Biology subjects

Larsen, J.

Publications and source records attributed to Larsen, J..

16 recordsLinked to original sources

bioRxiv2026

Hyaluronic acid-b-polylactic acid polymersomes facilitate CD44-mediated delivery of doxorubicin to glioblastoma in vitro

Glioblastoma represents a highly aggressive brain tumor with low survival and no response to chemotherapy and radiation therapy. Temozolomide, the current standard of care chemotherapy, improves patient survival by only about 6 months because of several resistance mechanisms, including unmethylated MGMT, which enables repair of chemotherapy-induced DNA damage. Thus, additional treatments strategies are necessary to investigate efficient responses towards glioblastoma. Doxorubicin (DOX) is a chemotherapeutic agent that is independent of MGMT methylation and instead works through inhibition of topoisomerase (TOPO) II, an enzyme necessary for DNA replication of the tumor. The inability of doxorubicin to cross the blood-brain barrier (BBB) precludes its use in glioblastoma. Polymersome nanoparticles have the potential to transport agents across the BBB. Here, we develop hyaluronic acid-b-polylactic acid (HA-PLA) polymeric nanoparticles called polymersomes, encapsulate them with DOX and investigate the ability of our system to induce apoptosis in a human glioblastoma cell line. The HA-PLA polymersomes show specificity and receptor-mediated endocytosis towards CD44-positive U87 glioblastoma cells due to the natural affinity of HA (hyaluronic acid) to CD44. Our HLA-PLA-DOX system promotes apoptosis of glioblastoma through inhibition of topoisomerase (TOPO) II. Thus, our system could allow tumor specificity through HA-CD44 affinity and slow drug release through pH sensitivity of PLA in the acidic tumor microenvironment.

bioengineering↗

bioRxiv2026

Endophytic fungi from avocado trees exhibit potential for multi-target biocontrol applications

BACKGROUNDEndophytic fungi are naturally inhabiting plant organs without causing disease symptoms. They can also contribute to their hosts pest and disease resistance by displaying entomopathogenic and/or antifungal traits. In this study, we evaluated the ability of 11 strains of avocado fungal endophytes to antagonize three important avocado plant pathogens: Colletotrichum gloeosporioides, Fusarium solani, and Phytophthora cinnamomi, and two insect pests: Sitophilus zeamais and Xyleborus bispinatus. RESULTSThe results show that Trichoderma spp. strains were the most effective against the evaluated plant pathogens in terms of growth inhibition, in direct contact assays or through metabolite production. Other fungi, such as Purpureocillium sp. and Pochonia sp., only exhibited pathogen inhibition through diffusible metabolites but displayed strong insecticidal capacity against the evaluated pests, hence being identified as promising multi-target biocontrol agents in the integrative analysis. CONCLUSIONOur findings evidence the potential of avocado fungal endophytes and their metabolites as multi-target biocontrol agents of crop pests and pathogens.

microbiology↗

bioRxiv2025

Protocell formation on micrometeorites

We report on the formation of membranous protocells by self-assembly of lipids on micrometeorites, the extraterrestrial particles that have been continuously reaching the surface of the Earth ever since its formation. Synergistic interactions of lipid compartments with pristine extraterrestrial surfaces are entirely unexplored, but constitute a possible scenario for early evolution of primitive cells by a surface energy-driven transformation mechanism. Lipids utilize the surface energy of the particles to adhere to them and autonomously transform into spherical compartments, typically through formation of lipid nanotubes. Natural sand particles of similar composition and shape were simultaneously investigated for reference, showing that certain lipid compositions prefer micrometeorite surfaces. The elemental composition of the particles, their surface texture and cleanness altogether may be contributing to the differences observed in lipid behavior. Lipid nanotubes on- and extending out of- the micrometeorites were observed to carry lipid particles and connect to other objects in the surrounding environment.

biophysics↗

bioRxiv2025

KHSRP-mediated Decay of Axonally Localized Prenyl-Cdc42 mRNA Slows Nerve Regeneration

