Search results for: genetic analysis

Authors: Sonal Sethi, Mukesh Yadav, Abhimanyu Gupta

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The upcoming field of radiogenomics has the potential to upgrade the role of imaging in lung cancer management by noninvasive characterization of tumor histology and genetic microenvironment. Receptor positivity like epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) genotyping are critical in lung adenocarcinoma for treatment. As conventional identification of receptor positivity is an invasive procedure, we analyzed the features on non-invasive computed tomography (CT), which predicts the receptor positivity in lung adenocarcinoma. Retrospectively, we did a comprehensive study from 77 proven lung adenocarcinoma patients with CT images, EGFR and ALK receptor genotyping, and clinical information. Total 22/77 patients were receptor-positive (15 had only EGFR mutation, 6 had ALK mutation, and 1 had both EGFR and ALK mutation). Various morphological characteristics and metastatic distribution on CT were analyzed along with the clinical information. Univariate and multivariable logistic regression analyses were used. On multivariable logistic regression analysis, we found spiculated margin, lymphangitic spread, air bronchogram, pleural effusion, and distant metastasis had a significant predictive value for receptor mutation status. On univariate analysis, air bronchogram and pleural effusion had significant individual predictive value. Conclusions: Receptor positive lung cancer has characteristic imaging features compared with nonreceptor positive lung adenocarcinoma. Since CT is routinely used in lung cancer diagnosis, we can predict the receptor positivity by a noninvasive technique and would follow a more aggressive algorithm for evaluation of distant metastases as well as for the treatment.

Keywords: lung cancer, multidisciplinary cancer care, oncologic imaging, radiobiology

Procedia PDF Downloads 104

Authors: Willian C. De Brito, Hernan D. C. Munoz, Erlan V. C. Carvalho, Helder L. C. De Oliveira

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In order to improve commute time for small distance trips and relieve large cities traffic, a new transport category has been the subject of research and new designs worldwide. The air taxi travel market promises to change the way people live and commute by using the concept of vehicles with the ability to take-off and land vertically and to provide passenger’s transport equivalent to a car, with mobility within large cities and between cities. Today’s civil air transport remains costly and accounts for 2% of the man-made CO₂ emissions. Taking advantage of this scenario, many companies have developed their own Vertical Take Off and Landing (VTOL) design, seeking to meet comfort, safety, low cost and flight time requirements in a sustainable way. Thus, the use of green power supplies, especially batteries, and fully electric power plants is the most common choice for these arising aircrafts. However, it is still a challenge finding a feasible way to handle with the use of batteries rather than conventional petroleum-based fuels. The batteries are heavy and have an energy density still below from those of gasoline, diesel or kerosene. Therefore, despite all the clear advantages, all electric aircrafts (AEA) still have low flight autonomy and high operational cost, since the batteries must be recharged or replaced. In this sense, this paper addresses a way to optimize the energy consumption in a typical mission of an aerial taxi aircraft. The approach and landing procedure was chosen to be the subject of an optimization genetic algorithm, while final programming can be adapted for take-off and flight level changes as well. A real tilt rotor aircraft with fully electric power plant data was used to fit the derived dynamic equations of motion. Although a tilt rotor design is used as a proof of concept, it is possible to change the optimization to be applied for other design concepts, even those with independent motors for hover and cruise flight phases. For a given trajectory, the best set of control variables are calculated to provide the time history response for aircraft´s attitude, rotors RPM and thrust direction (or vertical and horizontal thrust, for independent motors designs) that, if followed, results in the minimum electric power consumption through that landing path. Safety, comfort and design constraints are assumed to give representativeness to the solution. Results are highly dependent on these constraints. For the tested cases, performance improvement ranged from 5 to 10% changing initial airspeed, altitude, flight path angle, and attitude.

Keywords: air taxi travel, all electric aircraft, batteries, energy consumption, genetic algorithm, landing performance, optimization, performance improvement, tilt rotor, VTOL design

Procedia PDF Downloads 99

Authors: Ruchi Pathania, Ahmad Ahmad, Shireesh Srivastava

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Cyanobacteria is a promising microbe that can capture and convert atmospheric CO₂ and light into valuable industrial bio-products like biofuels, biodegradable plastics, etc. Among their most attractive traits are faster autotrophic growth, whole year cultivation using non-arable land, high photosynthetic activity, much greater biomass and productivity and easy for genetic manipulations. Cyanobacteria store carbon in the form of glycogen which can be hydrolyzed to release glucose and fermented to form bioethanol or other valuable products. Marine cyanobacterial species are especially attractive for countries with scarcity of freshwater. We recently identified a marine native cyanobacterium Synechococcus sp. BDU 130192 which has good growth rate and high level of polyglucans accumulation compared to Synechococcus PCC 7002. In this study, firstly we sequenced the whole genome and the sequences were annotated using the RAST server. Genome scale metabolic model (GSMM) was reconstructed through COBRA toolbox. GSMM is a computational representation of the metabolic reactions and metabolites of the target strain. GSMMs construction through the application of Flux Balance Analysis (FBA), which uses external nutrient uptake rates and estimate steady state intracellular and extracellular reaction fluxes, including maximization of cell growth. The model, which we have named isyn942, includes 942 reactions and 913 metabolites having 831 metabolic, 78 transport and 33 exchange reactions. The phylogenetic tree obtained by BLAST search revealed that the strain was a close relative of Synechococcus PCC 7002. The flux balance analysis (FBA) was applied on the model iSyn942 to predict the theoretical yields (mol product produced/mol CO₂ consumed) for native and non-native products like acetone, butanol, etc. under phototrophic condition by applying metabolic engineering strategies. The reported strain can be a viable strain for biotechnological applications, and the model will be helpful to researchers interested in understanding the metabolism as well as to design metabolic engineering strategies for enhanced production of various bioproducts.

