Genetic mapping of isozyme loci in Secale cereale L.

Summary The genetics and linkage relationships of several isozymatic and morphological markers have been investigated in different cultivars of rye (Secale cereale L.). The inheritance and the variability among cultivars of three new isozymatic zones are described: GOT2 and LAP, each of them under the control of a two-allele single locus, namely Got2 and Lap, respectively; and 6PGD1 controlled by two loci, 6Pgd1a and 6Pgd1b, which have alleles in common. Four linkage groups have been found: Acp2-Acp3, Got3-Mdh2-Lper4, Mdh1-6Pgd2-Pgi2, and Pgm-Eper2-[Eper1-Eper3]. The assignment of these four groups to the chromosomes 7R, 3R, 1R, and 4R is discussed.     

RF nonlinear interactions in living cells-I: nonequilibrium thermodynamic theory

Some biological experiments report effects that depend on low frequency modulation of a radiofrequency (RF) carrier. Such effects require nonlinear responses in biological preparations, which we show could be observed with great generality by the unique frequency signatures that would appear in the scattered RF energy. Following Illinger [Illinger (1982): Bioelectromagnetics 3:9-16], we considered a two part physical system. The greater part, dominated by the properties of water, interacts linearly with the RF field and is described by equilibrium thermodynamics. However, another, much smaller part, e.g., certain biological molecules and molecular subgroups, supports nonlinear interactions and is described by nonequilibrium thermodynamics. For example, a nonlinear interaction might result from scattering of RF photons from oscillators located in a region of strong field gradients, such as at membrane surfaces. A second nonlinear mechanism could appear if stress (elastic) waves were launched within the confines of the exposure vessel by RF heating. Amplitude modulation at angular frequency Omega of a carrier wave with angular frequency omega (omega < omega) produces two peaks in elastic stress in the cell structure during each period; that is, there is "full-wave demodulation." As a result of coherent nonlinear charge motion, modulation products could appear at frequencies omega +/- 2 omega and, in general, at omega +/- n 2 omega (n = 1, 2, em leader ) if vibrational harmonics at 2 n omega also are excited. Although in principle microwaves can alter the stability of a thermodynamic system by pumping a chemical transition, the degree of nonlinear coupling required for an observable instability is so great that its probability is effectively zero, unless field intensity is extremely high. A companion paper suggests an extremely sensitive method and the related instrumentation for detection of the spectrum scattered by living cells during exposure to amplitude modulated RF energy.     

RF nonlinear interactions in living cells--II: detection methods for spectral signatures

The presence of harmonic products due to possible nonlinear interaction of amplitude modulated RF signals in living cells is best detected by using a cavity with high quality factor. Harmonic products generated by elementary oscillators can be trapped and accumulated in a cavity, permitting detection sensitivity much greater than in an open environment, where they would be radiated in all directions. The experimental method described herein is a systematic approach to detection of the non-Planck RF energy (if any) emitted by an exposed sample of living cells. Balzano and Sheppard [Balzano and Sheppard (2003): Bioelectromagnetics 24:473-482] classified the non-Planck RF emissions from living cells as coming from (1). nonlinear interactions and (2). inelastic interactions. Nonlinear harmonic products would appear in the band at twice the frequency of an amplitude modulated RF carrier. Inelastic interaction products resulting from the interaction between the incident RF energy and normally occurring mechanical vibrations are found in the band immediately adjacent to the carrier. Detection of the latter signals is difficult because of this close spectral proximity, for example, 1 part in 10(7) for 100 Hz modulation of a GHz carrier. Modern audio spectrum analyzers have excellent selectivity, providing 60 dB rejections only 2 kHz away from the carrier. By judicious selection of the amplitude modulation (AM) frequency, frequency of the RF carrier, and size of the biological sample, it is possible to achieve very high sensitivity (about -90 dBm) with commercially available instrumentation. The presence (or absence) of harmonics in the band adjacent to the amplitude modulated RF carrier would establish (or negate) the existence of coherent interactions between mechanical vibrations in the cell ensemble and the incident RF signal.     

