Degeneracy and repertoire of the human HIV-1 Gag p17(77-85) CTL response

CD8+ CTL responses are important for the control of HIV-1 infection. The immunodominant HLA-A2-restricted Gag epitope, SLYNTVATL (SL9), is considered to be a poor immunogen because reactivity to it is rare in acute infection despite its paradoxical dominance in patients with chronic infection. We have previously reported SL9 to be a help-independent epitope in that it primes highly activated CTLs ex vivo from CD8+ T cells of seronegative healthy donors. These CTLs produce sufficient cytokines for extended autocrine proliferation but are sensitive to activation-induced cell death, which may cause them to be eliminated by a proinflammatory cytokine storm. Here we identified an agonist variant of the SL9 peptide, p41 (SLYNTVAAL), by screening a large synthetic combinatorial nonapeptide library with ex vivo-primed SL9-specific T cells. p41 invariably immunized SL9-cross-reactive CTLs from other donors ex vivo and H-2Db beta2m double knockout mice expressing a chimeric HLA-A*0201/H2-Db MHC class I molecule. Parallel human T cell cultures showed p41-specific CTLs to be less fastidious than SL9-CTLs in the level of costimulation required from APCs and the need for exogenous IL-2 to proliferate (help dependent). TCR sequencing revealed that the same clonotype can develop into either help-independent or help-dependent CTLs depending on the peptide used to activate the precursor CD8+ T cells. Although Ag-experienced SL9-T cells from two patients were also sensitive to IL-2-mediated cell death upon restimulation in vitro, the loss of SL9 T cells was minimized with p41. This study suggests that agonist sequences can replace aberrantly immunogenic native epitopes for the rational design of vaccines targeting HIV-1.     

Autophagy occurs upstream or parallel to the apoptosome during histolytic cell death

Histolysis refers to a widespread disintegration of tissues that is morphologically distinct from apoptosis and often associated with the stimulation of autophagy. Here, we establish that a component of the apoptosome, and pivotal regulator of apoptosis, is also required for histolytic cell death. Using in vivo and ex vivo assays, we demonstrate a global apoptogenic requirement for dark, the fly ortholog of Apaf1, and show that a required focus of dark(-) organismal lethality maps to the central nervous system. We further demonstrate that the Dark protein itself is a caspase substrate and find that alterations of this cleavage site produced the first hypermorphic point mutation within the Apaf1/Ced-4 gene family. In a model of ;autophagic cell death', dark was essential for histolysis but dispensable for characteristic features of the autophagic program, indicating that the induction of autophagy occurs upstream or parallel to histolytic cell death. These results demonstrate that stimulation of autophagy per se is not a ;killing event' and, at the same time, establish that common effector pathways, regulated by the apoptosome, can underlie morphologically distinct forms of programmed cell death.     

Infinite populations and counterfactual frequencies in evolutionary theory

One finds intertwined with ideas at the core of evolutionary theory claims about frequencies in counterfactual and infinitely large populations of organisms, as well as in sets of populations of organisms. One also finds claims about frequencies in counterfactual and infinitely large populations--of events--at the core of an answer to a question concerning the foundations of evolutionary theory. The question is this: to what do the numerical probabilities found throughout evolutionary theory correspond? The answer in question says that evolutionary probabilities are 'hypothetical frequencies' (including what are sometimes called 'long-run frequencies' and 'long-run propensities'). In this paper, I review two arguments against hypothetical frequencies. The arguments have implications for the interpretation of evolutionary probabilities, but more importantly, they seem to raise problems for biologists' claims about frequencies in counterfactual or infinite populations of organisms and sets of populations of organisms. I argue that when properly understood, claims about frequencies in large and infinite populations of organisms and sets of populations are not threatened by the arguments. Seeing why gives us a clearer understanding of the nature of counterfactual and infinite population claims and probability in evolutionary theory.     

Adaptive change in the resource-exploitation traits of a generalist consumer: the evolution and coexistence of generalists and specialists

Mathematical models of consumer-resource systems are used to explore the evolution of traits related to resource acquisition in a generalist consumer species that is capable of exploiting two resources. The analysis focuses on whether evolution of traits determining the capture rates of two resources by a consumer species produce one generalist, two specialists, or all three types, when all types are characterized by a common fitness function. In systems with a stable equilibrium, evolution produces one generalist or two specialists, depending on the second derivative of the trade-off relationship. When there are sustained population fluctuations, the nature of the trade-off between the consumer's capture rates of the two resources still plays a key role in determining the evolutionary outcome. If the trade-off is described by a choice variable between zero and one that is raised to a power n, polymorphic states are possible when n > 1, which implies a positive second derivative of the curve. These states are either dimorphism, with two relatively specialized consumer types, or trimorphism, with a single generalist type and two specialists. Both endogenously driven consumer-resource cycles, and fluctuations driven by an environmental variable affecting resource growth are considered. Trimorphic evolutionary outcomes are relatively common in the case of endogenous cycles. In contrast to a previous study, these trimorphisms can often evolve even when new lineages are constrained to have phenotypes very similar to existing lineages. Exogenous cycles driven by environmental variation in resource growth rates appear to be much less likely to produce a mixture of generalists and specialists than are endogenous consumer-resource cycles.     

