Biology subjects

Carlson, S.

Publications and source records attributed to Carlson, S..

11 recordsLinked to original sources

bioRxiv2025

IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry.

The identification and analysis of bacteria is central to the microbiological sciences. While gene sequencing methods have been the standard to achieve this, use of MALDI-TOF mass spectrometry (MS), particularly in clinical microbiology, provides high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical settings due to the lack of a centralized public database of MS protein signatures that would facilitate isolate identification via spectral comparison. Further, current platforms lack meaningful ways to compare multiple properties from large numbers of bacterial isolates. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase of protein MS signatures of >1400 strains spanning 6 bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections using metadata integration, and visualize specialized metabolite differences within groups of closely related bacteria. To highlight this utility and encourage wide community contribution, examples of each are presented.

microbiology↗

bioRxiv2025

Bacterial suppression of intestinal fungi via activation of human gut γδ T-cells

Gut symbionts condition mucosal immunity to resist infection by enteropathogens, but the specific microbes and mechanisms involved differ significantly between host species. In higher primates, bacterial metabolite HMB-PP is sensed by a specialized population of V{gamma}9V{delta}2+T-cells, which we now report can potently suppress growth of endogenous fungi in human intestinal organ cultures. In healthy intestine, HMB-PP-stimulated V{delta}2+T-cells restricted outgrowth of keystone fungus Candida albicans via a mechanism that required IL-22. In contrast, Crohns disease (CD) patients with reduced V{delta}2+T-cell numbers displayed outgrowth of C. albicans strains that readily formed toxin-producing filaments, triggered neutrophil extracellular traps, and induced macrophage IL-1{beta} release ex vivo. Genomic and proteomic analysis of the Candida isolates suggested increased tissue adhesion of CD-derived strains, which rapidly invaded the gut barrier in an intestine-on-a-chip model. These data reveal that bacterial activation of V{delta}2+T-cells suppresses fungal pathobionts in human gut via an IL-22-dependent mechanism that is dysregulated in CD.

immunology↗

bioRxiv2025

Mapping of individual somatosensory representations - comparison of fMRI and TMS

Invasive brain mapping, functional magnetic resonance imaging (fMRI) and navigated transcranial magnetic stimulation (nTMS) results indicate that somatosensory representations vary between individuals. However, it is unknown how well somatosensory representations determined using nTMS and fMRI correspond. Here, we used single-pulse nTMS and fMRI in 17 right-handed subjects to determine the S1 representation of the tip of the right index finger stimulated mechanically with a Braille device. In an nTMS mapping experiment, the S1 site at which tactile sensation was blocked by nTMS, was considered the S1 representation site (S1HS) of the fingertip. The location of S1HS varied up to 36 mm between subjects. In the fMRI experiment, passive and oddball tactile tasks were employed. The location of the somatosensory peak fMRI activation varied up to 39 mm between subjects in the passive condition and up to 84 mm in the oddball condition. Within subjects, the mean distance between the S1HS and the peak fMRI activation was 10 + 2 mm (S.E.M.) in the passive condition and 14 + 3 mm in the oddball task. Taken together, our findings underscore the importance of multimodal approaches to brain mapping in future studies.

neuroscience↗

bioRxiv2024

Prolonged low flows and non-native fish operate additively to alter insect emergence in mountain streams

Climate-induced flow alteration is subjecting mountain streams to more frequent and severe low-flow periods due to lower snowpack and earlier snowmelt. Yet, anticipating how stream ecosystems respond to prolonged low flows remains challenging because trophic levels can respond differently, and non-native predators could dampen or amplify responses. Here, we conducted a large-scale experiment to examine how early, prolonged low flows projected by the end of the century in Californias Sierra Nevada will alter mountain stream food webs and emerging insect flux--a critical stream-to-land cross-ecosystem linkage. Additionally, we tested whether Brown trout (Salmo trutta), a widespread non-native top predator, would change food-web responses to low-flow conditions. We found that early low flows and non-native fish effects were additive rather than synergistic or antagonistic. Early low flows did not alter the overall rate of emerging insects but they did shift community structure and reduce the prevalence of small-sized individuals--possibly reflecting larger size at emergence and faster growth rates due to warming. In contrast, non-native fish presence increased seasonally-aggregated abundance of stream insects up to 12%, mainly by increasing abundance of Chironomidae and small-sized Ephemeroptera and Trichoptera. In channels with fish, benthic algal biomass doubled and scraper-grazer and collector-gatherer insects emerged 60% and 55% more than channels without fish, likely benefiting from trout keeping mesopredators at bay. This experiment illustrates that prolonged low flows and invasions can profoundly alter mountain river food webs even when operating additively; and shows how mesocosm-based research may help understand global-change driven disruption of cross-ecosystem linkages.

ecology↗

bioRxiv2024

A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs)

