Relevant bibliographies by topics / Nucleoid Organization

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Nucleoid Organization'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Nucleoid Organization"

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Chen, Inês. "Nucleoid organization." Nature Structural & Molecular Biology 18, no. 10 (October 2011): 1085. http://dx.doi.org/10.1038/nsmb.2156.

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Farge, Géraldine, and Maria Falkenberg. "Organization of DNA in Mammalian Mitochondria." International Journal of Molecular Sciences 20, no. 11 (June 5, 2019): 2770. http://dx.doi.org/10.3390/ijms20112770.

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As with all organisms that must organize and condense their DNA to fit within the limited volume of a cell or a nucleus, mammalian mitochondrial DNA (mtDNA) is packaged into nucleoprotein structures called nucleoids. In this study, we first introduce the general modes of DNA compaction, especially the role of the nucleoid-associated proteins (NAPs) that structure the bacterial chromosome. We then present the mitochondrial nucleoid and the main factors responsible for packaging of mtDNA: ARS- (autonomously replicating sequence-) binding factor 2 protein (Abf2p) in yeast and mitochondrial transcription factor A (TFAM) in mammals. We summarize the single-molecule manipulation experiments on mtDNA compaction and visualization of mitochondrial nucleoids that have led to our current knowledge on mtDNA compaction. Lastly, we discuss the possible regulatory role of DNA packaging by TFAM in DNA transactions such as mtDNA replication and transcription.
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Bogenhagen, Daniel F. "Does mtDNA nucleoid organization impact aging?" Experimental Gerontology 45, no. 7-8 (August 2010): 473–77. http://dx.doi.org/10.1016/j.exger.2009.12.002.

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Macvanin, Mirjana, and Sankar Adhya. "Architectural organization in E. coli nucleoid." Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1819, no. 7 (July 2012): 830–35. http://dx.doi.org/10.1016/j.bbagrm.2012.02.012.

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Castellana, Michele, Sophia Hsin-Jung Li, and Ned S. Wingreen. "Spatial organization of bacterial transcription and translation." Proceedings of the National Academy of Sciences 113, no. 33 (August 2, 2016): 9286–91. http://dx.doi.org/10.1073/pnas.1604995113.

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In bacteria such as Escherichia coli, DNA is compacted into a nucleoid near the cell center, whereas ribosomes—molecular complexes that translate mRNAs into proteins—are mainly localized to the poles. We study the impact of this spatial organization using a minimal reaction–diffusion model for the cellular transcriptional–translational machinery. Although genome-wide mRNA-nucleoid segregation still lacks experimental validation, our model predicts that ∼90% of mRNAs are segregated to the poles. In addition, our analysis reveals a “circulation” of ribosomes driven by the flux of mRNAs, from synthesis in the nucleoid to degradation at the poles. We show that our results are robust with respect to multiple, biologically relevant factors, such as mRNA degradation by RNase enzymes, different phases of the cell division cycle and growth rates, and the existence of nonspecific, transient interactions between ribosomes and mRNAs. Finally, we confirm that the observed nucleoid size stems from a balance between the forces that the chromosome and mRNAs exert on each other. This suggests a potential global feedback circuit in which gene expression feeds back on itself via nucleoid compaction.
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Passot, Fanny Marie, Hong Ha Nguyen, Cloelia Dard-Dascot, Claude Thermes, Pascale Servant, Olivier Espéli, and Suzanne Sommer. "Nucleoid organization in the radioresistant bacteriumDeinococcus radiodurans." Molecular Microbiology 97, no. 4 (June 25, 2015): 759–74. http://dx.doi.org/10.1111/mmi.13064.

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Rebelo, Adriana P., Lloye M. Dillon, and Carlos T. Moraes. "Mitochondrial DNA transcription regulation and nucleoid organization." Journal of Inherited Metabolic Disease 34, no. 4 (May 4, 2011): 941–51. http://dx.doi.org/10.1007/s10545-011-9330-8.

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Hsu, Y. H. "Distribution of gyrase and topoisomerase IV on bacterial nucleoid: implications for nucleoid organization." Nucleic Acids Research 34, no. 10 (May 31, 2006): 3128–38. http://dx.doi.org/10.1093/nar/gkl392.

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Eltsov, Mikhail, and Jacques Dubochet. "Fine Structure of the Deinococcus radiodurans Nucleoid Revealed by Cryoelectron Microscopy of Vitreous Sections." Journal of Bacteriology 187, no. 23 (December 1, 2005): 8047–54. http://dx.doi.org/10.1128/jb.187.23.8047-8054.2005.

