ARTICLE | doi:10.20944/preprints201908.0010.v1
Subject: Engineering, Mechanical Engineering Keywords: genetic algorithm; Kalina cycle; energy efficiency; Exergy efficiency;
Online: 1 August 2019 (06:13:45 CEST)
In this paper, a thermodynamic investigation is done on a Kalina-flash cycle. This work is initially validated with the Kalina cycle power plant, Wich is commissioned in Husavic. Low-temperature Kalina-flash is considered for this study. This cycle is working with the ammonia-water mixture. The Kalina-flash cycle was optimized in the view of exergy and thermal efficiency. A multi-objective genetic algorithm is used to accomplish optimization. The optimum values of the objective functions are observed to be 40.20 and 11.70% respectively. At last, The influence of the separator inlet dryness fraction, basic ammonia mass fraction, temperature and flash pressure ratio on the first and second law efficiencies are analysed.
ARTICLE | doi:10.20944/preprints201804.0227.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: Ensemble clustering; cluster stability; F-measure; co-association matrix; genetic algorithm
Online: 17 April 2018 (15:58:22 CEST)
Nowadays, we live in a world in which people are facing with a lot of data that should be stored or displayed. One of the key methods to control and manage this data refers to grouping and classifying them in clusters. Today, clustering has a critical role in information retrieval methods for organizing large collections inside a few significant clusters. One of the main motivations for the use of clustering is to determine and reveal the hidden and inherent structure of a set of data. Ensemble clustering algorithms combine multiple clustering algorithms to finally reach an overall clustering system. Ensemble clustering methods by lack of information fusing utilize several primary partitions of data to find better ways. Since various clustering algorithms look at the different data points, they can produce various partitions from such data. It is possible to create a partition with high performance by combining the partitions obtained from different algorithms, even if the clusters to be very dense from each other. Most studies in this area have examined all the initial clusters. In this study, a new method is used in which the most sustainable clusters are utilized instead of all primary produced clusters. Consensus function based on co-association matrixes used to select more stable clusters. The most stable clusters selection method is done by cluster stability criterion based on F-measure. Optimization functions are used to optimize the obtained final clusters. The genetic algorithm is the optimizer used in this article to find the ultimate clusters participated in a consensus. Experimental results on several datasets show that the output of proposed method is various clusters with high stability.
ARTICLE | doi:10.20944/preprints202301.0075.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: EMG; optimization; genetic algorithm; deep learning
Online: 4 January 2023 (09:21:39 CET)
Hand gesture recognition has many valuable applications in engineering and health care. This study proposes a novel model which can accurately distinguish hand gestures using forearm muscles' surface electromyogram (sEMG) signals. A deep learning algorithm with hyper parameters impacting the final model’s accuracy and a convolutional neural network (CNN) were employed in the recognition stage. The number of convolutional layers, kernels per layer, and neurons in the dense layer were selected for optimization, while the remaining parameters, such as the learning rate, batch size, and number of epochs, were chosen based on trial and error and prior knowledge. The optimal values for the selected hyperparameters were obtained using a genetic algorithm to achieve maximum recognition accuracy. The UC2018 Dual-Myo database was used for training and testing the model based on EMG signals characterizing the activity of eight different hand gestures. The final structure of the model consisted of two convolutional layers with 131 and 28 kernels, a dense layer with 111 neurons, and a softmax layer with eight neurons. Upon optimizing the hyperparameters using the genetic algorithm, the accuracy of the proposed model increased from 91.86% to 96.4% at best and 95.3% on average in real-time applications and 99.6% in an offline mode. Future work is warranted towards improving the architecture and the computational cost.
ARTICLE | doi:10.20944/preprints202310.2104.v1
Subject: Engineering, Architecture, Building And Construction Keywords: ventilation system networks; design optimization; genetic algorithm
Online: 1 November 2023 (03:55:34 CET)
The COVID-19 pandemic has emphasized the crucial role of ventilation systems in mitigating cross-infections, especially in infectious disease hospitals. This study introduces a dual-design operation ventilation system that can operate under two sets of ventilation conditions for normal and epidemic times. A challenge is optimizing duct diameters for required airflow while maintaining hydraulic balance. We design a genetic algorithm with adaptive penalty factor, the velocity constraint and the improved crossover and mutation probability. The improved genetic algorithm is suitable for ventilation system networks, which can find a better air duct diameters combination to improve the hydraulic balance rate, and reduce the usage of air valves, resulting in efficient hydraulic balancing commissioning. Compared with the traditional genetic algorithm, it has a faster search speed and a better global search ability, which is effective for the optimal design of ventilation system networks.
ARTICLE | doi:10.20944/preprints202309.0114.v1
Subject: Physical Sciences, Applied Physics Keywords: photovoltaic system; LPSP; TLCC; optimization; genetic algorithm
Online: 4 September 2023 (03:50:12 CEST)
This study is focused on an optimal sizing method based on genetic algorithms (GA) in order to design a high-performance photovoltaic system that would be installed in the Alioune Diop University of Bambey, Senegal. The multi-objective optimization allowed us to find a better trade- off between the Total Life Cycle cost (TLCC) and the Loss of Power Supply Probability (LPSP). The goal is to minimize the TLCC while maintaining a good satisfactory of the system with a desired LPSP, under certain constraints. The expressions of the TLCC and the LPSP are established according to the total photovoltaic energy and the battery capacity. The toolbox of Matlab software is used to implement the optimization problem with twelve blocks of the site and its different corresponding loads. The obtained results have led to a several combinations of the photovoltaic and battery capacities of which the best one is selected based on the lowest LPSP, that guaranteed a better load coverage during the night. The results of this proposed method are compared with intuitive method that has been firstly applied. For the block with the lowest load demand, the proposed optimization model leads to a reduction a reduction of 70% and 48% in the storage capacity and the TLCC respectively for a LPSP of 0.007 %.
ARTICLE | doi:10.20944/preprints202201.0430.v1
Subject: Engineering, Civil Engineering Keywords: Water distribution networks; Optimization; Genetic Algorithm; EPANET
Online: 28 January 2022 (08:53:05 CET)
Water distribution networks are vital infrastructure, needed for providing consumers with sufficient water of appropriate quality. The cost of construction, operation, and maintenance of such networks is extremely large. The problem of optimization of a water distribution network is governed by the type of water distribution network and the size of pipelines placed in the distribution network. This problem of the optimal diameter allocation of pipes in a distribution network has been heavily researched over the past few decades. This study describes the development of a computer program, ‘Smart Optimization Program for Water Distribution Networks’ (SOP–WDN), which applies Genetic Algorithm to the problem of the least-cost design of water distribution networks. SOP–WDN demonstrates the application of an evolutionary optimization technique, Genetic Algorithm, linked with a hydraulic simulation solver EPANET, for the optimal design of water distribution networks. The developed program was applied to three benchmark water distribution network optimization problems and produced consistently good results. SOP–WDN can be utilized as a tool for guiding engineers during the design and rehabilitation of water distribution pipelines.
ARTICLE | doi:10.20944/preprints202306.1093.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Aedes albopictus; genetic sexing strain; insecticide selection; dieldrin quantification
Online: 15 June 2023 (07:45:18 CEST)
The mass production of mosquitoes at an industrial scale requires efficient sex separation, which can be achieved through mechanical, genetic or artificial intelligence means. Compared with others methods, the genetic sexing approach offers the advantage of limiting costs and space by removing females at larval stage. We recently developed a GSS in Aedes albopictus based on the sex linkage of the rdl gene to the M locus, conferring dieldrin resistance in males only. It has been previously reported that dieldrin ingested by larvae can be detected in adults and bioaccumulated in predators, raising the question of its use at a large-scale. In this context, we performed several experiments aiming at optimizing dieldrin selection by decreasing both dieldrin concentration and exposure time while maintaining a stable percentage of females averaging 1%. We showed that the previously used dieldrin exposure induced an important toxicity as it killed 60% of resistant males at larval stage. We could easily lower this toxicity by reducing the dose and/or the exposure time to recover nearly all resistant males. We then quantified the residues of dieldrin in resistant male adults and showed that dieldrin toxicity in larvae was positively correlated with dieldrin concentrations detected in adults. Interestingly, we showed that the use of reduced dieldrin exposure led to a dieldrin detection in adult males that was below the sensitivity threshold of the Gas Chromatography Mass Spectrometry detection method. Presented data show that dieldrin exposure can be adjusted to suppress toxicity in males while achieving efficient sexing and lowering the levels of dieldrin residues in adults to barely detectable levels.
ARTICLE | doi:10.20944/preprints202310.1810.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Global Optimization; COVID-19; Genetic Algorithms; Particle Swarm Optimization; Cat Swarm Optimization
Online: 27 October 2023 (12:55:48 CEST)
As the COVID-19 pandemic has caused enormous damage to society, economy and public health security, it is crucial to combat the epidemic and allocate social and health resources effectively. Global optimization algorithms are extensively used in many domains to find optimal solutions to complex problems. Thus, a survey of three typical global optimizations applied on the COVID-19 pandemic is timely. This article is structured into three typical global optimization algorithms - Genetic Algorithm, Particle Swarm Optimization, and Cat Swarm Optimization - and summarizes the framework models and practical applications, as well as other optimization methods that may be applied to COVID-19. Finally, current unresolved challenges and future research opportunities to be explored are summarized.
ARTICLE | doi:10.20944/preprints202304.0172.v1
Subject: Computer Science And Mathematics, Computer Networks And Communications Keywords: Genetic Algorithm; Uniform Crossover; Network Protocol Optimization; Routing Algorithm; Optimization; Oriented Crossover
Online: 11 April 2023 (02:43:26 CEST)
Optimization using Genetic Algorithms (GA) is a well-known strategy in several scientific disciplines. The crossover is an essential operator of the Genetic Algorithm. It has been an active area of research to develop sustainable forms for this operand. In this work, a new crossover operand is proposed. This operand depends on giving an elicited description for the chromosome with a new structure for alleles of the parents. It is suggested that each allele has two attitudes, one attitude differs contrastingly with the other, and both of them complement the allele. Thus, in case of one attitude is good, the other should be bad. This is suitable for many systems which contain admired parameters and unadmired parameters. The proposed crossover would improve the desired attitudes and damp the undesired attitudes. The proposed crossover can be achieved in two stages: the first stage is a mating method for both attitudes in one parent to improving one attitude at the expense of the other. The second stage comes after the first improvement stage for mating between different parents. Hence, two concurrent steps for improvement would be applied. Simulation experiments for the system shows improvement in the fitness function. The proposed crossover could be helpful in different fields, especially to optimize routing algorithms and network protocols, an application that has been tested as a case study in this work.
ARTICLE | doi:10.20944/preprints202309.1324.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: optimization; genetic algorithm methods; initialization distribution; evolutionary techniques; stochastic methods; termination rules
Online: 20 September 2023 (07:35:05 CEST)
The need to find the global minimum in multi-dimensional functions is a critical problem in many fields of science and technology. Effectively solving this problem requires the creation of initial solution estimates, which are subsequently used by the optimization algorithm to search for the best solution in the solution space. In the context of this article, a novel approach to generating the initial solution distribution is presented which is applied to a genetic optimization algorithm. Using the k-means clustering algorithm, a distribution based on data similarity is created. This helps in generating initial estimates that may be more tailored to the problem. Additionally, the proposed method employs a rejection sampling algorithm to discard samples that do not yield better solution estimates in the optimization process. This allows the algorithm to focus on potentially optimal solutions, thus improving its performance. Finally, the article presents experimental results from the application of this approach to various optimization problems, providing the scientific community with a new method for addressing this significant problem.
ARTICLE | doi:10.20944/preprints201712.0129.v1
Subject: Engineering, Automotive Engineering Keywords: semi-active suspension; feed energy; parameter optimization; genetic algorithm
Online: 19 December 2017 (06:53:01 CET)
In order to coordinate the damping performance and energy regenerative performance of energy regenerative suspension, this paper proposes a structure of vehicle semi-active energy regenerative suspension with electro-hydraulic actuator (EHA). In light of the proposed concept, a specific energy regenerative scheme is designed and the mechanical properties test is carried out. Based on the test results, the parameter identification for the system model is conducted using recursive least squares algorithm. On the basis of system principle, the nonlinear model of the semi-active energy regenerative suspension with EHA is built. Meanwhile, LQG control strategy of the system is designed. And then the influence of the main parameters of EHA on the damping performance and energy regenerative performance of suspension is analyzed. Finally, the main parameters of EHA actuator are optimized via genetic algorithm. The test results show that when sinusoidal is input at the frequency of 2Hz and the amplitude of 30mm, the spring mass acceleration RMS value of optimized EHA semi-active energy regenerative suspension is reduced by 22.23% and energy regenerative power RMS value is increased by 40.51%, which means while meeting the requirements of certain vehicle ride comfort and driving safety, energy regenerative performance is improved significantly.
ARTICLE | doi:10.20944/preprints202306.1263.v1
Subject: Engineering, Civil Engineering Keywords: genetic algorithms; optimization; band-gaps; beams; eigenproblem; dynamic analysis; finite element method
Online: 19 June 2023 (02:56:28 CEST)
The aim of this paper is to optimize thickness variation function of simply supported and cantilever beams, in terms of maximizing gaps between chosen neighboring frequencies and analyze obtained results. The optimization results are examined in terms of achieving the objective function (related to eigenproblem), but also in terms of their dynamics stiffness (forced vibrations excited by point harmonic load). In the optimization process, a Genetic Algorithm was used. Problems related to structural dynamics were solved by FEM implementation into the algorithm. Sample results were presented, and the developed algorithm was analyzed in terms of result convergence by examining several variable parameters. The authors demonstrated the validity of applying the described optimization tool to the presented problems. Conclusions were drawn regarding the correlation between stiffness and mass distribution in the optimized beams and the natural frequency modes in terms of which they were optimized.
REVIEW | doi:10.20944/preprints202309.1318.v1
Subject: Engineering, Chemical Engineering Keywords: reactor operations; Machine Learning (ML); optimization; Artificial Neural Networks (ANNs); Genetic Algorithms (GAs)
Online: 20 September 2023 (08:59:34 CEST)
Machine Learning (ML) has brought about a transformative era in reactor operations, reshaping monitoring, control, and optimization strategies. This survey comprehensively explores the diverse spectrum of ML applications in industrial reactors. From real-time sensor analysis ensuring reactor functionality to adaptive control algorithms ensuring stability, ML's impact is profound and multifaceted. The benefits of ML are equally evident in optimization, encompassing performance trend prediction, proactive maintenance, and fine-tuning of operations for enhanced efficiency. This review identifies dominant ML techniques, operations stages receptive to ML integration, core data sources, and critical input-output parameters. Aimed at both academics and practitioners, this exploration enriches reactor technologies, unlocking their full potential through insights driven by ML.
ARTICLE | doi:10.20944/preprints201705.0081.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: optimization; simulated annealing; genetic algorithm; power losses; power consumption
Online: 9 May 2017 (10:45:49 CEST)
In this paper a variable’s involved in assessing the quality of a distributed generation system are reviewed, aiming to minimize the electric power losses (unused power consumption) and optimize the voltage profile. To provide this assessment, several experiments have been made to the IEEE 34-bus test case and various actual test cases with the respect of multiple DG units. The possibility and effectiveness of the proposed algorithm for optimal placement and sizing of DG in distribution systems have been verified. Finally, four algorithms were trailed: simulated annealing (SA), hybrid genetic algorithm (HGA), genetic algorithm (GA) and variable neighbourhood search. The HGA algorithm was found to produce the best solution at a cost of longer processing time.
