Search results for: crude protein yield

Authors: M. Naimi, M. B. Khaled

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The present study consisted of an applied test in meat system to assess the effectiveness of three bio agents bacteriocinproducing strains: Lm24: Lactobacillus sakei, Lm14and Lm25: Pediococcus spp. Two tests were carried out: The ex-situ test was intended for three batches added with crude bacteriocin solutions at 12.48 AU/ml for Lm25 and 8.4 AU/ml for Lm14 and Lm24. However, the in situ one consisted of four batches; three of them inoculated with one bacteriocinogenic Lm25, Lm14, Lm24, respectively. The fourth one was used in mixture: Lm14+m24 at approximately of 107 CFU/ml. The two used tests were done in the presence of the pathogen St. aureus ATCC 6538, as a test strain at 103 CFU/ml. Another batch served as a positive or a negative control was used too. The incubation was performed at 7°C. Total viable counts, staphylococci and lactic acid bacteria, at the beginning and at selected times with interval of three days were enumerated. Physicochemical determinations (except for in situ test): pH, dry mater, sugars, fat and total protein, at the beginning and at end of the experiment, were done, according to the international norms. Our results confirmed the ex situ effectiveness. Furthermore, the batches affected negatively the total microbial load over the incubation days, and showed a significant regression in staphylococcal load at day seven, for Lm14, Lm24, and Lm25 of 0.73, 2.11, and 2.4 log units. It should be noticed that, at the last day of culture, staphylococcal load was nil for the three batches. In the in situ test, the cultures displayed less inhibitory attitude and recorded a decrease in staphylococcal load, for Lm14, Lm24, Lm25, Lm14+m24 of 0.73, 0.20, 0.86, 0.032 log units. Therefore, physicochemical analysis for Lm14, Lm24, Lm25, Lm14+m24 showed an increase in pH from 5.50 to 5.77, 6.18, 5.96, 7.22, a decrease in dry mater from 7.30% to 7.05%, 6.87%, 6.32%, 6.00%.This result reflects the decrease in fat ranging from 1.53% to 1.49%, 1.07%, 0.99%, 0.87%; and total protein from 6.18% to 5.25%, 5.56%, 5.37%, 5.5%. This study suggests that the use of selected strains as Lm25 could lead to the best results and would help in preserving and extending the shelf life of lamb meat.

Keywords: biocontrol, in situ, ex situ, meat system, St. aureus, Lactobacillus sakei, Pediococcus spp.

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Authors: Shohreh Rahimi Lascokalayeh, Hasan Yousefnia, Mojtaba Tajik, Samaneh Zolghadri, Bentehoda Abdolhosseini

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In this study, the production of terbium-161 as new therapeutic radionuclide was investigated using TALYS1.6& EMPIRE 3.2 codes. For this purpose, cross section for the reactions reactor to produce 161Tb were extracted by mean of this code In the following step, stopping power of the reactions reactor was calculated by SRIM code. The best reaction in the production of 161Tb is160 Gd(d,n)161Tb Production yield of the 161Tb was obtained by utilization of MATLAB calculation code and based on the charged particle reaction formalism.The results showed that Production yield of the 161Tb was obtained 0.8 (mci/ A*h).

Keywords: terbium161, TALYS1.6, EMPIRE3.2, yield, cross-section

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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

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Authors: Laila Nassiri, Aziza Irhza, Jamal Ibijbijen, Fouad Rachidi, Ghizlane Echchgadda

