ARTICLE | doi:10.20944/preprints202201.0465.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: genetic algorithm; deep neural network; hidden layer; optimal architecture; intrusion detection
Online: 31 January 2022 (13:26:18 CET)
Computer network attacks are evolving in parallel with the evolution of hardware and neural network architecture. Despite major advancements in Network Intrusion Detection System (NIDS) technology, most implementations still depend on signature-based intrusion detection systems, which can’t identify unknown attacks. Deep learning can help NIDS to detect novel threats since it has a strong generalization ability. The deep neural network’s architecture has a significant impact on the model’s results. We propose a genetic algorithm based model to find the optimal number of hidden layers and the number of neurons in each layer of the deep neural network (DNN) architecture for the network intrusion detection binary classification problem. Experimental results demonstrate that the proposed DNN architecture shows better performance than classical machine learning algorithms at a lower computational cost.
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/preprints201906.0241.v1
Subject: Computer Science And Mathematics, Applied Mathematics Keywords: cabinet dryer; genetic algorithm; neural network; temperature; air velocity; moisture
Online: 24 June 2019 (10:05:50 CEST)
Nowadays industrial dryers are used instead of traditional methods for drying. In designing dryers suitable for controlling the process of drying and reaching a high quality product, it is necessary to predict the instantaneous moisture loss during drying. For this purpose, ten mathematical-experimental models with a neural network model based on the kinetic data of pistachio drying are studied. The data obtained from the cabinet dryer will be evaluated at four temperatures of inlet air and different air velocities. The pistachio seeds will be placed in a thin layer on an aluminum sheet on a drying tray and weighed by a scale attached to the computer at different times. In the neural network, data are divided into three parts: educational (60%), validation (20%) and test (20%). Finally, the best mathematical-experimental model using genetic algorithm and the best neural network structure for predicting instantaneous moisture are selected based on the least squared error and the highest correlation coefficient.
ARTICLE | doi:10.20944/preprints202005.0002.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Grammar Evolution; Deep Learning; Network Architecture Search; Grammar Guided Genetic Programming
Online: 2 May 2020 (11:36:18 CEST)
Photogrammetry involves aerial photography of the earth’s surface and subsequently processing the images to provide a more accurate depiction of the area (Orthophotography). It’s used by the Spanish Instituto Geográfico Nacional to update road cartography but requires a significant amount of manual labor due to the need to perform visual inspection of all tiled images. Deep Learning techniques (artificial neural networks with more than one hidden layer) can perform road detection but it is still unclear how to find the optimal network architecture. Our system applies grammar guided genetic programming to the search of deep neural network architectures. In this kind of evolutive algorithm all the population individuals (here candidate network architectures) are constrained to rules specified by a grammar that defines valid and useful structural patterns to guide the search process. Grammar used includes well-known complex structures (e.g. Inception-like modules) combined with a custom designed mutation operator (dynamically links the mutation probability to structural diversity). Pilot results show that the system is able to design models for road detection that obtain test accuracies similar to that reached by state of the art models when evaluated over a dataset from the Spanish National Aerial Orthophotography Plan.
ARTICLE | doi:10.20944/preprints202301.0434.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: pan-cancer; mitotic network activity index; prognostic biomarker; genetic instability; immunotherapy; multimodal biomarker; cellular morphometric subtype
Online: 24 January 2023 (13:23:26 CET)
Increased mitotic activity is associated with the genesis and aggressiveness of many cancers. To assess the clinical value of mitotic activity as prognostic biomarker, we performed a pan-cancer study on the mitotic network activity index (MNAI) constructed based on 54-gene mitotic apparatus network. Our pan-cancer assessment on TCGA (33 tumor types, 10,061 patients) and validation on other publicly available cohorts (23 tumor types, 9,209 patients) confirmed the significant association of MNAI with overall survival, progression-free survival and other prognostic endpoints in multiple cancer types, including Lower-Grade Gliomas (LGG), Breast Invasive Carcinoma (BRCA) and many others. We also showed significant association of MNAI with genetic instability, which provides a biological explanation of its prognostic impact at pan-cancer landscape. Futhermore, we found that patients with high MNAI benefit more from anti-PD-1 and Anti-CTLA-4 treatment. In addition, we demonstrated on LGG and BRCA that the multimodal integration of MNAI and the AI-empowerd Cellular Morphometric Subtypes (CMS) significantly improved the predictive power of prognosis compared to MNAI and CMS alone. Our results suggest that MNAI can be used as a potential prognostic biomarker for different tumor types toward different clinical endpoints, and multimodal integration of MNAI and CMS exceeds individual biomarker for precision prognosis.
