Mapping the landscape of the lymphocytic choriomeningitis virus stable signal peptide reveals novel functional domains

The stable signal peptide (SSP) of the lymphocytic choriomeningitis virus surface glycoprotein precursor has several unique characteristics. The SSP is unusually long, at 58 amino acids, and contains two hydrophobic domains, and its sequence is highly conserved among both Old and New World arenaviruses. To better understand the functions of the SSP, a panel of point and deletion mutants was created by in vitro mutagenesis to target the highly conserved elements within the SSP. We were also able to confirm critical residues required for separate SSP functions by trans-complementation. Using these approaches, it was possible to resolve functional domains of the SSP. In characterizing our SSP mutants, we discovered that the SSP is involved in several distinct functions within the viral life cycle, beyond translocation of the viral surface glycoprotein precursor into the endoplasmic reticulum lumen. The SSP is required for efficient glycoprotein expression, posttranslational maturation cleavage of GP1 and GP2 by SKI-1/S1P protease, glycoprotein transport to the cell surface plasma membrane, formation of infectious virus particles, and acid pH-dependent glycoprotein-mediated cell fusion.

Entering dystopia, entering Erewhon

Abandon hope all ye who enter here: a society cannot be truly dystopian if travellers can come and go freely. Anti-utopias and 'satirical utopias' - that is, societies considered perfect by their advocates but not by the implied reader - must be well-regulated enough to prevent the possible disruption caused by a visitor. There is no exit at all from the classic twentieth-century dystopias, which end either in an actual death, like that of the Savage in Huxley's Brave New World (1932), or in a spiritual death like Winston Smith's in Orwell's Nineteen Eighty-Four (1949). Any glimmers of hope that the protagonist may have felt are quickly destroyed.

Reconciling biodiversity and carbon conservation

Climate change is leading to the development of land-based mitigation and adaptation strategies that are likely to have substantial impacts on global biodiversity. Of these, approaches to maintain carbon within existing natural ecosystems could have particularly large benefits for biodiversity. However, the geographical distributions of terrestrial carbon stocks and biodiversity differ. Using conservation planning analyses for the New World and Britain, we conclude that a carbon-only strategy would not be effective at conserving biodiversity, as have previous studies. Nonetheless, we find that a combined carbon-biodiversity strategy could simultaneously protect 90% of carbon stocks (relative to a carbon-only conservation strategy) and > 90% of the biodiversity (relative to a biodiversity-only strategy) in both regions. This combined approach encapsulates the principle of complementarity, whereby locations that contain different sets of species are prioritised, and hence disproportionately safeguard localised species that are not protected effectively by carbon-only strategies. It is efficient because localised species are concentrated into small parts of the terrestrial land surface, whereas carbon is somewhat more evenly distributed; and carbon stocks protected in one location are equivalent to those protected elsewhere. Efficient compromises can only be achieved when biodiversity and carbon are incorporated together within a spatial planning process.

Fire-free land use in pre-1492 Amazonian savannas

The nature and scale of pre-Columbian land use and the consequences of the 1492 “Columbian Encounter” (CE) on Amazonia are among the more debated topics in New World archaeology and paleoecology. However, pre-Columbian human impact in Amazonian savannas remains poorly understood. Most paleoecological studies have been conducted in neotropical forest contexts. Of studies done in Amazonian savannas, none has the temporal resolution needed to detect changes induced by either climate or humans before and after A.D. 1492, and only a few closely integrate paleoecological and archaeological data. We report a high-resolution 2,150-y paleoecological record from a French Guianan coastal savanna that forces reconsideration of how pre-Columbian savanna peoples practiced raised-field agriculture and how the CE impacted these societies and environments. Our combined pollen, phytolith, and charcoal analyses reveal unexpectedly low levels of biomass burning associated with pre-A.D. 1492 savanna raised-field agriculture and a sharp increase in fires following the arrival of Europeans. We show that pre-Columbian raised-field farmers limited burning to improve agricultural production, contrasting with extensive use of fire in pre-Columbian tropical forest and Central American savanna environments, as well as in present-day savannas. The charcoal record indicates that extensive fires in the seasonally flooded savannas of French Guiana are a post-Columbian phenomenon, postdating the collapse of indigenous populations. The discovery that pre-Columbian farmers practiced fire-free savanna management calls into question the widely held assumption that pre-Columbian Amazonian farmers pervasively used fire to manage and alter ecosystems and offers fresh perspectives on an emerging alternative approach to savanna land use and conservation that can help reduce carbon emissions.

