EquiFACS: the Equine Facial Action Coding System

Although previous studies of horses have investigated their facial expressions in specific contexts, e.g. pain, until now there has been no methodology available that documents all the possible facial movements of the horse and provides a way to record all potential facial configurations. This is essential for an objective description of horse facial expressions across a range of contexts that reflect different emotional states. Facial Action Coding Systems (FACS) provide a systematic methodology of identifying and coding facial expressions on the basis of underlying facial musculature and muscle movement. FACS are anatomically based and document all possible facial movements rather than a configuration of movements associated with a particular situation. Consequently, FACS can be applied as a tool for a wide range of research questions. We developed FACS for the domestic horse (Equus caballus) through anatomical investigation of the underlying musculature and subsequent analysis of naturally occurring behaviour captured on high quality video. Discrete facial movements were identified and described in terms of the underlying muscle contractions, in correspondence with previous FACS systems. The reliability of others to be able to learn this system (EquiFACS) and consistently code behavioural sequences was high—and this included people with no previous experience of horses. A wide range of facial movements were identified, including many that are also seen in primates and other domestic animals (dogs and cats). EquiFACS provides a method that can now be used to document the facial movements associated with different social contexts and thus to address questions relevant to understanding social cognition and comparative psychology, as well as informing current veterinary and animal welfare practices

The ice-nucleating activity of Arctic sea surface microlayer samples and marine algal cultures

In recent years, sea spray as well as the biological material it contains has received increased attention as a source of ice-nucleating particles (INPs). Such INPs may play a role in remote marine regions, where other sources of INPs are scarce or absent. In the Arctic, these INPs can influence water–ice partitioning in low-level clouds and thereby the cloud lifetime, with consequences for the surface energy budget, sea ice formation and melt, and climate. Marine aerosol is of a diverse nature, so identifying sources of INPs is challenging. One fraction of marine bioaerosol (phytoplankton and their exudates) has been a particular focus of marine INP research. In our study we attempt to address three main questions. Firstly, we compare the ice-nucleating ability of two common phytoplankton species with Arctic seawater microlayer samples using the same instrumentation to see if these phytoplankton species produce ice-nucleating material with sufficient activity to account for the ice nucleation observed in Arctic microlayer samples. We present the first measurements of the ice-nucleating ability of two predominant phytoplankton species: Melosira arctica, a common Arctic diatom species, and Skeletonema marinoi, a ubiquitous diatom species across oceans worldwide. To determine the potential effect of nutrient conditions and characteristics of the algal culture, such as the amount of organic carbon associated with algal cells, on the ice nucleation activity, Skeletonema marinoi was grown under different nutrient regimes. From comparison of the ice nucleation data of the algal cultures to those obtained from a range of sea surface microlayer (SML) samples obtained during three different field expeditions to the Arctic (ACCACIA, NETCARE, and ASCOS), we found that they were not as ice active as the investigated microlayer samples, although these diatoms do produce ice-nucleating material. Secondly, to improve our understanding of local Arctic marine sources as atmospheric INPs we applied two aerosolization techniques to analyse the ice-nucleating ability of aerosolized microlayer and algal samples. The aerosols were generated either by direct nebulization of the undiluted bulk solutions or by the addition of the samples to a sea spray simulation chamber filled with artificial seawater. The latter method generates aerosol particles using a plunging jet to mimic the process of oceanic wave breaking. We observed that the aerosols produced using this approach can be ice active, indicating that the ice-nucleating material in seawater can indeed transfer to the aerosol phase. Thirdly, we attempted to measure ice nucleation activity across the entire temperature range relevant for mixed-phase clouds using a suite of ice nucleation measurement techniques – an expansion cloud chamber, a continuous-flow diffusion chamber, and a cold stage. In order to compare the measurements made using the different instruments, we have normalized the data in relation to the mass of salt present in the nascent sea spray aerosol. At temperatures above 248 K some of the SML samples were very effective at nucleating ice, but there was substantial variability between the different samples. In contrast, there was much less variability between samples below 248 K. We discuss our results in the context of aerosol–cloud interactions in the Arctic with a focus on furthering our understanding of which INP types may be important in the Arctic atmosphere

Just how versatile are domains?

