Monte Carlo and Poisson–Boltzmann calculations of the fraction of counterions bound to DNA

The counterion density and the condensation region around DNA have been examined as functions of both ion size and added-salt concentration using Metropolis Monte Carlo (MC) and Poisson–Boltzmann (PB) methods. Two different definitions of the “bound” and “free” components of the electrolyte ion atmosphere were used to compare these approaches. First, calculation of the ion density in different spatial regions around the polyelectrolyte molecule indicates, in agreement with previous work, that the PB equation does not predict an invariance of the surface concentration of counterions as electrolyte is added to the system. Further, the PB equation underestimates the counterion concentration at the DNA surface, compared to the MC results, the difference being greatest in the grooves, where ionic concentrations are highest. If counterions within a fixed radius of the helical axis are considered to be bound, then the fraction of polyelectrolyte charge neutralized by counterions would be predicted to increase as the bulk electrolyte concentration increases. A second categorization—one in which monovalent cations in regions where the average electrostatic potential is ledd than ?kT are considered to be bound—provides an informative basis for comparison of MC and PB with each other and with counterion-condensation theory. By this criterion, PB calculations on the B from of DNA indicate that the amount of bound counterion charge per phosphate group is about .67 and is independent of salt concentration. A particularly provocative observatiob is that when this binding criterion is used, MC calculations quantitatively reproduce the bound fraction predicated by counterion-condensation theory for all-atom models of B-DNA and A-DNA as well as for charged cylindera of varying lineat charge densities. For example, for B-DNA and A-DNA, the fractions of phosphate groups neutralized by 2 Å hard sphere counterions are 0.768 and .817, respectively. For theoretical studies, the rediys enclosing the region in which the electrostatic potential is calculated studies, the radius enclosing the region in which the electrostatic potential is calculated to be less than ?kT is advocated s a more suitable binding or condensation radius that enclosing the fraction of counterions given by (1 – ξ^?1). A comparsion of radii calculated using both of these definitions is presented. © 1994 John Wiley & Sons, Inc.     

Peptide crystal growth via sulfonate salt formation: The structure of bis-glycylglycine-1,5-naphthalenedisulfonate hydrate

Summary Continuing a line of investigations on methods for formation and growth of high-quality crystals of peptides, the glycylglycine sequence has been crystallized by evaporation methods as a salt with 1,5-naphthalenedisulfonic acid. The structure of the peptide is highly extended, and is conformationally quite similar to the structures which have been characterized for other zwitterionic and salt forms of this sequence. Thus, crystallization as a salt with this sulfonic acid has imposed no undue influence upon the molecular conformation. These results offer further indication that the preparation of peptide sulfonate salts, particularly with arene templates, may have broad general utility for crystallization of interesting sequences which until now have not been approachable in their zwitterionic forms.     

Dietary circumvention of acorn tannins by blue jays

Blue jays consume large quantities of acorns to fuel energy-demanding caching flights in the fall. Yet blue jays possess no known physiological adaptation to counter the negative effects of a high tannin diet on protein digestion. Dietary experiments were conducted to determine if blue jays could subsist on an acorn-only diet, and if they could not, to determine whether supplements of acorn weevil larvae (Curculio), present inside acorns, enabled them to maintain their mass. Comparative tannin assays also were conducted on Lepidobalanus (low tannin; white oak) and Erythrobalanus (high tannin; pin oak) acorns using radial diffusion assay. Captive jays consumed considerable acorn material, yet were unable to maintain mass on ad lib. acorn-only diets or on an acorn +1.5 g larvae/day supplement. There were no significant differences in mass loss between high and low tannin diets. In contrast, blue jays were able to stabilize mass on a diet of acorns +5.0 g larvae supplement/day. These results suggest that acorn weevil larvae, or perhaps other insects, counteract the effects of acorn tannins in the jay diet allowing jays to subsist largely on acorns during the fall caching season. Oak demographic processes may be partly regulated by a tri-trophic relationship among plant, insect and bird. Acorn weevil larvae, considered damaging to oak populations, may actually facilitate oak recruitment and population vagility in the long-term.     

