Search results for: gene modification

Authors: Y. Landkocz, P. Gosset, A. Héliot, C. Corbière, C. Vendeville, V. Keravec, S. Billet, A. Verdin, C. Monteil, D. Préterre, J-P. Morin, F. Sichel, T. Douki, P. J. Martin

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Air Pollution produced by automobile traffic is one of the main sources of pollutants in urban atmosphere and is largely due to exhausts of the diesel engine powered vehicles. The International Agency for Research on Cancer, which is part of the World Health Organization, classified in 2012 diesel engine exhaust as carcinogenic to humans (Group 1), based on sufficient evidence that exposure is associated with an increased risk for lung cancer. Amongst the strategies aimed at limiting exhausts in order to take into consideration the health impact of automobile pollution, filtration of the emissions and use of biofuels are developed, but their toxicological impact is largely unknown. Diesel exhausts are indeed complex mixtures of toxic substances difficult to study from a toxicological point of view, due to both the necessary characterization of the pollutants, sampling difficulties, potential synergy between the compounds and the wide variety of biological effects. Here, we studied the potential indirect genotoxicity of emission of Diesel engines through on-line exposure of rats in inhalation chambers to a subchronic high but realistic dose. Following exposure to standard gasoil +/- rapeseed methyl ester either upstream or downstream of a particle filter or control treatment, rats have been sacrificed and their lungs collected. The following indirect genotoxic parameters have been measured: (i) telomerase activity and telomeres length associated with rTERT and rTERC gene expression by RT-qPCR on frozen lungs, (ii) γH2AX quantification, representing double-strand DNA breaks, by immunohistochemistry on formalin fixed-paraffin embedded (FFPE) lung samples. These preliminary results will be then associated with global cellular response analyzed by pan-genomic microarrays, monitoring of oxidative stress and the quantification of primary DNA lesions in order to identify biological markers associated with a potential pro-carcinogenic response of diesel or biodiesel, with or without filters, in a relevant system of in vivo exposition.

Keywords: diesel exhaust exposed rats, γH2AX, indirect genotoxicity, lung carcinogenicity, telomerase activity, telomeres length

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Authors: Vipin Kumar Verma, Neeta Sehgal, Om Prakash

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Cyprinus carpio has a wide spread occurrence in the lakes and rivers of Europe and Asia. Heavy losses in natural environment due to anthropogenic activities, including pollution as well as pathogenic diseases have landed this fish in IUCN red list of vulnerable species. The significance of a suitable diet in preserving the health status of fish is widely recognized. In present study, artificial feed supplemented with leaves of two weed plants, Eichhornia crassipes and Ricinus communis were evaluated for their role on the fish immune system. To achieve this objective fish were acclimatized to laboratory conditions (25 ± 1 °C; 12 L: 12D) for 10 days prior to start of experiment and divided into 4 groups: non-challenged (negative control= A), challenged [positive control (B) and experimental (C & D)]. Group A, B were fed with non-supplemented feed while group C & D were fed with feed supplemented with 5% Eichhornia crassipes and 5% Ricinus communis respectively. Supplemented feeds were evaluated for their effect on growth, health, immune system and disease resistance in fish when challenged with Vibrio harveyi. Fingerlings of C. carpio (weight, 2.0±0.5 g) were exposed with fresh overnight culture of V. harveyi through bath immunization (concentration 2 Χ 105) for 2 hours on 10 days interval for 40 days. The growth was monitored through increase in their relative weight. The rate of mortality due to bacterial infection as well as due to effect of feed was recorded accordingly. Immune response of fish was analyzed through differential leucocyte count, percentage phagocytosis and phagocytic index. The effect of V. harveyi on fish organs were examined through histo-pathological examination of internal organs like spleen, liver and kidney. The change in the immune response was also observed through gene expression analysis. The antioxidant potential of plant extracts was measured through DPPH and FRAP assay and amount of total phenols and flavonoids were calculates through biochemical analysis. The chemical composition of plant’s methanol extracts was determined by GC-MS analysis, which showed presence of various secondary metabolites and other compounds. Investigation revealed immuno-modulatory effect of plants, when supplemented with the artificial feed of fish.

Keywords: immuno-modulation, gc-ms, Cyprinus carpio, Eichhornia crassipes, Ricinus communis

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Authors: Selisha A. Sooklal, Phelelani Mpangase, Shaun Aron, Karl Rumbold

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Organically bound fluorine (C-F bond) is extremely rare in nature. Despite this, the first fluorinated secondary metabolite, fluoroacetate, was isolated from the plant Dichapetalum cymosum (commonly known as Gifblaar). However, the enzyme responsible for fluorination (fluorinase) in Gifblaar was never isolated and very little progress has been achieved in understanding this process in higher plants. Fluorinated compounds have vast applications in the pharmaceutical, agrochemical and fine chemicals industries. Consequently, an enzyme capable of catalysing a C-F bond has great potential as a biocatalyst in the industry considering that the field of fluorination is virtually synthetic. As with any biocatalyst, a range of these enzymes are required. Therefore, it is imperative to expand the exploration for novel fluorinases. This study aimed to gain molecular insights into secondary metabolite biosynthesis in Gifblaar using a high-throughput sequencing-based approach. Mechanical wounding studies were performed using Gifblaar leaf tissue in order to induce expression of the fluorinase. The transcriptome of the wounded and unwounded plant was then sequenced on the Illumina HiSeq platform. A total of 26.4 million short sequence reads were assembled into 77 845 transcripts using Trinity. Overall, 68.6 % of transcripts were annotated with gene identities using public databases (SwissProt, TrEMBL, GO, COG, Pfam, EC) with an E-value threshold of 1E-05. Sequences exhibited the greatest homology to the model plant, Arabidopsis thaliana (27 %). A total of 244 annotated transcripts were found to be differentially expressed between the wounded and unwounded plant. In addition, secondary metabolic pathways present in Gifblaar were successfully reconstructed using Pathway tools. Due to lack of genetic information for plant fluorinases, a transcript failed to be annotated as a fluorinating enzyme. Thus, a local database containing the 5 existing bacterial fluorinases was created. Fifteen transcripts having homology to partial regions of existing fluorinases were found. In efforts to obtain the full coding sequence of the Gifblaar fluorinase, primers were designed targeting the regions of homology and genome walking will be performed to amplify the unknown regions. This is the first genetic data available for Gifblaar. It has provided novel insights into the mechanisms of metabolite biosynthesis and will allow for the discovery of the first eukaryotic fluorinase.

Keywords: biocatalyst, fluorinase, gifblaar, transcriptome

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Authors: Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Y. Rafii

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Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system can facilitate targeted genome editing in organisms. Dual or single guide RNA (gRNA) can program the Cas9 nuclease to cut target DNA in particular areas; thus, introducing concise mutations either via error-prone non-homologous end-joining repairing or via incorporating foreign DNAs by homologous recombination between donor DNA and target area. In spite of high demand of such promising technology, developing a well-organized procedure in order for reliable mining of potential target sites for gRNAs in large genomic data is still challenging. Hence, we aimed to perform high-throughput detection of target sites by specific PAMs for not only common Streptococcus pyogenes (SpCas9) but also for Neisseria meningitides (NmCas9) CRISPR-Cas systems. Previous research confirmed the successful application of such RNA-guided Cas9 orthologs for effective gene targeting and subsequently genome manipulation. However, Cas9 orthologs need their particular PAM sequence for DNA cleavage activity. Activity levels are based on the sequence of the protospacer and specific combinations of favorable PAM bases. Therefore, based on the specific length and sequence of PAM followed by a constant length of the target site for the two orthogonals of Cas9 protein, we created a reliable procedure to explore possible gRNA sequences. To mine CRISPR target sites, four different searching modes of sgRNA binding to target DNA strand were applied. These searching modes are as follows i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching, and iv) paired-gRNA searching. Finally, a complete list of all potential gRNAs along with their locations, strands, and PAMs sequence orientation can be provided for both SpCas9 as well as another potential Cas9 ortholog (NmCas9). The artificial design of potential gRNAs in a genome of interest can accelerate functional genomic studies. Consequently, the application of such novel genome editing tool (CRISPR/Cas technology) will enhance by presenting increased versatility and efficiency.

