Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 80

Search results for: chromosome

80 A Second Order Genetic Algorithm for Traveling Salesman Problem

Authors: M. Munlin, T. Toathom, P. Sugunnasil

Abstract:

The traveling salesman problem (TSP) is one of the best-known problems in optimization problem. There are many research regarding the TSP. One of the most usage tool for this problem is the genetic algorithm (GA). The chromosome of the GA for TSP is normally encoded by the order of the visited city. However, the traditional chromosome encoding scheme has some limitations which are twofold: the large solution space and the inability to encapsulate some information. The number of solution for a certain problem is exponentially grow by the number of city. Moreover, the traditional chromosome encoding scheme fails to recognize the misplaced correct relation. It implies that the tradition method focuses only on exact solution. In this work, we relax some of the concept in the GA for TSP which is the exactness of the solution. The proposed work exploits the relation between cities in order to reduce the solution space in the chromosome encoding. In this paper, a second order GA is proposed to solve the TSP. The term second order refers to how the solution is encoded into chromosome. The chromosome is divided into 2 types: the high order chromosome and the low order chromosome. The high order chromosome is the chromosome that focus on the relation between cities such as the city A should be visited before city B. On the other hand, the low order chromosome is a type of chromosome that is derived from a high order chromosome. In other word, low order chromosome is encoded by the traditional chromosome encoding scheme. The genetic operation, mutation and crossover, will be performed on the high order chromosome. Then, the high order chromosome will be mapped to a group of low order chromosomes whose characteristics are satisfied with the high order chromosome. From the mapped set of chromosomes, the champion chromosome will be selected based on the fitness value which will be later used as a representative for the high order chromosome. The experiment is performed on the city data from TSPLIB.

Keywords: Genetic Algorithm, traveling salesman problem, initial population, chromosomes encoding

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79 Effect of Interaction between Colchicine Concentrations and Treatment Time Duration on the Percentage of Chromosome Polyploidy of Crepis capillaris (with and without 2B Chromosome) in vitro Culture

Authors: Payman A. A. Zibari, Mosleh M. S. Duhoky

Abstract:

These experiments were conducted at Tissue Culture Laboratory/ Faculty of Agriculture / University of Duhok during the period from January 2011 to May 2013. The objectives of this study were to study the effects of interaction between colchcine concentrations and treatment time duration of Creps capilaris (with and without 2B chromosome) on chromosome polyploidy during fifteen passages until regeneration of plants from the callus. Data showed that high percentage of chromosome polyploidy approximately can be obtained from high concentration of colchicin and long time of duration.

Keywords: Polyploidy, Crepis capilaris, colchicine, B chromosome

Procedia PDF Downloads 58
78 The Prevalence of X-Chromosome Aneuploidy in Recurrent Pregnancy Loss

Authors: Rim Frikha, Afifa Sellami, Tarek Rebai, Nouha Bouayed, Nozha Chakroun, Leila Keskes, Salima Douad

Abstract:

Recurrent pregnancy loss (RPL), classically defined as the occurrence of two or more failed pregnancies, is a serious reproductive problem, in which, chromosomal rearrangements in either carrier are a major cause; mainly the chromosome aneuploidy. This study was conducted to determine the frequency and contribution of X-chromosome aneuploidy in recurrent pregnancy loss. A retrospective study was carried out among 100 couples with more than 2 miscarriages, referred to our genetic counseling. In all the cases the detailed reproductive histories were taken. Chromosomal analysis was performed using RHG banding in peripheral blood. Of a total of 100 couples; 3 patients with a detected X-chromosome aneuploidy were identified with an overall frequency of 3%. Chromosome abnormalities are as below: a Turner syndrome with 45, X/46, XX mosaicism, a 47, XXX, and a Klinefelter syndrome with 46, XY/47, XXY. These data show a high incidence of X-chromosome aneuploidy; mainly with mosaicism; in RPL. Thus, couples with such chromosomal abnormality should be referred to a clinical geneticist with whom the option of pre-implantation genetic diagnosis in subsequent pregnancy should be discussed.

Keywords: Genetic Testing, recurrent pregnancy loss, aneuploidy, X-chromosome

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77 Chaos Fuzzy Genetic Algorithm

Authors: Mohammad Jalali Varnamkhasti

Abstract:

The genetic algorithms have been very successful in handling difficult optimization problems. The fundamental problem in genetic algorithms is premature convergence. This paper, present a new fuzzy genetic algorithm based on chaotic values instead of the random values in genetic algorithm processes. In this algorithm, for initial population is used chaotic sequences and then a new sexual selection proposed for selection mechanism. In this technique, the population is divided such that the male and female would be selected in an alternate way. The layout of the male and female chromosomes in each generation is different. A female chromosome is selected by tournament selection size from the female group. Then, the male chromosome is selected, in order of preference based on the maximum Hamming distance between the male chromosome and the female chromosome or The highest fitness value of male chromosome (if more than one male chromosome is having the maximum Hamming distance existed), or Random selection. The selections of crossover and mutation operators are achieved by running the fuzzy logic controllers, the crossover and mutation probabilities are varied on the basis of the phenotype and genotype characteristics of the chromosome population. Computational experiments are conducted on the proposed techniques and the results are compared with some other operators, heuristic and local search algorithms commonly used for solving p-median problems published in the literature.

