Search results for: population genetics

Authors: Junghwa An, Sungkyoung Choi, Eun Ye, San Hoon Han, Young-Gun Choi, Chul Oun Jung

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The copper-winged bat (Myotis rufoniger) is the widely distributed medium body-sized bat in Asia, including Korea. This bat population has been decreasing because of habitat loss. This study reported the isolation and characterization of ten polymorphic microsatellite loci in endangered M. rufoniger. To do genetic studies, we use saliva DNA of bats during winter sleep period. The number of alleles per locus ranged from 2 to 9, and the observed and expected heterozygosities ranged from 0.063 to 0.750 and from 0.063 to 0.865, respectively. The average polymorphic information content (PIC) value of these markers was 0.37. Two loci of M. rufoniger showed departure from Hardy-Weinberg equilibrium(HWE). This demonstrated that the ten microsatellite loci can be used as genetic markers for further investigation of the copper-winged bat.

Keywords: copper-winged bat, microsatellite, population genetics, South Korea

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Authors: Wesley H. Brewer, John C. Sanford

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SciPaaS is a prototype development of an execution platform/middleware designed to make it easy for scientists to rapidly deploy their scientific applications (apps) to the cloud. It provides all the necessary infrastructure for running typical IXP (Input-eXecute-Plot) style apps, including: a web interface, post-processing and plotting capabilities, job scheduling, real-time monitoring of running jobs, and even a file/case manager. In this paper, first the system architecture is described and then is demonstrated for a two scientific applications: (1) a simple finite-difference solver of the inviscid Burger’s equation, and (2) Mendel’s Accountant—a forward-time population genetics simulation model. The implications of the prototype are discussed in terms of ease-of-use and deployment options, especially in cloud environments.

Keywords: web-based simulation, cloud computing, Platform-as-a-Service (PaaS), rapid application development (RAD), population genetics

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Authors: Salma M. Wakil

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Advances in the field of genetics overwhelmed detecting large number of inherited disorders at the molecular level and directed to the development of innovative technologies. These innovations have led to gene sequencing, prenatal mutation detection, pre-implantation genetic diagnosis; population based carrier screening and genome wide analyses using microarrays. Microarrays are widely used in establishing clinical and diagnostic setup for genetic anomalies at a massive level, with the advent of cytoscan molecular karyotyping as a clinical utility card for detecting chromosomal aberrations with high coverage across the entire human genome. Unlike a regular karyotype that relies on the microscopic inspection of chromosomes, molecular karyotyping with cytoscan constructs virtual chromosomes based on the copy number analysis of DNA which improves its resolution by 100-fold. We have been investigating a large number of patients with Developmental Delay and Intellectual disability with this platform for establishing micro syndrome deletions and have detected number of novel CNV’s in the Arabian population with the clinical relevance.

Keywords: microarrays, molecular karyotyping, developmental delay, genetics

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

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Enzyme restriction site associated DNA (EzRAD) has recently emerged as a promising genomic approach for exploring fish genetic diversity on a genome-wide scale. This is a simplified method for genomic genotyping in non-model organisms and applied for SNPs discovery in the population genetics of freshwater and marine fish in the South of Vietnam. The observations of regional-scale differentiation of commercial freshwater fish (smallscale croakers Boesemania microlepis) and marine fish (emperor Lethrinus lentjan) are clarified. Samples were collected along Hau River and coastal area in the south and center Vietnam. 52 DNA samples from Tra Vinh, An Giang Province for Boesemania microlepis and 34 DNA samples of Lethrinus lentjan from Phu Quoc, Nha Trang, Da Nang Province were used to prepare EzRAD libraries from genomic DNA digested with MboI and Sau3AI. A pooled sample of regional EzRAD libraries was sequenced using the HiSeq 2500 Illumina platform. For Boesemania microlepis, the small scale population different from upstream to downstream of Hau river were detected, An Giang population exhibited less genetic diversity (SNPs per individual from 14 to 926), in comparison to Tra Vinh population (from 11 to 2172). For Lethrinus lentjan, the result showed the minor difference between populations in the Northern and the Southern Mekong River. The numbers of contigs and SNPs vary from 1315 to 2455 and from 7122 to 8594, respectively (P ≤ 0.01). The current preliminary study reveals regional scale population disconnection probably reflecting environmental changing. Additional sampling and EzRad libraries need to be implemented for resource management in the Mekong Delta.

