Santa Fe Institute

About: Santa Fe Institute is a nonprofit organization based out in Santa Fe, New Mexico, United States. It is known for research contribution in the topics: Population & Complex network. The organization has 558 authors who have published 4558 publications receiving 396015 citations. The organization is also known as: SFI.

Comparison of Viral Env Proteins from Acute and Chronic Infections with Subtype C Human Immunodeficiency Virus Type 1 Identifies Differences in Glycosylation and CCR5 Utilization and Suggests a New Strategy for Immunogen Design

Abstract: Understanding human immunodeficiency virus type 1 (HIV-1) transmission is central to developing effective prevention strategies, including a vaccine. We compared phenotypic and genetic variation in HIV-1 env genes from subjects in acute/early infection and subjects with chronic infections in the context of subtype C heterosexual transmission. We found that the transmitted viruses all used CCR5 and required high levels of CD4 to infect target cells, suggesting selection for replication in T cells and not macrophages after transmission. In addition, the transmitted viruses were more likely to use a maraviroc-sensitive conformation of CCR5, perhaps identifying a feature of the target T cell. We confirmed an earlier observation that the transmitted viruses were, on average, modestly underglycosylated relative to the viruses from chronically infected subjects. This difference was most pronounced in comparing the viruses in acutely infected men to those in chronically infected women. These features of the transmitted virus point to selective pressures during the transmission event. We did not observe a consistent difference either in heterologous neutralization sensitivity or in sensitivity to soluble CD4 between the two groups, suggesting similar conformations between viruses from acute and chronic infection. However, the presence or absence of glycosylation sites had differential effects on neutralization sensitivity for different antibodies. We suggest that the occasional absence of glycosylation sites encoded in the conserved regions of env, further reduced in transmitted viruses, could expose specific surface structures on the protein as antibody targets.

How Swarms Build Cognitive Maps

Abstract: Swarms of social insects construct trails and networks of regular traffic via a process of pheromone laying and following. These patterns constitute what is known in brain science as a cognitive map. The main difference lies in the fact that the insects write their spatial memories in the environment, while the mammalian cognitive map lies inside the brain. This analogy can be more than a poetic image, and can be further justified by a direct comparison with the neural processes associated with the construction of cognitive maps in the hippocampus. We investigate via analysis and numerical simulation the formation of trails and networks in a collection of insect-like agents. The agents interact in simple ways which are determined by experiments with real ants

Multihost Experimental Evolution of a Plant RNA Virus Reveals Local Adaptation and Host-Specific Mutations

Abstract: For multihost pathogens, adaptation to multiple hosts has important implications for both applied and basic research. At the applied level, it is one of the main factors determining the probability and the severity of emerging disease outbreaks. At the basic level, it is thought to be a key mechanism for the maintenance of genetic diversity both in host and pathogen species. Using Tobacco etch potyvirus (TEV) and four natural hosts, we have designed an evolution experiment whose strength and novelty are the use of complex multicellular host organism as hosts and a high level of replication of different evolutionary histories and lineages. A pattern of local adaptation, characterized by a higher infectivity and virulence on host(s) encountered during the experimental evolution was found. Local adaptation only had a cost in terms of performance on other hosts in some cases. We could not verify the existence of a cost for generalists, as expected to arise from antagonistic pleiotropy and other genetic mechanisms generating a fitness trade-off between hosts. This observation confirms that this classical theoretical prediction lacks empirical support. We discuss the reasons for this discrepancy between theory and experiment in the light of our results. The analysis of full genome consensus sequences of the evolved lineages established that all mutations shared between lineages were host specific. A low degree of parallel evolution was observed, possibly reflecting the various adaptive pathways available for TEV in each host. Altogether, these results reveal a strong adaptive potential of TEV to new hosts without severe evolutionary constraints.

The evolutionary ecology of technological innovations

Abstract: Technological evolution has been compared to biological evolution by many authors over the last two centuries. As a parallel experiment of innovation involving economic, historical, and social components, artifacts define a universe of evolving properties that displays episodes of diversification and extinction. Here, we critically review previous work comparing the two types of evolution. Like biological evolution, technological evolution is driven by descent with variation and selection, and includes tinkering, convergence, and contingency. At the same time, there are essential differences that make the two types of evolution quite distinct. Major distinctions are illustrated by current specific examples, including the evolution of cornets and the historical dynamics of information technologies. Due to their fast and rich development, the later provide a unique opportunity to study technological evolution at all scales with unprecedented resolution. Despite the presence of patterns suggesting convergent trends between man-made systems end biological ones, they provide examples of planned design that have no equivalent with natural evolution.

Human APOBEC3G-Mediated Editing Can Promote HIV-1 Sequence Diversification and Accelerate Adaptation to Selective Pressure

Abstract: Human apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G, hereinafter referred to as A3G) is an innate virus restriction factor that inhibits human immunodeficiency virus type 1 (HIV-1) replication and induces excessive deamination of cytidine residues in nascent reverse transcripts. To test the hypothesis that this enzyme can also help generate viral sequence diversification and the evolution of beneficial viral variants, we have examined the impact of A3G on the acquisition of (-)2',3'-dideoxy-3'-thiacytidine (3TC) resistance in vitro. That characteristic resistance mutations are rapidly fixed in the presence of A3G and 3TC suggests that A3G-mediated editing can be an important source of genetic variation on which natural selection acts to shape the structure of HIV-1 populations.