Biology subjects

Nelson, E.

Publications and source records attributed to Nelson, E..

16 recordsLinked to original sources

bioRxiv2026

Distinguishing Photoacoustic and Photothermal Neuron Stimulation Through Quantitative Mapping Spatiotemporal Field Evolution

Neuromodulation is a rapidly advancing strategy for modulating brain function and treating neurological disorders, yet the mechanisms of optical neural stimulation remain incompletely understood. A central challenge is that photoacoustic (PA) and photothermal (PT) effects are typically generated simultaneously and evolve on overlapping spatial and temporal scales, making their contributions to neuronal activation difficult to distinguish. Here, we overcome this limitation by integrating two carbon-based emitters with a spatial-offset pump-probe imaging platform to distinguish PA and PT neuromodulation through direct mapping of spatiotemporal field evolution. The two emitters produce nearly identical thermal fields while exhibiting a 26-fold difference in acoustic output, enabling decoupled comparison of thermal and acoustic contributions. To directly characterize the physical fields, we establish a spatial-offset pump-probe imaging system capable of visualizing both temperature and pressure evolution, confirming matched thermal profiles between the two emitters. Neuronal stimulation experiments further show that neurons are markedly more responsive to PA stimulation than to PT stimulation. Beyond resolving a longstanding mechanistic question, this work demonstrates the enhanced efficiency of PA stimulation and provides general guidance for designing high-performance optical neural interfaces.

neuroscience↗

bioRxiv2025

Whole brain fluorescence imaging in Drosophila reveals spreading depression and its initiation, propagation, and resilience dynamics.

Spreading depression (SD) is a wave of neuronal hyperactivity followed by depolarization block that propagates through large brain regions and is associated with disorders such as migraine, stroke, and brain injury. The mechanisms that initiate SD and alter susceptibility to it remain incompletely understood. Here, we use whole-brain fluorescence imaging with genetically encoded pan-neuronal calcium and voltage sensors to observe SD in Drosophila melanogaster. We show that rapid cooling, a naturally occurring environmental condition, as well as elevated extracellular potassium reliably elicit SD in both adult and larval flies. SD was characterized by a rapid and large rise in intracellular calcium that was accompanied by neuronal depolarization and stark changes in the transperineuronal potential. In adults, SD occurred at 6.7 {+/-} 0.6{degrees}C (N=15) and in larvae at 6.0 {+/-} 0.3{degrees}C (N=30). SD initiation was not restricted to specific sites, but initiated at multiple, variable sites across and within individuals, with an average of 3.0 {+/-} 0.7 (N=8) initiation points per brain. In all cases, SD spread throughout large areas of the nervous system. In a high-throughput larval assays that allows the simultaneous monitoring of up to 16 animals with repeated cooling cycles, we demonstrate that single SD events are followed by a transient refractory period lasting up to 45 minutes, during which the threshold for subsequent SD was significantly elevated. This was the case in adult and larval brains of all developmental stages. The refractory effect was independent of neuronal depolarization, suggesting that homeostatic processes alter SD susceptibility following an initial SD event. Taken together, our findings demonstrate that SD initiation and propagation are not restricted to specific regions, neuronal populations, or developmental stages, and they reveal fundamental properties of adaptive changes to SD susceptibility in a genetically tractable model. Building upon the extensive genetic toolkit available in Drosophila, this work establishes the fly as a complementary model for understanding conserved cellular and circuit-level mechanisms of SD relevant to human neurological disorders.

