Prediction of the three-dimensional structure of the rap-1A protein from its homology to theras-gene-encoded p21 protein

rap-1A, an anti-oncogene-encoded protein, is aras-p21-like protein whose sequence is over 80% homologous to p21 and which interacts with the same intracellular target proteins and is activated by the same mechanisms as p21, e.g., by binding GTP in place of GDP. Both interact with effector proteins in the same region, involving residues 32–47. However, activated rap-1A blocks the mitogenic signal transducing effects of p21. Optimal sequence alignment of p21 and rap-1A shows two insertions of rap-1A atras positions 120 and 138. We have constructed the three-dimensional structure of rap-1A bound to GTP by using the energy-minimized three-dimensional structure ofras-p21 as the basis for the modeling using a stepwise procedure in which identical and homologous amino acid residues in rap-1A are assumed to adopt the same conformation as the corresponding residues in p21. Side-chain conformations for homologous and nonhomologous residues are generated in conformations that are as close as possible to those of the corresponding side chains in p21. The entire structure has been subjected to a nested series of energy minimizations. The final predicted structure has an overall backbone deviation of 0.7 å from that ofras-p21. The effector binding domains from residues 32–47 are identical in both proteins (except for different side chains of different residues at position 45). A major difference occurs in the insertion region at residue 120. This region is in the middle of another effector loop of the p21 protein involving residues 115–126. Differences in sequence and structure in this region may contribute to the differences in cellular functions of these two proteins.     

Does Weeding Promote Regeneration of an Indigenous Tree Community in Felled Pine Plantations in Uganda?

The use of plantations to manage extensive tracks of deforested lands in the tropics is a conservation strategy that has recently received considerable attention. Plantation trees can promote seed dispersal by attracting dispersers and creating favorable site conditions, leading to increased germination and establishment of indigenous trees. Subsequently, plantation trees can be harvested for profit or left to senesce, leaving a native tree community. We evaluated the effect of vine, grass, and shrub cutting (weeding) over a 3‐year period on regeneration of indigenous trees subsequent to the removal of plantation softwoods in Kibale National Park, Uganda. Counter to what would be expected if weeding released trees from competition, we found no difference in the total number of stems or in the stems greater than 10 cm diameter at breast height between control and weeded plots; there were more stems greater than 1 cm diameter at breast height in the control plots. For species found in both control and weeded plots, the maximum size of individuals did not differ. At the end of the study, 61 species were found in the control plots and 43 species were found in the weeded plots, and in both types of plots the three most abundant species were the same. The number of species and stems classified as early or middle successional species did not differ between weeded and control plots. The fact that weeding did not promote regeneration of indigenous trees after the removal of plantation trees illustrates the importance of evaluating and field‐testing potential management options.     

Effect of phenolic acids and phenolics from plant cell walls on rumenlike fermentation in consecutive batch culture

Information on the interaction between mixed populations in the rumen and plant phenolics is required to fully elucidate the limitations of phenolic compounds on forage digestibility. The objective of this study was to examine the degradation of Italian ryegrass (Lolium multiflorum L.) hay incubated with mixed ruminal populations in consecutive batch culture (CBC) with or without phenolic acids or phenolic compounds extracted from plant cell walls. Each CBC consisted of a series of 10 cultures (3 replicates per culture) inoculated (10%, vol/vol) in sequence at 48-h intervals with microbial suspension from the previous set of cultures. All cultures were grown on a semidefined medium containing Italian ryegrass hay, and each CBC was initiated with an inoculum from the rumen. Rumenlike fermentation characteristics were maintained in control CBCs by repeated inoculum transfer. Treatment CBCs were transferred as described above, but cultures 5, 6, and 7 were incubated in the presence of trans-p-coumaric, cis-p-coumaric, or trans-ferulic acid or phenolics extracted from the cell walls of maize stem or barley straw. Mean apparent dry matter disappearance in control CBC cultures was 495 mg per g of hay, whereas the presence of phenolics reduced the initial dry matter disappearance by 6.3 to 25.6%. trans-p-Coumaric acid and, to a lesser extent, the phenolics from cell walls of maize stem were the most inhibitory compounds for dry matter disappearance and for the production of volatile fatty acids; trans-p-coumaric acid altered the molar ratio of acetate/propionate/butyrate. The CBC further showed variations in the ability of the rumen microbial population to adapt to phenolic compounds.     

The osmotic/calcium stress theory of brain damage: Are free radicals involved?

This overview presents data showing that glucose use increases and that excitatory amino acids (i.e., glutamate, aspartate), taurine and ascorbate increase in the extracellular fluid during seizures. During the cellular hyperactive state taurine appears to serve as an osmoregulator and ascorbate may serve as either an antioxidant or as a pro-oxidant. Finally, a unifying hypothesis is given for seizure-induced brain damage. This unifying hypothesis states that during seizures there is a release of excitatory amino acids which act on glutamatergic receptors, increasing neuronal activity and thereby increasing glucose use. This hyperactivity of cells causes an influx, of calcium (i.e. calcium stress) and water movements (i.e., osmotic stress) into the cells that culminate in brain damage mediated by reactive oxygen species.Special issue dedicated to Dr. Frederick E. Samson     

Effects of non-MHC loci on resistance to retrovirus-induced immunodeficiency in mice

Mice of certain strains are highly sensitive to development of a severe immunodeficiency disease following inoculation as adults with LP-BM5 murine leukemia viruses (MuLV) whereas others are extremely resistant. These strain-dependent differences in response to infection have been shown to be genetically determined with resistance to disease being, in general, associated with homozygosity for Fv-1 ⁿand H-2 haplotypes a and d and sensitivity with homozygosity for Fv-1 ^band other H-2 haplotypes including b, s, and q. The Fv-1 ^b, H-2 ^rstrain RIIIS/J (RIIIS) was found to be highly resistant to disease even though B10.RIII(71NS)/J (B10.RIII), also H-2 ^r, was very sensitive, thus excluding a role for H-2 in the resistance of RIIIS. The characteristics of RIIIS resistance were evaluated in studies of infected (B10.RIII×RIIIS) F₁, F₂ and reciprocal backcross mice. Resistance to disease was shown to be semidominant and determined by more than one gene, although a preponderant influence of a single gene was suggested. Studies of segregating populations showed that resistance was not associated with or linked to polymorphisms of the V _\complex or genes in proximity to the Emv-2 locus on chromosome 8. However, there was almost complete concordance between absence of disease in infected mice and inhibition of ecotropic virus spread. These results demonstrate that genes other than Fv-1 or H-2 can profoundly influence the development of retrovirus-induced immunodeficiency and replication of ecotropic viruses.Abbreviations MuLV murine leukemia virus - MCF mink cell focus-inducing MuLV - B6 C57BL/6 - BM5d the defective virus in LP-BM5 MuLV - MAIDS murine acquired immunodeficiency syndrome - RIIIS RIIIS/J - B10.RIII B10.RIII (71NS)/J - MLR mixed lymphocyte reaction - FACS fluorescence activated cell sorter     

pH-dependent processes in proteins

Recent improvements in the understanding of electrostatic interactions in proteins serve as a focus for the general topic of pH-dependent processes in proteins. The general importance of pH-dependent processes is first set out in terms of hydrogen ion equilibria, stability, ligand interactions, assembly, dynamics, and events in related molecular systems. The development of various theoretical treatments includes various formalisms in addition to the solvent interface model developed by Shire et al. as an extension of the Tanford-Kirkwood treatment. A number of detailed applications of the model are presented and future potentialities are sketched.