Search results for: gene circuit
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 2249

Search results for: gene circuit

1979 Light-Controlled Gene Expression in Yeast

Authors: Peter. M. Kusen, Georg Wandrey, Christopher Probst, Dietrich Kohlheyer, Jochen Buchs, Jorg Pietruszkau

Abstract:

Light as a stimulus provides the capability to develop regulation techniques for customizable gene expression. A great advantage is the extremely flexible and accurate dosing that can be performed in a non invasive and sterile manner even for high throughput technologies. Therefore, light regulation in a multiwell microbioreactor system was realized providing the opportunity to control gene expression with outstanding complexity. A light-regulated gene expression system in Saccharomyces cerevisiae was designed applying the strategy of caged compounds. These compounds are photo-labile protected and therefore biologically inactive regulator molecules which can be reactivated by irradiation with certain light conditions. The “caging” of a repressor molecule which is consumed after deprotection was essential to create a flexible expression system. Thereby, gene expression could be temporally repressed by irradiation and subsequent release of the active repressor molecule. Afterwards, the repressor molecule is consumed by the yeast cells leading to reactivation of gene expression. A yeast strain harboring a construct with the corresponding repressible promoter in combination with a fluorescent marker protein was applied in a Photo-BioLector platform which allows individual irradiation as well as online fluorescence and growth detection. This device was used to precisely control the repression duration by adjusting the amount of released repressor via different irradiation times. With the presented screening platform the regulation of complex expression procedures was achieved by combination of several repression/derepression intervals. In particular, a stepwise increase of temporally-constant expression levels was demonstrated which could be used to study concentration dependent effects on cell functions. Also linear expression rates with variable slopes could be shown representing a possible solution for challenging protein productions, whereby excessive production rates lead to misfolding or intoxication. Finally, the very flexible regulation enabled accurate control over the expression induction, although we used a repressible promoter. Summing up, the continuous online regulation of gene expression has the potential to synchronize gene expression levels to optimize metabolic flux, artificial enzyme cascades, growth rates for co cultivations and many other applications addicted to complex expression regulation. The developed light-regulated expression platform represents an innovative screening approach to find optimization potential for production processes.

Keywords: caged-compounds, gene expression regulation, optogenetics, photo-labile protecting group

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1978 Association of Vascular Endothelial Growth Factor Gene +405 C>G and -460 T>C Polymorphism with Type 2 Diabetic Foot Ulcer Patient in Cipto Mangunkusumo National Hospital Jakarta

Authors: Dedy Pratama, Akhmadu Muradi, Hilman Ibrahim, Raden Suhartono, Alexander Jayadi Utama, Patrianef Darwis, S. Dwi Anita, Luluk Yunaini, Kemas Dahlan

Abstract:

Introduction: Vascular endothelial growth factor (VEGF) gene shows association with various angiogenesis conditions including Diabetic Foot Ulcer (DFU) disease. In this study, we performed this study to examine VEGF gene polymorphism associated with DFU. Methods: Case-control study of polymorphism of VEGF gene +405 C>G and -460 T>C, of diabetes mellitus (DM) type 2 with Diabetic Foot Ulcer (DFU) in Cipto Mangunkusumo National Hospital (RSCM) Jakarta from June to December 2016. Results: There were 203 patients, 102 patients with DFU and 101 patients without DFU. Forty-nine point 8 percent of total samples is male and 50,2% female with mean age 56,06 years. Distribution of the wild-type genotype VEGF +405 C>G wild type CC was found in 6,9% of respondents, the number of mutant heterozygote CG was 69,5% and mutant homozygote GG was 19,7%. Cumulatively, there were 6,9% wild-type and 85,2% mutant and 3,9% of total blood samples could not be detected on PCR-RFLP. Distribution of VEGF allele +405 C>G C alleles were 43% and G alleles were 57%. Distribution of genotype from VEGF gene -460 T>C is wild type TT 42,9%, mutant heterozygote TC 37,9% and mutant homozygote CC 13,3%. Cumulatively, there were 42,9% wild-type and 51% mutant type. Distribution of VEGF -460 T>C were 62% T allele and 38% C allele. Conclusion: In this study we found the distribution of alleles from VEGF +405 C>G is C 43% and G 57% and from VEGF -460 T>C; T 62% and C 38%. We propose that G allele in VEGF +405 C>G can act as a protective allele and on the other hands T allele in VEGF -460 T>C could be acted as a risk factor for DFU in diabetic patients.

Keywords: diabetic foot ulcer, diabetes mellitus, polymorphism, VEGF

Procedia PDF Downloads 297
1977 A Review of Feature Selection Methods Implemented in Neural Stem Cells

Authors: Natasha Petrovska, Mirjana Pavlovic, Maria M. Larrondo-Petrie

Abstract:

Neural stem cells (NSCs) are multi-potent, self-renewing cells that generate new neurons. Three subtypes of NSCs can be separated regarding the stages of NSC lineage: quiescent neural stem cells (qNSCs), activated neural stem cells (aNSCs) and neural progenitor cells (NPCs), but their gene expression signatures are not utterly understood yet. Single-cell examinations have started to elucidate the complex structure of NSC populations. Nevertheless, there is a lack of thorough molecular interpretation of the NSC lineage heterogeneity and an increasing need for tools to analyze and improve the efficiency and correctness of single-cell sequencing data. Feature selection and ordering can identify and classify the gene expression signatures of these subtypes and can discover novel subpopulations during the NSCs activation and differentiation processes. The aim here is to review the implementation of the feature selection technique on NSC subtypes and the classification techniques that have been used for the identification of gene expression signatures.