Genetic Analysis of Aspartate Aminotransferase Isozymes from Hybrids between DROSOPHILA MELANOGASTER and DROSOPHILA SIMULANS and Mutagen-Induced Isozyme Variants

The aspartate aminotransferases (designated GOT1 and GOT2) are two enzymes of Drosophila melanogaster for which naturally occurring electrophoretic variants were not found. There is an electrophoretic difference between D. melanogaster and D. simulans. Since the F ₁ hybrid offspring of these species are sterile, a genetic analysis of the ordinary type cannot be done on differences between the two species. A method was devised to make "partial hybrids" in which one chromosome arm is homozygous for melanogaster genes in an otherwise hybrid background. By using this method, Got1 was localized to 2R and Got2 to 2L. Once a gene can be assigned to a chromosome, it may be followed in crossing schemes and mutations from mutagen treatments may be looked for. At the locus of Got1 a mutation with low activity was recovered and designated Got1^lo. It was located at a genetic map position of 75 on 2R. A Got2 mutant with a greater migration to the anode was recovered and designated Got2 ^J. It was located at a genetic map position of 3.0, and in the salivary chromosome was between 22B1 and 22B4 inclusive.     

Exotic Mammals Disperse Exotic Fungi That Promote Invasion by Exotic Trees

Biological invasions are often complex phenomena because many factors influence their outcome. One key aspect is how non-natives interact with the local biota. Interaction with local species may be especially important for exotic species that require an obligatory mutualist, such as Pinaceae species that need ectomycorrhizal (EM) fungi. EM fungi and seeds of Pinaceae disperse independently, so they may use different vectors. We studied the role of exotic mammals as dispersal agents of EM fungi on Isla Victoria, Argentina, where many Pinaceae species have been introduced. Only a few of these tree species have become invasive, and they are found in high densities only near plantations, partly because these Pinaceae trees lack proper EM fungi when their seeds land far from plantations. Native mammals (a dwarf deer and rodents) are rare around plantations and do not appear to play a role in these invasions. With greenhouse experiments using animal feces as inoculum, plus observational and molecular studies, we found that wild boar and deer, both non-native, are dispersing EM fungi. Approximately 30% of the Pinaceae seedlings growing with feces of wild boar and 15% of the seedlings growing with deer feces were colonized by non-native EM fungi. Seedlings growing in control pots were not colonized by EM fungi. We found a low diversity of fungi colonizing the seedlings, with the hypogeous Rhizopogon as the most abundant genus. Wild boar, a recent introduction to the island, appear to be the main animal dispersing the fungi and may be playing a key role in facilitating the invasion of pine trees and even triggering their spread. These results show that interactions among non-natives help explain pine invasions in our study area.     

The use of synthetic tandem repeats to isolate new VNTR loci: cloning of a human hypermutable sequence.

Synthetic tandem repeats (STRs) of oligonucleotides have previously been shown to detect polymorphic loci in the human genome. Here, we report results from the use of three such probes to screen a human cosmid library. Nine of the 45 positive clones that were analyzed appear to contain highly polymorphic minisatellite or VNTR loci. The degree of enrichment for minisatellite sequences varied with the choice of STR: one provided a 15- to 20-fold enrichment (4 polymorphic loci among 10 clones), whereas 2 others gave a 3- to 5-fold enrichment (5 polymorphic probes in a total of 35 clones) compared to random screening. The 9 VNTR markers have been localized by linkage analysis in the CEPH panel and/or by in situ hybridization. Eight probes identify new loci, one of which maps to an interstitial region. One of the VNTR loci (identified by probe CEB1) was found to be hypermutable, with 52 mutation events identified among 310 children characterized in 40 CEPH families. The parental origin of the mutation could be identified in all instances, and only one mutation was found to be of maternal origin. The mutation rate in males was estimated to be approximately 15%. Segregation analysis of flanking markers suggests that mutations are not associated with crossing over. As the only previously described hypermutable minisatellite loci in humans have equal rates of male and female mutations, these observations establish that a second type of hypermutable minisatellite exists in the human genome. In neither case does the generation of new alleles appear to be associated with unequal crossing over.     