The small GTPase CDC42 promotes axon growth through actin filament polymerization and this growth is driven by axonal localization of the mRNA encoding the prenylated CDC42 isoform (Prenyl-Cdc42). Here, we show that axonal Prenyl-Cdc42 mRNA transport and translation are decreased by growth-inhibiting stimulation and increased by growth-promoting stimulation. In contrast, axonal RhoA mRNA transport and translation are increased by growth inhibition but unaffected by growth promotion. Localized increase in KHSRP in response to growth inhibitory stimulation, through elevation of intracellular Ca2+, promotes decay of axonal Prenyl-Cdc42 mRNA. Distinct 3UTR motifs regulate transport and stability of axonal Prenyl-Cdc42 mRNA. KHSRP protein binds to a Prenyl-Cdc42 mRNA motif within nt 801-875 and the mRNA is remarkably increased in axons of Khsrp-/- mice. Selective depletion of Prenyl-Cdc42 mRNA from axons reverses the accelerated axon regeneration seen in Khsrp-/-mice.

neuroscience↗

bioRxiv2025

Diversity of culturable endophytic fungi associated with avocado orchards under organic and conventional management

Endophytic fungi constitute a great resource for the implementation of sustainable agricultural practices. However, their diversity may be altered by agrochemicals used in conventionally managed agrosystems. Here we explored the culturable diversity of endophytic fungi associated with avocado (Persea americana Mill.) in conventional and organic orchards from three counties of the worlds leading productive region. In total, 529 endophytic fungal isolates were obtained from branches and roots of avocado trees. Identification based on ITS sequencing showed that most isolates belonged to the Ascomycota phylum (98 %) and were grouped into 52 fungal genera, representing 102 tentative species. The endophytic fungal community was dominated by genera which were common to both management types, namely Fusarium, Colletotrichum, Dactylonectria, and Diaporthe / Phomopsis. Twenty fungal genera were exclusive to organic orchards (e.g., Hypoxylon and Talaromyces) and 10 were only found in conventional orchards (e.g., Trichoderma). Fungal species richness and diversity were higher in organic than in conventional orchards. Ordination and clustering analyses revealed a stronger effect of site than of management type on endophytic fungal community structure, highlighting the influence of local factors in shaping the culturable endophytic fungal community. Overall, our findings confirm the negative impact of conventional management on the diversity of crop-associated endophytic fungi and the significant influence of local factors on endophytic fungal assemblages. Moreover, our results emphasize the need to assess the risk that possible latent fungal pathogens may represent for the crop or dominant forest species surrounding avocado orchards.

microbiology↗

bioRxiv2024

Field monitoring and hydraulic modelling quantify untreated wastewater as dominant source of AMR in a small river running through a big city

Quantifying sources of antimicrobial resistance (AMR) in rivers receiving various waste streams is essential for targeting mitigation strategies yet rarely performed. This study combined field monitoring with hydraulic modelling and mass balance calculations to attribute sources of AMR in the Musi River running through Hyderabad, India, a city renowned for pharmaceutical manufacturing. We quantified antibiotic resistance genes (ARGs), resistant bacteria (ARBs), and physicochemical parameters in water and sediment samples in the dry and wet season. Absolute ARG and ARB abundances spiked in the city, declining again downstream. Changes were more gradual in the wet season. Pollution levels were significantly different between upstream, city and downstream stretches and seasons. Hydraulic modelling revealed that 60-80% or 20-40% of the river water in the city derived from untreated sewage during the dry or wet seasons, respectively. This established municipal waste, not pharmaceutical sources, as the dominant driver of AMR in the Musi. Linear discriminant analysis identified dissolved oxygen and total nitrogen as reliable proxies for distinguishing AMR-polluted from less-polluted sites. The Musi, with insufficient wastewater treatment and limited dilution of point-source loadings, is typical for many urban rivers in resource-limited countries highlighting the urgent need for improved wastewater management to reduce AMR exposures.

