Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids

Background  

Cichlid fish from East Africa are remarkable for phenotypic and behavioral diversity on a backdrop of genomic similarity. In 2006, the Joint Genome Institute completed low coverage survey sequencing of the genomes of five phenotypically and ecologically diverse Lake Malawi species. We report a computational and comparative analysis of these data that provides insight into the mechanisms that make closely related species different from one another.     

AnCF, the CCAAT Binding Complex of Aspergillus nidulans, Contains Products of the hapB, hapC, and hapE Genes and Is Required for Activation by the Pathway-Specific Regulatory Gene amdR

CCAAT binding factors (CBFs) positively regulating the expression of the amdS gene (encoding acetamidase) and two penicillin biosynthesis genes (ipnA and aatA) have been previously found in Aspergillus nidulans. The factors were called AnCF and PENR1, respectively. Deletion of the hapC gene, encoding a protein with significant similarity to Hap3p of Saccharomyces cerevisiae, eliminated both AnCF and PENR1 binding activities. We now report the isolation of the genes hapB and hapE, which encode proteins with central regions of high similarity to Hap2p and Hap5p of S. cerevisiae and to the CBF-B and CBF-C proteins of mammals. An additional fungus-specific domain present in HapE was revealed by comparisons with the homologs from S. cerevisiae, Neurospora crassa, and Schizosaccharomyces pombe. The HapB, HapC, and HapE proteins have been shown to be necessary and sufficient for the formation of a CCAAT binding complex in vitro. Strains with deletions of each of the hapB, hapC, and hapE genes have identical phenotypes of slow growth, poor conidiation, and reduced expression of amdS. Furthermore, induction of amdS by omega amino acids, which is mediated by the AmdR pathway-specific activator, is abolished in the hap deletion mutants, as is growth on γ-aminobutyric acid as a sole nitrogen or carbon source. AmdR and AnCF bind to overlapping sites in the promoters of the amdS and gatA genes. It is known that AnCF can bind independently of AmdR. We suggest that AnCF binding is required for AmdR binding in vivo.     

AN ULTRASTRUCTURAL STUDY OF SPERMATIUM FORMATION IN THE RUST FUNGUS GYMNOSPORANGIUM JUNIPERI-VIRGINIANAE

Spermatium formation in G. juniperi-virginianae is phialidic. The spermatia are blown out of the tips of spermatiophores which possess a thickened neck region and a distinct, flared collarette. Each spermatium initial is surrounded by a thin wall which is attached to the inner surface of the spermatiophore wall just below the thickened neck region. A spermatium is delimited by a centripetally developing septum and then pushed into the spermogonial cavity by the next spermatium initial. Mature spermatia are ellipsoid with tapered ends and are surrounded by a thin wall. Each contains a single nucleus, many ribosomes, a few small vacuoles, and a number of lipid bodies and mitochondria.     

Zinc metabolism in humans: a kinetic model

The development and testing of an integrated kinetic model describing both short and long term zinc metabolism in humans is discussed. The development took place in two stages. The first, based on a five day turnover study, details the early phases of zinc metabolism in several body tissues together with absorption and excretion. This model, however, accounts for only 10% of total body zinc. To describe the kinetics of total body zinc, a long term model which contains a reduced version of the five day model was developed. This model required an additional compartment for the liver system, but as postulated in the short term model, 90% of body zinc turns over slowly in a single compartment. The models are then used to describe the effect on zinc metabolism of different disease states and lietary perturbations. These additional studies enhance the models' validity while providing physiological insights.     

Local and global anatomy of antibody‐protein antigen recognition

Deciphering antibody‐protein antigen recognition is of fundamental and practical significance. We constructed an antibody structural dataset, partitioned it into human and murine subgroups, and compared it with nonantibody protein‐protein complexes. We investigated the physicochemical properties of regions on and away from the antibody‐antigen interfaces, including net charge, overall antibody charge distributions, and their potential role in antigen interaction. We observed that amino acid preference in antibody‐protein antigen recognition is entropy driven, with residues having low side‐chain entropy appearing to compensate for the high backbone entropy in interaction with protein antigens. Antibodies prefer charged and polar antigen residues and bridging water molecules. They also prefer positive net charge, presumably to promote interaction with negatively charged protein antigens, which are common in proteomes. Antibody‐antigen interfaces have large percentages of Tyr, Ser, and Asp, but little Lys. Electrostatic and hydrophobic interactions in the Ag binding sites might be coupled with Fab domains through organized charge and residue distributions away from the binding interfaces. Here we describe some features of antibody‐antigen interfaces and of Fab domains as compared with nonantibody protein‐protein interactions. The distributions of interface residues in human and murine antibodies do not differ significantly. Overall, our results provide not only a local but also a global anatomy of antibody structures.     

VARIATION IN THE OCCURRENCE OF EXTERNAL CARBONIC ANHYDRASE AMONG STRAINS OF THE MARINE DIATOM PHAEODACTYLUM TRICORNUTUM (BACILLARIOPHYCEAE)1

Eleven different strains of Phaeodactylum tricornutum Bohlin were obtained from three culture collections and were examined for the presence of external and internal carbonic anhydrase (CA). Cells of all strains, grown in standing culture at alkaline pH and low, dissolved inorganic carbon had internal CA, but only eight were found to have external CA. External CA activity was reduced when cultures were bubbled with air and was completely repressed when they were grown on 5% CO₂. Expression of external CA activity appears to be regulated by CO₂ concentration in the growth medium, but within one species, there appears to be a variation in occurrence of external CA and consequently in the mode of inorganic carbon acquisition.     

Production of antibody to lipopolysaccharide (LPS) after immunization with a LPS-polymyxin B-agarose immunogen

A method was devised to produce antibodies to lipopolysaccharide (LPS) in guineapigs following a single immunization, The antigen was prepared by mixing polymyxin B-agarose with LPS from Escherichia coli O55:B5. Use of the agarose support allowed purification of the complex by simple washing procedures. Twenty-nine days after a single injection of the immunogen mixed with Freund complete adjuvant all animals demonstrated antibody to the LPS portion of the complex. No antibodies were detected to the polymyxin B component. Typical titres of LPS as measured by ELISA were 2¹¹. After, a booster immunization, titres of LPS antibody were further inceased and a greater avidity was noted. In contrast to other methods which have been employed for production of antibody to LPS, use of the polymyxin B-agarose complex has the following advantages: ease of antigen preparation, ready purification of the complex, potent immunostimulation, and under the conditions employed here, LPS-specific antibody production, without accompanying antibody to polymyxin B.