A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome

Mural, Richard J.; Adams, Mark D.; Myers, Eugene W.; Smith, Hamilton O.; Miklos, George L. Gabor; Wides, Ron; Halpern, Aaron L.; Li, Peter W.; Sutton, Granger; Nadeau, Joe; Salzberg, Steven L.; Holt, Robert A.; Kodira, Chinnappa D.; Lu, Fu; Chen, Lin; Deng, Zuoming; Evangelista, Carlos; Gan, Weiniu; Heiman, Thomas J.; Li, Jiayin; Li, Zhen‐Ya; Merkulov, Gennady V.; Milshina, Natalia V.; Naik, Ashwinikumar K; Qi, Rong; Shue, Bixiong Chris; Wang, Aihui; Wang, Jian; Wang, Xin; Yan, Xianghe; Ye, Jane J.; Yooseph, Shibu; Zhao, Qi; Zheng, Liansheng; Zhu, Shiaoping C.; Biddick, Kendra; Bolanos, Randall; Delcher, Arthur L.; Dew, Ian; Fasulo, Daniel; Flanigan, Michael J.; Huson, Daniel H.; Kravitz, Saul; Miller, Jason R.; Mobarry, Clark; Reinert, Knut; Remington, Karin; Zhang, Qing; Zheng, Xiangqun H.; Nusskern, Deborah; Lai, Zhongwu; Lei, Yiding; Zhong, Wenyan; Yao, Alison; Guan, Peng; Ji, Rui-Ru; Gu, Zhiping; Wang, Zhenyuan; Zhong, Fei; Xiao, Chunlin; Chiang, Chia-Chien; Yandell, Mark; Wortman, Jennifer; Amanatides, P. G.; Hladun, Suzanne L; Pratts, Eric C; Johnson, Jeffery E; Dodson, Kristina L; Woodford, Kerry J.; Evans, Cheryl; Gropman, Barry; Rusch, Douglas B.; Venter, Eli; Wang, Mei; Smith, Thomas J.; Houck, Jarrett T; Tompkins, Donald E; Haynes, Charles A.; Jacob, Debbie; Chin, Soo H; Allen, David R.; Dahlke, Carl; Sanders, Robert D.; Li, Kelvin; Liu, Xiangjun; Levitsky, Alexander; Majoros, William H.; Chen, Quan; Xia, Ashley C; Lopez, John; Donnelly, Michael; Newman, Matthew; Glodek, Anna; Kraft, Cheryl; Nodell, Marc; Ali, Feroze; An, Hui-Jin; Baldwin-Pitts, Danita; Beeson, Karen; Cai, Shuang; Carnes, Mark; Carver, Amy; Caulk, Parris M; Center, Angela; Chen, Yen‐Hui; Cheng, Ming-Lai; Coyne, My D; Crowder, Michelle; Danaher, Steven; Davenport, Lionel B; Desilets, Raymond; Dietz, Susanne; Doup, Lisa; Dullaghan, Patrick; Ferriera, Steven; Fosler, Carl; Gire, Harold C; Gluecksmann, Andres; Gocayne, Jeannine D.; Gray, Jonathan; Hart, Brit J.; Haynes, Jason; Hoover, Jeffery; Howland, T. J.; Ibegwam, Chinyere; Jalali, Mena; Johns, David G.; Kline, Leslie; Daniel, Sandro Natal; MacCawley, Steven; Magoon, Anand; Mann, Felecia; May, David; McIntosh, Tina C; Mehta, Somil C.; Moy, Linda; Moy, Mee C; Murphy, Brian J.; Murphy, Sean D.; Nelson, Keith A; Nuri, Zubeda; Parker, Kimberly A.; Prudhomme, Alexandre C; Puri, Vinita; Qureshi, Hina; Raley, John C; Reardon, Matthew; Regier, Megan A.; Rogers, Yu-Hui C; Romblad, Deanna L; Schutz, Jakob; Scott, John L; Scott, Rodney J.; Sitter, Cynthia; Smallwood, Michella; Sprague, Arlan C; Stewart, Erin; Strong, Renee; Suh, Ellen; Sylvester, Karena; Thomas, Reginald; Tint, Ni Ni; Tsonis, Christopher; Wang, Gary; Wang, George; Williams, Monica S; Williams, S. M.; Windsor, Sandra M; Wolfe, Keriellen; Wu, Mitchell M; Zaveri, Jayshree; Chaturvedi, Kabir; Gabrielian, Andrei; Ke, Zhaoxi; Sun, Jing‐Tao; Subramanian, G.; Venter, J. Craig; Pfannkoch, Cynthia; Barnstead, Mary; Stephenson, Lisa D

doi:10.1126/science.1069193

Cited by 339 publications

(216 citation statements)

