Multipoint linkage analysis using sib pairs: an interval mapping approach for dichotomous outcomes

I propose an interval mapping approach suitable for a dichotomous outcome, with emphasis on samples of affected sib pairs. The method computes a lod score for each of a set of locations in the interval between two flanking markers and takes as its estimate of trait-locus location the maximum lod score in the interval, provided it exceeds the prespecified critical value. Use of the method depends on prior knowledge of the genetic model for the disease only through available estimates of recurrence risk to relatives of affected individuals. The method gives an unbiased estimate of location, provided the recurrence risk are correctly specified and provided the marker identity-by-descent probabilities are jointly, rather than individually, estimated. I also discuss use of the method for traits determined by two loci and give an approximation that has good power for a wide range of two-locus models.

Robust multipoint linkage analysis: an extension of the Haseman-Elston method

The use of multiple markers, rather than a single marker, can increase the likelihood of detecting linkage to a locus underlying a quantitative trait. In this paper, the Haseman-Elston sibpair method is extended to include information from multiple markers. The result is a linear regression of the squared pair trait difference on the jointly estimated proportions of genes shared identical by descent at the two closest flanking marker loci. The results strengthen the theoretical motivation for the interval mapping technique proposed by Fulker and Cardon [1994: Am J Hum Genet 54:1092-1103] and extend the method to include information from multiple markers, account for a trait dominance component, and examine the region just outside that defined by the markers. Simulations show that modest increases in power and substantial decreases in bias of parameter estimates are obtained when identity-by-descent probabilities are jointly estimated. The regression relationship is also developed for other types of relative pairs.

Design and sample-size considerations in the detection of linkage disequilibrium with a disease locus

The presence of linkage disequilibrium between closely linked loci can aid in the fine mapping of disease loci. We investigate the power of several designs for sampling individuals with different disease genotypes. As expected, haplotype data provide the greatest power for detecting disequilibrium, but, in the absence of parental information to resolve the phase of double heterozygotes, the most powerful design samples only individuals homozygous at the trait locus. For rare diseases, such a scheme is generally not feasible, and we also provide power and sample-size calculations for designs that sample heterozygotes. The results provide information useful in planning disequilibrium studies.

Robust estimation of gene frequency and association parameters

Methods based on generalized estimating equations are proposed for estimation and testing of gene frequency and association parameters using family data. In the problems considered, a marginal model is used to estimate the gene frequency and association parameters specified in the marginal distributions of the individuals. These procedures are robust in the sense that consistent estimates of the parameters of interest and their standard errors are obtained even though the marginal model is not fully correctly specified. In addition, the methods are shown to have good efficiency when compared with maximum likelihood methods. Specific procedures for application of the methods to the cases of allele frequency estimation, testing of linkage and Hardy-Weinberg disequilibrium parameters, and testing for marker-disease association are outlined and illustrated with data examples.

Gene therapy of rat 9L gliosarcoma tumors by transduction with selectable genes does not require drug selection

9L rat glioma cells have been used as a model for brain tumor therapies. It has been reported that in vivo infection of 9L cells with a replication-defective retrovirus expressing the herpes simplex thymidine kinase gene resulted in decreased tumor formation following treatment with the antiviral drug ganciclovir. In the study reported here, rats were injected either intracerebrally or subcutaneously with 9L glioma cells expressing a chimeric hygromycin phosphotransferase-thymidine kinase fusion protein or with unmodified 9L cells. Tumor formation was decreased in the rats receiving modified cells, even in the absence of treatment with ganciclovir. Suppression of tumor growth was also observed with cells modified to express the intracellular selectable marker neomycin phosphotransferase. These results indicate that an intracellular selectable marker, in the absence of pharmacologic selection, can inhibit tumor growth of 9L cells. The demonstration that intracellular marker genes can negatively influence the survival of transplanted cells has important implications for in vivo studies that use genetically modified cells.

