Human-specific gain of function in a developmental enhancer

Changes in gene regulation are thought to have contributed to the evolution of human development. However, in vivo evidence for uniquely human developmental regulatory function has remained elusive. In transgenic mice, a conserved noncoding sequence (HACNS1) that evolved extremely rapidly in humans acted as an enhancer of gene expression that has gained a strong limb expression domain relative to the orthologous elements from chimpanzee and rhesus macaque. This gain of function was consistent across two developmental stages in the mouse and included the presumptive anterior wrist and proximal thumb. In vivo analyses with synthetic enhancers, in which human-specific substitutions were introduced into the chimpanzee enhancer sequence or reverted in the human enhancer to the ancestral state, indicated that 13 substitutions clustered in an 81-base pair module otherwise highly constrained among terrestrial vertebrates were sufficient to confer the human-specific limb expression domain.     

The role of informal contracts in the growth of small cattle herds on the floodplains of the Lower Amazon

In the absence of access to formal credit, informal contracts with independent investors give the small ranchers of the Lower Amazon an acceptable means through which to surmount the high investment hurdle of starting a cattle herd. These contracts – called sociedades – allow small ranchers to raise an outside investor's cattle in return for a portion of the offspring and are commonplace in the cattle production systems of the Amazon. But, notwithstanding a vast literature on cattle production in the Amazon, informal contracts have been largely overlooked. This paper presents the results of a field survey and financial analysis for informal contracts on small ranches in the Lower Amazon. In the results, we suggest that informal contracts are an important means of cattle herd start-up and herd production for small ranchers. Internal rates of returns in cattle production under these contracts are in the range of –7 to –12% for the small rancher and 12% for the investor. The net present value of the contract to the small rancher ranges from –R$1219 to –R$8599 and from R$1681 to R$8845 for the investor, for a 10-year period, depending on herd size. Financial returns contracts are sensitive to the contract design – e.g., to who pays health costs – and to beef prices. The small ranchers have a negative IRR, lose money, and bear all the risk of loss, yet persist in using this form of herd development. We surmise that this is due to the non-financial benefits of cattle ownership and the lack of access to formal credit structures. In conclusion, although outside the formal economy and apparently financially unrewarding, these contracts are an important mechanism by which the small ranchers on the Amazon Floodplains create cattle herds.     

Adventurous food futures: knowing about alternatives is not enough,we need to feel them

This paper investigates how we can enact, collectively, affording food systems. Yet rather than asking simply what those assemblages might look like the author enquires as to how they might also feel. Building on existing literature that speaks to the radically relational, and deeply affective, nature of food the aims of this paper are multiple: to learn more about how moments of difference come about in otherwise seemingly banal encounters; to understand some of the processes by which novelty ripples out, up, and through social bodies; to speak to, and suggest ways to resolve, ontological asymmetries within the agrifood literature pertaining to Cartesian dualisms; and to offer ways forward that allow agrifood scholars to talk about phenomena such as feelings and structures/barriers in the same sentence. The empirical flesh of the paper comes from an admittedly unconventional case study. On December 10, 2012, Amendment 64 was added to Colorado’s constitution making it legal for adults to consume marijuana for recreational purposes. The case examined is not about pot, however. The paper, rather, is about hopeful, hydroponic-inspired, agrifood futures; novel doings, feelings, and thinkings sparked by, among other things, food grown in basements and spare bedrooms.     

Estimation of the rootzone depth above a gravel layer (in wild blueberry fields) using electromagnetic induction method

