High-resolution genome screen for bone mineral density in heterogeneous stock rat

We previously demonstrated that skeletal mass, structure, and biomechanical properties vary considerably in heterogeneous stock (HS) rat strains. In addition, we observed strong heritability for several of these skeletal phenotypes in the HS rat model, suggesting that it represents a unique genetic resource for dissecting the complex genetics underlying bone fragility. The purpose of this study was to identify and localize genes associated with bone mineral density in HS rats. We measured bone phenotypes from 1524 adult male and female HS rats between 17 and 20 weeks of age. Phenotypes included dual-energy X-ray absorptiometry (DXA) measurements for bone mineral content and areal bone mineral density (aBMD) for femur and lumbar spine (L3-L5), and volumetric BMD measurements by CT for the midshaft and distal femur, femur neck, and fifth lumbar vertebra (L5). A total of 70,000 polymorphic single-nucleotide polymorphisms (SNPs) distributed throughout the genome were selected from genotypes obtained from the Affymetrix rat custom SNPs array for the HS rat population. These SNPs spanned the HS rat genome with a mean linkage disequilibrium coefficient between neighboring SNPs of 0.95. Haplotypes were estimated across the entire genome for each rat using a multipoint haplotype reconstruction method, which calculates the probability of descent for each genotyped locus from each of the eight founder HS strains. The haplotypes were tested for association with each bone density phenotype via a mixed model with covariate adjustment. We identified quantitative trait loci (QTLs) for BMD phenotypes on chromosomes 2, 9, 10, and 13 meeting a conservative genomewide empiric significance threshold (false discovery rate [FDR] = 5%; p < 3 × 10(-6)). Importantly, most QTLs were localized to very small genomic regions (1-3 megabases [Mb]), allowing us to identify a narrow set of potential candidate genes including both novel genes and genes previously shown to have roles in skeletal development and homeostasis.

MAP ORDER OF THE STRUCTURAL GENES AND OPERATOR GENES

Ramakrishnan, T. (Yale University, New Haven, Conn.), and Edward A. Adelberg. Regulatory mechanisms in the biosynthesis of isoleucine and valine. III. Map order of the structural genes and operator genes. J. Bacteriol. 89:661-664. 1965.-A new method has been employed to determine the map order of the structural genes and operator genes governing the enzymes of the isoleucine-valine biosynthetic pathway. This method relies on the observation that phage transduction of markers carried on an F-genote leads to the establishment in the recipient of F-genotes of various lengths. Using this method, we have established that the order of loci is the following: F/ilvE ilvD ilvA oprA/ilvC/ilvB oprB. The operator locus, oprA, regulates the activity of structural genes ilvE (transaminase B), ilvD (dehydrase), and ilvA (threonine deaminase). The operator locus, oprB, regulates the activity of ilvB (condensing enzyme). An operator for ilvC (reductoisomerase) can be inferred to exist, but has not yet been detected genetically. The loci ilvB and oprB have been shown to be at the extreme right end of the sequence, but their positions relative to each other remain to be established.

IDENTIFICATION OF TWO OPERATOR GENES

Ramakrishnan, T. (Yale University, New Haven, Conn.), and Edward A. Adelberg. Regulatory mechanisms in the biosynthesis of isoleucine and valine. II. Identification of two operator genes. J. Bacteriol. 89:654-660. 1965.-A tightly clustered set of five structural genes governs the synthesis of the five enzymes of isoleucine and valine biosynthesis in Escherichia coli. Three of the genes governing transaminase B, dehydrase, and threonine deaminase, are controlled by a single operator locus, designated oprA. The structural gene governing the condensing enzyme is controlled by a second operator locus, designated oprB. Both oprA and oprB have been shown to regulate structural genes which are cis, but not trans, to their own operator. No mutations have yet been found which affect the level of reductoisomerase, but the existence of a third operator controlling the synthesis of this enzyme can be inferred. Enzyme derepression resulting from mutations in oprA confers resistance to high levels of valine. Derepression of the condensing enzyme resulting from mutations in oprB confers resistance to low levels of valine, and to alpha-aminobutyric acid. The significance of these findings with respect to the valine sensitivity of E. coli strain K-12 is discussed.

