Search results for: genetic diversity and viral proteins

Authors: Victor Prevost, Solene Landerneau, Michel Duhamel, Joel Sternheimer, Olivier Gallet, Pedro Ferrandiz, Marwa Mokni

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The search for homologous proteins is one of the ongoing challenges in biology and bioinformatics. Traditionally, a pair of proteins is thought to be homologous when they originate from the same ancestral protein. In such a case, their sequences share similarities, and advanced scientific research effort is spent to investigate this question. On this basis, we propose the Protein-Wave Alignment Tool (”P-WAT”) developed within the framework of the France Relance 2030 plan. Our work takes into consideration the mass-related wave aspect of protein biosynthesis, by associating specific frequencies to each amino acid according to its mass. Amino acids are then regrouped within their mass category. This way, our algorithm produces specific alignments in addition to those obtained with a common amino acid coding system. For this purpose, we develop the ”P-WAT” original algorithm, able to address large protein databases, with different attributes such as species, protein names, etc. that allow us to align user’s requests with a set of specific protein sequences. The primary intent of this algorithm is to achieve efficient alignments, in this specific conceptual frame, by minimizing execution costs and information loss. Our algorithm identifies sequence similarities by searching for matches of sub-sequences of different sizes, referred to as primers. Our algorithm relies on Boolean operations upon a dot plot matrix to identify primer amino acids common to both proteins which are likely to be part of a significant alignment of peptides. From those primers, dynamic programming-like traceback operations generate alignments and alignment scores based on an adjusted PAM250 matrix.

Keywords: protein, alignment, homologous, Genodic

Procedia PDF Downloads 115

Authors: Yasir Ali, Farhatullah

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The present study was conducted to estimate the genetic variability, heritability and genetic advance in six parental lines and their 56 genotypes derived from five introgressed brassica populations on the basis of morphological and biochemical traits. The experiment was laid out in a randomized complete block design with two replications at The University of Agriculture Peshawar-Pakistan during growing season of 2015-2016. The ANOVA of all traits of F5:6 populations showed highly significant differences (P ≤ 0.01) for all morphological and biochemical traits. Among F5:6 populations, the genotype 2(526) was earlier in flowering (108.65 days), and genotype 14(485) was earlier in maturity (170 days). Tallest plants (182.5 cm), largest main raceme (91.5 cm) and maximum number of pods (80.5) on main raceme were recorded for genotype 17(34). Maximum primary branches plant-1(6.2) and longest pods (10.26 cm) were recorded for genotype 15, while genotype 16(171) had more seeds pod⁻¹ (22) and gave maximum yield plant-1 (30.22 g). The maximum 100-seed weight (0.60 g) was observed for genotype 10(506) while high protein content (22.61%) was recorded for genotype 4(99). Maximum oil content (54.08 %) and low linoleic acid (7.07 %) were produced by genotype (12(138) and low glucosinolate (59.01 µMg⁻¹) was recorded for genotype 21(113). The genotype 27(303) having high oleic acid content (51.73 %) and genotype 1(209) gave low erucic acid (35.97 %). Among the F5:6 populations moderate to high heritability observed for all morphological and biochemical traits coupled with high genetic advance. Cluster analysis grouped the 56 F5:6 populations along their parental lines into seven different groups. Each group was different from the other group on the basis of morphological and biochemical traits. Moreover all the F5:6 populations showed sufficient variability. Genotypes 10(506) and 16(171) were superior for high seed yield⁻¹, 100-seeds weight, and seed pod⁻¹ and are recommended for future breeding program.

Keywords: Brassicaceae, biochemical characterization, introgression, morphological characterization

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Authors: Andrea Vasquez, Pedro Maldonado-Alvarado

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In general, 'gluten-free' foods like breadmaking products provide functional or nutraceutical benefits for the consumer's health and increased their demand on the market. In Ecuador, there is an overproduction of superfoods, and the food by-products are undervalued. For the first time, to the author's best knowledge, gluten-free bread mixtures from quinoa and banana flour, cassava starch, lupine flour (LF), or whey protein (WP) with hydroxypropylmethylcellulose (HPMC) and transglutaminase (TG) were evaluated on their functional and sensory properties. Free amino groups and thiols, rheology, and electrophoresis SDS PAGE were performed to analyze the crosslinking of TG at different concentrations with HC or PL proteins. Dough characterization, pasting properties were evaluated, respectively, by a MIXOLAB and a rheometer with a pasting cell. The texture, porosity, and loaf volume were characterized using a texturometer, ImageJ software, and breadmaking ability, respectively. Finally, a breadmaking aptitude and sensorial bread acceptability were performed. A significant decrease in the content of free amino groups (0.16 to 0.11 and 0.46 to 0.36 mM/mg of protein) and free thiol groups (0.37 to 0.21 and 1.79 to 1.32 mM/mg protein) was observed when 1.0% and 0.5% TG were added to LF and WP, respectively. In apparent viscosity analysis, the action of TG on HC proteins changes their viscosity, while the viscosity of LF is not modified by TG. Results of electrophoresis in PL showed bands of higher molecular weight of different fragments of proteins with 1% TG. Formulation with 59.8, 39.9, 160.8, 6.0, 1.0, and 1.5% of, respectively, QF, BF, CS, LF or WP, TG, and HPMC had the best properties in dough parameters, pasting parameters (lower pasting temperature and higher peak viscosity), best crumb structure, lower crumb hardness and higher loaf volume (2.24 and 2.28 mL/g). All the loaves of bread were acceptable in baking aptitude and general acceptability.

