A tyrosine-based motif in the cytoplasmic tail of pseudorabies virus glycoprotein B is important for both antibody-induced internalization of viral glycoproteins and efficient cell-to-cell spread

Pseudorabies virus (PRV), a swine alphaherpesvirus, is capable of causing viremia in vaccinated animals. Two mechanisms that may help PRV avoid recognition by the host immune system during this viremia are direct cell-to-cell spread in tissue and antibody-induced internalization of viral cell surface glycoproteins in PRV-infected blood monocytes, the carrier cells of the virus in the blood. PRV glycoprotein B (gB) is crucial during both processes. Here we show that mutating a tyrosine residue located in a YXXPhi motif in the gB cytoplasmic tail results in decreased efficiency of cell-to-cell spread and a strong reduction in antibody-induced internalization of viral cell surface glycoproteins. Mutating the dileucine motif in the gB tail led to an increased cell-to-cell spread of the virus and the formation of large syncytia.     

The evolution of courtship rituals in monogamous species

In this paper we propose an alternative explanation for theevolution of courtship rituals in monogamous species. We demonstrate,using computer simulations, how male courtship might developas males exploit response biases in females to manipulate thefemale into starting reproduction before she has been ableto assess the male's intentions. In our coevolutionary simulations, a recurrent, artificial neural network is used to model thefemale recognition mechanism, while the displaying male isrepresented by a sequence of signals. Our particular modelsituation is just one example of how a reproductive conflictcould result in the evolution of ritualized displays in monogamous species. Since reproductive conflicts occur even after pairformations, the explanation we propose may also apply to ritualsthat occur after pair formation.     

Correlations in fertility across generations: can low fertility persist?

Correlations in family size across generations could have a major influence on human population size in the future. Empirical studies have shown that the associations between the fertility of parents and the fertility of children are substantial and growing over time. Despite their potential long-term consequences, intergenerational fertility correlations have largely been ignored by researchers. We present a model of the fertility transition as a cultural process acting on new lifestyles associated with fertility. Differences in parental and social influences on the acquisition of these lifestyles result in intergenerational correlations in fertility. We show different scenarios for future population size based on models that disregard intergenerational correlations in fertility, models with fertility correlations and a single lifestyle, and models with fertility correlations and multiple lifestyles. We show that intergenerational fertility correlations will result in an increase in fertility over time. However, present low-fertility levels may persist if the rapid introduction of new cultural lifestyles continues into the future.     

John N. Brady (1952-2009): a Generous Spirit

John N. Brady, Chief of the Virus Tumor Biology Section of the Laboratory of Cellular Oncology, National Institutes of Health, died of cancer on 27 April 2009. John was a stellar member of the virology community. He was a longtime Journal of Virology reviewer and a member of the editorial board. He will be missed. Fatah Kashanchi of the George Washington University Medical Center has written John''s memorial. Fatah worked with John at the NIH and published more than 30 papers with him. Fatah thanks all the people who contributed to John''s obituary, including Kuan-Teh Jeang, Lou Laimins, Mary Loeken, Renaud Mehieux, Paul Lambert, Graziella Piras, Scott Gitlin, Paul Lindholm, Nadia Rosenthal, Sergi Nekhai, Brian Wigdahl, David Price, Susan J. Marriott, Cynthia Masison, Jurgen Dittmer, Eric Verdin, Bassel E. Sawaya, and John''s longtime assistants Janet Duvall Grimm and Michael Radonovich, who gave immense support to all the individuals who went through John''s lab.     

The taxonomic name resolution service: an online tool for automated standardization of plant names

Background

The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science.

Results

The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets.

Conclusions

We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/.     

An empirical assessment of tree branching networks and implications for plant allometric scaling models

Several theories predict whole‐tree function on the basis of allometric scaling relationships assumed to emerge from traits of branching networks. To test this key assumption, and more generally, to explore patterns of external architecture within and across trees, we measure branch traits (radii/lengths) and calculate scaling exponents from five functionally divergent species. Consistent with leading theories, including metabolic scaling theory, branching is area preserving and statistically self‐similar within trees. However, differences among scaling exponents calculated at node‐ and whole‐tree levels challenge the assumption of an optimised, symmetrically branching tree. Furthermore, scaling exponents estimated for branch length change across branching orders, and exponents for scaling metabolic rate with plant size (or number of terminal tips) significantly differ from theoretical predictions. These findings, along with variability in the scaling of branch radii being less than for branch lengths, suggest extending current scaling theories to include asymmetrical branching and differential selective pressures in plant architectures.     