Keywords: Chaos, Genetic Algorithm, fuzzy system, Sexual Selection

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76 Genome-Wide Analysis of Long Terminal Repeat (LTR) Retrotransposons in Rabbit (Oryctolagus cuniculus)

Authors: Faisal Nouroz, Zeeshan Khan, Shumaila Noureen

Abstract:

European or common rabbit (Oryctolagus cuniculus) belongs to class Mammalia, order Lagomorpha of family Leporidae. They are distributed worldwide and are native to Europe (France, Spain and Portugal) and Africa (Morocco and Algeria). LTR retrotransposons are major Class I mobile genetic elements of eukaryotic genomes and play a crucial role in genome expansion, evolution and diversification. They were mostly annotated in various genomes by conventional approaches of homology searches, which restricted the annotation of novel elements. Present work involved de novo identification of LTR retrotransposons by LTR_FINDER in haploid genome of rabbit (2247.74 Mb) distributed in 22 chromosomes, of which 7,933 putative full-length or partial copies were identified containing 69.38 Mb of elements, accounting 3.08% of the genome. Highest copy numbers (731) were found on chromosome 7, followed by chromosome 12 (705), while the lowest copy numbers (27) were detected in chromosome 19 with no elements identified from chromosome 21 due to partially sequenced chromosome, unidentified nucleotides (N) and repeated simple sequence repeats (SSRs). The identified elements ranged in sizes from 1.2 - 25.8 Kb with average sizes between 2-10 Kb. Highest percentage (4.77%) of elements was found in chromosome 15, while lowest (0.55%) in chromosome 19. The most frequent tRNA type was Arginine present in majority of the elements. Based on gained results, it was estimated that rabbit exhibits 15,866 copies having 137.73 Mb of elements accounting 6.16% of diploid genome (44 chromosomes). Further molecular analyses will be helpful in chromosomal localization and distribution of these elements on chromosomes.

Keywords: genome, rabbit, chromosome, LTR retrotransposons

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75 Analysis of the AZF Region in Slovak Men with Azoospermia

Authors: J. Bernasovská, I. Boroňová, R. Lohajová Behulová, E. Petrejčiková, I. Bernasovský

Abstract:

Y chromosome microdeletions are the most common genetic cause of male infertility and screening for these microdeletions in azoospermic or severely oligospermic men is now standard practice. Analysis of the Y chromosome in men with azoospermia or severe oligozoospermia has resulted in the identification of three regions in the euchromatic part of the long arm of the human Y chromosome (Yq11) that are frequently deleted in men with otherwise unexplained spermatogenic failure. PCR analysis of microdeletions in the AZFa, AZFb and AZFc regions of the human Y chromosome is an important screening tool. The aim of this study was to analyse the type of microdeletions in men with fertility disorders in Slovakia. We evaluated 227 patients with azoospermia and with normal karyotype. All patient samples were analyzed cytogenetically. For PCR amplification of sequence-tagged sites (STS) of the AZFa, AZFb and AZFc regions of the Y chromosome was used Devyser AZF set. Fluorescently labeled primers for all markers in one multiplex PCR reaction were used and for automated visualization and identification of the STS markers we used genetic analyzer ABi 3500xl (Life Technologies). We reported 13 cases of deletions in the AZF region 5,73%. Particular types of deletions were recorded in each region AZFa,b,c .The presence of microdeletions in the AZFc region was the most frequent. The study confirmed that percentage of microdeletions in the AZF region is low in Slovak azoospermic patients, but important from a prognostic view.

Keywords: Male Infertility, AZF, microdeletions, Y chromosome

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74 Effect of Interaction between Different Concentrations of Colchicine, Time Duration and Two Verities of Crepis capillaris on Chromosome Polyploidy in vitro Culture

Authors: Payman A. A. Zibari, Mosleh M. S. Duhoky

Abstract:

These experiments were conducted at Tissue Culture Laboratory/ Faculty of Agriculture and Forestry/ University of Duhok during the period from January 2011 to May 2013. The objectives of this study were to study the effects of interaction between three different factors on percentage of polyploidy of Crepis capillaris by using Tissue culture technology. Concerning the data it is obvious that shaking of Crepis capillaris with 2B chromosome with 0.15 mM for ten days inscribed a high percentage of polyploidy within most fifteen passages.

Keywords: Tissue Culture, Polyploidy, crepis capillaris

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73 Prevalence of Down Syndrome: A Single-Center Study in Bandung, Indonesia

Authors: Bremmy Laksono, Riksa Parikrama, Nur A. Rosyada, Willyanti Soewondo, Dadang S. H. Effendi, Eriska Rianti, Arlette S. Setiawan, Ine Sasmita, Risti S. Primanti, Erna Kurnikasari, Yunia Sribudiani

Abstract:

Down syndrome (DS) is a chromosomal abnormality characterised by complete 21 chromosome trisomy (classical or non-disjunction), or partial 21 chromosome trisomy (mosaicism), or chromosome rearrangement involving chromosome 21 (translocation). This study was carried out to describe the frequency of DS patients in a research institution in the city of Bandung, Indonesia. This descriptive study also provides a picture of the residential location and surrounding area of their dwellings. This study involved people with DS in various age whose chromosome were evaluated by conventional karyotyping method and FISH. Data were collected from 60 patients with DS from a total 150 patients during the period of September 2015 to August 2016 who were referred to Cell Culture and Cytogenetics Laboratory, Faculty of Medicine Universitas Padjadjaran, Indonesia. Results showed that the most common type of DS was non-disjunction (93%), followed by mosaicism (5%), no patient with translocation DS (0%), and a very rare type of tetrasomy 21 (2%). There were 39 males (65%) and 21 females (35%) of DS patient. Most of them live in suburban area beyond Bandung city (55%) while the rest live inside urban area of Bandung city (45%). They live mostly in dense area of greater Bandung area (65%) and only a few live in mid-density area (25%) and the least live in sparse populated area (10%). Their houses are mostly located in residential estate area (55%), nearby industrial area (37%), and around agricultural area (8%). Based on the study, it could be concluded that non-disjunction DS is the most common type. DS patients referred to the laboratory mostly came from dense residential zone in suburban area outside Bandung city. The low number of DS patients referred to the laboratory for chromosome analysis was the highlight to improve health service for people with genetic disorder. This study offered several information regarding area of DS patients’ residence and the condition of neighbourhood in Bandung city where they live as well.

Keywords: down syndrome, Prevalence, chromosome, descriptive

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72 Doubled Haploid Production in Wheat Using Imperata cylindrica Mediated Chromosome Elimination Technique

Authors: Jagdish Kumar, Madhu Patial, Dharam Pal, H. K. Chaudhary

Abstract:

Doubled haploid breeding serves as a useful technique in wheat improvement by providing instant and complete homozygosity. Of the various techniques employed for haploid production chromosome elimination has a large scale practical application in wheat improvement. Barclay (1975) initiated the technique in wheat by crossing wheat variety Chinese spring with Hordeum bulbosum, but due to presence of the dominant crossability inhibitor genes Kr7 and Kr2 in many wheat varieties, the technique was however genotypic specific. The discovery of wheat X maize system of haploid production being genotype non-specific is quite successful but still maize needs to be grown in greenhouse to coincide flowering with wheat crop. Recently, wheat X Imperate cylindrica has been identified as a new chromosome mediated DH approach for efficient haploid induction. An experiment to use this technique in wheat was set up by crossing six F1s and two three way F1s with Imperata cylindrica. The data was recorded for the three component traits of haploid induction viz., seed formation, embryo formation and regeneration frequency. Variation among wheat F1s was observed and higher frequency for all the traits were recorded in cross HD 2997/2*FL-8/DONSK-POLL and KLE/BER/2*FL-8/DONSK-POLL.

Keywords: Wheat, haploid, imperata cylindrica, chromosome elimination technique

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71 Medical Neural Classifier Based on Improved Genetic Algorithm

Authors: Fadzil Ahmad, Noor Ashidi Mat Isa

Abstract:

This study introduces an improved genetic algorithm procedure that focuses search around near optimal solution corresponded to a group of elite chromosome. This is achieved through a novel crossover technique known as Segmented Multi Chromosome Crossover. It preserves the highly important information contained in a gene segment of elite chromosome and allows an offspring to carry information from gene segment of multiple chromosomes. In this way the algorithm has better possibility to effectively explore the solution space. The improved GA is applied for the automatic and simultaneous parameter optimization and feature selection of artificial neural network in pattern recognition of medical problem, the cancer and diabetes disease. The experimental result shows that the average classification accuracy of the cancer and diabetes dataset has improved by 0.1% and 0.3% respectively using the new algorithm.

Keywords: Genetic Algorithm, Artificial Neural Network, pattern clasification, classification accuracy

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70 A Case Study of Misinterpretation of Results in Forensic DNA Cases Due to Expression of Y- Chromosome in Females

Authors: Garima Chaudhary

Abstract:

The gender of an individual in forensic DNA analysis is normally accessed by using the STR multiplexes with the incorporated gender based marker amelogenin or in other words by presence or absence of Y-Chromosome, but it may not be true in all the cases. We hereby report an interesting case of a phenotypic female carrying a male karyotype (46XY). In the alleged murder case, the deceased female with XY genotype was noticed. The expression of 18 Y-linked genes was studied to measure the extent of expression. Expression at 4 loci was observed that might have caused the misinterpretation in forensic casework. This clinical situation of the deceased in this case was diagnosed as testicular feminization syndrome, which characterize a female phenotype with a male karyotype (46, XY). Most of these cases have SRY (testis determining factor). The genetic explanation of this phenomenon is not very clear. Here, we are discussing the impact of such situations of genetic discrepancy in forensic interpretation of results. In the presented murder case of a phenotypic female, sexual assault was also suspected. For confirmation vaginal swabs and micro slides were also sent to us for DNA examination. After DNA analysis using STR markers, Y-chromosome was detected in the samples which supporting the suspicion of sexual assault before murder. When the reference blood sample of the deceased was analyzed, it was found to be case of testicular feminization syndrome. Interesting inferences were made from the results obtained.

Keywords: DNA profiling, females, Y chromosome, forensic case study

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69 Karyotyping the Date Palm (Phoenix dactylifera L.)