Keywords: CRISPR/Cas9 genome editing, gRNA mining, SpCas9, NmCas9

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Authors: Ashoke Priyadarshana Premananda

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As per the suggestions of previously conducted research in Counseling Psychology, the necessity of forming culture- friendly approaches has been strongly emphasized by a number of scholars in the field. In response to that, Multicultural-model of Buddhist Based Cognitive Behavioral Therapy (MMBCBT) has been formed as a culture-friendly therapeutic approach to address psychological disturbances (depression) in late adulthood. Elderly population in the world is on the rise by leaps and bounds, and forming a culture-based therapeutic model which is blended with Buddhist teachings has been the major objective of the study. Buddhist teachings and cultural applications, which were mapped onto Cognitive Behavioral Therapy (CBT) in the West, ultimately resulted in MMBCBT. Therefore, MMBCBT is a blend of cultural therapeutic techniques and the essence of certain Buddhist teachings extracted from five crucial suttas, which include CBT principles. In the process of mapping, MeghiyaSutta, GirimānandaSutta, SallekhaSutta, DvedhāvitakkaSutta, and Vitakka- SaṇṭhānaSutta have been taken into consideration mainly because of their cognitive behavioral content. The practical components of Vitakka- Saṇṭhānasutta (Aññanimittapabbaṃ) and Sallekhasutta (SallekhaPariyāya and CittuppādaPariyāya) have been used in the model while mindfulness of breathing was also carried out with the participants. Basically, multi-cultural therapeutic approaches of MMBCBT aim at modifying behavior (behavioral modification), whereas the rest is centered to the cognitive restructuring process. Therefore, MMBCBT is endowed with Behavioral Therapy (BT) and Cognitive Therapy(CT). In order to find out the validation of MMBCBT as a newly formed approach, it was then followed by mixed research (quantitative and qualitative research) with a sample selected from the elderly population following the purposive sampling technique. 40 individuals were selected from three elderly homes as per the purposive sampling technique. Elderly people identified to be depressed via Geriatric Depression Scale underwent MMBCBT for two weeks continuously while action research was being conducted simultaneously. Additionally, a Focus Group interview was carried out to support the action research. As per the research findings, people who identified depressed prior to the exposure to MMBCBT were found to be showing positive changes after they were exposed to the model. “Paired Sample t test” showed that the Multicultural Model of Buddhist based Cognitive Behavioral Therapy reduced depression of elderly people (The mean value (x̄) of the sample (level of depression) before the model was 10.7 whereas the mean value after the model was 7.5.). Most importantly, MMBCBT has been found to be effectively used with people from all walks of life despite religious diversities.

Keywords: buddhist psychotherapy, cognitive behavioral therapy in buddhism, counseling in cultural context, gerontology, and buddhism

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Authors: Eriko Ochiai, Fumiko Satoh, Keiko Miyashita, Yu Kakimoto, Motoki Osawa

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Sudden and unexpected deaths from unknown causes occur in infants and youths. Recently, molecular links between a part of these deaths and several genetic diseases are examined in the postmortem. For instance, hereditary long QT syndrome and Burgada syndrome are occasionally fatal through critical ventricular tachyarrhythmia. There are a large number of target genes responsible for such diseases, the conventional analysis using the Sanger’s method has been laborious. In this report, we attempted to analyze sudden deaths comprehensively using the next generation sequencing (NGS) technique. Multiplex PCR to subject’s DNA was performed using Ion AmpliSeq Library Kits 2.0 and Ion AmpliSeq Inherited Disease Panel (Life Technologies). After the library was constructed by emulsion PCR, the amplicons were sequenced 500 flows on Ion Personal Genome Machine System (Life Technologies) according to the manufacture instruction. SNPs and indels were analyzed to the sequence reads that were mapped on hg19 of reference sequences. This project has been approved by the ethical committee of Tokai University School of Medicine. As a representative case, the molecular analysis to a 40 years old male who received a diagnosis of Brugada syndrome demonstrated a total of 584 SNPs or indels. Non-synonymous and frameshift nucleotide substitutions were selected in the coding region of heart disease related genes of ANK2, AKAP9, CACNA1C, DSC2, KCNQ1, MYLK, SCN1B, and STARD3. In particular, c.629T-C transition in exon 3 of the SCN1B gene, resulting in a leu210-to-pro (L210P) substitution is predicted “damaging” by the SIFT program. Because the mutation has not been reported, it was unclear if the substitution was pathogenic. Sudden death that failed in determining the cause of death constitutes one of the most important unsolved subjects in forensic pathology. The Ion AmpliSeq Inherited Disease Panel can amplify the exons of 328 genes at one time. We realized the difficulty in selection of the true source from a number of candidates, but postmortem genetic testing using NGS analysis deserves of a diagnostic to date. We now extend this analysis to SIDS suspected subjects and young sudden death victims.

Keywords: postmortem genetic testing, sudden death, SIDS, next generation sequencing

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Authors: Guneet Saini, Shahrukh, Sunil Sharma

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Traffic congestion is the most critical issue faced by those in the transportation profession today. Over the past few years, roundabouts have been recognized as a measure to promote efficiency at intersections globally. In developing countries like India, this type of intersection still faces a lot of issues, such as bottleneck situations, long queues and increased waiting times, due to increasing traffic which in turn affect the performance of the entire urban network. This research is a case study of a non-conventional roundabout, in terms of geometric design, in a small town in India. These types of roundabouts should be analyzed for their functionality in mixed traffic conditions, prevalent in many developing countries. Microscopic traffic simulation is an effective tool to analyze traffic conditions and estimate various measures of operational performance of intersections such as capacity, vehicle delay, queue length and Level of Service (LOS) of urban roadway network. This study involves analyzation of an unsymmetrical non-circular 6-legged roundabout known as “Kala Aam Chauraha” in a small town Bulandshahr in Uttar Pradesh, India using VISSIM simulation package which is the most widely used software for microscopic traffic simulation. For coding in VISSIM, data are collected from the site during morning and evening peak hours of a weekday and then analyzed for base model building. The model is calibrated on driving behavior and vehicle parameters and an optimal set of calibrated parameters is obtained followed by validation of the model to obtain the base model which can replicate the real field conditions. This calibrated and validated model is then used to analyze the prevailing operational traffic performance of the roundabout which is then compared with a proposed alternative to improve efficiency of roundabout network and to accommodate pedestrians in the geometry. The study results show that the alternative proposed is an advantage over the present roundabout as it considerably reduces congestion, vehicle delay and queue length and hence, successfully improves roundabout performance without compromising on pedestrian safety. The study proposes similar designs for modification of existing non-conventional roundabouts experiencing excessive delays and queues in order to improve their efficiency especially in the case of developing countries. From this study, it can be concluded that there is a need to improve the current geometry of such roundabouts to ensure better traffic performance and safety of drivers and pedestrians negotiating the intersection and hence this proposal may be considered as a best fit.

Keywords: operational performance, roundabout, simulation, VISSIM

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Authors: Philippa Saunders, Claire Fletcher

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INTRODUCTION: Prostate cancer is the most prevalent malignancy affecting Western males. It is initially an androgen-dependent disease: androgens bind to the androgen receptor and drive the expression of genes that promote proliferation and evasion of apoptosis. Despite reduced androgen dependence in advanced prostate cancer, androgen receptor signaling remains a key driver of growth. Androgen deprivation therapy (ADT) is, therefore, a first-line treatment approach and works well initially, but resistance inevitably develops. Abiraterone and Enzalutamide are drugs widely used in ADT and are androgen synthesis and androgen receptor signaling inhibitors, respectively. The shortage of other treatment options means acquired resistance to these drugs is a major clinical problem. MicroRNAs (miRs) are important mediators of post-transcriptional gene regulation and show altered expression in cancer. Several have been linked to the development of resistance to ADT. Manipulation of such miRs may be a pathway to breakthrough treatments for advanced prostate cancer. This study aimed to validate ADT resistance-implicated miRs and their clinically relevant targets. MATERIAL AND METHOD: Small RNA-sequencing of Abiraterone- and Enzalutamide-resistant C42 prostate cancer cells identified subsets of miRs dysregulated as compared to parental cells. Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) was used to validate altered expression of candidate ADT resistance-implicated miRs 195-5p, 497-5p and 29a-5p in ADT-resistant and -responsive prostate cancer cell lines, patient-derived xenografts (PDXs) and primary prostate cancer explants. RESULTS AND DISCUSSION: This study suggests a possible role for miR-497-5p in the development of ADT resistance in prostate cancer. MiR-497-5p expression was increased in ADT-resistant versus ADT-responsive prostate cancer cells. Importantly, miR-497-5p expression was also increased in Enzalutamide-treated, castrated (ADT-mimicking) PDXs versus intact PDXs. MiR-195-5p was also elevated in ADT-resistant versus -responsive prostate cancer cells, while there was a drop in miR-29a-5p expression. Candidate clinically relevant targets of miR-497-5p in prostate cancer were identified by mining AGO-PAR-CLIP-seq data sets and may include AVL9 and FZD6. CONCLUSION: In summary, this study identified microRNAs that are implicated in prostate cancer resistance to androgen deprivation therapy and could represent novel therapeutic targets for advanced disease.

