Relevant bibliographies by topics / Chromosoms structure

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  2. Dissertations / Theses
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Academic literature on the topic 'Chromosoms structure'

Author: Grafiati
Published: 4 April 2023

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Journal articles on the topic "Chromosoms structure"

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Liehr, Thomas. "From Human Cytogenetics to Human Chromosomics." International Journal of Molecular Sciences 20, no. 4 (February 14, 2019): 826. http://dx.doi.org/10.3390/ijms20040826.

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Background: The concept of “chromosomics” was introduced by Prof. Uwe Claussen in 2005. Herein, the growing insights into human chromosome structure finally lead to a “chromosomic view” of the three-dimensional constitution and plasticity of genes in interphase nuclei are discussed. This review is dedicated to the memory of Prof. Uwe Claussen (30 April 1945–20 July 2008). Recent findings: Chromosomics is the study of chromosomes, their three-dimensional positioning in the interphase nucleus, the consequences from plasticity of chromosomal subregions and gene interactions, the influence of chromatin-modification-mediated events on cells, and even individuals, evolution, and disease. Progress achieved in recent years is summarized, including the detection of chromosome-chromosome-interactions which, if damaged, lead to malfunction and disease. However, chromosomics in the Human Genetics field is not progressing presently, as research interest has shifted from single cell to high throughput, genomic approaches. Conclusion: Chromosomics and its impact were predicted correctly in 2005 by Prof. Claussen. Although some progress was achieved, present reconsiderations of the role of the chromosome and the single cell in Human Genetic research are urgently necessary.
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Pelttari, Jeanette, Mary-Rose Hoja, Li Yuan, Jian-Guo Liu, Eva Brundell, Peter Moens, Sabine Santucci-Darmanin, et al. "A Meiotic Chromosomal Core Consisting of Cohesin Complex Proteins Recruits DNA Recombination Proteins and Promotes Synapsis in the Absence of an Axial Element in Mammalian Meiotic Cells." Molecular and Cellular Biology 21, no. 16 (August 15, 2001): 5667–77. http://dx.doi.org/10.1128/mcb.21.16.5667-5677.2001.

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ABSTRACT The behavior of meiotic chromosomes differs in several respects from that of their mitotic counterparts, resulting in the generation of genetically distinct haploid cells. This has been attributed in part to a meiosis-specific chromatin-associated protein structure, the synaptonemal complex. This complex consist of two parallel axial elements, each one associated with a pair of sister chromatids, and a transverse filament located between the synapsed homologous chromosomes. Recently, a different protein structure, the cohesin complex, was shown to be associated with meiotic chromosomes and to be required for chromosome segregation. To explore the functions of the two different protein structures, the synaptonemal complex and the cohesin complex, in mammalian male meiotic cells, we have analyzed how absence of the axial element affects early meiotic chromosome behavior. We find that the synaptonemal complex protein 3 (SCP3) is a main determinant of axial-element assembly and is required for attachment of this structure to meiotic chromosomes, whereas SCP2 helps shape the in vivo structure of the axial element. We also show that formation of a cohesin-containing chromosomal core in meiotic nuclei does not require SCP3 or SCP2. Our results also suggest that the cohesin core recruits recombination proteins and promotes synapsis between homologous chromosomes in the absence of an axial element. A model for early meiotic chromosome pairing and synapsis is proposed.
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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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S. Ramos, Ana Carolina, and Samara Cao Paixão. "Montando cromossomos: o ensino das alterações cromossômicas estruturais de maneira inovadora." Revista Científica Faesa 16, no. 2 (August 1, 2020): 07–27. http://dx.doi.org/10.5008/1809.7367.174.

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Dooner, H. K., and A. Belachew. "Chromosome breakage by pairs of closely linked transposable elements of the Ac-Ds family in maize." Genetics 129, no. 3 (November 1, 1991): 855–62. http://dx.doi.org/10.1093/genetics/129.3.855.

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Abstract Chromosome breaks and hence chromosomal rearrangements often occur in maize stocks harboring transposable elements (TEs), yet it is not clear what types of TE structures promote breakage. We have shown previously that chromosomes containing a complex transposon structure consisting of an Ac (Activator) element closely linked in direct orientation to a terminally deleted or fractured Ac (fAc) element have a strong tendency to break during endosperm development. Here we show that pairs of closely linked transposons with intact ends, either two Ac elements--a common product of Ac transposition--or an Ac and a Ds (Dissociation) element, can constitute chromosome-breaking structures, and that the frequency of breakage is inversely related to intertransposon distance. Similar structures may also be implicated in chromosome breaks in other eukaryotic TE systems known to produce chromosomal rearrangements. The present findings are discussed in light of a model of chromosome breakage that is based on the transposition of a partially replicated macrotransposon delimited by the outside ends of the two linked TEs.
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Uchida, Tetsuya, Naoto Ishihara, Hiroyuki Zenitani, Keiichiro Hiratsu, and Haruyasu Kinashi. "Circularized Chromosome with a Large Palindromic Structure in Streptomyces griseus Mutants." Journal of Bacteriology 186, no. 11 (June 1, 2004): 3313–20. http://dx.doi.org/10.1128/jb.186.11.3313-3320.2004.

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ABSTRACT Streptomyces linear chromosomes display various types of rearrangements after telomere deletion, including circularization, arm replacement, and amplification. We analyzed the new chromosomal deletion mutants Streptomyces griseus 301-22-L and 301-22-M. In these mutants, chromosomal arm replacement resulted in long terminal inverted repeats (TIRs) at both ends; different sizes were deleted again and recombined inside the TIRs, resulting in a circular chromosome with an extremely large palindrome. Short palindromic sequences were found in parent strain 2247, and these sequences might have played a role in the formation of this unique structure. Dynamic structural changes of Streptomyces linear chromosomes shown by this and previous studies revealed extraordinary strategies of members of this genus to keep a functional chromosome, even if it is linear or circular.
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Eidelman, Yuri, Ilya Salnikov, Svetlana Slanina, and Sergey Andreev. "Chromosome Folding Promotes Intrachromosomal Aberrations under Radiation- and Nuclease-Induced DNA Breakage." International Journal of Molecular Sciences 22, no. 22 (November 10, 2021): 12186. http://dx.doi.org/10.3390/ijms222212186.

