Search results for: complete genome sequencing

Authors: Mengying Wang, Dongjing Liu, Holger Schwender, Ping Wang, Hongping Zhu, Tao Wu, Terri H Beaty

Abstract:

Background: Maternal smoking is a recognized risk factor for nonsyndromic cleft lip with or without cleft palate (NSCL/P). It has been reported that the effect of maternal smoking on oral clefts is mediated through genes that influence nicotine dependence. The polymorphisms of cholinergic receptor nicotinic alpha (CHRNA) and beta (CHRNB) subunits genes have previously shown strong associations with nicotine dependence. Here, we attempted to investigate whether the above genes are associated with clefting risk through testing for potential gene-gene (G×G) and gene-environment (G×E) interaction. Methods: We selected 120 markers in 14 genes associated with nicotine dependence to conduct transmission disequilibrium tests among 806 Chinese NSCL/P case-parent trios ascertained in an international consortium which conducted a genome-wide association study (GWAS) of oral clefts. We applied Cordell’s method using “TRIO” package in R to explore G×G as well as G×E interaction involving environmental tobacco smoke (ETS) based on conditional logistic regression model. Results: while no SNP showed significant association with NSCL/P after Bonferroni correction, we found signals for G×G interaction between 10 pairs of SNPs in CHRNA3, CHRNA5, and CHRNB4 (p<10-8), among which the most significant interaction was found between RS3743077 (CHRNA3) and RS11636753 (CHRNB4, p<8.2×10-12). Linkage disequilibrium (LD) analysis revealed only low level of LD between these markers. However, there were no significant results for G×ETS interaction. Conclusion: This study fails to detect association between nicotine dependence genes and NSCL/P, but illustrates the importance of taking into account potential G×G interaction for genetic association analysis in NSCL/P. This study also suggests nicotine dependence genes should be considered as important candidate genes for NSCL/P in future studies.

Keywords: Gene-Gene Interaction, Maternal Smoking, Nicotine Dependence, Non-Syndromic Cleft Lip with or without Cleft Palate

Procedia PDF Downloads 326

Authors: Yayun Hsu, Henry Horng-Shing Lu

Abstract:

This paper proposes a data-driven, biology-inspired neural segmentation method of 3D drosophila Brainbow images. We use Bayesian Sequential Partitioning algorithm for probabilistic modeling, which can be used to detect somas and to eliminate cross talk effects. This work attempts to develop an automatic methodology for neuron image segmentation, which nowadays still lacks a complete solution due to the complexity of the image. The proposed method does not need any predetermined, risk-prone thresholds since biological information is inherently included in the image processing procedure. Therefore, it is less sensitive to variations in neuron morphology; meanwhile, its flexibility would be beneficial for tracing the intertwining structure of neurons.

Keywords: brainbow, 3D imaging, image segmentation, neuron morphology, biological data mining, non-parametric learning

Procedia PDF Downloads 477

Authors: K. Cartelier, D. Aime, V. Vernoud, J. Buitink, J. M. Prosperi, K. Gallardo, C. Le Signor

Abstract:

Legumes can produce protein-rich seeds without nitrogen fertilizer through root symbiosis with nitrogen-fixing rhizobia. Rich in lysine, these proteins are used for human nutrition and animal feed. However, the instability of seed protein yield and quality due to environmental fluctuations limits the wider use of legumes such as pea. Breeding efforts are needed to optimize and stabilize seed nutritional value, which requires to identify the genetic determinism of seed protein plasticity in response to the environment. Towards this goal, we have studied the plasticity of protein content and composition of seeds from a collection of 200 Medicago truncatula ecotypes grown under four controlled conditions (optimal, drought, and winter/spring sowing). A quantitative analysis of one-dimensional protein profiles of these mature seeds was performed and plasticity indices were calculated from each abundant protein band. Genome-Wide Association Studies (GWAS) from these data identified major GWAS hotspots, from which a list of candidate genes was obtained. A Gene Ontology Enrichment Analysis revealed an over-representation of genes involved in several amino acid metabolic pathways. This led us to propose that environmental variations are likely to modulate amino acid balance, thus impacting seed protein composition. The selection of candidate genes for controlling the plasticity of seed protein composition was refined using transcriptomics data from developing Medicago truncatula seeds. The pea orthologs of key genes were identified for functional studies by mean of TILLING (Targeting Induced Local Lesions in Genomes) lines in this crop. We will present how this study highlighted mechanisms that could govern seed protein plasticity, providing new cues towards the stabilization of legume seed quality.

Keywords: GWAS, Medicago truncatula, plasticity, seed, storage proteins

Procedia PDF Downloads 133

Authors: Anna Wiltshire, Rebecca Markham

Abstract:

Over the last decade, a growing body of evidence has indicated that children with disabilities are often amongst the most excluded and vulnerable in society. The World Bank estimates that 20% of those living in poverty in developing countries are disabled which means that those with the least bear the greatest burden. Furthermore, children with disabilities in Africa have to face a multitude of difficulties ranging from the physical to the psychological. Misconceptions and cultural beliefs are used to justify violence against, or complete shunning of these individuals and their families. In addition, discrimination can prevent access to both education and health services, further compromising these individuals. All children, irrespective of their disability should be able to enjoy human rights without discrimination, but this is often not the case. This poster explores how and why children with disabilities in Africa are subject to violations of their human rights, and suggests ways of addressing these problems.

