New T-cell receptor gamma haplotypes in wild mice and evidence for limited Tcrg-V gene polymorphism

Tcrg gene polymorphism was investigated by Southern blot analysis on a panel of laboratory and wild mouse strains using a set of probes which identify all known Tcrg-V and -C genes. Only three haplotypes are found in laboratory mice: gA, gB, and gC which are represented by BALB/c, AKR, and DBA/2 prototypes respectively. gA and gC haplotypes are the most frequent among laboratory mice whereas gB is poorly represented. Seven new haplotypes are described among 23 wild mice corresponding to four Mus musculus subspecies (Mus mus domesticus, castaneus, musculus, and molossinus). However, only a few new alleles of individual genes are observed. Tcrg-V genes located at the 5 end of the Tcrg locus (V7 and V4) appear to be nonpolymorphic whereas two Tcrg-V3,-V5,-V6,-C4 and three Tcr-V1,-V2,-C1,-C2, and -C3 specific restriction fragment length polymorphisms are detected. These results indicate a relatively high degree of conservation of Tcrg genes as compared to other members of the immunoglobulin (Ig) gene family and might be related to the specificity and function of T cells. Several of the new haplotypes described here result from point mutations in noncoding Tcrg-V or -C gene-flanking regions. Recombinations may have also participated in the evolution of the Tcrg locus. Finally, these new Tcrg haplotypes are unequally distributed among the four M. m. subspecies and support the idea that the gA and gC haplotypes found in laboratory mice are inherited from M. m. domesticus whereas gB might originated from asian subspecies (castaneus, musculus or molossinus).     

Natural killer cell enhancement factor-like gene in rainbow trout (Oncorhynchus mykiss)

The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence databse and have been assigned to the accession number U27125     

Natural killer (NK) cells are present in mice with severe combined immunodeficiency (scid)

Spleen cells from C.B- 17 scid mice with severe combined immunodeficiency disease exhibit natural killer cell (NK) activity against YAC lymphoma targets in a standard 4-hr 51Cr release assay. The cytolytic activity is demonstrable only at high effector to target ratios but can be augmented at least sevenfold by the interferon inducer poly I:C. The pattern of target lysis is specific, because splenocytes from poly I:C-primed C.B-17 scid mice lyse NK-sensitive YAC cells and not the insensitive P815 mastocytoma. The presence of several NK-associated antigens on C.B-17 scid splenocytes was tested by pretreating cells with the appropriate antiserum plus complement before testing for NK activity. The results indicate that a proportion of NK effectors in C.B-17 scid mice bear surface NK 2.1 and Asialo GM1 but are negative for Thy-1.     

TheD17Tu5 locus in thet complex: implications for the origin oft haplotypes and inbred strains

The mouse × Chinese hamster cell line R4 4-1 contains only one mouse chromosome, the bulk of which corresponds toMus musculus chromosomes 17 and 18 (MMU17 and MMU18, respectively). A genomic library was prepared from the R4 4-1 DNA, and a mouse clone was isolated from the library, which—with the help of somatic cell hybrids-could be mapped to the MMU17. A locus defined by a 2.7-kb longBam HI probe from this clone was designatedD17Tu5 (Tu for Tübingen). The locus proved to be polymorphic among inbred strains and wild mice. By testing of recombinant inbred strains and partialt haplotypes, theD17Tu5 locus could be mapped to a position between theD17Leh66E andD17Rp17 loci within thet complex. Two alleles were found at this locus,D17Tu5 ^a andD17Tu5 ^b , defined byTaq I restriction fragment length polymorphism. Both alleles are present among inbred strains and wild mice of the speciesM. domesticus. All completet haplotypes tested carry theD17Tu5 ^a allele and all tested wild mice of the speciesM. musculus, with the exception of those bearingt haplotypes, carry theD17Tu5 ^b allele. Additional alleles are found in some populations of wild mice and in other species of the genusMus. The distribution of the two alleles among the inbred strains correlates well with their known or postulated genealogy. Their distribution between the two species ofMus and among the mice withT haplotypes suggests a relatively recent origin of thet haplotypes.     

