Search results for: clonal fragment

Authors: Ismael Zamora, Elisabeth Ortega, Tatiana Radchenko, Guillem Plasencia

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The structure elucidation based on Mass Spectra (MS) data of unknown substances is an unresolved problem that affects many different fields of application. The recent overview of software available for structure elucidation of small molecules has shown the demand for efficient computational tool that will be able to perform structure elucidation of unknown small molecules and peptides. We developed an algorithm for De-Novo fragment analysis based on MS data that proposes a set of scored and ranked structures that are compatible with the MS and MSMS spectra. Several different algorithms were developed depending on the initial set of fragments and the structure building processes. Also, in all cases, several scores for the final molecule ranking were computed. They were validated with small and middle databases (DB) with the eleven test set compounds. Similar results were obtained from any of the databases that contained the fragments of the expected compound. We presented an algorithm. Or De-Novo fragment analysis based on only mass spectrometry (MS) data only that proposed a set of scored/ranked structures that was validated on different types of databases and showed good results as proof of concept. Moreover, the solutions proposed by Mass Spectrometry were submitted to the prediction of NMR spectra in order to elucidate which of the proposed structures was compatible with the NMR spectra collected.

Keywords: De Novo, structure elucidation, mass spectrometry, NMR

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Authors: Christina Roman, Deepak Koirala, Joseph A. Piccirilli

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Phage displaying synthetic Fab libraries have been used to obtain Fabs that bind to specific RNA targets with high affinity and specificity. These Fabs have been demonstrated to facilitate RNA crystallization. However, the antibody framework used in the construction of these phage display libraries contains numerous bulky, flexible, and charged residues, which facilitate solubility and hinder aggregation. These residues can interfere with crystallization due to the entropic cost associated with burying them within crystal contacts. To systematically reduce the surface entropy of the Fabs and improve their crystallization properties, a protein engineering strategy termed surface entropy reduction (SER) is being applied to the Fab framework. In this approach, high entropy residues are mutated to smaller ones such as alanine or serine. Focusing initially on Fab BL3-6, which binds an RNA AAACA pentaloop with 20nM affinity, the SER P server (http://services.mbi.ucla.edu/SER/) was used and analysis was performed on existing RNA-Fab BL3-6 co-crystal structures. From this analysis twelve surface entropy reduced mutants were designed. These SER mutants were expressed and are now being measured for their crystallization and diffraction performance with various RNA targets. So far, one mutant has generated 3.02 angstrom diffraction with the yjdF riboswitch RNA. Ultimately, the most productive mutations will be combined into a new Fab framework to be used in a optimized phage displayed Fab library.

Keywords: antibody fragment, crystallography, RNA, surface entropy reduction

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Authors: Akila Tayeb-Benmachiche, Saber-Mustapha Zendaoui, Salah-Eddine Bouaoud, Bachir Zouchoune

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The variation of the metal coordination site in π-coordinated polycyclic aromatic hydrocarbons (PAH) corresponds to the haptotropic rearrangement or haptotropic migration in which the metal fragment MLn is considered as the moveable moiety that is shifted between two rings of polycyclic or heteropolycyclic ligands. These structural characteristics and dynamical properties give to this category of transition metal complexes a considerable interest. We have investigated the coordination and the haptotropic shifts of (CO)3Ti and CpV moieties over the phenanthridine aromatic system and according to the metal atom nature. The optimization of (CO)3Ti(PHND) and CpV(PHND), using the Amsterdam Density Functional (ADF) program, without a symmetrical restriction of geometry gives an η6 coordination mode of the C6 and C5N rings, which in turn give rise to a six low-lying deficient 16-MVE of each (CO)3Ti(PHND) and CpV(PHND) structure (three singlet and three triplet state structures for Ti complexes and three triplet and three quintet state structures for V complexes). Thus, the η6–η6 haptotropic migration of the metal fragment MLn from the terminal C6 ring to the central C5N ring has been achieved by a loss of energy. However, its η6–η6 haptotropic migration from central C5N ring to the terminal C6 rings has been accomplished by a gain of energy. These results show the capability of the phenanthridine ligand to adapt itself to the electronic demand of the metal in agreement with the nature of the metal–ligand bonding and demonstrate that this theoretical study can also be applied to large fused π-systems.

Keywords: electronic structure, bonding analysis, density functional theory, coordination chemistry haptotropic migration

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Authors: Le Nguyen Binh, Luong Xuan Binh, Le Van Tuan, Tran Binh Duong, Truong Nguyen Khanh Hung, Do Le Hoang Son, Pham Quang Vinh, Hoang Quoc Huy, Nguyen Bach, Nguyen Quoc Khanh Le, Jiunn Horng Kang

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Introduction: Traumatic hip dislocation is an emergency in young adult which can cause avascular necrosis of femoral head or osteoarthritis of hip joint. The reasons for these may be the loose body of bony or chondral fragments, which are difficult to be detected on CT scan or MRI. In those cases, Hip arthroscopy may be the method of choice for diagnosis and treatment of loose bodies in hip joint after traumatic dislocation. Methods: A case report is performed. A 55-year-old male patient was under hip arthroscopy to retrieve the loose body in the right hip joint. Results: The patient’s hip was reduced under anesthesia in the opeation room. Xray and CT scan post-reduction showed that his right hip was wide and a small fragment of femoral head (< 5mm) locking inside the joint. A hip arthroscopy was done to take the fragment out. Post-operation, the patient went under rehabilition. After 6 months, he can walk with full-weight bearing; no further dislocaion was noted, and the Harris score was 84 points. Conclusions: Although acute traumatic injury of hip joint is usually treated with open surgeries, these methods have many drawbacks, such as soft tissue destruction, blood-loss,….Despite its technical requirement, hip arthroscopy is less invasive and effective treatment. Therefore, it may be an alternative treatment for a traumatic hip injury and can be applied frequently in the near future.