Keywords: feature selection, feature similarity, neural stem cells, genes, feature selection methods

Procedia PDF Downloads 153
1976 Electro Magnetic Tractor (E. M. Tractor)

Authors: Sijo Varghese

Abstract:

A space craft (E. M. Tractor) which is intended to deflect or tug the asteroids which possesses threat towards the planets is the whole idea behind this paper. In this case "Electro Magnetic Induction" is used where it is known that when two separate circuits are connected to the electro magnet and on application of electric current through the one circuit in to the coil induces magnetic fields which repels the other circuit.( Faraday's law of Electromagnetic Induction). Basically a Spacecraft is used to attach a large sheet of aluminum on to the surface of the asteroid, the Spacecraft acts as an electro magnet and the induced magnetic field would eventually repel the aluminum intern repelling the asteroid. This method would take less time as compared to use of gravity( which requires a larger spacecraft and process will take a long time).

Keywords: asteroids, electro magnetic induction, gravity, electro magnetic tractor

Procedia PDF Downloads 492
1975 Relationship Salt Sensitivity and с825т Polymorphism of gnb3 Gene in Patients with Essential Hypertension

Authors: Aleksandr Nagay, Gulnoz Khamidullayeva

Abstract:

It is known that an unbalanced intake of salt (NaCI), lifestyle and genetic predisposition to pathology is a key component of the risk and the development of essential hypertension (EH). Purpose: To study the relationship between salt-sensitivity and blood pressure (BP) on systolic (SBP) and diastolic (DBP) blood pressure, depending on the C825T polymorphism of GNB3 in individuals of Uzbek nationality with EH. Method: studied 148 healthy and 148 patients with EH with I-II degree (WHO/ISH, 2003) with disease duration 6,5±1,3 years. Investigation of the gene GNB3 was produced by PCR-RFLP method. Determination of salt-sensitivity was performed by the method of R. Henkin. Results: For a comparative analysis of BP, the groups with carriage of CТ and TT genotypes were combined. The analysis showed that carriers of CC genotype and low salt-sensitivity were determined by higher levels of SBP compared with carriers of CT and TT genotypes, and low salt-sensitivity of SBP: 166,2±4,3 against 158,2±9,1 mm Hg (p=0,000). A similar analysis on the values of DBP also showed significantly higher values of blood pressure in carriers of CC genotype DBP: 105,8±10,6 vs. 100,5±7,2 mm Hg, respectively (p=0,001). The average values of SBP and DBP in groups with carriers of CC genotype at medium or high salt-sensitivity in comparison with carriers of CT or TT genotype did not differ statistically SBP: 165,0±0,1 vs. 160,0±8,6 mm Hg (p=0,275) and DBP: 100,1±0,1 vs. 101,6±7,6 mm Hg (p=0,687), respectively. Conclusion: It is revealed that in patients with EH CC genotype of the gene GNB3 given salt-sensitivity has a negative effect on blood pressure profile. Since patients with EH with the CC genotype of GNB3 gene with low-salt taste sensitivity is determined by a higher level of blood pressure, both on SBP and DBP.

Keywords: salt sensitivity, essential hypertension EH, blood pressure BP, genetic predisposition

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1974 Recovery of Copper from Edge Trims of Printed Circuit Boards Using Acidithiobacillus Ferrooxidans: Bioleaching

Authors: Shashi Arya, Nand L. Singh, Samiksha Singh, Pradeep K. Mishra, Siddh N. Upadhyay

Abstract:

The enormous generation of E- waste and its recycling have greater environmental concern especially in developing countries like India. A major part of this waste comprises printed circuit boards (PCBs). Edge trims of PCBs have high copper content ranging between 25-60%. The extraction of various metals out of these PCBs is more or less a proven technology, wherein various hazardous chemicals are being used in the resource recovery, resulting into secondary pollution. The current trend of extracting of valuable metals is the utilization of microbial strains to eliminate the problem of a secondary pollutant. Keeping the above context in mind, this work aims at the enhanced recovery of copper from edge trims, through bioleaching using bacterial strain Acidithiobacillus ferrooxidans. The raw material such as motherboards, hard drives, floppy drives and DVD drives were obtained from the warehouse of the University. More than 90% copper could be extracted through bioleaching using Acidithiobacillus ferrooxidans. Inoculate concentration has merely insignificant effect over copper recovery above 20% inoculate concentration. Higher concentration of inoculation has the only initial advantage up to 2-4 days. The complete recovery has been obtained between 14- 24 days.

Keywords: acidithiobacillus ferrooxidans, bioleaching, e-waste, printed circuit boards

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1973 Resistance Training and Ginger Consumption on Cytokines Levels

Authors: Alireza Barari, Ahmad Abdi

Abstract:

Regular body trainings cause adaption in various system in body. One of the important effect of body training is its effect on immune system. It seems that cytokines usually release after long period exercises or some exercises which cause skeletal muscular damages. If some of the cytokines which cause responses such as inflammation of cells in skeletal muscles, with manipulating of training program, it can be avoided or limited from those exercises which induct cytokines release. Ginger plant is a kind of medicinal plants which is known as a anti inflammation plant. This plant is as most precedence medicinal plants in medicine science especially in inflammation cure. The aim of the present study was the effect of selected resistance training and consumption of ginger extract on IL-1α and TNFα untrained young women. The population includes young women interested in participating in the study with the average of 30±2 years old from Abbas Abad city among which 32 participants were chosen randomly and divided into 4 four groups, resistance training (R), resistance training and ginger consumption(RG), Ginger consumption(G)and Control group(C). The training groups performed circuit resistance training at the intensity of 65-75% one repeat maximum, 3 days a week for 6 weeks. Besides resistance training, subjects were given either ginseng (5 mg/kg per day) or placebo. Prior to and 48 hours after interventions body composition was measured and blood samples were taken in order to assess serum levels of IL-1α and TNFα. Plasma levels of cytokines were measured with commercially available ELISA Kits.IL-1α kit and TNFα kit were used in this research. To demonstrate the effectiveness of the independent variable and the comparison between groups, t-test and ANOVA were used. To determine differences between the groups, the Scheffe test was used that showed significant changes in any of the variables. we observed that circuit resistance training in R and RG groups can significant decreased in weight and body mass index in untrained females (p<0.05). The results showed a significant decreased in the mean level of IL-1α levels before and after the training period in G group (p=0.046) and RG group (p=0.022). Comparison between groups also showed there was significant difference between groups R-RG and RG-C. Intergroup comparison results showed that the mean levels of TNFα before and after the training in group G (p=0.044) and RG (p=0.037), significantly decreased. Comparison between groups also showed there was significant difference between groups R–RG , R-G ,RG-C and G-C. The research shows that circuit resistance training with reducing overload method results in systemic inflammation had significant effect on IL-1α levels and TNFα. Of course, Ginger can counteract the negative effects of resistance training exercise on immune function and stability of the mast cell membrane. Considerable evidence supported the anti-inflammatory properties of ginger for several constituents, especially gingerols, shogaols, paradols, and zingerones, through decreased cytokine gene TNF α and IL-1Α expression and inhibition of cyclooxygenase 1 and 2. These established biological actions suggest that ingested ginger could block the increase in IL-1α.

Keywords: resistance training, ginger, IL-1α , TNFα

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1972 Nonlinear Observer Canonical Form for Genetic Regulation Process

Authors: Bououden Soraya

Abstract:

This paper aims to study the existence of the change of coordinates which permits to transform a class of nonlinear dynamical systems into the so-called nonlinear observer canonical form (NOCF). Moreover, an algorithm to construct such a change of coordinates is given. Based on this form, we can design an observer with a linear error dynamic. This enables us to estimate the state of a nonlinear dynamical system. A concrete example (biological model) is provided to illustrate the feasibility of the proposed results.

Keywords: nonlinear observer canonical form, observer, design, gene regulation, gene expression

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1971 Multi Universe Existence Based-On Quantum Relativity using DJV Circuit Experiment Interpretation

Authors: Muhammad Arif Jalil, Somchat Sonasang, Preecha Yupapin

Abstract:

This study hypothesizes that the universe is at the center of the universe among the white and black holes, which are the entangled pairs. The coupling between them is in terms of spacetime forming the universe and things. The birth of things is based on exchange energy between the white and black sides. That is, the transition from the white side to the black side is called wave-matter, where it has a speed faster than light with positive gravity. The transition from the black to the white side has a speed faster than light with negative gravity called a wave-particle. In the part where the speed is equal to light, the particle rest mass is formed. Things can appear to take shape here. Thus, the gravity is zero because it is the center. The gravitational force belongs to the Earth itself because it is in a position that is twisted towards the white hole. Therefore, it is negative. The coupling of black-white holes occurs directly on both sides. The mass is formed at the saturation and will create universes and other things. Therefore, it can be hundreds of thousands of universes on both sides of the B and white holes before reaching the saturation point of multi-universes. This work will use the DJV circuit that the research team made as an entangled or two-level system circuit that has been experimentally demonstrated. Therefore, this principle has the possibility for interpretation. This work explains the emergence of multiple universes and can be applied as a practical guideline for searching for universes in the future. Moreover, the results indicate that the DJV circuit can create the elementary particles according to Feynman's diagram with rest mass conditions, which will be discussed for fission and fusion applications.

Keywords: multi-universes, feynman diagram, fission, fusion

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1970 Heterogeneity of Genes Encoding the Structural Proteins of Avian Infectious Bronchitis Virus

Authors: Shahid Hussain Abro, Siamak Zohari, Lena H. M. Renström, Désirée S. Jansson, Faruk Otman, Karin Ullman, Claudia Baule

Abstract:

Infectious bronchitis is an acute, highly contagious respiratory, nephropathogenic and reproductive disease of poultry that is caused by infectious bronchitis virus (IBV). The present study used a large data set of structural gene sequences, including newly generated ones and sequences available in the GenBank database to further analyze the diversity and to identify selective pressures and recombination spots. There were some deletions or insertions in the analyzed regions in isolates of the Italy-02 and D274 genotypes. Whereas, there were no insertions or deletions observed in the isolates of the Massachusetts and 4/91 genotype. The hypervariable nucleotide sequence regions spanned positions 152–239, 554–582, 686–737 and 802–912 in the S1 sub-unit of the all analyzed genotypes. The nucleotide sequence data of the E gene showed that this gene was comparatively unstable and subjected to a high frequency of mutations. The M gene showed substitutions consistently distributed except for a region between nucleotide positions 250–680 that remained conserved. The lowest variation in the nucleotide sequences of ORF5a was observed in the isolates of the D274 genotype. While, ORF5b and N gene sequences showed highly conserved regions and were less subjected to variation. Genes ORF3a, ORF3b, M, ORF5a, ORF5b and N presented negative selective pressure among the analyzed isolates. However, some regions of the ORFs showed favorable selective pressure(s). The S1 and E proteins were subjected to a high rate of mutational substitutions and non-synonymous amino acids. Strong signals of recombination breakpoints and ending break point were observed in the S and N genes. Overall, the results of this study revealed that very likely the strong selective pressures in E, M and the high frequency of substitutions in the S gene can probably be considered the main determinants in the evolution of IBV.