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The long-standing question in radiation and cancer biology is how principles of chromosome organization impact the formation of chromosomal aberrations (CAs). To address this issue, we developed a physical modeling approach and analyzed high-throughput genomic data from chromosome conformation capture (Hi-C) and translocation sequencing (HTGTS) methods. Combining modeling of chromosome structure and of chromosomal aberrations induced by ionizing radiation (IR) and nuclease we made predictions which quantitatively correlated with key experimental findings in mouse chromosomes: chromosome contact maps, high frequency of cis-translocation breakpoints far outside of the site of nuclease-induced DNA double-strand breaks (DSBs), the distinct shape of breakpoint distribution in chromosomes with different 3D organizations. These correlations support the heteropolymer globule principle of chromosome organization in G1-arrested pro-B mouse cells. The joint analysis of Hi-C, HTGTS and physical modeling data offers mechanistic insight into how chromosome structure heterogeneity, globular folding and lesion dynamics drive IR-recurrent CAs. The results provide the biophysical and computational basis for the analysis of chromosome aberration landscape under IR and nuclease-induced DSBs.
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Gunawardena, S., E. Heddle, and M. C. Rykowski. "‘Chromosomal puffing’ in diploid nuclei of Drosophila melanogaster." Journal of Cell Science 108, no. 5 (May 1, 1995): 1863–72. http://dx.doi.org/10.1242/jcs.108.5.1863.

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In situ hybridization has become a powerful technique for dissecting nuclear structure. By localizing nucleic acids with high precision, it is possible to infer the native structure of chromosomes, replication factories and transcript processing complexes. To increase the value of this technique, we have established the limits of resolution of two-color in situ hybridization to chromosomal DNA in diploid chromosomes of Drosophila embryonic nuclei. Using high-resolution 3-dimensional optical microscopy and computational image analysis, we establish that we can distinguish the location of chromosomal sequences that lie 27–29 kb apart within a 40 kb transcription unit with an accuracy of about 100 nm. Contrary to observations made in mammalian tissue culture cells, we find that when the gene is expressed, it assumes an open configuration, and that the extent of decondensation is variable from chromosome to chromosome. Further experiments suggest that variation in gene structure results from asynchrony in transcriptional elongation. We suggest that the phenomenon we observe is the diploid analog to chromosomal puffing that occurs in the transcriptionally active regions of Drosophila polytene chromosomes.
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Anderson, Lorinda K., Naser Salameh, Hank W. Bass, Lisa C. Harper, W. Z. Cande, Gerd Weber, and Stephen M. Stack. "Integrating Genetic Linkage Maps With Pachytene Chromosome Structure in Maize." Genetics 166, no. 4 (April 1, 2004): 1923–33. http://dx.doi.org/10.1093/genetics/166.4.1923.

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Abstract Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1) all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2) each RN corresponds to one crossover, and (3) the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r2 = 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well.
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Dissertations / Theses on the topic "Chromosoms structure"

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Heurteau, Alexandre. "Etude bioinformatique intégrative : déterminants et dynamique des interactions chromosomiques à longue distance." Electronic Thesis or Diss., Toulouse 3, 2019. http://www.theses.fr/2019TOU30343.

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Les protéines se liants aux insulateurs (IBPs) seraient impliquées dans la structuration tri-dimensionnelle des génomes en domaines topologiques (ou " TADs). Les TADs contribueraient notamment à séparer les compartiments inactifs/hétérochromatine et actifs/euchromatine. Les IBPs sont également capables de bloquer les contacts spécifiques entre les éléments activateurs ou "enhancers" d'un TAD et les promoteurs de gènes cibles présents dans un autre TAD. Ainsi, les insulateurs influenceraient l'expression des gènes selon plusieurs modes de régulations qui reste à être caractérisés à l'échelle du génome. Les résultats obtenus dans la première partie de ma thèse montrent comment les IBPs influenceraient l'expression des gènes selon un nouveau mécanisme de régulation, comme montré à l'échelle du génome de la Drosophile. Nos analyses bioinformatiques montrent que les IBPs régulent l'étalement de l'hétérochromatine répressive (H3K27me3) à la fois en cis et en trans. Les régulations en trans impliquent des boucles de chromatine entre insulateurs positionnés à la frontière de l'hétérochromatine et des insulateurs distants positionnés aux abords de gènes euchromatiniens. Ces étalements en trans conduisent à la formation de "micro-domaines" d'hétérochromatine réprimant ainsi les gènes distants. En particulier, un mutant d'insulateur qui empêche la formation de boucle diminue significativement l'établissement des micro-domaines. De plus, ces micro-domaines se formeraient au cours du développement suggérant un nouveau mécanisme insulateur-dépendant de régulation des gènes. De plus, nous un nouveau rôle de la Cohésine, un régulateur clé des boucles 3D chez l'homme, dans la régulation des ARN non codants (ncRNAs), incluant les "PROMoters uPstream Transcripts" (PROMPTs) et les enhancers RNAs (eRNAs). L'hélicase MTR4 est essentielle au contrôle de la stabilité des ARNs codants et non codants par son rôle dans les complexes nuclear-exosome targeting (NEXT) et pA-tail exosome targeting (PAXT). De manière intéressante, la déplétion de MTR4 et des sous-unités ZFC3H1 et ZCCHC8 (ou Z1 et Z8), a conduit à l'apparition de ncRNAs à l'échelle du génome. Curieusement, la cartographie des sites de liaison de MTR4 a mis en évidence que cette hélicase se lie sur des sites distants des PROMPTs. Plutôt que d'agir en cis, nos données suggèrent que la régulation des PROMPTs pourrait impliquer des contacts spécifiques à longue distance entre ces sites distants de liaison MTR4 et les promoteurs liés par Z1/Z8. Ainsi, l'intégration des données Hi-C et la détection des PROMPTS en conditions de déplétion de MTR4, Z1 ou Z8 ont souligné le rôle possible des interactions à longue distance dans la régulation des PROMPTs, depuis les sites distants MTR4. Ces travaux pourraient établir une nouvelle relation entre la structure 3D des génomes et la régulation des ARNs non codants
Insulator Binding Proteins (IBPs) could be involved in the three-dimensional folding of genomes into topological domains (or "TADs"). In particular, TADs would help to separate the inactive/heterochromatin and active/euchromatin compartments. IBPs are also able to block specific contacts between the activator or enhancer elements of one TAD and target gene promoters present in another TAD. Thus, insulators may influence gene expression according to several regulatory modes that have yet to be characterized at genome level. The results obtained in the first part of my thesis show how IBPs influence gene expression according to a new regulatory mechanism, as shown at the scale of the Drosophila genome. Our bioinformatics analyses show that IBPs regulate the spread of repressive heterochromatin (H3K27me3) both in cis and trans. Trans regulations involve chromatin loops between insulators positioned at the heterochromatin boundary and distant insulators positioned at the edges of euchromatic genes. Trans spreading leads to the formation of "micro-domains" of heterochromatin, thereby repressing distant genes. In particular, an insulator mutant that prevents loop formation significantly reduces the establishment of micro-domains. In addition, these micro-domains would be formed during development suggesting a new insulator-dependent mechanism for gene regulation. Furthermore, we could uncover a novel function of cohesion, a key regulator of 3D loops in humans, in regulating non-coding RNAs (ncRNAs), including "PROMoters uPstream Transcripts" (PROMPTs) and enhancers RNAs (eRNAs). The MTR4 helicase is essential to the control of coding and noncoding RNA stability by the human nuclear-exosome targeting (NEXT) complex and pA-tail exosome targeting (PAXT) complex. Remarkably, ncRNAs could be detected upon depletion of the Mtr4 helicase of the human NEXT complex. Moreover, depletion of additional NEXT subunits, ZFC3H1 and ZCCHC8 (or Z1 and Z8), also led to uncover ncRNAs often produced from the same loci as upon MTR4 depletion. Curiously however, mapping of Mtr4 binding sites highlighted that Mtr4 binds to sites that are distant from PROMPTs. Rather than acting in cis, our data suggest that regulation of PROMPTs could involve specific long-distance contacts between these distant MTR4 binding sites and promoters bound by Z1/Z8. As such, integration of Hi-C data together with the detection of PROMPTS upon MTR4-, Z1- or Z8- depletions highlight possible role of long-range interactions in regulating PROMPTs, from distant MTR4-bound sites. This work may establish a new relationship between the 3D structure of genomes and the regulation of ncRNAs
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Woodward, Jessica Christina. "Cell-lineage-specific chromosomal instability in condensin II mutant mice." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/22921.