Power output of scallop adductor muscle during contractions replicating the in vivo mechanical cycle

Because measurements on isolated skeletal muscles are often made with limited knowledge of in vivo kinematics, predictions of mechanical performance during natural movements are subject to considerable uncertainties. We used information on the in vivo length cycle and phase of activation of the scallop adductor during swimming at 10 degrees C to design an in vitro contractile regime that replicated the natural cycle. Replicating the in vivo length cycle and stimulation regime resulted in power output during cyclic contractions that matched in vivo performance both qualitatively and quantitatively. When sinusoidal length changes were used instead of the natural length trajectory, the adductor muscle produced a similar average power output (approximately 30 W kg-1 at 1.9 Hz), but the distribution of power throughout the cycles was quite different. We examined the instantaneous force-velocity properties during cyclic contractions and found that the muscle operated on or near its isotonic force-velocity curve for only 30-40% of the time required for shortening. During sinusoidal length cycles, the force-velocity trajectory was quite different. We conclude that during cyclic contractions the isotonic force-velocity curve of skeletal muscle sets an approximate boundary to the force-velocity trajectory, but the shape of this trajectory, and thus the distribution of power output, depends on the pattern of length change.

Low-temperature spectroscopy of isolated FMO-protein and a membrane-free reaction center complex from the green sulfur bacteriumChlorobium tepidum

We have isolated the water-soluble BChla-protein (FMO-protein) from the greer sulfur bacteriumChlorobium tepidum by a new procedure involving a salt-wash of isolated membranes at alkaline pH. The absorption spectrum of the isolated FMO-protein at 77 K was compared with that of a reaction-center complex containing the FMO-protein (FMO-RC complex) isolated fromC. tepidum following the procedure of Feiler U, Nitsche W and Michel H (1992) Biochemistry 31: 2608-2614. Oxidation or illumination of the FMO-RC complex caused bleaching of a component with a maximum at 836 nm which was not present in the purified FMO-protein.

The formation and characterization of the in vitro polymeric aggregates of bacteriochlorophyllc homologs fromChlorobium limicola in aqueous suspension in the presence of monogalactosyl diglyceride

Artificial aggregates of bacteriochlorophyllc (BChlc) were formed in an aqueous medium in the presence of a lipid, monogalactosyl diglyceride (MGDG), and the optical properties of those aggregates were studied by absorption and circular dichroism (CD) mainly. Four BChlc homologs, ([E,E]BChlc F, [P,E]BChlc F, [E,M]BChlc F and [I,E]BChlc F), were isolated from the green photosynthetic bacteriumChlorobium limicola strain 6230. Above 0.0004%, MGDG induced a red-shift of the absorption maxima of BChlc aggregates. At 0.003% MGDG BChlc aggregates showed absorption maxima in the range of 724 to 745 (±3) nm with a shift of 12 to 24 (±3) nm depending on the homolog species. Four kinds of BChlc-MGDG aggregates showed characteristic CD spectra. [E,M]BChlc F gave rise to a CD spectrum similar to that of chlorosomes, while the other three gave spectra of opposite sign. These aggregates are sensitive to 1-hexanol treatment; in a saturating amount (0.85%) of 1-hexanol, all the homologs gave a monomer-like absorption spectrum peaking at 670nm. At an intermediate concentration (0.5%), [E,M]BChlc F showed an enhanced CD intensity, as observed in native chlorosomes. Resonance Raman spectra of the monomer-like BChlc samples indicated that the keto vibrational band at ca. 1640 cm(-1) was considerably weakened by the 0.85% 1-hexanol treatment, however the 1680 cm(-1) band characteristic of a free keto group did not appear. These results indicate that the artificial aggregates formed by purified BChlc homologs and MGDG are good models for studying chlorosomes structure.

Reminiscence about'Chloropseudomonas ethylicum' and the FMO-protein

In 1961 the green sulfur bacterium-containing mixed culture known as'Chloropseudomonas ethylicum' was brought to Brookhaven National Laboratory (USA) from Moscow State University (USSR). The water-soluble bacteriochlorophylla-protein (FMO-protein) was extracted, purified and characterized by absorption and circular dichroism spectroscopy, by X-ray crystallography and by primary structure determination.