neuroscience↗

bioRxiv2025

OCcAM: A tool for rapidly assessing impacts of offshore wind farms on seabirds

Offshore wind energy generation has a key role in reducing reliance on fossil fuels and mitigating climate change. However, it also has the potential to negatively impact the environment, including seabird populations. Quantifying and minimising impacts of wind projects on seabirds is necessary for ensuring compliance with environmental legislation and safeguarding populations. However, the timescales and complexity involved in assessment processes can limit the extent to which estimates can be leveraged towards balancing environmental impact and energy generation. OCcAM is a simple, user-friendly and transparent industry-developed tool allowing rapid assessment of impacts on seabirds from offshore wind developments. Mortality rates of five seabird species are estimated using two UK industry-standard models: the Band collision risk model which predicts fatal collisions with turbine blades, and the matrix-based displacement approach that predicts mortalities associated with distributional responses to the presence of a wind farm. The tool supports simultaneous analysis of up to three input parameter sets and predictions can be expressed as a percentage of a focal population. OCcAM allows auditable analyses to be run quickly and easily with no requirement for specific technical expertise, making it accessible to all stakeholders. It presents a variety of opportunities to facilitate ornithological assessment at strategic to project-specific scales. Here we demonstrate three potential applications of OCcAM: (1) predicting the cumulative impact of Scottish offshore wind farms upon protected seabird populations, (2) updating fatality estimates calculated for worst-case consented values using as-built input parameters and (3) optioneering of project design parameters relative to seabird risk.

ecology↗

bioRxiv2025

OocystMeter, a machine-learning algorithm to count and measure Plasmodium oocysts, reveals clustering patterns in the Anopheles midgut

We present OocystMeter, a machine learning-based software developed to automate the segmentation of malaria oocysts from images of mosquito midguts stained with mercurochrome. Existing bioimage analysis tools, including machine learning-based ones, often struggle with the unique staining patterns, complex midgut backgrounds, and variable morphology of oocysts, making the determination of oocyst size and numbers cumbersome. To overcome these challenges, we curated a high-quality dataset comprised of 11,178 Plasmodium falciparum oocysts in Anopheles gambiae midguts annotated by expert parasitologists. Using this dataset, we fine-tuned a Mask R-CNN object detection model to achieve segmentation accuracy comparable to human parasitologists (Spearmans correlation of 0.998 for oocyst counts and 0.978 for size measurements). Applying this tool in conjunction with spatial analysis, we uncovered a non-random, clustered spatial distribution of oocysts independent of the midguts anatomical regions or geometric axes, particularly in infections with fewer than 75 oocysts/midgut. Our workflow significantly accelerates malaria oocyst intensity and size analysis, reduces human bias, and provides spatial coordinates for advanced parasitology studies. OocystMeter is freely available at https://github.com/duopeng/OocystMeter, and as a web tool at http://Oocystmeter.org/, offering a valuable resource for researchers investigating the oocyst stage of malaria development.

bioinformatics↗

bioRxiv2025

Comparison of oviposition and adult trapping to monitor wMel introgression for Wolbachia-based vector control

Wolbachia introgression into Aedes aegypti mosquito populations has been shown to be effective in preventing dengue and is being evaluated for WHO prequalification. Monitoring the long-term introgression of Wolbachia (wMel)-positive Aedes aegypti mosquitoes, however, requires labor-intensive and costly BG-Sentinel traps (BG-traps). More affordable alternatives, such as using oviposition traps (ovitraps), have not been fully evaluated. Ae. aegypti eggs and adults were collected from 124 ovitraps and 237 BG-traps, respectively, across 12 clusters in Belo Horizonte, Brazil from March to May 2023 as part of the EVITA Dengue trial. We used a qPCR assay to detect wMel in a sample of L3-L4 stage larvae (up to 29) that were reared from eggs in ovitraps and adults from BG-traps (up to 10 per BG-trap). We used mixed effects models to compare estimates of cluster-level wMel introgression from ovitrap and BG-trap data over time. Among 3,675 larvae reared from ovitraps, wMel prevalence was 0.50 (95% CI: 0.48-0.51). Among 1,244 adult Ae. aegypti tested from BG-traps, wMel prevalence was 0.45 (95% CI: 0.42-0.48). Cluster-level wMel introgression in larvae and adults was highly correlated (Spearmans r = 0.70, p = 6.71e-06). Multivariate analysis found that ovitrap estimates of introgression were associated with BG-trap estimates in the same month when models incorporated the previous months ovitrap wMel-positive count, the proportion of wMel in ovitraps in the current and previous month, and Ae. aegypti abundance. Leveraging this model, predicted wMel introgression from ovitrap data were highly correlated with observed introgression from BG-trap data (rs,counts=0.98, p=1.53e-14; rs,prevalences=0.82, p=0.11e-05) and provided greater precision than crude ovitrap-based estimates. These findings indicate that ovitrap-based monitoring represents a low cost, more efficient approach to evaluating introgression as the Wolbachia-based interventions are scaled up and implemented broadly in high burden regions for dengue and other arboviral diseases. Author SummaryDengue fever is a major global health burden, and one promising way to control it is by releasing Aedes aegypti mosquitoes infected with a bacteria called Wolbachia. This bacteria reduces the mosquitoes ability to spread dengue. However, monitoring the success of Wolbachia in mosquito populations over time requires expensive and labor-intensive traps. Our study explored a more affordable alternative: using oviposition traps (ovitraps), which collect mosquito eggs instead of adults. In Belo Horizonte, Brazil, we compared data from eggs collected in ovitraps with data from standard mosquito traps (BG-traps) that catch adult mosquitoes. By analyzing the mosquitoes for Wolbachia, we found that the egg-based method provided reliable estimates of Wolbachia levels in the mosquito population. These results suggest that ovitraps could be a cost-effective and efficient way to monitor Wolbachias spread. This approach could help improve dengue prevention efforts, making it easier for public health programs to track and expand this control strategy in areas where dengue is a major concern.