microbiology↗

bioRxiv2024

Targeted Polymersomes Enable Enhanced Delivery to Peripheral Nerves Post-Injury

The gold standard therapy for peripheral nerve injuries involves surgical repair, which is invasive and leads to major variations in therapeutic outcomes. Because of this, smaller injuries often go untreated. However, alternative, non-invasive routes of administration are currently unviable due to the presence of the blood-nerve barrier (BNB), which prevents passage of small molecules from the blood into the endoneurium and the nerve. This paper demonstrates that ligands on the surface of nanoparticles, called polymersomes, can enable delivery to the nerve through non-invasive intramuscular injections. Polymersomes made from polyethylene glycol (PEG)-b-polylactic acid (PLA) were conjugated with either apolipoprotein E (ApoE) or rabies virus glycoprotein-based peptide, RVG29 (RVG) and loaded with near infrared dye, AlexaFluor647. ApoE was used to target receptors upregulated in post-injury inflammation, while RVG targets neural specific receptors. Untagged, ApoE-tagged, and RVG-tagged polymersomes were injected at 100 mM either intranerve (IN) or intramuscular (IM) into Sprague Dawley rats post sciatic nerve injury. The addition of the ApoE and RVG tags enabled increased AlexaFluor647 fluorescence in the injury site at 1 hour post IN injection compared to the untagged polymersome control. However, only the RVG-tagged polymersomes increased AlexaFluor647 fluorescence after intramuscular injection. Ex vivo analysis of sciatic nerves demonstrated that ApoE-tagged polymersomes enabled the greatest retention of AlexaFluor647 regardless of the injection route. This led us to conclude that using ApoE to target inflammation enabled the greatest retention of polymersome-delivered payloads while RVG to target neural cells more specifically enabled the penetration of polymersome-delivered payloads. Observations were confirmed by calculating area under the curve pharmacokinetic parameters and the use of a two-compartment pharmacokinetic model.

bioengineering↗

bioRxiv2024

1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-Treated Adult Zebrafish as a Model for Parkinsons Disease

Dopamine (DA) is a catecholamine neurotransmitter that works to regulate cognitive functions. Patients affected by Parkinsons Disease (PD) experience a loss of dopaminergic neurons and downregulated neural DA production. This leads to cognitive and physical decline that is the hallmark of PD for which no cure currently exists.. Danio rerio, or zebrafish, have become an increasingly popular disease model used in PD pharmaceutical development. This model still requires extensive development to better characterize which PD features are adequately represented. Furthermore, the great majority of PD zebrafish models have been performed in embryos, which may not be relevant towards age-related human PD. As an improvement, mature D. rerio were treated with neurotoxic prodrug 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) through intraperitoneal injection to induce parkinsonism. Behavioral analysis confirmed disparities in movement between saline-injected control and the MPTP-injected experimental group, with swim distance and speed significantly lowered seven days after MPTP injection. Simultaneously, cognitive decline was apparent in MPTP-injected zebrafish, demonstrated by decreased alternation in a y-maze. RT-qPCR confirmed trends consistent with downregulation in Parkinsonian genetic markers, specifically DA transporter (DAT), MAO-B, PINK1. In summary, mature zebrafish injected with MPTP present with similar movement and cognitive decline as compared to human disease. Despite its benefits, this model does not appear to recapitulate full pathophysiology of the disease with the full profile of expected gene downregulation. Because of this, it is important that researchers looking for pharmacological interventions for PD only use this zebrafish model when targeting the human-relevant PD symptoms and causes that are represented.

neuroscience↗

bioRxiv2024

Personalized Molecular Signatures of Insulin Resistance and Type 2 Diabetes

HighlightsO_LIAdvanced proteomics analysis reveals personalized signatures of insulin resistance C_LIO_LIFasting muscle proteome and phosphoproteome predicts whole-body insulin sensitivity C_LIO_LIInsulin-stimulated phosphoproteome reveals selective insulin resistance signatures C_LIO_LIPhosphoproteome and proteome atlas explains sex-specific muscle metabolism C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/578994v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@a83000org.highwire.dtl.DTLVardef@1e77336org.highwire.dtl.DTLVardef@3d1ecdorg.highwire.dtl.DTLVardef@b1592b_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG Insulin resistance is a hallmark of type 2 diabetes, which is a highly heterogeneous disease with diverse pathology. Understanding the molecular signatures of insulin resistance and its association with individual phenotypic traits is crucial for advancing precision medicine in type 2 diabetes. Utilizing cutting-edge proteomics technology, we mapped the proteome and phosphoproteome of skeletal muscle from >120 men and women with normal glucose tolerance or type 2 diabetes, with varying degrees of insulin sensitivity. Leveraging deep in vivo phenotyping, we reveal that fasting proteome and phosphoproteome signatures strongly predict insulin sensitivity. Furthermore, the insulin-stimulated phosphoproteome revealed both dysregulated and preserved signaling nodes - even in individuals with severe insulin resistance. While substantial sex-specific differences in the proteome and phosphoproteome were identified, molecular signatures of insulin resistance remained largely similar between men and women. These findings underscore the need for precision medicine approaches in type 2 diabetes care, acknowledging disease heterogeneity.

