Relevant bibliographies by topics / Chromosomes

Academic literature on the topic 'Chromosomes'

Author: Grafiati
Published: 4 June 2021
Last updated: 30 July 2024

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Journal articles on the topic "Chromosomes"

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Zhao, J. T., M. Frommer, J. A. Sved, and A. Zacharopoulou. "Mitotic and polytene chromosome analyses in the Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)." Genome 41, no. 4 (August 1, 1998): 510–26. http://dx.doi.org/10.1139/g98-053.

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The Queensland fruit fly, Bactrocera tryoni, like the Mediterranean fruit fly, Ceratitis capitata, has a diploid complement of 12 chromosomes, including five pairs of autosomes and a XX/XY sex chromosome pair. Characteristic features of each chromosome are described. Chromosomal homology between B. tryoni and C. capitata has been determined by comparing chromosome banding pattern and in situ hybridisation of cloned genes to polytene chromosomes. Although the evidence indicates that a number of chromosomal inversions have occurred since the separation of the two species, synteny of the chromosomes appears to have been maintained.Key words: tephritid fruit fly, Bactrocera tryoni, polytene chromosomes, in situ hybridisation, chromosomal homology.
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Spell, R. M., and C. Holm. "Nature and distribution of chromosomal intertwinings in Saccharomyces cerevisiae." Molecular and Cellular Biology 14, no. 2 (February 1994): 1465–76. http://dx.doi.org/10.1128/mcb.14.2.1465-1476.1994.

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To elucidate yeast chromosome structure and behavior, we examined the breakage of entangled chromosomes in DNA topoisomerase II mutants by hybridization to chromosomal DNA resolved by pulsed-field gel electrophoresis. Our study reveals that large and small chromosomes differ in the nature and distribution of their intertwinings. Probes to large chromosomes (450 kb or larger) detect chromosome breakage, but probes to small chromosomes (380 kb or smaller) reveal no breakage products. Examination of chromosomes with one small arm and one large arm suggests that the two arms behave independently. The acrocentric chromosome XIV breaks only on the long arm, and its preferred region of breakage is approximately 200 kb from the centromere. When the centromere of chromosome XIV is relocated, the preferred region of breakage shifts accordingly. These results suggest that large chromosomes break because they have long arms and small chromosomes do not break because they have small arms. Indeed, a small metacentric chromosome can be made to break if it is rearranged to form a telocentric chromosome with one long arm or a ring with an "infinitely" long arm. These results suggest a model of chromosomal intertwining in which the length of the chromosome arm prevents intertwinings from passively resolving off the end of the arm during chromosome segregation.
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Spell, R. M., and C. Holm. "Nature and distribution of chromosomal intertwinings in Saccharomyces cerevisiae." Molecular and Cellular Biology 14, no. 2 (February 1994): 1465–76. http://dx.doi.org/10.1128/mcb.14.2.1465.

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To elucidate yeast chromosome structure and behavior, we examined the breakage of entangled chromosomes in DNA topoisomerase II mutants by hybridization to chromosomal DNA resolved by pulsed-field gel electrophoresis. Our study reveals that large and small chromosomes differ in the nature and distribution of their intertwinings. Probes to large chromosomes (450 kb or larger) detect chromosome breakage, but probes to small chromosomes (380 kb or smaller) reveal no breakage products. Examination of chromosomes with one small arm and one large arm suggests that the two arms behave independently. The acrocentric chromosome XIV breaks only on the long arm, and its preferred region of breakage is approximately 200 kb from the centromere. When the centromere of chromosome XIV is relocated, the preferred region of breakage shifts accordingly. These results suggest that large chromosomes break because they have long arms and small chromosomes do not break because they have small arms. Indeed, a small metacentric chromosome can be made to break if it is rearranged to form a telocentric chromosome with one long arm or a ring with an "infinitely" long arm. These results suggest a model of chromosomal intertwining in which the length of the chromosome arm prevents intertwinings from passively resolving off the end of the arm during chromosome segregation.
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Singchat, Worapong, Thitipong Panthum, Syed Farhan Ahmad, Sudarath Baicharoen, Narongrit Muangmai, Prateep Duengkae, Darren K. Griffin, and Kornsorn Srikulnath. "Remnant of Unrelated Amniote Sex Chromosomal Linkage Sharing on the Same Chromosome in House Gecko Lizards, Providing a Better Understanding of the Ancestral Super-Sex Chromosome." Cells 10, no. 11 (November 1, 2021): 2969. http://dx.doi.org/10.3390/cells10112969.

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Comparative chromosome maps investigating sex chromosomal linkage groups in amniotes and microsatellite repeat motifs of a male house gecko lizard (Hemidactylus frenatus, HFR) and a flat-tailed house gecko lizard (H. platyurus, HPL) of unknown sex were examined using 75 bacterial artificial chromosomes (BACs) from chicken and zebra finch genomes. No massive accumulations of microsatellite repeat motifs were found in either of the gecko lizards, but 10 out of 13 BACs mapped on HPL chromosomes were associated with other amniote sex chromosomes. Hybridization of the same BACs onto multiple different chromosome pairs suggested transitions to sex chromosomes across amniotes. No BAC hybridization signals were found on HFR chromosomes. However, HFR diverged from HPL about 30 million years ago, possibly due to intrachromosomal rearrangements occurring in the HFR lineage. By contrast, heterochromatin likely reshuffled patterns between HPL and HFR, as observed from C-positive heterochromatin distribution. Six out of ten BACs showed partial homology with squamate reptile chromosome 2 (SR2) and snake Z and/or W sex chromosomes. The gecko lizard showed shared unrelated sex chromosomal linkages—the remnants of a super-sex chromosome. A large ancestral super-sex chromosome showed a correlation between SR2 and snake W sex chromosomes.
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Singchat, Worapong, Syed Farhan Ahmad, Nararat Laopichienpong, Aorarat Suntronpong, Thitipong Panthum, Darren K. Griffin, and Kornsorn Srikulnath. "Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome." Cells 9, no. 11 (October 31, 2020): 2386. http://dx.doi.org/10.3390/cells9112386.