Crocodiles in the regulatory swamp: navigating the dangers of outsourcing, SaaS and shadow IT

Corporates are entering the brave new world of the internet and digitization without much regard for the fine print of a growing regulation regime. More traditional outsourcing arrangements are already falling foul of the regulators as rules and supervision intensifies. Furthermore, ‘shadow IT’ is proliferating as the attractions of SaaS, mobile, cloud services, social media, and endless new ‘apps’ drive usage outside corporate IT. Initial cost-benefit analyses of the Cloud make such arrangements look immediately attractive but losing control of architecture, security, applications and deployment can have far reaching and damaging regulatory consequences. From research in financial services, this paper details the increasing body of regulations, their inherent risks for businesses and how the dangers can be pre-empted and managed. We then delineate a model for managing these risks specifically focused on investigating, strategizing and governing outsourcing arrangements and related regulatory obligations

Natural Plasmodium infections in Brazilian wild monkeys: Reservoirs for human infections?

Four hundred and forty-eight samples of total blood from wild monkeys living in areas where human autochthonous malaria cases have been reported were screened for the presence of Plasmodium using microscopy and PCR analysis. Samples came from the following distinct ecological areas of Brazil: Atlantic forest (N = 140), semideciduous Atlantic forest (N = 257) and Cerrado (a savannah-like habitat) (N = 51). Thick and thin blood smears of each specimen were examined and Plasmodium infection was screened by multiplex polymerase chain reaction (multiplex PCR). The frequency of Plasmodium infections detected by PCR in Alouatta guariba clamitans in the Sao Paulo Atlantic forest was 11.3% or 8/71 (5.6% for Plasmodium malariae and 5.6% for Plasmodium vivax) and one specimen was positive for Plasmodium falciparum (1.4%); Callithrix sp. (N = 30) and Cebus apella (N = 39) specimens were negative by PCR tests. Microscopy analysis was negative for all specimens from the Atlantic forest. The positivity rate for Alouatta caraya from semideciduous Atlantic forest was 6.8% (16/235) in the PCR tests (5.5, 0.8 and 0.4% for P. malariae, P. falciparum and P. vivax, respectively), while C apella specimens were negative. Parasitological examination of I he samples using thick smears revealed Plasmodium sp. infections in only seven specimens, which had few parasites (3.0%). Monkeys from the Cerrado (a savannah-like habitat) (42 specimens of A. caraya, 5 of Callithrix jacchus and 4 of C. apella) were negative in both tests. The parasitological prevalence of P. vivax and P. malariae in wild monkeys from Atlantic forest and semideciduous Atlantic forest and the finding of a positive result for P.falciparum in Alouatta from both types of forest support the hypothesis that monkeys belonging to this genus could be a potential reservoir. Furthermore, these findings raise the question of the relationship between simian and autochthonous human malaria in extra-Amazonian regions. (C) 2008 Elsevier B.V. All rights reserved.

How does a riverine setting affect the lifestyle of shellmound builders in Brazil?

