Search results for: rational mutagenesis

Authors: Mark-Adam Kellerman

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Proteins are capable of exploring vast mutational spaces. This makes it difficult for protein engineers to devise rational methods to improve stability and function via mutagenesis. Deciding which residues to mutate requires knowledge of the characteristics they elicit. We probed the characteristics of residues in granulocyte-colony stimulating factor (G-CSF) using a thermal melt (from 295K to 323K) to denature it in a 700 MHz Bruker spectrometer. These characteristics included dynamics, micro-environmental changes experienced/ induced during denaturing and structure-function relationships. 15N-1H HSQC experiments were performed at 2K increments along with this thermal melt. We observed that dynamic residues that also undergo a lot of change in their microenvironment were predominantly in unstructured regions. Moreover, we were able to identify four residues (G4, A6, T133 and Q134) that we class as high priority targets for mutagenesis, given that they all appear in both the top 10% of measures for environmental changes and dynamics (∑Δ and ∆PI). We were also able to probe these NMR observables and combine them with molecular dynamics (MD) to elucidate what appears to be an opening motion of G-CSFs binding site III. V48 appears to be pivotal to this opening motion, which also seemingly distorts the loop region between helices A and B. This observation is in agreement with previous findings that the conformation of this loop region becomes altered in an aggregation-prone state of G-CSF. Hence, we present here an approach to profile the characteristics of residues in order to highlight their potential as rational mutagenesis targets and their roles in important conformational changes. These findings present not only an opportunity to effectively make biobetters, but also open up the possibility to further understand epistasis and machine learn residue behaviours.

Keywords: protein engineering, rational mutagenesis, NMR, molecular dynamics

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Authors: Iman Farasat, Howard M. Salis

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The CRISPR/Cas9 system has revolutionized genome engineering by enabling site-directed and high-throughput genome editing, genome insertion, and gene knockdowns in several species, including bacteria, yeast, flies, worms, and human cell lines. This technology has the potential to enable human gene therapy to treat genetic diseases and cancer at the molecular level; however, the current CRISPR/Cas9 system suffers from seemingly sporadic off-target genome mutagenesis that prevents its use in gene therapy. A comprehensive mechanistic model that explains how the CRISPR/Cas9 functions would enable the rational design of the guide-RNAs responsible for target site selection while minimizing unexpected genome mutagenesis. Here, we present the first quantitative model of the CRISPR/Cas9 genome mutagenesis system that predicts how guide-RNA sequences (crRNAs) control target site selection and cleavage activity. We used statistical thermodynamics and law of mass action to develop a five-step biophysical model of cas9 cleavage, and examined it in vivo and in vitro. To predict a crRNA's binding specificities and cleavage rates, we then compiled a nearest neighbor (NN) energy model that accounts for all possible base pairings and mismatches between the crRNA and the possible genomic DNA sites. These calculations correctly predicted crRNA specificity across 5518 sites. Our analysis reveals that cas9 activity and specificity are anti-correlated, and, the trade-off between them is the determining factor in performing an RNA-mediated cleavage with minimal off-targets. To find an optimal solution, we first created a scheme of safe-design criteria for Cas9 target selection by systematic analysis of available high throughput measurements. We then used our biophysical model to determine the optimal Cas9 expression levels and timing that maximizes on-target cleavage and minimizes off-target activity. We successfully applied this approach in bacterial and mammalian cell lines to reduce off-target activity to near background mutagenesis level while maintaining high on-target cleavage rate.

Keywords: biophysical model, CRISPR, Cas9, genome editing

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Authors: R. M. Kashim

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The study investigates the conceptual and procedural knowledge of rational number in primary school teachers, specifically, the primary school teachers level of conceptual knowledge about rational number and the primary school teachers level of procedural knowledge about rational numbers. The study was carried out in Bauchi metropolis in Bauchi state of Nigeria. A Conceptual and Procedural Knowledge Test was used as the instrument for data collection, 54 mathematics teachers in Bauchi primary schools were involved in the study. The collections were analyzed using mean and standard deviation. The findings revealed that the primary school mathematics teachers in Bauchi metropolis posses a low level of conceptual knowledge of rational number and also possess a high level of Procedural knowledge of rational number. It is therefore recommended that to be effective, teachers teaching mathematics most posses a deep understanding of both conceptual and procedural knowledge. That way the most knowledgeable teachers in mathematics deliver highly effective rational number instructions. Teachers should not ignore the mathematical concept aspect of rational number teaching. This is because only the procedural aspect of Rational number is highlighted during instructions; this often leads to rote - learning of procedures without understanding the meanings. It is necessary for teachers to learn rational numbers teaching method that focus on both conceptual knowledge and procedural knowledge teaching.

