Relevant bibliographies by topics / Gene orders

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
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Academic literature on the topic 'Gene orders'

Author: Grafiati
Published: 4 June 2021
Last updated: 2 February 2022

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Journal articles on the topic "Gene orders"

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Perseke, Marleen, Guido Fritzsch, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Detlef Bernhard, Peter F. Stadler, and Martin Schlegel. "Evolution of mitochondrial gene orders in echinoderms." Molecular Phylogenetics and Evolution 47, no. 2 (May 2008): 855–64. http://dx.doi.org/10.1016/j.ympev.2007.11.034.

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Perrin, Amandine, Jean-Stéphane Varré, Samuel Blanquart, and Aïda Ouangraoua. "ProCARs: Progressive Reconstruction of Ancestral Gene Orders." BMC Genomics 16, Suppl 5 (2015): S6. http://dx.doi.org/10.1186/1471-2164-16-s5-s6.

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Yang, Ning, Fei Hu, Lingxi Zhou, and Jijun Tang. "Reconstruction of Ancestral Gene Orders Using Probabilistic and Gene Encoding Approaches." PLoS ONE 9, no. 10 (October 10, 2014): e108796. http://dx.doi.org/10.1371/journal.pone.0108796.

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Markov, A. V., and I. A. Zakharov. "Evolution of gene orders in genomes of cyanobacteria." Russian Journal of Genetics 45, no. 8 (August 2009): 906–16. http://dx.doi.org/10.1134/s1022795409080031.

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Zhang, Yiwei, Fei Hu, and Jijun Tang. "A mixture framework for inferring ancestral gene orders." BMC Genomics 13, Suppl 1 (2012): S7. http://dx.doi.org/10.1186/1471-2164-13-s1-s7.

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Silander, Olin K., and Martin Ackermann. "The constancy of gene conservation across divergent bacterial orders." BMC Research Notes 2, no. 1 (2009): 2. http://dx.doi.org/10.1186/1756-0500-2-2.

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Markov, A. V., and I. A. Zakharov. "Evolution of gene orders in mycoplasmas (Bacteria, Firmicutes, Mollicutes)." Russian Journal of Genetics 45, no. 7 (July 2009): 781–87. http://dx.doi.org/10.1134/s1022795409070035.

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Kunisawa, Takashi. "Gene arrangements and branching orders of gram-positive bacteria." Journal of Theoretical Biology 222, no. 4 (June 2003): 495–503. http://dx.doi.org/10.1016/s0022-5193(03)00064-x.

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Perez Botero, Juliana, Lea Coon, Julie Majerus, Dong Chen, and Rajiv Pruthi. "Factor IX Gene (F9) Genotyping Trends and Spectrum of Mutations Identified: A Reference Laboratory Experience." Seminars in Thrombosis and Hemostasis 44, no. 03 (September 13, 2017): 287–92. http://dx.doi.org/10.1055/s-0037-1605567.

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AbstractIn hemophilia B (HB), factor IX gene (F9) genotyping is used for molecular confirmation of affected individuals, for carrier testing, to facilitate the identification of those at risk for anaphylaxis/inhibitors (associated with large deletions), and to assist in assigning disease severity. Owing to test costs, optimal test utilization involves pre/post-test counseling and appropriate patient and test selection (e.g., mutation screening [F9MS] vs. known mutation [F9KM] testing). This article aims to review the trends and outcomes of F9-genotyping orders and describe the spectrum of variants identified in a sample of individuals in our reference laboratory. We performed a retrospective review of consecutive orders submitted to the Special Coagulation DNA Diagnostic Laboratory, Mayo Clinic, between 2012 and 2015. A total of 133 orders (38%) were identified for men: 118 (88%) were F9MS and 15 (12%) were F9KM. Thirteen orders (10%) were cancelled. A total of 209 orders were identified for women: 178 (85%) were F9MS and 31 (15%) were F9KM. Thirty-seven orders (18%) were cancelled and 30% of the tests performed yielded negative results. A total of 164 samples (47%) were received without clinical information. Seventeen previously unreported variants were identified. F9 genotyping provides useful information for HB management; however, 18% of our orders were cancelled and almost half were received without relevant clinical information, thus reaffirming the need for ongoing scrutiny of submitted orders. Optimal patient and test selection is important as is the accurate interpretation of variants identified. Most of the pathogenic variants identified were point mutations, with very few large deletions, consistent with the literature.
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Hu, Fei, Jun Zhou, Lingxi Zhou, and Jijun Tang. "Probabilistic Reconstruction of Ancestral Gene Orders with Insertions and Deletions." IEEE/ACM Transactions on Computational Biology and Bioinformatics 11, no. 4 (July 2014): 667–72. http://dx.doi.org/10.1109/tcbb.2014.2309602.

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Dissertations / Theses on the topic "Gene orders"

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Goldman, Jacki P. "Regulated accessibility of variable region genes may control developmentally ordered T cell receptor [gamma] gene rearrangement." Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/32626.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1995.
On t.p., "[gamma] appears as the lower case Greek letter.
Includes bibliographical references (leaves 155-172).
by Jacki P. Goldman.
Ph.D.
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Zheng, Chunfang, Eric Chen, Victor Albert, Eric Lyons, and David Sankoff. "Ancient eudicot hexaploidy meets ancestral eurosid gene order." BioMed Central, 2013. http://hdl.handle.net/10150/610022.

