The initial attachment of transforming DNA to competent Bacillus subtilis.

Summary The initial attachment of transforming DNA to competent Bacillus subtilis is temperature independent between 25° and 45°. However, below 15° there is a significant reduction in the amount of DNA attached to competent cells. The DNA that is attached at 4° can lead to transformation or interfere effectively with the subsequent attachment of a distinctive DNA when the cells are shifted to a permissive temperature (37°). These data suggest that the attachment of DNA at 4° is to sites normally involved in the transformation process. The amount of DNA that is initially attached to the bacteria at 4° or 37° after perturbation of the cells by ionic strength changes, repetitive washings, or periodate oxidation varies with the temperature at which the treatment occurs. These results are consistent with a reorientation of the DNA attachment sites upon lowering the temperature to 4°, such that their affinity for DNA and susceptibility inhibitory treatments are reduced.National Institutes of Health Research Career Program Awardee, CA-K3-6487 during a portion of this investigation.     

A phylogenomic resolution for the taxonomy of Aegean green lizards

Lacerta pamphylica and Lacerta trilineata are two currently recognized green lizard species with a historically problematic taxonomy. In cases of tangled phylogenies, next-generation sequencing and double-digest restriction-site-associated DNA protocols can provide a wealth of genomic data and resolve difficult taxonomic issues. Here, we generated genome-wide SNPs and mitochondrial sequences, and applied molecular species delimitation approaches to provide a stable taxonomy for the Aegean green lizards. Mitochondrial gene trees, genetic cluster delimitation and population structure analyses converged into recognizing the populations of (a) L. pamphylica, (b) east Aegean islands, Anatolia and Thrace (diplochondrodes lineage), (c) central Aegean islands (citrovittata), and (d) remaining Balkan populations and islands (trilineata), as separate clusters. Phylogenomic analyses revealed a split into two major clades, east and west of the Aegean Barrier, unambiguously showing a sister–clade relationship between pamphylica and diplochondrodes, rendering L. trilineata paraphyletic. Species delimitation models were tested in a Bayesian framework using the genomic SNPs: lumping all populations into a single ‘species’ had the lowest likelihood but the current taxonomy was also outperformed by all other models. All lines of evidence support the Pamphylian green lizard as a valid species; thus, east Aegean L. trilineata should also be considered a distinct species under the name Lacerta diplochondrodes. Finally, evidence from the mitochondrial and nuclear genomes is overwhelmingly in favour of recognizing the morphologically distinct Cycladian green lizards as a distinct species. We propose their elevation to full species under the name Lacerta citrovittata. All remaining insular and continental populations of the Balkan Peninsula represent the species L. trilineata.     

Benzoylphenyl ureas inhibit chitin synthesis without interfering with amino sugar uptake in imaginal wing discs of Plodia interpunctella (Hübner)

We tested the hypothesis that the inhibition of chitin synthesis by benzoylphenyl ureas could be explained by their effect on the uptake of GlcNAc into chitin. Our test system consisted of organ cultures of wing imaginal discs from Plodia interpunctella. These wing discs synthesize chitin in response to 20-hydroxyecdysone or RH 5849, a non-steroidal ecdysteroid mimic. Two benzoylphenyl ureas, diflubenzuron and teflubenzuron, inhibited ecdysteroid-dependent chitin synthesis in the wing discs. However, although chitin synthesis was inhibited, there was no corresponding diminution of amino sugar uptake by the imaginal discs. In another experiment 20-hydroxyecdysone stimulated uptake of two sugars, 2-deoxy-D-glucose and 3-O-methyl-D-glucose, which are not synthesized into chitin. Transport of these non-metabolized sugars was unaffected by the inhibitors. In an additional test of the effects on precursor transport, the action of ecdysone (alpha-ecdysone) was examined. Ecdysone stimulated amino sugar uptake, but not chitin synthesis. Neither diflubenzuron nor teflubenzuron inhibited ecdysone-dependent precursor transport. Finally, we examined ecdysteroid-induced uptake of amino sugars by an imaginal disc derived cell line IAL-PID2. In this case, also, GlcNAc transport was not inhibited significantly by either diflubenzuron or teflubenzuron. From these observations we conclude that inhibition of uptake of amino sugars does not account for the ability of teflubenzuron and diflubenzuron to inhibit chitin synthesis in P. interpunctella wing discs.     

Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements

Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.     

Anaerobic CO2 Cabinet for the Cultivation of Strict Anaerobes

The design and construction of an anaerobic CO(2) cabinet are described. Air is displaced by a stream of oxygen-free CO(2), and anerobic conditions are produced in 3 hr. The equipment is simple and cheap to operate and has been found to be satisfactory for the isolation of strict anaerobes from the mouse intestine.     

Linking behavioral states to landscape features for improved conservation management

1. A central theme for conservation is understanding how animals differentially use, and are affected by change in, the landscapes they inhabit. However, it has been challenging to develop conservation schemes for habitat‐specific behaviors.
2. Here we use behavioral change point analysis to identify behavioral states of golden eagles (Aquila chrysaetos) in the Sonoran and Mojave Deserts of the southwestern United States, and we identify, for each behavioral state, conservation‐relevant habitat associations.
3. We modeled behavior using 186,859 GPS points from 48 eagles and identified 2,851 distinct segments comprising four behavioral states. Altitude above ground level (AGL) best differentiated behavioral states, with two clusters of short‐distance movement behaviors characterized by low AGL (state 1 AGL = 14 m (median); state 2 AGL = 11 m) and two associated with longer‐distance movement behaviors and characterized by higher AGL (state 3 AGL = 108 m; state 4 AGL = 450 m).
4. Behaviors such as perching and low‐altitude hunting were associated with short‐distance movements in updraft‐poor environments, at higher elevations, and over steeper and more north‐facing terrain. In contrast, medium‐distance movements such as hunting and transiting were over gentle and south‐facing slopes. Long‐distance transiting occurred over the desert habitats that generate the best updraft.
5. This information can guide management of this species, and our approach provides a template for behavior‐specific habitat associations for other species of management concern.

     

A process‐based metacommunity framework linking local and regional scale community ecology

The metacommunity concept has the potential to integrate local and regional dynamics within a general community ecology framework. To this end, the concept must move beyond the discrete archetypes that have largely defined it (e.g. neutral vs. species sorting) and better incorporate local scale species interactions and coexistence mechanisms. Here, we present a fundamental reconception of the framework that explicitly links local coexistence theory to the spatial processes inherent to metacommunity theory, allowing for a continuous range of competitive community dynamics. These dynamics emerge from the three underlying processes that shape ecological communities: (1) density‐independent responses to abiotic conditions, (2) density‐dependent biotic interactions and (3) dispersal. Stochasticity is incorporated in the demographic realisation of each of these processes. We formalise this framework using a simulation model that explores a wide range of competitive metacommunity dynamics by varying the strength of the underlying processes. Using this model and framework, we show how existing theories, including the traditional metacommunity archetypes, are linked by this common set of processes. We then use the model to generate new hypotheses about how the three processes combine to interactively shape diversity, functioning and stability within metacommunities.