Keywords: breadmaking, gluten-free, superfoods, by-products, Ecuador

Procedia PDF Downloads 135

Authors: Atilla Bayram

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This paper presents the trajectory tracking control of a spatial redundant hybrid manipulator. This manipulator consists of two parallel manipulators which are a variable geometry truss (VGT) module. In fact, each VGT module with 3-degress of freedom (DOF) is a planar parallel manipulator and their operational planes of these VGT modules are arranged to be orthogonal to each other. Also, the manipulator contains a twist motion part attached to the top of the second VGT module to supply the missing orientation of the endeffector. These three modules constitute totally 7-DOF hybrid (parallel-parallel) redundant spatial manipulator. The forward kinematics equations of this manipulator are obtained, then, according to these equations, the inverse kinematics is solved based on an optimization with the joint limit avoidance. The dynamic equations are formed by using virtual work method. In order to test the performance of the redundant manipulator and the controllers presented, two different desired trajectories are followed by using the computed force control method and a switching control method. The switching control method is combined with the computed force control method and genetic algorithm. In the switching control method, the genetic algorithm is only used for fine tuning in the compensation of the trajectory tracking errors.

Keywords: computed force method, genetic algorithm, hybrid manipulator, inverse kinematics of redundant manipulators, variable geometry truss

Procedia PDF Downloads 348

Authors: Faith Eweluegim Enahoro-Ofagbe, Alika Eke Joseph

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Information on genetic variation within a population is crucial for utilizing heterozygosity for breeding programs that aim to improve crop species. The study was conducted to ascertain the genotypic similarities among twelve sugarcane (Saccharum officinarum) varieties to group them for purposes of hybridizations for cane yield improvement. The experiment was conducted at the University of Benin, Faculty of Agriculture Teaching and Research Farm, Benin City. Twelve sugarcane varieties obtained from National Cereals Research Institute, Badeggi, Niger State, Nigeria, were planted in three replications in a randomized complete block design. Each variety was planted on a five-row plot of 5.0 m in length. Data were collected on 12 agronomic traits, including; the number of millable cane, cane girth, internode length, number of male and female flowers (fuss), days to flag leaf, days to flowering, brix%, cane yield, and others. There were significant differences, according to the findings among the twelve genotypes for the number of days to flag leaf, number of male and female flowers (fuss), and cane yield. The relationship between the twelve sugarcane varieties was expressed using hierarchical cluster analysis. The twelve genotypes were grouped into three major clusters based on hierarchical classification. Cluster I had five genotypes, cluster II had four, and cluster III had three. Cluster III was dominated by varieties characterized by higher cane yield, number of leaves, internode length, brix%, number of millable stalks, stalk/stool, cane girth, and cane length. Cluster II contained genotypes with early maturity characteristics, such as early flowering, early flag leaf development, growth rate, and the number of female and male flowers (fuss). The maximum inter-cluster distance between clusters III and I indicated higher genetic diversity between the two groups. Hybridization between the two groups could result in transgressive recombinants for agronomically important traits.

Keywords: sugarcane, Saccharum officinarum, genotype, cluster analysis, principal components analysis

Procedia PDF Downloads 83

Authors: Anxuan Xie, Chun-Chan Yu

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Survey evidence provides support that auditors can gain professional knowledge not only from client firms but also from teammates they work with. Furthermore, given that knowledge is accumulated in nature, along with the reality that auditors today must work in an environment of increased diversity, whether the attributes of teammates will influence the effects of knowledge sharing and accumulation and ultimately influence an audit partner’s audit quality should be interesting research issues. We test whether the gender of co-signers will moderate the effect of a lead partner’s cooperative experiences on financial restatements. Furthermore, if the answer is “yes”, we further investigate the underlying reasons. We use data from Taiwan because, according to Taiwan’s law, engagement partners, who are basically two certificate public accountants from the same audit firm, are required to disclose (i.e., sign) their names in the audit report of public companies since 1983. Therefore, we can trace each engagement partner’s historic direct cooperative (co-signing) records and get large-sample data. We find that the benefits of knowledge sharing manifest primarily via co-signing audit reports with audit partners of different gender from the lead engagement partners, supporting the argument that in an audit setting, accumulated gender-diverse working relationship is positively associated with knowledge sharing, and therefore improve lead engagements’ audit quality. This study contributes to the extant literature in the following ways. First, we provide evidence that in the auditing setting, the experiences accumulated from cooperating with teammates of a different gender from the lead partner can improve audit quality. Given that most studies find evidence of negative effects of surface-level diversity on team performance, the results of this study support the prior literature that the association between diversity and knowledge sharing actually hinges on the context (e.g., organizational culture, task complexity) and “bridge” (a pre-existing commonality among team members that can smooth the process of diversity toward favorable results) among diversity team members. Second, this study also provides practical insights with respect to the audit firms’ policy of knowledge sharing and deployment of engagement partners. For example, for audit firms that appreciate the merits of knowledge sharing, the deployment of auditors of different gender within an audit team can help auditors accumulate audit-related knowledge, which will further benefit the future performance of those audit firms. Moreover, nowadays, client firms also attach importance to the diversity of their engagement partners. As their policy goals, lawmakers and regulators also continue to promote a gender-diverse working environment. The findings of this study indicate that for audit firms, gender diversity will not be just a means to cater to those groups. Third, for audit committees or other stakeholders, they can evaluate the quality of existing (or potential) lead partners by tracking their co-signing experiences, especially whether they have gender-diverse co-signing experiences.