Authors: Abdullah M. Alzahrani

Abstract:

The karyotypes of Khalas (KH), Sukkary (SK), Sheeshi (SS), Shibeebi (SB) and Sillije (SJ) date palm cultivars were investigated. Data showed no variation in chromosome number, 2n = 36, 34 autosomes in addition to XX in females and XY in males. Mean autosomes length ranged from 3.85-9.93 μm and 3.71-2.73 μm for X and Y chromosomes, respectively. The formula of female date palm karyotype was 8m + 4sm +2st + 4t, and submedian Y chromosome. Relative chromosome length ranged from 3.3- 9.38 μm. SS cultivar showed high asymmetry levels by scoring low values of Syi (45.51), TF (42.8) and high values for A1 (0.53), A (0.41) and AI (0.29). Syi developed an inverse relation with A1 and A while A exhibited a direct correlation with A1. Cultivars SK, SB and SJ score medium values of Syi, A1, AI and A. KH cultivar exhibited high symmetry by scoring highest values of Syi (53.68), TF (51.81) and lowest values of A1 (0.44), A (0.34) and AI (0.18). Higher DI value was obtained in SB cultivar (1.34) followed by SJ (1.15) and low DI scores of 0.99, 0.86 and 0.71 were detected in KH, SS and SK, respectively. Stebbins classification assorted SS as 3B and the other cultivars as 2B, insuring the evolution and asymmetry of SS compared to the other karyotypes. Scatter diagram of Syi-A1 couple has the advantage of revealing high degree of sensitivity to present karyotype interrelationships, followed by AI-A and CVCL-CVCI couples.

Keywords: date palm, Karyotype, Khalas, Sukkary, Sheeshi

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68 High Expression Levels and Amplification of rRNA Genes in a Mentally Retarded Child with 13p+: A Familial Case Study

Authors: Irina S. Kolesnikova, Alexander A. Dolskiy, Natalya A. Lemskaya, Yulia V. Maksimova, Asia R. Shorina, Alena S. Telepova, Alexander S. Graphodatsky, Dmitry V. Yudkin

Abstract:

A cytogenetic and molecular genetic study of the family with a male child who had mental retardation and autistic features revealed an abnormal chromosome 13 bearing an enlarged p-arm with amplified ribosomal DNA (rDNA) in a boy and his father. Cytogenetic analysis using standard G-banding and FISH with labeled rDNA probes revealed an abnormal chromosome 13 with an enlarged p-arms due to rDNA amplification in a male child, who had clinically confirmed mental retardation and an autistic behavior. This chromosome is evidently inherited from the father, who has morphologically the same chromosome, but is healthy. The karyotype of the mother was normal. Ag-NOR staining showed brightly stained large whole-p-arm nucleolus organizer regions (NORs) in a child and normal-sized NORs in his father with 13p+-NOR-amount mosaicism. qRT-PCR with specific primers showed highly increased levels of 18S, 28S and 5,8 S ribosomal RNA (rRNA) in the patient’s blood samples compared to a normal healthy control donor. Both patient’s father and mother had no elevated levels of rRNAs expression. Thus, in this case, rRNA level seems to correlate with mental retardation in familial individuals with 13p+. Our findings of rRNA overexpression in a patient with mental retardation and his parents may show a possible link between the karyotype (p-arm enlargement due to rDNA amplification), rDNA functionality (rRNA overexpression), functional changes in the brain and mental retardation. The study is supported by Russian Science Foundation Grant 15-15-10001.

Keywords: Mental Retardation, ribosomal DNA–rDNA, ribosomal RNA–rRNA, nucleolus organizer region–NOR, chromosome 13

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67 The Usefulness of Premature Chromosome Condensation Scoring Module in Cell Response to Ionizing Radiation

Authors: K. Rawojć, J. Miszczyk, A. Możdżeń, A. Panek, J. Swakoń, M. Rydygier

Abstract:

Due to the mitotic delay, poor mitotic index and disappearance of lymphocytes from peripheral blood circulation, assessing the DNA damage after high dose exposure is less effective. Conventional chromosome aberration analysis or cytokinesis-blocked micronucleus assay do not provide an accurate dose estimation or radiosensitivity prediction in doses higher than 6.0 Gy. For this reason, there is a need to establish reliable methods allowing analysis of biological effects after exposure in high dose range i.e., during particle radiotherapy. Lately, Premature Chromosome Condensation (PCC) has become an important method in high dose biodosimetry and a promising treatment modality to cancer patients. The aim of the study was to evaluate the usefulness of drug-induced PCC scoring procedure in an experimental mode, where 100 G2/M cells were analyzed in different dose ranges. To test the consistency of obtained results, scoring was performed by 3 independent persons in the same mode and following identical scoring criteria. Whole-body exposure was simulated in an in vitro experiment by irradiating whole blood collected from healthy donors with 60 MeV protons and 250 keV X-rays, in the range of 4.0 – 20.0 Gy. Drug-induced PCC assay was performed on human peripheral blood lymphocytes (HPBL) isolated after in vitro exposure. Cells were cultured for 48 hours with PHA. Then to achieve premature condensation, calyculin A was added. After Giemsa staining, chromosome spreads were photographed and manually analyzed by scorers. The dose-effect curves were derived by counting the excess chromosome fragments. The results indicated adequate dose estimates for the whole-body exposure scenario in the high dose range for both studied types of radiation. Moreover, compared results revealed no significant differences between scores, which has an important meaning in reducing the analysis time. These investigations were conducted as a part of an extended examination of 60 MeV protons from AIC-144 isochronous cyclotron, at the Institute of Nuclear Physics in Kraków, Poland (IFJ PAN) by cytogenetic and molecular methods and were partially supported by grant DEC-2013/09/D/NZ7/00324 from the National Science Centre, Poland.