Keywords: Boesemania microlepis, EzRAD, Lethrinus lentjan, SNPs

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Authors: Masoud Sheidai

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Biologists with a special field of population genetics and phylogeny have different research tasks such as populations’ genetic variability and divergence, species relatedness, the evolution of genetic and morphological characters, and identification of DNA SNPs with adaptive potential. To tackle these problems and reach a concise conclusion, they must use the proper and efficient statistical and bioinformatic methods as well as suitable genetic and morphological characteristics. In recent years application of different bioinformatic and statistical methods, which are based on various well-documented assumptions, are the proper analytical tools in the hands of researchers. The species delineation is usually carried out with the use of different clustering methods like K-means clustering based on proper distance measures according to the studied features of organisms. A well-defined species are assumed to be separated from the other taxa by molecular barcodes. The species relationships are studied by using molecular markers, which are analyzed by different analytical methods like multidimensional scaling (MDS) and principal coordinate analysis (PCoA). The species population structuring and genetic divergence are usually investigated by PCoA and PCA methods and a network diagram. These are based on bootstrapping of data. The Association of different genes and DNA sequences to ecological and geographical variables is determined by LFMM (Latent factor mixed model) and redundancy analysis (RDA), which are based on Bayesian and distance methods. Molecular and morphological differentiating characters in the studied species may be identified by linear discriminant analysis (DA) and discriminant analysis of principal components (DAPC). We shall illustrate these methods and related conclusions by giving examples from different edible and medicinal plant species.

Keywords: GWAS analysis, K-Means clustering, LFMM, multidimensional scaling, redundancy analysis

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Authors: Masoud Sheidaei, Mohammad-Reza Kordasti, Fahimeh Koohdar

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Calotropis procera (Aiton) W.T.Aiton, (Apocynaceae), is an economically and medicinally important plant species which is an evergreen, perennial shrub growing in arid and semi-arid climates, and can tolerate very low annual rainfall (150 mm) and a dry season. The plant can also tolerate temperature ran off 20 to30°C and is not frost tolerant. This plant species prefers free-draining sandy soils but can grow also in alkaline and saline soils.It is found at a range of altitudes from exposed coastal sites to medium elevations up to 1300 m. Due to morpho-physiological adaptations of C. procera and its ability to tolerate various abiotic stresses. This taxa can compete with desirable pasture species and forms dense thickets that interfere with stock management, particularly mustering activities. Caloteropis procera grows only in southern part of Iran where in comprises a limited number of geographical populations. We used different population genetics and r landscape analysis to produce data on geographical populations of C. procera based on molecular genetic study using SCoT molecular markers. First, we used spatial principal components (sPCA), as it can analyze data in a reduced space and can be used for co-dominant markers as well as presence / absence data as is the case in SCoT molecular markers. This method also carries out Moran I and Mantel tests to reveal spatial autocorrelation and test for the occurrence of Isolation by distance (IBD). We also performed Random Forest analysis to identify the importance of spatial and geographical variables on genetic diversity. Moreover, we used both RDA (Redundency analysis), and LFMM (Latent factor mixed model), to identify the genetic loci significantly associated with geographical variables. A niche modellng analysis was carried our to predict present potential area for distribution of these plants and also the area present by the year 2050. The results obtained will be discussed in this paper.

Keywords: population genetics, landscape genetic, Calotreropis procera, niche modeling, SCoT markers

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Authors: Jinu Phonamontham

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Coronavirus, also referred to as COVID-19, is a virus caused by the SARS-Cov-2 virus. The pandemic has caused over 10 million cases and 500,000 deaths worldwide through the end of June 2020. In a previous study, HLA-DQA1*01:02 allele was associated with COVID-19 disease (p-value = 0.0121). Furthermore, there was a statistical significance between HLA- DQB1*06:02 and COVID-19 in the Italian population by Bonferroni’s correction (p-value = 0.0016). Nevertheless, there is no data describing the distribution of HLA alleles as a valid marker for prediction of COVID-19 in the Thai population. We want to investigate the prevalence of HLA-DQA1*01:02 and HLA-DQB1*06:02 alleles that are associated with severe COVID-19 in the Thai population. In this study, we recruited 200 healthy Thai individuals. Genomic DNA samples were isolated from EDTA blood using Genomic DNA Mini Kit. HLA genotyping was conducted using the Lifecodes HLA SSO typing kits (Immucor, West Avenue, Stamford, USA). The frequency of HLA-DQA1 alleles in Thai population, consisting of HLA-DQA1*01:01 (27.75%), HLA-DQA1*01:02 (24.50%), HLA-DQA1*03:03 (13.00%), HLA-DQA1*06:01 (10.25%) and HLA-DQA1*02:01 (6.75%). Furthermore, the distributions of HLA-DQB1 alleles were HLA-DQB1*05:02 (21.50%), HLA-DQB1*03:01 (15.75%), HLA-DQB1*05:01 (14.50%), HLA-DQB1*03:03 (11.00%) and HLA-DQB1*02:02 (8.25%). Particularly, HLA- DQA1*01:02 (29.00%) allele was the highest frequency in the NorthEast group, but there was not significant difference when compared with the other regions in Thais (p-value = 0.4202). HLA-DQB1*06:02 allele was similarly distributed in Thai population and there was no significant difference between Thais and China (3.8%) and South Korea (6.4%) and Japan (8.2%) with p-value > 0.05. Whereas, South Africa (15.7%) has a significance with Thais by p-value of 0.0013. This study supports the specific genotyping of the HLA-DQA1*01:02 and HLA-DQB1*06:02 alleles to screen severe COVID-19 in Thai and many populations.

