Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two South American cactus species.

Pilosocereus machrisii and P. aurisetus are cactus species within the P. aurisetus complex, a group of eight cacti that are restricted to rocky habitats within the Neotropical savannas of eastern South America. Previous studies have suggested that diversification within this complex was driven by distributional fragmentation, isolation leading to allopatric differentiation, and secondary contact among divergent lineages. These events have been associated with Quaternary climatic cycles, leading to the hypothesis that the xerophytic vegetation patches which presently harbor these populations operate as refugia during the current interglacial. However, owing to limitations of the standard phylogeographic approaches used in these studies, this hypothesis was not explicitly tested. Here we use Approximate Bayesian Computation to refine the previous inferences and test the role of different events in the diversification of two species within P. aurisetus group. We used molecular data from chloroplast DNA and simple sequence repeats loci of P. machrisii and P. aurisetus, the two species with broadest distribution in the complex, in order to test if the diversification in each species was driven mostly by vicariance or by long-dispersal events. We found that both species were affected primarily by vicariance, with a refuge model as the most likely scenario for P. aurisetus and a soft vicariance scenario most probable for P. machrisii. These results emphasize the importance of distributional fragmentation in these species, and add support to the hypothesis of long-term isolation in interglacial refugia previously proposed for the P. aurisetus species complex diversification.

Phylogeography's past, present, and future: 10 years after Avise, 2000.

Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and population genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phylogeography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally conceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of "likelihood-free" approximate Bayesian methods should permit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the concurrent rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evolutionary biology.

[An adaptation function for describing time-activity curves in nuclear medicine (author's transl)]. / Eine Anpassungsfunktion zur Beschreibung nuklearmedizinischer Zeit-Aktivitäts-Kurven.

Radioisotopic time-activity curves can be described by a function known from the physics of heat conduction. This function, called in this paper "tracer function", is a special solution of one-dimensional differential equation of heat conduction. The function is especially useful in the quantitation of left-to-right cardiac shunts by analysis of the pulmonary time-activity curve. The first transit curve is determined from the amplitudes on the ascending slope of the curve only including the maximum. The shunt curve analysis uses two parameters derived from the first transit curve and then the position and amplitude of the shunt curve maximum only.

[Typical presentation of sequential scintigraphy images in the diagnosis of cyanotic heart disease in the newborn, using a computer-assisted imaging technique (author's transl)]. / Typische Darstellung szintigraphischer Bildsequenzen zur Diagnose von zyanotischen Herzfehlern Neugeborener mit einer computergesteuerten Abbildungstechnik.

The technique of sequential scintigraphy in investigating newborn infants in order to exclude or detect cyanotic congenital heart disease has been improved. The primary scintigraphic data are recorded digitally (list mode, 1 ms, 128 by 128 pixels) and evaluated automatically as a sequence of 1/2 s frames in 1/8 s increments. A 35 mm film is exposed to a scanning pulsed light spot on a CRT-screen with quantitative correspondence between local count density and the local number of light pulses. A series of highly resolved images of the rapidly changing scintigraphic pattern is achieved in 30 min. The results of 3 investigations are discussed. They prove the importance of adequate spatial resolution and definition in time in nuclear angiocardiography in infancy. Three case results are discussed in detail. In one case cardiac catheterisation and angiocardiography had been omitted, since the radioisotopic findings excluded cyanotic congenital heart disease. Two further investigations are discussed with reference to the findings at cardiac catheterisation.

[The determination of the left ventrical volume curve without background correction and its validation by direct intercomparison with the ejection fractions as determined by biplane laevocardiography (author's transl)]. / Nuklearmedizinische Bestimmung linksventrikulärer Volumenkurven ohne Untergrundkorrektur und ihre Validisierung durch direkten Vergleich mit biplan laevokardiographisch ermittelten Auswurffraktionen.

Background corrections applied on the left ventricular volume curve determined by the "gated blood pool"--method are based on an estimated rather than on a directly measured background. This imposes an uncertainty on the values determined from the volume curve, especially on the ejection fraction. A method which does not require background correction may be applied if all available measurement and evaluation facilities are utilized fully. High temporal and spatial resolution is of fundamental importance, permitting the exact determination of the time-dependent scintigraphic contour variations of the left ventricle during the mechanical action of the heart. A good criterion of the validity of the volume curves with respect to interfering background radiation is the ejection fraction calculated from these curves. The direct intercomparison of 10 ejection fractions obtained by an expanded "gated blood pool"-method, employing cardiac catheterization, immediately before a biplane laevocardiography demonstrated very good agreement. A small systematic underestimation of the ejection fraction by the nuclear method was observed. This understimulation shows that the influence of the true background is small if other interfering count rate contributions or methodical uncertainties are excluded systematically.