Keywords: Africa, children, disability, discrimination, human rights

Procedia PDF Downloads 554

Authors: Preeyarach Whisetkhan, Malai Taweechotipatr, Ulisa Pachekrepapol

Abstract:

Elevated level of blood cholesterol or hypercholesterolemia may lead to atherosclerosis and poses a major risk for cardiovascular diseases. Probiotics play a crucial role in human health, and probiotic bacteria that possesses bile salt hydrolase (BSH) activity can be used to lower cholesterol level of the host. The aim of this study was to investigate whether lactic acid bacteria (LAB) isolated from traditional Thai fermented foods were able to exhibit bile salt hydrolase activity and their use in fermented milk. A total of 28 isolates were tested for BSH activity by plate method on MRS agar supplemented with 0.5% sodium salt of taurodeoxycholic acid and incubated at 37°C for 48 h under anaerobic condition. The results showed that FN1-1 and FN23-3 isolates possessed strong BSH activity. FN1-1 and FN23-3 isolates were then identified for phenotype, biochemical characteristics, and genotype (16S rRNA sequencing). FN1-1 isolate showed 99.92% similarity to Lactobacillus pentosus DSM 20314(T), while FN23-3 isolate showed 99.94% similarity to Enterococcus faecium CGMCC1.2136 (T). Lactobacillus pentosus FN1-1 and Enterococcus faecium FN23-3 were tolerant of pH 3-4 and 0.3 and 0.8% bile. Bacterial count and pH of milk fermented with Lactobacillus pentosus FN1-1 at 37°C and 43°C were investigated. The results revealed that Lactobacillus pentosus FN1-1 was able to grow in milk, which led to decrease in pH level. Fermentation at 37°C resulted in faster growth rate than at 43 °C. Lactobacillus pentosus FN1-1 was a candidate probiotic to be used in fermented milk products to reduce the risk of high-cholesterol diseases.

Keywords: probiotics, lactic acid bacteria, bile salt hydrolase, cholesterol

Procedia PDF Downloads 144

Authors: Omar Alhamd, Peter A. Thomas, Trevor J. Greenhough, Annette K. Shrive

Abstract:

The Pseudomonas syringae species complex includes many plant pathogenic strains with highly specific interactions with varied host species and cultivars. The rapid spread of these bacteria over the last ten years has become a cause for concern. Nanoparticles have previously shown promise in microbiological action. We have therefore investigated in vitro and in vivo the effects of different types and sizes of nanoparticles in order to provide quantitative information about their effect on the bacteria. The effects of several different nanoparticles against several bacteria strains were investigated. The effect of NP on bacterial growth was studied by measuring the optical density, biochemical and nutritional tests, and transmission electron microscopy (TEM) to determine the shape and size of NP. Our results indicate that their effects varied, with either a negative or a positive impact on both bacterial and plant growth. Additionally, the methods of exposure to nanoparticles have a crucial role in accumulation, translocation, growth response and bacterial growth. The results of our studies on the behaviour and effects of nanoparticles in model plants showed. Cerium oxide (CeO₂) and silver (Ag) NP showed significant antibacterial activity against several pathogenic bacteria. It was found that titanium nanoparticles (TiO₂) can have either a negative or a positive impact, according to concentration and size. It is also thought that environmental conditions can have a major influence on bacterial growth. Studies were therefore also carried out under some environmental stress conditions to test bacterial survival and to assess bacterial virulence. All results will be presented including information about the effects of different nanoparticles on Pseudomonas syringae bacteria.

Keywords: plant microbiome, nanoparticles, 16S rRNA gene sequencing, bacterial survival

Procedia PDF Downloads 197

Authors: Dipanshu Sur, Ratnabali Chakravorty

Abstract:

Background: Polycystic ovary syndrome (PCOS) is the most common metabolic abnormality such as changes in lipid profile, diabetes, hypertension and metabolic syndrome occurring in young women of reproductive age. Low vitamin D levels were found to be associated with the development of obesity and insulin resistance in women with PCOS. Variants on vitamin D receptor (VDR) gene have also been related to metabolic comorbidities in general population. Aim: The aim of this case-control study was to investigate whether the VDR gene polymorphisms are associated with susceptibility to PCOS. Methods: Women with PCOS and a control group, all aged 16-40 years, were enrolled. Genotyping of VDR Fok-I (rs2228570), VDR Apa-I (rs7975232) as well as GC (rs2282679), DHCR7 (rs12785878) SNPs between groups were determined by using direct sequencing. Serum 25-hydroxyvitamin D [25(OH)] levels were measured by ELISA. Results: Mean serum 25(OH)D in the PCOS and control samples were 19.08±7 and 23.27±6.03 (p=0.048) which were significantly lower in PCOS patients compared with controls. CC genotype of the VDR Apa-I SNP was same frequent in PCOS (25.6%) and controls (25.6%) (OR: 0.9995; 95%CI: 0.528 to 1.8921; p= 0.9987). The CC genotype was also significantly associated with both lower E2 (p=0.031) and Androstenedione levels (p=0.062). We observed a significant association of GC polymorphism with 25(OH)D levels. PCOS women carrying the GG genotype (in GC genes) had significantly higher risk for vitamin D deficiency than women carrying the TT genotype. Conclusions: In conclusion, data from this study indicate that vitamin D levels are lower, and vitamin D deficiency more frequent, in PCOS than in controls. The present findings suggest that the Apa-I, Fok-I polymorphism of the VDR gene is associated with PCOS and seems to modulate ovarian steroid secretion. Further studies are needed to better clarify the biological mechanisms by which the polymorphism influences PCOS risk.

