Non-human Systems Research Articles

Na+/Ca2+ Exchanger in Human iPSC Derived Cardiomyocytes: Functional Evidence and Relevance for Beating Behavior

The Na+/Ca2+-exchanger (NCX) plays an important role in cellular calcium homeostasis. Under physiological conditions NCX removes Ca2+ from the cell lumen of excitable cells and is involved in regulatory processes. Under pathological conditions, NCX can reverse direction and contribute to cell damage by Ca2+ overloading. These critical functions have fueled the debate over the pharmacological potential of NCX since many years. Inhibition of the reversed mode of NCX is thought to be beneficial in ischemia/reperfusion injury. Moreover, inhibition of NCX has been proposed to exhibit an anti-arrhythmic effect and implications for safety screening are discussed. Human iPSC derived cardiomyocytes (hiPSC-CMs) are an evolving model system in cardiac research. We investigated NCX function in hiPSC-CMs. By developing a suitable sensor based method (SSM based electrophysiology) we recorded specific NCX current responses of high amplitude. These currents showed similar calcium affinity compared to NCX1 expressed in HEK cells and were sensitive to nickel, KB-R7943 and SEA0400. The beating behavior of hiPSC-CMs was further investigated using an impedance based system. We observed a significant increase in beating rate as a long term effect when inhibiting NCX with SEA0400. These findings clearly demonstrate the presence of functional NCX in hiPSC-CMs which until now has been poorly investigated. The observed increase in beating rate after inhibition of NCX is to some extent in disagreement with other studies. However, previous studies have employed different methods using non-human systems and usually investigate short term effects of up to one hour. Further investigation is necessary, but at this time we can state that we have found an intriguing new combination of tools which will help to generate new insights into the physiology and pharmacology of NCX.

Internal acoustic structuring in pied babbler recruitment cries specifies the form of recruitment

Language is inherently combinatorial, and parallels of this combinatorial capacity are found in nonhuman systems, with animals combining sounds and calls into larger meaningful structures. However, further analogue examples are central in unveiling the diversity, distribution, and evolutionary drivers of combinatoriality. Here, we provide evidence for internal “meaning-refining” acoustic variation within a larger stereotyped signal in pied babblers (Turdoides bicolor). Using acoustic analyses, we demonstrate that males produce 2 long, raucous, “cry-like” structures, both starting with a wind-up segment grading into repetitions of A/single-note or AB/double-note motifs. Behavioral observations indicated that, consistent with similarities in their larger stereotyped structure, both variants function overall in recruiting group members during locomotion, but the internal A or AB substructure specifies the “precise” form of recruitment, from approaching the caller’s announced location to following it over longer distances. Playing back cries from a stationary loudspeaker further supported that the 2 variants elicit different responses, with more individuals approaching the loudspeaker in response to single-note compared with double-note cries. Additionally, despite similarities in overall distance travelled, group movement was only directional for single-note, but undefined for double-note cries. We suggest that the overall structure of the 2 cry variants conveys the same general meaning, with embedded variation refining this meaning. These results further illustrate the variability of generative mechanisms outside of human language and lend support to the hypothesis that combinatorial structuring may have emerged in species with limited or fixed vocal repertoires in order to enhance communicative output.

M3-subtype muscarinic receptor activation stimulates intracellular calcium oscillations and aldosterone production in human adrenocortical HAC15 cells.

A previous body of work in bovine and rodent models shows that cholinergic agonists modulate the secretion of steroid hormones from the adrenal cortex. In this study we used live-cell Ca2+ imaging to investigate cholinergic activity in the HAC15 human adrenocortical carcinoma cell line. The cholinergic agonists carbachol and acetylcholine triggered heterogeneous Ca2+ oscillations that were strongly inhibited by antagonists with high affinity for the M3 muscarinic receptor subtype, while preferential block of M1 or M2 receptors was less effective. Acute exposure to carbachol and acetylcholine modestly elevated aldosterone secretion in HAC15 cells, and this effect was also diminished by M3 inhibition. HAC15 cells expressed relatively high levels of mRNA for M3 and M2 receptors, while M1 and M5 mRNA were much lower. In conclusion, our data extend previous findings in non-human systems to implicate the M3 receptor as the dominant muscarinic receptor in the human adrenal cortex.

Expert Panel Discusses the Importance of Systems Medicine

Expert Panel Discusses the Importance of Systems Medicine

Is Climate Change Morally Good from Non-Anthropocentric Perspectives?

