assignPOP: An r package for population assignment using genetic, non-genetic, or integrated data in a machine-learning framework
Kuan-Yu Chen, Elizabeth A. Marschall, Michael G. Sovic, Anthony C. Fries, H. Lisle Gibbs, Stuart A. Ludsin. 2017. Methods Ecol Evol. 00:1–8. https://doi.org/10.1111/2041-210X.12897
The use of biomarkers (e.g., genetic, microchemical and morphometric characteristics) to discriminate among and assign individuals to a population can benefit species conservation and management by facilitating our ability to understand population structure and demography.
Tools that can evaluate the reliability of large genomic datasets for population discrimination and assignment, as well as allow their integration with non-genetic markers for the same purpose, are lacking. Our r package, assignPOP, provides both functions in a supervised machine-learning framework.
assignPOP uses Monte-Carlo and K-fold cross-validation procedures, as well as principal component analysis, to estimate assignment accuracy and membership probabilities, using training (i.e., baseline source population) and test (i.e., validation) datasets that are independent. A user then can build a specified predictive model based on the relative sizes of these datasets and classification functions, including linear discriminant analysis, support vector machine, naïve Bayes, decision tree and random forest.
assignPOP can benefit any researcher who seeks to use genetic or non-genetic data to infer population structure and membership of individuals. assignPOP is a freely available r package under the GPL license, and can be downloaded from CRAN or at https://github.com/alexkychen/assignPOP. A comprehensive tutorial can also be found at https://alexkychen.github.io/assignPOP/.
Fresh produce and their soils accumulate cyanotoxins from irrigation water: Implications for public health and food security
Seungjun Le, Xuewen Jiang, Manjunath Manubolu, Ken Riedl, Stuart A. Ludsin, Jay F. Martin, Jiyoung Lee. Food Research International. 2017. https://doi.org/10.1016/j.foodres.2017.09.079
Microcystin (MC), a hepatotoxin that can adversely affect human health, has become more prevalent in freshwater ecosystems worldwide, owing to an increase in toxic cyanobacteria blooms. While consumption of water and fish are well-documented exposure pathways of MCs to humans, less is known about the potential transfer to humans through consumption of vegetables that have been irrigated with MC-contaminated water. Likewise, the impact of MC on the performance of food crops is understudied. To help fill these information gaps, we conducted a controlled laboratory experiment in which we exposed lettuce, carrots, and green beans to environmentally relevant concentrations of MC-LR (0, 1, 5, and 10 μg/L) via two irrigation methods (drip and spray). We used ELISA and LC-MS/MS to quantify MC-LR concentrations and in different parts of the plant (edible vs. inedible fractions), measured plant performance (e.g., size, mass, edible leaves, color), and calculated human exposure risk based on accumulation patterns. MC-LR accumulation was positively dose-dependent, with it being greater in the plants (2.2–209.2 μg/kg) than in soil (0–19.4 μg/kg). MC-LR accumulation varied among vegetable types, between plant parts, and between irrigation methods. MC-LR accumulation led to reduced crop growth and quality, with MC-LR persisting in the soil after harvest. Observed toxin accumulation patterns in edible fractions of plants also led to estimates of daily MC-LR intake that exceeded both the chronic reference dose (0.003 μg/kg of body weight) and total daily intake guidelines (0.04 μg/kg of body weight). Because the use of MC-contaminated water is common in many parts of the world, our collective findings highlight the need for guidelines concerning the use of MC-contaminated water in irrigation, as well as consumption of these crops.
Photolysis- and Dissolved Organic Matter-Induced Toxicity of Triclocarban to Daphnia magna
Katie A. Albanese, Roman P. Lanno, Christopher M. Hadad, and Yu-Ping Chin. 2017. Environ. Sci. Technol. Lett. DOI: 10.1021/acs.estlett.7b00429
Triclocarban (TCC) is a common antimicrobial compound used in soaps and other household products and is found globally in many surface waters. This study investigated the acute toxicity of TCC and its photolyzed products to Daphnia magna using 50% 96-h lethal concentration (LC50) tests. The effects of dissolved organic matter (DOM) on the toxicity of TCC photoproducts to D. magna were also studied. Direct photolysis of TCC formed photoproducts that were significantly less toxic (LC50 value of 2.67 ± 0.6 μM) than the parent TCC compound (LC50 value of 0.087 ± 0.3 μM). In contrast, the indirect photolysis of TCC in the presence of DOM produced photoproducts that were significantly more toxic (LC50 value of 0.032 ± 0.015 μM). Chlorinated anilines and isocyanates, identified by mass spectrometry, were formed in the presence of DOM as indirect photolysis products of TCC and were shown to be partially responsible for the observed toxicity.