The contact of inland and coastal prehistoric groups in Brazil is believed to have been restricted to regions with no geographical barrier, as is the case in the Ribeira de Iguape valley. The inland osteological collection from the riverine shellmound Moraes (5800-4500 BP) represents a unique opportunity to test this assumption for this region. Despite cultural similarities between riverine and coastal shellmounds, important ecological and site distribution differences are expected to impact on lifestyle. The purpose of this study is thus to document and interpret health and lifestyle indicators in Moraes in comparison to coastal shellmound groups. Specifically we test if the rare evidence of fish and mollusc remains in the riverine shellmound led to (a) higher caries rates and (b) lower auditory exostosis frequency and (c) if the small size of the riverine shellmound translates into reduced demographic density and thus rarity of communicable infectious diseases. Of the three hypotheses, (a) was confirmed, (b) was rejected and (c) was partly rejected. Bioanthropological similarities between Moraes and coastal shellmounds include auditory exostoses with equally high frequencies; significantly more frequent osteoarthritis in upper than in lower limbs; cranial and dental morphological affinities and low frequencies of violent trauma. However, there are also important differences: Moraes subsisted on a much broader protein diet and consumed more cariogenic food, but showed a stature even shorter than coastal groups. Thus, despite the contact also suggested by treponematoses in both site types, there was enough time for the people at the riverine site to adapt to local conditions. (c) 2008 Elsevier GmbH. All rights reserved.

Skull Modularity in Neotropical Marsupials and Monkeys: Size Variation and Evolutionary Constraint and Flexibility

An organism is built through a series of contingent factors, yet it is determined by historical, physical, and developmental constraints. A constraint should not be understood as an absolute obstacle to evolution, as it may also generate new possibilities for evolutionary change. Modularity is, in this context, an important way of organizing biological information and has been recognized as a central concept in evolutionary biology bridging on developmental, genetics, morphological, biochemical, and physiological studies. In this article, we explore how modularity affects the evolution of a complex system in two mammalian lineages by analyzing correlation, variance/covariance, and residual matrices (without size variation). We use the multivariate response to selection equation to simulate the behavior of Eutheria and Metharia skulls in terms of their evolutionary flexibility and constraints. We relate these results to classical approaches based on morphological integration tests based on functional/developmental hypotheses. Eutherians (Neotropical primates) showed smaller magnitudes of integration compared with Metatheria (didelphids) and also skull modules more clearly delimited. Didelphids showed higher magnitudes of integration and their modularity is strongly influenced by within-groups size variation to a degree that evolutionary responses are basically aligned with size variation. Primates still have a good portion of the total variation based on size; however, their enhanced modularization allows a broader spectrum of responses, more similar to the selection gradients applied (enhanced flexibility). Without size variation, both groups become much more similar in terms of modularity patterns and magnitudes and, consequently, in their evolutionary flexibility. J. Exp. Zool. (Mol. Dev. Evol.) 314B:663-683, 2010. (C) 2010 Wiley-Liss, Inc.

SIZE AS A LINE OF LEAST RESISTANCE II: DIRECT SELECTION ON SIZE OR CORRELATED RESPONSE DUE TO CONSTRAINTS?

Evolutionary change in New World Monkey (NWM) skulls occurred primarily along the line of least resistance defined by size (including allometric) variation (g(max)). Although the direction of evolution was aligned with this axis, it was not clear whether this macroevolutionary pattern results from the conservation of within population genetic covariance patterns (long-term constraint) or long-term selection along a size dimension, or whether both, constraints and selection, were inextricably involved. Furthermore, G-matrix stability can also be a consequence of selection, which implies that both, constraints embodied in g(max) and evolutionary changes observed on the trait averages, would be influenced by selection Here, we describe a combination of approaches that allows one to test whether any particular instance of size evolution is a correlated by-product due to constraints (g(max)) or is due to direct selection on size and apply it to NWM lineages as a case study. The approach is based on comparing the direction and amount of evolutionary change produced by two different simulated sets of net-selection gradients (beta), a size (isometric and allometric size) and a nonsize set. Using this approach it is possible to distinguish between the two hypotheses (indirect size evolution due to constraints or direct selection on size), because although both may produce an evolutionary response aligned with g(max), the amount of change produced by random selection operating through the variance/covariance patterns (constraints hypothesis) will be much smaller than that produced by selection on size (selection hypothesis). Furthermore, the alignment of simulated evolutionary changes with g(max) when selection is not on size is not as tight as when selection is actually on size, allowing a statistical test of whether a particular observed case of evolution along the line of least resistance is the result of selection along it or not. Also, with matrix diagonalization (principal components [PC]) it is possible to calculate directly the net-selection gradient on size alone (first PC [PC1]) by dividing the amount of phenotypic difference between any two populations by the amount of variation in PC1, which allows one to benchmark whether selection was on size or not

