nils-herrmann/clean_scirepeval huggingface dataset:
Design of synthetic bacterial communities for predictable plant phenotypes
Venue: PLoS biology

Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant–bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation–responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities.
Vocal development through morphological computation
Venue: PLoS biology

The vocal behavior of infants changes dramatically during early life. Whether or not such a change results from the growth of the body during development—as opposed to solely neural changes—has rarely been investigated. In this study of vocal development in marmoset monkeys, we tested the putative causal relationship between bodily growth and vocal development. During the first two months of life, the spontaneous vocalizations of marmosets undergo (1) a gradual disappearance of context-inappropriate call types and (2) an elongation in the duration of context-appropriate contact calls. We hypothesized that both changes are the natural consequences of lung growth and do not require any changes at the neural level. To test this idea, we first present a central pattern generator model of marmoset vocal production to demonstrate that lung growth can affect the temporal and oscillatory dynamics of neural circuits via sensory feedback from the lungs. Lung growth qualitatively shifted vocal behavior in the direction observed in real marmoset monkey vocal development. We then empirically tested this hypothesis by placing the marmoset infants in a helium–oxygen (heliox) environment in which air is much lighter. This simulated a reversal in development by decreasing the effort required to respire, thus increasing the respiration rate (as though the lungs were smaller). The heliox manipulation increased the proportions of inappropriate call types and decreased the duration of contact calls, consistent with a brief reversal of vocal development. These results suggest that bodily growth alone can play a major role in shaping the development of vocal behavior.
A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila
Venue: PLoS biology

Insects determine their body segments in two different ways. Short-germband insects, such as the flour beetle Tribolium castaneum, use a molecular clock to establish segments sequentially. In contrast, long-germband insects, such as the vinegar fly Drosophila melanogaster, determine all segments simultaneously through a hierarchical cascade of gene regulation. Gap genes constitute the first layer of the Drosophila segmentation gene hierarchy, downstream of maternal gradients such as that of Caudal (Cad). We use data-driven mathematical modelling and phase space analysis to show that shifting gap domains in the posterior half of the Drosophila embryo are an emergent property of a robust damped oscillator mechanism, suggesting that the regulatory dynamics underlying long- and short-germband segmentation are much more similar than previously thought. In Tribolium, Cad has been proposed to modulate the frequency of the segmentation oscillator. Surprisingly, our simulations and experiments show that the shift rate of posterior gap domains is independent of maternal Cad levels in Drosophila. Our results suggest a novel evolutionary scenario for the short- to long-germband transition and help explain why this transition occurred convergently multiple times during the radiation of the holometabolan insects.
Identification of FAM173B as a protein methyltransferase promoting chronic pain
Venue: PLoS biology

Chronic pain is a debilitating problem, and insights in the neurobiology of chronic pain are needed for the development of novel pain therapies. A genome-wide association study implicated the 5p15.2 region in chronic widespread pain. This region includes the coding region for FAM173B, a functionally uncharacterized protein. We demonstrate here that FAM173B is a mitochondrial lysine methyltransferase that promotes chronic pain. Knockdown and sensory neuron overexpression strategies showed that FAM173B is involved in persistent inflammatory and neuropathic pain via a pathway dependent on its methyltransferase activity. FAM173B methyltransferase activity in sensory neurons hyperpolarized mitochondria and promoted macrophage/microglia activation through a reactive oxygen species–dependent pathway. In summary, we uncover a role for methyltransferase activity of FAM173B in the neurobiology of pain. These results also highlight FAM173B methyltransferase activity as a potential therapeutic target to treat debilitating chronic pain conditions.
Fruit flies are multistable geniuses
Venue: PLoS biology