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ABSTRACT Transmission electron microscopy revealed that the nucleoid of the extremely radioresistant bacteria Deinococcus radiodurans may adopt an unusual ring shape. This led to the hypothesis that the tight toroidal package of the D. radiodurans genome might contribute to radioresistance by preventing diffusion of ends of double-stranded DNA breaks. The molecular arrangement of DNA in the nucleoid, which must be determined to test this hypothesis, is not discernible by conventional methods of electron microscopy. We have applied cryoelectron microscopy of vitreous sections and found that the DNA arrangement in D. radiodurans differs from toroidal spooling. Diffuse coralline nucleoids of exponentially growing D. radiodurans do not reveal any particular molecular order. Electron-dense granules are generally observed in the centers of nucleoids. In stationary-phase cells, the nucleoid segregates from cytoplasm and DNA filaments show locally parallel arrangements, with increasing aspects of cholesteric liquid crystalline phase upon prolonged starvation. The relevance of the observed nucleoid organization to the radiation resistance of D. radiodurans is discussed.
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Sun, Qin, and William Margolin. "Effects of Perturbing Nucleoid Structure on Nucleoid Occlusion-Mediated Toporegulation of FtsZ Ring Assembly." Journal of Bacteriology 186, no. 12 (June 15, 2004): 3951–59. http://dx.doi.org/10.1128/jb.186.12.3951-3959.2004.

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ABSTRACT In Escherichia coli, assembly of the FtsZ ring (Z ring) at the cell division site is negatively regulated by the nucleoid in a phenomenon called nucleoid occlusion (NO). Previous studies have indicated that chromosome packing plays a role in NO, as mukB mutants grown in rich medium often exhibit FtsZ rings on top of diffuse, unsegregated nucleoids. To address the potential role of overall nucleoid structure on NO, we investigated the effects of disrupting chromosome structure on Z-ring positioning. We found that NO was mostly normal in cells with inactivated DNA gyrase or in mukB-null mutants lacking topA, although some suppression of NO was evident in the latter case. Previous reports suggesting that transcription, translation, and membrane insertion of proteins (“transertion”) influence nucleoid structure prompted us to investigate whether disruption of these activities had effects on NO. Blocking transcription caused nucleoids to become diffuse, and FtsZ relocalized to multiple bands on top of these nucleoids, biased towards midcell. This suggested that these diffuse nucleoids were defective in NO. Blocking translation with chloramphenicol caused characteristic nucleoid compaction, but FtsZ rarely assembled on top of these centrally positioned nucleoids. This suggested that NO remained active upon translation inhibition. Blocking protein secretion by thermoinduction of a secA(Ts) strain caused a chromosome segregation defect similar to that in parC mutants, and NO was active. Although indirect effects are certainly possible with these experiments, the above data suggest that optimum NO activity may require specific organization and structure of the nucleoid.
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Dissertations / Theses on the topic "Nucleoid Organization"

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Floc'h, Kevin. "Etude de l'organisation et de la dynamique du nucléoïde de Deinococcus radiodurans par microscopie de fluorescence avancée." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAV007/document.

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Durant ce projet, nous nous sommes intéressés à une bactérie, D. radiodurans, un coque particulièrement connu pour ces extraordinaires capacités de résistance à différents facteurs de stress. Cependant, à cause de ses capacités de radiorésistance, cette bactérie a surtout été étudiée dans cette optique. Certaines caractéristiques de son cycle cellulaire restent méconnues, notamment (i) sa morphologie au cours de sa division ainsi que (ii) l’organisation et (iii) la ségrégation de son nucléoïde. Ces méconnaissances touchent aussi de façon plus générale toutes les bactéries de types coques, notamment de par la petite taille relative des bactéries qui a été un frein pour leurs études en microscopie photonique.Le but du projet de thèse est donc de mieux comprendre comment les bactéries sont capables d’avoir un nucléoïde très compacté, mais en même temps, dynamique et restant accessible pour les différents mécanismes tels que la réplication de l’ADN, sa transcription ou sa réparation. Dans ce but, nous avons exploré l’organisation en 4D ainsi que la dynamique du nucléoïde de D. radiodurans, en fonction du cycle de vie de la bactérie, de sa phase de croissance. Afin de réaliser ces objectifs, plusieurs stratégies ont été poursuivies : (i) des timelapses en 3D par microscopie confocale (ii) l’étude dynamique du nucléoïde par FRAP et par SptPALM, et (iii) la cartographie des protéines associées au nucléoïde réalisé par microscopie de super-résolution (PALM)
During this PhD work, we have studied on D. radiodurans, a coccus, known for its intriguing outstanding resistance to different stress factors. Studies on D. radiodurans have been mainly focusing on its tremendous radioresistance. 52 years after its discovery, its nucleoid organization/segregation as well as its cell morphology during its cell cycle still remain elusive. Most of our knowledge on the bacteria shape during division and on the nucleoid organization/segregation arises from the study of a small number of “model bacteria”, that are mainly rod-shaped or ovoid. In contrast, little is known on the nucleoid organization/segregation of cocci. Moreover, the small relative size of bacteria and of their nucleoids (<1µm3) has limited their studies by conventional microscopy.Thus, one of the aims of this PhD project is to contribute to a better understanding of the cell morphology and the nucleoid organization/segregation in cocci. For that matter, we explored the 4D organization and the dynamics of D. radiodurans nucleoids, as a function of the cell cycle progression and growth phase. In order to achieve the objective of this PhD, several strategies were undertaken: (i) timelapse 3D stacks by spinning confocal microscopy (ii) dynamics studies with FRAP analysis and SptPALM acquisitions, and (iii) cartographies of nucleoid associated proteins using super-resolution microscopy (PALM)
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Rigoni, Giovanni. "ATAD3 protein family: Molecular dissection of the ATAD3A dual role on the maintenance of mitochondrial ultrastructure and mtDNA-Nucleoid organization." Doctoral thesis, Università degli studi di Padova, 2019. http://hdl.handle.net/11577/3423185.

