Search results for: gene identification

Authors: Punnoose A. K.

Abstract:

This paper presents an approach for identifying noisy speech recording using a multi-layer perception (MLP) trained to predict phonemes from acoustic features. Characteristics of the MLP posteriors are explored for clean speech and noisy speech at the frame level. Appropriate density functions are used to fit the softmax probability of the clean and noisy speech. A function that takes into account the ratio of the softmax probability density of noisy speech to clean speech is formulated. These phoneme independent scoring is weighted using a phoneme-specific weightage to make the scoring more robust. Simple thresholding is used to identify the noisy speech recording from the clean speech recordings. The approach is benchmarked on standard databases, with a focus on precision.

Keywords: noisy speech identification, speech pre-processing, noise robustness, feature engineering

Procedia PDF Downloads 127

Authors: Tayaba Dastgeer, Farhan Rasheed, Muhammad Saeed, Maqsood Ahmad, Zia Ashraf, Abdul Waheed, Muhammad Kamran, Mohsin Khurshid

Abstract:

Objectives: The study aimed to determine the efficacy of linezolid against clinical isolates of methicillin-resistant staphylococcus aureus (MRSA). Methodology: This cross-sectional study was conducted in the microbiology department of Allama Iqbal Medical College Lahore from August 2017 to September 2019. Isolates were confirmed as MRSA via the presence of the mec-A gene. Confirmed MRSA isolates were processed for susceptibility testing against different antimicrobials, especially linezolid, via the disc diffusion method. Zone sizes were interpreted according to CLSI guidelines. Results: Various types of clinical samples were included in the study; however, the highest frequency of MRSA isolates was found in pus samples, followed by other clinical samples. Among hospitalized patients, most MRSA isolates were obtained from patients in the surgical ward. Of 243 mec-A gene detected isolates, Vancomycin and linezolid showed 100% susceptibility, chloramphenicol showed declining resistance 78 (32.09%), and emerging sensitivity 165 (67.90%) against MRSA. Conclusion: Linezolid is a very efficient drug against MRSA, but the use of this novel drug must be conserved for vancomycin-resistant Staphylococcus aureus or when more resistant pathogens are suspected.

Keywords: MRSA, chloramphenicol, linezolid, nosocomial infections

Procedia PDF Downloads 97

Authors: Shauma L. Tamba

Abstract:

This study examined whether morality is the most important aspect in actual behavior. The prediction was that people tend to behave in line with moral (as compared to competence) norms, especially when such norms are presented by their ingroup. The actual behavior that was tested was support for a military intervention without a mandate from the UN. In addition, this study also examined whether identification with the ingroup and religion moderated the effect of group and norm on support for the norm that was prescribed by their ingroup. The prediction was that those who identified themselves higher with the ingroup moral would show a higher support for the norm. Furthermore, the prediction was also that those who have religion would show a higher support for the norm in the ingroup moral rather than competence. In an online survey, participants were asked to read a scenario in which a military intervention without a mandate was framed as either the moral (but stupid) or smart (but immoral) thing to do by members of their own (ingroup) or another (outgroup) society. This study found that when people identified themselves with the smart (but immoral) norm, they showed a higher support for the norm. However, when people identified themselves with the moral (but stupid) norm, they tend to show a lesser support towards the norm. Most of the results in the study did not support the predictions. Possible explanations and implications are discussed.

Keywords: morality, competence, ingroup identification, religion, group norm

Procedia PDF Downloads 408

Authors: Zaide Montes Ortiz, Jorge Alberto Molina, Alejandro Reyes

Abstract:

Insects are extremely successful organisms. A sophisticated olfactory system is in part responsible for their survival and reproduction. The detection of volatile organic compounds can positively or negatively affect many behaviors in insects. Compounds such as carbon dioxide (CO2), ammonium, indol, and lactic acid are essential for many species of mosquitoes like Anopheles gambiae in order to locate vertebrate hosts. For instance, in A. gambiae, the olfactory receptor AgOR2 is strongly activated by indol, which accounts for almost 30% of human sweat. On the other hand, in some insects of agricultural importance, the detection and identification of pheromone receptors (PRs) in lepidopteran species has become a promising field for integrated pest management. For example, with the disruption of the pheromone receptor, BmOR1, mediated by transcription activator-like effector nucleases (TALENs), the sensitivity to bombykol was completely removed affecting the pheromone-source searching behavior in male moths. Then, the detection and identification of olfactory receptors in the genomes of insects is fundamental to improve our understanding of the ecological interactions, and to provide alternatives in the integrated pests and vectors management. Hence, the objective of this study is to propose a bioinformatic workflow to enhance the detection and identification of potential olfactory receptors in genomes of relevant insects. Applying Hidden Markov models (Hmms) and different computational tools, potential candidates for pheromone receptors in Tuta absoluta were obtained, as well as potential carbon dioxide receptors in Rhodnius prolixus, the main vector of Chagas disease. This study showed the validity of a bioinformatic workflow with a potential to improve the identification of certain olfactory receptors in different orders of insects.

Keywords: bioinformatic workflow, insects, olfactory receptors, protein prediction

Procedia PDF Downloads 149

Authors: Alisha Akya, Afsaneh salami

Abstract:

Background and Objective: Pseudomonas aeruginosa is an opportunistic pathogen associated with nosocomial infections. One of the major concerns for the treatment of P. aeruginosa infections is its resistant to a variety of antibiotics. The purpose of this study was to assess the dissemination of p. aeruginosa isolates obtained from major hospitals in Kermanshah, west of Iran. Materials and Methods: Antibiotic susceptibility testing was performed using the minimal inhibitory concentrations. Mettalo-beta-lactamase was investigated using the double disk diffusion (DDST) test and PCR. Molecular typing was performed by pulsed-field gel electrophoresis (PFGE). Results: The 60 P. aeruginosa isolates, 30 (50%) were resistant to gentamicin, 38 (63/3%) to piperacilin, 42 (70%) to ceftazidime, and 45 (75%) to cefepime. Twenty-nine (48/3%) isolates were MBLs producer based on the DDST test. Five (8/3%) isolates were positive for VIM gene and 4 of them were from burn specimens. PFGE analysis among MBLs producers revealed 12 distinct genotype patterns. A pattern covering the highest number of strains was determined as the dominant clone. Conclusions: Our study showed that P. aeruginosa strains can be spread between patients in hospitals or acquired from different environmental sources. P. aeruginosa isolates were highly resistant to antibiotics and, therefore, the susceptibility of isolates to antibiotics should be tested before treatment. Given the clinical significance of MBLs producing isolates, identification of these organisms is essential in the hospitals in order to get a better therapeutic response and control of bacterial dissemination.