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BACKGROUND:A hexaploidization event over 125 Mya underlies the evolutionary lineage of the majority of flowering plants, including very many species of agricultural importance. Half of these belong to the rosid subgrouping, containing severals whose genome sequences have been published. Although most duplicate and triplicate genes have been lost in all descendants, clear traces of the original chromosome triples can be discerned, their internal contiguity highly conserved in some genomes and very fragmented in others. To understand the particular evolutionary patterns of plant genomes, there is a need to systematically survey the fate of the subgenomes of polyploids, including the retention of a small proportion of the duplicate and triplicate genes and the reconstruction of putative ancestral intermediates between the original hexaploid and modern species, in this case the ancestor of the eurosid clade.RESULTS:We quantitatively trace the fate of gene triples originating in the hexaploidy across seven core eudicot flowering plants, and fit this to a two-stage model, pre- and post-radiation. We also measure the simultaneous dynamics of duplicate orthologous gene loss in three rosids, as influenced by biological functional class. We propose a new protocol for reconstructing ancestral gene order using only gene adjacency data from pairwise genomic analyses, based on repeating MAXIMUM WEIGHT MATCHING at two levels of resolution, an approach designed to transcend limitations on reconstructed contig size, while still avoiding the ambiguities of a multiplicity of solutions. Applied to three high-quality rosid genomes without subsequent polyploidy events, our automated procedure reconstructs the ancestor of the eurosid clade.CONCLUSIONS:The gene loss analysis and the ancestor reconstruction present complementary assessments of post-hexaploidization evolution, the first at the level of individual gene families within and across sister genomes and the second at the chromosome level. Despite the loss of more than 95% of gene duplicates and triplicates, and despite major structural rearrangement, our reconstructed eurosid ancestor clearly identifies the three regions corresponding to each of the seven original chromosomes of the earlier pre-hexaploid ancestor. Functional analysis confirmed trends reported for more recent plant polyploidy events: genes involved with regulation and responses were retained in multiple copies, while genes involved with metabolic processes were lost.
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Silvestre, Daniela. "Seqüenciamento e análise do genoma mitocondrial de Melipona bicolor (Hymenoptera, Apidae, Meliponini)." Universidade de São Paulo, 2002. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-06052002-110339/.

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A seqüência completa do genoma mitocondrial de uma espécie pode ajudar no mapeamento de restrição e desenho de primers para PCR. Estes poderão servir para amplificação e posterior seqüenciamento de regiões específicas de outras espécies e populações relacionadas, para estudos filogenéticos e de dinâmica populacional. Até o momento, temos na literatura a seqüência completa do DNA mitocondrial (DNAmt) de um único himenóptero, Apis mellifera, espécie que é endêmica do Velho Mundo. Nenhum genoma mitocondrial de uma espécie de abelha nativa do Brasil foi até o momento descrito. Com a devastação crescente dos ecossistemas, há a perda de espécies de abelhas ainda pouco estudadas, e talvez até outras ainda não conhecidas. Entre os meliponíneos, há espécies-chave de diversos ecossistemas brasileiros, tendo portanto uma enorme importância ecológica. No decorrer deste projeto, foram amplificados via PCR e seqüenciados 77% do genoma mitocondrial da abelha sem ferrão Melipona bicolor (Apidae, Meliponini), contendo todos os 13 genes mitocondriais codificadores para proteínas, 18 dos 22 genes para RNAt e os dois genes para RNAr (sendo um integral e o outro parcialmente seqüenciado). Além do seqüenciamento, foram realizados neste trabalho: análise da organização do genoma (conteúdo e ordem gênica); análise da tradução dos genes para proteínas e código genético; análise de outras características moleculares (freqüência das bases, códons utilizados, iniciação e terminação de genes, freqüência de aminoácidos etc); e comparação das características acima mencionadas com o genoma mitocondrial de A. mellifera e também com outros insetos. O viés para o uso de bases A+T, bastante evidente em A. mellifera, mostrou-se ainda mais acentuado em M. bicolor. Foram encontradas diferenças no tamanho e composição dos genes. Pelo menos nove rearranjos na ordem gênica mitocondrial foram observados entre as duas espécies de abelhas, um fenômeno raro entre organismos tão próximos. Considerando que essas espécies compartilham um comportamento intrigante, a eussocialidade, esses rearranjos podem servir como um excelente marcador para estudar a origem e a evolução desse comportamento no grupo.
The complete sequence of the mitochondrial genome of a species may help on restriction mapping and to design PCR primers. These can be useful to amplify and sequence specific regions from other species and analyze populations, in phylogenetic and demographic studies. So far, there was reported on literature the mtDNA complete sequence for only one hymenopteran, Apis mellifera, endemic from the Old World. No mitocondrial genome of a Brazilian native bee was ever described. With the increasing devastation of natural environments, several bee species can be led to extinction, including those poorly studied and maybe some unknown species. The meliponines (stingless bees) include key species to several Brazilian ecosystems, so they play an important ecological role. In this project, we have PCR amplified and sequenced 77% of the mitochondrial genome of the stingless bee Melipona bicolor (Apidae, Meliponini). The sequenced region contains all of the 13 mitochondrial protein-coding genes, 18 of 22 tRNA genes, and both rRNA genes (one of them was only partially sequenced). Besides sequencing, this work consisted of: analysis of genome organization (gene content and order); analysis of gene translation and genetic code; analysis of other molecular features (base frequencies, codon usage, gene initiation and termination, amino acid frequencies etc.); and comparison of the characteristics mentioned above with A. mellifera mitocondrial genome and also other insects. The highly biased A+T content is a typical characteristic of A. mellifera mitochondrial genome, and it is even more extreme on M. bicolor mtDNA. There are length and compositional differences on genes between M. bicolor and A. mellifera. At least nine gene order rearrangements were observed by comparing the mtDNA of these species, what is a rare event on closely related organisms. Considering that both species share an intriguing behavior, eusociality, these gene rearrangements may be used as an excellent marker to study the origin and evolution of that behavior on bees.
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Bernt, Matthias. "Gene order rearrangement methods for the reconstruction of phylogeny." Doctoral thesis, Universitätsbibliothek Leipzig, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-38666.