Keywords: HLA-DQA1*01:02, HLA-DQB1*06:02, Asian, Thai population

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Authors: Mohamed Thani Ibouroi, Ali Cheha, Claudine Montgelard, Veronique Arnal, Dawiyat Massoudi, Guillelme Astruc, Said Ali Ousseni Dhurham, Aurelien Besnard

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The Livingstone's flying fox (Pteropus livingstonii) and the Comorian fruit bat (P.seychellensis comorensis) are two endemic fruit bat species among the mostly threatened animals of the Comoros archipelagos. Despite their role as important ecosystem service providers like all flying fox species as pollinators and seed dispersers, little is known about their ecologies, population genetics and structures making difficult the development of evidence-based conservation strategies. In this study, we assess spatial distribution and ecological niche of both species using Species Distribution Modeling (SDM) based on the recent Ensemble of Small Models (ESMs) approach using presence-only data. Population structure and genetic diversity of the two species were assessed using both mitochondrial and microsatellite markers based on non-invasive genetic samples. Our ESMs highlight a clear niche partitioning of the two sympatric species. Livingstone’s flying fox has a very limited distribution, restricted on steep slope of natural forests at high elevation. On the contrary, the Comorian fruit bat has a relatively large geographic range spread over low elevations in farmlands and villages. Our genetic analysis shows a low genetic diversity for both fruit bats species. They also show that the Livingstone’s flying fox population of the two islands were genetically isolated while no evidence of genetic differentiation was detected for the Comorian fruit bats between islands. Our results support the idea that natural habitat loss, especially the natural forest loss and fragmentation are the important factors impacting the distribution of the Livingstone’s flying fox by limiting its foraging area and reducing its potential roosting sites. On the contrary, the Comorian fruit bats seem to be favored by human activities probably because its diets are less specialized. By this study, we concluded that the Livingstone’s flying fox species and its habitat are of high priority in term of conservation at the Comoros archipelagos scale.

Keywords: Comoros islands, ecological niche, habitat loss, population genetics, fruit bats, conservation biology

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Authors: Abubakar Sadiq Mensah

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The Knowledge of the population growth of a nation is paramount to national planning. The population of a place is studied and a model developed over a period of time, Matrices is used to form model for population growth. The eigenvalue ƛ of the matrix A and its corresponding eigenvector X is such that AX = ƛX is calculated. The stable age distribution of the population is obtained using the eigenvalue and the characteristic polynomial. Hence, estimation could be made using eigenvalues and eigenvectors.

Keywords: eigenvalues, eigenvectors, population, growth/stability

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Authors: Sammy Kibor, Filip Huyghe, Marc Kochzius, James Kairo

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Goldstripe Sardinella, Sardinella gibbosa, (Bleeker, 1849) is a commercially and ecologically important small pelagic fish common in the Western Indian Ocean region. The present study aimed to assess genetic diversity and population structure of the species in the Kenya-Tanzania transboundary area using mtDNA and msDNA markers. Some 630 bp sequence in the mitochondrial DNA (mtDNA) Cytochrome C Oxidase I (COI) and five polymorphic microsatellite DNA loci were analyzed. Fin clips of 309 individuals from eight locations within the transboundary area were collected between July and December 2018. The S. gibbosa individuals from the different locations were distinguishable from one another based on the mtDNA variation, as demonstrated with a neighbor-joining tree and minimum spanning network analysis. None of the identified 22 haplotypes were shared between Kenya and Tanzania. Gene diversity per locus was relatively high (0.271-0.751), highest Fis was 0.391. The structure analysis, discriminant analysis of Principal component (DAPC) and the pair-wise (FST = 0.136 P < 0.001) values after Bonferroni correction using five microsatellite loci provided clear inference on genetic differentiation and thus evidence of population structure of S. gibbosa along the Kenya-Tanzania coast. This study shows a high level of genetic diversity and the presence of population structure (Φst =0.078 P < 0.001) resulting to the existence of four populations giving a clear indication of minimum gene flow among the population. This information has application in the designing of marine protected areas, an important tool for marine conservation.

Keywords: marine connectivity, microsatellites, population genetics, transboundary

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Authors: Sheena K. J., Jyoti Badge, Sayed Mohammed Zeeshan

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A Comparative Study of Exponential and Logistic Population Growth Models in India India is the second most populous city in the world, just behind China, and is going to be in the first place by next year. The Indian population has remarkably at higher rate than the other countries from the past 20 years. There were many scientists and demographers who has formulated various models of population growth in order to study and predict the future population. Some of the models are Fibonacci population growth model, Exponential growth model, Logistic growth model, Lotka-Volterra model, etc. These models have been effective in the past to an extent in predicting the population. However, it is essential to have a detailed comparative study between the population models to come out with a more accurate one. Having said that, this research study helps to analyze and compare the two population models under consideration - exponential and logistic growth models, thereby identifying the most effective one. Using the census data of 2011, the approximate population for 2016 to 2031 are calculated for 20 Indian states using both the models, compared and recorded the data with the actual population. On comparing the results of both models, it is found that logistic population model is more accurate than the exponential model, and using this model, we can predict the future population in a more effective way. This will give an insight to the researchers about the effective models of population and how effective these population models are in predicting the future population.

