Biology subjects

Patterson, A.

Publications and source records attributed to Patterson, A..

18 recordsLinked to original sources

bioRxiv2026

Whole-Brain, Region-Specific Astrocyte Reactivity and Morphological Remodeling After Diffuse Traumatic Brain Injury in A Gyrencephalic Ferret Model

Traumatic brain injury (TBI) triggers pathological cascades that evolve across acute, subacute, and chronic phases. Astrocytes play a central role across these phases, and astrocyte reactivity is commonly evaluated using glial fibrillary acidic protein (GFAP) immunolabeling. However, in many TBI studies GFAP changes are characterized qualitatively or with manual or simple threshold-based measures on a small set of sections, limiting throughput and constraining analysis of region-specific heterogeneity in astrocyte responses. To overcome these limitations, we employed a ferret model of diffuse TBI (5 TBI, 5 sham), leveraging the ferrets gyrencephalic cortex, human-like regional fractional brain volumes, and astrocyte features that more closely resemble the human brain than rodent models. An AI-driven segmentation model validated for GFAP-stained ferret histology was integrated with atlas-based mapping to achieve whole-brain, region-resolved quantification of astrocyte reactivity over an average of 10 coronal slices per animal. Morphometric analysis using a custom SMorph-based pipeline characterized branching complexity and spatial domain features across defined regions. At seven days post-injury, TBI animals showed elevated astrocyte reactivity and hypertrophic remodeling, with significant expansion of convex hull area and elongation of secondary branches at the whole-brain level, most pronounced in the atlas-defined gray-matter region and cerebellum and brain-stem subregions, whereas white-matter showed a similar but less marked trend. Morphological changes were also detected in the hippocampus that did not show significant increases in astrocyte reactivity, indicating that structural remodeling represents a partially independent dimension of the astroglial response. These regional patterns are consistent with expected large tissue deformation and axonal strain in brainstem-cerebellar pathways and gray-matter at gray-white junctions in sagittal rotation, motivating future computational studies to quantify these links more directly. By combining region-resolved GFAP mapping with large-scale morphometry, this work provides a scalable framework for region-specific astrocyte mapping to support future multimodal, computational, and targeted neuroprotective studies.

neuroscience↗

bioRxiv2026

Microbial Growth in an Enceladus Ocean Analog Medium Informed by Mineral Stability Modeling

Evidence from the Cassini mission confirmed that Saturns moon Enceladus hosts a subsurface alkaline ocean where rock-water reactions may generate redox disequilibria capable of supporting microbial metabolisms. To investigate potential microbial survival under simulated Enceladus ocean conditions, we used thermodynamic modeling to develop a salt formulation consistent with one possible Enceladus ocean composition and supplemented it with putative microbial energy sources to create a growth medium. The medium was inoculated with samples from diverse ocean world analog environments on Earth to determine which microorganisms could persist under Enceladus-like conditions. The microorganisms persisting in this geochemically bounded medium were heterotrophic, metabolically versatile bacteria with low carbon requirements. Genomic and physiological analyses further showed the presence of multiple stress-response pathways, sodium-based bioenergetic systems, osmoregulation strategies, and other adaptations consistent with survival in alkaline, low-nutrient settings. These results suggest that some stress-tolerant heterotrophic bacteria may serve as useful model organisms for life in Enceladus subsurface ocean. These findings demonstrate the value of geochemically modeled media as a framework for constraining habitability, identifying relevant biosignatures, and probing potential microbial survival strategies beyond Earth.

microbiology↗

bioRxiv2026

A phylogeny-guided framework for decoding mechanisms of human endogenous retrovirus regulation in health and disease

