Is a large-scale DNA-based inventory of ancient life possible?

A complete DNA-based inventory of the Earth's present biota using large-scale high-throughput DNA sequencing of signature region(s) (DNA barcoding) is an ambitious proposal rivaling the Human Genome Project. We examine whether this approach will also enable us to assess the past diversity of the earth's biota. To test this, we sequenced the 5' terminus of the mitochondrial cytochrome c oxidase I (COI) gene of individuals belonging to a group of extinct ratite birds, the moa of New Zealand. Moa comprised a large number of taxa that radiated in isolation on this oceanic landmass. Using a phylogenetic approach based on a large data set including protein coding and 12S DNA sequences as well as morphology, we now have precise information about the number of moa species that once existed. We show that each of the moa species detected using this extensive data set has a unique COI barcode(s) and that they all show low levels of within-species COI variation. Consequently, we conclude that COI sequences accurately identify the species discovered using the larger data set. Hence, more generally, this study suggests that DNA barcoding might also help us detect other extinct animal species and that a large-scale inventory of ancient life is possible.     

Recognition of the Trachypetidae stat.n. as a new extant family of Ichneumonoidea (Hymenoptera), based on molecular and morphological evidence

The Trachypetinae (type genus Trachypetus Guérin de Méneville) comprise seven species of large-bodied wasps in three genera (Cercobarcon Tobias, Megalohelcon Turner and Trachypetus) endemic to continental Australia. Historically they have been variously treated, as members of the Helconinae in the case of Megalohelcon, or as separate subfamilies (Cercobarconinae and Trachypetinae). Some 25 years ago they were united in a single subfamily, the Trachypetinae, based on a number of characters. Although there has been conflicting evidence from morphological and molecular phylogenetic studies as to how best to treat the group, there has been a growing consensus that they fall outside the rest of the Braconidae, although taxon sampling has been a limiting factor for molecular studies. We generated a molecular dataset comprising five gene fragments (nuclear 28S ribosomal rDNA, nuclear 18S, elongation factor 1-alpha, mitochondrial 16S rDNA, and mitochondrial cytochrome oxidase subunit 1) for a taxonomically broad range of Braconidae, Ichneumonidae, trachypetines and outgroup hymenopterans including the first molecular data for the trachypetines Cercobarcon and Trachypetus obtained using specially designed internal primers. Molecular and combined molecular and morphological analyses confirm the monophyly of the Trachypetinae and robustly place them as sister to the Braconidae. Detailed morphological analysis including newly recognized characters shows that trachypetines lack several synapomorphies that define the Braconidae, and that they possess a number of symplesiomorphies absent from this family but found in some ichneumonids. We conclude that family-level status is warranted for the group based on both molecular and morphological criteria, and hence we propose the new family, Trachypetidae Schulz stat.n. (type genus Trachypetus Guérin de Méneville), for it. As a result, the remaining extant Braconidae become clearly defined based on synapomorphies not present in Trachypetidae stat.n. This published work has been registered on ZooBank, http://zoobank.org/urn:lsid:urn:lsid:zoobank.org:pub:5418F709-D724-4F14-89D8-1E054D1D27D0 .     

Different effects of concentric and eccentric muscle actions on plasma volume

The effects of concentric (CON) and eccentric (ECC) contractions on Delta plasma volume (PV), heart rate (HR), and lactate in responses to protocols in different body positions were investigated. CON or ECC contractions were performed in either a single-exercise (6 sets of 12 repetitions of leg extensions completed at 80% of 12 repetition maximum [12RM] with 3-minute rest periods) or multiexercise (4 sets of 10 repetitions for both CON and ECC trials of bench press, leg extension, military press, and leg curl at 80% of 10RM with 90-second rest periods) protocols. HR and lactate increased significantly for both protocols from pre- to postexercise for CON but not ECC trials. DeltaPV was greater following both CON single-exercise (-11.48 +/- 1.38%) and multiexercise (-4.64 +/- 0.33%) trials vs. ECC single-exercise (-1.62 +/- 1.69%) and multiexercise (-1.26 +/- 1.20) trials. Data demonstrate ECC exercise in response to single and multiexercise protocols at the same absolute workload as CON exercise produces less cardiovascular stress.     

Biogeography,ecology and conservation of Erebia oeme (Hübner) in the Carpathians (Lepidoptera: Nymphalidae: Satyrinae)

The European endemic Erebia oeme (Hübner [1804]) (Lepidoptera: Nymphalidae: Satyrinae) is discovered in the Carpathian Chain, from where it was considered to be absent. The single population found is situated in the southern part of the Romanian Carpathians (Retezat Mountains), where it flies sympatrically and synchronically with Erebia medusa ([Denis & Schiffermüller] 1775). The similar external morphology of these two species probably caused E. oeme to be overlooked in the Carpathians, leading to an unexpected information gap in the otherwise thoroughly studied European continent. The morphology of the Romanian specimens is compared to populations from the rest of the species’ range and to E. medusa. In addition, we tested DNA barcoding as a method to discriminate between these species and confirmed that it represents an effective identification tool for the taxa involved. The habitat of E. oeme, adults of both sexes and their genitalia are illustrated in comparison with E. medusa. Based on the study of several collections, we show that E. oeme is likely to be extremely local in the Carpathians and provide arguments to consider the species as vulnerable in Romania.     