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In order to equally segregate their genetic material into daughter cells during mitosis, it is essential that chromosomes undergo major restructuring to facilitate compaction. However, the process of transforming diffuse, entangled interphase chromatin into discrete, highly organised chromosomal structures is extremely complex, and currently not completely understood. The complexes involved in chromatin compaction and sister chromatid decatenation in preparation for mitosis include condensins I and II. Mutations in condensin subunits have been identified in human tumours, reflecting the importance of accurate cell division in the prevention of aneuploidy and tumour formation. Most mutations described in TCGA (The Cancer Genome Atlas) and COSMIC (Catalogue of Somatic Mutations in Cancer) are missense, and therefore likely to only partially affect condensin function. Most functional genetic studies of condensin, however, have used loss of function systems, which typically cause severe chromosome segregation defects and cell death. Mice carrying global hypomorphic mutations within the kleisin subunit of the condensin II complex develop T cell lymphomas. The Caph2nes/nes mouse model is therefore a good system for understanding how condensin dysfunction can influence tumourigenesis. However, little is known about which cellular processes are affected in mutant cells before transformation. I therefore set out to use the Caph2nes/nes mouse model to study the consequences of the condensin II deficiency on cell cycle regulation in several different hematopoietic lineages. The Caph2nes/nes mice are viable and fertile, with no obvious abnormalities other than the thymus, which is drastically reduced in size. Previous studies reported greater than a hundred-fold reduction in the number of CD4+ CD8+ thymocytes. I set out to understand why the alteration of a ubiquitously expressed protein which functions in a fundamental cellular process would result in such a cell-type specific block in development. To achieve this, I investigated the possibility that condensin II is involved in interphase processes as well as in mitosis. In addition, I studied the aspects of T cell development that may make this lineage particularly vulnerable to condensin II deficiency. Finally, I carried out a preliminary investigation into the biochemical properties of the condensin complexes. During my PhD., I found strong evidence to suggest that the Caph2nes/nes T cell-specific phenotype arises due to abnormal cell division. However, I was unable to find any evidence to support the hypothesis that the phenotype is a consequence of abnormal interphase processes. Upon systematic analysis of several stages of hematopoietic differentiation, I found that at a specific stage of T cell development, the mutation results in an increased proportion of cells with abnormal ploidy, followed by a drastic reduction in cell numbers. Erythroid cells revealed a similar increase in the frequency of hyperdiploid cells, but no reduction in cell numbers. B cells and hematopoietic precursors did not reveal an increase in hyperdiploidy, or a reduction in cell numbers in wildtype relative to mutant. Subsequently, I found preliminary evidence to suggest that the T cell-specificity may be due to more rapid progression of CD4+ CD8+ T cells from S phase to M phase, relative to other hematopoietic stages. Finally, a preliminary investigation into the biochemical properties of the condensin complex revealed apparent imbalances in the expression of condensin subunits in T, B and erythroid cells. The sedimentation profile of CAP-H2 from whole-thymus extract did not exclude the possibility that condensin subunits might be forming heavier-weight complexes with non-SMC proteins. Further work must be carried out to determine whether this sedimentation pattern is unique to T cells.
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Stear, Jeffrey Hamilton. "Studies of chromosome structure and movement in C. elegans /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/5056.

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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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Minnen, Anita [Verfasser], and Thorsten [Akademischer Betreuer] Mascher. "Structural Maintenance of Chromosomes (SMC) localization on the Bacillus subtilis chromosome / Anita Minnen. Betreuer: Thorsten Mascher." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2015. http://d-nb.info/1101344172/34.

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Lindow, Janet C. (Janet Christine) 1974. "A role for the Bacillus subtilis Structural Maintenance of Chromosomes (BsSMC) protein in chromosome organization and compaction." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/8385.