Keywords: population growth, population models, exponential model, logistic model, fibonacci model, lotka-volterra model, future population prediction, demographers

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Authors: Aisling De Paor

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

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

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Authors: Masoud Sheidaei, Melica Tabasi, Fahimeh Koohdar, Mona Sheidaei

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Juglans regia L. is an economically important species of edible nuts. Iran is known as a center of origin of genetically rich walnut germplasm and expected to be found a large diversity within Iranian walnut populations. A detailed population genetic of local populations is useful for developing an optimal strategy for in situ conservation and can assist the breeders in crop improvement programs. Different phylogenetic studies have been carried out in this genus, but none has been concerned with genetic changes associated with geographical divergence and the identification of adaptive SNPs. Therefore, we carried out the present study to identify discriminating ITS nucleotides among Juglans species and also reveal association between ITS SNPs and geographical variables. We used different computations approaches like DAPC, CCA, and RDA analyses for the above-mentioned tasks. We also performed population genetics analyses for population effective size changes associated with the species expansion. The results obtained suggest that latitudinal distribution has a more profound effect on the species genetic changes. Similarly, multiple analytical approaches utilized for the identification of both discriminating DNA nucleotides/ SNPs almost produced congruent results. The SNPs with different phylogenetic importance were also identified by using a parsimony approach.

Keywords: Persian walnut, adaptive SNPs, data analyses, genetic diversity

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Authors: Luz Estrada

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The currents of evolutionary materialistic thought have argued that knowledge about an object is not obtained through the abstractive method. That is, the object cannot come to be understood if founded upon itself, nor does it take place by the encounter between form and matter. According to this affirmation, the research presented here identified as a problematic situation the absence of comprehension of the formal creation as a generative operation. This has been referred to as a recurrent lack in the production of objects and corresponds to the need to conceive the configurative process from the reality of its genesis. In this case, it is of interest to explore ways of creation that consider the object as if it were a living organism, as well as responding to the object’s experience as embodied in the designer since it unfolds its genesis simultaneously to the ways of existence of those who are involved in the generative experience.

Keywords: architecture, theoretical graphics, evolutionary genetics, formal perception

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Authors: Anthony F. Peressini

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The concept of race has recently come prominently back into discussion in the context of medicine and medical science, along with renewed effort to biologize racial concepts. This paper argues that this renewed effort to biologize race by way of medicine and population genetics fail on their own terms, and more importantly, that the philosophical project of biologizing race ought to be recognized for what it is—a retrograde racial project—and abandoned. There is clear agreement that standard racial categories and concepts cannot be grounded in the old way of racial naturalism, which understand race as a real, interest-independent biological/metaphysical category in which its members share “physical, moral, intellectual, and cultural characteristics.” But equally clear is the very real and pervasive presence of racial concepts in individual and collective consciousness and behavior, and so it remains a pressing area in which to seek deeper understanding. Recent philosophical work has endeavored to reconcile these two observations by developing a “thin” conception of race, grounded in scientific concepts but without the moral and metaphysical content. Such “thin,” science-based analyses take the “commonsense” or “folk” sense of race as it functions in contemporary society as the starting point for their philosophic-scientific projects to biologize racial concepts. A “philosophic-scientific analysis” is a special case of the cornerstone of analytic philosophy: a conceptual analysis. That is, a rendering of a concept into the more perspicuous concepts that constitute it. Thus a philosophic-scientific account of a concept is an attempt to work out an analysis of a concept that makes use of empirical science's insights to ground, legitimate and explicate the target concept in terms of clearer concepts informed by empirical results. The focus in this paper is on three recent philosophic-scientific cases for retaining “race” that all share this general analytic schema, but that make use of “medical necessity,” population genetics, and human genetic clustering, respectively. After arguing that each of these three approaches suffers from internal difficulties, the paper considers the general analytic schema employed by such biologizations of race. While such endeavors are inevitably prefaced with the disclaimer that the theory to follow is non-essentialist and non-racialist, the case will be made that such efforts are not neutral scientific or philosophical projects but rather are what sociologists call a racial project, that is, one of many competing efforts that conjoin a representation of what race means to specific efforts to determine social and institutional arrangements of power, resources, authority, etc. Accordingly, philosophic-scientific biologizations of race, since they begin from and condition their analyses on “folk” conceptions, cannot pretend to be “prior to” other disciplinary insights, nor to transcend the social-political dynamics involved in formulating theories of race. As a result, such traditional philosophical efforts can be seen to be disciplinarily parochial and to address only a caricature of a large and important human problem—and thereby further contributing to the unfortunate isolation of philosophical thinking about race from other disciplines.