Keywords: conceptual knowledge, primary school teachers, procedural knowledge, rational numbers

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Authors: R. M. Kashim

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The study investigated primary school teachers’ conceptual and procedural knowledge of rational numbers and its effects on pupil’s achievement in rational numbers. Specifically, primary school teachers’ level of conceptual knowledge about rational numbers, primary school teachers’ level of procedural knowledge about rational numbers, and the effects of teachers conceptual and procedural knowledge on their pupils understanding of rational numbers in primary schools is investigated. The study was carried out in Bauchi metropolis in the Bauchi state of Nigeria. The design of the study was a multi-stage design. The first stage was a descriptive design. The second stage involves a pre-test, post-test only quasi-experimental design. Two instruments were used for the data collection in the study. These were Conceptual and Procedural knowledge test (CPKT) and Rational number achievement test (RAT), the population of the study comprises of three (3) mathematics teachers’ holders of Nigerian Certificate in Education (NCE) teaching primary six and 210 pupils in their intact classes were used for the study. The data collected were analyzed using mean, standard deviation, analysis of variance, analysis of covariance and t- test. The findings indicated that the pupils taught rational number by a teacher that has high conceptual and procedural knowledge understand and perform better than the pupil taught by a teacher who has low conceptual and procedural knowledge of rational number. It is, therefore, recommended that teachers in primary schools should be encouraged to enrich their conceptual knowledge of rational numbers. Also, the superiority performance of teachers in procedural knowledge in rational number should not become an obstruction of understanding. Teachers Conceptual and procedural knowledge of rational numbers should be balanced so that primary school pupils will have a view of better teaching and learning of rational number in our contemporary schools.

Keywords: conceptual, procedural knowledge, rational number, pupils

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Authors: Raliatu Mohammed Kashim

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The study investigated primary school teachers conceptual and procedural knowledge of rational numbers to determine how it effects on pupil’s achievement on rational number. Specifically, primary school teachers’ level of conceptual and procedural knowledge about rational number and its effects on their pupils understanding of rational number in primary school was explored. The study was carried out in Bauchi state of Nigeria, Using a multistage design. The first stage was a descriptive design. The second stage involves a pre-test post-test only quasi experiment design. The population of the study comprises of six mathematics teachers holding the Nigerian Certificate in Education (NCE) teaching primary six and their two hundred and ten pupils in intact class. Two instrument namely Conceptual and Procedural knowledge Test (CPKT) and Rational number Achievement Test (RAT) were used for data collection. Data collected was analyzed using ANCOVA and Scheffe’s Test. The result revealed a significant differences between pupils taught by teachers with high conceptual and procedural knowledge and those target by teachers with low conceptual and procedural knowledge.

Keywords: conceptual knowledge, procedural knowledge, rational numbers, multistage design

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Authors: G. Ultanbekova, Zh. Suleimenova, Zh. Rakhmetova, G. Mombekova, S. Mantieva

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Plant Growth Promoting Rhizobacteria (PGPR) are a group of free-living bacteria that colonize the rhizosphere, enhance plant growth of many cereals and other important agricultural crops and protect plants from disease and abiotic stresses through a wide variety of mechanisms. The use of PGPR has been proven to be an environmentally sound way of increasing crop yields by facilitating plant growth. In the present study, strain improvement of PGPR isolates were carried out by chemical mutagenesis for the improvement of growth and yield of lima bean. Induced mutagenesis is widely used for the selection of microorganisms producing biologically active substances and further improving their activities. Strain improvement is usually done by classical mutagenesis which involves exposing the microbes to chemical or physical mutagens. The strains of Pseudomonas putida 4/1, Azotobacter chroococcum Р-29 and Bacillus subtilis were subjected to mutation process for strain improvement by treatment with a chemical agent (sodium nitrite) to cause mutation and were observed for its consequent action on the seeds germination and plant growth of lima bean (Phaseolus lunatus). Bacterial mutant strains of Pseudomonas putida M-1, Azotobacter chroococcum M-1 and Bacillus subtilis M-1, treated with sodium nitrite in the concentration of 5 mg/ml for 120 min, were found effective to enhance the germination of lima bean seeds compared to parent strains. Moreover, treatment of the lima bean seeds with a mutant strain of Bacillus subtilis M-1 had a significant stimulation effect on plant growth. The length of the stems and roots of lima bean treated with Bacillus subtilis M-1 increased significantly in comparison with parent strain in 1.6 and 1.3 times, respectively.

Keywords: chemical mutagenesis, germination, kidney bean, plant growth promoting rhizobacteria (PGPR)

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Authors: Uzma Bashir, Jamaludin Md. Ali

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This study is concerned with the visualization of monotone data using a piece-wise C1 rational trigonometric interpolating scheme. Four positive shape parameters are incorporated in the structure of rational trigonometric spline. Conditions on two of these parameters are derived to attain the monotonicity of monotone data and other two are left-free. Figures are used widely to exhibit that the proposed scheme produces graphically smooth monotone curves.