The prerequisites for and likelihood of generalist-specialist coexistence

Mathematical models of three-consumer-two-resource systems are used to explore the possibility of coexistence when one consumer is a generalist utilizing both resources, and the other two are specialists utilizing only one. Such coexistence requires strongly saturating functional or numerical responses in at least one consumer and the presence of sustained asynchronous variation in resource abundances. Given these conditions, the effects of three dichotomous factors on the range of parameters allowing coexistence are examined: flexible versus inflexible resource choice by the generalist, endogenous or exogenous cause of resource cycles, and location of the two resources in a single habitat versus two habitats. Coexistence of all three species is found to be possible for all combinations of these factors except for inflexible choice in a two-habitat environment. Generalists experience frequency-dependent fitness because, when they are abundant, they synchronize resource cycles and/or reduce their amplitude. When the generalist can adaptively adjust its relative foraging on the two resources, coexistence conditions are broadened considerably, and coexistence commonly occurs readily with exogenous variation in resource growth and with resources located in distinct habitats. Adaptive behavior increases the generalist's ability to both synchronize and dampen resource cycles.     

The synthesis and biological evaluation of a series of potent dual inhibitors of farnesyl and geranyl-Geranyl protein transferases

We have prepared a series of potent, dual inhibitors of the prenyl transferases farnesyl protein transferase (FPTase) and geranyl-geranyl protein transferase I (GGPTase). The compounds were shown to possess potent activity against both enzymes in cell culture. Mechanistic analysis has shown that the compounds are CAAX competitive for FPTase inhibition but geranyl-geranyl pyrophosphate (GGPP) competitive for GGPTase inhibiton.     

"DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop

We have characterized a large-scale inactive-to-active conformational change in the activation-loop of the insulin receptor kinase domain at the atomistic level via untargeted temperature-accelerated molecular dynamics (TAMD) and free-energy calculations using the string method. TAMD simulations consistently show folding of the A-loop into a helical conformation followed by unfolding to an active conformation, causing the highly conserved DFG-motif (Asp(1150), Phe(1151), and Gly(1152)) to switch from the inactive "D-out/F-in" to the nucleotide-binding-competent "D-in/F-out" conformation. The minimum free-energy path computed from the string method preserves these helical intermediates along the inactive-to-active path, and the thermodynamic free-energy differences are consistent with previous work on various other kinases. The mechanisms revealed by TAMD also suggest that the regulatory spine can be dynamically assembled/disassembled either by DFG-flip or by movement of the αC-helix. Together, these findings both broaden our understanding of kinase activation and point to intermediates as specific therapeutic targets.     

Interferon Regulatory Factor-8 Is Important for Histone Deacetylase Inhibitor-Mediated Antitumor Activity

The notion that epigenetic alterations in neoplasia are reversible has provided the rationale to identify epigenetic modifiers for their ability to induce or enhance tumor cell death. Histone deacetylase inhibitors (HDACi) represent one such class of anti-neoplastic agents. Despite great interest for clinical use, little is known regarding the molecular targets important for response to HDACi-based cancer therapy. We had previously shown that interferon regulatory factor (IRF)-8, originally discovered as a leukemia suppressor gene by regulating apoptosis, also regulates Fas-mediated killing in non-hematologic tumor models. Furthermore, we and others have shown that epigenetic mechanisms are involved in repression of IRF-8 in tumors. Therefore, in our preclinical tumor model, we tested the hypothesis that IRF-8 expression is important for response to HDACi-based antitumor activity. In the majority of experiments, we selected the pan-HDACi, Trichostatin A (TSA), because it was previously shown to restore Fas sensitivity to tumor cells. Overall, we found that: 1) TSA alone and more so in combination with IFN-γ enhanced both IRF-8 expression and Fas-mediated death of tumor cells in vitro; 2) TSA treatment enhanced IRF-8 promoter activity via a STAT1-dependent pathway; and 3) IRF-8 was required for this death response, as tumor cells rendered IRF-8 incompetent were significantly less susceptible to Fas-mediated killing in vitro and to HDACi-mediated antitumor activity in vivo. Thus, IRF-8 status may underlie a novel molecular basis for response to HDACi-based antitumor treatment.