Publications

@article{noKey,

title = {Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3},

author = {Chuang, Hsiu-Chun, Ruidong, Li, Li, Li, Kai-Hui, Sun},

url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-11036-0},

doi = {https://doi.org/10.1186/s12864-024-11036-0},

year  = {2024},

date = {2024-11-20},

journal = {BMC Genomics},

abstract = {We developed an automated high-throughput Smart-seq3 (HT Smart-seq3) workflow that integrates best practices and an optimized protocol to enhance efficiency, scalability, and method reproducibility. This workflow consistently produces high-quality data with high cell capture efficiency and gene detection sensitivity. In a rigorous comparison with the 10X platform using human primary CD4 + T-cells, HT Smart-seq3 demonstrated higher cell capture efficiency, greater gene detection sensitivity, and lower dropout rates. Additionally, when sufficiently scaled, HT Smart-seq3 achieved a comparable resolution of cellular heterogeneity to 10X. Notably, through T-cell receptor (TCR) reconstruction, HT Smart-seq3 identified a greater number of productive alpha and beta chain pairs without the need for additional primer design to amplify full-length V(D)J segments, enabling more comprehensive TCR profiling across a broader range of species. Taken together, HT Smart-seq3 overcomes key technical challenges, offering distinct advantages that position it as a promising solution for the characterization of single-cell transcriptomes and immune repertoires, particularly well-suited for low-input, low-RNA content samples.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {A ‘rich-get-richer’ mechanism drives patchy  dynamics and resistance evolution in  antibiotic-treated bacteria},

author = {Emrah, Şimşek, Kim, Kiyeri, You, Lingchong},

url = {https://www.embopress.org/doi/pdf/10.1038/s44320-024-00046-5},

doi = {https://doi.org/10.1038/s44320-024-00046-5},

year  = {2024},

date = {2024-06-13},

journal = {Molecular Systems Biology},

abstract = {Bacteria in nature often form surface-attached communities that initially comprise distinct subpopulations, or patches. For pathogens, these patches can form at infection sites, persist during antibiotic treatment, and develop into mature biofilms. Evidence suggests that patches can emerge due to heterogeneity in the growth environment and bacterial seeding, as well as cell-cell signaling. However, it is unclear how these factors contribute to patch formation and how patch formation might affect bacterial survival and evolution. Here, we demonstrate that a 'rich-get-richer' mechanism drives patch formation in bacteria exhibiting collective survival (CS) during antibiotic treatment. Modeling predicts that the seeding heterogeneity of these bacteria is amplified by local CS and global resource competition, leading to patch formation. Increasing the dose of a non-eradicating antibiotic treatment increases the degree of patchiness. Experimentally, we first demonstrated the mechanism using engineered Escherichia coli and then demonstrated its applicability to a pathogen, Pseudomonas aeruginosa. We further showed that the formation of P. aeruginosa patches promoted the evolution of antibiotic resistance. Our work provides new insights into population dynamics and resistance evolution during surface-attached bacterial growth.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Rapid high-throughput method for investigating physiological regulation of neutrophil extracellular trap formation},

author = {Zukas, Kieran},

url = {https://www.sciencedirect.com/science/article/pii/S1538783624003209},

doi = {https://doi.org/10.1016/j.jtha.2024.05.028},

year  = {2024},

date = {2024-06-09},

journal = {Journal of Thrombosis and Haemostasis},

abstract = {Background

Neutrophils, the most abundant white blood cells in humans, play pivotal roles in innate immunity, rapidly migrating to sites of infection and inflammation to phagocytose, neutralize, and eliminate invading pathogens. Neutrophil extracellular trap (NET) formation is increasingly recognized as an essential rapid innate immune response, but when dysregulated, it contributes to pathogenesis of sepsis and immunothrombotic disease.