Keywords: trigonometric splines, monotone data, shape preserving, C1 monotone interpolant

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Authors: Sarah Gaßmeyer, Nadine Hülsemann, Raphael Stoll, Kenji Miyamoto, Robert Kourist

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Enzymatic racemization allows the smooth interconversion of stereocenters under very mild reaction conditions. Racemases find frequent applications in deracemization and dynamic kinetic resolutions. Arylmalonate decarboxylase (AMDase) from Bordetella Bronchiseptica has high structural similarity to amino acid racemases. These cofactor-free racemases are able to break chemically strong CH-bonds under mild conditions. The racemase-like catalytic machinery of mutant G74C conveys it a unique activity in the racemisation of pharmacologically relevant derivates of 2-phenylpropionic acid (profenes), which makes AMDase G74C an interesting object for the mechanistic investigation of cofactor-independent racemases. Structure-guided protein engineering achieved a variant of this unique racemase with 40-fold increased activity in the racemisation of several arylaliphatic carboxylic acids. By saturation–transfer–difference NMR spectroscopy (STD-NMR), substrate binding during catalysis was investigated. All atoms of the substrate showed interactions with the enzyme. STD-NMR measurements revealed distinct nuclear Overhauser effects in experiments with and without molecular conversion. The spectroscopic analysis led to the identification of several amino acid residues whose variation increased the activity of G74C. While single-amino acid exchanges increased the activity moderately, structure-guided saturation mutagenesis yielded a quadruple mutant with a 40 times higher reaction rate. This study presents STD-NMR as versatile tool for the analysis of enzyme-substrate interactions in catalytically competent systems and for the guidance of protein engineering.

Keywords: racemase, rational protein design, STD-NMR, structure guided saturation mutagenesis

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Authors: Fakharuddin Ibrahim, Jamaludin Md. Ali, Ahmad Ramli

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In this paper, we will discuss about the data interpolation by using the rational cubic Ball curve. To generate a curve with a better and satisfactory smoothness, the curve segments must be connected with a certain amount of continuity. The continuity that we will consider is of type G¹ continuity. The conditions considered are known as the G¹ Hermite condition. A simple application of the proposed method is to generate an Arabic font satisfying the required continuity.

Keywords: data interpolation, rational ball curve, hermite condition, continuity

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Authors: A. Chillali, M. Sahmoudi

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In this paper we will give a method for encoding the elements of the ring of integers of sextic extension, namely L = Q(a,b) which is a rational quadratic over cubic field K =Q(a) where a^{2} is a rational square free integer and b is a root of irreducible polynomiale of degree 3.

Keywords: coding, integral bases, sextic, quadratic

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Authors: Ahlem Mougaida, Hedi Bel Hadj Salah

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Several methods are suggested to improve the numerical integration in Galerkin weak form for Meshless methods. In fact, integrating without taking into account the characteristics of the shape functions reproduced by Meshless methods (rational functions, with compact support etc.), causes a large integration error that influences the PDE’s approximate solution. Comparisons between different methods of numerical integration for rational functions are discussed and compared. The algorithms are implemented in Matlab. Finally, numerical results were presented to prove the efficiency of our algorithms in improving results.

Keywords: adaptive methods, meshless, numerical integration, rational quadrature

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Authors: Yakup Ulusu, Numan Eczacıoğlu, İsa Gökçe, Helen Waller, Jeremy H. Lakey

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Besides having the appropriate amino acid sequence to perform the function of proteins, it is important to have correct conformation after this sequence to process. To consist of this conformation depends on the amino acid sequence at the primary structure, hydrophobic interaction, chaperones and enzymes in charge of folding etc. Misfolded proteins are not functional and tend to be aggregated. Cysteine originating disulfide cross-links make stable this conformation of functional proteins. When two of the cysteine amino acids come side by side, disulfide bond is established that forms a cystine bridge. Due to this feature cysteine plays an important role on the formation of three-dimensional structure of many proteins. There are two cysteine amino acids (C44, C69) in the Tol-A-III protein. Unlike protein disulfide bonds from within his own, any non-specific cystine bridge causes a change in the three dimensional structure of the protein. Proteins can be expressed in various host cells as directly or fusion (chimeric). As a result of overproduction of the recombinant proteins, aggregation of insoluble proteins in the host cell can occur by forming a crystal structure called inclusion body. In general fusion proteins are produced for provide affinity tags to make proteins more soluble and production of some toxic proteins via fusion protein expression system like pTolT. Proteins can be modified by using a site-directed mutagenesis. By this way, creation of non-specific disulfide crosslinks can be prevented at fusion protein expression system via the present cysteine replaced by another amino acid such as serine, glycine or etc. To do this, we need; a DNA molecule that contains the gene that encodes for the target protein, required primers for mutation to be designed according to site directed mutagenesis reaction. This study was aimed to be replaced cysteine encoding codon TGT with serine encoding codon AGT. For this sense and reverse primers designed (given below) and used site-directed mutagenesis reaction. Several new copy of the template plasmid DNA has been formed with above mentioned mutagenic primers via polymerase chain reaction (PCR). PCR product consists of both the master template DNA (wild type) and the new DNA sequences containing mutations. Dpn-l endonuclease restriction enzyme which is specific for methylated DNA and cuts them to the elimination of the master template DNA. E. coli cells obtained after transformation were incubated LB medium with antibiotic. After purification of plasmid DNA from E. coli, the presence of the mutation was determined by DNA sequence analysis. Developed this new plasmid is called PtolT-δ.

