Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C

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Inter‐oceanic variation in patterns of host‐associated divergence in a seabird ectoparasite

Aim Parasites with global distributions and wide host spectra provide excellent models for exploring the factors that drive parasite diversification. Here, we tested the relative force of host and geography in shaping population structure of a widely distributed and common ectoparasite of colonial seabirds, the tick Ixodes uriae. Location Two natural geographic replicates of the system: numerous seabird colonies of the North Pacific and North Atlantic Ocean basins. Methods Using eight microsatellite markers and tick samples from a suite of multi‐specific seabird colonies, we examined tick population structure in the North Pacific and compare patterns of diversity and structure to those in the Atlantic basin. Analyses included population genetic estimations of diversity and population differentiation, exploratory multivariate analyses, and Bayesian clustering approaches. These different analyses explicitly took into account both the geographic distance among colonies and host use by the tick. Results Overall, little geographic structure was observed among Pacific tick populations. However, host‐related genetic differentiation was evident, but was variable among host types and lower than in the North Atlantic. Main conclusions Tick population structure is concordant with the genetic structure observed in seabird host species within each ocean basin, where seabird populations tend to be less structured in the North Pacific than in the North Atlantic. Reduced tick genetic structure in the North Pacific suggests that host movement among colonies, and thus tick dispersal, is higher in this region. In addition to information on parasite diversity and gene flow, our findings raise interesting questions about the subtle ways that host behaviour, distribution and phylogeographic history shape the genetics of associated parasites across geographic landscapes.     

Effects of ultraviolet-B radiation on plants during mild water stress. III. Effects on photosynthetic recovery and growth in soybean

Soybean { Glycine max (L.) Merr. ev. Essex} was grown from seed in a greenhouse under ultraviolet-B (UV-B, 280–320 nm) radiation supplied by filtered FS-40 sunlamps. On a weighted, total daily dose basis these plants received either 0 (control) or 2875 effective J m⁻² day⁻¹ UV-B_BE. When weighted with the generalized plant action spectrum (Caldwell 1971), this simulated the solar ultraviolet-B irradiance expected to occur at College Park, Maryland, USA (39°N) in the event the global stratospheric ozone column is reduced by 23%. The effects of ultraviolet radiation on the photosynthetic recovery from water stress were measured with an infrared gas analyzer. These effects were examined in plants which were either well-watered or previously preconditioned to water stress, during two distinct phenological stages of development. During the early stages of soybean growth, enhanced levels of UV-B reduced net photosynthesis by 25%, and water stress also reduced photosynthesis to nearly the same extent (by 20%). The combination of these two stresses resulted in smaller biomass than that produced by plants exposed to either stress independently. Photosynthesis in older, larger plants was much more sensitive to water stress and was reduced by as much as 50–60% in non-preconditioned plants. Although non-irradiated, non-preconditioned (control) plants recovered to only within 60% of their prestressed value, preconditioned plants recovered to within 70–80% during the 3 day recovery period. Both water stress and UV-B radiation affected non-stomatal conductance, while stomatal conductance was primarily affected by water stress.     

An NMR-based identification of a peptide fragment from the beta-subunit of a G-protein showing specific interactions with the GBB domain of the Ste20 kinase in budding yeast

In mitogen-activated protein kinase (MAPK) cascades of budding yeast, pheromone-induced mating signal is transmitted by interactions between the beta-subunit of a G-protein (G-beta) and the G-beta binding (GBB) domain of Ste20 kinase. Previously, mutational analyses of the beta-subunit of G-protein had identified two critical mutations which abrogate binding of the GBB domain of Ste20. In this work, we have identified, by use of NMR spectroscopy, a peptide fragment from the G-beta that shows specific interactions with the isolated GBB domain of Ste20. A model structure of the Ste20/G-beta complex reveals that the interface of the hetero-complex may be sustained by parallel orientation of two potentially interacting helical segments that are further stabilized by ionic, hydrogen bond, and helix macro-dipole interactions.     

Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains

Sequence-specific protein-nucleic acid recognition is determined, in part, by hydrogen bonding interactions between amino acid side-chains and nucleotide bases. To examine the repertoire of possible interactions, we have calculated geometrically plausible arrangements in which amino acids hydrogen bond to unpaired bases, such as those found in RNA bulges and loops, or to the 53 possible RNA base-pairs. We find 32 possible interactions that involve two or more hydrogen bonds to the six unpaired bases (including protonated A and C), 17 of which have been observed. We find 186 "spanning" interactions to base-pairs in which the amino acid hydrogen bonds to both bases, in principle allowing particular base-pairs to be selectively targeted, and nine of these have been observed. Four calculated interactions span the Watson-Crick pairs and 15 span the G:U wobble pair, including two interesting arrangements with three hydrogen bonds to the Arg guanidinum group that have not yet been observed. The inherent donor-acceptor arrangements of the bases support many possible interactions to Asn (or Gln) and Ser (or Thr or Tyr), few interactions to Asp (or Glu) even though several already have been observed, and interactions to U (or T) only if the base is in an unpaired context, as also observed in several cases. This study highlights how complementary arrangements of donors and acceptors can contribute to base-specific recognition of RNA, predicts interactions not yet observed, and provides tools to analyze proposed contacts or design novel interactions.     

The interaction of cationic antimicrobial peptides with vesicles containing synthetic glycolipids as models of the outer membrane of gram-negative bacteria.

Two simple lipid A analogues methyl 2,3-di-O-tetradecanoyl-alpha-D-glucopyranoside (GL1) and methyl 2,3-di-O-tetradecanoyl-alpha-D-glucopyranoside 4-O-phosphate (GL2) were synthesized and used for preparing mixed phosphocholine vesicles as models of the outer membrane of gram-negative bacteria. The interaction of these model membranes with magainin 2, a representative of the alpha-helical membrane active peptides, and apidaecin Ib and drosocin, two insect Pro-rich peptides which do not act at the level of the cellular membrane, were studied by CD and dye-releasing experiments. The CD spectra of apidaecin Ib and drosocin in the presence of GL1- or GL2-containing vesicles were consistent with largely unordered structures, whereas, according to the CD spectra, magainin 2 adopted an amphipathic alpha-helical conformation, particularly in the presence of negatively charged bilayers. The ability of the peptides to fold into amphipathic conformations was strictly correlated to their ability to bind and to permeabilize phospholipid as well as glycolipid membranes. Apidaecin Ib and drosocin, which are unable to adopt an amphipathic structure, showed negligible dye-leakage activity even in the presence of GL2-containing vesicles. It is reasonable to suppose that, as for the killing mechanism, the two classes of antimicrobial peptides follow different patterns to cross the bacterial outer membrane.