Search results for: whole genome sequence

Authors: Qi Liu, Jiqin Yao, Xiaohu Zhou, Bo Zheng

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The first artificial cell was produced by Thomas Chang in the 1950s when he was trying to make a mimic of red blood cells. Since then, many different types of artificial cells have been constructed from one of the two approaches: a so-called bottom-up approach, which aims to create a cell from scratch, and a top-down approach, in which genes are sequentially knocked out from organisms until only the minimal genome required for sustaining life remains. In this project, bottom-up approach was used to build a new cell-free expression system which mimics artificial cell that capable of protein expression and communicate with each other. The artificial cells constructed from the bottom-up approach are usually lipid vesicles, polymersomes, hydrogels or aqueous droplets containing the nucleic acids and transcription-translation machinery. However, lipid vesicles based artificial cells capable of communication present several issues in the cell communication research: (1) The lipid vesicles normally lose the important functions such as protein expression within a few hours. (2) The lipid membrane allows the permeation of only small molecules and limits the types of molecules that can be sensed and released to the surrounding environment for chemical communication; (3) The lipid vesicles are prone to rupture due to the imbalance of the osmotic pressure. To address these issues, the hydrogel-based artificial cells were constructed in this work. To construct the artificial cell, polyacrylamide hydrogel was functionalized with Acrylate PEG Succinimidyl Carboxymethyl Ester (ACLT-PEG2000-SCM) moiety on the polymer backbone. The proteinaceous factors can then be immobilized on the polymer backbone by the reaction between primary amines of proteins and N-hydroxysuccinimide esters (NHS esters) of ACLT-PEG2000-SCM, the plasmid template and ribosome were encapsulated inside the hydrogel particles. Because the artificial cell could continuously express protein with the supply of nutrients and energy, the artificial cell-artificial cell communication and artificial cell-natural cell communication could be achieved by combining the artificial cell vector with designed plasmids. The plasmids were designed referring to the quorum sensing (QS) system of bacteria, which largely relied on cognate acyl-homoserine lactone (AHL) / transcription pairs. In one communication pair, “sender” is the artificial cell or natural cell that can produce AHL signal molecule by synthesizing the corresponding signal synthase that catalyzed the conversion of S-adenosyl-L-methionine (SAM) into AHL, while the “receiver” is the artificial cell or natural cell that can sense the quorum sensing signaling molecule form “sender” and in turn express the gene of interest. In the experiment, GFP was first immobilized inside the hydrogel particle to prove that the functionalized hydrogel particles could be used for protein binding. After that, the successful communication between artificial cell-artificial cell and artificial cell-natural cell was demonstrated, the successful signal between artificial cell-artificial cell or artificial cell-natural cell could be observed by recording the fluorescence signal increase. The hydrogel-based artificial cell designed in this work can help to study the complex communication system in bacteria, it can also be further developed for therapeutic applications.

Keywords: artificial cell, cell-free system, gene circuit, synthetic biology

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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: K. S. Vimal, D. Bodhini, K. Ramya, N. Lakshmipriya, R. M. Anjana, V. Sudha, J. A. Lovegrove, V. Mohan, V. Radha

