Biology subjects

Gee, M.

Publications and source records attributed to Gee, M..

6 recordsLinked to original sources

bioRxiv2024

Antigen-specificity of clonally-enriched CD8+ T cells in multiple sclerosis

CD8+ T cells are the dominant lymphocyte population in multiple sclerosis (MS) lesions where they are highly clonally expanded. The clonal identity, function, and antigen specificity of CD8+ T cells in MS are not well understood. Here we report a comprehensive single-cell RNA-seq and T cell receptor (TCR)-seq analysis of the cerebrospinal fluid (CSF) and blood from a cohort of treatment-naive MS patients and control participants. A small subset of highly expanded and activated CD8+ T cells were enriched in the CSF in MS that displayed high activation, cytotoxicity and tissue-homing transcriptional profiles. Using a combination of unbiased and targeted antigen discovery approaches, MS-derived CD8+ T cell clonotypes recognizing Epstein-Barr virus (EBV) antigens and multiple novel mimotopes were identified. These findings shed vital insight into the role of CD8+ T cells in MS and pave the way towards disease biomarkers and therapeutic targets. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/611010v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1a0b738org.highwire.dtl.DTLVardef@5cf5c2org.highwire.dtl.DTLVardef@10abdccorg.highwire.dtl.DTLVardef@32c7b2_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical SummaryC_FLOATNO Created in BioRender. Sabatino, J. (2024) BioRender.com/e66l598 C_FIG

immunology↗

bioRxiv2024

Navigating the Landscape of Fear

O_LIAnimals searching for food must navigate complex landscapes with varying terrain, food availability, predator activity, and shelter. Where and when should they gather food? To what extent should they engage in anti-predator behaviors such as vigilance or seeking refuge if a predator is detected? Optimal foraging theory (OFT) posits that animals balance potentially conflicting goals (such as feeding versus escaping predation) by making decisions that maximize some expected utility or reward. However, OFT models have generally considered highly simplified landscapes, either ignoring spatial variability or assuming that the habitat consists of discrete, internally uniform habitat patches. As a result, OFT has largely avoided the question of how animals should move from one potential feeding area to another, or between feeding areas and refuges. C_LIO_LIWe develop methods based on stochastic dynamic programming to find optimal foraging strategies, including optimal movement paths, in a continuous landscape with spatially varying predation risk. Our approach accounts for switching from foraging to escape behavior when pursued by a predator. Because contingent escape paths are considered for all visited locations, they influence the optimal foraging path even before threats are encountered. The optimal strategy thus depends on the animals level of hunger, the distribution of food, and the perceived threat distribution. The realized path is further influenced by actual predator encounters. C_LIO_LIWe illustrate our approach with two numerical examples: the first hypothetical with two food-abundant regions accessible only via high-risk areas, the second based on empirical studies on foraging Samango monkeys, Cercopithecus albogularis schwarzi. We find that the shape of the foragers utility function (risk-averse, risk-neutral, or with state-dependent risk sensitivity) affects not only its choices of where to feed, but also the optimal paths to and from each feeding ground. C_LIO_LIOur methods make it possible to compare properties of observed foraging trajectories with those predicted for different goal functions. Foraging trajectories can then provide additional information, along with other behavioral choices, about what quantity, if any, animals aim to optimize while foraging. C_LI

ecology↗

bioRxiv2024

Designed fluorescent protein cages as fiducial markers for targeted cell imaging

Understanding how proteins function within their cellular environments is essential for cellular biology and biomedical research. However, current imaging techniques exhibit limitations, particularly in the study of small complexes and individual proteins within cells. Previously, protein cages have been employed as imaging scaffolds to study purified small proteins using cryo-electron microscopy (cryo-EM). Here we demonstrate an approach to deliver designed protein cages - endowed with fluorescence and targeted binding properties - into cells, thereby serving as fiducial markers for cellular imaging. We used protein cages with anti-GFP DARPin domains to target a mitochondrial protein (MFN1) expressed in mammalian cells, which was genetically fused to GFP. We demonstrate that the protein cages can penetrate cells, are directed to specific subcellular locations, and are detectable with confocal microscopy. This innovation represents a milestone in developing tools for in-depth cellular exploration, especially in conjunction with methods such as cryo-correlative light and electron microscopy (cryo-CLEM).