Keywords: IBV, avian infectious bronchitis, structural genes, genotypes, genetic diversity

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1969 Online Battery Equivalent Circuit Model Estimation on Continuous-Time Domain Using Linear Integral Filter Method

Authors: Cheng Zhang, James Marco, Walid Allafi, Truong Q. Dinh, W. D. Widanage

Abstract:

Equivalent circuit models (ECMs) are widely used in battery management systems in electric vehicles and other battery energy storage systems. The battery dynamics and the model parameters vary under different working conditions, such as different temperature and state of charge (SOC) levels, and therefore online parameter identification can improve the modelling accuracy. This paper presents a way of online ECM parameter identification using a continuous time (CT) estimation method. The CT estimation method has several advantages over discrete time (DT) estimation methods for ECM parameter identification due to the widely separated battery dynamic modes and fast sampling. The presented method can be used for online SOC estimation. Test data are collected using a lithium ion cell, and the experimental results show that the presented CT method achieves better modelling accuracy compared with the conventional DT recursive least square method. The effectiveness of the presented method for online SOC estimation is also verified on test data.

Keywords: electric circuit model, continuous time domain estimation, linear integral filter method, parameter and SOC estimation, recursive least square

Procedia PDF Downloads 383
1968 Genetics, Law and Society: Regulating New Genetic Technologies

Authors: Aisling De Paor

Abstract:

Scientific and technological developments are driving genetics and genetic technologies into the public sphere. Scientists are making genetic discoveries as to the make up of the human body and the cause and effect of disease, diversity and disability amongst individuals. Technological innovation in the field of genetics is also advancing, with the development of genetic testing, and other emerging genetic technologies, including gene editing (which offers the potential for genetic modification). In addition to the benefits for medicine, health care and humanity, these genetic advances raise a range of ethical, legal and societal concerns. From an ethical perspective, such advances may, for example, change the concept of humans and what it means to be human. Science may take over in conceptualising human beings, which may push the boundaries of existing human rights. New genetic technologies, particularly gene editing techniques create the potential to stigmatise disability, by highlighting disability or genetic difference as something that should be eliminated or anticipated. From a disability perspective, use (and misuse) of genetic technologies raise concerns about discrimination and violations to the dignity and integrity of the individual. With an acknowledgement of the likely future orientation of genetic science, and in consideration of the intersection of genetics and disability, this paper highlights the main concerns raised as genetic science and technology advances (particularly with gene editing developments), and the consequences for disability and human rights. Through the use of traditional doctrinal legal methodologies, it investigates the use (and potential misuse) of gene editing as creating the potential for a unique form of discrimination and stigmatization to develop, as well as a potential gateway to a form of new, subtle eugenics. This article highlights the need to maintain caution as to the use, application and the consequences of genetic technologies. With a focus on the law and policy position in Europe, it examines the need to control and regulate these new technologies, particularly gene editing. In addition to considering the need for regulation, this paper highlights non-normative approaches to address this area, including awareness raising and education, public discussion and engagement with key stakeholders in the field and the development of a multifaceted genetics advisory network.

Keywords: disability, gene-editing, genetics, law, regulation

Procedia PDF Downloads 361
1967 Harnessing Earth's Electric Field and Transmission of Electricity

Authors: Vaishakh Medikeri

Abstract:

Energy in this Universe is the most basic characteristic of every particle. Since the birth of life on this planet, there has been a quest undertaken by the living beings to analyze, understand and harness the precious natural facts of the nature. In this quest, one of the greatest undertaken is the process of harnessing the naturally available energy. Scientists around the globe have discovered many ways to harness the freely available energy. But even today we speak of “Power Crisis”. Nikola Tesla once said “Nature has stored up in this universe infinite energy”. Energy is everywhere around us in unlimited quantities; all of it waiting to be harnessed by us. Here in this paper a method has been proposed to harness earth's electric field and transmit the stored electric energy using strong magnetic fields and electric fields. In this paper a new technique has been proposed to harness earth's electric field which is everywhere around the world in infinite quantities. Near the surface of the earth there is an electric field of about 120V/m. This electric field is used to charge a capacitor with high capacitance. Later the energy stored is allowed to pass through a device which converts the DC stored into AC. The AC so produced is then passed through a step down transformer to magnify the incoming current. Later the current passes through the RLC circuit. Later the current can be transmitted wirelessly using the principle of resonant inductive coupling. The proposed apparatus can be placed in most of the required places and any circuit tuned to the frequency of the transmitted current can receive the energy. The new source of renewable energy is of great importance if implemented since the apparatus is not costly and can be situated in most of the required places. And also the receiver which receives the transmitted energy is just an RLC circuit tuned to the resonant frequency of the transmitted energy. By using the proposed apparatus the energy losses can be reduced to a very large extent.

Keywords: capacitor, inductive resonant coupling, RLC circuit, transmission of electricity

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1966 Intelligent and Optimized Placement for CPLD Devices

Authors: Abdelkader Hadjoudja, Hajar Bouazza

Abstract:

The PLD/CPLD devices are widely used for logic synthesis since several decades. Based on sum of product terms (PTs) architecture, the PLD/CPLD offer a high degree of flexibility to support various application requirements. They are suitable for large combinational logic, finite state machines as well as intensive I/O designs. CPLDs offer very predictable timing characteristics and are therefore ideal for critical control applications. This paper describes how the logic synthesis techniques, such as 1) XOR detection, 2) logic doubling, 3) complement of a Boolean function are combined, applied and used to optimize the CPLDs devices architecture that is based on PAL-like macrocells. Our goal is to use these techniques for minimizing the number of macrocells required to implement a circuit and minimize the delay of mapped circuit.

