Luis Villarreal

Luis Villarreal
University of California, Irvine | UCI · Center for Virus Research - Department of Molecular Biology and Biochemistry

Doctor of Philosophy

About

180
Publications
41,189
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Introduction
Luis Villarreal currently is professor emeritus and was founding director at the Center for Virus Research, University of California, Irvine. Luis does research in molecular evolution and the role of viruses in the origin and evolution of host. There is an ongoing collaboration with Gunther Witzany on 'Biocommunication and Natural Genome Editing'.

Publications

Publications (180)
Chapter
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This chapter (8.3) along with the chapter of Gunther Witzany (2.4) outlines a new paradigm for understand the origin and evolution of life in which communication is a core issue. Together they summarize the group interactions of RNA stem loops and viruses, the consortia dependence, the role of group identity, the minority roles in changing environm...
Preprint
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The role of viruses in the evolution of life has traditionally been seen to result from a predator/prey virus/host relationship in which viruses are selfish toxic replicators. Viral information found in host DNA was historically considered as mostly defective junk. Viral persistence or symbiosis is seldom considered, although these are exceedingly...
Preprint
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Two starting points of this dialogue, which is really unique in the history of science, are the basic knowledge on language and communication from an action theoretical perspective and on the other point, basic knowledge of virology and all the detailed interactional motifs of viruses on RNA networks, subviral agents and cellular organisms that con...
Article
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The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the h...
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The crucial difference of quasispecies consortia with former quasispecies-concepts (fittest type – mutant spectra) is the basically consortial organisation of functional RNA ensembles.
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Viruses and related infectious genetic parasites are the most abundant biological agents on this planet. They invade all cellular organisms, are key agents in the generation of adaptive and innate immune systems , and drive nearly all regulatory processes within living cells.
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Viruses and related infectious genetic parasites are the most abundant biological agents on this planet. They invade all cellular organisms, are key agents in the generation of adaptive and innate immune systems, and drive nearly all regulatory processes within living cells.
Book
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The study of DNA virus persistence and RNA virus evolution has de fi ned the concepts of addiction modules and quasispecies which can respectively explain the persistence of virus information and the cooperative evolution of viral populations (including defective virus). Together, these concepts can be applied to a wide array of phenomena that emer...
Chapter
This chapter examines the role of transmissible RNA populations (viruses) able to functions as a coherent consortia in the origin of RNA based life.
Article
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All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNA-mediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs an...
Book
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The 2018 symposium entitled “EVOLUTION—Genetic Novelty/Genomic Variations by RNA-Networks and Viruses” followed on “Natural Genetic Engineering and Natural Genome Editing” in 2008 (Ann. N.Y. Acad. Sci. Vol. 1178) and “DNA Habitats and Its RNA Inhabitants” in 2014 (Ann. N.Y. Acad. Sci. Vol. 1341). All three symposia were organized by philosopher Gue...
Book
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A new paradigmatic understanding of evolution, genetic novelty, code-generating, genome-formatting factors, infectious RNA Networks, viruses and other natural genetic content operators
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A virus first perspective is presented as an alternative hypothesis to explain the role of various endogenized retroviruses in the origin of the mammalian placenta. It is argued that virus–host persistence is a key determinant of host survival and the various ERVs involved have directly affected virus–host persistence.
Article
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In the early 1970s, Manfred Eigen and colleagues developed the quasispecies model (qs) for the population-based origin of RNAs representing the early genetic code. The Eigen idea is basically that a halo of mutants is generated by error-prone replication around the master fittest type which will behave similarly as a biological population. But almo...
Book
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The shifting perspective from a read-only-memory genome with copying errors to a readand-write genome with competent change operators is fundamental: For decades it was assumed that driving force of evolution is mutation (error) and selection. Now it is recognized that errors cannot explain genetic novelty and complexity. A variety of RNA based age...
Article
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Lytic viruses were thought to kill the most numerous host (i.e., kill the winner). But persisting viruses/defectives can also protect against viruses, especially in a ubiquitous virosphere. In 1991, Yarmolinsky et al. discovered the addiction modules of P1 phage, in which opposing toxic and protective functions stabilize persistence. Subsequently,...
Article
As vertebrates emerged from the oceans to become land‐dwelling animals, numerous basic changes in their physiology and organ structures were necessary. This chapter examines the roles that persistent viruses and especially endogenous retroviruses (ERVs) have had in the evolution of terrestrial vertebrates. The mammalian paramyxovirus lineage may tr...
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Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA va...
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Biological systems must employ a security or immunity system to ensure their survival. This chapter traces the early origins of biological identification and immune systems, first found in the prokaryotes, such as bacteria. It outlines the evolution of biological models of group identity and immunity and presents a thesis that links biological iden...