biochemistry↗

bioRxiv2022

Rigidified Scaffolds for 3-Angstrom Resolution Cryo-EM of Small Therapeutic Protein Targets

Numerous technical advances have made cryo-EM an attractive method for atomic structure determination. Cryo-EM is ideally suited for large macromolecular structures, while problems of low signal-to-noise prevent routine structure determination of proteins smaller than about 50 kDa. This size limitation excludes large numbers of important cellular proteins from structural characterization by this powerful technique, including many cell-signaling proteins of high therapeutic interest. In the present work, we use molecular engineering techniques to rigidify an imaging scaffold, based on a designed protein cage, to the point where 3 [A] resolution can be achieved, even for very small proteins. After optimizing the design of the rigidified scaffold on test proteins, we apply this imaging system to the key oncogenic signaling protein KRAS, which represents an outstanding challenge in the area of structure-based drug design. Despite its 19 kDa size, we show that the structure of KRAS, in multiple mutant forms, and bound to its GDP ligand, can be readily interpreted at a resolution slightly better than 3.0 [A]. This advance further expands the capability of cryo-EM to become an essentially universal method for protein structure determination, including for applications to small therapeutic protein targets.

biochemistry↗

bioRxiv2020

Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation

Host-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study found that the ground beetle microbiome is consistent across different host food sources. We used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ: Anisodactylus similis LeConte, 1851, Pterostichus serripes (LeConte, 1875), and Brachinus elongatulus Chaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets. Soil environment but not diet had a significant effect on bacterial diversity and composition. The three carabid species have patterns of microbial diversity similar to those previously found in other insect hosts. Metagenomic samples from two highly active tissue types -- guts, and pygidial gland secretory cells (which produce defensive compounds) -- were processed and sequenced separately from those of the remaining body. The observed similarity of the pygidial gland secretory cell microbiome across hosts suggests the possibility that it may be a conserved community, possibly due to functional interactions related to defensive chemistry. These results provide a baseline for future studies of the role of microbes in the diversification of defensive chemical biosynthesis in carabids.

ecology↗

bioRxiv2020

Cognitive and Motor Correlates of Grey and White Matter Pathology in Parkinsons Disease

IntroductionPrevious studies have found associations between grey matter atrophy and white matter hyperintensities (WMH) of vascular origin with cognitive and motor deficits in Parkinsons disease (PD). Here we investigate these relationships in a sample of PD patients and age-matched healthy controls. MethodsData included 50 PD patients and 45 age-matched controls with T1-weighted and FLAIR scans at baseline, 18-months, and 36-months follow-up. Deformation-based morphometry was used to measure grey matter atrophy. SNIPE (Scoring by Nonlocal Image Patch Estimator) was used to measure Alzheimers disease-like textural patterns in the hippocampi. WMHs were segmented using T1-weighted and FLAIR images. The relationship between MRI features and clinical scores was assessed using mixed-effects models. The motor subscore of the Unified Parkinsons Disease Rating Scale (UPDRSIII), number of steps in a walking trial, and Dementia Rating Scale (DRS) were used respectively as measures of motor function, gait, and cognition. ResultsSubstantia nigra atrophy was significantly associated with motor deficits, with a greater impact in PDs (p<0.05). Hippocampal SNIPE scores were associated with cognitve decline in both PD and controls (p<0.01). WMH burden was significantly associated with cognitive decline and increased motor deficits in the PD group, and gait deficits in both PD and controls (p<0.03). ConclusionWhile substantia nigra atrophy and WMH burden were significantly associated with additional motor deficits, WMH burden and hippocampal atrophy were associated with cognitive deficits in PD patients. These results suggest an additive contribution of both grey and white matter damage to the motor and cognitive deficits in PD.

neuroscience↗