biochemistry↗

bioRxiv2021

Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD

Efficient control of transcription is essential in all organisms. In bacteria, where DNA replication and transcription occur simultaneously, the replication machinery is at risk of colliding with highly abundant transcription complexes. This can be exacerbated by the fact that transcription complexes pause frequently. When pauses are long-lasting, the stalled complexes must be removed to prevent collisions with either another transcription complex or the replication machinery. HelD is a protein that represents a new class of ATP-dependent motor protein distantly related to helicases. It was first identified in the model Gram-positive bacterium Bacillus subtilis and is involved in removing and recycling stalled transcription complexes. To date, two classes of HelD have been identified: one in the low G+C and the other in the high G+C Gram-positive bacteria. In this work we have undertaken the first comprehensive investigation of the phylogenetic diversity of HelD proteins. We show that genes in certain bacterial classes have been inherited by horizontal gene transfer, many organisms contain multiple expressed isoforms of HelD, some of which are associated with antibiotic resistance, and that there is a third class of HelD protein found in Gram-negative bacteria. Therefore, HelD proteins represent an important new class of transcription factor associated with genome maintenance and antibiotic resistance that are conserved across the Eubacterial kingdom.

molecular biology↗

bioRxiv2021

Bacteriophages encoding human immune evasion factors adapt to livestock-associated MRSA through rounds of integration and excision

In recent years there has been an increase in human infections with methicillin-resistant Staphylococcus aureus (MRSA) originating from livestock and strains carrying bacterial viruses of the Sa3int-family have disseminated into the community. Sa3int phages express immune evasion factors and are common in human staphylococcal strains. As the bacterial attachment site (attB) for Sa3int phages is mutated in livestock-associated strains, the integration frequency is low and a key question is how the phages are established. Here we show that Sa3int phages adapt to alternative bacterial integration sites by mutating the phage attachment sequence, attP, leading to enhanced integration at these sites. Using a model strain carrying the mutated attBLA of livestock-associated strains we find that once established, the Sa3int phage, {Phi}13 is inducible with release of heterogenous phage populations carrying mutations in attP that in part increase homology to alternative integration sites or attBLA. Compared to the original phage, the adaptive mutations increase phage integration in new rounds of infection. Also, Sa3int phages induced from livestock-associated outbreak strains reveal mutated attP sequences. We suspect that promiscuity of the phage-encoded recombinase allows this adaptation and propose it may explain how phages mediate "host jumps" that are regularly observed for staphylococcal lineages.

microbiology↗

bioRxiv2020

Linking Enzyme Upregulation to Autophagic Failure: A Potential Biomarker for GM1 Gangliosidosis

With an increasing aging population, neurodegenerative diseases are having an increased impact on society. Typically, these diseases are diagnosed significantly past symptom onset, decreasing the possibility of effective treatment. A non-invasive biomarker and specific target are needed to diagnose and treat the disease before late-stage symptoms. GM1 Gangliosidosis is a lysosomal storage disease where lysosomal enzyme {beta}-galactosidase is missing. As a result, GM1 ganglioside is not broken down and accumulates in the cell, ultimately leading to cell death. One of the main aspects of GM1 Gangliosidosis, and other neurodegenerative diseases, is impaired autophagy: reduced fusion of autophagosomes and lysosomes to degrade cellular waste. In this paper, we show that healthy cells (NSV3) have approximately 13 times more co-localization of lysosomes and autophagosomes than GM1 Gangliosidosis-diseased cells (GM1SV3), as demonstrated via immunofluorescence. GM1SV3 fold normal enzyme activity of {beta}-galactosidase was downregulated while mannosidase, and hexosaminidase A were both upregulated. When inducing impaired autophagy in NSV3 via starvation, co-localization gradually decreases with increased starvation time. Most notably, after 48-hour starvation, healthy cells (NSV3) showed no significant difference in co-localization compared to GM1SV3. NSV3 under starvation conditions showed a significant increase between time starved and fold normal enzyme activity, with a positive correlation being observed. Activities of mannosidase, and hexosaminidase A of starved NSV3 closely resemble, and surpass, GM1SV3 after 12-hour starvation. These observations have the potential to expand the conversation regarding impaired autophagy as a potential biomarker for disease progression and diagnostics and as a treatment target.

pathology↗

bioRxiv2019

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

We present a chromosome-scale annotated assembly of the rye (Secale cereale L. inbred line Lo7) genome, which we use to explore Triticeae genomic evolution, and ryes superior disease and stress tolerance. The rye genome shares chromosome-level organization with other Triticeae cereals, but exhibits unique retrotransposon dynamics and structural features. Crop improvement in rye, as well as in wheat and triticale, will profit from investigations of rye gene families implicated in pathogen resistance, low temperature tolerance, and fertility control systems for hybrid breeding. We show that rye introgressions in wheat breeding panels can be characterised in high-throughput to predict the yield effects and trade-offs of rye chromatin.