Objectives

Current NETosis models are limited, routinely employing nonphysiological triggers that can bypass natural NET regulatory pathways. Models utilizing isolated neutrophils and immortalized cell lines do not reflect the complex biology underlying neutrophil activation and NETosis that occurs in whole blood. To our knowledge, we report the first human ex vivo model utilizing naturally occurring molecules to induce NETosis in whole blood. This approach could be used for drug screening and, importantly, inadvertent activators of NETosis.



Methods

Here we describe a novel, high-throughput ex vivo whole blood–induced NETosis model using combinatorial pooling of native NETosis-inducing factors in a more biologically relevant Synthetic-Sepsis model.



Results

We found different combinations of factors evoked distinct neutrophil responses in the rate of NET generation and/or magnitude of NETosis. Despite interdonor variability, similar sets of proinflammatory molecules induced consistent responses across donors. We found that at least 3 biological triggers were necessary to induce NETosis in our system including either tumor necrosis factor-α or lymphotoxin-α.



Conclusion

These findings emphasize the importance of investigating neutrophil physiology in a biologically relevant context to enable a better understanding of disease pathology, risk factors, and therapeutic targets, potentially providing novel strategies for disease intervention and treatment.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Protocol for generation of and high-throughput drug testing with patient-derived colorectal cancer organoids},

author = {Tan, Tao},

url = {https://www.sciencedirect.com/science/article/pii/S2666166724002557},

doi = {https://doi.org/10.1016/j.xpro.2024.103090},

year  = {2024},

date = {2024-05-27},

journal = {STAR Protocols},

abstract = {Drug sensitivity testing of patient-derived tumor organoids (PDTOs) is a promising tool for personalizing cancer treatment. Here, we present a protocol for generation of and high-throughput drug testing with PDTOs. We describe detailed steps for PDTO establishment from colorectal cancer tissues, preparation of PDTOs for high-throughput drug testing, and quantification of drug testing results using image analysis. This protocol provides a standardized workflow for PDTO testing of standard-of-care therapies, along with exploring the activity of new agents, for translational research.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts},

author = {Huertas, Luis Hernandez},

url = {https://www.biorxiv.org/content/10.1101/2024.05.22.595167v1.full},

doi = {https://doi.org/10.1101/2024.05.22.595167},

year  = {2024},

date = {2024-05-22},

journal = {Preprint},

abstract = {The Maternal-to-Zygotic transition (MZT) is a reprograming process encompassing zygotic genome activation (ZGA) and the clearance of maternally-provided mRNAs. While some factors regulating MZT have been identified, there are thousands of maternal RNAs whose function has not been ascribed yet. Here, we have performed a proof-of-principle CRISPR-RfxCas13d maternal screening targeting mRNAs encoding protein kinases and phosphatases in zebrafish and identified Bckdk as a novel post-translational regulator of MZT. Bckdk mRNA knockdown caused epiboly defects, ZGA deregulation, H3K27ac reduction and a partial impairment of miR-430 processing. Phospho-proteomic analysis revealed that Phf10/Baf45a, a chromatin remodeling factor, is less phosphorylated upon Bckdk depletion. Further, phf10 mRNA knockdown also altered ZGA and Phf10 constitutively phosphorylated rescued the developmental defects observed after bckdk mRNA depletion. Altogether, our results demonstrate the competence of CRISPR-RfxCas13d screenings to uncover new regulators of early vertebrate development and shed light on the post-translational control of MZT mediated by protein phosphorylation.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Dynamic Clinical Assay Pipeline for Detecting a Virus},

author = {Williams, Jonathan David},

url = {https://patents.google.com/patent/US20240141447A1/en},

doi = {US20240141447A1},

year  = {2024},

date = {2024-05-01},

journal = {Google Patents},

abstract = {Disclosed herein are methods and systems comprising obtaining nucleic acid from a sample that was obtained from a subject; capturing and amplifying a target molecule in the nucleic acid using a molecular inversion probe under hybridization conditions; ligating an adapter to create a circular molecule; sequencing the circular molecule to obtain sequence reads; generating a sequencing file comprising the sequence reads of each molecule and a position of each sequence read in a reference genome of a virus; and generating a reporting file for the subject comprising a predicted lineage of the virus in the sample.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {The transcription factor ZNF469 regulates collagen production in liver fibrosis},

