glu224Lys). These mutations were associated with endonucleases BseRI, NspI, PfrJS2IV, BspGI, BsaBI, and SpoDI, respectively. Gly27Ala/Leu38Gln mutations impacted the 3D structure of the Mef2c protein. Mef2c protein sequences across species showed a high percentage of similarity with a highly conserved MADS domain. Discussion: Mef2c, Pten, Prodh, Nme1, and Dhcr 7 gene mutation frequencies in the Malian population will be very informative. PCR coupled with restriction enzyme digestion can be used to screen the targeted gene mutations. Sanger sequencing will be used for confirmation only. This will cut down considerably the sequencing cost for gene-to-gene mutation screening. The knowledge of the 3D structure and potential impact of the mutations on Mef2c protein informed the protein family and altered function (ex. Leu38Gln). Conclusion & Future Work: Bio-informatics will positively impact autism research in Mali. Our approach can be applied to another neuropsychiatric disorder.

Keywords: bioinformatics, endonucleases, autism, Sanger sequencing, point mutations

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Authors: Joseph Clement Akan, Lami Jafiya, Zaynab Muhammad Chellube, Zakari Mohammed, Fanna Inna Abdulrahman

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Five vegetables (spinach, lettuce, cabbage, tomato, and onion) were freshly harvested from the Alau Dam and Gongulong agricultural areas for the determination of some organochlorine pesticide residues (o, p-DDE, p,p’-DDD, o,p’-DDD, p,p’-DDT, α-BHC, γ-BHC, metoxichlor, lindane, endosulfan dieldrin, and aldrin.) Soil samples were also collected at different depths for the determination of the above pesticides. Samples collection and preparation were conducted using standard procedures. The concentrations of all the pesticides in the soil and vegetable samples were determined using GC/MS SHIMADZU (GC-17A) equipped with electron capture detector (ECD). The highest concentration was that of p,p’-DDD (132.4±13.45µg/g) which was observed in the leaf of cabbage, while the lowest concentration was that of p,p’-DDT (2.34µg/g) was observed in the root of spinach. Similar trends were observed at the Gongulong agricultural area, with p,p’-DDD having the highest concentration of 153.23µg/g in the leaf of cabbage, while the lowest concentration was that of p,p’-DDT (12.45µg/g) which was observed in the root of spinach. α-BHC, γ-BHC, Methoxychlor, and lindane were detected in all the vegetable samples studied. The concentrations of all the pesticides in the soil samples were observed to be higher at a depth of 21-30cm, while the lowest concentrations were observed at a depth of 0-10cm. The concentrations of all the pesticides in the vegetables and soil samples from the two agricultural sites were observed to be at alarming levels, much higher than the maximum residue limits (MRLs) and acceptable daily intake values (ADIs) .The levels of the pesticides observed in the vegetables and soil samples investigated, are of such a magnitude that calls for special attention and laws to regulate the use and circulation of such chemicals. Routine monitoring of pesticide residues in these study areas is necessary for the prevention, control and reduction of environmental pollution, so as to minimize health risks.

Keywords: Alau Dam, gongulong, organochlorine, pesticide residues, soil, vegetables

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Authors: Pooja Kumari, Anandkumar Tengli

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Aurora kinase enzyme, a protein on overexpression, leads to metastasis and is extremely important for women’s health in terms of prevention or treatment. While creating a targeted technique, the aim of the work is to design purine molecules that inhibit in aurora kinase enzyme and helps to suppress breast cancer. Purine molecules attached to an amino acid in DNA block protein synthesis or halt the replication and metastasis caused by the aurora kinase enzyme. Various protein related to the overexpression of aurora protein was docked with purine molecule using Biovia Drug Discovery, the perpetual software. Various parameters like X-ray crystallographic structure, presence of ligand, Ramachandran plot, resolution, etc., were taken into consideration for selecting the target protein. A higher negative binding scored molecule has been taken for simulation studies. According to the available research and computational analyses, purine compounds may be powerful enough to demonstrate a greater affinity for the aurora target. Despite being clinically effective now, purines were originally meant to fight breast cancer by inhibiting the aurora kinase enzyme. In in-silico studies, it is observed that purine compounds have a moderate to high potency compared to other molecules, and our research into the literature revealed that purine molecules have a lower risk of side effects. The research involves the design, synthesis, and identification of active purine molecules against breast cancer. Purines are structurally similar to the normal metabolites of adenine and guanine; hence interfere/compete with protein synthesis and suppress the abnormal proliferation of cells/tissues. As a result, purine target metastasis cells and stop the growth of kinase; purine derivatives bind with DNA and aurora protein which may stop the growth of protein or inhibits replication and stop metastasis of overexpressed aurora kinase enzyme.