Keeping time without a spine: what can the insect clock teach us about seasonal adaptation?
David L. Denlinger, Daniel A. Hahn, Christine Merlin, Christina M. Holzapfel, William E. Bradshaw. 2017. Philosophical Transactions of the Royal Society B. 372(1737). DOI: 10.1098/rstb.2016.0257
Seasonal change in daylength (photoperiod) is widely used by insects to regulate temporal patterns of development and behaviour, including the timing of diapause (dormancy) and migration. Flexibility of the photoperiodic response is critical for rapid shifts to new hosts, survival in the face of global climate change and to reproductive isolation. At the same time, the daily circadian clock is also essential for development, diapause and multiple behaviours, including correct flight orientation during long-distance migration. Although studied for decades, how these two critical biological timing mechanisms are integrated is poorly understood, in part because the core circadian clock genes are all transcription factors or regulators that are able to exert multiple effects throughout the genome. In this chapter, we discuss clocks in the wild from the perspective of diverse insect groups across eco-geographic contexts from the Antarctic to the tropical regions of Earth. Application of the expanding tool box of molecular techniques will lead us to distinguish universal from unique mechanisms underlying the evolution of circadian and photoperiodic timing, and their interaction across taxonomic and ecological contexts represented by insects.
Infection of army ant pupae by two new parasitoid mites (Mesostigmata: Uropodina)
Adrian Brückner, Hans Klompen, Andrew Iain Bruce, Rosli Hashim, Christoph von Beeren. 2017. PeerJ 5:e3870. https://doi.org/10.7717/peerj.3870
A great variety of parasites and parasitoids exploit ant societies. Among them are the Mesostigmata mites, a particularly common and diverse group of ant-associated arthropods. While parasitism is ubiquitous in Mesostigmata, parasitoidism has only been described in the genus Macrodinychus. Yet information about the basic biology of most Macrodinychus species is lacking. Out of 24 formally described species, information about basic life-history traits is only available for three species. Here we formally describe two new Macrodinychus species, i.e. Macrodinychus hilpertae and Macrodinychus derbyensis. In both species, immature stages developed as ecto-parasitoids on ant pupae of the South-East Asian army ant Leptogenys distinguenda. By piercing the developing ant with their chelicera, the mites apparently suck ant hemolymph, ultimately killing host individuals. We compare infection rates among all studied Macrodinychus species and discuss possible host countermeasures against parasitoidism. The cryptic lifestyle of living inside ant nests has certainly hampered the scientific discovery of Macrodinychus mites and we expect that many more macrodinychid species await scientific discovery and description.
State-dependent metabolic partitioning and energy conservation: A theoretical framework for understanding the function of sleep
Markus H. Schmidt , Theodore W. Swang, Ian M. Hamilton, Janet A. Best. 2017. https://doi.org/10.1371/journal.pone.0185746
Metabolic rate reduction has been considered the mechanism by which sleep conserves energy, similar to torpor or hibernation. This mechanism of energy savings is in conflict with the known upregulation (compared to wake) of diverse functions during sleep and neglects a potential role in energy conservation for partitioning of biological operations by behavioral state. Indeed, energy savings as derived from state-dependent resource allocations have yet to be examined. A mathematical model is presented based on relative rates of energy deployment for biological processes upregulated during either wake or sleep. Using this model, energy savings from sleep-wake cycling over constant wakefulness is computed by comparing stable limit cycles for systems of differential equations. A primary objective is to compare potential energy savings derived from state-dependent metabolic partitioning versus metabolic rate reduction. Additionally, energy conservation from sleep quota and the circadian system are also quantified in relation to a continuous wake condition. As a function of metabolic partitioning, our calculations show that coupling of metabolic operations with behavioral state may provide comparatively greater energy savings than the measured decrease in metabolic rate, suggesting that actual energy savings derived from sleep may be more than 4-fold greater than previous estimates. A combination of state-dependent metabolic partitioning and modest metabolic rate reduction during sleep may enhance energy savings beyond what is achievable through metabolic partitioning alone; however, the relative contribution from metabolic partitioning diminishes as metabolic rate is decreased during the rest phase. Sleep quota and the circadian system further augment energy savings in the model. Finally, we propose that state-dependent resource allocation underpins both sleep homeostasis and the optimization of daily energy conservation across species. This new paradigm identifies an evolutionary selective advantage for the upregulation of central and peripheral biological processes during sleep, presenting a unifying construct to understand sleep function.
