The barbs (Barbus spp.) of Lake Tana: a forgotten species flock?

Synopsis All living species occupy an ecological niche, and are positioned within a trophic hierarchy. Extinct organisms presumably held similar behavioral and coevolutionary characteristics in the past, and were susceptible to the same kinds of natural ecological pressures operating today. Paleoecological investigations are limited by the incompleteness of the fossil record, and particularly by a lack of behavioral data that are so fundamental to ecological studies of living communities and habitats. Opportunities to examine the coevolutionary structure of ancient communities from empirical data are extremely rare. One such opportunity is provided by the Lower Cretaceous Santana Formation of north-eastern Brazil, a series of richly fossiliferous strata approximately 110 million years old. Many fossil fishes from the Santana Formation contain identifiable prey, including decapod crustaceans and fishes. A trophic hierarchy of these organisms is reconstructed here, and their ecological relationships are discussed. Comparison is made with a similar fish fauna from the Upper Jurassic Solnhofen Limestone of Germany. Low-level, intermediate and high-level predators are identified in each fauna. Predator-prey relationships in the Santana fauna are strongly hierarchical, and are more focussed at the intermediate predator level than in Solnhofen. Comparison with a model of predator-prey relationships between fishes and benthic fauna of the Baltic Sea (which like the Araripe Basin represents a semi-enclosed environment) suggests that heavy predation on teleosts such asRhacolepis, occupying an intermediate trophic level, may have permitted benthic decapods to proliferate and exclude other benthic organisms. Less intense predation on fishes at the intermediate trophic level would allow their numbers to increase, thereby increasing the intensity of predation on the benthos at the base of the trophic hierarchy.     

Slow conformational exchange in DNA minihairpin loops: A conformationalstudy of the circular dumbbell d〈pCGC-TT-GCG-TT〉

In recent years various examples of highly stable two-residue hairpin loops (miniloops) in DNA have been encountered. As the detailed structure and stability of miniloops appear to be determined not only by the nature and sequence of the two bases in the loop, but also by the closing base pair, it is desirable to carry out in-depth studies of especially designed small model DNA compounds. Therefore, a circular DNA dumbbell-like molecule is tailored to consist of a stem of three Watson–Crick base pairs, flanked on each side by a minihairpin loop. The resulting circular DNA decanter 5′-d〈pCGC- TT-GCG- TT〉 -3′ ( I ) is studied in solution by means of nmr spectroscope. At a temperature of 269 K the molecule occurs in a 50/50 mixture of two dumbbell structures (denoted L2L2 and L2L4). L2L2 contains three Watson–Crick C-G base pairs and two two-residue loops (H2-family type) in opposite parts of the molecule. On raising the temperature from 269 to 314 K. The L2L4 conformer becomes increasingly dominant (95% at 314 K). This conformer has a partially disrupted closing G-C base pair in the 5′-GTTC-3′ loop with only one remaining solvent-accessible hydrogen bond between NH_α of the cytosine C(1) and O6 of the guanine G(8), whereas the opposite 5′-CTTG-3′ loop remains stable. The disruption of the C(1)-G(8) base pair in the L2L4 form is correlated with the presence of a syn orientation for the C(1) base at the 5′-3′ loop-stem junction in the 5′-GTTC-3′ loop. The two conformers. L2L2 and L2L4, occur in slow equilibrium (2–20 s^?1). Moderate line broadening of specific ¹H, ¹³C, and ³¹P resonances of residues C(1), G(8), T(9), and T(10) at low temperatures, due to chemical exchange between L2L2 and L2L4, show that the interconversion from an anti to syn conformer in residue C(1) has a small local effect on the structure of the dumbbell. T₁ relaxation measurements, chemical-shift considerations, and complete hand-shape calculations of the exchange process of the G(8) imino proton reveal a possibility for the existence of multiconformational slates in the anti–syn equilibrium. © 1995 John Wiley & Sons, Inc.     

Interaction of 3'-fluoro-3'-deoxyanalogs of a trimer of (2'-5')oligoadenylic acid with (2'-5')A3-antibodies: stereochemical aspect

Mouse antibodies to (2'-5')oligoadenylates were obtained by the immunization of animals with the (2'-5')oligoadenylic acid trimer conjugated with bovine serum albumin through a 2',3'-levulinic acid residue. Using radioimmunoassay, the reactivity of mouse polyclonal antibodies to the (2'-5')oligoadenylic acid trimer was studied for the trimer analogues containing 9-(3-deoxy-3-fluro-beta-D- xylofuranosyl)adenine and 3'-deoxy-3'-fluoro-adenosine in various positions of the chain. It was found that (a) the three-dimensional structure of short oligonucleotides is an important factor in the antibody recognition; (b) antibodies are more sensitive to modifications of the 5'-terminal and central ribose fragments of the (2'-5')oligoadenylic acid trimer; (c) the 3'-hydroxyl group plays a secondary role in the formation of the antigen determinant.     

Larval growth patterns in Cyprinus carpio and Clarias gariepinus with attention to the finfold

During the larval period, most teleost fishes undergo a dramatic change in body form. Most functional systems are incomplete at hatching. Rapid development of swimming, feeding and respiration systems are expected. In this study, growth patterns of morphological characteristics related to these three functions were studied in two species of Ostariophysian teleosts: African catfish Clarias gariepinus and common carp Cyprinus carpio . Special attention was paid to the larval finfold, which is a remarkably common feature of fish larvae. The results confirmed that larval growth shows different phases. Many morphological characters showed fast allometric growth in early larvae, followed by isometric growth after an inflexion point. In carp, all larval growth curves showed such inflexion points at a total length of about 7 mm while in Clarias such a coupling was not found. The inflexion points in carp occur at a stage during which the typical larval swimming style changes towards the adult swimming style.     

