Compensatory evolution in RNA secondary structures increases substitution rate variation among sites

There is growing evidence that interactions between biological molecules (e.g., RNA-RNA, protein-protein, RNA-protein) place limits on the rate and trajectory of molecular evolution. Here, by extending Kimura's model of compensatory evolution at interacting sites, we show that the ratio of transition to transversion substitutions (kappa) at interacting sites should be equal to the square of the ratio at independent sites. Because transition mutations generally occur at a higher rate than transversions, the model predicts that kappa should be higher at interacting sites than at independent sites. We tested this prediction in 10 RNA secondary structures by comparing phylogenetically derived estimates of kappa in paired sites within stems (kappa(p)) and unpaired sites within loops (kappa(u)). Eight of the 10 structures showed an excellent match to the quantitative predictions of the model, and 9 of the 10 structures matched the qualitative prediction kappa(p) > kappa(u). Only the Rev response element from the human immunovirus (HIV) genome showed the reverse pattern, with kappa(p) < kappa(u). Although a variety of evolutionary forces could produce quantitative deviations from the model predictions, the reversal in magnitude of kappa(p) and kappa(u) could be achieved only by violating the model assumption that the underlying transition (or transversion) mutation rates were identical in paired and unpaired regions of the molecule. We explore the ability of the APOBEC3 enzymes, host defense mechanisms against retroviruses, which induce transition mutations preferentially in single-stranded regions of the HIV genome, to explain this exception to the rule. Taken as a whole, our findings suggest that kappa may have utility as a simple diagnostic to evaluate proposed secondary structures.     

Evolutionary histories of soil fungi are reflected in their large‐scale biogeography

Although fungal communities are known to vary along latitudinal gradients, mechanisms underlying this pattern are not well‐understood. We used high‐throughput sequencing to examine the large‐scale distributions of soil fungi and their relation to evolutionary history. We tested the Tropical Conservatism Hypothesis, which predicts that ancestral fungal groups should be more restricted to tropical latitudes and conditions than would more recently derived groups. We found support for this hypothesis in that older phyla preferred significantly lower latitudes and warmer, wetter conditions than did younger phyla. Moreover, preferences for higher latitudes and lower precipitation levels were significantly phylogenetically conserved among the six younger phyla, possibly because the older phyla possess a zoospore stage that is vulnerable to drought, whereas the younger phyla retain protective cell walls throughout their life cycle. Our study provides novel evidence that the Tropical Conservatism Hypothesis applies to microbes as well as plants and animals.     

Rapamycin analogs with reduced systemic exposure

The synthesis and biological activities of rapamycin (I) analogs modified at the C-40 position are reported. Emphasis placed on compounds that potentially have an improved safety profile on account of their shorter in vivo half-life when compared with rapamycin.     

Molecular engineering of proteins with predefined function. Part I: Design of a hemoglobin-based oxygen carrier

Molecular engineering refers to a collection of complex, computer-based methods used to study molecular structures and properties. These methods include ones for determining properties as well as for accessing prior knowledge about them. Applying these methods, one can generate, manipulate and calculate the energy involved with the three-dimensional conformation of a given molecule. These computational tools were utilized in this study, to design cross-linking reagents for cell-free Hb, for the purpose of O(2)-carriers development. Hb, when removed from the red blood cell, misses some of its functional characteristics required. Yet, these characteristics can be rebuilt into the Hb molecule by appropriate chemical modifications. These modifications have been devised to prevent dimer formation, increase the retention time in circulation, and decrease the high oxygen affinity of free Hb. The reagent reported in this study, namely, oxidized-NAD (o-NAD), has been designed to fulfill both criteria of retention time and oxygen affinity, in a single package. Feasibility of the cross-linking reaction of o-NAD with Hb was assessed by studying the docking process of o-NAD within the 2,3-DPG pocket of Hb. In this study, we provide an insight into how the overall factors involved with the potential energy calculations contribute to the hydrogen bonding network, formed within the complex. Conformational search analysis has shown a high proximity, of functional moieties on the Hb molecule, to reactive groups on the o-NAD molecule suggested. This is an important step in the design and later synthesis of O(2)-carrying materials to be used as blood substitutes.     

A lightweight microdrive for single-unit recording in freely moving rats and pigeons

A design for an inexpensive and reliable subminiature microdrive for recording single neurons in the freely moving animal is presented. The Scribe microdrive is small and lightweight and has been used successfully to record in freely moving rats and pigeons. It would also be suitable for recording in mice. The device is simple and inexpensive yet allows for stable and precise manipulation of the recording electrodes. As a result it supports stable recordings conducted over long periods. Because the Scribe microdrive is a small-diameter device it is also suitable for multisite, multielectrode applications. Here we discuss the construction of the device and comment on its use in recording from freely moving rats and pigeons.     

Guanosine 3',5'-cyclic monophosphate: a tapeworm-secreted signal molecule communicating with the rat host's small intestine

Tapeworms alter the physiological environment of the host's small intestinal lumen by contracting the intestinal smooth muscle, thereby slowing the transit of intestinal contents. We hypothesize that parasite-to-host molecular signaling is responsible for the specific patterns of small intestinal smooth muscle contraction observed both during tapeworm infection and after the infusion of tapeworm-secreted molecules into the intestinal lumen of unanesthetized rats. Of the tapeworm-secreted compounds tested, only lumenal infusion of guanosine 3',5'-cyclic monophosphate (cGMP) induced contractile patterns that mimic those observed during tapeworm infection. The response to cGMP occurred in a concentration-dependent fashion. Our study clearly demonstrates that cGMP can serve as an extracellular signal molecule regulating small intestinal motility mechanisms in vivo.     

Synovial fibroblasts from patients with rheumatoid arthritis, like fibroblasts from Graves' disease, express high levels of IL-16 when treated with Igs against insulin-like growth factor-1 receptor

We have reported recently that IgG from patients with Graves' disease (GD) can induce the expression of the CD4-specific T lymphocyte chemoattractant, IL-16, and RANTES, a C-C chemokine, in their fibroblasts. This induction is mediated through the insulin-like growth factor-1 receptor (IGF-1R) pathway. We now report that Abs from individuals with active rheumatoid arthritis (RA-IgG) stimulate in their synovial fibroblasts the expression of these same cytokines. IgG from individuals without known autoimmune disease fails to elicit this chemoattractant production. Furthermore, RA-IgG fails to induce IL-16 or RANTES expression in synovial fibroblasts from donors with osteoarthritis. RA-IgG-provoked IL-16 and RANTES production also appears to involve the IGF-1R because receptor-blocking Abs prevent the response. RA fibroblasts transfected with a dominant-negative mutant IGF-1R fail to respond to RA-IgG. IGF-1 and the IGF-1R-specific analog Des(1-3) also induce cytokine production in RA fibroblasts. RA-IgG-provoked IL-16 expression is inhibited by rapamycin, a specific macrolide inhibitor of the Akt/FRAP/mammalian target of rapamycin/p70(s6k) pathway, and by dexamethasone. GD-IgG can also induce IL-16 in RA fibroblasts, and RA-IgG shows similar activity in GD fibroblasts. Thus, IgGs from patients with RA, like those associated with GD, activate IGF-1R, and in so doing provoke T cell chemoattraction expression in fibroblasts, suggesting a potential common pathway in the two diseases. Immune-competent cell trafficking to synovial tissue is integral to the pathogenesis of RA. Recognition of this novel RA-IgG/fibroblast interaction and its functional consequences may help identify therapeutic targets.