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/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.
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.
ARTICLE | doi:10.20944/preprints201903.0161.v1
Subject: Engineering, Civil Engineering Keywords: Response Surface Methodology; Hybrid; Genetic Algorithm Artificial Neural Network; Concrete; Flexural Strength; Steel Fibre Reinforced Concrete; Civil Engineering
Online: 15 March 2019 (09:54:22 CET)
The study presents a comparative approach between response surface methodology (RSM) and hybridized, genetic algorithm artificial neural network (GA-ANN) in predicting the water absorption, compressive strength, flexural strength split tensile strength and slump for steel fiber reinforced concrete. The effect of process variables such as aspect ratio, water cement ratio and cement content were investigated using the central composite design of response surface methodology. This same experimental design was used in training the hybrid-training approach of artificial neural network. The predicting ability of both methodologies were compared using the root mean sqaured error (RMSE), mean absolute error (MAE), model predictive error (MPE) and absolute average deviation (AAD). The RSM model was found more accurate in prediction compared to hybrid GA-ANN.
ARTICLE | doi:10.20944/preprints201804.0327.v2
Subject: Engineering, Electrical And Electronic Engineering Keywords: Overcurrent Relay (OCR); Genetic Algorithm (GA); Time Dial Setting (TDS); Plug Setting Multiplier (PSM); Optimal OCR setting and coordination and DigSILENT power factory
Online: 27 April 2018 (15:49:58 CEST)
This paper presents a study on optimization of Overcurrent relay (OCR) coordination protection scheme for Sustainable Standalone Hydrokinetic Renewable Energy (SHRE) distribution network at Batang Rajang river, located at Kapit Sarawak, Malaysia by turning river stream into power generation source. The purpose of the project is to develop rural electrification system for native long houses along the river. The research study is tested on a DigSILENT develop model of the SHRE distribution network and in accordance with all respectively unique parameters and relevant standards. Since this is a new standalone distribution system, an efficient and properly coordinated overcurrent protection system must be provided. Improper and miscoordination among OCRs result in maloperation of the protection system that can lead to false tripping and an unnecessary outage and power system instability. Thus, the objective of this work is to employ Genetic Algorithm (GA) technique in Matlab/Simulink for optimal overcurrent coordination and settings among all OCRs in the proposed distribution network in order to improve the speed of OCR tripping operation. The GA is used because the project is fast track and requiring the simplest method available. In this strategy, time dial setting (TDS) is optimized by using plug setting multiplier (PSM) as the constraint. The obtained results show a significant improvement of the relay operating time of 36.01% faster than that of conventional numerical technique during fault occurrence. Thus, an efficient and reliable overcurrent protection scheme has been achieved for the SHRE distribution network.
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.
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/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/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.
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/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/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/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/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/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.
ARTICLE | doi:10.20944/preprints202105.0606.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Chi-squared; Genetic ratios; Progenies; Selfing; Variability analysis
Online: 25 May 2021 (10:34:35 CEST)
The present cultivated enset clonal landraces in Ethiopia originated from few wild progenitors. However, enset has a mixed mode of reproduction in which, the wild enset reproduces sexually through seeds, while cultivated enset is generally propagated vegetatively. The objective of this study was to understand the genetic structures of enset cultivars and estimate their genetic variability by evaluating the morphological data generated from progenies of cultivated and wild enset clones. Hence, seeds collected from six cultivated and four wild enset genotypes were used for this study. Data on four qualitative and six quantitative morphological traits were recorded from the progenies of the 10 enset genotypes. Progenies of seven enset genotypes segregated with 3:1 genetic ratio while progenies of the remaining genotypes segregated differently for the qualitative traits considered. With regard to the quantitative traits, the progenies of the 10 enset genotypes differed significantly for five of the six traits except pseudostem length. Generally the cultivated clones performed better than the wild types. This study demonstrated the possibility of creating genetic variation through selfing of the existing clones of enset for traits of interest and makes improvements either through selection or crossing the elite types to develop novel cultivar
ARTICLE | doi:10.20944/preprints202105.0305.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ISSR; Rosa spp.; DNA fingerprinting; genotypes; genetic diversity
Online: 13 May 2021 (14:01:21 CEST)
Genetic diversity is inevitable in making any crop improvement program successful. DNA fingerprinting technology to assess the genetic relationship among the selected genotypes for identification and cataloging of different species and cultivars of roses is a promising tool for Rosa genomes. The inter-simple sequence repeats markers (ISSRs) were used to investigate the genetic diversity among twenty-one diverse Rosa genotypes belonging to two different species, Rosa hybrida and R. damascena, and three distinct groups of rose varieties, namely Hybrid Tea, Floribunda, and Damask roses. Twenty-four ISSR primers yielded a total of 280 scorable amplified fragments from 250-1800 bp in length, from which 244 were polymorphic, resulting in an average of 86.4% polymorphism. UPGMA cluster analysis based on Jaccard’s pairwise similarity coefficient values ranged from 0.264 to 0.818, clearly distinguished different species and genotypes, grouping them into three distinct clusters. The results confirmed a high degree of variation in the rose germplasm studied highlighting the potential of improvement in roses for the ornamental and perfume industry.