ecology↗

bioRxiv2024

Mapping Plasmodium transitions and interactions in the Anopheles female

The human malaria parasite, Plasmodium falciparum, relies exclusively on Anopheles mosquitoes for transmission. Once ingested during blood feeding, most parasites die in the mosquito midgut lumen or during epithelium traversal1. How surviving ookinetes interact with midgut cells and form oocysts is poorly known, yet these steps are essential to initiate a remarkable growth process culminating in the production of thousands of infectious sporozoites2. Here, using single-cell RNA sequencing of both parasites and mosquito cells across different developmental stages and metabolic conditions, we unveil key transitions and mosquito-parasite interactions occurring in the midgut. Functional analyses uncover processes regulating oocyst growth and identify the transcription factor PfSIP2 as essential for sporozoite infection of human hepatocytes. Combining shared mosquito-parasite barcode analysis with confocal microscopy, we reveal that parasites preferentially interact with midgut progenitor cells during epithelial crossing, potentially using their basal location as an exit landmark. Additionally, we show tight connections between extracellular late oocysts and surrounding muscle cells that may ensure parasites adherence to the midgut. We confirm our major findings in several mosquito-parasite combinations, including field-derived parasites. Our study provides fundamental insight into the molecular events characterizing previously inaccessible biological transitions and mosquito-parasite interactions, and identifies candidates for transmission-blocking strategies.

microbiology↗

bioRxiv2024

Temporal multi-modal single-cell analyses reveal dynamic interactions of CAR-T cells with glioblastoma and targeting of antigen-negative neoplastic cells

CAR-T therapy is a promising new immunotherapy for cancers, but its efficacy for solid tumors requires improvement. A detailed understanding of the interplay between solid tumors and CAR-T cells is critical. Here we report temporal, multi-modal, single-cell profiling of patient-derived glioblastoma organoids with CAR-T treatment. We found that all tumor cell types responded to CAR-T cell activation and contributed to an initially anti-tumor, but subsequently pro-tumor and immune-inhibitory microenvironment, accompanied by CAR-T cell exhaustion. Unexpectedly, CAR-T treatment attenuated glioma stem-like states of both antigen-positive and antigen-negative neoplastic cells and reduced their proliferation via diffusible factors, including IFN{gamma}. Analysis of samples from additional patients, including those in clinical trials, supported these findings. Our study reveals the dynamic interplay among different tumor cells and T cells in adaptive responses to immunotherapy and identifies previously unappreciated benefits of CAR-T therapy directly on antigen-negative neoplastic cells that may be leveraged to enhance therapeutic efficacy.

cancer biology↗

bioRxiv2024

Overexpression of α-SNAPRhg1 can improve rhg1-a mediated soybean resistance to soybean cyst nematode

