@article {2374,
	title = {Orientation of DNA Minicircles Balances Density and Topological Complexity in Kinetoplast DNA.},
	journal = {PLoS One},
	volume = {10},
	year = {2015},
	month = {2015},
	pages = {e0130998},
	abstract = {<p>Kinetoplast DNA (kDNA), a unique mitochondrial structure common to trypanosomatid parasites, contains thousands of DNA minicircles that are densely packed and can be topologically linked into a chain mail-like network. Experimental data indicate that every minicircle in the network is, on average, singly linked to three other minicircles (i.e., has mean valence 3) before replication and to six minicircles in the late stages of replication. The biophysical factors that determine the topology of the network and its changes during the cell cycle remain unknown. Using a mathematical modeling approach, we previously showed that volume confinement alone can drive the formation of the network and that it induces a linear relationship between mean valence and minicircle density. Our modeling also predicted a minicircle valence two orders of magnitude greater than that observed in kDNA. To determine the factors that contribute to this discrepancy we systematically analyzed the relationship between the topological properties of the network (i.e., minicircle density and mean valence) and its biophysical properties such as DNA bending, electrostatic repulsion, and minicircle relative position and orientation. Significantly, our results showed that most of the discrepancy between the theoretical and experimental observations can be accounted for by the orientation of the minicircles with volume exclusion due to electrostatic interactions and DNA bending playing smaller roles. Our results are in agreement with the three dimensional kDNA organization model, initially proposed by Delain and Riou, in which minicircles are oriented almost perpendicular to the horizontal plane of the kDNA disk. We suggest that while minicircle confinement drives the formation of kDNA networks, it is minicircle orientation that regulates the topological complexity of the network.</p>
},
	keywords = {Cell Cycle, Crithidia fasciculata, DNA Replication, DNA, Kinetoplast, DNA, Mitochondrial},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0130998},
	author = {Diao, Yuanan and Rodriguez, Victor and Klingbeil, Michele and Arsuaga, Javier}
}
@article {383,
	title = {Unraveling the secrets of regulating mitochondrial DNA replication.},
	journal = {Mol Cell},
	volume = {35},
	year = {2009},
	month = {2009 Aug 28},
	pages = {398-400},
	abstract = {In this issue, Liu et al. (2009) report that maxicircle DNA copy number in trypanosomes is regulated by proteolysis of a helicase; the complex kinetoplast DNA system yields a clear view of how mitochondrial DNA replication can be regulated.},
	keywords = {Animals, DNA Helicases, DNA Replication, DNA, Kinetoplast, DNA, Mitochondrial, DNA, Protozoan, Gene Expression Regulation, Mutation, Peptide Hydrolases, Protozoan Proteins, Time Factors, Trypanosoma brucei brucei},
	issn = {1097-4164},
	doi = {10.1016/j.molcel.2009.08.007},
	author = {Klingbeil, Michele M and Shapiro, Theresa A}
}
@article {385,
	title = {Closing the gaps in kinetoplast DNA network replication.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {101},
	year = {2004},
	month = {2004 Mar 30},
	pages = {4333-4},
	keywords = {Animals, Crithidia fasciculata, DNA Ligases, DNA Replication, DNA, Kinetoplast, DNA, Mitochondrial, Microscopy, Electron, Trypanosoma brucei brucei},
	issn = {0027-8424},
	doi = {10.1073/pnas.0401400101},
	author = {Klingbeil, Michele M and Englund, Paul T}
}
@article {798,
	title = {Discriminating between Ixodes ticks by means of mitochondrial DNA sequences.},
	journal = {Mol Phylogenet Evol},
	volume = {4},
	year = {1995},
	month = {1995 Dec},
	pages = {361-5},
	abstract = {Ticks of the genus Ixodes have recently assumed prominence because they frequently serve as vectors of important zoonoses, including Lyme disease and babesiosis. The morphological characteristics that have been used in their identification often are ambiguous and are useful solely at a particular stage of development. Here we report the DNA sequence of the mitochondrially encoded 16S rRNA gene of nine different Ixodes ticks and an outgroup from another genus, Dermacentor. The sequences readily discriminate between these ticks. Samples of I. dammini from the northeastern and upper midwestern United States differ from southeastern I. scapularis at about 2\% of the nucleotides. This difference is about half that separating other members of the I. ricinus group of species, but exceeds typical levels of intraspecific variation. Two major clades exist within the I. ricinus complex. One includes I. cookei, I. hexagonus, and I. angustus. The other includes I. persulcatus, I. pacificus, I. muris, I. ricinus, I. scapularis, and I. dammini. We conclude that mtDNA sequences are useful for unravelling the systematics of these important vectors of human disease.},
	keywords = {Animals, Arachnid Vectors, Base Sequence, Dermacentor, DNA Primers, DNA, Mitochondrial, Genes, Humans, Ixodes, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Species Specificity},
	issn = {1055-7903},
	doi = {10.1006/mpev.1995.1033},
	author = {Caporale, D A and Rich, S M and Spielman, A and Telford, S R and Kocher, T D}
}
@article {799,
	title = {Distribution of the Ixodes ricinus-like ticks of eastern North America.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {92},
	year = {1995},
	month = {1995 Jul 3},
	pages = {6284-8},
	abstract = {We analyzed the geographic distribution of the Ixodes ricinus-like ticks in eastern North America by comparing the mitochondrial 16S rDNA sequences of specimens sampled directly from the field during the 1990s. Two distinct lineages are evident. The southern clade includes ticks from the southeastern and middle-eastern regions of the United States. The range of the northern clade, which appears to have been restricted to the northeastern region until the mid-1900s, now extends throughout the northeastern and middle-eastern regions. These phyletic units correspond to northern and southern taxa that have previously been assigned specific status as Ixodes dammini and Ixodes scapularis, respectively. The expanding range of I. dammini appears to drive the present outbreaks of zoonotic disease in eastern North America that include Lyme disease and human babesiosis.},
	keywords = {Animals, Base Sequence, Demography, DNA Primers, DNA, Mitochondrial, DNA, Ribosomal, Geography, Mitochondria, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Population, RNA, Ribosomal, 16S, Ticks, United States},
	issn = {0027-8424},
	author = {Rich, S M and Caporale, D A and Telford, S R and Kocher, T D and Hartl, D L and Spielman, A}
}
