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Showing 7 results for Folding


Volume 2, Issue 1 (3-2016)
Abstract

  Background: The over-expression of recombinant proteins in large amount is important for production of therapeutic proteins and structural study. There are several systems for expression of recombinant proteins. One of the most relevant expression systems is Escherichia coli (E. coli). Although this organism has many advantages, most of recombinant proteins expressed in E. coli hosts form inclusion bodies. For gaining biological activities, these structures should be refolded. Many techniques have been developed for in vitro protein refolding.   Methods: In this study, a method was designed for inclusion body solubilization and protein refolding. IBs were solubilized in the solution containing 2M urea. This is a mild solubilization method without creating random coil structures in the protein. Results : Inclusion bodies undergo mild solubilization with maintain native-like secondary structures. Solubilized proteins were refolded on chromatography column by using native buffer conditions. The results showed the recombinant proteins were purified with high efficiency without aggregation. Conclusions : The results suggest that this method is easy, efficient, cheap procedure and usable for obtaining refolded recombinant proteins. In addition, purified protein with the method can be used in diagnosis and/or treatment of diseases.

Volume 7, Issue 1 (6-2016)
Abstract

Lipases, as an important enzyme group, are able to catalyze hydrolysis or synthesis of esters.The lipase from pseudomonas fluorescens (E.C.3.1.1.3) is a thermophilic kind of lipases (MW around 33 Kd). In this study, the effect of different concentrations of sorbitol on the activity and conformational stability of Psedomonas fluorescence lipase was evaluated using UV/Vis and Circular Dichroism (CD), respectively. According to the results of thermodynamic studies the 0.6 M concentration of sorbitol was selected for refolding and unfolding kinetic measurements with stopped flow fluorescence apparatus. Kinetics data indicate that unfolding of lipase is performed via two different pathways; one of them is probably involves a synchronous unfolding and dissociation of subunits and the other one comprises a two step unfolding in which the subunits are first dissociated followed by complete unfolding of subunits. We found that more population of protein molecules unfolded with slow phase unfolding pathway when sorbitol is present in the unfolding buffer. Furthermore; refolding kinetics data suggest that in the presence of sorbitol the energy barrier of refolding is reduced.
A. Niknejad, G. H. Liaghat, H. Moslemi Naeini, A. H. Behravesh,
Volume 10, Issue 3 (12-2010)
Abstract

In this paper, a theoretical formula is derived to predict the instantaneous folding force of a single-cell square column under axial loading. Calculation is based on analys of “Basic Folding Mechanism” introduced by Wierzbicki and Abramowicz to calculate the instantaneous folding force. For this purpose, three mechanisms of energy dissipation were assumed. The formula obtained in this paper, can predicts the instantaneous folding force variations versus folding distance and versus folding angle with good precision and can predict folding force in each time instance instead of the average value. The results of theoretical formula were compared with experimental data and good agreement was observed. Keywords: Instantaneous Force, Folding, Honeycomb, Square Column.

Volume 10, Issue 3 (9-2019)
Abstract

Aims: Prediction of three-dimensional structure from a sequence of amino acids is one of the important problems in structural bioinformatics. Proteins select a special structure among many possible conformations in order of seconds. Levinthal paradox expresses that random searches could not be an effective way to form a native structure and a principal mechanism should be available. Reduced alphabet fewer than 20 have been interested in protein structure because it could sufficiently simplify the protein folding problem. It is generally assumed that the native structure form in the lowest free energy among all conformational states. Therefore, it is needed to design a trustworthy potential function that could discriminate protein fold from incorrect ones.
Materials and Methods: Knowledge-based potential functions are one type of energy functions derived from a database of known protein structures. In this study, we introduce a knowledge-based potential and assess the power of five amino acids ALA, LEU, ILE, VAL, and PHE in discrimination of native structure using the reduced model. In the reduced model only the energy between the aforementioned amino acids are calculated.
Finding: The reduced model was evaluated using four criteria. The results indicate that there is no significant difference between the 20- amino acid model and the reduced model.
Conclusion: The presented model indicates that the power of discrimination of native structure is originally from the interaction between the aforementioned amino acids. Therefore, it needed a new strategy to capture the remaining interactions to improve the power of knowledge-based potential function.