Characterization of allelic V kappa-1 region genes in inbred strains of mice

Germ line genes encoding mouse Ig kappa-chains belonging to the V kappa-1 group have been isolated from BALB/c, NZB, and CE, three inbred strains of differing kappa haplotype. The V kappa-1A and V kappa-1C germ line genes isolated from BALB/c (Ig kappa c) were identical to those previously described. These are the two major V kappa-1 germ line genes in BALB/c and together account for 40 of the 53 expressed V kappa-1 sequences that have been reported to date. Allelic differences in a single germ line variable region gene (V kappa-1A) in different strains of mice explain the differences in L chain IEF patterns previously associated with the Ig kappa-Ef2 locus. The rearranged kappa-gene expressed in the BALB/c myeloma MOPC-460 has been isolated and found to represent a V kappa-1A somatic variant differing by three nucleotides from the germ line V kappa-1A gene. Germ line genes isolated from NZB (Ig kappa b) and CE (Ig kappa f) show greater than 95% identity with the BALB/c genes over the 1700 nucleotides compared. Comparison by region indicated the greatest conservation of sequence occurs in and around the leader exon followed by the V-region exon. The NZB gene encodes the amino acid sequence found in the myeloma PC-2205, previously designated V kappa-1B. The V kappa-1 gene isolated from CE is likely an allele of the BALB/c V kappa-1C gene as the two share greater than 96% identity over 1700 nucleotides. The CE gene has been designated V kappa-1Cf. Ancient remnants of LINE-1 repetitive elements were detected approximately 400 bp downstream of all of the V kappa-1 genes. These possess greater homology with repetitive elements found near other kappa genes than they do with the native L1Md sequence.     

DNA sequence variation within the beta-glucuronidase gene complex among inbred strains of mice

Tightly linked to the gene that encodes murine beta-glucuronidase (GUS) are three GUS-specific regulatory elements. Together, these elements define the GUS gene complex. Specific alleles of each regulatory element are associated with a specific GUS structural allele. These associations define the three common forms (haplotypes) of the GUS gene complex, designated A, B, and H. As an initial step in defining the DNA determinants of each regulatory element and to develop DNA markers for the common haplotypes, we have identified several DNA variants by blot hybridization analysis of restricted genomic DNA using GUS-specific cDNA probes. Of 30 tested restriction endonucleases, 24 reveal DNA polymorphisms that distinguish B- and H-haplotype DNA from that of the A haplotype. Of these 24, 18 uncover a restriction fragment length polymorphism in which the polymorphic fragment of A-haplotype DNA is 200-300 bp larger than the corresponding fragment of B- or H-haplotype DNA. DNA sequence analysis of this polymorphic region reveals the presence of a short, interspersed repetitive element of the B2 family within A-haplotype DNA which is absent in DNAs of B- or H-haplotype mice. None of the DNA variations revealed by these analyses can be associated at this time with variation in the regulatory or structural properties of GUS among the common haplotypes. Nevertheless, they do provide useful haplotype-specific markers within the GUS gene complex which are of critical importance for DNA transfer experiments in transgenic mice and in cultured cells.     

Natural killer cell activity in reticulum cell sarcomas (RCS) of SJL/J mice.

Two transplantable reticulum cell sarcomas (RCS) of SJL mice expressed marked levels of natural killer (NK) activity when tested against susceptible ⁵¹Cr-labeled tumor targets. In contrast, normal SJL lymph node and spleen cells demonstrated low levels of NK activity. Neither depletion of macrophages nor pretreatment with anti-Thy-1.2 sera and complement reduced the capacity of RCS cells to express NK activity. Systemic injection of irradiated RCS cells into SJL mice induced a transient increase in NK activity at 3 and 7 days after injection. However, the NK activity observed in recipients of irradiated RCS cells never reached levels comparable to those of control mice injected with viable tumor cells. These data suggest that the transplantable reticulum cell sarcomas of SJL mice may represent a tumor of natural killer cells and thus provide an enriched source of these effectors that may be useful for further characterization of natural cytotoxicity.     