Keywords: clonal dissemination, mettalo-beta-lactamase, Pseudomonas aeruginosa, PFGE

Procedia PDF Downloads 326

Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

Abstract:

A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: bacteria chromosome, bacterial identification, sequence, primer generation

Procedia PDF Downloads 193

Authors: Xiaoxing Ye

Abstract:

To investigate complex rumen microbial communities, 16S ribosomal RNA (rRNA) sequencing is widely used. Here, we evaluated the impact of bioinformatics pipelines on the observation of OTUs and taxonomic classification of 750 cattle rumen microbial samples by comparing three commonly used pipelines (LotuS, UPARSE, and QIIME) with Usearch. In LotuS-based analyses, 189 archaeal and 3894 bacterial OTUs were observed. The observed OTUs for the Usearch analysis were significantly larger than the LotuS results. We discovered 1495 OTUs for archaea and 92665 OTUs for bacteria using Usearch analysis. In addition, taxonomic assignments were made for the rumen microbial samples. All pipelines had consistent taxonomic annotations from the phylum to the genus level. A difference in relative abundance was calculated for all microbial levels, including Bacteroidetes (QIIME: 72.2%, Usearch: 74.09%), Firmicutes (QIIME: 18.3%, Usearch: 20.20%) for the bacterial phylum, Methanobacteriales (QIIME: 64.2%, Usearch: 45.7%) for the archaeal class, Methanobacteriaceae (QIIME: 35%, Usearch: 45.7%) and Methanomassiliicoccaceae (QIIME: 35%, Usearch: 31.13%) for archaeal family. However, the most prevalent archaeal class varied between these two annotation pipelines. The Thermoplasmata was the top class according to the QIIME annotation, whereas Methanobacteria was the top class according to Usearch.

Keywords: cattle rumen, rumen microbial, 16S rRNA gene sequencing, bioinformatics pipeline

Procedia PDF Downloads 88

Authors: Mahsa Jalili, Essa Ehsan Khan, Signe Dille Lovmo, Augustine Akruwe, Egil Lien, Rolf Erik Olsen, Trygve Sigholt, Atle Magnus Bones

Abstract:

Data from the Norwegian Directorate of Fisheries reported that >1.2 million tons of Atlantic salmon were produced in Norway aquaculture industry in 2016. Peroxisome proliferator-activated receptors (PPARs) are one of the key transcription factor families that respond to nutritional ligands. Recent studies have shown the connection between PPARs with lipid and carbohydrate metabolism in aquaculture. To our knowledge, there is no published data about the effects of krill meal, soybean meal, Bactocell ® and butyrate feedings compared to control group on PPARs gene and protein expressions in Atlantic salmon. Fish, 1year +postsmolt, average weight 250 gram were cultured for 12 weeks after acclimatization by control commercial feeding in 2 weeks after hatchery. Water oxygen rate, salinity, and temperature were monitored every second day. At the end of the trial, fish were taken from tanks randomly, and four replicates per group were collected and stored in -80 freezers until analysis. Total RNA extracted from posterior part of dorsal fin muscle tissues and Nanodrop and Bioanalyzer was used to check the quality of RNA. Gene expression of PPAR α, β and γ were determined by RT-PCR. The expression of genes of interest was measured relative to control group after normalization to three reference genes. Total protein concentration was calculated by Bradford method, and protein expression was determined with primary PPARγ antibody by western blot. All data were analyzed by ANOVA followed by Benjamini-Hochberg and Bonferroni tests. Probability values <0.05 considered significant. Bactocell® and butyrate groups showed significantly lower PPARα expression. PPARβ and γ were not significantly different among groups. PPARγ mRNA expression was approximately consistent with protein expression pattern, except than butyrate group showed lower mRNA level. The order of PPARγ expression was Bactocell® > soy meal > butyrate > krill meal > control respectively. PPARβ gene expression decreased more in soy meal > butyrate > krill meal > Bactocell® > control groups respectively. In conclusion, the increased expression of PPARγ and α is proposed to represent a reduction tendency of lipid storage in fish fed by Bactocell®, butyrate, soy and krill meal.

Keywords: aquaculture, blotting western, gene expression, krill protein extract, prebiotics, probiotics, Salmo salar

Procedia PDF Downloads 225

Authors: Pattanapon Kayansamruaj, Ha Thanh Dong, Nopadon Pirarat, Channarong Rodkhum

Abstract:

Streptococcus iniae (SI) is a devastating pathogenic bacteria causing heavy mortality in farmed fish. The application of commercialized bacterin vaccine has been reported failures as the outbreaks of the new serotype of SI were emerged in farms after vaccination and subsequently caused severe losses. In the present study, we attempted to develop effective DNA vaccines against SI infection using Nile tilapia (Oreochromis niloticus) as an animal model. Two monovalent DNA vaccines were constructed by the insertion of coding sequences of cell wall-associated virulence factors-encoding genes, comprised of eno (α-enolase) and mtsB (hydrophobic membrane protein), into cytomegalovirus expression vector (pCI-neo). In the animal trial, 30-g Nile tilapia were injected intramuscularly with 15 µg of each vaccine (mock vaccine group was injected by naked pCI-neo) and maintained for 35 days prior challenging with pathogenic SI at the dosage of 107 CFU/fish. At 13 days post-challenge, the relative percent survival of pEno, pMtsB and mock vaccine were 57%, 45% and 27%, respectively. The expression levels of immune responses-associated genes, namely, IL1β, TNF-α, TGF-β, COX2, IL-6, IL-12 and IL-13, were investigated from the spleen of experimental animal at 7 days post-vaccination (PV) and 7 days post-challenge (PC) using quantitative RT-PCR technique. Generally, at 7 days PV, the pEno vaccinated group exhibited highest level of up-regulation (1.7 to 2.9 folds) of every gene, but TGF-β, comparing to pMtsB and mock vaccine groups. However, at 7 days PC, pEno group showed significant up-regulation (1.4 to 8.5 folds) of immune-related genes as similar as mock vaccine group, while pMtsB group had lowest level of up-regulation (0.7 to 3.3 folds). Summarily, this study indicated that the pEno and pMtsB vaccines could elicit the immune responses of the fish and the magnitude of gene expression at 7 days PV was also consistent with the protection level conferred by the vaccine.

Keywords: gene expression, DNA vaccine, Nile tilapia, Streptococcus iniae

Procedia PDF Downloads 329

Authors: Abdulwahab Kammon, Tan Sheau Wei, Abdul Rahman Omar, Abdunaser Dayhum, Ibrahim Eldghayes, Monier Sharif

Abstract:

Infectious bronchitis virus (IBV) is a very dynamic and evolving virus which causing major economic losses to the global poultry industry. Recently, the Libyan poultry industry faced severe outbreak of respiratory distress associated with high mortality and dramatic drop in egg production. Tracheal and cloacal swabs were analyzed for several poultry viruses. IBV was detected using SYBR Green I real-time PCR detection based on the nucleocapsid (N) gene. Sequence analysis of the partial N gene indicated high similarity (~ 94%) to IBV strain 3382/06 that was isolated from Taiwan. Even though the IBV strain 3382/06 is more similar to that of the Mass type H120, the isolate has been implicated associated with intertypic recombinant of 3 putative parental IBV strains namely H120, Taiwan strain 1171/92 and China strain CK/CH/LDL/97I. Complete sequencing and antigenicity studies of the Libya IBV strains are currently underway to determine the evolution of the virus and its importance in vaccine induced immunity. In this paper, we documented for the first time the presence of possibly variant IBV strain from Libya which required a dramatic change in the vaccination program.

Keywords: Libya, infectious bronchitis, molecular characterization, viruses, vaccine

Procedia PDF Downloads 470

Authors: Zaouche Mohamed, Amini Mohamed, Foughali Khaled, Aitkaid Souhila, Bouchiha Nihad Sarah

Abstract:

The aerodynamic coefficients are important in the evaluation of an aircraft performance and stability-control characteristics. These coefficients also can be used in the automatic flight control systems and mathematical model of flight simulator. The study of the aerodynamic aspect of flying systems is a reserved domain and inaccessible for the developers. Doing tests in a wind tunnel to extract aerodynamic forces and moments requires a specific and expensive means. Besides, the glaring lack of published documentation in this field of study makes the aerodynamic coefficients determination complicated. This work is devoted to the identification of an aerodynamic model, by using an aircraft in virtual simulated environment. We deal with the identification of the system, we present an environment framework based on Software In the Loop (SIL) methodology and we use Microsoft^TM Flight Simulator (FS-2004) as the environment for plane simulation. We propose The Total Least Squares Estimation technique (TLSE) to identify the aerodynamic parameters, which are unknown, variable, classified and used in the expression of the piloting law. In this paper, we define each aerodynamic coefficient as the mean of its numerical values. All other variations are considered as modeling uncertainties that will be compensated by the robustness of the piloting control.

Keywords: aircraft aerodynamic model, total least squares estimation, piloting the aircraft, robust control, Microsoft Flight Simulator, MQ-1 predator

Procedia PDF Downloads 287

Authors: Srijata Mitra, Mobina Parveen, Pranab Roy, Narayan Chandra Chattopadhyay

Abstract:

Chlorinated hydrocarbon can be a major pollution problem in groundwater as well as soil. Many people interact with these chemicals on daily accidentally or by professionally in the laboratory. One of the most common sources for Chlorinated hydrocarbon contamination of soil and groundwater are industrial effluents. The wide use and discharge of Trichloroethylene (TCE), a volatile chlorohydrocarbon from chemical industry, led to major water pollution in rural areas. TCE is an mainly used as an industrial metal degreaser in industries. Biotransformation of TCE to the potent carcinogen vinyl chloride (VC) by consortia of anaerobic bacteria might have role for the above purpose. For these reasons, the aim of current study was to isolate and characterized the genes involved in TCE metabolism and also to investigate the in silico study of those genes. To our knowledge, only one aromatic dioxygenase system, the toluene dioxygenase in Pseudomonas putida F1 has been shown to be involved in TCE degradation. This is first instance where Bacillus cereus group being used in biodegradation of trichloroethylene. A novel bacterial strain 2479 was isolated from oil depot site at Rajbandh, Durgapur (West Bengal, India) by enrichment culture technique. It was identified based on polyphasic approach and ribotyping. The bacterium was gram positive, rod shaped, endospore forming and capable of degrading trichloroethylene as the sole carbon source. On the basis of phylogenetic data and Fatty Acid Methyl Ester Analysis, strain 2479 should be placed within the genus Bacillus and species cereus. However, the present isolate (strain 2479) is unique and sharply different from the usual Bacillus strains in its biodegrading nature. Fujiwara test was done to estimate that the strain 2479 could degrade TCE efficiently. The gene for TCE biodegradation was PCR amplified from genomic DNA of Bacillus cereus 2479 by using todC1 gene specific primers. The 600bp amplicon was cloned into expression vector pUC I8 in the E. coli host XL1-Blue and expressed under the control of lac promoter and nucleotide sequence was determined. The gene sequence was deposited at NCBI under the Accession no. GU183105. In Silico approach involved predicting the physico-chemical properties of deduced Tce1 protein by using ProtParam tool. The tce1 gene contained 342 bp long ORF encoding 114 amino acids with a predicted molecular weight 12.6 kDa and the theoretical pI value of the polypeptide was 5.17, molecular formula: C559H886N152O165S8, total number of atoms: 1770, aliphatic index: 101.93, instability index: 28.60, Grand Average of Hydropathicity (GRAVY): 0.152. Three differentially expressed proteins (97.1, 40 and 30 kDa) were directly involved in TCE biodegradation, found to react immunologically to the antibodies raised against TCE inducible proteins in Western blot analysis. The present study suggested that cloned gene product (TCE1) was capable of degrading TCE as verified chemically.