REVIEW | doi:10.20944/preprints202104.0461.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Germplasm; Genetic plant resources; Preservation; Propagation; in vitro
Online: 19 April 2021 (11:28:31 CEST)
Germplasm is a valuable natural resource in plant diversity that is crucial for its potential use. It provides knowledge about a species genetic composition. Germplasm protection strategies are not just planting hope threatened with extinction, they preserve medicinal and other essential plants on which survival rests. The successful use of genetic plant resources necessitates diligent collection, storage, analysis, documentation, and germplasm exchange. Slow growth cultures, cryopreservation, pollen and DNA banks, botanic gardens, genetic reserves and farmer’s fields are few conservation techniques. However, usage of an in vitro procedure with any chance of genetic instability leads to the destruction of the entire substance. Improved understanding of basic regeneration biology would, in turn, undoubtedly increase the capacity to regenerate plants from in vitro harvested explants, thus expanding selection possibilities. Germplasm conservation seeks to conserve endangered and vulnerable plant species worldwide for future proliferation and development; it is also the bedrock of agricultural production.
ARTICLE | doi:10.20944/preprints202102.0470.v1
Subject: Engineering, Civil Engineering Keywords: Smooth rectangular channel; Tsallis entropy; Genetic Programming (GP)
Online: 22 February 2021 (13:09:13 CET)
One of the most important subjects of hydraulic engineering is the reliable estimation of the transverse distribution in rectangular channel of bed and wall shear stresses. This study makes use of the Tsallis entropy, Genetic Programming (GP) and (ANFIS) methods to assess the shear stress distribution (SSD) in rectangular channel. To evaluate the results of the Tsallis entropy, GP and ANFIS models, laboratory observations were used in which shear stress was measured using an optimized Preston tube. This is then used to measure the SSD in various aspect ratios in the rectangular channel. To investigate the shear stress percentage, 10 data series with a total of 112 different data for were used. The results of the sensitivity analysis show that the most influential parameter for the SSD in smooth rectangular channel is the dimensionless parameter B/H, Where the transverse co-ordinate is B, and the flow depth is H. With the parameters (b/B), (B/H) for the bed and (z/H), (B/H) for the wall as inputs, the modeling of the GP was better than the other one. Based on the analysis, it can be concluded that the use of GP and ANFIS algorithms is more effective in estimating shear stress in smooth rectangular channels than the Tsallis entropy-based equations.
ARTICLE | doi:10.20944/preprints202010.0303.v1
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: fuzzy genetic algorithm; reachability property; deadlock; model checking
Online: 14 October 2020 (10:58:37 CEST)
model checking techniques are often used for the verification of software systems. Such techniques are accompanied with several advantages. However, state space explosion is one of the drawbacks to model checking. During recent years, several methods have been proposed based on evolutionary and meta-heuristic algorithms to solve this problem. In this paper, a hybrid approach is presented to cope with the SSE problem in model checking of systems modeled by GTS with an ample state space. Most of existence proposed methods that aim to verify systems are applied to detect deadlocks by graph transformations. The proposed approach is based on the fuzzy genetic algorithm and is designed to decline the safety property by verifying the reachability property and detecting deadlocks. In this solution, the state space of the system is searched by a fuzzy genetic algorithm to find the state in which the specified property is refuted/verified. To implement and evaluate the suggested approach, GROOVE is used as a powerful designing and model checking toolset in GTS. The experimental results indicate that the presented hybrid fuzzy method improves speed and performance by comparing other techniques
ARTICLE | doi:10.20944/preprints202006.0028.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: genetic algorithm; search techniques; random tests; evolution; applications
Online: 4 June 2020 (07:44:03 CEST)
Nowadays genetic algorithm (GA) is greatly used in engineering pedagogy as an adaptive technique to learn and solve complex problems and issues. It is a meta-heuristic approach that is used to solve hybrid computation challenges. GA utilizes selection, crossover, and mutation operators to effectively manage the searching system strategy. This algorithm is derived from natural selection and genetics concepts. GA is an intelligent use of random search supported with historical data to contribute the search in an area of the improved outcome within a coverage framework. Such algorithms are widely used for maintaining high-quality reactions to optimize issues and problems investigation. These techniques are recognized to be somewhat of a statistical investigation process to search for a suitable solution or prevent an accurate strategy for challenges in optimization or searches. These techniques have been produced from natural selection or genetics principles. For random testing, historical information is provided with intelligent enslavement to continue moving the search out from the area of improved features for processing of the outcomes. It is a category of heuristics of evolutionary history using behavioral science-influenced methods like an annuity, gene, preference, or combination (sometimes refers to as hybridization). This method seemed to be a valuable tool to find solutions for problems optimization. In this paper, the author has explored the GAs, its role in engineering pedagogies, and the emerging areas where it is using, and its implementation.