Genetic and morphological variability in South American rodent Oecomys (Sigmodontinae, Rodentia): evidence for a complex of species

The rodent genus Oecomys (Sigmodontinae) comprises ~16 species that inhabit tropical and subtropical forests in Central America and South America. In this study specimens of Oecomys paricola Thomas, 1904 from Belém and Marajó island, northern Brazil, were investigated using cytogenetic, molecular and morphological analyses. Three karyotypes were found, two from Belém (2n = 68, fundamental number (FN) = 72 and 2n = 70, FN = 76) and a third from Marajó island (2n = 70, FN = 72). No molecular or morphological differences were found between the individuals with differing cytotypes from Belém, but differences were evident between the individuals from Belém and Marajó island. Specimens from Belém city region may represent two cryptic species because two different karyotypes are present in the absence of significant differences in morphology and molecular characteristics. The Marajó island and Belém populations may represent distinct species that have been separated for some time, and are in the process of morphological and molecular differentiation as a consequence of reproductive isolation at the geographic and chromosomal levels. Thus, the results suggest that O. paricola may be a complex of species.     

Bulbourethral (Cowper's) gland abnormalities in inbred laboratory mice

Abnormalities of the bulbourethral (Cowper's) glands are rare in most strains of inbred laboratory mice. Since the glands are covered with striated muscle and because of their small size, the bulbourethral glands are often overlooked at necropsy. We review the gross and microscopic anatomy of the bulbourethral glands in laboratory mice and report in SJL/J and RBF/DnJ mice a series of anomalies of this gland that appear to be common in these strains and relatively strain specific. From 14 different inbred strains of mice that had been submitted for necropsy over a period of 4.5 years for various clinical complaints, including enlargement of the perianal region, 23.8% of SJL/J mice (27/113) and 51.2% of RBF/DnJ mice (21/41) had cystic hyperplasia of the bulbourethal glands. Furthermore 7.3% of BALB/cByJ mice (3/41) had cystic glands and 6.7% of DBA/2J mice (4/60) had enlarged bulbourethal glands, three of which (5.0%) were abscessed. All selected mice were active male breeders older than 6 months of age from production colonies at The Jackson Laboratory. Detailed examination of bulbourethral glands of retired SJL/J breeders revealed cystic glands in 83.8% (109/130) of mice. No abnormalities were found in the other inbred strains of mice investigated.     

Reduced nucleotide variability at an androgen-binding protein locus (Abpa) in house mice: evidence for positive natural selection.

Previous work has shown that the gene for the alpha subunit of androgen-binding protein, Abpa, may be involved in premating isolation between different subspecies of the house mouse, Mus musculus. We investigated patterns of DNA sequence variation at Abpa within and between species of mice to test several predictions of a model of neutral molecular evolution. Intraspecific variation among 10 Mus musculus domesticus alleles was compared with divergence between M. m. domesticus and M. caroli for Abpa and two X-linked genes, Glra2 and Amg. No variation was observed at Abpa within M. m. domesticus. The ratio of polymorphism to divergence was significantly lower at Abpa than at Glra2 and Amg, despite the fact that all three genes experience similar rates of recombination. Interspecific comparisons among M. m. domesticus, Mus musculus musculus, Mus musculus castaneus, Mus spretus, Mus spicilegus, and Mus caroli revealed that the ratio of nonsynonymous substitutions to synonymous substitutions on a per-site basis (Ka/Ks) was generally greater than one. The combined observations of no variation at Abpa within M. m: domesticus and uniformly high Ka/Ks values between species suggest that positive directional selection has acted recently at this locus.     