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Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.
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Pazhenkova, Elena A., and Vladimir A. Lukhtanov. "Whole-Genome Analysis Reveals the Dynamic Evolution of Holocentric Chromosomes in Satyrine Butterflies." Genes 14, no. 2 (February 8, 2023): 437. http://dx.doi.org/10.3390/genes14020437.

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Butterfly chromosomes are holocentric, i.e., lacking a localized centromere. Potentially, this can lead to rapid karyotypic evolution through chromosome fissions and fusions, since fragmented chromosomes retain kinetic activity, while fused chromosomes are not dicentric. However, the actual mechanisms of butterfly genome evolution are poorly understood. Here, we analyzed chromosome-scale genome assemblies to identify structural rearrangements between karyotypes of satyrine butterfly species. For the species pair Erebia ligea–Maniola jurtina, sharing the ancestral diploid karyotype 2n = 56 + ZW, we demonstrate a high level of chromosomal macrosynteny and nine inversions separating these species. We show that the formation of a karyotype with a low number of chromosomes (2n = 36 + ZW) in Erebia aethiops was based on ten fusions, including one autosome–sex chromosome fusion, resulting in a neo-Z chromosome. We also detected inversions on the Z sex chromosome that were differentially fixed between the species. We conclude that chromosomal evolution is dynamic in the satyrines, even in the lineage that preserves the ancestral chromosome number. We hypothesize that the exceptional role of Z chromosomes in speciation may be further enhanced by inversions and sex chromosome–autosome fusions. We argue that not only fusions/fissions but also inversions are drivers of the holocentromere-mediated mode of chromosomal speciation.
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McAllister, Bryant F. "Sequence Differentiation Associated With an Inversion on the Neo-X Chromosome of Drosophila americana." Genetics 165, no. 3 (November 1, 2003): 1317–28. http://dx.doi.org/10.1093/genetics/165.3.1317.

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Abstract Sex chromosomes originate from pairs of autosomes that acquire controlling genes in the sex-determining cascade. Universal mechanisms apparently influence the evolution of sex chromosomes, because this chromosomal pair is characteristically heteromorphic in a broad range of organisms. To examine the pattern of initial differentiation between sex chromosomes, sequence analyses were performed on a pair of newly formed sex chromosomes in Drosophila americana. This species has neo-sex chromosomes as a result of a centromeric fusion between the X chromosome and an autosome. Sequences were analyzed from the Alcohol dehydrogenase (Adh), big brain (bib), and timeless (tim) gene regions, which represent separate positions along this pair of neo-sex chromosomes. In the northwestern range of the species, the bib and Adh regions exhibit significant sequence differentiation for neo-X chromosomes relative to neo-Y chromosomes from the same geographic region and other chromosomal populations of D. americana. Furthermore, a nucleotide site defining a common haplotype in bib is shown to be associated with a paracentric inversion [In(4)ab] on the neo-X chromosome, and this inversion suppresses recombination between neo-X and neo-Y chromosomes. These observations are consistent with the inversion acting as a recombination modifier that suppresses exchange between these neo-sex chromosomes, as predicted by models of sex chromosome evolution.
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Gonzalez de la Rosa, Pablo Manuel, Marian Thomson, Urmi Trivedi, Alan Tracey, Sophie Tandonnet, and Mark Blaxter. "A telomere-to-telomere assembly ofOscheius tipulaeand the evolution of rhabditid nematode chromosomes." G3 Genes|Genomes|Genetics 11, no. 1 (December 8, 2020): 1–17. http://dx.doi.org/10.1093/g3journal/jkaa020.

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AbstractEukaryotic chromosomes have phylogenetic persistence. In many taxa, each chromosome has a single functional centromere with essential roles in spindle attachment and segregation. Fusion and fission can generate chromosomes with no or multiple centromeres, leading to genome instability. Groups with holocentric chromosomes (where centromeric function is distributed along each chromosome) might be expected to show karyotypic instability. This is generally not the case, and in Caenorhabditis elegans, it has been proposed that the role of maintenance of a stable karyotype has been transferred to the meiotic pairing centers, which are found at one end of each chromosome. Here, we explore the phylogenetic stability of nematode chromosomes using a new telomere-to-telomere assembly of the rhabditine nematode Oscheius tipulae generated from nanopore long reads. The 60-Mb O. tipulae genome is resolved into six chromosomal molecules. We find the evidence of specific chromatin diminution at all telomeres. Comparing this chromosomal O. tipulae assembly with chromosomal assemblies of diverse rhabditid nematodes, we identify seven ancestral chromosomal elements (Nigon elements) and present a model for the evolution of nematode chromosomes through rearrangement and fusion of these elements. We identify frequent fusion events involving NigonX, the element associated with the rhabditid X chromosome, and thus sex chromosome-associated gene sets differ markedly between species. Despite the karyotypic stability, gene order within chromosomes defined by Nigon elements is not conserved. Our model for nematode chromosome evolution provides a platform for investigation of the tensions between local genome rearrangement and karyotypic evolution in generating extant genome architectures.
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Surosky, R. T., and B. K. Tye. "Meiotic disjunction of homologs in Saccharomyces cerevisiae is directed by pairing and recombination of the chromosome arms but not by pairing of the centromeres." Genetics 119, no. 2 (June 1, 1988): 273–87. http://dx.doi.org/10.1093/genetics/119.2.273.