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Gene-lifestyle interaction studies have been carried out in various populations. However, to date there are no studies in an Asian Indian population. Hence, we examined whether lifestyle factors such as diet and physical activity modify the association between fat mass and obesity–associated (FTO) gene variants and obesity and type 2 diabetes (T2D) in an Asian Indian population. We studied 734 unrelated T2D and 884 normal glucose-tolerant (NGT) participants randomly selected from the Chennai Urban Rural Epidemiology Study (CURES) in Southern India. Obesity was defined according to the World Health Organization Asia Pacific Guidelines (non-obese, BMI < 25 kg/m2; obese, BMI ≥ 25 kg/m2). Six single nucleotide polymorphisms (SNPs) in the FTO gene (rs9940128, rs7193144, rs8050136, rs918031, rs1588413 and rs11076023) identified from recent genome-wide association studies for T2D were genotyped by polymerase chain reaction-restriction fragment length polymorphism and direct sequencing. Dietary assessment was carried out using a validated food frequency questionnaire and physical activity was based upon the self-report. Interaction analyses were performed by including the interaction terms in the model. A joint likelihood ratio test of the main SNP effects and the SNP-diet/physical activity interaction effects was used in the linear regression analyses to maximize statistical power. Statistical analyses were performed using STATA version 13. There was a significant interaction between FTO SNP rs8050136 and carbohydrate energy percentage (Pinteraction=0.04) on obesity, where the ‘A’ allele carriers of the SNP rs8050136 had 2.46 times higher risk of obesity than those with ‘CC’ genotype (P=3.0x10-5) among individuals in the highest tertile of carbohydrate energy percentage. Furthermore, among those who had lower levels of physical activity, the ‘A’ allele carriers of the SNP rs8050136 had 1.89 times higher risk of obesity than those with ‘CC’ genotype (P=4.0x10-5). We also found a borderline interaction between SNP rs11076023 and carbohydrate energy percentage (Pinteraction=0.08) on T2D, where the ‘A’ allele carriers in the highest tertile of carbohydrate energy percentage, had 1.57 times higher risk of T2D than those with ‘TT’ genotype (P=0.002). There was also a significant interaction between SNP rs11076023 and physical activity (Pinteraction=0.03) on T2D. No further significant interactions between SNPs and macronutrient intake or physical activity on obesity and T2D were observed. In conclusion, this is the first study to provide evidence for a gene-diet and gene-physical activity interaction on obesity and T2D in an Asian Indian population. These findings suggest that the association between FTO gene variants and obesity and T2D is influenced by carbohydrate intake and physical activity levels. Greater understanding of how FTO gene influences obesity and T2D through dietary and exercise interventions will advance the development of behavioral intervention and personalised lifestyle strategies predicted to reduce the development of metabolic diseases in ‘A’ allele carriers of both SNPs in this Asian Indian population.

Keywords: dietary intake, FTO, obesity, physical activity, type 2 diabetes, Asian Indian.

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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: Oleg Reva, Ilya Korotetskiy, Marina Lankina, Murat Kulmanov, Aleksandr Ilin

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Molecular docking approaches are widely used for design of new antibiotics and modeling of antibacterial activities of numerous ligands which bind specifically to active centers of indispensable enzymes and/or key signaling proteins of pathogens. Widespread drug resistance among pathogenic microorganisms calls for development of new antibiotics specifically targeting important metabolic and information pathways. A generally recognized problem is that almost all molecular targets have been identified already and it is getting more and more difficult to design innovative antibacterial compounds to combat the drug resistance. A promising way to overcome the drug resistance problem is an induction of reversion of drug resistance by supplementary medicines to improve the efficacy of the conventional antibiotics. In contrast to well established computer-based drug design, modeling of drug resistance reversion still is in its infancy. In this work, we proposed an approach to identification of compensatory genetic variants reducing the fitness cost associated with the acquisition of drug resistance by pathogenic bacteria. The approach was based on an analysis of the population genetic of Mycobacterium tuberculosis and on results of experimental modeling of the drug resistance reversion induced by a new anti-tuberculosis drug FS-1. The latter drug is an iodine-containing nanomolecular complex that passed clinical trials and was admitted as a new medicine against MDR-TB in Kazakhstan. Isolates of M. tuberculosis obtained on different stages of the clinical trials and also from laboratory animals infected with MDR-TB strain were characterized by antibiotic resistance, and their genomes were sequenced by the paired-end Illumina HiSeq 2000 technology. A steady increase in sensitivity to conventional anti-tuberculosis antibiotics in series of isolated treated with FS-1 was registered despite the fact that the canonical drug resistance mutations identified in the genomes of these isolates remained intact. It was hypothesized that the drug resistance phenotype in M. tuberculosis requires an adjustment of activities of many genes to compensate the fitness cost of the drug resistance mutations. FS-1 cased an aggravation of the fitness cost and removal of the drug-resistant variants of M. tuberculosis from the population. This process caused a significant increase in genetic heterogeneity of the Mtb population that was not observed in the positive and negative controls (infected laboratory animals left untreated and treated solely with the antibiotics). A large-scale search for linkage disequilibrium associations between the drug resistance mutations and genetic variants in other genomic loci allowed identification of target proteins, which could be influenced by supplementary drugs to increase the fitness cost of the drug resistance and deprive the drug-resistant bacterial variants of their competitiveness in the population. The approach will be used to improve the efficacy of FS-1 and also for computer-based design of new drugs to combat drug-resistant infections.