Keywords: cloning, Bacillus cereus, in silico analysis, TCE

Procedia PDF Downloads 398

Authors: Thiago M. R. Dias, Patrícia M. Dias, Gray F. Moita

Abstract:

The production and publication of scientific works have increased significantly in the last years, being the Internet the main factor of access and distribution of these works. Faced with this, there is a growing interest in understanding how scientific research has evolved, in order to explore this knowledge to encourage research groups to become more productive. Therefore, the objective of this work is to explore repositories containing data from scientific publications and to characterize keyword networks of these publications, in order to identify the most relevant keywords, and to highlight those that have the greatest impact on the network. To do this, each article in the study repository has its keywords extracted and in this way the network is  characterized, after which several metrics for social network analysis are applied for the identification of the highlighted keywords.

Keywords: bibliometrics, data analysis, extraction and data integration, scientometrics

Procedia PDF Downloads 258

Authors: Kaomud Tyagi, Rajasree Chakraborty, Shantanu Kundu, Devkant Singha, Kailash Chandra, Vikas Kumar

Abstract:

The melon thrips, Thrips palmi is a serious pest of a wide range of agriculture crops and also act as vectors for plant viruses (genus Tospovirus, family Bunyaviridae). More molecular data on this species is required to understand the cryptic speciation and evolutionary affiliations. Mitochondrial genomes have been widely used in phylogenetic and evolutionary studies in insect. So far, mitogenomes of five thrips species (Anaphothrips obscurus, Frankliniella intonsa, Frankliniella occidentalis, Scirtothrips dorsalis and Thrips imaginis) is available in the GenBank database. In this study, we sequenced the first complete mitogenome T. palmi and compared it with available thrips mitogenomes. We assembled the mitogenome from the whole genome sequencing data generated using Illumina Hiseq2500. Annotation was performed using MITOS web-server to estimate the location of protein coding genes (PCGs), transfer RNA (tRNAs), ribosomal RNAs (rRNAs) and their secondary structures. The boundaries of PCGs and rRNAs was confirmed manually in NCBI. Phylogenetic analyses were performed using the 13 PCGs data using maximum likelihood (ML) in PAUP, and Bayesian inference (BI) in MrBayes 3.2. The complete mitogenome of T. palmi was 15,333 base pairs (bp), which was greater than the genomes of A. obscurus (14,890bp), F. intonsa (15,215 bp), F. occidentalis (14,889 bp) and S. dorsalis South Asia strain (SA1) (14,283 bp), but smaller than the genomes of T. imaginis (15,407 bp) and S. dorsalis East Asia strain (EA1) (15,343bp). Like in other thrips species, the mitochondrial genome of T. palmi was represented by 37 genes, including 13 PCGs, large and small ribosomal RNA (rrnL and rrnS) genes, 22 transfer RNA (tRNAs) genes (with one extra gene for trn-Serine) and two A+T-rich control regions (CR1 and CR2). Thirty one genes were observed on heavy (H) strand and six genes on the light (L) strand. The six tRNA genes (trnG,trnK, trnY, trnW, trnF, and trnH) were found to be conserved in all thrips species mitogenomes in their locations relative to a protein-coding or rRNA gene upstream or downstream. The gene arrangements of T. palmi is very close to T. imaginis except the rearrangements in tRNAs genes: trnR (arginine), and trnE (glutamic acid) were found to be located between cox3 and CR2 in T. imaginis which were translocated between atp6 and CR1 in T. palmi; trnL1 (Leucine) and trnS1(Serine) were located between atp6 and CR1 in T. imaginis which were translocated between cox3 and CR2 in T. palmi. The location of CR1 upstream of nad5 gene was suggested to be ancestral condition of the thrips species in subfamily Thripinae, was also observed in T. palmi. Both the Maximum likelihood (ML) and Bayesian Inference (BI) phylogenetic trees generated resulted in similar topologies. The T. palmi was clustered with T. imaginis. We concluded that more molecular data on the diverse thrips species from different hierarchical level is needed, to understand the phylogenetic and evolutionary relationships among them.

Keywords: thrips, comparative mitogenomics, gene rearrangements, phylogenetic analysis

Procedia PDF Downloads 168

Authors: D. P. Gangwar

Abstract:

Identification of human through facial images has got great importance in forensic science. The video recordings, CCTV footage, passports, driver licenses and other related documents are invariably sent to the laboratory for comparison of the questioned photographs as well as video recordings with suspected photographs/recordings to prove the identity of a person. More than 300 questioned and 300 control photographs received in actual crime cases, received from various investigation agencies, have been compared by me so far using various familiar analysis and comparison techniques such as Holistic comparison, Morphological analysis, Photo-anthropometry and superimposition. On the basis of findings obtained during the examination huge photo exhibits, a realistic and comprehensive technique has been proposed which could be very useful for forensic.