ARTICLE | doi:10.20944/preprints202003.0119.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: black rice; transcriptome sequencing; genic SSRs; genetic diversity
Online: 7 March 2020 (09:03:34 CET)
Study in black rice has gain prominence in recent times due to its high nutritive value, curative effect, and anti-oxidant properties. However, its poor agronomic traits, including low yield necessitates the incorporation of the colour-grain trait into elite varieties through plant breeding techniques. SSR markers play an important role in plant identification and breeding. Here, the generation of reference-based transcriptome, annotation of transcriptome datasets, and a large set of simple sequence repeat (SSR) markers derived from Black rice have been described. In all 28664 SSRs were predicted in 34978 (48.59%) expressed transcripts. However, 7068 (20.20%) transcripts were found to have more than one SSR. The identified SSRs were dominated by tri-nucleotide and tetra-nucleotide repeats representing about 54.11% and 33.31% respectively, of total SSRs. Validation of selected markers associated with anthocyanin trait performed across different black rice accessions established the reliability of the process used for mining SSR markers. The SSR markers identified in this study could be used to select varieties with desired traits, and to investigate the genetic mechanism underlying anthocyanin accumulation in the pericarps of black rice. Furthermore, the findings from this study may prove beneficial in future genetic diversity studies, primer development, and selective breeding programs.
Subject: Engineering, Electrical And Electronic Engineering Keywords: transient analysis; surge arrester allocation; genetic algorithm; ATP
Online: 1 September 2019 (09:59:23 CEST)
Lightning discharges in electric power networks generate voltage and current surges that are propagated through the electrical network causing damage and shutdowns in the electrical system. To protect the system against these phenomena, surge arresters are very effective and widely used by electrical utilities in their electric grids. This paper presents a methodology for optimized surge arrester allocation based on genetic algorithm (GA), creating a simulation environment in the software ATP (Alternative Transients Program) to implement the proposed methodology. The optimized allocation procedure is based on a fitness function that minimizes the cost of surge arresters and maximizes the number of protected equipment. To carry out this optimized arrester allocation procedure using ATP may demand too much processing time when running large distribution grids. To overcome this difficulty a procedure is proposed to obtain an overvoltage severity description of the grid and select the most critical electric nodes for the incidence of lightning discharges, in the GA allocation procedure. The case study is applied to the IEEE 123-bus electrical feeder to demonstrate the effectiveness of the proposed methodology.
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/preprints201904.0321.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chickpea; genetic diversity; linkage disequilibrium; DArTseq-SNP markers
Online: 29 April 2019 (07:56:52 CEST)
Characterization of genetic diversity, population structure and linkage disequilibrium is prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes were genotyped using DArTseq-Based SNP markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that covered by SNPs varied from 16236.36 kbp (LG8) to 67923.99 kbp (LG5), while LG4 showed higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6 and LG8 showed higher mean PIC value than average. Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and Discriminant Analysis of Principal Component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2≥0.8, while 2961 pairs of markers showed complete LD (r2=1) and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggesting the presence of a high genetic diversity among studied chickpea genotypes. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits such as seed yield, abiotic and biotic stresses and therefore can be efficiently used in breeding programs to improve chickpea.