Keywords: proton therapy, cell response to radiation exposure, drug induced premature chromosome condensation, premature chromosome condensation procedure

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66 From Primer Generation to Chromosome Identification: A Primer Generation Genotyping Method for Bacterial Identification and Typing

Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

Abstract:

A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: Bacterial Identification, Sequence, bacteria chromosome, primer generation

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65 Functional Gene Expression in Human Cells Using Linear Vectors Derived from Bacteriophage N15 Processing

Authors: Kumaran Narayanan, Pei-Sheng Liew

Abstract:

This paper adapts the bacteriophage N15 protelomerase enzyme to assemble linear chromosomes as vectors for gene expression in human cells. Phage N15 has the unique ability to replicate as a linear plasmid with telomeres in E. coli during its prophage stage of life-cycle. The virus-encoded protelomerase enzyme cuts its circular genome and caps its ends to form hairpin telomeres, resulting in a linear human-chromosome-like structure in E. coli. In mammalian cells, however, no enzyme with TelN-like activities has been found. In this work, we show for the first-time transfer of the protelomerase from phage into human and mouse cells and demonstrate recapitulation of its activity in these hosts. The function of this enzyme is assayed by demonstrating cleavage of its target DNA, followed by detecting telomere formation based on its resistance to recBCD enzyme digestion. We show protelomerase expression persists for at least 60 days, which indicates limited silencing of its expression. Next, we show that an intact human β-globin gene delivered on this linear chromosome accurately retains its expression in the human cellular environment for at least 60 hours, demonstrating its stability and potential as a vector. These results demonstrate that the N15 protelomerse is able to function in mammalian cells to cut and heal DNA to create telomeres, which provides a new tool for creating novel structures by DNA resolution in these hosts.

Keywords: Gene expression, Dna, chromosome, beta-globin, linear vector

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64 A Novel Chicken W Chromosome Specific Tandem Repeat

Authors: Alsu F. Saifitdinova, Alexey S. Komissarov, Svetlana A. Galkina, Elena I. Koshel, Maria M. Kulak, Stephen J. O'Brien, Elena R. Gaginskaya

Abstract:

The mystery of sex determination is one of the most ancient and still not solved until the end so far. In many species, sex determination is genetic and often accompanied by the presence of dimorphic sex chromosomes in the karyotype. Genomic sequencing gave the information about the gene content of sex chromosomes which allowed to reveal their origin from ordinary autosomes and to trace their evolutionary history. Female-specific W chromosome in birds as well as mammalian male-specific Y chromosome is characterized by the degeneration of gene content and the accumulation of repetitive DNA. Tandem repeats complicate the analysis of genomic data. Despite the best efforts chicken W chromosome assembly includes only 1.2 Mb from expected 55 Mb. Supplementing the information on the sex chromosome composition not only helps to complete the assembly of genomes but also moves us in the direction of understanding of the sex-determination systems evolution. A whole-genome survey to the assembly Gallus_gallus WASHUC 2.60 was applied for repeats search in assembled genome and performed search and assembly of high copy number repeats in unassembled reads of SRR867748 short reads datasets. For cytogenetic analysis conventional methods of fluorescent in situ hybridization was used for previously cloned W specific satellites and specifically designed directly labeled synthetic oligonucleotide DNA probe was used for bioinformatically identified repetitive sequence. Hybridization was performed with mitotic chicken chromosomes and manually isolated giant meiotic lampbrush chromosomes from growing oocytes. A novel chicken W specific satellite (GGAAA)n which is not co-localizes with any previously described classes of W specific repeats was identified and mapped with high resolution. In the composition of autosomes this repeat units was found as a part of upstream regions of gonad specific protein coding sequences. These findings may contribute to the understanding of the role of tandem repeats in sex specific differentiation regulation in birds and sex chromosome evolution. This work was supported by the postdoctoral fellowships from St. Petersburg State University (#1.50.1623.2013 and #1.50.1043.2014), the grant for Leading Scientific Schools (#3553.2014.4) and the grant from Russian foundation for basic researches (#15-04-05684). The equipment and software of Research Resource Center “Chromas” and Theodosius Dobzhansky Center for Genome Bioinformatics of Saint Petersburg State University were used.

Keywords: birds, lampbrush chromosomes, sex chromosomes, tandem repeats

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63 Atomic Force Microscopy Studies of DNA Binding Properties of the Archaeal Mini Chromosome Maintenance Complex

Authors: Amna Abdalla Mohammed Khalid, Pietro Parisse, Silvia Onesti, Loredana Casalis

Abstract:

Basic cellular processes as DNA replication are crucial to cell life. Understanding at the molecular level the mechanisms that govern DNA replication in proliferating cells is fundamental to understand disease connected to genomic instabilities, as a genetic disease and cancer. A key step for DNA replication to take place, is unwinding the DNA double helix and this carried out by proteins called helicases. The archaeal MCM (minichromosome maintenance) complex from Methanothermobacter thermautotrophicus have being studied using Atomic Force Microscopy (AFM), imaging in air and liquid (Physiological environment). The accurate analysis of AFM topographic images allowed to understand the static conformations as well the interaction dynamic of MCM and DNA double helix in the present of ATP.