Keywords: CCTV Images, facial features, photo-anthropometry, superimposition

Procedia PDF Downloads 529

Authors: Ruwani N. Nugara, Masashi Inafuku, Kensaku Takara, Hironori Iwasaki, Hirosuke Oku

Abstract:

Pteryxin from the partially purified hexane phase (HP) of Peucedanum japonicum Thunb (PJT) was identified as the active compound related to anti-obesity. Thus, in this study we investigated the mechanisms related to anti-obesity activity in-vitro. The HP was fractionated, and effect on the triglyceride (TG) content was evaluated in 3T3-L1 and HepG2 cells. Comprehensive spectroscopic analyses were used to identify the structure of the active compound. The dose dependent effect of active constituent on the TG content, and the gene expressions related to adipogenesis, fatty acid catabolism, energy expenditure, lipolysis and lipogenesis (20 μg/mL) were examined in-vitro. Furthermore, higher dosage of pteryxin (50μg/mL) was tested against 20μg/mL in 3T3-L1 adipocytes. The mRNA were subjected to SOLiD next generation sequencer and the obtained data were analyzed by Ingenuity Pathway Analysis (IPA). The active constituent was identified as pteryxin, a known compound in PJT. However, its biological activities against obesity have not been reported previously. Pteryxin dose dependently suppressed TG content in both 3T3-L1 adipocytes and HepG2 hepatocytes (P < 0.05). Sterol regulatory element-binding protein-1 (SREBP1 c), Fatty acid synthase (FASN), and acetyl-CoA carboxylase-1 (ACC1) were downregulated in pteryxin-treated adipocytes (by 18.0, 36.1 and 38.2%; P < 0.05, respectively) and hepatocytes (by 72.3, 62.9 and 38.8%, respectively; P < 0.05) indicating its suppressive effects on fatty acid synthesis. The hormone-sensitive lipase (HSL), a lipid catabolising gene was upregulated (by 15.1%; P < 0.05) in pteryxin-treated adipocytes suggesting improved lipolysis. Concordantly, the adipocyte size marker gene, paternally expressed gene1/mesoderm specific transcript (MEST) was downregulated (by 42.8%; P < 0.05), further accelerating the lipolytic activity. The upregulated trend of uncoupling protein 2 (UCP2; by 77.5%; P < 0.05) reflected the improved energy expenditure due to pteryxin. The 50μg/mL dosage of pteryxin completely suppressed PPARγ, MEST, SREBP 1C, HSL, Adiponectin, Fatty Acid Binding Protein (FABP) 4, and UCP’s in 3T3-L1 adipocytes. The IPA suggested that pteryxin at 20μg/mL and 50μg/mL suppress obesity in two different pathways, whereas the WNT signaling pathway play a key role in the higher dose of pteryxin in preadipocyte stage. Pteryxin in PJT play the key role in regulating lipid metabolism related gene network and improving energy production in vitro. Thus, the results suggests pteryxin as a new natural compound to be used as an anti-obesity drug in pharmaceutical industry.

Keywords: obesity, peucedanum japonicum thunb, pteryxin, food science

Procedia PDF Downloads 453

Authors: Ahmed Abdrabou, Medhat Abdalla

Abstract:

The studied stele dates back to Third Intermediate Period (1075-664) B.C in an ancient Egypt. It is made of wood and covered with painted gesso layers. This study aims to use a combination of multi spectral imaging {visible, infrared (IR), Visible-induced infrared luminescence (VIL), Visible-induced ultraviolet luminescence (UVL) and ultraviolet reflected (UVR)}, along with portable x-ray fluorescence in order to map and identify the pigments as well as to provide a deeper understanding of the painting techniques. Moreover; the authors were significantly interested in the identification of wood species. Multispectral imaging acquired in 3 spectral bands, ultraviolet (360-400 nm), visible (400-780 nm) and infrared (780-1100 nm) using (UV Ultraviolet-induced luminescence (UVL), UV Reflected (UVR), Visible (VIS), Visible-induced infrared luminescence (VIL) and Infrared photography. False color images are made by digitally editing the VIS with IR or UV images using Adobe Photoshop. Optical Microscopy (OM), potable X-ray fluorescence spectroscopy (p-XRF) and Fourier Transform Infrared Spectroscopy (FTIR) were used in this study. Mapping and imaging techniques provided useful information about the spatial distribution of pigments, in particular visible-induced luminescence (VIL) which allowed the spatial distribution of Egyptian blue pigment to be mapped and every region containing Egyptian blue, even down to single crystals in some instances, is clearly visible as a bright white area; however complete characterization of the pigments requires the use of p. XRF spectroscopy. Based on the elemental analysis found by P.XRF, we conclude that the artists used mixtures of the basic mineral pigments to achieve a wider palette of hues. Identification of wood species Microscopic identification indicated that the wood used was Sycamore Fig (Ficus sycomorus L.) which is recorded as being native to Egypt and was used to make wooden artifacts since at least the Fifth Dynasty.

Keywords: polychrome wooden stele, multispectral imaging, IR luminescence, Wood identification, Sycamore Fig, p-XRF

Procedia PDF Downloads 264

Authors: Daniel Aberdam

Abstract:

Haploinsufficiency of PAX6 in humans is the main cause of congenital aniridia, a rare eye disease characterized by reduced visual acuity. Patients have also progressive disorders including cataract, glaucoma and corneal abnormalities making their condition very challenging to manage. Aniridia-related keratopathy (ARK), caused by a combination of factors including limbal stem-cell deficiency, impaired healing response, abnormal differentiation, and infiltration of conjunctival cells onto the corneal surface, affects up to 95% of patients. It usually begins in the first decade of life resulting in recurrent corneal erosions, sub-epithelial fibrosis with corneal decompensation and opacification. Unfortunately, current treatment options for aniridia patients are currently limited. Although animal models partially recapitulate this disease, there is no in vitro cellular model of AKT needed for drug/therapeutic tools screening and validation. We used genome editing (CRISPR/Cas9 technology) to introduce a nonsense mutation found in patients into one allele of the PAX6 gene into limbal stem cells. Resulting mutated clones, expressing half of the amount of PAX6 protein and thus representative of haploinsufficiency were further characterized. Sequencing analysis showed that no off-target mutations were induced. The mutated cells displayed reduced cell proliferation and cell migration but enhanced cell adhesion. Known PAX6 targets expression was also reduced. Remarkably, addition of soluble recombinant PAX6 protein into the culture medium was sufficient to activate endogenous PAX6 gene and, as a consequence, rescue the phenotype. It strongly suggests that our in vitro model recapitulates well the epithelial defect and becomes a powerful tool to identify drugs that could rescue the corneal defect in patients. Furthermore, we demonstrate that the homeotic transcription factor Pax6 is able to be uptake naturally by recipient cells to function into the nucleus.

Keywords: Pax6, crispr/cas9, limbal stem cells, aniridia, gene therapy

Procedia PDF Downloads 207

Authors: Svetlana L. Mishlanova, Evgeniia V. Ermakova, Mariia E. Timirkina

Abstract:

The paper is concerned with the study of metaphor production in essays written by Russian and English native speakers in the framework of cognitive metaphor theory. It considers metaphorical competence as individual’s ability to recognize, understand and use metaphors in speech. The work analyzes the influence of visual metaphor on production and density of conventional and novel verbal metaphors. The main methods of research include experiment connected with image interpretation, metaphor identification procedure (MIPVU) and visual conventional metaphors identification procedure proposed by VisMet group. The research findings will be used in the project aimed at comparing metaphorical competence of native and non-native English speakers.

Keywords: metaphor, metaphorical competence, conventional, novel

Procedia PDF Downloads 286

Authors: L. K. Davis

Abstract:

The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time-based DNA codes, writing DNA code from scratch

Procedia PDF Downloads 114

Authors: Muhammad Imran, Sarfraz Shafiq, Xiangru Tang

Abstract:

Alternative splicing (AS) is an important post-transcriptional regulatory mechanism to generate transcripts variability and proteome diversity in plants. Fragrant rice (Oryza sativa L.) has a high economic and nutritional value, and the application of micronutrients regulate 2-acetyl-1-pyrroline (2-AP) production, which is responsible for aroma in fragrant rice. However, no systematic investigation of AS events in response to micronutrients (Zn) has been performed in fragrant rice. Furthermore, the post-transcriptional regulation of genes involved in 2-AP biosynthesis is also not known. In this study, a comprehensive analysis of AS events under two gradients of Zn treatment in two different fragrant rice cultivars (Meixiangzhan-2 and Xiangyaxiangzhan) was performed. A total of 386 and 598 significant AS events were found in Meixiangzhan-2 treated with low and high doses of Zn, respectively. In Xiangyaxiangzhan, a total of 449 and 598 significant AS events were found in low and high doses of Zn, respectively. Go analysis indicated that these genes were highly enriched in physiological processes, metabolism, and cellular process in both cultivars. However, genotype and dose-dependent AS events were also detected in both cultivars. By comparing differential AS (DAS) events with differentially expressed genes (DEGs), we found a weak overlap among DAS and DEGs in both fragrant rice cultivars, indicating that only a few genes are post-transcriptionally regulated in response to Zn treatment. We further report that Zn differentially regulates the expression of 2-AP biosynthesis-related genes in both cultivars, and Zn treatment altered the editing frequency of SNPs in the genes involved in 2-AP biosynthesis. Finally, we showed that epigenetic modifications associated with active gene transcription are generally enriched over 2-AP biosynthesis-related genes. Taken together, our results provide evidence of the post-transcriptional gene regulation in fragrant rice in response to Zn treatment and highlight that the 2-AP biosynthesis pathway may also be post-transcriptionally regulated through epigenetic modifications. These findings will serve as a cornerstone for further investigation to understand the molecular mechanisms of 2-AP biosynthesis in fragrant rice.

Keywords: fragrant rice, 2-acetyl-1-pyrroline, gene expression, zinc, alternative splicing, SNPs

Procedia PDF Downloads 112

Authors: Farahnaz Motamedi Sedeh, Homayoon Mahravani, Parvin Shawrang, Mehdi Behgar

Abstract:

Most countries use inactivated binary ethylenimine (BEI) vaccines to control and prevent Foot-and-Mouth Disease (FMD). However, this vaccine induces a short-term humoral immune response in animals. This study investigated the cellular and humoral immune responses in homologous and prime-boost (PB) groups in the BALB/c mouse model. FMDV strain O/IRN/1/2007 was propagated in the BHK-21 cell line and inactivated by three methods, including a chemical with BEI to produce a conventional vaccine (CV), a gamma irradiation vaccine (GIV), and an electron irradiated vaccine (EIV). Three vaccines were formulated with the adjuvant aluminum hydroxide gel. In addition, a DNA vaccine was prepared by amplifying the virus VP1 gene pcDNA3.1 plasmid. In addition, the plasmid encoding the granulocyte-macrophage colony-stimulating factor gene (GM-CSF) was used as a molecular adjuvant. Eleven groups of five mice each were selected, and the vaccines were administered as homologous and heterologous strategy prime-boost (PB) in three doses two weeks apart. After the evaluation of neutralizing antibodies, interleukin (IL)-2, IL-4, IL-10, interferon-gamma (INF-γ), and MTT assays were compared in the different groups. The pcDNA3.1+VP1 cassette was prepared and confirmed as a DNA vaccine. The virus was inactivated by gamma rays and electron beams at 50 and 55 kGy as GIV and EIV, respectively. Splenic lymphocyte proliferation in the inactivated vaccinated homologous groups was significantly lower (P≤0.05) compared with the heterologous prime-boosts (PB1, PB2, PB3) and DNA + GM-CSF groups (P≤0.05). The highest SNT titer was observed in the inactivated vaccine groups. IFN-γ and IL-2 were higher in the vaccinated groups. It was found that although there was a protective humoral immune response in the groups with inactivated vaccine, there was adequate cellular immunity in the group with the DNA vaccine. However, the strongest cellular and humoral immunity was observed in the PB groups. The primary injection was accompanied by DNA vaccine + GM-CSF and boosted injection with GIV or CV.