ABSTRACTAnthropogenic climate change poses some difficult ethical quandaries for non-anthropocentrists. While it is hard to deny that climate change is a substantial moral ill for humans, many non-human organisms and ecosystems stand to benefit from plausible climate change scenarios. Modelling studies provide evidence that net primary productivity (NPP) could be substantially boosted, both regionally and globally, as a result of warming from increased concentrations of greenhouse gases. The same holds for deployment of certain types of climate engineering. This has a surprising implication: from certain non-anthropocentric perspectives, some plausible scenarios of climate change and climate engineering might bring about morally better states of affairs when compared to both pre-industrial and emission-mitigation baselines. We present existing evidence that certain emissions trajectories and climate engineering scenarios are likely to benefit non-human organisms on the whole, using NPP as a proxy for non-human flourishing. We then argue that, on a non-anthropocentric perspective that affords independent moral value to non-human organisms or systems, there is reason to deem such emissions trajectories and climate engineering scenarios to be morally better than prominent alternatives, including aggressive mitigation. If we are to take non-anthropocentrism seriously, then we should view current discussions of the ethics of climate change and climate engineering as incomplete, for they pay little attention to the well-being of non-human organisms in their own right. However, giving non-anthropocentric perspectives a more prominent place might substantially alter how we view climate ethics, as it would challenge the widely held views that climate change and climate engineering constitute absolute moral ills.

Intentional communication between wild bonnet macaques and humans

Comparative studies of nonhuman communication systems could provide insights into the origins and evolution of a distinct dimension of human language: intentionality. Recent studies have provided evidence for intentional communication in different species but generally in captive settings. We report here a novel behaviour of food requesting from humans displayed by wild bonnet macaques Macaca radiata, an Old World cercopithecine primate, in the Bandipur National Park of southern India. Using both natural observations and field experiments, we examined four different behavioural components—coo-calls, hand-extension gesture, orientation, and monitoring behaviour—of food requesting for their conformity with the established criteria of intentional communication. Our results suggest that food requesting by bonnet macaques is potentially an intentionally produced behavioural strategy as all the food requesting behaviours except coo-calls qualify the criteria for intentionality. We comment on plausible hypotheses for the origin and spread of this novel behavioural strategy in the study macaque population and speculate that the cognitive precursors for language production may be manifest in the usage of combination of signals of different modalities in communication, which could have emerged in simians earlier than in the anthropoid apes.

Glycosphingolipid levels and glucocerebrosidase activity are altered in normal aging of the mouse brain.

Aging is the predominant risk factor for both genetic and sporadic Parkinson’s disease (PD). The majority of PD cases are nonfamilial, and the connection between aging and PD-associated genes is not well understood. Haploinsufficiency of the GBA gene, leading to a reduction in glucocerebrosidase (GCase) activity, is one of the most common genetic risk factors for PD. Furthermore, GCase activity is also reduced in brain regions of sporadic PD patients, with a corresponding accumulation of its glycosphingolipid (GSL) substrates. Recent findings in PD patients and aging control cases, and in human PD patient induced pluripotent stem cell neurons, have shown an age-dependent reduction in GCase activity and an elevation of some GSLs. We therefore asked whether aging-induced changes to both lysosomal and nonlysosomal GCase activity and GSL homeostasis in the brain could also be reflected in other nonhuman mammalian systems. Increases in brain polyubiquitin and the lysosomal-associated membrane protein, LAMP2A, were found in 24-month-old wild-type mice compared to 1.5-month-old mice. A lipidomic analysis was performed on brains of wild-type mice of different strains between 1.5 and 24 months of age. Aging created GSL changes that are reminiscent of sporadic PD. Levels of glucosylceramide, glucosylsphingosine, lactosylceramide, and GM1a were elevated in the brain of aged mice, and levels of complex gangliosides, GD1a, GD1b, and GT1b, were reduced with age. Parallel biochemical analyses revealed a change in lipid metabolism probably mediated by lysosomal hydrolases, with reduced GCase and increased neuraminidase activity. Based on these data, we hypothesize that perturbation of GSL metabolism in the aging brain may precede or may be part of abnormal protein handling and may accelerate PD pathophysiological processes in vulnerable neurons in PD and other age-related neurodegenerative disorders.

Alarm calls evoke a visual search image of a predator in birds

One of the core features of human speech is that words cause listeners to retrieve corresponding visual mental images. However, whether vocalizations similarly evoke mental images in animal communication systems is surprisingly unknown. Japanese tits (Parus minor) produce specific alarm calls when and only when encountering a predatory snake. Here, I show that simply hearing these calls causes tits to become more visually perceptive to objects resembling snakes. During playback of snake-specific alarm calls, tits approach a wooden stick being moved in a snake-like fashion. However, tits do not respond to the same stick when hearing other call types or if the stick's movement is dissimilar to that of a snake. Thus, before detecting a real snake, tits retrieve its visual image from snake-specific alarm calls and use this to search out snakes. This study provides evidence for a call-evoked visual search image in a nonhuman animal, offering a paradigm to explore the cognitive basis for animal vocal communication in the wild.