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Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Biology, 2002.
Includes bibliographical references.
All cells must compact their chromosomes in order for the DNA to fit inside the cell or nucleus. In Bacillus subtilis, and other bacteria, replication occurs simultaneously with the organization, compaction and segregation of newly duplicated chromosomal regions. My work indicates that the B. subtilis Structural Maintenance of Chromosomes (BsSMC) protein is involved in compacting and organizing the chromosome. Increasing the amount of supercoiling of DNA is a means to compact the chromosome. This thesis describes a role for BsSMC in supercoiling. I determined that BsSMC can alter the DNA topology of plasmids in vivo. There is also genetic evidence that BsSMC is involved in supercoiling. An smc null mutant is hypersensitive to inhibitors of DNA gyrase, which reduce the level of negative supercoiling in the cell. Conversely, depletion of Topoisomerase I, which increases the amount of negative supercoiling of the chromosome, partially suppresses the phenotype of an smc null mutant. These data are consistent with the model that BsSMC affects chromosome compaction by constraining positive supercoils. Interestingly, SMC-containing complexes in eukaryotes are able to constrain positive supercoils in vitro and affect chromosome architecture suggesting that there is a conserved function for SMC proteins in chromosome structure. I also determined the subcellular localization of BsSMC. I found that BsSMC is a moderately abundant protein that can bind to many regions of the chromosome. A portion of BsSMC localizes in a pattern similar to the replication machinery.
(cont.) Simultaneous localization of BsSMC and a component of the replisome revealed that they are usually in the same region of the cell but are not always colocalized. Finally, the formation of BsSMC foci is dependent on the presence of the nucleoid but not ongoing replication. I propose that BsSMC is acting to compact newly replicated DNA by affecting DNA topology and is thereby facilitating the partitioning of sister chromosomes to opposite halves of the cell.
by Janet C. Lindow.
Ph.D.
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Cinato, Elisa. "Structure et expression du gène IFNA R2 humain : identification de la deuxième chaîne du récepteur des interférons alpha/bêta." Montpellier 2, 1996. http://www.theses.fr/1996MON20042.

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Seule la premiere chaine du recepteur des ifn-alpha/beta avait ete caracterisee. Nous avons clone le gene ifnar2, qui appartient au groupe de genes de recepteurs des cytokines sur le chromosome 21 humain. Le gene ifnar2 est a l'origine de quatre messagers differents, codant pour trois proteines. Une est secretee, deux sont des proteines transmembranaires, partageant le meme domaine extracellulaire, mais avec queue cytoplasmique differente. Nous avons montre, par complementation dans les cellules humaines mutantes u5, que la proteine avec domaine intracellulaire long est un composant fonctionnel du recepteur des ifn-alpha/beta humain
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Francki, Michael G. "The midget chromosome as a model to study cereal chromosome structure /." Title page, contents and summary only, 1995. http://web4.library.adelaide.edu.au/theses/09PH/09phf823.pdf.

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Dadon, Daniel Benjamin. "3D chromosome structure and chromatin proteomics." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104174.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2016.
Cataloged from PDF version of thesis. "May 2016."
Includes bibliographical references.
The selective interpretation of the genome through transcription enables the production of every cell type's distinct gene expression program from a common genome. Transcription takes place within, and is controlled by, highly organized three-dimensional (3D) chromosome structures. The first part of the work presented here describes the generation of 3D chromosome regulatory landscape maps of human naive and primed embryonic stem cells. To create these 3D chromosome regulatory landscape maps, genome-wide enhancer and insulator locations were mapped and then placed into a 3D interaction framework formed by cohesin-mediated 3D chromosome structures. Enhancer (H3K27ac) and insulator (CTCF) locations were mapped using ChIP-sequencing, whereas 3D chromosome structures were detected by cohesin-ChIA-PET. 3D chromosome structures connecting insulators (CTCF-CTCF loops) were shown to form topologically associating domains (TADs) and insulated neighborhoods, which were mostly preserved in the transition between naive and primed states. Insulated neighborhoods are critical for proper gene expression, and their disruption leads to the improper regulation of local gene expression. Changes in enhancer-promoter loops occurred within preserved insulated neighborhoods during cell state transition. The CTCF anchors of CTCF-CTCF loops are conserved across species and are frequently mutated in cancer cells. These 3D chromosome regulatory landscapes provide a foundation for the future investigation of the relationship between chromosome structure and gene control in human development and disease. The work presented in the second part focuses on developing an approach called "chromatin proteomic profiling" to identify protein factors associated with various active and repressed portions of the genome marked by specific histone modifications. The histone modifications assayed by chromatin proteomic profiling are associated with genomic regions where specific transcriptional activities occur, thus implicating the identified proteins in these activities. This chromatin proteomic profiling study revealed a catalog of known, implicated, and novel proteins associated with these functionally characterized genomic regions.
by Daniel Benjamin Dadon.
Ph. D.
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Croft, Jenny Anne. "Correlating mammalian chromosome structure and function." Thesis, University of Edinburgh, 1998. http://hdl.handle.net/1842/13491.

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The euchromatin of mammalian chromosomes is broadly divided into two types with opposing characteristics: G-bands are revealed by Giemsa staining. These bands are generally late replicating, T-rich, low in gene density and appear to have a "closed" chromatin structure. R-bands are revealed by reverse Giemsa staining. These bands are generally early replicating, GC-rich, high in gene density and appear to have a more "open" chromatin structure. These two band types are intercalated throughout the mammalian genome making comparative studies of their behaviour difficult. However, in the human genome, chromosome 18 predominantly displays the features of G-bands and chromosome 19 generally displays the features of R-bands. These chromosomes were shown to be comparable in DNA content and size at metaphase and are, thus, ideal to investigate further the apparent links between chromosome structure and function. Some models of chromosome structure suggest differences in the higher order packaging of the different band types of metaphase chromosomes. Any differences should be reflected in the overall structure of chromosomes 18 and 19. Combining fluorescence in situ hybridisation and biochemical extraction of metaphase chromosomes, I detected no significant differences in their structure. In contrast, the two chromosomes demonstrated different structural characteristics in the interphase nucleus. I found that chromosome 18 occupies a relatively condensed territory, close to the periphery of the nucleus, while chromosome 19 occupies a considerably larger territory, more centrally located. My studies of different cell types and on cells at different stages of the cell cycle suggest that these characteristics generally apply in human cells, but not in a somatic cell hybrid background. Analysis of nuclei with a reciprocal 18:19 translocation showed that the translocated segments were orientated towards the positions occupied by their structurally normal homologues. The size but not the positioning of an interphase territory appears to be dependent on transcriptional activity.
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Books on the topic "Chromosoms structure"

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Therman, Eeva. Human chromosomes: Structure, behavior, effects. 2nd ed. New York: Springer-Verlag, 1985.

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Human chromosomes: Structure, behavior, effects. New York, New York, USA: Springer-Verlag, 1986.

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Millard, Susman, ed. Human chromosomes: Structure, behavior, and effects. 3rd ed. New York: Springer-Verlag, 1993.

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Gustafson, J. Perry, and R. Appels, eds. Chromosome Structure and Function. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4613-1037-2.