Keywords: cyanobacteria, flux balance analysis, genome scale metabolic model, metabolic engineering

Procedia PDF Downloads 139

Authors: I. Kade Wiratama

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As a result of the significant growth of wind turbines in size, blade load control has become the main challenge for large wind turbines. Many advanced techniques have been investigated aiming at developing control devices to ease blade loading. Amongst them, trailing edge flaps have been proven as effective devices for load alleviation. The present study aims at investigating the potential benefits of flaps in enhancing the energy capture capabilities rather than blade load alleviation. A software tool is especially developed for the aerodynamic simulation of wind turbines utilising blades equipped with flaps. As part of the aerodynamic simulation of these wind turbines, the control system must be also simulated. The simulation of the control system is carried out via solving an optimisation problem which gives the best value for the controlling parameter at each wind turbine run condition. Developing a genetic algorithm optimisation tool which is especially designed for wind turbine blades and integrating it with the aerodynamic performance evaluator, a design optimisation tool for blades equipped with flaps is constructed. The design optimisation tool is employed to carry out design case studies. The results of design case studies on wind turbine AWT 27 reveal that, as expected, the location of flap is a key parameter influencing the amount of improvement in the power extraction. The best location for placing a flap is at about 70% of the blade span from the root of the blade. The size of the flap has also significant effect on the amount of enhancement in the average power. This effect, however, reduces dramatically as the size increases. For constant speed rotors, adding flaps without re-designing the topology of the blade can improve the power extraction capability as high as of about 5%. However, with re-designing the blade pretwist the overall improvement can be reached as high as 12%.

Keywords: flaps, design blade, optimisation, simulation, genetic algorithm, WTAero

Procedia PDF Downloads 318

Authors: Rohit Kothari, Muneer Mohamed, Vivekanandh K., Sunmeet Sandhu, Preema Sinha, Anuj Bhatnagar

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Introduction: Hyper-IgE syndrome is a rare primary immunodeficiency syndrome characterised by triad of severe atopic dermatitis, recurrent pulmonary infections, and recurrent staphylococcal skin infections. The diagnosis requires a high degree of suspicion, typical clinical features, and not mere rise in serum-IgE levels, which may be seen in multiple conditions. Genetic studies are not always possible in a resource poor setting. This study highlights various presentations of Hyper-IgE syndrome in skin of color children. Case-series: Our study had six children of Hyper-IgE syndrome aged twomonths to tenyears. All had onset in first ten months of life except one with a late-onset at two years. All had recurrent eczematoid rash, which responded poorly to conventional treatment, secondary infection, multiple episodes of hospitalisation for pulmonary infection, and raised serum IgE levels. One case had occasional vesicles, bullae, and crusted plaques over both the extremities. Genetic study was possible in only one of them who was found to have pathogenic homozygous deletions of exon-15 to 18 in DOCK8 gene following which he underwent bone marrow transplant (BMT), however, succumbed to lower respiratory tract infection two months after BMT and rest of them received multiple courses of antibiotics, oral/ topical steroids, and cyclosporine intermittently with variable response. Discussion: Our study highlights various characteristics, presentation, and management of this rare syndrome in children. Knowledge of these manifestations in skin of color will facilitate early identification and contribute to optimal care of the patients as representative data on the same is limited in literature.

Keywords: absolute eosinophil count, atopic dermatitis, eczematous rash, hyper-immunoglobulin E syndrome, pulmonary infection, serum IgE, skin of color

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Authors: Mengjie Qu, Yi Wang, Jiawei Ding, Siyu Chen, Yanan Di

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Marine ecosystem is facing intensified multiple stresses caused by environmental contaminants from human activities. Xenobiotics, such as benzo(α)pyrene (BaP) have been discharged into marine environment and cause hazardous impacts on both marine organisms and human beings. As a filter-feeder, marine mussels, Mytilus spp., has been extensively used to monitor the marine environment. However, their genomic alterations induced by such xenobiotics are still kept unknown. In the present study, gills, as the first defense barrier in mussels, were selected to evaluate the genetic instability alterations induced by the exposure to BaP both in vivo and in vitro. Both random amplified polymorphic DNA (RAPD) assay and comet assay were applied as the rapid tools to assess the environmental stresses due to their low money- and time-consumption. All mussels were identified to be the single species of Mytilus coruscus before used in BaP exposure at the concentration of 56 μg/l for 1 & 3 days (in vivo exposure) or 1 & 3 hours (in vitro). Both RAPD and comet assay results were showed significantly increased genomic instability with time-specific altering pattern. After the recovery period in 'in vivo' exposure, the genomic status was as same as control condition. However, the relative higher genomic instabilities were still observed in gill cells after the recovery from in vitro exposure condition. Different repair mechanisms or signaling pathway might be involved in the isolated gill cells in the comparison with intact tissues. The study provides the robust and rapid techniques to exam the genomic stability in marine organisms in response to marine environmental changes and provide basic information for further mechanism research in stress responses in marine organisms.