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Abstract We explored the behavior of meiotic chromosomes in Saccharomyces cerevisiae by examining the effects of chromosomal rearrangements on the pattern of disjunction and recombination of chromosome III during meiosis. The segregation of deletion chromosomes lacking part or all (telocentric) of one arm was analyzed in the presence of one or two copies of a normal chromosome III. In strains containing one normal and any one deletion chromosome, the two chromosomes disjoined in most meioses. In strains with one normal chromosome and both a left and right arm telocentric chromosome, the two telocentrics preferentially disjoined from the normal chromosome. Homology on one arm was sufficient to direct chromosome disjunction, and two chromosomes could be directed to disjoin from a third. In strains containing one deletion chromosome and two normal chromosomes, the two normal chromosomes preferentially disjoined, but in 4-7% of the tetrads the normal chromosomes cosegregated, disjoining from the deletion chromosome. Recombination between the two normal chromosomes or between the deletion chromosome and a normal chromosome increased the probability that these chromosomes would disjoin, although cosegregation of recombinants was observed. Finally, we observed that a derivative of chromosome III in which the centromeric region was deleted and CEN5 was integrated at another site on the chromosome disjoined from a normal chromosome III with fidelity. These studies demonstrate that it is not pairing of the centromeres, but pairing and recombination along the arms of the homologs, that directs meiotic chromosome segregation.
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Yuan, Xiuyun, Siqi Yuan, Ya Liu, Yun Xia, and Xiaomao Zeng. "Microsatellites mapping for non-model species with chromosomal rearrangement: a case study in the frog Quasipaa boulengeri (Anura: Dicroglossidae)." Genome 60, no. 8 (August 2017): 707–11. http://dx.doi.org/10.1139/gen-2016-0200.

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Gene mapping is an important resource for understanding the evolution of genes and cytogenetics. Model species with a known genetic map or genome sequence allow for the selection of genetic markers on a desired chromosome, while it is hard to locate these markers on chromosomes of non-model species without such references. A frog species, Quasipaa boulengeri, shows chromosomal rearrangement polymorphisms, making itself a fascinating model for chromosomal speciation mediated by suppressed recombination. However, no markers have been located on its rearranged chromosomes. We present a complete protocol to map microsatellites based on mechanical microdissection and chromosome amplification techniques. Following this protocol, we mapped 71 microsatellites of Q. boulengeri at the chromosome level. In total, eight loci were assigned to rearranged chromosomes, and the other 63 loci might attach to other chromosomes. These microsatellites could be used to compare the gene flow and verify the chromosomal suppressed recombination hypothesis in Q. boulengeri. This integrated protocol could be effectively used to map genes to chromosomes for non-model species.
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Dissertations / Theses on the topic "Chromosomes"

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Morroll, Shaun Michael. "Mapping of yeast artificial chromosomes from Arabidopsis chromosome 5." Thesis, University of Nottingham, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308922.

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Downie, Sarah Elizabeth. "Detection of chromosomes and chromosomal abnormalities in human sperm." Title page, contents and overview only, 1999. http://web4.library.adelaide.edu.au/theses/09PH/09phd751.pdf.

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Bibliography: leaves 135-151. A study of chromosomal abnormalities and the localisation of chromosomes in human sperm, especially from men with TSD, using fluorescence in situ hybridization (FISH). The project entailed: 1. development of reliable FISH protocols, 2. determination of basline frequencies of aneuploidy, 3. analysis of chromosomal abnormalities in men with severe TSD and 4. assessment of the localisation of individual chromosomes within the sperm head.
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Morey, Céline. "Caractérisation du rôle de la région en aval du gène Xist lors de l'inactivation du chromosome X murin par mutagenèse ciblée dans les cellules ES." Paris 5, 2004. http://www.theses.fr/2004PA05N040.

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Chez les mammifères, la compensation de dose des gènes liés à l' X entre les sexes est assurée par l' inactivation transcriptionnelle de l' un des deux chromosomes X, au hasard, chez la femelle. Ce processus dépend des fonctions de comptage et de choix et recquiert l' expression du gène Xist localisé sur le chromosome X. Ce gène produit un grand ARN non-codant qui recouvre le chromosome X inactif. La délétion de 65 kb en aval de Xist, incluant le minisatellite DXPas 34 et l' initiation d' une transcription antisens (Tsix), dans des cellules ES-cellules récapitulant l' inactivation lors de leur différenciation in vitro-induit l'altération du choix et du comptage. Par une stratégie de complémentation cre/oxP, nous avons montré que la restitution de Tsix au site de la délétion de 65 kb dans les cellules XX est insuffisante au rétablissement de l' inactivation aléatoire. . .
In mammals, dosage compensation of X-linked genes is ensured by X-chromosome inactivation wherby one X chromosome in each female embryonic cell (ES) is chosen at random to become silenced. X-inactivation depends on the counting of X chromosomes and on the choice of the inactive X, It is mediated by the expression of the Xist non-coding RNA wich coats the inactive X and by the Tsix antisense transcipt, a Tsix antisense transcript, a Xist regulator. A 65 kb deletion extending 3' to Xist and including both Tsix and the DXPas34 minisatellite, disrupts choice and counting. Using a cre/loxP site-specific re-insertion strategy in XX deleted ES cells we showed that targeting back, at the 65 kb mutated locus, the Tsix antisense transcription fails to retore random X-inactivation. In contrast, normal counting can be restored in XO deleted ES cells. .
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Landmann, Cedric. "Rôles et régulations de Polo et BubR1 sur les cassures double-­‐brin de l'ADN en mitose." Thesis, Bordeaux, 2017. http://www.theses.fr/2017BORD0852/document.