Keywords: hip dislocation, hip arthroscopy, hip osteoarthritis, acute hip trauma

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Authors: Ramesh Joshi, Nisha Khatik

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Murraya koenigii (L.) Spreng locally known as “Curry patta” or “Meetha neem” belonging to the family Rutaceae that grows wildly in Southern Asia. Its aromatic leaves are commonly used as the raw material for traditional medicinal formulations in India. The leaves contain essential oil and also used as a condiment. Several monomeric and binary carbazol alkaloids present in the various plant parts. These alkaloids have been reported to possess anti-microbial, mosquitocidal, topo-isomerase inhibition and antioxidant properties. Some of the alkaloids reported in this plant have showed anti carcinogenic and anti-diabetic properties. The conventional method of propagation of this tree is limited to seeds only, which retain their viability for only a short period. Hence, a biotechnological approach might have an advantage edging over traditional breeding as well as the genetic improvement of M. koenigii within a short period. The development of a reproducible regeneration protocol is the prerequisite for ex situ conservation and micropropagation. An efficient protocol for high frequency regeneration of in vitro plants of Murraya koenigii via different explants such as- nodal segments, intermodal segments, leaf, root segments, hypocotyle, cotyledons and cotyledonary node explants is described. In the present investigation, assessment of clonal fidelity in the micropropagated plantlets of Murraya koenigii was attempted using RAPD and ISSR markers at different pathways of plant tissue culture technique. About 20 ISSR and 40 RAPD primers were used for all the samples. Genomic DNA was extracted by CTAB method. ISSR primer were found to be more suitable as compared to RAPD for the analysis of clonal fidelity of M. koenigii. The amplifications however, were finally performed using RAPD, ISSR markers owing to their better performance in terms of generation of amplification products. In RAPD primer maximum 75% polymorphism was recorded in OPU-2 series which exhibited out of 04 scorable bands, three bands were polymorphic with a band range of size 600-1500 bp. In ISSR primers the UBC 857 showed 50% polymorphism with 02 band were polymorphic of band range size between 400-1000 bp.

Keywords: genetic fidelity, Murraya koenigii, aromatic plants, ISSR primers

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Authors: P. M. Sreekanth

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Teak (Tectona grandis L. f.) is a tree species indigenous to India and other Southeastern countries. It produces high-value timber and is easily established in plantations. Reforestation requires a constant supply of high quality seeds. Seed Production Areas (SPA) of teak are improved stands used for collection of open-pollinated quality seeds in large quantities. Information on the genetic diversity of major teak SPAs in India is scanty. The genetic structure of four important seed production areas of Kerala State in Southern India was analyzed employing amplified fragment length polymorphism markers using ten selective primer combinations on 80 samples (4 populations X 20 trees). The study revealed that the gene diversity of the SPAs varied from 0.169 (Konni SPA) to 0.203 (Wayanad SPA). The percentage of polymorphic loci ranged from 74.42 (Parambikulam SPA) to 84.06 (Konni SPA). The mean total gene diversity index (HT) of all the four SPAs was 0.2296 ±0.02. A high proportion of genetic diversity was observed within the populations (83%) while diversity between populations was lower (17%) (GST = 0.17). Principal coordinate analysis and STRUCTURE analysis of the genotypes indicated that the pattern of clustering was in accordance with the origin and geographic location of SPAs, indicating specific identity of each population. A UPGMA dendrogram was prepared and showed that all the twenty samples from each of Konni and Parambikulam SPAs clustered into two separate groups, respectively. However, five Nilambur genotypes and one Wayanad genotype intruded into the Konni cluster. The higher gene flow estimated (Nm = 2.4) reflected the inclusion of Konni origin planting stock in the Nilambur and Wayanad plantations. Evidence for population structure investigated using 3D Principal Coordinate Analysis of FAMD software 1.30 indicated that the pattern of clustering was in accordance with the origin of SPAs. The present study showed that assessment of genetic diversity in seed production plantations can be achieved using AFLP markers. The AFLP fingerprinting was also capable of identifying the geographical origin of planting stock and there by revealing the occurrence of the errors in genotype labeling. Molecular marker-based selective culling of genetically similar trees from a stand so as to increase the genetic base of seed production areas could be a new proposition to improve quality of seeds required for raising commercial plantations of teak. The technique can also be used to assess the genetic diversity status of plus trees within provenances during their selection for raising clonal seed orchards for assuring the quality of seeds available for raising future plantations.

Keywords: AFLP, genetic structure, spa, teak

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Authors: Boris Djartov, Sanaz Mostaghim

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This paper presents a number-based dominance method. The main idea is how to fragment the many attributes of the problem into subsets suitable for the well-established concept of Pareto dominance. Although other similar methods can be found in the literature, they focus on comparing the solutions one objective at a time, while the focus of this method is to compare entire subsets of the objective vector. Given the nature of the method, it is computationally costlier than other methods and thus, it is geared more towards selecting an option from a finite set of alternatives, where each solution is defined by multiple objectives. The need for this method was motivated by dynamic alternate airport selection (DAAS). In DAAS, pilots, while en route to their destination, can find themselves in a situation where they need to select a new landing airport. In such a predicament, they need to consider multiple alternatives with many different characteristics, such as wind conditions, available landing distance, the fuel needed to reach it, etc. Hence, this method is primarily aimed at human decision-makers. Many methods within the field of multi-objective and many-objective decision-making rely on the decision maker to initially provide the algorithm with preference points and weight vectors; however, this method aims to omit this very difficult step, especially when the number of objectives is so large. The proposed method will be compared to Favour (1 − k)-Dom and L-dominance (LD) methods. The test will be conducted using well-established test problems from the literature, such as the DTLZ problems. The proposed method is expected to outperform the currently available methods in the literature and hopefully provide future decision-makers and pilots with support when dealing with many-objective optimization problems.