Our sensory systems have evolved to provide us with information about the external world. Such information is useful only insofar as it leads to actions that enhance fitness, and thus, the link between sensation and action has been thoroughly studied in many species. In insects, for example, specific visual stimuli lead to highly stereotyped responses. In contrast, humans can exhibit a wide range of responses to the same stimulus, as occurs most notably in the phenomenon of multistable perception. On this basis, one might think that humans have a fundamentally different way of generating actions from sensory inputs, but Toepfer et al. show that flies show evidence of multistable perception as well. Specifically, when confronted with a sensory stimulus that can yield different motor responses, flies switch from one response to another with temporal dynamics that are similar to those of humans and other animals. This suggests that the mechanisms that give rise to the rich repertoire of sensory experience in humans have correlates in much simpler nervous systems.
Multi-stability with ambiguous visual stimuli in Drosophila orientation behavior
Venue: PLoS biology

It is widely accepted for humans and higher animals that vision is an active process in which the organism interprets the stimulus. To find out whether this also holds for lower animals, we designed an ambiguous motion stimulus, which serves as something like a multi-stable perception paradigm in Drosophila behavior. Confronted with a uniform panoramic texture in a closed-loop situation in stationary flight, the flies adjust their yaw torque to stabilize their virtual self-rotation. To make the visual input ambiguous, we added a second texture. Both textures got a rotatory bias to move into opposite directions at a constant relative angular velocity. The results indicate that the fly now had three possible frames of reference for self-rotation: either of the two motion components as well as the integrated motion vector of the two. In this ambiguous stimulus situation, the flies generated a continuous sequence of behaviors, each one adjusted to one or another of the three references.
How the microbiome challenges our concept of self
Venue: PLoS biology

Today, the three classical biological explanations of the individual self––the immune system, the brain, the genome––are being challenged by the new field of microbiome research. Evidence shows that our resident microbes orchestrate the adaptive immune system, influence the brain, and contribute more gene functions than our own genome. The realization that humans are not individual, discrete entities but rather the outcome of ever-changing interactions with microorganisms has consequences beyond the biological disciplines. In particular, it calls into question the assumption that distinctive human traits set us apart from all other animals––and therefore also the traditional disciplinary divisions between the arts and the sciences.
Catecholamines alter the intrinsic variability of cortical population activity and perception
Venue: PLoS biology

The ascending modulatory systems of the brain stem are powerful regulators of global brain state. Disturbances of these systems are implicated in several major neuropsychiatric disorders. Yet, how these systems interact with specific neural computations in the cerebral cortex to shape perception, cognition, and behavior remains poorly understood. Here, we probed into the effect of two such systems, the catecholaminergic (dopaminergic and noradrenergic) and cholinergic systems, on an important aspect of cortical computation: its intrinsic variability. To this end, we combined placebo-controlled pharmacological intervention in humans, recordings of cortical population activity using magnetoencephalography (MEG), and psychophysical measurements of the perception of ambiguous visual input. A low-dose catecholaminergic, but not cholinergic, manipulation altered the rate of spontaneous perceptual fluctuations as well as the temporal structure of “scale-free” population activity of large swaths of the visual and parietal cortices. Computational analyses indicate that both effects were consistent with an increase in excitatory relative to inhibitory activity in the cortical areas underlying visual perceptual inference. We propose that catecholamines regulate the variability of perception and cognition through dynamically changing the cortical excitation–inhibition ratio. The combined readout of fluctuations in perception and cortical activity we established here may prove useful as an efficient and easily accessible marker of altered cortical computation in neuropsychiatric disorders.
The jaguar and the PhD
Venue: PLoS biology