Keywords: site directed mutagenesis, Escherichia coli, pTolT, protein expression

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Authors: Jan Franciszek Jacko

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This investigation presents the principle of methodological rationality of decision making and discusses the impact of an organisation's members' methodologically rational or irrational decisions on its security. This study formulates and partially justifies some research hypotheses regarding the impact. The thinking experiment is used according to Max Weber's ideal types method. Two idealised situations("models") are compared: Model A, whereall decision-makers follow methodologically rational decision-making procedures. Model B, in which these agents follow methodologically irrational decision-making practices. Analysing and comparing the two models will allow the formulation of some research hypotheses regarding the impact of methodologically rational and irrational attitudes of members of an organisation on its security. In addition to the method, phenomenological analyses of rationality and irrationality are applied.

Keywords: methodological rationality, rational decisions, security of organisations, philosophy of economics

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Authors: Akbar Jamali

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Hegel is the first great political philosopher who specifically contemplates on bureaucracy. For Hegel bureaucracy is the function of the state. Since state, essentially is a rational organization, its function; namely, bureaucracy must be rational. Since, what is rational is universal; Hegel had to explain how the bureaucracy could be understood as universal. Hegel discusses bureaucracy in his treatment of ‘executive power’. He analyses modern bureaucracy as a form of political organization, its constituent members, and its relation to the social environment. Therefore, the essence of bureaucracy in Hegel’s philosophy is the implementation of law and rules. Hegel argues that unlike the other social classes that are particular because they look for their own private interest, bureaucracy as a class is a ‘universal’ because their orientation is the interest of the state. State for Hegel is essentially rational and universal. It is the actualization of ‘objective Spirit’. Marx criticizes Hegel’s argument on the universality of state and bureaucracy. For Marx state is equal to bureaucracy, it constitutes a social class that based on the interest of bourgeois class that dominates the society and exploits proletarian class. Therefore, the main disagreement between these political philosophers is: whether the state (bureaucracy) is universal or particular. Growing e-government in modern state as an important aspect of development leads us to contemplate on the particularity and universality of e-government. In this article, we will argue that e-government essentially is universal. E-government, in itself, is impartial; therefore, it cannot be particular. The development of e-government eliminates many side effects of the private, personal or particular interest of the individuals who work as bureaucracy. Finally, we will argue that more a state is developed more it is universal. Therefore, development of e-government makes the state a more universal and affects the modern philosophical debate on the particularity or universality of bureaucracy and state.

Keywords: particularity, universality, rational bureaucracy, impartiality

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Authors: Debamitra Chakravorty, Pratap K. Parida

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Cold-adapted proteases enhance wash performance in low-temperature laundry resulting in a reduction in energy consumption and wear of textiles and are also used in the dehairing process in leather industries. Unfortunately, the possible drawbacks of using cold-adapted proteases are their instability at higher temperatures. Therefore, proteases with broad temperature stability are required. Unfortunately, wild-type cold-adapted proteases exhibit instability at higher temperatures and thus have low shelf lives. Therefore, attempts to engineer cold-adapted proteases by protein engineering were made previously by directed evolution and random mutagenesis. The lacuna is the time, capital, and labour involved to obtain these variants are very demanding and challenging. Therefore, rational engineering for cold stability without compromising an enzyme's optimum pH and temperature for activity is the current requirement. In this work, mutations were rationally designed with the aid of high throughput computational methodology of network analysis, evolutionary conservation scores, and molecular dynamics simulations for Savinase from Bacillus lentus with the intention of rendering the mutants cold stable without affecting their temperature and pH optimum for activity. Further, an attempt was made to incorporate a mutation in the most stable mutant rationally obtained by this method to introduce oxidative stability in the mutant. Such enzymes are desired in detergents with bleaching agents. In silico analysis by performing 300 ns molecular dynamics simulations at 5 different temperatures revealed that these three mutants were found to be better in cold stability compared to the wild type Savinase from Bacillus lentus. Conclusively, this work shows that cold adaptation without losing optimum temperature and pH stability and additionally stability from oxidative damage can be rationally designed by in silico enzyme engineering. The key findings of this work were first, the in silico data of H5 (cold stable savinase) used as a control in this work, corroborated with its reported wet lab temperature stability data. Secondly, three cold stable mutants of Savinase from Bacillus lentus were rationally identified. Lastly, a mutation which will stabilize savinase against oxidative damage was additionally identified.