Keywords: co-signing experiences, audit quality, knowledge sharing, gender diversity

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Authors: Ramona Moldovan, Doina Cosman, Sebastian Moldovan, Radu Popp, Victor Pop

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MENTALICA is a project aimed at developing and evaluating a platform that can assist individuals diagnosed with severe mental disorders and their families in managing the consequences associated with severe mental disorders, recurrence risks, prevention strategies and treatment options. MENTALICA is a platform based on guidance issued by some of the most prominent scientific organizations in the world. In order to personalize the information provided, the program explores details about the personal and family history of mental disorders. MENTALICA summarizes the answers and gives respondents a personal assessment. This includes personalized information and support about schizophrenia, bipolar disorder and schizoaffective disorder. MENTALICA includes several modules: Family history tools, Risk assessment tools and Risk factor sheets, Practical guides for patients, Practical guides for families, Guidelines for clinicians. Currently, there are no available guidelines for genetic counselling for mental disorders. Respondents can print out their reports and discuss them with family members or their doctors. We will briefly present the current status of MENTALICA and its implications for patients, professionals and the community.

Keywords: genetic counseling, mental disorders, platform

Procedia PDF Downloads 491

Authors: H. Naseh, M. Mirshams, M. Mirdamadian, H. R. Fazeley

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This paper presents an extension of fuzzy-genetic algorithm multi-objective optimization methodology that could effectively be used to find the overall satisfaction of objective functions (selecting the design variables) in the early stages of design process. The coupling of objective functions due to design variables in an engineering design process will result in difficulties in design optimization problems. In many cases, decision making on design variables conflicts with more than one discipline in system design. In space launch system conceptual design, decision making on some design variable (e.g. oxidizer to fuel mass flow rate O/F) in early stages of the design process is related to objective of liquid propellant engine (specific impulse) and Tanks (structure weight). Then, the primary application of this methodology is the design of a liquid propellant engine with the maximum specific impulse and cylindrical stiffened tank with the minimum weight. To this end, the design problem is established the fuzzy rule set based on designer's expert knowledge with a holistic approach. The independent design variables in this model are oxidizer to fuel mass flow rate, thickness of stringers, thickness of rings, shell thickness. To handle the mentioned problems, a fuzzy-genetic algorithm multi-objective optimization methodology is developed based on Pareto optimal set. Consequently, this methodology is modeled with the one stage of space launch system to illustrate accuracy and efficiency of proposed methodology.

Keywords: cylindrical stiffened tanks, multi-objective, genetic algorithm, fuzzy approach

Procedia PDF Downloads 656

Authors: M. Titaouine, T. Meziane, K. Deghnouche

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The purpose of this study was to determine reference serum biochemistry values from dromedary (Camelus dromedarius) in Algeria and to evaluate potential sources of physiological variability such as the sex, age and season on serum data. Usual serum biochemistry values were determined in blood samples from 26 apparently healthy dromedaries, 11 males and 15 females, divided into 3 lots (ender 4years), (between 5 and 10 years), (up 10 years). Parametric reference ranges and physiological variations are determined for calcium (Ca), organic phosphate (P), magnesium (Mg), natrium (Na), potassium (K), iron (Fe), glucose, triglycerides (TG), cholesterol, urea, creatinine, total proteins and albumin. The results demonstrate: * Values which agreed with literature * Significant statistically differences (Anova test, p < 0.05) depending on: -the sex for Na, glucose, TG, cholesterol, urea, creatinine, albumin, -the age for Ca, P, K, Mg, glucose, TG, b and g globulin, -and season for Fe, urea, total proteins, TG, cholesterol and glucose. These reference ranges for serum biochemical analysis can be used for metabolic and nutritional disorders detection in dromedary.

Keywords: age, biochemistry, dromadery, season, sex

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Authors: Santosh Kumar Suman, Vinod Kumar Giri

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The goal of this paper is to outline a speed controller of a DC motor by choice of a PID parameters utilizing genetic algorithms (GAs), the DC motor is extensively utilized as a part of numerous applications such as steel plants, electric trains, cranes and a great deal more. DC motor could be represented by a nonlinear model when nonlinearities such as attractive dissemination are considered. To provide effective control, nonlinearities and uncertainties in the model must be taken into account in the control design. The DC motor is considered as third order system. Objective of this paper three type of tuning techniques for PID parameter. In this paper, an independently energized DC motor utilizing MATLAB displaying, has been outlined whose velocity might be examined utilizing the Proportional, Integral, Derivative (KP, KI , KD) addition of the PID controller. Since, established controllers PID are neglecting to control the drive when weight parameters be likewise changed. The principle point of this paper is to dissect the execution of optimization techniques viz. The Genetic Algorithm (GA) for improve PID controllers parameters for velocity control of DC motor and list their points of interest over the traditional tuning strategies. The outcomes got from GA calculations were contrasted and that got from traditional technique. It was found that the optimization techniques beat customary tuning practices of ordinary PID controllers.