Keywords: vitamin D receptor, polymorphism, vitamin D, polycystic ovary syndrome

Procedia PDF Downloads 294

Authors: Asma Ansari, Afsheen Aman, Shah Ali Ul Qader

Abstract:

In the past few years, numerous concerns have been raised against increased bacterial resistance towards effective drugs and become a debated issue all over the world. With the emergence of drug resistant pathogens, the interaction of natural antimicrobial compounds and antibacterial nanoparticles has emerged as a potential candidate for combating infectious diseases. Microbial diversity in the biome provides an opportunity to screen new species which are capable of producing large number of antimicrobial compounds. Among these antimicrobial compounds, bacteriocins are highly specific and efficient antagonists. A combination of bacteriocin along with nanoparticles could prove to be more potent due to broadened antibacterial spectrum with possibly lower doses. In the current study, silver nanoparticles were synthesized through biological reduction using various isolated bacterial, fungal and yeast strains. Spectroscopy and scanning electron microscopy (SEM) was performed for the confirmation of nanoparticles. Bacteriocin was characterized and purified to homogeneity through gel permeation chromatography. The estimated molecular weight of bacteriocin was 10 kDa. Amino acid analysis and N-terminal sequencing revealed the novelty of the protein. Then antibacterial potential of silver nanoparticles and broad inhibitory spectrum bacteriocin was determined through agar well diffusion assay. These synthesized bacteriocin-Nanoparticles exhibit a good potential for clinical applications as compared to bacteriocin alone. This combination of bacteriocin with nanoparticles will be used as a new sort of biocide in the field of nano-proteomics. The advancement of nanoparticles-mediated drug delivery system will open a new age for rapid eradication of pathogens from biological systems.

Keywords: BAC-IB17, multidrug resistance, purification, silver nanoparticles

Procedia PDF Downloads 485

Authors: M. Khalid, G. N. Singh

Abstract:

In this paper, we have considered the problem of estimation for population mean, on current (second) occasion in the presence of random non response in two-occasion successive sampling under two phase set-up. Modified exponential type estimators have been proposed, and their properties are studied under the assumptions that numbers of sampling units follow a distribution due to random non response situations. The performances of the proposed estimators are compared with linear combinations of two estimators, (a) sample mean estimator for fresh sample and (b) ratio estimator for matched sample under the complete response situations. Results are demonstrated through empirical studies which present the effectiveness of the proposed estimators. Suitable recommendations have been made to the survey practitioners.

Keywords: successive sampling, random non-response, auxiliary variable, bias, mean square error

Procedia PDF Downloads 512

Authors: Omneya M. Helmy, Mona T. Kashef

Abstract:

Aminoglycosides are used in treating a wide range of infections caused by both Gram-negative and Gram positive bacteria. The presence of 16S rRNA methyl transferases (16S-RMTase) is among the newly discovered resistance mechanisms that confer high resistance to clinically useful aminoglycosides. Cephalosporins are the most commonly used antimicrobials in Egypt; therefore, this study was conducted to determine the isolation frequency of 16S rRNA methyl transferases among third generation cephalosporin-resistant clinical isolates in Egypt. One hundred and twenty three cephalosporin resistant Gram-negative clinical isolates were screened for aminoglycoside resistance by the Kirby Bauer disk diffusion method and tested for possible production of 16S-RMTase. PCR testing and sequencing were used to confirm the presence of 16S-RMTase and the associated antimicrobial resistance determinants, as well as the genetic region surrounding the armA gene. Out of 123 isolates, 66 (53.66%) were resistant to at least one aminoglycoside antibiotic. Only one Escherichia coli isolate (E9ECMO) which was totally resistant to all tested aminoglycosides, was confirmed to have the armA gene in association with blaTEM-1, blaCTX-M-15, blaCTX-M-14 and aac(6)-Ib genes. The armA gene was found to be carried on a large A/C plasmid. Genetic mapping of the armA surrounding region revealed, for the first time, the association of armA with aac(6)-Ib on the same transposon. In Conclusion, the isolation frequency of 16S-RMTase was low among the tested cephalosporin-resistant clinical samples. However, a novel composite transposon has been detected conferring high-level aminoglycosides resistance.

Keywords: aminoglcosides, armA gene, β lactmases, 16S rRNA methyl transferases

Procedia PDF Downloads 275

Authors: Shizra Waris, Saleem Akhtar

Abstract:

Big data is a research area receiving attention from academia and IT communities. In the digital world, the amounts of data produced and stored have within a short period of time. Consequently this fast increasing rate of data has created many challenges. In this paper, we use functionalism and structuralism paradigms to analyze the genesis of big data applications and its current trends. This paper presents a complete discussion on state-of-the-art big data technologies based on group and stream data processing. Moreover, strengths and weaknesses of these technologies are analyzed. This study also covers big data analytics techniques, processing methods, some reported case studies from different vendor, several open research challenges and the chances brought about by big data. The similarities and differences of these techniques and technologies based on important limitations are also investigated. Emerging technologies are suggested as a solution for big data problems.

