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Ernst Mayr used the geography of closely related species in various stages of increasing divergence to “animate” the process of geographic, or allopatric, speciation. This approach was applied to a wide set of taxa, and a seminal paper by Mayr used it to explore speciation patterns in tropical sea urchins. Since then, taxonomic information in several of these genera has been augmented by detailed molecular phylogenies. We compare Mayr's animation with the phylogenies of eight sea urchin genera placed by Mayr into four speciation groups. True to Mayr's predictions, early-stage genera have on average lower species divergence and more polytypic species than genera in later stages. For six of these genera, we also have information about the evolution of the gamete recognition protein bindin, which is critical to reproductive isolation. These comparisons show that later-stage genera with many sympatric species tend to be those with rapid bindin evolution. By contrast, early-stage genera with few sympatric species are not necessarily earlier in the divergence process; they happen to be those with slow rates of bindin evolution. These results show that the rate of speciation in sea urchins does not only depend on the steady accumulation of genome divergence over time, but also on the rate of evolution of gamete recognition proteins. The animation method used by Mayr is generally supported by molecular phylogenies. However, the existence of multiple rates in the acquisition of reproductive isolation complicates placement of different genera in an evolutionary series.

The genetic factors contributing to complex trait variation may reside in regulatory, rather than protein-coding portions of the genome. Within noncoding regions, SNPs in regulatory elements are more likely to contribute to phenotypic variation than those in nonregulatory regions. Thus, it is important to be able to identify and annotate noncoding regulatory elements. DNA conservation among diverged species successfully identifies noncoding regulatory regions. However, because rapidly evolving regulatory regions will not generally be conserved across species, these will not detected by using purely conservation-based methods. Here we describe additional approaches that can be used to identify putative regulatory elements via signatures of nonneutral evolution. An examination of the pattern of polymorphism both within and between populations of Drosophila melanogaster , as well as divergence with its sibling species Drosophila simulans , across 24.2 kb of noncoding DNA identifies several nonneutrally evolving regions not identified by conservation. Because different methods tag different regions, it appears that the methods are complementary. Patterns of variation at different elements are consistent with the action of selective sweeps, balancing selection, or population differentiation. Together with regions conserved between D. melanogaster and Drosophila pseudoobscura , we tag 5.3 kb of noncoding DNA as potentially regulatory. Ninety-seven of the 408 common noncoding SNPs surveyed are within putatively regulatory regions. If these methods collectively identify the majority of functional noncoding polymorphisms, genotyping only these SNPs in an association mapping framework would reduce genotyping effort for noncoding regions 4-fold.

One of Ernst Mayr's legacies is the consensus that the allopatry model is the predominant mode of speciation in most sexually reproducing lineages. In this model, reproductive isolation develops as a pleiotropic byproduct of the genetic divergence that develops among physically isolated populations. Presently, there is no consensus concerning which, if any, evolutionary process is primarily responsible for driving the specific genetic divergence that leads to reproductive isolation. Here, we focus on the hypothesis that inter-locus antagonistic coevolution drives rapid genetic divergence among allopatric populations and thereby acts as an important “engine” of speciation. We assert that only data from studies of experimental evolution, rather than descriptive patterns of molecular evolution, can provide definitive evidence for this hypothesis. We describe and use an experimental approach, called hemiclonal analysis, that can be used in the Drosophila melanogaster laboratory model system to simultaneously screen nearly the entire genome for both standing genetic variation within a population and the net-selection gradient acting on the variation. Hemiclonal analysis has four stages: ( i ) creation of a laboratory “island population”; ( ii ) cytogenetic cloning of nearly genome-wide haplotypes to construct hemiclones; ( iii ) measurement of additive genetic variation among hemiclones; and ( iv ) measurement of the selection gradient acting on phenotypic variation among hemiclones. We apply hemiclonal analysis to test the hypothesis that there is ongoing antagonistic coevolution between the sexes in the D. melanogaster laboratory model system and then discuss the relevance of this analysis to natural systems.

Converging experimental evidence indicates that CD4+regulatory T cells control progression of autoimmune insulitis in nonobese diabetic (NOD) mice. Here, we studied the nature of these regulatory T cells and their mode of action in diabetes-prone NODRag-/-or severe combined immunodeficient (SCID) mice harboring a transgenic T cell receptor derived from the diabetogenic T cell clone BDC2.5. We first show that diabetes onset is prevented in such mice by infusion of polyclonal CD4+T cells expressingl-selectin (CD62L) but not prevented or only marginally prevented by CD4+CD25+T cells. Similarly, we found with a cotransfer model that CD4+CD62L+T cells but not CD4+CD25+T cells inhibited diabetes transfer into NOD SCID recipients by transgenic NOD BDC2.5 SCID cells. Unexpectedly, cotransfer of transgenic NOD BDC2.5 SCID cells and spleen cells from WT diabetic NOD mice did not induce diabetes, whereas each individual population did so. Data are presented arguing for the role of CD4+CD62L+T cells present within the polyclonal diabetogenic population in mediating this apparently paradoxical effect. Collectively, these data confirm the central role of CD4+CD62L+regulatory T cells in controlling disease onset in a well defined transgenic model of autoimmune diabetes and suggest the intervention of homeostatic mechanisms as part of their mode of action.