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Mitochondria are key organelles in a variety of cellular functions such as ATP production, calcium homeostasis, cell differentiation, and apoptosis. All these functions are possible thanks to the complicated mitochondrial ultrastructure that results in the compartmentalization of the different biochemical processes. An example of this is the cristae compartment that host the oxidative phosphorylation machinery, existing a direct correlation between the cristae density and the respiratory capacity of mitochondria. Moreover, the mitochondrial ultrastructure is crucial for the mitochondrial function, indeed, thinner cristae favor the assembly of respiratory complexes in supercomplexes improving the respiratory efficiency. Therefore, the ultrastructure has become an indicator of the mitochondrial functional status and the study of specific ultrastructural parameters is currently used to describe a dysfunction. In this thesis, by using a dynamic complexomic analysis to identify new cristae remodeling modulators, we have recognized the protein ATAD3A as a highly interesting candidate to participate in the process. Although previous studies pointed to ATAD3A as a regulator of mitochondrial ultrastructure based on results obtained after silencing, no details about the molecular mechanism have been revealed. In addition, ATAD3A have been also implicated in many other cellular processes like cholesterol transport, apoptosis and nucleoid-mtDNA stability. The main goal of this work was to understand whether and how ATAD3A regulates mitochondrial structure and whether this is somehow correlated with its implication in mtDNA stability. To address these questions, we used a variety of biochemical and proteomic approaches, that in combination with proper genetic models have led us to the data presented in this work. We have identified by dynamic complexomic analysis three different complexes of ATAD3A at 1MDa, 500kDa and 250kDa. The observation that only the 500kDa complex is disrupted during the cristae remodeling, and that OPA1 was comigrating in the same disrupted complex, led us to hypothesize its involvement in the cristae maintenance. Indeed, ATAD3A silencing or overexpression was able to decrease or increase the number of cristae, respectively. Moreover, this effect was accompanied by alterations on the nucleoid and mtDNA copy number. By using specific ATAD3A mutant in the coiled-coil (CCD) or ATPase domain of ATAD3A we demonstrated that the ATPase is required for the cristae maintenance while the CCD seems to be involved in nucleoid organization. Our experiments also excluded the participation of the ATAD3A oligomerization in the cristae maintenance. The analysis of the ATAD3A complexes in presence of the different mutants further supported the involvement of the 500kDa complex in the process of cristae maintenance since the ATAD3A ATPase-mutant, that does not maintain cristae does not assemble on it. On the contrary, the CCD-mutant that induces cristae biogenesis assembles in the 500kDa complex. Our data also support the idea that ATAD3A 500kDa complex act as a scaffold protein that allows OPA1 to assemble together cooperating in the cristae biogenesis process. We have also studied the role of the ATAD3A 1MDa complex, which looking in our complexomic analysis, appeared enriched in mitoribosomal and other proteins suggested to be involved in nucleoid and mtDNA stability, suggesting the involvement in the process. To support this idea, cells lacking the mtDNA do not present the ATAD3A 1MDa complex, and also control treated shortly with EtBr display a significant reduction of the same complex. Since the CCD-mutant is not assembling in the 1MDa complex, we analyzed nucleoids in presence of the ATAD3A wild type or mutants after silencing of the endogenous protein. This results further confirm the involvement of the 1MDa in nucleoid organization since the CCD mutant exhibited a decrease in nucleoid are that was not present with the wild type or ATPase-mutant. Overall our data demonstrate a dual role of ATAD3A in cristae biogenesis and nucleoid-mtDNA stability that depends on the different domains: the coiled-coil domain is required for nucleoid organization and the ATPase domain for cristae biogenesis. Additional studies have been done in this PhD thesis to understand whether and how ATAD3B might be able or not to complement the absence of ATAD3A, or if as previously proposed it acts as a dominant negative for ATAD3A. Our work supports the latter hypothesis, that seems to be mediated by the direct interaction of ATAD3A and ATAD3B in the 1MDa complex. Surprisingly, our data show that ATAD3B can revert the pathological mitochondrial phenotype observed in cells expressing the ATPase mutant, suggesting that the nullifying effect of ATAD3B is not specific for the wild type protein. Further experiments are required to confirm these results.
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O'Brien, Brendan John. "The architecture, connectivity and organization of Macaca inferior pulvinar /." Thesis, Connect to this title online; UW restricted, 1997. http://hdl.handle.net/1773/10655.