Keywords: CPLD, doubling, optimization, XOR

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1965 Meditation and Insight Interpretation Using Quantum Circle Based-on Experiment and Quantum Relativity Formalism

Authors: Somnath Bhattachryya, Montree Bunruangses, Somchat Sonasang, Preecha Yupapin

Abstract:

In this study and research on meditation and insight, the design and experiment with electronic circuits to manipulate the meditators' mental circles that call the chakras to have the same size is proposed. The shape of the circuit is 4-ports, called an add-drop multiplexer, that studies the meditation structure called the four-mindfulness foundation, then uses an AC power signal as an input instead of the meditation time function, where various behaviors with the method of re-filtering the signal (successive filtering), like eight noble paths. Start by inputting a signal at a frequency that causes the velocity of the wave on the perimeter of the circuit to cause particles to have the speed of light in a vacuum. The signal changes from electromagnetic waves and matter waves according to the velocity (frequency) until it reaches the point of the relativistic limit. The electromagnetic waves are transformed into photons with properties of wave-particle overcoming the limits of the speed of light. As for the matter wave, it will travel to the other side and cannot pass through the relativistic limit, called a shadow signal (echo) that can have power from increasing speed but cannot create speed faster than light or insight. In the experiment, the only the side where the velocity is positive, only where the speed above light or the corresponding frequency indicates intelligence. Other side(echo) can be done by changing the input signal to the other side of the circuit to get the same result. But there is no intelligence or speed beyond light. It is also used to study the stretching, contraction of time and wormholes that can be applied for teleporting, Bose-Einstein condensate and teleprinting, quantum telephone. The teleporting can happen throughout the system with wave-particle and echo, which is when the speed of the particle is faster than the stretching or contraction of time, the particle will submerge in the wormhole, when the destination and time are determined, will travel through the wormhole. In a wormhole, time can determine in the future and the past. The experimental results using the microstrip circuit have been found to be by the principle of quantum relativity, which can be further developed for both tools and meditation practitioners for quantum technology.

Keywords: quantu meditation, insight picture, quantum circuit, absolute time, teleportation

Procedia PDF Downloads 64
1964 Predicting Dose Level and Length of Time for Radiation Exposure Using Gene Expression

Authors: Chao Sima, Shanaz Ghandhi, Sally A. Amundson, Michael L. Bittner, David J. Brenner

Abstract:

In a large-scale radiologic emergency, potentially affected population need to be triaged efficiently using various biomarkers where personal dosimeters are not likely worn by the individuals. It has long been established that radiation injury can be estimated effectively using panels of genetic biomarkers. Furthermore, the rate of radiation, in addition to dose of radiation, plays a major role in determining biological responses. Therefore, a better and more accurate triage involves estimating both the dose level of the exposure and the length of time of that exposure. To that end, a large in vivo study was carried out on mice with internal emitter caesium-137 (¹³⁷Cs). Four different injection doses of ¹³⁷Cs were used: 157.5 μCi, 191 μCi, 214.5μCi, and 259 μCi. Cohorts of 6~7 mice from the control arm and each of the dose levels were sacrificed, and blood was collected 2, 3, 5, 7 and 14 days after injection for microarray RNA gene expression analysis. Using a generalized linear model with penalized maximum likelihood, a panel of 244 genes was established and both the doses of injection and the number of days after injection were accurately predicted for all 155 subjects using this panel. This has proven that microarray gene expression can be used effectively in radiation biodosimetry in predicting both the dose levels and the length of exposure time, which provides a more holistic view on radiation exposure and helps improving radiation damage assessment and treatment.

Keywords: caesium-137, gene expression microarray, multivariate responses prediction, radiation biodosimetry

Procedia PDF Downloads 199
1963 GeneNet: Temporal Graph Data Visualization for Gene Nomenclature and Relationships

Authors: Jake Gonzalez, Tommy Dang

Abstract:

This paper proposes a temporal graph approach to visualize and analyze the evolution of gene relationships and nomenclature over time. An interactive web-based tool implements this temporal graph, enabling researchers to traverse a timeline and observe coupled dynamics in network topology and naming conventions. Analysis of a real human genomic dataset reveals the emergence of densely interconnected functional modules over time, representing groups of genes involved in key biological processes. For example, the antimicrobial peptide DEFA1A3 shows increased connections to related alpha-defensins involved in infection response. Tracking degree and betweenness centrality shifts over timeline iterations also quantitatively highlight the reprioritization of certain genes’ topological importance as knowledge advances. Examination of the CNR1 gene encoding the cannabinoid receptor CB1 demonstrates changing synonymous relationships and consolidating naming patterns over time, reflecting its unique functional role discovery. The integrated framework interconnecting these topological and nomenclature dynamics provides richer contextual insights compared to isolated analysis methods. Overall, this temporal graph approach enables a more holistic study of knowledge evolution to elucidate complex biology.

Keywords: temporal graph, gene relationships, nomenclature evolution, interactive visualization, biological insights

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1962 Air-Blast Ultrafast Disconnectors and Solid-State Medium Voltage DC Breaker: A Modified Version to Lower Losses and Higher Speed

Authors: Ali Kadivar, Kaveh Niayesh

Abstract:

MVDC markets for green power generations, Navy, subsea oil and gas electrification, and transportation electrification are extending rapidly. The lack of fast and powerful DC circuit breakers (CB) is the most significant barrier to realizing the medium voltage DC (MVDC) networks. A concept of hybrid circuit breakers (HCBs) benefiting from ultrafast disconnectors (UFD) is proposed. A set of mechanical switches substitute the power electronic commutation switches to reduce the losses during normal operation in HCB. The success of current commutation in such breakers relies on the behaviour of elongated, wall constricted arcs during the opening across the contacts inside the UFD. The arc voltage dependencies on the contact speed of UFDs is discussed through multiphysics simulations contact opening speeds of 10, 20 and 40 m/s. The arc voltage at a given current increases exponentially with the contact opening velocity. An empirical equation for the dynamic arc characteristics is presented for the tested UFD, and the experimentally verfied characteristics for voltage-current are utilized for the current commutation simulation prior to apply on a 14 kV experimental setup. Different failures scenarios due to the current commutation are investigated

Keywords: MVDC breakers, DC circuit breaker, fast operating breaker, ultra-fast elongated arc

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1961 Biophysically Motivated Phylogenies

Authors: Catherine Felce, Lior Pachter

Abstract:

Current methods for building phylogenetic trees from gene expression data consider mean expression levels. With single-cell technologies, we can leverage more information about cell dynamics by considering the entire distribution of gene expression across cells. Using biophysical modeling, we propose a method for constructing phylogenetic trees from scRNA-seq data, building on Felsenstein's method of continuous characters. This method can highlight genes whose level of expression may be unchanged between species, but whose rates of transcription/decay may have evolved over time.