DNA vaccines, comprised of plasmid DNA encoding proteins from pathogens, allergens, and tumors, are being evaluated as prophylactic vaccines and therapeutic treatments for infectious diseases, allergies, and cancer; plasmids encoding normal human proteins are likewise being tested as vaccines and treatments for autoimmune diseases. Examples of in vivo prophylaxis and immunotherapy, based on different types of immune responses (humoral and cellular), in a variety of disease models and under evaluation in early phase human clinical trials are presented. Viral vectors continue to show better levels of expression than those achieved by DNA plasmid vectors. We have focused our clinical efforts, at this time, on the use of recombinant viral vectors for both vaccine as well as cytokine gene transfer studies. We currently have four clinical programs in cancer immunotherapy. Two nonspecific immunotherapy programs are underway that apply adenoviral vectors for the transfer of cytokine genes into tumors in situ . An adenovirus-IFNγ construct (TG1042) is currently being tested in phase II clinical trials in cutaneous lymphoma. A similar construct, adenovirus-IL2 (TG1024), also injected directly into solid tumors, is currently being tested in patients with solid tumors (about one-half of which are melanoma). Encouraging results are seen in both programs. Two cancer vaccine immunotherapy programs focus on two cancer-associated antigens: human papilloma virus E6 and E7 proteins and the epithelial cancer-associated antigen MUC1. Both are encoded by a highly attenuated vaccinia virus vector [modified vaccinia Ankara (MVA)] and both are coexpressed with IL-2. Encouraging results seen in both of these programs are described.

Our recent clinical trials demonstrate that autologous cell transfer after lymphodepleting chemotherapy can cause the regression of large, vascularized tumors in patients with refractory metastatic melanoma. Eighteen of 35 patients treated with tumor-reactive lymphocyte cultures experienced an objective clinical response (>50% reduction in tumor), including four complete responders. In some patients, tumor regression was accompanied by a large in vivo expansion of the administered antitumor lymphocytes, which persisted in peripheral blood at >70% of total lymphocytes for many months after transfer. The cells capable of mediating tumor regression consisted of heterogeneous lymphocyte populations with high avidity for tumor antigens that were derived from tumor-infiltrating lymphocytes cultured for limited times in vitro . The success of this treatment likely results from the ability to infuse large numbers of activated antitumor lymphocytes into an appropriate host homeostatic environment depleted of regulatory T cells. These studies are elucidating the requirements for successful immunotherapy of patients with advanced metastatic disease and are leading to additional clinical trials with gene-modified lymphocytes.

One's present repertoire of antibodies encodes the history of one's past immunological experience. Can the present autoantibody repertoire be consulted to predict resistance or susceptibility to the future development of an autoimmune disease? Here, we developed an antigen microarray chip and used bioinformatic analysis to study a model of type 1 diabetes developing in nonobese diabetic male mice in which the disease was accelerated and synchronized by exposing the mice to cyclophosphamide at 4 weeks of age. We obtained sera from 19 individual mice, treated the mice to induce cyclophosphamide-accelerated diabetes (CAD), and found, as expected, that 9 mice became severely diabetic, whereas 10 mice permanently resisted diabetes. We again obtained serum from each mouse after CAD induction. We then analyzed, by using rank-order and superparamagnetic clustering, the patterns of antibodies in individual mice to 266 different antigens spotted on the chip. A selected panel of 27 different antigens (10% of the array) revealed a pattern of IgG antibody reactivity in the pre-CAD sera that discriminated between the mice resistant or susceptible to CAD with 100% sensitivity and 82% specificity (P= 0.017). Surprisingly, the set of IgG antibodies that was informative before CAD induction did not separate the resistant and susceptible groups after the onset of CAD; new antigens became critical for post-CAD repertoire discrimination. Thus, at least for a model disease, present antibody repertoires can predict future disease, predictive and diagnostic repertoires can differ, and decisive information about immune system behavior can be mined by bioinformatic technology. Repertoires matter.

Autoimmune T and B cell responses to CNS antigen(s) are thought to drive the pathogenesis of multiple sclerosis (MS), and thus are logical targets for therapy. Indeed, several immunomodulatory agents, including IFN-β1b, IFN-β1a, glatiramer acetate, and mitoxantrone, have had beneficial clinical effects in different forms of MS. However, because the available treatments are only partially effective, MS therapy needs to be further improved. Selective (antigen-specific) immunotherapies are especially appealing because in theory they combine maximal efficacy with minimal side effects. Indeed, several innovative immunotherapies have been successfully applied in experimental autoimmune encephalomyelitis. For example, autoreactive T cells can be selectively targeted by means of antigen, T cell receptor, or activation markers. However, experimental autoimmune encephalomyelitis is far from being a perfect approximation of MS because MS is more heterogeneous and the target antigen(s) is (are) not known. Further advances in MS therapy will depend on our growing understanding of the pathogenesis of this still incurable disease.