Keywords: microRNA, androgen deprivation therapy, Enzalutamide, abiraterone, patient-derived xenograft

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Authors: Marcin Jakiel, Maria Kurek, Karolina Gutkowska, Sylwia Sanakiewicz, Dominika Stolarczyk, Jakub Batko, Rafał Jakiel, Mateusz K. Hołda

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Proper imaging of the interventricular septum during endocavital lead implantation is essential for successful procedure. The interventricular septum is located oblique to the 3 main body planes and forms angles of 44.56° ± 7.81°, 45.44° ± 7.81°, 62.49° (IQR 58.84° - 68.39°) with the sagittal, frontal and transverse planes, respectively. The optimal left anterior oblique (LAO) projection is to have the septum aligned along the radiation beam and will be obtained for an angle of 53.24° ± 9,08°, while the best visualization of the septal surface in the right anterior oblique (RAO) projection is obtained by using an angle of 45.44° ± 7.81°. In addition, the RAO angle (p=0.003) and the septal slope to the transverse plane (p=0.002) are larger in the male group, but the LAO angle (p=0.003) and the dihedral angle that the septum forms with the sagittal plane (p=0.003) are smaller, compared to the female group. Analyzing the optimal RAO angle in cross-sections lying at the level of the connections of the septum with the free wall of the right ventricle from the front and back, we obtain slightly smaller angle values, i.e. 41.11° ± 8.51° and 43.94° ± 7.22°, respectively. As the septum is directed leftward in the apical region, the optimal RAO angle for this area decreases (16.49° ± 7,07°) and does not show significant differences between the male and female groups (p=0.23). Within the right ventricular apex, there is a cavity formed by the apical segment of the interventricular septum and the free wall of the right ventricle with a depth of 12.35mm (IQR 11.07mm - 13.51mm). The length of the septum measured in longitudinal section, containing 4 heart cavities, is 73.03mm ± 8.06mm. With the left ventricular septal wall formed by the interventricular septum in the apical region at a length of 10.06mm (IQR 8.86 - 11.07mm) already lies outside the right ventricle. Both mentioned lengths are significantly larger in the male group (p<0.001). For proper imaging of the septum from the right ventricular side, an oblique position of the visualization devices is necessary. Correct determination of the RAO and LAO angle during the procedure allows to improve the procedure performed, and possible modification of the visual field when moving in the anterior, posterior and apical directions of the septum will avoid complications. Overlooking the change in the direction of the interventricular septum in the apical region and a significant decrease in the RAO angle can result in implantation of the lead into the free wall of the right ventricle with less effective pacing and even complications such as wall perforation and cardiac tamponade. The demonstrated gender differences can also be helpful in setting the right projections. A necessary addition to the analysis will be a description of the area of the ventricular septum, which we are currently working on using autopsy material.

Keywords: anatomical variability, angle, electrocardiological procedure, intervetricular septum

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Authors: Shalini TV, Gangadharan GG, Sriranjini S Jaideep, ASN Seshasayee, Awadhesh Pandit

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Introduction: Prakriti (body-mind constitution of an individual) is a conventional, customized and unique understanding of which is essential for the personalized medicine described in Ayurveda, Indian System of Medicine. Based on the Doshas( functional, bio humoral unit in the body), individuals are categorized into three major Prakriti- Vata, Pitta, and Kapha. The human gut microbiome hosts plenty of highly diverse and metabolically active microorganisms, mainly dominated by the bacteria, which are known to influence the physiology of an individual. Few researches have shown the correlation between the Prakriti and the biochemical parameters. In this study, an attempt was made to explore any correlation between the Prakriti (phenotype of an individual) with the Genetic makeup of the gut microbiome in healthy individuals. Materials and methods: 270 multi-ethnic, healthy volunteers of both sex with the age group between 18 to 40 years, with no history of antibiotics in the last 6 months were recruited into three groups of Vata, Pitta, and Kapha. The Prakriti of the individual was determined using Ayusoft, a software designed by CDAC, Pune, India. The volunteers were subjected to initial screening for the assessment of their height, weight, Body Mass Index, Vital signs and Blood investigations to ensure they are healthy. The stool and saliva samples of the recruited volunteers were collected as per the standard operating procedure developed, and the bacterial DNA was isolated using Qiagen kits. The extracted DNA was subjected to 16s rRNA sequencing using the Illumina kits. The sequencing libraries are targeting the variable V3 and V4 regions of the 16s rRNA gene. Paired sequencing was done on the MiSeq system and data were analyzed using the CLC Genomics workbench 11. Results: The 16s rRNA sequencing of the V3 and V4 regions showed a diverse pattern in both the oral and stool microbial DNA. The study did not reveal any specific pattern of bacterial flora amongst the Prakriti. All the p-values were more than the effective alpha values for all OTUs in both the buccal cavity and stool samples. Therefore, there was no observed significant enrichment of an OTU in the patient samples from either the buccal cavity or stool samples. Conclusion: In healthy volunteers of multi-ethnicity, due to the influence of the various factors, the correlation between the Prakriti and the gut microbiome was not seen.

Keywords: gut microbiome, ayurveda Prakriti, sequencing, multi-ethnic urban population

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Authors: Soma Banerjee, Aamen Talukdar, Argha Mandal, Dipankar Chaudhuri

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Japanese Encephalitis is a major infectious disease with nearly half the world’s population living in areas where it is prevalent. Currently, treatment for it involves only supportive care and symptom management through vaccination. Due to the lack of antiviral drugs against Japanese Encephalitis Virus (JEV), the quest for such agents remains a priority. For these reasons, simulation studies of drug targets against JEV are important. Towards this purpose, docking experiments of the kinase inhibitors were done against the chosen target NS3 helicase as it is a nucleoside binding protein. Previous efforts regarding computational drug design against JEV revealed some lead molecules by virtual screening using public domain software. To be more specific and accurate regarding finding leads, in this study a proprietary software Schrödinger-GLIDE has been used. Druggability of the pockets in the NS3 helicase crystal structure was first calculated by SITEMAP. Then the sites were screened according to compatibility with ATP. The site which is most compatible with ATP was selected as target. Virtual screening was performed by acquiring ligands from databases: KinaseSARfari, KinaseKnowledgebase and Published inhibitor Set using GLIDE. The 25 ligands with best docking scores from each database were re-docked in XP mode. Protein structure alignment of NS3 was performed using VAST against MMDB, and similar human proteins were docked to all the best scoring ligands. The low scoring ligands were chosen for further studies and the high scoring ligands were screened. Seventy-three ligands were listed as the best scoring ones after performing HTVS. Protein structure alignment of NS3 revealed 3 human proteins with RMSD values lesser than 2Å. Docking results with these three proteins revealed the inhibitors that can interfere and inhibit human proteins. Those inhibitors were screened. Among the ones left, those with docking scores worse than a threshold value were also removed to get the final hits. Analysis of the docked complexes through 2D interaction diagrams revealed the amino acid residues that are essential for ligand binding within the active site. Interaction analysis will help to find a strongly interacting scaffold among the hits. This experiment yielded 21 hits with the best docking scores which could be investigated further for their drug like properties. Aside from getting suitable leads, specific NS3 helicase-inhibitor interactions were identified. Selection of Target modification strategies complementing docking methodologies which can result in choosing better lead compounds are in progress. Those enhanced leads can lead to better in vitro testing.

Keywords: antivirals, docking, glide, high-throughput virtual screening, Japanese encephalitis, ns3 helicase

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Authors: Oshma Chakoory, Sophie Comtet-Marre, Pierre Peyret

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Metagenomic classifiers are widely used for the taxonomic profiling of metagenomic data and estimation of taxa relative abundance. Small subunit rRNA genes are nowadays a gold standard for the phylogenetic resolution of complex microbial communities, although the power of this marker comes down to its use as full-length. We benchmarked the performance and accuracy of rRNA-specialized versus general-purpose read mappers, reference-targeted assemblers and taxonomic classifiers. We then built a pipeline called RiboTaxa to generate a highly sensitive and specific metataxonomic approach. Using metagenomics data, RiboTaxa gave the best results compared to other tools (Kraken2, Centrifuge (1), METAXA2 (2), PhyloFlash (3)) with precise taxonomic identification and relative abundance description, giving no false positive detection. Using real datasets from various environments (ocean, soil, human gut) and from different approaches (metagenomics and gene capture by hybridization), RiboTaxa revealed microbial novelties not seen by current bioinformatics analysis opening new biological perspectives in human and environmental health. In a study focused on corals’ health involving 20 metagenomic samples (4), an affiliation of prokaryotes was limited to the family level with Endozoicomonadaceae characterising healthy octocoral tissue. RiboTaxa highlighted 2 species of uncultured Endozoicomonas which were dominant in the healthy tissue. Both species belonged to a genus not yet described, opening new research perspectives on corals’ health. Applied to metagenomics data from a study on human gut and extreme longevity (5), RiboTaxa detected the presence of an uncultured archaeon in semi-supercentenarians (aged 105 to 109 years) highlighting an archaeal genus, not yet described, and 3 uncultured species belonging to the Enorma genus that could be species of interest participating in the longevity process. RiboTaxa is user-friendly, rapid, allowing microbiota structure description from any environment and the results can be easily interpreted. This software is freely available at https://github.com/oschakoory/RiboTaxa under the GNU Affero General Public License 3.0.