author = {Steinhauser, Sebastian},

url = {https://www.biorxiv.org/content/10.1101/2024.04.25.591188v1},

doi = {https://doi.org/10.1101/2024.04.25.591188},

year  = {2024},

date = {2024-04-24},

journal = {Preprint},

abstract = {Non-alcoholic fatty liver disease (NAFLD) - characterized by excess accumulation of fat in the liver - now affects one third of the world’s population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Machine learning accelerates pharmacophore-based virtual screening of MAO inhibitors},

author = {Cieślak, Marcin},

url = {https://www.nature.com/articles/s41598-024-58122-7},

doi = {https://doi.org/10.1038/s41598-024-58122-7},

year  = {2024},

date = {2024-04-07},

journal = {Scientific Reports},

abstract = {Nowadays, an efficient and robust virtual screening procedure is crucial in the drug discovery process, especially when performed on large and chemically diverse databases. Virtual screening methods, like molecular docking and classic QSAR models, are limited in their ability to handle vast numbers of compounds and to learn from scarce data, respectively. In this study, we introduce a universal methodology that uses a machine learning-based approach to predict docking scores without the need for time-consuming molecular docking procedures. The developed protocol yielded 1000 times faster binding energy predictions than classical docking-based screening. The proposed predictive model learns from docking results, allowing users to choose their preferred docking software without relying on insufficient and incoherent experimental activity data. The methodology described employs multiple types of molecular fingerprints and descriptors to construct an ensemble model that further reduces prediction errors and is capable of delivering highly precise docking score values for monoamine oxidase ligands, enabling faster identification of promising compounds. An extensive pharmacophore-constrained screening of the ZINC database resulted in a selection of 24 compounds that were synthesized and evaluated for their biological activity. A preliminary screen discovered weak inhibitors of MAO-A with a percentage efficiency index close to a known drug at the lowest tested concentration. The approach presented here can be successfully applied to other biological targets as target-specific knowledge is not incorporated at the screening phase.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {A novel micellular fluorogenic substrate for quantitating the activity of 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma (PLCγ) enzymes},

author = {Visvanathan, Ramya},

url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0299541},

doi = {https://doi.org/10.1371/journal.pone.0299541},

year  = {2024},

date = {2024-03-28},

journal = {Plos One},

abstract = {The activities of the phospholipase C gamma (PLCγ) 1 and 2 enzymes are essential for numerous cellular processes. Unsurprisingly, dysregulation of PLCγ1 or PLCγ2 activity is associated with multiple maladies including immune disorders, cancers, and neurodegenerative diseases. Therefore, the modulation of either of these two enzymes has been suggested as a therapeutic strategy to combat these diseases. To aid in the discovery of PLCγ family enzyme modulators that could be developed into therapeutic agents, we have synthesized a high-throughput screening-amenable micellular fluorogenic substrate called C16CF3-coumarin. Herein, the ability of PLCγ1 and PLCγ2 to enzymatically process C16CF3-coumarin was confirmed, the micellular assay conditions were optimized, and the kinetics of the reaction were determined. A proof-of-principle pilot screen of the Library of Pharmacologically Active Compounds 1280 (LOPAC1280) was performed. This new substrate allows for an additional screening methodology to identify modulators of the PLCγ family of enzymes.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Defining the function of disease variants with CRISPR editing and multimodal single cell sequencing},

