Benchmarking sample pooling for epigenomics of natural populations.

DNA methylation (DNAm) is a mechanism for rapid acclimation to environmental conditions. In natural systems, small effect sizes relative to noise necessitates large sampling efforts to detect differences. Large numbers of individually sequenced libraries are costly. Pooling DNA prior to library preparation may be an efficient way to reduce costs and increase sample size, yet there are to date no recommendations in ecological epigenetics research. We test whether pooled and individual libraries yield comparable DNAm signals in a natural system exposed to different pollution levels by generating whole-epigenome data from two invasive molluscs (Corbicula fluminea, Dreissena polymorpha) collected from polluted and unpolluted localities (Italy). DNA of the same individuals were used for pooled and individual epigenomic libraries and sequenced with equivalent resources per individual. We found that pooling effectively captures similar genome-wide and global methylation signals as individual libraries, highlighting that pooled libraries are representative of the global population signal. However, pooled libraries yielded orders of magnitude more data than individual libraries, which was a consequence of higher coverage. We would therefore recommend aiming for a high initial coverage of individual libraries (15×) in future studies. Consequently, we detected many more differentially methylated regions (DMRs) with the pooled libraries and a significantly lower statistical power for regions from individual libraries. Computationally pooled data from the individual libraries produced fewer DMRs and the overlap with wet-lab pooled DMRs was relatively low. We discuss possible causes for discrepancies, list benefits and drawbacks of pooling, and provide recommendations for future epigenomic studies.

Genetic heritage of the Baphuthi highlights an over-ethnicized notion of "Bushman" in the Maloti-Drakensberg, southern Africa.

Using contemporary people as proxies for ancient communities is a contentious but necessary practice in anthropology. In southern Africa, the distinction between the Cape KhoeSan and eastern KhoeSan remains unclear, as ethnicity labels have been changed through time and most communities were decimated if not extirpated. The eastern KhoeSan may have had genetic distinctions from neighboring communities who speak Bantu languages and KhoeSan further away; alternatively, the identity may not have been tied to any notion of biology, instead denoting communities with a nomadic "lifeway" distinct from African agro-pastoralism. The Baphuthi of the 1800s in the Maloti-Drakensberg, southern Africa had a substantial KhoeSan constituency and a lifeway of nomadism, cattle raiding, and horticulture. Baphuthi heritage could provide insights into the history of the eastern KhoeSan. We examine genetic affinities of 23 Baphuthi to discern whether the narrative of KhoeSan descent reflects distinct genetic ancestry. Genome-wide SNP data (Illumina GSA) were merged with 52 global populations, for 160,000 SNPs. Genetic analyses show no support for a unique eastern KhoeSan ancestry distinct from other KhoeSan or southern Bantu speakers. The Baphuthi have strong affinities with early-arriving southern Bantu-speaking (Nguni) communities, as the later-arriving non-Nguni show strong evidence of recent African admixture possibly related to late-Iron Age migrations. The references to communities as "San" and "Bushman" in historic literature has often been misconstrued as notions of ethnic/biological distinctions. The terms may have reflected ambiguous references to non-sedentary polities instead, as seems to be the case for the eastern "Bushman" heritage of the Baphuthi.

Metabolic labeling of secreted matrix to investigate cell-material interactions in tissue engineering and mechanobiology.

Re-creating features of the native extracellular matrix (ECM) with engineered biomaterials has become a valuable tool to probe the influence of ECM properties on cellular functions (e.g., differentiation) and toward the engineering of tissues. However, characterization of newly secreted (nascent) matrix and turnover, which are important in the context of cells interacting with these biomaterials, has been limited by a lack of tools. We developed a protocol to visualize and quantify the spatiotemporal evolution of newly synthesized and deposited matrix by cells that are either cultured atop (2D) or embedded within (3D) biomaterial systems (e.g., hydrogels, fibrous matrices). This technique relies on the incorporation of a noncanonical amino acid (azidohomoalanine) into proteins as they are synthesized. Deposited nascent ECM components are then visualized with fluorescent cyclooctynes via copper-free cycloaddition for spatiotemporal analysis or modified with cleavable biotin probes for identification. Here we describe the preparation of hyaluronic acid hydrogels through ultraviolet or visible light induced cross-linking for 2D and 3D cell culture, as well as the fluorescent labeling of nascent ECM deposited by cells during culture. We also provide protocols for secondary immunofluorescence of specific ECM components and ImageJ-based ECM quantification methods. Hyaluronic acid polymer synthesis takes 2 weeks to complete, and hydrogel formation for 2D or 3D cell culture is performed in 2-3 h. Lastly, we detail the identification of nascent proteins, including enrichment, preparation and analysis with mass spectrometry, which can be completed in 10 d.

Nanowire networks: how does small-world character evolve with dimensionality?

Networks of nanowires are currently under consideration for a wide range of electronic and optoelectronic applications. Nanowire devices are usually made by sequential deposition, which inevitably leads to stacking of the wires on top of one another. Here we demonstrate the effect of stacking on the topology of the resulting networks. We compare perfectly 2D networks with quasi-3D networks, and compare both nanowire networks to the corresponding Watts Strogatz networks, which are standard benchmark systems. By investigating quantities such as clustering, path length, modularity, and small world propensity we show that the connectivity of the quasi-3D networks is significantly different to that of the 2D networks, a result which may have important implications for applications of nanowire networks.

Flower orientation in Gloriosa superba (Colchicaceae) promotes cross-pollination via butterfly wings.

BACKGROUND AND AIMS: Complex modifications of angiosperm flowers often function for precise pollen placement on pollinators and to promote cross-pollination. We explore the functional significance of the unusually elaborate morphology of Gloriosa superba flowers, which are divided into one hermaphrodite meranthium and five male meranthia (functional pollination units of a single flower). METHODS: We used controlled pollination experiments, floral measurements, pollen load analyses and visitor observations in four populations of G. superba in South Africa to determine the breeding system, mechanism of pollination and role of flower in the promotion of cross-pollination. KEY RESULTS: We established that G. superba is self-compatible, but reliant on pollinators for seed production. Butterflies, in particular the pierid Eronia cleodora, were the primary pollinators (>90 % of visitors). Butterflies brush against the anthers and stigma during nectar feeding and pollen is carried on their ventral wing surfaces. Butterfly scales were positively correlated with the number of pollen grains on stigmas. We demonstrate that the styles were orientated towards clearings in the vegetation and we confirm that the highest proportion of initial visits was to hermaphrodite meranthia pointing towards clearings. CONCLUSIONS: The flower morphology of G. superba results in effective pollen transfer on the wings of butterfly visitors. The style-bearing hermaphrodite meranthium of the flowers orientates towards open spaces in the vegetation, thus increasing the probability that butterflies land first on the hermaphrodite meranthium. This novel aspect of flower orientation is interpreted as a mechanism that promotes cross-pollination.