Human endogenous retroviruses (HERVs) are remmants of ancient infections which make up to [~]8% of the human genome. Their activity influences development, immunity, and cancer, but studying them has been limited by a key technical challenge: short-read sequencing cannot uniquely assign reads to these highly repetitive elements. Here, we present ERVmancer, a phylogeny-informed method that resolves the read-mapping ambiguity and quantifies HERV expression across scales, from individual loci to entire retroviral clades, depending on mapping confidence. Benchmarking with sample-matched long- and short-read data generated in this study demonsrates that ERVmancer outperforms existing approaches in both sensitivity and specificity. Application of ERVmancer recapitulates known HERV expression patterns in multiple sclerosis and uncovers new biology in breast cancer, including suppression of HERVH-LTR7 by p53. By enabling accurate and scalable quantification of integrated retroviral elements, ERVmancer provides a broadly applicable resource for investigating retroviral mechanisms in health and disease.

bioinformatics↗

bioRxiv2025

Including fitness and health proxies can alter our understanding of habitat selection

Habitat selection analyses, which discern the environmental conditions individuals select, often inform conservation planning. Through a literature review, we demonstrate that recent habitat selection studies rarely include fitness and health information. With a simulation study, we show that ignoring such information could support the protection of sink habitats. Our case studies demonstrate how health and fitness proxies can modify our understanding of habitat selection: (1) incorporating mass gain of thick-billed murres shows the energetic benefit of areas deemed secondary by a naive resource selection function; (2) including number of chicks in a step selection function (SSF) exposes the complex relationships glaucous-winged gulls have with landscapes impacted by humans; and (3) including external signs of trauma in the movement kernel of SSFs demonstrate others ways in which narwhal distribution can be altered. We urge movement ecologists to collect and use health and fitness data to improve ecological inference and conservation action.

ecology↗

bioRxiv2025

Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance

Most advanced melanomas initially respond to targeted therapy but eventually relapse. Rather than acquiring new mutations, resistance is driven by drug-tolerant persister cells that enter a reversible drug-refractory state. We developed MeRLin, a high-resolution lineage tracing platform integrating cellular barcoding, single-cell transcriptomics, RNA fluorescence in situ hybridization (FISH), and computational analyses to track clonal and transcriptional dynamics in patient-derived melanoma models during prolonged therapy. Clonal dynamics revealed that persister subpopulations first responded to treatment but persisted and expanded during minimal residual disease, ultimately leading to tumor recurrence. Pre-treatment melanoma populations diversified into four conserved persister states characterized by stress-like, lipid metabolism, PI3K signaling, and extracellular matrix remodeling programs associated with adaptive resistance. Spatial transcriptomics showed the organization of these adaptive programs and a complex signaling network of autocrine and paracrine interactions among persister subpopulations. Barcoded RNA-FISH enabled spatial mapping of clonal identity and gene expression, revealing in situ co-localization of a dominant resistant clone with SLC2A1 expression. MeRLin provides a robust framework for dissecting cancer heterogeneity and identifying vulnerabilities in persister populations.

cancer biology↗

bioRxiv2025

Using wingbeat frequency to estimate mass gained by seabirds

1. Energy intake is a fundamental currency in ecology that is critical to reproductive success, survival and lifetime fitness. Measuring foraging success in wild animals via biologgers has been a long-standing challenge. 2. Flying animals gain mass during foraging, and they must counteract the associated increased gravitational force by creating additional lift. Pennycuick (1996) proposed that wingbeat frequency (w) should vary with the square root of body mass [Formula], when other variables influencing wingbeat frequency are held constant. 3. We present a state-space model that estimates instantaneous changes in body mass by modelling this relationship with wingbeat frequency using animal-borne accelerometer and depth data. To demonstrate the usefulness of our proposed method, we applied it to biologging data from 55 thick-billed murres (Uria lomvia) during the incubation period. 4. Our mass estimates allowed us to identify areas associated with higher gains, and to demonstrate that foraging success was generally higher farther from the colony. However, 79% of foraging trips were associated with mass deficits. We performed simulation studies to assess the sensitivity of our method to parameter misspecification and the increase in accuracy gained from including the known mass at recapture. As estimates of energy intake allow for testing of long-standing hypotheses in foraging ecology, our method provides a new tool to help answer these questions with any animal that engages in flapping flight.

ecology↗

bioRxiv2025

Mesenchymal-epithelial transition serves to rapidly, yet transiently, restore the endometrial epithelium during postpartum murine uterine regeneration