ARTICLE | doi:10.20944/preprints201811.0603.v1
Subject: Biology And Life Sciences, Virology Keywords: CCHFV, CD24, nucleocapsid, genetic adjuvant, immunogenicity, IFNAR-/- mice
Online: 27 November 2018 (12:15:59 CET)
Crimean Congo hemorrhagic fever virus (CCHFV) is the causative agent of a globally-spread tick-borne zoonotic infection with an eminent risk of fatal human disease. Imminent public health threat posed by disseminated virus activity and lack of an approved therapeutic make CCHFV an urgent target for vaccine development. We described the construction of a DNA vector expressing nucleocapsid protein (N) of CCHFV (pV-N13) and investigated its potential to stimulate cytokine and total/specific antibody responses in BALB/c and challenge experiment in IFNAR-/- mice. Due to lack of sufficient antibody stimulation towards N protein, we have selected CD24 protein as a potential adjuvant which has proliferative effect on B and T cells. Overall, our N expressing construct when administered solely or in combination with pCD24 vector elicited significant cellular and humoral responses in BALB/c, despite variations in particular cytokines and total antibodies. However, the stimulated antibodies produced due to expression of N protein have shown no neutralizing ability in VNA. Furthermore, challenge experiments were revealed protection potential of N expressing construct in IFNAR -/- mice model. In conclusion, we have shown that CD24 has prominent effect as a genetic adjuvant when co-delivers with a synergic foreign gene expressing vector. Besides, targeting of S segment of CCHFV can be considered as a practical way in developing vaccine against this virus due to its ability to induce immune response which leads to protection in challenge assays in IFN-gamma defective mice models.
ARTICLE | doi:10.20944/preprints201807.0164.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: PEM fuel cell; identification; genetic algorithm; model; LabVIEW
Online: 10 July 2018 (10:12:34 CEST)
PEM fuel cell is a technology successfully used in the production of energy from hydrogen, allowing the use of hydrogen as an energy vector. It is scalable for stationary and mobile applications. However, the technology demands more research. An important research topic is fault diagnosis and condition monitoring to improve the life and the efficiency and to reduce the operation costs of PEMFC devices. Consequently, there is a need of physical models that let deep analysis. These models must be accurate enough to represent the PEMFC behavior and to allow the identification of different internal signals of a PEM fuel cell. This work presents a PEM fuel cell model that uses the output temperature in a closed loop, so it can represent the thermal and the electrical behavior. The model is used to represent a NEXA Ballard 1.2 kW; therefore it is necessary to fit the coefficients to represent the real behavior. Five optimization algorithms were tested to fit the model, three of them were taken from literature and two were proposed. Finally, the model with the parameters identified was validated with real.
ARTICLE | doi:10.20944/preprints201805.0089.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: agrobiodiversity; vegetables; plant genetic resources; Italy; safeguarding; landraces
Online: 4 May 2018 (09:34:09 CEST)
The study attempts, above all, to provide a summary, with a strictly scientific basis, about the strategies of conservation of autochthonous agrobiodiversity followed in Italy. A special focus is dedicated on vegetables and, therefore, could represent a contribution to improve the national strategy for the safeguarding of its agrobiodiversity in general. The paper offers also an outlook on the most critical factors of the ex situ conservation and some actions which need to be taken. Some examples of ‘novel’ recovered neglected crops are also given. Finally a case study is proposed: ‘Mugnolicchio’, a neglected race of Brassica oleracea L., cultivated in Altamura (Ba) in southern Italy. ‘Mugnolicchio’ might be considered as an early step in the evolution of broccoli (B. oleracea L. var. italica Plenck) like ‘Mugnoli’ another neglected race described from Salento (Apulia).
ARTICLE | doi:10.20944/preprints201803.0199.v1
Subject: Engineering, Civil Engineering Keywords: Reservoir operation; SWAT; Genetic Algorithm; Urbanisation; Ganga River
Online: 23 March 2018 (15:07:22 CET)
Reservoirs are recognized as one of the most efficient infrastructure components in integrated water resources management and development. At present, with the ongoing advancement of social economy and requirement of water, the water resources shortage problem has worsened, and the operation of reservoirs, in terms of consumption of flood water, has become significantly important. Reservoirs perform both regulation of flood and integrated water resources management, in which the flood limited water level is considered as the most important parameter for trade-off between regulation of flood and conservation. To achieve optimal operating policies for reservoirs, large numbers of simulation and optimization models have been developed in the course of recent decades, which vary notably in their applications and working. Since each model has their own limitations, the determination of fitting model for derivation of reservoir operating policies is challenging and most often there is always a scope for further improvement as the selection of model depends on availability of data. Subsequently, assessment and evaluation associated with the operation of reservoir stays conventional. In the present study, the Soil and Water Assessment Tool (SWAT) models and a Genetic Algorithm model has been developed and applied to two reservoirs in Ganga River basin, India to derive the optimal operational policies. The objective function is set to minimize the annual sum of squared deviation form desired irrigation release and desired storage volume. The decision variables are release for irrigation and other demands (industrial and municipal demands), from the reservoir. As a result, a simulation-based optimization model was recommended for optimal reservoir operation, such as allocation of water, flood regulation, hydropower generation, irrigation demands and navigation and e-flows using a definite combination of decision variables. Since the rule curves are derived through random search it is found that the releases are same as that of demand requirements. Hence based on simulated result, in the present case study it is concluded that GA-derived policies are promising and competitive and can be effectively used operation of the reservoir.