The epithelial to mesenchymal transition (EMT) is a widely studied but poorly defined state change due to the variety of ways in which it has been characterized in cells. There is a need for reproducible cell model systems that enable the integration and comparison of different types of measured observations of cells across many distinct cellular contexts. We present human induced pluripotent stem (hiPS) cells as such a model system by demonstrating its utility through a comparative analysis of hiPS cell-EMT in 2D and 3D cell culture geometries. We developed live-imaging-based assays to directly compare examples of changes in cell function (via migration timing), molecular components (via expression of marker proteins), organization (via reorganization of cell junctions), and environment (via dynamics of basement membrane) in the same experimental system. The EMT-related changes we measured occurred earlier in 2D colonies than in 3D lumenoids, likely due to differences in the basement membrane environments associated with 2D vs. 3D initial hiPS cell culture geometries. We have made the 449 60-hour-long 3D time-lapse movies and the associated tools used for analysis and visualization open-source and easily accessible as a resource for future work in this field.

cell biology↗

bioRxiv2023

OptoPI3K, genetic code expansion, and click chemistry reveal mechanisms underlying reciprocal regulation between TRPV1 and PI3K

ABSTRACTLigands such as insulin, epidermal growth factor, platelet derived growth factor, and nerve growth factor (NGF) initiate signals at the cell membrane by binding to receptor tyrosine kinases (RTKs). Along with G-protein coupled receptors, RTKs are the main platforms for transducing extracellular signals into intracellular signals. Studying RTK signaling has been a challenge, however, due to the multiple signaling pathways to which RTKs typically are coupled, including MAP/ERK, PLC{gamma}, and Class 1A phosphoinositide 3-kinases (PI3K). The multi-pronged RTK signaling has been a barrier to isolating the effects of any one downstream pathway. Here, we used optogenetic activation of PI3K to decouple its activation from other RTK signaling pathways. In this context, we used genetic code expansion to introduce a click chemistry noncanonical amino acid into the extracellular side of membrane proteins. Applying a cell- impermeant click chemistry fluorophore allowed us to visualize delivery of membrane proteins to the plasma membrane in real time. Using these approaches, we demonstrate that activation of PI3K, without activating other pathways downstream of RTK signaling, is sufficient to traffic the TRPV1 ion channels and insulin receptors to the plasma membrane.

physiology↗

bioRxiv2023

Elevated Expression of srp RiPPs Across Bacterial Phyla in Marine Sponges

We investigated transcriptional activity, at a genome-resolved level, of bacterial communities in two S. officinalis and two I. felix sponges, both of which are considered high microbial abundance (HMA) sponges that harbor similar bacterial communities. Overlap of metatranscriptional data on genome-resolved metagenomic data showed that genome bins classified within the Chloroflexota and Poribacteria phyla were the most abundant and transcriptionally active. However, abundant bins in general were not the most transcriptionally active, instead less abundant bins of the same phyla were most active indicating that numerical dominance does not imply transcriptional dominance. We found that although some primary metabolic functions appeared upregulated, they were not obviously attributable to any particular bacterial species. However, assessment of transcription levels of biosynthetic gene clusters (BGCs) encoding secondary metabolites revealed a high transcription of ribosomally synthesized and post-translationally modified peptides (RiPPs) in genome bins across diverse bacterial phyla, most of which were likely srp RiPPs encoding brominated azol(in)e-containing compounds. However, the ecological role of these compounds remains elusive. IMPORTANCEMarine sponges and bacteria have formed close associations over several million years with many bacteria performing specialized functions within their sponge host. Previous studies have either assessed the genomes of a given sponge or the expression profile for a sponge holobiont as a whole. Here, we present the first genome-resolved transcriptomic study which gives us a snapshot of the transcriptional activity of individual bacteria in the context of four different sponge holobionts. Using this approach we found that the numerically dominant bacteria were not the most transcriptionally active and that relatively high expression of a ubiquitous biosynthetic gene cluster was evident in many different bacterial phyla in all four sponge samples.

ecology↗

bioRxiv2021

Coordination of di-acetylated histone ligands by the ATAD2 bromodomain

The ATPase Family, AAA domain-containing protein 2 (ATAD2) bromodomain (BRD) has a canonical bromodomain structure consisting of four -helices. ATAD2 functions as a co-activator of the androgen and estrogen receptors as well as the MYC and E2F transcription factors. ATAD2 also functions during DNA replication, recognizing newly synthesized histones. In addition, ATAD2 is shown to be up regulated in multiple forms of cancer including breast, lung, gastric, endometrial, renal, and prostate. Furthermore, up-regulation of ATAD2 is strongly correlated with poor prognosis in many types of cancer, making the ATAD2 bromodomain an innovative target for cancer therapeutics. In this study, we describe the recognition of histone acetyllysine modifications by the ATAD2 bromodomain. Residue-specific information on the complex formed between the histone tail and the ATAD2 bromodomain, obtained through nuclear magnetic resonance spectroscopy (NMR) and X-ray crystallography, illustrates key residues lining the binding pocket, which are involved in coordination of di-acetylated histone tails. Analytical ultracentrifugation, NMR relaxation data, and isothermal titration calorimetry further confirm the monomeric state of the functionally active ATAD2 bromodomain in complex with di-acetylated histone ligands. Overall, we describe histone tail recognition by ATAD2 BRD and illustrate that one acetyllysine group is primarily engaged by the conserved asparagine (N1064), the "RVF" shelf residues, and the flexible ZA loop. Coordination of a second acetyllysine group also occurs within the same binding pocket, but is essentially governed by unique hydrophobic and electrostatic interactions making the di-acetyllysine histone coordination more specific than previously presumed.