From a young age, I dreamed of studying big cats. My favorite cat was the African lion, and I had a recurring dream of having one in my backyard, which I fed bones. This love of cats (and wildlife in general) started with books, encyclopaedias, nature shows, and zoos. I eventually earned a Master’s in Science degree with a study on mountain lions in Baja California, Mexico. I produced a map with preferred habitat; analyzed scat contents to identify mountain lions’ prey species; and conducted numerous surveys of the local residents about economic activities, cattle grazing, and ranching activities. Not surprisingly, the results pointed to conflict in areas where humans or their activities converge with mountain lion distribution. Some years later, I was invited to be part of a new study of jaguars in Northwest Mexico. The study aimed to generate new information about the social organization and feeding habits of jaguars and mountain lions in the Sierra Madre Mountains of Sonora and about their dispersal movements into ranges along the United States–Mexico border, where they had been recently documented. The study would be the first of its type for this region, gathering new data with radio telemetry, remote camera photographs, scat, tracks, and sign data points collected in the field. The study area is about 120 miles south of the Arizona–Sonora border—a remote, rugged area of the Sierra Madre with low human population density and historically a region of extensive private lands, mostly dedicated to cattle grazing by private landowners. This project would be my PhD dissertation. Tropical and temperate species come together, at least for a season, in this transition area between the Sonoran Desert scrub and the oak and pine woodlands of higher elevation ranges on the western slope of the Sierra Madre, where canyons and streams lined with palm trees grow next to columnar cacti and wildflowers. The area sustains a great diversity of plants and animals at the edge of the Nearctic and Neotropical regions—bald eagles returning to places where military macaws live; ocelots moving through the same drainages as coatis and desert tortoises. The “research station” was located at the end of a long, winding dirt road, about 50 miles (80 km) from the closest town. It took at least nine hours to drive there. The remoteness meant living in very basic conditions and having simple arrangements for activities like sleeping, showering, and cooking—not the typical National Geographic or Discovery Channel adventures. Before my arrival, remote cameras were installed along creeks, game trails, and places where jaguar tracks or kills were found. Additionally, foot-hold snares—long metal cables attached to the base of a tree, with a loop and swivel at the other end where a jaguar or a mountain lion would walk in and get caught—were also set in order to capture them to place radio collars and monitor the big cats’ movements.
Empirical evidence that metabolic theory describes the temperature dependency of within-host parasite dynamics
Venue: PLoS biology

The complexity of host–parasite interactions makes it difficult to predict how host–parasite systems will respond to climate change. In particular, host and parasite traits such as survival and virulence may have distinct temperature dependencies that must be integrated into models of disease dynamics. Using experimental data from Daphnia magna and a microsporidian parasite, we fitted a mechanistic model of the within-host parasite population dynamics. Model parameters comprising host aging and mortality, as well as parasite growth, virulence, and equilibrium abundance, were specified by relationships arising from the metabolic theory of ecology. The model effectively predicts host survival, parasite growth, and the cost of infection across temperature while using less than half the parameters compared to modeling temperatures discretely. Our results serve as a proof of concept that linking simple metabolic models with a mechanistic host–parasite framework can be used to predict temperature responses of parasite population dynamics at the within-host level.
A case for conserving common species
Venue: PLoS biology

I grew up in a country where fish were, first and foremost, food. At the age of nine or so, I started following my dad and uncle to nearby rivers to fish on weekends, and soon I learned to make my own tackle and go back to the rivers to fish with my friends. We never caught a lot of fish, but every fish we caught came home with us to be eaten. It never occurred to us to consider what ecological role these fish might play or how they fit into the ecosystem. In Ghana, West Africa, like in almost all the developing countries in sub-Saharan Africa, viewing fish primarily as food flows naturally from the need to survive. Once survival is secured, humans can start thinking about other things, like prestige or social status, for example . As I entered my postdoc in ecology and conservation—me, a Ghanaian who identified more with fisheries and natural resource management—I felt the distinction keenly. I had not studied for any of my degrees under brand-name ecologists or conservation scientists, which I had come to realize was helpful in launching an academic career in our field. I understood then that professional pedigree really matters. What I know now is that this is not merely for the prestige and access such mentorship provides but for the intellectual shelter and sustenance I must provide as a principal investigator (PI). This is the story of building my niche as an ecosystem engineer. But it is also the story of recognizing the ecological role of species we take for granted—and why we should fund research on common species that may sustain the rare ones, some of which we have yet to discover. As a new PI, I would need to carve out my own niche to attract funding while also ensuring that my research program was interesting and topical enough to attract topnotch graduate students who would be proud to take a chance on my uncertain name recognition to advance their own careers. This is no small feat. My choice of research program was also constrained by the fact that my institution already had all sorts of established fish biologists, who studied game species; large river, reservoir, and marine ecosystems; and threatened and endangered species of streams. Of course, my colleagues had become established in these areas because that is where nearly all the research funding was and still is going. Driven by considerations of cost and convenience, I decided to go local. I recruited my first group of students to study the fishes of the wadeable tributaries of the upper and middle New River in Virginia and North Carolina in the United States. Because it is a rather depauperate system with almost no fish species listed as of conservation concern by state or federal agencies, we had no competition. But we didn’t have much idea of what we were looking to do either. I had no particular species of interest in mind but vaguely planned to characterize the fish communities and determine the relationship between community structure and land use and land cover in the watersheds.
Neutrophils kill the parasite Trichomonas vaginalis using trogocytosis
Venue: PLoS biology