(i)The rhg1-a and rhg1-b haplotypes of the soybean Rhg1 locus are economically effective tools for the control of soybean cyst nematode (SCN; Heterodera glycines), but ongoing SCN evolution requires improved sources of resistance. Both Rhg1 haplotypes carry multiple tandem repeat copies of a four-gene block encoding four disparate proteins; resistance efficacy scales with copy number. The haplotypes encode different variants of an unusual -SNAP protein whose abundance increases in the nematode-reprogrammed plant cells that form the syncytium (nematode feeding site), which subsequently collapses. Simultaneous presence of the two -SNAPRhg1 protein types, or substantially elevated expression of either type, was hypothesized to improve SCN resistance but has not been achievable by conventional plant breeding methods. We accomplished both, by transgenic additions to an rhg1-a Rhg4 soybean line. Existing resistance to HG type 0 and HG type 2.5.7 SCN was strengthened, but resistance was not improved against an HG type 1.3.6.7 SCN population that was already highly virulent on the parent line. No significant yield penalties from constitutive overexpression of transgenic -SNAP genes were observed in greenhouse or initial field studies. Cisgenic combination or elevated expression of the different -SNAP genes may extend the efficacy and/or durability of Rhg1-mediated resistance. We also observed differential protein abundances for some -SNAPRhg1 isoforms after inoculation with different HG type populations of SCN. These approaches provide opportunities to understand the different mechanisms of the two Rhg1 haplotypes and to possibly fine-tune them for better management of SCN.

plant biology↗

bioRxiv2022

Distinct Subsets of Multi-Lymphoid Progenitors Support Ontogeny-Related Changes in Human Lymphopoiesis

Changes in lymphocyte production patterns occurring across human ontogeny remain poorly defined. In this study, we demonstrate that human lymphopoiesis is supported by three waves of embryonic, fetal, and postnatal multi-lymphoid progenitors (MLPs) differing in CD7 and CD10 expression and their output of CD127-/+ early lymphoid progenitors (ELP). Our results reveal that, like the fetal-to-adult switch in erythropoiesis, transition to postnatal life coincides with a shift from multilineage to B lineage-biased lymphopoiesis and an increase in production of CD127+ ELPs which persists until puberty. A further developmental transition is observed in elderly individuals where B-cell differentiation bypasses the CD127+ compartment and branches directly from CD10+ MLPs. Functional analyses indicate that these changes are determined at the level of the hematopoietic stem cell. Besides reconciling controversies about the identity and function of human MLPs, these results may shed light on the causes of age-related differences in the incidence of lymphoblastic leukemia.

immunology↗

bioRxiv2022

Multimodal Mapping of Human Lymphopoiesis Reveals B and T/NK/ILC Lineages are Subjected to Cell-Intrinsic versus Flt3L-Dependent Regulation

The developmental cartography of human lymphopoiesis remains incompletely understood. Here, we establish a multimodal map that extends the current view of lymphoid development. Our results demonstrate that lymphoid specification follows independent direct or stepwise differentiation pathways converging toward the emergence of CD117lo multi-lymphoid progenitors (MLPs) that undergo a proliferation arrest before entering the CD127- (T/NK/ILC) or CD127+ (B) lymphoid pathways. While the emergence of CD127- early lymphoid progenitors is driven by Flt3 signaling, differentiation of their CD127+ counterparts is regulated cell-intrinsically and depends exclusively on the divisional history of their precursors. Single-cell mapping of lymphoid differentiation trajectories reveals that a dissociation between proliferation and differentiation phases allows amplification of the precursor pools prior to the onset of antigen receptor rearrangement. Besides demonstrating that B and T/NK/ILC lineages are subjected to differential cell-autonomous versus Flt3-inducible regulation, our results go a long way to reconciling human and mouse models of lymphoid architecture.

immunology↗

bioRxiv2022

Identification of a microbial sub-community from the feral chicken gut that reduces Salmonella colonization and improves gut health in a gnotobiotic chicken model.