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The study of phylogeny, i.e. the evolutionary history of species, is a central problem in biology and a key for understanding characteristics of contemporary species. Many problems in this area can be formulated as combinatorial optimisation problems which makes it particularly interesting for computer scientists. The reconstruction of the phylogeny of species can be based on various kinds of data, e.g. morphological properties or characteristics of the genetic information of the species. Maximum parsimony is a popular and widely used method for phylogenetic reconstruction aiming for an explanation of the observed data requiring the least evolutionary changes. A certain property of the genetic information gained much interest for the reconstruction of phylogeny in recent time: the organisation of the genomes of species, i.e. the arrangement of the genes on the chromosomes. But the idea to reconstruct phylogenetic information from gene arrangements has a long history. In Dobzhansky and Sturtevant (1938) it was already pointed out that “a comparison of the different gene arrangements in the same chromosome may, in certain cases, throw light on the historical relationships of these structures, and consequently on the history of the species as a whole”. This kind of data is promising for the study of deep evolutionary relationships because gene arrangements are believed to evolve slowly (Rokas and Holland, 2000). This seems to be the case especially for mitochondrial genomes which are available for a wide range of species (Boore, 1999). The development of methods for the reconstruction of phylogeny from gene arrangement data has made considerable progress during the last years. Prominent examples are the computation of parsimonious evolutionary scenarios, i.e. a shortest sequence of rearrangements transforming one arrangement of genes into another or the length of such a minimal scenario (Hannenhalli and Pevzner, 1995b; Sankoff, 1992; Watterson et al., 1982); the reconstruction of parsimonious phylogenetic trees from gene arrangement data (Bader et al., 2008; Bernt et al., 2007b; Bourque and Pevzner, 2002; Moret et al., 2002a); or the computation of the similarities of gene arrangements (Bergeron et al., 2008a; Heber et al., 2009). 1 1 Introduction The central theme of this work is to provide efficient algorithms for modified versions of fundamental genome rearrangement problems using more plausible rearrangement models. Two types of modified rearrangement models are explored. The first type is to restrict the set of allowed rearrangements as follows. It can be observed that certain groups of genes are preserved during evolution. This may be caused by functional constraints which prevented the destruction (Lathe et al., 2000; Sémon and Duret, 2006; Xie et al., 2003), certain properties of the rearrangements which shaped the gene orders (Eisen et al., 2000; Sankoff, 2002; Tillier and Collins, 2000), or just because no destructive rearrangement happened since the speciation of the gene orders. It can be assumed that gene groups, found in all studied gene orders, are not acquired independently. Accordingly, these gene groups should be preserved in plausible reconstructions of the course of evolution, in particular the gene groups should be present in the reconstructed putative ancestral gene orders. This can be achieved by restricting the set of rearrangements, which are allowed for the reconstruction, to those which preserve the gene groups of the given gene orders. Since it is difficult to determine functionally what a gene group is, it has been proposed to consider common combinatorial structures of the gene orders as gene groups (Marcotte et al., 1999; Overbeek et al., 1999). The second considered modification of the rearrangement model is extending the set of allowed rearrangement types. Different types of rearrangement operations have shuffled the gene orders during evolution. It should be attempted to use the same set of rearrangement operations for the reconstruction otherwise distorted or even wrong phylogenetic conclusions may be obtained in the worst case. Both possibilities have been considered for certain rearrangement problems before. Restricted sets of allowed rearrangements have been used successfully for the computation of parsimonious rearrangement scenarios consisting of inversions only where the gene groups are identified as common intervals (Bérard et al., 2007; Figeac and Varré, 2004). Extending the set of allowed rearrangement operations is a delicate task. On the one hand it is unknown which rearrangements have to be regarded because this is part of the phylogeny to be discovered. On the other hand, efficient exact rearrangement methods including several operations are still rare, in particular when transpositions should be included. For example, the problem to compute shortest rearrangement scenarios including transpositions is still of unknown computational complexity. Currently, only efficient approximation algorithms are known (e.g. Bader and Ohlebusch, 2007; Elias and Hartman, 2006). Two problems have been studied with respect to one or even both of these possibilities in the scope of this work. The first one is the inversion median problem. Given the gene orders of some taxa, this problem asks for potential ancestral gene orders such that the corresponding inversion scenario is parsimonious, i.e. has a minimum length. Solving this problem is an essential component 2 of algorithms for computing phylogenetic trees from gene arrangements (Bourque and Pevzner, 2002; Moret et al., 2002a, 2001). The unconstrained inversion median problem is NP-hard (Caprara, 2003). In Chapter 3 the inversion median problem is studied under the additional constraint to preserve gene groups of the input gene orders. Common intervals, i.e. sets of genes that appear consecutively in the gene orders, are used for modelling gene groups. The problem of finding such ancestral gene orders is called the preserving inversion median problem. Already the problem of finding a shortest inversion scenario for two gene orders is NP-hard (Figeac and Varré, 2004). Mitochondrial gene orders are a rich source for phylogenetic investigations because they are known for more than 1 000 species. Four rearrangement operations are reported at least in the literature to be relevant for the study of mitochondrial gene order evolution (Boore, 1999): That is inversions, transpositions, inverse transpositions, and tandem duplication random loss (TDRL). Efficient methods for a plausible reconstruction of genome rearrangements for mitochondrial gene orders using all four operations are presented in Chapter 4. An important rearrangement operation, in particular for the study of mitochondrial gene orders, is the tandem duplication random loss operation (e.g. Boore, 2000; Mauro et al., 2006). This rearrangement duplicates a part of a gene order followed by the random loss of one of the redundant copies of each gene. The gene order is rearranged depending on which copy is lost. This rearrangement should be regarded for reconstructing phylogeny from gene order data. But the properties of this rearrangement operation have rarely been studied (Bouvel and Rossin, 2009; Chaudhuri et al., 2006). The combinatorial properties of the TDRL operation are studied in Chapter 5. The enumeration and counting of sorting TDRLs, that is TDRL operations reducing the distance, is studied in particular. Closed formulas for computing the number of sorting TDRLs and methods for the enumeration are presented. Furthermore, TDRLs are one of the operations considered in Chapter 4. An interesting property of this rearrangement, distinguishing it from other rearrangements, is its asymmetry. That is the effects of a single TDRL can (in the most cases) not be reversed with a single TDRL. The use of this property for phylogeny reconstruction is studied in Section 4.3. This thesis is structured as follows. The existing approaches obeying similar types of modified rearrangement models as well as important concepts and computational methods to related problems are reviewed in Chapter 2. The combinatorial structures of gene orders that have been proposed for identifying gene groups, in particular common intervals, as well as the computational approaches for their computation are reviewed in Section 2.2. Approaches for computing parsimonious pairwise rearrangement scenarios are outlined in Section 2.3. Methods for the computation genome rearrangement scenarios obeying biologically motivated constraints, as introduced above, are detailed in Section 2.4. The approaches for the inversion median problem are covered in Section 2.5. Methods for the reconstruction of phylogenetic trees from gene arrangement data are briefly outlined in Section 2.6.3 1 Introduction Chapter 3 introduces the new algorithms CIP, ECIP, and TCIP for solving the preserving inversion median problem. The efficiency of the algorithm is empirically studied for simulated as well as mitochondrial data. The description of algorithms CIP and ECIP is based on Bernt et al. (2006b). TCIP has been described in Bernt et al. (2007a, 2008b). But the theoretical foundation of TCIP is extended significantly within this work in order to allow for more than three input permutations. Gene order rearrangement methods that have been developed for the reconstruction of the phylogeny of mitochondrial gene orders are presented in the fourth chapter. The presented algorithm CREx computes rearrangement scenarios for pairs of gene orders. CREx regards the four types of rearrangement operations which are important for mitochondrial gene orders. Based on CREx the algorithm TreeREx for assigning rearrangement events to a given tree is developed. The quality of the CREx reconstructions is analysed in a large empirical study for simulated gene orders. The results of TreeREx are analysed for several mitochondrial data sets. Algorithms CREx and TreeREx have been published in Bernt et al. (2008a, 2007c). The analysis of the mitochondrial gene orders of Echinodermata was included in Perseke et al. (2008). Additionally, a new and simple method is presented to explore the potential of the CREx method. The new method is applied to the complete mitochondrial data set. The problem of enumerating and counting sorting TDRLs is studied in Chapter 5. The theoretical results are covered to a large extent by Bernt et al. (2009b). The missing combinatorial explanation for some of the presented formulas is given here for the first time. Therefor, a new method for the enumeration and counting of sorting TDRLs has been developed (Bernt et al., 2009a).
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Munoz, Adriana, Chunfang Zheng, Qian Zhu, Victor Albert, Steve Rounsley, and David Sankoff. "Scaffold filling, contig fusion and comparative gene order inference." BioMed Central, 2010. http://hdl.handle.net/10150/610198.