Keywords: aurora kinases, in silico studies, medicinal chemistry, combination therapies, chronic cancer, clinical translation

Procedia PDF Downloads 86

Authors: Zi-Han Li, Lu Fang, Liang Wu, Dong-Yuan Chang, Manyuan Dong, Liang Ji, Qi Zhang, Ming-Hui Zhao, Sydney C.W. Tang, Lemin Zheng, Min Chen

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Uncoupling of mitochondrial respiration by chemical uncouplers has proven effective in ameliorating obesity, insulin resistance, and hyperglycemia, which were risk factors for diabetic nephropathy (DN). Recently, it was found that annexin A1(ANXA1) could improve mitochondrial function to mitigate DN progression. However, the underlying mechanism is not fully clear yet. Here, it was identified that uncoupling protein 1 (UCP1), an inner membrane protein of mitochondria, as a key to mitochondrial homeostasis improved by ANXA1. Specifically, ANXA1 attenuated mitochondrial dysfunction via appropriately upregulating UCP1 by stabilizing its transcription factor GATA binding protein 3 (GATA3) through combining with thioredoxin. Moreover, specific overexpression of UCP1 in renal cortex rescued renal injuries in diabetic Anxa1-KO mice. UCP1 deletion aggravated renal injuries in HFD/STZ-induced diabetic mice. Mechanistically, UCP1 reduced mitochondrial fission through the aristaless-related homeobox (ARX)/cardiolipin synthase 1 (CRLS1) pathway. Therapeutically, CL316243, a UCP1 agonist, could attenuate established DN in db/db mice. This work established a novel principle to harness the power of uncouplers for the treatment of DN.

Keywords: diabetic nephropathy, uncoupling protein 1, mitochondrial homeostasis, cardiolipin metabolism

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Authors: Farideh Halakou, Emel Sen, Attila Gursoy, Ozlem Keskin

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Protein–Protein Interactions (PPIs) mediate major biological processes in living cells. The study of PPIs as networks and analyze the network properties contribute to the identification of genes and proteins associated with diseases. In this study, we have created the sub-networks of brain and lung metastasis from primary tumor in breast cancer. To do so, we used seed genes known to cause metastasis, and produced their interactions through a network-topology based prioritization method named GUILDify. In order to have the experimental support for the sub-networks, we further curated them using STRING database. We proceeded by modeling structures for the interactions lacking complex forms in Protein Data Bank (PDB). The functional enrichment analysis shows that KEGG pathways associated with the immune system and infectious diseases, particularly the chemokine signaling pathway, are important for lung metastasis. On the other hand, pathways related to genetic information processing are more involved in brain metastasis. The structural analyses of the sub-networks vividly demonstrated their difference in terms of using specific interfaces in lung and brain metastasis. Furthermore, the topological analysis identified genes such as RPL5, MMP2, CCR5 and DPP4, which are already known to be associated with lung or brain metastasis. Additionally, we found 6 and 9 putative genes that are specific for lung and brain metastasis, respectively. Our analysis suggests that variations in genes and pathways contributing to these different breast metastasis types may arise due to change in tissue microenvironment. To show the benefits of using structural PPI networks instead of traditional node and edge presentation, we inspect two case studies showing the mutual exclusiveness of interactions and effects of mutations on protein conformation which lead to different signaling.

Keywords: breast cancer, metastasis, PPI networks, protein conformational changes

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Authors: Ishrat Jahan Saifi, Sheelu Shafiq Siddiqi, M. R. Ajmal

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Glycation of protein is very important as well as a harmful process, which may lead to develop DM in human body. Human Serum Albumin (HSA) is the most abundant protein in blood and it is highly prone to glycation by the reducing sugars. 2-¬deoxy d-¬Ribose (dRib) is a highly reactive reducing sugar which is produced in cells as a product of the enzyme thymidine phosphorylase. It is generated during the degradation of DNA in human body. It may cause glycation in HSA rapidly and is involved in the development of DM. In present study, we did in¬vitro glycation of HSA with different concentrations of 2-¬deoxy d-¬ribose and found that dRib glycated HSA rapidly within 4h incubation at 37◦C. UV¬ Spectroscopy, Fluorescence spectroscopy, Fourier transform infrared spectroscopy (FTIR) and Circular Dichroism (CD) technique have been done to determine the structural changes in HSA upon glycation. Results of this study suggested that dRib is the potential glycating agent and it causes alteration in protein structure and biophysical properties which may lead to development and progression of Diabetes mellitus.

Keywords: 2-deoxy D-ribose, human serum albumin, glycation, diabetes mellitus

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

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Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max, and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, brassinosteroids, phylogenetic analysis, transcription factor

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Authors: Javier Perez-Vaquero, Katryn Junker, Volker Lammers, Petra Foerst

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There is increasing importance to accelerate the transition to sustainable food systems by including environmentally friendly technologies. Our work focuses on protein enrichment and fractionation of agricultural side streams by dry triboelectrostatic separation technology. Materials are fed in particulate form into a system dispersed in a highly turbulent gas stream, whereby the high collision rate of particles against surfaces and other particles greatly enhances the electrostatic charge build-up over the particle surface. A subsequent step takes the charged particles to a delimited zone in the system where there is a highly uniform, intense electric field applied. Because the charge polarity acquired by a particle is influenced by its chemical composition, morphology, and structure, the protein-rich and fiber-rich particles of the starting material get opposite charge polarities, thus following different paths as they move through the region where the electric field is present. The output is two material fractions, which differ in their respective protein content. One is a fiber-rich, low-protein fraction, while the other is a high-protein, low-fiber composition. Prior to testing, materials undergo a milling process, and some samples are stored under controlled humidity conditions. In this way, the influence of both particle size and humidity content was established. We used two oilseed meals: lupine and rapeseed. In addition to a lab-scale separator to perform the experiments, the triboelectric separation process could be successfully scaled up to a mid-scale belt separator, increasing the mass feed from g/sec to kg/hour. The triboelectrostatic separation technology opens a huge potential for the exploitation of so far underutilized alternative protein sources. Agricultural side-streams from cereal and oil production, which are generated in high volumes by the industries, can further be valorized by this process.