A complex microbial community in the gut generally prevent the colonization of enteric pathogens such as Salmonella. Because of the high complexity, several species or combination of species in the gut can confer colonization resistance. To gain a better understanding of the colonization resistance against Salmonella enterica, we isolated a library of 1,300 bacterial strains from feral chicken gut microbiota which represented a total of 51 species. Using a co-culture assay, we screened the representative species from this library and identified 30 species that inhibited Salmonella enterica Typhimurium. To improve the Salmonella inhibition capacity, from a pool of fast-growing species, we formulated 66 bacterial blends, each of which composed of 10 species. Bacterial blends were more efficient in inhibiting Salmonella as compared to individual species. The blend that showed maximum inhibition (Mix10) also inhibited other serotypes of Salmonella frequently found in poultry. The in vivo effect of Mix10 was examined in a gnotobiotic and conventional chicken model. The Mix10 consortium reduced Salmonella colonization, intestinal tissue damage and inflammation in both models. Cell free supernatant of Mix10 did not show Salmonella inhibition, indicating that Mix10 inhibits Salmonella through either nutritional competition or reinforcement of host immunity. Out of ten species, three species in Mix10 did not colonize while three species constituted more than 70% of the community. Two of these species represents previously uncultured bacteria. Our approach could be used as a high-throughput screening system to identify additional bacterial sub-communities that confer colonization resistance against enteric pathogens and its effect on the host. ImportanceSalmonella colonization in chicken and human infections originating from Salmonella- contaminated poultry is a significant problem. Poultry has been identified as the most common food linked to enteric pathogen outbreaks in the United States. Since multi-drug resistant Salmonella often colonize chicken and cause human infections, methods to control Salmonella colonization in poultry are needed. The method we describe here could form the basis of developing gut microbiota-derived bacterial blends as a microbial ecosystem therapeutic against Salmonella.

microbiology↗

bioRxiv2021

Btbd11 is an inhibitory interneuron specific synaptic scaffolding protein that supports excitatory synapse structure and function

Synapses in the brain exhibit cell-type-specific differences in basal synaptic transmission and plasticity. Here, we evaluated cell-type-specific differences in the composition of glutamatergic synapses, identifying Btbd11, as an inhibitory interneuron-specific synapse-enriched protein. Btbd11 is highly conserved across species and binds to core postsynaptic proteins including Psd-95. Intriguingly, we show that Btbd11 can undergo liquid-liquid phase separation when expressed with Psd-95, supporting the idea that the glutamatergic post synaptic density in synapses in inhibitory and excitatory neurons exist in a phase separated state. Knockout of Btbd11 from inhibitory interneurons decreased glutamatergic signaling onto parvalbumin-positive interneurons. Further, both in vitro and in vivo, we find that Btbd11 knockout disrupts network activity. At the behavioral level, Btbd11 knockout from interneurons sensitizes mice to pharmacologically induced hyperactivity following NMDA receptor antagonist challenge. Our findings identify a cell-type-specific protein that supports glutamatergic synapse function in inhibitory interneurons--with implication for circuit function and animal behavior.

neuroscience↗

bioRxiv2021

In-solution buffer-free digestion for the analysis of SARS-CoV-2 RBD proteins allows a full sequence coverage and detection of post-translational modifications in a single ESI-MS spectrum

Subunit vaccines based on the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2, are among the most promising strategies to fight the COVID-19 pandemic. The detailed characterization of the protein primary structure by mass spectrometry (MS) is mandatory, as described in ICHQ6B guidelines. In this work, several recombinant RBD proteins produced in five expression systems were characterized using a non-conventional protocol known as in-solution buffer-free digestion (BFD). In a single ESI-MS spectrum, BFD allowed very high sequence coverage ([≥] 99 %) and the detection of highly hydrophilic regions, including very short and hydrophilic peptides (2-8 amino acids), the His6-tagged C-terminal peptide carrying several post-translational modifications at Cys538 such as cysteinylation, glutathionylation, cyanilation, among others. The analysis using the conventional digestion protocol allowed lower sequence coverage (80-90 %) and did not detect peptides carrying some of the above-mentioned post-translational modifications. The two C-terminal peptides of a dimer [RBD(319-541)-(His)6]2 linked by an intermolecular disulfide bond (Cys538-Cys538) with twelve histidine residues were only detected by BFD. This protocol allows the detection of the four disulfide bonds present in the native RBD and the low-abundance scrambling variants, free cysteine residues, O-glycoforms and incomplete processing of the N-terminal end, if present. Artifacts that might be generated by the in-solution BFD protocol were also characterized. BFD can be easily implemented and we foresee that it can be also helpful to the characterization of mutated RBD.

biochemistry↗

bioRxiv2019

The Low-Cost, Semi-Automated Shifter Microscope Stage Transforms Speed and Robustness of Manual Protein Crystal Harvesting