genomics↗

bioRxiv2019

Persistent Prolate Polymersomes for Enhanced Co-Delivery of Hydrophilic and Hydrophobic Drugs

Self-assembled polymersomes encapsulate, protect, and deliver hydrophobic and hydrophilic drugs. Though spherical polymersomes are effective, early studies suggest that non-spherical structures may enhance specificity of delivery and uptake due to similarity to endogenous uptake targets. Here we describe a method to obtain persistent non-spherical shapes, prolates, via osmotic pressure and the effect of prolates on uptake behavior. Polyethylene glycol-b-poly(lactic acid) polymersomes change in diameter from 175 {+/-} 5nm to 200 {+/-} 5nm and increase in polydispersity from 0.06 {+/-} 0.02 to 0.122 {+/-} 0.01 nm after addition of 50 mM salt. Transmission and scanning electron microscopy confirm changes from spheres to prolates. Prolate-like polymersomes maintain their shape in 50 mM NaCl for seven days. Nile Red and bovine serum albumin(BSA)-Fluorescein dyes are taken up in greater amounts by SH-SY5Y neural cells when encapsulated in polymersomes. Prolate polymersomes may be taken up more efficiently in neural cells than spherical polymersomes.

bioengineering↗

bioRxiv2019

Microbial Food Safety in the Maryland Direct-to-Consumer Poultry Supply Chain

Direct-to-consumer food marketing is a growing niche in the United States food supply chain. Food animal producers who use direct marketing may employ different production models and standard practices from producers selling animal products to the conventional food system. Direct-to-consumer food supply chains (generally and specifically regarding food animal products) are relatively unexplored in food safety and health research. We conducted a cross-sectional, market-basket analysis of the Maryland direct-to-consumer poultry supply chain to assess food safety. We analyzed 40 direct-to-consumer commercial poultry meat products (one product per farm) for Escherichia coli, Staphylococcus aureus and Salmonella spp. using culture-based methods. Isolates underwent antimicrobial susceptibility testing. E. coli and S. aureus were recovered from 9/40 (23%) and 12/40 (30%) of poultry meat samples, respectively. Of interest for comparing direct-market and mainstream supply chains for food safety risks, no Salmonella isolates were recovered from any direct-market sampled poultry products and no multidrug resistance was observed in E. coli and S. aureus isolates. Microbial outcomes were compared to a survey of poultry production and processing practices within the same study population.\n\nImportanceThis study demonstrates substantially lower rates of antimicrobial-resistant (AMR) microbial pathogens in the market-basket products from Maryland direct-market broiler poultry supply chain compared to rates of AMR in the conventional supply chain for similar retail meat products from NARMS. We further describe the landscape of the statewide supply chain for direct-market poultry, focusing on characteristics related to risk management strategies applied to microbial food safety. These findings are of public health significance for both the research and policy communities; these data provide an initial evidence base for more targeted research evaluating potential risk factors for microbial food safety in the direct-to-consumer supply chain. These data will also assist the Maryland Department of Agriculture and other state-level agencies with oversight of food safety issues to guide policy efforts for direct-market poultry production and sales.

microbiology↗

bioRxiv2017

Causal Associations Between Body Mass Index and Mental Health: A Mendelian Randomization Study

BackgroundBody Mass Index (BMI) is negatively correlated with subjective well-being and positively correlated with depressive symptoms. Whether these associations reflect causal effects or confounding is unclear.\n\nMethodsWe examined causal effects between BMI and subjective well-being/depressive symptoms with bi-directional, two-sample Mendelian randomization using summary-level data from large genome-wide association studies. Genetic variants robustly related to the exposure variable acted as instrumental variable (two thresholds were used; p<5e-08 and p<1e-05). These instruments were then associated with the outcome variable. Pleiotropy was corrected for by two sensitivity analyses.\n\nResultsSubstantial evidence was found for a causal effect of BMI on mental health, such that a higher BMI decreased subjective well-being and increased depressive symptoms. No consistent evidence was found for causality in the other direction.\n\nConclusionsThis study provides support for a higher BMI causing poorer mental health. Further research should corroborate these findings and consider non-linear effects and sex differences.

genetics↗