Studies in experimental models (1953–1956) demonstrated that acquired donor-specific allotolerance in immunologically immature or irradiated animals is strongly associated with donor leukocyte chimerism. Bone marrow transplantation in immune-deficient or cytoablated human recipients was a logical extension (1968). In contrast, clinical (1959) and then experimental organ transplantation was systematically accomplished in the apparent absence of leukocyte chimerism. Consequently, it was assumed for many years that success with organ and bone marrow transplantation involved fundamentally different mechanisms. With the discovery in 1992 of small numbers of donor leukocytes in the tissues or blood of long-surviving organ recipients (microchimerism), we concluded that organ engraftment was a form of leukocyte chimerism-dependent partial tolerance. In this initially controversial paradigm, alloengraftment after both kinds of transplantation is the product of a double immune reaction in which responses, each to the other, of coexisting donor and recipient immune systems results in variable reciprocal clonal exhaustion, followed by peripheral clonal deletion. It was proposed with Rolf Zinkernagel that the individual alloresponses are the equivalent of the MHC-restricted T cell recognition of, and host response to, intracellular parasites and that the mechanisms of immune responsiveness, or nonresponsiveness, are governed by the migration and localization of the respective antigens. Elucidation of the mechanisms of nonresponsiveness (clonal exhaustion-deletion and immune ignorance) and their regulation removed much of the historical mystique of transplantation. The insight was then applied to improve the timing and dosage of immunosuppression of current human transplant recipients.

By using data from three bibliographic databases in biology, physics, and mathematics, respectively, networks are constructed in which the nodes are scientists, and two scientists are connected if they have coauthored a paper. We use these networks to answer a broad variety of questions about collaboration patterns, such as the numbers of papers authors write, how many people they write them with, what the typical distance between scientists is through the network, and how patterns of collaboration vary between subjects and over time. We also summarize a number of recent results by other authors on coauthorship patterns.

A crossmapping technique is introduced for visualizing multiple and overlapping relations among entity types in collections of journal articles. Groups of entities from two entity types are crossplotted to show correspondence of relations. For example, author collaboration groups are plotted on the x axis against groups of papers (research fronts) on the y axis. At the intersection of each pair of author group/research front pairs a circular symbol is plotted whose size is proportional to the number of times that authors in the group appear as authors in papers in the research front. Entity groups are found by agglomerative hierarchical clustering using conventional similarity measures. Crossmaps comprise a simple technique that is particularly suited to showing overlap in relations among entity groups. Particularly useful crossmaps are: research fronts against base reference clusters, research fronts against author collaboration groups, and research fronts against term co-occurrence clusters. When exploring the knowledge domain of a collection of journal papers, it is useful to have several crossmaps of different entity pairs, complemented by research front timelines and base reference cluster timelines.

Usage data at a high-traffic web site can expose information about external events and surges in popularity that may not be accessible solely from analyses of content and link structure. We consider sites that are organized around a set of items available for purchase or download, consider, for example, an e-commerce site or collection of online research papers, and we study a simple indicator of collective user interest in an item, the batting average, defined as the fraction of visits to an item's description that result in an acquisition of that item. We develop a stochastic model for identifying points in time at which an item's batting average experiences significant change. In experiments with usage data from the Internet Archive, we find that such changes often occur in an abrupt, discrete fashion, and that these changes can be closely aligned with events such as the highlighting of an item on the site or the appearance of a link from an active external referrer. In this way, analyzing the dynamics of item popularity at an active web site can help characterize the impact of a range of events taking place both on and off the site.

From an informed critique of existing methods to the development of original tools, cartographic engagement can provide a unique perspective on knowledge domain visualization. Along with a discussion of some principles underlying a cartographically informed visualization methodology, results of experiments involving several thousand conference abstracts will be sketched and their plausibility reflected on.

Recent developments in question-answering systems have demonstrated that approaches based on propositional analysis of source text, in conjunction with formal inference systems, can produce substantive improvements in performance over surface-form approaches. [Voorhees, E. M. (2002) in Eleventh Text Retrieval Conference , eds. Voorhees, E. M. & Buckland, L. P., http://trec.nist.gov/pubs/trec11/t11_proceedings.html ]. However, such systems are hampered by the need to create broad-coverage knowledge bases by hand, making them difficult to adapt to new domains and potentially fragile if critical information is omitted. To demonstrate how this problem might be addressed, the Syntagmatic Paradigmatic model, a memory-based account of sentence processing, is used to autonomously extract propositional knowledge from unannotated text. The Syntagmatic Paradigmatic model assumes that people store a large number of sentence instances. When trying to interpret a new sentence, similar sentences are retrieved from memory and aligned with the new sentence by using String Edit Theory. The set of alignments can be considered an extensional interpretation of the sentence. Extracting propositional information in this way not only permits the model to answer questions for which the relevant facts are explicitly stated in the text but also allows the model to take advantage of “inference by coincidence,” where implicit inference occurs as an emergent property of the mechanism. To illustrate the potential of this approach, the model is tested for its ability to determine the winners of tennis matches as reported on the Association of Tennis Professionals web site.

A first step in identifying the content of a document is determining which topics that document addresses. We describe a generative model for documents, introduced by Blei, Ng, and Jordan [Blei, D. M., Ng, A. Y. & Jordan, M. I. (2003) J. Machine Learn. Res. 3, 993-1022], in which each document is generated by choosing a distribution over topics and then choosing each word in the document from a topic selected according to this distribution. We then present a Markov chain Monte Carlo algorithm for inference in this model. We use this algorithm to analyze abstracts from PNAS by using Bayesian model selection to establish the number of topics. We show that the extracted topics capture meaningful structure in the data, consistent with the class designations provided by the authors of the articles, and outline further applications of this analysis, including identifying “hot topics” by examining temporal dynamics and tagging abstracts to illustrate semantic content.