Craniodental morphology and diet of Leptarctus oregonensis (Mammalia, Carnivora, Mustelidae) from the Mascall Formation (Miocene) of central Oregon
Jonathan J. Calede, Winifred A. Kehl, and Edward B. Davis. 2017. Journal of Paleontology. in press. doi: 10.1017/jpa.2017.78
The Leptarctinae are an enigmatic subfamily of mustelids present in North America and Eurasia during the Miocene (Arikareean to Hemphillian North American Land Mammal Ages). Their diet and ecology have been particularly controversial. Some workers have suggested they were similar to koalas, whereas others suggested they were crushing omnivores analogous to raccoons. Leptarctus oregonensis Stock, 1930, a poorly known leptarctine from the early Barstovian, is represented by fragmented cranial elements and isolated teeth from the Mascall Formation of Oregon, and some fairly complete but undescribed material from the Olcott Formation of western Nebraska. Herein, we describe the first well-preserved skull of L. oregonensis from the type formation. Based on this new specimen, we confirm that L. oregonensis is a distinct species from L. primus Leidy, 1856 and L. ancipidens White, 1941 that is characterized by a distinct morphology of its tympanic projections and first upper molars. We are also able to describe intraspecific variation within L. oregonensis coinciding with the geographic distribution of the specimens (Oregon and Nebraska). The most variable characters are concentrated in the morphology of the frontals and the upper fourth premolar. Additional specimens will be needed to settle the debate over sexual dimorphism in this species, but this new specimen suggests that Leptarctus oregonensis, despite being one of the smallest members of the Leptarctinae, was an animal-dominated omnivore with considerable crushing ability.
Structure, folding and stability of a minimal homologue from Anemonia sulcata of the sea anemone potassium channel blocker ShK
Bankala Krishnarjuna, Christopher A. MacRaild, Punnepalli Sunanda, Rodrigo A.V. Morales, Steve Peigneur, Jason Macrander, Heidi H. Yu, Marymegan Daly, Srinivasarao Raghothama, Vikas Dhawan, Satendra Chauhan, Jan Tytgat, Michael W. Pennington, Raymond S.Norton. 2018. Peptides 99:169-178. https://doi.org/10.1016/j.peptides.2017.10.001
Peptide toxins elaborated by sea anemones target various ion-channel sub-types. Recent transcriptomic studies of sea anemones have identified several novel candidate peptides, some of which have cysteine frameworks identical to those of previously reported sequences. One such peptide is AsK132958, which was identified in a transcriptomic study of Anemonia sulcata and has a cysteine framework similar to that of ShK from Stichodactyla helianthus, but is six amino acid residues shorter. We have determined the solution structure of this novel peptide using NMR spectroscopy. The disulfide connectivities and structural scaffold of AsK132958 are very similar to those of ShK but the structure is more constrained. Toxicity assays were performed using grass shrimp (Palaemonetes sp) and Artemia nauplii, and patch-clamp electrophysiology assays were performed to assess the activity of AsK132958 against a range of voltage-gated potassium (KV) channels. AsK132958 showed no activity against grass shrimp, Artemia nauplii, or any of the KV channels tested, owing partly to the absence of a functional Lys-Tyr dyad. Three AsK132958 analogues, each containing a Tyr in the vicinity of Lys19, were therefore generated in an effort to restore binding, but none showed activity against any of KV channels tested. However, AsK132958 and its analogues are less susceptible to proteolysis than that of ShK. Our structure suggests that Lys19, which might be expected to occupy the pore of the channel, is not sufficiently accessible for binding, and therefore that AsK132958 must have a distinct functional role that does not involve KV channels.