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La présence de cassures double-brin de l'ADN en mitose est problématique pour les cellules, car cette situation produit des fragments de chromosome ne possédant pas de centromères. En l'absence d'un mécanisme permettant leur prise en charge, ces fragments acentriques n'étant pas attachés au fuseau mitotique, pourraient être ségrégés aléatoirement dans les cellules filles, causant de l'instabilité génomique. Nous avons découvert un mécanisme permettant la transmission correcte des fragments acentriques dans les cellules filles via une structure faisant le lien entre les deux fragments cassés. Plusieurs protéines sont recrutées sur les cassures, comme les kinases mitotiques BubR1 et Polo, et favorisent la ségrégation correcte de ces chromosomes cassés. Cependant, les mécanismes permettant le recrutement de BubR1 et Polo sur les cassures d'ADN en mitose sont inconnus. De plus, les mécanismes moléculaires par lesquels BubR1 et Polo favorisent la ségrégation correcte des fragments acentriques restent à être identifiés. La première partie de mon projet a été d'étudier le rôle et la régulation de BubR1 sur les cassures d'ADN pendant la mitose. Nous avons montré que BubR1 requiert Bub3 pour se localiser sur les chromosomes cassés afin de favoriser leur ségrégation correcte. Nous avons également détecté l'accumulation de FizzyCDC20, un cofacteur de l'E3 ubiquitine ligase APC/C (Anaphase-Promoting- Complex/Cyclosome), sur les cassures d'ADN, et son recrutement dépend de son interaction avec la KEN Box de BubR1. De plus, l'utilisation d'un substrat synthétique de l'APC/C nous a permis de démontrer que la dégradation par l'APC/C est inhibée localement autour du chromosome cassé, de manière dépendante de BubR1. Ces résultats suggèrent fortement que le complexe BubR1/Bub3 recrut é sur les cassures d'ADN inhibe localement l'APC/C en séquestrant FizzyCDC20 et empêche ainsi la dégradation de substrats clefs impliqués dans la ségrégation correcte des chromosomes cassés. La seconde partie de mon projet a été d'étudier les relations d'interdépendance entre Polo et BubR1/Bub3/Fizzy sur les cassures d'ADN en mitose. Nous avons utilisé un laser UV pulsé pour induire des cassures dans un chromosome à un instant précis pendant la mitose, puis nous avons suivi le recrutement de protéines tagguées GFP sur les cassures de chromosome. Cette étude révèle que Polo est rapidement recrutée sur les cassures d'ADN et précède BubR1, Bub3 et Fizzy. De plus, la disparition de BubR1, Bub3 et Fizzy des cassures d'ADN coïncide avec la télophase alors que Polo disparait des cassures pendant l'interphase. Nous avons également montré que le recrutement de BubR1, Bub3 et Fizzy sur les cassures d'ADN est retardé dans les mutants polo, indiquant que Polo est requis pour un recrutement efficace de BubR1, Bub3 et Fizzy sur les cassures d'ADN. Pour finir, nous avons montré que l'accumulation de Polo et BubR1/Bub3/Fizzy sur les cassures d'ADN dépend de deux composants de la réponse aux dommages à l'ADN, le complexe MRN (Mre11-Rad50-Nbs1) et ATM (ataxia-telangiectasia mutated). Ce travail a permis d'avoir une meilleure compréhension sur la dynamique de recrutement de Polo et BubR1/Bub3/Fizzy sur les cassures d'ADN en mitose. De plus, le mécanisme moléculaire par lequel le complexe BubR1/Bub3 agit pour faciliter la ségrégation des chromosomes cassés a pu être en partie élucidé
The presence of DNA double strand breaks (DSB) during mitosis is challenging for the cell, as it produces fragments of chromosome lacking a centromere. If not processed, this situation can cause genomic instability resulting in improper segregation of the broken fragments into daughter cells. We uncovered a mechanism by which broken chromosomes are faithfully transmitted to daughter cells via the tethering of the two broken chromosome ends. Several proteins including the mitotic kinase BubR1 and Polo are recruited to the breaks and mediate the proper segregation of the broken fragments. However, the mechanism underlying Polo and BubR1 recruitment to DNA breaks is unknown. Moreover, the molecular mechanisms by which Polo and BubR1 mediate the proper segregation of the broken fragments remain to be elucidated. We first investigated the role and regulation of BubR1 on DNA breaks during mitosis. We show that BubR1 requires Bub3 to localize on the broken chromosome fragment and to mediate its proper segregation. We also find that FizzyCdc20, a co--‐factor of the E3 ubiquitin ligase Anaphase--‐Promoting--‐Complex/Cyclosome (APC/C), accumulates on DNA breaks in a BubR1 KEN box--‐dependent manner. A biosensor for APC/C activity demonstrates a BubR1--‐dependent local inhibition of APC/C around the segregating broken chromosome. These results are consistent with a model where Bub3/BubR1 complex on DNA breaks functions to inhibit the APC/C locally via the sequestration of FizzyCdc20, thus preserving key substrates from degradation, which promotes proper transmission of broken chromosomes. In a second study, we investigated the dependency relationship between Polo and BubR1/Bub3/Fizzy on DNA breaks in mitosis. We used a pulsed UV laser to break one chromosome at a define time during mitosis. We immediately follow the recruitment of GFP--‐tagged proteins to laser--‐induced DNA breaks. My study reveals that Polo is promptly recruited to DNA breaks and precedes BubR1, Bub3 and Fizzy. In addition, while BubR1, Bub3 and Fizzy dissociation from the breaks coincide with telophase and the nuclear envelope reformation, Polo remains on the breaks well into interphase. We further show that the appearance of BubR1, Bub3 and Fizzy on DNA breaks is delayed in polo mutant, indicating that Polo is required for the robust and efficient recruitment of BubR1, Bub3 and Fizzy to DNA breaks. Finally, the timely accumulation of Polo, BubR1 and Bub3 to DNA breaks depends on two components of the DNA Damage Response, the MRN complex (Mre11--‐Rad50--‐Nbs1) and ATM (ataxia--‐telangiectasia mutated). This work gives us a better understanding on how Polo and BubR1, Bub3 and FizzyCdc20 are recruited to DNA breaks in mitosis and how they promote broken chromosomes segregation
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Prades, Catherine. "Recherche de marqueurs polymorphes dans les régions centromériques des chromosomes humains." Montpellier 1, 1997. http://www.theses.fr/1997MON1T007.