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Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code comp...
Chapter
Full-text available
The study of DNA virus persistence and RNA virus evolution has defined the concepts of addiction modules and quasispecies which can respectively explain the persistence of virus information and the cooperative evolution of viral populations (including defective virus). Together, these concepts can be applied to a wide array of phenomena that emerge...
Article
Full-text available
Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K(+) channels. To determine if these viral K(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the...
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Neighbor joining tree of K+ channel amino acid sequences from phycodnaviridae and host cells C. variabilis and E. siliculosus . (DOC)
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Information on source of K+ genes. (DOC)
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Parsimony tree of K+ channel amino acid sequences from phycodnaviridae and host cells C. variabilis and E. siliculosus . (DOC)
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Multiple sequence alignment of nucleotides coding for K+ channel pores from in C. variabilis, C. reinhardtii and phycodnaviridae . (DOCX)
Article
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Virus evolution has become a topic that involves population based selection. Both quasispecies based populations and reticulated mosaic exchange of populations of genetic elements are now well established. This has led us to the understanding that a cooperative consortia can be a crucial aspect of virus driven evolution. Thus viruses exist in group...
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All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review,...
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In contrast with former definitions of life limited to membrane-bound cellular life forms which feed, grow, metabolise and replicate (i) a role of viruses as genetic symbionts, (ii) along with peripheral phenomena such as cryptobiosis and (iii) the horizontal nature of genetic information acquisition and processing broaden our view of the tree of l...
Article
Stable colonization of the host by viruses (genetic parasites) can alter the systems of host identity and provide immunity against related viruses. To attain the needed stability, some viruses of prokaryotes (P1 phage) use a strategy called an addiction module. The linked protective and destructive gene functions of an addiction module insures both...
Article
Recently, we have realized that viruses numerically dominate all life. Although viruses are known to affect host survival in populations, this has not been previously evaluated in the context of host group selection. Group selection per se is not a currently accepted idea and its apparent occurrence is explained by statistical gene frequency models...
Book
From bacteria to humans, all life has ways to recognize themselves and differentiate themselves from similar life forms. The ability to recognize similarity can be called group identity or group membership and also relates to group cooperation. Even viruses have the capacity for group identity and cooperation. However, those viruses that stably col...
Chapter
In the last 30 years, the study of virus evolution has undergone a transformation. Originally concerned with disease and its emergence, virus evolution had not been well integrated into the general study of evolution. This chapter reviews the developments that have brought us to this new appreciation for the general significance of virus evolution...
Article
The eradication of smallpox by vaccination with vaccinia virus was probably one of the greatest achievements of vaccinology. However, the immunological basis of this protection is not fully understood. To this end, we have used protein microarrays of the vaccinia (Western Reserve, WR) proteome to profile antibody reactivities after primary infectio...
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In the last several years, numerous reports have suggested that viruses of various types might have contributed to the evolution of important and basic host characteristics. This would represent a symbiotic viral involvement in host evolution. Here, I outline many of these suggestions. However, in order for viruses to succeed as symbionts, they mus...
Conference Paper
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In the last several years, numerous reports have suggested that viruses of various types might have contributed to the evolution of important and basic host characteristics. This would represent a symbiotic viral involvement in host evolution. Here, I outline many of these suggestions. However, in order for viruses to succeed as symbionts, they mus...
Article
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Consideration of virus evolution only from a disease perspective has provided a limited view for of virus-host evolution. Such views assume all viruses fit predator/prey models replication, but fail to explain the origin of disease or how viruses might make significant contributions to host evolution. On a long evolutionary time scale, the ability...
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The Parvoviridae, a family of viruses with single-stranded DNA genomes widely spread from invertebrates to mammal and human hosts, display a remarkable evolutionary capacity uncommon in DNA genomes. Parvovirus populations show high genetic heterogeneity and large population sizes resembling the quasispecies found in RNA viruses. These viruses multi...
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The smallpox vaccine is the prototypic vaccine, yet the viral targets critical for vaccine-mediated protection remain unclear in humans. We have produced protein microarrays of a near-complete vaccinia proteome and used them to determine the major antigen specificities of the human humoral immune response to the smallpox vaccine (Dryvax). H3L, an i...
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Despite the increasing availability of genome sequences from many human pathogens, the production of complete proteomes remains at a bottleneck. To address this need, a high-throughput PCR recombination cloning and expression platform has been developed that allows hundreds of genes to be batch-processed by using ordinary laboratory procedures with...