Covariance structure in the skull of Catarrhini: a case of pattern stasis and magnitude evolution

The study of the genetic variance/covariance matrix (G-matrix) is a recent and fruitful approach in evolutionary biology, providing a window of investigating for the evolution of complex characters. Although G-matrix studies were originally conducted for microevolutionary timescales, they could be extrapolated to macroevolution as long as the G-matrix remains relatively constant, or proportional, along the period of interest. A promising approach to investigating the constancy of G-matrices is to compare their phenotypic counterparts (P-matrices) in a large group of related species; if significant similarity is found among several taxa, it is very likely that the underlying G-matrices are also equivalent. Here we study the similarity of covariance and correlation structure in a broad sample of Old World monkeys and apes (Catarrhini). We made phylogenetically structured comparisons of correlation and covariance matrices derived from 39 skull traits, ranging from between species to the superfamily level. We also compared the overall magnitude of integration between skull traits (r(2)) for all Catarrhim genera. Our results show that P-matrices were not strictly constant among catarrhines, but the amount of divergence observed among taxa was generally low. There was significant and positive correlation between the amount of divergence in correlation and covariance patterns among the 30 genera and their phylogenetic distances derived from a recently proposed phylogenetic hypothesis. Our data demonstrate that the P-matrices remained relatively similar along the evolutionary history of catarrhines, and comparisons with the G-matrix available for a New World monkey genus (Saguinus) suggests that the same holds for all anthropoids. The magnitude of integration, in contrast, varied considerably among genera, indicating that evolution of the magnitude, rather than the pattern of inter-trait correlations, might have played an important role in the diversification of the catarrhine skull. (C) 2009 Elsevier Ltd. All rights reserved.

The Evolution of Modularity in the Mammalian Skull I: Morphological Integration Patterns and Magnitudes

Morphological integration refers to the modular structuring of inter-trait relationships in an organism, which could bias the direction and rate of morphological change, either constraining or facilitating evolution along certain dimensions of the morphospace. Therefore, the description of patterns and magnitudes of morphological integration and the analysis of their evolutionary consequences are central to understand the evolution of complex traits. Here we analyze morphological integration in the skull of several mammalian orders, addressing the following questions: are there common patterns of inter-trait relationships? Are these patterns compatible with hypotheses based on shared development and function? Do morphological integration patterns and magnitudes vary in the same way across groups? We digitized more than 3,500 specimens spanning 15 mammalian orders, estimated the correspondent pooled within-group correlation and variance/covariance matrices for 35 skull traits and compared those matrices among the orders. We also compared observed patterns of integration to theoretical expectations based on common development and function. Our results point to a largely shared pattern of inter-trait correlations, implying that mammalian skull diversity has been produced upon a common covariance structure that remained similar for at least 65 million years. Comparisons with a rodent genetic variance/covariance matrix suggest that this broad similarity extends also to the genetic factors underlying phenotypic variation. In contrast to the relative constancy of inter-trait correlation/covariance patterns, magnitudes varied markedly across groups. Several morphological modules hypothesized from shared development and function were detected in the mammalian taxa studied. Our data provide evidence that mammalian skull evolution can be viewed as a history of inter-module parcellation, with the modules themselves being more clearly marked in those lineages with lower overall magnitude of integration. The implication of these findings is that the main evolutionary trend in the mammalian skull was one of decreasing the constraints to evolution by promoting a more modular architecture.