Natural killer cell activity in Naegleria fowleri infected mice]

The natural killer (NK) cell activity of splenocytes and recycling capacity of NK cells were observed by combining the 51Cr-release cytotoxicity assay and single cell cytotoxicity assay against YAC-1. The ICR mice were infected intranasally with Naegleria fowleri, that is a pathogenic free-living amoeba. The mice infected with 1 x 10(5) trophozoites showed mortality rate of 76.7% and mean survival time of 12.9 days. The cytotoxic activity of NK cells in infected mice was significantly higher than that of non-infected mice during the period between 12 hours and day 3 after infection, and highest on day 1. The target-binding capacity of NK cells in infected mice was not different from that of non-infected ones. Maximal killing potential and maximal recycling capacity were remarkably increased in infected mice as compared with the control. The results obtained in this observation indicated that elevated NK cell activity in mice infected with N. fowleri was not due to target-binding capacity of NK cells but due to the increased activity of NK cells and increased recycling capacity of individual NK cells.     

Molecular variability in the Celleporella hyalina (Bryozoa; Cheilostomata) species complex: evidence for cryptic speciation from complete mitochondrial genomes

The bryozoan Celleporella has been shown to be composed of multiple, often cryptic, lineages. We sequenced two complete mitochondrial (mt) genomes of the Celleporella hyalina species complex from Wales, UK and Norway (i) to determine genetic divergence at the complete mt genome level, and (ii) to design new molecular markers for examining the interrelationships amongst the major lineages. In addressing (i), we estimated genetic divergence at three levels: (a) nucleotide diversity (π), (b) genome size, and (c) gene order. Genes nad4L, nad6, and atp8 showed the highest levels of divergence, and rrnL, rrnS, and cox1 showed the lowest levels. Inter-genome nucleotide divergence of protein-coding and ribosomal RNA genes, measured as π, was 0.21. The two genomes differed substantially in size, with the Norwegian genome being 2,573 base pairs (bp) longer than the Welsh genome, 17,265 and 14,692 bp, respectively. This difference in size is attributable to long non-coding regions present in the Norwegian genome. Both genomes exhibit similar gene orders, except for the translocation of one transfer RNA (trnA). Considering the high nucleotide diversity, genome size difference and change in gene order, these mt genomes are considered sufficiently divergent to have originated from two distinct species. In addressing (ii) we designed PCR primers that flank the most conserved regions of the genome: 1,300 bp of cox1 and a contiguous 2,000 bp fragment of rrnL + rrnS. The primers have yielded products for tissue from Wales, Norway, New Zealand, Alaska and Chile and should provide useful tools in establishing species- and population-level diversity within the Celleporella complex.     

Large-scale in silico mapping of complex quantitative traits in inbred mice

Understanding the genetic basis of common disease and disease-related quantitative traits will aid in the development of diagnostics and therapeutics. The processs of gene discovery can be sped up by rapid and effective integration of well-defined mouse genome and phenome data resources. We describe here an in silico gene-discovery strategy through genome-wide association (GWA) scans in inbred mice with a wide range of genetic variation. We identified 937 quantitative trait loci (QTLs) from a survey of 173 mouse phenotypes, which include models of human disease (atherosclerosis, cardiovascular disease, cancer and obesity) as well as behavioral, hematological, immunological, metabolic, and neurological traits. 67% of QTLs were refined into genomic regions <0.5 Mb with approximately 40-fold increase in mapping precision as compared with classical linkage analysis. This makes for more efficient identification of the genes that underlie disease. We have identified two QTL genes, Adam12 and Cdh2, as causal genetic variants for atherogenic diet-induced obesity. Our findings demonstrate that GWA analysis in mice has the potential to resolve multiple tightly linked QTLs and achieve single-gene resolution. These high-resolution QTL data can serve as a primary resource for positional cloning and gene identification in the research community.     

Biochemical polymorphisms in feral and inbred mice (Mus musculus)

Examination of the frequencies of several loci controlling isozymes in three geographically distinct feral populations of mice showed the average animal to be heterozygous at 10.3% of his loci. There was no evidence for interaction between loci, nor any evidence for inbreeding in the populations. Thirty-nine inbred strains, including four newly derived ones, were also characterized for their alleles for as many as 16 polymorphic loci. Among these strains, variability is at least as great as in any single feral population, but probably less than that found among all feral populations of the species.This work was supported by NIH Research Grants GM-9966 and GM-07249 from the Division of General Medical Science, and by contracts AT(30-1)-1979 and AT(30-1)-3671 with the U.S. Atomic Energy Commission.     