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The introduction of agroecological practices in ecosystems can contribute to meeting the challenges posed by the diversion of current agricultural production systems towards efficient production methods that are more respectful of the environment, including a reasoned use of inputs and resources. Intercropping is one of these practices that requires the production of two or more crops on the same plot and during the same growing season. Organic fertilization also can contribute to increase the yield due to the potential availability of nutrients. The objective of this work is to study the effect of intercropping and organic fertilization, which are two important practices of agroecology, on potato yield. Intercropping of potato and faba bean was carried out at the Agroecology and Environment platform (ENA, Meknes). The soil is silty-clay, the climate is warm with an average temperature of 17.1°C, and the annual average rainfall of 511mm. Four treatments were tested: Potato sole crop (T1), potato + organic fertilization (T2), Potato + faba bean (T3), Potato + faba bean + organic fertilization (T4). The results showed that there is a significant effect of the treatment on the evolution of the agronomical characters studied, especially the number of leaves and the yield. The number of stems at t0 was equal to 1 in all treatments; it began to grow after 30 days from the date of sowing with a slight increase in treatments containing organic fertilization (T2-T4), then it stabilized 60 days after sowing. In terms of the mean value of the number of leaves, a significant difference was noted between the treatments, the highest value was recorded in treatment T2. The T2 treatment showed the highest average yield, followed by the control (T1). As for the yield, treatments T2 and T1 recorded the highest number of tubers. In order to evaluate two of the practices of agroecology, this work focuses on the evaluation of the effect of intercropping and organic fertilization on the growth and yield parameters of the potato. The results obtained show that agroecological practices have a significant effect on the measured parameters.

Keywords: agroecology, intercropping, organic fertilization, potato yield

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Authors: A. Kraiem, A. Ayadi

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The squeeze flow tests were studied by many authors to measure the rheological properties of fluid. Experimental squeezing flow test with constant area between two parallel disks of bitumen is investigated in the present work. The effect of the temperature, the process of preparing the sample and the gap between the discs were discussed. The obtained results were compared with the theoretical models. The behavior of bitumen depends on the viscosity and the yield stress. Thus, the bitumen was presented as a power law for a small power law exponent and as a biviscous fluid when the viscosity ratio was smaller than one. Also, the influence of the ambient temperature is required for the compression test. Therefore, for a high temperature the yield stress decrease.

Keywords: bitumen, biviscous fluid, squeeze flow, viscosity, yield stress

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Authors: Katja Ignatieva, Patrick Wong

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We investigated the dynamics of high frequency energy prices, including crude oil and electricity prices. The returns of underlying quantities are modelled using various parametric models such as stochastic framework with jumps and stochastic volatility (SVCJ) as well as non-parametric alternatives, which are purely data driven and do not require specification of the drift or the diffusion coefficient function. Using different statistical criteria, we investigate the performance of considered parametric and nonparametric models in their ability to forecast price series and volatilities. Our models incorporate possible seasonalities in the underlying dynamics and utilise advanced estimation techniques for the dynamics of energy prices.

Keywords: stochastic volatility, affine jump-diffusion models, high frequency data, model specification, markov chain monte carlo

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Authors: Adebola Ajayi, Olakunle M. Makanjuola

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Effect of sprouting period on proximate, functional and mineral properties of malted sorghum flour was evaluated. The study was carried out to determine the proximate, functional and mineral properties of sprouting period on malted sorghum flour produced. The malted sorghum flour was obtained by sorting, weighing, washing, steeping, draining, germination, drying, dry milling, sieving. Malted sorghum flour was evaluated for proximate composition, functional properties and mineral contents. Moisture, protein, fat content, crude fiber, ash contents and carbohydrate of 24 and 48 hours, were in the range of 10.50-11.0, 11.17-11.17, 1.50-4.00, 2.50-1.50, 1.50-1.54 and 73.15-70.79% respectively. Bulk density ranged between 0.64 and 0.59g/ml, water and oil absorption capacities ranged between 139.3 and 150.0 and 217.3 and 222.7g/g respectively. Calcium, Magnesium, Zinc, Iron and Manganese were also range of 12.5, 59.3-60.0, 3.22-3.25, 3.80-3.90 and 3.22-3.25 mg/100g respectively. The results indicate that the germination of red sorghum resulted in the enhancement of the nutritional quality and its functional properties.