Keywords: cold stability, molecular dynamics simulations, protein engineering, rational design

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Authors: Muhammad Shoaib

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Every society has a set of beliefs, norms, values, folkways, mores and laws. All the principles, customs, traditions and procedures of societies are directly or indirectly related to the religion of the society and changed with the passage of time by the mediation of democratic values attitudes and mass media influence. The main objective of the present study is to examine the effects of rational thinking values on forgiveness attitude by the mediation of democratic values and mass media attitude among family members. As many other developing settings, Pakistani society is undergoing a rapid and multifaceted social change, in which traditional thinking coexists and often clashes with modern thinking. Rational thinking attitude has great effects on the forgiveness attitude among family members as well as all the members of Pakistani society. For the present study 520 respondents were sampled from two urban areas of Punjab province; Lahore and Faisalabad, through proportionate random sampling technique. A survey method was used as a technique of data collection and an interview schedule was administered to collect information from the respondents. The results support that the net of other factors, favorable democratic values attitudes are positively associated rational thinking attitudes. The results also provide support that all other things equal, mass media attitudes also have a significant positive effect on rational thinking attitudes. Favorable democratic values attitudes have a significant net positive effect and the effect of mass media attitudes is positive and statistically highly significant. It shows that the effects of both democratic values attitudes and mass media attitudes diminish in magnitude when the rational thinking attitudes scale is included. However, the effect of democratic values remains highly significant. In comparison, the effect of mass media attitudes is only marginally significant.

Keywords: rationality, forgiveness, democratic values, mass media, attitudes, Pakistan

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Authors: Soniya Takshak, R. K. Sharma

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Let q and n be positive integers, then Fᵩ denotes the finite field of q elements, and Fqn denotes the extension of Fᵩ of degree n. Also, Fᵩ* represents the multiplicative group of non-zero elements of Fᵩ, and the generators of Fᵩ* are called primitive elements. A normal element α of a finite field Fᵩⁿ is such that {α, αᵠ, . . . , αᵠⁿ⁻¹} forms a basis for Fᵩⁿ over Fᵩ. Primitive normal elements have several applications in coding theory and cryptography. So, establishing the existence of primitive normal elements under certain conditions is both theoretically important and a natural issue. In this article, we provide a sufficient condition for the existence of a primitive normal element α in Fᵩⁿ of a prescribed primitive norm and non-zero trace over Fᵩ such that f(α) is also primitive, where f(x) ∈ Fᵩⁿ(x) is a rational function of degree sum m. Particularly, we investigated the rational functions of degree sum 4 over Fᵩⁿ, where q = 11ᵏ and demonstrated that there are only 3 exceptional pairs (q, n), n ≥ 7 for which such kind of primitive normal elements may not exist. In general, we show that such elements always exist except for finitely many choices of (q, n). To arrive to our conclusion, we used additive and multiplicative character sums.

Keywords: finite field, primitive element, normal element, norm, trace, character

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Authors: O. Starineca, I. Voronchuk

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Human Resources (HR) selection and training have various implementation possibilities depending on an organization’s abilities and peculiarities. We propose to base HR selection and training decisions about on a competence-based approach. HR selection and training of employees are topical as there is room for improvement in this field; therefore, the aim of the research is to propose rational decision-making approaches for an organization HR selection and training choice. Our proposals are based on the training development and competence-based selection approaches created within previous researches i.e. Analytic-Hierarchy Process (AHP) and Linear Programming. Literature review on non-formal education, competence-based selection, AHP form our theoretical background. Some educational service providers in Latvia offer employees training, e.g. motivation, computer skills, accounting, law, ethics, stress management, etc. that are topical for Public Administration. Competence-based approach is a rational base for rational decision-making in both HR selection and considering HR training.

Keywords: competence-based selection, human resource, training, decision-making

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Authors: Siddhant Sethi, Yasuharu Takashima, Shigetaka Nakamura, Kenzo Fujimoto