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BACKGROUND:There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to compare genomes available in scaffold form only? Can the comparative evidence predict the location of unsequenced genes?RESULTS:Our method involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is accomplished by an exact, polynomial-time algorithm. We then correct for the number of extra fusion/fission operations required to make scaffolds comparable to full assemblies. We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other. We estimate the parameters of this model through simulations and by comparing the angiosperm genomes Ricinus communis and Vitis vinifera.CONCLUSIONS:The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.
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Turner, Kyle Hugh. "Commanding officer's standing orders a powerful and unique genre." Thesis, Monterey, Calif. : Springfield, Va. : Naval Postgraduate School ; Available from National Technical Information Service, 2006. http://library.nps.navy.mil/uhtbin/hyperion/06Jun%5FTurner.pdf.

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Myhre, Susanna. "Genetic re-targeting and de-targeting of adenovirus type 5 in order to create vectors for gene therapy /." Göteborg : Department of Microbiology and Immunology, The Sahlgrenska Academy at Göteborg University, 2007. http://hdl.handle.net/2077/7498.

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Tiwari, Vijay Kumar. "The Epigenetics of Gene Transcription and Higher Order Chromatin Conformation." Doctoral thesis, Uppsala universitet, Zoologisk utvecklingsbiologi, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6302.

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It is becoming increasingly clear that long-range control of gene expression is mediated through direct physical interactions between genes and regulatory elements, either intra- or interchromosomally. In addition to transcriptional initiation, formation of active chromatin hubs seem to be crucial for increased transcriptional efficiency as well as insulation from neighbouring heterochromatic environment. Regulatory factors apparently have an important role in organization of such functional modules in a development and differentiated- dependent fashion. The relevance of trans-acting factors in the ‘choice’ process of X-Chromosome Inactivation (XCI) was highlighted by our observations where CTCF was shown to occupy a homologous position on the active mouse and human Xist/XIST promoters and its binding affinity was altered in familial cases of opposite skewed X-inactivation patterns. The paradigm of genomic imprinting, i.e. the Igf2-H19 locus, manifests its imprinted states through the H19 Imprinting Control Region (ICR). The repression of the maternal Igf2 allele depends on the insulator properties of the H19 ICR when this interacts with CTCF. The studies here detected a novel kind of CTCF-dependent tightly closed pocket- like higher order structure exclusively on maternal allele which was found to be essential for imprinted Igf2 expression as well as maintenance of precise epigenetic marks at various Differentially Methylated Regions (DMRs) across this locus. Despite the highly condensed state of the mitotic chromosome, the insulator protein CTCF was found to constitutively occupy its known target sites. Furthermore, pivotal CTCF-dependent long-range regulatory loops within Igf2-H19 locus were found to survive mitotic compaction and such mechanisms might serve as a novel kind of epigenetic memory to minimize transcriptional chaos and to reset proper expression domains in the daughter cells as soon as cells exit mitosis. Our observations also suggest that the epigenetic reprogramming of H19 ICR during spermatogenesis is initiated by a CTCF-dependent recruitment of chromatin remodeling factor Lsh to the H19 ICR followed by completion of the imprint acquisition process by a replacement of CTCF with its closely related paralogue termed BORIS. Overall, this thesis unravels the novel roles for CTCF as an architectural factor in the organization of higher order chromatin conformations and transcriptional regulation.
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Göndör, Anita. "Epigenetic Regulation of Higher Order Chromatin Conformations and Gene Transcription." Doctoral thesis, Uppsala universitet, Zoologisk utvecklingsbiologi, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8296.

