Biology subjects

Pickering, A. J.

Publications and source records attributed to Pickering, A. J..

10 recordsLinked to original sources

bioRxiv2025

Surface avidity of anionic polypeptide coatings target nanoparticles to cancer-associated amino acid transporters

Tumor-targeted drug delivery enhances therapeutic efficacy while minimizing toxicity. Layer-by-layer nanoparticles (LbL-NPs) coated with anionic polypeptides selectively bind to cancer cells, though the mechanisms have been unclear. Here, we integrated in silico and in vitro approaches--including gene expression analysis, receptor inhibition, and AI-based protein modeling--to show that poly(L-glutamate) (PLE)-coated LbL-NPs bind with high avidity to SLC1A5, a glutamine transporter overexpressed in cancer. We also discovered that PLE clusters SLC1A5 on the cell membrane, promoting prolonged cell surface retention. Poly(L-aspartate) (PLD)-coated NPs similarly bind SLC1A5 but also interact with faster internalizing transporters of anionic amino acids. Correlation analyses across cancer cell lines confirmed a strong link between transporter expression and nanoparticle association. These findings demonstrate that dense glutamate or aspartate presentation through electrostatically adsorbed polypeptides enables selective targeting of overexpressed transporters, providing a mechanistic framework for receptor-targeted delivery that leverages metabolic characteristics of a range of solid tumor types.

bioengineering↗

bioRxiv2025

Associations between floor material and E. coli contamination in rural Bangladeshi households

Soil floors are common in low-income countries and can harbor contamination from unsafely managed human and animal fecal waste. Soil/dust ingestion directly from floors or indirectly via hands, drinking water and food can significantly contribute to childrens ingestion of fecal organisms. We assessed if finished (e.g., concrete) floors are associated with lower E. coli contamination in the domestic environment in rural Bangladesh. We collected samples from 1864 households over 3.5 years, including stored drinking water, child and caregiver hand rinses, courtyard soil, food, and flies (n=24,118 samples), and enumerated E. coli using IDEXX Quanti-Tray/2000. Controlling for potential confounders (socio-demographics, water/sanitation status, animal ownership), households with finished floors had slightly lower log10-transformed E. coli counts ({Delta}log10= -0.10 (-0.20, 0.00)) and prevalence (prevalence ratio=0.90 (0.83, 0.98)) on child hands than households with soil floors; floor material was not associated with contamination levels in other sample types. Finished floors were associated with lower E. coli contamination of child hands, food and stored drinking water following periods of higher rainfall and temperature, and lower E. coli contamination of child hands in households with more domestic animals. Measures to control enteric infections in low-income countries should test flooring improvements to reduce exposure to fecal contamination.

microbiology↗

bioRxiv2024

Environmental surveillance of soil-transmitted helminths and other enteric pathogens in settings without networked wastewater infrastructure

Soil-transmitted helminths (STH) are one of the most prevalent enteric infections world-wide. To control STH-related morbidity, the World Health Organization recommends targeted deworming and improvements in water, sanitation and hygiene. Current surveillance strategies for STH focus on identifying and quantifying eggs in stool samples via microscopy, which exhibits poor specificity and sensitivity, especially in settings with low-intensity infections. Wastewater-based epidemiology is a surveillance tool used to monitor pathogen circulation and could replace stool- based approaches for STH detection. However, sampling strategies for settings lacking networked sanitation outside large urban settlements are not well developed. Here, we report evaluation of sampling strategies for soil and wastewater STH surveillance in rural and peri-urban settings without networked sanitation. We used multi-parallel qPCR assays to detect STH DNA in soil collected from high foot-traffic locations and three types of wastewater samples (passive Moore swabs, grab samples, and sediment from drainage ditches) in Come, Benin and Timiri and Jawadhu Hills in Tamil Nadu, India. We detected STH in soil (India = 32/95, Benin = 39/121) and wastewater (India = 24/60, Benin = 8/64) with a detection frequency across all sample types of 36% in India and 25% in Benin. We evaluated which sample locations and types allowed for more sensitive detection of STH DNA and determined that STH prevalence varied by sample site but did not vary significantly within a given sample site location (e.g., samples collected from multiple locations within one market). Further, we determined that wastewater sediment samples outperformed grab and Moore swab sample types for STH detection. Finally, we expanded our methods to include detection of other enteric pathogens using multiplexed qPCR for wastewater samples. Our results establish sampling strategies for environmental and wastewater surveillance of a wide range of enteric pathogens in settings without networked sanitation.

microbiology↗

bioRxiv2024

Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance

Precisely understanding how and to what extent antimicrobial resistance (AMR) is exchanged between animals and humans is needed to inform control strategies. Metagenomic sequencing has low detection for rare targets such as antibiotic resistance genes, while whole genome sequencing of isolates misses exchange between uncultured bacterial species. We introduce Context-Seq, CRISPR-Cas9 targeted sequencing of ARGs and their genomic context with long-reads. Using Context-Seq, we investigate genetically similar AMR elements containing the ARGs blaCTX-M and blaTEM between adults, children, poultry, and dogs in Nairobi, Kenya. We identify genetically distinct clusters containing blaTEM and blaCTX-M that are shared between animals and humans within and between households. We also uncover potentially pathogenic hosts of ARGs including Escherichia coli, Klebsiella pneumonia, and Haemophilus influenzae in this study context. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.