Keywords: population genetics, ontology of race, race-based medicine, racial formation theory, racial projects, racism, social construction

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Authors: Pager Mansaram Pandit

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The present paper aims to changing trends of population in Nashik district. The spatial variation of changing trends of population from 1901 to 2011. Nasik, lying between 19° 33’ and 20° 53’ north latitude and 73° 16’ and 75° 16’, with an area of 15530 Sq. K.M.North South length is 120 km. East West length is 200 km. Nashik has a population of 6,109,052 of which 3,164,261 are males and 2,944,791 and females. Average literacy rate of Nashik district in 2011 was 82.91 compared to 80.96 in 2001. In 1901 the density was 52 and in 2011 the density was 393 per sq. km. The progressive growth rate from 1901 to 2012 was 11.25 to 642.22 percent, respectively. The population trend is calculated with the help of time series. In 1901 population was 45.44% more and less in 1941 i.e. -13.86. From 1921 to 1981 the population was below the population trend but after 1991 population it gradually increased. The average rainfall it receives is 1034 mm. In the present times, because of advances in good climate, industrialization, development of road, University level educational facilities, religious importance, cargo services, good quality of grapes, pomegranates and onions, more and more people are being attracted towards Nashik districts. Another cause for the increase in the population is the main attraction of Ramkund, Muktidham Temple, Kalaram Temple, Coin Museum, and Trimbakeshwar.

Keywords: density, growth, population, population trend

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Authors: Nadzeya Marozkina, Joe Zein, Benjamin Gaston

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Introduction: We have observed that many patients with Primary Ciliary Dyskinesia (PCD) benefit from asthma medications. In healthy airways, the ciliary function is normal. Antigens and irritants are rapidly cleared, and NO enters the gas phase normally to be exhaled. In the PCD airways, however, antigens, such as Dermatophagoides, are not as well cleared. This defect leads to oxidative stress, marked by increased DUOX1 expression and decreased superoxide dismutase [SOD] activity (manuscript under revision). H₂O₂, in high concentrations in the PCD airway, injures the airway. NO is oxidized rather than being exhaled, forming cytotoxic peroxynitrous acid. Thus, antigen stasis on PCD airway epithelium leads to airway injury and may predispose PCD patients to asthma. Indeed, recent population genetics suggest that PCD genes may be associated with asthma. We therefore hypothesized that PCD patients would be predisposed to having asthma. Methods. We analyzed our database of 18 million individual electronic medical records (EMRs) in the Indiana Network for Patient Care research database (INPCR). There is not an ICD10 code for PCD itself; code Q34.8 is most commonly used clinically. To validate analysis of this code, we queried patients who had an ICD10 code for both bronchiectasis and situs inversus totalis in INPCR. We also studied a validation cohort using the IBM Explorys® database (over 80 million individuals). Analyses were adjusted for age, sex and race using a 1 PCD: 3 controls matching method in INPCR and multivariable logistic regression in the IBM Explorys® database. Results. The prevalence of asthma ICD10 codes in subjects with a code Q34.8 was 67% vs 19% in controls (P < 0.0001) (Regenstrief Institute). Similarly, in IBM*Explorys, the OR [95% CI] for having asthma if a patient also had ICD10 code 34.8, relative to controls, was =4.04 [3.99; 4.09]. For situs inversus alone the OR [95% CI] was 4.42 [4.14; 4.71]; and bronchiectasis alone the OR [95% CI] =10.68 (10.56; 10.79). For both bronchiectasis and situs inversus together, the OR [95% CI] =28.80 (23.17; 35.81). Conclusions: PCD causes antigen stasis in the human airway (under review), likely predisposing to asthma in addition to oxidative and nitrosative stress and to airway injury. Here, we show that, by several different population-based metrics, and using two large databases, patients with PCD appear to have between a three- and 28-fold increased risk of having asthma. These data suggest that additional studies should be undertaken to understand the role of ciliary dysfunction in the pathogenesis and genetics of asthma. Decreased antigen clearance caused by ciliary dysfunction may be a risk factor for asthma development.

Keywords: antigen, PCD, asthma, nitric oxide

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Authors: M. Sakthivel, A. Devaki, D. Balasubramanyam, P. Kumarasamy, A. Raja, R. Anilkumar, H. Gopi