Interpreting the role of phosphorus and growth rate in enhanced fungal induction of sesquiterpenes from Hyoscyamus muticus root cultures

The effect of thiamine limitation in combination with fungal elicitation on sesquiterpene (solavetivone) production was studied in Agrobacterium-transformed hairy-root cultures of Hyoscyamus muticus as a potential means of manipulating the growth rate independent of phosphorus availability. Limiting the initial supply of thiamine did not affect the growth of these cultures compared to growth at the control level of thiamine (0.01 g/l). There was also no enhancement in sesquiterpene production when thiamine supply was limited. Serial culturing in thiamine-free media suggests that these root cultures are not strictly auxotrophic for thiamine, in contrast to previously published results for untransformed root culture. The effect of phosphate limitation combined with elicitation on the production of solavetivone was examined at constant media volume to provide a constant elicitor concentration and to eliminate feedback-inhibition effects. Limiting the initial supply of phosphate to elicited cultures resulted in a twofold increase in solavetivone production as compared to the elicitation at control media phosphate levels (1.1mm). Because growth was attenuated, production per unit cell mass increased 11-fold compared to the control. The effect of phosphate limitation on solavetivone production at constant cell mass and elicitor per root mass was studied. Limiting the initial supply of phosphate to elicited cultures under these conditions did not result in enhanced production of solavetivone. The initially observed enhanced production of solavetivone at limiting initial phosphate concentrations is therefore due to factors other than the growth rate or phosphate involvement in secondary metabolism. Correspondence to: W. R. Curtis     

Structure of the intergenic spacer region from the ribosomal RNA gene family of white spruce (Picea glauca)

Five genomic clones containing ribosomal DNA repeats from the gymnosperm white spruce (Picea glauca) have been isolated and characterized by restriction enzyme analysis. No nucleotide variation or length variation was detected within the region encoding the ribosomal RNAs. Four clones which contained the intergenic spacer (IGS) region from different rDNA repeats were further characterized to reveal the sub-repeat structure within the IGS. The sub-repeats were unusually long, ranging from 540 to 990 bp but in all other respects the structure of the IGS was very similar to the organization of the IGS from wheat, Drosophila and Xenopus.     

Linkage analysis of idiopathic generalized epilepsy (IGE) and marker loci on chromosome 6p in families of patients with juvenile myoclonic epilepsy: no evidence for an epilepsy locus in the HLA region.

Evidence for a locus (EJM1) in the HLA region of chromosome 6p predisposing to idiopathic generalized epilepsy (IGE) in the families of patients with juvenile myoclonic epilepsy (JME) has been obtained in two previous studies of separately ascertained groups of kindreds. Linkage analysis has been undertaken in a third set of 25 families including a patient with JME and at least one first-degree relative with IGE. Family members were typed for eight polymorphic loci on chromosome 6p: F13A, D6S89, D6S109, D6S105, D6S10, C4B, DQA1/A2, and TCTE1. Pairwise and multipoint linkage analysis was carried out assuming autosomal dominant and autosomal recessive inheritance and age-dependent high or low penetrance. No significant evidence in favor of linkage was obtained at any locus. Multipoint linkage analysis generated significant exclusion data (lod score < -2.0) at HLA and for a region 10-30 cM telomeric to HLA, the extent of which varied with the level of penetrance assumed. These observations indicate that genetic heterogeneity exists within this epilepsy phenotype.     

A large, dominant pedigree of atrioventricular septal defect (AVSD): exclusion from the Down syndrome critical region on chromosome 21.

We describe a large pedigree of individuals with autosomal dominant atrioventricular septal defect (AVSD). The pedigree includes affected individuals and individuals who have transmitted the defect but are not clinically affected. AVSDs are a rare congenital heart malformation that occurs as only 2.8% of isolated cardiac lesions. They are the predominant heart defect in children with Down syndrome, making chromosome 21 a candidate for genes involved in atrioventricular septal development. We have carried out a linkage study in the pedigree by using 10 simple-sequence polymorphisms from chromosome 21. Multipoint linkage analysis gives lod scores of less than -2 for the region of trisomy 21 associated with heart defects, which excludes a locus within this region as the cause of the defect in this family.