Keywords: multi-objective decision-making, many-objective decision-making, multi-objective optimization, many-objective optimization

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Authors: Branislav Kovačević, Andrej Pilipović, Zoran Novčić, Marina Milović, Lazar Kesić, Milan Drekić, Saša Pekeč, Leopold Poljaković Pajnik, Saša Orlović

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Poplars present one of the most important tree species used for phytoremediation in the northern hemisphere. They can be used either as direct “cleaners” of the contaminated soils or as buffer zones preventing the contaminant plume to the surrounding environment. In order to produce appropriate planting material for this purpose, there is a long process of the breeding of the most favorable candidates. Although the development of the poplar propagation technology has been evolving for decades, white poplar nursery production, as well as the establishment of short-rotation coppice plantations, still considerably depends on the success of hardwood cuttings’ survival. This is why easy rooting is among the most desirable properties in white poplar breeding. On the other hand, there are many opportunities for the optimization of the technological procedures in order to meet the demands of particular genotype (clonal technology). In this study the effect of the term of hardwood cuttings’ preparation of four white poplar clones on their survival and further growth of rooted cuttings in nursery conditions were tested. There were three terms of cuttings’ preparation: the beginning of February (2nd Feb 2023), the beginning of March (3rd Mar 2023) and the end of March (21nd Mar 2023), which is regarded as the standard term. The cuttings were stored in cool chamber at 2±2°C. All cuttings were planted on the same date (11th Apr 2023), in soil prepared with rotary tillage, and then cultivated by usual nursey procedures. According to the results obtained after the bud set (29th Sept 2023) there were significant differences in the survival and growth of rooted cuttings between examined terms of cutting preparation. Also, there were significant differences in the reaction of examined clones on terms of cutting preparation. In total, the best results provided cuttings prepared at the first term (2nd Feb 2023) (survival rate of 39.4%), while performance after two later preparation terms was significantly poorer (20.5% after second and 16.5% after third term). These results stress the significance of dormancy preservation in cuttings of examined white poplar clones for their survival, which could be especially important in context of climate change. Differences in clones’ reaction to term of cutting preparation suggest necessity of adjustment of the technology to the needs of particular clone i.e. design of clone specific technology.

Keywords: rooting, Populus alba, nursery, clonal technology

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Authors: Ram Sharma, Esha Chatterjee, Santosh Kumar Guru, Kunal Nepali

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A tractable anti-lung cancer agent was identified via the installation of a Ring C expanded synthetic analogue of the alkaloid vasicinone [7,8,9,10-tetrahydroazepino[2,1-b] quinazolin-12(6H)-one (TAZQ)] as a surface recognition part in the HDAC inhibitory three-component model. Noteworthy to mention that the candidature of TAZQ was deemed suitable for accommodation in HDAC inhibitory pharmacophore as per the results of the fragment recruitment process conducted by our laboratory. TAZQ was pinpointed through the fragment screening program as a synthetically flexible fragment endowed with some moderate cell growth inhibitory activity against the lung cancer cell lines, and it was anticipated that the use of the aforementioned fragment to generate hydroxamic acid functionality (zinc-binding motif) bearing HDAC inhibitors would boost the antitumor efficacy of TAZQ. Consistent with our aim of applying epigenetic targets to the treatment of lung cancer, a strikingly potent anti-lung cancer scaffold (compound 6) was pinpointed through a series of in-vitro experiments. Notably, the compounds manifested a magnificent activity profile against KRAS and EGFR mutant lung cancer cell lines (IC50 = 0.80 - 0.96 µM), and the effects were found to be mediated through preferential HDAC6 inhibition (IC50 = 12.9 nM). In addition to HDAC6 inhibition, the compounds also elicited HDAC1 and HDAC3 inhibitory activity with an IC50 value of 49.9 nM and 68.5 nM, respectively. The HDAC inhibitory ability of compound 6 was also confirmed from the results of the western blot experiment that revealed its potential to decrease the expression levels of HDAC isoforms (HDAC1, HDAC3, and HDAC6). Noteworthy to mention that complete downregulation of the HDAC6 isoform was exerted by compound 6 at 0.5 and 1 µM. Moreover, in another western blot experiment, treatment with hydroxamic acid 6 led to upregulation of H3 acK9 and α-Tubulin acK40 levels, ascertaining its inhibitory activity toward both the class I HDACs and Class II B HDACs. The results of other assays were also encouraging as treatment with compound 6 led to the suppression of the colony formation ability of A549 cells, induction of apoptosis, and increase in autophagic flux. In silico studies led us to rationalize the results of the experimental assay, and some key interactions of compound 6 with the amino acid residues of HDAC isoforms were identified. In light of the impressive activity spectrum of compound 6, a pH-responsive nanocarrier (hyaluronic acid-compound 6 nanoparticles) was prepared. The dialysis bag approach was used for the assessment of the nanoparticles under both normal and acidic circumstances, and the pH-sensitive nature of hyaluronic acid-compound 6 nanoparticles was confirmed. Delightfully, the nanoformulation was devoid of cytotoxicity against the L929 mouse fibroblast cells (normal settings) and exhibited selective cytotoxicity towards the A549 lung cancer cell lines. In a nutshell, compound 6 appears to be a promising adduct, and a detailed investigation of this compound might yield a therapeutic for the treatment of lung cancer.