Chemotaxonomic differentiation of conifer families and genera based on the seed oil fatty acid compositions: multivariate analyses

 The fatty acid compositions of seed oils from 34 conifer species, mainly Pinaceae and secondarily Cupressaceae, have been determined by gas-liquid chromatography of the methyl esters. As noted in earlier studies, these oils were characterized by the presence of several Δ5-olefinic acids, i.e., 5,9-18:2, 5,9,12-18:3, 5,9,12,15-18:4, 5,11-20:2, 5,11,14-20:3, and 5,11,14,17-20:4 acids, in addition to the more common saturated, oleic, linoleic and α-linolenic acids. Based on these fatty acid compositions, and on those established in earlier systematic studies (totalling 82 species), we established a chemotaxonomic grouping of the main conifer families, i.e., of the Pinaceae, Taxodiaceae, Cupressaceae, and Taxaceae. This was achieved using multivariate analyses (principal component analysis and discriminant analysis). The fatty acids that discriminate best in this classification are the 5,11,14,17-20:4, 9,12,15-18:3 and 5,9,12-18:3 acids. Moreover, it was possible to differentiate between several genera of the Pinaceae: Pinus (including Tsuga and Pseudotsuga), Abies, Cedrus, and Picea plus Larix, represented quite distinct groups. Other fatty acids such as oleic, linoleic, and 5,9-18:2 acids were also important for this purpose. The fatty acid compositions, and particularly the Δ5-olefinic acid contents of conifer seed oils, may thus be applied to the chemosystematic distinction among conifer families as well as genera of the Pinaceae. Received: 3 January 1997 / Accepted: 17 April 1997     

Genetic variation in cultivars of diploid ryegrass,Lolium perenne andL. multiflorum,at five enzyme systems

Summary Samples of approximately 100 plants from each of 22 populations ofLolium perenne representing 15 cultivars, and from 13 populations ofLolium multiflorum representing six cultivars were scored for iso-zyme variants in five enzyme systems, PGI, GOT, ACP, PGM and 6-PGD. From the individual banding patterns a genetic interpretation of the variation was formulated and population studies of the resulting six polymorphic enzyme loci were performed. No strong indications of partial selfing was found since at four of the six loci,Pgi 2, Got 3, Pgm 1 andPgd 1, the genotypic proportions were in correspondence with the Hardy-Weinberg expectations. This indicated, further, that the genetical interpretations of the banding patterns might be correct. Deviations from Hardy-Weinberg proportions forAcp 1 andGot 2 indicated presumably selection working on the linkage group including these loci. Gametic phase disequilibrium was observed betweenPgi 2 andPgd 1 for populations of one cultivar. These results were discussed in relation to the variation expected within a cultivar.     

Interleukin 6 promoter polymorphisms influence the outcome of chronic hepatitis C

Host genetic variation may affect the outcome of chronic viral hepatitides, favoring viral clearance and/or modulating the inflammatory response to persistent infection. Our aims were to assess whether interleukin 6 (IL-6) promoter polymorphisms are associated with chronic hepatitis C virus (HCV) infection and to clarify the role of IL-6 haplotypes in facilitating progressive disease. The study included 424 Italian patients (233 males, median age 53 years) affected by HCV chronic infection. IL6 -1363, -597, -572, -174, and +2954 polymorphic loci were assayed by means of restriction fragment length polymorphism. Three hundred forty-four healthy Italian blood donors (245 males, median age 50 years) served as controls. Comparing patients and controls analysis of molecular variance was highly significant (p?相似文献   

Sequence-tagged-site (STS) markers of arbitrary genes: the utility of black spruce-derived STS primers in other conifers