biochemistry↗

bioRxiv2020

Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable?

Despite the intimate link between cell organization and function, the principles underlying intracellular organization and the relation between organization, gene expression and phenotype are not well understood. We address this by creating a benchmark for mean cell organization and the natural range of cell-to-cell variation. This benchmark can be used for comparison to other normal or abnormal cell states. To do this, we developed a reproducible microscope imaging pipeline to generate a high-quality dataset of 3D, high-resolution images of over 200,000 live cells from 25 isogenic human induced pluripotent stem cell (hiPSC) lines from the Allen Cell Collection. Each line contains one fluorescently tagged protein, created via endogenous CRISPR/Cas9 gene editing, representing a key cellular structure or organelle. We used these images to develop a new multi-part and generalizable analysis approach of the locations, amounts, and variation of these 25 cellular structures. Taking an integrated approach, we found that both the extent to which a structures individual location varied ("stereotypy") and the extent to which the structure localized relative to all the other cellular structures ("concordance") were robust to a wide range of cell shape variation, from flatter to taller, smaller to larger, or less to more polarized cells. We also found that these cellular structures varied greatly in how their volumes scaled with cell and nuclear size. These analyses create a data-driven set of quantitative rules for the locations, amounts, and variation of 25 cellular structures within the hiPSC as a normal baseline for cell organization.

cell biology↗

bioRxiv2018

Structural insights into the recognition of mono- and di-acetyllysine by the ATAD2B bromodomain

Bromodomains are chromatin reader modules that recognize acetylated lysine. Different bromodomains exhibit a preference for specific patterns of lysine acetylation marks on core and variant histone proteins, however, the functional relationships that exist between histone acetyllysine ligands and bromodomain recognition remain poorly understood. In this study, we examined the ligand specificity of the ATAD2B bromodomain and compared it to its closely related paralog in ATAD2. We show that the ATAD2B bromodomain selects for mono- and di-acetylated histones, and structural analysis identified key residues in the acetyllysine binding pocket that dictate ligand binding specificity. The X-ray crystal structure of the ATAD2B bromodomain in complex with an ATAD2 bromodomain inhibitor was solved at 2.4 [A] resolution. This structure demonstrated that critical contacts required for bromodomain inhibitor coordination are conserved between the ATAD2/B bromodomains, and many of these residues play a dual role in acetyllysine recognition. We further characterized a variant of the ATAD2B bromodomain that through alternative splicing loses critical amino acids required for histone ligand and inhibitor coordination. Altogether our results outline the structural and functional features of the ATAD2B bromodomain and identify a novel mechanism important for regulating the interaction of the ATAD2B protein with chromatin. HIGHLIGHTSO_LIThe ATAD2B bromodomain recognizes mono- and di-acetylated histone ligands. C_LIO_LIChemical shift perturbations outline the ATAD2B bromodomain acetyllysine binding pocket. C_LIO_LIAn ATAD2B bromodomain-inhibitor complex reveals important binding contacts. C_LIO_LIAn alternate splice variant in the ATAD2B bromodomain abolishes histone and inhibitor binding. C_LI

biochemistry↗

bioRxiv2017

Thirty-five experimental fisheries reveal the mechanisms of selection

Fisheries have been described as large-scale evolutionary experiments; yet such \"experiments\" tend to be poorly replicated and therefore lack the predictive power essential for designing appropriate management strategies to minimize the effects of fisheries-induced selection. Large-scale removal of non-native trout from 35 montane lakes in California provided repeated experimental fisheries that allowed us to explore how environmental parameters affect the three potential contributors to overall selection: the fitness-trait correlation, trait variability, and fitness variability. Our results demonstrate that fishing rapidly altered the size structure of harvested populations, and that the magnitude of change was primarily driven by the fitness-trait correlation (net selectivity). Fishing-induced selection was repeatable overall but was also influenced by environmental (lake size and quality) and demographic (size structure) parameters. Decomposing fishing-induced selection into its key components can improve the management of stocks experiencing fishing-induced selection by identifying the drivers of selection and therefore the appropriate target for management.

evolutionary biology↗