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Bhat, Tariq Ahmad, and Aijaz Ahmad Wani, eds. Chromosome Structure and Aberrations. New Delhi: Springer India, 2017. http://dx.doi.org/10.1007/978-81-322-3673-3.

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S, Risley Michael, ed. Chromosome structure and function. New York: Van Nostrand Reinhold Co., 1986.

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Houben, Andreas. Chromosome structure and function. Basel: Karger, 2009.

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Mitchell, Eddy E., Griswold Michael D, New York Academy of Sciences, and North American Testis Workshop (19th : 2007 : Tampa, Fla.), eds. Testicular chromosome structure and gene expression. Malden, MA: Published on behalf of the New York Academy of Sciences by Blackwell Pub., 2007.

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Hennig, Wolfgang, ed. Structure and Function of Eukaryotic Chromosomes. Berlin, Heidelberg: Springer Berlin Heidelberg, 1987. http://dx.doi.org/10.1007/978-3-540-47783-9.

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1941-, Hennig Wolfgang, ed. Structure and function of eukaryotic chromosomes. Berlin: Springer-Verlag, 1987.

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Book chapters on the topic "Chromosoms structure"

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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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Gill, Bikram S. "A Century of Cytogenetic and Genome Analysis: Impact on Wheat Crop Improvement." In Wheat Improvement, 277–97. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-90673-3_16.

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AbstractBeginning in the first decade of 1900, pioneering research in disease resistance and seed color inheritance established the scientific basis of Mendelian inheritance in wheat breeding. A series of breakthroughs in chromosome and genome analysis beginning in the 1920s and continuing into the twenty-first century have impacted wheat improvement. The application of meiotic chromosome pairing in the 1920s and plasmon analysis in the 1950s elucidated phylogeny of the Triticum-Aegilops complex of species and defined the wheat gene pools. The aneuploid stocks in the 1950s opened floodgates for chromosome and arm mapping of first phenotypic and later protein and DNA probes. The aneuploid stocks, coupled with advances in chromosome banding and in situ hybridization in the 1970s, allowed precise chromosome engineering of traits in wide hybrids. The deletion stocks in the 1990s were pivotal in mapping expressed genes to specific chromosome bins revealing structural and functional differentiation of chromosomes along their length and facilitating map-based cloning of genes. Advances in whole-genome sequencing, chromosome genomics, RH mapping and functional tools led to the assembly of reference sequence of Chinese Spring and multiple wheat genomes. Chromosome and genomic analysis must be integrated into wheat breeding and wide-hybridizaton pipeline for sustainable crop improvement.
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Elgin, S. C. R., S. A. Amero, J. C. Eissenberg, G. Fleischmann, D. S. Gilmour, and T. C. James. "Distribution Patterns of Nonhistone Chromosomal Proteins on Polytene Chromosomes: Functional Correlations." In Chromosome Structure and Function, 145–56. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4613-1037-2_6.

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Douglas, Ryan N., and James A. Birchler. "B Chromosomes." In Chromosome Structure and Aberrations, 13–39. New Delhi: Springer India, 2017. http://dx.doi.org/10.1007/978-81-322-3673-3_2.

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Pombo, A., J. McManus, T. A. Hughes, F. J. Iborra, D. A. Jackson, and P. R. Cook. "Transcription factories and chromosome structure." In Chromosomes Today, 147–60. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-009-1537-4_10.

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Appels, Rudi, Rosalind Morris, Bikram S. Gill, and Cedric E. May. "Variable Structure and Folding of DNA." In Chromosome Biology, 244–69. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4615-5409-7_17.

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Miller, Orlando J., and Eeva Therman. "Chromosome Structural Aberrations." In Human Chromosomes, 187–205. New York, NY: Springer New York, 2001. http://dx.doi.org/10.1007/978-1-4613-0139-4_13.

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Therman, Eeva. "Chromosome Structural Aberrations." In Human Chromosomes, 65–77. New York, NY: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-0269-8_7.

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Therman, Eeva, and Millard Susman. "Chromosome Structural Aberrations." In Human Chromosomes, 93–106. New York, NY: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4684-0529-3_9.

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Pettijohn, D. E. "Bacterial Chromosome Structure." In Nucleic Acids and Molecular Biology, 152–62. Berlin, Heidelberg: Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-84150-7_9.

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Conference papers on the topic "Chromosoms structure"

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Țurcan, Ana, Olesea Borozan, Silvia Munteanu, Constantin Ababii, Ana Nistiriuc, Andrei Șestacov, Vadim Struna, and Victor Lașco. "Multi-Criteria Distributed Decision-Making System Based on Genetic Algorithms." In 11th International Conference on “Electronics, Communications and Computing". Technical University of Moldova, 2022. http://dx.doi.org/10.52326/ic-ecco.2021/ce.06.

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This thesis comprises the results of designing a distributed decision-making system in multi-criteria areas. The distributed decision-making system is the architecture of homogenous data-processing devices that form a Wireless network with Mesh topology. The decision-making process is based on finding an optimal solution that is implemented through the use of genetic algorithms. Aiming to identify the initial population of the genetic algorithm, there shall be calculated the partial derivative for each variable for the ordered process. The results of partial derivative serve as an identifier of values from the Chromosome structure. There have been developed in this thesis: general algorithm of system functioning; population structure formed of Chromosomes and Genes; methodology of calculation of component values of the initial population; and an example of implementation of the distributed decision-making system based on Node MCU ESP32 devices.
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Bosma, P. J., E. A. van den Berg, and T. Kooistra. "ISOLATION OF THE GENE CODING FOR HUMAN PLASMINOGEN ACTIVATOR INHIBITOR TYPE 1 (PAI-1)." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644440.

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A human placenta genomic DNA cosmid library was screened for the presence of the PAI-1 gene using a cDNA probe coding for PAI-1. Two overlapping recombinant cosmids were obtained that contain human DNA spanning 55 kb. The cosmids were mapped using 3' and 5' end probes isolated from an almost full-length cDNA clone of 2.5 kb. The two cosmids were found to contain the entire structural PAI-1 gene (approximately 15 kb) and also included 25 kb 5' flanking sequences. The transcription initiation site was identified by SI nuclease protection experiments and the promotor region was sequenced. Further experiments will be directed at characterizing the regulatory elements of the PAI-1 gene.In order to determine the chromosomal localization of the PAI-1 gene we have hybridized our genomic clones in situ to metaphase chromosomes of a human blood cell culture. Preliminary experiments show a specific hybridization signal which will enable us to sublocalize the chromosomal position of the PAI-1 gene.
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"Chromosome synapsis and recombination in intraspecific and interspecific heterozygotes for chromosomal rearrangements in voles of the genus Alexandromys." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-384.