ARTICLE | doi:10.20944/preprints202308.1745.v1
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Genetic Algorithms; Digital Filters; Metaheuristic Optimization; Finite Impulse Response (FIR); Side Lobe Level (SLL).
Online: 24 August 2023 (10:46:40 CEST)
The advancement of technology and the availability of specialized digital signal processing chips have made digital filter design and implementation more feasible in a variety of fields, including biomedical engineering. This paper makes two key contributions. First, it uses a genetic algorithm to optimize the coefficients of Finite Impulse Response (FIR) filters. Second, it conducts a case study on using genetic algorithms to optimize FIR filters for electrocardiogram (ECG) biomedical signal noise removal. The goal of the proposed filter design approach is to achieve the desired signal bandwidth while minimizing the side lobe level and eliminating unwanted signals using a genetic algorithm. The results of the comprehensive analysis of the impact of different genetic operators show that the genetic algorithm-based filter outperforms conventional filter designs.
ARTICLE | doi:10.20944/preprints201703.0015.v1
Subject: Physical Sciences, Fluids And Plasmas Physics Keywords: colebrook equation; colebrook-white; moody diagram; turbulent flow; hydraulic resistance; darcy friction; pipes; genetic algorithms; optimization techniques; error analysis
Online: 2 March 2017 (07:57:54 CET)
Today, Colebrook’s equation is mostly accepted as an informal standard for modeling of turbulent flow in hydraulically smooth and rough pipes including transient zone in between. The empirical Colebrook’s equation relates the unknown flow friction factor (λ) with the known Reynolds number (R) and the known relative roughness of inner pipe surface (ε/D). It is implicit in unknown friction factor (λ). Implicit Colebrook’s equation cannot be rearranged to derive friction factor (λ) directly and therefore it can be solved only iteratively [λ=f(λ, R, ε/D)] or using its explicit approximations [λ≈f(R, ε/D)]. Of course, approximations carry in certain error compared with the iterative solution where the highest level of accuracy can be reached after enough number of iterations. The explicit approximations give a relatively good prediction of the friction factor (λ) and can reproduce accurately Colebrook’s equation and its Moody’s plot. Usually, more complex models of approximations are more accurate and vice versa. In this paper, numerical values of parameters in various existing approximations are changed (optimized) using genetic algorithms to reduce maximal relative error. After this improvement computational burden stays unchanged while accuracy of approximations increases in some of the cases very significantly.
ARTICLE | doi:10.20944/preprints202311.0613.v1
Subject: Engineering, Chemical Engineering Keywords: Phyllantus emblica leaf; bioactive extract; heat-assisted technology; multi gene genetic programming; reliability assessment
Online: 9 November 2023 (07:54:45 CET)
The feasibility of recovering bioactive antioxidants from Phyllantus emblica leaves using ethanol -water mixture (0 – 100%) and heat-assisted extraction technology (HAE-T) was investigated in this present study. To this effect, the process parameter of operating temperature (OT: 30 -50 oC), solid -to-liquid ratio (S:L: 1:20 - 1:60 g/mL) and extraction time (ET: 45 - 180 min) were investigated on the extract total phenolic content (TPC, mg GAE/g d.w), yield (EY, %) and antioxidant activity (μM AAE/g d.w) by employing the Box-Behnken experimental design (BBD) available in response surface methodology (RSM). Multi-objective process optimization using the desirability function algorithm to determine set of process variables that simultaneously optimize process responses of TPC, EY and AA was also investigated. The recovery process was thereafter modeled with BBD-RSM and multi gene genetic programming (MGGP) algorithm and model reliability assessment via Monte Carlo simulation were conducted for the best performing set of models for predicting TPC, EY and AA values. The HPLC characterization of the recovered extract was carried out to ascertain the phenolic compound constituents of the Phyllantus emblica leaf extract. The 50% ethanol solution was found to be the best for the optimal extraction of antioxidants from Phyllantus emblica leaves. The HAE-T was suitable for recovering bioactive extract from Phyllantus emblica leaves and investigated process parameters have impacts on the recovery process. The process parameters that simultaneously gave the optimum EY of 21.6565%, TPC of 67.116 mg GAE/g and AA of 3.68583 µM AAE/g were OT of 41.61 oC, S:L of 1:60 g/mL and ET of 180 min. The HPLC extract profiling revealed that the bioactive constituents present in the recovered extract were betulinic acid, gallic acid, chlorogenic acid, caffeic acid, ellagic acid, and ferulic acid. Both the developed BBD-RSM and evolved MGGP-based models predicted the observed process response of TPC, EY and AA satisfactorily with BBD-RSM models marginally better in their predictions. The reliability results showed that the BBD-RSM models predicted TPC, EY and AA values with high certainty of 99.985%, 97.569% and 98.661%, respectively.
ARTICLE | doi:10.20944/preprints201704.0148.v1
Subject: Engineering, Energy And Fuel Technology Keywords: francis turbine; draft tube; optimization design; experiment of design; non–dominated sorting genetic algorithm
Online: 24 April 2017 (10:52:28 CEST)
In order to improve the performance of the draft tube in hydraulic turbine, a multi–objective optimization method for the draft tube is developed by combining the design of experiment (DOE), the radial basis function (RBF) and the non–dominated sorting genetic algorithm (NSGA–II) in this paper. The geometrical design variables of the median section in the draft tube and the cross section in its exit diffuser are considered as design parameters in this optimization, which objective function is to maximize the pressure recovery factor (Cp) and minimize the energy loss coefficient (ζ). The limited numbers of design matrix required for the shape optimization of the draft tube is generated by optimal Latin hypercube (OLH) method of the DOE technique, of which performances are evaluated through computational fluid dynamic (CFD) numerical simulation. For reducing of the computational consumption, the approximate model is used based on the RBF. The Pareto optimal solutions are finally performed using the NSGA–II for obtaining the best geometrical parameters of the draft tube. The optimization result of the draft tube shows a marked performance improvement over the original, which verifies the theoretical validity and feasibility of the proposed method in this paper.
ARTICLE | doi:10.20944/preprints202308.1376.v1
Subject: Engineering, Architecture, Building And Construction Keywords: air supply optimization; double-objective optimization; surrogate-based optimization; Kriging model; genetic algorithm
Online: 21 August 2023 (03:23:07 CEST)
When using meta-heuristic optimization approaches for optimization, a large number of samples are required. In particular, when generating subgeneration, the utilization of existing samples is low and the number of individuals is high. Therefore, surrogate-based optimization has been developed, which greatly reduces the number of individuals in the subgeneration and the cost of optimization. In complex air supply scenarios, single-objective optimization results may not be comprehensive; therefore, this paper developed a double-objective air supply optimization method based on the Kriging surrogate model and Non-dominated Sorting Genetic Algorithms-II. And proposed the infill criteria based on clustering to advance the Pareto Frontier. The method was validated by an inverse prediction case, and in particular, the problems when based on 3D steady-state simulations were analyzed. The results showed that the method can quickly achieve an approximate prediction of the boundary conditions (when prediction were made based on experimental data, the number of simulations was 82 and the average error was 6.8%). Finally, the method was used to optimize the air supply parameters of a dual-aisle, single-row cabin. The Pareto set suggested that an airflow organization with dual circulation may be optimal.
ARTICLE | doi:10.20944/preprints201806.0317.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: device-to-device; LTE systems; resource allocation; particle swarm optimization algorithm; genetic algorithm; system capacity
Online: 20 June 2018 (09:31:54 CEST)
In this study, the resource blocks (RB) are allocated to user equipment (UE) according to the evolutional algorithms for long term evolution (LTE) systems. Particle Swarm Optimization (PSO) algorithm is one of the evolutionary algorithms, based on the imitation of a flock of birds foraging behavior through learning and grouping the best experience. In previous work, the Simple Particle Swarm Optimization (SPSO) algorithm was proposed for RB allocation to enhance the throughput of Device-to-Device (D2D) communications and improve the system capacity performance. In simulation results, with less population size of M = 10, the SPSO can perform quickly convergence to sub-optimal solution in the 100th generation and obtained sub-optimum performance with more 2 UEs than the Rand method. Genetic algorithm (GA) is one of the evolutionary algorithms, based on Darwinian models of natural selection and evolution. Therefore, we further proposed a Refined PSO (RPSO) and a novel GA to enhance the throughput of UEs and to improve the system capacity performance. Simulation results show that the proposed GA with 100 populations, in 200 generations can converge to suboptimal solutions. Therefore, with comparing with the SPSO algorithm the proposed GA and RPSO can improve system capacity performance with 1.8 and 0.4 UEs, respectively.
ARTICLE | doi:10.20944/preprints202101.0018.v1
Subject: Engineering, Automotive Engineering Keywords: conjunctive use; cropping pattern; genetic algorithm; bacterial foraging optimization; ant colony optimization; hybrid optimization; productivity
Online: 4 January 2021 (11:31:59 CET)
Increasing demand for food production with limited available water resources pose the threat to agricultural activities. The conjunctive allocation of water resources maximizes the net benefit of farmers efficiently. In this study, a novel hybrid optimization model was developed based on a genetic algorithm (GA), bacterial foraging optimization (BFO) and ant colony optimization (ACO) to maximize the net benefit of water deficit Sathanur reservoir command. The GA-based opti-mization model considered crop-related physical and economical parameters to derive optimal cropping patterns for three different conjunctive use policies and further allocation of surface and groundwater for different crops are enhanced with the BFO. The allocation of surface and groundwater for the head, middle and tail reach obtained from BFO is considered as input to ACO as a guiding mechanism to attain an optimal cropping pattern. Comparing the average produc-tivity values Policy 3 (3.665 Rs/m3) has better values relating to Policy 1 (3.662 Rs/m3) and Policy 2 (3.440 Rs/m3). Thus, the developed novel hybrid optimization model (GA-BFO-ACO) is very promising to enhance the farmer's net income as well as for the command area water conservation and can be replicated in other irrigated regions of the globe to overcome chronic land and water problems.
ARTICLE | doi:10.20944/preprints202003.0298.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: Data Mining; Breast Cancer; Hybrid Feature Selection; Machine learning; Support Vector Machine; Optimize Genetic Algorithm; boosting algorithms
Online: 19 March 2020 (11:13:15 CET)
Breast cancer is a significant health issue across the world. Breast cancer is the most widely-diagnosed cancer in women; early-stage diagnosis of disease and therapies increase patient safety. This paper proposes a synthetic model set of features focused on the optimization of the genetic algorithm (CHFS-BOGA) to forecast breast cancer. This hybrid feature selection approach combines the advantages of three filter feature selection approaches with an optimize Genetic Algorithm (OGA) to select the best features to improve the performance of the classification process and scalability. We propose OGA by improving the initial population generating and genetic operators using the results of filter approaches as some prior information with using the C4.5 decision tree classifier as a fitness function instead of probability and random selection. The authors collected available updated data from Wisconsin UCI machine learning with a total of 569 rows and 32 columns. The dataset evaluated using an explorer set of weka data mining open-source software for the analysis purpose. The results show that the proposed hybrid feature selection approach significantly outperforms the single filter approaches and principal component analysis (PCA) for optimum feature selection. These characteristics are good indicators for the return prediction. The highest accuracy achieved with the proposed system before (CHFS-BOGA) using the support vector machine (SVM) classifiers was 97.3%. The highest accuracy after (CHFS-BOGA-SVM) was 98.25% on split 70.0% train, remainder test, and 100% on the full training set. Moreover, the receiver operating characteristic (ROC) curve was equal to 1.0. The results showed that the proposed (CHFS-BOGA-SVM) system was able to accurately classify the type of breast tumor, whether malignant or benign.
ARTICLE | doi:10.20944/preprints202307.1870.v1
Subject: Engineering, Marine Engineering Keywords: multi-parameter 1; multi-objective 2; genetic algorithms 3; water jet pump 4; impellers 5; optimal design 6.
Online: 27 July 2023 (08:36:44 CEST)
As the core components of water jet propulsion system, water jet pump, directly affect the ship's propulsion performance. 3D reverse design method can effectively suppress the impeller secondary flow to get better performing hydraulic models. Aiming at fast and efficient optimization of the impellers, we parameterize the impellers and runner, and coupled with optimization algorithms and numerical calculations. It is an efficient and feasible way to coupling optimization based on multi-parameter, multi-objective and optimization algorithms, and parameterizing the impellers and guide vane geometry based on the 3D model designed by 3D reverse design method. In this paper, the waterjet propulsion pump is taken as the research object. According to the design method of the waterjet propulsion pump hydraulic model, the traditional axial flow blade design method, the modern ternary design theory of the blades, and the parametric three-dimensional reverse design method are selected to constructing an optimal design optimization strategy for the impeller of water-jet propulsion pump based on multi-parameter and multi-object genetic algorithm. Under the design conditions, the optimized pump efficiency reaches 89.28%, which is 1.24% higher than the original hydraulic model. The optimized pump head is 13.51 m, which is 0.39m more than the original hydraulic model. Under the design condition, the test measured head is 13.26m, the numerical calculation result is 1.88% higher than the test result, the test measured efficiency is 87.1%, the numerical calculation result is 2.5% higher than the test result. From the test results, the optimized impeller has higher hydraulic performance. Experiments have shown that it is feasible to optimize the design strategy.
ARTICLE | doi:10.20944/preprints202305.1314.v1
Subject: Engineering, Architecture, Building And Construction Keywords: RBFOpt model-based optimization; genetic algorithms; multi-objective optimization; Energy Use Intensity optimization; spatial Daylight Autonomy optimization; office building; layout optimization
Online: 18 May 2023 (09:37:53 CEST)
Advancements in Parametric Design, Generative Design, and automation in Building Information Modelling (BIM) have opened new opportunities for architects and engineers working on complex buildings, such as offices. These developments allow designers to enhance their designs, increase project efficiency, improve performance, and reduce project time and costs. To address conflicting objectives that arise during the design process, genetic algorithms with multi-objective optimization (MOO) have been employed in architectural design. The GENIUS project aims to optimize building shape, apertures, and shading systems in the concept and design stages, with a focus on energy and daylight performance. The project integrates BIM and visual programming tools with Artificial Intelligence techniques like Genetic Algorithms and RBFOpt model-based optimization. Optimization algorithms are used to identify the best solutions that meet all design objectives, helping architects optimize their designs and achieve desired outcomes. The workflow was tested on a case study of a large office building, with MOO focused on maximizing daylight performance using Spatial Daylight Autonomy metric and minimizing energy consumption using Energy Use Intensity metric. The project provides architects with a method to improve their designs using Algorithm Aided Design tools, which help identify the best solutions for complex design problems.
ARTICLE | doi:10.20944/preprints202303.0481.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: genetic fidelity; genetic diversity; IRAP; ISSR; Rhododendron
Online: 28 March 2023 (09:56:04 CEST)
Rhododendron is well-known for the colorful corolla. Molecular marker systems have the potentials to elucidate genetic diversity as well as to assess the genetic fidelity in rhododendrons. In the present study, the reverse transcription domains of long terminal repeat retrotransposons were cloned from rhododendrons and used to develop inter-retrotransposon amplified polymorphism (IRAP) marker system. Subsequently, 198 polymorphic loci were generated from the IRAP and inter-simple sequence repeat (ISSR) markers, of which 119 were derived from the IRAP markers. It was justified that in rhododendrons, IRAP markers were superior to the ISSRs in some polymorphic parameters such as the average number of polymorphic loci (14.88 versus 13.17). In comparison with the single one, the combination of IRAPs and ISSRs systems was more discriminative for detecting 46 rhododendron accessions. Further, IRAP markers demonstrated more efficiency in genetic fidelity detection of in vitro R. bailiens, an endangered species just recorded in Guizhzhou Province, China. The available evidences revealed the distinct properties of IRAP and ISSR markers in the rhododendron-associated applications, and highlighted the availability of highly informative ISSR and IRAP markers in the genetic diversity evaluation and the genetic fidelity assessment of rhododendrons, which may facilitate the preservation and genetic breeding in rhododendron plants.