BIOCHEMICAL AND GENETIC GROUPING OF ISOLEUCINE-VALINE MUTANTS OF PSEUDOMONAS AERUGINOSA

Pearce, L. E. (University of Otago, Dunedin, New Zealand), and J. S. Loutit. Biochemical and genetic grouping of isoleucine-valine mutants of Pseudomonas aeruginosa. J. Bacteriol. 89:58-63. 1965.-Isoleucine- and valine-requiring mutants of Pseudomonas aeruginosa, induced with ultraviolet and ethyl-methane-sulfonate, were isolated. The feeding properties and growth requirements of 56 of these mutants were examined, and evidence was found for at least four phenotypic groups, A, B, C, and D, controlling the biosynthesis of isoleucine and valine. Preliminary genetic mapping by use of bacteriophage-mediated transduction showed linkage between the mutant loci within groups A, B, and C. There was also evidence of linkage between the genes controlling groups A and B and some slight evidence of linkage between the other groups. There was insufficient evidence to suggest the arrangement of the genes.

LINKAGE RELATIONSHIPS OF GENES CONTROLLING ISOLEUCINE, VALINE, AND LEUCINE BIOSYNTHESIS IN BACILLUS SUBTILIS

Barat, M. (Centre National de la Recherche Scientifique, Gif-sur-Yvette, Seine et Oise, France), C. Anagnostopoulos, and A.-M. Schneider. Linkage relationships of genes controlling isoleucine, valine, and leucine biosynthesis in Bacillus subtilis. J. Bacteriol.90:357-369. 1965.-In Bacillus subtilis, the genetic loci controlling isoleucine and valine biosynthesis are not all clustered. Some of them were located on two distinct transforming deoxyribonucleic acid "molecules." One of these molecules (the "ileilva(2-4)-met segment") carries the threonine deaminase and the dihydroxy acid dehydrase loci linked to methionine markers. The other (the "ilva(1-3)-leu segment") bears the reductoisomerase locus and one or more loci involved in leucine synthesis. A phenylalanine marker was also shown to be weakly linked to this latter group. In transduction mediated by phage PBS-1, these groups are transferred jointly with other gene clusters. The phage appears to convey chromosome fragments considerably longer than the transforming "molecules." The genetic maps of both the above segments were extended by transduction. Some groups previously studied by transformation can be placed in the following linear order: the ile-ilva(2-4)-met segment, the cluster of loci involved in aromatic amino acid synthesis (try segment), and a lysine locus. An arginine locus is cotransduced with the phe-ilva(1-2)-leu segment. Recombination frequencies between linked markers are much lower in transduction by this phage than in transformation.

GROWTH OF MALE-SPECIFIC BACTERIOPHAGE IN PROTEUS MIRABILIS HARBORING F-GENOTES DERIVED FROM ESCHERICHIA COLI

Horiuchi, Kensuke (Yale University, New Haven, Conn.), and Edward A. Adelberg. Growth of male-specific bacteriophage in Proteus mirabilis harboring F-genotes derived from Escherichia coli. J. Bacteriol. 89:1231-1236. 1965.-Male-specific bacteriophage MS2 was shown to infect and grow in Proteus mirabilis strains which harbor F-genotes derived from Escherichia coli K-12. The burst size was 2,000 to 3,000, which is similar to that in E. coli K-12, whereas the latent period was 45 min, definitely longer than that in E. coli. In spite of the multiplication of MS2 in male P. mirabilis in broth, P. mirabilis strains failed to show plaque formation by MS2 on agar plates; this failure may be related to the low efficiency of phage adsorption. No host-controlled modification of MS2 by P. mirabilis was detected.

