Biology subjects

Fischer, S. E.

Publications and source records attributed to Fischer, S. E..

4 recordsLinked to original sources

bioRxiv2025

Parallel elevational replacement of hosts and parasites in a highly susceptible songbird genus

Elevational replacement distribution patterns underpin montane diversity and reflect the interaction of both biotic and abiotic pressures, but the degree to which parasites exhibit elevational zonation remains unclear. Investigating infection patterns in related host species across elevational gradients can reveal whether parasites and hosts show concordant patterns of elevational turnover, potentially due to shared historical and ecological factors. Here, we assessed patterns of elevational replacement in haemosporidian parasite assemblages that infect three congeneric songbird species: Bells vireo (Vireo bellii), gray vireo (V. vicinior), and plumbeous vireo (V. plumbeus), each of which breeds across distinct elevations and habitats in the southwestern United States. We screened a total of 248 individuals using cytochrome b PCR and microscopy. We identified 19 haemosporidian haplotypes, including eight novel lineages. We found that each of the three vireo species exhibited high haemosporidian prevalence (55.0-86.2%), with nearly all infections from the genus Haemoproteus (subgenus Parahaemoproteus). Haemosporidian assemblages varied across elevations; each sampled range of elevations harbored abundant, yet host-specific lineages with different environmental associations. Bells and plumbeous vireos, but not gray vireos, hosted several phylogenetically distinct, putative generalist lineages, likely reflecting spillover from more diverse local breeding bird communities. Repeated infections in individuals across breeding seasons, together with moderate parasitemia (x{square} {approx} 1%) suggest that these focal vireo species harbor chronic infections during their respective breeding seasons. These results demonstrate that elevational replacement patterns in avian hosts may be mirrored by their haemosporidian parasites, particularly among host-specialized lineages.

ecology↗

bioRxiv2023

Drab and distant birds are studied less than their fancy-feathered friends

Human decisions are influenced by implicit biases, and scientists do not exist in an objectivity vacuum. Subconscious biases in scientists choices about which species to study may beget distorted knowledge bases and stagnant paradigms. Disparities in biological knowledge can result from bias in study species selection within a cycle of policymaking, funding, and publication, all subject to implicit biases. Here, we show that ornithological research in the USA and Canada is biased toward birds with greater aesthetic salience and those with larger breeding ranges and ranges that encompass more universities. We quantified components of aesthetic salience (e.g., color, pattern/contrast, body size) of 293 passerines and near-passerines based on empirically documented human visual preferences and investigated whether these components were associated with research effort. We also quantified each species breeding range size and the number of universities within that range. Accounting for phylogenetic relatedness, we found that these metrics of aesthetics, familiarity, and accessibility combined to explain 45% of the variation in the number of published papers about each species from 1965-2020. On average, birds in the top 10% of aesthetic salience were studied 3.0X more than birds in the bottom 10%, and publication numbers were predicted most strongly by color and pattern components of aesthetic salience. Birds in the top 10% of breeding range size and university abundance were studied 3.8X and 3.5X more often than species in the bottom 10% of those categories, respectively. Species listed as Endangered and those featured on journal covers have greater aesthetic salience scores than other species. We discuss how these biases may influence perceived relative value of species with respect to culture and conservation. The disparities in empirical knowledge we describe here perpetuate a positive feedback loop, thus widening the gap between the avian "haves" and "have-nots", with some questions answered repeatedly while potentially critical discoveries are left undiscovered. O_QD"All animals are equal, but some animals are more equal than others." --George Orwell, Animal Farm (1945) C_QD

ecology↗

bioRxiv2022

Hourglass, a tool to mine bioimaging data, uncovers sex-disparities in the IL-6-associated T cell response in pancreatic tumors

Recent advances in digital pathology have led to an explosion in high-content multidimensional imaging approaches. Yet, our ability to gainfully process, visualize, integrate and mine the resulting mass of bioimaging data remains a challenge. We have developed Hourglass, an open access user-friendly software that streamlines complex biology-driven post-processing and visualization of multiparametric data. Directed at datasets derived from tissue microarrays or imaging methods that analyze multiple regions of interest per patient specimen, Hourglass systematically organizes observations across spatial and global levels as well as within patient subgroups. Application of Hourglass to our large and complex pancreatic cancer bioimaging dataset (540,617 datapoints derived from 26 bioimaging analyses applied to 596 specimens from 165 patients) consolidated a breadth of known IL-6 functions in a well-annotated human pancreatic cancer cohort and uncovered new unprecedented insights into a sex-linked Interleukin-6 (IL-6) association with immune phenotypes. Specifically, regional effects of IL-6 on the intratumoral T cell response were restricted to male patients only. In conclusion, Hourglass facilitates multi-layered knowledge extraction from complex multiparametric bioimaging datasets and provides tailored analytical means to productively harness heterogeneity at the sample and patient level.

cancer biology↗

bioRxiv2021

Spatially confined sub-tumor microenvironments orchestrate pancreatic cancer pathobiology

Pancreatic ductal adenocarcinoma (PDAC) remains resistant to most treatments and demonstrates a complex pathobiology. Here, we deconvolute regional heterogeneity in the human PDAC tumor microenvironment (TME), a long-standing obstacle, to define precise stromal contributions to PDAC progression. Large scale integration of histology-guided multiOMICs with clinical data sets and functional in vitro models uncovers two microenvironmental programs in PDAC that were anchored in fibroblast differentiation states. These sub-tumor microenvironments (subTMEs) co-occurred intratumorally and were spatially confined, producing patient-specific cellular and molecular heterogeneity associated with shortened patient survival. Each subTME was uniquely structured to support discrete aspects of tumor biology: reactive regions rich in activated fibroblast communities were immune-hot and promoted aggressive tumor progression while deserted regions enriched in extracellular matrix supported tumor differentiation yet were markedly chemoprotective. In conclusion, PDAC regional heterogeneity derives from biologically distinct reactive and protective TME elements with a defined, active role in PDAC progression. Graphical Abstract & Key findings O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/431890v1_ufig1.gif" ALT="Figure 1"> View larger version (73K): org.highwire.dtl.DTLVardef@17adabdorg.highwire.dtl.DTLVardef@aee778org.highwire.dtl.DTLVardef@deae00org.highwire.dtl.DTLVardef@1718272_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIPDAC regional heterogeneity originates in sub-tumor microenvironments (subTMEs) C_LIO_LISubTMEs exhibit distinct immune phenotypes and CAF differentiation states C_LIO_LIDifferent subTMEs are either tumor-promoting or chemoprotective C_LIO_LIIntratumoral subTME co-occurrence links stromal heterogeneity to patient outcome C_LI

cancer biology↗