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Chapman, Colin D., Kazuhiro Saitou, and Mark J. Jakiela. "Genetic Algorithms As an Approach to Configuration and Topology Design." In ASME 1993 Design Technical Conferences. American Society of Mechanical Engineers, 1993. http://dx.doi.org/10.1115/detc1993-0338.

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Abstract The Genetic Algorithm, a search and optimization technique based on the theory of natural selection, is applied to problems of structural topology optimization. Given a structure’s boundary conditions and maximum allowable design domain, a discretized design representation is created. Populations of genetic algorithm “chromosomes” are then mapped into the design representation, creating potentially optimal structure topologies. Utilizing genetics-based operators such as crossover and mutation, generations of increasingly-desirable structure topologies are created. In this paper, the use of the genetic algorithm (GA) in structural topology optimization is presented. An overview of the genetic algorithm will describe the genetics-based representations and operators used in a typical genetic algorithm search. After defining topology optimization and its relation to the broader area of structural optimization, a review of previous research in GA-based and non-GA-based structural optimization is provided. The design representations, and methods for mapping genetic algorithm “chromosomes” into structure topology representations, are then detailed. Several examples of genetic algorithm-based structural topology optimization are provided: we address the optimization of beam cross-section topologies and cantilevered plate topologies, and we also investigate efficient techniques for using finite element analysis in a genetic algorithm-based search. Finally, a description of potential future work in genetic algorithm-based structural topology optimization is offered.
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Chapman, Colin D., and Mark J. Jakiela. "Genetic Algorithm-Based Structural Topology Design With Compliance and Manufacturability Considerations." In ASME 1994 Design Technical Conferences collocated with the ASME 1994 International Computers in Engineering Conference and Exhibition and the ASME 1994 8th Annual Database Symposium. American Society of Mechanical Engineers, 1994. http://dx.doi.org/10.1115/detc1994-0141.

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Abstract The genetic algorithm, a search and optimization technique based on the theory of natural selection, is applied to structural topology design problems with compliance and manufacturability considerations. After describing the genetic algorithm and reviewing previous research in structural topology design, we detail the chromosome-to-design representation which enables the genetic algorithm to perform structural topology optimization. Extending our prior investigations, this article details the use of our genetic algorithm-based technique to minimize a structure’s compliance, subject to a maximum volume constraint. The resulting structure is then directly compared with a solution obtained using a mathematical programming technique and material homogenization methods. We also demonstrate how our technique can generate structures which combine high stiffness-to-weight ratio with high manufacturability. After a brief discussion of our findings, we describe potential future work in genetic algorithm-based structural topology design.
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"Composition of sex chromosomes of veiled chameleon (Chamaeleo calyptratus, Iguania, Squamata) reveals new insights into sex chromosome evolution of iguanian lizards." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-097.

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Kim, Il Yong, and Olivier de Weck. "Variable Chromosome Length Genetic Algorithm for Structural Topology Design Optimization." In 45th AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics & Materials Conference. Reston, Virigina: American Institute of Aeronautics and Astronautics, 2004. http://dx.doi.org/10.2514/6.2004-1911.

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"Chromosome evolution in Ruminantia." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-087.

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Greene, William A. "Schema disruption in tree-structured chromosomes." In the 2005 conference. New York, New York, USA: ACM Press, 2005. http://dx.doi.org/10.1145/1068009.1068233.

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"X-chromosome Inactivation in American Mink iPSCs." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-310.

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Reports on the topic "Chromosoms structure"

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Rill, R. The impact of energy related pollutants on chromosome structure. Office of Scientific and Technical Information (OSTI), October 1989. http://dx.doi.org/10.2172/5345926.

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Shapiro, Daniel Benjamin. Polarized light scattering as a probe for changes in chromosome structure. Office of Scientific and Technical Information (OSTI), October 1993. http://dx.doi.org/10.2172/10107208.

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Pawlowski, Wojtek P., and Avraham A. Levy. What shapes the crossover landscape in maize and wheat and how can we modify it. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600025.bard.

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Meiotic recombination is a process in which homologous chromosomes engage in the exchange of DNA segments, creating gametes with new genetic makeup and progeny with new traits. The genetic diversity generated in this way is the main engine of crop improvement in sexually reproducing plants. Understanding regulation of this process, particularly the regulation of the rate and location of recombination events, and devising ways of modifying them, was the major motivation of this project. The project was carried out in maize and wheat, two leading crops, in which any advance in the breeder’s toolbox can have a huge impact on food production. Preliminary work done in the USA and Israeli labs had established a strong basis to address these questions. The USA lab pioneered the ability to map sites where recombination is initiated via the induction of double-strand breaks in chromosomal DNA. It has a long experience in cytological analysis of meiosis. The Israeli lab has expertise in high resolution mapping of crossover sites and has done pioneering work on the importance of epigenetic modifications for crossover distribution. It has identified genes that limit the rates of recombination. Our working hypothesis was that an integrative analysis of double-strand breaks, crossovers, and epigenetic data will increase our understanding of how meiotic recombination is regulated and will enhance our ability to manipulate it. The specific objectives of the project were: To analyze the connection between double-strand breaks, crossover, and epigenetic marks in maize and wheat. Protocols developed for double-strand breaks mapping in maize were applied to wheat. A detailed analysis of existing and new data in maize was conducted to map crossovers at high resolution and search for DNA sequence motifs underlying crossover hotspots. Epigenetic modifications along maize chromosomes were analyzed as well. Finally, a computational analysis tested various hypotheses on the importance of chromatin structure and specific epigenetic modifications in determining the locations of double-strand breaks and crossovers along chromosomes. Transient knockdowns of meiotic genes that suppress homologous recombination were carried out in wheat using Virus-Induced Gene Silencing. The target genes were orthologs of FANCM, DDM1, MET1, RECQ4, and XRCC2.
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Glesne, D., E. Huberman, F. Collart, T. Varkony, and H. Drabkin. Chromosomal localization and structure of the human type II IMP dehydrogenase gene. Office of Scientific and Technical Information (OSTI), May 1994. http://dx.doi.org/10.2172/10148872.

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Bradbury, E. M. Structural studies of chromatin and chromosomes. Progress report, March 15--September 15, 1997. Office of Scientific and Technical Information (OSTI), November 1997. http://dx.doi.org/10.2172/548675.