Keywords: sprouting, sorghum, malted sorghum flour, cabinet dryer

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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: Alireza Nejadmohammad Namaghi

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Investigators have reported that mulches increase production potential in arid and semi arid lands. Mulches are covering materials that are used on soil surface for efficiency irrigation, erosion control, weed control, evaporation decrease and improvement of water perpetration. Our aim and local situation determine the kind of material that we can use. In this research we used different mulches including chemical mulch (M1), Aquasorb polymer, manure mulch (M2), Residue mulch (M3) and polyethylene mulch (M4), with control treatment (M0), without usage of mulch, on germination, biomass dry matter and cottonseed yield (Varamin variety) in Kashan area. Randomized complete block (RCB) design have measured the cotton yield with 3 replications for measuring the biomass dry matter and 4 replication in tow irrigation periods as 7 and 14 days. Germination percentage for M0, M1, M2, M3 and M4 treatment were receptivity 64, 65, 76, 57 and 72% Biomass dry matter average for M0, M1, M2, M3 and M4 treatment were receptivity 276, 306, 426, 403 and 476 gram per plot. M4 treatment (polyethylene Mulch) had the most effect, M2 and M3 had no significant as well as M0 and M1. Total yield average with respect to 7 days irrigation for M0, M1, M2, M3 and M4 treatment were receptivity 700, 725, 857, 1057 and 1273 gram per plot. Dunken ne multiple showed no significant different among M0, M1, M2, and M3, but M4 ahs the most effect on yield. Total yield average with respect to 14 days irrigation for M0, M1, M2, M3 and M4 treatment were receptivity 535, 507, 690, 957 and 1047 gram per plot. These were significant difference between all treatments and control treatment. Results showed that used different mulches with water decrease in dry situation can increase the yield significantly.

Keywords: mulch, cotton, arid land management, irrigation systems

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Authors: Yahya Al-Wahaibi, Saif Al-Bahry, Abdulkadir Elshafie, Ali Al-Bemani, Sanket Joshi

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Microbial enhanced oil recovery is one of the most economical and efficient methods for extending the life of production wells in a declining reservoir. There are a variety of metabolites produced by microorganisms that can be useful for oil recovery, like biopolymers-polysaccharides secreted by microbes, biodegradable thus environmentally friendly. Some fungi like Schizophyllum commune (a type of mushroom), and Aureobasidium pullulans are reported to produce biopolymers-schizophyllan and pullulan. Hence, we have procured a microbial strain (Schizophyllum commune) from American Type Culture Collection, which is reported for producing a biopolymer and also isolated several Omani strains of Aureobasidium pullulans from different samples. Studies were carried out for maintenance of the strains and primary screening of production media and environmental conditions for growth of S. commune and Omani A. pullulans isolates, for 30 days. The observed optimum growth and production temperature was ≤35 °C for S. commune and Omani A. pullulans isolates. Better growth was observed for both types of fungi under shaking conditions. The initial yield of lyophilized schizophyllan was ≥3.0 g/L, and the yield of pullulan was ≥0.5g/L. Both schizophyllan and pullulan were extracted in crude form and were partially identified by Fourier transform infrared spectroscopy (FTIR), which showed partial similarity in chemical structure with published biopolymers. The produced pullulan and schizophyllan increased the viscosity from 9-20 cp of the control media (without biopolymer) to 20 - 121.4 cp of the cell free broth at 0.1 s-1 shear rate at range of temperatures from 25–45 °C. Enhanced biopolymer production and its physicochemical and rheological properties under different environmental conditions (different temperatures, salt concentrations and wide range of pH), complete characterization and effects on oil recovery enhancement were also investigated in this study.

Keywords: Aureobasidium pullulans, biopolymer, oil recovery enhancement, Schizophyllum commune

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Authors: Cosmas Nathanailides, Fotini Kakali, Kostas Karipoglou

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The filleting yield and the chemical composition of farmed sea bass (Dicentrarchus labrax); rainbow trout (Oncorynchus mykiss) and meagre (Argyrosomus regius) was investigated in farmed fish in NW Greece. The results provide an estimate of the quantity of fish required to produce one kilogram of fillet weight, an estimation which is required for the operational management of fish processing companies. Furthermore in this work, the ratio of feed input required to produce one kilogram of fish fillet (FFCR) is presented for the first time as a useful indicator of the ecological footprint of consuming farmed fish. The lowest lipid content appeared in meagre (1,7%) and the highest in trout (4,91%). The lowest fillet yield and fillet yield feed conversion ratio (FYFCR) was in meagre (FY=42,17%, FFCR=2,48), the best fillet yield (FY=53,8%) and FYFCR (2,10) was exhibited in farmed rainbow trout. This research has been co-financed by the European Union (European Social Fund – ESF) and Greek national funds through the Operational Program "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF) - Research Funding Program: ARCHIMEDES III. Investing in knowledge society through the European Social Fund.