Keywords: DC motor, PID controller, optimization techniques, genetic algorithm (GA), objective function, IAE

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Authors: Agostinho Antunes

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The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: comparative genomics, adaptive evolution, bioinformatics, phylogenetics, genome mining

Procedia PDF Downloads 534

Authors: Olga Blagova, Yuliya Osipova, Evgeniya Kogan, Alexander Nedostup

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Purpose: to quantify the value of various clinical, laboratory and instrumental signs in the diagnosis of myocarditis in comparison with morphological studies of the myocardium. Methods: in 100 patients (65 men, 44.7±12.5 years) with «idiopathic» arrhythmias (n = 20) and dilated cardiomyopathy (DCM, n = 80) were performed 71 endomyocardial biopsy (EMB), 13 intraoperative biopsy, 5 study of explanted hearts, 11 autopsy with virus investigation (real-time PCR) of the blood and myocardium. Anti-heart antibodies (AHA) were also measured as well as cardiac CT (n = 45), MRI (n = 25), coronary angiography (n = 47). The comparison group included of 50 patients (25 men, 53.7±11.7 years) with non-inflammatory heart diseases who underwent open heart surgery. Results. Active/borderline myocarditis was diagnosed in 76.0% of the study group and in 21.6% of patients of the comparison group (p < 0.001). The myocardial viral genome was observed more frequently in patients of comparison group than in study group (group (65.0% and 40.2%; p < 0.01. Evaluated the diagnostic value of noninvasive markers of myocarditis. The panel of anti-heart antibodies had the greatest importance to identify myocarditis: sensitivity was 81.5%, positive and negative predictive value was 75.0 and 60.5%. It is defined diagnostic value of non-invasive markers of myocarditis and diagnostic algorithm providing an individual assessment of the likelihood of myocarditis is developed. Conclusion. The greatest significance in the diagnosis of latent myocarditis in patients with 'idiopathic' arrhythmias and DCM have AHA. The use of complex of noninvasive criteria allows estimate the probability of myocarditis and determine the indications for EMB.

Keywords: myocarditis, "idiopathic" arrhythmias, dilated cardiomyopathy, endomyocardial biopsy, viral genome, anti-heart antibodies

Procedia PDF Downloads 173

Authors: Alhaji Modu Bukar, Faez Firdaus Abdullah Jesse, Che Azurahanim Che Abdullah, Mustapha M. Noordin, Mohd-Lila Mohd Azmia

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Orf virus (ORFV) is the causative agent of a proliferative skin lesion known as contagious ecthyma in sheep and goats. Currently used live attenuated vaccines against ORFV infection have been reported to cause severe outbreaks in vaccinated animals. In this study, we investigated the immunogenicity of the B2L and F1L proteins of the virus, which are thought to elicit a protective immune response The 6-week-old 50 female mice were divided into 8 groups: seven experimental groups and one control group. Each animal in the experimental group received an initial immunisation with the nanoparticles or proteins coated with the nanoparticles, followed by two booster immunizations with the same products 14 days apart. Ten days after the last booster inoculation, the mice were either humanely killed or lethally challenged with UPM /HSN-2-ORFV at a dose of 106 TCID50/mL in a volume of 50 μl. The spleen was examined for histopathological changes and quantification of T cells by flow cytometry. On the other hand, the degree of protection of mice from the lethal virus was evaluated by lesion size, weight loss, and histopathological examination of skin and liver. The results showed that mice immunised with rB2L alone, rB2L-Al₂O₃-NPs, rB2L/rF1L, and rB2L/rF1L-Al₂O₃-NPs elicited statistically higher levels of anti-rB2L and/or rF1L-specific IgA/IgG and CD4/CD8 cell immune responses than mice in the control groups (p < 0.01). The vaccine candidate did not exhibit severe skin damage after monitoring histopathology, morbidity, and mortality. Overall, the results suggest that recombinant rB2L and rF1L antigens may be useful universal vaccine candidates against ORFV infections.

Keywords: orf virus, antigen nanoparticles, virus, nanoparticles

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Authors: H. Kadi-Hanifi, F. Amghar

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Steppes of arid Mediterranean zones are deeply threatened by desertification. To stop or alleviate ecological and economic problems associated with this desertification, management actions have been implemented since the last three decades. The struggle against desertification has become a national priority in many countries. In Algeria, several management techniques have been used to cope with desertification. This study aims at investigating the effect of exclosure on floristic diversity and chemical soil proprieties after four years of implementation. 167 phyto-ecological samples have been studied, 122 inside the exclosure and 45 outside. Results showed that plant diversity, composition, vegetation cover, pastoral value and soil fertility were significantly higher in protected areas.