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Epigenetic states constitute heritable features of the chromatin to regulate when, where and how genes are expressed in the developing conceptus. A special case of epigenetic regulation, genomic imprinting, is defined as parent of origin-dependent monoallelic expression. The Igf2-H19 locus is considered as paradigm of genomic imprinting with a growth-promoting gene, Igf2, expressed paternally and a growth antagonist, H19 encoding a non-coding transcript, expressed only from the maternal allele. The monoallelic expression patterns are regulated by the epigenetic status at an imprinting control region (ICR) in the 5´-flank of the H19 gene. The chromatin insulator protein CTCF interacts with only the maternal H19 ICR allele to prevent downstream enhancers to communicate with the Igf2 promoters. Mutations of these CTCF binding sites lead to biallelic Igf2 expression, increased size of the conceptus and predisposition for cancer. Reasoning that these effects cannot be explained by the regulation of Igf2 expression alone, a technique was invented to examine long-range chromatin interactions without prior knowledge of the interacting partners. Applying the circular chromosomal conformation capture (4C) technique to mouse neonatal liver cells, it was observed that 114 unique sequences interacted with the H19 ICR. A majority of these interactors was in complex with only the maternal H19 ICR allele and depended on the presence of functional CTCF binding sites. The functional consequence of chromosomal networks was demonstrated by the observation that the maternal H19 ICR allele regulated the transcription of two genes on another chromosome. As the chromosomal networks underwent reprogramming during the maturation of embryonic stem cells, attention was turned to human cancer cells, displaying features common with mouse embryonic stem cells. Subsequently, chromatin folding at the human H19 ICR suggested that stable chromatin loops were organized by synergistic interactions within and between baits and interactors. The presence of these interactions was linked to DNA methylation patterns involving repeat elements. A "flower" model of chromatin networks was formulated to explain these observations. This thesis has unravealed a novel feature of the epigenome and its functions to regulate gene expression in trans. The identified roles for CTCF as an architectural factor in the organization of higher order chromatin conformations may be of importance in understanding development and disease ontogeny from novel perspectives.
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WHEELER, COSETTE MARIE THERESE. "HEPATITIS A VIRUS: GROWTH CHARACTERISTICS, PURIFICATION, AND CAPSID GENE ORDER (PEPTIDES, IMMUNOREACTIVITIES, POLYPEPTIDES)." Diss., The University of Arizona, 1985. http://hdl.handle.net/10150/188108.

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A human isolate of hepatitis A virus (HAV) strain HAS-15 was adapted to rapid growth FRhK-4 cells and a one-step growth curve was determined. Detectable virion production was absent for approximately 20 h post-infection (p.i.) and was followed by a 4-day logarithmic phase of virus production. A maximum intracellular virus titer of 10⁹ radioimmunofocus-forming units (RFU) per milliliter was achieved and remained essentially constant for a period of up to 14 days p.i. An adsorption study with HAV HAS-15 using FRhK-4 cells demonstrated greater than 99.9% of infectious virus adsorbed at 25 C in less than 20 min. Milligram amounts of purified HAV HAS-15 were obtained from persistently-infected RFhK-4 cells. The HAV polypeptides were separated by sodium dodecyl sulfate - polyacrylamide gel electrophoresis and transferred to nitocellulose for detection by an enzyme-linked immunotransfer blot (EITB) procedure. HAV nucleotide-derived amino acid sequence was subjected to computer analysis to identify potential immunogenic regions within the HAV capsid polypeptides. Synthetic peptides corresponding to selected regions of each of the larger putative capsid polypeptides were coupled to keyhole limpet hemocyanin and used to immunize rabbits. EITB reactivities of HAV specific anti-peptide sera have allowed the identification of the gene order for the larger HAV P1 gene products and the determination of the following molecular weights: HAV VP2 or 1B (MW 27,000), HAV VP3 or 1C (MW 29,000), and HAV VP1 or 1D (MW 33,000). The disposition of the HAV capsid polypeptides with respect to the virion external surface was evaluated by EITB reactivity of HAV polypeptides with specific antisera. Hyperimmune rabbit anti-157S HAV and human IgM reacted with VP1, VP2, and VP3, while IgG reacted predominantly with VP1 and VP2. Further evaluation of the HAV virion structure was attempted by examining the relative accessibility of the virion polypeptides to various labeling reagents. Reaction of intact virions with Iodogen resulted in the predominant labeling of VP1 while labeling of VP2 and 3 was barely detectable. Selective labeling of VP1 under controlled conditions, combined with the anti-HAV IgG immunologic reactivity against VP1 and VP2, suggests that these two capsid components are more exposed on the virion surface and may play an important role in the generation of neutralizing antibodies.
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Books on the topic "Gene orders"

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Ridder, Jozef de. 't zijn al geen heiligen die grote paternosters dragen: Kleding van vrouwelijke religieuzen in de 19de en 20ste eeuw in België. Brugge: Vanhaecke, 2002.

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David, Sankoff, and Nadeau J. H, eds. Comparative genomics: Empirical and analytical approaches to gene order dynamics, map alignment and the evolution of gene families. Dordrecht: Kluwer Academic, 2000.

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Slack, Jonathan. 3. Mutations and gene variants. Oxford University Press, 2014. http://dx.doi.org/10.1093/actrade/9780199676507.003.0003.

