Meletemata quaedam de lectis : dissertatio inauguralis medica

http://tartu.ester.ee/record=b1922301~S1*es

Transfer of 13C between paired Douglas-fir seedlings reveals plant kinship effects and uptake of exudates by ectomycorrhizas

• Processes governing the fixation, partitioning, and mineralization of carbon in soils are under increasing scrutiny as we develop a more comprehensive understanding of global carbon cycling. Here we examined fixation by Douglas-fir seedlings and transfer to associated ectomycorrhizal fungi, soil microbes, and full-sibling or non-sibling neighbouring seedlings. • Stable isotope probing with 99% 13C-CO2 was applied to trace 13C-labelled photosynthate throughout plants, fungi, and soil microbes in an experiment designed to assess the effect of relatedness on 13C-transfer between plant pairs. The fixation and transfer of 13C-label to plant, fungal, and soil microbial tissue was examined in biomass and PLFAs. • After a 6-day chase period, approximately 26.8% of the 13C remaining in the system was translocated belowground. Enrichment was proportionally greatest in ectomycorrhizal biomass. The presence of mesh barriers (0.5 or 35 µm) between seedlings did not restrict 13C-transfer. • Fungi were the primary recipients of 13C-labelled photosynthate throughout the system, representing 60–70% of total 13C-enriched phospholipids. Full-sibling pairs exhibited significantly greater 13C-transfer to recipient roots in two of four Douglas-fir families, representing 3- and 4-fold increases (+ approx. 4 µg excess 13C) compared to non-sibling pairs. The existence of a root/mycorrhizal exudation – hyphal uptake pathway was supported

Actinorhodopsin genes discovered diverse in freshwater habitats and among cultivated Actinobacteria

Microbial rhodopsins are membrane proteins that utilize a retinal chromophore to harvest sunlight for energetic and photosensory functions. Recently, a group of novel rhodopsin sequences named ‘actinorhodopsins’ (ActRs) was hypothesized to exist among uncultured planktonic Actinobacteria. ActRs were discovered by mining metagenomic data obtained during the Venter Institute’s Global Ocean Sampling expedition, from a hypersaline lagoon, two estuaries and a freshwater lake. On the basis of these findings, and many studies that show Actinobacteria are common inhabitants of lakes, we predicted that ActR genes would likely be present in other freshwater habitats and among the genomes of cultivated Actinobacteria. Using degenerate polymerase chain reaction primers, we discovered an ActR gene present in an actinobacterial isolate of the family Microbacteriaceae. Isolate MWH-Uga1 was cultivated prior to this study from a freshwater pond in Uganda and belongs to a group of Actinobacteria previously identified in freshwater ecosystems. ActR genes were also discovered present in numerous mixed cultures containing freshwater Actinobacteria and among environmental DNA samples obtained from three freshwater sources; a small woodland pond and the Laurentian Great Lakes Superior and Erie. An analysis of small subunit ribosomal RNA genes from metagenomic DNA samples harboring ActR genes suggests that organisms belonging to the acI lineage, an uncultured group of Actinobacteria commonly present in fresh waters, may utilize rhodopsins. The co-occurrence of an acI organism with a specific ActR variant in a mixed culture supports our hypothesis

Assessing zoo giraffe survivorship: Methodological aspects, historical improvement and a rapid demographic shift

Giraffe have been kept in zoos for a long time. They have traditionally been considered difficult to maintain due to various husbandry requirements, including their nature as intrinsic browsers. However, zoo animals are expected to achieve higher survivorship than free-ranging conspecifics due to protection against dangers that would be experienced in their natural habitat. Global zoo giraffe data was analysed for historical developments of juvenile and adult survivorship, assessing the data with various demographic measures and comparing it to that of populations from natural habitats. Additionally, zoo population structure was analysed, in particular with respect to two events that occurred in parallel in 2014—a recommendation to restrict the number of new offspring given by the European Endangered Species Programme (EEP) studbook coordinator and the culling of a designated ‘surplus’ giraffe at Copenhagen Zoo that attracted global media attention. Both juvenile and adult giraffe survivorship has increased over time, suggesting advances in giraffe husbandry. For juveniles, this process has been continuous, whereas for adults the major progress has been in the most recent cohort (from 2000 onwards), in parallel with the publication of various husbandry guidelines. Zoo giraffe survivorship is now generally above that observed in natural habitats. Simple survivorship analyses appear suitable to describe these developments. Since 2014, the global giraffe population has undergone a rapid demographic shift from a growing to an ageing population, indicating a drastic limitation of reproduction rather than a system where reproduction is allowed and selected animals are killed (and possibly fed to carnivores). Thus, giraffe are both a showcase example for the historical progress made in zoo animal husbandry due to efforts of the zoo community and serve as an example to discuss implications of different methods of zoo population management

Stepwise bending of DNA by a single TATA-box Binding Protein

The TATA-box Binding Protein (TBP) is required by all three eukaryotic RNA polymerases for the initiation of transcription from most promoters. TBP recognizes, binds to, and bends promoter sequences called ``TATA-boxes'' in the DNA. We present results from the study of individual Saccharomyces cerevisia TBPs interacting with single DNA molecules containing a TATA-box. Using video microscopy, we observed the Brownian motion of beads tethered by short surface-bound DNA. When TBP binds to and bends the DNA, the conformation of the DNA changes and the amplitude of Brownian motion of the tethered bead is reduced compared to that of unbent DNA. We detected individual binding and dissociation events and derived kinetic parameters for the process. Dissociation was induced by increasing the salt concentration or by directly pulling on the tethered bead using optical tweezers. In addition to the well-defined free and bound classes of Brownian motion, we observed another two classes of motion. These extra classes were identified with intermediate states on a three-step, linear binding pathway. Biological implications of the intermediate states are discussed.Comment: Accepted for publication in: Biophysical Journa

Experimental Determination of the Dissociative Recombination Rate Coefficient for Rotationally Cold CH⁺ and Its Implications for Diffuse Cloud Chemistry

Observations of CH+ are used to trace the physical properties of diffuse clouds, but this requires an accurate understanding of the underlying CH+ chemistry. Until this work, the most uncertain reaction in that chemistry was dissociative recombination (DR) of CH+. Using an electron–ion merged-beams experiment at the Cryogenic Storage Ring, we have determined the DR rate coefficient of the CH+ electronic, vibrational, and rotational ground state applicable for different diffuse cloud conditions. Our results reduce the previously unrecognized order-of-magnitude uncertainty in the CH+ DR rate coefficient to ∼20% and are applicable at all temperatures relevant to diffuse clouds, ranging from quiescent gas to gas locally heated by processes such as shocks and turbulence. Based on a simple chemical network, we find that DR can be an important destruction mechanism at temperatures relevant to quiescent gas. As the temperature increases locally, DR can continue to be important up to temperatures of ∼600 K, if there is also a corresponding increase in the electron fraction of the gas. Our new CH+ DR rate-coefficient data will increase the reliability of future studies of diffuse cloud physical properties via CH+ abundance observations