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Berger, Imre. "Supramolecular organization of DNA and proteins in eukaryotic nuclei." Zürich : ETH - Department of Biology, 2005. http://e-collection.ethbib.ethz.ch/show?type=habil&nr=21.

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Höger, Geralin. "Self-Organization of β-Peptide Nucleic Acid Helices for Membrane Scaffolding." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2019. http://hdl.handle.net/21.11130/00-1735-0000-0003-C187-A.

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Juha, Mikael Lintuluoto. "Self-organization and Dynamic Molecular Recognition of Nucleoside Derivatives through Hydrogen Bonding." Kyoto University, 1997. http://hdl.handle.net/2433/202325.

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Anderson, Shirley Victoria. "The nucleotide sequence and genomic organization of the potato mop-top virus RNA-2 molecule." Thesis, Queen's University Belfast, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.334531.

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Niranjan, Shalini S. "Potential mismatches in structural and functional organization in the gracile nucleus." University of Toledo Health Science Campus / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=mco1223921577.

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Puig, Giribets Marta. "Evolution of the hsp70 gene family at the nucleotide, genome organization and gene expression levels in Drosophila subobscura." Doctoral thesis, Universitat Autònoma de Barcelona, 2018. http://hdl.handle.net/10803/663952.

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Nombrosos estudis han constatat el valor adaptatiu del ric polimorfisme d’inversions cromosòmiques al drosofíl· lid D. subobscura. No obstant això, fins ara es coneixien molt poc les bases moleculars que hi ha darrere del seu manteniment a les poblacions naturals. En cercar loci candidats, un experiment previ de xoc tèrmic va quantificar els nivells de la proteïna Hsp70 en soques homocariotípiques dels ordenaments OST, O3+4+8 i O3+4. Inesperadament, els individus de l’ordenament càlid O3+4 mostraven nivells incrementats d’aquesta proteïna, en absència d’estrès tèrmic, que no augmentaven després del xoc tèrmic. Malauradament, en el moment en què es va dur a terme l’experiment hi havia moltes incògnites sobre l’organització molecular del locus Hsp70IR a D. subobscura. Els resultats prèviament esmentats, van donar peu al present treball de tesi, els objectius del qual són localitzar el locus Hsp70IR al cariotip i conèixer-ne l’organització genòmica, característiques moleculars i expressió gènica en diversos ordenaments cromosòmics d’interès que inclouen la regió genòmica on es troba la família gènica hsp70: O3+4+16+2, O3+4+8, O3+4 i OST. Gràcies a la seqüència d’un clon de la genoteca d’una línia OST i a còntigs del genoma de D. subobscura, hem pogut dissenyar una sonda a partir de la regió codificant de hsp70 que ens ha permès determinar la localització del locus on es troba aquesta família gènica (Hsp70IR) mitjançant hibridació in situ (ISH). Paral· lelament, hem pogut completar la seqüenciació d’una regió de 9-10 kb al locus Hsp70IR en 12 línies isogèniques per als ordenaments esmentats i a les espècies properes D. madeirensis i D. guanche per aclarir l’evolució d’aquest locus en els darrers 1,8 - 2,8 milions d’anys (Ma). Els resultats de la ISH van mostrar un únic punt d’hibridació a la banda 94A del segment distal (SI) del cromosoma O que coincidia els 4 cariotips estudiats: O3+4+16+2, O3+4+8, O3+4 i OST. Les seqüències corresponents a les 12 línies isogèniques i a D. madeirensis i D. guanche indiquen que en aquestes tres espècies del clúster subobscura, el locus Hsp70IR consta de dues còpies paràloges de 2,5 – 3,0 kb en orientació divergent i separades per una regió espaiadora central no duplicada de 0,5 – 1,4 kb. Les dues còpies mostren un elevat grau de conservació entre els diferents ordenaments i espècies analitzats, mentre que la regió espaiadora central és altament polimòrfica. Entre els aspectes més rellevants de l’anàlisi del polimorfisme, destaquem l’elevada conservació de les regions codificadores (CDSs) i els diferents elements reguladors en cis (CREs) al promotor proximal de tots els gens hsp70 analitzats, que indicarien que aquests són funcionals a totes les línies estudiades, i que la seva regulació podria ser similar. Curiosament, a nivell de seqüència, les regions paràlogues del promotor proximal i el CDS tendeixen a ser significativament més similars dins del mateix ordenament i, en alguns casos, dins la mateixa línia, probablement com a resultat de