A review of data mining and analysis techniques that can be used for the mapping of knowledge domains is given. Literature mapping techniques can be based on authors, documents, journals, words, and/or indicators. Most mapping questions are related to research assessment or to the structure and dynamics of disciplines or networks. Several mapping techniques are demonstrated on a data set comprising 20 years of papers published in PNAS. Data from a variety of sources are merged to provide unique indicators of the domain bounded by PNAS. By using funding source information and citation counts, it is shown that, on an aggregate basis, papers funded jointly by the U.S. Public Health Service (which includes the National Institutes of Health) and non-U.S. government sources outperform papers funded by other sources, including by the U.S. Public Health Service alone. Grant data from the National Institute on Aging show that, on average, papers from large grants are cited more than those from small grants, with performance increasing with grant amount. A map of the highest performing papers over the 20-year period was generated by using citation analysis. Changes and trends in the subjects of highest impact within the PNAS domain are described. Interactions between topics over the most recent 5-year period are also detailed.

We are interested in tracking changes in large-scale data by periodically creating an agglomerative clustering and examining the evolution of clusters (communities) over time. We examine a large real-world data set: the NEC CiteSeer database, a linked network of >250,000 papers. Tracking changes over time requires a clustering algorithm that produces clusters stable under small perturbations of the input data. However, small perturbations of the CiteSeer data lead to significant changes to most of the clusters. One reason for this is that the order in which papers within communities are combined is somewhat arbitrary. However, certain subsets of papers, called natural communities, correspond to real structure in the CiteSeer database and thus appear in any clustering. By identifying the subset of clusters that remain stable under multiple clustering runs, we get the set of natural communities that we can track over time. We demonstrate that such natural communities allow us to identify emerging communities and track temporal changes in the underlying structure of our network data.

The World Wide Web provides a unprecedented opportunity to automatically analyze a large sample of interests and activity in the world. We discuss methods for extracting knowledge from the web by randomly sampling and analyzing hosts and pages, and by analyzing the link structure of the web and how links accumulate over time. A variety of interesting and valuable information can be extracted, such as the distribution of web pages over domains, the distribution of interest in different areas, communities related to different topics, the nature of competition in different categories of sites, and the degree of communication between different communities or countries.

Representations of scientific knowledge must reflect the dynamic nature of knowledge construction and the evolving networks of relations between scientific concepts. In this article, we describe initial work toward dynamic, visual methods and tools that support the construction, communication, revision, and application of scientific knowledge. Specifically, we focus on tools to capture and explore the concepts that underlie collaborative science activities, with examples drawn from the domain of human-environment interaction. These tools help individual researchers describe the process of knowledge construction while enabling teams of collaborators to synthesize common concepts. Our visualization approach links geographic visualization techniques with concept-mapping tools and allows the knowledge structures that result to be shared through a Web portal that helps scientists work collectively to advance their understanding. Our integration of geovisualization and knowledge representation methods emphasizes the process through which abstract concepts can be contextualized by the data, methods, people, and perspectives that produced them. This contextualization is a critical component of a knowledge structure, without which much of the meaning that guides the sharing of concepts is lost. By using the tools we describe here, human-environment scientists are given a visual means to build concepts from data (individually and collectively) and to connect these concepts to each other at appropriate levels of abstraction.

We present a method for creating a network of gene co-occurrences from the literature and partitioning it into communities of related genes. The way in which our method identifies communities makes it likely that the component genes of each community will be related by their function. The method processes a large database of article abstracts, synthesizing information from many sources to shed light on groups of genes that have been shown to interact. It is a tool to be used by researchers in the biomedical sciences to swiftly search for known interactions and to provide insight into unexplored connections. The partitioning procedure is designed to be particularly applicable to large networks in which individual nodes may play a role in more than one community. In this paper, we explain the details of the method, in particular the partitioning process. We also apply the method to produce communities of genes related to colon cancer and show that the results are useful.

Scientific research is highly dynamic. New areas of science continually evolve;others gain or lose importance, merge or split. Due to the steady increase in the number of scientific publications it is hard to keep an overview of the structure and dynamic development of one's own field of science, much less all scientific domains. However, knowledge of hot topics, emergent research frontiers, or change of focus in certain areas is a critical component of resource allocation decisions in research labs, governmental institutions, and corporations. This paper demonstrates the utilization of Kleinberg's burst detection algorithm, co-word occurrence analysis, and graph layout techniques to generate maps that support the identification of major research topics and trends. The approach was applied to analyze and map the complete set of papers published in the Proceedings of the National Academy of Sciences (PNAS) in the years 1982-2001. Six domain experts examined and commented on the resulting maps in an attempt to reconstruct the evolution of major research areas covered by PNAS.