Keywords: computer, it community, industry, big data

Procedia PDF Downloads 184

Authors: Quyen Vu Dang Ha, Oanh Truong Thi, Thuoc Tran Linh, Kent Carpenter, Thinh Doan Vu, Binh Dang Thuy

Abstract:

Enzyme restriction site associated DNA (EzRAD) has recently emerged as a promising genomic approach for exploring fish genetic diversity on a genome-wide scale. This is a simplified method for genomic genotyping in non-model organisms and applied for SNPs discovery in the population genetics of freshwater and marine fish in the South of Vietnam. The observations of regional-scale differentiation of commercial freshwater fish (smallscale croakers Boesemania microlepis) and marine fish (emperor Lethrinus lentjan) are clarified. Samples were collected along Hau River and coastal area in the south and center Vietnam. 52 DNA samples from Tra Vinh, An Giang Province for Boesemania microlepis and 34 DNA samples of Lethrinus lentjan from Phu Quoc, Nha Trang, Da Nang Province were used to prepare EzRAD libraries from genomic DNA digested with MboI and Sau3AI. A pooled sample of regional EzRAD libraries was sequenced using the HiSeq 2500 Illumina platform. For Boesemania microlepis, the small scale population different from upstream to downstream of Hau river were detected, An Giang population exhibited less genetic diversity (SNPs per individual from 14 to 926), in comparison to Tra Vinh population (from 11 to 2172). For Lethrinus lentjan, the result showed the minor difference between populations in the Northern and the Southern Mekong River. The numbers of contigs and SNPs vary from 1315 to 2455 and from 7122 to 8594, respectively (P ≤ 0.01). The current preliminary study reveals regional scale population disconnection probably reflecting environmental changing. Additional sampling and EzRad libraries need to be implemented for resource management in the Mekong Delta.

Keywords: Boesemania microlepis, EzRAD, Lethrinus lentjan, SNPs

Procedia PDF Downloads 496

Authors: Mariam Shah

Abstract:

This paper will examine the potential influence and role of unconscious cognition on judicial decision making. The theoretical underpinnings of this paper rest on phenomenological theory grounded predominantly in Schutzian phenomenology. Aspects of Husserlian and Gadamerian phenomenology will be included within the phenomenological framework put forward in this paper, in an attempt to provide a more complete and thorough account of how unconscious cognition can influence judicial decision making. This paper has far reaching implications, as the framework provides a foundation for unconscious cognitive factors which can work to influence decision making more generally.

Keywords: decision making, Gadamer, Gadamerian, Husserl, Husserlian, judicial decision making, phenomenology, Schutz, Schutzian

Procedia PDF Downloads 406

Authors: Z. Nourmohammadi, F. Farahani, M. Shaker

Abstract:

Aloe is an important commercial crop available in a wide range of species and varieties in international markets. The applications of this plant have been recorded in the ancient cultures of India, Egypt, Greece, Rome and China. Aloe has been used for centuries and is currently being actively studied for medicinal purposes. Aloe is propagated through lateral buds, which is slow, very expensive and low income practice. Nowadays, it has been cultured by in vitro propagation for rapid multiplication of plants, genetic improvement of crops, obtaining disease-free clones and for progressive valuable germplasm. The present study focused on the influence of different phytohormones on rapid in vitro propagation of Aloe plants. We also investigated the effect of gamma radiation on biochemical characters as well as genetic changes. Shoot tip of 2-3 cm were collected from offshoot of Aloe barbadensis and Aloe littoralis, and were inoculated with MS medium containing various concentrations of BA (0.5, 1, 2 mg/l), IAA (0.5, 1 mg/l). The best treatment for a highest shoot number and bud proliferation was MS medium containing 2 mg/l BAP and 0.5 mg/l IAA in A. barbadensis and A. littoralis. Maximum percentage of proliferated shoot buds (90% and 95%) from a single explant were obtained in MS medium after 4-5 weeks of the second and the first subcultures, respectively. Different genome sizes were also indicated among treatments and subcultures. The mixoploids identified in flow cytometery histograms in different treatments. The effect of gamma radiation on A. littoralis showed that by increasing the dose of gamma radiation, amounts of chlorophyll A, B, carotenoids, total protein content and superoxide dismutase were significantly increased compared to control plants. Genetic variation analysis also revealed significant genetic differences between control and gamma radiation treated regenerated plants by AMOVA test. Higher genetic heterozygocity was observed in radiation treated plants. Our findings may provide useful method for improving of Aloe plant proliferation with increasing of useful material such as antioxidant enzymes.

Keywords: aloe, antioxidant enzyme, micropropagation, gamma radiation, genetic variation

Procedia PDF Downloads 420

Authors: Rozeena Shaikh, Syed M Shahid, Jamil Ahmad, Qaisar Mansoor, Muhammad Ismail, Abid Azhar

Abstract:

