Triplex-forming ability of modified oligonucleotides

We present our studies on the ability of several different nucleotide analogs as triplex-forming oligonucleotides. The modifications tested include 4'-C-hydroxymethyl, LNA, 2'-amino-LNA and N2'-functionalized 2'-amino-LNA. Triplexes containing monomers of N2'-glycyl-functionalized 2'-amino-LNA are particularly stable.     

Formation of atroviridin by Hypocrea atroviridis is conidiation associated and positively regulated by blue light and the G protein GNA3

Species of the mycoparasitic fungal genus Hypocrea/Trichoderma are prominent producers of peptaibols, a class of small linear peptides of fungal origin. Some of these peptaibols have been shown to act synergistically with cell-wall-degrading enzymes in the inhibition of the growth of other fungi in vitro and in vivo. Here we present the structure of the Hypocrea atroviridis peptaibol synthetase gene (pbs1), deduced from the genome sequence of H. atroviridis. It consists of 19 typical peptide synthetase modules with the required additional modifying domains at the N and C termini. Phylogenetic and similarity analyses of the individual amino acid-activating modules is consistent with its ability to synthesize atroviridins. Matrix-assisted laser desorption ionization-time of flight mass spectrometry of surface-grown cultures of H. atroviridis showed that no peptaibols were formed during vegetative growth, but a microheterogenous mixture of atroviridins accumulated when the colonies started to sporulate. This correlation between sporulation and atroviridin formation was shown to be independent of the pathway inducing sporulation (i.e., light, mechanical injury and carbon starvation, respectively). Atroviridin formation was dependent on the function of the two blue light regulators, BLR1 and BLR2, under some but not all conditions of sporulation and was repressed in a pkr1 (regulatory subunit of protein kinase A) antisense strain with constitutively active protein kinase A. Conversely, however, loss of function of the Galpha-protein GNA3, which is a negative regulator of sporulation and leads to a hypersporulating phenotype, fully impairs atroviridin formation. Our data show that formation of atroviridin by H. atroviridis occurs in a sporulation-associated manner but is uncoupled from it at the stage of GNA3.     

Structural characterization of the pore forming protein TatAd of the twin-arginine translocase in membranes by solid-state N-NMR

The transmembrane protein TatA is the pore forming unit of the twin-arginine translocase (Tat), which has the unique ability of transporting folded proteins across the cell membrane. This ATP-independent protein export pathway is a recently discovered alternative to the general secretory (Sec) system of bacteria. To obtain insight in the translocation mechanism, the structure and alignment in the membrane of the well-folded segments 2-45 of TatA_d from Bacillus subtilis was studied here. Using solid-state NMR in bicelles containing anionic lipids, the topology and orientation of TatA_d was determined in an environment mimicking the bacterial membrane. A wheel-like pattern, characteristic for a tilted transmembrane helix, was observed in ¹⁵N chemical shift /¹⁵N-¹H dipolar coupling correlation NMR spectra. Analysis of this PISA wheel revealed a 14-16 residue long N-terminal membrane-spanning helix which is tilted by 17° with respect to the membrane normal. In addition, comparison of uniformly and selectively ¹⁵N-labeled TatA_2-45 samples allowed determination of the helix polarity angle.     

Critical summer foraging tradeoffs in a subarctic ungulate

Summer diets are crucial for large herbivores in the subarctic and are affected by weather, harassment from insects and a variety of environmental changes linked to climate. Yet, understanding foraging behavior and diet of large herbivores is challenging in the subarctic because of their remote ranges. We used GPS video‐camera collars to observe behaviors and summer diets of the migratory Fortymile Caribou Herd (Rangifer tarandus granti) across Alaska, USA and the Yukon, Canada. First, we characterized caribou behavior. Second, we tested if videos could be used to quantify changes in the probability of eating events. Third, we estimated summer diets at the finest taxonomic resolution possible through videos. Finally, we compared summer diet estimates from video collars to microhistological analysis of fecal pellets. We classified 18,134 videos from 30 female caribou over two summers (2018 and 2019). Caribou behaviors included eating (mean = 43.5%), ruminating (25.6%), travelling (14.0%), stationary awake (11.3%) and napping (5.1%). Eating was restricted by insect harassment. We classified forage(s) consumed in 5,549 videos where diet composition (monthly) highlighted a strong tradeoff between lichens and shrubs; shrubs dominated diets in June and July when lichen use declined. We identified 63 species, 70 genus and 33 family groups of summer forages from videos. After adjusting for digestibility, monthly estimates of diet composition were strongly correlated at the scale of the forage functional type (i.e., forage groups composed of forbs, graminoids, mosses, shrubs and lichens; r = 0.79, p < .01). Using video collars, we identified (1) a pronounced tradeoff in summer foraging between lichens and shrubs and (2) the costs of insect harassment on eating. Understanding caribou foraging ecology is needed to plan for their long‐term conservation across the circumpolar north, and video collars can provide a powerful approach across remote regions.     