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All gene variants originate as mutations. Most variants in the genome of any given individual are not new mutations but have been inherited from previous generations. ‘Mutations and gene variants’ shows that mutations can occur in any cell of the body, but in order to be inherited they must occur in the DNA of the reproductive cells. There are numerous genetic diseases caused by a single mutation in one gene, and the examples considered here are cystic fibrosis, haemophilia, achondroplasia, and Holt-Oram Syndrome. In such cases, the inheritance of the abnormal gene variant follows simple Mendelian rules. The origin of cancer is explained as a combination of mutations occurring in a single cell of the body. Inherited gene variants predisposing to cancer do so because they reduce the number of new mutations required.
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(Editor), D. Sankoff, and J. H. Nadeau (Editor), eds. Comparative Genomics - Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families (Computational Biology). Springer, 2000.

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Campbell, Joseph W. The Order and the Other. University Press of Mississippi, 2019. http://dx.doi.org/10.14325/mississippi/9781496824721.001.0001.

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The Order and the Other is a call to reexamine the relationship between dystopian literature and science fiction by thinking about the work that each genre does on and for the reader. The author believes that this is especially necessary in regards to dystopian literature intended for adolescents. Now that the cultural boom of YA Dystopian texts is over, this book attempts to understand that boom by placing dystopian works into the larger context of belonging to literary history of dystopian works. It attempts to help readers see how surveillance and power form the way that not only the characters within the films or books think about themselves, but also how it shapes the readers, as well. It also helps show that the surveillance culture and state that we see within such texts is not dependent on science fiction genre structures to exist. Finally, the book examines the most recent efforts to understand the genre and suggests ways inquiry into the genre might go forward.
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Steane, Andrew. Purpose and Cause. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198824589.003.0007.

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The distinction between purpose (‘in order that what?’) and cause (‘owing to what?’) is spelled out. The aim is to unpick the confusion of these concepts that takes place in the writing of Richard Dawkins, especially in The Selfish Gene. Science is a discipline which is competent to address the second question, but which mostly does not address the first. However, it does not follow from this that scientific discourse must conclude that there is no purpose, or that the question of purpose is meaningless. To think that is to misunderstand the very nature of the discourse which scientific model-making embarks upon. Rather, intellectual discipline must be respected. The question of purpose is informed by science, but not answered by it. Furthermore, high-level languages applied to human life are valid and insightful. The products of Darwinian evolution are not defined by their role in multiplication of genes.
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Holroyd, Christopher R., Nicholas C. Harvey, Mark H. Edwards, and Cyrus Cooper. Environment. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0038.

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Musculoskeletal disease covers a broad spectrum of conditions whose aetiology comprises variable genetic and environmental contributions. More recently it has become clear that, particularly early in life, the interaction of gene and environment is critical to the development of later disease. Additionally, only a small proportion of the variation in adult traits such as bone mineral density has been explained by specific genes in genome-wide association studies, suggesting that gene-environment interaction may explain a much larger part of the inheritance of disease risk than previously thought. It is therefore critically important to evaluate the environmental factors which may predispose to diseases such as osteorthritis, osteoporosis, and rheumatoid arthritis both at the individual and at the population level. In this chapter we describe the environmental contributors, across the whole life course, to osteoarthritis, osteoporosis and rheumatoid arthritis, as exemplar conditions. We consider factors such as age, gender, nutrition (including the role of vitamin D), geography, occupation, and the clues that secular changes of disease pattern may yield. We describe the accumulating evidence that conditions such as osteoporosis may be partly determined by the early interplay of environment and genotype, through aetiological mechanisms such as DNA methylation and other epigenetic phenomena. Such studies, and those examining the role of environmental influences across other stages of the life course, suggest that these issues should be addressed at all ages, starting from before conception, in order to optimally reduce the burden of musculoskeletal disorders in future generations.
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Holroyd, Christopher R., Nicholas C. Harvey, Mark H. Edwards, and Cyrus Cooper. Environment. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199642489.003.0038_update_001.

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Musculoskeletal disease covers a broad spectrum of conditions whose aetiology comprises variable genetic and environmental contributions. More recently it has become clear that, particularly early in life, the interaction of gene and environment is critical to the development of later disease. Additionally, only a small proportion of the variation in adult traits such as bone mineral density has been explained by specific genes in genome-wide association studies, suggesting that gene-environment interaction may explain a much larger part of the inheritance of disease risk than previously thought. It is therefore critically important to evaluate the environmental factors which may predispose to diseases such as osteorthritis, osteoporosis, and rheumatoid arthritis both at the individual and at the population level. In this chapter we describe the environmental contributors, across the whole life course, to osteoarthritis, osteoporosis and rheumatoid arthritis, as exemplar conditions. We consider factors such as age, gender, nutrition (including the role of vitamin D), geography, occupation, and the clues that secular changes of disease pattern may yield. We describe the accumulating evidence that conditions such as osteoporosis may be partly determined by the early interplay of environment and genotype, through aetiological mechanisms such as DNA methylation and other epigenetic phenomena. Such studies, and those examining the role of environmental influences across other stages of the life course, suggest that these issues should be addressed at all ages, starting from before conception, in order to optimally reduce the burden of musculoskeletal disorders in future generations.
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Schindler, Nina. An Order of Amelie, Hold the Fries. Annick Press, 2004.

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Schindler, Nina. An Order of Amelie, Hold the Fries. Annick Press, 2004.

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Book chapters on the topic "Gene orders"

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Blin, Guillaume, Eric Blais, Pierre Guillon, Mathieu Blanchette, and Nadia El-Mabrouk. "Inferring Gene Orders from Gene Maps Using the Breakpoint Distance." In Comparative Genomics, 99–112. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11864127_9.

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Bergeron, Anne, Mathieu Blanchette, Annie Chateau, and Cedric Chauve. "Reconstructing Ancestral Gene Orders Using Conserved Intervals." In Lecture Notes in Computer Science, 14–25. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-30219-3_2.

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Liu, Tao, Jijun Tang, and Bernard M. E. Moret. "Quartet-Based Phylogeny Reconstruction from Gene Orders." In Lecture Notes in Computer Science, 63–73. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11533719_9.

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Bernt, Matthias, Daniel Merkle, and Martin Middendorf. "The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders." In Computational Life Sciences II, 52–63. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11875741_6.