Keywords: complete genome sequencing, computational modeling, drug resistance reversion, Mycobacterium tuberculosis

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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: Zahra Mohajer, Afsaneh Soltani

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Doping is a major issue in competitive sports and is favored by vast groups of athletes. The feeling of being higher-ranking than others and gaining fame has caused many athletes to misuse drugs. The definition of doping is to use prohibited substances and/or methods that help physical or mental performances or both. Doping counts as the illegal use of chemical substances or drugs, excessive amounts of physiological substances to increase the performance at or out of competition or even the use of inappropriate medications to treat an injury to gain the ability to participate in a competition. The International Olympic Committee (IOC) and World Anti-Doping Agency (WADA) have forbidden these substances to ensure fair and equal competition and also the health of the competitors. As of 2004 WADA has published an international list of illegal substances used for doping, which is updated annually. In the process of the Genome Project scientists have gained the ability to treat numerous diseases by gene therapy, which may result in bodily performance increase and therefore a potential opportunity to misuse by some athletes. Gene doping is defined as the non-therapeutic direct and indirect genetic modifications using genetic materials that can improve the performances in sports events. Biosynthetic drugs are a form of indirect genetic engineering. The method can be performed in three ways such as injecting the DNA directly into the muscle, inserting the genetically engineered cells, or transferring the DNA using a virus as a vector. Erythropoietin is a hormone majorly released by the kidney and in small amounts by the liver. Its function is to stimulate the erythropoiesis and therefore the more production of red blood cells (RBC) which causes an increase in Hemoglobin (Hb). During this process, the oxygen delivery to muscles will increase, which will improve athletic performance and postpone exhaustion. There are ways to increase the oxygen transferred to muscles such as blood transfusion, stimulating the production of red blood cells by using Erythropoietin (EPO), and also using allosteric effectors of Hemoglobin. EPO can either be injected as a protein or can be inserted into the cells as the gene which encodes EPO. Adeno-associated viruses have been employed to deliver the EPO gene to the cells. Employing the genes that naturally exist in the human body such as the EPO gene can reduce the risk of detecting gene doping. The first research about blood doping was conducted in 1947. The study has shown that an increase in hematocrit (HCT) up to 55% following homologous transfusion makes it more unchallenging for the body to perform the exercise at the altitude. Thereafter athletes’ attraction to blood infusion escalated. Also, a study has demonstrated that by reinfusing their own blood 4 weeks after being drawn, three men have shown a rise in Hb level which improved the oxygen uptake, and a delay in exhaustion. The list of performance-enhancing drugs is published by WADA annually and includes the following drugs: anabolic agents, hormones, Beta-2 agonists, Beta-blockers, Diuretics, Stimulants, narcotics, cannabinoids, and corticosteroids.

Keywords: doping, PEDs, sports, WADA

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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: 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: Niamh Higgins, Dawn Howard

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The Irish agri-food sector is of major importance to Ireland’s manufacturing sector and to the Irish economy through employment and the exporting of animal products worldwide. Infectious diseases and parasites have an impact on farm animal health causing profitability and productivity to be affected. For the sustainability of Irish dairy farming, there must be the highest standard of animal health. There can be a lack of information in accounting for > 1% of complete microbial diversity in an environment. There is the tendency of culture-based methods of microbial identification to overestimate the prevalence of species which grow easily on an agar surface. There is a need for new technologies to address these issues to assist with animal health. Metagenomic approaches provide information on both the whole genome and transcriptome present through DNA sequencing of total DNA from environmental samples producing high determination of functional and taxonomic information. Nanopore Next Generation Technologies have the ability to be powerful sequencing technologies. They provide high throughput, low material requirements and produce ultra-long reads, simplifying the experimental process. The aim of this study is to use a metagenomics approach to analyze dairy cattle faecal samples using the Oxford Nanopore MinION Next Generation Sequencer and to establish an in-house pipeline for metagenomic characterization of complex samples. Faecal samples will be obtained from Irish dairy farms, DNA extracted and the MinION will be used for sequencing, followed by bioinformatics analysis. Of particular interest, will be the parasite Buxtonella sulcata, which there has been little research on and which there is no research on its presence on Irish dairy farms. Preliminary results have shown the ability of the MinION to produce hundreds of reads in a relatively short time frame of eight hours. The faecal samples were obtained from 90 dairy cows on a Galway farm. The results from Oxford Nanopore ‘What’s in my pot’ (WIMP) using the Epi2me workflow, show that from a total of 926 classified reads, 87% were from the Kingdom Bacteria, 10% were from the Kingdom Eukaryota, 3% were from the Kingdom Archaea and < 1% were from the Kingdom Viruses. The most prevalent bacteria were those from the Genus Acholeplasma (71 reads), Bacteroides (35 reads), Clostridium (33 reads), Acinetobacter (20 reads). The most prevalent species present were those from the Genus Acholeplasma and included Acholeplasma laidlawii (39 reads) and Acholeplasma brassicae (26 reads). The preliminary results show the ability of the MinION for the identification of microorganisms to species level coming from a complex sample. With ongoing optimization of the pipe-line, the number of classified reads are likely to increase. Metagenomics has the potential in animal health for diagnostics of microorganisms present on farms. This would support wprevention rather than a cure approach as is outlined in the DAFMs National Farmed Animal Health Strategy 2017-2022.