Introduction: Diabetes mellitus (DM) is a prevalent non-communicable disease worldwide. In most high-income countries as well as middle-income and low- income countries. DM is among the top causes of deaths. DM may lead to many vascular complications like hypertension, nephropathy, retinopathy, neuropathy, and foot. Diabetic nephropathy (DN) characterized by persistent albuminuria is a leading cause of end stage renal failure (ESRF). Pathogenesis of diabetic nephropathy is implicated by the polymorphisms in genes encoding the components of reninangiotensin- aldosteron system (RAAS) which include angiotensinogen (AGT), angiotensin-II receptor and particularly angiotensin converting enzyme (ACE) gene. Method: Study subjects include 110 control, 110 patients with DM without hypertension, 110 patients with DM with hypertension and 110 patients with DN. Blood samples were collected for Biochemical analysis and PCR and sequencing for the specific region of both genes. Results: The frequency of DD genotype and D allele of ACE (I/D) was significantly (p<0.05) high in DM normotensive, DM hypertensive and DN patients when compared to control. The ACE G2350A genotypes and allele frequencies were significantly different (p<0.05) in DM hypertensive patients as compared to control and DN, while no difference was observed between DM normotensive and DN when compared to control. The genotypes and alleles of AGT (M268T) polymorphism were significantly different (p<0.05) in DM normotensive, DM hypertensive and DN when compared to control. Conclusion: The DD genotype and D allele of ACE (I/D), GG genotype and G allele of ACE (G2350A) and the TT genotype and T allele of AGT (M268T) polymorphism have shown a significant difference in genotype and allele frequencies between controls and patients.

Keywords: genetic variations, ACE, AGT, diabetes mellitus, diabetic nephropathy, Pakistan

Procedia PDF Downloads 384

Authors: Gajanan V. Mane, Rashmi More, Mahesh S. Sonawane, Tushar Lodha, Rohit Sharma

Abstract:

The diversity of fungi isolated from two different termite species viz., Odontoterms assmuthi and O. abesus was investigated by dilution- plate method, combined with morphological characteristics and sequencing of internal transcribed spacer region. In total, ninety-six fungi were isolated and purified, out of which 69 isolates were obtained from O. assmuthi belonging to 18 genera and 31 species, whereas 27 isolates were obtained from O. abesus belonging to 15 genera and 17 species. The fungal strains were screened for laccase, amylase, cellulase and pectinase enzymes production. Twenty-seven strains were positive for laccase, 59 strains were positive for amylase, 71 strains were positive for cellulase and 72 strains were positive for pectinase enzymes. The antimicrobial activities of the isolated fungi were tested by the dual plate culture method against standard pathogens. Bioactive secondary metabolites were identified by HPLC and LCMS. Four isolates viz., Penicillium goetzii MG 57, Epicoccum sp. MG 39, Penicillium tanzanicum MG 30, Aspergillus polyporicola MG 54, showed positive antimicrobial activity against standard pathogens, Streptococcus pneumonia MCC 2425, Staphylococcus aureus MCC 2408, Pseudomonas aeruginosa MCC 2080, Escherichia coli MCC 2412, Enterococcus faecalis MCC 2409, Klebsiella pneumonia MCC 2451, Micrococcus luteus MCC 2155 and Candida albicans MCC 1151. In conclusion, the study showed that the insect gut harbor fungal diversity, which is futuristic with biotechnological potential and could be a good source of enzymes and antibiotics.

Keywords: termites, fungi, its, enzyme, antimicrobial activity

Procedia PDF Downloads 95

Authors: Alok Kumar, Hari Ram, Lebin Thomas, Ved Pal Singh

Abstract:

Organic solvent tolerant amylases and proteases of microbial origin are in great demand for their application in transglycosylation of water-insoluble flavanoids and in peptide synthesizing reaction in organic media. Most of the amylases and proteases are unstable in presence of organic solvent. In the present work two different bacterial strains M-11 and VP-07 were isolated from the soil sample of a dairy farm in Delhi, India, for the efficient production of extracellular amylase and protease through their screening on starch agar (SA) and skimmed milk agar (SMA) plates, respectively. Both the strains (M-11 and VP-07) were identified based on morphological, biochemical and 16S rRNA gene sequencing methods. After analysis through Ez-Taxon software, the strains M-11 and VP-07 were found to have maximum pairwise similarity of 98.63% and 100% with Bacillus subtilis subsp. inaquosorum BGSC 3A28 and Bacillus anthracis ATCC 14578 and were therefore identified as Bacillus sp. UKS1 and Bacillus sp. UKS2, respectively. Time course study of enzyme activity and bacterial growth has shown that both strains exhibited typical sigmoid growth behavior and maximum production of amylase (180 U/ml) and protease (78 U/ml) by these strains (UKS1 and UKS2) was commenced during stationary phase of growth at 24 and 20 h, respectively. Thereafter, both amylase and protease were tested for their tolerance towards organic solvents and were found to be active as well stable in p-xylene (130% and 115%), chloroform (110% and 112%), isooctane (119% and 107%), benzene (121% and 104%), n-hexane (116% and 103%) and toluene (112% and 101%, respectively). Owing to such properties, these enzymes can be exploited for their potential application in industries for organic synthesis.

Keywords: amylase, enzyme activity, industrial applications, organic solvent tolerant, protease

Procedia PDF Downloads 332

Authors: Sharjeel Aslam, Vassil Vassilev, Karim Ouazzane

Abstract:

Ontologies and various semantic repositories became a convenient approach for implementing model-driven architectures of distributed systems on the Web. SPARQL is the standard query language for querying such. However, although SPARQL is well-established standard for querying semantic repositories in RDF and OWL format and there are commonly used APIs which supports it, like Jena for Java, its parallel option is not incorporated in them. This article presents a complete framework consisting of an object algebra for parallel RDF and an index-based implementation of the parallel query engine capable of dealing with the distributed RDF ontologies which share common vocabulary. It has been implemented in Java, and for validation of the algorithms has been applied to the problem of organizing virtual exhibitions on the Web.