Keywords: bench-scale processing, dry separation, protein-enrichment, triboelectrostatic separation

Procedia PDF Downloads 190

Authors: John N. Idenyi, Hadimundeen Abdallah, Abigeal D. Adeyemi, Jonathan C. Eya

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Gut microbiomes play a significant role in the growth, metabolism, and health of fish. However, we know very little about the interactive effects of variations in dietary composition and temperature on rainbow trout gut microbiota. Exactly 288 rainbow trout weighing 45.6g ± 0.05 (average ± SD) were fed four isocaloric, isolipidic, and isonitrogenous diets comprising 40% crude protein and 20% crude lipid and formulated as 100 % animal-based protein (AP) and a blend of 50 fish oil (FO)/50 camelina oil (CO), 100 % AP and100 % CO, 100 % plant-based protein (PP) and a blend of 50FO/50CO or 100 % PP and 100 % CO in 14 or 18°C for 150 days. Gut content was analyzed using 16S rRNA gene and shotgun sequencing. The most abundant phyla identified regardless of diet were Tenericutes, Firmicutes, Proteobacteria, Spirochaetes, Bacteroidetes, and Actinobacteria, while Aeromonadaceae and Enterobacteriaceae were dominant families in 18°C. Moreover, gut microbes were dominated by genes relating to an amino acid, carbohydrate, fat, and energy metabolisms and influenced by temperature. The shared functional profiles for all the diets suggest that plant protein sources in combination with CO could be as good as the fish meal with 50/50 FO & CO in rainbow trout farming.

Keywords: aquafeed, aquaculture, microbiome, rainbow trout

Procedia PDF Downloads 91

Authors: Mohammad Hossein Modarressi, Mozhgan Mondeali, Khabat Barkhordari, Ali Etemadi

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The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant concerns worldwide due to its catastrophic effects on public health. The SARS-CoV-2 infection is initiated with the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Due to the error-prone entity of the viral RNA-dependent polymerase complex, the virus genome, including the coding region for the RBD, acquires new mutations, leading to the appearance of multiple variants. These variants can potentially impact transmission, virulence, antigenicity and evasive immune properties. S477N mutation located in the RBD has been observed in the SARS-CoV-2 omicron (B.1.1. 529) variant. In this study, we investigated the consequences of S477N mutation at the molecular level using computational approaches such as molecular dynamics simulation, protein-protein interaction analysis, immunoinformatics and free energy computation. We showed that displacement of Ser with Asn increases the stability of the spike protein and its affinity to ACE2 and thus increases the transmission potential of the virus. This mutation changes the folding and secondary structure of the spike protein. Also, it reduces antibody neutralization, raising concern about re-infection, vaccine breakthrough and therapeutic values.

Keywords: S477N, COVID-19, molecular dynamic, SARS-COV2 mutations

Procedia PDF Downloads 174

Authors: Muhammad Nauman Ahmad, Patrick Büker, Sofia Khalid, Leon Van Den Berg, Hamid Ullah Shah, Abdul Wahid, Lisa Emberson, Sally A. Power, Mike Ashmore

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Although ozone is well-documented to affect crop yields in the densely populated Indo-Gangetic Plain, there is little knowledge of its effects around cities in more remote areas of South Asia. We surveyed crops around the city of Peshawar, Pakistan for visible injury, linking this to passive measurements of ozone concentrations. Foliar injury was found in the field on potato, onion and cotton when the mean monthly ozone concentration reached 35-55ppb. The symptoms on onion were reproduced in ozone fumigation experiments, which also showed that daytime ozone concentrations of 60ppb and above significantly reduce the growth of Pakistani varieties of both spinach (Beta vulgaris) and onion. Aphid infestation on spinach was also reduced at these elevated ozone concentrations. The ozone concentrations in Peshawar are comparable to those through many parts of northern south Asia, where ozone may therefore be a significant threat to sensitive vegetable crops in peri-urban regions.

Keywords: ozone, air pollution, vegetable crops, peshawar, south asia

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Authors: S. Petrovska, D. Jonkus, D. Smiltiņa

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κ-casein is one of milk proteins which are very important for milk processing. Genotypes of κ-casein affect milk yield, fat, and protein content. The main factors which affect local Latvian dairy breed milk yield and composition are analyzed in research. Data were collected from 88 Latvian brown and 82 Latvian blue cows in 2015. AA genotype was 0.557 in Latvian brown and 0.232 in Latvian blue breed. BB genotype was 0.034 in Latvian brown and 0.207 in Latvian blue breed. Highest milk yield was observed in Latvian brown (5131.2 ± 172.01 kg), significantly high fat content and fat yield also was in Latvian brown (p < 0.05). Significant differences between κ-casein genotypes were not found in Latvian brown, but highest milk yield (5057 ± 130.23 kg), protein content (3.42 ± 0.03%), and protein yield (171.9 ± 4.34 kg) were with AB genotype. Significantly high fat content was observed in Latvian blue breed with BB genotype (4.29 ± 0.17%) compared with AA genotypes (3.42 ± 0.19). Similar tendency was found in protein content – 3.27 ± 0.16% with BB genotype and 2.59 ± 0.16% with AA genotype (p < 0.05). Milk yield increases by increasing parity. We did not obtain major tendency of changes of milk fat and protein content according parity.