References 52 publications

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“…Figure 2c depicts the zoomed quantitative perfusion map calculated by use of Eq. [1]. Figure 2d shows a representative perfusion map of a mouse with myocardial infarction that was anesthetized by isoflurane as well.…”

Section: Resultsmentioning

confidence: 99%

“…In addition, a local validation of the same technique against measurements with first pass perfusion imaging was performed for the isolated rat heart (15). Equation [1] provides information about the needed accuracy of the T 1 quantification for the assessment of myocardial perfusion with this technique. Assuming a T 1,glob of 1600 ms for murine myocardium, a T 1,blood of 1650 ms and a blood-tissue partition coefficient of 0.95 mL g Ϫ1 results in a T 1,sel of 1350 ms for a myocardial perfusion of 640 mL (100 g ⅐ min) Ϫ1 , a value that was determined in a microspheres study (5).…”

Section: Quantification Of Perfusionmentioning

confidence: 99%

“…[1] and [3] under the assumption of a blood-tissue partition coefficient of 0.95 mL/g in the myocardium (28).…”

Section: Postprocessingmentioning

confidence: 99%

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In vivo assessment of absolute perfusion and intracapillary blood volume in the murine myocardium by spin labeling magnetic resonance imaging

Streif¹,

Nahrendorf²,

Hiller³

et al. 2005

Magnetic Resonance in Med

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The absolute perfusion and the intracapillary or regional blood volume (RBV) in murine myocardium were assessed in vivo by spin labeling magnetic resonance imaging. Pixel-based perfusion and RBV maps were calculated at a pixel resolution of 469 ؋ 469 m and a slice thickness of 2 mm. The T 1 imaging module was a segmented inversion recovery snapshot fast low angle shot sequence with velocity compensation in all three gradient directions. The group average myocardial perfusion at baseline was determined to be 701 ؎ 53 mL (100 g ⅐ min) ؊1 for anesthesia with isoflurane (N ‫؍‬ 11) at a mean heart rate (HR) of 455 ؎ 10 beats per minute (bpm). This value is in good agreement with perfusion values determined by invasive microspheres examinations. For i.v. administration of the anesthetic Propofol, the baseline perfusion decreased to 383 ؎ 40 mL (100 g ⅐ min) ؊1 (N ‫؍‬ 17, P < 0.05 versus. isoflurane) at a mean heart rate of 261 ؎ 13 bpm (P < 0.05 versus isoflurane). In addition, six mice with myocardial infarction were studied under isoflurane anesthesia (HR 397 ؎ 7 bpm). The perfusion maps showed a clear decrease of the perfusion in the infarcted area. The perfusion in the remote myocardium decreased significantly to 476 ؎ 81 mL (100 g ⅐ min) ؊1 (P < 0.05 versus sham). Regarding the regional blood volume, a mean value of 11.8 ؎ 0.8 vol % was determined for healthy murine myocardium under anesthesia with Propofol (N ‫؍‬ 4, HR 233 ؎ 17 bpm). In total, the presented techniques provide noninvasive in vivo assessment of the perfusion and the regional blood volume in the murine myocardium for the first time and seem to be promising tools for the characterization of mouse models in cardiovascular research. Over the past decade, the mouse animal model has become an essential part of medical basic research. This is due to the high degree of similarity between the mouse and the human genomes of about 97% (1) and the resulting high relevance of mouse animal studies for human basic research. Regarding cardiovascular research, magnetic resonance imaging (MRI) provides noninvasive and accurate assessment of cardiac structure and function (2). Since the viability and the capability of the myocardium are strongly influenced by its microcirculation, a full characterization of the myocardium requires a quantification of parameters such as the perfusion and the intracapillary or regional blood volume (RBV). In particular, perfusion is of paramount importance as a physiologic parameter, since it strongly determines the function of organs and the severity of many diseases.Heart diseases involving ventricular dysfunction and hypertrophy show significant alterations of the myocardial perfusion and transgenic mouse models may be well suited to elucidate the underlying fundamental mechanisms.For the assessment of cardiac perfusion in mice, only a few methods have been presented to date. One possible approach is the quantification of the coronary flow in the isolated mouse heart by ultrasonic flow probes (3). The injection of labeled microsphe...