Keywords: foot and mouth disease, irradiated vaccine, immune responses, DNA vaccine, prime boost strategy

Procedia PDF Downloads 17

Authors: Maciej Sobczak, Julita Pietrzak, Tomasz Płoszaj, Agnieszka Robaszkiewicz

Abstract:

Brg1, a member of SWI/SNF complex, plays a role in chromatin remodeling, therefore, regulates expression of many genes. Brg1 is an ATPase of SWI/SNF complex, thus its activity requires ATP. Through its bromodomain recognizes acetylated histone residues and evicts them, thus promoting transcriptionally active state of chromatin. One of the enzymes that is responsible for acetylation of histone residues is Ep300. It was previously shown in the literature that cooperation of Brg1 and Ep300 occurs at the promoter regions that have binding sites for E2F-family transcription factors as well as CpG islands. According to literature, approximately 20% of human cancer possess mutation in Brg1 or any other crucial SWI/SNF subunit. That phenomenon makes Brg1-Ep300 a very promising target for anti-cancer therapy. Therefore in our study, we investigated if physical interaction between Brg1 and Ep300 exists and what impact those two proteins have on key for breast cancer cells processes such as DNA damage repair and cell proliferation. Bioinformatical analysis pointed out, that genes involved in cell proliferation and DNA damage repair are overexpressed in MCF7 and MDA-MB-231 cells. Moreover, promoter regions of these genes are highly acetylated, which suggests high transcriptional activity of those sites. Notably, many of those gene possess within their promoters an E2F, Brg1 motives, as well as CpG islands and acetylated histones. Our data show that Brg1 physically interacts with Ep300, and together they regulate expression of genes involved in DNA damage repair and cell proliferation. Upon inhibiting Brg1 or Ep300, expression of vital for cancer cell survival genes such as CDK2/4, BRCA1/2, PCNA, and XRCC1 is decreased in MDA-MB-231 and MCF7 cells. Moreover, inhibition or silencing of either Brg1 or Ep300 leads to cell cycle arrest in G1. After inhibition of BRG1 or Ep300 on tested gene promoters, the repressor complex including Rb, HDAC1, and EZH2 is formed, which inhibits gene expression. These results highlight potentially significant target for targeted anticancer therapy to be introduced as a supportive therapy.

Keywords: brg1, ep300, breast cancer, epigenetics

Procedia PDF Downloads 183

Authors: S. Pradhan, D. Pradhan, G. Tripathy, T. Dasmohapatra

Abstract:

Suppressors of cytokine signalling (SOCS3), a newly indentified anti-apoptotic molecule is a downstream effecter of the receptor tyrosine kinase-Ras signalling pathway. Current study has uncovered that SOCS3 may have wide and imperative capacities, particularly because of its close correlation with malignant tumors. To investigate the impact of SOCS3 on MDR, we analyzed the expression of P-gp and SOCS3 by immune-histochemistry and found there was positive correlation between them. At that point we effectively interfered with RNA translation by the contamination of siRNA of SOCS3 into MCF7/ADM breast cancer cell lines through a lentivirus, and the expression of the target gene was significantly inhibited. After RNAi the drug resistance was reduced altogether and the expression of MDR1 mRNA and P-gp in MCF7/ADM cell lines demonstrated a significant decrease. Likewise the expression of P53 protein increased in a statistically significant manner (p ≤ 0.01) after RNAi exposure. Moreover, flowcytometry analysis uncovers that cell cycle and anti-apoptotic enhancing capacity of cells changed after RNAi treatment. These outcomes proposed SOCS3 may take part in breast cancer MDR by managing MDR1 and P53 expression, changing cell cycle and enhancing the anti-apoptotic ability.

Keywords: SOCS3gene, breast cancer, multidrug resistance, MDR1 gene, RNA interference

Procedia PDF Downloads 337

Authors: Roihatul Mutiah, Sukardiman, Aty Widyawaruyanti

Abstract:

Calotropis gigantiea (L.) R. Br (Apocynaceae) commonly called as “Biduri” or “giant milk weed” is a well-known weed to many cultures for treating various disorders. Several studies reported that C.gigantea roots has anticancer activity. The main aim of this research was to isolate and identify an active marker compound of C.gigantea roots for quality control purpose of its extract in the development as anticancer natural product. The isolation methods was bioactivity guided column chromatography, TLC, and HPLC. Evaluated anticancer activity of there substances using MTT assay methods. Identification structure active compound by UV, 1HNMR, 13CNMR, HMBC, HMQC spectral and other references. The result showed that the marker active compound was identical as Calotropin.

Keywords: calotropin, Calotropis gigantea, anticancer, marker active

Procedia PDF Downloads 335

Authors: Nesrine Lenchi, Salima Kebbouche-Gana, Laddada Belaid, Mohamed Lamine Khelfaoui, Mohamed Lamine Gana

Abstract:

Saline lakes are extreme hypersaline environments that are considered five to ten times saltier than seawater (150 – 300 g L-1 salt concentration). Hypersaline regions differ from each other in terms of salt concentration, chemical composition and geographical location, which determine the nature of inhabitant microorganisms. In order to explore the diversity of moderate and extreme halophiles Bacteria in Chott Tinsilt (East of Algeria), an isolation program was performed. In the first time, water samples were collected from the saltern during pre-salt harvesting phase. Salinity, pH and temperature of the sampling site were determined in situ. Chemical analysis of water sample indicated that Na +and Cl- were the most abundant ions. Isolates were obtained by plating out the samples in complex and synthetic media. In this study, seven halophiles cultures of Bacteria were isolated. Isolates were studied for Gram’s reaction, cell morphology and pigmentation. Enzymatic assays (oxidase, catalase, nitrate reductase and urease), and optimization of growth conditions were done. The results indicated that the salinity optima varied from 50 to 250 g L-1, whereas the optimum of temperature range from 25°C to 35°C. Molecular identification of the isolates was performed by sequencing the 16S rRNA gene. The results showed that these cultured isolates included members belonging to the Halomonas, Staphylococcus, Salinivibrio, Idiomarina, Halobacillus Thalassobacillus and Planococcus genera and what may represent a new bacterial genus.