Warming up the system: higher predator feeding rates but lower energetic efficiencies

Predictions on the consequences of the rapidly increasing atmospheric CO₂ levels and associated climate warming for population dynamics, ecological community structure and ecosystem functioning depend on mechanistic energetic models of temperature effects on populations and their interactions. However, such mechanistic approaches combining warming effects on metabolic (energy loss of organisms) and feeding rates (energy gain by organisms) remain a key, yet elusive, goal. Aiming to fill this void, we studied the metabolic rates and functional responses of three differently sized, predatory ground beetles on one mobile and one more resident prey species across a temperature gradient (5, 10, 15, 20, 25 and 30 °C). Synthesizing metabolic and functional‐response theory, we develop novel mechanistic predictions how predator–prey interaction strengths (i.e., functional responses) should respond to warming. Corroborating prior theory, warming caused strong increases in metabolism and decreases in handling time. Consistent with our novel model, we found increases in predator attack rates on a mobile prey, whereas attack rates on a mostly resident prey remained constant across the temperature gradient. Together, these results provide critically important information that environmental warming generally increases the direct short‐term per capita interaction strengths between predators and their prey as described by functional‐response models. Nevertheless, the several fold stronger increase in metabolism with warming caused decreases in energetic efficiencies (ratio of per capita feeding rate to metabolic rate) for all predator–prey interactions. This implies that warming of natural ecosystems may dampen predator–prey oscillations thus stabilizing their dynamics. The severe long‐term implications; however, include predator starvation due to energetic inefficiency despite abundant resources.     

Venation networks and the origin of the leaf economics spectrum

The leaf economics spectrum describes biome-invariant scaling functions for leaf functional traits that relate to global primary productivity and nutrient cycling. Here, we develop a comprehensive framework for the origin of this leaf economics spectrum based on venation-mediated economic strategies. We define a standardized set of traits - density, distance and loopiness - that provides a common language for the study of venation. We develop a novel quantitative model that uses these venation traits to model leaf-level physiology, and show that selection to optimize the venation network predicts the mean global trait-trait scaling relationships across 2548 species. Furthermore, using empirical venation data for 25 plant species, we test our model by predicting four key leaf functional traits related to leaf economics: net carbon assimilation rate, life span, leaf mass per area ratio and nitrogen content. Together, these results indicate that selection on venation geometry is a fundamental basis for understanding the diversity of leaf form and function, and the carbon balance of leaves. The model and associated predictions have broad implications for integrating venation network geometry with pattern and process in ecophysiology, ecology and palaeobotany.     

A dual infection pseudorabies virus conditional reporter approach to identify projections to collateralized neurons in complex neural circuits

Replication and transneuronal transport of pseudorabies virus (PRV) are widely used to define the organization of neural circuits in rodent brain. Here we report a dual infection approach that highlights connections to neurons that collateralize within complex networks. The method combines Cre recombinase (Cre) expression from a PRV recombinant (PRV-267) and Cre-dependent reporter gene expression from a second infecting strain of PRV (PRV-263). PRV-267 expresses both Cre and a monomeric red fluorescent protein (mRFP) fused to viral capsid protein VP26 (VP26-mRFP) that accumulates in infected cell nuclei. PRV-263 carries a Brainbow cassette and expresses a red (dTomato) reporter that fills the cytoplasm. However, in the presence of Cre, the dTomato gene is recombined from the cassette, eliminating expression of the red reporter and liberating expression of either yellow (EYFP) or cyan (mCerulean) cytoplasmic reporters. We conducted proof-of-principle experiments using a well-characterized model in which separate injection of recombinant viruses into the left and right kidneys produces infection of neurons in the renal preautonomic network. Neurons dedicated to one kidney expressed the unique reporters characteristic of PRV-263 (cytoplasmic dTomato) or PRV-267 (nuclear VP26-mRFP). Dual infected neurons expressed VP26-mRFP and the cyan or yellow cytoplasmic reporters activated by Cre-mediated recombination of the Brainbow cassette. Differential expression of cyan or yellow reporters in neurons lacking VP26-mRFP provided a unique marker of neurons synaptically connected to dual infected neurons, a synaptic relationship that cannot be distinguished using other dual infection tracing approaches. These data demonstrate Cre-enabled conditional reporter expression in polysynaptic circuits that permits the identification of collateralized neurons and their presynaptic partners.