Biology subjects

Larson, A.

Publications and source records attributed to Larson, A..

9 recordsLinked to original sources

bioRxiv2026

IL-2- and IL-4-dependent signaling play separate and sequential roles in the differentiation of GATA3-hi TH2 cells in vivo

Naive CD4+ T cells differentiation into T-helper type 2 (TH2) cells requires Interleukin 2 (IL-2) and IL-4-dependent signaling as well as presentation of allergens by dendritic cells (DCs). The role of IL-2 and IL-4 in TH2 differentiation has been mostly studied in vitro, however, these models do not account for the heterogeneity of TH responses and bypass the DC-derived signals that are necessary in vivo. We used cytokine-blocking antibodies and IL-4RKO/IL-4RWT mixed bone marrow chimeras to show that IL-4 signaling was not required for initial upregulation of GATA3 by CD4+ T cells after intradermal immunization, but was necessary for later TH2 cell expansion and further GATA3 upregulation. Single-cell transcriptomics and computational analyses confirmed that IL-4 signaling was not necessary for TH2 identity but promoted TH2 proliferation and expression of a pathogenic signature. Early IL-2 blockade prevented GATA3 upregulation without affecting TH2 proliferation or the differentiation of TH1 and TFH subsets after immunization. Adoptive transfer experiments showed that reduced competition for IL-4 in vivo drove extensive T cell proliferation and preferential expansion of the GATA3hi population. Overall, our results suggest temporally and functionally distinct roles of IL-2 and IL-4 during TH2 differentiation: IL-2 is necessary for GATA3 upregulation, while IL-4 drives subsequent TH2 proliferation and licensing to effector activity. Therefore, IL-2 and IL-4 act in a co-ordinated manner to respectively promote TH2 differentiation, expansion, and effector commitment in the LN.

immunology↗

bioRxiv2025

A topologically conserved unstructured region helps positioning the evolutionarily conserved Prp40 WW domains to promote non-canonical intron splicing

Newly transcribed introns are immediately identified by early splicing factors that recognize the intron 5 splice site (5SS) and branch site (BS). In the budding yeast, these critical splice-site sequences are generally constrained, whereas degeneracy is the rule in higher eukaryotes. Yet, [~]40% of the yeast introns do diverge, to a certain degree, from the canonical sequences. Exactly how these non-canonical introns are recognized and spliced remains unknown. Here we show that the conserved Prp40 WW domains promote non-canonical intron splicing by enhancing stable U1 snRNP and BBP recruitments. AlphaFold predicts a topologically conserved unstructured region between Prp40 WW and FF domains. Alignment of the AlphaFold Prp40 structure with published U1 snRNP structure positions WW domains adjacent to 5SS and Luc7, which is known to be critical for 5SS recognition. Indeed, deletion of this unstructured region negatively impacts on splicing of the non-canonical 5SS introns. Taken together, our results suggest that the conserved WW domains may have evolved to deal with the highly degenerate 5SS and BS sequences in higher eukaryotes, so as to accommodate increased splicing complexity. HighlightsO_LIThe evolutionarily conserved Prp40 WW domains promote splicing of introns harboring non-canonical 5 splice site or branch site. C_LIO_LIPrp40 WW domains enhance stable U1 snRNP and BBP recruitments to nascent transcripts containing non-canonical splice sites. C_LIO_LIA topologically conserved unstructured region between WW and FF domains helps to position Prp40 WW domains close to the 5 splice site. C_LIO_LIThe N-terminal WW domain sterically hinders conformational rearrangements required for efficient release of a BBP variant during spliceosome assembly. C_LIO_LIA reporter assay identified 13 non-canonical introns whose splicing, under various environmental conditions, depend on Prp40 WW domains. C_LI

biochemistry↗

bioRxiv2025

Splice-switching antisense oligonucleotides correct cryptic exon inclusion and restore SDCCAG8 protein in Bardet-Biedl Syndrome