[Quantitative exercise scintigraphy of the myocardium with 201Tl--methods and normal values (author's transl)]. / Quantitative Belastungs-Szintigraphie des Myokards mit 201Tl--Methodik und Normalverhalten.

Quantitative myocardial scintigraphy was performed in 20 normal individuals after maximum exercise and after two hours of rest. A mobile Anger camera with converging collimator and a Data-General computer with a 128 x 128 matrix were used. Quantitative analysis of data was performed on the basis of a 14-halfsegment model. Quantitative normal values after exercise and after redistribution of activity during rest are presented.

Electromagnetic articulography treatment for an adult with Broca's aphasia and apraxia of speech.

Electromagnetic articulography (EMA) was explored as a means of remediating [s]/[symbol in text] articulation deficits in the speech of an adult with Broca's aphasia and apraxia of speech. Over a 1-month period, the subject was provided with 2 different treatments in a counterbalanced procedure: (1) visually guided biofeedback concerning tongue-tip position and (2) a foil treatment in which a computer program delivered voicing-contrast stimuli for simple repetition. Kinematic and perceptual data suggest improvement resulting from visually guided biofeedback, both for nonspeech oral and, to a lesser extent, speech motor tasks. In contrast, the phonetic contrast treated in the foil condition showed only marginal improvement during the therapy session, with performance dropping back to baseline 10 weeks post-treatment. Although preliminary, the findings suggest that visual biofeedback concerning tongue-tip position can be used to treat nonspeech oral and (to a lesser extent) speech motor behavior in adults with Broca's aphasia and apraxia of speech.

Testing population genetic structure using parametric bootstrapping and MIGRATE-N.

We present a method for investigating genetic population structure using sequence data. Our hypothesis states that the parameters most responsible for the formation of genetic structure among different populations are the relative rates of mutation (micro) and migration (M). The evolution of genetic structure among different populations requires rates of M << p because this allows population-specific mutation to accumulate. Rates of micro << M will result in populations that are effectively panmictic because genetic differentiation will not develop among demes. Our test is implemented by using a parametric bootstrap to create the null distribution of the likelihood of the data having been produced under an appropriate model of sequence evolution and a migration rate sufficient to approximate panmixia. We describe this test, then apply it to mtDNA data from 243 plethodontid salamanders. We are able to reject the null hypothesis of no population structure on all but smallest geographic scales, a result consistent with the apparent lack of migration in Plethodon idahoensis. This approach represents a new method of investigating population structure with haploid DNA, and as such may be particularly useful for preliminary investigation of non-model organisms in which multi-locus nuclear data are not available.

Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus.

Several theoretical studies have demonstrated the importance of accounting for coalescent stochasticity in phylogeographical studies, however, there are few empirical examples that do so in the context of explicit hypothesis testing. Here, we provide an example from the Idaho giant salamander (Dicamptodon aterrimus) using 118 mtDNA sequences, nearly 2 kb in length. This species is endemic to mesic forests in northern and central Idaho, and several a priori hypotheses have been erected based both on palaeoclimatic grounds and from phylogeographical studies of codistributed amphibians. Phylogenetic analysis of the D. aterrimus data suggests an expansion from a single refugium south of the Salmon River, whereas the inference from nested clade analysis is one of expansion from a single refugium in the Clearwater drainage. Explicit testing of these hypotheses, using geographically structured coalescent simulations to erect null distributions, indicates we can reject expansion from the Clearwater drainage (pCLW = 0.089), but not expansion from the South Fork of the Salmon drainage (pSAL = 0.329). Furthermore, data from codistributed amphibians suggest that there may have been two refugia, and an amova shows that most of the molecular variance partitioned between the Clearwater and the Salmon drainages (54.40%; P < 0.001) and within drainages (43.61%; P < 0.001). As a result, we also tested three a priori hypotheses which predicted that both the Clearwater and Salmon drainages functioned as refugia during the late Pleistocene; we could reject (PCORD = 0.019) divergence dates during the Cordilleran glacial maxima [c. 20 000 years before present (ybp)], during the Sangamon interglacial (c. 35 000 ybp; pSANG = 0.032), as well as pre-Pleistocene divergence (c. 1.7 Ma; ppP < 0.001). Mismatch distributions and Tajima's D within the individual drainages provide further support to recent population expansion. This work demonstrates coalescent stochasticity is an important phenomenon to consider in testing phylogeographical hypotheses, and suggests that analytical methods which fail to sufficiently quantify this uncertainty can lead to false confidence in the conclusions drawn from these methods.