<p>Abstract</p> <p>Background</p> <p>Creating new protein domain arrangements is a frequent mechanism of evolutionary innovation. While some domains always form the same combinations, others form many different arrangements. This ability, which is often referred to as versatility or promiscuity of domains, its a random evolutionary model in which a domain's promiscuity is based on its relative frequency of domains.</p> <p>Results</p> <p>We show that there is a clear relationship across genomes between the promiscuity of a given domain and its frequency. However, the strength of this relationship differs for different domains. We thus redefine domain promiscuity by defining a new index, <it>DV I </it>("domain versatility index"), which eliminates the effect of domain frequency. We explore links between a domain's versatility, when unlinked from abundance, and its biological properties.</p> <p>Conclusion</p> <p>Our results indicate that domains occurring as single domain proteins and domains appearing frequently at protein termini have a higher <it>DV I</it>. This is consistent with previous observations that the evolution of domain re-arrangements is primarily driven by fusion of pre-existing arrangements and single domains as well as loss of domains at protein termini. Furthermore, we studied the link between domain age, defined as the first appearance of a domain in the species tree, and the <it>DV I</it>. Contrary to previous studies based on domain promiscuity, it seems as if the <it>DV I </it>is age independent. Finally, we find that contrary to previously reported findings, versatility is lower in Eukaryotes. In summary, our measure of domain versatility indicates that a random attachment process is sufficient to explain the observed distribution of domain arrangements and that several views on domain promiscuity need to be revised.</p

Microphysical explanation of the RH-dependent water affinity of biogenic organic aerosol and its importance for climate

This is the final version of the article. Available from American Geophysical Union via the DOI in this record.A large fraction of atmospheric organic aerosol (OA) originates from natural emissions that are oxidized in the atmosphere to form secondary organic aerosol (SOA). Isoprene (IP) and monoterpenes (MT) are the most important precursors of SOA originating from forests. The climate impacts from OA are currently estimated through parameterizations of water uptake that drastically simplify the complexity of OA. We combine laboratory experiments, thermodynamic modeling, field observations, and climate modeling to (1) explain the molecular mechanisms behind RH-dependent SOA water-uptake with solubility and phase separation; (2) show that laboratory data on IP- and MT-SOA hygroscopicity are representative of ambient data with corresponding OA source profiles; and (3) demonstrate the sensitivity of the modeled aerosol climate effect to assumed OA water affinity. We conclude that the commonly used single-parameter hygroscopicity framework can introduce significant error when quantifying the climate effects of organic aerosol. The results highlight the need for better constraints on the overall global OA mass loadings and its molecular composition, including currently underexplored anthropogenic and marine OA sources.The data presented in the paper will be available through the Bolin Centre database (http://bolin.su.se/data/). The EC H2020 European Research Council ERC (ERC-StGATMOGAIN-278277 and ERC-StG-QAPPA-335478) and integrated project 641816 CRESCENDO Svenska Forskningsrådet Formas (Swedish Research Council Formas) (2015-749), Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation Wallenberg Fellowship AtmoRemove), Academy of Finland (grants 272041 and 259005), Natural Environment Research Council (NERC grants NE/M003531/1 and NE/J02175X/1), Norwegian Research Council (EVA grant 229771), Natural Sciences and Engineering Research Council of Canada (NSERC, grant RGPIN/04315-2014), National Science Foundation (NSF, grants ATM-1242258, AGS-1242932, and AGS-1360834), U.S. Environmental Protection Agency (EPA, STAR grant R835410), National Oceanic and Atmospheric Administration (NOAA, CPO award 538NA10OAR4310102), Electric Power Research Institute (EPRI, grant 10004734), U.S. Department of Energy (DOE, grants BER/ASR DE-SC0016559 and DE-SC0012792), Georgia Institute of Technology, and NordForsk (Nordic Centre of Excellence eSTICC) are gratefully acknowledged for funding. The climate model simulations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at the National Supercomputing Centre. Benjamin Murphy is acknowledged for useful discussions

Differences in the Number of Intrinsically Disordered Regions between Yeast Duplicated Proteins, and Their Relationship with Functional Divergence