The apolipoprotein E/CI/CII gene cluster and late-onset Alzheimer disease

The chromosome 19 apolipoprotein E/CI/CII gene cluster was examined for evidence of linkage to a familial Alzheimer disease (FAD) locus. The family groups studied were Volga German (VG), early-onset non-VG (ENVG; mean age at onset < 60 years), and late-onset families. A genetic association was observed between apolipoprotein E (ApoE) allele epsilon 4 and FAD in late-onset families; the epsilon 4 allele frequency was .51 in affected subjects, .37 in at-risk subjects, .11 in spouses, and .19 in unrelated controls. The differences between the epsilon 4 frequencies in affected subjects versus controls and in at-risk subjects versus controls were highly significant (standard normal deviate [ZSND]) = 7.37, P < 10(-9); and ZSND = 4.07, P < .00005, respectively). No association between the epsilon 4 allele and FAD was observed in the ENVG or VG groups. A statistically significant allelic association between epsilon 4 and AD was also observed in a group of unrelated subjects; the epsilon 4 frequency was .26 in affected subjects, versus .19 in controls (ZSND = 2.20, P < .03). Evidence of linkage of ApoE and ApoCII to FAD was examined by maximum-likelihood methods, using three models and assuming autosomal dominant inheritance: (1) age-dependent penetrance, (2) extremely low (1%) penetrance, and (3) age-dependent penetrance corrected for sporadic Alzheimer disease (AD). For ApoCII in late-onset families, results for close linkage were negative, and only small positive lod-score-statistic (Z) values were obtained (model 1, maximum Z[Zmax] = 0.61, recombination fraction [theta] = .30; model 2, Zmax = 0.47, theta = .20). For ApoE in late-onset kindreds, positive Z values were obtained when either allele frequencies from controls (model 1, Zmax = 2.02, theta = .15; model 2, Zmax = 3.42, theta = .05) or allele frequencies from the families (model 1, Zmax = 1.43, theta = .15; model 2, Zmax = 1.70, theta = .05) were used. When linkage disequilibrium was incorporated into the analysis, the Z values increased (model 1, Zmax = 3.17, theta = .23; model 3, Zmax = 1.85, theta = .20). For the ENVG group, results for ApoE and ApoCII were uniformly negative. Affected-pedigree-member analysis gave significant results for the late-onset kindreds, for ApoE (ZSND = 3.003, P = .003) and ApoCII (ZSND = 2.319, P = .016), when control allele frequencies were used but not when allele frequencies were derived from the families.

Some empirical properties of an all-relative-pairs linkage test

Olson and Wijsman [Genet Epidemiol 10:87-102, 1993] recently proposed a single test of linkage which combines information from different types of relative pairs in a pedigree. Relative-pair-type-specific regression parameters that relate the squared pair trait difference to the estimated number of marker genes shared identical by descent between the pair are estimated using generalized estimating equation methodology, then combined to give a single linkage test statistic. Questions remain concerning the small sample and robustness properties of this test statistic; these questions are addressed in the present paper using simulation. The test is substantially anti-conservative for samples with fewer than about ten families and are approximately valid for samples larger than about 15 families. In addition, the test appears robust in the presence of trait genotype by environment interaction, trait family-specific errors, a second major trait locus, and trait dominance. Surprisingly, the sibpair test was more powerful than the all-relative-pairs test for dominant traits with high heritability. Finally, adjusting for the presence of a marker known to be linked to one trait locus only marginally improves the power for detecting a second trait locus.

Testing the Hardy-Weinberg law across strata

The problem of testing the Hardy-Weinberg law when data are sampled from several populations with different allele frequencies is considered. An odds-ratio representation of disequilibrium is proposed. This ratio is assumed to be constant across strata, an assumption that seems more reasonable than that of previous authors of a constant difference in true and expected (under equilibrium) heterozygote proportions. A score-type test which optimally combines information from the separate strata is then derived using the theory of unbiased estimating equations. Simulations show that the new test has greater power than previously proposed tests when the disequilibrium ratio is constant across strata. The method is applied to glyoxalase genotype data from populations in India.