The uterus is a remarkable organ in its ability to undergo extensive tissue damage during menstruation and parturition, yet achieves efficient, scar-free repair. Coordinated regulation of this regenerative process is essential for uterine homeostasis and fertility; however, the underlying mechanisms remain incompletely understood. Here, we demonstrate that mesenchymal-epithelial transition (MET) contributed to postpartum endometrial re-epithelialization using PdgfrCreERT2/+; Rosa26-tdTomatofl/+ lineage tracing mice. Flow cytometry revealed a marked increase in mesenchymal-derived (MD) epithelial cells during active tissue repair. Notably, these cells were transient, undergoing clearance primarily via apoptosis following completed epithelial restoration. We also identified a migratory population of transitional cells of mesenchymal origin within the mesometrial stroma that incorporated into the luminal epithelium, consistent with an active MET program. Single-nucleus RNA sequencing (snRNA-seq) revealed that MD epithelial cells exhibited gene expression profiles associated with cell adhesion and cytoskeletal remodeling, while transitional cells were enriched for genes involved in junctional assembly and actin dynamics. MET-associated genes were significantly upregulated in both transitional and MD epithelial populations. Cell-cell communication analysis highlighted WNT, BMP, and EPHA signaling as candidate regulators of MET during regeneration. Together, these findings provide confirmation of MET as a physiologic mechanism of postpartum endometrial epithelial repair and uncover a coordinated signaling network that facilitates this process. Perturbations in MET may contribute to pathologies such as endometriosis or endometrial cancer, underscoring the importance of understanding mesenchymal-epithelial plasticity in both normal and disease states. SignificanceThe mammalian endometrium undergoes repeated injury and repair during menstruation (women) and pregnancy (most eutherians), yet exhibits a remarkable capacity for rapid, scar-free healing that mediates infection, inflammation and hemorrhage. Despite its clinical relevance, the molecular regulation of endometrial regeneration remains poorly defined. Using a transgenic lineage-tracing mouse model, we identified mesenchymal-derived (MD) epithelial and transitional cells during the regenerative window and revealed a critical role for mesenchymal-epithelial transition (MET) in this process. Single-nucleus RNA sequencing further uncovered functional characteristics of these cells and highlighted WNT, BMP, and EPHA signaling as potential regulators of MET. These findings provide new insight into the cellular and molecular framework of endometrial regeneration and have important implications for diseases involving aberrant tissue repair.

physiology↗

bioRxiv2024

Maternal diet alters offspring early life host-microbiota communication through goblet cells, resulting in long-lasting diseases susceptibility

A crucial early-life developmental phase regulates microbiome settling while establishing critical and long-lasting immune and metabolic processes. During this period, the influence of select components of maternal diet on offspring microbiota and health remains largely unknown. To investigate the potential transgenerational impact of maternal exposure to microbiota-disrupting factors, dams were subjected prior breeding to dietary emulsifiers, known to directly perturb the microbiota. Such maternal exposure induced early-life microbiota alterations in offspring which associated with long-lasting susceptibility to diet-induced obesity and intestinal inflammation. These detrimental effects were entirely prevented by early-life microbiota normalization through cross-fostering procedures. Mechanistically, maternal emulsifier exposure induces strong offsprings impairment in goblet cells-mediated host-microbiota communication which is central in driving the observed long-lasting deleterious effects. To conclude, this study underscores the central role played by maternal intake of microbiota-disrupting agents on the next generations microbiota, with long lasting consequences for intestinal and metabolic health.

microbiology↗

bioRxiv2024

Fine-scale movement data of the endangered Bermuda petrel highlights surface foraging and greater nocturnal flight activity.