The 500 different species of venomous cone snails (genus Conus ) use small, highly structured peptides (conotoxins) for interacting with prey, predators, and competitors. These peptides are produced by translating mRNA from many genes belonging to only a few gene superfamilies. Each translation product is processed to yield a great diversity of different mature toxin peptides (≈50,000–100,000), most of which are 12–30 aa in length with two to three disulfide crosslinks. In vitro , forming the biologically relevant disulfide configuration is often problematic, suggesting that in vivo mechanisms for efficiently folding the diversity of conotoxins have been evolved by the cone snails. We demonstrate here that the correct folding of a Conus peptide is facilitated by a posttranslationally modified amino acid, γ-carboxyglutamate. In addition, we show that multiple isoforms of protein disulfide isomerase are major soluble proteins in Conus venom duct extracts. The results provide evidence for the type of adaptations required before cone snails could systematically explore the specialized biochemical world of “microproteins” that other organisms have not been able to systematically access. Almost certainly, additional specialized adaptations for efficient microprotein folding are required.

Diversification of cytochrome P450 monooxygenases (P450s) is thought to result from antagonistic interactions between plants and their herbivorous enemies. However, little direct evidence demonstrates the relationship between selection by plant toxins and adaptive changes in herbivore P450s. Here we show that the furanocoumarin-metabolic activity of CYP6B proteins in two species of swallowtail caterpillars is associated with the probability of encountering host plant furanocoumarins. Catalytic activity was compared in two closely related CYP6B4 and CYP6B17 groups in the polyphagous congeners Papilio glaucus and Papilio canadensis . Generally, P450s from P. glaucus , which feeds occasionally on furanocoumarin-containing host plants, display higher activities against furanocoumarins than those from P. canadensis , which normally does not encounter furanocoumarins. These P450s in turn catalyze a larger range of furanocoumarins at lower efficiency than CYP6B1, a P450 from Papilio polyxenes , which feeds exclusively on furanocoumarin-containing host plants. Reconstruction of the ancestral CYP6B sequences using maximum likelihood predictions and comparisons of the sequence and geometry of their active sites to those of contemporary CYP6B proteins indicate that host plant diversity is directly related to P450 activity and inversely related to substrate specificity. These predictions suggest that, along the lineage leading to Papilio P450s, the ancestral, highly versatile CYP6B protein presumed to exist in a polyphagous species evolved through time into a more efficient and specialized CYP6B1-like protein in Papilio species with continual exposure to furanocoumarins. Further diversification of Papilio CYP6Bs has likely involved interspersed events of positive selection in oligophagous species and relaxation of functional constraints in polyphagous species.

The insect chemoreceptor superfamily in Drosophila melanogaster is predicted to consist of 62 odorant receptor (Or) and 68 gustatory receptor (Gr) proteins, encoded by families of 60 Or and 60 Gr genes through alternative splicing. We include two previously undescribed Or genes and two previously undescribed Gr genes; two previously predicted Or genes are shown to be alternative splice forms. Three polymorphic pseudogenes and one highly defective pseudogene are recognized. Phylogenetic analysis reveals deep branches connecting multiple highly divergent clades within the Gr family, and the Or family appears to be a single highly expanded lineage within the superfamily. The genes are spread throughout the Drosophila genome, with some relatively recently diverged genes still clustered in the genome. The Gr5a gene on the X chromosome, which encodes a receptor for the sugar trehalose, has transposed from one such tandem cluster of six genes at cytological location 64, as has Gr61a , and all eight of these receptors might bind sugars. Analysis of intron evolution suggests that the common ancestor consisted of a long N-terminal exon encoding transmembrane domains 1-5 followed by three exons encoding transmembrane domains 6-7. As many as 57 additional introns have been acquired idiosyncratically during the evolution of the superfamily, whereas the ancestral introns and some of the older idiosyncratic introns have been lost at least 48 times independently. Altogether, these patterns of molecular evolution suggest that this is an ancient superfamily of chemoreceptors, probably dating back at least to the origin of the arthropods.

All animals detect osmotic and mechanical stimuli, but the molecular basis for these responses is incompletely understood. The vertebrate transient receptor potential channel vanilloid subfamily 4 (TRPV4) (VR-OAC) cation channel has been suggested to be an osmo/mechanosensory channel. To assess its function in vivo , we expressed TRPV4 in Caenorhabditis elegans sensory neurons and examined its ability to generate behavioral responses to sensory stimuli. C. elegans ASH neurons function as polymodal sensory neurons that generate a characteristic escape behavior in response to mechanical, osmotic, or olfactory stimuli. These behaviors require the TRPV channel OSM-9 because osm-9 mutants do not avoid nose touch, high osmolarity, or noxious odors. Expression of mammalian TRPV4 in ASH neurons of osm-9 worms restored avoidance responses to hypertonicity and nose touch, but not the response to odorant repellents. Mutations known to reduce TRPV4 channel activity also reduced its ability to direct nematode avoidance behavior. TRPV4 function in ASH required the endogenous C. elegans osmotic and nose touch avoidance genes ocr-2, odr-3, osm-10 , and glr-1 , indicating that TRPV4 is integrated into the normal ASH sensory apparatus. The osmotic and mechanical avoidance responses of TRPV4-expressing animals were different in their sensitivity and temperature dependence from the responses of wild-type animals, suggesting that the TRPV4 channel confers its characteristic properties on the transgenic animals' behavior. These results provide evidence that TRPV4 can function as a component of an osmotic/mechanical sensor in vivo .