Failure of extraocular light to facilitate circadian rhythm reentrainment in humans

Although extraocular light can entrain the circadian rhythms of invertebrates and nonmammalian vertebrates, almost all studies show that the mammalian circadian system can only be affected by light to the eyes. The exception is a recent study by Campbell and Murphy that reported phase shifts in humans to bright light applied with fiber-optic pads behind the knees (popliteal region). We tested whether this extraocular light stimulus could accelerate the entrainment of circadian rhythms to a shift of the sleep schedule, as occurs in shift work or jet lag. In experiment 1, the sleep/dark episodes were delayed 8h from baseline for 2 days, and 3h light exposures were timed to occur before the temperature minimum to help delay circadian rhythms. There were three groups: (1) bright (about 13,000 lux) extraocular light from fiber-optic pads, (2) control (dim light, 10-20 lux), and (3) medium-intensity (about 1000 lux) ocular light from light boxes. In experiment 2, the sleep/dark episodes were inverted, and extraocular light was applied either before the temperature minimum to help delay circadian rhythms or after the temperature minimum to help advance rhythms. Circadian phase markers were the salivary dim light melatonin onset (DLMO) and the rectal temperature minimum. There was no evidence that the popliteal extraocular light had a phase-shifting effect in either experiment. Possible reasons for phase shifts in the Campbell and Murphy study and not the current study include the many differences between the protocols. In the current study, there was substantial sleep deprivation before the extraocular light was applied. There was a large shift in the sleep/dark schedule, rather than allowing subjects to sleep each day from midnight to noon, as in the Campbell and Murphy study. Also, when extraocular light was applied in the current protocol, subjects did not experience a change from sleeping to awake, a change in posture (from lying in bed to sitting in a chair), or a change in ocular light (from dark to dim light). Further research is necessary to determine the conditions under which extraocular light might produce phase shifts in human circadian rhythms. (Chronobiology International, 17(6), 807-826, 2000).     

Protein unfolding: mitochondria offer a helping hand

Post-translocational protein import into mitochondria requires that the protein be unfolded prior to import. Mapping the mitochondrial-assisted unfolding pathway of a cargo protein and demonstrating that it deviates from the spontaneous unfolding pathway have provided valuable insight into the energetics of the translocation process.     

Isolation and characterization of a slowly milk-coagulating variant of Lactobacillus helveticus deficient in purine biosynthesis

A slowly milk-coagulating variant (Fmc(-)) of Lactobacillus helveticus CRL 1062, designated S1, was isolated and characterized. Strain S1 possessed all the known essential components required to utilize casein as a nitrogen source, which include functional proteinase and peptidase activities as well as functional amino acid, di- and tripeptide, and oligopeptide transport systems. The amino acid requirements of strain S1 were similar to those of the parental strain. However, on a purine-free, chemically defined medium, the growth rate of the Fmc(-) strain was threefold lower than that of the wild-type strain. L. helveticus S1 was found to be defective in IMP dehydrogenase activity and therefore was deficient in the ability to synthesize XMP and GMP. This conclusion was further supported by the observation that the addition of guanine or xanthine to milk, a substrate poor in purine compounds, restored the Fmc(+) phenotype of L. helveticus S1.     

New insights into the distribution of polyploid Daphnia: the Holarctic revisited and Argentina explored

It has long been known that polyploid organisms are more prevalent in arctic than in temperate environments. Past explanations for this geographical trend have focused on the role of glacial cycles in generating polyploids and the influence of abiotic factors in favouring polyploidy in the north. In combination, these mechanisms probably suffice to explain the observed geographical cline in ploidy levels in members of the Daphnia pulex complex in the Holarctic. While only diploid members of the D. pulex complex are found in the temperate regions of North America and Europe, allozyme and DNA quantification analyses indicate that the southern Argentine pulex-complex fauna is dominated by polyploids. Indeed, the present study is the first to document the presence of polyploid members of the D. pulex complex in any temperate climate. The results of phylogeographic analyses suggest that this difference in polyploid distribution between the northern and southern hemispheres is based more on ecological and historical contingencies than direct selection for polyploidy. Specifically, competition with diploid relatives probably limits the lower latitudinal range of polyploids in the north, but appears not to have occurred in Argentina. Because of these differences, the present study provides important insights into the diverse factors that determine the distributions and evolutionary fates of polyploid organisms.     

A role for the exosome in the in vivo degradation of unstable mRNAs

In mammals, the mRNAs encoding many proteins involved in inflammation bear destabilizing AU-rich elements (AREs) in the 3'-untranslated region. The exosome, a complex of 3' --> 5' exonucleases, is rate limiting in the destruction of such mRNAs in a mammalian in vitro system, but a role in vivo has not been demonstrated. The phenomenon of ARE-mediated degradation also occurs in the protist parasite Trypanosoma brucei. Messenger RNAs with 3'-untranslated region U-rich elements, which strongly resemble AREs, are extremely unstable in the trypanosome form that parasitizes mammals. The first step in degradation of these mRNAs in vivo is rapid destruction of the 3'-untranslated region; subsequently the mRNA is destroyed by exonucleases acting in both 5' --> 3' and 3' --> 5' directions. We here investigated the roles of three subunits of the trypanosome exosome complex, RRP45, RRP4, and CSL4, in this process, depleting the individual subunits in vivo by inducible RNA interference. RRP45 depletion, which probably disrupts exosome integrity, caused a delay in the onset of degradation of the very unstable RNAs, but did not affect degradation of more stable species. Depletion of RRP4 or CSL4 does not affect the stability of the residual exosome and did not change mRNA degradation kinetics. We conclude that the exosome is required for the initiation of rapid degradation of unstable mRNAs in trypanosomes.