The int genes of bacteriophages P22 and λ are regulated by different mechanisms

Bacteriophage P22 and λ are related bacteriophages with similar gene organizations. In λ the cII-dependent P_I promoter is responsible for λint gene expression. The only apparent counterpart to P_I in P22 is oriented in the opposite direction, and cannot transcribe the P22 int gene. We show that this promoter, called P_al, is active both in vivo and in vitro, and is dependent upon the P22 cII-like gene, called c1. We have also determined the DNA sequence of a 3.3 kb segment that closes the gap between previously reported sequences to give a continuous sequence between the P22 p_L promoter and the int gene. The newly determined sequence is densely packed with genes from the p_L direction, and the proteins predicted by the sequence show excellent correlation with the proteins mapped by Youderian and Susskind in 1980. However, the sequence contains no apparent genes in the opposite (p_al) direction, and no additional binding motifs for the P22 c1 protein. We conclude that int gene expression in P22 is regulated by a different mechanism than in λ.     

Particle size influences decay rates of environmental DNA in aquatic systems

Environmental DNA (eDNA) analysis is a powerful tool for remote detection of target organisms. However, obtaining quantitative and longitudinal information from eDNA data is challenging, requiring a deep understanding of eDNA ecology. Notably, if the various size components of eDNA decay at different rates, and we can separate them within a sample, their changing proportions could be used to obtain longitudinal dynamics information on targets. To test this possibility, we conducted an aquatic mesocosm experiment in which we separated fish-derived eDNA components using sequential filtration to evaluate the decay rate and changing proportion of various eDNA particle sizes over time. We then fit four alternative mathematical decay models to the data, building towards a predictive framework to interpret eDNA data from various particle sizes. We found that medium-sized particles (1–10 μm) decayed more slowly than other size classes (i.e., <1 and > 10 μm), and thus made up an increasing proportion of eDNA particles over time. We also observed distinct eDNA particle size distribution (PSD) between our Common carp and Rainbow trout samples, suggesting that target-specific assays are required to determine starting eDNA PSDs. Additionally, we found evidence that different sizes of eDNA particles do not decay independently, with particle size conversion replenishing smaller particles over time. Nonetheless, a parsimonious mathematical model where particle sizes decay independently best explained the data. Given these results, we suggest a framework to discern target distance and abundance with eDNA data by applying sequential filtration, which theoretically has both metabarcoding and single-target applications.     

THE DIRECT ISOLATION OF THE MITOTIC APPARATUS

A method for isolating the mitotic apparatus from dividing sea urchin eggs without the use of ethyl alcohol or of detergents is described. In the present method, the eggs are dispersed directly in a medium containing 1 M (to 1.15 M) sucrose, 0.15 M dithiodiglycol, and 0.001 M Versene at pH 6, releasing the visibly intact mitotic apparatus. The method is designed for studies of enzyme activities, lipid components, and the variables affecting the stability of the apparatus.     

SENESCENCE IN NATURAL POPULATIONS OF MAMMALS: A COMPARATIVE STUDY

Here, I use published mortality data from 56 natural populations of mammals to examine evidence for senescence, an increase in the probability of mortality with age. Data on extent of senescence and life history characteristics are compared across taxa in an attempt to test theories for the evolution of senescence in natural populations. In accord with theoretical expectation, senescence is highest in short-lived species with short generation times. In contrast to theoretical expectation, however, senescent increases in mortality rate do not begin until well after age at maturity in most cases. I also present evidence in support of the hypothesis that senescence will be lower in large-brained taxa.     

SYSTEMATIC ANALYSIS OF SPHAEROPLEA (CHLOROPHYCEAE)1

A systematic investigation of the genus Sphaeroplea was conducted using cladistic analyses of both structural and isozyme characters for the same set of taxa. The structural data were not able to fully resolve some of the taxa while the isozyme data did produce a tree in which all nodes were supported by data. The structural characters were relatively consistent with one another, whereas the isozyme characters were much less internally consistent. Results from independent, cladistic analyses of both data sets support the concept that among those Sphaeroplea species investigated, S. fragilis Buchheim et Hoffman had an early divergence. The two data sets differed primarily in that the structural data support monophyly of the genus Sphaeroplea and the isozyme data do not. The greater relative consistency of the structural data suggests better support for trees inferred from its analysis. Furthermore, searches for character congruence between the two data sets revealed isozyme data which support monophyly of the genus Sphaeroplea, but had been overwhelmed by conflicting isozyme characters.     

ENTRANCE INTO STAGE III FASTING BY STARVELING NORTHERN ELEPHANT SEAL PUPS

Blood metabolites and urea kinetics were determined in starveling elephant seal pups to assess the transition to stage III fasting in this fasting-adapted species. Five postmolt and two premolt starvelings, denned as having a mass <50 kg, were studied until death or departure to sea. Premolt starvelings died on the rookery while postmolt starvelings departed to sea. Increased mass loss and a significant inverse relationship between mass and the ratio of blood urea nitrogen to creatinine suggested that premolt starvelings had enrered stage III starvation prior to death while urea kinetics suggested that postmolt pups engaged stage III starvation prior to departure. The mean rate of protein catabolism was estimated at 19.4 g/d for departing starvelings, twice the absolute rate and about four times the mass-specific rate estimated in healthy weanlings after eight weeks of fasting. Three starvelings stranded after departure, possibly as a result of thermoregulatory challenges and inefficient dive behavior. Entrance into stage III fasting interrupts the development of diving in emaciated pups (<50 kg) suggesting that an increased rate of protein catabolism might be linked to the cue to forage. This biochemical trigger is possibly different than the cue to feed in healthy weanlings, which depart the rookery with substantial fat stores.     

Selection of peptides inhibiting a beta-lactamase-like activity.

A library of random peptide sequences was used to select peptides that inhibit an anti-idiotypic catalytic Ig, immunoglobulin (IgG) 9G4H9, with a beta-lactamase-like activity. This library displays cyclic heptapeptides on the surface of bacteriophages and represents a collection of up to 4.5 x 109 peptides. The first selection step aimed at enriching the library in species that bind to the whole Ig molecule. The second step was to discriminate peptides that bind to part of the molecule other than the active site. Selected peptides were then screened by surface plasmon resonance analysis. Those displaying measurable Kd values were assayed for their ability to inhibit the catalytic Ig.