 Sequence-tagged-site primers, previously developed based upon black spruce (Picea mariana) cDNA sequences, were tested for their ability to direct specific amplification in two individuals of each of 12 additional conifer species. Nearly all (95–97%) of the primers functioned well in congeneric trials, while a lower proportion (21–33%) scored positively in other Pinaceae genera. Outside of the Pinaceae, amplification of homologous products was not achieved. Products from the various species often differed in size from their homologs in black spruce. In one case a large difference in size was due to the lack of an intron in a jack pine product while in several other cases the differences were due to the presence or absence of large direct repeats in the DNA sequences. Length polymorphism was occasionally evident between the two individuals examined of a given species. We investigated marker polymorphism in detail in a panel of 15 white spruce (Picea glauca) trees. Allelic segregation among haploid megagametophytes was revealed directly at 16 loci by standard agarose-gel electrophoresis without any additional manipulation of amplification products. Polymorphisms observed at 12 of these loci were exclusively co-dominant. For this subset of 12 loci, the average number of alleles was 3.2 and the average observed heterozygosity was 0.37. Received: 10 April 1998 / Accepted: 22 April 1998     

Enzyme Polymorphism and Cyclic Parthenogenesis in DAPHNIA MAGNA. I. Selection and Clonal Diversity

Genotype frequencies and fecundities were recorded over a period of two years for three polymorphic enzyme loci (Est, Mdh and Got) in a parthenogenetic natural population of Daphnia magna Straus (Crustacea: Cladocera). There was a large excess of heterozygotes at each locus, and some nonrandom association between loci, although 29 different three-locus genotypes were detected. There were small but significant changes in genotype frequencies that did not follow any clear seasonal cycles or overall trends, and the genotypes often differed significantly in fecundity, although the direction of the difference was not constant. These fitness differences were probably not attributable to the specific loci studied.--Models of balancing selection are of two types: segregation-balanced (e.g., heterosis) and competition-balanced (e.g., frequency dependence). Only the latter type can stabilize diversity in a clonal population. The observed selection was not heterotic, but it is not certain that it was stabilizing either. Clonal competition did not lead to victory by a single, fittest clone; genotypic diversity remained high.     

The red mutations impair the regulation of flavinogenesis and metal homeostas in yeast Pichia guilliermondii

A method of positive selection of mutants with impaired regulation of flavinogenesis and metal homeostasis in yeast Pichia guilliermondii was developed. This positive selection system was based on the isolation of pseudo-wild-type revertants (the Rib+ phenotype) in riboflavin-dependent rib1-86 mutant (the Rib- phenotype) of yeast P. guilliermondii. Mutation rib1-86 blocks activity of the GTP cyclohydrolase II catalyzing the first step in riboflavin (RF) biosynthesis. Study of a collection of spontaneous Rib+ revertants allowed the identification of a considerably large number of genetic loci responsible for the suppression of rib1-86, which include both previously identified three loci (rib80, rib81, and hit1) and six new loci designated red1-red6 (reduction). A comparative analysis of the wild-type strain and red mutants revealed that these mutants had higher activity levels of GTP cyclohydrolase and RF-synthase, elevated levels of RF biosynthesis, enhanced Fe/Cu reductase activity and higher total iron content in cells and that they are characterized by enhanced sensitivity to transition metals (Fe(III), Cu(II), Cd(II), Co(II), Zn(II), Ag(I), and to H2O2. The metal hypersensitivity of mutant cells can be prevented by an increased amount of extracellular iron ions. Mutations red1 and red6 synergistically interact with the locus rib81 in the course of RF biosynthesis. Obviously, each RED gene plays an important role in the regulation of both flavinogenesis and metal homeostasis in P. guilliermondii cells.     

