NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control

The three-dimensional structures of two DNA duplexes d(CATGAGTAC). d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high resolution nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Good convergence was observed between final structures derived from A- and B-form starting geometries for both 1 and 2. Structures of 1 and 2 are right-handed duplexes within the B-form conformational regime. Furthermore, the structures of 1 and 2 are highly similar, with differences in the structures localized to the vicinity of residue 14 (X versus T). The pyrrole group of 1 is in the syn conformation and it is displaced towards the major groove. Furthermore, unlike T14 in 2, the base of X14 has reduced pi-pi stacking interactions with C13 and C15 and the nitro group of X14 is pointing out of the major groove. The structures presented here establish the basis of the thermal data of DNA duplexes containing X and should be informative during the design of improved wild card nucleobase analogs.     

The mouse genome database: a resource for today and tomorrow

The Mouse Genome Database supports the use of mice in genome research, offering researchers information on gene characterization, genetic maps, comparative genomic data, and phenotypes.     

Neuromuscular ataxia: a new spontaneous mutation in the mouse

Neuromuscular ataxia, nma, is a new autosomal recessive mutation that arose spontaneously in CBA/J inbred mice at The Jackson Laboratory. The mutation, now maintained on the B6C3FeF₁ hybrid background, when homozygous, causes small size, uncoordinated gait, dysmetria, dystonia, general weakness, and death shortly after weaning. No biochemical or morphological abnormalities have been detected. We used an intercross between the B6C3FeF₁ mutant and CAST/Ei to map the nma mutation to the proximal end of Chr 12. The most likely gene order places the mutation between D12Mit270 and D12Mit54, non-recombinant with D12Mit2 in 96 tested meioses. Received: 27 March 2000 / Accepted: 17 May 2000     

Identifying sources of dissolved organic carbon in agriculturally dominated rivers using radiocarbon age dating: Sacramento–San Joaquin River Basin, California

We used radiocarbon measurements of dissolved organic carbon (DOC) to resolve sources of riverine carbon within agriculturally dominated landscapes in California. During 2003 and 2004, average Δ¹⁴C for DOC was ?254‰ in agricultural drains in the Sacramento–San Joaquin Delta, ?218‰ in the San Joaquin River, ?175‰ in the California State Water Project and ?152‰ in the Sacramento River. The age of bulk DOC transiting the rivers of California’s Central Valley is the oldest reported for large rivers and suggests wide-spread loss of soil organic matter caused by agriculture and urbanization. Using DAX 8 adsorbent, we isolated and measured ¹⁴C concentrations in hydrophobic acid fractions (HPOA); river samples showed evidence of bomb-pulse carbon with average Δ¹⁴C of 91 and 76‰ for the San Joaquin and Sacramento Rivers, respectively, with older HPOA, ?204‰, observed in agricultural drains. An operationally defined non-HPOA fraction of DOC was observed in the San Joaquin River with seasonally computed Δ¹⁴C values of between ?275 and ?687‰; the source of this aged material was hypothesized to be physically protected organic-matter in high clay-content soils and agrochemicals (i.e., radiocarbon-dead material) applied to farmlands. Mixing models suggest that the Sacramento River contributes about 50% of the DOC load in the California State Water Project, and agricultural drains contribute approximately one-third of the load. In contrast to studies showing stabilization of soil carbon pools within one or two decades following land conversion, sustained loss of soil organic matter, occurring many decades after the initial agricultural-land conversion, was observed in California’s Central Valley.     

Prp (proline-rich protein) genes linked to markers Es-12 (esterase-12), Ea-10 (erythrocyte alloantigen), and loci on distal mouse chromosome 6

The closely linked proline-rich protein (Prp) genes, coding for abundant salivary proteins, are located on distal mouse chromosome 6. They are part of a conserved linkage group that is represented on human chromosome 12p. Two other markers, Ea-10 and Es-12, that were previously unassigned to a chromosome are closely linked to Prp genes in the mouse.     

A spontaneous mutation in contactin 1 in the mouse

Mutations in the gene encoding the immunoglobulin-superfamily member cell adhesion molecule contactin1 (CNTN1) cause lethal congenital myopathy in human patients and neurodevelopmental phenotypes in knockout mice. Whether the mutant mice provide an accurate model of the human disease is unclear; resolving this will require additional functional tests of the neuromuscular system and examination of Cntn1 mutations on different genetic backgrounds that may influence the phenotype. Toward these ends, we have analyzed a new, spontaneous mutation in the mouse Cntn1 gene that arose in a BALB/c genetic background. The overt phenotype is very similar to the knockout of Cntn1, with affected animals having reduced body weight, a failure to thrive, locomotor abnormalities, and a lifespan of 2-3 weeks. Mice homozygous for the new allele have CNTN1 protein undetectable by western blotting, suggesting that it is a null or very severe hypomorph. In an analysis of neuromuscular function, neuromuscular junctions had normal morphology, consistent with previous studies in knockout mice, and the muscles were able to generate appropriate force when normalized for their reduced size in late stage animals. Therefore, the Cntn1 mutant mice do not show evidence for a myopathy, but instead the phenotype is likely to be caused by dysfunction in the nervous system. Given the similarity of CNTN1 to other Ig-superfamily proteins such as DSCAMs, we also characterized the expression and localization of Cntn1 in the retinas of mutant mice for developmental defects. Despite widespread expression, no anomalies in retinal anatomy were detected histologically or using a battery of cell-type specific antibodies. We therefore conclude that the phenotype of the Cntn1 mice arises from dysfunction in the brain, spinal cord or peripheral nervous system, and is similar in either a BALB/c or B6;129;Black Swiss background, raising a possible discordance between the mouse and human phenotypes resulting from Cntn1 mutations.     

Molecular characterization of the translocation breakpoints in the Down syndrome mouse model Ts65Dn

Ts65Dn is a mouse model of Down syndrome: a syndrome that results from chromosome (Chr) 21 trisomy and is associated with congenital defects, cognitive impairment, and ultimately Alzheimer's disease. Ts65Dn mice have segmental trisomy for distal mouse Chr 16, a region sharing conserved synteny with human Chr 21. As a result, this strain harbors three copies of over half of the human Chr 21 orthologs. The trisomic segment of Chr 16 is present as a translocation chromosome (Mmu17(16)), with breakpoints that have not been defined previously. To molecularly characterize the Chrs 16 and 17 breakpoints on the translocation chromosome in Ts65Dn mice, we used a selective enrichment and high-throughput paired-end sequencing approach. Analysis of paired-end reads flanking the Chr 16, Chr 17 junction on Mmu17(16) and de novo assembly of the reads directly spanning the junction provided the precise locations of the Chrs 16 and 17 breakpoints at 84,351,351 and 9,426,822?bp, respectively. These data provide the basis for low-cost, highly efficient genotyping of Ts65Dn mice. More importantly, these data provide, for the first time, complete characterization of gene dosage in Ts65Dn mice.