Foraging behavior plays a fundamental role in animal fitness and population dynamics, particularly in marine ecosystems where seabirds like petrels (small Procellariiformes) showcase a diverse array of foraging strategies finely adapted to the pelagic environment. The extent and remote nature of their foraging grounds makes direct observation of foraging behaviour impractical, thereby requiring the use of remote tracking technologies. We deployed miniaturized multi-sensor biologgers and collected fine scale movement data to investigate the at-sea behaviours of the Bermuda petrel Pterodroma cahow, a poorly studied and highly threatened gadfly petrel, specialised on mesopelagic prey. GPS-tracking data revealed extensive foraging trips, in consistent directions, over remote oceanic regions. Time-depth-recorders provided new insights into petrel feeding techniques suggesting that the meso-bathypelagic prey targeted by petrels must be available in the very upper layer of the water surface, given their very limited diving activity (99.99% of dives had 0.1 m of depth). Accelerometer data revealed 3 flying- and 3 water-related behaviours. Flying behaviours reflected the expected dynamic soaring flight strategy of procellariforms; individuals spent more than three-quarters of their time in flight with flying-non-flapping being the most common behaviour under all conditions. The behaviour classified as "flying-intensive" was infrequently observed but could indicate aerial dipping, a characteristic foraging technique of Pterodroma species. The remaining time was spent in three water behaviours: active, inactive and intensive, with the latter being less common but thought to reflect scavenging and prey seizing. Flying-related behaviours increased with negative sun elevation values, highlighting greater flight activity during night compared to the day, while water behaviours were more common during the day. While some of our findings may require further validation to confirm their relevance to foraging behaviour, our work offers new and valuable insights to consider when assessing the extent and nature of offshore anthropogenic-related risks faced by petrels.

animal behavior and cognition↗

bioRxiv2023

Extraordinary levels of per- and polyfluoroalkyl substances (PFAS) in vertebrate animals at a New Mexico desert oasis: multiple pathways for wildlife and human exposure

Per- and polyfluoroalkyl substances (PFAS) threaten human and wildlife health, but their movement through food webs remains poorly understood. Contamination of the physical environment is widespread, but particularly concentrated at military installations. Here we measured 17 PFAS in wild, free-living mammals and migratory birds at Holloman Air Force Base (AFB), New Mexico, USA, where wastewater catchment lakes form biodiverse oases. PFAS concentrations were among the highest ever reported in animal tissues, and high levels have persisted for at least three decades. The hazardous long carbon-chain form, perfluorooctanosulfonic acid (PFOS), was most abundant, with liver concentrations averaging tens of thousands of ng/g wet weight (ww), reaching as high 97,000 ng/g (ww) in a 1994 specimen of white-footed mouse (Peromyscus leucopus) and 38,000 ng/g ww in a duck, the American wigeon (Mareca americana). Perfluorohexanesulfonic acid (PFHxS) averaged thousands of ng/g ww in the livers of birds and house mice, but one order of magnitude lower in the livers of upland desert rodent species. PFAS levels were strikingly lower at control sites, even for highly mobile migratory species. Tissue concentrations were correlated within individuals, and consistently higher in liver than in muscle or blood. Twenty of 23 vertebrate species sampled at Holloman AFB were heavily contaminated, representing multiple trophic levels and microhabitats, and implicating a range of pathways for PFAS spread: ingestion of surface water, sediments, and dust; foraging on aquatic invertebrates and plants by secondary consumers; and preying upon small vertebrates by higher level consumers, including consumption of game species by hunters. Unlike in other aquatic systems, piscivory was not an important pathway of PFAS uptake. In sum, legacy PFAS at a desert wetland have permeated the local food web across a period of decades, severely contaminating resident and migrant animals, and likely exposing humans via game meat consumption and outdoor recreation. Five highlightsO_LIA biodiverse, wetland food web at a military base is heavily contaminated with PFAS. C_LIO_LILittoral-zone mice and aquatic birds had high liver PFOS, up to 97,000 ng/g ww. C_LIO_LISpecies and ecological variation were high among 16 PFAS detected in animal tissues. C_LIO_LIGame species had dangerously contaminated meat and can transport it long distances. C_LIO_LIBiorepositories provide key temporal and spatial sampling for contaminant studies. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/561778v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@96a640org.highwire.dtl.DTLVardef@7cd7f4org.highwire.dtl.DTLVardef@45fb67org.highwire.dtl.DTLVardef@7c33a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2023

Tofacitinib effects profound seizure suppression through mimicking EZH2 antagonism of a pro-inflammatory gene network in epilepsy.