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Imakaev, Maksim (Maksim Viktorovich). "Polymer models of chromosomes." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/103234.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, 2016.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 203-215).
Studies of chromosomes have a long history. Since late XIX century, microscopy studies have revealed that chromosomal organization as seen by light microscopy is different among organisms, cell types, or stages of the cell cycle. However, the internal organization of chromosomes at scales below the diffraction limit largely remained unexplored. Recently, genomic techniques to measure contacts between genomic regions were developed; the most advanced of them, Hi-C, measures probabilities of contact between all pairs of genomic regions. Throughout my Ph.D, we have been developing methods to analyze Hi-C data, and to infer principles of chromosomal organization from the contact map provided by Hi-C. As a first step, we developed a toolset to map, analyze, and correct the Hi-C data. We then we performed polymer simulations that implement hypothetical principles of chromosomal organization and compared them to the Hi-C data. We showed that mitotic chromosomes in humans are not organized hierarchically, as thought previously, and are likely folded as an array of consecutive chromosomal loops. In the bacterium Caulobacter Crescentus, we showed that the chromosome is organized as a dense array of supercoiled plectonemes interspersed by highly transcribed regions free of plectonemes. Finally, for human interphase chromosomes, we showed that the equilibrium state of a long unknoted polymer chain is inconsistent with the observed properties of chromosomes.
by Maksim Imakaev.
Ph. D.
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Mascarenhas, Judita. "Chromosome dynamics in Bacillus subtilis characterization of the structural maintenance of chromosomes (SMC) complex /." [S.l. : s.n.], 2004. http://archiv.ub.uni-marburg.de/diss/z2004/0125/.

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Kulharya, Anita S. (Anita Singh). "Cytogenetics of chromosome 22 and its clinical relevance." Thesis, University of North Texas, 1990. https://digital.library.unt.edu/ark:/67531/metadc798385/.

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This investigation reorganizes and identifies chromosomal anomalies and delineates the associated clinical findings. The present investigation involved 37 individuals with anomalies of chromosome 22. The clinical profile with the corresponding cytogenetic anomalies was studied.
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Coultas, Susan L. (Susan Lynette). "A comparison of straight-stained, Q-stained, and reverse flourescent-stained cell lines for detection of fragile sites on the human X chromosome." Thesis, North Texas State University, 1985. https://digital.library.unt.edu/ark:/67531/metadc798127/.

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Cell cultures were examined for percentage of fragile sites seen in straight-stained, Q-stained and reverse fluorescent-stained preparations. In all cases, percentage of fragile site expression was decreased when compared to straight-stained preparations. However, fragile sites seen in Q- and RF-stain could be identified as on X chromosomes.
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Khalil, Ahmad M. "Histone modifications and chromatin dynamics of the mammalian inactive sex chromosomes title." [Gainesville, Fla.] : University of Florida, 2004. http://purl.fcla.edu/fcla/etd/UFE0008329.

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Thesis (Ph.D.)--University of Florida, 2004.
Typescript. Title from title page of source document. Document formatted into pages; contains 102 pages. Includes Vita. Includes bibliographical references.
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Books on the topic "Chromosomes"

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Clark, M. S., and W. J. Wall. Chromosomes. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0073-8.

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Olmo, Ettore, and Carlo Alberto Redi, eds. Chromosomes Today. Basel: Birkhäuser Basel, 2000. http://dx.doi.org/10.1007/978-3-0348-8484-6.

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Therman, Eeva. Human Chromosomes. New York, NY: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-0269-8.

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Therman, Eeva, and Millard Susman. Human Chromosomes. New York, NY: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4684-0529-3.

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Miller, Orlando J., and Eeva Therman. Human Chromosomes. New York, NY: Springer New York, 2001. http://dx.doi.org/10.1007/978-1-4613-0139-4.

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Henriques-Gil, N., J. S. Parker, and M. J. Puertas, eds. Chromosomes Today. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-1537-4.

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Sumner, A. T., and A. C. Chandley. Chromosomes Today. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1510-0.

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Schmid, Michael, and Indrajit Nanda, eds. Chromosomes Today. Dordrecht: Springer Netherlands, 2004. http://dx.doi.org/10.1007/978-94-017-1033-6.

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Stahl, A., J. M. Luciani, and A. M. Vagner-Capodano, eds. Chromosomes Today. Dordrecht: Springer Netherlands, 1987. http://dx.doi.org/10.1007/978-94-010-9166-4.

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Callan, Harold Garnet. Lampbrush Chromosomes. Berlin, Heidelberg: Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-82792-1.

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Book chapters on the topic "Chromosomes"

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Paro, Renato, Ueli Grossniklaus, Raffaella Santoro, and Anton Wutz. "Dosage Compensation Systems." In Introduction to Epigenetics, 67–89. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-68670-3_4.

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AbstractThis chapter provides an introduction to chromosome-wide dosage compensation systems. We will examine the evolution of dosage compensation, which is thought to be driven by the appearance of differentiated sex chromosomes. In a subset of species with X chromosomal sex determination or XY sex chromosome systems, expression of X-linked genes is regulated by chromosome-wide modifications that equalize gene expression differences between males and females. The molecular mechanisms of X chromosome-wide dosage compensation have been studied in flies, worms, and mammals. Each of these species uses a distinct dosage compensation strategy with a different molecular mechanism. In the wormCaenorhabditis elegans, gene expression on the two X chromosomes of hermaphrodites is reduced to a level that approximates a single X chromosome in males. The fruit flyDrosophila melanogasterachieves dosage compensation by increased transcription of the single X chromosome in males to a level that is similar to the two X chromosomes in females. Lastly, in mammals, one of the two X chromosomes in female cells is transcriptionally inactive and a single X chromosome is transcribed in both sexes. Studies of dosage compensation systems provide insights into how epigenetic regulation controls gene expression and chromatin organization differentially within a cell.
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Li, Le, Trude Schwarzacher, Paulina Tomaszewska, Qing Liu, Xiaoyu Zoe Li, Kexian Yi, Weihuai Wu, and J. S. Pat Heslop-Harrison. "Protocols for Chromosome Preparations: Molecular Cytogenetics and Studying Genome Organization in Coffee." In Mutation Breeding in Coffee with Special Reference to Leaf Rust, 291–314. Berlin, Heidelberg: Springer Berlin Heidelberg, 2023. http://dx.doi.org/10.1007/978-3-662-67273-0_21.