Keywords: Dna, Atomic Force Microscopy (AFM), protein-DNA interaction, MCM (mini chromosome manteinance) complex

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62 An Improved Genetic Algorithm for Traveling Salesman Problem with Precedence Constraint

Authors: M. F. F. Ab Rashid, A. N. Mohd Rose, N. M. Z. Nik Mohamed, W. S. Wan Harun, S. A. Che Ghani

Abstract:

Traveling salesman problem with precedence constraint (TSPPC) is one of the most complex problems in combinatorial optimization. The existing algorithms to solve TSPPC cost large computational time to find the optimal solution. The purpose of this paper is to present an efficient genetic algorithm that guarantees optimal solution with less number of generations and iterations time. Unlike the existing algorithm that generates priority factor as chromosome, the proposed algorithm directly generates sequence of solution as chromosome. As a result, the proposed algorithm is capable of generating optimal solution with smaller number of generations and iteration time compare to existing algorithm.

Keywords: Genetic Algorithm, Sequencing, traveling salesman problem, precedence constraint

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61 Cytogenetic Investigation of Patients with Disorder of Sexual Development Using G-Banding Karyotype and Fluorescence In situ Hybridization

Authors: Bremmy Laksono, Riksa Parikrama, Dadang S. H. Effendi

Abstract:

Disorder of sexual development (DSD) covers various conditions with a specific term such as Klinefelter syndrome, Turner syndrome, androgen insensitivity syndrome, and many more. The techniques to accurately diagnose those conditions has developed extensively. However, conventional karyotype and fluorescence in situ hybridization (FISH) are still widely used in many genetic laboratories as the basic method to determine chromosomal condition of DSD patients. Cytogenetic study was conducted on 36 DSD patients in Cell Culture and Cytogenetics Laboratory, Faculty of Medicine Universitas Padjadjaran, Indonesia. Most of the patients referred to the laboratory diagnosed with primary amenorrhea, hypospadias, micropenis, genitalia ambiguity, or congenital adrenal hyperplasia. The study used G-banding technique to acquire complete karyotype and followed by FISH as either confirmation or comparison method. Among 36 patients, G-banding karyotype and FISH results showed that two were diagnosed with 45, X (Turner syndrome); three with 47, XXY (Klinefelter syndrome); five with 46, XX DSD; 22 with 46, XY DSD; and four with 46,XY complete androgen insensitivity syndrome. G-banding karyotype analysis were paired with FISH using X and Y chromosome probe produced similar results. The present analysis showed that FISH is a reliable method to attain a rapid and accurate chromosome analysis result of DSD patients. Nevertheless, conventional karyotype technique is still vital if other condition appeared in DSD patients in order to get more detailed karyotype result which FISH method cannot achieve.

Keywords: Fish, chromosome, DSD, Karyotype

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60 Hardware for Genetic Algorithm

Authors: Fariborz Ahmadi, Reza Tati

Abstract:

Genetic algorithm is a soft computing method that works on set of solutions. These solutions are called chromosome and the best one is the absolute solution of the problem. The main problem of this algorithm is that after passing through some generations, it may be produced some chromosomes that had been produced in some generations ago that causes reducing the convergence speed. From another respective, most of the genetic algorithms are implemented in software and less works have been done on hardware implementation. Our work implements genetic algorithm in hardware that doesn’t produce chromosome that have been produced in previous generations. In this work, most of genetic operators are implemented without producing iterative chromosomes and genetic diversity is preserved. Genetic diversity causes that not only do not this algorithm converge to local optimum but also reaching to global optimum. Without any doubts, proposed approach is so faster than software implementations. Evaluation results also show the proposed approach is faster than hardware ones.

Keywords: Computer Science, Engineering, Hardware, Genetic Algorithm

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59 Generalized Correlation Coefficient in Genome-Wide Association Analysis of Cognitive Ability in Twins

Authors: Afsaneh Mohammadnejad, Marianne Nygaard, Jan Baumbach, Shuxia Li, Weilong Li, Jesper Lund, Jacob v. B. Hjelmborg, Lene Christensen, Qihua Tan

Abstract:

Cognitive impairment in the elderly is a key issue affecting the quality of life. Despite a strong genetic background in cognition, only a limited number of single nucleotide polymorphisms (SNPs) have been found. These explain a small proportion of the genetic component of cognitive function, thus leaving a large proportion unaccounted for. We hypothesize that one reason for this missing heritability is the misspecified modeling in data analysis concerning phenotype distribution as well as the relationship between SNP dosage and the phenotype of interest. In an attempt to overcome these issues, we introduced a model-free method based on the generalized correlation coefficient (GCC) in a genome-wide association study (GWAS) of cognitive function in twin samples and compared its performance with two popular linear regression models. The GCC-based GWAS identified two genome-wide significant (P-value < 5e-8) SNPs; rs2904650 near ZDHHC2 on chromosome 8 and rs111256489 near CD6 on chromosome 11. The kinship model also detected two genome-wide significant SNPs, rs112169253 on chromosome 4 and rs17417920 on chromosome 7, whereas no genome-wide significant SNPs were found by the linear mixed model (LME). Compared to the linear models, more meaningful biological pathways like GABA receptor activation, ion channel transport, neuroactive ligand-receptor interaction, and the renin-angiotensin system were found to be enriched by SNPs from GCC. The GCC model outperformed the linear regression models by identifying more genome-wide significant genetic variants and more meaningful biological pathways related to cognitive function. Moreover, GCC-based GWAS was robust in handling genetically related twin samples, which is an important feature in handling genetic confounding in association studies.