All current drug treatments for epilepsy, a neurological disorder affecting over 50 million people(1, 2) merely treat symptoms, and a third of patients do not respond to medication. There are no disease modifying treatments that may be administered briefly to patients to enduringly eliminate spontaneous seizures and reverse cognitive deficits(3, 4). Applying network approaches to rodent models and human temporal lobectomy samples at both whole tissue and single-nuclei resolutions, we observe the well-characterized pattern of rapid induction and subsequent quenching exhibited of the JAK/STAT pathway within days of epileptogenic insult. This is followed by a resurgent activation weeks to months later with the onset of spontaneous seizures. Targeting the first wave of activation after epileptic insult does not prevent disease. However, brief inhibition of the second wave with CP690550 (Tofacitinib) (5, 6) enduringly suppresses seizures, rescues deficits in spatial memory, and alleviates epilepsy-associated histopathological alterations. Seizure suppression lasts for at least 2 months after the final dose. Using discovery-based transcriptomic analysis across models of epilepsy and validation of putative mechanisms with human data, we demonstrate a powerful approach to identifying disease modifying targets; this may be useful for other neurological disorders. With this approach, we find that reignition of inflammatory JAK/STAT3 signaling in chronic epilepsy opens a window for disease modification with the FDA-approved, orally available drug CP690550.

neuroscience↗

bioRxiv2023

Comammox bacterial preference for urea influences its interactions with aerobic nitrifiers.

While the co-existence of comammox bacteria with canonical nitrifiers is well documented in diverse ecosystems, there is still a dearth of knowledge about the mechanisms underpinning their interactions. Understanding these interaction mechanisms is important as they may play a critical role in governing nitrogen biotransformation in natural and engineered ecosystems. In this study, we tested the ability of two environmentally relevant factors (nitrogen source and availability) to shape interactions between strict ammonia and nitrite-oxidizing bacteria and comammox bacteria in continuous flow column reactors. The composition of inorganic nitrogen species in reactors fed either ammonia or urea was similar during the lowest nitrogen loading condition (1 mg-N/L), but higher loadings (2 and 4 mg-N/L) promoted significant differences in nitrogen species composition and nitrifier abundances. The abundance and diversity of comammox bacteria were dependent on both nitrogen source and loading conditions as multiple comammox bacterial populations were preferentially enriched in the urea-fed system. In contrast, their abundance was reduced in response to higher nitrogen loadings in the ammonia-fed system likely due to ammonia-based inhibition. The preferential enrichment of comammox bacteria in the urea-fed system could be associated with their ureolytic activity calibrated to their ammonia oxidation rates thus minimizing ammonia accumulation to inhibitory levels. However, an increased abundance of comammox bacteria was not associated with a reduced abundance of nitrite oxidizers in the urea-fed system while a negative correlation was found between them in the ammonia-fed system; the latter dynamic likely emerging from reduced availability of nitrite to strict nitrite oxidizers at low ammonia loading conditions. ImportanceNitrification is an essential biological process in drinking water and wastewater treatment systems for managing nitrogen and protecting downstream water quality. The discovery of comammox bacteria and their detection alongside canonical nitrifiers in these engineered ecosystems has made it necessary to understand the environmental conditions that regulate their abundance and activity relative to other better-studied nitrifiers. This study aimed to evaluate two important factors that could potentially influence the behavior of nitrifying bacteria, and therefore impact nitrification processes. Colum reactors fed with either ammonia or urea were systematically monitored to capture changes in nitrogen biotransformation and the nitrifying community as a function of influent nitrogen concentration, nitrogen source, and reactor depth. Our findings show that comammox bacterial abundance decreased and that of nitrite oxidizers increased with increased ammonia availability, while their abundance and diversity increased with increasing urea availability without driving a reduction in the abundance of canonical nitrifiers.