Keywords: metagenomics profiling, microbial diversity, SSU rRNA genes, full-length phylogenetic marker

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Authors: Sandisiwe Mangali, Graeme Bradley

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Genome is complete set of the organism's hereditary information encoded as either deoxyribonucleic acid or ribonucleic acid in most viruses. The three different types of genomes are nuclear, mitochondrial and the plastid genome and their sequences which are uncovered by genome sequencing are known as an archive for all genetic information and enable researchers to understand the composition of a genome, regulation of gene expression and also provide information on how the whole genome works. These sequences enable researchers to explore the population structure, genetic variations, and recent demographic events in threatened species. Particularly, genome sequencing refers to a process of figuring out the exact arrangement of the basic nucleotide bases of a genome and the process through which all the afore-mentioned genomes are sequenced is referred to as whole or complete genome sequencing. Gelidium pristoides is South African endemic Rhodophyta species which has been harvested in the Eastern Cape since the 1950s for its high economic value which is one motivation for its sequencing. Its endemism further motivates its sequencing for conservation biology as endemic species are more vulnerable to anthropogenic activities endangering a species. As sequencing, mapping and annotating the Gelidium pristoides genome is the aim of this study. To accomplish this aim, the genomic DNA was extracted and quantified using the Nucleospin Plank Kit, Qubit 2.0 and Nanodrop. Thereafter, the Ion Plus Fragment Library was used for preparation of a 600bp library which was then sequenced through the Ion S5 sequencing platform for two runs. The produced reads were then quality-controlled and assembled through the SPAdes assembler with default parameters and the genome assembly was quality assessed through the QUAST software. From this assembly, the plastid and the mitochondrial genomes were then sampled out using Gelidiales organellar genomes as search queries and ordered according to them using the Geneious software. The Qubit and the Nanodrop instruments revealed an A260/A280 and A230/A260 values of 1.81 and 1.52 respectively. A total of 30792074 reads were obtained and produced a total of 94140 contigs with resulted into a sequence length of 217.06 Mbp with N50 value of 3072 bp and GC content of 41.72%. A total length of 179281bp and 25734 bp was obtained for plastid and mitochondrial respectively. Genomic data allows a clear understanding of the genomic constituent of an organism and is valuable as foundation information for studies of individual genes and resolving the evolutionary relationships between organisms including Rhodophytes and other seaweeds.

Keywords: Gelidium pristoides, genome, genome sequencing and assembly, Ion S5 sequencing platform

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Authors: Sevde Altuntas, Fatih Buyukserin

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Alzheimer’s disease is responsible for irreversible neural damage of brain parts. One of the disease markers is Amyloid-β 1-42 protein that accumulates in the brain in the form plaques. The basic problem for detection of the protein is the low amount of protein that cannot be detected properly in body liquids such as blood, saliva or urine. To solve this problem, tests like ELISA or PCR are proposed which are expensive, require specialized personnel and can contain complex protocols. Therefore, Surface-enhanced Raman Spectroscopy (SERS) a good candidate for detection of Amyloid-β 1-42 protein. Because the spectroscopic technique can potentially allow even single molecule detection from liquid and solid surfaces. Besides SERS signal can be improved by using nanopattern surface and also is specific to molecules. In this context, our study proposes to fabricate diagnostic test models that utilize Au-coated nanopatterned polycarbonate (PC) surfaces modified with Thioflavin - T to detect low concentrations of Amyloid-β 1-42 protein in water and artificial saliva medium by the enhancement of protein SERS signal. The nanopatterned PC surface that was used to enhance SERS signal was fabricated by using Anodic Alumina Membranes (AAM) as a template. It is possible to produce AAMs with different column structures and varying thicknesses depending on voltage and anodization time. After fabrication process, the pore diameter of AAMs can be arranged with dilute acid solution treatment. In this study, two different columns structures were prepared. After a surface modification to decrease their surface energy, AAMs were treated with PC solution. Following the solvent evaporation, nanopatterned PC films with tunable pillared structures were peeled off from the membrane surface. The PC film was then modified with Au and Thioflavin-T for the detection of Amyloid-β 1-42 protein. The protein detection studies were conducted first in water via this biosensor platform. Same measurements were conducted in artificial saliva to detect the presence of Amyloid Amyloid-β 1-42 protein. SEM, SERS and contact angle measurements were carried out for the characterization of different surfaces and further demonstration of the protein attachment. SERS enhancement factor calculations were also completed via experimental results. As a result, our research group fabricated diagnostic test models that utilize Au-coated nanopatterned polycarbonate (PC) surfaces modified with Thioflavin-T to detect low concentrations of Alzheimer’s Amiloid – β protein in water and artificial saliva medium. This work was supported by The Scientific and Technological Research Council of Turkey (TUBITAK) Grant No: 214Z167.

Keywords: alzheimer, anodic aluminum oxide, nanotopography, surface enhanced Raman spectroscopy

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Authors: Hamed Ahari, Behrouz Akbari Adreghani, Vadood Razavilar, Amirali Anvar, Sima Moradi, Hourieh Shalchi

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Considering the ever increasing population and industrialization of the developmental trend of humankind's life, we are no longer able to detect the toxins produced in food products using the traditional techniques. This is due to the fact that the isolation time for food products is not cost-effective and even in most of the cases, the precision in the practical techniques like the bacterial cultivation and other techniques suffer from operator errors or the errors of the mixtures used. Hence with the advent of nanotechnology, the design of selective and smart sensors is one of the greatest industrial revelations of the quality control of food products that in few minutes time, and with a very high precision can identify the volume and toxicity of the bacteria. Methods and Materials: In this technique, based on the bacterial antibody connection to nanoparticle, a sensor was used. In this part of the research, as the basis for absorption for the recognition of bacterial toxin, medium sized silica nanoparticles of 10 nanometer in form of solid powder were utilized with Notrino brand. Then the suspension produced from agent-linked nanosilica which was connected to bacterial antibody was positioned near the samples of distilled water, which were contaminated with Staphylococcus aureus bacterial toxin with the density of 10-3, so that in case any toxin exists in the sample, a connection between toxin antigen and antibody would be formed. Finally, the light absorption related to the connection of antigen to the particle attached antibody was measured using spectrophotometry. The gene of 23S rRNA that is conserved in all Staphylococcus spp., also used as control. The accuracy of the test was monitored by using serial dilution (l0-6) of overnight cell culture of Staphylococcus spp., bacteria (OD600: 0.02 = 107 cell). It showed that the sensitivity of PCR is 10 bacteria per ml of cells within few hours. Result: The results indicate that the sensor detects up to 10-4 density. Additionally, the sensitivity of the sensors was examined after 60 days, the sensor by the 56 days had confirmatory results and started to decrease after those time periods. Conclusions: Comparing practical nano biosensory to conventional methods like that culture and biotechnology methods(such as polymerase chain reaction) is accuracy, sensitiveness and being unique. In the other way, they reduce the time from the hours to the 30 minutes.

Keywords: exotoxin, nanobiosensor, recognition, Staphylococcus aureus

Procedia PDF Downloads 365

Authors: Mirjana Petronijević, Sanja Panić, Aleksandra Cvetanović, Branko Kordić, Nenad Grba

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Enzyme peroxidases are biological catalysts and play a major role in phenolic wastewater treatments and other environmental applications. The most studied species from the peroxidases family is horseradish peroxidase (HRP). In environmental processes, HRP could be used in its free or immobilized form. Enzyme immobilization onto solid support is performed to improve the enzyme properties, prolong its lifespan and operational stability and allow its reuse in industrial applications. One of the enzyme supports of a newer generation is magnetic particles (MPs). Fe₃O₄ MPs are the most widely pursued immobilization of enzymes owing to their remarkable advantages of biocompatibility and non-toxicity. Also, MPs can be easily separated and recovered from the water by applying an external magnetic field. On the other hand, metals and metal oxides are not suitable for the covalent binding of enzymes, so it is necessary to perform their surface modification. Fe₃O₄ MPs functionalization could be performed during the process of their synthesis if it takes place in the presence of plant extracts. Extracts of plant material, such as wild plants, herbs, even waste materials of the food and agricultural industry (bark, shell, leaves, peel), are rich in various bioactive components such as polyphenols, flavonoids, sugars, etc. When the synthesis of magnetite is performed in the presence of plant extracts, bioactive components are incorporated into the surface of the magnetite, thereby affecting its functionalization. In this paper, the suitability of bio-magnetite as solid support for covalent immobilization of HRP across glutaraldehyde was examined. The activity of immobilized HRP at different pH values (4-9) and temperatures (20-80°C) and reusability were examined. Bio-MP was synthesized by co-precipitation method from Fe(II) and Fe(III) sulfate salts in the presence of water extract of the Allium cepa peel. The water extract showed 81% of antiradical potential (according to DPPH assay), which is connected with the high content of polyphenols. According to the FTIR analysis, the bio-magnetite contains oxygen functional groups (-OH, -COOH, C=O) suitable for binding to glutaraldehyde, after which the enzyme is covalently immobilized. The immobilized enzyme showed high activity at ambient temperature and pH 7 (30 U/g) and retained ≥ 80% of its activity at a wide range of pH (5-8) and temperature (20-50°C). The HRP immobilized onto bio-MPs showed remarkable stability towards temperature and pH variations compared to the free enzyme form. On the other hand, immobilized HRP showed low reusability after the first washing cycle enzyme retains 50% of its activity, while after the third washing cycle retains only 22%.

