Search results for: multilocus sequence typing

Authors: Boitumelo Setlhare, Mduduzi P. Mokoena, Ademola O. Olaniran

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Agricultural and industrial activities have led to increasing production of xenobiotics such as 2,4-dichlorophenol (2,4-DCP), a derivative of 2,4-dichlorophenoxyacetic acid (2,4-D), which is a widely used herbicide. Bioremediation offers an efficient, cost-effective and environmentally friendly method for degradation of the compound through the activities of the various microbial enzymes involved in the catabolic pathway. The aim of this study was to isolate and characterize bacterial isolate indigenous to contaminated sites in Durban, South Africa for 2,4-DCP degradation. One bacterium capable of utilizing 2,4-DCP as sole carbon source was isolated using culture enrichment technique and identified as Pseudomonas chlororaphis strain UFB2 via PCR amplification and analysis of 16S rRNA gene sequence. This isolate was able to degrade up to 75.11% of 2,4-DCP in batch cultures within 10 days, with the degradation rate constant of 0.14 mg/l/d. Phylogenetic analysis revealed the relatedness of this bacterial isolate to other Pseudomonas sp. previously characterized for chlorophenol degradation. PCR amplification of the catabolic genes involved in 2,4-DCP degradation revealed the presence of the correct amplicons for phenol hydroxylase (600 bp), catechol 1,2-dioxygenase (214 bp), muconate isomerase (851 bp), cis-dienelactone hydrolase (577 bp), and trans-dienelactone hydrolase (491 bp) genes. Enzyme assays revealed activity as high as 21840 mU/mg, 15630 mU/mg, 2340 mU/mg and 1490 mU/mg obtained for phenol hydroxylase, catechol 1,2-dioxygenase, cis-dienelactone hydroxylase and trans-dienelactone hydroxylase, respectively. The absence of catechol 2,3-dioxygenase gene and the corresponding enzyme in this isolate suggests that the organism followed ortho-pathway for 2,4-DCP degradation. Furthermore, the absence of malaycetate reductase genes showed that the bacterium may not be able to completely mineralize 2,4-DCP. Further studies are required to optimize 2,4-DCP degradation by this isolate as well as to elucidate the mechanism of 2,4-DCP degradation.

Keywords: biodegradation, catechol 1, 2-dioxygenase, 2, 4-dichlorophenol, phenol hydroxylase, Pseudomonas chlororaphis

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Authors: Vincent Murray

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The glycopeptide bleomycin is used in the treatment of testicular cancer, Hodgkin's lymphoma, and squamous cell carcinoma. Bleomycin damages and cleaves DNA in human cells, and this is considered to be the main mode of action for bleomycin's anti-tumor activity. In particular, double-strand breaks are thought to be the main mechanism for the cellular toxicity of bleomycin. Using Illumina next-generation DNA sequencing techniques, the genome-wide sequence specificity of bleomycin-induced double-strand breaks was determined in human cells. The degree of bleomycin cleavage was also assessed at the transcription start sites (TSSs) of actively transcribed genes and compared with non-transcribed genes. It was observed that bleomycin preferentially cleaved at the TSSs of actively transcribed human genes. There was a correlation between the degree of this enhanced cleavage at TSSs and the level of transcriptional activity. Bleomycin cleavage is also affected by chromatin structure and at TSSs, the peaks of bleomycin cleavage were approximately 200 bp apart. This indicated that bleomycin was able to detect phased nucleosomes at the TSSs of actively transcribed human genes. The genome-wide cleavage pattern of the bleomycin analogues 6′-deoxy-BLM Z and zorbamycin was also investigated in human cells. As found for bleomycin, these bleomycin analogues also preferentially cleaved at the TSSs of actively transcribed human genes. The cytotoxicity (IC₅₀ values) of these bleomycin analogues was determined. It was found that the degree of enhanced cleavage at TSSs was inversely correlated with the IC₅₀ values of the bleomycin analogues. This suggested that the level of cleavage at the TSSs of actively transcribed human genes was important for the cytotoxicity of bleomycin and analogues. Hence this study provided a deeper understanding of the cellular processes involved in the cancer chemotherapeutic activity of bleomycin.

Keywords: anti-tumour activity, bleomycin analogues, chromatin structure, genome-wide study, Illumina DNA sequencing

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Authors: M. A. Barros, M. V. Barros

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The aim of this work is to analyze the discursive dynamics of preservice teachers during the implementation of a didactic sequence on topics of Quantum Mechanics for High School. Our research methodology was qualitative, case study type, in which we selected two prospective teachers on the Physics Teacher Training Course of the Sao Carlos Institute of Physics, at the University of Sao Paulo/Brazil. The set of modes of communication analyzed were the intentions and interventions of the teachers, the established communicative approach, the patterns and the contents of the interactions between teachers and students. Data were collected through video recording, interviews and questionnaires conducted before and after an 8 hour mini-course, which was offered to a group of 20 secondary students. As teaching strategy we used an active learning methodology, called: Peer Instruction. The episodes pointed out that both future teachers used interactive dialogic and authoritative communicative approaches to mediate the discussion between peers. In the interactive dialogic dimension the communication pattern was predominantly I-R-F (initiation-response-feedback), in which the future teachers assisted the students in the discussion by providing feedback to their initiations and contributing to the progress of the discussions between peers. Although the interactive dialogic dimension has been preferential during the use of the Peer Instruction method the authoritative communicative approach was also employed. In the authoritative dimension, future teachers used predominantly the type I-R-E (initiation-response-evaluation) communication pattern by asking the students several questions and leading them to the correct answer. Among the main implications the work contributes to the improvement of the practices of future teachers involved in applying active learning methodologies in classroom by identifying the types of communicative approaches and communication patterns used, as well as researches on curriculum innovation in physics in high school.

Keywords: curricular innovation, high school, physics teaching, discursive dynamics

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Authors: Priya Varma, Denis John McKeown

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Psychological time, unlike physical time, is believed to be ‘compressive’ in the sense that the mental representations of a series of events may be internally arranged with ever decreasing inter-event spacing (looking back from the most recently encoded event). If this is true, the record within immediate memory of recent events is severely temporally distorted. Although this notion of temporal distortion of the memory record is captured within some theoretical accounts of human forgetting, notably temporal distinctiveness accounts, the way in which the fundamental nature of the distortion underpins memory and forgetting broadly is barely recognised or at least directly investigated. Our intention here was to manipulate the spacing of items for recall in order to ‘reverse’ this supposed natural compression within the encoding of the items. In Experiment 1 three schedules of presentation (expanding, contracting and fixed irregular temporal spacing) were created using logarithmic spacing of the words for both free and serial recall conditions. The results of recall of lists of 7 words showed statistically significant benefits of temporal isolation, and more excitingly the contracting word series (which we may think of as reversing the natural compression within the mental representation of the word list) showed best performance. Experiment 2 tested for effects of active verbal rehearsal in the recall task; this reduced but did not remove the benefits of our temporal scheduling manipulation. Finally, a third experiment used the same design but with Chinese characters as memoranda, in a further attempt to subvert possible verbal maintenance of items. One change to the design here was to introduce a probe item following the sequence of items and record response times to this probe. Together the outcomes of the experiments broadly support the notion of temporal compression within immediate memory.