Keywords: Cognition, gwas, twins, generalized correlation coefficient

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58 Comparison of Crossover Types to Obtain Optimal Queries Using Adaptive Genetic Algorithm

Authors: Khaled Almakadmeh, Wafa’ Alma'Aitah

Abstract:

this study presents an information retrieval system of using genetic algorithm to increase information retrieval efficiency. Using vector space model, information retrieval is based on the similarity measurement between query and documents. Documents with high similarity to query are judge more relevant to the query and should be retrieved first. Using genetic algorithms, each query is represented by a chromosome; these chromosomes are fed into genetic operator process: selection, crossover, and mutation until an optimized query chromosome is obtained for document retrieval. Results show that information retrieval with adaptive crossover probability and single point type crossover and roulette wheel as selection type give the highest recall. The proposed approach is verified using (242) proceedings abstracts collected from the Saudi Arabian national conference.

Keywords: Information Retrieval, Genetic Algorithm, crossover, optimal queries

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57 Brachypodium: A Model Genus to Study Grass Genome Organisation at the Cytomolecular Level

Authors: R. Hasterok, A. Betekhtin, N. Borowska, A. Braszewska-Zalewska, E. Breda, K. Chwialkowska, R. Gorkiewicz, D. Idziak, J. Kwasniewska, M. Kwasniewski, D. Siwinska, A. Wiszynska, E. Wolny

Abstract:

In contrast to animals, the organisation of plant genomes at the cytomolecular level is still relatively poorly studied and understood. However, the Brachypodium genus in general and B. distachyon in particular represent exceptionally good model systems for such study. This is due not only to their highly desirable ‘model’ biological features, such as small nuclear genome, low chromosome number and complex phylogenetic relations, but also to the rapidly and continuously growing repertoire of experimental tools, such as large collections of accessions, WGS information, large insert (BAC) libraries of genomic DNA, etc. Advanced cytomolecular techniques, such as fluorescence in situ hybridisation (FISH) with evermore sophisticated probes, empowered by cutting-edge microscope and digital image acquisition and processing systems, offer unprecedented insight into chromatin organisation at various phases of the cell cycle. A good example is chromosome painting which uses pools of chromosome-specific BAC clones, and enables the tracking of individual chromosomes not only during cell division but also during interphase. This presentation outlines the present status of molecular cytogenetic analyses of plant genome structure, dynamics and evolution using B. distachyon and some of its relatives. The current projects focus on important scientific questions, such as: What mechanisms shape the karyotypes? Is the distribution of individual chromosomes within an interphase nucleus determined? Are there hot spots of structural rearrangement in Brachypodium chromosomes? Which epigenetic processes play a crucial role in B. distachyon embryo development and selective silencing of rRNA genes in Brachypodium allopolyploids? The authors acknowledge financial support from the Polish National Science Centre (grants no. 2012/04/A/NZ3/00572 and 2011/01/B/NZ3/00177)

Keywords: Fish, nucleus, Brachypodium, B. distachyon, chromosome, molecular cytogenetics, plant genome organisation

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56 Polymorphism of Candidate Genes for Meat Production in Lori Sheep

Authors: Shahram Nanekarania, Majid Goodarzia

Abstract:

Calpastatin and callipyge have been known as one of the candidate genes in meat quality and quantity. Calpastatin gene has been located to chromosome 5 of sheep and callipyge gene has been localized in the telomeric region on ovine chromosome 18. The objective of this study was identification of calpastatin and callipyge genes polymorphism and analysis of genotype structure in population of Lori sheep kept in Iran. Blood samples were taken from 120 Lori sheep breed and genomic DNA was extracted by salting out method. Polymorphism was identified using the PCR-RFLP technique. The PCR products were digested with MspI and FaqI restriction enzymes for calpastatin gene and callipyge gene, respectively. In this population, three patterns were observed and AA, AB, BB genotype have been identified with the 0.32, 0.63, 0.05 frequencies for calpastatin gene. The results obtained for the callipyge gene revealed that only the wild-type allele A was observed, indicating that only genotype AA was present in the population under consideration.

Keywords: Polymorphism, calpastatin, callipyge, PCR-RFLP, Lori sheep

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55 Analysis of Saudi Breast Cancer Patients’ Primary Tumors using Array Comparative Genomic Hybridization

Authors: A. Chaudhary, L. M. Al-Harbi, A. M. Shokry, J. S. M. Sabir, J. Manikandan, K. S. Saini

Abstract:

Breast cancer is the second most common cause of cancer death worldwide and is the most common malignancy among Saudi females. During breast carcinogenesis, a wide-array of cytogenetic changes involving deletions, or amplification, or translocations, of part or whole of chromosome regions have been observed. Because of the limitations of various earlier technologies, newer tools are developed to scan for changes at the genomic level. Recently, Array Comparative Genomic Hybridization (aCGH) technique has been applied for detecting segmental genomic alterations at molecular level. In this study, aCGH was performed on twenty breast cancer tumors and their matching non-tumor (normal) counterparts using the Agilent 2x400K. Several regions were identified to be either amplified or deleted in a tumor-specific manner. Most frequent alterations were amplification of chromosome 1q, chromosome 8q, 20q, and deletions at 16q were also detected. The amplification of genetic events at 1q and 8q were further validated using FISH analysis using probes targeting 1q25 and 8q (MYC gene). The copy number changes at these loci can potentially cause a significant change in the tumor behavior, as deletions in the E-Cadherin (CDH1)-tumor suppressor gene as well as amplification of the oncogenes-Aurora Kinase A. (AURKA) and MYC could make these tumors highly metastatic. This study validates the use of aCGH in Saudi breast cancer patients and sets the foundations necessary for performing larger cohort studies searching for ethnicity-specific biomarkers and gene copy number variations.