Self-esteem and counterfactual thinking

Two studies examined the relation between self-esteem and counterfactual thinking (consideration of "might-have-been" alternatives to reality). Ss imagined themselves in scenarios with another actor that resulted in either success or failure. Ss then "undid" the outcome by altering events that preceded the outcome. Following success, high self-esteem (HSE) Ss were more likely than low self-esteem (LSE) Ss to mutate their own actions. Following failure, LSE Ss were more likely than HSE Ss to mutate their own actions. Also, the structure of counterfactuals was influenced by outcome valence but not by self-esteem: Subtractive structures (in which antecedents are removed) were elicited by success, whereas additive structures (in which antecedents are added) were elicited by failure. The importance of the self and individual differences in self-esteem to counterfactual thinking is discussed.

Cancer in twins of Wilms tumor patients

We interviewed families of 71 patients registered in the National Wilms Tumor Study and identified as having a twin sibling. Questions concerning zygosity and the occurrence of congenital anomalies and other forms of cancer in the twins were asked. Of the 71 twin pairs, 35 were dizygotic, 31 were monozygotic, and 5 were of unknown zygosity. The only pair concordant for Wilms tumor was dizygotic, leading to a heritability estimate of zero. In a monozygotic pair, one twin was diagnosed with Wilms tumor and the other with medulloblastoma. The estimated relative risk of Wilms tumor and childhood cancer in the co-twin was 250 times and 10 times the population rate, respectively. Four discordant pairs had a family history of Wilms tumor, suggesting that the penetrance of the condition is not complete. Because of the small sample size, caution should be exercised in the interpretation of these results.

Diabetes increases excretion of urinary malonaldehyde conjugates in rats

The effect of streptozotocin-induced diabetes on the urinary excretion of thiobarbituric acid test-positive materials was examined. In diabetic rats, urinary excretion of thiobarbituric acid reactive substances was increased 5-fold over that in nondiabetic animals. High-performance liquid chromatography of urine samples revealed that five of the six fractions previously found to be increased in vitamin E deficiency [Lee, H.-S., Shoeman, D.W., and Csallany, A.S. (1992) Lipids 27, 124-128] were also significantly increased in streptozotocin-induced diabetes. The data suggest that a high level of oxidative stress is induced by uncontrolled diabetes in rats.

Self-esteem and counterfactual thinking

Two studies examined the relation between self-esteem and counterfactual thinking (consideration of "might-have-been" alternatives to reality). Ss imagined themselves in scenarios with another actor that resulted in either success or failure. Ss then "undid" the outcome by altering events that preceded the outcome. Following success, high self-esteem (HSE) Ss were more likely than low self-esteem (LSE) Ss to mutate their own actions. Following failure, LSE Ss were more likely than HSE Ss to mutate their own actions. Also, the structure of counterfactuals was influenced by outcome valence but not by self-esteem: Subtractive structures (in which antecedents are removed) were elicited by success, whereas additive structures (in which antecedents are added) were elicited by failure. The importance of the self and individual differences in self-esteem to counterfactual thinking is discussed.

Wilms' tumour and parental age: a report from the National Wilms' Tumour Study

Age distributions of parents at birth of patients registered in the National Wilms' Tumour Study were compared to those of the general population. An increasing incidence of sporadic Wilms' tumour with increasing paternal age was found, with a relative risk of 2.1 of tumour in children of fathers over 55 compared to children of fathers younger than 20. A similar effect for maternal age was found, with a relative risk of 1.4 in children of mothers over 40 compared to children of mothers younger than 20. The maternal age effect was much weaker among patients registered later in the study; in the later, more completely ascertained cohort, paternal age appears to be the major contributor to the parental age effect. Little difference in paternal age distribution was found between patients with bilateral and unilateral tumour and between male and female patients. In contrast, patients with reported associated congenital anomalies, patients with evidence of nephrogenic rests, and patients with early or late age-of-onset of tumour had parents who were, on average, substantially older than the remainder. These findings lend support to the idea that many Wilms' tumours result from new germline mutations. Further, the histologic composition of such tumours may be sufficiently distinct as to provide a valuable diagnostic indicator of the etiology of these tumours.