Keywords: dairy cows, κ-casein, milk productivity, polymorphism

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Authors: Patarasuda Chaisupa, R. Clay Wright

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The selection of appropriate biomolecular targets is a crucial aspect of biopharmaceutical development. The Auxin-Inducible Degron Degradation (AID) technology has demonstrated remarkable potential in efficiently and rapidly degrading target proteins, thereby enabling the identification and acquisition of drug targets. The AID system also offers a viable method to deplete specific proteins, particularly in cases where the degradation pathway has not been exploited or when the adaptation of proteins, including the cell environment, occurs to compensate for the mutation or gene knockout. In this study, we have engineered an improved AID system tailored to deplete proteins of interest. This AID construct combines the auxin-responsive E3 ubiquitin ligase binding domain, AFB2, and the substrate degron, IAA17, fused to the target genes. Essential genes of fungi with the lowest percent amino acid similarity to human and plant orthologs, according to the Basic Local Alignment Search Tool (BLAST), were cloned into the AID construct in S. cerevisiae (AID-tagged strains) using a modular yeast cloning toolkit for multipart assembly and direct genetic modification. Each E3 ubiquitin ligase and IAA17 degron was fused to a fluorescence protein, allowing for real-time monitoring of protein levels in response to different auxin doses via cytometry. Our AID system exhibited high sensitivity, with an EC50 value of 0.040 µM (SE = 0.016) for AFB2, enabling the specific promotion of IAA17::target protein degradation. Furthermore, we demonstrate how this improved AID system enhances quantitative functional studies of various proteins in fungi. The advancements made in auxin-inducible protein degradation in this study offer a powerful approach to investigating critical target protein viability in fungi, screening protein targets for drugs, and regulating intracellular protein abundance, thus revolutionizing the study of protein function underlying a diverse range of biological processes.

Keywords: synthetic biology, bioengineering, molecular biology, biotechnology

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: okra leaf curl virus, AV1 gene, sequencing, phylogenetic, cloning, purified protein, genetic diversity and viral proteins

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Authors: Po-Jung Huang, Chi-Ching Lee, Bertrand Chin-Ming Tan, Yuan-Ming Yeh, Julie Lichieh Chu, Tin-Wen Chen, Cheng-Yang Lee, Ruei-Chi Gan, Hsuan Liu, Petrus Tang

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Whole-exome sequencing focuses on the protein coding regions of disease/cancer associated genes based on a priori knowledge is the most cost-effective method to study the association between genetic alterations and disease. Recent advances in high throughput sequencing technologies and proteomic techniques has provided an opportunity to integrate genomics and proteomics, allowing readily detectable mutated peptides corresponding to mutated genes. Since sequence database search is the most widely used method for protein identification using Mass spectrometry (MS)-based proteomics technology, a mutant proteome database is required to better approximate the real protein pool to improve disease-associated mutated protein identification. Large-scale whole exome/genome sequencing studies were launched by National Cancer Institute (NCI), Broad Institute, and The Cancer Genome Atlas (TCGA), which provide not only a comprehensive report on the analysis of coding variants in diverse samples cell lines but a invaluable resource for extensive research community. No existing database is available for the collection of mutant protein sequences related to the identified variants in these studies. CMPD is designed to address this issue, serving as a bridge between genomic data and proteomic studies and focusing on protein sequence-altering variations originated from both germline and cancer-associated somatic variations.

Keywords: TCGA, cancer, mutant, proteome

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Authors: Usha Kiran, M. Z. Abdin

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Osmotin is an abundant cationic multifunctional protein discovered in cells of tobacco (Nicotiana tabacum L. var Wisconsin 38) adapted to an environment of low osmotic potential. It provides plants protection from pathogens, hence placed in the PRP family of proteins. The osmotin induced proline accumulation has been reported in plants including transgenic tomato and strawberry conferring tolerance against both biotic and abiotic stresses. The exact mechanism of induction of proline by osmotin is however, not known till date. These observations have led us to hypothesize that osmotin induced proline accumulation could be due to its involvement as transcription factor and/or cell signal pathway modulator in proline biosynthesis. The present investigation was therefore, undertaken to analyze the osmotin protein as transcription factor /cell signalling modulator using bioinformatics tools. The results of available online DNA binding motif search programs revealed that osmotin does not contain DNA-binding motifs. The alignment results of osmotin protein with the protein sequence from DATF showed the homology in the range of 0-20%, suggesting that it might not contain a DNA binding motif. Further to find unique DNA-binding domain, the superimposition of osmotin 3D structure on modeled Arabidopsis transcription factors using Chimera also suggested absence of the same. We, however, found evidence implicating osmotin in cell signaling. With these results, we concluded that osmotin is not a transcription factor but regulating proline biosynthesis and accumulation through cell signaling during abiotic stresses.