Keywords: animal health, buxtonella sulcata, infectious disease, irish dairy cattle, metagenomics, minION, next generation sequencing

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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: Huyen T. Pham, Nhue P. Nguyen, Tien Q. Phi, Phuong T. Dang, Hy G. Le

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Since the marine environmental conditions are extremely different from the other ones, so that marine actinomycetes might produce novel bioactive compounds. Therefore, actinomycete strains were screened from marine water and sediment samples collected from the coastal areas of Northern Vietnam. Ninety-nine actinomycete strains were obtained on starch-casein agar media by dilution technique, only seven strains, named HP112, HP12, HP411, HPN11, HP 11, HPT13 and HPX12, showed significant antibacterial activity against both gram-positive and gram-negative bacteria (Bacillus subtilis ATCC 6633, Staphylococcus epidemidis ATCC 12228, Escherichia coli ATCC 11105). Further studies were carried out with the most active HP411strain against Candida albicans ATCC 10231. This strain could grow rapidly on starch casein agar and other media with high salt containing 7-10% NaCl at 28-30oC. Spore-chain of HP411 showed an elongated and circular shape with 10 to 30 spores/chain. Identification of the strain was carried out by employing the taxonomical studies including the 16S rRNA sequence. Based on phylogenetic and phenotypic evidence it is proposed that HP411 to be belongs to species Streptomyces variabilis. The potent of the crude extract of fermentation broth of HP411that are effective against wide range of pathogens: both gram-positive, gram-negative and fungi. Further studies revealed that the crude extract HP411 could obtain the anticancer activity for cancer cell lines: Hep-G2 (liver cancer cell line); RD (cardiac and skeletal muscle letters cell line); FL (membrane of the uterus cancer cell line). However, the actinomycetes from marine ecosystem will be useful for the discovery of new drugs in the furture.

Keywords: marine actinomycetes, antibacterial, anticancer, Streptomyces variabilis

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Authors: Gargi Prasad, Ashiho A. Mao, Deepu Vijayan, S. Mandal

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The main objective of the present study was to optimize and develop an efficient protocol for in vitro propagation of a medicinally important orchid Cephalantheropsis obcordata (Lindl.) Ormerod along with genetic stability analysis of regenerated plants. This plant has been traditionally used in Chinese folk medicine and the decoction of whole plant is known to possess anticancer activity. Nodal segments used as explants were inoculated on Murashige and Skoog (MS) medium supplemented with various concentrations of isopentenyl adenine (2iP). The rooted plants were successfully acclimatized in the greenhouse with 100% survival rate. Inter-simple sequence repeats (ISSR) markers were used to assess the genetic fidelity of in vitro raised plants and the mother plant. It was revealed that monomorphic bands showing the absence of polymorphism in all in vitro raised plantlets analyzed, confirming the genetic uniformity among the regenerants. Phytochemical analysis was done to compare the antioxidant activities and HPLC fingerprinting assay of 80% aqueous ethanol extract of the leaves and stem of in vitro and in vivo grown C. obcordata. The extracts of the plants were examined for their antioxidant activities by using free radical 1, 1-diphenyl-2-picryl hydrazyl (DPPH) scavenging method, 2,2’-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging ability, reducing power capacity, estimation of total phenolic content, flavonoid content and flavonol content. A simplified method for the detection of ascorbic acid, phenolic acids and flavonoids content was also developed by using reversed phase high-performance liquid chromatography (HPLC). This is the first report on the micropropagation, genetic integrity study and quantitative phytochemical analysis of in vitro regenerated plants of C. obcordata.

