HIV Evolution in Early Infection: Selection Pressures,Patterns of Insertion and Deletion,and the Impact of APOBEC

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual''s HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not of mutational hotspots. Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections.     

Overcoming resistance to rapalogs in gliomas by combinatory therapies

Glioblastoma is the most common and aggressive brain tumor type, with a mean patient survival of approximately 1 year. Many previous analyses of the glioma kinome have identified key deregulated pathways that converge and activate mammalian target of rapamycin (mTOR). Following the identification and characterization of mTOR-promoting activity in gliomagenesis, data from preclinical studies suggested the targeting of mTOR by rapamycin or its analogs (rapalogs) as a promising therapeutic approach. However, clinical trials with rapalogs have shown very limited efficacy on glioma due to the development of resistance mechanisms. Analysis of rapalog-insensitive glioma cells has revealed increased activity of growth and survival pathways compensating for mTOR inhibition by rapalogs that are suitable for therapeutic intervention. In addition, recently developed mTOR inhibitors show high anti-glioma activity. In this review, we recapitulate the regulation of mTOR signaling and its involvement in gliomagenesis, discuss mechanisms resulting in resistance to rapalogs, and speculate on strategies to overcome resistance. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).     

The nucleotide exchange factor Ric-8A is a chaperone for the conformationally dynamic nucleotide-free state of Gαi1

Heterotrimeric G protein α subunits are activated upon exchange of GDP for GTP at the nucleotide binding site of Gα, catalyzed by guanine nucleotide exchange factors (GEFs). In addition to transmembrane G protein-coupled receptors (GPCRs), which act on G protein heterotrimers, members of the family cytosolic proteins typified by mammalian Ric-8A are GEFs for Gi/q/12/13-class Gα subunits. Ric-8A binds to Gα?GDP, resulting in the release of GDP. The Ric-8A complex with nucleotide-free Gαi1 is stable, but dissociates upon binding of GTP to Gαi1. To gain insight into the mechanism of Ric-8A-catalyzed GDP release from Gαi1, experiments were conducted to characterize the physical state of nucleotide-free Gαi1 (hereafter referred to as Gαi1[ ]) in solution, both as a monomeric species, and in the complex with Ric-8A. We found that Ric-8A-bound, nucleotide-free Gαi1 is more accessible to trypsinolysis than Gαi1?GDP, but less so than Gαi1[ ] alone. The TROSY-HSQC spectrum of [(15)N]Gαi1[ ] bound to Ric-8A shows considerable loss of peak intensity relative to that of [(15)N]Gαi1?GDP. Hydrogen-deuterium exchange in Gαi1[ ] bound to Ric-8A is 1.5-fold more extensive than in Gαi1?GDP. Differential scanning calorimetry shows that both Ric-8A and Gαi1?GDP undergo cooperative, irreversible unfolding transitions at 47° and 52°, respectively, while nucleotide-free Gαi1 shows a broad, weak transition near 35°. The unfolding transition for Ric-8A:Gαi1[ ] is complex, with a broad transition that peaks at 50°, suggesting that both Ric-8A and Gαi1[ ] are stabilized within the complex, relative to their respective free states. The C-terminus of Gαi1 is shown to be a critical binding element for Ric-8A, as is also the case for GPCRs, suggesting that the two types of GEF might promote nucleotide exchange by similar mechanisms, by acting as chaperones for the unstable and dynamic nucleotide-free state of Gα.     

Miricatena prunicola (Hyphomycetes), a new genus and species causing leaf spots of Prunus serotina in the UK

A fungus causing conspicuous leaf spots of Prunus serotina was recently collected in Surrey, UK. It proved to represent an undescribed species which also cannot be referred to any known genus. The species is described as Miricatena prunicola gen. et sp. nov.     

Validation of an algorithm for real-time measurement of sheep activity in confinement by recording movement within a commercial weighing crate

This study reports a method of measuring sheep activity in confinement based on recording movement of sheep during weighing. The aim was to show that an algorithm to analyse continuous weight records could be used to measure activity quickly and efficiently using commercial weighing equipment and that this measurement is related to animal productivity, specifically liveweight. A prototype method required magnetic switches on the weighing crate to record gate positioning and enclosure of the animal, with data analysis subsequent to the completion of weighing. The method reported here does not require additional equipment, instead using a computer program to analyse weights in real-time to record the degree of sheep movement. The result is summarised as the coefficient of variation of the weight over a period of 8–20 s and reported as an activity score.The real-time method had a higher repeatability (P < 0.05) than the prototype method and gave a stronger association with liveweight with heavier lambs and heavier young sheep being less active under confinement at 6 months and 18 months, respectively (P < 0.05).These findings indicate that a simple system could be developed enabling real-time reporting of activity scores during normal weighing.     