Contractile properties of the striated adductor muscle in the bay scallop Argopecten irradians at several temperatures

The isometric and isotonic contractile properties of the cross-striated adductor muscle of the bay scallop (Argopecten irradians) were measured in vitro at 10, 15 and 20 degrees C. The length at which twitch force was maximal as a function of the closed length in situ (L0/Lcl) averaged 1.38 +/− 0.01 (mean +/− S.E.M.) at 10 degrees C. This length is very close to the typical length at maximum gape during natural swimming at this temperature. Passive force was very low over the range of lengths measured here; at L0, passive force averaged approximately 0.08 N cm-2, or only 0.5% of the corresponding peak twitch force. The mean peak isometric twitch force (Ptw,max) at 10 degrees C was 21.43 +/− 0.68 N cm-2 (S.E.M.), and the ratio of peak twitch force to tetanic force (Ptw,max/P0) averaged 0.89 +/− 0.01. Temperature did not affect either twitch force (Ptw), once fatigue was taken into account, or Ptw,max/P0. In contrast, the time-related properties of twitch contractions (latent period, tL; time to peak tension, tPtw; and time from peak tension to half-relaxation, t50%R) were positively modified by temperature at all temperatures measured (Q10 &gt; 1.8). All three properties were more temperature-sensitive over the range 10–15 degrees C than over the range 15–20 degrees C. The force-velocity relationships of the striated adductor muscle were fitted to the hyperbolic-linear (HYP-LIN) equation. The force-velocity curves of the striated adductor muscle of the scallop were strongly influenced by temperature. Maximal velocity at zero force (Vmax), and therefore maximal power output, increased significantly with temperature. The Q10 over the temperature range 10–15 degrees C (1.42) was significantly lower than that over the range 15–20 degrees C (2.41). The shape of the force-velocity relationship, assessed through comparisons of the power ratio (Wmax/VmaxP0), was not influenced by temperature.

Linkage analysis of Alzheimer's disease with methods using relative pairs

Four relative-pair methods for detecting genetic linkage were applied to familial Alzheimer's disease data. Results obtained using an extended Haseman-Elston test and a weighted rank pairwise correlation test, which both use information from all relative pairs, were consistent with previously published likelihood results and appear to be more powerful than affected sib pair methods.

Linkage between quantitative trait and marker loci: methods using all relative pairs

Relative-pair methods for detection of linkage between a quantitative trait and a marker locus have been proposed by a number of authors [e.g., Haseman and Elston, Behav Genet 3-19, 1972; Amos and Elston, Genet Epidemiol 349-360, 1989]. However, development of tests of significance that combine information from different types of relative pairs has been hampered by the presence of correlations between relative pairs from the same pedigree. In this paper, the methodology of generalized estimating equations is used to provide an estimate of the robust covariance matrix of the estimates of the set of relative-pair-type-specific regression parameters. Using this matrix, an asymptotically most powerful test of linkage which optimally combines the information contained in the different types of relative pairs is constructed. This test requires optimal weights that depend on unknown values of heritability and recombination fraction to be chosen a priori. However, simulations show that, in the regions of recombination fraction and heritability of practical interest, the power of the test does not depend strongly on the assumptions made when choosing the optimal weights; as a result, weights that depend only on the number of each type of relative pair and the variability of the marker identity-by-descent probabilities work well in practice. In addition, an approximation to the regression model leads to a simple approach to testing linkage in which only a single regression parameter is estimated from data containing different types of relative pairs. The resulting test is slightly less powerful than the test described above, but its computational simplicity and lack of dependence on a priori weighting schemes suggest potential usefulness in large linkage studies.

Dietary guar gum halts further renal enlargement in rats with established diabetes

Guar gum, a dietary fiber known to improve glucose tolerance, was fed to rats with established diabetes to determine its effect on renal enlargement and microalbuminuria. Diabetic rats were fed a modified AIN-76A (basal) diet for 4 wk, at which time half the rats continued to receive the same basal diet (DB-BA group) and half were switched to a 5% guar gum diet (DB-GG group). Nondiabetic rats fed the basal diet served as controls (NRL group). After 8 additional weeks the animals were killed. Glycated hemoglobin, a measure of long-term blood glucose control, was 14.4% in the DB-BA group and 12.4% in the DB-GG group, a statistically significant difference (P < 0.05). Kidney weight of the DB-BA group (3.51 g) was significantly greater than that of the DB-GG group (2.76 g) (P < 0.05). Eight weeks after induction of diabetes, 24-h urinary albumin excretion was highest in the DB-BA group and lowest in the NRL group; excretion in the DB-GG group (4 wk of guar feeding) was intermediate. However, by 12 wk no differences in albumin excretion among the groups were apparent. These results suggest that guar gum may be useful for slowing the progression of diabetic nephropathy and that guar gum deserves further study in this regard.