Keywords: Ecology, Molecular Biology, Environment, Breast Cancer

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54 Somatic Hybridization of between Citrus and Murraya paniculata Cells Applied by Electro-Fusion

Authors: Hasan Basri Jumin

Abstract:

Protoplasts isolated from embryogenic callus of Citrus sinensis were electrically used with mesophyll protoplasts isolated from seedless Citrus relatives. Hybrid of somatic embryos plantlets was obtained after 7 months of culture. Somatic hybrid plants were regenerated into normal seedlings and successfully transferred to soil after strictly acclimatization in the glass pot. The somatic hybrid plants were obtained by screening on the basis of chromosomes count. The number of chromosome of root tip counting revealed plantlets tetraploids (2n = 4x = 36) and the other were diploids (2n = 2x = 18) morphologically resembling the mesophyll parent. This somatic hybrid will be utilized as a possible pollen parent for improving the Citrus sinensis. A complete protoplast-to-plant system of somatic hybrid was developed for Citrus sinensis and Citrus relatives which could facilitate the transfer of nuclear and cytoplasmic genes from this species into cultivated Citrus through protoplast fusion.

Keywords: chromosome, Murraya paniculata, protoplast fusion, somatic hybrid, tetrapoliod

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53 Cytogenetic Characterization of the VERO Cell Line Based on Comparisons with the Subline; Implication for Authorization and Quality Control of Animal Cell Lines

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

Abstract:

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

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

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52 Identification of Quantitative Trait Loci Conferring Downy Mildew Resistance in Cucumis sativus

Authors: Pawinee Innark, Hudsaya Punyanitikul, Chanuluk Khanobdee, Chatchawan Jantasuriyarat, Sompid Samipak

Abstract:

One of the most devastating diseases in cucumber is downy mildew caused by the fungus Pseudoperonospora cubensis. To enable the use of marker-assisted breeding for resistance cultivars, sixty six microsatellite markers were used to map (quantitative trait loci) QTLs for DM resistance. Total of 315 F2 population from the cross between DM-resistant inbred line CSL0067 and susceptible CSL0139 were evaluated for downy mildew resistance in cotyledon, first and second true leaf at 7, 10, and 14 day after inoculation. The QTL analysis revealed that the downy mildew resistant genes were controlled by multiple recessive genes. From eight linkage groups (LG 1.1, 1.2, 2, 3, 4, 5.1, 5.2 and 6), fourteen QTL positions were detected on 4 linkage groups (LG 1.1, 2, 5.1 and 6) with the log of odd scores ranged from 3.538 to 9.165. Among them, Cot7_5.1_2 and Cot10_5.1 had major-effect QTL with the R2 values of 10.9 and 12.5%, respectively. The flanking markers for Cot7_5.1_2 were SSR19172 - SSR07531 markers and for Cot10_5.1 were SSR03943 - SSR00772. Besides QTLs on chromosome 1, 5 and 6 that were previously reported, this study also revealed a QTL for DM resistance on chromosome 2 that can be used as a new source in cucumber breeding program.

Keywords: qtl, cucumber, DNA marker, downy mildew

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51 Isolation and Expansion of Human Periosteum-Derived Mesenchymal Stem Cells in Defined Serum-Free Culture Medium

Authors: Ainur Mukhambetova, Miras Karzhauov, Vyacheslav Ogay

Abstract:

Introduction: Mesenchymal stem cells (MSCs) have the capacity to be differentiated into several cell lineages and are a promising source for cell therapy and tissue engineering. However, currently most MSCs culturing protocols use media supplemented with fetal bovine serum (FBS), which limits their application in clinic due to the possibility of zoonotic infections, contamination and immunological reactions. Consequently, formulating effective serum free culture medium becomes one of the important problems in contemporary cell biotechnology. Objectives: The aim of this study was to define an optimal serum-free medium for culturing of periosteum derived MSCs. Materials and methods: The MSCs were extracted from human periosteum and transferred to the culture flasks pretreated with CELLstart™. Immunophenotypic characterization, proliferation and in vitro differentiation of cells grown on STEM PRO® MSC SFM were compared to the cells cultured in the standard FBS containing media. Chromosome analysis and flow cytometry were also performed. Results: We have shown that cells were grown on STEM PRO® MSC SFM retained all the morphological, immunophenotypic (CD73, CD90, CD105, vimentin and Stro-1) and cell differentiation characteristics specific to MSCs. Chromosome analysis indicated no anomalies in the chromosome structure. Flow cytometry showed a high expression of cell adhesion molecules CD44 (98,8%), CD90 (97,4%), CD105 (99,1%). In addition, we have shown that cell is grown on STEM PRO® MSC SFM have higher proliferation capacity compared to cell expanded on standard FBS containing the medium. Conclusion: We have shown that STEM PRO® MSC SFM is optimal for culturing periosteum derived human MSCs which subsequently can be safely used in cell therapy.

Keywords: Regenerative medicine, cell technologies, periosteum-derived MSCs, serum-free medium

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