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The role of viruses as a gray area between living and nonliving is discussed. A research by Stanley and others established that a virus consist of nucleic acids (DNA or RNA) enclosed in protein coat that may also shelter viral proteins involved in infection. It is found that viruses depend on the host cell for the raw materials and energy necessary...
Conference Paper
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Recent concerns over the potential use of variola virus-commonly known as smallpox-and other orthopox viruses as weapons of bioterrorism have increased research efforts towards creating new antiviral drugs and safer more effective vaccines. Here we introduce a new resource for structural information of poxvirus proteins: the poxvirus proteomics dat...
Article
Cervical cancer, mainly caused by infection with human papillomaviruses (HPVs), is a major public health problem in Mexico. During a study of the prevalence of HPV types in northeastern Mexico, we identified, as expected from worldwide comparisons, HPV-16, 18, 31, and 35 as highly prevalent. It is well known that the genomes of HPV types differ geo...
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We analyzed genomic sequences of Mexican variants of HPV-16, 18, 31 and 35. Among 112 HPV- 16 samples, we detected 14 E variants and 98 AA. Among 15 HPV-18 samples, 13 E and 2 African were detected. We constructed phylogenetic trees with the variants of HPV-31 and 35. In 46 HPV-31 isolates we detected 35 nucleotidic changes. In 27 HPV-35 samples we...
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There is a glaring omission in the recent Tree of Life Special Issue (13 June, pp. [1691-1709][1]). For too long, viruses have been overlooked by biologists attempting to frame the big picture of life's history. Earlier views maintained that viruses are not alive because of their lifestyle as
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Memory B cells are a central component of humoral immunity, and yet little is known about their longevity in humans. Immune memory after smallpox vaccination (DryVax) is a valuable benchmark for understanding the longevity of B cell memory in the absence of re-exposure to Ag. In this study, we demonstrate that smallpox vaccine-specific memory B cel...
Article
To determine whether human polyomavirus (hPy) genomes are present in prostate tissues, we have carried out a polymerase chain reaction (PCR) screening in two sets of prostate samples, archival and fresh frozen, as well as performing in situ hybridization (ISH). The frozen prostate samples as well as the urine from the same patients were also screen...
Article
Human papillomavirus type 16 is a common sexually transmitted pathogen capable of giving rise to cervical intraepithelial neoplasia and invasive carcinoma through the expression and activity of two adjacent oncogenes: E6 and E7. Naturally occurring amino acid variation is commonly observed in the E6 protein but to a much lesser extent in E7. In ord...
Article
Human papillomavirus type 16 is a common sexually transmitted pathogen capable of giving rise to cervical intraepithelial neoplasia and invasive carcinoma through the expression and activity of two adjacent oncogenes: E6 and ET Naturally occurring amino acid variation is commonly observed in the E6 protein but to a much lesser extent in ET In order...
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A monoclonal antibody directed against the BK virus large T-antigen (clone BK.T-1) has previously been used to evaluate BKV-T antigen (BKV-TAg) expression. However, our experience showed a consistent reactivity to uninfected human, but not rodent cells and tissues. Using immunoprecipitation, Western analysis, amino acid sequencing and end-point dil...
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Interleukin 12 (IL-12) isa cytokine that promotesan antitumor Th1-type pattern of differentiation in mature naïveT cells. Despite its therapeutic success in multiple animal models of cancer, the utility of systemically administered recombinant cytokine has been limited by its toxicity. This has encouraged the development of local IL-12 delivery sys...
Article
S. L. Salzberg and colleagues reexamined data that had been published by the international human genome sequencing group in which it appeared that between 113 and 223 genes were present in the human genome but were absent from lower eukaryotes ( Caenorhabditis elegans, Saccharomyces cerrevisiae,
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Worldwide, cervical cancer is one of the most common cancers in women. This is especially true in developing countries, where Papanicolaou smear screening, an effective preventive measure against cervical cancer, is insufficiently implemented. With growing evidence for human papillomavirus as a central etiologic factor in cervical neoplasia, develo...
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"It has been commented by someone that 'polyoma' is an adjective composed of a prefix and suffix, with no root between--a meatless linguistic sandwich" (C. J. Dawe). The very name "polyomavirus" is a vague mantel: a name given before our understanding of these viral agents was clear but implying a clear tumor life-style, as noted by the late C. J....
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stinct life strategies. However, since various acute viruses can be both a virgin soil epidemic (r-selected) and a childhood infection at equilibrium in the population (K-selected), these life strategies cannot be applied to individual viral species (Villarreal, 1999). Yet viruses do appear to have distinct patterns of acute and persistent host inf...
Chapter
This chapter provides an introduction to the evolutionary ecology of viruses. It deals with condition and capacity of the selective environment in determining the evolutionary path of viruses. This selective environment is partitioned into many compartments, each of which has a role in shaping the overall adaptive landscape. This chapter demonstrat...
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The eukaryotic replicative DNA polymerases are similar to those of large DNA viruses of eukaryotic and bacterial T4 phages but not to those of eubacteria. We develop and examine the hypothesis that DNA virus replication proteins gave rise to those of eukaryotes during evolution. We chose the DNA polymerase from phycodnavirus (which infects microalg...
Article
The generation and accumulation of genetic mutations have been associated with carcinogenesis. Epidemiological and experimental evidence implicate parvoviruses in growth inhibition (oncosuppression) and selective destruction (oncolysis) of tumor cells. It is proposed here that parvoviruses can preferentially target genetically unstable tumor cells,...

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