Bardet-Biedl Syndrome (BBS) is a ciliopathy often associated with progressive blindness and obesity. A patient presenting with BBS was discovered to have two mutations within 55bp of each other in intron 7 of SDCCAG8 (BBS16). One of the biallelic mutations, c.740+356C>T, causes inclusion of cryptic exon(s) containing premature termination codons, while c.740+301G>A has not been characterized. We hypothesized that antisense oligonucleotides (ASOs) complementary to the patients mutations or to the cryptic exon splice sites would correct the splicing of SDCCAG8 between exons 7 and 8 to prevent cryptic exon inclusion and restore SDCCAG8 expression. We systematically screened 20nt-long ASOs tiled across each mutation and ASOs targeting the 3' splice sites of the cryptic exons in patient-derived fibroblasts, using RT-PCR assays to assess exon 7 and 8 splicing. We identified one ASO for each mutation and a cryptic exon-targeting ASO that restored the splicing pattern to that observed in an unaffected cell line. Lead ASOs were further investigated through RT-PCR, RNA sequencing, and western blotting to confirm ASO-mediated restoration of wild-type transcript and protein. Notably, ASO 20, which targets the cryptic exon 7a/7a' splice site rather than patient-specific mutations, achieved the greatest rescue effect, increasing exon 7-8 splicing from 0% to an average of 26% and restoring SDCCAG8 protein from undetectable levels to approximately 40% of wild-type expression. This mutation-agnostic approach could benefit multiple patients with cryptic exon inclusion in this region of SDCCAG8, expanding therapeutic impact beyond traditional N-of-1 ASO strategies. These findings establish a molecular foundation for clinical development of ASO therapy for BBS caused by SDCCAG8 splicing defects.

genetics↗

bioRxiv2025

Bacteriophage-mediated reduction of uropathogenic E. coli from the urogenital epithelium

Urinary tract infections (UTIs), primarily caused by uropathogenic Escherichia coli (UPEC), affect millions annually. UPEC gains access to the urinary tract through mucosal reservoirs including the vaginal tract. With rising antibiotic resistance and frequent recurrence, alternative non-antibiotic strategies like bacteriophage (phage) therapy are gaining attention. We explored the potential of a lytic phage, {Phi}HP3, as well as a phage cocktail to decolonize UPEC from the urogenital tract using in vitro and in vivo models. Phage significantly inhibited UPEC growth in both bacteriologic medium and simulated vaginal fluid. Pretreatment of human vaginal epithelial cells (VK2/E6E7) and bladder carcinoma cells (HTB-9) with phage reduced adhesion and invasion of UPEC compared with controls. Phage treatment was further able to reduce intracellular UPEC in VK2 cells. Notably, phage pretreatment did not impact phage resistant UPEC strains, indicating that phage lysis was the primary driver of phenotypes. Live confocal microscopy confirmed interaction of phage particles with UPEC and with both epithelial cell lines. In vivo, daily intravaginal {Phi}HP3 administration in humanized microbiota mice significantly reduced vaginal UPEC burden after 4 days. Treatment with a phage cocktail also reduced vaginal and cervical tissue burdens by day 7 post-treatment. UPEC dissemination was observed to uterine and kidney tissues, but burdens were not different between phage and mock-treated groups. In conclusion, we demonstrate that phage and phage cocktails can modestly reduce UPEC urogenital colonization, highlighting the potential of phage therapy as a viable treatment option for UTI prevention. IMPORTANCEUrinary tract infections (UTIs) are among the most common infections worldwide, with millions of cases each year. Due to frequent recurrence and increasing antibiotic resistance, UTIs are becoming more difficult to treat, and non-antibiotic prevention options remain limited. The bacteria responsible for UTIs, such as uropathogenic E. coli (UPEC), often colonize other body sites, such as the intestines or vagina, before causing infection. In this study, we investigated whether bacteriophage (phage), viruses that infect bacteria, could reduce UPEC colonization. We found that phage treatment decreased UPEC adherence to vaginal and bladder cell lines, but only modestly reduced UPEC vaginal colonization in a mouse model. These findings suggest that phages may offer a potential strategy for UTI prevention, though further research is needed to optimize their therapeutic use.

microbiology↗

bioRxiv2025

A dNmnat-sensitized in vivo platform for unbiased discovery of regulators of neurodegeneration

Axon degeneration drives nervous system dysfunction in diverse neurological diseases and injuries. While key regulators of injury-induced Wallerian degeneration have been identified, approaches have largely relied on axotomy, a particularly extreme injury for a neuron. Here, we developed a forward genetic screening platform in the adult Drosophila wing that sensitizes neurons to degeneration through depletion of nicotinamide mononucleotide adenylyltransferase (dNmnat), the essential NAD+ biosynthetic enzyme. We screened 9,393 mutagenized chromosomes and recovered 59 mutations that suppress neurodegeneration induced by dNmant depletion, including the known pro-degenerative molecule dSarm, thereby validating our approach. We show loss of CG4098, the Drosophila homolog of the mammalian enzyme NUDT9, robustly preserved axons and induced widespread remodeling of NAD+-related metabolites, which provides a new link between cADP-ribose hydrolase activity and neuronal survival. We further show mutations in the transcription factor Abrupt resulted in elevated dNmnat protein levels and blocked axon degeneration, suggesting Abrupt normally tunes dNmnat levels and neuronal NAD+ homeostasis. dNmnat depletion is thus a versatile approach for unbiased discovery of axon death pathway components, each of which may provide new entry points for therapeutic strategies to preserve axons in neurodegenerative diseases.