conversió gènica ectòpica. Per últim, hem dut a terme la quantificació dels nivells basals de mRNA i proteïna en mascles i femelles adults de sis línies isogèniques per a l’ordenament fred OST i sis per a l’ordenament càlid O3+4. La quantificació dels nivells de mRNA indica que els nivells són similars entre els dos ordenaments però en canvi aquests difereixen entre mascles i femelles de l’ordenament càlid O3+4. Així mateix, la quantificació dels nivells de la proteïna Hsp70 suggereix que no hi ha diferències entre sexes ni entre els dos ordenaments, però en canvi observem una interacció significativa entre sexe i ordenament. Aquests resultats, tant per a mRNA com per a proteïna, indiquen que l’expressió de hsp70 podria estar influïda pel sexe.
Numerous studies have confirmed the adaptive value of the rich chromosomal inversion polymorphism in the drosophilid D. subobscura. However, until recently very little was known about the molecular basis behind its maintenance in natural populations. In search of candidate loci, a previous heat shock experiment quantified Hsp70 protein levels in homokaryotypic strains for the OST, O3+4+8 and O3+4 arrangements. Unexpectedly, individuals of the warm climate-associated O3+4 arrangement showed increased levels in absence of thermal stress that did not boost after the heat shock. Unfortunately, by the time this experiment was performed there was very little data available on the molecular organization of the Hsp70IR locus in D. subobscura. The previously mentioned results led to the present thesis work, whose objectives are to locate the Hsp70IR locus in the karyotype and to know the genomic organization, molecular characteristics and gene expression patterns in several representative chromosomal arrangements that comprise the genomic region where the hsp70 gene family is located: O3+4+16+2, O3+4+8, O3+4 and OST. Using the sequence of a clone from an OST line genomic library and contigs from the unassembled genome of D. subobscura, we designed a probe from the hsp70 coding region that enabled us to determine the location of the locus by in situ (ISH) hybridization. Concomitantly, we completed the sequencing of a 9-10 kb region in the Hsp70IR locus in 12 lines isogenic for the aforementioned arrangements and in D. madeirensis and D. guanche to shed light on the evolution of this locus in the last 1.8 - 2.8 million years (myr). ISH results showed a single hybridization site in the 94A band in the distal segment (SI) of the O chromosome coincident in the 4 studied karyotypes: O3+4+16+2, O3+4+8, O3+4 and OST. The sequences corresponding to the 12 isogenic lines and to D. madeirensis and D. guanche indicated that in these three species of the subobscura cluster, the Hsp70IR locus consists of two 2.5 - 3.0 kb long paralogous copies in divergent orientation separated by a 0.5 - 1.4 kb nonduplicated central spacer region. The two copies show a high degree of conservation between the different gene arrangements and species analyzed, while the central spacer region is highly polymorphic. Among the most relevant aspects of polymorphism analyses, we highlight the high degree of conservation in the coding regions (CDSs) and the cis-regulatory elements (CREs) in the proximal promoter of all the analyzed hsp70 genes, which might indicate that these are functional in all studied lines, and that their regulation might be similar. Curiously, at the sequence level, the paralogous 5'-UTR and CDS regions tend to be significantly more similar within the same arrangement and, in some cases, within the same line, probably as a result of ectopic gene conversion. Lastly, we carried out the quantification of basal hsp70 mRNA and protein levels in adult males and females of six lines isogenic for the cold climate-associated OST and six for the warm climate-associated O3+4 arrangements. Basal mRNA quantification results indicate that the two arrangements exhibit similar levels, yet significant differences are observed between males and females of the warm O3+4 arrangement. Regarding the quantification of basal Hsp70 protein levels, these suggest that there are no differences between sexes nor between the two arrangements, but instead we observe a significant interaction between sex and arrangement. Overall, the results for both, mRNA and protein data, indicate that hsp70 expression might be influenced by sex.
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Highett, Martin I. "The organization of ribosomal DNA and transcripts in Pisum sativum nucleoli : a study using 3-D confocal microscopy." Thesis, University of East Anglia, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.332081.