author = {Baglaenko, Yuriy},

url = {https://www.biorxiv.org/content/10.1101/2024.03.28.587175v1.abstract},

doi = {https://doi.org/10.1101/2024.03.28.587175},

year  = {2024},

date = {2024-03-28},

journal = {Preprint},

abstract = {Genetic studies have identified thousands of individual disease-associated non-coding alleles, but identification of the causal alleles and their functions remain critical bottlenecks. Even though CRISPR-Cas editing has enabled targeted modification of DNA, inefficient editing leads to heterogeneous outcomes across individual cells, limiting the ability to detect functional consequences of disease alleles. To overcome these challenges, we present a multi-omic single cell sequencing approach that directly identifies genomic DNA edits, assays the transcriptome, and measures cell surface protein expression. We apply this approach to investigate the effects of gene disruption, deletions in regulatory regions, and non-coding single nucleotide polymorphisms. We identify the specific effects of individual SNPs, including the state-specific effects of an IL2RA autoimmune variant in primary human T cells. Multimodal functional genomic single cell assays including DNA sequencing bridge a crucial gap in our understanding of complex human diseases by directly identifying causal variation in primary human cells.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Topographical and cell type-specific connectivity of rostral and caudal forelimb corticospinal neuron populations},

author = {Carmona, Lina Marcela},

url = {https://www.cell.com/cell-reports/fulltext/S2211-1247(24)00321-8},

doi = {https://doi.org/10.1016/j.celrep.2024.113993},

year  = {2024},

date = {2024-03-26},

journal = {Cell Reports},

abstract = {Corticospinal neurons (CSNs) synapse directly on spinal neurons, a diverse assortment of cells with unique structural and functional properties necessary for body movements. CSNs modulating forelimb behavior fractionate into caudal forelimb area (CFA) and rostral forelimb area (RFA) motor cortical populations. Despite their prominence, the full diversity of spinal neurons targeted by CFA and RFA CSNs is uncharted. Here, we use anatomical and RNA sequencing methods to show that CSNs synapse onto a remarkably selective group of spinal cell types, favoring inhibitory populations that regulate motoneuron activity and gate sensory feedback. CFA and RFA CSNs target similar spinal neuron types, with notable exceptions that suggest that these populations differ in how they influence behavior. Finally, axon collaterals of CFA and RFA CSNs target similar brain regions yet receive highly divergent inputs. These results detail the rules of CSN connectivity throughout the brain and spinal cord for two regions critical for forelimb behavior.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Profiling Protein-Protein Interactions in the Human Brain by Refined Co-Fractionation Mass Spectrometry},

author = {Shrestha, Him K.},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11065482/},

doi = {https://doi.org/10.1021/acs.jproteome.3c00685},

year  = {2024},

date = {2024-03-19},

journal = {Journal of Proteome Research},

abstract = {Proteins usually execute their biological functions through interactions with other proteins and by forming macromolecular complexes, but global profiling of protein complexes directly from human tissue samples has been limited. In this study, we utilized co-fractionation mass spectrometry (CF-MS) to map protein complexes within the post-mortem human brain with experimental replicates. First, we used concatenated anion and cation Ion Exchange Chromatography (IEX) to separate native protein complexes in 192 fractions, then proceeded with Data-Independent Acquisition (DIA) mass spectrometry to analyze the proteins in each fraction, quantifying a total of 4,804 proteins with 3,260 overlapping in both replicates. We improved DIA quantitative accuracy by implementing a constant amount of bovine serum albumin (BSA) in each fraction as an internal standard. Next, advanced computational pipelines, which integrate both a database-based complex analysis and an unbiased protein-protein interaction (PPI) search, were applied to identify protein complexes and construct protein-protein interaction networks in the human brain. Our study led to the identification of 486 protein complexes and 10,054 binary protein-protein interactions, which represents the first global profiling of human brain PPIs using CF-MS. Overall, this study offers a resource and tool for a wide range of human brain research, including the identification of disease-specific protein complexes in the future.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {scAbsolute: measuring single-cell ploidy and replication status},

