In recent years, data-driven inference of cell-cell communication has helped reveal coordinated biological processes across cell types. Here, we integrate two tools, LIANA and Tensor-cell2cell, which, when combined, can deploy multiple existing methods and resources to enable the robust and flexible identification of cell-cell communication programs across multiple samples. In this work, we show how the integration of our tools facilitates the choice of method to infer cell-cell communication and subsequently perform an unsupervised deconvolution to obtain and summarize biological insights. We explain how to perform the analysis step by step in both Python and R and provide online tutorials with detailed instructions available at https://ccc-protocols.readthedocs.io/. This workflow typically takes ∼1.5 h to complete from installation to downstream visualizations on a graphics processing unit-enabled computer for a dataset of ∼63,000 cells, 10 cell types, and 12 samples.

Research Highlight: Ferraro, K. M., Welker, L., Ward, E. B., Schmitz, O. J., & Bradford, M. A. (2023). Plant mycorrhizal associations mediate the zoogeochemical effects of calving subsidies by a forest ungulate. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.14002. Animals play large roles in ecosystem elemental cycling but predicting effects in diverse contexts remains a substantial challenge. Fundamental to progress is (1) identifying mechanisms by which animals impact nutrient distribution and cycling, and (2) disentangling how environmental context mediates the operation of alternative mechanisms. In an elegant field experiment, Ferraro et al. (2023) provide the first detailed exploration of the impact of nutrient inputs from mammalian parturition on soil functioning and the stoichiometry of plant tissues. The authors find that nitrogen from experimental additions of ungulate parturition material (natal fluids) is rapidly incorporated into microsite soil organic pools and plant tissues. They also find that soil processes (soil microbial biomass, rates of carbon mineralization, nitrogen mineralization and nitrification) and the nitrogen content of plant tissues above- and belowground are increased by addition of parturition material. Notably, the authors identify that increases in some soil processes and plant tissue nitrogen are weaker in microsites dominated by ericoid mycorrhizal plants than those dominated by ectomycorrhizal plants. These findings demonstrate that parturition depositions, a ubiquitous but overlooked mechanism of mammalian impacts on ecosystems, impact ecosystem processes and plant tissue stoichiometry. Furthermore, plant-fungal associations are a predictive axis of context dependency mediating zoogeochemical effects at fine scales. Ferraro et al.\'s (2023) novel approach simultaneously advances mechanistic understanding of animal-ecosystem interactions at fine scales and facilitates prediction of ungulate effects on nutrient availability at landscape extents.

G-quadruplexes (GQs) are secondary nucleic acid structures that play regulatory roles in various cellular processes. G-quadruplex-forming sequences present within the 5\' UTR of mRNAs can function not only as repressors of translation but also as elements required for optimum function. Based upon previous reports, the majority of the 5\' UTR GQ structures inhibit translation, presumably by blocking the ribosome scanning process that is essential for detection of the initiation codon. However, there are certain mRNAs containing GQs that have been identified as positive regulators of translation, as they are needed for translation initiation. While most cellular mRNAs utilize the 5\' cap structure to undergo cap-dependent translation initiation, many rely on cap-independent translation under certain conditions in which the cap-dependent initiation mechanism is not viable or slowed down, for example, during development, under stress and in many diseases. Cap-independent translation mainly occurs via Internal Ribosomal Entry Sites (IRESs) that are located in the 5\' UTR of mRNAs and are equipped with structural features that can recruit the ribosome or other factors to initiate translation without the need for a 5\' cap. In this review, we will focus only on the role of RNA GQs present in the 5\' UTR of mRNAs, where they play a critical role in translation initiation, and discuss the potential mechanism of this phenomenon, which is yet to be fully delineated.

GPR37 is an orphan G-protein-coupled receptor, a substrate of parkin which is linked to Parkinson\'s disease (PD) and affective disorders. In this study, we sought to address the effects of early life stress (ELS) by employing the paradigm of limited nesting material on emotional behaviors in adult GPR37 knockout (KO) mice. Our results showed that, while there was an adverse effect of ELS on various domains of emotional behaviors in wild type (WT) mice in a sex specific manner (anxiety in females, depression and context-dependent fear memory in males), GPR37KO mice subjected to ELS exhibited less deteriorated emotional behaviors. GPR37KO female mice under ELS conditions displayed reduced anxiety compared to WT mice. This was paralleled by lower plasma corticosterone in GPR37KO females and a lower increase in P-T286-CaMKII by ELS in the amygdala. GPR37KO male mice, under ELS conditions, showed better retention of hippocampal-dependent emotional processing in the passive avoidance behavioral task. GPR37KO male mice showed increased immobility in the forced swim task and increased P-T286-CaMKII in the ventral hippocampus under baseline conditions. Taken together, our data showed overall long-term effects of ELS-deleterious or beneficial depending on the genotype, sex of the mice and the emotional context.

Task-related information is widely distributed across the brain with different coding properties, such as persistency. We found in mice that coding persistency of action history and value was variable across areas, learning phases, and task context, with the highest persistency in the retrosplenial cortex of expert mice performing value-based decisions where history needs to be maintained across trials. Persistent coding also emerged in artificial networks trained to perform mouse-like reinforcement learning. Persistency allows temporally untangled value representations in neuronal manifolds where population activity exhibits cyclic trajectories that transition along the value axis after action outcomes, collectively forming cylindrical dynamics. Simulations indicated that untangled persistency facilitates robust value retrieval by downstream networks. Even leakage of persistently maintained value through non-specific connectivity could contribute to the brain-wide distributed value coding with different levels of persistency. These results reveal that context-dependent, untangled persistency facilitates reliable signal coding and its distribution across the brain.