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Books on the topic "Nucleoid Organization"

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A, Merchán Miguel, North Atlantic Treaty Organization. Scientific Affairs Division., and NATO Advanced Research Workshop on the Mammalian Cochlear Nuclei: Organization and Function (1991 : Salamanca, Spain), eds. The Mammalian cochlear nuclei: Organization and function. New York: Plenum Press, 1993.

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Chadwick, Derek. Nuclear organization in development and disease. Edited by Goode Jamie. Hoboken, NJ: Wiley, 2005.

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Berghmans, Koen. Zwarte dageraad: Nucleair terrorisme in België: een reële bedreiging. Antwerpen: Standaard, 2006.

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Meier, Iris. Functional organization of the plant nucleus. Berlin: Springer, 2009.

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Functional organization of the plant nucleus. Berlin: Springer, 2009.

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Egel, Richard. Origins of Life: The Primal Self-Organization. Berlin, Heidelberg: Springer-Verlag Berlin Heidelberg, 2011.

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Highett, Martin I. The organization of ribosomal DNA and transcripts in "Pisum sativum" nucleoli: A study using 3-D confocal microscopy. Norwich: University of East Anglia, 1993.

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van, Driel Roeland, and Otte Arie P, eds. Nuclear organization, chromatin structure, and gene expression. Oxford: Oxford University Press, 1997.

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Laboratory, Cold Spring Harbor, ed. Abstracts of papers presented at the 2004 meeting on Dynamic organization of nuclear function: September 29-October 3, 2004. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory, 2004.

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Wente, Susan. Abstracts of papers presented at the 2006 meeting on dynamic organization of nuclear function: September 27-October 1, 2006. Cold Spring Harbor: Cold Spring Harbor Laboratory, 2006.

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Book chapters on the topic "Nucleoid Organization"

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Le Gall, Antoine, Diego I. Cattoni, and Marcelo Nollmann. "Imaging of Bacterial Chromosome Organization by 3D Super-Resolution Microscopy." In The Bacterial Nucleoid, 253–68. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7098-8_19.

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Adams, Roger L. P., John T. Knowler, and David P. Leader. "Chromosome organization." In The Biochemistry of the Nucleic Acids, 35–86. Dordrecht: Springer Netherlands, 1986. http://dx.doi.org/10.1007/978-94-009-4103-8_3.

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Drlica, Karl, and Conrad L. Woldringh. "Chromosomal Organization: Nucleoids, Chromosomal Folding, and DNA Topology." In Bacterial Genomes, 12–22. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4615-6369-3_2.

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Voogd, Jan, Yoshikazu Shinoda, Tom J. H. Ruigrok, and Izumi Sugihara. "Cerebellar Nuclei and the Inferior Olivary Nuclei: Organization and Connections." In Handbook of the Cerebellum and Cerebellar Disorders, 377–436. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-1333-8_19.

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Voogd, Jan, Yoshikazu Shinoda, Tom J. H. Ruigrok, and Izumi Sugihara. "Cerebellar Nuclei and the Inferior Olivary Nuclei: Organization and Connections." In Handbook of the Cerebellum and Cerebellar Disorders, 1–61. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-319-97911-3_19-2.

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Voogd, Jan, Yoshikazu Shinoda, Tom J. H. Ruigrok, and Izumi Sugihara. "Cerebellar Nuclei and the Inferior Olivary Nuclei: Organization and Connections." In Handbook of the Cerebellum and Cerebellar Disorders, 497–557. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-23810-0_19.

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Garrard, W. T. "Chromosomal Loop Organization in Eukaryotic Genomes." In Nucleic Acids and Molecular Biology, 163–75. Berlin, Heidelberg: Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-84150-7_10.

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Le Bescond, Loïc, Marvin Lerousseau, Ingrid Garberis, Fabrice André, Stergios Christodoulidis, Maria Vakalopoulou, and Hugues Talbot. "Unsupervised Nuclei Segmentation Using Spatial Organization Priors." In Lecture Notes in Computer Science, 325–35. Cham: Springer Nature Switzerland, 2022. http://dx.doi.org/10.1007/978-3-031-16434-7_32.

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Benedetti, G., P. De Santis, M. Fua’, S. Morosetti, A. Palleschi, M. Savino, and A. Scipioni. "Superstructural Informations in the Base Sequences of Nucleic Acids." In Topics in Molecular Organization and Engineering, 93–108. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-0822-5_9.