ARTICLE | doi:10.20944/preprints202311.1357.v1
Subject: Engineering, Control And Systems Engineering Keywords: genetic algorithm; genetic programming; control design; control tuning
Online: 22 November 2023 (07:49:09 CET)
This paper introduces the implementation of a genetic programming (GP)-based procedure to the automatic design and tuning of process controllers. The proposed approach makes a significant contribution to the field of artificial intelligence (AI) in control engineering. Unlike other controller design methods, the GP-based program handles the entire design in the time domain, including differential operations like derivatives and integrals, without the need for intermediate inverse Laplace transformation. This approach not only simplifies the design process but also ensures that all generated controllers are implementable in physical systems. Furthermore, GP’s functions set includes various mathematical operations beyond basic arithmetic operators, such as trigonometric, exponential, and logarithmic operators. The performance and validity of the resulting controllers generated by the proposed GP-based approach are evaluated by verifying whether the generator can replicate the structure and performance of those produced by traditional controller design methods and, in some cases, achieve even better results. As a result, the GP-based approach presents a promising solution for automating the controller design process and addressing control problems in various engineering applications.
ARTICLE | doi:10.20944/preprints202309.1532.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Neural networks; Genetic algorithms; Genetic programming; Grammatical evolution
Online: 22 September 2023 (08:37:54 CEST)
RBF networks are used in a variety of real-world applications such as medical data or signal processing problems. The success of these parametric models lies in the successful adaptation of their parameters using efficient computational techniques. In the current work, a method of adjusting the parameters of these networks using Grammatical Evolution is presented. Grammatical Evolution will be used to successfully discover the most promising range of parameter values and then the training of the parameter set will be achieved using a Genetic Algorithm. The new method was applied to a wide range of data fitting and classification problems, and the results were more than promising.
REVIEW | doi:10.20944/preprints202007.0583.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic association studies; extreme phenotype; genetic epidemiology; tinnitus
Online: 24 July 2020 (13:43:00 CEST)
Exome sequencing has been commonly used in rare diseases by selecting multiplex families or singletons with an extreme phenotype (EP) to search for rare variants in coding regions. The EP strategy covers both extreme ends of a disease spectrum and it has been also used to investigate the contribution of rare variants to heritability in complex clinical traits. We have conducted a systematic review to find evidence supporting the use of EP strategies to search for rare variants in genetic studies of complex diseases, to highlight the contribution of rare variation to the genetic structure of multiallelic conditions. After performing the quality assessment of the retrieved records, we selected 19 genetic studies considering EP to demonstrate genetic association. All the studies successfully identified several rare variants, de novo mutations and many novel candidate genes were also identified by selecting an EP. There is enough evidence to support that the EP approach in patients with an early onset of the disease can contribute to the identification of rare variants in candidate genes or pathways involved in complex diseases. EP patients may contribute to a better understanding of the underlying genetic architecture of common heterogeneous disorders such as tinnitus or age-related hearing loss.
ARTICLE | doi:10.20944/preprints202311.1729.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: genetic diversity; genetic variability; microsatellites; allele frequencies; population structure
Online: 28 November 2023 (08:08:48 CET)
Guava (Psidium guajava L.) is a species is widely distributed in Córdoba, despite this, there are few studies that have been carried out to understand its genetic diversity. For this reason, the objective of this research was to evaluate the genetic diversity and variability of guava (Psidium guajava L) using microsatellite markers in Montería, Córdoba-Colombia. Forty-five accessions were evaluated. For DNA extraction, the CTAB 2x extraction protocol was used with modifications. The extracted DNA was amplified by the PCR technique using seven microsatellite markers. A total of 46 alleles were found with an average of 6.5 alleles per locus. A total of 28 private alleles were identified in the populations, possibly fixed by different evolutionary forces. The evaluated population presented an average expected heterozygosity of 0.572 and the observed heterozygosity was lower (0.058). The fixation index presented a total average of 0.906, indicating that in Montería there is an excess of homozygotes. The PIC values allowed us to determine that the markers mPgCIR9, mPgCIR11, mPgCIR13, mPgCIR16, mPgCIR19 and mPgCIR22 are highly informative, while mPgCIR23 is moderately informative. The guava population in Montería presented a low genetic diversity within the subpopulations, which could be related to inbreeding events such as self-pollination..
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: forensic genetic genealogy; investigative genetic genealogy; DNA; forensic DNA
Online: 1 August 2020 (16:29:22 CEST)
Forensic genetic genealogy, a technique leveraging new DNA capabilities and public genetic databases to identify suspects, raises specific considerations in a law enforcement context. Use of this technique requires consideration of its scientific and technical limitations, including the composition of current online datasets, and consideration of its scientific validity. Additionally, forensic genetic genealogy needs to be considered in the relevant legal context to determine the best way in which to make use of its potential to generate investigative leads while minimising its impact on individual privacy. This article presents these issues from an Australian perspective, with the observations and conclusions likely to be applicable to other jurisdictions.
CONCEPT PAPER | doi:10.20944/preprints202011.0387.v1
Subject: Social Sciences, Anthropology Keywords: genetic music; genetic code; music composition; steam disciplines; notch1 gene
Online: 13 November 2020 (15:34:47 CET)
In the present work we present a methodology for teaching the basis of the genetic code through music composition, with the aim to combine science and arts learning. The project was carried out by 155 students, the so-called MARGA Consortium, with ages comprised between 10 and 17 years from different public schools located in the Principality of Asturias, Spain. The different groups generated 8 different music works using a short genetic sequence obtained from the human notch1 gene, receptor of mutations leading to chronic lymphocytic leukemia.
ARTICLE | doi:10.20944/preprints201707.0047.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Festuca ovina L.; AFLP, genetic diversity; genetic barriers; environmental factors
Online: 18 July 2017 (10:05:56 CEST)
Glaciation and mountain orogeny have generated new ecologic opportunities for plants, favoring an increase in the speciation rate. Moreover, they also act as corridors or barriers for plant lineages and populations. High genetic diversity ensures that species are able to survive and adapt. Gene flow is one of the most important determinants of the genetic diversity and structure of out-crossed species, and it is easily affected by biotic and abiotic factors. The aim of this study was to characterize the genetic diversity and structure of an alpine species, Festuca ovina L., in Xingjiang, China. A total of 100 individuals from 10 populations were analyzed using six amplified fragment length polymorphism (AFLP) primer pairs. A total of 583 clear bands were generated, of which 392 were polymorphic; thus, the percentage of polymorphic bands (PPB) was 67.24%. The total and average genetic diversities were 0.2722 and 0.2006 (0.1686-0.2225), respectively. The unweighted group method with arithmetic mean (UPGMA) tree, principal coordinates analysis (PCoA) and STRUCTURE analyses revealed that these populations or individuals could be clustered into two groups. The analysis of molecular variance analysis (AMOVA) suggested that most of the genetic variance existed within a population, and the genetic differentiation (Fst) among populations was 20.71%. The Shannon differentiation coefficient (G’st) among populations was 0.2350. Limited gene flow (Nm = 0.9571) was detected across all sampling sites. The Fst and Nm presented at different levels under the genetic barriers due to fragmentation. The population genetic diversity was significant relative to environmental factors such as temperature, altitude and precipitation.
REVIEW | doi:10.20944/preprints202012.0738.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Next generation sequencing; Genetic disorders; Genomic medicine; Genetic counseling; Rare diseases
Online: 29 December 2020 (16:47:01 CET)
Genetic disorders are preeminent determinants of infant mortality. The inherited pediatric-onset genetic disorders have consequential stress on child growth and development: several congenital, complex and rare disorders with indistinguishable clinical symptoms where diagnosis always remains a challenging task. Traditional diagnosis methods include biochemical tests followed by chromosomal microarray and sequencing of a single gene or panel of genes. These methods had several limitations, but with the advent of whole-exome sequencing (WES), genetic testing has become cost-effective and transformative. Exome sequencing has been known for its effectiveness, which appropriately elucidates and distinguishes the heterogeneous disorders to avoid misdiagnosis and decode the underlying genetic alterations. WES has led to discovering genes and genomic variants in a broad spectrum of diseases, including autism, epilepsy, congenital heart diseases, neurodevelopmental diseases, cancer, nephrotic disorders, neural tube defects and fetal structural anomalies. WES is significant in producing immense genomic biomarkers that can be made as appropriate pharmacogenomic targets for drug therapy. In this article, we analyze the recent exploration of WES technology to revolutionize not only the process of genetic variation and disease detection but also the convention of preventative and targeted drug discovery.
REVIEW | doi:10.20944/preprints202012.0144.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Antimicrobial resistance; blaCTX-M-15; genetic environment; mobile genetic elements; Africa
Online: 7 December 2020 (12:49:16 CET)
The most widely distributed blaCTX-M gene on a global scale is blaCTX-M-15. The dissemination has been associated with clonal spread and different types of mobile genetic elements. This study aimed to review and describe the genetic environments of blaCTX-M-15 gene detected from Enterobacteriaceae in published literature from Africa. A literature search for relevant articles was done through PubMed, and Google Scholars electronic databases, 43 articles from 17 African countries were included in the review based on the eligibility criteria. Insertion sequences were reported as part of the genetic environment of blaCTX-M-15 gene in 32 studies, integrons in 13 studies, and plasmids in 23 studies. In this review, five insertion sequences including ISEcp1, IS26, orf447, IS903, and IS3 have been detected associated with the genetic environment of blaCTX-M-15 in Africa. Seven different genetic patterns were seen in blaCTX-M-15 genetic environment. Insertion sequence ISEcp1 was commonly located upstream of the end of the blaCTX-M-15 gene while insertion sequence orf477 was located downstream. In some studies, ISEcp1 was truncated upstream of blaCTX-M-15 by insertion sequences IS26 and IS3. Class 1 integron (Intl1) was most reported to be associated with blaCTX-M-15 (13 studies), with Intl1/dfrA17–aadA5 being the most common gene cassette array. IncFIA-FIB-FII multi-replicons and IncHI2 replicon types were the most common plasmid replicon types that horizontally transfer blaCTX-M-15 gene. Aminoglycoside modifying enzymes, and plasmid-mediated quinolone resistance genes were commonly collocated with blaCTX-M-15 gene on plasmids. This review revealed the predominant role of ISEcp1, Intl1and IncF plasmid in the mobilization and continental dissemination of the blaCTX-M-15 gene in Africa.
ARTICLE | doi:10.20944/preprints202307.1185.v1
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: microRNA; isomiR; genetic association
Online: 18 July 2023 (07:52:22 CEST)
MicroRNA plays a critical role in regulating gene expression post-transcriptionally. Variations in mature microRNA sequences, known as isomiRs, arise from imprecise cleavage and nucleotide substitution or addition. These isomiRs can target different mRNAs or compete with their canonical counterparts, thereby expanding the scope of miRNA post-transcriptional regulation. Our study investigated the relationship between cis-acting single nucleotide polymorphisms (SNPs) in precursor miRNA regions and isomiR composition, represented by the ratio of a specific 5’-isomiR subtype to all isomiRs identified for a particular mature miRNA. Significant associations between 95 SNP-isomiR pairs were identified. Of note, rs6505162 was significantly associated with both 5’-extension of hsa-miR-423-3p and 5’-trimming of hsa-miR-423-5p. Comparison of breast cancer and normal samples revealed that expression of both isomiRs was significantly higher in tumors than in normal tissues. This study sheds light on the genetic regulation of isomiR maturation and advances our understanding of post-transcriptional regulation by microRNA.
ARTICLE | doi:10.20944/preprints202106.0710.v1
Online: 29 June 2021 (13:30:30 CEST)
In recent years, several industries have registered an impressive improvement in technological advances such as Internet of Things (IoT), e-commerce, vehicular networks, etc. These advances have sparked an increase in the volume of information that gets transmitted from different nodes of a computer network (CN). As a result, it is crucial to safeguard CNs against security threats and intrusions that can compromise the integrity of those systems. In this paper, we propose a machine mearning (ML) intrusion detection system (IDS) in conjunction with the Genetic Algorithm (GA) for feature selection. To assess the effectiveness of the proposed framework, we use the NSL-KDD dataset. Furthermore, we consider the following ML methods in the modelling process: decision tree (DT), support vector machine (SVM), random forest (RF), extra-trees (ET), extreme gradient boosting (XGB), and naïve Bayes (NB). The results demonstrated that using the GA algorithm has a positive impact on the performance of the selected classifiers. Moreover, the results obtained by the proposed ML methods were superior to existing methodologies.
REVIEW | doi:10.20944/preprints202001.0276.v1
Subject: Biology And Life Sciences, Insect Science Keywords: genetic improvement; genetic variation; heritability; systematic review; biocontrol agent; life history traits
Online: 24 January 2020 (10:39:55 CET)
The concept of genetic improvement in relation to biological control involves the exploitation of natural genetic variation for the benefit of existing biological control agents (BCAs). Despite recent calls for this process to be adopted in biological control research, there is no clear overview of the current state of research into genetic variation within a biological control context, including quantifiable estimates such as narrow-sense heritability (h2). In this systematic review, we aim to determine the current state of research on the genetic variation of biological control traits in natural enemies. After the searching process, screening for papers that can deliver on our research question reduced the initial 2,927 search hits to only a mere 69 papers for data extraction. Of these, the majority (73.6%) did not report quantitative values for genetic variation. Extracting the traits measured in these papers, we categorized them according to two approaches; the first related to fitness components, and the second related to biological control importance. This systematic review highlights the need for more rigorous reporting of the quantitative values of genetic variation to enable the successful genetic improvement of biological control agents.
CASE REPORT | doi:10.20944/preprints202312.0328.v1
Subject: Biology And Life Sciences, Other Keywords: COVID-19; SARS-CoV-2; oncology; genetic variants; NGS; severity; genetic associations; exome
Online: 6 December 2023 (08:52:54 CET)
The COVID-19 pandemic has created unique challenges for people with comorbidities, including hereditary diseases and cancer cancers. Several studies have reported a link between the presence of disease-causing genetic variants and the outcome of the COVID-19 infection. In this study, we used clinical exome sequencing in a cohort of 840 COVID-19 patients to identify pathogenic and likely pathogenic genetic variants present in these individuals. While we did not identify any statistically significant differences in the overall burden of pathogenic variants between different patient groups, we discovered three known pathogenic alleles associated with hereditary cancer syndromes, including a frameshift mutation in MSH6 and two missense mutations in TP53. The patients carrying these mutations presented with different severity of the disease and outcome. Thus, a 58-year old male subject with an MSH6 mutation developed a severe form of COVID-19 that resulted in death, even though the patient had few pre-existing conditions and no evidence of malignant tumors. On the other hand, two female subjects carrying pathogenic TP53 variants successfully recovered from the disease despite suffering from various forms of cancer. Our results highlight the importance of personalized approaches to the diagnosis, management and treatment of COVID-19 in patients with specific genetic mutations. Further studies are needed to elucidate the complex relationship between these mutations and COVID-19.