Keywords: farmed fish, flesh quality, filleting yield, lipid

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Authors: F. N. U. Abdullah, A. M. H. Ibrahim, Shuyu Liu

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Hybrid wheat root system is the major plant organ for water and nutrient acquisition. An initial wheat root study with Winrhizo scanner showed that entries with high root surface area but narrow root angle are associated with past drought tolerance in Texas, while those with wide angle can perform best under normal growing conditions. In a hybrid field experiment, commercial heterosis up to 8.3% in grain yield was obtained from diverse parents selected from male and female diverse groups. These hybrids showed promising yield at Greenville and McGregor, Texas, with grain yield up to 4412 Kg ha⁻¹ as compared to best performing commercial varieties ‘TAM-304’ (4075 Kg ha⁻¹) and ‘Gallagher’ (3981 Kg ha⁻¹). Among 130 hybrids produced, a subset of 50 better-performing hybrids and parents was subjected to one-month-old plant root studies scanned with Winrhizo. The results showed a significant positive correlation of grain yield with initial root angle and a negative correlation with root length.

Keywords: hybrids, root studies, heterosis, wheat breeding

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Authors: Bensaid Boulekbache, Mostefa Hamrat, Mohamed Chemrouk, Sofiane Amziane

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This study aims in examining the influence of the paste yield stress and compressive strength on the behaviour of fibre-reinforced concrete (FRC) versus direct shear. The parameters studied are the steel fibre contents, the aspect ratio of fibres and the concrete strength. Prismatic specimens of dimensions 10x10x35cm made of concrete of various yield stress reinforced with steel fibres hooked at the ends with three fibre volume fractions (i.e. 0, 0.5, and 1%) and two aspects ratio (65 and 80) were tested to direct shear. Three types of concretes with various compressive strength and yield stress were tested, an ordinary concrete (OC), a self-compacting concrete (SCC) and a high strength concrete (HSC). The concrete strengths investigated include 30 MPa for OC, 60 MPa for SCC and 80 MPa for HSC. The results show that the shear strength and ductility are affected and have been improved very significantly by the fibre contents, fibre aspect ratio and concrete strength. As the compressive strength and the volume fraction of fibres increase, the shear strength increases. However, yield stress of concrete has an important influence on the orientation and distribution of the fibres in the matrix. The ductility was much higher for ordinary and self-compacting concretes (concrete with good workability). The ductility in direct shear depends on the fibre orientation and is significantly improved when the fibres are perpendicular to the shear plane. On the contrary, for concrete with poor workability, an inadequate distribution and orientation of fibres occurred, leading to a weak contribution of the fibres to the direct shear behaviour.

Keywords: concrete, fibre, direct shear, yield stress, orientation, strength

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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: Areej Javaid, Nishat Fatima, Mehwish Naseer

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There is a tremendous use of biofertilizers in agriculture to increase crop productivity. Pakistan spends a huge amount on the purchase of synthetic fertilizers every year. The use of natural compounds to harness crop productivity is the major area of interest nowadays due to being safe for human health and the environment as well. Legumes have the intrinsic quality to enrich the nutrient status of soil because of the presence of nitrogen fixation bacteria on nodules. This research determined the effect of biofertilizer on nodulation attributes and yield of the pea plant. Seeds of pea varieties were treated with a slurry of biofertilizer prepared in a 10% sugar solution just before seed sowing. The impact of biofertilizer on different parameters of growth, yield and nodulation was observed. Analysis of variance showed that plant height, days to flowering, number of nodes, days to first pod, root length and plant height exhibited significant genetic variation. All the yield parameters, including the number of pods per plant, number of seeds per pod, seed fresh and dry weight showed significant results under treatment. Among nodulation parameters, nodule number responded positively to biofertilizer treatment. Genotypes 2001-40 showed better performance followed by 2001-20 and LINA-PAK in all the parameters, whereas 2001-40 and 2001-20 performed well in nodulation and yield parameters. Consequently, seed treatment with biofertilizer before sowing is recommended to obtain higher crop yield.