Keywords: osmotin, cell signaling modulator, bioinformatic tools, protein

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Authors: Abayomi O. Adetuyi, Jamiu M. Jabar, Samuel O. Afolabi

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Vegetable fibres are classes of fibres of low density, biodegradable and non-abrasive that are largely abundant fibre materials with specific properties and mostly found/ obtained in plants on earth surface. They are classified into three categories, depending on the part of the plant from which they are gotten from namely: fruit, Blast and Leaf fibre. Ever since four/five millennium B.C, attention has been focussing on the commonest and highly utilized cotton fibre obtained from the fruit of cotton plants (Gossypium spp), for the production of cotton fabric used in every home today. The present study, therefore, focused on the ability of three underutilized vegetable (fruit) fibres namely: coir fiber (Eleas coniferus), palm kernel fiber and empty fruit bunch fiber (Elias guinensis) through chemical modifications for better composite value addition performance to polyurethane form and dye adsorption. These fibres were sourced from their parents’ plants, identified and cleansed with 2% hot detergent solution 1:100, rinsed in distilled water and oven-dried to constant weight, before been chemically modified through alkali bleaching, mercerization and acetylation. The alkali bleaching involves treating 0.5g of each fiber material with 100 mL of 2% H2O2 in 25 % NaOH solution with refluxing for 2 h. While that of mercerization and acetylation involves the use of 5% sodium hydroxide NaOH solution for 2 h and 10% acetic acid- acetic anhydride 1:1 (v/v) (CH3COOH) / (CH3CO)2O solution with conc. H2SO4 as catalyst for 1 h, respectively on the fibres. All were subsequently washed thoroughly with distilled water and oven dried at 105 0C for 1 h. These modified fibres were incorporated as composite into polyurethane form and used in dye adsorption study of indigo. The first two treatments led to fiber weight reduction, while the acidified acetic anhydride treatment gave the fibers weight increment. All the treated fibers were found to be of less hydrophilic nature, better mechanical properties, higher thermal stabilities as well as better adsorption surfaces/capacities than the untreated ones. These were confirmed by gravimetric analysis, Instron Universal Testing Machine, Thermogravimetric Analyser and the Scanning Electron Microscope (SEM) respectively. The fiber morphology of the modified fibers showed smoother surfaces than unmodified fibres.The empty fruit bunch fibre and the coconut coir fibre are better than the palm kernel fibres as reinforcers for composites or as adsorbents for waste-water treatment. Acetylation and alkaline bleaching treatment improve the potentials of the fibres more than mercerization treatment. Conclusively, vegetable fibres, especially empty fruit bunch fibre and the coconut coir fibre, which are cheap, abundant and underutilized, can replace the very costly powdered activated carbon in wastewater treatment and as reinforcer in foam.

Keywords: chemical modification, industrial application, value addition, vegetable fibre

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Authors: Janneth Gonzalez, Marco Avila, George Barreto

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GRP78 participates in multiple functions in the cell during normal and pathological conditions, controlling calcium homeostasis, protein folding and unfolded protein response. GRP78 is located in the endoplasmic reticulum, but it can change its location under stress, hypoxic and apoptotic conditions. NF-κB represents the keystone of the inflammatory process and regulates the transcription of several genes related with apoptosis, differentiation, and cell growth. The possible relationship between GRP78-NF-κB could support and explain several mechanisms that may regulate a variety of cell functions, especially following brain injuries. Although several reports show interactions between NF-κB and heat shock proteins family members, there is a lack of information on how GRP78 may be interacting with NF-κB, and possibly regulating its downstream activation. Therefore, we assessed the computational predictions of the GRP78 (Chain A) and NF-κB complex (IkB alpha and p65) protein-protein interactions. The interaction interface of the docking model showed that the amino acids ASN 47, GLU 215, GLY 403 of GRP78 and THR 54, ASN 182 and HIS 184 of NF-κB are key residues involved in the docking. The electrostatic field between GRP78-NF-κB interfaces and molecular dynamic simulations support the possible interaction between the proteins. In conclusion, this work shed some light in the possible GRP78-NF-κB complex indicating key residues in this crosstalk, which may be used as an input for better drug design strategy targeting NF-κB downstream signaling as a new therapeutic approach following brain injuries.

Keywords: computational biology, protein interactions, Grp78, bioinformatics, molecular dynamics

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Authors: Hak-Ryul Kim, Hyung-Geun Lee, Qi Long, Ching Hou

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Structural modification of natural lipids via chemical reaction or microbial bioconversion can change their properties or even create novel functionalities. Enzymatic oxidation of lipids leading to formation of oxylipin is one of those modifications. Hydroxy fatty acids, one of those oxylipins have gained important attentions because of their structural and functional properties compared with other non-hydroxy fatty acids. Recently 7,10-dihydroxy-8(E)-octadecenoic acid (DOD) was produced with high yield from lipid-containing oleic acid by microbial conversion, and the further study confirmed that DOD contained strong antimicrobial activities against a broad range of microorganisms. In this study, we tried to modify DOD molecules by the enzymatic or physical reaction to create new functionality or to enhance the antimicrobial activity of DOD. After modification of DOD molecules by different ways, we confirmed that the antimicrobial activity of DOD was highly enhanced and presented strong antimicrobial activities against multidrug-resistant Staphylococcus aureus, suggesting that DOD and its derivatives can be used as efficient antimicrobial agents for medical and industrial applications.