Keywords: HDAC inhibitors, lung cancer, scaffold, hyaluronic acid, nanoparticles

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Authors: Martin Juckel

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Probably no other field of inorganic chemistry has undergone such a rapid development in the past two decades than the low oxidation state chemistry of main group elements. This rapid development has only been possible by the development of new bulky ligands. In case of our research group, super-bulky monodentate amido ligands and β-diketiminate ligands have been used to a great success. We first synthesized the unprecedented magnesium(I) dimer [ᴹᵉˢNacnacMg]₂ (ᴹᵉˢNacnac = [(ᴹᵉˢNCMe)₂CH]-; Mes = mesityl, which has since been used both as reducing agent and also for the synthesis of new metal-magnesium bonds. In case of the zinc bromide precursor [L*ZnBr] (L*=(N(Ar*)(SiPri₃); (Ar* = C₆H₂{C(H)Ph₂}₂Me-2,6,4, the reduction with [ᴹᵉˢNacnacMg]₂ led to such a metal-magnesium bond. This [L*ZnMg(ᴹᵉˢNacnac)] compound can be seen as an ‘inorganic Grignard reagent’, which can be used to transfer the metal fragment onto other functional groups or other metal centers; just like the conventional Grignard reagent. By simple addition of (TBoN)GeCl (TBoN = N(SiMe₃){B(DipNCH)₂) to the aforesaid compound, we were able to transfer the amido-zinc fragment to the Ge center of the germylene starting material and to synthesize the first example of a germanium(II)-zinc bond: [:Ge(TBoN)(ZnL*)]. While these reactions typically led to complex product mixture, [:Ge(TBoN)(ZnL*)] could be isolated as dark blue crystals in a good yield. This new compound shows interesting reactivity towards small molecules, especially dihydrogen gas. This is of special interest as dihydrogen is one of the more difficult small molecules to activate, due to its strong (BDE = 108 kcal/mol) and non-polar bond. In this context, the interaction between H₂ σ-bond with the tetrelylene p-Orbital (LUMO), with concomitant donation of the tetrelylene lone pair (HOMO) into the H₂ σ* orbital are responsible for the activation of dihydrogen gas. Accordingly, the narrower the HOMO-LUMO gap of tertelylene, the more reactivity towards H₂ it typically is. The aim of a narrow HOMO-LUMO gap was reached by transferring electropositive substituents respectively metal substituents with relatively low Pauling electronegativity (zinc: 1.65) onto the Ge center (here: the zinc-amido fragment). In consideration of the unprecedented reactivity of [:Ge(TBoN)(ZnL*)], a computational examination of its frontier orbital energies was undertaken. The energy separation between the HOMO, which has significant Ge lone pair character, and the LUMO, which has predominantly Ge p-orbital character, is narrow (40.8 kcal/mol; cf.∆S-T= 24.8 kcal/mol), and comparable to the HOMO-LUMO gaps calculated for other literature known complexes). The calculated very narrow HOMO-LUMO gap for the [:Ge(TBoN)(ZnL*)] complex is consistent with its high reactivity, and is remarkable considering that it incorporates a π-basic amide ligand, which are known to raise the LUMO of germylenes considerably.

Keywords: activation of dihydrogen gas, narrow HOMO-LUMO gap, first germanium(II)-zinc bond, inorganic Grignard reagent

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Authors: Sekena H. Abd El-Aziem, Heba A. M. Abd El-Kader, Sally S. Alam, Othman E. Othman

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Growth hormone (GH) is an anabolic hormone synthesized and secreted by the somatotroph cells of the anterior lobe of the pituitary gland in a circadian and pulsatile manner, the pattern of which plays an important role in postnatal longitudinal growth and development, tissue growth, lactation, reproduction as well as protein, lipid and carbohydrate metabolism. The aim of this study was to detect the genetic polymorphism of GH gene in five camel breeds reared in Egypt; Sudany, Somali, Mowaled, Maghrabi and Falahy, using PCR-RFLP technique. Also this work aimed to identify the single nucleotide polymorphism between different genotypes detected in these camel breeds. The amplified fragment of camel GH at 613-bp was digested with the restriction enzyme MspI and the result revealed the presence of three different genotypes; CC, CT and TT in tested breeds and significant differences were recorded in the genotype frequencies between these camel breeds. The result showed that the Maghrabi breed that is classified as a dual purpose camels had higher frequency for allele C (0.75) than those in the other tested four breeds. The sequence analysis declared the presence of a SNP (C→T) at position 264 in the amplified fragment which is responsible for the destruction of the restriction site C^CGG and consequently the appearance of two different alleles C and T. The nucleotide sequences of camel GH alleles T and C were submitted to nucleotide sequences database NCBI/Bankit/GenBank and have accession numbers: KP143517 and KP143518, respectively. It is concluded that only one SNP C→T was detected in GH gene among the five tested camel breeds reared in Egypt and this nucleotide substitution can be used as a marker for the genetic biodiversity between camel breeds reared in Egypt. Also, due to the possible association between allele C and higher growth rate, we can used it in MAS for camels and enter the camels possess this allele in breeding program as a way for enhancement of growth trait in camel breeds reared in Egypt.

Keywords: camel breeds in Egypt, GH, PCR-RFLP, SNPs

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Authors: Galina Portnova, Kseniya Gladun

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In our EEG experiment participated 27 children with ASD with the average age of 6.13 years and the average score for CARS 32.41 and 25 healthy children (of 6.35 years). Six types of musical stimulation were presented, included Gluck, Javier-Naida, Kenny G, Chopin and other classic musical compositions. Children with autism showed orientation reaction to the music and give behavioral responses to different types of music, some of them might assess stimulation by scales. The participants were instructed to remain calm. Brain electrical activity was recorded using a 19-channel EEG recording device, 'Encephalan' (Russia, Taganrog). EEG epochs lasting 150 s were analyzed using EEGLab plugin for MatLab (Mathwork Inc.). For EEG analysis we used Fast Fourier Transform (FFT), analyzed Peak alpha frequency (PAF), correlation dimension D2 and Stability of rhythms. To express the dynamics of desynchronizing of different rhythms we've calculated the envelope of the EEG signal, using the whole frequency range and a set of small narrowband filters using Hilbert transformation. Our data showed that healthy children showed similar EEG spectral changes during musical stimulation as well as described the feelings induced by musical fragments. The exception was the ‘Chopin. Prelude’ fragment (no.6). This musical fragment induced different subjective feeling, behavioral reactions and EEG spectral changes in children with ASD and healthy children. The correlation dimension D2 was significantly lower in autists compared to healthy children during musical stimulation. Hilbert envelope frequency was reduced in all group of subjects during musical compositions 1,3,5,6 compositions compared to the background. During musical fragments 2 and 4 (terrible) lower Hilbert envelope frequency was observed only in children with ASD and correlated with the severity of the disease. Alfa peak frequency was lower compared to the background during this musical composition in healthy children and conversely higher in children with ASD.