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Rill, R. L. The impact of energy related pollutants on chromosome structures. Final performance report, May 1, 1987--April 30, 1992. Office of Scientific and Technical Information (OSTI), March 1998. http://dx.doi.org/10.2172/607511.

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Breiman, Adina, Jan Dvorak, Abraham Korol, and Eduard Akhunov. Population Genomics and Association Mapping of Disease Resistance Genes in Israeli Populations of Wild Relatives of Wheat, Triticum dicoccoides and Aegilops speltoides. United States Department of Agriculture, December 2011. http://dx.doi.org/10.32747/2011.7697121.bard.

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Wheat is the most widely grown crop on earth, together with rice it is second to maize in total global tonnage. One of the emerging threats to wheat is stripe (yellow) rust, especially in North Africa, West and Central Asia and North America. The most efficient way to control plant diseases is to introduce disease resistant genes. However, the pathogens can overcome rapidly the effectiveness of these genes when they are wildly used. Therefore, there is a constant need to find new resistance genes to replace the non-effective genes. The resistance gene pool in the cultivated wheat is depleted and there is a need to find new genes in the wild relative of wheat. Wild emmer (Triticum dicoccoides) the progenitor of the cultivated wheat can serve as valuable gene pool for breeding for disease resistance. Transferring of novel genes into elite cultivars is highly facilitated by the availability of information of their chromosomal location. Therefore, our goals in this study was to find stripe rust resistant and susceptible genotypes in Israeli T. dicoccoides population, genotype them using state of the art genotyping methods and to find association between genetic markers and stripe rust resistance. We have screened 129 accessions from our collection of wild emmer wheat for resistance to three isolates of stripe rust. About 30% of the accessions were resistant to one or more isolates, 50% susceptible, and the rest displayed intermediate response. The accessions were genotyped with Illumina'sInfinium assay which consists of 9K single nucleotide polymorphism (SNP) markers. About 13% (1179) of the SNPs were polymorphic in the wild emmer population. Cluster analysis based on SNP diversity has shown that there are two main groups in the wild population. A big cluster probably belongs to the Horanum ssp. and a small cluster of the Judaicum ssp. In order to avoid population structure bias, the Judaicum spp. was removed from the association analysis. In the remaining group of genotypes, linkage disequilibrium (LD) measured along the chromosomes decayed rapidly within one centimorgan. This is the first time when such analysis is conducted on a genome wide level in wild emmer. Such a rapid decay in LD level, quite unexpected for a selfer, was not observed in cultivated wheat collection. It indicates that wild emmer populations are highly suitable for association studies yielding a better resolution than association studies in cultivated wheat or genetic mapping in bi-parental populations. Significant association was found between an SNP marker located in the distal region of chromosome arm 1BL and resistance to one of the isolates. This region is not known in the literature to bear a stripe rust resistance gene. Therefore, there may be a new stripe rust resistance gene in this locus. With the current fast increase of wheat genome sequence data, genome wide association analysis becomes a feasible task and efficient strategy for searching novel genes in wild emmer wheat. In this study, we have shown that the wild emmer gene pool is a valuable source for new stripe rust resistance genes that can protect the cultivated wheat.
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Medrano, Juan, Adam Friedmann, Moshe (Morris) Soller, Ehud Lipkin, and Abraham Korol. High resolution linkage disequilibrium mapping of QTL affecting milk production traits in Israel Holstein dairy cattle. United States Department of Agriculture, March 2008. http://dx.doi.org/10.32747/2008.7696509.bard.

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Original objectives: To create BAC contigs covering two QTL containing chromosomal regions (QTLR) and obtain BAC end sequence information as a platform for SNP identification. Use the SNPs to search for marker-QTL linkage disequilibrium (LD) in the test populations (US and Israel Holstein cattle). Identify candidate genes, test for association with dairy cattle production and functional traits, and confirm any associations in a secondary test population. Revisions in the course of the project: The selective recombinant genotyping (SRG) methodology which we implemented to provide moderate resolution QTL mapping turned out to be less effective than expected, due to problems introduced by incomplete marker informativity. This required a no-cost one-year extension of the project. Aside from this, the project was implemented essentially as envisaged, but only with respect to a single QTLR and single population association-test. Background to the topic. Dairy cattle breeders are looking to marker-assisted selection (MAS) as a means of identifying genetically superior sires and dams. MAS based on population-wide LD can be many times more effective than MAS based on within-family linkage mapping. In this proposal we developed a protocol leading from family based QTL mapping to population-wide LD between markers and the QTL Major conclusions, solutions, achievements. The critical importance of marker informativity for application of the SRG design in outcrossing random mating populations was identified, and an alternative Fractioned Pool Design (FPD) based on selective DNA pooling was developed. We demonstrated the feasibility of constructing a BAC contig across a targeted chromosomal region flanking the marker RM188 on bovine chromosome BTA4, which was shown in previous work to contain a QTL affecting milk production traits. BAC end sequences were obtained and successfully screened for SNPs. LD studies of these SNPs in the Israel population, and of an independent set of SNPs taken across the entire proximal region of BTA4 in the USA population, showed a much lower degree of LD than previously reported in the literature. Only at distances in the sub-cM level did an appreciable fraction of SNP marker-pairs show levels of LD useful for MAS. In contrast, studies in the Israel population using microsatellite markers, presented an equivalent degree of LD at a 1-5 separation distance. SNP LD appeared to reflect historical population size of Bostaurus (Ne=5000- 10,000), while microsatellite LD appeared to be in proportion to more recent effective population size of the Holstein breed (Ne=50-100). An appreciable fraction of the observed LD was due to Family admixture structure of the Holstein population. The SNPs MEOX2/IF2G (found within the gene SETMAR at 23,000 bp from RM188) and SNP23 were significantly associated with PTA protein, Cheese dollars and Net Merit Protein in the Davis bull resource population, and were also associated with protein and casein percentages in the Davis cow resource population. Implications. These studies document a major difference in degree of LD presented by SNPs as compared to microsatellites, and raise questions as to the source of this difference and its implications for QTL mapping and MAS. The study lends significant support to the targeted approach to fine map a previously identified QTL. Using high density genotyping with SNP discovered in flanking genes to the QTL, we have identified important markers associated with milk protein percentage that can be tested in markers assisted selection programs.
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Fallik, Elazar, Robert Joly, Ilan Paran, and Matthew A. Jenks. Study of the Physiological, Molecular and Genetic Factors Associated with Postharvest Water Loss in Pepper Fruit. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593392.bard.