The challenges of a Big Data Earth

The potential of big data fused with the vision of a digital Earth offers powerful opportunities to deepen understanding of the whole Earth system and the management of a sustainable planet. It is important to stand back from often confusing detail to clarify what those opportunities are and how they might be seized. The essential scientific potential of data, big or small, is to reveal patterns, which have often been the fundamental first step in stimulating inquiry, leading to new questions, new perspectives and potentially to new answers. The digital revolution has created a “digital microscope” that permits us to see patterns that have not been seen before, and when coupled with machine learning technologies to analyse them in creating statistical predictions of the behaviour of both human and non-human systems. These potentials converge with the imperative to represent an Earth system with interacting non-human and human components, as a vital contribution to the understanding and actions required in working towards planetary sustainability. But a digital Earth is also capable of being represented mathematically as a digitally networked phenomenon, analogous to an analogue computer, and should be an important target for a Big Earth Data Journal. We should also return to Al Gore’s vision of an accessible digital Earth with wide usability. Pre-determining the separate functions of parallel digital Earths risks losing one of the great potentials of big data and learning algorithms, the identification and analysis of unanticipated relationships and processes.

What have humans done for evolutionary biology? Contributions from genes to populations.

Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future.

Ancient human miRNAs are more likely to have broad functions and disease associations than young miRNAs

BackgroundmicroRNAs (miRNAs) are essential to the regulation of gene expression in eukaryotes, and improper expression of miRNAs contributes to hundreds of diseases. Despite the essential functions of miRNAs, the evolutionary dynamics of how they are integrated into existing gene regulatory and functional networks is not well understood. Knowledge of the origin and evolutionary history a gene has proven informative about its functions and disease associations; we hypothesize that incorporating the evolutionary origins of miRNAs into analyses will help resolve differences in their functional dynamics and how they influence disease.ResultsWe computed the phylogenetic age of miRNAs across 146 species and quantified the relationship between human miRNA age and several functional attributes. Older miRNAs are significantly more likely to be associated with disease than younger miRNAs, and the number of associated diseases increases with age. As has been observed for genes, the miRNAs associated with different diseases have different age profiles. For example, human miRNAs implicated in cancer are enriched for origins near the dawn of animal multicellularity. Consistent with the increasing contribution of miRNAs to disease with age, older miRNAs target more genes than younger miRNAs, and older miRNAs are expressed in significantly more tissues. Furthermore, miRNAs of all ages exhibit a strong preference to target older genes; 93% of validated miRNA gene targets were in existence at the origin of the targeting miRNA. Finally, we find that human miRNAs in evolutionarily related families are more similar in their targets and expression profiles than unrelated miRNAs.ConclusionsConsidering the evolutionary origin and history of a miRNA provides useful context for the analysis of its function. Consistent with recent work in Drosophila, our results support a model in which miRNAs increase their expression and functional regulatory interactions over evolutionary time, and thus older miRNAs have increased potential to cause disease. We anticipate that these patterns hold across mammalian species; however, comprehensively evaluating them will require refining miRNA annotations across species and collecting functional data in non-human systems.

Activation of PKC triggers rescue of NPC1 patient specific iPSC derived glial cells from gliosis