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AbstractCytological preparations from cell nuclei are required to count the number of chromosomes (including determining ploidy or aneuploidy), to investigate their morphology and organization. The results are valuable for genetic and evolutionary studies, and in breeding programs to understand species relationships, polyploidy, and potential introgression of chromosomes in hybrids between different species. Preparation of good chromosome spreads with well-separated metaphase chromosomes is the foundation of cytogenetic research including chromosomal mapping based on FISH (fluorescence in situ hybridization). FISH combined with specific locus probes correlated with molecular markers to specific chromosomes for integrating physical and linkage maps as well as studying the genetic evolution of allopolyploidization, has rarely been applied in Coffea spp. despite being a global high-value crop. Cytogenetic studies of Coffea are limited by the small size and similar morphology of the chromosomes, but FISH can help to map sequences to chromosome arms and identify individual chromosomes. This chapter presents protocols for germinating seeds and growing coffee plants involving pre-treatment and fixation of root-tips where the meristems of actively growing roots have many divisions. Mitotic metaphase chromosome preparation on microscope slides is described, as well as preparing probes of 5S and 18S rDNA to be used for FISH. The FISH experiments involve a two-step protocol with pre-treatments and setting up the hybridization on day 1 and the detection of probe sites on day 2 after overnight hybridization. A final section gives advice about visualization using a fluorescent microscope and capturing images.
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Feldman, Moshe, and Avraham A. Levy. "B Chromosomes." In Wheat Evolution and Domestication, 71–84. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-30175-9_4.

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AbstractThis chapter describes supernumerary or accessory chromosomes (B-chromosomes) in several grasses focusing on those in species of the sub-tribe Triticineae of the tribe Triticeae. It refers to their origin, molecular characterization, preferential transmission (accumulation mechanism), effect on morphology, fitness, and chromosomal pairing in species and hybrids, and their transcriptional activity.
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Clark, M. S., and W. J. Wall. "Chromatin structure and replication." In Chromosomes, 1–26. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0073-8_1.

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Clark, M. S., and W. J. Wall. "Artificial manipulation of genomes." In Chromosomes, 258–88. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0073-8_10.

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Clark, M. S., and W. J. Wall. "Historical aspects of cytogenetics." In Chromosomes, 289–302. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0073-8_11.

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Clark, M. S., and W. J. Wall. "Chromosome form and function." In Chromosomes, 27–71. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0073-8_2.

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Clark, M. S., and W. J. Wall. "Chromosome identification." In Chromosomes, 72–93. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0073-8_3.

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Clark, M. S., and W. J. Wall. "Nuclear division." In Chromosomes, 94–132. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0073-8_4.

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Clark, M. S., and W. J. Wall. "Gene control by position and origin." In Chromosomes, 133–46. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0073-8_5.

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Conference papers on the topic "Chromosomes"

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Rodrigues, Rodrigo, Rubens Pasa, Karine Kavalco, and João Fernando Mari. "Segmentation of fish chromosomes in microscopy images: A new dataset." In Workshop de Visão Computacional. Sociedade Brasileira de Computação - SBC, 2020. http://dx.doi.org/10.5753/wvc.2020.13481.

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The chromosome segmentation is the most important step in automatic karyotype assembling. In this work, we presented a brand new chromosome image dataset and proposed methods for segmenting the chromosomes. Chromosome images are usually low quality, especially fish chromosomes. In order to overcome this issue, we tested three filters to reduce noise and improve image quality. After filtering, we applied adaptive threshold segmentation combined with mathematical morphology and supervised classification methods. Support Vector Machine and k-nearest neighbors were applied to discriminate between chromosomes and image background. The proposed method was applied to segment chromosomes in a new dataset. To enable measure the performance of the methods all chromosomes were manually delineated. The results are evaluated considering the Hausdorff distance and normalized sum of distances between segmented and reference images.
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Smith, Warren E., and Seth A. Maislin. "Fluorescent imaging approach to the automatic determination of chromosome damage." In OSA Annual Meeting. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/oam.1992.thnn6.

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Chromosome damage is produced by several types of agents, including ionizing radiation. There is a need for rapid measurement of such damage in the event of an accident to assist in the determination of the extent of exposure and the planning of consequent therapy. In current practice, radiation damage is measured by operator-intensive analysis of microscope images of suitably prepared lymphocyte chromosomes from the exposed individual. Some of the features looked for are chromosome breakage, dicentrics (chromosomes with two centromeres), and chromosome translocations (unnatural joining of chromosomes).
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Alekseeva, S. S., Yu V. Andreeva, I. E. Wasserlauf, A. K. Sibataev, and V. N. Stegniy. "SPECIES SPECIFICITY OF HETEROCHROMATIN BLOCK DISTRIBUTION AND rDNA LOCALIZATION IN MITOTIC CHROMOSOMES OF MOSQUITOES SPECIES AEDES EXCRUCIANS, AE. BEHNINGI AND AE. PUNCTOR." In V International Scientific Conference CONCEPTUAL AND APPLIED ASPECTS OF INVERTEBRATE SCIENTIFIC RESEARCH AND BIOLOGICAL EDUCATION. Tomsk State University Press, 2020. http://dx.doi.org/10.17223/978-5-94621-931-0-2020-2.