Keywords: bio-magnetite, enzyme immobilization, water extracts, environmental protection

Procedia PDF Downloads 195

Authors: Robert Pellerin, Michel Gamache, Remi Trudeau, Nathalie Perrier

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The context of large engineering projects is particularly favorable to the appearance of engineering changes and contractual modifications. These elements are potential causes for claims. In this paper, we investigate one of the critical components of the claim management process: the calculation of the impacts of changes in terms of losses of productivity due to the need to accelerate some project activities. When project changes are initiated, delays can arise. Indeed, project activities are often executed in fast-tracking in an attempt to respect the completion date. But the acceleration of project execution and the resulting rework can entail important costs as well as induce productivity losses. In the past, numerous methods have been proposed to quantify the duration of delays, the gains achieved by project acceleration, and the loss of productivity. The calculation related to those changes can be divided into two categories: direct cost and indirect cost. The direct cost is easily quantifiable as opposed to indirect costs which are rarely taken into account during the calculation of the cost of an engineering change or contract modification despite several research projects have been made on this subject. However, proposed models have not been accepted by companies yet, nor they have been accepted in court. Those models require extensive data and are often seen as too specific to be used for all projects. These techniques are also ignoring the resource constraints and the interdependencies between the causes of delays and the delays themselves. To resolve this issue, this research proposes a simulation model that mimics how major engineering changes or contract modifications are handled in large construction projects. The model replicates the use of overtime in a reactive scheduling mode in order to simulate the loss of productivity present when a project change occurs. Multiple tests were conducted to compare the results of the proposed simulation model with statistical analysis conducted by other researchers. Different scenarios were also conducted in order to determine the impact the number of activities, the time of occurrence of the change, the availability of resources, and the type of project changes on productivity loss. Our results demonstrate that the number of activities in the project is a critical variable influencing the productivity of a project. When changes occur, the presence of a large number of activities leads to a much lower productivity loss than a small number of activities. The speed of reducing productivity for 30-job projects is about 25 percent faster than the reduction speed for 120-job projects. The moment of occurrence of a change also shows a significant impact on productivity. Indeed, the sooner the change occurs, the lower the productivity of the labor force. The availability of resources also impacts the productivity of a project when a change is implemented. There is a higher loss of productivity when the amount of resources is restricted.

Keywords: engineering changes, indirect costs overtime, productivity, scheduling, simulation

Procedia PDF Downloads 220

Authors: Kamran Jawed, Anu Jose Mattam, Zia Fatma, Saima Wajid, Malik Z. Abdin, Syed Shams Yazdani

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Worldwide demand of natural and sustainable fuels and chemicals have encouraged researchers to develop microbial platform for synthesis of short chain fatty acids as they are useful precursors to replace petroleum-based fuels and chemicals. In this study, we evaluated the role of fatty acid synthesis and β-oxidation cycle of Escherichia coli to produce butyric acid, a 4-carbon short chain fatty acid, with the help of three thioesterases, i.e., TesAT from Anaerococcus tetradius, TesBF from Bryantella formatexigens and TesBT from Bacteroides thetaiotaomicron. We found that E. coli strain transformed with gene for TesBT and grown in presence of 8 g/L glucose produced maximum butyric acid titer at 1.46 g/L, followed by that of TesBF at 0.85 g/L and TesAT at 0.12 g/L, indicating that these thioesterases were efficiently converting short chain fatty acyl-ACP intermediate of fatty acid synthesis pathway into the corresponding acid. The titer of butyric acid varied significantly depending upon the plasmid copy number and strain genotype. Deletion of genes for fatty acyl-CoA synthetase and acyl-CoA dehydrogenase, which are involved in initiating the fatty acid degradation cycle, and overexpression of FadR, which is a dual transcriptional regulator and exerts negative control over fatty acid degradation pathway, reduced up to 30% of butyric acid titer. This observation suggested that β-oxidation pathway is working synergistically with fatty acid synthesis pathway in production of butyric acid. Moreover, accelerating the fatty acid elongation cycle by overexpressing acetyl-CoA carboxyltransferase (Acc) and 3-hydroxy-acyl-ACP dehydratase (FabZ) or by deleting FabR, the transcription suppressor of elongation, did not improve the butyric acid titer, rather favored the long chain fatty acid production. Finally, a balance between cell growth and butyric acid production was achieved with the use of phosphorous limited growth medium and 14.3 g/L butyric acid, and 17.5 g/L total free fatty acids (FFAs) titer was achieved during fed-batch cultivation. We have engineered an E. coli strain which utilizes the intermediate of both fatty acid synthesis and degradation pathway, i.e. butyryl-ACP and -CoA, to produce butyric acid from glucose. The strategy used in this study resulted in highest reported titers of butyric acid and FFAs in engineered E. coli.

Keywords: butenoic acid, butyric acid, Escherichia coli, fed-batch fermentation, short chain fatty acids, thioesterase

Procedia PDF Downloads 350

Authors: Valliyil Govindankutty

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Human civilizations across the globe stand testimony to water being one of the major interaction points with nature. The interactions with nature especially in drier areas revolve around water, be it harnessing, transporting, usage and management. Many ingenious ideas were born, nurtured and developed for harnessing, transporting, storing and distributing water through the areas in the drier parts of the world. Many methods of water extraction, collection and management could be found throughout the world, some of which are associated with efficient, sustained use of surface water, ground water and rain water. Karez is one such ingenious method of collection, transportation, storage and distribution of ground water. Most of the Karez systems in India were developed during reign of Muslim dynasties with ruling class descending from Persia or having influential connections and inviting expert engineers from there. Karez have strongly influenced the village socio-economic organisations due to multitude of uses they were brought into. These are masterpiece engineering structures to collect groundwater and direct it, through a subsurface gallery with a gradual slope, to surface canals that provide water to settlements and agricultural fields. This ingenious technology, karez was result of need for harnessing groundwater in arid areas like that of Bidar. The study views this traditional technology in historical perspective linked to sustainable utilization and management of groundwater and above all the immediate environment. The karez system is one of the best available demonstration of human ingenuity and adaptability to situations and locations of water scarcity. Bidar, capital of erstwhile Bahmani sultanate with a history of more than 700 years or more is one of the heritage cities of present Karnataka State. The unique water systems of Bidar along with other historic entities have been listed under World Heritage Watch List by World Monument Fund. The Historical or cultural landscape in Bidar is very closely associated to the natural resources of the region, Karez systems being one of the best examples. The Karez systems were the lifeline of Bidar’s historical period providing potable water, fulfilling domestic and irrigation needs, both within and outside the fort enclosures. These systems are still functional, but under great pressure and threat of rapid and unplanned urbanisation. The change in land use and fragmentation of land are already paving way for irreversible modification of the karez cultural and geographic landscape. The Paper discusses the significance of character defining elements of Naubad Karez Landscape, highlights the importance of conserving cultural heritage and presents a geographical approach to its revival.

Keywords: Karez, groundwater, traditional water harvesting, cultural heritage landscape, urban planning

Procedia PDF Downloads 472

Authors: David Taillis, Oussama Becissa, Julien Gabaston, Jean-Michel Merillon, Tristan Richard, Stephanie Cluzet

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Nowadays, there is a strong pressure to reduce the phytosanitary inputs of synthetic chemistry in vineyards. It is, therefore, necessary to find viable alternatives in order to protect the vine against its major diseases. For this purpose, we suggest the use of a plant extract enriched in antimicrobial compounds. Being produced from vine trunks and roots, which are co-products of wine production, the extract produced is part of a circular economy. The antimicrobial molecules present in this plant material are polyphenols and, more particularly, stilbenes, which are derived from a common base, the resveratrol unit, and that are well known vine phytoalexins. The stilbenoids were extracted from trunks and roots (30/70, w/w) by a double extraction with ethyl acetate followed by enrichment by liquid-liquid extraction. The produced extract was characterized by UHPLC-MS, then its antimicrobial activities were tested on Plasmopara viticola and Botrytis cinerea in the laboratory and/or in greenhouse and in vineyard. The major compounds were purified, and their antimicrobial activity was evaluated on B. cinerea. Moreover, after its spraying, the effect of the stilbene extract on the plant defence status was evaluated by analysis of defence gene expression. UHPLC-MS analysis revealed that the extract contains 50% stilbenes with resveratrol, ε-viniferin and r-viniferin as major compounds. The extract showed antimicrobial activities on P. viticola with IC₅₀ and IC₁₀₀ respectively of 90 and 300 mg/L in the laboratory. In addition, it inhibited 40% of downy mildew development in greenhouse. However, probably because of the sensitivity of stilbenes to the environment, such as UV degradation, no activity has been observed in vineyard towards P. viticola development. For B. cinerea, the extract IC50 was 123 mg/L, with resveratrol and ε-viniferin being the most active stilbenes (IC₅₀ of 88 and 142 mg/L, respectively). The analysis of the expression of defence genes revealed that the extract can induce the expression of some defence genes 24, 48, and 72 hours after treatment, meaning that the extract has a defence-stimulating effect at least for the first three days after treatment. In conclusion, we produced a plant extract enriched in stilbenes with antimicrobial properties against two major grapevine pathogenic agents P. viticola and B. cinerea. In addition, we showed that this extract displayed eliciting activity of plant defences. This extract can therefore represent, after formulation development, a viable eco-friendly alternative for vineyard protection. Subsequently, the effect of the stilbenoid extract on primary metabolism will be evaluated by quantitative NMR.