Aggregation of bacteriochlorophyll c homologs to dimers, tetramers, and polymers in water-saturated carbon tetrachloride

Three homologs of BChl c, 2-(R)-(1-hydroxyethyl)-4-n-propyl-5-ethyl-farnesyl BChl c (PEF-BChl c), 2-(R)-(1-hydroxyethyl)-4-ethyl-5-ethyl-farnesyl BChl c (EEF-BChl c), and 2-(S)-(1-hydroxyethyl)-4-isobutyl-5-methyl/ethyl-farnesyl BChl c (iBM/EF-BChl c), formed aggregates in water-saturated carbon tetrachloride (H2O-satd CCl4). The water content was about 100 times higher than that of the dried CCl4 previously used. Absorption spectra were recorded for 8 concentrations for the three homologs of BChl c and were deconvoluted in terms of standard spectra of monomer, dimer, tetramer and polymer (747-nm aggregate, Olson and Pedersen (1990) Photosynthe Res 25: 25). PEF- and EEF-BChl c formed dimers (680 nm maximum) and tetramers (705-710 nm maximum), but iBM/EF-BChl c formed polymers. Inhibition of dimer formation by water faciliated the study of the initial stages of the polymerization of BChl c. When the logarithm of polymer concentration was plotted versus the logarithm of the monomer concentration for iBM/EF-BChl c, the initial slope was 30±10 and indicated the cooperation of 20-40 BChl c molecules to form a polymer from a seed. Circular dichroism spectra of the polymers with positive and negative bands at 743 and 760 nm, respectively, were similar to those for chlorosomes (Brune et al. (1990) Photosynth Res 24: 253).

Mechanical performance of scallop adductor muscle during swimming

Mechanical performance of skeletal muscle has long been the subject of intense interest, but the details of in vivo performance of individual skeletal muscles during normal locomotion remain largely unknown. Performance in vitro has been described with considerable precision under simplified loading conditions. The force production and shortening velocity of most muscles, however, probably change continuously during natural movements. Therefore, modelling in vivo performance on the basis of in vitro contractile properties is subject to large degrees of uncertainty. Designing in vitro experiments that effectively examine the limits of mechanical performance requires increasing knowledge of precisely how muscles are used during normal movements. We report here measurements of the mechanical performance of the adductor muscle in scallops during jet-propulsion swimming. Swimming in scallops is powered solely by the striated portion of the single adductor muscle. Exploiting this simple locomotor morphology with simultaneous high-resolution measurements of pressure and flow rate, we have recorded nearly instantaneous measurements of the performance of a single skeletal muscle during normal locomotion.

Localization of the peripheral-type benzodiazepine binding site to mitochondria of human glioma cells

Subcellular fractionation was performed on human U251 glioblastoma cultures. In all subcellular fractions, the binding of the peripheral benzodiazepine ligand, [3H]PK 11195, correlated with the specific activity of monoamine oxidase (r = 0.95, p less than 0.001) and succinate dehydrogenase (r = 0.93, p less than 0.001), two mitochondrial enzymes. The specific activity of plasma membrane and nuclear markers correlated poorly with the presence of PK 11195 binding sites. These data support the mitochondrion as the primary location of peripheral-type benzodiazepine binding sites (PBBS) in human glioma cells. Mitochondria-rich preparations were then assayed for [3H]Ro5-4964 binding. Six nM [3H]Ro5-4964 failed to specifically bind to human U251 mitochondria, but bound vigorously to mitochondria from rat C6 glioma. These data indicate that the low affinity of Ro5-4864 for PBBS in human glioma cells compared to those in rat is due to interspecies receptor variation rather than impaired drug transport into human cells.

Psychological Barriers to Behavior Change: How to indentify the barriers that inhibit change

Adopting a healthy lifestyle often requires changing patterns of behavior. This article describes three categories of psychological barriers to behavior change: those that prevent the admission of a problem, those that interfere with initial attempts to change behavior, and those that make long-term change difficult. Strategies are identified that family physicians can use to overcome the barriers.