Keywords: memory, serial position curves, temporal isolation, temporal schedules

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Authors: Tae-Hoon Kim, Kwon-Ha Yoon, Hong Young Jun, Ki-Jong Kim, Young Hwan Lee, Myeung Su Lee, Keum Ha Choi, Ki Jung Yun, Eun Young Cho, Yong-Yeon Jeong, Chung-Hwan Jun

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Purpose: To assess the changes of hepatic metabolite for differentiation between non-alcoholic steatohepatitis (NASH) and simple steatosis on proton magnetic resonance spectroscopy (1H-MRS) in both humans and animal model. Methods: The local institutional review board approved this study and subjects gave written informed consent. 1H-MRS measurements were performed on a localized voxel of the liver using a point-resolved spectroscopy (PRESS) sequence and hepatic metabolites of alanine (Ala), lactate/triglyceride (Lac/TG), and TG were analyzed in NASH, simple steatosis and control groups. The group difference was tested with the ANOVA and Tukey’s post-hoc tests, and diagnostic accuracy was tested by calculating the area under the receiver operating characteristics (ROC) curve. The associations between metabolic concentration and pathologic grades or non-alcoholic fatty liver disease(NAFLD) activity scores were assessed by the Pearson’s correlation. Results: Patient with NASH showed the elevated Ala(p<0.001), Lac/TG(p < 0.001), TG(p < 0.05) concentration when compared with patients who had simple steatosis and healthy controls. The NASH patients were higher levels in Ala(mean±SEM, 52.5±8.3 vs 2.0±0.9; p < 0.001), Lac/TG(824.0±168.2 vs 394.1±89.8; p < 0.05) than simple steatosis. The area under the ROC curve to distinguish NASH from simple steatosis was 1.00 (95% confidence interval; 1.00, 1.00) with Ala and 0.782 (95% confidence interval; 0.61, 0.96) with Lac/TG. The Ala and Lac/TG levels were well correlated with steatosis grade, lobular inflammation, and NAFLD activity scores. The metabolic changes in human were reproducible to a mice model induced by streptozotocin injection and a high-fat diet. Conclusion: 1H-MRS would be useful for differentiation of patients with NASH and simple hepatic steatosis.

Keywords: non-alcoholic fatty liver disease, non-alcoholic steatohepatitis, 1H MR spectroscopy, hepatic metabolites

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Authors: Sharique Ahmed, Khushtar Anwar Salman

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Alpha-1-antitrypsin (AAT) is a major plasma serine protease inhibitor (SERPIN). Hereditary AAT deficiency is one of the common diseases in some part of the world. AAT is mainly produced in the liver and functions to protect the lung against proteolytic damage (e.g., from neutrophil elastase) acting as the major inhibitor for neutrophil elastase. α (1)-Antitrypsin (AAT) deficiency is an under recognized genetic condition that affects approximately 1 in 2,000 to 1 in 5,000 individuals and predisposes to liver disease and early-onset emphysema. Not only does α-1-antitrypsin deficiency lead to disabling syndrome of pulmonary emphysema, there are other disorders too which include ANCA (antineutrophilic cytoplasmic antibody) positive Wegener's granulomatosis, diffuse bronchiectasis, necrotizing panniculitis in α-1-antitrypsin phenotype (S), idiopathic pulmonary fibrosis and steroid dependent asthma. Augmentation therapy with alpha-1 antitrypsin (AAT) from human plasma has been available for specific treatment of emphysema due to AAT deficiency. Apart from this several observations have also suggested a role for endogenous suppressors of HIV-1, alpha-1 antitrypsin (AAT) has been identified to be one of those. In view of its varied important role in humans, serum from a mammalian source was chosen for the isolation and purification. Studies were performed on the homogeneous fraction. This study suggests that the buffalo serum α-1-antritrypsin has characteristics close to ovine, dog, horse and more importantly to human α-1-antritrypsin in terms of its hydrodynamic properties such as molecular weight, carbohydrate content, etc. The similarities in the hydrodynamic properties of buffalo serum α-1-antitrypsin with other sources of mammalian α-1-antitrypsin mean that it can be further studied and be a potential source for "augmentation therapy", as well as a source of AAT replacement therapy to raise serum levels above the protective threshold. Other parameters like the amino acid sequence, the effect of denaturants, and the thermolability or thermostability of the inhibitor will be the interesting basis of future studies on buffalo serum alpha-1 antitrypsin (AAT).

Keywords: α-1-antitrypsin, augmentation therapy , hydrodynamic properties, serine protease inhibitor

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Authors: Yang Ye, Hongfei Qiu, Yaqi Li

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The planning and construction of traditional cities are oriented by cars, which leads to the problems of insufficient urban public space, fragmentation, and low utilization efficiency. With the development of driverless technology, the urban structure will change from the traditional single-core grid structure to the multi-core model. In terms of traffic organization, with the release of land for traffic facilities, public space will become more continuous and integrated with traffic space. In the context of driverless technology, urban public reconstruction is characterized by modularization and high efficiency, and its planning and layout features accord with points (service facilities), lines (smart lines), surfaces (activity centers). The public space of driverless urban roads will provide diversified urban public facilities and services. The intensive urban layout makes the commercial public space realize the functions of central activities and style display, respectively, in the interior (building atrium) and the exterior (building periphery). In addition to recreation function, urban green space can also utilize underground parking space to realize efficient dispatching of shared cars. The roads inside the residential community will be integrated into the urban landscape, providing conditions for the community public activity space with changing time sequence and improving the efficiency of space utilization. The intervention of driverless technology will change the thinking of traditional urban construction and turn it into a human-oriented one. As a result, urban public space will be richer, more connected, more efficient, and the urban space justice will be optimized. By summarizing the frontier research, this paper discusses the impact of unmanned driving on cities, especially urban public space, which is beneficial for landscape architects to cope with the future development and changes of the industry and provides a reference for the related research and practice.