Keywords: antimicrobial, bioprotection, grapevine, Plasmopara viticola, stilbene

Procedia PDF Downloads 190

Authors: Zeynep Yazgan, Gökhan Aygün, Reyhan Çalışkan

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Objective: Invasive fungal infections are a serious threat in terms of morbidity and mortality, especially in immunocompromised patients. The most frequently isolated agents are Aspergillus genus fungi, and sensitivity to azoles, which are the first choice in treatment, decreases. In our study, we aimed to investigate the use of the agar plate screening method as a fast, easy, and practical method in determining azole resistance in Aspergillus spp. species. Methods: Our study was conducted with 125 Aspergillus spp. isolates produced from various clinical samples. Aspergillus spp. isolates were identified by conventional methods and azole resistance was determined by gradient test and agar plate screening method. Broth microdilution method was applied to resistant isolates, and CypA-L98H and CypA-M220 mutations in the cyp51A gene were investigated. Results: In our study, 55 A. fumigatus complex (44%), 42 A. flavus (33.6%), 6 A. terreus (5%), 4 A. niger (3%) and 18 Aspergillus spp. (14%) were identified. With the gradient test method, resistance to VOR and POS was detected in 1 (1.8%) of A.fumigatus isolates, and resistance to ITR was detected in 3 (5.45%). With the agar plate method, 1 of the A.fumigatus isolates (1.8%) had VOR, ITR, POS, 1 of the A.terreus isolates (16.7%) had VOR, 1 of the A.niger isolates (25%) had ITR. Resistance to VOR and POS was detected in 2 Aspergillus spp. isolates (11%), and resistance to ITR was detected in 1 (5.6%). Sensitivity and specificity were determined as 100% for VOR and POS in A. fumigatus species, 33.3% and 100% for ITR, respectively, 100% for ITR in A. flavus species, and 100% for ITR and POS in A. terreus species. By broth microdilution method in 7 isolates in which resistance was detected by gradient test and/or agar plate screening method; 1 A.fumigatus resistant to ITR, VOR, POS, 2 A.fumigatus resistant to ITR, 2 Aspergillus spp. ITR, VOR, POS MICs were determined as 2µg/ml and 8µg/ml, 8µg/ml and >32µg/ml, 0.5µg/ml and 4µg/ml, respectively. CypA-L98H mutations were detected in 5 of these isolates, CypA-M220 mutations were detected in 6, and no mutation was detected in 1. CypA-L98H and CypA-M220 mutations were detected in 1 isolate for which resistance was not detected. Conclusion: The need for rapid antifungal susceptibility screening tests is increasing in the treatment of aspergillosis. Although the sensitivity of the agar plate method was determined to be 33.3% for A.fumigatus ITR in our study, its sensitivity and specificity were determined to be 100% for ITR, VOR, and POS in other species. The low sensitivity value detected for A.fumigatus showed that agar plate drug concentrations should be updated in accordance with the latest regulations of EUCAST guidelines. The CypA-L98H and CypA-M220 mutations detected in our study suggested that the distribution of azole resistance-related mutations in different regions in our country should be investigated. In conclusion, it is thought that the agar plate method, which can be easily applied to detect azole resistance, is a fast and practical method in routine use and can contribute to both the determination of effective treatment strategies and the generation of epidemiological data.

Keywords: Aspergillus, agar plate, azole resistance, cyp51A, cypA-L98H, cypA-M220

Procedia PDF Downloads 45

Authors: Thomas Folegot, Arnaud Levaufre, Léna Bourven, Nicolas Kermagoret, Alexis Caillard, Roger Gallou

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Concern for negative impacts of anthropogenic noise on the ocean’s ecosystems has increased over the recent decades. This concern leads to a similar increased willingness to regulate noise-generating activities, of which shipping is one of the most significant. Dealing with ship noise requires not only knowledge about the noise from individual ships, but also how the ship noise is distributed in time and space within the habitats of concern. Marine mammals, but also fish, sea turtles, larvae and invertebrates are mostly dependent on the sounds they use to hunt, feed, avoid predators, during reproduction to socialize and communicate, or to defend a territory. In the marine environment, sight is only useful up to a few tens of meters, whereas sound can propagate over hundreds or even thousands of kilometers. Directive 2008/56/EC of the European Parliament and of the Council of June 17, 2008 called the Marine Strategy Framework Directive (MSFD) require the Member States of the European Union to take the necessary measures to reduce the impacts of maritime activities to achieve and maintain a good environmental status of the marine environment. The Ocean-Planner is a web-based platform that provides to regulators, managers of protected or sensitive areas, etc. with a decision support tool that enable to anticipate and quantify the effectiveness of management measures in terms of reduction or modification the distribution of underwater noise, in response to Descriptor 11 of the MSFD and to the Marine Spatial Planning Directive. Based on the operational sound modelling tool Quonops Online Service, Ocean-Planner allows the user via an intuitive geographical interface to define management measures at local (Marine Protected Area, Natura 2000 sites, Harbors, etc.) or global (Particularly Sensitive Sea Area) scales, seasonal (regulation over a period of time) or permanent, partial (focused to some maritime activities) or complete (all maritime activities), etc. Speed limit, exclusion area, traffic separation scheme (TSS), and vessel sound level limitation are among the measures supported be the tool. Ocean Planner help to decide on the most effective measure to apply to maintain or restore the biodiversity and the functioning of the ecosystems of the coastal seabed, maintain a good state of conservation of sensitive areas and maintain or restore the populations of marine species.

Keywords: underwater noise, marine biodiversity, marine spatial planning, mitigation measures, prediction

Procedia PDF Downloads 92

Authors: Taro Komori, Toshiki Gushi, Akihito Anzai, Taku Hirose, Kaoru Toko, Shinji Isogami, Takashi Suemasu

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Ferrimagnetic antiperovskite Mn₄₋ₓNiₓN thin film exhibits both small saturation magnetization and rather large perpendicular magnetic anisotropy (PMA) when x is small. Both of them are suitable features for application to current induced domain wall motion devices using spin transfer torque (STT). In this work, we successfully grew antiperovskite 30-nm-thick Mn₄₋ₓNiₓN epitaxial thin films on MgO(001) and STO(001) substrates by MBE in order to investigate their crystalline qualities and magnetic and magneto-transport properties. Crystalline qualities were investigated by X-ray diffraction (XRD). The magnetic properties were measured by vibrating sample magnetometer (VSM) at room temperature. Anomalous Hall effect was measured by physical properties measurement system. Both measurements were performed at room temperature. Temperature dependence of magnetization was measured by VSM-Superconducting quantum interference device. XRD patterns indicate epitaxial growth of Mn₄₋ₓNiₓN thin films on both substrates, ones on STO(001) especially have higher c-axis orientation thanks to greater lattice matching. According to VSM measurement, PMA was observed in Mn₄₋ₓNiₓN on MgO(001) when x ≤ 0.25 and on STO(001) when x ≤ 0.5, and MS decreased drastically with x. For example, MS of Mn₃.₉Ni₀.₁N on STO(001) was 47.4 emu/cm³. From the anomalous Hall resistivity (ρAH) of Mn₄₋ₓNiₓN thin films on STO(001) with the magnetic field perpendicular to the plane, we found out Mr/MS was about 1 when x ≤ 0.25, which suggests large magnetic domains in samples and suitable features for DW motion device application. In contrast, such square curves were not observed for Mn₄₋ₓNiₓN on MgO(001), which we attribute to difference in lattice matching. Furthermore, it’s notable that although the sign of ρAH was negative when x = 0 and 0.1, it reversed positive when x = 0.25 and 0.5. The similar reversal occurred for temperature dependence of magnetization. The magnetization of Mn₄₋ₓNiₓN on STO(001) increases with decreasing temperature when x = 0 and 0.1, while it decreases when x = 0.25. We considered that these reversals were caused by magnetic compensation which occurred in Mn₄₋ₓNiₓN between x = 0.1 and 0.25. We expect Mn atoms of Mn₄₋ₓNiₓN crystal have larger magnetic moments than Ni atoms do. The temperature dependence stated above can be explained if we assume that Ni atoms preferentially occupy the corner sites, and their magnetic moments have different temperature dependence from Mn atoms at the face-centered sites. At the compensation point, Mn₄₋ₓNiₓN is expected to show very efficient STT and ultrafast DW motion with small current density. What’s more, if angular momentum compensation is found, the efficiency will be best optimized. In order to prove the magnetic compensation, X-ray magnetic circular dichroism will be performed. Energy dispersive X-ray spectrometry is a candidate method to analyze the accurate composition ratio of samples.