microbiology↗

bioRxiv2023

Inactivation of face selective neurons alters eye movements when free viewing faces

During free viewing, faces attract gaze and induce specific fixation patterns corresponding to the facial features. This suggests that neurons encoding the facial features are in the causal chain that steers the eyes. However, there is no physiological evidence to support a mechanistic link between face encoding neurons in high-level visual areas and the oculomotor system. In this study, we targeted the middle face patches of inferior temporal (IT) cortex in two macaque monkeys using an fMRI localizer. We then utilized muscimol microinjection to unilaterally suppress IT neural activity inside and outside the face patches and recorded eye movements while the animals free viewing natural scenes. Inactivation of the face selective neurons altered the pattern of eye movements on faces: the monkeys found faces in the scene but neglected the eye contralateral to the inactivation hemisphere. These findings reveal the causal contribution of the high-level visual cortex in eye movements. SignificanceIt has been shown, for more than half a century, that eye movements follow distinctive patterns when free viewing faces. This suggests causal involvement of the face-encoding visual neurons in the eye movements. However, the literature is scant of evidence for this possibility and has focused mostly on the link between low-level image saliency and eye movements. Here, for the first time, we bring causal evidence showing how face-selective neurons in inferior temporal cortex inform and steer eye movements when free viewing faces.

neuroscience↗

bioRxiv2022

Subset-specific mitochondrial and DNA damage shapes T cell responses to fever and inflammation

Heat is a cardinal feature of inflammation. Despite temperature variability and dependence of enzymes and complexes, how heat and fever affect immune cells remains uncertain. We found that heat broadly increased inflammatory activity of CD4+ T cell subsets and decreased Treg suppressive function. Th1 cells, however, also selectively developed mitochondrial dysfunction with high levels of ROS production and DNA damage. This led Th1 cells to undergo Tp53-dependent death, which was required to minimize the accumulation of mutations in heat and inflammation. Th1 cells with similar DNA damage signatures were also detected in Crohns disease and rheumatoid arthritis. Fever and inflammation-associated heat thus selectively induce mitochondrial stress and DNA damage in activated Th1 cells that requires p53 to maintain genomic integrity of the T cell repertoire. One Sentence SummaryFever temperatures augment CD4+ T cell-mediated inflammation but induce differential metabolic stress and DNA damage in T cell subsets, with Th1 cells selectively sensitive and dependent on p53 to induce apoptosis and maintain genomic integrity.

immunology↗

bioRxiv2022

Dynamic states of eIF6 and SDS variants modulate interactions with uL14 of the 60S ribosomal subunit.

Assembly of ribosomal subunits into active ribosomal complexes is integral to protein synthesis. Release of eIF6 from the 60S ribosomal subunit primes 60S to associate with the 40S subunit and engage in translation. The dynamics of eIF6 interaction with the uL14 (RPL23) interface of 60S and its regulation by somatic mutations acquired in Shwachman-Diamond Syndrome (SDS) is yet to be clearly understood. Here, by using a modified strategy to obtain high yields of recombinant human eIF6 we have uncovered the critical interface entailing 8 key residues in the C-tail of RPL23 that is essential for physical interactions between 60S and eIF6. Disruption of the complementary binding interface by conformational changes in eIF6 disease variants provide a mechanism for weakened interactions of variants with the 60S. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) analyses uncovered dynamic configurational rearrangements in eIF6 induced by binding to RPL23 and exposed an allosteric interface regulated by the C-tail of eIF6. Disrupting a key residue in the eIF6-60S binding interface markedly limits proliferation of cancer cells, which highlights the significance of therapeutically targeting this interface. Establishing these key interfaces thus provide a therapeutic framework for targeting eIF6 in cancers and SDS.

biochemistry↗

bioRxiv2022

In macrophages fatty acid oxidation spares glutamate for use in diverse metabolic pathways required for alternative activation