Keywords: biocatalysis, antimicrobial agent, multidrug-resistant bacteria, vegetable oil

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Authors: A. Gramza-Michałowska, J. Skręty, M. Antczak, J. Kobus-Cisowska, D. Kmiecik, J. Korczak, Kulczyński Bartosz

Abstract:

Background: Modern consumer highly appreciates the correlation between eating habits and health. Intensified research showed many proofs confirming that food besides its basic nutritional function, possess also significant prophylactic and therapeutic potential. Preventive potential of selected food is commonly used as improvement factor of patients life standard. World Health Organization indicates that diabetes (Diabetes mellitus) and obesity are two of the most common and dangerous diseases. Diet therapy is an element of diabetes education program and a part of healing process, allowing maintaining and remaining the optimal metabolic state of the system. It must be remembered that diabetes treatment should be individualized to each patient. One of highly recommended vegetable for diabetes is asparagus (Asparagus officinalis L.), low calories common plant, growing in European countries. Objective: To propose the technology of unsweetened muesli production with addition of new components, we investigated the effects of selected vegetable addition on antioxidative capacity and consumer’s acceptance of muesli as representative of breakfast product. Methods: Muesli was formulated from a composition of oat flakes, flaxseed, bran, carrots, broccoli and asparagus. Basic composition of muesli was evaluated as content of protein, lipids, fatty acid composition, ash, selected minerals and caloricity. Antioxidant capacity of muesli was evaluated with use radical scavenging methods (DPPH, ABTS), ORAC value and PCL - photochemiluminescence antiradical potential. Proposed muesli as new product was also characterized with sensory analysis, which included color, scent, taste, consistency and overall acceptance of a product. Results: Results showed that addition of freeze-dried asparagus into muesli allowed to lower the fat content and caloricity of a product according to the base product. No significant loss in antioxidant potential was evaluated, also the sensory value of a product was not negative. Conclusion: Designed muesli would be an answer for obese people looking for healthy snack during the daytime. Results showed that product with asparagus addition would be accepted by the consumers and because of its antidiabetic potential could be a n important factor in prevention of diabetes or obesity. Financial support by the UE Project no PO IG 01.01.00.00-061/09

Keywords: muesli, vegetables, asparagus, antioxidant potential, lipids

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Authors: A. Rajabpour, A. Hadizadeh Kheirkhah

Abstract:

Heat transfer is of great importance to biological systems in order to function properly. In the present study, specific heat capacity as one of the most important heat transfer properties is calculated for a soluble in water Lysozyme protein. Using equilibrium molecular dynamics (MD) simulation, specific heat capacities of pure water, dry lysozyme, and lysozyme-water solution are calculated at 300K for different weight fractions. It is found that MD results are in good agreement with ideal binary mixing rule at small weight fractions. Results of all simulations have been validated with experimental data.

Keywords: specific heat capacity, molecular dynamics simulation, lysozyme protein, equilibrium

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Authors: Abdorrasoul Malekpour, Mohammad Ghorbani Mojtaba Mortazavi, Mohammadreza Fattahi, Mohammad Hassan Meshkibaf, Ali Fakhrzad, Saeid Salehi, Saeideh Zahedi, Amir Ahmadimoghaddam, Parviz Farzadnia Dr., Mohammadreza Hajyani Asl Bs

Abstract:

Hepatitis B as an infectious disease has eight main genotypes (A–H). The aim of this study is to Bioinformatically identify Rare Codon Clusters (RCC) in proteins structure of HBV. For detection of protein family accession numbers (Pfam) of HBV proteins; used of uni-prot database and Pfam search tool were used. Obtained Pfam IDs were analyzed in Sherlocc program and RCCs in HBV proteins were detected. In further, the structures of TrEMBL entries proteins studied in PDB database and 3D structures of the HBV proteins and locations of RCCs were visualized and studied using Swiss PDB Viewer software. Pfam search tool have found nine significant hits and 0 insignificant hits in 3 frames. Results of Pfams studied in the Sherlocc program show this program not identified RCCs in the external core antigen (PF08290) and truncated HBeAg protein (PF08290). By contrast the RCCs become identified in Hepatitis core antigen (PF00906) Large envelope protein S (PF00695), X protein (PF00739), DNA polymerase (viral) N-terminal domain (PF00242) and Protein P (Pf00336). In HBV genome, seven RCC identified that found in hepatitis core antigen, large envelope protein S and DNA polymerase proteins and proteins structures of TrEMBL entries sequences that reported in Sherlocc program outputs are not complete. Based on situation of RCC in structure of HBV proteins, it suggested those RCCs are important in HBV life cycle. We hoped that this study provide a new and deep perspective in protein research and drug design for treatment of HBV.

Keywords: rare codon clusters, hepatitis B virus, bioinformatic study, infectious disease

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Authors: Angela U. Makolo

Abstract:

Protein-coding and Non-coding regions determine the biology of a sequenced transcriptome. Research advances have shown that Non-coding regions are important in disease progression and clinical diagnosis. Existing bioinformatics tools have been targeted towards Protein-coding regions alone. Therefore, there are challenges associated with gaining biological insights from transcriptome sequence data. These tools are also limited to computationally intensive sequence alignment, which is inadequate and less accurate to identify both Protein-coding and Non-coding regions. Alignment-free techniques can overcome the limitation of identifying both regions. Therefore, this study was designed to develop an efficient sequence alignment-free model for identifying both Protein-coding and Non-coding regions in sequenced transcriptomes. Feature grouping and randomization procedures were applied to the input transcriptomes (37,503 data points). Successive iterations were carried out to compute the gradient vector that converged the developed Protein-coding and Non-coding Region Identifier (PNRI) model to the approximate coefficient vector. The logistic regression algorithm was used with a sigmoid activation function. A parameter vector was estimated for every sample in 37,503 data points in a bid to reduce the generalization error and cost. Maximum Likelihood Estimation (MLE) was used for parameter estimation by taking the log-likelihood of six features and combining them into a summation function. Dynamic thresholding was used to classify the Protein-coding and Non-coding regions, and the Receiver Operating Characteristic (ROC) curve was determined. The generalization performance of PNRI was determined in terms of F1 score, accuracy, sensitivity, and specificity. The average generalization performance of PNRI was determined using a benchmark of multi-species organisms. The generalization error for identifying Protein-coding and Non-coding regions decreased from 0.514 to 0.508 and to 0.378, respectively, after three iterations. The cost (difference between the predicted and the actual outcome) also decreased from 1.446 to 0.842 and to 0.718, respectively, for the first, second and third iterations. The iterations terminated at the 390th epoch, having an error of 0.036 and a cost of 0.316. The computed elements of the parameter vector that maximized the objective function were 0.043, 0.519, 0.715, 0.878, 1.157, and 2.575. The PNRI gave an ROC of 0.97, indicating an improved predictive ability. The PNRI identified both Protein-coding and Non-coding regions with an F1 score of 0.970, accuracy (0.969), sensitivity (0.966), and specificity of 0.973. Using 13 non-human multi-species model organisms, the average generalization performance of the traditional method was 74.4%, while that of the developed model was 85.2%, thereby making the developed model better in the identification of Protein-coding and Non-coding regions in transcriptomes. The developed Protein-coding and Non-coding region identifier model efficiently identified the Protein-coding and Non-coding transcriptomic regions. It could be used in genome annotation and in the analysis of transcriptomes.

Keywords: sequence alignment-free model, dynamic thresholding classification, input randomization, genome annotation

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Authors: Tety Hartatik, Dian Kurniawati, Adiarto

Abstract:

The aim of the research was to determine the associations between polymorphism of the bovine growth hormone (GH) gene (Leu/Val, L/V) and milk production of Friesian Holstein Cattle. A total of 62 cows which consist of two Friesian Holstein groups (cattle from New Zealand are 19 heads and cattle from Australia are 43 heads). We perform the PCR and RFLP method for analyzing the genotype of the target gene GH 211 bp in the part of intron 4 and exon 5 of GH gene. The frequencies of genotypes LL were higher than genotype LV. The number of genotype LL in New Zealand and Australia groups are 84% and 79%, respectively. The number of genotype LV in New Zealand and Australia groups are 16% and 21%, respectively. The association between Leu/Val polymorphism on milk production, fat and protein content in both groups does not show the significant effect. However base on the groups (cows from New Zealand compare with those from Australia) show the significant effect on fat and protein content.

Keywords: Friesian Holstein, fat content, growth hormone gene, milk production, PCR-RLFP, protein content

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Authors: Leila Najafian

Abstract:

Sarcoplasmic protein hydrolysates (SPHs) and myofibrillar protein hydrolysates (MPHs) from patin (Pangasius sutchi) were produced using two types of proteases: Papain and Alcalase. 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS) radical scavenging activities and metal chelating activity assays for antioxidant activities were carried out on the SPHs and MPHs. The hydrolysates were isolated and purified by ultrafiltration, gel filtration and reverse phase high-performance liquid chromatography (RP-HPLC) and liquid chromatography with tandem mass spectrometry detection (LC-MS/MS) was used in identifying peptide sequences. The results showed that when the DH of MPHs increased, the protein solubility increased, while the highest amount of the protein solubility of SPHs was after 60 min incubation. The effect of DH on antioxidant activities of SPHs and MPHs was investigated. Among the hydrolysates, papain-MPH and Alcalase-SPH, which had the highest antioxidant activities, were purified. The potent fractions obtained from RP-HPLC of sarcoplasmic (SI 3 fraction) and myofibrillar (MI 4 fraction) hydrolysates showed the highest DPPH radical scavenging activity. The FVNQPYLLYSVHMK peptide for MPH and the LVVDIPAALQHA peptide for SPH exhibited the highest antioxidant activity. The presence of hydrophobic and hydrophilic amino acids, namely leucine (L), valine (V), phenylalanine (F), histidine (H) and proline (P), in the peptide sequences of SPH and MPH are believed to contribute to high antioxidant activity. Hence, SPH and MPH from patin have the potential as a natural functional ingredient in food and pharmaceutical industry.

