Evolution of assortative mating following selective introgression of pigmentation genes between two Drosophila species

Adaptive introgression is ubiquitous in animals but experimental support for its role in driving speciation remains scarce. In the absence of conscious selection, admixed laboratory strains of Drosophila asymmetrically and progressively lose alleles from one parental species and reproductive isolation against the predominant parent ceases after 10 generations. Here, we selectively introgressed during one year light pigmentation genes of D. santomea into the genome of its dark sibling D. yakuba, and vice versa. We found that the pace of phenotypic change differed between the species and the sexes, and identified through genome sequencing common as well as distinct introgressed loci in each species. Mating assays showed that assortative mating between introgressed flies and both parental species persisted even after four years (~ 60 generations) from the end of the selection. Those results indicate that selective introgression of as low as 0.5% of the genome can beget morphologically-distinct and reproductively-isolated strains, two prerequisites for the delimitation of new species. Our findings hence represent a significant step towards understanding the genome-wide dynamics of speciation-through-introgression.

Phenotypic change of mesenchymal stem cells into smooth muscle cells regulated by dynamic cell-surface interactions on patterned arrays of ultrathin graphene oxide substrates

The topographical interface of the extracellular environment has been appreciated as a principal biophysical regulator for modulating cell functions, such as adhesion, migration, proliferation, and differentiation. Despite the existed approaches that use two-dimensional nanomaterials to provide beneficial effects, opportunities evaluating their impact on stem cells remain open to elicit unprecedented cellular responses. Herein, we report an ultrathin cell-culture platform with potential-responsive nanoscale biointerfaces for monitoring mesenchymal stem cells (MSCs). We designed an intriguing nanostructured array through self-assembly of graphene oxide sheets and subsequent lithographical patterning method to produce chemophysically defined regions. MSCs cultured on anisotropic micro/nanoscale patterned substrate were spontaneously organized in a highly ordered configuration mainly due to the cell-repellent interactions. Moreover, the spatially aligned MSCs were spontaneously differentiated into smooth muscle cells upon the specific crosstalk between cells. This work provides a robust strategy for directing stem cells and differentiation, which can be utilized as a potential cell culture platform to understand cell–substrate or cell–cell interactions, further developing tissue repair and stem cell-based therapies. Graphical Abstract

Reciprocal interactions between the gut microbiome and mammary tissue mast cells promote metastatic dissemination of HR+ breast tumors

Establishing commensal dysbiosis, defined as an inflammatory gut microbiome with low biodiversity, prior to breast tumor initiation, enhances early dissemination of hormone-receptor positive (HR+) mammary tumor cells. Here, we sought to define mammary tissue mediators of dysbiosis-induced tumor dissemination. We found that commensal dysbiosis increased both the frequency and profibrogenicity of mast cells in the mammary tissue, a phenotypic change that persisted after tumor implantation. Fibroblast activation and tissue remodeling associate with enhanced breast tumor metastasis. We employed pharmacological and adoptive transfer approaches to demonstrate that mammary tissue mast cells from dysbiotic animals enhances dissemination of HR+ tumor cells. Collagen levels in mammary tissues from HR+ breast cancer patients correlated with mast cell abundance, suggesting clinical relevance of mast cell-mediated fibroblast activation. Together, these data demonstrate that a gut-mast cell axis exists that induces fibroblast activation and orchestrates early dissemination of HR+ breast tumors.

Cell-Projection Pumping of Fibroblast Contents into Osteosarcoma SAOS-2 Cells Correlates with Increased SAOS-2 Proliferation and Migration, as well as Altered Morphology

We earlier reported that cell-projection pumping transfers fibroblast contents to cancer cells and this alters the cancer cell phenotype. Here, we report on single-cell tracking of time lapse recordings from co-cultured fluorescent fibroblasts and SAOS-2 osteosarcoma cells, tracking 5201 cells across 7 experiments. The fluorescent lipophilic marker DiD was used to label fibroblast organelles and to trace the transfer of fibroblast cytoplasm into SAOS-2 cells. We related SAOS-2 phenotypic change to levels of fluorescence transfer from fibroblasts to SAOS-2 cells, as well as what we term ‘compensated fluorescence’, that numerically projects mother cell fluorescence post-mitosis into daughter cells. The comparison of absolute with compensated fluorescence allowed us to deduct if the phenotypic effects in mother SAOS-2 cells were inherited by their daughters. SAOS-2 receipt of fibroblast fluorescence correlated by Kendall’s tau with cell-profile area and without evidence of persistence in daughter cells (median tau = 0.51, p < 0.016); negatively and weakly with cell circularity and with evidence of persistence (median tau = −0.19, p < 0.05); and very weakly with cell migration velocity and without evidence of persistence (median tau = 0.01, p < 0.016). In addition, mitotic SAOS-2 cells had higher rates of prior fluorescence uptake (median = 64.9 units/day) than non-dividing cells (median = 35.6 units/day, p < 0.016) and there was no evidence of persistence post-mitosis. We conclude that there was an appreciable impact of cell-projection pumping on cancer cell phenotype relevant to cancer histopathological diagnosis, clinical spread and growth, with most effects being ‘reset’ by cancer cell mitosis.