Keywords: compensation, ferrimagnetism, Mn₄N, PMA

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Authors: E. Nemes-Nagy, E. Fogarasi, M. Croitoru, A. Nyárádi, K. Komlódi, S. Pál, A. Kovács, O. Kopácsy, R. Tripon, Z. Fazakas, C. Uzun, Z. Simon-Szabó, V. Balogh-Sămărghițan, E. Ernő Nagy, M. Szabó, M. Tilinca

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Intense oxidative stress, increased glycated hemoglobin and mineral imbalance represent risk factors for complications in diabetic patients. Cardiovascular complications are most common in these patients, including nephropathy. This study was conducted in 2015 at the Procardia Laboratory in Tîrgu Mureș, Romania on 40 type 2 diabetic adults. Routine biochemical tests were performed on the Konleab 20XTi analyzer (serum glucose, total cholesterol, LDL and HDL cholesterol, triglyceride, creatinine, urea). We also measured serum uric acid, magnesium and calcium concentration by photometric procedures, potassium, sodium and chloride by ion selective electrode, and chromium by atomic absorption spectrometry in a group of patients. Glycated hemoglobin (HbA1c) dosage was made by reflectometry. Urine analysis was performed using the HandUReader equipment. The level of oxidative stress was measured by serum malondialdehyde dosage using the thiobarbituric acid reactive substances method. MDRD (Modification of Diet in Renal Disease) formula was applied for calculation of creatinine-derived glomerular filtration rate. GraphPad InStat software was used for statistical analysis of the data. The diabetic subject included in the study presented high MDA concentrations, showing intense oxidative stress. Calcium was deficient in 5% of the patients, chromium deficiency was present in 28%. The atherogenic cholesterol fraction was elevated in 13% of the patients. Positive correlation was found between creatinine and MDRD-creatinine values (p<0.0001), 68% of the patients presented increased creatinine values. The majority of the diabetic patients had good control of their diabetes, having optimal HbA1c values, 35% of them presented fasting serum glucose over 120 mg/dl and 18% had glucosuria. Intense oxidative stress and mineral deficiencies can increase the risk of cardiovascular complications in diabetic patients in spite of their good metabolic balance. More than two third of the patients present biochemical signs of nephropathy, cystatin C dosage and microalbuminuria could reveal better the kidney disorder, but glomerular filtration rate calculation formulas are also useful for evaluation of renal function.

Keywords: cardiovascular risk, homocysteine, malondialdehyde, metformin, minerals, type 2 diabetes, vitamin B12

Procedia PDF Downloads 299

Authors: J. R. Büttler, T. Pham

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Basic understanding of interfacial mechanisms is of importance for the development of polymer composites. For this purpose, we need techniques to analyze the quality of interphases, their chemical and physical interactions and their strength and fracture resistance. In order to investigate the interfacial phenomena in detail, advanced characterization techniques are favorable. Dynamic mechanical thermal analysis (DMTA) using a rheological system is a sensitive tool. T-peel tests were performed with this system, to investigate the temperature-dependent peel behavior of woven textile composites. A model system was made of polyamide (PA) woven fabric laminated with films of polypropylene (PP) or PP modified by grafting with maleic anhydride (PP-g-MAH). Firstly, control measurements were performed with solely PP matrixes. Polymer melt investigations, as well as the extensional stress, extensional viscosity and extensional relaxation modulus at -10°C, 100 °C and 170 °C, demonstrate similar viscoelastic behavior for films made of PP-g-MAH and its non-modified PP-control. Frequency sweeps have shown that PP-g-MAH has a zero phase viscosity of around 1600 Pa·s and PP-control has a similar zero phase viscosity of 1345 Pa·s. Also, the gelation points are similar at 2.42*104 Pa (118 rad/s) and 2.81*104 Pa (161 rad/s) for PP-control and PP-g-MAH, respectively. Secondly, the textile composite was analyzed. The extensional stress of PA66 fabric laminated with either PP-control or PP-g-MAH at -10 °C, 25 °C and 170 °C for strain rates of 0.001 – 1 s^-1 was investigated. The laminates containing the modified PP need more stress for T-peeling. However, the strengthening effect due to the modification decreases by increasing temperature and at 170 °C, just above the melting temperature of the matrix, the difference disappears. Independent of the matrix used in the textile composite, there is a decrease of extensional stress by increasing temperature. It appears that the more viscous is the matrix, the weaker the laminar adhesion. Possibly, the measurement is influenced by the fact that the laminate becomes stiffer at lower temperatures. Adhesive lap-shear testing at room temperature supports the findings obtained with the T-peel test. Additional analysis of the textile composite at the microscopic level ensures that the fibers are well embedded in the matrix. Atomic force microscopy (AFM) imaging of a cross section of the composite shows no gaps between the fibers and matrix. Measurements of the water contact angle show that the MAH grafted PP is more polar than the virgin-PP, and that suggests a more favorable chemical interaction of PP-g-MAH with PA, compared to the non-modified PP. In fact, this study indicates that T-peel testing by DMTA is a technique to achieve more insights into polymeric textile composites.

Keywords: dynamic mechanical thermal analysis, interphase, polyamide, polypropylene, textile composite

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Authors: Andrey A. Lipovskii, Alexey V. Redkov, Vyacheslav V. Rusan, Dmitry K. Tagantsev, Valentina V. Zhurikhina

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The presented research is related to the development of recently proposed technique of the formation of composite materials, like optical glass-ceramics, with predetermined structure and properties of the crystalline component. The technique is based on the control of the size and concentration of the crystalline grains using the phenomenon of glass-ceramics decrystallization (vitrification) induced by ion-exchange. This phenomenon was discovered and explained in the beginning of the 2000s, while related theoretical description was given in 2016 only. In general, the developed theory enables one to model the process and optimize the conditions of ion-exchange processing of glass-ceramics, which provide given properties of crystalline component, in particular, profile of the average size of the crystalline grains. The optimization is possible if one knows two dimensionless parameters of the theoretical model. One of them (β) is the value which is directly related to the solubility of crystalline component of the glass-ceramics in the glass matrix, and another (γ) is equal to the ratio of characteristic times of ion-exchange diffusion and crystalline grain dissolution. The presented study is dedicated to the development of experimental technique and simulation which allow determining these parameters. It is shown that these parameters can be deduced from the data on the space distributions of diffusant concentrations and average size of crystalline grains in the glass-ceramics samples subjected to ion-exchange treatment. Measurements at least at two temperatures and two processing times at each temperature are necessary. The composite material used was a silica-based glass-ceramics with crystalline grains of Li2OSiO2. Cubical samples of the glass-ceramics (6x6x6 mm3) underwent the ion exchange process in NaNO3 salt melt at 520 oC (for 16 and 48 h), 540 oC (for 8 and 24 h), 560 oC (for 4 and 12 h), and 580 oC (for 2 and 8 h). The ion exchange processing resulted in the glass-ceramics vitrification in the subsurface layers where ion-exchange diffusion took place. Slabs about 1 mm thick were cut from the central part of the samples and their big facets were polished. These slabs were used to find profiles of diffusant concentrations and average size of the crystalline grains. The concentration profiles were determined from refractive index profiles measured with Max-Zender interferometer, and profiles of the average size of the crystalline grains were determined with micro-Raman spectroscopy. Numerical simulation were based on the developed theoretical model of the glass-ceramics decrystallization induced by ion exchange. The simulation of the processes was carried out for different values of β and γ parameters under all above-mentioned ion exchange conditions. As a result, the temperature dependences of the parameters, which provided a reliable coincidence of the simulation and experimental data, were found. This ensured the adequate modeling of the process of the glass-ceramics decrystallization in 520-580 oC temperature interval. Developed approach provides a powerful tool for fine tuning of the glass-ceramics structure, namely, concentration and average size of crystalline grains.