Keywords: electroencephalogram (EEG), emotional perception, ASD, musical perception, childhood Autism rating scale (CARS)

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Authors: Khalid Alshallash

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Small fragments of the roots of some Rumex species including R. obtusifolius and R. crispus have been found to regenerate readily, contributing to the severity of infestations by these very common, widespread and difficult to control perennial weeds of agricultural crops and grasslands. Their root fragments are usually created during routine agricultural practices. We found that fresh root fragments of both species containing 65-70 % of moisture, progressively lose their moisture content when desiccated under controlled growth room conditions matching summer weather of southeast England, with the greatest reduction occurring in the first 48 hours. Probability of shoot emergence and the time taken for emergence in glasshouse conditions were also reduced significantly by desiccation, with R. obtusifolius least affected up to 48-hour. However, the effects converged after 120 hours. In contrast, R. obtusifolius was significantly slower to emerge after up to 48 hours desiccation, again effects converging after longer periods, R. crispus entirely failed to emerge at 120 hours. The dry weight of emerged shoots was not significantly different between the species, until desiccated for 96 hours when R. obtusifolius was significantly reduced. At 120 hours, R. obtusifolius did not emerge. In outdoor trials, desiccation for 24 or 48 hours had less effect on emergence when planted at the soil surface or up to 10 cm of depth, compared to deeper plantings. In both species, emergence was significantly lower when desiccated fragments were planted at 15 or 20 cm. Time taken for emergence was not significantly different between the species until planted at 15 or 20 cm when R. obtusifolius was slower than R. crispus and reduced further by increasing desiccation. Similar variation in effects of increasing soil depth interacting with increasing desiccation was found in reductions in dry weight, the number of tillers and leaf area, with R obtusifolius generally but not exclusively better able to withstand more extreme trial conditions. Our findings suggest that infestations of these highly troublesome weeds may be partly controlled by appropriate agricultural practices, notably exposing cut fragments to drying environmental conditions followed by deep burial.

Keywords: regeneration, root fragment, rumex crispus, rumex obtusifolius

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Authors: Asghar Ebrahimzadeh, Sattar Malekian, Mohammad Ali Aazami, Mohammad Bagher Hassanpouraghdam

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Roses are of main ornamental flowers worldwide. Rosa damascena Mill., besides being an ornamental plant, has major pharmaceutical, cosmetic and fragrance applications. Traditional propagation methods of the plant are using suckers, cutting and grafting. In the present experiment, we used the different explants (leaf section, petioles and nodal cutting) for the optimization of this high-valued ornamental from a native clonal plant. Diverse explants were acquired from mature plants during the growing season and were planted on MS medium supplemented with different hormonal combinations. 70% alcohol and sodium hypochloride were utilized for the surface sterilization. For proliferation, BAP and BA (1-5 mg L-1) and NAA (1-2 mg L-1) were tested. The highest proliferation rate was afforded from MS medium supplemented with 1.5 mg L-1 BA and 5 mg L-1 BAP. Callogenesis from leaf samples and petioles was the best with 1/2 MS medium enriched with 1mg L-1 BAP and 4 mg L-1 2,4-D. Rooting was occurred with the highest frequency in a medium containing 0.1 mg L-1 IBA.

Keywords: Rosa damascene, micropropagation, petiole, IBA, BAP

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Authors: Krishna Poudel, Tahar Katuwal, Sujan Karki

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A rapid propagation and acclimatization method of large cardamom was optimized in this study. Sprouted rhizome buds were collected. The excised rhizome bud explants were cultured on semi solid culture media. The explants were cultured on Murashige and Skoog’s (MS) medium supplemented with different concentration and combinations of BAP (6-Benzyl-amino-purine) and IBA (Indole-3-butyric acid) for shoot and root induction. Explants cultured on MS basal medium supplemented with 1.0 mg/l BAP + 0.5 gm/l IBA showed the highest rate of shoot multiplication. In vitro shoots were rooted on to the half-strength MS basal media supplemented with 0.5 mg/l IBA. Rooted shoots were transplanted in the screen house for hardening process. These hardened plants were subsequently shifted into the netted nursery for further multiplication process.

Keywords: concentration, explants, hardening, rhizome

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Authors: Diwei Lin, Amanda Jh. Tan

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We present a very rare case of de novo large cell neuroendocrine carcinoma of the prostate (LCNEC) in an 84-year-old male on a background of high-grade, muscle-invasive transitional cell carcinoma of the bladder. While NE tumours account for 1% to 5% of all cases of prostate cancer and scattered NE cells can be found in 10% to 100% of prostate adenocarcinomas, pure LCNEC of the prostate is extremely rare. Most LCNEC of the prostate is thought to originate by clonal progression under the selection pressure of therapy and refractory to long-term hormonal treatment for adenocarcinoma of the prostate. De novo LCNEC is only described in case reports and is thought to develop via direct malignant transformation. Limited data in the English literature makes it difficult to accurately predict the prognosis of LCNEC of the prostate. However, current evidence suggesting that increasing NE differentiation in prostate adenocarcinoma is associated with a higher stage, high-grade disease, and a worse prognosis.

Keywords: large cell neuroendocrine cancer, prostate cancer, refractory cancer, medical and health sciences

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Authors: Muhammad Faisal Khilji, Rana Shoaib Hamid, Asim Qureshi

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A fifty years old female presented in the emergency department of a tertiary care hospital with complaints of migraine type headache for the last few months. Her last episode of headache was severe, increasing in intensity, associated with nausea but no fever, lasting more than 24 hours and not resolving with analgesics. On examination there was no neurological deficit. CT scan of brain showed a large Pedunculated, non-expansible, non-aggressive bony lesion in the clivus with its sharp fragment impinging into the pons. Findings were further confirmed with MRI brain. Trans-sphenoidal excision biopsy was done and histopathology proved the lesion to be osteochondroma of clivus.