Keywords: driverless, urban public space, construction strategy, urban design

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Authors: Othman E. Othman, Hassan R. Darwish, Amira M. Nowier

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Lactoferrin (LF) is a multifunctional protein involved in economically production traits like milk protein composition and skeletal structure in small ruminants including sheep and goat. So, LF gene - with its genetic polymorphisms associated with production traits - is considered a candidate genetic marker used in marker-assisted selection in goats. This study aimed to identify the different alleles and genotypes of this gene in three Egyptian goat breeds using PCR-SSCP (polymerase chain reaction-single-strand conformation polymorphism) and DNA sequencing. Genomic DNA was extracted from 120 animals belonging to Barki, Zaraibi, and Damascus goat breeds. Using specific primers, PCR amplified 247-bp fragments from exon 2 of LF goat gene. The PCR products were subjected to Single-Strand Conformation Polymorphism (SSCP) technique. The results showed the presence of two genotypes GG and AG in the tested animals. The frequencies of both genotypes varied among the three tested breeds with the highest frequencies of GG genotype in all tested goat breeds. The sequence analysis of PCR products representing these two detected genotypes declared the presence of an SNP (single nucleotide polymorphisms) substitution (G/A) among G and A alleles of this gene. The association between different LF genotypes and milk composition as well as body measurement was estimated. The comparison showed that the animals possess AG genotypes are superior over those with GG genotypes for different parameters of milk protein compositions and skeletal structures. This finding declared that allele A of LF gene is considered the promising marker for the productive traits in goat. In conclusion, the Egyptian goat breeds will be needed to enhance their milk protein composition and growth trait parameters through the increasing of allele A frequency in their herds depending on the superior production traits of this allele in goats.

Keywords: lLactoferrin gene, PCR-SSCP, SNPs, Egyptian goat

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Authors: Alejandro Arnaldo Barroso Martinez

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Unlike sex, which is constituted by anatomic-physiological differences, gender is a social construction. Our thoughts and behaviors as females and males are not etched in stone by our biology but rather from how society expects us to think and behave based on our sex assignment in the womb. Social expectations, values, and roles are taken on by individuals and shape the ways considered acceptable and linked to our bodies, feelings, and interpersonal relationships. Furthermore, these evolve into dire consequences for those who do not meet these disciplinary, economic, and cultural standards. Then, the social learning of gender identity implies the individual’s psychological sense of being, and it might be highly linked to a sense of life and suicide attempts. As a result, suicide has been considered a gender issue with differences in the rates and means used by men and women worldwide. Nevertheless, there has been a misunderstanding of the meaning of being male or female in a particular context and how it becomes a risk process for suicide attempts. For this reason, the general objective of the current research is to explain how this process occurs in Cuba. From a Critical Sociology and Social Psychology, a qualitative methodology was developed through six case studies and qualitative in-depth interviews. The analysis is focused on the sequence and interplay between two dimensions of meaning: signifiers and voices. Findings show that the risk process of suicide attempts in Cuba means some patriarchal beliefs and practices as part of informal educational models and some positivist practices in mental health attention. Findings also show that community relations create a sense of belonging, and it is a protection against suicide attempts in Cuba. Those frames of signifiers and voices explain in both males and females but differently when and how they are suffering from isolation, violence, the normalization of emotional awareness, and emotional distress expression. Suicide prevention programs should take gender learning into account as a cultural process.

Keywords: social constructions, gender identity, meanings, suicide attempt

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Authors: Chingwen Yeh, I. Chen Huang

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This paper aims to conduct a case study on kinesthetic intelligence development intervention with a child who has Asperger symptom identified by physician. First, the characteristics of Asperger were defined based on the related literature. Some Asperger's people are born with outstanding insight and are good at solving complex and difficult problems. In contrast to high-functioning autistic, Asperger children do not lose their ability to express themselves verbally. However in the cognitive function, they focus mainly on the things they are interested in instead of paying attention to the whole surrounding situation. Thus it is difficult for them not only to focus on things that they are not interesting in, but also to interact with people. Secondly, 8-weeks of kinesthetic intelligence development courses were designed within a series of physical action that including the following sections: limbs coordination, various parts of body rhythm changes, strength and space awareness and breathing practice. In classroom observations were recorded both on words and with video as the qualitative research data. Finally, in-depth interview with the case child’s teachers, parents and other in class observers were documented on a weekly base in order to examine the effectiveness of before and after the kinesthetic intelligence development course and to testify the usefulness of the lesson plan. This research found that the case child has improved significantly in terms of attention span and body movement creativity. In the beginning of intervention, the case child made less eyes contact with others. The instructor needed to face the case child to confirm the eyes contact. And the instructor also used various adjective words as guiding language for all kinds of movement sequence practice. The result can cause the case child’s attention and learning motivation. And the case child understand what to do to enhance kinesthetic intelligence. These authors hope findings of this study can contribute as reference for the further research on the related topic.

Keywords: asperger symptom, body rhythm, kinesthetic intelligence, space awareness

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Authors: Mohammadreza Hajialigol, Nargues Falahi Charkhabi, Fatemeh Shahryari, Saadat Sarikhani

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BACKGROUND AND OBJECTIVES Walnut canker is characterized by brown to blackish roundish blotches on the trunks and main branches, necrosis of inner bark and bleeding with dark brown to black-colored exudates. The present study aimed to identify the causative agents of walnut decline by their phenotypic features, approval of pathogenicity, the partial sequencing of the housekeeping genes in Razavi Khorasan. MATERIAL AND METHODS Ten Symptomatic samples were collected from walnut orchards of Razavi Khorasan in 2019. Pathogenicity of all isolated strains was carried out on walnut immature fruits cv. ‘Hartley’ and young green twigs of cv. ‘Chandler’. All pathogenic strains were subjected to physiological, morphological and biochemical tests. 16S rRNA and housekeeping genes (fusA, leuS, and pyrG) were partially amplified and sequenced. RESULTS Eight strains were able to cause necrosis and a dark-colored region in the mesocarp of immature walnut fruits, and three representative strains caused necrosis on young inoculated twigs. Strains utilized starch, however, did not utilized esculin, Tween 20, Tween 80, and gelatin. The partial 16S rRNA gene sequence of strain KH7 indicated 99.63 % similarity to that of Citrobacter braakii ATCC5113T. The phylogenetic analyses based on the partial sequencing of three housekeeping genes, fusA (633 bp), pyrG (305), and leuS (640 bp), demonstrated that strains KH1, KH3, and KH7 belong to C. braakii species in a monophyletic clade with high bootstrap support. CONCLUSION To the best of our knowledge, this is the first report of C. braakii as a new plant pathogen which cause walnut decline. Identification of bacteria associated with walnut decline will eventually improve our understanding of the etiology of the disease and may result in improved management techniques for control.