4-Isobutyl homologs of farnesyl bacteriochlorophyll c in carbon tetrachloride

Absorption (ABS) and circular dichroism (CD) spectra were recorded for 3 concentrations (2.3, 19 and ca. 75 μM) of 4-isobutyl homologs. Monomer spectra were the same as those for 4-n-propyl-5-ethyl farnesyl bacteriochlorophyll c. Pure polymer spectra were obtained by subtracting the 2.3-μM spectra appropriately scaled from the ca. 75-μM spectra. The polymer showed an ABS peak at 742 nm and a CD trough at ca. 742 nm. These properties are in harmony with the aggregate model proposed by Smith KM, Kehrs LA and Fajer J (1983, J Am Chem Soc 105: 1387-1389). A log-logplot of absorbance at 742 nm vs. monomer concentration could be fitted by a straight line of slope 1.6.

Monomers, dimers, and tetramers of 4-n-propyl-5-ethyl farnesyl bacteriochlorophyll c in dichloromethane and carbon tetrachloride

Absorption (ABS) and circular dichroism (CD) spectra were recorded for 6 concentrations (2.0-290 μM) of bacteriochlorophyll (BChl) c in each solvent. Monomer spectra were obtained by adding methanol (1:200) to each sample. The monomer showed an ABS peak and a CD trough at 664 nm in CH2Cl2 (ABS peak at 665 nm in CCl4). Dimer-plus-monomer spectra were obtained by subtracting high concentration (e.g., 290 μM) spectra appropriately scaled from lower concentration (e.g., 26 μM) spectra. Pure dimer spectra were then obtained by subtracting monomer spectra appropriately scaled from dimer-plus-monomer spectra. The dimer showed an ABS peak at 679 nm in both CH2Cl2 and CCl4 and a CD trough at ca. 670 nm in CH2Cl2. The optical properties of the dimer do not agree with the model for bacteriochlorophyllide d [Smith KM, Bobe FW, Goff DA and Abraham RJ (1986) J Am Chem Soc 108: 1111-1120]. Higher aggregate spectra were obtained by subtracting appropriately scaled monomer and dimer spectra from high concentration (e.g., 290 μM) spectra. The aggregate showed ABS shoulders at ca. 636 and 678 nm with a peak at 702 nm in CH2Cl2 and at 708 nm in CCl4; the CD spectrum in either solvent showed peaks at 638 and 679 nm with troughs at 658 and ca. 710 nm. These spectra are consistent with an excitonic interaction between 4 chromophores in the aggregate. Each of the 12 original ABS spectra was deconvoluted in terms of the appropriate monomer, dimer and aggregate spectra, and the concentrations of each component were determined. Plots of log aggregate concentration vs. log dimer concentration lay on or near a line of slope 1.9 for CH2Cl2 and on or near a line of slope 2.1 for CCl4. The aggregate was thus shown to be a tetramer. The theoretical relationship between dimers and monomers (slope 2.0) was not observed in all cases.

The amino acid sequence of a major protein component in the light harvesting complex of the green photosynthetic bacterium Chlorobium limicola f. thiosulfatophilum

A 7.5-kDa protein has been isolated from chlorosomes of Chlorobium limicola f. thiosulfatophilum and the complete primary structure determined by a combination of automatic Edman degradation and plasma desorption mass spectrometry. The 74-residue protein shows great homology to a similar protein of unknown function which has been isolated from Pelodictyon luteolum but otherwise no significant homology to other proteins can be found. The possible role of the protein in the structure and function of the chlorosome is discussed.

Monte Carlo comparison of preliminary methods for ordering multiple genetic loci

We carried out a simulation study to compare the power of eight methods for preliminary ordering of multiple genetic loci. Using linkage groups of six loci and a simple pedigree structure, we considered the effects on method performance of locus informativity, interlocus spacing, total distance along the chromosome, and sample size. Method performance was assessed using the mean rank of the true order, the proportion of replicates in which the true order was the best order, and the number of orders that needed to be considered for subsequent multipoint linkage analysis in order to include the true order with high probability. A new method which maximizes the sum of adjacent two-point maximum lod scores divided by the equivalent number of informative meioses and the previously described method which minimizes the sum of adjacent recombination fraction estimates were found to be the best overall locus-ordering methods for the situations considered, although several other methods also performed well.