Intersegmental interneurons serving larval and pupal mechanosensory reflexes in the moth Manduca sexta

1. Intersegmental interneurons (INs) that participate in the larval bending reflex and the pupal gin trap closure reflex were identified in the isolated ventral nerve cord of Manduca sexta. INs 305, 504, and 703 show qualitatively different responses in the pupa than in the larva to electrical stimulation of sensory neurons that are retained during the larval-pupal transition to serve both reflexes. Action potentials produced by current injected into the 3 interneurons excite motor neurons that are directly involved in the larval and pupal reflexes. The excitation of the motor neurons is not associated with EPSPs at a fixed latency following action potentials in the interneurons, and thus there do not seem to be direct synaptic connections between the interneurons and the motor neurons. 2. IN 305 (Fig. 2) has a lateral soma, processes in most of the dorsal neuropil ipsilateral to the soma, and a crossing neurite that gives rise to a single contralateral descending axon. IN 305 is excited by stimulation of the sensory nerve ipsilateral to its soma in the larva and the pupa. Stimulation of the sensory nerve contralateral to its soma produces an inhibitory response in the larva, but a mixed excitatory/inhibitory response to the identical stimulus in the pupa. 3. IN 504 (Fig. 3) has a lateral soma, processes throughout most of the neuropil ipsilateral to the soma, and a crossing neurite that bifurcates to give rise to a process extending to the caudal limit of the neuropil and an ascending axon. IN 504 is excited by stimulation of the sensory nerve ipsilateral to its soma in both larvae and pupae, while the response to stimulation of the sensory nerve contralateral to its soma is inhibitory in the larva but mixed (excitatory/inhibitory) in the pupa. 4. IN 703 has a large antero-lateral soma, a neurite that extends across to the contralateral side giving rise to processes located primarily dorsally in both ipsilateral and contralateral neuropils, and two axons that ascend and descend in the connectives contralateral to the soma (Fig. 4). IN 703 responds to stimulation of the sensory nerves on either side of the ganglion, but the form of the response changes during the larval-pupal transition. In the larva, the response consists of very phasic (0-2 spikes) excitation, but in the pupa there is a prolonged excitation that greatly outlasts the stimulus (Fig. 6).(ABSTRACT TRUNCATED AT 400 WORDS)     

Aldosterone regulates rapid trafficking of epithelial sodium channel subunits in renal cortical collecting duct cells via protein kinase D activation

Aldosterone elicits rapid physiological responses in target tissues such as the distal nephron through the stimulation of cell signaling cascades. We identified protein kinase D (PKD1) as an early signaling response to aldosterone treatment in the M1-cortical collecting duct (M1-CCD) cell line. PKD1 activation was blocked by the PKC inhibitor chelerythrine chloride and by rottlerin, a specific inhibitor of PKCdelta. The activation of PKCdelta and PKCepsilon coincided with PKD1 activation and while a complex was formed between PKD1 and PKCepsilon after aldosterone treatment, there was a concurrent reduction in PKD1 association with PKCdelta. A stable PKD1 knockdown M1-CCD-derrived clone was developed in which PKD1 expression was 90% suppressed by gene silencing with a PKD1-specific siRNA. The effect of aldosterone treatment on the subcellular distribution of enhanced cyan fluorescent protein (eCFP)-tagged epithelial sodium channel (ENaC) subunits in wild type (WT) and PKD1 suppressed cells was examined using confocal microscopy. In an untreated confluent monolayer of M1-CCD cells, alpha, beta, and gamma ENaC subunits were evenly distributed throughout the cytoplasm of WT and PKD1-suppressed cells. After 2 min treatment, aldosterone stimulated the localization of each of the ENaC subunits to discrete regions within the cytoplasm of WT cells. The translocation of eCFP-ENaC subunits in WT cells was inhibited by rottlerin and the mineralocorticoid receptor (MR) antagonist spironolactone. No subcellular translocation of eCFP-ENaC subunits was observed in PKD1-suppressed cells treated with aldosterone. These data demonstrate the involvement of a novel MR/PKCdelta /PKD1 signaling cascade in the earliest ENaC subunit intracellular trafficking events that follow aldosterone treatment.