Keywords: osteochondroma, clivus, headache, CT scan

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Authors: Jianrong Wu, Xuan Fu, Akihiro Higashi, Zhiming Tan

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CMOS image sensors with a rolling shutter are used broadly in the digital cameras embedded in mobile devices. The rolling shutter suffers the flicker artifacts from the fluorescent lamp, and it could be observed easily. In this paper, the characteristics of illumination flicker in motion case were analyzed, and two efficient detection methods based on matching fragment selection were proposed. According to the experimental results, our methods could achieve as high as 100% accuracy in static scene, and at least 97% in motion scene.

Keywords: illumination flicker, embedded camera, rolling shutter, detection

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Authors: H. Imad, Y. Cheah, O. Aamera

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The aims of this research are to study the mitochondrial non-coding region by using the Sanger sequencing technique and establish the degree of variation characteristics of a fragment. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. A portion of a non-coding region encompassing positions 37 to 340 amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column then sequenced and detected by using the ABI 3730xL DNA Analyzer. New polymorphic positions 57, 63, and 101 are described may in future be suitable sources for identification purpose. The data obtained can be used to identify variable nucleotide positions characterized by frequent occurrence most promising for identification variants.

Keywords: encompassing nucleotide positions 37 to 340, HVII, Iraq, mitochondrial DNA, polymorphism, frequency

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Authors: Asma'u Mahe, Abdullahi A. Imam, Adamu J. Alhassan, Nasiru Abdullahi, Sadiya A. Bichi, Nura Lawal, Kamaluddeen Babagana

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Malaria is a disease with global health significance. It is caused by parasites and transmitted by Anopheles mosquitoes. Increase in insecticide resistance threatens the disease vector control. The strength of selection pressure acting on a mosquito population in relation to insecticide resistance can be assess by determining the genetic diversity of a fragment spanning exon- 20 of IIS6 of the voltage gated sodium channel (VGSC). Larval samples reared to adulthood were identified and kdr (knock down resistance) profile was determined. The DNA sequences were used to assess the patterns of genetic differentiation by determining the levels of genetic variability between the Anopheles mosquitoes. Genetic differentiation of the Anopheles mosquitoes based on a portion of the voltage gated sodium channel gene was obtained. Polymorphisms were detected; sequence variation and analysis were presented as a phylogenetic tree. Phylogenetic tree of VGSC haplotypes was constructed for samples of the Anopheles mosquitoes using the maximum likelihood method in MEGA 6.0 software. DNA sequences were edited using BioEdit sequence editor. The edited sequences were aligned with reference sequence (Kisumu strain). Analyses were performed as contained in dnaSP 5.10. Results of genetic parameters of polymorphism and haplotype reconstruction were presented in count. Twenty sequences were used for the analysis. Regions selected were 1- 576, invariable (monomorphic) sites were 460 while variable (polymorphic) sites were 5 giving the number of total mutations observed in this study. Mutations obtained from the study were at codon 105: TTC- Phenylalanine replaces TCC- Serine, codon 513: TAG- Termination replaces TTG- Leucine, codon 153, 300 and 553 mutations were non-synonymous. From the constructed phylogenetic tree, some groups were shown to be closer with Exon20Gambiae Kisumu (Reference strain) having some genetic distance, while 5-Exon20Gambiae-F I13.ab1, 18-Exon20Gambiae-F C17.ab1, and 2-Exon20Gambiae-F C13.ab1 clustered together genetically differentiated away from others. Mutations observed in this study can be attributed to the high insecticide resistance profile recorded in the study areas. Haplotype networks of pattern of genetic variability and polymorphism for the fragment of the VGSC sequences of sampled Anopheles mosquitoes revealed low haplotypes for the present study. Haplotypes are set of closely linked DNA variation on X-chromosome. Haplotypes were scaled accordingly to reflect their respective frequencies. Low haplotype number, four VGSC-1014F haplotypes were observed in this study. A positive association was previously established between low haplotype number of VGSC diversity and pyrethroid resistance through kdr mechanism. Significant values at (P < 0.05) of Tajima D and Fu and Li D’ were observed for some of the results indicating possible signature of positive selection on the fragment of VGSC in the study. This is the first report of VGSC-1014F in the study site. Based on the results, the mutation was present in low frequencies. However, the roles played by the observed mutations need further investigation. Mutations, environmental factors among others can affect genetic diversity. The study area has recorded increase in insecticide resistance that can affect vector control in the area. This finding might affect the efforts made against malaria. Sequences were deposited in GenBank for Accession Number.

Keywords: anopheles mosquitoes, insecticide resistance, kdr, malaria, voltage gated sodium channel

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Authors: Jyothi Nagraj, Sudeshna Mukherjee, Rajdeep Chowdhury

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Autophagy has recently been linked with cancer cell survival post drug insult contributing to acquisition of resistance. However, the molecular signaling governing autophagic survival response is poorly explored. In our study, in osteosarcoma (OS) cells cisplatin shock was found to activate both MAPK and autophagy signaling. An activation of JNK and autophagy acted as pro-survival strategy, while ERK1/2 triggered apoptotic signals upon cisplatin stress. An increased sensitivity of the cells to cisplatin was obtained with simultaneous inhibition of both autophagy and JNK pathway. Furthermore, we observed that the autophagic stimulation upon drug stress regulates other developmentally active signaling pathways like the Hippo pathway in OS cells. Cisplatin resistant cells were thereafter developed by repetitive drug exposure followed by clonal selection. Basal levels of autophagy were found to be high in resistant cells to. However, the signaling mechanism leading to autophagic up-regulation and its regulatory effect differed in OS cells upon attaining drug resistance. Our results provide valuable clues to regulatory dynamics of autophagy that can be considered for development of improved therapeutic strategy against resistant type cancers.

