Collective Action and Decision Making: An Analysis of Economic Modeling and Environmental Free-Riding

It is hypothesized that tool-assisted excavation of plant underground storage organs (USOs) played an adaptive role in hominin evolution and was also once considered a uniquely human behavior. Recent data indicate that savanna chimpanzees also use tools to excavate edible USOs. However, those chimpanzees remain largely unhabituated and we lack direct observations of this behavior in the wild. To fill this gap in our knowledge of hominoid USO extractive foraging, we conducted tool-mediated excavation experiments with captive chimpanzees naive to this behavior. We presented the chimpanzees with the opportunity to use tools in order to excavate artificially-placed underground foods in their naturally forested outdoor enclosure. No guidance or demonstration was given to the chimpanzees at any time. The chimpanzees used tools spontaneously in order to excavate the underground foods. They exhibited six different tool use behaviors in the context of excavation: probe, perforate, dig, pound, enlarge and shovel. However, they still excavated manually more often than they did with tools. Chimpanzees were selective in their choice of tools that we provided, preferring longer tools for excavation. They also obtained their own tools mainly from naturally occurring vegetation and transported them to the excavation site. They reused some tools throughout the study. Our new data provide a direction for the study of variables relevant to modeling USO extractive foraging by early hominins.Funding Agencies|La Caixa Foundation Spain [LCF/BQ/EU15/10350002]; University of Oslo, Department of Biosciences, Norway</p

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Effect of different levels of collembolan grazing on interspecific competition between microfungi, decomposition of organic matter and bio-availability of nitrogen

The effect of selective grazing by a collembolan (Folsomia fimetaria) on the reproduction and ability to degrade wheat straw by 2 species of microfungi was measured. The experiment was performed with 3 different grazing pressures and a control without grazing. The 3 grazing pressures correspond to an initial density of 10.000, 20.000 or 100.000 collembolans/m2. The density cannot however be directly related to a field density, because the soil column was only approximately 2 cm high. Results show that the most preferred fungus to F. fimetaria, Alternaria infectoria, were only affected in terms of reproduction at the highest grazing pressure of 30 collembolans (as initial density). Both respiration rates and the content of bio-available nitrogen in the microcosms containing A. infectoria either alone or in competition with Mucor hiemalis, at all grazing pressures, showed that the fungus was very resilient to grazing. M. hiemalis reproduced most, respired most and retained most bio-available nitrogen at a grazing pressure of 6 F. fimetaria (initial density) compared to 3 or 30 collembolans as initial density. Apart from this there was no effect of collembolan grazing on reproduction. The results suggest that A. infectoria and M. hiemalis are able to avoid competition in this study, as a result of different ecological strategies

Life-history traits of soil collembolans in relation to food quality

Preference studies of many different collembolan species have categorised collembolans being selective in their food choice. To clarify whether collembolan food selectivity is related to fitness parameters, three species, Folsomia fimetaria, Protaphorura armata and Heteromurus nitidus, were fed three fungal species, Alternaria infectoria, Mucor hiemalis and Penicillium hordei, representing fungi of high, medium and low preference. The fungal diets were grown on soil and collembolan growth, survival and fecundity were measured. The fungus A. infectoria supported growth, survival and reproduction best in all three species of collembolans, while the fungus P. hordei was of low food quality. M. hiemalis was of medium quality and F. fimetaria was the only collembolan reproducing on M. hiemalis. F. fimetaria favoured reproduction over growth when confined to M. hiemalis. When P. armata was fed M. hiemalis it reached a size where reproduction normally starts, but no young were produced. This suggests that M. hiemalis lacks nutrients necessary for reproduction. H. nitidus did not perform well on any of the fungi offered, which were generally of low food quality for this species. In this study, where the fungal growth substrate is soil, there is a clear relationship between collembolan fitness and their food choice in contrast to some other studies where substrates optimised for fungal growth had been used. We show that specific fungal species are important for resource allocation to growth or reproduction and closely connected with food choice. Further, we argue that natural fungal growth substrates, such as soil, should be used in experiments of this kind

Carbonic anhydrases reduce the acidity of the tumor microenvironment, promote immune infiltration, decelerate tumor growth, and improve survival in ErbB2/HER2-enriched breast cancer

Abstract Background Carbonic anhydrases catalyze CO2/HCO3 – buffer reactions with implications for effective H+ mobility, pH dynamics, and cellular acid–base sensing. Yet, the integrated consequences of carbonic anhydrases for cancer and stromal cell functions, their interactions, and patient prognosis are not yet clear. Methods We combine (a) bioinformatic analyses of human proteomic data and bulk and single-cell transcriptomic data coupled to clinicopathologic and prognostic information; (b) ex vivo experimental studies of gene expression in breast tissue based on quantitative reverse transcription and polymerase chain reactions, intracellular and extracellular pH recordings based on fluorescence confocal microscopy, and immunohistochemical protein identification in human and murine breast cancer biopsies; and (c) in vivo tumor size measurements, pH-sensitive microelectrode recordings, and microdialysis-based metabolite analyses in mice with experimentally induced breast carcinomas. Results Carbonic anhydrases—particularly the extracellular isoforms CA4, CA6, CA9, CA12, and CA14—undergo potent expression changes during human and murine breast carcinogenesis. In patients with basal-like/triple-negative breast cancer, elevated expression of the extracellular carbonic anhydrases negatively predicts survival, whereas, surprisingly, the extracellular carbonic anhydrases positively predict patient survival in HER2/ErbB2-enriched breast cancer. Carbonic anhydrase inhibition attenuates cellular net acid extrusion and extracellular H+ elimination from diffusion-restricted to peripheral and well-perfused regions of human and murine breast cancer tissue. Supplied in vivo, the carbonic anhydrase inhibitor acetazolamide acidifies the microenvironment of ErbB2-induced murine breast carcinomas, limits tumor immune infiltration (CD3+ T cells, CD19+ B cells, F4/80+ macrophages), lowers inflammatory cytokine (Il1a, Il1b, Il6) and transcription factor (Nfkb1) expression, and accelerates tumor growth. Supporting the immunomodulatory influences of carbonic anhydrases, patient survival benefits associated with high extracellular carbonic anhydrase expression in HER2-enriched breast carcinomas depend on the tumor inflammatory profile. Acetazolamide lowers lactate levels in breast tissue and blood without influencing breast tumor perfusion, suggesting that carbonic anhydrase inhibition lowers fermentative glycolysis. Conclusions We conclude that carbonic anhydrases (a) elevate pH in breast carcinomas by accelerating net H+ elimination from cancer cells and across the interstitial space and (b) raise immune infiltration and inflammation in ErbB2/HER2-driven breast carcinomas, restricting tumor growth and improving patient survival

Additional file 1 of Carbonic anhydrases reduce the acidity of the tumor microenvironment, promote immune infiltration, decelerate tumor growth, and improve survival in ErbB2/HER2-enriched breast cancer

Additional file 1. Supplementary tables and figures. Table S1 summarizes the clinical and pathological patient characteristics. Table S2 and S3 provide sequence information for primers and probes used for quantitative RT-PCR analyses. Table S4 and S5 give detailed information on the statistics analyses in Figs. 1 and 9. Figure S1 shows patterns of gene expression for carbonic anhydrases across breast cancer molecular subtypes. Figure S2 and S3 provide survival curves for Luminal A (Fig. S2) and Luminal B (Fig. S3) breast cancer patients stratified for carbonic anhydrase expression