East-West cranial differentiation in pre-Columbian populations from Central and North America

In a recent study we found that crania from South Amerindian populations on each side of the Andes differ significantly in terms of craniofacial shape. Western populations formed one morphological group, distributed continuously over 14,000 km from the Fuegian archipelago (southern Chile) to the Zulia region (northwestern Venezuela). Easterners formed another group, distributed from the Atlantic Coast up to the eastern foothills of the Andes. This differentiation is further supported by several genetic studies, and indirectly by ecological and archaeological studies. Some authors suggest that this dual biological pattern is consistent with differential rates of gene flow and genetic drift operating on both sides of the Cordillera due to historical reasons. Here we show that such East-West patterning is also observable in North America. We suggest that the ""ecological zones model"" proposed by Dixon, explaining the spread of the early Americans along a Pacific dispersal corridor, combined with the evolution of different population dynamics in both regions, is the most parsimonious mechanism to explain the observed patterns of within- and between-group craniofacial variability. (c) 2007 Elsevier Ltd. All rights reserved.

Taxonomy of the Threadsnakes of the tribe Epictini (Squamata: Serpentes: Leptotyphlopidae) in Colombia

Threadsnakes of the tribe Epictini are endemic to the New World, occurring from the United States to Argentina, mostly in the Neotropical region. Currently, the taxonomic status of most species is unclear and there has been no previous attempt of a comprehensive taxonomic revision of Neotropical taxa. Taxonomy of the group is a difficult task due to the paucity of geographic samples, general homogeneous morphology and brevity of species descriptions. Therefore, the only way to address the taxonomic status of existing names is through detailed characterization of the types and the search for additional material of the poorly known species. In this study, we evaluated the taxonomic status of the Colombian threadsnakes and report on geographical variation of meristic, morphometric, colour pattern, and hemipenis characters. On the basis of available samples we recognize the following species in Colombia: Epictia goudotii, E. magnamaculata, E. signata, Rena nicefori, Tricheilostoma brevissimum, T. dugandi, T. joshuai and T. macrolepis. We discuss the systematic position of Rena nicefori and propose its allocation in the genus Tricheilostoma based on a unique combination of morphological characters. Furthermore, we provide a key to the representatives of the tribe Epictini in Colombia.

Rod bipolar cells in the retina of the capuchin monkey (Cebus apella): Characterization and distribution

Rod bipolar cells in Cebus apella monkey retina were identified by an antibody against the alpha isoform of protein kinase C (PKC alpha). which has been shown to selectively identify rod bipolars in two other primates and various mammals. Vertical sections were used to confirm the identity of these cells by their characteristic morphology of dendrites and axons. Their topographic distribution was assessed in horizontal sections; counts taken along the dorsal, ventral, nasal, and temporal quadrants. The density of rod bipolar cells increased from 500 to 2900 cells/mm(2) at 1 mm from the fovea to reach a peak of 10,000-12,000 cellss/mm(2) at 4 mm, approximately 5 deg of eccentricity, and then gradually decreased toward retinal periphery to values of 5000 cells/mm(2) or less. Rod to rod bipolar density ratio remained between 10 and 20 across most of the retinal extension. The number of rod bipolar cells per retina was 6,360,000 +/- 387,433 (mean +/- S.D., n = 6). The anti-PKC alpha antibody has shown to be a good marker of rod bipolar cells of Cebus, and the cell distribution is similar to that described for other primates. In spite of the difference in the central retina, the density variation of rod bipolar cells in the Cebus and Macaca as well as the convergence from rod to rod bipolar cells are Generally similar, suggesting that both retinae stabilize similar sensitivity (as measured by rod density) and convergence.