Keywords: phylogenetics, single-cell, biophysical modeling, transcription

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1960 Intracellular Strategies for Gene Delivery into Mammalian Cells Using Bacteria as a Vector

Authors: Kumaran Narayanan, Andrew N. Osahor

Abstract:

E. coli has been engineered by our group and by others as a vector to deliver DNA into cultured human and animal cells. However, so far conditions to improve gene delivery using this vector have not been investigated, resulting in a major gap in our understanding of the requirements for this vector to function optimally. Our group recently published novel data showing that simple addition of the DNA transfection reagent Lipofectamine increased the efficiency of the E. coli vector by almost 3-fold, providing the first strong evidence that further optimization of bactofection is possible. This presentation will discuss advances that demonstrate the effects of several intracellular strategies that improve the efficiency of this vector. Conditions that promote endosomal escape of internalized bacteria to evade lysosomal destruction after entry in the cell, a known obstacle limiting this vector, are elucidated. Further, treatments that increase bacterial lysis so that the vector can release its transgene into the mammalian environment for expression will be discussed. These experiments will provide valuable new insight to advance this E. coli system as an important class of vector technology for genetic correction of human disease models in cells and whole animals.

Keywords: DNA, E. coli, gene expression, vector

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1959 Microarray Gene Expression Data Dimensionality Reduction Using PCA

Authors: Fuad M. Alkoot

Abstract:

Different experimental technologies such as microarray sequencing have been proposed to generate high-resolution genetic data, in order to understand the complex dynamic interactions between complex diseases and the biological system components of genes and gene products. However, the generated samples have a very large dimension reaching thousands. Therefore, hindering all attempts to design a classifier system that can identify diseases based on such data. Additionally, the high overlap in the class distributions makes the task more difficult. The data we experiment with is generated for the identification of autism. It includes 142 samples, which is small compared to the large dimension of the data. The classifier systems trained on this data yield very low classification rates that are almost equivalent to a guess. We aim at reducing the data dimension and improve it for classification. Here, we experiment with applying a multistage PCA on the genetic data to reduce its dimensionality. Results show a significant improvement in the classification rates which increases the possibility of building an automated system for autism detection.

Keywords: PCA, gene expression, dimensionality reduction, classification, autism

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1958 A Nucleic Acid Extraction Method for High-Viscosity Floricultural Samples

Authors: Harunori Kawabe, Hideyuki Aoshima, Koji Murakami, Minoru Kawakami, Yuka Nakano, David D. Ordinario, C. W. Crawford, Iri Sato-Baran

Abstract:

With the recent advances in gene editing technologies allowing the rewriting of genetic sequences, additional market growth in the global floriculture market beyond previous trends is anticipated through increasingly sophisticated plant breeding techniques. As a prerequisite for gene editing, the gene sequence of the target plant must first be identified. This necessitates the genetic analysis of plants with unknown gene sequences, the extraction of RNA, and comprehensive expression analysis. Consequently, a technology capable of consistently and effectively extracting high-purity DNA and RNA from plants is of paramount importance. Although model plants, such as Arabidopsis and tobacco, have established methods for DNA and RNA extraction, floricultural species such as roses present unique challenges. Different techniques to extract DNA and RNA from various floricultural species were investigated. Upon sampling and grinding the petals of several floricultural species, it was observed that nucleic acid extraction from the ground petal solutions of low viscosity was straightforward; solutions of high viscosity presented a significant challenge. It is postulated that the presence of substantial quantities of polysaccharides and polyphenols in the plant tissue was responsible for the inhibition of nucleic acid extraction. Consequently, attempts were made to extract high-purity DNA and RNA by improving the CTAB method and combining it with commercially available nucleic acid extraction kits. The quality of the total extracted DNA and RNA was evaluated using standard methods. Finally, the effectiveness of the extraction method was assessed by determining whether it was possible to create a library that could be applied as a suitable template for a next-generation sequencer. In conclusion, a method was developed for consistent and accurate nucleic acid extraction from high-viscosity floricultural samples. These results demonstrate improved techniques for DNA and RNA extraction from flowers, help facilitate gene editing of floricultural species and expand the boundaries of research and commercial opportunities.

Keywords: floriculture, gene editing, next-generation sequencing, nucleic acid extraction

Procedia PDF Downloads 29
1957 Open Circuit MPPT Control Implemented for PV Water Pumping System

Authors: Rabiaa Gammoudi, Najet Rebei, Othman Hasnaoui

Abstract:

Photovoltaic systems use different techniques for tracking the Maximum Power Point (MPPT) to provide the highest possible power to the load regardless of the climatic conditions variation. In this paper, the proposed method is the Open Circuit (OC) method with sudden and random variations of insolation. The simulation results of the water pumping system controlled by OC method are validated by an experimental experience in real-time using a test bench composed by a centrifugal pump powered by a PVG via a boost chopper for the adaptation between the source and the load. The output of the DC/DC converter supplies the motor pump LOWARA type, assembly by means of a DC/AC inverter. The control part is provided by a computer incorporating a card DS1104 running environment Matlab/Simulink for visualization and data acquisition. These results show clearly the effectiveness of our control with a very good performance. The results obtained show the usefulness of the developed algorithm in solving the problem of degradation of PVG performance depending on the variation of climatic factors with a very good yield.

