Organic Fertilization and Sufficient Nutrient Status in Prehistoric Agriculture? – Indications from Multi-Proxy Analyses of Archaeological Topsoil Relicts

Neolithic and Bronze Age topsoil relicts revealed enhanced extractable phosphorus (P) and plant available inorganic P fractions, thus raising the question whether there was targeted soil amelioration in prehistoric times. This study aimed (i) at assessing the overall nutrient status and the soil organic matter content of these arable topsoil relicts, and (ii) at tracing ancient soil fertilizing practices by respective stable isotope and biomarker analyses. Prehistoric arable topsoils were preserved in archaeological pit fillings, whereas adjacent subsoils served as controls. One Early Weichselian humic zone represented the soil status before the introduction of agriculture. Recent topsoils served as an additional reference. The applied multi-proxy approach comprised total P and micronutrient contents, stable N isotope ratios, amino acid, steroid, and black carbon analyses as well as soil color measurements. Total contents of P and selected micronutrients (I, Cu, Mn, Mo, Se, Zn) of the arable soil relicts were above the limits for which nutrient deficiencies could be assumed. All pit fillings exhibited elevated δ¹⁵N values close to those of recent topsoils (δ¹⁵N>6 to 7‰), giving first hints for prehistoric organic N-input. Ancient legume cultivation as a potential source for N input could not be verified by means of amino acid analysis. In contrast, bile acids as markers for faecal input exhibited larger concentrations in the pit fillings compared with the reference and control soils indicating faeces (i.e. manure) input to Neolithic arable topsoils. Also black carbon contents were elevated, amounting up to 38% of soil organic carbon, therewith explaining the dark soil color in the pit fillings and pointing to inputs of burned biomass. The combination of different geochemical analyses revealed a sufficient nutrient status of prehistoric arable soils, as well as signs of amelioration (inputs of organic material like charcoal and faeces-containing manure).     

Mating Resets Male Cricket Aggression

An animal’s motivational state can significantly impact its behavior. We examined the effects of mating on the aggression of male Acheta domesticus crickets. Pairs of males were allowed to establish dominance and subordinance and were then physically separated. Subordinate males were then allowed to either copulate with a female or to have chemo-tactile contact with, but to not copulate with, a female. Less than 15 min after separation, all male pairs engaged in a second agonistic encounter. Subordinate males that copulated with females were significantly more aggressive toward their dominant partners than un-mated subordinate males. Many mated subordinates became dominant. Allowing a subordinate male to contact, but not copulate with, a female had a similar effect, suggesting that chemo-tactile cues from the female are sufficient to elicit this change in aggression.     

An approach to functionally relevant clustering of the protein universe: Active site profile‐based clustering of protein structures and sequences

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification—amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two‐Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure‐Function Linkage Database, SFLD) self‐identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self‐identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well‐curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP‐identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F‐measure and performance analysis on the enolase search results and comparison to GEMMA and SCI‐PHY demonstrate that TuLIP avoids the over‐division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results.     

Engaging with Dementia: Moral Experiments in Art and Friendship

The box-office as well as critical success of the 2014 major motion picture Still Alice, starring Julianne Moore in the title role and based on the bestselling novel of the same name by the Harvard-trained neuroscientist Lisa Genova (Still Alice. Simon & Schuster, New York, 2009), marked an important moment in public cultural representations of people with dementia. Still Alice tells the story of Alice Howland, an eminent scientist whose increasing memory lapses are eventually diagnosed as early-onset Alzheimer’s, and chronicles the transformations in her family relationships as her husband and three children respond to her decline in different ways. Alice’s husband, her son, and her older daughter all respond by turning toward science, while her younger daughter Lydia seeks to engage her mother as she is now, and turns toward art and relationships. Taking Still Alice and the figure of Lydia as an entry point, I discuss arts-focused efforts to improve the lives of people with dementia, and draw upon ongoing interview-based research on the topic of dementia and friendship, to offer an account of some of the ways that people I have spoken with are actively experimenting with art and with relationships in the face of dementia. I argue that these efforts can be understood as “moral experiements,” in the sense articulated by Cheryl Mattingly (Moral Laboratories: Family Peril and the Struggle for a Good Life. University of California Press, Berkeley, 2014). Although Lydia is a fictional character, her response to Alice’s dementia points toward the kinds of moral experimentation that are in fact possible, and quietly being practiced, by ordinary people every day.     

High-content single-cell drug screening with phosphospecific flow cytometry

Drug screening is often limited to cell-free assays involving purified enzymes, but it is arguably best applied against systems that represent disease states or complex physiological cellular networks. Here, we describe a high-content, cell-based drug discovery platform based on phosphospecific flow cytometry, or phosphoflow, that enabled screening for inhibitors against multiple endogenous kinase signaling pathways in heterogeneous primary cell populations at the single-cell level. From a library of small-molecule natural products, we identified pathway-selective inhibitors of Jak-Stat and MAP kinase signaling. Dose-response experiments in primary cells confirmed pathway selectivity, but importantly also revealed differential inhibition of cell types and new druggability trends across multiple compounds. Lead compound selectivity was confirmed in vivo in mice. Phosphoflow therefore provides a unique platform that can be applied throughout the drug discovery process, from early compound screening to in vivo testing and clinical monitoring of drug efficacy.