Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

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Comparative analysis of complete plastid genome reveals powerful barcode regions for identifying wood of Dalbergia odorifera and D. tonkinensis (Leguminosae)

Dalbergia odorifera T. C. Chen (Leguminosae), a rare and endangered tree species endemic to Hainan Island of China, produces the most expensive and rarest wood in China. The wood characteristics of D. odorifera are remarkably similar to those of D. tonkinensis (a much less sought-after species from Vietnam), and the DNA from wood is often highly degraded, making it very difficult to identify the two species using anatomical features or DNA barcoding based on regular DNA markers. To solve the confusion of identifying wood reliably from the two species, we built and analyzed the plastome library of 26 samples from 18 Dalbergia species, of which 12 samples from eight closely related species of D. odorifera are newly sequenced in this study. Phylogenomic analysis suggested that the relationships among the 26 samples are mostly well resolved, and conspecific individuals from different populations of D. odorifera and D. tonkinensis clustered together. Between the plastid genomes of the two species, we identified 129 indels and 114 single nucleotide polymorphisms. By assessing a subset of 20 nucleotide polymorphisms and 10 indels using 37 population-level samples (20 samples of D. odorifera and 17 samples of D. tonkinensis), we recovered eight species-specific barcode regions that could be suitable for identifying the wood D. odorifera and D. tonkinensis. To examine their utility in wood identification, we amplified the eight DNA barcodes using six wood samples and recovered an amplification success rate of 83.3%, demonstrating a reliable method for precise wood identification of the two species.     

The Wilms' tumor suppressor Wt1 encodes a transcriptional activator of the class IV POU-domain factor Pou4f2 (Brn-3b)

The Wilms' tumor gene Wt1 encodes a zinc finger protein, which is required for normal formation of the genitourinary system and mesothelial tissues. Our recent findings indicate that Wt1 also plays a critical role in the development of ganglion cells in the vertebrate retina. Here we show that the POU-domain factor Pou4f2 (formerly Brn-3b), which is necessary for retinal ganglion cell survival, is up-regulated in human embryonic kidney (HEK)293 cells with stable Wt1 expression. Consistent with our previous observations of increased Pou4f2 mRNA in stably Wt1-transfeced HEK293 cells [EMBO J. 21 (2002) 1398], endogenous Pou4f2 was also elevated at the protein level in the HEK293 transfectants as well as in U2OS osteosarcoma cells that expressed an inducible Wt1 isoform. Transient co-transfection of a Wt1 expression construct activated a Pou4f2 promoter-reporter construct approximately 4-fold. Stimulation of the Pou4f2 promoter required a Wt1 binding element that was similar to a degenerative consensus site previously identified in other Wt1 responsive genes. Double-immunofluorescent labeling revealed co-expression of Pou4f2 and Wt1 in glomerular podocytes of adult kidney and in developing retinal ganglion cells of mouse embryos. Pou4f2 immunoreactivity was absent from the retinas of Wt1(-/-) embryos. In conclusion, we identified Pou4f2 as a novel downstream target gene of Wt1. Co-localization of both proteins in glomerular podocytes of the kidney and in developing retinal ganglion cells suggests a role for Wt1-Pou4f2 interaction in these tissues.     

Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling,multiple markers and simulations

Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method''s power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events.     

Reliable routine method for determination of perazine in serum by thin-layer chromatography with an internal standard

The use of a high-performance thin-layer chromatography linear chamber and of thioridazine as internal standard increases the performance of thin-layer chromatography (TLC) with direct densitometric scanning, and allows the rapid determination of serum levels of the neuroleptic drug perazine under usual therapeutic conditions. TLC is superior to gas—liquid chromatography in so far as the main metabolite desmethylperazine can be easily separated and detected by the same procedure.     

Principles and pitfalls in designing site-directed peptide ligands

An immunoglobulin light chain dimer with a large generic binding cavity was used as a host molecule for designing a series of peptide guest ligands. In a screening procedure peptides coupled to solid supports were systematically tested for binding activity by enzyme linked immunosorbent assays (ELISA). Key members of the binding series were synthesized in milligram quantities and diffused into crystals of the host molecule for X-ray analyses. These peptides were incrementally increased in size and affinity until they nearly filled the cavity. Progressive changes in binding patterns were mapped by comparisons of crystallo-graphically refined structures of 14 peptide–protein complexes at 2.7 Å resolution. These comparisons led to guidelines for ligand design and also suggested ways to modify previously established binding patterns. By manipulating equilibria involving histidine, for example, it was possible to abolish one important intramolecular interaction of the bound ligand and substitute another. These events triggered a change inconformation of the ligand from a compact to an extended form and a comprehensive change in the mode of binding to the protein. In dipeptides of histidine and proline, protonation of both imidazolium nitrogen atoms was used to program anend-to-end reversal of the direction in which the ligand was inserted into the binding cavity. Peptides cocrystallized with proteins produced complexes somewhat different in structure from those in which ligandswere diffused into preexisting crystals. In sucha large and malleable cavity, space utilization was thus different when a ligand was introduced before the imposition of crystal packing restraints. © 1993 Wiley-Liss, Inc.     

Socio-spatial organization of urban stone martens

Stone martens Martes foina are common occupants of urban environments across continental Europe. We predicted that like other 'urban adapters', urban stone martens should exhibit smaller home ranges, more extensive home-range overlap and higher population densities than their rural counterparts. We radio-tracked 13 stone martens (10 females, three males) in two towns in southern Luxembourg during a 2-year period, in order to investigate nocturnal ranging behaviour. All martens maintained stable, year-round territories almost wholly within the urban perimeter of the respective study towns. Socio-spatial organization was based on intra-sexual territoriality. Territories (100% minimum convex polygon) were small in size (males: 112.6±24.8 ha; females: 37.0±22.2 ha) and population densities moderately high (4.7–5.8 adults km⁻²) by comparison with previous studies of rural populations. We conclude that although stone martens are clearly well adapted to urban conditions, urbanization has surprisingly little impact on their socio-spatial organization by comparison with its effects on other mesocarnivores. This apparent inflexibility in the spacing patterns of stone martens lends support to the view that spacing in martens ( Martes spp.) is a predominantly phylogenetic trait that is under limited environmental influence.     

The role of context in risky choice

Human choice behavior was assessed in a concurrent-chain schedule, where two equal initial links (IL) each led to a distinct terminal-link (TL). One TL was associated with a fixed ratio schedule of reinforcement, while the other was associated with a bi-valued mixed ratio schedule of reinforcement, whose arithmetic mean equaled the Fixed TL schedule. The fixed component (FR50; FR25; FR5) was arranged to be equal to the alternative mixed component in each condition (FR1/99; FR1/49; FR1/9), and choice behavior was measured by proportion of responses to each IL. In addition, the IL duration varied across conditions (VI 30 s; VI 15 s; FI 1 s). Preference for the mixed option was observed with longer durations (e.g., when IL = VI 30 s and TL = FR1/99). Participants were relatively indifferent in other conditions, though the results suggested a monotonic increase in preference as either durations or programmed efforts increased. It is concluded that both choice and the conditioned reinforcement value of the mixed option is contextually based, so that the value of a stimulus correlated with an immediate reward (i.e., FR 1) is enhanced the greater the temporal context in which the FR1 is embedded.