Competition alters species’ plastic and genetic response to environmental change

Species react to environmental change via plastic and evolutionary responses. While both of them determine species’ survival, most studies quantify these responses individually. As species occur in communities, competing species may further influence their respective response to environmental change. Yet, how environmental change and competing species combined shape plastic and genetic responses to environmental change remains unclear. Quantifying how competition alters plastic and genetic responses of species to environmental change requires a trait-based, community and evolutionary ecological approach. We exposed unicellular aquatic organisms to long-term selection of increasing salinity—representing a common and relevant environmental change. We assessed plastic and genetic contributions to phenotypic change in biomass, cell shape, and dispersal ability along increasing levels of salinity in the presence and absence of competition. Trait changes in response to salinity were mainly due to mean trait evolution, and differed whether species evolved in the presence or absence of competition. Our results show that species’ evolutionary and plastic responses to environmental change depended both on competition and the magnitude of environmental change, ultimately determining species persistence. Our results suggest that understanding plastic and genetic responses to environmental change within a community will improve predictions of species’ persistence to environmental change.

Cell-Projection Pumping of Fibroblast Contents into Osteosarcoma SAOS-2 Cells Correlates with Increased SAOS-2 Proliferation and Migration, and also with Altered Morphology

We earlier reported that cell-projection pumping transfers fibroblast contents to cancer cells, and this alters cancer cell phenotype. We now report on single-cell tracking of time lapse recordings from co-cultured fluorescent fibroblasts and SAOS-2 osteosarcoma cells, tracking 5,201 cells across 7 experiments. The fluorescent lipophilic marker DiD was used to label fibroblast organelles, and to trace transfer of fibroblast cytoplasm into SAOS-2. We related SAOS-2 phenotypic change to levels of fluorescence transfer from fibroblasts to SAOS-2, and also to what we term 'compensated fluorescence', that numerically projects mother cell fluorescence post-mitosis, into daughter cells. Comparison of absolute with compensated fluorescence, allowed deduction if phenotypic effects in mother SAOS-2, were inherited by their daughters. SAOS-2 receipt of fibroblast fluorescence correlated by Kendall's tau: with cell-profile area, and without evidence for persistence in daughter cells (median tau = 0.51, p < 0. 016); negatively and weakly with cell circularity, and with evidence for persistence (median tau = -0.19, p < 0.05); and very weakly with cell migration velocity, and without evidence for persistence (median tau = 0.01, p < 0.016). Also, mitotic SAOS-2 had higher rates of prior fluorescence uptake (median = 64.9 units/day), compared with non dividing cells (median = 35.6 units/day, p < 0.016), and there was no evidence for persistence post-mitosis. We conclude there is appreciable impact of cell-projection pumping on cancer cell phenotype, relevant to cancer histopathological diagnosis, clinical spread, and growth, with most effects 'reset' by cancer cell mitosis.

Rapid phenotypic change in a polymorphic salamander over 43 years

Color polymorphic animals offer a unique system for studying intraspecific phenotypic responses to climate change. Discrete color morphs are easy to identify, and correlated trait responses of morphs can indicate how climate warming may facilitate long-term maintenance of polymorphisms. We use a historical dataset spanning 43 years to examine temporal shifts in color morph frequency and body size in response to climate in the Eastern Red-backed Salamander, Plethodon cinereus, which contains a widespread striped/unstriped color polymorphism. We created a pipeline to extract high-throughput trait data from fluid-preserved museum specimens where we batch-photographed salamanders, de-aggregated individual specimens from photographs, and solicited help of community scientists to score color morphs. We used a linear modeling framework that includes information about spatial population structure to demonstrate that color morph frequency and body size vary in response to climate, elevation, and over time, with an overall trend of higher frequency and decreased body size of the striped morph, but increased size of the unstriped morph. These surprising results suggest that morphs may be responding to multiple climate and geographic drivers through co-adapted morphological changes. This work highlights new practices of extracting trait data from museum specimens to demonstrate species phenotypes response to climate change.