Keywords: Cephalantheropsis obcordata, genetic fidelity, ISSR markers, HPLC

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Authors: Maria Manzoor, Iram Gul, Muhammad Arshad, Jean Kallerhoff

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The potential of fungal isolates to be used in phytoremediation of widespread lead contaminated soil has been evaluated in this study. Five different fungal isolates (Trichoderma harzianum, Penicillium simplicissimum, Aspergillus flavus, Aspergillus niger and Mucor spp.) were obtained and tested for their tolerance to increasing concentration of lead (Pb) i.e. 100, 200, 300, 400 and 500 mgL-1 on PDA and PDB culture experiment. All strains were tolerant up to 500 mgL-1 following sequence; A. flavus > A. niger > Mucor spp. > P. simplicissimum > T. harzianum. Further the isolates were then monitored for possible effect on Pb solubility/mobility through soil incubation experiments and characterized for essays including pathogenicity, germination and root elongation and plant growth promoting activities including IAA (indole acetic acid), phosphorus solubilization and gibberellic acid (GA3) production. Results revealed that fungal isolates have positive effect on Pb mobility in soil and plant biomass production. Pb solubility was significantly (P> 0.05) increased in soil upon application of Mucor spp. P. simplicissimum and T. harzianum. when compared to control. Among different strains three isolates (Mucor spp., P. simplicissimum and T. harzianum) were nonpathogenic because no inhibitory effect of fungus was observed to plant growth when exposed to these strains in root shoot elongation essay. Particularly T. harzianum and P. simplicissimum showed great ability to increase root length by 1.1 and 1.3 folds and shoot length by 1.47 and 1.5 folds respectively under Pb stress (500 mgL-1). Significantly high production of IAA was observed in A. niger (26.7 μg/ml), Phosphorus solubilization was observed in T. harzianum (9.15 μg/ml) and GA3 production was observed in P. simplicissimum (11.02 μg/ml). From results it is concluded that Mucor spp., P. simplicissimum and T. harzianum have potential to increase Pb mobility and improving plant growth under highy Pb contamination, therefore can be used in microbially assisted phytoremediation of Pb contaminated soil.

Keywords: Pb tolerant fungus, Pb mobility, plant growth promoting activities, indole acetic acid (IAA)

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Authors: Ishani D. Goonasekara, Erio Camporesi, Timur Bulgakov, Rungtiwa Phookamsak, Kevin D. Hyde

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Phaeosphaeriaceae comprises a large number of species occurring mainly on grasses and cereal crops as endophytes, saprobes and especially pathogens. Parastagonospora is an important genus in Phaeosphaeriaceae that includes pathogens causing leaf and glume blotch on cereal crops. Currently, there are fifteen Parastagonospora species described, including both pathogens and saprobes. In this study, one sexual morph species and an asexual morph species, occurring as saprobes on members of Poaceae are introduced based on morphology and a combined molecular analysis of the LSU, SSU, ITS, and RPB2 gene sequence data. The sexual morph species Parastagonospora elymi was isolated from a Russian sample of Elymus repens, a grass commonly known as couch grass, and important for grazing animals, as a weed and used in traditional Austrian medicine. P. elymi is similar to the sexual morph of P. avenae in having cylindrical asci, bearing 8, overlapping biseriate, fusiform ascospores but can be distinguished by its subglobose to conical shaped, wider ascomata. In addition, no sheath was observed surrounding the ascospores. The asexual morph species was isolated from a specimen from Italy, on Dactylis glomerata, a commonly found grass distributed in temperate regions. It is introduced as Parastagonospora macrouniseptata, a coelomycete, and bears a close resemblance to P. allouniseptata and P. uniseptata in having globose to subglobose, pycnidial conidiomata and hyaline, cylindrical, 1-septate conidia. However, the new species could be distinguished in having much larger conidiomata. In the phylogenetic analysis which consisted of a maximum likelihood and Bayesian analysis P. elymi showed low bootstrap support, but well segregated from other strains within the Parastagonospora clade. P. neoallouniseptata formed a sister clade with P. allouniseptata with high statistical support.