Keywords: distributed ontologies, parallel querying, semantic indexing, shared vocabulary, SPARQL

Procedia PDF Downloads 193

Authors: Zhenyu Du, Ed Collings, James Meredith

Abstract:

The high cost of composite materials versus conventional materials remains a major barrier to uptake in the transport sector. This is exacerbated by a shortage of skilled labour which makes the labour content of a hand laid composite component (~40 % of total cost) an obvious target for reduction. Automation is a method to remove labour cost and improve quality. This work focuses on the challenges and benefits to automating the manufacturing process from raw fibre to trimmed component. It will detail the experimental work required to complete an automation cell, the control strategy used to integrate all machines and the final benefits in terms of throughput and cost.

Keywords: automation, low cost technologies, processing and manufacturing technologies, resin transfer moulding

Procedia PDF Downloads 283

Authors: Sumit Kumar, Sunil Kumar, Chandan Deep Singh

Abstract:

This paper presents modeling and simulation of flexible robot in an underwater environment. The underwater environment completely contrasts with ground or space environment. The robot in an underwater situation is subjected to various dynamic forces like buoyancy forces, hydrostatic and hydrodynamic forces. The underwater robot is modeled as Rayleigh beam. The developed model further allows estimating the deflection of tip in two directions. The complete dynamics of the underwater robot is analyzed, which is the main focus of this investigation. The control of robot trajectory is not discussed in this paper. Simulation is performed using Symbol Shakti software.

Keywords: bond graph modeling, dynamics. modeling, rayleigh beam, underwater robot

Procedia PDF Downloads 576

Authors: Shuo Liu

Abstract:

In Chinese text classification tasks, redundant words and phrases can interfere with the formation of extracted and analyzed text information, leading to a decrease in the accuracy of the classification model. To reduce irrelevant elements, extract and utilize text content information more efficiently and improve the accuracy of text classification models. In this paper, the text in the corpus is first extracted using the TextRank algorithm for abstraction, the words in the abstract are used as nodes to construct a text graph, and then the graph attention network (GAT) is used to complete the task of classifying the text. Testing on a Chinese dataset from the network, the classification accuracy was improved over the direct method of generating graph structures using text.

Keywords: Chinese natural language processing, text classification, abstract extraction, graph attention network

Procedia PDF Downloads 88

Authors: Shield B. Lin, Sameer Abdali

Abstract:

Computer simulations were performed using MATLAB/Simulink for a vibration isolation system for astronaut’s exercise platform. Simulation parameters initially were based on an on-going experiment in a laboratory at NASA Johnson Space Center. The authors expanded later simulations to include other parameters. A discrete proportional-integral-derivative controller with a low-pass filter commanding a linear actuator served as the active control unit to push and pull a counterweight in balancing the disturbance forces. A spring-damper device is used as an optional passive control unit. Simulation results indicated such design could achieve near complete vibration isolation with small displacements of the exercise platform.

Keywords: control, counterweight, isolation, vibration

Procedia PDF Downloads 144

Authors: Mahmoud Huleihel, George Abu-Aqil, Manal Suleiman, Klaris Riesenberg, Itshak Lapidot, Ahmad Salman

Abstract:

Urinary tract infections (UTIs) are considered to be the most common bacterial infections worldwide, which are caused mainly by Escherichia (E.) coli (about 80%). Klebsiella pneumoniae (about 10%) and Pseudomonas aeruginosa (about 6%). Although antibiotics are considered as the most effective treatment for bacterial infectious diseases, unfortunately, most of the bacteria already have developed resistance to the majority of the commonly available antibiotics. Therefore, it is crucial to identify the infecting bacteria and to determine its susceptibility to antibiotics for prescribing effective treatment. Classical methods are time consuming, require ~48 hours for determining bacterial susceptibility. Thus, it is highly urgent to develop a new method that can significantly reduce the time required for determining both infecting bacterium at the species level and diagnose its susceptibility to antibiotics. Fourier-Transform Infrared (FTIR) spectroscopy is well known as a sensitive and rapid method, which can detect minor molecular changes in bacterial genome associated with the development of resistance to antibiotics. The main goal of this study is to examine the potential of FTIR spectroscopy, in tandem with machine learning algorithms, to identify the infected bacteria at the species level and to determine E. coli susceptibility to different antibiotics directly from patients' urine in about 30minutes. For this goal, 1600 different E. coli isolates were isolated for different patients' urine sample, measured by FTIR, and analyzed using different machine learning algorithm like Random Forest, XGBoost, and CNN. We achieved 98% success in isolate level identification and 89% accuracy in susceptibility determination.