Keywords: PVWPS (PV Water Pumping System), maximum power point tracking (MPPT), open circuit method (OC), boost converter, DC/AC inverter

Procedia PDF Downloads 454
1956 Bio-Genetic Activities Associated with Resistant in Peppers to Phytophthora capsici

Authors: Mehdi Nasr-Esfahani, Leila Mohammad Bagheri, Ava Nasr-Esfahani

Abstract:

Root and collar rot disease caused by Phytophthora capsici (Leonian) is one of the most serious diseases in pepper, Capsicum annuum L. In this study, a diverse collection of 37 commercial edible and ornamental pepper genotypes infected with P. capsici were investigated for biomass parameters and enzymatic activity of peroxidase or peroxide reductases (EC), superoxide dismutase (SOD), polyphenol oxidase (PPOs), catalase (CAT) and phenylalanine ammonia-lyase (PAL). Seven candidate DEG genes were also evaluated on resistant and susceptible pepper cultivars, through measuring product formation, using spectrophotometry and real-time polymerase chain reaction. All the five enzymes and seven defense-gene candidates were up-regulated in all inoculated pepper accessions to P. capsici. But, the enzymes and DEG genes were highly expressed in resistant cv. 19OrnP-PBI, 37ChillP-Paleo, and “23CherryP-Orsh". The expression level of enzymes were 1.5 to 5.6-fold higher in the resistant peppers, than the control non-inoculated genotypes. Also, the transcriptional levels of related candidate DEG genes were 3.16 to 5.90-fold higher in the resistant genotypes. There was a direct and high correlation coefficient between resistance, bio-mass parameters, enzymatic activity, and resistance gene expression. The related enzymes and candidate genes expressed herein will provide a basis for further gene cloning and functional verification studies, and also will aid in an understanding of the regulatory mechanism of pepper resistance to P. capsici.

Keywords: AP2/ERF, cDNA, enzymes, MIP gene, q-RTPCR, XLOC

Procedia PDF Downloads 155
1955 High Speed Response Single-Inductor Dual-Output DC-DC Converter with Hysteretic Control

Authors: Y. Kobori, S. Tanaka, N. Tsukiji, N. Takai, H. Kobayashi

Abstract:

This paper proposes two kinds of new single-inductor dual-output (SIDO) DC-DC switching converters with ripple-based hysteretic control. First SIDO converters of type 1 utilize the triangular signal generated by the CR-circuit connected across the inductor. This triangular signal is used for generating the PWM signal instead of the saw-tooth signal used in the conventional converters. Second SIDO converters of type 2 utilize the triangular signal generated by the CR-circuit connected across the voltage error amplifier. This paper describes circuit topologies, Operation principles, simulation results and experimental results of the proposed SIDO converters. In simulation results of both type of SIDO converters, static output voltage ripples are less than 5mVpp and over/under shoots of the dynamic load regulations for the output current step are less than +/- 10mV. In experimental results of single output converter of type 2, static output voltage ripples are about 20mVpp. Output ripples of SIDO type 1 converter are about 80mVpp.

Keywords: DC-DC converter, switching converter, SIDO converter, hysteretic control, ripple-based control

Procedia PDF Downloads 575
1954 Parkinson's Disease Gene Identification Using Physicochemical Properties of Amino Acids

Authors: Priya Arora, Ashutosh Mishra

Abstract:

Gene identification, towards the pursuit of mutated genes, leading to Parkinson’s disease, puts forward a challenge towards proactive cure of the disorder itself. Computational analysis is an effective technique for exploring genes in the form of protein sequences, as the theoretical and manual analysis is infeasible. The limitations and effectiveness of a particular computational method are entirely dependent on the previous data that is available for disease identification. The article presents a sequence-based classification method for the identification of genes responsible for Parkinson’s disease. During the initiation phase, the physicochemical properties of amino acids transform protein sequences into a feature vector. The second phase of the method employs Jaccard distances to select negative genes from the candidate population. The third phase involves artificial neural networks for making final predictions. The proposed approach is compared with the state of art methods on the basis of F-measure. The results confirm and estimate the efficiency of the method.

Keywords: disease gene identification, Parkinson’s disease, physicochemical properties of amino acid, protein sequences

Procedia PDF Downloads 141
1953 Investigation of the Association of Vitamin D Receptor Gene Polymorphism in Female Genital: Tuberculosis Cases

Authors: Swati Gautam, Amita Jain, Shyampyari Jaiswar

Abstract:

Objective: To elucidate the role of (ApaI&TaqI) VDR gene polymorphism in the pathogenesis of female genital tuberculosis (FGTB) cases. Background: Female genital TB represents about 15-20% of total extra-pulmonary TB (EPTB). Female subjects with vitamin D deficiency have been shown to be at higher risk of pulmonary TB as well as FGTB. In same context few functional polymorphism in vitamin D receptor (VDR) gene has been considered as an important genetic risk factor that modulate the development of FGTB. Therefore we aimed, to elucidate the role of (ApaI&TaqI) VDR gene polymorphism in the pathogenesis of FGTB. Study design: Case-Control study. Sample size: Cases (60) and Controls (60). Study site: Department of Obstetrics & Gynecology & Department of Microbiology, K.G.M.U. Lucknow, (UP). Inclusion criteria: Cases: Women with age group 20-35 years, premenstrual endometrial aspiration collected and included in the study, those were positive with acid-fast bacilli (AFB)/ TB-PCR/ LJ culture/ liquid culture. Controls: Women with age group 20-35 years having no history of ATT and all test negative for TB recruited as control. Exclusion criteria: -Women with endometriosis, polycystic ovaries (PCOD), positive on Chlamydia & gonorrhea, already on anti-tubercular therapy (ATT) excluded. Materials and Methods: Blood samples were collected in EDTA tubes from cases and controls stored at -20ºC. Genomic DNA extraction was carried out by salting-out method. Genotyping of VDR gene (ApaI&TaqI) polymorphism was performed by using single amplification refractory mutation system (ARMS) PCR technique. PCR products were analyzed by electrophoresis on 2% agarose gel. Statistical analysis was done by SPSS16.3 software & computing odds ratio (OR) with 95% CI. Results: Increased risk of female genital tuberculosis was observed in AA genotype (OR =1.1419-6.212 95% CI, P*<0.036) and A allele (OR =1.255-3.518, 95% CI, P* < 0.006) in FGTB as compared to controls. Moreover A allele was found more frequent in FGTB patients. No significant difference was observed in TaqI gene polymorphism of VDR gene. Conclusion: The ApaI polymorphism is significantly associated with etiology of FGTB and plays an important role as a genetic risk factor in FGTB women.

