Pituophis ruthveni

Number of Pages: 16Geological SciencesIntegrative Biolog

Incorporating molecular data in fungal systematics: a guide for aspiring researchers

The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that draws from molecular data involves a long series of steps, ranging from taxon sampling through the various laboratory procedures and data analysis to the publication process. All steps are important and influence the results and the way they are perceived by the scientific community. The present paper provides a reflective overview of all major steps in such a project with the purpose to assist research students about to begin their first study using DNA-based methods. We also take the opportunity to discuss the role of taxonomy in biology and the life sciences in general in the light of molecular data. While the best way to learn molecular methods is to work side by side with someone experienced, we hope that the present paper will serve to lower the learning threshold for the reader.Comment: Submitted to Current Research in Environmental and Applied Mycology - comments most welcom

Anthracycline-Induced Cardiotoxicity: Cardiac Monitoring by Continuous Wave-Doppler Ultrasound Cardiac Output Monitoring and Correlation to Echocardiography

Background: Anthracyclines are agents with a well-known cardiotoxicity. The study sought to evaluate the hemodynamic response to an anthracycline using real-time continuous-wave (CW)-Doppler ultrasound cardiac output monitoring (USCOM) and echocardiography in combination with serum biomarkers. Methods: 50 patients (26 male, 24 female, median age 59 years) suffering from various types of cancer received an anthracycline-based regimen. Patients' responses were measured at different time points (T0 prior to infusion, T1 6 h post infusion, T2 after 1 day, T3 after 7 days, and T4 after 3 months) with CW-Doppler ultrasound (T0-T4) and echocardiography (T1, T4) for hemodynamic parameters such as stroke volume (SV; SVUSCOM ml) and ejection fraction (EF; EFechocardiography%) and with NT-pro-BNP and hs-Troponin T (T0-T4). Results: During the 3-month observation period, the relative decrease in the EF determined by echocardiography was -2.1% (Delta T0-T4, T0 71 +/- 7.8%, T4 69.5 +/- 7%, p = 0.04), whereas the decrease in SV observed using CW-Doppler was -6.5% (Delta T0-T4, T0 54 +/- 19.2 ml, T4 50.5 +/- 20.6 ml, p = 0.14). The kinetics for serum biomarkers were inversely correlated. Conclusions: Combining real-time CW-Doppler USCOM and serum biomarkers is feasible for monitoring the immediate and chronic hemodynamic changes during an anthracycline-based regimen; the results obtained were comparable to those from echocardiography

Subsurface Geometry of the San Andreas Fault in Southern California: Results from the Salton Seismic Imaging Project (SSIP) and Strong Ground Motion Expectations

The San Andreas fault (SAF) is one of the most studied strike‐slip faults in the world; yet its subsurface geometry is still uncertain in most locations. The Salton Seismic Imaging Project (SSIP) was undertaken to image the structure surrounding the SAF and also its subsurface geometry. We present SSIP studies at two locations in the Coachella Valley of the northern Salton trough. On our line 4, a fault‐crossing profile just north of the Salton Sea, sedimentary basin depth reaches 4 km southwest of the SAF. On our line 6, a fault‐crossing profile at the north end of the Coachella Valley, sedimentary basin depth is ∼2–3  km and centered on the central, most active trace of the SAF. Subsurface geometry of the SAF and nearby faults along these two lines is determined using a new method of seismic‐reflection imaging, combined with potential‐field studies and earthquakes. Below a 6–9 km depth range, the SAF dips ∼50°–60° NE, and above this depth range it dips more steeply. Nearby faults are also imaged in the upper 10 km, many of which dip steeply and project to mapped surface fault traces. These secondary faults may join the SAF at depths below about 10 km to form a flower‐like structure. In Appendix D, we show that rupture on a northeast‐dipping SAF, using a single plane that approximates the two dips seen in our study, produces shaking that differs from shaking calculated for the Great California ShakeOut, for which the southern SAF was modeled as vertical in most places: shorter‐period (T<1  s) shaking is increased locally by up to a factor of 2 on the hanging wall and is decreased locally by up to a factor of 2 on the footwall, compared to shaking calculated for a vertical fault

Images of Crust Beneath Southern California Will Aid Study of Earthquakes and Their Effects

The Whittier Narrows earthquake of 1987 and the Northridge earthquake of 1991 highlighted the earthquake hazards associated with buried faults in the Los Angeles region. A more thorough knowledge of the subsurface structure of southern California is needed to reveal these and other buried faults and to aid us in understanding how the earthquake-producing machinery works in this region

Ab initio alpha-alpha scattering

Processes involving alpha particles and alpha-like nuclei comprise a major part of stellar nucleosynthesis and hypothesized mechanisms for thermonuclear supernovae. In an effort towards understanding alpha processes from first principles, we describe in this letter the first ab initio calculation of alpha-alpha scattering. We use lattice effective field theory to describe the low-energy interactions of nucleons and apply a technique called the adiabatic projection method to reduce the eight-body system to an effective two-cluster system. We find good agreement between lattice results and experimental phase shifts for S-wave and D-wave scattering. The computational scaling with particle number suggests that alpha processes involving heavier nuclei are also within reach in the near future.Comment: 6 pages, 6 figure

Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation

During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual.In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively.These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation

Finite-size effects in heavy halo nuclei from effective field theory

Halo/Cluster Effective Field Theory describes halo/cluster nuclei in an expansion in the small ratio of the size of the core(s) to the size of the system. Even in the point-particle limit, neutron-halo nuclei have a finite charge radius, because their center of mass does not coincide with their center of charge. This point-particle contribution decreases as 1 / Ac, where Ac is the mass number of the core, and diminishes in importance compared to other effects, e.g., the size of the core to which the neutrons are bound. Here we propose that for heavy cores the EFT expansion should account for the small factors of 1 / Ac. As a specific example, we discuss the implications of this organizational scheme for the inclusion of finite-size effects in expressions for the charge radii of halo nuclei. We show in particular that a short-range operator could be the dominant effect in the charge radius of one-neutron halos bound by a P-wave interaction. The point-particle contribution remains the leading piece of the charge radius for one-proton halos, and so Halo EFT has more predictive power in that case