Keywords: urinary tract infections (UTIs), E. coli, Klebsiella pneumonia, Pseudomonas aeruginosa, bacterial, susceptibility to antibiotics, infrared microscopy, machine learning

Procedia PDF Downloads 158

Authors: A. Ferasat, S. Rostampour Yasouri

Abstract:

Seasonal flu is a highly contagious infection caused by influenza viruses. These viruses undergo genetic changes that result in new epidemics across the globe. Medical attention is crucial in severe cases, particularly for the elderly, frail, and those with chronic illnesses, as their immune systems are often weaker. The purpose of this study was to detect new subtypes of the influenza A virus rapidly using a specific RT-PCR method based on the HA gene (hemagglutinin). In the winter and spring of 2022_2023, 120 embryonated egg samples were cultured, suspected of seasonal influenza. RNA synthesis, followed by cDNA synthesis, was performed. Finally, the PCR technique was applied using a pair of specific primers designed based on the HA gene. The PCR product was identified after purification, and the nucleotide sequence of purified PCR products was compared with the sequences in the gene bank. The results showed a high similarity between the sequence of the positive samples isolated from the patients and the sequence of the new strains isolated in recent years. This RT-PCR technique is entirely specific in this study, enabling the detection and multiplication of influenza and its subspecies from clinical samples. The RT-PCR technique based on the HA gene, along with sequencing, is a fast, specific, and sensitive diagnostic method for those infected with influenza viruses and its new subtypes. Rapid molecular diagnosis of influenza is essential for suspected people to control and prevent the spread of the disease to others. It also prevents the occurrence of secondary (sometimes fatal) pneumonia that results from influenza and pathogenic bacteria. The critical role of rapid diagnosis of new strains of influenza is to prepare a drug vaccine against the latest viruses that did not exist in the community last year and are entirely new viruses.

Keywords: influenza, molecular diagnosis, patients, RT-PCR technique

Procedia PDF Downloads 60

Authors: Alexander A. Tokmakov

Abstract:

Cell-free protein synthesis is widely used to synthesize recombinant proteins. It allows genome-scale expression of various polypeptides under strictly controlled uniform conditions. However, only a minor fraction of all proteins can be successfully expressed in the systems of protein synthesis that are currently used. The factors determining expression success are poorly understood. At present, the vast volume of data is accumulated in cell-free expression databases. It makes possible comprehensive bioinformatics analysis and identification of multiple features associated with successful cell-free expression. Here, we describe an approach aimed at identification of multiple physicochemical and structural properties of amino acid sequences associated with protein solubility and aggregation and highlight major correlations obtained using this approach. The developed method includes: categorical assessment of the protein expression data, calculation and prediction of multiple properties of expressed amino acid sequences, correlation of the individual properties with the expression scores, and evaluation of statistical significance of the observed correlations. Using this approach, we revealed a number of statistically significant correlations between calculated and predicted features of protein sequences and their amenability to cell-free expression. It was found that some of the features, such as protein pI, hydrophobicity, presence of signal sequences, etc., are mostly related to protein solubility, whereas the others, such as protein length, number of disulfide bonds, content of secondary structure, etc., affect mainly the expression propensity. We also demonstrated that amenability of polypeptide sequences to cell-free expression correlates with the presence of multiple sites of post-translational modifications. The correlations revealed in this study provide a plethora of important insights into protein folding and rationalization of protein production. The developed bioinformatics approach can be of practical use for predicting expression success and optimizing cell-free protein synthesis.

Keywords: bioinformatics analysis, cell-free protein synthesis, expression success, optimization, recombinant proteins

Procedia PDF Downloads 407

Authors: Subhayan Maity

Abstract:

Complete scenario of cosmic evolution from emergent phase to late time acceleration (i.e. non-singular ever expanding Universe) is a popular preference in the recent cosmology. Yet one can’t exclude the idea that other type of evolution pattern of the Universe may also be possible. Especially, the bouncing scenario is becoming a matter of interest now a days. The present work is an exhibition of such a different pattern of cosmic evolution where the evolution of Universe has been shown as a cyclic thermodynamic process. Under diffusion mechanism (non-equilibrium thermodynamic process), the cosmic evolution has been modelled as [ emergent - accelerated expansion - decelerated expansion - decelerated contraction - accelerated contraction - emergent] .

Keywords: non-equilibrium thermodynamics, non singular evolution of universe, cyclic evolution, diffusive fluid

Procedia PDF Downloads 131

Authors: Bello Muhammad Dogon Kade

Abstract:

The study was conducted to determine the effect of a treated groundnut (Arachis hypogaea) shell in a complete diet on blood metabolites and microbial load in fattening Yankasa rams. The study was conducted at the Teaching and Research Farm (Small Ruminants Unit of Animal Science Department, Faculty of Agriculture, Ahmadu Bello University, Zaria. Each kilogram of groundnut shell was treated with 5% urea and 5% lime for treatments 2 (UTGNS) and 3 (LTGNS), respectively. For treatment 4 (ULTGNS), 1 kg of groundnut shell was treated with 2.5% urea and 2.5% lime, but the shell in treatment 1 was not treated (UNTGNS). Sixteen Yankasa rams were used and randomly assigned to the four treatment diets with four animals per treatment in a completely randomized design (CRD). The diet was formulated to have 14% crude protein (CP) content. Rumen fluid was collected from each ram at the end of the experiment at 0 and 4 hours post-feeding. The samples were then put in a 30 ml bottle and acidified with 5 drops of concentrated sulphuric (0.1N H₂SO4) acid to trap ammonia. The results of the blood metabolites showed that the mean values of NH₃-N differed significantly (P<0.05) among the treatment groups, with rams in the ULTGNS diet having the highest significant value (31.96 mg/L). TVFs were significantly (P<0.05) higher in rams fed UNTGNS diet and higher in total nitrogen; the effect of sampling periods revealed that NH3N, TVFs and TP were significantly (P<0.05) higher in rumen fluid collected 4hrs post feeding among the rams across the treatment groups, but rumen fluid pH was significantly (p<0.05) higher in 0-hour post-feeding in all the rams in the treatment diets. In the treatment and sampling period’s interaction effects, animals on the ULTGNS diet had the highest mean values of NH3N in both 0 and 4 hours post-feeding and were significantly (P<0.5) higher compared to rams on the other treatment diets. Rams on the UTGNS diet had the highest bacteria load of 4.96X105/ml, which was significantly (P<0.05) higher than a microbial load of animals fed UNTGNS, LTGNS and ULTGNS diets. However, protozoa counts were significantly (P<0.05) higher in rams fed the UTGNS diet than those followed by the ULTGNS diet. The results showed that there was no significant difference (P>0.05) in the bacteria count of the animals at both 0 and 4 hours post-feeding. But rumen fungi and protozoa load at 0 hours were significantly (P<0.05) higher than at 4 hours post-feeding. The use of untreated ground groundnut shells in the diet of fattening Yankasa ram is therefore recommended.