Isozyme analysis of primary trisomies in beet (Beta vulgaris L.). Genetical characterization and techniques for chromosomal assignment of two enzyme-coding loci: leucine aminopeptidase and glutamate oxaloacetate transaminase

Segregating families of beet (Beta vulgaris) were used to verify the monofactorial inheritance of two enzyme-coding loci, leucine aminopeptidase (Lap1) and glutamate oxaloacetate transaminase (Got3). With a series of primary trisomies and using three methods to discriminate between the critical trisomic (the locus is situated on the triplicated chromosome) and the non-critical ones, it was possible to allocate the two loci to beet chromosomes I and II, respectively. For the locus Lap1 distorted segregation ratios were estimated, and the incorporation of three alleles into one plant was attempted. In the case of Got3 the measurement of the allele dosage effect after electrophoresis was chosen as the major strategy. The output of laser densitometric scans were subjected to the non-parametrical Wilcoxon-Mann-Whitney test.     

A Direct Assessment of the Role of Genetic Drift in Determining Allele Frequency Variation in Populations of EUPHYDRYAS EDITHA

Estimates of allele frequencies at six polymorphic loci were collected over eight generations in two populations of Euphydryas editha. We have estimated, in addition, the effective population size for each generation for both populations with results from mark-recapture and other field data. The variation in allele frequencies generated by random genetic drift was then studied using computer simulations and our direct estimates of effective population size. Substantial differences between observed values and computer-generated expected values assuming drift alone were found for three loci (Got, Hk, Pgi) in one population. These observations are consistent with natural selection in a variable environment.     

Genetic control and intracellular localization of glutamate oxaloacetic transaminase in maize

Glutamate oxaloacetic transaminase (L-aspertate: 2-oxoglutarate aminotransferase, E.C. 2.6.1.1; GOT) was found to occur in five distinct electrophoretic forms in different tissue extracts from a number of highly inbred strains of Zea mays L. No major qualitative differences were detected in the various tissues examined, and the isozyme patterns did not undergo changes during temporal development of any given inbred strain. Cell fractionation studies showed one isozyme to be associated with the mitochondria (mGOT), another to be exclusively associated with the soluble fraction (sGOT), and a third to be associated with the glyoxysomes (gGOT). The glyoxysomal form occurs as two electrophoretically distinct variants which exist in different inbred strains of maize. The gGOT variants are under the control of two codiminant alleles (Got1A and Got1B) at the Got1 locus (isozyme5, gGOT). The genetic data and gene dosage effects suggest that GOT in maize is functionally a dimer.     

New Sporulation Loci in Streptomyces coelicolor A3(2)

Sporulation mutants of Streptomyces coelicolor appear white because they are defective in the synthesis of the grey polyketide spore pigment, and such white (whi) mutants had been used to define eight sporulation loci, whiA, whiB, whiD, whiE, whiG, whiH, whiI, and whiJ (K. F. Chater, J. Gen. Microbiol. 72:9-28, 1972; N. J. Ryding, Ph.D. thesis, University of East Anglia, 1995). In an attempt to identify new whi loci, we mutagenized S. coelicolor M145 spores with nitrosoguanidine and identified 770 mutants with colonies ranging from white to medium grey. After excluding unstable strains, we examined the isolates by phase-contrast microscopy and chose 115 whi mutants with clear morphological phenotypes for further study. To exclude mutants representing cloned whi genes, self-transmissible SCP2*-derived plasmids carrying whiA, whiB, whiG, whiH, or whiJ (but not whiD, whiE, or whiI) were introduced into each mutant by conjugation, and strains in which the wild-type phenotype was restored either partially or completely by any of these plasmids were excluded from further analysis. In an attempt to complement some of the remaining 31 whi mutants, an SCP2* library of wild-type S. coelicolor chromosomal DNA was introduced into 19 of the mutants by conjugation. Clones restoring the wild-type phenotype to 12 of the 19 strains were isolated and found to represent five distinct loci, designated whiK, whiL, whiM, whiN, and whiO. Each of the five loci was located on the ordered cosmid library: whiL, whiM, whiN, and whiO occupied positions distinct from previously cloned whi genes; whiK was located on the same cosmid overlap as whiD, but the two loci were shown by complementation to be distinct. The phenotypes resulting from mutations at each of these new loci are described.     