Keywords: ARMS, ATT, EPTB, FGTB, VDR

Procedia PDF Downloads 287
1952 Studies on the Feasibility of Cow Dung as a Non-Conventional Energy Source

Authors: Raj Kumar Rajak, Bharat Mishra

Abstract:

Bio-batteries represent an entirely new long-term, reasonable, reachable and ecofriendly approach to produce sustainable energy. In the present experimental work, we have studied the effect of generation of power by bio-battery using different electrode pairs. The tests show that it is possible to generate electricity using cow dung as an electrolyte. C-Mg electrode pair shows maximum voltage and SCC (Short Circuit Current) while C-Zn electrode pair shows less OCV (Open Circuit Voltage) and SCC. We have chosen C-Zn electrodes because Mg electrodes are not economical. By the studies of different electrodes and cow dung, it is found that C-Zn electrode battery is more suitable. This result shows that the bio-batteries have the potency to full fill the need of electricity demand for lower energy equipment.

Keywords: bio-batteries, electricity, cow-dung, electrodes, non-conventional

Procedia PDF Downloads 205
1951 Nucleotide Based Validation of the Endangered Plant Diospyros mespiliformis (Ebenaceae) by Evaluating Short Sequence Region of Plastid rbcL Gene

Authors: Abdullah Alaklabi, Ibrahim A. Arif, Sameera O. Bafeel, Ahmad H. Alfarhan, Anis Ahamed, Jacob Thomas, Mohammad A. Bakir

Abstract:

Diospyros mespiliformis (Hochst. ex A.DC.; Ebenaceae) is a large deciduous medicinal plant. This plant species is currently listed as endangered in Saudi Arabia. Molecular identification of this plant species based on short sequence regions (571 and 664 bp) of plastid rbcL (ribulose-1, 5-biphosphate carboxylase) gene was investigated in this study. The endangered plant specimens were collected from Al-Baha, Saudi Arabia (GPS coordinate: 19.8543987, 41.3059349). Phylogenetic tree inferred from the rbcL gene sequences showed that this species is very closely related with D. brandisiana. The close relationship was also observed among D. bejaudii, D. Philippinensis and D. releyi (≥99.7% sequence homology). The partial rbcL gene sequence region (571 bp) that was amplified by rbcL primer-pair rbcLaF-rbcLaR failed to discriminate D. mespiliformis from the closely related plant species, D. brandisiana. In contrast, primer-pair rbcL1F-rbcL724R yielded longer amplicon, discriminated the species from D. brandisiana and demonstrated nucleotide variations in 3 different sites (645G>T; 663A>C; 710C>G). Although D. mespiliformis (EU980712) and D. brandisiana (EU980656) are very closely related species (99.4%); however, studied specimen showed 100% sequence homology with D. mespiliformis and 99.6% with D. brandisiana. The present findings showed that rbcL short sequence region (664 bp) of plastid rbcL gene, amplified by primer-pair rbcL1F-rbcL724R, can be used for authenticating samples of D. mespiliforformis and may provide help in authentic identification and management process of this medicinally valuable endangered plant species.

Keywords: Diospyros mespiliformis, endangered plant, identification partial rbcL

Procedia PDF Downloads 433
1950 Evolution of DNA-Binding With-One-Finger Transcriptional Factor Family in Diploid Cotton Gossypium raimondii

Authors: Waqas Shafqat Chattha, Muhammad Iqbal, Amir Shakeel

Abstract:

Transcriptional factors are proteins that play a vital role in regulating the transcription of target genes in different biological processes and are being widely studied in different plant species. In the current era of genomics, plant genomes sequencing has directed to the genome-wide identification, analyses and categorization of diverse transcription factor families and hence provide key insights into their structural as well as functional diversity. The DNA-binding with One Finger (DOF) proteins belongs to C2-C2-type zinc finger protein family. DOF proteins are plant-specific transcription factors implicated in diverse functions including seed maturation and germination, phytohormone signalling, light-mediated gene regulation, cotton-fiber elongation and responses of the plant to biotic as well as abiotic stresses. In this context, a genome-wide in-silico analysis of DOF TF family in diploid cotton species i.e. Gossypium raimondii has enabled us to identify 55 non-redundant genes encoding DOF proteins renamed as GrDofs (Gossypium raimondii Dof). Gene distribution studies have shown that all of the GrDof genes are unevenly distributed across 12 out of 13 G. raimondii chromosomes. The gene structure analysis illustrated that 34 out of 55 GrDof genes are intron-less while remaining 21 genes have a single intron. Protein sequence-based phylogenetic analysis of putative 55 GrDOFs has divided these proteins into 5 major groups with various paralogous gene pairs. Molecular evolutionary studies aided with the conserved domain as well as gene structure analysis suggested that segmental duplications were the principal contributors for the expansion of Dof genes in G. raimondii.

Keywords: diploid cotton , G. raimondii, phylogenetic analysis, transcription factor

Procedia PDF Downloads 148