Keywords: dothideomycetes, multi-gene analysis, Poaceae, saprobes, taxonomy

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Authors: Yemima Dani Riani, Anggraini Barlian

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Green turtle (Chelonia mydas) is one of well known long-lived turtle. Its age can reach 100 years old. Senescence in green turtle is an interesting process to study because until now no clear explanation has been established about senescence at cellular or molecular level in this species. Since 1999, green turtle announced as an endangered species. Hence, establishment of fibroblast skin cell culture of green turtle may be material for future study of senescence. One common marker used for detecting senescence is telomere shortening. Reduced telomerase activity, the reverse transcriptase enzyme which adds TTAGGG DNA sequence to telomere end, may also cause senescence. The purpose of this research are establish and identify green turtle fibroblast skin cell culture and also compare telomere length and telomerase activity from passage 5 and 14. Primary cell culture made with primary explant method then cultured in Leibovitz-15 (Sigma) supplemented by 10% Fetal Bovine Serum (Sigma) and 100 U/mL Penicillin/Streptomycin (Sigma) at 30 ± 1oC. Cells identified with Rabbit Anti-Vimentin Polyclonal Antibody (Abcam) and Goat Polyclonal Antibody (Abcam) using confocal microscope (Zeiss LSM 170). Telomere length obtained using TeloTAGGG Telomere Length Assay (Roche) while telomerase activity obtained using TeloTAGGG Telomerase PCR ElisaPlus (Roche). Primary cell culture from green turtle skin had fibroblastic morphology and immunocytochemistry test with vimentin antibody proved the culture was fibroblast cell. Measurement of telomere length and telomerase activity showed that telomere length and telomerase activity of passage 14 was greater than passage 5. However, based on morphology, green turtle fibroblast skin cell culture showed senescent morphology. Based on the analysis of telomere length and telomerase activity, suspected fibroblast skin cell culture of green turtles is not undergo aging through telomere shortening.

Keywords: cell culture, chelonia mydas, telomerase, telomere, senescence

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Authors: Armando A. Rodríguez, Emilio Salceda, Anoland Garateix, André J. Zaharenko, Steve Peigneur, Omar López, Tirso Pons, Michael Richardson, Maylín Díaz, Yasnay Hernández, Ludger Ständker, Jan Tytgat, Enrique Soto

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Acid-sensing ion channels are cation (Na+) channels activated by a pH drop. These proteins belong to the ENaC/degenerin superfamily of sodium channels. ASICs are involved in sensory perception, synaptic plasticity, learning, memory formation, cell migration and proliferation, nociception, and neurodegenerative disorders, among other processes; therefore those molecules that specifically target these channels are of growing pharmacological and biomedical interest. Sea anemones produce a large variety of ion channels peptide toxins; however, those acting on ligand-gated ion channels, such as Glu-gated, Ach-gated ion channels, and acid-sensing ion channels (ASICs), remain barely explored. The peptide PhcrTx1 is the first compound characterized from the sea anemone Phymanthus crucifer, and it constitutes a novel ASIC inhibitor. This peptide was purified by chromatographic techniques and pharmacologically characterized on acid-sensing ion channels of mammalian neurons using patch-clamp techniques. PhcrTx1 inhibited ASIC currents with an IC50 of 100 nM. Edman degradation yielded a sequence of 32 amino acids residues, with a molecular mass of 3477 Da by MALDI-TOF. No similarity to known sea anemone peptides was found in protein databases. The computational analysis of Cys-pattern and secondary structure arrangement suggested that this is a structurally ICK (Inhibitor Cystine Knot)-type peptide, a scaffold that had not been found in sea anemones but in other venomous organisms. These results show that PhcrTx1 represents the first member of a new structural group of sea anemones toxins acting on ASICs. Also, this peptide constitutes a novel template for the development of drugs against pathologies related to ASICs function.

Keywords: animal toxin, inhibitor cystine knot, ion channel, sea anemone

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