Curiously Modern DNA for a ``250 Million-Year-Old' Bacterium

Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the ∼59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies. Received: 12 April 2001 / Accepted: 9 June 2001     

Urinary profiles of volatile and acid metabolites in germfree and conventional rats

Qualitative and quantitative differences in the urinary excretion of volatile and acidic metabolites in germfree and conventional rats were examined by capillary gas chromatography and gas chromatography/mass spectrometry. A number of carbonyl compounds, including several short-chain aliphatic ketones and acetophenone, were higher in the conventional urines, while many heterocyclic compounds (furan derivatives, benzothiazole and others) were lower. Both qualitative and quantitative differences were observed in the urinary excretion of acidic metabolites. Three meta-hydroxy phenolic acids appeared only in the conventional rat urines, while levels of many other aromatic and aliphatic acids were also higher.     

Receiver operating characteristic (ROC) analysis of neural code efficacies

 Nerve cell signals are different in form from the stimuli that evoke them and they exhibit complex spatio-temporal characteristics. This defines a neural coding problem which is addressed by two current theories: Multiple Meaning Theory holds that neural signals contain patterns that make statements about combinations of stimulus properties; the Task Dependence Hypothesis suggests that different features of identical neural signals mediate performance in different behavioral tasks. These coding issues were addressed by investigating the representation of sensory information in the distal nervous system after transduction of visual stimuli into bio-electric signals. The objects of study were light-evoked neural responses which had been intracellularly recorded from single retinula (photoreceptor) cells in Limulus lateral eyes. The efficacies with which sensory information was represented by various candidate neural codes were calculated using receiver operating characteristic (ROC) analyses to provide objective indices. The specific visual problem under investigation was discrimination between light flashes whose intensities differed by a very small amount. A wide range of light adaptation states and relative stimulus intensities were explored. Extremely stringent data quality standards were applied which restricted the investigation to cells whose potentials did not exhibit any statistically significant drift during the hours required for data collection. Seven cellular characterizations were simultaneously monitored to detect drift in a given cell’s potentials; these characterizations included the value of the membrane potential and the values of six candidate codes. These codes were: the area under the light-evoked receptor potential (RP), the mean value of the RP, the peak height of the RP, the slope of the onset of the RP, the duration required for the RP to drop from its peak by a given amount, and the duration required for the RP to end. The results were: (1) Light adaptation increases efficacy. (2) Thus, light adaptation trades sensitivity for acuity (as characterized by ROC discriminations). (3) Increasing relative light flash intensity also increases efficacy. (4) The efficacies of the various codes are significantly different and fall in the following order: area?peak=mean?duration-end=slope= duration-drop. These findings further demonstrate that arbitrary characterizations of stimulus-response relationships are very likely to be incomplete. They particularly indicate that many commonly used and quite conventional neural analysis strategies may substantially underestimate system performance. Received: 21 August 1995/Accepted in revised form: 19 April 1996     

Fluorescence analysis of late DNA replication in mouse metaphase chromosomes using BUdR and 33258 Hoechst

A late replicating X or Y chromosome can be detected by 33258 Hoechst staining and fluorescence microscopy in a large proportion of female or male mouse embryo cells, respectively, which have been cultured in medium containing 5-bromodeoxyuridine (BUdR) for part of one DNA synthesis period, The observed distribution of late replicating chromosome regions also includes centromeric heterochromatin and some quinacrine positive bands.     

Discovery of 3(S)-thiomethyl pyrrolidine ERK inhibitors for oncology

Compound 5 (SCH772984) was identified as a potent inhibitor of ERK1/2 with excellent selectivity against a panel of kinases (0/231 kinases tested @ 100?nM) and good cell proliferation activity, but suffered from poor PK (rat AUC PK @10?mpk?=?0?μM?h; F%?=?0) which precluded further development. In an effort to identify novel ERK inhibitors with improved PK properties with respect to 5, a systematic exploration of sterics and composition at the 3-position of the pyrrolidine led to the discovery of a novel 3(S)-thiomethyl pyrrolidine analog 28 with vastly improved PK (rat AUC PK @10?mpk?=?26?μM?h; F%?=?70).     

Multiple origins of secondary temporal fenestrae and orbitozygomatic junctions in birds

Orbitozygomatic junctions (bony connections between the postorbital and zygomatic processes) and secondary temporal fenestrae have long been known to occur in a few avian species, but no comprehensive study of this phenomenon has ever been published. Having surveyed all non‐passerine and most passerine families, we established that the orbitozygomatic junction evolved 18–20 times independently in Cracidae, Phasianoidea (Odontophoridae and Phasianidae), Gastornis, Columbidae (three times), Pteroclidae (Syrrhaptes), Aptornis, Thinocoridae (Thinocorus), Scolopacidae (possibly twice), Ciconiidae (twice), Brachypteraciidae (Uratelornis), Picidae (Picus spp.), Psittacidae (Melopsittacus), Cacatuidae, and Alaudidae (twice). The junction arises in evolution as a result of either elongation of the two processes that meet at angles or the appearance of a bony cross‐bridge in place of a ligament or aponeurosis. In the first case, the junction is initially non‐adaptive, as indicated by its extreme variation (e.g., in Cracinae and Ciconiidae), and may or may not prove functional as an exaptation. Whenever adaptive, the junction supports an expansion of the adductor mandibulae externus (primarily its pars media). In addition, a rostral extension of the tympanic wing has come to cross the temporal fossa in Strigidae (at least twice) and probably Podargus. Altogether, secondary bony connections across the temporal fossa evolved independently at least 21–23 times in neornithine birds.