Volume 12, Issue 1 (3-2021)
Abstract

Despite growing interest in the studies on ZPD, its operation in the forms of individualized and group-wide has been controversial. To cast some empirical light on the issue, this study was designed to quantitatively and comparatively study the applicability of the two scenarios of ZPD-based instructions to the writing accuracy of Iranian EFL learners in terms of learners' types (low vs. high scorers). To this end, 118 EFL learners identified as homogeneous based on TOEFL ITP test were randomly assigned into two equal experimental groups (individualized and group-wide ZPD-based) which respectively received compatible instructions utilizing individual and whole-class scaffolding techniques. The treatments were allocated to the groups in a random manner within homogeneous blocks. Prior to and after the treatments, three tests (two writing tests and one ZPD test) were administered to measure both groups’ writing accuracy and their ZPD levels. A ZPD test was also administered in the mid of treatments. Results revealed that I-ZPD-based instruction is constructive to the low scorers, and GW-ZPD-based instruction is not constructive to both low and high scorers. The findings pointed to the use of ZPD-based instructions in TEFL writing in meaningful contexts and thereby showing impacts made on the writing accuracy of learners. The study, indeed, yield support to the feasibility of GW-ZPD measurement along with I-ZPD approach.

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1. Introduction

Vygotsky’s (1978) Socio-Cultural Theory (SCT) is regarded as a major breakthrough in the field of social psychology and as a resultant in education in general and language education in particular given the significant role of sign system in social construction. SCT is based on certain macro principles mainly including developmental analysis of mental program, social basis of human cognition, scaffolding, mediated learning, and ZPD. In Vygotsky’s sense, scaffolding is defined as the “role of teachers and others in supporting the learner’s development and providing support structures to get to that next stage or level” (Raymond, 2000, p.176, as cited in Van Der Stuyf, 2002).

While SCT principles have been implemented as to certain skills of language ability, writing skill seems to have been left intact to some extent. While writing is one of the main and productive skills, as well as a significant requirement for EFL learners. It is the most difficult skill to master because of its difficulties in generating, organizing, and translating ideas into a readable text (Richards & Renandya, 2002). At the same time, writing is often considered as the most difficult skill to be mastered (Hapsari, 2011). Researchers (Ellis, 2003; Skehan 1998) are now in agreement that L2 proficiency, in general, and writing proficiency, in particular, are multi-componential in nature, and that their principal dimensions can be adequately and comprehensively captured by the notions of complexity, accuracy and fluency (CAF; Housen and Kuiken, 2009).

Writing accuracy refers to “the extent to which the language produced conforms to the target language norms” (Skehan & Foster, 1996, p. 232). Accuracy refers to the production of error-free language. It is estimated by considering the percentage of errorfree clauses (Skehan & Foster, 1996; Skehan & Foster, 1999; Yuan & Ellis, 2004) and the percentage of correct use of target features (Crookes, 1989, as cited in Ellis, 2004).

Scaffolding associates peer-and cooperative endeavor but its implementation seems unimaginable in the absence of ZPD measurement and operationalization. Analogous to society, classroom setting is the combination individuals working and cooperating in a community. It is a must and, of course, to some extent more feasible to identify and probably measure one’s ZPD in a bid to offer some kind of compatible education and input. Nevertheless, pure individualization may look at odd with the other principles of SCT, which is strongly in favor of socially-mediated learning and defining learning as movement along the continuum of intra-personal and inter-personal processes. Such a social, cooperative, and collaborative nature of learning and development requires an initiative to measure both I-ZPD along with GW-ZPD such that the expected mediation, scaffolding and inter-personal and intra-personal processes can be compatible and cooperative. Then, the main problem to be addressed is twofold: operationalization of the varieties of ZPD-based instruction (i.e. I-ZPD vs. GW-ZPD), and incorporation of these two varieties in teaching writing skills in relation to the learners’ variables such as their proficiency level in the form of e,g, test scores.

Based on the significance of the two categories of ZDP and writing in EFL contexts on one hand and the undesirable status of the writing performance of Iranian EFL learners (Hasani and Moghadam, 2012) on the other, this very study is rationalized on the following two premises:

-            the interfaces between EFL learners’ writing quality in terms of accuracy and the two types of ZPD-based instructions (i.e. individualized and group-wide)

-            these instructions’ effect on enhancing writing quality (i.e. accuracy) of Iranian EFL learners in terms of learners' types (i.e. low and high scorers).