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Ma, Jian, Aakrosh Ratan, Louxin Zhang, Webb Miller, and David Haussler. "A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications." In Comparative Genomics, 122–35. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-74960-8_10.

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Makarenkov, Vladimir, Alix Boc, and Pierre Legendre. "A New Algorithm for Inferring Hybridization Events Based on the Detection of Horizontal Gene Transfers." In Clusters, Orders, and Trees: Methods and Applications, 273–93. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0742-7_17.

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Xu, Qiaoji, Lingling Jin, Chunfang Zheng, James H. Leebens Mack, and David Sankoff. "RACCROCHE: Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-occurrences." In Computational Advances in Bio and Medical Sciences, 97–115. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-79290-9_9.

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Aganezov, Sergey, and Max A. Alekseyev. "Multi-genome Scaffold Co-assembly Based on the Analysis of Gene Orders and Genomic Repeats." In Bioinformatics Research and Applications, 237–49. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-38782-6_20.

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Tan, Ian H., and Louis D. Druehl. "Phylogeny of the Northeast Pacific brown algal (Phaeophycean) orders as inferred from 18S rRNA gene sequences." In Fourteenth International Seaweed Symposium, 699–704. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1998-6_94.

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El-Mabrouk, Nadia, and David Sankoff. "Analysis of Gene Order Evolution Beyond Single-Copy Genes." In Methods in Molecular Biology, 397–429. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-582-4_15.

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Conference papers on the topic "Gene orders"

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SWENSON, KRISTER M., WILLIAM ARNDT, JIJUN TANG, and BERNARD M. E. MORET. "PHYLOGENETIC RECONSTRUCTION FROM COMPLETE GENE ORDERS OF WHOLE GENOMES." In The 6th Asia-Pacific Bioinformatics Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2007. http://dx.doi.org/10.1142/9781848161092_0026.

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Trösser, Fulya, Simon de Givry, and George Katsirelos. "Improved Acyclicity Reasoning for Bayesian Network Structure Learning with Constraint Programming." In Thirtieth International Joint Conference on Artificial Intelligence {IJCAI-21}. California: International Joint Conferences on Artificial Intelligence Organization, 2021. http://dx.doi.org/10.24963/ijcai.2021/584.

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Bayesian networks are probabilistic graphical models with a wide range of application areas including gene regulatory networks inference, risk analysis and image processing. Learning the structure of a Bayesian network (BNSL) from discrete data is known to be an NP-hard task with a superexponential search space of directed acyclic graphs. In this work, we propose a new polynomial time algorithm for discovering a subset of all possible cluster cuts, a greedy algorithm for approximately solving the resulting linear program, and a generalized arc consistency algorithm for the acyclicity constraint. We embed these in the constraint programming-based branch-and-bound solver CPBayes and show that, despite being suboptimal, they improve performance by orders of magnitude. The resulting solver also compares favorably with GOBNILP, a state-of-the-art solver for the BNSL problem which solves an NP-hard problem to discover each cut and solves the linear program exactly.
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Brewer, Bryson M., Yandong Gao, Rebecca M. Sappington, and Deyu Li. "Microfluidic Molecular Trap: Probing Extracellular Signaling by Selectively Blocking Exchange of Specific Molecules in Cell-Cell Interactions." In ASME 2013 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/imece2013-64489.

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Communication among cell populations is achieved via a wide variety of soluble, extracellular signaling molecules [1]. In order to investigate the role of specific molecules in a cellular process, researchers often utilize in vitro cell culture techniques in which the molecule under question has been removed from the signaling pathway. Traditionally, this has been accomplished by eliminating the gene in the cell that is responsible for coding the targeted ligand/receptor by using modern DNA technology such as gene knockout; however, this process is expensive, time-consuming, and labor intensive. Previously, we have demonstrated a microfluidic platform that uses a semi-permeable barrier with embedded receptor-coated nanoparticles to selectively remove a specific molecule or ligand from the extracellular signaling pathway in a cell co-culture environment [2]. This initial proof-of-principle was conducted using biotinylated nanoparticles and fluorescently tagged avidin molecules, as the avidin/biotin complex is the strongest known non-covalent interaction between a protein and a ligand (Dissociation constant kd = 10−15 M). Also, the trap was only effective for short time periods (<15 min) because the high concentration of fluorescently tagged avidin molecules required for visualization quickly saturated the barrier. However, nearly all biologically relevant ligand-receptor interactions have lower binding affinities than the avidin-biotin complex, with dissociation constants that are larger by several orders of magnitude. In addition, many in vitro cell culture experiments are conducted over multiple hours or days. Thus, a practically useful molecular trap device must be able to operate in a lower binding affinity regime while also lasting for extended time periods. Here we present results in which a biotinylated-particle barrier was used to successfully block lower concentrations of fluorescently tagged avidin for multiple days, showcasing the applicability of the device for long term experiments. In addition, we introduce a modified molecular trap in which the protein A/goat IgG complex was used to demonstrate the effectiveness of the platform for lower binding affinity protein-ligand interactions. These results indicate the potential usefulness of the microfluidic molecular trap platform for probing extracellular signaling pathways.
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Rezaei, S., and J. Bai. "Multiple Gene Order Alignment." In 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference. IEEE, 2005. http://dx.doi.org/10.1109/iembs.2005.1615536.

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Guan, Yingxue, Aili Zhang, and Lisa X. Xu. "Study of Interaction Energy Between Nanoparticles and Cell Membrane." In 2010 14th International Heat Transfer Conference. ASMEDC, 2010. http://dx.doi.org/10.1115/ihtc14-23187.