ARTICLE | doi:10.20944/preprints202212.0099.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Genetic parameters, (Co)variance components, Mecheri sheep, Animal models, Maternal genetic influence, Inbreeding
Online: 6 December 2022 (10:03:11 CET)
Determining genetic and non-genetic sources of variation in a breed is vital for the formulation of strategies for its conservation and improvement. The present study was aimed at estimating the (co)variance components and genetic parameters of Mecheri sheep by fitting six different animal models in the restricted maximum likelihood method, with a preliminary investigation on the performance of animals for non-genetic sources of variation. A total of 2616 lambs were studied, and varying levels of significance were found for the effect of period, season, parity of dam and birth type on different body weight traits. Direct heritability estimates derived from the best animal model for body weight at birth, 3 months, 6 months, 9 months and 12 months were 0.21, 0.24, 0.10, 0.15 and 0.09, respectively, and maternal heritabilities of the corresponding traits were 0.12, 0.05, 0.04, 0.04 and 0.04, respectively. The genetic correlations between body weight traits were all positive and moderate to strong except for birth weight with the other body weight traits. The significance of non-genetic factors studied in this work demanded a correction to improve the accuracy of the direct selection of lambs for body weight traits. The estimated genetic parameters identified the weaning weight as a selection criterion for the improvement in body weight of Mecheri lambs at different ages. Inbred individuals accounted for approximately 13% of the total population in the Mecheri sheep population studied. There were 877 founders in the population, and the actual effective size of the population was 128.48. The population's mean generation interval was 3.26. The mean inbreeding values ranged from 0.005 to 0.010 across generations. The population's average relatedness ranged from 0.001 to 0.014 across generations. Individual inbreeding was found to be 0.45 per cent for the entire population and 3.4 per cent for the inbred population.
ARTICLE | doi:10.20944/preprints202107.0509.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Perilla crop; genetic resources; morphological traits; principal component analysis; SSR marker; genetic variation
Online: 22 July 2021 (08:04:28 CEST)
Using morphological characteristics and SSR markers, we evaluated the morphological and genetic variation of 200 Perilla accessions collected from the five regions of South Korea and other region. In morphological characteristics analysis, particularly, leaf color, stem color, degree of pubescence, leaf size were found to be useful for distinguishing the characteristics of native Perilla accessions cultivated in South Korea. A total of 137 alleles were identified in the 20 simple sequence repeat (SSR) markers, and the number of alleles per locus ranged from 3 to 13, and the average number of alleles per locus was 6.85. The average gene diversity (GD) was 0.649, with a range of 0.290-0.828. From analysis of SSR markers, accessions from the Jeolla-do and Gyeongsang-do regions showed comparatively high genetic diversity values compared with those from other regions in South Korea. In the unweighted pair group method with arithmetic mean (UPGMA) analysis, the 200 Perilla accessions were found to cluster into three major groups and an outgroup with a genetic similarity of 42%, and did not showed a clear geographic structure from the five regions of South Korea. Therefore, it is believed that landrace Perilla seeds are frequently exchanged by farmers through various routes between the five regions of South Korea. The results of this study are expected to provide useful information for conservation of these genetic resources and selection of useful resources for the development of varieties for seeds and leafy vegetables of cultivated var. frutescens of Perilla crop in South Korea.
REVIEW | doi:10.20944/preprints202308.0706.v2
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Interferon; Innate; Adaptive; Genetic; Molecular
Online: 26 September 2023 (11:35:53 CEST)
Interferons were the original prototype cytokine system discovered in 20th-century research. As the name implies, they were originally thought to be synthesised and secreted between cells. Thanks to technological advances, the processes involved in protein secretion can be explained comparatively more clearly at both the genetic and biochemical levels. The discovery of interferon (IFN) occurred when genetic research was still in its infancy. Franklin and Wilkins discovered the structure and function of deoxyribonucleic acid (DNA) at the same time as Crick and Watson; however, Isaacs and Lindemann, two scientists, described the first IFN in 1957. Mutations can be caused by inherent genetic protein synthesis and during infection as well as within IFN regulation pathways affecting cell proliferation. This remains central to host cell IFN synthesis and effects through IFN protein receptor subunits defined by 6 protein domains. Type II IFN is key to immune cell function secreted by a variety of immune cells, mainly natural killer (NK) as well as T cells. Single–stranded and/or double–stranded RNA/DNA viruses, as well as bacterial infections (e.g., Escherichia coli) and fungal infections (e.g., Aspergillus), also affect IFN regulation. Pathogenic proteins utilise intra/extracellular proteins that sense foreign antigens like Toll–like Receptors (TLRs), affected by mutations within the human cellular IFN transduction pathways. Since the discovery of the third IFN type in 2003, when immune cell phenotypes were further characterised, questions remain about the immunological mechanisms contributing to the regulation of the innate and adaptive host immune system. Alterations in the synthesis of type I/II/III host IFNs can differentially and beneficially alter homeostatic cellular pathways in pathological disease, with type I IFN being synthesised in cancer as well as by homeostatic cells. Therefore, considered here are the overall IFN molecular, cell regulatory mechanisms in the context of immune cell research developments.
CASE REPORT | doi:10.20944/preprints202306.0239.v1
Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Cardiomyopathy; Genetic disorders; Cardiovascular Imagen
Online: 5 June 2023 (05:02:25 CEST)
A 52-y/o asymptomatic male with history of hypertension, was referred to our Heart Failure Clinic due to report of hypertrophic cardiomyopathy, TTE with an increased end-diastolic thick-ness (basal inferoseptal of 23 mm, and basal anteroseptal of 21 mm). CMR demonstrated late gadolinium enhancement at the septum, anterior, inferolateral, and inferior walls with a mid-myocardial distribution, T1 mapping which reported an average T1 of 929 ms. A next-generation sequencing panel was requested. Results demonstrated hemizygosis, in the ga-lactosidase alpha gene, consistent with Fabry Disease. The replacement of the enzyme was start-ed. Extended familial genetic counseling and testing were done.
ARTICLE | doi:10.20944/preprints202304.0114.v1
Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Dyslipidemia; atherogenic indexes; genetic associations
Online: 7 April 2023 (05:24:09 CEST)
Atherogenesis and dyslipidemia increase the risk of cardiovascular disease, which is the leading cause of death in developed countries. While blood lipid levels have been studied as disease predictors, their accuracy in predicting cardiovascular risk is limited due to its high interindividual and interpopulation variability. The lipid ratios: atherogenic index of plasma (AIP=log TG/HDL-C) and the Castelli risk index 2 (CI2=LDL-C/HDL-C) have been proposed as better predictors of cardiovascular risk, but the genetic variability associated to these ratios has not been investigated. This study aimed to identify genetic associations with these indexes. The study population (n=426) included males (40%) and females (60%) aged 18-52 years (mean 39 years), the Infinium GSA array was used for genotyping. Regression models were developed using R and PLINK. AIP was associated with variation on APOC3, KCND3, CYBA, CCDC141/TTN, and ARRB1 (p-value < 2.1E-6) the three former previously associated to blood lipids, while CI2 was associated with variants on DIPK2B, LIPC, and 10q21.3 rs11251177 (p-value 1.1E-7) the latter previously linked to coronary atherosclerosis and hypertension. KCND3 rs6703437 was associated with both indexes. This study is the first to characterize the potential link between genetic variation and atherogenic indexes, AIP and CI2, highlighting the relation between genetic variation and dyslipidemia predictors. These results also contribute to consolidating the genetics of blood lipid and lipid indexes.
REVIEW | doi:10.20944/preprints202206.0284.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Symbiodinaceae; genetic diversity; coral symbiosis
Online: 21 June 2022 (04:49:04 CEST)
Within microeukaryotes, genetic and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellies), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
ARTICLE | doi:10.20944/preprints202305.1960.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: C. dactylon; C. transvaalensis; interspecific hybrids; cluster analysis; genetic similarity; genetic diversity; directional breeding
Online: 29 May 2023 (08:55:06 CEST)
Bermudagrass (Cynodon spp.) is one of the drought-resistant warm-season turfgrasses adapted to the southern and transitional zones in the United States. Multiple hybrid varieties have been developed and released for use as a turfgrass and others are in pipeline. Increasing genetic di-versity of commercial varieties is vital to tackle stress tolerance. A DNA profiling study of 21 experimental selections from the Oklahoma State University (OSU) turfgrass breeding program and 11 cultivars was conducted using 51 simple sequence repeat (SSR) primer pairs that spread across the bermudagrass genome. Pairwise genetic relationship analysis among the genotypes using 352 polymorphic bands showed genetic similarity coefficients ranging from 0.59 to 0.89. Cluster analysis using the un-weighted paired group method with arithmetic average (UPGMA) method grouped the entries into six clusters. Correlation analysis identified different levels of pairwise genetic relationship among the entries that largely reflected parental relationship. Di-rectional breeding and selection for cold hardiness or drought resistance created progeny that had distinct genetic diversity in the tested bermudagrasses. It is evident that an increase in genetic diversity of the existing cultivar pool with the release of one or more of the experimental selec-tions for commercial use will strengthen and improve bermudagrass systems.
REVIEW | doi:10.20944/preprints201912.0021.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: protein 0th-order structure; origin of gene; origin of protein; origin of genetic code; GNC primeval genetic code hypothesis; SNS primitive genetic code hypothesis
Online: 3 December 2019 (11:10:12 CET)
Understanding the mechanism, how entirely new (EntNew) gene/protein or the first ancestral gene/protein of a family was created, should be one of the most important issues in the biological sciences. However, the mechanism is totally unknown still now. On the other hand, it is well known that mature protein is generally rigid and one catalytic center exists on the protein. Creation of such a mature EntNew gene/protein should be, of course, carried out through random process, because it cannot be designed in advance. However, the EntNew gene/protein never be created by random polymerization of the respective monomeric units, because of the extraordinary large sequence diversities of ~10180 and ~10130, respectively. Protein 0th-order structure or a specific amino acid composition, in which immature but water-soluble protein can be produced even through random process, holds the key for solving the difficult problem. As it was fragmentally described in the previous papers how and where EntNew gene/protein was created, I describe in detail in this review three processes generating EntNew gene/protein with some flexibility under three genetic codes, the universal genetic code, SNS primitive code and GNC primeval code, and discuss why the mature gene/protein could be created through the processes.
ARTICLE | doi:10.20944/preprints202310.0169.v1
Subject: Biology And Life Sciences, Other Keywords: genetic code symmetry, mitochondrial genetic code, energy code, DNA quadruplet symmetry, classification of trinucleotides/codons
Online: 4 October 2023 (07:43:22 CEST)
The Supersymmetry Genetic code (SSyGC) table is based on five physicochemical symmetries: 1) double mirror symmetry on the principle of the horizontal and vertical mirror symmetry axis between all bases (purines [A, G) and pyrimidines (U, C)], and 2) of bases in form of codons 3) direct – complement like codon/anticodon symmetry in the sixteen alternating boxes of the genetic code columns, 4) A+T rich and C+G rich alternate codons in the same row between both columns of the genetic code, 5) the same position between divided and undivided codon boxes in relation to horizontal mirror symmetry axes. The SSyGC table has a unique physicochemical purine – pyrimidine symmetry net which is as the core symmetry common for all, more than thirty different nuclear and mitochondrial genetic codes. This net is present in the SSyGC table of all RNA and DNA living species. None of these symmetries is present in the Standard Genetic Code (SGC) table which is constructed on the alphabetic horizontal and vertical U-C-A-G order of bases. Here we show that the free energy value of each codon incorporated as fundamentally mapping the “energy code” in the SSyGC table is compatible with mirror symmetry. On the other hand, in the SGC table the same free energy values of codons are dispersed and a mirror symmetry between them is not recognizable. At the same time the mirror symmetry of the SSyGC table and the DNA quadruplets together with our classification of codons/trinucleotides are perfectly imbedded in the mirror symmetry energy mapping of codons/trinucleotides and point out in favor of maintaining the integrity of the genetic code and DNA genome. We also argue that physicochemical symmetries of the SSyGC table in the manner of the purine – pyrimidine symmetry net, the quadruplet symmetry of DNA molecule and the free energy of codons have remined unchanged during all of evolution. The unchangeable and universal symmetry properties of the genetic code, DNA molecule and energy code are decreasing disorder between codons/trinucleotides and shed a new light on evolution. Diversity in all living species on Earth is broad, but the symmetries of the Supersymmetry Genetic Code as the code of life and the DNA quadruplets related to the” energy code” are unique, unchangeable and have the power of natural laws.
ARTICLE | doi:10.20944/preprints202212.0234.v1
Subject: Biology And Life Sciences, Virology Keywords: reassortant virus; recombinant virus; chimeric virus; genetic engineering; reverse genetic; SARS-CoV-2; COVID-19
Online: 13 December 2022 (08:47:51 CET)
Due to the fact that to date, the question of the origin of SARS-CoV-2 has not been resolved yet, the author analyzed the main advances in the development of genetic engineering of viruses that took place before the onset of the COVID-19 pandemic. The first artificial genetically modified viruses could appear in nature in the mid-1950s. The technique of nucleic acid hybridization was developed by the end-1960s. In the late 1970s, a method called the "reverse genetics" emerged to synthesize RNA and DNA molecules. In the early 1980-s, it became possible to combine the genes of different viruses and insert the genes of one virus into the genome of another virus. Since that time, the production of vector vaccines began. Currently, by modern technologies one can assemble any virus based on the nucleotide sequence available in the virus database or designed by a computer as a virtual model.Scientists around the world are invited to answer the call of Neil Harrison and Jeffrey Sachs of Columbia University, for a thorough and independent investigation into the origin of SARS-CoV-2. Only a full understanding of the origin of the new virus can minimize the likelihood of a similar pandemic in the future.
ARTICLE | doi:10.20944/preprints202310.0274.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Neural networks; Genetic algorithms; Grammatical Evolution
Online: 5 October 2023 (10:59:20 CEST)
Artificial neural networks are widely established models of computational intelligence that have been tested for effectiveness in a variety of real-world applications. These models require fitting a set of parameters through the use of some optimization technique. However, an issue that researchers often face is finding an efficient range of values for the parameters of the artificial neural network. This paper proposes an innovative technique of generating a promising range of values for the parameters of the artificial neural network. Finding the value field is done by a series of rules for partitioning the original set of values or expanding it, which rules are generated using Grammatical Evolution. After finding a promising interval of values, any optimization technique such as a genetic algorithm can be used to train the artificial neural network on that interval of values. The new technique was tested on a wide range of problems from the relevant literature and the results were extremely promising.
ARTICLE | doi:10.20944/preprints202305.1482.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic manipulation; pleiotropic effects; systems biology
Online: 22 May 2023 (09:03:52 CEST)
In T. gondii, as well as in other model organisms, gene knock-out using CRISPR-Cas9 is a suitable tool to identify the role of specific genes. The general consensus implies that only the gene of interest is affected by the knock-out. Is this really the case? In a previous study, we have generated knock-out (KO) clones of TgRH88_077450 (SRS29B; SAG1) which differed in the numbers of integrated dihydrofolate-reductase-thymidylate-synthase (MDHFR-TS) drug-selectable marker. Clones 18 and 33 had a single insertion of MDHFR-TS within SRS29B. Clone 6 was disrupted by the insertion of a short unrelated DNA-sequence, but the marker was integrated elsewhere. In clone 30, the marker was inserted into SRS29B and several other MDHFR-TS copies were found in the genome. KO and wild-type (WT) tachyzoites had similar shape, dimensions and vitality. This prompted us to investigate the impact of the genetic engineering as such on the overall proteome patterns of the four clones as compared to the respective WT. Comparative shotgun proteomics of the five strains was performed. Overall, 3236 proteins were identified. Principal component analysis of the proteomes revealed five distinct clusters corresponding to the five strains by both iTop3 and iLFQ algorithms. Detailed analysis of the differentially expressed proteins revealed that the target of the KO, srs29B, was lacking in all KO clones. Besides this protein, twenty other proteins were differentially expressed between KO clones and WT or between different KO clones. The protein exhibiting the highest variation between the five strains was srs36D encoded by TgRH_016110. The deregulated expression of SRS36D was further validated by quantitative PCR. Moreover, the transcript levels of three other selected SRS genes, namely SRS36B, SRS46, and SRS57 exhibited significant differences between individual strains. These results indicate that knocking out a given gene may affect the expression of other genes. Therefore, care must be taken when specific phenotypes are regarded as a direct consequence of the KO of a given gene.