Keywords: diffusion, glass-ceramics, ion exchange, vitrification

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Authors: M. M. Essa, S. Subash, M. Akbar, S. Al-Adawi, A. Al-Asmi, G. J. Guillemein

Abstract:

Transgenic (tg) mice which contain an amyloid precursor protein (APP) gene mutation, develop extracellular amyloid beta (Aβ) deposition in the brain, and severe memory and behavioral deficits with age. These mice serve as an important animal model for testing the efficacy of novel drug candidates for the treatment and management of symptoms of Alzheimer's disease (AD). Several reports have suggested that oxidative stress is the underlying cause of Aβ neurotoxicity in AD. Date palm fruits contain very high levels of antioxidants and several medicinal properties that may be useful for improving the quality of life in AD patients. In this study, we investigated the effect of dietary supplementation of Omani date palm fruits on the memory, anxiety and learning skills along with inflammation in an AD mouse model containing the double Swedish APP mutation (APPsw/Tg2576). The experimental groups of APP-transgenic mice from the age of 4 months were fed custom-mix diets (pellets) containing 2% and 4% Date palm fruits. We assessed spatial memory and learning ability, psychomotor coordination, and anxiety-related behavior in Tg and wild-type mice at the age of 4-5 months and 18-19 months using the Morris water maze test, rota rod test, elevated plus maze test, and open field test. Further, inflammatory parameters also analyzed. APPsw/Tg2576 mice that were fed a standard chow diet without dates showed significant memory deficits, increased anxiety-related behavior, and severe impairment in spatial learning ability, position discrimination learning ability and motor coordination along with increased inflammation compared to the wild type mice on the same diet, at the age of 18-19 months In contrast, PPsw/Tg2576 mice that were fed a diet containing 2% and 4% dates showed a significant improvements in memory, learning, locomotor function, and anxiety with reduced inflammatory markers compared to APPsw/Tg2576 mice fed the standard chow diet. Our results suggest that dietary supplementation with dates may slow the progression of cognitive and behavioral impairments in AD. The exact mechanism is still unclear and further extensive research needed.

Keywords: Alzheimer's disease, date palm fruits, Oman, cognitive decline, memory loss, anxiety, inflammation

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Authors: Konstantin S. Vainutis, Mark E. Andreev, Anastasia N. Voronova, Mikhail Yu. Shchelkanov

Abstract:

Introduction: The trematodes from the family Cyclocoelidae (cyclocoelids) belong to the superfamily Echinostomatoidea infecting air sacs and trachea of wild birds. At present, the family Cyclocoelidae comprises nine valid genera in three subfamilies: Cyclocoelinae (type taxon), Haematotrephinae, and Typhlocoelinae. To our best knowledge, in this study, molecular genetic methods were used for the first time for studying cyclocoelids from the Russian Far East. Here we provide the data on the morphology and phylogeny of cyclocoelids from gadwall from the Russian Far East. The morphological and genetic data obtained for cyclocoelids indicated the necessity to revise the previously proposed classification within the family Cyclocoelidae. Objectives: The first objective was performing the morphological study of cyclocoelids found in M. strepera from the Russian Far East. The second objective is to reconstruct the phylogenetic relationships of the studied trematodes with other cyclocoelids using the 28S gene. Material and methods: During the field studies in the Khasansky district of the Primorsky region, 21 cyclocoelids were recovered from the air sacs of a single gadwall Mareca strepera. Seven samples of cyclocoelids were overstained in alum carmine, dehydrated in a graded ethanol series, cleared in clove oil, and mounted in Canada balsam. Genomic DNA was extracted from four cyclocoelids using the alkaline lysis method HotShot. The 28S rDNA fragment was amplified using the forward primer Digl2 and the reverse primer 1500R. Results: According to morphological features (ovary intratesticular, forming a triangle with the testes), the studied worms belong to the subfamily Cyclocoelinae Stossich, 1902. In particular, the highest morphological similarity was observed in relation to the trematodes of the genus Cyclocoelum Brandes, 1892 – genital pores are pharyngeal. However, the genetic analysis has shown significant discrepancies between the trematodes studied regarding the genus Cyclocoelum. On the phylogenetic tree, these trematodes took the sister position in relation to the genus Morishitium (previously considered in the subfamily Szidatitrematinae). Conclusion: Based on the results of the morphological and genetic studies, cyclocoelids isolated from Mareca strepera are suggested to be described in the previously unknown genus and differentiated from the type genus Cyclocoelum of the type subfamily Cyclocoelinae. Considering the available molecular data, including described cyclocoelids, the family Cyclocoelidae comprises ten valid genera in the three subfamilies mentioned above.

Keywords: new species, trematoda, phylogeny, cyclocoelidae

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Authors: Francesco Pantano, Marta Fogolari, Michele Iuliani, Sonia Simonetti, Silvia Cavaliere, Marco Russano, Fabrizio Citarella, Bruno Vincenzi, Silvia Angeletti, Giuseppe Tonini

Abstract:

Background: Although immune checkpoint inhibitors (ICIs) have changed the treatment paradigm of non–small cell lung cancer (NSCLC), these drugs fail to elicit durable responses in the majority of NSCLC patients. The gut microbiota, able to regulate immune responsiveness, is emerging as a promising, modifiable target to improve ICIs response rates. Since the oral microbiome has been demonstrated to be the primary source of bacterial microbiota in the lungs, we investigated its composition as a potential predictive biomarker to identify and select patients who could benefit from immunotherapy. Methods: Thirty-five patients with stage IV squamous and non-squamous cell NSCLC eligible for an anti-PD-1/PD-L1 as monotherapy were enrolled. Saliva samples were collected from patients prior to the start of treatment, bacterial DNA was extracted using the QIAamp® DNA Microbiome Kit (QIAGEN) and the 16S rRNA gene was sequenced on a MiSeq sequencing instrument (Illumina). Results: NSCLC patients were dichotomized as “Responders” (partial or complete response) and “Non-Responders” (progressive disease), after 12 weeks of treatment, based on RECIST criteria. A prevalence of the phylum Candidatus Saccharibacteria was found in the 10 responders compared to non-responders (abundance 5% vs 1% respectively; p-value = 1.46 x 10-7; False Discovery Rate (FDR) = 1.02 x 10-6). Moreover, a higher prevalence of Saccharibacteria Genera Incertae Sedis genus (belonging to the Candidatus Saccharibacteria phylum) was observed in "responders" (p-value = 6.01 x 10-7 and FDR = 2.46 x 10-5). Finally, the patients who benefit from immunotherapy showed a significant abundance of TM7 Phylum Sp Oral Clone FR058 strain, member of Saccharibacteria Genera Incertae Sedis genus (p-value = 6.13 x 10-7 and FDR=7.66 x 10-5). Conclusions: These preliminary results showed a significant association between oral microbiota and ICIs response in NSCLC patients. In particular, the higher prevalence of Candidatus Saccharibacteria phylum and TM7 Phylum Sp Oral Clone FR058 strain in responders suggests their potential immunomodulatory role. The study is still ongoing and updated data will be presented at the congress.

Keywords: oral microbiota, immune checkpoint inhibitors, non-small cell lung cancer, predictive biomarker

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Authors: Ali H. Daraji, Jack M. Hale, Ye Jianqiao

Abstract:

With the extensive use of high specific strength structures to optimise the loading capacity and material cost in aerospace and most engineering applications, much effort has been expended to develop intelligent structures for active vibration reduction and structural health monitoring. These structures are highly flexible, inherently low internal damping and associated with large vibration and long decay time. The modification of such structures by adding lightweight piezoelectric sensors and actuators at efficient locations integrated with an optimal control scheme is considered an effective solution for structural vibration monitoring and controlling. The size and location of sensor and actuator are important research topics to investigate their effects on the level of vibration detection and reduction and the amount of energy provided by a controller. Several methodologies have been presented to determine the optimal location of a limited number of sensors and actuators for small-scale structures. However, these studies have tackled this problem directly, measuring the fitness function based on eigenvalues and eigenvectors achieved with numerous combinations of sensor/actuator pair locations and converging on an optimal set using heuristic optimisation techniques such as the genetic algorithms. This is computationally expensive for small- and large-scale structures subject to optimise a number of s/a pairs to suppress multiple vibration modes. This paper proposes an efficient method to determine optimal locations for a limited number of sensor/actuator pairs for active vibration reduction of a flexible structure based on finite element method and Hamilton’s principle. The current work takes the simplified approach of modelling a structure with sensors at all locations, subjecting it to an external force to excite the various modes of interest and noting the locations of sensors giving the largest average percentage sensors effectiveness measured by dividing all sensor output voltage over the maximum for each mode. The methodology was implemented for a cantilever plate under external force excitation to find the optimal distribution of six sensor/actuator pairs to suppress the first six modes of vibration. It is shown that the results of the optimal sensor locations give good agreement with published optimal locations, but with very much reduced computational effort and higher effectiveness. Furthermore, it is shown that collocated sensor/actuator pairs placed in these locations give very effective active vibration reduction using optimal linear quadratic control scheme.

Keywords: optimisation, plate, sensor effectiveness, vibration control

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