Purification of a fragment of MDM2 for production of polyclonal antisera.

A histidine-tagged, carboxy-terminal fragment of the murine double minute 2 gene product, p90(MDM2), was purified by Ni--NTA chromatography and preparative gel electrophoresis. The purified MDM2 fragment was used to generate polyclonal antisera that recognize multiple species of MDM2 proteins, including the inhibitor of p53, p90(MDM2), as well as the activator of p53, p76(MDM2). The antibodies are useful for Western analysis, immunoprecipitation, and immunofluorescence.

Exploring population genetic structure in three species of Lesser Antillean bats.

We explore population genetic structure in phyllostomid bats (Ardops nichollsi, Brachyphylla cavernarum and Artibeus jamaicensis) from the northern Lesser Antilles by investigating the degree to which island populations are genetically differentiated. Our hypothesis, that the island populations are genetically distinct because of a combination of founding events, limited migration and genetic drift exacerbated by catastrophe-induced fluctuations in population size, is derived from a priori hypotheses erected in the literature. The first prediction of this hypothesis, that within each species island populations are monophyletic, was tested using a parametric bootstrap approach. Island monophyly could not be rejected in Ardops nichollsi (P = 0.718), but could be rejected in B. cavernarum (P < 0.001) and Artibeus jamaicensis (P < 0.001). A second prediction, that molecular variance is partitioned among islands, was tested using an amova and was rejected in each species [Ardops nichollsi (P = 0.697); B. cavernarum (P = 0.598); Artibeus jamaicensis (P = 0.763)]. In B. cavernarum and Artibeus jamaicensis, the admixture in mitochondrial haplotypes from islands separated by > 100 km of ocean can be explained either by interisland migration or by incomplete lineage sorting of ancestral polymorphism in the source population. As an a posteriori test of lineage sorting, we used simulations of gene trees within a population tree to suggest that lineage sorting is an unlikely explanation for the observed pattern of nonmonophyly in Artibeus jamaicensis (PW < 0.01; PSE = 0.04), but cannot be rejected in B. cavernarum (PW = 0.81; PSE = 0.79). A conservative interpretation of the molecular data is that island populations of Artibeus jamaicensis, although isolated geographically, are not isolated genetically.

Chromium(VI) reductase activity is associated with the cytoplasmic membrane of anaerobically grown Shewanella putrefaciens MR-1.

Shewanella putrefaciens MR-1 can reduce a diverse array of compounds under anaerobic conditions, including manganese and iron oxides, fumarate, nitrate, and many other compounds. These reductive processes are apparently linked to a complex electron transport system. Chromium (Cr) is a toxic and mutagenic metal and bacteria could potentially be utilized to immobilize Cr by reducing the soluble and bioavailable state, Cr(VI), to the insoluble and less bioavailable state, Cr(III). Formate-dependent Cr(VI) reductase activity was detected in anaerobically grown cells of S. putrefaciens MR-1, with highest specific activity in the cytoplasmic membrane. Both formate and NADH served as electron donors for Cr(VI) reductase, whereas L-lactate or NADPH did not support any activity. The addition of 10 micromol l(-1) FMN markedly stimulated formate-dependent Cr(VI) reductase, and the activity was almost completely inhibited by diphenyliodonium chloride, an inhibitor of flavoproteins. Cr(VI) reductase activity was also inhibited by p-chloromercuriphenylsulphonate, azide, 2-heptyl-4-hydroxyquinolone-N-oxide, and antimycin A, suggesting involvement of a multi-component electron transport chain which could include cytochromes and quinones. Cr(V) was detected by electron paramagnetic resonance (EPR) spectroscopy, suggesting a one-electron reduction as the first step.

Regulation of transcriptional activation of mdm2 gene by p53 in response to UV radiation.

The mdm2 oncogene is expressed at elevated levels in a variety of human tumors, and its product inactivates the p53 tumor suppressor protein. MDM2 forms an autoregulatory loop with p53, because the mdm2 gene contains a promoter that is responsive to p53. Synthesis of MDM2 protein increases in a p53-dependent manner in response to DNA-damaging agents such as UV light. Although this increase likely results from enhanced transcription, the amount of MDM2 protein does not correspond to the amount of p53 protein in cells exposed to UV light. Here we show that the p53-specific internal promoter in the mdm2 gene is induced after exposure to UV light, whereas the upstream constitutive promoter is not induced. The amount of the mdm2 transcript does not parallel the ability of p53 to bind DNA, indicating that transcription is regulated at a step distinct from activation of the DNA-binding function of p53.