Keywords: biological nitrogen fixation, correlation analysis, quantitative inheritance, varietal responses

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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: H. B. Torane, M. C. Kasture, S. S. Prabhudesai, P. B. Sanap, V. N. Palsande, J. J. Palkar

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The present investigation entitled “Response of briquettes application with different coating materials on yield and quality of Cucumber [Cucumis sativus (L.)]” was conducted at Central Experiment Center, Wakawali during kharif season 2013. The field experiment was laid out in Factorial Randomized Block Design with three replicate. The four coating materials viz., Co – Non coating, C1 – Wax coating, C2 – Jaggary coating, and C3 – Tar coating was applied to Konkan Annapurna Briquette along with three sub treatments of application time i.e B1 – ½ at sowing, B2 - ½ at sowing and ½ at 30 days after sowing and B3 - 1/3 at sowing, 1/3 at 30 days after sowing and 1/3 at 60 days after sowing. It was observed that the application of tar coated Konkan Annapurna Briquettes (KAB) in three times @1/3 quantity of briquettes at sowing time, 1/3 quantity of briquettes at 30 days after sowing and 1/3 quantity of briquettes at 60 days after sowing was found promising to enhancing the cucumber fruit yield, higher vine length, number of fruits vine-1, girth of fruit, length of fruit. It was also observed that the quality of the cucumber fruit increased in terms of ascorbic acid. UB-Godavari forms of briquettes .i.e. are promising source of N, P2O5 and K2O fertilizers as compared to straight fertilizers for enhancing green cucumber fruit yield of Sheetal variety of cucumber in lateritic soil. Amongst the three types of coated briquettes, the tar coated briquettes application was found to be superior for increasing cucumber fruit yield applied in three times @1/3 quantity of briquettes at sowing time, 1/3 quantity of briquettes at 30 days after sowing and 1/3 quantity of briquettes at 60 days after sowing @ 5 briquettes per plant at an interval of 30 days after sowing.

Keywords: briquettes, coating, yield, tar, wax and quality

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Authors: A. Rajabpour, A. Hadizadeh Kheirkhah

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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

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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: Amr A. EL Hanafy, Yasir Anwar, Saleh A. Mohamed, Saleh Mohamed Saleh Al-Garni, Jamal S. M. Sabir , Osama A. H. Abu Zinadah, Mohamed Morsi Ahmed

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In the vicinity of the red sea about 15 fungi species were isolated from oil contaminated sites. On the basis of aptitude to degrade the crude oil and DCPIP assay, two fungal isolates were selected amongst 15 oil degrading strains. Analysis of ITS-1, ITS-2 and amplicon pyrosequencing studies of fungal diversity revealed that these strains belong to Penicillium and Aspergillus species. Two strains that proved to be the most efficient in degrading crude oil was Aspergillus niger (54 %) and Penicillium commune (48 %) Subsequent to two weeks of cultivation in BHS medium the degradation rate were recorded by using spectrophotometer and GC-MS. Hence, it is cleared that these fungal strains has the capability of degradation and can be utilized for cleaning the Saudi Arabian environment.