Disease resistance of plants involves two distinct forms of chemical communication with the pathogen: recognition and defense. Both are essential components of a highly complex, multifaceted defense response, which begins with non-self recognition through the perception of pathogen-derived signal molecules and results in the production, inter alia, of antibiotically active compounds (phytoalexins) and cell wall-reinforcing material around the infection site. To elucidate the molecular details and the genomic basis of the underlying chains of events, we used two different experimental systems: suspension-cultured cells of Petroselinum crispum (parsley) and wild-type as well as mutant plants of Arabidopsis thaliana . Particular emphasis was placed on the structural and functional identification of signal and defense molecules, and on the mechanisms of signal perception, intracellular signal transduction and transcriptional reprogramming, including the structural and functional characterization of the responsible cis-acting gene promoter elements and transacting regulatory proteins. Comparing P. crispum and A. thaliana allows us to distinguish species-specific defense mechanisms from more universal responses, and furthermore provides general insights into the nature of the interactions. Despite the complexity of the pathogen defense response, it is experimentally tractable, and knowledge gained so far has opened up a new realm of gene technology-assisted strategies for resistance breeding of crop plants.

Numerous plant species have been known for decades that respond to herbivore attacks by systemically synthesizing defensive chemicals to protect themselves from predators. The nature of systemic wound signals remained obscure until 1991, when an 18-aa peptide called systemin was isolated from tomato leaves and shown to be a primary signal for systemic defense. More recently, two new hydroxyproline-rich, glycosylated peptide defense signals have been isolated from tobacco leaves, and three from tomato leaves. Because of their origins in plants, small sizes, hydroxyproline contents (tomato systemin is proline-rich), and defense-signaling activities, the new peptides are included in a functionally defined family of signals collectively called systemins. Here, we review structural and biological properties of the systemin family, and discuss their possible roles in systemic wound signaling.

Many animals show intimate interactions with bacterial symbionts that provision hosts with limiting nutrients. The best studied such association is that between aphids and Buchnera aphidicola , which produces essential amino acids that are rare in the phloem sap diet. Genomic studies of Buchnera have provided a new means for inferring metabolic capabilities of the symbionts and their likely contributions to hosts. Despite evolutionary reduction of genome size, involving loss of most ancestral genes, Buchnera retains capabilities for biosynthesis of all essential amino acids. In contrast, most genes duplicating amino acid biosynthetic capabilities of hosts have been eliminated. In Buchnera of many aphids, genes for biosynthesis of leucine and tryptophan have been transferred from the chromosome to distinctive plasmids, a feature interpreted as a mechanism for overproducing these amino acids through gene amplification. However, the extent of plasmid-associated amplification varies between and within species, and plasmid-borne genes are sometimes fewer in number than single copy genes on the (polyploid) main chromosome. This supports the broader interpretation of the plasmid location as a means of achieving regulatory control of gene copy number and/or transcription. Buchnera genomes have eliminated most regulatory sequences, raising the question of the extent to which gene expression is moderated in response to changing demands imposed by host nutrition or other factors. Microarray analyses of the Buchnera transcriptome reveal only slight changes in expression of nutritionrelated genes in response to shifts in host diet, with responses less dramatic than those observed for the related nonsymbiotic species, Escherichia coli .

Tissue stem cells form the cellular base for organ homeostasis and repair. Stem cells have the unusual ability to renew themselves over the lifetime of the organ while producing daughter cells that differentiate into one or multiple lineages. Difficult to identify and characterize in any tissue, these cells are nonetheless hotly pursued because they hold the potential promise of therapeutic reprogramming to grow human tissue in vitro , for the treatment of human disease. The mammalian skin epithelium exhibits remarkable turnover, punctuated by periods of even more rapid production after injury due to burn or wounding. The stem cells responsible for supplying this tissue with cellular substrate are not yet easily distinguishable from neighboring cells. However, in recent years a significant body of work has begun to characterize the skin epithelial stem cells, both in tissue culture and in mouse and human skin. Some epithelial cells cultured from skin exhibit prodigious proliferative potential; in fact, for >20 years now, cultured human skin has been used as a source of new skin to engraft onto damaged areas of burn patients, representing one of the first therapeutic uses of stem cells. Cell fate choices, including both self-renewal and differentiation, are crucial biological features of stem cells that are still poorly understood. Skin epithelial stem cells represent a ripe target for research into the fundamental mechanisms underlying these important processes.