ARTICLE | doi:10.20944/preprints202201.0414.v1
Subject: Medicine And Pharmacology, Tropical Medicine Keywords: Giardia duodenalis; Assemblages; Epidemiology; Genetic diversity
Online: 27 January 2022 (11:18:33 CET)
Gut protozoan parasites are neglected and not targeted by specific control initiatives and this have led to a knowledge gap concerning their regional diversity and epidemiology. The present study aims to explore Giardia duodenalis genetic diversity and assess the epidemiologic scenario of subclinical infections in different Brazilian biogeographic regions. Cross-sectional surveys (n=1,334 subjects) were conducted in the Amazon, Cerrado, Semiarid and Atlantic Forest. Microscopy of non-diarrheal feces and nucleotide sequencing of a β-giardin gene fragment were performed. Twenty-seven (52.9%) β-giardin sequences were characterized as assemblage A and 24 (47.1%) as assemblage B. In Amazon, assemblage B was the most frequently detected with 2 novel sub-assemblages. Assemblage A predominated in the extra-Amazon region, with 5 novel sub-assemblages. Prevalence rates reached 17.8% in Amazon, 8.8% in Atlantic Forest, 7.4% in Cerrado and 2.3% in the Semiarid. People living in poverty and extreme poverty presented significantly higher positivity rates, reaching 11.9% and 14.5%, respectively. Giardiasis tended to be more frequent in stunted (21.6%) than in eutrophic children (12.9%). In conclusion, subclinical giardiasis in endemic in Brazilian communities in different biogeographic regions, presenting high genetic diversity and a heterogeneous genotypic distribution.
ARTICLE | doi:10.20944/preprints202111.0533.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chloroplast; genetic resources; genomics capirona; phylogenomics
Online: 29 November 2021 (12:32:24 CET)
Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of de major lineages in the Rubiaceae family, and is an important timber tree, with origin in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct librar-ies. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes and 01 pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotide (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than invert regions. Finally, phylogenetic analysis resolved that C. spruceanum is a sister species to Emmenopterys henryi, and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.
ARTICLE | doi:10.20944/preprints202103.0692.v1
Subject: Engineering, Civil Engineering Keywords: Genetic algorithms, structures, algorithms, generative design
Online: 29 March 2021 (12:50:16 CEST)
The prevalence of algorithms and computational tools in the modern-day has intersected with nearly every field. Generative design, specifically those using genetic algorithms, is an increasingly effective, yet cost efficient way to generate architectural designs in modern engineering. Thus, we adopt a genetic algorithm model in pursuit of maximizing the durability of a structure when it is stressed while minimizing the material cost. After the model is formulated, the algorithm is able to approximate with high accuracy the load a small-scale structure is able to bear, as well as iterate upon its designs to maximize a fitness function.
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Genetic affinity; STR; Rajasthan; Heterozygosity; Polymorphic
Online: 21 June 2020 (14:12:03 CEST)
Rajasthan is a state located in the north-western part of India and it has been cited as a major route of human migration since ancient times. The present study was conducted to find out the genetic affinity of Rajasthani population with the population living in its east and the west. In particular, we compared them with the population of Pakistan which shares the common geographical boundary with the Rajasthan while also having a look at their inter and intra population affinities with the population belonging to other Indian states. We investigated the genetic structure and population parameters of Rajasthani populations obtained for twenty polymorphic autosomal STR loci from 669 unrelated individuals belonging to its three population groups including Mina, Gujjar and the admixed population of Rajasthan. The studied populations showed a wide range of genetic diversity and besides the genetic structure of the studied populations, it was found that the average heterozygosity value was highest among the populations of Rajasthan, possibly, because of gene flow from different directions. Various statistical analyses suggested that the Rajasthani populations had a higher affinity with the North Indian populations rather than with the Pakistani population.
Subject: Biology And Life Sciences, Biophysics Keywords: evolution; genetic code; RNA; protein; physicochemistry
Online: 28 November 2019 (09:38:55 CET)
The current framework of evolutionary theory postulates that evolution relies on random mutations generating a diversity of phenotypes on which natural selection acts. This framework was established using a top-down approach as it originated from Darwinism, which is based on observations made on complex multicellular organisms, and then modified to fit a DNA-centric view. In this article, I argue that, based on a bottom-up approach starting from the physicochemical properties of nucleic and amino acid polymers, we should reject the facts that: i) natural selection plays a dominant role in evolution, and ii) the probability of mutations is independent of the generated phenotype. I will show that the adaptation of a phenotype to an environment does not correspond to organism fitness but rather corresponds to maintaining the genome stability and integrity. In a stable environment, the phenotype maintains the stability of its originating genome, and both (genome and phenotype) are reproduced identically. In an unstable environment (i.e., corresponding to variations in physicochemical parameters above a physiological range), the phenotype no longer maintains the stability of its originating genome but instead influences its variations. Indeed, environment- and cellular-dependent physicochemical parameters define the probability of mutations in terms of frequency, nature and location in a genome. Evolution is non-deterministic because it relies on probabilistic physicochemical rules, and evolution is driven by a bidirectional interplay between genome and phenotype, the phenotype ensuring the stability of the genotype in a cellular and environment physicochemical parameter-depending manner.
ARTICLE | doi:10.20944/preprints201911.0349.v1
Subject: Biology And Life Sciences, Forestry Keywords: Bemisia tabaci; genetic diversity; distribution; haplotype
Online: 28 November 2019 (03:24:39 CET)
Bemisia tabaci (Gennadius) is a polyphagous, highly destructive pest capable of vectoring viruses in most agricultural crops. Currently, information on the distribution and genetic diversity of B. tabaci in South Sudan is not available. The objectives of this study were to investigate the genetic variability of B. tabaci infesting sweet potato and cassava in South Sudan. Field surveys were conducted between August 2017 and July and August 2018 in 10 locations in Juba County, Central Equatoria State, South Sudan. Sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) were used to determine the phylogenetic relationships between sampled B. tabaci. Six distinct genetic groups of B. tabaci were identified including three non-cassava haplotypes (Mediterranean (MED), Indian Ocean (IO) and Uganda) and three cassava haplotypes (Sub-Saharan Africa 1 sub-group 1 (SSA1-SG1), SSA1-SG3 and SSA2). MED predominated on sweet potato and SSA2 on cassava in all the sampled locations. The Uganda haplotype was also widespread, occurring in five of the sampled locations. This study provides important information on the diversity of B. tabaci species in South Sudan. A comprehensive assessment of the genetic diversity, geographical distribution, population dynamics and host range of B. tabaci species in South Sudan is vital for its effective management.
ARTICLE | doi:10.20944/preprints201806.0201.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic architecture; Africa; GWAS; health disparities
Online: 13 June 2018 (11:17:04 CEST)
Human genetic studies have long been vastly Eurocentric, raising a key question about the generalizability of these study findings to other populations. Because humans originated in Africa, these populations retain more genetic diversity, and yet individuals of African descent have been tremendously underrepresented in genetic studies. The diversity in Africa affords ample opportunities to improve fine-mapping resolution for associated loci, discover novel genetic associations with phenotypes, build more generalizable genetic risk prediction models, and better understand the genetic architecture of complex traits and diseases subject to varying environmental pressures. Thus, it is both ethically and scientifically imperative that geneticists globally surmount challenges that have limited progress in African genetic studies to date while meaningfully including African investigators, as greater inclusivity and enhanced research capacity affords enormous opportunities to accelerate genomic discoveries that translate more effectively to all populations. We review the advantages and challenges of studying the genetic architecture of complex traits and diseases in Africa. For example, with greater genetic diversity comes greater ancestral heterogeneity; this higher level of understudied diversity can yield novel genetic findings, but some methods that assume homogeneous population structure and work well in European populations may work less well in the presence of greater diversity and heterogeneity in African populations. Consequently, we advocate for methodological development that will accelerate studies important for all populations, especially those currently underrepresented in genetics.
ARTICLE | doi:10.20944/preprints202308.1951.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: Aminoacyl-tRNA synthetases; Standard Genetic Code; Symmetry groups; Origin and evolution of the genetic code; Group Theory
Online: 29 August 2023 (08:34:06 CEST)
Aminoacyl-tRNA synthetases (aaRSs) originated from an ancestral bidirectional gene (mirror symmetry) and through the evolution of the genetic code the twenty aaRSs exhibit a symmetrical distribution in a 6-dimensional hypercube of the Standard Genetic Code. In this work, we assume a primeval RNY code, and the Extended Genetic RNA code type II which includes codons of the type YNY, YNR and RNR. Each of the 4 subsets of codons can be represented in a 4-dimensional hypercube. Altogether these 4 subcodes constitute the 6-dimensional representation of the SGC. We identify the aaRSs' symmetry groups in each of these hypercubes. We show that each of the four hypercubes contains the following sets of symmetries for the two known Classes of synthetases: RNY: dihedral group D2; YNY: binary group Z2; YNR: amplified octahedral group Oh; and RNR: binary group Z2. We demonstrate that for each hypercube, the group of symmetries of Class 1 is the same as the group of symmetries of Class 2. The biological implications of these findings are discussed.
ARTICLE | doi:10.20944/preprints202310.0827.v1
Subject: Engineering, Bioengineering Keywords: Genetic syndrome; Acoustical analysis; Artificial Intelligence; Classification
Online: 12 October 2023 (12:03:32 CEST)
Perceptual and statistical evidence has underlined voice characteristics of individuals affected by genetic syndromes different from that of normophonic subjects. In this paper we propose a procedure for the systematic collection of such pathological voices and the development of AI-based automatic tools to support differential diagnosis. Guidelines are provided concerning most suitable recording devices, vocal tasks and acoustical parameters, in order to simplify, speed up and make the whole procedure homogenous and replicable. The proposed procedure was applied to a set of 56 subjects, affected by Costello syndrome (CS), Down syndrome (DS), Noonan syndrome (NS) and Smith-Magenis syndrome (SMS). The whole database has been divided into three groups, respectively called: paediatric subjects (PS, individuals < 12 years of age), female adults (FA) and male adults (MA) subjects. In line with literature results, the Kruskal-Wallis test and post-hoc analysis with Dunn-Bonferroni test highlighted several significant differences in acoustical features not only between healthy subjects and patients, but also across syndromes within PS, FA and MA groups. Machine learning provided for the PS group a k-nearest neighbour classifier with 75% accuracy, for the FA group a support vector machine (SVM) model with 84% accuracy and for the MA group a SVM model with 97% accuracy. These preliminary results suggest that the proposed procedure, based on acoustical analysis and AI, might be helpful for an effective non-invasive automatic characterization of genetic syndromes.
INTERESTING IMAGES | doi:10.20944/preprints202309.1918.v1
Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: multidrug-resistant tuberculosis; genetic mutations; clinical cases.
Online: 28 September 2023 (08:02:58 CEST)
The emergence of M. tuberculosis strains resistant to Isoniazid (INH) and Rifampicin (RIF), the two most potent drugs of first-line anti-TB therapy is termed multidrug drug-resistant TB (MDR-TB). Multidrug-resistant tuberculosis has been a serious medical and epidemic problem all over the world. We present here a series of clinical cases consist of two patients diagnosed with isoniazid resistant tuberculosis. Histopathological examination supports the diagnosis of tuberculous granulomas. And the pathology molecular examination revealed the presence of Isoniazid-resistant Mycobacterium tuberculosis1,2 via the following mutation c.947G>A; p.Gly316Asp. Isoniazid-resistance is associated with mutations in the furA-katG and fabG1-inhA operons, as well as mutations in the ahpC gene. 64% of the isoniazid-resistance phenotypes were associated with the katG315 mutation worldwide. The second most common mutation is inhA-15, and it has been reported in 19% of the Isoniazid-resistant isolates. The significant association between the two mutations, inhA c-15 and katG 315 respectively, and the high-level resistance is of interest in the interpretation of current and future molecular diagnostic testing, as an early prediction of the level of Isoniazid-resistance is essential to decide the benefit of high-dose Isoniazid use.
CASE REPORT | doi:10.20944/preprints202309.1060.v1
Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: interrupted aortic arch; 22q11.2DS; ultrasound; genetic tests
Online: 18 September 2023 (05:41:23 CEST)
The 22q11.2 deletion syndrome (22q11.2DS) is the most common chromosomal microdeletion disorder caused by hemizygous microdeletion of the long arm of chromosome 22. It is now known to have a heterogenous presentation that includes multiple additional congenital anomalies and later-onset conditions, such as gastrointestinal and renal abnormalities, autoimmune disease, variable cognitive delays, behavioral phenotypes and psychiatric illness. The purpose of our paper is to present the case of a fetus diagnosed with a rare and complex cardiac malformation (interrupted aortic arch (IAA) type B, large malalignment-type ventricular septal defect (VSD), pulmonary valve dysplasia, aberrant right subclavian artery (ARSA). The result of the genetic testing revealed 22q11.2 deletion and after genetic counselling the patient decided to continue the pregnancy. She was regularly followed until delivery which took place in Germany so that neonatal cardiac surgery could be performed in an experienced center for cardiac malformations. We emphasize on the ultrasound aspects regarding the cardiac anomaly and specific features of 22q11.2DS in a continuous manner from diagnosis until delivery.
ARTICLE | doi:10.20944/preprints202307.0697.v1
Subject: Biology And Life Sciences, Horticulture Keywords: Fragaria × ananassa; genetic parameters; selection index; clusterin
Online: 11 July 2023 (08:40:08 CEST)
Strawberry is produced in tropical regions using imported cultivars adapted to temperate and subtropical climates. These cultivars, under tropical conditions, produce below their genetic potential. Through multivariate analyses, the objective was to evaluate and select short-day strawberry genotypes based on intraspecific crosses, product characteristics, and fruit quality. The genotypes were obtained from the cross between 'Camino Real' (female parent) and the first-generation genotypes RVCA16, RVCS44, RVFS06, RVFS07, and RVDA11 (male parent), obtained in previous selections. The experimental design consisted of augmented blocks with standard controls, consisting of first-generation genotypes and commercial cultivars. The fruits were harvested and evaluated for productivity and post-harvest characteristics: Total Fruit Mass (MTF); Total Number of Fruits (TFN); Average Fruit Mass (AFM); Commercial Fruit Mass (CFM); Fruit Commercial Number (CFN); Average Commercial Mass of Fruits (ACFM); Total Soluble Solids (TSS); Firmness (F); Brightness (L); Hue Angle (°Hue); Chroma (C). The selection index of Mulamba and Mock (1978) was used with an intensity of 3% to obtain superior genotypes and submitted to multivariate analysis for comparative purposes. Of the 1500 genotypes evaluated, it was possible to select 44 genotypes with characteristics superior to the 13 controls. The RVDA11CR59 genotype showed better values for the attributes of interest, but the RVCS44CR population, from the cross between 'Camino Real' × RVCS44 ('Camarosa' × 'Sweet Charlie'), obtained the highest number (16) of individuals among those selected. Significant traits had high heritability but were not necessarily reflected in high selection gain. Coefficients of genetic variation were high, indicating sufficient genetic variability to select genotypes for these traits. When multivariate analyses were used, it was possible to group the selected genotypes into the same cluster according to the similarity and balance in the responses to the evaluated variables, demonstrating that these analyses help other parameters choose superior genotypes. The multivariate analysis allowed the selection of more balanced genotypes for production and post-harvest traits for tropical climates.