Bacteriochlorophyll c monomers, dimers, and higher aggregates in dichloromethane, chloroform, and carbon tetrachloride

Bacteriochlorophyll c in vivo is a mixture of at least 5 homologs, all of which form aggregates in CH2Cl2, CHCl3 and CCl4. Three homologs exist mainly in the 2-R-(1-hydroxyethyl) configuration, whereas the other two homologs, 4-isobutyl-5-ethyl and 4-isobutyl-5-methyl farnesyl bacteriochlorophyll c, exist mainly in the 2-S-(1-hydroxyethyl) configuration (Smith KM, Craig GW, Kehres LA and Pfennig N (1983) J. Chromatograph. 281: 209-223). In CCl4 the S-homologs form an aggregate of 2-3 molecules whose absorption (747 nm maximum) and circular dichroism spectra resemble those of the chlorosome. In CH2Cl2, CHCl3 and CCl4 the 4-n-propyl homolog (R-configuration) forms dimers absorbing at ca. 680 nm and higher aggregates absorbing at 705-710 nm. In CCl4 the dimerization constant is approx. 10 µM(-1) (1000 times that for chlorophyll a). The difference between the types of aggregates formed by the 4-n-propyl and 4-isobutyl homologs is attributed to the difference between the R- and S-configurations of the 2-(1-hydroxyethyl) groups in each chlorophyll.

Fluorescence lifetimes of dimers and higher oligomers of bacteriochlorophyll c from Chlorobium limicola

Fluorescence lifetimes have been measured for bacteriochlorophyll (BChl) c isolated from Chlorobium limicola in different states of aggregation in non-polar solvents. Two different homologs of BChl c were used, one with an isobutyl group at the 4 position, the other with n-propyl. Species previously identified as dimers (Olson and Pedersen 1990, Photosynth Res, this issue) decayed with lifetimes of 0.64 ns for the isobutyl homolog, 0.71 ns for n-propyl. Decay-associated spectra indicate that the absorption spectrum of the isobutyl dimer is slightly red-shifted from that of the n-propyl dimer. Aggregates absorbing maximally at 710 nm fluoresced with a principal lifetime of 3.1 ns, independent of the homolog used. In CCl4, only the isobutyl homolog forms a 747-nm absorbing oligomer spectrally similar to BChl c in vivo. This oligomer shows non-exponential fluorescence decay with lifetimes of 67 and 19 ps. Because the two components show different excitation spectra, the higher oligomer is probably a mixture of more than one species, both of which absorb at ∼747 nm.

Circular dichroism of green bacterial chlorosomes

Positive and negative bands in previously measured circular dichroism (CD) spectra of Chlorobium limicola chlorosomes appeared to be sign-reversed relative to those of Chloroflexus aurantiacus chlorosomes in the 740-750 nm spectral region where bacteriochlorophyll (BChl) c absorbs maximally. It was not clear, however, whether this difference was intrinsic to the chlorosomes or was due to differences in the procedures used to prepare them. We therefore repeated the CD measurements using chlorosomes isolated from both Cb. limicola f. thiosulfatophilum and Cf. aurantiacus using the method of Gerola and Olson (1986, Biochim. Biophys. Acta 848: 69-76). Contrary to the earlier results, both types of chlorosomes had very similar CD spectra, suggesting that both have similar arrangements of BChl c molecules. The previously reported difference between the CD spectra of Chlorobium and Chloroflexus chlorosomes is due to the instability of Chlorobium chlorosomes, which can undergo a hypsochromic shift in their near infrared absorption maximum accompanied by an apparent inversion in their near infrared CD spectrum during isolation. Treating isolated chlorosomes with the strong ionic detergent sodium dodecylsulfate, which removes BChl a, does not alter the arrangement of BChl c molecules in either Chloroflexus or Chlorobium chlorosomes, as indicated by the lack of an effect on their CD spectra.