Keywords: Algeria, arid, desertification, pastoral management, soil fertility

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Authors: Rithvik Reddy Adapa, Xin Wang

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Phasor Measurement Units (PMUs) are very sophisticated measuring devices that find amplitude, phase and frequency of various voltages and currents in a power system. Particle filter is a state estimation technique that uses Bayesian inference. Particle filters are widely used in pose estimation and indoor navigation and are very reliable. This paper studies and compares four different particle filters as PMUs namely, generic particle filter (GPF), genetic algorithm particle filter (GAPF), particle swarm optimization particle filter (PSOPF) and adaptive particle filter (APF). Two different test signals are used to test the performance of the filters in terms of responsiveness and correctness of the estimates.

Keywords: phasor measurement unit, particle filter, genetic algorithm, particle swarm optimisation, state estimation

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Authors: E. L. Queiroz, S. M. A. Souza, R. T. S. Santos

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The cereal bars have emerged as a healthy alternative in the food sector, by presenting a remarkable functional appeal, being a product of high nutritional value. Cereals have an important function in feeding because they have features that particularize them as their variety, smooth flavour and aroma and easy digestion and absorption in the body. Brazil is the largest producer of cassava in the world, and the flour produced from this raw material is a source of nutrients for much of the low-income population, however it is little explored industrially. The northeast region of Brazil has great potential for honey production, which is a source of vitamins, proteins, minerals and organic acids but it is much used as a medicine. Aiming to combine the production of healthy food with the sustainable utilization and enhancement of family farming products, was created a cereal bar using regional raw materials of desirable nutritional characteristics: honey, umbu pulp and cassava flour. The cereal bar was characterized by physicochemical analyzes quantifying the content of lipids, proteins, moisture and ashes, microbiological and sensory evaluation showed that the cereal bar is a safe, and nutritious food with good sensory properties.

Keywords: cassava flour, cereal bar, honey, insoluble fibre

Procedia PDF Downloads 472

Authors: Mabtho Moreroa-Monyelo, Grace Ijoma, Rosina Nkuna, Tonderayi Matambo

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A moving bed biofilm reactor (MBBR) was used for the bioremediation of high strength chemical oxygen demand (COD) Fisher-Tropsch (FT) wastewater. The aerobic MBBR system was operated over 60 days. For metagenomics profile assessment of the targeted 16S sequence of bacteria involved in the bioremediation of the chemical compounds, sludge samples were collected every second day of operation. Parameters such as pH and COD were measured daily to compare the system efficiency as the changedin microbial diversity progressed. The study revealed that pH was a contributing factor to microbial diversity, which further affected the efficiency of the MBBR system. The highest COD removal rate of 86.4% was achieved at pH 8.3. It was observed that when there was more, A higher bacterial diversity led to an improvement in the reduction of COD. Furthermore, an OTUof 4530 was obtained, which were divided into 12 phyla, 27 classes, 44 orders, 74 families, and 138 genera across all sludge samples from the MBBR. A determination of the relative abundance of microorganisms at phyla level indicates that the most abundant phylum on day it was Firmicutes (50%); thereafter, the most abundant phylum changed toProteobacteria.

Keywords: biodegradation, fischer-tropsch wastewater, metagenomics, moving bed biofilm reactor

Procedia PDF Downloads 161

Authors: Fumio Kasai, Noriko Hirayama, Jorge Pereira, Azusa Ohtani, Masashi Iemura, Malcolm A. Ferguson Smith, Arihiro Kohara

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The VERO cell line was established in 1962 from normal tissue of an African green monkey, Chlorocebus aethiops (2n=60), and has been commonly used worldwide for screening for toxins or as a cell substrate for the production of viral vaccines. The VERO genome was sequenced in 2014; however, its cytogenetic features have not been fully characterized as it contains several chromosome abnormalities and different karyotypes coexist in the cell line. In this study, the VERO cell line (JCRB0111) was compared with one of the sublines. In contrast to 59 chromosomes as the modal chromosome number in the VERO cell line, the subline had two peaks of 56 and 58 chromosomes. M-FISH analysis using human probes revealed that the VERO cell line was characterized by a translocation t(2;25) found in all metaphases, which was absent in the subline. Different abnormalities detected only in the subline show that the cell line is heterogeneous, indicating that the subline has the potential to change its genomic characteristics during cell culture. The various alterations in the two independent lineages suggest that genomic changes in both VERO cells can be accounted for by progressive rearrangements during their evolution in culture. Both t(5;X) and t(8;14) observed in all metaphases of the two cell lines might have a key role in VERO cells and could be used as genetic markers to identify VERO cells. The flow karyotype shows distinct differences from normal. Further analysis of sorted abnormal chromosomes may uncover other characteristics of VERO cells. Because of the absence of STR data, cytogenetic data are important in characterizing animal cell lines and can be an indicator of their quality control.