Keywords: genotoxic impacts, in vivo/vitro exposure, marine mussels, RAPD and comet assay

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Authors: N. R. Prasannakumar, M. N. Maruthi

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The whitefly, Bemisia tabaci (Gennadius) (Hemiptera; Aleyrodidae) is a highly polyphagous pest reported to infest over 600 plant hosts globally. About 42 genetic groups/cryptic species of B. tabaci exist in the world on different hosts. The species have variable behaviour with respect to feeding, development and transmission of viral diseases. Feeding on diverse host plants affect both whitefly development and the population of the endosymbionts harboured by the insects. Due to changes in the level of endosymbionts, the virus transmission efficiency by the vector also gets affected. We investigated these interactions on five host plants – egg plant, tomato, beans, okra and cotton - using a single whitefly species Asia 1 infected with three different bacteria Portiera, Wolbachia and Arsenophonus. The Asia 1 transmits the Tomato leaf curl Bangalore virus (ToLCBV) effectively and thus was used in the interaction studies. We found a significant impact of hosts on whitefly growth and development; eggplant was most favourable host, while okra and tomato were least favourable. Among the endosymbiotic bacteria, the titre of Wolbachia was significantly affected by feeding of B. tabaci on different host plants whereas Arsenophonus and Portiera were unaffected. When whitefly fed on ToLCBV-infected tomato plants, the Arsenophonus population was significantly increased, indicating its previously confirmed role in ToLCBV transmission. Further, screening of total proteins of B. tabaci Asia 1 genetic group interacting with ToLCBV coat protein was carried out using Y2H system. Some of the proteins found to be interacting with ToLCBV CP were HSPs 70kDa, GroEL, nucleoproteins, vitellogenins, apolipophorins, lachesins, enolase. The reported protein thus would be the potential targets for novel whitefly control strategies such as RNAi or novel insecticide target sites for sustainable whitefly management after confirmation of genuine proteins.

Keywords: cDNA, whitefly, ToLCBV, endosymbionts, Y2H

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Authors: Doo Byong Bae, Jae Jun Yoo, Il Gyu Park, Choi Seowon, Oh Chang Kook

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There are several wind load provisions to evaluate the wind response on tank structures such as API, Euro-code, etc. the assessment of wind action applying these provisions is made by performing the finite element analysis using both linear bifurcation analysis and geometrically nonlinear analysis. By comparing the pressure patterns obtained from the analysis with the results of wind tunnel test, most appropriate wind load criteria will be recommended.

Keywords: wind load, finite element analysis, linear bifurcation analysis, geometrically nonlinear analysis

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Authors: Rouhollah Radjabi, Mojtaba Zarei, Elham Sanatgar, Hossein Shouhani

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RAPD molecular markers in order to discrimination of the Iranian native Bombyx mori silkworm breeds were used. DNA extraction using phenol - chloroform was and the qualitative and quantitative measurements of extracted DNA and its dilution, the obtained bands on agarose gel 1.5 percent were marked and analyzed. Results showed that the bands are observed between 250-2500 bp and most bands have been observed as Gilani-orange, the lowest bands observed are Khorasani-lemon. Primer 3 with 100% polymorphism with the highest polymorphism and primer 2 with 61.5 polymorphism had the lowest percentage of polymorphism. Cluster analysis of races and placed them in three main groups, races Gilani - orange, Baghdad and Khorasani -pink if the first group, camel's thorn, Herati - yellow race was alone in the second group and Khorasani – lemon was alone in the third group. The greatest similarity between the races, between Khorasani- pink and Baghdad (0.64). RAPD markers have been determined different silkworm races based on various morphological or economic characteristics except geographic origin.

Keywords: silkworm, molecular marker, RAPD, Iran

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Authors: Behrang Ekrami, Amin Tamadon

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Persian fallow deer (Dama dama mesopotamica) is belonging to the family Cervidae and is only found in a few protected areas in the northwest, north, and southwest of Iran. The aims of this study were analysis of inbreeding and morphometric parameters of semen in male Persian fallow deer to investigate the cause of reduced fertility of this endangered species in Dasht-e-Naz National Refuge, Sari, Iran. The Persian fallow deer semen was collected from four adult bucks randomly during the breeding and non-breeding season from five dehorned and horned deer's BY an artificial vagina. Twelve blood samples was taken from Persian fallow deer and mitochondrial DNA was extracted, amplified, extracted, sequenced, and then were considered for genetic analysis. The Persian fallow deer semen, both with normal and abnormal spermatozoa, is similar to that of domestic ruminants but very smaller and difficult to observe at the primary observation. The post-mating season collected ejaculates contained abnormal spermatozoa, debris and secretion of accessory glands in horned bucks and accessory glands secretion free of any spermatozoa in dehorned or early velvet budding bucks. Microscopic evaluation in all four bucks during the mating season showed the mean concentration of 9×106 spermatozoa/ml. The mean ±SD of age, testes length and testes width was 4.60±1.52 years, 3.58±0.32 and 1.86±0.09 cm, respectively. The results identified 1120 loci (assuming each nucleotide as locus) in which 377 were polymorphic. In conclusion, reduced fertility of male Persian fallow deer may be caused by inbreeding of the protected herd in a limited area of Dasht-e-Naz National Refuge.