ARTICLE | doi:10.20944/preprints201705.0109.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Turnip mosaic virus; Potyvirus; Genetic structure; Population; China
Online: 15 May 2017 (11:38:11 CEST)
Turnip mosaic virus (TuMV) is one of the most widespread and economically important virus infecting both crop and ornamental species of the family Brassicaceae. TuMV isolates can be classified to five phylogenetic lineages, basal-B, basal-BR, Asian-BR, world-B and Orchis. To understand the genetic structure of TuMV from radish in China, the 3′-terminal genome of 90 TuMV isolates were determined and analyzed with other Chinese isolates available. The results showed that the Chinese TuMV isolates from radish formed three groups: Asian-BR, basal-BR and world-B. More than half of these isolates (52.54%) were clustered to basal-BR group, and could be further divided into three sub-groups. The TuMV basal-BR isolates in the sub-groups I and II were genetically homologous with Japanese ones, while those in sub-group III formed a distinct lineage. Sub-populations of TuMV basal-BR II and III were new emergent and in a state of expansion. The Chinese TuMV radish populations were under negative selection. Gene flow between TuMV populations from Tai’an, Weifang and Changchun was frequent.
ARTICLE | doi:10.20944/preprints202309.1723.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Mango tree; SSR markers; mango varieties; genetic diversity; cultivar identification diagram, loci, polymorphism; genetic resources in Pakistan; breeding; cultivar development
Online: 26 September 2023 (03:48:00 CEST)
Assessment of the genetic distinctiveness of a cultivar through morphological descriptors is an important tool for both the registration and the protection. New mango genotypes have been improved using valuable diverse germplasm resources to ensure food security. DNA fingerprinting based simple sequence repeats (SSR)-markers have been the most broadly used, effective and accurate in evaluation of genetic characterization of a cultivar. Molecular breeding is an effective source of genetic gain after improvement of fruit trees using marker assisted genomic selection. Mango (Mangifera indica L.) is an allotetraploid (2n = 4X= 40) drupe fruit and has high nutritional value belongs to genus Mangifera and family Anacardiaceae. Mango cultivars are used with worldwide acceptance to pharmacological, ethnomedical, and phytochemical industries. This study investigated the molecular evaluation of a new mango cultivar ‘Azeem Chaunsa’ using a set of the most effective 50 hyper-variable polymorphic SSR markers. Highly specific DNA fingerprints were identified in the genome of this mango cultivar, ‘Azeem Chaunsa’ compared with three standard cultivars such as Sindhri, Samar Bahisht (S.B) Chaunsa and Sufaid Chaunsa. Our results showed that SSR markers could efficiently assess genetic diversity in mango. An agglomerative hierarchical clustering method was used to construct dendrogram based on the ‘Unweighted Pair- Group Method with Arithmetic Mean’ (UPGMA). The genetic similarity coefficients were recorded between the mangos cultivars ranged from 0.49 to 0.67. Cultivar identification (CID) evaluates association among standard cultivars and Azeem Chaunsa and further concludes significant variations. CID results concluded that cultivar ‘Azeem Chaunsa’ varied significantly from the check cultivar, Sindhri (46.2%), S.B Chaunsa (45%) and Sufaid Chaunsa (46.7%). The results obtained in this study will orient cultivar identification strategies for a successful future mango breeding programmes in the context of climate change.