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The New Zealand White breed of rabbit is one of the most commonly used, well adapted exotic breeds in India. Earlier studies were limited only to analyze the environmental factors affecting the growth and reproductive performance. In the present study, the population of the New Zealand White rabbits in a closed herd was evaluated for its genetic structure. Data on pedigree information (n=2508) for 18 years (1995-2012) were utilized for the study. Pedigree analysis and the estimates of population genetic parameters based on gene origin probabilities were performed using the software program ENDOG (version 4.8). The analysis revealed that the mean values of generation interval, coefficients of inbreeding and equivalent inbreeding were 1.489 years, 13.233 percent and 17.585 percent, respectively. The proportion of population inbred was 100 percent. The estimated mean values of average relatedness and the individual increase in inbreeding were 22.727 and 3.004 percent, respectively. The percent increase in inbreeding over generations was 1.94, 3.06 and 3.98 estimated through maximum generations, equivalent generations, and complete generations, respectively. The number of ancestors contributing the most of 50% genes (fₐ₅₀) to the gene pool of reference population was 4 which might have led to the reduction in genetic variability and increased amount of inbreeding. The extent of genetic bottleneck assessed by calculating the effective number of founders (fₑ) and the effective number of ancestors (fₐ), as expressed by the fₑ/fₐ ratio was 1.1 which is indicative of the absence of stringent bottlenecks. Up to 5th generation, 71.29 percent pedigree was complete reflecting the well-maintained pedigree records. The maximum known generations were 15 with an average of 7.9 and the average equivalent generations traced were 5.6 indicating of a fairly good depth in pedigree. The realized effective population size was 14.93 which is very critical, and with the increasing trend of inbreeding, the situation has been assessed to be worse in future. The proportion of animals with the genetic conservation index (GCI) greater than 9 was 39.10 percent which can be used as a scale to use such animals with higher GCI to maintain balanced contribution from the founders. From the study, it was evident that the herd was completely inbred with very high inbreeding coefficient and the effective population size was critical. Recommendations were made to reduce the probability of deleterious effects of inbreeding and to improve the genetic variability in the herd. The present study can help in carrying out similar studies to meet the demand for animal protein in developing countries.

Keywords: effective population size, genetic structure, pedigree analysis, rabbit genetics

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Authors: Marsudi, Noor Hidayat, Ratno Bagus Edy Wibowo

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This paper considers a deterministic model for the transmission dynamics of HIV/AIDS in which condom campaign and treatment are both important for the disease management. In modelling of the spread of AIDS, the population is divided into six subpopulations, namely susceptible population, susceptible population who change their behavior due to education condom campaign, infected population, pre-AIDS population, treated population and full-blown AIDS population. We calculate the effective reproduction number using the next generation matrix method and investigate the existence and stability of the equilibrium points. A sensitivity analysis discovers parameters that have a high impact on effective reproduction number and should be targeted by intervention strategies. Numerical simulations are given to illustrate and verify our analytic results.

Keywords: HIV/AIDS, condom campaign, antiretroviral treatment, effective reproduction number, stability and sensitivity analysis

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Authors: Siriniya Siribrahmanakul

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Introduction:SARsCOVID-19 is rapidly spreading, and some people may exhibit severe symptoms. Mortality rate of 2.0–3.0% with COVID-19 infection atworldwide. Human leukocyte antigen (HLA), located on chromosome 6, consist of HLA class I and class II. HLA are used by the immune system to attach self-antigens. Previous studies, HLA-DRB1*01:01,HLA-DRB1*12:01and HLA-DRB1*14:04 were, showed significant difference with severe COVID-19 in the Chinese population by p-value < 0.05. Objective: We investigated the prevalence of HLA-DRB1 alleles associated with severe COVID-19 in Thai population. Materials and Methods:200 DNA samples were isolated from EDTA blood using the MagNAprue Compact Nucleic Acid Isolation kits.HLA-DRB1alleles were genotyped using sequence-specific oligonucleotides (PCR-SSOs). Results:The frequency of HLA-DRB1 alleles in Thai population wereHLA-DRB1*12:02 (15.75%), HLA-DRB1*15:02 (14.50%), HLA-DRB1*09:01 (11.50%), HLA-DRB1*07:01 (9.50%), HLA-DRB1*03:01,HLA-DRB1*05:01 (5.75%), HLA-DRB1*14:01 (5.50%), HLA-DRB1*16:02 (4.50%), HLA-DRB1*04:05 (4.00%), HLA-DRB1*14:03 (3.25%), HLA-DRB1*10:01 (2.25%) and HLA-DRB1*13:02 (2.00%). Particularly, HLA-DRB1*12:02 allele was the highest allele frequency presented in the four regions groups of Thai population. Furthermore, the HLA-DRB1* alleles associated with severe COVID-19, which consists ofHLA-DRB1*14:04(2.00 %) and HLA-DRB1*12:01(0.50%) in Thai population, whereas HLA-DRB1*01:01 allele was not found in this population. HLA-DRB1*14:04 and HLA-DRB1*12:01alleles were similarly distributed in four regions populations in Thailand (p-value > 0.05). The alleles frequencies of HLA-DRB1*14:04 and HLA-DRB1*12:01, which associated with severe COVID-19, had no significant differences between Thai population, South China population, South Africa population, and South Koreapopulation (p-value > 0.05). Conclusions: Particularly, this study has focused on allele frequency of HLA-DRB1*14:04in a healthy Thai population to evaluating their impact on the severe COVID-19. Furthermore, our research needs to be done in larger numbers of Thai patients.