We recently showed that a rare cell from murine bone marrow, which we termed multipotent adult progenitor cells (MAPCs), can be expanded for >120 population doublings. Mouse (m)MAPCs differentiate into mesenchymal lineage cells as well as endothelium and endoderm, and, when injected in the blastocyst, mMAPCs contribute to most if not all somatic cell lineages including the different cell types of the brain. Our results, reported herein, demonstrate that mMAPCs can also be induced to differentiate into cells having anatomical and electrophysiological characteristics similar to those of midbrain neurons. Differentiation to a neuronal phenotype was achieved by coculturing mMAPCs with astrocytes, suggesting that neuronal differentiation may require astrocyte-derived factors similar to what is required for the differentiation of embryonic stem cells and neural stem cells to neurons. Differentiation of mMAPCs to neuron-like cells follows similar developmental steps as described for embryonic stem cells and neural stem cells. MAPCs therefore may constitute a source of cells for treatment of central nervous system disorders. ispartof: pages:11854-60 ispartof: Proceedings of the National Academy of Sciences of the United States of America vol:100 issue:Suppl 1 pages:11854-60 ispartof: Arthur M Sackler Colloquium of the National-Academy-of-Sciences on Regenerative Medicine location:CA, IRVINE date:18 Oct - 22 Oct 2002 status: published

We have tested the ability of bone marrow (BM) cells (BMCs) to form hepatocytes in liver injury models. We used three models: ( i ) carbon tetrachloride (CCl 4 ) treatment, ( ii ) albumin-urokinase transgenic mouse [TgN(Alb1Plau)], and ( iii ) hepatitis B transgenic mouse [TgN(Alb1HBV)]. As a nonselective liver injury model, irradiated C57BL/6 (B6) mice were transplanted with BMCs from GFP transgenic mouse [TgN(ActbEGFP)] or β-galactosidase transgenic mouse [TgN(MtnLacZ)] followed by the administration of CCl 4 . Irradiated TgN(Alb1HBV) and TgN(Alb1Plau) were also transplanted with BMCs from TgN(ActbEGFP) or TgN(MtnLacZ). Approximately 1.5 × 10 6 hepatocytes per liver were analyzed for GFP-positive cells, and the whole livers were inspected for β-galactosidase expression. No GFP-positive hepatocytes and no gross blue staining of the livers with 5-bromo-4-chloro-3-indolyl β- d -galactoside in any of the 18 recipient mice analyzed were detected. The livers from female animals with gender-mismatched BM transplantation were also tested with Y chromosome fluorescent in situ hybridization analysis to detect donor-derived cells. A total of five isolated hepatocytes were positive for Y chromosome in 4.1 × 10 5 hepatocytes analyzed. Our results demonstrate that there is little or no contribution of BMCs to the replacement of injured livers in these models. We conclude that BM-derived cells cannot generally lead to a cure of liver damage.

In mammalian epidermis, the level of β-catenin signaling regulates lineage selection by stem cell progeny. High levels of β-catenin stimulate formation of hair follicles, whereas low levels favor differentiation into interfollicular epidermis and sebocytes. In transgenic mouse epidermis, overexpression of β-catenin leads to formation of hair follicle tumors, whereas overexpression of N-terminally truncated Lef1, which blocks β-catenin signaling, results in spontaneous sebaceous tumors. Accompanying overexpression of β-catenin is up-regulation of Sonic hedgehog (SHH) and its receptor, Patched (PTCH/Ptch). In ΔNLef1 tumors Ptch mRNA is up-regulated in the absence of SHH. We now show that PTCH is up-regulated in both human and mouse sebaceous tumors and is accompanied by overexpression of Indian hedgehog (IHH). In normal sebaceous glands IHH is expressed in differentiated sebocytes and the transcription factor GLI1 is activated in sebocyte progenitors, suggesting a paracrine signaling mechanism. PTCH1 and IHH are up-regulated during human sebocyte differentiation in vitro and inhibition of hedgehog signaling inhibits growth and stimulates differentiation. Overexpression of ΔNLef1 up-regulates IHH and stimulates proliferation of undifferentiated sebocytes. We present a model of the interactions between β-catenin and hedgehog signaling in the epidermis in which SHH promotes proliferation of progenitors of the hair lineages whereas IHH stimulates proliferation of sebocyte precursors.

The transcription factor Sox1 is the earliest and most specific known marker for mammalian neural progenitors. During fetal development, Sox1 is expressed by proliferating progenitor cells throughout the central nervous system and in no tissue but the lens. We generated a reporter mouse line in which egfp is inserted into the Sox1 locus. Sox1 GFP animals faithfully recapitulate the expression of the endogenous gene. We have used the GFP reporter to purify neuroepithelial cells by fluorescence-activated cell sorting from embryonic day 10.5 embryos. RNAs prepared from Sox1 GFP+ and Sox1 GFP- embryo cells were then used to perform a pilot screen of subtracted cDNAs prepared from differentiating embryonic stem cells and arrayed on a glass chip. Fifteen unique differentially expressed genes were identified, all previously associated with fetal or adult neural tissue. Whole mount in situ hybridization against two genes of previously unknown embryonic expression, Lrrn1 and Musashi2 , confirmed the selectivity of this screen for early neuroectodermal markers.

Understanding the nonmonotonic behavior in the temperature dependent resistance $R$$(T)$ of strongly correlated two-dimensional (2D) carriers in clean semiconductors has been a central issue in the studies of 2D metallic states and metal-insulator transitions. We have studied the transport of high mobility 2D holes in 20-nm-wide GaAs quantum wells with varying short-range disorder strength by changing the Al fraction $x$ in the ${\mathrm{Al}}_{x}{\mathrm{Ga}}_{1\ensuremath{-}x}$As barrier. Via varying the short-range interface roughness and alloy scattering, it is observed that increasing $x$ suppresses both the strength and characteristic temperature scale of the 2D metallicity, pointing to the distinct role of short-range vs long-range disorder in the 2D metallic transport in this correlated 2D hole system with interaction parameter ${r}_{s}\ensuremath{\sim}20$.