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A karyotypic analysis of three mosquito species Aedes excrucians, Ae. behningi and Ae. punctor (Diptera: Culicidae). Differences in the lengths of chromosomes, the distribution of C- and DAPI blocks of heterochromatin, and the localization of rDNA genes on chromosomes were revealed. Aedes excrucians has the largest chromosome length among the three species represented. Ae. punctor differs in the localization of rDNA on the second chromosome, while in Aedes excrucians and Ae. behningi, rDNA genes are located on chromosome 1. All three species have different C-banding and species-specific localization of heterochromatin DAPI blocks. Consequently, chromosome analysis can serve as an additional mechanism for species identification of mosquitoes of the genus Aedes.
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Anderson, Kurt S., and YuHung Hsu. "Crossover Strategy for Improved Solution Space Exploration With Genetic Algorithms." In ASME 1998 Design Engineering Technical Conferences. American Society of Mechanical Engineers, 1998. http://dx.doi.org/10.1115/detc98/dac-5617.

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Abstract The following paper presents a modified crossover operator to extend the exploration capability in Genetic Algorithms for high dimensional optimization problems. Traditional strategies apply crossover once on a pair of selected chromosomes to generate two offspring by randomly selecting a single crossover location within the chromosomal length. The proposed method applies crossover once on each separate gene (variable) instead of on the entire chromosome. To further accelerate exploration of the Genetic Algorithm, nonuniform distribution of the respective crossover position on each gene has also been studied. The empirical results show that Genetic Algorithms with the proposed crossover strategies can find optimal or near optimal solutions within fewer generations than traditional single point crossover.
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Saranya, S., and S. Lakshmi. "Classification of Chromosomes to Diagnose Chromosomal Abnormalities using CNN." In 2023 International Conference on Artificial Intelligence and Knowledge Discovery in Concurrent Engineering (ICECONF). IEEE, 2023. http://dx.doi.org/10.1109/iceconf57129.2023.10083710.

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Trykin, Alexander Mikhailovich. "Interphase FISH-analysis Processing of Chromosomal Mosaicism on Blood Cell Nuclei Preparations." In 33rd International Conference on Computer Graphics and Vision. Keldysh Institute of Applied Mathematics, 2023. http://dx.doi.org/10.20948/graphicon-2023-633-642.

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Fluorescence in situ hybridization (FISH) is a molecular cytogenetic technique. It provides a powerful tool for understanding genetic and genomic processes, diagnosing genetic disorders, and studying the structure and function of genes and chromosomes. This paper proposes a method for automatic object segmentation of preparations of blood cell nuclei and a method for detecting chromosomes with the aim of further studying them for chromosomal mosaicism. Based on the data provided by the laboratory of the Institute of Biology and Biomedicine of Lobachevsky University, the SOTA deep learning model YOLOv8-seg was trained. This was made possible by marking up a small portion of the 87 images. Experiment on model training for segmentation showed very good quality metrics: Precision = 0.940, Recall = 0.980, mAP[0.5] = 0.991 and mAP[0.5:0.95] = 0.764. After that, a method for detecting chromosomes was proposed, based on the classical principles of image processing and computer vision, due to the lack of the necessary labelled data.
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Zaccaron, Alex. "Impact of genomic structural variations on virulence of the tomato pathogen Cladosporium fulvum." In IS-MPMI Congress. IS-MPMI, 2023. http://dx.doi.org/10.1094/ismpmi-2023-1.

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Cladosporium fulvum causes tomato leaf mold and has been extensively used in the past as a model species to study plant-microbe interactions. Although the first chromosome-scale reference genome of the fungus was released in 2022, still little is known about how its genome architecture and structural variations (SVs) thereof impact its virulence. In this study, we used PacBio HiFi to sequence the genomes of four additional C. fulvum isolates and further assembled them at chromosome level. Comparative genome analyses revealed high chromosomal synteny among the five isolates, and a set of 13 core and two dispensable chromosomes, one of which carries pseudogenized copies of effector genes and likely emerged by duplication of subtelomeric regions of core chromosome. Between 14906 and 14993 genes were predicted in each C. fulvum genome with an estimated completeness of >99%. A pangenome analysis of the five isolates revealed a low number of 331 accessory genes, indicating high conservation of gene content among isolates of the fungus. An analysis of SVs showed no enriched of effectors or of other pathogenicity-related genes in these regions. However, SVs in subtelomeric regions affected virulence by prompting the loss of effector genes residing in them, as we have found is the case for the Avr9 effector gene of C. fulvum. Collectively, these results provide new insights of how genomic SVs can contribute to virulence of fungal pathogens.
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Gao, X. Q., and M. R. Chapron. "Interactive classification of chromosomes." In 1992 14th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 1992. http://dx.doi.org/10.1109/iembs.1992.5760918.

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Gao and Chapron. "Interactive Classification Of Chromosomes." In Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 1992. http://dx.doi.org/10.1109/iembs.1992.589614.

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Kumar, Sushrut, Priyam Gupta, and Raj Kumar Singh. "A Natural Evolution Based Numerical Optimisation Framework to Develop and Enhance Airfoil-Slat Arrangement." In ASME 2019 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2019. http://dx.doi.org/10.1115/imece2019-10846.

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Abstract Leading Edge Slats are popularly being put into practice due to their capability to provide a significant increase in the lift generated by the wing airfoil and decrease in the stall. Consequently, their optimum design is critical for increased fuel efficiency and minimized environmental impact. This paper attempts to develop and optimize the Leading-Edge Slat geometry and its orientation with respect to airfoil using Genetic Algorithm. The class of Genetic Algorithm implemented was Invasive Weed Optimization as it showed significant potential in converging design to an optimal solution. For the study, Clark Y was taken as test airfoil. Slats being aerodynamic devices require smooth contoured surfaces without any sharp deformities and accordingly Bézier airfoil parameterization method was used. The design process was initiated by producing an initial population of various profiles (chromosomes). These chromosomes are composed of genes which define and control the shape and orientation of the slat. Control points, Airfoil-Slat offset and relative chord angle were taken as genes for the framework and different profiles were acquired by randomly modifying the genes within a decided design space. To compare individual chromosomes and to evaluate their feasibility, the fitness function was determined using Computational Fluid Dynamics simulations conducted on OpenFOAM. The lift force at a constant angle of attack (AOA) was taken as fitness value. It was assigned to each chromosome and the process was then repeated in a loop for different profiles and the fittest wing slat arrangement was obtained which had an increase in CL by 78% and the stall angle improved to 22°. The framework was found capable of optimizing multi-element airfoil arrangements.
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Reports on the topic "Chromosomes"

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Antonarakis, S. E. Human Chromosome 21: Mapping of the chromosomes and cloning of cDNAs. Office of Scientific and Technical Information (OSTI), September 1991. http://dx.doi.org/10.2172/6397375.