Despite the tremendous success of x-ray cryocrystallography over recent decades, the transfer of crystals from the drops where they grow to diffractometer sample mounts, remains a manual process in almost all laboratories. Here we describe the Shifter, a semi-automated microscope stage that offers an accessible and scalable approach to crystal mounting that exploits on the strengths of both humans and machines. The Shifter control software manoeuvres sample drops beneath a hole in a clear protective cover, for human mounting under a microscope. By allowing complete removal of film seals the tedium of cutting or removing the seal is eliminated. The control software also automatically captures experimental annotations for uploading to the users data repository, removing the overhead of manual documentation. The Shifter facilitates mounting rates of 100-240 crystals per hour, in a more controlled process than manual mounting, which greatly extends the lifetime of drops and thus allows for a dramatic increase in the number of crystals retrievable from any given drop, without loss of X-ray diffraction quality. In 2015 the first in a series of three Shifter devices was deployed as part of the XChem fragment screening facility at Diamond Light Source (DLS), where they have since facilitated the mounting of over 100,000 crystals. The Shifter was engineered to be simple, allowing for a low-cost device to be commercialised and thus potentially transformative as many research initiatives as possible. SynopsisA motorised X/Y microscope stage is presented that combines human fine motor control with machine automation and automated experiment documentation, to transform productivity in protein crystal harvesting.

biophysics↗

bioRxiv2018

Gut Microbial succession during conventionalization of germfree chicken

A gnotobiotic chicken model was developed to study the succession of intestinal microflora from hatching to 18 days of age. Intestinal samples were collected from a local population of feral chickens and administered orally to germ-free 3 day old chicks. Animals were enthanized on 0, 9 and 18 days of age and intestinal samples were collected and subjected to genomic analysis. The five most prevalent phyla were Bacteroidetes (45.73{+/-}3.35%), Firmicutes (36.47{+/-}2.60%), Proteobacteria (8.28{+/-}0.91%), Actinobacteria (5.09{+/-}0.52%), and Spriochetes (2.10{+/-}0.38%). Principle coordinate analysis indicated the 0, 9 day and 18 day variables clustered together and the microbial communities changed temporally. The Morista-Horn index values ranged from 0.72 to 1, indicating the communities at 0, 9 or 18 days were more similar than dissimilar. The predicted functional profiles of the microbiomes of 0, 9 and 18 days were also similar. These results indicate the gnotobiotic chicks stably maintain the phylogentic diversity and predicted metabolic functionality of the inoculum community.\n\nImportanceThe domestic chicken is the cornerstone of animal agriculture worldwide with a flock population exceeding 40 billion birds/year. It serves as the economically valuable source of protein globally. Microbiome of poultry has important effects on chicken growth, feed conversion, immune status and pathogen resistance. The significance of our research is in developing a gnotobiotic chicken model to study chicken gut microbiota function. Our experimental model shows that young germfree chicks are able to colonize diverse set of gut bacteria. Therefore, besides using this model to study mechanisms of gut microbiota interactions in the chicken gut, our model could be also used for applied aspects such as determining the safety and efficacy of new probiotic strains derived from chicken gut microbiota.

microbiology↗

bioRxiv2018

Genome sequence and description of Blautia brookingsii str SG772 nov., a new species of anaerobic bacterium isolated from healthy human gut

Strain SG-772 is a Gram positive, strictly anoxic bacterium isolated from the feces of a healthy human fecal donor. Based on 16S rRNA gene sequence, the strain showed maximum similarity (94.39%) with Blautia stercoris GAM6-1 in EZ-Taxon server and thus assigned the genus Blautia. The scanning electron micrograph of the bacterium revealed the characteristic coccobacillus shape as well as the complete absence of flagellum, suggesting its non-motile phenotype. This strain was found to utilize 27 substrates based on Biolog AN plates assay, with maximum preference for D-mannitol. Additionally, the strain was found to be resistant to tetracycline and streptomycin. Genome sequencing and analysis revealed an overall genome size of 3.49 Mbp and GC content of 43.97%. Based on RAST annotation server, the closest neighbor was Blautia hansenii DSM20583. Average Nucleotide Identity (ANI) of these strains were 81.69%, suggesting a high level of genomic variation. The comparative genome analysis of strain SG772 with B. hansenii DSM20583 revealed a total of 411 orthologous genes coding for basic metabolic functions. Furthermore, the genomes were functionally distinct based on COG categories. Thus, based on all these differences, we propose a novel species of genus Blautia named as Blautia brookingsii SG772.

microbiology↗