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Applications of nanoparticles in the bio-medical field like nano-medicine, molecular imaging probes, fluorescence marker, gene carriers, are developing quickly owing to the unique characteristics of nanoparticles. Among these applications, the interaction of nano-particles with the living cells is of critical importance. The complex chemical properties and biological activities of the particles bring about undesirable cytotoxic potentials and special cell internalization. According to previous studies, the cell uptake kinetics of nanoparticles mainly depend on the concentration difference between extracellular and intracellular nanoparticles, the surface electric charge of the nanoparticle, and the active transport of the cell. For example, Ginzburg’s thermodynamic simulation and Park’s three-dimensional phase-field model quantitatively explain the transitions in membrane morphology after exposure to nanoparticles with different surface charge, respectively. However, recent studies have shown that the gold nanoparticles coated with hydrophilic and hydrophobic functional groups with the same concentration but in different orders, completely exhibit quite different intrusion ability at 4°C when the active transport of the cell is greatly inhibited. The results suggest that the interaction energy of nanoparticles and cell membranes may be another driving force for the nanopartcles’ mass transfer across the cell membrane. Thus, in this paper, the interaction energy of the differently coated nanoparticles (P) with cell membrane (M) in water (W) is studied theoretically and results are used to explain the former experimental findings.
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Pannekok, H., A. J. Van Zonneveid, C. J. M. de vries, M. E. MacDonald, H. Veerman, and F. Blasi. "FUNCTIONAL PROPERTIES OF DELETION-MUTANTS OF TISSUE-TYPE PLASMINOGEN ACTIVATOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643724.

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Over the past twenty-five years, genetic methods have generated a wealth of information on the regulation and the structure-function relationship of bacterial genes.These methods are based on the introduction of random mutations in a gene to alter its function. Subsequently, genetic techniques cure applied to localize the mutation, while the nature of the impairedfunction could be determined using biochemical methods. Classic examples of this approach is now considered to be the elucidation of the structure and function of genes, constituting the Escherichia coli lactose (lac) and tryptophan (trp) operons,and the detailed establishment of the structure and function of the repressor (lacl) of the lac operon. Recombinant DNA techniques and the development of appropriate expression systems have provided the means both to study structure and functionof eukaryotic (glyco-) proteins and to create defined mutations with a predestinedposition. The rationale for the construction of mutant genes should preferentiallyrely on detailed knowledge of the three-dimensional structure of the gene product.Elegant examples are the application of in vitro mutagenesis techniques to substitute amino-acid residues near the catalytic centre of subtilisin, a serine proteasefrom Bacillus species and to substituteanamino acid in the reactive site (i.e. Pi residue; methionine) of α-antitrypsin, a serine protease inhibitor. Such substitutions have resulted into mutant proteins which are less susceptible to oxidation and, in some cases, into mutant proteins with a higher specific activity than the wild-type protein.If no data are available on the ternary structure of a protein, other strategies have to be developed to construct intelligent mutants to study the relation between the structure and the function of a eukaryotic protein. At least for a number of gene families, the gene structure is thought to be created by "exon shuffling", an evolutionary recombinational process to insert an exon or a set of exons which specify an additional structural and/or functional domain into a pre-existing gene. Both the structure of the tissue-type plasminogen activator protein(t-PA) and the t-PA gene suggest that this gene has evolved as a result of exon shuffling. As put forward by Gilbert (Science 228 (1985) 823), the "acid test"to prove the validity of the exon shuffling theory is either to delete, insert or to substitute exon(s) (i.e. in the corresponding cDNA) and toassay the properties of the mutant proteins to demonstrate that an exon or a set of adjacent exons encode (s) an autonomousfunction. Indeed, by the construction of specific deletions in full-length t-PA cDNA and expression of mutant proteins intissue-culture cells, we have shown by this approach that exon 2 of thet-PA gene encodes the function required forsecretion, exon 4 encodes the "finger" domain involved in fibrin binding(presumably on undegraded fibrin) and the set of exons 8 and 9 specifies kringle 2, containing a lysine-binding sit(LBS) which interacts with carboxy-terminal lysines, generated in fibrin after plasmic digestion. Exons 10 through 14 encode the carboxy-ter-minal light chain of t-PA and harbor the catalytic centre of the molecule and represents the predominant "target site" for the fast-acting endothelial plasminogen activator inhibitor (PAI-1).As a follow-up of this genetic approach to construct deletion mutants of t-PA, we also created substitution mutants of t-PA. Different mutants were constructed to substitute cDNA encoding thelight chain of t-PA by cDNA encoding the B-chain of urokinase (u-PA), in order to demonstrate that autonomous structural and functional domains of eitherone of the separate molecules are able toexert their intrinsic properties in a different context (C.J.M. de Vries et al., this volume). The possibilities and the limitations of this approach to study the structure and the function of t-PA and of other components of the fibrinolytic process will be outlined.
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Sirotinina, E. A., E. V. Romanova, and D. Yu Sherbakov. "GENE ORDER VARIABILITY IN BAIKALIAN AMPHIPODS." In The Second All-Russian Scientific Conference with international participation "Regulation Mechanisms of Eukariotic Cell Organelle Functions". SIPPB SB RAS, 2018. http://dx.doi.org/10.31255/978-5-94797-318-1-117-119.

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Haiyan Hu and Xiaoman Li. "Hierarchical order of gene expression levels." In 2010 International Conference on Bioinformatics and Biomedical Technology. IEEE, 2010. http://dx.doi.org/10.1109/icbbt.2010.5479017.

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Lai, Yinglei. "The analysis of ordered changes of gene expression and gene-gene co-expression patterns." In 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2011. http://dx.doi.org/10.1109/iccabs.2011.5729863.

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Fei Hu, Nan Gao, Meng Zhang, and Jijun Tang. "Maximum likelihood phylogenetic reconstruction using gene order encodings." In 2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology - Part of 17273 - 2011 Ssci. IEEE, 2011. http://dx.doi.org/10.1109/cibcb.2011.5948459.

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Reports on the topic "Gene orders"

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Moret, Bernard M., and Tandy Warnow. Advances in Phylogeny Reconstruction from Gene Order and Content Data. Fort Belvoir, VA: Defense Technical Information Center, October 2004. http://dx.doi.org/10.21236/ada482523.

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