Keywords: VERO, cell culture passage, chromosome rearrangement, heterogeneous cells

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Authors: Michael Aupetit, Mahmoud Al-ismail, Khaled Mohamed

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Cancer is a major public health problem all over the world. Breast cancer has the highest incidence rate over all cancers for women in Qatar making its study a top priority of the country. Human cancer is a dynamic disease that develops over an extended period through the accumulation of a series of genetic alterations. A Darwinian process drives the tumor cells toward higher malignancy growing the branches of a progression tree in the space of genes expression. Although it is not possible to track these genetic alterations dynamically for one patient, it is possible to reconstruct the progression tree from the aggregation of thousands of tumor cells’ genetic profiles from thousands of different patients at different stages of the disease. Analyzing the progression tree is a way to detect pivotal molecular events that drive the malignant evolution and to provide a guide for the development of cancer diagnostics, prognostics and targeted therapeutics. In this work we present the development of a Visual Analytic web platform CanVis enabling users to upload gene-expression data and analyze their progression tree. The server computes the progression tree based on state-of-the-art techniques and allows an interactive visual exploration of this tree and the gene-expression data along its branching structure helping to discover potential driver genes.

Keywords: breast cancer, progression tree, visual analytics, web platform

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Authors: Zhen Cao, Yu Zhu, Junxue Fu

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Immunoassay, i.e., antigen-antibody reaction, is crucial for disease diagnostics. To achieve the adequate signal of the antigen protein detection, a large amount of sample and long incubation time is needed. However, the amount of protein is usually small at the early stage, which makes it difficult to detect. Unlike cells and DNAs, no valid chemical method exists for protein amplification. Thus, an alternative way to improve the signal is through particle manipulation techniques to concentrate proteins, among which dielectrophoresis (DEP) is an effective one. DEP is a technique that concentrates particles to the designated region through a force created by the gradient in a non-uniform electric field. Since DEP force is proportional to the cube of particle size and square of electric field gradient, it is relatively easy to capture larger particles such as cells. For smaller ones like proteins, a super high gradient is then required. In this work, three-dimensional Ag/SiO2 nanorods arrays, fabricated by an easy physical vapor deposition technique called as oblique angle deposition, have been integrated with a DEP device and created the field gradient as high as of 2.6×10²⁴ V²/m³. The nanorods based DEP device is able to enrich bovine serum albumin (BSA) protein by 1800-fold and the rate has reached 180-fold/s when only applying 5 V electric potential. Based on the above nanorods integrated DEP platform, an immunoassay of mouse immunoglobulin G (IgG) proteins has been performed. Briefly, specific antibodies are immobilized onto nanorods, then IgG proteins are concentrated and captured, and finally, the signal from fluorescence-labelled antibodies are detected. The limit of detection (LoD) is measured as 275.3 fg/mL (~1.8 fM), which is a 20,000-fold enhancement compared with identical assays performed on blank glass plates. Further, prostate-specific antigen (PSA), which is a cancer biomarker for diagnosis of prostate cancer after radical prostatectomy, is also quantified with a LoD as low as 2.6 pg/mL. The time to signal saturation has been significantly reduced to one minute. In summary, together with an easy nanorod fabrication and integration method, this nanorods based DEP platform has demonstrated highly sensitive immunoassay performance and thus poses great potentials in applications for early point-of-care diagnostics.

Keywords: dielectrophoresis, immunoassay, oblique angle deposition, protein concentration

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Authors: Hamed K. Esfahani, Bithin Datta

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Transport of reactive chemical contaminant species in groundwater aquifers is a complex and highly non-linear physical and geochemical process especially for real life scenarios. Simulating this transport process involves solving complex nonlinear equations and generally requires huge computational time for a given aquifer study area. Development of optimal remediation strategies in aquifers may require repeated solution of such complex numerical simulation models. To overcome this computational limitation and improve the computational feasibility of large number of repeated simulations, Genetic Programming based trained surrogate models are developed to approximately simulate such complex transport processes. Transport process of acid mine drainage, a hazardous pollutant is first simulated using a numerical simulated model: HYDROGEOCHEM 5.0 for a contaminated aquifer in a historic mine site. Simulation model solution results for an illustrative contaminated aquifer site is then approximated by training and testing a Genetic Programming (GP) based surrogate model. Performance evaluation of the ensemble GP models as surrogate models for the reactive species transport in groundwater demonstrates the feasibility of its use and the associated computational advantages. The results show the efficiency and feasibility of using ensemble GP surrogate models as approximate simulators of complex hydrogeologic and geochemical processes in a contaminated groundwater aquifer incorporating uncertainties in historic mine site.

Keywords: geochemical transport simulation, acid mine drainage, surrogate models, ensemble genetic programming, contaminated aquifers, mine sites

Procedia PDF Downloads 278

Authors: A. Mansouri, F. Krim

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This paper presents two techniques for DC motor parameters identification. We propose a numerical method using the adaptive extensive recursive least squares (AERLS) algorithm for real time parameters estimation. This algorithm, based on minimization of quadratic criterion, is realized in simulation for parameters identification of DC motor autoregressive moving average with extra inputs (ARMAX). As advanced technique, we use genetic algorithms (GA) identification with biased estimation for high dynamic performance speed regulation. DC motors are extensively used in variable speed drives, for robot and solar panel trajectory control. GA effectiveness is derived through comparison of the two approaches.