Keywords: emerging pathogens, Iran, juglans regia, MLSA

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Authors: Shringika Soni, Utkarsh Jain, Nidhi Chauhan

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Aptamers are recently discovered ~80-100 bp long artificial oligonucleotides that not only demonstrated their applications in therapeutics; it is tremendously used in diagnostic and sensing application to detect different biomarkers and drugs. Synthesizing aptamers for proteins or genomic template is comparatively feasible in laboratory, but drugs or other chemical target based aptamers require major specification and proper optimization and validation. One has to optimize all selection, amplification, and characterization steps of the end product, which is extremely time-consuming. Therefore, we performed asymmetric PCR (polymerase chain reaction) for random oligonucleotides pool synthesis, and further use them in Systematic evolution of ligands by exponential enrichment (SELEX) for anti-psychotic drugs based aptamers synthesis. Anti-psychotic drugs are major tranquilizers to control psychosis for proper cognitive functions. Though their low medical use, their misuse may lead to severe medical condition as addiction and can promote crime in social and economical impact. In this work, we have approached the in-vitro SELEX method for ssDNA synthesis for anti-psychotic drugs (in this case ‘target’) based aptamer synthesis. The study was performed in three stages, where first stage included synthesis of random oligonucleotides pool via asymmetric PCR where end product was analyzed with electrophoresis and purified for further stages. The purified oligonucleotide pool was incubated in SELEX buffer, and further partition was performed in the next stage to obtain target specific aptamers. The isolated oligonucleotides are characterized and quantified after each round of partition, and significant results were obtained. After the repetitive partition and amplification steps of target-specific oligonucleotides, final stage included sequencing of end product. We can confirm the specific sequence for anti-psychoactive drugs, which will be further used in diagnostic application in clinical and forensic set-up.

Keywords: anti-psychotic drugs, aptamer, biosensor, ssDNA, SELEX

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Authors: Zintle Kolo, Ndiko Ludidi

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The enzymatic activity of p-coumarate 3-hydroxylase (C3H) synthesize caffeic acid from p-coumaric acid. We recently showed that exogenously applied caffeic acid confers salinity tolerance in soybean (Glycine max) by inducing antioxidant enzymatic activity to promote enhanced scavenging or reactive oxygen species, thus limiting salinity-induced oxidative stress. Recent evidence also establishes that pre-treatment of plants with exogenously supplied caffeic acid improves plant tolerance to osmotic stress by improving plant antioxidant capacity and enhancing biosynthesis of compatible solutes. We aimed to identify a C3H in maize (Zea mays) and evaluate the effect of drought on the spatial and temporal expression of the gene encoding the candidate maize C3H (ZmC3H). Primary sequence analysis shows that ZmC3H shares 71% identity with an Arabidopsis thaliana C3H that is implicated in the control of Arabidopsis cell expansion, growth, and responses to stress. In silico ZmC3H promoter analysis reveals the presence of cis-acting elements that interact with transcription factors implicated in plant responses to drought. Spatial expression analysis by semi-quantitative RT-PCR shows that ZmC3H is expressed in both leaves and roots under normal conditions. However, drought represses the expression of ZmC3H in leaves whereas it up-regulates its expression in roots. These changes in ZmC3H expression correlate with the changes in the content of caffeic acid in maize in response to drought. We illustrate the implications of these changes in the expression of the gene in relation to maize responses to drought and discuss the potential of regulating caffeic acid biosynthesis towards genetic improvement of maize tolerance to drought stress. These findings have implications for food security because of the potential of the implications of the study for drought tolerance in maize.

Keywords: caffeic acid, drought-responsive expression, maize drought tolerance, p-coumarate 3-hydroxylase

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Authors: J. U. Santhosh Kumar, V. Krishna, Sebin Sebastian, G. S. Seethapathy, G. Ravikanth, R. Uma Shaanker

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Food is one of the basic needs of human beings. It requires the normal function of the body part and a healthy growth. Recently, food adulteration increases day by day to increase the quantity and make more benefit. Animal source foods can provide a variety of micronutrients that are difficult to obtain in adequate quantities from plant source foods alone. Particularly in the meat industry, products from animals are susceptible targets for fraudulent labeling due to the economic profit that results from selling cheaper meat as meat from more profitable and desirable species. This work presents an overview of the main PCR-based techniques applied to date to verify the authenticity of beef meat and meat products from beef species. We were analyzed 25 market beef samples in South India. We examined PCR methods based on the sequence of the cytochrome b gene for source species identification. We found all sample were sold as beef meat as Bos Taurus. However, interestingly Male meats are more valuable high price compare to female meat, due to this reason most of the markets samples are susceptible. We were used sex determination gene of cattle like TSPY(Y-encoded, testis-specific protein TSPY is a Y-specific gene). TSPY homologs exist in several mammalian species, including humans, horses, and cattle. This gene is Y coded testis protein genes, which only amplify the male. We used multiple PCR products form species-specific “fingerprints” on gel electrophoresis, which may be useful for meat authentication. Amplicons were obtained only by the Cattle -specific PCR. We found 13 market meat samples sold as female beef samples. These results suggest that the species-specific PCR methods established in this study would be useful for simple and easy detection of adulteration of meat products.

Keywords: authentication, meat products, species-specific, TSPY

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Authors: El Harraj Abdeslam, Raissouni Naoufal

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The detection of moving objects from a video image sequences is very important for object tracking, activity recognition, and behavior understanding in video surveillance. The most used approach for moving objects detection / tracking is background subtraction algorithms. Many approaches have been suggested for background subtraction. But, these are illumination change sensitive and the solutions proposed to bypass this problem are time consuming. In this paper, we propose a robust yet computationally efficient background subtraction approach and, mainly, focus on the ability to detect moving objects on dynamic scenes, for possible applications in complex and restricted access areas monitoring, where moving and motionless persons must be reliably detected. It consists of three main phases, establishing illumination changes in variance, background/foreground modeling and morphological analysis for noise removing. We handle illumination changes using Contrast Limited Histogram Equalization (CLAHE), which limits the intensity of each pixel to user determined maximum. Thus, it mitigates the degradation due to scene illumination changes and improves the visibility of the video signal. Initially, the background and foreground images are extracted from the video sequence. Then, the background and foreground images are separately enhanced by applying CLAHE. In order to form multi-modal backgrounds we model each channel of a pixel as a mixture of K Gaussians (K=5) using Gaussian Mixture Model (GMM). Finally, we post process the resulting binary foreground mask using morphological erosion and dilation transformations to remove possible noise. For experimental test, we used a standard dataset to challenge the efficiency and accuracy of the proposed method on a diverse set of dynamic scenes.

Keywords: video surveillance, background subtraction, contrast limited histogram equalization, illumination invariance, object tracking, object detection, behavior understanding, dynamic scenes