Keywords: fungal strains, hydrocarbon contaminants, molecular identification, biodegradation, GC-MS

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Authors: Dalia G. Aseel

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The potato (Solanum tubersum, L.) has become one of the major vegetable crops in Egypt and all over the world. Potato leafroll virus(PLRV) was observed on potato plants collected from different governorates in Egypt. Three cultivars, Spunta, Diamont, and Cara, infected with PLRV were collected; RNA was extracted and subjected to Real-Time PCR using the coat protein gene primers. The results showed that the expression of the coat protein was 39.6-fold, 12.45-fold, and 47.43-fold, respectively, for Spunta, Diamont, and Cara cultivars. Differential Display Polymerase Chain Reaction (DD-PCR) using pathogenesis-related protein 1 (PR-1), β-1,3-glucanases (PR-2), chitinase (PR-3), peroxidase (POD), and polyphenol oxidase (PPO) forward primers for pathogenesis-related proteins (PR). The obtained data revealed different banding patterns depending on the viral type and the region of infection. Regarding PLRV, 58 up-regulated and 19 down-regulated genes were detected. Sequence analysis of the up-and down-regulated genes revealed that infected plants were observed in comparison with the healthy control. Sequence analysis of the up-regulated gene was performed, and the encoding sequence analysis showed that the obtained genes include: induced stolen tip protein. On the other hand, two down-regulated genes were identified: disease resistance RPP-like protein and non-specific lipid-transfer protein. In this study, the expressions of PR-1, PR-2, PR-3, POD, and PPO genes in the infected leaves of three potato cultivars were estimated by quantitative real-time PCR. We can conclude that the PLRV-infection of potato plants inhibited the expression of the five PR genes. On the contrary, infected leaves by PLRV elevated the expression of some defense genes. This interaction may also induce and/or suppress the expression of some genes responsible for the plant's defense mechanisms.

Keywords: PLRV, pathogenesis-related proteins (PRs), DD-PCR, sequence, real-time PCR

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Authors: Kahina Bedda, Boudjema Hamada

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Environmental regulations have been introduced in many countries around the world to reduce the sulfur content of diesel fuel to ultra low levels with the intention of lowering diesel engine’s harmful exhaust emissions and improving air quality. Removal of sulfur containing compounds from diesel feedstocks to produce ultra low sulfur diesel fuel by extraction with selective solvents has received increasing attention in recent years. This is because the sulfur extraction technologies compared to the hydrotreating processes could reduce the cost of desulfurization substantially since they do not demand hydrogen, and are carried out at atmospheric pressure. In this work, the desulfurization of distillate gasoil by liquid-liquid extraction with N, N-dimethylformamide was investigated. This fraction was recovered from a mixture of Hassi Messaoud crude oils and Hassi R'Mel gas-condensate in Algiers refinery. The sulfur content of this cut is 281 ppm. Experiments were performed in six-stage with a ratio of solvent:feed equal to 3:1. The effect of the extraction temperature was investigated in the interval 30 ÷ 110°C. At 110°C the yield of refined gas oil was 82% and its sulfur content was 69 ppm.

Keywords: desulfurization, gasoil, N, N-dimethylformamide, sulfur content

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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: Nelson Rotimi Osungbemiro, Sanni Rafiu Olugbenga, Abayomi Olufemi Olajuyigbe

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Ninety Fingerlings of Clarias gariepinus were exposed to the pathogenic Flavobacterium columnare a Gram Negative bacteria responsible for high mortality in fish pond raised young fish (fries and fingerlings) of Clarias sp. in Southwestern Nigeria. After feeding with 40% crude protein pelletized fish feed for 5 days, the fishes were divided into two groups, one group was treated with extracts from Calendula officinalis flowers, while the second group was not treated (control). The results indicated that, at day 5, colony formation had been manifesting and at day 7, skin lesion occurred and at the 8th day, first mortality of fish occurred, and this continued steadily on the 9th-12th day when all the fishes were dead. Whereas, in the group that was treated with Calendula sp., no single mortality was recorded. This research shows that plant extract from Calendula flowers is an effective antimicrobial agent against the virulent pathogenic Flavobacterium columnare disease.