AbstractChanges in temperature associated with climate change can alter species\' distributions, drive adaptive evolution, and in some cases cause extinction. Research has tended to focus on the direct effects of temperature, but changes in temperature can also have indirect effects on populations and species. Here, we test whether temperature can indirectly affect the fitness of Drosophila santomea and Drosophila yakuba by altering the nature of interspecific competition. We show that when raised in isolation, both D. santomea and D. yakuba display similar variation in relative fitness across temperatures of 18°, 22°, and 25°C. However, D. santomea has higher fitness than D. yakuba when experiencing interspecific competition at 18°C, while the inverse is true at 25°C. Patterns of fitness across thermal and competitive environments therefore indicate that the outcome of interspecific competition varies with temperature. We then use a coexistence experiment to show that D. santomea is rapidly (within eight generations) extirpated when maintained with D. yakuba at 25°C. By contrast, D. santomea remains as (or more) abundant than D. yakuba over the course of ∼10 generations when maintained at 18°C. Our results provide an example of how the thermal environment can affect interspecific competition and suggest that some species may become more prone to extinction under scenarios of climate change through indirect effects of the thermal environment on competitive advantages between species.

Social animals flexibly use a variety of vocalizations to communicate in complex and dynamic environments. However, it remains unknown whether the auditory perception of different vocalizations changes according to the ecological context. By using miniature wireless devices to synchronously record vocal interactions and local neural activity in freely-behaving zebra finches in combination with playback experiments, we investigate whether the auditory processing of vocalizations changes across life-history stages. We show that during breeding, females (but not males) increase their estrogen levels and reply faster to their mates when interacting vocally. These changes are associated with an increase in the amplitude of the female\'s neural auditory responses. Furthermore, the changes in auditory response are not general, but specific to a subset of functionally distinct vocalizations and dependent on the emitter\'s identity. These results provide novel insights into auditory plasticity of communication systems, showing that the perception of specific signals can shift according to ecologically-determined physiological states.

Epichloë endophytes have been shown to be mutualistic symbionts of cool-season grasses under most environmental conditions. Although pairwise interactions between hemiparasites and their hosts are heavily affected by host-associated symbiotic microorganisms, little attention has been paid to the effects of microbe-plant interactions, particularly endophytic symbiosis, in studies examining the effects of parasitic plants on host performance. In this study, we performed a greenhouse experiment to examine the effects of hereditary Epichloë endophyte symbiosis on the growth of two host grasses (Stipa purpurea and Elymus tangutorum) in the presence or absence of a facultative root hemiparasite (Pedicularis kansuensis Maxim). We observed parasitism of both hosts by P. kansuensis: when grown with a host plant, the hemiparasite decreased the performance of the host while improving its own biomass and survival rate of the hemiparasite. Parasitized endophyte-infected S. purpurea plants had higher biomass, tillers, root:shoot ratio, and photosynthetic parameters and a lower number of functional haustoria than the endophyte-free S. purpurea conspecifics. By contrast, parasitized endophyte-infected E. tangutorum had a lower biomass, root:shoot ratio, and photosynthetic parameters and a higher number of haustoria and functional haustoria than their endophyte-free counterparts. Our results reveal that the interactions between the endophytes and the host grasses are context dependent and that plant-plant interactions can strongly affect their mutualistic interactions. Endophytes originating from S. purpurea alleviate the host biomass reduction by P. kansuensis and growth depression in the hemiparasite. These findings shed new light on using grass-endophyte symbionts as biocontrol methods for the effective and sustainable management of this weedy hemiparasite.

Evolution in nature occurs in the proverbial tangled bank. The species interactions characterizing this tangled bank can be strongly affected by global change and can also influence the fitness and selective effects of a global change on a focal population. As a result, species interactions can influence which traits will promote adaptation and the magnitude or direction of evolutionary responses to the global change. First, we provide a framework describing how species interactions may influence evolutionary responses to global change. Then, we highlight case studies that have explicitly manipulated both a global change and the presence or abundance of interacting species and used either experimental evolution or quantitative genetics approaches to test for the effects of species interactions on evolutionary responses to global change. Although still not frequently considered, we argue that species interactions commonly modulate the effects of global change on the evolution of plant and animal populations. As a result, predicting the evolutionary effects of the multitude of global changes facing natural populations requires both community ecology and evolutionary perspectives.

Interactions with resident species can affect the rate that expanding species invade novel areas. These interactions can be antagonistic (biotic resistance), where resident species hinder invasive establishment, or facilitative (biotic assistance), where residents promote invasive establishment. The predominance of resistance or assistance could vary with the abiotic context. We examined how the effects of a resident ecosystem engineer interact with abiotic stress to resist or assist the establishment of an expanding competitor. In Florida salt marshes, native cordgrass, Spartina alterniflora, is an influential ecosystem engineer that, when dead, exerts a legacy effect by forming persistent wrack patches. We examined how the legacy effect of Spartina wrack varies with spatial context and abiotic conditions to influence establishment of the northward-expanding black mangrove, Avicennia germinans. Field surveys documented that Spartina wrack and Avicennia propagules co-occur in the high intertidal zone, and we conducted two outdoor mesocosm experiments to investigate this association. Wrack positively affected propagule establishment when propagules were beneath wrack, but negatively affected establishment when propagules were above wrack. The abiotic tidal regime influences the magnitude of wrack effects by controlling ambient moisture, and the positive and negative effects of wrack were stronger in low moisture conditions that simulated desiccation stress during harsh neap tides. Thus, the same resident engineer can either resist or assist an expanding competitor and the magnitude of these effects depends on abiotic conditions. We propose that under harsh conditions, there is greater scope for an engineer\'s mediating influence to affect associated species, both positively and negatively.