Keywords: blood metabolites, microbial load, volatile fatty acid, ammonia, total protein

Procedia PDF Downloads 48

Authors: Narin Salehiyan

Abstract:

The three iodothyronine selenodeiodinases catalyze the start and end of thyroid hormone impacts in vertebrates. Auxiliary examinations of these proteins have been prevented by their indispensably film nature and the wasteful eukaryotic-specific pathway for selenoprotein blend. Hydrophobic cluster examination utilized in combination with Position-specific Iterated Impact uncovers that their extramembrane parcel has a place to the thioredoxin-fold superfamily for which test structure data exists. Besides, a expansive deiodinase locale imbedded within the thioredoxin overlay offers solid similitudes with the dynamic location of iduronidase, a part of the clan GH-A-fold of glycoside hydrolases. This show can clarify a number of comes about from past mutagenesis examinations and grants unused irrefutable experiences into the auxiliary and utilitarian properties of these proteins.

Keywords: glycoside, hydrolase, GH-A-like structure, catalyze

Procedia PDF Downloads 64

Authors: Sumeeta Khurana, Kirti Megha, Amit Gupta, Rakesh Sehgal

Abstract:

Background: Amoebic keratitis is a painful vision threatening infection caused by a free living pathogenic amoeba Acanthamoeba. It can be misdiagnosed and very difficult to treat if not suspected early. The epidemiology of Acanthamoeba genotypes causing infection in our geographical area is not yet known to the best of our knowledge. Objective: To characterize Acanthamoeba isolates from amoebic keratitis patients. Methods: A total of 19 isolates obtained from patients with amoebic keratitis presenting to the Advanced Eye Centre at Postgraduate Institute of Medical Education and Research, a tertiary care centre of North India over a period of last 10 years were included. Their corneal scrapings, lens solution and lens case (in case of lens wearer) were collected for microscopic examination, culture and molecular diagnosis. All the isolates were maintained in the Non Nutrient agar culture medium overlaid with E.coli and 13 strains were axenised and maintained in modified Peptone Yeast Dextrose Agar. Identification of Acanthamoeba genotypes was based on amplification of diagnostic fragment 3 (DF3) region of the 18srRNA gene followed by sequencing. Nucleotide similarity search was performed by BLAST search of sequenced amplicons in GenBank database (http//www.ncbi.nlm.nih.gov/blast). Multiple Sequence alignments were determined by using CLUSTAL X. Results: Nine out of 19 Acanthamoeba isolates were found to belong to Genotype T4 followed by 6 isolates of genotype T11, 3 T5 and 1 T3 genotype. Conclusion: T4 is the predominant Acanthamoeba genotype in our geographical area. Further studies should focus on differences in pathogenicity of these genotypes and their clinical significance.

Keywords: Acanthamoeba, free living amoeba, keratitis, genotype, ocular

Procedia PDF Downloads 229

Authors: Hela Gargouri, Nizar Moalla, Hassen Hadj Kacem

Abstract:

Meat adulteration affecting the safety and quality of food is becoming one of the main concerns of public interest across the world. The drastic consequences on the meat industry highlighted the urgent necessity to control the products' quality and to point out the complexity of both supply and processing circuits. Due to the expansion of this problem, the authentic testing of foods, particularly meat and its products, is deemed crucial to avoid unfair market competition and to protect consumers from fraudulent practices of meat adulteration. The adoption of authentication methods by the food quality-control laboratories is becoming a priority issue. However, in some developing countries, the number of food tests is still insignificant, although a variety of processed and traditional meat products are widely consumed. Little attention has been paid to provide an easy, fast, reproducible, and low-cost molecular test, which could be conducted in a basic laboratory. In the current study, the 359 bp fragment of the cytochrome-b gene was mapped by PCR-RFLP using firstly fresh biological supports (DNA and meat) and then turkey salami as an example of commercial processed meat. This technique has been established through several optimizations, namely: the selection of restriction enzymes. The digestion with BsmAI, SspI, and TaaI succeed to identify the seven included animal species when meat is formed by individual species and when the meat is a mixture of different origin. In this study, the PCR-RFLP technique using universal primer succeed to meet our needs by providing an indirect sequencing method identifying by restriction enzymes the specificities characterizing different species on the same amplicon reducing the number of potential tests.

Keywords: adulteration, animal species, authentication, meat, mtDNA, PCR-RFLP

Procedia PDF Downloads 102