Keywords: JNK, autophagy, drug resistance, cancer

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Authors: Jma Hannan, Prawej Ansari, Yasser H. A. Abdel-Wahab, Peter R. Flatt

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Spirulina platensis (SP, Blue-green algae) have been accepted as a supplement for the treatment of pre and post-diabetes. The present study investigated the effects of butanol fraction from ethanol extract of S. platensis on insulin release from BRIN BD11 cells, isolated mouse islets, and perfused rat pancreas, as well as glucose homeostasis in type 2 diabetic rats and their molecular pathways. In a dose-dependent manner, S. platensis increased insulin release from mouse islets and pancreatic β-cells. The extract also elevated insulin release in perfused rat pancreas. Glucose, isobutylmethylxanthine, tolbutamide, and a depolarizing concentration of KCl significantly potentiated insulin release from BRIN BD11 cells. The effect of diazoxide and verapamil, as well as the absence of extracellular Ca2+ showed a reduction in insulin secretion. When administered orally together with glucose (2.5g/kg bw), S. platensis extract improved fasting and postprandial blood glucose in type 2 diabetes. These data suggest that the anti-diabetic activity of S. platensis is partly mediated by insulin secretion via the KATP channel-dependent pathway/the intracellular cAMP pathway.

Keywords: Insulin, glucose, S. platensis, type 2 diabetes, medicinal plants

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Authors: Li Hung-Hui, Chen Chi-Chieh, Yang Zon-Yee

Abstract:

This study aims to explore the impact energy absorption in the fragmented processes of rock samples during the split-Hopkinson-pressure-bar tests. Three kinds of rock samples including granite, marble and sandstone were tested. The impact energy absorptions were calculated according to the incident, reflected and transmitted strain wave histories measured by a oscilloscope. The degree of fragment rocks after tests was quantified by the box dimension of the fractal theory. The box dimension of rock fragments was obtained from the particle size distribution curve by the sieve analysis. The results can be concluded that: (1) the degree of rock fragments after tests can be well described by the value of box dimension; (2) with the impact energy absorption increasing, the degrees of rock fragments are varied from the very large fragments to very small fragments, and the corresponding box dimension varies from 2.9 to 1.2.

Keywords: SHPB test, energy absorption, rock fragments, impact loading, box dimension

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Authors: Cuneyt Yucelbas, Seral Ozsen, Sule Yucelbas, Gulay Tezel

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Due to the fact that there exist only a small number of complex systems in artificial immune system (AIS) that work out nonlinear problems, nonlinear AIS approaches, among the well-known solution techniques, need to be developed. Gaussian function is usually used as similarity estimation in classification problems and pattern recognition. In this study, diagnosis of breast cancer, the second type of the most widespread cancer in women, was performed with different distance calculation functions that euclidean, gaussian and gaussian-euclidean hybrid function in the clonal selection model of classical AIS on Wisconsin Breast Cancer Dataset (WBCD), which was taken from the University of California, Irvine Machine-Learning Repository. We used 3-fold cross validation method to train and test the dataset. According to the results, the maximum test classification accuracy was reported as 97.35% by using of gaussian-euclidean hybrid function for fold-3. Also, mean of test classification accuracies for all of functions were obtained as 94.78%, 94.45% and 95.31% with use of euclidean, gaussian and gaussian-euclidean, respectively. With these results, gaussian-euclidean hybrid function seems to be a potential distance calculation method, and it may be considered as an alternative distance calculation method for hard nonlinear classification problems.

Keywords: artificial immune system, breast cancer diagnosis, Euclidean function, Gaussian function

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Authors: Tetyana Baydyk, Ernst Kussul, Sandra Bonilla Meza

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There are many articles that attempt to establish the role of different facial fragments in face recognition. Various approaches are used to estimate this role. Frequently, authors calculate the entropy corresponding to the fragment. This approach can only give approximate estimation. In this paper, we propose to use a more direct measure of the importance of different fragments for face recognition. We propose to select a recognition method and a face database and experimentally investigate the recognition rate using different fragments of faces. We present two such experiments in the paper. We selected the PCNC neural classifier as a method for face recognition and parts of the LFW (Labeled Faces in the Wild) face database as training and testing sets. The recognition rate of the best experiment is comparable with the recognition rate obtained using the whole face.

Keywords: face recognition, labeled faces in the wild (LFW) database, random local descriptor (RLD), random features

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Authors: Shu Hui

Abstract:

Since 2010, the genre of comedy became predominant in film market in China. However, compared with the huge commercial success, these films received severe public criticism. These films are referred as trash (lan pian) by the public because of the fragment narrative, the non-professional photographing and advocating money warship. The paper aims to explain the contradictive phenomena between the higher box office and the lower mouth of word within hegemony theory. Four popular comedies that ranked top 20 in domestic revenue in the year the film released will be chosen to analyze their popularity in general. Differing from other popular films, these comedies’ popularity is generated from their disruptive pleasures instead of good stories or photographing. The destruction in Confucianism and socialism formulated the public consent or popularity, and caused the public criticism as well. Moreover, the happy-endings restore the normality at the superficial level.