T. vaginalis, a human-infective parasite, causes the most common nonviral sexually transmitted infection (STI) worldwide and contributes to adverse inflammatory disorders. The immune response to T. vaginalis is poorly understood. Neutrophils (polymorphonuclear cells [PMNs]) are the major immune cell present at the T. vaginalis–host interface and are thought to clear T. vaginalis. However, the mechanism of PMN clearance of T. vaginalis has not been characterized. We demonstrate that human PMNs rapidly kill T. vaginalis in a dose-dependent, contact-dependent, and neutrophil extracellular trap (NET)-independent manner. In contrast to phagocytosis, we observed that PMN killing of T. vaginalis involves taking “bites” of T. vaginalis prior to parasite death, using trogocytosis to achieve pathogen killing. Both trogocytosis and parasite killing are dependent on the presence of PMN serine proteases and human serum factors. Our analyses provide the first demonstration, to our knowledge, of a mammalian phagocyte using trogocytosis for pathogen clearance and reveal a novel mechanism used by PMNs to kill a large, highly motile target.
Witnessing extinction in real time
Venue: PLoS biology

I started my amphibian research a little like Thoreau, living alone in a cabin in the woods and recording the seasonal variation in the natural world. I lived in a shack without plumbing or electricity, an hour away from the closest house, in a cloud forest on the top of a mountain that straddled the border between Costa Rica and Panama. I scrambled along mountain streams chasing seasonal reproductive data on treefrogs. The species I studied, Isthmohyla calypsa, remains one of the most spectacular frogs I have ever seen; adults were a brilliant, iridescent green with a bright white throat pouch, and their skin was as textured as the spikey moss they lived on, apparently camouflaging them from predators . I was living a field biologist’s dream and expected to spend my career studying tropical montane amphibians in one of the most beautiful and least studied regions in the world. I couldn’t know that my study site in this remote cloud forest would give me a front row seat to one of the most distressing ecological mysteries of our time. As a graduate student, I had heard the ominous reports describing the mysterious disappearances of amphibian populations around the world. At the time, scientists were debating whether this was a real phenomenon, what might cause it, and whether these events were connected. The large number of species affected was especially worrisome; of the suspected threats, none typically caused extirpation or extinction of multiple species while leaving the habitat intact. It was more than a search for a needle in a haystack—we were still debating the existence of the haystack. I was just a graduate student, and while I wasn’t actively looking for the needle, I would step right on it. That was triggered with my intent to capture the early breeding season of an interesting toad (Incilius fastidiosus). These toads would emerge from underground to lay rosary-like strands of eggs amidst torrential downpours that turned the pastures into swampy meadows. I returned to my cloud forest site weeks earlier than usual, at the beginning of the rainy season in 1993, to continue some preliminary work from the previous year. But the toads never came out. I knew that a related species—the golden toad (Incilius periglenes)—had recently disappeared from its entire range just a few hundred miles north of me. But I was soon focused on other, more immediate concerns as I realized that it wasn’t just the toads that were gone, my mossy green treefrogs and the other stream frogs were also missing. I blamed the weather, my technique, the bright light of my headlamp—I was grasping at straws and I knew it, but I couldn’t really believe that this might be another “enigmatic decline.” Maybe it would have been different if I had found hundreds of dead frogs, but they had disappeared when I wasn’t looking. When I returned in 1996, the streams were dead silent—no frogs were calling, species were missing, overall abundance was down by 90%, and even the gelatinous egg masses were