Keywords: Persian fallow deer, spermatozoa, reproductive characteristics, morphometric parameters

Procedia PDF Downloads 559

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

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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 486

Authors: Yuzhen Hu, Sirui Wang

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As a training base for intellectual talents, universities have a large number of students. Teaching is a primary activity in universities, and during the teaching process, a large number of people gather both inside and outside the teaching buildings, posing a strong risk of close contact. The class schedule is the fundamental basis for teaching activities in universities and plays a crucial role in the management of teaching order. Different class schedules can lead to varying degrees of indoor gatherings and trajectories of class attendees. In recent years, highly contagious diseases have frequently occurred worldwide, and how to reduce the risk of infection has always been a hot issue related to public safety. "Reducing gatherings" is one of the core measures in epidemic prevention and control, and it can be controlled through scientific scheduling in specific environments. Therefore, the scientific prevention and control goal can be achieved by considering the reduction of the risk of excessive gathering of people during the course schedule arrangement. Firstly, we address the issue of personnel gathering in various pathways on campus, with the goal of minimizing congestion and maximizing teaching effectiveness, establishing a nonlinear mathematical model. Next, we design an improved genetic algorithm, incorporating real-time evacuation operations based on tracking search and multidimensional positive gradient cross-mutation operations, considering the characteristics of outdoor crowd evacuation. Finally, we apply undergraduate course data from a university in Harbin to conduct a case study. It compares and analyzes the effects of algorithm improvement and optimization of gathering situations and explores the impact of path blocking on the degree of gathering of individuals on other pathways.

Keywords: the university timetabling problem, risk prevention, genetic algorithm, risk control

Procedia PDF Downloads 60

Authors: Rim Sghiri, Samia Al Shouli, Hana Benhassine, Nejla Elamri, Zahid Shakoor, Foued Slama, Adel Almogren, Hala Zeglaoui, Elyes Bouajina, Ramzi Zemni

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Objectives: Little is known about genes predisposing to systemic bone loss (SBL) in rheumatoid arthritis (RA). Therefore, we examined the association between SBL and a variant of CD40 gene, which is known to play a critical role in both immune response and bone homeostasis among patients with RA. Methods: CD40 rs48104850 was genotyped in 176 adult RA patients. Bone mineral density (BMD) was measured using dual-energy X-ray absorptiometry (DXA). Results: Low BMD was observed in 116 (65.9%) patients. Among them, 60 (34.1%) had low femoral neck (FN) Z score, 72 (40.9%) had low total femur (TF) Z score, and 105 (59.6%) had low lumbar spine (LS) Z score. CD40 rs4810485 was found to be associated with reduced TF Z score with the CD40 rs4810485 T allele protecting against reduced TF Z score (OR = 0.40, 95% CI = 0.23-0.68, p = 0.0005). This association was confirmed in the multivariate logistic regression analysis (OR=0.31, 95% CI= 0.16-0.59, p=3.84 x 10₋₄). Moreover, median FN BMD was reduced among RA patients with CD40 rs4810485 GG genotype compared to RA patients harbouring CD40 rs4810485 TT and GT genotypes (0.788± 0.136 versus 0.826± 0.146g/cm², p=0.001). Conclusion: This study, for the first time ever, demonstrated an association between a CD40 genetic variant and SBL among patients with RA.

Keywords: rheumatoid arthritis, CD40 gene, bone mineral density, systemic bone loss, rs48104850

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Authors: Samson Abayomi Olasoju, Olufemi Adekunle, Titilope Edun, Johnson Owoseni

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Science offers opportunities for revolutionizing human activities, enriched by input from scientific research and technology. Biotechnology is a major force for development in developing countries such as Nigeria. It is found to contribute to solving human problems like water and food insecurity that impede national development and threaten peace wherever it is applied. This review identified the problems of agricultural biotechnology in Nigeria. On the part of rural farmers, there is a lack of adequate knowledge or awareness of biotechnology despite the fact that they constitute the bulk of Nigerian farmers. On part of the government, the problems include: lack of adequate implementation of government policy on bio-safety and genetically modified products, inadequate funding of education as well as research and development of products related to biotechnology. Other problems include: inadequate infrastructures (including laboratory), poor funding and lack of national strategies needed for development and running of agricultural biotechnology. In spite of all the challenges associated with agricultural biotechnology, its prospects still remain great if Nigeria is to meet with the food needs of the country’s ever increasing population. The introduction of genetically engineered products will lead to the high productivity needed for commercialization and food security. Insect, virus and other related diseases resistant crops and livestock are another viable area of contribution of biotechnology to agricultural production. In conclusion, agricultural biotechnology will not only ensure food security, but, in addition, will ensure that the local farmers utilize appropriate technology needed for large production, leading to the prosperity of the farmers and national economic growth, provided government plays its role of adequate funding and good policy implementation.

Keywords: biosafety, biotechnology, food security, genetic engineering, genetic modification

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Authors: Othman E. Othman, Agnés Germot, Daniel Petit, Abderrahman Maftah