Held on October 25, 2013, the Open Access Colloquium: Redefining Impact was the inaugural colloquium event for the Research Enterprise and Scholarly Communication Team, a unit based out of the Library at the University of Guelph. Especially for a first time event, the colloquium was a great success pulling together over 80 University of Guelph administrative leaders, faculty, students, staff, librarians and regional colleagues. The goal was to provide an inspirational and collaborative opportunity to learn, discuss, and celebrate the new imperative to scholarly communication, open access. In addition to being well attended, the colloquium was well received. Many attendees expressed positive feedback about the relevance and quality of the speakers and their presentations. Rebecca Graham, CIO and Chief Librarian opened the day with a welcoming message. Of note were the three keynote speakers: Leslie Chan, Chad Gaffield and Michael Geist. Six short lightning talk presentations were delivered by faculty who submitted interesting and related ideas about open access, Open Humanities, Open Data, Open Science, Community Engagement, and Intellectual property rights management. The day was closed by Catherine Steeves, who summed up the day by weaving together the themes and messages heard throughout the day. The following pages contain specific information and feedback about the colloquium.  KTT/OMAFRA  Open Learning & Educational Support  The Catalyst Centre  The College of Biological Science  The College of Management & Economics  The College of Social Science & Applied Human Sciences  The Library  The Ontario Agricultural College  The Ontario Veterinary College  BERESKIN & PARR LLP  Springer  Wiley

We study a quantum Otto engine operating on the basis of a helical spin- 1/2 multiferroic chain with strongly coupled magnetic and ferroelectric order parameters. The presence of a finite spin chirality in the working substance enables steering of the cycle by an external electric field that couples to the electric polarization. We observe a direct connection between the chirality, the entanglement and the efficiency of the engine. An electric-field dependent threshold temperature is identified above which the pair correlations in the system, as quantified by the thermal entanglement, diminish. In contrast to the pair correlations, the collective many-body thermal entanglement is less sensitive to the electric field, and in the high temperature limit converges to a constant value. We also discuss the correlations between the threshold temperature of the pair entanglement, the spin chirality and the minimum of the fidelities in relation to the electric and magnetic fields. The efficiency of the quantum Otto cycle shows a saturation plateau with increasing electric field amplitude., Comment: 29 pages, 17 figures, accepted for publication by New Journal of Physics

An outline of a two-hour law school colloquium discussing antebellum slave law. Topics include required reading materials, class structure, and student assessments.

Este dossiê nasceu do Colóquio “Pierre Clastres: pensar a política a contracorrente”, realizado em outubro de 2009 no Sesc Pinheiros, sob organização de Beatriz Perrone-Moisés, Renato Sztutman e Sérgio Cardoso. Reunindo antropólogos, politólogos e filósofos, o evento foi pensado como parte integrante e como movimento paralelo a um colóquio internacional em torno da obra deste autor – “Pierre Clastres e nós: liberdade política e Estado coercitivo” – que ocorreu em Paris, em novembro do mesmo ano, sob a coordenação de Miguel Abensour e Anne Kupiec. This dossier was born the Colloquium "Pierre Clastres: thinking politics to counter" held in October 2009 at SESC Pinheiros under organization

Колоквіум є формою індивідуальної роботи студентів із фахової дисципліни “Хорове диригування”. Навчальне видання містить перелік питань, критерії оцінювання відповіді та список джерел, рекомендованих для використання. Питання охоплюють історію розвитку європейської, в тому числі української, хорової творчості від епохи Відродження до наших днів, а також основні диригентсько-хорові поняття та музичні терміни. Видання адресується студентам і викладачам музично-педагогічних факультетів вищих навчальних закладів.

Колоквіум є формою індивідуальної роботи студентів із фахової дисципліни “Естрадний спів”. Навчальне видання містить перелік питань, критерії оцінювання відповіді та список джерел, рекомендованих для використання. Питання охоплюють історію розвитку світового, в тому числі українського, джазового та естрадного мистецтва від його витоків до панорами наших днів, основні аспекти розвитку рок-культури. Подаються найбільш розповсюджені музичні терміни. Видання адресується студентам і викладачам музично- педагогічних і факультетів вищих навчальних закладів.

We present a detailed numerical study of the electronic transport properties of bilayer and trilayer graphene within a framework of single-electron tight-binding model. Various types of disorder are considered, such as resonant (hydrogen) impurities, vacancies, short- or long-range Gaussian random potentials, and Gaussian random nearest neighbor hopping. The algorithms are based on the numerical solution of the time-dependent Schr \"{o}dinger equation and applied to calculate the density of states and conductivities (via the Kubo formula) of large samples containing millions of atoms. In the cases under consideration, far enough from the neutrality point, depending on the strength of disorders and the stacking sequence, a linear or sublinear electron-density dependent conductivity is found. The minimum conductivity $\sigma_{\min}\approx 2e^{2}/h$ (per layer) at the charge neutrality point is the same for bilayer and trilayer graphene, independent of the type of the impurities, but the plateau of minimum conductivity around the neutrality point is only observed in the presence of resonant impurities or vacancies, originating from the formation of the impurity band., Comment: 14 pages, 11 figures