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Authors: Nacer Hamza

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Naturally radiation exposure that present due to the cosmic ray or the naturel occurring radioactives materials(NORMs) that originated in the earth's crust and are present everywhere in the environment(1) , a significant concentration of NORMs reported in the produced water which comes out during the oil extraction process, so that the management of this produced water is a challenge for oil and gas companies which include either minimization of produced water which considered as the best way in the term of environment based in the fact that ,the lower water produced the lower cost in treating this water , recycling and reuse by reinjected produced water that fulfills some requirements to enhance oil recovery or disposal in the case that the produced water cannot be minimize or reuse. In the purpose of produced water management, the investigation of NORMs activity concentration present in it considered as the main step for more understanding of the radionuclide’s distribution. Many studies reported the present of NORMs in produced water and investigated the correlation between 〖Ra〗^226and the different metals present in produced water(2) including Cations and anions〖Na〗^+,〖Cl〗^-, 〖Fe〗^(2+), 〖Ca〗^(2+) . and lead, nickel, zinc, cadmium, and copper commonly exist as heavy metal in oil and gas field produced water(3). However, there are no real interesting to investigate the correlation between 〖Rn〗^222and the different metals exist in produced water. methods using, in first to measure the radon concentration activity in produced water samples is a RAD7 .RAD7 is a radiometer instrument based on the solid state detectors(4) which is a type of semi-conductor detector for alpha particles emitting from Rn and their progenies, in second the concentration of different metals presents in produced water measure using an atomic absorption spectrometry AAS. Then to investigate the correlation between the 〖Rn〗^222concentration activity and the metals concentration in produced water a statistical method is Pearson correlation analysis which based in the correlation coefficient obtained between the 〖Rn〗^222 and metals. Such investigation is important to more understanding how the radionuclides act in produced water based on this correlation with metals , in first due to the fact that 〖Rn〗^222decays through the sequence 〖Po〗^218, 〖Pb〗^214, 〖Bi〗^214, 〖Po〗^214, and〖Pb〗^210, those daughters are metals thus they will precipitate with metals present in produced water, secondly the short half-life of 〖Rn〗^222 (3.82 days) lead to faster precipitation of its progenies with metals in produced water.

Keywords: norms, radon concentration, produced water, heavy metals

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Authors: Dina Athariah, Desriani Desriani, Bugi Ratno Budiarto, Abinawanto Abinawanto, Dwi Wulandari

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Breast cancer is a regulated by many genes. Defect in PIK3CA gene especially at position of exon 9 (E542K and E545K), called hot spot mutation induce early transformation of breast cells. The early detection of breast cancer based on mutation profile of this hot spot region would be hampered by the existence of pseudogene, marked by its substitution mutation at base 1658 (E545A) and deletion at 1659 that have been previously proven in several cancers. To the best of the authors’ knowledge, until recently no studies have been reported about pseudogene phenomenon in breast cancer. Here, we reported PCR optimization to to obtain true exon 9 of PIK3CA gene from its pseudogene hence increasing the validity of data. Material and methods: two genomic DNA with Dev and En code were used in this experiment. Two pairs of primer were design for Standard PCR method. The size of PCR products for each primer is 200bp and 400bp. While other primer was designed for Nested-PCR followed with DNA sequencing method. For Nested-PCR, we optimized the annealing temperature in first and second run of PCR, and the PCR cycle for first run PCR (15x versus 25x). Result: standard PCR using both primer pairs designed is failed to detect the true PIK3CA gene, appearing a substitution mutation at 1658 and deletion at 1659 of PCR product in sequence chromatogram indicated pseudogene. Meanwhile, Nested-PCR with optimum condition (annealing temperature for the first round at 55oC, annealing temperatung for the second round at 60,7oC with 15x PCR cycles) and could detect the true PIK3CA gene. Dev sample were identified as WT while En sample contain one substitution mutation at position 545 of exon 9, indicating amino acid changing from E to K. For the conclusion, pseudogene also exists in breast cancer and the apllication of optimazed Nested-PCR in this study could detect the true exon 9 of PIK3CA gene.

Keywords: breast cancer, exon 9, hotspot mutation, PIK3CA, pseudogene

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Authors: Sidra Pervez, Afsheen Aman, Shah Ali Ul Qader

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The importance of attaining an optimum performance of an enzyme is often a question of devising an effective method for its immobilization. Cross-linked enzyme aggregate (CLEAs) is a new approach for immobilization of enzymes using carrier free strategy. This method is exquisitely simple (involving precipitation of the enzyme from aqueous buffer followed by cross-linking of the resulting physical aggregates of enzyme molecules) and amenable to rapid optimization. Among many industrial enzymes, amyloglucosidase is an important amylolytic enzyme that hydrolyzes alpha (1→4) and alpha (1→6) glycosidic bonds in starch molecule and produce glucose as a sole end product. Glucose liberated by amyloglucosidase can be used for the production of ethanol and glucose syrups. Besides this amyloglucosidase can be widely used in various food and pharmaceuticals industries. For production of amyloglucosidase on commercial scale, filamentous fungi of genera Aspergillus are mostly used because they secrete large amount of enzymes extracellularly. The current investigation was based on isolation and identification of filamentous fungi from genus Aspergillus for the production of amyloglucosidase in submerged fermentation and optimization of cultivation parameters for starch saccharification. Natural isolates were identified as Aspergillus niger KIBGE-IB36, Aspergillus fumigatus KIBGE-IB33, Aspergillus flavus KIBGE-IB34 and Aspergillus terreus KIBGE-IB35 on taxonomical basis and 18S rDNA analysis and their sequence were submitted to GenBank. Among them, Aspergillus fumigatus KIBGE-IB33 was selected on the basis of maximum enzyme production. After optimization of fermentation conditions enzyme was immobilized on CLEA. Different parameters were optimized for maximum immobilization of amyloglucosidase. Data of enzyme stability (thermal and Storage) and reusability suggested the applicability of immobilized amyloglucosidase for continuous saccharification of starch in industrial processes.

Keywords: aspergillus, immobilization, industrial processes, starch saccharification

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Authors: Carmela Perta

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In Italy the coexistence of standard language, its varieties and different minority languages - historical and migration languages - has been a way to study language contact in different directions; the focus of most of the studies is either the relations among the languages of the social repertoire, or the study of contact phenomena occurring in a particular structural level. However, studies on contact facts in relation to a given sociolinguistic situation of the speech community are still not present in literature. As regard the language level to investigate from the perspective of contact, it is commonly claimed that the lexicon is the most volatile part of language and most likely to undergo change due to superstrate influence, indeed first lexical features are borrowed, then, under long term cultural pressure, structural features may also be borrowed. The aim of this paper is to analyse language contact in two historical minority communities where Francoprovençal is spoken, in relation to their sociolinguistic situation. In this perspective, firstly lexical borrowings present in speakers’ speech production will be examined, trying to find a possible correlation between this part of the lexicon and informants’ sociolinguistic variables; secondly a possible correlation between a particular community sociolinguistic situation and lexical borrowing will be found. Methods used to collect data are based on the results obtained from 24 speakers in both the villages; the speaker group in the two communities consisted of 3 males and 3 females in each of four age groups, ranging in age from 9 to 85, and then divided into five groups according to their occupations. Speakers were asked to describe a sequence of pictures naming common objects and then describing scenes when they used these objects: they are common objects, frequently pronounced and belonging to semantic areas which are usually resistant and which are thought to survive. A subset of this task, involving 19 items with Italian source is examined here: in order to determine the significance of the independent variables (social factors) on the dependent variable (lexical variation) the statistical package SPSS, particularly the linear regression, was used.