BackgroundNiemann-Pick disease Type C1 (NPC1) is a rare progressive neurodegenerative disorder caused by mutations in the NPC1 gene. The pathological mechanisms, underlying NPC1 are not yet completely understood. Especially the contribution of glial cells and gliosis to the progression of NPC1, are controversially discussed. As an analysis of affected cells is unfeasible in NPC1-patients, we recently developed an in vitro model system, based on cells derived from NPC1-patient specific iPSCs. Here, we asked if this model system recapitulates gliosis, observed in non-human model systems and NPC1 patient post mortem biopsies. We determined the amount of reactive astrocytes and the regulation of the intermediate filaments GFAP and vimentin, all indicating gliosis. Furthermore, we were interested in the assembly and phosphorylation of these intermediate filaments and finally the impact of the activation of protein kinase C (PKC), which is described to ameliorate the pathogenic phenotype of NPC1-deficient fibroblasts, including hypo-phosphorylation of vimentin and cholesterol accumulation.MethodsWe analysed glial cells derived from NPC1 patient specific induced pluripotent stem cells, carrying different NPC1 mutations. The amount of reactive astrocytes was determined by means of immuncytochemical stainings and FACS-analysis. Semi-quantitative western blot was used to determine the amount of phosphorylated GFAP and vimentin. Cholesterol accumulation was analysed by Filipin staining and quantified by Amplex Red Assay. U18666A was used to induce NPC1 phenotype in unaffected cells of the control cell line. Phorbol 12-myristate 13-acetate (PMA) was used to activate PKC.ResultsImmunocytochemical detection of GFAP, vimentin and Ki67 revealed that NPC1 mutant glial cells undergo gliosis. We found hypo-phosphorylation of the intermediate filaments GFAP and vimentin and alterations in the assembly of these intermediate filaments in NPC1 mutant cells. The application of U18666A induced not only NPC1 phenotypical accumulation of cholesterol, but characteristics of gliosis in glial cells derived from unaffected control cells. The application of phorbol 12-myristate 13-acetate, an activator of protein kinase C resulted in a significantly reduced number of reactive astrocytes and further characteristics of gliosis in NPC1-deficient cells. Furthermore, it triggered a restoration of cholesterol amounts to level of control cells.ConclusionOur data demonstrate that glial cells derived from NPC1-patient specific iPSCs undergo gliosis. The application of U18666A induced comparable characteristics in un-affected control cells, suggesting that gliosis is triggered by hampered function of NPC1 protein. The activation of protein kinase C induced an amelioration of gliosis, as well as a reduction of cholesterol amount. These results provide further support for the line of evidence that gliosis might not be only a secondary reaction to the loss of neurons, but might be a direct consequence of a reduced PKC activity due to the phenotypical cholesterol accumulation observed in NPC1. In addition, our data support the involvement of PKCs in NPC1 disease pathogenesis and suggest that PKCs may be targeted in future efforts to develop therapeutics for NPC1 disease.

Elite Power under Advanced Neoliberalism

The financial crisis, and associated scandals, created a sense of a juridical deficit with regard to the financial sector. Forms of independent judgement within the sector appeared compromised, while judgement over the sector seemed unattainable. Elites, in the classical Millsian sense of those taking tacitly coordinated ‘big decisions’ over the rest of the public, seemed absent. This article argues that the eradication of jurisdictional elites is an effect of neoliberalism, as articulated most coherently by Hayek. It characterizes the neoliberal project as an effort to elevate ‘unconscious’ processes over ‘conscious’ ones, which in practice means elevating cybernetic, non-human systems and processes over discursive spheres of politics and judgement. Yet such a system still produces its own types of elite power, which come to consist in acts of translation, rather than judgement. Firstly, there are ‘cyborg intermediaries’: elites which operate largely within the system of codes, data, screens and prices. Secondly, there are ‘diplomatic intermediaries’: elites who come to narrate and justify what markets (and associated technologies and bodies) are ‘saying’. The paper draws on Lazzarato’s work on signifying vs asignifying semiotics in order to articulate this, and concludes by considering the types of elite crisis which these forms of power tend to produce.

Subjectivity of political knowledge: gonoseological dimension

The article explores the specifics of the separation of political gnoseology, political epistemology and political cognition as directions of penetration of the subject of knowledge into the essence of political phenomena and processes at the methodological level. It is emphasized that the classical and non-classical theory of cognition has paved the way for a modern scientific understanding of experimental methodology and generally accepted standards of scientific novelty. The attention is focused on the formation of one-dimensional political views on political cognition as a reflective reflection of the political world in a certain period of time by the actual means of cognition. It is emphasized that the question of the significance of the classical directions of cognition, mono-ideological and monodoctrynnyh structures of political world perception is actualized. It is argued that in the conditions of informatization and the growth of the importance of machine intelligence systems in the practice of obtaining new knowledge, it is necessary to find out the problem of the value of artificial intelligence and non-human systems of thinking for political knowledge of the future. It is substantiated that the scientific paradigm of thinking defines standard requirements for the effectiveness and efficiency of political activity. Considered the importance of part of political knowledge, which may not meet the criteria of natural or technical scientific.

Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

BackgroundDetection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic processes. However, most of the routinely used mutation calling algorithms are not optimised for the simultaneous analysis of multiple samples, or for non-human experimental model systems with no reliable databases of common genetic variations. Most standard tools either require numerous in-house post filtering steps with scarce documentation or take an unpractically long time to run. To overcome these problems, we designed the streamlined IsoMut tool which can be readily adapted to experimental scenarios where the goal is the identification of experimentally induced mutations in multiple isogenic samples.MethodsUsing 30 isogenic samples, reliable cohorts of validated mutations were created for testing purposes. Optimal values of the filtering parameters of IsoMut were determined in a thorough and strict optimization procedure based on these test sets.ResultsWe show that IsoMut, when tuned correctly, decreases the false positive rate compared to conventional tools in a 30 sample experimental setup; and detects not only single nucleotide variations, but short insertions and deletions as well. IsoMut can also be run more than a hundred times faster than the most precise state of art tool, due its straightforward and easily understandable filtering algorithm.ConclusionsIsoMut has already been successfully applied in multiple recent studies to find unique, treatment induced mutations in sets of isogenic samples with very low false positive rates. These types of studies provide an important contribution to determining the mutagenic effect of environmental agents or genetic defects, and IsoMut turned out to be an invaluable tool in the analysis of such data.

Cyborg landscapes: Choreographing resilient interactions between infrastructure, ecology, and society

Contemporary challenges of climate change, population growth, resource scarcity, and environmental decline prompt designers to envision new relationships between nature and culture. Infrastructure design and adaptation are key to addressing theses issues. This article argues for the formulation of a landscape approach that integrates biotic and abiotic systems to envision more dynamic interactions among infrastructure, ecology, and urbanism. Conceptualized as cyborg landscapes, this approach embraces notions of change, adaptation, and feedback to create hybrid infrastructures of human and non-human systems, of living and non-living entities, across a range of spatial and temporal scales. Three examples illustrate that the profession is already (knowingly or unknowingly) working within this framework. Designed as co-dependent socioecological networks, these projects transform and choreograph landscape processes across multiple spatial and temporal scales. They promote an aesthetic that is predicated on relationships between dynamic things and systems. By stressing co-evolutionary processes between human agency and ecological systems, cyborg landscapes aspire to create multifunctional landscapes that do not simply operate in the present, but learn from experiences in order to adapt and grow smarter.

Reframing The Postindustrial: Landscapes of Extraction between Reclamation and Reinvention

Sites created for and abandoned by hardrock mining operations in the Rocky Mountain West are among the most layered, complex, and noteworthy landscapes in America, expressive of the entangled relationships between the human processes of extraction and reclamation and nonhuman processes of geological and ecological change. Few types of landscape have involved such localized drastic change of the surface of the earth and such significant impacts on associated nonhuman and human systems. The spatial and temporal scales of mining and postmining operations and their impacts extend far beyond the immediate local context, recent history, and immediate future. The complexity of such landscapes transcends the physical and lies in the various values that drove the processes of extraction, as well as those at play in addressing postextraction conditions. They pose fundamental challenges to many disciplines and have prompted a rethinking of traditional concepts and practices of preservation and reclamation. This paper develops a framework that meaningfully responds to the complexities of postmining landscapes (PMLs). It is connected to a critical investigation of functional-performative and aesthetic-experiential considerations and an engagement of underlying meanings and values. It casts PMLs as dynamic and ever-changing sites to model and render legible new forms of human-environment relationships.

Evaluating a Self-Access Centre’s Effectiveness and Efficiency: A Case Study and Reflection

This article discusses changes that occurred after a case study that examined the effectiveness and efficiency of a Self-access Centre (SAC) within a university in Hong Kong using Morrison’s (2003) Evaluation of Self-access Language Learning Centre framework. The case study addressed issues from a stakeholder’s perspective by collecting data from learners through an online questionnaire and conducting 15 semi-structured interviews, an advisers’ focus group and management interviews and reports. The outcome of the study showed that a wider perspective for senior managers and insights for evaluation of the support services is vital to making key decisions in context. Upon reflection of the findings with the new SAC manager, more acute decision-making and continuous improvement is needed to enhance effectiveness and efficiency of the running of the SAC. To achieve this, regular feedback from various stakeholders, also re-structuring human and non-human support systems is vital.

Posthuman Ecologies and the More-than-Human World

Posthuman Ecologies and the More-than-Human World

Developmental changes of cognitive vocal control in monkeys.

The evolutionary origins of human language are obscured by the scarcity of essential linguistic characteristics in non-human primate communication systems. Volitional control of vocal utterances is one such indispensable feature of language. We investigated the ability of two monkeys to volitionally utter species-specific calls over many years. Both monkeys reliably vocalized on command during juvenile periods, but discontinued this controlled vocal behavior in adulthood. This emerging disability was confined to volitional vocal production, as the monkeys continued to vocalize spontaneously. In addition, they continued to use hand movements as instructed responses during adulthood. This greater vocal flexibility of monkeys early in ontogeny supports the neoteny hypothesis in human evolution. This suggests that linguistic capabilities were enabled via an expansion of the juvenile period during the development of humans.