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Site-directed mutagenesis is a renowned technique to introduce specific mutations in the genome. To achieve site-directed mutagenesis, many chemical and enzymatic approaches have been reported in the past like disulphite induced genome editing, CRISPR-Cas9, TALEN etc. The chemical methods are invasive whereas the enzymatic approaches are time-consuming and expensive. Most of these techniques are unusable in the cellular application due to their toxicity and other limitations. Photo-chemical cytosine deamination, introduced in 2010, is one of the major technique for enzyme-free single-point mutation of cytosine to uracil in DNA and RNA, wherein, 3-cyanovinylcarbazole nucleoside (CNVK) containing oligodeoxyribonucleotide (ODN) having CNVK at -1 position to that of target cytosine is reversibly crosslinked to target DNA strand using 366 nm and then incubated at 90ºC to accommodate deamination. This technique is superior to enzymatic methods of site-directed mutagenesis but has a disadvantage that it requires the use of high temperature for the deamination step which restricts its applicability in the in vivo applications. This study has been focused on improving the technique by reducing the temperature required for deamination. Firstly, the photo-cross-linker, CNVK has been modified by replacing cyano group attached to vinyl group with methyl ester (OMeVK), amide (NH2VK), and carboxylic acid (OHVK) to observe the acceleration in the deamination of target cytosine cross-linked to vinylcarbazole derivative. Among the derivatives, OHVK has shown 2 times acceleration in deamination reaction as compared to CNVK, while the other two derivatives have shown deceleration towards deamination reaction. The trend of rate of deamination reaction follows the same order as that of hydrophilicity of the vinylcarbazole derivatives. OHVK being most hydrophilic has shown highest acceleration while OMeVK is least hydrophilic has proven to be least active for deamination. Secondly, in the related study, the counter-base of the target cytosine, guanine has been replaced by inosine, 2-aminopurine, nebularine, and 5-nitroindole having distinct hydrogen bonding patterns with target cytosine. Among the ODNs with these counter bases, ODN with inosine has shown 12 fold acceleration towards deamination of cytosine cross-linked to CNVK at physiological conditions as compared to guanosine. Whereas, when 2-aminopurine, nebularine, and 5-nitroindole were used, no deamination reaction took place. It can be concluded that inosine has potential to be used as the counter base of target cytosine for the CNVK mediated photo-cross-linking induced deamination of cytosine. The increase in rate of deamination reaction has been attributed to pattern and number of hydrogen bonding between the cytosine and counter base. One of the important factor is presence of hydrogen bond between exo-cyclic amino group of cytosine and the counter base. These results will be useful for development of more efficient technique for site-directed mutagenesis for C → U transformations in the DNA/RNA which might be used in the living system for treatment of various genetic disorders and genome engineering for making designer and non-native proteins.

Keywords: C to U transformation, DNA editing, genome engineering, ultra-fast photo-cross-linking

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Authors: Said Algarni

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The purpose of this study was to investigate selected numerical methods that demonstrate good performance in solving PDEs. We adapted alternative method that involve rational polynomials. Padé time stepping (PTS) method, which is highly stable for the purposes of the present application and is associated with lower computational costs, was applied. Furthermore, PTS was modified for our study which focused on diffusion equations. Numerical runs were conducted to obtain the optimal local error control threshold.

Keywords: Padé time stepping, finite difference, reaction diffusion equation, PDEs

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Authors: Hunmin Jung, Michael Hawkins, Seongmin Lee

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The exocyclic amines of nucleobases can undergo deamination by various DNA damaging agents such as reactive oxygen species, nitric oxide, and water. The deamination of guanine and adenine generates the promutagenic xanthine and hypoxanthine, respectively. The exocyclic amines of bases in DNA are hydrogen bond donors, while the carbonyl moiety generated by the base deamination acts as hydrogen bond acceptors, which can alter base pairing properties of the purines. Xanthine is known to base pair with both cytosine and thymine, while hypoxanthine predominantly pairs with cytosine to promote A to G mutations. Despite the known promutagenicity of the major deaminated purines, structures of DNA polymerase bypassing these lesions have not been reported. To gain insights into the deaminated-induced mutagenesis, we solved crystal structures of human DNA polymerase η (polη) catalyzing across xanthine and hypoxanthine. In the catalytic site of polη, the deaminated guanine (i.e., xanthine) forms three Watson-Crick-like hydrogen bonds with an incoming dCTP, indicating the O2-enol tautomer of xanthine involves in the base pairing. The formation of the enol tautomer appears to be promoted by the minor groove contact by Gln38 of polη. When hypoxanthine is at the templating position, the deaminated adenine uses its O6-keto tautomer to form two Watson-Crick hydrogen bonds with an incoming dCTP, providing the structural basis for the high promutagenicity of hypoxanthine.

