Factors affecting the early life history of yellow perch,Perca flavescens

Synopsis From 1979 to 1981 we followed the movement, diet, and growth of yellow perch,Perca flavescens, for their first 70 days after hatching in Lake Itasca, Minnesota. Perch spawned inshore during early spring; hatching occurred 10–20 days after spawning. Newly hatched perch were 5.6–6.2 mm total length (TL). Soon after hatching the larvae moved into the limnetic zone where they began feeding. This movement is probably a mechanism to escape intense predation in the littoral zone. Normally the first food of perch was immature copepods, but within a week they incorporated all common zooplankters into their diet. When the perch reached 25 mm TL (about day 40) they returned to the littoral zone, where they ate larger and more abundant prey than was present in the limnetic habitat. There is no correlation between growth rates and zooplankton abundances, which suggests that food quantity is not a limiting factor in the early life history of perch in Lake Itasca.     

Phylogenetic Analysis of the Aminoacyl-tRNA synthetases

Numerous aminoacyl-tRNA synthetase sequences have been aligned by computer and phylogenetic trees constructed from them for the two classes of these enzymes. Branching orders based on a consensus of these trees have been proposed for the two groups. Although the order of appearance can be rationalized to fit many different scenarios having to do with the genetic code, the invention of a system for translating nucleic acid sequences into polypeptide chains must have predated the existence of these proteins. In the past, a variety of schemes has been proposed for matching amino acids and tRNAs. Most of these have invoked direct recognition of one by the other, whether or not the anticodon was involved. Often ignored is the possibility of a nonprotein (presumably RNA) matchmaker for bringing the two into conjunction. If such had been the case, then the contemporary aminoacyl-tRNA synthetases could have entered the system gradually, each specific type replacing its matchmaking RNA counterpart in turn. A simple displacement scheme of this sort accommodates the existence of two different families of these enzymes, the second being introduced well before the first had undergone sufficient genetic duplications to specify the full gamut of amino acids. Such a scheme is also consistent with similar amino acids often, but not always, being the substrates of enzymes with the most similar amino acid sequences.Based on a presentation made at a workshop—Aminoacyl-tRNA Synthetases and the Evolution of the Genetic Code—held at Berkeley, CA, July 17–20, 1994 Correspondence to: R.F. Doolittle     

Evolutionary analysis of the hisCGABdFDEHI gene cluster from the archaeon Sulfolobus solfataricus P2.

While sequencing the genome of the archaeon Sulfolobus solfataricus P2, we found an 8,313-bp sequence containing a cluster of nine histidine biosynthesis genes in an order different from that of any known his operon. Results of phylogenetic analysis of the coding regions in the putative operon give conflicting evolutionary histories for individual his genes.     

Genome mapping in halobacteria

The goal of our research is to produce an ordered set of cosmid clones for each of several species of halobacteria for use in physical and genetic mapping. These maps will answer questions about genome evolution and about gene organization and regulation in this archaebacterial lineage. Progress in cloning and mapping the genome of Halobacterium volcanii DS2 (synonym Haloferax volcanii DS2) is reported. Overlapping cosmids are recognized by a strategy which makes use of the distinctive restriction fragments around relatively rare restriction sites. Each site recognized by the infrequently cutting restriction enzymes is a landmark from which to identify different regions of the genome. The main advantage of this strategy is that only a small overlap (10-20%) between cosmid clones is required, resulting in a correspondingly small number of cosmid clones to be analyzed. The certainty of overlap is high, and computation is simple. The final 5-10% of each genome is cloned, linked, and identified by chromosome walking methods. Hybridization of cloned homologous or heterologous genes and of stable RNAs to the minimal cosmid set localizes these genes on the physical map. Additional genes have been and will be cloned by complementation of auxotrophic mutants, or as determinants of resistance to antibiotics.     