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Threats to the biodiversity are increasing due to the loss of genetic diversity within the species utilized in agriculture. Due to the progressive substitution of the less productive, locally adapted and native breeds by highly productive breeds, the number of threatened breeds is increased. In these conditions, it is more strategically important than ever to preserve as much the farm animal diversity as possible, to ensure a prompt and proper response to the needs of future generations. Mitochondrial (mtDNA) sequencing has been used to explain the origins of many modern domestic livestock species. Studies based on sequencing of sheep mitochondrial DNA showed that there are five maternal lineages in the world for domestic sheep breeds; A, B, C, D and E. Because of the eastern location of Egypt in the Mediterranean basin and the presence of fat-tailed sheep breeds- character quite common in Turkey and Syria- where genotypes that seem quite primitive, the phylogenetic studies of Egyptian sheep breeds become particularly attractive. We aimed in this work to clarify the genetic affinities, biodiversity and phylogeny of five Egyptian sheep breeds using cytochrome B sequencing. Blood samples were collected from 63 animals belonging to the five tested breeds; Barki, Rahmani, Ossimi, Saidi and Sohagi. The total DNA was extracted and the specific primer allowed the conventional PCR amplification of the cytochrome B region of mtDNA (approximately 1272 bp). PCR amplified products were purified and sequenced. The alignment of Sixty-three samples was done using BioEdit software. DnaSP 5.00 software was used to identify the sequence variation and polymorphic sites in the aligned sequences. The result showed that the presence of 34 polymorphic sites leading to the formation of 18 haplotypes. The haplotype diversity in five tested breeds ranged from 0.676 in Rahmani breed to 0.894 in Sohagi breed. The genetic distances (D) and the average number of pairwise differences (Dxy) between breeds were estimated. The lowest distance was observed between Rahmani and Saidi (D: 1.674 and Dxy: 0.00150) while the highest distance was observed between Ossimi and Sohagi (D: 5.233 and Dxy: 0.00475). Neighbour-joining (Phylogeny) tree was constructed using Mega 5.0 software. The sequences of the 63 analyzed samples were aligned with references sequences of different haplogroups. The phylogeny result showed the presence of three haplogroups (HapA, HapB and HapC) in the 63 examined samples. The other two haplogroups described in literature (HapD and HapE) were not found. The result showed that 50 out of 63 tested animals cluster with haplogroup B (79.37%) whereas 7 tested animals cluster with haplogroup A (11.11%) and 6 animals cluster with haplogroup C (9.52%). In conclusion, the phylogenetic reconstructions showed that the majority of Egyptian sheep breeds belonging to haplogroup B which is the dominant haplogroup in Eastern Mediterranean countries like Syria and Turkey. Some individuals are belonging to haplogroups A and C, suggesting that the crosses were done with other breeds for characteristic selection for growth and wool quality.

Keywords: cytochrome B, diversity, phylogheny, Egyptian sheep breeds

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Authors: Dalave S. C., S. G. Auti, B. J. Apparao

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Centella asiatica (L) Urban, commonly known as Brahmi and Mandookaparni is a valuable medicinal plant highly valued for its asiaticoside and madecassoside. It is widely used in Ayurveda and Unani systems of medicine. Attempts are made in the present investigation to improve the genotype of Centella plant that can yield higher amount of the therapeutically active compounds viz., asiaticosides and madecassosides, employing techniques of polyploidy breeding. Young developing shoots of Centella were treated with different concentrations of colchicine for varying time intervals. 0.4 % colchicine for 6 hours duration at room temperature was effective in inducing autopolyploidy in this plant. The colchicine treated plants were allowed to reproduce vegetatively for several generations in a polyhouse. The colchicine treated plants showed significant increase in plant size, fresh & dry weights, vigorous growth, broad leaves and double the number of chromosomes. HPTLC analysis of dried leaves of control and polyploid plants, even after 9th generations, revealed that the tetraploids synthesized at two times more asiaticoside and madecassoside, as compared to control, untreated diploid plants.

Keywords: Centella asiatica, polyploidy, asiaticosides, madecassoside, HPTLC

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Authors: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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Authors: Enea Danut Nicolae, Osman (Defta) Aurelia, Vidu Livia, Marginean Gheorghe, Defta Nicoleta, Moise Andrada

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Today, as a result of population growth, there is an increase in demand for animal products; milk and dairy products are an important part of this category. Maintaining production at maximum levels for as long as possible is one of the main objectives of dairy farmers. Over the course of lactation, a cow's milk production is not uniform. During the initial stage of lactation, the cow's milk production follows an upward slope, a plateau, and then a downward slope, which is a reflection of the lactation curve. The evolution of the lactation curve is influenced by numerous factors, which are genetic, exploitation, physiological, environmental and technological. The aim of this study was to observe the lactation curve of Holstein cows in Romania and determine the extent to which they conform to the expected pattern. In addition, there has been an analysis of the factors which have an influence on this curve and the extent of this influence. In order to be able to carry out the present study, data were collected from three farms located in three different geographical areas. To highlight the findings, the data collected was then statistically processed and graphically interpreted. All the farms have only Holstein cows, which are kept in free stalls.

Keywords: lactation curve, Holstein, milk production, influencing factors

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Authors: Shivani Sharma, Prashant Saxena, Inamul Hasan Madar

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Since the time of Darwin, it has been considered that genetic change is the direct indicator of variation in phenotype. But a few studies in system biology in the past years have proposed that epigenetic developmental processes also affect the phenotype thus shifting the focus from a linear genotype-phenotype map to a non-linear G-P map. In this paper, we attempt at explaining the evolution of colour vision in mammals by taking LWS/ Long-wave sensitive gene under consideration.

Keywords: evolution, phenotypes, epigenetics, LWS gene, G-P map

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Authors: B. Grygalewicz, R. Woroniecka, J. Rygier, K. Borkowska, A. Labak, B. Nowakowska, B. Pienkowska-Grela