Keywords: DNA damage, DNA polymerase, deamination, mutagenesis, tautomerization, translesion synthesis

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Authors: Zakir H. Shaik, Punam L. Vartak

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Management By Objectives (MBO) is a management technique in which objectives of an organisation are conveyed to the employees to establish the individual goals. These objectives and goals are then monitored and assessed jointly by management and the employee time to time. This tool can be used for planning, monitoring as well as for performance appraisal. The success of an organisation is largely dependent on its’s Vision. Thus, it is of paramount importance to achieve the realm of vision through a mission which is well crafted within the organisation to address the objectives. The success of the mission depends upon how realistic and action oriented philosophical approach, an organisation caters to; and how the individual goals are set to track and meet the objectives. Thus, focused and passionate efforts of the team, assigned for the mission, are an absolute obligation for achieving the vision of any organisation. Any construction site is generally a controlled disorder having huge investments, resources and logistics involved. The Construction progression is time-consuming with many isolated as well as interconnected activities. Traditional MBO approach can be unsuccessful if planning and control is non-realistic and inflexible. Moreover, the Construction Industry is far behind understanding these concepts. It is important to address the employee engagement in defining and creating awareness to achieve the targets. Besides, current economic environment and competitive world demands refined management tools to achieve profit, growth and survival of the business. Therefore, the necessity of rational MBO becomes vital part towards the success of an organisation. This paper details about the philosophical assumptions to develop the grounded theory in lieu of achieving objectives through RATIONAL MBO approach in Construction Contracting Organisations. The goals and objectives of the Construction Contracting Organisations can be achieved efficiently by adopting this RATIONAL MBO approach, as those are based on realistic, logical and balanced assumptions.

Keywords: growth, leadership, management by objectives, Management By Objectives (MBO), profit, rational

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Authors: Anass Hsissi, Hakim Allali, Abdelmajid Hajami

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This article presents the results of a doctoral research which aims to integrate metacognitive dimension in the design of human learning computing environments (ILE). We conducted a detailed study on the relationship between metacognitive processes and learning, specifically their positive impact on the performance of learners in the area of reading comprehension. Our contribution is to implement methods, using an intelligent agent based on BDI paradigm to ensure intelligent and reliable support for low readers, in order to encourage regulation and a conscious and rational use of their metacognitive abilities.

Keywords: metacognition, text comprehension EIAH, autoregulation, BDI agent

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Authors: D. Shehu, Z. Alias

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Glutathione S-transferases (GSTs) are family of enzymes that function in the detoxification of variety of electrophilic substrates. In the present work, we report a novel zeta-like GST (designated as KKSG9) from the biphenyl/polychlorobiphenyl degrading organism Acidovorax sp. KKS102. KKSG9 possessed low sequence similarity but similar biochemical properties to zeta class GSTs. The gene for KKSG9 was cloned, purified and biochemically characterized. Functional analysis showed that the enzyme exhibits wider substrate specificity compared to most zeta class GSTs by reacting with 1-chloro-2,4-dinitrobenzene (CDNB), p-nitrobenzyl chloride (NBC), ethacrynic acid (EA), hydrogen peroxide, and cumene hydroperoxide (CuOOH). The enzyme also displayed dehalogenation function against dichloroacetate (a common substrate for zeta class GSTs) in addition to permethrin, and dieldrin. The functional role of Tyr12 was also investigated by site-directed mutagenesis. The mutant (Y12C) displayed low catalytic activity and dehalogenation function against all the substrates when compared with the wild type. Kinetic analysis using NBC and GSH as substrates showed that the mutant (Y12C) displayed a higher affinity for NBC when compared with the wild type, however, no significant change in GSH affinity was observed. These findings suggest that the presence of tyrosine residue in the motif might represent an evolutionary trend toward improving the catalytic activity of the enzyme. The enzyme as well could be useful in the bioremediation of various types of organochlorine pollutants.

Keywords: Acidovorax sp. KKS102, bioremediation, glutathione s-transferase, site-directed mutagenesis, zeta

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Authors: Dumasari, Pujiati Utami

Abstract:

The bargaining position is important for a craftsman in every transaction. A strong bargaining position to encourage craftsmen to gain feasible prices on souvenirs tourism products are sold in several market segments. Some social actions of craftsmen turned out to also determine the conditions bargaining. The main goal of this study is to assess the range of social action to strengthen the bargaining position of craftsmen in marketing various products of tourism souvenir. Location of the study is set intentionally in the Sub-District of Baturaden, Banyumas Regency and also the Sub-District of Purbalingga Wetan, Purbalingga Regency. Both of them are located in the Central Java Province, Indonesia. The research method is the descriptive case study. The results showed that the craftsmen not only carry out one or two type of social action. They do all of the social action: the first is rational based instrumental, the second is rational based on the values, the third is affective, and the fourth is traditional. However, craftsmen also develop other social actions namely: collective, productive and creative action. At respondents in Baturaden dominant type of social action that is instrumentally rational, productive and creative. Meanwhile, respondents in Purbalingga more dominant social action collective, productive and creative. Some social actions implemented simultaneously by the respondents. Because of this, they concluded that the rational action that modified by themselves is more easily for strengthening the bargaining position when facing the craftsmen traders collectors. Collective and rationality social action has the highest sensitivity value for strengthening the bargaining position of craftsmen.