neuroscience↗

bioRxiv2023

The genome of the colonial hydroid Hydractinia reveals their stem cells use a toolkit of genes shared with all animals

Hydractinia is a colonial marine hydroid that exhibits remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, H. symbiolongicarpus and H. echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinias i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinias stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from non-self.

genomics↗

bioRxiv2021

Establishing Normative Reference Values for the Utah Seated Medicine Ball Throw Protocol in Adolescents

The seated medicine ball throw (SMBT) is a field test intended to assess upper-body muscular power by measuring the maximal distance an individual can throw a medicine ball from an isolated, seated position (25). The SMBT has been used to assess upper-body power in various populations and to establish concurrent validity for other measures of upper-body power such as the bench press power test and the plyometric push-up. The SMBT is less costly and simpler to incorporate into a field test battery than other upper body power assessments. While the SMBT is a valid, reliable field test for upper-body power, normative reference standards for most populations, including adolescent (12-15 years old) physical education students, do not exist. PurposeThis study reports distances thrown in the SMBT to establish normative reference values in male and female physical education students, ages 12-15 years old. MethodsOne hundred thirteen untrained male and female physical education students aged 12-15 years performed the SMBT field test three times on a single testing day. Participants threw a 2kg medicine ball with a 19.5 cm diameter while seated at a 90{degrees} after recording height, body mass, and BMI. ResultsParticipant data was separated by age gender for analysis. Mean and standard deviation for the SMBT for males was 4.3{+/-}0.7m and 5.2{+/-}0.8 m for ages 12-13 and 14-15, respectively, and for females was 3.4{+/-}0.5m and 3.7{+/-}0.5m for ages 12-13 and 14-15, respectively. Pearson correlation coefficients for between-trials comparisons for males and females ranged from r=0.85-0.97. Pearson correlation coefficients for average SMBT and age of participants was r=0.93. Normative reference values as percentile ranks for the SMBT scores for age groups 12-13 and 14-15 among males and females, respectively, were also established. ConclusionThe data presented provides an initial set of normative reference standards for coaches and students to determine upper-body muscular power using the SMBT.

scientific communication and education↗

bioRxiv2020

PlanktonScope: Affordable modular imaging platform for citizen oceanography

The planktonic communities within our oceans represent one of the most diverse and understudied ecosystems on the planet. A major hurdle in describing these systems is the sheer scale of the oceans along with logistical and economic constraints associated with their sampling. This is due to the limited amount of scientifically equipped fleets and affordable equipment. Here we demonstrate a modular approach for building a versatile, re-configurable imaging platform that can be adapted to a number of field applications, specifically focusing on oceanography. By using a modular hardware/software approach for building microscopes, we demonstrate high-throughput imaging of lab and field samples while enabling rapid device reconfiguration in order to match diverse applications and the evolving needs of the sampler. The presented versions of PlanktonScope are capable of autonomously imaging 1.7 ml per minute with a 1.5 {micro}m resolution, and are built with under $400 in parts. This low cost enables new applications in laboratory settings such as the continuous imaging of suspension cultures, and in-field settings with the ability to scale up for long-term deployment on an international fleet of sailing boats enabling citizens based oceanographic research

bioengineering↗

bioRxiv2019

Scale-free Vertical Tracking Microscopy: Towards Bridging Scales in Biological Oceanography

Understanding key biophysical phenomena in the ocean often requires one to simultaneously focus on microscale entities, such as motile plankton and sedimenting particles, while maintaining the macroscale context of vertical transport in a highly stratified environment. This poses a conundrum: How to measure single organisms, at microscale resolution, in the lab, while allowing them to freely move hundreds of meters in the vertical direction? We present a solution in the form of a scale-free, vertical tracking microscope based on a circular \"hydrodynamic-treadmill\". Our technology allows us to transcend physiological and ecological scales, tracking organisms from marine zooplankton to single-cells over vertical scales of meters while resolving microflows and behavioral processes. We demonstrate measurements of sinking particles, including marine snow as they sediment tens of meters while capturing sub-particle-scale phenomena. We also demonstrate depth-patterned virtual-reality environments for novel behavioral analyses of microscale plankton. This technique offers a new experimental paradigm in microscale ocean biophysics by combining physiological-scale imaging with free movement in an ecological-scale patterned environment.\n\nOne sentence summaryScale-free vertical tracking microscopy captures, for the first time, untethered behavioral dynamics at cellular resolution for marine plankton.

biophysics↗