author = {Schneider, Michael P.},

url = {https://link.springer.com/article/10.1186/s13059-024-03204-y},

doi = {https://doi.org/10.1186/s13059-024-03204-y},

year  = {2024},

date = {2024-03-03},

journal = {Genome Biology},

abstract = {Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single-cell genomes is paramount for downstream analysis. Based only on single-cell DNA sequencing information, scAbsolute achieves accurate and unbiased measurement of single-cell ploidy and replication status, including whole-genome duplications. We demonstrate scAbsolute’s capabilities using experimental cell multiplets, a FUCCI cell cycle expression system, and a benchmark against state-of-the-art methods. scAbsolute provides a robust foundation for single-cell DNA sequencing analysis across different technologies and has the potential to enable improvements in a number of downstream analyses.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Cis inhibition of NOTCH1 through JAGGED1 sustains embryonic hematopoietic stem cell fate},

author = {Thambyrajah, Roshana},

url = {https://www.nature.com/articles/s41467-024-45716-y},

doi = {https://doi.org/10.1101/2023.04.19.537430},

year  = {2024},

date = {2024-02-20},

journal = {Nature Communications},

abstract = {Hematopoietic stem cells (HSCs) develop from the hemogenic endothelium (HE) in the aorta- gonads-and mesonephros (AGM) region and reside within Intra-aortic hematopoietic clusters (IAHC) along with hematopoietic progenitors (HPC). The signalling mechanisms that distinguish HSCs from HPCs are unknown. Notch signaling is essential for arterial specification, IAHC formation and HSC activity, but current studies on how Notch segregates these different fates are inconsistent. We now demonstrate that Notch activity is highest in a subset of, GFI1 + , HSC-primed HE cells, and is gradually lost with HSC maturation. We uncover that the HSC phenotype is maintained due to increasing levels of NOTCH1 and JAG1 interactions on the surface of the same cell (cis) that renders the NOTCH1 receptor from being activated. Forced activation of the NOTCH1 receptor in IAHC activates a hematopoietic differentiation program. Our results indicate that NOTCH1-JAG1 cis-inhibition preserves the HSC phenotype in the hematopoietic clusters of the embryonic aorta.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {High-throughput screening assay for PARP-HPF1 interaction inhibitors to affect DNA damage repair},

author = {Dhakar, Saurabh S.},

url = {https://www.nature.com/articles/s41598-024-54123-8},

doi = {https://doi.org/10.1038/s41598-024-54123-8},

year  = {2024},

date = {2024-02-15},

journal = {Scientific Reports},

abstract = {ADP-ribosyltransferases PARP1 and PARP2 play a major role in DNA repair mechanism by detecting the DNA damage and inducing poly-ADP-ribosylation dependent chromatin relaxation and recruitment of repair proteins. Catalytic PARP inhibitors are used as anticancer drugs especially in the case of tumors arising from sensitizing mutations. Recently, a study showed that Histone PARylation Factor (HPF1) forms a joint active site with PARP1/2. The interaction of HPF1 with PARP1/2 alters the modification site from Aspartate/Glutamate to Serine, which has been shown to be a key ADP-ribosylation event in the context of DNA damage. Therefore, disruption of PARP1/2-HPF1 interaction could be an alternative strategy for drug development to block the PARP1/2 activity. In this study, we describe a FRET based high-throughput screening assay to screen inhibitor libraries against PARP-HPF1 interaction. We optimized the conditions for FRET signal and verified the interaction by competing the FRET pair in multiple ways. The assay is robust and easy to automate. Validatory screening showed the robust performance of the assay, and we discovered two compounds Dimethylacrylshikonin and Alkannin, with µM inhibition potency against PARP1/2-HPF1 interaction. The assay will facilitate the discovery of inhibitors against HPF1-PARP1/2 complex and to develop potentially new effective anticancer agents.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interactions during Primordial Follicle Activation},