Directed Evolution and Discovery of Nitroreductase Enzymes for Targeted Cell Ablation

<p>Nitroreductase enzymes are a superfamily of bacterial flavoproteins that can catalyze the reduction of aromatic nitro groups. The reduction of an aromatic nitro group, a highly electronegative functionality, causes a large electronic shift that can profoundly affect the activity of other substituents on the aromatic ring. For example, upon nitroreduction, initially non-toxic compounds known as prodrugs can be converted into a cytotoxic form. The ability of nitroreductases to alter the activity of compounds has lead to their development as tools for multiple biotechnological applications. Of particular note is the use of nitroreductase enzymes in combination with a nitroaromatic prodrug to study the role of specific cell populations in zebrafish (Danio rerio). Zebrafish are used as model organisms to study processes such as embryonic development and tissue regeneration. By expressing a nitroreductase enzyme in a specific tissue of a zebrafish, it is possible to selectively ablate that tissue upon administration of a prodrug. The subsequent phenotypic change induced by the ablation can provide information on the physiological role of the ablated tissue, or of the regenerative processes that can be recruited to repair the damage. The goal of this thesis was to engineer or discover new nitroreductase enzymes that could expand the capabilities of cell ablation studies in zebrafish. In particular, this work sought to develop a system that would enable the dual, or multiplexed, ablation of two tissues independently within the same organism. Control over the ablation of two distinct tissues could be useful for studying tissue interactions during developmental or regenerative processes. For this to be achievable, two different nitroreductase enzymes, each possessing distinct and non-overlapping prodrug selectivities would be required. Previous studies in the Ackerley lab had identified NfsA from Escherichia coli (NfsA_Ec) and NfsA from Pseudomonas putida (NfsA_Pp) as nitroreductase enzymes that were slightly more selective for the prodrug tinidazole compared than metronidazole. In contrast the NfsB nitroreductase from Vibrio vulnificus (NfsB_Vv) was substantially more selective for metronidazole than tinidazole. To further improve the tinidazole selectivity of the NfsA enzymes, directed evolution was employed as a tool to further enhance the substrate selectivity of each enzyme. The primary outcome of this work was the evolution of an NfsA_Ec mutant that was 12 fold more selective for tinidazole over metronidazole than wild type NfsA_Ec. In addition to engineering new enzymes for cell ablation experiments, this work also sought to discover new nitroreductase enzymes from unculturable bacteria, a previously unplumbed source. The genes and gene products of unculturable bacteria can be identified and studied by expressing fragments of their DNA in a readily culturable host such as E. coli. A variety of different screening methodologies were tested for identifying nitroreductase enzymes from eDNA inserts. The compound 4-nitroimidazole was found to be capable of detecting nitroreductase expression at the level of a single colony. While no novel nitroreductase enzymes were discovered in the scope of this work, the preliminary results are encouraging that a screening strategy centred on 4-nitroimidazole in particular could successfully do so in the near future.</p>

Ly6Chi monocytes are metabolically reprogrammed in the blood during inflammatory stimulation allowing for macrophage lineage commitment

Acute inflammation is a rapid and dynamic process involving the recruitment and activation of multiple cell types in a co-ordinated and precise manner. Using cell tracking, linage tracing and single cell transcriptomics we investigated the origin and transcriptional reprogramming of monocytes and macrophages in acute inflammation. Monocyte trafficking and adoptive transfer experiments revealed that monocytes undergo rapid phenotypic change as they exit the blood and give rise to monocyte-derived macrophages that persist during the resolution of inflammation. Single cell transcriptomics revealed significant heterogeneity within the surface marker defined CD11b+Ly6G-Ly6Chi monocyte population within the blood and at the site of inflammation. Lineage trajectory analysis revealed that Ly6Chi monocytes in the blood are re-programmed into a defined differentiation pathway following inflammatory stimulus. We show that two major transcriptional reprogramming events occur during the initial 6h of Ly6Chi monocyte mobilisation, one in the blood priming monocytes for migration and a second at the site of inflammation. Pathway analysis revealed an important role for oxidative phosphorylation (OxPhos) during both these reprogramming events in a subset of M2-like cells. Experimentally we also demonstrate that OxPhos is essential for murine and human monocyte chemotaxis. These new findings opening up the possibility that altering monocyte metabolic capacity towards OxPhos could facilitate enhanced macrophage M2-like polarisation to aid inflammation resolution and tissue repair.