ARTICLE | doi:10.20944/preprints202306.0020.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: molecular evolution; genetic drift; human papillomavirus (HPV)
Online: 1 June 2023 (03:52:59 CEST)
Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history. Whereas the role of selection on, and drift of, non-coding DNA elements on HPV diversification is poorly understood. More than a thousand complete genomes representing Alphapapillomavirus types, lineages and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions and Phylogenetic Independent Contrasts. For anciently diverged Alphapapillomavirus types, composition of the 4 nucleotides (A,C,G,T), codon usage, trimer usage and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured Alphapapillomavirus genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages
ARTICLE | doi:10.20944/preprints202305.1634.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: genetic resources; molecular markers; local cultivar; certification
Online: 23 May 2023 (09:55:00 CEST)
Andalusia is a Spanish region that is home to numerous minority varieties due to its diversity and territorial extension, offering the local viticulture the possibility of diversifying its wine production. The molecular identification of 98 specimens from six areas with a winemaking tradition in Andalusia was carried out between the years 2020 and 2022. Thirteen microsatellite markers were used in this study, including the nine recommended by the OIV. 31 different genotypes were obtained, 20 of which corresponded to profiles of already described varieties (11 of them are of minority cultivation in Andalusia: 'Rojal Tinto', 'Beba', 'Zurieles', 'Rome', 'Hebén', 'Mollar Cano', 'Listán Prieto', 'Listán del Condado', 'Jarrosuelto', 'Negra Dorada' and 'Mantúo de Pilas'), while the other 11 profiles did not match with previously identified varieties. This profiles were integrated into the database of the IFAPA “Rancho de la Merced” Germplasm Bank. The eco-geographical groups of the new identified genotypes were determined through analysis of genetic diversity. The presence of the Grapevine Fanleaf Virus, the Grapevine Fleck Virus and the Grapevine Leafroll associated Viruses was also analyzed using an ELISA test due to the necessity of having certifiable clones of the new varieties for their potential interest in being authorized for its cultivation in Spain.
REVIEW | doi:10.20944/preprints202305.1454.v1
Subject: Medicine And Pharmacology, Other Keywords: Catastrophes; Genetic identification; Kinship analysis; DNA degradation
Online: 22 May 2023 (03:01:25 CEST)
Different types of disasters, whether natural or human character, lead to the significant loss of human lives. In the latter case, the quick action of identification of corpses and human remains is mandatory. There are a variety of protocols to identify victims, however, genetics is one of the tools that allow an exact identification of the victim. However, several factors may interfere with this identification, from the biological samples’ degradation not allowing the analysis of nuclear information, to failure to dispose of biological samples from family members. Access to certain family members could be a determinant of the proper choice of genetic markers that allow the identification of the victim, or his/her inclusion in a given genetic maternal or paternal lineage. With the new advances in the genetic field, it is expected to allow soon the identification of victims from disasters only with his/her biological postmortem samples, being possible to draw a robot portrait and its most likely physical characteristics. In all cases, genetics is the only modern tool with universal character and can be used in essentially all biological samples, giving and identification of more or less accurate statistical character, depending on whether nuclear or lineage markers are used.
COMMUNICATION | doi:10.20944/preprints202305.0087.v1
Subject: Biology And Life Sciences, Virology Keywords: Japanese encephalitis virus; Population dynamic; Genetic diversity
Online: 2 May 2023 (11:02:54 CEST)
Japanese encephalitis virus (JEV) causes acute viral encephalitis in humans and reproductive disorders in pigs. JEV emerged during the 1870s in Japan and since that time, JEV has been transmitted exclusively throughout Asia, according to known reporting and sequencing records. A recent JEV outbreak occurred in Australia which affected commercial piggeries across different temperate southern Australian states and caused confirmed infections in humans. A total of 47 human cases and seven deaths were reported. The recent evolving situation of JEV needs to be reported due to its continuous circulation in endemic regions and spread to non-endemics areas. Here, we reconstructed the phylogeny and population dynamics of JEV using recent JEV isolates for the future perception of disease spread. Phylogenetic analysis shows the most recent common ancestor occurred about 3120 years ago (YA) (95% Highest posterior density [HPD], 2680 to 3715). Our results of the Bayesian skyline plot (BSP) demonstrates that JEV demography lacks fluctuations for the last two decades, but it shows that JEV genetic diversity has increased during the last ten years. This indicates the potential JEV replication in the reservoir host, which is helping it to maintain its genetic diversity, and to continue its dispersal into non-endemic areas. The continuous spread in Asia and recent detection from Australia further support these findings. Therefore, an enhanced surveillance system is needed along with precautionary measures such as regular vaccination and mosquito control to avoid future JEV outbreaks.
ARTICLE | doi:10.20944/preprints202302.0505.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: phylogeny; salivary effectors; effector 84; genetic diversity
Online: 28 February 2023 (04:44:34 CET)
Herbivores have evolved several strategies to cope with plant defences. Some herbivores are able to resist toxic compounds, while others can manipulate host immunity. Previously it was found that spider mites collected from non-solanaceous wild host plants consist mostly of individuals that induce tomato defences, but also at low frequencies of individuals that can suppress these defences. Also, it has been shown that mites collected from non-solanaceous plants can adapt to tomato by evolving traits that allow them to suppress defences. Hence, we wanted to know if this trait is also common among mites naturally occurring on tomatoes. Here, we compared three T. urticae populations sampled from tomato at three field sites, and also an outbred population created from them through controlled crosses. We then assessed their fecundity on wild-type (WT) tomato plants and def-1 mutants impaired in inducible JA-defences. We also assessed the magnitude of JA defences they induce in WT plants to discriminate between resistant types (high induction and high performance) and those that can suppress defences (low induction, high performance). We then aligned these data with data on variation in mitochondrial DNA cytochrome oxidase I (COI) and effector 84 (a suppressor of JA-defences in planta), in order to compare genetic diversity patterns among mite lines that induce or suppress defences. We found that suppression is the dominant phenotype in mite strains collected from field-grown tomatoes and that inducers and suppressors predominantly cluster in distinct effector 84 clades. We speculate that effector allelic diversity may be subject to natural selection when these mites colonize a novel host plant, promoting traits to cope with plant resistance, such as defence suppression, which facilitates adaptation.
REVIEW | doi:10.20944/preprints202302.0305.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: genetic databases; mutation disorders; ethnic specific databases
Online: 17 February 2023 (07:59:08 CET)
The mutation databases have vital importance in detecting genetic mutation and their corresponding phenotypes. The emergence of next generation sequencing genetic technologies has accelerated this process, and the growth of genetic disease identification has created a need for quality control and documentation of mutation-related information. Ethnic-specific mutation databases offer valuable information for researchers, and the article evaluates the homogeneity and effectiveness of these databases. The aim to raise awareness of NEMDBs to healthcare professionals, the general public, and researchers studying genetic disorders. The article also recommendations to improve the effectiveness of these databases.
REVIEW | doi:10.20944/preprints202301.0197.v1
Subject: Social Sciences, Behavior Sciences Keywords: Biomarkers; Genetic; Suicidal behavior; Suicide; Mexican; Genomic.
Online: 11 January 2023 (10:34:57 CET)
Suicide is defined as the action of harming oneself with the intention of dying. It is estimated that worldwide one suicide occurs every 40 seconds, making it a major health problem. Studies in families have suggested that suicide has a genetic component, around the world studies have been carried out in search of genetic variants associated with suicidal behavior, these variants could be useful as potential biomarkers to identify people at risk of suicide. In this area in Mexico, some studies of variants in genes related to neurotransmission and other important pathways have been carried out and a possible association of variants located in genes has been suggested: SLC6A4, SAT-1, TPH-2, ANKK1, GSHR, SCARA50, RGS10, STK33, COMT, and FKBP5. This systematic review shows the genetic studies on the Mexican population. This article contributes by compiling the existing information on genetic variants and genes associated with suicidal behavior, said variants in the future could be used as potential biomarkers to identify people at risk of suicide.
ARTICLE | doi:10.20944/preprints202103.0400.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Lipid metabolism; NAFLD; genetic variants; PSRC1; HCC
Online: 15 March 2021 (16:30:15 CET)
Background and Aims: Dyslipidemia and cardiovascular diseases (CAD) are comorbidities of nonalcoholic fatty liver disease (NAFLD), which ranges from steatosis to hepatocellular carcinoma (HCC). The rs599839 A>G variant, in the CELSR2-PSRC1-SORT1 cluster, has been associated CAD, but its impact on metabolic traits and liver damage in NAFLD has not been investigated yet. Methods: We evaluated the effect of the rs599839 variant in 1426 NAFLD patients (Overall cohort) of whom 131 have HCC (NAFLD-HCC), in 500,000 individuals from the UK Biobank Cohort (UKBBC) and in 366 HCC samples from The Cancer Genome Atlas (TCGA). Hepatic PSRC1, SORT1 and CELSR2 expressions were evaluated by RNAseq (n=125). Results: The rs599839 variant was associated with reduced circulating LDL, carotid intima-media thickness, carotid plaques and hypertension (p<0.05) in NAFLD patients and with protection against dyslipidemia in UKBBC. The G allele was associated with higher risk of HCC and advanced tumor stage (p<0.05) in the Overall cohort. Hepatic PSRC1, SORT1 and CELSR2 expressions were increased in NAFLD patients carrying the rs599839 variant (p<0.0001). SORT1 mRNA levels negatively correlated with circulating lipids and with those of genes involved in lipoprotein turnover (p<0.0001). Conversely, PSRC1 expression was positively related to that of genes implicated in cell proliferation (p<0.0001). In TCGA, PSRC1 over-expression promoted more aggressive HCC development (p<0.05). Conclusions: In sum, the rs599839 A>G variant improves dyslipidemia thus protecting against CAD in NAFLD patients, but as one it might promote HCC development by modulating SORT1 and PSRC1 expressions which impact on lipid metabolism and cell proliferation, respectively
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: evolution; darwinism; genetic code; RNA; homoestasis; physics
Online: 6 January 2021 (15:06:41 CET)
The physics–biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the physical coupling between the synthesis of nucleic acids and the synthesis of amino acid polymers. Owing to this physical coupling, amino acid polymers (or proto-phenotypes) maintained the physicochemical parameter equilibria (proto-homeostasis) in the immediate environment of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical stresses, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome generating an internal environment whose physicochemical parameters guarantee homeostasis and genome integrity has a higher probability to be reproduced without variation and therefore to reproduce the same phenotype in offspring. Otherwise, the genome is modified by the imbalances of the internal physicochemical parameters it generates, until new emerging biological activities maintain homeostasis. In sum, evolution depends on feedforward and feedback loops between genome and phenotype, since the internal physicochemical conditions that a genome generates in response to environmental fluctuations in turn either guarantee the stability or direct the variation of the genome.
ARTICLE | doi:10.20944/preprints202012.0003.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: DNA repair; NHEJ; synthetic lethality; genetic interaction
Online: 15 December 2020 (10:41:58 CET)
Non-homologous end-joining (NHEJ) is a major DNA repair pathway in mammalian cells that recognizes, processes and fixes DNA damages throughout the cell cycle, and is specifically important for homeostasis of post-mitotic neurons and developing lymphocytes. Neuronal apoptosis increases in the mice lacking NHEJ factors Ku70 and Ku80. Inactivation of other NHEJ genes, either Xrcc4 or Lig4, leads to massive neuronal apoptosis in the central nervous system (CNS) that correlates with embryonic lethality in mice. Inactivation of either Paxx, Mri or Dna-pkcs NHEJ gene results in normal CNS development due to compensatory effects of Xlf. Combined inactivation of Xlf/Paxx, Xlf/Mri and Xlf/Dna-pkcs, however, results in late embryonic lethality and high levels of apoptosis in CNS. To determine the impact of NHEJ factors on early stages of neurodevelopment, we isolated neural stem and progenitor cells from mouse embryos and investigated proliferation, self-renewal and differentiation capacity of these cells lacking either Xlf, Paxx, Dna-pkcs, Xlf/Paxx or Xlf/Dna-pkcs. We found that XLF, DNA-PKcs and PAXX maintain the neural stem and progenitor cell populations and neurodevelopment in mammals, which is particularly evident in the double knockout models.
ARTICLE | doi:10.20944/preprints202009.0653.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ionizing radiation; radiation resistance; genetic mechanisms; microorganisms
Online: 26 September 2020 (17:24:56 CEST)
Nuclear pollution is an urgent environmental issue as a consequence of rapid industrialization and nuclear accidents in the past. Remediation of nuclear polluted sites using microbial vital activity (bioremediation) is a promising approach to recover contaminated areas in an environmentally friendly and cost-saving way. At the same time, the number of known bacterial and archaeal species able to withstand extremely high doses of ionizing radiation is steadily growing every year, together with growing knowledge about mechanisms of radioresistance. This opens up new opportunities for developing new biotechnological solutions. However, these data are often not systemized and it can be difficult to access. Here, we present the Determinants of Radioresistance Database, or DetR DB (http://extremebiolab.com/detr-db/), gathering a comprehensive catalog of radioresistant microbes and their molecular and genetic determinants of enhanced ionizing radiation tolerance. The database provides search tools including taxonomy, common gene name, and BLAST. DetR DB will be a useful tool for research community by facilitating the extraction of the necessary information to help further analysis of radiation-resistant mechanisms.
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; severe symptoms; inactivation; genetic diversity
Online: 16 April 2020 (09:15:49 CEST)
The rapid spread of the coronavirus disease 2019 (COVID-19) is a serious threat to public health systems globally and is subsequently, a cause of anxiety and panic within human society. Understanding the mechanisms and reducing the chances of having severe symptoms from COVID-19 will play an essential role in treating the disease, and become an urgent task to calm the panic. However, the COVID-19 test developed to identify virus carriers is unable to predict symptom development in individuals upon infection. Experiences from other plagues in human history and COVID-19 statistics suggest that genetic factors may determine the compliance with the virus, i.e., severe, mild, and asymptomatic. Here, a hypothesis is put forward based on the epidemiological characteristics and traits of COVID-19, and our gene expression analysis. It proposes that COVID-19 inactivation in the blood by blocking virus entry into other internal organs for reproduction through the blood circulation after lung cell invasion prevents severe symptoms. Additionally, we investigated a genetic connection between candidate genes and severe COVID-19 symptoms through the utilization of strategies combining hypothesis and data-driven approaches. A list of genes and important SNPs that require further investigation to aid the screening of individuals who may suffer severe illness if exposed to the virus is present. Those individuals should be intensively safeguarded and prioritised for treatment. Concurrently to further research on the COVID-19 pathogenesis, our results also offer a new research strategy for pandemic prevention and health maintenance.