Wild blueberry (Vaccinium angustifolium Ait.) fields in the north east Canada are naturally grown in a course textured thin layer of soil and below this layer is a soilless layer of gravel. The root zone depth of this crop varies from 10 to 15 cm. Investigating the depth to the gravel layer below the course textured soil is advantageous, as it affects the water holding capacity of the root zone. Water and nutrient management are the two primary determinants of crop yield and the amount of leaching. The objective of this study was to estimate the depth to the gravel layer using DualEM-2 instrument. A C++ program written in Visual Studio 2010 was used to develop mathematical models for estimating the depth to the gravel layer from the outputs of DualEM-2 sensor. Two wild blueberry fields were selected in central Nova Scotia, Canada to evaluate the performance of DualEM-2 instrument in estimating the rootzone depth above the gravel layer. The mid points of squares created by grid lines were used as the sampling points at each experimental site. The actual depth to the interface was measured manually at selected grid points (n = 50). The apparent ground conductivity (EC_a) values of DualEM-2 were recorded and the depth to the interface was estimated for the same sampling points within the selected fields. The fruit yield samples were also collected from the same grid points to identify the impact of the depth to the gravel layer on crop yield. After calibrations, comprehensive surveys were conducted and the actual and estimated depths to the interface were established. The interpolated maps of fruit yield, and the actual (z_in) and estimated (\( {\text{z}}_{\text{in}}^{*} \)) depths to the interface were created in ArcGIS 10 software. Results indicated that the z_in was significantly correlated with \( {\text{z}}_{\text{in}}^{*} \) for the North River (R ² = 0.73; RMSE = 0.27 m) and the Carmel (R ² = 0.45; RMSE = 0.20 m) sites. Results revealed that the areas with shallow depth to the gravel layer were low yielding, indicating that the variation in the depth to the gravel layer can have an impact on crop productivity. Non-destructive estimations of the depth to the gravel layer can be used to develop erosion control strategies, which will result in an increased crop production.     

Trans-endocytosis of CD80 and CD86: a molecular basis for the cell-extrinsic function of CTLA-4

Cytotoxic T lymphocyte antigen 4 (CTLA-4) is an essential negative regulator of T cell immune responses whose mechanism of action is the subject of debate. CTLA-4 shares two ligands (CD80 and CD86) with a stimulatory receptor, CD28. Here, we show that CTLA-4 can capture its ligands from opposing cells by a process of trans-endocytosis. After removal, these costimulatory ligands are degraded inside CTLA-4-expressing cells, resulting in impaired costimulation via CD28. Acquisition of CD86 from antigen-presenting cells is stimulated by T cell receptor engagement and observed in vitro and in vivo. These data reveal a mechanism of immune regulation in which CTLA-4 acts as an effector molecule to inhibit CD28 costimulation by the cell-extrinsic depletion of ligands, accounting for many of the known features of the CD28-CTLA-4 system.     

The historic influence of dams on diadromous fish habitat with a focus on river herring and hydrologic longitudinal connectivity

The erection of dams alters habitat and longitudinal stream connectivity for migratory diadromous and potamodromous fish species and interrupts much of organismal exchange between freshwater and marine ecosystems. In the US, this disruption began with colonial settlement in the seventeenth century but little quantitative assessment of historical impact on accessible habitat and population size has been conducted. We used published surveys, GIS layers and historical documents to create a database of 1356 dams, which was then analyzed to determine the historical timeline of construction, use and resultant fragmentation of watersheds in Maine, US. Historical information on the anadromous river herring was used to determine natural upstream boundaries to migration and establish total potential alewife spawning habitat in nine watersheds with historic populations. Dams in Maine were constructed beginning in 1634 and by 1850 had reduced accessible lake area to less than 5% of the virgin 892 km² habitat and 20% of virgin stream habitat. There is a near total loss of accessible habitat by 1860 that followed a west-east pattern of European migration and settlement. Understanding historic trends allows current restoration targets to be assessed and prioritized within an ecosystem-based perspective and may inform expectations for future management of oceanic and freshwater living resources.     

Weak effect of edges on avian nesting success in fragmented and forested landscapes in Ontario,Canada

We studied the effects of anthropogenic edges on predation and parasitism of forest bird nests in an agriculturally fragmented landscape and a continuously forested landscape in Ontario, Canada. Nesting data were collected at 1937 nests across 10 species in the fragmented landscape from 2002–2008, and 464 nests across 4 species in the continuously forested landscape from 2006–2008. Brood parasitism only occurred in the fragmented landscape, and was positively related to the proportion of rural grassland and row crop habitats within 500-m of nests. Daily nest survival was negatively related to the density of roads within 500-m of nests in the fragmented landscape, but was not influenced by distance to anthropogenic edge in either landscape. Predation rates were higher in the fragmented landscape for Ovenbird and Rose-breasted Grosbeak nests, but did not differ between landscapes for Veery and American Redstart nests. Uniformly high predation in the fragmented landscape may be a result of (1) matrix predators that penetrate deep (>300 m) into the forest interior, or (2) the additive effect of forest-dependent and matrix-associated predators that results in high predation pressure in both edge and interior habitats. Further research focused on the identification of nest predators, their population dynamics, and habitat use is required to understand the underlying mechanisms leading to uniformly high nest predation in fragmented landscapes.