Keywords: ARMAX model, DC motor, AERLS, GA, optimization, parameter identification, PID speed regulation

Procedia PDF Downloads 381

Authors: Amita Barik, Ranjit Prasad Bahadur

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We investigate the role of water molecules in 89 protein-RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein-RNA interfaces are hydrated less than protein-DNA interfaces, but more than protein-protein interfaces. Majority of the waters at protein-RNA interfaces makes multiple H-bonds; however, a fraction does not make any. Those making Hbonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively ‘dry’ than interfaces with tRNA and duplex RNA. In contrast to protein-DNA interfaces, mainly due to the presence of the 2’OH, the ribose in protein-RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein-RNA interfaces is hydrated more than the major groove, while in protein-DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein-RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein-RNA recognition and should be carefully treated while engineering protein-RNA interfaces.

Keywords: h-bonds, minor-major grooves, preserved water, protein-RNA interfaces

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Authors: Benjamin A. Ha, Marco Morselli, Xinhui Paige Zhang, Elizabeth A. C. Heath-Heckman, Jonathan B. Puritz, David K. Jacobs

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Next-generation sequencing has enhanced the ability to acquire massive amounts of sequence data to address classic population genetic questions for non-model organisms. Targeted approaches allow for cost effective or more precise analyses of relevant sequences; although, many such techniques require a known genome and it can be costly to purchase probes from a company. This is challenging for non-model organisms with no published genome and can be expensive for large population genetic studies. Expressed exome capture sequencing (EecSeq) synthesizes probes in the lab from expressed mRNA, which is used to capture and sequence the coding regions of genomic DNA from a pooled suite of samples. A normalization step produces probes to recover transcripts from a wide range of expression levels. This approach offers low cost recovery of a broad range of genes in the genome. This research project expands on EecSeq to investigate if mRNA from one taxon may be used to capture relevant sequences from a series of increasingly less closely related taxa. For this purpose, we propose to use the endangered Northern Tidewater goby, Eucyclogobius newberryi, a non-model organism that inhabits California coastal lagoons. mRNA will be extracted from E. newberryi to create probes and capture exomes from eight other taxa, including the more at-risk Southern Tidewater goby, E. kristinae, and more divergent species. Captured exomes will be sequenced, analyzed bioinformatically and phylogenetically, then compared to previously generated phylogenies across this group of gobies. This will provide an assessment of the utility of the technique in cross-species studies and for analyzing low genetic variation within species as is the case for E. kristinae. This method has potential applications to provide economical ways to expand population genetic and evolutionary biology studies for non-model organisms.

Keywords: coastal lagoons, endangered species, non-model organism, target capture method

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Authors: Qinghua Xing, Xinyi Tao, Haisheng Wang, Baisuo Zhao

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The first true anaerobic, halophilic alkali thermophile, Natranaerobius thermophilus DSM 18059T, serves as a valuable model for studying cellular adaptations to saline, alkaline and thermal extremes. To uncover the adaptive strategies employed by N. thermophilus in coping with these challenges, we conducted a comprehensive iTRAQ-based quantitative proteomic analysis under different conditions of salinity (3.5 M vs. 2.5 M Na+), pH (pH 9.6 vs. pH 8.6), and temperature (52°C vs. 42°C). The increased intracellular accumulation of glycine betaine, through both synthesis and transport, plays a critical role in N. thermophilus' adaptation to these combined stresses. Under all three stress conditions, the up-regulation of Trk family proteins responsible for K+ transport is observed. Intracellular K+ concentration rises in response to salt and pH levels. Multiple types of Na+/H+ antiporter (NhaC family, Mrp family and CPA family) and a diverse range of FOF1-ATP synthase are identified as vital components for maintaining ionic balance under different stress conditions. Importantly, proteins involved in amino acid metabolism, carbohydrate metabolism, ABC transporters, signaling and chemotaxis, as well as biological macromolecule repair and protection, exhibited significant up-regulation in response to these extreme conditions. These metabolic pathways emerge as critical factors in N. thermophilus' adaptation mechanisms under extreme environmental stress. To validate the proteomic data, ddPCR analysis confirmed changes in mRNA expression, thereby corroborating the up-regulation and down-regulation patterns of 19 co-up-regulated and 36 key proteins under saline, alkaline and thermal stresses. This research enriches our understanding of the complex regulatory systems that enable polyextremophiles to survive in combined extreme conditions.

Keywords: polyextremophiles, natranaerobius thermophilus, saline- alkaline- thermal stresses, combined extremes

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Authors: Ilknur Tuncer, Nihayet Bizsel

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The scarcity of research in bacterial diversity and antimicrobial resistance in coastal environments as in Turkish coasts leads to difficulties in developing efficient monitoring and management programs. In the present study, biogeochemical analysis of sediments and antimicrobial susceptibility analysis of bacteria in Izmir Bay, eastern Aegean Sea under high anthropogenic pressure were aimed in summer period when anthropogenic input was maximum and at intertidal zone where the first terrigenious contact occurred for aquatic environment. Geochemical content of the intertidal zone of Izmir Bay was firstly illustrated such that total and organic carbon, nitrogen and phosphorus contents were high and the grain size distribution varied as sand and gravel. Bacterial diversity and antibiotic resistance were also firstly given for Izmir Bay. Antimicrobially assayed isolates underlined the multiple resistance in the inner, middle and outer bays with overall 19% high MAR (multiple antibiotic resistance) index. Phylogenetic analysis of 16S rRNA gene sequences indicated that 67 % of isolates belonged to the genus Bacillus and the rest included the families Alteromonadaceae, Bacillaceae, Exiguobacteriaceae, Halomonadaceae, Planococcaceae, and Staphylococcaceae.

