Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana

The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and approximately 4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.     

The foot and ankle of Australopithecus sediba

A well-preserved and articulated partial foot and ankle of Australopithecus sediba, including an associated complete adult distal tibia, talus, and calcaneus, have been discovered at the Malapa site, South Africa, and reported in direct association with the female paratype Malapa Hominin 2. These fossils reveal a mosaic of primitive and derived features that are distinct from those seen in other hominins. The ankle (talocrural) joint is mostly humanlike in form and inferred function, and there is some evidence for a humanlike arch and Achilles tendon. However, Au. sediba is apelike in possessing a more gracile calcaneal body and a more robust medial malleolus than expected. These observations suggest, if present models of foot function are correct, that Au. sediba may have practiced a unique form of bipedalism and some degree of arboreality. Given the combination of features in the Au. sediba foot, as well as comparisons between Au. sediba and older hominins, homoplasy is implied in the acquisition of bipedal adaptations in the hominin foot.     

Immersive landscapes: modelling ecosystem reference conditions in virtual reality

Landscape Ecology - Understanding the variability and dynamics of ecosystems, as well as their responses to climate or land use change, is challenging for policy makers and natural resource...     

Activity of feline interferon-omega after ocular or oral administration in cats as indicated by Mx protein expression in conjunctival and white blood cells

OBJECTIVE: To assess the biological response to recombinant feline interferon-omega (rFeIFN-omega) following ocular or oral administration in cats via estimation of Mx protein expression in conjunctival cells (CCs) and WBCs. ANIMALS: 10 specific pathogen-free cats. PROCEDURES: In multiple single-dose drug experiments, each cat received various concentrations of rFeIFN-omega administered topically into both eyes (50 to 10,000 U/eye) and orally (200 to 20,000 units). The same cats received saline (0.9% NaCl) solution topically and orally as control treatments. The CCs and WBCs were collected prior to treatment (day 0), on day 1, and every third or seventh day thereafter until samples yielded negative results for Mx protein. Samples were examined for Mx protein expression via immunohistochemistry and immunoblotting procedures involving murine anti-Mx protein monoclonal antibody M143. RESULTS: After topical application of 10,000 U of rFeIFN-omega/eye, CCs stained for Mx protein for a minimum of 7 days, whereas WBCs were positive for Mx protein for a minimum of 31 days. After topical application of lower concentrations, CCs did not express Mx protein, in contrast to WBCs, which stained for Mx protein at 1,000 units for at least 1 day. Following oral administration, Mx protein was expressed in WBCs at rFeIFN-omega concentrations as low as 200 units, whereas CCs did not stain for Mx protein at any concentration. CONCLUSIONS AND CLINICAL RELEVANCE: Results indicate that Mx protein expression (a marker of the biological response to rFeIFN-omega) in CCs and WBCs of rFeIFN-omega-treated cats depends on the dose of rFeIFN-omega, site of administration, and cell type.     

Hydraulic traits and tree-ring width in <Emphasis Type="Italic">Larix sibirica</Emphasis> Ledeb. as affected by summer drought and forest fragmentation in the Mongolian forest steppe

Key message

Wood-anatomical traits determining the hydraulic architecture of Larix sibirica in the drought-limited Mongolian forest steppe at the southern fringe of the boreal forest respond to summer drought, but only weakly to variations in microclimate that depend on forest stand size.

Context

Siberian larch (L. sibirica Ledeb.) is limited by summer drought and shows increasing mortality rates in the Mongolian forest steppe. The climate sensitivity of stemwood formation increases with decreasing forest stand size. The trees’ hydraulic architecture is crucial for drought resistance and thus the capability to deal with climate warming.

Aims

We studied whether hydraulic traits were influenced by temporal or forest size-dependent variations in water availability and were related to tree-ring width.

Methods

Hydraulic traits (tracheid diameter, tracheid density, potential sapwood area-specific hydraulic conductivity) of earlywood were studied in stemwood series of 30 years (1985–2014) and were related to climate data. Tree-ring width was measured for the same period. Trees were selected in stands of four different size classes with increasing drought exposure with decreasing stand size.

Results

Tracheid diameters and hydraulic conductivity decreased with decreasing late summer precipitation of the previous year and were positively correlated with tree-ring width. Forest stand size had only weak effects on hydraulic traits, despite known effects on stemwood increment.

Conclusion

Decreasing tracheid diameters and thus hydraulic conductivity are a drought acclimation of L. sibirica in the Mongolian forest steppe. These acclimations occur as a response to drought periods but are little site-dependent with respect to stand size.

     

Metropolitan farmers markets in Minneapolis and Vienna: a values-based comparison

Farmers markets (FMs) have traditionally served as a space for farmers to sell directly to consumers. Recently, many FMs in the US and other regions have experienced a renaissance. This article compares the different value sets embedded in the rules and norms of two metropolitan FM regions—Minneapolis, Minnesota and in Vienna, Austria. It uses a values-based framework that reflects the relationships among FM operating structures (OS) and their values reflected by the key FM participants—i.e., farmer/vendors, consumers and market managers. The framework allows us to focus on two very contrasting value sets of metropolitan FM regions in (1) presenting and discussing the values found and embedded in the two metropolitan market regions; (2) illustrating how the values found are embodied as rules and norms in each FM region; (3) considering the alignment or not of FM participant values with their corresponding FM values; and (4) the differences and commonalities as well as the benefits and challenges of the two market regions. In contrasting metropolitan FMs we explain that FM value sets are complex and differ among and within FM participant groups and are dependent on their respective OS. We show that contrasting two metropolitan FM regions can be useful in understanding beneficial and disadvantageous relationships between the values and structures of, and in FMs, and specifically in examining institutional impediments such as governance. Thus we illustrate the possibilities and limitations of values for and within metropolitan FMs.