In order to accomplish these objectives, the present study, focusing first and foremost on measuring each target learner’s I-ZPD and then on their GW-ZPD or average ZPD, and second on the feasibility and application of each ZPD scenarios in developing writing ability of Iranian EFL learners. More specifically, the following main question realized through four minor ones were posed:

1.         Is there any significant difference in the effect of group-wide ZPD-based instruction and individualized ZPD-based instruction on the writing accuracy of Iranian EFL learners in terms of learners' types (low vs. high scorers)?

1.1     Does GW-ZPD-based instruction and I-ZPD-based instruction have different impact on the accuracy of EFL low-scored learners’ writing?

1.2     Minor Q: Does GW-ZPD-based instruction and I-ZPD-based instruction have different impact on the accuracy of EFL high-scored learners’ writing?

1.3     Minor Q: Does GW-ZPD-based instruction have significantly different effect on low scorers compared to high scorers in developing their writing accuracy?

1.4     Minor Q: Does I-ZPD-based instruction have significantly different effect on low scorers compared to high scorers in developing their writing accuracy?

2. Methodology

The research was conducted empirically through the implementation of the pretest-treatment-posttest design. A homogeneous group of 118 undergraduate, intermediate Persian EFL learners of both genders in the age range of 18 to 22 years old majored in Translation Studies from a university in Tehran students was selected based on their performance on their TOEFL ITP. Then, three pre- and post-tests (two writing tests and a ZPD test) were administered in the first and the last sessions, respectively. The two treatment groups were formed randomly to receive two types of ZPD-based instructions (individualized and group-wide). Another ZPD-test was also administered in the sixth session of the treatment in order to study ZPD development of the two treatment groups and give them their most suitable ZPD-based instructions.

Ultimately, comparison was made between the pre- and post-tests’ scores of the two intact writing classes. The learners’ ZPD development was measured before, after and in the mid of treatment using Raven’s Standard Progressive Matrices (SPM; Raven, 1998). Their ZPD development was, indeed, assessed and analyzed on a weekly basis and a monthly basis (three times in the semester -- before, after, and in the mid of treatment) taking the advantage of Kozulin and Garb’s (2002) learning potential score’s (LPS) formula.

To estimate the inter-rater reliability between the two raters, a randomly selected cluster of writing papers, including 28 sets of papers, scored by the two raters. Running Pearson correlations between these score sets indicated that there were significant agreements between the scores of writing accuracy (r (27) = .73, P < .05 representing a large effect size) as provided by the two raters. As a result, the researcher employed the mean of the two scores provided by the two raters as the final score for each participant’s writing performance in terms of their writing complexity, accuracy.

The treatment was applied for two consequent semesters in order to increase the intra-rater reliability of the findings. Running Pearson correlations between the score sets taken from the first and second semester’s participants of the study indicated that there were significant agreements between the two sets of scores of the participants’ writing performance (r (32) = .83, P < .05 representing a large effect size). As a result, the researcher employed the mean of the two sets of scores taken from the participants during the first and the second semesters as the final score for each participant’s writing performance in terms of their writing accuracy.    

 

3. Results and Discussion

Due to the non-interval nature of the data, all research questions were probed through non-parametric analysis of covariance (ANCOVA) and Friedman’s test.

As to the first and the second minor research questions about the impact of the two types of ZPD-based instructions on the writing accuracy of the low scorers, and the high-scorers, the researchers taking advantage of the criteria proposed by Wigglesworth and Storch (2009) for the measurement of writing accuracy, came up with the following findings:

-            The I-ZPD-based instruction helped the low-scored learners outperform GW-ZPD-based instruction group on the accuracy of writing (+.003 vs. -.136).

-            While the I-ZPD-based instruction acted as a stronger deterrent against writing accuracy of the high-scored learners than the GW-ZPD-based instruction (-.037 vs. -.078).

As to the third and the fourth minor research questions on the effect of the GW-ZPD-based instruction, and the effect of the I-ZPD-based instruction on the writing accuracy of the low scorers compared to high scorers, the respective ANCOVA came up with the following findings:

-            The GW-ZPD-based instruction act as a deterrent against writing accuracy of the low scorers (-.136) and high scorers (-.037) respectively significantly and slightly.