Mutational Analysis of Dark Endogenous Metabolism in the Blue-Green Bacterium Anacystis nidulans

We describe a mutant (strain 704) of the obligate photoautotroph Anacystis nidulans which behaves like the wild type under continuous illumination but which in the dark rapidly loses viability, respires little, and incorporates label into ribonucleic acid and protein at rates considerably less than observed with the darkened wild type. Extracts of this mutant strain show no detectable 6-phosphogluconate dehydrogenase (EC 1.1.1.44) activity. Spontaneous revertants of mutant 704 were selected as survivors of prolonged incubation in darkness. Of 10 such strains examined, none had regained 6-phosphogluconate dehydrogenase activity, and all had lost detectable glucose-6-phosphate dehydrogenase (EC 1.1.1.49) activity. Although dark survival of these revertants paralleled that of the wild type, rates of dark endogenous respiration and incorporation of labeled precursors into ribonucleic acid were still very low, comparable to those observed with strain 704. These results are consistent with the following hypotheses concerning dark endogenous metabolism in unicellular blue-green bacteria. (i) Although the oxidative pentose phosphate cycle (hexose monophosphate shunt) may play a major role in endogenous metabolism in A. nidulans, as proposed by others, it is not the only pathway capable of providing energy for maintenance of viability in darkness. (ii) Much of the endogenous metabolic activity (respiration and macromolecular synthesis) observed in darkened cultures of wild-type A. nidulans is not required for survival alone, and must therefore serve other functions.     

A comparative study of hepatic DNA repair, DNA replication and hepatotoxicity in the CD-1 mouse following multiple administrations of dimethylnitrosamine

The objective of this study was to quantify hepatic DNA repair and DNA replication following multiple administrations of dimethylnitrosamine (DMN) and to determine if these events were correlated with hepatotoxicity. Male CD-1 mice, 50-100 days old, were dosed daily, p.o., with DMN in water at dose levels of 2, 4, 7 and 10 mg/kg for 2 weeks. After 2, 7 and 14 days of dosing, hepatocytes were isolated by an in situ perfusion procedure, incubated in the presence of [3H] thymidine, and fixed. Unscheduled as well as scheduled DNA synthesis were assessed by quantitative autoradiography. Unscheduled DNA synthesis (UDS) represents DNA repair while scheduled DNA synthesis (S phase) represents DNA replication. In addition, the animals' serum was examined for enzymes which indicate hepatic toxicity. After 1, 7 and 14 days of dosing, animals were orbital-bled and the serum was analyzed for serum glutamic pyruvic transaminase (SGPT), serum glutamic oxalacetic transaminase (SGOT), alkaline phosphatase (AP) and gamma-glutamyl transpeptidase (GGT). No morbidity or mortality was observed at dose levels of 2 and 4 mg/kg, but all animals receiving 7 and 10 mg/kg died after 4-6 days of dosing. GGT or AP were not elevated at any dose level or at any time point examined. At 4 mg/kg only a slight increase (less than or equal to 2 X) in the concentration of SGOT and SGPT was observed but a sharp increase (greater than 20 X) in replicative DNA synthesis was seen. The 2 mg/kg dose level of DMN did not increase replicative DNA synthesis and SGOT and SGPT were not elevated above control values at any time point following dosing at 2 mg/kg. A weakly positive DNA repair response was observed for dose levels of 4, 7 and 10 mg/kg DMN after two consecutive days of dosing. No DNA repair was observed after either 7 or 14 days of dosing at the 2 and 4 mg/kg/day levels. These results indicate that hepatic toxicity is associated with the induction of replicative DNA synthesis (S phase) but not with the induction of DNA repair. The results also confirm and extend a previous study (Doolittle et al., 1987b) indicating that a significant elevation in hepatic DNA replication is induced by hepatocarcinogens after multiple administrations of dose levels which do not alter hepatic DNA replication after a single administration. This finding indicates that the utility of the in vivo-in vitro hepatocyte assay may be enhanced by using a multi-dose protocol.