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Section: Resultsmentioning

confidence: 99%

Section: Quantification Of Perfusionmentioning

confidence: 99%

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In vivo assessment of absolute perfusion and intracapillary blood volume in the murine myocardium by spin labeling magnetic resonance imaging

Streif¹,

Nahrendorf²,

Hiller³

et al. 2005

Magnetic Resonance in Med

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“…However, the recent availability of public and private sequence assemblies (Marshall 2001;Mural et al 2002;Waterston et al 2002) has simplified the development of additional polymorphic markers that afford higher resolution break-point mapping and often circumvent the need for outcrossing to wild-derived strains. These new markers have been used to characterize both previously described deletions and the new ones reported here.…”

Section: Overviewmentioning

confidence: 99%

“…In total, the five deletion complexes span 25 Mbp on the proximal end of Chr 17 and provide a valuable resource for the functional annotation of a region whose analysis has heretofore been refractory to traditional genetic analysis. With the recent construction of highly detailed public and private sequence assemblies (Mural et al 2002;Waterston et al 2002), functional maps now can be correlated with detailed physical maps and sequence annotation. …”

mentioning

confidence: 99%

Overlapping deletions spanning the proximal two-thirds of the mouse t complex

Bergstrom¹,

Bergstrom²,

Munroe³

et al. 2003

Mammalian Genome

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Chromosome deletion complexes in model organisms serve as valuable genetic tools for the functional and physical annotation of complex genomes. Among their many roles, deletions can serve as mapping tools for simple or quantitative trait loci (QTLs), genetic reagents for regional mutagenesis experiments, and, in the case of mice, models of human contiguous gene deletion syndromes. Deletions also are uniquely suited for identifying regions of the genome containing haploinsufficient or imprinted loci. Here we describe the creation of new deletions at the proximal end of mouse Chromosome (Chr) 17 by using the technique of ES cell irradiation and the extensive molecular characterization of these and previously isolated deletions that, in total, cover much of the mouse t complex. The deletions are arranged in five overlapping complexes that collectively span about 25 Mbp. Furthermore, we have integrated each of the deletion complexes with physical data from public and private mouse genome sequences, and our own genetic data, to resolve some discrepancies. These deletions will be useful for characterizing several phenomena related to the t complex and t haplotypes, including transmission ratio distortion, male infertility, and the collection of t haplotype embryonic lethal mutations. The deletions will also be useful for mapping other loci of interest on proximal Chr 17, including T-associated sex reversal (Tas) and head-tilt (het). The new deletions have thus far been used to localize the recently identified t haplolethal (Thl1) locus to an approximately 1.3-Mbp interval.Chromosomal deletions have long served as valuable genetic tools for geneticists. For Drosophila melanogaster, collections of deletion (deficiency) strains are available that collectively encompass virtually the entire genome (http://flybase.bio.indiana.edu/aberrations) and allow loss-of-function alleles to be mapped to specific subchromosomal intervals by crossing flies carrying such alleles to lines of flies bearing overlapping deficiencies. Likewise, in a classic set of experiments known as the "specific locus test," mouse geneticists used large-scale, whole-body irradiation to create sets of overlapping deletions centered around several "visible" loci (Davis and Justice 1998). These experiments allowed molecular genetic analyses of phenotypes arising from the combinatorial mating of mice carrying deletions within each complex (Dhar and Johnson 1997;Rikke et al. 1997;Roix et al. 2001;Simpson et al. 2000), and from region-specific mutagenesis with the point mutagen ENU (Justice et al. 1997; Carpenter 1993, 1999;Rinchik et al. 1990Rinchik et al. , 2002 NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript now possible to develop deletion complexes throughout the genome and without the logistical complexities of whole-body radiation (Ramirez-Solis et al. 1995;You et al. 1997b).We previously described a chromosomal deletion complex at the proximal end of mouse Chr 17 centered at the D17Aus9 locus (You et al. 1997a;1997b). ...

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The mouse genome sequence

Jackson

2005

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

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The mouse is the leading mammalian model organism for the study of genetics. Its genome consists of about 2500 Mb of DNA and contains about 30 000 genes, virtually all of which have close homologs in the human genome. Comparison of the mouse with other mammalian genomes indicates that it is not only the coding sequences of genes that have been maintained in evolution; putative conserved control elements can be identified by aligning multiple genomes. The DNA of the mouse (and rat) is accumulating changes at a much more rapid rate than the human genome. Base substitutions in neutral sequences have accumulated about twice as fast in the mouse when compared to humans, since their last common ancestor 75 million years ago. Furthermore, transposable elements have been more active in the rodent lineage, and there have been more chromosomal rearrangements that alter long‐range relationships between genes.

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A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome

Cited by 339 publications

References 52 publications

In vivo assessment of absolute perfusion and intracapillary blood volume in the murine myocardium by spin labeling magnetic resonance imaging

In vivo assessment of absolute perfusion and intracapillary blood volume in the murine myocardium by spin labeling magnetic resonance imaging

Overlapping deletions spanning the proximal two-thirds of the mouse t complex

The mouse genome sequence

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