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The fruit of pepper (Capsicum annuum) commonly wilts (or shrivels) during postharvest storage due to rapid water loss, a condition that greatly reduces its shelf life and market value. The fact that pepper fruit are hollow, and thus have limited water content, only exacerbates this problem in pepper. The collaborators on this project completed research whose findings provided new insight into the genetic, physiological, and biochemical basis for water loss from the fruits of pepper (Capsicum annuum and related Capsicum species). Well-defined genetic populations of pepper were used in this study, the first being a series of backcross F₁ and segregating F₂, F₃, and F₄ populations derived from two original parents selected for having dramatic differences in fruit water loss rate (very high and very low water loss). The secondly population utilized in these studies was a collection of 50 accessions representing world diversity in both species and cultivar types. We found that an unexpectedly large amount of variation was present in both fruit wax and cutin composition in these collections. In addition, our studies revealed significant correlations between the chemical composition of both the fruit cuticular waxes and cutin monomers with fruit water loss rate. Among the most significant were that high alkane content in fruit waxes conferred low fruit water loss rates and low permeability in fruit cuticles. In contrast, high amounts of terpenoids (plus steroidal compounds) were associated with very high fruit water loss and cuticle permeability. These results are consistent with our models that the simple straight chain alkanes pack closely together in the cuticle membrane and obstruct water diffusion, whereas lipids with more complex 3-dimensional structure (such as terpenoids) do not pack so closely, and thus increase the diffusion pathways. The backcross segregating populations were used to map quantitative trait loci (QTLs) associated with water loss (using DART markers, Diversity Arrays Technology LTD). These studies resulted in identification of two linked QTLs on pepper’s chromosome 10. Although the exact genetic or physiological basis for these QTLs function in water loss is unknown, the genotypic contribution in studies of near-isogenic lines selected from these backcross populations reveals a strong association between certain wax compounds, the free fatty acids and iso-alkanes. There was also a lesser association between the water loss QTLs with both fruit firmness and total soluble sugars. Results of these analyses have revealed especially strong genetic linkages between fruit water loss, cuticle composition, and two QTLs on chromosome 10. These findings lead us to further speculate that genes located at or near these QTLs have a strong influence on cuticle lipids that impact water loss rate (and possibly, whether directly or indirectly, other traits like fruit firmness and sugar content). The QTL markers identified in these studies will be valuable in the breeding programs of scientists seeking to select for low water loss, long lasting fruits, of pepper, and likely the fruits of related commodities. Further work with these newly developed genetic resources should ultimately lead to the discovery of the genes controlling these fruit characteristics, allowing for the use of transgenic breeding approaches toward the improvement of fruit postharvest shelf life.
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Sela, Hanan, Eduard Akhunov, and Brian J. Steffenson. Population genomics, linkage disequilibrium and association mapping of stripe rust resistance genes in wild emmer wheat, Triticum turgidum ssp. dicoccoides. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598170.bard.

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The primary goals of this project were: (1) development of a genetically characterized association panel of wild emmer for high resolution analysis of the genetic basis of complex traits; (2) characterization and mapping of genes and QTL for seedling and adult plant resistance to stripe rust in wild emmer populations; (3) characterization of LD patterns along wild emmer chromosomes; (4) elucidation of the multi-locus genetic structure of wild emmer populations and its correlation with geo-climatic variables at the collection sites. Introduction In recent years, Stripe (yellow) rust (Yr) caused by Pucciniastriiformis f. sp. tritici(PST) has become a major threat to wheat crops in many parts of the world. New races have overcome most of the known resistances. It is essential, therefore, that the search for new genes will continue, followed by their mapping by molecular markers and introgression into the elite varieties by marker-assisted selection (MAS). The reservoir of genes for disease and pest resistance in wild emmer wheat (Triticumdicoccoides) is an important resource that must be made available to wheat breeders. The majority of resistance genes that were introgressed so far in cultivated wheat are resistance (R) genes. These genes, though confering near-immunity from the seedling stage, are often overcome by the pathogen in a short period after being deployed over vast production areas. On the other hand, adult-plant resistance (APR) is usually more durable since it is, in many cases, polygenic and confers partial resistance that may put less selective pressure on the pathogen. In this project, we have screened a collection of 480 wild emmer accessions originating from Israel for APR and seedling resistance to PST. Seedling resistance was tested against one Israeli and 3 North American PST isolates. APR was tested on accessions that did not have seedling resistance. The APR screen was conducted in two fields in Israel and in one field in the USA over 3 years for a total of 11 replicates. We have found about 20 accessions that have moderate stripe rust APR with infection type (IT<5), and about 20 additional accessions that have novel seedling resistance (IT<3). We have genotyped the collection using genotyping by sequencing (GBS) and the 90K SNP chip array. GBS yielded a total 341K SNP that were filtered to 150K informative SNP. The 90K assay resulted in 11K informative SNP. We have conducted a genome-wide association scan (GWAS) and found one significant locus on 6BL ( -log p >5). Two novel loci were found for seedling resistance. Further investigation of the 6BL locus and the effect of Yr36 showed that the 6BL locus and the Yr36 have additive effect and that the presence of favorable alleles of both loci results in reduction of 2 grades in the IT score. To identify alleles conferring adaption to extreme climatic conditions, we have associated the patterns of genomic variation in wild emmer with historic climate data from the accessions’ collection sites. The analysis of population stratification revealed four genetically distinct groups of wild emmer accessions coinciding with their geographic distribution. Partitioning of genomic variance showed that geographic location and climate together explain 43% of SNPs among emmer accessions with 19% of SNPs affected by climatic factors. The top three bioclimatic factors driving SNP distribution were temperature seasonality, precipitation seasonality, and isothermality. Association mapping approaches revealed 57 SNPs associated with these bio-climatic variables. Out of 21 unique genomic regions controlling heading date variation, 10 (~50%) overlapped with SNPs showing significant association with at least one of the three bioclimatic variables. This result suggests that a substantial part of the genomic variation associated with local adaptation in wild emmer is driven by selection acting on loci regulating flowering. Conclusions: Wild emmer can serve as a good source for novel APR and seedling R genes for stripe rust resistance. APR for stripe rust is a complex trait conferred by several loci that may have an additive effect. GWAS is feasible in the wild emmer population, however, its detection power is limited. A panel of wild emmer tagged with more than 150K SNP is available for further GWAS of important traits. The insights gained by the bioclimatic-gentic associations should be taken into consideration when planning conservation strategies.
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