BACKGROUND: Intrinsically disordered regions are enriched in short interaction motifs that play a critical role in many protein-protein interactions. Since new short interaction motifs may easily evolve, they have the potential to rapidly change protein interactions and cellular signaling. In this work we examined the dynamics of gain and loss of intrinsically disordered regions in duplicated proteins to inspect if changes after genome duplication can create functional divergence. For this purpose we used Saccharomyces cerevisiae and the outgroup species Lachancea kluyveri. PRINCIPAL FINDINGS: We find that genes duplicated as part of a genome duplication (ohnologs) are significantly more intrinsically disordered than singletons (p<2.2(e)-16, Wilcoxon), reflecting a preference for retaining intrinsically disordered proteins in duplicate. In addition, there have been marked changes in the extent of intrinsic disorder following duplication. A large number of duplicated genes have more intrinsic disorder than their L. kluyveri ortholog (29% for duplicates versus 25% for singletons) and an even greater number have less intrinsic disorder than the L. kluyveri ortholog (37% for duplicates versus 25% for singletons). Finally, we show that the number of physical interactions is significantly greater in the more intrinsically disordered ohnolog of a pair (p = 0.003, Wilcoxon). CONCLUSION: This work shows that intrinsic disorder gain and loss in a protein is a mechanism by which a genome can also diverge and innovate. The higher number of interactors for proteins that have gained intrinsic disorder compared with their duplicates may reflect the acquisition of new interaction partners or new functional roles

A fresh look at the evolution and diversification of photochemical reaction centers

In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments. I show, for example, that the protein folds at the C-terminus of the D1 and D2 subunits of Photosystem II, which are essential for the coordination of the water-oxidizing complex, were already in place in the most ancestral Type II reaction center subunit. I then evaluate the evolution of reaction centers in the context of the rise and expansion of the different groups of bacteria based on recent large-scale phylogenetic analyses. I find that the Heliobacteriaceae family of Firmicutes appears to be the earliest branching of the known groups of phototrophic bacteria; however, the origin of photochemical reaction centers and chlorophyll synthesis cannot be placed in this group. Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria. Finally, I argue that the discrepancies among the phylogenies of the reaction center proteins, chlorophyll synthesis enzymes, and the species tree of bacteria are best explained if both types of photochemical reaction centers evolved before the diversification of the known phyla of phototrophic bacteria. The primordial phototrophic ancestor must have had both Type I and Type II reaction centers

Dealing with Feelings: Characterization of Trait Alexithymia on Emotion Regulation Strategies and Cognitive-Emotional Processing

Background: Alexithymia, or "no words for feelings'', is a personality trait which is associated with difficulties in emotion recognition and regulation. It is unknown whether this deficit is due primarily to regulation, perception, or mentalizing of emotions. In order to shed light on the core deficit, we tested our subjects on a wide range of emotional tasks. We expected the high alexithymics to underperform on all tasks. Method: Two groups of healthy individuals, high and low scoring on the cognitive component of the Bermond-Vorst Alexithymia Questionnaire, completed questionnaires of emotion regulation and performed several emotion processing tasks including a micro expression recognition task, recognition of emotional prosody and semantics in spoken sentences, an emotional and identity learning task and a conflicting beliefs and emotions task (emotional mentalizing). Results: The two groups differed on the Emotion Regulation Questionnaire, Berkeley Expressivity Questionnaire and Empathy Quotient. Specifically, the Emotion Regulation Quotient showed that alexithymic individuals used more suppressive and less reappraisal strategies. On the behavioral tasks, as expected, alexithymics performed worse on recognition of micro expressions and emotional mentalizing. Surprisingly, groups did not differ on tasks of emotional semantics and prosody and associative emotional-learning. Conclusion: Individuals scoring high on the cognitive component of alexithymia are more prone to suppressive emotion regulation strategies rather than reappraisal strategies. Regarding emotional information processing, alexithymia is associated with reduced performance on measures of early processing as well as higher order mentalizing. However, difficulties in the processing of emotional language were not a core deficit in our alexithymic group

Intrinsically Disordered Proteins Display No Preference for Chaperone Binding In Vivo