Structural evolution of nrDNA ITS in Pinaceae and its phylogenetic implications

Nuclear ribosomal DNA (nrDNA) has been considered as an important tool for inferring phylogenetic relationships at many taxonomic levels. In comparison with its fast concerted evolution in angiosperms, nrDNA is symbolized by slow concerted evolution and substantial ITS region length variation in gymnosperms, particularly in Pinaceae. Here we studied structure characteristics, including subrepeat composition, size, GC content and secondary structure, of nrDNA ITS regions of all Pinaceae genera. The results showed that the ITS regions of all taxa studied contained subrepeat units, ranging from 2 to 9 in number, and these units could be divided into two types, longer subrepeat (LSR) without the motif (5'-GGCCACCCTAGTC) and shorter subrepeat (SSR) with the motif. Phylogenetic analyses indicate that the homology of some SSRs still can be recognized, providing important informations for the evolutionary history of nrDNA ITS and phylogeny of Pinaceae. In particular, the adjacent tandem SSRs are not more closely related to one another than they are to remote SSRs in some genera, which may imply that multiple structure variations such as recombination have occurred in the ITS1 region of these groups. This study also found that GC content in the ITS1 region is relevant to its sequence length and subrepeat number, and could provide some phylogenetic information, especially supporting the close relationships among Picea, Pinus, and Cathaya. Moreover, several characteristics of the secondary structure of Pinaceae ITS1 were found as follows: (1) the structure is dominated by several extended hairpins; (2) the configuration complexity is positively correlated with subrepeat number; (3) paired subrepeats often partially overlap at the conserved motif (5'-GGCCACCCTAGTC), and form a long stem, while other subrepeats fold onto itself, leaving part of the conserved motif exposed in hairpin loops.     

Performance of random forest when SNPs are in linkage disequilibrium

Background  

Single nucleotide polymorphisms (SNPs) may be correlated due to linkage disequilibrium (LD). Association studies look for both direct and indirect associations with disease loci. In a Random Forest (RF) analysis, correlation between a true risk SNP and SNPs in LD may lead to diminished variable importance for the true risk SNP. One approach to address this problem is to select SNPs in linkage equilibrium (LE) for analysis. Here, we explore alternative methods for dealing with SNPs in LD: change the tree-building algorithm by building each tree in an RF only with SNPs in LE, modify the importance measure (IM), and use haplotypes instead of SNPs to build a RF.     

Common breast cancer-predisposition alleles are associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers

Germline mutations in BRCA1 and BRCA2 confer high risks of breast cancer. However, evidence suggests that these risks are modified by other genetic or environmental factors that cluster in families. A recent genome-wide association study has shown that common alleles at single nucleotide polymorphisms (SNPs) in FGFR2 (rs2981582), TNRC9 (rs3803662), and MAP3K1 (rs889312) are associated with increased breast cancer risks in the general population. To investigate whether these loci are also associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers, we genotyped these SNPs in a sample of 10,358 mutation carriers from 23 studies. The minor alleles of SNP rs2981582 and rs889312 were each associated with increased breast cancer risk in BRCA2 mutation carriers (per-allele hazard ratio [HR] = 1.32, 95% CI: 1.20-1.45, p(trend) = 1.7 x 10(-8) and HR = 1.12, 95% CI: 1.02-1.24, p(trend) = 0.02) but not in BRCA1 carriers. rs3803662 was associated with increased breast cancer risk in both BRCA1 and BRCA2 mutation carriers (per-allele HR = 1.13, 95% CI: 1.06-1.20, p(trend) = 5 x 10(-5) in BRCA1 and BRCA2 combined). These loci appear to interact multiplicatively on breast cancer risk in BRCA2 mutation carriers. The differences in the effects of the FGFR2 and MAP3K1 SNPs between BRCA1 and BRCA2 carriers point to differences in the biology of BRCA1 and BRCA2 breast cancer tumors and confirm the distinct nature of breast cancer in BRCA1 mutation carriers.