-            And, the I-ZPD-based instruction acted slightly as a deterrent against writing accuracy of the high scorers (-.078) while acting as a very slight developer of writing accuracy of the low scorers (+.003).

As to the main question on the significant difference in the effect of the g-wide ZPD-based instruction and the I-ZPD-based instruction on the writing accuracy of Iranian EFL learners in terms of the learners' levels (i.e., low vs. high scorers), the researcher defined the I-ZPD-based instruction’s positive impacts on the writing accuracy of the low scorers, and the g-wide ZPD-based instruction’s negative impacts on the writing accuracy of the both levels of the learners (more on the low scorers than the high scorers).

 

4. Conclusion and Implications

In brief, two main conclusions from the above-mentioned discussion were drawn: 1) I-ZPD-based instruction is constructive to the writing accuracy of the low-scored learners. 2) GW-ZPD-based instruction is more destructive to the writing accuracy of the low scorers than the high scorers.

The results of the present study cast new light on the nature of ZPD, highlighting the significant difference between the two ways of its running (i.e. individualized vs. group-wide) and the achievements of the two types of EFL learners (i.e. low scorers vs. high scorers). These findings were in line with the results of the studies conducted by many other researchers on the individualized scaffolding technique of conference writing (e.g. Aljaafreh & Lantolf, 1994; De Guerrero & Villamil, 1996; Nassaji & Swain, 2010) and on the whole-class scaffolding technique of template studied by several other scholars (e.g. Baleghizadeh et al., 2011; and Smit et al.,2013).

This study has significant pedagogical implications. Syllabus designers can apply two types of scaffoldings (used in the two types of ZPD-based instructions; i.e. group-wide and individualized) effective for the writing accuracy of the relevant low- and high-scored EFL learners to textbooks. The merit of these two types of ZPD-based instructions is that they challenge writing accuracy of the two types of EFL learners differently but in their ZPD providing guided free exploration.

 



Volume 13, Issue 3 (8-2022)
Abstract

Scaffolding research has been widely investigated involving parent-child within the first language (L1) context without considering the cognitive issues and Intelligence Quotients (IQ) aspects as crucial precursors of the scaffolding process. This case study aims to find emergent themes and theorize potential scaffolding theory from the interaction of two-second language (L2) Autism Spectrum Disorder (ASD) children and normal parents with minimum English exposure, cognitive disorders, and different IQ levels on the mobile story-sharing application. Participant observations and in-depth interviews on scaffolding using story-sharing activities among children, parents, and researchers were conducted every week for six months. Thematic analysis was implemented inductively and interpreted by two experts to find the emerging variation of scaffolding theories. The results showed that ASD learners' scaffolding process involved more complex stages than the previous studies. The complexities of scaffolding involved repetitive recall, translating, imitating, cooperating, target and crises. ASD learners could write a simple phrase and short sentence after exhaustive efforts. Since ASD learners’ previous vocabulary mastery was excluded, it is worth pursuing further researchers to examine learners’ vocabulary and story writing development using the same application.

Volume 15, Issue 3 (6-2024)
Abstract

The countries’ social and economic conditions have been threatened by corona epidemic and a large number of people’s death in the world.  SARS-CoV-2 virus, a form of corona virus family, is responsible for corona disease and its spread in the present century. The study of the receptor binding region (RBD) in the spike protein is very important for scientists because the new corona virus uses its surface spike protein for binding to the ACE2 surface protein and entering its genetic material to the host cells. By this protein and its receptor binding region inhibition, the prevention of virus entrance to the cell is possible. The virus’s genes can be multiplied by cloning and its protein can be purified. The usage of antiviral peptides as the most practical methods and binding inhibitory peptides of RBD to the ACE2 receptor for SARS-CoV-2 treatment, are of great interest to scientists. In the present research, RBD cloning in PET28a expression vector, RBD protein expression and GFP/RBD fusion protein were performed in prokaryotic host. Due to this protein’s insolubility in the prokaryotic host, column refolding was performed with urea gradient with a nickel-agarose column and the synthesized protein was confirmed through western blot technique. Three nominated peptides from articles used to compare their binding to RBD using bioinformatics and their tendency to bind to each other was investigated by molecular docking. The mentioned peptides can be used in this virus infection treatment due to their binding potential to RBD, if their interaction is proven.
 

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