Keywords: bacteria, Chott, halophilic, 16S rRNA

Procedia PDF Downloads 281

Authors: Ghazanfar Ali, Fahad N Almajhdi

Abstract:

This study provides data on the viral diagnosis and molecular epidemiology of influenza A(H3N2) virus isolated in Riyadh, Saudi Arabia. Nasopharyngeal aspirates from 80 clinically infected patients in the peak of the 2010-2011 winter seasons were processed for viral diagnosis by RT-PCR. Sequencing of entire HA and NA genes of representative isolates and molecular epidemiological analysis were performed. A total of 06 patients were positive for influenza A, B and respiratory syncytial viruses by RT-PCR assays; out of these only one sample was positive for influenza A(H3N2) by RT-PCR. Phylogenetic analysis of the HA and NA gene sequences showed identities higher than 99-98.8 % in both genes. They were also similar to reference isolates in HA sequences (99 % identity) and in NA sequences (99 % identity). Amino acid sequences predicted for the HA gene were highly identical to reference strains. The NA amino acid substitutions identified did not include the oseltamivir-resistant H275Y substitution. Conclusion: Viral isolation and RT-PCR together were useful for diagnosis of the influenza A (H3N2) virus. Variations in HA and NA sequences are similar to those identified in worldwide reference isolates and no drug resistance was found.

Keywords: influenza A (H3N2), genetic characterization, viral isolation, RT-PCR, Saudi Arabia

Procedia PDF Downloads 262

Authors: Chengcao Sun, Shujun Li, Cuili Yang, Yongyong Xi, Liang Wang, Feng Zhang, Dejia Li

Abstract:

Recently, the long non-coding RNA (lncRNA) NEAT1 has been identified as an oncogenic gene in multiple cancer types and elevated expression of NEAT1 was tightly linked to tumorigenesis and cancer progression. However, the molecular basis for this observation has not been characterized in progression of non-small cell lung cancer (NSCLC). In our studies, we identified NEAT1 was highly expressed in NSCLC patients and was a novel regulator of NSCLC progression. Patients whose tumors had high NEAT1 expression had a shorter overall survival than patients whose tumors had low NEAT1 expression. Further, NEAT1 significantly accelerates NSCLC cell growth and metastasis in vitro and tumor growth in vivo. Additionally, by using bioinformatics study and RNA pull down combined with luciferase reporter assays, we demonstrated that NEAT1 functioned as a competing endogenous RNA (ceRNA) for has-miR-377-3p, antagonized its functions and led to the de-repression of its endogenous targets E2F3, which was a core oncogene in promoting NSCLC progression. Taken together, these observations imply that the NEAT1 modulated the expression of E2F3 gene by acting as a competing endogenous RNA, which may build up the missing link between the regulatory miRNA network and NSCLC progression.

Keywords: long non-coding RNA NEAT1, hsa-miRNA-377-3p, E2F3, non-small cell lung cancer, tumorigenesis

Procedia PDF Downloads 369

Authors: Khaled M. El Naggar

Abstract:

This paper introduces a digital method for fault section identification in transmission lines. The method uses digital set of the measured short circuit current to locate faults in electrical power systems. The digitized current is used to construct a set of overdetermined system of equations. The problem is then constructed and solved using the proposed digital optimization technique to find the fault distance. The proposed optimization methodology is an application of simulated annealing optimization technique. The method is tested using practical case study to evaluate the proposed method. The accurate results obtained show that the algorithm can be used as a powerful tool in the area of power system protection.

Keywords: optimization, estimation, faults, measurement, high voltage, simulated annealing

Procedia PDF Downloads 393

Authors: Elham Ahmadi, Mehrdad Ravanshad, Joyce Fingeroth, Mazyar Ziyaeyan, Rajesh Panigrahi, Jun Xie, Gao Guangping

Abstract:

B-cell proliferative disorders often occur among persons that are T-cell compromised. These disorders are primarily EBV+ and can first present with a focal lesion. Direct introduction of oncolytic viruses into localized tumors provides theoretical advantages over chemotherapy and immunotherapy by reducing systemic toxicity, to which the immunocompromised host is most vulnerable. Widely studied as a vehicle for gene therapy, AAV has only rarely been applied to treat cancer. As a prelude to development of a therapeutic vehicle, we assessed the ability of 15 distinct recombinant AAV serotypes (rAAV1, rAAV2, rAAV3b, rAAV4, rAAV5, rAAV6, rAAV6.2, rAAV6TM, rAAV7, rAAV8, rAAVrh8, rAAV9, rAAVrh10, rAAV39, rAAV43) bearing eGFP to infect human B-cell tumor lines compared with primary B-cells in vitro. Enhanced infection of tumor lines by AAV 6.2 was demonstrated by flow cytometry. EBV superinfection of EBV negative B-cell tumor lines increased susceptibility to AAV6.2 infection. As proof of concept, AAV6.2 bearing HSV-1 thymidine kinase in place of eGFP eliminated tumor cells upon exposure to ganciclovir.

Keywords: AAV, gene therapy, lymphoma, malignancy, tropism

Procedia PDF Downloads 120