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Introduction: Chronic lymphocytic leukemia (CLL) is the most common form of adult leukemia in the Western world. Hemizygous and or homozygous loss at 13q14 occur in more than half of cases and constitute the most frequent chromosomal abnormality in CLL. It is believed that deletions 13q14 play a role in CLL pathogenesis. Two microRNA genes miR-15a and miR- 16-1 are targets of 13q14 deletions and plays a tumor suppressor role by targeting antiapoptotic BCL2 gene. Deletion size, as a single change detected in FISH analysis, has haprognostic significance. Patients with small deletions, without RB1 gene involvement, have the best prognosis and the longest overall survival time (OS 133 months). In patients with bigger deletion region, containing RB1 gene, prognosis drops to intermediate, like in patients with normal karyotype and without changes in FISH with overall survival 111 months. Aim: Precise delineation of 13q14 deletions regions in two groups of CLL patients, with mono- and biallelic deletions and qualifications of their prognostic significance. Methods: Detection of 13q14 deletions was performed by FISH analysis with CLL probe panel (D13S319, LAMP1, TP53, ATM, CEP-12). Accurate deletion size detection was performed by CGH Haematological Cancer and SNP array (8x60K). Results: Our investigated group of CLL patients with the 13q14 deletion, detected by FISH analysis, comprised two groups: 18 patients with monoallelic deletions and 18 patients with biallelic deletions. In FISH analysis, in the monoallelic group the range of cells with deletion, was 43% to 97%, while in biallelic group deletion was detected in 11% to 94% of cells. Microarray analysis revealed precise deletion regions. In the monoallelic group, the range of size was 348,12 Kb to 34,82 Mb, with median deletion size 7,93 Mb. In biallelic group discrepancy of total deletions, size was 135,27 Kb to 33,33 Mb, with median deletion size 2,52 Mb. The median size of smaller deletion regions on one copy chromosome 13 was 1,08 Mb while the average region of bigger deletion on the second chromosome 13 was 4,04 Mb. In the monoallelic group, in 8/18 deletion region covered RB1 gene. In the biallelic group, in 4/18 cases, revealed deletion on one copy of biallelic deletion and in 2/18 showed deletion of RB1 gene on both deleted 13q14 regions. All minimal deleted regions included miR-15a and miR-16-1 genes. Genetic results will be correlated with clinical data. Conclusions: Application of CGH microarrays technique in CLL allows accurately delineate the size of 13q14 deletion regions, what have a prognostic value. All deleted regions included miR15a and miR-16-1, what confirms the essential role of these genes in CLL pathogenesis. In our investigated groups of CLL patients with mono- and biallelic 13q14 deletions, patients with biallelic deletion presented smaller deletion sizes (2,52 Mb vs 7,93 Mb), what is connected with better prognosis.

Keywords: CLL, deletion 13q14, CGH microarrays, SNP array

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Authors: Chih-Jer Lin, Jian-Hong Hou

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Industry 4.0 is a vision of integrated industry implemented by artificial intelligent computing, software, and Internet technologies. The main goal of industry 4.0 is to deal with the difficulty owing to competitive pressures in the marketplace. For today’s manufacturing factories, the type of production is changed from mass production (high quantity production with low product variety) to medium quantity-high variety production. To offer flexibility, better quality control, and improved productivity, robot manipulators are used to combine material processing, material handling, and part positioning systems into an integrated manufacturing system. To implement the automated system for sheet metal bending operations, motion planning of a 7-degrees of freedom (DOF) robot is studied in this paper. A virtual reality (VR) environment of a bending cell, which consists of the robot and a bending machine, is established using the virtual robot experimentation platform (V-REP) simulator. For sheet metal bending operations, the robot only needs six DOFs for the pick-and-place or tracking tasks. Therefore, this 7 DOF robot has more DOFs than the required to execute a specified task; it can be called a redundant robot. Therefore, this robot has kinematic redundancies to deal with the task-priority problems. For redundant robots, Pseudo-inverse of the Jacobian is the most popular motion planning method, but the pseudo-inverse methods usually lead to a kind of chaotic motion with unpredictable arm configurations as the Jacobian matrix lose ranks. To overcome the above problem, we proposed a method to formulate the motion planning problems as optimization problem. Moreover, a genetic algorithm (GA) based method is proposed to deal with motion planning of the redundant robot. Simulation results validate the proposed method feasible for motion planning of the redundant robot in an automated sheet-metal bending operations.

Keywords: redundant robot, motion planning, genetic algorithm, obstacle avoidance

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Authors: Liu Yao, B. T. Wan Maseri, Wan Mohd, B. T. Nurul Izzah, Mohd Shah, Wei Wei

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Effectively managing knowledge has become a vital weapon for businesses to survive or to succeed in the increasingly competitive market. But do they perform environmental analysis when managing knowledge? If yes, how is the level and significance? This paper established a conceptual framework covering the basic knowledge management activities (KMA) to examine their contribution towards organizational performance (OP). Environmental analysis (EA) was then investigated from both internal and external aspects, to identify its effects on that contribution. Data was collected from 400 Chinese SMEs by questionnaires. Cronbach's α and factor analysis were conducted. Regression results show that the external analysis presents higher level than internal analysis. However, the internal analysis mediates the effects of external analysis on the KMA-OP relation and plays more significant role in the relation comparing with the external analysis. Thus, firms shall improve environmental analysis especially the internal analysis to enhance their KM practices.

Keywords: knowledge management, environmental analysis, performance, mediating, small sized enterprises, medium sized enterprises