An integrated in silico gene mapping strategy in inbred mice

In recent years in silico analysis of common laboratory mice has been introduced and subsequently applied, in slightly different ways, as a methodology for gene mapping. Previously we have demonstrated some limitation of the methodology due to sporadic genetic correlations across the genome. Here, we revisit the three main aspects that affect in silico analysis. First, we report on the use of marker maps: we compared our existing 20,000 SNP map to the newly released 140,000 SNP map. Second, we investigated the effect of varying strain numbers on power to map QTL. Third, we introduced a novel statistical approach: a cladistic analysis, which is well suited for mouse genetics and has increased flexibility over existing in silico approaches. We have found that in our examples of complex traits, in silico analysis by itself does fail to uniquely identify quantitative trait gene (QTG)-containing regions. However, when combined with additional information, it may significantly help to prioritize candidate genes. We therefore recommend using an integrated work flow that uses other genomic information such as linkage regions, regions of shared ancestry, and gene expression information to obtain a list of candidate genes from the genome.     

The genetic structure of recombinant inbred mice: High-resolution consensus maps for complex trait analysis

Background

Recombinant inbred (RI) strains of mice are an important resource used to map and analyze complex traits. They have proved particularly effective in multidisciplinary genetic studies. Widespread use of RI strains has been hampered by their modest numbers and by the difficulty of combining results derived from different RI sets.

Results

We have increased the density of typed microsatellite markers 2- to 5-fold in each of several major RI sets that share C57BL/6 as a parental strain (AXB, BXA, BXD, BXH, and CXB). A common set of 490 markers was genotyped in just over 100 RI strains. Genotypes of another ~1100 microsatellites were generated, collected, and error checked in one or more RI sets. Consensus RI maps that integrate genotypes of ~1600 microsatellite loci were assembled. The genomes of individual strains typically incorporate 45-55 recombination breakpoints. The collected RI set - termed the BXN set - contains approximately 5000 breakpoints. The distribution of recombinations approximates a Poisson distribution and distances between breakpoints average about 0.5 cM. Locations of most breakpoints have been defined with a precision of < 2 cM. Genotypes deviate from Hardy-Weinberg equilibrium in only a small number of intervals.

Conclusions

Consensus maps derived from RI strains conform almost precisely with theoretical expectation and are close to the length predicted by the Haldane-Waddington equation (X3.6 for a 2-3 cM interval between markers). Non-syntenic associations among different chromosomes introduce predictable distortions in QTL data sets that can be partly corrected using two-locus correlation matrices.     

Natural killer cells, bone, and the bone marrow: studies in estrogen-treated mice and in congenitally osteopetrotic (mi/mi) mice.

Mice lose natural killer cells after 6 weeks of treatment with 17 beta-estradiol. We here demonstrate that the same protocol leads to loss of genetic resistance to bone marrow transplantation and to significant osteoproliferation with loss of bone marrow. We also show that mice with reduced marrow because of congenital osteopetrosis are deficient in natural killing. These findings are consistent with previous evidence that natural killing and genetic resistance to bone marrow transplantation are dependent upon the marrow. Temporal studies of bone histology and radiology during and after treatment with estrogen reveal that alterations in natural killing proceed more rapidly than changes in bone marrow volume. These studies also demonstrate that estrogens induce osteoproliferation only at endosteal surfaces that are adjacent to hematopoietic marrow. From these observations, we conclude that estrogens do not reduce natural killer cells simply by reducing the volume of bone marrow. Estrogens may instead have an effect on bone marrow. Estrogens may instead have an effect on bone marrow cells that leads both to osteoproliferation and to a deficiency of marrow-dependent cells.