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Honrubia, Vicente, Larry F. Hoffman, Anita Newman, Eri Naito, Yasushi Naito, and Karl Beykirch. "Sensoritopic and Topologic Organization of the Vestibular Nerve." In The Mammalian Cochlear Nuclei, 437–49. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2932-3_35.

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Conference papers on the topic "Nucleoid Organization"

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Vierling, Elizabeth. "Mitochondrial Nucleoid Organization is Linked to Mitochondrial Gene Expression and Stress Tolerance." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.1053088.

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Velasco, Vera. "Mitochondrial Nucleoid Organization is Linked to Mitochondrial Gene Expression and Stress Tolerance." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.1007204.

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"Search of new type of spatial organization of nucleic acids in human genome." 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-2020-084.

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"Search for a new type of spatial organization of nucleic acids in human genome." In SYSTEMS BIOLOGY AND BIOINFORMATICS (SBB-2020). Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences., 2020. http://dx.doi.org/10.18699/sbb-2020-40.

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Sussman, Michael. "ISO TC 34/SC 16 Horizontal methods for molecular biomarker analysis—international standards for molecular biomarker analysis/isothermal nucleic acid amplification methods." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/fnwh5573.

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Harmonized, easy to handle methods of analysis with defined patterns and known nomenclatures bring more customers to the market. The International Organization for Standardization (ISO.org) was formed in 1946. It is an independent, non-governmental voluntary consensus standard body based in Geneva, Switzerland with a membership of 165 national standards bodies. The US ISO member is the American National Standards Institute (ANSI.org), a consortium of US standardization organizations. There are 45 participating countries. The US delegation responsible for developing the US position for standards development in agricultural molecular biomarker analysis was delegated to the American Oil Chemist’s Society (AOCS.org) by ANSI. The AOCS US TAG also hosts the TC 34/SC 16 international secretariat. TC 34/SC 16 has published 31 standards with another 6 under development. The six under development are: ISO/AWI 5354 Molecular biomarkers of agricultural fibers. Screening of genetically modified organisms (GMOs) in cotton and textiles; ISO/DIS 16577 Molecular biomarker analysis. Vocabulary for molecular biomarker analytical methods in agriculture and food production; ISO/CD 16578 Molecular biomarker analysis. Requirements for microarray detection of specific nucleic acid sequences; ISO/DTS 20224-8 Molecular biomarker analysis. Detection of animal-derived materials in foodstuffs and feedstuffs by real-time PCR Part 8: Turkey DNA detection method; ISO/DTS 20224-9; Molecular biomarker analysis. Detection of animal-derived materials in foodstuffs and feedstuffs by real-time PCR. Part 9: Goose DNA detection method and ISO/FDIS 22942-1 Molecular biomarker analysis. Isothermal polymerase chain reaction (isoPCR) methods. Part 1: General requirements. We will discuss details and publication of these new standards.
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Cheung, Tracy M., and George A. Truskey. "Aging Endothelial Cells Exhibit Decreased Response to Atheroprotective Shear Stress." In ASME 2013 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/sbc2013-14402.

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As endothelial cells (ECs) age, morphological and physiological changes occur that may alter macromolecular transport and cause subsequent disease development. ECs in atherosclerotic regions exhibit high cell turnover and high levels of oxidative stress due to transient flow patterns and low and oscillating shear stress. This leads to replicative or stress-induced senescence. Resveratrol indirectly reverses senescence-associated phenotypes via competitive inhibition of cAMP-degrading phosphodiesterases (PDEs). Elevated levels of membrane-associated cAMP activate the cyclic AMP-regulated guanosine nucleotide exchange factor Epac1 which, in turn, leads to guanosine triphosphate (GTP) binding to the small G protein Rap1. GTP bound Rap1 activates the deacetylase SIRTUIN1 (SIRT1) but also causes changes to the cortical cytoskeleton and organization of VE-cadherin mechanosensor in the endothelial junctions (Figure 1).
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Dahl, Kris Noel, Elizabeth A. Booth-Gauthier, Alexandre J. S. Ribeiro, and Zhixia Zhong. "The Role of Nuclear Stiffness and Resilience in Mechanotransduction." In ASME 2010 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2010. http://dx.doi.org/10.1115/sbc2010-19514.