author = {Takase, Hinako M.},

url = {https://www.biorxiv.org/content/10.1101/2024.02.08.579446v2},

doi = {https://doi.org/10.1101/2024.02.08.579446},

year  = {2024},

date = {2024-02-12},

journal = {Preprint},

abstract = {Primordial follicle activation (PFA) is a pivotal event in female reproductive biology, coordinating the transition from quiescent to growing follicles. This study employed comprehensive single-cell RNA sequencing to gain insights into the detailed regulatory mechanisms governing the synchronized dormancy and activation between granulosa cells (GCs) and oocytes with the progression of the PFA process. Wntless (Wls) conditional knockout (cKO) mice served as a unique model, suppressing the transition from pre-GCs to GCs, and disrupting somatic cell-derived WNT signaling in the ovary. Our data revealed immediate transcriptomic changes in GCs post-PFA in Wls cKO mice, leading to a divergent trajectory, while oocytes exhibited modest transcriptomic alterations. Subpopulation analysis identified the molecular pathways affected by WNT signaling on GC maturation, along with specific gene signatures linked to dormant and activated oocytes. Despite minimal evidence of continuous up-regulation of dormancy-related genes in oocytes, the loss of WNT signaling in (pre-)GCs impacted gene expression in oocytes even before PFA, subsequently influencing them globally. The infertility observed in Wls cKO mice was attributed to compromised GC-oocyte molecular crosstalk and the microenvironment for oocytes. Our study highlights the pivotal role of the WNT-signaling pathway and its molecular signature, emphasizing the importance of intercellular crosstalk between (pre-)GCs and oocytes in orchestrating folliculogenesis.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory},

author = {Sun, Wenfei},

url = {https://www.nature.com/articles/s41586-023-07011-6},

doi = {https://doi.org/10.1038/s41586-023-07011-6},

year  = {2024},

date = {2024-02-06},

journal = {Nature},

abstract = {Memory encodes past experiences, thereby enabling future plans. The basolateral amygdala is a centre of salience networks that underlie emotional experiences and thus has a key role in long-term fear memory formation1. Here we used spatial and single-cell transcriptomics to illuminate the cellular and molecular architecture of the role of the basolateral amygdala in long-term memory. We identified transcriptional signatures in subpopulations of neurons and astrocytes that were memory-specific and persisted for weeks. These transcriptional signatures implicate neuropeptide and BDNF signalling, MAPK and CREB activation, ubiquitination pathways, and synaptic connectivity as key components of long-term memory. Notably, upon long-term memory formation, a neuronal subpopulation defined by increased Penk and decreased Tac expression constituted the most prominent component of the memory engram of the basolateral amygdala. These transcriptional changes were observed both with single-cell RNA sequencing and with single-molecule spatial transcriptomics in intact slices, thereby providing a rich spatial map of a memory engram. The spatial data enabled us to determine that this neuronal subpopulation interacts with adjacent astrocytes, and functional experiments show that neurons require interactions with astrocytes to encode long-term memory.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Global genomic diversity of Pseudomonas aeruginosa in bronchiectasis},

author = {Harrington, Niamh E.},

url = {https://www.biorxiv.org/content/10.1101/2024.01.30.577916v1},

doi = {https://doi.org/10.1101/2024.01.30.577916},

year  = {2024},

date = {2024-01-30},

journal = {Preprint},

abstract = {Background Pseudomonas aeruginosa is the dominant pathogen causing lung infections in people with both cystic fibrosis (CF) and bronchiectasis, associated with poorer outcomes. Unlike CF, bronchiectasis has been a neglected disease. More extensive genomic studies of larger bronchiectasis patient cohorts and within patient sampling are needed to improve understanding of the evolutionary mechanisms underpinning P. aeruginosa infections to guide novel and improved treatments.



Methods We have performed genome sequencing of 2,854 P. aeruginosa isolates from 180 patients attending clinics worldwide to analyse the genomic diversity between and within patient infections.



Results We observed high genetic diversity between infections with low incidence of highly transmissible strains. Our genomic data provide evidence for the mutational targets driving P. aeruginosa evolution in bronchiectasis. Some functions found to gain mutations were comparable to CF, including biofilm and iron acquisition, whilst others highlighted distinct evolutionary paths in bronchiectasis such as pyocin production and resistance, and a novel efflux pump gene (PA1874). We also show a high incidence of antimicrobial resistance-associated mutations and acquired resistance genes, in particular multidrug efflux and fluoroquinolone resistance mechanisms.