microbiology↗

bioRxiv2024

'Target-and-release' nanoparticles for effective immunotherapy of metastatic ovarian cancer

Immunotherapies such as checkpoint inhibitors (CPI) are effective in treating several advanced cancers, but these treatments have had limited success in metastatic ovarian cancer (OC). Here, we engineered liposomal nanoparticles (NPs) carrying a layer-by-layer (LbL) polymer coating that promotes their binding to the surface of OC cells. Covalent anchoring of the potent immunostimulatory cytokine interleukin-12 (IL-12) to phospholipid headgroups of the liposome core enabled the LbL particles to concentrate IL-12 in disseminated OC tumors following intraperitoneal administration. Shedding of the LbL coating and serum protein-mediated extraction of IL-12-conjugated lipids from the liposomal core over time enabled IL-12 to disseminate in the tumor bed following rapid NP localization in tumor nodules. Optimized IL-12 LbL-NPs promoted robust T cell accumulation in ascites and tumors in mouse models, extending survival compared to free IL-12 and remarkedly sensitizing tumors to CPI, leading to curative treatments and immune memory.

bioengineering↗

bioRxiv2024

Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline

Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.

microbiology↗

bioRxiv2022

Core material and surface chemistry of Layer-by-Layer (LbL) nanoparticles independently direct uptake, transport, and trafficking in preclinical blood-brain barrier (BBB) models

Development of new treatments for neurological disorders, especially brain tumors and neurodegenerative diseases, is hampered by poor accumulation of new therapeutic candidates in the brain. Drug carrying nanoparticles are a promising strategy to deliver therapeutics, but there is a major need to understand interactions between nanomaterials and the cells of the blood-brain barrier (BBB), and to what degree these interactions can be predicted by preclinical models. Here, we use a library of eighteen layer-by-layer electrostatically assembled nanoparticles (LbL-NPs) to independently assess the impact of nanoparticle core stiffness and surface chemistry on in vitro uptake and transport in three common assays, as well as intracellular trafficking in hCMEC/D3 endothelial cells. We demonstrate that nanoparticle core stiffness impacts the magnitude of material transported, while surface chemistry influences how the nanoparticles are trafficked within the cell. Finally, we demonstrate that these factors similarly dictate in vivo BBB transport using intravital imaging through cranial windows in mice, and we discover that a hyaluronic acid surface chemistry provides an unpredicted boost to transport. Taken together, these findings highlight the importance of considering factors such as assay geometry, nanomaterial labelling strategies, and fluid flow in designing preclinical assays to improve nanoparticle screening throughput for drug delivery to the brain.

bioengineering↗

bioRxiv2022

Effects of high temperature and heavy precipitation on drinking water quality and child hand contamination levels in rural Kenya

Climate change may impact human health through the influence of weather on environmental transmission of diarrhea. Previous studies have found that high temperatures and heavy precipitation are associated with increased diarrhea prevalence, but the underlying causal mechanisms are not clear. We linked measurements of Escherichia coli in source water (n=1,673), stored drinking water (n=8,924), and hand rinses from children <2 years old (n=2,660) with publicly available gridded temperature and precipitation data (at [≤]0.2 degree spatial resolution and daily temporal resolution) by the GPS coordinates and date of sample collection. Measurements were collected over a 3-year period across a 2500 km2 area in rural Kenya. In drinking water sources, high 7-day temperature was associated with a 0.16 increase in log10 E. coli levels (p<0.001), while heavy 7-day total precipitation was associated with a 0.29 increase in log10 E. coli levels (p<0.001). In household stored drinking water, heavy 7-day precipitation was associated with a 0.079 increase in log10 E. coli levels (p=0.042). On child hands, high 7-day temperature was associated with a 0.39 decrease in log10 E. coli levels (p<0.001). Our findings provide insight on how climate change could impact environmental transmission of bacterial pathogens in Kenya, and suggest water treatment could be a mitigation strategy.

microbiology↗

bioRxiv2021

Leakiness at the human-animal interface in Southeast Asia and implications for the spread of antibiotic resistance

International efforts to curb antimicrobial resistance have focused on drug development and limiting unnecessary use. However, in areas where water, sanitation, and hygiene infrastructure is lacking, and where biosecurity in food-animal production is poor, pathogen-flow between humans and animals could exacerbate the emergence and spread of resistant pathogens. Here, we compared mobile resistance elements among Escherichia coli recovered from humans and meat in Cambodia, a country with substantial connectivity between humans and animals, unregulated antibiotic use, and poor environmental controls. We identified multiple resistance-encoding plasmids and a novel, blaCTX-M and qnrS1-encoding transposon that were widely dispersed in both humans and animals, a phenomenon rarely observed in high-income settings. Our findings indicate that plugging leaks at human-animal interfaces should be a critical part of addressing antimicrobial resistance in low and middle-income countries.

ecology↗

bioRxiv2021

StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities

Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify nearest known references and find variants for multiple conspecific strains within a sample at relative abundances below 0.1% in typical metagenomic datasets.

bioinformatics↗