Keywords: antimicrobial, Flavobacterium columnare, Clarias gariepinus, fish

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Authors: Golaleh Ghaffari

Abstract:

A basin sediment yield refers to the amount of sediment exported by a basin over a period of time, which will enter a reservoir located at the downstream limit of the basin. The Soil and Water Assessment Tool (SWAT, 2008) was used to hydrology and sediment transport modeling at daily and monthly time steps within the Gheshlagh dam basin in north-west of Iran. The SWAT model and Geographic Information System (GIS) techniques were applied to evaluate basin hydrology and sediment yield using historical flow and sediment data and to identify and prioritize critical sub-basins based on sediment transport. The results of this study indicated that simulated daily discharge and sediment values matched the observed values satisfactorily. The model predicted that mean annual basin precipitation for the total study period (413 mm) was partitioned in to evapotranspiration (36%), percolation/groundwater recharge (21%) and stream water (25%), yielding 18% surface runoff. Potential source areas of erosion were also identified with the model. The range of the annual contributing erosive zones varied spatially from 0.1 to 103 t/ha according to the slope and land use at the basin scale. Also the fifteen sub basins create the 60% of the total sediment yield between the all (102) sub basins. The results of the study indicated that SWAT can be a useful tool for assessing hydrology and sediment yield response of the watersheds in the region.

Keywords: erosion, Gheshlagh dam, sediment yield, SWAT

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Authors: Wali Ullah, Muhammad Nishat

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The study investigates the extent to which the so called Nelson-Siegel model (DNS) and its extended version that accounts for time varying volatility (DNS-EGARCH) can optimally fit the yield curve and predict its future path in the context of an emerging economy. For the in-sample fit, both models fit the curve remarkably well even in the emerging markets. However, the DNS-EGARCH model fits the curve slightly better than the DNS. Moreover, both specifications of yield curve that are based on the Nelson-Siegel functional form outperform the benchmark VAR forecasts at all forecast horizons. The DNS-EGARCH comes with more precise forecasts than the DNS for the 6- and 12-month ahead forecasts, while the two have almost similar performance in terms of RMSE for the very short forecast horizons.

Keywords: yield curve, forecasting, emerging markets, Kalman filter, EGARCH

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Authors: M. Jahanandish, M. B. Zeydabadinejad

Abstract:

In this paper, von Mises and Drucker-Prager yield criteria, as typical ones that consider the effect of intermediate principal stress σ2, have been selected and employed for investigating the influence of σ2 on the solution of a typical stability problem. The bearing capacity factors have been calculated under plane strain condition (strip footing) and axisymmetric condition (circular footing) using the method of stress characteristics together with the criteria mentioned. Different levels of σ2 relative to the other two principal stresses have been considered. While a higher σ2 entry in yield criterion gives a higher bearing capacity; its entry in equilibrium equations (axisymmetric) causes substantial reduction.

Keywords: intermediate principal stress, plane strain, axisymmetric, yield criteria

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Authors: Abdollah Javanmard, Fariborz Shekari

Abstract:

Barley (Hordeum vulgare L.), vetch (Vicia villosa), and grass pea (Lathyrus sativus L.) monocultures as well as mixtures of barley with each of the above legumes, in three seeding ratios (i.e., barley: legume 75:25, 50:50 and 25:75 based on seed numbers) were used to investigate forage yield and competition indices. The results showed that intercropping reduced the dry matter yield of the three component plants, compared with their respective monocrops. The greatest value of total dry matter yield was obtained from barley25-grasspea75 (5.44 t ha-1) mixture, followed by grass pea sole crop (4.99 t ha-1). The total AYL values were positive and greater than 0 in all mixtures, indicating an advantage from intercropping over sole crops. Intercropped barley had a higher relative crowding coefficient (K=1.64) than intercropped legumes (K=1.20), indicating that barley was more competitive than legumes in mixtures. Furthermore, grass pea was more competitive than vetch in mixtures with barley. The highest LER, SPI and MAI were obtained when barley was mixed at a rate of 25% with 75% seed rate of grass pea. It is concluded that intercropping of barley with grass pea has a good potential to improve the performance of forage with high land-use efficiency.

Keywords: forage, grass pea, intercropping, LER, monetary advantage

Procedia PDF Downloads 387