Biology subjects

Fitzpatrick, M.

Publications and source records attributed to Fitzpatrick, M..

4 recordsLinked to original sources

bioRxiv2020

Relationships between climate and phylogenetic community structure of fossil pollen assemblages are not constant during the last deglaciation

Disentangling the influence of environmental drivers on community assembly is important to understand how multiple processes influence biodiversity patterns and can inform understanding of ecological responses to climate change. Phylogenetic Community Structure (PCS) is increasingly used in community assembly studies to incorporate evolutionary perspectives and as a proxy for trait (dis)similarity within communities. Studies often assume a stationary relationship between PCS and climate, though few if any studies have tested this assumption over long time periods with concurrent community data. We estimated Nearest Taxon Index (NTI) and Net Relatedness index (NRI), two PCS metrics, of fossil pollen assemblages of angiosperms in eastern North America data over the last 21 ka BP at 1ka intervals. We analyzed spatiotemporal relationships between PCS and seven climate variables, evaluated the potential impact of deglaciation on PCS, and tested for the stability of climate-PCS relationships. The broad scale patterns of PCS, with overdispersion increasing towards the southern and eastern parts of the study area, remained largely stable across time. Most importantly, we found that significant relationships between climate variables and PCS (slope) were unstable as climate changed during the last deglaciation and new ice-free regions were colonized. We also found weak, but significant, relationships between both PCS metrics (i.e., NTI and NRI) and climate and time-since-deglaciation, which were stable even though the baselines (intercepts) changed through time. Overall, our results suggest that (1) PCS of fossil Angiosperm assemblages during the last 21ka BP have had predictable spatial patterns, but (2) the instability in the relationships between PCS and climate brings into question their usefulness in predictive modeling of community assembly.

ecology↗

bioRxiv2020

Multiplexed imaging of human tuberculosis granulomas uncovers immunoregulatory features conserved across tissue and blood

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that is distinctly characterized by granuloma formation within infected tissues. Granulomas are dynamic and organized immune cell aggregates that limit dissemination, but can also hinder bacterial clearance. Consequently, outcome in TB is influenced by how granuloma structure and composition shift the balance between these two functions. To date, our understanding of what factors drive granuloma function in humans is limited. With this in mind, we used Multiplexed Ion Beam Imaging by Time-of-Flight (MIBI-TOF) to profile 37 proteins in tissues from thirteen patients with active TB disease from the U.S. and South Africa. With this dataset, we constructed a comprehensive tissue atlas where the lineage, functional state, and spatial distribution of 19 unique cell subsets were mapped onto eight phenotypically-distinct granuloma microenvironments. This work revealed an immunosuppressed microenvironment specific to TB granulomas with spatially coordinated co-expression of IDO1 and PD-L1 by myeloid cells and proliferating regulatory T cells. Interestingly, this microenvironment lacked markers consistent with T-cell activation, supporting a myeloid-mediated mechanism of immune suppression. We observed similar trends in gene expression of immunoregulatory proteins in a confirmatory transcriptomic analysis of peripheral blood collected from over 1500 individuals with latent or active TB infection and healthy controls across 29 cohorts spanning 14 countries. Notably, PD-L1 gene expression was found to correlate with TB progression and treatment response, supporting its potential use as a blood-based biomarker. Taken together, this study serves as a framework for leveraging independent cohorts and complementary methodologies to understand how local and systemic immune responses are linked in human health and disease.

immunology↗

bioRxiv2020

The low complexity motif of cytoplasmic polyadenylation element binding protein 3 (CPEB3) is critical for the trafficking of its targets in neurons

Biomolecular condensates, membraneless organelles found throughout the cell, play critical roles in many aspects of cellular function. Ribonucleoprotein granules (RNPs), a type of biomolecular condensate found in neurons that are necessary for local protein synthesis and are involved in long-term potentiation (LTP). Several RNA-binding proteins present in RNPs are necessary for the synaptic plasticity involved in LTP and long-term memory. Most of these proteins possess low complexity motifs, allowing for increased promiscuity. We explore the role the low complexity motif plays for RNA binding protein cytoplasmic polyadenylation element binding protein 3 (CPEB3), a protein necessary for long-term memory persistence. We found that RNA binding and SUMOylation are necessary for CPEB3 localization to the P body, thereby having functional implications on translation. Here, we investigate the role of the low complexity motif of CPEB3 and find that it is necessary for P body localization and downstream targeting for local protein synthesis.

neuroscience↗

bioRxiv2017

A system-wide approach to monitor responses to synergistic BRAF and EGFR inhibition in colorectal cancer cells

Intrinsic and/or acquired resistance represents one of the great challenges in targeted cancer therapy. A deeper understanding of the molecular biology of cancer has resulted in more efficient strategies, where one or multiple drugs are adopted in novel therapies to tackle resistance. This beneficial effect of using combination treatments has also been observed in colorectal cancer patients harboring the BRAF(V600E) mutation, whereby dual inhibition of BRAF(V600E) and EGFR increases antitumor activity. Notwithstanding this success, it is not clear whether this combination treatment is the only or most effective treatment to block intrinsic resistance to BRAF inhibitors. Here, we investigate molecular responses upon single and multi-target treatments, over time, using BRAF(V600E) mutant colorectal cancer cells as a model system. Through integration of transcriptomic, proteomic and phosphoproteomics data we obtain a comprehensive overview, revealing both known and novel responses. We primarily observe widespread upregulation of receptors tyrosine kinases and metabolic pathways upon BRAF inhibition. These findings point to mechanisms by which the drug-treated cells switch energy sources and enter a quiescent-like state as a defensive response, while additionally reactivating the MAPK pathway.

cancer biology↗