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Mechanical force is found to be increasingly important during development and for proper homeostatic maintenance of cells and tissues. The nucleus occupies a large volume fraction of the cell and is interconnected with the cytoskeleton. Here, to determine the direct role of the nucleus itself in converting forces to changes in gene expression, also known as, mechanotransduction, we examine changes in nuclear mechanics and gene reorganization associated with cell fate and with extracellular force. We measure mechanics of nuclei in many model cell systems using micropipette aspiration to show changes in nuclear mechanics. In intact cells we characterize the rheological changes induced in the genome organization with live cell imaging and particle tracking, and we suggest how these changes relate to gene expression.
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Marmolejo Duarte, Carlos Ramiro, Carlos Andrés Aguirre Núñez, and Manuel A. Ruiz Lineros. "¿Hacia un sistema de metrópolis españolas policéntricas?: caracterización de su estructura metropolitana." In International Conference Virtual City and Territory. Mexicali: Universidad Autónoma de Baja California, 2010. http://dx.doi.org/10.5821/ctv.7672.

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Las metrópolis han sufrido en la última mitad de siglo un proceso de descentralización de la actividad económica y el desarrollo de nuevas centralidades fuera de sus cascos tradicionales. Este proceso, ha permitido la generación de subcentros de actividad, que captan actividad económica de los centros urbanos generando nuevos patrones de ocupación del territorio, que coexisten con los procesos de dispersión. En esta investigación, mediante el análisis de la densidad de empleo, se caracteriza la estructura policentrica de 7 áreas metropolitanas españolas: Madrid, Barcelona, Valencia, Bilbao, Sevilla, Zaragoza, y Málaga; en el sentido de identificar la forma en cómo la población y la actividad económica se distribuye en 4 tipos de asentamientos: 1) núcleos centrales de actividad, 2) continuos centrales, 3) núcleos satelitales de actividad, y 4) resto del área metropolitana. Los resultados sugieren que el nivel de policentrismo está asociado a dos factores: el tamaño de los sistemas metropolitanos y la matriz territorial en la que se ubican éstos; así, cuanto más grandes son los primeros y más accidentada es la segunda, el proceso de autoorganización espacial de la economía tiende a generar sistemas policéntricos. The cities have suffered in the last half century a process of decentralization of economic activity and development of new centralities outside their traditional helmets. This process has allowed the generation of sub-centers, that capture economic activity to generate new patterns in the territory, which coexist with the scattering processes. In this research, by analyzing the density of employment, polycentric structure characterized by seven metropolitan areas Spanish: Madrid, Barcelona, Valencia, Bilbao, Seville, Zaragoza, and Málaga, in the sense of identifying how and how people and economic activity is settled in into four types of settlement: 1) nuclei central activity, 2) Central continuous, 3) satellite nucleos , and 4) rest of the metropolitan area. The results suggest that the level of polycentrism is associated with two factors: the size of metropolitan system and the territorial matrix in which are located they, thus, the larger the first and most rugged is the second, the process of spatial self-organization of the economy tends to generate polycentric system.
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Heo, Su-Jin, Nandan L. Nerurkar, Tristan P. Driscoll, and Robert L. Mauck. "Differentiation and Dynamic Tensile Loading Alter Nuclear Mechanics and Mechanoreception in Mesenchymal Stem Cells." In ASME 2011 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2011. http://dx.doi.org/10.1115/sbc2011-53432.

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Mesenchymal stem cells (MSCs) are a promising cell source for tissue engineering applications, given their ease of isolation and multi-potential differentiation capacity [1]. Passive and active mechanical signals can direct MSC lineage commitment [2], however, the subcellular machinery that translates physical cues to biologic response remains unclear. Direct deformation of the nucleus may influence differentiation by inducing mechanical reorganization of nuclear chromatin. Because the nuclei of differentiated cells are stiffer than progenitor cells [3], it is possible that such mechanoregulatory mechanisms vary with differentiation state. Lamin A/C is a filamentous protein that largely defines nuclear shape, size and stiffness [3]. Recent work suggests that Lamin A/C also regulates chromatin organization and transcriptional activity [4]. Recently, we have developed an in vitro system to direct the functional differentiation of MSCs into fibrochondrocytes, using electrospun polymeric nanofiber substrates [5]. Alignment of nanofibers directs cell alignment, allowing external forces to be applied uniformly along the long axes of cells, emulating the mechanical microenvironment experienced by embryonic progenitors during fibrous tissue morphogenesis [6]. We have noted, however, that as MSCs undergo fibrochondrogenesis, translation of scaffold deformation to nuclear deformation is attenuated [7]. From those studies, it was not clear whether this was due to changes in cellular mechanics or to accretion of extracellular matrix during differentiation. Thus the objective of the present work was to specifically identify how fibrochondrogenesis of MSCs on aligned nanofibrous scaffolds alters nuclear mechanics and mechanoreception, and further to ascertain whether mechanical stimulation alone can elicit similar mechanoregulatory changes.
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