DOMINANCE OF THE INDUCIBLE STATE IN STRAINS OF STAPHYLOCOCCUS AUREUS CONTAINING TWO DISTINCT PENICILLINASE PLASMIDS

Richmond, Mark H. (National Institute for Medical Research, Mill Hill, London, England). Dominance of the inducible state in strains of Staphylococcus aureus containing two distinct penicillinase plasmids. J. Bacteriol. 90:370-374. 1965.-The phenotypic expression of penicillinase synthesis is studied in a strain of S. aureus containing two distinct plasmids, each carrying the penicillinase structural gene and its associated control (inducibility) gene. One plasmid in the heterodiploid carries the genes responsible for the normal, fully inducible synthesis of a structural mutant of type A penicillinase, and the second plasmid carries the genes required for constitutive synthesis of C-type enzyme. The heterodiploid is phenotypically fully inducible, indicating that the inducible state dominates the constitutive in penicillinase synthesis. The heterodiploid synthesizes approximately equal quantities of A- and C-type enzyme when fully induced. Parental types are obtained from the heterodiploid by spontaneous segregation at a frequency of about 1 per 1,000 divisions of each character. Recombination between the two plasmids in such a persistent heterodiploid is a rare event.

UNSTABLE LINKAGE BETWEEN GENETIC MARKERS IN TRANSFORMATION

Kelly, M. (Hammersmith Hospital, London, England), and R. H. Pritchard. Unstable linkage between genetic markers in transformation. J. Bacteriol. 89:1314-1321. 1965.-A new type of association of genetic markers in a transformation system has been discovered. Linkage between certain markers is detectable only under particular conditions of deoxyribonucleic acid (DNA) extraction and is sensitive to dilution of the DNA. The data suggest that this unstable association occurs between markers which are on the same molecule but separated by a molecular distance sufficiently great for linkage to be preserved only by mild DNA extraction procedures and at high concentrations of DNA. Linkage can be stabilized by dilution in the presence of a carrier DNA. By use of these unstable linkages, the genetic map of Bacillus subtilis has been extended in both directions from the aromatic gene cluster.

EFFECT OF INTEGRATED SEX FACTOR ON TRANSDUCTION OF CHROMOSOMAL GENES IN ESCHERICHIA COLI

Pittard, James (Yale University, New Haven, Conn.). Effect of integrated sex factor on the transduction of chromosomal genes in Escherichia coli. J. Bacteriol. 89:680-686. 1965.-Generalized transducing phage P1kc can contransduce the markers tna and ilv in Escherichia coli K-12 at a frequency of approximately 25%. When sex factor is integrated into the donor chromosome between tna and ilv, as in Hfr AB313, the entire sequence tna F ilv is not cotransduced at a detectable frequency, nor is F cotransduced with either tna or ilv. The frequency with which ilv is transduced from Hfr AB313 to female recipients is approximately one-eighth the frequency obtained when either F(+) or female strains are used as donors. This reduction of transduction frequency does not occur if the recipient is an Hfr male similar to AB313. The reduction is attributed to pairing difficulties which occur when the transduced fragment carrying the ilv genes also carries sex-factor material. When ilv(+) is transduced from a female to an ilv(-) derivative of AB313, 70% of the transductants are converted to F(+) males. A model is proposed to account for all of these observations.