Keywords: HLA-DRB1, allele frequency, Thai population, COVID-19 marker

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Authors: Jarmila Bernasovska, Pavel Ružbarský, Ivan Bernasovsky, Regina Lohajová Behulová

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The paper presents the results of the application of molecular genetics methods in sport research, with special emphasis on the most advanced methods and trends in diagnosing of motoric predispositions for the sake of identifying talented children. Genetic tests differ in principle from the traditional motoric tests, because the DNA of an individual does not change during life. Genetics is important in determining the capacity of an individual and for professional sport level. Genetic information can be used for individual genetic predispositions in early childhood. The phenotypes are influenced by a combination of genetic and environmental factors. The aim of the presented study was to examine physical condition, coordination skills, motoric docility and to determine the frequency of ACTN3 (R577X) gene in Romany children from Eastern Slovakia and compared their motoric performance with non-Romany children. This paper is not looking just for a performance, but also its association to genetic predispositions in relation to ACTN3 gene and its R577X polymorphism. Genotype data were obtained from 175 Romany children from 6 to 15 years old and 218 non-Romany children at the same age from Eastern Slovakia. Biological material for genetic analyses comprised samples of buccal swabs. Genotypes were determined using Real Time High resolution melting PCR method (Rotor Gene 6000 Corbett and LightCycler 480 Roche). Romany children of analyzed group legged to non-Romany children at the same age in all the compared tests. The % distribution of R and X alleles in children was different from controls. The frequency of XX genotype was 11,45% which is comparable to a frequency of an Indian population. Data were analysed with the ANOVA statistical programme and parametric and nonparametric tests. This work was supported by grants APVV-0716-10, ITMS 26220120023 and ITMS 26220120041.

Keywords: ACTN3 gene, R577X polymorphism, Romany children, sport performance, Slovakia

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Authors: Evelyn Nwamaka Ogbeide-Osaretin, Bright Orhewere

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This study examined the role of the population in the linkage between energy consumption and economic development in Nigeria. Time series data on energy consumption, population, and economic development were used for the period 1995 to 2020. The Autoregressive Distributed Lag -Error Correction Model (ARDL-ECM) was engaged. Economic development had a negative substantial impact on energy consumption in the long run. Population growth had a positive significant effect on energy consumption. Government expenditure was also found to impact the level of energy consumption, while energy consumption is not a function of oil price in Nigeria.

Keywords: dynamic analysis, energy consumption, population, economic development, Nigeria

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Authors: Maimuna Nontji

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The life cycle of rice plant has three phases of growth; they are the vegetative, reproductive and maturation phase. They greatly affect the life of dynamics metanotrof bacterial as reducer methane emissions in the rice field, both of population and on the rate of growth. The aim of this study was to analyze the population and growth rate of methanotrof isolates which has been isolated in previous studies. Isolates were taken at all the life cycle of rice plant. Population of analysis was conducted by standard plate count method and growth rate was analysed by logarithmic calculation. The results showed that each isolate varied in population and growth rate. The highest population was obtained in the isolates Gowa Methanotrof Reproductive (GMR 8) about 7.06 x 10 11 cfu / ml on 3 days of incubation and the lowest population was obtained in the Gowa Methanotrof Maturation (GMP 5) about 0.27 x 10 11 cfu / ml on 7 day of incubation. Some isolate were demonstrated in long growth rate about 5 days of incubation and another are 3 days.

Keywords: emission, methanotrof, methane, population

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Authors: Ziyi Zhou, Qiuxiao Chen, Shuang Wu

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Population diversification phenomena becomes quite common in villages located in China’s developed coastal area. Based on the analysis of the traditional rural society and its landscape characteristics, and in consideration of diversified landscape requirements due to the population diversification, with dual ideas of heritage and innovation, methods for rural landscape design were explored by taking Duxuao Village in Zhejiang Province of China as an example.

Keywords: rural landscape, population diversification, landscape design, urban management

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Authors: Shorena Tsiklauri, Avtandil Sulaberidze, Nino Gomelauri

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In the years followed independence, an economic crisis and some conflicts led to the displacement of many people inside Georgia. The growing poverty, unemployment, low income and its unequal distribution limited access to basic social service have had a clear direct impact on Georgian population dynamics and its age-sex structure. Factors influencing the changing population age structure and urbanization include mortality, fertility, migration and expansion of urban. In this paper presents the main factors of changing the distribution by urban and rural areas. How different are the urban and rural age and sex structures? Does Georgia have the same age-sex structure among their urban and rural populations since 1950s?

Keywords: age and sex structure of population, georgia, migration, urban-rural population

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Authors: K. H. Reeta, Bhavana Prasher, Mitali Mukerji, Dhwani Dholakia, Sangeeta Khanna, Archana Vats, Shivam Pandey, Sandeep Seth, Subir Kumar Maulik