Keywords: Confucianism, destruction, reconcilation, socialism

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Authors: Asim Mehmood, Abdul Karim, Muhammad J. Jaskani, Faisal S. Awan, Muhammad W. Sajid

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Guava (Psidium guajava L.) is an important commercial fruit crop of Pakistan. It is an allogamous crop having 25-40% cross pollination which on the one hand leads to clonal degradation and on the other hand can add variations to generated new cultivars. Morpho-genetic characterization of 37 guava accessions was carried out for study of the genetic diversity among guava accessions located in province Punjab, Pakistan. For morphological analysis, 17 morphological traits were studied, and strong positive correlation was found among the 7 morphological traits which included thickness of outer flesh in relation to core diameter, fruit length, fruit width, fruit juiciness, fruit size, fruit sweetness and number of seeds. For genetic characterization, 18 microsatellites were used, and the sizes of reproducible and scorable bands ranged from 150 to 320 bp. These 18 primer pairs amplified a total of 85 alleles in P. guajava, with an average total number of 4.7 alleles per locus and no more than two displayed bands (nuclear SSR loci). The phylogenetic tree based on the morphological and genetic traits showed the diversity of these 37 guava genotypes into two major groups. These results indicated that Pakistani guava is quite diverse and a more detail study is needed to define the level of genetic variability.

Keywords: Psidium guajava L, genetic diversity, SSR markers, polymorphism, dendrogram

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Authors: Ashish Kumar Agrahari, Amit Kumar

Abstract:

Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal blood disorder that manifests with hemolytic anemia, thrombosis, and peripheral blood cytopenias. The disease is caused by the deficiency of two glycosylphosphatidylinositols (GPI)-anchored proteins (CD55 and CD59) in the hemopoietic stem cells. The deficiency of GPI-anchored proteins has been associated with the somatic mutations in phosphatidylinositol glycan class A (PIGA). However, the mutations that do not cause PNH is associated with the multiple congenital anomalies-hypotonia-seizures syndrome 2 (MCAHS2). To best of our knowledge, no computational study has been performed to explore the atomistic level impact of PIGA mutations on the structure and dynamics of the protein. In the current work, we are mainly interested to get insights into the molecular mechanism of PIGA mutations. In the initial step, we screened the most pathogenic mutations from the pool of publicly available mutations. Further, to get a better understanding, pathogenic mutations were mapped to the modeled structure and subjected to 50ns molecular dynamics simulation. Our computational study suggests that four mutations are highly vulnerable to altering the structural conformation and stability of the PIGA protein, which illustrates its association with PNH and MCAHS2 phenotype.

Keywords: homology modeling, molecular dynamics simulation, missense mutations PNH, MCAHS2, PIGA

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Authors: Shu Hui

Abstract:

From 2013 to 2015, Tiny Times series gained huge commercial success. However, compared with the successful box office, these films received severe public criticism. Some scholars refer to these films as trash (lan pian) because of the fragment narrative, the non-professional photographing, and advocating money warship. Differing from other popular films, the popularity of Tiny Times series is actually generated from the fantasy that presented on screen instead of good stories or photographs. The fantasy is desired by the public and then formulates its popularity. Based on Jacques Lacan’s fantasy theory, the paper aims to explain what kind of fantast the films present. Then, according to hegemony theory, the paper will illustrate why the public desires such a fantasy and how the fantasy causes the criticism as well. The dominant ideology (patriarchy) conspires with or manipulates consumerism, which brings about the female's fantasy in Tiny Times. Because consumerism interrogates Confucianism, the film received public criticism for highlighting the former.

Keywords: fantasy, desire, ideology, popularity

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Authors: Yakup Ulusu, Faruk Ozel, Numan Eczacioglu, Abdurrahman Ozen, Sabriye Acikgoz

Abstract:

GFP discovered in the mid-1970s, has been used as a marker after replicated genetic study by scientists. In biotechnology, cell, molecular biology, the GFP gene is frequently used as a reporter of expression. In modified forms, it has been used to make biosensors. Many animals have been created that express GFP as an evidence that a gene can be expressed throughout a given organism. Proteins labeled with GFP identified locations are determined. And so, cell connections can be monitored, gene expression can be reported, protein-protein interactions can be observed and signals that create events can be detected. Additionally, monitoring GFP is noninvasive; it can be detected by under UV-light because of simply generating fluorescence. Moreover, GFP is a relatively small and inert molecule, that does not seem to treat any biological processes of interest. The synthesis of GFP has some steps like, to construct the plasmid system, transformation in E. coli, production and purification of protein. GFP carrying plasmid vector pBAD–GFPuv was digested using two different restriction endonuclease enzymes (NheI and Eco RI) and DNA fragment of GFP was gel purified before cloning. The GFP-encoding DNA fragment was ligated into pET28a plasmid using NheI and Eco RI restriction sites. The final plasmid was named pETGFP and DNA sequencing of this plasmid indicated that the hexa histidine-tagged GFP was correctly inserted. Histidine-tagged GFP was expressed in an Escherichia coli BL21 DE3 (pLysE) strain. The strain was transformed with pETGFP plasmid and grown on LuiraBertoni (LB) plates with kanamycin and chloramphenicol selection. E. coli cells were grown up to an optical density (OD 600) of 0.8 and induced by the addition of a final concentration of 1mM isopropyl-thiogalactopyranoside (IPTG) and then grown for additional 4 h. The amino-terminal hexa-histidine-tag facilitated purification of the GFP by using a His Bind affinity chromatography resin (Novagen). Purity of GFP protein was analyzed by a 12 % sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). The concentration of protein was determined by UV absorption at 280 nm (Varian Cary 50 Scan UV/VIS spectrophotometer). Synthesis of GFP-Polymer composite nanofibers was produced by using GFP solution (10mg/mL) and polymer precursor Polyvinylpyrrolidone, (PVP, Mw=1300000) as starting materials and template, respectively. For the fabrication of nanofibers with the different fiber diameter; a sol–gel solution comprising of 0.40, 0.60 and 0.80 g PVP (depending upon the desired fiber diameter) and 100 mg GFP in 10 mL water: ethanol (3:2) mixtures were prepared and then the solution was covered on collecting plate via electro spinning at 10 kV with a feed-rate of 0.25 mL h-1 using Spellman electro spinning system. Results show that GFP-based nano-fiber can be used plenty of biomedical applications such as bio-imaging, bio-mechanic, bio-material and tissue engineering.

Keywords: biomaterial, GFP, nano-fibers, protein expression

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