GENETIC MAPPING OF VI AND SOMATIC ANTIGENIC DETERMINANTS IN SALMONELLA

Johnson, E. M. (Walter Reed Army Institute of Research, Washington, D.C.), Barbara Krauskopf, and L. S. Baron. Genetic mapping of Vi and somatic antigenic determinants in Salmonella. J. Bacteriol. 90:302-308. 1965.-The Vi antigen and somatic antigen 9 were transferred to Salmonella typhimurium recipients by mating with S. typhosa Hfr TD-7, and the genetic determinants of these antigens were located. A gene responsible for Vi antigen expression, ViB was found to be associated with the inlpurA-pyrB linkage group, and the order ViB-inl-purA-pyrB was established. The determinant of somatic antigen 9 was found closely linked to the his gene, and cotransduction of these determinants was accomplished with phage PLT-22. Moreover, all conjugation and transduction hybrids which received the somatic antigen 9 determinant concurrently lost somatic antigen 4. Similarly, S. typhosa hybrids produced by transfer of his and the gene for somatic antigen 4 from S. typhimurium Hfr B2, or by cotransduction of these genes with PLT-22, also lost somatic antigen 9. These results indicated that the genetic determinants of the somatic antigen 9 and 4 are probably allelic. A second Vi antigen determinant, ViA, located near his, was discovered in matings of S. typhimurium Hfr B2 with a Vi-negative S. typhosa recipient. Vi-positive S. typhosa hybrids were obtained from this cross in which neither parent expressed the Vi antigen, indicating that this Vi determinant of S. typhosa is present also in S. typhimurium.

EPISOME-MEDIATED TRANSFER OF DRUG RESISTANCE IN ENTEROBACTERIACEAE. VII. TWO TYPES OF NATURALLY OCCURRING R FACTORS

Watanabe, Tsutomu (Keio University, Tokyo, Japan), Hiroshi Nishida, Chizuko Ogata, Toshihiko Arai, and Sachiko Sato. Episome-mediated transfer of drug resistance in Enterobacteriaceae. VII. Two types of naturally occurring R factors. J. Bacteriol. 88:716-726. 1964.-Naturally occurring R factors are classified into two types, fi(+) and fi(-), depending on their fi characters. The term fi is an abbreviation of fertility inhibition and fi(-) and fi(-) mean, respectively, the presence and absence of suppression of the functions of the sex factor F of Escherichia coli K-12. It was found that fi(-) R factors reduce the efficiency of plating of phages lambda and T(1) in K-12; fi(+) R factors did not have this inhibitory action. One of the fi(-) R factors reduced the efficiency of plating of phage T(7) as well. Phages lambda and T(1) underwent host-induced modifications in the host carrying some fi(-) R factors. At least two types of fi(-) R factors were recognized by the types of their restriction and host-induced modification of these phages. CaCl(2) exhibited antagonistic actions against the restrictions of phages lambda and T(1) by fi(-) R factors. Transduction of the ability to ferment galactose with HFT lysates of lambda was reduced by fi(-) R factors. Ultraviolet induction of lambda was not affected by any R factors. Furthermore, adsorption of phages lambda and T(1) was not altered by the presence of any R factors. From these results, we concluded that the suppression of progeny formation of these phages by fi(-) R factors is due to some step(s) after adsorption of the phages to the bacteria. Superinfection immunity and mutual exclusion were found between two different fi(+) R factors but not between fi(+) and fi(-) R factors. The two different fi(-) R factors were frequently genetically recombined. but fi(+) and fi(-) R factors were not genetically recombined, as indicated by findings of independent transfer of these R factors by conjugation and by transduction from the donors having these two R factors. It was assumed from these findings that fi(+) and fi(-) R factors are considerably different episomes having different resistance-transfer factors.

CHARACTERIZATION OF AN HFR STRAIN OF SHIGELLA FLEXNERI

Schneider, Herman (Walter Reed Army Institute of Research, Washington, D.C.), and Stanley Falkow. Characterization of an Hfr strain of Shigella flexneri. J. Bacteriol. 88:682-689. 1964.-A Hfr Shigella flexneri, strain 69, was obtained by terminal marker selection in a cross between Hfr Escherichia coli and S. flexneri. The chromosome of this Hfr Shigella bears gross homology to the E. coli chromosome: it can conjugate with both Shigella and E. coli; its order of gene transmission is the same as E. coli; and interrupted matings show that distance between gene loci is the same as for E. coli. The kinetics of transfer of the pro(+), thr(+) + leu(+), and arg(+) loci by Hfr S. flexneri differ from Hfr E. coli, and may indicate that function of the sex factor, F, derived from E. coli, is modified when integrated into the Shigella chromosome.