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Authors: Debabrata Biswas

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The current trend in the development of antibiotic resistance by multiple bacterial pathogens has resulted in a troubling loss of effective antibiotic options for human. The emergence of multi-drug-resistant pathogens has necessitated higher dosages and combinations of multiple antibiotics, further exacerbating the problem of antibiotic resistance. Zoonotic bacterial pathogens, such as Salmonella, Campylobacter, Shiga toxin-producing Escherichia coli (such as enterohaemorrhagic E. coli or EHEC), and Listeria are the most common and predominant foodborne enteric infectious agents. It was observed that these pathogens gained/developed their ability to survive in the presence of antibiotics either in farm animal gut or farm environment and researchers believe that therapeutic and sub-therapeutic antibiotic use in farm animal production might play an important role in it. The mechanism of action of antimicrobial components used in farm animal production in genomic interplay in the gut and farm environment, has not been fully characterized. Even the risk of promoting the exchange of mobile genetic elements between microbes specifically pathogens needs to be evaluated in depth, to ensure sustainable farm animal production, safety of our food and to mitigate/limit the enteric infection with multiple antibiotic resistant bacterial pathogens. Due to the consumer’s demand and considering the current emerging situation, many countries are in process to withdraw antibiotic use in farm animal production. Before withdrawing use of the sub-therapeutic antibiotic or restricting the use of therapeutic antibiotics in farm animal production, it is essential to find alternative natural antimicrobials for promoting the growth of farm animal and/or treating animal diseases. Further, it is also necessary to consider whether that compound(s) has the potential to trigger the acquisition or loss of genetic materials in zoonotic and any other bacterial pathogens. Development of alternative therapeutic and sub-therapeutic antimicrobials for farm animal production and food processing and preservation and their effective implementation for sustainable strategies for farm animal production as well as the possible risk for horizontal gene transfer in major enteric pathogens will be focus in the study.

Keywords: food safety, natural antimicrobial, sustainable farming, antibiotic resistance

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Authors: Ayse Ozge Demir, Nihat Mert

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This study has been carried out in order to determine the polymorphic traits of various biochemical parameters in goat breeds which are native to Turkey. For this purpose, Angora and Hair goats breeds were chosen as live materials. Two different herds for each breed were selected from Ankara and Antalya, respectively. Blood samples were taken from a total of 120 goats aged between 2 and 4 which was made up of 60 Angora goats and 60 Hair goats. All which derived equally from 4 lots of herds. Analyses were performed for the polymorphic determination of the Haemoglobin (Hb), Transferrine (Tf), Ceruloplasmin (Cp) and Glutathione (GSH). Hb types were determined by starch gel electrophoresis and Tf types were detected by SDS-PAGE electrophoresis. Furthermore, Cp and GSH analyses were performed by spectrophotometrically. Following the analysis, Hb types were found as 3 genotypes (AA, AB, BB) controlled by 2 allel genes. Tf types were found as 6 genotypes (AA, AB, AC, BB, BC, CC) controlled by 3 allele genes. Findings for Hb was in line with the Hardy-Weinberg Equilibrium (HWE) in Angora goats while the Hair goat was not found to be in line. Moreover, Tf was found in line with the HWE for 2 separate goat breeds. The levels of Cp and GSH of two breeds were significantly different from other (P<0.0001). The findings are recorded as a source of reference for prospective polymorphism studies.

Keywords: electrophoresis, genetic resources, goats, spectrophotometer

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Authors: Zahra Mohajer, Afsaneh Soltani

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

Keywords: doping, PEDs, sports, WADA

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Authors: Talal Alsulaiman, Khaldoun Khashanah

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In this paper, we provided a literature survey on the artificial stock problem (ASM). The paper began by exploring the complexity of the stock market and the needs for ASM. ASM aims to investigate the link between individual behaviors (micro level) and financial market dynamics (macro level). The variety of patterns at the macro level is a function of the AFM complexity. The financial market system is a complex system where the relationship between the micro and macro level cannot be captured analytically. Computational approaches, such as simulation, are expected to comprehend this connection. Agent-based simulation is a simulation technique commonly used to build AFMs. The paper proceeds by discussing the components of the ASM. We consider the roles of behavioral finance (BF) alongside the traditionally risk-averse assumption in the construction of agent's attributes. Also, the influence of social networks in the developing of agents’ interactions is addressed. Network topologies such as a small world, distance-based, and scale-free networks may be utilized to outline economic collaborations. In addition, the primary methods for developing agents learning and adaptive abilities have been summarized. These incorporated approach such as Genetic Algorithm, Genetic Programming, Artificial neural network and Reinforcement Learning. In addition, the most common statistical properties (the stylized facts) of stock that are used for calibration and validation of ASM are discussed. Besides, we have reviewed the major related previous studies and categorize the utilized approaches as a part of these studies. Finally, research directions and potential research questions are argued. The research directions of ASM may focus on the macro level by analyzing the market dynamic or on the micro level by investigating the wealth distributions of the agents.

Keywords: artificial stock markets, market dynamics, bounded rationality, agent based simulation, learning, interaction, social networks

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Authors: Lydia Tan, Philippe Lemey, Lieselot Houspie, Marco Viveen, Darren Martin, Frank Coenjaerts