Keywords: bacterial phylogeny, multiple antibiotic resistance, 16S rRNA genes, Izmir Bay, Aegean Sea

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Authors: Elhem Zaatir, Taher Hamza

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Several governments seek to implement gender parity on boards, but the results of doing so are not clear and could harm corporations and economies. The present paper aims to investigate the relationship between women’s presence on boards and firms’ performance in the context of the French listed firms during the quota period. A dynamic panel generalized method of moment estimation is applied to control the endogenous effect of board structure and reverse the causality impact of the financial performance. Our results show that the impact of gender diversity manifests in conflicting directions, positively affecting accounting performance and negatively influencing market performance. These results suggest that female directors create economic value, but the market discounts their impact. Apparently, they are subject to a biased evaluation by the market, which undervalues their presence on boards. Added to that, our results confirm a twofold nature of female representation in the French market. The effect of female directorship on firm performance varies with the affiliation of the directors. In other words, the positive impact of gender diversity on return on assets primarily originates from the positive effect of non-family-affiliated women directors on market performance rather than on the effect of family-affiliated women directors on ROA. Finally, according to our results, women’s demographic attributes namely the level of education and multiple directorships strongly and positively impact firm performance as measured by return on assets (ROA). Obviously, women directors seem to be appointed to the business case rather than as token directors.

Keywords: corporate governance, board of directors, women, gender diversity, demographic attributes, firm performance

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Authors: I. Agboola Julius, Christopher A. Kumolu-Johnson, O. Kolade Rafiu, A. Saba Abdulwakil

Abstract:

This work elucidates on mangrove diversity, trends of change, factors responsible for loss over the years and implications for sustainable livelihoods of locals in four villages (Ajido (L1), Tarkwa bay (L2), University of Lagos (L3), and Ikosi (L4)) along the coast of Lagos, Nigeria. Primary data were collected through field survey, questionnaires, interviews, and review of existing literature. Field observation and data analysis reveals mangrove diversity as low and varied on a spatial scale, where Margalef’s Diversity Index (D) was 0.368, 0.269, 0.326, and 0.333, respectively for L1, L2, L3, and L4. Shannon Weiner’s Index (H) was estimated to be 1.003, 1.460, 1.160, 1.046, and Specie Richness (E) 0.913, 0.907, 0.858, and 0.015, respectively, for the four villages. Also, The Simpson’s index of diversity was analyzed to be 0.632, 0. 731, 0.647, 0.667, and Simpson’s reciprocal index 2.717, 3.717, 3.060, and 3.003, respectively, for the four villages. Chi-square test was used to analyze the impact of mangrove loss on the sustainable livelihood of coastal communities. Calculated Chi-square (X2) value (5) was higher than tabulated value (4.30), suggesting that loss of mangrove wetlands impacted on local communities’ livelihood at the four villages. Analyses of causes and trends of mangrove wetland loss over the years suggest that urbanization, fuel wood and agricultural activities are major causes. Current degradation observed in mangrove wetlands on the Lagos coast suggest a reduction in mangroves biodiversity and associated fauna with potential cascading effects on higher trophic levels such as fisheries. Low yield in fish catch, reduction in income and increasing cases of natural disaster has culminated in threats to sustainable livelihoods of local communities along the coast of Lagos.

Keywords: Mangroves, lagos coast, fisheries, management

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Authors: Agostinho Antunes

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The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: marine genomics, evolutionary bioinformatics, human genome sequencing, genomic analyses

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Authors: Mohammed Taleb

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Morocco is characterized by an important genetic diversity represented by a rich and varied flora with 5211 species and subspecies and many natural ecosystems. Biodiversity and natural ecosystems provide the local population with highly diversified services represented by aromatic and medicinal plants, forage plants, melliferous plants, firewood, lumber, mushrooms, etc. Ecosystem services are currently subject to many pressures: overgrazing and deforestation, climate change, including increased drought, urbanization and forest fire. Conscious of the risks that weigh on biodiversity and ecosystem services, Morocco had made an important effort to reverse the tendencies by developing a consistent biodiversity conservation strategy focused on in-situ and ex-situ conservation. This presentation will be focused on the current state of biodiversity and ecosystem services and their role for the human development and their decline under the action of different pressures (grazing, timber harvest, harvesting of medicinal and aromatic plants, charcoal making...) while emphasizing efforts constructed by Morocco to conserve and sustainably manage biodiversity and ecosystem services.

Keywords: morocco, biodiversity, ecosystem services, local population

Procedia PDF Downloads 95