Conclusions Our findings highlight important differences between P. aeruginosa infections in bronchiectasis and CF and provide evidence of the relatively minor role transmissible strains play in bronchiectasis. Our study provides a 10-fold increase in the available genomic data for these infections and is a global resource to improve our knowledge and understanding, to facilitate better patient outcomes.



Summary The largest genomic study of Pseudomonas aeruginosa bronchiectasis isolates to-date, providing an unprecedented global genomic resource. We highlight important differences between bronchiectasis and cystic fibrosis, including key genes under selection.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {High-Throughput GPCRome Screen of Pollutants Reveals the Activity of Polychlorinated Biphenyls at Melatonin and Sphingosine-1-phosphate Receptors},

author = {Wilkinson, Joshua C.},

url = {https://pubs.acs.org/doi/full/10.1021/acs.chemrestox.3c00388},

doi = {https://doi.org/10.1021/acs.chemrestox.3c00388},

year  = {2024},

date = {2024-01-30},

journal = {Chemical Research in Toxicology},

abstract = {Exposure to environmental pollutants is linked to numerous toxic outcomes, warranting concern about the effect of pollutants on human health. To assess the threat of pollutant exposure, it is essential to understand their biological activity. Unfortunately, gaps remain for many pollutants’ specific biological activity and molecular targets. A superfamily of signaling proteins, G-protein-coupled receptors (GPCRs), has been shown as potential targets for pollutant activity. However, research investigating the pollutant activity at the GPCRome is scarce. This work explores pollutant activity across a library of human GPCRs by leveraging modern high-throughput screening techniques devised for drug discovery and pharmacology. We designed and implemented a pilot screen of eight pollutants at 314 human GPCRs and discovered specific polychlorinated biphenyl (PCB) activity at sphingosine-1-phosphate and melatonin receptors. The method utilizes open-source resources available to academic and governmental institutions to enable future campaigns that screen large numbers of pollutants. Thus, we present a novel high-throughput approach to assess the biological activity and specific targets of pollutants.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {A comparison between low-cost library preparation kits for low coverage sequencing},

author = {Stewart et, Caitlin M.},

url = {https://www.biorxiv.org/content/10.1101/2024.01.30.578044v1},

doi = {https://doi.org/10.1101/2024.01.30.578044},

year  = {2024},

date = {2024-01-30},

journal = {Preprint},

abstract = {In the fields of human health and agricultural research, low coverage whole-genome sequencing followed by imputation to a large haplotype reference panel has emerged as a cost-effective alternative to genotyping arrays for assaying large numbers of samples. However, a systematic comparison of library preparation methods tailored for low coverage sequencing remains absent in the existing literature. In this study, we evaluated one full sized kit from IDT and miniaturized and evaluated three Illumina-compatible library preparation kits—the KAPA HyperPlus kit (Roche), the DNA Prep kit (Illumina), and an IDT kit—using 96 human DNA samples. Metrics evaluated included imputation concordance with high-depth genotypes, coverage, duplication rates, time for library preparation, and additional optimization requirements. Despite slightly elevated duplication rates in IDT kits, we find that all four kits perform well in terms of imputation accuracy, with IDT kits being only marginally less performant than Illumina and Roche kits. Laboratory handling of the kits was similar: thus, the choice of a kit will largely depend on (1) existing or planned infrastructure, such as liquid handling capabilities, (2) whether a specific characteristic is desired, such as the use of full-length adapters, shorter processing times, or (3) use case, for instance, long vs short read sequencing. Our findings offer a comprehensive resource for both commercial and research workflows of low-cost library preparation methods suitable for high-throughput low coverage whole genome sequencing.},

keywords = {Mantis®},

pubstate = {published},

tppubtype = {article}

}