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Introduction Research has demonstrated a connection between coronary artery disease (CAD) and genetics. We did a deep literature mining using both bioinformatics and manual efforts to identify the susceptible polymorphisms in coronary artery disease. Further, the study sought to validate these findings in an Asian population. Methodology In first phase, we used an automated pipeline which organizes and presents structured information on SNPs, Population and Diseases. The information was obtained by applying Natural Language Processing (NLP) techniques to approximately 28 million PubMed abstracts. To accomplish this, we utilized Python scripts to extract and curate disease-related data, filter out false positives, and categorize them into 24 hierarchical groups using named Entity Recognition (NER) algorithms. From the extensive research conducted, a total of 466 unique PubMed Identifiers (PMIDs) and 694 Single Nucleotide Polymorphisms (SNPs) related to coronary artery disease (CAD) were identified. To refine the selection process, a thorough manual examination of all the studies was carried out. Specifically, SNPs that demonstrated susceptibility to CAD and exhibited a positive Odds Ratio (OR) were selected, and a final pool of 324 SNPs was compiled. The next phase involved validating the identified SNPs in DNA samples of 96 CAD patients and 37 healthy controls from Indian population using Global Screening Array. ResultsThe results exhibited out of 324, only 108 SNPs were expressed, further 4 SNPs showed significant difference of minor allele frequency in cases and controls. These were rs187238 of IL-18 gene, rs731236 of VDR gene, rs11556218 of IL16 gene and rs5882 of CETP gene. Prior researches have reported association of these SNPs with various pathways like endothelial damage, susceptibility of vitamin D receptor (VDR) polymorphisms, and reduction of HDL-cholesterol levels, ultimately leading to the development of CAD. Among these, only rs731236 had been studied in Indian population and that too in diabetes and vitamin D deficiency. For the first time, these SNPs were reported to be associated with CAD in Indian population. Conclusion: This pool of 324 SNP s is a unique kind of resource that can help to uncover risk associations in CAD. Here, we validated in Indian population. Further, validation in different populations may offer valuable insights and contribute to the development of a screening tool and may help in enabling the implementation of primary prevention strategies targeted at the vulnerable population.

Keywords: coronary artery disease, single nucleotide polymorphism, susceptible SNP, bioinformatics

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Authors: Kamel Allaw, Jocelyne Adjizian Gerard, Makram Chehayeb, Nada Badaro Saliba

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In developing countries, such as Lebanon, the demographic data are hardly available due to the absence of the mechanization of population system. The aim of this study is to evaluate, using only remote sensing data, the correlations between the number of population and the characteristics of roads network (length of primary roads, length of secondary roads, total length of roads, density and percentage of roads and the number of intersections). In order to find the influence of the different factors on the demographic data, we studied the degree of correlation between each factor and the number of population. The results of this study have shown a strong correlation between the number of population and the density of roads and the number of intersections.

Keywords: population, road network, statistical correlations, remote sensing

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Authors: Muneeba Butt

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One of the most important physical evidence which leaves suspects at the crime scene is footprints. Analysis of footprints, which can provide useful information for personal identification, is helpful in crime scene investigation. For the current study, 200 samples collected (144 male and 56 female) from Pakistani population with a consent form. The footprints were collected by using black ink with an ink pad. The entire samples were photographed, and then the magnifying glass was used for visualization of individual characteristics including detail of toes, humps, phalange mark, and flat foot cracks in footprint patterns. The descriptive results of individualizing characteristics features were presented in tabular form with respective frequency and percentage. In the result in the male population, the prevalence of tibialis type (T-type) is highest. In the female population, the prevalence of midularis type (M-type) is highest. Humps on the first toe are more found in the male population rather than other humps. In the female population, humps on the third toe are more found rather than other humps. In the male population, the prevalence of phalange mark by toe 1 is highest followed by toe 3, toe 5, toe 2, toe 4 and in female population the prevalence of phalange mark by toe 1 is highest followed by toe 5, 4, 3 and 2. Creases marks are found highest in male population as compared to the female population.

Keywords: foot prints, toes, humps, cracks

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Authors: Marinela Istrate, Ionel Muntele, Alexandru Bănică

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The authors propose the identification, analysis and prognosis of the quantitative and qualitative evolution of the elderly population in the functional urban areas. The present paper takes into account the analysis of some representative indicators (the weight of the elderly population, ageing index, dynamic index of economic ageing of productive population etc.) and the elaboration of an integrated indicator that would help differentiate the population ageing forms in the 48 functional urban areas that were defined based on demographic and social-economic criteria for all large and medium cities in Romania.

Keywords: ageing, demographic transition, functional urban areas, spatial resilience

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Authors: Sabiu Abdullahi Yau

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Nigeria is a high fertility country that experiences eye-popping population growth, with no end in sight. However, there is evidence that its large population inhibits government’s efforts in meeting the basic needs of the people. Moreover, past and present governments of Nigeria have been committing huge amount of financial resources to meet the basic infrastructural requirements capable of propelling growth and development. Despite the country’s large population and abundant natural resources, poverty, unemployment, rural-urban migration, deforestation and inadequate infrastructural facilities have been persistently on the increase resulting in consistent failure of government policies to impact positively on the economy. This paper, however, identifies and critically analyses the major development challenges caused by population growth in Nigeria using secondary data. The paper concludes that for the Nigeria’s economy to develop, all the identified challenges posed by rapid population growth must be promptly and squarely addressed.

Keywords: economic development, population, growth, Nigeria

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