Keywords: borrowing, Francoprovençal, language change, lexicon

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Authors: Manuel A. Alonso-Tarajano, Roberto Mosca, Patrick Aloy

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Protein kinases participate in a myriad of cellular processes of major biomedical interest. The in vivo substrate specificity of these enzymes is a process determined by several factors, and despite several years of research on the topic, is still far from being totally understood. In the present work, we have quantified the contributions to the kinase substrate specificity of i) the phosphorylation sites and their surrounding residues in the sequence and of ii) the association of kinases to adaptor or scaffold proteins. We have used position-specific scoring matrices (PSSMs), to represent the stretches of sequences phosphorylated by 93 families of kinases. We have found negative correlations between the number of sequences from which a PSSM is generated and the statistical significance and the performance of that PSSM. Using a subset of 22 statistically significant PSSMs, we have identified specificity determinant residues (SDRs) for 86% of the corresponding kinase families. Our results suggest that different SDRs can function as positive or negative elements of substrate recognition by the different families of kinases. Additionally, we have found that human proteins with known function as adaptors or scaffolds (kAS) tend to interact with a significantly large fraction of the substrates of the kinases to which they associate. Based on this characteristic we have identified a set of 279 potential adaptors/scaffolds (pAS) for human kinases, which is enriched in Pfam domains and functional terms tightly related to the proposed function. Moreover, our results show that for 74.6% of the kinase– pAS association found, the pAS colocalize with the substrates of the kinases they are associated to. Finally, we have found evidence suggesting that the association of kinases to adaptors and scaffolds, may contribute significantly to diminish the in vivo substrate crossed- specificity of protein kinases. In general, our results indicate the relevance of several SDRs for both the positive and negative selection of phosphorylation sites by kinase families and also suggest that the association of kinases to pAS proteins may be an important factor for the localization of the enzymes with their set of substrates.

Keywords: kinase, phosphorylation, substrate specificity, adaptors, scaffolds, cellular colocalization

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Authors: Mohammad W. Dewan, Jahangir Alam, Khurshida Sharmin

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Synthetic fibers (carbon, glass, aramid, etc.) are generally utilized to make composite materials for better mechanical and thermal properties. However, they are expensive and non-biodegradable. In the perspective of Bangladesh, jute fibers are available, inexpensive, and comprising good mechanical properties. The improved properties (i.e., low cost, low density, eco-friendly) of natural fibers have made them a promising reinforcement in hybrid composites without sacrificing mechanical properties. In this study, jute and e-glass fiber reinforced hybrid composite materials are fabricated utilizing hand lay-up followed by a compression molding technique. Room temperature cured two-part epoxy resin is used as a matrix. Approximate 6-7 mm thick composite panels are fabricated utilizing 17 layers of woven glass and jute fibers with different fiber layering sequences- only jute, only glass, glass, and jute alternatively (g/j/g/j---) and 4 glass - 9 jute – 4 glass (4g-9j-4g). The fabricated composite panels are analyzed through fiber volume calculation, tensile test, bending test, and water absorption test. The hybridization of jute and glass fiber results in better tensile, bending, and water absorption properties than only jute fiber-reinforced composites, but inferior properties as compared to only glass fiber reinforced composites. Among different fiber layering sequences, 4g-9j-4g fibers layering sequence resulted in better tensile, bending, and water absorption properties. The effect of chemical treatment on the woven jute fiber and chopped glass microfiber infusion are also investigated in this study. Chemically treated jute fiber and 2 wt. % chopped glass microfiber infused hybrid composite shows about 12% improvements in flexural strength as compared to untreated and no micro-fiber infused hybrid composite panel. However, fiber chemical treatment and micro-filler do not have a significant effect on tensile strength.

Keywords: compression molding, chemical treatment, hybrid composites, mechanical properties

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Authors: I. Gusti Agung Aditya Surya Wibawa, Andri Syafriya, Beiruny Syam

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Gumai Formation which acts as regional seal for Talang Akar Formation becomes one of the most prolific reservoir in South Sumatra Basin and the primary exploration target in this area. Marine conditions were eventually established during the continuation of transgression sequence leads an open marine facies deposition in Early Miocene. Marine clastic deposits where calcareous shales, claystone and siltstones interbedded with fine-grained calcareous and glauconitic sandstones are the domination of lithology which targeted as the hydrocarbon reservoir. All this time, the main objective of PetroChina’s exploration and production in Betara area is only from Lower Talang Akar Formation. Successful testing in some exploration wells which flowed gas & condensate from Gumai Formation, opened the opportunity to optimize new reservoir objective in Betara area. Limitation of conventional wireline logs data in Gumai interval is generating technical challenge in term of geological approach. A utilization of Gas While Drilling indicator initiated with the objective to determine the next Gumai reservoir candidate which capable to increase Jabung hydrocarbon discoveries. This paper describes how Gas While Drilling indicator is processed to generate potential and non-potential zone by cut-off analysis. Validation which performed by correlation and comparison with well logs, Drill Stem Test (DST), and Reservoir Performance Monitor (RPM) data succeed to observe Gumai reservoir in Betara Complex. After we integrated all of data, we are able to generate a Betara Complex potential map and overlaid with reservoir characterization distribution as a part of risk assessment in term of potential zone presence. Mud log utilization and geophysical data information successfully covered the geological challenges in this study.

Keywords: Gumai, gas while drilling, classification, reservoir, potential

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Authors: Xiaoqing Liu, Kurt Friese, Karsten Rinke

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Lacustrine sediment archives rich paleoenvironmental information in lake and surrounding environment. Additionally, modern sediment is used as an effective medium for the monitoring of lake. Organic carbon in sediment is a heterogeneous mixture with varying turnover times and qualities which result from the different biogeochemical processes in the deposition of organic material. Therefore, the isolation of different carbon pools is important for the research of lacustrine condition in the lake. However, the numeric available fractionation procedures can hardly yield homogeneous carbon pools on terms of stability and age. In this work, a multi-step fractionation protocol that treated sediment with hot water, HCl, H2O2 and Na2S2O8 in sequence was adopted, the treated sediment from each step were analyzed for the isotopic and structural compositions with Isotope Ratio Mass Spectrometer coupled with element analyzer (IRMS-EA) and Solid-state 13C Nuclear Magnetic Resonance (NMR), respectively. The sequential extractions with hot-water, HCl, and H2O2 yielded a more homogeneous and C3 plant-originating OC fraction, which was characterized with an atomic C/N ratio shift from 12.0 to 20.8, and 13C and 15N isotopic signatures were 0.9‰ and 1.9‰ more depleted than the original bulk sediment, respectively. Additionally, the H2O2- resistant residue was dominated with stable components, such as the lignins, waxes, cutans, tannins, steroids and aliphatic proteins and complex carbohydrates. 6M HCl in the acid hydrolysis step was much more effective than 1M HCl to isolate a sedimentary OC fraction with higher degree of homogeneity. Owing to the extremely high removal rate of organic matter, the step of a Na2S2O8 oxidation is only suggested if the isolation of the most refractory OC pool is mandatory. We conclude that this multi-step chemical fractionation procedure is effective to isolate more homogeneous OC pools in terms of stability and functional structure, and it can be used as a promising method for OC pools fractionation of sediment or soil in future lake research.