REVIEW | doi:10.20944/preprints202305.0472.v1
Subject: Public Health And Healthcare, Health Policy And Services Keywords: diagnostic molecular pathology; genetic testing; diagnostic services; technology assess- ment; biomedical; genetic services; financial support; clinical governance; health technology; healthcare innovation
Online: 8 May 2023 (08:36:59 CEST)
1) Background: Genomic medicine harbors the real potential to improve the health and healthcare jour-ney of patients, care provider experiences, and improve health system efficiency – even reducing health care costs. There is expected to be an exponential growth in medically necessary new genome- based tests and test approaches in coming years. Testing can also create scientific research and commercial opportu-nities beyond healthcare decision-making. The purpose of this research is to generate a better under-standing of Canada’s state of readiness for genomic medicine, and to provide some insights for other healthcare systems; (2) Methods: a mixed-methodsapproach of literature review and key informant in-terviews with a purposive sample of experts was used. Health system readiness was assessed using a pre-viously published set of conditions. (3) Results: Canada has created some of the established conditions but more needs to be done to improve the state of readiness for genome-based medicine. Important gaps are the need for linked information systems and data integration; evaluative processes that are timely, and transparent; navigational tools for care providers; dedicated funding to facilitate rapid onboarding and supports test development and proficiency testing; and broader engagement with a broader set of inno-vation stakeholders. These findings highlight the known role of organizational context, social influence, and other factors that are known to affect the diffusion of innovation within health systems
REVIEW | doi:10.20944/preprints202309.2089.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: maize; global nutrition; macronutrients; biofortification; genetic modification; maize processing
Online: 29 September 2023 (10:15:15 CEST)
This chapter explores the pivotal role of maize (Zea mays L.) in global nutrition, emphasizing its status as a staple food worldwide. It discusses maize's complex nutritional profile, including macronutrients, micronutrients, and dietary fiber. The chapter also covers biofortification efforts to enhance maize with essential nutrients, addresses nutritional concerns related to maize-centric diets, and explores genetic modification and agronomic strategies to boost nutrient-rich maize yields. Additionally, it delves into maize processing traditions, nutrient retention techniques, and the importance of promoting nutrient-rich maize varieties. The chapter outlines post-harvest strategies to combat nutrient loss and prevent contamination while emphasizing the significance of consumer education and diverse diets. Case studies illustrate the impact of improved maize nutrition and provide replicable strategies. The chapter concludes by considering emerging research and technology, identifying challenges, and proposing solutions to enhance maize's nutritional value in the future.
REVIEW | doi:10.20944/preprints202309.1600.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Plastic degrading bacteria; sustainable environment; genetic enhancement; recycling; biodegradation
Online: 25 September 2023 (12:56:55 CEST)
The drastically increasing amount of plastic waste is causing an environmental crisis that requires innovative technologies for recycling post-consumer plastics to achieve waste valorization while meeting environmental quality goals. Biocatalytic depolymerization mediated by enzymes has emerged as an efficient and sustainable alternative for plastic treatment and recycling. A variety of plastic- degrading enzymes have been discovered from microbial sources. Meanwhile, protein engineering has been exploited to modify and optimize plastic-degrading enzymes. This review highlights the recent trends and up-to-date advances in mining novel plastic-degrading enzymes through state-of-the-art omics-based techniques and improving the enzyme catalytic efficiency and stability via various protein engineering strategies. Future research prospects and challenges are also discussed
ARTICLE | doi:10.20944/preprints202309.1515.v1
Subject: Engineering, Mechanical Engineering Keywords: composite material; laminates orientation; optimization; simulated annealing; genetic algorithm
Online: 22 September 2023 (09:07:46 CEST)
The present work sets out the evaluation of composite laminates through optimization objective functions. Genetic Algorithms (GA), as well as Simulated Annealing (SA), were performed in order to determine the optimal ply orientations of a fiber-reinforced polymer laminate for three given load cases: 1) in-plane loads, 2) combined moments, and 3) in-plane loads and combined moments. It searches the optimal orientation layup, which fulfills at the same time both the maximum strain criterion and the Tsai-Wu failure criterion. Construction of an objective function based on the strains and the stresses involves a minimization process to deformations and a maximization of the safety factor. For the first load case, the initial solution is [±45/0/90/±45]s, and the best solution is [(45/135)2/452]s. For the second load case, [-45/45/45/-45/0/90]s is the initial layup sequence, then the best solution obtained is [(45/-45)2/452]s, where plies at 0° and 90º are not necessary even when axial loads are applied. For the third study case, the original layup sequence is [0/45/-45/45/0/90]s; meanwhile, the best solution calculated is [21/24/145/140/45/49]s. An interesting observation is that each pair of layers has a 5º gap. The simulations show that the qualitative results from the GA are better than the SA, but with a significantly higher computational cost. These kinds of computational tools are expected to be used as a reference guide for an optimal fiber configuration with respect to the common orientations used when composite laminates are designed for a structural application.