Novel non-peptide lead structures forBradykinin B2-receptor antagonists

Summary A series of new non-peptide Bradykinin (BK) B₂-receptor antagonists is reported. These new leads belong to a larger set including both commercially or otherwise available potential candidates found by proprietary database searches using 3D-pharmacophore models as query, and several bis-benzamidino compounds selected from our tryptase-like protease inhibitor library on the basis of topological considerations, derived from the same models. Some of these compounds show functional competitive antagonistic activity, inhibiting in vitro the BK-induced contraction of isolated guinea-pig ileum (GPI) and rat uterus with a pA₂ up to 5.3 and 7.0, respectively. They display also binding affinity (IC₅₀ up to 0.56 μM) to the BK B₂-receptor in radioligand binding assays on GPI membrane preparations and on human IMR-90 fetal lung fibroblast cells expressing this receptor subtype. Furthermore, the results with the commercially available compounds, in some cases developed as therapeutics, show that the used 3D-pharmacophore model allows to predict to some certainty possible side actions of potential drugs.     

Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.     

Negative Feedback Loop of Wnt Signaling through Upregulation of Conductin/Axin2 in Colorectal and Liver Tumors

Activation of Wnt signaling through beta-catenin/TCF complexes is a key event in the development of various tumors, in particular colorectal and liver tumors. Wnt signaling is controlled by the negative regulator conductin/axin2/axil, which induces degradation of beta-catenin by functional interaction with the tumor suppressor APC and the serine/threonine kinase GSK3beta. Here we show that conductin is upregulated in human tumors that are induced by beta-catenin/Wnt signaling, i.e., high levels of conductin protein and mRNA were found in colorectal and liver tumors but not in the corresponding normal tissues. In various other tumor types, conductin levels did not differ between tumor and normal tissue. Upregulation of conductin was also observed in the APC-deficient intestinal tumors of Min mice. Inhibition of Wnt signaling by a dominant-negative mutant of TCF downregulated conductin but not the related protein, axin, in DLD1 colorectal tumor cells. Conversely, activation of Wnt signaling by Wnt-1 or dishevelled increased conductin levels in MDA MB 231 and Neuro2A cells, respectively. In time course experiments, stabilization of beta-catenin preceded the upregulation of conductin by Wnt-1. These results demonstrate that conductin is a target of the Wnt signaling pathway. Upregulation of conductin may constitute a negative feedback loop that controls Wnt signaling activity.     

Temperature‐specific acclimation effects on adult locomotor performance of inbred and crossbred Drosophila melanogaster

Climate change poses a serious threat to the existence of many species. The combination of habitat fragmentation and increasing temperatures is of particular concern because it can alter demographic and population genetic processes, which may ultimately lead to extinction. Locomotion is very important in mitigating the negative impacts of these processes by upholding migration and contributing to random mating within and between populations. In the present study, a T‐maze, constituting a relatively complex laboratory assay, is used to investigate whether inbreeding affects the capacity to reach a food source in male Drosophila melanogaster Meigen 1830 (Diptera: Drosophilidae) reared at 20, 25 or 30 °C, respectively. The effects of inbreeding and crossbreeding are highly temperature‐specific. Strong heterosis for the ability to reach food in the maze is observed in flies developed and maintained at 30 °C, whereas inbred flies locate the food significantly faster than crossbreds when reared at 25 °C in four of six runs. No clear pattern is evident in flies reared at 20 °C. The results suggest that complex traits such as locomotor performance in a maze are highly informative in the evaluation and detection of inbreeding depression under different thermal conditions. The effect of inbreeding is most pronounced at high temperature, which is a characteristic of the conditions that many natural populations may have to face under climate change.     

Solution‐Based Silicon in Thin‐Film Solar Cells

Solution‐based semiconductors give rise to the next generation of thin‐film electronics. Solution‐based silicon as a starting material is of particular interest because of its favorable properties, which are already vastly used in conventional electronics. Here, the application of a silicon precursor based on neopentasilane for the preparation of thin‐film solar cells is reported for the first time, and, for the first time, a performance similar to conventional fabrication methods is demonstrated. Because three different functional layers, n‐type contact layer, intrinsic absorber, and p‐type contact layer, have to be stacked on top of each other, such a device is a very demanding benchmark test of performance of solution‐based semiconductors. Complete amorphous silicon n‐i‐p solar cells with an efficiency of 3.5% are demonstrated, which significantly exceeds previously reported values.