Non-radioactive in situ hybridization for the detection of cytomegalovirus infections

Summary Acetylaminofluorene (AAF) modified cytomegalovirus (CMV) DNA probes have been applied for the rapid detection of CMV genomes by non-radioactive in situ hybridization in routinely obtained pathological material. To establish proper protocols, AAF modified mouse satellite DNA and mouse liver were used to investigate the procedural variables. Among these were type and time of fixation, glass slide coating for improved tissue adherence, protease permeabilization of sections, type and time of denaturation and hybridization, probe concentration, post-hybridization washing conditions and immunocytochemical detection. This research has led to a user-friendly procedure which, in addition to cells displaying a cytopathological effect typical for CMV infection detects with high sensitivity CMV carrying cells that show no histo-pathological alterations. It can be readily applied in routine clinical-diagnostic laboratories.Dedicated to Professor Dr. T.H. Schiebler on the occasion of his 65th birthdaySubsidized in part by Het Praeventiefonds, The Hague, The Netherlands (project no. 28-801)     

Eimeria refractile body proteins contain two potentially functional characteristics: Transhydrogenase and carbohydrate transport

Abstract cDNA encoding an immunogenic protein from partially sporulated oocysts of Eimeria acervulina was cloned and used to search for the homologous counterpart in Eimeria tenella . Monospecific antibodies were raised against the recombinant expression product. Using these antibodies, the parasite proteins were found to be localised in the refractile bodies. The derived amino-acid sequences were compared by computer using the SWISSPROT protein database. In addition to high homology between the Eimeria species, extensive similarity was found with pyridine nucleotide transhydrogenase from Escherichia coli . Comparison with the sugar signature database also resulted in a possible sugar binding domain present only in the Eimeria proteins. It is possible that the corresponding parasite proteins play a role in the recently discovered mannitol cycle of Eimeria .     

An NMR study of the conformation and thermodynamics of the circular dumbbell d [formula: see text] Slow exchange between two- and four-membered hairpin loops.

The circular DNA decamer 5'-d [formula: see text] 3' is studied in solution by means of NMR spectroscopy. At low temperature the molecule adopts a dumbbell structure with three Watson-Crick C-G base pairs and two two-residue loops in opposite parts of the molecule. On raising the temperature another conformer appears, in which the closing C-G base pair in the 5'-GTTC-3' loop is disrupted, whereas the opposite 5'-CTTG-3' loop remains stable. The two conformers are in slow equilibrium over a limited temperature range.     

Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives

The cultivated Brassica species are the group of crops most closely related to Arabidopsis thaliana (Arabidopsis). They represent models for the application in crops of genomic information gained in Arabidopsis and provide an opportunity for the investigation of polyploid genome formation and evolution. The scientific literature contains contradictory evidence for the dynamics of the evolution of polyploid genomes. We aimed at overcoming the inherent complexity of Brassica genomes and clarify the effects of polyploidy on the evolution of genome microstructure in specific segments of the genome. To do this, we have constructed bacterial artificial chromosome (BAC) libraries from genomic DNA of B. rapa subspecies trilocularis (JBr) and B. napus var Tapidor (JBnB) to supplement an existing BAC library from B. oleracea. These allowed us to analyse both recent polyploidization (under 10,000 years in B. napus) and more ancient polyploidization events (ca. 20 Myr for B. rapa and B. oleracea relative to Arabidopsis), with an analysis of the events occurring on an intermediate time scale (over the ca. 4 Myr since the divergence of the B. rapa and B. oleracea lineages). Using the Arabidopsis genome sequence and clones from the JBr library, we have analysed aspects of gene conservation and microsynteny between six regions of the genome of B. rapa with the homoeologous regions of the genomes of B. oleracea and Arabidopsis. Extensive divergence of gene content was observed between the B. rapa paralogous segments and their homoeologous segments within the genome of Arabidopsis. A pattern of interspersed gene loss was identified that is similar, but not identical, to that observed in B. oleracea. The conserved genes show highly conserved collinearity with their orthologues across genomes, but a small number of species-specific rearrangements were identified. Thus the evolution of genome microstructure is an ongoing process. Brassica napus is a recently formed polyploid resulting from the hybridization of B. rapa (containing the Brassica A genome) and B. oleracea (containing the Brassica C genome). Using clones from the JBnB library, we have analysed the microstructure of the corresponding segments of the B. napus genome. The results show that there has been little or no change to the microstructure of the analysed segments of the Brassica A and C genomes as a consequence of the hybridization event forming natural B. napus. The observations indicate that, upon polyploid formation, these segments of the genome did not undergo a burst of evolution discernible at the scale of microstructure.     

An NMR Study of the Conformation and Thermodynamics of the Circular Dumbbell d<pCGC-TT-GCG-TT>

Abstract

The circular DNA decamer 5′-d<pCGC-TT-GCG-TT>3′ is studied in solution by means of NMR spectroscopy. At low temperature the molecule adopts a dumbbell structure with three Watson-Crick C-G base pairs and two two-residue loops in opposite parts of the molecule. On raising the temperature another conformer appears, in which the closing C-G base pair in the 5′-GTTC-3′ loop is disrupted, whereas the opposite 5′-CTTG-3′ loop remains stable. The two conformers are in slow equilibrium over a limited temperature range.