Fatty acid oxidation (FAO) is upregulated in IL-4-stimulated (alternatively activated) macrophages (M(IL-4)). We examined the effect of loss of function of the enzyme Cpt1a, which facilitates the entry of long chain fatty acids (FA) into mitochondria for FAO, on alternative activation. Expression of M(IL-4) markers ARG1, CD301 and RELM, was impaired in tamoxifen-treated ERT2Cre x Cpt1afl/fl macrophages and in macrophages expressing shRNA targeting Cpt1a (Cpt1a-shRNA). In contrast, VaviCre x Cpt1afl/fl and LysmCre x Cpt1afl/fl M(IL-4) responded normally to IL-4. Reduced alternative activation due to Cpt1a loss of function was linked to decreased cellular pools of -ketoglutarate, glutamate, and glutathione, diminished commitment of glucose carbon to serine/glycine synthesis, and decreased expression of genes in the Nrf2-oxidative stress response pathway. Consistent with this, reactive oxygen species were increased. Restoration of glutathione pools with N-acetyl cysteine normalized oxidative stress and allowed alternative activation in the face of Cpt1a-deficiency, pointing to a role for FAO in the control of ROS and as being important for alternative activation. In VaviCre x Cpt1afl/fl M(IL-4), glutamine uptake was increased, compensating for the loss of FAO to meet necessary metabolic demands, to allow alternative activation. The data indicate that macrophages are able to regulate glutamine metabolism to compensate for chronic disruption of FAO to meet metabolic needs.

immunology↗

bioRxiv2022

Rtt105 configurationally staples RPA and blocks facilitated exchange and interactions with RPA-interacting proteins

Replication Protein A (RPA) binds to single-stranded DNA (ssDNA) and recruits over three dozen RPA-interacting proteins (RIPs) to coordinate multiple aspects of DNA metabolism including DNA replication, repair, and recombination. Rtt105 is a molecular chaperone that regulates nuclear localization of RPA. Whether and how Rtt105 regulates the activities of RPA is poorly understood. Here, we show that Rtt105 binds to multiple DNA binding and protein-interaction domains of RPA and configurationally staples the complex. In the absence of ssDNA, Rtt105 inhibits RPA binding to Rad52, thus preventing spurious binding to RPA-interacting proteins (RIPs). When ssDNA is available, Rtt105 promotes formation of high-density RPA nucleoprotein filaments and dissociates during this process. Free Rtt105 further stabilizes the RPA-ssDNA filaments by inhibiting RPA facilitated exchange. Collectively, our data suggest that Rtt105 sequesters free RPA in the nucleus to prevent untimely RIP interaction, while stabilizing RPA-ssDNA filaments at DNA lesion sites.

biochemistry↗

bioRxiv2020

Hydrogen-deuterium exchange reveals a dynamic DNA binding map of Replication Protein A

Replication Protein A (RPA) binds to single-stranded DNA (ssDNA) and interacts with over three dozen enzymes and serves as a recruitment hub to coordinate most DNA metabolic processes including DNA replication, repair, and recombination. RPA binds ssDNA utilizing six oligosaccharide/oligonucleotide binding (OB) domains within a heterotrimeric complex of RPA70, RPA32 and RPA14 subunits. Based on their DNA binding affinities they are classified as high versus low-affinity DNA binding domains (DBDs). However, recent evidence suggests that the DNA-binding dynamics of DBDs better define their roles. Utilizing hydrogen-deuterium exchange mass spectrometry (HDX-MS) we assessed the contacts and dynamics of the individual domains of human RPA to determine the landscape of conformational changes upon binding to ssDNA. As expected, ssDNA interacts with the major DBDs (A, B, C, and D). However, DBD-A and DBD-B are dynamic and do not show robust DNA-dependent protection. DBD-C displays the most extensive changes in HDX, suggesting a major role in stabilizing RPA on ssDNA. DNA-dependent HDX kinetics are also captured for DBD-D and DBD-E. Slower allosteric changes transpire in the protein-protein interaction domains and the linker regions. We propose a dynamics-based DNA binding model for RPA utilizing a dynamic half and a less-dynamic half.

biochemistry↗