Keywords: patin (Pangasius sutchi), protein hydrolysates, antioxidative peptides, mass spectrometry

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Authors: María José Bugueño, Natalia Jaime, Cristian Castro, Diego Naranjo, Guido Trautmann, Mario Pérez-Won, Vilbett Briones-Labarca

Abstract:

Proteins play a crucial role in various prepared foods, including dairy products, drinks, emulsions, and ready meals. These food proteins are naturally present in food waste and byproducts. The alkaline extraction and acid precipitation method is commonly used to extract proteins from plants and animals due to its product stability, cost-effectiveness, and ease of use. This study aimed to investigate the impact of pH-shifting storage at two different pH levels on the conformational changes affecting the physicochemical and functional properties of quinoa protein isolate (QPI) and yellow shrimp byproduct protein isolate (YSPI). The QPI and YSPI were extracted using the alkaline extraction-isoelectric precipitation method. The dispersions were adjusted to pH 4 or 12, stirred for 2 hours at 20°C to achieve a uniform dispersion, and then freeze-dried. Various analyses were conducted, including flexibility (F), free sulfhydryl content (Ho), emulsifying activity (EA), emulsifying capacity (EC), water holding capacity (WHC), oil holding capacity (OHC), intrinsic fluorescence, ultraviolet spectroscopy, differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR) to assess the properties of the protein isolates. pH-shifting at pH 11 and 12 for QPI and YSPI, respectively, significantly improved protein properties, while property modification of the samples treated under acidic conditions was less pronounced. Additionally, the pH 11 and 12 treatments significantly improved F, Ho, EA, WHC, OHC, intrinsic fluorescence, ultraviolet spectroscopy, DSC, and FTIR. The increase in Ho was due to disulfide bond disruption, which produced more protein sub-units than other treatments for both proteins. This study provides theoretical support for comprehensively elucidating the functional properties of protein isolates, promoting the application of plant proteins and marine byproducts. The pH-shifting process effectively improves the emulsifying property and stability of QPI and YSPI, which can be considered potential plant-based or marine byproduct-based emulsifiers for use in the food industry.

Keywords: quinoa protein, yellow shrimp by-product protein, physicochemical properties, structural properties

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Authors: Hongping Lu, Kelbinur Tursun, Yaru Li, Yu Zhang, Shunai Liu, Ming Han

Abstract:

Objective: To investigate whether NS5ATP9 is involved in IL-6 mediated autophagy and the relationship between IL-6 and NS5ATP9 in liver cancer cells. Methods: 1. Detect the mRNA and protein levels of Beclin 1 after HepG2 cells were treated with or without recombinant human IL-6 protein. 2. Measure and compare of the changes of autophagy-related genes with their respective control, after IL-6 was silenced or neutralized with monoclonal antibody against human IL-6. 3. HepG2 cells were incubated with 50 ng/ml of IL-6 in the presence or absence of PDTC. The expression of NS5ATP9 was analyzed by Western blot after 48 h. 4. After NS5ATP9-silenced HepG2 cells had been treated with 50 ng/ml recombinant IL-6 protein, we detected the Beclin 1 and LC3B (LC3Ⅱ/Ⅰ) expression. 5. HepG2 cells were transfected with pNS5ATP9, si-NS5ATP9, and their respective control. Total RNA was isolated from cells and analyzed for IL-6. 6. Silence or neutralization of IL-6 in HepG2 cells which has been transfected with NS5ATP9. Beclin 1 and LC3 protein levels were analyzed by Western blot. Result: 1. After HepG2 were treated with recombinant human IL-6 protein, the expression of endogenous Beclin 1 was up-regulated at mRNA and protein level, and the conversion of endogenous LC3-I to LC3-II was also increased. These results indicated that IL-6 could induce autophagy. 2. When HepG2 cells were treated with IL-6 siRNA or monoclonal antibody against human IL-6, the expression of autophagy-related genes were decreased. 3. Exogenous human IL-6 recombinant protein up-regulated NS5ATP9 via NF-κB activation. 4. The expression of Beclin 1 and LC3B was down-regulated after IL-6 treated NS5ATP9-silenced HepG2 cells. 5. NS5ATP9 could reverse regulates IL-6 expression in HepG2 cells. 6. Silence or neutralization of IL-6 attenuates NS5ATP9-induced autophagy slightly. Conclusion: Our results implied that in HCC patients, maybe the higher level of IL-6 in the serum promoted the expression of NS5ATP9 and induced autophagy in cancer cells. And the over-expression of NS5ATP9 which induced by IL-6, in turn, increased IL-6 expression, further, promotes the IL-6/NS5ATP9-mediated autophagy and affects the progression of tumor. Therefore, NS5ATP9 silence might be a potential target for HCC therapy.

Keywords: autophagy, Hepatocellular carcinoma, IL-6, microenvironment, NS5ATP9

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Authors: Virender Singh Gurau, Akash Deep, Sarbjot S. Sandhu

Abstract:

Vegetable oils are produced from numerous oil seed crops. While all vegetable oils have high energy content, most require some processing to assure safe use in internal combustion engines. Some of these oils already have been evaluated as substitutes for diesel fuels. In the present research work Bitter Apricot kernel oil was employed as a feedstock for the production of biodiesel. The physicochemical properties of the Bitter Apricot kernel oil methyl ester were investigated as per ASTM D6751. From the series of engine testing, it is concluded that the brake thermal efficiency (BTE) with biodiesel blend was little lower than that of diesel. BSEC is slightly higher for Bitter apricot kernel oil methyl ester blends than neat diesel. For biodiesel blends, CO emission was lower than diesel fuel as B 20 reduced CO emissions by 18.75%. Approximately 11% increase in NOx emission was observed with 20% biodiesel blend. It is observed that HC emissions tend to decrease for biodiesel based fuels and Smoke opacity was found lower for biodiesel blends in comparison to diesel fuel.

Keywords: biodiesel, transesterification, bitter apricot kernel oil, performance and emission testing

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