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic diversity; Dioscorea praehensilis; SSR markers; Ghana
Online: 8 March 2020 (14:55:19 CET)
Dioscorea praehensilis Berth is one of the wild yam species resistance to many yam disease (yam anthracnose disease and yam mosaic virus) grow in Ghana especially in the cocoa grown regions of the country. It is a crucial crop that has been known to contribute to poverty reduction and food gap. Genetic diversity in this yam species has been discovered to be eroding and neglected. In this study we evaluated the genetic diversity among 43 D. praehensilis collected from Ghana using simple sequence repeat (SSR). Using 11 SSR marker, a total of 99 number of alleles were generated with an average of 8.48 alleles per locus. The mean gene diversity was 0.81, mean polymorphism information content was 0.82 while mean Shannon information index was 1.94. Principal coordinate analysis (PCoA) revealed a contribution of 40.16% of the first three coordinate axes and grouped the 43 morphotypes into 2 groups while hierarchical cluster through UPGMA revealed the presence of 3 main clusters. Molecular variance (AMOVA) alongside the Fst revealed low genetic diversity and differentiation among accessions and population. Result of this study assess the genetic diversity and will facilitate the use D. praehensilis as sources of resistance gene into yam breeding program.
COMMUNICATION | doi:10.20944/preprints201912.0176.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: conservation; genetic diversity; decision-making; ex situ
Online: 12 December 2019 (12:43:13 CET)
The rapid and extensive loss of biodiversity globally has resulted in an increased urgency to capture and conserve the diversity which is present, including genetic diversity within species. However, for many species there is currently no detailed genetic data available to inform the collection and use of material held in ex situ collections and this can hamper the consideration of genetic issues and reduce the likelihood collection represent the diversity present. Even in the absence of direct genetic data, however, it is possible to consider genetic issues using the existing theoretical and empirical evidence-based and biological, ecological and demographic data for a given species. Here a framework to facilitate the consideration of genetic diversity and genetic issues, even where genetic data is lacking, is presented.
ARTICLE | doi:10.20944/preprints201811.0046.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: DNA replication, DNA repair, genetic recombination, mutagenesis
Online: 2 November 2018 (10:19:18 CET)
Covalent DNA protein crosslinks (DPCs) are common lesions that block replication. We examine here the consequence of DPCs on mutagenesis involving replicational template-switch reactions in Escherichia coli. 5-azacytidine (5azaC) is a potent mutagen for template-switching, dependent on DNA cytosine methylase (Dcm), implicating the trapped Dcm-DNA covalent complex as the initiator for mutagenesis. The leading strand of replication is more mutable than the lagging strand, explained by blocks to the replicative helicase and/or fork regression. We find that template-switch mutagenesis induced by 5-azaC does not require DSB repair via RecABCD. The ability to induce the SOS response is anti-mutagenic by an unknown mechanism. Mutants in recB, but not recA, exhibit high constitutive rates of template-switching and we suggest that RecBCD-mediated DNA degradation prevents template-switching associated with fork regression. A mutation in the DnaB fork helicase also promotes high levels of template-switching. We also find that other DPC-inducers, formaldehyde (a non-specific crosslinker) and ciprofloxacin (a topoisomerase II poison) are also strong mutagens for template-switching. Induction of mutations and genetic rearrangements that occur by template-switching may constitute a previously unrecognized component of the genotoxicity and genetic instability promoted by DPCs.
REVIEW | doi:10.20944/preprints201807.0089.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: multidisciplinary; Gaucher; genotype/phenotype correlation; genetic counselling
Online: 5 July 2018 (08:51:35 CEST)
Managing the multisystemic symptoms of type I Gaucher Disease (GD) requires a multidisciplinary team approach that includes disease-specific treatments, as well as supportive care. This involves a range of medical specialists, general practitioners, supportive care providers, and patients. Phenotype classification and the setting of treatment goals are important for optimizing the management of type I GD, and providing personalized care. The ability to classify disease severity using validated measurement tools allows the standardization of patient monitoring, and the measurement of disease progression and treatment response. Defining treatment goals is useful to provide a benchmark for assessing treatment response, and managing the expectations of patients and their families. Although treatment goals will vary depending on disease severity, they include the stabilization, improvement or reversal (if possible) of clinical manifestations. Enzyme replacement therapy (ERT) is the standard care for patients with type I GD, but a novel substrate reduction therapy (SRT), Eliglustat has demonstrated safety and efficacy in selected patients. To ensure that treatment goals are being achieved, regular, comprehensive follow up is necessary.
ARTICLE | doi:10.20944/preprints201806.0329.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Alzheimer’s disease; Parkinson’s disease; Genetic testing; bioethics
Online: 21 June 2018 (04:38:35 CEST)
Over the last decade, advances in our understanding about the genetic architecture of complex traits and common diseases, have increased our ability to perform susceptibility genetic testing for diseases in asymptomatic individuals. These technological developments raise complex ethical, legal and social considerations. Here we discuss a series of ethical issues associated with susceptibility genetic testing for Alzheimer's and Parkinson's disease. These include, amongst others, informed consent, disclosure of results and unexpected findings, mandatory screening, privacy and confidentiality, and stigma and genetic discrimination. As knowledge of the genetic basis of these diseases continues growing, and as genetic testing becomes more widespread, we anticipate that it will become increasingly important for scientists and clinicians to engage in the conversation about the ethical, social and policy implications of these technologies.
REVIEW | doi:10.20944/preprints201806.0191.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: rare disease; functional genomics; genetic variant validation
Online: 12 June 2018 (12:36:08 CEST)
Many insights into human disease have been built on experimental results in Drosophila, and research in fruit flies is often justified on the basis of its predictive value for questions related to human health. Additionally, there is now a growing recognition of the value of Drosophila for the study of rare human genetic diseases, either as a means of validating the causative nature of a candidate genetic variant found in patients, or as a means of obtaining functional information about a novel disease-linked gene when there is little known about it. For these reasons, funders in the US, Europe, and Canada have launched targeted programs to link human geneticists working on discovering new rare disease loci with researchers who work on the counterpart genes in Drosophila and other model organisms. Several of these initiatives are described here, as are a number of output publications that validate this new approach.
ARTICLE | doi:10.20944/preprints201803.0215.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Phaseolus vulgaris L.; REML/BLUP; genetic diversity
Online: 26 March 2018 (10:35:00 CEST)
In the international scenario of agriculture, Brazil stands out as the main producer and consumer of common bean (Phaseolus vulgaris L.) The increase in the productive potential of the crop is mainly due to breeding programs. The objective of this study was to estimate genetic parameters, predict genotypic values with REML/BLUP (Restricted Maximum Likelihood/Best Linear Unbiased Prediction) and, based on these values, study the variability in common bean cultivars with carioca and black grain. Twenty three agromorphological descriptors were evaluated, among them grain yield. Deviance analysis detected significant differences between the cultivars in both groups. Selective accuracy (Ac) was considered high for most of the traits. Broad-sense heritability (hg2 ) ranged from 0.05 to 0.72, but it was low for the trait yield (YLD). In the carioca grain group, the hg2 values for the traits related to plant morphology were higher than in the black group. Nevertheless, the hg2 values in the black group were higher in relation to the pod and seed traits. The correlations for YLD were moderate but different in the two commercial groups studied. In the black group, variables related to the seed morphology were correlated with grain yield, and in the carioca group, traits related to seed quantity. Based on the groupings, variability among the cultivars was observed. Three distinct clusters were formed for the carioca group and four for the black group. Based on the predicted genetic values, genetic variability and the most adapted and stable cultivars were detected among the cultivars in the studied environments.
ARTICLE | doi:10.20944/preprints201707.0005.v1
Subject: Engineering, Control And Systems Engineering Keywords: Acrobot; Artificial Intelligence; SARSA; PWM; Genetic Algorithm
Online: 4 July 2017 (16:12:37 CEST)
An acrobot is a planar robot with a passive actuator in its first joint. The control problem of the acrobot tries to make it rise from the rest position to the inverted pendulum position. This control problem can be divided in the swing-up problem, when the robot has to rise itself through swinging up as a human acrobat does, and the balancing problem, when the robot has to maintain itself on the inverted pendulum position. We have developed three controllers for the swing-up problem applied to two types of motors: small and big. For small motors, we used the SARSA controller and the PD with a trajectory generator. For big motors, we propose a new controller to control the acrobot, a PWM controller. All controllers except SARSA are tuned using a Genetic Algorithm.
ARTICLE | doi:10.20944/preprints202311.1015.v1
Subject: Computer Science And Mathematics, Computational Mathematics Keywords: SDN; DDoS; genetic algorithm; Grammatical Evolution; packet classification
Online: 16 November 2023 (03:03:51 CET)
Software-Defined Networking (SDN) is a network implementation paradigm of great importance, as it has a profound impact on the pace of technological progress. While SDN doesn’t directly address the technical complexities of routing, congestion control, traffic engineering, security, mobility, reliability, or real-time communication, it paves the way for innovative solutions to emerge for these and similar challenges. Security is of utmost importance in SDN with Distributed Denial of Service (DDoS) being an attack which creates large scale problems. DDoS creates malicious traffic that resembles normal traffic in order to create service problems. As such, mechanisms that distinguish between benign and malicious traffic is essential, since this is the first step to mitigate the problem of DDoS. In this paper, we take a dataset onboard which exhibits benign and malicious traffic in SDN. There are 23 features that are used for classification purposes. Here we utilise classification procedure based on three methods based Grammatical Evolution applied on the aforementioned data. We provide results that show the efficiency of our approach and show that all three methods exhibits satisfactory results.
REVIEW | doi:10.20944/preprints202310.0243.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Lupinus mutabilis; genetic diversity; breeding; anthracnose resistance; alkaloids
Online: 5 October 2023 (02:38:00 CEST)
Lupinus mutabilis, also known as tarwi or chocho, is an important agricultural species cultivated in South America since ancient times. Tarwi is native from the Andean regions of Peru, Bolivia, and Ecuador and has a very high protein content. Despite its high nutritional value and promotion efforts by regional researchers and breeders, tarwi is not a widely cultivated crop in its center of origin. In this review, we present the work carried out by public breeding programs of L. mutabilis at national agricultural research institutes, universities, and other institutions in Ecuador, Peru, and Bolivia. The main breeding method used in the Andes to improve local landraces has been mass selection to adapt lines to specific environments. At least 25 cultivars or ecotypes have been selected and released over the last 40 years using this breeding system. Notwithstanding, breeders are currently struggling to develop new varieties that are high yielding, suitable for mechanized harvesting, have a low content of alkaloids or other anti-nutritional properties, and to anthracnose (Colletotrichum acutatum). Therefore, it is necessary to reassess the potential of this crop and invest in its research to incorporate new techniques and breeding strategies to optimize the development of new varieties in the Andes which address the current cultivation challenges of the species.
ARTICLE | doi:10.20944/preprints202308.0463.v1
Subject: Medicine And Pharmacology, Dermatology Keywords: alopecia areata; androgenetic alopecia; genetic test; DNA analysis
Online: 7 August 2023 (10:13:57 CEST)
Background: Androgenetic alopecia (AGA) and alopecia areata (AA) are most common types of non-cicatricial alopecia. Both diseases have limited effective therapeutic options and affect patients' quality of life. Pharmacogenetic tests can help predict the most appropriate treatment option by evaluating the single nucleotide polymorphisms (SNPs) corresponding to genes related to alopecia. The objective of the study was to evaluate and compare selected SNPs and genes in AA and AGA patients from Romania and Brazil. Materials and methods: We investigated associations between AA and AGA and 45 tag SNPs of 13 genes in 287 Romanian and 882 Brazilian patients. The DNA samples were extracted from saliva using qPCR technique. Results: GR-alpha gene, GPR44-2 gene, SULT1A1 gene and CRABP2 gene were statistically significantly different in Brazil compared to Romania. Minoxidil may be recommended in half of the cases of AGA and AA. Patients with AGA and high expression of SRD5A1 or PTGFR-2 may benefit from Dutasteride, respectively Latanoprost treatment. Most of the studied genes showed no differences between the two population. Conclusion: The DNA analysis of the patients with alopecia may contribute to a successful treatment.
BRIEF REPORT | doi:10.20944/preprints202306.2051.v1
Subject: Biology And Life Sciences, Aquatic Science Keywords: Microsatellites; Centropomus parallelus; Centropomus undecimalis; Centropomidae, genetic polymorphism
Online: 28 June 2023 (15:31:25 CEST)
Centropomus undecimalis (common snook, sergeant fish or robalo) and Centropomus parallelus (fat snook, smallscale fat snook, little snook or chucumite) have tropical and subtropical wide distribution from southern Florida (Gulf of Mexico) to southern Brazil (Rio Grande do Sul) waters, and due the value of their flesh, these species have been explored with predatory fishing, generating a deficiency for their conservation. Adequate conservation of this species depends on population genetic parameters. Thus, in this study, we used microsatellite markers to investigate the genetic variability and the genetic characterization of C. undecimalis and C. parallelus populations, identifying if the citations species are geographically connected, using 10 loci of microsatellites, bringing strategies of management, sustainability, and conservation for species citations, and providing genetic subsidies needed to be used in breeding programs for snooks. Microsatellite molecular genetic markers were efficient in the study of the genetic variability of the samples of C. parallelus and C. undecimalis, resulting in data on the genetic structuring of these populations, thus aiding in their management and conservation. The data presented may provide subsidies for future use in programs aimed at animal breeding of sea bass, establishing tools for use in fish farming. In addition, despite being two species that are not on the endangered list, we can observe that there are genetic differences between the studied populations of the same species.
ARTICLE | doi:10.20944/preprints202306.1721.v1
Subject: Environmental And Earth Sciences, Geochemistry And Petrology Keywords: Jiuzhaigou; Tufa particulate matter; Sedimentation; Genetic analysis; Paleoearthquake
Online: 25 June 2023 (07:11:39 CEST)
The sedimentary characteristics of the special interlayer contained in the section of the Sparking Lake dam revealed by the 8.8 Jiuzhaigou earthquake in 2017 are obviously different from the tufa in the dam body, and they are considered to be prehistoric flood relics. Based on the study of the particulate matter from the 8.8 Jiuzhaigou earthquake, this paper combines comparative petrographic, mineralogical, geochemical and chronological studies of the special interbedded sediments of the Sparking Lake dam with other genetic samples to obtain homology information and genetic links, as well as to explore the tufa depositional dynamics and earthquake disaster subsidence. The palaeoseismic benefit in the discontinuity layer is explored, and the palaeoseismic information embedded in the profiles is extracted, providing a new idea to reconstruct the palaeoseismic events in the tufa deposition sequence. According to X-ray diffraction, laser particle size analysis and scanning electron microscope experiments, the particulate matter in the Jiuzhaigou mountains has its own specific mineralogical characteristics. The mineral composition of the particulate matter is basically calcite. The particle size is large, and the single particle is mostly angular and subangular. The fracture morphology observed under the single particle microscope is uneven, showing the characteristics of dust caused by earthquake disasters. Geochemical analysis data show that the provenance of various types of particles in the same area is stable, indicating the homology of terrestrial carbonate sedimentation in the karst system. Combined with mineralogy and grain size morphology, the interbedded particles in the tufa depositional profile have the potential application of palaeoseismic archives to record extreme seismic events. The palaeoseismic date was inferred from the chronological data of special interlayered sediments in the tufa dam body. Therefore, the tufa bedding can be related to the palaeoearthquake, and the special interlayer of the tufa section can be used to reconstruct palaeoearthquakes.