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Introduction: Human respiratory syncytial virus (hRSV) is the leading cause of severe respiratory tract infections in infants under the age of two. Genomic substitutions and related evolutionary dynamics of hRSV are of great influence on virus transmission behavior. The evolutionary patterns formed are due to a precarious interplay between the host immune response and RSV, thereby selecting the most viable and less immunogenic strains. Studying genomic profiles can teach us which genes and consequent proteins play an important role in RSV survival and transmission dynamics. Study design: In this study, genetic diversity and evolutionary rate analysis were conducted on 36 RSV subgroup B whole genome sequences and 37 subgroup A genome sequences. Clinical RSV isolates were obtained from nasopharyngeal aspirates and swabs of children between 2 weeks and 5 years old of age. These strains, collected during epidemic seasons from 2001 to 2011 in the Netherlands and Belgium by either conventional or 454-sequencing. Sequences were analyzed for genetic diversity, recombination events, synonymous/non-synonymous substitution ratios, epistasis, and translational consequences of mutations were mapped to known 3D protein structures. We used Bayesian statistical inference to estimate the rate of RSV genome evolution and the rate of variability across the genome. Results: The A and B profiles were described in detail and compared to each other. Overall, the majority of the whole RSV genome is highly conserved among all strains. The attachment protein G was the most variable protein and its gene had, similar to the non-coding regions in RSV, more elevated (two-fold) substitution rates than other genes. In addition, the G gene has been identified as the major target for diversifying selection. Overall, less gene and protein variability was found within RSV-B compared to RSV-A and most protein variation between the subgroups was found in the F, G, SH and M2-2 proteins. For the F protein mutations and correlated amino acid changes are largely located in the F2 ligand-binding domain. The small hydrophobic phosphoprotein and nucleoprotein are the most conserved proteins. The evolutionary rates were similar in both subgroups (A: 6.47E-04, B: 7.76E-04 substitution/site/yr), but estimates of the time to the most recent common ancestor were much lower for RSV-B (B: 19, A: 46.8 yrs), indicating that there is more turnover in this subgroup. Conclusion: This study provides a detailed description of whole RSV genome mutations, the effect on translation products and the first estimate of the RSV genome evolution tempo. The immunogenic G protein seems to require high substitution rates in order to select less immunogenic strains and other conserved proteins are most likely essential to preserve RSV viability. The resulting G gene variability makes its protein a less interesting target for RSV intervention methods. The more conserved RSV F protein with less antigenic epitope shedding is, therefore, more suitable for developing therapeutic strategies or vaccines.

Keywords: drug target selection, epidemiology, respiratory syncytial virus, RSV

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Authors: Faheem Shahzad Baloch, Muhammad Azhar Nadeem, Muhammad Amjad Nawaz, Ephrem Habyarimana, Gonul Comertpay, Tolga Karakoy, Rustu Hatipoglu, Mehmet Zahit Yeken, Vahdettin Ciftci

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Turkey is considered a bridge between Europe, Asia, and Africa and possibly played an important role in the distribution of many crops including common bean. Hundreds of common bean landraces can be found in Turkey, particularly in farmers’ fields, and they consistently contribute to the overall production. To investigate the existing genetic diversity and hybridization events between the Andean and Mesoamerican gene pools in the Turkish common bean, 188 common bean accessions (182 landraces and 6 modern cultivars as controls) were collected from 19 different Turkish geographic regions. These accessions were characterized using phenotypic data (growth habit and seed weight), geographic provenance, 12557 high-quality whole-genome DArTseq markers, and 3767 novel DArTseq loci were also identified. The clustering algorithms resolved the Turkish common bean landrace germplasm into the two recognized gene pools, the Mesoamerican and Andean gene pools. Hybridization events were observed in both gene pools (14.36% of the accessions) but mostly in the Mesoamerican (7.97% of the accessions), and was low relative to previous European studies. The lower level of hybridization witnessed the existence of Turkish common bean germplasm in its original form as compared to Europe. Mesoamerican gene pool reflected a higher level of diversity, while the Andean gene pool was predominant (56.91% of the accessions), but genetically less diverse and phenotypically more pure, reflecting farmers greater preference for the Andean gene pool. We also found some genetically distinct landraces and overall, a meaningful level of genetic variability which can be used by the scientific community in breeding efforts to develop superior common bean strains.

Keywords: bean germplasm, DArTseq markers, genotyping by sequencing, Turkey, whole genome diversity

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Authors: Alime Cengiz, Talip Kahyaoglu

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Roasting process has the major importance to obtain desired aromatic taste of nuts. In this study, two kinds of roasting process were applied to hulled sesame seeds - vacuum oven and hot air roasting. Efficiency of Gene Expression Programming (GEP), a new soft computing technique of evolutionary algorithm that describes the cause and effect relationships in the data modelling system, and response surface methodology (RSM) were examined in the modelling of roasting processes over a range of temperature (120-180°C) for various times (30-60 min). Color attributes (L*, a*, b*, Browning Index (BI)), textural properties (hardness and fracturability) and moisture content were evaluated and modelled by RSM and GEP. The GEP-based formulations and RSM approach were compared with experimental results and evaluated according to correlation coefficients. The results showed that both GEP and RSM were found to be able to adequately learn the relation between roasting conditions and physical and textural parameters of roasted seeds. However, GEP had better prediction performance than the RSM with the high correlation coefficients (R2 >0.92) for the all quality parameters. This result indicates that the soft computing techniques have better capability for describing the physical changes occuring in sesame seeds during roasting process.

Keywords: genetic expression programming, response surface methodology, roasting, sesame seed

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Authors: Lavinia Ruta, Ileana Farcasanu

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The yeast surface display (YSD) technique enables the expression of proteins on yeast cell surfaces, facilitating the identification and isolation of proteins with targeted binding properties, such as nanobodies. Nanobodies, derived from camelid species, are single-domain antibody fragments renowned for their high affinity and specificity towards target proteins, making them valuable in research and potentially in therapeutics. Their advantages include a compact size (~15 kDa), robust stability, and the ability to target challenging epitopes. The project endeavors to establish and validate a platform for producing Green Fluorescent Protein (GFP) and mCherry nanobodies using the yeast surface display method. mCherry, a prevalent red fluorescent protein sourced from coral species, is commonly utilized as a genetic marker in biological studies due to its vibrant red fluorescence. The GFP-nanobody, a single variable domain of heavy-chain antibodies (VHH), exhibits specific binding to GFP, offering a potent means for isolating and engineering fluorescent protein fusions across various biological research domains. Both GFP and mCherry nanobodies find specific utility in cellular imaging and protein analysis applications.

Keywords: YSD, nanobodies, GFP, Saccharomyces cerevisiae

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