ARTICLE | doi:10.20944/preprints202309.0826.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: proso millet collection; genetic diversity; SSR markers; agronomic traits
Online: 13 September 2023 (10:37:54 CEST)
Proso millet is an important allotetraploid cereal crop, however, it is the least studied species of the Poaceae family as it is an under-utilized crop. Genomic resources of proso millet are very limited compared to the major crops. Understanding of genetic relationships among germplasm resources is important for future breeding endeavors. In the present study, the SSR markers were employed to assess the polymorphism and genetic diversity of 100 millet accessions from different countries, which were tested in the dry steppe zone conditions of the Akmola region from 2020 to 2022. The use of 20 SSR markers detected a total of 47 alleles with an average allele number of 2.35 per locus among these proso accessions. Nine of them were polymorphic among genotypes, which suggests that these SSR markers can be used for genetic studies. The results showed a moderate level of polymorphism information content (PIC) averaged at 0.424, ranging from 0.125 to 0.795. The markers SSR 67, SSR-82, SSR-85 and SSR-109 showed high PIC values, 0.536, 0.756, 0.795 and 0.758 respectively. Markers SSR 85 and SSR 86 significantly correlated to agronomic traits, such as productive tillering (PT) and grain yield (GY). The genetic structure, UPGMA cluster and PCoA assay indicated that the accessions originated from Central Asia had higher genetic diversity. Based on Structure (K=3), all the accessions were divided into three groups, whereas the gene pool originated from Central Asia were detected in all the three clusters. Based on principal component analysis (PCA), the accessions of Central Asian origin were genetically closer to the North Asian group.
REVIEW | doi:10.20944/preprints202309.0496.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: plant genetic resources; population genomics; crop evolution; food legumes
Online: 7 September 2023 (09:23:38 CEST)
Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA (aDNA) from historical or long-dead organisms to reconstruct and analyze their genomes. The aDNA is commonly obtained from remains found in paleontological and archaeological sites, conserved in museums and in other archival collections. Herbarium collections represent a great source of phenotypic and genotypic information, and their exploitation allowed to infer and to clarify previously unsolved taxonomic and systematic relationships. Moreover, Herbarium specimens offered a new source to study phenological traits in plants and to disentangle biogeography and evolutionary scenarios of species. More recently, advances in the molecular technologies went in parallel with the decreasing costs of the next-generation sequencing (NGS) approaches, that paved the way to the utilization of aDNA for whole-genome studies. Although many studies have been carried out combining modern analytic techniques and Herbarium specimens, this research field is still relatively unexplored, due to the need of improving strategies for aDNA manipulation and exploitation. The higher susceptibility of aDNA to degradation and contamination during the Herbarium conservation and manipulation, and the occurrence of biochemical post-mortem damages, can result in the more challenging reconstruction of the original DNA sequence. Here, we review the methodological approaches that have been developed for the exploitation of historical Herbarium plant materials, such as the best practices for aDNA extraction, amplification and genotyping. We also focus on some strategies to overcome the main problems related to the utilization of Herbarium specimens for their exploitation in plant evolutionary studies.
REVIEW | doi:10.20944/preprints202309.0297.v1
Subject: Biology And Life Sciences, Virology Keywords: influenza A virus; virulence; genetic fitness; disease transmission; review
Online: 6 September 2023 (03:12:41 CEST)
Influenza A (IAV) is a major human respiratory pathogen, causing illness, hospitalizations, and mortality annually worldwide. IAV is also a zoonotic pathogen with a multitude of hosts, allowing for interspecies transmission, reassortment events, and the emergence of novel pandemics, as was seen in 2009 with the emergence of a swine origin H1N1 (pdmH1N1) virus into humans, causing the first influenza pandemic of the 21st century. While the 2009 pandemic was considered to have high morbidity and low mortality, studies have linked the pdmH1N1 virus and its gene segments to increased disease in humans and animal models. Genetic components of the pdmH1N1 virus currently circulate in the swine population, reassorting with endemic swine viruses that co-circulate and occasionally spillover into humans. This is evidenced by the regular detection of variant swine IAVs in humans associated with state fairs and other intersections of humans and swine. Defining genetic changes that support species adaptation, virulence, and cross-species transmission, as well as mutations that enhance or attenuate these features will improve our understanding of influenza biology, aid in surveillance and virus risk assessment, and guide the establishment of counter measures for emerging viruses. Here, we review current understanding of determinants of specific IAV phenotypes, focusing on the fitness, transmission, and virulence determinants that have been identified in swine IAVs and/or in relation to the 2009 pdmH1N1 virus.