Intrinsically disordered/unstructured proteins (IDPs) are extremely sensitive to proteolysis in vitro, but show no enhanced degradation rates in vivo. Their existence and functioning may be explained if IDPs are preferentially associated with chaperones in the cell, which may offer protection against degradation by proteases. To test this inference, we took pairwise interaction data from high-throughput interaction studies and analyzed to see if predicted disorder correlates with the tendency of chaperone binding by proteins. Our major finding is that disorder predicted by the IUPred algorithm actually shows negative correlation with chaperone binding in E. coli, S. cerevisiae, and metazoa species. Since predicted disorder positively correlates with the tendency of partner binding in the interactome, the difference between the disorder of chaperone-binding and non-binding proteins is even more pronounced if normalized to their overall tendency to be involved in pairwise protein–protein interactions. We argue that chaperone binding is primarily required for folding of globular proteins, as reflected in an increased preference for chaperones of proteins in which at least one Pfam domain exists. In terms of the functional consequences of chaperone binding of mostly disordered proteins, we suggest that its primary reason is not the assistance of folding, but promotion of assembly with partners. In support of this conclusion, we show that IDPs that bind chaperones also tend to bind other proteins

Recognising and reacting to angry and happy facial expressions: a diffusion model analysis.

Researchers have reported two biases in how people recognise and respond to angry and happy facial expressions: (1) a gender-expression bias (Becker et al. in J Pers Soc Psychol, 92(2):179-190, https://doi.org/10.1037/0022-3514.92.2.179 , 2007)-faster identification of male faces as angry and female faces as happy and (2) an approach-avoidance bias-faster avoidance of people who appear angry and faster approach responses people who appear happy (Heuer et al. in Behav Res The, 45(12):2990-3001, https://doi.org/10.1016/j.brat.2007.08.010 2007; Marsh et al. in Emotion, 5(1), 119-124, https://doi.org/10.1037/1528-3542.5.1.119 , 2005; Rotteveel and Phaf in Emotion 4(2):156-172, https://doi.org/10.1037/1528-3542.4.2.156 , 2004). The aim of the current research is to gain insight into the nature of such biases by applying the drift diffusion model to the results of an approach-avoidance task. Sixty-five participants (33 female) identified faces as either happy or angry by pushing and pulling a joystick. In agreement with the original study of this effect (Solarz 1960) there were clear participant gender differences-both the approach avoidance and gender-expression biases were larger in magnitude for female compared to male participants. The diffusion model results extend recent research (Krypotos et al. in Cogn Emot 29(8):1424-1444, https://doi.org/10.1080/02699931.2014.985635 , 2015) by indicating that the gender-expression and approach-avoidance biases are mediated by separate cognitive processes

Intranasal Administration of poly(I:C) and LPS in BALB/c Mice Induces Airway Hyperresponsiveness and Inflammation via Different Pathways

BACKGROUND: Bacterial and viral infections are known to promote airway hyperresponsiveness (AHR) in asthmatic patients. The mechanism behind this reaction is poorly understood, but pattern recognizing Toll-like receptors (TLRs) have recently been suggested to play a role. MATERIALS AND METHODS: To explore the relation between infection-induced airway inflammation and the development of AHR, poly(I:C) activating TLR3 and LPS triggering TLR4, were chosen to represent viral and bacterial induced interactions, respectively. Female BALB/c or MyD88-deficient C57BL/6 mice were treated intranasally with either poly(I:C), LPS or PBS (vehicle for the control group), once a day, during 4 consecutive days. RESULTS: When methacholine challenge was performed on day 5, BALB/c mice responded with an increase in airway resistance. The maximal resistance was higher in the poly(I:C) and LPS treated groups than among the controls, indicating development of AHR in response to repeated TLR activation. The proportion of lymphocytes in broncheoalveolar lavage fluid (BALF) increased after poly(I:C) treatment whereas LPS enhanced the amount of neutrophils. A similar cellular pattern was seen in lung tissue. Analysis of 21 inflammatory mediators in BALF revealed that the TLR response was receptor-specific. MyD88-deficient C57BL/6 mice responded to poly (I:C) with an influx of lymphocytes, whereas LPS caused no inflammation. CONCLUSION: In vivo activation of TLR3 and TLR4 in BALB/c mice both caused AHR in conjunction with a local inflammatory reaction. The AHR appeared to be identical regardless of which TLR that was activated, whereas the inflammation exhibited a receptor specific profile in terms of both recruited cells and inflammatory mediators. The inflammatory response caused by LPS appeared to be dependent on MyD88 pathway. Altogether the presented data indicate that the development of AHR and the induction of local inflammation might be the result of two parallel events, rather than one leading to another