Keywords: 13C-CPMAS-NMR, 13C signature, lake sediment, OC fractionation

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Authors: You-Lin Wu, Yi-Hsing Sung, Shih-Hung Lin, Jing-Jenn Lin

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Performance improvement in optoelectronic devices such as solar cells and photodetectors has been reported when a polymer/ZnO nanorods stack is used. Resistance switching of polymer/ZnO nanocrystals (or nanorods) hybrid has also gained a lot of research interests recently. It has been reported that high- and low-resistance states of a metal/insulator/metal (MIM) structure diode with a polystyrene (PS) and ZnO hybrid as the insulator layer can be switched by applied bias after a high-voltage forming process, while the same device structure merely with a PS layer does not show any forming behavior. In this work, we investigated the current-voltage (I-V) characteristics of an MIM device with a PS/ZnO nanorods stack deposited on fluorine-doped tin oxide (FTO) glass substrate. The ZnO nanorods were grown by a hydrothermal method using a mixture of zinc nitrate, hexamethylenetetramine, and DI water. Following that, a PS layer was deposited by spin coating. Finally, the device with a structure of Ti/ PS/ZnO nanorods/FTO was completed by e-gun evaporated Ti layer on top of the PS layer. Semiconductor parameters analyzer Agilent 4156C was then used to measure the I-V characteristics of the device by applying linear ramp sweep voltage with sweep sequence of 0V → 4V → 0V → 3V → 0V → 2V → 0V → 1V → 0V in both positive and negative directions. It is interesting to find that the I-V characteristics are bias dependent and hysteretic, indicating that the device Ti/PS/ZnO nanorods/FTO structure has ferroelectricity. Our results also show that the maximum hysteresis loop height of the I-V characteristics as well as the voltage at which the maximum hysteresis loop height of each scan occurs increase with increasing maximum sweep voltage. It should be noticed that, although ferroelectricity has been found in ZnO at its melting temperature (1975℃) and in Li- or Co-doped ZnO, neither PS nor ZnO has ferroelectricity at room temperature. Using the same structure but with a PS or ZnO layer only as the insulator does not give and hysteretic I-V characteristics. It is believed that a charge polarization layer is induced near the PS/ZnO nanorods stack interface and thus causes the ferroelectricity in the device with Ti/PS/ZnO nanorods/FTO structure. Our results show that the PS/ZnO stack can find a potential application in a resistive switching memory device with MIM structure.

Keywords: ferroelectricity, hysteresis, polystyrene, resistance switching, ZnO nanorods

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Authors: Huan Ting Liao

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In a typical manufacturing environment, computer numerical control (CNC) machining is essential for automating production through precise computer-controlled tool operations, significantly enhancing efficiency and ensuring consistent product quality. However, traditional CNC production lines often rely on manual loading and unloading, limiting operational efficiency and scalability. Although automated loading systems have been developed, they frequently lack sufficient intelligence and configuration efficiency, requiring extensive setup adjustments for different products and impacting overall productivity. This research addresses the job shop scheduling problem (JSSP) in CNC machining environments, aiming to minimize total completion time (makespan) and maximize CNC machine utilization. We propose a novel approach using reinforcement learning (RL), specifically the Q-learning algorithm, to optimize scheduling decisions. The study simulates the JSSP, incorporating robotic arm operations, machine processing times, and work order demand allocation to determine optimal processing sequences. The Q-learning algorithm enhances machine utilization by dynamically balancing workloads across CNC machines, adapting to varying job demands and machine states. This approach offers robust solutions for complex manufacturing environments by automating decision-making processes for job assignments. Additionally, we evaluate various layout configurations to identify the most efficient setup. By integrating RL-based scheduling optimization with layout analysis, this research aims to provide a comprehensive solution for improving manufacturing efficiency and productivity in CNC-based job shops. The proposed method's adaptability and automation potential promise significant advancements in tackling dynamic manufacturing challenges.

Keywords: job shop scheduling problem, reinforcement learning, operations sequence, layout optimization, q-learning

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Authors: Danielle C. B. Honorato, Rafael H. Carvalho, Adriana L. Soares, Ana Paula F. R. L. Bracarense, Paulo D. Guarnieri, Massami Shimokomaki, Elza I. Ida

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Over the past decade, the Brazilian production of turkey meat increased by more than 50%, indicating that the turkey meat is considered a great potential for the Brazilian economy contributing to the growth of agribusiness at the marketing international scenario. However, significant color changes may occur during its processing leading to the pale, soft and exudative (PSE) appearance on the surface of breast meat due to the low water holding capacity (WHC). Changes in PSE meat functional properties occur due to the myofibrils proteins denaturation caused by a rapid postmortem glycolysis resulting in a rapid pH decline while the carcass temperature is still warm. The aim of this study was to analyze the physical, chemical and histological characteristics of PSE turkey meat obtained from a Brazilian commercial processing plant. The turkey breasts samples were collected (n=64) at the processing line and classified as PSE at L* ≥ 53 value. The pH was also analyzed after L* measurement. In sequence, PSE meat samples were evaluated for WHC, cooking loss (CL), shear force (SF), myofibril fragmentation index (MFI), protein denaturation (PD) and histological evaluation. The abnormal color samples presented lower pH values, 16% lower fiber diameter, 11% lower SF and 2% lower WHC than those classified as normal. The CL, PD and MFI were, respectively, 9%, 18% and 4% higher in PSE samples. The Pearson correlation between the L* values and CL, PD and MFI was positive, while that SF and pH values presented negative correlation. Under light microscopy, a shrinking of PSE muscle cell diameter was approximately 16% shorter in relation to normal samples and an extracellular enlargement of endomysium and perimysium sheaths as the consequence of higher water contents lost as observed previously by lower WHC values. Thus, the results showed that PSE turkey breast meat presented significant changes in their physical, chemical and histological characteristics that may impair its functional properties.