Keywords: bargaining position, craftsmen, strengthen, social actions, marketing of tourism souvenir

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Authors: Maria Hussin, Malik Zawwar Hussain, Mubashrah Saddiqa

Abstract:

We present a trigonometric scheme to approximate a circular arc with its two end points and two end tangents/unit tangents. A rational cubic trigonometric Bézier curve is constructed whose end control points are defined by the end points of the circular arc. Weight functions and the remaining control points of the cubic trigonometric Bézier curve are estimated by variational approach to reproduce a circular arc. The radius error is calculated and found less than the existing techniques.

Keywords: control points, rational trigonometric Bézier curves, radius error, shape measure, weight functions

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Authors: Vano Tsertsvadze, Marina Chavchanidze, Lali Khurtsia

Abstract:

Problem of drug use is often seen as a combination of psychological and social problems, but this problem can be considered as economically rational decision in the process of buying pleasure (looking after children, reading, harvesting fruits in the fall, sex, eating, etc.). Before the adoption of the decisions people face to a trade-off - when someone chooses a delicious meal, she takes a completely rational decision, that the pleasure of eating has a lot more value than the pleasure which she will experience after two months diet on the summer beach showing off her beautiful body. This argument is also true for alcohol, drugs and cigarettes. Smoking has a negative effect on health, but smokers are not afraid of the threat of a lung cancer after 40 years, more valuable moment is a pleasure from smoking. Our hypothesis - unsatisfied pleasure and frustration, probably determines the risk of dependence on drug abuse. The purpose of research: 1- to determine the relative measure unit of pleasure, which will be used to measure and assess the intensity of various human pleasures. 2- to compare the intensity of the pleasure from different kinds of activity, with pleasures received from drug use. 3- Based on the analysis of data, to identify factors affecting the rational decision making. Research method: Respondents will be asked to recall the greatest pleasure of their life, which will be used as a measure of the other pleasures. The study will use focus groups and structured interviews.

Keywords: drug, drug-user, measurement, satisfaction

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Authors: Benhenni Abdellaziz

Abstract:

Irrigation is a limiting factor for agricultural production and socio-economic development of many countries in arid and semiarid in the world. However, the sustainability of irrigation systems requires a rational management of the water resource that is becoming increasingly rare in these regions. The objective of this work is to apply a geographic information system (GIS) coupled to a model for calculating crop water requirements (CROPWATER) for the management of irrigation water in irrigated area and offer managers with an effective tool to better manage water resources in these areas. The application area of GIS is the irrigated perimeter of Western Middle Cheliff which is located in a semi-arid region (Middle Cheliff). The scope in question is a considerable agrarian dynamics and an increased need for irrigation of most crops.

Keywords: geographical information, irrigation, economical, use rational

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Authors: Shweta Jha, Digambar Darekar, Krishna Kadam

Abstract:

Major Depressive Disorder (MDD) is one of the most common of psychiatric disorders. It has a wide range of symptoms, aetiologies and risk factors, and these reasons make MDD affect not only the primary patient, but also their family, caregivers and associates; by negatively impacting their self dignity, economic condition and self-confidence. Thus, it is important to help individuals suffering from MDD learn adaptive mechanism and deal effectively with their environment, with that aim this study focused on a comparative therapeutic intervention using Behaviour Activation (BA), Rational Emotive Behaviour Therapy (REBT) and Waiting list control (WLC) for management of MDD. This study apart from enhancing personal skills will also help us understand which therapeutic method would be more beneficial in treating and prolonging relapse in patients with MDD in Indian population. Fifteen individuals following application of inclusion and exclusion criteria were selected as study samples. They were randomly assigned to three treatment groups. Ten sessions of therapy, forty-five minutes each according to the proposed sessions plan were conducted for each group. The individuals selected as samples were re–assessed after 2 months and 6 months post intervention. The overall result showed that individuals treated with BA and REBT showed more improvement in comparison to those in WLC.

Keywords: behaviour activation, major depressive disorder, rational emotive behaviour therapy, therapeutic intervention

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Authors: Lola Rosalia Saavedra Guzman, Plamen Neytchev Netchev

Abstract:

In general, agnosticism is perceived as an uncertainty between a well-structured (religious) belief (in some Christian or pagan deity) and its absolute and total absence, often causing the suspicion that an agnostic is an atheist, which is "reinsured" in case if their personal belief is wrong. All of this, along with the prevailing view among the naturalists that science has already demonstrated the inexistence of God, has compelled us to seek the foundation of agnosticism and faith in the contemporary formal human logic, advanced mathematics, and the natural sciences. Along the way, we will find that no natural science can demonstrate the existence of God, nor could it discard it for rational considerations, which show that there is something beyond. After all, it seems that the human intellect is insufficient to respond surely with yes or no to the existence of higher intelligences leaving unconditional faith as the only path to God for Christians and transcendent techniques, for pagan religious beliefs.

Keywords: agnosticism, formal logic, axioms and postulates, Gödel theorems, and logical faults

Procedia PDF Downloads 167