ARTICLE | doi:10.20944/preprints202306.0613.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Accessions; genetic diversity; morphological traits; SSRs; winged bean
Online: 8 June 2023 (09:25:39 CEST)
Winged bean productivity and the potential to enhance food and nutrition security in sub-Saharan Africa are recurrently affected by several constraints, including but not limited to the lack of genetic improvement. The dearth of adequate information on the genetic diversity that guides the choice of progenitors’ selection among other advantages has been a major setback in planning appropriate improvement programs. This study assessed 15 winged bean accessions for genetic diversity using 10 quantitative traits and 10 microsatellites (SSRs) markers. These accessions were evaluated using RCBD with three replicates for two growing seasons. Ten plants constitute each accession during evaluation from where leaf samples were obtained for SSR marker genotyping. Phenotypic results revealed significant variation (p < 0.05) in the performances of the accessions for the measured traits. H2 estimates varied from 18.92% for seed length to 72.67% for seed weight per plant. Pod weight had a positive and significant correlation with pod length (0.53), pod width (0.70), and number of seeds per pod (0.64). However, the number of seeds per pod negatively correlated with days to maturity (-0.71). The number of seeds per pod was positively predicted by pod weight, seed thickness, and days to maturity. Cluster analysis revealed two genetic groups characterized by different traits. The ten SSRs revealed an average allele count of 4.2, gene diversity of 0.25, and polymorphic information content of 0.22. Analysis of molecular variance revealed within the population of 95% as compared to between population variance of 5%. Phylogeny analysis revealed two primary genetic groups from where five secondary genetic subgroups were identified and only three accessions (TPt-6, TPt-126, and TPt-48) showed genetic purity. This study provides the basis for further studies aimed at exploiting existing variations in winged bean germplasm for its improvement.
ARTICLE | doi:10.20944/preprints202306.0016.v1
Subject: Medicine And Pharmacology, Dermatology Keywords: psoriasis; psoriatic arthritis; IFIH1; MDA5; polymorphism; genetic association
Online: 1 June 2023 (03:40:11 CEST)
The melanoma differentiation-associated protein 5 (MDA5; encoded by the IFIH1 gene) mediates the activation of the interferon pathway in response to viral infection. This protein is also upregulated in autoimmune diseases and psoriasis skin lesions. IFIH1 gene variants that increased the MDA5 activity have been associated with increased risk for immune mediated diseases, including psoriasis. Our aim was to determine the association between three IFIH1 variants (rs35337543, intron8 +1G>C; rs35744605, Glu627Stop; and rs1990760, Ala946Thr) and the main clinical findings in a cohort of Spanish patients with psoriatic disease (N=572; 77% early-onset). Early-onset psoriasis (EOPs) had a significant higher frequency of severe disease and Cw6+. Carriers of the 946Thr variant were more common in EOPs (p<0.001), and the effect was more pronounced among Cw6-negatives. This variant was also associated with an increased risk of psoriatic arthritis (PsA) independently of other factors (OR=1.62, 95%CI=1.11-2.37). The rs3533754 and rs35744605 have been reported as risk factors for viral infection and protective for autoimmune diseases, but we did not find significant differences between the two onset age or PsA groups. However, due to the reduced frequency of the two variants (<0.02) the size of our cohort was too low to conclude a significant effect. In conclusion, the common IFIH1 rs1990760 T allele that has been linked to increased gene expression was significantly more frequent in EOPs patients. This variant was also an independent risk factor for PsA in our cohort. This risk allele was in linkage disequilibrium with other variants previously associated with the risk of psoriasis and PsA. Our study reinforces the widely reported role of IFIH1 gene variants on psoriatic disease and other immune mediated diseases.
REVIEW | doi:10.20944/preprints202305.1297.v1
Subject: Medicine And Pharmacology, Other Keywords: genetic kidney disease; knockout; nephrotic syndrome; proteinuria; transgenic
Online: 18 May 2023 (08:10:21 CEST)
Proteinuria is known to be associated with all-cause and cardiovascular mortality, and nephrotic syndrome is defined by the level of proteinuria and hypoalbuminemia. With advances in medicine, new causative genes for genetic kidney diseases are being discovered increasingly frequently. We reviewed articles on proteinuria/nephrotic syndrome, focal segmental glomerulosclerosis, membranous nephropathy, diabetic kidney disease/nephropathy, hypertension/nephrosclerosis, Alport syndrome, and rare diseases, which have been studied in mouse models. Significant progress has been made in understanding the genetics and pathophysiology of kidney diseases thanks to advances in science, but research in this area is ongoing. In the future, genetic analyses of patients with proteinuric kidney disease/nephrotic syndrome may ultimately lead to personalized treatment options.
ARTICLE | doi:10.20944/preprints202305.1095.v1
Subject: Biology And Life Sciences, Horticulture Keywords: Prunus tenella; genome; assembly; almond; population genetic structure
Online: 16 May 2023 (05:13:20 CEST)
Prunus tenella is a rare and precious relict plant in China. It is an important genetic resource for almond improvement and an indispensable material in ecological protection and landscaping. However, the research of molecular breeding and genetic evolution has been severely restricted, due to the lack of genome information. In this investigation, we created a chromosome-level genomic pattern of P. tenella, 231Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32088 protein-coding genes, and an examination of the genome assembly indicated that 94.7% among all assembled transcripts were alignable to the genome assembly; most (97.24%) were functionally annotated. By phylogenomic genome comparison, we found that P. tenella is an ancient group that diverged approximately 13.4 million years ago (Mya) from 13 additional closely related species and about 6.5 Mya from the cultivated almond. Collinearity analysis revealed that P. tenella is highly syntenic and has high sequence conservation with almond and peach. However, this species also exhibit many presence/absence variants. Moreover, a large inversion at the 7,588 kb position of chromosome 5 was observed, which may have a significant association with phenotypic traits. Lastly, population genetic structure analysis in eight different populations indicated a high genetic differentiation among the natural distribution of P. tenella. This high-quality genome assembly provides critical clues and comprehensive information for the systematic evolution, genetic characteristics, and functional gene research of P. tenella. Moreover, it provides a valuable genomic resource for in-depth study in protecting, developing, and utilizing P. tenella germplasm resources.
ARTICLE | doi:10.20944/preprints202304.1057.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: genetic polymorphism; ACE1 rs4646994; lung cancer; pulmonary nodules
Online: 27 April 2023 (07:47:55 CEST)
Background: Currently, many detection methods have high sensitivity to the diagnosis of lung cancer. However, some postoperative patients with pulmonary nodule were eventually diagnosed as benign nodules. The ideal evaluation of an individual with a pulmonary nodule would expedite therapy for a malignant nodule and minimize testing for those with a benign nodule.Methods: This case-control study is designed to explore the relationship between ACE1 rs4646994 polymorphism and the risk of lung cancer in patients with pulmonary nodules, 400 individuals with lung cancer and benign pulmonary nodules were included. A DNA extraction kit was used to extract plasm DNA from peripheral blood. The relationship between ACE1 rs4646994 and the risk of lung cancer in patients with pulmonary nodules was determined by chi-square test, logistic regression analysis and cross analysis. Results: The results showed that the DD genotype of ACE1 rs4646994 may increase the risk of lung cancer in patients with pulmonary nodules, and this correlation was more significant in the female subgroup. In the age stratification analysis, it was found that the risk of lung cancer was significantly increased in the DD genotype of ACE1 rs4646994 in the older subgroup (> 45 years). In addition, the possibility of EGFR mutation in lung adenocarcinoma patients with ACE1 rs4646994 DD genotype was lower than that of II or ID genotype carriers. Conclusions: Our study indicated that ACE1 rs4646994 polymorphism increases the risk of lung cancer in patients with pulmonary nodules from China.
REVIEW | doi:10.20944/preprints202212.0453.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: wheat; resistance; leaf rust; genetic loci; genome-wide
Online: 23 December 2022 (08:11:48 CET)
Due to the global warming and dynamic changes in pathogenic virulence, leaf rust caused by Puccinia triticina has greatly expanded its epidermic region and become a severe threat to global wheat production. Genetic bases of wheat resistance to leaf rust mainly relies on the leaf rust resistance (Lr) gene or quantitative trait locus (QLr). Although these genetic loci have been insensitively studied during the last two decades, an updated overview of Lr/QLr in a genome-wide level is urgently needed. This review summarized recent progresses in genetic studies of wheat resistance to leaf rust. Wheat germplasms with great potentials in genetic improvement of resistance to leaf rust were highlighted. Key information about the genetic loci carrying Lr/QLr were summarized. A genome-wide chromosome distribution map for all the Lr/QLr was generated based on the released wheat reference genome. In conclusion, this review has provided valuable sources for both wheat breeders and researchers to understand the genetics of resistance to leaf rust in wheat.
ARTICLE | doi:10.20944/preprints202212.0427.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Plankton; Monitoring; Harmful algae; microscopic; genetic; Western Channel
Online: 22 December 2022 (11:34:13 CET)
Plankton monitoring by microscopy offers long-term ecological perspective of plankton com-munities but different detection approaches are biased uniquely. Genetic identification of marine plankton has become standard but is still not used in routine monitoring. This study assessed the diversity of plankton taxa using 18S high throughput sequencing from 2011-2012 from small-volume (~200ml) samples from the Water and Microplankton Sampler (WaMS) deployed on the Continuous Plankton Recorder platform (CPR). The 18S-HTS survey revealed a bias towards heterotrophic taxa, and phototrophs under 10µm within the photosynthetic community. In comparison with phytoplankton microscopic counts from the CPR survey and Western Channel Observatory station L4, only 8-12 taxonomic families were common to all three surveys, with a bias towards larger diatoms and dinoflagellate taxa in microscopy surveys. The WaMS survey detected a contrasting but complementary taxa set to that of microscopic surveys. Additional Quantitative PCR was carried out on the picoeukaryotic pelagophyte, Aureococcus anophagefferens, and the nanoeukaryotic potential harmful algae, Pseudo-nitzschia delicatissima, from 2011-2013. This confirmed the persistence presence of A. anophagefferens in the Western Channel and an elevated abundance of both species in 2011. Species specific seasonality were distinct from those of aggregrate phytoplankton groups.
REVIEW | doi:10.20944/preprints202212.0210.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Maize; drought; landrace; climate-change; crop genetic resources
Online: 13 December 2022 (01:07:51 CET)
To meet an ever global population's food demand, crop yields must be sustained and increased. Drought, which is getting harsher as a result of global warming, is largely impeding the agricultural productivity. Maize is widely used as food and animal feed in many regions of the world, but its yields are largely effected by drought and heat stress. Historical data on climate change predicts that drought and heat stress becoming major threat for maize cultivation in coming years, which will have huge impact on food security of the world especially in Africa and Asia. Thus there is an immense necessary to develop drought tolerant and climate resilient maize to feed the predicted population of the world. Availability and accessibility of crop genetic resources plays a huge role in development of drought-tolerant maize cultivars. A huge genetic resources of maize, including its landraces and crop wild relatives (CWR) have been reported naturally and many of them have stored in National and International gene banks globally. Conventional breeding methods have been tremendously increased maize yields, but these methods frequently fall short of achieving the demand for improved drought stress resistance. In this article, we have briefly discussed about impact of climate variability on crop production, maize yield losses due to drought, drought tolerance in maize landraces and CWR, and origin and evolution of Mexican landraces. This information may help in utilization of these potential resources in various pre-breeding programs.
ARTICLE | doi:10.20944/preprints202211.0244.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: aromatic rice; salt screening; RAPD marker; genetic diversity
Online: 14 November 2022 (07:43:36 CET)
Salinity is abiotic stress, which causes adverse environmental conditions for rice cultivation. In particular, local aromatic rice cultivation is heavily influenced by soil salinity stress, which has an impact on global food security. This study aimed to screen local aromatic rice genotypes in a hydroponics experiment using Yoshida solutions to evaluate the effect of increasing NaCl concentrations on the early growth stages of rice seedlings. Genetic diversity along with phylogenetic relationship was assessed using the random amplified polymorphic DNA (RAPD) markers. Out of 20 RAPD markers, 17 markers produced reproducible polymorphic bands. Individuals of all genotypes shared 88 (89.80%) of the 98 total RAPD elements amplified. The genetic distance-focused similarity index ranged from 0.05 to 0.94. The highest genetic distance (0.94) was discovered between genotypes Nayanmoni and Kalijira Barisal, and the lowest was between Badshabhog and Kataribhog (0.05). In addition, the OPS 3(510bp) and OPA 14(1100bp) markers could be used to identify salt-tolerant genotypes. According to genetic distance, the salt stress tolerant check genotype, Pokkali was genetically related to Chinigura as well as Kalijira Barisal. This study established a simple and consistent method for evaluating variability across various aromatic rice genotypes, which will benefit in genotype selection for breeding salinity stress tolerant aromatic rice varieties in Bangladesh.
REVIEW | doi:10.20944/preprints202211.0106.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Keywords: chloroplast genetic engineering; Homologus recombination; ORF; photosynthesis
Online: 7 November 2022 (04:31:29 CET)
Abstract: Chloroplast is a new hotspot in the field of plant transformation system of plant genetic engineering. Initially developed in Chlamydomonas and tobacco, it is now feasible in a broad range of species. They exploit the homologous recombination and segregation pathways acting on chloroplast genomes and are based on direct repeats, transient co-integration or co-transformation and segregation of trait and marker genes. Foreign site-specific recombinases and their target sites provide an alternative and effective method for removing marker genes from plastids.Chloroplast genetic engineering has many advantages over nuclear genetic enginering, especially site-specific introduction of foreign genes ,leading to the absence of gene siliency and positon effect,which providing the available to explore the regulation and mechanism of chloroplast genes`expression in vitro .It also can identify the structure and function of the chloroplast genome , the expression of chloroplast affect the nulear genome. In this paper, the basic methodology of chloroplast transformation, the current techniques and applications, and the future possibilities for Chloroplast genetic engineering was reviewed[1-3].
ARTICLE | doi:10.20944/preprints202207.0332.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Plankton; Monitoring; Harmful algae; microscopic; genetic; Western Channel
Online: 22 July 2022 (03:33:40 CEST)
Plankton monitoring by microscopy offers long-term ecological perspective of plankton communities but is biased towards those organisms that can be distinguished using the microscope. Genetic identification of marine plankton has become standard but is still not used. This study is a comprehensive study genetically measured taxa in the Western Channel of UK using a small-volume automated water sampler deployed on the CPR platform. The study present one year of high-throughput sequencing data focussing on smaller plankton and separate community to that measured by microscopy that can complement each other for a holistic view of plankton. Quantitative tests of two harmful algae show relatively high abundance of the Pelagophyte Aureococcus anophagefferens during 2011 with low nitrite levels. Three years of Pseudo-nitzschia delicatissima quantitative monitoring also shows a greater abundance of this potentially harmful taxa in 2011. Flow cytometry reveals distinct seasonal cycles with distinct timings.
REVIEW | doi:10.20944/preprints202112.0331.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Genetic code expansion; unnatural amino acid; fluorescence imaging
Online: 21 December 2021 (12:42:35 CET)
Genetic code expansion has emerged as an enabling tool to provide insight into functions of understudied proteinogenic species such as small proteins and peptides, and to probe protein biophysics in the cellular context. Here we discuss recent technical advances and applications of genetic code expansion in cellular imaging of complex mammalian protein species, along with considerations and challenges upon using the method.
ARTICLE | doi:10.20944/preprints202110.0334.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: Nesting; cutting; irregular pattern; genetic algorithm; smart manufacturing
Online: 22 October 2021 (15:41:54 CEST)
In industrial environments, nesting consists in cutting or extracting pieces from a material sheet, with the purpose of minimizing the surface of the sheet used. This problem is present in different types of industries, such as shipping, aeronautics, woodworking, footwear, and so on. In this work, the aim is to find an acceptable solution to solve complex nesting problems. The research developed is oriented to sacrifice accuracy for speed so as to obtain robust solutions in less computational time. To achieve this, a greedy method and a genetic algorithm have been implemented, being the latter responsible for generating a sequence for the placement of the pieces, where each piece is placed in its current optimal position with the help of a representation system for both the pieces and the material sheet.