Keywords: functional properties, histological evaluation, meat quality, PSE

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Authors: Arushi Singh, Anjana Jain, Prakash Vyavahare

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Recently, Li-Fi(light-fiedelity) has been launched based on VLC(visible light communication) technique, 100 times faster than WiFi. Now 5G mobile communication system is proposed to use VLC-OFDM as the transmission technique. The VLC system focused on visible rays, is considered for efficient spectrum use and easy intensity modulation through LEDs. The reason of high speed in VLC is LED, as they flicker incredibly fast(order of MHz). Another advantage of employing LED is-it acts as low pass filter results no out-of-band emission. The VLC system falls under the category of ‘green technology’ for utilizing LEDs. In present scenario, OFDM is used for high data-rates, interference immunity and high spectral efficiency. Inspite of the advantages OFDM suffers from large PAPR, ICI among carriers and frequency offset errors. Since, the data transmission technique used in VLC system is OFDM, the system suffers the drawbacks of OFDM as well as VLC, the non-linearity dues to non-linear characteristics of LED and PAPR of OFDM due to which the high power amplifier enters in non-linear region. The proposed paper focuses on reduction of PAPR in VLC-OFDM systems. Many techniques are applied to reduce PAPR such as-clipping-introduces distortion in the carrier; selective mapping technique-suffers wastage of bandwidth; partial transmit sequence-very complex due to exponentially increased number of sub-blocks. The paper discusses three companding techniques namely- µ-law, A-law and advance A-law companding technique. The analysis shows that the advance A-law companding techniques reduces the PAPR of the signal by adjusting the companding parameter within the range. VLC-OFDM systems are the future of the wireless communication but non-linearity in VLC-OFDM is a severe issue. The proposed paper discusses the techniques to reduce PAPR, one of the non-linearities of the system. The companding techniques mentioned in this paper provides better results without increasing the complexity of the system.

Keywords: non-linear companding techniques, peak to average power ratio (PAPR), visible light communication (VLC), VLC-OFDM

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Authors: Sutapa Som Chaudhury, Chitrangada Das Mukhopadhyay

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Alzheimer’s disease is a well-known form of dementia since its discovery in 1906. Current Food and Drug Administration approved medications e.g. cholinesterase inhibitors, memantine offer modest symptomatic relief but do not play any role in disease modification or recovery. In last three decades many small molecules, chaperons, synthetic peptides, partial β-secretase enzyme blocker have been tested for the development of a drug against Alzheimer though did not pass the 3rd clinical phase trials. Here in this study, we designed a PEGylated, aminogenic, tripeptidic polymer with two different molecular weights based on the aggregation prone amino acid sequence 17-20 in amyloid beta (Aβ) 1-42. Being conjugated with poly-ethylene glycol (PEG) which self-assembles into hydrophilic nanoparticles, these PEGylated tripeptides constitute a very good drug delivery system crossing the blood brain barrier while the peptide remains protected from proteolytic degradation and non-specific protein interactions. Moreover, being completely aminogenic they would not raise any side effects. These peptide inhibitors were evaluated for their effectiveness against Aβ42 fibrillation at an early stage of oligomer to fibril formation as well as preformed fibril clearance via Thioflavin T (ThT) assay, dynamic light scattering analyses, atomic force microscopy and scanning electron microscopy. The inhibitors were proved to be safe at a higher concentration of 20µM by the reduction assay of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) dye. Moreover, SHSY5Y neuroblastoma cells have shown a greater survivability when treated with the inhibitors following Aβ42 fibril and oligomer treatment as compared with the control Aβ42 fibril and/or oligomer treated neuroblastoma cells. These make the peptidic inhibitors a promising compound in the aspect of the discovery of alternative medication for Alzheimer’s disease.

Keywords: Alzheimer’s disease, alternative medication, amyloid beta, PEGylated peptide

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Authors: Othman Elmahdy Othman, Agnés Germot, Daniel Petit, Muhammad Khodary, Abderrahman Maftah

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Recently, the control (D-loop) and cytochrome b (Cyt b) regions of mtDNA have received more attention due to their role in the genetic diversity and phylogenetic studies in different livestock which give important knowledge towards the genetic resource conservation. Studies based on sequencing of sheep mitochondrial DNA showed that there are five maternal lineages in the world for domestic sheep breeds; A, B, C, D and E. By using cytochrome B sequencing, we aimed to clarify the genetic affinities and phylogeny of six Egyptian sheep breeds. Blood samples were collected from 111 animals belonging to six Egyptian sheep breeds; Barki, Rahmani, Ossimi, Saidi, Sohagi and Fallahi. The total DNA was extracted and the specific primers were used for conventional PCR amplification of the cytochrome B region of mtDNA. PCR amplified products were purified and sequenced. The alignment of sequences was done using BioEdit software and DnaSP 5.00 software was used to identify the sequence variation and polymorphic sites in the aligned sequences. The result showed that the presence of 39 polymorphic sites leading to the formation of 29 haplotypes. The haplotype diversity in six tested breeds ranged from 0.643 in Rahmani breed to 0.871 in Barki breed. The lowest genetic distance was observed between Rahmani and Saidi (D: 1.436 and Dxy: 0.00127) while the highest distance was observed between Ossimi and Sohagi (D: 6.050 and Dxy: 0.00534). Neighbour-joining (Phylogeny) tree was constructed using Mega 5.0 software. The sequences of 111 analyzed samples were aligned with references sequences of different haplogroups; A, B, C, D and E. The phylogeny result showed the presence of four haplogroups; HapA, HapB, HapC and HapE in the examined samples whereas the haplogroup D was not found. The result showed that 88 out of 111 tested animals cluster with haplogroup B (79.28%), whereas 12 tested animals cluster with haplogroup A (10.81%), 10 animals cluster with haplogroup C (9.01%) and one animal belongs to haplogroup E (0.90%).

Keywords: phylogeny, genetic biodiversity, MtDNA, cytochrome B, Egyptian sheep

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Authors: Neelma Ashraf

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Actinomycetes, particularly genus Streptomyces is of great importance due to their role in the discovery of new natural products, particularly antimicrobial secondary metabolites in the medicinal science and biotechnology industry. Different Streptomyces strains were isolated from Helianthus annuus plants and tested for antibacterial and antifungal activities. The most promising five strains were chosen for further investigation, and growth conditions for antibiotic synthesis were optimised. The supernatants were extracted in different solvents, and the extracted products were analyzed using liquid chromatography-mass spectrometry (LC-MS) and biological testing. From one of the potent strains Streptomyces globusus sp. BR123, a compound lavendamycin was identified using these analytical techniques. In addition, this potent strain also produces a strong antifungal polyene compound with a quasimolecular ion of 2072. Streptomyces sp. BR123 was genome sequenced because of its promising antimicrobial potential in order to identify the gene cluster responsible for analyzed compound “lavendamycin”. The genome analysis yielded candidate genes responsible for the production of this potent compound. The genome sequence of 8.15 Mb of Streptomyces sp. isolate BR123 with a GC content of 72.63% and 8103 protein coding genes was attained. Many antimicrobial, antiparasitic, and anticancerous compounds were detected through multiple biosynthetic gene clusters predicted by in-Silico analysis. Though, the novelty of metabolites was determined through the insignificant resemblance with known biosynthetic gene clusters. The current study gives insight into the bioactive potential of Streptomyces sp. isolate BR123 with respect to the synthesis of bioactive secondary metabolites through genomic and spectrometric analysis. Moreover, the comparative genome study revealed the connection of isolate BR123 with other Streptomyces strains, which could expand the knowledge of this genus and the mechanism involved in the discovery of new antimicrobial metabolites.

Keywords: streptomyces, secondary metabolites, genome, biosynthetic gene clusters, high performance liquid chromatography, mass spectrometry

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