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Antonarakis, S. E. Human chromosome 21: Linkage mapping and cloning in yeast artificial chromosomes. Office of Scientific and Technical Information (OSTI), January 1991. http://dx.doi.org/10.2172/6278130.

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Giddings, J. C. Field-flow fractionation of chromosomes. Office of Scientific and Technical Information (OSTI), April 1993. http://dx.doi.org/10.2172/6434224.

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Giddings, J. C. Field-flow fractionation of chromosomes. Office of Scientific and Technical Information (OSTI), September 1990. http://dx.doi.org/10.2172/6370502.

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Giddings, J. C. Field-flow fractionation of chromosomes. Office of Scientific and Technical Information (OSTI), September 1991. http://dx.doi.org/10.2172/5745557.

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Feldman, Moshe, Eitan Millet, Calvin O. Qualset, and Patrick E. McGuire. Mapping and Tagging by DNA Markers of Wild Emmer Alleles that Improve Quantitative Traits in Common Wheat. United States Department of Agriculture, February 2001. http://dx.doi.org/10.32747/2001.7573081.bard.

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The general goal was to identify, map, and tag, with DNA markers, segments of chromosomes of a wild species (wild emmer wheat, the progenitor of cultivated wheat) determining the number, chromosomal locations, interactions, and effects of genes that control quantitative traits when transferred to a cultivated plant (bread wheat). Slight modifications were introduced and not all objectives could be completed within the human and financial resources available, as noted with the specific objectives listed below: 1. To identify the genetic contribution of each of the available wild emmer chromosome-arm substitution lines (CASLs) in the bread wheat cultivar Bethlehem for quantitative traits, including grain yield and its components and grain protein concentration and yield, and the effect of major loci affecting the quality of end-use products. [The quality of end-use products was not analyzed.] 2. To determine the extent and nature of genetic interactions (epistatic effects) between and within homoeologous groups 1 and 7 for the chromosome arms carrying "wild" and "cultivated" alleles as expressed in grain and protein yields and other quantitative traits. [Two experiments were successful, grain protein concentration could not be measured; data are partially analyzed.] 3. To derive recombinant substitution lines (RSLs) for the chromosome arms of homoeologous groups 1 and 7 that were found previously to promote grain and protein yields of cultivated wheat. [The selection of groups 1 and 7 tons based on grain yield in pot experiments. After project began, it was decided also to derive RSLs for the available arms of homoeologous group 4 (4AS and 4BL), based on the apparent importance of chromosome group 4, based on early field trials of the CASLs.] 4. To characterize the RSLs for quantitative traits as in objective 1 and map and tag chromosome segments producing significant effects (quantitative trait loci, QTLs by RFLP markers. [Producing a large population of RSLs for each chromosome arm and mapping them proved more difficult than anticipated, low numbers of RSLs were obtained for two of the chromosome arms.] 5. To construct recombination genetic maps of chromosomes of homoeologous groups 1 and 7 and to compare them to existing maps of wheat and other cereals [Genetic maps are not complete for homoeologous groups 4 and 7.] The rationale for this project is that wild species have characteristics that would be valuable if transferred to a crop plant. We demonstrated the sequence of chromosome manipulations and genetic tests needed to confirm this potential value and enhance transfer. This research has shown that a wild tetraploid species harbors genetic variability for quantitative traits that is interactive and not simply additive when introduced into a common genetic background. Chromosomal segments from several chromosome arms improve yield and protein in wheat but their effect is presumably enhanced when combination of genes from several segments are integrated into a single genotype in order to achieve the benefits of genes from the wild species. The interaction between these genes and those in the recipient species must be accounted for. The results of this study provide a scientific basis for some of the disappointing results that have historically obtained when using wild species as donors for crop improvement and provide a strategy for further successes.
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Barker, D. F. Molecular mapping of chromosomes 17 and X. Office of Scientific and Technical Information (OSTI), January 1989. http://dx.doi.org/10.2172/6697096.

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Durham, Mary. Demonstrating Meiosis Using Manipulatable Chromosomes and Cells. Genetics Society of America Peer-Reviewed Education Portal (GSA PREP), May 2015. http://dx.doi.org/10.1534/gsaprep.2015.002.

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Barker, D. F. Molecular mapping of chromosomes 17 and X. Office of Scientific and Technical Information (OSTI), January 1991. http://dx.doi.org/10.2172/6659529.

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Dubcovsky, Jorge, and T. (Tzion) Fahima. Validation of candidate genes for a QTL responsible for water stress tolerance and their diversity in wheat. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2022. http://dx.doi.org/10.32747/2022.8134149.bard.

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The main goals of this project as stated in the original proposal were to identify which of the candidate gene(s) identified in a 1.5 Mb region of wheat and rye chromosomes 1RS and 1BS were responsible for the differences in root architecture, reveal their natural variation and characterize the epistatic interactions that modulate their effect in different backgrounds. Background: Wheat is an essential crop for global food security and is well adapted to a wide variety of soils. However, the gene networks regulating different wheat root architectures remain poorly understood. Root depth and biomass distribution in the soil profile are critical traits for adaptation to water stress, and a good source for these traits is the introgression of the short arm of rye chromosome one (1RS) into common wheat. A recombinant 1RS chromosome with a small wheat 1BS introgressions and a duplicated 1RS segment (1RW) showed reduced drought tolerance and was used for the identification of the causal genes.
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